bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of circadian clock and light-input pathway genes in Hemiptera
Authors: Smykal Vlastimil , Tobita Hisashi , Dolezel David 
Published: January 2025

AbstractCircadian clocks are timekeeping mechanisms that help organisms anticipate periodic alterations of day and night. These clocks are widespread, and in the case of animals, they rely on genetically related components. At the molecular level, the animal circadian clock consists of several interconnected transcription-translation feedback loops. Although the clock setup is generally conserved, some important differences exist even among various insect groups. Therefore, we decided to identifyin silicoall major clock components and closely related genes in Hemiptera. Our analyses indicate several lineage-specific alterations of the clock setup in Hemiptera, derived from gene losses observed in the complete gene set identified in the outgroup, Thysanoptera, which thus presents the insect lineage with a complete clock setup.Nilaparvataand Fulgoroidea, in general, lost the (6-4) photolyase, while all Hemiptera lost FBXL3, and several lineage-specific losses of dCRY and jetlag were identified. Importantly, we identified non-canonical splicing variants ofperiodandm-crygenes, which might provide another regulatory mechanism for clock functioning. Lastly, we performed a detailed reconstruction of Hemiptera’s light input pathway genetic repertoire and explored the horizontal gene transfer of cryptochrome-DASH from plant toBemisia. Altogether, this inventory reveals important trends in clock gene evolution and provides a reference for clock research in Hemiptera, including several lineages of important pest species.Bullet points (highlights)○Evolution of clock genes (including light input pathway) was reconstructed in Hemiptera○Newm-cryandpersplicing variants were identified in certain species○A unique horizontal gene transfer of plant/fungal CRY-DASH was found inBemisia○Clock setup was identified for pests:Nilaparvata,Bemisia,Halyomorpha, and aphids○Future clock research directions in Hemiptera are proposed
Independent and repeated acquisition of endosymbiotic bacteria across the diversification of feather lice
Authors: Soto-Patiño Juliana , Walden Kimberly K. O. , Doña Jorge , Alessio Lorenzo D’ , Bush Sarah E. , Clayton Dale H. , Dale Colin , Johnson Kevin P. 
Published: January 2025

AbstractMany parasitic insects, including lice, form close relationships with endosymbiotic bacteria that are crucial for their survival. In this study, we used genomic sequencing to investigate the distribution and evolutionary history of the bacterial genusSodalisacross a broad range of feather louse species spanning 156 genera. Phylogenomic analysis revealed significant diversity amongSodalislineages in feather lice, and robust evidence for their independent and repeated acquisition by different louse clades throughout their radiation. Among the 1,020 louse genomes analyzed, at least 22% containedSodalis, distributed across 57 louse genera. Cophylogenetic analyses between theSodalisand feather louse phylogenies indicated considerable mismatch. This phylogenetic incongruence between lice andSodalis, along with the presence of distantly relatedSodalislineages in otherwise closely related louse species, strongly indicates repeated independent acquisition of this endosymbiont. Additionally, evidence of cospeciation among a few closely related louse species, coupled with frequent acquisition of these endosymbionts from free-living bacteria, further highlights the diverse evolutionary processes shapingSodalisendosymbiosis in feather lice.
Urbanisation and Habitat Shape Resource-Driven Dietary Shifts in Wild Birds
Authors: Chatelain Marion , Rennstam Rubbmark Oskar , Rüdisser Johannes , Traugott Michael 
Published: January 2025

AbstractUrbanisation affects bird ecology and evolution, with changes in nutritional intake considered a key driver. However, most studies provide only snapshots of urban bird feeding ecology due to methodological limitations in analysing diets across space and time. Here, we address this gap by examining the diets of two common species with differing feeding ecologies: the great tit (Parus major) and blue tit (Cyanistes caeruleus). Diet samples from 370 birds, captured over a year at 147 locations across an urbanised landscape in Innsbruck, Austria, were molecularly analysed. Results revealed species-and season-specific diet patterns influenced by urbanisation: urban great tits exhibited higher diet diversity but reduced arthropod consumption during the breeding season, while urban blue tits compensated for lower moth intake by increasing their consumption of crab spiders and aphids. Prey consumption mirrored prey availability, highlighting resource-driven dietary shifts. Habitat type also played a significant role, with urban green spaces enhancing plant-based food diversity and residential areas increasing anthropogenic food consumption. These findings support the hypothesis that diet drives fitness and phenotypic differences between urban and rural bird populations. They highlight the need to consider both urbanisation levels and habitat characteristics to fully understand its ecological and evolutionary impacts.
Prenatal maternal infection promotes maternal microchimeric cells to alter infection risk in male offspring
Authors: Jimena Brittany , Kazimierczyk Daniel , Kazimierczyk Simon , Moya Haley , Shin Eva , Li Li , Korgaonkar Parimal , Porter Caryn , Seed Brian , Cherayil Bobby J. , Jain Nitya 
Published: January 2025

