bluuebunny/crossref_metadata_2025 huggingface dataset:
Decoding Host-Pathogen Interactions inStaphylococcus aureus: Insights into Allelic Variation and Antimicrobial Resistance Prediction Using Artificial Intelligence and Machine Learning based approaches
Authors: Ghosh Joyeta , Taneja Jyoti , Kant Ravi
Published: February 2025

This novel study leveraged advanced machine learning techniques to elucidate the molecular mechanisms of antimicrobial resistance (AMR) in 300Staphylococcus aureusisolates across six critical antibiotics. Employing a diverse array of deep learning and ensemble models, we conducted an in-depth analysis of genetic markers and allelic variations to characterize resistance determinants. Our investigation revealed that the XGBoost ensemble model demonstrated the most exceptional performance, achieving a remarkable 95% test accuracy, 100% training accuracy, and an unprecedented ROC AUC of 0.9855.

Comparative analysis of multiple machine learning approaches, including Long Short-Term Memory (LSTM), Convolutional Neural Network (CNN), Multi-Layer Perceptron (MLP), Decision Tree, and Stochastic Gradient Descent (SGD) models, provided detailed insights into resistance prediction. The SHAP (SHapley Additive exPlanations) analysis unveiled critical genetic markers, with “cat_allele_Cluster_1015_Allele_8” emerging as the most influential feature driving resistance predictions. Notably, the models exhibited varying performance across different antibiotics, with consistently high accuracy and F1-scores for ciprofloxacin, clindamycin, gentamicin, and sulfamethoxazole/trimethoprim.

Our findings not only demonstrate the potential of advanced machine learning techniques in predicting antimicrobial resistance but also provide crucial insights into the molecular mechanisms underlyingS. aureusdrug resistance. By identifying key genetic determinants and their relative importance, this study offers a sophisticated approach to understanding resistance patterns, potentially guiding future diagnostic strategies, targeted therapies, and antimicrobial stewardship practices in clinical settings.
Lancet2: Improved and accelerated somatic variant calling with joint multi-sample local assembly graphs
Authors: Musunuri Rajeeva Lochan , Zhu Bryan , Clarke Wayne E. , Hooper William , Chu Timothy , Shelton Jennifer , Corvelo André , Chung Dickson , Sundar Shreya , Novak Adam M , Paten Benedict , Zody Michael C. , Robine Nicolas , Narzisi Giuseppe
Published: February 2025

Here, we present Lancet2, an open-source somatic variant caller designed to improve detection of small variants in short-read sequencing data. Lancet2 introduces significant enhancements, including: 1) Improved variant discovery and genotyping through partial order multiple sequence alignment of assembled haplotype contigs and re-alignment of sample reads to the best supporting allele. 2) Optimized somatic variant scoring with Explainable Machine Learning models leading to better somatic filtering throughout the sensitivity scale. 3) Integration with Sequence Tube Map for enhanced visualization of variants with aligned sample reads in graph space. When benchmarked against enhanced two-tech truth sets generated using high-coverage short-read (Illumina) and long-read (Oxford Nanopore) data from four well characterized matched tumor/normal cell lines, Lancet2 outperformed other industry-leading tools in variant calling performance, especially for InDels. In addition, significant runtime performance improvements compared to Lancet1 (∼10x speedup and 50% less peak memory usage) and most other state of the art somatic variant callers (at least 2x speedup with 8 cores or more) make Lancet2 an ideal tool for accurate and efficient somatic variant calling.
Odor-evoked respiratory responses throughout development in sighted and blind mice
Authors: Bouguiyoud N. , Litaudon P. , Frasnelli J. , Garcia S. , Messaoudi B. , Mouly AM. , Al Aïn S. , Courtiol E.
Published: February 2025

Congenital blindness affects olfactory function depending on developmental stage. However, when studying the ontogeny of olfactory abilities, not all behaviors are expressed at every age making the longitudinal comparisons difficult. Odor-evoked respiratory responses, which are unlearned and do not require complex motor coordination, may serve as sensitive measures of olfactory abilities throughout ontogeny. Using a non-invasive measure of respiration in an olfactory perceptual paradigm, we assessed odor-evoked respiratory responses in a model of congenital blindness at 3 ages, infant, juvenile and adult, in the same mice and in both males and females. We demonstrated the differential outcome of two respiratory parameters (i.e. frequency and amplitude) in a mouse model of congenital blindness. We showed that blind mice have similar olfactory abilities than sighted mice throughout ontogeny but display enhanced sniffing frequency and amplitude, starting at the juvenile age for the latter one, that may help them better explore their environment. We also demonstrated that respiratory frequency is a robust index of age and of olfactory detection, habituation and discrimination at all ages. On the other side, respiratory amplitude does not provide a proxy of olfactory performance at all ages, however, it does highlight differences between sexes and phenotypes associated with visual deprivation. To conclude, our data highlight that respiratory parameters can be used as a complementary approach to assess olfactory performance throughout development and provide an index of olfactory plasticity.
PHYTOCHROME INTERACTING FACTORS are required to coordinate microtubule dynamics and differential cell growth during Arabidopsis apical hook opening
Authors: Burachik Natalia , Vacs Paula , Franco Santin , Mazzella María Agustina , González-Schain Nahuel
Published: February 2025

Background

Differential cell growth is a key strategy that enables plants to adjust their morphology in response to internal and external cues. Apical hook opening in dark- grown Arabidopsis seedlings serves as an excellent model to study how coordinated cell expansion generates organ bending. Several works highlight the influence of hormone signaling, cell wall mechanics, and environmental cues on cortical microtubule (cMT) arrangement in bending tissues. However, the precise genetic hierarchy governing these processes remains largely unknown.

