bluuebunny/crossref_metadata_2025_split huggingface dataset:
Testing for the genomic footprint of conflict between life stages in an angiosperm and a moss species
Authors: Yuan Meng , Kollar Leslie M. , Sacchi Bianca M. , Carey Sarah B. , Choudhury Baharul I. , Jones Teresa , Grimwood Jane , Barrett Spencer C. H. , McDaniel Stuart F. , Wright Stephen I. , Stinchcombe John R. 
Published: October 2024

AbstractThe maintenance of genetic variation by balancing selection is of considerable interest to evolutionary biologists. An important but understudied potential driver of balancing selection is antagonistic pleiotropy between diploid and haploid stages of the plant life cycle. Despite sharing a common genome, sporophytes (2n) and gametophytes (n) may undergo differential or even opposing selection. Theoretical work suggests the antagonistic pleiotropy between life stages can generate balancing selection and maintain genetic variation. Despite the potential for far-reaching consequences of gametophytic selection, empirical tests of its pleiotropic effects (neutral, synergistic, or antagonistic) on sporophytes are generally lacking. Here, we examined the population genomic signals of selection across life stages in the angiospermRumex hastatulusand the mossCeratodon purpureus. We compared gene expression among life stages and between sexes, combined with neutral diversity statistics and the analysis of the distribution of fitness effects. In contrast to what would be predicted under balancing selection due to antagonistic pleiotropy, we found that unbiased genes between life stages are under stronger purifying selection, likely explained by a predominance of synergistic pleiotropy between life stages and strong purifying selection on broadly expressed genes. In addition, we found that 30% of candidate genes under balancing selection inR. hastatulusare located within inversion polymorphisms. Our findings provide novel insights into the genome-wide characteristics and consequences of plant gametophytic selection.SignificanceThe genome-wide importance of balancing selection has been a key question in evolutionary biology. Despite theoretical support for the potential of balancing selection generated by antagonistic pleiotropy between plant life stages, no empirical studies have investigated this problem. Our results revealed genome-wide patterns more consistent with synergistic pleiotropy, with gametophyte-biased genes mostly likely to be under relaxed purifying selection in both angiosperm and moss species we investigated. In addition, our study suggests gene expression level and breadth has a greater effect on selection efficacy than differences between ploidy levels in different life stages.
Ixochymostatin, a trypsin inhibitor-like (TIL) protein fromIxodes scapularis, inhibits chymase and impairs vascular permeability
Authors: Martins Larissa Almeida , Berger Markus , Kotál Jan , Lu Stephen , Sousa-Paula Lucas C. , Smith Brian J. , Zhang Yixiang , Andersen John F. , Tirloni Lucas 
Published: October 2024

AbstractTicks, as pool feeders, obtain a blood meal by lacerating small blood vessels and ingesting the blood that flows to the feeding site, which triggers various host-derived responses. However, ticks face the challenge of wound healing, a process involving hemostasis, inflammation, cell proliferation and migration, and remodeling, hindering blood acquisition. To overcome these obstacles, tick salivary glands produce a diverse array of bioactive molecules. Here, we characterize ixochymostatin, anIxodes scapularisprotein belonging to the trypsin inhibitor-like (TIL) family. It is expressed in multiple developmental stages and in tick salivary glands and acts as a slow and tight-binding inhibitor of chymase, cathepsin G, and chymotrypsin. Predictions for the tertiary structure complex between ixochymostatin and chymase suggest a direct interaction between the inhibitor’s reactive site loop and protease active sites.In vitro, ixochymostatin protects the endothelial cell barrier against chymase degrading action, decreasing cell permeability.In vivo, it reduces vascular permeability induced by chymase and compound 48/80, a mast cell degranulator agonist, in a mouse model. Additionally, ixochymostatin inhibits the chymase-dependent generation of vasoconstrictor peptides. Antibodies against ixochymostatin neutralize its inhibitory properties, with epitope mapping identifying potential neutralization regions. Ixochymostatin emerges as a novel tick protein modulating host responses against tick feeding, facilitating blood acquisition.HighlightsIxochymostatin is a newly described trypsin inhibitor-like (TIL) protein fromIxodes scapularis.Ixochymostatin inhibits chymase and reduces vascular permeability.Ixochymostatin inhibits chymase-dependent generation of vasoconstrictive peptides.Antibodies generated against ixochymostatin neutralize its inhibitory functions.Potential epitopes responsible for anti-ixochymostatin neutralization were mapped.
Intrinsic molecular identifiers enable robust molecular counting in single-cell sequencing
Authors: Fontanez Kristina M. , Agam Yigal , Bevans Sophia , May-Zhang Aaron A. , Hayford Corey , Xue Yi , Ishibashi Jacob S. A. , Komuhendo Rachael , Yoder Lucas , Hettige Pabodha , Rickner Hannah D. , Zhang Jesse Q. , Osman Ahmad , D’Amato Chris , Smithers Trinity , Calkins Sarah , Rahman Muntasir , Mutafopulos Kiryakos S. , Kiani Sepehr , Meltzer Robert H. 
Published: October 2024

