bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ion occupancy of the selectivity filter controls opening of a cytoplasmic gate in the K2P channel TALK-2
Authors: Neelsen Lea C. , Riel Elena B. , Rinné Susanne , Schmid Freya-Rebecca , Jürs Björn C. , Bedoya Mauricio , Langer Jan P. , Eymsh Bisher , Kiper Aytug K. , Cordeiro Sönke , Decher Niels , Baukrowitz Thomas , Schewe Marcus 
Published: November 2023

AbstractTwo-pore domain K+(K2P) channel activity was previously thought to be controlled primarily via a selectivity filter (SF) gate. However, recent crystal structures of TASK-1 and TASK-2 revealed a lower gate at the cytoplasmic pore entrance. Here, we report functional evidence of such a lower gate in the K2Pchannel K2P17.1 (TALK-2, TASK-4). We identified compounds (drugs and lipids) and mutations that opened the lower gate allowing the fast modification of pore cysteine residues. Surprisingly, stimuli that exclusively target the SF gate (i.e., pHe., Rb+permeation, membrane depolarization) also opened the cytoplasmic gate suggesting that the SF can induce global structural changes in TALK-2. Reciprocally, opening of the lower gate reduced the electrical work required to force ions into the SF to induce its opening as apparent in large shifts of the conductance-voltage (G-V) curves. These shifts, thereby, represent the mechanical work done by the SF to induce a global structural re-arrangement that opened the lower gate. In conclusion, it appears that the SF is so rigidly locked into the TALK-2 protein structure that changes in ion occupancy can pry open a distant lower gate. Vice versa, we show that opening of the lower gate concurrently forces the SF gate to open. This concept might extent to other K+channels that contain two gates (e.g., voltage-gated K+channels) for which such a positive gate coupling has been suggested, but so far not directly demonstrated.SynopsisTALK-2 channels, like most K2Pchannels, possess a functional gate in the selectivity filter (SF; the upper gate) that is opened by rising extracellular pH and voltage-dependent ion binding (voltage gating).A second (lower) permeation gate in TALK-2 at the cytoplasmic end of TM4 is identified using cysteine modification, scanning mutagenesis and structural modelling. This gate can be opened by anionic lipids (LC-CoA) as well as pharmacological ligands (e.g., 2-APB).The modification reactivity of a cysteine introduced between the two gates reveal that stimuli targeting the SF gate also open the lower gate. Furthermore, stimuli that open the lower gate reduce the voltage (i.e., electrical work or mechanical load) required to open the SF gate. These findings demonstrate a tight positive coupling between the two gates.The concept of strong positive gate coupling might extend to other K+channels with two gates (e.g., voltage-gated K+channels) for which positive gate coupling has been suggested but so far not directly demonstrated.
Impact of blood meals taken on ivermectin-treated livestock on survival and fecundity of the malaria vectorAnopheles coluzziiunder laboratory conditions
Authors: Pooda Sié Hermann , de Salle Hien François , Pagabeleguem Soumaïla , Heinrich Andre Patrick , Porciani Angélique , Sagna André Barembaye , Zela Lamidi , Percoma Lassane , Lefèvre Thierry , Dabiré Roch Kounbobr , Koffi Amnan Alphonsine , Düring Rolf-Alexander , Pennetier Cédric , Moiroux Nicolas , Mouline Karine 
Published: November 2023

AbstractTreatment of livestock with endectocides such as ivermectin is viewed as a complementary vector control approach to address residual transmission of malaria. However, efficacy of this treatment may vary between animal species. Hence, our purpose was to investigate the effects of ivermectin treatments of common livestock species on life history traits of the opportunistic malaria vectorAnopheles coluzzii.Sheep, goats and pigs were treated using injectable veterinary ivermectin formulation at the species-specific doses (recommended dose for all species and high dose in pig). Mosquito batches were exposed to treated and control (not injected) animals at different days after treatment. Daily mosquito mortality was recorded and fecundity assessed through the count of gravid females and the number of eggs they developed.The recommended dose of ivermectin induced a significant decrease in mosquito survival for up to 7 days after injection (DAI), with a decrease of 89.7%, 66.7%, and 48.4% in treated pigs, goats and sheep, respectively, compared to control animals. In treated pigs, the triple therapeutic dose decreased mosquito survival of 68.97% relatively to controls up to 14 DAI. The average number in gravid femalesAnophelesthat survived after feeding on treated animals were reduced when blood-meals were taken on sheep (2.57% and 42.03% at 2 and 7 DAI), or on goats (decrease of the 28.28% and 73.64% respectively at 2 and 7 DAI).This study shows that ivermectin treatments to animals negatively impactsAn. coluzziilife history traits and could reduce vector densities in areas where livestock live near humans. However, due to short-term efficacy of single dose treatments, repeated treatments and potentially increased dosages would be required to span the transmission season. The use of long-acting ivermectin formulations is discussed as a mean for extending efficacy while remaining cost effective.
Functional characterization of RNA profiles in processing bodies of human embryonic stem cells and mesodermal cells
Authors: Jiang Jin , Shao Qizhe , Xie Sisi , Xiao Xiaoying , Guo Ruisi , Jin Min , Chen Di 
Published: November 2023

