Document:

<PAGE>

                                                                   Exhibit 10.29

                                          Effective as of January 3, 2000

Robert C. Bishop, Ph.D.
47 Carisbrooke Road
Wellesley, MA 02481

Dear Bob:

      This will confirm our agreement pursuant to which you will act as a
consultant to us ("AutoImmune").

      As a consultant, you will provide senior management services to
AutoImmune. Your services will include technology licensing; assistance in the
preparation of press releases; assistance in the preparation of AutoImmune's
filings with the Securities and Exchange Commission; assistance in the
preparation of AutoImmune's proxy statement and annual report to stockholders;
supervision of persons responsible for AutoImmune's financial statements; and
assistance to AutoImmune's Board of Directors with respect to strategic planning
and initiatives.

      For these services, AutoImmune shall pay you at the rate of two hundred
dollars ($200) per hour but in no event more than one thousand, six hundred
dollars ($1,600) per day. You shall be paid for your services within thirty (30)
days after AutoImmune's receipt of your invoice for such services. Such invoice
shall be accompanied by a report setting forth in reasonable detail the nature
of your activities and time spent. You shall also be reimbursed for expenses
incurred by you in the performance of your services under this agreement to the
extent these expenses were approved in advance by AutoImmune and upon submission
of appropriate documentation.

      This agreement may be terminated by either you or AutoImmune effective
upon thirty (30) days' prior written notice.

      Your status as a consultant to AutoImmune will be that of an Independent
contractor and not as an employee of AutoImmune.

      This agreement constitutes the entire agreement between us with respect to
the subject matter hereof and may not be modified or changed or its provisions
waived, except by an agreement in writing. This agreement shall inure to the
benefit of and be binding upon our respective heirs, personal representatives,
successors and assigns.
<PAGE>

      If the foregoing accurately sets forth our agreement, please so indicate
by signing and returning to AutoImmune the enclosed copy of this letter.

                                  Very truly yours,

                                  AUTOIMMUNE INC.

                                  By /s/ Allan R. Ferguson
                                     -----------------------
                                     Allan R. Ferguson
                                     Chairman of the Compensation
                                     Committee of the Board of Directors

AGREED:

/s/ Robert C. Bishop
-----------------------
Robert C. Bishop, Ph.D.

                                      -2-<PAGE>

                                                                  Exhibit 10.30

                                        Effective as of November 20, 1999

Heather Ellerkamp
8 Summer Street
Ipswich, MA 01938

Dear Heather:

      This will confirm our agreement pursuant to which you will act as a
consultant to us ("AutoImmune").

      As a consultant, you will provide such financial services to AutoImmune as
the Chairman of the Board of Directors of AutoImmune or his designee shall
reasonably require. Your services will include assistance in the quarterly close
of AutoImmune's books; preparation of quarterly Reports on Form 10-Q and Annual
Reports on Form 10-K; working with the Audit Committee of AutoImmune's Board of
Directors; preparation of tax returns on behalf of AutoImmune; assistance in the
preparation and dissemination of press releases; assistance in the preparation
of AutoImmune's annual report to stockholders; assistance in the preparation of
AutoImmune's proxy statements; attendance to insurance and benefits matters
involving AutoImmune; and assistance with the calling and holding of meetings of
AutoImmune's stockholders.

      For these services, AutoImmune shall pay you at the rate of one hundred
dollars ($100) per hour but in no event less than eight thousand dollars
($8,000) per calendar quarter during the term of this Agreement. You shall be
paid for your services within thirty (30) days after AutoImmune's receipt of
your invoice for such services. Such invoice shall be accompanied by a report
setting forth in reasonable detail the nature of your activities and time spent.
You shall also be reimbursed for expenses incurred by you in the performance of
your services under this agreement to the extent these expenses were approved in
advance by AutoImmune and upon submission of appropriate documentation.

      This agreement may be terminated by either you or AutoImmune effective as
of February 19, May 19, August 19 or November 19 of a calendar year upon thirty
(30) days' prior written notice.

      Your status as a consultant to AutoImmune will be that of an independent
contractor and not as an employee of AutoImmune.
<PAGE>

      This agreement constitutes the entire agreement between us with respect to
the subject matter hereof and may not be modified or changed or its provisions
waived, except by an agreement in writing. This agreement shall inure to the
benefit of and be binding upon our respective heirs, personal representatives,
successors and assigns.

      If the foregoing accurately sets forth our agreement, please so indicate
by signing and returning to AutoImmune the enclosed copy of this letter.

