Biology subjects

Garcia, J.

Publications and source records attributed to Garcia, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Stress-dependent responses of grapevine wood and fungal pathogen activity under esca and drought

O_LIBiotic and abiotic stresses alter the physiology of perennial plants, with consequences for fungal endophytes and disease expression. In grapevine, one of the worlds most valuable crops, drought inhibits esca disease expression, but the underlying molecular interactions between plant and fungi are unknown. C_LIO_LIWe combined wood metatranscriptomics, metabolomics, and metabarcoding to investigate these interactions in 30-year-old grapevines and eight wood-pathogenic fungi under conditions of drought or esca leaf symptom expression. C_LIO_LIBoth esca and drought decreased grapevine transpiration, but with different transcriptomic and metabolic signatures. Similar pathways were also activated, including the phenylpropanoid and stilbenoid synthesis pathways. These stress responses could potentially confer cross-tolerance, and elicit different fungal molecular responses. The levels of putative fungal virulence factors increased significantly under both stresses. Under drought, only the relative abundance of Phaeomoniella chlamydospora and gene expression involved in anti-oxidative mechanisms, growth, and reproduction increased. Under esca expression conditions, only the relative abundance of Fomitiporia mediterranea and gene expression involved in wood degradation, competition, detoxification, and growth increased. C_LIO_LIThe grapevine defense mechanisms induced by drought coupled with a low transpiration rate and a low abundance and virulence of F. mediterranea may account for esca leaf symptom inhibition upon water deficit. C_LI

plant biology↗

bioRxiv2025

Intraspecies sequence-graph analysis of the Phytophthora theobromicola genome reveals a dynamic structure and variable effector repertoires

Phytophthora theobromicola is an emerging cacao pathogen recently identified in Brazil as an aggressive agent of black pod rot. We generated genome assemblies for two P. theobromicola isolates using long-read sequencing and five additional isolates using short reads. Comparative analysis revealed a genome size and predicted gene content comparable to P. citrophthora, a closely related species with a broad host range that includes both citrus and cacao. An intraspecies sequence-graph analysis revealed a highly dynamic genome structure with high proportion of variable effectors. Syntenic orthology analysis across 13 Phytophthora species identified orthologous gene groups conserved only in cacao pathogens and others specific to P. theobromicola. RxLR effectors and CAZymes were particularly enriched among lineage-specific syntenic groups, with RxLRs preferentially located near transposable elements and within gene-sparse, repeat-rich regions. Transcriptome analysis of infected cacao tissues showed that 88% of predicted effectors were expressed, with pods exhibiting the highest number of upregulated genes. Notably, several RxLRs classified as P. theobromicola-specific syntenic orthologs were highly expressed in infected tissues, suggesting that these lineage-specific effectors may play key roles in host-pathogen interactions unique to cacao. Together, our findings highlight the dynamic architecture and functional plasticity of the P. theobromicola genome, providing foundational insights into its virulence strategies and supporting future studies on host adaptation and effector evolution in emerging cacao pathogens.

genomics↗

bioRxiv2025

Epithelial tumor cells utilize mast cell-derived histamine to regulate perineural invasion

Cancer dissemination by perineural invasion (PNI) is associated with poor outcomes in epithelial malignancies, yet the cellular interactions critical to this process are not fully defined. Single-cell transcriptomic analysis of cutaneous squamous cell carcinoma (cSCC) with PNI highlighted KITLG-KIT signaling activation between keratinocytes and mast cells. Additionally, we observed increased expression of HRH1 on tumor cells, which encodes the H1 histamine receptor. We confirmed these changes in other cancers, including PNI-positive hepatobiliary and oral mucosal tumors. Histamine enhanced tumor invasion into nerve in organoids that recapitulate key features of PNI, an effect rescued by H1-antihistamines. Mechanistically, broad upregulation of matrix metalloproteinases (MMPs) through P38 activation underscored histamine-mediated PNI by enabling collagen degradation in the nerve sheath. Examination of multiple cancer types with PNI showed co-expression of HRH1 and MMP2 on tumor cells as well as type IV collagen loss in involved nerves. Retrospective analysis of >15,000 patient health records in two independent databases demonstrated that H1-antihistamine use improved overall survival and immunotherapy response in cancers that spread by PNI. Together, these data reveal a critical role for mast cells in PNI and present a new therapeutic strategy for targeting this process in epithelial cancers.

