bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relative Effects of Habitat Amount and FragmentationPer Seon the Genetic Diversity of The Glanville Fritillary Butterfly
Authors: Fernandez Multigner Lola , Bras Audrey , DiLeo Michelle , Saastamoinen Marjo 
Published: November 2024

AbstractHabitat loss and fragmentation are considered the key drivers of biodiversity loss. Understanding their relative roles is difficult as habitat loss and fragmentation tend to co-occur. It has been proposed that the total habitat amount available in the local landscape mainly drives species richness while fragmentationper se– the breaking apart of habitat independent of habitat amount - has negligible or even a positive effect on biodiversity. Several studies support this at the species richness level. Yet, the potential effects of fragmentationper seon genetic diversity at the landscape scale are understudied. Using the Glanville fritillary butterfly metapopulation in the Åland islands, we tested the effects of fragmentationper seon genetic diversity using a landscape-based approach and 2,610 individuals genotyped at 40 neutral SNP markers. We assessed the independent effect of habitat amount and fragmentation (i.e. number of patches) within the local landscape on the focal patch genetic diversity. The amount of habitat in the local landscape had a positive effect on genetic diversity, while fragmentationper sehad a more negligible impact on the genetic diversity. Our results thus highlight that all fragments, even the small ones, likely contribute to the maintenance of genetic diversity of the focal population.
Denoising Reveals Low-Occupancy Populations in Protein Crystals
Authors: Fadini Alisia , Apostolopoulou Virginia , Lane Thomas J. , van Thor Jasper J. 
Published: November 2024

AbstractAdvances in structural biology increasingly focus on uncovering protein dynamics and transient or weak macromolecular complexes. Such studies require modeling of low-occupancy species, for instance time-evolving intermediates and bound ligands. In protein crystallography, difference maps that compare paired perturbed and reference datasets are a powerful way to identify and aid modeling of low-occupancy species. Current methods to generate difference maps, however, rely on manually tuned parameters and, in cases of weak signal due to low occupancy, can fail to extract clear, chemically interpretable signals.We address these issues, first by showing negentropy is an effective metric to assess difference map quality and can therefore be used to automatically determine parameters needed during difference map calculation. Leveraging this, we apply total variation denoising, an image restoration technique that requires a choice of regularization parameter, to crystallographic difference maps. We show that total variation denoising improves map signal-to-noise and enables us to estimate the latent phase contribution of low-occupancy states. This technology opens new possibilities for time-resolved and ligand-screening crystallography in particular, allowing the detection of states that previously could not be resolved due to their inherently low occupancy.
Co-Therapy with S1P and Heparan Sulfate Derivatives to Restore Endothelial Glycocalyx and Combat Pro-Atherosclerotic Endothelial Dysfunction
Authors: Mitra Ronodeep , Pentland Kaleigh , Kolev Svilen , Eden Matthew , Levine Erel , Oakes Jessica M. , Ebong Eno E. 
Published: November 2024

ABSTRACTEndothelial cell (EC) glycocalyx (GCX) shedding due to disturbed blood flow and chemical factors leads to low-density lipoprotein infiltration and reduced nitric oxide synthesis, causing vascular dysfunction and atherosclerosis. This study evaluates a novel therapy combining sphingosine-1-phosphate (S1P) and heparin (heparan sulfate derivative). We hypothesized that heparin/S1P would repair mechanically damaged EC GCX in disturbed flow (DF) regions and restore anti-atherosclerotic mechanotransduction function, addressing cardiovascular disease. We used a parallel-plate flow chamber to simulate flow conditions in vitro and a partial carotid ligation mouse model to mimic DF in vivo. Heparin and albumin-bound S1P were administered to assess their reparative effects on the endothelial GCX. Immunocytochemistry, fluorescent staining, confocal microscopy, cellular alignment studies, and ultrasound were performed to evaluate EC function and endothelial-dependent vascular function. Barrier functionality was assessed via macrophage uptake. Heparin/S1P mechanism-of-action insights were gained through fluid dynamics simulations and staining of GCX synthesis enzyme as well as S1P receptor. Statistical analyses validated results. In vitro data showed that heparin/S1P therapy improves the function of DF-conditioned ECs by restoring EC GCX and promoting EC alignment and elevated vasodilator eNOS (endothelial-type nitric oxide synthase) expression. The in vivo studies confirmed GCX degradation, increased vessel inflammation and hyperpermeability, and vessel wall thickening in the partially ligated left carotid artery. Heparin/S1P treatment restored GCX in the left carotid artery, enhancing GCX thickness and coverage of the blood vessel wall. This work advances a new approach to regenerating the EC GCX and restoring its function in ECs under DF conditions.
Tear secretionviaa paracellular pathway in lacrimal gland is regulated by myosin-mediated modulation of tight junction permeability
Authors: Ohno Yuta , Hu Gaizun , Robak Dominik , Zheng W. Sharon , Ebrahim Seham 
Published: November 2024