SummaryVertically transferred maternal cells or maternal microchimeric cells (MMCs) engraft the fetus and persist in offspring for long periods of time. How altered maternal immune states arising from infection affect MMCs and their function in offspring is poorly understood. Here, we show that pregnancy-associated transient maternal infection alters MMCs to differentially regulate immunity in offspring. In male offspring of dams previously infected withYersinia pseudotuberculosis, MMCs confer a pro-inflammatory type 17 T effector phenotype that leads to enhanced protective immunity to an unrelatedSalmonellainfection. Thus, acquired maternal cells imprinted by microbial exposure during pregnancy exert an antigen agnostic and sex-differential effect on offspring immunity, and may potentially be targeted to deliver immune benefits to infants in the vulnerable early life period.
Alginate-εPLL core-shell hydrogel beads as a tool for an effective, stable and scalable microbial encapsulation
Authors: Amaro-Cruz Alba , García-Román Miguel , Moya-Ramírez Ignacio 
Published: January 2025

AbstractSynthetic microbial consortia offer significant potential for biotechnological applications. However, achieving stable and reproducible co-cultures is challenging due to competitive dynamics and unbalanced growth rates among species. Here, we present an effective method for microbial encapsulation based on alginate-based core-shell hydrogel beads coated with ε-poly-L-lysine (εPLL-HB). This method ensures complete microbial containment while allowing for consistent growth inside the beads of several microbial species with a wide variability in their features. Compared to chitosan and α-poly-L-lysine, two of the most used coating agents for this kind of encapsulation, εPLL demonstrated superior performance in avoiding cellular escape across diverse culture conditions and for all the microbial strains tested, while allowing their proliferation inside the capsule. εPLL-HB enabled the construction of spatially organized co-cultures, effectively balancing populations between microorganisms with different growth rates. Furthermore, εPLL-HB provided protection against toxic compounds in lignocellulosic-derived media and maintained their encapsulation efficacy and viability after long-term storage at -80°C. The superior microbial containment, structural integrity and chemical resistance of εPLL-HB, combined with their low price and ease of preparation, makes them a versatile tool for engineering synthetic microbial consortia, with broad applicability in biotechnological processes.
Pervasive and programmed nucleosome distortion patterns on single mammalian chromatin fibers
Authors: Yang Marty G , Richter Hannah J , Wang Simai , McNally Colin P , Harris Nicole , Dhillon Simaron , Maresca Michela , de Wit Elzo , Willenbring Holger , Maher Jacquelyn , Goodarzi Hani , Ramani Vijay 
Published: January 2025

