bluuebunny/crossref_metadata_2025_split huggingface dataset:
Collagen type VI regulates TGFβ bioavailability in skeletal muscle
Authors: Mohassel Payam , Rooney Jachinta , Zou Yaqun , Johnson Kory , Norato Gina , Hearn Hailey , Nalls Matthew A , Yun Pomi , Ogata Tracy , Silverstein Sarah , Sleboda David A , Roberts Thomas J , Rifkin Daniel B , Bönnemann Carsten G 
Published: June 2023

AbstractCollagen VI-related disorders (COL6-RDs) are a group of rare muscular dystrophies caused by pathogenic variants in collagen VI genes (COL6A1, COL6A2,andCOL6A3). Collagen type VI is a heterotrimeric, microfibrillar component of the muscle extracellular matrix (ECM), predominantly secreted by resident fibroadipogenic precursor cells in skeletal muscle. The absence or mislocalizatoion of collagen VI in the ECM underlies the non-cell autonomous dysfunction and dystrophic changes in skeletal muscle with an as of yet elusive direct mechanistic link between the ECM and myofiber dysfunction. Here, we conduct a comprehensive natural history and outcome study in a novel mouse model ofCOL6-RDs (Col6a2-/-mice) using standardized (Treat-NMD) functional, histological, and physiologic parameter. Notably, we identify a conspicuous dysregulation of the TGFβ pathway early in the disease process and propose that the collagen VI deficient matrix is not capable of regulating the dynamic TGFβ bioavailability at baseline and also in response to muscle injury. Thus, we propose a new mechanism for pathogenesis of the disease that links the ECM regulation of TGFβ with downstream skeletal muscle abnormalities, paving the way for developing and validating therapeutics that target this pathway.
Genetic characterization of a captive marmoset colony using genotype-by-sequencing
Authors: Cole SA , Lyke MM , Christensen C , Newman D , Bagwell A , Galindo S , Glenn J , Layne-Colon D , Sayers K , Tardif SD , Cox LA , Ross CN , Cheeseman IH 
Published: June 2023

ABSTRACTThe marmoset is a fundamental non-human primate model for the study of aging, neurobiology, and many other topics. Genetic management of captive marmoset colonies is complicated by frequent chimerism in the blood and other tissues, a lack of tools to enable cost-effective, genome-wide interrogation of variation, and historic mergers and migrations of animals between colonies. We implemented genotype-by-sequencing (GBS) of hair follicle derived DNA (a minimally chimeric DNA source) of 82 marmosets housed at the Southwest National Primate Research Center (SNPRC). Our primary goals were the genetic characterization of our marmoset population for pedigree verification and colony management and to inform the scientific community of the functional genetic makeup of this valuable resource. We used the GBS data to reconstruct the genetic legacy of recent mergers between colonies, to identify genetically related animals whose relationships were previously unknown due to incomplete pedigree information, and to show that animals in the SNPRC colony appear to exhibit low levels of inbreeding. Of the >99,000 single-nucleotide variants (SNVs) that we characterized, >9,800 are located within gene regions known to harbor pathogenic variants of clinical significance in humans. Overall, we show the combination of low-resolution (sparse) genotyping using hair follicle DNA is a powerful strategy for the genetic management of captive marmoset colonies and for identifying potential SNVs for the development of biomedical research models.
Multichannel joint image reconstruction allows for artifact-free focused small field of view magnetic particle imaging
Authors: Gevaert Julia J. , Konkle Justin , Goodwill Patrick , Foster Paula J. 
Published: June 2023

