bluuebunny/crossref_metadata_2025_split huggingface dataset:
Absolute abundance unveilsBasidiobolusas a cross-domain bridge indirectly bolstering gut microbiome homeostasis
Authors: Ghotbi Mitra , Stajich Jason E. , Dallas Jason , Rurik Alexander , Cummins Chloe , Vargas-Gastélum Lluvia , Ghotbi Marjan , Spatafora Joseph W. , Kelly Kian , Alexander N. Reed , Moe Kylie C. , Syring Kimberly C. , Shadmani Leila , Perez-Marron Julissa , Walker Donald M. 
Published: January 2025

AbstractThe host microbiome is integral to metabolism, immune function, and resilience against pathogens. However, reliance on relative abundance (RA) to estimate host-associated microbiomes introduces compositional biases, while limited tools for absolute abundance (AA) quantification hinder broader applications. To address these challenges, we developed DspikeIn (https://github.com/mghotbi/DspikeIn), an R package paired with a versatile wet-lab methodology for AA quantification. Using RA and AA to compare core microbiome distributions across herpetofauna orders and their natural histories revealed starkly distinct results, driven by aggregate effects, including inherited compositional biases in RA and additional multifactorial influences. Focusing on two closely relatedDesmognathusspecies demonstrated that AA quantification enhanced resolution in differential abundance analyses and minimized false discovery rates (FDR) when identifying enriched taxa in their gut microbiomes. Keystone taxa identified through network associations also differed between RA and AA data. For example,LactococcusandCetobacteriumwere core members in Anura and Caudata, whileBasidiobolusandMortierellawere core to Chelonia and Squamata, facilitating host adaptation to diverse environments, insights undetectable with RA data. AA-based network analysis further revealed that removing theBasidiobolussubnetwork increased negative interactions, highlighting its role in promoting gut homeostasis through cross-domain connectivity. Despite low redundancy, theBasidiobolusnode exhibited high betweenness, efficiency, and degree, serving as a critical bridge linking disconnected nodes or modules and indirectly supporting microbiome stability, consistent with Burt’s structural hole theory. DspikeIn represents a transformative tool for microbiome research, enabling the transition from RA to AA quantification and delivering more accurate, consistent, and comparable results across studies.Graphical abstract DspikeIn cheatsheet
Stick together: Isolation and characterization of exopolysaccharide producing bacteria from degraded permafrost soils
Authors: Waqas Muhammad , Zelenková Simona , Vogel Cordula , Rühmann Broder , Varsadiya Milan , Liebmann Patrick , Wang Haitao , Shibistova Olga , Urich Tim , Guggenberger Georg , Bárta Jiří 
Published: January 2025

ABSTRACTPermafrost thaw can result in two distinct environmental landscapes (i.e. “wet condition” soils rich in ice wedges and low drainage, and “dry condition” well-drained areas with higher evapotranspiration). These different conditions influence the bacterial communities and may impact their capacity to produce exopolysaccharides (EPSs), which are crucial for bacterial survival and adaptation. This study aimed to isolate and characterize EPSs-producing bacteria from the active layer of two permafrost degrading landscapes and from undisturbed permafrost soil. A total of 54 bacterial isolates were obtained, representing three phyla: Firmicutes, Actinomycetota, and Pseudomonadota. EPSs production was assessed by determining the polysaccharide content measured as glucose equivalent, and 26 isolates were identified as potential EPSs-producers. Among the isolates,Curtobacterium oceanosedimentum, Frigoribacterium faeni,Streptomycesstrains,Neobacillus bataviensisandMesobacillus subterraneushad the highest polysaccharide yield. They were also found inhabiting in the different horizons of degraded permafrost soil and undisturbed permafrost soil, by determining their relative proportion within the total bacterial community based on 16S rRNA gene sequences similarities.
Topical application of carbon dots and mesoporous silica nanoparticle-derived dsRNA-nanocomposites for the control of beet curly top virus and turnip mosaic virus
Authors: Zarrabi Sara , Rangel Carmen , Martínez-Campos Emanuel , Delgado-Martín Josemaría , Arpanaei Ayyoob , Shams-bakhsh Masoud , Velasco Leonardo 
Published: January 2025