SUMMARYProcessing bodies (P-bodies) are the membraneless organelles that play critical roles in RNA storage and decay. Abnormalities in P-bodies contribute to diseases and developmental disorders. Huge efforts have been applied to the identification of the protein components in P-bodies, however, the dynamics of RNA components of P-bodies in human embryonic stem cells (hESCs) during maintenance and differentiation remain largely elusive. Here, we characterized the RNA profiles of P-bodies from HEK293T cells, hESCs, and hESC-derived mesodermal cells. The number of P-bodies decreases upon hESC differentiation towards mesodermal fate, accompanied with the decreased RNAs within P-bodies. By functional analysis of the P-body enriched and P-body depleted genes across different cell types, we discovered the cell type-specific enrichment of P-body-genes and the potential association with human diseases. We also captured the non-coding RNAs, including long intergenic non-coding RNAs and transposable elements in P-bodies in a cell type-specific manner. Furthermore, we verified the involvement P-bodies in regulating the differentiation of hESCs towards mesoderm by over-expression of LSM14A and knocking down ofSPTAN1. In summary, we characterized the mRNAs and non-coding RNAs in P-bodies of hESCs and hESC-derived mesodermal cells, discovering the potential roles that P-bodies play for the precise differentiation of hESCs.
Boosting performance of generative diffusion model for molecular docking by training on artificial binding pockets
Authors: Voitsitskyi Taras , Bdzhola Volodymyr , Stratiichuk Roman , Koleiev Ihor , Ostrovsky Zakhar , Vozniak Volodymyr , Khropachov Ivan , Henitsoi Pavlo , Popryho Leonid , Zhytar Roman , Yesylevskyy Semen O , Nafiiev Alan , Starosyla Serhii 
Published: November 2023

AbstractThis study introduces the PocketCFDM generative diffusion model, aimed at improving the prediction of small molecule poses in the protein binding pockets. The model utilizes a novel data augmentation technique, involving the creation of numerous artificial binding pockets that mimic the statistical patterns of non-bond interactions found in actual protein-ligand complexes. An algorithmic method was developed to assess and replicate these interaction patterns in the artificial binding pockets built around small molecule conformers. It is shown that the integration of artificial binding pockets into the training process significantly enhanced the model’s performance. Notably, PocketCFDM surpassed DiffDock in terms of non-bond interaction quality, number of steric clashes, and inference speed. Future developments and optimizations of the model are discussed.AvailabilityThe inference code and final model weights of PocketCFDM are accessible publicly via the GitHub repository:https://github.com/vtarasv/pocket-cfdm.git.
Rifampicin tolerance and growth fitness among isoniazid-resistant clinicalMycobacterium tuberculosisisolates: an in-vitro longitudinal study
Authors: Vijay Srinivasan , Bao Nguyen Le Hoai , Vinh Dao Nguyen , Nhat Le Thanh Hoang , Thu Do Dang Anh , Quang Nguyen Le , Trieu Le Pham Tien , Nhung Hoang Ngoc , Ha Vu Thi Ngoc , Thai Phan Vuong Khac , Ha Dang Thi Minh , Lan Nguyen Huu , Caws Maxine , Thwaites Guy E. , Javid Babak , Thuong Nguyen Thuy Thuong 
Published: November 2023

