bluuebunny/crossref_metadata_2025_split huggingface dataset:
A highly scalable method for joint whole genome sequencing and gene expression profiling of single cells
Authors: Zachariadis Vasilios , Cheng Huaitao , Andrews Nathanael J , Enge Martin 
Published: March 2020

AbstractUnderstanding how genetic variation alters gene expression - how genotype affects phenotype - is a central challenge in biology. To address this question in complex cell mixtures, we developed Direct Nuclear Tagmentation and RNA-sequencing (DNTR-seq), which enables whole genome and mRNA sequencing jointly in single cells. When applied to biobanked leukemia samples, DNTR-seq readily identified minor subclones within patients, as well as cell-type specific gene editing such as T-cell receptor rearrangements. mRNA-seq quality is equal to RNA-only methods, and the high yield combined with low positional bias of the genomic library preparation allows detection of sub-megabase aberrations at ultra low coverage of 0.5-3M read pairs per genome. Since each cell library is individually addressable, rare subpopulations can be re-sequenced at increased depth, allowing multi-tiered study designs where depth of sequencing is informed by previous results. In addition, the direct tagmentation protocol enables coverage-independent estimation of ploidy, which can be used to unambiguously identify cell singlets. Thus, DNTR-seq directly links each cell’s state to its corresponding genome at a scale enabling routine analysis of heterogeneous tumors and other complex tissues.
Within-Family Validation of Polygenic Risk Scores and Complex Trait Prediction
Authors: Lello Louis , Raben Timothy G. , Hsu Stephen D.H. 
Published: March 2020

AbstractWe test a variety of polygenic predictors using tens of thousands of genetic siblings for whom we have SNP genotypes, health status, and phenotype information in late adulthood. Siblings have typically experienced similar environments during childhood, and exhibit negligible population stratification relative to each other. Therefore, the ability to predict differences in disease risk or complex trait values between siblings is a strong test of genomic prediction in humans. We compare validation results obtained using non-sibling subjects to those obtained among siblings and find that typically most of the predictive power persists in within-family designs. In the case of disease risk we test the extent to which higher polygenic risk score (PRS) identifies the affected sibling, and also compute Relative Risk Reduction as a function of risk score threshold. For quantitative traits we examine between-sibling differences in trait values as a function of predicted differences, and compare to performance in non-sibling pairs. Example results: Given 1 sibling with normal-range PRS score (<84 percentile) and 1 sibling with high PRS score (top few percentiles), the predictors identify the affected sibling about 70-90% of the time across a variety of disease conditions, including Breast Cancer, Heart Attack, Diabetes, etc. For height, the predictor correctly identifies the taller sibling roughly 80 percent of the time when the (male) height difference is 2 inches or more.
Analyzing and interpreting DNA double-strand break sequencing data
Authors: Mitra Abhishek , Dojer Norbert , Fongang Bernard , Nde Jules , Zhu Yingjie , Rowicka Maga 
Published: March 2020

AbstractDNA double-strand breaks (DSBs), are a major threat to genomic stability and may lead to cancer. Several technologies to accurately detect DSBs genome-wide have been developed recently, but still lacking publicly available tools for analysis of the resulting data. Here, we present a step-by-step iSeq package (http://breakome.utmb.edu/software.html), custom designed for analysis and interpretation of DSB-sequencing data. iSeq performs barcode trimming and read counting, and identifies DSB-enriched regions by statistical test and annotate them to the desired genomic features. Applying this package, users can identify and annotate DSB-enriched regions from base pair (eg. Cas9 cleavage sites) up to megabase (eg. DNA replication stress-induced) resolution, and if possible quantify DSB frequencies per cell genome-wide by combining with qDSB-Seq. iSeq can be used for any sequencing-based DSB detection techniques. The analysis for Steps 1-19 can be performed within ~4 hours.
The gliopeptide ODN, a ligand for the benzodiazepine site of GABAAreceptors, boosts functional recovery after stroke
Authors: Lamtahri Rhita , Hazime Mahmoud , Gowing Emma K , Nagaraja Raghavendra Y. , Maucotel Julie , Alasoadura Michael , Quilichini Pascale , Lehongre Katia , Lefranc Benjamin , Gach-Janczak Katarzyna , Marcher Ann-Britt , Mandrup Susanne , Vaudry David , Clarkson Andrew N. , Leprince Jérôme , Chuquet Julien 
Published: March 2020

