bluuebunny/crossref_metadata_2025 huggingface dataset:
GSLab: Open-Source Platform for Advanced Phasor Analysis in Fluorescence Microscopy
Authors: Vallmitjana Alexander , Torrado Belen , Durkin Amanda F , Dvornikov Alexander , Rajil Navid , Ranjit Suman , Balu Mihaela
Published: February 2025

GSLab addresses the need for effective image analysis tools in fluorescence microscopy by providing an open-source platform that enhances traditional phasor analysis with advanced features. Key capabilities include machine learning-based clustering, real-time monitoring, and quantitative unmixing of fluorescent species. Designed for both commercial and custom systems, GSLab provides researchers with comprehensive lifetime and spectral phasor image analysis tools to tackle complex biological problems.
A Study of Calibration as a Measurement of Trustworthiness of Large Language Models in Biomedical Research
Authors: de Oliveira Rodrigo , Garber Matthew , Gwinnutt James M , Rashidi Emaan , Hwang Jwu-Hsuan (Shantina) , Gilmour William , Nanavati Jay , El Abidine Khaldoun Zine , Mack Christina DeFilippo
Published: February 2025

Objectives

To assess the calibration of 9 large language models (LLMs) within biomedical natural language processing (BioNLP) tasks, furthering understanding of trustworthiness and reliability in real-world settings.

Materials and Methods

For each LLM, we collected responses and corresponding confidence scores for all 13 datasets (grouped into 6 tasks) of the Biomedical Language Understanding & Reasoning Benchmark (BLURB). Confidence scores were assigned using 3 strategies: Verbal, Self-consistency, Hybrid. For evaluation, we introduced Flex-ECE (Flexible Expected Calibration Error): a novel adaptation of ECE that accounts for partial correctness in model responses, allowing for a more realistic assessment of calibration in language-based settings. Two post-hoc calibration techniques—isotonic regression and histogram binning—were evaluated.

Results

Across tasks, mean calibration ranged from 23.9% (Population-Intervention-Comparison-Outcome extraction) to 46.6% (Relation Extraction). Across LLMs, Medicine-Llama3-8B had the best mean overall calibration (29.8%); Flan-T5-XXL had the highest ranking on 5/13 datasets. Across strategies, self-consistency (mean: 27.3%) had better calibration than Verbal (mean: 42.0%) and Hybrid (mean: 44.2%). Post-hoc methods substantially improved calibration, with best mean calibrated Flex-ECEs ranging from 0.1% to 4.1%.

Discussion

The poor out-of-the-box calibration of LLMs poses a risk to trustworthy deployment of such models in real-world BioNLP applications. Calibration can be improved post-hoc and is a recommended practice. Non-binary metrics for LLM evaluation such as Flex-ECE provide a more realistic assessment of trustworthiness of LLMs, and indeed any model that can be partially right/wrong.

Conclusion

This study shows that out-of-the-box calibration of LLMs is very poor, but traditional post-hoc calibration techniques are useful to calibrate LLMs.
In vivovalidation of kinematic relationships for epithelial morphogenesis
Authors: Namba Toshinori , Sugimura Kaoru , Ishihara Shuji
Published: February 2025

Tissue growth and deformation result from the combined effects of various cellular events, including cell shape change, cell rearrangement, cell division, and cell death. Resolving and integrating these cellular events is essential for understanding the coordination of tissue-scale growth and deformation by individual cellular behaviors that are critical for morphogenesis, wound healing, and other collective cellular phenomena. For epithelial tissues composed of tightly connected cells, the texture tensor method provides a unified framework for quantifying tissue and cell strains by tracking individual cells in live imaging data. The corresponding kinematic relationships have been introduced in a continuum model that we previously reported. In this study, we validated the kinematic equations proposed in the continuum model using experimental data from a growingDrosophilawing. To accomplish this, we introduced modified definitions of the texture tensor and validated that one of these modifications more accurately represents approximated cellular shapes without relying onad hocscaling factors. By utilizing the modified tensor, we demonstrated the compatibility of the strain rate tensors and validated both the kinematic and cell number density equations. These results crossvalidate the modified texture analysis and continuum model. Further, the precision in the kinematic relationships achieved in this study provide a robust and solid foundation for more advanced integration of modeling and experiments.
Heterogeneous T cell responses across Hepatitis B virus clinical phases revealed by rapid whole-blood HBV T cell analysis
Authors: Le Bert Nina , Koffas Apostolos , Kumar Rajneesh , Facchetti Floriana , Tan Anthony T , Gill Upkar S , Mak Lung-Yi , Stretch Sophie W , Miao Tizong , Hariharaputran Smrithi , Hang Shou Kit , Guo Yifei , Chen Qi , Degasperi Elisabetta , Lampertico Pietro , Chow Wan Cheng , Bertoletti Antonio , Kennedy Patrick TF
Published: February 2025

Background & Aims

There is an unmet need for immunological biomarkers in chronic hepatitis B (CHB), where patient management relies on virological and biochemical markers despite the crucial role of virus-specific T cells in controlling viral replication and disease progression. To address this, we developed the HBV-cytokine release assay (HBV-CRA), a rapid, point-of-care test that measures multiple cytokines in whole blood after HBV-peptide stimulation.

