bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interrogation of the integrated mobile genetic elements in gut-associated Bacteroidaceae with a consensus prediction approach
Authors: Campbell Danielle E. , Leigh Joseph R. , Kim Ted , England Whitney E. , Whitaker Rachel J. , Degnan Patrick H. 
Published: September 2021

ABSTRACTExploration of mobile genetic element (MGE) diversity and relatedness is vital to understanding microbial communities, especially the gut microbiome, where the mobilization of antibiotic resistance and pathogenicity genes has important clinical consequences. Current MGE prediction tools are biased toward elements similar to previously-identified MGEs, especially tailed phages of proteobacterial hosts. Further, there is a need for methods to examine relatedness and gene sharing among MGEs. We present VICSIN, a consensus approach for MGE prediction and clustering of predictions to provide classification. Testing of VICSIN on datasets of Pseudomonas aeruginosa and Bacteroides fragilis genomes suggests VICSIN is the optimal approach to predict integrated MGEs from poorly-explored host taxa, because of its increased sensitivity and accuracy. We applied VICSIN to a dataset of gut-associated Bacteroidaceae genomes, identifying 816 integrated MGEs falling into 95 clusters, most of which are novel. VICSIN’s fast and simple network-building scheme revealed a high degree of gene sharing within and between related MGE clusters. Shared gene functions across MGEs include core mobilization functions and accessory gene content, such as type VI secretion systems and antibiotic resistance genes. The MGEs identified here encode a large portion of unknown gene content, emphasizing the fact that the full diversity of MGEs and the factors they encode remain very poorly understood. Together, this work motivates more exploration of the gut mobilome, which is likely one of the most potent drivers of microbial evolution in the human microbiome.IMPORTANCEMobile genetic elements (MGEs), including phages and integrative and conjugative elements (ICEs), drive the diversity and function of microbial communities through horizontal gene transfer. Current tools to predict MGEs in genomic sequence data are highly focused on phages, and are biased against the discovery of novel MGEs. We present VICSIN, a consensus approach to MGE prediction that is able to find a diversity of MGEs, particularly in poorly-understood bacterial taxa. By applying VICSIN to a large database of diverse Bacteroidaceae genomes, we have been able to get a distinct view of the gut mobilome, extending beyond the phageome. These novel MGEs belong to related groups, sharing a significant amount of functional gene content within and between groups, supporting a mosaic model of evolution for ICEs. Understanding how phages evolve in Bacteroidaceae hosts, however, remains elusive and highlights the need for more experimental research.
Mutations at the Alphavirus E2/E1 inter-dimer interface have host-specific phenotypes
Authors: Ren Sophia C. , Qazi Shefah A. , Towell Brian , Wang Joseph CY , Mukhopadhyay Suchetana 
Published: September 2021

ABSTRACTAlphaviruses are enveloped viruses transmitted by arthropod vectors to vertebrate hosts. The surface of the virion contains 80 glycoprotein spikes embedded in the membrane and these spikes mediate attachment to the host cell and initiate viral fusion. Each spike consists of a trimer of E2-E1 heterodimers. These heterodimers interact at two interfaces: (1) the intra-dimer interactions between E2 and E1 of the same heterodimer, and (2) the inter-dimer interactions between E2 of one heterodimer and E1 of the adjacent heterodimer (E1’). We hypothesized that the inter-dimer interactions are essential for trimerization of the E2-E1 heterodimers into a functional spike. In this work, we made a mutant virus (CPB) where we replaced six inter-dimeric residues in the E2 protein of Sindbis virus (WT SINV) with those from the E2 protein from chikungunya virus, and studied its effect in both mammalian and mosquito cell lines. CPB produced fewer infectious particles in mammalian cells than in mosquito cells, relative to WT SINV. When CPB virus was purified from mammalian cells, particles showed reduced amounts of glycoproteins relative to capsid protein, and contained defects in particle morphology compared to virus derived from mosquito cells. Using cryo-EM, we determined that the spikes of CPB had a different conformation than WT SINV. Last, we identified two revertants, E2-H333N and E1-S247L, that restored particle growth and assembly to different degrees. We conclude the inter-dimer interface is critical for spike trimerization and is a novel target for potential antiviral drug design.IMPORTANCEAlphaviruses, which can cause disease when spread to humans by mosquitoes, have been classified as an emerging pathogen, with infections occurring worldwide. The spikes on the surface of the alphavirus particle are absolutely required for the virus to enter a new host cell and initiate an infection. Using a structure-guided approach, we made a mutant virus that alters spike assembly in mammalian cells but not mosquito cells. This is important because it identifies a region in the spike that could be a target for antiviral drug design.
Multifaceted N-degron recognition and ubiquitylation by GID/CTLH E3 ligases
Authors: Chrustowicz Jakub , Sherpa Dawafuti , Teyra Joan , Loke Mun Siong , Popowicz Grzegorz , Basquin Jerome , Sattler Michael , Prabu J. Rajan , Sidhu Sachdev S. , Schulman Brenda A. 
Published: September 2021

