bluuebunny/crossref_metadata_2025_split huggingface dataset:
Activity of DNA polymerase κ across the genome in human fibroblasts
Authors: Torres Mariela C. , Sun Dongxiao , Spratt Thomas E. 
Published: February 2024

AbstractDNA polymerase κ (Pol κ) is a specialized polymerase that has multiple cellular roles such as translesion DNA synthesis, replicating repetitive sequences, and nucleotide excision repair. We have developed a method for capturing DNA synthesized by Pol κ utilizing a Pol κ - specific substrate,N2-(4-ethynylbenzyl)-2′-deoxyguanosine (EBndG). After shearing of the DNA into 200-500bp lengths, the EBndG-containing DNA was covalently bound to biotin using the Cu(I)- catalyzed alkyne–azide cycloaddition reaction, and isolated with streptavidin beads. Isolated DNA was then ligated to adaptors, followed by PCR amplification and next-generation sequencing (NGS) to generate genome-wide repair maps. We have termed this method polymerase κ sequencing (polK-seq). Here we present the human genome maps for pol κ activity in an undamaged cell line. We found that pol κ activity was enhanced in euchromatin regions, the promoter of genes, and in DNA that is replicated early in S-phase.
Drug-Target Interactions Prediction at Scale: the Komet Algorithm with the LCIdb Dataset
Authors: Guichaoua Gwenn , Pinel Philippe , Hoffmann Brice , Azencott Chloé-Agathe , Stoven Véronique 
Published: February 2024

AbstractDrug-target interactions (DTIs) prediction algorithms are used are various stages of the drug discovery process. In this context, specific problems such as de-orphanization of a new therapeutic target, or target identification of a drug candidate arising from phenotypic screens require large-scale predictions across the protein and molecule spaces. DTI prediction heavily relies on supervised learning algorithms that use known DTIs to learn associations between molecule and protein features, allowing for the prediction of new interactions based on learned patterns. The algorithms must be broadly applicable to enable reliable predictions, even in regions of the protein or molecule spaces where data may be scarce. In this paper, we address two key challenges to fulfil these goals: building large, high-quality training datasets and designing prediction methods that can scale, in order to be trained on such large datasets. First, we introduce LCIdb, a curated, large-sized dataset of DTIs, offering extensive coverage of both the molecule and druggable protein spaces. Notably, LCIdb contains a much higher number of molecules than publicly available benchmarks, expanding coverage of the molecule space. Second, we propose Komet (Kronecker Optimized METhod), a DTI prediction pipeline designed for scalability without compromising performance. Komet leverages a three-step framework, incorporating efficient computation choices tailored for large datasets and involving the Nyström approximation. Specifically, Komet employs a Kronecker interaction module for (molecule, protein) pairs, which efficiently captures determinants in DTIs, and whose structure allows for reduced computational complexity and quasi-Newton optimization, ensuring that the model can handle large training sets, without compromising on performance. Our method is implemented in open-source software, leveraging GPU parallel computation for efficiency. We demonstrate the interest of our pipeline on various datasets, showing that Komet displays superior scalability and prediction performance compared to state-of-the-art deep learning approaches. Additionally, we illustrate the generalization properties of Komet by showing its performance on an external dataset, and on the publicly availableℒℌbenchmark designed for scaffold hopping problems. Komet is available open source athttps://komet.readthedocs.ioand all datasets, including LCIdb, can be found athttps://zenodo.org/records/10731712.
Protein aggregation is a consequence of the dormancy-inducing membrane toxin TisB inEscherichia coli
Authors: Leinberger Florian H. , Cassidy Liam , Edelmann Daniel , Schmid Nicole E. , Blumenkamp Patrick , Schmidt Sebastian , Natriashvili Ana , Ulbrich Maximilian H. , Tholey Andreas , Koch Hans-Georg , Berghoff Bork A. 
Published: February 2024