ABSTRACTParticle-templated instant partition sequencing (PIPseq), is an emerging approach for massively scalable single-cell gene expression studies that does not require complex instrumentation or expensive consumables. We present PIPseqTMV, a novel implementation of the PIPseq workflow with significant improvements in assay performance and sensitivity compared to prior methods. Among the innovations driving the improved performance in PIPseq V is a new approach for transcript counting using Intrinsic Molecular Identifiers (IMIs) from the captured transcript sequence, eliminating the need for traditional Unique Molecular Identifiers (UMIs). IMIs are the starting positions for molecules generated by random fragmentation after limited cycle PCR, which can be used to uniquely identify individual transcript copies of genes expressed within individual cells. To correct for experimental variation in IMI generation, we have developed a dynamic correction strategy that can adapt to different sample cell input, transcript expression, and sequencing depth without the need for external benchmarking or controls. Our results demonstrate that PIPseq V with IMI-based analysis provides biological information comparable to established UMI-based approaches while avoiding UMI-associated biases. Dynamic correction offers a robust and data-driven analysis strategy for scRNAseq.
A combination of expansion microscopy and proximity labelling reveals conserved and unique asymmetric functional hubs at the trypanosome nuclear pore
Authors: Gabiatti Bernardo Papini , Odenwald Johanna , Braune Silke , Krüger Timothy , Zoltner Martin , Kramer Susanne 
Published: October 2024

ABSTRACTNuclear export of mRNAs requires loading the mRNP to the transporter Mex67/Mtr2 in the nucleoplasm, controlled access to the pore by the basket-localized TREX2 complex and mRNA release at the cytoplasmic site by the DEAD-box RNA helicase Dbp5. Asymmetric localisation of nucleoporins (NUPs) and transport components as well as the ATP dependency of Dbp5 ensure unidirectionality of transport. Trypanosomes possess homologues of the mRNA transporter Mex67/Mtr2, but not of TREX2 or Dbp5. Instead, nuclear export is likely fuelled by the GTP/GDP gradient created by the Ran GTPase. However, it remains unclear, how directionality is achieved since the current model of the trypanosomatid pore is mostly symmetric.We have revisited the architecture of the trypanosome nuclear pore complex using a novel combination of expansion microscopy, proximity labelling and streptavidin imaging. We could confidently assign the NUP76 complex, a known Mex67 interaction platform, to the cytoplasmic site of the pore. The resulting availability of reference proteins for basket, inner ring and cytoplasmic site allowed mapping of all 75 trypanosome proteins with known nuclear pore localisation to a sub-region of the pore based on mass spectrometry data from proximity labelling. This approach defined many further asymmetrically localised nuclear pore components. At the nuclear site, we identified several trypanosome-unique proteins, for instance the FG-NUPs NUP64/NUP98, but also proteins with structural homology to TREX-2 components. We mapped the components of the Ran-based nuclear export system and confirm the absence of a Dbp5 homologue. Lastly, we demonstrate, by deploying an auxin degron system, that NUP76 holds an essential role in mRNA export consistent with a functional orthology to NUP82/88.Altogether, the combination of proximity labelling with expansion microscopy revealed an asymmetric architecture of the trypanosome nuclear pore supporting inherent roles fort directed transport. Our approach delivered novel nuclear pore associated components inclusive positional information, which can now be interrogated for functional roles to explore trypanosome specific adaptions of the nuclear basket, export control and mRNP remodelling.
The FunCoup Cytoscape App: multi-species network analysis and visualization
Authors: Buzzao Davide , Steininger Lukas , Guala Dimitri , Sonnhammer Erik L.L. 
Published: October 2024

