bluuebunny/crossref_metadata_2025_split huggingface dataset:
gplasCC: classification and reconstruction of plasmids from short-read sequencing data for any bacterial species
Authors: Paganini Julian A. , Kerkvliet Jesse J. , Teunis Gijs , Jordan Oscar , Plantinga Nienke L. , Meneses Rodrigo , Willems Rob J.L. , Arredondo-Alonso Sergio , Schürch Anita C. 
Published: December 2024

ABSTRACTPlasmids play a pivotal role in the spread of antibiotic resistance genes. Accurately reconstructing plasmids often requires long-read sequencing, but bacterial genomic data in publicly accessible repositories has historically been derived from short-read sequencing technology. We recently presented an approach for reconstructingEscherichia coliantimicrobial resistance plasmids using Illumina short reads. This method consisted of combining a robust binary classification tool named plasmidEC with gplas2, which is a tool that makes use of features of the assembly graph to bin predicted plasmid contigs into individual plasmids. Here, we developed gplasCC, a plasmidEC-simplification, capable of classifying plasmid contigs using Centrifuge databases. We have developed seven plasmidCC databases in addition to the database forE. coli: six species-specific models (Acinetobacter baumannii,Enterococcus faecium,Enterococcus faecalis,Klebsiella pneumoniae,Staphylococcus aureusandSalmonella enterica) and one species-independent model for less frequently studied bacterial species. We combined these models with gplas2 (now, gplasCC) to reconstruct plasmids from more than 100 bacterial species. This approach allows comprehensive analysis of the wealth of bacterial short-read sequencing data available in public repositories and advance our understanding of microbial plasmids.
Mammalian enhancers and GWASs act proximally and seldom skip active genes
Authors: Narita Takeo , Choudhary Chunaram 
Published: December 2024

SummaryEnhancers play a critical role in regulating transcription. Nearly 90% of human genetic variants identified in genome-wide association studies (GWAS) are located in distal regions, underscoring the importance of enhancers in human development, diseases, and traits. It is widely suggested that mammalian enhancers frequently skip active genes, and thus, linear proximity is a poor predictor of their targets. A key unresolved question is how often mammalian enhancers skip proximal active genes to specifically target distal genes. Genome-wide enhancer-promoter mapping shows that enhancers frequently bypass active genes, while ultra-deep locus-specific analyses reveal extensive multi-way interactions between enhancers and promoters, forming nested microcompartments. The functional significance of these seemingly contrasting phenomena remains unclear.Here, we compared hundreds of enhancer-target gene pairs identified using enhancer-promoter chromatin contact maps, enhancer-promoter RNA interaction data, and genome-scale CRISPR interference (CRISPRi) perturbations. Our findings reveal limited overlap between active gene-skipping enhancer-gene pairs identified through physical interaction mapping and CRISPRi. Additionally, promoters involved in multi-way enhancer interactions are not co-regulated by shared coactivators. Notably, gene-skipping and non-skipping enhancers identified via CRISPRi differ fundamentally in chromatin features, gene activation strength, false discovery rates, target gene distance, coactivator requirements, and cell-type specificity of target genes. These results suggest that gene-skipping enhancer-promoter interactions observed in chromatin and RNA-based analyses do not reliably predict functional enhancer-gene relationships. We propose that linear enhancer-promoter proximity and coactivator dependency offer a simple, scalable, and cost-effective method for genome-wide prediction of enhancer and GWAS targets, with accuracy comparable to state-of-the-art experimental techniques. While enhancers can skip active genes, such deliberate skipping appears to be the exception rather than the rule.
Prognostic Model Construction Based on Platinum-Free Interval in Ovarian Cancer and Its Implication for Chemotherapy Resistance
Authors: Zhang Yang , Kang Jihui , Wu Chuling , Xu Huishan , Ling Qin , Tan Hao , Zhang Zuwei , He Weipeng , Yao Shuzhong , Gu Langyu , Yang Guofen 
Published: December 2024

