bluuebunny/crossref_metadata_2025_split huggingface dataset:
Body temperature regulates glucose metabolism and torpid behavior
Authors: Lee Ming-Liang , Chang Ching-Pu , Toda Chitoku , Nemoto Tomomi , Enoki Ryosuke 
Published: January 2024

SummaryGlucose is a significant energy resource for maintaining physiological activities, including body temperature homeostasis, and glucose homeostasis is tightly regulated in mammals. Although ambient temperature tunes glucose metabolism to maintain euthermia, the significance of body temperature in metabolic regulation remains unclear owing to strict thermoregulation. Activation of Qrfp neurons in the preoptic area induced a harmless hypothermic state known as Q-neuron-induced hypothermia and hypometabolism (QIH), which is suitable for studying glucose metabolism under hypothermia. In this study, we first observed that QIH mice had hyperinsulinemia and insulin resistance. This glucose hypometabolic state was abolished by increasing the body temperature to euthermia. Moreover, QIH-mediated inappetence and locomotor inactivity were recovered in euthermia QIH mice. These results indicate that body temperature is considerably more powerful than ambient temperature in regulating glucose metabolism and behavior, and hypometabolism in QIH is secondary to hypothermia rather than modulated by Qrfp neurons.HighlightsQIH reorganizes glucose homeostasis which is unchanged by fasting.QIH mice exhibit glucose hypometabolism with hyperinsuliemia and insulin resistance.Increased body temperature abolishes QIH-mediated hypometabolism and torpid behaviors.Body temperature is a strong factor in controlling metabolism and behavior.Body temperature-mediated glucose metabolism is reversible.
The interplay between peptides and RNA is critical for protoribosome compartmentalization and stability
Authors: Codispoti Simone , Yamaguchi Tomoko , Makarov Mikhail , Giacobelli Valerio G. , Mašek Martin , Kolář Michal H. , Sanchez Rocha Alma Carolina , Fujishima Kosuke , Zanchetta Giuliano , Hlouchová Klára 
Published: January 2024

AbstractThe ribosome, owing to its exceptional conservation and biological importance, harbours a remarkable molecular fossil known as the protoribosome. It surrounds the peptidyl transferase center (PTC), responsible for peptide bond formation. While previous studies have demonstrated the PTC activity in RNA alone, our investigation reveals the intricate roles of the ribosomal protein fragments (rPeptides) within the ribosomal core.This research highlights the significance of rPeptides in stability and coacervation of two distinct protoribosomal evolutionary stages. The 617nt “big” protoribosome model which associates with rPeptides specifically, exhibits a structurally defined and rigid nature, further stabilised by the peptides. In contrast, the 136nt “small” model, previously linked to peptidyltransferase activity, displays greater structural flexibility. While this construct interacts with rPeptides with lower specificity, they induce coacervation of the “small” protoribosome across a wide concentration range, which is concomitantly dependent on the RNA sequence and structure. Moreover, these conditions protect RNA from degradation. This phenomenon suggests a significant evolutionary advantage in the RNA-protein interaction at the early stages of ribosome evolution.The distinct properties of the two protoribosomal stages suggest that rPeptides initially provided compartmentalization and prevented RNA degradation, preceding the emergence of specific RNA-protein interactions crucial for the ribosomal structural integrity.3keypoints- The most ancient fragments of ribosomal peptides trigger coacervation of protoribosome- The protoribosome coacervation provides protection against RNA degradation- Coacervation is more profound with a smaller and more flexible model of the protoribosome
Rewriting endogenous human transcripts withtrans-splicing
Authors: Chandrasekaran Sita S. , Tau Cyrus , Nemeth Matthew , Pawluk April , Konermann Silvana , Hsu Patrick D. 
Published: January 2024

