bluuebunny/crossref_metadata_2025 huggingface dataset:
ASTRO: Automated Spatial Whole-Transcriptome RNA-Expression Workflow
Authors: Zhang Dingyao , Chu Zhiyuan , Huo Yiran , Bai Zhiliang , Fan Rong , Lu Jun , Gerstein Mark
Published: January 2025

Motivation

Despite significant advances in spatial transcriptomics, the analysis of formalin-fixed paraffin-embedded (FFPE) tissues, which constitute most clinically available samples, remains challenging. Additionally, capturing both coding and noncoding RNAs in a spatial context poses significant challenges. We recently introduced Patho-DBiT, a technology designed to address these unmet needs. However, the marked differences between Patho-DBiT and existing spatial transcriptomics protocols necessitate specialized computational tools for comprehensive whole-transcriptome analysis in FFPE samples.

Results

Here, we present ASTRO, an automated pipeline developed to process spatial transcriptomics data. In addition to supporting standard datasets, ASTRO is optimized for whole-transcriptome analyses of FFPE samples, enabling the detection of various RNA species, including non-coding RNAs such as miRNAs. To compensate for the reduced RNA quality in FFPE tissues, ASTRO incorporates a specialized filtering step and optimizes spatial barcode calling, increasing the mapping rate. These optimizations allow ASTRO to spatially quantify coding and non-coding RNA species in the entire transcriptome and achieve robust performance in FFPE samples.

Availability

Codes are available at GitHub (https://github.com/gersteinlab/ASTRO).
Evaluating Seqstant LiveGene Analysis in Real-Time Assessment of Metagenomic Next-Generation Sequencing (mNGS) Data from Respiratory Samples
Authors: Boutin Sébastien , Klein Sabrina , Untergasser Gerold , Loka Tobias P. , Jakob Suzan , Khatamzas Elham , Wrettos Georg , Knobloch Henri , Nurjadi Dennis
Published: January 2025

Background

The detection of pathogens causing infections by conventional diagnostic methods can be challenging and next-generation sequencing (NGS) technology offers a promising alternative method. In this study, we evaluated the performance of real-time metagenomic next-generation sequencing (rt-mNGS) for the detection of pathogens in respiratory samples.

Method

We used rt-mNGS, using the Seqstant LiveGene Analysis platform, on 335 respiratory samples in comparison to conventional culture results.

Results

We observed an overall good concordance in 71.64% (240/335) of the methods. The rt-mNGS outperformed the gold standard culture in 16.12% (54/335) of the samples, while the culture was superior in detecting the clinically relevant pathogen in 12.24% (41/335) of the samples. The non-inferiority of rt-mNGS was statistically significant (δ = 10,α= 0.05, 1− β= 0.8). We also observed that the real-time analysis of NGS data is beneficial in obtaining reliable timely results as the initial report at cycle 46 exhibits a Positive Predictive Value (PPV) of 93.75% at the species-level with a sensitivity of 32.09%.

Conclusion

Overall, our study showed the non-inferiority of rt-mNGS compared to the standard-of-care microbiology for respiratory samples with statistical significance. Moreover, the rt-mNGS method exhibited superior sensitivity and superior overall performance. It also uniquely detected certain organisms that are typically hard to culture. However, rt-mNGS reported a higher number of false positives and faced limitations in detectingAspergillusspp. In conclusion, the study highlights the potential of rt-mNGS as a powerful tool in clinical diagnostics of respiratory infections and beyond.
Pooled long-read sequencing for structural variant characterization in schistosome populations
Authors: Nair Shalini , Li Xue , Anderson Tim , Platt Roy Nelson
Published: January 2025

Pooled sequencing provides a rapid cost-effective approach to assess genetic variation segregating within populations of organisms. However, such studies are typically limited to single nucleotide variants and small indels (≤ 50bp), and have not been used for structural variants (SVs; >50bp) which impact large portions of most genomes and may significantly impact phenotype. Here, we examined SVs circulating in five laboratory populations of the human parasiteSchistosoma mansoniby generating long-read sequences from pools of worms (92 -152 per population). We were able identify and genotype 17,446 SVs, representing 6.5% of the genome despite challenges in identifying low frequency variants. SVs included deletions (n=8,525), duplications (n=131), insertions (n=8,410), inversions (n=311), and translocations (n=69) and were enriched in repeat regions. More than half (59%) of the SVs were shared between ≥4 populations, but 12% were found in only one of the five populations. Within this subset, we identified 168 population-specific SVs that were at-or-near fixation (>95% alternate allele frequency) in one population but missing (<5%) in the other four populations. Five of these variants impact the coding sequence of 6 genes. We also identified 8 SVs with extreme allele frequency differences between populations within quantitative trait loci for biomedically important pathogen phenotypes (drug resistance, larval stage production) identified in prior genetic mapping studies. These results demonstrate that long-read sequence data from pooled individuals is a viable method to quickly catalogue SVs circulating within populations. Furthermore, some of these variants may be responsible for, or linked to, regions experiencing, population-specific directional selection.
Applied Machine Learning for human bacteria MALDI-TOF Mass Spectrometry: a systematic review
Authors: Schmidt Santiago Lucía , Guerrero-López Alejandro , Sevilla-Salcedo Carlos , Rodríguez Temporal David , Rodríguez-Sánchez Belén , Gómez-Verdejo Vanessa
Published: January 2025

