Document:

exv10w11

Exhibit 10.11

Pages where confidential treatment has been requested are stamped ‘Confidential Treatment Requested and the
Redacted Material has been separately filed with the Commission,’ and the confidential section has been
marked as follows: [***].

EXCLUSIVE LICENSE AGREEMENT

          This Exclusive License Agreement (Agreement), effective as of this day of November 1, 2001
(the “Effective Date”), is by and between Cambridge University Technical Services Ltd., an English
limited company (“CUTS”) and Ceres, Inc. (“Ceres”), a Delaware corporation, having a principal
place of business at 3007 Malibu Canyon Road, Malibu, California 90265.

W I T N E S S E T H:

          WHEREAS, The Chancellor, Masters and Scholars of the University of Cambridge and Ceres have
entered into that certain Sponsored Research Agreement dated June 1, 2000 in support of research
and development work, including the screening of certain transgenic plants;

          WHEREAS, CUTS is the owner of certain patent rights and other intellectual property developed
by Dr. Haseloff relating to (i) Arabidopsis transgenic plants and (ii) the HAP-1 and other
extensin-GFP constructs and Ceres desires to license such rights from CUTS;

          WHEREAS, CUTS desires to provide to Ceres certain first rights of refusal to Other Project
Technology (defined below); and

          WHEREAS, Ceres desires to grant to the University of Cambridge license rights to certain of
Ceres’ technologies for the University’s non-commercial research and teaching activities.

          NOW, THEREFORE, in consideration of the foregoing premises and the following mutual covenants,
and other good and valuable consideration, the receipt of which is hereby acknowledged, and
intending to be legally bound hereby, the Parties agree as follows:

1. DEFINITIONS

          As used in this Agreement, the following terms will have the meaning set forth below:

     1.1 “Affiliate(s)” shall mean (a) any company owned or controlled to the extent of at least
fifty percent (50%) of its issued and voting capital by a Party to this Agreement and any other
company so owned or controlled (directly or indirectly) by any such company or the owner of any
such company, or (b) any partnership, joint venture or other entity directly or indirectly
controlled by, controlling, or under common control with, to the extent of at least fifty percent
(50%) of voting power (or otherwise having power to control its general activities), a Party to
this Agreement.

 

 

     1.2 “Background Technology” shall mean the Technologies developed prior to the Effective Date
of the Sponsored Research Agreement, which CUTS or Ceres owns, or has license rights to, and which
are useful for the Purpose. The Party’s respective Background Technology shall be referred to as
Ceres Background Technology and CUTS Background Technology. CUTS Background Technology shall
include certain CUTS Technology Rights relating to Arabidopsis transgenic plants, as listed in
Exhibit A; except that CUTS Background Technology shall not include any HAP-1 Technology, nor any
Project Technology. In addition, Ceres Background Technology shall include Technologies relating to
recombinant transmembrane proteins as defined in Exhibit I to Amendment I to the Sponsored Research
Agreement, developed prior to the Effective Date of such Amendment I.

     1.3 “Biological Material” means any plants, seeds, microorganisms, cells, parts of cells, DNA,
RNA, cDNA, proteins, peptides, enzymes, and any combination of the foregoing, and/or other organic
matter and/or biologically active compounds.

     1.4 “Biological Product(s)” means any product comprising the Biological Materials.

     1.5 “Confidential Information” means any information, disclosed by one Party to this Agreement
to the other Party, that has any commercial value to the disclosing Party’s business, research,
development or other activities. Confidential Information includes, without limitation,
inventions, biological materials, technical information, trade secrets, financial information,
product plans, customer lists, marketing plans and strategies, forecasts and other business
information, improvements, ideas, works of authorship, processes, computer programs, techniques,
schematics, data, gene sequences, gene expression data, protein sequences, protein structures,
regulatory sequences, and other data.

     1.6 “HAP-1 Patent” shall mean any Patent Rights based on the patent application listed in
Exhibit B, which includes the HAP-1 Technology.

     1.7 “HAP-1 Products” shall mean all products, processes, or services including Biological
Products that are to be commercialized, the manufacture, use or sale of which is covered by any
valid and subsisting claim of the HAP-1 Patent.

     1.8 “HAP-1 Technology” means any and all Technology related to and including (i) the HAP-1
sequences or constructs and (ii) the extensin GFP gene constructs, as further described in Exhibit
B.

     1.9 “Net Sales” shall mean the gross amount actually received on sales of HAP-1 Products to
third parties (except as set forth below) by Ceres, and its Affiliates, less the following: (i)
customary trade, quantity, or cash discounts and commissions to non-affiliated brokers or agents to
the extent actually allowed and taken; (ii) amounts repaid or credited by reason of rejection or
return; (iii) any sales, use, tariff, customs duties, V.A.T. and/or other taxes, duties and similar
governmental assessments (except taxes based on income), which are paid by or on behalf of Ceres;
and (iv) outbound transportation, shipping, packing, costs of insurance in transit, and other costs
paid or allowed by Ceres; subject in all cases (i) to (iii) being separately

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charged on customer invoices or credit notes. In any transfers of Product between Ceres and
an Affiliate, Net Sales shall be calculated based only on the final sale of the Product to an
independent third party.

     1.10 “Non-Commercial Research and Teaching” shall mean research and teaching activities whose
primary purpose is the advancement of science or academic learning and dissemination of knowledge
excluding (a) any research sponsored by a commercial entity other than Ceres or (b) any research
where the results will be provided to a commercial entity other than Ceres, either directly by CUTS
or the University or via collaboration or otherwise, and other than through publication in a
learned journal.

     1.11 “Other Project Technology” shall mean any Technology, which the University develops,
which is based on or created by using Project Technology and/or which furthers the Purpose without
funding or information from Ceres during the Research Project.

     1.12 “Party” means, CUTS or Ceres, collectively they are sometimes referred to as the
“Parties”.

     1.13 “Patent Rights” shall mean all patents and patent applications throughout the world,
including any reissues, extensions, substitutions, continuations, divisions, and
continuations-in-part applications, reexaminations or extensions or other government actions which
extend the life of a patent, and all rights to apply for patent protection and all rights, if any,
to sue or bring other actions for past, present or future infringement of such rights. The Party’s
respective Patent Rights shall be referred to as Ceres Patent Rights and CUTS Patent Rights.

     1.14 “Products” shall mean all products, processes, or services including Biological Products
that are to be commercialized, the manufacture, use or sale of which is covered by any valid and
subsisting claim of the Patent Rights within CUTS Background Technology, and/or the Project
Technology, except that Products shall not include any HAP-1 Products.

     1.15 “Project Technology” shall mean any and all Technology developed or obtained during and
resulting from the Research Project, but excluding any Background Technology, HAP-1 Technology and
Other Project Technology.

     1.16 “Purpose” shall mean the generation and analysis and transfer to Ceres of data and large
numbers of transgenic Arabidopsis plants and/or seeds transformed with constructs containing the
GFP gene the expression of which is indirectly driven by a large amount of different plant
promoters, as further described in the Research Plan.

     1.17 “Research Project” shall mean the collaborative research program under which the
University and Ceres have performed and shall perform certain research and development activities
in pursuit of the Purpose and in accordance with the Research Plan, as defined in the Sponsored
Research Agreement.

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     1.18 “Research Plan” shall mean the mutually agreed document attached as Exhibit A to the
Sponsored Research Agreement that describes the respective research experiments and the specific
responsibilities of Ceres and University in performing the Research Project.

     1.19 “Sublicense Income” shall mean the gross amount actually received by either Ceres or its
Affiliates in consideration for sublicenses of any of the rights under the HAP-1 Patent granted
hereunder, including up-front fees, lump sum payments and any running royalties (on a
product-by-product and country-by-country basis), without deduction of any kind, but excluding the
following, in relation to which no payments shall be due to CUTS:

          (a) Payments received by either Ceres or its Affiliates solely for performance of research and
development, including but not limited to milestone payments for achievement of objectives in
research and development, only to the extent that such payments (i) cover the actual cost of the
research and development work; (ii) cover the amounts of the milestone payments due under Paragraph
5.5 hereof; or, (iii) are directly related to development of products that would be covered by this
Agreement;

          (b) Investments made by a sublicensee in either Ceres or its Affiliates;

          (c) Payments made to either Ceres or its Affiliates solely to the extent that they cover the
actual costs of conducting testing and other activities in connection with obtaining regulatory
approval for a Product;

          (d) Reimbursed expenses of either Ceres or its Affiliates.

     1.20 “Sponsored Research Agreement” shall mean that certain sponsored research agreement dated
June 1, 2000, between the University and Ceres in respect of the Research Project.

     1.21 “Technological Element” shall mean any individual Biological Material, data, methods,
protocols, procedures, processes arising out of the University’s performance of the Research
Project and which is employed or embodied in a Product and which can be separated from other such
Biological Material, data, methods, protocols, procedures, processes employed or embodied in the
Product and which, in the absence of a license, would infringe CUTS Patent Rights. There shall be
three (3) mutually exclusive types of Technological Elements, (i) those solely owned by CUTS, (ii)
those jointly owned by CUTS and Ceres, and (iii) all other Technological Elements. A non-inclusive
list of examples of Technological Elements can be found in Exhibit C hereto.

     1.22 “Technology” shall mean any Biological Material, Biological Product, data, methods,
protocols, procedures, processes and the like, and the Patent Rights and Technology Rights relating
thereto.

     1.23 “Technology Rights” shall mean existing and future proprietary rights, including but not
limited to know-how rights, trade secret rights, copyrights, design rights, and all other

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intellectual property rights (including without limitation the right, if any, to sue or bring
other actions for past, present or future infringement of such proprietary rights), but excluding
Patent Rights. The Party’s respective Technology Rights shall be referred to as Ceres Technology
Rights and CUTS Technology Rights.

     1.24 “Term” shall mean the period beginning on the Effective Date, and ending on the earlier
of (i) the date of the expiration of the last to expire patent licensed hereunder, or if no patents
are licensed hereunder, ten (10) years from the Effective Date, or (ii) the termination hereof
pursuant to the terms of Section 6 of this Agreement.

     1.25 “University” shall mean the University of Cambridge.

2. PROJECT TECHNOLOGY

     CUTS acknowledges and agrees with Section 4.2 of the Sponsored Research Agreement on Ownership
of Project Technology.

3. LICENSE GRANTS

     3.1 Subject to all the terms of this Agreement, CUTS hereby grants to Ceres, under CUTS Patent
Rights and CUTS Technology Rights, a fully paid-up, irrevocable, world-wide, non-exclusive license,
including the right to grant sublicenses, to make, have made, use, or have used, CUTS Background
Technology.

     3.2 Subject to all the terms of this Agreement Ceres hereby grants to CUTS a limited license
to use the Project Technology solely for Non-Commercial Research and Teaching purposes. Ceres
acknowledges and agrees that such license will be implemented by CUTS solely at the University,
under the full responsibility of CUTS.

     3.3 Subject to all the terms of this Agreement CUTS hereby grants to Ceres, under CUTS Patent
Rights and CUTS Technology Rights an irrevocable, world-wide, exclusive license, including the
right to grant sublicenses: (a) to possess, to make (e.g. propagate), have made, use, sell, have
sold, offer for sale, import and have imported the HAP-1 Technology, and (b) to make, have made,
use, sell, have sold, offer for sale, import and have imported HAP-1 Products; except that CUTS
shall retain the limited right to use such HAP-1 Technology for Non-Commercial Research and
Teaching purposes solely at the University under the full responsibility of CUTS.

     3.4 Ceres will notify CUTS of each sublicense granted hereunder.

     3.5 Subject to all the terms of this Agreement, and only in respect of Ceres Background
Technology that Ceres makes available to the University for conducting the Research Project, Ceres
hereby grants to CUTS, under Ceres Patent Rights and Ceres Technology Rights, a limited, fully
paid-up, non-exclusive license to use such Ceres Background Technology solely at the University and
only (i) to perform the Research Project and (ii) for

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Non-Commercial Research and Teaching purposes.

4. OTHER PROJECT TECHNOLOGY

     Prior to commercializing or granting any rights to any third party to commercialize any Other
Project Technology, CUTS shall offer to Ceres in writing terms for the commercialization of such
Other Project Technology (“Offer”), and Ceres will have a sixty (60) day period from the date of
delivery of the Offer in which to indicate its desire to accept such Offer, subject to negotiation
of definitive agreements. If the Offer is declined or is not accepted during such sixty (60) day
period, CUTS may either commercialize itself or grant a license to a third party on terms no more
favorable to the third party than the terms of the Offer. If Ceres indicates its desire to accept
the Offer in writing within said sixty (60) day period, the Parties agree to negotiate in good
faith the definitive agreements for such commercialization; provided, however, that if the Parties
are unable to agree upon the terms and conditions of any such license or acquisition agreement
within twelve months of delivery of the written notice of Ceres’ desire to accept the Offer, CUTS
may either commercialize itself or grant a license to a third party on terms no more favorable to
the third party than the terms offered by CUTS to Ceres. In determining whether the terms offered
to a third party are more favorable than those received or accepted by Ceres, all terms and
conditions of the respective offers shall be considered, including but not limited to, monetary
terms, scope of rights granted, warranties and indemnities.

5. CONSIDERATION

     5.1 License Initiation Fee. Ceres agrees to pay to CUTS the amount of [***] United
States dollars (U.S. $[***]) within thirty (30) business days of the Effective Date. Such fee
includes the reimbursement of all costs incurred by CUTS in connection with the filing and
prosecution of the HAP-1 Patent.

     5.2 Royalty on Net Sales. Ceres shall pay to CUTS an earned royalty on Net Sales on a
product-by-product and country-by-country basis. Earned royalties shall accrue in each country for
the duration of CUTS Patent Rights covering such HAP-1 Product in that country. Ceres shall pay
royalties to CUTS on Net Sales from the first date of commercial introduction of a HAP-1 Product,
which royalty shall be A. A is defined as follows: the lesser of [***] percent ([***]%) or
(W/X)(MRNS); where X shall be the total number of Technological Elements in the HAP-1 Product; W is
the sum of one half of the number of Technological Elements contributed to the HAP-1 Product which
are jointly owned by CUTS and Ceres plus the total number of Technological Elements contributed to
the HAP-1 Product solely by CUTS; and, MRNS shall be the maximum royalty on Net Sales, which is
[***] percent ([***]%). The Parties further agree to negotiate in good faith for another royalty
rate in the event of substantial market considerations.

     5.3 Royalty on Sublicense Income. Ceres shall pay to CUTS an earned royalty on
Sublicense Income actually received by Ceres, which royalty shall be A. A is defined as follows:
the lesser of [***] percent ([***]%) or (W/X)(MRNS); where X shall be the total number of
Technological Elements in the sublicense; W is the sum of one half of the number of Technological
Elements contributed to the sublicense which are jointly owned by CUTS and

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	Confidential Treatment Requested and the Redacted Material has been separately filed with
the Commission.

 

Ceres plus the total number of Technological Elements contributed to the sublicense solely by
CUTS; and, MRNS shall be the maximum royalty on Sublicense Income, which is [***] percent ([***]%).
The Parties further agree to negotiate in good faith for a lower royalty rate in the event of
substantial market considerations.

     5.4 Milestone Payments. Ceres shall pay to CUTS the following Milestone payments:

          (a) within thirty (30) days of Ceres’ successful validation of the technical evaluation
protocol for a dicotyledon plant, such as Arabidopsis, associated with the HAP-1 Technology and
described in Exhibit B of this Agreement, Ceres shall pay to CUTS [***] United States dollars (U.S.
$[***]). Ceres shall use all reasonable efforts to complete such validation within two (2) years
of the Effective Date;

          (b) within thirty (30) days of Ceres’ successful validation of the technical evaluation
protocol for a monocotyledon plant, such as rice, associated with the HAP-1 Technology and
described in Exhibit B of this Agreement, Ceres shall pay to CUTS [***] United States dollars (U.S.
$[***]);

          (c) within thirty (30) days of CUTS’ notice to Ceres that a United States patent under the
HAP-1 Patent, licensed to Ceres hereunder has been issued to CUTS, Ceres shall pay to CUTS [***]
United States dollars (U.S. $[***]);

          (d) within thirty (30) days of CUTS’ notice to Ceres that a European patent under the HAP-1
Patent licensed to Ceres hereunder, has been issued to CUTS, Ceres shall pay to CUTS [***] United
States dollars (U.S. $[***]).

     5.5 Royalty Reports; Payments; Records

          (a) First Sale. Ceres shall report to CUTS the date of first commercial sale of any HAP-1
Product within thirty (30) business days of occurrence in each country.

          (b) Reports and Payments. Within sixty (60) days after the conclusion of each calendar year
following First Sale, Ceres shall deliver to CUTS a report containing the following information:

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	Confidential Treatment Requested and the Redacted Material has been separately filed with
the Commission.

 

(i) the number of HAP-1 Products sold to independent third parties in each
country;

(ii) the gross sales price for each HAP-1 Product sold by Ceres and its
Affiliates during the applicable year in each country;

(iii) the calculation of Net Sales and Sublicense Income for the applicable
year in each country, including a listing of applicable deductions and
credits applied;

(iv) the total royalty payable on Net Sales in U.S. dollars, together with
the exchange rates used for conversion; and,

(v) a statement indicating whether any Milestones have been attained
pursuant to Section 5.5.

          All such reports shall be considered Ceres Confidential Information pursuant to Section 7, and
shall not be transferred to a third party. If no royalties are due to CUTS for any year, the
report shall so state. Concurrent with this report, Ceres shall remit to CUTS any payment due in
respect of Net Sales, Sublicense Income or Milestones for the applicable year. CUTS shall instruct
Ceres as to the method of payment.

          (c) Records. Ceres shall maintain, and shall cause its Affiliates to maintain, reasonably
complete and accurate records of HAP-1 Product that is made, used, sold, or performed and
Sublicense Income received under this Agreement and any amounts payable to CUTS in relation to such
HAP-1 Product, which records shall contain sufficient information to permit CUTS to confirm the
accuracy of any reports delivered to CUTS under this Section 5.6. The relevant party shall retain
such records relating to a given royalty period for at least three (3) years after the conclusion
of that royalty period, during which time CUTS shall have the right, at its sole expense, to cause
an independent, certified public accountant to inspect such records once per calendar year, upon
thirty (30) days’ prior written notice, during normal business hours for the sole purpose of
verifying any reports and payments delivered under this Agreement. The parties shall reconcile any
underpayment or overpayment within thirty (30) days after the accountant delivers the results of
the audit. In the event that any audit performed under this Section reveals an aggregate
underpayment in excess of five percent (5%) during any calendar year, Ceres or the applicable
sublicensee or Affiliate shall bear the full cost of such audit.

6. TERM AND TERMINATION

     6.1 Term. Unless otherwise terminated by operation of law or by acts of the Parties
in accordance with the terms of this Agreement, this Agreement will be in force for the Term.

     6.2 Monies Due/Accrued Rights. Any termination of this Agreement shall not relieve
Ceres of its obligation to pay any monies due or owing at the time of such termination and will not
impair any accrued right of CUTS arising under this Agreement prior to such termination.

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     6.3 Termination Upon Breach. Upon material breach or default of any of the terms and
conditions of this Agreement, the defaulting Party shall be given notice of such default in writing
and a period of sixty (60) days after receipt of such notice to correct the breach or default. If
(a) the default or breach (i) is material to this Agreement taken as a whole, and (ii) is not
corrected within said sixty (60) day period and the defaulting Party has not taken reasonable steps
to cure the same, and (b) the Party not in default has fully complied with all of its obligations
under this Agreement and (c) the Party not in default has no adequate remedy from monetary changes,
the Party not in default shall have the right to terminate this Agreement. In the event that this
Agreement is terminated due to a breach by CUTS, Sections 3.1 and 3.3 of this Agreement shall
survive such termination.

     6.4 Termination upon Bankruptcy. A Party shall have the right to terminate this
agreement upon the first to occur of the following events: (i) a petition of action is filed or
action taken by or against the other Party under any law dealing with insolvency or bankruptcy;
(ii) a receiver is appointed over the assets or undertaking of the other Party; (iii) the other
Party enters into a deed of arrangement or makes an assignment for the benefit of creditors; or
(iv) the other Party ceases to function as a going concern or an order is made or a resolution
passed to that effect.

     6.5 Ceres Termination Rights. In addition to the above termination rights, Ceres
shall be entitled to terminate this Agreement at any time, with or without cause, upon providing
CUTS with ninety (90) days’ notice of termination in writing.

7. CONFIDENTIALITY

     7.1 Mutual Non-Disclosure Obligations. Without prejudice to Sections 7.7 and 7.8 of
the Sponsored Research Agreement, each Party hereby agrees that it shall keep confidential and not
use for any purpose, except as provided herein, all Confidential Information supplied to it (the
“Recipient”) by the other Party (the “Disclosing Party”) during the term of this Agreement and for
five (5) years after termination or expiration hereof; provided, however, that the foregoing
obligations of confidentiality and non-use shall not apply to the extent that any Confidential
Information is demonstrated by written records to be (a) already known to the Recipient or one of
its Affiliates at the time of disclosure hereunder (provided the Recipient and/or its Affiliates
comply with any restrictions imposed by third parties); or (b) is hereafter developed by the
Recipient or one of its Affiliates in the course of work entirely independent of any disclosure
hereunder; or (c) publicly known prior to or after disclosure hereunder other than through acts or
omissions of the Recipient or one of its Affiliates; or (d) disclosed in good faith to the
Recipient or one of its Affiliates by a third party (provided the Recipient and/or its Affiliates
comply with any restrictions imposed by third parties). This does not prevent disclosure to third
parties by the Recipient under a secrecy or confidentiality agreement with essentially the same
confidentiality provisions provided herein in connection with the exercise of its rights under this
Agreement (but only to the extent permitted herein). In addition, disclosure may be made (i) to
Recipient’s employees, consultants, representatives, agents and advisors provided that such persons
are subject to confidentiality obligations consistent with the ones set

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forth in this Section 7.1, and (ii) to governmental agencies to the extent required to secure
governmental approval for marketing of the Products; provided, however, that the Recipient shall
seek to limit disclosure and to obtain confidential treatment therefor.

     7.2 Affiliates, Licensee and Sublicensees. Nothing herein shall be construed as
preventing Ceres from disclosing any information received from CUTS to an Affiliate, licensee or to
a sublicensee of Ceres, provided such Affiliate, licensee or sublicensee has undertaken a similar
obligation of confidentiality with respect to the Confidential Information.

     7.3 Internet Communications. To the extent that the Parties use the Internet as a
means of communication, all e-mail and/or other Internet-based communications containing
Confidential Information shall be encrypted.

8. PRESS RELEASES AND USE OF NAMES AND TRADEMARKS

     8.1 Press Releases. All press releases which one Party desires to make relating to
the Research Project or any of the matters contemplated hereunder shall be prepared by such Party
as a joint press release of the Parties and shall not be publicly released or released to the press
without the prior written consent of the other Party.

     8.2 Use of Tradenames. Neither Party shall disclose or use the name of the other for
any purpose without the prior written consent of the named Party, except for the purposes of
referring to this Agreement in disclosures to be made in documents in connection with financings
and/or as required by law.

9. REPRESENTATIONS AND WARRANTIES

     9.1 Ceres Representations and Warranties. Ceres represents to CUTS that:

          (a) Ceres is a corporation duly organized, validly existing and in good standing under the
laws of the State of Delaware and has all requisite corporate power and authority to carry on its
business as now conducted;

          (b) All corporate action on the part of Ceres and its officers and directors necessary for the
authorization, execution and delivery of this Agreement and the performance of all obligations of
Ceres hereunder has been taken, and this Agreement constitutes a valid and legally binding
obligation of Ceres, enforceable in accordance with its terms; and,

          (c) Ceres warrants to CUTS that it has the lawful right to grant the licenses granted to CUTS
under this Agreement.

     9.2 CUTS Representations and Warranties.

          (a) CUTS is a company duly organized, validly existing and in good standing under the laws of
England and Wales has all requisite power and authority to carry on its

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business as now conducted;

          (b) All action on the part of CUTS and its officers and directors necessary for the
authorization, execution and delivery of this Agreement and the performance of all obligations of
CUTS hereunder has been taken, and this Agreement constitutes a valid and legally binding
obligation of CUTS, enforceable in accordance with its terms; and

          (c) CUTS warrants to Ceres that it has the lawful right to grant the licenses granted to Ceres
under this Agreement. CUTS warrants that, to the best of its knowledge, CUTS owns and has full
rights, title and interest, through assignment by the University and/or inventors associated with
the University, in all Technology Rights, Patent Rights or other rights which are or shall or may
be licensed to Ceres pursuant to this Agreement; including without limitation, Technology Rights,
Patent Rights and other rights on CUTS Background Technology, on the HAP-1 Patent and HAP-1
Technology, and on Other Project Technology.

10. DISCLAIMERS

     10.1 Project Technology and CUTS Background Technology. The Parties accept no
responsibility whatsoever for any use which may be made of any work carried out under or pursuant
to this Agreement, of the Project Technology, or of its Background Technology, and no liability
whatsoever either direct or indirect shall rest upon the a Party, its employees, students, agents
or appointees for the effects of any Product or process that may be developed, manufactured, used,
sold, imported or distributed by or on behalf of the other Party or any Affiliate or sublicensee of
the other Party, notwithstanding that such Product or process may be based upon the findings of the
Research Project, the results or upon any other advice or information furnished by a Party, its
employees, students, agents or appointees under this Agreement.

     10.2 General. Except as expressly provided for in this Agreement the licenses granted
to the Parties under this Agreement and the associated Technology, Biological Materials, Patent
Rights, property rights, Products, and patent methods are provided WITHOUT WARRANTY OF
MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER REPRESENTATION OR WARRANTY,
EXPRESS OR IMPLIED.

11. LIMITATION OF LIABILITY

     11.1 EXCLUSIONS. IN NO EVENT WILL ANY PARTY BE LIABLE UNDER ANY CONTRACT, NEGLIGENCE,
STRICT LIABILITY OR OTHER THEORY FOR ANY INDIRECT, INCIDENTAL, SPECIAL OR CONSEQUENTIAL DAMAGES
INCLUDING, BUT NOT LIMITED TO, LOSS OF REVENUES AND LOSS OF PROFITS IN CONNECTION WITH THIS
AGREEMENT OR IN CONNECTION WITH THE USE OF THE TECHNOLOGY, BIOLOGICAL MATERIALS, PATENT RIGHTS,
PROPERTY RIGHTS OR PRODUCTS.

     11.2 Limitation. Under no circumstances whatsoever shall CUTS liability to Ceres

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under or otherwise in connection with this Agreement exceed sums paid by Ceres to CUTS under
this Agreement together with the sums paid by Ceres to the University under the Sponsored Research
Agreement.

12. INDEMNIFICATION

     12.1 Ceres Indemnity. Ceres agrees to indemnify, defend and hold harmless CUTS, its
employees, students, agents and appointees, including but not limited to, Dr. Haseloff, from and
against any and all liability, loss, damage, cost or expense (including reasonable legal fees,
court costs and other expenses of litigation) arising out of or in connection with third party
claims relating to:

          (a) any alleged infringement of a third party’s intellectual property rights by reason of
Ceres’ activities in relation to the Research Project or this Agreement; or

          (b) any HAP-1 Product or process developed, manufactured, used, sold, imported or distributed
by or on behalf of Ceres, its Affiliates or sublicensees arising out of the Research Project or in
any way out of this Agreement.

13. PATENT PROSECUTION AND MAINTENANCE

     13.1 Responsibility.

          (a) CUTS will diligently prosecute and maintain at its own expense, CUTS Patent Rights related
to CUTS Background Technology and Other Project Technology using counsel of its choice.

          (b) Ceres shall have the sole right and discretion, at its own expense, to prepare, file,
prosecute and maintain patent applications and patents claiming Project Technology and the HAP-1
Patent, using patent counsel of its own choosing. CUTS will cause inventors to assign their
ownership rights in the Project Technology to Ceres and will cooperate with and assist Ceres in
preparation of such patents and patent applications. CUTS will cooperate with and assist Ceres, and
will cause the University to cooperate with and assist Ceres in assuming any ongoing patent
prosecution relating to the HAP-1 Patent or in the preparation and prosecution of any further such
patents and patent applications as may arise.

          (c) The Parties will promptly provide each other with copies of all relevant documentation
associated with their respective Patent Rights to the extent that such Patent Rights relate to
Project Technology, the HAP-1 Patent, CUTS Background Technology or Other Project Technology and
all other reasonable assistance so that both Parties may be currently and promptly informed and
apprised of the continuing prosecution and may comment upon such documentation sufficiently in
advance of any initial deadline for filing a response; provided, however, that if the receiving
Party has not commented upon such documentation prior to ten (10) business days before the initial
deadline for filing a response with the relevant government patent office, then the Party providing
the documentation will be free to respond appropriately

- 12 -

 

without consideration of comments by the receiving Party, if any. Both Parties hereto will
keep this documentation in confidence in accordance with the provisions of Section 7 herein.

     13.2 Choice to Not Prosecute. If subsequent to filing a patent application that
claims Project Technology or the HAP-1 Patent, Ceres elects not to prosecute or maintain such
patent application or ensuing patent or fund such prosecution, filing or maintenance, Ceres shall,
on a country-by-country basis, give CUTS notice thereof within a reasonable period prior to
allowing such patent application or patent to lapse or become abandoned or unenforceable and CUTS
may continue prosecution or maintenance of such patent application or patent at its sole expense
and for its exclusive benefit.

     13.3 Claims. CUTS will use all reasonable efforts to amend any patent application to
include claims requested by Ceres and required to protect the products contemplated to be sold or
methods contemplated to be practiced under this Agreement.

     13.4 Interferences/Oppositions. The costs of all interferences and oppositions
relating to such Patent Rights will be considered prosecution expenses and also will be borne by
the prosecuting Party.

14. PATENT INFRINGEMENT

     14.1 Notice. In the event that a Party learns of any infringement of any Patent Right
licensed under this Agreement, that Party will call the attention of the other Party thereto in
writing and will provide the other Party with reasonable evidence of such infringement. The
Parties to this Agreement acknowledge and agree that during the period and in a jurisdiction where
Ceres has exclusive rights under this Agreement, CUTS will not notify a third party of the
infringement of any of Patent Rights without first obtaining consent of Ceres. The Parties will
use their diligent efforts in cooperation with each other to terminate such infringement without
litigation. Ceres shall have no obligation and CUTS shall have no right, to grant any rights to
such infringing third party in derogation of the exclusive licenses granted to Ceres under this
Agreement.

     14.2 Legal Action. Ceres may request that CUTS take legal action against the
infringement of Patent Rights. Such request must be made in writing and must include reasonable
evidence of such infringement and damages to Ceres. If the infringing activity has not been abated
within ninety (90) days following the effective date of such request, CUTS will have the right to
elect to:

          (a) commence suit on its own account; or

          (b) refuse to participate in such suit;

and CUTS will give notice of its election in writing to Ceres by the end of the 100th day after
receiving notice of such request from Ceres. Ceres may thereafter bring suit for patent
infringement if and only if CUTS elects not to commence suit and if the infringement occurred

- 13 -

 

during the period and in a jurisdiction where Ceres had exclusive rights under this Agreement.
However, in the event Ceres elects to bring suit in accordance with this Section 14.2, CUTS may
thereafter join such suit at its own expense.

     14.3 Expenses and Awards. Such legal action as is decided upon will be at the expense
of the Party on account of whom suit is brought and all recoveries recovered thereby will belong to
such Party; provided, however, that legal action brought jointly by CUTS and Ceres and participated
in by both will be at the joint expense of the Parties and all recoveries from such joint legal
action will be allocated in the following order:

          (a) to each Party as reimbursement in equal amounts of the outside attorney’s costs, fees, and
other related expenses to the extent each Party paid for such costs, fees, and expenses until all
such costs, fees, and expenses are consumed for each Party, provided that if one Party paid more
for such costs, fees, and expenses, all of such Party’s costs, fees, and expenses shall be
reimbursed in full prior to the allocation of any remaining recovery to either Party under
Subsection 14.3(b); and

          (b) any remaining amount to be divided by the Parties in the following manner: (i)
seventy-five percent (75%) to Ceres and twenty-five percent (25%) to CUTS of any recoveries based
on actual damages and lost profits; and (ii) fifty percent (50%) to Ceres and fifty percent (50%)
to CUTS of any recoveries based on punitive and statutory enhanced damages.

     14.4 Cooperation. Each Party will cooperate with the other in litigation proceedings
instituted hereunder but at the expense of the Party on account of whom suit is brought. Such
litigation will be controlled by the Party bringing the suit, except that CUTS may be represented
by counsel of its choice, at its expense, in any suit brought by Ceres.

15. PATENT MARKING

          Ceres will mark all Products made, used, or sold under the terms of this Agreement, or their
containers, in accordance with the applicable patent marking laws.

16. GOVERNMENT APPROVAL OR REGISTRATION

          If this Agreement or any associated transaction is required by the law of any nation to be
either approved or registered with any governmental agency, Ceres will assume all legal obligations
to do so. Ceres will notify CUTS if it becomes aware that this Agreement is subject to a United
States or foreign government reporting or approval requirement. Ceres will make or cause to be
made all necessary filings and pay all costs including fees, penalties, and all other out-of-pocket
costs associated with such reporting or approval process. CUTS shall cooperate with Ceres, to the
extent it is able to do so within the law and established policy of CUTS, by providing
documentation and testimony to assist Ceres in obtaining such approval or registration. Any
expenses incurred by CUTS in cooperating with Ceres in obtaining approval or registration of this
Agreement in any country will be reimbursed within thirty (30) days after

- 14 -

 

receiving an itemized invoice for such expenses from CUTS.

17. MISCELLANEOUS

     17.1 Reserved Rights. Ceres may during or after the Term of this Agreement
independently or with third parties perform any research, including, without limitation, research
related to the Purpose in any plant. Cambridge retains the right, after the Research Project is
complete, to perform research and development work related to the Purpose independent of Ceres.

     17.2 Mediation and Governing Law.

          (a) If any dispute arises out of or in connection with this Agreement the Parties will attempt
in good faith to settle it by negotiation.

          (b) If the Parties are unable to settle any dispute by negotiation within twenty-eight (28)
days the Parties will attempt to settle it by mediation in accordance with the Centre for Dispute
Resolution (CEDR) Model Mediation Procedure.

          (c) To initiate a mediation, a Party must give notice in writing to the other Parties
requesting a mediation in accordance with Section 17.7.

          (d) This Agreement and all questions of construction, validity and performance under this
Agreement shall be governed by English law.

     17.3 Independent Contractors. Nothing in this Agreement is intended or shall be
deemed to constitute a partnership, agency, employer-employee or joint venture relationship between
the Parties. All activities by the Parties hereunder shall be provided as independent contractors.
Neither Party shall incur any debts or make any commitments for the other except to the extent, if
at all, specifically provided herein.

     17.4 Force Majeure. If the performance of any part of this Agreement by a Party is
prevented, restricted, interfered with or delayed by reason of any cause beyond the reasonable
control of the Party liable to perform, unless conclusive evidence to the contrary is provided, the
Party so affected shall use its diligent efforts to avoid or remove such causes of non-performance
and shall continue performance with the utmost dispatch whenever such causes are removed. When
such circumstances arise, the Parties shall discuss what, if any, modification of the terms of this
Agreement may be required in order to arrive at an equitable solution.

     17.5 Construction. In the event any portion of this Agreement shall be held illegal,
void or ineffective, the remaining portions hereof shall remain in full force and effect, as long
as it does not materially alter the purpose and performance of this Agreement. If any of the terms
or provisions of this Agreement are in conflict with any applicable statute or rule of law, then
such terms or provisions shall be deemed inoperative to the extent that they may conflict therewith
and shall be deemed to be modified to conform with such statute or rule of law. In the

- 15 -

 

event that the terms and conditions of this Agreement are materially altered as a result of
this Section, the Parties will renegotiate the terms and conditions of this Agreement to resolve
any inequities.

     17.6 Entire Agreement. Without prejudice to the Sponsored Research Agreement, this
Agreement constitutes the entire agreement between the Parties relating to the subject matter
hereof and supersedes all prior agreements, understandings, writings, and discussions between the
Parties relating to said subject matter. No terms or provisions of this Agreement shall be varied
or modified by any prior or subsequent statement, conduct or act of the Parties, except that the
Parties may amend this Agreement by written instruments specifically referring to and executed in
the same manner as this Agreement.

     17.7 Notices. All notices pertaining to this Agreement, including but not limited to
notices concerning progress reports and royalty and other payments, shall be in writing and sent by
two-day delivery via an internationally recognized delivery service, to the Parties at the
following addresses or such other address as such Party shall have furnished in writing to the
other Parties in accordance with this Section 17.7:

          For CUTS:

Cambridge University Technical Services, Ltd.

Research Services Division

16 Mill Lane

Cambridge CB2 1SB

Great Britain

Attention: Contracts Officer

          For Ceres:

Ceres, Inc.

3007 Malibu Canyon Road

Malibu, CA 90265

U.S.A.

Attention: Chief Operating Officer

          A notice shall be deemed to have been received on the day after deposit with the delivery
service, if sent by overnight delivery.

     17.8 No Third Party Beneficiaries and No Assignment. This Agreement shall be binding
upon and inure to the benefit of the successors in interest of the respective Parties. This
Agreement shall not be assigned by any Party without the written consent of the other Parties;
provided, however, Ceres may assign this Agreement to any Affiliates or to any corporation with
which it may merge or consolidate, or to which it may transfer all or substantially all of its
assets or business, without obtaining the consent of CUTS.

- 16 -

 

     17.9 Further Assurances. Each Party hereto shall execute such further papers or
agreements as may be necessary to effect the purposes of this Agreement and carry out its
provisions.

     17.10 Export Control Laws. The Parties will observe all applicable national laws with
respect to the transfer of materials and related technical data to foreign countries, including,
without limitation, the International Traffic in Arms Regulations (ITAR) and the Export
Administration Regulations.

     17.11 No Waiver. The failure of either Party at any time or times to require
performance of any provision hereof shall in no manner affect its right at a later time to enforce
the same. No waiver by either Party of any condition or term in any one or more instances shall be
construed as a further or continuing waiver of such condition or term or of any other condition or
term.

     17.12 Severability. If any term of this Agreement is held by a court of competent jurisdiction
to be unenforceable because it is invalid or in conflict with any law of any relevant jurisdiction,
the validity of the remaining provisions shall not be affected.

     17.13
Headings. The headings of the several sections are inserted for convenience of
reference only and are not intended to be a part of or to affect the meaning or interpretation of
this Agreement.

     17.14 Survival. Upon termination of this Agreement for any reason, Sections 3, 6, 7,
8, 10, 11, 12, 13, 14 and 17.2 and any accrued rights, obligations and causes of action shall
survive termination of this Agreement.

- 17 -

 

          In Witness Whereof, both CUTS and Ceres have executed this Exclusive License Agreement, in
duplicate originals, by their respective officers hereunto duly authorized, as of the date and year
written on page one hereof.

	 	 	 	 	 	 	 

	CAMBRIDGE UNIVERSITY TECHNICAL
SERVICES LTD.	 	CERES, INC.
	 
