bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extension of ade novoTIM barrel with a rationally designed secondary structure element
Authors: Wiese Jonas Gregor , Shanmugaratnam Sooruban , Höcker Birte 
Published: October 2020

SummaryThe ability to construct novel enzymes is a major aim inde novoprotein design. A popular enzyme fold for design attempts is the TIM barrel. This fold is a common topology for enzymes and can harbor many diverse reactions. The recently publishedde novodesign of a four-fold symmetric TIM barrel provides a well understood minimal scaffold for potential enzyme designs. Here we explore opportunities to extend and diversify this scaffold by adding a shortde novohelix on top of the barrel. Due to the size of the protein we developed a design pipeline based on computationalab initiofolding that solves a less complex sub-problem focused around the helix and its vicinity and adapt it to the entire protein. We provide biochemical characterization and a high-resolution X-ray structure for one variant and compare it to our design model. The successful extension of this robust TIM-barrel scaffold opens opportunities to diversify it towards more pocket like arrangements and as such can be considered a building block for future design of binding or catalytic sites.
Targeting androgen regulation of TMPRSS2 and ACE2 as a therapeutic strategy to combat COVID-19
Authors: Deng Qu , Rasool Reyaz ur , Russell Ronnie M. , Natesan Ramakrishnan , Asangani Irfan A. 
Published: October 2020

SummaryEpidemiological data showing increased severity and mortality of COVID-19 in men suggests a potential role for androgen in SARS-CoV-2 infection. Here, we present evidence for the transcriptional regulation of SARS-CoV-2 host cell receptor ACE2 and TMPRSS2 by androgen in mouse and human cells. Additionally, we demonstrate the endogenous interaction between TMPRSS2 and ACE2 in human cells and validate ACE2 as a TMPRSS2 substrate. Further, Camostat – a TMPRSS2 inhibitor, blocked the cleavage of pseudotype SARS-CoV-2 surface Spike without disrupting TMPRSS2-ACE2 interaction. Thus providing evidence for the first time a direct role of TMPRSS2 in priming the SARS-CoV-2 Spike, required for viral fusion to the host cell. Importantly, androgen-deprivation, anti-androgens, or Camostat attenuated the SARS-CoV-2 S-mediated cellular entry. Together, our data provide a strong rationale for clinical evaluations of TMPRSS2 inhibitors, androgen-deprivation therapy/androgen receptor antagonists alone or in combination with antiviral drugs as early as clinically possible to prevent COVID-19 progression.
Coexistence holes characterize the assembly and disassembly of multispecies systems
Authors: Angulo Marco Tulio , Kelley Aaron , Montejano Luis , Song Chuliang , Saavedra Serguei 
Published: October 2020

AbstractA central goal of life science has been to understand the limits of species coexistence. However, we know surprisingly little about the structure of species coexistence below such limits, and how it affects the assembly and disassembly of ecological systems. Here we introduce a novel hypergraph-based formalism that fully captures the structure of coexistence in multispecies systems. Our formalism uncovers that, below its limits, coexistence in ecological systems has ubiquitous discontinuities that we call “coexistence holes.” These coexistence holes do not occur arbitrarily but tend to obey patterns that make them predictable. We provide direct evidence showing that the biotic and abiotic constraints of empirical systems produce an over-representation of coexistence holes. By highlighting discontinuities in the form of coexistence holes, our work provides a new platform to uncover the order and structure of the assembly and disassembly of ecological systems.
The role of the rodent lateral orbitofrontal cortex in simple Pavlovian cue-outcome learning depends on training experience
Authors: Panayi Marios C. , Killcross Simon 
Published: October 2020

