Top Peer Reviewed Journals – Molecular Biology & Genetics
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Applied Category Theory for Genomics – an Initiative
Applied Category Theory for Genomics { An Initiative Yanying Wu1,2 1Centre for Neural Circuits and Behaviour, University of Oxford, UK 2Department of Physiology, Anatomy and Genetics, University of Oxford, UK 06 Sept, 2020 Abstract The ultimate secret of all lives on earth is hidden in their genomes { a totality of DNA sequences. We currently know the whole genome sequence of many organisms, while our understanding of the genome architecture on a systematic level remains rudimentary. Applied category theory opens a promising way to integrate the humongous amount of heterogeneous informations in genomics, to advance our knowledge regarding genome organization, and to provide us with a deep and holistic view of our own genomes. In this work we explain why applied category theory carries such a hope, and we move on to show how it could actually do so, albeit in baby steps. The manuscript intends to be readable to both mathematicians and biologists, therefore no prior knowledge is required from either side. arXiv:2009.02822v1 [q-bio.GN] 6 Sep 2020 1 Introduction DNA, the genetic material of all living beings on this planet, holds the secret of life. The complete set of DNA sequences in an organism constitutes its genome { the blueprint and instruction manual of that organism, be it a human or fly [1]. Therefore, genomics, which studies the contents and meaning of genomes, has been standing in the central stage of scientific research since its birth. The twentieth century witnessed three milestones of genomics research [1]. It began with the discovery of Mendel's laws of inheritance [2], sparked a climax in the middle with the reveal of DNA double helix structure [3], and ended with the accomplishment of a first draft of complete human genome sequences [4]. -
Tissue and Cell
TISSUE AND CELL AUTHOR INFORMATION PACK TABLE OF CONTENTS XXX . • Description p.1 • Impact Factor p.1 • Abstracting and Indexing p.1 • Editorial Board p.1 • Guide for Authors p.3 ISSN: 0040-8166 DESCRIPTION . Tissue and Cell is devoted to original research on the organization of cells, subcellular and extracellular components at all levels, including the grouping and interrelations of cells in tissues and organs. The journal encourages submission of ultrastructural studies that provide novel insights into structure, function and physiology of cells and tissues, in health and disease. Bioengineering and stem cells studies focused on the description of morphological and/or histological data are also welcomed. Studies investigating the effect of compounds and/or substances on structure of cells and tissues are generally outside the scope of this journal. For consideration, studies should contain a clear rationale on the use of (a) given substance(s), have a compelling morphological and structural focus and present novel incremental findings from previous literature. IMPACT FACTOR . 2020: 2.466 © Clarivate Analytics Journal Citation Reports 2021 ABSTRACTING AND INDEXING . Scopus PubMed/Medline Cambridge Scientific Abstracts Current Awareness in Biological Sciences Current Contents - Life Sciences Embase Embase Science Citation Index Web of Science EDITORIAL BOARD . Editor Pietro Lupetti, University of Siena, Siena, Italy AUTHOR INFORMATION PACK 1 Oct 2021 www.elsevier.com/locate/tice 1 Managing Editor Giacomo Spinsanti, University of Siena, -
New Editor on Journal of Cell Science Michael Way (Editor-In-Chief)
© 2019. Published by The Company of Biologists Ltd | Journal of Cell Science (2019) 132, jcs229740. doi:10.1242/jcs.229740 EDITORIAL New Editor on Journal of Cell Science Michael Way (Editor-in-Chief) As someone who has worked on things related to the actin cytoskeleton my whole research career, the nucleus was not something I paid much attention to. Yes, there were scattered historical reports of actin in the nucleus long before I started my PhD, but no one believed actin was really there of course – it was all an artefact of fixation, you know. Nuclear actin was taboo and no one talked about it at the meetings I went to as a student and postdoc. How wrong we were – today nuclear actin is alive and kicking, although there are definitely more questions than answers concerning what it is actually doing there. We now appreciate that the nucleus contains a wide assortment of proteins associated with the cytoplasmic actin cytoskeleton including myosin motors and actin nucleators such as the Arp2/3 complex. In addition, it should not be forgotten that many chromatin-associated complexes including SWI/SNF and INO80/ SWR also contain multiple actin-related proteins, as well as actin itself. It strikes me that maybe we should all be paying more attention to the nucleus and not just because it contains my favourite proteins! Maybe that’s why, in recent years, we’ve been seeing more submissions to JCS that are focused on different aspects of the nucleus and that traditionally appeared in journals with ‘molecular’ in their titles. -
Distinctive Regulatory Architectures of Germline-Active and Somatic Genes in C
