bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational Study of Ion Permeation Through Claudin-4 Paracellular Channels
Authors: Berselli Alessandro , Alberini Giulio , Benfenati Fabio , Maragliano Luca 
Published: March 2022

ABSTRACTClaudins (Cldns) form a large family of protein homologs that are essential for the assembly of paracellular tight junctions (TJs), where they form channels or barriers with tissue-specific selectivity for permeants. In contrast to several family members whose physiological role has been identified, the function of claudin 4 (Cldn4) remains elusive, despite experimental evidence suggesting that it can form anion-selective TJ channels in the renal epithelium. Computational approaches have recently been employed to elucidate the molecular basis of Cldns’ function, and hence could help in clarifying Cldn4 role. In this work, we use structural modeling and all-atom molecular dynamics simulations to transfer two previously introduced structural models of Cldn-based paracellular complexes to Cldn4, in order to reproduce a paracellular anion channel. Free energy (FE) calculations for ionic transport through the pores allow us to establish the thermodynamic properties driving the ion-selectivity of the structures. While one model shows a cavity permeable to chloride and repulsive to cations, the other forms barrier to the passage of all the major physiological ions. Furthermore, our results confirm the charge selectivity role of the residue Lys65 in the first extracellular loop of the protein, rationalizing Cldn4 control of paracellular permeability.
Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome depleted regions
Authors: Donovan Benjamin T. , Chen Hengye , Eek Priit , Meng Zhiyuan , Jipa Caroline , Tan Song , Bai Lu , Poirier Michael G. 
Published: March 2022

SUMMARYNucleosomes drastically limit transcription factor (TF) occupancy, while pioneer transcription factors (PFs) somehow circumvent this nucleosome barrier. In this study, we compare nucleosome binding of two conserved S. cerevisiae basic helix-loop-helix (bHLH) TFs, Cbf1 and Pho4. A Cryo-EM structure of Cbf1 in complex with the nucleosome reveals that the Cbf1 HLH region can electrostatically interact with exposed histone residues within a partially unwrapped nucleosome. Single molecule fluorescence studies show that the Cbf1 but not the Pho4 HLH region facilitates efficient nucleosome invasion by slowing its dissociation rate relative to DNA through interactions with histones. In vivo studies show that this enhanced binding provided by the Cbf1 HLH region enables nucleosome invasion and ensuing repositioning. These structural, single molecule, and in vivo studies reveal the mechanistic basis of dissociation rate compensation by pioneer factors and how this translates to facilitating chromatin opening inside cells.
Single-cell multiomics atlas of organoid development uncovers longitudinal molecular programs of cellular diversification of the human cerebral cortex
Authors: Uzquiano Ana , Kedaigle Amanda J. , Pigoni Martina , Paulsen Bruna , Adiconis Xian , Kim Kwanho , Faits Tyler , Nagaraja Surya , Antón-Bolaños Noelia , Gerhardinger Chiara , Tucewicz Ashley , Murray Evan , Jin Xin , Buenrostro Jason , Chen Fei , Velasco Silvia , Regev Aviv , Levin Joshua Z. , Arlotta Paola 
Published: March 2022

AbstractRealizing the full utility of brain organoids as experimental systems to study human cortical development requires understanding whether organoids replicate the cellular and molecular events of this complex process precisely, reproducibly, and with fidelity to the embryo. Here we present a comprehensive single-cell transcriptomic, epigenetic, and spatial atlas of human cortical organoid development, comprising over 610,000 cells, spanning initial generation of neural progenitors through production of differentiated neuronal and glial subtypes. We define the lineage relationships and longitudinal molecular trajectories of cortical cell types during development in organoids, and show that developmental processes of cellular diversification in organoids correlate closely to endogenous ones, irrespective of metabolic state. Using this data, we identify genes with predicted human-specific roles in lineage establishment, and discover a developmental origin for the transcriptional diversity of human callosal projection neurons, a population that has undergone dramatic expansion and diversification during human evolution. Our work provides a comprehensive, single-cell molecular map of human corticogenesis in vitro, identifying developmental trajectories and molecular mechanisms associated with human cellular diversification.
A model for determining the length distribution of actin filaments in cells
Authors: Ueda Yuika , Matsunaga Daiki , Deguchi Shinji 
Published: March 2022

