bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interplay between bacterial clone and plasmid in the spread of antibiotic resistance genes in the gut: lessons from a temporal study in veal calves
Authors: Massot Méril , Châtre Pierre , Condamine Bénédicte , Métayer Véronique , Clermont Olivier , Madec Jean-Yves , Denamur Erick , Haenni Marisa 
Published: June 2021

AbstractIntestinal carriage of extended spectrum β-lactamase (ESBL)-producing Escherichia coli is a frequent, increasing and worrying phenomenon, but little is known about the molecular scenario and the evolutionary forces at play. We screened 45 veal calves, known to have high prevalence of carriage, for ESBL-producing E. coli on 514 rectal swabs (one randomly selected colony per sample) collected over six months. We characterized the bacterial clones and plasmids carrying blaESBL genes with a combination of genotyping methods, whole genome sequencing and conjugation assays. One hundred and seventy-three ESBL-producing E. coli isolates [blaCTX-M-1 (64.7%), blaCTX-M-14 (33.5%) or blaCTX-M-15 (1.8%)] were detected, belonging to 32 bacterial clones, mostly of phylogroup A. Calves were colonized successively by different clones with a trend in decreasing carriage. The persistence of a clone in a farm was significantly associated with the number of calves colonized. Despite a high diversity of E. coli clones and blaCTX-M-carrying plasmids, few blaCTX-M gene/plasmid/chromosomal background combinations dominated, due to (i) efficient colonization of bacterial clones and/or (ii) successful plasmid spread in various bacterial clones. The scenario ‘clone vs. plasmid spread’ depended on the farm. Thus, epistatic interactions between resistance genes, plasmids and bacterial clones contribute to optimize fitness in specific environments.
Mapping the host protein interactome of non-coding regions in SARS-CoV-2 genome
Authors: Jiang Liuyiqi , Xiao Mu , Liao Qing-Qing , Zheng Luqian , Li Chunyan , Liu Yuemei , Yang Bing , Ren Aiming , Jiang Chao , Feng Xin-Hua 
Published: June 2021

AbstractA deep understanding of SARS-CoV-2-host interactions is crucial to the development of effective therapeutics. The role of non-coding regions of viral RNA (ncrRNAs) has not been scrutinized. We developed a method using MS2 affinity purification coupled with liquid chromatography-mass spectrometry (MAMS) to systematically map the interactome of SARS-CoV-2 ncrRNA in different human cell lines. Integration of the results defined the core and cell-type-specific ncrRNA-host protein interactomes. The majority of ncrRNA-binding proteins were involved in RNA biogenesis, protein translation, viral infection, and stress response. The 5′ UTR interactome is enriched with proteins in the snRNP family and is a target for the regulation of viral replication and transcription. The 3′ UTR interactome is enriched with proteins involved in the cytoplasmic RNP granule (stress granule) and translation regulation. We show that the ORF10 is likely to be a part of 3′ UTR. Intriguingly, the interactions between negative-sense ncrRNAs and host proteins, such as translation initiation factors and antiviral factors, suggest a pathological role of negative-sense ncrRNAs. Moreover, the cell-type-specific interactions between ncrRNAs and mitochondria may explain the differences of cell lines in viral susceptibility. Our study unveils a comprehensive landscape of the functional SARS-CoV-2 ncrRNA-host protein interactome, providing a new perspective on virus-host interactions and the design of future therapeutics.
Mutations within the Open Reading Frame (ORF) including Ochre stop codon of the Surface Glycoprotein gene of SARS-CoV-2 virus erase potential seed location motifs of human non-coding microRNAs
Authors: Goyani Krishna Himmatbhai , Vaniawala Shalin , Mukhopadhyaya Pratap Narayan 
Published: June 2021

