bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global hypo-methylation in a subgroup of glioblastoma enriched for an astrocytic signature is associated with increased invasion and altered immune landscape
Authors: Boot James R , Rosser Gabriel , Kancheva Daliya , Vinel Claire , Lim Yau Mun , Pomella Nicola , Zhang Xinyu , Guglielmi Loredana , Sheer Denise , Barnes Michael R. , Brandner Sebastian , Nelander Sven , Movahedi Kiavash , Marino Silvia 
Published: February 2022

AbstractWe describe a new molecular subgroup of glioblastoma, the most prevalent malignant adult brain tumour, harbouring a bias towards hypomethylation at defined differentially methylated regions. This epigenetic signature correlates with an enrichment for an astrocytic gene signature, which together with the identification of enriched predicted binding sites of transcription factors known to cause demethylation and to be involved in astrocytic/glial lineage specification, point to a shared ontogeny between this glioblastoma subgroup and astroglial progenitors. At functional level, increased invasiveness, at least in part mediated by SRPX2, and macrophage infiltration characterise this glioblastoma subgroup.
Fibrosis resolution in the mouse liver: role of Mmp12 and potential role of Calpain 1/2
Authors: Sato Toshifumi , Head Kimberly Z. , Li Jiang , Dolin Christine E. , Wilkey Daniel , Skirtich Nolan , McCreary Dylan D. , Liu Sylvia , Beier Juliane I , McEnaney Ryan M. , Merchant Michael L , Arteel Gavin E 
Published: February 2022

AbstractAlthough most work has focused on resolution of collagen ECM, fibrosis resolution involves changes to several ECM proteins. The purpose of the current study was two-fold: 1) to examine the role of MMP12 and elastin; and 2) to investigate the changes in degraded proteins in plasma (i.e., the “degradome”) in a preclinical model of fibrosis resolution. Fibrosis was induced by 4 weeks carbon tetrachloride (CCl4) exposure, and recovery was monitored for an additional 4 weeks. Some mice were treated with daily MMP12 inhibitor (MMP408) during the resolution phase. Liver injury and fibrosis was monitored by clinical chemistry, histology and gene expression. The release of degraded ECM peptides in the plasma was analyzed using by 1D-LC-MS/MS, coupled with PEAKS Studio (v10) peptide identification. Hepatic fibrosis and liver injury rapidly resolved in this mouse model. However, some collagen fibrils were still present 28d after cessation of CCl4. Despite this persistent collagen presence, expression of canonical markers of fibrosis were also normalized. The inhibition of MMP12 dramatically delayed fibrosis resolution under these conditions. LC-MS/MS analysis identified that several proteins were being degraded even at late stages of fibrosis resolution. Calpains 1/2 were identified as potential new proteases involved in fibrosis resolution. CONCLUSION. The results of this study indicate that remodeling of the liver during recovery from fibrosis is a complex and highly coordinated process that extends well beyond the degradation of the collagenous scar. These results also indicate that analysis of the plasma degradome may yield new insight into the mechanisms of fibrosis recovery, and by extension, new “theragnostic” targets. Lastly, a novel potential role for calpain activation in the degradation and turnover of proteins was identified.
Antisense oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types
Authors: Yip Chi Wai , Hon Chung-Chau , Yasuzawa Kayoko , Sivaraman Divya M. , Ramilowski Jordan A. , Shibayama Youtaro , Agrawal Saumya , Prabhu Anika V. , Parr Callum , Severin Jessica , Lan Yan Jun , Dostie Josée , Petri Andreas , Nishiyori-Sueki Hiromi , Tagami Michihira , Itoh Masayoshi , López-Redondo Fernando , Kouno Tsukasa , Chang Jen-Chien , Luginbühl Joachim , Kato Masaki , Murata Mitsuyoshi , Yip Wing Hin , Shu Xufeng , Abugessaisa Imad , Hasegawa Akira , Suzuki Harukazu , Kauppinen Sakari , Yagi Ken , Okazaki Yasushi , Kasukawa Takeya , de Hoon Michiel , Carninci Piero , Shin Jay W. 
Published: February 2022

