bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure-based discovery of inhibitors of the SARS-CoV-2 Nsp14N7-methyltransferase
Authors: Singh Isha , Li Fengling , Fink Elissa , Chau Irene , Li Alice , Rodriguez-Hernández Annía , Glenn Isabella , Zapatero-Belinchón Francisco J. , Rodriguez Mario , Devkota Kanchan , Deng Zhijie , White Kris , Wan Xiaobo , Tolmachova Nataliya A. , Moroz Yurii S. , Kaniskan H. Ümit , Ott Melanie , Gastía-Sastre Adolfo , Jin Jian , Fujimori Danica Galonić , Irwin John J. , Vedadi Masoud , Shoichet Brian K. 
Published: January 2023

AbstractAn under-explored target for SARS-CoV-2 is non-structural protein 14 (Nsp14), a crucial enzyme for viral replication that catalyzes the methylation ofN7-guanosine of the viral RNA at 5′-end; this enables the virus to evade the host immune response by mimicking the eukaryotic post-transcriptional modification mechanism. We sought new inhibitors of the S-adenosyl methionine (SAM)-dependent methyltransferase (MTase) activity of Nsp14 with three large library docking strategies. First, up to 1.1 billion make-on-demand (“tangible”) lead-like molecules were docked against the enzyme’s SAM site, seeking reversible inhibitors. On de novo synthesis and testing, three inhibitors emerged with IC50values ranging from 6 to 43 μM, each with novel chemotypes. Structure-guided optimization andin vitrocharacterization supported their non-covalent mechanism. In a second strategy, docking a library of 16 million tangible fragments revealed nine new inhibitors with IC50values ranging from 12 to 341 μM and ligand efficiencies from 0.29 to 0.42. In a third strategy, a newly created library of 25 million tangible, virtual electrophiles were docked to covalently modify Cys387 in the SAM binding site. Seven inhibitors emerged with IC50values ranging from 3.2 to 39 μM, the most potent being a reversible aldehyde. Initial optimization of a second series yielded a 7 μM acrylamide inhibitor. Three inhibitors characteristic of the new series were tested for selectivity against 30 human protein and RNA MTases, with one showing partial selectivity and one showing high selectivity. Overall, 32 inhibitors encompassing eleven chemotypes had IC50values <50 μM and 5 inhibitors in four chemotypes had IC50values <10 μM. These molecules are among the first non-SAM-like inhibitors of Nsp14, providing multiple starting points for optimizing towards antiviral activity.
Incorporating discovery and replication GWAS into summary data Mendelian randomization studies: A review of current methods and a simple, general and powerful alternative
Authors: Mounier Ninon , Robertson David S. , Kutalik Zoltán , Dudbridge Frank , Bowden Jack 
Published: January 2023

AbstractMendelian Randomization (MR) is a popular method for using genetics to estimate the causal effect of a modifiable exposure on a health outcome. Single Nucleotide Polymorphisms (SNPs) are typically selected for inclusion if they pass a genome-wide significance threshold in order to guarantee that they are strong genetic instruments, but this also induces Winner’s curse, as SNP-exposure associations tend to be overestimated. In this paper, we consider how to combine SNP-exposure data from discovery and replication samples using two-sample and three-sample approaches to best account for Winner’s curse, weak instrument bias, and pleiotropy within a summary data MR framework, using only GWAS summary statistics. After reviewing several existing methods, that often correct for Winner’s curse at the individual SNP level, we propose a simple alternative based on the technique of regression calibration that enacts a global correction to the causal effect estimate directly. This approach does not only correct for Winner’s curse, but also simultaneously accounts for weak instruments bias. Regression calibration can be used with a wide range of existing MR methods, including pleiotropy-robust methods such as median-based and mode-based estimators. Extensive simulations and real data examples are used to illustrate the utility of the new approach. Software is provided for users to implement the method in practice.Author SummaryMendelian randomization is a method to explore causation in health research which exploits the random inheritance of genes from parents to offspring as a ‘natural experiment’. It attempts to quantify the effect of intervening and modifying a health exposure, such as a person’s body mass, on a downstream outcome such as blood pressure. Causal estimates obtained using this method can be strongly influenced by the set of genes used, or more specifically, the rationale used to select them. For example, selecting only genes that are strongly associated with the health exposure can induce bias due to the ‘Winner’s curse’. Unfortunately, using genes with a small association can lead to so-called ‘weak instrument’ bias leading to a no-win paradox. In this paper, we present a novel approach based on the technique of regression calibration to de-bias causal estimates in an MR study. Our approach relies on the use of two independent samples for the exposure (discovery and replication) to estimate the amount of bias that is expected for a specific set of genes, so that causal estimates can be re-calibrated accordingly. We use extensive simulations and applied examples to compare our approach to current methods and provide software for researchers to implement our approach in future studies.
iTie controls intestinal tolerance through suppressing the NLRP6 inflammasome
Authors: Qin Xiwen , Zhu Fangrui , Li Weitao , Wang Shuo , Xia Pengyan 
Published: January 2023

