bioRxiv Preprints

{
  "doi": "10.64898/2026.07.24.740384",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.24.740384v1",
  "title": "Paralog diversification masks conserved diel regulatory programs during cold acclimation in Brassica rapa",
  "source": "biorxiv",
  "authors": "Ricono, A. M.; Myers, Z. A.; Schoenecker, D.; Menon, A.; Such, D.; Hazen, A.; Wise, A.; Bruna, T.; Jenkins, J.; Plott, C.; Webber, J.; Boston, L.; Shu, S.; Qiu, Y.; Barry, K.; Nwakama, C. K.; Grimwood, J.; Schmutz, J.; Lovell, J. T.; Greenham, K. M.",
  "version": "1",
  "abstract": "Plant stress responses occur within daily cycles of physiology, metabolism, and growth, making timing a critical dimension of acclimation. In Arabidopsis, circadian and diel regulation influence responses to abiotic stress, including cold, but how this temporal regulation is conserved, diversified, or expanded in crop genomes remains unclear. This question is especially challenging in Brassica rapa, which underwent a genome triplication after diverging from Arabidopsis, resulting in multiple retained paralogs that can be grouped by Arabidopsis orthology and ancient homeologous relationships. Here, we generated a B. rapa pangenome spanning six morphotypes and used it to profile diel (24 h) cold acclimation responses across diverse accessions differing in freeze tolerances. Cold altered peak expression time for thousands of genes, which we grouped into distinct phase-change groups. Circadian leaf movement assays revealed accession-specific differences in clock period and temperature compensation under cold, suggesting that altered clock behavior may contribute in part to the diel transcriptome retiming. At the individual gene level, inferred gene regulatory networks (GRNs) were highl",
  "category": "plant biology",
  "published_at": "2026-07-27T00:00:00.000Z",
  "corresponding_author": "Kathleen M Greenham",
  "journal_published_doi": null,
  "corresponding_institution": "University of Minnesota"
}

{
  "doi": "10.64898/2026.07.24.740530",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.24.740530v1",
  "title": "A missing PEPC1 exaptation restricts C₄ evolution in palms (Arecaceae)",
  "source": "biorxiv",
  "authors": "You, N.; Chen, Y.; Martin, J.; Zhou, N.; Li, W.; Cao, H.; Sun, C.",
  "version": "1",
  "abstract": "O_LIC4 and CAM photosynthesis evolved repeatedly across angiosperms, yet the four palm species examined here -- representing three of five Arecaceae subfamilies ([~]2,600 species total) -- all lack both. We hypothesized that this reflects the absence of PEPC1, a phosphoenolpyruvate carboxylase isoform required for C4 carbon fixation initiation and present in commelinids (Poaceae + Bromeliaceae) but whose distribution across monocots is unknown. C_LIO_LIWe surveyed six core C4 enzyme families by HMMER profiling across nine plant genomes -- four palms (Cocos nucifera, Elaeis guineensis, Phoenix dactylifera, Nypa fruticans), two grasses, one bromeliad, one basal monocot, and one fern. We constructed maximum-likelihood PEPC phylogenies and performed codon-based branch-site likelihood ratio tests using PAML. C_LIO_LIAll six enzyme families were present in palms. PEPC1 was detected in all commelinids (rice, maize, pineapple) but absent from all four palm species and outgroups. No palm PEPC sequence fell within the PPC-1 clade. Molecular dating indicates the Arecaceae-commelinid divergence ([~]120 Mya) predates PEPC1 origin ([~]105 Mya). Branch-site tests on the maize C4-PEPC1 branch were",
  "category": "plant biology",
  "published_at": "2026-07-27T00:00:00.000Z",
  "corresponding_author": "Chengxu Sun",
  "journal_published_doi": null,
  "corresponding_institution": "Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan 571339, China"
}

