bluuebunny/crossref_metadata_2025 huggingface dataset:
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

Background

The 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.

Results

We 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.

Conclusion

Our 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

Calcium 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.

Highlights

Swimming 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

To 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

There 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

Neutrophil 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 sentence

Neutrophils, 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
Multi-organ and Multi-omics Aging Clocks Digitize Human Biological Age
Authors: Wen Junhao
Published: February 2025

Multi-organ biological aging clocks derived from clinical phenotypes and neuroimaging have emerged as valuable tools for studying human aging and disease1,2,3,4. Plasma proteomics provides an additional molecular dimension to enrich these clocks5. Building on previous work1,3, I developed 11 multi-organ proteome-based biological age gaps (ProtBAGs) using 2448 plasma proteins from 43,498 participants in the UK Biobank. I highlighted key methodological and clinical considerations for developing and using ProtBAG, including age bias correction6, and investigated the impact of training data sample size, protein organ specificity, and the underlying pathologies of the training data on model generalizability and clinical interpretability. I then integrated the 11 ProtBAGs with our previously developed 9 multi-organ phenotype-based biological age gaps (PhenoBAG1) to investigate their genetic underpinnings, causal associations with 525 disease endpoints (DE) from FinnGen and PGC, and their clinical potential in predicting 14 disease categories and mortality. Genetic analyses revealed overlap between ProtBAGs and PhenoBAGs via shared loci, genetic correlations, and colocalization signals. A three-layer causal network linked ProtBAG, PhenoBAG, and DE, exemplified by the pathway of obesity→renal PhenoBAG→renal ProtBAG to holistically understand human aging and disease. Combining features across multiple organs improved predictions for disease categories and mortality. These findings provide a framework for integrating multi-organ and multi-omics biological aging clocks in biomedicine. All results are publicly disseminated athttps://labs-laboratory.com/medicine/.
Exploring the 'Visible Versus Invisible' Paradigm in Cavernous Sinus Dural Arteriovenous Fistula
Authors: Zheng Jingwei , Su Shixing , Lu Hua , Liu Sheng , Zhou Shengjun , Jia Qi , Bao Xiang , Li Zhenqiang , Zhou Haihang , Zhang Guoqiang , Jiang Zhijie , Liu Fei , Hu Si , Wang Zixin , yu jun , liang xu
Published: February 2025

Abstract Background: Cavernous sinus dural arteriovenous fistulas (CS-DAVFs) present significant treatment challenges when the inferior petrosal sinus (IPS) is not opacified during cerebral angiography. However, the widely accepted transvenous IPS recanalization approach is associated with a high failure rate. The consistently visible superior ophthalmic vein (SOV) offers a promising alternative, though it has yet to be fully evaluated in large-scale studies. Methods: This retrospective, case-control study was conducted between May 2017 and October 2024. Data collection for this multicenter, population-based study took place across eight tertiary referral centers. Eligible patients were diagnosed with CS-DAVF with occluded IPS. Endovascular treatment via the transvenous SOV approach versus the IPS recanalization approach in patients with occluded IPS. Results: Of 178 eligible cases, 70 cases (39.3%) were treated using the transvenous SOV approach, while 108 cases (60.7%) underwent the transvenous IPS approach. The initial treatment success rate was significantly higher in the SOV group compared to the IPS group (91.4% vs. 75.9%; odds ratio [OR], 3.38; 95% CI, 1.30-8.35; P = 0.0092). The overall complication rate was 1.4% in the SOV group and 2.8% in the IPS group (OR, 0.51; 95% CI, 0.04-3.47; P > 0.9999). After classifying the SOV approach into simple and complex types, the SOV-simple type further demonstrated significant advantages, including shorter average operation times (126.20 ± 46.99 minutes, P = 0.0197) and a higher initial treatment success rate (95.7%, P = 0.0027) compared to the IPS group. Conclusion: The SOV approach should be considered a first-line treatment for CS-DAVF patients with invisible IPS. These findings establish a new treatment standard, underscoring the importance of precise preoperative classification and individualized surgical planning.
Changing Physician Performance: A Systematic Review and Meta-Analysis (75 years 1950-2024) of the Effect of Continuing Medical Education Strategies, Continuous Professional Development and knowledge Translation
Authors: Abbasi Ebrahim
Published: February 2025

Introduction

Medical education has always been considered an essential component for improving the knowledg and performance of physicians and medical assistants. However, this education must be carried out continuously t update the knowledge of physicians and improve their performance. Various strategies are used to achieve this goal, the most important of which are CME, CPD, and CBME strategies. This study aimed to investigate the effect of using these strategies on improving the performance of physicians in the world using a systematic review method.