AbstractBacterial dormancy is a valuable strategy to survive stressful conditions. Toxins from chromosomal toxin-antitoxin systems have the potential to halt cell growth, induce dormancy and eventually promote a stress-tolerant persister state. Due to their potential toxicity when overexpressed, sophisticated expression systems are needed when studying toxin genes. Here, we present an optimized plasmid expression system for toxin genes based on an artificial 5’ untranslated region. We applied the system to induce expression of the toxin genetisBfrom the chromosomal type I toxin- antitoxin systemtisB/istR-1inEscherichia coli. TisB is a small hydrophobic protein that targets the inner membrane, resulting in depolarization and ATP depletion. We analyzed TisB-producing cells by RNA- sequencing and revealed several genes with a role in recovery from TisB-induced dormancy, including the chaperone genesibpB,spyandcpxP. The importance of chaperone genes suggested that TisB- producing cells are prone to protein aggregation, which was validated by anin vivofluorescent reporter system. We moved on to show that TisB is an essential factor for protein aggregation upon DNA damage mediated by the fluoroquinolone antibiotic ciprofloxacin inE. coliwild-type cells. The occurrence of protein aggregates correlates with an extended dormancy duration, which underscores their importance for the life cycle of TisB-dependent persister cells.ImportanceProtein aggregates occur in all living cells due to misfolding of proteins. In bacteria, protein aggregation is associated with cellular inactivity, which is related to dormancy and tolerance to stressful conditions, including the exposure to antibiotics. InEscherichia coli, the membrane toxin TisB is an important factor for dormancy and antibiotic tolerance upon DNA damage mediated by the fluoroquinolone antibiotic ciprofloxacin. Here, we show that TisB provokes protein aggregation, which in turn promotes a deeper state of cellular dormancy. Our study suggests that protein aggregation is a consequence of membrane toxins with the potential to affect the duration of dormancy and the outcome of antibiotic therapy.
TNFR1-mediated senescence and lack of TNFR2-signaling limit human intervertebral disc cell repair in back pain conditions
Authors: Gansau Jennifer , Grossi Elena , Rodriguez Levon , Wang Minghui , Laudier Damien M. , Chaudhary Saad , Hecht Andrew C. , Fu Wenyu , Sebra Robert , Liu Chuanju , Iatridis James C. 
Published: February 2024

ABSTRACTPoor intervertebral disc (IVD) healing causes IVD degeneration (IVDD) and progression to herniation and back pain. This study identified distinct roles of TNFα-receptors (TNFRs) in contributing to poor healing in painful IVDD. We first isolated IVDD tissue of back pain subjects and determined the complex pro-inflammatory mixture contained many chemokines for recruiting inflammatory cells. Single-cell RNA-sequencing of human IVDD tissues revealed these pro- inflammatory cytokines were dominantly expressed by a small macrophage-population. Human annulus fibrosus (hAF) cells treated with IVDD-conditioned media (CM) underwent senescence with greatly reduced metabolic rates and limited inflammatory responses. TNFR1 inhibition partially restored hAF cell metabolism sufficiently to enable a robust chemokine and cytokine response to CM. We showed that the pro-reparative TNFR2 was very limited on hIVD cell membranes so that TNFR2 inhibition with blocking antibodies or activation using Atsttrin had no effect on hAF cells with CM challenge. However, TNFR2 was expressed in high levels on macrophages identified in scRNA-seq analyses, suggesting their role in repair responses. Results therefore point to therapeutic strategies for painful IVDD involving immunomodulation of TNFR1 signaling in IVD cells to enhance metabolism and enable a more robust inflammatory response including recruitment or delivery of TNFR2 expressing immune cells to enhance IVD repair.SUMMARY STATEMENTTNFR1 signaling drives cells towards senesce and muted inflammatory response in painful intervertebral disc degeneration, while limited TNFR2 signaling may limit disc cell repair responses.
Kinetochores grip microtubules with directionally asymmetric strength
Authors: Larson Joshua D. , Heitkamp Natalie A. , Murray Lucas E. , Popchock Andrew R. , Biggins Sue , Asbury Charles L. 
Published: February 2024