AbstractThe management of emerging phytoviruses in current agriculture confronts many challenges, including the appearance of new strains or the arrival of new species, requiring a multidisciplinary approach. The usual methods for the control of these pathogens are based on management practices, vector control, seed control, etc., and the introgression of genetic resistance in cultivars. But the development of resistances by classical genetic methods is a costly and time-consuming process. A promising alternative is the control of these pathogens by means of the so-called SIGS (Spray-Induced Gene Silencing) that consists of topical treatments with specific molecules derived from the viruses as double-stranded RNA (dsRNA), triggering the plant defense mechanisms. In this work, we show the control of two viruses, the potyvirus turnip mosaic virus (TuMV) and the curtovirus beet curly top virus (BCTV) by dsRNA nanocomposites with carbon dots or mesoporous silica nanoparticles inNicotiana benthamiana. In the case of TuMV, the disease was significantly reduced in terms of plant photosynthetic capacity and viral titers, in the dsRNA treated plants. Moreover, when the treatments were carried out with dsRNAs as nanocomposites, the differences were even more noticeable with respect to untreated inoculated plants. In the case of BCTV, a significant delay in symptoms appearance was observed after the treatments with the dsRNA nanocomposites, but not with the naked dsRNAs. Viral titers were reduced either with the naked or the nanoparticle-delivered dsRNAs. The increased efficiency of dsRNA for virus control when supplied with the nanoparticles can be related with the enhanced dsRNA delivery reported in this work.
Identification of QTL-by-Environment Interaction by Controlling Polygenic Background Effect
Authors: Zhao Fuping , Wang Lixian , Xu Shizhong 
Published: January 2025

AbstractThe QTL by environment interaction (Q×E) effect is hard to detect because there are no effective ways to control the genomic background. In this study, we propose a novel linear mixed model that simultaneously analyzes data from multiple environments to detect Q×E interactions. This model incorporates two different kinship matrices derived from the genome-wide markers to control both main and interaction polygenic background effects. Simulation studies demonstrated that our approach was more powerful than the meta-analysis and inclusive composite interval mapping methods. We further analyzed four agronomic traits of rice across four environments. A main effect QTL was identified for 1000-grain weight (KGW), while no QTLs were found for tiller number. Additionally, a large QTL with a significant Q×E interaction was detected on chromosome 7 affecting grain number, yield and KGW. This region harbored two important genes,PROG1andGhd7. Furthermore, we applied our mixed model to analyze lodging in barley across six environments. The six regions exhibiting Q×E interaction effects identified by our approach overlapped with the SNPs previously identified using EM and MCMC-based Bayesian methods, further validating the robustness of our approach. Both simulation studies and empirical data analyses showed that our method outperformed all other methods compared.
Effectiveness of COVID-19 vaccines against SARS-CoV-2 infection and symptomatic infection in the England Winter Coronavirus (COVID-19) Infection Study cohort
Authors: Abdul Aziz Nurin , Andrews Nick , Rawlinson Christopher , Buckley Andrew , Allen Alexander 
Published: January 2025

AbstractBackgroundThe Winter Coronavirus (COVID-19) Infection Study (WCIS) was a sample-based household study in England and Scotland aiming to inform COVID-19-related epidemiology and health pressures over the 2023-2024 winter period. We aim to estimate vaccine effectiveness (VE) against both SARS-CoV-2 infection in general and specifically symptomatic infection (COVID-19) within the WCIS cohort in England.MethodsData from self-reported lateral flow device (LFD) tests for SARS-CoV-2 were collected from participants alongside self-completed questionnaires from November 2023 to March 2024. A test-negative case-control design was used to estimate VE of the Autumn 2023 COVID-19 boosters against SARS-CoV-2 infection and symptomatic infection compared with being unboosted, regardless of previous vaccination history. Symptomatic infection as an outcome was restricted to participants who reported an ARI symptom associated with their test. Logistic regression was used to calculate VE, with LFD test result as the outcome, vaccination status as primary exposure variable, and adjustment for covariates. Analyses were also stratified by bivalent BA4/5 and monovalent XBB vaccines to assess VE of individual vaccine types.ResultsThe analysis included 109,929 English residents primarily in the 60-80 age range (54%), of White ethnic background (95%), and in the least deprived quintile (31%). Participants contributed 114,066 eligible tests in the analysis, of which 42,340 were associated with a symptomatic outcome. VE against infection peaked at 49% (95% Confidence Interval (CI): 35-60%) at 2-4 weeks post-vaccination, with waning to a null effect occurring after 10 weeks (VE: 5% (95% CI: -5-14%)). Similarly, VE against symptomatic infection peaked at 49% (95% CI: 32-63%) after 2-4 weeks, waning after 10 weeks (VE: 5% (95% CI: -7-16%)). The bivalent vaccine showed low and mainly non-significant evidence of protection against either outcome, whereas the monovalent vaccine showed a peak VE of 49% (95% CI: 34-60%) at 2-4 weeks against infection and 49% (95% CI: 31-63%) at 2-4 weeks against symptomatic infection.ConclusionsThe Autumn 2023 COVID-19 vaccine campaign provided moderate protection against infection and symptomatic infection during the 2023 winter period, with a differential effect between vaccine type. Household studies such as WCIS are useful to understand impacts of vaccination campaigns within the community, especially in the post-pandemic period where testing capacity is restricted to hospital settings.
YnaI exemplifies the diversity of structural gating mechanisms in mechanosensitive channels of small conductance
Authors: Flegler Vanessa J. , Rasmussen Akiko , Hedrich Rainer , Rasmussen Tim , Böttcher Bettina 
Published: January 2025