                                            Very truly yours,

                                            AUTOIMMUNE INC.

                                            By /s/ Robert C. Bishop
                                               -----------------------
                                               Robert C. Bishop, Ph.D.
                                               Its Chief Executive Officer

AGREED:

/s/ Heather A. Ellerkamp
-----------------------
Heather Ellerkamp

                                      -2-<PAGE>

                                                                  Exhibit 10.31

                     [LETTERHEAD OF FLETCHER SPAGHT, INC.]

R. John Fletcher
Chief Executive Officer

                                                 September 20, 1999

Transmitted via Facsimile (781) 860-0705
Originals Forwarded via First Class Mail

Robert C. Bishop, Ph.D.
Chief Executive Officer
AutoImmune, Inc.
128 Spring Street
Lexington, MA 02421

Dear Bob:

      It was a pleasure to speak with you and Joanne last week. Linda Tufts and
I incorporated your suggestions relative to our proposal. We would be pleased to
undertake the work required to ascertain the potential of Colloral as a
neutraceutical. If the product does have potential we would assist your efforts
to determine the commercialization strategy which would optimize that potential.

      We are enthusiastic about the work you requested. Our firm can commence
the assignment soon and believe there is value to doing so. The balance of this
letter represents our proposal for assisting you.

CHARTER

      Fletcher Spaght, Inc. ("FSI") will analyze the market potential, business
requirements and likely returns associated with the launch of Colloral as a
neutraceutical. A major emphasis of the work will be formulating alternative
market entry strategies and evaluating the relative attractiveness of those
options. FSI will work with you to determine whether, and how, AutoImmune could
best realize value from Colloral.
<PAGE>

Robert C. Bishop, Ph.D.
Page 2
September 20, 1999

      At this point, we anticipate the major tasks which need to be completed
include:

      .     Estimate the market potential (units) of Colloral

            -  relevant population - appropriate market segments

            -  overall size and growth races of relevant segments

            -  achievable share

            -  what is the most likely manner in which the product will be
               used?

            -  expected distribution of usage rates (per year, per segment)

      .     Research the appropriate price level of Colloral considering such
            factors as:

            -  price levels of competitive products

            -  price levels of analogous products

            -  economic characteristics of key segments

            -  full costs of bringing Colloral to market (i.e., including
               distribution, marketing, sales)

            -  likely price elasticity of the product

      .     Quantify the achievable revenue level of Colloral given its likely
            price level and unit potential

      .     Estimate the rate at which Colloral is likely to penetrate and ramp
            to its potential

      .     Project annual revenue levels from market launch through ramp-up

      .     Evaluate alternative sales channels including their requirements,
            capabilities, and economics relative to Colloral

      .     Determine how Colloral should be packaged and distributed within the
            context of the likely sales channel(s)

      .     Identify the types and costs of marketing efforts which would be
            required to educate and generate interest among target customers

      .     Determine manufacturing requirements and likely costs levels
            (investment and operating) to support the projected level of demand

      .     Assess whether partners could be helpful to the manufacturing,
            marketing and/or sales of Colloral i.e., evaluate the trade-offs
            between leveraging AutoImmune's infrastructure vs. partnering with
            others. If partnering is attractive, determine which companies are
            the more attractive prospects and the likely economic
            characteristics of the partnership (at this point, for planning
            purposes)
<PAGE>

Robert C. Bishop, Ph.D.
Page 3
September 20, 1999

      .     Develop annual projections of the financials (revenues, costs,
            profits, cash flow) for each of the major scenarios in which
            Colloral could be launched

      .     Evaluate the alternative commercialization options and identify the
            most promising alternative based upon criteria relevant to
            AutoImmune

      .     Create a Business Plan documenting the potential, market entry
            strategy, requirements and pay-offs of the preferred alternative for
            commercializing Colloral

      .     Negotiate partnerships which are part of the optimal entry strategy

APPROACH

      To address and complete the major work efforts listed in the Charter
section, FSI plans to structure its work as outlined in the phases described
below.

                           Overview of FSI's Approach

Phase   Work Effort
-----   -----------

I.      Market Analysis      ------------------
                                  Phase V              ------------
II.     Commercialization         Financial              Phase VI
        Assessment                Planning               Business
                             ------------------            Plan
III.    Manufacturing         Commercialization        ------------
        Analysis              Option Assessment        ------------
IV.     Partners             ------------------         Phase VII
                                  Financial             Partnering
                                  Strategy             Arrangement
                             ------------------        ------------

Note: Shaded work efforts to be done if decide to commercialize following go/no
go decision.
<PAGE>

Robert C. Bishop, Ph.D.
Page 4
September 20, 1999

      Phase I: Market Analysis

      During this phase, FSI will work on the issues related to determining the
overall potential of Colloral as a neutraceutical: market potential in units,
pricing, achievable revenue and ramp-up rate.