AbstractBackgroundWhile platinum sensitivity and resistance have long been central to treatment decisions in high-grade serous ovarian cancer (HGSOC), these categories are increasingly questioned in real-world clinical settings. This study seeks to develop a prognostic model based on platinum-free interval (PFI) as a reliable indicator of patient prognosis, with additional exploration of chemotherapy resistance-related genes and pathways.Methods70 HGSOC patients with varied gene expression profiles and corresponding clinical information of platinum-based chemotherapy responses were analysed. We first identified PFI-related genes (PRGs) that constituted a predictive signature for HGSOC by using univariate COX and LASSO regression analysis. We determined the optimal PFI indicative using linear correlation equations between gene expression levels and PFI. This time point was then employed to categorize patients into cohorts with good and poor prognosis, followed by an analysis of differentially expressed genes (DEGs) and their enriched pathways. Additionally, we utilized public available drug database to evaluate chemotherapeutic agents effective against the poor prognosis group.ResultsA signature comprising 10 PRGs (TUBA4A, ENSG00000232325.3, ENSG00000268080.1, KCNK9, ENSG00000230567.3, CST6, KNTC1, LINC02167, ENSG00000267469.1, NKAIN4) was established. Patients within the high-risk category defined by this signature exhibited a poorer prognosis and earlier recurrence than low-risk group. The prognostic model had a robust accuracy in predicting prognosis with an area under curve value >0.90. We estimated a PFI threshold of 22.37 months, which serves as a cutoff point to further differentiate groups with good and poor prognosis. KEGG pathways enrichment analysis revealed that taurine and hypotaurine metabolism, melanogenesis, Cushing syndrome, and mTOR signaling pathways were enriched in the poor prognosis group. We also performed drug resistance assessment and found that patients from the poor prognosis group were more sensitive to anti-cancer drugs such as Pevonedistat and GDC0810 than the good prognosis group.ConclusionsOur study constructed a prognostic model based on PFI for HGSOC and further explored its implications for chemotherapy resistance. These findings could enhance clinical applications and inform novel anticancer therapeutic strategies targeting HGSOC.
Pushing the boundary of child well-being: A spatial examination of child mortality in transition zones of extreme economic inequality and material hardship
Authors: Barboza-Salerno Gia Elise , Liebhard Brittany , Schockley-McCarthy Karla , Duhaney Sharefa 
Published: December 2024

AbstractHow do patterns of socioeconomic inequality shape the risk of child fatality in urban areas? Studies have demonstrated that intentional and accidental deaths of children are highly clustered into areas of social disadvantage. However, in complex urban settings, the risk of death to children is likely to exhibit a more localized spatial structure characterized by rapid changes in child fatality risk. The present research uses Bayesian hierarchical modeling to detect spatial discontinuities in child fatality risk in transition areas defined by elevated levels of economic hardship and inequality (EHI). The analysis detected 413 neighborhood boundaries characterized by extreme differences in EHI (i.e., a difference of four deciles). Living in proximity to a boundary of extreme difference, called a social frontier, is associated with a 22% higher relative risk of child fatality beyond measures of neighborhood racial segregation, concentrated disadvantage, residential mobility, and immigrant concentration. The significance of identifying neighborhoods characterized as a social frontier where children may benefit from additional preventive interventions is discussed in context.
Direct high-throughput deconvolution of unnatural bases via nanopore sequencing and bootstrapped learning
Authors: Perez Mauricio Lisboa , Kimoto Michiko , Rajakumar Priscilla , Suphavilai Chayaporn , da Silva Rafael Peres , Tan Hui Pen , Xun Ong Nicholas Ting , Nicholas Hannah , Hirao Ichiro , Leong Chew Wei , Nagarajan Niranjan 
Published: December 2024

AbstractThe discovery of synthetic xeno-nucleic acids (XNAs) that can basepair as unnatural bases (UBs) to expand the genetic alphabet has spawned interest in many applications, from synthetic biology to DNA storage. However, the inability to read XNAs in a direct, high-throughput manner has been a significant limitation for xenobiology. Here we demonstrate that XNA-containing templates can be directly and robustly sequenced (>2.3 million reads/flowcell, similar to DNA controls) on a MinION sequencer from Oxford Nanopore Technologies to obtain signal data that is significantly distinct from DNA controls (median fold-change >6×). To enable training of machine learning models that deconvolve these signals and basecall XNAs along with natural bases, we developed a framework to synthesize a complex pool of 1,024 UB-containing oligonucleotides with diverse 6-mer sequence contexts and high XNA purity (>90% UB-insertion on average). Bootstrapped models to enable data preparation, and data augmentation with spliced XNA reads to provide high context diversity, enabled learning of a generalizable model to call natural as well as unnatural bases with high accuracy (>80%) and specificity (99%). These results highlight the versatility of nanopore sequencing as a platform for interrogating nucleic acids for xenobiology applications, and the potential to transform the study of genetic material beyond those that use canonical bases.
Analysis of gene expression inAedes aegyptisuggests changes in early genetic control of mosquito development
Authors: Coutinho-dos-Santos Renata , Santos Daniele G. , Ribeiro Lupis , Mucherino-Muñoz Jonathan J. , Uhl Marcelle , Logullo Carlos , Mendonça-Amarante A , Fantappie M , Nunes-da-Fonseca Rodrigo 
Published: December 2024

