Progress 09/01/24 to 08/31/25
Outputs
Target Audience:This program aims to reach both internal and external participants in the fields of omics, bioinformatics, and computer-data sciences, including the PD, Co-PDs, research staff, post-docs, graduate students, and clients. Additionally, the college dean, associate deans, university administrators, and facility staff will play administrative roles in supporting this project. Once the DNA core is established, the project's outreach activities will extend to high school and community college students and teachers, university faculty and students, and local communities. It supportsall students andcommunities by offering graduate research opportunities and Core extension programs. The project efforts go through a variety of formal and informal activities such as lab experiments, classroom instruction, workshops, special seminars, summer programs, extension programs, and access to DNA Core services such as NGS, library prep, bioinformatics, and big data analysis, the project will deliver new technology and science-based knowledge to its target audiences and stakeholders. Changes/Problems:The PD and DSU Facilities were prepared to move forward with the renovation and construction of the DNA Core lab, as well as the procurement of core equipment as outlined for the project's second year. However, both activities have been delayed due to internal administrative processes at DSU and the incomplete return of funds from another project by the DSU Accounting Department. These issues delayed the project's progress. Nevertheless, DSU remains committed to complying with NIFA guidelines and has submitted the required supporting documents as requested by the agency. In the meantime, the PD continues to make active progress on other project objectives, as outlined in this annual report, while awaiting NIFA's approval. What opportunities for training and professional development has the project provided?Training Activities The PD and research staff have been actively enhancing their expertise in next-generation sequencing (NGS), third-generation sequencing (TGS), and data science technologies through the use of a high-performance computing (HPC) cluster. Currently, the PD is developing bioinformatics pipelines to support high-throughput sequencing and big data analysis, while also designing new graduate-level courses and professional development workshops in genomics and bioinformatics. This training encompasses a broad range of topics, including: 1. Core principles of NGS and TGS technologies, 2. Sequencing library preparation and system operations, 3. Big data generation and analysis, 4. IT infrastructure and high-performance computing, 5.Integration of NGS systems with server networks, 6. Utilization of the SMRT Link platform for experimental design, sample preparation, quality control, analysis, and data management These self-guided training activities are establishing a strong knowledge base that will support the delivery of sequencing and bioinformatics services once the DNA Core Lab renovation is complete. During the second year of the project, the PD continued engaging with representatives from scientific vendors and biotechnology firms to stay informed about the latest innovations that could enhance the DNA Core Facility. These meetings provided valuable insights into advanced NGS and TGS platforms, single-cell sorters, automation technologies, and HPC systems. The PD and staff gained a deeper understanding of equipment specifications, analytical capabilities, software/hardware integration, and potential applications across various research areas, further strengthening DSU's research capacity. Professional Development Activities To support ongoing professional growth, company representatives conducted both on-site and virtual seminars showcasing their technologies. The PD recommended that the Core Development Committee regularly invite vendors to host workshops and presentations tailored to DSU faculty, staff, and students, especially as equipment needs for the DNA Core are assessed and prioritized. Looking ahead, a DNA Core Genomics Seminar Series is planned for launch following completion of the lab renovations. This series will include guest speakers from omics technology companies and academic institutions, aimed at engaging the DSU community and regional stakeholders in discussions about cutting-edge genomic research and applications. How have the results been disseminated to communities of interest?The PD and DNA Core Manager have been working closely with the DSU webmaster to develop and maintain the DSU DNA Core website, which serves as a key platform to introduce the facility to both internal and external audiences. The website features information about the Core's mission and vision, team members, available services, equipment, educational programs, and outreach initiatives. The team is also coordinating with iLab to expand the site with additional functionality for service scheduling and payment processing for core users. In addition, the Core Manager and the CAST event coordinator have engaged with various internal and external stakeholders to promote awareness of the DNA Core. Informational brochures and booklets have been distributed to DSU faculty, research staff, and local school educators. These materials will also be available at the DSU booth during the upcoming 1890 ARD Symposium next year.? What do you plan to do during the next reporting period to accomplish the goals?Goals for the Next Reporting Period: 1. Initiate the renovation of the Genomics Core Lab on the Downtown campus, with completion targeted for early 2026; 2. Begin the design phase, environmental assessments, and other pre-construction processes for the development of the Proteomics Core Lab on the Main Campus; 3. Procure and install a high-throughput, short-read NGS system to support transcriptomics services; 4. Submit proposals for new graduate-level courses in genomics and bioinformatics to the DSU Graduate Program Committee and Faculty Senate for approval; 5. Officially launch the DSU DNA Core facility.
Impacts
What was accomplished under these goals?
