ARGONAUT TECHNOLOGIES, INC. AMENDED AND RESTATED CHANGE OF CONTROL SEVERANCE AGREEMENT

Exhibit 10.1

ARGONAUT TECHNOLOGIES, INC.

AMENDED AND RESTATED CHANGE OF CONTROL SEVERANCE AGREEMENT

This Amended and Restated Change of Control Severance Agreement (the “Agreement”) is made and entered into effective as of June 6, 2005 (the “Effective Date”), by and between Gordon Tredger (the “Employee”) and Argonaut Technologies, Inc., a Delaware corporation (the “Company”). Certain capitalized terms used in this Agreement are defined in Section 1 below.

R E C I T A L S

A. The Company and the Employee are parties to an Amended and Restated Change of Control Severance Agreement dated August 3, 2004, as last amended on March 17, 2005 (the “Prior Agreement”), which the parties desire to amend and restate in its entirety.

B. The Company has entered into a Purchase Agreement with Biotage AB to sell substantially all the Company’s assets (the “Asset Sale”). On or about June 1, 2005 the Company will call a special meeting of its stockholders, to approve the Asset Sale. If the Asset Sale is approved, the Company will complete the sale in accordance with the terms of and subject to satisfaction of the closing conditions set forth in the Purchase Agreement with Biotage AB. Following the closing of the Asset Sale, the Company will wind up its affairs and seek to dispose of its remaining assets.

C. In connection with the Asset Sale, which constitutes a Negotiated Change of Control as defined herein, the Company will appoint the Employee as President and begin the wind down process.

AGREEMENT

In consideration of the mutual covenants herein contained and the continued employment of Employee by the Company, the parties agree that the Prior Agreement is amended and restated in full as follows:

1. Definition of Terms. The following terms referred to in this Agreement shall have the following meanings:

(a) Cause. “Cause” shall mean (i) any act of personal dishonesty taken by the Employee in connection with his responsibilities as an employee which is intended to result in substantial personal enrichment of the Employee, (ii) Employee’s conviction of a felony which the board of directors of the Company (the “Board of Directors”) reasonably believes has had or will have a material detrimental effect on the Company’s reputation or business, (iii) a willful act by the Employee which constitutes gross misconduct and is materially injurious to the Company, and (iv) continued willful violations by the Employee of the Employee’s principal duties and obligations of employment after there has been delivered to the Employee a written demand for performance from the Company which describes the basis for the Company’s reasonable belief that the Employee has repeatedly failed to substantially and materially perform his duties; provided, however, that no act

shall be deemed to constitute “Cause” if committed at the direction of the Board or otherwise by Employee in good faith and in the reasonable belief that such act is in the Company’s best interest.

(b) Change of Control. “Change of Control” shall mean the occurrence of any of the following events:

(i) the approval by shareholders of the Company of a merger or consolidation of the Company with any other corporation, other than a merger or consolidation which would result in the voting securities of the Company outstanding immediately prior thereto continuing to represent (either by remaining outstanding or by being converted into voting securities of the surviving entity) more than fifty percent (50%) of the total voting power represented by the voting securities of the Company or such surviving entity outstanding immediately after such merger or consolidation;

(ii) the approval by the shareholders of the Company of a plan of complete liquidation of the Company or an agreement for the sale or disposition by the Company of all or substantially all of the Company’s assets;

(iii) any “person” (as such term is used in Sections 13(d) and 14(d) of the Securities Exchange Act of 1934, as amended) becoming the “beneficial owner” (as defined in Rule 13d-3 under said Act), directly or indirectly, of securities of the Company representing 50% or more of the total voting power represented by the Company’s then outstanding voting securities; or

(iv) a change in the composition of the Board, as a result of which fewer than a majority of the directors are Incumbent Directors. “Incumbent Directors” shall mean directors who either (A) are directors of the Company as of the date hereof, or (B) are elected, or nominated for election, to the Board with the affirmative votes of at least a majority of those directors whose election or nomination was not in connection with any transactions described in subsections (i), (ii), or (iii) or in connection with an actual or threatened proxy contest relating to the election of directors of the Company.