ABSTRACTAedes aegypti,a critical vector for tropical diseases, poses significant challenges for studying its embryogenesis due to difficulties in removing its rigid chorion and achieving effective fixation for in situ hybridization. Here, we present novel methodologies for fixation, dechorionation, DAPI staining, and in situ hybridization, enabling the detailed analysis of gene expression throughoutAe. aegyptiembryogenesis. By synchronizing eggs at various developmental stages (0–72 h), we localized the transcripts of the gap genemille-pattes (mlpt),the dorsoventral gene cactus(cact),and the pioneer transcription factor (pTF)zelda (zld).In situ hybridization and RT-qPCR analyses revealed thatmlpt and cactare maternally expressed, while zldexpression begins zygotically during cellularization and later becomes prominent in neuroblasts. Analysis of previously published transcriptomes suggests that three other pTFs,CLAMP, grainyheadandGAF,are also maternally expressed and may function as pioneer transcription factors duringAe. aegyptiembryogenesis. These findings suggest that the transcription factors responsible for genome activation in mosquitoes differ from those in fruit flies, highlighting significant divergence in the genetic regulation of early Dipteran embryogenesis.
Expanding the CarD interaction network: CrsL is a novel transcription factor inMycobacterium smegmatis
Authors: Shoman Mahmoud , Jirát Matějčková Jitka , Schwarz Marek , Černý Martin , Borah Nabajyoti , Vaňková Hausnerová Viola , Šiková Michaela , Šanderová Hana , Halada Petr , Hubálek Martin , Dvořáková Věra , Převorovský Martin , Holubová Jana , Staněk Ondřej , Krásný Libor , Žídek Lukáš , Hnilicová Jarmila 
Published: December 2024

ABSTRACTBacterial transcription regulation is critical for adaptation and survival. CarD is an essential transcription factor in mycobacteria involved in regulation of gene expression. We searched for CarD interaction partners in the model organismMycobacterium smegmatisand identified two proteins: ApeB (MSMEG_5828) and an uncharacterized protein, which we named CrsL (MSMEG_5890). While ApeB interacted with CarD only when CarD was overexpressed, CrsL associated with CarD at its physiological levels. CrsL is a 5.7 kDa protein shown by NMR to be intrinsically disordered. CrsL homologs are present in actinobacteria including pathogenic species such asMycobacterium tuberculosis. CrsL directly interacts with CarD and binds RNAP. ChIP-seq showed that CrsL associates with promoters of actively transcribed genes and ∼75 % of these regions are also associated with CarD. RNA-seq showed ∼50% and ∼66% overlap in differentially expressed genes between CrsL and CarD knockdowns during exponential and stationary phases, respectively. CrsL represses expression of DesA desaturase (MSMEG_5773) and DEAD/DEAH-box RNA helicaseMSMEG_1930, which are important for adaptation to cold stress. Furthermore, CrsL promotes the growth ofM. smegmatisat elevated temperature. In summary, this study identifies CrsL as a novel actinobacterial transcription factor and provides a basis for its further investigation.
Distinct roles for theStaphylococcus aureusPOT transporter DtpT in di/tripeptide uptake and glutathione utilisation inside human macrophages
Authors: Khan Imran , MacDonald Sandy J , Markusson Sigurbjörn , Robson Callum , Parker Joanne L , Newstead Simon , Boucher Dave , Van Der Woude Marjan , Thomas Gavin H 
Published: December 2024