SummaryWithin the scope of FANTOM6 consortium, we perform a large-scale knockdown of 200 long non-coding RNAs (lncRNAs) in human induced pluripotent stem (iPS) cells, and systematically characterize their roles in self-renewal and pluripotency. We find 36 lncRNAs (18%) exhibiting cell growth inhibition From the knockdown of 123 lncRNAs with transcriptome profiling, 36 lncRNAs (29.3%) show molecular phenotypes. Integrating the molecular phenotypes with chromatin-interaction assays further revealscis- andtrans-interacting partners as potential primary targets. Additionally, cell type enrichment analysis identifies lncRNAs associated with pluripotency while the knockdown ofLINC02595,CATG00000090305.1andRP11-148B6.2modulates colony formation of iPS cells. We compare our results with previously published fibroblasts phenotyping data and find that 2.9% of the lncRNAs exhibit consistent cell growth phenotype, whereas we observe 58.3% agreement in molecular phenotypes. This highlights molecular phenotyping is more comprehensive in revealing affected pathways.
Contribution of the Wolffian duct mesenchyme to the formation of the female reproductive tract
Authors: Zhao Fei , Grimm Sara A , Jia Shua , Yao Humphrey Hung-Chang 
Published: February 2022

AbstractThe female reproductive tract develops from its embryonic precursor, the Müllerian duct.In close proximity to the Müllerian duct lies the precursor for the male reproductive tract, the Wolffian duct, which is eliminated in the female embryo during sexual differentiation. We discovered that a component of the Wolffian duct, its mesenchyme, is not eliminated after sexual differentiation. Instead, the Wolffian duct mesenchyme underwent changes in transcriptome and chromatin accessibility from male tract to female tract identity, and became a unique mesenchymal population in the female reproductive tract with localization and transcriptome distinct from the mesenchyme derived from the Müllerian duct. Partial ablation of the Wolffian duct mesenchyme stunted the growth of the fetal female reproductive tract. These findings reveal a new fetal origin of mesenchymal tissues for female reproductive tract formation and reshape our understanding of sexual differentiation of reproductive tracts.Significance statementA female embryo initially possesses both the primitive female and male reproductive tracts, also known as the Müllerian and Wolffian duct. During sexual differentiation, the female eliminates the Wolffian duct and maintains the Müllerian duct that eventually differentiates into the female reproductive tract organs. However, in this paper, we show the female embryo retains mesenchymal cells surrounding the Wolffian duct for its reproductive tract formation. When incorporated into the female reproductive tract organs, the Wolffian duct mesenchyme shows unique anatomical localization and transcriptome and plays critical roles in female reproductive tract growth. This discovery provides new insights into female reproductive tract development and advances our understanding of sexual differentiation of reproductive tracts.
Predicted structure of the hepatitis B virus polymerase reveals an ancient conserved protein fold
Authors: Tajwar Razia , Bradley Daniel P. , Ponzar Nathan L. , Tavis John E. 
Published: February 2022

AbstractHepatitis B virus (HBV) replicates by protein-primed reverse transcription. It chronically infects >250 million people, and the dominant anti-HBV drugs are nucleos(t)ide analogs targeting the viral polymerase (P). P has four domains, the terminal protein (TP) that primes DNA synthesis, a spacer, the reverse transcriptase (RT), and the ribonuclease H (RNaseH). Despite being a major drug target and catalyzing a reverse transcription pathway very different from the retroviral pathway, HBV P has resisted structural analysis for decades. Here, we exploited advances in protein structure prediction to model the structure of P. The predicted HBV RT and RNaseH domains aligned to the HIV RT-RNaseH at 3.75 Å RMSD, had a nucleic acid binding groove spanning the two active sites, had DNA polymerase active site motifs in their expected positions, and accommodated two Mg++ ions in both active sites. Surprisingly, the TP domain wrapped around the RT domain, with the priming tyrosine poised over the RT active site. This model was validated using published mutational analyses, and by docking RT and RNaseH inhibitors, RNA:DNA heteroduplexes, and the HBV ε RNA stem-loop that templates DNA priming into the model. The HBV P fold, including the orientation of the TP domain, was conserved among hepadnaviruses from rodents to fish and in P from a fish nackednavirus, but not in other non-retroviral RTs. Therefore, this protein fold has persisted since the hepadnaviruses diverged from nackednaviruses >400 million years ago. This model will guide drug development and mechanistic studies into P’s function.SignificanceThe hepatitis B virus (HBV) polymerase (P) catalyzes an unusual reverse transcription pathway and is a major drug target. However, P’s insolubility and instability have long prevented its structural analyses. This work predicts the structure of P proteins from human to fish viruses, revealing an unanticipated conserved protein fold that is at least 400 million years old. The HBV P model was validated by mechanistically interpreting mutations with strong phenotypes and by computationally docking nucleic acids to P and inhibitors into both of its active sites. The model will advance mechanistic studies into the function of P and enable drug discovery against targets on P other than the reverse transcriptase and ribonuclease H active sites.
Accessibility and Disability Inclusion Among Top-Funded U.S. Undergraduate Institutions
Authors: Campanile Jessica , Cerilli Caroline , Varadaraj Varshini , Sweeney Fiona , Smith Jared , Zhu Jiafeng , Yenokyan Gayane , Swenor Bonnielin K. 
Published: February 2022

