{"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\/2026.07.10.737762v1?rss=1'>Using BONCAT-FACS to probe the active soil microbial community during nitrous oxide production<\/a><\/div><time datetime=\"2026-07-13T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">July 13, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Gray, J., Harris, J. E., Kaye, J. P., Couradeau, E.<\/span><div class=\"wp-block-rss__item-excerpt\">Nitrous oxide (N2O) is a potent greenhouse gas and is largely produced by incomplete denitrification. Although we know many of the microbial species that denitrify, we are still unable to reliably predict N2O production from soils. Recent work in microbial ecology has shown that when key microbes are considered as members of functional ensembles rather than isolated, the predictive power linking their activity to emergent properties increases dramatically. We hypothesized that the active microbial community during high N2O production would [&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\/2026.07.10.737761v1?rss=1'>Macroalgal fucoidan can activate the biological carbon pump<\/a><\/div><time datetime=\"2026-07-13T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">July 13, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Hellige, I., Buck-Wiese, H., Bligh, M., Thomson, T., White, L., Arnosti, C., Baiko, D., Biehler, L., Fernandez-Mendez, M., Ghobrial, S., Gu, B., Gustafsson, C., Kajee, M., Lloyd, C. C., Nguyen, N. P., Philippi, M., Potin, D., Potin, P., Rothman, M., S. Murillo, B., Seidel, M., Uth, C., Wieters, E., Magnusson, M., Hehemann, J.-H.<\/span><div class=\"wp-block-rss__item-excerpt\">Macroalgae secrete complex carbohydrate polymers, their extracellular matrix, as protection against microbial degradation. By resisting breakdown, these carbohydrates can contribute to marine carbon sequestration, though mechanisms, extent, and timescales remain unknown. Using ship-based sampling and experiments, we found that brown macroalgae release 1.7-4.2% of carbon fixation as fucoidan, equivalent to 0.32-0.88 mg fucoidan per gram of dry seaweed tissue per day. A Bayesian model trained on our empirical data, coupled with Monte Carlo simulations suggests an annual global release 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\/2026.07.10.737747v1?rss=1'>Plastome phylogenomics of the tribe Spermacoceae (Rubiaceae): taxonomic implications and a key to the genera<\/a><\/div><time datetime=\"2026-07-13T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">July 13, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Nunez Florentin, M., Claypool, K., Huda, N., Green, K., Monzel, G., Schafran, P. W., Neupane, S.<\/span><div class=\"wp-block-rss__item-excerpt\">The tribe Spermacoceae (Rubiaceae) comprises a morphologically diverse assemblage of approximately 1,400 species distributed across the Neotropics, Africa, Asia, Australia, and Pacific region. It remains one of the most taxonomically intractable groups in the family, with generic limits repeatedly redefined for more than two centuries. Previous phylogenetic studies based on a limited number of plastid and nuclear markers left numerous relationships unresolved and provided sparse representation of Neotropical lineages. Here, we present the first phylogenomic study of the tribe based [&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\/2026.07.10.737583v1?rss=1'>An ice-bucket challenge: investigating ice algae physiology in laboratory microcosms.<\/a><\/div><time datetime=\"2026-07-13T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">July 13, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Baker, M. L., Forss, E., Kolzenburg, R., Collins, S., Kranz, S. A.<\/span><div class=\"wp-block-rss__item-excerpt\">John Raven pioneered the field of algae ecophysiology, advancing our understanding of cellular resource economics, carbon acquisition, and energy allocation. His work laid the foundation for investigating integrative physiology, linking growth-survival trade-offs across diverse environments. The sea ice habitat provides an excellent framework to continue the research John championed. With steep temperature-salinity gradients, algae survival requires a shift in physiology that we are only beginning to understand. We developed two small scale, reproducible icecosms to investigate physiological changes associated with [&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\/2026.07.10.737758v1?rss=1'>ARCHIVE: Machine-Guided Design of an Efficient Open-Ended DNA Recording Device to Increase Resolution of Multiplexed Cell History Tracking<\/a><\/div><time datetime=\"2026-07-13T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">July 13, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Rosenstein, A. H., Garton, M.