bluuebunny/crossref_metadata_2025_split huggingface dataset:
Altered co-stimulatory and inhibitory receptors on monocyte subsets in patients with visceral leishmaniasis
Authors: Adem E. , Yizengaw E. , Mulaw T. , Nibret E. , Müller I. , Takele Y. , Kropf P. 
Published: March 2024

ABSTRACTVisceral leishmaniasis (VL) is a neglected tropical disease caused by parasites from theLeishmania(L.)donovanicomplex. VL is characterised by uncontrolled parasite replication in spleen, liver and bone marrow, and by an impaired immune response and high systemic levels of inflammation. Monocytes have been poorly characterised in VL patients. The aim of this study was to evaluate the expression levels of markers involved in the regulation of T cell responses on different subsets of monocytes from the blood of VL patients and healthy non-endemic controls (HNEC). Monocytes can broadly be divided into three subsets: classical, intermediate and non-classical monocytes. Our results show that the percentages of all three subsets stay similar at the time of VL diagnosis (ToD) and at the end of anti-leishmanial treatment (EoT). We first looked at co-stimulatory receptors: the expression levels of CD40 were significantly increased on classical and intermediate, but not non-classical monocytes, at ToD as compared to EoT and HNEC. CD80 expression levels were also increased on intermediate monocytes at ToD as compared to EoT and HNEC, and on classical monocytes only as compared to HNEC. The levels of CD86 were similar at EoT and ToD and in HNEC on classical and intermediate monocytes, but significantly higher at EoT on non-classical monocytes. We also looked at an inhibitory molecule, PD-L1. Our results show that the expression levels of PD-L1 is significantly higher on all three monocyte subsets at ToD as compared to HNEC, and to EoT on classical and intermediate monocytes.These results show that monocytes from the blood of VL patients upregulate both co-stimulatory and inhibitory receptors and that their expression levels are restored at EoT.
In vivooptogenetics using a Utah Optrode Array with enhanced light output and spatial selectivity
Authors: McAlinden Niall , Reiche Christopher F. , Clark Andrew M. , Scharf Robert , Cheng Yunzhou , Sharma Rohit , Rieth Loren , Dawson Martin D. , Angelucci Alessandra , Mathieson Keith , Blair Steve 
Published: March 2024

AbstractOptogenetics allows manipulation of neural circuitsin vivowith high spatial and temporal precision. However, combining this precision with control over a significant portion of the brain is technologically challenging (especially in larger animal models). Here, we have developed, optimised, and tested in vivo, the Utah Optrode Array (UOA), an electrically addressable array of optical needles and interstitial sites illuminated by 181 µLEDs and used to optogenetically stimulate the brain. The device is specifically designed for non-human primate studies. Thinning the combined µLED and needle backplane of the device from 300 µm to 230 µm improved the efficiency of light delivery to tissue by 80%, allowing lower µLED drive currents, which improved power management and thermal performance. The spatial selectivity of each site was also improved by integrating an optical interposer to reduce stray light emission. These improvements were achieved using an innovative fabrication method to create an anodically bonded glass/silicon substrate with through-silicon vias etched, forming an optical interposer. Optical modelling was used to demonstrate that the tip structure of the device had a major influence on the illumination pattern. The thermal performance was evaluated through a combination of modelling and experiment, in order to ensure that cortical tissue temperatures did not rise by more than 1°C. The device was testedin vivoin the visual cortex of macaque expressing ChR2-tdTomato in cortical neurons. It was shown that the strongest optogenetic response occurred in the region surrounding the needle tips, and that the extent of the optogenetic response matched the predicted illumination profile based on optical modelling – demonstrating the improved spatial selectivity resulting from the optical interposer approach. Furthermore, different needle illumination sites generated different patterns of low-frequency potential (LFP) activity.
Post-transcriptional RNA stabilization of telomere-proximal RNAs FRG2, DBET, D4Z4 at human 4q35 in response to genotoxic stress and D4Z4 macrosatellite repeat length
Authors: Salsi Valentina , Losi Francesca , Salani Monica , Kaufman Paul D. , Tupler Rossella 
Published: March 2024

