{"id":3087,"date":"2023-01-17T11:53:53","date_gmt":"2023-01-17T17:53:53","guid":{"rendered":"https:\/\/kermitmurray.com\/msblog\/?page_id=3087"},"modified":"2023-01-17T20:57:06","modified_gmt":"2023-01-18T02:57:06","slug":"biorxiv","status":"publish","type":"page","link":"https:\/\/kermitmurray.com\/msblog\/links\/journal-feeds\/biochemistry-journal-feeds\/biorxiv\/","title":{"rendered":"bioRxiv"},"content":{"rendered":"\n<div class=\"wp-block-caxton-grid relative\"><div class=\"absolute absolute--fill\"><div class=\"absolute absolute--fill cover bg-center\" style=\"background-color:;background-image:linear-gradient( );\"><\/div><div class=\"absolute absolute--fill\" style=\"background-color:;background-image:linear-gradient( );opacity:1;\"><\/div><\/div><div class=\"relative caxton-columns caxton-grid-block\" style=\"padding-top:0;padding-left:0;padding-bottom:0;padding-right:0;grid-template-columns:repeat(12, 1fr)\" data-tablet-css=\"padding-left:em;padding-right:em;\" data-mobile-css=\"padding-left:em;padding-right:em;\">\n<div class=\"wp-block-caxton-section relative\" style=\"grid-area:span 1\/span 8\"><div class=\"absolute absolute--fill\"><div class=\"absolute absolute--fill cover bg-center\" style=\"background-color:;background-image:linear-gradient( );\"><\/div><div class=\"absolute absolute--fill\" style=\"background-color:;background-image:linear-gradient( );opacity:1;\"><\/div><\/div><div class=\"relative caxton-section-block\" style=\"padding-top:5px;padding-left:5px;padding-bottom:5px;padding-right:5px\" data-mobile-css=\"padding-left:1em;padding-right:1em;\" data-tablet-css=\"padding-left:1em;padding-right:1em;\">\n<p><strong><a href=\"https:\/\/www.biorxiv.org\/alertsrss\" target=\"_blank\" rel=\"noreferrer noopener\">Journal Home<\/a><\/strong><\/p>\n<\/div><\/div>\n\n\n\n<div class=\"wp-block-caxton-section relative\" style=\"grid-area:span 1\/span 4\"><div class=\"absolute absolute--fill\"><div class=\"absolute absolute--fill cover bg-center\" style=\"background-color:;background-image:linear-gradient( );\"><\/div><div class=\"absolute absolute--fill\" style=\"background-color:;background-image:linear-gradient( );opacity:1;\"><\/div><\/div><div class=\"relative caxton-section-block\" style=\"padding-top:5px;padding-left:5px;padding-bottom:5px;padding-right:5px\" data-mobile-css=\"padding-left:1em;padding-right:1em;\" data-tablet-css=\"padding-left:1em;padding-right:1em;\">\n<p><strong><a href=\"http:\/\/connect.biorxiv.org\/biorxiv_xml.php?subject=all\" target=\"_blank\" rel=\"noreferrer noopener\">RSS<\/a><\/strong><\/p>\n<\/div><\/div>\n<\/div><\/div>\n\n\n<ul class=\"su-subpages\"><li class=\"page_item page-item-3099\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/journal-feeds\/biochemistry-journal-feeds\/biorxiv\/biorxiv-biochemistry\/\">BioRxiv Biochemistry<\/a><\/li>\n<li class=\"page_item page-item-3112\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/journal-feeds\/biochemistry-journal-feeds\/biorxiv\/biorxiv-bioinformatics\/\">BioRxiv Bioinformatics<\/a><\/li>\n<li class=\"page_item page-item-3132\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/journal-feeds\/biochemistry-journal-feeds\/biorxiv\/biorxiv-biophysics\/\">BioRxiv Biophysics<\/a><\/li>\n<li class=\"page_item page-item-3188\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/journal-feeds\/biochemistry-journal-feeds\/biorxiv\/biorxiv-cancer-biology\/\">BioRxiv Cancer Biology<\/a><\/li>\n<li class=\"page_item page-item-3190\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/journal-feeds\/biochemistry-journal-feeds\/biorxiv\/biorxiv-pharmacology-and-toxicology\/\">BioRxiv Pharmacology and Toxicology<\/a><\/li>\n<li class=\"page_item page-item-3114\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/journal-feeds\/biochemistry-journal-feeds\/biorxiv\/biorxiv-systems-biology\/\">BioRxiv Systems Biology<\/a><\/li>\n<li class=\"page_item page-item-3193\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/journal-feeds\/biochemistry-journal-feeds\/biorxiv\/biorxiv-zoology\/\">BioRxiv Zoology<\/a><\/li>\n<\/ul>\n\n\n<ul class=\"has-dates has-authors has-excerpts wp-block-rss\"><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.biorxiv.org\/content\/10.64898\/2026.06.21.733640v1?rss=1'>MALDI Tandem Mass Spectrometry for Colony-Based Dereplication of Natural Products<\/a><\/div><time datetime=\"2026-06-22T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">June 22, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Shepherd, R. A., Gad, L. Y., Strobel, M., Luu, G. T., Feng, J., De Silva, C., McKinnie, S. M., Wang, M., Sanchez, L. M.