AbstractMagnetic Particle Imaging (MPI) directly detects superparamagnetic iron oxide (SPIO) labeled cells. We have used MPI to detect SPIO-labeled dendritic cells (DC) migrated to the popliteal lymph nodes (pLN) after injection into the hind footpads. However, in some cases the low pLN signal could not be resolved from nearby higher footpad signal where window leveling to pLN signal oversaturated the footpad signal. The same limitation occurs when SPIO is injected intravenously, accumulates in the liver, and prevents isolation of regions of interest with lower signals. Previous studies have reported on the issue of resolving a wide range of differing iron concentration. A small focused field of view (FOV), to exclude high sources of nearby signal cannot be performed with the standard reconstruction algorithm equipped on the MomentumTM MPI scanner because it is assumed that there is no signal at the edge of the FOV and these values are set to zero for each line along the transmit axis. However, when there is signal at the FOV edge, an inverted negative artifact is created. The multichannel joint reconstruction method uses an iterative reconstruction technique to recover edge information using information from an orthogonal axis, preventing this artifact and allowing the user to prescribe a small FOV on the region of interest. Here we describe the implementation of this method to isolate and quantify low regions of MPI signal from higher regions.
TRAILS: tree reconstruction of ancestry using incomplete lineage sorting
Authors: Rivas-González Iker , Schierup Mikkel H , Wakeley John , Hobolth Asger 
Published: June 2023

AbstractGenome-wide genealogies of multiple species carry detailed information about demographic and selection processes on individual branches of the phylogeny. Here, we introduce TRAILS, a hidden Markov model that accurately infers time-resolved population genetics parameters, such as ancestral effective population sizes and speciation times, for ancestral branches using a multi-species alignment of three species and an outgroup. TRAILS leverages the information contained in incomplete lineage sorting fragments by modelling genealogies along the genome as rooted three-leaved trees, each with a topology and two coalescent events happening in discretized time intervals within the phylogeny. Posterior decoding of the hidden Markov model can be used to infer the ancestral recombination graph for the alignment and details on demographic changes within a branch. Since TRAILS performs posterior decoding at the base-pair level, genome-wide scans based on the posterior probabilities can be devised to detect deviations from neutrality. Using TRAILS on a human-chimp-gorilla-orangutan alignment, we recover speciation parameters and extract information about the topology and coalescent times at high resolution.Author summaryDNA sequences can be compared to reconstruct the evolutionary history of different species. While the ancestral history is usually represented by a single phylogenetic tree, speciation is a more complex process, and, due to the effect of recombination, different parts of the genome might follow different genealogies. For example, even though humans are more closely related to chimps than to gorillas, around 15% of our genome is more similar to the gorilla genome than to the chimp one. Even for those parts of the genome that do follow the same human-chimp topology, we might encounter a last common ancestor at different time points in the past for different genomic fragments. Here, we present TRAILS, a new framework that utilizes the information contained in all these genealogies to reconstruct the speciation process. TRAILS infers unbiased estimates of the speciation times and the ancestral effective population sizes, improving the accuracy when compared to previous methods. TRAILS also reconstructs the genealogy at the highest resolution, inferring, for example, when common ancestry was found for different parts of the genome. This information can also be used to detect deviations from neutrality, effectively inferring natural selection that happened millions of years ago. We validate the method using extensive simulations, and we apply TRAILS to a human-chimp-gorilla multiple genome alignment, from where we recover speciation parameters that are in good agreement with previous estimates.
A benchmark study of data normalisation methods for PTR-TOF-MS exhaled breath metabolomics
Authors: Roquencourt Camille , Lamy Elodie , Bardin Emmanuelle , Deviller Philippe , Grassin-Delyle Stanislas 
Published: June 2023

AbstractBackgroundVolatilomics is the branch of metabolomics dedicated to the analysis of volatile organic compounds (VOCs) in exhaled breath for medical diagnostic or therapeutic monitoring purposes. Real-time mass spectrometry technologies such as proton transfer reaction mass spectrometry (PTR-MS) are commonly used, and data normalisation is an important step to discard unwanted variation from non-biological sources, as batch effects and loss of sensitivity over time may be observed. As normalisation methods for real-time breath analysis have been poorly investigated, we aimed to benchmark known metabolomic data normalisation methods and apply them to PTR-MS data analysis.MethodsWe compared seven normalisation methods, five statistically based and two using multiple standard metabolites, on two datasets from clinical trials for COVID-19 diagnosis in patients from the emergency department or intensive care unit. We evaluated different means of feature selection to select the standard metabolites, as well as the use of multiple repeat measurements of ambient air to train the normalisation methods.ResultsWe show that the normalisation tools can correct for time-dependent drift. The methods that provided the best corrections for both cohorts were Probabilistic Quotient Normalisation and Normalisation using Optimal Selection of Multiple Internal Standards. Normalisation also improved the diagnostic performance of the machine learning models, significantly increasing sensitivity, specificity and area under the ROC curve for the diagnosis of COVID-19.ConclusionsOur results highlight the importance of adding an appropriate normalisation step during the processing of PTR-MS data, which allows significant improvements in the predictive performance of statistical models.
Nanobiopsy investigation of the subcellular mtDNA heteroplasmy in human tissues
Authors: Bury Alexander , Vincent Amy E. , Pyle Angela , Actis Paolo , Hudson Gavin 
Published: June 2023

