bluuebunny/crossref_metadata_2025 huggingface dataset:
Larval diet affects adult reproduction but not survival regardless of injury and infection stress inDrosophila melanogaster
Authors: Savola Eevi , Vale Pedro , Walling Craig
Published: October 2020

Early-life conditions have profound effects on many life-history traits. In particular, early-life diet affects both juvenile development, and adult survival and reproduction. Early-life diet also has consequences for the ability of adults to withstand stressors such as starvation, temperature and desiccation. However, it is less well known how early-life diet influences the ability of adults to respond to infection. Here we test whether varying the larval diet of femaleDrosophila melanogaster(through altering protein to carbohydrate ratio, P:C) influences the long-term response to injury and infection with the bacterial pathogenPseudomonas entomophila. Given previous work manipulating adult dietary P:C, we predicted that adults from larvae raised on higher P:C diets would be more likely to survive infection and have increased reproduction, but shorter lifespans and an increased rate of ageing. For larval development, we predicted that low P:C would lead to a longer development time and lower viability. We found that early-life and lifetime egg production were highest at intermediate to high larval P:C diets, but there was no effect of larval P:C on adult survival. Larval diet had no effect on survival or reproduction post-infection. Larval development was quickest on intermediate P:C and egg-to-pupae and egg-to-adult viability were higher on higher P:C. Overall, despite larval P:C affecting several traits measured in this study, we saw no evidence that larval P:C altered the consequence of infection or injury for adult survival and early-life and lifetime reproduction. Taken together, these data suggest that larval diets appear to have a limited impact on adult response to infection.
Single cell transcriptome sequencing on the Nanopore platform with ScNapBar
Authors: Wang Qi , Bönigk Sven , Böhm Volker , Gehring Niels , Altmüller Janine , Dieterich Christoph
Published: October 2020

The current ecosystem of single cell RNA-seq platforms is rapidly expanding, but robust solutions for single cell and single molecule full-length RNA sequencing are virtually absent. A high-throughput solution that covers all aspects is necessary to study the complex life of mRNA on the single cell level. The Nanopore platform offers long read sequencing and can be integrated with the popular single cell sequencing method on the 10x Chromium platform. However, the high error-rate of Nanopore reads poses a challenge in downstream processing (e.g. for cell barcode assignment). We propose a solution to this particular problem by using a hybrid sequencing approach on Nanopore and Illumina platforms. Our software ScNapBar enables cell barcode assignment with high accuracy, especially if sequencing saturation is low. ScNapBar uses unique molecular identifier (UMI) or Naïve Bayes probabilistic approaches in the barcode assignment, depending on the available Illumina sequencing depth. We have benchmarked the two approaches on simulated and real Nanopore datasets. We further applied ScNapBar to pools of cells with an active or a silenced non-sense mediated RNA decay pathway. Our Nanopore read assignment distinguishes the respective cell populations and reveals characteristic nonsense-mediated mRNA decay events depending on cell status.
Evolutionary recent dual obligatory symbiosis among adelgids indicates a transition between fungus and insect associated lifestyles
Authors: Szabó Gitta , Schulz Frederik , Manzano-Marín Alejandro , Toenshoff Elena Rebecca , Horn Matthias
Published: October 2020

Adelgids (Insecta: Hemiptera: Adelgidae) form a small group of insects but harbor a surprisingly diverse set of bacteriocyte-associated endosymbionts, which suggest multiple replacement and acquisition of symbionts over evolutionary time. Specific pairs of symbionts have been associated with adelgid lineages specialized on different secondary host conifers. Using a metagenomic approach, we investigated the symbiosis of theAdelges laricis/tardusspecies complex containing betaproteobacterial (‘CandidatusVallotia tarda’) and gammaproteobacterial (‘CandidatusProfftia tarda’) symbionts. Genomic characteristics and metabolic pathway reconstructions revealed thatVallotiaandProfftiaare evolutionary young endosymbionts, which complement each other’s role in essential amino acid production. Phylogenomic analyses and a high level of genomic synteny indicate an origin of the betaproteobacterial symbiont from endosymbionts ofRhizopusfungi. This evolutionary transition was accompanied with substantial loss of functions related to transcription regulation, secondary metabolite production, bacterial defense mechanisms, host infection and manipulation. The transition from fungus to insect endosymbionts extends our current framework about evolutionary trajectories of host-associated microbes.
De NovoLipid Labeling for Comprehensive Analysis of Subcellular Distribution and Trafficking in Live Cells
Authors: Zhang Jun , Nie Jia , Sun Haoran , Andersen John-Paul , Shi Yuguang
Published: October 2020