Bacterial identification, antimicrobial resistance prediction, and strain typification are critical tasks in clinical microbiology, essential for guiding patient treatment and controlling the spread of infectious diseases. While machine learning (ML) and deep learning (DL) have shown immense promise in enhancing MALDI-TOF mass spectrometry applications for these tasks, a comprehensive review from a technical perspective remains lacking. To address this gap, we systematically reviewed 93 studies published between 2004 and 2024, focusing on key ML/DL aspects such as data size and balance, preprocessing pipelines, peak selection methods, algorithms, evaluation techniques, and the availability of open-source data and code. Our analysis highlights the predominant use of classical ML models like random forests and support vector machines, alongside emerging interest in DL approaches for handling complex, high-dimensional data. Despite significant progress, challenges such as inconsistent preprocessing workflows, reliance on blackbox models, limited external validation, and insufficient opensource resources persist, hindering transparency, reproducibility, and broader adoption. By addressing these critical gaps, this review provides actionable insights to bridge microbiological and technical perspectives, paving the way for more robust, scalable, and interpretable solutions in diagnostic microbiology.
Epigenetic priming promotes acquisition of tyrosine kinase inhibitor resistance and oncogene amplification in human lung cancer
Authors: Starble Rebecca M. , Sun Eric G. , Gbyli Rana , Radda Jonathan , Lu Jiuwei , Jensen Tyler B. , Sun Ning , Khudaverdyan Nelli , Hu Bomiao , Melnick Mary Ann , Zhao Shuai , Roper Nitin , Wang Gang Greg , Song Jikui , Politi Katerina , Wang Siyuan , Xiao Andrew Z.
Published: January 2025

In mammalian cells, gene copy number is tightly controlled to maintain gene expression and genome stability. However, a common molecular feature across cancer types is oncogene amplification, which promotes cancer progression by drastically increasing the copy number and expression of tumor-promoting genes. For example, in tyrosine kinase inhibitor (TKI)-resistant lung adenocarcinoma (LUAD), oncogene amplification occurs in over 40% of patients’ tumors. Despite the prevalence of oncogene amplification in TKI-resistant tumors, the mechanisms facilitating oncogene amplification are not fully understood. Here, we find that LUADs exhibit a unique chromatin signature demarcated by strong CTCF and cohesin deposition in drug-naïve tumors, which correlates with the boundaries of oncogene amplicons in TKI-resistant LUAD cells. We identified a global chromatin priming effect during the acquisition of TKI resistance, marked by a dynamic increase of H3K27Ac, cohesin loading, and inter-TAD interactions, which occurs before the onset of oncogene amplification. Furthermore, we have found that the METTL7A protein, which was previously reported to localize to the endoplasmic reticulum and inner nuclear membrane, has a novel chromatin regulatory function by binding to amplified loci and regulating cohesin recruitment and inter-TAD interactions.

Surprisingly, we discovered that METTL7A remodels the chromatin landscape prior to large-scale copy number gains. Furthermore, while METTL7A depletion has little effect on the chromatin structure and proliferation of drug-naïve cells, METTL7A depletion prevents the formation and maintenance of TKI resistant-clones, highlighting the specific role of METTL7A as cells are becoming resistant. In summary, we discovered an unexpected mechanism required for the acquisition of TKI resistance regulated by a largely uncharacterized factor, METTL7A. This discovery sheds light into the maintenance of oncogene copy number and paves the way to the development of new therapeutics for preventing TKI resistance in LUAD.
Avoidance of pyroptosis accounts for the relatively high metastatic potential observed in early hybrid EMT states
Authors: Verma Aakanksha , Genna Alessandro , Vinik Yaron , Nataraj Nishanth Belugali , Abedrabbo Maha , Selvadurai Boobash Raj , Bhandari Tithi , Aharoni Noa , Ramesh Palaniappan , Boguslavski Boris , Drago Diana , Salame Tomer-Meir , Prior Amir , Levin Yishai , Weizman Eviatar , Zhu Rong , Caldas Carlos , Rueda Oscar M. , Lev Sima , Yarden Yosef
Published: January 2025

EMT converts epithelial (E) phenotypes to invasive mesenchymal (M) states. However, analyses of circulating tumor cells (CTCs) indicated that biphenotypic (E+M) CTCs better correlate with metastasis. Similarly, investigations of murine tumors undergoing EMT concluded that early E+M states posses the highest metastatic potential. To explore this, we selected in animals with breast cancer CTCs having progressively increasing intravasation abilities. This revealed that downregulation of arrestin Arrdc4 associates with CTC aggressiveness. In xenografts, depleting Arrdc4 accelerated tumor progression, whereas overexpression hindered progression in immunocompetent, but not in immunocompromised mice. Mechanistically, high Arrdc44 suppresses glucose uptake and enhances gasdermin E, triggering pyroptosis a type of pro-inflammatory cell death. Consistently, Arrdc4’s lowest levels characterize the most metastatic biphenotypic states. In patients, both epigenetic and chromosomal aberrations downregulate ARRDC4 and predict poor prognosis. In summary, the uncovered mechanism portrays pyroptosis of biphenotypic EMT cells as a rheostat of CTCs, which may resolve the controversy on the role played by EMT in metastasis.
Genetic dissection of cyclic di-GMP signaling inPseudomonas aeruginosa viadiguanylate cyclase disruption
Authors: Martino Román A. , Volke Daniel C. , Tenaglia Albano H. , Tribelli Paula M. , Nikel Pablo I. , Smania Andrea M.
Published: January 2025