Downloaded from genome.cshlp.org on October 7, 2021 - Published by Cold Spring Harbor Laboratory Press Research Distinctive regulatory architectures of germline-active and somatic genes in C. elegans Jacques Serizay, Yan Dong, Jürgen Jänes, Michael Chesney, Chiara Cerrato, and Julie Ahringer The Gurdon Institute and Department of Genetics, University of Cambridge, CB2 1QN Cambridge, United Kingdom RNA profiling has provided increasingly detailed knowledge of gene expression patterns, yet the different regulatory ar- chitectures that drive them are not well understood. To address this, we profiled and compared transcriptional and regu- latory element activities across five tissues of Caenorhabditis elegans, covering ∼90% of cells. We find that the majority of promoters and enhancers have tissue-specific accessibility, and we discover regulatory grammars associated with ubiquitous, germline, and somatic tissue–specific gene expression patterns. In addition, we find that germline-active and soma-specific promoters have distinct features. Germline-active promoters have well-positioned +1 and −1 nucleosomes associated with a periodic 10-bp WW signal (W = A/T). Somatic tissue–specific promoters lack positioned nucleosomes and this signal, have wide nucleosome-depleted regions, and are more enriched for core promoter elements, which largely differ between tissues. We observe the 10-bp periodic WW signal at ubiquitous promoters in other animals, suggesting it is an ancient conserved signal. Our results show fundamental differences in regulatory architectures of germline and somatic tissue–specific genes, uncover regulatory rules for generating diverse gene expression patterns, and provide a tissue-specific resource for future studies. [Supplemental material is available for this article.] Cell type–specific transcription regulation underlies production tissues are achieved and whether expression is governed by dis- of the myriad of different cells generated during development. -
Personal and Population Genomics of Human Regulatory Variation
Downloaded from genome.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press Research Personal and population genomics of human regulatory variation Benjamin Vernot, Andrew B. Stergachis, Matthew T. Maurano, Jeff Vierstra, Shane Neph, Robert E. Thurman, John A. Stamatoyannopoulos,1 and Joshua M. Akey1 Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA The characteristics and evolutionary forces acting on regulatory variation in humans remains elusive because of the difficulty in defining functionally important noncoding DNA. Here, we combine genome-scale maps of regulatory DNA marked by DNase I hypersensitive sites (DHSs) from 138 cell and tissue types with whole-genome sequences of 53 geo- graphically diverse individuals in order to better delimit the patterns of regulatory variation in humans. We estimate that individuals likely harbor many more functionally important variants in regulatory DNA compared with protein-coding regions, although they are likely to have, on average, smaller effect sizes. Moreover, we demonstrate that there is sig- nificant heterogeneity in the level of functional constraint in regulatory DNA among different cell types. We also find marked variability in functional constraint among transcription factor motifs in regulatory DNA, with sequence motifs for major developmental regulators, such as HOX proteins, exhibiting levels of constraint comparable to protein-coding regions. Finally, we perform a genome-wide scan of recent positive selection and identify hundreds of novel substrates of adaptive regulatory evolution that are enriched for biologically interesting pathways such as melanogenesis and adipo- cytokine signaling. These data and results provide new insights into patterns of regulatory variation in individuals and populations and demonstrate that a large proportion of functionally important variation lies beyond the exome. -
Theory of Cytoskeletal Reorganization During Crosslinker-Mediated Mitotic Spindle Assembly
bioRxiv preprint doi: https://doi.org/10.1101/419135; this version posted March 1, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Theory of cytoskeletal reorganization during crosslinker-mediated mitotic spindle assembly A. R. Lamson, C. J. Edelmaier, M. A. Glaser, and M. D. Betterton Abstract Cells grow, move, and respond to outside stimuli by large-scale cytoskeletal reorganization. A prototypical example of cytoskeletal remodeling is mitotic spindle assembly, during which micro- tubules nucleate, undergo dynamic instability, bundle, and organize into a bipolar spindle. Key mech- anisms of this process include regulated filament polymerization, crosslinking, and motor-protein activity. Remarkably, using passive crosslinkers, fission yeast can assemble a bipolar spindle in the absence of motor proteins. We develop a torque-balance model that describes this reorganization due to dynamic microtubule bundles, spindle-pole bodies, the nuclear envelope, and passive crosslink- ers to predict spindle-assembly dynamics. We compare these results to those obtained with kinetic Monte Carlo-Brownian dynamics simulations, which include crosslinker-binding kinetics and other stochastic effects. Our results show that rapid crosslinker reorganization to microtubule overlaps facilitates crosslinker-driven spindle assembly, a testable prediction for future experiments. Combin- ing these two modeling techniques, we illustrate a general method for studying cytoskeletal network reorganization. 1 bioRxiv preprint doi: https://doi.org/10.1101/419135; this version posted March 1, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. -
