bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced stress tolerance through reduction of G3BP and suppression of stress granules
Authors: Lee Anna K. , Klein Jonathon , Tacer Klementina Fon , Lord Tessa , Oatley Melissa J. , Oatley Jon M. , Porter Shaina N. , Pruett-Miller Shondra M. , Tikhonova Elena B. , Karamyshev Andrey L. , Yang Peiguo , Kim Hong Joo , Taylor J. Paul , Potts Patrick Ryan 
Published: February 2020

SUMMARYStress granules (SG) are membrane-less ribonucleoprotein condensates that form in response to various stress stimuli via phase separation. SG act as a protective mechanism to cope with acute stress, but persistent SG have cytotoxic effects that are associated with several age-related diseases. Here, we demonstrate that the testis-specific protein, MAGE-B2, increases cellular stress tolerance by suppressing SG formation through translational inhibition of the key SG nucleator G3BP. MAGE-B2 reduces G3BP protein levels below the critical concentration for phase separation and suppresses SG initiation. Importantly, knockout of the MAGE-B2 mouse ortholog confers hypersensitivity of the male germline to heat stressin vivo. Thus, MAGE-B2 provides cytoprotection to maintain mammalian spermatogenesis, a highly thermo-sensitive process that must be preserved throughout reproductive life. These results demonstrate a mechanism that allows for tissue-specific resistance against stress through fine-tuning phase separation and could aid in the development of male fertility therapies.
Poecivirus is present in individuals with beak deformities in seven species of North American birds
Authors: Zylberberg Maxine , Van Hemert Caroline , Handel Colleen M. , Liu Rachel M. , DeRisi Joseph L. 
Published: February 2020

ABSTRACTAvian keratin disorder (AKD), a disease characterized by debilitating beak overgrowth but with unknown etiology, has increasingly affected wild bird populations since the 1990s. We previously showed that a novel picornavirus, Poecivirus, is closely correlated with disease status in Black-capped Chickadees (Poecile atricapillus) in Alaska. However, our knowledge of the relationship between Poecivirus and beak deformities in other species and other geographic areas remains limited. The growing geographic scope and number of species affected by AKD-like beak deformities require a better understanding of the causative agent to evaluate the population-level impacts of this epizootic. Here, we tested eight individuals from six avian species with AKD-consistent deformities for the presence of Poecivirus: Mew Gull (Larus canus), Hairy Woodpecker (Picoides villosus), Black-billed Magpie (Pica hudsonia), Northwestern Crow (Corvus caurinus), Red-breasted Nuthatch (Sitta canadensis), and Blackpoll Warbler (Setophaga striata); individuals were sampled in Alaska and Maine (1999-2016). We used targeted PCR followed by Sanger sequencing to test for the presence of Poecivirus in each specimen, and to obtain viral genome sequence from virus-positive host individuals. We detected Poecivirus in all individuals tested, but not in negative controls. Furthermore, we used unbiased metagenomic sequencing to test for the presence of other pathogens in six of these specimens (Hairy Woodpecker, two Northwestern Crows, two Red-breasted Nuthatches, Blackpoll Warbler). This analysis yielded additional viral sequence from several specimens, including the complete coding region of Poecivirus from one Red-breasted Nuthatch, which we confirmed via targeted PCR followed by Sanger sequencing. This study demonstrates that Poecivirus is present in individuals with AKD-consistent deformities from six avian species other than Black-capped Chickadee. While further investigation will be required to explore whether there exists a causal link between this virus and AKD, this study demonstrates that Poecivirus is not geographically restricted to Alaska, but rather occurs elsewhere in North America.
Human cytomegalovirus protein pUL36: a dual cell death pathway inhibitor
Authors: Fletcher-Etherington Alice , Nobre Luis , Nightingale Katie , Antrobus Robin , Nichols Jenna , Davison Andrew J. , Stanton Richard J. , Weekes Michael P. 
Published: February 2020