AbstractThe orbitofrontal cortex (OFC) is a critical structure in the flexible control of value-based behaviours. OFC dysfunction is typically only detected when task or environmental contingencies change, against a backdrop of apparently intact initial acquisition and behaviour. While intact acquisition following OFC lesions in simple Pavlovian cue-outcome conditioning is often predicted by models of OFC function, this predicted null effect has not been thoroughly investigated. Here we test the effects of lesions and temporary muscimol inactivation of the rodent lateral OFC on the acquisition of a simple single cue-outcome relationship. Surprisingly, pre-training lesions significantly enhanced acquisition after over-training whereas post-training lesions and inactivation significantly impaired acquisition. This impaired acquisition to the cue reflects a disruption of behavioural control and not learning since the cue could also act as an effective blocking stimulus in an associative blocking procedure. These findings suggest that even simple cue-outcome representations acquired in the absence of OFC function are impoverished. Therefore, while OFC function is often associated with flexible behavioural control in complex environments, it is also involved in very simple Pavlovian acquisition where complex cue-outcome relationships are irrelevant to task performance.
DNA, Morphology, and Ecology Resurrect Previously Synonymized Species of North AmericanStereumand Suggest Extensive Undescribed Global Diversity
Authors: DeLong-Duhon Sarah , Bagley Robin K. , Forbes Andrew A. 
Published: October 2020

AbstractStereumis an exceedingly common but taxonomically confounding genus of basidiomycete fungus with a cosmopolitan distribution. Lack of consensus about morphological and geographic boundaries of manyStereumspecies has resulted in a lack of consistency in identification of physical specimens, a problem that cascades to their associated published DNA sequences. A critical initial step towards addressing these issues is determining the scope of the problem. Here, we first use integrative taxonomy to delimit species in the North AmericanStereum ostreacomplex. We use morphological and ecological characters, alongside ITS rDNA sequences of specimens from midwestern and eastern North America to show that “Stereum ostrea”in this region is a complex of at least three reproductively isolated sister species:S. lobatum,S. fasciatum, andS. subtomentosum. We then extend lessons from this case study to a set of publicly availableStereumITS sequences to assess the accuracy of species names represented by existing sequence data. ASAP species delimitation successfully discriminates among the three newly revealed species in theS. ostreaspecies complex, but also reveals considerable cryptic diversity across globalStereumand widespread inconsistency in application of species names. Though ITS alone should not be used to delimit species or describe evolutionary relationships, its application here helps direct new hypotheses and suggests several areas ofStereumtaxonomy that require revision. The critical future work of disentanglingStereumtaxonomy and evolution should combine a multilocus genetic approach with morphology, ecology, and a global sampling strategy.
Genotype-dependent and heat-induced grain chalkiness in rice correlates with the expression patterns of starch biosynthesis genes
Authors: Gann Peter James , Esguerra Manuel , Counce Paul Allen , Srivastava Vibha 
Published: October 2020

ABSTRACTTo understand the molecular basis of environment-induced and genotype-dependent chalkiness, six rice genotypes showing variable chalk levels were subjected to gene expression analysis during reproductive stages. In the high chalk genotypes, the peak expressions ofADP-Glucose Pyrophosphorylase (AGPase) Large Subunit 4(AGPL4) occurred in the stages before grain filling commenced, creating a temporal gap with the upregulation ofGranule Bound Starch Synthase I(GBSSI) andStarch Synthase IIA(SSIIA). Whereas, in the low chalk genotypes,AGPL4expression generally occurred in later stages, close to the upregulation ofGBSSIandSSIIA. However, heat treatment altered the expression pattern and created a gap between the expression peaks ofAGPL4, andGBSS1andSSIIA. This change was accompanied by transformed granular morphology, increased protein content, and chalkiness in the grains.AGPL4expression pattern may partially explain chalkiness as it contributes to the pool of ADP-Glucose for producing amylose and amylopectin, the major components of the starch. Down-regulation of AGPase during grain filling stages could result in a limited pool of ADP-Glucose leading to inefficient grain filling and air pockets that contribute to chalkiness. The study suggests a mechanism of grain chalkiness based on the coordination of the three starch biosynthesis genes in rice.Significance statementGenotype-dependent and heat-induced grain chalkiness in rice is partially based on the increased gap between the upregulationAGPaseand that ofGBSSIandSSIIAthrough reproductive stages. This temporal gap could limit starch accumulation and alter granular morphology, eventually leading to grain chalkiness.
Functional assessments ofPTENvariants using machine-assisted phenotype scoring
Authors: Chao Jesse T. , Roskelley Calvin D. , Loewen Christopher J.R. 
Published: October 2020

