Document:

EXHIBIT 10.17

AMENDMENT NO. 2 TO

VEECO INSTRUMENTS INC.

2000 STOCK INCENTIVE PLAN

Effective January 1,
2006

The Veeco Instruments Inc. 2000 Stock Incentive Plan,
formerly known as the 2000 Stock Option Plan, as amended (the “Plan”), is
hereby amended as follows:

Section 4(c)of the Plan is hereby amended by
restating such section in its entirety to read as follows:

(c)         Notwithstanding
the above, no Committee member may participate in any action of the Committee
with respect to any claim or dispute regarding only that Committee member.

Section 7(a)(ii) of the Plan is hereby
amended by restating such section in its entirety to read as follows:

(ii)        Eligible Directors. For periods prior to December 31,
2005, each Participant who is a Non-Employee Director of the Company shall
receive upon initial election to office and thereafter annually on the date of
the Company’s annual meeting of stockholders (provided
that such date is at least 6 months following such Eligible Director’s initial
election to office) an Option to acquire 10,000 shares of Stock at a price
equal to the Fair Market Value of the shares of Stock subject to such Option on
the Date of Grant.

Section 8 of the Plan is hereby amended by adding
at the end of paragraph (a) of such section the following:

(iv)        Upon
initial election to office, each Non-Employee Director shall receive 5,000
shares of Restricted Stock.

(v)         On
the day following the date of each annual meeting of the Company’s
stockholders, each Non-Employee Director with service greater than six months
prior to such date shall receive 5,000 shares of Restricted Stock.

(vi)        The
Restricted Stock granted pursuant to clause (iv) or (v) above shall
be granted pursuant to a Restricted Stock Agreement in a form, and having such
terms as are, approved by the Committee including, without limitation, that (A) the
purchase price for such shares shall consist solely of such Director’s service
as a Director and (B) the Restrictions with respect to such Restricted
Stock shall lapse on the first anniversary of the Date of Grant, provided that
the director remains continuously in active service as a director for at least
nine months following the Date of Grant; provided further that the service
requirement shall be deemed to be satisfied with respect to a particular
Director in the event of a termination of such Director’s service as described
in clause (i) of the definition of “Normal Termination.”

*     *    
*     *     *

This Amendment was approved by the Compensation
Committee and by the Board of Directors of Veeco Instruments Inc. on October 19,
2005 and October 20, 2005, respectively, to be effective January 1,
2006.Exhibit 4.1

 

CUBIST

PHARMACEUTICALS

 

	
  NUMBER

  	
   

  	
  SHARES

  
	
   

  	
   

  	
   

  
	
  CBST

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
  COMMON STOCK

  	
   

  	
  SEE REVERSE
  SIDE

  
	
   

  	
   

  	
  CERTAIN
  DEFINITIONS

  
	
   

  	
   

  	
   

  
	
  INCORPORATED UNDER THE LAWS OF THE STATE OF DELAWARE

  
	
   

  	
   

  	
   

  
	
  THIS
  CERTIFICATE IS TRANSFERABLE

  	
   

  	
  CUSIP 229678
  10 7

  
	
  IN CANTON,
  MA, JERSEY CITY, NJ

  	
   

  	
   

  
	
  AND NEW YORK
  CITY, NY

  	
   

  	
   

  

 

THIS CERTIFIES THAT

 

is
the owner of

 

FULLY PAID AND NON-ASSESSABLE SHARES OF COMMON STOCK $.001 PAR VALUE, OF
 
======================== CUBIST PHARMACEUTICALS, INC. =======================
--------------------------- CERTIFICATE OF STOCK -----------------------------
 
transferable only on the books of the Corporation by the holder hereof in person or by duly authorized attorney upon surrender of this Certificate properly endorsed. This Certificate and the shares represented hereby are issued under and subject to the laws of the State of Delaware and to the Certificate of Incorporation and By-laws of the Corporation, all as amended from time to time. This Certificate is not countersigned and registered by the Transfer Agent and Registrant.
 
IN WITNESS WHEREOF, the Corporation has caused this Certificate to be signed by the facsimile signatures of its duly authorized officers and a facsimile of its corporate seal to be hereunto affixed.
 

	Dated:

	 

	/s/ Christopher D.T. Guiffre
	[CORPORATE SEAL APPEARS HERE]
	/s/ Michael W. Bonney

	Secretary
	 
	President

	 

	Countersigned and registered:

	 

	EquiServe Trust Company, N.A.

	Transfer Agent and Registrar

	 

	By
	/s/ ILLEGIBLE
	 

	Authorized Signature

	CUBIST PHARMACEUTICALS, INC.

					

 

 

The Corporation has more than one class of stock authorized to be issued.  The Corporation will furnish without charge to each stockholder upon written request, a copy of the full text of the preferences, qualifications and special and relative rights of the shares of each class of stock (and any series thereof) authorized to be issued by the Corporation.
 
The following abbreviations, when used in the inscription on the face of this Certificate, shall be construed at though they were written out in full according to applicable laws or regulations:
 

	TEN COM - as tenants in common
	 
	UNIF GIFT MIN ACT -----Custodian-----

	TEN ENT - as tenant by the entities
	 
	 
	   (Cust)      (Minor)

	JT TEN - as joint tenants with
	 
	 
	under Uniform Gifts to

	right of survivorship
	 
	 
	Minors Act
	 
	 
	 
	 

	and not as tenants in
	 
	 
	 
	(State)
	 
	 
	 

	common
	 
	 
	 

 
Additional abbreviations may also be used though not in the above list.
 