The second messengerbis-(3′→5′)-cyclic dimeric guanosine monophosphate (c-di-GMP) governs adaptive responses in the opportunistic pathogenPseudomonas aeruginosa, including biofilm formation and the transition from acute to chronic infections. Understanding the intricate c-di-GMP signaling network remains challenging due to the overlapping activities of numerous diguanylate cyclases (DGCs). In this study, we employed a CRISPR-based multiplex genome-editing tool to disrupt all 32 GGDEF domain-containing proteins (GCPs) implicated in c-di-GMP signaling inP.aeruginosaUCBPP-PA14. Phenotypic and physiological analyses revealed that the resulting mutant was unable to form biofilms and had attenuated virulence. Residual c-di-GMP levels were still detected despite the extensive GCP disruption, underscoring the robustness of this regulatory network. Taken together, these findings provide insights into the complex c-di-GMP metabolism and showcase the importance of functional overlapping in bacterial signaling. Moreover, our design overcomes the native redundancy in c-di-GMP synthesis, providing a framework to dissect individual DGC functions and paving the way for targeted strategies to address bacterial adaptation and pathogenesis.
The evolution of Hutchinsonian climatic niche hypervolumes in gymnosperms
Authors: Caron Fernanda S. , Burslem David F. R. P. , Morimoto Juliano
Published: January 2025

The niche is a fundamental concept in ecology. One way to represent the niche is to use multidimensional geometry known as the Hutchinsonian niche hypervolume. However, hypervolume data are complex and the biological significance of niche hypervolume properties needs to be better understood. Here, we conducted for the first time a systematic and comprehensive test of the evolution of Hutchinsonian niche hypervolume properties (volume and holes) across 65 genera and 12 families of gymnosperms, which includes many species that are endangered or threatened. Using cutting-edge computational algorithms, we measured the evolution of geometric (i.e. volume) and topological (i.e. holes) properties of gymnosperm hypervolumes across a comprehensive calibrated phylogeny. Our comparative analysis revealed weak evidence of the non-independent evolution of niche hypervolume volume and no evidence of the non-independent evolution of hypervolume holes. We also found that genera and families with low hypervolume volume such as monotypic groups likeGingko, likely experienced shifts in hypervolume evolutionary rates. Our results show that geometric and topological properties of gymnosperm climatic niche hypervolumes evolve independently. This agrees with competitive exclusion hypothesis where extant groups are likely to be the ones which minimise niche overlap and competition.
Brain connectivity using EEG data
Authors: AGGARWAL ANU
Published: January 2025

The goal of this work was to use EEG data from epilepsy patients and analyze it for connectivity between brain regions using cross-power spectral density (CPSD). We took data from 76 EEG sessions by removing those with epileptic seizures. Then, we calculated CPSD for the 210 electrode pairs for each patient. Initially, we calculated CPSD in the entire sample and then stratified it based on frequency bands related to different brain states. We observed the brain hubs, the default mode network (DMN) and the anti-correlated network attached to the DMN. The connectivity of the brain changed with change in frequency and hence, brain states. EEG analysis with CPSD is a relatively inexpensive, longer duration and more convenient method over fMRI but provides similar information. Similar study can be used to identify brain connectivity patterns while brain is performing a specific task by collecting EEG data for the task.
GO Big or Go Home: A New Gene Ontology Subset that Improves Plant Gene Function Prediction
Authors: Fattel Leila , Lawrence-Dill Carolyn J.
Published: January 2025

Background

The availability of gene function prediction datasets helps researchers to consider possible functions for uncharacterized genes for hypothesis generation, candidate gene prioritization, and many other applications. Many such datasets are based on the Gene Ontology (GO) function graph. For plants this can be problematic because the most specific GO terms available are often derived from the biology of non-plant taxa (e.g., functions specific to nerve function would not seem likely to map to plant biological processes given that plants lack nerves). To balance the need for functional specificity while limiting to functions relevant to plant biology, researchers often limit to the GO Slim plant subset, but, by design, that subset consists of very general terms and limits real utility for e.g., specific hypothesis generation. Worse yet, sometimes researchers choose to simply throw out terms if they are not relevant to plant biology (rather than traversing the GO graph to select the most specific term in that hierarchy that is compatible with plant biology).

Results

We created GO Big, a Gene Ontology subset type, to improve the biological relevance of gene function predictions for taxon-specific biology applications. GO Big plant subsets retain maximal functional specificity for hypothesis generation while limiting to terms applicable to the biology of plants. In brief, we used a curatorial approach to generate two GO Big subsets, a general subset derived from terms with experimentally validated functions across Viridiplantae species, and a species-specific subset for maize (Zea maysssp.mays).

