AWARD
B -- SABLEFISH CAPTIVE BROOD STOCK RESEARCH
- Notice Date
- 9/14/2011
- Notice Type
- Award Notice
- NAICS
- 541990
— All Other Professional, Scientific, and Technical Services
- Contracting Office
- Department of Commerce, National Oceanic and Atmospheric Administration (NOAA), Western Region Acquisition Division, 7600 Sand Point Way, Northeast, Seattle, Washington, 98115-6349
- ZIP Code
- 98115-6349
- Point of Contact
- Anthony R. Buch, Phone: 206-526-6033
- E-Mail Address
-
Anthony.R.Buch@noaa.gov
(Anthony.R.Buch@noaa.gov)
- Small Business Set-Aside
- N/A
- Award Number
- WADAB133F-11-CN-0146
- Award Date
- 9/14/2011
- Awardee
- University of Washington, 4333 Brooklyn Ave. NE, Seattle, Washington 98195, United States
- Award Amount
- $349,407.00
- Description
- In accordance with the requirements of the Competition in Contracting Act (41 U.S.C. 253), as implemented by FAR 6.303, the following information is submitted to support an acquisition without full and open competition. I.Agency and Contracting Activity NOAA Acquisition & Grants Office Western Acquisition Division (WAD) 7600 Sand Point Way NE Seattle, WA 98115 II.Description of Action Being Approved NOAA National Marine Fisheries Service (NMFS), Northwest Fisheries Science Center, is seeking to negotiate a sole-source, firm-fixed-price contract, with a base period consisting of two years with the University of Washington's School of Aquatic & Fishery Sciences, similar to services procured in the past. Substantially similar services have been provided by the University of Washington before, but never by Dr. Roberts, the head research scientist. III.Description of Services Required to Meet the Agency's Needs NMFS, Northwest Fisheries Science Center, requires researchers to assist NOAA research in developing the resources and techniques for intensive aquaculture of sablefish (Anoplopoma fimbria, aka black cod). Thus, the goals of this work are to produce the molecular (genomic) tools and information required for NOAA to help establish sablefish brood stock for commercial aquaculture (i.e. genomic markers that can be used in selective breeding and to assess impacts of 17a-MT on growth and metabolism). The following tasks are required for this work: 1) Sablefish tissue collection- Assist NOAA scientists with collection of tissues (liver, muscle, brain, gonads, spleen, kidney, heart, gills) from wild, adult sablefish collected off the coast of Washington annually. NOAA scientists will provide euthanized commercially-harvested wild fish and individuals from a captive brood stock maintained at the NMFS Manchester Marine Field Station (MMFS) near Manchester, WA. Samples from 100 fish per year will be harvested for RNA processing. Sample collection will require 5 trips per year to Westport, WA and approximately 3 days overnight in a hotel for each trip. Approximately 20 day-trips to MMFS in Manchester, WA will be required to assist NOAA scientists with tissue collection from fish maintained by NOAA scientists at the MMFS. 2) Sablefish transcriptome sequence analysis- Bioinformatically analyze approximately 2 million (0.25 million/tissue) sequences from the sablefish tissues that have been sequenced by Roche 454 GS-FLX pyrosequencing. Using CLC Genomics and Newbler software assemble sequences into a unified reference genome for sablefish and annotate by aligning against the existing NCBI database. Using software, interrogate the assembled sequences for potential microsatellites and single nucleotide polymorphisms (SNPs) for use as genetic markers in future pedigree tracking. 