AbstractTensional homeostasis is a cellular process whereby nonmuscle cells such as fibroblasts keep a constant level of intracellular tension and signaling activities. Cells are allowed thanks to tensional homeostasis to adapt to mechanical stress, but the detailed mechanism remains unclear. Here we address from a theoretical point of view what is required for maintaining cellular tensional homeostasis. A constrained optimization problem is formulated to analytically determine the probability function of the length of individual actin filaments (AFs) responsible for sustaining cellular tension. An objective function composed of two entropic quantities measuring the extent of formation and dispersion of AFs within cells is optimized under two constraint functions dictating a constant amount of actin molecules and tension that are arguably the two most salient features of tensional homeostasis. We then derive a specific probability function of AFs that is qualitatively consistent with previous experimental observations, in which short AF populations preferably appear. Regarding the underlying mechanism, our analyses suggest that the constraint for keeping the constant tension level makes long AF populations smaller in number because long AFs have a higher chance to be involved in bearing larger forces. The specific length distribution of AFs is thus required for achieving the constrained objectives, by which individual cells are endowed with the ability to stably maintain a homeostatic tension throughout the cell, thereby potentially allowing cells to locally detect deviation in the tension, keep resulting biological functions, and hence enable subsequent adaptation to mechanical stress. Although minimal essential factors are included given the actual complexity of cells, our approach would provide a theoretical basis for understanding complicated homeostatic and adaptive behavior of the cell.
Diagnostic performance of non-invasive fibrosis markers for chronic hepatitis B in sub-Saharan Africa: a Bayesian individual patient data meta-analysis
Authors: Johannessen Asgeir , Stockdale Alexander J. , Henrion Marc Y.R. , Okeke Edith , Seydi Moussa , Wandeler Gilles , Sonderup Mark , Spearman C. Wendy , Vinikoor Michael , Sinkala Edford , Desalegn Hailemichael , Fall Fatou , Riches Nicholas , Davwar Pantong , Duguru Mary , Maponga Tongai , Taljaard Jantjie , Matthews Philippa C. , Andersson Monique , Sombie Roger , Shimakawa Yusuke , Lemoine Maud 
Published: March 2022

ABSTRACTObjectiveIn sub-Saharan Africa, hepatitis B is the principal cause of liver disease. Non-invasive biomarkers of liver fibrosis are needed to identify patients requiring antiviral treatment. We assessed aspartate aminotransferase-to-platelet ratio index (APRI), gamma-glutamyl transferase-to-platelet ratio (GPR) and FIB-4 to diagnose significant fibrosis and cirrhosis in an individual patient data (IPD) meta-analysis.DesignIn total, 3,549 patients from 12 cohorts of HBsAg positive individuals in 8 sub-Saharan African countries were included. Transient elastography was used as a reference test for cirrhosis (>12.2 kPa), excluding patients who were pregnant, had hepatitis C, D, or HIV co-infection, were on hepatitis B therapy, or had acute hepatitis. A bivariate Bayesian IPD model was fitted with patient-level covariates and study-level random effects.ResultsAPRI and GPR had the best discriminant performance (area under receiver operating curve 0.81 and 0.82) relative to FIB-4 (0.77) for cirrhosis. The World Health Organization (WHO) recommended APRI threshold of ≥2.0 was associated with a sensitivity and specificity (95% credible interval) of 16.5% (12.5-20.5) and 99.5% (99.2-99.7) for cirrhosis. For APRI, we identified an optimised rule-in threshold for cirrhosis (cut-off 0.65) with a sensitivity and specificity of 56.2% (50.5-62.2) and 90.0% (89.0-91.0), and an optimised rule-out threshold (cut-off 0.36) with a sensitivity and specificity of 80.6% (76.1-85.1) and 64.3% (62.8-65.8).ConclusionsThe WHO recommended APRI threshold of 2.0 is too high to diagnose cirrhosis in sub-Saharan Africa. We identified new and optimised rule-in and rule-out thresholds for cirrhosis, with direct consequences for treatment guidelines in this setting.
The SUMO activating enzyme subunit, SAE2, contributes SUMO protein bias for mitotic fidelity
Authors: Walker Alexandra K. , Lanz Alexander J. , Jamshad Mohammed , Garvin Alexander J. , Wotherspoon Peter , Cooper Benjamin F. , Knowles Timothy J. , Morris Joanna R. 
Published: March 2022

