bluuebunny/crossref_metadata_2025_split huggingface dataset:
Broiler house environment and litter management practices impose selective pressures on antimicrobial resistance genes and virulence factors ofCampylobacter
Authors: Woyda Reed , Oladeinde Adelumola , Endale Dinku , Strickland Timothy , Lawrence Jodie Plumblee , Abdo Zaid 
Published: February 2023

AbstractCampylobacterinfections are a leading cause of bacterial diarrhea in humans globally. Infections are due to consumption of contaminated food products and are highly associated with chicken meat, with chickens being an important reservoir forCampylobacter. Here, we characterized the genetic diversity ofCampylobacterspecies detected in broiler chicken litter over three consecutive flocks and determined their antimicrobial resistance and virulence factor profiles. Antimicrobial susceptibility testing and whole genome sequencing were performed onCampylobacter jejuni(n = 39) andCampylobacter coli(n = 5) isolates. AllC. jejuniisolates were susceptible to all antibiotics tested whileC. coli(n =4) were resistant to only tetracycline and harbored the tetracycline-resistant ribosomal protection protein (TetO). Virulence factors differed within and across grow houses but were explained by the isolates’ flock cohort, species and multilocus sequence type. Virulence factors involved in the ability to invade and colonize host tissues and evade host defenses were absent from flock cohort 3C. jejuniisolates as compared to flock 1 and 2 isolates. Our results show that virulence factors and antimicrobial resistance genes differed by the isolates’ multilocus sequence type and by the flock cohort they were present in. These data suggest that the house environment and litter management practices performed imposed selective pressures on antimicrobial resistance genes and virulence factors. In particular, the absence of key virulence factors within the final flock cohort 3 isolates suggests litter reuse selected forCampylobacterstrains that are less likely to colonize the chicken host.ImportanceCampylobacteris a leading cause of foodborne illness in the United States due to the consumption of contaminated food products or from mishandling of food products, often associated with chicken meat.Campylobacteris common in the microbiota of avian and mammalian gut; however, the acquisition of antimicrobial resistance genes and virulence factors may result in strains that pose a significant threat to public health. Although there are studies that have investigated the genetic diversity ofCampylobacterstrains isolated from post-harvest chicken samples, there is limited data on the genome characteristics of isolates recovered from pre-harvest broiler production. In this study, we show thatCampylobacter jejuniandCampylobacter colithat differ in their carriage of antimicrobial resistance and virulence factors may differ in their ability to evade host defense mechanisms and colonize the gut of chickens and humans. Furthermore, we found that differences in virulence factor profiles were explained by the species ofCampylobacterand its multilocus sequence type.
Engineering a symbiont as a biosensor for the honey bee gut environment
Authors: Chhun Audam , Moriano-Gutierrez Silvia , Zoppi Florian , Cabirol Amélie , Engel Philipp , Schaerli Yolanda 
Published: February 2023

AbstractThe honey bee is a powerful model system to probe host-gut microbiota interactions, and an important pollinator species for natural ecosystems and for agriculture. While bacterial biosensors can provide critical insight into the complex interplay occurring between a host and its associated microbiota, the lack of methods to non-invasively sample the gut content, and the limited genetic tools to engineer symbionts, have so far hindered their development in honey bees. Here, we built a versatile molecular toolkit to genetically modify symbionts and report for the first time in the honey bee a technique to sample their feces. We reprogrammed the native bee gut bacteriumSnodgrassella alvias a biosensor for IPTG, with engineered cells that stably colonize the gut of honey bees and report in a dose-dependent manner exposure through the expression of a fluorescent protein. We showed that fluorescence readout can be measured in the gut tissues or non-invasively in the feces. These tools and techniques will enable rapid building of engineered bacteria to answer fundamental questions in host-gut microbiota research.
Following the fate of lytic polysaccharide monooxygenases (LPMOs) under oxidative conditions by NMR spectroscopy
Authors: Christensen Idd A. , Eijsink Vincent G. H. , Stepnov Anton A. , Courtade Gaston , Aachmann Finn L. 
Published: February 2023

AbstractLytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that catalyze oxidative cleavage of polysaccharides, such as cellulose and chitin. LPMO action is key to the efficient varlorization of biomass, but the instability of LPMOs in turnover conditions limits their efficiency. LPMO catalysis requires the presence of a reductant, such as ascorbic acid, and hydrogen peroxide, which can be generatedin situin the presence of molecular oxygen and various electron donors.. While it is known that reduced LPMOs are prone to auto-catalytic oxidative damage due to off-pathway reactions with the oxygen co-substrate, little is known about the structural consequences of such damage. Here, we present atomic-level insight into how the structure of the chitin-activeSmLPMO10A is affected by oxidative damage, using NMR and CD spectroscopy. Incubation with ascorbic acid, led to rearrangements of aromatic residues, followed by more profound structural changes near the copper active site and loss of activity. Longer incubation times induced changes in larger parts of the structure, indicative of progressing oxidative damage. Incubation with ascorbic acid in the presence of chitin led to similar changes in the observable (i.e., not substrate-bound) fraction of the enzyme. Upon subsequent addition of H2O2, which drastically speeds up chitin hydrolysis, NMR signals corresponding to seemingly intactSmLPMO10A reappeared, indicating dissociation of catalytically competent LPMO. Activity assays confirmed thatSmLPMO10A retained catalytic activity when pre-incubated with chitin before being subjected to conditions that induce oxidative damage. Overall, this study provides structural insights into the process of oxidative damage ofSmLPMO10A and demonstrates the protective effect of the substrate. The impact of turnover conditions on aromatic residues in the core of the enzyme suggests a role for these residues in dealing with redox-active species generated in the copper center.
DandD: efficient measurement of sequence growth and similarity
Authors: Bonnie Jessica K. , Ahmed Omar , Langmead Ben 
Published: February 2023

AbstractGenome assembly databases are growing rapidly. The sequence content in each new assembly can be largely redundant with previous ones, but this is neither conceptually nor algorithmically easy to measure. We propose new methods and a new tool called DandD that addresses the question of how much new sequence is gained when a sequence collection grows. DandD can describe how much human structural variation is being discovered in each new human genome assembly and when discoveries will level off in the future. DandD uses a measure called δ (“delta”), developed initially for data compression. Computing δ directly requires counting k-mers, but DandD can rapidly estimate it using genomic sketches. We also propose δ as an alternative to k-mer-specific cardinalities when computing the Jaccard coefficient, avoiding the pitfalls of a poor choice of k. We demonstrate the utility of DandD’s functions for estimating δ, characterizing the rate of pangenome growth, and computing allpairs similarities using k-independent Jaccard. DandD is open source software available at:https://github.com/jessicabonnie/dandd.
Effective networks mediate right hemispheric dominance of human 40 Hz auditory steady-state response
Authors: Kumar Neeraj , Jaiswal Amit , Roy Dipanjan , Banerjee Arpan 
Published: February 2023

AbstractAuditory steady-state responses (ASSR) are induced from the brainstem to the neocortex when humans hear periodic amplitude-modulated tonal signals. ASSRs have been argued to be a key marker of auditory temporal processing and pathological reorganization of ASSR – a biomarker of neurodegenerative disorders. However, most of the earlier studies reporting the neural basis of ASSRs were focused on looking at individual brain regions. Here, we seek to characterize the large-scale directed information flow among cortical sources of ASSR entrained by 40 Hz external signals. Entrained brain rhythms with power peaking at 40 Hz were generated using both monaural and binaural tonal stimulation. First, we confirm the presence of ASSRs and their well-known right hemispheric dominance during binaural and both monaural conditions. Thereafter, reconstruction of source activity employing individual anatomy of the participant and subsequent network analysis revealed that while the sources are common among different stimulation conditions, differential levels of source activation and differential patterns of directed information flow using Granger causality among sources underlie processing of binaurally and monaurally presented tones. Particularly, we show bidirectional interactions involving the right superior temporal gyrus and inferior frontal gyrus underlie right hemispheric dominance of 40 Hz ASSR during both monaural and binaural conditions. On the other hand, for monaural conditions, the strength of inter-hemispheric flow from left primary auditory areas to right superior temporal areas followed a pattern that comply with the generally observed contralateral dominance of sensory signal processing.
Meningeal P2X7 signaling mediates migraine-related intracranial mechanical hypersensitivity
Authors: Zhao Jun , Harrison Samantha , Levy Dan 
Published: February 2023