<\/span><div class=\"wp-block-rss__item-excerpt\">Engineering cell-based devices to record events into DNA has potential both as a non-ablative research tool and in the clinic for enacting gene-circuit-based logic of cell therapies conditional on cell history. Whether as a means of understanding interactions on the single-cell level, or reconstructing histories of cellular events, a cellular DNA recording device has widespread utility, with prime editing-based methods at the forefront of this endeavor, notably peCHYRON. Yet, the resolution of such open-ended recording tools are inherently constrained 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\/2026.07.10.737750v1?rss=1'>Coordinated leaf hydraulic thresholds maintain virtually null stomatal safety margins in poplar despite genetic variation and nutrient-induced phenotypic plasticity<\/a><\/div><time datetime=\"2026-07-13T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">July 13, 2026<\/time> <span class=\"wp-block-rss__item-author\">by CHASSAGNAUD, D., BEZON, L., LE JAN, I., FICHOT, R.<\/span><div class=\"wp-block-rss__item-excerpt\">The sequence of leaf physiological thresholds underlying plant responses to water deficit is thought to be functionally coordinated; yet, to what extent this coordination is maintained across genotypes and environments remains poorly documented at the intraspecific level. We characterized the sequence of stomatal closure, turgor loss and xylem embolism in the leaves of two genotypes of the riparian species Populus nigra (DRA-038 vs. PG-31) subjected to control, additional nitrogen or additional potassium treatments. Under control conditions, embolism measurements using 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\/2026.07.10.737742v1?rss=1'>Tissue nanotransfection-mediated induction of neurogenic programs promotes myoprotective responses in denervated skeletal muscle<\/a><\/div><time datetime=\"2026-07-13T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">July 13, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Salazar Puerta, A. I., Kheirkhah, S., Moore, J. T., Vasquez Martinez, C. A., Velasquez Quintero, C., Harris, H., Fukuda, M., Fukuda, M. E., Stranan, J. P., Zhao, F., Dathathreya, K., Albert, J., Bobbili, P., Wendt, C. D., Winograd, J., Valerio, I. L., Askwith, C., Moore, A. M., Arnold, W. D., Gallego Perez, D.<\/span><div class=\"wp-block-rss__item-excerpt\">Peripheral nerve injuries often result in prolonged skeletal muscle denervation, leading to progressive atrophy, fibrosis, neuromuscular instability, and loss of regenerative capacity before axons can reinnervate distal targets. Here, we developed a non-viral strategy using tissue nanotransfection (TNT) to deliver the neurogenic transcription factor cocktail Ascl1, Brn2, and Myt1l (ABM) directly to denervated skeletal muscle. In vitro, ABM-transfected myoblasts sustained expression of the reprogramming factors, acquired neuron-like morphologies, upregulated neuronal markers including Tuj1, Map2, and Syp, and exhibited electrophysiological properties [&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\/2026.07.12.738054v1?rss=1'>NPC1 deficiency engages a lysosome &#8211; genome &#8211; immune program linked to neurodegeneration and cellular aging signatures<\/a><\/div><time datetime=\"2026-07-13T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">July 13, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Abyadeh, M., Zarei, M., Hou, P.-C., Sari, V., Lee, K., Hameed, R., Mehkri, B., Malaugh, E., Newton, J., Kordula, T., Wang, Y.-H., Kaya, A.<\/span><div class=\"wp-block-rss__item-excerpt\">Lysosomal dysfunction is a prominent feature of neurodegeneration and aging, yet how primary defects in lysosomal trafficking are converted into progressive cellular decline remains poorly understood. Niemann Pick disease type C (NPC), caused by impaired NPC1 dependent cholesterol export, provides a genetically defined model to address this question. Here, we show that NPC1 deficiency activates a lysosome, genome, immune axis linking cholesterol trafficking failure to neurodegeneration and hallmarks of cellular aging. In Npc1 mutant mice, NPC1 loss triggered DNA damage, [&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\/2026.07.09.737582v1?rss=1'>Electrostatics and Local Aromatic Residues Govern Lipid Binding and Membrane Penetration of Synaptotagmin C2 Domains<\/a><\/div><time datetime=\"2026-07-13T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">July 13, 2026<\/time> <span class=\"wp-block-rss__item-author\">by An, D., Lindau, M.