bluuebunny/crossref_metadata_2025_split huggingface dataset:
dar: A Consensus-Based Framework for Differential Abundance Testing in Microbiome Data
Authors: Farré-Badia Judit , Noguera-Julian Marc , Paredes Roger , Català-Moll Francesc 
Published: February 2025

ABSTRACTSummaryThedarR package streamlines differential abundance (DA) testing in microbiome research by integrating state-of-the-art DA methods—such as DESeq2, ALDEx2, ANCOM-BC, and MetagenomeSeq—within a customizable consensus-based framework, thereby enhancing the robustness and reproducibility of DA results. Leveraging microbiome data inphyloseqorTreeSummarizedExperimentformats,darorganizes analysis steps in a modularrecipeobject, enabling users to easily incorporate preprocessing tasks such as taxonomic filtering, rarefaction, and subsetting, alongside multiple DA analysis methods. Dedicated visualization tools facilitate the definition of a consensus by illustrating the overlap among methods, empowering users to refine analysis strategies and display final results. Reproducibility is supported through functions that export and import entire analysis workflows, makingdara comprehensive solution for addressing the complex, high-dimensional nature of microbiome data.Availability and implementationdaris an R package available from Bioconductor ≥ 3.19 (https://www.bioconductor.org/packages/dar) for R ≥ 4.4. The software is distributed under the MIT License and includes example datasets.Contactfcatala@irsicaixa.esSupplementary informationAdditional documentation is available athttps://microbialgenomics-irsicaixaorg.github.io/dar
Insights From Protein Frustration Analysis of BRD4-Cereblon Degrader Ternary Complexes Show Separation of Strong from Weak Degraders
Authors: Yang Tianyi , Mukhaleva Elizaveta , Wei Wenyuan , Weiss Dahlia , Ma Ning , Shanmugasundaram Veerabahu , Vaidehi Nagarajan 
Published: February 2025

AbstractPROteolysis TArgeting Chimeras (PROTACs), also known as Ligand-Directed Degraders (LDDs), are an innovative class of small molecules that leverage the ubiquitin-proteasome system to induce the degradation of target proteins. Structure based design methods are not readily applicable for designing LDDs due to the dynamic nature of the ternary complexes. This study investigates the dynamic properties of five LDD-mediated BRD4-Cereblon complexes, focusing on the challenges of evaluating linker efficiency due to the difficulty in identifying suitable computational metrics that correlate well with the cooperativity or degradation propensity of LDDs. We uncovered that protein frustration, a concept originally developed to understand protein folding, calculated for the residues in the protein-protein interface of the LDD-mediated ternary complexes recapitulate the strength of degradation of the LDDs. Our findings indicated that hydrophobic residues in the interface are among the highly frustrated residues pairs, and they are crucial in distinguishing strong degraders from weak ones. By analyzing frustration patterns, we identified key residues and interactions critical to the effectiveness of the ternary complex. These insights provide practical guidelines for designing and prioritizing more efficient degraders, paving the way for the development of next-generation LDDs with improved therapeutic potential.
Identification of new interactors of eIF3f by endogenous proximity-dependent biotin labelling in human muscle cells
Authors: Tintignac Lionel , Mittal Nitish , Alam Shahidul , Ataman Meric , Ertuna Yusuf I. , Bock Thomas , Erne Beat , Zavolan Mihaela , Sinnreich Michael 
Published: February 2025