ABSTRACTWe present a genome-scale method to map the single-molecule co-occupancy of structurally distinct nucleosomes, subnucleosomes, and other protein-DNA interactions via long-read high-resolution adenine methyltransferase footprinting.IterativelyDefinedLengths of Inaccessibility (IDLI) classifies nucleosomes on the basis of shared patterns of intranucleosomal accessibility, into: i.) minimally-accessible chromatosomes; ii.) octasomes with stereotyped DNA accessibility from superhelical locations (SHLs) ±1 through ±7; iii.) highly-accessible unwrapped nucleosomes; and iv.) subnucleosomal species, such as hexasomes, tetrasomes, and other short DNA protections. Applying IDLI to mouse embryonic stem cell (mESC) chromatin, we discover widespread nucleosomal distortion on individual mammalian chromatin fibers, with >85% of nucleosomes surveyed displaying degrees of intranucleosomally accessible DNA. We observe epigenomic-domain-specific patterns of distorted nucleosome co-occupancy and positioning, including at enhancers, promoters, and mouse satellite repeat sequences. Nucleosome distortion is programmed by the presence of bound transcription factors (TFs) at cognate motifs; occupied TF binding sites are differentially decorated by distorted nucleosomes compared to unbound sites, and degradation experiments establish direct roles for TFs in structuring binding-site proximal nucleosomes. Finally, we apply IDLI in the context of primary mouse hepatocytes, observing evidence for pervasive nucleosomal distortionin vivo.Further genetic experiments reveal a role for the hepatocyte master regulator FOXA2 in directly impacting nucleosome distortion at hepatocyte-specific regulatory elementsin vivo. Our work suggests extreme—but regulated—plasticity in nucleosomal DNA accessibility at the single-molecule level. Further, our study offers an essential new framework to model transcription factor binding, nucleosome remodeling, and cell-type specific gene regulation across biological contexts.
Breaking the Phalanx: Overcoming Bacterial Drug Resistance with Quorum Sensing Inhibitors that Enhance Therapeutic Activity of Antibiotics
Authors: Beasley Jon-Michael , Dorjsuren Dorjbal , Jain Sankalp , Rath Marielle , Tieghi Ricardo Scheufen , Tropsha Alexander , Simeonov Anton , Zakharov Alexey V. , Muratov Eugene 
Published: January 2025

AbstractAntibiotic-resistant bacterial infections loom over humanity as an increasing deadly threat. There exists a dire need for new treatments, especially those that synergize with our existing arsenal of antibiotic drugs to help overcome the gap in antibiotic efficacy and attenuate the development of new antibiotic-resistance in the most dangerous pathogens. Quorum sensing systems in bacteria drive the formation of biofilms, increase surface motility, and enhance other virulence factors, making these systems attractive targets for the discovery of novel antibacterials. Quorum sensing inhibitors (QSIs) are hypothesized to synergize with existing antibiotics, making bacteria more sensitive to the effects of these drugs. In this study, we aimed to find the synergistic combinations between the QSIs and known antibiotics to combat the two deadliest hospital infections -Pseudomonas aeruginosaandAcinetobacter baumannii.We mined biochemical activity databases and literature to identify known, high efficacy QSIs against these bacteria. We used these data to develop and validate a Quantitative Structure-Activity Relationship (QSAR) model for predicting QSI activity and then employed this model to identify new potential QSIs from the Inxight database of approved and investigational drugs. We then tested binary mixtures of the identified QSIs with 11 existing antibiotics using a combinatorial matrix screening approach with ten (five of each) clinical isolates ofP. aeruginosaandA. baumannii. Amongst explored drug combinations, 31 exhibited a synergistic effect, including mixtures involving naldemedine and telotristat, two drugs predicted by our model with previously undescribed QSI activity. Although no mixture inhibiting all the strains was found, piperacillin combined with curcumin, ketoprofen, indomethacin, and piroxicam demonstrated the broadest antimicrobial action. We anticipate that further preclinical investigation of these combinations of novel repurposed QSIs with a known antibiotic may lead to novel clinical candidates.Table of Content Graphic
Ketone body b-Hydroxybutyrate does not extend lifespan, but upregulates fecundity in food-limitedDaphnia, with a transgenerational effect
Authors: Pearson A. C. , Bhadra S. , Yampolsky L. Y. 
Published: January 2025