Results

Here, we reveal a two-step growth rate during apical hook opening, in which an initial phase of differential cell expansion is followed by a phase of more balanced growth. We show that cMT re-arrangement precedes and predicts cell expansion patterns, suggesting a central role in coordinating differential growth. Our findings indicate that PIF transcription factors regulate this process, aspifqmutants fail to align cMT reorganization with growth dynamics, resulting in premature hook opening. RNA- seq analysis further supports a role for PIFs in coordinating cell wall remodeling and microtubule-associated gene expression, including kinesins and cell wall-modifying enzymes.

Conclusions

Our study uncovers a PIF-dependent regulatory mechanism that orchestrates cytoskeletal dynamics and cell expansion to control apical hook opening.
Conservation and discovery of regulatory motifs across oomycetes through comparative genomic analysis
Authors: Bharti Sakshi , Thines Marco
Published: February 2025

Promoter sequences contain specific transcription factor (TFs) binding sites that regulate gene expression. While the conservation of TFs in pathogen development and infection among oomycetes is known, little is understood about TFs bind to conserved promoter regions across species. This study employs a robust comparative computational genomics approach to identify the TFs binding to orthologous DNA motifs in oomycetes. By integrating high-confidence TF binding site (TFBS) profiles,in-silicomotif discovery, sequence conservation analysis and protein sequence similarity searches, the study revealed conserved regulatory mechanisms in oomycetes. The multi-layered computational framework identified two major TF classes in oomycetes: Cys2-His2 (C2H2) zinc finger proteins and winged helix repressor proteins, binding to orthologous motifs regulating gene clusters involved in epigenetic regulation, effectors, intracellular trafficking, host cell wall degrading enzymes, RNA processing and cytoskeletal organization. Structural comparisons indicate high sequence similarity between oomycete TFs and well-characterized eukaryotic TFs, supporting the predictive power of the computational approach. Moreover, motif plasticity analysis across developmental phases revealed conserved and phase-specific motifs emphasizing dynamic transcriptional regulation during infection and colonization. The presence of highly conserved motifs across multiple oomycete species suggests strong evolutionary selection pressure on key regulatory elements. The results provide a computational foundation for future experimental validation, guiding functional characterization of transcriptional regulation in oomycetes. This study highlights the potential ofin-silicoTFBS discovery for understanding gene regulation, paving the way for targeted experimental approaches such as ChIP-seq or electrophoretic mobility shift assays (EMSA).
Collisional cross-section prediction for multiconformational peptide ions with IM2Deep
Authors: Devreese Robbe , Nameni Alireza , Declercq Arthur , Terryn Emmy , Gabriels Ralf , Impens Francis , Gevaert Kris , Martens Lennart , Bouwmeester Robbin
Published: February 2025

Peptide collisional cross-section (CCS) prediction is complicated by the tendency of peptide ions to exhibit multiple conformations in the gas phase. This adds further complexity to downstream analysis of proteomics data, for example for identification or quantification through feature finding. Here, we present an improved version of IM2Deep that is trained on a carefully curated dataset to predict CCS values of multiconformational peptides. The training data is derived from a large and comprehensive set of publicly available datasets. This comprehensive training dataset together with a tailored architecture allows for the accurate CCS prediction of multiple peptide conformational states. Furthermore, the enhanced IM2Deep model also retains high precision for peptides with a single observed conformation. IM2Deep is publicly available under a permissive open source license athttps://github.com/compomics/IM2Deep.
The geometry of pMHC-coated nanoparticles and T cell receptor clusters governs the sensitivity-specificity trade-off in T cell response
Authors: Richez Louis , Khadra Anmar
Published: February 2025

T cells must reliably discriminate between foreign-derived antigens that require an adaptive immune response from non-specific self-antigens that do not. This discrimination is highly specific to the affinity of the bond between ligand and T cell receptors (TCRs), as well as highly sensitive to the concentration of ligand. In this study, we examined these features of T cell mediated immunity in the context of multivalent ligand-receptor interactions between clusters of TCRs with pMHC-coated nanoparticles (NPs). Using Monte Carlo simulations of NP-T cell surface interactions, we compared the effect of TCR clustering on the dose-response profiles of various NP designs. These simulations revealed a trade-off between sensitivity and specificity, mediated by the spatial clustering of TCRs and the geometry of the NP. In particular, large clusters of TCRs were more sensitive to both NP valence and ligand concentration at the expense of antigen specificity. Conversely, uniformly distributed TCR landscapes were better suited to affinity-based ligand discrimination, while sacrificing sensitivity to ligand concentration. These features of NP-mediated T cell activation depended significantly on NP size and valence rather than on the average ligand concentration. Furthermore, we demonstrated how kinetic proofreading mechanisms may help compensate for the limitations associated with TCR clustering. These findings thus highlight the importance of interacting geometries of NP design and TCR landscape in modulating the specificity and sensitivity of the T cell response.