AbstractAntibiotic tolerance inMycobacterium tuberculosisleads to less effective bacterial killing, poor treatment responses and resistant emergence. Therefore, we investigated the rifampicin tolerance ofM. tuberculosisisolates, with or without pre-existing isoniazid-resistance. We determined thein-vitrorifampicin survival fraction by minimum duration of killing assay in isoniazid susceptible (IS, n=119) and resistant (IR, n=84)M. tuberculosisisolates. Then we correlated the rifampicin tolerance with bacterial growth, rifampicin minimum inhibitory concentrations (MICs) and isoniazid-resistant mutations. The longitudinal IR isolates collected from patients were analyzed for changes in rifampicin tolerance and associated emergence of genetic variants. The median duration of rifampicin exposure reducing theM. tuberculosissurviving fraction by 90% (minimum duration of killing-MDK90) increased from 1.23 (95%CI 1.11; 1.37) and 1.31 (95%CI 1.14; 1.48) to 2.55 (95%CI 2.04; 2.97) and 1.98 (95%CI 1.69; 2.56) days, for IS and IR respectively, during 15 to 60 days of incubation. This indicated the presence of fast and slow growing tolerant sub-populations. A range of 6 log10-fold survival fraction enabled classification of tolerance as low, medium or high and revealed IR association with increased tolerance with faster growth (OR=2.68 for low vs. medium, OR=4.42 for low vs. high,P-trend=0.0003). The high tolerance in IR isolates was specific to those collected during rifampicin treatment in patients and associated with bacterial genetic microvariants. Furthermore, the high rifampicin tolerant IR isolates have survival potential similar to multi-drug resistant isolates. These findings suggest that IR tuberculosis needs to be evaluated for high rifampicin tolerance to improve treatment regimen and prevent the risk of MDR-TB emergence.
Long-term evolution ofStreptococcus mitisandStreptococcus pneumoniaeleads to higher genetic diversity within rather than between human populations
Authors: Davison Charlotte , Tallman Sam , de Ste-Croix Megan , Antonio Martin , Oggioni Marco R. , Kwambana-Adams Brenda , Freund Fabian , Beleza Sandra 
Published: November 2023

AbstractEvaluation of the apportionment of genetic diversity of bacterial commensals within and between populations is an important step in the characterization of their evolutionary potential. Recent studies showed a correlation between the genomic diversity of human commensal strains and that of their host, but the strength of this correlation and of the geographic structure among populations is a matter of debate. Here, we studied the genomic diversity and evolution of the phylogenetically related oronasopharingeal healthy-carriageStreptococcus mitisandStreptococcus pneumoniae, whose lifestyles range from stricter commensalism to high pathogenic potential. A total of 119S. mitisgenomes showed higher within- and among-host variation than 810S. pneumoniaegenomes in European, East Asian and African populations. Summary statistics of the site-frequency spectrum for synonymous and non-synonymous variation and ABC modelling showed this difference to be due to higher historical population effective size (Ne) inS. mitis,whose genomic variation been maintained close to mutation-drift equilibrium across (at least many) generations, whereasS. pneumoniaehas been expanding from a smaller ancestral population and has been subjected to adaptive selection. Strikingly, both species show limited differentiation among populations. As genetic differentiation is inversely proportional to the product of effective population size and migration rate (Nem),we argue that largeNehave led to similar differentiation patterns, even ifmis very low forS. mitis. We conclude that more diversity within than among human populations and limited population differentiation must be common features of the human microbiome due to largeNe.
Towards new AQP4 inhibitors: ORI-TRN-002
Authors: Thormann Michael , Traube Nadine , Yehia Nasser , Koestler Roland , Galabova Gergana , MacAulay Nanna , Toft-Bertelsen Trine L. 
Published: November 2023

AbstractCerebral edema is a life-threatening condition that can cause permanent brain damage or death if left untreated. Existing therapies aim at mitigating the associated elevated intracranial pressure, yet they primarily alleviate pressure rather than preventing edema formation. Prophylactic anti-edema therapy necessitates novel drugs targeting edema formation. Aquaporin 4 (AQP4), an abundantly expressed water pore in mammalian glia and ependymal cells, has been proposed to be involved in cerebral edema formation. A series of novel compounds have been tested for their potential inhibitory effects on AQP4. However, selectivity, toxicity, functional inhibition, sustained therapeutic concentration, and delivery into the central nervous system are major challenges. Employing extensive DFT calculations, we identified a previously unreported thermodynamically stable tautomer of the recently identified AQP4-specific inhibitor TGN-020. This novel form, featuring a distinct hydrogen bonding pattern, served as a template for a COSMOsim-3D based virtual screen of proprietary compounds from Origenis™. The screening identified ORI-TRN-002, an electronic homologue of TGN-020, demonstrating high solubility and low protein binding. Evaluating ORI-TRN-002 on AQP4-expressingXenopus laevisoocytes using a high-resolution volume recording system revealed an IC50of 2.9 ± 0.6 μM, establishing it as a novel AQP4 inhibitor. ORI-TRN-002 exhibits superior solubility and free fraction limitations compared to other reported AQP4 inhibitors, suggesting its potential as a promising antiedema therapy for treating cerebral edema in the future.
Imaging genetics of language network functional connectivity reveals links with language-related abilities, dyslexia and handedness
Authors: Amelink Jitse S. , Postema Merel C. , Kong Xiang-Zhen , Schijven Dick , Castillo Amaia Carrion , Soheili-Nezhad Sourena , Sha Zhiqiang , Molz Barbara , Joliot Marc , Fisher Simon E. , Francks Clyde 
Published: November 2023

