bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing
Authors: Lind Abigail L. , Pollard Katherine S. 
Published: July 2020

AbstractBackgroundMicrobial eukaryotes are found alongside bacteria and archaea in natural microbial systems, including host-associated microbiomes. While microbial eukaryotes are critical to these communities, they are challenging to study with shotgun sequencing techniques and are therefore often excluded.ResultsHere we present EukDetect, a bioinformatics method to identify eukaryotes in shotgun metagenomic sequencing data. Our approach uses a database of 521,824 universal marker genes from 241 conserved gene families, which we curated from 3,713 fungal, protist, non-vertebrate metazoan, and non-streptophyte archaeplastid genomes and transcriptomes. EukDetect has a broad taxonomic coverage of microbial eukaryotes, performs well on low-abundance and closely related species, and is resilient against bacterial contamination in eukaryotic genomes. Using EukDetect, we describe the spatial distribution of eukaryotes along the human gastrointestinal tract, showing that fungi and protists are present in the lumen and mucosa throughout the large intestine. We discover that there is a succession of eukaryotes that colonize the human gut during the first years of life, mirroring patterns of developmental succession observed in gut bacteria. By comparing DNA and RNA sequencing of paired samples from human stool, we find that many eukaryotes continue active transcription after passage through the gut, though some do not, suggesting they are dormant or nonviable. We analyze metagenomic data from the Baltic Sea and find that eukaryotes differ across locations and salinity gradients. Finally, we observe eukaryotes inArabidopsisleaf samples, many of which are not identifiable from public protein databases.ConclusionsEukDetect provides an automated and reliable way to characterize eukaryotes in shotgun sequencing datasets from diverse microbiomes. We demonstrate that it enables discoveries that would be missed or clouded by false positives with standard shotgun sequence analysis. EukDetect will greatly advance our understanding of how microbial eukaryotes contribute to microbiomes.
Cell type-specific immune dysregulation in severely ill COVID-19 patients
Authors: Yao Changfu , Bora Stephanie A , Parimon Tanyalak , Zaman Tanzira , Friedman Oren A , Palatinus Joseph A , Surapaneni Nirmala S , Matusov Yuri P , Chiang Giuliana Cerro , Kassar Alexander G , Patel Nayan , Green Chelsi ER , Aziz Adam W , Suri Harshpreet , Suda Jo , Lopez Andres A , Martins Gislaine A , Stripp Barry R , Gharib Sina A , Goodridge Helen S , Chen Peter 
Published: July 2020

AbstractCoronavirus disease 2019 (COVID-19) has quickly become the most serious pandemic since the 1918 flu pandemic. In extreme situations, patients develop a dysregulated inflammatory lung injury called acute respiratory distress syndrome (ARDS) that causes progressive respiratory failure requiring mechanical ventilatory support. Recent studies have demonstrated immunologic dysfunction in severely ill COVID-19 patients. To further delineate the dysregulated immune response driving more severe clinical course from SARS-CoV-2 infection, we used single-cell RNA sequencing (scRNAseq) to analyze the transcriptome of peripheral blood mononuclear cells (PBMC) from hospitalized COVID-19 patients having mild disease (n = 5), developing ARDS (n = 6), and recovering from ARDS (n = 6). Our data demonstrated an overwhelming inflammatory response with select immunodeficiencies within various immune populations in ARDS patients. Specifically, their monocytes had defects in antigen presentation and deficiencies in interferon responsiveness that contrasted the higher interferon signals in lymphocytes. Furthermore, cytotoxic activity was suppressed in both NK and CD8 lymphocytes whereas B cell activation was deficient, which is consistent with the delayed viral clearance in severely ill COVID-19 patients. Finally, we identified altered signaling pathways in the severe group that suggests immunosenescence and immunometabolic changes could be contributing to the dysfunctional immune response. Our study demonstrates that COVID-19 patients with ARDS have an immunologically distinct response when compared to those with a more innocuous disease course and show a state of immune imbalance in which deficiencies in both the innate and adaptive immune response may be contributing to a more severe disease course in COVID-19.
Local structure of DNA toroids reveals curvature-dependent intermolecular forces
Authors: Barberi Luca , Livolant Françoise , Leforestier Amélie , Lenz Martin 
Published: July 2020

