bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of cell membrane tension on the lifetime and size of mature clathrin-coated pits and their spatial distribution
Authors: Liu Xinyue , Xi Wang , Gong Xiaobo 
Published: March 2023

ABSTRACTClathrin-mediated endocytosis is the most characterized pathway for cells to internalize diverse receptor-bound cargo, such as proteins, nanoparticles, and viruses. However, the effect of membrane tension on clathrin-coated pit (CCP) maturation remains inadequately characterized. This study aimed to determine the effect of membrane tension on CCP maturation both spatially and temporarily, which remains a controversial and elusive issue. We obtained the sizes and spatial distributions of CCPs by the structured illumination microscopy of fixed cells and observed CCP lifetimes in live cells by total internal reflection fluorescence microscopy. The processes of CCP maturation and abortion were reproduced numerically through Monte Carlo simulation. The results showed that the growth time of CCP was more reasonably proportional to its volume rather than its surface area. We further investigated the spatial distribution of the membrane tension and size of CCPs, finding a significant positive correlation between the membrane tension and the size of mature CCPs spatially. This indicates that the CCPs tend to enrich in the highest-tension region, especially the mature ones. These results agreed with our numerical prediction that the CCP structure grew larger to overcome a higher energy barrier caused by higher background cell membrane tension. Our findings enhance the understanding of CCP maturation dynamics and underscore the importance of membrane tension in regulating CCP development.
Efficient differential expression analysis of large-scale single cell transcriptomics data using dreamlet
Authors: Hoffman Gabriel E. , Lee Donghoon , Bendl Jaroslav , Prashant N.M. , Hong Aram , Casey Clara , Alvia Marcela , Shao Zhiping , Argyriou Stathis , Therrien Karen , Venkatesh Sanan , Voloudakis Georgios , Haroutunian Vahram , Fullard John F. , Roussos Panos 
Published: March 2023

AbstractAdvances in single-cell and -nucleus transcriptomics have enabled generation of increasingly large-scale datasets from hundreds of subjects and millions of cells. These studies promise to give unprecedented insight into the cell type specific biology of human disease. Yet performing differential expression analyses across subjects remains difficult due to challenges in statistical modeling of these complex studies and scaling analyses to large datasets. Our open-source R package dreamlet (DiseaseNeurogenomics.github.io/dreamlet) uses a pseudobulk approach based on precision-weighted linear mixed models to identify genes differentially expressed with traits across subjects for each cell cluster. Designed for data from large cohorts, dreamlet is substantially faster and uses less memory than existing workflows, while supporting complex statistical models and controlling the false positive rate. We demonstrate computational and statistical performance on published datasets, and a novel dataset of 1.4M single nuclei from postmortem brains of 150 Alzheimer’s disease cases and 149 controls.
The vasodilator-stimulated phosphoprotein (VASP) supports the conduction of vasodilator signals and NO-induced arteriolar dilations in murine arteriolesin vivo
Authors: Poley Philip , Benz Peter M. , de Wit Cor 
Published: March 2023

AbstractVASP is a member of the Enabled/VASP protein family that is involved in cortical actin dynamics and may also contribute to the formation of gap junctions. In vessels, gap junctional coupling allows the transfer of signals along the vessel wall and coordinates vascular behavior. Moreover, VASP is reportedly a mediator of NO-induced inhibition of platelet aggregation. Therefore, we hypothesized that VASP exerts also important physiologic functions in arterioles. We examined the spread of vasodilations enabled by gap junctional coupling in endothelial cells as well as NO-induced arteriolar dilations in VASP-deficient mice by intravital microscopy of the microcirculation in a skeletal muscle in anesthetized mice. Conducted dilations were initiated by brief, locally confined stimulation of the arterioles with acetylcholine. The maximal diameters of the arterioles under study ranged from 30 to 40 μm. Brief stimulation with acetylcholine induced a short dilation at the local site that was also observed at remote, upstream sites without an attenuation of the amplitude up to a distance of 1.2 mm in control animals (wild-type). In contrast, remote dilations were reduced in VASP-deficient mice despite a similar local dilation indicating an impairment of conducted dilations. Superfusion of NOdonors induced a concentration-dependent dilation in wild-type mice. However, these dilations were slightly reduced in VASP-deficient animals. In contrast, dilations induced by the endothelial stimulator acetylcholine were fully preserved in VASP-deficient mice. In summary, this study suggests that VASP exerts critical functions in arteriolar diameter control. It is crucial for the conduction of dilator signals along the endothelial cell layer. The impairment possibly reflects a perturbed formation of gap junctions in the endothelial cell membrane. VASP also participates in the full dilatory potential of NOdonors although the effect of its deficiency is only subtle. In contrast, VASP is not required for dilations initiated by endothelial stimulation which are mediated in the murine microcirculation by an EDH-mechanism.
Detecting Material State Changes in the Nucleolus by Label-free Digital Holographic Microscopy
Authors: Zorbas Christiane , Soenmez Aynur , Léger Jean , De Vleeschouwer Christophe , Lafontaine Denis L.J. 
Published: March 2023

