bluuebunny/crossref_metadata_2025_split huggingface dataset:
Life history evolution of insects in response to climate variation: seasonal timing versus thermal physiology
Authors: Gotthard Karl , Berger David , Rohner Patrick 
Published: February 2025

AbstractClimate adaptation in insects can proceed via responses in life history traits and their thermal plasticity, and through phenological shifts mediated by responses to photoperiodic cues (“photoperiodism”). While, experimental studies demonstrate evolutionary potential for both modes of adaptation, it remains unclear how evolution will unfold in natural populations, limiting our ability to predict how insects will respond to climate change. Here we review the literature and perform an analysis of published studies revealing that photoperiodism for diapause induction evolves predictably along latitude, with high-latitude populations entering diapause earlier. In contrast, although a few species showed clinal variation in life history and thermal plasticity, the direction of these clines were not consistent across taxa. This suggests that while life history traits sometime evolve rapidly, photoperiodism is a more predictable response to climate, and thus, climate adaptation is more likely to proceed via phenological shifts than physiological adaptations to changing temperatures.
The Cause of Most Common Antler Abnormality is Not a Fracture But an Osteomyelitis Like Disease the Pedunculitis Chronica Deformans
Authors: Sukosd Farkas , Lakatos Istvan , Urmos Adam , Babarczi Bianka , Skoda Gabriella , Molnar Zsofia , Pankotai Tibor , Borsos Barbara N , Karkas Reka , Sukosd Akos , Palanki Gabor , Dobrosy Szabolcs , Toth Attila Arany , Erdelyi Karoly , Horvath Gyozo , Horvath Adrienn , Toth Daniel , Maurer Mate , Miso Mihaly , Plank Patrik , Czeh Arpad , Nagyeri Gyorgy , Ferenczi Szilamer , Gobolos Peter , Kemenesi Gabor , Posta Katalin , Kovacs Ferenc , Mezes Miklos , Szemethy Laszlo , Szoke Zsuzsanna 
Published: February 2025

AbstractClimate change is increasing the incidence of certain diseases in wildlife, offering a deeper understanding of their underlying causes. Traditionally, the most common antler abnormalities have been attributed to trauma, based on their morphology. However, this explanation does not account for the epidemic-like spread of abnormalities in specific regions, suggesting that they might be a previously undescribed aspect of this anomaly. In fallow deer (Dama dama), using advanced medical diagnostic tools, we identified an osteomyelitis-like condition, Pedunculitis Chronica Deformans (PCD) which is also observed in otherCervidae. The incidence of this disease shows a strong correlation with the production of mycotoxins by molds that are becoming more prevalent with global warming. Mycotoxins can inhibit wound healing through scar formation after the antlers are cast, leading to the development of PCD. In this report we characterize PCD pathomorphology and introduce a scoring system to differentiate it from other deformities. Moreover, we argue that the most common anomalies such as fractures, antler losses, fatal meningoencephalitis and brain abscesses are complications of PCD. Our research underscores the potential of antlers to serve as biomarkers for mycotoxin exposure.
PARP inhibitors elicit distinct transcriptional programs in homologous recombination competent castration-resistant prostate cancer
Authors: Cunningham Moriah L. , Vasquez-Gonzalez Jasibel , Barnada Samantha , Tchotorlishvili Salome , Jones Latese , Shankle Hailey , Mulders Tessa , Ajmal Namra , Solomides Charalambos , Shafi Ayesha A. , Gomella Leonard G. , Kelly Wm Kevin , McMahon Steven B. , Schiewer Matthew J. 
Published: February 2025