AbstractMicroRNA are short and non-coding RNA, 18-25 nucleotides in length. They are produced at the early stage of viral infection. The roles played by cellular miRNAs and miRNA-mediated gene-silencing in the COVID-19 epidemic period is critical in order to develop novel therapeutics. We analysed SARS-CoV-2 Surface Glycoprotein (S) nucleotide sequence originating from India as well as Iran, Australia, Germany, Italy, Russia, China, Japan and Turkey and identified mutation in potential seed location of several human miRNA. Seventy single nucleotide polymorphisms (SNP) were detected in the S gene out of which, 36, 32 and 2 were cases of transitions, transversions and deletions respectively. Eleven human miRNA targets were identified on the reference S gene sequence with a score >80 in the miRDB database. Mutation A845S erased a common binding site of 7 human miRNA (miR-195-5p, miR-16-5p, miR-15b-5p, miR-15a-5p, miR-497-5p, miR-424-5p and miR-6838-5p). A synonymous mutation altered the wild type Ochre stop codon within the S gene sequence (Italy) to Opal thereby changing the seed sequence of miR-511-3p. Similar (synonymous) mutations were detected at amino acid position 659 and 1116 of the S gene where amino acids serine and threonine were retained, abolishing potential seed location for miR-219a-1-3p and miR-20b-3p respectively. The significance of this finding in reference to the strategy to use synthetic miRNA combinations as a novel therapeutic tool is discussed.
A framework for evaluating the performance of SMLM cluster analysis algorithms
Authors: Nieves Daniel J. , Pike Jeremy A. , Levet Florian , Griffié Juliette , Sage Daniel , Cohen Edward A.K. , Sibarita Jean-Baptiste , Heilemann Mike , Owen Dylan M. 
Published: June 2021

AbstractSingle molecule localisation microscopy (SMLM) generates data in the form of Cartesian coordinates of localised fluorophores. Cluster analysis is an attractive route for extracting biologically meaningful information from such data and has been widely applied. Despite the range of developed cluster analysis algorithms, there exists no consensus framework for the evaluation of their performance. Here, we use a systematic approach based on two metrics, the Adjusted Rand Index (ARI) and Intersection over Union (IoU), to score the success of clustering algorithms in diverse simulated clustering scenarios mimicking experimental data. We demonstrate the framework using three analysis algorithms: DBSCAN, ToMATo and KDE, show how to deduce optimal analysis parameters and how they are affected by fluorophore multiple blinking. We propose that these standard conditions and metrics become the basis for future analysis algorithm development and evaluation.
SARS-CoV-2 mRNA Vaccine Induces Robust Specific and Cross-reactive IgG and Unequal Strain-specific Neutralizing Antibodies in Naïve and Previously Infected Recipients
Authors: Narowski Tara M. , Raphel Kristin , Adams Lily E. , Huang Jenny , Vielot Nadja A. , Jadi Ramesh , de Silva Aravinda M. , Baric Ralph S. , Lafleur John E. , Premkumar Lakshmanane 
Published: June 2021

AbstractWith the advance of SARS-CoV-2 vaccines, the outlook for overcoming the global COVID-19 pandemic has improved. However, understanding of immunity and protection offered by the SARS-CoV-2 vaccines against circulating variants of concern (VOC) is rapidly evolving. We investigated the mRNA vaccine-induced antibody responses against the referent WIV04 (Wuhan) strain, circulating variants, and human endemic coronaviruses in 168 naïve and previously infected people at three-time points. Samples were collected prior to vaccination, after the first and after the second doses of one of the two available mRNA-based vaccines. After full vaccination, both naïve and previously infected participants developed comparable robust SARS-CoV-2 specific spike IgG levels, modest IgM and IgA binding antibodies, and varying degrees of HCoV cross-reactive antibodies. However, the strength and frequency of neutralizing antibodies produced in naïve people were significantly lower than in the previously infected group. We also found that 1/3rdof previously infected people had undetectable neutralizing antibodies after the first vaccine dose; 40% of this group developed neutralizing antibodies after the second dose. In all subjects neutralizing antibodies produced against the B.1.351 and P.1 variants were weaker than those produced against the reference and B.1.1.7 strains. Our findings provide support for future booster vaccinations modified to be active against the circulating variants.
The Cx43 Carboxyl-Terminal Mimetic Peptide αCT1 Protects Endothelial Barrier Function in a ZO1 Binding-Competent Manner
Authors: Strauss Randy E. , Mezache Louisa , Veeraraghavan Rengasayee , Gourdie Robert G. 
Published: June 2021

