bluuebunny/crossref_metadata_2025_split huggingface dataset:
Taxonomic, temporal, and spatial variation in the dynamics of High-Arctic arthropod populations
Authors: Høye Toke T. , Loboda Sarah , Koltz Amanda M. , Gillespie Mark A. K. , Bowden Joseph J. , Schmidt Niels M. 
Published: April 2020

ABSTRACTTime-series data on arthropod populations are critical for understanding the magnitude, direction, and drivers of abundance changes. However, most arthropod monitoring programs are short-lived and limited in taxonomic resolution and spatial extent. Consequently, variation in population dynamics among taxa and habitats remains poorly understood. Monitoring data from the Arctic are particularly underrepresented, yet important to assessments of species abundance changes because many anthropogenic drivers of change that are present in other regions are absent in polar regions. Here, we utilise 24 years of abundance data from Zackenberg in High-Arctic Greenland, which is the longest running Arctic arthropod monitoring program, to study temporal trends in abundance. Despite a strong warming signal in air temperature, we only find evidence of weak temporal trends in arthropod abundances across most taxa. These trends are more pronounced in the most recent decade, with change point analyses suggesting distinct non-linear dynamics within some functional groups such as predators and detritivores. Although the abundances of many taxa were correlated, we detected both positive and negative correlations, suggesting that multiple processes are affecting arthropod populations even in this relatively simple Arctic food web. Finally, we found clear differences among species within single families of arthropods, indicating that an apparent lack of change in abundance at broader taxonomic or functional levels could mask substantial species-specific trends. Our results reiterate the need for more basic research into the life-history, ecology, and adaptation of arthropod species to better understand their sensitivity to global changes.Significance statementTerrestrial arthropods, including insects and spiders, serve critical ecosystem functions and are excellent indicators of environmental change due to their physiology, short generation time, and abundance. The Arctic, with its rapid climate change and limited direct anthropogenic impact, is ideal for examining arthropod population dynamics. We use the most comprehensive, standardized dataset available on Arctic arthropods to evaluate the variability in population dynamics for the most common arthropod groups at various taxonomic levels across 24 years. Our results highlight that temporal trends of arthropod populations seem less directional in the Arctic than in temperate regions. Although abundances of some arthropod taxa are declining, particularly in recent decades, population trends still display high variation among time periods, taxa, and habitats.
The qBED track: a novel genome browser visualization for point processes
Authors: Moudgil Arnav , Li Daofeng , Hsu Silas , Purushotham Deepak , Wang Ting , Mitra Robi D. 
Published: April 2020

AbstractSummaryTransposon calling cards is a genomic assay for identifying transcription factor binding sites in both bulk and single cell experiments. Here we describe the qBED format, an open, text-based standard for encoding and analyzing calling card data. In parallel, we introduce the qBED track on the WashU Epigenome Browser, a novel visualization that enables researchers to inspect calling card data in their genomic context. Finally, through examples, we demonstrate that qBED files can be used to visualize non-calling card datasets, such as CADD scores and GWAS/eQTL hits, and may have broad utility to the genomics community.Availability and ImplementationThe qBED track is available on the WashU Epigenome Browser (http://epigenomegateway.wustl.edu/browser), beginning with version 46. Source code for the WashU Epigenome Browser with qBED support is available on GitHub (http://github.com/arnavm/eg-reactandhttp://github.com/lidaof/eg-react). We have also released a tutorial on how to upload qBED data to the browser (dx.doi.org/10.17504/protocols.io.bca8ishw).
HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data
Authors: Jain Dhawal , Chu Chong , Alver Burak Han , Lee Soohyun , Lee Eunjung Alice , Park Peter J. 
Published: April 2020