AbstractProstate cancer (PCa) is the second most lethal cancer in men in the United States. African American (AA) men have twice the incidence and death rate from the disease than European American (EA) men. Early-stage PCa is treated with hormone deprivation therapy, although patients frequently experience relapse. Advanced stage PCa is associated with increased expression and activity of the DNA damage/repair pathway enzyme, poly (ADP-ribose) polymerase 1 (PARP1). Furthermore, PARP1 inhibitors are FDA-approved for the treatment of advanced PCa tumors that carry mutations in components of a specific DNA damage/repair pathway termed homologous recombination repair (HRR). However, PARPi also provide benefit in model systems without HRR incompetencies.A number of different PARPi have now been developed, tested and approved for use in PCa. These inhibitors utilize multiple biochemical mechanisms of action and exhibit distinct potencies and toxicity profiles. While there is emerging evidence of differences in DNA damage/repair pathway enzyme expression between EA and AA men, PARP1 itself has not been fully explored in the context of race.This study hypothesized that 1) AA and EA PCa may respond differently to PARPi and 2) different PARPi may differentially impact the transcriptome, irrespective of HRR status.To test these hypotheses, PCa patient samples from a racially diverse cohort were examined to define race-based differences in PARP activity/expression. Additionally, biologically relevant doses of five clinically relevant PARPi were established across multiple PCa lines carrying different genetic backgrounds, HRR status, and hormone therapy sensitivities. Collectively, these findings demonstrate a link between racial background and PARP1 expression/activity and define a core transcriptional response that lies downstream of all five PARPi, while simultaneously defining transcriptional programs unique to each inhibitor. These findings broaden our understanding of the effector pathways downstream of individual PARPi and provide a compelling rationale for a broader exploration of the impact of race on the response to PARPi. They may also help refine personalized recommendations for use of specific PARPi.
Actin Painting: a multicolor fluorescence staining method highlighting cell type-specific differences in the composition of filamentous actin architectures
Authors: Nagasaki Akira , Kijima Saku T. , Shinkai Yoichi , Ohtsuka Yukio , Ochiishi Tomoyo , Sasaki Yasnory T.F. , Hata Saori , Hirano Kazumi , Kato Yoshio , Doi Motomichi , Uyeda Taro Q.P. 
Published: February 2025

AbstractActin is a major structural component of the cytoskeleton in eukaryotic cells, and filamentous actin (F-actin) forms a variety of types of cellular structures. Many actin probes have been developed to visualize F-actin architectures in eukaryotic cells. However, it is known that double-stained images of F-actin obtained by two different types of actin probes often show partial inconsistencies. While developing actin probes, we observed that the merged images of three distinct actin probes, each labeled with a different fluorescent dye (red, green and blue), enabled various F-actin architectures to be distinguished based on color. This differentiation arises from slight variations in the distribution of each actin probe, and results in a unique color combination of actin probes that reflects the relative intensities of the three fluorescent dyes. In this report, we introduce a new cell staining method, named Actin Painting, which exploits the unique affinity of actin-binding molecules in each actin probe to F-actin architectures. This technique allows the classification of various cell types based on their specific actin cytoskeleton.
Functional diversity of soil microbial communities increases with ecosystem development
Authors: Ranheim Sveen Tord , Viketoft Maria , Bengtsson Jan , Lejoly Justine , Buegger Franz , Pritsch Karin , Strengbom Joachim , Fritscher Joachim , Hildebrand Falk , Osburn Ernest , Hannula Emilia , Bahram Mo 
Published: February 2025

ABSTRACTLand abandonment is the single largest process of land-use change in the Global North driving succession and afforestation at continental scales, but assessing its impacts on soil microbial communities remains a challenge. Here, we established a nationwide successional gradient of paired grassland and forest sites to track developments in microbial structure and functioning following land abandonment and gradually changing plant communities. We show that microbes generally respond through threshold dynamics, leading to increasing functional but decreasing taxonomic diversity. Succession also increased the specialization of microbial nutrient (C-N-P) cycling genes while decreasing genetic redundancy, highlighting a putative trade-off between two desirable ecosystem properties: functional diversity and functional redundancy. Increasing fungal functional diversity underpinned higher microbial C-cycling capacity, underscoring the causal link between functional traits and ecosystem processes. Changing litter quality similarly provided a mechanistic link between plant and microbial communities despite otherwise largely decoupled successional developments. Land abandonment is frequently touted as an opportunity to increase biodiversity and carbon storage. Our results show that deeper knowledge about the multifaceted development of soil microbial communities and its links to plant communities during succession may be needed to fully grasp the impacts of global land abandonment processes.
Fast and Accuratein silicoAntigen Typing with Kaptive 3
Authors: Stanton Thomas D. , Hetland Marit A.K. , Löhr Iren H. , Holt Kathryn E. , Wyres Kelly L. 
Published: February 2025