Significance

T cells rely on surface T cell receptors (TCRs) to recognize foreign antigens presented as peptide-major histocompatibility complex (pMHC) molecules. TCR clustering is crucial for T cell activation, though its full role remains not entirely clear. Using Monte Carlo simulations, we demonstrate that TCR clustering profoundly influences both surface binding dynamics of multivalent pMHC-coated nanoparticles, used in autoimmune disease therapies, as well as downstream intracellular signals leading to T cell activation. Our findings thus provide important insights into the role of interaction geometries in shaping T cell response, with implications for optimizing nanoparticle design to enhance their therapeutic efficacy.
Dynamic Lipidome Reorganization in Response to Heat Shock Stress
Authors: Solano Luis , Keshet Uri , Reinschmidt Andrew , Chavez Yonny , Hulsy William Drew , Fiehn Oliver , Nikolaidis Nikolas
Published: February 2025

The heat shock response (HSR) is a conserved cellular mechanism critical for adaptation to environmental and physiological stressors, with broad implications for cell survival, immune responses, and cancer biology. While the HSR has been extensively studied at the proteomic and transcriptomic levels, the role of lipid metabolism and membrane reorganization remains underexplored. Here, we integrate mass spectrometry-based lipidomics with RNA sequencing to characterize global lipidomic and transcriptomic changes in HeLa cells exposed to three conditions: control, heat shock (HS), and HS with eight hours of recovery. Heat shock-induced extensive lipid remodeling, including significant increases in fatty acids, glycerophospholipids, and sphingolipids, with partial normalization during recovery. Transcriptomic analysis identified over 2,700 upregulated and 2,300 downregulated genes under heat shock, with GO enrichment suggesting potential transcriptional contributions to lipid metabolism. However, transcriptional changes alone did not fully explain the observed lipidomic shifts, suggesting additional layers of regulation. Joint pathway analysis revealed enrichment in glycerophospholipid and sphingolipid metabolism, while network analysis identified lipid transport regulators (STAB2, APOB), stress-linked metabolic nodes (KNG1), and persistent sphingolipid enrichment during recovery. These findings provide a comprehensive framework for understanding lipid-mediated mechanisms of the HSR and highlight the importance of multi-omics integration in stress adaptation and disease biology.
EPIraction - an atlas of candidate enhancer-gene interactions in human tissues and cell lines
Authors: Nurtdinov Ramil N. , Guigó Roderic
Published: February 2025

Enhancer-gene maps are essential to understand gene regulation. The identification of enhancers contributing to regulating a given gene, however, is challenging as they may lie far from the gene and act in a tissue-specific manner. Here we present EPIraction, an enhancer-gene atlas in the human genome. As H3K27ac is a typical mark of enhancer function, EPIraction relies on an exhaustive collection of 1,538 H3K27ac ChIP-Seq datasets. We used these data together with other epigenomic data to measure enhancer activity. To predict enhancer-gene interactions we first applied the conventional Activity By Contact algorithm to score enhancer-gene pairs in individual tissues. Then, we re-scored the interaction rewarding those present in biologically similar tissues. We used our predictions to annotate the candidate target genes for 1,664,956 SNPs from 3,693 UK Biobank and 760 FinnGen GWAS traits. The EPIraction predictions can be accessed through the portal athttps://epiraction.crg.es. The portal can be employed to produce annotations for user-provided lists of SNPs or genomic intervals.
Chronic sleep curtailment expediates brain aging by activating the complement and coagulation cascades in mice
Authors: Jha Pawan K. , Valekunja Utham K. , Reddy Akhilesh B.
Published: February 2025

Chronic sleep insufficiency is prevalent in modern society and has been associated with age-related neurodegenerative diseases. Loss of sleep accelerates the progression of neurodegeneration in animal models of neurological diseases. Here, we study whether chronic sleep curtailment leads to brain aging in wild-type animals without a genetic predisposition. We used a wild-type mouse model to simulate modern-day conditions of restricted sleep and compared the brain (cortex) proteome of young sleep-restricted animals with different aged control groups. We report the alteration of 149 proteins related to sleep and 1269 related to age with 96 proteins common between them. Through pathway analysis of proteins common to sleep restriction and aging, we discovered that the complement and coagulation cascade pathways were enriched by alterations of complement component 3 (C3), alpha-2-macroglobulin (A2M), fibrinogen alfa and beta chain (FGA and FGB). This is the first study indicating the possible role of the complement and coagulation pathways in brain aging and by chronic sleep restriction (CSR) in mice.
A Genetic Analysis of Lipid Metabolism Regulation in Han Chinese Youth in Xinjiang via Extreme Phenotypic Strategies
Authors: Yu Jiaqing , Ma Yitong
Published: February 2025

The Xinjiang Uyghur Autonomous Region of the People’s Republic of China has been influenced by its natural ecological environment, historical evolution, and cultural customs since ancient times. The aim of this study was to investigate new genes that contribute to lipid metabolism regulation in Han Chinese youth in the Xinjiang region through sequencing analysis. Based on the threshold value of triglycerides (TG), we selected two groups of Han Chinese university students, namely, individuals with extremely low TG levels and individuals with normal TG levels, and conducted whole-exome sequencing on samples from these individuals. Ten genes (ACTN2, DHTKD1, NLRP9, PTPRA, INPP4B, PHGDH, PYROXD2, RIN1, MYRIP, and PRSS57) were selected via bioinformatics analysis of the sequencing results. Subsequently, we can conduct further validation at the cellular and animal levels to screen for emerging genes associated with lipid metabolism.
ABL Kinases Modulate EZH2 Phosphorylation and Signaling in Metastatic Triple Negative Breast Cancer
Authors: Colemon Ashley , Prioleau Tatiana , Rouse Clay , Pendergast Ann Marie
Published: February 2025