AbstractIn viruses and cells, DNA is closely packed and tightly curved thanks to polyvalent cations inducing an effective attraction between its negatively charged filaments. Our understanding of this effective attraction remains very incomplete, partly because experimental data is limited to bulk measurements on large samples of mostly uncurved DNA helices. Here we use cryo electron microscopy to shed light on the interaction between highly curved helices. We find that the spacing between DNA helices in spermine-induced DNA toroidal condensates depends on their location within the torus, consistent with a mathematical model based on the competition between electrostatic interactions and the bending rigidity of DNA. We use our model to infer the characteristics of the interaction potential, and find that its equilibrium spacing strongly depends on the curvature of the filaments. In addition, the interaction is much softer than previously reported in bulk samples using different salt conditions. Beyond viruses and cells, our characterization of the interactions governing DNA-based dense structures could help develop robust designs in DNA nanotechnologies.
NF-kappa-B activation unveils the presence of inflammatory hotspots in human gut xenografts
Authors: Nissim-Eliraz Einat , Nir Eilam , Marsiano Noga , Yagel Simcha , Shpigel Nahum Y. 
Published: July 2020

ABSTRACTThe single-epithelial cell layer of the gut mucosa serves as an essential barrier between the host and luminal microflora and plays a major role in innate immunity against invading pathogens. Nuclear factor kB (NF-κB), a central component of the cellular signaling machinery, regulates immune response and inflammation. NF-κB proteins are activated by signaling pathways downstream to microbial recognition receptors and cytokines receptors. Highly regulated NF-κB activity in intestinal epithelial cells (IEC) is essential for normal gut homeostasis; dysregulated activity has been linked to a number of disease states, including inflammatory bowel diseases (IBD) such as Crohn’s Disease (CD). Our aim was to visualize and quantify spatial and temporal dynamics of NF-κB activity in steady state and inflamed human gut. Lentivirus technology was used to transduce the IEC of human gut xenografts in SCID mice with a NF-κB luminescence reporter system. NF-κB signaling was visualized and quantified using low resolution, intravital imaging of the whole body and high resolution, immunofluorescence microscopic imaging of the tissues. We show that NF-κB is activated in select subset of IEC with low “leaky” NF-κB activity. These unique inflammatory epithelial cells are clustered in the gut into discrete hotspots of NF-κB activity that are visible in steady state and selectively activated by systemic LPS and human TNFα or luminal bacteria. The presence of inflammatory hotspots in the normal and inflamed gut might explain the patchy mucosal lesions characterizing CD and thus could have important implications for diagnosis and therapy.
The effect of absent blood flow on the zebrafish cerebral and trunk vasculature
Authors: Kugler Elisabeth , Snodgrass Ryan , Bowley George , Plant Karen , Serbanovic-Canic Jovana , Evans Paul C. , Chico Timothy , Armitage Paul 
Published: July 2020

AbstractThe role of blood flow is complex and context-dependent. In this study, we quantify the effect of the lack of blood flow on vascular development and compare its impact in two vascular beds, namely the cerebral and trunk vasculature, using zebrafish as preclinical model. We performed this by analysing vascular topology, endothelial cell number, apoptosis, and inflammatory response in animals with normal blood flow or absent blood flow. We find that absent blood flow reduced vascular area and endothelial cell number significantly in both examined vascular beds, but the effect is more severe in the cerebral vasculature. Similarly, while stereotypic vascular patterning in the trunk is maintained, intra-cerebral vessels show altered patterning. Absent blood flow lead to an increase in non-EC-specific apoptosis without increasing tissue inflammation, as quantified by cerebral immune cell numbers and nitric oxide. In conclusion, blood flow is essential for cellular survival in both the trunk and cerebral vasculature, but particularly intra-cerebral vessels are affected by the lack of blood flow, suggesting that responses to blood flow differ between these two vascular beds.Key pointsWe here use zebrafish as a model to quantitatively assess the impact of the lack of blood flow in development and compare its impact in two vascular beds, namely the cerebral to trunk vasculature.In both vascular beds, vascular growth and endothelial cell number are reduced by lack of blood flow, with increasing effect size from 2-5 days post fertilisation.Examination of vascular patterning shows that while stereotypic patterning in the trunk is preserved, the intra-cerebral vasculature patterning is altered.We found non-EC-specific cell death to be increased in both vascular beds, with a larger effect size in the brain, but that this cell death occurs without triggering tissue inflammation.
Protein kinase A controls the hexosamine pathway by tuning the feedback inhibition of GFAT-1
Authors: Ruegenberg Sabine , Mayr Felix A.M.C. , Miethe Stephan , Atanassov Ilian , Baumann Ulrich , Denzel Martin S. 
Published: July 2020