AbstractOsmotically varying environments are challenging for bacterial cells. Sudden drops in osmolytes cause an increased membrane tension and rupture the cells in the absence of protective mechanisms. One family of protective proteins are mechanosensitive channels of small conductance that open in response to membrane tension. Although these channels have a common architecture, they vary widely in the number of transmembrane helices, conductivity, and gating characteristics. Despite of several structures of channels in the open and closed state, the underlying common principles of the gating mechanism are not well understood. Here we show that YnaI opens by radial relocation of the transmembrane sensor paddles together with a shortening of the pore. This contrasts the prototypic smaller MscS which tilts the sensor paddles and retains the pore length. A chimera of both channels with the YnaI sensor paddles and the pore containing C-terminal part of MscS has the conductivity of the pore donor and the tension response of the paddle donor together with the conformational changes of the respective donor. Our research shows that elements with different types of structural rearrangements can be mixed and matched within one channel as long as they support the common area expansion on the periplasmic side.
Exploring the effects of metformin on the body by urine proteome
Authors: Chen Yuzhen , Wang Haitong , Yang Minhui , Shen Ziyun , Gao Youhe 
Published: January 2025

AbstractMetformin is the first-line medication for treating type 2 diabetes mellitus (T2DM), with over 200 million patients taking it daily. Its effects are extensive and play a positive role in multiple areas. Can we explore its effects and potential mechanisms by urine proteome? In this study, a total of 166 differential proteins were identified after rats were given a dose of 150 mg/(kg·d) of metformin for 5 consecutive days, including complement component C6, pyruvate kinase, coagulation factor X, growth differentiation factor 15 (GDF15), carboxypeptidase A4, chymotrypsin-like elastase family member 1, and L-lactate dehydrogenase C chain (LDH-C). Several of these proteins have been reported to be directly affected by metformin or associated with the effects of metformin. Several biological pathways enriched by the differential proteins or proteins where the differentially modified peptides are located have been reported to be associated with metformin, including glutathione metabolic process, negative regulation of gluconeogenesis, and renin-angiotensin system. Additionally, some significantly enriched biological pathways that have not been reported to be related to the effects of metformin may provide clues for the study of metformin’s potential mechanisms. In conclusion, the application of urine proteome offers a comprehensive and systematic approach to exploring both the known and unknown effects of drugs, thus opening a new window to study the mechanisms of metformin.
Does non-Mendelian chromosome transmission and unusual sex determination affect male mate choice in the flyBradysia coprophila?
Authors: Hodson Christina N , Baird Robert , Hodgemen Maddy , Dury Shona , Ross Laura 
Published: January 2025