ABSTRACTSummaryFunctional association networks, such as FunCoup, are crucial for analyzing complex gene interactions. To facilitate the analysis and visualization of such genome-wide networks, there is a need for seamless integration with powerful network analysis tools like Cytoscape.The FunCoup Cytoscape App integrates the FunCoup web service API with Cytoscape, allowing users to visualize and analyze gene interaction networks for 640 species. Users can input gene identifiers and customize search parameters, employing various network expansion algorithms like group or independent gene search, MaxLink, and TOPAS. The app maintains consistent visualizations with the FunCoup website, providing detailed node and link information, including tissue and pathway gene annotations. The integration with Cytoscape plugins, such as ClusterMaker2, enhances the analytical capabilities of FunCoup, as exemplified by the identification of theMyasthenia gravisdisease module along with potential new therapeutic targets.Availability and implementationThe FunCoup Cytoscape App is developed using the Java OSGi framework, with UI components implemented in Java Swing and build support from Maven. The App is available as a JAR file athttps://bitbucket.org/sonnhammergroup/funcoup_cytoscape/repo, and can be downloaded from the Cytoscape App storehttps://apps.cytoscape.org/.Contacterik.sonnhammer@scilifelab.se
Genetically encoded biosensor for fluorescence lifetime imaging of PTEN dynamics in the intact brain
Authors: Kagan Tomer , Gabay Matan , Levi Yossi , Eid Sharbel , Malchenko Nikol , Maman Maya , Nitzan Anat , Ravotto Luca , Zaidel-Bar Ronen , Gal Maayan , Laviv Tal 
Published: October 2024

AbstractThe phosphatase and tensin homolog (PTEN) is a vital signaling protein which maintains an inhibitory brake that is critical for cellular metabolism, proliferation, and growth. The importance of PTEN signaling is evident from the broad spectrum of human pathologies associated with its loss of function. Moreover, loss or gain of PTEN function in animal models leads to aberrant cellular morphology, function, and metabolic regulation. However, despite the important role of PTEN signaling, there is currently no method to dynamically monitor its activity with cellular specificity within intact biological systems. Here, we describe the development of a novel PTEN biosensor, optimized for two-photon fluorescence lifetime imaging microscopy (2pFLIM). This biosensor is designed to measure PTEN activity within intact cells, tissues, and organisms. Our approach is based on monitoring FRET-dependent changes in PTEN conformation, which serves as a proxy for the activity state in living cells. We identify a point mutation that allow us to express this biosensor with minimal interference to endogenous PTEN signaling and cellular function. We demonstrate the utility of imaging PTEN signaling in cell lines, developingC. elegans,and in the living mouse brain. To complement this approach, we developed a red-shifted PTEN sensor variant that permits simultaneous imaging with GFP-based sensors. Finally, we use in vivo PTEN imaging in the mouse brain to identify cell-type specific dynamics of PTEN activity in excitatory and inhibitory cortical cells. In summary, our approach enables dynamic imaging of PTEN activity in vivo with unprecedented spatial and temporal resolution.
Evolutionary history with chronic malnutrition enhances pathogen susceptibility at older ages
Authors: Sarkar Saubhik , Shit Biswajit , Bose Joy , De Souvik , Kawecki Tadeusz J. , Khan Imroze 
Published: October 2024

AbstractJuvenile malnutrition is a global public health concern that negatively impacts the development and maturation of the immune system, leading to increased susceptibility to infectious diseases. Such adverse effects on immunity might increase with ageing, worsening disease conditions later in life. Furthermore, malnutrition may persist across generations, imposing strong natural selection to survive the nutrient shortage. However, it is unclear how the evolutionary history of ancestral generations with chronic malnutrition could influence pathogen resistance and infection susceptibility, as well as their age-specific changes in extant generations. To address this, we usedDrosophila melanogasterpopulations adapted against chronic juvenile malnutrition and exposed them to a bacterial pathogen,Providencia rettgeri, during their early and late adulthood. Surprisingly, we observed that in populations adapted to chronic malnutrition, young flies survived infection better by tolerating the infection, while control flies displayed higher infection susceptibility despite carrying a similar pathogen load. However, this pattern in post-infection survival is reversed with ageing. There was no change in pathogen resistance, but evolved flies succumbed more to infection than control flies regardless of the input infection doses. Our study thus revealed new evolutionary insights into the development of contrasting early vs late-life immune strategies and age-specific vulnerabilities to infection as a function of early-life malnutrition.
Chemically defined lipid diets reveal the versatility of lipidome remodeling in genomically minimal cells
Authors: Safronova Nataliya , Junghans Lisa , Oertel Jana , Fahmy Karim , Saenz James P. 
Published: October 2024