Conclusion

Annotating genes with assignments that better reflect the biology of a taxon can pave the way for more biologically accurate and testable hypotheses for genes of interest. The subsets produced here can help plant biologists limit genome-wide gene function prediction sets to functions possible for plant genes, and the process to generate GO Big subsets is described in detail to enable others to create GO Big subsets for additional taxon sets, including ones for protists, fungi, and other phylogenetic categories.
Integrating bulk and single cell RNA-seq refines transcriptomic profiles of individualC. elegansneurons
Authors: Barrett Alec , Varol Erdem , Weinreb Alexis , Taylor Seth R. , McWhirter Rebecca M. , Cros Cyril C. , Vidal Berta , Basaravaju Manasa , Poff Abigail , Tipps John A. , Majeed Maryam , Wang Chen , Bayer Emily A. , Reilly Molly B. , Yemini Eviatar , Sun HaoSheng , Hobert Oliver , Miller David M. , Hammarlund Marc
Published: January 2025

Neuron-specific morphology and function are fundamentally tied to differences in gene expression across the nervous system. We previously generated a single cell RNA-seq (scRNA-Seq) dataset for every anatomical neuron class in theC. eleganshermaphrodite. Here we present a complementary set of bulk RNA-seq samples for 52 of the 118 canonical neuron classes inC. elegans. We show that the bulk RNA-seq dataset captures both lowly expressed and noncoding RNAs that are not detected in the scRNA-Seq profile, but also includes false positives due to contamination by other cell types. We present an analytical strategy that integrates the two datasets, preserving both the specificity of scRNA-Seq data and the sensitivity of bulk RNA-Seq. We show that this integrated dataset enhances the sensitivity and accuracy of transcript detection and differential gene analysis. In addition, we show that the bulk RNA-Seq data set detects differentially expressed non-coding RNAs across neuron types, including multiple families of non-polyadenylated transcripts. We propose that our approach provides a new strategy for interrogating gene expression by bridging the gap between bulk and single cell methodologies for transcriptomic studies. We suggest that these datasets advance the goal of delineating the mechanisms that define morphology and connectivity in the nervous system.
Particular Amino Acid on Lateral Interface Maintains FtsZ Function Under Acid Stress inStreptococcus mutans
Authors: Chen Yuxing , Li Yongliang , Niu Jiahao , Yang Liuchang , Chi Yaqi , Cai Xue , Xin Fengjiao , Zhang Jie , Fang Xianyang , Mondal Manas , Gao Yiqin , Wang Xiaoyan
Published: January 2025

FtsZ is the core protein for cell division in bacteria that can polymerize into Z-rings and drive cytokinesis. Understanding how bacteria maintain the correct function of FtsZ under various environmental stresses is crucial for novel antibacterial drug discovery. Our previous study revealed that the FtsZ inS. mutanshas higher self-assembly and GTPase activity under acidic stress, which may be responsible for the cariogenesis ofS. mutans. However, the mechanism is still unknown. Here, we further reported the crystal structure ofS. mutansFtsZ, revealing a unique lateral interface. Through protein polymerization and GTPase ability assay, we experimentally demonstrated that mutation of Arg68 on this lateral interface significantly reduced the functional activity of FtsZ in an acidic environment. The phenotype assay and rat caries model further showed that mutation of Arg68 effectively inhibited the acid resistance ofS. mutansand the occurrence and progress of dental caries in vivo. By employing a molecular dynamics simulation analysis, we conclude that mutation of Arg68 disrupts the conformation change necessary for SmFtsZ polymerization under acidic conditions. Our study proposes a novel mechanism to maintain FtsZ function in bacteria and could be a potential target for antimicrobial drugs to inhibit the growth ofS. mutansin an acidic environment.

Significance Statement

FtsZ is the core protein that drives cytokinesis. Maintaining the self-assembly and GTPase activity of FtsZ plays a critical role in cell growth under environmental stress. Currently, research on FtsZ function maintenance under stress mainly focuses on model organisms, with less on other pathogenic bacteria. This study reveals a novel structural mechanism for the acidic tolerance of FtsZ inS. mutanswhich survives in strongly acidic surroundings. Meanwhile, Arg68 on the lateral interface of SmFtsZ may be a potential therapeutic target to regulate microecology and combatS. mutans-associated dental caries.
Lepidoptera Diversity, Richness, and Distribution in Semi-Urban Farmland and other Habitats around Lumbini, Rupandehi
Authors: Baral Celeus , Baral Hem Sagar , Inskipp Carol , Maharjan Rajana
Published: January 2025

This study comprehensively examined Lepidoptera diversity in the semi-urban agricultural landscapes of Lumbini, Nepal, documenting 30 moth species from six families and 39 butterfly species from five families over 14 days. Field methods included moth traps with 50 Watts LED lights inside a box with egg cartons for moth trapping and butterfly transect surveys across various habitats—grasslands, shrublands, and agricultural areas for recording butterfly species. The Erebidae family dominated moth populations, while Nymphalidae led butterfly diversity, showing resilience in disturbed habitats influenced by environmental factors such as weather patterns, lunar phases, and habitat characteristics. Statistical analyses using Simpson’s Diversity Index, Shannon-Wiener Diversity Index, Pielou’s Evenness Index, and Margalef’s Richness Index revealed that shrubland and agricultural habitats supported the highest species richness and evenness, while grasslands hosted fewer species. The study highlighted the importance of agricultural and shrubland ecosystems for biodiversity, emphasizing ongoing monitoring to understand how Lepidoptera populations respond to environmental changes, offering essential insights for future conservation efforts.
Dose response comparison of Nipah virus strains Malaysia and Bangladesh in hamsters exposed by the intranasal or intraperitoneal route
Authors: Johnston Sara C. , Qiu Ju , Norris Sarah LW , Panchal Rekha , Punger Elizabeth M. , Teague Melissa , Moore Joshua L. , Dyer David N. , Frick Ondraya M. , Stevens Stephen C. , Fiallos Jimmy , Mills Harold L. , Blue Eugene L. , Sifford Willie B. , McCarson Trevor , Casselman Amanda , Latty Jonathan D. , Huie Kathleen E. , Adolphi Ryan , Nalca Aysegul
Published: January 2025