Using Open Access Literature to Guide Full-Text Query Formulation Heather A
Using open access literature to guide full-text query formulation Heather A. Piwowar and Wendy W. Chapman Background Much scientific knowledge is contained in the details of the full-text biomedical literature. Most research in automated retrieval presupposes that the target literature can be downloaded and preprocessed prior to query. Unfortunately, this is not a practical or maintainable option for most users due to licensing restrictions, website terms of use, and sheer volume. Scientific article full-text is increasingly queriable through portals such as PubMed Central, Highwire Press, Scirus, and Google Scholar. However, because these portals only support very basic Boolean queries and full text is so expressive, formulating an effective query is a difficult task for users. We propose improving the formulation of full-text queries by using the open access literature as a proxy for the literature to be searched. We evaluated the feasibility of this approach by building a high-precision query for identifying studies that perform gene expression microarray experiments. Methodology and Results We built decision rules from unigram and bigram features of the open access literature. Minor syntax modifications were needed to translate the decision rules into the query languages of PubMed Central, Highwire Press, and Google Scholar. We mapped all retrieval results to PubMed identifiers and considered our query results as the union of retrieved articles across all portals. Compared to our reference standard, the derived full- text query found 56% (95% confidence interval, 52% to 61%) of intended studies, and 90% (86% to 93%) of studies identified by the full-text search met the reference standard criteria. -
Genomic Approaches for Understanding the Genetics of Complex Disease
Downloaded from genome.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Perspective Genomic approaches for understanding the genetics of complex disease William L. Lowe Jr.1 and Timothy E. Reddy2,3 1Division of Endocrinology, Metabolism and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA; 2Department of Biostatistics and Bioinformatics, Duke University Medical School, Durham, North Carolina 27708, USA; 3Center for Genomic and Computational Biology, Duke University Medical School, Durham, North Carolina 27708, USA There are thousands of known associations between genetic variants and complex human phenotypes, and the rate of novel discoveries is rapidly increasing. Translating those associations into knowledge of disease mechanisms remains a fundamental challenge because the associated variants are overwhelmingly in noncoding regions of the genome where we have few guiding principles to predict their function. Intersecting the compendium of identified genetic associations with maps of regulatory activity across the human genome has revealed that phenotype-associated variants are highly enriched in candidate regula- tory elements. Allele-specific analyses of gene regulation can further prioritize variants that likely have a functional effect on disease mechanisms; and emerging high-throughput assays to quantify the activity of candidate regulatory elements are a promising next step in that direction. Together, these technologies have created the ability to systematically and empirically test hypotheses about the function of noncoding variants and haplotypes at the scale needed for comprehensive and system- atic follow-up of genetic association studies. Major coordinated efforts to quantify regulatory mechanisms across genetically diverse populations in increasingly realistic cell models would be highly beneficial to realize that potential. -
Journal of Cell Science & Therapy
Journal of Cell Science & Therapy 2021 Conference Announcement Mark on Your Calendar, Stem Cell 2021 is coming soon!! Ahmed Hegazi Pursued by the Successful Completion of the Stem Cell discuss the latest developments in the field of Stem Cell and Conference, we are facilitating its next version “International Regenerative Medicine as well. Current studies of Stem cell Conference on Stem Cell” in Osaka, Japan on March 16-17, are examining how undifferentiated organisms might be 2021. utilized to anticipate or fix sicknesses and wounds, for The theme attracts for the Stem Cell 2021 is “Frontiers in example, Parkinson's illness, type 1 diabetes, coronary illness, Stem Cells & Turning Ideas into Reality”. spinal string damage, strong dystrophy, Alzheimer's malady, Welcoming all of you for our Stem Cell 2021 involves strokes, osteoarthritis, vision and hearing misfortune. extraordinary delight, warmth and passion. We anticipate all Immature microorganisms could likewise be utilized to of you sharing your knowledge and information, look into supplant or repair tissue harmed by ailment or damage. thoughts and to make a sprinkle with new upgrades at this 2- days occasion. This time we have introduced some contemporary and recently updated and advanced highlights of Life sciences in Stem Cell 2021. Stem Cell 2021 wish to bring all the medicinal science, chemical engineering & tissue regeneration professionals and scientists under material science fields for our Smart Materials Meeting to collaborate and share their insight and their most Cancer Stem Cells, Bio-Makers Of Cancer Stem Cells, Stem current research to the whole Material Science Community. Cell Biology & Advances, Advanced In Tissue Regeneration, Also this time, Our International Conference on Stem Cell Embryonic Stem Cell, Reprogramming In Stem Cell & will be aims to haven for Multinational organizations, Transplantation, Treatment Of Diseases By Stem Cell entrepreneurs across the globe, the researchers and Therapeutics, Stem Cell Banking, Novel Stem Cell Therapy, academicians. -