AbstractMate quality and the cost of mating affect the evolution of mating preferences and is one reason females often show stronger mate preferences than males. Fungus gnats in the family Sciaridae (Diptera) are a family in which we might expect to see the evolution of strong male mate preferences. Many Sciaridae species are monogenic, where females exclusively produce offspring of one sex. Sciaridae species also exhibit paternal genome elimination, a reproductive system where males only transmit maternally inherited chromosomes to offspring. Therefore, Sciaridae males would benefit from exhibiting mating preferences for females that produce female offspring, as a male’s genes are only transmitted to future generations through his daughters, not his sons. We explore male mate choice in the sciarid flyBradysia(formerlySciara)coprophila. We find that mating is costly, as males become sperm limited through multiple matings, and that males exhibit preferences for larger females, suggesting that males are selected to be choosy. However, we do not find male preferences for females that produce female offspring, instead we find that males prefer mating with females that produce male offspring. We speculate that this seemingly maladaptive behaviour may be due to female receptivity rather than male preference, or that males are unable to distinguish between females of different types, which is perhaps surprising since these females differ genetically by 1000s of genes (through a large paracentric inversion on the X chromosome). Together we show how the interplay between unusual genetics and sex determining systems may affect mating system evolution.Summary statementIn the fungus gnatBradysia coprophilafemales are genetically predetermined to produce broods of just one sex and males only transmit maternally inherited genes to offspring. These factors suggest males should have strong mating preferences for females that produce daughters, which we explore. We find that while males would benefit from being “choosy”, they appear unable to distinguish the two female types, possibly because females are selected to hide their sex determining phenotype.
Cadmium ingestion does not disrupt the social transmission of the microbiome in juveniles of a subsocial insect
Authors: Cheutin Marie-Charlotte , Honorio Romain , Meunier Joël 
Published: January 2025

AbstractSymbiotic microbes are essential for host health and fitness. In family-living species, these microbes are often acquired through vertical transmission from parents and horizontal transmission from siblings. However, it is unclear how environmental stressors, such as chemical pollution, influence these contributions to the juvenile microbiome. Here, we tested the independent and interactive effects of social environment and cadmium ingestion - a common heavy metal pollutant - on the microbiome of juvenile European earwigs. We reared juveniles either alone, with siblings or with siblings plus the mother, exposed them to cadmium at 0, 25 or 100mg/L, and analysed their microbiome composition and diversity. Our results showed that both social environment and cadmium independently influenced the phylogenetic beta-diversity of the juvenile microbiome although neither factor nor their interaction affected alpha-diversity. Moreover, we found that observed specific bacterial taxa in the social groups, including the overabundance of putatively pathogenic (Serratia) and mutualistic (Lactobacillus) symbionts were more abundant in juveniles reared with family members than isolated ones. Overall, our findings suggest that while both social environment and cadmium shape the juvenile microbiome, family does not amplify the effects of chemical exposure. This highlights the resilience of microbial transmission within families, even under environmental stress.
Nde1 Promotes Lis1 Binding to Full-Length Autoinhibited Human Dynein-1
Authors: Yang Jun , Zhao Yuanchang , Chai Pengxin , Yildiz Ahmet , Zhang Kai 
Published: January 2025

AbstractCytoplasmic dynein-1 (dynein) is the primary motor for the retrograde transport of intracellular cargoes along microtubules. The activation of the dynein transport machinery requires the opening of its autoinhibited Phi conformation by Lis1 and Nde1/Ndel1, but the underlying mechanism remains unclear. Using biochemical reconstitution and cryo-electron microscopy, we show that Nde1 significantly enhances Lis1 binding to autoinhibited dynein and facilitates the opening of Phi. We discover a key intermediate step in the dynein activation pathway where a single Lis1 dimer binds between the Phi-like (PhiL) motor rings of dynein. In this “PhiL-Lis1”, Lis1 interacts with one of the motor domains through its canonical interaction sites at the AAA+ ring and stalk and binds to the newly identified AAA5, AAA6, and linker regions of the other motor domain. Mutagenesis and motility assays confirm the critical role of the PhiL-Lis1 interface. This intermediate state is instantly and efficiently formed in the presence of Nde1, but Nde1 is not part of the PhiL-Lis1. These findings provide key insights into the mechanism of how Nde1 promotes the Lis1-mediated opening of Phi dynein.
Control of limb loading during active horizontal perturbations at moderate and fast trots in rats
Authors: Andrada Emanuel , Fischer Martin S. , Stark Heiko , Arnold Dirk 
Published: January 2025