Methods

We first assessed the assay’s sensitivity by spiking whole blood with engineered HBV-specific T cells. Next, we compared sensitivity and consistency of HBV-CRA to ex vivo IFN-γ ELISpot assays. We then applied the assay in a cross-sectional study of 235 CHB patients and longitudinally in acute HBV patients during HBsAg sero-clearance.

Results

The HBV-CRA detected T cell function in 80% of CHB cases and showed that elevated IL-2 and IFN-γ levels after Core peptide stimulation were associated with HBsAg clearance. Importantly, unsupervised clustering identified distinct immune response patterns independent of established clinical and virological classifications. The assay also demonstrated the functional impact of NUC treatment on HBV-specific T cell responses.

Conclusions

The HBV-CRA is a rapid and easy-to-use assay that identifies immune profiles associated with HBsAg clearance and differentiates CHB patients based on antiviral T cell function. Its application in a large CHB cohort revealed that traditional disease phase classifications, based on viral and clinical parameters, cannot predict HBV-specific T cell profiles. The HBV-CRA has the potential to guide patient stratification for immunotherapeutic interventions.
A single decreasing ramp friction sprint for torque-cadence relationship assessment during cycling
Authors: Rozier-Delgado Pablo , Bowen Maximilien , Dussauge Marion , Samozino Pierre , Morel Baptiste
Published: February 2025

This study aimed to introduce and validate a novel method for assessing dynamic fatigue components through a single-sprint test, addressing the limitations of traditional multi-sprint evaluations. We tested this method on twenty-one participants by computing torque-cadence relationships from two iso-friction sprints at varying friction levels (3% and 9% of body mass), the traditional combination of these iso-friction sprints and a novel decreasing ramp friction sprint (FrD). The accuracy of this new method through fatigue was also tested with ten 6-s FrDsprints interspersed with a 24-s passive rest. FrDoutperformed single iso-friction sprints and provided accurate and valid torque-cadence relationship’s parameters estimates (T0, C0, and Pmax) with systematic bias < 3%, typical error of estimate < 6% and very high r2(median of 0.962). The quality of the input data from this method was also high, as evidenced by the well-distributed and wide-range cadence spectrum (51.3% of C0; skewness = −0.51, p < 0.05) and was maintained throughout the fatiguing exercise. Our novel method not only allows the dynamic fatigue components evaluation with only one sprint but also maintains accuracy and validity across varying fatigue states, offering significant advantages for both research and practical applications.
A harmonized ovarian cancer scRNA-seq atlas to dissect disease heterogeneity underlying metastatization and chemoresistance
Authors: Sallese Marta Rosa , Aiello Vittorio , Villa Carlo Emanuele , Lo Riso Pietro , Testa Giuseppe
Published: February 2025

The advent of single cell technology has enabled researchers with the ability to achieve unprecedented resolution in the characterization of biological systems. The consequent increasing availability of single cell dataset brought about the possibility to obtain comprehensive reference atlases, to shed light on the molecular and cellular foundations of healthy and diseased tissues. This process has highlighted the need to integrate datasets from different sources while being able to distinguish true biological signal from technical confounders. While this issue is widespread to most biological settings, it holds especially true for cancer samples, which are characterized by a diffused inter- and intra-patient phenotypic heterogeneity. To address this issue, here we developed a novel integration method tailored to highly heterogeneous single cell transcriptomic data and applied it to one of the quintessential heterogeneous cancer type, namely high-grade serous ovarian cancer, to generate the first reference atlas for this disease. By identifying patient-specific cell populations and deriving metacells, we were able to preserve inter-patient biological variability. Using a variational autoencoder, we integrated metacell data, revealing an evolving landscape of cell states along disease progression and treatment for each of the main cell types constituting the dataset. Also, we showed the potential of this resource by identifying diffused and tissue/treatment-specific cell-to-cell interactions. Finally, the generated integration model allowed to expand the atlas with additional data, granting iterative refinement over time of this disease reference. Our strategy now provides a valuable resource for the cancer research community, facilitating the investigation of tumor heterogeneity towards the development of novel therapeutic strategies.
cfDecon: Accurate and Interpretable methylation-based cell type deconvolution for cell-free DNA
Authors: Wang Yixuan , Li Jiayi , Li Jingqi , Yang Shen , Huang Yuhan , Liu Xinyuan , Fan Yimin , King Irwin , Li Yumei , Li Yu
Published: February 2025