AbstractIntestines are full of commensal bacteria that possess numerous pathogen-associated molecular patterns. How the intestinal epithelial cells are tolerant to these stimuli under normal conditions is still elusive. Here we show that iTie is expressed in small intestinal enterocytes and its deficiency leads to body weight loss in mice, accompanied by length reduce of small intestines and intestinal villi. The activation of NLRP6 inflammasome is exacerbated uponiTiedeletion. iTie has a higher binding affinity for NLRP6 than NLRP6’s physiological ligand LTA does.iTiedeficiency gives rise to uncontrolled GSDMD activation and pyroptosis of small intestinal enterocytes. Inhibition of GSDMD permeabilization on cell membrane ameliorates the damage caused byiTiedeficiency. iTe’s expression is diminished in small intestines of patients with Crohn’s disease. Our results uncover a self-control system for mouse intestine to tolerate commensal bacteria which might shed new light on the treatment of bowel diseases.
Cryo-EM structure of the endothelin-1-ETB-Gicomplex
Authors: Sano Fumiya K. , Akasaka Hiroaki , Shihoya Wataru , Nureki Osamu 
Published: January 2023

AbstractThe endothelin ETBreceptor is a promiscuous G-protein coupled receptor, activated by vasoactive peptide endothelins. ETBsignaling induces reactive astrocytes in the brain and vasorelaxation in vascular smooth muscle, and thus ETBagonists are expected to be utilized for neuroprotection and improved anti-tumor drug delivery. Here, we report a cryo-electron microscopy structure of the endothelin-1-ETB-Gicomplex at 2.8-Å resolution, with complex assembly stabilized by a newly established method. Comparisons with the inactive ETBreceptor structures revealed how endothelin-1 activates the ETBreceptor. The NPxxY motif, which is essential for G-protein activation, is not conserved in ETB, resulting in a unique structural change upon G-protein activation. As Compared with other GPCR-G-protein complexes, ETBbinds Giat the shallowest position, thus expanding the diversity of G-protein binding. This structural information will facilitate the elucidation of G-protein activation and the rational design of ETB-agonists.
The dietary polyphenol metabolite protocatechuic acid produces acute and sustained effects on hippocampal electrical activity
Authors: Montero-Atalaya Marta , Muñoz-Arnaiz Ricardo , Makarova Julia , Bartolomé Begoña , Moreno-Arribas María-Victoria , Herreras Oscar 
Published: January 2023

AbstractDietary polyphenols and in particular bioavailable metabolites resulting from gut microbiota transformations appear to have beneficial effects in situations of impaired cognition, combatting memory deficits in acute pathological models of neurodegeneration. Modifications to blood flow may underlie the effects of these molecules and although some such metabolites cross the blood-brain barrier, their targets and electrophysiological effects remain unknown. Hence, we explored the systemic and direct effects of protochatechuic acid (PCA) on electrical activity in the hippocampus and cortex of anesthetized female rats, recording evoked and spontaneous high-density field potentials (FPs) to mathematically derive pathway-specific FP generators. We found transient and sustained effects of PCA on evoked activity in the CA1 field, including paradoxical actions on excitatory transmission that depend on the route of administration. Systemic delivery of PCA altered the ongoing activity of some FP generators, albeit with marked inter-animal variation. Interestingly, PCA induced the detachment of infraslow cortico-hippocampal activities over a scale of minutes. These results point to direct actions of polyphenols on cell and network electrical activity, some of which reflect non-specific actions. Thus, dietary-derived polyphenols appear to fulfill neuromodulatory roles, encouraging the search for additional targets to better guide their use in preventing brain pathologies.
Multiparametric senescent cell phenotyping reveals CD24 osteolineage cells as targets of senolytic therapy in the aged murine skeleton
Authors: Doolittle Madison L. , Saul Dominik , Kaur Japneet , Rowsey Jennifer L. , Vos Stephanie J. , Pavelko Kevin D. , Farr Joshua N. , Monroe David G. , Khosla Sundeep 
Published: January 2023

