[{"id":"cms890kmbb4hpkh0ckx0wxbct","channel":"knowledge","topic":"biorxiv","title":"New histone deposition recruits the DNA methylation maintenance machinery at sites of DNA damage repair","summary":"Faithful inheritance of DNA methylation contributes to the memory of epigenetic states and protects against disease. While the mechanisms underlying DNA methylation maintenance at replication forks are well characterized, whether and how DNA methylation is altered or maintained at sites of DNA damag","payload":{"doi":"10.64898/2026.07.27.740930","url":"https://www.biorxiv.org/content/10.64898/2026.07.27.740930v1","title":"New histone deposition recruits the DNA methylation maintenance machinery at sites of DNA damage repair","source":"biorxiv","authors":"Mori, M.; Piquet, S.; Girard, L.; Ferry, L.; Yamaguchi, K.; Farshchi, M.; Bethouel, E.; Kirsh, O.; Hennion, M.; Defossez, P.-A.; Polo, S. E.","version":"1","abstract":"Faithful inheritance of DNA methylation contributes to the memory of epigenetic states and protects against disease. While the mechanisms underlying DNA methylation maintenance at replication forks are well characterized, whether and how DNA methylation is altered or maintained at sites of DNA damage repair is still poorly understood. Here, by exploiting sequencing, imaging and proteomic approaches in mammalian cells exposed to UV radiation, we show that the majority of DNA methylation marks are maintained during UV damage repair and we dissect the molecular machinery involved in DNA methylation control. We detect the recruitment to sites of repair synthesis of the DNMT1 and DNMT3A DNA methylating enzymes, driven by the DNMT1 cofactor UHRF1 and by UV damage repair endonucleases. We also uncover a crosstalk with histone dynamics, whereby newly deposited H3.3 histones at UV damage sites promote the recruitment of DNMT1. Functionally, we reveal the importance of the DNA methylation maintenance machinery for the transcriptional response to UV damage and sustained cell proliferation. This work provides a comprehensive picture of DNA methylation control mechanisms following DNA damage, w","category":"molecular biology","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Sophie E Polo","journal_published_doi":null,"corresponding_institution":"Laboratory of Epigenome Integrity, Epigenetics & Cell Fate Centre, UMR7216 CNRS, Universite Paris Cite, Paris, 75013, France"},"public_metadata":null,"published_at":"2026-07-31T01:13:08.195Z"},{"id":"cms890k35b4hnkh0cynf4w3ey","channel":"knowledge","topic":"biorxiv","title":"Wobble Vaccines: Complex Vaccine Antigen Pools Promote Increased Antibody Breadth and Cross-Strain Viral Targeting in SARS-CoV-2","summary":"Vaccination remains the most successful preventative measure against viral infection, but methods to stably deter rapidly-evolving pathogens have remained elusive. Vaccines capable of incorporating and anticipating viral evolution could address current challenges in seasonal vaccination efforts agai","payload":{"doi":"10.64898/2026.07.01.735277","url":"https://www.biorxiv.org/content/10.64898/2026.07.01.735277v2","title":"Wobble Vaccines: Complex Vaccine Antigen Pools Promote Increased Antibody Breadth and Cross-Strain Viral Targeting in SARS-CoV-2","source":"biorxiv","authors":"McIlroy, P. R.; Zinzow-Kramer, W. M.; Ellis, M. L.; Melief, E.; Ali, M.; Peck, H. E.; Sasser, L. E.; Vanover, D.; Santangelo, P. J.; Suthar, M. S.; Voigt, E. A.; Woodruff, M. C.","version":"2","abstract":"Vaccination remains the most successful preventative measure against viral infection, but methods to stably deter rapidly-evolving pathogens have remained elusive. Vaccines capable of incorporating and anticipating viral evolution could address current challenges in seasonal vaccination efforts against SARS-CoV-2 and influenza where economic and disease burdens remain high despite decades of combined study. Rare epitope suppression (RES) is an underutilized concept within vaccine design, where humoral epitope targeting can be molded using complex antigen pools. Based in mRNA vaccine technology, wobble vaccines represent the novel application of RES to human pathogens designed to anticipate and resist viral evolution. To establish this platform, public SARS-CoV-2 sequencing data was compiled from the first two years of the COVID-19 pandemic to identify high-diversity sites across the receptor binding domain (RBD) of the spike protein. Wobble RBD (WobbRBD) libraries reflecting that entropy were synthesized and incorporated into established self-amplifying (SA) vaccine constructs. Animals immunized with these complex antigen pools showed no obvious adverse effects. By three days-post ","category":"immunology","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Matthew C Woodruff","journal_published_doi":null,"corresponding_institution":"Emory University"},"public_metadata":null,"published_at":"2026-07-31T01:13:07.505Z"},{"id":"cms890jjub4hlkh0c81ctjty4","channel":"knowledge","topic":"biorxiv","title":"Gelsolin Counteracts ER Stress-Driven Inflammatory Circuits in Psoriasis-like Dermatitis","summary":"Psoriasis is a chronic inflammatory skin disorder driven by amplified communication between immune cells and keratinocytes. Here, we show that imiquimod (IMQ) triggers organelle stress responses that directly contribute to this pathogenic circuit. In dendritic cells (DCs), IMQ promotes formation of ","payload":{"doi":"10.1101/2025.11.20.689413","url":"https://www.biorxiv.org/content/10.1101/2025.11.20.689413v2","title":"Gelsolin Counteracts ER Stress-Driven Inflammatory Circuits in Psoriasis-like Dermatitis","source":"biorxiv","authors":"Ori, D.; Okude, H.; Konishi, R.; Murase, M.; Hiroki, S.; Takahara, S.; Tanaka, T.; Toyodome, R.; Kano, N.; Kawasaki, T.; Ishii, K.; Kobiyama, K.; Nakashima, H.; Nakashima, K.; Sasai, M.; Yamamoto, M.; Kumagai, Y.; Tsuru, A.; Kohno, K.; Kawai, T.","version":"2","abstract":"Psoriasis is a chronic inflammatory skin disorder driven by amplified communication between immune cells and keratinocytes. Here, we show that imiquimod (IMQ) triggers organelle stress responses that directly contribute to this pathogenic circuit. In dendritic cells (DCs), IMQ promotes formation of ER-mitochondria contact sites (MAMs), inducing ER stress and activation of the unfolded protein response (UPR). These pathways act independently of, yet converge with, TLR7/MyD88 signaling to enhance IL-23 expression. IMQ also increases cytosolic Ca{superscript 2}+, facilitating NLRP3 inflammasome activation and release of mitochondrial DNA (mtDNA). In parallel, keratinocytes exposed to IMQ activate UPR-dependent genes, including Defb14 (mBD14), a psoriasis-associated antimicrobial peptide. Extracellular mtDNA and mBD14 then cooperatively stimulate plasmacytoid DCs through TLR9, establishing a feed-forward inflammatory loop. We further identify Gelsolin as a direct IMQ-binding protein that mitigates IMQ-induced ER stress; its loss amplifies ER stress, UPR activation, and oxidative stress, and its expression is reduced in human psoriatic lesions. Thus, MAM-UPR signaling links intracellula","category":"immunology","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Taro Kawai","journal_published_doi":null,"corresponding_institution":"Nara Institute of Science and