Rigor, Reproducibility, and Transparency in Shared Research Resources: Follow-Up Survey and Recommendations for Improvements.

Rigor, reproducibility, and transparency (RR&T) are essential components of all scientific pursuits. Shared research resources, also known as core facilities, are on the frontlines of ensuring robust RR&T practices. The Association of Biomolecular Resource Facilities Committee on Core Rigor and Reproducibility conducted a follow-up survey 4 years after the initial 2017 survey to determine if core facilities have seen a positive impact of new RR&T initiatives (including guidance from the National Institutes of Health, new scientific journal requirements on transparency and data provenance, and educational tools from professional organizations). While there were fewer participants in the most recent survey, the respondents' opinions on the role of core facilities and level of best practices adoption remained the same. Overall, the respondents agreed that procedures should be implemented by core facilities to ensure scientific RR&T. They also indicated that there is a strong correlation between institutions that emphasize RR&T and core customers using this expertise in grant applications and publications. The survey also assessed the impact of the COVID-19 pandemic on core operations and RR&T. The answers to these pandemic-related questions revealed that many of the strategies aimed at increasing efficiencies are also best practices related to RR&T, including the development of standard operating procedures, supply chain management, and cross training. Given the consistent and compelling awareness of the importance of RR&T expressed by core directors in 2017 and 2021 contrasted with the lack of apparent improvements over this time period, the authors recommend an adoption of RR&T statements by all core laboratories. Adhering to the RR&T guidelines will result in more efficient training, better compliance, and improved experimental approaches empowering cores to become "rigor champions."

Maximizing Shared Research Resources: Next Steps.

Shared research resources (SRRs) promote access and training to advanced technologies and applications for a diverse array of trainees, faculty, students, and staff. Institutions and the broader research community benefit from the expertise and reputation of SRRs, their efficient use of research funds, and their positive impact on faculty recruitment and retention. Moreover, as contemporary science has become increasingly multidisciplinary and team based, SRRs are the nexus for basic discovery and the application of new groundbreaking technologies, with data as the key deliverable. However, despite their track record of accomplishments, barriers continue to exist, hindering SRRs essential role in modern research and highlighting the need for a national strategy to ensure their sustainability. The recommendations from the Federation of American Societies for Experimental Biology (FASEB) SRR Task Force publication "Maximizing SRR part III" and subsequent roundtable meetings have spurred efforts for strengthening shared resources, achieving career recognition and parity, and elevating team science to its full potential. This JBT special issue focuses on these efforts, with contributions from members of the Association of Biomolecular Resource Facilities and FASEB Task Force.

Addressing the Environmental Impact of Science Through a More Rigorous, Reproducible, and Sustainable Conduct of Research.

The pervasiveness of irreproducible research remains a thorny problem for the progress of scientific endeavor, spawning an abundance of opinion, investigation, and proposals for improvement. Irreproducible research has negative consequences beyond the obvious impact on achieving new scientific discoveries that can advance healthcare and enable new technologies. The conduct of science is resource intensive, resulting in a large environmental impact from even the smallest research programs. There is value in making explicit connections between the conduct of more rigorous, reproducible science and commitments to environmental sustainability. Shared research resources (also commonly known as cores) often have an institutional role in supporting researchers in the responsible conduct of research through training, informal mentorship, and services and are particularly well suited to promulgating essential principles of scientific rigor, reproducibility, and transparency. Shared research resources can also play a role in advancing sustainability by virtue of their inherently efficient science model in which singular shared equipment, technology, and expertise resources can serve many different research programs. Programs that elevate shared research resources, scientific rigor, reproducibility, transparency, and environment sustainability in harmony may achieve a unique synergy. Several case studies and quality paradigms are discussed that offer tools and concepts that can be adapted whole or in part by individual shared research resources or research-intensive institutions as part of an overall program of sustainability.

Establishing a national strategy for shared research resources in biomedical sciences.

