bluuebunny/crossref_metadata_2025_split huggingface dataset:
Secreted folate receptor-gamma drives fibrogenesis in nonalcoholic steatohepatitis by amplifying TGFβ signaling in hepatic stellate cells
Authors: Quinn Connor R. , Rico Mario C. , Merali Carmen , Perez-Leal Oscar , Mischley Victoria , Karanicolas John , Friedman Scott L. , Merali Salim 
Published: July 2022

AbstractHepatic fibrosis is the primary determinant of mortality in nonalcoholic steatohepatitis (NASH) patients. Antagonism of transforming growth factor β (TGFβ), a master profibrogenic cytokine, is a promising therapeutic target that has not yet been translated into an effective therapy, due in part to the lack of animal models resembling the human phenotype of NASH. Here we have identified that soluble secreted folate receptor gamma (FOLR3), expressed in humans but not rodents, is a secreted protein that is elevated in livers of NASH subjects but not in subjects with nonalcoholic fatty liver, type II diabetes, or healthy subjects. FOLR3, based on global proteomics, was the most highly expressed NASH-specific protein and positively correlated with increasing fibrosis stages, suggesting an impact on activated hepatic stellate cells (HSCs), the key fibrogenic cell in the liver. Exposure of stellate cells to exogenous FOLR3 led to elevated extracellular matrix (ECM) protein production, an effect synergistic with TGFβ1. Structurally, FOLR3 interacts with serine protease HTRA1, which downregulates TGFβ signaling through the degradation of its receptor TGFBR2. Administration of human FOLR3 to mice induced severe bridging fibrosis and an ECM pattern resembling human NASH. Our study uncovers a novel role of FOLR3 in enhancing fibrosis and identifies FOLR3 as a potential therapeutic target in NASH fibrosis.Abstract Figure
Establishment of Measles Virus Receptor-expressing Vero Cells Lacking Functional Poliovirus Receptors
Authors: Someya Kenji , Okemoto-Nakamura Yuko , Kurata Takako , Kanbayashi Daiki , Saito Noriko , Itamochi Masae , Otsuki Noriyuki , Hanada Kentaro , Takeda Makoto 
Published: July 2022

AbstractGlobal efforts are underway to eliminate measles and rubella and active viral surveillance is key to achieving this goal. In addition to this, the World Health Organization announced guidelines for handling materials potentially infectious for poliovirus (PV) to minimize the risk of PV reintroduction and achieve PV eradication. To support the global efforts, we have established new PV-non-susceptible cell lines useful for the isolation of measles virus (MeV) and rubella virus (RuV) (Vero ΔPVR1/2 hSLAM+). In the cell lines, MeV and RuV replicated efficiently with no concern about PV replication.
SNM1A (DCLRE1A) is crucial for efficient repair of complex DNA breaks in human cells
Authors: Swift Lonnie P. , Lagerholm B. Christoffer , Baddock Hannah T. , Henderson Lucy R. , Ratnaweera Malitha , Sengerova Blanka , Lee Sook , Cruz-Migoni Abimael , Waithe Dominic , Renz Christian , Ulrich Helle D. , Newman Joseph A. , Schofield Christopher J. , McHugh Peter J. 
Published: July 2022

AbstractDNA double-strand breaks (DSBs), such as those produced by radiation and radiomimetics, are amongst the most toxic forms of cellular damage, in part because they involve extensive oxidative modifications at the break termini. Prior to completion of DSB repair, the chemically modified termini must be removed. Various DNA processing enzymes have been implicated in the processing of these ‘dirty ends’, but molecular knowledge of this process is limited. Here, we demonstrate a role for the metallo-β-lactamase fold 5ʹ-3ʹ exonuclease SNM1A in this vital process. Cells disrupted for SNM1A manifest increased sensitivity to radiation and radiomimetic agents and show defects in DSB damage repair. SNM1A is recruited and is retained at the sites of DSB damageviathe concerted action of its three highly conserved PBZ, PIP box and UBZ interaction domains, which mediate interactions with poly-ADP-ribose chains, PCNA and the ubiquitinated form of PCNA, respectively. SNM1A can resect DNA containing oxidative lesions induced by radiation damage at break termini. The combined results reveal a crucial role for SNM1A to digest chemically modified DNA during the repair of DSBs and imply that the catalytic domain of SNM1A is an attractive target for potentiation of radiotherapy.
Cardiolipin, and not monolysocardiolipin, preferentially binds to the interface of Complexes III and IV
Authors: Corey Robin A. , Harrison Noah , Stansfeld Phillip J. , Sansom Mark S.P. , Duncan Anna 
Published: July 2022