ABSTRACTHuman cytomegalovirus (HCMV) is an important human pathogen and a paradigm of intrinsic, innate and adaptive viral immune evasion. Here, we employed multiplexed tandem mass tag-based proteomics to characterise host proteins targeted for degradation late during HCMV infection. This approach revealed that mixed lineage kinase domain-like protein (MLKL), a key terminal mediator of cellular necroptosis, was rapidly and persistently degraded by the minimally passaged HCMV strain Merlin but not the extensively passaged strain AD169. The strain Merlin viral inhibitor of apoptosis pUL36 was necessary and sufficient both to degrade MLKL and to inhibit necroptosis. Furthermore, mutation of pUL36 Cys131abrogated MLKL degradation and restored necroptosis. As the same residue is also required for pUL36-mediated inhibition of apoptosis by preventing proteolytic activation of pro-caspase 8, we define pUL36 as a multifunctional inhibitor of both apoptotic and necroptotic cell death.SIGNIFICANCE STATEMENTCell death is a key defence against viral infection, preventing spread from infected to uninfected cells. Correspondingly, certain viruses encode inhibitors of apoptotic and necroptotic cell death pathways in order to facilitate their persistence. Human cytomegalovirus (HCMV) is an important human pathogen that can block apoptosis, but hitherto it has been unclear whether or how the virus blocks necroptosis. Here, we used a proteomic screen to identify human proteins targeted for destruction by HCMV, finding that the key necroptosis mediator MLKL is degraded throughout infection. MLKL is targeted for degradation by HCMV protein pUL36, which is also instrumental in inhibiting apoptosis. Thus, pUL36 is a dual cell death pathway inhibitor, and may represent an important therapeutic target.
SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data
Authors: Giguere Collin , Dubey Harsh Vardhan , Sarsani Vishal Kumar , Saddiki Hachem , He Shai , Flaherty Patrick 
Published: February 2020

AbstractBackgroundRecently, it has become possible to collect next-generation DNA sequencing data sets that are composed of multiple samples from multiple biological units where each of these samples may be from a single cell or bulk tissue. Yet, there does not yet exist a tool for simulating DNA sequencing data from such a nested sampling arrangement with single-cell and bulk samples so that developers of analysis methods can assess accuracy and precision.ResultsWe have developed a tool that simulates DNA sequencing data from hierarchically grouped (correlated) samples where each sample is designated bulk or single-cell. Our tool uses a simple configuration file to define the experimental arrangement and can be integrated into software pipelines for testing of variant callers or other genomic tools.ConclusionsThe DNA sequencing data generated by our simulator is representative of real data and integrates seamlessly with standard downstream analysis tools.
QTG-Finder2: a generalized machine-learning algorithm for prioritizing QTL causal genes in plants
Authors: Lin Fan , Lazarus Elena Z. , Rhee Seung Y. 
Published: February 2020

AbstractLinkage mapping has been widely used to identify quantitative trait loci (QTL) in many plants and usually requires a time-consuming and labor-intensive fine mapping process to find the causal gene underlying the QTL. Previously, we described QTG-Finder, a machine-learning algorithm to rationally prioritize candidate causal genes in QTLs. While it showed good performance, QTG-Finder could only be used in Arabidopsis and rice because of the limited number of known causal genes in other species. Here we tested the feasibility of enabling QTG-Finder to work on species that have few or no known causal genes by using orthologs of known causal genes as training set. The model trained with orthologs could recall about 64% of Arabidopsis and 83% of rice causal genes when the top 20% ranked genes were considered, which is similar to the performance of models trained with known causal genes. We further extended the algorithm to include polymorphisms in conserved non-coding sequences and gene presence/absence variation as additional features. Using this algorithm, QTG-Finder2, we trained and cross-validatedSorghum bicolorandSetaria viridismodels. TheS. bicolormodel was validated by causal genes curated from the literature and could recall 70% of causal genes when the top 20% ranked genes were considered. In addition, we applied theS. viridismodel and public transcriptome data to prioritize a plant height QTL and identified 13 candidate genes. QTL-Finder2 can accelerate the discovery of causal genes in any plant species and facilitate agricultural trait improvement.
A double role of the Gal80 N-terminus in activation of transcription by Gal4p
Authors: Reinhardt-Tews Annekathrin , Krutyhołowa Rościsław , Günzel Christian , Glatt Sebastian , Breunig Karin D 
Published: February 2020