Abstract“Dry eye”, characterized by symptoms of ocular discomfort and visual disturbances due to decreased tear secretion, affects 16 million Americans. Yet, there is currently no cure for dry eye as the mechanistic details of water secretion in the tear-producing lacrimal gland have not been fully elucidated. While a transcellular water secretion pathwayviawater channels like AQP5 has been reported, the existence and function of a paracellular pathwayviatight junctions between epithelial cells remains controversial. The actomyosin cytoskeleton localizes to the apical junctions of epithelial cells across organs and regulates tight junction integrity. Here, we report that non-muscle myosin IIC (NMIIC) is enriched at apical junctions of ductal epithelial cells in the lacrimal gland, leading us to hypothesize that NMIIC regulates tear secretion through modulation of tight junction permeability. Consistent with this hypothesis, we found that tear volume after carbachol stimulation was significantly increased in mice lacking NMIIC, and levels of the tight junction protein ZO-1 were significantly reduced. Furthermore, pharmacological activation of NMIIC by 4-Hydroxyacetophenone in wildtype mice significantly inhibited tear secretion. In summary, our findings reveal a paracellular water secretion pathway in the lacrimal gland, which is regulated by NMIIC-mediated modulation of ductal cell tight junctional permeability, and can be targeted by small molecules.Significance StatementWhile dry eye affects more than 16 million Americans, there is currently no cure as the mechanisms underlying tear secretion are incompletely understood. Here, we report first evidence for the existence and function of a paracellular water pathway, in which water flows between cells, in the lacrimal gland. We also show that this pathway is directly regulated by the modulation of tight junction permeability by non-muscle myosin IIC (NMIIC). This study thus identifies a new mechanism for exocrine secretion, which can be targeted towards developing treatments for dry eye/mouth syndrome.
TomoScore: A Neural Network Approach for Quality Assessment of Cellular cryo-ET
Authors: Tan Xuqian , Boniuk Ethan , Abraham Anisha , Zhou Xueting , Yu Zhili , Ludtke Steven J. , Wang Zhao 
Published: November 2024

AbstractElectron cryo-tomography (cryo-ET) is a powerful imaging tool that allows three-dimensional visualization of subcellular architecture. During morphological analysis, reliable tomogram segmentation can only be achieved through high-quality data. However, unlike single-particle analysis or subtomogram averaging, the field lacks a useful quantitative measurement of cellular tomogram quality. Currently, the most prevalent method to determine cellular tomogram resolvability is an empirical judgment by experts, which is time-consuming. Methods like FSC between split tilt series suffer from severe geometrical artifacts. We address this gap with a neural network model to predict per-slice resolvability that can apply to tomograms collected from various species and magnifications. We introduce a novel metric, “TomoScore”, providing a single-value evaluation of cellular tomogram quality, which is a powerful tool for pre-screening tomograms for subsequent automatic segmentation. We further explore the relationship between accumulated electron dose and resulting quality, suggesting an optimum dose range for cryo-ET data collection. Overall, our study streamlines data processing and reduces the need for human involvement during pre-selection for tomogram segmentation.
Genetic and Environmental Determinants of Streaming and Aggregation inMyxococcus xanthus
Authors: Khan Trosporsha T , Murphy Patrick , Zhang Jiangguo , Igoshin Oleg A , Welch Roy D 
Published: November 2024

