bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection and characterization of circulating microvesicles containing Shiga toxin type 2 (Stx2) in a rat model of Hemolytic Uremic Syndrome
Authors: Sacerdoti Flavia , Gomez Fernando , Jancic Carolina , Moretton Marcela A. , Chiappetta Diego A. , Ibarra Cristina , Amaral María Marta 
Published: February 2022

AbstractShiga toxin (Stx) producing Escherichia coli (STEC) are foodborne pathogens that release Stx and may develop Hemolytic Uremic Syndrome (HUS). Stx causes endothelial cell damage and leads to platelets deposition and thrombi formation within the microvasculature. It has been described that Stx activates blood cells and induces the shedding of proinflammatory and prothrombotic microvesicles (MVs) containing the toxin. In this sense, it has been postulated that MVs containing Stx2 (MVs-Stx2+) can contribute to the physiopathology of HUS, allowing Stx to reach the target organs and evading the immune system. In this work, we propose that circulating MVs-Stx2+ can be a potential biomarker for the diagnosis and prognosis of STEC infections and HUS progression. In this regard, we developed a rat HUS model by the intreperitoneal injection of a sublethal dose of Stx2 and observed: decrease in body weight, increase of creatinine and urea levels, decrease of creatinine clearance and histological renal damages. After characterization of renal damages we investigated circulating total MVs and MVs-Stx2+ by flow cytometry at different times after Stx2 injection. Additionally, we evaluated the correlation of biochemical parameters such as creatinine and urea in plasma with MVs-Stx2+. As a result, we found a significant circulation of Mvs-Stx2+ at 96 hours after Stx2 injection, nevertheless no correlation with creatinine and urea plasma levels were detected. Our results suggest that MVs-Stx2+ may be an additional biomarker for the characterization and diagnosis of HUS progression. Further analysis is required in order to validate MVs-Stx2+ as biomarker of the disease.
The brassinosteroid biosynthesis gene TaD11-2A controls grain size and its elite haplotype improves wheat grain yields
Authors: Xu Huiyuan , Sun Han , Dong Jiajin , Ma Chengxue , Li Jingxue , Li Zhuochun , Wang Yihuan , Ji Junqi , Hu Xinrong , Wu Meihui , Zhao Chunhua , Qin Ran , Wu Jiajie , Ni Fei , Cui Fa , Wu Yongzhen 
Published: February 2022

AbstractBrassinosteroids (BRs) control many important agronomic traits, therefore the manipulation of BR components could improve crop productivity and performance. However, the potential effects of BR-related genes on yield-related traits and stress tolerance in wheat (Triticum aestivum L.) remain poorly understood. Here, we identified TaD11 genes in wheat (rice D11 orthologs) that encoded enzymes involved in BR biosynthesis. TaD11 genes were highly expressed in roots (Zadoks scale: Z11) and grains (Z75), while expression was significantly suppressed by exogenous BR (24-epiBL). Ectopic expression of TaD11-2A rescued the abnormal panicle structure and plant height (PH) of the cpb1 mutant, and also increased endogenous BR levels, resulting in improved grain yields and grain quality in rice. Natural variations in TaD11-2A were associated with significant differences in yield-related traits, including PH, grain width (GW), 1000-grain weight (TGW), and grain yield per plant (GYPP), and its favorable haplotype, TaD11-2A-HapI was subjected to positive selection during wheat breeding. Additionally, TaD11-2A influenced root length and salt tolerance in rice and wheat at seedling stages. These results indicated the important role of BR TaD11 biosynthetic genes in controlling grain size and root length, and also highlighted their potential in the molecular biological analysis of wheat.HighlightThe brassinosteroid biosynthesis gene TaD11-2A regulates grain size and root length and its haplotype favorably improves grain yields and salt tolerance in wheat.
Bayesian inference of phylogeny is robust to substitution model over-parameterization
Authors: Fabreti Luiza Guimarães , Höhna Sebastian 
Published: February 2022