ABSTRACTThe yeast galactose switch operated by the Gal4p-Gal80p-Gal3p regulatory module is a textbook model of transcription regulation in eukaryotes. The Gal80 protein inhibits Gal4p-mediated transcription activation by binding to the transcription activation domain. Inhibition is relieved by formation of an alternative Gal80-Gal3 complex. In yeasts lacking a Gal3p ortholog the Gal1 protein combines regulatory and enzymatic activity. The data presented here reveal a so-far unknown role of the Gal80 N-terminus in the mechanism of Gal4p activation. The N-terminus contains an NLS, which is responsible for nuclear accumulation of KlGal80p and galactokinase inhibitionin vitro.Herein we propose a model where the N-terminus of KlGal80p reaches into the catalytic center of KlGal1p of the nuclear fraction of KlGal1p triggering dissociation of the KlGal80-KlGal4 complex. We corroborate this model by genetic analyses and structural modelling and provide a rationale for the divergent evolution of the mechanism activating Gal4p.Summary blurbActivation of gene expression by Gal4p inK. lactisrequires an element in the N-terminus of KlGal80 that mediates nuclear import, KlGal1 interaction and galactokinase inhibition
Zebrafish Kit ligands cooperate with erythropoietin to promote erythroid cell expansion
Authors: Oltova Jana , Svoboda Ondrej , Machonova Olga , Svatonova Petra , Traver David , Kolar Michal , Bartunek Petr 
Published: February 2020

AbstractKit ligand (Kitlg) is pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Although the role of Kitlg in this process has not yet been reported inDanio rerio(zebrafish), in the present study, we show that its function is evolutionary conserved. Zebrafish possess two copies of Kitlg genes (Kitlga and Kitlgb) due to whole genome duplication. To determine the role of each ligand in zebrafish, we performed a series ofex vivoandin vivogain- and loss-of-function experiments. First, we tested the biological activity of recombinant Kitlg proteins in suspension culture from zebrafish whole kidney marrow and we demonstrate that Kitlga is necessary for expansion of erythroid progenitorsex vivo. To further address the role ofkitlgaandkitlgbin hematopoietic developmentin vivo, we performed gain-of-function experiments in zebrafish embryos, showing that both ligands cooperate with erythropoietin (Epo) to promote erythroid cell expansion. Finally, using thekitamutant (kitab5/b5orsparse), we show that Kita receptor is crucial for Kitlga/b cooperation with Epo in erythroid cells. In summary, using optimized suspension culture conditions with recombinant cytokines (Epo, Kitlga), we are reporting for the first timeex vivosuspension cultures of zebrafish hematopoietic progenitor cells, which can serve as an indispensable tool to study normal and aberrant hematopoiesis in zebrafish. Furthermore, we conclude that although partial functional diversification of Kit ligands has been described in other processes, in erythroid development, both paralogs play a similar role and their function is evolutionary conserved.Key points:Kit signaling contributes to erythroid cell development and is conserved from fish to manEx vivo expansion and self-renewal of zebrafish erythroid progenitors requires addition of recombinant Kitlga
Gene loss and acquisition in lineages of bacteria evolving in a human host environment
Authors: Gabrielaite Migle , Johansen Helle K. , Molin Søren , Nielsen Finn C. , Marvig Rasmus L. 
Published: February 2020

AbstractWhile genome analyses have documented that there are differences in the gene repertoire between evolutionary distant lineages of the same bacterial species, less is known about micro-evolutionary dynamics of gene loss and acquisition within lineages of bacteria as they evolve over the timescale of years. This knowledge is valuable to understand both the basic mutational steps that on long timescales lead to evolutionary distant bacterial lineages, and the evolution of the individual lineages themselves. In the case that lineages evolve in a human host environment, gene loss and acquisition may furthermore have implication for disease.We analyzed the genomes of 45Pseudomonas aeruginosalineages evolving in the lungs of cystic fibrosis patients to identify genes that are lost or acquired during the first years of infection in each of the different lineages. On average, the lineage genome content changed with 88 genes (range 0–473). Genes were more often lost than acquired, and prophage genes were more variable than bacterial genes. We identified genes that were lost or acquired independently across different clonal lineages, i.e. convergent molecular evolution. Convergent evolution suggests that there is a selection for loss and acquisition of certain genes in the host environment. We find that a significant proportion of such genes are associated with virulence; a trait previously shown to be important for adaptation. Furthermore, we also compared the genomes across lineages to show that within-lineage variable genes more often belonged to genomic content not shared across all lineages. Finally, we used 4,760 genes shared by 446P. aeruginosagenomes to develop a stable and discriminatory typing scheme forP. aeruginosaclone types (Pactyper,https://github.com/MigleSur/Pactyper). In sum, our analysis adds to the knowledge on the pace and drivers of gene loss and acquisition in bacteria evolving over multiple years in a human host environment and provides a basis to further understand how gene loss and acquisition plays a role in lineage differentiation and host adaptation.Data SummaryP. aeruginosagenome sequencing data has been made publicly available by Marviget al.(2015) and is deposited in Sequence Read Archive (SRA) under accession ERP004853.
High through-put identification of miR-145 targets in human articular chondrocytes
Authors: Martinez-Sanchez Aida , Lazzarano Stefano , Sharma Eshita , Murphy Chris L. 
Published: February 2020