Methods

This study was conducted using a systematic review method on the effect of educational strategies o improving the performance of physicians in the world. Accordingly, all relevant articles published between 195 and 2024 were extracted and reviewed through a search in the scientific databases PubMed/Medline, Web of Science, ProQuest, and Scopus. The quality of the articles was assessed using the CONSORT checklist an Newcastle-Ottawa Scale.

Results

twenty articles conducted between 1993 and 2024 were included in the systematic review process. According to the findings, providing continuing education based on CME, CPD, CBME, and knowledge translatio strategies positively affected the knowledge, skills, and performance of physicians and medical assistants i providing health services. This can be used to train medical students and practicing physicians on an ongoing basis.

Conclusion

Medical education using CME, CPD, and CBME strategies can improve physicians’ knowledge and performance, and subsequently increase job satisfaction, self-efficacy, communication skills, medical knowledge, performance, and skill. However, individual, structural, and content limitations that can prevent success in learnin and training programs should be considered and addressed.
Formation of amyloid-like HTTex1 aggregates in neurons, downregulation of synaptic proteins and early mortality of Huntington’s disease flies are causally linked
Authors: Ast Anne , Roth Leonard , Brusendorf Lydia , Schindler Franziska , Ammar Orchid Wael Mostapha , Berberich Simon , Edel Juliane , Bonsor Megan , Georgii Elisabeth , Hänig Christian , Langnick Claudia , Ivanov Andranik , Beule Dieter , Piraud Marie , Kunz Severine , Popp Oliver , Mertins Philipp , Petzoldt Astrid G. , Wanker Erich E.
Published: February 2025

Amyloidogenic mutant huntingtin exon-1 (mHTTex1) protein aggregates with pathogenic polyglutamine (polyQ) tracts are the potential root cause of Huntington’s disease (HD). Here, we assessed the gain-of-function toxicity of mHTTex1 aggregation in neurons of HD transgenic flies. We show that the rate of mHTTex1 aggregation in neurons and early mortality of HD transgenic flies are correlated. We observed sequestration of key synaptic proteins into amyloid-like mHTTex1 aggregates and a concomitant decrease of their transcript levels, suggesting that progressive mHTTex1 aggregate stress in neurons leads to an impairment of synaptic function. Machine learning-based data analysis revealed that the abundance of synaptic proteins such as the vesicular monoamine transporter Vmat in the brain is predictive of fly survival. RNAi knockdown of Vmat-encoding transcripts in neurons with pathogenic amyloid-like HTTex1Q97 aggregates further shortened the lifespan of HD flies, supporting the hypothesis that mHTTex1 aggregation drives impairment of synaptic processes and pathogenesis of HD.
The molecular properties of the bHLH TCF4 protein as an intrinsically disordered hub transcription factor
Authors: Nikola Sozańska , Klepka Barbara P. , Anna Niedźwiecka , Lilia Żukowa , Michał Dadlez , Beata Greb-Markiewicz , Andrzej Ożyhar , Aneta Tarczewska
Published: February 2025

1.

Background

Transcription factor 4 (TCF4) is a member of the basic helix-loop-helix (bHLH) family of transcription factors and guides proper embryogenesis, particularly neurogenesis, myogenesis, heart development and hematopoiesis. bHLH proteins exhibit variations in length, expression patterns and the presence of defined motifs. The interaction of TCF4 with DNA is dependent on the presence of a conserved bHLH domain, particularly the presence of a basic (b) motif. Most mutations in theTcf4gene are either associated with the development of serious nervous system disorders, such as Pitt-Hopkins syndrome or schizophrenia, or are lethal. Although TCF4 is essential for the proper development and function of the human body, apart from the isolated bHLH domain, there is a lack of fundamental knowledge about the structure of TCF4.

Methods

Recombinant full-length TCF4 was expressed inE. colicells and purified using chromatographic techniques. To determine the conformation of the polypeptide chain of TCF4, we performedin vitroanalysis using hydrogen/deuterium exchange mass spectrometry (HDX-MS). We then determined the dissociation constant (KD) of the TCF4:DNA complex using independent methods, including fluorescence polarization (FP), electrophoretic mobility shift assay (EMSA), and fluorescence correlation spectroscopy (FCS). Finally, we compared the properties of TCF4 in itsapoandholoform in relation to the changes of the conformation of the polypeptide chain (HDX-MS), hydrodynamic properties (e.g., sedimentation-velocity analytical ultracentrifugation; SV-AUC), and stability (thermal shift, circular dichroism; CD).