Contemporary science has become increasingly multi-disciplinary and team-based, resulting in unprecedented growth in biomedical innovation and technology over the last several decades. Collaborative research efforts have enabled investigators to respond to the demands of an increasingly complex 21st century landscape, including pressing scientific challenges such as the COVID-19 pandemic. A major contributing factor to the success of team science is the mobilization of core facilities and shared research resources (SRRs), the scientific instrumentation and expertise that exist within research organizations that enable widespread access to advanced technologies for trainees, faculty, and staff. For over 40 years, SRRs have played a key role in accelerating biomedical research discoveries, yet a national strategy that addresses how to leverage these resources to enhance team science and achieve shared scientific goals is noticeably absent. We believe a national strategy for biomedical SRRs-led by the National Institutes of Health-is crucial to advance key national initiatives, enable long-term research efficiency, and provide a solid foundation for the next generation of scientists.

Reopening During the Unprecedented: The Association of Biomolecular Resource Facilities Community Coronavirus Disease 2019 Pandemic Response. Part 2: Efforts to Effectively Ramp Up Core Facility Activities.

Shared research resources, also known as core facilities, serve a crucial role in supporting research, training, and other needs for their respective institutions. In response to the coronavirus disease (COVID-19) pandemic, all but the most critical laboratory research was halted in many institutions around the world. The Association of Biomolecular Resource Facilities conducted 2 surveys to understand and document institutional responses to the COVID-19 pandemic from core facility perspectives. The first survey was focused on initial pandemic response and efforts to sustainably ramp down core facility operations. The second survey, which is the subject of this study, focused on understanding the approaches taken to ramp up core facility operations after these ramp-down procedures. The survey results revealed that many cores remained active during the ramp-down, performing essential COVID-19 research, and had a more coordinated institutional response for ramping up research as a whole. The lessons gained from this survey will be indexed to serve as a resource for the core facility community to understand, plan, and mitigate risk and disruptions in the event of future disasters.

Preparing for the Unprecedented: The Association of Biomolecular Resource Facilities (ABRF) Community Coronavirus Disease 2019 (COVID-19) Pandemic Response Part 1: Efforts to Sustainably Ramp Down Core Facility Activities.

The coronavirus disease 2019 (COVID-19) pandemic has curtailed all but the most critical laboratory research in many institutions around the world. These unplanned and unprecedented operational changes have put considerable stress on every aspect of the research enterprise, from funding agencies to research institutes, individual and core laboratories, researchers, and research administrators, with drastic changes in demands and deliverables. The Association of Biomolecular Resource Facilities Core Administrators Network Coordinating Committee initiated a forum-wide discussion followed by a global survey to gain information on how institutions and, specifically, shared resource core facilities were responding to the COVID-19 pandemic. The survey aimed to identify shared resource core facility challenges and opportunities related to operational ramp downs, shutdowns, or research "pauses" during the COVID-19 pandemic, as well as new practices and resources needed to ensure business continuity. Although a number of positive outcomes from remote work hold promise for improved core operations, the survey results revealed a surprising level of unfamiliarity with business continuity planning for cores and limited coordination within institutions. Recommendations for business continuity planning include key stakeholders working together to assess risk, prioritize work, and promote transparency across campus.

A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups.

Shared research resource facilities, also known as core laboratories (Cores), are responsible for generating a significant and growing portion of the research data in academic biomedical research institutions. Cores represent a central repository for institutional knowledge management, with deep expertise in the strengths and limitations of technology and its applications. They inherently support transparency and scientific reproducibility by protecting against cognitive bias in research design and data analysis, and they have institutional responsibility for the conduct of research (research ethics, regulatory compliance, and financial accountability) performed in their Cores. The Association of Biomolecular Resource Facilities (ABRF) is a FASEB-member scientific society whose members are scientists and administrators that manage or support Cores. The ABRF Research Groups (RGs), representing expertise for an array of cutting-edge and established technology platforms, perform multicenter research studies to determine and communicate best practices and community-based standards. This review provides a summary of the contributions of the ABRF RGs to promote scientific rigor and reproducibility in Cores from the published literature, ABRF meetings, and ABRF RGs communications.