	 	 	 	 	 	 
	By

	 	/s/
R.C. Jennings	 	By	 	/s/
Richard Flavell
	 

	 	 
	 	 	 	 
	Name:	 	Dr. R.C. Jennings	 	Name: Richard Flavell, CBE, FRS
	Title:	 	Director	 	Title: Chief Scientific Officer
	 
	 	 	 	 	 	 
	 

	 	 	 	By	 	/s/
Peter Mascia
	 

	 	 	 	 	 	 
	 	 	 	 	Name: Dr. Peter Mascia
	 	 	 	 	Title: Director of Product Development

- 18 -

 

Exhibit A

CUTS Background Technology

HAP1 ENHANCER TRAP LINES

HAP1-VP16:HAP1-UAS-Extensin-emdGFP

HC10 — stomatal guard cells

HC03 — root base, cortex, endodermis

HC128.3 — petal vasculature

HC104.2 — leaf vasculature

HAP1-VP16:HAP1-UAS-histone-mCFP

With expression patterns in first screen:

HS69 — epidermis of roots, pili, abscission zones

HS135 — mature vasculature of silique and petals

HS151 — base of silique

HS164 — epidermis of roots, cotyledons, siliques, flowers

HS165 — style epidermis

HS176 — mature leaves

HS181 — silique vascular

HS222 — YOUNG ROOTS

HS230 — sepals and leaves

HS238 — vascular tissue roots, shoot meristem of embryo

HS241a — root tips

HS241b — hypocotyls and cotyledons, stem

HS251 — epidermis of stem/flower

HS357 — lateral root primordial

No expression in untreated seedlings, mature plants:

HS42

HS57

HS62

 

 

HS130

HS138

HS168

HS179

HS181

HS186

HS192

HS202

HS204

HS210

HS216

HS217

Hs220

HS221

HS225

HS228

HS231

HS232

HS243

HS247

HS250

HS253

HS359

HS630

HS361

HS364

HS366

HS368

HS369

HS371

 

 

Exhibit B

HAP-1 Technology

Description of HAP-1 technology:

ET HAP1 EXT emdGFP [diagram of linear T-DNA vector transformation]

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

ET HAP1 H2BECFP [diagram of linear T-DNA vector transformation]

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

HAP-1 Patent:

UK priority patent application number 0122828.7 filed on September 21, 2001, with title: Gene
expression construct.

Protocol associated with the validation of the use of HAP1 within the HAP-1 Technology:

Transgene activation by HAP1 in dicots: the following milestones should be achieved by
December 2002:

	 	§ 	 	Create Arabidopsis lines using a vector that contains a Ceres’ constitutive promoter
directing HAP1-VP16 expression as well as UASHAP1 — driven expression of a
fluorescent protein (line A)
	 
	 	•	 	Create Arabidopsis lines using a vector that contains a “weak” cell/tissue specific
promoter directing HAP1-VP16 expression as well as UASHAP1 — driven
expression of a fluorescent protein (line B)
	 
	 	•	 	Create Arabidopsis lines using a vector that contains UASHAP1 — driven
aequorin or a spectrally distinct fluorescent protein (line C)
	 
	 	•	 	Cross line C into lines A and B (or retransform construct from C into A or B using a
novel, non-PPT based selectable marker)
	 
	 	•	 	Evaluate RNA levels, and demonstrate presence of transactivated protein function in
a range of at least 10 cell types in statistically relevant sets of independent
Arabidopsis transformants.

	 	 	Transgene activation by HAP1 in monocots: the following milestones should be achieved by
December 2003:

	 	•	 	Create rice lines using a vector that contains a Ceres’ constitutive promoter
directing HAP1-VP16 expression as well as UASHAP1 — driven expression of a
fluorescent protein (line A)
	 
	 	•	 	Create rice lines using a vector that contains a “weak” cell/tissue specific
promoter directing HAP1-VP16 expression as well as UASHAP1 — driven
expression of a fluorescent protein (line B)
	 
	 	•	 	Create rice lines using a vector that contains UASHAP1 — driven aequorin
or a spectrally distinct fluorescent protein (line C)
	 
	 	•	 	Cross line C into lines A and B (or retransform construct from C into A or B using a
novel, non-PPT based selectable marker)
	 
	 	•	 	Evaluate RNA levels, and demonstrate presence of transactivated protein function in
a range of at least 10 cell types in statistically relevant sets of independent rice
transformants.

 

 

Exhibit C

Exemplary Technological Elements

A polynucleotide sequence encoding a protein or polypeptide

A polynucleotide sequence regulating the expression of a coding sequence

A polynucleotide sequence regulating the transcription of a coding sequence

A polynucleotide regulating the stability of a transcript

A polynucleotide regulating the translation of a transcript

A polynucleotide sequence capable of suppressing the activity of another polynucleotide

A polynucleotide sequence capable of suppressing the activity of a polypeptide or protein

A process or method to transform a plant or a plant cell

A process or method to select a desirable transformant

 

 

SPONSORED RESEARCH AGREEMENT

          This Sponsored Research Agreement (the “Agreement”), effective as of the 1st day of
June, 2000 (the “Effective Date”), is by and between The Chancellor, Masters and Scholars of The
University of Cambridge (“University”) and Ceres, Inc., a Delaware corporation (“Ceres”).

W I T N E S S E T H :

          WHEREAS, University, as a center for academic knowledge and research and development, and
through the work of Dr. Haseloff and others, has expertise, information and technology rights in
the field of plant genomics and developmental biology;

          WHEREAS, Dr. Haseloff is an employee of University and has special expertise and know-how in
screening transformed tissues for analyzing expression in certain cell types using Green
Fluorescent Protein (“GFP”);

          WHEREAS, University is interested in performing certain research and development work for
Ceres, including the making and screening of certain transgenic plants of interest to one or both
Parties, and Ceres is willing to fund such research and development work, all subject to the terms
and conditions of this Agreement;

          NOW, THEREFORE, in consideration of the foregoing premises and the following mutual covenants,
and other good and valuable consideration, the receipt of which is hereby acknowledged, and
intending to be legally bound hereby, the Parties agree as follows:

1. DEFINITIONS

          For purposes of this Agreement the following terms shall have the following meanings:

     1.1 “Affiliates” shall mean (a) any company owned or controlled to the extent of at least
fifty percent (50%) of its issued and voting capital by a Party to this Agreement and any other
company so owned or controlled (directly or indirectly) by any such company or the owner of any
such company, or (b) any partnership, joint venture or other entity directly or indirectly
controlled by, controlling, or under common control with, to the extent of at least fifty percent
(50%) of voting power (or otherwise having power to control its general activities), a Party to
this Agreement

     1.2 “Background Technology” shall mean the Technologies developed prior to the Effective Date,
which the University or Ceres owns, or has license rights to, and which are useful for the Purpose.
The Party’s respective Background Technology shall be referred to as Ceres Background Technology
and University Background Technology. The University Background Technology shall include in
particular certain Patent Rights and Technology Rights relating to (i) Arabidopsis transgenic
plants and (ii) the hap1 and other extensin-gfp gene constructs. The Patent Rights related hereto
are listed in Exhibit D.

 

 

     1.3 “Biological Materials” shall mean any plants, seeds, microorganisms, cells, parts of
cells, DNA, RNA, cDNA, proteins, peptides, enzymes, and any combination of the foregoing, and/or
other organic matter and/or other biologically active compounds.

     1.4 “Biological Product(s)” means any product comprising the Biological Materials.

     1.5 “University Patent Rights” means all Patent Rights owned or co-owned by University, but on
which no Ceres’ inventors are named.

     1.6 “Ceres’ Patent Rights” means all Patent Rights owned or co-owned by Ceres.

     1.7 “Confidential Information” means any information, disclosed by one Party to this Agreement
to the other Party, that has any commercial value to the disclosing Party’s business, research,
development or other activities. Confidential Information includes, without limitation,
inventions, biological materials, technical information, trade secrets, financial information,
product plans, customer lists, marketing plans and strategies, forecasts and other business
information, improvements, ideas, works of authorship, processes, computer programs, techniques,
schematics, data, gene sequences, gene expression data, protein sequences, protein structures,
regulatory sequences, and other data.

     1.8 “Exclusive License Agreement” shall mean these or that certain exclusive license
agreement(s) to be negotiated between the Parties on fair and reasonable terms on commencement of
the Research Project.

     1.9 “Other Project Technology” shall mean any Technology which the University develops which
is based on or created by using Project Technology and/or which furthers the Purpose without
funding or information from Ceres during the Research Project..

     1.10 “Patent Rights” means all patents and patent applications throughout the world, including
any reissues, extensions, substitutions, continuations, divisions, and continuations-in-part
applications, reexaminations or extensions or other government actions which extend the life of a
patent, and all rights to apply for patent protection and all rights, if any, to sue or bring other
actions for past, present or future infringement of such rights.

     1.11 “Products” shall mean all products, processes, or services including Biological Products
that are to be commercialized, the manufacture, use or sale of which is covered by any claim of one
or more patents within the University Background Technology, and/or Project Technology.

     1.12 “Party” means University or Ceres, collectively they are sometimes referred to as the
“Parties”.

     1.13 “Project Technology” shall mean any and all Technology developed or obtained during and
resulting from the Research Project, but excluding any Background Technology and Other Project
Technology.

     1.14 “Purpose” shall mean the generation and analysis and transfer to Ceres of data and large
numbers of transgenic Arabidopsis plants and/or seeds transformed with constructs

 

 

containing the GFP gene the expression of which is indirectly driven by a large amount of
different plant promoters, as further described in the Research Plan.

     1.15 “Research Budget” shall mean the mutually agreed document attached hereto as Exhibit B
that specifies the funding for the Research Project.

     1.16 “Research Funds” shall mean any funds paid or credited to the University by Ceres under
this Agreement as further specified in the Research Budget.

     1.17 “Research Project” shall mean the collaborative research program under which University
and Ceres shall perform certain research and development activities in pursuit of the Purpose and
in accordance with the Research Plan. The Research Project shall continue until the earlier of (i)
the completion of the last task performed with the aid of the Research Funds, or (ii) the
expiration or termination of this Agreement.

     1.18 “Research Plan” shall mean the mutually agreed document attached hereto as Exhibit A,
that describes the respective research experiments and the specific responsibilities of the Parties
in performing the Research Project.

     1.19 “Technology” shall mean any Biological Material, Biological Products, data, methods,
protocols, procedures, processes and the like, and the Patent Rights and Technology Rights relating
thereto.

     1.20 “Technology Rights” shall mean existing and future proprietary rights, including but not
limited to know-how rights, trade secret rights, copyrights, design rights, and all other
intellectual property rights (including without limitation the right, if any, to sue or bring other
actions for past, present or future infringement of such proprietary rights), but excluding Patent
Rights.

2. THE RESEARCH PROJECT

     2.1 Research Project. University and Ceres shall carry out the Research Project in
accordance with the Research Plan attached hereto as Exhibit A.

     2.2 Research Plan. The Research Plan shall be signed by the Parties and shall include
a detailed outline of the Research Project, time schedules for performance of specific tasks, and
an annual budget. The Parties recognize that changes to the Research Plan may be required, and
therefore agree to negotiate in good faith the terms of amendments to the Research Plan.
Modifications to the Research Plan shall only become effective, however, through a written
amendment to the Research Plan executed by the Parties

     2.3 The Parties agree to fully cooperate, including making their respective personnel
available at reasonable times, in order to expedite carrying out the Research Project efficiently
and avoiding unwarranted expenditure of effort.

 

 

     2.4 Research Performed by University.

          2.4.1 University shall use all reasonable efforts to carry out its responsibilities under the
Research Project in accordance with the Research Plan, and within the timetables set forth therein.

          2.4.2 University shall allocate its resources substantially as set forth in the Research Plan
including, but not limited to, providing at least three (3) full time equivalent personnel
(“FTEs”), who shall work on the Research Project. At least two (2) of the FTEs shall be at least
at the postdoctoral level. The other one (1) FTE shall be the technician level.

          2.4.3 The principal scientist or investigator who will direct the performance of the Research
Project on behalf of University is, unless the Parties otherwise agree, Dr. James Haseloff. All
inventions and research information disclosed pursuant to this Agreement, and all other
communications concerning the Research Project shall be directed to Dr. James Haseloff.

          2.4.4 Dr. Haseloff and his team shall not, during the conduct of the Research Project, engage
in any research in pursuit of the Purpose and the Research Project to which any other commercial
entity would receive rights.

     2.5 Research Performed by Ceres.

          2.5.1 In order to accelerate and facilitate the Research Project, Ceres may, in its sole
discretion:

               2.5.1.1 provide certain of its Background Technology to University and provide certain
Confidential Information relating thereto to University, and

               2.5.1.2 perform analysis on Project Technology provided by University.

          2.5.2 Any results arising from work performed under this Section 2.5 shall be deemed to be
Project Technology.

3. CONSIDERATION

     3.1 Research Funds. Ceres shall provide Research Funds over a three-year period to
support the Research Project, in accordance with the Research Budget attached hereto as Exhibit B.
The Research Funds paid under this Agreement shall not exceed £ (English pounds) 575,478 in total.
Installments of the Research Funds shall be provided on a quarterly basis with the first payment
occurring within thirty (30) days from the signature date of this Agreement and thereafter within
thirty (30) days from the start of each quarter. The foregoing notwithstanding, the Parties may,
from time to time, discuss the scope, direction, and pace of the Research Project, and Ceres may
agree to provide greater amounts of funding if University agrees to commit greater resources to the
Research Project.

     3.2 Equipment. On the expiration or termination of this Agreement, the University
shall retain title to any equipment provided by Ceres, or purchased with funds provided by Ceres,
under this Agreement.

 

 

4. OWNERSHIP

     4.1 Background Technology. For the avoidance of doubt, each Party shall have and
retain all rights, title and interest to its respective Background Technology used in the Research
Project.

     4.2 Project Technology. Ceres shall be the sole owner of all right, title and
interest to Project Technology. University hereby assigns to Ceres all of its rights, title and
interest to the Project Technology. . If University is prevented by law or otherwise prevented
from assigning any Project Technology to Ceres, University hereby grants to Ceres all licenses, to
the fullest extent possible, to effectuate the intent of this Agreement that Ceres be assigned all
Project Technology, and to otherwise effectuate the purposes of this Agreement.

     4.3 Other Project Technology. University shall have and retain all rights, title and
interest to the Other Project Technology.

5. PATENT RIGHTS

     5.1 University Patent Rights. Subject to all of the terms and conditions of the
Exclusive License Agreement, University will diligently prosecute and maintain the patents and
patent applications throughout the world comprising University Patent Rights covering University
Background Technology and Other Project Technology or relating to any other technology exclusively
licensed to Ceres under the Exclusive License Agreements. To aid in effectuating the purposes of
this Agreement and the Exclusive License Agreement, University shall use all reasonable endeavors
to ensure that each University’ inventor of Patent Rights covering Project Technology shall do all
acts and execute documents as may be necessary by patent laws to give effect of this clause 5.1.

     5.2 Ceres Patent Rights. Subject to all of the terms and conditions of the Exclusive
License Agreement, Ceres will diligently prosecute and maintain the patents and patent applications
throughout the world comprising Ceres Patent Rights arising out of the Research Project. In the
event patent laws require the naming of University inventors as co-inventors on Ceres’ Patent
Rights, University will assign its ownership rights of these Patent Rights to Ceres. University
shall use all reasonable endeavors to ensure that each University’ inventor of Patent Rights
covering Project Technology shall do all acts and execute documents as may be necessary by patent
laws to give effect of this clause 5.2

6. EXCLUSIVE LICENSE AGREEMENT

          During the period of negotiation of the Exclusive License Agreement neither Dr. Haseloff nor
any member of his team or any person appointed to represent the University on behalf of Dr.
Haseloff or his team shall enter into any arrangements with third parties which may conflict with
the Results, the field of research or terms of this Agreement.

7. DISCLOSURE OBLIGATIONS

     7.1 Disclosure to Ceres. Upon execution of this Agreement University shall promptly
disclose in writing or other tangible form to Ceres all of University Background Technology

 

 

existing as of the Effective Date which University has already used or plans to use in the
Research Project.

     7.2 Disclosure during Research Project. During the term of the Agreement University
shall promptly disclose to Ceres any and all Project Technology as it arises, in carrying out the
Research Project. Immediately after University becomes aware of the existence of any Other Project
Technology, University shall disclose such Other Project Technology to Ceres.

     7.3 Means of Disclosure. Any disclosure as required by this Section 7 shall be made
in tangible forms, which are mutually acceptable to both Parties. To facilitate such transfer, the
Parties shall agree upon mutually acceptable means of accomplishing such end, which means shall
include correspondence via telephone, mail, e-mail and fax as well as meetings at least every six
(6) months during the term. Such meetings shall be held at the University facilities or at Ceres,
or at such other locations as may be mutually agreed upon. About two (2) weeks prior to each such
meeting, the University shall provide Ceres with written reports concerning the Research Project.
All costs incurred in undertaking all communications relating to the Research Project shall be
borne by Ceres. Ceres shall reimburse the University for reasonable travel costs incurred in
traveling to Ceres or other locations selected by Ceres. All transportation will be coach class or
equivalent. The University or its employees shall itemize each expense and provide Ceres with
receipts for all expenses that are to be reimbursed.

     7.4 Mutual Non-Disclosure Obligations. Each Party hereby agrees that it shall keep
confidential and not use for any purpose, except as provided herein, all Confidential Information
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     7.5 Affiliates, Licensee and Sublicensees. Nothing herein shall be construed as
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     7.6 Publication and Patentability. In order to avoid the loss of, or the diminution
in value of, valuable patent rights the University agrees to ensure that the University, the
University’ inventors of the Patent Rights covering Project Technology and other University
employees and consultants involved in the Research Project delay the dissemination or publication
of any information developed in the course of performance of the Research Project or based upon any
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     7.7 Deposit of Seeds. In order to avoid the loss of, or diminution in value of,
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     7.8 Disclosure to Collaborators. Dr. Haseloff may choose to transfer selected seed
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9. LIMITATION OF LIABILITY

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11. TERM AND TERMINATION

     11.1 Term. This Agreement shall come into effect on the Effective Date and shall
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     11.2 Termination upon Breach. Upon breach or default of any of the terms and
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     11.3 Termination upon Bankruptcy. A Party shall have the right to terminate this
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     11.4 Ceres Termination Rights. In addition to the above termination rights, Ceres
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          11.4.1 If Dr. Haseloff leaves University during the term of this Agreement, and is not
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          11.4.2 Ceres believes that the intended objectives of the Research Project are not being
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12. MISCELLANEOUS

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contractors. Neither Party shall incur any debts or make any commitments for the other except
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     12.6 Entire Agreement. This Agreement together with the Exclusive License Agreement
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For the University:

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Attention: Head of Research Grants and Contracts

 

 

For Ceres:

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     12.11 No Waiver. The failure of either Party at any time or times to require
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     12.12 Headings. The headings of the several sections are inserted for convenience of
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     12.13 Survival. Upon termination of this Agreement for any reason, Sections 4, 5, 6,
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termination of this Agreement.

 

 

IN WITNESS WHEREOF the respective Parties hereto have executed this Sponsored Research
Agreement by their duly authorized officers as of the Effective Date.

	 	 	 	 	 	 	 	 	 

	THE UNIVERSITY OF CAMBRIDGE	 	 	 	CERES, INC.
	 
	 	 	 	 	 	 	 	 
	By
	 	 	 	 	 	 	 	 
	 

	 	 

	 	 	 	 	 	 
	 

	 	 	 	 	 	By:
	 	/s/ Mark Vaeck
	 

	 	Title Director of Research Services	 	 	 	 	 	 
	 

	 	 	 	 	 	 	 	Title Chief Operating Officer

	 	 	 	 	 
	DR. JAMES HASELOFF

 	 
	Signature:     /s/ James Haseloff 

 	 	 	 
	 
	 	 	 	 	 	 	 	 
	Title University Lecturer 
	 
	 	 
	 

 

 

Exhibit A

Research Plan

Decoding gene expression and plant cell fate.

Dr. Jim Haseloff,

Department of Plant Sciences, University of Cambridge,

Downing Street, Cambridge. CB2 3EA.

Tel: +44-1223-766546, Fax: +44-1223-333953,

Email: jh295@cam.ac.uk, web site: http://www.weed3D.com

Objectives of the proposed research.

The genetic control of plant development is mediated by cellular interactions, and an exchange
of positional information contributes to the self-organisation and coordination of cells during
development. The Arabidopsis root meristem provides an ideal test-bed for probing these
interactions. The root meristem grows indeterminately, is genetically amenable, has a simple and
transparent architecture, and can be induced to form de novo in adult tissues. We have developed
new genetic and optical techniques for visualising and manipulating cells within living meristems,
using a modified green fluorescent protein (GFP).

With these new approaches, it is crucial to obtain GAL4-independent markers for precisely
monitoring cell fate, and to understand the patterns of gene expression that underlie different
cell fates. I believe that recent technical advances will allow both of these objectives to
be simply realised. The first part of this proposal describes our general approach and new
methods that we have developed. The second part describes a high throughput scheme for rapidly
generating a library of Arabidopsis lines that express a cell wall localised form of GFP in
specific cell types. These enhancer trap lines will contain a novel transcription factor based on
HAPI, similar to a GAL4-based strategy that we have already developed.

The enhancer trap lines will:

(i) provide GAL4-independent GFP markers for cell fate, (Ii) allow precise
HAP1-dependent transactivation of genes in Arabidopsis,

(iii) allow histological clearing of GFP expressing tissues for detailed 3D mapping of
cell arrangements in meristems and during embryogenesis, and

(iv) the presence of a new fluorescent cell wall epitope will allow the simple isolation of highly
specific cell types in relatively large quantities for gene expression analysis using microarrays
or DNA chips and protein and biochemical analyses.

					
	 	 	 	 	 
	 
	 	Page 1
	 	 

 

 

Background.

Developing multicellular tissues or organs generally demonstrate a capacity for
self-organisation. For example, wounded tissues generally respond in a robust and coordinated
fashion to allow repair, and local induction events can initiate prolonged and coordinated
developmental processes. These types of developmental plasticity and functional autonomy are
particularly evident in plant tissues. The basic features of a plant’s body plan are established
during embryogenesis, however its final form results from the continued growth of meristems and the
formation of organs throughout its life, often in a modular and indeterminate fashion. Plant cells
are constrained by rigid cell walls and are generally non-motile, so there is the clear possibility
that cell fates within a meristem are determined by lineage. However, evidence from plant chimera
and wounding studies have demonstrated a more important role for cell-cell interactions during fate
determination (reviewed in Steeves & Sussex, Patterns in Plant Development, 1989) and
laser ablation of cells within the Arabidopsis root meristem has shown that after the death of a
cell, a neighbouring cell can be triggered to divide and compensate for the loss (van der Berg et
al., Nature 37Q:62-65, 1995). It is likely that positional information
during plant development is obtained via cell-cell contact, and that the coordination and fate of
cells within a developing meristem may be determined by a network of local cellular interactions.
We have chosen the Arabidopsis root meristem as a model system for investigating intercellular
interactions. The root meristem possesses indeterminate growth and has a simple and transparent
architecture. Arabidopsis is genetically amenable, and one can routinely generate transgenic lines
for work with the intact organism.

In order to dissect local cell-cell interactions it is crucial that we can (i) clearly image
individual cells inside living meristems and (ii) have the means to perturb them.

					
	 	 	 	 	 
	 
	 	Page 2
	 	 

 

 

Over the past several years, we have developed a set of new genetic and optical techniques which
allow us to visualise and manipulate cells within living plants.

(i) Visible gene reporters.

The jellyfish green fluorescent protein (GFP) has been adapted for use as a bright marker in
transgenic plants. The wild-type GFP cDNA is not expressed in Arabidopsis. We have extensively
modified the gfp gene to remove a cryptic intron, to introduce mutations that confer improved
folding and spectral properties and to alter the subcellular localisation of the protein. All of
these alterations have been incorporated into a single modified form of the gene (mgfp5-ER) which
we now routinely use for monitoring gene expression and marking cells in live transgenic plants
(Siemering et al., Current Biology §: 1653-1663, 1996; Haseloff et al., PNAS 94:2122-2127, 1997).

(ii) Multispectral dynamic imaging.

We have developed fluorescence microscopy techniques for high resolution observation of living
cells. The expression of GFP within an organism produces an intrinsic fluorescence that colours
normal cellular processes, and high resolution optical techniques can be used non-invasively to
monitor the dynamic activities of these living cells. Using coverslip-based culture vessels,
specialised microscope objectives and the optical sectioning properties of the confocal microscope,
it is possible to monitor simply and precisely both the arrangement of living cells within a
meristem, and their behaviour through long time-lapse observations (see
http://celldev4.plantsci.cam.ac.uk). We have recently constructed cyan and yellow emitting GFP
variants that can be distinguished from the green fluorescent protein during confocal microscopy.
These colour variants have enabled simultaneous imaging of different tagged proteins in living
cells.

					
	 	 	 	 	 
	 
	 	Page 3
	 	 

 

 

(iii) GAL4 targeted GFP expression.

In order to genetically manipulate cells during meristem development, we have devised a scheme
for targeted gene expression, which is based on a method widely used in Drosophila (Brand and
Perrimon, Development 118:401-415, 1993). We have used an “enhancer-trap” strategy to generate many
transgenic plants which express different patterns of a yeast transcription activator, GAL4. A
chosen target gene can then be placed under the control of GAL4 upstream activation sequences
(VAS), transformed into plants, and maintained silently in the absence of GAL4. Genetic crosses
between this single line and any of the library of GAL4-containing lines specifically activates the
target gene in a · particular tissue or cell type (Fig. 1). The phenotypic consequences of
mis-expression, including those deleterious to the organism, can be conveniently studied.

We found that GAL4 is not expressed in Arabidopsis due to a high A/T content, which can interfere
with mRNA processing in plants. We have produced a modified form, mGAL4-VPI6, that it is expressed
efficiently in plants, and randomly inserted the modified gene into the Arabidopsis genome, using
Agrobacterium tumefaciens-mediated transformation. The transformation vector was designed so that
expression of the mGAL4-VP16 gene would be dependent upon the fortuitous proximity of an
Arabidopsis enhancer element. The inserted DNA also contained a GAL4-responsive mGFP5-ER gene.
Thus, interesting “enhancer-trap” patterns of GAL4 gene expression were immediately and directly
visible, with each GAL4-expressing cell marked by bright green fluorescence. We have used in vivo
detection of GFP to directly screen for GAL4-directed GFP expression in 8000 regenerated plantlets.
We have documented a collection of over 250 Arabidopsis lines with distinct and stable patterns of
mGAL4-VPI6 and GFP expression in the root. These lines provide a valuable set of markers, where
particular cell types are tagged and can be visualised with unprecedented ease and clarity in
living plants (Fig. 2).

(iv) Targeted misexpression.

Most importantly, mGAL4-VP16 expression within these lines can be used to direct the
expression of a chosen gene at a precise time and place within the organism. We have produced
transgenic plants which maintain regulatory proteins or toxins, silent behind a GAL4-responsive
promoter. We can now activate these genes in specific cells by crossing to a chosen mGAL4-VPI6
expressing line. For the first time, we have a system with the potential to both precisely perturb
and to monitor the behaviour of particular cells within a living plant. For example, we are (i)
using GAL4dependent expression of the A-chain of diphtheria toxin (DTA) to kill specific cells
within the root meristem, (ii) driving misexpression of cell cycle regulatory proteins, to activate
or inhibit particular cell divisions within the root meristem (in collaboration with Dr. Sue
Bougourd, University of York), and (iii) triggering ectopic expression of homeodomain proteins in
order to affect cell fate determination. In order to better interpret these experiments, it is
crucial to gain an improved understanding of the precise timing and arrangement of gene expression
and cell architecture within normal meristems, and in these genetically perturbed tissues.
Accordingly, we have developed better techniques for the three dimensional visualisation of cell
arrangements within meristems.

(v) 3D visualisation.

The architecture of primary meristems is established early, during embryogenesis.
Unfortunately, this process is occluded by the silique and ovary walls, making direct live
observations difficult. The 3D arrangements of plant cells can be observed using either physical or
optical sectioning techniques.

					
	 	 	 	 	 
	 
	 	Page 4
	 	 

 

 

However the laborious nature of thin sectioning, the problem of obtaining the desired plane of
section, and difficulty of obtaining a complete series of sections has limited its use somewhat to
the skilled and patient. Optical sectioning has many advantages from the point of view of speed and
simplicity, and it can allow the direct viewing of living wholemounts. Here, transverse
sections need to be reconstructed from a series of Z-axis images. Nomarski optics have proved
useful for examining details within living tissues, but do not provide sufficient contrast and
resolution to allow precise 3D reconstruction of cell arrangements. Confocal laser scanning
microscopy provides a substantial improvement, but it has still proved difficult to optically
section deep into tissues due to light scattering and spherical aberration caused by particulate
subcellular matter and layers of refractile cell walls. I have been struggling with this problem
for some time, and have recently found some solutions.

Periodic acid treatment of carbohydrates produces aldehyde groups which can be reacted with various
fluorescent pseudoSchiff reagents. If fixed plant tissue is treated in this way, cell walls (and
starch-containing plastids, if present) become intensely and covalently labeled with the chosen
fluor. The tissue can then be directly cleared in a high refractive index agent containing chloral
hydrate, and mounted for microscopy. The combination of high levels of fluorescence and high
refractive index mountant allows the collection of extended Z-series images at very fine resolution
(0.2 -0.5 μM steps), using minimum confocal aperture, and without fear of photobleaching or signal
and resolution loss due to spherical aberration. The depth of image collection is limited mainly by
the working distance of the objective (>200JlM), and this allows simple optical sectioning
throughout an entire Arabidiopsis root at high resolution. In fact every cell within a
mature Arabidopsis embryo can be clearly visualised (Fig. 3). We now face the exciting
prospect of being able to clearly visualise the relative arrangement of every cell during meristem
initiation and development, and to be able to accurately map the order and pattern of cell
proliferation during meristem development.

We can routinely reconstruct the cellular structure of entire meristems for various experiments.
The large data files, between 100MB and 200MB in size, allow excavation of the data, production of
sections in arbitrary planes, and rendering of surface features. We can also use computer
visualisation methods, borrowed from the medical imaging field, to reduce large data sets to a
simple description of the 3D shapes and arrangement of cells in a meristem. These advanced software
methods for 3D segmentation allow visualisation of the dimensions, shapes and relative arrangements
of cells within optically sectioned

					
	 	 	 	 	 
	 
	 	Page 5
	 	 

 

 

meristems (Fig. 4). These same methods can be used to analyse meristems that have been genetically
perturbed by GAL4 targeted cell ablation or misexpression.

(vi) Naturally insolubilised GFP marker.

With the techniques that we have already developed, one can readily visualise living
GFP-expressing cel1s, do precise 3D analysis of fixed and stained tissues and use the GAL4 system
for targeted misexpression experiments. These experiments have led us to look for better
GAL4-independent cel1 markers, and to search for ways of retaining the GFP signal in cleared
tissues for detailed 3D analysis of marked cel1s. (The 3D visualisation methods described above
result in bleaching and loss of GFP from cleared, stained tissues). Accordingly, we have recently
developed a natural1y insolublised form of GFP.

We have fused a variant of GFP to the coding sequence of a carrot extensin. Expression of this gene
fusion in transgenic Arabidopsis tissues results in the decoration of cel1 wal1s with bright
fluorescence (Fig. 5). Extensin becomes covalently linked to the cel1 wall matrix, and the
GFP-extensin marker is resistant to various clearing techniques that normal1y result in complete
loss of the protein from treated tissues. For example, the cel1 wall bound signal is retained after
complete alcohol dehydration or glycerol infiltration. In addition, the externalised GFP provides
an epitope tag that will be useful for the physical sorting of cells using simple immunological
methods. These properties would provide a substantial benefit for the screen outlined below.

PROPOSAL

We have constructed a novel enhancer trap vector that will allow the generation of stable
Arabidopsis lines with a robust fluorescent marker within specific cell walls. It will be possible
to see developing cells, deep in cleared embryonic and meristem tissues. The marker will also
provide a cell surface epitope. For the first time, it will be possible both to
visualise the precise 3D arrangements of different cell types and to simply and rapidly isolate
those same cell types for genetic or biochemical analysis.

1. HAP1-VP16 enhancer trap vector.

The yeast GAL4 protein is a member of a family of zinc-finger (Cys4) transcription factors
which are limited to fungi, and homologues have not been found in plants to date. In order to
generate a GAL4-independent system for targeted gene expression and generation of cel1 markers, we
have constructed a synthetic HAPI-VP16 gene. HAPI is another yeast zinc-finger transcription factor
related to GAL4, but with a different binding specificity. Yeast genes have a high A/T content and
are often poorly expressed in Arabidopsis due to aberrant post-transcriptional processing.
Therefore we have constructed a synthetic gene which has an elevated G/C content, and in which the
DNA binding domain is fused to the highly active and G/C-rich transcription activator domain of
VP16. We have also synthesised an optimised

					
	 	 	 	 	 
	 
	 	Page 6
	 	 

 

 

multimeric binding site for HAP1, and cloned this behind a GFP reporter (Marion Bauch &
J.R., unpublished results). These elements have been used for the construction of an enhancer
trap vector, following the methods proven for the GAL4-based vector. We are in the process
of biologically testing this construction at present.

If this construction proves active, we will use this as the basis for a HAPI driven,
extensin-GFP enhancer trap screen. If verification of the HAPI vector is delayed for any reason, we
will use the proven GAL4-based vector. The extensin-GFP reporter gene will be inserted into the
appropriate enhancer trap vector and used to generate transgenic Arabidopsis lines.

2. High throughput screen.

All necessary reagents and techniques for a new enhancer trap screen are in place. We have
proven the feasibility of using: a cell wall GFP marker, a transcription factor based enhancer trap
screen, epifluorescence techniques for rapid screening and image documentation of primary
transformants,

					
	 	 	 	 	 
	 
	 	Page 7
	 	 

 

 

confocal microscopy techniques for precise 3D visualisation of GFP expression patterns, and have
generated hundreds of highly specific GFP tagged Arabidopsis lines. At this point, the main
limitation to using cell wall tagged lines for cell sorting or misexpression experiments, is the
new screen itself. From a practical point of view, this is the most important part of this proposal
and is based upon our experiences with the earlier GAL4-GFP screen.

For speed, I propose that we use an Arabidopsis root transformation based protocol for the
generation of transgenic plantlets. In each experiment, large numbers of transgenic calli can be
regenerated over the course of a few weeks, induced to form shoots and roots, and directly screened
by epifluorescence microscopy for extensin-GFP expression in the developing meristems. GFP
fluorescence can be seen from 4 days after Agrobacterium inoculation, depending on the expression
pattern. This ensures very rapid and obvious indication of the efficiency of each transformation
experiment. We will use a microplate based format for the growth and tracking of individual
transformants. We routinely use digital imaging techniques for archive and database construction,
and this information can be easily shared with colleagues at Ceres.

The main goal of this screen is to rapidly generate lines that possess highly specific patterns of
extensin-GFP expression for use as markers and for cell sorting experiments. Ideally, we wish to
collect lines where expression is limited or is absent from one or a few cell types (e.g. Fig 2). A
major advantage of screening primary transformants is that lines with no or broad expression
patterns can be discarded or pooled, and more interesting lines can be identified immediately. By
concentrating our initial efforts in this way, we expect to screen at least 12,000 transformed
lines The alternative (perhaps complementary) approach would be to generate transgenic lines using
an Agrobacterium -floral infiltration based approach. However, this would require much more
glasshouse space than we have available, and would not allow rapid prescreening for extensin-GFP
expression in primary transformants. I expect that the first batches of characterised seed could be
sent to Ceres within 6 months of starting the screen.

I am seeking funds to support two postdoctoral workers and one research technician to support this
screen. The screen will require a large amount of media preparation, basic microbial and plant
tissue growth and glasshouse planting and seed collection, and the efforts of a full time
technician will be required to support the work. The postdoctoral workers will be responsible for
the generation, screening, documentation and amplification of the extensin-GFP expressing lines.
The workers will have access to three confocal microscope systems and computers for 3D
reconstruction and detailed description of interesting lines. However, I have requested funds for a
Leica MZ FLIII epifluorescence stereomicroscope and computer for rapid screening and documentation
of transgenic plantlets. Our current system, based on an aging inverted epifluorescence microscope
is already over taxed. In addition, I have included a request for an additional
computer with CD-R writer to allow storage and physical segregation of Ceres-related data. The
consumables budget includes the cost of a large amount of plasticware, media, computer and
microscopy items and glasshouse supplies, including ara-cons for seed collection.

					
	 	 	 	 	 
	 
	 	Page 8
	 	 

 

 

3. Screen for embryonic expression patterns.

The primary screen (described above) will result in the generation of over 12,000 transgenic
plantlets, which will be screened for specific patterns of extensin-GFP gene expression. On the
basis of our first GAL4-GFP screen, I expect that over 1000 lines will show extensin-GFP expression
as plantlets, and 200-400 of these should maintain stable and limited patterns of expression as
transgenic lines. All or as many as possible that space allows of those plantlets that do not
express the marker will be grown for seed collection. Ideally, we would like to rescue as many of
these 12,000 primary transformants as possible, and generate independent transformed lines. Lines
which possess bright and specific embryo and floral expression patterns often show little GFP
expression as plantlets. Therefore a secondary screen is necessary for detection of these
interesting patterns.

We performed a secondary screen using pooled seed from our first GAL4-GFP experiments. This
involved the microscope dissection of flowers and siliques from hundreds of transgenic plants, and
video documentation of fluorescence within dissected embryos and floral parts. This was slow and
tedious but allowed us to obtain a useful additional collection of GAL4-GFP expressing lines.
However, use of the

					
	 	 	 	 	 
	 
	 	Page 9
	 	 

 

 

cell-wall tethered GFP marker and recent technical developments promise radical improvements in
this type of secondary screen.

The GFP-extensin marker is resistant to various clearing techniques that normally result in
complete loss of the protein from tissues prepared for microscopy. For example, the cell wall bound
signal is retained after complete alcohol dehydration or glycerol infiltration. We are now
experimenting with various gentle clearing treatments that will allow deep optical sectioning and
detailed 3D analysis of extensin-GFP marked tissues. For example, embryos can be optically
sectioned within ovules in benzyl alcohol: benzyl benzoate cleared intact siliques (Fig. 6). In
this case the clearing agent induces autofluorescence which would provide a useful counterstain. We
are continuing to experiment with different histological techniques, and I anticipate that a
judicious choice of clearing agent (which doesn’t adversely affect GFP fluorescence) will allow the
direct and highly precise observation of GFP-extensin expression deep within developing tissues.
Clearing agents include benzyl benzoate and glycerol based formulations. Of course, effective
clearing of GFP labelled tissues will have profound implications for the speed and precision of a
screen for floral and embryo expression patterns.

With some part-time support from undergraduate labour, the large number of the non-expressing
plantlets could be transferred to soil and coaxed to set seed. Flowers and siliques corresponding
to a range of developmental stages could be excised from the individual plants, dehydrated, cleared
and scored for extension-GFP expression by epifluorescence and confocal microscopy. In particular,
it should be relatively straightforward to document specific patterns of expression within embryos
at different stages of development. Unfortunately, one major impediment to a large scale secondary
screen is the lack of high quality glasshouse space (suitable for transgenic plants) in the
Department of Plant Sciences, University of Cambridge. The Department has a number of ancient
glasshouses and space for growth rooms, that are suitable for upgrading or equipping, and I am
raising funds for this. I have included a request for partial support of this necessary upgrading.