AbstractModel selection aims to choose the most adequate model for the statistical analysis at hand. The model must be complex enough to capture the complexity of the data but should be simple enough to not overfit. In phylogenetics, the most common model selection scenario concerns selecting an appropriate substitution and partition model for sequence evolution to infer a phylogenetic tree. Here we explored the impact of substitution model over-parameterization in a Bayesian statistical framework. We performed simulations under the simplest substitution model, the Jukes-Cantor model, and compare posterior estimates of phylogenetic tree topologies and tree length under the true model to the most complex model, the GTR+Γ+I substitution model, including over-splitting the data into additional subsets (i.e., applying partitioned models). We explored four choices of prior distributions: the default substitution model priors of MrBayes, BEAST2 and RevBayes and a newly devised prior choice (Tame). Our results show that Bayesian inference of phylogeny is robust to substitution model over-parameterization but only under our new prior settings. All three default priors introduced biases for the estimated tree length. We conclude that substitution and partition model selection are superfluous steps in Bayesian phylogenetic inference pipelines if well behaved prior distributions are applied.
Experience-dependent learning and myelin plasticity in individuals with stroke
Authors: Rubino Cristina , Larssen Beverley C. , Chiu Larissa K. , Liu Hanwen , Kraeutner Sarah N. , Mahendran Niruthikha , Denyer Ronan , Lakhani Bimal , Borich Michael R. , Laule Cornelia , Boyd Lara A. 
Published: February 2022

AbstractBackgroundInjury to brain myelin disrupts motor performance and learning, however it is not clear if myelination is modulated by skilled motor practice or by recovery after stroke. Multi-component relaxation imaging can be used to measure water trapped between myelin bilayers which is expressed as myelin water fraction.The purpose of this study was to examine the effect of experience-dependent learning on myelin plasticity using multi-component relaxation imaging in individuals with stroke.MethodsThirty-two individuals with chronic stroke (>6 months) and twenty-seven healthy controls completed 4 weeks of skilled motor practice using a complex, gamified reaching task. Multi-component relaxation imaging-derived myelin water fraction was obtained before and after training. Seven brain regions associated with motor learning and sensorimotor function were investigated.ResultsAll participants improved task-specific reaching movements after training. In individuals with stroke: 1) pre-training myelin water fraction was lower in motor brain regions but higher in the cingulum compared to controls, 2) pre-training myelin water fraction in motor and sensorimotor regions was positively associated with learning rate, and 3) myelin water fraction was increased in the ipsilesional (contralateral to the trained arm) superior longitudinal fasciculus following skilled motor practice.ConclusionsFindings indicate that after stroke, myelin water fraction is related to measures of motor learning and modulated by 4 weeks of skilled motor practice with the paretic limb. Myelin water fraction can be enhanced in the chronic stage of stroke and may be an important target for upper-limb motor recovery.
Species-Specific Formation of Paraspeckles in Intestinal Epithelium Revealed by Characterization ofNEAT1in Naked Mole-rat
Authors: Yamada Akihiro , Toya Hikaru , Tanahashi Mayuko , Kurihara Misuzu , Mito Mari , Iwasaki Shintaro , Kurosaka Satoshi , Takumi Toru , Fox Archa , Kawamura Yoshimi , Miura Kyoko , Nakagawa Shinichi 
Published: February 2022

AbstractParaspeckles are mammalian-specific nuclear bodies built on the long noncoding RNANEAT1_2. The molecular mechanisms of paraspeckle formation have been mainly studied using human or mouse cells, and it is not known if the same molecular components are involved in the formation of paraspeckles in other mammalian species. We thus investigated the expression pattern ofNEAT1_2in naked mole-rats (nNEAT1_2), which exhibit extreme longevity and lower susceptibility to cancer. In the intestine, nNEAT1_2is widely expressed along the entire intestinal epithelium, which is different from the expression of mNeat1_2, that is restricted to the cells of the distal tip in mice. Notably, the expression of FUS, a FET family RNA binding protein, essential for the formation of paraspeckles both in humans and mice, was absent in the distal part of the intestinal epithelium in naked mole-rats. Instead, mRNAs of other FET family proteins EWSR1 and TAF15 were expressed in the distal region. Exogenous expression of these proteins in Fus-deficient murine embryonic fibroblast cells rescued the formation of paraspeckles. These observations suggest that nNEAT1_2recruits different set of RNA binding proteins in a cell type-specific manner during the formation of paraspeckles in different organisms.
γ-aminobutyrate (GAB) functions as a bioenergetic and signaling gatekeeper to control T cell inflammation
Authors: Kang Siwen , Liu Lingling , Wang Tingting , Cannon Matthew , Lin Penghui , Fan Teresa W.-M. , Scott David A. , Wu Hsin-Jung Joyce , Lane Andrew N. , Wang Ruoning 
Published: February 2022