AbstractAll cells are encapsulated in a lipid membrane that provides a responsive interface between life and its environment. Although simple membranes can be built from a single type of lipid, cellular membranes contain 10s to 100s of unique lipid species. Deciphering the significance of lipidome complexity is a central challenge in understanding the design principles of living membranes. While functions of individual lipids have been extensively studied, understanding how lipidomes collectively contribute to membrane function and cell phenotypes is experimentally challenging in most organisms. To address this challenge, we turned to the simple pathogenic organismMycoplasma mycoidesand its genomically derived “Minimal Cell” JCVI-syn3B, to establish a living minimal membrane model system in which lipidome complexity can be experimentally manipulated. By complexing lipids with cyclodextrins, we introduce a chemically defined approach to deliver lipid ‘diets’ with different chemistries to cells, resulting in cellular lipidomes with as few as seven to nearly 30 lipids species. We explored how lipidome size and composition influences cell growth, osmotic sensitivity, and membrane adaptability to changes in growth temperature. Our findings indicate that lipidome composition dictates membrane adaptation to temperature change. Moreover, we show that lipidome diversity enhances cellular robustness to hypoosmotic shock. We further show that impaired acyl chain remodeling in the minimal cell is associated with impaired membrane temperature adaptation. Finally, we demonstrate as a proof of principle, how cells with tuneable lipidomes can be used as experimental chassis for screening membrane active antimicrobial peptides. Our study introduces an experimental resource and foundation for deciphering the role of lipidome complexity in membrane function and cellular fitness.
An iterative design approach to development of an ex-vivo normothermic multivisceral perfusion platform
Authors: van Leeuwen L. Leonie , Holzner Matthew L. , McKenney Ceilidh , Todd Rachel , Frost Jamie K. , Gudibendi S. , Kim-Schluger Leona , Schiano Thomas , Florman Sander , Akhtar M. Zeeshan 
Published: October 2024

AbstractChallenges in normothermic machine perfusion (NMP) remain, particularly concerning the duration for which individual organs can be safely preserved. We hypothesize that optimal preservation can be achieved by perfusing organs together in a multivisceral block. Therefore, our aim was to establish a platform forex vivomultivisceral organ perfusion.Multivisceral grafts containing the liver, kidneys, pancreas, spleen and intestine were obtained from Yorkshire pigs. Three generation (gen) setups were tested during the iterative design process, and minor changes were made throughout. Gen1 (n=4) used a custom-designed single perfusion circuit. Gen2 (n=3) employed a dual perfusion circuit. Gen3 (n=4) featured a single perfusion circuit with an optimized basin and reservoir. Grafts underwent NMP using an autologous blood-based perfusate, while hemostatic parameters and function were assessed.With each iteration, aortic flow improved, resistance decreased, urine output increased, oxygen consumption rose, perfusate lactate levels dropped, and pH stability improved. Cellular injury trended lower in Gen3. Histological evaluation demonstrated minimal differences in Gen2 and 3.We demonstrate the feasibility of abdominal multivisceral NMP for up to 8 hours. Adequate arterial flow, stable perfusate pH, and high oxygen consumption in setup 3 indicate organ viability. Multivisceral perfusion may serve as a platform for long-term NMP.
Pool PaRTI: A PageRank-based Pooling Method for Robust Protein Sequence Representation in Deep Learning
Authors: Tartici Alp , Nayar Gowri , Altman Russ B 
Published: October 2024

