bluuebunny/crossref_metadata_2025_split huggingface dataset:
Presynaptic Mitochondrial Volume and Density Scale with Presynaptic Power Demand
Authors: Justs Karlis A. , Lu Zhongmin , Chouhan Amit K. , Borycz Jolanta A. , Lu Zhiyuan , Meinertzhagen Ian A. , Macleod Gregory T. 
Published: June 2021

AbstractStable neural function requires an energy supply that can meet the intense episodic power demands of neuronal activity. The bioenergetic machinery of glycolysis and oxidative phosphorylation is highly responsive to such demands, but it must occupy a minimum volume if it is to accommodate these demands. We examined the trade-off between presynaptic power demands and the volume available to the bioenergetic machinery. We quantified the energy demands of sixDrosophilamotor nerve terminals through direct measurements of neurotransmitter release and Ca2+entry, and via theoretical estimates of Na+entry and power demands at rest. Electron microscopy revealed that terminals with the highest power demands contained the greatest volume of mitochondria, indicating that mitochondria are allocated according to presynaptic power demands. In addition, terminals with the greatest power demand-to-volume ratio (∼66 nmol·min-1·μL-1) harbor the largest mitochondria packed at the greatest density. If we assume sequential and complete oxidation of glucose by glycolysis and oxidative phosphorylation, then these mitochondria are required to produce ATP at a rate of 52 nmol·min-1·μL-1at rest, rising to 963 during activity. Glycolysis would contribute ATP at 0.24 nmol·min-1·μL-1of cytosol at rest, rising to 4.36. These data provide a quantitative framework for presynaptic bioenergeticsin situ, and reveal that, beyond an immediate capacity to accelerate ATP output from glycolysis and oxidative phosphorylation, over longer time periods presynaptic terminals optimize mitochondrial volume and density to meet power demand.Significance StatementThe remarkable energy demands of the brain are supported by the complete oxidation of its fuel but debate continues regarding a division of labor between glycolysis and oxidative phosphorylation across different cell types. Here we leverage the neuromuscular synapse, a model for studying neurophysiology, to elucidate fundamental aspects of neuronal energy metabolism that ultimately constrain rates of neural processing. We quantified energy production rates required to sustain activity at individual nerve terminals and compared these data with the volume capable of oxidative phosphorylation (mitochondria) and glycolysis (cytosol). We find strong support for oxidative phosphorylation playing a primary role in presynaptic terminals and provide the firstin vivoestimates of energy production rates per unit volume of presynaptic mitochondria and cytosol.
Dynamic interplay between reward and voluntary attention determines stimulus processing in visual cortex
Authors: Grahek Ivan , Schettino Antonio , Koster Ernst H.W. , Andersen Søren K. 
Published: June 2021

AbstractReward enhances stimulus processing in the visual cortex, but the mechanisms through which this effect occurs remain unclear. Reward prospect can both increase the deployment of voluntary attention and increase the salience of previously neutral stimuli. In this study we orthogonally manipulated reward and voluntary attention while human participants performed a global motion detection task. We recorded steady-state visual evoked potentials (SSVEPs) to simultaneously measure the processing of attended and unattended stimuli linked to different reward probabilities, as they compete for attentional resources. The processing of the high rewarded feature was enhanced independently of voluntary attention, but this gain diminished once rewards were no longer available. Neither the voluntary attention nor the salience account alone can fully explain these results. Instead, we propose how these two accounts can be integrated to allow for the flexible balance between reward-driven increase in salience and voluntary attention.
Task-Dependent Warping of Semantic Representations During Search for Visual Action Categories
Authors: Shahdloo Mo , Çelik Emin , Ürgen Burcu A. , Gallant Jack L. , Çukur Tolga 
Published: June 2021

SummaryObject and action perception in cluttered dynamic natural scenes relies on efficient allocation of limited brain resources to prioritize the attended targets over distractors. It has been suggested that during visual search for objects, distributed semantic representation of hundreds of object categories is warped to expand the representation of targets. Yet, little is known about whether and where in the brain visual search for action categories modulates semantic representations. To address this fundamental question, we studied human brain activity recorded via functional magnetic resonance imaging while subjects viewed natural movies and searched for either communication or locomotion actions. We find that attention directed to action categories elicits tuning shifts that warp semantic representations broadly across neocortex, and that these shifts interact with intrinsic selectivity of cortical voxels for target actions. These results suggest that attention serves to facilitate task performance during social interactions by dynamically shifting semantic selectivity towards target actions, and that tuning shifts are a general feature of conceptual representations in the brain.
PLEKHA5, PLEKHA6 and PLEKHA7 bind to PDZD11 to target the Menkes ATPase ATP7A to the cell periphery and regulate copper homeostasis
Authors: Sluysmans Sophie , Méan Isabelle , Xiao Tong , Boukhatemi Amina , Ferreira Flavio , Jond Lionel , Chang Christopher J. , Citi Sandra 
Published: June 2021