ABSTRACTObjectiveMicroRNAs play a key role in biological processes, including cartilage development and homeostasis and are dysregulated in many diseases, including osteoarthritis. MiR-145 modulation induces profound changes in the human articular chondrocyte (HAC) phenotype, partially through direct repression ofSOX9. Since miRNAs can simultaneously silence multiple targets, we aimed to identify the whole targetome of miR-145 in HACs. This information is critical if miR-145 is to be considered a target for cartilage repair.MethodsRIP-seq (RNA-immunoprecipitation plus HT-sequencing) of miRISC (miRNA-induced silencing complex) was performed in HACs overexpressing miR-145 to identify miR-145 direct targets. The motif discovery method cWords was used to assess enrichment on miR-145 seed matches in the identified targets. RT-qPCR, Western (immuno-)blot and luciferase assays were used to validate miRNA-target interactions.ResultsMiR-145 overexpression affects the expression of over 350 genes and directly targets more than 50 mRNAs through the 3’UTR or, more commonly, the coding region.We also demonstrate that miR-145 targets DUSP6, involved in cartilage organization and development, at the translational level. DUSP6 depletion using specific siRNAs lead to MMP13 up-regulation, suggesting that miR-145-mediated DUSP6 depletion contributes to the effect of miR-145 on MMP13 expression.ConclusionWe demonstrate that miR-145 directly targets several genes in primary chondrocytes including those involved in the expression of the extracellular matrix and inflammation. Thus, we propose miR-145 as an important regulator of chondrocyte function and a new target for cartilage repair.
Prioritizing conservation actions for Pacific salmon in Canada
Authors: Walsh Jessica C. , Connors Katrina , Hertz Eric , Kehoe Laura , Martin Tara G. , Connors Brendan , Bradford Michael J. , Freshwater Cameron , Frid Alejandro , Halverson Jessica , Moore Jonathan W. , Price Michael H.H. , Reynolds John D. 
Published: February 2020

AbstractCurrent investment in conservation is insufficient to adequately protect and recover all ecosystems and species. The challenge of allocating limited funds is acute for Pacific salmon (Oncorhynchusspp.) in Canada, which lack a strategic approach to ensure that resources are spent on actions that would cost-effectively recover diminished populations.We applied the Priority Threat Management framework to prioritize strategies that are most likely to maximize the number of thriving Pacific salmon populations on the Central Coast of British Columbia, Canada. These included 79 genetically, ecologically and spatially distinct population groups called Conservation Units (CUs) for five salmon species. This region has high salmon biodiversity and spans the territories of four First Nations: the Heiltsuk, Nuxalk, Kitasoo/Xai’xais and Wuikinuxv.Using structured expert elicitation of Indigenous and other experts, we quantified the estimated benefits, costs and feasibility of implementing 10 strategies. Under a business-as-usual scenario (i.e., no additional investments in salmon conservation or management), experts predicted that only one in four CUs would have >50% chance of achieving a thriving status within 20 years. Limiting future industrial development, which was predicted to safeguard CUs from future declines, was identified as the most cost-effective strategy. Investment in three strategies: 1) removal of artificial barriers to fish migration, 2) watershed protection, and 3) stream restoration – at 11.3M CAD per year – was predicted to result in nearly half (34 of 79) of the CUs having a >60% chance of meeting the conservation objective.If all conservation strategies were implemented, experts estimated a >50% probability of achieving a thriving status for 78 of 79 CUs, at an annual cost of 17.3M CAD. However, even with the implementation of all strategies, most sockeye salmon CUs were unlikely to achieve higher probability targets of reaching the objective.Policy implications: We illustrate how Priority Threat Management can incorporate the perspectives and expertise of Indigenous peoples and other experts to evaluate and prioritize conservation strategies based on their cost, benefit and feasibility. Timely investment in the strategies outlined in this assessment could help safeguard and recover Pacific salmon in this region of Canada.
DOT1L Methyltransferase Activity Preserves SOX2-Enhancer Accessibility And Prevents Activation of Repressed Genes In Murine Stem Cells
Authors: Ferrari F. , Arrigoni L. , Franz H. , Butenko L. , Trompouki E. , Vogel T. , Manke T. 
Published: February 2020