Nipah virus, a zoonotic pathogen, can cause debilitating disease and death in humans. Currently, countermeasures are limited, with several in various stages of testing but none yet FDA-approved for human use. Evaluation of countermeasure candidates requires safety testing in humans, as well as efficacy testing against lethal challenge in animal models. Herein, we describe the characterization and comparison of the intraperitoneal and intranasal Syrian golden hamster models for Nipah virus strains Malaysia and Bangladesh. Overall, the intraperitoneal route of exposure resulted in a more consistent lethal outcome, regardless of virus strain. Therefore, the IP model was subsequently used to evaluate the use of Favipiravir as a potential positive control for future studies investigating NiV countermeasures. In contrast to prior reported results regarding Favipiravir in Nipah virus-infected hamsters, Favipiravir was only fifty percent effective at preventing death following lethal challenge, regardless of Nipah virus strain. The data suggest that Favipiravir is only partially protective against Nipah virus in hamsters, and, thus, would likely not be an ideal candidate as a positive control in future efficacy studies.
Complete genome sequence assembly elucidates evolution and regulation of 5S rDNA loci in the greater duckweedSpirodela polyrhiza
Authors: Stepanenko Anton , Schubert Veit , Chen Guimin , Kishchenko Olena , Michael Todd P. , Lam Eric , Hrmova Maria , Schubert Ingo , Borisjuk Nikolai
Published: January 2025

We resolved the molecular architecture of the 5S rDNA loci in an aquatic monocotSpirodela polyrhiza. Measurements of fluorescencein situhybridization signals revealed two loci with 5S rDNA clusters. A combination of the extra-long DNA reads and conventional sequencing of 5S rDNA repeats allowed the assembling of complete loci sequences located on ChrSp6 and ChrSp13. The homologous chromosomes of the ChrSp6 locus contain clusters of 40 and >60 copies of 5S rDNA repeat units with intergenic spacer (IGS) of 400 bp. The ChrSp13 locus is represented by 5S rDNA clusters of rRNA genes spaced by IGSs of 1,056 or 1,069 bp arranged in two sub-clusters, suggesting a different rate of repeat homogenization between loci. The G/C-rich 5S rDNA arrays in both loci are embedded in A/T-enriched chromosome regions with possible regulatory functions. The TATA-like boxes of the 5S rDNA repeat on ChrSp6 and ChrSp13 exhibit different affinities for the TATA-binding protein in 3D modeling of protein/DNA interactions, suggesting a locus-specific regulation of rRNA transcription. Our findings shed light on the molecular architecture of the 5S rDNA loci, which could foster an innovative era for the principles of evolution and regulation of rRNA genes in plants.
Single-Cell Genomics Elucidates Molecular Variations and Regulatory Mechanisms in Circulating Immune Cells
Authors: Yin Jianhua , Zheng Yuhui , Huang Zhuoli , Zhou Wenwen , Yuan Yue , Cai Pengfei , Bai Yong , Yang Shichen , Gao Yue , Duan Shanshan , Wang Yang , Zhang Wenxi , Zhang Xinyu , Wei Yilin , Xu Zekai , Huang Yaling , Liu Ying , Wang Weikai , Yang Tao , Lv Jingzhi , Zhang Zhongjin , Chen Xiaoya , Zhang Xiru , Li Fupeng , Zhang Yan , Zeng Guodan , Wang Xue , Ma Wen , Hou Guixue , Hao Shijie , Liu Chang , Lai Yiwei , Wang Bo , Li Yuxiang , Zhang Wenwei , Gao Peng , Xie Jun , Esteban Miguel A. , Gu Ying , Ji Jiansong , Qi Ting , Liu Boxiang , Wang Jian , Yang Jian , Xu Xun , Liu Longqi , Jin Xin , Liu Chuanyu
Published: January 2025

The human peripheral blood displays diverse molecular characteristics across populations, understanding the drivers and underlying mechanisms of which remains challenging. Here, we introduce the Chinese Immune Multi-Omics Atlas (CIMA), elucidating sex-, age-, and genetic-related molecular variations by analyzing multi-omics data from 428 adults with over 10 million immune cells. CIMA generated an enhancer-driven gene regulatory network, identifying 237 high-quality regulons and revealing cell type-specific regulatory mechanisms. Additionally, 11,521 leadcis-expression quantitative trait loci (eQTLs) and 46,339 chromatin accessibility QTLs (caQTLs) were identified at cell type level. CIMA also uncovered pleiotropic associations among immune-related disease risk loci, eQTLs, and caQTLs in a cell type-specific manner. Lastly, a novel cell language model, CIMA-CLM, was developed to predict chromatin accessibility and noncoding variant effects using chromatin sequences and gene expressions. This work represents a population-scale multi-omics resource of human immune cells, providing a valuable reference for future investigation of immune-related diseases.
Reproducible Boolean model analyses and simulations with the CoLoMoTo software suite: a tutorial
Authors: Noël Vincent , Naldi Aurélien , Calzone Laurence , Paulevé Loic , Thieffry Denis
Published: January 2025

This tutorial provides stepwise instructions to install the 20 tools integrated in the CoLoMoTo software suite, to develop reproducible dynamical analyses of logical models of complex biological molecular networks.