4. Sorting cell types and screening for gene expression patterns.

There is a compelling motivation for the screens described above. Tissues from transgenic
Arabidopsis lines that contain specific patterns of extensin-GFP expression can be treated with
pectinase to liberate individual cell types. The fluorescent extensin-GFP tagged cell types may
then be incubated with anti-GFP antibody coated magnetic particles, and specifically fished out of
the population of cells. The isolated cells can be checked by fluorescence microscopy to ensure
purity. If the cells are gently fixed (e.g formaldehyde treated) immediately before isolation, then
mRNA extracts will reflect the original

					
	 	 	 	 	 
	 
	 	Page 10
	 	 

 

 

state of the cells. Extracted mRNAs can then be used for the construction of specific cDNA
libraries or for scoring gene expression patterns using various PCR-based or DNA chip technologies.
The access to different cell types will only be limited by availability of an appropriate
extensin-GFP expressing line. Clearly, our aim will be to provide as near a complete collection of
highly localised patterns as possible.

The same fishing technique will be useful for studying the protein components of specific cell
types, for example using antibody assays or fluorescent 20 gel display techniques. If one uses
unfixed cells, it will be possible to assay biochemical activities. In addition, it may be possible
to use sequential selection for different epitopes, to isolate cellular subpopulations.

I anticipate that this part of the work will be carried out largely at Ceres. However, our own work
involves mapping the functional and positional relationships between cell types within the
developing Arabidopsis root meristem. The root meristem is a highly dynamic network of related
cells, and the accurate mapping of changing patterns of gene expression will need to be correlated
with the 3D arrangements of particular cellular domains. In my view, 3D visualisation techniques,
live imaging of gene expression and targeted misexpression will be essential adjuncts to this
effort. I think that we will be in a position to provide some of these extra elements. In return,
we recognise the need to understand the expression patterns of key regulators within the root
meristem -both during normal development, and after selective genetic perturbation. For example, we
are selectively misexpressing certain homeodomain proteins in the root meristem, finding
post-translational regulation, and attempting to derive constitutively active variants. Cell
sorting and DNA chip analysis of potential target genes would be an immense help in decoding
potential networks of interacting regulators.

Schedule of work.

We aim to generate and characterise more than 12,000 Arabidopsis HAPI -extensin-GFP enhancer trap
lines over 3 years. This will be the most extensive screen of its kind to date. We will use a
combination of transformation techniques to generate these lines. First, tissue culture based root
transformation methods (A) allow rapid testing of vector efficiency and direct selection of
fluorescent primary transformants in the early stages of a screen. Second, floral dip
transformation methods (B) allow simple scaling up of the process, with little requirement for
experienced personnel, allowing postdoctoral workers to concentrate on the analysis and
documentation of the lines. The unique properties of the extensin-GFP marker will aid these
screens.

	(i)	 	Individual primary transformants can be directly screened for expression during
culture. This allows the use of rapid, high efficiency tissue culture methods, and minimises
the need for amplification of subsequent generations by large scale glasshouse plantings.
(Previous large scale screens, which used Agrobacterium infiltration and the GUS
marker, have involved teams of up to a dozen workers and hundreds of square metres of
glasshouse space over many years, simply to generate the transformed material).
	 
	(ii)	 	Cell-specific expression patterns can be immediately identified. Extensin-GFP provides a
bright, insoluble fluor and tissue-specific expression can be precisely visualised and
documented in live regenerated plantlets, and cleared floral and embryonic tissues, using
epifluorescence and confocal microscopy.

Such an immediate screen allows the rapid establishment of Arabidopsis lines with
highly selective patterns of HAPI -extensin-GFP expression, within a single generation in the case
of tissue culture based

					
	 	 	 	 	 
	 
	 	Page 11
	 	 

 

 

transformation. Production of the Arabidopsis lines will involve (1) a series of
transformation experiments, (2) microscopic imaging, documentation and database construction, and
(3) amplification of selected lines. Two postdoctoral workers and a technician will be employed in
the generation and cataloguing of the lines.

(A). Tissue culture tranformation method

	 	 	 

	 

	 	Suface sterilization of Arabidopsis seed (20 mg, ~1000 seed)
	 
	 	 
	 

	 	addition to liquid media
	 
	 	 
	2 weeks

	 	Germination and growth of wild-type seedlings
	 
	 	 
	 

	 	addition of 2,4 D to liquid media
	 
	 	 
	3 days

	 	Callus induction & root harvesting
	 
	 	 
	 

	 	inoculation and transfer to CIM agar media in Petri dishes
	 
	 	 
	2 days

	 	Agrobacterium cocultivation (~10,000 explants)
	 
	 	 
	 

	 	transfer to selective SIM agar media
	 
	 	 
	4 weeks

	 	Shoot induction (up to 1500 regenerated transformants)
	 
	 	 
	 

	 	transfer to RIM agar media in 24-well dishes
	 
	 	 
	2 weeks

	 	Root induction (60 dishes)
	 
	 	 
	1 day

	 	Screen 1: root and shoot expression of extensin-GFP; document
patterns by video fluorescence microscopy
transfer to agar media in magenta boxes
	 
	 	 
	4 weeks

	 	Grow plantlets to maturity (1500 lines)
	 
	 	 
	4 days

	 	Screen 2: floral, ovule and embryonic expression of extensin-GFP.
Collect flowers and siliques in (60) 24-well dishes, dehydrate,
clear and document patterns by video fluorescence microscopy
	 
	 	 
	2 weeks

	 	Dry plants; collect and archive the seed.

(B). Floral dip tranformation method

	 	 	 

	 

	 	Planting of seed in glasshouse.
	 
	 	 
	4-6 weeks

	 	Infiltrate emerging floral bolts with Agrobacterium culture containing the
mHAP1-extensinGFP enhancer trap vector.
	 
	 	 
	4 weeks

	 	Harvest transformed seed.
	 
	 	 
	2 weeks

	 	Dry seed
	 
	 	 
	 

	 	Surface sterilise seed and transfer to petri dishes containing selective media
	 
	 	 
	1 week

	 	Score seedlings for presence of antibiotic resistance marker
	 
	 	 
	1 day

	 	Screen 1: root and shoot expression of extensin-GFP; document patterns by
video fluorescence microscopy
	 
	 	 
	 

	 	transfer transformed seedlings to soil
	 
	 	 
	4 weeks

	 	Grow plantlets to maturity

					
	 	 	 	 	 
	 
	 	Page 12
	 	 

 

 

	 	 	 

	4 days

	 	Screen 2: floral, ovule and embryonic expression of extensin-GFP.
Collect flowers and siliques in 24-well dishes, dehydrate, clear
and document patterns by video fluorescence microscopy.
	 
	 	 
	2 weeks

	 	Dry plants; collect and archive the seed.

1. Generation of enhancer trap lines.

The time course of a typical transformation experiment is shown above. In this example, a
single worker would expect to produce around 1,500 transformants in 4 months, with some technical
support for the preparation of sterile media and growth vessels. There is considerable scope for
increasing the scale of individual transformation experiments, depending on coordination and
enthusiasm of those involved, or the recruitment of additional undergraduate labour. The
application includes funds for a technician who will be required to prepare considerable quantities
of plant tissue culture media.

2. Documentation of gene expression patterns.

With each transformation experiment, there will be a need to document all expression patterns.
About 15-25% of all lines will show some form of extension-GFP expression, based on our experience
with the GAL4-GFP screen. This documentation of the primary transformants is crucial, and we have
designed schemes to streamline the process as much as possible, using digital imaging and database
techniques. In addition, those lines which possess highly specific, bright and stable expression of
the GFP marker will be examined in detail, using confocal 3D imaging techniques to precisely map
expression patterns.

Each cycle of transformation, screening and documentation of the lines and seed collection will
take 6 months. It will be feasible to generate 2,500 — 3,500 transgenic Arabidopsis plants over a
6 month period, with the support of 2 post-doctoral workers and a technician. This will allow the
screening of 12,000 individual transformants over the 3 year time period of the grant.

Projected timetable

Cambridge

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	6 months	 	 	12 months	 	 	18 months	 	 	24 months	 	 	30 months	 	 	36 months	 
	Vector optimization
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Plant transformation
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Confocal 3D imaging
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Database construction
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Number of plantlets
	 	 	1,000	 	 	 	3,000	 	 	 	6,000	 	 	 	9,000	 	 	 	12,000	 	 	 	 	 
	Establishment of lines
	 	 	 	 	 	 	1,000	 	 	 	3,000	 	 	 	6,000	 	 	 	9,000	 	 	 	12,000	 

   Ceres

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	6 months	 	 	12 months	 	 	18 months	 	 	24 months	 	 	30 months	 	 	36 months	 
	Seed from Cambridge
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Growth of lines
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Cell isolation and
microarray
screening
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 

					
	 	 	 	 	 
	 
	 	Page 13
	 	 

 

 

Funding Request

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	Year 1	 	 	Year 2	 	 	Year 3	 	 	total	 
	Dr. Smita Kurup
	 	£	28,099	 	 	£	30,350	 	 	£	32,722	 	 	£	91,171	 
	Post-doc 2
	 	£	26,922	 	 	£	29,083	 	 	£	31,412	 	 	£	87,417	 
	Technician
	 	£	18,000	 	 	£	19,205	 	 	£	20,076	 	 	£	57,281	 
	Overhead costs1
	 	£	51,115	 	 	£	55,047	 	 	£	58,947	 	 	£	165,109	 
	Glasshouse
services2
	 	£	10,000	 	 	£	10,000	 	 	£	10,000	 	 	£	30,000	 
	Consumables
	 	£	31,000	 	 	£	32,000	 	 	£	33,000	 	 	£	96,000	 
	Equipment 3
	 	£	24,000	 	 	 	 	 	 	 	 	 	 	£	24,000	 
	Glasshouse upgrade
	 	£	20,000	 	 	 	 	 	 	 	 	 	 	£	20,000	 
	Travel
	 	£	1,500	 	 	£	1,500	 	 	£	1,500	 	 	£	4,500	 
	Total
	 	£	210,636	 	 	£	177,185	 	 	£	187,657	 	 	£	575,478	 

 

			
	1	 	Overhead costs are levied by the University of Cambridge at 70%
of the salary costs. Salaries are calculated according to the University Salary Scale, and include
a salary calculated for Dr. Smita Kurup who I am supporting at present; a postdoctoral worker of 30
years of age at start, and a technician starting at grade T4/05, with cost-of-living
increments calculated at 3.5% per annum. Salaries include N.I. and U.S.S. subscriptions.
	 
	2	 	Glasshouse services includes funding for part-time undergraduate
labour.
	 
	3	 	Equipment for primary screen.

	 	 	 	 	 

	Leica MZ FLIII epifluorescence stereomicroscope with
integrating digital camera and image capture computer
	 	£	20,000	 
	 
	Apple Macintosh G3 with additional 18 GB hard disk and CD-R writer
and monitor.
	 	£	4,000	 

 

 

Exhibit B

Research Budget

 

Exhibit C

Material Transfer Agreements TYPE A and TYPE B

 

[For Purpose of Article 7.7]

UNIVERSITY OF CAMBRIDGE

MATERIALS TRANSFER AGREEMENT TYPE A

Biological Materials to which this Agreement applies:

and any related confidential information (“Information”) and/or biological materials supplied in
connection therewith by the University of Cambridge (U of C), and any products that are replicated
or obtained through use therefrom by Recipient (the “Biological Materials”).

We are pleased to provide Recipient with the Biological Materials and related Information from the
laboratory of Dr. James Haseloff (“Scientist”) of U of C, subject to the following terms:

	1.	 	Recipient agrees that the Biological Materials shall be used solely for noncommercial
research purposes to:

      

      

      

hereinafter called “Research”. This work is to be conducted in the Recipient Scientist’s
Laboratories at the Institution identified below. The Biological Materials and related Information
will not be used for testing in or treatment of humans, and shall not be used, directly or
indirectly, for commercial purposes or on behalf of or to the benefit of any commercial entity or
business.

2. The Biological Materials will not be distributed further to third parties for any purpose. In
addition, Recipient shall obtain acceptance of the terms of this Agreement of all persons under its
direct control and supervision who have access to the Biological Materials and Information.

It is further understood by Recipient that any and all proprietary rights, including but not
limited to patent rights, trademarks and proprietary rights, in and to the Biological Materials and
Information shall be and remain in U of C, subject to the rights granted herein and subject to any
rights that Ceres, Inc. may have.

3. Nothing in this Agreement grants any rights under any patents or in any know-how of U of C nor
any rights to use the Biological Materials and related Information or any product or process
related thereto or obtained through use therefrom for profit-making or commercial purposes such as,
but not limited to, production, sale, screening or design.

4. U of C makes no representation that the use of the Biological Materials will not infringe any
patent or other proprietary right of any third party. The Biological Materials are provided only
to
Recipient and only for research purposes. Such materials are provided without warranty of
merchantability or fitness for a particular purpose or any other warranty, express or implied.

 

It is understood that U of C and its employees and agents have no liability in connection with such
Biological Materials or their use.

5. In no event shall U of C be liable for any use of the Biological Materials and related
Information by the Recipient. Ceres shall not be liable for the Biological Materials and the
related Information, or their use by Recipient.

6. This Agreement will terminate in twenty (20) years after its signature date.

7. This Agreement may not be assigned by Recipient without the prior written consent of the U of C.

8. This Agreement sets forth the entire agreement and understanding between the parties and cannot
be changed or amended except by written agreement executed by both parties.

9. This agreement shall be construed in accordance with English law.

The authorized signatures below verify agreement between the parties.

	 	 	 	 	 	 	 	 	 

	FOR THE UNIVERSITY of CAMBRIDGE	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	By

	: 	
	 	 	 	DATE:	 	 
	 

	 	 

	 	 	 	 
	 	 
 
	 
	 	 	 	 	 	 	 	 
	 

	 	    Richard C Jennings Ph.D.	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	 

	 	    Director	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	 

	 	    Wolfson Industrial Liaison Office	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	 

	 	    University of Cambridge	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	 

	 	    20 Trumpington Street, Cambridge CB2 1QA	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	By

	: 	
	 	 	 	DATE:	 	 
	 

	 	 

	 	 	 	 
	 	 
 
	 

	 	          SCIENTIST’s SIGNATURE	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	FOR THE RECIPIENT:	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	[Insert Institution Name and Address]	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	By

	: 	
	 	 	 	DATE:	 	 
	 

	 	 

	 	 	 	 
	 	 
 

 

	 	 	 	 	 	 	 	 	 

	 

	 	Authorized Institutional Representative:	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	 

	 	Position:	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	By

	: 	
	 	 	DATE:	 	 	 
	 

	 	 

	 	 	 	 
	 
 	 
	 

	 	           RECIPIENT SCIENTIST’s SIGNATURE	 	 	 	 	 	 

 

[For Purpose of Article 7.8]

UNIVERSITY OF CAMBRIDGE

MATERIALS TRANSFER AGREEMENT TYPE B

Biological Materials to which this Agreement applies:

and any related confidential information (“Information”) and/or biological materials supplied in
connection therewith by the University of Cambridge (U of C), and any products that are replicated
or obtained through use therefrom by Recipient (the “Biological Materials”).

We are pleased to provide Recipient with the Biological Materials and related Information from the
laboratory of Dr. James Haseloff (“Scientist”) of U of C, subject to the following terms:

	1.	 	Recipient agrees that the Biological Materials shall be used solely for noncommercial
research purposes to:

      

      

      

hereinafter called “Research”. This work is to be conducted in the Recipient Scientist’s
Laboratories at the Institution identified below. The Biological Materials and related Information
will not be used for testing in or treatment of humans, and shall not be used, directly or
indirectly, for commercial purposes or on behalf of or to the benefit of any commercial entity or
business.

2. The Biological Materials will not be distributed further to third parties for any purpose. In
addition, Recipient shall obtain acceptance of the terms of this Agreement of all persons under its
direct control and supervision who have access to the Biological Materials and Information.

It is further understood by Recipient that any and all proprietary rights, including but not
limited to patent rights, trademarks and proprietary rights, in and to the Biological Materials and
Information shall be and remain in U of C, subject to the rights granted herein and subject to any
rights that Ceres, Inc. may have.

3. Nothing in this Agreement grants any rights under any patents or in any know-how of U of C nor
any rights to use the Biological Materials and related Information or any product or process
related thereto or obtained through use therefrom for profit-making or commercial purposes such as,
but not limited to, production, sale, screening or design.

 

4. U of C makes no representation that the use of the Biological Materials will not infringe any
patent or other proprietary right of any third party. The Biological Materials are provided only
to Recipient and only for research purposes. Such materials are provided without warranty of
merchantability or fitness for a particular purpose or any other warranty, express or implied. It
is understood that U of C and its employees and agents have no liability in connection with such
Biological Materials or their use.

5. Thirty (30) days before their submission, Recipient shall provide to U of C copies of all
posters, abstracts and publication manuscripts describing data obtained under the Research. U of
C will promptly disclose these posters, abstracts and publication manuscripts to Ceres in
confidence for the purposes of Ceres initiating a dialog with the Recipient to explore
opportunities for collaboration.

6. Confidentiality. Recipient agrees to hold in strictest confidence the Biological Materials, the
nature of the Biological Materials and Information being used except for information which:

a. is included in publications of results of the Research which are made in accordance
with the term of this Agreement; or

b. was lawfully in Recipient’s possession or control prior to the date of disclosure;
or

c. was in the public domain or enters into the public domain through no improper act on
Recipient’s part or on the part of any of Recipient’s employees; or

d. is rightfully given to Recipient from sources independent of U of C; or

e. was independently developed by employees of the Recipient without knowledge of the
Information provided by U of C, as demonstrated with written records; or

f. must be disclosed for minimum lawful compliance with court orders, regulations and
statutes.

7. In no event shall U of C be liable for any use of the Biological Materials and related
Information by the Recipient. Ceres shall not be liable for the Biological Materials and the
related Information, or their use by Recipient.

8. This Agreement will terminate when the Biological Materials become generally available to third
parties through an M.T.A. Type A (enclosed herewith as Exhibit), and such M.T. A. Type A will
substitute the present M.T.A. Type B.

9. This Agreement may not be assigned by Recipient without the prior written consent of the U of C.

 

10. This Agreement sets forth the entire agreement and understanding between the parties and cannot
be changed or amended except by written agreement executed by both parties.

11. This agreement shall be construed in accordance with English law.

The authorized signatures below verify agreement between the parties.

	 	 	 	 	 	 	 	 	 

	FOR THE UNIVERSITY of CAMBRIDGE	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	By

	: 	
	 	 	DATE:	 	 	 
	 

	 	 

	 	 	 	 
	 
 	 
	 
	 	 	 	 	 	 	 	 
	 

	 	    Richard C Jennings Ph.D.	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	 

	 	    Director	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	 

	 	    Wolfson Industrial Liaison Office	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	 

	 	    University of Cambridge	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	 

	 	    20 Trumpington Street, Cambridge CB2 1QA	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	By

	: 	
	 	 	DATE:	 	 	 
	 

	 	 

	 	 	 	 
	 
 	 
	 

	 	          SCIENTIST’s SIGNATURE	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	FOR THE RECIPIENT:	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	[Insert Institution Name and Address]	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	By

	: 	
	 	 	DATE:	 	 	 
	

		 

				
	 
	 
	 

	 	Authorized Institutional Representative:	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	 

	 	Position:	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	By

	: 	
	 	 	DATE:	 	 	 
	 

	 	 

	 	 	 	 
	 
 	 
	 

	 	RECIPIENT SCIENTIST’s SIGNATURE	 	 	 	 	 	 

 

Exhibit D

List of Patent Rights related to University Background Technology

 

Exhibit E

List of Collaborators of Dr. Haseloff

Dr. Frederic Berger

RCAP/INRA

Ecole Normale Superior Lyon

46 Allee d’Italie

Lyon

France

Dr. Susan Bougourd

Department of Biology

University of York

York

United Kingdom

Dr Alex Webb

Department of Plant Sciences

University of Cambridge

Downing Street

Cambridge CB2 3EA

United Kingdom

Dr. Mark Tester

Department of Plant Sciences

University of Cambridge

Downing Street

Cambridge CB2 3EA

United Kingdom

Dr. Scott Poethig

Department of Biology

University of Pennsylvania

415 S. University Avenue

Philadelphia, PA 19104-6018

USA

 

Draft: October 17, 2001

Stricly Confidential

Amendment I

          Effective as of October 1, 2001 (the Amendment I Effective Date)

to the Sponsored Research Agreement between The Chancellor, Masters and Scholars of the University
of Cambridge (“University”) and Ceres, Inc. (“Ceres”) of June 1, 2000 (the “Agreement”).

WHEREAS certain Technology was developed at Ceres that may be useful for the Research Project;

WHEREAS the parties wish to expand the Research Project in order to include certain activities
based on such Technology;

NOW THERFORE, the Parties agree as follows:

	 	1.	 	Section 1.2. of the Agreement — definition of “Background Technology”
shall be amended by adding at the end of the present text:

“. . .Exhibit D. In addition, Ceres Background Technology shall include
Technologies relating to recombinant transmembrane proteins as defined in
Exhibit I to Amendment I to this Agreement, developed prior to the Amendment
I Effective Date.”

	 	2.	 	A new paragraph is inserted between the first and the second paragraph
of Section 4 in the Chapter “Proposal” in Exhibit A to the Agreement, the text of
which paragraph is set forth in Exhibit I to this Amendment I. This addition to
the Research Project is referred to hereinafter, when distinguished from the
remainder of the Research Project, as Addition to Research Project.

	 	3.	 	A new Section is added to the Chapter Funding request in Exhibit A to
the Agreement, the text of which is set forth in Exhibit I to this Amendment I.

	 	4.	 	For the avoidance of doubt, any results arising from work performed by
University with the Ceres Background Technology referred to in Exhibit I to this
Amendment I shall be deemed to be Project Technology.

Page 1 of 4

 

Draft: October 17, 2001

Stricly Confidential

	 	5.	 	In Section 7.6 on Publication and Patentability, the following clauses
shall be added at the end:

	 	7.6.1.	 	Notwithstanding the above, any student of the University working on
the Addition to the Research Project (Student) may include some or all
of the results acquired during the work on the Addition to the Research
Project in a thesis submitted for a degree of the University. The
thesis shall be examined by examiners appointed by the University and a
successful thesis deposited in the University library in accordance
with University Regulations. The Student shall, on request of Ceres,
request that access to the thesis be restricted initially for two (2)
years and then for a period of up to five (5) years, for one year at a
time. This request by Ceres shall not be unreasonably denied by the
University.
	 
	 	7.6.2	 	The examiners of the thesis will examine the
thesis in confidence according to University regulations, but Ceres
may, at its discretion, request that the examiners agree in writing to
be bound by the terms of confidentiality as set out in Sections 7.4 and
7.6 of the Agreement.

	 	6.	 	For the remainder, the Agreement shall be unchanged and continue in
full force and effect, and this Amendment shall constitute an integral part
thereof.

IN WITNESS WHEREOF the respective Parties hereto have executed this Amendment I by their duly
authorized officers as of the Amendment I Effective Date.

	 	 	 	 	 	 	 

	THE UNIVERSITY OF CAMBRIDGE	 	CERES, INC.
	 
	 	 	 	 	 	 
	By:

	 	 	 	By:
	 	/s/ Mark Vaeck
	

		

				 

	 

	 	 	 	 	 	Mark Vaeck
	Title:

	 	Director of Research Services
	 	Title:
	 	Chief Operating Officer
	 
	 	 	 	 	 	 
	By:

	 	/s/ James Haseloff
	 	By:
	 	/s/ Richard Flavell
	

		

				 

	 

	 	James Haseloff
	 	 	 	Richard Flavell, CBE, FRS
	Title:

	 	Lecturer
	 	Title:
	 	Chief Scientific Officer

Page 2 of 4

 

Draft: October 17, 2001

Stricly Confidential

Exhibit I

                         to Amendment I to the Sponsored Research Agreement

	1.	 	Certain Ceres Background Technology: Recombinant transmembrane
proteins.
	 
	 	 	There are a range of other opportunities for cell sorting in addition to using
cell wall-insolubilized GFP-extensin. Protoplasts can be isolated from a variety of
tissues in Arabidopsis and many other plant species, and it might be possible to use
ligands exposed at and attached to the surface of the plasma membrane for sorting.
One possibilty is to explore GFP-tagged proteins arising from random gene fusion
that localize to the plasma membrane, such as the PIP fusion from the Carnegie
Institute. Another possibility is to engineer transmembrane proteins such as
receptor kinases or other proteins with secretion signals and hydrophobic domains
such that they carry a fluorescing protein such as GFP to the cytosolic face of the
membrane, and a ligand such as an antigen to the extracellular face. Protoplasts
prepared from tissues carrying a bifunctional protein such as this could allow
sorting of protoplasts visualized by fluorescence. A recombinant receptor kinase and
a recombinant permease have already been assembled at Ceres, and these could form
the basis of these experiments.
	 
	2.	 	Proposal: New text to be included as paragraph 2 of Section 4
	 
	 	 	Two recombinant transmembrane proteins — a receptor kinase and a permease -
have also been generated at Ceres, and both have been introduced into plants. To
explore the potential of these proteins for protoplast sorting, we will use confocal
microscopy to see if these recombinant proteins carry GFP to the inner face of the
plasma membane. If either of them do, we will use anti-FLAG antibody to see if they
also deliver FLAG epitopes to the other face. This can be done by immunofluorescence
on sectioned material or protoplasting and addition of anti-FLAG antibody carrying
small beads. Proteins that provide GFP and FLAG to opposite surfaces of the plasma
membranes will be expressed in Hap1-activation lines, the cells and tissue so
identified being targets for confocal imaging and cell sorting. Fluorescing
protoplasts can be sorted from nonfluorescing protoplasts by applying magnetic beads
to the extracellular ligands. These magnetic beads will be applied as antibody
conjugates or other kinds of conjugates. Scientists at Ceres have direct experience
with magnetic separation procedures and can help with the sorting.
	 
	 	 	In case the Ceres Background Technology referred to in Exhibit I to Amendment I to
the Agreement does not work correctly, a set of transmembrane proteins will be
engineered such that GFPs are added to the exposed cytosolic domains and FLAG,
histidine or c-myc tags added to the extracellular domains. This can be in

Page 3 of 4

 

Draft: October 17, 2001

Stricly Confidential

	 	 	a systematic way, so that all the receptor kinases, for example, in the Arabidopsis
genome are processed for cell sorting applications. When expressed in plants,
	 
	 	 	these recombinant proteins will also allow visualization of cells that are also
marked by extracellular tags.
	 
	3.	 	Funding request: addition

	 	 	 	 	 	 	 	 	 
	 	 	Year 1	 	 	 	 
	 	 	October 1, 2001 to	 	 	 	 
	 	 	September 30, 2002	 	 	Total	 
	Graduate Student
	 	£ 28,000	 	 	£	28,000	 

Page 4 of 4

 

Miss Helen Atkinson

Contracts Manager

	 	 	 

	Richard Flavell
	 	
	Chief Scientific Officer

	 
	Ceres Inc
	 
	3007 Malibu Canyon Road

	 	Research Services Division
	Malibu
	 	 
	CA 90265
	 	 
	USA
	 	 

			
	 
	22 May 2003
	 	When replying please quote: RG31274

Dear Mr Flavell,

Studentship for Alex Navid — Continuation to PhD

‘Decoding gene expression and plant cell fate’

I am writing with reference to your correspondence with Alex Navid and Professor Haseloff of
October 2002, in which you state that you are willing to provide $40,000 funding per year for 2003
and 2004, for the continuation of Alex Navid’s research.

In order that this additional funding can be activated on our system, I would be grateful if you
could confirm that you are willing for the end date of the original contract to be extended in
order to cover the renewed time period for Alex Navid’s funding. If this acceptable to you please
could you sign and return the duplicate of this letter, which shall be taken as your agreement that
the duration of the Sponsored Research Agreement shall be extended to 31st December
2004.

May I take this opportunity to thank you for sponsoring this research and for the additional
funding for Alex Navid.

If you have any questions relating to this, please do not hesitate to contact me.

Best Regards,

	 	 	 	 	 
	 	 
	/s/ Helen Atkinson
 	 
	Helen Atkinson	 
	 	 
	 

I agree to extension of the Sponsored Research Agreement between The University of Cambridge
and Ceres, Inc. as outlined above.

	 	 	 

	Signed: /s/ Richard Flavell
 

	 	Date: June 4, 2003

Title: CSO

	 	 	 

	 

	 	16 Mill Lane

Cambridge
	 

	 	CB2 1SB
	 
	 	 
	 

	 	Telephone: 01223 765056
	 

	 	Fax: 01223 332988
	 

	 	E-mail: helen.atkinson@rsd.cam.ac.ukexv10w12

Pages where confidential treatment has been requested are stamped

‘Confidential Treatment
Requested and the Redacted Material has been separately filed with the Commission,’ and the
confidential section has been marked as follows: [***].

Exhibit 10.12

EXECUTION COPY

AMENDED AND RESTATED SPONSORED RESEARCH AGREEMENT

BETWEEN

CERES, INC.

and

TEXAS AGRILIFE RESEARCH

This Amended and Restated Sponsored Research Agreement (“Agreement”)

is made and entered into as of
September 24, 2011 (the “Effective Date”) by and between Ceres, Inc., a corporation with principal
offices in Thousand Oaks, California, a Delaware corporation (“CERES”) and Texas AgriLife Research
(“AGRILIFE”) with principal offices in College Station, Texas, a member of The Texas A&M University
System (“TAMUS”), an agency of the State of Texas. CERES and AGRILIFE are collectively referred to
as “Parties” and individually as a “Party.”

WHEREAS, AGRILIFE and CERES have in common the desire to encourage and

facilitate the discovery,
dissemination and application of new knowledge, and CERES desires to support said research;

WHEREAS, AGRILIFE, formerly known as The Texas Agricultural Experiment Station,

a member of TAMUS
(“TAES”), and CERES have conducted such research under that certain Sponsored Research Agreement,
dated as of August 29, 2007 (as amended, supplemented and otherwise modified by way of those
certain written amendments entered into by the Parties, effective as of June 18, 2008, July 15,
2008, October 22, 2008 and August 29, 2007, the “Original Agreement”);

WHEREAS, the Parties desire to continue to improve germplasm, develop lines and

hybrids of sorghum
and its interbreeding species and develop DNA markers and marker platform technology to advance the
development of biomass/bioenergy crops and enter into a master research agreement to facilitate
such activities;

WHEREAS, the Parties desire for CERES to have rights to commercialize such

technologies, germplasm
and other results arising out of the research conducted by AGRILIFE under this Agreement in
connection with the production of bioenergy, biofuels, biochemical, sugar, and other bioproducts;
and

WHEREAS, pursuant to Article 16.A of the Original Agreement the Parties

desire to amend and restate
the Original Agreement in its entirety, incorporating by reference the Appendices to the Original
Agreement as provided in Article II.C hereof, and proceed with the Program (as defined below) under
this Agreement.

NOW THEREFORE, in consideration of the mutual covenants and premises contained

in

			
	 	 	 
	Amended and Restated Sponsored Research Agreement
	 	Page 1 of 34

 

 

this Agreement, the receipt and sufficiency of which is acknowledged, the

Parties agree as follows:

	I.	 	PROJECT MANAGEMENT
	 
	 	 	A. AGRILIFE will perform research projects as agreed upon by the Parties (each such
research project, a “Project,” and all such Projects, together, the “Program”). The
proposals for, review of, recommendations to the Executive Committee for approval of, and
implementation of the Projects under the Program will be overseen by a committee of four
members (the “Management Committee”). Two members will be nominated by each Party to serve
on the Management Committee.
	 
	 	 	B. The Management Committee will be a forum for communication and exchange of information
regarding the implementation of the Projects under the Program. It shall have no authority
to make any modifications to this Agreement, but may formulate recommendations to change
the Projects under the Program or to take advantage of additional funding opportunities and
present such recommendations to CERES and AGRILIFE for consideration. AGRILIFE agrees to
permit CERES representatives to confer as necessary with Principal Investigators. It is
understood and agreed that the Management Committee and CERES representatives have no
authority to supervise, direct or control the work performed hereunder.
	 
	 	 	C. Recommendations of the Management Committee shall be made by unanimous agreement and
recorded in a manner prescribed by the Management Committee as a true record of the
recommendations. If the Management Committee cannot come to a unanimous agreement on any
matter for which it is responsible, then the Management Committee shall refer the matter to
the Executive Committee.
	 
	 	 	D. The Management Committee shall have the discretion to designate any selected gene or
group of genes as a cloning target (“Cloning Target”). The Management Committee shall also
have the discretion to decide that a selected gene or group of genes is no longer a Cloning
Target. The selection or deselection of a Cloning Target will be communicated to all
Principal Investigators conducting Projects under the Agreement at the time of such
selection or deselection.
	 
	 	 	E. The Management Committee will meet at least once every four (4) months with additional
meetings as mutually agreed upon and exchange information and data regarding the
implementation of the Program. At least one (1) week before each Management Committee
meeting, AGRILIFE will provide CERES with a report on the Program activities performed
since the last Management Committee meeting. A preferred format for such reports will be
created by the Management Committee. Such reports will contain at least the following with
respect to each pending Project (“Basic Report Information”):

			
	 	 	 
	Amended and Restated Sponsored Research Agreement
	 	Page 2 of 34

 

 

	 	•	 	status update;
	 
	 	•	 	actual spending relative to budget, including FTE breakout;
	 
	 	•	 	description of Subject Inventions and germplasm generated during the period; and
	 
	 	•	 	copies of slide presentations summarizing research progress.

	 	 	Upon CERES’ request, additional information, if not specifically included in the Basic
Report Information, shall be delivered to CERES as supporting information with respect to
each pending Project at the related meeting (“Additional Information”), including, without
limitation:

	 	•	 	breeding records;
	 
	 	•	 	copies of field or greenhouse books and records;
	 
	 	•	 	DNA sequencing results of genotypes;
	 
	 	•	 	detailed descriptions of each genotype sequenced including phenotypes collected;
	 
	 	•	 	other genotyping data collected including QTL’s and markers;
	 
	 	•	 	current markers being utilized for genotyping breeding materials; and
	 
	 	•	 	as may be requested from time to time, copies of raw field trial data.

	 	 	In addition to providing the Basic Report Information and Additional Information to CERES
in connection with such Management Committee meetings, upon CERES’ request, AGRILIFE shall
update the Basic Report Information and Additional Information and provide such updated
Basic Report Information and Additional Information to CERES within ten (10) days after
AGRILIFE’s receipt of such request.

	II.	 	PROGRAM MANAGEMENT

	 	 	A. A committee of four (4) members (the “Executive Committee”) will oversee the activities
between the Parties for the Program. Two (2) members will be nominated by each Party to
serve on the Executive Committee. The Executive Committee will meet at least once every
six (6) months with additional meetings as mutually agreed upon by the Parties. Each Party
will ensure that at least one nominee has sufficient signature authority to enact the
obligations of the Executive Committee set forth in this Agreement. Any of the members of
the Management Committee may join any such meetings of the Executive Committee unless the
Executive Committee unanimously indicates otherwise.
	 
	 	 	B. The Executive Committee will be responsible and have authority for the approval,
rejection, modification, extension and cancellation of Projects and for overseeing the
budget for Projects. In connection with each Project, the Executive Committee

1. will be responsible for tracking the milestones specified in

the work statement
for such Project and will have authority to cancel such

			
	 	 	 
	Amended and Restated Sponsored Research Agreement
	 	Page 3 of 34

 

 

Project in the event any
such milestone is not met; and

2. will have authority to increase or decrease the budget on a

semi-annual basis
for such Project.

	 	 	In addition, the Executive Committee will have authority for re-allocating priorities
within the Program based on, among other things, any market events and/or any technical
successes achieved or difficulties encountered in connection with any Project.
	 
	 	 	C. Notwithstanding the meeting frequency described in Article II.A., the Executive
Committee shall hold a special meeting within ten (10) business days of the Effective Date.
At such special meeting, the Executive Committee will consider and take actions it deems
appropriate with respect to the following matters: (1) reviewing and confirming the status
of the Parties’ existing activities under the Original Agreement as further described in
Appendices A, B and C as amended, of the Original Agreement, (collectively, the “Original
Workplan”); (2) determining which aspects of the Original Workplan will remain active and
transition into Projects under this Agreement; (3) determining the handling of any aspects
of the Original Workplan which will not transition into Projects under this Agreement; and
(4) any other matters which the Executive Committee deems appropriate to facilitate the
transition of Original Workplan activities under the Original Agreement to Projects under
this Agreement. The Original Workplan is incorporated herein by reference; however, the
Parties acknowledge that each Proposed Project will have a budget and that Appendix B is
incorporated herein for informational purposes only.
	 
	 	 	D. Either Party may submit proposals to the Management Committee for any research and
development project that such Party wishes to include as a Project under this Agreement
(“Proposed Project”). Any such proposal shall be in the form of Appendix A and shall
include at least a reasonably detailed description of such Proposed Project, the goal(s) of
such Proposed Project and the proposed timeline, milestones and budget for such Proposed
Project. The Management Committee will decide whether to recommend acceptance of the
Proposed Project to the Executive Committee within twelve (12) months after its receipt of
the proposal for such Proposed Project. The Executive Committee shall consider the
Management Committee’s recommended Proposed Projects, if any, at each regular meeting of
the Executive Committee, and make the final decision whether to accept or reject each
Proposed Project. If the Executive Committee decides to accept and proceed with any such
Proposed Project as a new Project under this Agreement, the Executive Committee shall
request that the Management Committee develop a scope of work statement (including, without
limitation, budget, targeted start date and completion date and agreed upon milestones and
deliverables) with respect to such new Project, substantially in the form of Appendix A.
Upon the execution of such work statement by the Parties, the
research project described in such work statement shall be a Project under this Agreement.

			
	 	 	 
	Amended and Restated Sponsored Research Agreement
	 	Page 4 of 34

 

 

	 	 	E. In the event that, following completion of the Proposed Project process set forth in
Article II.C., the Executive Committee decides not to fund a Proposed Project within the
CERES Field (“Unfunded Proposed Project”), such Unfunded Proposed Project shall be referred
by the Executive Committee back to the Management Committee. If AGRILIFE desires to pursue
alternate funding opportunities, AGRILIFE shall present not more than one (1) Unfunded
Proposed Project annually to the Executive Committee for reconsideration at a regular
meeting of the Executive Committee. Upon the Parties’ mutual written agreement, the
Management Committee may recommend in writing that the Executive Committee reconsider
certain additional Unfunded Proposed Projects from time to time as part of the Executive
Committee’s regular meeting agenda. The Executive Committee shall be responsible for
determining the outcome of any such Unfunded Proposed Project in a manner which shall not
unduly impact the respective interests of the Parties and which is subject to the
provisions of Article IV hereof. The Parties contemplate that such potential outcomes may
include, but not be limited to, engaging in joint efforts to obtain funding from agencies
or organizations that provide grants for research, creating jointly-owned companies that
may pursue the Proposed Project, delaying the funding by CERES of such Proposed Project for
a reasonable period, or revising the statement of work and budget for the Proposed Project.
	 