Technology"},"public_metadata":null,"published_at":"2026-07-31T01:13:06.810Z"},{"id":"cms890j08b4hjkh0c3gui9yqw","channel":"knowledge","topic":"biorxiv","title":"Language-aligned models and structured scene descriptions reveal sensitivity to compositional scene structure in the high-level visual cortex","summary":"Natural scenes are defined not only by their contained objects, but also by the structured relations among those objects. Using 7T fMRI data from the Natural Scenes Dataset, we tested whether the high-level visual cortex is sensitive to this compositional scene structure. We related narrative scene ","payload":{"doi":"10.64898/2026.07.27.740322","url":"https://www.biorxiv.org/content/10.64898/2026.07.27.740322v1","title":"Language-aligned models and structured scene descriptions reveal sensitivity to compositional scene structure in the high-level visual cortex","source":"biorxiv","authors":"Rajaei, K.; Afshar, A.; Cichy, R. M.; Soltanian-Zadeh, H.","version":"1","abstract":"Natural scenes are defined not only by their contained objects, but also by the structured relations among those objects. Using 7T fMRI data from the Natural Scenes Dataset, we tested whether the high-level visual cortex is sensitive to this compositional scene structure. We related narrative scene descriptions to cortical responses in an encoding framework, contrasting intact narrative descriptions with lexical control descriptions that preserved word content while disrupting compositional structure via word randomization. Intact narrative descriptions better predicted cortical responses in high-level visual cortex, indicating sensitivity to structured scene information beyond lexical content alone. This advantage was particularly pronounced for scenes with richer compositional structure. Further, a language-aligned vision model outperformed a self-supervised vision-only model, and this advantage showed a similar high-level cortical distribution. These findings suggest that the high-level visual cortex represents structured scene information beyond simple entity co-occurrence and language supervision may help induce similar representations in artificial vision models.","category":"neuroscience","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Karim Rajaei","journal_published_doi":null,"corresponding_institution":"Institute for Research in Fundamental Sciences (IPM)"},"public_metadata":null,"published_at":"2026-07-31T01:13:06.104Z"},{"id":"cms890ih5b4hhkh0cjrbz82i7","channel":"knowledge","topic":"biorxiv","title":"Seasonal hepatic plasticity follows a temporal response hierarchy in a Neotropical frog","summary":"BackgroundSeasonal climate variation drives physiological change across levels of biological organization in ectotherms, yet whether these responses follow a predictable temporal hierarchy remains untested in wild populations. In a year-round field study of the Lesser Treefrog (Dendropsophus minutus","payload":{"doi":"10.64898/2026.07.26.740824","url":"https://www.biorxiv.org/content/10.64898/2026.07.26.740824v1","title":"Seasonal hepatic plasticity follows a temporal response hierarchy in a Neotropical frog","source":"biorxiv","authors":"Franco-Belussi, L. B.; Moraes, L. T.; de Oliveira, C.; Fernandes, C. E.; Provete, D. B.","version":"1","abstract":"BackgroundSeasonal climate variation drives physiological change across levels of biological organization in ectotherms, yet whether these responses follow a predictable temporal hierarchy remains untested in wild populations. In a year-round field study of the Lesser Treefrog (Dendropsophus minutus, Anura: Hylidae) in Sao Jose do Rio Preto, southeastern Brazil, we sampled 40 to 68 adult males across a full annual cycle to quantify seasonal variation in four hepatic phenotypic modules spanning multiple organizational levels: liver histochemistry (pigments and glycogen; intracellular), cell and nucleus morphometry (cellular), tissue volumetric composition of hepatocytes, sinusoids, melanomacrophage centres and portal structures (tissue), and whole-body somatic indices of liver mass and body condition (organismal). We asked whether lower organizational levels respond faster to seasonal climate, as predicted by the bottom-up cascade framework originally proposed for toxicant exposure, or whether alternative hierarchies emerge when climate acts first through whole-organism physiology. To test whether climatic change precedes each biological response, we extended Procrustean superimposi","category":"zoology","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Lilian B. Franco-Belussi","journal_published_doi":null,"corresponding_institution":"UNESP"},"public_metadata":null,"published_at":"2026-07-31T01:13:05.417Z"},{"id":"cms890hxmb4hfkh0cxq8pbhqj","channel":"knowledge","topic":"biorxiv","title":"Proteome-wide QTL mapping enables gene-protein-phenotype metabolic network construction in a genetically diverse MASLD mouse model","summary":"The limited treatment options available for the estimated 38% of adults worldwide affected by Metabolic Dysfunction Associated Steatotic Liver Disease (MASLD) are largely due to an incomplete understanding of the complex molecular networks underlying disease pathogenesis. To dissect the genetic arch","payload":{"doi":"10.64898/2026.07.26.740836","url":"https://www.biorxiv.org/content/10.64898/2026.07.26.740836v1","title":"Proteome-wide QTL mapping enables gene-protein-phenotype metabolic network construction in a genetically diverse MASLD mouse model","source":"biorxiv","authors":"Robinson, M. L.; Benegiamo, G.; Liu, W.; Williams, M. T.; Smith, G. I.; Klein, S.; Auwerx, J.; Coon, J. J.","version":"1","abstract":"The limited treatment options available for the estimated 38% of adults worldwide affected by Metabolic Dysfunction Associated Steatotic Liver Disease (MASLD) are largely due to an incomplete understanding of the complex molecular networks underlying disease pathogenesis. To dissect the genetic architecture and proteomic regulation underlying MASLD, we generated a genetically diverse mouse cohort through a four-way cross of founder strains with varying susceptibility to liver disease, producing 444 F2 mice with a spectrum of phenotypes and genotypes. Utilizing deep proteomic profiling of the livers of this population, we identified quantitative trait loci (QTL) for 2,652 proteins, spanning over 4,000 unique genomic loci, and distinguished cis- and trans-acting regulatory mechanisms. Integrating proteomic, genomic, and phenotypic data reveals key regulatory loci and candidate proteins influencing disease progression, creating a mineable proteogenomic resource for MASLD research. We utilize this resource to identify the E3 ubiquitin ligase Ubr1 as a candidate central regulator connecting proteostasis and lipid metabolism, with genetic polymorphisms that may alter its abundance and pr","category":"systems biology","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Joshua J Coon","journal_published_doi":null,"corresponding_institution":"University of Wisconsin - Madison"},"public_metadata":null,"published_at":"2026-07-31T01:13:04.715Z"},{"id":"cms890he2b4hdkh0cxakikxjk","channel":"knowledge","topic":"biorxiv","title":"Cross-Species Efficacy of Combinatorial Gene Therapy for Osteoarthritis and Correction of Neuro-Inflammatory Pain Mechanisms","summary":"Osteoarthritis is a leading cause of chronic pain and disability, which lacks disease-modifying treatment. Given the complex multi-tissue and multifactorial drivers behind disease progression, effective treatments will require simultaneously targeting several mechanisms underlying joint degeneration","payload":{"doi":"10.64898/2026.07.27.740924","url":"https://www.biorxiv.org/content/10.64898/2026.07.27.740924v1","title":"Cross-Species Efficacy of Combinatorial Gene Therapy for Osteoarthritis and Correction of Neuro-Inflammatory Pain Mechanisms","source":"biorxiv","authors":"Secor, E.; Wang, J.; Dou, Z.; Yan, J.; Majano, C.; Woodman, M.; Ruiz, O.; Al Azaat, J.; Crosby, D.; Cela, R.; Pownder, S.; Engiles, J. B.; Palmer, D.; Jiang, M.; Leynes, C.; Yaman, I.; Jeong, M.; Sponder, G.; Plutziki, S.; Yuva, L.; Veeragavan, S.; Ray, R. S.; Wythe, J. D.; Arenkiel, B. R.; Chen, R.; Worley, K. C.; Consortium, R.