AbstractThe hexosamine pathway (HP) is a key anabolic pathway whose product uridine 5’-diphospho-N-acetyl-D-glucosamine (UDP-GlcNAc) is an essential precursor for all glycosylation processes in mammals. It modulates the ER stress response, is implicated in cancer and diabetes, and HP activation extends lifespan inCaenorhabditis elegans. The highly conserved glutamine fructose-6-phosphate amidotransferase 1 (GFAT-1) is the first and rate-limiting HP enzyme. GFAT-1 activity is modulated through UDP-GlcNAc feedback inhibition and by kinase signaling, including Ser205 phosphorylation by protein kinase A (PKA). The consequence and molecular mechanism of GFAT-1 phosphorylation, however, remains poorly understood. Here, we identify the GFAT-1 R203H substitution that elevates UDP-GlcNAc levels inC. elegans, leading to ER stress resistance. In human GFAT-1, the R203H substitution interfered with both UDP-GlcNAc inhibition and PKA-mediated Ser205 phosphorylation. Of note, Ser205 phosphorylation had two discernible effects: It lowered baseline GFAT-1 activity and abolished UDP-GlcNAc feedback inhibition. Thus, GFAT-1 phosphorylation by PKA uncoupled the feedback loop of the HP and, depending on UDP-GlcNAc availability, phosphorylation by PKA results in lower or enhanced GFAT-1 activityin vivo. Mechanistically, our data indicate that the relative positioning of the two GFAT-1 domains might be affected by phosphorylation and we propose a model how Ser205 phosphorylation modulates the activity and feedback inhibition of GFAT-1.
Genomic epidemiology and evolution ofEscherichia coliin wild animals
Authors: Murphy Robert , Palm Martin , Mustonen Ville , Warringer Jonas , Farewell Anne , Moradigaravand Danesh , Parts Leopold 
Published: July 2020

AbstractEscherichia coliis a common bacterial species in the gastrointestinal tracts of warm-blooded animals and humans. Pathogenic and antimicrobial resistance inE. colimay emerge via host switching from animal reservoirs. Despite its potential clinical importance, knowledge of the population structure of commensalE. coliwithin wild hosts and the epidemiological links betweenE. coliin non-human hosts andE. coliin humans is still scarce. In this study, we analysed the whole genome sequencing data of a collection of 119 commensalE. colirecovered from the guts of 68 mammal and bird species in Mexico and Venezuela in the 1990s. We observed low concordance between the population structures ofE. colicolonizing wild animals and the phylogeny, taxonomy and ecological and physiological attributes of the host species, with distantly relatedE. colioften colonizing the same or similar host species and distantly related host species often hosting closely relatedE. coli. We found no evidence for recent transmission ofE. coligenomes from wild animals to either domesticated animals or humans. However, multiple livestock- and human-related virulence factor genes were present inE. coliof wild animals, including virulence factors characteristic for Shiga toxin-producingE. coli(STEC) and atypical enteropathogenicE. coli(aEPEC), where several isolates from wild hosts harboured the locus of enterocyte effacement (LEE) pathogenicity island. Moreover,E. coliin wild animal hosts often harboured known antibiotic resistance determinants, including against ciprofloxacin, aminoglycosides, tetracyclines and beta-lactams, with some determinants present in multiple, distantly relatedE. colilineages colonizing very different host animals. We conclude that although the genome pools ofE. colicolonizing wild animal and human gut are well separated, they share virulence and antibiotic resistance genes andE. coliunderscoring that wild animals could serve as reservoirs forE. colipathogenicity in human and livestock infections.ImportanceEscherichia coliis a clinically importance bacterial species implicated in human and livestock associated infections worldwide. The bacterium is known to reside in the guts of humans, livestock and wild animals. Although wild animals are recognized to serve as potential reservoirs for pathogenicE. colistrains, the knowledge of the population structure ofE. coliin wild hosts is still scarce. In this study we used the fine resolution of whole genome sequencing to provide novel insights into the evolution ofE. coligenomes within a broad range of wild animal species (including mammals and birds), the co-evolution ofE. colistrains with their hosts and the genetics of pathogenicity ofE. colistrains in wild hosts. Our results provide evidence for the clinical importance of wild animals as reservoirs for pathogenic strains and necessitate the inclusion of non-human hosts in the surveillance programs forE. coliinfections.
Revealing the unique features of each individual’s muscle activation signatures
Authors: Aeles Jeroen , Horst Fabian , Lapuschkin Sebastian , Lacourpaille Lilian , Hug François 
Published: July 2020

