SOLICITATION NOTICE
B -- Analysis for Oxidized Amino Acids
- Notice Date
- 8/12/2008
- Notice Type
- Combined Synopsis/Solicitation
- NAICS
- 541380
— Testing Laboratories
- Contracting Office
- Environmental Protection Agency, Office of Acquisition Management, RTP Procurement Operations Division, E105-02, RTP Procurement Operations Division (D143-01) Research Triangle Park, NC 27711
- ZIP Code
- 27711
- Solicitation Number
- PR-NC-08-10748
- Response Due
- 8/22/2008
- Archive Date
- 9/21/2008
- Point of Contact
- JENNIFER B. HILL, Contract Specialist, Phone: 919-541-3083, E-Mail: hill.jennifer@epa.gov<br />
- Small Business Set-Aside
- N/A
- Description
- THIS IS A COMBINED SYNOPSIS/SOLICITATION FOR COMMERCIAL SERVICES 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. PROPOSALS ARE BEING REQUESTED AND A WRITTEN SOLICITATION WILL NOT BE ISSUED. The solicitation number is PR-NC-08-10748, and the solicitation is being issued as a full and open competition Request for Quotation (RFQ)using FAR Part 13 Simplified Acquisition Procedures. The solicitation document and incorporated provisions and clauses are those in effect through Federal Acquisition Circular 05-26. The associated North American Industry Classification System (NAICS) Code 541380, which has a size standard of $11.0 to qualify as a small business, is applicable. A firm fixed-price contract is anticipated to result from the award of this solicitation. This procurement is for the Analysis for Oxidized Amino Acids. A price proposal is required to perform the analysis in accordance with the Statement of Work. PART I. GENERAL INFORMATION. 1)TITLE / INTRODUCTION. The contractor shall develop a quantitative analytical method for the detection of a comprehensive array of oxidized amino acids, including: 3-chlorotyrosine (3-CT), 3,5-dichlorotyrosine (3,5-diCT), 3-nitrotyrosine (3NT) and 3-bromotyrosine (3BT) in either tissue samples of the upper respiratory tract (URT) and lower respiratory tract (LRT) or in cell culture samples. The method shall be based on contractor experience with methods published in the literature, and shall include internal standardization using stable isotope-substituted standards. The contractor shall then conduct quantitative analysis for the aforementioned oxidized amino acids in cellular and extracellular samples for the U.S. EPA, National Health and Environmental Toxicology Division, Research Triangle Park, NC, 27711. The U.S. EPA expects to provide a minimum of 360 biological samples over a 2-year period, with options, at the discretion of the Government, to include up to a maximum of 700 additional samples. These chlorotyrosine, nitrotyrosine, and bromotyrosine protein adducts have been chosen for analysis to serve as internal dosimeters of chlorine exposure and as biomarkers of inflammation (Gaut et al., 2002). 3-Nitrotyrosine is formed by the activity of reactive nitrogen species and is indicative of NO production via iNOS (Tarpey, et al., 2004). Chlorotyrosine in tissue has been established both as a relevant biomarker for inflammation (Hazen et al., 1996, 1997; Winterbourn and Kettle, 2000; Chapman et al., 2000; Gaut et al., 2002) and as a dosimeter for chlorine exposures per se (Roberts et al., 2007; Sochaski et al., 2008; Jarabek et al., In preparation). The results of these analyses for the protein adducts will be used to verify dosimetry model development and as an endpoint to track the pathogenesis of inflammation induced by inhaled chlorine. 2) BACKGROUND. As with other inhaled reactive gases of interest to the U.S. EPA (e.g., aldehydes, organic esters, acylating [phosgene] or alkylating agents [mustards]), the sentinel effect of inhaled chlorine is irritant and corrosive damage in the respiratory tract of experimental animals and humans (Wolf et al., 1995). Lesions typically show a proximal to distal distribution pattern, indicating that airflow patterns and exposure concentration play a key role in their pathogenesis. Due to the differences in airway architecture, ventilation rate, and breathing mode across species, characterization of gas uptake and epithelial responses using anatomically accurate computational models is necessary for accurate dose, duration, and interspecies extrapolation. Dosimetry models such as hybrid computational fluid dynamics- physiologically-based pharmacokinetic (CFD-PBPK) models afford the flexibility to predict different dose metrics and have been instrumental in dose-response analysis for irritants such as ozone and formaldehyde (Kimbell et al, 1997, 2001; Overton et al., 2001; Schroeter et al., 2006). A hybrid CFD-PBPK model has been developed for chlorine (Jarabek et al., 2007). Because recent studies have established that the mode of action (MOA) for chlorine is oxidative stress mediated by hypochlorous acid (HOCl) which forms in epithelial tissues by hydrolysis and downstream biological responses (Martin et al., 2003; Roberts et al., 2007), the PBPK portion of the CFD-PBPK model extends the dose description into the tissue phase to address epithelial reactions. Results for the protein adducts in these tissue samples performed with the analytical method developed for this contract will be used to verify the dosimetry model structure and as an endpoint to track the pathogenesis of inflammation induced by inhaled chlorine. 