ABSTRACTBackgroundReduced copy number of the D4Z4 macrosatellite at human chromosome 4q35 is associated with facioscapulohumeral muscular dystrophy (FSHD). A pervasive idea is that chromatin alterations at the 4q35 locus following D4Z4 repeat unit deletion lead to disease via inappropriate expression of nearby genes. Here, we sought to analyze transcription and chromatin characteristics across 4q35 and how these are affected by D4Z4 deletions and exogenous stresses.ResultsWe found that the 4q subtelomere is subdivided into discrete domains, each with characteristic chromatin features associated with distinct gene expression profiles. Centromere-proximal genes within 4q35 (ANT1,FAT1andFRG1)display active histone marks at their promoters. In contrast, poised or repressed markings are present at telomere-proximal loci includingFRG2, DBE-TandD4Z4. We discovered that these discrete domains undergo region-specific chromatin changes upon treatment with chromatin enzyme inhibitors or genotoxic drugs. We demonstrated that the 4q35 telomere-proximalFRG2, DBE-TandD4Z4-derived transcripts are induced upon DNA damage to levels inversely correlated with the D4Z4 repeat number, are stabilized through post-transcriptional mechanisms upon DNA damage, and are bound to chromatin.ConclusionOur study reveals unforeseen biochemical features of RNAs from clustered transcription units within the 4q35 subtelomere. Specifically, theFRG2, DBE-TandD4Z4-derived transcripts are chromatin-associated and are stabilized post-transcriptionally after induction by genotoxic stress. Remarkably, the extent of this response is modulated by the copy number of the D4Z4 repeats, raising new hypotheses about their regulation and function in human biology and disease.
Fibroblast diversification is an embryonic process dependent on muscle contraction
Authors: Coren Lavi , Zaffryar-Eilot Shelly , Odeh Anas , Kaganovsky Anna , Hasson Peleg 
Published: March 2024

SUMMARYFibroblasts are the most common cell type found in connective tissues, known to play major roles in development, homeostasis, regeneration and disease. Although specific fibroblast subpopulations were associated with different biological processes, the mechanisms and unique activities underlying their diversity has not been thoroughly examined. Turning to skeletal muscle development, we set to dissect the variation of muscle-resident fibroblasts (mrFibroblasts). Our results demonstrate mrFibroblasts diversify following the transition from embryonic to fetal myogenesis prior to birth. We find mrFibroblast segregate into two major subpopulations occupying distinct niches, with interstitial fibroblasts residing between the muscle fibers, and delineating fibroblasts sheathing the muscle mass. We further show these subpopulations entail distinct cellular dynamics and transcriptomes. Notably, we find mrFibroblast subpopulations exert distinct regulatory roles on myoblast proliferation and differentiation. Finally, we demonstrate this diversification depends on muscle contraction. Altogether, these findings establish mrFibroblast diversify in a spatio-temporal embryonic process into distinct cell types, entailing different characteristics and roles.
CACNA1Ahaploinsufficiency leads to reduced synaptic function and increased intrinsic excitability
Authors: Hommersom Marina P. , Doorn Nina , Puvogel Sofía , Lewerissa Elly I. , Mordelt Annika , Ciptasari Ummi , Kampshoff Franziska , Dillen Lieke , van Beusekom Ellen , Oudakker Astrid , Kogo Naoki , Frega Monica , Schubert Dirk , van de Warrenburg Bart P.C. , Nadif Kasri Nael , van Bokhoven Hans 
Published: March 2024

AbstractHaploinsufficiency of theCACNA1Agene, encoding the pore-forming α1 subunit of P/Q-type voltage-gated calcium channels, is associated with a clinically variable phenotype ranging from cerebellar ataxia, to neurodevelopmental syndromes with epilepsy and intellectual disability.To understand the pathological mechanisms ofCACNA1Aloss-of-function variants, we characterized a human neuronal model forCACNA1Ahaploinsufficiency, by differentiating isogenic induced pluripotent stem cell lines into glutamatergic neurons, and investigated the effect ofCACNA1Ahaploinsufficiency on mature neuronal networks through a combination of electrophysiology, gene expression analysis, andin silicomodeling.We observed an altered network synchronization inCACNA1A+/−networks alongside synaptic deficits, notably marked by an augmented contribution of GluA2-lacking AMPA receptors. Intriguingly, these synaptic perturbations coexisted with increased non-synaptically driven activity, as characterized by inhibition of NMDA and AMPA receptors on micro-electrode arrays. Single-cell electrophysiology and gene expression analysis corroborated this increased intrinsic excitability through reduced potassium channel function and expression. Moreover, we observed partial mitigation of theCACNA1A+/−network phenotype by 4-aminopyridine, a therapeutic intervention for episodic ataxia type 2.In summary, our study pioneers the characterization of a human induced pluripotent stem cell-derived neuronal model forCACNA1Ahaploinsufficiency, and has unveiled novel mechanistic insights. Beyond showcasing synaptic deficits, this neuronal model exhibited increased intrinsic excitability mediated by diminished potassium channel function, underscoring its potential as a therapeutic discovery platform with predictive validity.
NFIB influences progenitor competence in maturation of GABAergic neurons in mice
Authors: Bright Ann Rose , Kotlyarenko Yana , Neuhaus Florian , Rodrigues Diana , Feng Chao , Peters Christian , Vitali Ilaria , Dönmez Elif , Myoga Michael H. , Dvoretskova Elena , Mayer Christian 
Published: March 2024