ABSTRACTBackgroundThere is limited data to assess, track, or quantify accessibility and disability inclusion across universities.ObjectiveThis study assessed disability inclusion and accessibility at the top 50 National Institutes of Health (NIH)-funded undergraduate programs in the United States. We hypothesized that there is no association between NIH funding and the University Disability Inclusion ScoreMethodsA novel tool, the University Disability Inclusion Score assessed disability inclusion and accessibility using 10 indicators spanning 4 categories: (1) accessibility of built and virtual environment, (2) public image of disability inclusion, (3) accommodations processes and procedures, and (4) grievance policy. Based upon the total points (out of a total score of 100), each university was assigned a letter grade (A-F).ResultsOf the top 50 NIH-funded institutions, 6% received an A grade on the Score, while 60% received D or F. The mean scores were 15.2 (SD=5) for accessibility of built and virtual environment (20 points), 10 (SD=3) for public image of disability inclusion (20 points), 30.6 (SD=10) for accommodations processes and procedures (50 points), and 8.1 (SD=3) for grievance policy (10 points).ConclusionsOur findings suggest room for improvement in disability inclusion and accessibility among top university recipients of NIH funding. To provide an equitable academic experience, universities must prioritize disability inclusion.
COVID-19-related Smell and Taste Impairment with Widespread Diffusion of SARS-CoV-2 Omicron Variant
Authors: Boscolo-Rizzo Paolo , Tirelli Giancarlo , Meloni Pierluigi , Hopkins Claire , Madeddu Giordano , De Vito Andrea , Gardenal Nicoletta , Valentinotti Romina , Tofanelli Margherita , Borsetto Daniele , Lechien Jerome R. , Polesel Jerry , De Riu Giacomo , Vaira Luigi Angelo 
Published: February 2022

AbstractBackgroundThe aim of this study was to estimate the prevalence of self-reported chemosensory dysfunction in a study cohort of subjects who developed a mild-to-moderate COVID-19 in the period from January 17, 2022 to February 4, 2022 (Omicron proxy period) and compared that with a historical series of patients tested positive for SARS-CoV-2 infection between March and April, 2020 (comparator period).MethodsProspective study based on the sinonasal outcome tool 22 (SNOT-22), item “sense of smell or taste” and additional outcomes.ResultsPatients’ characteristics and clinical presentations of COVID-19 were evaluated and compared in 779 patients, 338 of the study cohort and 441 of the historical series. The prevalence of self-reported chemosensory dysfunction during the proxy Omicron period (32.5%; 95% CI, 27.6-37.8) was significantly lower from that during the comparator period (66.9%; 95% CI, 62.3-71.3) (p<.001). 24.6% (95% CI, 20.1-29.5) of patients reported an altered sense of smell during the proxy Omicron period compared to 62.6% (95% CI, 57.9-67.1) during the comparator period (p<.001). Similarly, the prevalence of an altered sense of taste dropped from 57.4% (95% CI, 52.6-62.0) during the comparator period to 26.9% (95% CI, 22.3-32.0) during the proxy Omicron period (p<.001). The severity of chemosensory dysfunction was lower in proxy Omicron period compared to comparator period (p<.001).ConclusionsThe prevalence and the severity of COVID-19 associated smell and taste dysfunction has dropped significantly with the advent of the Omicron variant.
Serological responses and six-month trajectories to COVID-19 Comirnaty and Spikevax booster vaccine, September 2021 to January 2022, London, United Kingdom
Authors: Ireland Georgina , Whitaker Heather , Ladhani Shamez N , Baawuah Frances , Subbarao Sathyvani , Elgohari Suzanne , Smith Alexandra , O’Brien Michelle , Whillock Corinne , Martin Oliver , Moss Paul , Ramsay Mary E , Amirthalingam Gayatri , Brown Kevin E 
Published: February 2022