{
  "doi": "10.64898/2026.07.23.740003",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.23.740003v1",
  "title": "Bioenergetic profiling of fresh human kidney tissue reveals compensatory metabolic adaptation and intrinsic mitochondrial dysfunction in diabetes",
  "source": "biorxiv",
  "authors": "Granata, C.; Laskowski, A.; Thallas-Bonke, V.; Ramm, G.; Macisaac, R.; Chang, C.; Campbell, N.; Royce, P.; Cooper, M. E.; Ekinci, E.; Grummet, J.; Wilson, S. G.; McLean, C. A.; Coughlan, M. T.",
  "version": "1",
  "abstract": "The kidney is a highly energetic organ, requiring substantial ATP production through mitochondrial oxidative phosphorylation to support tubular reabsorption. Metabolic reprogramming and impaired mitochondrial function are implicated in diabetic kidney disease, yet direct assessment of mitochondrial respiratory flux in the human kidney has been constrained by limited access to freshly obtained tissue. Consequently, much of the evidence supporting altered renal mitochondrial function in diabetes derives from animal models that do not fully recapitulate the human condition. We established a workflow for real-time bioenergetic profiling of fresh kidney cortex obtained during nephrectomy from living individuals with diabetes and preserved kidney function. Mitochondrial respiration, electron transport system activity and tubular mitochondrial morphology were compared with age- and sex-matched, histopathologically normal non-diabetic controls. High-resolution respirometry revealed increased mitochondrial respiratory flux in permeabilised diabetic kidney cortex. In contrast, mitochondria isolated from the same tissue exhibited reduced respiratory capacity and impaired complex I activity. Q",
  "category": "pathology",
  "published_at": "2026-07-27T00:00:00.000Z",
  "corresponding_author": "Melinda T Coughlan",
  "journal_published_doi": null,
  "corresponding_institution": "Monash University"
}

{
  "doi": "10.1101/2025.07.17.665344",
  "url": "https://www.biorxiv.org/content/10.1101/2025.07.17.665344v3",
  "title": "WITHDRAWN: Regulatory Rewiring in Adrenocortical Carcinoma: Tumor-Suppressive microRNAs Modulate Cell Cycle, ER Stress, and Sterol Metabolism Axes",
  "source": "biorxiv",
  "authors": "Omidi, J.",
  "version": "3",
  "abstract": "Adrenocortical carcinoma (ACC) is a rare endocrine malignancy with poor prognosis and limited therapeutic strategies. In this study, transcriptomic profiles from TCGA, GTEx 2025, and miRNATissueAtlas 2025 were integrated to construct ceRNA networks specific to tumor and normal adrenal tissues, leveraging a novel integrative analytical framework specifically developed in this study. Network topology revealed substantial rewiring in tumors, with miR-940 emerging as a tumor-exclusive hub, and miR-375 and miR-326 losing centrality despite marked downregulation. Experimentally validated and negatively correlated miRNA-mRNA interactions were identified, highlighting suppression of key oncogenes. Functional enrichment and PPI analyses demonstrated that the targets of these miRNAs are involved in pathways such as cell cycle regulation, EMT, and transcriptional activation. Survival analysis of target genes confirmed their prognostic relevance. Notably, miR-940 exhibited increased expression in radiation-treated patients, indicating therapy-responsive regulatory response, while miR-375 and miR-326 showed stable profiles. Cross-cancer expression analysis further supported the tumor-suppressiv",
  "category": "cancer biology",
  "published_at": "2026-07-27T00:00:00.000Z",
  "corresponding_author": "Javad Omidi",
  "journal_published_doi": null,
  "corresponding_institution": "Columbia University"
}

{
  "doi": "10.64898/2026.07.24.740526",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.24.740526v1",
  "title": "Circulating colorectal tumor cells remodel their surfaceome to increase their viability and metastatic potential in the bloodstream",
  "source": "biorxiv",
  "authors": "Cabaud, O.; Aulas, A.; Lopresti, A. M.; Acquaviva, C.; Finetti, P.; Dessaux, C.; Ganier, L.; Da-Costa, Q.; Germier, C.; Mescam, L.; Elkaoutari, A.; Audebert, S.; Camoin, L.; de Rauglaudre, B.; Boudin, L.; Denicolai, E.; Lumet, G.; Cohendet, A.; Picard, M.; Birnbaum, D.; Gouarne, C.; Chanez, B.; De Chaisemartin, C.; Lelong, B.; Marchetto, S.; Goncalves, A.; Bertucci, F.; Borg, J.-P.; Mamessier, E.",
  "version": "1",
  "abstract": "Circulating tumor cells (CTCs) are the potential seeds of distant metastases; however, little is known about how they survive in the bloodstream. Using a large cohort of colorectal cancer (CRC) patients, we found that the pseudokinase receptor PTK7 is highly expressed in primary tumors and metastatic lesions. Consistent with previous reports, high PTK7 expression is associated with reduced disease-free survival and increased metastatic dissemination. Surprisingly, PTK7 is absent from most CTCs and undergoes a cell-autonomous ONtumor/OFFCTC/ONmetastasis switch that can be recapitulated in a xenografted mouse model, in in vitro systems, and a fluidic platform. PTK7-negative cancer cells exhibit increased expression of YAP1-driven genes, senescence-like features, and enhanced resistance to hemodynamic stress following loss of cell-cell and cell-matrix adhesion. This adaptive phenotype depends on metalloproteases, notably ADAM17, whose cleavage activity remodels the CTCs surfaceome. Functionally, the PTK7 OFFCTC state confers enhanced metastatic potential in vivo, and can be pharmacologically suppressed using metalloprotease inhibitors. Collectively, our findings identify a reversible,",
  "category": "cancer biology",
  "published_at": "2026-07-27T00:00:00.000Z",
  "corresponding_author": "Emilie Mamessier",
  "journal_published_doi": null,
  "corresponding_institution": "Aix Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue Contre le Cancer, Predictive Oncology laboratory, Marseille, France"
}