AbstractThe Cx43 CT mimetic peptide, αCT1, originally designed to bind to ZO1 and thereby inhibit Cx43/ZO1 interaction, was used as a tool to probe the role of Cx43/ZO1 association in regulation of epithelial/endothelial barrier function. Using both in vitro and ex vivo methods of barrier function measurement, including Electric Cell-Substrate Impedance Sensing(ECIS), a FITC-dextran transwell permeability assay, and a FITC-dextran cardiovascular leakage protocol involving Langendorff-perfused mouse hearts, αCT1 was found to protect the endothelium from thrombin-induced breakdown in cell-cell contacts. Barrier protection was accompanied by significant remodeling of the F-actin cytoskeleton, characterized by a redistribution of F-actin away from the cytoplasmic and nuclear regions of the cell, towards the endothelial cell periphery, in association with alterations in cellular orientation distribution. In line with observations of increased cortical F-actin, αCT1 upregulated cell-cell border localization of endothelial VE-cadherin, the Tight Junction protein Zonula Occludens 1 (ZO1), and the Gap Junction Protein (GJ) Connexin43 (Cx43). A ZO1-binding-incompetent variant of αCT1, αCT1-I, indicated that these effects on barrier function and barrier-associated proteins, were likely associated with Cx43 CT sequences retaining ability to interact with ZO1. These results implicate the Cx43 CT and its interaction with ZO1, in the regulation of endothelial barrier function, while revealing the therapeutic potential of αCT1 in the treatment of vascular edema.
Yet another mitochondrial genome of the Pacific cupped oyster: the published mitogenome of Alectryonella plicatula (Ostreinae) is based on a misidentified Magallana gigas (Crassostreinae)
Authors: Salvi Daniele , Berrilli Emanuele , Garzia Matteo , Mariottini Paolo 
Published: June 2021

AbstractThe recently published mitochondrial genome of the fingerprint oyster Alectryonella plicatula (Gmelin, 1791) with GenBank accession number MW143047 was resolved in an unexpected phylogenetic position, as sister to the Pacific cupped oyster Magallana gigas (Thunberg, 1793) and share with this species three typical gene duplications that represent robust synapomorphies of the Magallana clade. In this study, we verified the identity of MW143047 using direct comparisons of single gene sequences, DNA barcoding and phylogenetic analyses. BLAST searches using each of the 12 protein coding genes and rRNA genes extracted from MW143047 as query retrieved M. gigas as best hit with 100% sequence identity. MW143047 is nested within the clade formed by M. gigas sequences, with virtually no difference between their terminal branch lengths, both in the cox1 gene tree (based on 3639 sequences) and in the 16S gene tree (based on 1839 sequences), as well as in the Maximum Likelihood mitogenomic tree based on concatenated sequence of 12 PCGs. Our findings suggest that the original specimen used for mitogenome sequencing was misidentified and represents an individual of M. gigas. This study reinforces the notion that morphological shell analysis alone is not sufficient for oyster identification, not even at high taxonomic ranks such as subfamilies. While it is well established that morphological identification of oysters should be validated by molecular data, this study emphasizes that also molecular data should be taxonomically validated by means of DNA barcoding and phylogenetic analyses. The implications of the publication of taxonomically misidentified sequences and mitogenomes are discussed.
Recycling of cell surface membrane proteins from yeast endosomes is regulated by ubiquitinated Ist1
Authors: Laidlaw Kamilla ME. , Calder Grant , MacDonald Chris 
Published: June 2021