AbstractThe mitochondrial electron transport chain comprises a series of protein complexes embedded in the inner mitochondrial membrane that generate a proton motive force via oxidative phosphorylation, ultimately generating ATP. These protein complexes can oligomerize to form larger structures called supercomplexes. Cardiolipin (CL), a conical lipid, unique within eukaryotes to the inner mitochondrial membrane, has proven essential in maintaining the stability and function of supercomplexes. Monolysocardiolipin (MLCL) is a CL variant that accumulates in people with Barth syndrome (BTHS). BTHS is caused by defects in CL biosynthesis and characterised by abnormal mitochondrial bioenergetics and destabilised supercomplexes. However, the mechanisms by which MLCL causes pathogenesis remain unclear. Here, multiscale molecular dynamics characterise the interactions of CL and MLCL with yeast and mammalian mitochondrial supercomplexes containing Complex III (CIII) and Complex IV (CIV). Coarse-grained simulations reveal that both CL and MLCL bind to sites at the interface between CIII and CIV of the supercomplex. Free energy perturbation calculations show that MLCL interaction is weaker than that of CL and suggest that interaction with CIV drives this difference. Atomistic contact analyses show that, although interaction with CIII is similar for CL and MLCL, CIV makes more contacts with CL than MLCL, demonstrating that CL is a more successful “glue” between the two complexes. Simulations of the human CIII2CIV supercomplex show that this interface site is maintained between species. Our study suggests that MLCL accumulation in people with BTHS disrupts supercomplex stability by formation of relatively weak interactions at the interface lipid binding site.
A gas phase fractionation acquisition scheme integrating ion mobility for rapid diaPASEF library generation
Authors: Penny Jack , Schroeder Gunnar N. , Bengoechea José A. , Collins Ben C. 
Published: July 2022

AbstractData independent acquisition (DIA or DIA/SWATH) mass spectrometry has emerged as a primary measurement strategy in the field of quantitative proteomics. diaPASEF is a recent adaptation that leverages trapped ion mobility spectrometry (TIMS) to improve selectivity and increase sensitivity. The complex fragmentation spectra generated by co-isolation of peptides in DIA mode are most typically analyzed with reference to prior knowledge in the form of spectral libraries. The best-established method for generating libraries uses data dependent acquisition (DDA) mode, or DIA mode if appropriately deconvoluted, often including offline fractionation to increase depth of coverage. More recently strategies for spectral library generation based on gas phase fractionation (GPF), where a representative sample is injected serially using narrow DIA windows that cover different mass ranges of the complete precursor space, have been introduced that performed comparably to deep offline fractionation-based libraries for DIA data analysis. Here, we investigated whether an analogous GPF-based library building approach that accounts for the ion mobility (IM) dimension is useful for the analysis of diaPASEF data and can remove the need for offline fractionation. To enable a rapid library development approach for diaPASEF we designed a GPF acquisition scheme covering the majority of multiply charged precursors in the m/z vs 1/K0 space requiring 7 injections of a representative sample and compared this with libraries generated by direct deconvolution-based analysis of diaPASEF data or by deep offline fractionation and ddaPASEF. We found that library generation by IM-GPF outperformed direct deconvolution of the diaPASEF data and had performance approaching that of a deep offline fractionation library, when analysing diaPASEF data. This establishes the ion mobility integrated GPF scheme as a pragmatic approach to rapid library generation for the analysis of diaPASEF data.
Differential Role of GABAergic and Cholinergic Ventral Pallidal Neurons in Behavioral Despair, Conditioned Fear Memory and Active Coping
Authors: Akmese Cemal , Sevinc Cem , Halim Sahar , Unal Gunes 
Published: July 2022