(c) Negotiated Change of Control. “Negotiated Change of Control” shall mean the occurrence of a Change of Control by virtue of clause (i), (ii) or (iii) of the definition of “Change of Control” that is approved in advance by the Board.

(d) Involuntary Termination. “Involuntary Termination” shall mean, following the closing of the Asset Sale, (i) without the Employee’s express written consent, a reduction by the Company of the Employee’s Base Salary (as such term is defined below) as in effect immediately prior to such reduction; (ii) a material reduction by the Company in the kind or level of employee benefits to which the Employee is entitled immediately prior to such reduction with the result that the Employee’s overall benefits package is significantly reduced; (iii) without the Employee’s express written consent, the relocation of the Employee to a facility or a location more than twenty-five (25) miles from the Company’s current location; or (iv) any purported termination of the Employee by the Company which is not effected for Cause or for which the grounds relied upon are not valid.

-2-

(e) Severance Payments. “Severance Payments” shall mean lump sum cash payments in amounts totaling $200,000.00, payable in accordance with the terms herein.

(f) Value of the Company. “Value of the Company” shall mean (i) in the case of a Negotiated Change of Control, the value of the consideration actually received per share of common stock of the Company (the “Price Per Share”) multiplied by the total number of common shares (including the number of shares which would be outstanding upon exercise of any options or warrants, or upon conversion of any securities convertible into common stock) of the Company (the “Fully Diluted Outstanding Shares”); provided, however, that, if any portion of the consideration received by the Company’s shareholders consists of common stock of any other company merging with or acquiring the Company (the “Acquisition Partner”), that portion of the Price Per Share shall be calculated using the applicable exchange ratio contained in the definitive agreement multiplied by the average closing price of the Acquisition Partner’s common stock over the five trading day period up to and including the trading day preceding the closing of such Negotiated Change of Control, (ii) in all other cases where the Company’s common stock trades on an established stock exchange or a national market system, the average closing price of the Company’s common stock over the five trading day period up to and including the trading day preceding the occurrence of a Negotiated Change of Control multiplied by the Fully Diluted Outstanding Shares or (iii) in all other cases, the fair market value of the Fully Diluted Outstanding Shares on the date of the Negotiated Change of Control, as determined in good faith by the Board concurrent with or up to thirty (30) days in advance of such Negotiated Change of Control or, if such a timely determination is not made, following such Negotiated Change of Control.

2. Term of Agreement. This Agreement shall terminate upon the date that all obligations of the parties hereto under this Agreement have been satisfied (pursuant to Section 3 or otherwise), or, if earlier, on the date, prior to a Change of Control, Employee is no longer employed by the Company.

3. Employment and Duties. Subject to Section 4 below, the Company agrees to employ and Employee agrees to serve as the Company’s President following the closing of the Asset Sale. The duties and responsibilities of Employee shall include the duties and responsibilities as the Board may from time to time reasonably assign to Employee, which shall include, but not be limited to, managing a team of employees and contractors who will wind-down the Company’s affairs in order to return any remaining cash to the Company’s stockholders. It is contemplated that Employee will devote his full time and attention to the Company from the date of this Agreement through the date which is nine (9) months from the date of the Agreement. Following such time, it is expected that Employee shall devote the lesser of twenty-five percent (25%) of his full time and attention to the Company, or such time as necessary in order to wind-down the affairs of the Company, until such time as a final distribution to the stockholders is made and the Company is dissolved (and after which time this Agreement shall terminate). Nothing in this Section 3 shall be deemed to prevent Employee from seeking and undertaking additional employment following the date which is nine (9) months from the date of the Agreement.

4. At-Will Employment. The Company and the Employee acknowledge that the Employee’s employment is and shall continue to be at-will, as defined under applicable law. If the Employee’s employment terminates for any reason, the Employee shall not be entitled to any

-3-

payments, benefits, damages, awards or compensation other than as provided by this Agreement, or as may otherwise be established under the Company’s then existing employee benefit plans or policies at the time of termination.