AbstractThere is growing evidence that each individual has unique movement patterns, or signatures. The exact origin of these movement signatures however, remains unknown. We developed an approach that can identify individual muscle activation signatures during two locomotor tasks (walking and pedalling). A linear Support Vector Machine was used to classify 78 participants based on their electromyographic (EMG) patterns measured on eight lower limb muscles. To provide insight into decision making by the machine learning classification model, a Layer-wise Relevance Propagation (LRP) approach was implemented. This enabled the model predictions to be decomposed into relevance scores for each individual input value. In other words, it provided information regarding which features of the time-varying EMG profiles were unique to each individual. Through extensive testing, we have shown that the LRP results, and by extent the activation signatures, are highly consistent between conditions and across days. In addition, they are minimally influenced by the dataset used to train the model. Additionally, we proposed a method for visualising each individual’s muscle activation signature, which has several potential clinical and scientific applications. This is the first study to provide conclusive evidence of the existence of individual muscle activation signatures.
Single-cell transcriptome analysis of the immunosuppressive effect of differential expression of tumor PD-L1 on responding TCR-T cells
Authors: Ding Renpeng , Liu Shang , Wang Shanshan , Chen Huanyi , Wang Fei , Xu Qumiao , Zhu Linnan , Dong Xuan , Gu Ying , Chao Cheng-Chi , Gao Qianqian 
Published: July 2020

AbstractPD-L1 expression levels in tumors do not consistently predict cancer patients’ response to PD-(L)1 inhibitors. We therefore evaluated how tumor PD-L1 levels affect the anti-PD-(L)1 efficacy and T cell function. We used MART-1-specific TCR-T cells (TCR-TMART-1) stimulated with MART-127-35peptide-loaded MEL-526 tumor cells with different proportions of them expressing PD-L1 to perform cellular assays and high-throughput single-cell RNA sequencing. Compared to control T cells, TCR-TMART-1were more sensitive to exhaustion and secreted lower pro-inflammatory but higher anti-inflammatory cytokines with increasing proportions of PD-L1+tumor cells. The colocalization of T cells and tumor cells in gene clusters correlated negatively with the proportion of PD-L1+tumor cells and positively with immune cell cytotoxicity. Moreover, elevated proportion of PD-L1+tumor cells increased PD-L1 expression and decreased PD-1 expression on T cells and enhanced T cell death. The expression of PD-1 and PD-L1 in T cells and macrophages also correlated positively with COVID-19 severity.
An in-silico study on SARS-CoV-2: Its compatibility with human tRNA pool, and the polymorphism arising in a single lineage over a month
Authors: Victor Manish Prakash , Das Rohit , Ghosh Tapash Chandra 
Published: July 2020