AbstractPeptides available in biological niches inhabited by the human pathogenStaphylococcus aureusserve as a rich source of amino acids required for growth and successful host colonisation. Uptake of peptides byS. aureusinvolves at least two transport systems: the POT family di/tri-peptide permease DtpT and the oligopeptide ABC transporter Opp3. Here we study the individual and combined functions of DtpT and Opp3 in enabling utilisation of 282 di-/tri-peptides via a high-throughput phenotypic screen. We reveal that many peptides can be utilised via either transporter, though DtpT appears to be the primary route of uptake for dipeptides. Intriguingly, we demonstrate a preference for Asp/Glu-containing peptides among putative DtpT substrates. To measure DtpT-mediated peptide transport directly, the protein was purified and reconstituted into proteoliposomes and active transport of diverse di- and tri-peptides was demonstrated, supporting the conclusions of the phenotypic screen. During thisin vitroanalysis, we also found that DtpT could transport the biologically prevalent tripeptide reduced glutathione (GSH). In the absence of the known glutathione transporter Gis,dtpTis essential for growth under conditions where GSH is supplied as the sole sulphur source, identifying DtpT as the predicted second GSH uptake system ofS. aureus. Site-directed mutagenesis of the predicted ligand binding site of DtpT suggests GSH binds the protein vertically in a manner dependent on interactions with Gln310. Finally, we demonstrate that GSH transport is required byS. aureusfor complete fitness duringin vitromacrophage infection experiments, and our data suggest that GSH uptake plays a role in modulating host-pathogen interactions in these infections. Together, these data reveal important new functions for DtpT, both in the utilisation of diverse peptides for growth but also providing the first clues toward a distinct role of DtpT during intracellular infection.
Bilingual Exposure and Sex Shape Developmental Trajectories of Brain Responses to Speech-Sound Features in Infants
Authors: Puertollano Marta , Gorina-Careta Natàlia , Ijjou-Kadiri Siham , Mondéjar-Segovia Alejandro , Gómez-Roig María Dolores , Escera Carles 
Published: December 2024

AbstractAs the auditory brain becomes functional during the third trimester of pregnancy, both biological and environmental processes begin shaping its maturation, influencing how speech sounds are perceived. Biological factors, such as sex, introduce early genetic differences, while environmental experiences, like bilingualism, modulate the auditory input that infants receive. Although existing research highlights the impact of sex and bilingualism on the development of speech perception, the neural mechanisms remain unclear. In this study, we recorded frequency-following responses (FFRs) longitudinally, at birth, six months, and twelve months of age in 73 infants exposed to varying degrees of bilingual input. We modeled the developmental trajectories for neural encoding of voice pitch and speech formant structure, finding significant maturation during the first six months, followed by stabilization through the first year. Distinct developmental patterns emerged as a function of sex and bilingualism, revealing their influence on neural attunement to key speech-sound features. Bilingual exposure notably predicted lower neural pitch encoding values at six months, but higher values by twelve months. A positive effect of bilingualism on speech formant encoding was observed throughout the first year. These findings reveal how biological and environmental factors contribute to individual variability in early auditory development and speech acquisition.HighlightsBilingualism and sex impact early developmental trajectories in neural speech encodingResults suggest a female advantage in early neural encoding of speech-sound featuresBilingual exposure positively modulates infant neural speech encoding
Drug screening targeting TREM2-TYROBP transmembrane binding
Authors: Cobas-Carreño M. , Esteban-Martos A. , Tomas-Gallardo L. , Iribarren I. , Gonzalez-Palma L. , Rivera-Ramos A. , Elena-Guerra J. , Alarcon-Martin E. , Ruiz R. , Bravo M.J. , Venero J.L. , Morató X. , Ruiz A. , Royo J.L. 
Published: December 2024

AbstractTREM2encodes a microglial membrane receptor involved in the disease-associated microglia (DAM) phenotype whose activation requires the transmembrane interaction with TYROBP. Mutations inTREM2represent a high-impact risk factor for Alzheimer’s disease (AD) which turned TREM2 into a significant drug target. We present a bacterial two-hybrid (B2H) system designed for high-throughput screening of modulators for the TREM2-TYROBP transmembrane interaction. In a pilot study, 315 FDA-approved drugs were analyzed to identify potential binding modifiers. Our pipeline includes multiple filtering steps to ensure candidate specificity. The screening suggested two potential candidates that were finally assayed in the human microglial cell line HMC3. Upon stimulation with anti-TREM2 mAb, pSYK/SYK ratios were calculated in the presence of the candidates. As a result, we found that varenicline, a smoking cessation medication, can be considered as a transmembrane agonist of the TREM2-TYROBP interaction.
Explainable AI-guided identification of a novel protein-RNA interactive frame for selective siRNA accumulation in plants
Authors: Enoki Natsumi , Kuwada Eriko , Matsuo Shinnosuke , Fujita Naoko , Noda Saki , Matsubayashi Yoshikatsu , Uchida Seiichi , Akagi Takashi 
Published: December 2024

