bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parapipe: a Pipeline for Handling Parasite NGS Datasets and its Application to Cryptosporidium
Authors: Morris Arthur V. , Robinson Guy , Chalmers Rachel , Caccio Simone , Connor Tom 
Published: January 2025

0.0AbstractCryptosporidium, a protozoan parasite of significant public health concern, is responsible for severe diarrheal diseases, particularly in immunocompromised individuals and young children in resource-limited settings. Analysis of whole genome next generation sequencing (NGS) data is a critical next step in improving our understanding ofCryptosporidiumepidemiology, transmission dynamics, and genetic diversity. However, effective analysis of NGS data in a public health context necessitates the development of robust, validated bioinformatics tools. Here, we present Parapipe, a modular ISO accreditable bioinformatics pipeline designed for high-throughput processing and analysis ofCryptosporidiumNGS datasets. Built using Nextflow DSL2 and containerized with Singularity, Parapipe is portable, scalable, and capable of end-to-end analyses, including quality control, variant calling, multiplicity of infection (MOI) investigations and phylogenomic clustering analysis.Using both simulated and real-world datasets, we demonstrate Parapipe’s ability to resolve genetic heterogeneity, identify mixed infections, and generate high-resolution phylogenomic insights. Here, we use it to carry out a comparison between whole genome single nucleotide polymorphism (wgSNP) typing and the conventionally used gp60 molecular typing scheme. Compared to existing pipelines, Parapipe uniquely integrates MOI analysis, enabling the differentiation of mixed infections and supporting epidemiological investigations. Parapipe’s design facilitates integration with geographic, demographic, epidemiological and environmental data, enhancing its utility for tracking transmission pathways and outbreak sources.Parapipe represents a significant advance in utilising genomics for public health surveillance ofCryptosporidium, offering a streamlined and reproducible framework for analysis with potential application to other pathogenic protozoa. By automating complex workflows and enabling detailed genomic characterization, Parapipe provides a valuable tool for public health agencies and researchers, supporting efforts to mitigate the global burden of cryptosporidiosis.
High-throughput assessment of exercise-induced adaptations and muscle function in health and ageing
Authors: Malita Alina , Texada Michael J. , Kubrak Olga , Lassen Mette , Skakkebaek Anne H. , Bradic Ivan , Larsen Martin R. , Ahrentløv Nadja , Rewitz Kim 
Published: January 2025

AbstractExercise improves metabolic health, enhances insulin sensitivity, and preserves muscle function, making it a core intervention to combat age-related decline and metabolic disorders. However, large-scale genetic and pharmacological screens to uncover exercise-induced adaptations remain challenging in mammalian models due to their complexity and cost. Here, we present the ClimbMaster, a fully automated, computer-controlled platform for assessing exercise-induced adaptations and physical performance in the fruit flyDrosophila. The system uses repeated climbing exercises to simulate endurance training, enabling precise measurements of climbing speed and endurance across different conditions and life stages. Using the ClimbMaster, we demonstrate that exercise improves endurance, promotes fat loss, and enhances insulin-mediated glucose uptake and modulates insulin sensitivity in muscle, highlighting key conserved features of exercise physiology between flies and mammals. We also show that rapamycin, a TOR inhibitor, mitigates age-related performance decline. This platform enables high-throughput screens to investigate genetic and environmental factors influencing muscle health, aging, and insulin resistance, providing a scalable and versatile tool for the identification of novel therapeutic targets to improve healthspan and physical performance.
Unveiling the Conformational Dynamics of the Histone Tails Using Markov State Modeling
Authors: Patel Rutika , Loverde Sharon M. 
Published: January 2025