Results

In this study, we demonstrate the molecular characteristics of full-length TCF4, the dimer of which is one of the largest intrinsically disordered proteins (IDPs) described to date. According to our findings, the structure of TCF4 is extensively disordered. Only the bHLH domain, which comprises 10% of the polypeptide chain, exhibits a stable fold. Strikingly, Ephrussi-box (E-box) binding via the bHLH domain has no significant effect on the disordered nature of TCF4, but it does influence the stability of TCF4.

Conclusions

We suggest that bHLH plays the role of an anchor localizing TCF4 to specific gene sequences. The dual nature of the TCF4 structure, as well as the fact that the intrinsically disordered regions (IDRs) represents most of the protein sequence, suggests that TCF4 may act as a hub transcription factor regulating the expression of specific genes through the interaction of IDRs with gene-specific partners.
BTK Autoinhibition Analyzed by High-Throughput SH2 Domain Swaps
Authors: Eisen Timothy J , Ghaffari-Kashani Sam , Hung Chien-Lun , Groves Jay T , Kuriyan John
Published: February 2025

BTK, a Tec-family tyrosine kinase, resembles the Src and Abl kinases in that an SH2-SH3 module regulates the activity of the kinase domain, principally through an inhibitory interaction between the SH3 and kinase domains. In Src kinases, phosphorylation of a C-terminal tail latches the SH2 domain onto the kinase domain, positioning the SH3 domain in an inhibitory conformation; in Abl, interaction between the kinase domain and a myristoyl group on the N-terminal segment provides the same latching function. The structure of autoinhibited BTK resembles that of the Src and Abl kinases, but BTK lacks an SH2-kinase latch. To assess autoinhibition in BTK, we generated hundreds of chimeric BTK molecules and measured their fitness using a high-throughput assay in T and B cells. Surprisingly, many SH2 domains increased fitness when substituted into BTK. Analysis of one set of chimeric proteins demonstrated that the increase in fitness stems from the ability of the substituted SH2 domains to disrupt BTK autoinhibition while maintaining phosphotyrosine targeting. These results reveal the importance of distributed interactions between the SH2 and kinase domains of BTK in stabilizing the inhibitory conformation, and suggest that the specialized latching mechanisms in Src and Abl kinases may be later evolutionary refinements.
Tier-based standards for FAIR sequence data and metadata sharing in microbiome research
Authors: Kim Lina , Lavrinienko Anton , Sebechlebska Zuzana , Stoltenberg Sven , Bokulich Nicholas A.
Published: February 2025

Microbiome research is a growing, data-driven field within the life sciences. While policies exist for sharing microbiome sequence data and using standardized metadata schemes, compliance among researchers varies. To promote open research data best practices in the microbiome research community, we (1) propose two tiered badge systems to evaluate data/metadata sharing compliance, and (2) showcase an automated evaluation tool to determine adherence to data reporting standards in publications with amplicon and metagenome sequence data. In a systematic evaluation of publications (n ∼ 3000) spanning human gut microbiome research, we found that nearly half of publications do not meet minimum standards for sequence data availability. Moreover, poor standardization of metadata creates a high barrier to harmonization and cross-study comparison. Using this badge system and evaluation tool, our proof-of-concept work exposes (i) the ineffectiveness of sequence data availability statements, and (ii) the lack of consistent metadata standards for annotating microbial data. In this Perspective, we highlight the need for improved practices and infrastructure that reduce barriers to data submission and maximize reproducibility in microbiome research. We anticipate our tiered badge framework will promote dialogue regarding data sharing practices and facilitate microbiome data reuse, supporting best practices that make microbiome data FAIR.
Dissection of retrosplenial cortex inputs: ubiquitous drive from anterior thalamus
Authors: Margetts-Smith Gabriella , Andrianova Lilya , Kohli Shivali , Randall Andrew D , Aggleton John P , Witton Jonathan , Craig Michael T
Published: February 2025

The retrosplenial cortex (RSC) is a highly interconnected brain region involved in spatial navigation and associative learning. It forms extensive, reciprocal connections with sensory, hippocampal, parahippocampal, prefrontal, and thalamic areas. RSC comprises granular (gRSC) and dysgranular (dRSC) subdivisions with distinct connectivity and functions. Despite its emerging role in behaviour and its implication in memory-related disorders such as Alzheimer’s disease, the nature of its synaptic inputs remains poorly understood.

Here, we combined viral anatomical tracing, optogenetic stimulation, and patch-clamp electrophysiology to investigate inputs from the anterior cingulate cortex (ACC), dorsal subiculum (dSub), and anterior thalamic nuclei (ATN) to gRSC and dRSC. Strikingly, all recorded RSC pyramidal neurons received ATN input, regardless of subdivision or cortical layer. Activation of ATN inputs evoked significantly larger post-synaptic responses than those from dSub or ACC, though both regions maintained substantial connectivity with RSC. While dSub projections appeared denser in gRSC, synaptic responses were larger in dRSC, albeit with lower input probability. Notably, NMDA receptor-mediated components of RSC excitatory inputs were weaker than expected, potentially explaining the reported inability to induce long-term potentiation in RSC inex vivoneurophysiology experiments.

