Editorial: Bioinformatics of Genome Regulation, Volume II
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ABSTRACT:
SUBMITTER: Orlov Y
PROVIDER: S-EPMC8606529 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Recent experiments reveal that the volume of adhered cells is reduced as their basal area is increased. During spreading, the cell volume decreases by several thousand cubic micrometers, corresponding to large pressure changes of the order of megapascals. We show theoretically that the volume regulation of adhered cells is determined by two concurrent conditions: mechanical equilibrium with the extracellular environment and a generalization of Donnan (electrostatic) equilibrium that accounts for active ion transport. Spreading affects the structure and hence activity of ion channels and pumps, and indirectly changes the ionic content in the cell. We predict that more ions are released from the cell with increasing basal area, resulting in the observed volume-area dependence. Our theory is based on a minimal model and describes the experimental findings in terms of measurable, mesoscale quantities. We demonstrate that two independent experiments on adhered cells of different types fall on the same master volume-area curve. Our theory also captures the measured osmotic pressure of adhered cells, which is shown to depend on the number of proteins confined to the cell, their charge, and their volume, as well as the ionic content. This result can be used to predict the osmotic pressure of cells in suspension.
| S-EPMC7084104 | biostudies-literature
Project description:Forkhead box O (FOXO) transcription factors are key players in diverse cellular processes affecting tumorigenesis, stem cell maintenance and lifespan. To gain insight into the mechanisms of FOXO-regulated target gene expression, we studied genome-wide effects of FOXO3 activation. Profiling RNA polymerase II changes shows that FOXO3 regulates gene expression through transcription initiation. Correlative analysis of FOXO3 and RNA polymerase II ChIP-seq profiles demonstrates FOXO3 to act as a transcriptional activator. Furthermore, this analysis reveals a significant part of FOXO3 gene regulation proceeds through enhancer regions. FOXO3 binds to pre-existing enhancers and further activates these enhancers as shown by changes in histone acetylation and RNA polymerase II recruitment. In addition, FOXO3-mediated enhancer activation correlates with regulation of adjacent genes and pre-existence of chromatin loops between FOXO3 bound enhancers and target genes. Combined, our data elucidate how FOXOs regulate gene transcription and provide insight into mechanisms by which FOXOs can induce different gene expression programs depending on chromatin architecture.
| S-EPMC3564262 | biostudies-literature
Project description:BackgroundWe provide volume II of a distributional atlas of aquatic insects for the eastern USA state of Ohio. This treatment of stoneflies (Plecoptera) is companion to Armitage et al. (2011) on caddisflies (Trichoptera). We build on a recent analysis of Ohio stonefly diversity patterns based on large drainages (DeWalt et al. 2012), but add 3717 new records to the data set. We base most analyses on the United States Geological Survey Hierarchical Unit Code eight (HUC8) drainage scale. In addition to distributional maps for each species, we provide analyses of species richness versus HUC8 drainage area and the number of unique locations in a HUC8 drainage, species richness versus Ohio counties, analyze adult presence phenology throughout the year, and demonstrate stream size range affiliation for each species.New informationThis work is based on a total of 7797 specimen records gathered from 21 regional museums, agency data, personal collections, and from the literature Table 1. To our knowledge this is the largest stonefly data set available for a similarly sized geopolitical area anywhere in the world. These data are made available as a Darwin Core Archive supported by the Pensoft Integrated Publishing Toolkit (DeWalt et al. 2016b). All known published papers reporting stoneflies from Ohio are detailed in Suppl. material 1. We recovered 102 species from Ohio, including all nine Nearctic families Table 2?. Two species were removed from the DeWalt et al. (2012) list and two new state records added. Perlidae (32 spp.) was most speciose, compared to the low diversity Pteronarcyidae (2 spp.) and Peltoperlidae (1 sp.). The richest HUC8 drainages occurred in northeastern, south-central, and southern regions of the state where drainages were heavily forested, had the highest slopes, and were contained within or adjacent to the unglaciated Allegheny and Appalachian Plateaus. Species poor drainages occurred mainly in the northwestern region where Wisconsinan aged lake plains climaxed to an expansive wooded wetland, the Black Swamp. The unglaciated Lower Scioto drainage (72 spp.) in south-central Ohio supported the greatest species richness. There was no relationship between species richness and HUC8 drainage size, but the number of unique locations in a drainage strongly related to species richness. All Ohio counties were represented in the data set with Hocking County (59 spp.) of the Lower Scioto drainage being the richest and most heavily sampled. Adult presence phenology was influenced by phylogenetic relationships such that the superfamily Nemouroidea (Capniidae, Leuctridae, Nemouridae, and Taeniopterygidae) generally emerged in winter and spring while the superfamilies Pteronarcyoidea (Pteronarcyidae, Peltoperlidae) and Perloidea (Chloroperlidae, Perlidae, Perlodidae) emerged later, some species continuing emergence through summer months. Species often occupied specific stream size ranges, while others were generalists. Two species once histrorically abundant in the western Lake Erie Bass Islands no longer reside there. Each of the 102 species is discussed in detail, including several that require additional collecting efforts to confirm their identities, presence, and distribution in Ohio.
