bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid differentiation of regulatory CD4+ T cells in the infarcted myocardium blunts in situ inflammation
Authors: Delgobo Murilo , Weiß Emil , Ashour Diyaa ElDin , Popiolkowski Lisa , Arampatzi Panagiota , Stangl Verena , Arias-Loza Paula , Rainer Peter P. , Saliba Antoine-Emmanuel , Ludewig Burkhard , Hofmann Ulrich , Frantz Stefan , Ramos Gustavo Campos 
Published: March 2022

AbstractBackgroundMyocardial infarction (MI) is a sterile inflammatory condition associated with tissue injury that results in the activation of T helper cell targeting cardiac antigens. However, the differentiation trajectories and in situ activity of heart-specific CD4+T cells activated in the MI context remain poorly understood.MethodsHerein, we combined T-cell receptor transgenic models targeting myocardial protein, single-cell transcriptomics, and functional phenotyping to elucidate how the myosin-specific CD4+ T cells (TCR-M) differentiate in the murine infarcted myocardium and ultimately influence tissue repair. Furthermore, we adoptively transferred heart-specific T-cells that were pre-differentiated in vitro towards pro-inflammatory versus regulatory phenotypic states to dissect how they differentially regulate post-myocardial infarction (MI) inflammation.ResultsFlow cytometry and single-cell transcriptomics findings reveled that transferred TCR-M cells rapidly acquired an induced regulatory phenotype (iTreg) in the infarcted myocardium and blunt local inflammation. Myocardial TCR-M cells differentiated into two main lineages enriched with cell activation and pro-fibrotic transcripts (e.g. Tgfb1) or with suppressor immune checkpoints (e.g. Pdcd1), which we also found in human myocardial tissue. These cells produced high levels of latency-associated peptide (LAP) and inhibited interleukine-17 (IL-17) responses. Notably, TCR-M cells that were pre-differentiated in vitro towards a regulatory phenotype maintained a stable in vivo FOXP3 expression and anti-inflammatory activity when adoptively transferred prior to MI induction. In contrast, TCR-M cells that were pre-differentiated in vitro towards a pro-inflammatory TH17 phenotype were partially converted towards a regulatory phenotype in the injured myocardium and blunted myocardial inflammation.ConclusionsThese findings reveal that the myocardial milieu provides a suitable environment for iTreg differentiation and reveals novels mechanisms by which the healing myocardium shapes local immunological processes.
Structural basis of transcription antitermination by Qλ: NusA induces refolding of Qλ to form nozzle for RNA polymerase exit channel
Authors: Yin Zhou , Bird Jeremy G. , Kaelber Jason T. , Nickels Bryce E. , Ebright Richard H. 
Published: March 2022

ABSTRACTLambdoid bacteriophage Q proteins are transcription antipausing and antitermination factors that enable RNA polymerase (RNAP) to read through pause and termination sites. Q proteins load onto RNAP engaged in promoter-proximal pausing at a Q binding element (QBE) and adjacent sigma-dependent pause element to yield a Q-loading complex, and translocate with RNAP as a pausing-deficient, termination-deficient Q-loaded complex. In previous work, we showed that the Q protein from bacteriophage 21 (Q21) functions by forming a “nozzle” that narrows and extends the RNAP RNA-exit channel, preventing formation of pause and termination RNA hairpins. Here, we report atomic structures of four states on the pathway of antitermination by the Q protein from bacteriophage λ (Qλ), a Q protein that shows no sequence similarity to Q21 and that, unlike Q21, requires the transcription elongation factor NusA for efficient antipausing and antitermination. We report structures of Qλ, the Qλ-QBE complex, the NusA-free “pre-engaged” Qλ-loading complex, and the NusA-containing “engaged” Qλ-loading complex. The results show that Qλ, like Q21, forms a nozzle that narrows and extends the RNAP RNA-exit channel, preventing formation of RNA hairpins. However, the results show that Qλ has no three-dimensional structural similarity to Q21, employs a different mechanism of QBE recognition than Q21, and employs a more complex process for loading onto RNAP than Q21, involving recruitment of Qλ to form a “pre-engaged” loading complex, followed by NusA-facilitated refolding of Qλ to form an “engaged” loading complex. The results establish Qλ and Q21 are not structural homologs and are solely functional analogs.SIGNIFICANCE STATEMENTBacteriophage Q proteins are textbook examples of regulators of gene expression that function at the level of transcription antitermination. Here, we report structures defining the mechanism of antitermination by the Q protein of bacteriophage λ (Qλ). The results show Qλ forms a “nozzle” that narrows and extends the RNA polymerase RNA-exit channel, precluding the formation of terminator RNA hairpins. The results show Qλ exhibits no structural similarity to the Q protein of bacteriophage 21 (Q21), employs a different mechanism for DNA binding than Q21, and employs a more complex process of loading onto RNA polymerase than Q21. We conclude Qλ and Q21 are not structural homologs and are solely functional analogs, akin to a bird wing and a bat wing.
Fast synaptic-like axo-axonal transmission from striatal cholinergic interneurons onto dopaminergic fibers
Authors: Kramer Paul F. , Brill-Weil Samuel , Cummins Alex C. , Zhang Renshu , Camacho-Hernandez Gisela A. , Newman Amy H. , Eldridge Mark A. , Averbeck Bruno B. , Khaliq Zayd M. 
Published: March 2022