ABSTRACTSplicing bridges the gap between static DNA sequence and the diverse and dynamic set of protein products that execute a gene’s biological functions. While exon skipping technologies enable influence over splice site selection, many desired perturbations to the transcriptome require replacement or addition of exogenous exons to target mRNAs: for example, to replace disease-causing exons, repair truncated proteins, or engineer protein fusions. Here, we report the development ofRNA-guidedtrans-splicing withCaseditor (RESPLICE), inspired by the rare, natural process of trans-splicing that joins exons from two distinct primary transcripts. RESPLICE uses two orthogonal RNA-targeting CRISPR effectors to co-localize a trans-splicing pre-mRNA and to inhibit the cis-splicing reaction, respectively. We demonstrate efficient, specific, and programmable trans-splicing of multi-kilobase RNA cargo into nine endogenous transcripts across two human cell types, achieving up to 45% trans-splicing efficiency in bulk, or 90% when sorting for high effector expression. Our results present RESPLICE as a new mode of RNA editing for fine-tuned and transient control of cellular programs without permanent alterations to the genetic code.
Multiplex PCR reveals population structure in an inbred communal bird
Authors: Babaei Sarah , Grieves Leanne A. , Evans Ben , Quinn James S. 
Published: January 2024

AbstractWe sampled communally breeding pūkeko (Porphyrio melanotus melanotus, family Rallidae) populations on the North (Tāwharanui Park) and South (Otokia Reserve) Islands of New Zealand that differ in climate and ecology. North Island populations have year-round territories, philopatry, and form kin groups, resulting in inbreeding. South Island populations have seasonal territories, high dispersal rates, and form non-kin groups, leading to outbreeding. Given behavioural evidence of inbreeding we predicted that the North Island population would exhibit lower heterozygosity and higher inbreeding coefficients than the South Island population. We hypothesized that the South Island population originated via a range expansion from the north and predicted that South Island birds would have lower allelic diversity due to founder effects. To test these predictions, we developed microsatellite primers, optimized multiplex PCRs, and genotyped breeding groups from the North and South Island. Breeding groups from North Island were genetically differentiated, whereas population structure was not detected in the South Island birds. North Island birds had higher inbreeding coefficients and levels of within group kinship, but not allelic diversity, compared to South Island birds. Our results are thus inconclusive about whether the South Island population originated via a range expansion from the north. This pilot study validated microsatellite markers and PCR methods and is the first genetic analysis of population structure and relatedness within communal breeding pūkeko groups. These genetic tools will be used for larger-scale studies to help resolve the origins of the South Island population and provide further insights into the effects of ecology and behaviour on inbreeding, reproductive success, and population demographics in this species. Pūkeko may provide an excellent model for experimental analyses of inbreeding effects on wild avian populations without the attendant concerns that come with small, endangered populations. This work may thus inform conservation efforts, including translocations of endangered species.
Variant calling and genotyping accuracy of ddRAD-seq: comparison with 20X WGS in layers
Authors: Doublet Mathilde , Degalez Fabien , Lagarrigue Sandrine , Lagoutte Laetitia , Gueret Elise , Allais Sophie , Lecerf Frédéric 
Published: January 2024

AbstractWhole Genome Sequencing (WGS) remains a costly or unsuitable method for routine genotyping of laying hens methods, thus alternatives have been developed. Among these, reduced representation sequencing approaches can offer both sequencing quality and cost-effectiveness by reducing the genomic regions covered by sequencing. The aim of this study was to evaluate the ability ofdouble digested Restriction site Associated DNA sequencing(ddRAD-seq) to identify and genotype SNPs in laying hens, by comparison with a presumed reliable WGS approach. Firstly, the sensitivity and precision of variant calling and the genotyping reliability of ddRADseq were determined. Next, the SNP Call Rate (CRSNP) and mean depth of sequencing per SNP (DPSNP) were compared between both methods. Finally, the effect of multiple combinations of thresholds for these parameters on genotyping reliability and amount of remaining SNPs in ddRAD-seq was studied. In raw form, the ddRAD-seq identified 349,497 SNPs evenly distributed on the genome with a CRSNPof 0.55, a DPSNPof 11X and a mean genotyping reliability rate per SNP of 80%. Considering genomic regions covered by expected enzymatic fragments (EFs), the sensitivity of the ddRAD-seq was estimated at 32.4% and its precision at 96.4%. The low CRSNPand DPSNPvalues were explained by the detection of SNPs outside the EFs theoretically generated by the ddRAD-seq protocol. Indeed, SNPs outside the EFs had significantly lower CRSNP(0.25) and DPSNP(1X) values than SNPs within the EFs (0.7 and 17X, resp.). The study demonstrated the relationship between CRSNP, DPSNP, genotyping reliability and the number of SNPs retained, to provide a decision-support tool for defining filtration thresholds. Severe quality control over ddRAD-seq data allowed to retain a minimum of 40% of the SNPs with a CcR of 98%. Then, ddRAD-seq was defined as a suitable method for variant calling and genotyping in layers.
West Nile virus is transmitted within mosquito populations through infectious mosquito excreta
Authors: Hamel Rodolphe , Narpon Quentin , Serrato-Pomar Idalba , Gauliard Camille , Berthomieu Arnaud , Wichit Sineewanlaya , Missé Dorothée , Sofonea Mircea T. , Pompon Julien 
Published: January 2024