{
  "doi": "10.64898/2026.07.23.740353",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.23.740353v1",
  "title": "SyntenyPair Explorer: an installation-free, browser-based tool for interactive pairwise genome synteny visualization",
  "source": "biorxiv",
  "authors": "Gibbons, J. G.",
  "version": "1",
  "abstract": "Comparisons of genome structure between related organisms are central to understanding genome evolution, gene family dynamics, and the genomic basis of phenotypic variation. Synteny, the conserved co-localization of genes along chromosomes, is most readily interpreted visually, yet many existing synteny visualization tools require local software installation, command-line proficiency, and/or dedicated server infrastructure, and produce static images that cannot be explored interactively. Here, I present SyntenyPair Explorer, a lightweight, installation-free tool for interactive visualization of synteny between two genomes. The application runs entirely within a standard web browser as a single, self-contained HTML file with no external dependencies and no server-side component. SyntenyPair Explorer accepts standard file formats already produced by common comparative genomics workflows, including FASTA genome assemblies (used to compute optional assembly summary statistics), GFF3/GTF gene annotations, and either BLAST tabular output (outfmt 6) or MCScanX collinearity files. Syntenic relationships are resolved by gene-identifier matching between the relationship file and the gene ann",
  "category": "bioinformatics",
  "published_at": "2026-07-27T00:00:00.000Z",
  "corresponding_author": "John G Gibbons",
  "journal_published_doi": null,
  "corresponding_institution": "University of Massachusetts Amherst"
}

{
  "doi": "10.1101/2025.09.16.676551",
  "url": "https://www.biorxiv.org/content/10.1101/2025.09.16.676551v2",
  "title": "Overcoming Biosynthetic Limitations to Enhance Bacterial Polyketide Production",
  "source": "biorxiv",
  "authors": "Bravo, S. C.; Hu, J.; Kushnir, S.; Brandenburger, M.; Schulz, F.",
  "version": "2",
  "abstract": "The objective of this study was to enhance the production of monensin and its derivatives in Streptomyces sp. ATCC 15413. To this end the contributions of medium composition and enzyme engineering on polyketide biosynthesis were assessed. Enzyme engineering was implemented through a single-point mutation in KS5 of the polyketide synthase (PKS). This mutation increased premonensin productivity up to 29-fold, revealing and alleviating a rate-limiting step in the multi-enzyme biosynthetic pathway. Medium optimization proved comparably effective, raising titers by at least an order of magnitude across strains. Moreover, medium optimization and ketosynthase mutagenesis acted additively in the premonensin strain, further boosting its production. Overall, our findings show that medium optimization is the dominant factor in maximizing monensin yields, while enzyme engineering can deliver targeted benefits in specific contexts.",
  "category": "biochemistry",
  "published_at": "2026-07-27T00:00:00.000Z",
  "corresponding_author": "Frank Schulz",
  "journal_published_doi": null,
  "corresponding_institution": "Ruhr-University Bochum"
}

{
  "doi": "10.64898/2026.07.24.740592",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.24.740592v1",
  "title": "BRCA2 and RAD54B FxPP motifs Bind DMC1 Filaments through Persistent and Transient Interfaces",
  "source": "biorxiv",
  "authors": "Dupaigne, P.; Miron, S.; Baconnais, S.; Legrand, P.; Van Rossum Fikkert, S.; Sato, K.; Majeed, A.; Le Hingrat, M.; Ouldali, M.; Zelensky, A. N.; Kanaar, R.; Cuniasse, P.; ZINN-JUSTIN, S.",
  "version": "1",
  "abstract": "During meiosis, double-strand DNA breaks are programmed to initiate homologous recombination. The DMC1 recombinogenic filament is central to the repair of these breaks. However, the three-dimensional structures of the protein-protein interfaces regulating the assembly and activity of this filament have not been described yet. We and others previously reported that in BRCA2, a P-motif called PhePP binds to DMC1 in its oligomeric and filament states. Here we identified a similar P-motif in the DNA translocase RAD54B. We solved the cryo-electron microscopy (cryo-EM) structures of BRCA2 and RAD54B P-motif peptides bound to a ssDNA-DMC1 filament at 1.9-2.0 [A] resolution. While these peptides only share the sequence F-[IV]-P-P, they bind to the filament through larger 9-10 residue core sequences with superimposable structures. Both peptides bind to a hydrophobic and negatively charged site, named the P-site, on a single DMC1 protomer and stabilize the ssDNA-DMC1 filament. Mutagenesis experiments and molecular dynamics simulations identified additional transient interactions between positively charged residues of the peptides and negatively charged patches distributed on the DMC1 protome",
  "category": "biochemistry",
  "published_at": "2026-07-27T00:00:00.000Z",
  "corresponding_author": "SOPHIE ZINN-JUSTIN",
  "journal_published_doi": null,
  "corresponding_institution": "I2BC-CEA"
}

