bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental Mixtures Analysis (E-MIX) Workflow and Methods Repository
Authors: Joubert Bonnie R. , Palmer Glenn , Dunson David , Kioumourtzoglou Marianthi-Anna , Coull Brent A. 
Published: December 2024

AbstractHuman exposure to complex, changing, and variably correlated mixtures of environmental chemicals has presented analytical challenges to epidemiologists and human health researchers. There have been a wide variety of recent advances in statistical methods for analyzing mixtures data, with most of these methods having open-source software for implementation. However, there is no one-size-fits-all method for analyzing mixtures data given the considerable heterogeneity in scientific focus and study design. For example, some methods focus on predicting the overall health effect of a mixture and others seek to disentangle main effects and pairwise interactions. Some methods are only appropriate for cross-sectional designs, while other methods can accommodate longitudinally measured exposures or outcomes. This article focuses on greatly simplifying the daunting task of identifying which methods are most suitable for a particular study design, data type, and scientific focus. With this goal in mind, we present an organized workflow for statistical analysis considerations in environmental mixtures data. This systematic strategy builds on epidemiological and statistical principles, considering specific nuances for the mixtures’ context. We also describe an accompanying online methods repository in development to increase awareness of and inform application of existing methods and new methods as they are developed and identify gaps in existing methods warranting further development.
Acquisition of an immunosuppressive microenvironment after CAR-T therapy drives T-cell dysfunction and resistance
Authors: Ponzo Marianna , Drufuca Lorenzo , Buracchi Chiara , Sindoni Marco M. , Nucera Silvia , Bugarin Cristina , Bason Ramona , Rossetti Grazisa , Bonnal Raoul , Meli Cristian , Rambaldi Benedetta , Lussana Federico , Ferrari Silvia , Moretti Alex , Risca Giulia , Pellegrino Christian , Manz Markus G. , Galimberti Stefania , Rambaldi Alessandro , Gaipa Giuseppe , Biondi Andrea , Pagani Massimiliano , Magnani Chiara F. 
Published: December 2024

AbstractChimeric antigen receptor (CAR) T cells targeting CD19 induce durable responses in B-cell acute lymphoblastic leukemia (B-ALL). However, the contribution of the tumor microenvironment to the therapeutic response after CAR-T cell treatment remains incompletely understood. We performed single-cell RNA sequencing and spectral flow cytometry-based analyses of bone marrow-resident immune cells from B-ALL patients before and after CAR T-cell treatment. We observed profound changes in the microenvironment in response to CAR T cell-mediated inflammation, including an increase in myeloid cells. Significant induction of the IFN response, hypoxia, and TGF-β-signaling was associated with expansion of myeloid-derived suppressor cells (MDSCs) and endogenous exhausted CD8+ T cells. PD1 expression in endogenous T cells post-treatment was associated with a lack of durable response in the cohort of patients analyzed. Further, we revealed that HIF1α, VEGF, and TGFBR2 are key players in the intercellular communication between CAR T cells and the immune niche, driving widespread T-cell dysfunction. Infusion of anti-CD19 CAR T cells led to increased accumulation of human MDSCs, exacerbation of a hypoxic environment and T-cell exhaustion in HSPC-humanized mice bearing a human tumor. In conclusion, CAR T-cell-mediated myeloid activation is associated with pathways of immune dysregulation that may antagonize the effects of therapy.Key pointsThe tumor immune context post-treatment affects CAR T-cell fate and endogenous immunity in B-cell acute lymphoblastic leukemia.IFN response, hypoxia, and TGF-β-signaling result in endogenous T-cell exhaustion and compromise CAR T-cell efficacy.
Benchmarking AI Models forIn SilicoGene Perturbation of Cells
Authors: Li Chen , Gao Haoxiang , She Yuli , Bian Haiyang , Chen Qing , Liu Kai , Wei Lei , Zhang Xuegong 
Published: December 2024