<\/span><div class=\"wp-block-rss__item-excerpt\">Microbial libraries remain an important resource for natural product discovery; however, constructing taxonomically and chemically diverse collections remains a challenge. Advances in dereplication strategies, including molecular networking, have reduced the rediscovery of known bioactive molecules and facilitated the identification of novel chemical scaffolds, but these approaches are typically applied after library construction or to existing repositories. Furthermore, many dereplication workflows require scaled fermentation and extraction, increasing the time needed to assess a microbe&#039;s metabolite profile. Here, we integrate matrix-assisted laser [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.biorxiv.org\/content\/10.64898\/2026.06.21.733238v1?rss=1'>Single-molecule insights into DNA gyrase in live bacteria<\/a><\/div><time datetime=\"2026-06-22T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">June 22, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Syeda, A. H., Leek, V. A., Maxwell, A., Leake, M. C.<\/span><div class=\"wp-block-rss__item-excerpt\">Molecular motors travelling along DNA introduce positive supercoils that present as barriers to replication leading to genome instability. To counter these, bacterial cells express DNA gyrase, a topoisomerase that introduces negative supercoils. While much is known about DNA gyrase from genetic and in vitro biochemical studies, the spatiotemporal dynamics of this enzyme remain a mystery. Only recently have we been able to observe the in vivo spatiotemporal dynamics down to single molecule level using advanced super-resolution microscopy techniques. We used [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.biorxiv.org\/content\/10.64898\/2026.06.17.732903v1?rss=1'>A novel texture backward masking method to locate critical recurrent processes in human vision<\/a><\/div><time datetime=\"2026-06-22T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">June 22, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Ollikka, N., Bergstrom, A., Kilpelainen, M., Deny, S.<\/span><div class=\"wp-block-rss__item-excerpt\">Mounting evidence suggests that recurrent neural processes taking place within the visual system are recruited when we recognize challenging images&#8212;such as objects seen from unusual viewpoints. Backward masking techniques have traditionally been used as a non-invasive method for studying recurrent processes in the human visual system: A mask follows the target image, presumably disrupting recurrent processes of the visual system. However, these techniques have the limitation that they do not allow to identify the stage of the visual system where [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.biorxiv.org\/content\/10.64898\/2026.06.19.728400v1?rss=1'>IL-38 limits alloreactivity through modulating myeloid and T cell activation<\/a><\/div><time datetime=\"2026-06-22T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">June 22, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Kiprina, A., Xu, W., Macinkovic, I., Boeffinger, N., Namgaladze, D., Elewa, M. A. F., Jacomin, A.-C., Kur, I. M., Aliraj, B., Imkeller, K., Bruene, B., Weigert, A.<\/span><div class=\"wp-block-rss__item-excerpt\">Interleukin-38 (IL-38) is a cytokine of the IL-1 cytokine family that promotes the resolution of inflammation. Resolution mechanisms comprise the induction or recovery of immune tolerance that is lacking in various acute and chronic inflammatory pathologies, including Graft-versus-Host Disease (GvHD). The role of IL-38 in the context of immune tolerance, its primary immune cell targets and underlying molecular mechanisms are not defined. In this study, we investigated the impact of IL-38 on human alloreactivity and in a mouse model of [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.biorxiv.org\/content\/10.64898\/2026.06.17.733038v1?rss=1'>Conserved T cell receptor usage underpins recognition of CD1c presenting a mycobacterial lipid<\/a><\/div><time datetime=\"2026-06-22T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">June 22, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Cao, T.