{
  "doi": "10.64898/2026.06.09.731167",
  "url": "https://www.biorxiv.org/content/10.64898/2026.06.09.731167v2",
  "title": "Reading the gut microbiome by its fermentative engine and host-facing channels reveals dysbiosis and defines eubiosis.",
  "source": "biorxiv",
  "authors": "Soverini, M.; Lotfollahzadeh, A.; di Rito, L.; Padella, A.; Santacroce, B.; Marcante, A.; Monaldi, C.; Velichevskaya, A.; Viciani, E.; Castagnetti, A.",
  "version": "2",
  "abstract": "Taxonomy gives only a partial description of a gut microbiome, since phylogenetically distinct communities encode much the same metabolism and composition is confounded by lifestyle and geography. Here we introduce TAGMOS, an annotation-verified enzymatic architecture aimed at reading gut-microbiome function, built on a fermentative engine and a set of host-facing channels. The engine reports whether the community disposes of fermentative hydrogen through anaerobic sinks or through respiration, and it is the causal driver of the state: antibiotics drive it to an oxidised, respiratory state while faecal transplantation restores the fermentative milieu, and across 73 cohorts the oxidised state is where facultatively anaerobic Enterobacteriaceae bloom. We observe that the engines disease signal lies in the tail of a population, and a threshold criterion detects disease that a comparison of means overlooks, whereas the channels describe condition-specific mechanistic signatures. Engine and channels transfer across pipelines and populations where taxon-based indices fail. Combining engine and specific channels defines a portable, quantitative measure of eubiosis and dysbiosis, and shows",
  "category": "microbiology",
  "published_at": "2026-07-27T00:00:00.000Z",
  "corresponding_author": "Andrea Castagnetti",
  "journal_published_doi": null,
  "corresponding_institution": "Wellmicro Srl, Via Antonio Canova 30, 40128 Bologna, Italy"
}

{
  "doi": "10.64898/2026.07.24.740503",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.24.740503v1",
  "title": "Metagenomic Discovery of Neutral Lipid Metabolism Pathways in the Arctic Ocean Microbiomes Suggests a Potential New Role in Survival and Oceanic Carbon Cycling",
  "source": "biorxiv",
  "authors": "Grevesse, T.; Walsh, D. A.; McLatchie, S.; Onana, V. E.",
  "version": "1",
  "abstract": "The Arctic Ocean microbiomes experience extreme seasonal fluctuations in light, nutrient availability, and organic carbon supply. In this environment, neutral lipid storage may provide a key survival strategy. Here, we investigated the diversity, distribution, and ecological role of neutral lipid metabolism in Arctic microbiomes using metagenome-resolved analyses and global ocean comparisons. Arctic photic-zone microbiomes were strongly enriched in triacylglycerol (TAG) biosynthesis genes relative to other oceans, primarily due to picoeukaryotic phytoplankton, including the ecologically dominant Micromonas and Bathycoccus. In contrast, prokaryotic communities exhibited diverse TAG-degrading taxa and fatty acid transport systems, supporting a previously unrecognized lipotrophic bacterial guild exploiting phytoplankton-derived lipids as carbon and energy sources. Genome-resolved analyses further revealed distinct bacterial lipid-storage strategies: TAG-producing taxa preferentially encoded fatty acid uptake and carbohydrate utilization pathways, whereas polyhydroxyalkanoate-producing taxa were associated with aromatic compound degradation, linking terrestrial organic matter to lipid ",
  "category": "microbiology",
  "published_at": "2026-07-27T00:00:00.000Z",
  "corresponding_author": "Thomas Grevesse",
  "journal_published_doi": null,
  "corresponding_institution": "New York University Abu Dhabi"
}