For value received,                                hereby sell, assign and transfer unto
 

	Please Insert Social Security

	or other identifying number

	of assignee

	 
	 

	 

	 
	 

	 

	 
	 

	(Please print or typewrite name and address, including zip code, of assignee)

	 
	 

	 
	 

	 
	 

	 

	                                                         shares of the capital stock represented by the within Certificate, and do hereby irrevocably constitute and appoint

	 

	 
	 
	Attorney

	 
	 

	to transfer the said stock on the books of the within named Corporation with

	full power of substitution in the premises.

	 

	Dated.

	 
	 
	 

	 

	 
	(Signature)

	 
	 
	 

	 
	NOTICE:
	 
	The signature to this assignment must correspond

	 
	with the name as written upon the face of the

														

 

 

	 
	Certificate in every particular, without alteration

	 
	or enlargement or any change whatever.

 

	(Signature Guaranteed)

	 
	 
	 
	 

	 
	 
	All guarantees must be made by a financial

	 
	 
	institution (such as a bank or broker) which is a

	 
	 
	participant in the Securities Transfer Agents

	 
	 
	Medallion Program (“STAMP”), the New York Stock

	 
	 
	Exchange, Inc. Medallion Signature Program (“MSP”)

	 
	 
	or the Stock Exchanges Medallion Program (“SEMP”)

	 
	 
	and must not be dated. Guarantees by a notary

	 
	 
	public are not accepted.

 
This Certificate also evidences and entitles to holder hereof to certain rights as set forth in a Rights Agreement between Cubist Pharmaceuticals, Inc. and EquiServe Trust Company, N.A., dated as of June 21, 1999, (as amended to date, the “Rights Agreement”), the terms of which are hereby incorporated herein by reference and a copy of which is on file at the principal executive offices of Cubist Pharmaceuticals, Inc. Under certain circumstances, as set forth in the Rights Agreement, such Rights may be redeemed, may expire, or may be evidenced by separate certificates and will no longer be evidenced by this certificate. Cubist Pharmaceuticals, Inc. will mail to the registered holder of this certificate a copy of the Rights Agreement without charge after receipt of a written request therefor. As described in the Rights Agreement, under certain circumstances, Rights held by Acquiring Persons (as defined in the Rights Agreement), or certain related Persons, and any subsequent holder of such Rights, may become null and void.Exhibit
10.1

 

TAPESTRY
PHARMACEUTICALS, INC. 

Schedule Required by Instruction 2 to Item 601

of Regulation S-K 

 

	
  Name of Executive Officer

  Signing Amendment to

  Employment Agreement

  
	
   

  
	
  Leonard Shaykin

  
	
  Gordon Link

  
	
  Kai Larson

  

 

Amendment to Employment Agreement

 

February 27, 2006

 

This Amendment is made to that Employment Agreement dated October 1,
2001 by and between Tapestry Pharmaceuticals, Inc. (Tapestry) and                       
(Executive).

 

Whereas, Executive and Tapestry are desirous to conform the terms of
the Employment Agreement to changes made in the law relating to taxation of
severance payments.

 

Now, therefore, Executive and Tapestry hereby agree as follows:

 

In the event that the Company determines that any severance benefit
provided under the Employment Agreement fails to satisfy the distribution
requirement of Section 409A(a)(2)(A) of the Internal Revenue Code of 1986, as
amended (the “Code”), as a result of Executive’s status as a “specified
employee” within the meaning of Section 409A(a)(2)(B)(i) of the Code, then
the payment of such benefits shall be automatically delayed to the minimum
extent necessary so that such benefits are not subject to the provisions of
Section 409A(a)(1) of the Code.

 

All other provisions of the Employment Agreement shall remain
unchanged.

 

Tapestry Pharmaceuticals, Inc.

 

	
  By:

  	
   

  	
   

  
	
   

  
	
   

  
	
   

  	
   

  
	
  [Name of Executive]Exhibit
10.2

 

Schedule
Required by Instruction 2 to Item 601

of Regulation S-K 

 

	
  Name of Executive Officer

  Signing Waiver Letter

  
	
   

  
	
  Leonard Shaykin

  
	
  Gordon Link

  
	
  Kai Larson

  

 

Tapestry Pharmaceuticals, Inc

4840 Pearl East Circle, Suite 300W

Boulder, CO 80301

 

Re:  Employment Agreement of
October 1, 2001 (the “Employment Agreement”)

 

Gentlemen:

 

I refer you to paragraph 6(f) of the Employment Agreement. Capitalized
terms not defined in this letter have the meanings given them in that
Employment Agreement.

 

Please be advised that the undersigned Executive hereby waives any
right to assert that he has Good Reason to resign from employment with the
Company if the Company fails to comply with section 6(f)ii of the Employment
Agreement. This waiver is limited solely to any Change of Control that may be
deemed to have occurred as a result of the acquisition of beneficial ownership
of securities of the Company by investors (the “Investors”) in the private
placement described in the preliminary proxy statement of the Company filed with
the Securities and Exchange Commission on February 6, 2006.

 

This waiver shall not apply to any other acquisition of stock or other
transaction that results in a Change of Control, including a Change of Control
that results from the acquisition of beneficial ownership of additional securities
of the Company by an Investor. Furthermore, this waiver shall be null and void
if, in the reasonable opinion of the Executive, any Investor takes action to change
the Company’s business or management in a manner materially detrimental to either
the Company’s business and operations or to the Executive’s interest as an
employee of the Company. Such action could include, without limitation, any action
affecting the Company’s strategic direction, management, corporate governance, compensation
or personnel. For the avoidance of doubt, the exercise by SSF of its right to
designate up to two persons for election to the Company’s board of directors
shall not of itself constitute the taking any such action

 

Executive shall give the Company notice promptly if he determines that
action has been taken rendering this waiver to be null and void.

 

Very truly yours,

 

 

[Executive]

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