The tutorial specifically focuses on the analysis of a previously published model of the regulatory network controlling mammalian cell proliferation. It includes chunks of python code to reproduce several of the results and figures published in the original article and further extend these results with the help of a selection of tools included in the CoLoMoTo suite.

The notebook covers the visualisation of the network with the tool GINsim, an attractor analysis with bioLQM, the computation of synchronous attractors with BNS, the extraction of modules from the full model, MaBoSS simulations of the wild-type model, as well as of selected mutants, and finally the delineation of compressed probabilistic state transition graphs.

The integration of all these analyses in an executable Jupyter notebook greatly eases their reproducibility, as well as the inclusion of further extensions. This notebook can further be used as a template and enriched with other ColoMoTo tools to enable comprehensive dynamical analyses of biological network models.
Variability in intrinsic promoter strength underlies the temporal hierarchy of theCaulobacterSOS response induction
Authors: Kamat Aditya , Joseph Asha M. , Rathour Deeksha , Badrinarayanan Anjana
Published: January 2025

Bacteria encode for gene regulatory networks crucial for sensing and repairing DNA damage. Upon exposure to genotoxic stress, these transcriptional networks are induced in a temporally structured manner. A case in point is of the highly conserved SOS response thwat is regulated by the LexA repressor. Studies have proposed that affinity of LexA towards promoters of SOS response genes is the primary determinant of its expression dynamics. Here, we describe an additional level of regulation beyond LexA properties that modulates the SOS response gene expression pattern. Using transcriptomic analyses, we reveal a distinct temporal hierarchy in the induction of SOS-regulated genes inCaulobacter crescentus. We observe that LexA properties are insufficient in predicting the temporal hierarchy of these genes. Instead, we find that intrinsic promoter strength underlies the order of gene activation, with differential sigma factor association as a key factor in modulating gene expression timing. Our findings highlight a novel regulatory layer in SOS dynamics and underscore the importance of promoter properties in shaping bacterial stress responses.
Rapid catecholamine trafficking regulates neutrophil functions and neutrophil-platelet interactions
Authors: Mohr Jennifer , Schmitz Anne , Dinarvand Meshkat , Shankar Sangeetha , Hill Bjoern F. , Wulfert Franziska , Neubert Elsa , Shumanska Magdalena , Kaushik Sofia , Kartaschew Linda , Bogeski Ivan , Daniel James , Jung Sebastian , Eble Johannes , Erpenbeck Luise , Kruss Sebastian
Published: January 2025

Neutrophils are key effector cells of the innate immune system that respond to small signaling molecules regulating immune responses. For a long time, similarities between neuronal and immune cells have been discussed. Here, we show that human neutrophils rapidly take up, package and use catecholamine neurotransmitters such as dopamine or epinephrine via the machinery known from neurons. Uptake and release of catecholamines as well as trafficking and packaging into MPO/VMAT2-positive primary vesicles is visualized with false fluorescent neurotransmitters. We also directly image the fast (> 10 s) and transient release of catecholamines from neutrophils with near infrared fluorescent nanosensors. Serotonin or activated platelets trigger calcium (Ca2+) signaling and consequently exocytosis of catecholamines. They reduce NET-formation but increase platelet aggregation. Thus, we establish similarities between neurons and neutrophils and identify a paracrine neutrophil-platelet feedback loop relevant for inflammatory and coagulatory conditions.
Non-Visual Light Sensing Enhances Behavioral Memory and Drives Gene Expression inC. elegans
Authors: Ji Zhijian , Wang Bingying , Chandra Rashmi , Liu Junqiang , Yang Supeng , Long Yong , Egan Michael , L’Etoile Noelle , Ma Dengke K.
Published: January 2025

Visible light influences a range of physiological processes, yet how animals respond to it independently of the visual system remains largely unknown. Here, we uncover a previously undescribed light-induced transcriptional pathway that modulates behavioral plasticity inC. elegans, a roundworm without eyes. We demonstrate that ambient visible light or controlled-intensity visible-spectrum LED activates an effector genecyp-14A5in non-neuronal tissues through the bZIP transcription factors ZIP-2 and CEBP-2. Light induction ofcyp-14A5is more prominent at shorter wavelengths but is independent of the known blue light receptors LITE-1 and GUR-3 inC. elegans. This bZIP-dependent genetic pathway in non-neuronal tissues enhances behavioral adaptability and olfactory memory, suggesting a body-brain communication axis. Furthermore, we use the light-responsivecyp-14A5promoter to drive ectopic gene expression, causing synthetic light-induced sleep and rapid aging phenotypes inC. elegans. These findings advance our understanding of light-responsive mechanisms outside the visual system and offer a new genetic tool for visible light-inducible gene expression in non-neuronal tissues.
Optimized Detection and Inference of Names in scRNA-seq data
Authors: Tulyeu Janyerkye , Priest David , Wing James B. , Søndergaard Jonas Nørskov
Published: January 2025