AbstractDiverse types of GABAergic projection neurons and interneurons of the telencephalon derive from progenitors in a ventral germinal zone, called the ganglionic eminence. Using single-cell transcriptomics, chromatin accessibility profiling, lineage tracing, birthdating, heterochronic transplantation, and perturbation sequencing in mouse embryos, we investigated how progenitor competence influences the maturation and differentiation of these neurons. We found that the progression of neurogenesis over developmental time shapes maturation competence in ganglionic eminence progenitors, influencing how they progress into mature states. In contrast, differentiation competence, which defines the ability to produce diverse transcriptomic identities, remains largely unaffected by the stages of neurogenesis. Chromatin remodeling alongside a NFIB-driven regulatory gene module influences maturation competence in late-born neurons. These findings provide key insights into how transcriptional programs and chromatin accessibility govern neuronal maturation and the diversification of GABAergic neuron subtypes during neurodevelopment.
A Developmental Mechanism to Regulate Alternative Polyadenylation in an Adult Stem Cell Lineage
Authors: Gallicchio Lorenzo , Matias Neuza R. , Morales-Polanco Fabian , Nava Iliana , Stern Sarah , Zeng Yi , Fuller Margaret T. 
Published: March 2024

AbstractAlternative Cleavage and Polyadenylation (APA) often results in production of mRNA isoforms with either longer or shorter 3’UTRs from the same genetic locus, potentially impacting mRNA translation, localization and stability. Developmentally regulated APA can thus make major contributions to cell-type-specific gene expression programs as cells differentiate. DuringDrosophilaspermatogenesis, approximately 500 genes undergo APA when proliferating spermatogonia differentiate into spermatocytes, producing transcripts with shortened 3’ UTRs, leading to profound stage-specific changes in the proteins expressed. The molecular mechanisms that specify usage of upstream polyadenylation sites in spermatocytes are thus key to understanding the changes in cell state. Here, we show that upregulation of PCF11 and Cbc, the two components of Cleavage Factor II (CFII), orchestrates APA duringDrosophilaspermatogenesis. Knock down ofPCF11orcbcin spermatocytes caused dysregulation of APA, with many transcripts normally cleaved at a proximal site in spermatocytes now cleaved at their distal site, as in spermatogonia. Forced overexpression of CFII components in spermatogonia switched cleavage of some transcripts to the proximal site normally used in spermatocytes. Our findings reveal a developmental mechanism where changes in expression of specific cleavage factors can direct cell-type-specific APA at selected genes.
Natural history of eukaryotic DNA viruses with double jelly-roll major capsid proteins
Authors: Krupovic Mart , Kuhn Jens H. , Fischer Matthias G. , Koonin Eugene V. 
Published: March 2024