Cell-free DNA (cfDNA) analysis has emerged as a powerful tool for noninvasive diagnostics and monitoring of aberrant methylation. However, computational deconvolution of cfDNA remains challenging due to the complexity of methylation data, the diverse cellular compositions in cfDNA mixtures, and the limited interpretability of current methods. We present cfDecon, an efficient deep-learning framework for cfDNA deconvolution at the resolution of individual reads. cfDecon employs a multichannel autoencoder core module and an iterative refinement process to estimate cell-type proportions and generate condition-aware cell-type-specific methylation profiles. We rigorously evaluate cfDecon through comprehensive simulation experiments, including scenarios with normal cellular compositions, rare cell types, and unknown cell types, where cfDecon consistently outperforms previous state-of-the-art methods in deconvolution. Using strict data separation and careful control for potential data leakage, cfDecon shows scalability and applicability to large-scale studies by raising Lin’s Concordance Correlation Coefficient (CCC) over 33% on an atlas-level reference dataset. We further validate cfDecon’s utility in disease diagnosis on two clinical datasets, Amyotrophic Lateral Sclerosis (ALS) and Hepatocellular Carcinoma (HCC). cfDecon raises the performance of disease detection from 0.53 to 0.79 compared to existing methods on the ALS dataset and 0.55 to 0.77 on the HCC dataset. The capacity of cfDecon to predict condition-specific DNA methylation patterns across cell types offers a valuable framework for studying differentially methylated CpGs. Furthermore, integrating cfDecon with enrichment analysis facilitates the exploration of functional variations in CpGs across different conditions. cfDecon represents a significant advancement in cfDNA analysis, offering improved accuracy, interpretability, and potential for personalized medicine applications. The codebase is available athttps://github.com/Susanxuan/cfDecon.
Predicting the responses of the world's bird species to increases in agricultural production
Authors: Busana Michela , Phalan Ben , Balmford Andrew , Buchanan Graeme M , Butchart Stuart H M , Eyres Alison , Simkins Ashley T , Williams David R , Ball Thomas S , Berger Iris , Clark Michael , Dicks Lynn V , Fajardo Javier , Green Rhys E , Scott Emma , Donald Paul F
Published: February 2025

The intensification and expansion of croplands are among the greatest threats to biodiversity, but the likely responses to these changes remain unknown for most species. Using data on responses of 862 bird species to changes in yields of arable crops, we extrapolate vulnerability to agriculture for the world's other terrestrial birds based on their traits and taxonomy. We estimate that 74-78% of terrestrial bird species globally suffer population declines where natural habitats are replaced by croplands, and that over half cannot persist in cropland at even the lowest current yields. Past impacts of agriculture on birds have been greatest in the tropics, particularly in coastal forest regions of Central and South America and West Africa and in southern and South-East Asia. Using these estimates to model the impacts of future scenarios of agricultural change, we find that continuing current rates of cropland expansion and yield increases (i.e. extrapolating 'business-as-usual' trends to 2050) is expected to have more negative impacts on birds (particularly in Central and South America, Eastern Europe, sub-Saharan Africa and South and East Asia) than a potential alternative of a targeted strategy of closing yield gaps while limiting cropland expansion. However, we also identify biodiverse regions of the world where closing yield gaps may have more severe impacts on birds than business-as-usual, such as the Pampas of South America and parts of the Sahel region in West Africa. The strategy of least impact for a particular area can be predicted from the response characteristics of the communities of species present there, offering opportunities to take account of regional context for designing less damaging global food production systems.
Predicting Potential Spawning Areas: a novel framework for elasmobranch conservation and spatial management
Authors: Ruiz-García David , Barría Claudio , Colmenero Ana I. , Raga Juan A. , March David
Published: February 2025

Defining and protecting critical habitats for elasmobranchs (sharks and rays), such as spawning areas, is essential for mitigating anthropogenic pressures that threaten their populations, primarily driven by fisheries and habitat degradation. This study presents a novel modelling-based framework to identify Potential Spawning Areas (PSAs) - habitats offering optimal conditions for oviposition. Using fisheries-dependent trawl bycatch data combined with environmental and anthropogenic predictors, we applied machine-learning models to delineate PSAs for the smallspotted catshark (Scyliorhinus canicula) and skates (Raja spp.) in the western Mediterranean. Static environmental predictors, including depth and slope, were primary drivers, while dynamic predictors, including sea bottom temperature and salinity played seasonally relevant roles. Trawl fishing pressure also influenced importantly the distribution of PSAs, revealing a concerning positive feedback loop between exploitation and habitat degradation. While PSAs experienced lower fishing effort than the rest of the study area, a substantial proportion of egg case bycatch still occurs within them. The current network of Marine Protected Areas in the region fails to adequately safeguard these habitats due to limited coverage and enforcement. Our findings underscore significant gaps in spatial management and the urgent need for targeted conservation measures. The PSA framework provides a robust, scalable tool for identifying critical habitats across regions and species, offering actionable insights for marine spatial planning and ecosystem-based management. This adaptable approach can support global conservation efforts for elasmobranchs and their ecosystems.

Significance

Sharks and rays are vital to marine ecosystems but face alarming extinction risks due to overfishing and habitat loss. Identifying critical reproductive habitats, such as spawning areas, is essential for protection but remains a significant challenge. This study introduces a novel framework for identifying Potential Spawning Areas (PSAs) - habitats offering optimal conditions for oviposition - using machine-learning and fisheries bycatch data. Applied in the western Mediterranean for the smallspotted catshark and skates, it demonstrates how environmental factors and fishing pressures shape these habitats, highlighting significant management gaps. The PSAs framework offers a scalable approach to guide the establishment of marine protected areas and fisheries management plans, providing a novel approach for conserving vulnerable marine species and their habitats.
Perivascular RELM⍺-positive synovial macrophages recruit monocytes at the onset of inflammatory arthritis
Authors: Schonfeldova Barbora , Chibwana Marah , Gentek Rebecca , Zec Kristina , Udalova Irina A
Published: February 2025