AbstractSurface polysaccharides are common antigens in priority pathogens and therefore attractive targets for novel control strategies such as vaccines, monoclonal antibody and phage therapies. Distinct serotypes correspond to diverse polysaccharide structures that are encoded by distinct biosynthesis gene clusters, e.g. theKlebsiella pneumoniaespecies complex (KpSC) K- and O-loci encode the synthesis machinery for the capsule (K) and outer-lipopolysaccharides (O), respectively. We previously presented Kaptive and Kaptive 2, programs to identify K and O-loci directly from KpSC genome assemblies (later adapted forAcinetobacter baumannii), enabling sero-epidemiological analyses to guide vaccine and phage therapy development. However, for some KpSC genome collections, Kaptive (v≤2) was unable to type a high proportion of K-loci. Here we identify the cause of this issue as assembly fragmentation, and present a new version of Kaptive (v3) to circumvent this problem, reduce processing times and simplify output interpretation.We compared the performance of Kaptive v2 and Kaptive v3 for typing genome assemblies generated from subsampled Illumina read sets (decrements of 10x depth), for which a corresponding high quality completed genome was also available to determine the ‘true’ loci (n=549 KpSC, n=198A. baumannii). Both versions of Kaptive showed high rates of agreement to the matched true locus among ‘typeable’ locus calls (≥96% for ≥20x read depth), but Kaptive v3 was more sensitive, particularly for low depth assemblies (at <40x depth, v3 ranged 0.85-1 vs v2 0.09-0.94) and/or typing KpSC K-loci (e.g. 0.97 vs 0.82 for non-subsampled assemblies). Overall, Kaptive v3 was also associated with a higher rate of optimal outcomes i.e. loci matching those in the reference database were correctly typed and genuine novel loci were reported as untypeable (73-98% for v3 vs 7-77% for v2 for KpSC K-loci).Kaptive v3 was >1 order of magnitude faster than Kaptive v2 making it easy to analyse thousands of assemblies on a desktop computer, facilitating broadly accessible in silico serotyping that is both accurate and sensitive. The Kaptive v3 source code is freely available on GitHub (https://github.com/klebgenomics/Kaptive), and has been implemented in Kaptive Web (https://kaptive-web.erc.monash.edu).
The ABCG1 transporter facilitates sesquiterpene accumulation inMarchantia polymorphaoil bodies
Authors: Forestier Edith C. F. , Asprilla Paola , Romani Facundo , Bonter Ignacy , Frangedakis Eftychios , Haseloff Jim 
Published: February 2025

ABSTRACTMarchantia polymorphaoil bodies (OBs) are specialised cell structures housing a diverse array of C15-terpenes, called sesquiterpenes. These compounds are known for their roles as herbivore repellents, yet the enzymes responsible for the biosynthesis of their precursors (C5 isoprenoid units) remain poorly characterized. Discrepancies remain between enzyme localizations suggested by computational predictions and those observed in earlier experimental studies, complicating our understanding of terpene biosynthesis. We investigated the localization of isoprenoid biosynthetic enzymes using translational and transcriptional reporters, coupled with confocal microscopy. Most enzymes localized as predicted (e.g., cytosol, chloroplast and the endoplasmic reticulum), and OB cells were identified as the primary sites of terpene biosynthesis.To explore OBs as potential storage sites for terpenes, we attempted to produce exogenous but easily identifiable compounds inMarchantia, such as the diterpene taxadiene and the triterpene β-amyrin. Targeting to OB cells resulted in measurable amounts of these compounds, but their yields remained unaffected by the over-expression of key precursor genes, underscoring challenges in redirecting metabolic flux.To further investigate terpene accumulation in OBs, we focused on ABCG1, an ABC transporter previously reported to localize at the OB membrane. Overexpression of ABCG1 in OB cells, alongside an exogenous sesquiterpene synthase, only increased the levels of endogenous sesquiterpenes, while CRISPR-mediated disruption of ABCG1 resulted in a dramatic reduction in sesquiterpene accumulation. These findings establish ABCG1 as a critical factor for sesquiterpene retention within OBs and provide new insights into the mechanisms governing terpene metabolism and storage inMarchantia polymorpha.
MethylProphet: A Generalized Gene-Contextual Model for Inferring Whole-Genome DNA Methylation Landscape
Authors: Huang Xiaoke , Liu Qi , Zhao Yifei , Tang Xianfeng , Zhou Yuyin , Hou Wenpin 
Published: February 2025