Lipids exert dynamic biological functions which are determined both by their fatty acyl compositions and precise spatiotemporal distributions inside the cell. There are more than 1000 lipid species in a typical mammalian cell. However, it remains a daunting task to investigate any of these features in live cells for each of the more than 1000 lipid species. Here we resolved this issue by developing ade novolipid labeling method for major lipid species, including glycerolipids, glycerophospholipids, and cholesterol esters by using a single fluorescent probe. The method not only allowed us to probe the precise subcellular distribution and trafficking of individual lipid species in live cells, but also uncovered some unexpected biological functions of previously reported lipid metabolic enzymes that were not possible by conventional biochemical methods. We envision that this method will become an indispensable tool for the functional analysis of individual lipid species and numerous lipid metabolic enzymes and transporters in live cells.
High-Resolution Phylogenetic and Population Genetic Analysis of Microbial Communities with RoC-ITS
Authors: Rusch Douglas B. , Huang Jie , Hemmerich Chris , Hahn Matthew W.
Published: October 2020

Microbial communities are inter-connected systems of incredible complexity and dynamism that play crucial roles in health, energy, and the environment. To better understand microbial communities and how they respond to change, it is important to know which microbes are present and their relative abundances at the greatest taxonomic resolution possible. Here, we describe a novel protocol (RoC-ITS) that uses the single-molecule Nanopore sequencing platform to assay the composition of microbial communities in unprecedented detail. This methodology produces long-read sequences including multiple copies of the same complete 16S ribosomal gene and its neighboring internally transcribed spacer (ITS) using rolling-circle amplification. The ribosomal 16S gene provides phylogenetic information down to the species-level, while the much less conserved ITS region contains strain-level information. When linked together, this combination of markers allows for the identification of individual ribosomal units within a specific organism, the assessment of their relative stoichiometry, and the ability to monitor subtle shifts in microbial community composition with a single generic assay. We applied RoC-ITS to a mock microbial community that was also sequenced using the Illumina platform, demonstrating its accuracy in quantifying the relative abundance and identity of each species.
Resolving transcriptional states and predicting lineages in the annelidCapitella teletausing single-cell RNAseq
Authors: Sur Abhinav , Meyer Néva P.
Published: October 2020

Evolution and diversification of cell types has contributed to animal evolution. However, gene regulatory mechanisms underlying cell fate acquisition during development remains largely uncharacterized in spiralians. Here we use a whole-organism, single-cell transcriptomic approach to map larval cell types in the annelidCapitella teletaat 24- and 48-hours post gastrulation (stages 4 and 5). We identified eight unique cell clusters (undifferentiated precursors, ectoderm, muscle, ciliary-band, gut, neurons, neurosecretory cells and protonephridia), thus helping to identify previously uncharacterized molecular signatures such as novel neurosecretory cell markers. Analysis of coregulatory programs in individual clusters revealed gene interactions that can be used for comparisons of cell types across taxa. We examined the neural and neurosecretory clusters more deeply and characterized a differentiation trajectory starting from dividing precursors to neurons using Monocle3 and velocyto. Pseudotime analysis along this trajectory identified temporally-distinct cell states undergoing progressive gene expression changes over time. Our data revealed two potentially distinct neural differentiation trajectories including an early trajectory for brain neurosecretory cells. This work provides a valuable resource for future functional investigations to better understanding neurogenesis and the transitions from neural precursors to neurons in an annelid.
Modeling airway dysfunction in asthma using synthetic mucus biomaterials
Authors: Song Daniel , Iverson Ethan , Kaler Logan , Bader Shahed , Scull Margaret A. , Duncan Gregg A.
Published: October 2020