SummaryTransmission from striatal cholinergic interneurons (CINs) controls dopamine release through nicotinic acetylcholine receptors (nAChRs) on dopaminergic axons. Anatomical studies suggest that cholinergic terminals signal predominantly through non-synaptic volume transmission. However, the influence of cholinergic transmission on electrical signaling in axons remains unclear. We examined axo-axonal transmission from CINs onto dopaminergic axons using perforated-patch recordings which revealed rapid spontaneous EPSPs with properties characteristic of fast synapses. Pharmacology showed that axonal EPSPs (axEPSPs) were mediated primarily by high-affinity α6-containing receptors. Remarkably, axEPSPs triggered spontaneous action potentials locally in dopaminergic axons, suggesting these axons perform integration to convert synaptic input into spiking, a function associated with somatodendritic compartments. We investigated cross-species validity of cholinergic axo-axonal transmission by recording dopaminergic axons in macaque putamen and found similar axEPSPs. Thus, we reveal that fast synaptic-like neurotransmission underlies cholinergic signaling onto dopaminergic axons, providing insight into how nicotinic receptors shape electrical signaling directly in axon terminals.
ChromDMM: A Dirichlet-Multinomial Mixture Model For Clustering Heterogeneous Epigenetic Data
Authors: Osmala Maria , Eraslan Gökçen , Lähdesmäki Harri 
Published: March 2022

AbstractMotivationResearch on epigenetic modifications and other chromatin features at genomic regulatory elements elucidates essential biological mechanisms including the regulation of gene expression. Despite the growing number of epigenetic datasets, new tools are still needed to discover novel distinctive patterns of heterogeneous epigenetic signals at regulatory elements.ResultsWe introduce ChromDMM, a product Dirichlet-multinomial mixture model for clustering genomic regions that are characterised by multiple chromatin features. ChromDMM extends the mixture model framework by profile shifting and flipping that can probabilistically account for inaccuracies in the position and strand-orientation of the genomic regions. Owing to hyper-parameter optimisation, ChromDMM can also regularise the smoothness of the epigenetic profiles across the consecutive genomic regions. With simulated data, we demonstrate that ChromDMM clusters, shifts, and strand-orients the profiles more accurately than previous methods. With ENCODE data, we show that the clustering of enhancer regions in the human genome reveals distinct patterns in several chromatin features. We further validate the enhancer clusters by their enrichment for transcriptional regulatory factor binding sites.AvailabilityThe software is available at https://github.com/MariaOsmala/ChromDMM
Multiplexed Label-Free Biomarker Detection by Targeted Disassembly of Variable-Length DNA Payload Chains
Authors: Aquilina Matthew , Dunn Katherine E. 
Published: March 2022