	 	 	F. If the Executive Committee cannot come to a unanimous agreement on any matter for which
it is responsible, then the members of the Executive Committee nominated by CERES shall
make the final decision with regard to such matter, except that the members of the
Executive Committee nominated by AGRILIFE shall make the final decision with regard to
whether AGRILIFE has the capacity and capability to perform any Project or whether any
proposed budget for any Project is reasonably feasible.

	III.	 	RESEARCH MANAGEMENT
	 
	 	 	A. The research under each Project will be supervised by the Principal Investigator(s)
identified in such Project. No substitution of any such Principal Investigator(s) will be
made without the prior written consent of CERES.
	 
	 	 	B. Each Party acknowledges and agrees that the Projects are research in nature and hence
the achievement of the deliverables and/or milestones specified in the Projects cannot be
guaranteed. Neither Party guarantees any particular outcome or specific yield arising from
any Project.
	 
	 	 	C. Each Party will require any and all of its employees and researchers who will perform
Program activities to sign a statement stating that they have read and understand the
obligations of AGRILIFE under Article VI and Article XI. AGRILIFE affirms that, as per The
Texas A&M University System Policy 17.01, Subsection 2.2.1, intellectual property conceived
or developed with support from
TAMUS or any of its members in the form of administered funds shall be owned by TAMUS, and
that the funding received from CERES will constitute such administered funds under such
policy.

			
	 	 	 
	Amended and Restated Sponsored Research Agreement
	 	Page 5 of 34

 

 

	 	 	D. Except in the case of permitted subcontracting as provided in Article III.H, below, each
Party will conduct Program activities exclusively in laboratories, greenhouses or fields
under full control of or owned by that Party. Each Party will take all reasonable
precautions to prevent damage to or third party access to any information related to, or
unintentional destruction of or release of, any germplasm created in the Program.
	 
	 	 	E. Each Party will strictly comply, and use its commercially reasonable efforts to cause
its employees and researchers conducting Program activities to comply, with notebook and
breeding book keeping policies of the highest standards as applicable in the field. Each
Party will record and keep all field evaluation, composition and marker data in
user-friendly and secure electronic database format with limited access.
	 
	 	 	F. Each Party shall be responsible for its compliance, and will comply, with all applicable
laws, rules and regulations, including, without limitation, those relating to genetically
modified organisms (to the extent the Program involves such organisms), and will obtain any
and all permits or authorizations or proceed to any notifications which may be required by
such laws, rules and regulations.
	 
	 	 	When contributing sorghum germplasm for Program activities, the contributing Party will
verify what the origin of the material is and inform the other Party in writing from
whom/where and approximately on what date such Party initially obtained such germplasm. If
the germplasm contributed is governed by the Convention on Biological Diversity (“CBD”) or
the International Treaty on Plant Genetic Resources for Food and Agriculture (“ITPGRFA”),
the contributing Party will be responsible for obtaining all necessary authorizations to
commercialize any such genetic material and the results arising from the use of such
genetic material, as applicable under the CBD and/or ITPGRFA, under financial terms and
conditions defined by the applicable authorizing body under the CBD or ITPGRFA, as
applicable, and neither Party will use any germplasm in the Program for which the preceding
condition is not satisfied. Further, each Party shall only contribute germplasm to the
Program for which such Party has breeding rights with the right to commercialize the
progeny.
	 
	 	 	G. Any subcontracting of Program activities to a third party by AGRILIFE will be subject to
CERES’ prior written approval which will not be unreasonably withheld. CERES may
subcontract any Program activities to any third party.

	IV.	 	RESTRICTIONS ON AGRILIFE RESEARCH.

	 	A.	 	Definitions

1. “Biomass/Bioenergy/Sweet Sorghum” means

	 	 	 	a)
sorghum or Sorghum [***] which has
been identified, bred, or selected
for the purpose of conversion to fuels, chemicals, sugar, energy or other
bioproducts, including, but not limited to, sorghum

			
	 	 	 
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	 	Page 6 of 34

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which has been bred to
produce higher biomass yields, higher yields of cellulose, higher yields
of sugar, other improved composition, improved agronomics, improved net
energy balance or improved energy density or which has been bred to make
its cellulose or sugars more available to conversion or more efficiently
converted, or

b) sorghum or Sorghum [***] lines that enable better

breeding or
contribute to the development of commercial products, including, but not
limited to, energy, fuels, chemicals, sugar or other bioproducts.

Biomass/Bioenergy/Sweet Sorghum shall not include

c) sorghum or Sorghum [***] which has been improved

through breeding for
increased starch yields, including, but not limited to, grain sorghums
(even where such sorghum must necessarily produce increased yields of
sugar to achieve increased starch content), or

d) sorghum or Sorghum [***] which has been improved

through breeding for
a purpose that does not include conversion to fuels, chemicals, sugar,
energy or other bioproducts, including, but not limited to, the purposes
of silage, forage, grain or other traditional uses for sorghum for feed or
food purposes

2. “CERES Field” means Germplasm Improvement to

develop Biomass/Bioenergy/Sweet
Sorghum.

3. “Germplasm Improvement” means any activities to

improve sorghum or Sorghum
[***], including without limitation selection, breeding, marker development or
marker assisted breeding or transgenic improvement.

4. “Sorghum [***]” or “Sorghum

[***]” means [***] plants (those which do [***] and
[***] or [***]) created utilizing the [***] and [***] of the [***] sorghum

[***].

	 	B.	 	AGRILIFE acknowledges and agrees that during the term of this Agreement:

1. To the extent that AGRILIFE conducts, directly or

indirectly, any research in
the CERES Field, other than in the Program, under any funding or any collaboration
agreement other than this Agreement, AGRILIFE agrees not to grant any rights in the
CERES Field to any person or entity other than CERES.

2. AGRILIFE will notify CERES in advance in writing of any

			
	 	 	 
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	 	 	 	contemplated projects
in Germplasm Improvement in sorghum and/or Sorghum [***], outside the CERES Field,
that would result in the grant of any rights by AGRILIFE, TAMUS and/or any other
TAMUS member to a for-profit person or entity pursuant to a sponsored research
agreement or other funded collaboration agreement in which such for-profit person
or entity finances such research and, at CERES’ request, to discuss in good faith
any such project with CERES, subject to any applicable confidentiality provisions.
	 
	 	 	 	3. AGRILIFE’s participation in any third-party sponsored research in
Biomass/Bioenergy/Sweet Sorghum, outside the CERES Field, shall be subject to
AGRILIFE’S compliance with the Guidelines for Future Collaborative Opportunities
(“Guidelines”) which are included in the Amended and Restated Intellectual Property
Rights Agreement entered into as of August 27, 2007 by and between TAMUS and CERES,
as amended and restated as of September 24, 2011, the “IPRA”). Both Parties agree
to comply with such Guidelines.
	 
	 	 	 	4. Unfunded Proposed Projects in the CERES Field shall be handled as set forth in
Article II.E.
	 
	 	 	 	5. AGRILIFE agrees that germplasm developed using any Lines will only be released
or made available to third parties for commercialization or Germplasm Improvement
if such germplasm

a) is less than five percent (5%) identical to any of the

Lines under
exclusive option or exclusive license to CERES based on genetic
contribution as determined by pedigree,

b) contains no specific Allele(s) optioned or exclusively

licensed to
CERES to which a Line’s specific valuable phenotype or trait is
attributable,

c) contains no Subject Inventions optioned or exclusively

licensed to
CERES, and

d) contains no CERES proprietary technology or intellectual

property.

The foregoing provisions in this Article IV.B.5 do not

limit and are subject to
Article IV.B.1, Article IV.B.2, Article IV.B.3 and Article IV.B.4.

	V.	 	IN-KIND SUPPORT
	 
	 	 	A. In partial consideration for the covenants of AGRILIFE contained in this
Agreement, within sixty (60) days of the Effective Date or as otherwise set forth in
Appendix B, the Parties will enter into good faith negotiations, for a period not to exceed
one hundred twenty (120) days without mutual written agreement of the

			
	 	 	 
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	 	 	 	Parties, for
appropriate contractual agreements as applicable for CERES’ provision to AGRILIFE of
certain in-kind research support as further described in Appendix B (collectively, “In-Kind
Support”) for AGRILIFE’s use in performing Program activities. For the avoidance of doubt,
the obligation to enter into good faith negotiations is a material obligation under this
Agreement. Any such use of In-Kind Support by AGRILIFE shall be subject to the terms and
conditions of a separate written agreement to be negotiated in good faith and entered into
by the Parties. Unless otherwise agreed to by CERES in any such separate written
agreement, any such use by AGRILIFE shall be solely for Program activities. Unless
otherwise agreed by the Parties in such separate written agreements, any Materials,
Derivatives, Progeny, germplasm, Hybrids, Lines or other intellectual property arising out
of any use by AGRILIFE of In-Kind Support shall be deemed Program Intellectual Property
subject to Article IX.
	 
	 	 	 	B. Notwithstanding anything else in Article IV, Article IX, this Article or otherwise, in
no event shall AGRILIFE publish, use or exploit outside of the Program any CERES Original
Materials, Derivatives, Progeny, data, information, intellectual property, technology or
in-kind research support (including, without limitation, any In-Kind Support) provided or
made available by CERES for use in or otherwise in connection with the Program, or any
Derivatives, Progeny or information developed or derived therefrom, without in each
instance the prior written consent of CERES, which consent may be granted, withheld or
conditioned in CERES’ sole discretion.

	VI.	 	TRANSFER OF MATERIALS

	 	A.	 	DEFINITIONS

1. “Derivatives” means plants made by a Receiving

Party from the Original Materials
of the other Party through traditional or artificial means, excluding, however,
Progeny of the Original Materials. “Derivatives” further means any plant part or
seed of Derivatives or biological samples made from Derivatives, or any Progeny of
Derivatives.

2. “Existing License and Material Transfer

Agreements” means the license and
material transfer agreements listed in Appendix C:

3. “Materials” means Original Materials, Derivatives

and Progeny of such Original
Materials.

4. “Original Materials” means (i) any plant

materials owned, jointly owned or
otherwise controlled by a Party (“Originating Party”) and transferred to the other
Party (“Receiving Party”) under this Agreement, and any Progeny of such materials,
and (ii) any plant part or seed of plant
materials included in Article VI.A.4.(i) or biological samples made from plant
materials included in Article VI.A.4.(i).

			
	 	 	 
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	 	 	 	5. “Progeny” means the offspring of a plant produced through asexual propagation or
sexual multiplication or maintenance where such offspring is not substantially
genetically different from such plant.

	 	 	 	B. It is contemplated that either Party may supply samples to the other Party under the
terms of this Article VI.
	 
	 	 	 	C. Within thirty (30) days after the Effective Date, CERES shall provide to the OTC (as
defined in Article XIV) a list of all Original Materials received by CERES from AGRILIFE,
including for each Original Material the designation of the implementing letter it was
received under, which are not the subject of any Existing License and Material Transfer
Agreement (excluding any publicly available lines or CERES Confidential Information). For
any Original Material which has been received by CERES which was not received under an
implementing letter, the Parties shall promptly generate an implementing letter. Both
Parties shall periodically update such lists of Original Materials transferred and
implementing letters during the term of this Agreement.
	 
	 	 	 	D. The Parties agree that any Original Materials provided by AGRILIFE to CERES pursuant to
this Agreement may be used by CERES and its Affiliated Companies for the following purposes
and such other purposes as the Parties may mutually agree upon in writing:

	 	1.	 	creating Progeny;
	 
	 	2.	 	creating Derivatives;
	 
	 	3.	 	research activities, evaluation and the conduct of trials using Materials;

	 	 	 	CERES acknowledges that no right in Materials, markers, or DNA sequence data and
information, is granted nor grantable herein or in the Original Agreement for CERES’ use
for commercial exploitation purposes, and that any grant of commercial exploitation rights
must occur through the instrument of a separate agreement, and that such grants of
commercial exploitation rights, including without limitation those set forth in the
Existing License and Material Transfer Agreements, supersede the limitations on the use for
commercial exploitation of Materials, markers, or DNA sequence information, set forth in
this Agreement. CERES shall be responsible for its Affiliated Companies’ compliance with
this Agreement or any of its provisions.
	 
	 	 	 	E. All Original Materials provided by the Originating Party to the Receiving Party should
be considered experimental and should be handled by the Receiving Party with appropriate
safety precautions. The Receiving Party agrees to exclusively and restrictedly use all
Materials under suitable containment conditions, in a safe manner, and in compliance with
all applicable state and federal laws and regulations, and not to use Materials on human
subjects.
	 
	 	 	 	F. The Originating Party of the Original Materials will obtain any permits required for the
delivery of such Original Materials to the Receiving Party or

			
	 	 	 
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	 	 	 	proceed to any required
notifications prior to the delivery of such Original Materials to the Receiving Party, and
such Receiving Party will reasonably cooperate with such Originating Party in order to
facilitate the issuance of any required permits. The Receiving Party will obtain any
authorizations or permits which may be required for its activities with Materials.
	 
	 	 	 	G. The Receiving Party agrees that Materials will be used solely for the purpose of the
Program and, in the case where CERES is the Receiving Party, for the purposes described in
Article VI.D above.
	 
	 	 	 	H. The Receiving Party will only grant access to Materials intended for Program activities
to its employees or researchers who need access to such Materials for the purpose of the
Program and, in the case where CERES is the Receiving Party, for the purposes described in
Article VI.D above.
	 
	 	 	 	I. The Receiving Party agrees that Materials will not be supplied or made available to any
other persons or entities, either within or outside of the Receiving Party, without the
prior written approval of the Originating Party. Such Materials will not be sold or
transferred for commercial exploitation purposes.
	 
	 	 	 	J. Notwithstanding anything to the contrary in this Article VI, the Parties agree that the
Materials provided to CERES by AGRILIFE, or made available to CERES by AGRILIFE, or derived
by CERES from AGRILIFE Original Materials, in each case under this Agreement or the
Original Agreement, may be supplied to any third parties with whom CERES has entered into
any collaboration, evaluation (including, without limitation, field evaluation, composition
and/or conversion) and/or material transfer agreements or any agreement similar to any of
the foregoing (each a “Collaborator”) or any subcontractors of CERES (each a
“Subcontractor”), provided that such Collaborator or Subcontractor, as the case may be, (i)
will only be allowed to use such Materials for the purpose of the implementation of, and
the exercise of its rights and performance of its obligations under, its agreement or
agreements with CERES, (ii) will be subject to applicable obligations with respect to such
Materials that are consistent with this Agreement and (iii) will have no greater scope of
rights in using such Materials than CERES. Upon AGRILIFE’s reasonable written request,
CERES will provide to AGRILIFE reasonable, non-confidential information with respect to
such Materials provided pursuant to CERES’ agreements with Collaborators provided that
CERES has the right to disclose such information to AGRILIFE; any such information will be
deemed Confidential Information of CERES.
	 
	 	 	 	K. In the event that the Receiving Party desires to utilize Materials for any uses beyond
the scope of this Agreement, the Parties shall enter into good faith negotiations to
establish the terms and conditions for any such purposes; however, nothing in this
Agreement shall be construed as a representation that the Originating Party guarantees the
grant of such rights.
	 
	 	 	 	L. The Receiving Party will keep and maintain written or electronic records

			
	 	 	 
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	 	 	 	of all use by
the Receiving Party of the Original Materials provided or made available by the Originating
Party under this Agreement and the Original Agreement, including records of Derivatives and
Progeny that have been made, and shall provide such records to the OTC and to the other
Party within thirty (30) days after each anniversary of the Effective Date of this
Agreement.
	 
	 	 	 	M. AGRILIFE shall make available to CERES for potential selection and transfer under this
Agreement materials developed in the Program in which CERES has indicated an interest or
which relate to the CERES Field, subject to the limits of such materials’ physical
availability.
	 
	 	 	 	N. The Originating Party will accompany each transfer of Original Materials with a
transmittal letter that specifies: (i) the roles of each Party involved in the transfer,
e.g., who is the Originating Party, (ii) the experimental designation of the Materials and
(iii) a statement confirming that the subject Materials are being transferred under the
terms of this Agreement. Each Party will provide to the OTC a copy of each such
transmittal letter that it provides to the other Party.
	 
	 	 	 	O. No transfer of any Material under this Agreement shall change the ownership of such
Material.

	VII.	 	TERM AND TERMINATION

	 	 	 	A. The term of this Agreement shall begin on the Effective Date and continue for fifteen
(15) years unless sooner terminated in accordance with this Article VII or extended by the
mutual written agreement of the Parties.
	 
	 	 	 	B. This Agreement may be terminated for convenience by CERES at any time prior to the full
term of this Agreement set forth in Article VII.A, provided that a written notice is given
to AGRILIFE thirty (30) days in advance. However, CERES shall be obligated to pay AGRILIFE
for all services, orders, materials, or facilities committed in good faith (and not
cancelable or re-allocatable despite AGRILIFE’s efforts to cancel or re-allocate) prior to
the effective date of termination.
	 
	 	 	 	C. AGRILIFE shall have the right to terminate this Agreement unilaterally with written
notice to CERES in case of failure of CERES to satisfy its material obligations under this
Agreement, if CERES fails to cure such failure(s) within (i) thirty (30) days for failures
to remit payment for amounts due under this Agreement and (ii) ninety (90) days for all
other obligations, in each case after receipt of written notice from AGRILIFE specifying
such failure(s).
	 
	 	 	 	D. If there are no active Projects at any time during the term of this Agreement, then,
upon written notice by either Party to the other Party, the Executive Committee will meet
to define and decide upon any further research projects to perform under this Agreement.
If no such research projects are decided upon by the Executive Committee within three (3)
months after such
meeting, CERES will have the option to continue any previous Projects that were

			
	 	 	 
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	 	 	 	part of the
Program, on the same annual budget (adjusted for inflation under the Consumer Price Index
(CPI) applicable as of the first day of the calendar quarter in which such continuation is
agreed upon) for the remainder of the fifteen (15) year term set forth in Article VII.A.
In the event that CERES does not exercise such option within three (3) months from the
aforementioned meeting of the Executive Committee, this Agreement may be terminated by
either Party upon delivery of a written notice of termination to the other Party with
immediate effect.
	 
	 	 	 	E. Promptly upon the delivery of a notice of termination of this Agreement, the Parties
will meet to discuss the Program, and each Party will provide to the other Party any data,
information, germplasm and any other materials that constitute Joint Inventions or Jointly
Owned Lines, if still in existence as of the notice of termination and which has not been
provided to such other Party prior to the notice of termination.
	 
	 	 	 	F. Termination of this Agreement shall not affect the rights and obligations of the Parties
under this Agreement accrued prior to termination hereof nor any license grants then in
existence, subject to payment of remuneration as set forth in any relevant
license/commercialization agreements. Further, at or about the effective date of
termination, the Parties will negotiate in good faith to reach agreement as to the rights
for CERES to use and commercially exploit Subject Inventions and Lines not covered by any
relevant license/commercialization agreement between the Parties, which rights will be
addressed in one or more written agreements. Such Subject Inventions and Lines shall be
deemed subject to the options set forth in this Agreement and to the terms and conditions
of the IPRA. In the event of the expiration or any termination of this Agreement, the
following provisions shall survive: Articles IV.A, IV.B.5, V.B., VI.A, VI.D, VI.E, VI.F,
VI.G, VI.H,VI.I, VI.K, VI.L and VI.O; VII.E and VII.F.; IX, X, XI, XII, XIII, XIV, XV, XVI,
XVIII, XXI, XXII.C, XXII.D, XXII.E, XXII.F, XXII.G, XXII.H, XXII.I, XXII.J, XXII.L, and
XXIII.

	VIII.	 	PAYMENT
	 
	 	 	A. CERES agrees to pay for the direct and indirect cost of work performed under each
Project under this Agreement as described in, and up to the maximum amount specified in,
the budget for such Project. Within thirty (30) days after the last day of each calendar
quarter during the term of this Agreement, AGRILIFE shall provide a written invoice to
CERES for the amount of the annual budget for each Project allocated to such calendar
quarter as set forth in the work statement for such Project. CERES shall pay such amount
within thirty (30) days after CERES’ receipt of such invoice. All payments to AGRILIFE
under this Agreement shall be made payable to Texas AgriLife Research and forwarded to the
address designated in Article XIV. AGRILIFE acknowledges and agrees that, except with
respect to its invoice dated September 30, 2011, all payments required to be made by CERES
under the Original Agreement between September 3, 2007
and the Effective Date of this Agreement have been timely made and that CERES

			
	 	 	 
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	 	 	otherwise has
no further payment obligations under the Original Agreement.
	 
	 	 	B. AGRILIFE will expend these funds as needed for labor, equipment, travel, and other
operating costs solely in connection with the research conducted under and in accordance
with this Agreement. The unexpended balance or any unused supplies with respect to the
Program remaining at the completion of the Program shall remain the sole property of
AGRILIFE. Notwithstanding the foregoing sentence, the Parties agree that unexpended funds
will be used to extend the term and/or scope of the Program as determined by the Executive
Committee and that the Parties shall amend the relevant work statement accordingly.
	 
	 	 	C. If, at any time, AGRILIFE has reason to believe that the cost of the work with respect
to any Project will exceed the applicable amount set forth in any Project work statement,
AGRILIFE will promptly notify CERES in writing, giving a revised budget for completion of
such work. CERES will not be obligated to reimburse AGRILIFE for any cost in excess of the
applicable amount set forth in any Project work statement, and, subject to diligent
performance of the Program activities, AGRILIFE will not be obligated to continue such work
or incur costs in excess of that amount unless and until this Agreement is amended to
increase the maximum amount for such work as mutually agreed upon by the Parties in
writing.
	 
	 	 	D. CERES and AGRILIFE may jointly seek additional funding opportunities from Federal and
State funding sources in support of the Program or in support of expansion of the Program.
Where accepting funds from such additional sources would conflict with the obligations of
AGRILIFE to CERES or with any of CERES’ rights under this Agreement, the IPRA or the
Existing License and Material Transfer Agreements, such acceptance of funds will be
contingent upon the approval and subsequent amendment of the Agreement by the Parties.

	IX.	 	PROGRAM INTELLECTUAL PROPERTY

	 
	 	A.	 	Definitions

	 	 	 	1. “AGRILIFE Genetic Contribution” means, for any specific Hybrid or New Parental
Line: (a) the proportion of the nuclear genes of the Hybrid or the New Parental
Line, as applicable, arising from Lines licensed by AGRILIFE to CERES, based on
genetic contribution as determined by pedigree and (b) a contribution to be
determined on a case-by-case basis in each case where a specific valuable phenotype
of that Hybrid or New Parental Line, as applicable, is attributable to specific
Allele(s) optioned or licensed to CERES by AGRILIFE.
	 
	 	 	 	2. “Allele” means a particular form of one or more genes determinant for a valuable
characteristic of a plant (e.g. drought tolerance, specific flowering time),
discovered in the Program by AGRILIFE or CERES solely or by AGRILIFE and CERES
jointly.

			
	 	 	 
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	 	 	 	3. “Copyright” means any copyrightable material and its associated copyright.
	 
	 	 	 	4. “Developed by Breeding” means originated by any form of genetic manipulation
including but not limited to single or multiple hybridization, backcrossing,
genetic transformation or other rearrangement or recombination of genes with or
without associated selection.
	 
	 	 	 	5. “Hybrid” means a seed or plant that has resulted from genetic crossbreeding
between two or more lines where those lines include one or more (i) Lines or (ii)
New Parental Lines.
	 
	 	 	 	6. “Invention” means any invention or discovery that is or may be patentable or
otherwise protectable under title 35 of the U.S. Code.
	 
	 	 	 	7. “Jointly-Owned Lines” means Lines which are jointly developed by employees,
contractors and/or consultants (other than AGRILIFE) of CERES and employees and/or
researchers of AGRILIFE, and Lines where the Materials or Other Contributions of
CERES and AGRILIFE have been combined through traditional or artificial means in
the Program.
	 
	 	 	 	8. “Lines” means (i) sorghum lines or Sorghum [***] or populations created by
AGRILIFE in the course of the Program, or (ii) new genetic lines or populations
developed by or for CERES (other than by AGRILIFE) through further selection within
any sorghum lines or populations created in the course of the Program, as
distinguished from crossing followed by selection.
	 
	 	 	 	9. “New Parental Lines” means new genetic lines or populations which are Developed
by Breeding by CERES and which have one or more of the Lines as progenitors.
	 
	 	 	 	10. “Other Contributions” means (i) intellectual and technical contributions to the
development of Lines or if from CERES, to the development of Lines, New Parental
Lines or Hybrids, such as, without limitation, markers, gene-trait association
knowledge or composition knowledge, that inform the breeding and selection process,
or transgenic traits and (ii) except with respect to Article IX.A.7 and Article
IX.D.1, financial contributions to the development of Lines, or if from CERES, to
the development of Lines, New Parental Lines or Hybrids.
	 
	 	 	 	11. “Subject Invention” means any Invention conceived and reduced to practice
during the term of this Agreement in the conduct of a Project.

	 	B.	 	Copyright

	 	 	 	1. Title. Title to and the right to determine the disposition of any 

			
	 	 	 
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Confidential Treatment Requested and the Redacted Material has been separately filed with the Commission

 

 

	 	 	 	copyrights
or copyrightable material first produced or composed in the performance of the
Program by AGRILIFE employees and/or researchers only shall remain with AGRILIFE.
Title to and the right to determine the disposition of any copyrights or
copyrightable material first produced or composed in the performance of the Program
by CERES employees only shall remain with CERES. Title to and the right to
determine the disposition of any copyrights or copyrightable material first
produced or composed in the performance of the Program by employees and/or
researchers of AGRILIFE and CERES shall remain with AGRILIFE and CERES.
	 
	 	 	 	2. License to Copyrightable Materials (excluding software). AGRILIFE grants to
CERES an irrevocable, royalty-free, non-transferable, non-exclusive and license in
AGRILIFE’s rights in any copyrightable materials (technical data, reports, etc.)
first developed in the performance of the Program to use, reproduce, display,
perform and otherwise exploit (to the extent not prohibited by applicable law) such
copyrightable materials. Such grant excludes rights in computer software
(including both source and executable code) first developed under this Agreement,
its documentation, and/or information databases (“Software”).
	 
	 	 	 	3. Invention Notice (Software). AGRILIFE will notify CERES, in writing stating
expressly that each disclosure is a software invention notice under this Agreement
within thirty (30) days of receiving a disclosure on Software solely made by
employees and/or researchers of AGRILIFE, or of Software jointly made by employees
of AGRILIFE and CERES, and each such notice will describe the Software with
sufficient specificity to allow assessment by CERES. CERES shall hold such
disclosure in confidence and shall not reveal the disclosure to any third party
without the written consent of AGRILIFE.
	 
	 	 	 	4. First Right to Negotiate for Commercial Exploitation License. Additionally,
AGRILIFE grants to CERES a time-limited first right to negotiate a non-exclusive or
exclusive, at CERES’ election, commercial exploitation license (i) to use,
reproduce, display, perform and otherwise exploit any Software for commercial
exploitation purposes, and to distribute and/or sublicense such Software to third
parties. CERES shall advise AGRILIFE in writing within ninety (90) days following
delivery of such Software to CERES (“Option Period”) whether or not CERES elects to
negotiate a license agreement to obtain commercial exploitation rights to such
Software. In the event that CERES elects to negotiate for a commercial
exploitation license to such Software, the Parties shall initiate negotiation of
such license agreement, such negotiations not to extend beyond one hundred eighty
(180) days from CERES’ notice of election (“Negotiation Period”) without the mutual
consent of both Parties. Such
license shall be negotiated in good faith between the Parties, and shall

			
	 	 	 
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	 	 	 	contain
reasonable business terms common to CERES’ field of commercial interest and
proposed application.

	 	C.	 	Subject Inventions

	 	 	 	1. Inventorship and Title. Inventorship of inventions, developments, or
discoveries in the performance of the Program (“Subject Inventions”) shall be
determined in accordance with U.S. Patent Law, whether or not patent applications
are pursued. All rights to Subject Inventions invented solely by employees or
researchers of AGRILIFE shall belong solely to AGRILIFE (“AGRILIFE Inventions”).
All rights to Subject Inventions invented solely by employees, contractors and/or
consultants (other than AGRILIFE) of CERES shall belong solely to CERES (“CERES
Inventions”). All rights to Subject Inventions invented jointly by employees or
researchers of AGRILIFE and employees, contractors and/or consultants (other than
AGRILIFE) of CERES (“Joint Inventions”) shall belong jointly to AGRILIFE and CERES.
	 
	 	 	 	2. Marker-Trait Inventions. In the event that a Party uses a mapping population
provided by the other Party to discover a marker, Allele or trait, such marker,
Allele or trait shall be a Joint Invention, provided, however, that such mapping
population is only available to third parties subject to the same condition that
the resulting discoveries of markers, Alleles or traits shall be jointly owned by
the Party providing the mapping population to the third party, and such third
party.
	 
	 	 	 	3. Invention Notice (Subject Invention). AGRILIFE will notify CERES, in writing
stating expressly that each disclosure is an invention notice under this Agreement
within thirty (30) days of reduction to practice or knowledge of conception or
discovery of a Subject Invention solely invented by employees and/or researchers of
AGRILIFE, or of a Joint Invention, and each such notice will describe the Subject
Invention with sufficient specificity to allow assessment by CERES. CERES shall
hold such disclosure in confidence and shall not reveal the disclosure to any third
party without the written consent of AGRILIFE.
	 
	 	 	 	4. Option to Obtain a Commercial Exploitation License. AGRILIFE grants to CERES a
time-limited option to obtain an exclusive world-wide commercial exploitation
license in AGRILIFE’s rights in Subject Inventions and in Joint Inventions, with
the right to grant sublicenses, as set forth below.
	 
	 	 	 	5. Exercise of Option to a Commercial Exploitation License. CERES shall advise
AGRILIFE in writing within ninety (90) days of such disclosure to CERES of a
Subject Invention (“Option Period”) whether or not CERES elects to obtain exclusive
commercial exploitation rights to
such Subject Invention. In the event that CERES elects to exercise its

			
	 	 	 
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	 	 	 	option to
obtain a commercial exploitation license to such Subject Invention, the Parties
shall initiate negotiation of a license agreement in compliance with the IPRA, such
negotiations not to extend beyond one hundred eighty (180) days from CERES’ notice
of election (“Negotiation Period”) without the mutual written consent of both
Parties. Such license shall be negotiated in good faith between the Parties and
shall contain reasonable business terms common to CERES’ field of commercial
interest and proposed application and shall allow CERES to direct patent
prosecution for the Subject Invention.
	 
	 	 	 	6. AGRILIFE shall not file a non-provisional application on any Subject Invention
without CERES’ written approval prior to the expiration of the later of (i) the
Option Period for such Subject Invention and (ii) the Negotiation Period for such
Subject Invention.

	 	D.	 	Lines

	 	 	 	1. Ownership (General). Lines developed by employees, contractors and/or
consultants (other than AGRILIFE) of CERES alone without the use of AGRILIFE
Materials or Other Contributions, will be owned by CERES. Lines developed by
employees and/or researchers of AGRILIFE alone without the use of CERES Materials
or Other Contributions will be owned by AGRILIFE. Jointly-Owned Lines jointly
developed by employees, contractors and/or consultants (other than AGRILIFE) of
CERES and employees and/or researchers of AGRILIFE shall be jointly owned. Lines
where the Materials or Other Contributions of CERES and AGRILIFE have been combined
through traditional or artificial means in the Program shall be jointly owned.
	 
	 	 	 	2. Ownership (CERES breeding program). In the event that CERES or its Affiliated
Companies use Jointly-Owned Lines or Lines owned by AGRILIFE in its or its
Affiliated Companies’ own breeding program outside the Program in compliance with
this Agreement or a license agreement for Lines as provided in Article IX.D.4, the
resulting Lines, New Parental Lines or Hybrids developed by CERES or its Affiliated
Companies shall be solely owned by CERES, without regard to whether or not the
operative license agreement for Lines was in effect at the time of CERES or its
Affiliated Companies’ development of such Lines, New Parental Lines or Hybrids.
Any use for commercial exploitation of any Lines, New Parental Lines or Hybrids by
CERES or its Affiliated Companies shall be subject to CERES obtaining a license
under this Article IX.D and pursuant to the IPRA.
	 
	 	 	 	3. Option to Obtain a Commercial Exploitation License. AGRILIFE grants to CERES a
time-limited option to obtain an exclusive world-wide commercial exploitation
license in AGRILIFE’s rights in Lines and in
Jointly-Owned Lines with the right to grant sublicenses, as set forth

			
	 	 	 
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	 	 	 	below.
	 
	 	 	 	4. Exercise of Option to a Commercial Exploitation License. CERES may at any time
identify a Line for which it elects to exercise its option. In addition, the
Management Committee may nominate a Line in writing to the Executive Committee
which, in the Management Committee’s judgment, exhibits valuable characteristics
which may be of interest to CERES. The Executive Committee is responsible for
determining whether or not to validate each such Line nomination as a formal
written disclosure to CERES (“Lines Disclosure”). Any Lines Disclosure by the
Executive Committee will state that such disclosure is a Lines Disclosure under
this Agreement and describe the Line with sufficient specificity to allow
assessment by CERES. CERES shall advise AGRILIFE in writing within ninety (90)
days of any such Lines Disclosure to CERES (“Option Period”) whether or not CERES
elects to exercise its option to obtain exclusive commercial exploitation rights to
such Line to maintain and increase seed of Lines; develop New Parental Lines;
develop Hybrids; and sell Hybrids. In the event that CERES elects to obtain a
commercial exploitation license to one or more or all Line(s), the Parties shall
initiate negotiation of such license agreement in compliance with the IPRA and
substantially in the form of the Annexes thereto, such negotiations not to extend
beyond one hundred eighty (180) days from CERES’ notice of election (“Negotiation
Period”) without the mutual consent of both Parties.
	 
	 	 	 	5. The Parties agree that any such license as negotiated by the Parties for Line(s)
shall be negotiated in good faith and shall contain reasonable business terms
common to CERES’ field of commercial interest and proposed application, and shall
contain royalty rates customary in the seed industry, taking into consideration,
(i) AGRILIFE Genetic Contribution, (ii) Other Contributions of CERES, (iii)
financial contributions of each Party, and (iv) germplasm contributed by CERES, if
any, all of the foregoing (i) through (iv) to the development of such Lines, New
Parental Lines and Hybrids.
	 
	 	 	 	6. Jointly-Owned Lines. Neither AGRILIFE nor CERES shall have the right to
commercialize Jointly-Owned Lines without a written agreement between the Parties.
	 
	 	 	 	7. In the event that CERES’ option to license a Line has expired and/or CERES does
not license a Line developed under the Program, AGRILIFE shall be able to use such
Line for any purpose but subject to the restrictions set forth in this Agreement,
including but not limited to those restrictions set forth in Article IV, Article V
and Article XI and the restrictions set forth in the IPRA.

	 	E.	 	Intellectual Property Protection for Joint Inventions and Jointly-Owned
Lines

			
	 	 	 
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	 	 	 	1. CERES shall have the responsibility to pursue statutory protection of Joint
Inventions or Jointly-Owned Lines, and shall be the “Administering Party” for the
purposes of this Agreement.
	 
	 	 	 	2. CERES may, at its sole discretion, make a written request that AGRILIFE be the
Administering Party for certain Joint Inventions or Jointly-Owned Lines. Should
AGRILIFE agree, it shall provide notice of its agreement in writing and shall be
the Administering Party for such Joint Inventions or Jointly-Owned Lines.
	 
	 	 	 	3. The Administering Party shall be responsible for retaining counsel, overseeing
the process of securing intellectual property protection (i.e., the preparation,
filing and prosecution of patent or plant variety rights application(s)) and
maintaining intellectual property protection for the mutual benefit of the Parties,
in its best judgment, for that which it had prosecution responsibility. In
addition to other reporting responsibilities provided below, the Administering
Party shall promptly notify the other Party following retention of counsel. The
Parties will provide, and cause their respective employees, researchers and agents
to provide, all reasonable assistance which may be required in connection with the
filing and prosecution of such intellectual property rights, including without
limitation the signing of documents.
	 
	 	 	 	4. The Administering Party shall keep the non-administering Party advised as to all
developments with respect to all patent and plant variety rights application(s) and
issued patents and plant variety rights covering AGRILIFE owned or Subject
Inventions or Joint Inventions or AGRILIFE owned or Jointly-Owned Lines, which
includes supplying copies of all papers received and filed in connection with such
applications and patents in sufficient time for the non-administering Party to
comment thereon. Any decision which would result in a change of legal inventorship
or ownership of a patent, patent application or plant variety rights certificate
shall not be taken by an Administering Party unless it has first received
authorization in writing from the non-administering Party, provided that the
Parties shall comply with U.S. law on inventorship.
	 
	 	 	 	5. Each Party agrees to bear all legal expenses incurred by that Party as an
Administering Party in obtaining and maintaining patents and plant variety rights,
U.S. and foreign, covering Joint Inventions and jointly-owned Lines.
	 
	 	 	 	6. Joint Inventions. Subject to the restrictions set forth in Articles IV and V,
for Joint Inventions conceived in the performance of the Program, AGRILIFE and
CERES shall be deemed independent owners under 35
USC 262, in the absence of a written agreement between the Parties to the

			
	 	 	 
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	 	 	 	contrary.

	 	 	 	F. All grants of intellectual property rights to CERES pursuant to this Agreement or the
IPRA will be subject to the reservation by AGRILIFE of an irrevocable, nonexclusive,
royalty-free right to use or practice such intellectual property for research and
educational purposes only and for the conduct of third-party sponsored research subject to
the terms of this Agreement including without limitation Article IV, Article V and Article
XI and the IPRA. This reservation excludes Jointly-Owned Lines and any other intellectual
property rights of CERES.
	 
	 	 	 	G. If the Parties fail to reach agreement within a Negotiation Period, within thirty (30)
days after the end of such Negotiation Period either Party may request through written
notification to the other Party that the matter shall be settled in accordance with the
following procedures: the disputed contract terms shall be referred to a mutually agreed
impartial expert whose decision shall be final. Each Party shall submit to the expert
within fifteen (15) days of his/her appointment its position in writing on the disputed
contract terms and conditions. Such expert shall be limited to choosing one of such two
(2) Party positions on each of the contract terms and conditions or related group of
contract terms and conditions that the expert considers most reasonable in the
circumstances and shall not make any other determination. Neither Party shall be bound by
any determination by the expert which, in the opinion of Party’s counsel, will result or be
likely to result in that Party violating any applicable law or regulation.