ABSTRACTGenetic testing is widely used in evaluating a patient’s predisposition for developing a malignancy. In the case of cancer, when a functionally impactful inherited mutation (i.e. genetic variant) is identified in a disease-relevant gene, the patient is at elevated risk of developing a lesion in their lifetime. Unfortunately, as the rate and coverage of genetic testing has accelerated, our ability to make informed assessments regarding the functional status of the variants has lagged. Currently, there are two main strategies for assessing variant functions:in silicopredictions orin vitrotesting. The first approach is to build generalist computational prediction software using theoretical parameters such as amino acid conservation as feature inputs. These types of software can classify any variant of any gene. Although versatile, their non-specific design and theoretical assumptions result in different models frequently producing conflicting classifications. The second approach is to develop gene-specific assays. Although each assay is tailored to the physiological function of the gene, this approach requires significant investments. Therefore, there is an urgent need for more practical, streamlined and cost-effective methods. To directly address these issues, we designed a new approach of using alterations in protein subcellular localization as a key indicator of loss of function. Thus, new variants can be rapidly functionalized by using high-content microscopy. To facilitate the analysis of large amounts of image data, we developed a new software, named MAPS for machine-assisted phenotype scoring, that utilizes deep learning (DL) techniques to extract and classify cell-level phenotypes. This new Python-based toolkit helps users leverage commercial cloud-based DL services that are easy to train and deploy to fit varying experimental conditions. Model training is entirely code-free and can be done with limited number of images. Users simply input the trained endpoints into MAPS to accomplish cell detection, phenotype discovery and phenotype classification. Thus, MAPS allows cell biologists to easily apply DL to accelerate their image analysis workflow.
Cytoplasmic innate immune sensing by the caspase-4 non-canonical inflammasome promotes cellular senescence
Authors: Fernández-Duran Irene , Tarrats Núria , Birch Jodie , Hari Priya , Millar Fraser R. , Muir Morwenna , Quintanilla Andrea , Brunton Valerie G. , Passos João F. , Acosta Juan Carlos 
Published: October 2020

SummaryCytoplasmic recognition of microbially derived lipopolysaccharides (LPS) in human cells is elicited by the inflammatory cysteine aspartic proteases caspase-4 and caspase-5, which activate non-canonical inflammasomes inducing a form of inflammatory programmed cell death termed pyroptosis. Here we show that LPS mediated activation of the non-canonical inflammasome also induces cellular senescence and the activation of tumour suppressor stress responses in human diploid fibroblasts. Interestingly, this LPS-induced senescence is dependent on caspase-4, the pyroptotic effector protein gasdermin-D and the tumour suppressor protein p53. Also, experiments with a catalytically deficient mutant suggest that caspase-4 proteolytic activity is not necessary for its role in senescence. Furthermore, we found that the caspase-4 non-canonical inflammasome is induced and assembled during Ras-mediated oncogene-induced senescence (OIS). Moreover, targeting caspase-4 in OIS showed that the non-canonical inflammasome is critical for SASP activation and contributes to reinforcing the cell cycle arrest in OIS. Finally, we observed that caspase-4 induction occursin vivoin models of tumour suppression and ageing. Altogether, we are unveiling that cellular senescence is induced by cytoplasmic microbial LPS recognition by the caspase-4 non-canonical inflammasome and that this pathway is conserved in the senescence program induced by oncogenic stress.
The discovery, distribution and diversity of DNA viruses associated withDrosophila melanogasterin Europe
Authors: Wallace Megan A. , Coffman Kelsey A. , Gilbert Clément , Ravindran Sanjana , Albery Gregory F. , Abbott Jessica , Argyridou Eliza , Bellosta Paola , Betancourt Andrea J. , Colinet Hervé , Eric Katarina , Glaser-Schmitt Amanda , Grath Sonja , Jelic Mihailo , Kankare Maaria , Kozeretska Iryna , Loeschcke Volker , Montchamp-Moreau Catherine , Ometto Lino , Onder Banu Sebnem , Orengo Dorcas J. , Parsch John , Pascual Marta , Patenkovic Aleksandra , Puerma Eva , Ritchie Michael G. , Rota-Stabelli Omar , Schou Mads Fristrup , Serga Svitlana V. , Stamenkovic-Radak Marina , Tanaskovic Marija , Veselinovic Marija Savic , Vieira Jorge , Vieira Cristina P. , Kapun Martin , Flatt Thomas , González Josefa , Staubach Fabian , Obbard Darren J. 
Published: October 2020