Abstractγ-Aminobutyrate (GAB) is the biochemical form of γ-aminobutyric acid (GABA) at physiological pH and functions as an essential neurotransmitter in the vertebrate’s central nervous system (CNS). Growing evidence suggests that GAB may also mediate intercellular communications to shape various physiological processes, including immune response. Beyond acting as a paracrine signaling molecule, how GAB metabolism is controlled to exert many distinct functions remains elusive. By an integrated analysis of the extracellular metabolome, stable isotope traced metabolic pathway analysis, and metabolic transcriptome, we revealed that GAB is one of the most abundant metabolites produced through glutamine and arginine catabolism in CD4+ T help 17 (TH17) and induced T regulatory (iTreg) cells. GAB functions as a bioenergetic and signaling gatekeeper by reciprocally controlling pro-inflammatory TH17 cell and anti-inflammatory iTreg cell differentiation through distinct mechanisms. The expression of 4-aminobutyrate aminotransferase (ABAT) funnels GAB, as an anaplerotic substrate, into the TCA cycle to maximize carbon allocation in promoting TH17 cell differentiation. By contrast, the absence of ABAT activities in iTreg cells enables GAB exporting to the extracellular environment and acting as an autocrine signaling metabolite to promote iTreg cell differentiation. Accordingly, genetic or pharmacological ablation of ABAT activity in T cells confers protection against experimental autoimmune encephalomyelitis (EAE) pathogenic progression. Conversely, genetic ablation of GABA(A) receptor in T cells deteriorates EAE pathogenic progression. Collectively, our results suggest that the cell-autonomous control exerted by GAB on CD4+ T cell is bimodal and consists of the sequential action of two discrete processes, ABAT–dependent mitochondrial anaplerosis and the receptor-dependent autocrine signaling response, both of which are required for a properly controlled T cell-mediated inflammation.
Duplicated binding site for RIC-3 in 5-Hydroxytryptamine Receptors Subtype 3
Authors: Do Hoa Quynh , Jansen Michaela 
Published: February 2022

AbstractSerotonin or 5-hydroxytryptamine receptors type 3 (5-HT3) belong to the family of pentameric ligand-gated ion channels (pLGICs), which also includes other neurotransmitter-gated ion channels such as nicotinic acetylcholine receptors (nAChRs). pLGICs have been long-standing therapeutic targets for psychiatric disorders such as anxiety, schizophrenia, and addiction, and neurological diseases like Alzheimer’s and Parkinson’s disease. Due to structural conservation and significant sequence similarities of pLGICs’ extracellular and transmembrane domains across the more than 40 subunits found in humans, clinical trials for drug candidates targeting these two domains have been largely hampered by undesired effects mediated by off-subunit modulation. With the present study, we explore the interaction interface of the 5-HT3Aintracellular domain (ICD) with the resistance to inhibitors of choline esterase (RIC-3) protein. Previously, we have shown that RIC-3 directly interacts with the ICD of 5-HT3Asubunits. Using a sequential deletion approach, we identified the L1-MX segment of the ICD fused to maltose-binding protein as sufficient for the interaction. For the present study, synthetic L1-MX-based peptides, Ala-scanning, and a pull-down assay identified positions W347, R349, and L353 as critical for binding to RIC-3. In complementary studies with full-length 5-HT3Asubunits, the identified Ala substitutions reduced the modulation of functional surface expression by co-expression of RIC-3. Additionally, we found and characterized a duplication of the binding motif at the transition between the ICD MA-helix and transmembrane segment M4. Analogous Ala substitutions at W447, R449, and L454 disrupt MAM4-peptide RIC-3 interactions and reduce modulation of functional surface expression. In summary we identify two binding sites for RIC-3 with a shared duplicated motif in 5-HT3Asubunits, one in the MX-helix and one at the MAM4-helix transition.
Contribution of spontaneous mutations to quantitative and molecular variation at the highly repetitive rDNA locus in yeast
Authors: Sharp Nathaniel P. , Smith Denise R. , Driscoll Gregory , Sun Kexin , Vickerman Catherine M. , Martin Sterling C.T. 
Published: February 2022