AbstractSARS-CoV-2 has caused a global pandemic that has costed enormous human lives in the recent past. The present study is an investigation of the viral codon adaptation, ORFs’ stability and tRNA co-adaptation with humans. We observed that for the codon usage bias in viral ssRNA, ORFs have near values of folding free energies and codon adaptation index with mRNAs of the human housekeeping CDS. However, the correlation between the stability of the ORFs in ssRNA and CAI is stronger than the mRNA stability and CAI of HKG, suggesting a greater expression capacity of SARS-CoV-2. Mutational analysis reflects polymorphism in the virus for ORF1ab, surface glycoprotein and nucleocapsid phosphoprotein ORFs. Non-synonymous mutations have shown non-polar substitutions. Out of the twelve mutations nine are for a higher t-RNA copy number. Viruses in general have high mutation rates. To understand the chances of survival for the mutated SARS-CoV-2 we did simulation for synonymous mutations. It resulted in 50% ORFs with higher stability than their native equivalents. Thus, considering only the synonymous mutations the virus can exhibit a lot of polymorphism. Collectively our data provides new insights for SARS-CoV-2 mutations and the human t-RNA compatibility.SignificanceSurvivability of SARS-CoV-2 in humans is essential for its spread. It has overlapping genes exhibiting a high codon optimization with humans even after a higher codon usage bias. They seem to possess cognizance for high copy number t-RNA (cognate or near-cognate) in humans, while mutating. Even though, it has been well established that native transcripts posses the highest stability, our in-silico studies show that SARS-CoV-2 under mutations give rise to ORFs with higher stability. These results significantly present the virus’s ability and the credibility of survival for the mutants. Despite its focus on a geographical location it explains the ongoing behavior of SARS-CoV-2 for a steady existence in humans as all the different lineages have a common origin. Wuhan, China.
Limits and Convergence properties of the Sequentially Markovian Coalescent
Authors: Sellinger Thibaut , Awad Diala Abu , Tellier Aurélien 
Published: July 2020

AbstractMany methods based on the Sequentially Markovian Coalescent (SMC) have been and are being developed. These methods make use of genome sequence data to uncover population demographic history. More recently, new methods have extended the original theoretical framework, allowing the simultaneous estimation of the demographic history and other biological variables. These methods can be applied to many different species, under different model assumptions, in hopes of unlocking the population/species evolutionary history. Although convergence proofs in particular cases have been given using simulated data, a clear outline of the performance limits of these methods is lacking. We here explore the limits of this methodology, as well as present a tool that can be used to help users quantify what information can be confidently retrieved from given datasets. In addition, we study the consequences for inference accuracy violating the hypotheses and the assumptions of SMC approaches, such as the presence of transposable elements, variable recombination and mutation rates along the sequence and SNP call errors. We also provide a new interpretation of the SMC through the use of the estimated transition matrix and offer recommendations for the most efficient use of these methods under budget constraints, notably through the building of data sets that would be better adapted for the biological question at hand.
An integrate-and-fire spiking neural network model simulating artificially induced cortical plasticity
Authors: Shupe Larry , Fetz Eberhard E. 
Published: July 2020

AbstractWe describe an integrate-and-fire (IF) spiking neural network that incorporates spike-timing dependent plasticity (STDP) and simulates the experimental outcomes of four different conditioning protocols that produce cortical plasticity. The original conditioning experiments were performed in freely moving non-human primates with an autonomous head-fixed bidirectional brain-computer interface. Three protocols involved closed-loop stimulation triggered from (a) spike activity of single cortical neurons, (b) EMG activity from forearm muscles, and (c) cycles of spontaneous cortical beta activity. A fourth protocol involved open-loop delivery of pairs of stimuli at neighboring cortical sites. The IF network that replicates the experimental results consists of 360 units with simulated membrane potentials produced by synaptic inputs and triggering a spike when reaching threshold. The 240 cortical units produce either excitatory or inhibitory post-synaptic potentials in their target units. In addition to the experimentally observed conditioning effects, the model also allows computation of underlying network behavior not originally documented. Furthermore, the model makes predictions about outcomes from protocols not yet investigated, including spike-triggered inhibition, gamma-triggered stimulation and disynaptic conditioning. The success of the simulations suggests that a simple voltage-based IF model incorporating STDP can capture the essential mechanisms mediating targeted plasticity with closed-loop stimulation.