-P., Soliman, C., Redmond, S. J., Tappen, T., Kollmorgen, J., Geng, Q., Moody, D. B., Scriba, T. J., Uldrich, A. P., Minnaard, A. J., Seshadri, C., Venugopal, H., Shahine, A., Rossjohn, J., Godfrey, D. I., Gherardin, N. A.<\/span><div class=\"wp-block-rss__item-excerpt\">The mechanism by which T cell receptors (TCR) recognise mycobacterial lipids presented by CD1 family members not well understood. We used CD1c tetramers loaded with the mycobacterial phosphomycoketide (PM) or mannosyl-PM (MPM) to isolate T cells ex vivo in healthy blood donors and in individuals from a tuberculosis (TB)-endemic region of South Africa, with higher frequencies observed in individuals from the TB-endemic region. High throughput analysis of &gt;200 paired CD1c-mycoketide tetramer+ alpha-beta TCRs identified a conserved TCR motif, encoded by [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.biorxiv.org\/content\/10.64898\/2026.06.22.733315v1?rss=1'>Active non-redundancy and viral orchestration sustain diel microbial successions in the coastal ocean<\/a><\/div><time datetime=\"2026-06-22T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">June 22, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Pereira, O., Ottesen, E. A., DePoy, A. N., Ramond, P., Chen, S., Ji, F., Hou, S., Jiao, N., Zhang, C.<\/span><div class=\"wp-block-rss__item-excerpt\">Ecosystem resilience in dynamic coastal oceans is conventionally ascribed to functional redundancy, where taxonomically distinct microbes buffer environmental fluctuations through interchangeable metabolic roles. In this study, we reveal a deterministic succession architecture sustained by active non redundancy and temporal metabolic coupling, uncovered via autonomous drone array metatranscriptomic sampling in Daya Bay, China. By resolving the transcriptional landscape into six chronometrically phased modules rather than simple time points, we demonstrate a near total renewal of the active gene pool, with greater [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.biorxiv.org\/content\/10.64898\/2026.06.21.733656v1?rss=1'>A representative of a ubiquitous bacterial lineage parasitically feeds on host RNA<\/a><\/div><time datetime=\"2026-06-22T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">June 22, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Katayama, T., Hosogi, N., Meng, X.-Y., Kamagata, Y., Tamaki, H., Nobu, M. K.<\/span><div class=\"wp-block-rss__item-excerpt\">Cellular metabolism is widely understood as an integrated network of redox reactions, energy conservation, and biosynthetic pathways. Here we show that across diverse prokaryotic lineages, loss of redox-associated functions is coupled with loss of nucleotide biosynthesis, raising a fundamental question of how such metabolically reduced organisms sustain cell growth. One of the most widespread and diverse lineages of prokaryotes, Minisyncoccota or Patescibacteriota, constitutes the majority of lineages exhibiting this pattern. To investigate how such organisms persist, we cultivated and characterized [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.biorxiv.org\/content\/10.64898\/2026.06.22.733705v1?rss=1'>PanRes: A database of latent and acquired antimicrobial resistance allowing 3D-based protein homology search<\/a><\/div><time datetime=\"2026-06-22T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">June 22, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Vojtkova, M., Baltusis, M., Martiny, H.-M., Baral, A., Pyrounakis, N., Beleon, A., Freitag, R., Pico-Tomas, A., Kaas, R. S., Petersen, T. N., Munk, P.