AbstractUnderstanding perturbations at the single-cell level is essential for unraveling cellular mechanisms and their implications in health and disease. The growing availability of biological data has driven the development of a variety ofin silicoperturbation methods designed for single-cell analysis, which offer a means to address many inherent limitations of experimental approaches. However, these computational methods are often tailored to specific scenarios and validated on limited datasets and metrics, making their evaluation and comparison challenging. In this work, we introduce a comprehensive benchmarking framework to systematically evaluatein silicoperturbation methods across four key scenarios: predicting effects of unseen perturbations in known cell types, predicting effects of observed perturbations in unseen cell types, zero-shot transfer to bulk RNA-seq of cell lines, and application to real-world biological cases. For each scenario, we curated diverse and abundant datasets, standardizing them into flexible formats to enable efficient analysis. Additionally, we developed multiple metrics tailored to each scenario, facilitating a thorough and comparative evaluation of these methods. Our benchmarking study assessed 10 methods, ranging from linear baselines to advanced machine learning approaches, across these scenarios. While some methods demonstrated surprising efficacy in specific contexts, significant challenges remain, particularly in zero-shot predictions and the modeling of complex biological processes. This work provides a valuable resource for evaluating and improvingin silicoperturbation methods, serving as a foundation for bridging computational predictions with experimental validation and real-world biological applications.
Conserved heavy/light contacts and germline preferences revealed by a large-scale analysis of natively paired human antibody sequences and structural data
Authors: Dudzic Pawel , Chomicz Dawid , Bielska Weronika , Jaszczyszyn Igor , Zieliński Michał , Janusz Bartosz , Wróbel Sonia , Pannérer Marguerite-Marie Le , Philips Andrew , Ponraj Prabakaran , Kumar Sandeep , Krawczyk Konrad 
Published: December 2024

AbstractAntibody next-generation sequencing (NGS) datasets have become crucial to develop computational models addressing this successful class of therapeutics. Although antibodies are composed of both heavy and light chains, most NGS sequencing depositions provide them in unpaired form, reducing their utility. Here we introduce PairedAbNGS, a novel database with paired heavy/light antibody chains. To the best of our knowledge, this is the largest resource for paired natural antibody sequences with 58 bioprojects and over 14 million assembled productive sequences. We make the database accessible athttp://naturalantibody.com/paired-ngsas a valuable tool for biological and machine-learning applications. Using this dataset, we investigated heavy and light chain variable (V) gene pairing preferences and found significant biases beyond gene usage frequencies, possibly due to receptor editing favoring less autoreactive combinations. Analyzing the available antibody structures from the Protein Data Bank, we studied conserved contact residues between heavy and light chains, particularly interactions between the CDR3 region of one chain and the FWR2 region of the opposite chain. Examination of amino acid pairs at key contact sites revealed significant deviations of amino acids distributions compared to random pairings, in the heavy chain’s CDR3 region contacting the opposite chain, indicating specific interactions might be crucial for proper chain pairing. This observation is further reinforced by preferential IGHV-IGLJ and IGLV-IGHJ pairing preferences. We hope that both our resources and the findings would contribute to improving the engineering of biological drugs.
Black flying foxes in Australia harbor novelBorrelialineages adjacent to zoonotic clades
Authors: Verrett Taylor B. , Falvo Caylee A. , Benson Evelyn , Jones-Slobodian Devin N. , Crowley Daniel E. , Dale Adrienne S. , Lunn Tamika J. , Ruiz-Aravena Manuel ,   Bat One Health, McKee Clifton D. , Clark Kerry L. , Peel Alison J. , Plowright Raina K. , Becker Daniel J. 
Published: December 2024

AbstractWe explore the role of Australian black flying foxes (Pteropus alecto) as reservoir hosts of potentially zoonoticBorreliabacteria. Across six sites, 2% of 840 bats were infected with one of two novelBorreliahaplotypes. Phylogenetic reconstruction indicated these infections are distinct from Lyme or relapsing fever clades.
Modes of action and bio-fungicide potential of peptides derived from the bi-domain plant defensin MtDef5
Authors: Kalunke Raviraj M. , Pokhrel Ambika , Tetorya Meenakshi , Nath Vishnu Sukumari , Czymmek Kirk J. , Shah Dilip M. 
Published: December 2024