AbstractN-degron E3 ubiquitin ligases recognize specific residues at the N-termini of substrates. Although molecular details of N-degron recognition are known for several E3 ligases, the range of N-terminal motifs that can bind a given E3 substrate binding domain remains unclear. Here, studying the Gid4 and Gid10 substrate receptor subunits of yeast “GID”/human “CTLH” multiprotein E3 ligases, whose known substrates bear N-terminal prolines, we discovered capacity for high-affinity binding to diverse N-terminal sequences determined in part by context. Screening of phage displaying peptide libraries with exposed N-termini identified novel consensus motifs with non-Pro N-terminal residues distinctly binding Gid4 or Gid10 with high affinity. Structural data reveal that flexible loops in Gid4 and Gid10 conform to complementary folds of diverse interacting peptide sequences. Together with analysis of endogenous substrate degrons, the data show that degron identity, substrate domains harboring targeted lysines, and varying E3 ligase higher-order assemblies combinatorially determine efficiency of ubiquitylation and degradation.
Optimization of single dose VSV-based COVID-19 vaccination in hamsters
Authors: O’Donnell Kyle L. , Clancy Chad S. , Griffin Amanda J. , Shifflett Kyle , Gourdine Tylisha , Thomas Tina , Long Carrie M. , Furuyama Wakako , Marzi Andrea 
Published: September 2021

AbstractThe ongoing COVID-19 pandemic has resulted in global effects on human health, economic stability, and social norms. The emergence of viral variants raises concerns about the efficacy of existing vaccines and highlights the continued need the for the development of efficient, fast-acting, and cost-effective vaccines. Here, we demonstrate the immunogenicity and protective efficacy of two vesicular stomatitis virus (VSV)-based vaccines encoding the SARS-CoV-2 spike protein either alone (VSV-SARS2) or in combination with the Ebola virus glycoprotein (VSV-SARS2-EBOV). Intranasally vaccinated hamsters showed an early CD8+ T cell response in the lungs and a greater antigen-specific IgG response, while intramuscularly vaccinated hamsters had an early CD4+ T cell and NK cell response. Intranasal vaccination resulted in protection within 10 days with hamsters not showing clinical signs of pneumonia when challenged with three different SARS-CoV-2 variants. This data demonstrates that VSV-based vaccines are viable single-dose, fast-acting vaccine candidates that are protective from COVID-19.
Directed evolution predicts cytochrome b G37V target site modification as probable adaptive mechanism towards the QiI fungicide fenpicoxamid in Zymoseptoria tritici
Authors: Fouché Guillaume , Michel Thomas , Lalève Anaïs , Wang Nick X , Young David H , Meunier Brigitte , Debieu Danièle , Fillinger Sabine , Walker Anne-Sophie 
Published: September 2021