ABSTRACTRibosome biogenesis is initiated in the nucleolus, a multiphase biomolecular condensate formed by liquid-liquid phase separation. The nucleolus is a powerful disease biomarker and stress biosensor whose morphology reflects its function. Here we have used digital holographic microscopy (DHM), a label-free quantitative phase contrast microscopy technique, to detect nucleoli in adherent and suspension cells. Subtle nucleolar alterations induced by drug treatment or by depletion of ribosomal proteins were efficiently detected by DHM. We trained convolutional neural networks to detect and quantify nucleoli automatically on DHM images of cultured human cells (HeLa). Holograms containing cell optical thickness information allowed us to define a novel nucleolar index which we used to distinguish nucleoli whose material state had been optogenetically modulated. We conclude that DHM is a powerful tool for quantitatively characterizing nucleoli, including material state, without any staining.
Rigid Scaffolds are Promising for Designing Macrocyclic Kinase Inhibitors
Authors: Zhao Zheng , Bourne Philip E. 
Published: March 2023

AbstractMacrocyclic kinase inhibitors (MKIs) are gaining attention due to their favorable selectivity and potential to overcome drug resistance, yet they remain challenging to design because of their novel structures. To facilitate the design and discovery of MKIs, we investigate MKI rational design starting from initial acyclic compounds by performing microsecond-scale atomistic simulations for multiple MKIs, constructing an MKI database, and analyzing MKIs using hierarchical cluster analysis. Our studies demonstrate that the binding modes of MKIs are like that of their corresponding acyclic counterparts against the same kinase targets. Importantly, within the respective binding sites, the MKI scaffolds retain the same conformations as their corresponding acyclic counterparts, demonstrating the rigidity of scaffolds before and after molecular cyclization. The MKI database includes 641 nanomole-level MKIs from 56 human kinases elucidating the features of rigid scaffolds, and the tendency of core structures among MKIs. Collectively these results and resources can facilitate MKI development.
Does nonlinear blood-brain barrier transport matter for morphine dosing strategies?
Authors: Gülave Berfin , Budda Divakar , Saleh Mohammed AA , van Hasselt JG Coen , de Lange Elizabeth CM 
Published: March 2023

AbstractMorphine blood-brain barrier (BBB) transport is governed by passive diffusion, active efflux and saturable active influx. These processes may be associated with nonlinear concentration-dependencies which impact plasma and brain extracellular fluid (brainECF) pharmacokinetics of morphine. In this study, we aim to evaluate the impact of nonlinear BBB transport on brainECFpharmacokinetics of morphine and its metabolites for different dosing strategies using a physiologically based pharmacokinetic simulation study. We extended the human physiologically based pharmacokinetic, LeiCNS-PK3.0, model with equations for nonlinear BBB transport of morphine. Simulations for brainECFpharmacokinetics were performed for various dosing strategies: intravenous (IV), oral immediate (IR) and extended release (ER) with dose range of 0.25-150mg and dosing frequencies of 1-6 times daily. The impact of nonlinear BBB transport on morphine CNS pharmacokinetics was evaluated by quantifying (i) the relative brainECFto plasma exposure (AUCu,brainECF/AUCu,Plasma) and (ii) the impact on the peak-to-trough ratio (PTR) of concentration-time profiles in brainECFand plasma. We found that the relative morphine exposure and PTRs are dose dependent for the evaluated dose range. The highest relative morphine exposure value of 1.4 was found for once daily 0.25mg ER and lowest of 0.1 for 6-daily 150mg IV dosing. At lower doses the PTRs were smaller and increased with increasing dose and stabilized at higher doses independent of dosing frequency. Relative peak concentrations of morphine in relation to its metabolites changed with increasing dose. We conclude that nonlinearity of morphine BBB transport affect the relative brainECFexposure and the fluctuation of morphine and its metabolites.HighlightsNonlinear transport affects relative morphine exposure in brainECF.Nonlinear transport affects PK fluctuations of morphine in brainECF.Nonlinear transport affects brainECFPK relationship of morphine and its metabolites.Graphical abstract
Sculpting DNA-based synthetic cells through phase separation and phase-targeted activity
Authors: Malouf Layla , Tanase Diana A. , Fabrini Giacomo , Paez-Perez Miguel , Leathers Adrian , Booth Michael J. , Di Michele Lorenzo 
Published: March 2023