ABSTRACTSimultaneously studying different types of biomarkers (DNA, RNA, proteins, metabolites) has the potential to significantly improve understanding and diagnosis for many complex diseases. However, extracting biomarkers of different types involves using several technically complex or expensive methodologies, often requiring specialized laboratories and personnel. Streamlining detection through the use of a single multiplexed assay would greatly facilitate the process of accessing and interpreting patient biomarker data. In this work, we present a method for multiplexed biomarker detection based on variable-length DNA payload chains, which are systematically disassembled in the presence of specific biomolecular targets, leading to fragments of different sizes that yield characteristic band patterns in gel electrophoresis. This strategy has enabled us to detect with high sensitivity and specificity DNA sequences including BRCA1, an RNA sequence (miR-141) and the steroid aldosterone. We show that our assay can be multiplexed, enabling simultaneous detection of different types of biomarker. Furthermore, we show that our method suffers no loss of sensitivity when conducted in fetal bovine serum and can be applied using capillary electrophoresis, which may be more amenable to automation and integration in healthcare settings.ToC Graphic
Lis1-dynein drives corona compaction and error-correction at kinetochores
Authors: Mitevska Olivera , Lam Pak Wing , Auckland Philip 
Published: March 2022

AbstractMitotic cell division requires that kinetochores form microtubule attachments that can segregate chromosomes and control mitotic progression via the spindle assembly checkpoint. During prometaphase, kinetochores shed a distal domain called the fibrous corona as microtubule attachments form and mature. This shedding is mediated, in part, by the minus-end directed motor dynein, which ‘strips’ kinetochore cargoes along K-fibre microtubules towards the pole. While the main molecular players are well understood, relatively little is known about how dynein stripping is regulated and how it responds to increasing microtubule occupancy. Lis1 is a conserved dynein regulator that associates with kinetochores and is mutated in the severe neurodevelopmental disease lissencephaly. Here, we have combined loss-of-function studies, high-resolution imaging and engineered separation-of-function mutants to define how Lis1 contributes to dynein-mediated corona stripping. We show that cells depleted of Lis1 fail to fully dissemble the corona and delay in metaphase as a result of persistent checkpoint activation. Furthermore, we find that while kinetochore-tethered Lis1-dynein is required for attachment error-correction, the contribution of Lis1 to corona disassembly can be mediated by a rapidly cycling cytosolic pool. These findings support the idea that Lis1 contextualises dynein function at kinetochores to maintain corona disassembly into metaphase and prevent chromosome mis-segregation.
The general anesthetic isoflurane inhibits calcium activity in cerebrovascular endothelial cells and disrupts vascular tone
Authors: Shi Lingyan , Rodríguez-Contreras Adrián 
Published: March 2022

AbstractCalcium signaling in cerebrovascular endothelial cells (CVECs) has been identified to play key physiological and pathological roles in blood brain barrier function and neurovascular coupling, which involve dynamic changes in vessel diameter. However, there are no studies that measured correlated changes in vessel diameter and calcium activity in CVECs in vivo. In this study, we used the general anesthetic isoflurane (ISO) to induce a maximally dilated state in cortical blood vessels and measured the effects of the manipulation on CVEC calcium reporter activity in awake Cdh5BAC-GCaMP mice by use of two-photon fluorescence microscopy through thinned skull cranial windows. For the first time, we report dual effects of ISO on calcium activity in cerebral blood vessels of different diameter. During anesthesia induction ISO exposure triggered a short latency synchronous increase in calcium activity, followed by a period of activity suppression in small, medium, and large diameter vessels. Furthermore, during anesthesia maintenance calcium activity was desynchronized, and the relationship between vascular tone and calcium activity was disrupted in all vessel types. Based on these results we propose that there is a feedback mechanism between intracellular calcium fluctuations in CVECs and the maintenance of cerebrovascular tone.
Comparative Genome Analysis ofLactobacillus acidophilusIsolates from Different Ecological Niches
Authors: Liu Xudong , Hu Tongyuan , Lin Xiaoqian , Liang Hewei , Li Wenxi , Jin Xin , Xiao Liang , Fang Xiaodong , Zou Yuanqiang 
Published: March 2022