ABSTRACTAcquired resistance is a threat for antifungal efficacy in medicine and agriculture. The diversity of possible resistance mechanisms, as well as the highly adaptive traits of pathogens make it difficult to predict evolutionary outcomes of treatments. We used directed evolution as an approach to assess the risk of resistance to the new fungicide fenpicoxamid in the wheat pathogenic fungus Zymoseptoria tritici. Fenpicoxamid inhibits complexIII of the respiratory chain at the ubiquinone reduction site (Qi site) of the mitochondrially encoded cytochrome b, a different site than the widely-used strobilurins which the respiratory complex by binding to the ubiquinol oxidation site (Qo site). We identified the G37V change, within the cytochrome b Qi site, as the most likely resistance mechanism to be selected in Z. tritici. This change triggered high fenpicoxamid resistance and halved the enzymatic activity of cytochrome b, despite no significant penalty for in vitro growth. In addition, we identified a negative cross-resistance between isolates harboring G37V or G143A, a Qo site change previously selected by strobilurins. Moreover, double mutants were less resistant to both QiIs and QoIs compared to single mutants. This work is a proof of concept that experimental evolution can be used to predict adaptation to fungicides, and provides new perspectives for the management of QiIs.Originality-Significance StatementThe highly adaptive traits of pathogens render evolutionary outcomes of antifungal treatments difficult to predict.We used directed evolution to assess the risk of resistance to the new fungicide fenpicoxamid in the wheat pathogenic fungus Zymoseptoria tritici.We identified a target modification as the most likely resistance mechanism to be selected.This change triggered high fenpicoxamid resistance and halved the activity of the target enzyme despite no significant penalty for in vitro growth.This work supports the use of experimental evolution as a method to predict adaptation to fungicides and provides important information for the management of QiIs.
Detection of F1 hybrids from single-genome data reveals frequent hybridization in Hymenoptera and particularly ants
Authors: Weyna Arthur , Bourouina Lucille , Galtier Nicolas , Romiguier Jonathan 
Published: September 2021

AbstractHybridization occupies a central role in many fundamental evolutionary processes, such as speciation or adaptation. Yet, despite its pivotal importance in evolution, little is known about the actual prevalence and distribution of hybridization across the tree of life. Here we develop and implement a new statistical method enabling the detection of F1 hybrids from single-individual genome sequencing data. Using simulations and sequencing data from known hybrid systems, we first demonstrate the specificity of the method, and identify its statistical limits. Next, we showcase the method by applying it to available sequencing data from more than 1500 species of Arthropods, including Hymenoptera, Hemiptera, Coleoptera, Diptera and Archnida. Among these taxa, we find Hymenoptera, and especially ants, to display the highest number of candidate F1 hybrids, suggesting higher rates of recent hybridization in these groups. The prevalence of F1 hybrids was heterogeneously distributed across ants, with taxa including many candidates tending to harbor specific ecological and life history traits. This work shows how large-scale genomic comparative studies of recent hybridization can be implemented, uncovering the determinants of hybridization frequency across whole taxa.
Quantitative accuracy and precision in multiplexed single-cell proteomics
Authors: Ctortecka Claudia , Stejskal Karel , Krššáková Gabriela , Mendjan Sasha , Mechtler Karl 
Published: September 2021

AbstractSingle-cell proteomics workflows have considerably improved in sensitivity and reproducibility to characterize yet unknown biological phenomena. With the emergence of multiplexed single-cell proteomics, studies increasingly present single-cell measurements in conjunction with an abundant congruent carrier to improve precursor selection and enhance identifications. While these extreme carrier spikes are often >100-times more abundant than the investigated samples, undoubtedly the total ion current increases, but quantitative accuracy possibly is affected. We here focus on narrowly titrated carrier spikes (i.e., <20x) and assess their elimination for comparable sensitivity at superior accuracy. We find that subtle changes in the carrier ratio can severely impact measurement variability and describe alternative multiplexing strategies to evaluate data quality. Lastly, we demonstrate elevated replicate overlap while preserving acquisition throughput at improved quantitative accuracy with DIA-TMT and discuss optimized experimental designs for multiplexed proteomics of trace samples. This comprehensive benchmarking gives an overview of currently available techniques and guides conceptualizing the optimal single-cell proteomics experiment.
A critical role of brain network architecture in a continuum model of autism spectrum disorders spanning from healthy individuals with genetic liability to individuals with ASD
Authors: Khundrakpam Budhachandra , Bhutani Neha , Vainik Uku , Al-Sharif Noor , Dagher Alain , White Tonya , Evans Alan C. 
Published: September 2021