AbstractCortical spreading depolarization (CSD) is a key pathophysiological event that underlies visual and sensory auras in migraine. CSD is also thought to drive the headache phase in migraine by promoting the activation and mechanical sensitization of trigeminal primary afferent nociceptive neurons that innervate the cranial meninges. The factors underlying meningeal nociception in the wake of CSD remain poorly understood but potentially involve the parenchymal release of algesic mediators and damage-associated molecular patterns, particularly ATP. Here, we explored the role of ATP-P2X purinergic receptor signaling in mediating CSD-evoked meningeal afferent activation and mechanical sensitization. Male rats were subjected to a single CSD episode. In vivo, extracellular single-unit recording was used to measure meningeal afferent ongoing activity changes. Quantitative mechanical stimuli using a servomotor force-controlled stimulator assessed changes in the afferent’s mechanosensitivity. Manipulation of meningeal P2X receptors was achieved via local administration of pharmacological agents. Broad-spectrum P2X receptor inhibition, selective blockade of the P2X7 receptor, and its related pannexin 1 channel suppressed CSD-evoked afferent mechanical sensitization but did not affect the accompanying afferent activation response. Surprisingly, inhibition of the pronociceptive P2X2/3 receptor did not affect the activation or sensitization of meningeal afferents post-CSD. P2X7 signaling underlying afferent mechanosensitization was localized to the meninges and did not affect CSD susceptibility. We propose that meningeal P2X7 and Pannexin 1 signaling, potentially in meningeal macrophages or neutrophils, mediates the mechanical sensitization of meningeal afferents, which contributes to migraine pain by exacerbating the headache during normally innocuous physical activities.Significance StatementActivation and sensitization of meningeal afferents play a key role in migraine headache, but the underlying mechanisms remain unclear. Here, using a rat model of migraine with aura involving cortical spreading depolarization (CSD), we demonstrate that meningeal purinergic P2X7 signaling and its related Pannexin 1 pore, but not nociceptive P2X2/3 receptors, mediate prolonged meningeal afferent sensitization. Additionally, we show that meningeal P2X signaling does not contribute to the increased afferent ongoing activity in the wake of CSD. Our finding points to meningeal P2X7 signaling as a critical mechanism underlying meningeal nociception in migraine, the presence of distinct mechanisms underlying the activation and sensitization of meningeal afferents in migraine, and highlight the need to target both processes for effective migraine therapy.
Sex and interferon gamma signaling regulate microglia migration in adult mouse cortexin vivo
Authors: Boghozian Roobina , Sharma Sorabh , Cheema Manjinder , Brown Craig E. 
Published: February 2023

SummaryAlthough microglia possess the unique ability to migrate, whether mobility is evident in all microglia, is sex dependent, and what molecular mechanisms drive this, is poorly understood in the adult brain. Using longitudinalin vivoimaging of sparsely labelled microglia, we find a relatively small population of microglia are mobile under normal conditions. Following injury (microbleed), the population of mobile microglia increased in a sex-dependent manner, with male microglia migrating significantly greater distances towards the microbleed relative to their female counterparts. To understand the signaling pathways involved, we interrogated the role of interferon gamma (IFNγ). Our data show that in male mice, stimulating microglia with IFNγ or inducible microglial specific knockdown of IFNγ receptor 1 stimulates or inhibits migration, respectively, whereas female microglia were generally unaffected. These findings highlight the diversity of microglia migratory responses to injury, its dependence on sex and the signaling mechanisms that modulate this behavior.
Discovery of A Polymorphic Gene Fusion via Bottom-Up Chimeric RNA Prediction
Authors: Elfman Justin , Goins Lynette , Heller Tessa , Singh Sandeep , Wang Yuh-Hwa , Li Hui 
Published: February 2023

