bluuebunny/crossref_metadata_2025_split huggingface dataset:
Staphylococcus aureus virulence factor expression matters: input from targeted proteomics shows Panton-Valentine leucocidin impact on mortality
Authors: Pivard Mariane , Bastien Sylvere , Macavei Iulia , Mouton Nicolas , Rasigade Jean-Philippe , Couzon Florence , Carrière Romain , Moreau Karen , Lemoine Jérôme , Vandenesch Francois 
Published: September 2022

AbstractIn the case of commensal bacteria such as Staphylococcus aureus, the transition from commensalism to invasion and disease as well as disease severity in the course of an infection remain poorly predictable on the sole basis of virulence gene content. To determine whether variations in the levels of expression of the numerous S. aureus virulence factors could affect disease occurrence and/or severity, we developed a targeted proteomic approach that monitored 149 peptide surrogates targeting 44 proteins. Semi-quantification was achieved by normalization on the signal of ribosomal proteins. We then evaluated this approach on a series of S.aureus strains from 136 patients presenting a severe community-acquired pneumonia, all admitted to an intensive care unit. After adjusting to the Charlson Comorbidity Index score the multivariate analysis of severity parameters found that HlgB, Nuc, and Tsst-1 were positively associated while BlaI and HlgC were negatively associated with leucopenia. BlaZ and HlgB were positively associated with hemoptysis and HlgC was negatively associated with hemoptysis. Regarding mortality, both the multivariate (1.28; 95%CI[1.02;1.60]) and survival (1.15; 95%CI[1.016;1.302]) analyses showed that only PVL was associated with death in a dose-dependent manner. Beyond highlighting the decisive role of PVL in community-acquired pneumonia severity, this study brings the proof of concept that “expression matters” and proposes a method that can be routinely implemented in laboratories, for any Staphylococcal disease, and which could be developed for other commensal bacteria.One Sentence SummaryA highly multiplexed semi-quantitative mass spectrometry method was developed for 44 Staphylococcus aureus virulence factors; applied to a 136-strain collection from severe community-acquired pneumonia patients, it showed that Panton-Valentine leucocidin was the only factor to impact mortality in a dose-dependent manner.
Cold-induced Suspension and Resetting of Ca2+ and Transcriptional Rhythms in the Suprachiasmatic Nucleus Neurons
Authors: Enoki Ryosuke , Kon Naohiro , Shimizu Kimiko , Kobayashi Kenta , Yamaguchi Yoshifumi , Tomomi Nemoto 
Published: September 2022

AbstractMammalian circadian rhythms are coordinated by the master clock located in the hypothalamic suprachiasmatic nucleus (SCN). Under severe environmental conditions, such as during the harsh winter season for food, certain mammalian species reduce their basal metabolism and thermogenesis, thereby undergoing torpor, a controlled state of hypothermia, which naturally returns to the normothermic state. A long-lasting debate focused on whether the SCN with a temperature-compensated clock remains functional during hypothermia. However, so far, no direct and quantitative evidence has been reported of temperature sensitivity in living SCN neurons.In this study, we performed dual-color fluorescence imaging of clock gene transcriptions and intracellular Ca2+ in mouse SCN neurons, using slices at various temperatures. We demonstrated that the Bmal1 transcription and Ca2+ circadian rhythms persisted at 22°C–28°C, although the two rhythms underwent temporal dissociation at 22 °C. Notably, Ca2+, Bmal1, and Per2 rhythms were suspended at 15°C, coupled with a significant Ca2+ increase, and all rhythms were reset by rewarming to 35°C. Upon rewarming, the Ca2+ rhythm showed stable oscillations immediately, whereas the Bmal1 and Per2 rhythms took several days to reach stable oscillations and recover their phase relationship with the Ca2+ rhythm.Taken together, we concluded that SCN neurons remain functional under moderate hypothermic conditions at approximately 22°C–28°C but stop ticking time in deep hypothermia at 15°C and that the rhythms reset after deep hypothermia. These data also indicate that the stable Ca2+ oscillation precedes clock gene transcriptional rhythms in the SCN neurons.
Higher-order dialectic variation and syntactic convergence in the complex warble song of budgerigars
Authors: Madabhushi Abhinava Jagan , Wewhare Nakul , Binwal Priya , Krishnan Anand 
Published: September 2022