AbstractKetone bodies accumulate on ketogenic diets and are known to have numerous beneficial health and longevity effects. Here we investigate the effects of exposure to environmental b-hydroxybutyrate (BHB), a ketone body, on longevity and fecundity of a model organismDaphnia magna,a plankton crustacean, maintained at limited food availability. We report that exposure to continuous or intermittent lifetime exposure to 2.5 – 10 mM of BHB reducesDaphnialifespan, while intermittent exposure administered for 20-day periods has little effect on post-exposure survival, regardless of the age at exposure onset. On the other hand, various BHB exposure regimes significantly increased fecundity, including fecundity up to 100 days past a 20-day exposure. We further demonstrate that even relatively brief early life maternal exposure to BHB can increase daughters’ fecundity, although this transgenerational effect is genotype-specific. We argue that this effect must have a signaling nature rather than simply manifestation of additional source of energy provided by BHB and discuss potential significance of genetic variation in transmission of such signals.
Pyruvate and Related Energetic Metabolites Modulate Resilience Against High Genetic Risk for Glaucoma
Authors: Li Keva , Tolman Nicholas , Segrè Ayellet V. , Stuart Kelsey V. , Zeleznik Oana A. , Vallabh Neeru A. , Hu Kuang , Zebardast Nazlee , Hanyuda Akiko , Raita Yoshihiko , Montgomery Christa , Zhang Chi , Hysi Pirro G. , Do Ron , Khawaja Anthony P. , Wiggs Janey L. , Kang Jae H. , John Simon WM , Pasquale Louis R. ,   UK Biobank Eye and Vision Consortium
Published: January 2025

AbstractGlaucoma polygenic risk scores (PRS) effectively identify disease risk, but some individuals with high PRS do not develop glaucoma. Factors contributing to this resilience remain unclear. Using 4,658 glaucoma cases and 113,040 controls in a cross-sectional study in the UK Biobank, we investigated whether plasma metabolites enhanced glaucoma prediction and if a metabolomic signature of resilience in high-genetic risk individuals existed. Logistic regression models incorporating 168 NMR-based metabolites into PRS-based glaucoma assessments were developed, with multiple comparison corrections applied. While metabolites weakly predicted glaucoma (Area Under the Curve=0.579), they offered modest prediction improvement in PRS-only-based models (P=0.004). We identified a metabolomic signature associated with resilience in the top PRS decile, with elevated glycolysis-related metabolites—lactate (P=8.8E-12), pyruvate (P=1.9E-10), and citrate (P=0.02)—linked to reduced glaucoma prevalence. These metabolites combined significantly modified the PRS-glaucoma relationship (Pinteraction=0.011). Higher total resilience metabolite levels within the highest PRS quartile corresponded to lower glaucoma prevalence (Odds Ratiohighest vs. lowest total resilience metabolite quartile=0.71, 95% Confidence Interval [CI]=0.64–0.80). As pyruvate is a foundational metabolite linking glycolysis to tricarboxylic acid cycle metabolism and ATP generation, we pursued experimental validation for this putative resilience biomarker in a human-relevant Mus musculus glaucoma model. Dietary pyruvate mitigated elevated intraocular pressure (P=0.002) and optic nerve damage (P<0.0003) inLmx1bV265Dmice. These findings highlight the protective role of pyruvate-related metabolism against glaucoma and suggest potential avenues for therapeutic intervention.
Fluid and White Matter Suppression Contrasts MRI Improves Deep Learning Detection of Multiple Sclerosis Cortical Lesions
Authors: Gordaliza Pedro M. , Müller Jannis , Cagol Alessandro , Molchanova Nataliia , La Rosa Francesco , Tsagkas Charidimos , Granziera Cristina , Bach Cuadra Meritxell 
Published: January 2025