Macrophages, monocytes and neutrophils are major types of myeloid cells involved in inflammatory diseases, such as rheumatoid arthritis (RA). Recent scRNA-seq studies identified a remarkable diversity of synovial macrophages but, with the exception of lining macrophages, their geographical location and specific roles remain largely unexplored. Here, we localised the RELMa-positive macrophages, predicted to produce high levels of monocyte-recruiting chemokines, to the synovial interstitium and more specifically, to the vicinity of interstitial blood vessels. Using complementary reporter mouse models, CCL2-mCherry to label CCL2-producing cells, and CCR2-CRE/mKate2 marking CCR2 expressing monocytes, we demonstrated that RELMa-positive perivascular macrophages secrete CCL2 to recruit monocytes predominantly to the synovial interstitium at the onset of antigen-induced arthritis. The inflamed synovial environment guides the differentiation of the recruited monocytes into tissue-resident macrophages, including but not limited to macrophages expressing VSIG4, a characteristic marker of lining macrophages. Thus, RELMa-positive macrophages orchestrate monocyte recruitment to the synovium during articular inflammation, contributing to a local replenishment of synovial lining macrophages.
ActSeek: Fast and accurate search algorithm of active sites in Alphafold database
Authors: Castillo Sandra , Ollila O. H. Samuli
Published: February 2025

Finding proteins with specific functions by mining modern databases can potentially lead to substantial advancements in wide range of fields, from medicine and biotechnology to material science. Currently available algorithms enable mining of proteins based on their sequence or structure. However, activities of many proteins, such as enzymes and drug targets, are dictated by active site residues and their surroundings rather than the overall structure or sequence of a protein. Here we present ActSeek – a computer vision-inspired fast program – that searches structural databases for proteins with active sites similar to the seed protein. ActSeek is implemented to mine proteins with desired active site environments from the Alphafold database. The potential of ActSeek to find innovative solutions to the world’s most pressing challenges is demonstrated by finding enzymes that may be used to produce biodegradable plastics or degrade plastics, as well as potential off-targets for common drug molecules.
Genomic and functional adaptations in guanylate-binding protein 5 (GBP5) highlight specificities of bat antiviral innate immunity
Authors: Le Corf Amandine , Maesen Sarah , Loyer Clara , Vazquez Juan Manuel , Lauterbur M. Elise , Sareoua Lucas , Gray-Sandoval Genevieve , Cimarelli Andrea , Rey Carine , Sudmant Peter H , Enard David , Etienne Lucie
Published: February 2025

Bats are asymptomatic reservoirs of several zoonotic viruses. This may result from long-term coevolution between viruses and bats, that have led to host adaptations contributing to an effective balance between strong antiviral responses with innate immune tolerance. To better understand these virus-host interactions, we combined comparative transcriptomics, phylogenomics and functional assays to characterize the evolution of bat innate immune antiviral factors. First, we stimulated the type I interferon immune pathway inMyotis yumanensisprimary cells and identified guanylate-binding protein 5 (GBP5) as the most differentially expressed interferon-stimulated gene (ISG). Phylogenomic analyses showed that bat GBP5 has been under strong episodic positive selection, with numerous rapidly evolving sites and species-specific gene duplications, suggesting past evolutionary arms races. Functional tests on GBP5 orthologs from ten bat species covering the >60 million years of Chiroptera evolution revealed species- and virus-specific restrictions against RNA viruses (retrovirus HIV, and rhabdoviruses European bat lyssavirus and VSV), which are typical signatures of adaptations to past viral epidemics. Interestingly, we also observed a lineage-specific loss of the GBP5 prenylation motif in the common ancestor ofPipistrellusandEptesicusbats, associated with different GBP5 subcellular localization and loss of antiviral functions. Resurrection of the ancestral prenylation motif inEptesicus fuscusGBP5 rescued its subcellular localization, but not the complete antiviral activities, suggesting that additional determinants are necessary for the antiviral restriction. Altogether, our results highlight adaptations that contribute to bat specific immunity and provide insights into the functional evolution of antiviral effector GBP5.

Key Findings

GBP5 is the most differentially expressed gene upon type I interferon stimulation ofMyotis yumanensisprimary cells.

Bat GBP5 has evolved under strong episodic genomic and genetic diversification, including early stop codon leading to protein truncation and loss of prenylation motif.

GBP5 diversification in bats impacts their subcellular localization and antiviral functions.

Bat GBP5s exhibit species- and virus-specificity in their ability to inhibit infectivity of viral particles, bearing glycoproteins from retroviral HIV, vesicular stomatitis virus and European bat lyssavirus-1.