AbstractThe ventral pallidum (VP), a core structure of the reward circuit, is well-associated with appetitive behaviors. Recent evidence suggests that this basal forebrain nucleus may have an overarching role in affective processing, including behavioral responses to aversive stimuli. We investigated this possibility by utilizing selective immunotoxin lesions and a series of behavioral tests in adult male Wistar rats. We made bilateral GAT1-Saporin, 192-IgG-Saporin or PBS (vehicle) injections into the VP to respectively eliminate GABAergic and cholinergic neurons, and tested the animals in the forced swim test (FST), open field test (OFT), elevated plus maze (EPM), Morris water maze (MWM) and cued fear conditioning. Both GAT1-Saporin and 192-IgG-Saporin injections reduced behavioral despair without altering general locomotor activity. This antidepressant-like effect was accompanied by reduced freezing and increased darting in the acquisition phase of cued fear conditioning. In the test phase, cholinergic, but not GABAergic lesions, impaired context-dependent fear memory, while both groups showed diminished conditioned freezing in a novel context. In line with this, selective cholinergic lesions impaired spatial memory in the MWM as compared to GAT1-Saporin or vehicle-injected animals. No differential effect was observed in anxiety-like behavior assessed in the OFT or EPM. These findings show that both the GABAergic and cholinergic cell groups of the VP contribute to behavioral despair and acquired fear responses by suppressing active coping. In conditioned learning, cholinergic ventral pallidal neurons contribute to the fear response in a context-independent manner, while the GABAergic population is required when the context information is missing.Significance StatementThe ventral pallidum (VP), associated with motivation and appetitive behaviors, is tested for its role in behavioral responses to aversive stimuli. Findings show that both the GABAergic and cholinergic neuronal groups of the VP contribute to behavioral despair and acquired fear response by suppressing active coping. In conditioned learning, the cholinergic neurons are required for the acquired fear response, while the VP GABAergic population becomes necessary only when the context information is missing. These results suggest that ventral pallidal GABAergic and cholinergic projections to the amygdaloid complex may constitute therapeutic targets for affective disorders.
Molecular Underpinnings and Environmental Drivers of Spontaneous Loss of Heterozygosity in Drosophila Intestinal Stem Cells
Authors: zouabi Lara Al , Stefanutti Marine , Riddiford Nick , Rubanova Natalia , Bohec Mylène , Servant Nicolas , Bardin Allison 
Published: July 2022

AbstractThe genome stability of adult stem cells is of particular importance as these cells maintain long-term self-renewal capacity and can contribute extensively to adult tissues. During development and aging, genome mutation leading to loss of heterozygosity (LOH) can uncover recessive phenotypes and be propagated within tissue compartments. This phenomenon occurs in normal human tissues, and is prevalent in pathological genetic conditions and cancers. While previous studies in yeast have defined distinct DNA repair mechanisms that can promote LOH, the predominant pathways underlying LOH in complex somatic tissues of multicellular organisms arenot well understood. In addition, how environmental triggers such as pathogenic bacterial infection may impact LOH is unclear. Here, we investigate the mechanisms giving rise to LOH in adult intestinal stem cells in Drosophila. Our data indicate that infection with the enteric pathogenic bacteria, Erwinia carotovora carotovora 15 but not Pseudomonas entomophila increases LOH frequency. Using whole-genome sequencing of somatic LOH events, we demonstrate that they arise primarily via mitotic recombination. Molecular features of recombination sites and genetic evidence argue against formation via break-induced replication and instead support cross-over events arising from double Holliday junction-based repair. This study provides a mechanistic understanding of mitotic recombination in stem cells in vivo, an important mediator of LOH.
Sex differences in default mode network connectivity in healthy aging adults
Authors: Ficek-Tani Bronte , Horien Corey , Ju Suyeon , Li Nancy , Lacadie Cheryl , Shen Xilin , Scheinost Dustin , Constable R Todd , Fredericks Carolyn 
Published: July 2022