AbstractDNA methylation (DNAm), an epigenetic modification, regulates gene expression, influences phenotypes, and encodes inheritable information, making it critical for disease diagnosis, treatment, and prevention. While human genome contains approximately28 millionCpG sites where DNAm can be measured, only 1–3% of these sites are typically available in most datasets due to complex experimental protocols and high costs, hindering insights from DNAm data. Leveraging the relationship between gene expression and DNAm offers promise for computational inference, but existing statistical, machine learning, and masking-based generative Transformers face critical limitations: they cannot infer DNAm at unmeasured CpGs or in new samples effectively. To overcome these challenges, we introduce MethylProphet, a gene-guided, context-aware Transformer model designed for DNAm inference. MethylProphet employs a Bottleneck MLP for efficient gene profile compression and a specialized DNA sequence tokenizer, integrating global gene expression patterns with local CpG context through a Transformer encoder architecture. Trained on whole-genome bisulfite sequencing data from ENCODE (1.6B training CpG-sample pairs; 322B tokens), MethylProphet demonstrates strong performance in hold-out evaluations, effectively inferring DNAm for unmeasured CpGs and new samples. In addition, its application to 10842 pairs of gene expression and DNAm samples at TCGA chromosome 1 (450M training CpGsample pairs; 91B tokens) highlights its potential to facilitate pan-cancer DNAm landscape inference, offering a powerful tool for advancing epigenetic research and precision medicine. All codes, data, protocols, and models are publicly available viahttps://github.com/xk-huang/methylprophet/.
Rumenomics: Evaluation of rumen metabolites from healthy sheep identifies differentially produced metabolites across sex, age, and weight
Authors: Munoz Briones Javier , Ball Brendan K. , Jena Smrutiti , Lescun Timothy B. , Chan Deva D. , Brubaker Douglas K. 
Published: February 2025

ABSTRACTBackgroundThe rumen harbors a diverse and dynamic microbiome vital in digesting vegetation into metabolic byproducts for energy and general biological function. Although previous studies have reported connections between the rumen and the overall health of the sheep, the exact biological process by which this occurs is not well understood. Therefore, our study aimed to quantify sheep rumen metabolites to determine if enriched biological pathways are differentiable across phenotypic features of sex, age, and weight.ResultsWe collected and quantified metabolites of rumen samples from sixteen sheep using liquid chromatography-tandem mass spectrometry. We performed a series of univariate and multivariate statistical analyses to interpret the rumen metabolomics data. To identify metabolic pathways associated with the phenotypic features of sex, weight, and age, we used MetaboAnalyst, which identified amino acid metabolism as a distinguishing factor. Among the pathways, phenylalanine metabolism emerged as a key pathway differentiating sheep based on sex and age. Additionally, phenylalanine, tyrosine, and tryptophan biosynthesis were exclusively associated with age. In univariate linear models, we also discovered that these amino acid and protein pathways were associated with weight by age-corrected effect. Finally, we identified arginine and proline biosynthesis as a pathway linked to metabolites with weight.ConclusionOur study identified differential pathways based on the sex, age, and weight features of sheep. Metabolites produced by the rumen may act as an indicator for sheep health and other ruminants. These findings encourage further investigation of the differentially produced metabolites to assess overall sheep health.
Swimming motions evoke Ca2+events in vascular endothelial cells of larval zebrafish via mechanical activation of Piezo1
Authors: Jia Bill Z. , Tang Xin , Rossmann Marlies P. , Zon Leonard I. , Engert Florian , Cohen Adam E. 
Published: February 2025

SummaryCalcium signaling in blood vessels regulates their growth1,2, immune response3, and vascular tone4. Vascular endothelial cells are known to be mechanosensitive5–7, and it has been assumed that this mechanosensation mediates calcium responses to pulsatile blood flow8–10. Here we show that in larval zebrafish, the dominant trigger for vascular endothelial Ca2+events comes from body motion, not heartbeat-driven blood flow. Through a series of pharmacological and mechanical perturbations, we showed that body motion is necessary and sufficient to induce endothelial Ca2+events, while neither neural activity nor blood circulation is either necessary or sufficient. Knockout and temporally restricted knockdown ofpiezo1eliminated the motion-induced Ca2+events. Our results demonstrate that swimming-induced tissue motion is an important driver of endothelial Ca2+dynamics in larval zebrafish.HighlightsSwimming motions in larval zebrafish evoke large, rapid, and pervasive Ca2+transients in vascular endothelial cells.These Ca2+transients do not require neural firing, muscular electrical activity, endocrine factors, or heart-driven blood flow.Mechanical forces are necessary and sufficient for endothelial Ca2+transients.Endothelial Ca2+transients require the mechanosensitive ion channel Piezo1.
The Translation Termination Factor eRF3 Interacts Sequentially with eRF1 and ABCE1 on the Ribosome
Authors: Wada Miki , Ito Koichi 
Published: February 2025