<\/span><div class=\"wp-block-rss__item-excerpt\">Antimicrobial resistance databases are central to genomic surveillance, but resistance determinants remain distributed across resources with different scopes, structures, and annotations. We developed PanRes, a curated resistance database of 11,717 genes integrating acquired and latent determinants of antibiotic, biocide, and metal resistance within a unified ontology. We predicted representative protein structures and clustered them by structural similarity, grouping proteins into 598 structurally conserved clusters coherent despite sequence divergence. Their structure-guided alignments were used to build Hidden Markov Models (HMMs) for [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.biorxiv.org\/content\/10.64898\/2026.06.18.733166v1?rss=1'>First outbreak of Lumpy Skin disease in Catalonia, Spain, 2025-2026<\/a><\/div><time datetime=\"2026-06-22T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">June 22, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Obregon-Gutierrez, P., Correa-Fiz, F., Fonseca-Rodriguez, O., Cortey, M., Cobos, A., Riera, C., Soler, M., Ribas, N., Domenes, F., Pailler-Garcia, L., Domingo, M., Majo, N., Vidal, E., Lorca-Oro, C.<\/span><div class=\"wp-block-rss__item-excerpt\">Lumpy skin disease (LSD) is an emerging cattle disease caused by lumpy skin disease virus (LSDV), with major impacts on the industry, being classified as a Category A disease. Although it was historically confined to Africa, LSD has expanded into the Middle East, Asia and Europe. Here, we report two LSDV genomes from the first outbreak detected in Catalonia, Spain, in October 2025. The genomes were assembled from high-throughput sequencing data generated from two homogenized skin nodules. Comparative phylogenetic analyses [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.biorxiv.org\/content\/10.64898\/2026.06.18.733270v1?rss=1'>The Dilated Cardiomyopathy E525K \u03b2-Myosin Mutation Causes Hypocontractility in Cardiomyocytes Without Altering Crossbridge Cycling<\/a><\/div><time datetime=\"2026-06-22T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">June 22, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Robeson, K. Z., McMillen, T. S., Cooiker, K., Kao, K. Y., Frebis, K., Geeves, M. A., Wescott, A. P., Soriano, R., Goldstein, A. J., Childers, M. C., Goluguri, R. R., Pathak, D., Sniadecki, N. J., Powers, J. D., Davis, J., Moussavi-Harami, F., Spudich, J. A., Ruppel, K. M., Regnier, M.<\/span><div class=\"wp-block-rss__item-excerpt\">The {beta}-cardiac myosin (MYH7) mutation E525K was first identified in 2012 in a patient with dilated cardiomyopathy (DCM). Work using engineered myosin constructs has shown that this mutation causes hypocontractility by stabilizing the interacting heads motif (IHM) of myosin despite the mutant E525K motor head exhibiting increased ATPase activity. However, no measurements have been made in myofilaments or cardiomyocytes to determine how this mutation affects contractile function. Here, we present force and contractile kinetics measurements from induced pluripotent stem cell [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.biorxiv.org\/content\/10.64898\/2026.06.21.733642v1?rss=1'>EMAlign: accurate alignment of cryo-EM maps through main-chain probability using deep learning<\/a><\/div><time datetime=\"2026-06-22T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">June 22, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Cao, H., Chen, J., Li, T., Huang, S.-Y.<\/span><div class=\"wp-block-rss__item-excerpt\">Accurate alignment of cryo-EM density maps is essential for comparing conformational states, searching map libraries, and guiding atomic model building, but remains challenging for noisy experimental maps and partially overlapping structures. Existing alignment methods are often based on raw maps, which may result in reduced accuracy due to the density noise, or require manual intervention for local alignment, which suffers from limited general applicability. Addressing the limitations, we present EMAlign, an automatic global and local cryo-EM map alignment with predicted [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.biorxiv.org\/content\/10.64898\/2026.06.20.733545v1?rss=1'>Simulation of cell-size systems at long timescales with flexible protein structures<\/a><\/div><time datetime=\"2026-06-22T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">June 22, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Yunas, K., Singh, A., Copeland, M. M., Tytarenko, A. M., Kundrotas, P. J., Halfmann, R., Kasyanov, P. O., Feinberg, E. A., Vakser, I. A.