• Building Genomic Core Facility - Development of the DNA Core Lab Major Activities Conducted: To continue developing a DNA core facility on the Downtown campus, the PD and the DSU Facilities Department have held regular biweekly meetings, both on-site and online. The lab construction team, comprising the PD; Mrs. Zerrad and Mr. Willis from the DSU Facilities; and Mr. Mengers and Ms. Robbins from StudioJAED, has been actively discussing project goals, lab renovation design, scheduling, and post-construction expectations. The DSU Facilities Department consulted several architectural and engineering firms to evaluate their qualifications and experience with academic construction projects. StudioJAED was selected for further project planning. In parallel, the Facilities team sought project approvals from the Delaware State Historic Preservation Office (SHPO) and requested environmental assessments and remediation estimates from Harvard Environmental Inc., Verdantas, and Plymouth Environmental. The Facilities team also collaborated with the PD to prepare the Year 2 and Year 3 budgets, following NIFA guidelines for core lab renovations on both the main and downtown campuses. Data Collected: During regular meetings and site visits, the PD, DSU Facilities team, and consultants documented requirements for flooring, ceilings, plumbing, temperature and humidity control, internet/network systems, electrical receptacles, and lab benches to accommodate core equipment. Equipment specifications were also collected. Following data collection, the environmental agencies conducted site visits to prepare project estimates. Results and Outcomes: The architectural and engineering consultants submitted and revised the lab design, including a detailed scope of work, lab specifications, and a budget estimate. The environmental agencies submitted assessment reports. The SHPO approved the project. In compliance with NIFA FGP guidelines, the required pre-construction A&E reports, environmental assessments, SHPO approval, equipment procurement requests, and supporting documents were submitted to the agency for final approval. - DNA Core Development Committee Major Activities Conducted: The PD convenes monthly DNA Core Development Committee meetings. The committee includes the PD, Co-PDs, DSU faculty, the Core Director and Manager, and the DSU Vice President for Research. Recently, the Director of the DSU Data Science Facility and the DNA Core Manager were added to the committee. Meeting agendas include: 1. Project progress and outcome updates, 2 Goal alignment review, 3.Recommendations for genomics and proteomics equipment, 4. Development of new curricula and educational programs, 5. Core user guideline development, 6.Promotion and sustainability of the DNA Core, 7.New agenda suggestions and feedback collection. During meetings, the PD provided updates on lab design and renovation, equipment selection, environmental assessments, core staff recruitment, and budget planning. The PD also met with the DSU VP for Research as needed to resolve emerging issues. Committee meetings will continue throughout and beyond the FGP project. Data Collected: In each meeting, the PD gathered feedback from committee members. Members requested that lab renovations be completed by the end of 2025 and recommended equipment such as mid-/high-throughput short-read NGS systems, automation tools, HPC units, and proteomics systems. They also discussed implementing NGS services using Illumina and PacBio platforms, with customized pipelines for WGS, targeted sequencing, and RNA-seq across diverse biological samples. Additionally, the PD collected responses from PIs regarding desired core services. To recruit a new DNA Core Manager, the PD and a search committee conducted interviews and evaluated candidates' skills, knowledge, and experience. Results and Outcomes: Based on the recommendations, the NextSeq 2000 and MiSeq Plus NGS systems were selected as the initial acquisitions for Year 2. These systems will support a wide range of core services, from small prokaryotic genomes to complex eukaryotic studies, serving both research and educational purposes. To manage the DNA Core, a staff position--DNA Core and Data Science Research Staff in Genomics and Bioinformatics--was filled by the PD and VP for Research. The new manager has recently started core operations. - Project Initiation and Collaboration Major Activities Conducted: Project initiation involved collaboration among the Dean, college budget administrator, Office of Sponsored Programs (OSP), Facilities Department, and university administration. The Dean of CAST convened a project meeting with the PD, Facility Manager, and NIFA to ensure compliance with Facilities Checklists during the DNA Core development. The PD also met with the VP for Research, Associate Dean for Research, and Department Chair to present the FGP project overview, goals, and target audiences, and to discuss the DNA Core's affiliation with DE-INBRE Core Facilities. Simultaneously, the DNA Core Manager engaged PIs, postdocs, research staff, and graduate students on both campuses to introduce the core's functions and services. The PD, OSP Compliance Officer, and college budget analyst also held regular meetings to prepare budget modifications, improve documentation, and enhance internal communication. Data Collected: The team conducted site visits to various buildings, including the OSCAR Center, Agriculture Annex, and Cannon Hall, assessing factors such as location, accessibility, and adaptability. The PD also visited the Core Facility at the University of Massachusetts Amherst to learn best practices in management, research support, innovation, and maintenance. Additionally, the PD and DNA Core Manager collected feedback from faculty and staff regarding preferred core lab locations and the projected opening date. Results and Outcomes: Based on assessments and feedback, the physics teaching lab in Cannon Hall was selected to house the DNA Core Lab. The Food Microbiology Lab in the Agriculture Annex was tentatively selected for the future Proteomics Core. The project is supported by the VP for Research. The DSU OSP submitted pre-construction reports and other required documents to the agency in accordance with NIFA guidelines.