	X.	 	PUBLICATIONS

	 
	 	A. AGRILIFE shall be free to publish the results of research performed under this Agreement
after providing CERES with a sixty (60) day period in which to review each publication for
patent purposes (enabling disclosures), to identify any inadvertent disclosure of CERES’
Confidential Information (as such term is defined in Article XI), to identify any
disclosure of any copyrights, copyrightable materials, Subject Inventions, germplasm,
Hybrids, Lines, Alleles or other intellectual property arising out of the Program (“Program
Intellectual Property”) and to identify information generated in the Program relating to
Materials, Derivatives, Progeny or the association of marker(s) with a gene which has been
defined as a Cloning Target. AGRILIFE agrees to delete, at the request of CERES, any
disclosure of CERES Confidential Information and/or any information generated in the
Program relating to the association of marker(s) with a gene which has been defined as a
Cloning Target. Notwithstanding the foregoing, AGRILIFE shall not be required to remove
from publications information generated in the Program relating to the association of
marker(s) with a gene which has been defined as a Cloning Target after the earliest of the
following events: (i) a patent application is filed on the Cloning Target in the U.S.; or
(ii) the Management Committee decides that the Cloning Target is no longer a Cloning Target
and such decision is reflected in a written document; or
(iii) at the conclusion of the Program, except if otherwise agreed by the Parties at

			
	 	 	 
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	 	 	that
time.
	 
	 	 	B. If necessary to permit the preparation and filing of patent applications and/or to
delete any disclosure of CERES’ Confidential Information, or the association of marker(s)
with a gene which has been defined as a Cloning Target, AGRILIFE shall agree to an
additional delay of publication not to exceed sixty (60) days to prepare and file necessary
applications and/or delete such CERES Confidential Information and/or information generated
in the Program relating to the association of marker(s) with a gene which has been defined
as a Cloning Target. In the event that CERES asks AGRILIFE to file a patent, CERES shall
reimburse AGRILIFE for all reasonable, documented costs incurred in such patent application
filing(s) as set forth in Article IX. Any further delay of publication shall require a
separate agreement between AGRILIFE and CERES. AGRILIFE shall reasonably and in good faith
consider and negotiate with CERES with respect to any other requests by CERES to delay any
publication.

	XI.	 	CONFIDENTIAL INFORMATION

	 	a)	 	The Parties intend to reasonably share all information and data that they develop
during the course and for the purpose of the Program. At its sole discretion, either
Party may designate information and data that it develops and shares with the other as
Confidential Information and such Confidential Information shall be subject to the terms
of this Article XI.
	 
	 	b)	 	It is contemplated that the disclosing Party (“Discloser”) may be disclosing certain
confidential and/or proprietary information to the receiving Party (“Recipient”) unknown
to the general public (hereinafter referred to as “Confidential Information”). The
Parties agree that the terms of this Article XI shall apply to any confidential and/or
proprietary information that may be disclosed under this Agreement, and that such
Confidential Information shall be used solely by Recipient for the purposes contemplated
and permitted by this Agreement or the IPRA (“Purpose”). Recipient acknowledges that the
above-described Confidential Information is confidential and/or proprietary to Discloser
and is claimed to be a valuable, special, and unique asset of Discloser.
	 
	 	c)	 	Identification of Confidential Information. Confidential Information disclosed that
Discloser, in good faith, regards as confidential and/or proprietary shall be clearly
marked as “Confidential,” “Proprietary,” or bear any other appropriate notice indicating
the sensitive nature of such Confidential Information. Any Confidential Information not
easily marked, including Confidential Information that may be orally disclosed, shall,
within thirty (30) days of its disclosure, be referenced in writing and designated
confidential by Discloser.
	 
	 	d)	 	Information shall not be afforded the protection of this Article XI of this Agreement
if such information:

			
	 	 	 
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	 	i)	 	has been, is now, or later becomes publicly available through no fault of
Recipient;
	 
	 	ii)	 	has been, is now, or later becomes rightfully learned by Recipient from a
third party who is not under restriction or duty imposed by Discloser;
	 
	 	iii)	 	has been, is now, or later is furnished to third parties by Discloser, if
such disclosure is, or has been, made to third parties without similar restriction,
duty or limitation of use;
	 
	 	iv)	 	was known to Recipient prior to the date it received such Confidential
Information from Discloser; or
	 
	 	v)	 	has been, is now, or later is independently developed by Recipient without
use of or resort to such Confidential Information, and can be so proven by clear and
convincing evidence prepared contemporaneously with such independent development.

	 	e)	 	Protection of Confidential Information. For a period of three (3) years from the
date of termination of a Project under which Confidential Information is disclosed,
Recipient will:

	 	i)	 	Maintain the Confidential Information in confidence;
	 
	 	ii)	 	Not use any such Confidential Information received from Discloser except for
the above-stated Purpose;
	 
	 	iii)	 	Disclose such Confidential Information received from Discloser only to its
employees that have a need to know such Confidential Information in order to fulfill
the Purpose; and
	 
	 	iv)	 	Not disclose any portion of the Confidential Information received from
Discloser to any third party without the prior written consent of Discloser, even if
such third party is under similar restriction on disclosure with Discloser.

	 	f)	 	Recipient agrees to use the same degree of care to protect the confidentiality of all
Confidential Information it receives as it uses to protect its own confidential and
proprietary information which it does not wish to have published or disseminated.
However, in no event shall Recipient use less than a reasonable degree of care to protect
the Confidential Information received from Discloser. Recipient further agrees that
without Discloser’s written consent, Recipient will not electronically record any
conversation or meeting with Discloser personnel or photograph any Discloser facility or
premises. In the case where AGRILIFE is the Recipient, access to Confidential Information
shall be limited to the employees and
researchers of AGRILIFE that have a need to access or know such Confidential

			
	 	 	 
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	 	 	 	Information.
	 
	 	g)	 	Notice of Legal Action. If Recipient is under a legal obligation (including, but not
limited to, pursuant to law (including Texas Government Code Chapter 552) or court order)
to disclose Confidential Information received under this Agreement, Recipient will use
reasonable efforts to promptly provide notice to Discloser, and, to the extent permitted
by applicable law and, if applicable, authorized by the Office of the Attorney General of
the State of Texas will cooperate with Discloser to protect Confidential Information, but
only to the extent required by such legal obligation. The Recipient will provide
reasonable advance written notice to the Discloser of any such legal requirement and will
use reasonable efforts to secure confidential treatment of such Confidential Information
prior to its production or disclosure.
	 
	 	h)	 	Miscellaneous Requirements for Confidential Information. All Confidential
Information disclosed under this Agreement shall remain the property of Discloser. At
Discloser’s request, all Confidential Information received by Recipient in tangible form
shall be promptly returned or destroyed, provided that each Party may retain one (1) copy
of such Confidential Information for record keeping purposes and/or for purposes of
exercising any rights or performing any obligations that survive any expiration or
termination of this Agreement. Nothing in this Article XI shall be construed as granting
a license to any patent or copyright. The disclosure of Confidential Information shall
likewise not be construed as any representation, warranty, assurance, or inducement by
either Party with respect to infringement of any patent or other proprietary right.

	XII.	 	TITLE TO EQUIPMENT
	 
	 	 	AGRILIFE shall retain title to all equipment, supplies and other items purchased and/or
fabricated with funds provided by CERES under this Agreement.
	 
	XIII.	 	GOVERNING LAW
	 
	 	 	The validity, interpretation, and enforcement of this Agreement shall be governed and
determined by the laws of the State of Texas, excluding the conflict of laws rules which
might require the application of the laws of another jurisdiction.
	 
	XIV.	 	NOTICES
	 
	 	 	Formal notices provided under this Agreement must be in writing and delivered by (i)
certified mail, return receipt requested, postage prepaid; (ii) hand delivered, costs
prepaid; (iii) facsimile with receipt of a successful transmission confirmation; (iv)
email; or (v) delivery by a reputable overnight courier service, costs prepaid (in the case
of delivery by facsimile or email the notice must be followed immediately by a copy of the
notice being delivered by a means
provided in (i), (ii), or (v)). The notice will be deemed given on the day the notice

			
	 	 	 
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	 	Page 24 of 34

 

 

	 	 	is received.
In the case of notice by facsimile or email, the notice is deemed received at the local time of the receiving machine,
and if not received, then the date the follow-up copy is received. Notices must be delivered to the following addresses or
at such other addresses as may be later designated in writing.
Notices may be required to be delivered under this Agreement to AGRILIFE, to CERES, and to
 The Texas A&M University System’s Office of Technology Commercialization (“OTC”) acting on behalf of AGRILIFE.

	 	 	 	 	 

	 

	 	AGRILIFE:
	 	Diane Gilliland
	 

	 	 	 	Director, Contracts and Grants
	 

	 	 	 	Texas AgriLife Research
	 

	 	 	 	The Office of Sponsored Research Services
	 

	 	 	 	400 Harvey Mitchell Parkway South, Suite 300
	 

	 	 	 	College Station, TX 77845-3578
	 

	 	 	 	E-Mail: d-gilliland@tamu.edu
	 

	 	 	 	Phone: (979) 845-4781
	 

	 	 	 	Fax: (979) 862-7775
	 
	 	 	 	 
	 

	 	CERES:
	 	Director of Business Development
	 

	 	 	 	cc: Legal Department
	 

	 	 	 	Ceres, Inc.
	 

	 	 	 	1535 Rancho Conejo Blvd.
	 

	 	 	 	Thousand Oaks, CA 91320
	 

	 	 	 	Phone: (805) 376-6500
	 

	 	 	 	Fax: (805) 376-6549
	 
	 	 	 	 
	 

	 	OTC:
	 	Director, Licensing and Intellectual Property
	 

	 	 	 	Office of Technology Commercialization
	 

	 	 	 	800 Raymond Stotzer Parkway, Suite 2020
	 

	 	 	 	College Station, TX 77845
	 

	 	 	 	Phone: (979) 847-8682
	 

	 	 	 	Fax: (979) 845-1402

	XV.	 	PUBLICITY
	 
	 	 	A. AGRILIFE shall have the right to acknowledge the CERES investigator, the AGRILIFE
investigator, the nature of the research, and the dollar value of the Agreement and
Projects thereunder in AGRILIFE’s records and reports.
	 
	 	 	B. Neither Party shall indicate, directly or indirectly, any endorsement by the other
Party, or any component institution or agency of such other Party, of any products or
services of such Party for any reason whatsoever, without obtaining the express, prior
written consent of such other Party. CERES shall not use the name of TAMUS, AGRILIFE, or
any component institution or agency of TAMUS, nor the names of any of their employees or
researchers nor any
adaptation in any advertising, promotional or sales literature to be disseminated to

			
	 	 	 
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	 	 	the
public without prior written consent obtained from AGRILIFE in each case, except that CERES
may continue any such use that was approved by AGRILIFE or TAMUS prior to the Effective
Date without obtaining such consent. Neither AGRILIFE nor TAMUS shall use the name of
CERES or any of its Affiliated Companies, nor the names of any of their respective
employees or researchers nor any adaptation in any advertising, promotional or sales
literature to be disseminated to the public without prior written consent obtained from
CERES in each case.
	 
	 	 	C. Notwithstanding any provision of this Article XV, either of the Parties can disclose or
otherwise acknowledge, without restriction, the existence of this Agreement as well as the
collaborative relationship between the Parties without the prior consent of the other
Party. Notwithstanding the unilateral disclosure rights provided for in this Article XV, if
the disclosure or acknowledgement takes the form of a written release by the disclosing
Party, the disclosing Party shall provide the other Party a copy of any such unilateral
disclosure prior to its release so as to allow the other Party to comment and shall take
such comments reasonably into account. However, no advance copy needs to be provided of any
releases referred to in this Article XV.C. or of any releases which are identical to
previous releases.
	 
	 	 	D. The Parties may issue joint press releases regarding their collaboration. Any such press
release and any press release by either Party will be subject to the prior written approval
of both Parties; provided however, that (i) CERES shall have the right to otherwise
disclose information as may be required in CERES’ judgment to comply with SEC or IRS
regulations or other laws, rules or regulations governing disclosure of information or to
(potential) investors or business partners and (ii) AGRILIFE shall have the right to
otherwise disclose information as may be required in AGRILIFE’s judgment to comply with
laws, rules or regulations governing disclosure of information. Notwithstanding the
unilateral disclosure rights provided for in this Article XV, the disclosing Party shall
provide the other Party a copy of any such unilateral disclosure preferably prior to its
release.

	XVI.	 	EXPORT ADMINISTRATION

	 
	 	 	The results of the Research Program obtained by AGRILIFE are expected to be ordinarily
published and shared broadly with the scientific community and therefore are expected to
constitute “fundamental research” as defined under the International Traffic in Arms
Regulations (ITAR, 22 CFR Sections 120-130) and the Export Administration Regulations (EAR, 15
CFR Sections 730-774). If CERES discloses to AGRILIFE any CERES Confidential Information that
is subject to export control, CERES will alert AGRILIFE in writing at the time of disclosure,
at which time AGRILIFE will advise CERES if it desires to take receipt of the export-controlled
materials. Neither Party shall export or re-export any United States-origin
technology, software, or products, or the direct products of that technology, software 

			
	 	 	 
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	 	 	or
products under this Agreement, in violation of United States export control regulations.

	XVII.	 	INDEPENDENT CONTRACTOR

	 
	 	 	For the purposes of this Agreement and all services to be provided hereunder, the Parties shall
be, and shall be deemed to be, independent contractors, and neither Party is acting as a
partner, joint venturer, agent or employee of the other Party. The employees, researchers,
officers or agents of AGRILIFE shall not be considered or deemed to be employees, researchers,
officers or agents of CERES. Neither Party shall have authority to make any statements,
representations nor commitments of any kind, or to take any action which shall be binding on
the other Party, except as may be explicitly provided for herein or authorized in writing by
such other Party.

	 
	XVIII.	 	SEVERABILITY

	 
	 	 	If any of the provisions of this Agreement in the application thereof to any person or
circumstance, is rendered or declared illegal for any reason, or shall be invalid or
unenforceable, the remainder of this Agreement and the application of such provision to other
persons or circumstances shall not be affected thereby, but shall be enforced to the greatest
extent permitted by applicable law.

	 
	XIX.	 	HEADINGS

	 
	 	 	The headings used herein are for reference and convenience only and shall not enter into the
interpretation hereof.

	 
	XX.	 	COUNTERPARTS

	 
	 	 	This Agreement may be executed in duplicate counterparts, which taken together shall constitute
one single representation between the Parties.

	 
	XXI.	 	DISPUTE RESOLUTION

	 	a)	 	The Parties shall make every possible attempt to resolve in an amicable manner all
disputes between the Parties concerning this Agreement.
	 
	 	b)	 	The Parties must use the dispute resolution process provided in Chapter 2260, Texas
Government Code, and the related rules adopted by the Texas Attorney General to attempt to
resolve in the ordinary course of business. CERES must submit written notice of a claim
of breach of contract under this Chapter to Dr. Craig Nessler, Director, who will examine
CERES’ claim and any counterclaim and negotiate with CERES in an effort to resolve the
claim.
	 
	 	XXII.	 	MISCELLANEOUS

			
	 	 	 
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	 	 	A. This Agreement, the IPRA and the Existing License and Material Transfer Agreements
constitute the entire agreement between the Parties relative to the subject matter hereof
and thereof, and may be modified or amended only by a written agreement signed by both
Parties. As of the Effective Date, all active, ongoing or proposed activities (including
materials developed) by either Party which were initiated under the Original Agreement and
are not the subject of the Existing License and Material Transfer Agreements, including
without limitation the activities which are the subject of the Original Workplan
incorporated by reference as provided in Article II.C, shall be deemed Program activities
governed by this Agreement and for the avoidance of doubt, not by the terms and conditions
of the Original Agreement which were applicable prior to the Effective Date; subject
however to Article II.C and the last sentence of Article VIII.A. This Agreement shall be
governed and construed in accordance with the laws of the State of Texas.
	 
	 	 	B. This Agreement binds and inures to the benefit of the Parties, their successor or
assigns, but may not be assigned by either Party without the prior written consent of the
other Party; provided however, CERES shall have the right to assign its rights and
obligations under this Agreement to any Affiliated Company without such prior consent.
CERES shall also have the right to assign its rights and obligations under this Agreement
to a third party in conjunction with the transfer to such third party of substantially all
of the assets of CERES associated with performance under this Agreement or substantially
all of the stock of CERES, in each case without such prior consent. “Affiliated Company”
means any company owned or controlled by, under common control with or controlling CERES,
“control” meaning in this context the direct or indirect ownership of more than fifty
percent (50%) of the voting stock/shares of a company, or the power to nominate at least
half of the directors. Ceres Sementes do Brasil Ltda., a company incorporated under the
laws of Brazil, is an Affiliated Company of CERES.
	 
	 	 	C. The failure of either Party at any time to require performance by the other Party of any
provision of this Agreement shall in no way affect the right to require such performance at
any time thereafter nor shall the waiver by either Party of a breach of any provision be
taken or held to be a waiver of any succeeding breach of such provision or as a waiver of
the provision itself. The waiver of any provision of this Agreement must be in a writing
signed by both Parties.
	 
	 	 	D. This Agreement, to the greatest extent possible, shall be construed so as to give
validity to all of the provisions hereof. If any provision of this Agreement is or becomes
invalid, is ruled illegal by a court of competent jurisdiction or is deemed unenforceable
under the current applicable law from time to time in effect during the term of this
Agreement, the remainder of this Agreement will not be affected or impaired thereby and
will continue to be construed to the maximum extent permitted by law. In lieu of each
provision which is invalid, illegal or
unenforceable, there will be substituted or added as part of this Agreement by

			
	 	 	 
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	 	 	mutual
written agreement of the Parties, a provision which will be as similar as possible, in
economic and business objectives as intended by the Parties, to such invalid, illegal or
unenforceable provision, but will be valid, legal and enforceable.
	 
	 	 	E. Neither Party shall be liable to the other Party for any incidental, indirect, special,
or consequential damage, however caused, and on any theory of liability, arising out of or
related to this Agreement.
	 
	 	 	F. If either Party fails to fulfill its obligations hereunder (other than an obligation for
the payment of money), when such failure is due to a circumstance beyond its reasonable
control, including but not limited to fire, flood, civil commotion, riot, war (declared and
undeclared), revolution, acts of foreign or domestic terrorism, or embargos, then said
failure shall be excused for the duration of such event and for such a time thereafter as
is reasonable to enable the Parties to resume performance under this Agreement, provided
however, that in no event shall such time extend for period or more than (30) days.
	 
	 	 	G. NEITHER PARTY MAKES ANY WARRANTIES, EXPRESS OR IMPLIED, AS TO ANY MATTER WHATSOEVER,
INCLUDING, WITHOUT LIMITATION, WARRANTIES WITH RESPECT TO THE CONDUCT, COMPLETION, SUCCESS
OR PARTICULAR RESULTS OF THE PROGRAM, OR THE CONDITION, OWNERSHIP, MERCHANTABILITY, OR
FITNESS FOR A PARTICULAR PURPOSE OF THE PROGRAM OR ANY INTELLECTUAL PROPERTY OR RESEARCH
RESULTS OR THAT THE USE OF ANY INTELLECTUAL PROPERTY OR RESEARCH RESULTS WILL NOT INFRINGE
ON ANY PATENT, COPYRIGHT, TRADEMARK OR OTHER INTELLECTUAL PROPERTY RIGHT OF A THIRD PARTY.
NEITHER PARTY SHALL BE LIABLE FOR ANY DIRECT, INDIRECT, CONSEQUENTIAL, PUNITIVE OR OTHER
DAMAGES SUFFERED BY THE OTHER PARTY OR ANY OTHER PERSON OR ENTITY RESULTING FROM THE
PROGRAM OR THE USE OF ANY INTELLECTUAL PROPERTY, ANY RESEARCH RESULTS OR ANY PRODUCTS
RESULTING THEREFROM.
	 
	 	 	H. CONCERNING THE INFORMATION AND DATA PROVIDED UNDER THIS AGREEMENT, NEITHER PARTY MAKES
ANY REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE OR USE AND
NON-INFRINGEMENT.
	 
	 	 	I. CONCERNING THE MATERIALS PROVIDED UNDER THIS AGREEMENT NO REPRESENTATIONS AND NO
WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES
OF MERCHANTABILITY OR FITNESS FOR A
PARTICULAR PURPOSE, ARE PROVIDED HEREIN BY EITHER PARTY,

			
	 	 	 
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	 	 	NOR ARE ANY OBLIGATIONS WITH
RESPECT TO INFRINGEMENT OF LICENSED PATENTS OR OTHER RIGHTS OF THIRD PARTIES PROVIDED
HEREIN.
	 
	 	 	J. All representations, warranties, covenants and agreements made in this Agreement and
which by their express terms or by implication are to be performed after the execution
and/or termination hereof, or are prospective in nature, shall survive such execution
and/or termination, as the case may be.
	 
	 	 	K. In compliance with federal law, including provisions of Title IX of the Education
Amendments of 1972, Sections 503 and 504 of the Rehabilitation Act of 1973, and the
Americans with Disabilities Act of 1990, AGRILIFE and CERES will not discriminate on the
basis of race, sex, religion, color, national or ethnic origin, age, disability or military
service in their administration of policies, programs, or activities, admission policies,
other programs or employment.
	 
	 	 	L. Nothing in this Agreement waives or relinquishes the right of either Party to claim any
exemptions, privileges and immunities as may be provided by law.
	 
	 	 	M. The individuals executing this Agreement on behalf of each Party represent that they are
each the duly authorized representatives of such Party on whose behalf the individuals are
signing, each with full power and authority to bind said Party to each term and condition
set forth in this Agreement.

	XXIII.	 	ORDER OF PRECEDENCE
	 
	 	 	In the event of an inconsistency between the provisions of this Agreement, the
inconsistency shall be resolved by giving precedence in the following order:

	 	i)	 	Any license agreement between CERES and The Texas A&M University System
	 
	 	ii)	 	This Agreement
	 
	 	iii)	 	The IPRA
	 
	 	iv)	 	Project
	 
	 	v)	 	Other provisions, documents and/or specifications that are expressly
incorporated by reference into this Agreement under any Project.

[Signature page follows.]

			
	 	 	 
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IN WITNESS WHEREOF, the Parties hereto have caused this Agreement to be executed

by their duly
authorized representatives.

	 	 	 	 	 	 	 	 	 	 	 

	For Ceres, Inc. (“CERES”)	 	 	 	For Texas AgriLife Research
(“AGRILIFE”)	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/ Richard Flavell	 	 	 	By:	 	/s/ Bill McCutchen	 	 
	 

	 	 

	 	 
	 	 	 	 

	 	 
	Name: Richard Flavell, CBE, FRS	 	 	 	Bill McCutchen	 	 
	Title: Chief Scientific Officer	 	 	 	Executive Associate Director, Texas
AgriLife Research	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	Date:

	 	 	 	 	 	Date:	 	9-24-2011	 	 
	 

	 	 

	 	 
	 	 	 	 

	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	For Ceres, Inc. (“CERES”)	 	 	 	For Texas AgriLife Research
(“AGRILIFE”)	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/ Richard Hamilton	 	 	 	By:	 	/s/ Craig Nessler	 	 
	 

	 	 

	 	 
	 	 	 	 

	 	 
	Name: Richard Hamilton	 	 	 	Craig Nessler	 	 
	Title: President & Chief Executive
Officer	 	 	 	Director, Texas AgriLife Research	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	Date:

	 	9/24/11	 	 	 	Date:	 	9/24/2011	 	 
	 

	 	 

	 	 
	 	 	 	 

	 	 

			
	 	 	 
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Appendix A

Proposed Project Format

Confidential and Proprietary

TITLE

Research Project Plan

Project Leads:

Ceres Contacts:

Revised/Updated:

ID:

Background

	 	1.	 	PURPOSE
	 
	 	2.	 	RATIONALE
	 
	 	3.	 	REFERENCES (if any)

Goals and Deliverables

LIST DELIVERABLES AND MILESTONES:

COMPLETION DATE:

Work Plan

	1.	 	EXPERIMENTAL DESIGN:
	 
	2.	 	TIMELINE and SCHEDULE:
	 
	3.	 	RESPONSIBLE PARTIES:

Resource Impacts

Future Directions

			
	 	 	 
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Appendix B

In-Kind Support

Technology:

Persephone.

	 	 	 	Phase I. Within sixty (60) days of the Effective Date of this Agreement, CERES and AGRILIFE
will begin good faith negotiations for a software access agreement to enable AGRILIFE’s
remote access by up to three (3) named AGRILIFE personnel to access certain Program data
solely for AGRILIFE’S use in the Program for a period not to exceed two (2) years from the
Effective Date.
	 
	 	 	 	Phase II. No later than eighteen (18) months from the Effective Date, CERES and AGRILIFE
will begin good faith negotiations for a software license agreement to enable AGRILIFE to
deploy software for up to three (3) computers, solely for AGRILIFE’s use in the Program.
Upon execution of such software license agreement, the software access agreement
contemplated in Phase I will terminate.

Services: Within the later of (i) sixty (60) days after the

Effective Date of this Agreement and
(ii) the time(s) expressly stated below, CERES and AGRILIFE will begin good faith negotiations for
appropriate contractual agreements as applicable for CERES’ provision of the following services to
AGRILIFE, solely for AGRILIFE’s use in the Program.

	1)	 	CERES will provide AGRILIFE with certain services for single marker assays as directed by
Program objectives, the scope of such services to be discussed and mutually agreed upon at the
next regular meeting of the Management Committee following the Effective Date of this
Agreement.
	 
	2)	 	CERES will provide AGRILIFE with access to certain CERES breeding nursery locations in the
U.S. and Brazil as directed by the Program objectives, the scope of such access to be
discussed and mutually agreed upon at the next regular meeting of the Management Committee
following the Effective Date of this Agreement.

			
	 	 	 
	Amended and Restated Sponsored Research Agreement
	 	Page 33 of 34

 

 

Appendix C

Existing License and Material Transfer Agreements

	(1)	 	The Line License Agreement entered into by Ceres, Inc. and The Texas A&M University System
(of which AGRILIFE is a part) dated October 16, 2009 covering the sorghum Line known as
R07007.
	 
	(2)	 	The Line License Agreement entered into by Ceres, Inc. and The Texas A&M University System
(of which AGRILIFE is a part) dated July 12, 2011 covering the Lines known as
A/B.05040-08CS6466/6465 and A/B.05038-08CS6460/6459.
	 
	(3)	 	The Material Transfer Agreement entered into by Ceres, Inc. and The Texas A&M University
System (of which AGRILIFE is a part) dated April 23, 2008, as amended covering the S1-S2
Materials as defined therein.
	 
	(4)	 	The Material Transfer Agreement entered into by Ceres, Inc. and The Texas A&M University
System (of which AGRILIFE is a part) dated April 23, 2008, as amended covering the S3
Materials as defined therein.
	 
	(5)	 	The Material Transfer Agreement entered into by Ceres, Inc. and The Texas A&M University
System (of which AGRILIFE is a part) dated April 23, 2008, as amended covering the S4a
Materials as defined therein.
	 
	(6)	 	The Material Transfer Agreement entered into by Ceres, Inc. and The Texas A&M University
System (of which AGRILIFE is a part) dated April 23, 2008, as amended covering the S4b
Materials as defined therein.

			
	 	 	 
	Amended and Restated Sponsored Research Agreement
	 	Page 34 of 34

 

 

Pages where confidential treatment has been requested are stamped ‘Confidential Treatment Requested and the Redacted Material
has been separately filed with the Commission,’ and the confidential section has been marked as follows: [***].

SPONSORED RESEARCH AGREEMENT

between

Ceres, Inc.

and

The Texas Agricultural Experiment Station

of The Texas A&M University System

     This agreement (“Agreement”) is made and entered into by and between Ceres, Inc., a
corporation with principal offices in Thousand Oaks, California, a Delaware corporation (“CERES”)
and The Texas Agricultural Experiment Station (“TAES”) with principal offices in College Station,
Texas, a member of The Texas A&M University System (“TAMUS”), an agency of the State of Texas,
collectively referred to as “Parties” and individually as “Party.”

WITNESSETH:

WHEREAS, TAES and CERES have in common the desire to encourage and facilitate the discovery,
dissemination and application of new knowledge, and CERES desires to support said research;

WHEREAS, the Parties desire to improve germplasm, develop lines and hybrids of sorghum and its
interbreeding species and develop DNA markers and marker platform technology to advance the
development of biomass/bioenergy crops;

WHEREAS, the Parties have agreed on guidelines setting forth how CERES and TAES will cooperate to
make the benefits of such crops available to the public.

NOW THEREFORE, in consideration of the mutual covenants and premises contained in this Agreement,
the receipt and sufficiency of which is acknowledged, the Parties agree as follows:

Article 1. Scope and Management of Work

A. TAES agrees to perform the work set forth in Appendix A (the “Program”) entitled “Crop
Development Using Marker-Assisted Breeding.” Any additional work not specifically identified in
the scope of work statement, but which is indicated during the course of the study shall be
separately negotiated and funded for the appropriate amounts to be agreed upon by CERES and TAES.

B. The work will be under the direction of TAES’ principal investigators, Prof. William Rooney and
Prof. John Mullet (each a “Principal Investigator”). No substitution may be made for TAES’
principal investigator without the prior written concurrence of CERES.

C. A committee of four members (the “Management Committee”) will oversee the

Page 1 of 45

 

implementation of the Program. Two members will be nominated by each Party to serve on the
Management Committee.

D. The Management Committee will be a forum for communication and exchange of information regarding
the implementation of the Program. It shall have no authority to make any modifications to this
Agreement, but may formulate recommendations to change the Program or to take advantage of
additional funding opportunities and present such recommendations to CERES and TAES for
consideration. TAES agrees to permit CERES representatives to confer as necessary with Principal
Investigators. It is understood and agreed that the Management Committee and CERES representatives
have no authority to supervise, direct or control the work performed hereunder.

E. Recommendations of the Management Committee shall be made by unanimous agreement and recorded in
a manner prescribed by the Management Committee as a true record of the recommendations. If the
Management Committee cannot come to a unanimous agreement on any matter then the Management
Committee shall make no recommendation on that matter.

F. TAES’ contact for administrative matters relating to the work performed hereunder is:

Diane Gilliland

Agriculture Program Contracts & Grants

2147 TAMU

College Station, TX 77843-2147

d-gilliland@tamu.edu

Phone: (979) 845-4761

Fax: (979) 862-7775

Physical Address:

3000 Briarcrest Dr. Suite 101

Bryan, TX 77802

G. Each Party will require any and all of its employees and researchers who will perform Program
activities to sign a statement stating that they have read and understand the obligations of TAES
under Article 11 (Confidentiality) and Article 15 (Materials). TAES affirms that, as per The Texas
A&M University System Policy 17.01, Subsection 2.2.1, intellectual property conceived or developed
with support from the System or any of its members in the form of administered funds shall be owned
by the System, and that the funding received from CERES will constitute such administered funds
under such policy.

H. Each Party will conduct Program activities exclusively in laboratories, greenhouses or fields
under full control of or owned by that Party. Each Party will take all reasonable precautions to
prevent damage to, or unintentional destruction of or release of any germplasm created in the
Program.

Page 2 of 45

 

I. Each Party will strictly comply, and use its best efforts to cause its employees and researchers
conducting Program activities to comply, with notebook and breeding book keeping policies of the
highest standards as applicable in the field. Each Party will record and keep all field evaluation,
composition and marker data in user-friendly electronic database format.

J. Each Party shall be responsible for its compliance with all applicable laws, rules and
regulations, including, without limitation, those relating to genetically modified organisms (to
the extent the Program involves such organisms), and for obtaining any and all permits or
authorizations or proceed to any notifications which may be required by such laws, rules and
regulations.

K. When contributing sorghum germplasm for Program activities, the contributing Party will verify
what the origin of the material is and inform the other Party in writing from whom/where and
approximately on what date such Party initially obtained such germplasm. If the germplasm
contributed is governed by the Convention on Biological Diversity (“CBD”), the contributing Party
will be responsible for obtaining all necessary authorizations to commercialize any progeny of such
material under defined financial terms and conditions, and neither Party will use any germplasm in
the Program for which the preceding condition is not satisfied. Further, each Party shall only
contribute germplasm to the Program for which such Party has breeding rights with the right to
commercialize the progeny.

L. Any subcontracting of Program activities to a third party by TAES will be subject to CERES’
prior written approval which will not be unreasonably withheld.

M. TAES agrees not to conduct Germplasm Improvement (as defined in Article 8.A.2) under a funding
or collaboration agreement which grants rights to any person or entity other than CERES in
Biomass/Bioenergy Sorghum (as defined in Article 8.A.2) during the term of this Agreement.

Article 2. Period of Performance

The period of performance for this Agreement shall begin on September 3, 2007, and shall end on
September 2, 2012 (“Program Term”). This period may be extended by mutual agreement of the Parties
in writing.

Article 3. Consideration and Payment

A. CERES agrees to pay for the direct and indirect cost of work of this Agreement to a maximum
amount of four million three hundred ninety three thousand one
hundred fifty eight dollars ($4,393,158) as described in the budget and attached as Appendix B. Twenty
payments in the amount of $193,157.90 shall be made quarterly with the first payment being due and
payable within thirty (30) days of execution of this Agreement. In addition to the quarterly
payments, CERES agrees to pay $470,000.00 within thirty

Page 3 of 45

 

(30) days
of execution of this Agreement and $60,000.00 upon the first anniversary of this Agreement
for the purchase of equipment as described in Appendix B. TAES will invoice CERES when the
payments become due. All payments to TAES under this Agreement shall be made payable to The Texas
Agricultural Experiment Station and forwarded to the address designated in Article 5.

B. TAES will expend these funds as needed for labor, equipment, travel, and other operating costs
in connection with the research. The unexpended balance or any unused supplies remaining at the
completion of the project shall remain the sole property of TAES. The Parties agree that
unexpended funds will be used to extend the term and/or scope of the Program and that they shall
amend this Agreement accordingly. Title to all equipment purchased under this Agreement shall
vest with TAES upon acquisition.

C. If, at any time, TAES has reason to believe that the cost of the work will exceed the amount set
forth in Article 3.A, TAES will notify CERES in writing, giving a revised budget for completion of
the work. CERES will not be obligated to reimburse TAES for any cost in excess of the amount set
forth in Article 3.A, and, subject to diligent performance of the Program activities, TAES will not
be obligated to continue the work or incur costs in excess of that amount unless and until this
Agreement is amended to increase the maximum amount.

D. CERES and TAES may jointly seek additional funding opportunities from Federal and State funding
sources in support of the Program or in support of expansion of the Program. Where accepting
funds from such additional sources would conflict with the obligations of TAES to CERES, such
acceptance of funds will be contingent upon the approval and subsequent amendment of the Agreement
by the Parties.

Article 4. Exchange of Information, Data and Germplasm

The Parties intend to reasonably share all information and data that they develop during the course
and for the purpose of the Program. At its sole discretion, CERES may designate information and
data that it develops and shares with TAES as CERES Confidential Information and such Confidential
Information shall be subject to the terms of Article 11. The Management Committee will meet at
least quarterly with additional meetings as mutually agreed upon and exchange information and data
regarding the implementation of the Program. At least one (1) week before each Management
Committee meeting, each Party will provide the other Party with a report on the Program activities
performed since the last Management Committee meeting. A preferred format for such reports will be
created by the Management Committee. Such reports will contain at least the following:

—     quarterly status update and FTE breakout;

—     actual spending relative to budget;

—     description of Subject Inventions and germplasm generated during the period; and

—     copies of slide presentations summarizing research progress.

Page 4 of 45

 

Additional information, if not specifically included in the reports, shall be delivered as
supporting information at the related quarterly meeting, if available:

—    breeding records;

—    copies of field or greenhouse books and records; and

—    copies of raw field trial data.

TAES shall supply samples of germplasm and Lines developed in the course of the Program activities
upon request by CERES. Further, the following procedure will be followed for release of Lines.
“Release Date” means the date that a Line developed, tested and evaluated pursuant to the terms of
this Agreement is ready for release for commercialization, wherein upon such decision, such variety
will be formally released by TAES (if owned by TAES) or CERES and TAES jointly (if jointly owned).
CERES, on advice of the breeder(s) of each Line, shall establish, in its sole discretion, an
appropriate Release Date for such Lines. The Parties agree that the development of new Lines will
not always result in Lines that are commercially acceptable or releasable.

Article 5. Notices

Formal notices provided under this Agreement must be in writing and delivered by (i) certified
mail, return receipt requested; (ii) hand delivered; (iii) facsimile with receipt of a successful
transmission confirmation; (iv) email; or (v) delivery by a reputable overnight courier service (in
the case of delivery by facsimile or email the notice must be followed immediately by a copy of the
notice being delivered by a means provided in (i), (ii), or (v)). The notice will be deemed given
on the day the notice is received. In the case of notice by facsimile or email, the notice is
deemed received at the local time of the receiving machine, and if not received, then the date the
follow-up copy is received. Notices must be delivered to the following addresses or at such other
addresses as may be later designated in writing.

	 	 	 

	TAES:

	 	Diane Gilliland
	 

	 	Agriculture Program Contracts & Grants
	 

	 	2147 TAMU
	 

	 	College Station, TX 77843-2147
	 

	 	d-gilliland@tamu.edu
	 

	 	Phone: (979) 845-4761
	 

	 	Fax: (979) 862-7775
	 
	 	 
	 

	 	Physical Address:
	 

	 	3000 Briarcrest Dr. Suite 101
	 

	 	Bryan, TX 77802
	 
	 	 
	CERES:

	 	Director of Business Development
	 

	 	cc: Legal Department
	 

	 	Ceres, Inc.
	 

	 	1535 Rancho Conejo Blvd.

Page 5 of 45

 

	 	 	 

	 

	 	Thousand Oaks, CA 91320
	 

	 	Phone: (805) 376-6500
	 

	 	Fax: (805) 376-6549

Article 6. Independent Contractor

A. It is expressly understood and agreed that TAES is an independent contractor in the performance
of the research and is not acting as a partner, joint venturer, or agent of CERES under this
Agreement. The employees, researchers, officers, or agents of TAES or TAMUS shall not be considered
or deemed to be employees, researchers, officers, or agents of CERES. TAES shall have exclusive
direction and control over the manner and method of carrying out the tasks for accomplishing the
research to be performed pursuant to this Agreement, CERES being interested only in the completed
performance of the research contemplated.

B. Neither Party is authorized or empowered to act as an agent for the other for any purpose and
shall not on behalf of the other enter into any contract, warranty, or representation as to any
matter. Neither shall be bound by the acts or conduct of the other.

Article 7. Publicity

A. CERES shall not indicate, directly or indirectly, any endorsement by TAMUS, TAES, or any
component institution or agency of TAMUS, of any products or services of CERES for any reason
whatsoever, without obtaining the express, prior written consent of TAMUS. CERES shall not use the
name of TAMUS, TAES, or any component institution or agency of TAMUS, nor the names of any of their
employees or researchers nor any adaptation in any advertising, promotional or sales literature to
be disseminated to the public without prior written consent obtained from TAMUS in each case.

B. Notwithstanding any provision of this Article, either of the Parties can disclose or otherwise
acknowledge, without restriction, the existence of this Agreement as well as the collaborative
relationship between the Parties without the prior consent of the other Party. Notwithstanding the
unilateral disclosure rights provided for in this Article, if the disclosure or acknowledgement
takes the form of a written release by the disclosing Party, the disclosing Party shall provide the
other Party a copy of any such unilateral disclosure prior to its release so as to allow the other
Party to comment and shall take such comments reasonably into account. However, no advance copy
needs to be provided of any releases referred to in Article 7.C. or of any releases which are
identical to previous releases.