SUMMARYFor accurate mitosis, all chromosomes must achieve ‘bi-orientation’, with replicated sister chromatids coupled via kinetochores to the plus ends of opposing microtubules. However, kinetochores first bind the sides of microtubules and subsequently find plus ends by directed transport or when side-attached microtubules shorten and bring their ends to the kinetochores. Mitotic accuracy depends on the selective release of erroneous attachments and proposed mechanisms have focused mainly on plus-end attachments. Whether erroneous side-attachments are distinguished from correct side-attachments is unknown. Here we show that side-attached kinetochores are very sensitive to microtubule polarity, gripping six-fold more strongly when pulled toward plus versus minus ends. This directionally asymmetric grip correlates with changes in the axial arrangement of subcomplexes within the kinetochores, suggesting that internal architecture dictates attachment strength. We propose that the kinetochore’s directional grip promotes accuracy specifically during early mitosis, by stabilizing correct attachments even before both sisters have found plus ends.
Effects of childhood hearing loss on the subcortical and cortical representation of speech
Authors: Calcus Axelle , Rosen Stuart 
Published: February 2024

AbstractLittle is known about the effects of childhood mild-to-moderate sensorineural hearing loss (MM HL) on the function of the auditory pathway. We aimed to examine the effect of childhood MM HL and the benefit of frequency-specific amplification on both subcortical and cortical auditory processing, and to relate it to speech-perceptual abilities. We recorded subcortical and cortical responses to speech syllables in nineteen children with congenital MM HL (unamplified and amplified), and sixteen children with typical hearing (unamplified sounds only). Speech perception was measured behaviourally. Congenital HL led to smaller subcortical and cortical responses to unamplified speech sounds. There was a significant benefit of amplification on subcortical and early, but not late, cortical responses, with some effects differing across age. No relationship was found between the neural and behavioural measures. Childhood MM HL affects both subcortical and cortical processing of speech. Amplification mostly benefits subcortical processing of speech in younger children. Childhood HL leads to functional changes in the processing of sounds, with amplification differentially affecting subcortical and cortical levels of the auditory pathway.
Drivers of Vessel Progenitor Fate Define Intermediate Mesoderm Dimensions by Inhibiting Kidney Progenitor Specification
Authors: Perens Elliot A. , Yelon Deborah 
Published: February 2024

ABSTRACTProper organ formation depends on the precise delineation of organ territories containing defined numbers of progenitor cells. Kidney progenitors reside in bilateral stripes of posterior mesoderm that are referred to as the intermediate mesoderm (IM). Previously, we showed that the transcription factors Hand2 and Osr1 act to strike a balance between the specification of the kidney progenitors in the IM and the vessel progenitors in the laterally adjacent territory. Recently, the transcription factor Npas4l – an early and essential driver of vessel and blood progenitor formation – was shown to inhibit kidney development. Here we demonstrate how kidney progenitor specification is coordinated byhand2,osr1, andnpas4l. We find thatnpas4lis necessary to inhibit IM formation. Consistent with the expression ofnpas4lflanking the medial and lateral sides of the IM, our findings suggest roles fornpas4lin defining the IM boundaries at each of these borders. At the lateral IM border,hand2promotes andosr1inhibits the formation ofnpas4l-expressing lateral vessel progenitors, andhand2requiresnpas4lto inhibit IM formation and to promote vessel formation. Meanwhile,npas4lappears to have an additional role in suppressing IM fate at the medial border:npas4lloss-of-function enhanceshand2mutant IM defects and results in excess IM generated outside of the lateralhand2-expressing territory. Together, our findings reveal that establishment of the medial and lateral boundaries of the IM requires inhibition of kidney progenitor specification by the neighboring drivers of vessel progenitor fate.
Hypoxia disrupts circadian rhythms in astrocytes and causes synapse engulfment defects
Authors: Li Li , Choi Jong Bin , Shin Chi Hong , Htun Saw , Mestan Sherry , Voss Anna , Shadrach Jennifer L. , Puno Alyssa , Nagar Dhriti , Ramirez Nephy , Rojo Daniela , Lee Samuel H. , Gibson Erin M. , Kaltschmidt Julia A. , Sloan Steven A. , Chung Won-Suk , Pasca Anca M. 
Published: February 2024