-J.; Ng, P.; Suzuki, M.; Guse, K.; Bae, Y.; Haelterman, N. A.; Reesink, H.; Lee, B.","version":"1","abstract":"Osteoarthritis is a leading cause of chronic pain and disability, which lacks disease-modifying treatment. Given the complex multi-tissue and multifactorial drivers behind disease progression, effective treatments will require simultaneously targeting several mechanisms underlying joint degeneration and pain. Here, we developed and evaluated a combinatorial gene therapy, consisting of a high-capacity adenoviral vector carrying two therapeutic genes to target distinct pathological mechanisms: inflammation (IL-1Ra) and chondrocyte health (PRG4). Intra-articular delivery of this treatment improved functional, structural, and pain outcomes in murine and equine osteoarthritis models. In addition, treatment normalized inflammatory environments in joint tissues, as well as in the dorsal root ganglia (DRG) known to harbor joint-innervating sensory neurons. Moreover, gene therapy reversed OA-induced molecular signatures of neural hyperexcitability, suggesting amelioration of peripheral sensitization. Collectively, these findings support combinatorial gene therapy as a promising treatment for osteoarthritis, while identifying neuroinflammatory signatures for correction of disease progression","category":"systems biology","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Brendan Lee","journal_published_doi":null,"corresponding_institution":"Department of Molecular and Human Genetics, Baylor College of Medicine; Houston, USA."},"public_metadata":null,"published_at":"2026-07-31T01:13:04.010Z"},{"id":"cms890gutb4hbkh0cuvimm6qz","channel":"knowledge","topic":"biorxiv","title":"Unlocking substrate specificities of human solute carrier proteins using untargeted metabolomics","summary":"The limited understanding of transporter substrate spectra constrains our ability to interpret cell and membrane function, highlighting the need for methods that enable transporter deorphanization and characterization of promiscuous transport activities. Here, we present a Xenopus oocyte-based platf","payload":{"doi":"10.64898/2026.07.27.740914","url":"https://www.biorxiv.org/content/10.64898/2026.07.27.740914v1","title":"Unlocking substrate specificities of human solute carrier proteins using untargeted metabolomics","source":"biorxiv","authors":"Zhang, Y.; Stanchev, L. D.; Schulz, F. C.; Rago, D.; Acevedo-Rocha, C. G.; Santos Delgado, A.; Kell, D. B.; Borodina, I.","version":"1","abstract":"The limited understanding of transporter substrate spectra constrains our ability to interpret cell and membrane function, highlighting the need for methods that enable transporter deorphanization and characterization of promiscuous transport activities. Here, we present a Xenopus oocyte-based platform for unbiased transporter substrate discovery. Oocytes expressing heterologous solute carrier proteins (SLC) were incubated in human blood serum, a chemically complex metabolite library containing thousands of endogenous metabolites and xenobiotics, followed by paired untargeted LC-MS/MS profiling of intracellular extracts and surrounding medium to capture metabolite exchange events. Across the five human SLC transporters, viz. SLC10A2, SLC10A6, SLC13A2, SLC16A10, and SLC46A1, metabolite exchange signatures were detected, and automated feature annotation was refined by manual chromatographic peak inspection. The workflow recovered known substrates of SLC10A2 and SLC16A10 and identified additional transported metabolites with MS/MS confirmation. This method provides a scalable framework for transporter substrate profiling and prioritization of candidates for targeted validation.","category":"systems biology","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Irina Borodina","journal_published_doi":null,"corresponding_institution":"The Novo Nordisk Foundation Biotechnology Research Institute for the Green Transition, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark"},"public_metadata":null,"published_at":"2026-07-31T01:13:03.317Z"},{"id":"cms890gb2b4h9kh0c7btzm4zd","channel":"knowledge","topic":"biorxiv","title":"Beige/brown fat-mediated cardiac protection from high-fat diet is dependent on adipocyte beta3-adrenergic receptor","summary":"Cardiometabolic diseases associated with obesity are continuously increasing worldwide. Yet, current therapeutic strategies remain insufficient to improve patient outcomes. The beta3-adrenergic receptor ({beta}3AR) promotes lipolysis in adipose tissue (AT) and thermogenesis specifically in brown adi","payload":{"doi":"10.64898/2026.07.27.739389","url":"https://www.biorxiv.org/content/10.64898/2026.07.27.739389v1","title":"Beige/brown fat-mediated cardiac protection from high-fat diet is dependent on adipocyte beta3-adrenergic receptor","source":"biorxiv","authors":"Cascarano, L.; Michel, L.; Esfahani, H.; De Mulder, D.; Melecchi, A.; Bouzin, C.; Loriot, A.; Ambroise, J.; Pezzica, S.; Carli, F.; Sabatini, S.; Gatto, L.; Dessy, C.; Gastaldelli, A.; Balligand, J.-L.","version":"1","abstract":"Cardiometabolic diseases associated with obesity are continuously increasing worldwide. Yet, current therapeutic strategies remain insufficient to improve patient outcomes. The beta3-adrenergic receptor ({beta}3AR) promotes lipolysis in adipose tissue (AT) and thermogenesis specifically in brown adipose tissue (BAT). In mice, BAT activation also improves systemic metabolism and limits cardiometabolic damage. While BAT is limited in humans (e.g., with ageing and obesity), {beta}3AR activation induces beige adipocytes within white adipose depots with similar thermogenic properties. To study the role of adipocyte {beta}3AR in the regulation of cardiac metabolism and remodeling, mice with/without adipocyte-specific {beta}3AR genetic deletion were fed a high-fat-sucrose (HF-S) diet and treated with the selective {beta}3AR agonist CL316,243 (CL). The metabolic and cardiac protection following {beta}3AR activation was abrogated upon {beta}3AR deletion in adipocytes, together with the beiging of the epididymal (visceral) AT, highlighting a critical role of adipose {beta}3AR signalling in mediating these benefits. Multi-omic analysis of AT and cardiac samples identified CL-induced secreted ","category":"systems biology","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Lorena Cascarano","journal_published_doi":null,"corresponding_institution":"Institute of Experimental and Clinical Research (IREC), Universite Catholique de Louvain, Belgium"},"public_metadata":null,"published_at":"2026-07-31T01:13:02.606Z"},{"id":"cms890frnb4h7kh0chskgr6d9","channel":"knowledge","topic":"biorxiv","title":"Leaf hydraulics is a core component of plant immunity","summary":"Hydathodes at leaf margins mediate guttation of xylem-derived fluids and serve as primary entry sites for adapted vascular bacterial pathogens such as Xanthomonas campestris. Infection of Arabidopsis mutants with fewer hydathodes resulted in spontaneous mesophyll water-soaking and revealed unexpecte","payload":{"doi":"10.64898/2026.07.27.740543","url":"https://www.biorxiv.org/content/10.64898/2026.07.27.740543v1","title":"Leaf hydraulics is a core component of plant immunity","source":"biorxiv","authors":"Marty, S.; Bellenot, C.; vasselon, d.; Goussot, M.; Boulanger, A.; Audran, C.; Savourat, P.; Sarthou, A.