As asthma worsens, occlusion of airways with mucus significantly contributes to airflow obstruction and reduced lung function. Recent evidence from clinical studies has shown mucus obtained from adults and children with asthma possesses altered mucin composition. However, how these changes alter the functional properties of the mucus gel is not yet fully understood. To study this, we have engineered a synthetic mucus biomaterial to closely mimic the properties of native mucus in health and disease. We demonstrate this model possesses comparable biophysical and transport properties to native mucusex vivocollected from human subjects andin vitroisolated from human airway epithelial (HAE) tissue cultures. We found by systematically varying mucin composition that mucus gel viscoelasticity is enhanced when predominantly composed of mucin 5AC (MUC5AC), as is observed in asthma. As a result, asthma-like synthetic mucus gels are more slowly transported on the surface of HAE tissue cultures and at a similar rate to native mucus produced by HAE cultures stimulated with the type 2 cytokine IL-13, known to contribute to airway inflammation and MUC5AC hypersecretion in asthma. We also discovered the barrier function of asthma-like synthetic mucus towards influenza A virus was impaired as evidenced by the increased frequency of infection in MUC5AC-rich hydrogel coated HAE cultures. Together, this work establishes a biomaterial-based approach to understand airway dysfunction in asthma and related muco-obstructive lung diseases.

Graphical Abstract
Extension of ade novoTIM barrel with a rationally designed secondary structure element
Authors: Wiese Jonas Gregor , Shanmugaratnam Sooruban , Höcker Birte
Published: October 2020

The 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

Epidemiological 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

A 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

The 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

Stereumis 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

To 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 statement

Genotype-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

Genetic 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

Cytoplasmic 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

Drosophila 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

Sorghum 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

Recent 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

Inbreeding 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

Over 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

We 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].
The Orbitofrontal Cortex in Temporal Cognition
Authors: Romero Sosa Juan Luis , Buonomano Dean , Izquierdo Alicia
Published: October 2020

One of the most important factors in decision making is estimating the value of available options. Subregions of the prefrontal cortex, including the orbitofrontal cortex (OFC), have been deemed essential for this process. Value computations require a complex integration across numerous dimensions, including, reward magnitude, effort, internal state, and time. The importance of the temporal dimension is well-illustrated by temporal discounting tasks, in which subjects select between smaller-sooner versus larger-later rewards. The specific role of OFC in telling time and integrating temporal information into decision making remains unclear. Based on the current literature, in this review we reevaluate current theories of OFC function, accounting for the influence of time. Incorporating temporal information into value estimation and decision making requires distinct, yet interrelated, forms of temporal information including the ability to tell time, represent time, create temporal expectations, and the ability to use this information for optimal decision making in a wide range of tasks, including temporal discounting and wagering. We use the term ‘temporal cognition’ to refer to the integrated use of these different aspects of temporal information. We suggest that the OFC may be a critical site for the integration of reward magnitude and delay, and thus important for temporal cognition.
Genomic analysis ofCryaa-R49C andCryab-R120G knockin mutant mice: 10-year follow-up
Authors: Kolling Fred , Ringelberg Carol , Wallace Mia , Andley Usha
Published: October 2020

Objective

Two experimental samples from a mouse line containing Cryaa or Cryab modifications on a predominantly C57Bl/6 background using 129Sv mouse strain embryonic stem cells were investigated. The objective was to reexamine the precise genetic background of the mice 10 years after they were converted to the C57Bl/6 background.