ABSTRACTSenescence drives organismal aging, yet the deep characterization of senescent cellsin vivoremains incomplete. Here, we applied mass cytometry by time-of-flight (CyTOF) using carefully validated antibodies to analyze senescent cells at single-cell resolution. We used multiple criteria to identify senescent mesenchymal cells that were growth arrested and resistant to apoptosis (p16+/Ki67-/BCL-2+; “p16KB” cells). These cells were highly enriched for senescence-associated secretory phenotype (SASP) and DNA damage markers and were strongly associated with age. p16KB cell percentages were also increased in CD24+ osteolineage cells, which exhibited an inflammatory SASP in aged mice and were robustly cleared by both genetic and pharmacologic senolytic therapies. Following isolation, CD24+ skeletal cells exhibited growth arrest, SA-βgal positivity, and impaired osteogenesisin vitro. These studies thus provide a new approach using multiplexed protein profiling by CyTOF to define senescent mesenchymal cellsin vivoand identify a highly inflammatory, senescent CD24+ osteolineage population cleared by senolytics.
Goal-seeking compresses neural codes for space in the human hippocampus and orbitofrontal cortex
Authors: Muhle-Karbe PS , Sheahan H , Pezzulo G , Spiers H , Chien S , Schuck NW , Summerfield C 
Published: January 2023

AbstractHumans can navigate flexibly to meet their goals. Here, we asked how the neural representation of allocentric space is distorted by goal-directed behaviour. Participants navigated an agent to two successive goal locations in a grid world environment comprising four interlinked rooms, with a contextual cue indicating the conditional dependence of one goal location on another. Examining the neural geometry by which room and context were encoded in fMRI signals, we found that map-like representations of the environment emerged in both hippocampus and neocortex. Cognitive maps in hippocampus and orbitofrontal cortices were compressed so that locations cued as goals were coded together in neural state space, and these distortions predicted successful learning. This effect was captured by a computational model in which current and prospective locations are jointly encoded in a place code, providing a theory of how goals warp the neural representation of space in macroscopic neural signals.
End Binding protein 1 promotes specific motor-cargo association in the cell body prior to axonal delivery of Dense Core Vesicles
Authors: Park Junhyun , Miller Kenneth G. , De Camilli Pietro , Yogev Shaul 
Published: January 2023