AbstractLanguage is supported by a distributed network of brain regions with a particular contribution from the left hemisphere. A multi-level understanding of this network requires studying its genetic architecture. We used resting-state imaging data from 29,681 participants (UK Biobank) to measure connectivity between 18 left-hemisphere regions involved in multimodal sentence-level processing, as well as their right-hemisphere homotopes, and interhemispheric connections. Multivariate genome-wide association analysis of this total network, based on genetic variants with population frequencies>1%, identified 14 genomic loci, of which three were also associated with asymmetry of intrahemispheric connectivity. Polygenic dispositions to lower language-related abilities, dyslexia and left-handedness were associated with generally reduced leftward asymmetry of functional connectivity. Exome-wide association analysis based on rare, protein-altering variants (frequencies≤1%) suggested 7 additional genes. These findings shed new light on genetic contributions to language network organization and related behavioural traits.
Pyroptosis leads to loss of centrosomal integrity in macrophages
Authors: Bai Siyi , Martin-Sanchez Fatima , Brough David , Lopez-Castejon Gloria 
Published: November 2023

AbstractNLRP3 forms a multiprotein inflammasome complex to initiate the inflammatory response when macrophages sense infection or tissue damage, which leads to caspase-1 activation and maturation and release of the inflammatory cytokines interleukin-1β (IL-1β) and IL-18, and Gasdermin-D (GSDMD) mediated pyroptosis. NLRP3 inflammasome activity must be controlled as unregulated and chronic inflammation underlies inflammatory and autoimmune diseases. Several findings uncovered that NLRP3 inflammasome activity is under the regulation of centrosome localized proteins such as NEK7 and HDAC6, however, whether the centrosome composition or structure is altered during the inflammasome activation is not known. Our data show that levels of the centrosomal scaffold protein pericentrin (PCNT) are reduced upon NLRP3 inflammasome activation via different activators in human and murine macrophages. PCNT loss occurs in the presence of membrane stabilizer punicalagin, suggesting this is not a consequence of membrane rupture. We found that PCNT loss is dependent on NLRP3 and active caspases as MCC950 and pan caspase inhibitor ZVAD prevent its degradation. Moreover, caspase-1 and GSDMD are both required for this NLRP3-mediated PCNT loss because absence of caspase-1 or GSDMD triggers an alternative regulation of PCNT via its cleavage by caspase-3 in response to nigericin stimulation. PCNT degradation occurs in response to nigericin, but also other NLRP3 activators including lysomotropic agent L-Leucyl-L-Leucine methyl ester (LLOMe) and hypotonicity. Our work reveals that the NLRP3 inflammasome activation affects centrosome composition and structure which may deepen our understandings of how activated NLRP3 inflammasomes are involved in the pathogenesis of inflammatory diseases.
Comparative single-cell transcriptomic atlases reveal conserved and divergent features of drosophilid central brains
Authors: Lee Daehan , Benton Richard 
Published: November 2023