AbstractUnder starvation conditions, a spot of a few millionMyxococcus xanthuscells on agar will migrate inward to form aggregates that mature into dome-shaped fruiting bodies. This migration is thought to occur within structures called ‘streams,’ which are considered crucial for initiating aggregation. The prevailing traffic jam model hypothesizes that intersections of streams cause cell crowding and ‘jamming,’ thereby initiating the process of aggregate formation. However, this hypothesis has not been rigorously tested, in part due to the lack of a standardized, quantifiable definition of streams. To address this gap, we captured time-lapse movies and conducted fluorescent cell tracking experiments using wild-type and two motility-deficient mutantM. xanthusstrains. By quantitatively defining streams and developing a novel stream detection mask, we show that streams are not essential for nascent aggregate formation, though they may accelerate the process. Moreover, our results indicate that streaming has a genetic component: disrupting only one of the twoM. xanthusmotility systems hinders stream formation. Together, these findings challenge the idea that stream intersections are required to drive aggregate formation and suggest thatM. xanthusaggregation may be driven by mechanisms independent of streaming, highlighting the need for alternative models to fully explain aggregation dynamics.
Differential Equation Modeling of Cell Population Dynamics in Skeletal Muscle Regeneration from Single-Cell Transcriptomic Data
Authors: Al-Ghazawi Renad , Shao Xiaojian , Perkins Theodore J. 
Published: November 2024

AbstractSkeletal muscle regeneration is a complex process orchestrated by diverse cell populations within a dynamic niche. In response to muscle damage and intercellular signaling, these cells undergo cell fate and migration decisions including quiescence, activation, proliferation, differentiation, infiltration, apoptosis, and exfiltration. The emergence of single-cell RNA sequencing (scRNA-seq) studies of muscle regeneration offers a significant opportunity to refine models of regeneration and enhance our understanding of cellular interactions. To better understand how crosstalk between cell types governs cell fate decisions and cell population dynamics, we developed a novel non-linear ordinary differential equation model guided by scRNA-seq data. Our model consists of 9 variables and 19 parameters, capturing the dynamics of key myogenic lineage and immune cell types. We calibrated time-series scRNA-seq data to units of cells per cubic millimeter of tissue and fit our model’s parameters to capture the observed dynamics, validating on an independent time series. The model successfully captures regeneration dynamics, particularly after incorporating a novel type of regulatory interaction between M2 macrophages and satellite cells that has been hypothesized in the literature. Our model lays a foundation for future computational explorations of muscle regeneration, modeling of disease conditions, and in silico testing of therapeutic strategies.
sCellST: a Multiple Instance Learning approach to predict single-cell gene expression from H&E images using spatial transcriptomics
Authors: Chadoutaud Loïc , Lerousseau Marvin , Herrero-Saboya Daniel , Ostermaier Julian , Fontugne Jacqueline , Barillot Emmanuel , Walter Thomas 
Published: November 2024

AbstractAdvancing our understanding of tissue organization and its disruptions in disease remains a key focus in biomedical research. Histological slides stained with Hematoxylin and Eosin (H&E) provide an abundant source of morphological information, while Spatial Transcriptomics (ST) enables detailed, spatiallyresolved gene expression (GE) analysis, though at a high cost and with limited clinical accessibility. Predicting GE directly from H&E images using ST as a reference has thus become an attractive objective; however, current patch-based approaches lack single-cell resolution. Here, we present sCellST, a multipleinstance learning model that predicts GE by leveraging cell morphology alone, achieving remarkable predictive accuracy. When tested on a pancreatic ductal adenocarcinoma dataset, sCellST outperformed traditional methods, underscoring the value of basing predictions on single-cell images rather than tissue patches. Additionally, we demonstrate that sCellST can detect subtle morphological differences among cell types by utilizing marker genes in ovarian cancer samples. Our findings suggest that this approach could enable single-cell level GE predictions across large cohorts of H&E-stained slides, providing an innovative means to valorize this abundant resource in biomedical research.
Salt-dependent non-catalytic allostery of human USP14-regulated 26S proteasome
Authors: Zou Shitao , Zhang Shuwen , Zhao Lihong , Mao Youdong 
Published: November 2024