AbstractBiomolecules predominantly exert their function through altering conformational dynamics. The nucleosome core particle (NCP) is the fundamental unit of chromatin. DNA with ∼146 base pairs wrap around the histone octamer to form a nucleosome. The histone octamer is comprised of two copies of each histone protein (H3, H4, H2A, and H2B) with a globular core and disordered N-terminal tails. Epigenetic modifications of the histone N-terminal tails play a critical role in the regulation of chromatin structure and biological processes such as transcription and DNA repair. Here, we report all-atomistic molecular dynamics (MD) simulations of the nucleosome at microsecond timescales to construct Markov state models (MSMs) to elucidate distinct conformations of the histone tails. We employ the time-lagged independent component analysis (tICA) to capture their essential slow dynamics, with k-means clustering used to discretize the conformational space. MSMs unveil distinct states and transition probabilities to characterize the dynamics and kinetics of the tails. Next, we focus on the H2B tail, one of the least studied tails. We show that acetylation increases secondary structure formation, with an increase in transition rates. These findings will aid in understanding the functional implications of tail conformations in nucleosome stability and gene regulation.Significance StatementThe nucleosome is the fundamental repeat unit of chromatin, composed of a histone octamer and DNA. Each histone has a globular core and N-terminal tail regions. N-terminal tails are major sites for post-translational modifications, chromatin structure, and gene regulation. Using all-atom molecular dynamics simulations of the nucleosome to examine the dynamics of histone tails and analyze the effects of one of the histone modifications, such as acetylation on histone tails. We explore tail dynamics and kinetics using Markov State Models (MSMs) to gain insight into histone tail structural changes. Acetylation of the H2B tail shows an increased dynamics of the tail based on transition rates. Our study characterizes transition rates of all histone tails that can influence nucleosome plasticity and gene regulation.
The epigenetic factorZrf1regulates intestinal stem cell proliferation during midgut regeneration
Authors: Shun Li Joshua Shing , Liu Ying , Kim Ah-Ram , Qadiri Mujeeb , Xu Jun , Xia Baolong , Binari Richard , Asara John M. , Hu Yanhui , Perrimon Norbert 
Published: January 2025

AbstractStem cells are essential for tissue maintenance and regeneration, balancing self-renewal and differentiation to support homeostasis and repair. Through an RNAi screen in theDrosophilamidgut, we identified the epigenetic factor Zrf1 as a critical regulator of intestinal stem cell (ISC) proliferation. Functional analyses reveal that Zrf1 integrates inputs from multiple signaling pathways and interacts with components of the RNA-induced silencing complex (RISC). Zrf1 mutants exhibit elevated expression of transposable elements (TEs) and chromatin disruption, highlighting a broader role in genome stability. Single-nuclei RNA sequencing (snRNA-seq) further demonstrated the influence of Zrf1 on chromatin organization and TE repression, particularly within stem cell progenitors. Our findings suggest that Zrf1 is potentially a key chromatin regulator necessary for maintaining stem cell proliferation and genome integrity, enhancing our understanding of the molecular controls underlying stem cell function and chromatin dynamics.
Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes
Authors: Kellom Matthew , Berg Maureen , Chen I-Min A. , Chu Ken , Clum Alicia , Huntemann Marcel , Ivanova Natalia N. , Kyrpides Nikos C. , Mukherjee Supratim , Reddy T. B. K. , Roux Simon , Seshadri Rekha , Szabo Gitta , Varghese Neha J. , Woyke Tanja , Eloe-Fadrosh Emiley A. 
Published: January 2025