AbstractFollowing stroke, the survival of neurons and their ability to re-establish connections is critical to functional recovery. This is strongly influenced by the balance between neuronal excitation and inhibition. In the acute phase of experimental stroke, lethal hyperexcitability can be attenuated by positive allosteric modulation of GABAAreceptors (GABAAR). Conversely, in the late phase, negative allosteric modulation of GABAAR can correct the sub-optimal excitability and improves both sensory and motor recovery. Here, we hypothesized that octadecaneuropeptide (ODN), an endogenous allosteric modulator of the GABAAR synthesized by astrocytes, influences the outcome of ischemic brain tissue and subsequent functional recovery. We show that ODN boosts the excitability of cortical neurons, which make it deleterious in the acute phase of stroke. However, if delivered after day 3, ODN is safe and improves motor recovery over the following month in two different paradigms of experimental stroke in mice. Furthermore, we bring evidence that during the sub-acute period after stroke, the repairing cortex can be treated with ODN by means of a single hydrogel deposit into the stroke cavity.SIGNIFICANCE STATEMENTStroke remains a devastating clinical challenge because there is no efficient therapy to either minimize neuronal death with neuroprotective drugs or to enhance spontaneous recovery with neurorepair drugs. Around the brain damage, the peri-infarct cortex can be viewed as a reservoir of plasticity. However, the potential of wiring new circuits in these areas is restrained by a chronic excess of GABAergic inhibition. Here we show that an astrocyte-derived peptide (ODN), can be used as a delayed treatment, to safely correct cortical excitability and facilitate sensorimotor recovery after stroke.
Identification of potential biomarkers associated with pathogenesis of primary prostate cancer based on meta-analysis approaches
Authors: Sepahi Neda , Piran Mehrdad , Piran Mehran , Ghanbariasad Ali 
Published: March 2020

AbstractWorldwide prostate cancer (PCa) is recognized as the second most common diagnosed cancer and the fifth leading cause of cancer death among men globally. Rising incidence rates of PCa have been observed over the last few decades. It is necessary to improve prostate cancer detection, diagnosis, treatment and survival. However, there are few reliable biomarkers for early prostate cancer diagnosis and prognosis. In the current study, systems biology method was applied for transcriptomic data analysis to identify potential biomarkers for primary PCa. We firstly identified differentially expressed genes (DEGs) between primary PCa and normal samples. Then the DEGs were mapped in Wikipathways and gene ontology database to conduct functional categories enrichment analysis. 1575 unique DEGs with adjusted p-value < 0.05 were achieved from two sets of DEGs. 132 common DEGs between two sets of DEGs were retrieved. The final DEGs were selected from 60 common upregulated and 72 common downregulated genes between datasets. In conclusion, we demonstrated some potential biomarkers (FOXA1, AGR2, EPCAM, CLDN3, ERBB3, GDF15, FHL1, NPY, DPP4, and GADD45A) and HIST2H2BE as a candidate one which are tightly correlated with the pathogenesis of PCa.
Targeted Esterase induced Dye loading supports Calcium Imaging in Eukaryotic Cell-Free Systems
Authors: Dhandapani Priyavathi , Dondapati Srujan Kumar , Zemella Anne , Bräuer Dennis , Wüstenhagen Doreen Anja , Kubick Stefan 
Published: March 2020