3) Determine effects of 17 a-MT on growth and metabolism- Assist NOAA scientists with determining effects of 17a-methyltestosterone (17a-MT) on expression of genes involved in growth regulation and metabolism. NOAA scientists will treat juvenile sablefish with several doses of 17a-MT via the diet and provide euthanized control and 17a-MT treated-fish for tissue collection. Contractor will harvest liver and muscle tissue from control and treated fish, isolate RNA and perform sequencing of the transcriptome using the ABI SOLiD or Illumina Solexa platforms. Using CLC Genomic software, compare the ABI SOLiD or Illumina Solexa sequences in treated versus untreated tissues using RNAseq analysis aligned against the sablefish reference genome. Analyze RNAseq results and perform quantitative RT PCR to obtain information on the molecular changes in growth pathways occurring under 17a-MT treatment. 4) Genome analysis - Provide NOAA scientists with an annotated sablefish reference genome for future analysis and lists of potential sablefish microsatellites and SNPs. Based on RNAseq analysis advise NOAA scientist on the molecular effects of 17a-MT on sablefish. 5) Report and Document Deliverables- Present results at three scientific meetings along with NOAA scientists such as the Annual Meeting of the American Fisheries Society (Little Rock, Arkansas; September 8-12, 2013) and Aquaculture America (Las Vegas, Nevada; February 28-March 2, 2012 and Nashville, Tennessee, February 21- 25, 2013). Provide results from tasks 1-4 in the form of electronic databases stored on NOAA computers. Assist NOAA scientists with project reports and preparation of manuscripts for publication in peer reviewed journals. The total estimated dollar amount for the proposed contract is $350,045.00 for a two year base period. IV.Statutory Authority Permitting Other than Full and Open Competition Pursuant to 41 U.S.C. 253(c) (1), as implemented by FAR 6.302-1, full and open competition is not required when only one responsible source and no other supplies or services will satisfy agency requirements. V.Applicability of Authority The University of Washington has been continually performing similar scientific research with NOAA's NMFS for many years. The University of Washington's Dr. Roberts has 10 years of research experience on the hormonal control of growth in fish, particularly focusing on the molecular pathways involved. He also has unique expertise on the use and bioinformatic analysis of sequences obtained from Next Gen sequencing platforms such as the Roche 454 GS-FLX and ABI SOLiD. For example, he has used the Roche 454 GS-FLX to investigate the differences in liver transcriptomes between different forms of fish (Goetz, F., Rosauer, D., Sitar, S., Goetz, G., Simchick, C., Roberts, S., Johnson, R., Murphy, C., Bronte, C., MacKenzie, S. (2010). A genetic basis for the phenotypic differentiation between siscowet and lean lake trout (Salvelinus namaycush). Molecular Ecology 19 (Suppl. 1): 176-196), and the ABI SOLiD to look at differences between experimental treatments in fish (Morera, D., Roher, N., Ribas, L., Balasch, J.C., Doñate, C., Callol, A., Boltaña, S., Roberts, S., Goetz, G., Goetz, F.W., and MacKenzie, S.A. (2011). RNA-Seq reveals an integrated immune response in nucleated erythrocytes. PloS ONE (in press)). He has also used these platforms for gene marker discovery (Seeb JE, Pascal CE, Grau ED, Seeb LW, Templin WD, Harkins T, Roberts SB. (2010) Transcriptome sequencing and high-resolution melt analysis advance single nucleotide polymorphism discovery in duplicated salmonids. Molecular Ecology Resources, 11:2 335-348). Dr. Roberts' unique combination of skills in both growth and genomics, coupled with the fact that NOAA knows of no other capable source, other than Dr. Roberts, makes sole source award justified. Dr. Roberts maintains a specialized computer cluster with dedicated software (e.g., CLC Genomics) specifically for the treatment and analysis of sequences obtained from Next Gen sequencing platforms. This cluster and software