Accurate identification of immune cell subsets in single-cell (sc)RNA-seq data is critical for understanding immune responses in autoimmune diseases, infections, and cancer. One caveat of scRNA-seq is the inability to properly assign rare immune cell subsets due to gene dropout events. To circumvent this caveat, we here developed Optimized Detection and Inference of Names in scRNA-seq data (scODIN). scODIN uses an informed holistic two-step approach combining expert knowledge with machine learning to rapidly assign cell type identities to large scRNA-seq dataset. First, scODIN uses key lineage-defining markers to identify a set of core cell types. Second, scODIN compensates for dropout events by integrating a k-nearest neighbors (kNN) algorithm. We additionally programmed scODIN to detect dual and transitional phenotypes, which are usually overlooked in conventional analyses. Consequently, scODIN may enhance our understanding of immune cell heterogeneity and provides comprehensive insights into immune regulation, with broad implications for immunology and personalized medicine.
PID-controller enhanced artificialβ-cells
Authors: Liu Lin , Jacobson Bruna , Stefanovic Darko
Published: January 2025

Conventional management of diabetes via injection or external insulin pumps suffers from inconvenience and inability to accurately maintain blood glucose levels. A potential solution to these problems consists of implanting synthetic artificialβ-cells that can sense glucose and transcribe insulin protein. We focus on one such artificialβ-cell recently described in the work of Xie et al. Experimental results show these cells are able to release insulin and somewhat improve postprandial glucose levels in diabetic mice. However, they fail to achieve the degree of glucose regulation as in healthy mice. In our analysis, we explain that this artificialβ-cell system has a major disadvantage: it is a high-dimensional dynamic system but with little tuning space. Here, we propose a PID-controller-based enhanced artificialβ-cell design to solve this issue. Our results based on an analytical model and numerical simulations show that the computational method of PID-control can enhance engineered artificialβ-cells, such that they could perform better in regulating glucose levels in Type 1 diabetic mice compared with artificialβ-cells without PID-control: they could shut down the production of insulin in time and maintain a proper glycemia level, and there is more tuning space for artificialβ-cells with PID control.
Fitting multiple bacterial growth data using continued fraction of straight lines
Authors: Shruti I S , Vijay Prakash S
Published: January 2025

The growth of a population is the net result of growth and decline in the number of individuals over time. When the growth in number is more than the decline, the population is said to be growing and vice versa. In other words, the growth rate of a population is influenced by two opposing factors, a growth promoting factor and a growth restricting factor. In this work, we estimate growth rates by applying a biological growth model that is based on the continued fraction of straight lines with two parametersaandm. The parametersaandmrepresent nonlinear i.e. growth restricting and linear i.e. growth promoting parts of the model, respectively. To fit this model, we use a publicly available dataset that exhibits the growth of three different strains of bacteria depending on the concentration gradient of the antibiotic Tetracycline. We also propose a method to automatically estimate growth rates for large-scale applications. Finally, a growth coordinate system withaandmas the axes is used to interpret the estimations.
Progenitor Heterogeneity in the Developing Cortex: Divergent and Complementary Roles of NG2-Progenitors and RGCs
Authors: Ojalvo-Sanz Ana Cristina , Figueres-Oñate María , Barriola Sonsoles , Pernia-Solanilla Carolina , Sanchez-Gonzalez Rebeca , García Lina Delgado , López-Mascaraque Laura
Published: January 2025

Brain development is a highly coordinated process that arises from a pool of neural progenitor cells (NPCs). Traditionally, research has largely focused on Radial Glial Cells (RGCs), which produce neurons and glia. However, recent findings revealed that the progenitor landscape is more complex and heterogeneous than previously understood. Emerging evidence indicates that NG2 glia, also known as oligodendrocyte precursor cells (OPCs), may contribute to generating other cell types, including neurons and astrocytes. This suggests that NG2 glia, or a specific subset, may act as multipotent NPCs, expanding their role in brain development beyond their known lineage.

We explore the cellular, molecular, and functional differences between NG2- and GFAP- expressing progenitors (NG2-NPCs and GFAP-NPCs) across different developmental stages. Usingin-uteroelectroporation and StarTrack technology, we examined whether these progenitors represent distinct populations and analyzed how their differences influence their functional roles based on cell fate decisions. Our findings uncover functional divergence between NG2-NPCs and GFAP-NPCs, particularly regarding their cell fate decisions. While both populations contribute to the formation of neurons and glial cells, the progeny of NG2-NPCs and GFAP-NPCs differ markedly in their contributions to neurogenesis and gliogenesis. Further, we conducted a comprehensive transcriptomic analysis of NG2-NPCs and GFAP-NPCs to elucidate the molecular basis for these functional differences. This study demonstrates distinct gene expression profiles. While NG2-NPCs show enrichment for genes associated with neurogenesis and synaptic transport, GFAP-NPCs displayed upregulation of genes involved in progenitor cell maintenance. This indicates that each progenitor type is governed by distinct molecular programs, shaping their contributions to brain architecture and function. In summary, our findings underscore the divergent roles of NG2-NPCs and GFAP-NPCs in driving cellular diversity and functional maturation in brain development, providing new insights into how these progenitor populations contribute to neural diversity and brain function.