This is the first study to characterise the synaptic properties of retrosplenial afferents. Our findings highlight the dominant influence of ATN inputs and raise important questions about how RSC’s long-range connectivity supports its roles in memory and spatial navigation.
Cascades of effectiveness of new-generation insecticide-treated nets against malaria, from entomological trials to real-life conditions
Authors: Champagne Clara , Lemant Jeanne , Assenga Alphonce , Kibondo Ummi A. , Lekundayo Ruth G. , Mbuba Emmanuel , Moore Jason , Muganga Joseph B. , Ntabaliba Watson S. , Odufuwa Olukayode G. , Swai Johnson Kyeba , Alexa Maria , Goers Roland , Golumbeanu Monica , Chitnis Nakul , Ross Amanda , Moore Sarah , Pothin Emilie
Published: February 2025

As insecticide resistance spreads in Africa, new-generation insecticide-treated nets (ITNs) are increasingly being deployed to protect vulnerable populations against malaria. While these nets provide greater entomological efficacy against resistant mosquitoes, their effectiveness against malaria transmission also depends on other factors, such as durability, access, usage, and activity patterns of hosts and vectors. Here, we quantify the impact of two new-generation ITNs, namely Interceptor®G2 (chlorfenapyr-pyrethroid) and Olyset®Plus (piperonyl butoxide-pyrethroid), in a cascade from entomological efficacy to population-level effectiveness. We use a mathematical model that we parameterize with entomological data and validate against results from randomized controlled trials. We found that, beyond entomological factors, operational factors including functional survival, ITN use and in-bed exposure critically impact ITN effectiveness overall and per ITN types. Our results obtained for Tanzania can be extended to other contexts in a dashboard (https://aimswisstph.shinyapps.io/ITNcascadesdashboard) allowing users to explore product selection based on setting-specific factors that influence ITN effectiveness.
Appraising Cardiovascular 10-yr Risk Prediction Scores: A Rapid Systematic Review
Authors: Adhikari Chiranjivi , Shah Komal , Shukla Aakansha , Karmacharya Biraj Man , Mavalankar Dileep
Published: February 2025

Globally, the burden of cardiovascular disease is on the rise. Despite WHO’s and the UN’s frantic efforts, it appears less probable that the 25 by 25 aim will be met. Early identification of at-risk cases using a risk scoring system can aid in achieving these goals, however for primary and secondary prevention, suitability of these scoring systems, for the countries with medium to low resources, including Asians, with respect to accuracies is a challenge as majority of them are developed from non-Asian cohorts. In light of methodological considerations, risk attribution, and policy consequences, we included and described, restricting our search but sytematically, with five widely used global tools for CVD risk 10-year prediction—FRS, WHO CVD, QRISK, ASCVD, and SCORE—and their updated versions, altogether 11, published during 1970-2023. In general, the results of consolidated risk ratings and summarization showed that these algorithms can differentiate CVD 10-yr risk by 63-86% accurately, considering both for internal and external validity. Further, we discuss their methodological perspectives, ad hoc use, and suggest prospects.

Registration

Open Science Framework (https://osf.io/72v48)

Highlights

Globally and optimally used cardiovascular disease (CVD) risk scoring algorithms have diverse accuracies, generalizability, and levels of evidence based on study designs, analyses, and given gold standards.

Although validated fair to excellent, still the performance of these tools can be increased from 12 to 37%, both for internal and external accuracy, which can have a positive impact on cost and public health.

Lifestyle and related changes due to gene-environment interaction, these algorithms are liable to change, so we need to update, validate, and fit them accordingly.

Implementational, methodological, technological, and cost-related issues need to be addressed for a country or a state-specific algorithm to be up taken, updated, or validated.
Reconstructing the silent circulation of West Nile Virus in a Caribbean island during 15 years using sentinel serological data
Authors: Hamouche Celia , Pradel Jennifer , Pagès Nonito , Chevalier Véronique , Lecollinet Sylvie , Bastard Jonathan , Durand Benoit
Published: February 2025