AbstractDialectic signatures in animal acoustic signals are key in identification and association with group members. Complex vocal sequences may also convey information about behavioral state, and may thus vary according to social environment. Many bird species learn and modify their complex acoustic signals throughout their lives. However, the structure and function of vocal sequences in perennial vocal learners remains understudied. Here, we examined vocal sequence variation in the warble song of budgerigars, and how these change upon contact between social groups. Budgerigars are perennial vocal learners which exhibit fission-fusion flock dynamics in the wild. We found that two captive colonies of budgerigars exhibited colony-specific differences in the syntactic structure of their vocal sequences. Individuals from the two colonies differed in the propensity to repeat certain note types, forming repetitive motifs which served as higher-order signatures of colony identity. When the two groups were brought into contact, their vocal sequences converged within months of contact, and these colony-specific repetitive patterns disappeared, with males from both erstwhile colonies now producing similar sequences with similar syntactic structure. Our data suggests that budgerigars can encode substantial information in the higher-order temporal arrangement of notes/vocal units, which is modified throughout life by social learning as groups of birds continually associate and dissociate. Our study sheds light on the importance of examining signal structure at multiple levels of organisation, and the potential for psittaciform birds as model systems to examine the influence of learning and social environment on acoustic signals.
Brain transcriptome of gobies inhabiting natural CO2 seeps reveal acclimation strategies to long-term acidification
Authors: Suresh Sneha , Mirasole Alice , Ravasi Timothy , Vizzini Salvatrice , Schunter Celia 
Published: September 2022

AbstractOcean acidification (OA) is known to affect the physiology, survival, behaviour, and fitness of various fish species with repercussions at the population, community, and ecosystem levels. Some fish species, however, seem to acclimate rapidly to OA conditions and even thrive in acidified environments. The molecular mechanisms that enable species to successfully inhabit high CO2environments has not been fully elucidated especially in wild fish populations. Here, we used the natural CO2seep in Vulcano Island, Italy to study the effects of elevated CO2exposure on the brain transcriptome of the anemone goby, a species with high population density in the CO2seep and investigate their potential for acclimation. When compared to fish from environments with ambient CO2, gobies living in the CO2seep showed differences in expression of transcripts involved in ion transport and pH homeostasis, cellular stress, immune response, circadian rhythm, and metabolism. We also found evidence of potential adaptive mechanisms to restore the functioning of GABAergic pathways, whose activity can be affected by exposure to elevated CO2levels. Our findings indicate that gobies living in the CO2seep may be capable of mitigating CO2induced oxidative stress and maintaining physiological pH while meeting the consequent increased energetic costs. The conspicuous difference in expression of core circadian rhythm transcripts could provide an adaptive advantage by increasing flexibility of physiological processes in elevated CO2conditions thereby facilitating acclimation. Our results show potential molecular processes of acclimation to elevated CO2in gobies enabling them to thrive in the acidified waters of Vulcano Island.
B cell receptor induced IL-10 production from neonatal CD19+CD43- cells depends on STAT5 mediated IL-6 secretion
Authors: Sakai Jiro , Yang Jiyeon , Chou Chao-Kai , Wu Wells W. , Akkoyunlu Mustafa 
Published: September 2022