Abstract Figure
Dynein-2 is tuned for the A-tubule of the ciliary doublet through tubulin tyrosination
Authors: He Haoqiang K. , Kubo Shintaroh , Lv Qianru H. , Kage Azusa , Ichikawa Muneyoshi
Published: January 2025

Eukaryotic cilia and flagella are thin structures present on the surface of cells, playing vital roles in signaling and cellular motion. Cilia structures rely on intraflagellar transport (IFT), which involves dynein-2 for retrograde and kinesin-2 for anterograde movements along doublet microtubules. Unlike dynein-1, which works on singlet microtubules within the cytoplasm, dynein-2 specifically works on the doublet microtubules inside the cilia. Previous cryo-electron tomography studies have shown that retrograde IFT, driven by dynein-2, occurs on the A-tubule of the doublet, suggesting a specialized regulatory mechanism involving dynein-2. However, the molecular basis of this specificity remains unclear. Here, we investigated this mechanism using cryo-electron tomography (cryo-ET) with Volta Phase Plate (VPP), molecular dynamics (MD) simulations, and biochemical analysis. Our biochemical assay revealed that the microtubule-binding domain of dynein-2 exhibits a higher affinity for the ciliary doublet microtubule compared to dynein-1. Cryo-ET with VPP further visualized the preferential binding of dynein-2 to the A-tubule of the doublet microtubule. MD simulations suggest that the preferential binding of dynein-2 is attributed to the tyrosinated tubulin in the A-tubule. These findings uncover a tyrosination-dependent regulatory mechanism that governs the bidirectional transport of IFT on doublet microtubules, providing new insights into the spatial and functional specialization of ciliary transport systems.
The emergence of E-Cadherin spot junctions between germline and somatic cells facilitates late stage oogenesis inDrosophila
Authors: Weichselberger Vanessa , Balaji Ramya , Rodriguez-Franco Marta , Classen Anne-Kathrin
Published: January 2025

Coordinated tissue morphogenesis relies on precise interactions between distinct cell lineages. During development of theDrosophilaoocyte, interactions between di_erent somatic follicle cell types and the germline-derived nurse cells and the future oocyte are crucial for coordinating oogenesis. However, the molecular basis of their interaction throughout enormous morphological changes remains largely unexplored. During late oogenesis, nurse cells transfer their cytoplasmic content into the oocyte, while anterior follicle cells (AFCs) must closely envelop the nurse cells to induce phagoptosis and remove their remnants. We identify E-cadherin-based spot junctions as novel adhesive complexes at this essential soma-germline interface. AFCs reorganize their E-cadherin from intraepithelial adherens junctions to their apical surface to form interlineage spot junctions with nurse cells, representing a switch in adhesive and thus mechanical coupling. The distribution and density of these junctions is stably organized, even as the interface undergoes dramatic size changes. Additionally, we show that these junctions integrate into a microvilli-rich nurse cell surface, influencing microvilli architecture. Importantly, disruption of E-cadherin spot junctions impairs nurse cell enveloping. Our findings reveal a switch from intra-lineage to inter-lineage mechanical coupling that is driven by the formation of E-Cadherin spot junctions and highlights their essential role in ensuring robust soma-germline coupling and coordination during nurse cell dumping in late oogenesis.
Redefining catecholaminergic polymorphic ventricular tachycardia (CPVT) as a neurocardiac condition
Authors: O’Reilly Molly , Verkerk Arie , Remme Carol Ann
Published: January 2025

Catecholaminergic polymorphic ventricular tachycardia (CPVT) is an inherited arrhythmia syndrome characterised by adrenergic activity-induced sudden cardiac death. It is most often caused by mutations in theRYR2gene encoding ryanodine receptor 2 (RyR2), which is essential for intracellular calcium handling. Research has traditionally focused on the consequences of mutations at the cardiomyocyte level. However, RyR2 is also expressed in neuronal tissue, and patients often present with clinical signs of autonomic dysfunction. Here, we assessed if there is a neuronal phenotype in this classically cardiac condition.

Using the established CPVT mouse modelRyr2-R2474S, we found that RyR2 is abundantly expressed in stellate ganglia neurons (SGNs) - the adrenergic neurons that project directly to the myocardium and modulate heart function. We revealed that in isolatedRyr2-R2474S SGNs there is altered calcium homeostasis suggestive of intracellular calcium leakage, and increased neurite projections when maintained in culture. We furthermore showed that hearts ofRyr2-R2474S mice are sympathetically hyper-innervated, with an increased heterogeneity in innervation within the myocardium. This led to changes in the quantities of neurotransmitters and their metabolites within the heart, indicating increased norepinephrine turnover.

CPVT may therefore be redefined as a neurocardiac disorder, with neuronal dysregulation being a prominent component of the disease. In addition to cardiomyocytes,RYR2mutations also affect stellate ganglia neuron function and cardiac innervation, with potential implications for arrhythmogenesis, risk stratification and therapy.

Graphical abstract

In wildtype hearts, activation of sympathetic neurons leads to their release of norepinephrine (NE), which binds to beta adrenergic receptors (β-ARs) on the cardiomyocyte membrane. The resultant initiation of intracellular signalling cascades involving cyclic AMP (cAMP) leads to reduced inhibition of the sarcoendoplasmic reticulum (SR) calcium ATPase (SERCA) pump and consequent calcium overload in the SR. This triggers the opening of ryanodine receptor 2 (RyR2), causing SR calcium to be released into the cytoplasmic space resulting in a calcium wave which triggers contraction.

In CPVT hearts, there is increased sympathetic neuron innervation of the ventricular myocardium. When cardiac sympathetic nerves are activated, there is an enhanced release of NE. This excess NE causes increased activation of β-ARs and an augmented intracellular cAMP response, which in turn leads to a greater reduction of the inhibition of SERCA, augmented SR calcium overload, and a heightened propensity for spontaneous calcium leakage to trigger a calcium wave, delayed afterdepolarisations, and arrhythmias.

Figure created withBioRender.com.