B -- GENE ARRAY ANALYSIS OF SHEEPSHEAD MINNOW

Notice Date

December 27, 2000

Contracting Office

U. S. Environmental Protection Agency, Contracts Management Division (MD-33), Attention: OARSC, Research Triangle Park, NC 27711

ZIP Code

27711

Solicitation Number

XQ8E40

Response Due

January 12, 2001

Point of Contact

JENNIFER HILL, Contract Specialist (919-541-3083)

E-Mail Address

Click here to contact the contract specialist via (hill.jennifer@epa.gov)

Description

THIS IS A COMBINED SYNOPSIS/SOLICITATION FOR COMMERCIAL ITEMS PREPARED IN ACCORDANCE WITH THE FORMAT IN SUBPART 12.6, AS SUPPLEMENTED WITH ADDITIONAL INFORMATION INCLUDED IN THIS NOTICE. THIS ANNOUNCEMENT CONSTITUTES THE ONLY SOLICITATION. QUOTES ARE BEING REQUESTED AND A WRITTEN SOLICITATION WILL NOT BE ISSUED. The solicitation number is XQ8E40, and the solicitation is being issued as a Request for Quotation (RFQ). The solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 97-20. The associated North American Industry Classification System (NAICS) code is 541710 which has a size standard of 500 employees to qualify as a small business; however, it is anticipated that the contract will be awarded as a result of full and open competition. A firm, fixed-price purchase order with option quantities is anticipated to result from the award of this solicitation. This procurement is for the preparation of cDNA membrane arrays containing 50 genes from sheepshead minnow (SHM, Cyprinodon variegatus) and subsequent evaluation of feral SHM liver samples collected from multiple locations over a two year period. This procurement requires the contractor to prepare and evaluate 200 to 400 samples provided by EPA. A minimum of 200 liver samples is guaranteed and will be shipped as a single unit. The additional quantities are optional and will be shipped in blocks of 25 samples. Exercising this option will be at the discretion of the EPA. CONTRACT LINE ITEM NUMBER (CLIN) 1. The contractor shall prepare membrane bound cDNA arrays by robotic application of 50 genes encompassed in plasmids provided by the EPA. The cDNAs will be amplified by M13 forward and reverse primers (or other specific primers as needed). In addition, three cDNAs corresponding to known sheepshead minnow genes for -actin, vitellogenin and the estrogen receptor will be prepared and used as positive controls. EPA will provide these three cDNAs. SHM liver samples will be supplied by EPA in individual coded cryovials which should be maintained at -70 C until analysis. The contractor shall provide EPA with a price on a per sample basis for the contract line item above, based on the minimum number of samples projected including the cost of the contractor picking up or shipping the samples from Gulf Breeze, Florida to the contractor's analytical facility. An additional price should be provided on a per sample basis for batches of 25 samples up to the projected maximum number of samples. The remaining tissue from each sample will be retained at the contractor's facility for one year following final report submission or returned on ice to EPA's Project Officer. The contractor shall first prepare high quality poly A+ RNA (or total RNA as required) using the Qiagen system and then 33P-labeled cDNAs from flash frozen livers of sheepshead minnows from feral populations provided by the EPA. The contractor shall provide photographs of gels showing total RNA and that the larger rRNA band staining more intensely than the lower rRNA band. The RNA will be copied into cDNA using reverse transcriptase and random primers (or poly dT) in the presence of 33P-dCTP to label the probes. The amplified products will be verified by agarose gel electrophoresis. Those that fail to amplify will be repeated until they are amplified. This may require returning to the original E. coli stocks to grow out and repurify the plasmids. Equal amounts of purified, amplified products from each plasmid will be placed into a 96 well format, denatured and diluted appropriately with binding buffer. A robot will be used to print equal volumes of the plasmids onto prepared nylon membranes. The cDNA will be crosslinked to the membranes with a UV light. Membranes will be checked randomly for quality control by staining with methylene blue and by hybridization with 33P-labeled probes made from the -actin, vitellogenin and estrogen receptor controls. The contractor shall treat the membranes with Ambion's prehybridization buffer "Ultrahyb", add denatured 33P-labeled cDNA probes in hybridization buffer such that the positive and negative controls are clearly expressed. Optimization of binding and washing steps will be required. Control and supplied field samples must be probed the same day. Radioactivity bound to each spot should be quantified using a phosphorimager and suitable software. This information will be used to evaluate the relative binding efficiency of probes from control and field samples. The contractor shall track and report assay results based on EPA sample specific code numbers. Deliverables for analyses: 1) Date of sample homogenization, extraction and analysis; 2) Tabulated sample results by designated EPA code number; 3) Summary of homogenization, extraction and analytical procedures; 4) Explanations for all data qualifications; 5) Reference analytical methods; and 6) Explanations for all departures from the analytical protocols and discussion of possible effects on the data. Quality Assurance Requirements: The contractor shall submit a copy of their Quality Assurance/Quality Control protocols to the EPA Project Officer prior to analysis of samples. The contractor must permit a QA audit of laboratory and/or data entry procedures by an