ABSTRACTCalcium imaging is an important functional tool for addressing ion channels, transporters and pumps for drug screening in living cells. Depicted eukaryotic cell-free systems utilize microsomes, derived from endoplasmic reticulum to incorporate the synthesized membrane proteins. Absence or inadequate amount of carboxylesterase in the endoplasmic reticulum of eukaryotic cells, which is necessary to cleave the acetoxymethyl ester moiety of the chemical calcium indicators, advocates the hindrance to perform calcium imaging in microsomes. In this work, we try to overcome this drawback and adapt the cell-based calcium imaging principle to a cell-free protein synthesis platform. Carboxylesterase synthesized in a Spodoptera frugiperda Sf21 lysate translation system is established as a viable calcium imaging tool and hTRPV1 is used as a model channel protein to demonstrate the realization of this concept.
Prolonged deficit of gamma oscillations in the peri-infarct cortex of mice after stroke
Authors: Hazime M , Alasoadura M , Lamtahri R , Quilichini P , Leprince J , Vaudry D , Chuquet J 
Published: March 2020

AbstractDays and weeks after an ischemic stroke, the peri-infarct area adjacent to the necrotic tissue exhibits very intense synaptic reorganization aimed at regaining lost functions. In order to enhance functional recovery, it is important to understand the mechanisms supporting neural repair and neuroplasticity in the cortex surrounding the lesion. Brain oscillations of the local field potential (LFP) are rhythmic fluctuations of neuronal excitability aimed at synchronizing neuronal activity to organize information processing and plasticity. Although the oscillatory activity of the brain has been probed after stroke in both animals and humans using electroencephalography (EEG), the latter is ineffective to precisely map the oscillatory changes in the peri-infarct zone where synaptic plasticity potential is high. Here, we worked on the hypothesis that brain oscillatory system is altered in the surviving peri-infarct cortex, which may slow down functional repair and reduce the capacity to recovery. In order to document the relevance of this hypothesis, oscillatory power was measured at various distances from the necrotic core at 7 and 21 days after a permanent cortical ischemia induced in mice. Delta and theta oscillations remained at a normal power in the peri-infarct cortex, in contrast to gamma oscillations that displayed a rapid decrease, the closer we get to the lesion core. A broadband increase of power was also observed in the homotopic contralateral sites. Thus, the proximal peri-infarct cortex could become a target of therapeutic interventions aimed at correcting the oscillatory regimen. These results argue for the usefulness of therapeutic intervention aimed at boosting gamma oscillations in order to improve post-stroke functional recovery.
Evolutionary dynamics of transposable elements following a shared polyploidization event in the tribe Andropogoneae
Authors: Ramachandran Dhanushya , McKain Michael R. , Kellogg Elizabeth A. , Hawkins Jennifer S. 
Published: March 2020

AbstractBoth polyploidization and transposable element (TE) activity are known to be major drivers of plant genome evolution. Here, we utilize theZea-Tripsacumclade to investigate TE activity and accumulation after a recent shared polyploidization event. Comparisons of TE evolutionary dynamics in variousZeaandTripsacumspecies, in addition to two closely related diploid species,Urelytrum digitatumandSorghum bicolor, revealed existing variation in repeat content among all taxa included in the study. The repeat composition ofUrelytrumis more similar to that ofZeaandTripsacumcompared toSorghum, despite the similarity in genome size with the latter. Although the genomes of all species studied had abundant LTR-retrotransposons, we observed an expansion of thecopiasuperfamily, specifically inZ. maysandT. dactyloides, species that have adapted to more temperate environments. Additional analyses of the genomic distribution of thesecopiaelements provided evidence of biased insertions near genes involved in various biological processes including plant development, defense, and macromolecule biosynthesis. The lack ofcopiainsertions near the orthologous genes inS. bicolorsuggests that duplicate gene copies generated during polyploidization may offer novel neutral sites for TEs to insert, thereby providing an avenue for subfunctionalization via TE insertional mutagenesis.
Mechanism of BceAB-type transporter: Resistance by lipid II flipping
Authors: Zaschke-Kriesche Julia , Unsleber Sandra , Voitsekhovskaia Irina , Kulik Andreas , Behrmann Lara V. , Overbeck Nina , Stühler Kai , Stegmann Evi , Smits Sander H.J. 
Published: March 2020