AbstractAxonal transport is key to neuronal function. Efficient transport requires specific motor-cargo association in the soma, yet the mechanisms regulating this early step remain poorly understood. We found that EBP-1, theC. elegansortholog of the canonical microtubule end binding protein EB1, promotes the specific association between kinesin-3/KIF1A/UNC-104 and Dense Core Vesicles (DCVs) prior to their axonal delivery. Using single-neuron,in vivolabelling of endogenous cargo and EBs, we observed reduced axonal abundance and reduced secretion of DCV cargo, but not other KIF1A/UNC-104 cargo, inebp-1mutants. This reduction could be traced back to fewer exit events from the cell body, where EBP-1 colocalized with the DCV sorting machinery at the trans Golgi, suggesting that this is the site of EBP-1 function. In addition to its microtubule binding CH domain, mammalian EB1 interacted with mammalian KIF1A in an EBH domain dependent manner, and expression of mammalian EB1 or the EBH domain was sufficient to rescue DCV transport inebp-1mutants. Our results suggest a model in which kinesin-3 binding and microtubule binding by EBP-1 cooperate to transiently enrich the motor near sites of DCV biogenesis to promote motor-cargo association. In support of this model, tethering either EBP-1 or a kinesin-3 KIF1A/UNC-104 interacting domain from an unrelated protein to the Golgi restored the axonal abundance of DCV proteins inebp-1mutants. These results uncover an unexpected role for a microtubule associated protein and provide insight into how specific kinesin-3 cargo are delivered to the axon.
A highly conserved neuronal microexon in DAAM1 controls actin dynamics, RHOA/ROCK signaling, and memory formation
Authors: Poliński Patryk , Miret Cuesta Marta , Zamora-Moratalla Alfonsa , Mantica Federica , Cantero-Recasens Gerard , Normanno Davide , Iñiguez Luis P. , Morenilla-Palao Cruz , Ordoño Patricia , Bonnal Sophie , Ellis Jonathan D , Gómez Riera Raúl , De Lagrán Cabredo María Martínez , Fernández-Blanco Álvaro , Rodríguez-Marin Cristina , Permanyer Jon , Fölsz Orsolya , Dominguez-Sala Eduardo , Sierra Cesar , Legutko Diana , Wojnacki José , Musoles Lleo Juan Luis , Muñoz López Francisco José , Blencowe Benjamin J , Herrera Eloisa , Dierssen Mara , Irimia Manuel 
Published: January 2023

AbstractActin cytoskeleton dynamics is critical for nervous system development and function, yet the role of alternative splicing in controlling these processes is poorly understood. A highly conserved subset of neuronal-specific microexons coordinates fundamental aspects of nervous system biology. A subset of these exons is enriched in genes involved in actin cytoskeleton, yet their functions are unknown. Here, we focus on a microexon in DAAM1, a member of the formin-homology-2 (FH2) domain class of proteins, which have diverse functions associated with the reorganization of the actin cytoskeleton. Remarkably, splicing of the microexon extends the linker region of the DAAM1 FH2 domain and leads to qualitative and quantitative changes in actin polymerization. Deletion of the microexon results in neuritogenesis defects and increased calcium influx in differentiated neurons. Moreover, mice harboring the deletion exhibit postsynaptic defects, reduced number of immature dendritic spines, impaired long-term potentiation, and deficits in memory formation. These deficits are associated with increased RHOA/ROCK signaling, pivotal in controlling actin-cytoskeleton dynamics, and were rescued by treatment with a ROCK inhibitor. We thus demonstrate that a conserved neuronal microexon in DAAM1 is critical for controlling actin dynamics through the RHOA/ROCK signaling pathway and is necessary for normal cognitive functioning.
Imputation of label-free quantitative mass spectrometry-based proteomics data using self-supervised deep learning
Authors: Webel Henry , Niu Lili , Nielsen Annelaura Bach , Locard-Paulet Marie , Mann Matthias , Jensen Lars Juhl , Rasmussen Simon 
Published: January 2023

AbstractImputation techniques provide means to replace missing measurements with a value and are used in almost all downstream analysis of mass spectrometry (MS) based proteomics data using label-free quantification (LFQ). Here we demonstrate how collaborative filtering, denoising autoencoders, and variational autoencoders can impute missing values in the context of LFQ at different levels. We applied our method, proteomics imputation modeling mass spectrometry (PIMMS), to an alcohol-related liver disease (ALD) cohort with blood plasma proteomics data available for 358 individuals. Removing 20 percent of the intensities we were able to recover 15 out of 17 significant abundant protein groups using PIMMS-VAE imputations. When analyzing the full dataset we identified 30 additional proteins (+13.2%) that were significantly differentially abundant across disease stages compared to no imputation and found that some of these were predictive of ALD progression in machine learning models. We, therefore, suggest the use of deep learning approaches for imputing missing values in MS-based proteomics on larger datasets and provide workflows for these.
CoVar: A generalizable machine learning approach to identify the coordinated regulators driving variational gene expression
Authors: Roy Satyaki , Sheikh Shehzad Z. , Furey Terrence S. 
Published: January 2023