AbstractUSP14, a deubiquitylating enzyme, regulates 26S proteasome function both catalytically and non-catalytically through multiple checkpoints. How USP14 non-catalytically regulates the proteasome activity remains elusive. Here, we combined genetic engineering and cryo-EM to disentangle how USP14 non-catalytically regulates proteasome activity in a salt-dependent manner. By solving 16 high-resolution cryo-EM structures of substrate-engaged human 26S proteasome complexed with a catalytically deficient mutant USP14, we demonstrate that USP14’s non-catalytic activity alone can induce parallel pathways of proteasome state transitions, leading to opposing substrate fates. The USP14 mutant allosterically reprograms the AAA-ATPase motor, inducing novel substrate-engaged conformations and filling major gaps in understanding asymmetric ATP-hydrolysis cycling around the ATPase ring. Time-resolved cryo-EM and functional analysis reveal that sodium or potassium promotes substrate-engaged pathways and suppresses USP14 activity for enhanced degradation, uncovering another layer of complexity in proteasome regulation.
Copper induces p53 unfolding in cancer cells, resulting in invasion and chemoresistance
Authors: von Grabowiecki Yannick , Bell Steven J , Richards Hannah L , Massey Ellie J , Newson Zoe , Tarrant Emma , Morrison Matthew S , Galvin Melanie , Simpson Kathryn L. , Le Quesne John , Aschauer Lydia , Muller Patricia AJ 
Published: November 2024

SummaryCopper has been shown to play an important role in cancers, enhancing cell proliferation, remodelling the microenvironment and enhancing the function of oncogenes. Here we show that copper turns the tumour suppressor p53 protein into a pro-oncogenic protein.Mutations in theTP53gene often lead to expression of various mutant p53 proteins. Mutant proteins often lose some or all wild type function and gain novel pro-tumourigenic functions, which can be partially attributed to protein unfolding. Here we show that copper accumulates in tumours, unfolds WTp53 and promotes chemoresistance. Unfolding of WT p53 results in interaction with mutant p53-specific interacting proteins TAp63 and Ago2 and promotes invasion. Interestingly, partially-functional p53 mutants that are frequently observed in lung cancers, are more affected by copper than WTp53. Our results suggest that small increases in copper impair WT p53 function and augment mutant p53 function, which could partially be restored by the chelator Trien.
Metabolic and neuroactivity imbalances in plasma from aniridia patients withPAX6haploinsufficiency
Authors: Cunha Dulce Lima , Kit Vivienne , Skinner Jane , Welch Ailsa A , Moosajee Mariya 
Published: November 2024

AbstractPAX6 is a transcription factor crucial for the development of the eye, pancreas, and brain. Heterozygous variants resulting inPAX6haploinsufficiency are the main genetic cause of congenital aniridia, characterized by both anterior and posterior ocular defects and sight loss. The extra-ocular features ofPAX6haploinsufficiency are becoming more widely recognised, with systemic manifestations like obesity, diabetes, and neurological/behavioural disorders being reported. In this study, we uncovered the metabolomic profile of the blood plasma from 25PAX6-related aniridia patients compared to gender and age-matched controls. We found significant disruptions in lipid and energy metabolism, increased oxidative stress and neurotransmitters imbalances, as well as alterations linked to the gut microbiome. This study identified novel metabolic changes associated withPAX6haploinsufficiency, providing evidence for the systemic aetiology of congenital aniridia and emphasizing the need for multidisciplinary management and further exploration into ocular and systemic therapeutic approaches.
Menadione reduces the expression of virulence- and colonisation-associated genes inHelicobacter pylori
Authors: Thompson Stephen , Ojo Rebecca Omoyemi , Hoyles Lesley , Winter Jody 
Published: November 2024