<\/span><div class=\"wp-block-rss__item-excerpt\">Protein behavior inside cells is dominated by the crowded nature of the intracellular environment. Progress in structure determination of proteins and protein complexes, based on advances in Artificial Intelligence, provides an opportunity for structure-based modeling of cellular phenomena. Such modeling at the atomic resolution has been advanced by the traditional simulation techniques, e.g. molecular dynamics. A recently developed docking-based approach implements Markov Chain Monte Carlo sampling of intermolecular energy landscapes, offering several orders of magnitude faster simulation protocols. The approach [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.biorxiv.org\/content\/10.64898\/2026.06.17.732787v1?rss=1'>Spatial Orchestration of Skin Fibrosis by a CD8+ T cell-Myofibroblast Axis<\/a><\/div><time datetime=\"2026-06-22T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">June 22, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Boothby, I. C., Gan, T. C., Flynn, E., Johri, V., Kazmi, M., Maliskova, L., Shaikh, S., Yellamilli, S., Fragiadakis, G. K., Neuhaus, I., Eckalbar, W., Cohen, J. N., Combes, A. J., Haemel, A., Rosenblum, M. D., Kinet, M. J.<\/span><div class=\"wp-block-rss__item-excerpt\">Fibrosing skin diseases are highly morbid conditions with diverse clinical and histopathologic features. Prior work, primarily in systemic sclerosis (SSc), has yielded mixed data regarding the immune drivers of fibrosis, as well as the identity and spatial localization of pro-fibrotic fibroblast cell subsets. Here, we focus on morphea and eosinophilic fasciitis (EF), which cause more acutely inflammatory skin fibrosis. Using multimodal single-nucleus and spatial transcriptomics, we find that effector CD8+ T cells are highly enriched in fibrotic skin. These cells [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.biorxiv.org\/content\/10.64898\/2026.06.22.733661v1?rss=1'>Label-free Pathogen Identification with Microscopy Imaging and Deep Learning<\/a><\/div><time datetime=\"2026-06-22T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">June 22, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Zhang, X., Zhou, T., Guo, S., Du, W., Tong, Z., Zheng, J., Shen, N., Zhu, J., Wang, J.<\/span><div class=\"wp-block-rss__item-excerpt\">Rapid and accurate pathogen identification is crucial for the clinical management of infectious diseases, particularly sepsis and severe respiratory infections, yet standard clinical workflows remain slow and resource-intensive. Here, we developed an automated, high-throughput imaging platform built on standard, clinically accessible bright-field microscopy, and generated a large dataset comprising 24.9 million label-free bacterial cells across six focal pathogens. Leveraging this resource, we trained a neural network (ESKAPe-ResNet) to identify ESKAPe species at the single-bacterium level. The model achieved &gt;92% accuracy [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.biorxiv.org\/content\/10.64898\/2026.06.20.733556v1?rss=1'>Organic availability and microbial competition for acetate suppress methane emissions during the conversion of gypsum in sewage sludge<\/a><\/div><time datetime=\"2026-06-22T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">June 22, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Coon, G. R., Kouadio, V., Murphy, C. W. M., Sun, H., Jagoutz, O., Bosak, T.<\/span><div class=\"wp-block-rss__item-excerpt\">Conventional anaerobic digestion emits methane from organic waste. Here, we investigate a sulfate-based alternative that suppresses methane production and generates alkaline solutions that may sequester carbon by carbonate precipitation. Although methanogenesis is known to occur when reduced organic carbon is replete and sulfate is limiting, it remains unclear whether methane emissions during microbial conversion of waste gypsum are primarily driven by community composition or organic availability. By comparing fluxes of electrons from organic matter toward sulfate or methane in microbial [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.biorxiv.org\/content\/10.64898\/2026.06.20.733521v1?rss=1'>Genetic introgression and transcriptomic plasticity are associated with enhanced Leishmania infantum pathogenicity causing human cutaneous leishmaniasis in Tunisia<\/a><\/div><time datetime=\"2026-06-22T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">June 22, 2026<\/time> <span class=\"wp-block-rss__item-author\">by SANTI, A. M. M., LI, B., PIEL, L., PIPOLI DA FONSECA, J., BACQ-DAIAN, D., OLASO, R., DELEUZE, J. F., COKELAER, T., AOUN, K., BOURATBINE, A., SPA\u0308TH, G. F.