3)SCOPE. The contract requires development of a quantitative analytical method for the detection of a comprehensive array of oxidized amino acids, including 3-chlorotyrosine (3-CT), 3,5-dichlorotyrosine (3,5-diCT), 3-nitrotyrosine (3-NT), and 3-bromotyrosine (3-BT) as biomarkers of oxidative stress in cellular and extracellular proteins. The method shall be aimed at analysis of tissue samples of the upper respiratory tract (URT) and lower respiratory tract (LRT) or of cell culture samples. Oxidized amino acids shall be quantified by LC-MS/MS with internal standardization using stable isotope-substituted standards or quantitative methods of similar sensitivity. Stable isotope-substituted standard amino acids shall be purchased from Cambridge Isotope Laboratories (Andover, MA) and used to prepare the internal standards (Heinecke et al., 1999). Quantification of the biomarkers shall be determined after delipidification and hydrolysis of tissue or cell culture protein samples. The method for sample analysis shall be based on contractor experience and published methods in the literature (Gaut et al., 2002, Rosen et al., 2002; Shao et al., 2005a,b; Shao et al., 2006; Sochaski et al., 2008), such as by LC-MS/MS using an Ultrahigh pressure liquid chromatography module with a Quattro Ultima triple quadrupole mass spectrometric detector (Waters-Micromass, Manchester, U.K.) and a reverse-phase column. Oxidized amino acids shall be detected by electrospray positive ionization-mass spectrometric multiple reaction monitoring with programmed molecular ions. The contractor shall then conduct chemical analysis of such tissue and cell culture samples for the aforementioned oxidized amino acid biomarkers for the U.S. EPA, National Health and Environmental Toxicology Division, Research Triangle Park, NC, 27711. The U.S. EPA expects to provide a minimum of 360 biological samples over the total 2-year period of performance. 3.1SPECIFIC OBJECTIVES ? BASE PHASE. Specific objectives for the base phase are as follows and shall be accomplished within 6 months of contract award: Objective 1. Synthesis of Internal Standards. A suitable isotopes (e.g., 13C9 and 15N) to serve as an internal standard for each oxidized amino acid shall be synthesized. Objective 2. Development of Analytical Method for Detection of Oxidized Amino Acids (3-CT, 3,5-diCT, 3-NT and 3-BT) in tissue samples. An analytical method of sufficient sensitivity and specificity to detect nanomolar quantities of oxidized amino acids in tissues (e.g., LC-MS/MS or GC-MS) shall be developed based upon published methods (Gaut et al., 2002, Rosen et al., 2002; Shao et al., 2005a,b; Shao et al., 2006;Sochaski et al., 2008; Hazen et al., 1996, 1997; Chapman et al., 2000; Crow,1999; Elserich et al., 1996; Heinecke et al., 1999; Ishida et al., 2000; Pietzsh et al., 2003; Van den Berg et al., 1993). Objective 3. Analysis of Pilot Tissue Samples. To verify the method and establish its level of detection (LOD) / level of quantitation (LOQ), tissue samples from a pilot study performed by the U.S. EPA shall be analyzed for the specified set of oxidized amino acids. The tissue samples will be provided by the U.S. EPA. Tissue sample locations will include four sites in the URT (septal respiratory epithelium, SEP RE; septal olfactory epithelium, SEP OE; lateral respiratory epithelium, LAT RE; and ethmoid olfactory epithelium, ETH), and two from the LRT (trachea and lung lobe). 3.2 OPTIONS FOR ADDITIONAL ANALYSES. The U.S. EPA may choose to exercise options to obtain analyses for additional data sets of up to 700. These analyses will be the same as those developed and conducted in the base phase. The period of performance for the options is 18 months and the total contract period of performance is 24 months. Option 1. (NTE 336 samples). Analysis of Respiratory Tract Tissue Samples from Acute Exposures to Chlorine. Available to be exercised from 1 month of award of contract. Option 2. (NTE 144 samples). Analysis of Respiratory Tract Tissue Samples from Subacute Exposures to Chlorine. Available to be exercised from 2 months of award of contract. Option 3. (NTE 120 samples). Analysis of Respiratory Tract Tissue Samples from Suchronic Exposure to Chlorine. Available to be exercised 6 months of award of contract. Option 4. (NTE 100 samples). Analysis of Cell Culture Samples. Available to be exercised from 2 months of award of contract. APPLICABLE DOCUMENTS. The list of documents are included in the Statement of Work document located on the EPA Procurement Website at http://www.epa.gov/oam/rtp_cmd/. PART II. WORK REQUIREMENTS. 