AbstractTreatment of bacterial infections are the great challenge of our era due to the evolved resistance mechanisms against antibiotics. The Achilles heel of bacteria is the cell wall especially during the needs of its synthesis and cell division. Here lipid II is an essential cell wall precursor component synthesized in the cytosol and flipped into the outer leaflet of the membrane prior to its incorporation into the cell wall.Compounds targeting the cell wall or its biosynthesis precursors have been around for decades and have been used as antibiotics against bacterial infections like meningitis, pneumonia and endocarditis. Antimicrobial peptides (AMPs) have proven to be a promising weapon against multiresistant bacteria. However, theBacitracinefflux (BceAB)-type ATP binding cassette transporters expressed in the membrane of human pathogenic bacteria have been shown to confer resistance to these alternative antibiotics, thereby hampering their medical development.InStreptococcus agalactiaeCOH1 the BceAB-type transporter NsrFP (SaNsrFP) confers high-level resistance against the antimicrobial peptide nisin, a member of the lantibiotic subfamily. We showed thatSaNsrFP provides a novel resistance mechanism by flipping lipid II back into the cytosol, thereby preventing the binding of nisin as well as other lipid II targeting compounds. This is intriguing since a relatively simple reaction mediates resistance to human pathogenic bacteria to lipid II targeting antibiotics, regardless of their structure.Significance StatementThe ABC-transporter NsrFP fromStreptococcus agalactiae(SaNsrFP) belongs to the BceAB-type transporters. Several BceAB-type transporters are known to confer resistance against multiple antimicrobial peptides. In this study a new resistance mechanism was identified, which is based on the reduction of the number of cell wall precursor lipid II molecules on the cell surface mediated bySaNsrFP.SaNsrFP flips lipid II, which are considered to be the target for many antibiotics, back into the cytoplasm. With this newly gained knowledge about the resistance mechanism of BceAB-type transporters, novel strategies can be established to overcome or bypass this resistance in human pathogenic bacteria.
Differential roles of pyramidal and fast-spiking, GABAergic neurons in the control of glioma cell proliferation
Authors: Tantillo Elena , Vannini Eleonora , Cerri Chiara , Spalletti Cristina , Colistra Antonella , Mazzanti Chiara Maria , Costa Mario , Caleo Matteo 
Published: March 2020

AbstractRecent studies have demonstrated an active role for neurons in glioma progression. Specifically, peritumoral neurons establish functional excitatory synapses with glioma cells, and optogenetic stimulation of cortical pyramidal neurons drives tumor progression. However, the specific role of different subsets of cortical neurons, such as GABAergic interneurons, remains unexplored. Here, we directly compared the effects of optogenetic stimulation of pyramidal cells vs. fast-spiking, GABAergic neurons. In mice inoculated with GL261 cells into the motor cortex, we show that optogenetic stimulation of pyramidal neurons enhances glioma cell proliferation. In contrast, optogenetic stimulation of fast-spiking, parvalbumin-positive interneurons reduces proliferation as measured by BrdU incorporation and Ki67 immunolabelling. Since both principal cells and fast-spiking interneurons are directly activated by sensory afferent input, we next placed tumors in the occipital cortex to test the impact of visual stimulation/deprivation. We report that total lack of visual input via dark rearing enhances the density of proliferating glioma cells, while daily visual stimulation by gratings of different spatial frequencies and contrast reduces tumor growth. The effects of sensory input are region-specific, as visual deprivation has no significant effect on tumor proliferation in mice with gliomas in the motor cortex. We also report that sensory stimulation combined with temozolomide administration delays the loss of visual responses in peritumoral neurons. Altogether, these data demonstrate complex effects of different neuronal subtypes in the control of glioma proliferation.HighlightsActivity of GABAergic neurons reduces glioma cell proliferationLevels of sensory afferent input regulate tumor proliferationEffects of sensory input are region-specific
A porcine bimicrobial abscess model for testing interventional treatments
Authors: Wang Yak-Nam , Brayman Andrew A. , Chan Keith T. , Richmond Keith , Monsky Wayne L. , Matula Thomas J. 
Published: March 2020