ABSTRACTBackgroundDuring cellular differentiation, the chromatin landscape changes dynamically and contributes to the activation of cell-type specific transcriptional programs. Disruptor of telomeric silencing 1-like (DOT1L) is a histone methyltransferase that mediates mono-, di- and trimethylation of lysine 79 of histone H3 (H3K79me1, 2, 3). Its enzymatic activity is critical for driving cellular differentiation into cardiomyocytes, chondrocytes and neurons, from embryonic or other type of stem cells in physiological settings. Ectopic localization of DOT1L in MLL-rearranged leukemias is causative for leukemogenesis and relapse. Little is known about the causal relevance of DOT1L methyltransferase activity in the global chromatin context and how its enzymatic function affects transcriptional and global chromatin states. Recent reports conducted in leukemia cell models have suggested that deposition of H3K79me2 may be critical to preserve histone H3K27 acetylation (ac) and enhancer activity, and to sustain expression of highly transcribed genes. If and to what extent DOT1L affects chromatin states and enhancer activity during physiological differentiation processes is currently unknown.ResultsWe measure global changes of seven histone modifications during the differentiation process via high-throughput and quantitative ChIP-seq in anin-vitroneuronal differentiation model of mouse embryonic stem cells (mESC). We observe that H3K27ac globally decreases, whereas H3K79me2 globally increases during differentiation, while other modifications remain globally unaltered. Pharmacological inhibition of DOT1L in mESC and mESC-derived neural progenitors results in decreased expression of highly transcribed genes and increased expression of normally repressed genes. Acute DOT1L inhibition primes neural progenitors towards a mature differentiation state. Transcriptional downregulation associates with decreased accessibility of enhancers specifically bound by the master regulator SOX2.ConclusionsIn-vitroneuronal differentiation couples with a genome-wide accumulation of H3K79me2, never described previously in mammalian cells. Acute inhibition of DOT1L is sufficient to initiate a defined transcriptional program, which biases the transcriptome of neural progenitor cells towards neuronal differentiation. H3K79me2 is not generally causative for maintaining transcriptional levels at a genome-wide scale. In contrast, DOT1L inactivation reduces the chromatin accessibility of enhancers bound by SOX2in-vivo, thereby reducing the expression level of a restricted number of genes. Our work establishes that DOT1L activity gates differentiation of progenitors by allowing SOX2-dependent transcription of stemness programs.
Microbial grazers may aid in controlling infections caused by aquatic zoosporic fungi
Authors: Farthing Hazel N. , Jiang Jiamei , Henwood Alexandra J. , Fenton Andy , Garner Trent , Daversa David R. , Fisher Matthew C. , Montagnes David J. S. 
Published: February 2020

AbstractFree-living eukaryotic microbes may reduce animal diseases. We evaluated the dynamics by which micrograzers (primarily protozoa) apply top-down control on the chytridBatrachochytrium dendrobatidis(Bd) a devastating, panzootic pathogen of amphibians. Although micrograzers consumed zoospores (∼3 µm), the dispersal stage of chytrids, not all species grew monoxenically on zoospores. However, the ubiquitous ciliateTetrahymena pyriformis, which likely co-occurs withBd, grew at near its maximum rate (r= 1.7 d-1). A functional response (ingestion vs. prey abundance) forT. pyriformis, measured using spore-surrogates (microspheres) revealed maximum ingestion (Imax) of 1.63 × 103zoospores d-1, with a half saturation constant (k) of 5.75 × 103zoospores ml-1. Using these growth and grazing data we developed and assessed a population model that incorporated chytrid-host and micrograzer dynamics. Simulations using our data and realistic parameters obtained from the literature suggested that micrograzers could controlBdand potentially prevent chytridiomycosis (defined as 104sporangia host-1). However, simulated inferior micrograzers (0.7 xImaxand 1.5 xk) did not prevent chytridiomycosis, although they ultimately reduced pathogen abundance to below levels resulting in disease. These findings indicate how micrograzer responses can be applied when modelling disease dynamics forBdand other zoosporic fungi.