      We will begin with a working session with you and Joanne to discuss your
perspectives, review any existing research, and agree on the appropriate level
and emphasis of the work.

      Thereafter, we anticipate that to complete our work we will need to:

      .     Collect and analyze relevant information regarding the Rheumatoid
            Arthritis (RA) population

      .     Review the current status of treatments for RA, including the use of
            non-prescription solutions

      .     Research the experience of analogous situations which involve the
            use of neutraceuticals

      .     Conduct a limited market research effort with key physicians,
            focusing on those involved in the clinical trials, regarding their
            perspective and likely level of support relative to their patients

      .     Interview selected patients from the AutoImmune clinical trials

      .     Analyze the pricing patterns of neutraceuticals in context with
            presumed levels of effectiveness, cost of alternatives, size of
            re1evant populations, etc.

      .     Analyze and synthesize the results of the market research and other
            information developed

      Phase II: Commercialization Assessment

      During this phase, FSI will determine the alternative sales channels which
would be appropriate for Colloral. For each channel type, we plan to:

      .     Conduct research to identify the key players
<PAGE>

Robert C. Bishop, Ph.D.
Page 5
September 2O, 1999

      .     Conduct field work to discuss the receptivity of those companies to
            distributing the product, define the requirements for achieving
            success within that channel and determine the level of potential
            which Colloral might achieve

      .     Analyze the financial characteristics of operating within the
            channel

      The above work will address, for each channel, such factors as:

      .     Types of customers served

      .     Market share of customer segments

      .     Price levels/margin expectations

      .     Inventory turn expectations

      .     Viewpoint on branding

      .     Typical distribution cycle and thus shelf-life requirements,
            refrigeration, order size and other distribution characteristics

      .     Packaging requirements

      .     Level of marketing support provided by/required by the channel

      .     Other benefits/risks during the start-up phase

      .     Implications for working with/conflicting with other channels

      The above work will enable us to resolve the issues related to sales
channels and distribution. As well, the work in this phase will provide valuable
inputs into FSI's work regarding pricing strategy, marketing, partnering and
financial planning.

      Phase III: Manufacturing Analysis

      The investments and operating costs associated with producing Colloral are
important inputs to developing strategic alternatives for commercializing the
product. During this phase, FSI will review the cost data available within
AutoImmune, and analyze the likely dynamics of those costs under alternative
scenarios of market success. To develop inputs for an analysis which are not
available within AutoImmune, FSI will rely on its past experience with analogous
clients, manufacturers of comparable products and equipment and raw materials
suppliers -- as required.
<PAGE>

Robert C. Bishop, Ph.D.
Page 6
September 20, 1999

      Phase IV: Partners

      It is likely that AutoImmune will want to partner with another company to
provide some or all of the capabilities required for commercialization. During
this phase FSI will determine the areas in which AutoImmune most benefits from a
partnership versus go-it-alone. Essentially, we plan to trade-off partnering
versus not, based upon the relative cost, for any step of value-added of having
a partner versus developing the capability de novo. Ultimately, whether or not
to have a partner will also depend on other factors, e.g., market size, type of
distribution available, capital access, etc. Nevertheless, at this point, the
planning process requires that the major types of partnerships be evaluated in
the context of relative cost and capabilities trade-offs.

      As a result of its work in this phase, FSI expects to:

      .     Determine the areas of value added for which a partner is preferred

      .     Identify prospective partners

      .     Incorporate benchmarks regarding partnerships economics into the
            overall financial projections

      Phase V: Financial Planning

      FSI will develop projections reflecting the more promising
commercialization options. During this phase our work will build upon the
revenue projections developed in Phase I and include:

      .     Analyzing the expense and investment levels required for the
            roll-out

      .     Creation of projected financia1s (3-5 years)

            -  P&L

            -  Balance Sheet

            -  Cash Flow

      Each major scenario will be evaluated in the context of likelihood of
success and types/levels of risk.