Resurrection of the ancestral prenylation motif in a bat GBP5 rescues its subcellular localization but not its full antiviral activity
Investigating Gene Expression Noise Reduction by MicroRNAs and MiRISC Reinforcement by Self-Feedback Regulation of mRNA Degradation
Authors: Tian Shuangmei , Zhao Ziyu , Kassie Meharie G. , Zhang Fangyuan , Ren Beibei , Wang Degeng
Published: February 2025

MicroRNA (miRNA) induced silencing complex (miRISC) is the targeting apparatus and arguably rate-limiting step of the miRNA-mediated regulatory subsystem – the major noise reducing though metabolically wasteful mechanism. Recently, we reported that miRISC channels miRNA-mediated regulatory activity back onto their own mRNAs to form negative self-feedback loops, a noise-reduction technique in engineering and synthetic/systems biology. Here, we describe mathematical modeling that predicts mRNA expression noise to correlate negatively with degradation rate (Kdeg) and noise reduction by self-feedback control of Kdeg. We also calculated Kdegand expression noise of mRNAs detected in a cutting-edge total-RNA single-cell RNA-seq (scRNA-seq) dataset. As predicted, miRNA-targeted mRNAs exhibited higher Kdegvalues in conjunction with lower inter-cell expression noise. Moreover, as predicted by our self-feedback loop model, miRISC mRNAs (AGO1/2/3 and TNRC6A/B/C) exhibited further reduced expression noise. In short, mathematical-modeling and total-RNA scRNA-seq data-analysis shed insight into operational trade-off between noise reduction and metabolic/energetic expenditure in producing miRNA-targeted mRNAs destined for enhanced degradation and translational inhibition, as well as negative self-feedback loop reinforcement of miRISC – the core of miRNA-mediated noise-reduction subsystem. To our knowledge, this is the first report of concurrent mRNA degradation and expression noise analyses and of noise reduction by self-feedback control of mRNA degradation.
CycleMix: Gaussian Mixture Modeling of the Cell Cycle
Authors: Peplinski Jack Edward , Andrews Tallulah
Published: February 2025

The cell cycle is a crucial component of many biological processes, including cancer, tissue repair, and inflammation. However, due to the heterogeneity of this cycle it has been difficult to assess the extent of proliferation in clinical tissues. Single-cell RNAseq (scRNAseq) and spatial transcriptomics enables high resolution measurement of gene expression enabling the classification of individual cells into their cycling state. The most widely used method for cell-cycle assignment is Seurat, however their approach is limited to classifying cells into only 3 states: G1, S, G2M and frequently incorrectly labels fully mature non-cycling cells (e.g. neurons) as S/G2M. Here we propose CycleMix, an alternative cell-cycle assignment algorithm that can flexibly assign cells into any number of states provided sufficient marker genes as well as being capable of identifying when cells are not cycling.
CyclicBoltz1, fast and accurately predicting structures of cyclic peptides and complexes containing non-canonical amino acids using AlphaFold 3 Framework
Authors: Xie Xuezhi , Li Christina Z , Lee Jin Sub , Kim Philip M
Published: February 2025

Cyclic peptides exhibit favourable properties making them promising candidates as therapeutics. While the design and modeling of peptides in general has seen rapid advances since the advent of modern machine learning methods, existing deep learning models cannot effectively predict cyclic peptide structures containing non-canonical amino acids (ncAAs), which are often crucial for peptide therapeutics. To address this limitation, we here extend the recent AF3-style model Boltz to cyclic peptides with ncAAs. In addition to the positional encoding offset, we used a simple yet effective extension of the cyclic offset encoding based on AlphaFold3’s tokenization scheme that allows the modeling of cyclic peptides with modified residues. On a test set of peptides with ncAAs, our approach outperforms HighFold2 on 13/17 cases, with an average CαRMSD of 1.877Å and an average all-atom RMSD of 3.361Å. Our results show that the cyclic offset encoding shown for AlphaFold2 generalizes to AlphaFold3-based models and can be extended to incorporate ncAAs, showing potential in the design of novel cyclic peptides with ncAAs for therapeutic applications.
p21-activated kinase regulates Rab3a vesicles to repair plasma membrane damage caused by Amyloid-β oligomers
Authors: Valappil Deepak Kunhi , Veerabhadraswamy Priyadarshini , Sarathi Shylaja Partha , Hegde Prakhyath , Gowda Jeevan M , Kumar Anujith , Gandasi Nikhil R , Nath Sangeeta
Published: February 2025

The interaction of amyloid-β (Aβ) peptides with the plasma membrane (PM) is a potential trigger that initiates the formation of higher-order aggregates, membrane alterations/damage, and progressive neurotoxicity in Alzheimer’s disease (AD). In a previous study, we showed that oligomers of Aβ1-42(oAβ1-42) induced PM damage, resulting in PM repair cascade via lysosomal exocytosis coupled with endocytosis, and facilitation of tunneling nanotubes (TNTs)-like membrane protrusions to promote direct cell-to-cell transfer of aggregates. In this study, we demonstrated that PM damage induced by oligomers of the aggregation-prone peptide Aβ1-42significantly facilitates PM repair by enhancing phosphorylated p21-activated kinase 1 (pPAK1)-dependent endocytosis and Rab3a-dependent exocytosis in SH-SY5Y and SK-N-SH neuronal cells compared to control and oAβ1-40treated cells. We studied the kinetics of pPAK1-dependent endocytosis and the fusion of EGFP-Rab3a vesicles near the PM using total internal reflection fluorescence (TIRF) microscopy. IPA-3, a selective non-ATP competitive inhibitor of PAK1, inhibits endocytosis of oAβ peptides and Rab3a-dependent PM repair. Further, shRNA-mediated knockdown of the Rab3a gene inhibits pPAK1 and disrupts PM repair. Repair of damaged PM is a vital protective mechanism for non-proliferative cells like neurons, as disruption in PM repair leads to gradual neuronal cell death. However, there was no explicit understanding of PM repair in response to Aβ oligomers. This study revealed the interconnected action of Rab3a and pPAK1 in PM repair in response to oAβ-mediated damage, and its potential correlation in AD pathogenesis.
A Novel TRPC6 Mutation Causes Autosomal Dominant FSGS
Authors: Bhattacharya Rohan , Mou Xingrui , Leeman Sophia M. , Mishra Alekshyander , Kalejaiye Titilola D. , Stangl Megan , Silas Daniel , Soldano Karen , Sperati C. John , Olabisi Opeyemi , Hall Gentzon , Musah Samira
Published: February 2025