AbstractTo elucidate the molecular mechanisms connecting translation termination and ribosome recycling, interactions among eRF1, eRF3, and ABCE1, were genetically investigated inSaccharomyces cerevisiae. Heterologous factors fromPneumocystis cariniiand humans, along with their mutants were successfully used for co-functional studies in conditional double knockout, double tetOFF strains. Combination ofP. cariniieRF3 mutants withS. cerevisiaeeRF1 and ABCE1 revealed that all the eRF3 mutants co-functioned with eRF1, but exhibited varying interactions with ABCE1 depending on the mutants. These findings provide evidence that eRF3 remains bound to the GTPase center of the ribosome, awaiting ABCE1. Thus, eRF3 sequentially interacts with eRF1 and ABCE1 during the final steps of translation.
Integration of climate change and health components in medical education worldwide- a scoping review
Authors: Maisoon Basima , Narayanan Prakash , Shetty Ranjitha S 
Published: February 2025

AbstractThere is growing recognition of the health impacts of climate change, prompting numerous calls and proposals in recent years for its inclusion in medical curricula. A scoping review was conducted according to JBI methodology to map and assess the integration of climate change and health content in undergraduate medical education globally and to identify existing curricula, educational strategies, and thematic coverage. Three scientific databases were searched for studies and articles that had instances of climate change integration in undergraduate medical curricula. The screening was done in stages following the PRISMA-ScR process, and there were 24 final inclusions. Data extracted include course type, duration, content, year of implementation, motive, challenges, enablers and recommendations. The review synthesized evidence from schools in North America, Europe, and Australia. There was a lack of studies from Low- and Middle-Income Countries (LMICs). The earliest instance of integration of climate change and health education was found to be in 2018, most schools started between 2020 and 2021. Common methods included stand-alone modules, electives, workshops, and modifying existing core curricula to include climate change and health components. Student-led initiatives significantly drove efforts in some schools. Courses emphasized climate change fundamentals, health impacts, vulnerabilities, communication and advocacy, interdisciplinary perspectives, and some practical applications. Challenges included integrating new content into existing curricula, requiring strategic planning and support. Recommendations include core curricular integration, experiential and practical learning, and encouraging research and advocacy.
A comprehensive phenome wide analysis of the role of neutrophils in health and disease
Authors: Fleming K , Cornish N , Vincent EE , Mumford AD , Amulic B , Burley K 
Published: February 2025

ABSTRACTNeutrophil release of cytoplasmic granules containing antimicrobial agents is a critical component of innate immunity. Neutrophils are widely implicated in other disease responses yet the overall extent of the neutrophil contribution to human health and disease is incompletely characterized. To explore this further, we leveraged publicly available genetic data to conduct a Mendelian randomization phenome-wide association study (MR-PheWAS) of neutrophil traits and 14,983 outcomes.Genetic proxies for neutrophil count, granularity, and serum myeloperoxidase were linked to 146 outcomes. Higher neutrophil count was associated with lower body weight, reduced obesity risk, and increased vascular activation markers but not with atherosclerosis. Elevated neutrophil count was robustly linked to Alzheimer’s disease and neutrophil granularity with gut microbiota abundance and dental pathology.Our findings reveal the diverse roles of neutrophils extending beyond pathogen defense and underscore the potential for MR-PheWAS in identifying novel neutrophil-related pathophysiology.Summary sentenceNeutrophils, essential for immunity, also influence other aspects of health, as shown in our MR-PheWAS study linking genetic proxies for neutrophil traits to 146 outcomes, including obesity, Alzheimer’s disease, endothelial activation markers and gut microbiota.VISUAL ABSTRACT