AbstractNewborns are unable to reach the adult-level humoral immune response partly due to the potent immunoregulatory role of IL-10. Increased IL-10 production by neonatal B cells has been attributed to the larger population of IL-10-producting CD43+B-1 cells in neonates. Here, we show that neonatal CD43-non-B-1 cells also produce substantial amounts of IL-10 following B cell antigen receptor (BCR) activation. In neonatal CD43-non-B-1 cells, BCR engagement activated STAT5 under the control of phosphorylated forms of signaling molecules Syk, Btk, PKC, FAK and Rac1. STAT5 activation led to IL-6 production, which in turn was responsible for IL-10 production in an autocrine/paracrine fashion through the activation of STAT3. In addition to the increased IL-6 production in response to BCR stimulation, elevated expression of IL-6Rα expression in neonatal B cells rendered them highly susceptible to IL-6 mediated STAT3 phosphorylation and IL-10 production. Finally, IL-10 secreted from neonatal CD43-non-B-1 cells was sufficient to inhibit TNF-α secretion by macrophages. Our results unveil a distinct mechanism of IL-6-dependent IL-10 production in BCR-stimulated neonatal CD19+CD43-B cells.
Inositol pyrophosphate profiling reveals regulatory roles of IP6K2-dependent enhanced IP7 metabolism in enteric nervous system
Authors: Ito Masatoshi , Fujii Natsuko , Kohara Saori , Hori Shuho , Tanaka Masayuki , Wittwer Christopher , Kikuchi Kenta , Iijima Takatoshi , Kakimoto Yu , Hirabayashi Kenichi , Kurotaki Daisuke , Jessen Henning J. , Saiardi Adolfo , Nagata Eiichiro 
Published: September 2022

AbstractInositol pyrophosphates (PP-IPs) regulate diverse physiological processes; to better understand their functional roles, assessing their tissue-specific distribution is important. Here, we profiled PP-IP levels in mammalian organs using a novel HILIC-MS/MS protocol and discovered that the gastrointestinal tract (GIT) contained the highest levels of IP7 and its precursor IP6. Although their absolute levels in the GIT is diet-dependent, elevated IP7 metabolism still exists under dietary regimes devoid of exogenous IP7. Of the major GIT cells, enteric neurons selectively express the IP7-synthesizing enzyme IP6K2. IP6K2-knockout mice exhibited significantly impaired IP7 metabolism in the various organs including the proximal GIT. Additionally, HILIC-MS/MS analysis displayed that genetic ablation of IP6K2 significantly impaired IP7 metabolism in the gut and duodenal muscularis externa containing myenteric plexus. Whole transcriptome analysis of duodenal muscularis externa further suggested that IP6K2 inhibition induced the gene sets associated with mature neurons such as inhibitory, GABAergic and dopaminergic neurons, concomitantly with suppression of those for neural progenitor/stem cells and glial cells. In addition, IP6K2 inhibition explicitly affected transcript levels of certain genes modulating neuronal differentiation and functioning, implying critical roles of IP6K2-IP7 axis in developmental and functional regulation of enteric nervous system. These results collectively reveal an unexpected role of mammalian IP7—a highly active IP6K2-IP7 pathway is conducive to enteric nervous system.
Deep Learning Architectures For the Prediction of YY1-Mediated Chromatin Loops
Authors: Fazeel Ahtisham , Asim Muhammad Nabeel , Trygg Johan , Dengel Andreas , Ahmed Sheraz 
Published: September 2022

AbstractYY1-mediated chromatin loops play substantial roles in basic biological processes like gene regulation, cell differentiation, and DNA replication. YY1-mediated chromatin loop prediction is important to understand diverse types of biological processes which may lead to the development of new therapeutics for neurological disorders and cancers. Existing deep learning predictors are capable to predict YY1-mediated chromatin loops in two different cell lines however, they showed limited performance for the prediction of YY1-mediated loops in the same cell lines and suffer significant performance deterioration in cross cell line setting. To provide computational predictors capable of performing large-scale analyses of YY1-mediated loop prediction across multiple cell lines, this paper presents two novel deep learning predictors. The two proposed predictors make use of Word2vec, one hot encoding for sequence representation and long short-term memory, and a convolution neural network along with a gradient flow strategy similar to DenseNet architectures. Both of the predictors are evaluated on two different benchmark datasets of two cell lines HCT116 and K562. Overall the proposed predictors outperform existing DEEPYY1 predictor with an average maximum margin of 4.65%, 7.45% in terms of AUROC, and accuracy, across both of the datases over the independent test sets and 5.1%, 3.2% over 5-fold validation. In terms of cross-cell evaluation, the proposed predictors boast maximum performance enhancements of up to 9.5% and 27.1% in terms of AUROC over HCT116 and K562 datasets.
In-Depth Characterization of Apoptosis N-terminome Reveals a Link Between Caspase-3 Cleavage and Post-Translational N-terminal Acetylation
Authors: Hanna Rawad , Rozenberg Andrey , Saied Layla , Ben-Yosef Daniel , Lavy Tali , Kleifeld Oded 
Published: September 2022