5. Base Salary. For all services to be rendered by Employee pursuant to this Agreement, the Company agrees to pay Employee an initial base salary at an annual rate of not less than $200,000.00 for such period beginning on the date of this Agreement and continuing through the date which is nine (9) months from the date of the Agreement (the “Employment Period”), and, after the Employment Period, the Company shall pay Employee a base salary at an annual rate of not less than $50,000.00 (the “Base Salary”). The Base Salary shall be paid in periodic installments in accordance with the Company’s regular payroll practices. During the Employment Period, the Company will use commercially reasonable efforts to continue to provide such employee benefits to Employee (including, but not limited to, healthcare benefits and paid time off) that are consistent with a company of similar size and operational history and equivalent to those benefits provided to Employee by the Company on the date of this Agreement.

6. Bonus Upon The Closing of the Asset Sale. Upon the closing of the Asset Sale, Employee shall be entitled to receive a cash bonus equal to 0.375% of the Value of the Company at the time of the Asset Sale, less applicable withholding. Additionally, Employee shall be entitled to shall receive the first portion of the Severance Payments in a lump sum cash payment equal to $80,000.00, less applicable withholding.

7. Bonus Upon Completion of 2005 End-Of-Year Matters. Following the Asset Sale and upon the Company’s completion of its tax, audit and compliance requirements (including the completion of tax filings, the delivery of audited year-end financial statements, and the filing of any reports with the Securities and Exchange Commission, if applicable), as determined in good faith by the Board, Employee shall be entitled to shall receive a the second portion of the Severance Payments in a lump sum cash payment equal to $80,000.00, less applicable withholding.

8. Bonus Upon Completion of Final Distribution to Stockholders and Dissolution. Following an Asset Sale and immediately prior to the Company’s successful completion of the final distribution to its stockholders and the Company’s dissolution, Employee shall be entitled to shall receive a lump sum cash payment equal to $70,000.00, less applicable withholding. Additionally, Employee shall be entitled to (i) receive the third and final portion of the Severance Payments in a lump sum cash payment equal to $40,000.00, less applicable withholding, and (ii) reimbursement for health insurance premiums at Employee’s then current rate of coverage for three months, provided that (a) Employee is not then receiving health insurance coverage from a third party, and (b) Employee timely elects continued coverage under COBRA. Payments under this Section 8 shall be shall be expressly conditioned on Employee’s execution of a general release of claims against the Company or any of its successors or assigns.

9. Severance Payments; Involuntary Termination or Termination Without Cause. If Employee’s employment with the Company is terminated as a result of an Involuntary Termination or Employee is terminated without Cause, regardless of whether Employee obtains employment elsewhere, Employee shall be entitled, upon Employee’s execution of a general release of claims against the Company or any of its successors or assigns, to a lump sum cash payment equal to all unpaid Severance Payments, less applicable withholding.

-4-

10. Accrued Wages and Vacation; Expenses. Without regard to the reason for, or the timing of, Employee’s termination of employment: (i) the Company shall pay the Employee any unpaid base salary due for periods prior to the Termination Date; (ii) the Company shall pay the Employee all of the Employee’s accrued and unused vacation through the Termination Date; and (iii) following submission of proper expense reports by the Employee, the Company shall reimburse the Employee for all expenses reasonably and necessarily incurred by the Employee in connection with the business of the Company prior to the Termination Date. These payments shall be made promptly upon termination and within the period of time mandated by law.

11. Limitation on Payments. In the event that the benefits provided for in this Agreement or otherwise payable to the Employee (i) constitute “parachute payments” within the meaning of Section 280G of the Code, and (ii) would be subject to the excise tax imposed by Section 4999 of the Code (the “Excise Tax”), then Employee’s benefits under this Agreement shall be either

(a) delivered in full, or

(b) delivered as to such lesser extent which would result in no portion of such benefits being subject to the Excise Tax,

whichever of the foregoing amounts, taking into account the applicable federal, state and local income taxes and the Excise Tax, results in the receipt by Employee on an after-tax basis, of the greatest amount of benefits, notwithstanding that all or some portion of such benefits may be taxable under Section 4999 of the Code.