AbstractBackgroundAbscess formation is a host defense mechanism to contain the spread of infection. Abscesses can affect any part of the body and are commonsequelaeto complications of trauma, surgery, systemic infections and other disease states. Most models for abscesses are in small animals. Pursuant to the goal of developing more advanced treatments for abscesses, we sought to develop a large animal model which would reasonably mimic a fluid-filled human abscess.MethodsDomestic swine were inoculated with a bimicrobial mixture ofBacteroides fragilis(B. fragilis) andEscherichia coli(E. coli) supplemented with an irritant (dextran). Inoculations were performed under ultrasound guidance in the muscle, subcutaneously or intradermally within the same animal. Fourteen days after inoculation, lesions were imaged with ultrasound, resected and prepared for histological evaluation.ResultsInjection of bimicrobial (aerobic and anaerobic) bacterial mixtures at multiple sites in a pig produced multiple lesions with histological features similar to encapsulated and multiloculated/multichamber abscesses often observed clinically in humans. Important salient features include the formation of a connective tissue capsule surrounding histologically nearly amorphous pus.ConclusionsThis paper provides the first description of a pig model for multiloculated abscesses. This animal model could potentially enable the evaluation of new technologies to replace or augment the current standard of care (image-guided percutaneous abscess drainage with antibiotics).
Functional delineation of tissue-resident CD8+T cell heterogeneity during infection and cancer
Authors: Milner J. Justin , Toma Clara , He Zhaoren , Kurd Nadia S. , Nguyen Quynh P. , McDonald Bryan , Quezada Lauren , Widjaja Christella E. , Witherden Deborah A. , Crowl John T. , Yeo Gene W. , Chang John T. , Omilusik Kyla D. , Goldrath Ananda W. 
Published: March 2020

AbstractUnremitting defense against diverse pathogens and malignancies requires a dynamic and durable immune response. Tissue-resident memory CD8+T cells (Trm) afford robust protection against infection and cancer progression through continuous surveillance of non-lymphoid tissues. Here, we provide insight into how Trmconfer potent and persistent immunity through partitioning of distinct cellular subsets differing in longevity, effector function, and multipotency. Antigen-specific CD8+T cells localized to the epithelium of the small intestine are primarily comprised of a shorter-lived effector population most prominent early following both acute viral and bacterial infections, and a longer-lived Id3hiTrmpopulation that subsequently accumulates at later memory timepoints. We define regulatory gene-programs driving these distinct Trmstates, and further clarify roles for Blimp1, T-bet, Id2, and Id3 in supporting and maintaining intestinal Trmheterogeneity during infection. Further, through single-cell RNAseq analysis we demonstrate that tumor-infiltrating lymphocytes broadly differentiate into discrete populations of short-lived and long-lived Trm-like subsets, which share qualities with terminally-exhausted and progenitor-exhausted cells, respectively. As the clinical relevance of Trmcontinues to widen from acute infections to settings of chronic inflammation and malignancy, clarification of the spectrum of phenotypic and functional states exhibited by CD8+T cells that reside in non-lymphoid tissues will provide a framework for understanding their regulation and identity in diverse pathophysiological contexts.
Innate immune signalling drives loser cell elimination during stem cell competition in theDrosophilatestis
Authors: Hof-Michel Silvana , Cigoja Ljubinka , Huhn Sabina , Bökel Christian 
Published: March 2020

AbstractIn theDrosophilatestis, a group of stromal cells termed hub provides multiple niche signals for the surrounding germline and somatic stem cells. Stem cells of both populations compete for physical retention in the niche, and stem cell clones unable to transduce any one niche signal are rapidly eliminated by differentiation. We have recently mapped the transcriptomes of isolated somatic cyst stem cells and differentiated cyst cells, and found that the stem cells but not their differentiated progeny activate an immune response involving the NF-κB transcription factor Relish (Rel).Here we show i) that Rel activation is not required for stemness but occurs physiologically in “losers” of stem cell competition, ii) that loss of Rel or the upstream receptor Toll suppresses loser elimination irrespective of how loser fate was induced, and iii) that clonal Rel activation is sufficient for the displacent of neutral or winner cells from the niche, even if the winners otherwise retain stem cell properties.This generalized mechanism for the elimination of “loser” stem cells may mask the compound nature of stem cell behaviour, and instead generate the impression of a binary cell fate decision between stemness and differentiation.