AbstractHi-C is a common technique for assessing three-dimensional chromatin conformation. Recent studies have shown that long-range interaction information in Hi-C data can be used to generate chromosome-length genome assemblies and identify large-scale structural variations. Here, we demonstrate the use of Hi-C data in detecting mobile transposable element (TE) insertions genome-wide. Our pipeline HiTea (Hi-C basedTransposableelementanalyzer) capitalizes on clipped Hi-C reads and is aided by a high proportion of discordant read pairs in Hi-C data to detect insertions of three major families of active human TEs. Despite the uneven genome coverage in Hi-C data, HiTea is competitive with the existing callers based on whole genome sequencing (WGS) data and can supplement the WGS-based characterization of the TE insertion landscape. We employ the pipeline to identify TE insertions from human cell-line Hi-C samples. HiTea is available athttps://github.com/parklab/HiTeaand as a Docker image.
Age-dependent VDR peak DNA methylation as a mechanism for latitude-dependent MS risk
Authors: Ong Lawrence T C , Schibeci Stephen D , Fewings Nicole L , Booth David R , Parnell Grant P 
Published: April 2020

AbstractBackgroundThe mechanisms linking UV radiation and vitamin D exposure to the risk of acquiring the latitude and critical period dependent autoimmune disease, multiple sclerosis, is unclear. We examined the effect of vitamin D on DNA methylation as well as DNA methylation at vitamin D receptor binding sites in adult and paediatric myeloid cells.ResultsVery few DNA methylation changes occurred in adult and paediatric cells treated with calcitriol. However, several VDR binding sites across the genome demonstrated increased DNA methylation in cells of adult origin. Genes associated with these VDR binding sites were enriched for intracellular signalling and cell activation pathways, suggesting that age-dependent potential for myeloid cell differentiation and adaptive immune system regulation may be encoded for by DNA methylation.ConclusionsThese results suggest vitamin D exposure at critical periods in immune system development may contribute to the well characterised latitude related differences in autoimmune disease incidence.
Evolutionary Genetic Species Detected in Prokaryotes by Applying the K/θ Ratio to DNA Sequences
Authors: Birky C. William , Maughan Heather 
Published: April 2020

AbstractPrevious papers in this series described the “evolutionary genetic species concept” which is based on population genetic theory and should be applicable to any organism. Also described was a species criterion, the K/θ ratio, that delimits independently evolving evolutionary species based on single-gene sequences, and its application to sexual and asexual eukaryotes was illustrated. Here, we show how the evolutionary genetic species concept and the K/θ ratio can be applied to bacteria, using the sequences from some genes of the core genome that are rarely, if ever, transferred horizontally between different species. This completes the demonstration that K/θ is a general method for species delimitation, applicable to all organisms. Also, it adds to the evidence that bacteria have species in the most general sense, even though they have the ability to exchange genes across species boundaries. Finally, we show that a published critique of the use of K/θ ≥ 4 as a criterion for independently evolving species rests on two errors in the application of population/evolutionary genetic theory.
Overexpressed Nup88 stabilized through interaction with Nup62 promotes NFκB dependent pathways in cancer
Authors: Singh Usha , Samaiya Atul , Mishra Ram Kumar 
Published: April 2020

AbstractNuclear pores control nucleo-cytoplasmic trafficking and directly or indirectly regulate vital cellular processes. Nup88, important for Crm1 mediated nuclear export process, is overexpressed in many cancers. A positive correlation exists between progressive stages of cancer and Nup88 expression. However, links between Nup88 overexpression and head and neck cancer are insignificant, and mechanistic details are non-existent. Here, we report that Nup88 exhibits positive correlation in head and neck cancer in addition to elevated Nup62 levels. We demonstrate that Nup88 interacts with Nup62 in a cell-cycle and glycosylation independent manner. The overexpression of Nup88 or Nup62 imparts proliferation and migration advantages to cells. We further report that the interaction with Nup62 stabilizes Nup88 by inhibiting proteasome-mediated degradation of overexpressed Nup88. Overexpressed Nup88 is stabile and partly inside the nucleus and can interact with NFκB (p65). Nup88 overexpression induces proliferative and inflammatory responses downstream of p65. Altogether, we suggest that simultaneous overexpression of Nup62 and Nup88 in head and neck cancer stabilizes overexpressed Nup88. Stable Nup88 interacts with p65 and induces inflammatory, proliferative, and migratory advantages to cells, which perhaps is the underlying mechanism driving tumorigenic transformations.
Transient high glucose causes delayed wound healing by the DNMT1-mediated Ang-1/NF-κB pathway
Authors: Zhao Jingling , Yang Shuai , Chen Lei , Yang Ronghua , Xu Yingbin , Xie Julin , Liu Xusheng , Shu Bin , Qi Shaohai 
Published: April 2020