| S-EPMC5136677 | biostudies-literature
Project description:Three-dimensional ultrasound is an established diagnostic imaging technique in many specialties. However, in neonates, infants and children three-dimensional ultrasound still is underutilized, partially due to time constraints for post-processing and restricted availability, of devices as well as dedicated pediatric transducers. Also reimbursement issues still need to be addressed. This editorial review presents more or less established pediatric three-dimensional ultrasound applications with proven diagnostic benefit as well as potential future applications of three-dimensional/four-dimensional ultrasound in infants and children, aiming at enhancing research and promoting practical use of three-dimensional ultrasound in relevant pediatric conditions. Particularly, applications in neonatal neurosonography, ultrasound of the urogenital tract as well as some other small part and miscellaneous queries are highlighted. Additional other potential and future indications are discussed briefly, also mentioning restrictions and potential future developments. In summary, three-dimensional ultrasound holds some potential to widen sonographic diagnostic capabilities throughout childhood and hopefully will be increasingly investigated and introduced into clinical practice provided respective equipment and pediatric three-dimensional/four-dimensional ultrasound transducers become available.
| S-EPMC4579731 | biostudies-literature
Project description:BACKGROUND: We have compared 38 isolates of the SARS-CoV complete genome. The main goal was twofold: first, to analyze and compare nucleotide sequences and to identify positions of single nucleotide polymorphism (SNP), insertions and deletions, and second, to group them according to sequence similarity, eventually pointing to phylogeny of SARS-CoV isolates. The comparison is based on genome polymorphism such as insertions or deletions and the number and positions of SNPs. RESULTS: The nucleotide structure of all 38 isolates is presented. Based on insertions and deletions and dissimilarity due to SNPs, the dataset of all the isolates has been qualitatively classified into three groups each having their own subgroups. These are the A-group with "regular" isolates (no insertions / deletions except for 5' and 3' ends), the B-group of isolates with "long insertions", and the C-group of isolates with "many individual" insertions and deletions. The isolate with the smallest average number of SNPs, compared to other isolates, has been identified (TWH). The density distribution of SNPs, insertions and deletions for each group or subgroup, as well as cumulatively for all the isolates is also presented, along with the gene map for TWH. Since individual SNPs may have occurred at random, positions corresponding to multiple SNPs (occurring in two or more isolates) are identified and presented. This result revises some previous results of a similar type. Amino acid changes caused by multiple SNPs are also identified (for the annotated sequences, as well as presupposed amino acid changes for non-annotated ones). Exact SNP positions for the isolates in each group or subgroup are presented. Finally, a phylogenetic tree for the SARS-CoV isolates has been produced using the CLUSTALW program, showing high compatibility with former qualitative classification. CONCLUSIONS: The comparative study of SARS-CoV isolates provides essential information for genome polymorphism, indication of strain differences and variants evolution. It may help with the development of effective treatment.
| S-EPMC434493 | biostudies-literature
Project description:A dataset of 103 SARS-CoV isolates (101 human patients and 2 palm civets) was investigated on different aspects of genome polymorphism and isolate classification. The number and the distribution of single nucleotide variations (SNVs) and insertions and deletions, with respect to a "profile", were determined and discussed ("profile" being a sequence containing the most represented letter per position). Distribution of substitution categories per codon positions, as well as synonymous and non-synonymous substitutions in coding regions of annotated isolates, was determined, along with amino acid (a.a.) property changes. Similar analysis was performed for the spike (S) protein in all the isolates (55 of them being predicted for the first time). The ratio Ka/Ks confirmed that the S gene was subjected to the Darwinian selection during virus transmission from animals to humans. Isolates from the dataset were classified according to genome polymorphism and genotypes. Genome polymorphism yields to two groups, one with a small number of SNVs and another with a large number of SNVs, with up to four subgroups with respect to insertions and deletions. We identified three basic nine-locus genotypes: TTTT/TTCGG, CGCC/TTCAT, and TGCC/TTCGT, with four subgenotypes. Both classifications proposed are in accordance with the new insights into possible epidemiological spread, both in space and time.
| S-EPMC5172477 | biostudies-literature