ABSTRACTRegulation of protein synthesis is central to maintaining skeletal muscle integrity and its understanding is important for the treatment of muscular and neuromuscular pathologies. The eIF3f subunit of the translation initiation factor eIF3 has a key role, as it stands at the crossroad between protein-synthesis-associated hypertrophy and MAFbx/atrogin-1-dependent. To decipher the molecular mechanisms underpinning the role of eIF3f in regulating muscle mass, we established a cellular model that enables interrogation of eIF3f functionality via identification of proximal interactors. Using CRISPR-Cas9 molecular scissors, we generated single cell clones of immortalised human muscle cells expressing eIF3f fused to the BirA biotin ligase (eIF3f-BioID1 chimera) from the endogenousEIF3Flocus. Biotinylated proteins, representing interactors of eIF3f in nanometer range distance, were identified by streptavidin pull-downs and mass spectrometry. In both proliferating and differentiated muscle cells, the eIF3f-BioID1 chimera co-sedimented with ribosomal complexes in polysome profiles and interacted mainly with components of the eIF3 complex, and with the eIF4E, eIF4G, and eIF5 initiation factors. Surprisingly, we identified several nucleus-localised interactors of eIF3f, and the immunofluorescence analyses revealed a previously unknown nuclear localization of eIF3f in both myoblasts and myotubes. We also identified novel cytoplasmic partners of eIF3f, responsible for the maintenance of skeletal muscle ultrastructure (sarcomeric/Z-disc (SYNPO2) bound proteins) and proteins of the lysosomal compartment (LAMP1). The established tagging system should be useful to further advance studies of eIF3f function in hypertrophic and atrophic conditions in skeletal muscle.
Inhibitors of the PqsR Quorum-Sensing Receptor Reveal Differential Roles for PqsE and RhlI in Control of Phenazine Production
Authors: Valastyan Julie S. , Shine Emilee E. , Mook Robert A. , Bassler Bonnie L. 
Published: February 2025

AbstractPseudomonas aeruginosais a leading cause of hospital-acquired infections and it is resistant to many current antibiotic therapies, making development of new anti-microbial treatments imperative. The cell-to-cell communication process called quorum sensing controlsP. aeruginosapathogenicity. Quorum sensing relies on the production, release, and group-wide detection of extracellular signal molecules called autoinducers. Quorum sensing enables bacteria to synchronize group behaviors.P. aeruginosapossesses multiple quorum-sensing systems that control overlapping regulons, including those required for virulence and biofilm formation. Interventions that targetP. aeruginosaquorum-sensing receptors are considered a fruitful avenue to pursue for new therapeutic advances. Here, we developed aP. aeruginosastrain that carries a bioluminescent reporter fused to a target promoter that is controlled by twoP. aeruginosaquorum-sensing receptors. The receptors are PqsR, which binds and responds to the autoinducer called PQS (2-heptyl-3-hydroxy-4(1H)-quinolone) and RhlR, which binds and responds to the autoinducer called C4-HSL (C4-homoserine lactone). We used this reporter strain to screen >100,000 compounds with the aim of identifying inhibitors of either or both the PqsR and RhlR quorum-sensing receptors. We report results for 30 PqsR inhibitors from this screen. All of the identified compounds inhibit PqsR with IC50values in the nanomolar to low micromolar range and they are readily docked into the autoinducer binding site of the PqsR crystal structure, suggesting they function competitively. The majority of hits identified are not structurally related to previously reported PqsR inhibitors. Recently, RhlR was shown to rely on the accessory protein PqsE for full function. Specifically, RhlR controls different subsets of genes depending on whether it is bound to PqsE or to C4-HSL, however, the consequences of differential regulation on the quorum-sensing output response have not been defined. PqsR regulatespqsE. That feature of the system enabled us to exploit our new set of PqsR inhibitors to show that RhlR requires PqsE to activate the biosynthetic genes for pyocyanin, a keyP. aeruginosavirulence factor, while C4-HSL is dispensable. These results highlight the promise of inhibition of PqsR as a possibleP. aeruginosatherapeutic to suppress production of factors under RhlR-PqsE control.
Spatiotemporal analysis ofde novoKSHV infection using Crispr/Cas9-based 3D live cell imaging at single episome resolution
Authors: Günther Thomas , Weissmann Simon , Hamann Martin V. , Scheibel Henry , Bosse Jens B. , Ziegler Marion , Grundhoff Adam 
Published: February 2025