AbstractMedicago truncatulabi-domain defensin MtDef5 exhibits antifungal activity at sub-micromolar concentrations against some fungal pathogens. It comprises two single-domain defensins, MtDef5A and MtDef5B, connected with a linker APKKVEP. MtDef5B is a more potent antifungal defensin than MtDef5A. We identified amino acid residues important for antifungal activity of MtDef5B and elucidated its modes of action (MoA). MtDef5B inhibited spore germination ofBotrytis cinerea (Bc)at low micromolar concentrations. However, it did not inhibit spore germination ofColletotrichum gloeosporioides (Cg). MtDef5B permeabilized the plasma membrane, induced reactive oxygen species and traveled to the nucleoli in germlings ofBc. Furthermore, a carboxy-terminal MtDef5A-derived GMA5AC peptide was selected for mutagenesis because of its lower cationicity than the corresponding MtDef5B-derived peptide. GMA5AC inhibited spore germination ofBc, but not ofCg. However, GMA5AC_V2, a variant of GMA5AC, inhibited spore germination ofCgand exhibited multi-faceted MoA. Spray-application of GMA5AC_V2 on the leaves of pepper plants demonstrated preventive and curative control of the gray mold disease. Furthermore, when applied topically on tomato fruits pre-inoculated with the pathogenCg, this peptide reduced anthracnose disease symptoms. This study highlights the potential of short chain defensin-derived peptides for management of fungal diseases.HighlightsThe bi-domain MtDef5-derived antifungal peptides exhibit multiple modes of action and confer resistance against the gray mold and anthracnose diseases in pepper plants and tomato fruits, respectively.
Genetic and behavioral analyses suggest that larval and adult stages ofLucilia cuprinaemploy different sensory systems to detect rotten beef
Authors: Wulff Juan P. , Laminack Rachel K. , Scott Maxwell J. 
Published: December 2024

AbstractBackgroundThe blowflyLucilia cuprinais a destructive parasite of sheep that causes flystrike or myiasis. Larvae consume the animal’s living flesh, producing large wounds that can lead to death. Growing resistance to conventional control methods has prompted the analysis of alternative strategies.MethodsAn RNA-Seq analysis was used to identify sensory receptors and other genes relevant to the physiology ofL. cuprinalarvae. Adult females and larvae of the same species carrying a loss-of-function mutation for theL. cuprinaodorant coreceptor gene (LcupOrco) were obtained by gene editing. Their response to fresh and rotten meat at different temperatures was evaluated.ResultsThe RNA-Seq analysis of whole larvae at different stages and third instar head and gut tissues, suggested that odorant (OR), gustatory, ionotropic andpickpocket receptors may not play a central role in theL. cuprinalarval sensory signaling and digestive systems. Rather, ATP-binding cassettes (ABCs) were highly enriched in head and gut RNA, and odorant-binding proteins (OBPs) only in the head. To confirm that ORs are not essential for larval detection of rotten beef, diet-choice assays were performed including larvae and adults homozygous for a null mutation inLcupOrco. While the attraction of adult females to rotten beef was fully disrupted,LcupOrcomutant larvae showed no change in diet preference.ConclusionsThe expression pattern of the ABC and OBP gene families suggests a central role in the sensory system of theL. cuprinalarva for these receptors. Behavioral assays showed that ORs are essential for the adult female response to rotten beef, but not for larval behavior. These findings are consistent with high levels of expression ofLcupOrcoin the adult female antenna but very low expression in larvae.
Trans-regulatory loci shape natural variation of gene expression plasticity in Arabidopsis
Authors: Lensink Mariele , Monroe Grey , Kliebenstein Dan 
Published: December 2024

AbstractOrganisms regulate gene expression in response to environmental cues, a process known as plasticity, to adjust to changing environments. Research into natural variation and the evolution of plasticity frequently studiescis-regulatory elements with theory suggesting they are more important evolutionarily thantrans-regulatory elements. Genome-wide association studies have supported this idea, observing a predominance ofcis-loci affecting plasticity. However, studies in structured populations provide a contrasting image, raising questions about the genetic architecture of natural variation in plasticity. To circumvent potential statistical difficulties present in genome-wide association studies, we mapped loci underlying transcriptomic plasticity in response to salicylic acid using recombinant inbred lines generated from two randomArabidopsis thalianaaccessions. We detected extensive transgressive segregation in the salicylic acid response, suggesting that plasticity to salicylate in Arabidopsis is polygenic. Most loci (>75%) underlying this variation act intrans, especially for loci influencing plasticity.Trans-acting loci were enriched in genome hotspots, with predominantly small effect sizes distributed across many genes. This could potentially explain their under-discovery in genome-wide association studies. This work reveals a potentially important role fortrans-acting loci in plastic expression responses, with implications for understanding plant adaptation to different environments.
Protocol for assessing DNA damage levelsin vivoin rodent testicular germ cells in the Alkaline Comet Assay
Authors: Olsen Ann-Karin , Ma Xiaoxiong , Zheng Congying , Dahl Hildegunn , Dirven Yvette , Boisen Anne-Mette Zenner , Sharma Anoop , Eide Dag. M. , Brunborg Gunnar 
Published: December 2024