-S.; Pouzet, C.; Routaboul, J.-M.; Laufs, P.; NOEL, L. D.","version":"1","abstract":"Hydathodes at leaf margins mediate guttation of xylem-derived fluids and serve as primary entry sites for adapted vascular bacterial pathogens such as Xanthomonas campestris. Infection of Arabidopsis mutants with fewer hydathodes resulted in spontaneous mesophyll water-soaking and revealed unexpectedly-large pathogen populations explained by direct infection of the mesophyll niche through stomata and subsequent proliferation. Physical blockage of hydathodes also induced mesophyll water-soaking and enhanced bacterial growth in both Arabidopsis and cauliflower leaves. These findings reveal a dual role for hydathodes as primary sites of infection while being essential to restrict pathogen proliferation in nonvascular tissues. More broadly, our study identifies leaf hydraulics and guttation as central components of water immunity in vascular plants.","category":"plant biology","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Laurent D NOEL","journal_published_doi":null,"corresponding_institution":"LIPME"},"public_metadata":null,"published_at":"2026-07-31T01:13:01.907Z"},{"id":"cms890f7zb4h5kh0cccbtziq6","channel":"knowledge","topic":"biorxiv","title":"Breakdown of sporophytic self-incompatibility: Diploids versus tetraploids","summary":"Many angiosperm species possess self-incompatibility (SI) systems that prevent self-fertilization. Because empirical studies often report higher selfing rates in tetraploids than in diploids, we investigate whether sporophytic self-incompatibility (SSI) is more likely to break down after the introdu","payload":{"doi":"10.64898/2026.07.27.740979","url":"https://www.biorxiv.org/content/10.64898/2026.07.27.740979v1","title":"Breakdown of sporophytic self-incompatibility: Diploids versus tetraploids","source":"biorxiv","authors":"Douet, D.; Billiard, S.; Vekemans, X.; Clo, J.","version":"1","abstract":"Many angiosperm species possess self-incompatibility (SI) systems that prevent self-fertilization. Because empirical studies often report higher selfing rates in tetraploids than in diploids, we investigate whether sporophytic self-incompatibility (SSI) is more likely to break down after the introduction of a self-compatible (SC) allele in tetraploid populations. To address this question, we use analytical models and individual-based simulations to compare diploid and tetraploid populations under two main scenarios: (1) all SI alleles are codominant, and (2) SI alleles are structured into dominance classes. Overall, our results indicate that SSI is more difficult to maintain in tetraploids than in diploids, with dominance relationships playing a key role in the invasion success of an SC allele. When SI alleles are organized into dominance classes, increasing the dominance of the SC allele generally favors SSI breakdown in tetraploids, while diploids show weaker sensitivity to dominance, with SSI maintained across all dominance scenarios for the SC allele under sufficiently high inbreeding depression. However, when the SC allele is dominant over all SI alleles, SSI is more readily m","category":"plant biology","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Diane Douet","journal_published_doi":null,"corresponding_institution":"Université de Lille"},"public_metadata":null,"published_at":"2026-07-31T01:13:01.200Z"},{"id":"cms890eolb4h3kh0c8ja4t466","channel":"knowledge","topic":"biorxiv","title":"Semenogelin-1 Inhibition of Mouse Sperm Hyperactivation Reveals Two Functional Domains Modulating CatSper Channel","summary":"Seminal plasma is essential for sperm survival and function after ejaculation. Semenogelin-1 (SEMG1), the predominant seminal plasma protein, transiently suppresses sperm motility and hyperactivation after ejaculation through epididymal protease inhibitor (EPPIN) binding. However, the molecular mech","payload":{"doi":"10.1101/2025.09.05.674523","url":"https://www.biorxiv.org/content/10.1101/2025.09.05.674523v5","title":"Semenogelin-1 Inhibition of Mouse Sperm Hyperactivation Reveals Two Functional Domains Modulating CatSper Channel","source":"biorxiv","authors":"Mariani, N. A. P.; Santos, N. C. M.; Andrade, J. J.; Andrade, A. D.; Rezende, B.; Steeman, T. J.; Novero, A. G.; de Lima-Junior, J. C.; Calderaro, G.; Themer, A. C. F.; Kushima, H.; Buffone, M. G.; Krapf, D.; Lishko, P. V.; Silva, E. J. R.","version":"5","abstract":"Seminal plasma is essential for sperm survival and function after ejaculation. Semenogelin-1 (SEMG1), the predominant seminal plasma protein, transiently suppresses sperm motility and hyperactivation after ejaculation through epididymal protease inhibitor (EPPIN) binding. However, the molecular mechanism underlying SEMG1-mediated inhibition of hyperactivation remains unclear. Here, we tested the hypothesis that SEMG1 inhibits CatSper, a sperm-specific calcium channel crucial for hyperactivation. Full-length recombinant mouse SEMG1 (mSEMG1; Q32-G375) inhibited both progressive motility and hyperactivation; the latter was not recovered with NH4Cl-induced alkalinization, indicating an effect downstream of capacitation-associated intracellular alkalinization. Electrophysiological recordings revealed that mSEMG1 reduced CatSper currents at physiologically relevant concentrations. Truncated mSEMG1 fragments mSEMG1Q32-V118 and mSEMG1R98-G375, but not mSEMG1Y221-G375, inhibited sperm hyperactivation and CatSper currents to a similar extent as full- length mSEMG1. Notably, only mSEMG1R98-G375 retained full EPPIN-binding capacity. Together, our findings identify two functional domains within","category":"physiology","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Erick J. R. Silva","journal_published_doi":null,"corresponding_institution":"Universidade Estadual Paulista"},"public_metadata":null,"published_at":"2026-07-31T01:13:00.501Z"},{"id":"cms890e5bb4h1kh0cawv7hdjm","channel":"knowledge","topic":"biorxiv","title":"A p53-dependent FBXO44-RAD18 axis limits mutagenesis by terminating translesion DNA synthesis","summary":"DNA lesions continually challenge genome replication and threaten genome integrity. DNA damage tolerance pathways, including translesion DNA synthesis (TLS), allow cells to bypass lesions and prevent stalled forks from collapsing into double-strand breaks. Because TLS polymerases are