ABSTRACTTrafficking of cell surface membrane proteins to and from the plasma membrane impinges on myriad biological processes and ensures correct cellular function. Upon internalization, many surface proteins are recycled back to the plasma membrane. Although these endosomal trafficking pathways control surface protein activity, the precise regulatory features and division of labour between interconnected pathways is poorly defined. Furthermore, how well endosomal trafficking mechanisms are conserved is unclear. In yeast, we show cargo recycling back to the surface occurs through distinct pathways. In addition to retrograde recycling pathways via the late Golgi, used by synaptobrevins and driven by cargo ubiquitination, we find nutrient transporter recycling bypasses the Golgi in a pathway driven by cargo deubiquitination. Nutrient transporters rapidly internalize to, and recycle from, endosomes marked by Vps4 and the ESCRT-III associated factor Ist1. This compartment serves as both ‘early’ and ‘recycling’ endosome, implying these features are evolutionarily conserved. Ist1 has previously been implicated in recycling in yeast and other eukaryotes. We show Ist1 is ubiquitinated and this is required for proper endosomal recruitment and cargo recycling to the surface. Additionally, the ubiquitin-binding adaptor Npl4 and the essential ATPase Cdc48 are required for cargo recycling possibly through regulation of ubiquitinated Ist1. This collectively suggests mechanistic features of recycling from endosomes to the plasma membrane are also conserved.
Disruption of VGLUT1 in cholinergic medial habenula projections increases nicotine self-administration
Authors: Souter Elizabeth A. , Chen Yen-Chu , Zell Vivien , Lallai Valeria , Steinkellner Thomas , Conrad William S. , Wisden William , Harris Kenneth D. , Fowler Christie D. , Hnasko Thomas S. 
Published: June 2021

ABSTRACTCholinergic projections from the medial habenula (MHb) to the interpeduncular nucleus (IPN) have been studied for their complex contributions to nicotine addiction and have been implicated in nicotine reinforcement, aversion, and withdrawal. While it has been established that MHb cholinergic projections co-release glutamate, no direct evidence has demonstrated a role for this specific glutamate projection in nicotine consumption. In the present study, a novel floxed Slc17a7 (VGLUT1) mouse was generated and used to create conditional knockout (cKO) mice that lack VGLUT1 in MHb cholinergic neurons. Histochemical approaches and optogenetics-assisted electrophysiology were used to validate the disruption of VGLUT1 from cholinergic MHb to IPN projections. The mice displayed no gross phenotypic abnormalities and exhibited normal exploratory and locomotor behavior in the open-field assay. However, the loss of VGLUT1-mediated glutamate co-release led to increased nicotine self-administration. These findings indicate that glutamate co-release from ventral MHb cholinergic neurons opposes nicotine consumption and provide additional support for targeting this synapse to develop potential treatments to nicotine addiction.
Ensuring that fundamentals of quantitative microbiology are reflected in microbial diversity analyses based on next-generation sequencing
Authors: Schmidt Philip J. , Cameron Ellen S. , Müller Kirsten M. , Emelko Monica B. 
Published: June 2021

AbstractDiversity analysis of amplicon sequencing data is mainly limited to plug-in estimates calculated using normalized data to obtain a single value of an alpha diversity metric or a single point on a beta diversity ordination plot for each sample. As recognized for count data generated using classical microbiological methods, read counts obtained from a sample are random data linked to source properties by a probabilistic process. Thus, diversity analysis has focused on diversity of (normalized) samples rather than probabilistic inference about source diversity. This study applies fundamentals of statistical analysis for quantitative microbiology (e.g., microscopy, plating, most probable number methods) to sample collection and processing procedures of amplicon sequencing methods to facilitate inference reflecting the probabilistic nature of such data and evaluation of uncertainty in diversity metrics. Types of random error are described and clustering of microorganisms in the source, differential analytical recovery during sample processing, and amplification are found to invalidate a multinomial relative abundance model. The zeros often abounding in amplicon sequencing data and their implications are addressed, and Bayesian analysis is applied to estimate the source Shannon index given unnormalized data (both simulated and real). Inference about source diversity is found to require knowledge of the exact number of unique variants in the source, which is practically unknowable due to library size limitations and the inability to differentiate zeros corresponding to variants that are actually absent in the source from zeros corresponding to variants that were merely not detected. Given these problems with estimation of diversity in the source even when the basic multinomial model is valid, sample-level diversity analysis approaches are discussed.HighlightsRandom error in amplicon sequencing method should be considered in diversity analysisClustering, amplification, and differential recovery distort sample diversityThe multinomial model for compositional count data is compromised by amplificationThere are three types of zeros in amplicon sequencing data, including missing zerosSource alpha diversity estimates are biased by unknown number of unique variants
A dose-sensitive OGT-TET3 complex is necessary for normal Xist RNA distribution and function
Authors: Martin Elizabeth Allene , Maynard Jason C. , Hrit Joel , Augspurger Katherine , Picard Colette L. , Feng Suhua , Jacobsen Steven E. , Burlingame Alma L. , Panning Barbara 
Published: June 2021