AbstractTo understand how small animals cope with complex, unstructured, and unpredictable substrates, we analyzed the kinetics of rats (n = 10) moving at a fast and at a moderate trot over an unperturbed substrate and a substrate subjected to active horizontal perturbations. Perturbations were active single forwards or backwards displacements of an instrumented platform by amplitudes of 5mm or 10mm in 0.05s. Single leg ground reaction forces (SLGRF) were collected for unperturbed and perturbed locomotion (hindlimbs: 50/102, forelimbs: 45/130, respectively). When negotiating horizontal perturbations, rats displayed gait resetting (braking, accelerating) and non-resetting behaviors. Feedforward strategies differed between the fore- and hindlimbs. In circa 60% of the perturbed trials, forelimbs started the step in acceleration mode, while hindlimbs began the stance mostly in non-resetting mode (∼45%). In about 50% of all perturbed steps, the impulse provided by the SLGRF displayed a change in behavior according to the expected response to the perturbation. The remaining 50% retained the feedforward strategy. Still, most perturbed trials displayed changes in SLGRF patterns that indicated passive and active reactions to platform shifts.Our results indicate that rats’ sensorimotor control system tunes fore- and hindlimbs differently in expectation of a perturbation. In addition, the tendon-muscle systems of the limbs are recruited to prevent leg collapse at the beginning and end of the stance. At lower speeds, spinal and/or higher center commands have enough time to re-adapt limb behavior. At higher speeds of locomotion, rats rely more on their limbs’ intrinsic stability and on feedforward control.
Neurodegenerative and neurodevelopmental roles for bulk lipid transportersVPS13AandBLTP2in movement disorders
Authors: Neuman Sarah D. , Thakur Rajan S. , Gratz Scott J. , O’Connor-Giles Kate M. , Bashirullah Arash 
Published: January 2025

ABSTRACTBackgroundBridge-like lipid transfer proteins (BLTPs) mediate bulk lipid transport at membrane contact sites. Mutations in BLTPs are linked to both early-onset neurodevelopmental and later-onset neurodegenerative diseases, including movement disorders. The tissue specificity and temporal requirements of BLTPs in disease pathogenesis remain poorly understood.ObjectivesTo determine the age-of-onset and tissue-specific roles ofVPS13AandBLTP2in movement disorder pathogenesis usingDrosophilamodels.MethodsWe generated tissue-specific knockdowns of theVPS13Aortholog (Vps13) and theBLTP2ortholog (hobbit) in neurons and muscles ofDrosophila. We analyzed age-dependent locomotor behavior, neurodegeneration, and synapse development and function.ResultsNeuron-specific loss of theVPS13Aortholog caused neurodegeneration followed by age- onset movement deficits and reduced lifespan, while muscle-specific loss affected only lifespan, revealing neurodegeneration and myopathy as independent comorbidities inVPS13Adisease. In contrast, neuronal loss of theBLTP2ortholog resulted in severe early-onset locomotor defects without neurodegeneration, while muscle loss impaired synaptogenesis and neurotransmission at the neuromuscular junction (NMJ).ConclusionsVPS13Amaintains neuronal survival, whileBLTP2orchestrates synaptic development.VPS13Afunction in muscle does not play a role in movement defects. The phenotypic specificity of BLTP function provides mechanistic insights into distinct disease trajectories for BLTP-associated movement disorders.
Boosting the detection of enhancer-promoter loops via novel normalization methods for chromatin interaction data
Authors: Wang Xiaotao , Shi Detong , Xue Feiyang , Liu Yunxia , Yang Hongbo , Jiang Linghan 
Published: January 2025

AbstractAccurately detecting enhancer-promoter loops from genome-wide interaction data, such as Hi-C, is crucial for understanding gene regulation. Current normalization methods, such as Iterative Correction and Eigenvector decomposition (ICE), are commonly used to remove biases in Hi-C data prior to chromatin loop detection. However, while structural or CTCF-associated loop signals are retained, enhancer-promoter interaction signals are often greatly diminished after ICE normalization and similar methods, making these regulatory loops harder to detect. To address this limitation, we developed Raichu, a novel method for normalizing chromatin contact data. Raichu identifies nearly twice as many chromatin loops as ICE, recovering almost all loops detected by ICE and revealing thousands of additional enhancer-promoter loops missed by ICE. With its enhanced sensitivity for regulatory loops, Raichu detects more biologically meaningful differential loops between conditions in the same cell type. Furthermore, Raichu performs consistently across different sequencing depths and platforms, including Hi-C, HiChIP, and single-cell Hi-C, making it a versatile tool for uncovering new insights into three- dimensional (3D) genomic organization and transcriptional regulation.