Results

The genetic backgrounds of the mice were assessed at the DartMouse™ Speed Congenic Core Facility at the Geisel School of Medicine at Dartmouth. DartMouse used the Illumina, Inc. Infinium Genotyping Assay to interrogate a custom panel of 5307 SNPs that were spread throughout the genome. The raw SNP data were analyzed using the DartMouse SNaP-Map™ and Map-Synth™ software, which allowed for genetic background identification at each SNP location for every mouse. As part of the analysis, 323 SNPs were eliminated from the data prior to generating chromosome maps due to internal quality control protocols. Of the remaining 4984 SNPs, 44.56% were uninformative (not polymorphic between the two relevant genetic backgrounds) and approximately 0.91% gave uninterpretable data. The remaining 54.53% of the returned SNPs were well distributed throughout the genome. The genetic backgrounds were determined to be 98-99% C57Bl/6J, which was the desired background.
Non-phylogenetic identification of co-evolving genes for reconstructing the archaeal Tree of Life
Authors: Rangel L. Thibério , Soucy Shannon M. , Setubal João C. , Gogarten Johann Peter , Fournier Gregory P.
Published: October 2020

Assessing the phylogenetic compatibility between individual gene families is a crucial and often computationally demanding step in many phylogenomics analyses. Here we describe the Evolutionary Similarity Index (IES) to assess shared evolution between gene families using a weighted Orthogonal Distance Regression applied to sequence distances. This approach allows for straightforward pairing of paralogs between co-evolving gene families without resorting to multiple tests, ora prioriassumptions of molecular interactions between protein products from assessed genes. The utilization of pairwise distance matrices, while less informative than phylogenetic trees, circumvents error-prone comparisons between trees whose topologies are inherently uncertain. Analyses of simulated gene family evolution datasets showed thatIESwas more accurate and less susceptible to noise than popular tree-based methods (Robinson-Foulds and geodesic distance) for assessing evolutionary signal compatibility, since it bypasses phylogenetic reconstruction and its inherent uncertainty. ApplyingIESto a real dataset of 1,322 genes from 42 archaeal genomes identified eight major clusters of gene families with compatible evolutionary trends. Four of these clusters included genes with a taxonomic distribution across all archaeal phyla, while other clusters included a subset of taxa that do not map to generally accepted archaeal clades, indicating possible shared horizontal transfers by clustered gene families. We identify one strongly connected set of 62 genes from the same cluster, occurring as both single-copy and multiple homologs per genome, with compatible phylogenetic reconstructions closely matching previously published species trees for Archaea. AnIESimplementation is available athttps://github.com/lthiberiol/evolSimIndex.
Target cell-specific synaptic dynamics of excitatory to inhibitory neuron connections in supragranular layers of human neocortex
Authors: Kim Mean-Hwan , Radaelli Cristina , Thomsen Elliot R. , Machen Deja , Chartrand Tom , Jorstad Nikolas L. , Mahoney Joseph T. , Taormina Michael J. , Long Brian , Baker Katherine , Campagnola Luke , Casper Tamara , Clark Michael , Dee Nick , D’Orazi Florence , Gamlin Clare , Kalmbach Brian , Kebede Sara , Lee Brian R. , Ng Lindsay , Trinh Jessica , Cobbs Charles , Gwinn Ryder P. , Keene C. Dirk , Ko Andrew L. , Ojemann Jeffrey G. , Silbergeld Daniel L. , Sorensen Staci A. , Berg Jim , Smith Kimberly , Nicovich Philip R. , Jarsky Tim , Murphy Gabe , Zeng Hongkui , Ting Jonathan T. , Levi Boaz P. , Lein Ed S.
Published: October 2020

Rodent studies have demonstrated that synaptic dynamics from excitatory to inhibitory neuron types are often dependent on the target cell type. However, these target cell-specific properties have not been well investigated in human cortex, where there are major technical challenges in reliably identifying cell types. Here, we take advantage of newly developed methods for human neurosurgical tissue analysis with multiple patch-clamp recordings,post-hocfluorescentin situhybridization (FISH), and prospective GABAergic AAV-based labeling to investigate synaptic properties between pyramidal neurons and PVALB- vs. SST- positive interneurons. We find that there are robust molecular differences in synapse-associated genes between these neuron types, and that individual presynaptic pyramidal neurons evoke postsynaptic responses with heterogeneous synaptic dynamics in different postsynaptic cell types. Using molecular identification with FISH and classifiers based on transcriptomically identified PVALB neurons analyzed with Patch-seq methods, we find that PVALB neurons typically show depressing synaptic characteristics, whereas other interneuron types including SST-positive neurons show facilitating characteristics. Together, these data support the existence of target cell-specific synaptic properties in human cortex that are similar to rodent, thereby indicating evolutionary conservation of local circuit connectivity motifs from excitatory to inhibitory neurons and their synaptic dynamics.
Multiple neuronal networks coordinate Hydra mechanosensory behavior
Authors: Badhiwala Krishna N. , Primack Abby S. , Juliano Celina E. , Robinson Jacob T.
Published: October 2020