AbstractMammalian cells possess three conjugatable SUMO variants: SUMO1 and the largely indistinguishable SUMO2 and SUMO3 (designated SUMO2/3). Some SUMOylated substrates are modified by both SUMO1 and SUMO2/3, while others show biased modifications towards SUMO1 or SUMO2/3. How preferential SUMO protein conjugation is coordinated is poorly understood.Here, we examine a modification of the catalytic component of the human SUMO Activation Enzyme, SAE2. We observe that lysine 164 of SAE2 is deacetylated during mitosis in an HDAC6-dependent manner. We find that an acetyl-analogue mutant, SAE2-K164Q, biases the activation and conjugation of SUMO2>SUMO1 and discriminates SUMO1 and SUMO2/3 through their C-terminal tails.Complementation of SAE2-depleted or inhibited cells with SAE2-K164Q restricts mitotic SUMO1-conjugates and increases multipolar spindle formation. We confirm the SUMO E1-dependent modification of the nuclear mitotic apparatus, NuMA, and find that the mitotic defects of both SAE2-K164Q complemented cells and HDAC6-inhibitor-treated cells are corrected by either over-expression of SUMO1 or by expression of a GFP-SUMO1-NuMA-K1766R fusion protein.Our observations suggest a model in which the SAE1:SAE2 enzyme is deacetylated on early mitosis to encourage the conjugation of SUMO1 to support mitotic fidelity. These surprising data reveal that the SUMO-activating enzyme can bias SUMO variant conjugation.
COVID-19 patients have increased levels of membrane-associated and soluble CD48
Authors: Pahima Hadas , Zaffran Ilan , Ben-Chetrit Eli , Jarjoui Amir , Gaur Pratibha , Manca Maria Laura , Reichmann Dana , Orenbuch-Harroch Efrat , Puxeddu Ilaria , Zinner Carl , Tzankov Alexandar , Levi-Schaffer Francesca 
Published: March 2022

AbstractCOVID-19 is a respiratory-centered systemic disorder caused by SARS-CoV-2. The disease can progress into a severe form causing acute lung injury.CD48 is a co-signaling receptor, existing as both membrane-bound and soluble forms reported to be dysregulated in several inflammatory conditions. Therefore, we reasoned that CD48 could be deregulated in COVID-19 as well.Here we analyzed CD48 expression in autoptic sections and peripheral blood leukocytes and sera of COVID-19 patients by gene expression profiling (HTG® autoimmune panel), immunohistochemistry, flow cytometry and ELISA.Lung tissue of COVID-19 patients showed increased CD48 mRNA expression and infiltration of CD48+ lymphocytes. In the peripheral blood, mCD48 was considerably increased on all evaluated cells, and additionally, sCD48 levels were significantly higher in COVID-19 patients independently of disease severity. Considering the alterations of mCD48 and sCD48, a specific role for CD48 in COVID-19 can be assumed, suggesting it as a potential target for therapy.
Hsp multichaperone complex buffers pathologically modified Tau
Authors: Moll Antonia , Ramirez Lisa Marie , Ninov Momchil , Schwarz Juliane , Urlaub Henning , Zweckstetter Markus 
Published: March 2022

AbstractAlzheimer’s disease is a neurodegenerative disorder in which misfolding and aggregation of pathologically modified Tau is critical for neuronal dysfunction and degeneration. The two central chaperones Hsp70 and Hsp90 coordinate protein homeostasis, but the nature of the interaction of Tau with the Hsp70/Hsp90 machinery has remained enigmatic. Here we show that Tau is a high-affinity substrate of the human Hsp70/Hsp90 machinery. Complex formation involves extensive intermolecular contacts, blocks Tau aggregation and depends on Tau’s aggregation-prone repeat region. The Hsp90 co-chaperone p23 directly binds Tau and stabilizes the multichaperone/substrate complex, whereas the E3 ubiquitin-protein ligase CHIP efficiently disassembles the machinery targeting Tau to proteasomal degradation. Because phosphorylated Tau binds the Hsp70/Hsp90 machinery but is not recognized by Hsp90 alone, the data establish the Hsp70/Hsp90 multichaperone complex as a critical regulator of Tau in neurodegenerative diseases.
Loop extrusion driven volume phase transition of entangled chromosomes
Authors: Yamamoto Tetsuya , Schiessel Helmut 
Published: March 2022