SummaryThe N-termini of proteins contain information about their biochemical properties and functions. These N-termini can be processed by proteases and can undergo other co- or post-translational modifications. We have developed LATE (LysN Amino Terminal Enrichment), a method that uses selective chemical derivatization of α-amines to isolate the N-terminal peptides, in order to improve N-terminome identification in conjunction with other enrichment strategies. We applied LATE alongside another N-terminomic method to study caspase-3 mediated proteolysis bothin vitroand during apoptosis in cells. This has enabled us to identify many unreported caspase-3 cleavages, some of which cannot be identified by other methods. Moreover, we have found direct evidence that neo-N-termini generated by caspase-3 cleavage can be further modified by Nt-acetylation. Some of these neo-Nt-acetylation events occur in the early phase of the apoptotic process and may have a role in translation inhibition. This has provided a comprehensive overview of the caspase-3 degradome and has uncovered previously unrecognized crosstalk between post-translational Nt-acetylation and caspase proteolytic pathways.
Insights from CRISPR/Cas9-mediated gene editing of centromeric histone H3 (CENH3) in carrot (Daucus carotasubsp.sativus)
Authors: Dunemann Frank , Krüger Antje , Maier Kerstin , Struckmeyer Sabine 
Published: September 2022

AbstractThe generation of haploids is one of the most powerful means to accelerate the plant breeding process. In most crop species, an efficient haploid technology is not yet available or only applicable to a limited set of genotypes. Recent results published forArabidopsis thalianaand major cereal crops like maize and wheat about successful haploid induction by CRISPR/Cas9-mediated editing of the centromeric histone H3 gene (CENH3) suggest that this novel method for the production of haploid plants might also be applicable to vegetable species like carrot. Here, we report and summarize the different experimental and genetic approaches that have been focused in the past few years on CRISPR/Cas9-based editing of the carrot CENH3 gene. We also describe the discovery of a second CENH3 locus in the carrot genome, which complicates the attempts to generate and to analyse putative haploid inducer genotypes. We show that three different CRISPR/Cas9 target constructs, used alone or in combinations, could successfully target carrot CENH3. Promising mutants such as in-frame indel or in-frame deletion mutants have been found, but their successful usage as putative haploid inducer is uncertain yet. Next generation sequencing of amplicons spanning CRISPR target sites and transcript-based amplicon sequencing seemed to be appropriate methods to select promising mutants, to estimate mutation frequencies, and to allow a first prediction which gene was concerned. Another aim of this study was the simultaneous knockout and complementation of the endogenous carrot CENH3 gene by an alien CENH3 gene. Co-transformation of a CRISPR/Cas9-based carrot CENH3 knockout construct together with a CENH3 gene cloned from ginseng (Panax ginseng) was performed by usingRhizobium rhizogenes. It was shown, that ginseng CENH3 protein is accumulated inside the kinetochore region of carrot chromosomes, indicating thatPgCENH3might be a suited candidate for this approach. However, presently it is unclear, if this gene is fully functioning during the meiotic cell divisions and able to complement lethal gametes. Challenges and future prospects to develop a CENH3-based HI system for carrot are discussed.
Deciphering the genetic structure of the Quebec founder population using genealogies
Authors: Gagnon Laurence , Moreau Claudia , Laprise Catherine , Vézina Hélène , Girard Simon L. 
Published: September 2022