ABSTRACTGene fusions and their chimeric products are typically considered hallmarks of cancer. However, recent studies have found chimeric transcripts in non-cancer tissues and cell lines. In addition, efforts to annotate structural variation at large scale have found examples of gene fusions with potential to produce chimeric transcripts in normal tissues. In this report, we provide a means for targeting population-specific chimeric RNAs to enrich for those generated by gene fusion events. We identify 57 such chimeric RNAs from the GTEx cohort, includingSUZ12P1-CRLF3 and TFG-ADGRG7, whose distribution we assessed across the populations of the 1000 Genomes Project. We reveal thatSUZ12P1-CRLF3results from a common complex structural variant in populations with African heritage, and identify its likely mechanism for formation. Additionally, we utilize a large cohort of clinical samples to characterize theSUZ12P1-CRLF3chimeric RNA, and find an association between the variant and indications of Neurofibramatosis Type I. We present this gene fusion as a case study for identifying hard-to-find and potentially functional structural variants by selecting for those which produce population-specific fusion transcripts.KEY POINTS- Discovery of 57 polymorphic chimeric RNAs- Characterization of SUZ12P1-CRLF3 polymorphic chimeric RNA and corresponding rearrangement- Novel bottom-up approach to identify structural variants which produce transcribed gene fusions
RTCpredictor: Identification of Read-Through Chimeric RNAs from RNA Sequencing Data
Authors: Singh Sandeep , Shi Xinrui , Ahmad Syed Basil , Manley Tommy , Piczak Claire , Phung Christopher , Sun Yunan , Lynch Sarah , Sharma Aadi , Li Hui 
Published: February 2023

ABSTRACTRead-through chimeric RNAs are gaining attention in cancer and other research fields, yet current tools often fail in predicting them. We have thus developed the first read-through chimeric RNA specific prediction method, RTCpredictor, utilizing a fast ripgrep algorithm to search for all possible exon-exon combinations of parental gene pairs. Compared with other ten popular tools, RTCpredictor achieved top performance on both simulated and real datasets. We randomly selected up to 30 candidate read-through chimeras predicted from each software method and experimentally validated a total of 109 read-throughs and on this set, RTCpredictor outperformed all the other methods. In addition, RTCpredictor (https://github.com/sandybioteck/RTCpredictor) has less memory requirements and faster execution time.
TheDrosophila melanogasterY-linked gene,WDY, is required for sperm to swim in the female reproductive tract
Authors: Hafezi Yassi , Omurzakov Arsen , Carlisle Jolie A. , Caldas Ian V. , Wolfner Mariana F. , Clark Andrew G. 
Published: February 2023

ABSTRACTUnique patterns of inheritance and selection on Y chromosomes lead to the evolution of specialized gene functions. Yet characterizing the function of genes on Y chromosomes is notoriously difficult. We report CRISPR mutants in Drosophila of the Y-linked gene,WDY, which is required for male fertility.WDYmutants produce mature sperm with beating tails that can be transferred to females but fail to enter the female sperm storage organs. We demonstrate that the sperm tails ofWDYmutants beat approximately half as fast as wild-type sperm’s and that the mutant sperm do not propel themselves within the male ejaculatory duct or female reproductive tract (RT). These specific motility defects likely cause the sperm storage defect and sterility of the mutants. Regional and genotype-dependent differences in sperm motility suggest that sperm tail beating and propulsion do not always correlate. Furthermore, we find significant differences in the hydrophobicity of key residues of a putative calcium-binding domain between orthologs ofWDYthat are Y-linked and those that are autosomal. Given thatWDYappears to be evolving under positive selection, our results suggest thatWDY’s functional evolution coincides with its transition from autosomal to Y-linked inDrosophila melanogasterand its most closely related species. Finally, we show that mutants for another Y-linked gene,PRY, also show a sperm storage defect that may explain their subfertility. In contrast toWDY, PRYmutants do swim in the female RT, suggesting they are defective in yet another mode of motility, navigation, or a necessary interaction with the female RT. Overall, we provide direct evidence for the long-held presumption that protein-coding genes on the Drosophila Y regulate sperm motility.
Experience-Dependent Plasticity in Nucleus Laminaris of the Barn Owl
Authors: Carr Catherine E. , Wang Tiffany , Kraemer Ira , Capshaw Grace , Ashida Go , Köppl Christine , Kempter Richard , Kuokkanen Paula T. 
Published: February 2023