AbstractMicrobiomes are constrained by physicochemical conditions, nutrient regimes, and community interactions across diverse environments, yet genomic signatures of this adaptation remain unclear. Metagenome sequencing is a powerful technique to analyze genomic content in the context of natural environments, establishing concepts of microbial ecological trends. Here, we developed a data discovery tool - a tetranucleotide-informed metagenome stability diagram - that is publicly available in the Integrated Microbial Genomes and Microbiomes (IMG/M) platform for metagenome-ecosystem analyses. We analyzed the tetranucleotide frequencies from quality-filtered and unassembled sequence data of over 12,000 metagenomes to assess ecosystem-specific microbial community composition and function. We found that tetranucleotide frequencies can differentiate communities across various natural environments, and that specific functional and metabolic trends can be observed in this structuring. Our tool places metagenomes sampled from diverse environments into clusters and along gradients of tetranucleotide frequency similarity, suggesting microbiome community compositions specific to gradient conditions. Within the resulting metagenome clusters, we identify protein-coding gene identifiers that are most differentiated between ecosystem classifications. We plan for annual updates to the metagenome stability diagram in IMG/M with new data, allowing for refinement of the ecosystem classifications delineated here. This framework has the potential to inform future studies on microbiome engineering, bioremediation, and the prediction of microbial community responses to environmental change.ImportanceMicrobes adapt to diverse environments influenced by factors like temperature, acidity, and nutrient availability. We developed a new tool to analyze and visualize the genetic makeup of over 12,000 microbial communities, revealing patterns linked to specific functions and metabolic processes. This tool groups similar microbial communities and identifies characteristic genes within environments. By continually updating this tool, we aim to advance our understanding of microbial ecology, enabling applications like microbial engineering, bioremediation, and predicting responses to environmental change.
A Single-Cell Atlas of the Upper Respiratory Epithelium Reveals Heterogeneity in Cell Types and Patterning Strategies
Authors: Foote Alexander G. , Sun Xin 
Published: January 2025

SUMMARYThe upper respiratory tract, organized along the pharyngolaryngeal-to-tracheobronchial axis, is essential for homeostatic functions such as breathing and vocalization. The upper respiratory epithelium is frequently exposed to pollutants and pathogens, making this an area of first-line defense against respiratory injury and infection. The respiratory epithelium is composed of a rich array of specialized cell types, each with unique capabilities in immune defense and injury repair. However, the precise transcriptomic signature and spatial distribution of these cell populations, as well as potential cell subpopulations, have not been well defined. Here, using single cell RNAseq combined with spatial validation, we present a comprehensive atlas of the mouse upper respiratory epithelium. We systematically analyzed our rich RNAseq dataset of the upper respiratory epithelium to reveal 17 cell types, which we further organized into three spatially distinct compartments: theTmprss11a+ pharyngolaryngeal, theNkx2-1+ tracheobronchial, and theDmbt1+ submucosal gland epithelium. We profiled/analyzed the pharyngolaryngeal epithelium, composed of stratified squamous epithelium, and identified distinct regional signatures, including a Keratin gene expression code. In profiling the tracheobronchial epithelium, which is composed of a pseudostratified epithelium-with the exception of the hillock structure-we identified that regional luminal cells, such as club cells and basal cells, show varying gradients of marker expression along the proximal-distal and/or dorsal-ventral axis. Lastly, our analysis of the submucosal gland epithelium, composed of an array of cell types, such as the unique myoepithelial cells, revealed the colorful diversity of between and within cell populations. Our single-cell atlas with spatial validation highlights the distinct transcriptional programs of the upper respiratory epithelium and serves as a valuable resource for future investigations to address how cells behave in homeostasis and pathogenesis.Highlights- Defined three spatially distinct epithelial compartments,Tmprss11a+ pharyngolaryngeal,Nkx2-1+ tracheobronchial, andDmbt1+ submucosal gland, comprising 17 total cell types- Profiled Keratin gene expression code along proximal-distal and basal-luminal axes and highlighted “stress-induced” Keratins KRT6A and KRT17 at homeostasis- Demarcated expression gradients ofScgb1a1+ andScgb3a2+club cells along the proximal-distal axes- Specified submucosal gland cell heterogeneity includingNkx3-1+mucin-producing cells, with ACTA2+ basal myoepithelial cells exhibiting gene profile for neuroimmune mediated signaling
Decoding Mechanisms of PTEN Missense Mutations in Cancer and Autism Spectrum Disorder using Interpretable Machine Learning Approaches
Authors: Yang Miao , Wang Jingran , Zhou Ziyun , Li Wentian , Verkhivker Gennady , Xiao Fei , Hu Guang 
Published: January 2025