AbstractWomen show an increased lifetime risk of Alzheimer’s disease (AD) compared to men. Characteristic brain connectivity changes, particularly within the default mode network (DMN), have been associated with both symptomatic and preclinical AD, but the impact of sex on DMN function throughout aging is poorly understood. We investigated sex differences in DMN connectivity over the lifespan in 595 cognitively healthy participants from the Human Connectome Project - Aging cohort. We used the intrinsic connectivity distribution (a robust voxel-based metric of functional connectivity) and a seed connectivity approach to determine sex differences within the DMN and between the DMN and whole brain.Compared with men, women demonstrated increased connectivity with age in posterior DMN nodes and decreased connectivity in the medial prefrontal cortex. Differences were most prominent in the decades surrounding menopause. Seed-based analysis revealed increased connectivity in women from the posterior cingulate to angular gyrus and parahippocampal gyrus, which correlated with neuropsychological measures of declarative memory. Taken together, we show significant sex differences in DMN subnetworks over the lifespan, including patterns in aging women that resemble changes previously seen in preclinical AD. These findings highlight the importance of considering sex in neuroimaging studies of aging and neurodegeneration.
DNA Methylation is stable after MMEJ and NHEJ double strand break repair
Authors: Bnaya Ester , Shilo Shay , Feldman Tzah , Bacharach Tal , Moskovitz Yoni , Kadam Aditee , Yedidim Paz , Azogy Hadas , Kaushansky Nathali , Chapal-Ilani Noa , Shlush Liran I. 
Published: July 2022

AbstractDNA double strand breaks (DSBs) are a major source of mutations. Both non-homologous-end-joining (NHEJ) and microhomology-mediated-end-joining (MMEJ) DSB repair pathways are error prone and produce deletions, which can lead to cancer. DSBs also lead to epigenetic changes, including demethylation, which is involved in carcinogenesis. Of specific interest is the MMEJ repair pathway, as it requires methylation restoration around the break, as a result of the resection and formation of single stranded (ssDNA) intermediates. While, methylation patterns after homologous recombination (HR) have been partially studied, the methylation status after MMEJ and NHEJ remains poorly reported, and can be relevant for cancer. To study methylation patterns around DSB after NHEJ and MMEJ repair, we used targeted bisulfite-sequencing (BS-seq) to quantify methylation of dozens of single cell clones after induction of DSB by CRISPR. Each single cell clone was classified according to the sequence signature to a specific repair mechanism: NHEJ or MMEJ. Comparison of single cell clones after DSB to control cells, without DSB, demonstrated correct restoration of the methylation levels. No difference in methylation patterns was noticed when comparing NHEJ to MMEJ. Methylation levels in gene body, highly methylated CpGs (n=61, 4000 base pairs around DSB) and in low methylation CpGs (n=19), remained stable after both MMEJ and NHEJ. Gene body methylation persisted even on the background of DNMT3A R882C mutation, the most prevalent preleukemic mutation, in which the de novo methylation machinery is compromised. An exception observed in a single CpG site (ASXL1 995) which demonstrated elevated methylation rate after DSB repair only in the presence of WT DNMT3A. In summary, DNA methylation restoration demonstrated high fidelity after DSB both in methylated and unmethylated gene body, even in cases where DNA resections and deletions occurred.Author SummaryDNA holds the genetic information. Modifications on the DNA molecule such as DNA methylation are crucial for the genetic regulation. DNA damage is harmful to the cell and needs to be repaired. Different repair mechanisms may result in mutations that can be identified according to their sequence signature. In the work presented here we examined changes in DNA methylation after different types of DNA repair, MMEJ and NHEJ. We found that DNA methylation is highly stable after DNA repair regardless to the repair mechanism and genomic context.
Live-cell imaging and mathematical analysis of the “community effect” in apoptosis
Authors: Coursier Diane , Coulette David , Leman Hélène , Grenier Emmanuel , Ichim Gabriel 
Published: July 2022

AbstractAs a cellular intrinsic mechanism leading to cellular demise, apoptosis was thoroughly characterized from a mechanistic perspective. Nowadays there is an increasing interest in describing the non-cell autonomous or community effects of apoptosis, especially in the context of resistance to cancer treatments. Transitioning from cell-centered to cell population-relevant mechanisms adds a layer of complexity for imaging and analyzing an enormous number of apoptotic events. In addition, the community effect between apoptotic and living cells is difficult to be taken into account for complex analysis. We describe here a robust and easy to implement method to analyze the interactions between cancer cells, while under apoptotic pressure. Using this approach we showed as proof-of-concept that apoptosis is insensitive to cellular density, while the proximity to apoptotic cells increases the probability of a given cell to undergo apoptosis.
DNA methylation patterns of transcription factor binding regions characterize their functional and evolutionary contexts
Authors: Rimoldi Martina , Wang Ning , Zhang Jilin , Villar Diego , Odom Duncan T. , Taipale Jussi , Flicek Paul , Roller Maša 
Published: July 2022