AbstractUsing genealogy to study the demographic history of a population makes it possible to overcome the models and assumptions often used in population genetics. The Quebec founder population is one of the few populations in the World having access to the complete genealogy of the last 400 years. The goal of this paper is to follow the evolution of the Quebec population structure generation per generation from the beginning of European colonization until the present day. To do so, we calculated the kinship coefficients of all ancestors’ pairs in the ascending genealogy of 665 individuals from eight regional and ethnocultural groups per 25-year period. We show that the Quebec population structure appeared in the St. Lawrence valley as early as 1750. At that time, the ancestors of two groups, the Sagueneans and the Acadians from the Gaspé Peninsula, experienced a marked increase in kinship and inbreeding levels which have shaped the contemporary population structure. Interestingly, this structure arose before the colonization of the Saguenay region and at the very beginning of the Gaspé Peninsula settlement. The resulting regional founder effects in these two groups, but also in the other regional groups, led to differences in the present-day identity-by-descent sharing and are directly linked to the number of most recent common ancestors and their genetic contribution to the studied subjects.
Revealing the structure of somatic cell membranes by in situ cryo-electron tomography
Authors: Liu Chao , Zhou Yiting , Zou Tianyi , Zhao Guanfang , Zhang Jinrui , Wang Huili , Wang Hongda 
Published: September 2022

AbstractThe cell membrane, which separates the cell from the environment, plays a key role in signal transduction, energy conversion and substance transport. Although previous membrane models have successfully interpreted some functions of the cell membrane, no consensus has been reached for the lack of direct and in situ evidence. Here, we characterized the high-resolution 3D structure of 293T cell membranes in situ for the first time by cryo-electron tomography. Due to the excellent thickness of our cryo-samples, we could clearly observe membrane proteins with an average molecular weight of 100 kD. By analysing tomograms, we found that the total thickness of a 293T plasma membrane is approximately 20 nm and that there is a 4-nm lipid bilayer structure within the membrane. We observed that membrane proteins and protein complexes with a similar height (7-11 nm) are densely embedded in the ectoplasmic side of 293T plasma membranes, whereas membrane proteins aggregate to form islands with heights reaching dozens of nanometres on the cytoplasmic side. Additionally, we measured the average sizes of membrane proteins on the cytoplasmic side of 293T plasma membranes and found them to be approximately 7 nm in length and 4 nm in width. Moreover, if more precise structural information is obtained in future studies, we will identify the molecular interactions and detailed structures of membrane protein clusters that can be easily distinguished on a 293T cell membrane. Our work represents the first in situ structural characterization of a native somatic cell membrane with cryo-electron tomography and advances cell membrane structural studies from the model prediction stage to the real structure observation stage.
Functional analysis of V2 protein of Beet curly top Iran virus
Authors: Bahari Atiyeh , Garriga Araceli Castillo , Safaie Naser , Bejarano Eduardo Rodriguez , Luna Ana Isabel Perez , Shams-Bakhsh Masoud 
Published: September 2022

AbstractThe geminivirus beet curly top Iran virus (BCTIV) is one of the main causal agents of the beet curly top disease in Iran and the newly established Becurtovirus genus type species. Although the biological features of known becurtoviruses are similar to those of curtoviruses, they only share a limited sequence identity, and no information is available on the function of their viral genes. In this work, we demonstrate that BCTIV V2, as the curtoviral V2, is also a strong local silencing suppressor in Nicotiana benthamiana and can delay the systemic silencing spreading, although it cannot block the cell-to-cell movement of the silencing signal to adjacent cells. BCTIV V2 shows the same subcellular localization as curtoviral V2, being detected in the nucleus and perinuclear region, and its ectopic expression from a PVX-derived vector also causes the induction of necrotic lesions in N. benthamiana like the ones produced during the HR, both at local and systemic levels. The results from the infection of N. benthamiana with a V2 BCTIV mutant showed that V2 is required for systemic infection but not for viral replication in a local infection. Considering all these results, we can conclude that BCTIV V2 is a functional homologue of curtoviral V2 and plays a crucial role in viral pathogenicity and systemic movement.