The dynamics of zoonotic infectious diseases with silent circulation may be imperfectly understood and monitored using passive (or reactive) epidemiological surveillance data only, highlighting the interest of quantitative methods like modelling. West Nile virus (WNV) is a widespread mosquito-borne virus transmitted from birds to “dead-end” hosts including humans and horses, in whom it can be fatal. It was first detected in Guadeloupe archipelago, Caribbean, in 2002, although no WNV clinical case in humans nor horses had been reported before 2024. Undetected infections represent a risk as WNV can be transmittedviablood and organ donations. In Guadeloupe, epidemiological surveillance started in 2002 in sentinel chickens and horses and in 2015 in mosquitoes, to detect WNV and to improve knowledge on its epidemiology and dynamics. In order to reconstruct the WNV force of infection (FOI), we built a model assessing different hypotheses regarding its dynamics using serological results in respectively 1,022 and 3,649 blood samples collected from 256 horses and 317 chickens between 2002 and 2018. We fitted the model to the serological data using Markov Chains Monte Carlo. We found that WNV FOI in Guadeloupe Island presented both within-year (seasonal) and between-years fluctuations. We identified three main episodes of WNV circulation on the island between 2002 and 2017. During years with circulation, the FOI was predicted to be highest around the months of October-November, although transmission could occur all year long. We estimated a very low weekly seroreversion rate, which is consistent with a lifelong persistence of WNV IgG antibodies in many infected individuals. To conclude, combining longitudinal serological data to a mathematical model allowed reconstructing the recurrent and silent circulation of WNV in this Caribbean island, which could improve surveillance design for better virus detection.
Validating data from Multiplex Assays of Variant Effect (MAVEs): A CanVIG-UK National Survey of NHS Clinical Scientists
Authors: Allen Sophie , Garrett Alice , Rowlands Charlie F. , Durkie Miranda , Burghel George J. , Robinson Rachel , Callaway Alison , Field Joanne , Frugtniet Bethan , Palmer-Smith Sheila , Grant Jonathan , Pagan Judith , McDevitt Trudi , Snape Katie , Hanson Helen , McVeigh Terri , Adams David J. , Findlay Gregory M. , Villani Rehan M. , Spurdle Amanda B. , Turnbull Clare ,   CanVIG-UK
Published: February 2025

Advances in technology have made possible Multiplex Assays of Variant Effect (MAVEs), systematically generating functional data for many thousands of genetic variants. Robust clinical validation and accessible online resources for MAVE data have previously been identified as barriers to clinical adoption of new MAVEs.

We delivered a survey during the November 2024 Cancer Variant Interpretation Group (CanVIG-UK) meeting comprising NHS clinical scientists and clinical geneticists, and received 46 responses from individuals regularly performing variant classification for diagnostic reporting.

Only 35% reported they would accept clinical validation of the MAVE provided by its authors: 20% reported they would attempt clinical validation themselves whilst 61% would await clinical validation by a trusted central body. 72% reported they would use MAVE data ahead of formal peer-reviewed publication if reviewed and clinically validated by a trusted central body. When scoring such central bodies on a scale 1-5 for confidence in their review and validation of MAVEs, CanVIG-UK (median=5), VCEPs (median=5) and ClinGen SVI Functional Working Group (median=4) all scored highly. Participants supported making variant-level data accessible via a relevant web resource (although the majority of participants expressed that additional assay-level or variant-level information would have a low likelihood to alter validation scores provided by a trusted central body). These findings, from a comparatively homogenous clinical diagnostic group operating in a resource-constrained healthcare setting, indicate that clinical application of new MAVEs for variant classification will be delayed unless robust clinical validations are performed by a trusted central body and made readily accessible.
Variable pharmacokinetics of coagulation factor VIII in the perioperative setting complicates personalisation of treatment in patients with haemophilia A
Authors: Janssen Alexander , van Moort Iris , Bennis Frank C. , Cnossen Marjon H. , Mathôt Ron A.A.
Published: February 2025

Pharmacokinetic (PK)-guided dosing of factor concentrates in patients with haemophilia A is generally recommended for the optimisation of prophylactic treatment. PK-guided dosing can also be useful in the perioperative setting, where guidelines advise to keep factor VIII (FVIII) activity levels within tight target ranges to prevent bleeding. Previous studies suggest changes in FVIII PK following medical procedures as well as potential time-dependent effects, meaning that population PK models specific to the perioperative setting are required. In this study, we use data from haemophilia A patients collected during the prophylactic and perioperative setting to identify covariates that explain changes in FVIII PK. Additionally, we use machine learning methods to find potential time-dependent effects on FVIII clearance. Perioperative FVIII clearance was generally lower compared to the prophylactic setting. Covariates related to the complexity of the medical procedures were correlated to larger decreases in clearance. Importantly, subjects undergoing more complex procedures also depicted potentially relevant time-dependent effects on clearance. These effects could be highly variable between subjects. Directly using PK parameters obtained from the prophylactic setting resulted in relatively high mean absolute percentage error (MAPE) at 26.3%, while the perioperative model including time-dependent effects depicted markedly reduced error (10.3%). The presence of high variability between subjects and potential time-dependent effects complicates the selection of optimal dosing regimens before the start of medical procedures. Our method can be used to optimise treatment in real-time, but close monitoring of FVIII levels will likely remain necessary.
Bioimaging with fluorescent nucleic-acid aptamers for the specific detection and quantification ofPseudomonas aeruginosaalone and in heterogeneous bacterial populations
Authors: Mezouarhi Chaimae , Vauchelles Romain , Abdallah Basma , Régine Janel , Ouadghiri Mouna , Ait Benhassou Hassan , Fechter Pierre , Choulier Laurence
Published: February 2025