AbstractCopper homeostasis is crucial for cellular physiology and development, and its dysregulation leads to disease. The Menkes ATPase ATP7A plays a key role in copper efflux, by trafficking from the Golgi to the plasma membrane upon cell exposure to elevated copper, but the mechanisms that target ATP7A to the cell periphery are poorly understood. PDZD11 interacts with the C-terminus of ATP7A, which contains sequences involved in ATP7A trafficking, but the role of PDZD11 in ATP7A localization is unknown. Here we identify PLEKHA5 and PLEKHA6 as new interactors of PDZD11, which similarly to the junctional protein PLEKHA7 bind to PDZD11 N-terminus through their WW domains. Using CRISPR-KO kidney epithelial cells, we show by immunofluorescence that WW-PLEKHAs (PLEKHA5, PLEKHA6, PLEKHA7) recruit PDZD11 to distinct plasma membrane localizations, and that they are required for the efficient anterograde targeting of ATP7A to the cell periphery in elevated copper. Pulldown experiments show that WW-PLEKHAs promote PDZD11 interaction with the C-terminus of ATP7A. However, WW-PLEKHAs and PDZD11 are not necessary for ATP7A Golgi localization in basal copper, ATP7A copper-induced exit from the Golgi, and ATP7A retrograde trafficking to the Golgi. Finally, measuring bioavailable copper with the labile copper probe CF4 shows that WW-PLEKHAs and PDZD11 are required to maintain low intracellular copper levels when cells are exposed to elevated copper. These data indicate that WW-PLEKHAs-PDZD11 complexes regulate the localization and function of ATP7A to modulate cellular copper homeostasis.
TMEM120A contains a specific coenzyme A-binding site and might not mediate poking- or stretch-induced channel activities in cells
Authors: Rong Yao , Jiang Jinghui , Gao Yiwei , Guo Jianli , Song Danfeng , Liu Wenhao , Zhao Yan , Xiao Bailong , Liu Zhenfeng 
Published: June 2021

AbstractTMEM120A, a member of the Transmembrane protein 120 (TMEM120) family, has pivotal function in adipocyte differentiation and metabolism, and may also contribute to sensing mechanical pain by functioning as an ion channel named TACAN. Here we report that expression of TMEM120A is not sufficient in mediating poking- or stretch-induced currents in cells, and have solved cryo-EM structures of human TMEM120A (HsTMEM120A) in complex with an endogenous metabolic cofactor (coenzyme A, CoASH) and in the apo form. HsTMEM120A forms a symmetrical homodimer with each monomer containing an amino-terminal coiled-coil motif followed by a transmembrane domain with six membrane-spanning helices. Within the transmembrane domain, a CoASH molecule is hosted in a deep cavity and forms specific interactions with nearby amino acid residues. Mutation of a central tryptophan residue involved in binding CoASH dramatically reduced the binding affinity of HsTMEM120A with CoASH. HsTMEM120A exhibits distinct conformations at the states with or without CoASH bound. Our results suggest that TMEM120A may have alternative functional roles potentially involved in CoASH transport, sensing or metabolism.
Interpreting ciliopathy-associated missense variants of uncertain significance (VUS) in an animal model
Authors: Lange Karen I. , Best Sunayna , Tsiropoulou Sofia , Berry Ian , Johnson Colin A. , Blacque Oliver E. 
Published: June 2021