intrinsically e","payload":{"doi":"10.64898/2026.07.27.739831","url":"https://www.biorxiv.org/content/10.64898/2026.07.27.739831v1","title":"A p53-dependent FBXO44-RAD18 axis limits mutagenesis by terminating translesion DNA synthesis","source":"biorxiv","authors":"Butera, A.; Caporali, S.; Capradossi, F.; Smith, P.; Tabagari, N.; Nikoloska, N.; Mayans, O.; Janic, A.; Gruber, A. J.; D'Angiolella, V.; Amelio, I.","version":"1","abstract":"DNA lesions continually challenge genome replication and threaten genome integrity. DNA damage tolerance pathways, including translesion DNA synthesis (TLS), allow cells to bypass lesions and prevent stalled forks from collapsing into double-strand breaks. Because TLS polymerases are intrinsically error-prone, however, this pathway must be tightly restrained; persistent or deregulated TLS can increase mutagenesis, create therapeutic vulnerabilities, and promote aggressive cancer phenotypes. Through integrated transcriptional profiling, genome-wide CRISPR/Cas9 screening for replication-stress sensitivity, and complementary proteomic analyses, we identify F-box protein 44 (FBXO44) as a late p53-responsive regulator of the TLS mediator RAD18. FBXO44 promotes RAD18 ubiquitination during recovery from replication stress and facilitates shutdown of RAD18-dependent PCNA monoubiquitination. Consistently, FBXO44 loss delays resolution of replication stress and TLS signaling, increases mutation frequency, and is associated with elevated mutational burden and therapy resistance in experimental models and patient datasets. These findings define a p53-FBXO44-RAD18 regulatory axis that limits mu","category":"cancer biology","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Ivano Amelio","journal_published_doi":null,"corresponding_institution":"University of Konstanz"},"public_metadata":null,"published_at":"2026-07-31T01:12:59.808Z"},{"id":"cms890dlub4gzkh0cb27xcupv","channel":"knowledge","topic":"biorxiv","title":"ProNA3D: Distance-Based Analysis of Nucleic Acid-Containing Interfaces","summary":"1.Biomolecular interactions are central to many essential cellular processes, but RNA-containing complexes remain challenging to resolve structurally, even as experimental methods and AI-based prediction have expanded structural coverage. Tools for the integrated analysis of complex interfaces remai","payload":{"doi":"10.64898/2026.04.16.719043","url":"https://www.biorxiv.org/content/10.64898/2026.04.16.719043v2","title":"ProNA3D: Distance-Based Analysis of Nucleic Acid-Containing Interfaces","source":"biorxiv","authors":"Genz, L. R.; Topf, M.","version":"2","abstract":"1.Biomolecular interactions are central to many essential cellular processes, but RNA-containing complexes remain challenging to resolve structurally, even as experimental methods and AI-based prediction have expanded structural coverage. Tools for the integrated analysis of complex interfaces remain limited. We present ProNA3D, a tool that provides a unified platform for analyzing protein-nucleic acid and nucleic acid-only complexes, bridging the gap between structure prediction and functional interpretation. ProNA3D supports both experimental and computationally predicted structures, incorporating scoring metrics for AlphaFold3 predictions. It also offers interactive two-dimensional interface visualization and secondary-structure topology plots for RNA and DNA. An interface-based density zoning feature facilitates structure analysis in cryo-EM maps, allowing evaluation of dynamic complexes in the context of heterogeneous density. We demonstrate ProNA3D on diverse complexes solved by X-ray crystallography or cryo-EM, as well as on computational models. For example, in a trimeric complex of HIV-1 RNA and a human antibody, ProNA3D identified a high-connectivity nucleotide with poten","category":"bioinformatics","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Maya Topf","journal_published_doi":null,"corresponding_institution":"Leibniz-Institut fuer Virologie (LIV) and Universitaetsklinikum Hamburg Eppendorf (UKE)"},"public_metadata":null,"published_at":"2026-07-31T01:12:59.106Z"},{"id":"cms890d2cb4gxkh0cdedworym","channel":"knowledge","topic":"biorxiv","title":"Bio-CM{superscript 2}: Distributed computational optics for cortex-widecellular imaging","summary":"Understanding distributed biological systems, particularly neural circuits, requires simultaneous cellular-resolution imaging across millimeter-scale fields of view (FOV). Existing miniature microscopes remain fundamentally constrained by trade-offs among FOV, spatial resolution, and optical complex","payload":{"doi":"10.64898/2026.07.27.740823","url":"https://www.biorxiv.org/content/10.64898/2026.07.27.740823v1","title":"Bio-CM{superscript 2}: Distributed computational optics for cortex-widecellular imaging","source":"biorxiv","authors":"Hu, G.; Deng, Q.; Qi, T.; Chen, Z.; Rauscher, B. C.; Chai, N.; Bogatova, D.; Weinberg, B.; Smith, J.; Davison, I. G.; Thunemann, M.; Devor, A.; Tian, L.","version":"1","abstract":"Understanding distributed biological systems, particularly neural circuits, requires simultaneous cellular-resolution imaging across millimeter-scale fields of view (FOV). Existing miniature microscopes remain fundamentally constrained by trade-offs among FOV, spatial resolution, and optical complexity, limiting their ability to bridge cellular microscopy with cortex-scale imaging. Here we introduce distributed computational optics, a framework that distributes image formation across coordinated optical modules and computationally integrates their measurements into a unified image. We realize this framework in Bio-CM2, a computational miniature mesoscope that partitions the imaging field across four optical modules while converging their measurements onto a common image sensor. This architecture overcomes the aberration-scaling limitations of conventional miniature optics while avoiding the hardware complexity of multi-camera systems and the contrast degradation associated with optical multiplexing. Bio-CM2 achieves a 7.5 x 10 mm2 FOV while enabling cellular-resolution in vivo imaging at video rates. We demonstrate its utility through two complementary imaging modalities in head-fi","category":"bioengineering","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Lei Tian","journal_published_doi":null,"corresponding_institution":"Boston University"},"public_metadata":null,"published_at":"2026-07-31T01:12:58.405Z"},{"id":"cms890ciob4gvkh0cg41co976","channel":"knowledge","topic":"biorxiv","title":"Self-Actuating 4D Cell-Strand Bioprinting","summary":"Engineering biomimetic tissues with dynamically evolving 3D architectures represents an important direction for next-generation tissue engineering, as it enables recapitulation of the continuous morphogenesis of native tissues during development and regeneration. Here, a self-actuating 4D cell-stran","payload":{"doi":"10.64898/2026.07.27.740975","url":"https://www.biorxiv.org/content/10.64898/2026.07.27.740975v1","title":"Self-Actuating 4D Cell-Strand Bioprinting","source":"biorxiv","authors":"Ding, A.; Cunha, A. F.; Oliveira, M. B.; Mano, J. F.; Alsberg, E.","version":"1","abstract":"Engineering biomimetic tissues with dynamically evolving 3D architectures represents an important direction for