Ultrastructure in Ochromonas Danica
EFFECTS OF CHLORAMPHENICOL ON CHLOROPLAST AND MITOCHONDRIAL ULTRASTRUCTURE IN OCHROMONAS DANICA HEIDI SMITH-JOHANNSEN and SARAH P . GIBBS From the Department of Biology, McGill University, Montreal 110, P. Q., Canada ABSTRACT The effect of chloramphenicol (CAP) on cell division and organelle ultrastructure was studied during light-induced chloroplast development in the Chrysophyte alga, Ochromonas danica . Since the growth rate of the CAP-treated cells is the same as that of the control cells for the first 12 hr in the light, CAP is presumed to be acting during that interval solely by inhibiting protein synthesis on chloroplast and mitochondrial ribosomes. CAP markedly inhibits chloroplast growth and differentiation . During the first 12 hr in the light, chloro- phyll synthesis is inhibited by 9317/c , the formation of new thylakoid membranes is reduced by 91 70, and the synthesis of chloroplast ribosomes is inhibited by 81 %. Other chloroplast- associated abnormalities which occur during the first 12 hr and become more pronounced with extended CAP treatment are the presence of prolamellar bodies and of abnormal stacks of thylakoids, the proliferation of the perinuclear reticulum, and the accumulation of dense granular material between the chloroplast envelope and the chloroplast endo- plasmic reticulum . CAP also causes a progressive loss of the mitochondrial cristae, which is paralleled by a decline in the growth rate of the cells, but it has no effect on the synthesis of mitochondrial ribosomes. We postulate that one or more chloroplast ribosomal proteins are synthesized on chloroplast ribosomes, whereas mitochondrial ribosomal pro- teins are synthesized on cytoplasmic ribosomes. INTRODUCTION Both chloroplasts and mitochondria are known insoluble inner membrane proteins, are believed to contain DNA and RNA and to have all the to be synthesized on mitochondrial ribosomes (3) . -
Since January 2020 Elsevier Has Created a COVID-19 Resource Centre with Free Information in English and Mandarin on the Novel Coronavirus COVID- 19
Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID- 19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. Available online at www.sciencedirect.com ScienceDirect Editorial overview: Membrane traffic in the time of COVID-19 Frances M. Brodsky and Jennifer L. Stow Current Opinion in Cell Biology 2020, 65:iii–v This overview comes from a themed issue on Membrane Trafficking Edited by Frances M. Brodsky and Jennifer L. Stow https://doi.org/10.1016/j.ceb.2020.09.003 0955-0674/© 2020 Published by Elsevier Ltd. Frances M. Brodsky We write this editorial emerging from lockdown in countries across the Division of Biosciences, University College world in the face of the COVID-19 pandemic. These have been chal- London, Gower Street, London, WC1E 6BT, lenging, frightening, and too often catastrophic times for many. Such times UK lead to evaluation of one’s own enterprise in the context of a global *Corresponding author: Brodsky, Frances M. -
New Doors to Open…And So Many! | Journal of Cell Science
New doors to open…and so many! | Journal of Cell Science Advertisement California Institute of Technology Log in Advanced search Home Articles About us For authors Journal info Contacts EDITORIAL New doors to open…and so many! Previous Article Next Article D.M. Glover Journal of Cell Science 2000 113: 359-360; This Issue Article Info & metrics Email Summary Share The pursuit of science is a wonderful journey of Citation Tools discovery along which there are a myriad of avenues to Alerts be explored. There have always been so many objects of fascination, so many questions to ask along the way, © Request Permissions We use cookies to help us improve this website. Learn more so many possibilities to understand new principles, that making the decision about which problem to address Article navigation and then having the self-discipline to explore it in depth Top challenge all who practice the art. How then are we, as Article cell biologists, to cope with the mountain of information Info & metrics that is accumulating as we enter the twenty-first https://jcs.biologists.org/content/113/3/359.long[8/10/2020 3:19:01 PM] New doors to open…and so many! | Journal of Cell Science century? We now have the potential to decipher the primary sequences of every single cellular protein for Related articles several model organisms. Just how are we to put this Web of Science PubMed information into an intelligible framework for Google Scholar understanding cell physiology? The turn of a century is a time at which we can permit ourselves the luxury of Cited by..