ABSTRACTMissense mutations in oncogenic proteins that are concurrently associated with neurodevelopmental disorders have garnered significant attention. Phosphatase and tensin homolog (PTEN) serves as a paradigmatic model for mapping its mutational landscape and identifying genotypic predictors of distinct phenotypic outcomes, including cancer and autism spectrum disorder (ASD). Despite extensive research into the genotype-phenotype correlations of PTEN mutations, the mechanisms underlying the dual association of specific PTEN mutations with both cancer and ASD (PTEN-cancer/ASD mutations) remain elusive. This study introduces an integrative approach that combines machine learning (ML) with structural dynamics to elucidate the molecular effects of PTEN-cancer/ASD mutations. Analysis of biophysical and network biology-based signatures reveals a complex energetic and functional landscape. Subsequently, an ML model and corresponding integrated score were developed to classify and predict PTEN-cancer/ASD mutations, underscoring the significance of protein dynamics in predicting cellular phenotypes. Further molecular dynamics simulations demonstrated that PTEN-cancer/ASD mutations induce dynamic alterations characterized by open conformational changes restricted to the P loop and coupled with inter-domain allosteric regulation. This research aims to enhance the genotypic and phenotypic understanding of PTEN-cancer/ASD mutations through an interpretable ML model integrated with structural dynamics analysis. By identifying shared mechanisms between cancer and ASD, the findings pave the way for the development of novel therapeutic strategies.
Multiparametric optimization of human primary B-cell cultures using Design of Experiments
Authors: Rovsing Anne Bruun , Green Kenneth , Jensen Lisbeth , Nielsen Ian Helstrup , Mikkelsen Jacob Giehm , Degn Søren E. 
Published: January 2025

AbstractB cells are essential in the immune system, driving antibody production, cytokine secretion, and antigen presentation. Studies in mouse models have illuminated key mechanisms underlying B-cell activation, differentiation, class-switch recombination, and somatic hypermutation. However, the extent to which these findings translate to human biology remains unclear. To address this, we developed a human primary B-cell culture system using feeder cells engineered to express CD40L, supplemented with the cytokines BAFF, IL-4, and IL-21. Using a Design of Experiments (DOE) approach, we optimized critical parameters and dissected the individual contributions of each specific factor. Our results reveal that BAFF plays a negligible role, and IL-21 has more subtle effects, whereas CD40L and IL-4 are critical determinants of cell viability, proliferation and IgE class-switching. Furthermore, we find that engineered feeder cells can serve equally well as a source of cytokines, but providing these in purified form increases the flexibility of the system. This platform enables detailed investigation of human B-cell biology, offering insights into intrinsic and extrinsic regulators of antibody responses and providing a foundation forin vitroproduction of human primary antibodies.
Proximal relationships of moonlighting Proteins inEscherichia coli: a mathematical genomic perspective
Authors: Nawn Debaleena , Hassan Sk. Sarif , Sil Moumita , Ghosh Ankita , Goswami Arunava , Uversky Vladimir N. 
Published: January 2025

AbstractMoonlighting proteins inEscherichia coli(E.coli) perform multiple independent functions without altering their primary amino acid sequence, challenging the “one gene-one enzyme” hypothesis. Bacterial proteins serve various functions, including host cell adhesion, extracellular matrix interaction, and immune modulation, while also supporting essential physiological processes within the bacteria. Identifying these proteins in pathogens and tracking their genetic changes is crucial for understanding bacterial survival and virulence. A quantitative understanding of these proteins is pivotal as it enables the identification of specific patterns and relationships between amino acid composition, protein stability, and functional versatility. This study quantitatively analyzes fiftyE. colimoonlighting proteins, focusing on their structural and functional features. Key findings include variability in amino acid composition, with alanine predominating, and a preference for non-polar residues, which may enhance protein stability. Quantitative features analyses identified seven distinct proximal sets, reflecting the proteins’ spatial arrangements of amino acids, structural diversity, and functional roles in processes such as metabolism, stress response, and gene regulation. These results deepen our understanding of the multifunctionality ofE. colimoonlighting proteins, indicating their adaptability and implications for bacterial survival and pathogenicity.
A field-focused systems approach reveals mRNA covalent modifications linked to sorghum growth and development under drought stress
Authors: Yu Li’ang , Melandri Giovanni , Nelson Dittrich Anna C. , Calleja Sebastian , Palos Kyle , Srinivasan Aparna , Brewer Emily K. , Henderson Riley , Garcia Ciara Denise , Zhang Xiaodan , Rozzi Bruno , Eveland Andrea , Schroeder Susan J. , Stern David , Skirycz Aleksandra , Lyons Eric , Arnold A. Elizabeth , Gregory Brian D. , Nelson Andrew D. L. , Pauli Duke 
Published: January 2025