ABSTRACTAstrocytes are emerging as key regulators of neuronal synaptic network maturation and function, through control of synaptic pruning. This is important, because individuals with ASD have excess glutamatergic synapses in the cortex, but the biological mechanisms underlying this phenotype remain unclear.Here, we used human cortical organoids (hCO) derived from induced pluripotent stem cells (hiPSCs), to examine the effect of hypoxia on synapse engulfment in human astrocytes at postnatal-equivalent stages of development. We identified that hypoxia significantly inhibits the synaptosome phagocytosis, and that this phenotype is mediated through disruptions in the astrocytic circadian rhythm molecular pathway and subsequent decreased expression of MEGF10. Lastly, we demonstrated that circadian clock disruptions are sufficient to induce these observed phenotypes even in the absence of hypoxia, both in hCOs and within the mouse hippocampusin vivo.Our study uncovers a novel mechanistic link between hypoxia, circadian rhythms disruptions, and synapse pruning by astrocytes, and provides insight into the pathophysiology of ASD, and other neuropsychiatric diseases. Separately, the demonstration of the presence of circadian rhythms in hCOs opens an unprecedented opportunity to dissect the role of circadian clocks in normal brain development and how it contributes to specific diseases of environmental or genetic origin.
Discovery of novel compounds and target mechanisms using a high throughput, multiparametric phenotypic screen in a human neuronal model of Tuberous Sclerosis
Authors: Williams Luis A. , Ryan Steven J. , Joshi Vaibhav , Lewarch Caitlin , Elder Amy , McManus Owen , Godard Patrice , Sridhar Srinidhi , Jacques Jane , Grooms Jennifer , Fink James J. , Zhang Hongkang , Gillard Michel , Pegurier Cécile , Sabnis Yogesh , André Véronique , Steward Lucinda , Dedeurwaerdere Stefanie , Devinsky Orrin , Wolff Christian , Dempsey Graham T. 
Published: February 2024

SUMMARYTuberous sclerosis complex (TSC) is a rare genetic disorder caused by mutations in the mTOR pathway genesTSC1orTSC2. TSC can affect multiple organs including the brain, and most patients (75-90%) present with seizures during early childhood and intractable epilepsy throughout life. mTOR inhibitors, part of the current standard of care, lack the optimal characteristics to fully address patient phenotypes. Here, we report on the application of our all-optical electrophysiology platform for phenotypic screening in a human neuronal model of TSC. We used CRISPR/Cas9-isogenicTSC2−/−iPS cell lines to identify disease-associated changes to neuronal morphology, transcript expression and neuronal excitability. We established a robust multiparametric electrophysiological phenotype which we then validated in TSC patient-derived neurons. We used this phenotype to conduct a screen of ∼30,000 small molecule compounds in human iPS cell-derived neurons and identified chemical scaffolds that rescued the functional TSC disease parameters. Confirmed hits may act via different mechanisms than direct mTOR pathway inhibition. This strategy provides molecular starting points for therapeutic development in TSC and a framework for phenotype discovery and drug screening in other neurological disorders.
WITHDRAWN: Investigating the ability of music to induce calm in young adults
Authors: Shepherd Daniel , Pedersen Mangor , Vashista Geet , Kercher Amy , Hautus Michael J. 
Published: February 2024

Withdrawal StatementThe authors have withdrawn their manuscript owing to reviewer feedback. A revised version of this work will be uploaded with significant changes. Therefore, the authors do not wish this work to be cited as a reference for the project. If you have any questions, please contact the corresponding author.
Direction-aware functional class scoring enrichment analysis of Infinium DNA methylation data
Authors: Ziemann Mark , Abeysooriya Mandhri , Bora Anusuiya , Lamon Séverine , Kasu Mary Sravya , Norris Mitchell W. , Wong Yen Ting , Craig Jeffrey M. 
Published: February 2024