AbstractSynthetic cells, like their biological counterparts, require internal compartments with distinct chemical and physical properties where different functionalities can be localised. Inspired by membrane-less compartmentalisation in biological cells, here we demonstrate how micro-phase separation can be used to engineer heterogeneous cell-like architectures with programmable morphology and compartment-targeted activity. The synthetic cells selfassemble from amphiphilic DNA nanostructures, producing core-shell condensates due to size-induced de-mixing. Lipid deposition and phase-selective etching are then used to generate a porous pseudo-membrane, a cytoplasm analogue, and membrane-less organelles. The synthetic cells can sustain RNA synthesisvia in vitrotranscription, leading to cytoplasm and pseudo-membrane expansion caused by an accumulation of the transcript. Our approach exemplifies how architectural and functional complexity can emerge from a limited number of distinct building blocks, if molecular-scale programmability, emergent biophysical phenomena, and biochemical activity are coupled to mimic those observed in live cells.
Spatial-temporal expression analysis of lineage-restricted shell matrix proteins reveals shell field regionalization and distinct cell populations in the slipper snailCrepidula atrasolea
Authors: Lopez-Anido Rebecca N. , Batzel Grant O. , Ramirez Gabriela , Goodheart Jessica A. , Wang Yiqun , Neal Stephanie , Lyons Deirdre C. 
Published: March 2023

AbstractMolluscs are one of the most morphologically diverse clades of metazoans, exhibiting an immense diversification of calcium carbonate structures, such as the shell. Biomineralization of the calcified shell is dependent on shell matrix proteins (SMPs). While SMP diversity is hypothesized to drive molluscan shell diversity, we are just starting to unravel SMP evolutionary history and biology. Here we leveraged two complementary model mollusc systems,Crepidula fornicataandCrepidula atrasolea, to determine the lineage-specificity of 185CrepidulaSMPs. We found that 95% of the adultC. fornicatashell proteome belongs to conserved metazoan and molluscan orthogroups, with molluscan-restricted orthogroups containing half of all SMPs in the shell proteome. The low number ofC. fornicata-restricted SMPs contradicts the generally-held notion that an animal’s biomineralization toolkit is dominated by mostly novel genes. Next, we selected a subset of lineage-restricted SMPs for spatial-temporal analysis usingin situhybridization chain reaction (HCR) during larval stages inC. atrasolea. We found that 12 out of 18 SMPs analyzed are expressed in the shell field. Notably, these genes are present in 5 expression patterns, which define at least three distinct cell populations within the shell field. These results represent the most comprehensive analysis of gastropod SMP evolutionary age and shell field expression patterns to date. Collectively, these data lay the foundation for future work to interrogate the molecular mechanisms and cell fate decisions underlying molluscan mantle specification and diversification.
LIFR recruits HGF-producing neutrophils to promote liver injury repair and regeneration
Authors: Deng Yalan , Zhao Zilong , Sheldon Marisela , Zhao Yang , Teng Hongqi , Martinez Consuelo , Zhang Jie , Lin Chunru , Sun Yutong , Yao Fan , Zhu Hao , Ma Li 
Published: March 2023