AbstractStudies have shown cortical alterations in individuals with autism spectrum disorders (ASD) as well as in individuals with high polygenic risk for ASD. An important addition to the study of altered cortical anatomy is the investigation of the underlying brain network architecture that may reveal brain-wide mechanisms in ASD and in polygenic risk for ASD. Such an approach has been proven useful in other psychiatric disorders by revealing that brain network architecture shapes (to an extent) the disorder-related cortical alterations. This study uses data from a clinical dataset – 560 male subjects (266 individuals with ASD and 294 healthy individuals, CTL, mean age at 17.2 years) from the Autism Brain Imaging Data Exchange database, and data of 391 healthy individuals (207 males, mean age at 12.1 years) from the Pediatric Imaging, Neurocognition and Genetics database. ASD-related cortical alterations (group difference, ASD-CTL, in cortical thickness) and cortical correlates of polygenic risk for ASD were assessed, and then statistically compared with structural connectome-based network measures (such as hubs) using spin permutation tests. Next, we investigated whether polygenic risk for ASD could be predicted by network architecture by building machine-learning based prediction models, and whether the top predictors of the model were identified as disease epicenters of ASD. We observed that ASD-related cortical alterations as well as cortical correlates of polygenic risk for ASD implicated cortical hubs more strongly than non-hub regions. We also observed that age progression of ASD-related cortical alterations and cortical correlates of polygenic risk for ASD implicated cortical hubs more strongly than non-hub regions. Further investigation revealed that structural connectomes predicted polygenic risk for ASD (r=0.30,p<0.0001), and two brain regions (the left inferior parietal and left suparmarginal) with top predictive connections were identified as disease epicenters of ASD. Our study highlights a critical role of network architecture in a continuum model of ASD spanning from healthy individuals with genetic risk to individuals with ASD. Our study also highlights the strength of investigating polygenic risk scores in addition to multi-modal neuroimaging measures to better understand the interplay between genetic risk and brain alterations associated with ASD.
Dopamine-dependent cAMP dynamics in basal amygdala glutamatergic neurons
Authors: Lutas Andrew , Fernando Kayla , Zhang Stephen X. , Sambangi Abhijeet , Andermann Mark L. 
Published: September 2021

SummaryDopaminergic inputs to basal amygdala (BA) instruct learning of motivational salience. Here, we investigated the dynamics of dopamine release and downstream signaling during multiple salient events occurring within tens of seconds. We established in vitro and in vivo real-time tracking and manipulation of cAMP – a key intracellular plasticity signal downstream of dopamine receptor activation. Optogenetically-evoked release of dopamine drove proportional increases in cAMP in almost all BA glutamatergic neurons, suggesting widespread actions of dopamine across neurons preferring positive or negative valence. These cAMP responses decayed more slowly than dopamine release, potentially extending the window of plasticity. cAMP levels accumulated following direct photostimulation of cAMP but not repeated stimulation of dopamine axons, due to potent depression of dopamine release. cAMP and protein kinase A (PKA) responses to repeated appetitive or aversive stimuli also exhibited pronounced depression. Thus, history-dependent dynamics of dopamine and cAMP may regulate learning of temporally clustered, salient stimuli.
Sex differences in central and peripheral fatigue induced by sustained isometric ankle plantar flexion
Authors: Jo Donguk , Goubran Miriam , Bilodeau Martin 
Published: September 2021

AbstractThe main aim of this study was to determine sex differences in central and peripheral fatigue produced by a sustained isometric exercise of ankle plantar flexors in healthy young adults. Ten males and fourteen females performed a sustained isometric ankle exercise until task failure. Maximal voluntary isometric contraction torque (plantarflexion), voluntary activation level (using the twitch interpolation technique), and twitch contractile properties (twitch peak torque, twitch half relaxation time, and low frequency fatigue index) were measured before, immediately after, and throughout a recovery period (1, 2, 5, and 10 min) following the exercise protocol in order to characterize neuromuscular fatigue. Fatigue had a significant effect (p ≤ 0.05) on all dependent variables. Other than for the maximal voluntary contraction torque, where males showed a greater fatigue-related decrease than females, males and females showed generally similar changes with fatigue. Altogether, our findings indicate no major differences in central or peripheral fatigue mechanisms between males and females to explain a somewhat greater fatigability in males.
Automatic variable selection in ecological niche modeling: A case study using Cassin’s Sparrow (Peucaea cassinii)
Authors: Schnase John L. , Carroll Mark L. 
Published: September 2021