AbstractDrosophila melanogasteris an important model for antiviral immunity in arthropods, but very few DNA viruses have been described from the family Drosophilidae. This deficiency limits our opportunity to use natural host-pathogen combinations in experimental studies, and may bias our understanding of theDrosophilavirome. Here we report fourteen DNA viruses detected in a metagenomic analysis of approximately 6500 pool-sequencedDrosophila, sampled from 47 European locations between 2014 and 2016. These include three new Nudiviruses, a new and divergent Entomopox virus, a virus related toLeptopilina boulardifilamentous virus, and a virus related toMusca domesticasalivary gland hypertrophy virus. We also find an endogenous genomic copy of Galbut virus, a dsRNA Partitivirus, segregating at very low frequency. Remarkably, we find thatDrosophilaVesanto virus, a small DNA virus previously described as a Bidnavirus, may be composed of up to 12 segments and represent a new lineage of segmented DNA viruses. Two of the DNA viruses,DrosophilaKallithea nudivirus andDrosophilaVesanto virus are relatively common, found in 2% or more of wild flies. The others are rare, with many likely to be represented by a single infected fly. We find that virus prevalence in Europe reflects the prevalence seen in publicly-available datasets, withDrosophilaKallithea nudivirus andDrosophilaVesanto virus the only ones commonly detectable in public data from wild-caught flies and large population cages, and the other viruses being rare or absent. These analyses suggest that DNA viruses are at lower prevalence than RNA viruses inD. melanogaster, and may be less likely to persist in laboratory cultures. Our findings go some way to redressing an earlier bias toward RNA virus studies inDrosophila, and lay the foundation needed to harness the power ofDrosophilaas a model system for the study of DNA viruses.
Genomics-accelerated discovery of diverse fungicidal bacteria
Authors: Biggs Matthew B , Craig Kelly , Gachango Esther , Ingham David , Twizeyimana Mathias 
Published: October 2020

AbstractSorghum Anthracnose and Black Sigatoka of bananas are problematic fungal diseases worldwide, with a particularly devastating impact on small-holder farmers in Sub-Saharan Africa. We screened a total of 1,227 bacterial isolates for antifungal activity against these pathogens using detached-leaf methods and identified 72 isolates with robust activity against one or both of these pathogens. These bacterial isolates represent a diverse set of five phyla, 14 genera and 22 species, including taxa for which this is the first observation of fungal disease suppression. We identified biosynthetic gene clusters associated with activity against each pathogen. Through a machine learning workflow we discovered additional active isolates, including an isolate from a genus that had not been included in previous screening or model training. Machine-learning improved the discovery rate of our screen by 3-fold. This work highlights the wealth of biocontrol mechanisms available in the microbial world for management of fungal pathogens, generates opportunities for future characterization of novel fungicidal mechanisms, and provides a set of genomic features and models for discovering additional bacterial isolates with activity against these two pathogens.
Soil disturbance affects plant growth via soil microbial community shifts
Authors: Seitz Taylor J. , Schütte Ursel M. E. , Drown Devin M. 
Published: October 2020