Unless the Company and the Employee otherwise agree in writing, any determination required under this Section shall be made in writing by the Company’s independent public accountants (the “Accountants”), whose determination shall be conclusive and binding upon the Employee and the Company for all purposes. For purposes of making the calculations required by this Section, the Accountants may make reasonable assumptions and approximations concerning applicable taxes and may rely on reasonable, good faith interpretations concerning the application of Section 280G and 4999 of the Code. The Company and the Employee shall furnish to the Accountants such information and documents as the Accountants may reasonably request in order to make a determination under this Section. The Company shall bear all costs the Accountants may reasonably incur in connection with any calculations contemplated by this Section.

12. Successors.

(a) Company’s Successors. Any successor to the Company (whether direct or indirect and whether by purchase, lease, merger, consolidation, liquidation or otherwise) to all or substantially all of the Company’s business and/or assets shall assume the Company’s obligations under this Agreement and agree expressly to perform the Company’s obligations under this Agreement in the same manner and to the same extent as the Company would be required to perform such obligations in the absence of a succession. For all purposes under this Agreement, the term

-5-

“Company” shall include any successor to the Company’s business and/or assets which executes and delivers the assumption agreement described in this subsection (a) or which becomes bound by the terms of this Agreement by operation of law.

(b) Employee’s Successors. Without the written consent of the Company, Employee shall not assign or transfer this Agreement or any right or obligation under this Agreement to any other person or entity. Notwithstanding the foregoing, the terms of this Agreement and all rights of Employee hereunder shall inure to the benefit of, and be enforceable by, Employee’s personal or legal representatives, executors, administrators, successors, heirs, distributees, devisees and legatees.

13. Notices. Notices and all other communications contemplated by this Agreement shall be in writing and shall be deemed to have been duly given when personally delivered or when mailed by U.S. registered or certified mail, return receipt requested and postage prepaid. In the case of the Employee, mailed notices shall be addressed to him at the home address which he most recently communicated to the Company in writing. In the case of the Company, mailed notices shall be addressed to its corporate headquarters, and all notices shall be directed to the attention of its Secretary.

14. Attorney Fees, Costs and Expenses. The Company shall promptly reimburse Employee, on a monthly basis, for the reasonable attorney fees, costs and expenses incurred by the Employee in connection with any action brought by Employee to enforce his rights hereunder. In the event Employee is not the prevailing party, determined without regard to whether or not the action results in a final judgment, employee shall repay such reimbursements.

-6-

15. Arbitration and Equitable Relief.

(a) Arbitration. In consideration of Employee’s employment with the Company, the Company’s promise to arbitrate all employment-related disputes and Employee’s receipt of the compensation, pay raises and other benefits paid to Employee by the Company, at present and in the future, the parties agree that any and all controversies, claims, or disputes with anyone (including the Company and any employee, officer, director, shareholder or benefit plan of the Company in their capacity as such or otherwise) arising out of, relating to, or resulting from Employee’s employment with the Company or the termination of Employee’s employment with the Company, including any breach of this Agreement, shall be subject to binding arbitration under the arbitration rules set forth in California Code of Civil Procedure Section 1280 through 1294.2, including Section 1283.05 (the “Rules”) and pursuant to California law. Disputes which the parties agree to arbitrate, and thereby agree to waive any right to a trial by jury, include any statutory claims under state or federal law, including, but not limited to, claims under Title VII of the Civil Rights Act of 1964, the Americans With Disabilities Act of 1990, the Age Discrimination in Employment Act of 1967, the Older Workers Benefit Protection Act, the California Fair Employment and Housing Act, the California Labor Code, claims of harassment, discrimination or wrongful termination and any statutory claims. The parties further understand that this Agreement to arbitrate also applies to any disputes that the Company may have with Employee.