AbstractThe ribosomal DNA array inSaccharomyces cerevisiaeconsists of many tandem repeats whose copy number is believed to be functionally important but highly labile. Regulatory mechanisms have evolved to maintain copy number by directed mutation, but how spontaneous variation at this locus is generated and selected has not been well characterized. We applied a mutation accumulation approach to quantify the impacts of mutation and selection on this unique genomic feature across hundreds of mutant strains. We find that mutational variance for this trait is relatively high, and that un-selected mutations throughout the genome can disrupt copy number maintenance. In consequence, copy number generally declines, consistent with a model of regulation where copy number is normally increased when low. This pattern holds across ploidy levels and strains in the standard lab environment, but differs under some stressful conditions. We identify several alleles, gene categories and genomic features that likely affect copy number, including aneuploidy for chromosome XII. Copy number change is associated with reduced growth in diploids, consistent with stabilizing selection. Levels of standing variation in copy number are well predicted by a balance between mutation and stabilizing selection, suggesting this trait is not subject to strong diversifying selection in the wild. The rate and spectrum of point mutations within the rDNA locus itself is distinct from the rest of the genome, and predictive of polymorphism locations. Our findings help differentiate the roles of mutation and selection and indicate that spontaneous mutation patterns shape several aspects of ribosomal DNA evolution.
An NKX-COUP-TFII genomic code for mucosal vascular addressins and organ morphogenesis
Authors: Dinh Thanh Theresa , Xiang Menglan , Rajaraman Anusha , Wang Yongzhi , Salazar Nicole , Roper Walter , Rhee Siyeon , Brulois Kevin , O’Hara Ed , Kiefel Helena , Dinh Truc , Bi Yuhan , Gonzalez Dalila , Bao Evan , Red-Horse Kristy , Balogh Peter , Gábris Fanni , Gaszner Balázs , Berta Gergely , Pan Junliang , Butcher Eugene C. 
Published: February 2022

SUMMARYImmunoglobulin family and carbohydrate vascular addressins encoded byMadcam1andSt6gal1control lymphocyte homing into intestinal tissues, regulating immunity and inflammation. The addressins are developmentally programmed to decorate endothelial cells lining gut post-capillary and high endothelial venules, providing a prototypical example of organ- and segment-specific endothelial specialization. We identify conserved NKX-COUP-TFII composite elements (NCCE) in regulatory regions ofMadcam1andSt6gal1that bind intestinal homeodomain protein NKX2-3 cooperatively with venous nuclear receptor COUP-TFII to activate transcription. TheMadcam1element also integrates repressive signals from arterial/capillary Notch effectors. Pan-endothelial COUP-TFII overexpression induces ectopic addressin expression in NKX2-3+capillaries, while NKX2-3 deficiency abrogates expression by HEV. Phylogenetically conserved NCCE are enriched in genes involved in neuron migration and morphogenesis of the heart, kidney, pancreas and other organs. Our results define a genomic address code for targeted expression of mucosal vascular addressins and implicate NCCE in fundamental processes in cell specification and development.
A statistical approach for identifying primary substrates of ZSWIM8-mediated microRNA degradation in small-RNA sequencing data
Authors: Wang Peter Y. , Bartel David P. 
Published: February 2022