AbstractMitotic chromosomes without nucleosomes have been reconstituted in recent experiments. When topo II is depleted from the reconstituted chromosomes, these chromosomes are entangled and form ‘sparklers’, where DNA is condensed in the core with linker histone H1.8 and condensin is localized at the periphery. To understand the mechanism of the assembly of sparklers, we here take into account the loop extrusion by condensin in an extension of the theory of entangled polymer gels. The loop extrusion stiffens an entangled DNA network because DNA segments in the elastically effective chains are translocated to loops, which are elastically ineffective. Our theory predicts that the loop extrusion by condensin drives the volume phase transition that collapses a swollen entangled DNA gel as the stiffening of the network destabilizes the swollen phase. This is an important element to understand the mechanism of the assembly of the reconstituted chromosomes.
Per-Pathogen Virulence of HIV-1 subtypes A, C and D
Authors: Bouman Judith A , Venner Colin M , Walker Courtney , Arts Eric J , Regoes Roland R 
Published: March 2022

AbstractHIV-1 subtypes differ, among other things, in their clinical manifestations and the speed in which they spread. In particular, the frequency of subtype C is increasing relative to subtype A and D. We aim to investigate whether HIV-1 subtype A, C and D differ in their per-pathogen virulence and to what extend this can explain the difference in spread between these subtypes.We use data from the Hormonal Contraception and HIV-1 Genital Shedding and Disease Progression among Women with Primary HIV Infection (GS) Study. For each study participant, we determine the set-point viral load value, CD4+ T cell level after primary infection and CD4+ T cell decline. Based on both the CD4+ T cell count after primary infection and CD4+ T cell decline, we estimate the time until AIDS for each individual. We then obtain our newly introduced measure of virulence as the inverse of the estimated time until AIDS. This new measure of virulence has an improved correlation with the set-point viral load compared to the decline of CD4+ T cells alone. After fitting a model to the measured virulence and set-point viral load values, we tested if this relation varies per subtype. We found that subtype C has a significantly higher per-pathogen virulence than subtype A. Based on an evolutionary model, we then hypothesize that differences in the primary length of infection period cause the observed variation in the speed of spread of the subtypes.Author summaryHIV-1 subtype C is currently spreading relatively fast in various parts of the world. Data from a study that followed many women infected with different HIV-1 subtypes (A, C and D) before they started treatment shows that neither their viral load nor the disease duration are increased for subtype C compared to subtype A and D. Thus, it seems that subtype C does not have a transmission advantage, neither per contact nor due to longer infection, making the observed relative rise in subtype C a puzzle. We used the same data to test if subtype C has optimized its potential to spread by decreasing the disease duration per unit of viral load (per-pathogen virulence) compared to subtype A and D. However, we find that subtype C has a significantly higher per-pathogen virulence than subtype A and D. This result makes the rise of subtype C even more counter-intuitive.In a last step, we develop an evolutionary model, in which we synthesize all our empirical results. With this model we can show that the most likely explanation for the global spread of subtype C is a difference in the duration of primary infection between the subtypes.
The RNA-binding protein EIF4A3 promotes axon development by direct control of the cytoskeleton
Authors: Alsina Fernando C. , Lupan Bianca M. , Lin Lydia J. , Musso Camila M. , Mosti Federica , Newman Carly R. , Wood Lisa M. , Agostino Mark , Moore Jeffrey K. , Silver Debra L. 
Published: March 2022