Triple-negative breast cancer (TNBC) remains a leading cause of cancer associated deaths in women owing to its highly metastatic potential and limited treatment options. Recent studies have shown that expression of proteins associated with epigenetic regulation of gene expression are associated with metastatic relapse, however targeting epigenetic regulatory proteins has not resulted in effective therapies for TNBC in the clinic. The ABL tyrosine kinases promote metastasis of breast cancer cells in mouse models. However, a role of ABL kinases in the regulation of epigenetic processes in solid tumor metastasis remains unexplored. Here we show that inactivation of ABL kinases in bone metastatic TNBC cells led to a significant enrichment in gene signatures associated with the PRC2 protein complex, revealing a functional link between ABL kinases and the PRC2 complex. ABL inactivation promotes EZH2-T487 phosphorylation through the regulation of a FAK-CDK1 signaling axis. We find that phosphorylated EZH2 T487 or a phosphomimic EZH2 T487D mutant exhibit increased binding to non-canonical binding partners of EZH2 including c-MYC and ZMYND8. Notably, we identify a therapeutic vulnerability in TNBC cells whereby combination treatment with ABL allosteric inhibitors and EZH2 inhibitors elicits a synergistic decrease in TNBC cell survival in vitro, and impairs TNBC metastasis, prolonging survival of tumor-bearing mice treated with the combination therapy.

One Sentence Summary

ABL Kinases indirectly impact EZH2 catalytic activity by blocking a signaling cascade that leads to changes in the phosphorylation, protein interactions, and function of the PRC2 catalytic component EZH2 in TNBC.
Is Tanimoto a metric?
Authors: Surendran Akash , Zsigmond Krisztina , López-Pérez Kenneth , Miranda-Quintana Ramón Alain
Published: February 2025

No. However, here we show how to generate a metric consistent with the Tanimoto similarity. We also explore new properties of this index, and how it relates to other popular alternatives.
Comparative Transcriptomic Analysis of Perfluoroalkyl Substances-Induced Responses of Exponential and Stationary PhaseEscherichia coli
Authors: Wintenberg Molly E. , Vasilyeva Olga B. , Schaffter Samuel W.
Published: February 2025

Per- and polyfluoroalkyl substances (PFAS) are highly stable chemical contaminants of emerging concern for human and environmental health due to their non-natural chemistry, widespread use, and environmental persistence. Despite conventional metrology, mitigation strategies, and removal technologies, the complexity of this growing problem necessitates the need for alternative approaches to tackle the immense challenges associated with complex environmental PFAS contamination. Recently, biology has emerged as an alternative approach to detect and mitigate PFAS and understand the molecular-level responses of living organisms, including microorganisms, to these compounds. However, further study is needed to understand how microorganisms in different environments and growth phases respond to PFAS. In this study, we performed RNA sequencing at mid-exponential, early stationary phase, and late stationary phase of bacterial growth to determine the global transcriptional response of a model chassis,Escherichia coliMG1655, induced by two PFAS, perfluorooctanoic acid (PFOA) and perfluorododecanoic acid (PFDoA), and equivalent non-fluorinated carboxylic acids (NFCA), octanoic acid and dodecanoic acid. Differential gene expression analysis revealed PFOA and PFDoA induced distinct changes in gene expression throughout cultivation. Specifically, we identified significant changes in expression of the formate regulon and sulfate assimilation at mid-exponential phase and ferrous iron transport, central metabolism, the molecular chaperone network, and motility processes during stationary phase. Importantly, many of these changes are not induced by NFCAs. In summary, we found PFAS induced a system-level change in gene expression, and our results expand the understanding of bacterial-PFAS interactions that could enable the development of future real-time environmental monitoring and mitigation technologies.

Importance

The prevalence and persistence of PFAS in the environment is a growing area of concern. However, little is understood of the impacts of PFAS on the environment, particularly impacts on microorganisms that play pivotal roles in nearly every ecosystem. Thus, comprehensive measurements that provide systems-level insight into how microorganisms respond and adapt to PFAS in the environment are paramount. Here, we use RNA sequencing to study the global transcriptional response ofE. coliMG1655 to two PFAS and non-fluorinated equivalent compounds across growth phases. We find that PFAS induce system-level changes in metabolic, transport, and gene regulatory pathways, providing insight into how these non-natural chemicals interact with a model bacterium. Additionally, the transcriptomic dataset associated with this work provides the community with PFSA-specific gene expression patterns and possible PFAS degradation pathways for the development of future whole-cell biosensors and mitigation efforts.
The immunometabolic topography of tuberculosis granulomas governs cellular organization and bacterial control
Authors: McCaffrey Erin F. , Delmastro Alea C. , Fitzhugh Isobel , Ranek Jolene S. , Douglas Sarah , Peters Joshua M. , Fullaway Christine Camacho , Bosse Marc , Liu Candace C. , Gillen Craig , Greenwald Noah F. , Anzick Sarah , Martens Craig , Winfree Seth , Bai Yunhao , Sowers Cameron , Goldston Mako , Kong Alex , Boonrat Potchara , Bigbee Carolyn L. , Venugopalan Roopa , Maiello Pauline , Klein Edwin , Rodgers Mark A. , Scanga Charles A. , Lin Philana Ling , Kirschner Denise , Fortune Sarah , Bryson Bryan D. , Butler J. Russell , Mattila Joshua T. , Flynn JoAnne L. , Angelo Michael
Published: February 2025

