Journal of biomolecular techniques : JBT最新文献

Shared Research Resources (SRRs) are essential for sustaining research excellence, particularly in financially constrained environments. This study examines how federal policy uncertainties exacerbate existing challenges in SRR operations and management. Findings from focus groups-including over 220 leaders in academic administration and SRRs-highlight that staffing, funding, and cross-campus collaboration disproportionately impact resource-limited institutions, widening disparities in research capabilities. Evaluating SRRs' role in supporting research during financial instability is critical. Active administrative engagement in supporting SRRs helps institutions to secure funding and align priorities with institutional goals. SRRs improve operational efficiency through shared infrastructure models and standardized procurement policies, reducing duplication and optimizing resource utilization. Workforce adaptability is key to sustainability, with cross-training and strategic recruitment fostering resilience amid financial uncertainty. This study underscores the interconnected nature of funding diversification, leadership alignment, operational efficiency, workforce adaptability, and policy reform in sustaining SRR systems. This study draws on collective insights from SRR staff across all organizational levels, from technical personnel and directors to administrators and institutional leaders, to capture a comprehensive, ground-level perspective on the conditions necessary for long-term viability. Institutions that recognize SRRs as strategic partners in addressing systemic research barriers will be better positioned to foster a more equitable, efficient, and sustainable research ecosystem.

Core facilities provide essential institutional infrastructure for answering a broad variety of technical research questions. Funding pilot programs through a core facility voucher system provides opportunities not only for researchers to collaborate with core facilities to further their research aims and produce scholarly output, but also for core directors to gain new long-term customers, develop new pipelines, and bring new services and assays into the core's portfolio. The University of North Carolina at Chapel Hill School of Medicine manages a core voucher program unique in several regards, including its requirement for a core consultation to ensure all proposals meet core facility standards for rigor and reproducibility, as well as its accessibility to trainees. The operational parameters and return on investment of this core voucher program are described and discussed.

Shared Research Resources (SRRs), also known as Core Facilities or Research Service Centers are essential for advancing scientific research in academic, government, industry, and non-profit institutions since they provide access to advanced resources like innovative research technologies, latest equipment in variety of platforms, and expert personnel with skills to solve complex problems as well as providing training and pursue technology development. Traditionally, SRRs are thought of as confined to academic R1 universities and non-profit organizations. However, many regional centers and national laboratories also feature core facilities that cater to local, regional, national, and international users. Like traditional SRRs, these facilities provide user training, in-person access, and remote access to instruments and services. In this section, we will discuss some of the opportunities these cores provide to scientists worldwide. We will also discuss some of the challenges these facilities face in running and maintaining such a large and continuous operation with many users.

Primers for 16S rRNA gene amplification are generally degenerate to account for mismatches between primers and templates, but primer lengths are typically not adjusted. However, prior research has shown that primers are most sensitive to mismatches at the 3' end, and 3' mismatches can limit the ability of primers to amplify target genes from complex microbial communities. We present here a novel approach to primer design by creating staggered and truncated (both the 5' and 3' ends) versions of commonly used microbial 16S ribosomal RNA (rRNA) primers while maintaining consistent melting temperatures. Genomic DNA extracted from complex microbial communities (skin, feces, wastewater, soil) was profiled using deep sequencing of 16S rRNA gene amplicons generated with standard and truncated primers. Sequence data were compared using standard bioinformatics pipelines evaluating alpha and beta diversity. Despite using primers as short as 10 bases, observed microbial communities generated with truncated primer pools were highly similar to those generated with standard primer pools. In analyses of skin, truncated amplicons had significantly increased relative abundance of Cutibacterium which contain 3' mismatches with standard primers. Further analysis revealed a single nucleotide position in a common 16S rRNA gene primer that enriched microorganisms from the domain Archaea with truncated primers. These results demonstrate the viability of using short primers for amplicon NGS, indicating the availability of greater primer design flexibility for future studies.

This report reflects the authors personal experiences as they navigated our own paths through the meeting, focusing on the sessions we each attended and the interactions we benefited from. ABRF 2025 was a large meeting with nearly 1,000 participants over 4 days (23rd-26th March 2025), featuring parallel sessions that catered to a diverse audience, ranging from dedicated technical professionals to senior leadership.

Shared Research Resources (SRRs), also known as core facilities or research cores, play a pivotal role in advancing scientific discovery by providing specialized equipment, services, and expert guidance. SRRs provide integral contributions to research and have an active role in upholding, rigor, reproducibility, and adherence to FAIR principles (Findability, Accessibility, Interoperability, and Reuse), but are frequently underacknowledged in scientific publications. This paper underscores the importance of formally recognizing SRRs in research outputs, both to enhance transparency and to support institutional efforts in securing funding, recruiting faculty, and sustaining infrastructure. Drawing on guidelines from the Association of Biomolecular Resource Facilities, we explore the challenges to widespread SRR acknowledgment and propose actionable strategies for researchers and SRR staff to ensure proper credit is given. Acknowledgment not only validates the intellectual and technical contributions of SRRs, ranging from experimental design to data interpretation, but also serves as a critical metric for career advancement within the SRR sector. By fostering a culture of recognition, the research community can better uphold standards of excellence and collaboration.

The field of metabolomics leverages advanced analytical techniques, such as nuclear magnetic resonance (NMR) and liquid chromatography-mass spectrometry (LC-MS), to identify and quantify metabolites that are integral to biology. The scope of untargeted metabolomics methods is highly dependent on the protocols employed prior to analysis. These include homogenization and extraction processes, which directly influence the metabolites detected and, consequently, the biological interpretations drawn. Given the substantial variability introduced by different homogenization and extraction parameters, the optimization of these protocols for non-routine or novel sample matrices is essential, particularly in core facilities where a diverse range of matrices are expected to be analyzed. In response to this need, we demonstrate the utility of a Taguchi design of experiments (DOE) method for the systematic optimization of matrix-specific sample preparation parameters using the model organism Caenorhabditis elegans. This methodology was applied to optimize four critical factors: (1) extraction solvent, (2) solvent volume, (3) extraction duration, and (4) LC reconstitution solvent, during a sequential non-polar and polar metabolite extraction for LC-MS and NMR spectroscopy. Despite its infrequent use in metabolomics, the Taguchi DOE method offers a structured and efficient pathway for optimizing multiple sample preparation variables, enhancing throughput, reproducibility, and cost-effectiveness. This approach is particularly valuable for the metabolomics community, as it provides a scalable, adaptable framework applicable across various sample types and research objectives. This work serves as a demonstration of the methodology, underscoring its potential to enhance method development and optimization across diverse metabolomics applications.

The most recent national Canadian Network for Scientific Platforms (CNSP) Scientific Platform Meeting was held from November 20 to 22, 2023, at the Montreal Neurological Institute, "The Neuro," affiliated with McGill University. This conference, attended by 114 representatives from 44 scientific platforms, was structured around three themes. Day 1 focused on open science, emphasizing transparency and the free sharing of scientific discoveries to enhance research efficiency. Discussions included panel talks on initiatives and resources related to open science and featured award presentations for 2023 CNSP National Platform Scientist Award winners for both the Platform Administrator Award and Platform Scientist Award. The day concluded with a conference dinner. Day 2 highlighted the critical role of scientific platforms in advancing research by providing essential infrastructure and expertise by hearing about different successful national and international networks. This day featured a poster session and a networking reception. Day 3 offered a professional development workshop and tours of McGill University's leading scientific platforms, showcasing the expertise within the scientific platform community.