authorized agent of EPA at any time during the conduct of analyses (given advance and reasonable notice). Results shall be reported to the EPA Project Officer no later than 180 days after receiving a shipment of samples. The contractor shall provide the results in an electronic format using Microsoft EXCEL and a hard-copy output of data files (i.e. spreadsheets) for the purpose of quality assurance. A report containing a written evaluation and interpretation of the data analysis and detailing the methods used and the results of QA measures shall also be provided by the contractor. Any laboratory notes discussing problems encountered must be included as an appendix to this report. Original records such as laboratory notebooks and printouts from analytical devices shall be retained by the contractor for at least three (3) years following the submission of the final report, as they may be requested by EPA. The contractor is required to transfer copies of all technical, fiscal, and programmatic files regarding this contract to the Project Officer. These files must be boxed in accordance with Federal Record Keeping Standards in boxes required by the Records Center and labeled as "Gene Array Analysis of Sheepshead Minnows -- Contractor Name / Contract Number" and contain an internal and external packing slip that identifies the specific contents of each box. The external packing slip shall be affixed to the exterior of the box. The offeror must have proven experience in molecular genetics techniques and the application of gene arrays. Previous documented experience in analytical molecular techniques and application of gene arrays is required. A Quality Assurance / Quality Control program shall be in place at the contractor's laboratory and shall address, at a minimum, the following topics: accuracy and precision; calibration; physical processing of samples; analytical methods utilized; and data reporting. The following FAR provisions apply to this solicitation: 52-212-1, Instructions to Offerors -- Commercial Items; 52.212-2, Evaluation -- Commercial Items. Evaluation criteria to be included in paragraph (a) of provision 52.212-2 are as follows: (i) TECHNICAL CAPABILITIES CRITERIA: 1) Provide a copy of QA/QC protocols; 2) Demonstrate previous experience in application and interpretation of gene arrays; 3) Demonstrate previous analytical experience with proposed molecular genetic techniques/methods; 4) Explanation of methods used for each area with references; 5) Experience with similar size/scope projects; 6) Ability to meet the deadlines for the project; 7) Plan to submit a final report (electronic format) as required; and 8) Description of Record Management Program; (ii) PAST PERFORMANCE: Provide 3 references (quality of product or service, timeliness of performance, ability to adhere to deadlines, and overall customer satisfaction); and (iii) PRICE. Award will be made to the offeror whose offer is the lowest priced offer meeting all of the technical requirements. Offerors must satisfactorily meet all of the technical requirements to be considered "technically acceptable". All offerors are to include with their offers a completed copy of provision 52.212-3, Offeror Representations and Certifications -- Commercial Items. The following FAR clause applies to this acquisition: 52.212-4, Contract Terms and Conditions -- Commercial Items. The following additional FAR clauses which are cited in Clause 52.212-5 are applicable to the acquisition: 52.203-6, Restrictions on Subcontractor Sales to the Government, with Alternate I; 52.203-10, Price or Fee Adjustment for Illegal or Improper Activity; 52.219-14, Limitation on Subcontracting; 52.222-26, Equal Opportunity, 52.222-35, Affirmative Action for Special Disabled and Vietnam Era Veterans; 52.222-36 Affirmative Action for Handicapped Workers; 52.222-37, Employment Reports on Special Disabled Veterans and Veterans of the Vietnam Era; 52.222-41, Service Contract Act of 1965, As Amended. Any applicable wage determination(s) will be made a part of the resultant purchase order. Price and technical information should be submitted in separate proposals. It is requested that the completed Representations and Certifications be included with the price proposal. All technical questions are to be forwarded via email to the Contract Specialist at the following email address: hill.jennifer@epa.gov. Offerors should review the Statement of Work and other information posted with this Request for Quotation on EPA's website at the following address: http://www.epa.gov/oam/rtp_cmd. Offerors should frequently go to the website and click on this RFQ to check the status of this procurement and to ascertain if any amendments have been issued. The Contract Specialist will also try to notify any offerors who have emailed expressing an interest in the solicitation when and if amendments have been posted to the web site above; however, it is the offeror's responsibility to frequently check the web site for an updated status and for any amendments. Please submit two copies of the technical proposal and two copies of the price proposal to Jennifer B. Hill, Contract Specialist, U.S. Environmental Protection Agency, MD-33, Research Triangle Park, NC 27711. Courier delivery address is U.S. Environmental Protection Agency, Receptionist-Administration Bldg., Lobby, Attn: Jennifer B. Hill (MD-33), 79 T.W. Alexander Drive, Research Triangle Park, NC 27709. All offers are due by January 12, 2001, 3:30 p.m., ET. No telephonic or faxed requests will be honored.

Web Link

Click here to visit the site that has information about (http://www.epa.gov/oam/rtp_cmd)

Record

Loren Data Corp. 20001229/BSOL002.HTM (W-362 SN509731)