FSGS is the most common primary glomerular lesion that causes kidney failure in the US. FSGS results from injury or loss of glomerular visceral epithelial cells (i.e. podocytes). Pathogenic variants inTRPC6can cause FSGS through dysregulated calcium conductance and associated disturbances in podocyte physiology. Here, we describe a 5-generation kindred with FSGS caused by a novel compound C-terminal TRPC6 mutation. Analysis of patient-specific iPSC-derived podocytes and glomerular capillary wall-on-a-chip systems revealed that the compound variants disrupt TRPC6 protein structure, intermolecular interactions, and membrane localization. Combined therapy with Sildenafil and Losartan ameliorated these disturbances compared to conventional immunosuppressive treatment.
Intermittent Fasting Reprograms Chromatin Accessibility to Modulate Gene Expression in Brain and Muscle
Authors: Fan Yibo , Peng Xiangyuan , Ebrahimi Mansour , Tabassum Nishat I. , Cheng Xiangru , Kumar Yatendra , Liu Yong U. , Chen Guobing , Okun Eitan , Johns Terrance G. , Sobey Christopher G. , Lai Mitchell K. P. , Gunaratne Jayantha , Mattson Mark P. , Jo Dong-Gyu , Arumugam Thiruma V.
Published: February 2025

Intermittent fasting (IF), a dietary regimen that mimics the natural feeding patterns observed across diverse organisms—from single-celled life to mammals—is thought to activate systemic survival responses and confer health benefits. However, the molecular mechanisms underlying these effects remain poorly understood. In this study, we utilized ATAC-Seq and RNA-Seq to investigate how IF influences chromatin accessibility and gene expression in brain and muscle tissues of mice, compared to ad libitum feeding. Our results reveal that IF induces significant changes in chromatin accessibility, modulating pathways related to metabolism, ribosome function, HIF-1 signaling, and glycolysis. Motif analysis identified tissue-specific transcription factors enriched in IF-regulated regions, including Sp1, Mef2a, NeuroD2, Banp, and NFIA in the brain, and SMAD4, TCF4, STAT5B, NKX3-1, and ZEB2 in muscle. Integrative analysis of ATAC-Seq and RNA-Seq data demonstrated that IF upregulates 50 genes and downregulates 15 in the cortex, while upregulating 31 genes and downregulating 10 in muscle. These gene expression changes are linked to pathways associated with neuroprotection and enhanced muscle function, offering mechanistic insights into the health benefits of IF. Our findings underscore the role of IF-induced chromatin remodeling in driving adaptive gene regulation.
SMCLMDA: statistical meta-paths contrastive learning for predicting miRNA-disease multidimensional relationships
Authors: Zhu Yangfeng , Fan Yongxian , Sun Guicong , Li Xueping
Published: February 2025

The accurate identification of miRNA-disease associations plays a crucial role in biomedical research and clinical applications. However, most research focuses on the existence of the association, without conducting further exploration. In this study, we propose a novel statistical meta-path contrastive learning-based approach (SMCLMDA), which aims to accurately identify the multidimensional relationships(up/down-regulation and causal/non-causal) between miRNAs and diseases. SMCLMDA first obtains the local structural information of miRNAs and diseases based on Node2Vec and uses it as the initial node input of the graph convolutional neural network (GCN). Then, the meta-path view constructed by the statistical method further enhances the representation of the similarity view via a contrastive learning strategy. Finally, SMCLMDA calculates the predicted probability of the multidimensional relationships of miRNA-disease via a multilayer perceptron(MLP). The experimental results demonstrate that SMCLMDA surpasses current state-of-the-art computational methods in predicting traditional associations, as well as up/down-regulation and causality/non-causality relationships. The case study additionally validates the effectiveness of SMCLMDA in identifying potential miRNA-disease associations.
A cellular solution to a robotics problem
Authors: Wang Zitong , Thomson Matt
Published: February 2025