AbstractThe progression of diabetic complications does not halt despite termination of hyperglycemia, suggesting a “metabolic memory” phenomenon. However, whether metabolic memory exists in and affects the healing of diabetic wounds, as well as the underlying molecular mechanisms, remain unclear. In this study, we found that wound healing was delayed and angiogenesis was decreased in diabetic mice, despite normalization of glycemic control. Thus, we hypothesized that transient hyperglycemic spikes may be a risk factor for diabetic wound healing. We showed that transient hyperglycemia caused persistent damage to the vascular endothelium. Transient hyperglycemia directly upregulated DNMT1 expression, leading to the hypermethylation of Ang-1 and reduced Ang-1 expression, which, in turn, induced long-lasting activation of nuclear factor (NF)-κB and subsequent endothelial dysfunction. An in vivo study further showed that inhibition of DNMT1 promoted angiogenesis and accelerated diabetic wound healing by regulating the Ang-1/NF-κB signaling pathway. These results highlight the dramatic and long-lasting effects of transient hyperglycemic spikes on wound healing and suggest that DNMT1 is a novel target for diabetic vascular complications.
Genomic and immunogenic changes over the history of the Viral Hemorrhagic Septicemia (VHS-IVb) fish virus (=Piscine novirhabdovirus) in the Laurentian Great Lakes
Authors: Niner Megan D. , Stepien Carol A. , Gorgoglione Bartolomeo , Leaman Douglas W. 
Published: April 2020

AbstractViral Hemorrhagic Septicemia Virus (VHSV) (=Piscine novirhabdovirus) appeared in the Laurentian Great Lakes in 2005, constituting a unique and highly virulent genogroup (IVb), which killed >32 fish species in large 2005 and 2006. Periods of apparent dormancy punctuated smaller outbreaks in 2007, 2008, and 2017. We conducted the first whole genome analysis of IVb, evaluating its evolutionary changes using 46 isolates, in reference to immunogenicity in cell culture, and the genomes of other VHS genogroups (I–IVa) and other Novirhabdoviruses. IVb isolates had 253 genomic nucleotide substitutions (2.3% of the total 11,158 nucleotides), with 85 (16.6%) being non-synonymous. The greatest number of substitutions occurred in the non-coding region (NCDS; 4.3%) followed by theNv-(3.8%), andM-(2.8%) genes. TheM-gene possessed the greatest proportions of amino acid changes (52.9%), followed by theNv-(50.0%),G-(48.6%),N-(35.7%) andL-(23.1%) genes. Among VHS genogroups, IVa from the northeastern Pacific exhibited the fastest substitution rate (2.01×10-3), followed by Ivb (6.64×10−5), and I/III from Europe (4.09×10−5). A 2016 gizzard shad isolate from Lake Erie was the most divergent IVb isolate (38 NT, 15.0%, 15 AA), yet exhibited reduced virulence within vitroimmunogenicity analyses, as did other 2016 isolates, in comparison to the first IVb isolate (2003). The 2016 isolates exhibited lower impact on innate antiviral responses, suggesting phenotypic effects. Results suggest continued sequence change and lower virulence over the history of IVb, which may facilitate its long-term persistence in fish host populations.
A validation scale to determine the readiness of environmental DNA assays for routine species monitoring
Authors: Thalinger Bettina , Deiner Kristy , Harper Lynsey R. , Rees Helen C. , Blackman Rosetta C. , Sint Daniela , Traugott Michael , Goldberg Caren S. , Bruce Kat 
Published: April 2020