Publications
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2025
Citation:
The Microbiome of Catfish (Ictalurus punctatus) Treated with Natural Preservatives During Refrigerated Storage
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Progress 09/01/23 to 08/31/24
Outputs
Target Audience:This program aims to reach both internal and external participants in the fields of genomics, bioinformatics, and computer sciences, including the PD, Co-PDs, research staff, post-docs, graduate students, and clients. Additionally, the college dean, associate deans, university administrators, and facility staff will play administrative roles in supporting this project. Once the DNA core is established, the project's outreach activitieswill extend to high school and community college students, university students, and local communities. It supports African American students and underserved communities by offering graduate research opportunities and Core extension programs. The project efforts go through a variety of formal and informal activities such as lab experiments, classroom instruction, workshops, special seminars, summer programs, extension programs, and access to DNA Core services such as NGS, library prep, and bioinformatics, the project will deliver new technology and science-based knowledge to its target audiences. Changes/Problems:The PD and DSU facility are prepared to proceed with the lab renovation and construction to develop the DNA Core as planned in the project's first year. However, the renovation has been delayed due to unforeseen issues;after multiple meetings with external A&E contractor teams, we realized that the estimated costs for lab renovation, associated fees, and preconstruction environmental assessment fees far exceeded what the original budget had been made. In response to NIFA guidance, the DSU OSP submitted requests and supporting documents for budget changes and approvals for A&E and EA to NIFA. After reviewing the submission, the agency requested budget revisions and additional documents, which the OSP resubmittedaccordingly. These events, combinedwith DSU's internal processes, have delayed the project initiation. Despite these delays, the PD continues to actively work onother project goalsas detailed in this annual report, while awaiting NIFA's approval. What opportunities for training and professional development has the project provided?Training Activities The PD and research staff have been expanding ourknowledge of IT and data science technology using the SMRT Link platform. Currently, the PD receives weekly training from a bioinformatician at PacBio. This training covers a range of topics, including IT technology and high-performance computing, networking between NGS systems and servers, and using the SMRT Link platformfor design, sample setup, QC, operation, analysis, and data management. This training provides a strong foundation for offering bioinformatics services once the DNA Core lab renovations are complete. In the project's first year, the PD met with representatives from scientific vendors and biotech companies to learn about recent equipment using new innovative technologythat could strengthen the DNA Core facility.These discussions included information on NGS systems, single-cell sorters, automated systems, and HPC clusters. The PD and staff gained insights into the scientific principles of the equipment, sample analysis capabilities, hardware and software specifications, applications in various studies, and the potential impact on DSU research communities. Professional Development Activities The training activities were conducted both onsite and online. The bioinformatics training was held virtually through presentations, remote demonstrations, videos, and Q&A sessions. System networkingincluded onsite meetings with IT personnel, with occasional virtual involvement from the DSU IT team. Company representatives offered virtual seminars to showcase their products. The PD will suggest that the Core Development Committee invite companies to present on-site seminars or workshops for DSU faculty, staff, and students, as the committee determines the necessary core equipment for the campus. How have the results been disseminated to communities of interest?The PD collaborated with the DSU webmaster to develop a DSU DNA Core website to introduce the facility to internal and external audiences. The website includes information about the core's introduction, mission and vision, services, equipment, educational program, and outreach service. Currently, the website is being expanded with additional pages on service scheduling, payment options, video links, and details about the core team. The PD and the CAST event coordinator created brochures and booklets to promote the DNA Core to internal and external communities. These materials have been distributed to DSU faculty, research staff, and local school teachers. Thosewere also made available at the DSU booth during the 1890 ARD symposium, along with contact information. What do you plan to do during the next reporting period to accomplish the goals?The goals for the next reporting period are to: 1. complete the renovation of the genomics core lab on the downtown campus and begin the development of the proteomics core lab on the main campus, 2. purchase a high-throughput, short-read NGS system and set it up for transcriptomics services, and 3. hire a senior research staff member to manage the DNA Core facility.
Impacts
What was accomplished under these goals?