SummaryThe exon junction complex (EJC), nucleated by EIF4A3, is indispensable for mRNA fate and function throughout eukaryotes. Unexpectedly, we discover that EIF4A3 directly controls microtubules independent of RNA, and this is critical for neural wiring. While neuronal survival in the developing mouse cerebral cortex depends upon an intact EJC, axonal tract formation requires only Eif4a3. Using human cortical organoids, we demonstrate that EIF4A3 disease mutations also impair neuronal maturation, highlighting conserved functions relevant for neurodevelopmental pathology. Employing biochemistry and molecular modeling we discover that EIF4A3 directly binds to microtubules, mutually exclusive of the RNA-binding complex. In growing neurons, EIF4A3 is essential for microtubule dynamics, and sufficient to promote microtubule polymerization and stability in vitro. Together, our data show that tubulin-bound EIF4A3 orchestrates microtubule dynamics, underlying key events of neuronal development. This reveals a new mechanism by which neurons re-utilize core gene expression machinery to rapidly and directly control the cytoskeleton.HighlightsThe Exon Junction Complex controls neuronal survival but only EIF4A3 directs axonal growthEIF4A3 controls axonal tract formation in vivo.Human EIF4A3 deficient iPSC-derived cortical organoids recapitulate neuronal defects.EIF4A3 directly binds to microtubules to control their growth and stability in neurons.
Technology applications in bovine gait analysis: a scoping review
Authors: Nejati Amir , Bradtmueller Anna , Shepley Elise , Vasseur Elsa 
Published: March 2022

AbstractQuantitative bovine gait analysis using technology has evolved significantly over the last two decades. However, subjective methods of gait assessment using visual locomotion scoring remain the primary on-farm and experimental approach. The objective of this review is to map research trends in quantitative bovine gait analysis and to explore the technologies that have been utilized to measure biomechanical parameters of gait. A scoping literature review was conducted according to PRISMA guidelines. A search algorithm based on PICO framework generated three components – bovine, gait, and technology – to address our objectives. Three online databases were searched for original work published from January 2000 to June 2020. A two-step screening process was then conducted, starting with the review of article titles and abstracts based on inclusion criteria. A remaining 125 articles then underwent a full-text assessment, resulting in 82 final articles. Thematic analysis of research aims resulted in four major themes among the studies: gait/claw biomechanics, lameness detection, intervention/comparison, and system development. Lameness detection (55 % of studies) was the most common reason for technology use. Studies in the field of bovine gait analysis used three main technologies: force and pressure platforms (FPP), vision-based systems (VB), and accelerometers. FPP were the first and most popular technologies to evaluate bovine gait and were used in 58.5 % of studies. They include force platforms, pressure mapping systems, and weight distribution platforms. The second most applied technology was VB (34.1 % of studies), which predominately consists of video analysis and image processing systems. Accelerometers, another technological method to measure gait characteristics, were used in 14.6 % of studies. A strong demand for automatic lameness detection influences the path of development for quantitative gait analysis technologies. Although progress has been made, more research is needed to achieve more accurate, practical, and user-friendly technologies.
Synapses and Ca2+activity in oligodendrocyte precursor cells can predict where myelin sheaths form
Authors: Li Jiaxing , Miramontes Tania , Czopka Tim , Monk Kelly R. 
Published: March 2022

SUMMARYIn the nervous system, only one type of neuron-glial synapse is known to exist: that between neurons and oligodendrocyte precursor cells (OPCs). Neuron-OPC synapses are thought to bridge neuronal activity to OPCs. However, their composition, assembly, downstream signaling, andin vivofunctions remain largely unclear. Here, we use zebrafish to address these questions and identify postsynaptic molecules PSD-95 and Gephyrin in OPCs. They increase during early development and decrease upon OPC differentiation. PSD-95 and Gephyrin in OPCs are highly dynamic and frequently assemble at “hotspots.” Gephyrin hotspots and synapse-associated Ca2+activity in OPCs predict where a subset of myelin sheaths form in oligodendrocytes. Further analyses reveal that spontaneous synaptic release is integral to OPC Ca2+activity, while evoked synaptic release contributes only in early development. Finally, disruption of the synaptic genesdlg4a&b,gephyrinb, andnlgn3bimpairs OPC differentiation and myelination. Together, we propose that neuron-OPC synapses are dynamically assembled and can predetermine myelination patterns through Ca2+signaling.