AbstractInfinium Methylation BeadChip arrays remain one of the most popular platforms for epigenome-wide association studies, but tools for downstream pathway analysis have their limitations. Functional class scoring (FCS) is a group of pathway enrichment techniques that involve the ranking of genes and evaluation of their collective regulation in biological systems, but the implementations described for Infinium methylation array data do not retain direction information, which is important for mechanistic understanding of genomic regulation. Here, we evaluate several candidate FCS methods that retain directional information. According to simulation results, the best-performing method involves the mean aggregation of probe limma t-statistics by gene followed by a rank-ANOVA enrichment test using the mitch package. This method, which we call “LAM”, outperformed an existing over-representation analysis method in simulations, and showed higher sensitivity and robustness in an analysis of real lung tumour-normal paired datasets. Using matched RNA-seq data we examine the relationship of methylation differences at promoters and gene bodies with RNA expression at the level of pathways in lung cancer. To demonstrate the utility of our approach, we apply it to three other contexts where public data were available. Firstly, we examine differential pathway methylation associated with chronological age. Secondly, we investigate pathway methylation differences in infants conceived with in vitro fertilisation. Lastly, we analyse differential pathway methylation in 19 disease states, identifying hundreds of novel associations. These results show LAM is a powerful method for the detection of differential pathway methylation as compared to existing methods. A reproducible vignette is provided to illustrate how to implement this method.
Identification and characterization of a bacterial periplasmic solute binding protein that binds L-amino acid amides
Authors: Smith Oliver B. , Frkic Rebecca L. , Rahman Marina G. , Jackson Colin J. , Kaczmarski Joe A. 
Published: February 2024

ABSTRACTPeriplasmic solute-binding proteins (SBPs) are key ligand recognition components of bacterial ATP-binding cassette (ABC) transporters that allow bacteria to import nutrients and metabolic precursors from the environment. Periplasmic SBPs comprise a large and diverse family of proteins, of which only a small number have been empirically characterized. In this work, we identify a set of 610 unique uncharacterized proteins within the SBP_bac_5 family that are found in conserved operons comprising genes encoding (i) ABC transport systems and (ii) putative amidases from the FmdA_AmdA family. From these uncharacterized SBP_bac_5 proteins, we characterize a representative periplasmic SBP fromMesorhizobiumsp. A09 (MeAmi_SBP) and show thatMeAmi_SBP bindsl-amino acid amides but not the correspondingl-amino acids. An X-ray crystal structure ofMeAmi_SBP bound tol-serinamide highlights the residues that impart distinct specificity forl-amino acid amides and reveals a structural Ca2+binding site within one of the lobes of the protein. We show that the residues involved in ligand and Ca2+binding are conserved amongst the 610 SBPs from experimentally uncharacterized FmdA_AmdA amidase-associated ABC transporter systems, suggesting these homologous systems are also likely to be involved in the sensing, uptake and metabolism ofl-amino acid amides across many Gram-negative nitrogen-fixing soil bacteria. We propose thatMeAmi_SBP is involved in the uptake of such solutes to supplement pathways such as the citric acid cycle and the glutamine synthetase-glutamate synthase pathway. This work expands our currently limited understanding of microbial interactions withl-amino acid amides and bacterial nitrogen utilization.
Power-to-Vitamins: Producing Folate (Vitamin B9) from Renewable Electric Power and CO2with a Microbial Protein System
Authors: Schmitz Lisa Marie , Kreitli Nicolai , Obermaier Lisa , Weber Nadine , Rychlik Michael , Angenent Largus T. 
Published: February 2024

AbstractMeeting a surging demand for superior micronutrient-rich protein sources and finding production practices that are less detrimental to the climate will be critical challenges of the 21stcentury. New technologies are needed to decouple food production from land use. Our group previously proposed a two-stage Power-to-Protein technology to produce microbial protein from renewable electric power and CO2. Two stages were operatedin series:(1)Clostridium ljungdahliiin Stage A to utilize H2 to reduce CO2 into acetate; and(2)Saccharomyces cerevisiaein Stage B to utilize O2 and produce microbial protein from acetate. Renewable energy would power water electrolysis to produce H2 and O2. A disadvantage ofC. ljungdahliiin Stage A is the need to continuously feed vitamins to sustain growth and acid production. Changing to the more robust thermophilic acetogenThermoanaerobacter kivuiavoids providing any vitamins. Additionally,S. cerevisiaeproduces folate when grown with acetate as a sole carbon source under aerobic conditions. A total folate concentration of 6.7 mg per 100 g biomass with an average biomass concentration of 3 g L-1in Stage B is achieved. The developed Power-to-Vitamin system enables folate production from renewable power and CO2 with zero or negative net-carbon emissions.