AbstractMitochondrial function is critical to continued cellular vitality and is an important contributor to a growing number of human diseases. Mitochondrial dysfunction is typically heterogeneous, mediated through the clonal expansion of mitochondrial DNA (mtDNA) variants in a subset of cells in a given tissue. To date, our understanding of the dynamics of clonal expansion of mtDNA variants has been technically limited to the single cell-level. Here, we report the use of nanobiopsy for subcellular sampling from human tissue, combined with next-generation sequencing to assess subcellular mtDNA mutation load in human tissue from mitochondrial disease patients. The ability to map mitochondrial mutation loads within individual cells of diseased tissue samples will further our understanding of mitochondrial genetic diseases.
Tumor-derived exosomal miR-222-3p induce cancer-associated fibroblasts activation to foster progression of renal cancer
Authors: Yang Yang , Zhu Jie , Shen Dong-lai , Han Ce , Wang Chen-feng , Cui Bo , Fan Wen-mei , Huang Yan , Li Xiu-bin , Zhang Xu , Gao Yu 
Published: June 2023

AbstractThe interaction between tumor-derived exosomes and stroma is crucial for tumor progression. However, the mechanisms by which tumor cells influence stromal changes are not yet fully understood. Our study revealed that high-metastatic renal cancer cells are more effective in converting normal fibroblasts into cancer-associated fibroblasts (CAFs) compared to low-metastatic renal cancer cells. Meanwhile, high-metastatic renal cancer cells secrete more exosomal miR-222-3p, which can directly target PANK3, activate NF-kB signaling pathway in fibroblasts and induce intracellular metabolic reprogramming to produce more lactic acid through Warburg effect. The activated CAFs further promote renal cancer progression by secreting lactic acid and inflammatory cytokines, including IL-6 and IL-8. Patients with renal cancer who have high levels of serum exocrine miR-222-3p are more likely to experience progression. These findings suggest that the intercellular communication between renal cancer cells and fibroblasts is facilitated by tumor exosomes. Targeting this communication may hold promise for the prevention and treatment of renal cancer.
CD95L concatemers highlight difference in the manner CD95-mediated apoptotic and non-apoptotic pathways are triggered
Authors: Lebrault Eden , Oblet Christelle , Kurma Keerthi , Levoin Nicolas , Jean Mickael , Vacher Pierre , Legembre Patrick 
Published: June 2023

AbstractTo better understand the stoichiometry of CD95L required to trigger apoptotic and non-apoptotic signals, we generated several CD95L concatemers from dimer to hexamer conjugatedviaa flexible link (GGGGS)2. These ligands reveal that although the hexameric structure is the best stoichiometry to trigger cell death, a dimer is sufficient to induce the apoptotic response in CD95-sensitive Jurkat cells. Interestingly, only trimeric and hexameric forms can implement a potent Ca2+response, suggesting that while CD95 aggregation controls the implementation of the apoptotic signal, both aggregation and conformation are required to implement the Ca2+pathway.
Single-molecule imaging reveals the kinetics of non-homologous end-joining in living cells
Authors: Mikhova Mariia , Goff Noah J. , Janovič Tomáš , Heyza Joshua R. , Meek Katheryn , Schmidt Jens C. 
Published: June 2023