(b) Procedure. The parties agree that any arbitration will be administered by the American Arbitration Association (“AAA”) and that a neutral arbitrator will be selected in a manner consistent with its National Rules for the Resolution of Employment Disputes. The parties agree that any arbitration under this section shall be conducted in San Mateo, California. The arbitration proceedings will allow for discovery according to the AAA National Rules for the Resolution of Employment Disputes, or the Rules. The parties agree that the arbitrator shall have the power to decide any motions brought by any party to the arbitration, including motions for summary judgment and/or adjudication and motions to dismiss and demurrers, prior to any arbitration hearing. The parties agree that the arbitrator shall issue a written decision on the merits. The parties also agree that the arbitrator shall have the power to award any remedies, including attorneys’ fees and costs, available under applicable law. The parties agree that the Company will pay for any administrative or hearing fees charged by the arbitrator or AAA except that Employee shall pay the first $200.00 of any filing fees associated with any arbitration Employee initiates. The parties agree that the arbitrator shall administer and conduct any arbitration in a manner consistent with the Rules and that to the extent that the AAA’s National Rules for the Resolution of Employment Disputes conflict with the Rules, the Rules shall take precedence.

(c) Remedy. Except as provided by the Rules, arbitration shall be the sole, exclusive and final remedy for any dispute between Employee and the Company. Accordingly, except as provided for by the Rules, neither Employee nor the Company will be permitted to pursue court action regarding claims that are subject to arbitration. Notwithstanding, the arbitrator will not have the authority to disregard or refuse to enforce any lawful company policy, and the arbitrator shall not order or require the Company to adopt a policy not otherwise required by law which the Company has not adopted.

-7-

(d) Availability of injunctive relief. In accordance with Rule 1281.8 of the California Code of Civil Procedure, the parties agree that any party may also petition the court for injunctive relief where either party alleges or claims a violation of the Employment, Confidential Information, Invention Assignment Agreement between Employee and the Company or any other agreement regarding trade secrets, confidential information, nonsolicitation or Labor Code §2870. In the event either party seeks injunctive relief, the prevailing party shall be entitled to recover reasonable costs and attorneys’ fees.

(e) Administrative relief. The parties understand that this Agreement does not prohibit Employee from pursuing an administrative claim with a local, state or federal administrative body such as the Department of Fair Employment and Housing, the Equal Employment Opportunity Commission or the Workers’ Compensation Board. This Agreement does, however, preclude Employee from pursuing court action regarding any such claim.

(f) Voluntary nature of agreement. Employee acknowledges and agrees that Employee is executing this Agreement voluntarily and without any duress or undue influence by the Company or anyone else. Employee further acknowledges and agrees that Employee has carefully read this Agreement and that Employee has asked any questions needed for Employee to understand the terms, consequences and binding effect of this Agreement and fully understand it, including that EMPLOYEE IS WAIVING HIS RIGHT TO A JURY TRIAL. Finally, Employee agrees that he has been provided an opportunity to seek the advice of an attorney of his choice before signing this Agreement.

16. Miscellaneous Provisions.

(a) No Duty to Mitigate. The Employee shall not be required to mitigate the amount of any payment contemplated by this Agreement, nor shall any such payment be reduced by any earnings that the Employee may receive from any other source.

(b) Waiver. No provision of this Agreement may be modified, waived or discharged unless the modification, waiver or discharge is agreed to in writing and signed by the Employee and by an authorized officer of the Company (other than the Employee). No waiver by either party of any breach of, or of compliance with, any condition or provision of this Agreement by the other party shall be considered a waiver of any other condition or provision or of the same condition or provision at another time.

(c) Integration. This Agreement and any outstanding stock option agreements and restricted stock purchase agreements referenced herein represent the entire agreement and understanding between the parties as to the subject matter herein and supersede all prior or contemporaneous agreements, whether written or oral, with respect to this Agreement (including the Prior Agreement) and any stock option agreement or restricted stock purchase agreement.

(d) Choice of Law. The validity, interpretation, construction and performance of this Agreement shall be governed by the internal substantive laws, but not the conflicts of law rules, of the State of California.

-8-

(e) Severability. The invalidity or unenforceability of any provision or provisions of this Agreement shall not affect the validity or enforceability of any other provision hereof, which shall remain in full force and effect.

(f) Employment Taxes. All payments made pursuant to this Agreement shall be subject to withholding of applicable income and employment taxes.

(g) Counterparts. This Agreement may be executed in counterparts, each of which shall be deemed an original, but all of which together will constitute one and the same instrument.

-9-

IN WITNESS WHEREOF, each of the parties has executed this Agreement, in the case of the Company by its duly authorized officer, as of the day and year first above written.

-10-