ABSTRACTBackgroundDNA methylation is an important epigenetic modification which has numerous roles in modulating genome function. Its levels are spatially correlated across the genome, typically high in repressed regions but low in transcription factor (TF) binding sites and active regulatory regions. However, the mechanisms establishing genome-wide and TF binding site methylation patterns are still unclear.ResultsWe used a comparative approach to investigate the association of DNA methylation to TF binding evolution in mammals. Specifically, we experimentally profiled DNA methylation and combined this with published occupancy profiles of five distinct TFs (CTCF, CEBPA, HNF4A, ONECUT1, FOXA1) in the liver of five mammalian species (human, macaque, mouse, rat, dog). TF binding sites were lowly methylated, but they often also had intermediate methylation levels. Employing a classification and clustering approach, we extracted distinct and species conserved patterns of DNA methylation levels at TF bound regions. CEBPA, HNF4A, ONECUT1 and FOXA1 shared the same methylation patterns, while CTCF’s differed. These patterns characterize alternative functions and chromatin landscapes of TF bound regions. Leveraging our phylogenetic framework, we found DNA methylation gain upon evolutionary loss of TF occupancy, indicating coordinated evolution. Furthermore, each methylation pattern has its own evolutionary trajectory reflecting its genomic contexts.ConclusionsOur epigenomic analyses found that specific DNA methylation profiles characterize TF binding, and are associated to their regulatory activity, chromatin contexts, and evolutionary trajectories.
Structure and host specificity ofStaphylococcus epidermidisbacteriophage Andhra
Authors: Hawkins N’Toia C. , Kizziah James L. , Hatoum-Aslan Asma , Dokland Terje 
Published: July 2022

AbstractStaphylococcus epidermidisis an opportunistic pathogen of the human skin, often associated with infections of implanted medical devices. An increase in antibiotic resistance inS. epidermidisand other bacterial pathogens has led to renewed interest in the use of bacteriophages as an alternative to conventional antibiotics. Staphylococcal picoviruses are a group of strictly lytic, short-tailed bacteriophages with compact genomes that are attractive candidates for therapeutic use. Here, we report the structure of the complete virion ofS. epidermidis-infecting phage Andhra, determined using high-resolution cryo-electron microscopy, allowing atomic modeling of the capsid and tail proteins, including twelve trimers of a unique receptor binding protein, the hexameric tail knob that acts as a gatekeeper for DNA ejection, and the tail tip, which is a heterooctamer of two different lytic proteins. Our findings elucidate critical features that enable host recognition and penetration, facilitating the development of this group of phages for therapeutic applications.
Benzimidazoles cause lethality by inhibiting the function of Caenorhabditis elegans neuronal beta-tubulin
Authors: Gibson Sophia B. , Ness-Cohn Elan , Andersen Erik C. 
Published: July 2022

AbstractParasitic nematode infections cause an enormous global burden to both human and livestock populations. Resistance to the limited arsenal of anthelmintic drugs used to combat these infections is widespread, including resistance to benzimidazole (BZ) compounds commonly found in livestock parasites. Previous studies using the free-living nematode Caenorhabditis elegans to model parasitic nematode resistance have shown that loss-of-function mutations in the beta-tubulin gene ben-1 confer resistance to BZ drugs. However, the mechanism of resistance and the tissue-specific susceptibility are not well known in any nematode species. To identify in which tissue(s) ben-1 function underlies BZ susceptibility, transgenic strains that express ben-1 in different tissues, including hypodermis, muscles, neurons, intestine, and ubiquitous expression were generated. High-throughput fitness assays were performed to measure and compare the quantitative responses to BZ compounds among different transgenic lines. Significant BZ susceptibility was observed in animals expressing ben-1 in neurons, comparable to expression using the ben-1 promoter. This result suggests that ben-1 function in neurons underlies susceptibility to BZ. Subsetting neuronal expression of ben-1 based on neurotransmitter system further restricted ben-1 function in cholinergic neurons to cause BZ susceptibility. These results better inform our current understanding of the cellular mode of action of BZ and also suggest additional treatments that might potentiate the effects of BZs.HighlightsExpressing wild-type ben-1 only in neurons restores susceptibility to benzimidazolesExpression of ben-1 in cholinergic neurons restores susceptibility to benzimidazolesGABAergic neurons might also play a role in benzimidazole sensitivityBroad implications for molecular mechanisms of benzimidazole mode of actionGraphical Abstract