C. The Parties may issue joint press releases regarding their collaboration. Any such press release
and any press release by either Party will be subject to the prior written approval of both
Parties; provided however, that (i) CERES shall have the right to otherwise disclose information as
may be required in CERES’ judgment to comply with SEC or IRS regulations or other laws, rules or
regulations governing disclosure of information or to (potential) investors or business partners
and (ii) TAES shall have the

Page 6 of 45

 

right to otherwise disclose information as may be required in TAES’ judgment to comply with laws,
rules or regulations governing disclosure of information. Notwithstanding the unilateral disclosure
rights provided for in this Article, the disclosing Party shall provide the other Party a copy of
any such unilateral disclosure preferably prior to its release.

Article 8. Intellectual Property

A. General

(1) Except for grants of copyright, all grants of intellectual property rights as set forth in this
Article 8 will be made through the instrument of license agreement substantially in the forms
included in the Intellectual Property Rights Agreement (“IPRA”) of even date herewith between TAMUS
and CERES.

(2) All grants of intellectual property rights as set forth in this Article 8 will be subject to
TAES reservation of an irrevocable, nonexclusive, royalty-free right to use or practice the
intellectual property for research and educational purposes only and for the conduct of third party
sponsored research; subject, however, to compliance with the Guidelines for Future Collaborative
Opportunities which both Parties agree to comply with and which are included in the IPRA. This
reservation excludes Lines developed by CERES or other intellectual property rights of CERES. TAES
agrees that such sponsored research will not grant to third party sponsors any rights already
granted to CERES, and that such third party sponsors will be notified of TAES’ use of Subject
Inventions and Lines which are licensed or optioned to CERES. Further, TAES agrees that germplasm
developed using Lines will only be released or made available to third parties for
commercialization or Germplasm Improvement when (i) such germplasm is less than five percent (5%)
identical to any of the Lines under exclusive option or exclusive license to CERES based on DNA
Marker Analysis, (ii) contains no specific Allele(s) optioned or exclusively licensed to CERES to
which a Line’s specific valuable phenotype is attributable and (iii) contains no Subject Inventions
optioned or exclusively licensed to CERES, or other CERES proprietary technology. The foregoing
provisions do not limit and are subject to Article 1.M hereof. “Germplasm Improvement” shall mean
any activities to improve sorghum to produce Biomass/Bioenergy Sorghum, including without
limitation selection, breeding, marker development or marker assisted breeding or transgenic
improvement. “Biomass/Bioenergy Sorghum” shall mean sorghum which has been bred for the purpose of
conversion to fuels or energy, including but not limited, bred to produce higher biomass yields,
higher yields of cellulose, higher yields of sugar , other improved composition, improved
agronomics, improved net energy balance, improved energy density or which has been bred to make its
cellulose or sugars more available to conversion or more efficiently converted. Biomass/Bioenergy
Sorghum shall not include (i) sorghum which has been improved through breeding for increased starch
yields, including but not limited to grain sorghums, even where such sorghum must necessarily
produce increased yields of sugar to achieve increased starch content or (ii) sorghum which has
been improved through breeding for a purpose that does not include conversion to fuels or energy,
including but not limited to the purposes of sugar

Page 7 of 45

 

production, silage, forage, grain or other traditional uses for sorghum. TAES will notify CERES in
advance in writing of any contemplated projects under (i) or (ii) which would result in the grant
of rights by TAES or TAMUS to a for-profit party, and at CERES’ request discuss such project with
CERES, subject to any applicable confidentiality provisions, “DNA Marker Analysis” shall mean a
comparison according to a mutually agreed process based on a mutually agreed set of approximately
one hundred (100) markers. The Management Committee will define DNA Marker Analysis within two (2)
years of the latest signature date of this Agreement.

(3) The Parties shall consult as soon as possible but in any case within twenty (20) days of
receiving an Invention Notice. Such consultation shall concern whether to proceed to obtain
intellectual property protection on disclosed CERES Inventions, TAES Inventions and/or Joint
Inventions or whether to protect the same through other methods. (All such terms are as defined
hereinafter in Article 8 C.(1).)

Each Party shall be responsible for securing intellectual property protection for its own Subject
Inventions. CERES shall have the first option to pursue protection of Joint Inventions, and any
protection of Lines which are jointly owned, in the joint names of both Parties. If CERES so
elects by written notice within sixty (60) days of such initial consultation or with respect to
Lines, at any time but before ninety (90) days after the end of the period set forth in Article 2,
CERES shall be the “Administering Party” for the purposes of this Agreement. If CERES does not so
elect, TAES shall be the Administering Party for the purposes of this Agreement.

TAES may, at its sole discretion, make a written request that CERES be the Administering Party for
certain TAES Inventions or other Subject Inventions for which it is the Administering Party.
Should CERES agree, it shall provide notice of its agreement in writing and shall be the
Administering Party for such Inventions.

The Administering Party shall be responsible for retaining counsel, overseeing the process of
securing intellectual property protection (i.e., the preparation, filing and prosecution of patent
or plant variety rights application(s)) and maintaining intellectual property protection for the
mutual benefit of the Parties, in its best judgment, for that which it had prosecution
responsibility. In addition to other reporting responsibilities provided below, the Administering
Party shall promptly notify the other Party following retention of counsel. The Parties will
provide, and cause their respective employees, researchers and agents to provide, all reasonable
assistance which may be required in connection with the filing and prosecution of such intellectual
property rights, including without limitation the signing of documents.

The Administering Party shall keep the non-administering Party advised as to all developments with
respect to all patent and plant variety rights application(s) and issued patents and plant variety
rights covering TAES owned or jointly owned Subject Inventions or TAES owned or jointly owned
Lines, which includes supplying copies of all papers received and filed in connection with such
applications and patents in sufficient time for the non-administering Party to comment thereon.
Any decision which would

Page 8 of 45

 

result in a change of legal inventorship or ownership of a patent, patent application or plant
variety rights certificate shall not be taken by an Administering Party unless it has first
received authorization in writing from the non-administering Party, provided that the Parties shall
comply with U.S. law on inventorship.

CERES agrees to bear all legal expenses incurred by CERES as an Administering Party in obtaining
and maintaining patents and plant variety rights, U.S. and foreign, covering Subject Inventions and
Lines.

B. Copyright

(1) Title. Title to and the right to determine the disposition of any copyrights or copyrightable
material first produced or composed in the performance of the Program by TAES employees and/or
researchers only shall remain with TAES. Title to and the right to determine the disposition of
any copyrights or copyrightable material first produced or composed in the performance of the
Program by CERES employees only shall remain with CERES. Title to and the right to determine the
disposition of any copyrights or copyrightable material first produced or composed in the
performance of the Program by employees and/or researchers of both TAES and CERES shall remain with
TAES and CERES.

(2) License to Copyrightable Materials (excluding software). TAES grants to CERES an irrevocable,
royalty-free, non-transferable, non-exclusive right and license in TAES’ rights in any
copyrightable materials (technical data, reports, etc.) first developed in the performance of the
Program to use, reproduce, display and perform (to the extent not prohibited by applicable law).
Such grant excludes rights in computer software (including both source and executable code) first
developed under this Agreement, its documentation, and/or information databases (“Software”).

(3) First Right to Negotiate for Commercial License. Additionally, TAES grants to CERES a
time-limited first right to negotiate a non-exclusive or exclusive, at CERES’ election, commercial
license (i) to use, reproduce, display, and perform Software for commercial purposes, and to
distribute and/or sublicense such Software to third parties. CERES shall advise TAES in writing
within ninety (90) days following delivery of such Software to CERES whether or not CERES elects to
negotiate a license agreement to obtain commercial rights to such Software. In the event that
CERES elects to negotiate for a commercial license to such Software, the Parties shall initiate
negotiation of such license agreement, such negotiations not to extend beyond one hundred eighty
(180) days from notice of election without the mutual consent of both Parties. Such license shall
be negotiated in good faith between the Parties, and shall contain reasonable business terms common
to CERES’ field of commercial interest and proposed application. If the Parties fail to reach
agreement within one hundred eighty (180) days after the start of such negotiations which shall be
evidenced by written notice from one Party to the other initiating such negotiations, the terms and
conditions of the license on which no agreement was reached shall be settled in accordance with the
following procedures: the disputed contract terms shall be referred to a mutually agreed impartial
expert whose

Page 9 of 45

 

decision shall be final. Each Party shall submit to the expert within fifteen (15) days of his
appointment its position in writing on the disputed contract terms and conditions. Such expert
shall be limited to choosing one of such two (2) party positions on each of the contract terms and
conditions or related group of contract terms and conditions that the expert considers most
reasonable in the circumstances and shall not make any other determination. Neither Party shall be
bound by any determination by the expert which, in the opinion of Party’s counsel, will result or
be likely to result in that Party violating any applicable law or regulation.

C. Patentable Inventions

(1) Inventorship and Title. Inventorship of inventions, developments, or discoveries first
conceived or actually reduced to practice in the performance of the Program (“Subject Inventions”)
shall be determined in accordance with U.S. Patent Law, whether or not patent applications are
pursued. All rights to Subject Inventions invented solely by employees or researchers of TAES shall
belong solely to TAES (“TAES Inventions”). All rights to Subject Inventions invented solely by
employees of CERES shall belong solely to CERES (“CERES Inventions”). All rights to Subject
Inventions invented jointly by employees or researchers of TAES and employees of CERES (“Joint
Inventions”) shall belong jointly to TAES and CERES. In the event that a Party uses a mapping
population provided by the other Party to discover a marker or Allele, such marker or Allele shall
be a Joint Invention, provided however, that such mapping population is only available to third
parties subject to the same condition that the resulting discoveries of markers or Alleles shall be
jointly owned by TAES and such third party. TAES will notify CERES, in a writing stating expressly
that it is an invention notice under this Agreement (“Invention Notice”), within thirty (30) days
of reduction to practice or knowledge of conception or discovery of a Subject Invention solely
invented by employees and/or researchers of TAES, or of a Joint Invention, and each Invention
Notice will describe the Subject Invention with sufficient specificity to allow assessment by the
other Party.

(2) Option to Obtain a Commercial License. TAES grants to CERES a time-limited option to obtain
an exclusive world-wide commercial license in TAES’ rights in Subject Inventions, with the right to
grant sublicenses, as set forth in the IPRA.

(3) Exercise of Option to a Commercial License. TAES shall promptly disclose to CERES any Subject
Invention pursuant to an Invention Notice. CERES shall hold such disclosure in confidence and shall
not reveal the disclosure to any third party without the written consent of TAES. CERES shall
advise TAES in writing within ninety (90) days of such disclosure to CERES whether or not CERES
elects to obtain exclusive commercial rights to such Subject Invention. In the event that CERES
elects to obtain a commercial license to such Subject Invention, the Parties shall initiate
negotiation of a license agreement in compliance with the IPRA, such negotiations not to extend
beyond one hundred eighty (180) days from notice of election without the mutual consent of both
Parties. Such license shall be negotiated in good faith between the Parties and shall

Page 10 of 45

 

contain reasonable business terms common to CERES’ field of commercial interest and proposed
application.

(4) Joint Inventions. For Joint Inventions conceived in the performance of the Program, TAES and
CERES shall be deemed independent owners under 35 USC 262, in the absence of a written agreement to
the contrary. TAES’ rights in such Joint Inventions shall be subject to the option set forth in
(2) and (3) hereinabove.

D. Germplasm

(1) Definitions:

	 	a.	 	“Hybrid” means a seed or plant that has resulted from genetic crossbreeding between
two or more lines where those lines include one or more (i) Lines or (ii) New Parental
Lines.
	 
	 	b.	 	“TAES Genetic Contribution” means, for any specific Line: (a) the proportion of the
nuclear genes of a Line arisen from Lines licensed by TAES to CERES, based on DNA Marker
Analysis (as defined in Article 8 A. (2)); (b) a contribution to be determined on a
case-by-case basis in each case where a specific valuable phenotype of that Line is
attributable to specific Allele(s) optioned or licensed to CERES by TAES; and (c) Other
Contributions from TAES.
	 
	 	c.	 	“Other Contributions” means intellectual and technical contributions to the
development of Lines or if from CERES, to the development of Lines, New Parental Lines or
Hybrids, such as, without limitation, markers, gene-trait association knowledge or
composition knowledge, that inform the breeding and selection process, or transgenic
traits.
	 
	 	d.	 	“Developed by Breeding” means originated by any form of genetic manipulation
including but not limited to single or multiple hybridization, backcrossing, genetic
transformation or other rearrangement or recombination of genes with or without associated
selection.
	 
	 	e.	 	“New Parental Lines” means new genetic lines or populations which are Developed by
Breeding by CERES and which have one or more of the Lines as progenitors.
	 
	 	f.	 	“Lines” means sorghum lines or populations created in the course of the Program and
new genetic lines or populations developed by CERES through further selection within the
Lines, as distinguished from crossing followed by selection.
	 
	 	g.	 	“Allele” means a particular form of a gene determinant for a valuable characteristic
of a plant (e.g. drought tolerance, specific flowering time), discovered in the Program by
TAES or by TAES and CERES jointly.

Page 11 of 45

 

(2) Ownership. Lines developed by employees of CERES alone will be owned by
CERES. Lines developed by employees and/or researchers of TAES alone will be owned by TAES. CERES
and TAES shall jointly own Lines where the germplasm and Other Contributions of CERES and TAES have
been combined through traditional or artificial means in the Program. When a Party uses jointly
owned Lines or Lines owned by TAES in its own breeding programs outside the Program in compliance
with this Agreement or a license agreement for Lines as referred to in Article 8.D. (4), the
resulting Lines shall be solely owned by that Party. CERES’ use of a jointly owned Line or Line
owned by TAES in its own breeding programs, or any commercial use of such Line(s), shall be subject
to CERES obtaining a license under this Article 8.D and pursuant to the IPRA. In the event that
CERES’ option to license a Line has expired and/or CERES does not license a Line developed under
the Program, TAES shall be able to use such Line for any purpose but subject to the restrictions
set forth in this Agreement, including but not limited to those restrictions set forth in Articles
1.M and 8.A.(2), and the restrictions set forth in the IPRA.

(3) Option to Obtain a Commercial License. TAES grants to CERES a time-limited option to obtain an
exclusive world-wide commercial license to TAES’ rights in Lines, with the right to grant
sublicenses, as set forth in the IPRA.

(4) Exercise of Option to a Commercial License. CERES shall advise TAES in writing at any time,
but before ninety (90) days after the end of the period set forth in Article 2, whether or not
CERES elects to obtain an exclusive world-wide license to maintain and increase seed of Lines;
develop New Parental Lines; develop Hybrids; and sell Hybrids. Such license shall contain royalty
rates customary in the seed industry, taking into consideration (i) TAES Genetic Contribution, (ii)
Other Contributions of CERES, (iii) financial contributions of each Party, and (iv) germplasm
contributed by CERES, if any, all to the development of the Lines and Hybrids. In the event that
CERES elects to obtain a commercial license to one or more or all Line(s), the Parties shall
initiate negotiation of such license agreement in compliance with the IPRA, such negotiations not
to extend beyond one hundred eighty (180) days from notice of election without the mutual consent
of both Parties.

Article 9. Publications

Subject to what is set forth hereinafter with respect to marker-trait associations, TAES shall be
free to publish the results of research performed under this Agreement after providing CERES with a
sixty (60) day period in which to review each publication for patent purposes (enabling
disclosures), and to identify any inadvertent disclosure of CERES’ Confidential Information (as
such term is defined in Article 11). If necessary to permit the preparation and filing of patent
applications, TAES shall agree to an additional delay of publication not to exceed sixty (60) days
to prepare and file necessary applications, and CERES shall agree to reimburse TAES for all
reasonable costs incurred in such filing(s). Any further delay of publication shall require a
separate agreement between TAES and CERES. The Parties agree that neither Party shall publish or
disclose to any third party any information generated in the Program relating to the association of

Page 12 of 56

 

(a) marker(s) with a gene which has been defined in the Program in Appendix A or by
the Management Committee as a cloning target (“Cloning Target”). Such restriction on publication
and disclosure shall cease, and the other provisions on Confidential Information and Publications
of this Agreement shall apply, with respect to each Cloning Target, until the earliest of the
following events: (i) a patent application is filed on the Cloning Target in the U.S.; or (ii) the
Management Committee decides that the Cloning Target is no longer a Cloning Target and such
decision is reflected in a written document; or (iii) at the conclusion of the Program, except if
otherwise agreed by the Parties at that time.

Article 10. Warranty

CONCERNING THE INFORMATION AND DATA PROVIDED UNDER THIS AGREEMENT, TAES MAKES NO REPRESENTATIONS OR
WARRANTIES, EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE OR USE.

Article 11. Confidential Information

A. Any confidential or proprietary information disclosed by CERES to TAES for use in the research
work conducted under this Agreement (“CERES Confidential Information”) shall be designated as
confidential in writing at the time of disclosure to TAES. For the purpose of keeping such
information derived from CERES confidential, TAES shall make all reasonable efforts not to disclose
such information to third parties or release it for publication without the prior written consent
of CERES for a period of five (5) years from the date of this Agreement, but TAES shall not be
liable for unauthorized disclosures of information which occur in spite of such efforts. TAES will
not use CERES Confidential Information for any purpose other than the implementation of the
Program. TAES will only make CERES Confidential Information available to TAES employees or
researchers on a need-to-know basis.

B. TAES shall not be obligated to keep information received from CERES confidential if any such
information; (a) was already in the possession of TAES as evidenced by existing documentation prior
to receipt of information from CERES; (b) appears in issued patents or printed publications; (c) is
now or hereafter becomes generally available to the public on a non-confidential basis through no
fault or action or failure to act on the part of TAES; (d) is disclosed to TAES by third parties
having a bona fide right to make such disclosures; or (e) is ordered produced or disclosed by a
court or administrative body of competent jurisdiction or otherwise required by law, or required to
be disclosed by the Attorney General of The State of Texas, but only to the extent of such required
production or disclosure.

C. Any disclosure by TAES of results of the research performed under this Agreement shall be
subject to compliance with Article 9. Publications.

Page 13 of 45

 

Article 12. Disputes

A. The Parties shall make every possible attempt to resolve in an amicable manner all disputes
between the Parties concerning the interpretation of this Agreement.

B. The Parties must use the dispute resolution process provided in Chapter 2260, Texas Government
Code, and the related rules adopted by the Texas Attorney General to attempt to resolve in the
ordinary course of business. CERES must submit written notice of a claim of breach of contract
under this Chapter to Dr. Mark Hussey, Director, who will examine CERES’ claim and any counterclaim
and negotiate with CERES in an effort to resolve the claim.

Article 13. Governing Law

The validity, interpretation, and enforcement of this Agreement shall be governed and determined by
the laws of the State of Texas, excluding the conflict of laws rules which might require the
application of the laws of another jurisdiction.

Article 14. Termination

A. This Agreement may be terminated for convenience by CERES at any time prior to the full term of
the Agreement period, set forth in Article 2, provided that a written notice is given to TAES
thirty (30) days in advance. However, CERES shall be obligated to pay TAES for all services,
orders, materials, or facilities committed in good faith prior to the effective date of
termination.

B. TAES shall have the right to terminate this Agreement unilaterally with written notice to CERES
in case of failure of CERES to satisfy its material obligations under this Agreement, if CERES
fails to cure such failure(s) within (i) thirty (30) days for failures to remit payment for amounts
due under this Agreement and (ii) ninety (90) days for all other obligations in each case after
receipt of written notice from TAES specifying such failure(s).

C. Promptly upon the delivery of a notice of termination of this Agreement, the Parties will meet
to discuss the Program, and each Party will provide to the other Party any data, information and
germplasm that constitutes Joint Inventions or jointly owned Lines and which has not been provided
prior to the notice of termination.

D. Termination of this Agreement shall not affect the rights and obligations of the Parties accrued
prior to termination hereof nor any license grants then in existence, subject to payment of
remuneration as set forth in any relevant license/commercialization agreements. Further, at or
about the effective date of termination, the Parties will negotiate in good faith to reach
agreement as to the rights to use and commercially exploit Subject Inventions and Lines not covered
by any relevant license/commercialization agreement between the Parties, which rights will be
addressed in one or more written agreements. Such Subject Inventions and Lines shall be deemed

Page 14 of 45

 

subject to the options set forth in this Agreement and to the terms and conditions of the
IPRA.

Article 15. Transfer of Materials

A. “Materials” means plant materials or biological samples owned or otherwise controlled by a Party
(“Originating Party”) and transferred to the other Party under this Agreement.

B. The Party receiving Material(s) (“Receiving Party”) agrees that the Materials will be used
solely for the purpose of the Program, or in the case of CERES, for commercial purposes in
accordance with any applicable license agreement between the Parties.

C. The Receiving Party agrees to use the Material(s) in a safe manner and in compliance with all
applicable state and federal laws and regulations. The Party who makes a delivery of certain
Material(s) will obtain any required permits or proceed to any required notifications prior to the
delivery; the other Party will reasonably cooperate in order to facilitate the issuance of any
required permits.

D. The Receiving Party will only grant access to Material(s) intended for Program activities to its
employees or researchers who need access to such Material(s) for the purpose of the Program.

E. The Receiving Party will exclusively and restrictedly use the Material(s) under suitable
containment conditions, and in accordance with all applicable regulations, and will not use it on
human subjects. The Receiving Party will obtain any authorizations or permits which may be
required for its activities with the Material(s).

F. The Receiving Party agrees that the original Material(s) received from the Originating Party
will not be supplied to other entities, either within or outside of the Receiving Party, without
the prior written approval of the Originating Party. The original Material(s) will not be sold or
transferred for commercial purposes.

G. In the event that Receiving Party desires to utilize the original Material(s) for any uses
beyond the scope of this Agreement, the Parties shall enter into good faith negotiations to
establish the terms and conditions for any such purposes; however, nothing in this Agreement shall
be construed as a representation that the Originating Party may guarantee the grant of such rights.

H. The Receiving Party will keep and maintain written records of all use of the Material(s)
received.

I. All Material provided should be considered experimental and should be handled by the Receiving
Party with appropriate safety precautions. NO REPRESENTATIONS AND NO WARRANTIES OF ANY KIND,
EITHER EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF MERCHANTABILITY OR

Page 15 of 45

 

FITNESS
FOR A PARTICULAR PURPOSE, ARE PROVIDED HEREIN, NOR ARE
ANY OBLIGATIONS WITH RESPECT TO INFRINGEMENT OF LICENSED PATENTS OR OTHER RIGHTS OF THIRD PARTIES
PROVIDED HEREIN.

J. In the event of termination or expiration of this Agreement, the Receiving Party will return or
destroy, at the sole election of the Originating Party, the Materials no later than thirty (30)
days from such termination or expiration, unless the Originating Party has entered into a written
agreement for the Receiving Party’s continued use of the Materials.

K. Subject to Article 4, the selection of Material(s) for transfer under this Agreement will be at
the sole discretion of the Originating Party. The Originating Party will accompany each transfer
of Material with a transmittal letter that specifies: (i) the roles of each Party involved in the
transfer, e.g., who is the Originating Party, (ii) the experimental designation of the Material(s)
being transferred, and (iii) a statement confirming that the subject Material(s) are being
transferred under the terms of this Agreement.

L. All right and title in Material(s) will remain with the Originating Party in each case. CERES
and TAES shall each retain ownership of their respective contribution in derivatives produced using
Materials where the Materials of CERES and TAES have been combined through traditional or
artificial means. Notwithstanding the foregoing, ownership of derivatives which are Lines shall be
as set forth in Article 8.D.(2).

Article 16. Miscellaneous

A. This Agreement and the IPRA constitutes the entire agreement between the Parties relative to the
subject matter, and may be modified or amended only by a written agreement signed by both Parties.
In this Agreement, the words “includes” and “including” mean “includes” and “including” without
limitation.

B. This Agreement binds and enures to the benefit of the Parties, their successor or assigns, but
may not be assigned by either Party without the prior written consent of the other Party; provided
however, CERES shall have the right to assign its rights and obligations under this Agreement to
any Affiliated Company without such prior consent. CERES shall also have the right to assign its
rights and obligations under this Agreement to a third party in conjunction with the transfer to
such third party of substantially all of the assets of CERES associated with performance under this
Agreement without such prior consent. “Affiliated Company” means any company owned or controlled
by, under common control with or controlling CERES, “control” meaning in this context the direct or
indirect ownership of more than fifty percent (50%) of the voting stock/shares of a company, or the
power to nominate at least half of the directors.

C. The failure of either Party at any time to require performance by the other Party of any
provision of this Agreement shall in no way affect the right to require such performance at any
time thereafter nor shall the waiver by either Party of a breach of any provision be taken or held
to be a waiver of any succeeding breach of such provision or

Page 16 of 45

 

as a waiver of the provision itself.

D. This Agreement, to the greatest extent possible, shall be construed so as to give validity to
all of the provisions hereof. If any provision of this Agreement is or becomes invalid, is ruled
illegal by a court of competent jurisdiction or is deemed unenforceable under the current
applicable law from time to time in effect during the term of this Agreement, the remainder of this
Agreement will not be affected or impaired thereby and will continue to be construed to the maximum
extent permitted by law. In lieu of each provision which is invalid, illegal or unenforceable,
there will be substituted or added as part of this Agreement by mutual written agreement of the
Parties, a provision which will be as similar as possible, in economic and business objectives as
intended by the Parties to such invalid, illegal or unenforceable provision, but will be valid,
legal and enforceable.

E. Neither Party shall be liable to the other Party for any incidental, indirect, special, or
consequential damage, however caused, and on any theory of liability, arising out of or related to
the work performed under this Agreement.

F. Each Party must excuse any breach of this Agreement by the other which is proximately caused by
government regulation, war, strike, act of God, or other similar circumstance normally deemed
outside the control of well-managed business.

IN WITNESS WHEREOF, the Parties hereto have caused this Agreement to be executed by their duly
authorized representatives.

	 	 	 	 	 	 	 	 	 	 	 

	For Ceres, Inc. (“CERES”)	 	 	 	For The Texas Agricultural
Experiment Station (“TAES”)	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:
/s/ Peter Mascia

	 	 	 	By: /s/
Mark A. Hussey	 
	 
	 

	 	 	 	 	 

	 	 
	Name: Peter Mascia	 	 	 	Mark A. Hussey	 	 
	Title: Vice President of Product
Development	 	 	 	Director, Texas Agricultural
Experiment Station	 	 
	Date: August 28, 2007

 
	 	 	 	Date: 8-29-2007
 
	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	For Ceres, Inc. (“CERES”)	 	 	 	For The Texas Agricultural
Experiment Station (“TAES”)	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/
Richard Hamilton	 	 	 	By:	 	/s/
Elsa Murano	 	 
	 

	 	 

	 	 	 	 	 	 

	 	 
	Name: Richard Hamilton	 	 	 	Elsa Murano	 	 
	Title: President & Chief Executive
Officer	 	 	 	Vice Chancellor & Dean of College
of Agriculture and Life Sciences	 	 
	Date: August 29, 2007
 
	 	 	 	Date: 8/29/07
 
	 	 

Page 17 of 45

 

Appendix A

to the Sponsored Research Agreement

between Ceres, Inc. and The Texas Agricultural Experiment Station of The Texas

A&M University System

Program

“Crop Development Using Marker-Assisted Breeding”

Technical Plan for the Development of Bioenergy Sorghum

Texas A&M University System and Ceres

TABLE OF CONTENTS

	 	 	 	 	 
	 	 	Page	 
	I. Executive Summary
	 	 	19	 
	 
	 	 	 	 
	II. Overall Goals
	 	 	19	 
	 
	 	 	 	 
	III. Technical Plan
	 	 	 	 
	 
	 	 	 	 
	A. Sorghum Breeding
	 	 	20	 
	A-1. Sweet sorghum
	 	 	 	 
	A-2. High-biomass cellulosic sorghum
	 	 	 	 
	 
	 	 	 	 
	B. Sorghum Composition/Conversion Testing
	 	 	22	 
	B-1. Biomass composition analysis
	 	 	 	 
	B-2. Biomass conversion testing
	 	 	 	 
	 
	 	 	 	 
	C. Genotyping/Marker-Assisted-Breeding
	 	 	23	 
	 
	 	 	 	 
	D. Technology Development
	 	 	24	 
	 
	 	 	 	 
	E. Sorghum Genome Platform
	 	 	26	 
	 
	 	 	 	 
	F. Bioenergy Traits/Gene Discovery
	 	 	27	 

Page 18 of 45

 

I. Executive Summary:

     Sorghum is one of the most promising biomass feedstocks for the emerging bioenergy/biofuels
industry due to its high yield, drought tolerance, and established production systems. Sorghum is
also an excellent genetic system with relatively simple genetics, a large and diverse germplasm
collection, established genetic/genomic platform and complete genome sequence. Therefore, sorghum
has significant commercial value as a biofuels and bioenergy feedstock, as source of genes and IP,
and as a source of information useful for a wide range of other grass species being developed for
the bioenergy industry (i.e., switchgrass, miscanthus, energy cane).

     The technical plan described in this document is the result of extensive discussion between
CERES and TAES. The scope of work includes; (1) breeding for improved sweet sorghum and high
biomass cellulosic sorghum, (2) analysis of sorghum for biomass composition and conversion
properties, and (3) development of technology for advanced graphical genotyping, enhancement of the
sorghum genome platform, and discovery of QTL and genes for bioenergy traits. The technical plan
integrates germplasm screening, breeding, composition/conversion analysis, and genomics enabled QTL
mapping/gene discovery and marker-assisted breeding (Appendix C, Project Diagram).

     The elements of the technical plan and corresponding budgets are described in sections III and
IV. The background and rationale for each near term budgeted objective/activity is provided in
outline form, followed by a brief description of research objectives and milestones/deliverables.
The technical plan and corresponding budget was designed to identify the most important targets and
milestones based on our current understanding of what needs to be done and to build a technology
platform that would enable accelerated progress over time. A key feature of the proposed agreement
is to establish a sustained investment in the areas of activity described herein for the duration
of the contract assuming reasonable progress towards objectives and milestones. This is essential
because the research and development activities will often involve graduate students who need
support for the duration of their thesis work and because the project requires population and
genotype construction and evaluation that requires many years to come to fruition. However, we
expect that the distribution of funds relative to technical objectives, and the specifics of the
technical plan will change over time as progress occurs, challenges arise, and new opportunities
are identified. Therefore the PIs, in consultation with CERES, expect to modify the specific
research objectives and distribution of funding to projects over the time course of the Agreement
to maximize the impact of investment and overall progress.

II. Overall Goals:

1. Develop bioenergy sorghum inbreds/hybrids that are high yielding, widely adapted, and have
optimum biomass composition for biofuels and bioenergy production systems.

2. Identify and capture IP on key genes/alleles that contribute to bioenergy traits to protect the
value of sorghum bioenergy genotypes co-developed by TAES/CERES.

Page 19 of 45

 

3. Develop sorghum as a model C4 bioenergy grass genetic system for trait assessment and gene
discovery for use in other biomass crops such as switchgrass and energycane.

III. TECHNICAL PLAN DESCRIPTION.

A. SORGHUM BREEDING.

Introduction: Sorghum (Sorghum bicolor) can be used as a feedstock for biofuels production in
several different ways. First, grain sorghum is easily converted to ethanol using the same
methodologies used for the conversion of corn to ethanol and ethanol yields from grain sorghum and
corn are similar. Second, sweet sorghum cultivars that produce high levels of sugar in the stalk
can also be harvested, milled and the juice fermented to ethanol using the same methods that
sugarcane processors use. Third, photoperiod sensitive sorghum hybrids have the capability of
amassing large tonnages for cellulosic production of biofuels while maintaining the highest
water-use efficiency of any crop widely grown in the United States. Moreover, sorghum (all types)
is widely adapted and fits very well into production systems throughout the U.S. and world.
Combined with the water use efficiency, biofuels production from sorghum is feasible in many
regions of the country and the crop will support ecologically sustainable use of the land.

     Grain sorghum hybrids are already available for use in ethanol production. Therefore, over
the past 5 years, TAES researchers have focused on the development of sweet and high biomass
sorghums for biofuels production. Seed supplies of sweet sorghum varieties are limited; their tall
stature and limited seed yields make producing and harvesting seed difficult. Sweet sorghum
hybrids will have two advantages over traditional sweet sorghum cultivars. First, seed production
and processing will use short grain-type female lines that can easily be harvested using technology
already used by the sorghum seed industry. Second, use of hybrids will allow breeders and
producers to capture hybrid vigor; early estimates indicate that hybrids will average 120% the
yield of the high producing parent in the hybrid. Photoperiod sensitive hybrids that produce large
quantities of biomass are commercially available and they are now used for forage production.
However, within the TAES program, we have identified specific genotypes from the world collections
that have even higher yield potential that would likely be superior for biofuels production in a
lignocellulosic conversion system. The manipulation of these lines to develop effective parents
for high biomass sorghum hybrid production has been initiated.

Objectives: This proposal requests funds to accelerate the development of both sweet sorghum and
high biomass cellulosic bioenergy sorghum genotypes. This activity will complement a recently
funded DOE proposal to enhance genomic research into the development of sorghums for biofuels
production. At the completion of both proposals, the sorghum hybrids for energy production will be
developed for commercial use.

Page 20 of 45

 

A-1. Sweet Sorghum: Complete the development of A/B lines that have high stem sugar content.
Utilize existing varieties as pollinators for hybrid production.

A-2. High-Biomass Cellulosic Sorghum: Develop new pollinators for the production of high biomass
photoperiod sensitive sorghum hybrids. Photoperiod sensitive germplasm with very high biomass
potential has been identified. To utilize these characters, insensitive versions will be generated
that can produce seed in the U.S. allowing these lines to hybridized to existing photoperiod
insensitive A/B lines of the right genotypes to produce photoperiod sensitive high biomass sorghum
bioenergy hybrids.

Technical Plan:

	 	 	A-1. Sweet Sorghum [***]

	 	 	20[***]: Offseason Nursery: [***] of next generation [***] of best [***]. Create [***] seed
for additional evaluation of the best lines in multiple [***] to identify the best [***].
Traditional Season: Evaluate selected [***] in multiple locations, measure agronomic
potential and [***] potential. If feasible, evaluate [***] potential. Continue completion
of selected [***] lines.

	 	 	20[***]-20[***]: Offseason Nursery: [***] the best lines for [***] (both [***] line and
[***] ) to facilitate large scale growouts in the summer of 20[***]. Evaluate sweet
sorghum [***]; continue [***] to complete [***] lines of most promising [***].
Traditional Season: Evaluate selected [***] in multiple locations, measure agronomic
potential and [***] potential. If feasible, evaluate [***] potential. Release best [***]
or [***] lines to [***] for [***] and eventual release. Release of [***]lines in fall of
20[***] is expected if all testing proves their worthiness. Seed of the lines and [***]
should be commercially available in the summer of 20[***].

A detailed breeding plan for sweet sorghum is provided in Appendix D.

	 	 	A-2: High Biomass [***] 

	 	 	20[***] Summer: Grow [***] population, select [***] lines with high biomass potential.

	 	 	20[***]-20[***]: Offseason: Advance selections to the [***] generation and [***] to [***]line
testers

	 	 	20[***] Summer: Grow [***] generation and evaluate [***]  to identify those that produce
the highest [***].

	 	 	20[***]-20[***] Offseason: Grow [***] generation and create [***]. Further improvement
of additional new lines will be completed through 20[***].

	 	 	20[***] Summer: Multilocation testing and evaluation for selection of best [***]. Further
advancement of the lines and additional [***]

	 	 	20[***] Summer: Multilocation testing and evaluation for selection of best [***]. Selected
lines released to [***] for [***] and release.

	 	 	20[***] Summer: Seed of the lines and
[***] should be commercially available.

A detailed breeding plan for high biomass cellulosic sorghum is provided in Appendix D.

	B.	 	SORGHUM BIOMASS COMPOSITION/CONVERSION TESTING.

Background and Rationale: The chemical composition of sorghum biomass will significantly influence
the logistics of harvesting, transport, storage, processing, pretreatment processes, conversion
efficiency and yield of biofuels per dry ton. Therefore, an early objective of this project is to
characterize the range of biomass composition present in sorghum germplasm and to identify biomass
composition traits that need to be selected for during the breeding process. In addition, the
capability to conduct rapid NIR-based composition analysis for sorghum will allow allelic variation
that modulates composition to be mapped and the corresponding genes identified and patented. CERES
is establishing a state-of-the-art biomass composition-testing laboratory in

Page 21 of 45

Confidential Treatment Requested and the Redacted Material has been separately filed with the Commission

 

California. This laboratory will be able to carry out chemical analysis of biomass required to
establish standard curves for NIR-based analysis. TAES/CERES propose to establish a biomass
composition-testing laboratory at TAES in order to assay several thousand samples generated each
cycle of sorghum breeding and to enable genetic analysis of composition traits. The details of
this activity are described below.

Technical Plan:

	 	 	B-1. Sorghum Biomass Composition Analysis.
	 
	1.1.	 	Establish NIR calibration curves for sorghum biomass samples.

 — TAES will sample a range of [***] ([***] of [***])

 — TAES will obtain samples from a range of duration, environments, locations

 — TAES will provide ~[***] samples to CERES for analysis

 — ~[***] gm of dry ([***]% water content)
tissue

 — whole plant biomass sample = [***] sample

 — selected lines sampled for [***]/[***]/[***] separately

 — if [***] is present, this needs to be noted or separated out

 — CERES will establish calibration curves for NIR

 — CERES will conduct [***] of selected samples

	1.2.	 	TAES/CERES will establish a biomass composition-testing lab at TAES.

 — laboratory space will be identified for this activity at TAES

 — ovens will be purchased for tissue drying

 — biomass tissue milling instrumentation will be set up (dust/noise issue)

 — NIR instrumentation will be purchased and calibrated

	1.3.	 	Biomass composition testing activity.

 — ~[***] samples will be analyzed by NIR per breeding cycle

 — additional samples of germplasm and from [***] mapping populations

 — selected samples will require [***] analysis
validation

 — TAES may conduct [***]/[***]/[***] analysis of [***]

	 	 	B-2. Biomass Pretreatment/Conversion-Testing Activity.

 — CERES is developing a range of conversion testing capability

 — TAES has developed MixAlco conversion testing capability

 — CERES/TAES will also co-develop third party testing agreements

Milestones:

1.       Establish NIR standard curves for sorghum biomass composition analysis (20[***]).

2.      Establish a biomass composition laboratory at TAES (20[***]).

3.      Establish sorghum biomass conversion testing activity (20[***]).

4.      Characterize biomass composition of breeding lines and germplasm.

5.      Characterize biomass composition variation associated with [***].

Page 22 of 45

Confidential Treatment Requested and the Redacted Material
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	C.	 	GENOTYPING AND MARKER-ASSISTED-BREEDING (MAB).

Background: Genotyping technology is now routinely used to analyze germplasm, select parents for
crossing, accelerate breeding through marker-assisted-selection, and for map-based gene discovery.
Genotyping technology is evolving rapidly from gel-based platform technologies (i.e., AFLP, SSR) to
a wide range of platforms (i.e., TaqMan, MassArray, SNPlex). Recent advances in high throughput
DNA sequencing will also allow sequence-based genotyping using Restriction-Site-Localized
Sequencing on instruments such as the Solexa sequencer. This technology is proposed for
development in Section D.