AbstractKaposi Sarcoma-associated herpesvirus (KSHV) persists as a latent episome in infected cells. While the virus efficiently infects established cell lines and primary cellsin vitro, the early events guiding establishment of latent infection and the dynamic interplay between viral episomes and host factors remain incompletely understood. Here, we describe the development and application of a CRISPR/Cas9-based 3D live cell imaging system capable of tracking single KSHV episomes in real-time. Our approach exploits the SunTag technology, wherein deactivated Cas9 (dCas9) molecules are fused to repetitive epitope arrays recognized by superfolder GFP-fused single-chain antibodies. By targeting these complexes to terminal repeat units of KSHV, we achieve high level signal amplification, allowing us not only to detect newly incoming viral genomes within the first hours ofde novoinfection, but also to follow their spatiotemporal trajectories through different stages of the viral lifecycle. Furthermore, to facilitate efficient generation of stable reporter cell lines, we adapted the transposon-based piggyBac system to combine all SunTag components into a single-vector targeting system (SunSeT).Using these systems, we demonstrate the ability to observe both transient and stable interactions between KSHV episomes and key cellular regulators, including the variant polycomb-repressive complex 1 (vPRC) component KDM2B and the innate immune sensor IFI16. Furthermore, our platform allows detailed visualization of episodic changes in episome localization, abundance and distribution duringde novoand long-term infection, providing critical insights into how viral genome positioning and dynamics correlate with host subnuclear environments.Overall, our study introduces a robust and adaptable imaging platform to dissect the earliest events of KSHV infection. The ability to track viral episomes in living cells offers a powerful tool to advance our understanding of the spatial and temporal regulation of individual KSHV genomes, shedding light on fundamental mechanisms of herpesvirus latency and persistence.
Persistence of large conjugative plasmids relies on the combination of active partitioning and addiction mechanisms
Authors: Effe Johannes , Santer Mario , Wang Yiqing , Feenstra Theresa E. , Hülter Nils F. , Dagan Tal 
Published: February 2025

AbstractExtrachromosomal and mobile genetic elements, including transposable elements, plasmids, and accessory chromosomes, are found across all domains of life. The replication and segregation of elements integrated into the host chromosome are ensured by the host life cycle. In contrast, the persistence of autonomously replicating elements relies on their ability to remain within the host population. Here, we assess the evolutionary success of different persistence strategies of prokaryotic plasmids. Through intracellular competitions between plasmid genotypes, we find that combining active partitioning during cell division with a toxin-antitoxin (TA) system for post-segregational killing is more effective than either strategy alone. Mathematical modeling of long-term plasmid evolution, calibrated with empirical plasmid persistence probabilities, further supports these findings. A survey of enterobacterial genomes indicates that partitioning and TA systems are core features of large conjugative plasmids. Indeed, we confirm the presence of a previously unrecognized type I TA system in IncX3 plasmids, which serve as important vectors of antibiotic resistance in human pathogens. These findings suggest that large conjugative plasmids likely encode TA systems, including those yet to be identified. The combination of TA and partitioning systems emerges as the most effective strategy for the persistence of low-copy extrachromosomal elements with unstable segregation.
Complex interplay between gene deletions and the environment uncovers cellular roles for genes of unknown function inEscherichia coli
Authors: Sondervorst Kaat , Nesporova Kristina , Herdman Matthew , Steemans Bart , Rosseels Joëlle , Govers Sander K. 
Published: February 2025

AbstractPhenotypic outcomes can be heavily affected by environmental factors. In this study, we exploited the previously observed nutrient-dependency of cell biological phenotypic features, captured by a cross-condition image-based profiling assay ofEscherichia colideletion strains, to examine this in more detail. We identified several general principles, including the existence of a spectrum of deviating phenotypes across nutrient conditions (i.e., from nutrient- or feature-specific to pleiotropic phenotypic deviations), limited conservation of phenotypic deviations across nutrient conditions (i.e., limited phenotypic robustness), and a subset of nutrient-independent phenotypic deviations (indicative of consistent genetic determinants of specific phenotypic features). In a subsequent step, we used this cross-condition dataset to identify five genes of unknown function of which the deletion displayed either nutrient-independent phenotypic deviations or phenotypic similarities to genes of known function:yibN,yaaY,yfaQ,ybiJ, andyijD. These genes showed different levels of phylogenetic conservation, ranging from conserved across the tree of life (yibN) to only present in some genera of the Enterobacterales (yaaY). Analysis of the structural properties of the proteins encoded by these y-genes, identification of structural similarities to other proteins, and the examination of their subcellular localization yielded new insights into their contribution toE. colicell morphogenesis, cell cycle progression and cell growth. Together, our approach showcases how bacterial image-based profiling assays and datasets can serve as a gateway to reveal the function of uncharacterized proteins.ImportanceDespite unprecedented access to genomic information, predicting phenotypes based on genotypes remains notoriously difficult. One major confounding factor is the environment and its ability to modulate phenotypic outcomes. Another is the fact that a large fraction of protein-coding genes in bacterial genomes remains uncharacterized and have no known function. In this work, we use a large-scale cross-condition image-based profiling dataset to characterize nutrient-dependent phenotypic variability ofE. colideletion strains and exploit it to provide insight into the cellular role of genes of unknown function. Through our analysis, we identified five genes of unknown function that we subsequently further characterized by examining their phylogenetic conservation, predicted structural properties and similarities, and their intracellular localization. Combined, this approach highlights the potential of cross-condition image-based profiling, which extracts many cell biological phenotypic readouts across multiple conditions, to better understand nutrient-dependent phenotypic variability and uncover protein function.
Eukaryotic MAGs recovered from deep metagenomic sequencing of the seagrass,Zostera marina,include a novel chytrid in the order Lobulomycetales
Authors: Ettinger Cassandra L. , Eisen Jonathan A. , Stajich Jason E. 
Published: February 2025