The rising prevalence of bacterial infections, antibiotic resistance, and emerging pathogens underscores the urgent need for innovative diagnostic approaches. Aptamers, short nucleic acid sequences with high specificity and affinity for their targets, are promising candidates for diagnostic applications due to their ability to detect a wide range of pathogens. In this study, we present a fluorescent aptamer-based bioimaging approach for detectingPseudomonas aeruginosa, a multidrug-resistant pathogen of significant clinical concern. Conjugated with fluorescent dye, the detection efficacy of the F23 aptamer was evaluated on 15 different Gram-negative and Gram-positive bacteria, including fixed and lived cells, as well as homogeneous and heterogeneous population. To quantify microscopy images, we developed an automated, open-access identification software using ImageJ. Its high sensitivity provides a robust platform for accurately quantifying bacteria labeled with aptamers and potentially other fluorescent ligands. For instance, it successfully detected 1122P. aeruginosacells labeled with aptamer F23 out of a total of 1123P. aeruginosacells in a single image. With almost 200,000 analyzed bacteria and an exceptionally clear signal-to-noise ratio, we demonstrated that the F23 aptamer effectively detects various reference and clinical strains ofPseudomonas aeruginosa, while failing to detect Gram-positiveStaphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus epidermidisandCorynebacterium striatum, as well as Gram-negativeKlebsiella pneumonia, Acinetobacter baumannii, andEscherichia coli. The F23 aptamer is therefore a promising tool to distinguishPseudomonas aeruginosafrom different strains of the skin microbiota. However, our quantitative method also revealed partial labeling to other bacterial cells, highlighting the issue of refining aptamer selection to improve selectivity.
Stable states in an unstable landscape: microbial resistance at the front line of climate change
Authors: Cronin Dylan , Holland-Moritz Hannah , Smith Derek , Aroney Samuel T. N. , Hodgkins Suzanne , Borton Mikayla , Li Yueh-Fen , Healy Kieran ,   IsoGenie Field & Analytic Teams 2010-2017,   EMERGE Institute Coordinators, Tfaily Malak M. , Crill Patrick , McCalley Carmody K. , Wrighton Kelly , Varner Ruth , Tyson Gene W. , Woodcroft Ben , Bagby Sarah C. , Ernakovich Jessica , Rich Virginia I.
Published: February 2025

Microbiome responses to warming may amplify or ameliorate terrestrial carbon loss and thus are a critical unknown in predicting climate outcomes. We quantified microbial warming response over seven years in a thawing permafrost peatland, using large-scale multi-omics data. We integrated analyses of organisms (via taxonomy), functions (via metabolic pathways and proteins), and community organization (via network structure and ecological assembly) to deeply characterize response mechanisms. This revealed unexpected and comprehensive microbiome stability. This resistance to change appeared bolstered by habitat-specific dispersal and community-level functional redundancy, particularly via versatile carbon generalists. Our findings challenge widespread assumptions of significant soil microbiome alteration with climate change, and reveal key genome-inferred processes that underlie microbiome stability. This suggests that future research should reorient towards critical habitat transitions.

One Sentence Summary

In a warming permafrost peatland, microbiome shifts are concerted and correspond to habitat change, rather than proceeding gradually with rising temperature, with multiple lines of evidence indicating that this microbiome ecological resistance is linked to functional redundancy and high dispersal.
Verification of emerging genomic mutations inMycobacterium tuberculosisallows transmission chains to be distinguished in an epidemiological typing cluster extending over thirty years
Authors: de Zwaan Rina , de Vries Gerard , Ubbelohde Ella , Mulder Arnout , Kamst Miranda , Rebel Karin , Kautz Saskia , Kremer Kristin , Anthony Richard M , van Soolingen Dick
Published: February 2025

Whole genome sequencing (WGS) is able to identify epidemiological links betweenMycobacterium tuberculosisisolates. Recent clustering can be ruled out using a pre-defined single nucleotide polymorphism (SNP) threshold. If WGS clusters grow significantly over time limited genetic variability hampers epidemiological investigations.