AbstractUnderstanding transmission routes of arboviruses is key to control their epidemiology and global health burden. Using West Nile virus andCulexmosquitoes, we tested whether arboviruses are transmitted through mosquito excreta. First, we determined the presence of infectious virions in excreta and quantified a high concentration of infectious units per excreta. Second, we showed that virion excretion starts early after oral infection and remains constant for a long period, regardless of mosquito infection level. These results highlight the infectiousness of excreta from infected mosquitoes. Third, we found that both larvae and pupae were susceptible to infection, although pupae were highly permissive. Forth, we established the proof-of-concept that immature mosqui-toes can be infected by infectious excreta, demonstrating a new excreta-mediated mode of transmission. Finally, by mathematically modelling excreta-mediated transmission in the field, we demonstrated its potential impact on arbovirus epidemiology. Our study uncovers a new route of transmission for arboviruses, unveiling mechanisms of viral maintenance in mosquito reservoirs and of vector species shift that contribute to zoonotic emergence.
Cost-benefit analysis of cryogenic electron tomography subtomogram averaging of chaperonin MmCpn at near atomic resolution
Authors: Zhao Yanyan , Schmid Michael F. , Chiu Wah 
Published: January 2024

SummaryCryogenic electron microscopy single particle reconstruction (cryoEM-SPR) has evolved into a routine approach for determining macromolecule structures to near-atomic resolution. Cryogenic electron tomography subtomogram averaging (cryoET-STA) towards similar resolution, in contrast, is still under active development. CryoET can capture the 3D snapshot of individual macromolecules by stage tilting, offering multiple angular views per particle than the single particle reconstruction approach. Here we use the archaea chaperonin MmCpn as a model macromolecule to investigate the resolution limiting factors of cryoET-STA in terms of cumulative electron dose, ice thickness, subtomogram numbers and tilt angle ranges. By quantitative analysis of these factors against the STA reconstruction resolution, we delineate the feasibility of attaining high resolution structure determination with cryoET-STA. This study provides biophysical guidance for the application of cryoET-STA towards high resolution and the cost against benefit of using cryoET-STA to achieve an efficient outcome at the desired resolution.
Genetic diversity within diagnostic sputum samples is mirrored in the culture ofMycobacterium tuberculosis
Authors: Mariner-Llicer Carla , Goig Galo A. , Torres-Puente Manuela , Vashakidze Sergo , Villamayor Luis M. , Saavedra-Cervera Belén , Mambuque Edson , Khurtsilava Iza , Avaliani Zaza , Rosenthal Alex , Gabrielian Andrei , Shurgaia Marika , Shubladze Natalia , García-Basteiro Alberto L. , López Mariana G. , Comas Iñaki 
Published: January 2024