Localizing and navigating toward a signal source in noisy environments remains a fundamental challenge in robotics. Similarly, cells in tissues must navigate noisy, fragmented molecular gradients, shaped by fluid flow and extracellular matrix interactions. We show that cells can perform source localization using a biophysical implementation of a computational algorithm called Bayes filtering, where the spatial distribution of molecules encodes a probability distribution over source location and intracellular transport processes update this distribution. Unlike conventional Bayes filtering, the cellular implementation can adjust the weight of past observations based on current environmental signals. When translated to traditional robotics algorithms, this signal-aware learning rate significantly improves navigation performance in high-noise conditions, revealing how biological mechanisms can advance engineered systems.
Immune response to co-administration of bovine tuberculosis and contraceptive vaccines in badgers (Meles meles)
Authors: Palphramand Kate L. , Anderson Paul , Bellamy Fiona , Birch Colin , Davé Dipesh , Eckery Doug , Gomm Matt , Jinks Rachel , Massei Giovanna , Pinkham Rebecca , Rahou Sabah , Simmons Hugh , Vial Flavie , Williams Gareth A. , Smith Graham C.
Published: February 2025

Controlling bovine tuberculosis (bTB) in livestock is often hindered by the presence of a wildlife reservoir, such as the Eurasian badger in the UK and Ireland. Vaccinating badgers against bTB can reduce the severity ofMycobacterium bovisinfection and potential onwards transmission to cattle, badgers and other species, thus combined with population control might provide additional benefits (and reference models). To evaluate the effects of co-administration of a bTB vaccine (BCG) and a contraceptive vaccine (GonaCon), captive badgers were injected intramuscularly with either BCG only, GonaCon only or BCG+GonaCon (phase 1). The duration of immune response to BCG vaccination and booster vaccination was also evaluated in the BCG only group over a 24-month period (phase 2). The cellular immune responses to purified protein derivatives PPDA and PPDB, used to measure the effects of BCG, did not differ significantly between the BCG only and BCG+GonaCon badgers but were significantly different between the BCG only and GonaCon only badgers. Anti-GnRH antibody titres, quantified to measure the effect of GonaCon, peaked at the first sampling point for the majority of badgers in the GonaCon only and BCG+GonaCon groups. Throughout phase 1, lasting three months post-vaccination, badgers in both GonaCon treatment groups maintained high anti-GnRH antibody titres (1:128,000 or above) that are associated with infertility in this species, with no significant difference between the two GonaCon groups. The immune responses to BCG vaccination in the BCG only badgers (phase 2) were elevated at the first sampling point, approximately three weeks after initial vaccination and booster vaccination, generally declining thereafter. The results from the current study suggest that co-administration of BCG and GonaCon do not have notable deleterious effects on either of the vaccines and that the protective effect of BCG is enhanced by booster vaccination. The protective effects afforded by both vaccines when given together, in terms of reduced disease burden or fecundity, should be determined by further studies.
Over half of the phylogenetic diversity accumulated on the African plant tree of life may be eroded under current biodiversity crisis even though threatened species are not evolutionarily unique
Authors: Tiawoun Makuete A.P. , Phogole Bopaki , Kandolo Bahati Samuel , Yessoufou Kowiyou
Published: February 2025

Although Africa contributes tremendously to global biodiversity, we have a poor understanding of how the African tree of life might be pruned owing to the ongoing biodiversity crisis. Here, we investigated this question integrating statistics and phylogenetics of ∼24000 African vascular plants. We found that 54% of African plant families are hot nodes of threatened species, thus heightening the risk of losing entire clades. We also found that, if all threatened species go extinction, 59% of the evolutionary history of the African plant tree of life would be eroded, and this loss is more than expected at random, although threatened species are not evolutionarily unique. Unfortunately, ∼72% of threatened species and ∼79% of the top-1000-EDGE species are not found in any form of protected areas. Overall, our analysis reveals the extent of biodiversity crisis in Africa and the need for steadfast commitments to i) increased data collection efforts particularly in central African regions and ii) implementation of existing policy for an accelerated recovery.
Cholesterol depletion activates trafficking-coupled sphingolipid synthesis
Authors: Kim Yeongho , Parolek Jan , Burd Christopher G.
Published: February 2025

Within cellular membranes, sphingomyelin is associated with cholesterol and this complex facilitates homeostatic regulation of membrane viscosity. Acute cholesterol depletion increases the synthesis of very-long-chain (VLC) sphingomyelin, but a link between lipid sensing and sphingolipid synthesis is lacking. Using sphingolipid metabolic flux analysis, we observed that VLC-ceramide, the precursor to VLC complex sphingolipids that are produced in the Golgi apparatus, was rapidly consumed after cholesterol depletion, while synthesis of long-chain sphingolipids was unaffected. Sphingolipid trafficking assays showed that cholesterol depletion enhances VLC-Ceramide trafficking from the endoplasmic reticulum to the Golgi apparatus. Changes in the sizes of coatomer II ER exit sites were correlated with increased VLC-Ceramide trafficking and concomitant increase in sphingomyelin. Depletion of Sec16A, a component of the COPII network, abolished VLC-SM synthesis. This study reveals ER-to-Golgi trafficking of VLC-Ceramide as a key regulatory node in organelle membrane homeostasis pathways.