Despite being heavily infiltrated by immune cells, tuberculosis (TB) granulomas often subvert the host response toMycobacterium tuberculosis(Mtb) infection and support bacterial persistence. We previously discovered that human TB granulomas are enriched for immunosuppressive factors typically associated with tumor-immune evasion, raising the intriguing possibility that they promote tolerance to infection. In this study, our goal was to identify the prime drivers for establishing this tolerogenic niche and to determine if the magnitude of this response correlates with bacterial persistence. To do this, we conducted a multimodal spatial analysis of 52 granulomas from 16 non-human primates (NHP) who were infected with low dose Mtb for 9-12 weeks. Notably, each granuloma’s bacterial burden was individually quantified allowing us to directly ask how granuloma spatial structure and function relate to infection control. We found that a universal feature of TB granulomas was partitioning of the myeloid core into two distinct metabolic environments, one of which is hypoxic. This hypoxic environment associated with pathologic immune cell states, dysfunctional cellular organization of the granuloma, and a near-complete blockade of lymphocyte infiltration that would be required for a successful host response. The extent of these hypoxia-associated features correlated with worsened bacterial burden. We conclude that hypoxia governs immune cell state and organization within granulomas and is a potent driver of subverted immunity during TB.
A complete mitochondrial genome-based phylogeny of gooseneck barnacles confirms the sister group relationship between the easternPacific Pollicipeselegans and the eastern AtlanticP. pollicipes
Authors: Alfaro Ruben , Mantilla Guillermo , Marín Alan
Published: February 2025

Background

Gooseneck barnacles are a fascinating invertebrate group and their taxonomic classification has attracted the attention of several specialists, including Charles Darwin, who was the first to note the close relationship between two species of gooseneck barnacles found on the eastern coasts of the Pacific,Pollicipes elegans, and the Atlantic,P. pollicipes. Additionally, a third species from the eastern Pacific,P. polymerus, was believed to have diverged earlier from the group.

Methods and results

Here, we used genomic short-read sequences publicly available in GenBank to assemble the first complete mitochondrial genome ofP. elegans. We conducted a phylogenetic analysis to assess the relationships among its related species and other cirripede species from the superorder Thoracicalcarea. Our phylogenetic findings based on complete mitogenomes reinforce the close relationship betweenP. elegansandP. pollicipes, withP. polymerusemerging as a basal branch, indicating an earlier divergence from the group.

Conclusions

Our analysis provided the first robust phylogenetic assessment ofP. elegans, strongly supporting its close relationship withP. pollicipes. Further efforts should aim to sequence the complete mitogenomes of other species within the order Pollicipedomorpha. This endeavor will enable a more comprehensive phylogenetic analysis of this group, whose classification remains a subject of debate.
Growth vs. Diversity: A Time-Evolution Analysis of the Chemical Space
Authors: Perez Kenneth Lopez , López-López Edgar , Soulage Flavie , Felix Eloy , Medina-Franco José L. , Miranda-Quintana Ramon Alain
Published: February 2025

Chemical space is a core and theoretical concept in cheminformatics, and it also has practical applications in drug discovery and other research areas. Chemical space is frequently associated with the number of molecules in the universe (e.g., chemical universe). It is well known that the number of compounds (both synthesized and theoretical ones) is rapidly increasing. It would be obvious to affirm that the chemical space is expanding (as a proxy of growth). But is the chemical diversity of compound libraries growing? In this study, we tackle this question by assessing quantitatively the time evolution of chemical libraries in terms of the chemical diversity as measured with molecular fingerprints. To tackle this task, we employed innovative cheminformatics methods to assess the progress over time of the chemical diversity of compound libraries available in the public domain. Using the iSIM and the BitBIRCH clustering algorithm, we conclude that, based on the fingerprints used to represent the chemical structures, just an increasing number of molecules cannot be directly translated to diversity for the analyzed libraries. With these tools, we have identified what releases contributed to the diversity of the library and the zones it did.
Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization
Authors: Sang Mankun , Johnson Margaret E
Published: February 2025