AbstractIn contrast to the increasing levels of high avidity S antibody measured by the Roche assay in the first 6 months following natural infection, marked waning is seen post 2 or 3 doses of vaccine. Although the kinetics differ between those with vaccine-induced immunity compared to those infected prior to vaccination (hybrid immunity), waning rates appear to be similar following 2 or 3 doses of vaccine. These data should allow countries to optimise the timing of future doses of vaccine.
CriSNPr: a single interface for the curated and de-novo design of gRNAs for CRISPR diagnostics using diverse Cas systems
Authors: Ansari Asgar Hussain , Kumar Manoj , Sarkar Sajal , Maiti Souvik , Chakraborty Debojyoti 
Published: February 2022

AbstractNucleic acid detection and variant calling through CRISPR-based diagnostics (CRISPRDx) has facilitated clinical decision-making, particularly during the COVID-19 pandemic. This has been further accelerated through the discovery of newer and engineered CRISPR effectors, expanding the portfolio of such diagnostic applications to a wide variety of pathogenic and non-pathogenic conditions. However, each diagnostic CRISPR pipeline requires customized detection schemes originating from fundamental principles of the Cas protein used, its guide RNA (gRNA) design parameters, and the assay readout. This is particularly relevant for variant detection, an attractive low-cost alternative to sequencing-based approaches for which no in silico pipeline for the ready-to-use design of CRISPR-based diagnostics currently exists. In this manuscript, we fill this lacuna using a unified webserver CriSNPr (CRISPR based SNP recognition), which provides the user the opportunity to de-novo design gRNAs based on six CRISPRDx proteins of choice (Fn/enFnCas9, LwCas13a, LbCas12a, AaCas12b, and Cas14a) and query for ready-to-use oligonucleotide sequences for validation on relevant samples. In addition, we provide a database of curated pre-designed gRNAs and target/off-target for all human and SARS-CoV-2 variants reported so far. CriSNPr has been validated on multiple Cas proteins and highlights its broad and immediate scope of utilization across multiple detection platforms. CriSNPr is available at URL http://crisnpr.igib.res.in/.
Accelerating the Validation of Endogenous On-Target Engagement and In-cellulo Kinetic Assessment for Covalent Inhibitors of KRASG12C in Early Drug Discovery
Authors: Kantae Vasudev , Polanski Radoslaw , Lewis Hilary J. , Barratt Derek , Srinivasan Bharath 
Published: February 2022

AbstractCovalent inhibition is a valuable modality in drug-discovery due to its potential ability in decoupling pharmacokinetics from pharmacodynamics by prolonging the residence time of the drug on the target of interest. This increase in target occupancy is limited only by the rate of target turnover. However, a limitation in such studies is to translate the in-vitro inhibition assessment to the appropriate in-cellulo target engagement parameter by covalent probes. Estimation of such parameters is often impeded by the low-throughput nature of current label-free approaches. In this study, an ultra-performance liquid chromatography-multiple reaction monitoring (UPLC-MRM) mass spectrometry platform was utilised to develop a targeted proteomics workflow that can evaluate cellular on-target engagement of covalent molecules in an increased throughput manner. This workflow enabled a throughput increase of 5-10 fold when compared to traditional nanoLC-based proteomics studies. To demonstrate the applicability of the method, KRASG12C was used as a model system to interrogate the interaction of an irreversible covalent small-molecule, compound 25, both in-vitro and in-cellulo. Initial biochemical studies confirmed that the small-molecule forms an adduct with the targeted cysteine on the protein, as assessed at the level of both intact protein and on the target peptide. In-cellulo studies were carried out to quantify target engagement and selectivity assessment in heterozygous NCI-H358 cell line with both WT type and KRASG12C alleles. The workflow enabled evaluation of in-cellulo target engagement kinetics providing mechanistic insights into the irreversible mode of inhibition. In summary, the method has the potential for target agnostic application in the assessment of on-target engagement of covalent probes compatible with the high-throughput requirements of early drug discovery.
The stationary phase-specific sRNAfimR2is a multifunctional regulator of bacterial motility, biofilm formation and virulence
Authors: Raad Nicole , Tandon Disha , Hapfelmeier Siegfried , Polacek Norbert 
Published: February 2022