Survey on Scientific Shared Resource Rigor and Reproducibility.

Shared scientific resources, also known as core facilities, support a significant portion of the research conducted at biomolecular research institutions. The Association of Biomolecular Resource Facilities (ABRF) established the Committee on Core Rigor and Reproducibility (CCoRRe) to further its mission of integrating advanced technologies, education, and communication in the operations of shared scientific resources in support of reproducible research. In order to first assess the needs of the scientific shared resource community, the CCoRRe solicited feedback from ABRF members via a survey. The purpose of the survey was to gain information on how U.S. National Institutes of Health (NIH) initiatives on advancing scientific rigor and reproducibility influenced current services and new technology development. In addition, the survey aimed to identify the challenges and opportunities related to implementation of new reporting requirements and to identify new practices and resources needed to ensure rigorous research. The results revealed a surprising unfamiliarity with the NIH guidelines. Many of the perceived challenges to the effective implementation of best practices (i.e., those designed to ensure rigor and reproducibility) were similarly noted as a challenge to effective provision of support services in a core setting. Further, most cores routinely use best practices and offer services that support rigor and reproducibility. These services include access to well-maintained instrumentation and training on experimental design and data analysis as well as data management. Feedback from this survey will enable the ABRF to build better educational resources and share critical best-practice guidelines. These resources will become important tools to the core community and the researchers they serve to impact rigor and transparency across the range of science and technology.

Disaster and Contingency Planning for Scientific Shared Resource Cores.

Progress in biomedical research is largely driven by improvements, innovations, and breakthroughs in technology, accelerating the research process, and an increasingly complex collaboration of both clinical and basic science. This increasing sophistication has driven the need for centralized shared resource cores ("cores") to serve the scientific community. From a biomedical research enterprise perspective, centralized resource cores are essential to increased scientific, operational, and cost effectiveness; however, the concentration of instrumentation and resources in the cores may render them highly vulnerable to damage from severe weather and other disasters. As such, protection of these assets and the ability to recover from a disaster is increasingly critical to the mission and success of the institution. Therefore, cores should develop and implement both disaster and business continuity plans and be an integral part of the institution's overall plans. Here we provide an overview of key elements required for core disaster and business continuity plans, guidance, and tools for developing these plans, and real-life lessons learned at a large research institution in the aftermath of Superstorm Sandy.

Chemical cleavage of proteins in solution.

Described in this unit are five basic protocols that are widely used for specific and efficient chemical cleavage of proteins in solution. Cyanogen bromide (CNBr) cleaves at methionine (Met) residues; BNPS-skatole cleaves at tryptophan (Trp) residues; formic acid cleaves at aspartic acid-proline (Asp-Pro) peptide bonds; hydroxylamine cleaves at asparagine-glycine (Asn-Gly) peptide bonds, and 2-nitro-5-thiocyanobenzoic acid (NTCB) cleaves at cysteine (Cys) residues. Because the above loci are at relatively low abundance in most proteins, digestion with these agents will yield relatively long peptides.

Expression, purification, crystallization and preliminary crystallographic analysis of human Pim-1 kinase.

Pim kinases, including Pim-1, Pim-2 and Pim-3, belong to a distinctive serine/threonine protein-kinase family. They are involved in cytokine-induced signal transduction and the development of lymphoid malignancies. Their kinase domains are highly homologous to one another, but share low sequence identity to other kinases. Specifically, there are two proline residues in the conserved hinge-region sequence ERPXPX separated by a residue that is non-conserved among Pim kinases. Full-length human Pim-1 kinase (1-313) was cloned and expressed in Escherichia coli as a GST-fusion protein and truncated to Pim-1 (14-313) by thrombin digestion during purification. The Pim-1 (14-313) protein was purified to high homogeneity and monodispersity. This protein preparation yielded small crystals in the initial screening and large crystals after optimization. The large crystals of apo Pim-1 enzyme diffracted to 2.1 A resolution and belong to space group P6(5), with unit-cell parameters a = b = 95.9, c = 80.0 A, beta = 120 degrees and one molecule per asymmetric unit.