SummaryFew protocols are available for retrieving male germ cell-specific information on DNA damage dynamics or assessing the potential harmful effects of environmental contaminants, drugs, or lifestyle factors related to genotoxicity. Here, we present a protocol for evaluating testicular germ cell genotoxicity using a modified version of the alkaline comet assay in rodent testicular germ cells. The protocol includes experimental design, preparation of testicular cell suspensions, comet analysis, germ cell-specific scoring, and data curation methods to collect information on testicular male germ cells, specifically spermatids and spermatocytes.For complete details on the use of this protocol please refer to Olsen et al., in preparationGraphical abstractHighlightsDNA damage levels can be specifically measured in testicular germ cells using the developed revised version of the alkaline comet assay1C spermatids as well as 4C primary spermatocytes can be assessedBoth manual- and modeling-based approaches were developed that facilitate user-friendly protocols to select 1C spermatid comets.This protocol expands the limited methodologies available to study germ cell DNA damage dynamics
Chemical Proteomics Identifies Protein Ligands for Monoacylglycerol Lipids
Authors: Shanbhag Karthik , Mhetre Amol B. , Saharan Ojal , Devarajan Archit , Rai Anisha , Madhusudhan M. S. , Chakrapani Harinath , Kamat Siddhesh S. 
Published: December 2024

ABSTRACTSignaling lipids are hormone-like small biomolecules that regulate many critical facets of physiology in mammals, including humans. Given their biomedical importance, the past few decades have seen a tremendous increase in our mechanistic understanding of the physiological processes regulated by a handful of such signaling lipids (e.g.: endocannabinoids, lysophospholipids, prostaglandins). However, a significant number of signaling lipid classes still remain poorly characterized, despite their direct associations to human pathophysiology and disease. Over the past decade, the advent of chemical proteomics technologies coupled with the development of multifunctional lipid probes has rapidly expanded our knowledge in terms of the protein ligands and biological pathways that the different signaling lipids interact with and modulate respectively. While the signaling pathways regulated by the endocannabinoid 2-arachidonoyl-glycerol in mammals are extensively characterized, the same cannot be said for the other members of the monoacylglycerol (MAG) family of signaling lipids. To understand this, here, we report the synthesis of a bifunctional MAG probe, containing a photoreactive group and a biorthogonal handle. Using established chemical proteomics approaches, we profile this bifunctional MAG probe in mouse brain and mammalian cell lysates, and leveraging probe competition experiments identify hitherto unknown protein ligands for MAG lipids. Finally, we biochemically validate the neuronal calcium sensor Hippocalcin as a putative MAG protein ligand, and show for the first time, that MAG may have a role to play in calcium sensing and downstream signaling in the mammalian brain.
Multi-Omic Atlas reveals cytotoxic phenotype and ROS-linked metabolic quiescence as key features of CTL-resistant HIV-infected CD4+T-cells
Authors: Herrera Alberto , Leyre Louise , Weiler Jared , Linden Noemi Luise , Huynh Tan Thinh , Wang Feng , Kovacs Colin , Caskey Marina , Zumbo Paul , Amiama Maider Astorkia , Terry Sandra , Ho Ya-Chi , Betel Doron , Jones R. Brad 
Published: December 2024

SummaryCytotoxic T-lymphocytes (CTL) exert sustained pressure on reservoirs of HIV-infected cells that persist through years of antiretroviral therapy (ART). This selects for latently infected cells, but also potentially for cells that express HIV but possess intrinsic CTL resistance. We demonstrate that such resistance exists in HIV-infected CD4+T-cells that survive rigorous CTL attack and map CTL susceptibility to cell identities and states defined by single-cell multi-omics and functional metabolic profiling. Cytotoxic CD4+T-cells were prominently overrepresented amongst survivors, as were cells with quiescent metabolic profiles and low levels of reactive oxygen species (ROS) production. The induction of ROS production by treatment with deferoxamine sensitized these cells to CTL-mediated elimination. Reservoir-harboring cells from clinical samples share the above transcriptional features, being enriched for quiescent states. Our results provide an atlas for elucidating features of CTL resistance in HIV reservoirs, and identify oxidative stress as a therapeutic target to facilitate reservoir elimination.
Structural Insights into the Activation and Inhibition of the ADAM17-iRhom2 Complex
Authors: Maciag Joseph J. , Slone Conner , Alnajjar Hala F. , Rich Maria F. , Guion Bryce , Blobel Carl P. , Seegar Tom C.M. 
Published: December 2024