SUMMARYNon-homologous end joining (NHEJ) is the predominant pathway that repairs DNA double-stranded breaks (DSBs) in vertebrates. However, due to challenges in detecting DSBs in living cells, the repair capacity of the NHEJ pathway is unknown. The DNA termini of many DSBs must be processed to allow ligation while minimizing genetic changes that result from break repair. Emerging models propose that DNA termini are first synapsed ~115Å apart in one of several long-range synaptic complexes before transitioning into a short-range synaptic complex that juxtaposes DNA ends to facilitate ligation. The transition from long-range to short-range synaptic complexes involves both conformational and compositional changes of the NHEJ factors bound to the DNA break. Importantly, it is unclear how NHEJ proceedsin vivobecause of the challenges involved in analyzing recruitment of NHEJ factors to DSBs over time in living cells. Here, we develop a new approach to study the temporal and compositional dynamics of NHEJ complexes using live cell single-molecule imaging. Our results provide direct evidence for stepwise maturation of the NHEJ complex, pinpoint key regulatory steps in NHEJ progression, and define the overall repair capacity NHEJ in living cells.
A CDC-42-regulated actin network is necessary for nuclear migration through constricted spaces inC. elegans
Authors: Ho Jamie , Guerrero Leslie A. , Libuda Diana , Luxton GW Gant , Starr Daniel A 
Published: June 2023

AbstractSuccessful nuclear migration through constricted spaces between cells or in the extracellular matrix relies on the ability of the nucleus to deform. Little is known of how this takes placein vivo. We study confined nuclear migration inCaenorhabditis eleganslarval P-cells, which is mediated by the LINC complex to pull nuclei towards the minus ends of microtubules. Null mutations of LINC componentunc-84lead to a temperature-dependent phenotype, suggesting a parallel pathway for P-cell nuclear migration. A forward genetic screen for enhancers ofunc-84identifiedcgef-1(CDC-42Guanine NucleotideExchangeFactor). Knockdown of CDC-42 in the absence of the LINC complex led to a P-cell nuclear migration defect. Expression of constitutively active CDC-42 rescued nuclear migration incgef-1; unc-84double mutants suggesting CDC-42 functions downstream of CGEF-1. The Arp2/3 complex and non-muscle myosin II (NMY-2) were also found to function parallel to the LINC pathway. In our model, CGEF-1 activates CDC-42, induces actin polymerization through the Arp2/3 complex to deform the nucleus during nuclear migration while NMY-2 helps push the nucleus through confined spaces.
HuR-miRNA complex Activates RAS GTPase RalA to Facilitate Endosome Targeting and Extracellular Export of miRNAs
Authors: Ghosh Syamantak , Choudhury Sourav Hom , Mukherjee Kamalika , Bhattacharyya Suvendra N. 
Published: June 2023

AbstractExtracellular vesicles-mediated exchange of miRNA cargos between diverse types of mammalian cells is a major mechanism of controlling cellular miRNA levels and activity and thus to regulate expression of miRNA-target genes in both donor and recipient cells. Despite tremendous excitement related to extracellular vesicles-associated miRNAs as biomarkers or having therapeutic potential, the mechanism of selective packaging of miRNAs into endosomes and multivesicular bodies for subsequent extracellular export is a poorly studied area due to lack of assay system to study such processesin vitro. We have developed anin vitroassay with endosomes isolated from mammalian macrophage cells to follow miRNA packaging into endocytic organelles. The synthetic miRNAs, used in the assay, get imported inside the isolated endosomes during thein vitroreaction and become protected from RNase in a time and concentration dependent manner. The selective miRNA accumulation inside endosomes requires both ATP and GTP hydrolysis and the miRNA binding protein HuR. The HuR-miRNA complex binds and stimulates the endosomal RalA GTPase to facilitate the import of miRNAs into endosomes and their subsequent export as part of the extracellular vesicles. The endosomal targeting of miRNAs is also very much dependent on endosome maturation process that is controlled by Rab5 protein and ATP.Graphical Abstract◦miRNAs get imported to endosomesin vitro andare become protected to RNase◦Endosomal miRNA import is sequence specific and requires miRNA exporter protein HuR◦HuR-miRNA complex activates RalA GTPases to complete miRNA import.◦Rab5 protein and ATP hydrolysis is required for endosome maturation and miRNA import
Koalas, cameras and a primary school: Obtaining ecological insights for land management through a mini-citizen science project with young students
Authors: Williams Sharon , Salmon Gerard , Dempsey Daniel , Philpot David , Faulkner Geoff 
Published: June 2023