ABSTRACTPurposeBetter methods are required to interpret the pathogenicity of disease-associated variants of uncertain significance (VUS), which cannot be actioned clinically. In this study, we explore the use of a tractable animal model (Caenorhabditis elegans) for in vivo interpretation of missense VUS alleles of TMEM67, a cilia gene associated with ciliopathies.MethodsCRISPR/Cas9 gene editing was used to generate homozygous knock-in C. elegans worm strains carrying TMEM67 patient variants engineered into the orthologous gene (mks-3). Quantitative phenotypic assays of sensory cilia structure and function measured if the variants affect mks-3 gene function. Results from worms were validated by a genetic complementation assay in a human TMEM67 knock-out hTERT-RPE1 cell line that tests a TMEM67 signaling function.ResultsAssays in C. elegans accurately distinguished between known benign (Asp359Glu, Thr360Ala) and known pathogenic (Glu361Ter, Gln376Pro) variants. Analysis of eight missense VUS generated evidence that three are benign (Cys173Arg, Thr176Ile, Gly979Arg) and five are pathogenic (Cys170Tyr, His782Arg, Gly786Glu, His790Arg, Ser961Tyr).ConclusionEfficient genome editing and quantitative functional assays in C. elegans make it a tractable in vivo animal model that allows rapid, cost-effective interpretation of ciliopathy-associated missense VUS alleles.
Zebrafish pigment cells develop directly from persistent highly multipotent progenitors
Authors: Nikaido Masataka , Subkhankulova Tatiana , Uroshlev Leonid A. , Kasianov Artem J. , Sosa Karen Camargo , Bavister Gemma , Yang Xueyan , Rodrigues Frederico S. L. M. , Carney Thomas J. , Schwetlick Hartmut , Dawes Jonathan H.P. , Rocco Andrea , Makeev Vsevelod , Kelsh Robert N. 
Published: June 2021

AbstractNeural crest cells (NCCs) are highly multipotent stem cells. A long-standing controversy exists over the mechanism of NCC fate specification, specifically regarding the presence and potency of intermediate progenitors. The direct fate restriction (DFR) model, based on early in vivo clonal studies, hypothesised that intermediates are absent and that migrating cells maintain full multipotency1–6. However, most authors favour progressive fate restriction (PFR) models, with fully multipotent early NCCs (ENCCs) transitioning to partially-restricted intermediates before committing to individual fates7–12. Here, single cell transcriptional profiling of zebrafish pigment cell development leads to us proposing a Cyclical Fate Restriction mechanism of NCC development that reconciles the DFR and PFR models. Our clustering of single NCC Nanostring transcriptional profiles identifies only broadly multipotent intermediate states between ENCCs and differentiated melanocytes and iridophores. Leukocyte tyrosine kinase (Ltk) marks the multipotent progenitor and iridophores, consistent with biphasic ltk expression13–15. Ltk inhibitor and constitutive activation studies support expression at an early multipotent stage, whilst lineage-tracing of ltk-expressing cells reveals their multipotency extends beyond pigment cell-types to neural fates. We conclude that pigment cell development does not involve a conventional PFR mechanism, but instead occurs directly and more dynamically from a broadly multipotent intermediate state.
splatPop: simulating population scale single-cell RNA sequencing data
Authors: Azodi Christina B. , Zappia Luke , Oshlack Alicia , McCarthy Davis J. 
Published: June 2021

AbstractWith improving technology and decreasing costs, single-cell RNA sequencing (scRNA-seq) at the population scale has become more viable, opening up the doors to study functional genomics at the single-cell level. This development has lead to a rush to adapt bulk methods and develop new single-cell-specific methods and tools for computational analysis of these studies. Many single-cell methods have been tested, developed, and benchmarked using simulated data. However, current scRNA-seq simulation frameworks do not allow for the simulation of population-scale scRNA-seq data. Here, we present splatPop, a new Splatter model, for flexible, reproducible, and well documented simulation of population-scale scRNA-seq data with known expression quantitative trait loci (eQTL) effects. The splatPop model also allows for the simulation of complex batch effects, cell group effects, and conditional effects between individuals from different cohorts.
Transcription factor-like 5 is a potential DNA/RNA-binding protein essential for maintaining male fertility in mice
Authors: Xu Weiya , Zhang Yiyun , Qin Dongdong , Gui Yiqian , Wang Shu , Du Guihua , Yang Fan , Li Lufan , Yuan Shuiqiao , Wang Mei , Wu Xin 
Published: June 2021

