Statement of Work v2.docx

STATEMENT OF WORK

A. BACKGROUND

The USDA-ARS Grape Genetics Research Unit in Geneva, New York, requires services for widely targeted metabolite and lipid quantification of grapevine bud tissues collected from vineyards during the winter season. The service provider must have demonstrated expertise in handling plant samples from species with complex genetics, including clonally propagated crops. The provider should possess in-house capabilities to profile over 30,000 plant-related metabolites, drawing from experience across more than 1,000 plant species. The firm must manage all aspects of the experimental workflow, from sample preparation to metabolite quantification. Technology used must be able to achieve sub-picogram/ml limits of quantitation to achieve the trace-level detection bioanalysis data that is sought after. The MRM Capacity must be at least 500/sec to accommodate the complexity of the sample matrices. Furthermore, when integrated with transcriptomic data, the provider should deliver comprehensive analyses, including co-expression network maps, gene enrichment circular diagrams, and detailed insights into converging metabolic pathways. The analysis should employ advanced high-throughput technologies to generate high-quality analytical data, utilizing Ultra Performance Liquid Chromatography (UPLC) for separation and tandem mass spectrometry (MS/MS), coupled with transcriptome analysis. The work will be carried out by Metware Biotechnology Inc., a recognized leader in this field.

B. OBJECTIVES

The objective of this Statement of Work (SOW) is to gain a holistic understanding of grapevine bud responses to winter temperature fluctuations by evaluating both metabolomic and transcriptomic profiles in bud tissue. The resulting data will be used to correlate differentially expressed genes with corresponding differential metabolites, with the goal of identifying key genes, metabolites, and metabolic pathways associated with internal physiological changes. This integrative analysis will help elucidate the biological basis of bud viability during winter and identify traits that can be targeted for the genetic improvement of cold hardiness in grapevines.

C. SCOPE

The contractor shall provide comprehensive information on a wide range of metabolites in grapevine using a large, curated database of over 30,000 plant metabolites and genes. This will be achieved through proprietary, ultra-sensitive, high-throughput, widely targeted metabolomics and transcriptome sequencing technologies. Ultra Performance Liquid Chromatography (UPLC) for compound separation and tandem mass spectrometry (MS/MS) for detection will be employed to ensure the best possible research outcomes.

D. TASKS

The contractor shall process Quality check and sample extraction, data quality control, re-processing as needed, data on compound/gene identity and quantification table. Contractor shall conduct differential compound/gene expression analysis data across biological samples that are currently prepared and ready for described sample processing and data analysis with a turnaround time of 6-8 weeks. RNA extractions from grapevine bud tissue samples, LC-MS, and data analysis. The samples will be analyzed on QqQ, quantitative LC-MS/MS system for high throughput capacity of 12,000 Da/sec with a polarity switching capability of 5ms for superior quantification with sacrificing data quality. The compound annotation process will be searched against a plant-centric database with over 60000 metabolites. With the annotation and quantification, we will perform statistical analysis using OPLS-DA, T-test and/or Wilcoxon Rank Sum Test to identify differential metabolites between sample groups. We will perform KEGG pathway enrichment analysis based on the differential metabolites.

D. DELIVERABLES

The contractor shall deliver, but is not limited to the following:

· Detect and quantify over 30,000 plant metabolites using Ultra LC-MS/MS and provide a comprehensive metabolite quantification table for the 48 submitted samples.

· Extract RNA, perform quality control checks, conduct library preparation, and carry out 150 bp paired-end RNA sequencing for all 48 samples, targeting a depth of 20 million reads per sample.

· Provide data analysis, including co-expression profiles of metabolites and genes, gene enrichment mapping, correlation network construction, and identification of converging metabolic pathways involved in cold tolerance in grapevine.

· Provide transcriptomics and metabolomics conjoint analysis using Pearson correlation, canonical correlation analysis, O2PLS, and KEGG pathway co-enrichment analysis.

· GOVERNMENT FURNISHED EQUIPMENT AND GOVERNMETN FURNISHED INFORMATION

The government will not provide the current existing workspace, desk, computer, internet access, but will not provide a telephone, printer, or access to duplicating machines or fax.

· REPORTING REQUIREMENTS

The contractor shall provide periodic updates to the Technical Point of Contact (TPOC) to include information in regard to the services provided.