ABSTRACTThe endopeptidase activity of ADAM (a disintegrin and metalloprotease) -17, the primary processor of several EGFR ligands and tumor necrosis factor-alpha (TNF-α), is essential for proper embryonic development and immune regulation. Dysregulated ADAM17 activity is prevalent in a wide array of human diseases, including cancer, chronic inflammation, and SARS-CoV-2 viral progression. Initially translated as an inactive enzyme zymogen, ADAM17 maturation and enzymatic function are tightly regulated by its obligate binding partners, the inactive rhomboid proteins (iRhom) -1 and -2. Here, we present the cryo-EM structure of the ADAM17 zymogen bound to iRhom2. Our findings elucidate the interactions within the ADAM17-iRhom2 complex, the inhibitory mechanisms of the therapeutic MEDI3622 antibody and ADAM17 prodomain, and the previously unknown role of a membrane-proximal cytoplasmic re-entry loop of iRhom2 involved in the mechanism of activation. Importantly, we perform cellular assays to validate our structural findings and provide further insights into the functional implications of these interactions, paving the way for developing therapeutic strategies targeting this biomedically critical enzyme complex.
Circumferential actomyosin bundles drive endothelial cell deformations to constrict blood vessels
Authors: Chen Yan , Taberner Nuria , da Silva Jason , Kondrychyn Igor , Aswani Nitish , Chen Guihua , Okada Yasushi , Lagendijk Anne Karine , Okuda Satoru , Phng Li-Kun 
Published: December 2024

AbstractFollowing the formation of new blood vessels, vascular remodelling ensues to generate a hierarchical network of vascular tubes with optimal connections and diameters for efficient blood perfusion of tissues. How transitions in endothelial cell (EC) number and shape are coordinated to define vessel diameter during development remains an open question. In this study, we discovered EC deformations, rearrangements and transient formation of self-seam junctions as key mechanisms that explain a negative relationship between cell number and vessel diameter. High-resolution analysis of actin cytoskeleton organization disclosed the generation of tension-bearing, circumferential actomyosin bundles in the endothelial cortex that drive EC deformation and vessel constriction. Importantly, the loss of circumferential actin bundles inkrit1/ccm1-deficient ECs causes cell enlargement and impaired vessel constriction that culminate in dilated vessels, characteristic of cerebral cavernous malformation. Our multiscale study therefore underpins circumferential actomyosin-driven EC deformations in controlling vessel size and in the prevention of vascular malformations.
Endocytic Patch Dynamics are Differentially Regulated at Distinct Cell Sites in Fission Yeast
Authors: Campbell Bethany F. , Patel Uma J. , Williams Ashlei R. , Das Maitreyi E. 
Published: December 2024

ABSTRACTEndocytosis promotes polarity and growth in eukaryotes. InSchizosaccharomyces pombefission yeast, endocytosis occurs at the polarized cell ends and division site and at the non-polarized cell sides. Our characterization of endocytic actin patches show that they are differentially regulated. The patches at the cell ends and division site internalize successfully while those at the sides are weak and erratic. The major regulator of cell polarity, Cdc42, and its target Pak1 kinase only localize to the cell ends and division site. We find that these proteins regulate assembly and internalization of patches at these sites but not at the cell sides. Moreover, Cdc42 specifically activated by the GEF Gef1 promotes proper patch dynamics. Endocytosis requires phosphorylation of the Type I Myosin Myo1 by the Pak1 kinase. Myo1 localizes to the cell ends, division site, and the cell sides. We find that unlike Cdc42 and Pak1, Myo1 also promotes patch assembly at the cell sides. Our data indicate that while Myo1 can globally promote branched actin assembly, successful endocytic patch dynamics and internalization at polarized sites require Cdc42 and Pak1 kinase.SUMMARY STATEMENTEndocytic patch dynamics are differentially regulated at distinct sites such as the cell ends, division site and the cell sides by Cdc42 and its downstream targets Pak1 kinase and the Type 1 myosin.