ABSTRACTCulturingMycobacterium tuberculosis(MTB) from tuberculosis cases is the basis for many research and clinical applications. Paradoxically, it is assumed to impose a diversity bottleneck, which, if true, would entail unexplored consequences. The alternative, culture-free sequencing from diagnostic samples, is a promising but challenging approach both to obtain and analyse the MTB genome from the complex sample. This study obtains high-quality genomes of sputum-culture pairs from two different settings after developing a workflow for sequencing from sputum and a tailored bioinformatics pipeline. Our approach reveals that 88% of variants called in culture-free sequencing analysis are false positives due to supplementary alignments, mostly in enriched-sputa samples. Overall, contrary to the bottleneck dogma, we identify a 97% variant agreement within sputum-culture pairs, with a high correlation also in the variants’ frequency (0.98). Our findings extrapolate to all publicly available data, thus demonstrating that in most cases culture accurately mirrors clinical samples.
scMicrobe PTA: Near Complete Genomes from Single Bacterial Cells
Authors: Bowers Robert M , Gonzalez-Pena Veronica , Wardhani Kartika , Goudeau Danielle , Blow Matthew James , Udwary Daniel , Klein David , Vill Albert C , Brito Ilana L , Woyke Tanja , Malmstrom Rex , Gawad Charles 
Published: January 2024

ABSTRACTMicrobial genomes produced by single-cell amplification are largely incomplete. Here, we show that primary template amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard amplification approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.
A benchmark of computational methods for correcting biases of established and unknown origin in CRISPR-Cas9 screening data
Authors: Vinceti Alessandro , Iannuzzi Raffaele , Boyle Isabella , Trastulla Lucia , Campbell Catarina D. , Vazquez Francisca , Dempster Joshua , Iorio Francesco 
Published: January 2024

AbstractCRISPR-Cas9 dropout screens stand as formidable tools for investigating biology with unprecedented precision and scale. One of their principal applications involves probing large panels of immortalised human cancer cell lines for viability reduction responses upon systematic genetic knock-out at a genome-wide level, to identify novel cancer dependencies and therapeutic targets. However, biases in CRISPR-Cas9 screens’ data pose challenges, leading to potential confounding effects on their interpretation and compromising their overall quality. The mode of action of the Cas9 enzyme, exerted by the induction of DNA double-strand breaks at a locus targeted by a specifically designed single-guide RNA (sgRNA), is influenced by structural features of the target site, including copy number amplifications (CN bias). More worryingly, proximal targeted loci tend to generate similar gene-independent responses to CRISPR-Cas9 targeting (proximity bias), possibly due to Cas9-induced whole chromosome-arm truncations or other unknown genomic structural features and different chromatin accessibility levels.Different computational methods have been proposed to correct these biasesin silico, each based on different modelling assumptions. We have benchmarked seven of the latest methods, rigorously evaluating for the first time their ability to reduce both CN and proximity bias in the two largest publicly available cell-line-based CRISPR-Cas9 screens to date. We have also evaluated the capability of each method to preserve data quality and heterogeneity by assessing the extent to which the processed data allows accurate detection of true positive essential genes, established oncogenetic addictions, and known/novel biomarkers of cancer dependency.Our analysis sheds light on the ability of each method to correct biases arising from structural properties and other possible unknown factors associated with CRISPR-Cas9 screen data under different scenarios. In particular, it shows that AC-Chronos outperforms other methods in correcting both CN and proximity biases when jointly processing multiple screens of models with available CN information, whereas CRISPRcleanR is the top performing method for individual screens or when CN information is not available for the screened models. In addition, Chronos and AC-Chronos yield a final dataset better able to recapitulate known sets of essential and non-essential genes.Overall, our investigation provides guidance for the selection of the most appropriate bias-correction method, based on its strengths, weaknesses and experimental settings.
Arc mediates intercellular synaptic plasticity via IRSp53-dependent extracellular vesicle biogenesis
Authors: Ravens Alicia , Sullivan Kaelan , Einstein Jenifer , Keceli Sevnur Kömürlü , Kicmal Tom , Tyagi Mitali , Hantak Michael P. , Shepherd Tate , Stewart Alyson , Lyon Kenneth , Dharan Adarsh , Gallagher Thomas , Campbell Edward M. , Shepherd Jason D. 
Published: January 2024