· TRAVEL REQUIREMENTS

Travel is not required for this service as it is provided locally on-site.

· PLACE OF PERFORMANCE

The place of performance will be Metware Biotechnology Inc., located at 8A Henshaw Street, Woburn, MA 01801, or on equivalent sequencing equipment at an alternative location and/or vendor.

· SECURITY REQUIREMENTS

All conversations and interactions will be held in strict confidence by the contract facilitators not to be shared with anyone internal or external to USDA unless otherwise mentioned in the agreement.

By accepting this contract/agreement, the Contractor providing IT services to the REE agrees to comply with this IT security policy. The Contractor is responsible for IT security for all systems connected to the USFS network or operated by the Contractor for the REE, regardless of location. This clause is applicable to all or any part of the contract that includes IT resources or services in which the Contractor must have physical or electronic access to REE sensitive information that directly supports the mission of the REE. The term 'information technology', as used in this clause, means any equipment or interconnected system or subsystem of equipment, that is used in the automatic acquisition, storage, manipulation, management, movement, control, display, switching, interchange, transmission, or reception of data or information. This includes both major applications and general support systems as defined by OMB Circular A-130 Security Training: The Contractor and other external organizations will ensure that its employees performing under this contract fulfill all REE requirements for mandatory security awareness and role-based advanced security training in accordance with OMB Circular A-130, FISMA, and NIST requirements, and sign all applicable FS statements of responsibilities.

Section 508 Compliance for IT Services, Hardware, Software, and Equipment: All Electronic and Information Technology (EIT) services procured through this task must meet the applicable accessibility standards at 36 CFR 1194, unless an agency exception to this requirement exists. 36 CFR 1194 implements Section 508 of the Rehabilitation Act of 1973, as amended, and is available at: http://www.access-board.gov/sec508/standards.htm Protection: The Contractor shall be responsible for properly protecting all information used, gathered, or developed under this task. The Contractor shall also protect all unclassified Government data, equipment, etc., by treating information as sensitive business, confidential information, controlling and limiting access to the information, and securing the data and equipment within their facility.

Non-Disclosure: The Contractor or other external organization will not publish or disclose in any manner, without the REE Contracting Officer's written consent, the details of any programs, documentation, data, or safeguards either designed or developed by the Contractor or other external organization under this Contract or otherwise provided by the Government. Contractors may be required to sign nondisclosure or other appropriate security agreements. Contractor(s) and other external organizations will enter into written agreements with the REE before the REE will disclose data or information otherwise exempt from public disclosure to the contractors and other external organizations. The contractor and other external organizations will agree to establish and follow security precautions considered by the REE as necessary to ensure proper handling of data and information. As may be identified elsewhere in this contract, the Contractor agrees that:

Documentation Ownership: The U.S. Government owns all draft and final deliverables, working papers, and other relevant materials generated by the Contractor during the contract’s performance. These materials must be submitted to the TPOC upon the conclusion of the tasks. The Government does not require the rights to testing. For example, if the Myers Briggs Type Indicator (MBTI) is used to evaluate employees, the MBTI itself does not become Government property. However, each employee’s MBTI results, and any additional custom resources created to support an employee, given their MBTI results, are property of the U.S. Government and must be delivered to the TPOC. Vendors are not allowed to retain employee responses to such instruments or custom materials based on those responses beyond the life of the contract.

Document Reproduction: Documents produced for this project are the property of the U.S. Government and cannot be reproduced or retained by the Contractor.

USDA will be authorized to make copies of any non-commercial, non-copyrighted material for use, without notification to the vendor. At the time of record disposition or contract transition, the vendor shall box, label, and deliver all records, files, materials and work papers to the TPOC or a location identified by the TPOC.

· POST AWARD ADMINISTRATION

Contractor’s performance will be monitored in accordance with this statement of work by review of monthly status reports. Status reports will be emailed to the TPOC and will include accounting of hours listed by contractor staff for each task. The contractor shall meet with the TPOC during a regularly scheduled meeting or conference call to review the most recent status report and discuss any issues or concerns. Because the nature of this contract is service oriented, the contractor shall ensure completion of tasks as requested by the TPOC within the specified deadlines.