Newly emerging (informative) SNPs in isolates of an extended cluster growing for more than 30 years to >150 cases in the Netherlands were analysed. WGS data was analyzed from 61 sequencing files from 54 patients. Genomic positions that varied within the cluster isolates were carefully screened for minority populations in other isolates from the cluster. A transmission scheme was generated on the basis of WGS data alone then compared to the epidemiological information available.

Fifty-two informative SNPs were identified, eight of which were also detected as mixed variants. One emerging SNP indnaA(1199G>A R400H) has been observed in other transmitted strains and may be under selection. There was high concordance between the transmission chains suggested on basis of the newly emerging SNPs and scenario’s identified using classical epidemiological cluster investigations.

Analysis of filtered SNPs accumulating in the genome ofM. tuberculosisin large clusters contains information on transmission dynamics and can be used to support epidemiological investigations.
Drosophilalarval gut transcriptome reveals a microbe-mediated intestinal tissue growthviaEcdysone during adaptive growth
Authors: Bai Longwei , Bellemin Stéphanie , Drelon Coralie , Joncour Pauline , Guillemot Elodie , Strigini Maura , Gillet Benjamin , Leulier François , Ramos Cathy Isaura
Published: February 2025

Juvenile growth is an adaptive trait since chronic undernutrition leads to reduced growth rate and delayed maturation. UsingDrosophilaand mouse gnotobiotic models, we previously established the evolutionarily conserved influence of the intestinal microbiota and selectedLactobacillistrains on juvenile growth. Here we aimed to identify the molecular mechanisms underlying microbe-mediatedDrosophilaadaptive growth. Since the intestine is the interface of host-microbe interactions, we conducted an analysis of the larval midgut transcriptome in presence or absence of an intestinalLactobacillistrain representative of theDrosophilamicrobiota. Among the different biological processes identified, Ecdysone signaling has emerged as a newLactobacilli-mediated signature. Through functional and morphometrical approaches, we show that, upon bacteria association, intestinal Ecdysone is not rate limiting for the larval systemic plastic growth but required for the adaptation of midgut growth toLactobacilli. Our results reveal a tissue-specific contribution of the pleiotropic hormone Ecdysone in the control of midgut adaptive growth and maturation.
Kinetic characterization of three human DExD/H-box RNA helicases
Authors: Li Fengling , Chan U Hang , Perez Julia Garcia , Zeng Hong , Chau Irene , Li Yanjun , Seitova Alma , Halabelian Levon
Published: February 2025

Human DExD/H-box RNA helicases are ubiquitous molecular motors that unwind and rearrange RNA secondary structures in an ATP-dependent manner. These enzymes play essential roles in nearly all aspects of RNA metabolism. While their biological functions are well-characterized, the kinetic mechanisms remain relatively understudiedin vitro. In this study, we describe the development and optimization of a bioluminescence-based assay to kinetically characterize three human RNA helicases: MDA5, LGP2, and DDX1. The assays were conducted using annealed 24-mer RNA (blunt-ended double-stranded RNA) or double-stranded RNA (ds-RNA) with a 25- nt 3ʹ overhang. These findings establish a robust and high-throughputin vitroassay suitable for a 384-well format, enabling the discovery and characterization of inhibitors targeting MDA5, LGP2, and DDX1. This work provides a valuable resource for advancing our understanding of these helicases and their therapeutic potential in Alzheimer’s disease.
A silicon rhodamine-fused glibenclamide to label and detect malaria-infected red blood cells
Authors: Bastl Claudia , Close Cindy M. , Holtz Ingo , Gatin-Fraudet Blaise , Eis Mareike , Werum Michelle , Konrad Smilla , Roßmann Kilian , Huhn Christiane , Ghosh Souvik , Ast Julia , Roosen Dorien A. , Lehmann Martin , Haucke Volker , Reymond Luc , Hodson David J. , Tinnefeld Philip , Johnsson Kai , Glembockyte Viktorija , Kilian Nicole , Broichhagen Johannes
Published: February 2025