ABSTRACTBackgroundOne strategy for identifying targets of a regulatory factor is to perturb the factor and use high-throughput RNA sequencing to examine the consequences. However, distinguishing direct targets from secondary effects and experimental noise can be challenging when confounding signal is present in the background at varying levels.ResultsHere, we present a statistical modeling strategy to identify microRNAs (miRNAs) that are primary substrates of target-directed miRNA degradation (TDMD) mediated by ZSWIM8. This method uses a bi-beta-uniform mixture (BBUM) model to separate primary from background signal components, leveraging the expectation that primary signal is restricted to upregulation and not downregulation upon loss of ZSWIM8. The BBUM model strategy retained the apparent sensitivity and specificity of the previous ad hoc approach but was more robust against outliers, achieved a more consistent stringency, and could be performed using a single cutoff of false discovery rate (FDR).ConclusionsWe developed the BBUM model, a robust statistical modeling strategy to account for background secondary signal in differential expression data. It performed well for identifying primary substrates of TDMD and should be useful for other applications in which the primary regulatory targets are only upregulated or only downregulated. The BBUM model, FDR-correction algorithm, and significance-testing methods are available as an R package athttps://github.com/wyppeter/bbum.
Assessing Protein Homology Models with Docking Reproducibility
Authors: Plonski Alexander P. , Reed Scott M. 
Published: February 2022

AbstractResults of the most recent Critical Assessment of Protein Structure (CASP) competition demonstrate that protein backbones can be predicted with very high accuracy. In particular, the artificial intelligence methods of AlphaFold 2 from DeepMind were able to produce structures that were similar enough to experimental structures that many described the problem of protein prediction solved. However, for such structures to be used for drug docking studies requires precision in the placement of side chain atoms as well. Here we built a library of 1334 small molecules and examined how reproducibly they bound to the same site on a protein using QuickVina-W, a branch of the program Autodock that is optimized for blind searches. We discovered that the higher the backbone quality of the homology model the greater the similarity between the small molecule docking to the experimental and modeled structures. Furthermore, we found that specific subsets of this library were particularly useful for identifying small differences between the best of the best modeled structures. Specifically, when the number of rotatable bonds in the small molecule increased, differences in binding sites became more apparent.
Sequential action of a tRNA base editor in conversion of cytidine to pseudouridine
Authors: Kimura Satoshi , Srisuknimit Veerasak , McCarty Kacie , Dedon Peter C. , Kranzusch Philip J. , Waldor Matthew K. 
Published: February 2022

SummaryPost-transcriptional RNA editing modulates gene expression in a condition-dependent fashion. We recently discovered C-to-Ψ editing in Vibrio cholerae tRNA. Here, we characterize the biogenesis, regulation, and functions of this previously undescribed RNA editing process. We show that an enzyme, TrcP, mediates the editing of C-to-U followed by the conversion of U to Ψ, consecutively. AlphaFold-2 predicts that TrcP consists of two globular domains, including a novel cytidine deaminase and a pseudouridylase, along with a long helical domain. The latter domain tethers tRNA substrates during both the C-to-U editing and pseudouridylation, likely enabling a substrate channeling mechanism for efficient catalysis all the way to the terminal product. C-to-Ψ editing both requires and suppresses other modifications, creating an interdependent network of modifications in the tRNA anticodon loop that facilitates coupling of tRNA modification states to iron availability. Our findings provide mechanistic insights into an RNA editing process that likely promotes environmental adaptation.
A protein semisynthesis-based strategy to probe the impact of site-specific serine ADP-ribosylation on linker histone function
Authors: Tashiro Kyuto , Mohapatra Jugal , Brautigam Chad A. , Liszczak Glen 
Published: February 2022

AbstractRecently developed chemical and enzyme-based technologies to install serine ADP-ribosylation onto synthetic peptides have enabled new approaches to study PARP biology. Here, we establish a generalizable strategy to prepare ADP-ribosylated peptides that are compatible with N-terminal, C-terminal and sequential protein ligation reactions. Two unique protein-assembly routes are employed to generate full-length linker histone constructs that are homogenously ADP-ribosylated at known DNA damage-dependent modification sites. We found that serine mono-ADP-ribosylation is sufficient to alleviate linker histone-dependent chromatin compaction, and that this effect is amplified by ADP-ribose chain elongation. Our work will greatly expand the scope of ADP-ribose-modified proteins that can be constructed via semisynthesis, which is rapidly emerging as a robust approach to elucidate the direct effects that site-specific serine mono- and poly-ADP-ribosylation have on protein function.