<\/span><div class=\"wp-block-rss__item-excerpt\">Synaptotagmins (Syts) are Ca2+-sensing exocytosis regulators whose tandem C2 domains interact with phosphoinositides and membranes to trigger neurotransmitter and hormone release. Although Ca2+-sensing binding is known to enhance C2 domain-membrane interactions, the sequence determinants governing lipid binding and membrane penetration across Syt isoforms remain incompletely understood. Here, we performed MARTINI coarse-grained molecular dynamics simulations of isolated C2A and C2B domains from eight Ca2+-sensing-sensing Syt isoforms (Syt1, Syt2, Syt3, Syt5, Syt6, Syt7, Syt9, and Syt10) interacting with phosphatidylinositol 4,5-bisphosphate (PIP2)-containing plasma [&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\/2026.07.10.737846v1?rss=1'>golgi: open-source software for automated nerve model generation and recruitment simulation<\/a><\/div><time datetime=\"2026-07-13T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">July 13, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Lung, D., Jia, Y., Moro, A., Fachino, M., Haberbusch, M.<\/span><div class=\"wp-block-rss__item-excerpt\">golgi is an open-source platform that takes a peripheral nerve from image to stimulated fiber population through a single graphical interface, with an equivalent scriptable Python API and command-line interface for batch and high-performance use. It integrates promptable image segmentation, automated multi-region tetrahedral meshing, anisotropic finite-element solution of the extracellular field with an explicit perineurium contact impedance, generation of realistic fiber populations and their three-dimensional trajectories, and biophysical activation thresholds through interchangeable backends&#8211;NEURON (via PyFibers) and a GPU-accelerated surrogate (AxonML). [&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\/2026.07.10.737486v1?rss=1'>Genetically distinct microenvironment determines cancer survival and response to therapy in mice<\/a><\/div><time datetime=\"2026-07-13T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">July 13, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Warner, M. A., Sargent, J. K., Farley, S. R., Dumont, B. L., Hasham, M. G.<\/span><div class=\"wp-block-rss__item-excerpt\">Genetic uniqueness of the tumor microenvironment significantly influences cancer growth, survival, and response to therapy, independent of the cancer cell&#039;s intrinsic properties or the adaptive immune system. Using genetically distinct Rag1-\/- mouse models, this study shows that different strains exhibit varied tumor growth kinetics and survival outcomes when xenografted with identical leukemic and solid tumor cell lines. This study further highlights the critical role of the myeloid immune compartment and shows that disrupting both lymphoid and myeloid systems alters cancer [&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\/2026.07.10.737821v1?rss=1'>Specific F1 ATP synthase inhibition delivers transient mitochondrial stress for selective targeting of acute myeloid leukemia<\/a><\/div><time datetime=\"2026-07-13T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">July 13, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Villaume, M. T., Ramsey, H. E., Impedovo, V., Davidson, M., Arrate, M. P., Singh, A. K., Lee, Y., Skwarska, A., Almadani, Y. F., Baran, N., Chaudhry, S., Reisman, B. J., TenBarge, E. G., Jiang, M., Monteith, A. J., Olmstead, S., Gorska, A. E., Zhao, Z., Grace, P. M., Bachmann, B. O., Konopleva, M., Tiziani, S., Savona, M. R.<\/span><div class=\"wp-block-rss__item-excerpt\">Targeting oxidative phosphorylation (OXPHOS) represents an attractive therapeutic strategy in acute myeloid leukemia, which exhibits exceptional dependence on mitochondrial respiration compared to normal hematopoietic cells. However, clinical attempts to exploit this vulnerability have been limited by on-target toxicity to healthy tissue. Here, we comprehensively compare the cellular consequences of inhibiting distinct nodes of the electron transport chain in AML. We demonstrate that selective inhibition of the F1 subunit of ATP synthase with EB2023 (ammocidin A) delivers an energetic stress to [&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\/2026.07.10.737736v1?rss=1'>Microbial Invasion and Immunosuppression Drives Adenoma Progression in Early Colorectal Cancer Development<\/a><\/div><time datetime=\"2026-07-13T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">July 13, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Liang, W., Falk, L., Lucarelli, D., Putze, P., Metwaly, A., Zheng, Y., Springer, F., Winogrodzki, T., Chan, Q., Zhang, Y., Zeller, G., Meier, M., Schnieke, A., Ebner, F., Haller, D., Flisikowska, T., Saur, D., Flisikowski, K.