AbstractRecent advances in climate research have discovered that permafrost is particularly vulnerable to the changes occurring in the atmosphere and climate, especially in Alaska where 85% of the land is underlain by mostly discontinuous permafrost. As permafrost thaws, research has shown that natural and anthropogenic soil disturbance causes microbial communities to undergo shifts in membership composition and biomass, as well as in functional diversity. Boreal forests are home to many plants that are integral to the subsistence diets of many Alaska Native communities. Yet, it is unclear how the observed shifts in soil microbes can affect above ground plant communities that are relied on as a major source of food. In this study, we tested the hypothesis that microbial communities associated with permafrost thaw affect plant growth by growing five plant species found in Boreal forests and Tundra ecosystems, including low-bush cranberry and bog blueberry, with microbial communities from the active layer soils of a permafrost thaw gradient. We found that plant growth was significantly affected by the microbial soil inoculants. Plants inoculated with communities from above thawing permafrost showed decreased growth compared to plants inoculated with microbes from undisturbed soils. We used metagenomic sequencing to determine that microbial communities from disturbed soils above thawing permafrost have differences in taxonomy from microbial communities in undisturbed soils above intact permafrost. The combination of these results indicates that a decrease in plant growth can be linked to soil disturbance driven changes in microbial community membership and abundance. These data contribute to an understanding of how microbial communities can be affected by soil disturbance and climate change, and how those community shifts can further influence plant growth in Boreal forests and more broadly, ecosystem health.
Strong whole life-cycle inbreeding depression inDaphnia magnaenhanced by partial asexuality
Authors: Tambovtseva Valentina G. , Zharov Anton A. , Haag Christoph R. , Galimov Yan R. 
Published: October 2020

ABSTRACTInbreeding depression is a key factor in the evolution of mating strategies and breeding systems across the eukaryotic tree of life. Yet its potential impact in partially asexual species has only received little attention. We studied inbreeding depression in the cyclical parthenogenDaphnia magnaby following mixtures of inbred and outbred genotypes from an early embryonic stage through hatching to adulthood and then across several asexual generations. We found that, across asexual generations, the frequency of inbred genotypes strongly and constantly decreased, until the experimental populations were almost entirely made up of outbred genotypes. The resulting estimate of inbreeding depression across the entire life cycle was almost 100 %, much higher than previous estimates for this and other similar species. Our results illustrate that the magnitude of inbreeding depression may be severely underestimated in studies that use fitness components or proxies instead of compound fitness estimates across the entire life, as well as in experimental studies with substantial pre-experimental mortality. More generally, our results suggest that inbreeding depression may play an important role in the evolution of partially asexual life cycles because clonal reproduction maintains inbreeding levels, and hence the negative effects of inbreeding accumulate across subsequent asexual generations.
Diverse Changes in Microglia Morphology and Axonal Pathology Over One Year after Mild Traumatic Brain Injury in Pigs
Authors: Grovola Michael R. , Paleologos Nicholas , Brown Daniel P. , Tran Nathan , Wofford Kathryn L. , Harris James P. , Browne Kevin D. , Wolf John A. , Cullen D. Kacy , Duda John E. 
Published: October 2020

AbstractOver 2.8 million people experience mild traumatic brain injury (TBI) in the United States each year, which may lead to long-term neurological dysfunction. The mechanical forces that occur due to TBI propagate through the brain to produce diffuse axonal injury (DAI) and trigger secondary neuroinflammatory cascades. The cascades may persist from acute to chronic time points after injury, altering the homeostasis of the brain. However, the relationship between the hallmark axonal pathology of diffuse TBI and potential changes in glial cell activation or morphology have not been established in a clinically relevant large animal model at chronic time points. In this study, we assessed tissue from pigs subjected to rapid head rotation in the coronal plane to generate mild TBI. Neuropathological assessments for axonal pathology, microglial morphological changes, and astrocyte reactivity were conducted in specimens out to 1 year post injury. We detected an increase in overall amyloid precursor protein pathology, as well as periventricular white matter and fimbria/fornix pathology after a single mild TBI. We did not detect changes in corpus callosum integrity or astrocyte reactivity. However, detailed microglial skeletal analysis revealed changes in morphology, most notably increases in the number of microglial branches, junctions, and endpoints. These subtle changes were most evident in periventricular white matter and certain hippocampal subfields, and were observed out to 1 year post injury in some cases. These ongoing morphological alterations suggest persistent change in neuroimmune homeostasis. Additional studies are needed to characterize the underlying molecular and neurophysiological alterations, as well as potential contributions to neurological deficits.
On the global attractors in one mathematical model of antiviral immunity
Authors: Tsygvintsev Alexei 
Published: October 2020

AbstractWe consider the mathematical model introduced by Batholdyet al.[1] describing the interaction between viral pathogens and immune system. We prove the global asymptotic stability of the infection steady-state if the basic reproductive ratioR0is greater than unity. That solves the conjecture announced in [7].