ABSTRACTTissue-specific transcription factors often play key roles in the development of specific cell lineages. Transcription factor-like 5 (TCFL5) is a testis-specific protein that contains the basic helix-loop-helix domain, although the in vivo functions of TCFL5 remain unknown. Herein, we generated CRISPR/Cas9-mediated knockout mice to dissect the function of TCFL5 in mouse testes. Surprisingly, we found that it was difficult to generate homozygous mice with the Tcfl5 deletion since the heterozygous males (Tcfl5+/−) were infertile. We did, however, observe markedly abnormal phenotypes of spermatids and spermatozoa in the testes and epididymides of Tcfl5+/− mice. Mechanistically, we demonstrated that TCFL5 transcriptionally regulated a set of genes participating in male germ cell development, which we uncovered via RNA-sequencing and TCFL5 ChIP-sequencing. We also found that TCFL5 interacted with RNA-binding proteins (RBPs) that regulated RNA processing, and further identified the fragile X mental retardation gene 1, autosomal homolog (FXR1, a known RBP) as an interacting partner of TCFL5 that may coordinate the transition and localization of TCFL5 in the nucleus. Collectively, we herein report for the first time that Tcfl5 is haploinsufficient in vivo and hypothesize that TCFL5 may be a dual-function protein that mediates DNA and RNA to regulate spermatogenesis.
The endoplasmic reticulum membrane protein complex localizes to the mitochondrial - endoplasmic reticulum interface and its subunits modulate phospholipid biosynthesis in Trypanosoma brucei
Authors: Iyer Advaitha , Niemann Moritz , Serricchio Mauro , Dewar Caroline E. , Oeljeklaus Silke , Farine Luce , Warscheid Bettina , Schneider André , Bütikofer Peter 
Published: June 2021

AbstractThe endoplasmic reticulum membrane complex (EMC) is a versatile complex that plays a key role in membrane protein biogenesis in the ER. Deletion of the complex has wide-ranging consequences including ER stress, disturbance in lipid transport and organelle tethering, among others. Here we report the function and organization of the evolutionarily conserved EMC (TbEMC) in the highly diverged eukaryote, Trypanosoma brucei. Using (co-) immunoprecipitation experiments in combination with mass spectrometry and whole cell proteomic analyses of parasites after depletion of select TbEMC subunits, we demonstrate that the TbEMC is composed of 9 subunits that are present in a high molecular mass complex localizing to the mitochondrial-endoplasmic reticulum interface. Knocking out or knocking down of single TbEMC subunits led to growth defects of T. brucei procyclic forms in culture. Interestingly, we found that depletion of individual TbEMC subunits lead to disruption of de novo synthesis of phosphatidylcholine (PC) or phosphatidylethanolamine (PE), the two most abundant phospholipid classes in T. brucei. Downregulation of TbEMC1 or TbEMC3 inhibited formation of PC while depletion of TbEMC8 inhibited PE synthesis, pointing to a role of the TbEMC in phospholipid synthesis. In addition, we found that in TbEMC7 knock-out parasites, TbEMC3 is released from the complex, implying that TbEMC7 is essential for the formation or the maintenance of the TbEMC.
MatrixQCvis: shiny-based interactive data quality exploration for omics data
Authors: Naake Thomas , Huber Wolfgang 
Published: June 2021

AbstractMotivationFirst-line data quality assessment and exploratory data analysis are integral parts of any data analysis workflow. In high-throughput quantitative omics experiments (e.g. transcriptomics, proteomics, metabolomics), after initial processing, the data are typically presented as a matrix of numbers (feature IDs × samples). Efficient and standardized data-quality metrics calculation and visualization are key to track the within-experiment quality of these rectangular data types and to guarantee for high-quality data sets and subsequent biological question-driven inference.ResultsWe present MatrixQCvis, which provides interactive visualization of data quality metrics at the per-sample and per-feature level using R’s shiny framework. It provides efficient and standardized ways to analyze data quality of quantitative omics data types that come in a matrix-like format (features IDs × samples). MatrixQCvis builds upon the Bioconductor SummarizedExperiment S4 class and thus facilitates the integration into existing workflows.AvailabilityMatrixQCVis is implemented in R. It is available via Bioconductor and released under the GPL v3.0 license.Contactthomas.naake@embl.deSupplementary informationSupplementary Information is available at bioRxiv online.
Dual Dysfunction of Kir2.1 Underlies Conduction and Excitation-Contraction Coupling Defects Promoting Arrhythmias in a Mouse Model of Andersen-Tawil Syndrome Type 1
Authors: Macías Álvaro , González-Guerra Andrés , Moreno-Manuel Ana I. , Cruz Francisco M. , García-Quintáns Nieves , Gutiérrez Lilian K. , Roche-Molina Marta , Bermúdez-Jiménez Francisco , Andrés Vicente , Vera-Pedrosa María Linarejos , Martínez-Carrascoso Isabel , Bernal Juan A. , Jalife José 
Published: June 2021