next-generation tissue engineering, as it enables recapitulation of the continuous morphogenesis of native tissues during development and regeneration. Here, a self-actuating 4D cell-strand bioprinting platform is developed to engineer complex tissue architectures through autonomous cell contractile force (CCF)-driven morphing without requiring external stimuli. The platform integrates a mechanically compliant and self-softening base hydrogel with embedded high-density cell strands printed using a fast-degrading carrier bioink. During culture, the carrier bioink rapidly degrades while the encapsulated cells proliferate and establish connected cellular networks, generating localized contraction that drives programmable shape transformation. Through spatial patterning of embedded cell strands, constructs with diverse morphologies, including V-shaped, helical, folded, and tubular architectures, are generated via controllable self-actuated morphogenesis. The platform further enables engineering of cartilage-like and bone-like tissues with well-defined curvature configurations","category":"bioengineering","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Eben Alsberg","journal_published_doi":null,"corresponding_institution":"University of Illinois Chicago"},"public_metadata":null,"published_at":"2026-07-31T01:12:57.696Z"},{"id":"cms890bzbb4gtkh0cpx5uxuz8","channel":"knowledge","topic":"biorxiv","title":"DCGAN-Based Synthetic MRI Augmentation for Data-centric Brain Tumor Segmentation","summary":"Accurate brain tumor segmentation from magnetic resonance imaging (MRI) remains a challenging task because supervised deep learning models require large quantities of annotated data, which are expensive and time-consuming to obtain. This study investigates whether synthetic MRI images generated usin","payload":{"doi":"10.64898/2026.07.26.740722","url":"https://www.biorxiv.org/content/10.64898/2026.07.26.740722v1","title":"DCGAN-Based Synthetic MRI Augmentation for Data-centric Brain Tumor Segmentation","source":"biorxiv","authors":"Das, P.; Rath, J.; Jaiswal, A.; Dash, B. B.","version":"1","abstract":"Accurate brain tumor segmentation from magnetic resonance imaging (MRI) remains a challenging task because supervised deep learning models require large quantities of annotated data, which are expensive and time-consuming to obtain. This study investigates whether synthetic MRI images generated using a Deep Convolutional Generative Adversarial Network (DCGAN) can improve U-Net-based brain tumor segmentation using synthetic data augmentation. Experiments were performed on the LGG-MRI dataset comprising 3,929 image-mask pairs. A baseline U-Net was first trained using the original training dataset. Synthetic MRI images were subsequently generated using a DCGAN, and threshold-derived pseudo-masks were assigned to the generated images to construct an augmented training dataset. The same U-Net architecture was then retrained using the augmented dataset and evaluated on an identical held-out test set. Compared with the baseline model, DCGAN-based augmentation increased the Dice coefficient from 0.2067 to 0.3037 and the Intersection over Union (IoU) from 0.1243 to 0.1918, while reducing the final test loss from 0.0474 to 0.0275. These results indicate that synthetic MRI augmentation was as","category":"bioengineering","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Bibhuti Bhusan Dash","journal_published_doi":null,"corresponding_institution":"School of Computer Applications, KIIT Deemed to be University, Bhubaneswar, Odisha, India"},"public_metadata":null,"published_at":"2026-07-31T01:12:56.999Z"},{"id":"cms890bg0b4grkh0c279tb1o8","channel":"knowledge","topic":"biorxiv","title":"A Modular Bio-Hybrid Skin Model for Optical Testing Applications","summary":"Synthetic optical skin models offer reproducible, tunable optical properties but lack biological responsiveness, while tissue engineered skin models provide cellular authenticity but suffer from optical variability and limited controllability. The growing demand for alternatives to animal models in ","payload":{"doi":"10.64898/2026.07.27.740463","url":"https://www.biorxiv.org/content/10.64898/2026.07.27.740463v1","title":"A Modular Bio-Hybrid Skin Model for Optical Testing Applications","source":"biorxiv","authors":"Bajrami, D.; Wei, K.; Spano, F.; Agah, N.; Bonmarin, M.; Rossi, R.","version":"1","abstract":"Synthetic optical skin models offer reproducible, tunable optical properties but lack biological responsiveness, while tissue engineered skin models provide cellular authenticity but suffer from optical variability and limited controllability. The growing demand for alternatives to animal models in the development and validation of optical biomedical technologies highlights the need for a new class of test system that combines the strengths of both approaches while addressing their respective limitations. Here, we introduce the concept of a modular biohybrid skin model, a new testing concept that integrates an optically defined artificial epidermal layer, incorporating polydopamine nanoparticles for changes in skin tone, with living human keratinocytes in two and three-dimensional configurations. In the Optical Protection Model, UV-B-induced apoptosis in primary keratinocytes is quantitatively modulated by model pigmentation level, demonstrating a relationship between optical attenuation and caspase 3/7 activity across three artificial skin tone conditions. In a Structured Dermal Model, keratinocytes seeded onto a hydrogel scaffold localize within follicle-like microcavities, as co","category":"bioengineering","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Dardan Bajrami","journal_published_doi":null,"corresponding_institution":"Empa, Swiss Federal Laboratories for Materials Science and Technology"},"public_metadata":null,"published_at":"2026-07-31T01:12:56.304Z"},{"id":"cms890aweb4gpkh0cfkud1x3s","channel":"knowledge","topic":"biorxiv","title":"An integrated biomaterials-centred approach of the ageing thymic microenvironment reveals design principles for regenerative biomaterials","summary":"Thymic involution is commonly addressed as a loss of epithelial and lymphoid tissue, yet the accompanying remodelling of the microenvironment remains poorly defined. This work applied a biomaterials-centered approach to compare young and aged bovine thymus by integrating histology, oscillatory rheol","payload":{"doi":"10.64898/2026.07.27.740917","url":"https://www.biorxiv.org/content/10.64898/2026.07.27.740917v1","title":"An integrated biomaterials-centred approach of the ageing thymic microenvironment reveals design principles for regenerative biomaterials","source":"biorxiv","authors":"Di Bernarndo, A.; Zanirato, C.; Briatico, F.; Petrini, P.; Butnarasu, C. S.; Leo, F.; Ambrogio, C.; Patrucco, E.; Locatelli, A.; Oliva, F.; Passoni, A.; Medana, C.; Visentin, S.; Sardelli, L.","version":"1","abstract":"Thymic involution is commonly addressed as a loss of epithelial and lymphoid tissue, yet the accompanying remodelling of the microenvironment remains poorly defined. This work applied a biomaterials-centered approach to compare young and aged bovine thymus by integrating histology, oscillatory rheology, untargeted lipidomics, ICP-MS and AP-MALDI mass spectrometry imaging. This