AbstractTo explore how brains change upon species evolution, we generated single-cell transcriptomic atlases of the central brains of three closely-related but ecologically-distinct drosophilids: the generalistsDrosophila melanogasterandDrosophila simulans, and the noni fruit specialistDrosophila sechellia. The global cellular composition of these species’ central brains is well-conserved, but we predicted a few cell types (perineurial glia, sNPF and Dh44 peptidergic neurons) with divergent frequencies. Gene expression analysis revealed that distinct cell types within the central brain evolve at different rates and patterns; notably, glial cell types exhibit the greatest divergence between species. Compared toD. melanogaster, the cellular composition and gene expression patterns of the central brain inD. sechelliadisplay greater deviation than those ofD. simulans- despite their similar phylogenetic distance fromD. melanogaster- that the distinctive ecological specialization ofD. sechelliais reflected in the structure and function of its brain. Expression changes inD. sechelliaencompass metabolic and ecdysone signaling genes, suggestive of adaptations to its novel ecological demands. Additional single-cell transcriptomic analysis onD. sechelliarevealed genes and cell types responsive to dietary supplement with noni, pointing to glia as sites for both physiological and genetic adaptation to novel conditions. Our atlases represent the first comparative analyses of “whole” central brains, and provide a comprehensive foundation for studying the evolvability of nervous systems in a well-defined phylogenetic and ecological framework.
Utilization of the genetically encoded calcium indicator Salsa6F in cardiac applications
Authors: Márquez-Nogueras Karla M. , Bovo Elisa , Cao Quan , Zima Aleksey V. , Kuo Ivana Y. 
Published: November 2023

AbstractCalcium signaling is a critical process required for cellular mechanisms such as cardiac contractility. The inability of the cell to properly activate or regulate calcium signaling can lead to contractile dysfunction. In isolated cardiomyocytes, calcium signaling has been primarily studied using calcium fluorescent dyes, however these dyes have limited applicability to whole organs. Here, we crossed the Salsa6f mouse which expresses a genetically encoded ratiometric cytosolic calcium indicator with a cardiomyocyte specific inducible cre to temporally-induce expression and studied cytosolic calcium transients in isolated cardiomyocytes and modified Langendorff heart preparations. Isolated cardiomyocytes expressing Salsa6f or Fluo-4AM loaded were compared. We also crossed the Salsa6f mouse with a floxed Polycystin 2 (PC2) mouse to test the feasibility of using the Salsa6f mouse to measure calcium transients in PC2 heterozygous or homozygous knock out mice. Although there are caveats in the applicability of the Salsa6f mouse, there are clear advantages to using the Salsa6f mouse to measure whole heart calcium signals.
YY1 binding is a gene-intrinsic barrier to Xist-mediated gene silencing
Authors: Bowness Joseph S , Almeida Mafalda , Nesterova Tatyana B , Brockdorff Neil 
Published: November 2023

AbstractX chromosome inactivation (XCI) in mammals is mediated by Xist RNA which functions incisto silence genes on a single X chromosome in XX female cells, thereby equalising levels of X-linked gene expression relative to XY males. XCI progresses over a period of several days, with some X-linked genes silencing faster than others. Chromosomal location of a gene is an important determinant of silencing rate, but uncharacterised gene-intrinsic features also mediate resistance or susceptibility to silencing. In this study, we integrate time-course data of gene silencing and decreasing inactive X (Xi) chromatin accessibility in mouse embryonic stem cell lines with an inducibleXistallele (iXist-ChrX mESCs). Our analysis reveals that motifs bound by the transcription factor YY1 are associated with persistently accessible regulatory elements, including many promoters and enhancers of slow-silencing genes. We further show that YY1 is evicted relatively slowly from target sites on Xi, and that silencing of X-linked genes is increased upon YY1 degradation. Together our results indicate that YY1 acts as barrier to Xist-mediated silencing that is removed only at late stages of the XCI process.
Cadherins modulate the self-organizing potential of gastruloids
Authors: Mayran Alexandre , Kolly Dominique , Lopez-Delisle Lucille , Romaniuk Yuliia , Leonardi Maxine , Cossy Anne-Catherine , Lacroix Theo , Amândio Ana Rita , Osteil Pierre , Duboule Denis 
Published: November 2023

ABSTRACTGastruloids have recently emerged as an efficient four-dimensional model for studying some aspects of post-implantation embryonic patterning. They undergo gastrulation-like processes leading to the self-organization into highly reproducible biological objects. Here, we sought to uncover the molecular and cellular mechanism underlying this remarkable property. We report that self-organization competence is associated with a cell-specific coordination of a Cadherin switch. We find that N-Cadherin hinders gastruloids morphogenetic competence, for its inactivation leads to the formation of trunk-like structures in absence of extra-cellular matrix analogues. In contrast,E-Cadherinrepression bySnai1is critical for self-organization:Snai1establishes a cell-specific repressive pace by triggering the repression of a pluripotency-associated transcription program and its chromatin landscape, thus allowing a proper transition from E-to N-Cadherin to occur. Altogether, this work establishes a molecular mechanism that integrates the exit from pluripotency and the pace of cell differentiation, leading to the observed self-organizing potential of gastruloids.