AbstractSmall interference RNA (siRNA) selectively accumulates and acts in RNA interference (RNAi). Although the components involved in siRNA production have long been the focus of studies to elucidate RNAi processes, the mechanism(s) for selectivity of siRNA (or RNAi effectivity) remains unclear. In a novel approach, we developed a progressive deep learning (DL) framework integrating Transformer and convolutional neural networks to predict the sequences of selectively accumulated siRNAs across various land plant species. These approaches achieved high-accuracy prediction of selectively accumulated 21-nt siRNAs and further identified their key signals, which are positionally and linguistically flexible sequences surrounding the target siRNA. We experimentally validated the contribution of these flexible key signal sequences to siRNA accumulation selectivity using virus-induced gene silencing (VIGS) inNicotiana benthamiana, and identified RNA-binding proteins that directly recognize the key signal sequences to act for selective siRNA accumulation. These insights provide a novel framework for investigating RNAi mechanisms in plants.One sentence summaryWe discovered a novel mechanism centered on RNA-protein interactions involving the selective accumulation of small-RNAs in plants by applying advanced deep learning frames.
Control of Epithelial Tissue Organization by mRNA Localization
Authors: Mason Devon E. , Madsen Thomas D. , Gasparski Alexander N. , Jiwnani Neal , Lechler Terry , Weigert Roberto , Iglesias-Bartolome Ramiro , Mili Stavroula 
Published: December 2024

AbstractmRNA localization to specific subcellular regions is common in mammalian cells but poorly understood in terms of its physiological roles1–6,7. This study demonstrates the functional importance ofNet1mRNA, which we find prominently localized at the dermal-epidermal junction (DEJ) in stratified squamous epithelia.Net1mRNA accumulates at DEJ protrusion-like structures that interact with the basement membrane and connect to a mechanosensitive network of microfibrils. DisruptingNet1mRNA localization in mouse epithelium alters DEJ morphology and keratinocyte-matrix connections, affecting tissue homeostasis. mRNA localization dictates Net1 protein distribution and its function as a RhoA GTPase exchange factor (GEF). Altered RhoA activity is in turn sufficient to alter the ultrastructure of the DEJ. This study provides a high-resolutionin vivoview of mRNA targeting in a physiological context. It further demonstrates how the subcellular localization of a single mRNA can significantly influence mammalian epithelial tissue organization, thus revealing an unappreciated level of post-transcriptional regulation that controls tissue physiology.
Heat-Induced Phosphatidylserine Changes Drive HSPA1A’s Plasma Membrane Localization
Authors: Low Jensen , Altman Rachel , Badolian Allen , Cuaresma Azalea Blythe , Briseño Carolina , Keshet Uri , Fiehn Oliver , Stahelin Robert V. , Nikolaidis Nikolas 
Published: December 2024

AbstractHeat shock protein A1A (HSPA1A) is a molecular chaperone crucial in cell survival. In addition to its cytosolic functions, HSPA1A translocates to heat-shocked and cancer cells’ plasma membrane (PM). In cancer, PM-localized HSPA1A (mHSPA1A) is associated with increased tumor aggressiveness and therapeutic resistance, suggesting that preventing its membrane localization could have therapeutic value. This translocation depends on HSPA1A’s interaction with PM phospholipids, including phosphatidylserine (PS). Although PS binding regulates HSPA1A’s membrane localization, the exact trigger for this movement remains unclear. Given that lipid modifications are a cancer hallmark, we hypothesized that PS is a crucial lipid driving HSPA1A translocation and that heat-induced changes in PS levels trigger HSPA1A’s PM localization in response to heat stress. We tested this hypothesis using pharmacological inhibition and RNA interference (RNAi) targeting PS synthesis, combined with confocal microscopy, lipidomics, and western blotting. Lipidomic analysis and PS-specific biosensors confirmed a heat shock-induced PS increase, peaking immediately post-stress. Inhibition of PS synthesis with fendiline and RNAi significantly reduced HSPA1A’s PM localization, while depletion of cholesterol or fatty acids had minimal effects, confirming specificity for PS. Further experiments showed that PS saturation and elongation changes did not significantly impact HSPA1A’s PM localization, indicating that the total PS increase, rather than specific PS species, is the critical factor. These findings reshape current models of HSPA1A trafficking, demonstrating that PS is a crucial regulator of HSPA1A’s membrane translocation during the heat shock response. This work offers new insights into lipid-regulated protein trafficking and highlights the importance of PS in controlling cellular responses to stress.