AbstractThe phylumPreplasmiviricota(kingdomBamfordvirae, realmVaridnaviria) is a broad assemblage of diverse viruses with comparatively short double-stranded DNA genomes (<50 kbp) that produce icosahedral capsids built from double jelly-roll major capsid proteins. Preplasmiviricots infect hosts from all cellular domains, testifying to their ancient origin and, in particular, are associated with six of the seven supergroups of eukaryotes. Preplasmiviricots comprise four major groups of viruses, namely, polintons, polinton-like viruses (PLVs), virophages, and adenovirids. We employed protein structure modeling and analysis to show that protein-primed DNA polymerases (pPolBs) of polintons, virophages, and cytoplasmic linear plasmids encompass an N-terminal domain homologous to the terminal proteins (TPs) of prokaryotic PRD1-like tectivirids and eukaryotic adenovirids that are involved in protein-primed replication initiation, followed by a viral ovarian tumor-like cysteine deubiquitinylase (vOTU) domain. The vOTU domain is likely responsible for the cleavage of the TP from the large pPolB polypeptide and is inactivated in adenovirids, in which TP is a separate protein. Many PLVs and transpovirons encode a distinct derivative of polinton-like pPolB that retains the TP, vOTU and pPolB polymerization palm domains but lacks the exonuclease domain and instead contains a supefamily 1 helicase domain. Analysis of the presence/absence and inactivation of the vOTU domains, and replacement of pPolB with other DNA polymerases in eukaryotic preplasmiviricots enabled us to outline a complete scenario for their origin and evolution.SignificanceStructural modeling of protein domains using advanced artificial intelligence-based methods such as AlphaFold2 may lead to insights into evolutionary relationships among proteins that are unreachable by sequence analysis. We applied this approach to elucidate the evolutionary relationships of four major groups of eukaryotic viruses: polintons, polinton-like viruses (PLVs), virophages, and adenovirids. We identified previously uncharacterized protein domains predicted to be essential for virus genome replication. Analysis of the presence/absence and inactivation of these domains suggests a complete scenario for the origin and evolution of this major part of the eukaryotic virosphere.
Single-cell genomics and regulatory networks for 388 human brains
Authors: Emani Prashant S. , Liu Jason J. , Clarke Declan , Jensen Matthew , Warrell Jonathan , Gupta Chirag , Meng Ran , Lee Che Yu , Xu Siwei , Dursun Cagatay , Lou Shaoke , Chen Yuhang , Chu Zhiyuan , Galeev Timur , Hwang Ahyeon , Li Yunyang , Ni Pengyu , Zhou Xiao ,   PsychENCODE Consortium, Bakken Trygve E. , Bendl Jaroslav , Bicks Lucy , Chatterjee Tanima , Cheng Lijun , Cheng Yuyan , Dai Yi , Duan Ziheng , Flaherty Mary , Fullard John F. , Gancz Michael , Garrido-Martín Diego , Gaynor-Gillett Sophia , Grundman Jennifer , Hawken Natalie , Henry Ella , Hoffman Gabriel E. , Huang Ao , Jiang Yunzhe , Jin Ting , Jorstad Nikolas L. , Kawaguchi Riki , Khullar Saniya , Liu Jianyin , Liu Junhao , Liu Shuang , Ma Shaojie , Margolis Michael , Mazariegos Samantha , Moore Jill , Moran Jennifer R. , Nguyen Eric , Phalke Nishigandha , Pjanic Milos , Pratt Henry , Quintero Diana , Rajagopalan Ananya S. , Riesenmy Tiernon R. , Shedd Nicole , Shi Manman , Spector Megan , Terwilliger Rosemarie , Travaglini Kyle J. , Wamsley Brie , Wang Gaoyuan , Xia Yan , Xiao Shaohua , Yang Andrew C. , Zheng Suchen , Gandal Michael J. , Lee Donghoon , Lein Ed S. , Roussos Panos , Sestan Nenad , Weng Zhiping , White Kevin P. , Won Hyejung , Girgenti Matthew J. , Zhang Jing , Wang Daifeng , Geschwind Daniel , Gerstein Mark 
Published: March 2024

AbstractSingle-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet, little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multi-omics datasets into a resource comprising >2.8M nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550K cell-type-specific regulatory elements and >1.4M single-cell expression-quantitative-trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized ∼250 disease-risk genes and drug targets with associated cell types.Summary Figure
The putative Type 4 secretion system effector BspD is involved in maintaining envelope integrity of the pathogenBrucella
Authors: Ketterer Maren , Chiquet Petra , Sedzicki Jaroslaw , Québatte Maxime , Dehio Christoph 
Published: March 2024