AbstractCurrent models of learning and memory have focused on cell-autonomous regulation of synaptic strength; however, intercellular signaling between cells in the brain is critical for normal cognition. The immediate early geneArcis a repurposed retrotransposon critical for long-term forms of synaptic plasticity and memory. Arc protein forms virus-like capsids released in extracellular vesicles (EVs) that signal cell-to-cell. Here, we find that long-term potentiation (LTP) stimuli induce the biogenesis of Arc EVs by recruiting the I-BAR protein IRSp53 to dendrites, which facilitates Arc capsid assembly and release. Arc EVs transfer Arc protein and mRNA to neighboring neurons, where translation of transferredArcmRNA induces a loss of surface AMPA-type glutamate receptors. These results show that Arc EVs mediate non-cell autonomous long-term depression (LTD), revealing an intercellular form of synaptic plasticity that may be critical for memory consolidation.
Identifying the function of the NMDA NR1C2subunit through its interaction with Magi-2 during inflammatory pain
Authors: Sheehan Garrett D. , Martin Molly K. , Roszczyk Adam , Hao Katherient , Bhattacharjee Arin 
Published: January 2024

SummaryMuch is understood about the structure and gating properties of NMDA receptors (NMDAR), but the function of the carboxy-terminal splice variant of the NR1 subunit, NR1C2has never been identified. By studying the scaffolding protein Magi-2 in animal models of inflammatory pain, we discovered how NR1C2protein is specifically regulated. We found that Magi-2 deficiency resulted in decreased pain behavior and a concomitant reduction in NR1C2protein. Magi-2 contains WW domains, domains typically found in ubiquitin ligases. We identified an atypical WW-binding domain within NR1C2which conferred susceptibility to Nedd4-1 ubiquitin-ligase dependent degradation. We used lipidated peptidomimetics derived from the NR1C2sequence and found that NR1C2protein levels and pain behavior can be pharmacologically targeted. The function of NR1C2is to give lability to a pool of NMDAR, important for pain signaling.
Radiative transition decay width of
ψ2(3823)→γχc1
from lattice QCD
Authors: Li Ning , Gao Yan , Chen Feiyu , Chen Ying , Jiang Xiangyu , Shi Chunjiang , Sun Wei 
Published: January 2024

We present an exploratory Nf=2 lattice QCD study of ψ2(3823)→γχc1 at a pion mass mπ≈350  MeV. The related two-point and three-point functions are calculated using the distillation method. The electromagnetic multipole form factor V^(0)=2.083(11) for J/ψ→γηc is consistent with previous lattice results. The form factors E^1(0), M^2(0), and E^3(0) for Γ(χc2→γJ/ψ) have the same hierarchy as that derived from experiments, and the predicted decay width Γ(χc2→γJ/ψ)=368(5)  keV is in excellent agreement with the Particle Data Group value 374(10) keV and previous lattice QCD results in the quenched approximation. The same strategy is applied to the study of the process ψ2(3823)→γχc1, and the partial decay width is predicted to be 337(27) keV. According to the BESIII constraints on the ψ2(3823) decay channels and some phenomenological results, we estimate the total width Γ(ψ2(3823))=520(100)  keV.

Published by the American Physical Society
2024
Limiting Light Dark Matter with Luminous Hadronic Loops
Authors: Diamond Melissa , Cappiello Christopher V. , Vincent Aaron C. , Bramante Joseph 
Published: January 2024

Dark matter is typically assumed not to couple to the photon at tree level. While annihilation to photons through quark loops is often considered in indirect detection searches, such loop-level effects are usually neglected in direct detection, as they are typically subdominant to tree-level dark-matter–nucleus scattering. However, when dark matter is lighter than around 100 MeV, it carries so little momentum that it is difficult to detect with nuclear recoils at all. We show that loops of low-energy hadronic states can generate an effective dark-matter–photon coupling, and thus lead to scattering with electrons even in the absence of tree-level dark-matter–electron scattering. For light mediators, this leads to an effective fractional electric charge that may be very strongly constrained by astrophysical observations. Current and upcoming searches for dark-matter–electron scattering can thus set limits on dark-matter–proton interactions down to 1 MeV and below.

Published by the American Physical Society
2024