AbstractNovel treatment options are needed for the gastric pathogenHelicobacter pyloridue to its increasing antibiotic resistance. The vitamin K analogue menadione has been extensively studied due to interest in its antibacterial and anti-cancer properties. Here, we investigated the effects of menadione onH. pylorigrowth, viability, antibiotic resistance, motility and gene expression using clinical isolates. The minimum inhibitory concentration (MIC) of menadione was 313 µM for 11/13 isolates and 156 µM for 2/13 isolates. The minimum bactericidal concentrations were 1.25-2.5 mM, indicating that concentrations in the micromolar range were bacteriostatic rather than bactericidal. We were not able to experimentally evolve resistance to menadionein vitro. Sub-MIC menadione (16 µM for 24 h) did not significantly inhibit bacterial growth but significantly (p < 0.05) changed the expression of 1291/1615 (79.9 %) genes encoded by strain 322A. Expression of the virulence factor genescagAandvacAwas downregulated in the presence of sub-MIC menadione, while genes involved in stress responses were upregulated. Sub-MIC menadione significantly (p < 0.0001) inhibited the motility ofH. pylori, consistent with the predicted effects of the observed significant (p < 0.05) downregulation ofcheY, upregulation ofrpoN, and changes in expression of flagellar assembly pathway genes seen in the transcriptomic analysis. Through in-depth interrogation of transcriptomics data, we concluded that sub-MIC menadione elicits a general stress response inH. pyloriwith survival in the stationary phase likely mediated by upregulation ofsurEandrpoN. Sub-MIC menadione caused some modest increases inH. pylorisusceptibility to antibiotics, but the effect was variable with strain and antibiotic type and did not reach statistical significance. Menadione (78 µM) was minimally cytotoxic to human gastric adenocarcinoma (AGS) cells after 4 hours but caused significant loss of cell viability after 24 hours.Given its inhibitory effects on bacterial growth, motility and expression of virulence and colonisation- associated genes, menadione at low micromolar concentrations may have potential utility as a virulence-attenuating agent againstH. pylori.Data summaryRNAseq data reported on in this study are available to download from ArrayExpress under accession E-MTAB-14439. Supplementary materials associated with this publication are available fromhttps://figshare.com/projects/Menadione_reduces_the_expression_of_virulence-_and_colonisation-associated_genes_in_Helicobacter_pylori/219631.
FOXPGenes Regulate Purkinje Cell Diversity in Cerebellar Development and Evolution
Authors: Khouri-Farah Nagham , Guo Qiuxia , Perry Thomas A. , Dussault Ryan , Li James Y.H. 
Published: November 2024

SUMMARYMammalian cerebellar development is thought to be influenced by distinct Purkinje cell (PC) subtypes. However, the degree of PC heterogeneity and the molecular drivers of this diversity have remained unclear, hindering efforts to manipulate PC diversification and assess its role in cerebellar development. Here, we demonstrate the critical role ofFoxpgenes in cerebellar development by regulating PC diversification. We identified 11 PC subtypes in the embryonic mouse cerebellum through single-cell RNA sequencing. Using a novel unsupervised method, we mapped these subtypes in three-dimensional space, revealing discrete PC subtypes predictive of adult cerebellar organization, including longitudinal stripes and lobules. These subtypes exhibit unique combinations ofFoxp1,Foxp2, andFoxp4expression. Deletion ofFoxp2andFoxp1disrupts PC diversification, leading to altered cerebellar patterning, including the loss of a specificFoxp1-expressing subtype and the cerebellar hemisphere. TheFoxp1-expressing PC subtype is much more abundant in the fetal human cerebellum than in mice, but rare in the chick cerebellum, correlating with cerebellar hemisphere size in these species. This highlights the significance ofFoxp1-expressing PCs in cerebellar hemisphere development and evolution. Therefore, our study identifiesFoxpgenes as key regulators of PC diversity, providing new insights into the developmental and evolutionary underpinnings of the cerebellum.