ABSTRACTLactobacillus acidophilushas been extensively applied in plentiful probiotic products and is mostly found in the gastrointestinal tract, vagina, and oral cavity of human and animal, and fermented foods. Although several studies have been performed to investigate the beneficial characteristics and genome function ofL. acidophilus, comparative genomic analysis remains scarce. In this study, we collected 74L. acidophilusgenomes from our gut bacterial genome collection and the public database and conducted a comprehensive comparative genomic analysis. The analysis of average nucleotide identity (ANI), phylogenetic, gene distribution of COG and KEGG database, carbohydrates utilization, and secondary metabolites revealed the potential correlation of the genomic diversity and niches adaptation ofL. acidophilusfrom different perspectives. In addition, the pan-genome ofL. acidophiluswas found to be open, with metabolism, information storage and processing genes mainly distributed in the core genome. Phage- and peptidase-associated genes were found in the genome of the specificity of animal-derived strains, which were related to adaptation of animal gut. SNP analysis showed the differences of the utilization of Vitamin B12 in cellular ofL. acidophilusstrains from animal gut and others. This work provides new insights for the genomic diversity analysis ofLactobacillus acidophilusand uncovers the ecological adaptation of the specific strains.
Deterioration of patients with mental disorders in Denmark coinciding with the invasion of Ukraine
Authors: Østergaard Søren Dinesen , Rohde Christopher , Jefsen Oskar Hougaard 
Published: March 2022

AbstractThe Russian invasion of Ukraine on February 24, 2022 has led to a humanitarian crisis of immense proportions. In turn, this will, inevitably, also lead to a mental health crisis among those affected by the war - either directly or by proxy. The mental health impact of the war in Ukraine is also likely to affect people beyond the borders of the countries directly involved. Here, we investigated whether Danish patients with mental disorders seem to be affected by the war in Ukraine. Specifically, we searched the Electronic Patient Record system of the Psychiatric Services of the Central Denmark Region in the period from January 1, 2022 to March 8, 2022 for clinical notes containing the word *ukrain* (*irrespective of letters and symbols prior to- or following ukrain). We then manually assessed (read) 100 randomly drawn notes containing *ukrain* to determine whether they described worsening of the mental health/symptoms of the patients that was likely attributable to the war in Ukraine. We identified a total of 16,341 adult patients (57% women, mean age 40 years, SD=18) who were registered with at least one clinical note in the Electronic Patient Record system of the Psychiatric Services of the Central Denmark Region in the period from January 1, 2022 to March 8, 2022. During this period, 567,647 clinical notes were entered into the electronic patient record system. Among these, 502 notes from 369 unique patients contained *ukrain* with a sharp rise in incidence following the Russian invasion of Ukraine on February 24, 2022. Among the 100 randomly drawn clinical notes containing *ukrain* (stemming from 94 unique patients), 62 notes from 58 unique patients described worsening of the mental health/symptoms of the patients that seemed attributable to the war in Ukraine. Although causal inference is challenging in this regard, the results of this study suggest that even individuals remotely distanced from the war in Ukraine may be psychologically affected by it - serving as an early warning sign of the potential width of the negative mental health impact from the war, which will, inevitably, hit the Ukrainian population the hardest.
RNAseq analysis reveals prominent and distinct expressed variants that are related to disease severity in SARS-CoV-2 infected patients with mild-to-severe disease
Authors: Okendo Javan , Okanda David 
Published: March 2022

AbstractBackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to be a significant public health challenge globally. SARS-CoV-2 is a novel virus, and the understanding of what constitutes expressed RNAseq variants in healthy, convalescent, severe, moderate and to those admitted at the Intensive Care Unit (ICU) is yet to be presented. We set to characterize the different expressed RNAseq variants in healthy, severe, moderate, ICU, and convalescent individuals.Materials and methodsThe bulk RNA sequencing data with identifier PRJNA639275 was download from Sequence Reads Archive (SRA). The individuals were divided into: (i) healthy, n=34, severe, n=16, ICU, n=8, moderate, n=8, and convalescent, n=2. Fastqc version 0.11.9 and Cutadapt version 3.7 was used to asses the reads quality and to perform adapter trimming respectively. STAR was using to align reads to the reference genome and GATK best practice was followed to call variants using rnavar pipeline, part of the nf-core pipelines.ResultsOur analysis demonstrated that convalescent, moderate, severe and those admitted to the ICU are characterized by different sets of unique RNAseq variants. The data shows that the individuals who recover from SARS-CoV-2 infection have the same set of expressed variants as in the healthy controls. We showed that the healthy and SARS-CoV-2 infected individuals display different sets of expressed varinats which is characteristic of the patient phenotype.ConclusionThe individuals with severe, moderate, those admitted at the ICU, and convalescent individuals display a unique set of variants. The findings in this study will inform the test kit development and SARS-CoV-2 patients classification to enhance management and control of SARS-CoV-2 infection in our population.
Sexual selection on a female copulatory device in an insect with nuptial gifts
Authors: Browne Jessica H. , Gwynne Darryl T. 
Published: March 2022

AbstractMale genitalia are rapidly evolving structures, often driven sexual selection to increase fertilization success. Although sexual selection on females can be strong in systems where males provide offspring care or feed their mates, sometimes resulting in the evolution of female ornamentation, there are no actual estimates of direct sexual selection on female genitalia. In a New Zealand ground weta,Hemiandrus pallitarsis(Orthoptera: Ensifera, Anostostomatidae), females possess a genitalic device (the accessory organ) that is necessary for successful copulation and the acquisition of glandular food-gifts from males. These nutritious gifts are known to result in sexual competition among females in other ensiferan species. In ground weta, the gifts are probably important in avoiding starvation during a months-long period when caring for (their lifetime production of) eggs and offspring. Here, we test the hypothesis that the accessory organ is a sexually selected device inH. pallitarsisby measuring the female Bateman gradient and directional sexual selection on the accessory organ. Using newly developed and characterized microsatellite loci, we analyze offspring and/or stored sperm to estimate female mating frequency for the first time in ground weta. As predicted, we found positive Bateman gradients for females, and some evidence of directional sexual selection on accessory organ length. Although organ length does not correlate well with female fecundity, it may increase mating success by indicating her condition and thus quality of her offspring care.
Sex-specific role of the circadian transcription factor NPAS2 in opioid tolerance, withdrawal, and analgesia
Authors: Puig Stephanie , Shelton Micah A. , Barko Kelly , Seney Marianne L. , Logan Ryan W. 
Published: March 2022

ABSTRACTOpioids like fentanyl are the mainstay treatment for chronic pain. Unfortunately, opioids high addiction liability has led to the current opioid crisis. This is in part related to long-term use side-effects, including analgesic tolerance (gradual decrease in analgesia), and physical dependence (withdrawal symptoms upon opioid interruption), causing dose-escalation and preventing usage interruption. Altered circadian rhythmicity and sleep patterns are common in patients on opioid therapy. Prior research showed intricate bidirectional interactions between circadian rhythmicity, opioid analgesic efficacy, and side-effects. However, underlying mechanisms are largely unknown. Neuronal PAS domain protein 2 (NPAS2) is a circadian transcription factor that is highly expressed in structures of the central nervous system that modulate pain and opioids. In this study, we used male and female mice expressing non-functional NPAS2 (NPAS2 deficient, NPAS2-/-) to investigate the role of NPAS2 in fentanyl analgesia, tolerance, hyperalgesia, and dependence. In NPAS2-/- mice, we found that thermal pain thresholds, acute analgesia, and tolerance to a fixed dose of fentanyl were largely like wild-type mice. However, female NPAS2-/- mice augmented behavioral state of analgesic tolerance and exhibited significantly more behavioral symptoms of physical dependence. Conversely, only male NPAS2-/- mice had increased fentanyl-induced hypersensitivity, when compared to matched-sex littermate controls. Together, our findings suggest sex-specific effects of NPAS2 signaling in the regulation of fentanyl-induced tolerance, hyperalgesia, and dependence.