AbstractNetwork inference is used to model transcriptional, signaling, and metabolic interactions among genes, proteins, and metabolites that identify biological pathways influencing disease pathogenesis. Advances in machine learning (ML)-based inference models exhibit the predictive capabilities of capturing latent patterns in genomic data. Such models are emerging as an alternative to the statistical models identifying causative factors driving complex diseases. We present CoVar, an inference framework that builds upon the properties of existing inference models, to find the central genes driving perturbed gene expression across biological states. We leverage ML-based network inference to find networks that capture the strength of regulatory interactions. Our model first pinpoints a subset of genes, termed variational, whose expression variabilities typify the differences in network connectivity between the control and perturbed data. Variational genes, by being differentially expressed themselves or possessing differentially expressed neighbor genes, capture gene expression variability. CoVar then creates subnetworks comprising variational genes and their strongly connected neighbor genes and identifies core genes central to these subnetworks that influence the bulk of the variational activity. Through the analysis of yeast expression data perturbed by the deletion of the mitochondrial genome, we show that CoVar identifies key genes not found through independent differential expression analysis.
The phenotype and genotype of fermentative microbes
Authors: Hackmann Timothy J. 
Published: January 2023

ABSTRACTFermentation is a major type of metabolism carried out by many organisms. The study of this metabolism cuts across many fields, including cell biology, animal and human health, and biofuel production. Despite this broad importance, there has been no systematic study of fermentation across many organisms. Here we explore the phenotype and genotype of fermentative prokaryotes in order to gain insight into this metabolism. We assembled a dataset containing phenotypic records of 8,350 organisms (type strains) plus 4,355 genomes and 13.6 million genes. Fermentation was widespread, being found in 30% of all organisms and across the tree of life. Fermentative organisms were more likely than non-fermentative ones to have certain phenotypic traits. Some traits (such as oxygen insensitivity) were expected, but others (such as long cells) were surprising. Fermentative organisms also had a distinct genotype, with 9,450 gene functions and 337 metabolic pathways being more common in them. In a related analysis, we identified end products (metabolites) for 1,455 organisms fermenting 100 substrates. We found 55 products were formed in nearly 300 combinations, showing fermentation is more complex than previously realized. Additionally, we built metabolic models for 406 organisms and predicted which products they form. These models did not predict all products accurately, revealing gaps in our knowledge of metabolic pathways. Our study paints a full picture of fermentation while showing there is still much to learn about this type of metabolism. The microbiology community can explore resources in this work with an interactive tool (https://github.com/thackmann/FermentationExplorer).
Distinct subpopulations of D1 medium spiny neurons exhibit unique transcriptional responsiveness to cocaine
Authors: Phillips Robert A. , Tuscher Jennifer J. , Fitzgerald N. Dalton , Wan Ethan , Zipperly Morgan E. , Duke Corey G. , Ianov Lara , Day Jeremy J. 
Published: January 2023

SummaryDrugs of abuse increase extracellular concentrations of dopamine in the nucleus accumbens (NAc), resulting in transcriptional alterations that drive long-lasting cellular and behavioral adaptations. While decades of research have focused on the transcriptional mechanisms by which drugs of abuse influence neuronal physiology and function, few studies have comprehensively defined NAc cell type heterogeneity in transcriptional responses to drugs of abuse. Here, we used single nucleus RNA-seq (snRNA-seq) to characterize the transcriptome of over 39,000 NAc cells from male and female adult Sprague-Dawley rats following acute or repeated cocaine experience. This dataset identified 16 transcriptionally distinct cell populations, including two populations of medium spiny neurons (MSNs) that express the Drd1 dopamine receptor (D1-MSNs). Critically, while both populations expressed classic marker genes of D1-MSNs, only one population exhibited a robust transcriptional response to cocaine. Validation of population-selective transcripts using RNA in situ hybridization revealed distinct spatial compartmentalization of these D1-MSN populations within the NAc. Finally, analysis of published NAc snRNA-seq datasets from non-human primates and humans demonstrated conservation of MSN subtypes across rat and higher order mammals, and further highlighted cell type-specific transcriptional differences across the NAc and broader striatum. These results highlight the utility in using snRNA-seq to characterize both cell type heterogeneity and cell type-specific responses to cocaine and provides a useful resource for cross-species comparisons of NAc cell composition.