<\/span><div class=\"wp-block-rss__item-excerpt\">The protozoan parasite Leishmania infantum exhibits significant genetic variability among isolates, influencing disease manifestation and treatment response. Although L. infantum is classically described as the causative agent of Visceral Leishmaniasis (VL) &#8212; often associated with immune deficiency, cases of Cutaneous Leishmaniasis (CL) caused by this species in immunocompetent individuals have been reported in different countries. To investigate the molecular basis of this unusual shift in tissue tropism and pathogenicity, we applied comparative genomic and transcriptomic approaches on two canine isolates [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.biorxiv.org\/content\/10.64898\/2026.06.18.733207v1?rss=1'>The primate gut bacterial microbiome: a systematic review of research methodologies, taxonomic coverage, and conservation implications<\/a><\/div><time datetime=\"2026-06-22T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">June 22, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Burch, T. C., Badrock, P. G., Boubli, J. P., Guimaraes Sales, N.<\/span><div class=\"wp-block-rss__item-excerpt\">Primates are central to both human evolutionary research and ecosystem functioning, serving as seed dispersers, predators, pollinators, and prey. Despite their value to human and ecosystem science, global primate populations continue to decline, with ~65% of species currently threatened with extinction. Conservation biology increasingly recognises that survival depends not only on protecting habitats and populations, but also on safeguarding the microbial communities that underpin host health, nutrition, and resilience. The gut bacterial microbiome plays a critical role in digestion, immune [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.biorxiv.org\/content\/10.64898\/2026.06.19.733336v1?rss=1'>Sex differences in PRDM9-independent fine-scale recombination patterns<\/a><\/div><time datetime=\"2026-06-22T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">June 22, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Joseph, J.<\/span><div class=\"wp-block-rss__item-excerpt\">Meiotic recombination rates exhibit strong, fine-scale variation along the genome of many eukaryotes. In some animals, including humans, the protein PRDM9 directs recombination toward so-called recombination hotspots. However, in birds and dogs, which have lost PRDM9, hotspots generally occur in promoter sequences called CpG islands. Furthermore, in many species, recombination rates and patterns differ between the sexes, a phenomenon known as heterochiasmy. While sex differences in recombination rates and broad-scale genomic variation are rather well documented, far less is known [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.biorxiv.org\/content\/10.64898\/2026.06.22.733644v1?rss=1'>DNA cytosine methylation modulates UV resistance and nucleotide excision repair gene expression in Escherichia coli<\/a><\/div><time datetime=\"2026-06-22T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">June 22, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Ichikawa, S., Okazaki, M.