AbstractBarn owls experience increasing interaural time differences (ITDs) during development, because their head width more than doubles in the month after hatching. We therefore hypothesized that their ITD detection circuit might be modified by experience. To test this, we raised owls with unilateral ear inserts that delayed and attenuated the acoustic signal, then measured the ITD representation in the brainstem nucleus laminaris (NL) when they were adult. The ITD circuit is composed of delay line inputs to coincidence detectors, and we predicted that plastic changes would lead to shorter delays in the axons from the manipulated ear, and complementary shifts in ITD representation on the two sides. In owls that received ear inserts starting around P14, the maps of ITD shifted in the predicted direction, but only on the ipsilateral side, and only in those tonotopic regions that hadnotexperienced auditory stimulation prior to insertion. The contralateral map did not change. Experience-dependent plasticity of the ITD circuit occurs in NL, and our data suggest that ipsilateral and contralateral delays are independently regulated. Thus, altered auditory input during development leads to long-lasting changes in the representation of ITD.Significance StatementThe early life of barn owls is marked by increasing sensitivity to sound, and by increasing ITDs. Their prolonged post-hatch development allowed us to examine the role of altered auditory experience on the development of ITD detection circuits. We raised owls with a unilateral ear insert and found that their maps of ITD were altered by experience, but only in those tonotopic regions that hadnotexperienced auditory stimulation prior to insertion. Thus experience-induced plasticity allows the sound localization circuits to be customized to individual characteristics, such as the size of the head, and potentially to compensate for natural conductive hearing losses.
Predicting the Sequence-Dependent Backbone Dynamics of Intrinsically Disordered Proteins
Authors: Qin Sanbo , Zhou Huan-Xiang 
Published: February 2023

AbstractHow the sequences of intrinsically disordered proteins (IDPs) code for functions is still an enigma. Dynamics, in particular residue-specific dynamics, holds crucial clues. Enormous efforts have been spent to characterize residue-specific dynamics of IDPs, mainly through NMR spin relaxation experiments. Here we present a sequence-based method, SeqDYN, for predicting residue-specific backbone dynamics of IDPs. SeqDYN employs a mathematical model with 21 parameters: one is a correlation length and 20 are the contributions of the amino acids to slow dynamics. Training on a set of 45 IDPs reveals aromatic, Arg, and long-branched aliphatic amino acids as the most active in slow dynamics whereas Gly and short polar amino acids as the least active. SeqDYN predictions not only provide an accurate and insightful characterization of sequence-dependent IDP dynamics but may also serve as indicators in a host of biophysical processes, including the propensities of IDP sequences to undergo phase separation.
PhylteR: efficient identification of outlier sequences in phylogenomic datasets
Authors: Comte Aurore , Tricou Théo , Tannier Eric , Joseph Julien , Siberchicot Aurélie , Penel Simon , Allio Rémi , Delsuc Frédéric , Dray Stéphane , de Vienne Damien M. 
Published: February 2023

AbstractIn phylogenomics, incongruences between gene trees, resulting from both artifactual and biological reasons, can decrease the signal-to-noise ratio and complicate species tree inference. The amount of data handled today in classical phylogenomic analyses precludes manual error detection and removal. However, a simple and efficient way to automate the identification of outliers from a collection of gene trees is still missing.Here, we present PhylteR, a method that allows a rapid and accurate detection of outlier sequences in phylogenomic datasets, i.e. species from individual gene trees that do not follow the general trend. PhylteR relies on DISTATIS, an extension of multidimensional scaling to 3 dimensions to compare multiple distance matrices at once. In PhylteR, these distance matrices extracted from individual gene phylogenies represent evolutionary distances between species according to each gene.On simulated datasets, we show that PhylteR identifies outliers with more sensitivity and precision than a comparable existing method. We also show that PhylteR is not sensitive to ILS-induced incongruences, which is a desirable feature. On a biological dataset of 14,463 genes for 53 species previously assembled for Carnivora phylogenomics, we show (i) that PhylteR identifies as outliers sequences that can be considered as such by other means, and (ii) that the removal of these sequences improves the concordance between the gene trees and the species tree. Thanks to the generation of numerous graphical outputs, PhylteR also allows for the rapid and easy visual characterisation of the dataset at hand, thus aiding in the precise identification of errors. PhylteR is distributed as an R package on CRAN and as containerized versions (docker and singularity).