Open Biology in a new decade.
Ontology highlight
ABSTRACT:
SUBMITTER: Glover DM
PROVIDER: S-EPMC7058933 | biostudies-literature | 2020 Feb
REPOSITORIES: biostudies-literature
Publications
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Project description:Systems biology provides a framework for assembling models of biological systems from systematic measurements. Since the field was first introduced a decade ago, considerable progress has been made in technologies for global cell measurement and in computational analyses of these data to map and model cell function. It has also greatly expanded into the translational sciences, with approaches pioneered in yeast now being applied to elucidate human development and disease. Here, we review the state of the field with a focus on four emerging applications of systems biology that are likely to be of particular importance during the decade to follow: (a) pathway-based biomarkers, (b) global genetic interaction maps, (c) systems approaches to identify disease genes, and (d) stem cell systems biology. We also cover recent advances in software tools that allow biologists to explore system-wide models and to formulate new hypotheses. The applications and methods covered in this review provide a set of prime exemplars useful to cell and developmental biologists wishing to apply systems approaches to areas of interest.
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Project description:Rural Healthy People is a companion piece to the federal Healthy People initiative released once a decade to identify the most important Healthy People priorities for rural America, as identified by rural stakeholders, for the current decade. This study reports on the findings of Rural Healthy People 2030. The study relied on a survey of rural health stakeholders collected from July 12, 2021, to February 14, 2022, and: 1) identified the 20 Healthy People priorities most frequently selected as priorities for rural America, 2) studied the priorities that were most frequently selected as a "top 3" priority within each Healthy People 2030 category, and 3) investigated Healthy People 2030 priorities in terms of ranked importance for rural Americans. The analysis finds that for the first time across 3 decades of Rural Healthy People, a greater proportion of respondents selected "Mental Health and Mental Disorders" and "Addiction" as Healthy People priorities for rural America, than did "Health Care Access and Quality". Even still, respondents ranked "Health Care Access and Quality" as the single-most important rural priority. "Economic Stability," a new priority within the Social Determinant of Health category, debuted within the 10 most frequently selected priorities for rural America for the coming decade. As public health practitioners, researchers, and policymakers work toward closing the urban-rural divide, the most important rural priorities to address in the coming decade are mental health and substance use disorders, access to high quality health care services, and social determinants of health, such as economic stability.
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Project description:Helping B cells and antibody responses is a major function of CD4+ T cells. It has been 10 years since the publication of Bcl6 as the lineage-defining transcription factor for T follicular helper (Tfh) differentiation and the requirement of Tfh cells as the specialized subset of CD4+ T cells needed for germinal centers (the microanatomical sites of B cell mutation and antibody affinity maturation) and related B cell responses. A great deal has been learned about Tfh cells in the past 10 years, particularly regarding their roles in a surprising range of diseases. Advances in the understanding of Tfh cell differentiation and function are discussed, as are the understanding of Tfh cells in infectious diseases, vaccines, autoimmune diseases, allergies, atherosclerosis, organ transplants, and cancer. This includes discussion of Tfh cells in the human immune system. Based on the discoveries to date, the next decade of Tfh research surely holds many more surprises. VIDEO ABSTRACT.
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Project description:The increasingly multidisciplinary nature of scientific research necessitates a need for Open Data repositories that can archive data in support of publications in scientific journals. Recognising this need, even before GigaScience launched in 2012, GigaDB was already in place and taking data for a year before (making it 11 this year). Since GigaDB launched, there has been a consistent growth in this resource in terms of data volume, data discoverability and data re-use. In this commentary, we provide a retrospective of key changes over the last decade, and the role of Data Curation in enhancing the user experience. Furthermore we explore a much needed emphasis on enabling researchers to interact with and explore datasets prior to data download.
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Project description:Open science is key to PLOS Biology's mission, both in its daily operations and in the role we aspire to have in the scholarly ecosystem. Here, we reflect on open science at the journal and discuss how and why we shall continue to hold it central to everything we do.
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Project description:The abundant existence of proteins and regions that possess specific functions without being uniquely folded into unique 3D structures has become accepted by a significant number of protein scientists. Sequences of these intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) are characterized by a number of specific features, such as low overall hydrophobicity and high net charge which makes these proteins predictable. IDPs/IDPRs possess large hydrodynamic volumes, low contents of ordered secondary structure, and are characterized by high structural heterogeneity. They are very flexible, but some may undergo disorder to order transitions in the presence of natural ligands. The degree of these structural rearrangements varies over a very wide range. IDPs/IDPRs are tightly controlled under the normal conditions and have numerous specific functions that complement functions of ordered proteins and domains. When lacking proper control, they have multiple roles in pathogenesis of various human diseases. Gaining structural and functional information about these proteins is a challenge, since they do not typically "freeze" while their "pictures are taken." However, despite or perhaps because of the experimental challenges, these fuzzy objects with fuzzy structures and fuzzy functions are among the most interesting targets for modern protein research. This review briefly summarizes some of the recent advances in this exciting field and considers some of the basic lessons learned from the analysis of physics, chemistry, and biology of IDPs.
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Project description:Cryptococcus neoformans is the etiologic agent of cryptococcosis, a lethal worldwide disease. Synthetic biology could contribute to its better understanding through engineering genetic networks. However, its major challenge is the requirement of accessible genetic parts. The database presented here provides 23 biological parts for this organism in Synthetic Biology Open Language.
| S-EPMC9476951 | biostudies-literature
Project description:Our understanding of complex living systems is limited by our capacity to perform experiments in high throughput. While robotic systems have automated many traditional hand-pipetting protocols, software limitations have precluded more advanced maneuvers required to manipulate, maintain, and monitor hundreds of experiments in parallel. Here, we present Pyhamilton, an open-source Python platform that can execute complex pipetting patterns required for custom high-throughput experiments such as the simulation of metapopulation dynamics. With an integrated plate reader, we maintain nearly 500 remotely monitored bacterial cultures in log-phase growth for days without user intervention by taking regular density measurements to adjust the robotic method in real-time. Using these capabilities, we systematically optimize bioreactor protein production by monitoring the fluorescent protein expression and growth rates of a hundred different continuous culture conditions in triplicate to comprehensively sample the carbon, nitrogen, and phosphorus fitness landscape. Our results demonstrate that flexible software can empower existing hardware to enable new types and scales of experiments, empowering areas from biomanufacturing to fundamental biology.
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