ABSTRACTAndersen-Tawil Syndrome (ATS) is associated with life threatening arrhythmias of unknown mechanism. We report on a mouse model carrying the trafficking-deficient mutant Kir2.1Δ314-315. The mouse recapitulates the electrophysiological phenotype of type 1 (ATS1), with slower conduction velocities in response to flecainide, QT prolongation exacerbated by isoproterenol, and increased vulnerability to calcium-mediated arrhythmias resembling catecholaminergic polymorphic ventricular tachycardia (CPVT). Kir2.1Δ314-315 expression significantly reduced inward rectifier K+ and Na+ inward currents, depolarized resting membrane potential and prolonged action potential duration. Immunolocalization in wildtype cardiomyocytes and skeletal muscle cells revealed a novel sarcoplasmic reticulum (SR) microdomain of functional Kir2.1 channels contributing to intracellular Ca2+ homeostasis. Kir2.1Δ314-315 cardiomyocytes showed defects in SR Kir2.1 localization and function, which contributed to abnormal spontaneous Ca2+ release events. This is the first in-vivo demonstration of a dual arrhythmogenic mechanism of ATS1 defects in Kir2.1 channel function at the sarcolemma and the SR, with overlap between ATS1 and CPVT.
The predicted bZIP transcription factor ZIP-1 promotes resistance to intracellular infection in Caenorhabditis elegans
Authors: Lažetić Vladimir , Wu Fengting , Cohen Lianne B. , Reddy Kirthi C. , Chang Ya-Ting , Gang Spencer S. , Bhabha Gira , Troemel Emily R. 
Published: June 2021

AbstractDefense against intracellular infection has been extensively studied in vertebrate hosts, but less is known about invertebrate hosts. For example, almost nothing is known about the transcription factors that induce defense against intracellular intestinal infection in the model nematode Caenorhabditis elegans. Two types of intracellular pathogens that naturally infect the C. elegans intestine are the Orsay virus, which is a positive-sense RNA virus, and microsporidia, which are fungal pathogens. Surprisingly, these molecularly distinct pathogens induce a common host transcriptional response called the Intracellular Pathogen Response (IPR). Here we describe zip-1 as an IPR regulator that functions downstream of all known IPR activating and regulatory pathways. zip-1 encodes a putative bZIP transcription factor of previously unknown function, and we show how zip-1 controls induction of a subset of genes upon IPR activation. ZIP-1 protein is expressed in the nuclei of intestinal cells, and is required in the intestine to upregulate IPR gene expression. Importantly, zip-1 promotes resistance to infection by the Orsay virus and by microsporidia in intestinal cells. Altogether, our results indicate that zip-1 represents a central hub for all triggers of the IPR, and that this transcription factor plays a protective role against intracellular pathogen infection in C. elegans.
Heparan Sulfate-dependent RAGE oligomerization is indispensable for pathophysiological functions of RAGE
Authors: Li Miaomiao , Ong Chih Yean , Langouët-Astrié Christophe J , Tan Lisi , Verma Ashwni , Yang Yimu , Zhang Xiaoxiao , Shah Dhaval K. , Schmidt Eric P. , Xu Ding 
Published: June 2021

ABSTRACTRAGE, a druggable inflammatory receptor, is known to function as an oligomer but the exact oligomerization mechanism remains poorly understood. Previously we have shown that heparan sulfate (HS) plays an active role in RAGE oligomerization. To understand the physiological significance of HS-induced RAGE oligomerization in vivo, we generated RAGE knock-in mice (RageAHA/AHA) by introducing point mutations to specifically disrupt HS–RAGE interaction. The RAGE mutant demonstrated normal ligand-binding but impaired capacity of HS-binding and oligomerization. Remarkably, RageAHA/AHA mice phenocopied Rage−/− mice in two different pathophysiological processes, namely bone remodeling and neutrophil-mediated liver injury, which demonstrates that HS-induced RAGE oligomerization is essential for RAGE signaling. Our findings suggest that it should be possible to block RAGE signaling by inhibiting HS-RAGE interaction. To test this, we generated a monoclonal antibody that targets the HS-binding site of RAGE. This antibody blocks RAGE signaling in vitro and in vivo, recapitulating the phenotype of RageAHA/AHA mice. By inhibiting HS-RAGE interaction genetically and pharmacologically, our work validated an alternative strategy to antagonize RAGE. Finally, we have performed RNA-seq analysis of neutrophils and lungs and found that while Rage−/− mice had a broad alteration of transcriptome in both tissues compared to wild-type mice, the changes of transcriptome in RageAHA/AHA mice were much more restricted. This unexpected finding suggests that by preserving the expression of RAGE protein (in a dominant-negative form), RageAHA/AHA mouse might represent a cleaner genetic model to study physiological roles of RAGE in vivo compared to Rage−/− mice.