will be instrumental in the analysis of sablefish genome data and since he has customized this for the analysis of fish gene this would be difficult to duplicate or find elsewhere. VI.Efforts to Obtain Competition To identify potential contractors with expertise and experience, an internet scientific literature search was performed on Web of Science using various search terms related to the task, including fish, growth, gene expression, transcriptome, sequencing and RNA-Seq. Although over one dozen scientific publications from laboratories with general expertise in this area was found, only the University of Washington lab of Dr. Roberts had the combination of genomic analysis experience and expertise in fish growth. Search results as follows: Zhang, ZP; Wang, YL; Wang, SH; Liu, JT; Warren, W; Mitreva, M; Walter, R, Zhang, Ziping; Wang, Yilei; Wang, Shuhong; Liu, Jingtao; Warren, Wesley; Mitreva, Makedonka; Walter, Ronald B. 2011Transcriptome Analysis of Female and Male Xiphophorus maculatus PLOS ONE 6:4, e18379 J. Pirooznia, M; Pozhitkov, A; Perkins, EJ; Deng, YP; Brouwer, M, Pirooznia, Mehdi; Pozhitkov, Alexander; Perkins, Edward J.; Deng, Youping; Brouwer, Marius. 2010. Generation, analysis and functional annotation of expressed sequence tags from the sheepshead minnow (Cyprinodon variegatus) BMC GENOMICS Suppl. 2: S4 J. Goetz, F; Rosauer, D; Sitar, S; Goetz, G; Simchick, C; Roberts, S; Johnson, R; Murphy, C; Bronte, CR; Mackenzie, S. Goetz, Frederick; Rosauer, Daniel; Sitar, Shawn; Goetz, Giles; Simchick, Crystal; Roberts, Steven; Johnson, Ronald; Murphy, Cheryl; Bronte, Charles R.; Mackenzie, Simon. 2010. A genetic basis for the phenotypic differentiation between siscowet and lean lake trout (Salvelinus namaycush). MOLECULAR ECOLOGY 19:176-196. J, Jeukens, J; Renaut, S; St-Cyr, J; Nolte, AW; Bernatchez, L, Julie; Renaut, Sebastien; St-Cyr, Jerome; Nolte, Arne W.; Bernatchez, Louis 2010. The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing. MOLECULAR ECOLOGY 24: 5389-5403. JSalem, M; Rexroad, CE; Wang, JN; Thorgaard, GH; Yao, JB, Mohamed; Rexroad, Caird E., III; Wang, Jiannan; Thorgaard, Gary H.; Yao, Jianbo. 2010Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches BMC GENOMICS 11: 564. J. Hale, MC; Jackson, JR; DeWoody, JA Hale, Matthew C.; Jackson, James R.; DeWoody, J. Andrew 2010. Discovery and evaluation of candidate sex-determining genes and xenobiotics in the gonads of lake sturgeon (Acipenser fulvescens) GENETICA 138: 745-756 J. Liu, D; Liu, SJ; You, CP; Chen, L; Liu, Z; Liu, LG; Wang, J; Liu, Y, Liu, Dong; Liu, Shaojun; You, Cuiping; Chen, Lin; Liu, Zhen; Liu, Liangguo; Wang, Jing; Liu, Yun. 2010. Identification and Expression Analysis of Genes Involved in Early Ovary Development in Diploid Gynogenetic Hybrids of Red Crucian Carp x Common Carp MARINE BIOTECHNOLOGY 12 2:186-194. Cerda, J; Bobe, J; Babin, PJ; Admon, A; Lubzens, E; Cerda, Joan; Bobe, Julien; Babin, Patrick J.; Admon, Arie; Lubzens, Esther 2008. Functional Genomics and Proteomic Approaches for the Study of Gamete Formation and Viability in Farmed Finfish REVIEWS IN FISHERIES SCIENCE Suppl. 1 vol 56 pp. 72 JRossi, F; Chini, V; Cattaneo, AG; Bernardini, G; Terova, G; Saroglia, M; Gornati, RRossi, Federica; Chini, Valentina; Cattaneo, Anna Giulia; Bernardini, Giovanni; Terova, Genciana; Saroglia, Marco; Gornati, Rosalba 2007 EST-based identification of genes expressed in perch (Perca fluviatilis, L.) GENE EXPRESSION Vol :117 pp.1052-2166 J Liu, ZJ, Liu, Zhanjiang Transcriptome characterization through the generation and analysis of expressed sequence tags: Factors to consider for a successful EST project ISRAELI JOURNAL OF AQUACULTURE-BAMIDGEH Sp. Iss. SI 328 -340 Knoll-Gellida, A; Andre, M; Gattegno, T; Forgue, J; Admon, A; Babin, PJ; Knoll-Gellida, Anja; Andre, Michele; Gattegno, Tamar; Forgue, Jean; Admon, Arie; Babin, Patrick