AbstractThe use of environmental DNA (eDNA) analysis for species monitoring requires rigorous validation - from field sampling to the analysis of PCR-based results - for meaningful application and interpretation. Assays targeting eDNA released by individual species are typically validated with no predefined criteria to answer specific research questions in one ecosystem. Hence, the general applicability of assays as well as associated uncertainties and limitations, often remain undetermined. The absence of clear guidelines for assay validation prevents targeted eDNA assays from being incorporated into species monitoring and policy; thus, their establishment is essential for realizing the potential of eDNA-based surveys. We describe the measures and tests necessary for successful validation of targeted eDNA assays and the associated pitfalls to form the basis of guidelines. A list of 122 variables was compiled, consolidated into 14 thematic blocks, (e.g. “in silicoanalysis”), and arranged on a 5-level validation scale from “incomplete” to “operational” with defined minimum validation criteria for each level. These variables were evaluated for 546 published single-species assays. The resulting dataset was used to provide an overview of current validation practices and test the applicability of the validation scale for future assay rating. Of the 122 variables, 20% to 76% were reported; the majority (30%) of investigated assays were classified as Level 1 (incomplete), and 15% did not achieve this first level. These assays were characterised by minimalin silicoandin vitrotesting, but their share in annually published eDNA assays has declined since 2014. The meta-analysis demonstrates the suitability of the 5-level validation scale for assessing targeted eDNA assays. It is a user-friendly tool to evaluate previously published assays for future research and routine monitoring, while also enabling the appropriate interpretation of results. Finally, it provides guidance on validation and reporting standards for newly developed assays.
Direct readout of heterochromatic H3K9me3 regulates DNMT1-mediated maintenance DNA methylation
Authors: Ren Wendan , Fan Huitao , Grimm Sara A , Guo Yiran , Kim Jae Jin , Li Linhui , Petell Christopher James , Tan Xiao-Feng , Zhang Zhi-Min , Coan John P. , Yin Jiekai , Gao Linfeng , Cai Ling , Detrick Brittany , Çetin Burak , Wang Yinsheng , Cui Qiang , Strahl Brian D. , Gozani Or , Miller Kyle M. , O’Leary Seán E. , Wade Paul A. , Patel Dinshaw J. , Wang Gang Greg , Song Jikui 
Published: April 2020

ABSTRACTIn mammals, repressive histone modifications such as trimethylation of histone H3 Lys9 (H3K9me3), frequently coexist with DNA methylation, producing a more stable and silenced chromatin state. However, it remains elusive how these epigenetic modifications crosstalk. Here, through structural and biochemical characterizations, we identified the replication foci targeting sequence (RFTS) domain of maintenance DNA methyltransferase DNMT1, a module known to bind the ubiquitylated H3 (H3Ub), as a specific reader for H3K9me3/H3Ub, with the recognition mode distinct from the typical trimethyl-lysine reader. Disruption of the interaction between RFTS and the H3K9me3Ub affects the localization of DNMT1 in stem cells and profoundly impairs the global DNA methylation and genomic stability. Together, this study reveals a previously unappreciated pathway through which H3K9me3 directly reinforces DNMT1-mediated maintenance DNA methylation.
On a Reef Far, Far Away: Anthropogenic Impacts Following Extreme Storms Affect Sponge Health and Bacterial Communities
Authors: Shore Amanda , Sims Jordan A. , Grimes Michael , Howe-Kerr Lauren I. , Grupstra Carsten G.B. , Doyle Shawn M. , Stadler Lauren , Sylvan Jason B. , Shamberger Kathryn E.F. , Davies Sarah W. , Santiago-Vázquez Lory Z. , Correa Adrienne M.S. 
Published: April 2020

ABSTRACTTerrestrial runoff can negatively impact marine ecosystems through stressors including excess nutrients, freshwater, sediments, and contaminants. Severe storms, which are increasing with global climate change, generate massive inputs of runoff over short timescales (hours to days); such runoff impacted offshore reefs in the northwest Gulf of Mexico (NW GoM) following severe storms in 2016 and 2017. Several weeks after coastal flooding from these events, NW GoM reef corals, sponges, and other benthic invertebrates -185 km offshore experienced mortality (2016 only) and/or sub-lethal stress (both years). To assess the impact of storm-derived runoff on reef filter feeders, we characterized the bacterial communities of two sponges,Agelas clathrodesandXestospongia muta, from offshore reefs during periods of sub-lethal stress and no stress over a three-year period (2016-2018). Sponge-associated bacterial communities were altered during both flood years. Additionally, we found evidence of wastewater contamination (based on 16S rRNA gene libraries and quantitative PCR) in offshore sponges following these flood years, but not during the no-flood year. We show that flood events from severe storms have the capacity to reach offshore reef ecosystems and impact resident benthic organisms. Such impacts are most readily detected if baseline data on organismal physiology and associated microbiome composition are available. This highlights the need for molecular and microbial time series of benthic organisms in near- and offshore reef ecosystems, and the continued mitigation of stormwater runoff and climate change impacts.
Population dynamics analysis ofSaccharomyces cerevisiaedeletion library during fed-batch cultivation using Bar-seq
Authors: Wehrs Maren , Thompson Mitchell G. , Banerjee Deepanwita , Prahl Jan-Philip , Barcelos Carolina A. , Moon Jadie , Morella Norma M. , Costello Zak , Keasling Jay D. , Shih Patrick M. , Tanjore Deepti , Mukhopadhyay Aindrila 
Published: April 2020