AbstractFemale (XX) mouse embryonic stem cells (mESCs) differ from their male (XY) counterparts because they have lower levels of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). This difference in DNA modifications is a result of having two X chromosomes (Xs), both of which are active at this developmental stage. We identified an X-linked gene, Ogt, that controls levels of 5mC and 5hmC in mESCs. OGT is a post-translational modification enzyme and we identified the 5-methylcytosine dioxygenase TET3 as an OGT target that is differentially modified in XX and XY mESCs. In addition to influencing 5mC and 5hmC abundance, OGT dose also controls TET3 and OGT distribution. OGT and TET3 are predominantly nuclear in XX mESCs and cytoplasmic in XY mESCs. Furthermore, these proteins are present in different complexes in XX and XY mESCs. Mutational analysis revealed that TET3 determines the XX-specific abundance of 5mC and 5hmC in mESCs. While TET3 null XX mESCs exhibited modest changes in gene expression, there were substantial alterations upon differentiation into epiblast-like cells (mEpiLCs). In addition, these TET3 null XX mESCs did not undergo X-chromosome inactivation (XCI) when differentiated. These data suggest that an X-dose sensitive complex containing OGT and TET3 regulates cytosine modifications and XCI.
The effect of self- vs. externally generated actions on timing, duration and amplitude of BOLD response for visual feedback processing
Authors: Kavroulakis Eleftherios , van Kemenade Bianca M. , Arikan B. Ezgi , Kircher Tilo , Straube Benjamin 
Published: June 2021

AbstractIt has been widely assumed that internal forward models use efference copies to create predictions about the sensory consequences of our own actions. While these predictions had been frequently associated with reduced neural processing in sensory cortices, the timing and duration of the hemodynamic response of self-generated as opposed to externally generated movements is poorly investigated. In the present study we tested the hypothesis that predictive mechanisms for self-generated actions lead to early and shorter neural processing compared with externally generated movements. Using a first and second-order Taylor approximation in terms of the temporal (TD) and dispersion (DD) derivatives of a canonical hemodynamic response function, we investigated the timing and duration of activation for self-generated and externally generated movements using a custom-made fMRI-compatible movement device. Visual video feedback of the active and passive hand movements were presented in real time or with variable delays (0 - 417 ms). Participants had to judge, whether the feedback was delayed. We found earlier feedback processing for self-generated compared to externally generated movements in several regions including the supplementary motor area, cerebellum, subcortical structures such as the putamen and visual cortices. Shorter processing was found in areas, which show also lower blood oxygen level dependent (BOLD) amplitudes, such as the SMA, occipital and parietal cortex. Specifically, earlier activation in the putamen, of self-generated movements was associated with worse performance in detecting delays. These findings support our hypothesis, that efference copy based predictive mechanisms enable earlier processing of action feedback, as potential source for behavioral effects.
Pathway-based approach reveals differential sensitivity of glioblastoma to E2F1 inhibition
Authors: Alvarado Alvaro G. , Tessema Kaleab , Muthukrishnan Sree Deepthi , Sober Mackenzie , Kawaguchi Riki , Bhaduri Aparna , Swarup Vivek , Nathanson David A , Goldman Steven A. , Kornblum Harley I. 
Published: June 2021

AbstractTargeting glioblastoma (GBM) based on molecular subtyping have not yet translated into successful therapies. Here, we used gene set enrichment analysis (GSEA) to conduct an unsupervised clustering analysis to condense the gene expression data from bulk patient samples and patient-derived gliomasphere lines into new gene lists. We then identified key molecular pathways differentially regulated between tumors. These gene lists associated not only with cell cycle and stemness signatures, but also with cell-type specific markers and different cellular states of GBM. We identified the transcription factor E2F1 as a key regulator of tumor cell proliferation and self-renewal in only the subset of proliferating gliomasphere cultures predicted to be E2F1-activated and validated its functional significance in tumor formation capacity. E2F1 inhibition also sensitized E2F1-activated gliomasphere cultures to radiation treatment. Our findings indicate that a pathway-based approach can be leveraged to deconstruct inter-tumoral heterogeneity and uncover key therapeutic vulnerabilities for targeting GBM.