AbstractMERRA/Max provides a feature selection approach to dimensionality reduction that enables direct use of global climate model outputs in ecological niche modeling. The system accomplishes this reduction through a Monte Carlo optimization in which many independent MaxEnt runs, operating on a species occurrence file and a small set of randomly selected variables in a large collection of variables, converge on an estimate of the top contributing predictors in the larger collection. These top predictors can be viewed as potential candidates in the variable selection step of the ecological niche modeling process. MERRA/Max’s Monte Carlo algorithm operates on files stored in the underlying filesystem, making it scalable to large data sets. Its software components can run as parallel processes in a high-performance cloud computing environment to yield near real-time performance. In tests using Cassin’s Sparrow (Peucaea cassinii) as the target species, MERRA/Max selected a set of predictors from Worldclim’s Bioclim collection of 19 environmental variables that have been shown to be important determinants of the species’ bioclimatic niche. It also selected biologically and ecologically meaningful predictors from a more diverse set of 86 environmental variables derived from NASA’s Modern-Era Retrospective Analysis for Research and Applications Version 2 (MERRA-2) reanalysis, an output product of the Goddard Earth Observing System Version 5 (GEOS-5) modeling system. We believe these results point to a technological approach that could expand the use global climate model outputs in ecological niche modeling, streamline the modeling process, and, eventually, enable automated bioclimatic modeling as a practical, readily accessible, low-cost, commercial cloud service.
Reovirus sensitizes microsatellite stable colorectal cancer to anti-PD-1 treatment via cross-talk in innate and adaptive immune systems
Authors: Augustine Titto , John Peter , Friedman Tyler , Jiffry Jeeshan , Guzik Hillary , Mannan Rifat , Gupta Riya , Delano Catherine , Mariadason John M. , Zang Xingxing , Maitra Radhashree , Goel Sanjay 
Published: September 2021

AbstractBackgroundMicrosatellite stable (MSS) colorectal cancer (CRC) represents ~85% of all CRCs. These tumors are poorly immunogenic and largely resistant to immunotherapy, necessitating a need to develop new immune enhancing strategies. Oncolytic reovirus has a high propensity to replicate in KRAS mutant tumors which account for ~50% of MSS CRCs. Current study explores the ability of reovirus to potentiate the effect of immune checkpoint inhibition in MSS CRC.MethodsEffectiveness of reovirus infection was quantified through MTT assay for cell viability, and expression of immune-response genes by flow cytometry, RT-qPCR, and microarray. Computational analysis of differentially expressed genes was performed by TAC, DAVID and STRING. Combinatorial approach using anti-PD-1 monoclonal antibody was assessed in ex vivo and in vivo models. Live-cell imaging, tumor volume and survival were measured for quantification of anti-tumor activity. Expression of pattern recognition receptors (PRRs), cell surface and activation markers of immune cells, and PD-1/PD-L1 axis were studied using multi-color flow cytometry, immunoblotting, immunohistochemistry, and immunofluorescence.ResultsReovirus infection exerted growth arrest and expression of immune-response genes in CRCs cell lines in a KRAS-dependent manner. However, microsatellite instability, rather than KRAS status determined immune-repose pathways, functionalities and biological processes post-reovirus infection. Furthermore, reovirus significantly enhanced the anti-tumor activity of anti-human PD-1 [nivolumab] treatment in MSS CRC cell lines ex vivo. Similarly, reovirus increased the activity of anti-mouse PD-1 treatment in the CT26 [MSS, KRASMut], but not the MC38 [MSI, KRASWt] syngeneic mouse model of CRC. Combinatorial treatment has reduced the proliferative index, increased apoptosis and differentially altered PD-L1/PD-1 signaling among CT26 and MC38 tumors. Activation of innate immune system and expression of PRRs and antigen presentation markers were observed under reovirus and anti-PD-1 treatment that additionally reduced immunosuppressive macrophages. This led to an increase in T cell subsets, increase in effector T cell activation, and decrease in exhaustion markers specifically within CT26 microenvironment.ConclusionThe current study systematically evaluates immune characteristics and immune microenvironment of CRC under reovirus/anti-PD-1 combination treatment that proves increased effectiveness among MSS compared to MSI CRCs. This is a promising regimen warranting translation into clinical trials.One Sentence SummaryOncolytic reovirus alters innate and adaptive immune system and potentiates MSS type colorectal cancer to checkpoint inhibition therapy.