<\/span><div class=\"wp-block-rss__item-excerpt\">Bacterial survival after ultraviolet (UV) exposure is shaped not only by the extent of DNA damage but also by the physiological state-dependent capacity for DNA repair. Here, we examined the mechanisms underlying growth phase-dependent UV resistance in Escherichia coli K-12 exposed to 262 nm UV irradiation. Stationary-phase cells required higher UV fluence for log inactivation than exponential-phase cells, whereas the levels of UV-induced DNA damage, assessed by cyclobutane pyrimidine dimer staining and real-time PCR, did not differ markedly between the [&hellip;]<\/div><\/li><li class='wp-block-rss__item'><div class='wp-block-rss__item-title'><a href='https:\/\/www.biorxiv.org\/content\/10.64898\/2026.06.18.733066v1?rss=1'>Neuroendocrine arylhydrocarbon receptor regulates gut microbiome of C. elegans via redox tone<\/a><\/div><time datetime=\"2026-06-22T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">June 22, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Hosea, C., Assie, A., Zhang, F., Samuel, B. S.<\/span><div class=\"wp-block-rss__item-excerpt\">The gut microbiome profoundly influences host health, with disrupted microbial communities implicated in inflammatory, metabolic, and neurological diseases. The aryl hydrocarbon receptor (AHR) shapes intestinal immunity and microbial composition, yet the mechanisms by which AHR mediates selective microbiome assembly remain poorly understood. Whether distant organ systems such as the nervous system actively participate in microbial community regulation is unexplored. Here we show that Caenorhabditis elegans neuronal AHR-1 orchestrates selective gut microbiome assembly through a neuroendocrine cascade that calibrates intestinal redox [&hellip;]<\/div><\/li><\/ul>\n\n\n<hr class=\"wp-block-separator has-alpha-channel-opacity is-style-wide\"\/>\n\n\n\n<h4 class=\"wp-block-heading\">Related Journals<\/h4>\n\n\n<ul class=\"su-siblings\"><li class=\"page_item page-item-2806\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/journal-feeds\/biochemistry-journal-feeds\/biochemistry\/\">Biochemistry<\/a><\/li>\n<li class=\"page_item page-item-1465\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/journal-feeds\/biochemistry-journal-feeds\/biochimica-et-biophysica-acta\/\">Biochimica et Biophysica Acta &#8211; Proteins and Proteomics<\/a><\/li>\n<li class=\"page_item page-item-2808\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/journal-feeds\/biochemistry-journal-feeds\/biomedical-chromatography\/\">Biomedical Chromatography<\/a><\/li>\n<li class=\"page_item page-item-1467\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/journal-feeds\/biochemistry-journal-feeds\/cell\/\">Cell<\/a><\/li>\n<li class=\"page_item page-item-1485\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/journal-feeds\/biochemistry-journal-feeds\/chemical-research-in-toxicology\/\">Chemical Research in Toxicology<\/a><\/li>\n<li class=\"page_item page-item-2814\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/journal-feeds\/biochemistry-journal-feeds\/chemical-science\/\">Chemical Science<\/a><\/li>\n<li class=\"page_item page-item-1489\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/journal-feeds\/biochemistry-journal-feeds\/clinical-proteomics\/\">Clinical Proteomics<\/a><\/li>\n<li class=\"page_item page-item-1492\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/journal-feeds\/biochemistry-journal-feeds\/current-opinion-in-biotechnology\/\">Current Opinion in Biotechnology<\/a><\/li>\n<li class=\"page_item page-item-2843\"><a href=\"https:\/\/kermitmurray.com\/msblog\/links\/journal-feeds\/biochemistry-journal-feeds\/journal-of-proteome-research\/\">Journal of Proteome Research<\/a><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Related Journals<\/p>\n","protected":false},"author":1,"featured_media":2652,"parent":1524,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-3087","page","type-page","status-publish","has-post-thumbnail","hentry","entry"],"_links":{"self":[{"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/pages\/3087","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/comments?post=3087"}],"version-history":[{"count":3,"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/pages\/3087\/revisions"}],"predecessor-version":[{"id":3116,"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/pages\/3087\/revisions\/3116"}],"up":[{"embeddable":true,"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/pages\/1524"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/media\/2652"}],"wp:attachment":[{"href":"https:\/\/kermitmurray.com\/msblog\/wp-json\/wp\/v2\/media?parent=3087"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}