SummaryBacterial pathogens employ a plethora of virulence factors for host invasion, and their use is tightly regulated to maximize infection efficiency and manage resources in a nutrient-limited environment. Here we show that duringEscherichia colistationary phase the small non-coding RNAfimR2regulates fimbrial and flagellar biosynthesis at the post-transcriptional level, leading to biofilm formation as the dominant mode of survival under conditions of nutrient depletion.fimR2interacts with the translational regulator CsrA, antagonizing its functions and firmly tightening control over motility and biofilm formation. Generated through RNase E cleavage,fimR2regulates stationary phase biology independently of the chaperones Hfq and ProQ. TheSalmonella entericaversion offimR2induces effector protein secretion by the type III secretion system and stimulates infection, thus linking the sRNA to virulence. This work reveals the importance of bacterial sRNAs in modulating various aspects of bacterial physiology including stationary phase and virulence.HighlightsfimR2expression causes biofilm formation and alters bacterial outer membrane architecturefimR2modulates CsrA activity and sequesters it from its targetsTheSalmonella fimR2variant is functional inE. colifimR2is generated through RNase E processing and enhances infectivity
Clonal behaviour of myogenic precursor cells throughout the vertebrate lifespan
Authors: Hughes Simon M. , Escaleira Roberta C. , Wanders Kees , Koth Jana , Wilkinson David G. , Xu Qiling 
Published: February 2022

AbstractTo address questions of stem cell diversity during skeletal myogenesis, a Brainbow-like genetic cell lineage tracing method, dubbed Musclebow, was derived by enhancer trapping in zebrafish. It is shown that at least 15 muscle precursor cells (mpcs) seed each somite, where they proliferate but contribute little to muscle growth prior to hatching. Thereafter, dermomyotome-derived mpc clones rapidly expand while some progeny undergo terminal differentiation, leading to stochastic clonal drift. No evidence of cell lineage-based clonal fate diversity was obtained. Neither fibre nor mpc death was observed in uninjured animals. Individual marked muscle fibres persist across much of the lifespan indicating low rates of nuclear turnover. In adulthood, early-marked mpc clones label stable blocks of tissue comprising a significant fraction of either epaxial or hypaxial somite. Fusion of cells from separate early-marked clones occurs in regions of clone overlap. Wounds are regenerated from many/most local mpcs; no evidence for specialised stem mpcs was obtained. In conclusion, our data indicate that most mpcs in muscle tissue contribute to local growth and repair and suggest that cellular turnover is low in the absence of trauma.Summary StatementMusclebow clonal cell lineage analysis is introduced to reveal the cellular dynamics of skeletal muscle formation, repair and maintenance throughout the life of zebrafish.
Sex differences in insular gyri responses to the cold pressor challenge
Authors: Krause-Sorio Beatrix , Macey Katherine E. , Kumar Rajesh , Ogren Jennifer A. , Thomas Albert , Henderson Luke A. , Harper Ronald M. , Macey Paul M. 
Published: February 2022

AbstractIntroductionSex differences in autonomic control may contribute to physiological sex differences in cardiovascular disease, thermoregulation, and the experience of pain. We previously showed sex differences in functional mapping of autonomic responses across the insula, a central autonomic control region. Anterior insula response patterns to sympathetic activation (Valsalva) and parasympathetic withdrawal (handgrip) differed between men and women. We here assessed sex differences in autonomic insula gyrus responses to a cold pressor challenge, which involves temperature and pain regulation.MethodsFunctional MRI (fMRI) involved a 1-minute right-foot cold pressor challenge in 22 women (age; mean±std: 50±4 yrs), and 39 men (45±3 yrs). Regions of interest (ROI) comprised left and right anterior short gyrus (ASG), middle short gyrus (MSG), posterior short gyrus (PSG), anterior long gyrus (ALG), and posterior long gyrus (PLG). Two-second time intervals of fMRI signal responses per ROI and concurrently recorded heart rate and blood oxygen saturation (SaO2) were tested for within- and between-group effects over time (repeated measures ANOVA P≤0.05). We tested sex differences in 1) each ROI; 2) lateralization effects; and 3) posterior-to-anterior gradients in responses.ResultsNo sex differences emerged in heart rate or SaO2. Women showed larger signal changes in several gyri than men after cold pressor onset and offset. Most consistently, women showed a greater right-over-left hemisphere dominance in cold pressor response compared to men in the MSG, PSG and ALG. Greater right-over-left hemisphere anterior-to-posterior dominance was more pronounced in men.ConclusionsThe findings confirm anterior and right-hemispheric dominance of insular responses during sympathetic activation that includes pain and cold. Although distinct transient male-female differences in fMRI responses appeared during the cold pressor, unlike the Valsalva and handgrip, no sex differences in ASG lateralization emerged, suggesting that the previously found sex differences may not solely relate to regulating blood pressure responses.