     We propose to develop TaqMan assays for MAB of selected QTL in the near term. This technology
is being used by CERES and is readily developed for small numbers of loci. In the longer term we
plan to transition to RSL/Solexa-based graphical genotyping as soon as this technology is
developed. Graphical genotyping could replace the need for MAB in most applications and much more
information for selection and genetic mapping experiments.

Technical Plan:

	 	 	C-1. Marker-assisted-breeding (MAB) activity:
	 
	1.1.	 	Taqman assay development for MAB.

 — [***], [***] initial targets

 — sequence ~[***] genes [***] each [***] for [***] discovery

 — sequence ~[***] [***] lines, [***], [***]-lines

 — optimize [***]based Taqman assays (ABI7900 platform)

 — add new markers each year ([***], [***], [***], etc.)

 — test BioTrove Taqman platform to explore cost/assay reduction

 — test new methods for DNA extraction, tracking, [***] assays

	1.2	 	MAB assay throughput per year.

 — ~[***] [***] plants X [***] markers ([***]/[***]) in spring 20[***]; fall 20[***]

 — seed from [***] plants will be collected and sent to MAB lab

 — seedlings will be grown out and sampled

 — DNA extraction via Genogrinder

 — [***] breeding cycles requiring MAB per year

	 	 	C-2. [***]; MAB and [***] analysis.
	 
	2.1	 	Develop [***] technology (20[***])

 — technology development described in Section D

 — transition to [***] based [***] for MAB (20[***])

	2.2	 	[***] applications.

 — collect [***] of all bioenergy germplasm ([***])

 — collect [***] of breeding progeny (MAB)

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 — collect [***] of trait mapping populations ([***])

Milestones and deliverables:

1.      [***]/[***] Taqman assay development (20[***]).

2.      ~[***] MAB assays in 20[***].

3.      New Taqman assay development ([***], [***], [***], etc.) (20[***]-20[***]).

4.      Deployment of [***] based [***] technology (20[***])

5.      Collect [***] of bioenergy germplasm ([***]) (20[***]).

6.      Collect [***] of breeding and trait mapping populations.

	D.	 	TECHNOLOGY DEVELOPMENT.
	 
	 	 	D-1. Graphical genotyping using RSL/Solexa technology.

Background and rationale:

 — sequencing platforms allow sequence-based genotyping

 — sequencing platforms allow digital expression profiling

 — (i.e., Genome Sequencer-20 System, Solexa, ABI-based systems)

 — Sb genome sequence/genetic map alignment allows sequence/SNP mapping

 — haplotypes or graphical genotypes are revealed at sufficient marker density

 — graphical genotypes of germplasm will allow better parent/progeny selection

 — graphical genotyping will accelerate QTL mapping to gene discovery

 — graphical genotyping may replace targeted marker-assisted-breeding

 — TAES has developed a graphical genotyping method called Restriction Site Localized sequencing technology (RSL sequencing technology)

 — TAES has tested RSL-technology on rice/sorghum using 454 technology

 — RSL-sequencing provides a way to sequence genomes at specific sites

 — RSL provides a way to re-sequence the same sub-sample of any genome

 — the number of sites sequenced can be varied depending on need

 — Solexa can collect 1B bp of sequence per run (25-35bp/read) (~$3,000/run)

 — sequence sampling every ~4 kbp (two reads/site) = 10 Mbp of sequence

 — predicted SNP discovery rate = 1 SNP/82kbp (@ 1SNP/1000bp)

 — indexing allows ~100 genotypes per run (~$30/genotype for sequencing)

 — more genotypes can be run at lower sequence/SNP coverage

 — @ $3/~500 marker-genotype this may replace the need for MAB

 — a high quality genome sequence aligned to a genetic map is required

Technical Plan:

	1.1	 	Test RSL-technology on the Solexa sequencing system.

 — conduct simulations on [***]/sorghum to select restriction enzymes

 — prepare templates from different genotypes of [***], sorghum

 — submit templates to [***] for sequencing (~$10,000 per test)

 — analyze results; # unique sequences, map location, error rate, etc.

 — SNP frequency, distribution, dependence on restriction enzyme used

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 — streamline DNA extraction, template preparation, sample indexing

 — establish a bioinformatics pipeline for sequence processing

 — test low pass coverage to allow MAB by [***]

	1.2	 	Applications:

 — purchase and set up [***] at TAES and CERES

 — transfer technology to the MAB laboratory

 — genotype all relevant germplasm lines being used for bioenergy

 — genotype breeding lines for MAB

 — genotype [***] [***]/[***] populations

Milestones and deliverables:

1.      Test [***] technology on the [***] (20[***])

2.      Refine the technology, test
[***] MAB application (20[***])

3.      Utilize [***] technology for bioenergy germplasm/breeding analysis (20[***]-20[***])

4.      Utilize [***] technology for [***] mapping (20[***]-20[***])

D-2. Gene expression platform development: (Solexa/SAGE, qRT-PCR):

Background: A large portion of the phenotypic variation present in germplasm is due to differences
in gene expression. Differences in gene expression can be associated with phenotypic variation by
combining phenotypic QTL analysis and expression QTL analysis in the same population. This type of
eQTL analysis often identifies candidate genes associated with QTL and providing a molecular
understanding of mechanism through analysis of cis- and trans-acting factors that modulate gene
expression. Gene expression profiling also identifies co-regulated genes and regulon structure and
provides diagnostic information about the molecular basis of differences in plant performance. In
recent years, TAES has used microarray studies to characterize expression patterns of ~22,000
genes. A more powerful approach is to acquire [***] from [***] using [***]- or [***]-technology
combined with a [***] platform. Therefore, we propose to optimize and utilize [***] technology in
combination with the Solexa sequencer to obtain [***] of sorghum [***] that varies in [***]. This
activity will aid bioenergy pathway gene annotation being done with funding from DOE using
SorghumCyc and accelerate the identification of key genes that modulate bioenergy traits.

Technical Plan:

2.1       Optimize [***] profiling technology on the [***].

2.2       Map [***] to genes and genome locations.

2.3       Collect reference profiles of selected treatments/tissues ([***], [***], [***]).

2.4      Utilize [***]/[***] for [***]/[***] discovery/[***] screening projects.

2.5       Conduct qRT-PCR-based [***] analysis to further map out [***].

Milestones and deliverables:

2.1      Optimize [***]/[***] profiling technology (20[***]).

2.2       [***] mapped to genes and the genome sequence (20[***])

2.3       Reference [***] profiles collected from selected treatments (20[***]).

2.4      [***] profiles from sorghum bioenergy genotypes/populations (20[***]).

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	E.	 	SORGHUM GENOME PLATFORM.

Background and Rationale: Scientists at TAES have been developed a sorghum genome technology
platform consisting of integrated genetic, cytogenetic and comparative genome maps since 1998. The
TAES sorghum genetic map contains over 3,000 DNA markers based on data collected from 137 RIL lines
derived from BTx623 X IS3620C. A physical map that is aligned to the sorghum genetic map has been
constructed from ~16X deep BAC libraries, HICF fingerprinting, 6D BAC pooling, and ~5,000 EST-STS
linkers. BACs from this map have been end-sequences and sequence scanned providing information for
aligning DOE sequence assemblies to the map. The sorghum genome sequence assemblies produced by
DOE based on 8X shotgun coverage of the genome are large (up to 14 Mbp). Test alignment of DOE
sequence assemblies to SBI03 is promising revealing 6 miss-assemblies in the euchromatic region
(~47Mbp) that were easily corrected.

     Funding is requested to accelerate the next set of sorghum genome map platform improvements
including aligning the DOE [***] to the TAES [***] and [***] followed by [***] and resolution of
issues related to [***] [***]/[***]. In addition, [***] of the [***] will be done in a targeted
manner ([***], [***]/[***]) at different levels depending on need (automated [***] and by [***]
analysis, [***] models, [***], etc.). For example, DOE funding will allow implementation of [***]
of sorghum [***] matching [***] in [***] in 20[***] in collaboration with Doreen Ware/Lincoln Stein
(Cold Spring Harbor). We will focus [***] efforts on [***] relevant to [***] with funding from
DOE. We also plan to bring in [***] of [***] (from prior [***], RT-PCR data, plus [***]/[***] data
when it becomes available). Comparative genetic maps and the comparative aligned genome sequences
focused on sorghum, rice, maize, and switchgrass will be updated on a regular basis.

     The TAES sorghum genome map platform is a key resource for all future QTL mapping, annotation,
and gene discovery projects done at TAES and those carried out in collaboration with CERES. As
such, the genome map/sequence platform provides our group an advantage in terms of gene
discovery/IP capture. For QTL mapping and gene discovery research it would be ideal if TAES and
CERES were operating with a common genome sequence/genetic map framework. If CERES provides
funding to help TAES to continue development of the TAES genome map/sequence platform, then TAES
will make the genome map/sequence platform available to CERES with regular quality and annotation
updates. CERES will be free to do their own in house annotation of the aligned sorghum genome
map/sequence provided by TAES and to use the information provided by TAES for commercial purposes.

Technical Plan:

1.      Phase I alignment of DOE [***] to [***] (20[***]).

2.      Phase II alignment [***], [***] using [***].

3.      Align [***]/[***]/[***]/[***] [***] maps and [***].

4.      Conduct selected [***]and [***].

5.      Identify the location of [***] [***]/[***] ([***]).

6.      Identify the location of [***]-[***] on the [***] ([***]).

7.      Provide bioinformatics support for [***] mapping and other projects.

Milestones and deliverables:

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1.      DOE sorghum [***] to [***] (20[***]).

2.      Refined [***] X [***] (20[***]).

3.      Targeted [***] of sorghum [***], [***], [***] (20[***]).

4.      Improved [***]/[***] [***] ([***], [***], [***], [***]) (20[***]).

5.      [***] onto the [***] (20[***]).

6.      [***] derived from [***]/[***] onto the [***] (20[***]).

	F.	 	BIOENERGY TRAITS AND GENE DISCOVERY.
	 
	 	 	F-1.  Flowering time/duration:

Background:

 — duration of growth contributes significantly to biomass yield

 — vegetative growth stops upon initiation of flowering

 — sorghum is a short day plant that responds to photoperiod, thermoperiods

 — dominant forms of maturity (Ma) loci repress time to flowering

 — Ma1-Ma6 modulate time to flowering; additional Ma loci have been identified

 — Ma1 has been mapped (Lin et al., 1995; R. Klein et al., 2007)

 — Ma2 mapping in progress (Mullet/Rooney, 2007/8)

 — Ma3 = PHYB (Childs et al., 1998 — TAES)

 — Ma4 has been mapped, cloning in progress (Mullet/Rooney et al.)

 — Ma5/Ma6 have been mapped, cloning in progress (Mullet et al., 2006-8)

 — CO/FT mapped; mutations in CO modulate [***] ( = [***])

 — [***]+ [***]= [***] when both are [***] ([***] days in College Station)

 — [***]/[***] or [***]/[***] [***] is [***] (~[***] days in College Station)

 — [***]/[***] [***] regardless of [***] at [***]-[***] ([***] needs checking)

 — most [***] germplasm is [***] ([***]) ([***], [***], [***]) and [***]

 — [***]-high biomass ([***]) lines will be ‘converted’ to [***] using [***]

 — [***] lines will be used as [***] lines for [***]

 — [***] [***]-lines X [***]-lines = [***] for testing

 — MAB for [***], [***] during the [***] process will save time, cost

 — modifiers of Ma5 and Ma6 action have been identified (Mullet et al., unpublished)

 — useful for producing hybrids with uniform long duration growth

 — useful for releasing hybrids with flowering times optimized to different regions

Technical Plan:

	1.1.	 	Clone [***] (patent) and map modifiers of [***] action to aid MAB.

 — [***] has been mapped in a large [***] population (~[***] plants)

 — [***] map-based [***] is in progress (~[***] months to candidate [***])

 — a [***] with [***]-like action was detected and is now being mapped

	1.2.	 	Clone [***] (patent) and map modifiers of [***] action to aid MAB.

 — [***] has been mapped in a large [***] population (~[***] plants)

 — a [***] that modifies [***]-action was detected and will be mapped

 — [***] map-based [***] will be carried out.

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Milestones and deliverables:

1.1.      DNA markers for [***]/[***] for use in TAES and CERES breeding programs (20[***]).

1.2.     [***] cloning, IP capture (20[***]).

1.3.     [***] cloning, IP capture (20[***]).

1.4.     Map/markers for [***]/[***] [***] (20[***]).

	 	 	F-2. Biomass yield, traits, and composition:

Background:

 — goal is to optimize biomass yield and composition

 — biomass yield is highly heritable in Arabidopsis

 — biomass heterosis is observed in At

 — biomass plant traits to map include lodging, leaf/stem ratio, stem thickness/mass

 — biomass composition traits to map include lignin, cellulose, etc.

 — DOE has provided TAES with partial funding for QTL mapping (2/3 years)

Technical Plan:

	2.1	 	Map [***] for [***] and [***] traits in [***]/[***] populations:

 — phase I mapping population; [***] [***] lines Dr. Rooney identified in 20[***]

 — phase II mapping population; [***] [***] X [***]-line

 — select parents based on [***] and [***] data

 — assay [***] among top [***] lines (in progress)

 — assay [***] of [***] (CERES)/ [***] among [***] lines

 — [***] [***] lines (in progress), [***], [***]; assay [***] lines (20[***])

 — select for [***] lines that have fairly [***] ([***])/ [***] for [***]

 — population size of ~[***] is sufficient for initial [***] mapping

 — assay [***] ([***], etc) and [***] at end of season, replicated

 — College Station; other sites when time, funding permit

 — construct a [***] for [***] mapping (use [***]/[***] technology)

 — conduct [***] assays, [***] ([***]/[***])

[***] and follow-up:

 — expand sub-populations for [***]

 — identify [***]/[***]/[***] region, [***], generate a large [***] population

 — identify useful [***], [***] for target trait(s)

 — candidate [***], [***] analysis, and validation

 — capture IP

 — [***] germplasm for [***]

 — translate to other [***]

	2.2.	 	[***] analysis of [***] for [***].
	 
	 	 	Rationale:

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 — [***] production is highly [***] in Arabidopsis (At) ([***]%)

 — [***] main [***] for [***] were identified in At

 — [***] for [***] could be mapped at the [***] (=[***] plants)

 — best parent [***] was [***] ([***]%); observed at the [***]

 — [***]  not obvious in At; also less well defined in [***] than [***]

 — [***] for specific [***] has also been identified in different systems

 — sorghum germplasm is [***]; sorghum shows [***]

 — multiple sources of [***] for [***] are likely in sorghum

 — goal is to determine if the [***] basis of [***] can be mapped

 — if so, [***] contributing to [***] from several sources could be pyramided

 — [***] basis of [***] could also be valuable

 — [***] basis of [***] might be too complex, too much [***], etc.

 — high risk, potentially high reward research activity

Proposed research:

 — [***] mapping for [***] can be tested using breeding materials

 — ~[***] [***] lines will be derived from each [***]/[***]-[***]

 — [***] lines will contain different portions of the [***]-[***] genome

 — ~[***] [***]-line-[***] sources will be [***] to [***]-lines each year

 — [***] data will be collected to advance the breeding program

 — genotype all [***] lines that are [***] to obtain [***]

 — utilize [***] technology for [***] (see below)

 — test if it is possible to map [***] for [***] of [***]

 — we will be mapping [***] (and [***]) [***] in [***]

 — [***] for [***] could come from several [***] sources

 — expand to other [***] X [***]-lines if this proves useful

 — [***] from different sources in phase II breeding activity (20[***])

Milestones and deliverables:

2.1       Construct [***], [***], [***] mapping populations (20[***]).

2.2       [***] data collection on [***] lines (20[***]); [***], (20[***]).

2.3       [***] profiling data (parental lines, [***] lines) (20[***]).

2.4       [***] and [***] map construction (20[***]).

2.5       [***], [***], IP capture, [***], etc. (20[***]).

2.6      Obtain [***] genotypes of [***] population (20[***]).

2.7      Test ability to map [***] basis of variation in [***]/[***] (20[***]).

2.8      If test is positive, analyze other [***]/[***]-line [***] populations (20[***]).

	 	 	F-3. Height (Dw1-4):

Background:

 — variation in plant height is often associated with differences in biomass yield

 — Quinby et al. identified four main loci that modulate height (Dw1-4)

 — Dw2 and Dw3 have been mapped; Dw3 has been cloned

 — map-based cloning of Dw2 is in progress (TAES-ARS collaboration)

 — Dw1, Dw4 require further genetic analysis

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 — most [***] lines will be [***] (but this will vary)

 — [***] = [***] (used for conversion of [***] lines)

 — ‘converted’ [***]-lines need to be at least [***], [***] (and maybe + [***], [***])

 — most [***]-lines will be [***]

 — [***] need to be at least [***], possibly + [***], [***]

 — select [***] lines that are [***] with markers (20[***])

Technical Plan:

	3.1	 	[***] DNA marker development: (budgeted in MAB platform development)

 — sequence genes flanking [***] for [***] discovery

 — sequence the [***] corresponding to [***]

 — sequence genes from [***], [***] germplasm used in breeding

 — optimize Taqman assays for MAB

 — assay [***] plants for [***]

	3.2	 	Determine if [***] or [***] have an impact on [***]:

 — utilize [***] populations and [***] populations

 — test association between height and [***] (in [***] backgrounds)

 — variation in [***], [***] and other [***] will be present

	3.3	 	Map [***], [***] and other genes for height if an association with [***] is found.

 — map height [***] impacting [***] in [***] populations (see below)

 — set up specific populations to map [***], [***] genes

 — [***]: [***] ([***]) X [***] ([***])

 — [***]: [***] ([***]) X Std. [***] ([***])

Milestones and deliverables:

3.1       DNA markers for [***], [***] (20[***]) (included in MAB budget objectives)

3.2       Assessment of [***] or [***] impact on [***] in [***] backgrounds.

3.3       [***], [***] mapping and DNA markers depending on results and funding.

	 	 	F-4. Other traits:

     The traits listed below were identified as important for the development of superior bioenergy
sorghum hybrids in addition to the traits described above that will be targeted for immediate
funding. Research on the traits listed below will be initiated as soon as new funding becomes
available or as other CERES funded objectives are completed.

4.1      [***] resistance (and other [***], [***] resistance)

4.2       [***] tolerance including [***]

4.3      Response to [***] ([***])

4.4      [***] tolerance ([***])

4.5      [***] efficiency

4.6      [***] ([***], [***])

4.7      [***] tolerance; [***] X [***]

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Appendix B

to the Sponsored Research Agreement

between Ceres, Inc. and The Texas Agricultural Experiment Station of The Texas

A&M University System

Budget

A. SORGHUM BREEDING

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	Year	 	 	 	 
	A. SORGHUM BREEDING	 	Year 1	 	 	Year 2	 	 	Year 3	 	 	Year 4	 	 	Year 5	 	 	TOTAL	 
	PI: Bill Rooney
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Salaries
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	To Be Named **
	 	 	32,000	 	 	 	32,960	 	 	 	33,949	 	 	 	34,967	 	 	 	36,016	 	 	 	169,892	 
	Technician
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	To Be Named **
	 	 	18,000	 	 	 	18,540	 	 	 	19,096	 	 	 	19,669	 	 	 	20,259	 	 	 	95,564	 
	Graduate Student
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	50% Time, 12 Cal Mos.
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Student Workers
	 	 	12,000	 	 	 	12,000	 	 	 	12,000	 	 	 	12,000	 	 	 	12,000	 	 	 	60,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Subtotal
	 	 	62,000	 	 	 	63,500	 	 	 	65,045	 	 	 	66,636	 	 	 	68,275	 	 	 	325,457	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Fringe Benefits
	 	 	16,698	 	 	 	16,922	 	 	 	17,154	 	 	 	17,392	 	 	 	17,637	 	 	 	85,803	 
	Total Personnel Costs
	 	 	78,698	 	 	 	80,422	 	 	 	82,199	 	 	 	84,028	 	 	 	85,912	 	 	 	411,260	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Materials & Supplies
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Breeding
	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	75,000	 
	Agronomic
	 	 	5,000	 	 	 	5,000	 	 	 	10,000	 	 	 	10,000	 	 	 	10,000	 	 	 	40,000	 
	Quality
	 	 	15,000	 	 	 	15,000	 	 	 	10,000	 	 	 	10,000	 	 	 	10,000	 	 	 	60,000	 
	Total Materials & Supplies
	 	 	35,000	 	 	 	35,000	 	 	 	35,000	 	 	 	35,000	 	 	 	35,000	 	 	 	175,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Travel
	 	 	16,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	76,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Other Costs
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	GreenHouse
	 	 	2,000	 	 	 	2,000	 	 	 	2,000	 	 	 	2,000	 	 	 	2,000	 	 	 	10,000	 
	Field Fees
	 	 	8,000	 	 	 	8,000	 	 	 	8,000	 	 	 	8,000	 	 	 	8,000	 	 	 	40,000	 
	Tuition & Fees
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	24 hrs @ $276/hr
	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	33,120	 
	Total Other Costs
	 	 	16,624	 	 	 	16,624	 	 	 	16,624	 	 	 	16,624	 	 	 	16,624	 	 	 	83,120	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Capital Costs
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Equipment
	 	 	80,000	 	 	 	40,000	 	 	 	0	 	 	 	0	 	 	 	0	 	 	 	120,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Total Cost — BREEDING
	 	$	226,322	 	 	$	187,046	 	 	$	            148,823	 	 	$	150,652	 	 	$	152,536	 	 	$	            865,380	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 

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B. COMPOSITION LAB

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	PI: Bill Rooney	 	Year 1	 	 	Year 2	 	 	Year 3	 	 	Year 4	 	 	Year 5	 	 	TOTAL	 
	Salaries
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	To Be Named **
	 	 	8,000	 	 	 	8,240	 	 	 	8,487	 	 	 	8,742	 	 	 	9,004	 	 	 	42,473	 
	.25 Technician
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Student Workers
	 	 	5,000	 	 	 	5,000	 	 	 	5,000	 	 	 	5,000	 	 	 	5,000	 	 	 	25,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Subtotal
	 	 	13,000	 	 	 	13,240	 	 	 	13,487	 	 	 	13,742	 	 	 	14,004	 	 	 	67,473	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Fringe Benefits
	 	 	3,340	 	 	 	3,382	 	 	 	3,426	 	 	 	3,471	 	 	 	3,518	 	 	 	17,138	 
	Total Personnel Costs
	 	 	16,340	 	 	 	16,622	 	 	 	16,913	 	 	 	17,213	 	 	 	17,522	 	 	 	84,611	 
	 
	 	 
	Materials & Supplies
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	NIR
	 	 	4,000	 	 	 	4,000	 	 	 	4,000	 	 	 	4,000	 	 	 	4,000	 	 	 	20,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Total Materials & Supplies
	 	 	4,000	 	 	 	4,000	 	 	 	4,000	 	 	 	4,000	 	 	 	4,000	 	 	 	20,000	 
	Travel
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	0	 
	Other Costs
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Wet Chemistry
	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	75,000	 
	Total Other Costs
	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	75,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Capital Costs
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Equipment
	 	 	120,000	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	120,000	 
	(grinder, dryer, NIR)
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Total Cost — Composition Lab
	 	$	155,340	 	 	$	35,622	 	 	$	            35,913	 	 	$	             36,213 	 	 	$	            36,522	 	 	$	299,611	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 

Page 32 of 45

 

C. GENOTYPING/MAB

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Co-PI: Patricia Klein
	 	Year 1	 	Year 2	 	Year 3	 	Year 4	 	Year 5	 	TOTAL
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Salaries
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Natalie Unruh (0.5-1.0)
	 	 	19,339	 	 	 	19,919	 	 	 	41,033	 	 	 	42,264	 	 	 	43,532	 	 	 	166,089	 
	Student workers
	 	 	5,000	 	 	 	5,000	 	 	 	5,000	 	 	 	5,000	 	 	 	5,000	 	 	 	25,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	subtotal
	 	 	24,339	 	 	 	24,919	 	 	 	46,033	 	 	 	47,264	 	 	 	48,532	 	 	 	191,089	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Fringe benefits
	 	 	6,766	 	 	 	6,869	 	 	 	13,444	 	 	 	13,662	 	 	 	13,886	 	 	 	54,627	 
	Total Personnel Costs
	 	 	31,105	 	 	 	31,788	 	 	 	59,477	 	 	 	60,926	 	 	 	62,419	 	 	 	245,715	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Materials and Supplies
	 	 	20,000	 	 	 	20,000	 	 	 	20,000	 	 	 	20,000	 	 	 	20,000	 	 	 	100,000	 
	Capital Costs
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Genogrinder, Nanospectrometer
	 	 	20,000	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	20,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Total Cost — Genotyping/MAB
	 	$	71,105	 	 	$	51,788	 	 	$	             79,477	 	 	$	             80,926  	 	 	$	           82,419	 	 	$	365,715	 

Page 33 of 45

 

D. TECHNOLOGY/SOLEXA

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 

	PI: John Mullet
	 	Year 1	 	Year 2	 	Year 3	 	Year 4	 	Year 5	 	TOTAL
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Salaries
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Post-doc (To be named)
	 	 	40,000	 	 	 	41,200	 	 	 	42,436	 	 	 	—	 	 	 	—	 	 	 	123,636	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	subtotal
	 	 	40,000	 	 	 	41,200	 	 	 	42,436	 	 	 	 	 	 	 	 	 	 	 	123,636	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Fringe Benefits
	 	 	12,756	 	 	 	12,968	 	 	 	13,187	 	 	 	 	 	 	 	 	 	 	 	38,912	 
	Total Personnel Costs
	 	 	52,756	 	 	 	54,168	 	 	 	55,623	 	 	 	 	 	 	 	 	 	 	 	162,548	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Materials and Supplies
	 	 	30,000	 	 	 	25,000	 	 	 	20,000	 	 	 	—	 	 	 	—	 	 	 	75,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Capital Costs
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Nanospectrometer, PCR machines
	 	 	35,000	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	35,000	 
	Solexa sequencer (TAES)
	 	 	200000	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	200,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Total Cost — Technology/Solexa 
	 	$	317,756	 	 	$	79,168	 	 	$	75,623	 	 	 	 	 	 	 	 	 	 	$	472,548	 

Page 34 of 45

 

E. GENOME PLATFORM

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 

	Co-PI: Patricia Klein
	 	Year 1	 	Year 2	 	Year 3	 	Year 4	 	Year 5	 	TOTAL
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Salaries
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Natalie Unruh (0.5)
	 	 	19,339	 	 	 	19,919	 	 	 	0	 	 	 	0	 	 	 	0	 	 	 	39,258	 
	Arun Sharma
	 	 	10,012	 	 	 	10,312	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	20,324	 
	CS student (0.5)
*
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	TEES
	 	 	13,000	 	 	 	13,390	 	 	 	13,792	 	 	 	14,205	 	 	 	14,632	 	 	 	69,019	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	subtotal
	 	 	42,351	 	 	 	43,621	 	 	 	13,792	 	 	 	14,205	 	 	 	14,632	 	 	 	128,600	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Fringe Benefits
	 	 	13,207	 	 	 	13,402	 	 	 	3,721	 	 	 	3,763	 	 	 	3,806	 	 	 	37,898	 
	Total Personnel Costs
	 	 	55,557	 	 	 	57,023	 	 	 	17,513	 	 	 	17,968	 	 	 	18,437	 	 	 	166,498	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Materials & Supplies
	 	 	10,000	 	 	 	10,000	 	 	 	2,500	 	 	 	2,500	 	 	 	2,500	 	 	 	27,500	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Other
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Tuition & Fees
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	24 hrs @ $276/hr *
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	TEES
	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	33,120	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Capital Costs
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Linex computers
	 	 	15,000	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	15,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Total Costs — Genome Platform
	 	$	87,181	 	 	$	73,647	 	 	$	             26,637	 	 	$	27,092	 	 	$	27,561	 	 	$	242,118	 

Page 35 of 45

 

F. TRAITS/QTL/GENES

3.1 Duration (Ma5/6)

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	PI: John Mullet	 	Year 1	 	 	Year 2	 	 	Year 3	 	 	Year 4	 	 	Year 5	 	 	TOTAL	 
	Salaries
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Graduate student (Bio/Bio)
	 	 	22,000	 	 	 	22,660	 	 	 	23,340	 	 	 	24,040	 	 	 	24,761	 	 	 	116,801	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	subtotal
	 	 	22,000	 	 	 	22,660	 	 	 	23,340	 	 	 	24,040	 	 	 	24,761	 	 	 	116,801	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Fringe benefits
	 	 	4,550	 	 	 	4,617	 	 	 	4,685	 	 	 	4,756	 	 	 	4,829	 	 	 	23,437	 
	Total Personnel Costs
	 	 	26,550	 	 	 	27,277	 	 	 	28,025	 	 	 	28,796	 	 	 	29,590	 	 	 	140,238	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Materials & Supplies
	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	75,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Other
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Tuition & Fees
	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	33,120	 
	Subtotal
	 	 	48,174	 	 	 	48,901	 	 	 	49,649	 	 	 	50,420	 	 	 	51,214	 	 	 	248,358	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	3.2 Biomass traits
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 
	 	 
	PI: John Mullet
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Salaries
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Post-doc
	 	 	40,000	 	 	 	41,200	 	 	 	42,436	 	 	 	43,709	 	 	 	45,020	 	 	 	212,365	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	subtotal
	 	 	40,000	 	 	 	41,200	 	 	 	42,436	 	 	 	43,709	 	 	 	45,020	 	 	 	212,365	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Fringe benefits
	 	 	12,756	 	 	 	12,968	 	 	 	13,187	 	 	 	13,413	 	 	 	13,645	 	 	 	65,969	 
	Total Personnel Costs
	 	 	52,756	 	 	 	54,168	 	 	 	55,623	 	 	 	57,122	 	 	 	58,665	 	 	 	278,334	 
	Materials & Supplies
	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	15,000	 	 	 	75,000	 
	Subtotal
	 	 	67,756	 	 	 	69,168	 	 	 	70,623	 	 	 	72,122	 	 	 	73,665	 	 	 	353,334	 

Page 36 of 45

 

3.3 Height/anthracnose

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Co-PI: Patricia Klein	 	Year 1	 	 	Year 2	 	 	Year 3	 	 	Year 4	 	 	Year 5	 	 	TOTAL	 
	Salaries
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Graduate student (MEPS)
	 	 	20,000	 	 	 	20,600	 	 	 	21,218	 	 	 	21,855	 	 	 	22,510	 	 	 	106,183	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	subtotal
	 	 	20,000	 	 	 	20,600	 	 	 	21,218	 	 	 	21,855	 	 	 	22,510	 	 	 	106,183	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Fringe benefits
	 	 	4,348	 	 	 	4,409	 	 	 	4,471	 	 	 	4,535	 	 	 	4,602	 	 	 	22,364	 
	Total Personnel Costs
	 	 	24,348	 	 	 	25,009	 	 	 	25,689	 	 	 	26,390	 	 	 	27,112	 	 	 	128,547	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Materials and Supplies
	 	 	12,500	 	 	 	12,500	 	 	 	12,500	 	 	 	12,500	 	 	 	12,500	 	 	 	62,500	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Other
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Tuition & Fees
	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	6,624	 	 	 	33,120	 
	Subtotal
	 	 	43,472	 	 	 	44,133	 	 	 	44,813	 	 	 	45,514	 	 	 	46,236	 	 	 	224,167	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 

3.4 Other traits

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	PI: John Mullet	 	Year 1	 	 	Year 2	 	 	Year 3	 	 	Year 4	 	 	Year 5	 	 	TOTAL	 
	Salaries
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Post-doc (To be named)
	 	 	—	 	 	 	—	 	 	 	—	 	 	 	40,000	 	 	 	41,200	 	 	 	81,200	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	subtotal
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	40,000	 	 	 	41,200	 	 	 	81,200	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Fringe Benefits
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	11,948	 	 	 	12,141	 	 	 	24,089	 
	Total Personnel Costs
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	51,948	 	 	 	53,341	 	 	 	105,289	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Materials and Supplies
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	15,000	 	 	 	15,000	 	 	 	30,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Capital Costs
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Freeze-mill grinder
	 	 	 	 	 	 	20,000	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	20,000	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Subtotal
	 	 	 	 	 	 	20,000	 	 	 	 	 	 	 	66,948	 	 	 	68,341	 	 	 	155,289	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Total for Traits/Genes
	 	$	159,402	 	 	$	182,202	 	 	$	165,085	 	 	$	235,003	 	 	$	239,456	 	 	$	981,148	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Operating Summary
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	A. Breeding
	 	 	865,380	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	B. Composition
	 	 	299,611	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	C. Genotyping/MAB
	 	 	365,715	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	D. Technology
	 	 	472,548	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	E. Genome Platform
	 	 	242,118	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	F. Traits/Genes	 	 	981,148	 	 	 	 	 	 	 	 	 	 	TEES Direct Costs	 	 	102,139	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Total Direct Costs	 	 	3,226,520	 	 	 	 	 	 	 	 	 	 	TEES Indirect Costs	 	 	31,404	 
	Indirect (45.5% MTDC)
	 	 	1,166,638	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	TAES Direct Costs	 	 	3,124,381	 
	Total Request	 	 	4,393,158	 	 	 	 	 	 	 	 	 	 	TAES Indirect Costs	 	 	1,135,235	 

Budget Justification

A. Breeding

Personnel: Funds are budgeted for a 100% FTE research assistant (B.S., Agronomy) to coordinate the
daily activities of the program. Funds for a 50% FTE graduate student are included to address
specific research issues in the project. Student workers will be needed to assist in planting,
harvesting, pollinating, and seed production. Fringe benefits and insurance are charged per Texas
A&M University System policy.

Materials and Supplies: Included all necessary material for managing the breeding program,
including but not limited to pollinating bags, herbicides, sample bags, shipments, grinding costs
for samples, storage and shipping of seed.

Page 37 of 45

 

Travel: Includes expenses associated with travel, lodging and subsistence for working

breeding nurseries, evaluation sites and any promotion and research related presentations.
Other Costs: Greenhouse facilities will be needed to induce flowering in some PS progeny. Field
fees will cover costs of land rental for nursery space in Weslaco and Puerto Rico (as well as
others). Tuition and partial fees for 24 credit hours is budgeted per Texas A&M University System
Policy.

Equipment: Equipment is budgeted to purchase a used experimental plot silage harvester and a pickup
and trailer on which to transport it.

B. Composition

Personnel: Funds are budgeted for a 25% FTE research assistant to coordinate the daily activities
of NIR analysis. Student workers will assist in sample preparation and analysis. Fringe benefits
and insurance have been charged per Texas A&M University System policy.

Materials and Supplies: Includes all necessary material for NIR analysis, including but not limited
to sample bags, grinding and sample vials.

Other Costs: Wet chemistry will be required for a subset of samples.

Equipment: Includes NIR spectrophotometer, grinder and drier for preparing samples.

C. Genotyping/MAB

Personnel: 50% time salary for Natalie Unruh (senior technician) is requested for year one and two
increasing to 100% in years 3-5 reflecting the increasing need for marker-assisted breeding and
graphical genotyping anticipated as the project moves forward. Wages for student workers are
included to help with tissue and DNA preparation. Fringe benefits and insurance are charged per
Texas A&M University System policy.

Materials and Supplies: Includes all reagents for DNA extraction, marker development and
application of Taqman assays and graphical genotyping assays.

Capital costs: A genogrinder is required for tissue disruption and DNA isolation and a
nanospectrometer is required for quantification of DNA.

D. Technology Development/Solexa.

Personnel: Support for a 100% FTE post-doc is requested to carry out the development and testing of
RSL-graphical genotyping and expression profiling technology using the Solexa sequencer. Fringe
Benefits and insurance are charged per Texas A&M University policy.

Materials and Supplies: Funding is requested for the preparation of samples, sequence validation on
capillary platforms, for trial runs on the Solexa sequencer and reagent costs associated with data
collection once a sequencer is installed at TAES. Supplies will also be used for RNA preparation,
qRT-PCR validation and preparation of SAGE samples for digital profiling experiments.

Capital Costs: A nanospectrophotometer and
additional PCR machines are required to quantify and
amplify small amounts of RNA and DNA involved in the proposed studies. Partial support towards the
purchase of a Solexa sequencer is requested in the amount of $200,000.

E. Genome Platform.

Page 38 of 45

 

Personnel: Support for 50% of Natalie Unruh’s time, 27% of Dr. Arun Sharma’s salary,

and 50% of a CS (computer science) graduate student’s time is requested for two years to help with
alignment of the DOE sequence to the TAES genetic and physical map and related genome map
enhancement activity (including support for graphical genotyping, expression tag mapping and QTL
mapping studies). Continued support for the computer science graduate student for bioinformatics
is requested for the duration of the project. Fringe benefits and insurance are charged per Texas
A&M University System policy.

Material and Supplies: Materials such as primers, PCR, gels and other reagents for mapping
sequence contigs onto the genome map is requested for two years. A baseline budget for genome
platform enhancement is requested for years 3-5.

Other: Tuition and partial fees are requested for the graduate student per Texas A&M University
System policy.

Capital Costs: Computers to enhance our ability to handle genome sequence data, genotyping
information and Solexa data are needed to carry out the proposed research.

F. Traits, QTL and Gene Discovery.

Three projects involving genetic mapping and the discovery of genes associated with bioenergy
traits are described, with a fourth project starting in year 4 on a trait target to be named.
Personnel, materials and supplies associated with these projects have been estimated based on past
map-based gene discovery projects. Capital costs are for a freeze-mill grinder needed to isolate
tissue for RNA extraction.

Page 39 of 45

 

Appendix C

to the Sponsored Research Agreement

between Ceres, Inc. and The Texas Agricultural Experiment Station of The Texas

A&M University System

Project Diagram

Process for Developing Sorghum Bioenergy Genotypes 

[***]

Page 40 of 45

Confidential Treatment Requested and the Redacted Material has been separately filed with the Commission

 

Appendix D

to the Sponsored Research Agreement

between Ceres, Inc. and The Texas Agricultural Experiment Station of The Texas

A&M University System

Breeding Plan

	 	 	 

	Objective

	 	Develop bioenergy sorghum [***]
	 
	 	 
	Product:

	 	(1) High biomass cellulosic [***] and
	 
	 	 
	 

	 	(2) high [***] sorghum [***]

	 	 	 
	Year	 	Task
	 
	Objective 1

	 	Sweet Sorghum Line and [***] Development ([***]-line, Fig. 1; [***]-line, Fig. 2)
	 
	 	 
	Year 0
	 	 
	 
	 	 
	Summer

	 	Make Breeding [***]
	 
	 	 
	Winter

	 	Grow out [***] and [***]
	 
	 	 
	Year 1
	 	 
	 
	 	 
	Summer

	 	Grow out [***] populations, crush and select for [***], [***] quantity and agronomic desirability
	 
	 	 
	Winter

	 	For [***]-lines, [***] to [***] for [***]
	 
	 	 
	 

	 	For [***]-lines, advance, [***] and select ([***], [***] and agronomic)
	 
	 	 
	Year 2
	 	 
	 
	 	 
	Summer

	 	For [***]-lines, advance in [***]
	 
	 	 
	 

	 	For [***]-lines, [***] and make [***] for evaluation
	 
	 	 
	Winter

	 	For [***]-lines, advance in [***]
	 
	 	 
	 

	 	For [***]-lines, make preliminary evaluation of [***], and advance lines with selection
	 
	 	 
	Year 3
	 	 
	 
	 	 
	Summer

	 	For [***]-lines, advance in [***]
	 
	 	 
	 

	 	For [***]-lines, evaluate [***] and advance lines to [***] status. Evaluate lines for
[***] and [***], make additional [***] for further testing and selection
	 
	 	 
	Winter

	 	For [***]-lines, advance in [***], make [***] for evaluation

Page 41 of 45

Confidential Treatment Requested and the Redacted Material has been separately filed with the Commission

 

	 	 	 
	 	 	 
	Year 4
	 	 
	 
	 	 
	Summer

	 	For [***]-lines, advance in [***] until [***], make additional [***] for evaluation, and
evaluate [***] in multiple locations, including evaluations of line in [***] areas, rating for [***], etc.
	 