J.2006. Molecular phenotype of zebrafish ovarian follicle by serial analysis of gene expression and proteomic profiling, and comparison with the transcriptomes of other animals BMC GENOMICS 7: 46 J. Corredor-Adamez, M; Welten, MCM; Spaink, HP; Jeffery, JE; Schoon, RT; de Bakker, MAG; Bagowski, CP; Meijer, AH; Verbeek, FJ; Richardson, MK. 2005 Genomic annotation and transcriptome analysis of the zebrafish (Danio rerio) hox complex with description of a novel member, hoxb13a. EVOLUTION & DEVELOPMENT 5:362 375. J,Carton, MW; Schmitz, M; Cutts, CJ; Kelly, AK; Hill, JA; Brabazon, ED; Adams, CE; Byrnes, L 2002 Expressed sequence tags in larval Arctic charr (Salvelinus alpinus) FISH PHYSIOLOGY AND BIOCHEMISTRY 26:231-238 A Notice of Intent to award a sole-source contract to University of Washington will be posted on the FedBizOpps website once the approval of this justification is received. If, as a result of posting the Notice of Intent, another firm demonstrates the ability to provide the required components, within the required time frame, the sole source nature of this procurement will be reevaluated VII.Determination of Fair and Reasonable Cost The University of Washington is a non-profit entity. They also have an interest in the research, and we anticipate they will give us the lowest overhead rates they can and still have their costs recovered. In addition, it is believed that a fair and reasonable contract price can be negotiated using pricing based upon contracts with major universities (including the University of Washington) for similar types of work in the areas of fish reproduction that had similar costs and by reviewing University of Washington employee pay tables. Also, prices from recent orders with Wildlife Computers placed by NMML, along with prices from an IDIQ contract with Pacific Islands Fisheries Science Center (AB133F-08-CQ-0035) will be reviewed to establish price reasonableness. VIII.Market Research To this date, no other firms have been identified that possess the unique qualifications required for this work. Additionally, to identify potential contractors with expertise and experience, an internet scientific literature search was performed on Web of Science using various search terms related to the task, including fish, growth, gene expression, transcriptome, sequencing and RNA-Seq. Although over one dozen scientific publications from laboratories with general expertise in this area was found, only the University Washington lab of Dr. Roberts had the combination of genomic analysis experience and expertise in fish growth. A SBA Dynamic Small Business Search using the NAICS code 541990 and the key word Sablefish had no results. A goggle search of the key words "sable fish brood stock" returned results for a firm named Troutlodge, however Cheryl Laufle indicated that Troutlodge would be positioned to make use of the research, but not to conduct it. IX.Other Facts Supporting The Use of Other Than Full And Open Competition A form CD-492 (Justification for Other Than Full & Open Competition) was submitted by NMFS and is located in the contract file and the sole-source request was approved by John Oliver, Deputy Assistant Administrator for NMFS. X.List of Interested Sources: None identified at this time. XI.Steps to Foster Competition Future research requirements will be advertised in FedBizOpps; however, competition will most likely be limited due to the highly specialized nature of the research. XII.Contracting Officer's Certification Based on the above information, negotiating and awarding a sole-source contract to the University of Washington's School of Aquatic & Fishery Sciences is in the best interest of the Government in accordance with FAR 6.302-1.
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