AbstractCovalent RNA modifications (RCMs) are post-transcriptional changes to the chemical composition of RNA. RCMs influence mRNA stability, regulate transcription and translation efficiency, and play critical roles in the growth and development of eukaryotes. However, their role in plants remains poorly understood, particularly as they relate to performance in the field under stress conditions. In this study, we grew a panel of six diverse sorghum (S. bicolor) accessions in the field during the summer in central Arizona and examined their physiological and molecular responses to drought and heat stress over time. We then explored the molecular features that contributed to plant performance under stress. To do so, we combined genomic, transcriptomic, epitranscriptomic, physiological, and metabolomic data in a systems-level approach. Co-expression network analyses uncovered two modules of interest, one controlled primarily by a single stress-responsive transcription factor, SbCDF3, and the other by an RCM, dihydrouridine. While the CDF3 module largely contained a set of stress response and photosynthesis-associated genes that were positively correlated with plant performance, the dihydrouridine-associated module was largely comprised of photosynthesis and metabolism genes, including SbPPDK1, which is integral to C4 photosynthesis in the grasses. In addition, the transcript encoding the enzyme responsible for this RCM, dihydrouridine synthase (SbDUS2), was also present in this module, and its abundance was positively correlated with photosynthetic traits andSbPPDK1abundance. Given that this highly conserved RCM has never been characterized in plants, we examined loss of function mutants for the DUS2 enzyme in Arabidopsis, demonstrating decreases in plant growth and performance under heat stress in this background. Our work highlights both a key transcription factor, CDF3, for breeding in thePoaceae. In addition, for the xfirst time in plants, we reveal a role for the RCM dihydrouridine in modifying conserved, core metabolic and photosynthesis-associated transcripts in plants.
Towards a comprehensive anatomical matrix for crown birds: phylogenetic insights from the pectoral girdle and forelimb skeleton
Authors: Chen Albert , Steell Elizabeth M. , Benson Roger B. J. , Field Daniel J. 
Published: January 2025

AbstractPhylogenetic analyses of phenotypic characters in crown-group birds often recover results that are strongly incongruous with the findings of recent phylogenomic analyses. Furthermore, existing morphological datasets for crown birds are frequently limited by restricted taxon or character sampling, inconsistent character construction, incorrect scoring, or a combination of several of these factors. As part of an effort to address these limitations, in this study we focus on identifying phylogenetically informative characters of the avian pectoral girdle and forelimb skeleton, elements of which are commonly preserved as avian fossils. We assembled and vetted a dataset of 204 characters, which were then scored for a phylogenetically diverse range of 75 extant avian taxa and incorporated into phylogenetic analyses. Analyses run without topological constraints exhibited notable conflicts with the results of recent phylogenomic studies, possibly due to functional convergence and rapid cladogenesis in the early evolutionary history of crown birds. Qualitative anatomical comparisons and quantitative metrics of homoplasy further highlighted the fact that similar morphologies in pectoral girdle and forelimb elements have evolved repeatedly in distantly related groups of birds, representing a major confounding factor in avian morphological phylogenetics. However, the implementation of molecular scaffolds allowed identification of diagnostic character combinations for numerous avian clades previously only recognized through molecular data, such as Phaethontimorphae, Aequornithes, and Telluraves. Although large morphological datasets may not guarantee increased congruence with molecular phylogenetic studies, they can nonetheless be valuable tools for identifying anatomical synapomorphies of key clades, placing fossils into phylogenetic context, and studying macroevolutionary patterns within major groups of organisms.