Successful DNA transcription demands coordination between proteins that bind DNA while simultaneously binding to one another into dimers or higher-order complexes. Measurements that report on the lifetime or occupancy of an individual protein on DNA thus represent a convolution over the protein interactions with specific DNA, nonspecific DNA, or protein partners on DNA. For some DNA-binding proteins, dimerization is considered an essential step for stable DNA association, but here we show that protein dimerization can also reduce dwell times on specific DNA targets, enhance or impair occupancy on target sequences, and spatially redistribute proteins on DNA. We use mass-action kinetic models of pairwise association reactions between proteins and DNA (specific and nonspecific) and protein dimers, along with theory and spatial stochastic simulations to isolate the role of dimerization on observed dwell times and occupancy. For proteins binding a spatially localized cluster of targets, dimerization can drive up dwell time by 1000-fold and produce high selectivity for clustered over isolated targets. However, this effect can become negligible when proteins outnumber target sequences. In contrast, for isolated DNA targets, dimerization often reduces dwell times by sequestering proteins from their target sites, in some cases thus reducing overall occupancy. The ability of these proteins to bind DNA nonspecifically and diffuse in 1D to exploit dimensional reduction is a key determinant controlling degree of enhancement, despite the presence of nucleosome barriers to 1D diffusion. By comparison with ChipSeq data, our model explains how the distribution of the GAF pioneer proteins throughout the genome is highly selective for clustered targets due to protein interactions and provides a framework to predict how even weak dimerization can redistribute or stabilize proteins on DNA.
Lack of motor defects and ALS-like neuropathology in heterozygousSptlc1Exon 2 deletion mice
Authors: Pant Devesh C. , Lone Museer A. , Parameswaran Janani , Ma Fuying , Dutta Prisha , Wang Zitong , Park Jaekeun , Verma Sumit , Hornemann Thorsten , Jiang Jie
Published: February 2025

Mutations in the humanSPTLC1gene have recently been linked to early onset amyotrophic lateral sclerosis (ALS), characterized by global atrophy, motor impairments, and symptoms such as tongue fasciculations. All known ALS-linkedSPTLC1mutations cluster within exon 2 and a specific variant, c.58G>T, results in exon 2 skipping. However, it is unclear how the exon 2 deletion affects SPTLC1 functionin vivoand contributes to ALS pathogenesis. Leveraging the high genomic sequence similarity between mouse and humanSPTLC1, we created a novel mouse model with a CRISPR/Cas9-mediated deletion of exon 2 in the endogenous murineSptlc1locus. While heterozygous mice did not develop motor defects or ALS-like neuropathology, homozygous mutants died prematurely. These findings indicate thatSptlc1ΔExon2 heterozygous mice do not replicate the disease phenotype but provide valuable insights into SPTLC1 biology and serve as a useful resource for future mechanistic studies.
Genome-wide mapping of 5ʹ-aldehyde terminus induced by reactive oxygen species
Authors: Wu Junzhou , Jiang Yang , Sun Jingjing , Dedon Peter C. , Sturla Shana J.
Published: February 2025

DNA single strand breaks (SSBs) are abundant lesions due to cell metabolism and reactive oxygen species (ROS) and can lead to replication folk collapse, double strand break formation, genome rearrangements, cell death and disease. Among numerous chemical forms of SSBs, 5ʹ-aldehyde terminus are the most abundant generated by hydroxyl radicals and pose significant challenge for cellular repair machinery due to the lack of specific end processing process, potentially leading to more severe biological consequences than other readily repairable SSBs. Herein we developed a new strategy to locate 5ʹ-aldehyde terminus in genomic DNA at single-nucleotide resolution. The principle involves labelling the 5ʹ-aldehyde terminus with an aminooxy-functionalized oligonucleotide, giving rise to a biocompatible altered DNA linkage and allowing labelled sites to be amplified by polymerase chain reaction. We sequenced the 5ʹ-aldehyde terminus distribution in genomic DNA, nuclei, and cells following activation of the Fenton reaction. The results revealed a significant preference for adenine bases in DNA lesions and provided insights into the genome-wide distribution of such DNA damage, correlating with genomic features and chromatin accessibility. This method provide a new strategy for studies aiming to understand the biological and toxicological impacts of 5ʹ-aldehyde termini in DNA as the form species of single strand break induced by reactive oxygen species from a human genome.
Rapid pronucleus assembly using cytoplasmic RNAs in fertilized eggs ofXenopus laevis
Authors: Ikeda Mizuki , Tanaka Yuto , Shohoji Tatsuya , Hara Yuki
Published: February 2025

The size of the nucleus, which serves as the site for essential cellular functions such as replication and transcription, is dynamically altered to support these functions in response to the surrounding environment. During the brief cleavage period in metazoan embryos, the small, hypercondensed sperm nucleus with silenced chromatin undergoes a dramatic transformation into a large, round pronucleus with relaxed chromatin, enabling the activation of chromatin functions necessary for subsequent development. However, it remains unclear whether the egg cytoplasm-specific molecular environment plays a role in pronucleus assembly. In this study, we evaluated the impact of abundant RNAs in eggs on pronucleus assembly by utilizing a cell-free reconstruction of interphase nuclei inXenopus laevisegg extract. We found that when RNA levels deviated from the conventional concentration, the growth rate of the interphase nucleus decreased. Additionally, the addition of RNAs led to a more dispersed chromatin distribution and the dissociation of sperm-specific nuclear proteins from the chromatin. These chromatin remodeling properties, which were reproducible with the introduction of cationic compounds, facilitated the incorporation of somatic histones into the chromatin in reconstructed nuclei. Based on these findings, we propose that cytoplasmic RNAs promote the rapid decondensation of negatively charged chromatin from a hypercompacted state and the removal of positively charged protamines from sperm chromatin via electrical interactions. This remodeling accelerates pronucleus assembly during the brief cleavage period following fertilization and promotes the rapid growth in nucleus size.
Simultaneous immunomodulation and epithelial-to-mesenchymal transition drives lung adenocarcinoma progression
Authors: Kim Junbum , Ravichandran Hiranmayi , Yoffe Liron , Bhinder Bhavneet , Finos Kyle , Singh Arshdeep , Pua Bradley B , Bates Stewart , Huang Bevan Emma , Rendeiro Andre F. , Mittal Vivek , Altorki Nasser K. , McGraw Timothy E. , Elemento Olivier
Published: February 2025