AbstractBrucellosis is a debilitating disease caused by the Gram-negative, facultative intracellular zoonotic pathogenBrucella.En routeto its intracellular replicative niche,Brucellaencounters various stressful environments that may compromise envelop integrity. Here we show, that the proposed Type 4 secretion system (T4SS) effector BspD is a conserved protein of the Rhizobiales, which does not show signs of co-evolution with the presence of a T4SS or a certain lifestyle. We further present data indicating that BspD is critical forBrucella abortusenvelope integrity in the stationary phase and in the presence of EDTA, a compound known to destabilize the outer membrane. Deletion ofbspDresulted in abnormal bacterial morphologies, indicating its involvement in maintaining envelope integrity. Additionally, the absence of BspD led to the formation of fewer and smaller intracellular microcolonies in a macrophage infection model. From our observations, we propose that BspD ofB. abortusis critical for preserving the integrity of the bacterial envelope, particularly under stressful conditions, which may enhanceBrucella’s ability to survive within host cells.ImportanceBrucellosis, caused by the intracellular pathogenBrucella, poses a significant health threat. Understanding howBrucellaadapts to stressful environments is crucial. This study unveils BspD, a conserved protein within the Rhizobiales order, as a key player in maintainingBrucella’s envelope integrity. Remarkably, BspD’s function appears independent of the presence of a Type 4 Secretion System (T4SS) or specific lifestyle. Deletion ofbspDresulted in compromised envelope integrity, abnormal bacterial morphologies, and reduced intracellular microcolony formation. These findings underscore BspD’s critical role, particularly in stressful conditions like the stationary phase and EDTA exposure, and highlight its significance inBrucella’s survival within host cells. This elucidation deepens our understanding ofBrucellapathogenesis and may inform future therapeutic strategies against brucellosis.
GGCX promotes Eurasian avian-like H1N1 swine influenza virus adaption to interspecies receptor binding
Authors: Zou Jiahui , Jiang Meijun , Xiao Rong , Sun Huimin , Liu Hailong , Peacock Thomas , Tu Shaoyu , Chen Tong , Guo Jinli , Zhao Yaxin , Barclay Wendy , Xie Shengsong , Zhou Hongbo 
Published: March 2024

AbstractThe Eurasian avian-like (EA) H1N1 swine influenza virus (SIV) possesses the capacity to instigate the next influenza pandemic, owing to its heightened affinity for the human-type α-2,6 sialic acid (SA) receptor. Nevertheless, the molecular mechanisms underlying the switch in receptor binding preferences of EA H1N1 SIV remain elusive. In this study, we conducted a comprehensive genome-wide CRISPR/Cas9 knockout screen utilizing EA H1N1 SIV in porcine kidney cells. Knocking out the enzyme gamma glutamyl carboxylase (GGCX) reduced virus replicationin vitroandin vivoby inhibiting the carboxylation modification of viral haemagglutinin (HA) and the adhesion of progeny viruses, ultimately impeding the replication of EA H1N1 SIV. Furthermore, GGCX was revealed to be the determinant of the D225E substitution of EA H1N1 SIV, and GGCX-medicated carboxylation modification of HA 225E contributed to the receptor binding adaption of EA H1N1 SIV to the α-2,6 SA receptor. Taken together, our CRISPR screen has elucidated a novel function of GGCX in the support of EA H1N1 SIV adaption for binding to α-2,6 SA receptor. Consequently, GGCX emerges as a prospective antiviral target against the infection and transmission of EA H1H1 SIV.
Structural analysis of genetic variants of the human tumor suppressor Palb2 coiled-coil domain
Authors: Reddy Pothula Purushotham , Phale Apurva , Das Ranabir 
Published: March 2024

AbstractHomologous recombination (HR) is an obligate pathway to repair DNA lesions and maintain genome integrity. The tumor suppressor Palb2 is an integral part of the HR pathway that functionally connects BRCA proteins at the site of DNA damage. The N-terminal coiled-coil domain in Palb2 switches from an inactive to an active complex during HR. In the inactive form, Palb2 forms homodimers, and during HR, it assumes the active state, forming a heterodimeric complex with BRCA1. However, the structural details of the human Palb2 coiled-coil domain are unknown. About 600 missense variants have been reported in Palb2, and several are in the coiled-coil domain. The structure-function relationship of such variants is poorly understood, which challenges genetic counseling. Here, we report the solution structure of the human Palb2 coiled-coil domain, which forms an antiparallel homodimer. We then use the structure to study the effect of a few well-characterized missense mutations on the fold and interactions of the Palb2 coiled-coil domain. The structural impact of mutations correlates excellently with their efficiency in homologous recombination, signifying that the approach can be exploited to study other genetic variations in the Palb2.