AbstractFungi play pivotal roles in terrestrial ecosystems as decomposers, pathogens, and endophytes, yet their significance in marine environments is often understudied. Seagrasses, as globally distributed marine flowering plants, have critical ecological functions, but knowledge about their associated fungal communities remains relatively limited. Previous amplicon surveys of the fungal community associated with the seagrass,Zostera marinahave revealed an abundance of potentially novel chytrids. In this study, we employed deep metagenomic sequencing to extract metagenome-assembled genomes (MAGs) from these chytrids and other microbial eukaryotes associated withZ. marinaleaves. Our efforts resulted in the recovery of five eukaryotic MAGs, including a single fungal MAG in the order Loubulomycetales (65% BUSCO completeness), three MAGs representing diatoms in the family Bacillariaceae (93%, 70% and 31% BUSCO completeness) and a single MAG representing a haptophyte algae in the genusPrymnesium(40% BUSCO completeness). Whole-genome phylogenomic assessment of these MAGs suggests they all largely represent under sequenced, and possibly novel eukaryotic lineages. Of particular interest, the chytrid MAG was placed within the order Lobulomycetales, consistent with the identity of the dominant chytrid from previousZ. marinaamplicon survey results. Annotation of this MAG yielded 5,650 gene models of which 77% shared homology to current databases. With-in these gene models, we predicted 121 carbohydrate-active enzymes and 393 secreted proteins (103 cytoplasmic effectors, 30 apoplastic effectors). Exploration of orthologs between the Lobulomycetales MAG and existing Chytridiomycota genomes have revealed a landscape of high-copy gene families related to host recognition and interaction. Further machine learning analyses based on carbohydrate-active enzyme composition predict that this MAG is a symbiont. Overall, these five eukaryotic MAGs represent substantial genomic novelty and valuable community resources, contributing to a deeper understanding of the roles of fungi and other microbial eukaryotes in the larger seagrass ecosystem.
Hoi1 targets the yeast BLTP2 protein to ER-PM contact sites to regulate lipid homeostasis
Authors: Dziurdzik Samantha K. , Sridhar Vaishnavi , Eng Hailey , Neuman Sarah D. , Yan Junran , Davey Michael , Taubert Stefan , Bashirullah Arash , Conibear Elizabeth 
Published: February 2025

AbstractMembrane contact sites between organelles are important for maintaining cellular lipid homeostasis. Members of the recently identified family of bridge-like lipid transfer proteins (BLTPs) span opposing membranes at these contact sites to enable the rapid transfer of bulk lipids between organelles. While the VPS13 and ATG2 family members use organelle-specific adaptors for membrane targeting, the mechanisms that regulate other bridge-like transporters remain unknown. Here, we identify the conserved protein Ybl086c, which we name Hoi1 (Hob interactor 1), as an adaptor that targets the yeast BLTP2-like proteins Fmp27/Hob1 and Hob2 to ER-PM contact sites. Two separate Hoi1 domains interface with alpha-helical projections that decorate the central hydrophobic channel on Fmp27, and loss of these interactions disrupts cellular sterol homeostasis. The mutant phenotypes of BLTP2 and HOI1 orthologs indicate these proteins act in a shared pathway in worms and flies. Together, this suggests that Hoi1-mediated recruitment of BLTP2-like proteins represents an evolutionarily conserved mechanism for regulating lipid transport at membrane contact sites.
Daily modulation of low-energy nuclear recoils from sub-GeV dark matter
Authors: Stratman Connor , Lin Tongyan 
Published: February 2025