1) TECHNICAL REQUIREMENTS. The contractor shall develop a quantitative analytical method for detection of an array of oxidized amino acids, including: 3-CT, 3,5-diCT, 3-NT and 3-BT as described above, and then apply the method to quantification of these analytes in tissue samples provided by the U.S. EPA. The contractor shall then write a series of reports and be available to discuss the findings and technical approach. The reports shall adhere to the tenets of proper grammar usage and spelling, and will be of an overall scientific quality similar to that demonstrated in top tier peer reviewed journals. One bound and one unbound hardcopies and an electronic file copy shall be submitted to the COR. All technical reports, spreadsheets, and presentations shall be delivered electronically in Microsoft Office product formats (Word, Excel, PowerPoint; version 2003 or later), and provided via email to the EPA COR. 2) DELIVERABLES. Report on Method Development. The contractor shall report on the development of the analytical method. The report shall contain a flowchart of the analytical steps, discussion of the internal standard, level of detection (LOD) / level of quantitation (LOQ), evaluation of the sensitivity and specificity of the method, comparison with previously published approaches, and discussion of its verification and applications. This report should be delivered at the end of the 6-month base phase. Report(s) on Sample Analysis. The contractor shall submit a report for each set of samples submitted for analysis. The report shall provide an Excel spreadsheet of the raw data for each analyte as an attachment. The report shall be due no later than one month from receipt of the samples by the contractor. PART III ? OTHER SPECIAL INFORMATION / CONSIDERATIONS AS APPLICABLE. 1) Schedule. The development of the analytical method and performance of sample analyses described in this Statement of Work (SOW) are high priority objectives of the U.S. EPA which must be completed as rapidly as possible while still providing scientific accuracy and integrity. The contractor shall take all steps necessary to ensure timely development of the method and proceed with sample analysis, and shall notify the EPA COR of any obstacles as they occur which may impede the completion of the studies. The technical requirements section above describes the sequence of tasks to be completed, and the deliverables section above describes the sequence of reports to be delivered to the EPA. 2) Review and Acceptance. The U.S. EPA will review each draft report within 30 working days of receipt and either accept the report as final or provide written comments to the contractor. When written comments on draft reports are made, the contractor shall address the written comments, including any additional sample analysis that may be required, and provide the revised report to the U.S. EPA within 15 working days of receipt. The U.S. EPA will review the revised report and either accept it as final within 15 working days of receipt, or request additional changes. The only exception to this 3-week review and reply schedule will be when the EPA COR is out of the office during this time period. In such an event, the 15-business day turn around period becomes 15 business days that the COR is in the office. The COR will notify the contractor via email in the event of such an occurrence. 3) Publication Restrictions. The Contractor may not publish, present briefings or release any material resulting directly or indirectly from work performed under this contract in any conference, presentation, forum, publication or other discussions without the prior approval of the EPA COR. 4) Acronyms. CFD ? Computational fluid dynamics; 3-BT ? 3-Bromotyrosine; 3-CT ? 3-Chlorotyrosine; COR ? Contracting Officer?s Representative; 3,5-diCT ? 3,5-Dichlorotyrosine; LOD ? Level of detection; LOQ ? Level of quantification; LRT ? Lower respiratory tract; NHEERL ? National Health and Environmental Effects Research Laboratory; 3-NT ? 3-Nitrotyrosine; PBPK ? Physiologically-based Pharmacokinetic; URT ? Upper respiratory tract; U.S. EPA ? United States Environmental Protection Agency. QUALITY ASSURANCE. The contractor shall submit a written hybrid quality management plan/quality assurance project plan (QM/QAPP) and detailed project plans within 60 days after award. Upon request by the government representative, the contractor shall allow a site visit to the laboratory. With the method development report and each sample analysis report, the contractor shall provide the calibration curve used for analysis of this set of samples. U.S. GOVERNMENT RESPONSIBILITIES. 1. The U.S. EPA will provide the contractor with a minimum of 3 weeks (15 working days) of notice before shipping or transport of tissue samples to the contractor. 2. The U.S. EPA will provide all biological tissue samples that the contractor shall analyze. Whenever available sample volume permits, the U.S. EPA will provide larger sample volumes than required so that the contractor can run additional analyses. The contractor shall hold the residual sample volume in reserve for additional analyses in case of unexpected results or results that may require confirmation. If desired by the contractor, the U.S. EPA will hold the reserve (residual) volume at its RTP facilities. If the contractor desires this option, the contractor shall bear the cost of overnight shipment of the reserve sample, rather than the U.S. EPA (see U.S. government responsibility #3 below). 