• Budling Genomic Core Facility - Development of the DNA core lab Major Activities Conducted: To develop a DNA core facility on the Downtown campus, the PD and the DSU facility department have regular meetings every two weeks. The lab construction team, comprising the PD, Mrs. Zerrad, and Willis, discusses the project's goals, the scope of renovation and construction, and expectations after DNA core development. The team consulted with several architectural and engineering consultants to assess their professional capabilities and experience with construction projects at academic institutes. They selected two consultants, StudioJAED and Bernardfor further project preparation. Additionally, the facility consulted environmental assessment services from Harvard Environmental Inc. and Verdantas to obtain project overviews and estimates. The facility also collaborated with the PD to prepare budgets in accordance with NIFA guidelines for core lab renovations on both main and downtown campuses. Data Collected: Each architectural and engineering consultant conducted three site visits to gather information about the lab space, includingflooring, ceiling, and plumbing conditions; temperature and humidity control; LAN/internet network system; and number of receptacles and lab benches required to accommodate the core equipment. After collecting the necessary data, the environmental assessment agencies visited the lab to estimate the project. Results and Outcomes: The architectural and engineering consultants submitted a project proposal outlining the scope of work, terms and conditions, service and billing rates, specifications for the DNA core lab, and a budget estimate. The environmental assessment agencies also submitted proposals and service estimates. Based on the DSU facility review, StudioJAED, Harvard Environmental, and Verdantas were selected for architectural and engineering, inspection, and phase I environmental assessment services, respectively. To complywith the NIFA FGP guidelines for pre-construction environmental assessments, the required documents have been submitted to the agency for approval. - Development of DNA corecommittee Major Activities Conducted: The PD appointed DSU PIs and an administrator to form a DNA core development committee. This committee includes the PD, Co-PDs, DSU faculty, and the DSU Vice President of Research. The main goals of the committee are: 1. updating on project progress and outcomes,2. ensuring the project aligns with its goals,3. listing and recommending core genomics and proteomics equipment,4. developing core user guidelines,5. Suggesting new agendas and collecting feedback, and 6. promoting and sustaining the DNA Core. The committee meets monthly, during which the PD provides updates on the internal process for lab renovation, pre-construction environmental assessment, core staff recruitment, and budget estimates. Additionally, the PD holds meetings with the DSU VP of Research as needed to address any issues that arise. Committee meetings will continue during and after the FGP project. Data Collected: In each core development meeting, the PD gathers feedback and suggestions from committee members. They recommend core equipment such as short-readingmid/high-throughput NGS systems, automation systems, high-performance computing units, and proteomics systems. For recruiting a new DNA Core manager, the PD collects the committee's suggestions regarding essential functions, required skills, knowledge, abilities, and performance standards. The committee also discusses NGS services usingthe Illumina and PacBio systems to develop customized pipelines for library preps of whole genome sequencing, target DNA sequencing, and RNA sequencing for various studies in bacteria, plants, worms, and animal cells. Results and Outcomes: From the equipment lists, the NextSeq NGS system was chosen as the first equipment to be introduced on campus in project year 2. This system is crucial for transcriptomics studies in eukaryotic subjects and is expected to be used for research, teaching, and services. To manage the DNA Core facility, the position of DNA Core and Data Science Research Staff in Genomics and Bioinformatics has been requested by the PD and the VP of Research. The position is anticipated to be announced on DSU HR and recruitment websites following internal approvals. - Project initiation and collaboration Major Activities Conducted: The project initiation involved collaboration between the Dean, college, office of the sponsored program, facility department, and university administrators. The Dean of CAST called a project meeting that included the PD, facility manager, VP for Strategic Initiatives on the downtown campus, and Associate Dean for Research. The PD presented the FGP project overview, including rationales, goals, target audiences, and the yearly plan for DNA Core development at DSU. The PD, VP for Research, and VP for Strategic Initiatives met several times to evaluate labs and office rooms on both main and downtown campuses to find the optimal locations. Simultaneously, the PD, OSP compliance officer, and college budget analyst met regularly to prepare budget modifications and documentation, as well as to improve internal processes and communications. Data Collected: The project team visited labs and rooms in the OSCAR Center, Agriculture Annex building, and Cannon Hall. They assessed factors such as location, accessibility, and transformability. Additionally, the PD gathered feedback and expectations from faculty and staffregarding the core location and opening date. Results and Outcomes: Based on site visits and feedback, the teaching lab and rooms in Cannon Hall were confirmed for the DNA Core in Genomics. The Food Lab in the Agriculture Annex building was tentatively chosen for the DNA Core lab in Proteomics. The PD received approval from the Dean and AOR for budget changes to support lab renovations. DSU OSP submitted the request for budget changes to the agency according to NIFA guidance.
Publications
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