AbstractKoalas are an endangered species in Eastern Australia and the management of habitat revegetation sites is essential for the marsupial’s survival. This report summarises the results of a partnership between revegetation managers and a local primary school that connected children to real world scientific practice. Ten infrared motion sensor cameras were installed on a five-year-old revegetation offset site in south-east Queensland, Australia to capture movements of koalas and other fauna. Primary school students screened images from these cameras for animal presence in a mini-citizen science project through an easy-to-use website created specifically for this project. Aspects of these results were used to modify the land’s management by site supervisors. This report outlines processes involved in having Queensland primary school students participate in a mini web-based citizen science project, presents some of the ecological results obtained through the investigation and makes recommendations for future projects of this type.
Control of stem cell behavior by CLE–JINGASA signaling in the shoot apical meristem inMarchantia polymorpha
Authors: Takahashi Go , Kiyosue Tomohiro , Hirakawa Yuki 
Published: June 2023

SummaryLand plants undergo indeterminate growth by the activity of meristems in both gametophyte (haploid) and sporophyte (diploid) generations1-3. In the sporophyte of the flowering plantArabidopsis thaliana, the apical meristems are located at the shoot and root tips, in which a number of regulatory gene homologs are shared for their development, implying deep evolutionary origins4-7. However, little is known about their functional conservation with gametophytic meristems in distantly related land plants such as bryophytes8-17, even though genomic studies have revealed the subfamily-level diversity of regulatory genes is mostly conserved throughout land plants18-23. Here we show that a NAM/ATAF/CUC (NAC) domain transcription factor, JINGASA (MpJIN), acts downstream of CLV3/ESR-related (CLE) peptide signaling and controls stem cell behavior in the gametophytic shoot apical meristem of the liverwortMarchantia polymorpha. We found that MpJINshows heterogeneous expression in space and time within the stem cell zone, associated with the loss andde novospecification of stem cell identity at the branching event. Consistent with the expression pattern, induction of MpJINresults in ectopic periclinal cell division in the stem cell zone and meristem termination. Comparative expression analysis suggests that the function of JIN/FEZ subfamily genes was shared between the shoot apical meristems in the gametophyte and sporophyte generations in early land plants but was lost in certain lineages including the flowering plantA. thaliana.
Hypoxia-driven deSUMOylation of EXOSC10 promotes adaptive changes in the transcriptome profile
Authors: Filippopoulou Chrysa , Thome Chairini C. , Perdikari Sofia , Ntini Evgenia , Simos George , Bohnsack Katherine E. , Chachami Georgia 
Published: June 2023

AbstractReduced oxygen availability (hypoxia) triggers adaptive cellular responses via hypoxia-inducible factor (HIF)-dependent transcriptional activation. Adaptation to hypoxia also involves transcription-independent processes like post-translational modifications, however these mechanisms are poorly characterized. Investigating the involvement of protein SUMOylation in response to hypoxia, we discovered that hypoxia strongly decreases the SUMOylation of Exosome subunit 10 (EXOSC10), the catalytic subunit of the RNA exosome, in a HIF-independent manner. EXOSC10 is a multifunctional exoribonuclease enriched in the nucleolus that mediates the processing and degradation of various RNA species. We demonstrate that the Ubiquitin-specific protease 36 (USP36) SUMOylates EXOSC10 and we reveal SUMO1/sentrin-specific peptidase 3 (SENP3) as the enzyme mediating deSUMOylation of EXOSC10. Under hypoxia, EXOSC10 dissociates from USP36 and translocates from the nucleolus to the nucleoplasm concomitant with its deSUMOylation. Loss of EXOSC10 SUMOylation does not detectably affect rRNA maturation but affects the mRNA transcriptome by modulating the expression levels of hypoxia-related genes. Our data suggest that dynamic modulation of EXOSC10 SUMOylation and localization under hypoxia regulates the RNA degradation machinery to facilitate cellular adaptation to low oxygen conditions.