<\/span><div class=\"wp-block-rss__item-excerpt\">Several inherited predispositions to colorectal cancer exist, most notably familial adenomatous polyposis (FAP), which typically involves a germline loss-of-function mutation in one APC allele. A second hit in APC or related loci leads to aberrant Wnt signalling, triggering adenoma formation with near-complete penetrance. Yet, substantial variability in disease onset and severity, even among siblings with identical APC germline mutations, implicates environmental modifiers. Emerging evidence points to the gut microbiome as a critical regulator of adenoma initiation and progression, particularly in [&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\/2026.07.11.737633v1?rss=1'>First O-demethylation activity in Arabidopsis specialized metabolism resolves the missing step in esculetin biosynthesis<\/a><\/div><time datetime=\"2026-07-13T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">July 13, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Dobek, A., Charles, C., Perkowska, I., Munakata, R., Grosjean, J., Hehn, A., Lojkowska, E., Ihnatowicz, A., Olry, A.<\/span><div class=\"wp-block-rss__item-excerpt\">Coumarins are phenylpropanoid-derived specialized metabolites that contribute to plant defence, shape plant-microbe interactions in the rhizosphere, and promote iron acquisition. In Arabidopsis thaliana, a model plant for iron-responsive coumarin metabolism, the enzymatic origin of the catecholic coumarin esculetin has long remained unresolved. Here we identify the first O-demethylation reaction in Arabidopsis specialized metabolism and show that 2-oxoglutarate- and Fe(II)-dependent dioxygenases catalyze scopoletin 6-O-demethylation to form esculetin. We designate these enzymes scopoletin 6-O-demethylases (S6ODs) and validate their activity through biochemical characterization, [&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\/2026.07.10.737764v1?rss=1'>Anisotropic Thermal Conductivity in Topologically Networked Protein-MXene Composites<\/a><\/div><time datetime=\"2026-07-13T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">July 13, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Demirel, M., Hopkins, P., Vural, M., Jung, H., Tomko, J.<\/span><div class=\"wp-block-rss__item-excerpt\">Governing thermal transport in engineered materials creates opportunities to redirect and recover the excess heat generated in electronic and energy-conversion devices. Materials that pair low cross-plane thermal conductivity with high in-plane thermal conductivity are particularly valuable because they confine heat and channel it away from sensitive regions, preventing localized device failure. Two-dimensional crystals are efficient building blocks for such anisotropic thermal conductors, but they are brittle, and the polymer composites used to toughen them usually forfeit much of the intrinsic [&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\/2026.07.10.737757v1?rss=1'>Ultra-low oxygen tension during in vitro fertilization improves embryonic and adult outcomes in mice<\/a><\/div><time datetime=\"2026-07-13T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">July 13, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Hemphill, C. N., Rhon-Calderon, E. A., Savage, A. J., Domingo-Muelas, A., Krapp, C. J., Plachta, N., Schultz, R. M., Bartolomei, M. S.<\/span><div class=\"wp-block-rss__item-excerpt\">Embryo culture, a required step during in vitro fertilization (IVF), exposes developing embryos to altered environmental conditions not normally experienced in vivo, including altered oxygen (O2) tension. Importantly, O2 influences gene expression, metabolism, and the activity of enzymes that sculpt the epigenetic landscape. The lowest O2 tension currently used in clinics during embryo culture is 5%, despite evidence that sections of the mammalian female reproductive tract have O2 levels as low at 2%. Lower O2 may therefore better mimic 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\/2026.07.10.737795v1?rss=1'>Peptide additives reprogram the lipid nanoparticle corona and enhance gene delivery in a serum-free environment for lung epithelium<\/a><\/div><time datetime=\"2026-07-13T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">July 13, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Hu, J., Papah, M. B., Ramirez, A., Alapati, D., Sullivan, M. O.