AbstractMotivationProtein language models generate token-level embeddings for each residue, necessitating a method to pool these into a single vector representation of the entire protein. Traditional pooling methods often result in substantial information loss, impacting downstream task performance. We aim to develop a task-agnostic pooling method that preserves more information from token embeddings while offering biological interpretability.ResultsWe introduce Pool PaRTI, a novel pooling method that leverages internal transformer attention matrices and PageRank to assign token importance weights. Pool PaRTI demonstrates statistically significant performance improvements across three diverse protein machine learning tasks, outperforming traditional pooling methods. It enhances accuracy, AUPRC, and MCC while offering interpretability by identifying biologically relevant regions without explicit structural training. Our approach is generalizable to encoder-containing protein language models.Availability and ImplementationPool PaRTI is implemented in Python with PyTorch and is available athttps://github.com/Helix-Research-Lab/Pool_PaRTI.git
Insights into the role of phosphorylation on microtubule crosslinking by PRC1
Authors: Tai Ellinor , Henglein Austin , Alfieri Angus , Saxena Gauri , Forth Scott 
Published: October 2024

AbstractThe mitotic spindle is composed of distinct networks of microtubules, including interpolar bundles that can bridge sister kinetochore fibers and bundles that organize the spindle midzone in anaphase. The crosslinking protein PRC1 can mediate such interactions between antiparallel microtubules. PRC1 is a substrate of mitotic kinases including CDK/cyclin-B, suggesting that it can be phosphorylated in metaphase and dephosphorylated in anaphase. How these biochemical changes to specific residues regulate its function and ability to organize bundles is not known. Here, we perform biophysical analyses on microtubule networks crosslinked by two PRC1 constructs, one a wild-type reflecting a dephosphorylated state, and one phosphomimetic construct with two threonine to glutamic acid substitutions near PRC1’s microtubule binding domain. We find that the wild-type construct builds longer and larger bundles that form more rapidly and are much less resistant to mechanical disruption than the phosphomimetic PRC1. Interestingly, microtubule pairs organized by both constructs behave similarly within the same assays. Our results suggest that phosphorylation of PRC1 in metaphase would tune the protein to stabilize smaller and more flexible bundles, while removal of these PTMs in anaphase would favor the assembly of larger more mechanically robust bundles to resist chromosome and pole separation forces at the spindle midzone.
Gum Arabic (Acacia senegal) enhances reproduction and modulates the microbiota-gut-brain axis of zebrafish in a sex-specific and dosage-dependent manner
Authors: Abi Assaf Justin , de Coriolis Jean-Charles , Godden Alice May , Redhead Eve , Bartram Jamie , Cohen-Krais Jayme , Silova Karina , Crighton Zoe , Le Gall Gwenaelle , Sami Saber , Khalid Sami Ahmed , Immler Simone 
Published: October 2024

AbstractDietary fibres (DFs) constitute a wide range of heterogeneous compounds that resist digestion and have beneficial effects on general health. Gum Arabic (GA) is a tree exudate consisting of 90% arabinogalactan, a polymer of arabinose and galactose sugars with prebiotic properties. As a dietary fibre, GA improves renal function, metabolism, and immune response in humans and animals. However, the underlying mechanisms leading to these health benefits are poorly understood. We supplemented female and male zebrafish (Danio rerio) with two concentrations of GA (6% and 60%) for two weeks. We assessed the effects of GA supplementation on the gut microbiome composition, intestinal and brain metabolic profiles, reproductive fitness, and brain gene expression. We found that GA supplementation resulted in changes to the gut microbiome with a relative increase in Fusobacteria and a relative decrease in Proteobacteria where the beneficial genusCetobacteriumwas significantly more abundant after supplementation. GA supplementation increased acetate levels, particularly in the brain, causing a decreased expression ofcart1in the brain of female zebrafish. While GA supplementation increased overall activity in male and female fish, reproductive fitness was negatively affected by GA supplementation in females. Our results suggest that while GA supplementation may have positive effects on metabolic rate and overall activity, it may come at a trade-off with reproductive fitness.Significance StatementDietary fibres, found in plant-based food sources, can improve health. They include natural gums like gum Arabic, a highly sought-after food additive used as a homogeniser. Despite our better understanding of nutrition, a fibre gap is still prevalent in the Western world with efforts being made to incorporate new sources to close this gap and boost well-being. Here, we showed that when gum Arabic was supplemented into the zebrafish diet, it had a beneficial modulatory effect on the microbiota-gut-brain axis and reproductive fitness. Our findings support the benefits of dietary fibres but also link their impact to sexual dimorphism and dosage. This has implications for developing nutrition guidelines for both animals and humans.