holistic approach connects the mechanical, compositional, and spatial features of the native thymus with the development of thymus-inspired biomaterials. Ageing increased both storage and loss moduli by more than one order of magnitude and reduced the linear viscoelastic region approximately fivefold, defining a markedly stiffer and more strain-sensitive material state. This mechanical transition was accompanied by lipid remodelling, with double realtive contribution of triacylglycerols to the lipid pool doubled and loss of membrane-associated phospholipids. The elemental profile also contracted, with total metal content decreasing by one-third and zinc showing a reduction of 70%. At the architectural level, the corticomedullary ratio was more than halved, while AP-MALDI imaging revealed an approximately 40% ","category":"bioengineering","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Lorenzo Sardelli","journal_published_doi":null,"corresponding_institution":"Department of Molecular Biotechnology and Health Science, University of Torino, Torino, Italy"},"public_metadata":null,"published_at":"2026-07-31T01:12:55.598Z"},{"id":"cms890ad1b4gnkh0cjewo5uk5","channel":"knowledge","topic":"biorxiv","title":"Coupling Luciferase Activation and BRET Enables High-Contrast Red-Window Calcium Imaging","summary":"Genetically encoded bioluminescent calcium indicators enable excitation-free imaging of Ca2+ dynamics with low background, no photobleaching, and improved tissue penetration. However, many exhibit lower dynamic ranges than their fluorescent counterparts, motivating the development of new sensor conf","payload":{"doi":"10.64898/2026.07.26.740815","url":"https://www.biorxiv.org/content/10.64898/2026.07.26.740815v1","title":"Coupling Luciferase Activation and BRET Enables High-Contrast Red-Window Calcium Imaging","source":"biorxiv","authors":"Sharma, R.; Xiong, Y.; Tian, X.; Ai, H.","version":"1","abstract":"Genetically encoded bioluminescent calcium indicators enable excitation-free imaging of Ca2+ dynamics with low background, no photobleaching, and improved tissue penetration. However, many exhibit lower dynamic ranges than their fluorescent counterparts, motivating the development of new sensor configurations, particularly for imaging in the red optical window, where tissue absorption and scattering are reduced. Here, we developed HyBRIC and HyBRIC2, two hybrid indicators that integrate Ca2+-dependent luciferase activation and bioluminescence resonance energy transfer (BRET) within a single molecular architecture. When paired with pyCTZ luciferin, they exhibited an approximately 55-fold Ca2+-dependent signal increase in the red optical window in vitro. Compared with HyBRIC, HyBRIC2 showed improved brightness and responsiveness in mammalian cells. It robustly resolved induced Ca2+ dynamics in HEK293T and HeLa cells, with particularly strong red-window responses. Together, these findings expand the limited repertoire of responsive red-window bioluminescent calcium indicators and establish hybrid multiplicative sensing as a modular strategy for improving biosensor contrast.","category":"biochemistry","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Huiwang Ai","journal_published_doi":null,"corresponding_institution":"University of Virginia"},"public_metadata":null,"published_at":"2026-07-31T01:12:54.901Z"},{"id":"cms8909twb4glkh0c791gala3","channel":"knowledge","topic":"biorxiv","title":"Computational evolutionary approach to generate antimicrobial peptides","summary":"As a consequence of the overuse of conventional antibiotics, there is currently an unprecedented increase in antibiotic resistance in newer generations of pathogenic bacteria. This growing problem has led scientists to discover novel medications that could potentially reduce the usage of antibiotics","payload":{"doi":"10.64898/2026.07.26.738612","url":"https://www.biorxiv.org/content/10.64898/2026.07.26.738612v1","title":"Computational evolutionary approach to generate antimicrobial peptides","source":"biorxiv","authors":"Harrison, T.; Zhang, T.; Parmar, M.; Praveen, P.; Menekse, A.; Darmawan, K. K.; Hung, A.; Li, W.","version":"1","abstract":"As a consequence of the overuse of conventional antibiotics, there is currently an unprecedented increase in antibiotic resistance in newer generations of pathogenic bacteria. This growing problem has led scientists to discover novel medications that could potentially reduce the usage of antibiotics, such as antimicrobial peptides (AMPs). Recent study has demonstrated that pardaxin could bind deeply into the surface of a lipid model membrane and inhibit the growth of pathogenic bacteria, including Staphylococcus aureus and Escherichia coli. In this work, the antibacterial efficacy of pardaxin was extended further by performing selective in silico substitution, driven by deep learning, Evolutionary-Scale Cambrian (ESMC) combined with conventional AMP design principles. Principal component analyses of the ESMC embeddings combined with conventional design models produced a set of single-and multiple-mutant analogues of pardaxin, which were predicted and validated with experimental data to exhibit selective antimicrobial properties against either E. coli or S. aureus, respectively. Atomistic molecular dynamics simulations further supported the notion that alpha-helical stability is a c","category":"biochemistry","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Wenyi Li","journal_published_doi":null,"corresponding_institution":"La Trobe University"},"public_metadata":null,"published_at":"2026-07-31T01:12:54.213Z"},{"id":"cms8909adb4gjkh0cnoi5qval","channel":"knowledge","topic":"biorxiv","title":"When Does Reaction Norm GWAS Discover Plasticity? The Residual Channel in Environmental Index-Based Genetic Dissection","summary":"CERIS-JGRA replaces the environmental mean in Finlay-Wilkinson regression with a climate-derived index, so that reaction norm association mapping can dissect the genetics of phenotypic plasticity. Its defining design choice forecloses that objective. An index correlated at{rho} with the environmenta","payload":{"doi":"10.64898/2026.07.27.741005","url":"https://www.biorxiv.org/content/10.64898/2026.07.27.741005v1","title":"When Does Reaction Norm GWAS Discover Plasticity? The Residual Channel in Environmental Index-Based Genetic Dissection","source":"biorxiv","authors":"Jenkins, S. D.; Graef, G. L.","version":"1","abstract":"CERIS-JGRA replaces the environmental mean in Finlay-Wilkinson regression with a climate-derived index, so that reaction norm association mapping can dissect the genetics of phenotypic plasticity. Its defining design choice forecloses that objective. An index correlated at{rho} with the environmental means decomposes exactly into{rho} times the mean plus a residual, and its loading on informative variation orthogonal to the mean,{tau} , cannot exceed {surd}(1 -{rho} {superscript 2}). Sensitivity independent of mean performance is orthogonal to the mean by definition, reaching the slope only through{tau} , and the non-centrality of a plasticity-specific test goes as{tau} {superscript 2}. The algorithm maximizes{rho} , minimizing by construction the channel carrying the signal it is used to detect. Simulation confirms this. A parameter-free expression