	 	 
	 

	 	For [***]-lines, evaluate [***] and advance lines to [***] status. Evaluate lines for
[***] and [***], make additional [***] for further testing and selection
	 
	 	 
	Winter

	 	For [***] lines, use only if additional [***] or [***] are needed.
	 
	 	 
	Year 5
	 	 
	 
	 	 
	Summer

	 	For [***]-lines, use only if additional [***] or [***] are needed, make additional [***]
for evaluation, and evaluate [***] in multiple locations, including evaluations of line in
[***] areas, rating for [***], etc.
	 
	 	 
	 

	 	For [***]-lines, as conditions merit, release and [***] of [***] for new [***]
	 
	 	 
	Winter

	 	Identify the best [***], [***] for eventual [***] to [***]
	 
	 	 
	Year 6
	 	 
	 
	 	 
	Summer

	 	Release
	 
	 	 
	NOTES

	 	1. The primary need in sweet sorghum [***] is for sweet, [***] type [***]-lines for use as
[***] in [***]. Initial material is [***], but additional material is in the pipeline
which will have enhanced [***], specifically [***] and possibly [***].
	 
	 	 
	 

	 	2. [***] have not been used to date in this process, but they could be useful in several phases.
	 
	 	 
	 

	 	3. Mapping of [***] for [***] and [***] is being completed, and these would be candidates for MAB.
	 
	 	 
	 

	 	4. The [***] process was initiated earlier, but takes longer than the [***]-line process. Thus,
the new [***]-lines will be out slightly ahead of [***]-line material. As a [***], we envision
using the [***] sweet sorghum [***].

Figure 1. Flow Diagram for the development of [***] lines for sweet sorghum [***].
The [***] diagram depicts the [***] of the program with the pipeline behind being
filled as well.

	 	 	 	 	 	 	 
	Summer 0

	 	[***]
	 	 	 	Texas
	 
	 	 	 	 	 	 
	Winter 0

	 	 	 	 	 	S. TX
	 
	 	 	 	 	 	 
	Summer 1

	 	 	 	Select specific genotypes, [***], [***], etc.
	 	Texas
	 
	 	 	 	 	 	 
	Winter 1

	 	 	 	Initiate [***]
	 	S. TX
	 
	 	 	 	 	 	 
	Summer 2

	 	 	 	 	 	Texas
	 
	 	 	 	 	 	 
	Winter 2

	 	 	 	 	 	S TX
	 
	 	 	 	 	 	 
	Summer 3

	 	 	 	 	 	Texas
	 
	 	 	 	 	 	 
	Winter 3

	 	 	 	Make [***]
	 	S TX
	 
	 	 	 	 	 	 
	Summer, Winter
4 and 5

	 	 	 	[***] Evaluation
	 	TX, others
	 
	 	 	 	 	 	 
	Summer 6

	 	 	 	[***] Evaluation
	 	TX, others
	 
	 	 	 	 	 	 
	 

	 	Release [***]	 	 	 	 

Page 42 of 45

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Figure 2. Flow Diagram for the development of [***] lines for sweet sorghum [***]. The
[***] diagram depicts the [***] of the program with the pipeline behind being filled
as well. We envision that [***] will be made using [***] sweet [***] as [***]. This
program is designed to [***]-lines.

	 	 	 	 	 	 	 

	Summer 0

	 	[***]
	 	 	 	Texas
	 
	 	 	 	 	 	 
	Winter 0

	 	 	 	 	 	S. TX
	 
	 	 	 	 	 	 
	Summer 1

	 	 	 	 	 	Texas
	 
	 	 	 	 	 	 
	Winter 1

	 	 	 	Select specific genotypes, [***], [***], etc.
	 	S. TX
	 
	 	 	 	 	 	 
	Summer 2

	 	 	 	Make Preliminary [***]	 	Texas
	 
	 	 	 	 	 	 
	Winter 2

Summer 3

	 	 	 	[***] Evaluation
	 	S TX
	 
	 	 	 	 	 	 
	Summer 3

	 	Make [***] 	 	 [***] Evaluation
	 	Texas
	 
	 	 	 	 	 	 
	Summer 4, 5

	 	 	 	Advanced [***] Evaluation
	 	Texas, others
	 
	 	 	 	 	 	 
	 	 	Release [***] based line, [***] performance	 	 

	 	 	 
	Year	 	Task
	 
	Objective 2

	 	High Biomass [***] (Figure 3)
	 
	 	 
	Year 0
	 	 
	 
	 	 
	Summer

	 	Evaluation of germplasm and identification of best genotypes (select [***] genotypes)
	 
	 	 
	Winter

	 	[***] of Selected Germplasm
	 
	 	 
	 

	 	[***] selected Germplasm to Potential [***] and Harvest [***] 
	 
	 	 
	 

	 	Make [***] to introgress the appropriate [***], [***], and [***] into [***] germplasm
	 
	 	 
	Year 1
	 	 
	 
	 	 
	Summer

	 	Evaluation of [***] to identify those with [***] (with the goal of selecting the top [***]-[***]
and identifying the [***] of this material).
	 
	 	 
	 

	 	Save [***] sample of parents and [***]  to assess [***] and [***] potential and to determine [***] of
the [***] in [***] ([***], [***], [***]).
	 
	 	 
	 

	 	Growout and [***] (treat to [***], [***], [***])

Page 43 of 45

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	Winter

	 	Based on [***] in [***], growout [***] population of each selected [***]. Plan on growing at least [***]
(possibly more). MAB screening of breeder-selected material to identify the most desirable [***] and
recovery of [***] genotype ([***]).
	 
	 	 
	 

	 	Marker analysis with [***] ([***]/[***]/[***]), [***] ([***]), other selected genes, and ~[***].
	 
	 	 
	 

	 	[***] with [***], selected [***] and [***]% or greater [***] of the adapted parent
	 
	 	 
	 

	 	[***] selected individuals in each population [***] to the [***] germplasm ([***])
	 
	 	 
	Year 2
	 	 
	 
	 	 
	Summer

	 	Growout selected [***] progeny (total of [***]), evaluate for [***], and make [***] for future
evaluation. Goal
	 
	 	 
	 

	 	Save [***] sample of parents to assess [***]; use as [***] based on information from Summer 1
	 
	 	 
	 

	 	Growout and [***] (treat to [***], [***], [***])
	 
	 	 
	Winter

	 	Growout [***] populations ([***]). MAB screening of breeder-selected material to identify the most
desirable [***] and recovery of [***] genotype ([***] Q: Bill do we still plan to do this?).
	 
	 	 
	 

	 	Marker analysis with [***] ([***]/[***]/[***]), [***] ([***]), other selected genes, and ~[***].
	 
	 	 
	 

	 	[***] with [***], selected [***] and [***]% (more?) or greater [***] of the adapted parent
	 
	 	 
	 

	 	Advance [***] through [***]
	 
	 	 
	Year 3
	 	 
	 
	 	 
	Summer

	 	Growout [***] lines and [***]populations
	 
	 	 
	 

	 	For [***], grow in multiple locations: CS for [***], advance and additional [***]. In SE US, evaluate
for [***] and [***] for adaptation and [***] to [***]. For the [***], grow in College Station
and [***].
	 
	 	 
	 

	 	Marker analysis, and [***] and cleanup (for [***])
	 
	 	 
	 

	 	Evaluate [***] in at least [***], replicated, preferably on [***] different testers.
	 
	 	 
	 

	 	Samples for [***] if appropriate
	 
	 	 
	Winter

	 	Selected [***] lines grown for final [***], expanded [***] to identify specific [***]
	 
	 	 
	 

	 	Advance [***] lines
	 
	 	 
	Year 4
	 	 
	 
	 	 
	Summer

	 	Single [***] Lines: Expanded [***] Testing and Evaluation, [***] logistics, [***] evaluation, [***], etc.
	 
	 	 
	 

	 	[***] lines; grow in multiple locations: CS for [***], advance and additional [***]. In SE US, evaluate
for [***] and [***] for adaptation and [***] to [***].

Page 44 of 45

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	 	Marker analysis, and [***] and cleanup
	 
	 	 
	Winter

	 	Selected [***], evaluation as needed
	 
	 	 
	Year 5
	 	 
	 
	 	 
	Summer

	 	Multilocation testing and evaluation for selection of best [***]. Selected lines released to [***] for
[***] and release.
	 
	 	 
	Year 6
	 	 
	 
	 	 
	Summer

	 	Seed of the lines and [***] commercially available.

Figure 3. Flow Diagram of Breeding Program for the development of [***] for [***] bioenergy
[***].

	 	 	 	 	 	 	 
	Summer 0

	 	[***]
	 	Screen [***] Germplasm
	 	Texas
	 
	 	 	 	 	 	 
	Winter 0

	 	 	 	Make [***] with Selected [***]
	 	Puerto Rico
	 
	 	 	 	 	 	 
	Summer 1

	 	 	 	[***] eval (check [***] status)
	 	Texas
	 
	 	 	 	 	 	 
	Winter 1

	 	 	 	Select
	 	Puerto Rico
	 
	 	 	 	 	 	 
	Summer 2

	 	 	 	Make Preliminary [***]
	 	Texas
	 
	 	 	 	 	 	 
	Winter 2

	 	 	 	 	 	Puerto Rico
	 
	 	 	 	 	 	 
	Summer 3

	 	 	 	[***] Eval.
	 	Texas
	 
	 	 	 	 	 	 
	Winter 3

	 	 	 	select
	 	Texas
	 
	 	 	 	 	 	 
	Summer 4, 5

	 	 	 	[***] Eval.
	 	Texas, others
	 
	 	 	 	 	 	 
	 	 	Release [***] based on [***] 	 	 

Page 45 of 45

Confidential Treatment Requested and the Redacted Material has been separately filed with the Commission

 

AMENDMENT I

to the Sponsored Research Agreement between Ceres, Inc. (“CERES”) and Texas AgriLife Research
(formerly The Texas Agricultural Experiment Station) of The Texas A&M University System
(“AGRILIFE”) effective as of August 29, 2007 (the “Agreement”).

	 	1.	 	The Parties agree to amend Article 1.A. to read as follows:
	 
	 	 	 	“AGRILIFE agrees to perform the work set forth in Appendix A and Appendix A-I
(jointly the “Program”) entitled respectively “Crop Development Using
Marker-Assisted Breeding” and “Enhancing the Sweet Sorghum Breeding Program”.”
	 
	 	2.	 	The Parties agree to add the “Enhancing the Sweet Sorghum Breeding Program” attached
hereto as Attachment I as Appendix A-I to the Agreement and Attachment II
as Appendix B-I to the Agreement.
	 
	 	3.	 	The Parties agree to add a sentence in Article 3.A. to read as follows:
	 
	 	 	 	“CERES agrees to pay for the direct and indirect cost of work of this Agreement to a
maximum amount of  four million three hundred ninety three thousand one hundred fifty eight dollars ($4,393,158) as described in the budget and attached as
Appendix B... Further, Ceres agrees to pay for the direct and indirect cost of this
Agreement to a maximum amount of  five hundred thousand dollars
($500,000) as described in the budget and
attached as Appendix B-I. AGRILIFE will invoice CERES when the payments become due.”
	 
	 	4.	 	The Parties agree that this Amendment I is effective as of June 18, 2008.
	 
	 	5.	 	For the remainder, the Agreement remains unchanged and this Amendment I shall form an
integral part thereof.

Made in two (2) copies.

	 	 	 	 	 	 	 	 	 	 	 

	For Ceres, Inc. (“CERES”)	 	 	 	For Texas AgriLife Research (“AGRILIFE”)	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:
/s/ Richard Flavell

	 	 	By: /s/
Mark A. Hussey
	 

	 

	 	 	 	 	 

	 	 
	Name: Richard Flavell, CBE, FRS	 	 	 	Mark A. Hussey	 	 
	Title: Chief Scientific Officer	 	 	 	Director, Texas AgriLife Research

Interim Vice Chancellor for Agriculture
and Life Sciences

Interim Dean, College of
Agriculture and Life Sciences	 	 

Page 1 of 7

 

	 	 	 	 	 

	For Ceres, Inc. (“CERES”)	 	 
	 
	 	 	 	 
	By:
	 	/s/ Richard Hamilton	 	 
	Name:

	 	 

Richard Hamilton
	 	 
	Title:

	 	President & Chief Executive Officer	 	 

Page 2 of 7

 

Attachment I

Appendix A-I

“Enhancing the Sweet Sorghum Breeding Program”

W.L. Rooney, Sorghum Breeding, Texas A&M University

Summary: Ceres and Texas AgriLife Research have an existing relationship to develop
bioenergy sorghums. Initial efforts have focused on the development of photoperiod-sensitive high
biomass sorghums with secondary emphasis on the development of sweet sorghum. Recent developments
in energy production and regions of production have focused additional importance on sweet sorghum.
Thus, there is a need to enhance and increase the development of sweet sorghum germplasm, parental
lines and hybrids. This describes the enhancement and activities that would be associated with
increased funding for sweet sorghum improvement.

Introduction: The DOE has set a goal of supplying 30% of 2004 transportation fuels consumed
with biofuels by 2030 to curb America’s addiction to oil, but it is clear that starch- and
sucrose-based feedstocks are not sufficient to achieve this goal. As a result, the conversion of
cellulosic feedstocks into ethanol has been recognized as an essential component of the overall
biofuel strategy in the U.S.

Several different plant species, such as (sorghum, switchgrass, energycane) are now being proposed
as lignocellulosic bioenergy crops. There are several different types of sorghum that have
potential as a biofuel crop. Initial interest in sorghum was focused on cellulosic biomass
production, but many regions of the world have realized that production of a sweet sorghum maybe a
better fit for their situation. Sweet sorghums have the potential to produce high total biomass,
sugar, starch and cellulose. A major limitation to the use of sweet sorghums is that paucity of
sweet sorghum hybrids. Current forage hybrids do not work and sweet cultivars are limited in
distribution by seed production problems.

Currently, Agrilife Research has developed a set of sweet A/B pairs that can be used to produce
sweet sorghum hybrids. We envision that first generation hybrids will use existing sweet sorghum
cultivars as pollinators. While this is not optimized, it is the most effective method to produce
hybrids quickly. Significant improvements on both the seed parent and the pollinator will result
in second generation hybrids that have better agronomics, higher yields, and improved quality.
The sorghum program at Agrilife Research has been developing populations to produce lines for the
second generation of sweet sorghum hybrids.

Ceres and Agrilife Research have an existing relationship to develop sorghum as a bioenergy crop.
While sweet sorghum is included in this relationship, it was initially listed as a lower priority
than the development of a cellulosic sorghum biofuel feedstock. Given the increased interest in
the sweet sorghum germplasm, the funding requested in this proposal is designed to increase
research and development activities specifically in the sweet sorghum development.

Page 3 of 7

 

Research Approach:

Research
Approach: For both [***] and [***] line sweet sorghum breeding efforts, a [***]
breeding approach is currently is used (Fig. 1 and 2); this approach is supplemented in the [***]
with a [***] breeding approach to incorporate [***] to produce the [***]-line from the [***]-lines.
The [***] procedure does add time to the process; this modified through the use of [***] to
produce [***]a [***].

In the [***]-line breeding program, the breeding pipeline is composed of germplasm in the [***],
[***] ([***]), [***] ([***]) and [***] ([***]) generations ([***]number in parentheses). The
populations represent [***] of sweet [***]existing [***] with [***]. These lines have been selected for
[***] content (>[***]%), [***] as a [***], and agronomic desirability. As they advance, [***],
[***], and [***] (specifically, [***] and [***]) will be evaluated. Additional populations are
continually being developed and emphasis will be placed on [***].

In the [***]-line breeding program, the breeding pipeline is composed of germplasm in the [***],
[***] ([***]), [***] ([***]) and [***] ([***]) generations ([***] number in parentheses). The
populations represent [***] of sweet [***] existing [***] with [***] as well as sweet [***] as
well. These lines have been selected for [***] content (>[***]%), complementary [***] as a
[***], and agronomic desirability. As they advance, we will evaluate [***] as a [***] and [***],
[***], and [***] (specifically, [***] and [***]) will be evaluated.

As experimental [***] hybrids are developed, Ceres will conduct [***] evaluations in multiple
environments to identify the best [***] and the specific [***] for further testing. Evaluation
shall include, but is not limited to [***] to [***], [***], [***] ([***] and [***]), and [***] and
[***].

The approaches described herein are not unlike those to be used in a traditional breeding program;
current Ceres funding is primarily directed at the high biomass research. If the sweet sorghum
program is continue at a similar pace, the funding requested is required.

Expected Results: This funding will expand the size and scope of the sweet sorghum
breeding program, allowing our cooperative efforts to advance for both the high biomass sorghums
(for cellulosic conversion applications) and the sweet sorghums (for sugar based conversion
applications). From this program, we expect to produce the lines needed for the second generation
of sweet sorghum hybrids. First generation hybrids have emphasized the development of hybrids that
are sweet and produce sugar as primary trait; there has been less attention devoted to improved
quality, enhanced yield, more desirable maturity, and improved disease resistance. The sweet
sorghum breeding program has been engaged in sweet sorghum breeding for over four years, we have a
4 year advantage on other projects that are now being initiated. This funding is critical to
maintain this advantage.

Page 4 of 7

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Attachment II

Appendix B-I

Budget and Timeline for Enhancing the Sweet Sorghum Breeding Program: We propose a four
year program that will match the minimum terms for the existing breeding and genomics proposal.

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Item	 	Year 1	 	Year 2	 	Year 3	 	Year 4	 	Total
	 
	Labor
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Research Associate
(salary, fringe)
	 	$	61,775	 	 	$	55,675	 	 	$	57,345	 	 	$	59,066	 	 	$	233,861	 
	Undergraduate Labor
	 	$	10,000	 	 	 	 	 	 	 	 	 	 	 	 	 	 	$	10,000	 
	Equipment
	 	$	18,000	 	 	 	 	 	 	 	 	 	 	 	 	 	 	$	18,000	 
	Expendable Supplies
	 	$	15,457	 	 	$	3,585	 	 	$	3,415	 	 	$	2,565	 	 	$	25,022	 
	Composition Analysis
	 	$	10,000	 	 	$	3,000	 	 	$	2,500	 	 	$	2,000	 	 	$	17,500	 
	Field Expense
	 	$	15,000	 	 	$	3,000	 	 	$	2,500	 	 	$	2,028	 	 	$	22,528	 
	Travel
	 	$	12,000	 	 	$	3,000	 	 	$	2,500	 	 	$	2,601	 	 	$	20,101	 
	 
	Direct Cost
	 	$	142,232	 	 	$	68,260	 	 	$	68,260	 	 	$	68,260	 	 	$	347,012	 
	 
	Indirect Costs
	 	$	57,768	 	 	$	31,740	 	 	$	31,740	 	 	$	31,740	 	 	$	152,988	 
	 
	Total
	 	$	200,000	 	 	$	100,000	 	 	$	100,000	 	 	$	100,000	 	 	$	500,000	 
	 

Budget Justification: A research assistant will be hired and this individual will be
responsible for coordinating and managing the breeding program for sweet sorghum line development
hybrid evaluations. A modest amount of funding for undergraduate labor is included. These
individuals will assist in the day to day activities associated with the program. Capital
equipment is budgeted in this project for a vehicle. Expendable supplies will include bags, tags,
envelopes, fuel and maintenance expenses associated with the project. Composition analysis
includes cost associated with quality analysis of the juice, bagasse or total biomass. It may
include both NIR and HPLC measurements as needed. Field expenses include land preparation, rental,
and fertilization/insecticide applications. Finally, travel funds are requested to offset cost
associated with travel to and from research locations within Texas as well as a winter nursery site
in Puerto Rico. It is expected that in-kind contributions from Ceres in seed production in off
season nurseries and the evaluation of testcross hybrids will be necessary to meet the goals of
this project at its current funding level.

Figure 1. Flow Diagram for the development of A/B lines for sweet sorghum hybrid production. This
scheme is similar to the original plan but modified to reflect the more advanced state of
development.

Page 5 of 7

 

	 	 	 	 	 	 	 

	Summer 0

	 	[***]
	 	 	 	Texas
	 
	 	 	 	 	 	 
	Winter 0

	 	 	 	 	 	S.TX
	 
	 	 	 	 	 	 
	Summer 1

	 	 	 	 	 	Texas, other locations
	 
	 	 	 	 	 	 
	Winter 1

	 	 	 	Head to row selection
specific genotypes
[***],[***],
agronomics, [***],[***], etc.
	 	S.TX
	Summer 2

	 	 	 	 	 	Texas
	 
	 	 	 	 	 	 
	Winter 2

	 	 	 	Initiate [***]
	 	S TX
	 
	 	 	 	 	 	 
	Summer 3

	 	 	 	Make [***]
	 	Texas
	 
	 	 	 	 	 	 
	Winter 3

	 	 	 	
	 	S TX
	 
	 	 	 	 	 	 
	Summer, Winter
4 and 5

	 	 	 	[***]
	 	TX, others
	 
	 	 	 	 	 	 
	Summer x

	 	Release [***]
	 	[***]
	 	TX, others

Figure 2. Flow Diagram for the development of R-lines for sweet sorghum hybrid production. We
envision that initial hybrids will be made using currently available sweet varieties as
pollinators. This program is designed to produce future R-lines.

Page 6 of 7

Confidential Treatment Requested and the Redacted Material has been separately filed with the Commission

 

	 	 	 	 	 	 	 

	Summer 0

	 	[***]
	 	 	 	Texas
	 
	 	 	 	 	 	 
	Winter 0

	 	 	 	 	 	S. Texas
	 
	 	 	 	 	 	 
	Summer 1

	 	 	 	Head to row selection
specific genotypes [***],[***], agronomics,
[***],[***], etc.
	 	Texas
	Summer 2

	 	 	 	 	 	Texas, Other
	 
	 	 	 	 	 	 
	Winter 2

	 	 	 	 	 	S. Texas
	 
	 	 	 	 	 	 
	Summer 3

	 	 	 	Make Preliminary

[***]
	 	Texas
	 
	 	 	 	 	 	 
	Summer 4

	 	Make [***]
	 	[***]Evaluation	 	Texas, Other
	 
	 	 	 	 	 	 
	Summer 5, 6

	 	Release [***]based on
line and [***] performance
	 	Advanced [***]

Evaluation
	 	Texas, others

Page 7 of 7

Confidential Treatment Requested and the Redacted Material has been separately filed with the Commission

 

AMENDMENT II

to the Sponsored Research Agreement between Ceres, Inc. (“CERES”) and Texas AgriLife Research
(formally The Texas Agricultural Experiment Station) of The Texas A&M University System
(“AGRILIFE”) effective as of August 29, 2007 (the “Agreement”).

	 	1.	 	The Parties agree to amend Article 1.A. to read as follows:
	 
	 	 	 	“AGRILIFE agrees to perform the work set forth in Appendix A, Appendix A-I and
Appendix A-II (jointly the “Program”) entitled respectively “Crop Development
Using Marker-Assisted Breeding”, “Enhancing the Sweet Sorghum Breeding Program”
and “Management Practices for Efficient Production of High Biomass and Sweet
Sorghums”.”
	 
	 	2.	 	The Parties agree to add the “Management Practices for Efficient Production of High
Biomass and Sweet Sorghums” attached hereto as Attachment I as Appendix A-II to the
Agreement and Attachment II as Appendix B-II to the Agreement.
	 
	 	3.	 	The Parties agree to add a sentence in Article 3.A. to read as follows:
	 
	 	 	 	“CERES agrees to pay for the direct and indirect cost of work of this Agreement to a
maximum amount of four million three hundred ninety three thousand
one hundred fifty eight dollars ($4,393,158) as described in the budget and attached as
Appendix B... Further, Ceres agrees to pay for the direct and indirect cost of this
Agreement to a maximum amount of five hundred thousand dollars
($500,000) as described in the budget and
attached as Appendix B-I. Further, Ceres agrees to pay for the direct and indirect cost
of this Agreement to a maximum amount of one hundred ninety nine
thousand nine hundred seventy six dollars ($199,976) as described in the
budget and attached as Appendix B-II. AGRILIFE will invoice CERES when the payments
become due.”
	 
	 	4.	 	The Parties agree that this Amendment II is effective as of July 15, 2008.
	 
	 	5.	 	For the remainder, the Agreement remains unchanged and this Amendment II shall form an
integral part thereof.

Made in two (2) copies.

Page 1 of 6

 

	 	 	 	 	 	 	 	 	 	 	 

	For Ceres, Inc. (“CERES”)	 	 	 	For Texas AgriLife Research (“AgriLife”)	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/ Richard Flavell	 	 	 	By:	 	/s/ Mark A. Hussey	 	 
	 

	 	 

	 	 	 	 	 	 

	 	 
	Name: Richard Flavell, CBE, FRS 

Title: Chief Scientific Officer	 	 	 	Mark A. Hussey

Director, Texas AgriLife Research

Interim Vice Chancellor for Agriculture
and Life Sciences

Interim Dean, College of Agriculture and
Life Sciences	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	For Ceres, Inc. (“CERES”)	 	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:
	 	/s/ Richard Hamilton	 	 	 	 	 	 	 	 
	 

	 	 

	 	 	 	 	 	 	 	 
	Name: Richard Hamilton	 	 	 	 	 	 	 	 
	Title: President & Chief
Executive Officer	 	 	 	 	 	 	 	 

Page 2 of 6

 

Attachment I

Appendix A-II

Proposal to Ceres

Management Practices for Efficient Production of

High Biomass and Sweet Sorghums

J.M. Blumenthal, Sorghum Cropping Systems Specialist

1. Introduction:

Many plant species have the potential to be used as dedicated bioenergy crops and each has unique
ecological and botanical features. For Texas and the Southern and Central U.S. region, sorghum
(Sorghum bicolor L. Moench) is a logical choice due to its high productivity, drought tolerance,
established production systems, and genetic diversity. Sorghum is a versatile feedstock for
conversion to renewable fuels utilizing three crop component approaches. Starch in the sorghum
grain is already utilized since it is easily converted to ethanol with similar efficiency using the
same methodologies as corn. Sweet sorghum stalks, traditionally used to produce sorghum syrup, can
be milled and sugar from extracted juice can be fermented to ethanol using the same methods as in
sugarcane processing. Finally, as cellulosic conversion technologies progress, newly developed
high-biomass sorghum hybrids have the potential to become an ideal lignocellulosic feedstock,
because of their ability to produce high tonnage with a higher water-use efficiency that
conventional forage sorghum(Bean and McCollum, 2006; TCE publication SCS-2006-04).

Management guidelines for producing either sweet or high biomass sorghums in Texas (or anywhere
else) are almost non-existent. While management recommendations for producing hay or silage from
forage sorghums are available, they are of limited relevance for sucrose production in sweet
sorghum stalks or management of high biomass sorghums that have plant heights of 4-6 m and stalk
diameters of 3-6 cm. The most closely related production information may be found in management
guidelines for sugarcane. Therefore, we believe that production information and management
guidelines for these novel sorghums should be developed simultaneously with the breeding effort in
an interdisciplinary approach.

Using this approach, the release of new genotypes will be integrated with deployment of associated
management practices into appropriate agricultural regions of Texas. Adaptation of these new
sorghums will be evaluated across the diverse agroecological zones of Texas and basic production
practices such as optimum seeding rate, planting and harvesting guidelines, and other cropping
components can be assessed. In addition, it is essential that optimum nutrient and water management
guidelines be determined because these inputs are critical to overall profitability and energy
balance associated with biomass cropping systems. Potential disease and insect problems will be
identified and addressed. All crop production factors can be incorporated into appropriate crop
production budgets and modeling efforts. This comprehensive plan will simultaneously promote rapid
adoption of new genotypes and their associated management systems to increase likelihood of
producer success and maximize economic impact.

2. Specific Objectives:

Page 3 of 6

 

1) Examine adaptability of high biomass sorghum and sweet sorghum to the High Plains, Central, and
Coastal areas of Texas.

2) Evaluate the effect of plant population on yield, agronomics, plant composition, sugar
concentration, and profitability of high biomass sorghum and sweet sorghum.

3) Determine nutrient requirement of high biomass sorghum and sweet sorghum under various
environments.

3. Material and Methods:

Objective 1: Hybrid adaptation and evaluation

Experiments will be conducted at Amarillo (irrigated), College Station (rainfed and irrigated),
east Texas (China) (rainfed), and the Rio Grande Valley (Monte Alto) (irrigated). In each
experiment, most advanced materials from the TAMU-Ceres biomass and sweet sorghum program will be
planted in small plots (min. of 4 rows × 15’). Plants will be grown in 30-inch rows (Amarillo,
College Station and China), or 40-inch rows (Monte Alto), respectively. Initially seeding rates for
the different regions will be based on conventional forage sorghum guidelines. The fertilization
requirement will be estimated based on the difference between nutrient measured in deep soil
samples (N: 0’—3’; P, K, Micronutrients: 0-8”) and the plant requirement estimated by yield goal.
Weed control will be atrazine applied preplant or early post emergence. Experiments requiring
irrigation at Amarillo, College Station, and Monte Alto will be furrow irrigated. Insect control
measures will be taken as warranted by pest pressure. At College Station, China, and Monte Alto all
sorghum plants will be harvested for the first time when the head-producing hybrids are in the
soft-dough growth stage. Thereafter a ratoon crop will be grown and all sorghum plants will be
harvested when the head-producing plants reach the soft-dough growth stage for the second time
(dependent on growing conditions and hybrid maturity, a third crop will be harvested at Monte
Alto). At Amarillo, due to is shorter growing season, it is likely that only one harvest will be
performed in late September. Agronomic data (such as plant height, lodging, biomass production, and
plant moisture) and compositional data (analyzed at the TAMU sorghum quality lab for the biomass
hybrids and sucrose yield and concentration for the sweet sorghums and nutrient removal of both the
sweet and biomass sorghums) will be collected at all locations. Experimental design will be a
randomized complete block with 4 replicates. Data will be subjected to ANOVA.

Page 4 of 6

 

Objective 2: Plant populations

Experiments will be conducted at Amarillo (irrigated), College Station (rainfed and irrigated),
China (rainfed), and Monte Alto (irrigated). With the exception of plant populations, agronomic
practices will be as described for objective 1. In this study we will evaluate the effect of
varying plant populations on the two most promising biomass sorghums and the two most promising
sweet sorghums developed by the TAMU-Ceres program. Plant populations tested are 40,000, 60,000,
80,000, 100,000, and 120,000 plants per acre. Agronomic and quality data will be gathered as
described in objective 1. Experimental design will be a randomized complete block with 4
replicates. Data will be subjected to ANOVA and regression analysis.

Objective 3: Nutrient requirement

Experiments will be conducted at Amarillo (rainfed and irrigated), College Station (rainfed and
irrigated), China (rainfed), and Monte Alto (irrigated). With the exception of nitrogen management,
agronomic practices will be as described for objective 1. In this study we will evaluate the effect
of N fertilization on the two most promising biomass sorghums and the two most promising sweet
sorghums developed by the TAMU-Ceres program. Nitrogen rates tested are 0, 60, 120, 180, 240, and
300 lb N per acre. Agronomic and quality data will be gathered as described in objective 1.
Experimental design will be a randomized complete block with 4 replicates. Data will be subjected
to ANOVA and regression analysis.

4. Timeline:

	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	Obj. 1	 	Obj. 2	 	Obj. 3
	Year 1
	 	 	X	 	 	 	X	 	 	 	 	 
	Year 2
	 	 	X	 	 	 	X	 	 	 	 	 
	Year 3
	 	 	X	 	 	 	 	 	 	 	X	 
	Year 4
	 	 	X	 	 	 	 	 	 	 	X	 

5. Deliverables:

Annual reports will be submitted to Ceres. Studies will be featured at AgriLife Research and
Extension field days. Extension bulletins will be prepared discussing high biomass sorghum and
sweet sorghum hybrid adaptation and best management practices. Presentations will also be made at
local, regional, and national level to showcase research and to introduce producers and industry to
the potential of high biomass sorghum and sweet sorghum as biofuel crops.

Page 5 of 6

 

Attachment II

Appendix B-II

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	Year 1	 	Year 2	 	Year 3	 	Year 4
	Program specialist (20%)
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Salary
	 	$	12,950	 	 	$	12,950	 	 	$	12,950	 	 	$	12,950	 
	Fringe Benefits & Insurance
	 	$	3,410	 	 	$	3,410	 	 	$	3,410	 	 	$	3,410	 
	Salary enhancement program
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Dr. Blumenthal
	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	Salary
	 	$	14,553	 	 	$	14,553	 	 	$	14,553	 	 	$	14,553	 
	Fringe Benefits & Insurance
	 	$	3,447	 	 	$	3,447	 	 	$	3,447	 	 	$	3,447	 
	Total Direct Costs
	 	 	34,360	 	 	 	34,360	 	 	 	34,360	 	 	 	34,360	 
	Institutional overhead (45.5%)
	 	 	15,634	 	 	 	15,634	 	 	 	15,634	 	 	 	15,634	 
	Total costs
	 	 	49,994	 	 	 	49,994	 	 	 	49,994	 	 	 	49,994	 

Page 6 of 6

 

CONFIDENTIAL

AMENDMENT III

to the Sponsored Research Agreement between Ceres, Inc. (“CERES”) and Texas AgriLife Research
(formerly the Texas Agricultural Experiment Station) of The Texas A&M University System
(“AgriLife”) effective as of August 29, 2007, as amended (the “Agreement”).

	 	1.	 	The Parties agree to add a new Article 15.M as follows:
	 
	 	 	 	“M. Notwithstanding anything to the contrary in this Article 15, the Parties
agree that the Materials provided to CERES pursuant to Section B of Appendix A
of the SRA may be supplied to parties with whom CERES has entered into
collaboration or evaluation agreements (“Collaborators”), provided that
Collaborators (i) will only be allowed to use such Materials for the purpose of
the implementation of their agreement or agreements with CERES, and (ii) will be
subject to obligations consistent with Articles 15.C, 15.D, 15.E, 15.F and 15.I.
CERES will provide to AgriLife information with respect to the Materials
feedstock composition generated pursuant to CERES’ agreements with Collaborators
and which CERES has the right to communicate to AgriLife; such information will
be deemed Confidential Information of CERES.
	 
	 	2.	 	The Parties agree that this Amendment III is effective as of October 22, 2008.
	 
	 	3.	 	For the remainder, the Agreement remains unchanged and this Amendment III shall form an
integral part thereof.

Made in two (2) copies.

	 	 	 	 	 	 	 	 	 	 	 

	For Ceres, Inc. (“CERES”)	 	 	 	For Texas AgriLife Research	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/ Richard Flavell
	 	 	 	By:
	 	/s/ Bill Dugas	27/1/09 	 
	 

	 	 

	 	 	 	 	 	 

	 	 
	Name: Richard Flavell, CBE, FRS	 	 	 	Bill Dugas	 	 
	Title: Chief Scientific Officer	 	 	 	Deputy Director, Texas AgriLife Research	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	For Ceres, Inc. (“CERES”)	 	 	 	For Texas AgriLife Research	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/ Richard Hamilton
	 	 	 	By:
	 	/s/ Mark A. Hussey	27/1/09 	 
	 

	 	 

	 	 	 	 	 	 

	 	 
	Name: Richard Hamilton	 	 	 	Mark A. Hussey	 	 
	Title: President & Chief Executive
Officer	 	 	 	Vice Chancellor & Dean of College of
Agriculture and Life Sciences	 	 

Page 1 of 1

 

CONFIDENTIAL

AMENDMENT IV

to the Sponsored Research Agreement between Ceres, Inc. (“CERES”) and Texas AgriLife Research
(formerly the Texas Agricultural Experiment Station) of The Texas A&M University System (“TAES”)
effective as of August 29, 2007, as amended (the “Agreement”).

	 	1.	 	The Parties agree to add a new Article 15.N as follows:
	 
	 	 	 	“N. Notwithstanding anything to the contrary in this Agreement, the Parties
agree that any Materials provided by TAES to CERES pursuant to this Agreement
which are germplasm or Lines may be used by CERES for the following purposes:
(a) creating hybrids using Materials and/or other germplasm or lines and (b)
research activities with, and trialing and evaluating of (i) the Materials and
any hybrids made using Materials and (ii) any plant material or seed derived
from such Materials or hybrids. Further, such Materials and any hybrids derived
therefrom and any plant material or seed of any of the foregoing may be supplied
by CERES to parties with whom CERES has entered into collaboration, evaluation,
material transfer or field evaluation agreements (“Collaborators”) or to any
subcontractors of Ceres (“Subcontractors”), provided that Collaborators and
Subcontractors (i) will only be allowed to use such Materials for the purpose of
the implementation of their agreement or agreements with CERES, (ii) will be
subject to obligations consistent with Articles 15.C, 15.D, 15.E, 15.F and 15.I
and (iii) will only perform activities as referred to in (a) or (b) hereinabove.
Any commercialization by CERES of Material or hybrids therefrom will be
governed by the relevant clauses of this Agreement, the IPRA and/or license
agreements which may be entered into by the Parties.”
	 
	 	2.	 	The Parties agree that this Amendment IV is effective as of the start of the Program
Term.
	 
	 	3.	 	For the remainder, the Agreement remains unchanged and this Amendment IV shall form an
integral part thereof.

Made in two (2) copies.

	 	 	 	 	 	 	 	 	 	 	 

	For Ceres, Inc. (“CERES”)	 	 	 	For Texas AgriLife Research (“AgriLife”)	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/ Richard Flavell	 	 	 	By:	 	/s/ Bill Dugas	7/4/09	 
	 

	 	 

	 	 	 	 	 	 

	 
	Name: Richard Flavell, CBE, FRS	 	 	 	Bill Dugas	 	 
	Title: Chief Scientific Officer	 	 	 	Interim Director, Texas Agricultural
Experiment Station	 	 

Page 1 of 2

 

	 	 	 	 	 	 	 	 	 	 	 

	For Ceres, Inc. (“CERES”)	 	 	 	For Texas AgriLife Research (“AgriLife”)	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/
Richard Hamilton	 	 	 	By:	 	/s/
Mark A. Hussey	 	 
	 

	 	 

	 	 	 	 	 	 

	 	 
	Name: Richard Hamilton	 	 	 	Mark A. Hussey	 	 
	Title: President & Chief Executive
Officer	 	 	 	Vice Chancellor & Dean, Agriculture and
Life Sciences	 	 

Page 2 of 2

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