3. The U.S. EPA will bear responsibility for sample shipment. If the contractor is local, the U.S. EPA will provide the local transport by motor vehicle of samples to the contractor. If the contractor is not within a 30-mile radius of the RTP, or at the convenience of the government, the U.S. EPA will ship the samples via overnight courier (FedEx) to the contractor, to be received Monday through Friday. All tissue samples will be transported frozen (i.e., ice chest / cooler with frozen samples placed on dry ice or frozen ice packs). If tissue samples are to be shipped by Fedex, a trial shipment of nontreated tissues will be conducted to ensure that the samples arrive frozen and sample vials remain intact when then they arrive at the contractor facility. 4. The U.S. EPA will provide the contractor with estimates of the concentration range to be expected within the biological samples so that the contractor can use this information to construct calibration curves that bracket the expected tissue concentrations. The accuracy of these estimates will vary based on how much prior information is known about these adducts under investigation and the sensitivity and specificity of the analytical method developed by the contractor. It is expected that the estimated concentration ranges provided by the U.S. EPA will improve with the refinement and improvement of the hybrid CFD-PBPK dosimetry model. 5. The U.S. EPA will review each draft report and will either approve it or recommend modification according to the schedule as described above under Review & Acceptance. 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: A. TECHNICAL CRITERIA: 1. Experience in development of quantitative analytical methods with sufficient sensitivity for detection as demonstrated by both publications and the discussion of proposed approach and potential technical challenges. 2. Proficiency in quantitative analytical methods of various biological tissues for comprehensive array of specified oxidized amino acids (i.e., 3-chloro and 3,5-dichlorotyrosine; 3-nitrotyrosine; 3-bromotyrosine) as demonstrated by publications. 3. Established laboratory for quantitative analytical chemistry as evidenced by equipment and routine functions of core facilities. 4. Capacity to provide timely throughput as demonstrated by discussion of laboratory capabilities. 5. Technical writing ability for written reports as demonstrated by publications and written proposal. B. PAST PERFORMANCE: Submit a list of 3 customers for whom like or similar analysis services have been performed within the past 3 years. Include specific points of contact and phone numbers. Past performance will be evaluated on 1) quality of product or service; 2) timeliness of performance (ability to adhere to deadlines); and overall customer satisfaction. C. PRICE. The Government intends to award a single contract to the responsible offeror whose technically acceptable quotation represents the best overall value to the Government based on the evaluation of the technical criteria, past performance, and price. Only those offerors submitting technically acceptable quotations shall be considered for award. For the purpose of this best value evaluation of technically acceptable proposals, technical criteria and past performance, when combined, are significantly more important than price. The government will make award to the responsible offeror whose offer conforms to the solicitation and represents the best value to the government, price and other factors considered. 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 clauses apply to this acquisition: 52.212-4, Contract Terms and Conditions--Commercial Items; 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders--Commercial Items and the following additional FAR clauses which are cited in Clause 52.212-5: 52.203-6, Restrictions on Subcontractor Sales to the Government; 52.222-3, Convict Labor; 52.222-21, Prohibition of Segregated Facilities; 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; 52.222-39 Notification of Employee Rights Concerning Payment of Union Dues or Fees; 52.222-50, Combating Trafficking in Persons; 52.225-13 Restrictions on Certain Foreign Purchases; 52-232-33, Payment by Electronic Funds Transfer-Central Contractor Registration. All technical questions are to be forwarded via email to the Contracting Officer 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. Click on the CURRENT SOLICITATIONS section and click on the solicitation for viewing applicable documents. Near the top of the page COMMERCIAL BUY CLAUSES AND FORMS sections are provided for your convenience. Please submit the technical proposal and price proposal via EMAIL to hill.jennifer@epa.gov or Jennifer B. Hill, Contracting Officer, U.S. Environmental Protection Agency, RTP Procurement Operations Division (D143- 01), Research Triangle Park, NC 27711 if using the US Postal Service. Courier delivery address is U.S. Environmental Protection Agency, Attn: Jennifer B. Hill, RTP Procurement Operations Division (D143-01), 4930 Old Page Road, Durham, NC 27703. All offers are due by August 22, 2008, 12:00 p.m., ET. No telephonic or faxed responses will be honored.
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