reproduces observed power across 189 conditions to a root mean square error of 0.030. Power to detect plasticity-specific loci falls from 0.64 at{rho} = 0 to 0.009 at{rho} = 0.99 and 0.003 at{rho} = 0.996, invariant to architecture, coupling and environment count. Holding{rho} at 0.5 while reducing{tau} from 0.87 to zero drops power fro","category":"genetics","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Shawn D. Jenkins","journal_published_doi":null,"corresponding_institution":"University of Nebraska-Lincoln"},"public_metadata":null,"published_at":"2026-07-31T01:12:53.509Z"},{"id":"cms8908qcb4ghkh0c1orxyi48","channel":"knowledge","topic":"biorxiv","title":"Field persistence of entomopathogenic fungi and network-level associations within the soil microbial community as biocontrol agents","summary":"The effects of entomopathogenic fungi (EPF) on native soil microbiota are poorly understood. Here, we investigated the persistence of the EPF Metarhizium brunneum and Beauveria bassiana as preventive treatments for date palms against the red palm weevil, Rhynchophorus ferrugineus, and monitored the ","payload":{"doi":"10.1101/2025.11.02.686131","url":"https://www.biorxiv.org/content/10.1101/2025.11.02.686131v3","title":"Field persistence of entomopathogenic fungi and network-level associations within the soil microbial community as biocontrol agents","source":"biorxiv","authors":"Matveev, S.; Reingold, V.; Doron-Faigenboim, A.; Livne, Y.; Davidovitz, M.; Ment, D.","version":"3","abstract":"The effects of entomopathogenic fungi (EPF) on native soil microbiota are poorly understood. Here, we investigated the persistence of the EPF Metarhizium brunneum and Beauveria bassiana as preventive treatments for date palms against the red palm weevil, Rhynchophorus ferrugineus, and monitored the microbial community within the palms. We assessed the changes in the soil microbiota of the palms following application by fungal soil isolation techniques, high-throughput metagenomics, EPF persistence assays, and accompanied that with a continuous monitoring of date palm health. EPF preemptive treatments significantly improved palm protection against the weevil. While both EPF species persisted for 180 days post-application, their effectiveness diverged, with B. bassiana providing longer palm protection. Overall microbial community composition showed no major changes following EPF applications; however, transient alterations increased the relative abundance of local EPF genera, with dominant taxa being more likely to persist. Both EPF treatments enhanced the relative abundance of nitrogen-fixing bacteria, organic matter decomposers, and ammonia-oxidizing archaea, suggesting potential i","category":"ecology","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Dana Ment","journal_published_doi":null,"corresponding_institution":"ARO"},"public_metadata":null,"published_at":"2026-07-31T01:12:52.789Z"},{"id":"cms89086nb4gfkh0cqbtqtfv8","channel":"knowledge","topic":"biorxiv","title":"The consequences of mixed-mode transmission for disease prevalence","summary":"Host-parasite relationships are defined by transmission. Transmission takes diverse forms, with horizontal transmission modes generally characterized as density- or frequency-dependent. However, many observed parasites display mixed-mode transmission using both density- and frequency-dependent route","payload":{"doi":"10.64898/2026.07.22.740081","url":"https://www.biorxiv.org/content/10.64898/2026.07.22.740081v1","title":"The consequences of mixed-mode transmission for disease prevalence","source":"biorxiv","authors":"Amundson, I.; Antonovics, J.","version":"1","abstract":"Host-parasite relationships are defined by transmission. Transmission takes diverse forms, with horizontal transmission modes generally characterized as density- or frequency-dependent. However, many observed parasites display mixed-mode transmission using both density- and frequency-dependent routes. To investigate how mixed-mode transmission impacts epidemics, we assessed infection prevalence under single- and mixed-mode transmission when there was a linear trade-off between the probability of infection by the two modes. Our results show that the prevalence of a parasite with mixed-mode transmission can be greater than one with a single-mode only when density- and frequency-dependent routes are associated with different effects of the parasite on host fitness. This work shows that mixed transmission modes per se may not necessarily increase disease prevalence, and that substituting two transmission modes for a single one may result in higher prevalence under limited conditions.","category":"ecology","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Irish Amundson","journal_published_doi":null,"corresponding_institution":"University of Virginia"},"public_metadata":null,"published_at":"2026-07-31T01:12:52.080Z"},{"id":"cms8907mib4gdkh0c7v8t478e","channel":"knowledge","topic":"biorxiv","title":"Macronutrient balance generates distinct nutritional optima for growth, immune function and stress responses in the specialist herbivore Plutella xylostella","summary":"Nutrition plays a fundamental role in insect physiology, yet whether growth, immunity and stress responses share a common nutritional optimum remains poorly understood. Using the Geometric Framework for Nutrition, we investigated how dietary protein and carbohydrate balance regulate multiple physiol","payload":{"doi":"10.64898/2026.07.27.740871","url":"https://www.biorxiv.org/content/10.64898/2026.07.27.740871v1","title":"Macronutrient balance generates distinct nutritional optima for growth, immune function and stress responses in the specialist herbivore Plutella xylostella","source":"biorxiv","authors":"Venkatesan, R.; Ghosh, A.","version":"1","abstract":"Nutrition plays a fundamental role in insect physiology, yet whether growth, immunity and stress responses share a common nutritional optimum remains poorly understood. Using the Geometric Framework for Nutrition, we investigated how dietary protein and carbohydrate balance regulate multiple physiological functions in the specialist herbivore Plutella xylostella. Growth was jointly determined by protein and carbohydrate intake, with maximal biomass accumulation constrained primarily by protein availability. Immune traits showed distinct nutritional optima: total hemocyte counts and phenoloxidase activity were maximised at intermediate protein-carbohydrate (P:C) ratios, whereas survival following Bacillus thuringiensis challenge depended predominantly on protein intake. Antioxidant and detoxification responses likewise varied non-linearly across the nutrient landscape, with individual enzyme systems each exhibiting distinct nutrient-dependent optima. Importantly, no single macronutrient balance simultaneously maximised growth, immune performance and oxidative homeostasis, demonstrating that these functions have divergent nutritional requirements. Together, these findings show that m","category":"ecology","published_at":"2026-07-28T00:00:00.000Z","corresponding_author":"Radhika Venkatesan","journal_published_doi":null,"corresponding_institution":"Indian Institute of Science Education and Research (IISER) Kolkata"},"public_metadata":null,"published_at":"2026-07-31T01:12:51.355Z"}]