At sufficiently low nuclear recoil energy, the scattering of dark matter (DM) in crystals gives rise to single phonon and multiphonon excitations. In anisotropic crystals, the scattering rate into phonons modulates over each sidereal day as the crystal rotates with respect to the DM wind. This gives a potential avenue for directional detection of DM. The daily modulation for single phonons has previously been calculated. Here we calculate the daily modulation for multiphonon excitations from DM in the mass range 1 MeV–1 GeV. We generalize previous multiphonon calculations, which made an isotropic approximation, and implement results in the DarkELF package. We find daily modulation rates up to 1%–10% for an Al2O3 target and DM mass below 30 MeV, depending on the recoil energies probed. We obtain similar results for SiC, while modulation in Si, GaAs, and SiO2 is negligible.

Published by the American Physical Society
2025
High-rise building density optimization for air quality improvement and investment potential
Authors: Vidanapathirana Malithie , Perera Narein , Emmanuel Rohinton , Coorey Shaleeni 
Published: February 2025

PurposeAir pollution and air quality are key environmental factors that impact an investor’s willingness to pay (WTP) and are negatively correlated. Hedonic pricing quantifies the relationship between air pollutants and property values but is a backward-looking tool. Similarly, limited research links investment potential to urban planning and air pollution. This research aims to predict variation in investor WTP due to air pollution concentrations within a high-dense high-rise building cluster.Design/methodology/approachPossible building configurations of Port City, Colombo, were modelled using Ansys Fluent. While maintaining the same Floor Area Ratio (FAR), building heights and volumes, the density of towers is changed by introducing wind corridors to enable pollutant dispersion. A trace pollutant is used as a comparative study to determine the effect of each building form on pollution concentration and potential WTP.FindingsThe introduction of wind corridors along the ambient wind direction increased building porosity, positively affecting WTP overall. Wind corridors perpendicular to the ambient wind reduced porosity, which reduced dispersion at upper levels, negatively affecting WTP.Research limitations/implicationsWTP is site-specific, and due to limited data for property values and volatility, the study was limited to a comparison study.Practical implicationsVarying building configurations affect pollutant dispersion at different heights. The findings of the study can refine investments based on air quality and natural ventilation requirements.Originality/valueThis paper fulfils a need to determine investment potential and air quality.
The influence mechanism of responsible leadership on sustainable reconfiguring in multi-tier supply chains
Authors: Zhou Ranran , Xu Jianzhong , Zhai Jiaqi , Kong Qingwei 
Published: February 2025

PurposeThis study examines how responsible leadership drives sustainable reconfiguring in multi-tier supply chains, addressing the recognized challenges of implementing sustainable practices in complex, global value chains, particularly in the face of the management challenges posed by the high complexity of multi-tier supply chains.Design/methodology/approachData were collected from 475 Chinese manufacturing firms between December 2023 and June 2024. Structural equation modeling with maximum likelihood estimation was used to assess linear relationships, followed by least-squares linear regression to verify model robustness. Neural network modeling was then applied to explore potential nonlinear relationships among variables.FindingsThe study empirically confirms that responsible leadership was a direct driver of sustainable reconfiguring, and social capital partially mediated the relationship between responsible leadership and sustainable reconfiguring. In addition, it was found that in highly complex supply chains, responsible leadership has a more significant driving effect on sustainable reconfiguring, i.e. supply chain complexity positively moderates the relationship between responsible leadership and sustainable reconfiguring.Originality/valueThis study contributes to the field by uniquely examining responsible leadership as a driver of sustainable supply chain reconfiguration, highlighting its role in resource acquisition through social capital from a resource dependence perspective. Unlike prior studies that treat supply chain complexity primarily as a management obstacle, this research uncovers its role as a “demand driver” in sustainable reconfiguration, offering fresh insights into complexity’s strategic impact. This approach provides a novel framework for understanding the nuanced pathways through which leadership style and situational factors collectively shape sustainable practices in supply chains.