Structural basis of constitutive activity and a unique nucleotide binding mode of human Pim-1 kinase.

Pim-1 kinase is a member of a distinct class of serine/threonine kinases consisting of Pim-1, Pim-2, and Pim-3. Pim kinases are highly homologous to one another and share a unique consensus hinge region sequence, ER-PXPX, with its two proline residues separated by a non-conserved residue, but they (Pim kinases) have <30% sequence identity with other kinases. Pim-1 has been implicated in both cytokine-induced signal transduction and the development of lymphoid malignancies. We have determined the crystal structures of apo Pim-1 kinase and its AMP-PNP (5'-adenylyl-beta,gamma-imidodiphosphate) complex to 2.1-angstroms resolutions. The structures reveal the following. 1) The kinase adopts a constitutively active conformation, and extensive hydrophobic and hydrogen bond interactions between the activation loop and the catalytic loop might be the structural basis for maintaining such a conformation. 2) The hinge region has a novel architecture and hydrogen-bonding pattern, which not only expand the ATP pocket but also serve to establish unambiguously the alignment of the Pim-1 hinge region with that of other kinases. 3) The binding mode of AMP-PNP to Pim-1 kinase is unique and does not involve a critical hinge region hydrogen bond interaction. Analysis of the reported Pim-1 kinase-domain structures leads to a hypothesis as to how Pim kinase activity might be regulated in vivo.

IKKalpha, IKKbeta, and NEMO/IKKgamma are each required for the NF-kappa B-mediated inflammatory response program.

The IKKbeta and NEMO/IKKgamma subunits of the NF-kappaB-activating signalsome complex are known to be essential for activating NF-kappaB by inflammatory and other stress-like stimuli. However, the IKKalpha subunit is believed to be dispensable for the latter responses and instead functions as an in vivo mediator of other novel NF-kappaB-dependent and -independent functions. In contrast to this generally accepted view of IKKalpha's physiological functions, we demonstrate in mouse embryonic fibroblasts (MEFs) that, akin to IKKbeta and NEMO/IKKgamma, IKKalpha is also a global regulator of tumor necrosis factor alpha- and IL-1-responsive IKK signalsome-dependent target genes including many known NF-kappaB targets such as serum amyloid A3, C3, interleukin (IL)-6, IL-11, IL-1 receptor antagonist, vascular endothelial growth factor, Ptx3, beta(2)-microglobulin, IL-1alpha, Mcp-1 and -3, RANTES (regulated on activation normal T cell expressed and secreted), Fas antigen, Jun-B, c-Fos, macrophage colony-stimulating factor, and granulocyte-macrophage colony-stimulating factor. Only a small number of NF-kappaB-dependent target genes were preferentially dependent on IKKalpha or IKKbeta. Constitutive expression of a trans-dominant IkappaBalpha superrepressor (IkappaBalphaSR) in wild type MEFs confirmed that these signalsome-dependent target genes were also dependent on NF-kappaB. A subset of NF-kappaB target genes were IKK-dependent in the absence of exogenous stimuli, suggesting that the signalsome was also required to regulate basal levels of activated NF-kappaB in established MEFs. Overall, a sizable number of novel NF-kappaB/IKK-dependent genes were identified including Secreted Frizzled, cadherin 13, protocadherin 7, CCAAT/enhancer-binding protein-beta and -delta, osteoprotegerin, FOXC2 and FOXF2, BMP-2, p75 neurotrophin receptor, caspase-11, guanylate-binding proteins 1 and 2, ApoJ/clusterin, interferon (alpha and beta) receptor 2, decorin, osteoglycin, epiregulin, proliferins 2 and 3, stromal cell-derived factor, and cathepsins B, F, and Z. SOCS-3, a negative effector of STAT3 signaling, was found to be an NF-kappaB/IKK-induced gene, suggesting that IKK-mediated NF-kappaB activation can coordinately illicit negative effects on STAT signaling.