The malaria parasitePlasmodium falciparumaffects the lives of millions of people worldwide every year. The detection of replicating parasites within human red blood cells is of paramount importance, requiring appropriate diagnostic tools. Herein, we design and apply a silicon rhodamine-fused glibenclamide (SiR-glib). We first test this far-red fluorescent, fluorogenic and endoplasmic reticulum-targeting sulfonylurea in mammalian cells and pancreatic tissues, before characterizing its labeling performance in red blood cells infected with the asexual developmental stages ofPlasmodium falciparum. We further combineSiR-glibwith a portable smartphone-based microscope to easily and rapidly identify parasitized red blood cells, providing proof of principle for diagnostic use in rural endemic areas without major healthcare facilities.
Spatial transcriptomics reveals heterogeneous cell–cell interactions among brain regions in a cuprizone model consistent with multiple sclerosis lesions
Authors: Tsai Hui-Hsin , Piya Sarbottam , Wang Jing , Zhu Jing , Hu Wenxing , Gehrke Andrew R. , Cao Shaolong , Guise Amanda J. , Chan Su Jing , Sheehan Mark , Chu Jenhwa , Ouyang Zhengyu , Ryals Matthew , Lee Michelle , Wang Wanli , Zhao Edward , Cullen Patrick , Challa Ravi , Marshall Eric , Zeng Wanyong , Kaeser-Woo Yea Jin , Ehrenfels Chris , Jandreski Luke , McLaughlin Helen , Carlile Thomas M. , Gagnon Jake , Reynolds Taylor L. , Li Mingyao , Li Kejie , Zhang Baohong
Published: February 2025

The cuprizone (CPZ) model is widely used for modeling demyelination in multiple sclerosis (MS) and for testing potential remyelination therapies. We integrated single-cell and spatial transcriptomics (ST) to fine map the spatial cellular and molecular responses during de and remyelination. ST revealed global demyelination and neuroinflammation in the brain beyond the corpus callosum, with region-specific differences. We identified oligodendroglia and microglia as two major cell types with significant transcriptomic changes in the model. Ligand receptor pairing analyses predicted growth factor and phagocytic pathway enrichment during demyelination, which is consistent with changes in MS lesions. During remyelination, while mature oligodendrocytes nearly reversed their phenotype back to the control state, microglia remained associated with the demyelination phenotype. Finally, astrocytes in the CPZ model had the greatest preservation of disease-associated modules to MS lesions, while the MOL, OPC, and microglia showed moderate to low preservation, which overall suggested that the CPZ model had moderate translatability to chronically active MS lesions.
Natural Variation in Photoprotection: Rapid NPQ Kinetics in Ferns
Authors: Maryn Nina M. , Chaparro Antonio , Short Audrey , Fleming Graham R. , Niyogi Krishna K.
Published: February 2025

Land plants perform oxygenic photosynthesis but are unable to use all of the solar radiation that they absorb on a daily basis. To minimize the production of reactive oxygen species in excess light, photosynthetic organisms use non-photochemical quenching (NPQ) mechanisms to dissipate excess excitation energy. However, the on-off transition of these mechanisms is slower than the light fluctuations themselves. In high-to-low light transitions, this can be costly to the overall productivity and carbon gain of the organism across its lifetime, because useful light energy is wasted. Here, we characterize the rapid kinetics of NPQ found in species across the fern lineage. Most of the 23 examined fern species showed faster NPQ induction and faster and more complete NPQ relaxation. Curve fitting suggested that energy-dependent quenching was the dominant contributor to the kinetics. The xerophytic fernAstrolepis windhamiiexhibited rapid, dithiothreitol-resistant accumulation of zeaxanthin during NPQ induction, and it maintained low residual NPQ after NPQ relaxation, which however was not associated with rapid re-epoxidation of zeaxanthin. Rapid NPQ kinetics might have been an adaptive trait as ferns radiated in sunflecked forest understories during angiosperm diversification and expansion during the Cretaceous.
Single-Cell Transcriptomics Reveals Dynamic Microglial States and Neural-Immune Networks in Human Diabetic Retinopathy
Authors: Yang Luning , Lin Sen , Tao Yiwen , Pan Qi , Cai Tengda , Ye Yunyan , Liu Jianhui , Zhou Yang , Yi Quanyong , Lu Zen Haut , Chen Lie , McKay Gareth , Rankin Richard , Shao Yongqing , Meng Weihua
Published: February 2025

Diabetic retinopathy (DR) is a major cause of vision loss worldwide. Here, we perform single-cell RNA sequencing of thirteen human retina samples (from living and post-mortem donors) across non-diabetic, diabetic, and DR states to create a comprehensive transcriptomic atlas. We uncover three distinct microglial states—homeostatic, stress-response, and inflammatory—along a functional continuum, rather than discrete activation states, with dynamic transitions occurring throughout disease progression. Trajectory analysis indicates bifurcating paths starting from the homeostatic state branching toward stress-response and inflammatory states. Three major functional modules: ribosomal/translation, coordinated immune cell function, and inflammatory/transcriptional regulation, showing disease-specific activation patterns were identified. Cell communication analysis further highlights sophisticated neural-immune interactions, particularly between photoreceptors and microglia. Our findings provide insights into the complex cellular dynamics of DR progression and suggest potential therapeutic targets for early intervention.