AbstractThe molecular links between tissue repair and tumorigenesis remain elusive. Here, we report that loss of the liver tumor suppressorLifrin mouse hepatocytes impairs the recruitment and activity of reparative neutrophils, resulting in the inhibition of liver regeneration after partial hepatectomy or toxic injuries. On the other hand, overexpression of LIFR promotes liver repair and regeneration after injury. Interestingly, LIFR deficiency or overexpression does not affect hepatocyte proliferationex vivoorin vitro. In response to physical or chemical damage to the liver, LIFR from hepatocytes promotes the secretion of the neutrophil chemoattractant CXCL1 (which binds CXCR2 to recruit neutrophils) and cholesterol in a STAT3-dependent manner. Cholesterol, in turn, acts on the recruited neutrophils to secrete hepatocyte growth factor (HGF) to accelerate hepatocyte proliferation and regeneration. Altogether, our findings reveal a LIFR-STAT3- CXCL1-CXCR2 axis and a LIFR-STAT3-cholesterol-HGF axis that mediate hepatic damage- induced crosstalk between hepatocytes and neutrophils to repair and regenerate the liver.
FBXO38 does not control PD-1 stability
Authors: Dibus Nikol , Salyova Eva , Kolarova Karolina , Pagano Michele , Stepanek Ondrej , Cermak Lukas 
Published: March 2023

AbstractSKP1-CUL1-F-box protein (SCF) ubiquitin ligases are versatile protein complexes that mediate the ubiquitination of substrates, which are recognized by their F-box-domain- containing subunits1. One of these substrate receptors is FBXO38. Its gene has been found to be mutated in several families with early-onset distal hereditary motor neuronopathy2. SCFFBXO38ubiquitin ligase controls the stability of ZXDB, a nuclear factor associated with the centromeric chromatin protein CENP-B3. Moreover, the loss of FBXO38 results in growth retardation and defect in spermatogenesis characterized by deregulation of the Sertoli cell transcription program and centromere integrity4. A report by Meng et al. proposed that SCFFBXO38regulates the protein levels of the PD-1 inhibitory receptor (also known as CD279, PDCD1) in T cells5. Here, we have re-addressed the conclusions by Meng et al. usingFbxo38KO/KOmice and cell systems. We have found no evidence indicating that FBXO38 controls the abundance and stability of PD-1.
Organization and replicon interactions within the highly segmented genome ofBorrelia burgdorferi
Authors: Ren Zhongqing , Takacs Constantin N. , Brandão Hugo B. , Jacobs-Wagner Christine , Wang Xindan 
Published: March 2023

AbstractBorrelia burgdorferi, a causative agent of Lyme disease, contains the most segmented bacterial genome known to date, with one linear chromosome and over twenty plasmids. How this unusually complex genome is organized, and whether and how the different replicons interact are unclear. We recently demonstrated thatB. burgdorferiis polyploid and that the copies of the chromosome and plasmids are regularly spaced in each cell, which is critical for faithful segregation of the genome to daughter cells. Regular spacing of the chromosome is controlled by two separate partitioning systems that involve the protein pairs ParA/ParZ and ParB/SMC. Here, using chromosome conformation capture (Hi-C), we characterized the organization of theB. burgdorferigenome and the interactions between the replicons. We uncovered that although the linear chromosome lacks contacts between the two replication arms, the two telomeres are in frequent contact. Moreover, several plasmids specifically interact with the chromosomeoriCregion, and a subset of plasmids interact with each other more than with others. We found that SMC and the SMC-like MksB protein mediate long-range interactions on the chromosome, but they minimally affect plasmid-chromosome or plasmid-plasmid interactions. Finally, we found that disruption of the two partition systems leads to chromosome restructuring, correlating with the mis-positioning of chromosomeoriC. Altogether, this study revealed the conformation of a complex genome and analyzed the contribution of the partition systems and SMC family proteins to this organization. This work expands the understanding of the organization and maintenance of multipartite bacterial genomes.
Sustained activation in basal ganglia and cerebellum after repetitive movement in a non-task-specific dystonia
Authors: Kuster John K , Levenstein Jacob M. , Waugh Jeff , Multhaupt-Buell Trisha J. , Lee Myung Joo , Kim Byoung Woo , Pagnacco Guido , Makhlouf Miriam L. , Sudarsky Lewis R. , Breiter Hans C. , Sharma Nutan , Blood Anne J. 
Published: March 2023