Lung cancer remains the deadliest cancer in the United States, with lung adenocarcinoma (LUAD) as its most prevalent subtype. While computed tomography (CT)-based screening has improved early detection and enabled curative surgeries, the molecular and cellular dynamics driving early-stage LUAD progression remain poorly understood, limiting non-surgical treatment options. To address this gap, we profiled 2.24 million cells from 122 early-stage LUAD patients using multiplexed imaging mass cytometry (IMC). This analysis revealed the molecular, spatial, and temporal dynamics of LUAD development.

Our findings uncover a binary progression model. LUAD advances through either inflammation, driven by a balance of cytotoxic and regulatory immune activity, or fibrosis, characterized by stromal activation. Surprisingly, tumor cell populations did not increase significantly. Instead, they displayed a mixed phenotypic profile consistent with epithelial-to-mesenchymal transition (EMT), effectively masking the expansion of malignant cells.

Furthermore, we addressed discrepancies between CT-based and histology-based subtyping. CT scans, while non-invasive, often mischaracterize invasive fibrotic tumors—which account for 20.5% of LUAD cases—as mild, non-solid ground glass opacities (GGOs). Using high-content IMC imaging, we demonstrate that these tumors harbor significant risks and advocate for improved diagnostic strategies. These strategies should integrate molecular profiling to refine patient stratification and therapeutic decision-making.

Altogether, our study provides a high-resolution, systems-level view of the tumor microenvironment in early-stage LUAD. We characterize key transitions in oncogenesis and propose a precision-driven framework to enhance the detection and management of aggressive disease subtypes.
Cochliobolus miyabeanusspecies-specific identification using nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS)-encoding genes associated with virulence to rice
Authors: Mohd Zainudin Nur Ain Izzati , Kusai Nor Azizah , Abd Murad Nur Baiti , Wu Dongliang , Condon Bradford J. , Turgeon B. Gillian
Published: February 2025

Cochliobolus miyabeanuscauses brown spot disease of rice. For necrotrophicCochliobolusspp., some small molecule products of nonribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) are known pathogenicity and/or virulence factors, often acting in a host-specific manner. Previous whole genome analyses acrossCochliobolusspecies identified 11 NRPS- and 21 PKS-encoding genes inC. miyabeanus. First purpose of the current study was to examine the effect of deletion of ten of the discontinuously distributed genes (corresponding to JGI protein IDs 4446, 5802, 6546, 7015, 9064, 41693, 41753, 83551, 98843 and 107726) on virulence ofC.miyabeanusto rice. A second purpose, based on results of the first, was to develop a PCR method to specifically identifyC. miyabeanusand to distinguish it from other closely related Cochliobolus spp. We show that deletion of seven of the genes resulted in mutants that were reduced in virulence compared to the wild-type strain WK1C. Wild-type developed large dark brown necrotic lesions surrounded by chlorotic halos, while the mutants produced smaller, light brown spots with chlorosis. These results suggest that the products of these genes contribute to brown spot disease. In addition, we identifiedPKSandNPSSNPs that discriminate betweenC. miyabeanusand other species ofCochliobolus.
The Knock-In Atlas: A web resource for targeted protein trap by CRISPR/Cas9 in human and mouse cell lines
Authors: Hanai Yuma , Hilario Patrick Louis Lagman , Shiraishi Yuriko , Kano Norisuke , Kojima Minami , Murai Kokoro , Kawai Taro , Okamura Katsutomo
Published: February 2025

Various cell engineering techniques have been developed by leveraging the CRISPR-Cas9 technology, but large-scale resources for targeted gene knock-in are still limited. Here we introduce a tool kit for tagging genes by inserting artificial exons encoding fluorescent protein tags in target gene introns. To produce knock-in cells efficiently and reproducibly, we carefully chose and catalogued guide RNAs (gRNAs) for targeting genes in the human and mouse genomes by taking the gRNA efficacy scores and protein structures around the insertion sites into account. So far, we have constructed 427 gRNA expression plasmids to target 178 genes as the first set. The transfection and flow cytometry protocols were optimized for several cell lines including HEK293T, eHAP1, HeLa, THP-1, Neuro2a, mouse embryonic fibroblast (MEF) and mouse embryonic stem cell (mESC). A website has been launched to organize the results of initial characterization including flow cytometry data after transfection, confocal microscopy, and western blot results for the genes for which knock-in HEK293T cell lines were already made. We provide a user-friendly database to organize the information of the cell line and pre-designed gRNAs at .
Photoperiod decoder 1regulates seasonal changes in energy metabolism through the growth hormone signaling pathway
Authors: Nakayama Tomoya , Yamaguchi Taiki , Maruyama Michiyo , Ansai Satoshi , Kashima Makoto , Fontaine Romain , Henkel Christiaan , Naruse Kiyoshi , Yoshimura Takashi
Published: February 2025