In cellular membranes, sphingomyelin is associated with cholesterol. Metabolic flux analysis of sphingolipid metabolism showed that synthesis rate of sphingomyelin, but not ceramide, was increased after depletion of cholesterol due increased rate of COPII-dependent ER-to-Golgi transport of ceramide.
A functional map of phosphoprotein phosphatase regulation identifies an evolutionary conserved reductase for the catalytic metal ions
Authors: Meeusen Bob , Ambjørn Sara M. , Veis Jiri , Riley Rachel C. , Vit Gianmatteo , Brauer Brooke L. , Møller Mads H. , Greiner Elora C. , Chan Camilla B. , Weisser Melanie B. , Garvanska Dimitriya H. , Zhu Hao , Davey Norman E. , Kettenbach Arminja N. , Ogris Egon , Nilsson Jakob
Published: February 2025

Serine/Threonine phosphoprotein phosphatases (PPPs, PP1-PP7) are conserved metalloenzymes and central to intracellular signaling in eukaryotes, but the details of their regulation is poorly understood. To address this, we performed genome-wide CRISPR knockout and focused base editor screens in PPP perturbed conditions to establish a high-resolution functional map of PPP regulation that pinpoints novel regulatory mechanisms. Through this, we identify the orphan reductase CYB5R4 as an evolutionarily conserved activator of PP4 and PP6, but not the closely related PP2A. Heme binding is essential for CYB5R4 function and mechanistically involves the reduction of the metal ions in the active site. Importantly, CYB5R4-mediated activation of PP4 is critical for cell viability when cells are treated with DNA damage-inducing agents known to cause oxidative stress. The discovery of a dedicated PPP reductase points to shared regulatory principles with protein tyrosine phosphatases, where specific enzymes dictate activity by regulating the active site redox state. In sum, our work provides a resource for understanding PPP function and the regulation of intracellular signaling.
Epsin1 enforces a condensation-dependent checkpoint for ubiquitylated cargo during clathrin-mediated endocytosis
Authors: Sarkar Susovan , Liu Hao-Yang , Yuan Feng , Malady Brandon T. , Wang Liping , Perez Jessica , Lafer Eileen M. , Huibregtse Jon M. , Stachowiak Jeanne C.
Published: February 2025

Clathrin-mediated endocytosis internalizes proteins and lipids from the cell surface, supporting nutrient uptake, signaling, and membrane trafficking. Recent work has demonstrated that a flexible, liquid-like network of initiator proteins is responsible for catalyzing assembly of clathrin-coated vesicles in diverse organisms including yeast, mammals, and plants. How do cells regulate the assembly of this dynamic network to produce cargo-loaded vesicles? Here we reveal the ability of an endocytic adaptor protein, Epsin1, to conditionally stabilize the initiator protein network, creating a cargo-dependent checkpoint during clathrin-mediated endocytosis. Epsin1 is known to recruit ubiquitylated transmembrane proteins to endocytic sites. Usingin vitroassays, we demonstrate that Epsin1 uses competitive binding and steric repulsion to destabilize condensation of initiator proteins in the absence of ubiquitin. However, when polyubiquitin is present, Epsin1 binds to both ubiquitin and initiator proteins, creating attractive interactions that stabilize condensation. Similarly, in mammalian cells, endocytic dynamics and ligand uptake are disrupted by removal of either ubiquitin or Epsin1. Surprisingly, when Epsin1 and ubiquitin are removed simultaneously, endocytic defects are rescued to near wildtype levels, although endocytic sites lose the ability to distinguish between ubiquitylated and non-ubiquitylated cargos. Taken together, these results suggest that Epsin1 tunes protein condensation to ensure the presence of ubiquitylated cargo during assembly of clathrin-coated vesicles. More broadly, these findings illustrate how a balance of attractive and repulsive molecular interactions controls the stability of liquid-like protein networks, providing dynamic control over key cellular events.
Polo-like kinase 1 maintains transcription and chromosomal accessibility during mitosis
Authors: Shen Zhouyuan , Adams Kristin , Moreno Ryan , Lera Robert , Kaufman Emily , Lang Jessica D. , Burkard Mark
Published: February 2025

Transcription persists at low levels in mitotic cells and plays essential roles in mitotic fidelity and chromosomal dynamics. However, the detailed regulatory network of mitotic transcription remains largely unresolved. Here, we report the novel role of Polo-like kinase 1 (Plk1) in maintaining mitotic transcription. Using 5-ethynyl uridine (5-EU) labeling of nascent RNAs, we found that Plk1 inhibition leads to significant downregulation of nascent transcription in prometaphase cells. Chromatin-localized Plk1 activity is required for transcription regulation and mitotic fidelity. Plk1 sustains global chromosomal accessibility in mitosis, especially at promoter and transcription start site (promoter-TSS) regions, facilitating transcription factor binding and ensuring proper transcriptional activity. We identified SMC4, a common subunit of condensin I and II, as a potential Plk1 substrate. Plk1 activity is fundamental to these processes across non-transformed and transformed cell lines, underscoring its critical role in cell cycle regulation. This study elucidates a novel regulatory mechanism of global mitotic transcription, advancing our understanding of cell cycle control.

Significance Statement

Cells retain a low level of transcription during mitosis, while the regulatory network and specific contributions of mitotic transcription are not well understood.

We identify Polo-like kinase 1 (Plk1) as a novel regulator of mitotic transcription, crucial for chromosome condensation, genome accessibility, and maintaining mitotic fidelity.

This study enhances our understanding of Plk1’s multifaceted role in mitotic progression, advancing cell cycle regulation knowledge, and informing new cancer therapies’ development.