<\/span><div class=\"wp-block-rss__item-excerpt\">Lipid nanoparticles (LNPs) have become a clinical standard for systemically-administered nucleic acid drugs and vaccines, but the LNP pipeline for locally-delivered LNP therapies remains much less mature. Local delivery in lung represents a particularly compelling application space for DNA-LNP therapeutics, as local gene therapies could support sustained epithelial recovery and functional restoration in various lung diseases. However, locally-delivered DNA-LNPs face multiple barriers, including the limited availability of serum components that often support conventional LNP activity, and the additional delivery barriers [&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\/2026.07.10.737877v1?rss=1'>Engineering a flexible loop in S-adenosyl-L-methionine synthetase enables production of SAM nucleobase analogues with selective biochemical and cellular activity<\/a><\/div><time datetime=\"2026-07-13T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">July 13, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Hazra, A. B., Kalita, D. B., Bhattacharyya, A., Gupte, V., Venugopal, V., Pattathil, A.<\/span><div class=\"wp-block-rss__item-excerpt\">S-adenosyl-L-methionine (SAM), an essential cofactor in all forms of life, is synthesized by the enzyme methionine adenosyltransferase (MAT) from methionine and ATP. The adenine moiety in SAM appears to have no direct function in catalysis, and some MAT homologs can utilize natural nucleotide triphosphates in vitro, producing the corresponding SAM nucleobase analogues. However, the molecular determinants of nucleotide choice of the MAT enzyme and the cellular significance of the nucleobase in SAM are unclear. In this study, using structure- and [&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\/2026.07.10.737529v1?rss=1'>golgi: an open-source graphical platform for image-to-recruitment modeling of peripheral nerve stimulation<\/a><\/div><time datetime=\"2026-07-13T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">July 13, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Lung, D., Jia, Y., Blumer, R., Reissig, L., Zopf, L. M., Heimel, P., Kraus, C., Moro, A., Fachino, M., Haberbusch, M.<\/span><div class=\"wp-block-rss__item-excerpt\">Computational models of peripheral nerve stimulation-coupling finite-element bioelectric fields to biophysical axon models-have become essential for designing electrodes and waveforms for neuromodulation therapies. Yet the established open tools are code-first and assume substantial modeling expertise, and several depend on commercial finite-element solvers, placing realistic nerve modeling out of reach for many experimentalists and clinicians. We present golgi, an open-source platform that takes a peripheral nerve from image to stimulated fiber population through a single graphical interface, with an equivalent scriptable [&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\/2026.07.12.738062v1?rss=1'>Air-driven aldehyde synthesis in engineered bacteria via gene deletion and aryl-alcohol oxidase profiling<\/a><\/div><time datetime=\"2026-07-13T00:00:00-05:00\" class=\"wp-block-rss__item-publish-date\">July 13, 2026<\/time> <span class=\"wp-block-rss__item-author\">by Dickey, R. M., Bryan, J., Somasundaram, V., Anderson, S. R., Phan, N., Kunjapur, A. M.<\/span><div class=\"wp-block-rss__item-excerpt\">Engineered bacterial routes for oxidation of non-native alcohols face three challenges: Nicotinamide-dependent enzymes are coupled to cellular redox metabolism, nicotinamide-independent aryl-alcohol oxidases (AAOs) usually express poorly in bacteria, and aldehyde products are rapidly modified by host enzymes. Here, we address these limitations by engineering aldehyde-retaining Escherichia coli for discovery and application of soluble bacterial AAOs. Screening 51 candidates revealed a high-expression sequence cluster containing enzymes that are active on diverse aromatic and furan-based alcohols. 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