Seasonal changes in metabolism are crucial for animals to adapt to annual environmental fluctuations. However, the molecular mechanisms underlying these adaptations remain poorly understood. Here, we identified a novel gene,photoperiod decoder 1(phod1), which exhibits a unique bimodal expression pattern under long-day conditions in Japanese medaka fish (Oryzias latipes). Whilephod1is conserved across many vertebrates, except for eutherians, its function remained unknown. Single-cell RNA sequencing analysis revealed thatphod1is predominantly expressed in specific pituitary cells that co-express opsin and circadian clock genes. Transcriptomic analysis usingphod1knockout fish demonstrated thatphod1is essential for photoperiodic regulation of growth hormone. Furthermore, transcriptomic and metabolomic analyses of the liver, the primary target of growth hormone, revealed significant alterations in energy metabolism. Behavioral analysis also showed thatphod1knockout fish exhibited significantly reduced locomotor activity. These findings indicate thatphod1plays a crucial role in seasonal metabolic adaptation through modulation of the growth hormone signaling pathway.
Object representations drive emotion schemas across a large and diverse set of daily-life scenes
Authors: Gao Chuanji , Ajith Susan , Peelen Marius V.
Published: February 2025

The rapid emotional evaluation of objects and events is essential in daily life. While visual scenes reliably evoke emotions, it remains unclear whether emotion schemas evoked by daily-life scenes depend on object processing systems or are extracted independently. To explore this, we collected emotion ratings for 4913 daily-life scenes from 300 participants, and predicted these ratings from representations in deep neural networks and fMRI activity patterns in visual cortex. AlexNet, an object-based model, outperformed EmoNet, an emotion-based model, in predicting emotion ratings for everyday scenes, while EmoNet excelled for explicitly evocative stimuli. Emotion information was processed hierarchically within the object recognition system, consistent with the visual cortex’s organization. Activity patterns in the lateral occipital complex (LOC), an object-selective region, reliably predicted emotion ratings and outperformed other visual regions. These findings suggest that emotion processing in everyday scenes follows visual object recognition, with additional mechanisms engaged when object content is uninformative.
PLK4 inhibition as a strategy to enhance non-small cell lung cancer radiosensitivity
Authors: Dominguez-Vigil Irma G. , Banik Kishore , Baro Marta , Contessa Joseph N. , Hayman Thomas J.
Published: February 2025

Lung cancer is the leading cause of cancer-related mortality worldwide. Non-small cell lung cancer (NSCLC) is the most common subtype of lung cancer and comprises 85% of cases. Despite treatment advances, local control after curative-intent chemoradiation for NSCLC remains suboptimal. Polo-like kinase 4 (PLK4) is a serine-threonine kinase that plays a critical role in the regulation of centrosome duplication and cell cycle progression and is overexpressed in NSCLC, thus, making it a potential therapeutic target. CFI-400945 is an orally available PLK4 inhibitor currently undergoing clinical trial evaluation. As radiation causes cell death primarily by mitotic catastrophe, a process enhanced by alterations in centrosome amplification, we hypothesized that disruption of the mitotic machinery by inhibition of PLK4 would enhance the effects of radiation in NSCLC. PLK4 inhibition by CFI-400945 resulted in radiosensitization of NSCLC cell lines. In contrast, CFI-400945 had no effect on the radiosensitivity of normal lung fibroblasts. PLK4 inhibition did not affect cell-cycle phase distribution prior to radiation, but rather the combination of CFI-400945 and radiation resulted in increased G2/M cell cycle arrest, increased centrosome amplification, and a concomitant increase in cell death through mitotic catastrophe. Lastly, CFI-400945 treatment enhanced the radiation-induced tumor growth delay of NSCLC tumor xenografts. These data indicate that targeting PLK4 is a novel approach to enhance the radiation sensitivity of NSCLCin vitroandin vivothrough potentiation of centrosome amplification and cell death through mitotic catastrophe.
‘SpikeNburst’ and ‘Nicespike’: Advanced Tools for Enhancing and AcceleratingIn VitroHigh-Density Electrophysiology Analysis
Authors: Wolff Robert , Polito Alessia , Buccino Alessio Paolo , Chiappalone Michela , Tucci Valter
Published: February 2025

High-density multi-electrode arrays (HD-MEAs) have revolutionized electrophysiology by enabling the recording of neuronal activity with unprecedented spatial and temporal resolution. However, analysing these large-scale datasets poses significant challenges, including artefact removal, spike sorting, and accurate assessments of neuronal synchronization. Here, we present two Python-based tools, ‘spikeNburst’ and ‘nicespike’, designed to address these challenges and provide a scalable solution for the comprehensive analysis of HD-MEA recordings.

ThespikeNbursttool integrates advanced methodologies for spike train filtering, burst and network burst detection, and synchronization analysis, and we implemented a full analysis pipeline in thenicespiketool, which includes GPU-accelerated spike sorting using template matching with Kilosort to accurately identify neuronal units spanning multiple electrodes. Together, these tools enable more precise analyses by mitigating redundancy and overestimation inherent in single-channel approaches. Their graphical user and command-line interfaces ensure accessibility for diverse user needs.

We validated the tools on neuronal culture recordings, demonstrating their ability to identify somatic and dendritic features of neuronal units, characterize bursting behaviour, and quantify synchronization at both unit and network levels. By addressing critical limitations of existing methods,spikeNburstandnicespikeprovide a robust, scalable, and user-friendly framework for HD-MEA data analysis, advancing our ability to study neural network dynamics and single-cell activity in detail.