AbstractTo understand the genetic basis of changes in strain physiology during industrial fermentation, and the corresponding roles these genes play in strain performance, we employed a barcoded yeast deletion library to assess genome-wide strain fitness across a simulated industrial fermentation regime. Our results demonstrate the utility of Bar-seq to assess fermentation associated stresses in yeast populations under industrial conditions. We find that mutant population diversity is maintained through multiple seed trains, enabling for large scale fermentation selective pressures to act upon the community. We identify specific deletion mutants that were enriched in all processes, independent of the cultivation conditions, which includeMCK1, RIM11, MRK1, andYGK3that encode homologues of mammalian glycogen synthase kinase 3 (GSK-3). Further, we show that significant changes in the population diversity during fed-batch cultivations reflect the presence of significant external stresses, such as the accumulation of the fermentative byproduct ethanol. The mutants that were lost during the time of most extreme population selection suggest that specific biological processes may be required to cope with these specific stresses. Overall our work highlights a promising avenue to identify genetic loci and biological stress responses required for fitness under industrial conditions.
Visualization and sequencing of accessible chromatin reveals cell cycle and post romidepsin treatment dynamics
Authors: Estève Pierre-Olivier , Vishnu Udayakumar S. , Chin Hang Gyeong , Pradhan Sriharsa 
Published: April 2020

AbstractChromatin accessibility is a predictor of gene expression, cell division and cell type specificity. NicE-viewSeq (NickingEnzyme assistedviewing andSequencing) allows accessible chromatin visualization and sequencing with overall lower mitochondrial DNA and duplicated sequences interference relative to ATAC-see. Using NicE-viewSeq, we interrogated the accessibility of chromatin in a cell cycle (G1, S and G2/M) - specific manner using mammalian cells. Despite DNA replication and subsequent condensation of chromatin to chromosomes, chromatin accessibility remained generally preserved with minimal subtle alterations. Genome-wide alteration of chromatin accessibility within TSS and enhancer elements gradually decreased as cells progressed from G1 to G2M, with distinct differential accessibility near consensus transcription factors sites. Inhibition of histone deacetylases promoted accessible chromatin within gene bodies, correlating with apoptotic gene expression. In addition, reduced chromatin accessibility for the MYC oncogene pathway correlated with down regulation of pertinent genes. Surprisingly, repetitive RNA loci expression remained unaltered following histone acetylation-mediated increased accessibility. Therefore, we suggest that subtle changes in chromatin accessibility is a prerequisite during cell cycle and histone deacetylase inhibitor mediated therapeutics.
New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics
Authors: Knyshov A. , Gordon E.R.L. , Weirauch C. 
Published: April 2020

AbstractDespite many bioinformatic solutions for analyzing sequencing data, few options exist for targeted sequence retrieval from whole genomic sequencing (WGS) data. Available tools especially struggle at deep phylogenetic levels and necessitate amino-acid space searches, increasing rates of false positive results. Many such tools also suffer from difficult installation processes and lack adequate user resources. Here, we describe a program using freely available similarity search tools to find homologs in assembled WGS data with unparalleled freedom to modify parameters. We evaluate its performance as well as that of other utilized bioinformatics tools on two divergent insect species (>200 My) for which annotated genomes exist, as well as on one large set each of highly conserved and more variable loci. Our software is capable of retrieving orthologs from well-curated, low and high depth shotgun, and target capture assemblies as well or better than other software as assessed by finding the most genes with maximal coverage and with a low rate of false positives throughout all datasets. The software (implemented in Python), tutorials, and manual are freely available athttps://github.com/AlexKnyshov/alibaseq.