      If AutoImmune decides to commercialize Colloral as a neutraceutical and
once a commercialization alternative is agreed upon, FSI will also provide
AutoImmune with the information needed to fund the start-up:

      .     Determination of financing requirements
<PAGE>

Robert C. Bishop, Ph.D.
Page 7
September 20, 1999

      .     Valuation

            -  analytical approaches

            -  comparables

      .     Development of prospect list for funding sources

      .     Determination of type of fundraising assistance required

      .     Recommendations regarding how best to proceed

      Phase VI: Business Plan

      If AutoImmune requires a business plan to raise capital or effect a
partnership relative to Colloral, FSI will build upon its prior work to develop
the plan. As appropriate, the document will cover the traditional business plan
topics, including, relevant:

      .     Executive Summary

      .     Definition of the business

      .     Market opportunity

            -  Segmentation

            -  size and growth, overall and by major segment

      .     Competition

            -  characteristics

            -  Colloral's advantage

      .     Roll-our strategy

      .     Marketing and sales strategy

      .     Organization, Human Resources

      .     Management Team and Board

      .     Ownership

      .     Goals, milestones, timing

      .     Risks
<PAGE>

Robert C. Bishop, Ph.D.
Page B
September 20, 1999

      .     Financials

            -  budget second half 1999

            -  3-5 year projections (P&L, Balance Sheet, Cash Flow)

            -  level of investment, timing, use of funds

            -  returns; value

      If other topics are important to include in the plan, FSI will do so.

      Following completion of the plan, FSI will develop an executive
presentation suitable for briefing prospective funding and/or partnering sources
on the Colloral opportunity. FSI will also develop an Action Plan for moving
ahead with fundraising efforts.

      Phase VII: Partnering Arrangement

      FSI will be available to assist AutoImmune, as appropriate, with effecting
partnerships which are deemed beneficial to commercializing Colloral. We have
been instrumental in many such partnerships and would be pleased to either take
the lead or play a supporting role relative to your efforts. If we assume
primary responsibility, we would do the work primarily on a success fee basis.

SCOPE

      Within the context of this proposal, FSI will focus on the U.S. market.
We would be pleased to assist you with the markets in Europe and/or Japan,
should you so require.

      We are pleased that Joanne will be available to contribute to the work and
we have taken her availability into account when we agreed upon the cost for the
work outlined herein.

OUTPUT

      At the conclusion of each major analytical effort we will develop an
interim summary of findings, supporting analyses and conclusions. At the
completion of Phase V we will synthesize our findings to date and prepare a
formal presentation for the Board and management team. We will provide bound
copies of the material presented as documentation of our work.
<PAGE>

Robert C. Bishop, Ph.D.
Page 9
September 20, 1999

WORKING RELATIONSHIP

      We will look to you, Bob, as our client and to Joanne as the focal point
for day-to-day interaction on behalf of AutoImmune. As well, Joanne will be
participating in the work. During this assignment we will update you on our
progress on no less than a biweekly basis.

QUALIFICATIONS

      Fletcher Spaght, Inc. was founded in 1983. The focus of our firm is to
provide strategy and corporate development assistance to high growth companies
and new ventures. The specific work we perform is directed at:

      .     Providing management with information which will facilitate making
            choices to maximize the potential of a business

      .     Developing options for improving existing businesses or
            creating/launching new businesses

      .     Assisting companies with the implementation of their strategic and
            operational choices

      .     Arranging corporate partnerships and equity investments

      Our practice areas of specialization include Healthcare, High Technology
and Corporate Growth/Development. In Healthcare. our work encompasses
pharmaceuticals, biotechnology, medical devices, innovative services for the
physician hospital and insurance markets and other technology opportunities,
including e-commerce applications, for the physician and hospital communities.
In High Technology, we include software, computers and computer peripherals, a
variety of other analog and digital devices, and advanced materials. Many of our
High Technology clients have applications in medical areas. In Corporate
Growth/Development we include distribution, service and transaction-intensive
businesses in a multiplicity of industries.

      The staff of FSI is comprised of strategy consultants with prior
experience in premier strategy firms, such as The Boston Consulting Group, Bain
and Company, The Wilkerson Group, Gemini Consulting and people with backgrounds
in our areas of expertise. On average, our staff has a greater level of
experience than members of competitor firms, thereby allowing us to quickly
grasp the issues of an evolving business. Our industry expertise provides a
broad spectrum of related experience and contacts. Thus, we avoid a costly
start-up in learning our client's industry and instead, can devote our resources
to in-depth pursuit of the issues comprising a specific assignment.
<PAGE>

Robert C. Bishop, Ph.D.
Page 10
September 20, 1999

      Selected assignments relevant to this work include:

      .     Assessment of the U.S. and European opportunity for a nutritional
            product/medical food line designed for Parkinson's patients (to be
            sold OTC mail-order) which, based on clinical trials, enhanced drug
            therapy/minimized on-off; this effort included market research with
            physicians, patients and key associations.
             -  post-launch, FSI conducted follow-up market research with
               patients to examine the purchase/rebuy decision and evaluated
               potential distribution partnerships to accelerate revenue
               growth/ramp-up

      .     Development of a strategic plan for a wound care company with a
            proprietary therapeutic (non-FDA approved) which included
            incorporating their solution into a services business and the
            creation of win/win service partnerships with hospitals for
            alternative/customized models of care

      .     Evaluation of the market opportunity, including development of the
            patient profile, likely patient market size and assessment of
            physician reaction relative to a drug with a problematic
            pharmacokinetic profile used to symptomatically treat a neurological
            disease, and which was historically available in the U.S. through
            compounding pharmacies and the "black market", but could be
            improved through reformulation/time-modulated delivery

      .     Strategy assistance for a company with a therapy, not subject to FDA
            approval (due to off-label use), to regulate the metabolic uptake
            for a subset of patients with short-bowel syndrome

      .     Strategy assistance for a food/nutrition company interested in
            enhancing sales of specific products through innovative
            cross-product promotions to selected customer segments

      As well, FSI has identified and negotiated many licensing and partnership
agreements with companies in the U.S., Europe and Japan for therapeutics,
diagnostics and devices.

      I believe FSI is unique in terms of its focus, expertise and scope of
operations. It is our perception that FSI enjoys a reputation for excellent
work, responsiveness, and objectivity. Importantly, we know our firm has helped
clients improve their performance, earn attractive returns on new investments,
and avoid pursuing business opportunities which have ultimately proven to be
unsuccessful.
<PAGE>

Robert C. Bishop, Ph.D.
Page 11
September 20, 1999

PROJECT STAFFING

      I will take primary responsibility for this assignment and Linda Tufts
will assume day-to-day case management. Assisting us in this effort will be key
team members from our Healthcare Practice including Mary Anne Poole, Geeta Bahl,
Joanna Chin and Brian Fox.

      An attachment with abbreviated profiles of each key team member
accompanies this proposal. Other professionals will be utilized as needed.

TIMING AND COST

      In accordance with your request, we will organize the work to be complete
by the end of November.

      The fees for our assistance for Phases I-V will be $150,000. Our policy is
to bill only for time productively spent on behalf of the client. Therefore,
actual accrued amounts could be less than proposed. In no case, however, will we
exceed the amount proposed for fees without your prior approval. The effort
required for subsequent phases will depend on the conclusions of Phase V and,
therefore, will be scoped at that time.

      We have structured the work in accordance with our current understanding
of what is needed. If this does not meet your expectations we would be pleased
to discuss alternatives to the scope of effort described.

      Our policy is to invoice our clients twice monthly on a progress billing
at the lower end of the projected budget estimate of professional fees. For this
project, we request an upfront payment of $30,000 and four progress payments of
$30,000 towards professional fees. We will invoice you for the progress
payments. At the completion of our work, we will reconcile all fees and submit a
final invoice for any remaining expenses due.

      In addition to our fees we will request reimbursement for expenses such as
those associated with communications (e.g., telephone, fax, photocopy),
overnight delivery (e.g., FedEx services), database searches, travel, honoraria,
etc. We will invoice for expenses at the end of each calendar month. Expense
documentation will accompany each invoice. Telephone expense is not documented
and thus will be charged at 3% of fees.

      FSI asks that you honor all invoices within fifteen days of receipt.
<PAGE>

Robert C. Bishop. Ph.D.
Page 12
September 20, 1999

CONFIDENTIALITY

      FSI recognizes the confidential nature of the work proposed. We commit to
treating all of the information developed on your behalf as proprietary to
AutoImmune.

SUMMARY

      We recognize the vital importance of this project to AutoImmune and we are
enthusiastic about assisting you.

      We look forward to hearing from you to discuss the next steps relative to
getting started. Please call Linda or me at your earliest convenience.

                                                 Sincerely,

                                                 /s/ John
                                                 -----------------
                                                 R. John Fletcher

APPROVED for AutoImmune, Inc. by:

/s/ Robert C. Bishop                             Sept 28, 1999
---------------------                            -----------------
Robert C. Bishop, Ph.D.                          Date
Chief Executive Officer

RJF/jmw
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