AbstractWe previously observed sustained fMRI BOLD signal in the basal ganglia in focal hand dystonia patients after a repetitive finger tapping task. Since this was observed in a task-specific dystonia, for which excessive task repetition may play a role in pathogenesis, in the current study we asked if this effect would be observed in a focal dystonia (cervical dystonia [CD]) that is not considered task-specific or thought to result from overuse. We evaluated fMRI BOLD signal time courses before, during, and after the finger tapping task in CD patients. We observed patient/control differences in post-tapping BOLD signal in left putamen and left cerebellum during the non-dominant (left) hand tapping condition, reflecting abnormally sustained BOLD signal in CD. BOLD signals in left putamen and cerebellum were also abnormally elevated in CD during tapping itself and escalated as tapping was repeated. There were no cerebellar differences in the previously studied FHD cohort, either during or after tapping. We conclude that some elements of pathogenesis and/or pathophysiology associated with motor task execution/repetition may not be limited to task-specific dystonias, but there may be regional differences in these effects across dystonias, associated with different types of motor control programs.
A beneficial adaptive role for CHOP in driving cell fate selection during ER stress
Authors: Liu Kaihua , Zhao Chaoxian , Adajar Reed C. , DeZwaan-McCabe Diane , Rutkowski D. Thomas 
Published: March 2023

ABSTRACTCellular stresses elicit signaling cascades that are capable of either mitigating the inciting dysfunction or initiating cell death. During endoplasmic reticulum (ER) stress, the transcription factor CHOP is widely recognized to promote cell death. However, it is not clear whether CHOP also has a beneficial role during adaptation. Here, we have combined a new, versatile, genetically modifiedChopallele with single cell analysis and with stresses of physiological intensity, to rigorously examine the contribution of CHOP to cell fate. Paradoxically, we found that CHOP promoted death in some cells, but proliferation—and hence recovery—in others. Strikingly, this function of CHOP conferred to cells a stress-specific competitive growth advantage. The dynamics of CHOP expression and UPR activation at the single cell level suggested that CHOP maximizes UPR activation, which in turn favors stress resolution, subsequent UPR deactivation, and proliferation. Taken together, these findings suggest that CHOP’s function can be better described as a “stress test” that drives cells into either of two mutually exclusive fates—adaptation or death—during stresses of physiological intensity.
Non-additive effects of schizophrenia risk genes reflect convergent downstream function
Authors: Deans PJ Michael , Seah Carina , Johnson Jessica , Gonzalez Judit Garcia , Townsley Kayla , Cao Evan , Schrode Nadine , Stahl Eli , O’Reilly Paul , Huckins Laura M. , Brennand Kristen J. 
Published: March 2023

ABSTRACTGenetic studies of schizophrenia (SCZ) reveal a complex polygenic risk architecture comprised of hundreds of risk variants, the majority of which are common in the population at-large and confer only modest increases in disorder risk. Precisely how genetic variants with individually small predicted effects on gene expression combine to yield substantial clinical impacts in aggregate is unclear. Towards this, we previously reported that the combinatorial perturbation of four SCZ risk genes (“eGenes”, whose expression is regulated by common variants) resulted in gene expression changes that were not predicted by individual perturbations, being most non-additive among genes associated with synaptic function and SCZ risk. Now, across fifteen SCZ eGenes, we demonstrate that non-additive effects are greatest within groups of functionally similar eGenes. Individual eGene perturbations reveal common downstream transcriptomic effects (“convergence”), while combinatorial eGene perturbations result in changes that are smaller than predicted by summing individual eGene effects (“sub-additive effects”). Unexpectedly, these convergent and sub-additive downstream transcriptomic effects overlap and constitute a large proportion of the genome-wide polygenic risk score, suggesting that functional redundancy of eGenes may be a major mechanism underlying non-additivity. Single eGene perturbations likewise fail to predict the magnitude or directionality of cellular phenotypes resulting from combinatorial perturbations. Overall, our results indicate that polygenic risk cannot be extrapolated from experiments testing one risk gene at a time and must instead be empirically measured. By unravelling the interactions between complex risk variants, it may be possible to improve the clinical utility of polygenic risk scores through more powerful prediction of symptom onset, clinical trajectory, and treatment response, or to identify novel targets for therapeutic intervention.