AbstractPurposeTo investigate, for the first time, the efficacy of Fluid and White Matter Suppression (FLAWS) MRI sequence in improving Deep Learning (DL)-based detection and segmentation of cortical lesions in Multiple Sclerosis (MS) patients even, with applicability to clinical settings where only standard T1-weighted images are available.Materials and MethodsIn this retrospective multi-site study, we analyzed 204 MS patients using DL models developed with FLAWS and Magnetization Prepared 2 Rapid Acquisition Gradient Echoes (MP2RAGE) sequences. Reference standard annotations were established through two approaches: (1) consensus of three expert raters across all contrasts, and (2) single-rater annotations for individual modalities. Models were validated on both internal and external datasets, with performance assessed usingF1-score for detection and DSC for segmentation accuracy.ResultsModels involving FLAWS demonstrated superior performance over MP2RAGE-only models. The combined MP2RAGE+FLAWS model achieved CL detection with medianF1-score of 0.667[0.339−0.840] compared to multirater consensus. Models trained on comprehensive consensus annotations outperformed those trained on single-modality annotations. Notably, a model exclusively based on MP2RAGE images and trained with FLAWS-derived annotations showed, showed strong generalization to external Magnetization Prepared Rapid Gradient-Echo (MPRAGE) clinical datasets (medianF1-score: 0.55[0.211−0.998]).ConclusionIntegration of FLAWS-derived contrasts and annotations significantly improves DL-based CL detection and segmentation. The models demonstrate capability in identifying lesions missed by individual raters and maintain robust performance even without FLAWS sequences in standard clinical settings. This advancement facilitates clinical translation, supported by publicly available inference models on DockerHub.Graphical AbstractHighlightsMP2RAGE+FLAWS MRI sequences achieves superior cortical lesion detection performanceQuantitative validation shows medianF1of 0.667[0.339−0.840] with combined sequencesFLAWS-trained model generalizes well to standard MPRAGE images (F1: 0.55[0.211−0.998)Model demonstrates immediate clinical applicability on standard MPRAGE without FLAWS inputImplementation publicly accessible via DockerHub for widespread clinical adoption
Effect of Hyperbaric Oxygen After Moderate-Intensity Exercise on Fatigue: A Single-blind Crossover Randomized Trial
Authors: Yagishita Kazuyoshi , Aizawa Junya , Ohji Shunske , Hoshino Takashi , Oyaizu Takuya 
Published: January 2025

AbstractObjectivesAlthough insufficient delivery of oxygen might be a factor in physical and perceived fatigue, the relationship between exposure to hyperbaric oxygen (HBO) and recovery from perceived fatigue remains unexplained. The purpose of this study was to investigate the effects of exposure to HBO after long-duration, medium-intensity training on recovery from perceived fatigue in a single-blind study.MethodsFatigue was induced in nine male university students (mean age: 21.3 years) using an ergometer exercise bike at a moderate intensity of 75% of their maximum heart rate for 60 min. Post-workout, subjects randomly received an intervention comprising exposure to HBO or an air placebo in a single-blind experimental trial. Blood tests were conducted, and perceived fatigue was evaluated by using visual analog scales (VAS) at five time points. One week later, a crossover trial was conducted.ResultsFor the HBO group, pre- to post-intervention mean VAS scores for whole-body fatigue significantly improved from 48.4 to 28.7 (p<0.001). However, in the placebo group, the improvement was not statistically significant. Hematological evaluations, including C-reactive protein level, white blood cell count, creatine kinase level, lactic acid level, T-cell count, CD4/CD8 ratio, and natural killer cell count, did not show any significant between-group differences except only BUN and free fatty acids levels 1.5 h after intervention and Mg levels immediately after intervention. There were also no significant differences in the results of other hematological assessments.ConclusionsThe results of this study showed that perceived fatigue evaluated by VAS scores significantly improved in the HBO group in a blinded trial. However, this was not objectively supported by blood test results. HBO may have effects on recovery from perceived fatigue following long-duration, moderate-intensity exercise. However, the results of this study could not determine the efficacy of HBO on exercise-induced fatigue.
Unbiased co-occurring mutational landscapes in tumorigenesis
Authors: Li Yizhou , Xiong Yangfang , Wei Wensheng 
Published: January 2025

SummaryMutations with a synergistic effect on tumorigenesis were positively selected during tumor evolution, showing a tendency to co-occur in cancer genomes. To systematically gain insight of tumorigenic crosstalk at the mutation level, we utilized the FP-Growth algorithm in frequent pattern mining to create an unbiased map of co-occurring mutations from clinical genome sequencing data. We identified 100,933 frequent co-occurring mutation pairs across 22 cancer types. The co-mutation pairs involving cancer driver genes highlighted potential mechanisms for collaborative tumor formation, suggesting promising targets to disrupt tumorigenesis. Additionally, the large number of intra-gene co-mutations with strong dependencies indicated possible combinational effects on the oncogenic properties of specific proteins, which might be overlooked when individual mutations are not hotspots. Furthermore, our whole-genome mining strategy revealed a significant number of co-mutations in non-coding regions, with an enrichment of regulatory elements suggesting their potential role in modulating the co-expression of related genes. Finally, we demonstrated that our pipeline could systematically identify high-order co-mutations. In summary, our study provides the most extensive co-occurring mutations in tumor development, offering valuable insights into mechanisms and potential therapeutic targets.