Hydra vulgaris is an emerging model organism for neuroscience due to its small size, transparency, genetic tractability, and regenerative nervous system; however, fundamental properties of its sensorimotor behaviors remain unknown. Here, we use microfluidic devices combined with fluorescent calcium imaging and surgical resectioning to study how the diffuse nervous system coordinates Hydra’s mechanosensory response. Mechanical stimuli cause animals to contract, and we find this response relies on at least two distinct networks of neurons in the oral and aboral regions of the animal. Different activity patterns arise in these networks depending on whether the animal is contracting spontaneously or contracting in response to mechanical stimulation. Together, these findings improve our understanding of how Hydra’s diffuse nervous system coordinates sensorimotor behaviors. These insights help reveal how sensory information is processed in an animal with a diffuse, radially symmetric neural architecture unlike the dense, bilaterally symmetric nervous systems found in most model organisms.
EfgA is a conserved formaldehyde sensor that halts bacterial translation in response to elevated formaldehyde
Authors: Bazurto Jannell V. , Nayak Dipti D. , Ticak Tomislav , Davlieva Milya , Lee Jessica A. , Lambert Leah B. , Benski Olivia J. , Quates Caleb J. , Johnson Jill L. , Patel Jagdish Suresh , Ytreberg F. Marty , Shamoo Yousif , Marx Christopher J.
Published: October 2020

Normal cellular processes give rise to toxic metabolites that cells must mitigate. Formaldehyde is a universal stressor and potent metabolic toxin that is generated in organisms from bacteria to humans. Methylotrophic bacteria such asMethylorubrum extorquensface an acute challenge due to their production of formaldehyde as an obligate central intermediate of single-carbon metabolism. Mechanisms to sense and respond to formaldehyde were speculated to exist in methylotrophs for decades but had never been discovered. Here we identify a member of the DUF336 domain family, namedefgAfor enhanced formaldehyde growth, that plays an important role in endogenous formaldehyde stress response inM. extorquensPA1 and is found almost exclusively in methylotrophic taxa. Our experimental analyses reveal that EfgA is a formaldehyde sensor that inhibits translation in response to elevated levels of formaldehyde. Heterologous expression of EfgA inEscherichia coliincreases formaldehyde resistance, indicating that its interaction partners are widespread and conserved and may include translational machinery. EfgA represents the first example of a formaldehyde stress response system that does not involve enzymatic detoxification. Thus, EfgA comprises a unique stress response mechanism in bacteria, whereby a single protein directly senses elevated levels of a toxic intracellular metabolite and modulates translational activity.
Diverse viral proteases activate the NLRP1 inflammasome
Authors: Tsu Brian V. , Beierschmitt Christopher , Ryan Andrew P. , Agarwal Rimjhim , Mitchell Patrick S. , Daugherty Matthew D.
Published: October 2020

The NLRP1 inflammasome is a multiprotein complex that is a potent activator of inflammation. Mouse NLRP1B can be activated through proteolytic cleavage by the bacterial Lethal Toxin (LeTx) protease, resulting in degradation of the N-terminal domains of NLRP1B and liberation of the bioactive C-terminal domain, which includes the caspase activation and recruitment domain (CARD). However, a natural pathogen-derived effector that can activate human NLRP1 remains unknown. Here, we use an evolutionary model to identify several proteases from diverse picornaviruses that cleave human NLRP1 within a rapidly evolving region of the protein, leading to host-specific and virus-specific activation of the NLRP1 inflammasome. Our work demonstrates that NLRP1 acts as a “tripwire” to recognize the enzymatic function of a wide range of viral proteases, and suggests that host mimicry of viral polyprotein cleavage sites can be an evolutionary strategy to activate a robust inflammatory immune response.