cancer biology↗

bioRxiv2025

Parental exposure to wet and dry conditions shapes the viability and thermotolerance of eggs in Aedes aegypti

Aedes aegypti, a primary vector of dengue, Zika, and chikungunya, displays remarkable adaptability across ecological gradients. Central to this resilience is the egg stage, which must withstand fluctuating moisture and temperature conditions. Environmental transitions, particularly changes in moisture availability, significantly influence egg hatching success in mosquitoes. This study investigates how parental exposure to variable hydration conditions shapes key reproductive traits in Ae. aegypti. Using four environmental regimes, continuous wet, continuous dry, wet-to- dry, and dry-to-wet, we assessed egg output, hatching success, thermotolerance, and egg nutrient composition across three Ae. aegypti populations. Our results show that oviposition timing and egg production are significantly affected by the hydration environment experienced by the parental generation. While the wet, dry, and dry-to-wet groups exhibited a consistent oviposition peak beginning four days post-blood feeding, the wet-to-dry group showed delayed reproductive investment, with peak egg production occurring later. Egg output was highest under continuous wet conditions and significantly reduced in the dry and wet-to-dry treatments across all populations. Interestingly, the wet-to-dry group showed significantly higher egg-thermotolerance than any other group, and this pattern was consistent across all three populations under high- temperature stress conditions (41{degrees}C and 45{degrees}C). Nutritional composition showed an increased glycogen level in eggs when parents were exposed to wet conditions before blood feeding. By integrating physiological and ecological metrics such as hatching rates and thermal stress resilience, we demonstrate how parental environments shape subsequent egg performance, highlighting adaptive responses that enable Ae. aegypti persistence under increasing climate variability.

physiology↗

bioRxiv2025

Genomic insights into the virulence repertoire and hemibiotrophic lifestyle of the grapevine black rot pathogen Phyllosticta ampelicida

Phyllosticta ampelicida, the causal agent of grapevine black rot, is a globally emerging pathogen that infects all grapevine green tissues, with young shoots and berries being particularly susceptible. Severe infections can result in total crop loss. To investigate its virulence repertoire, we generated a high-quality genome assembly of strain GW18.1 using long-read sequencing, resulting in 22 scaffolds, including four complete chromosomes and 12 chromosome arms, with a total genome size of 35.6 Mb and 10,289 predicted protein-coding genes. Two additional strains (TN2 and LB22.1) were sequenced with short reads to assess intraspecies diversity. Comparative genomics revealed a conserved virulence factor repertoire, including 314 carbohydrate-active enzymes (CAZymes), 17 cytochrome P450s, 35 peroxidases, and 20 secondary metabolite biosynthetic gene clusters (BGCs). Trophic lifestyle prediction based on gene content supports a biotrophic-like lifestyle consistent with hemibiotrophic pathogens. Broader comparisons with other Phyllosticta species and ten plant-pathogenic fungi pointed to species-specific features, while analysis of gene family evolution identified expansions and contractions in transporters and CAZymes. These genomic resources will support efforts to better understand and manage grapevine black rot.

genomics↗

bioRxiv2025

Oligomerization enables the selective targeting of intrinsically disordered regions by small molecules

Intrinsically disordered regions (IDRs) are challenging drug targets because they lack stable interaction sites for drug-like molecules. We studied the first small molecule targeting an IDR to be evaluated in a clinical trial and found that it interacts selectively with an oligomeric form of the protein, more structured than the monomeric state, that is stabilized by interactions involving aromatic residues in regions with helical propensity. We also found that this compound alters the network of interactions defining the conformational ensemble of its target, thus affecting its condensation properties, linked to its function as a transcription factor. These findings provide a framework for developing strategies to target intrinsically disordered regions with small molecules.

biophysics↗

bioRxiv2025

Mechanistic Modeling of Periodontal Pathogen Fusobacterium nucleatum-Induced Epithelial Oncogenic Transformation in Carcinomas via Selected FadA-Lactate-Angiogenesis Pathway

Periodontal pathogens, commonly found in the normal oral flora, have been implicated in cancer progression, yet their metabolic influence remains underexplored. This study investigates the role of Fusobacterium nucleatum in tumorigenesis by modeling bacterial-induced inflammation and metabolic shifts. Using computational simulations, we analyze key enzymatic fluxes and their impact on cancer development. Our findings highlight significant lactate accumulation and subsequent VEGF upregulation, suggesting potential biomarkers for early detection and novel therapeutic targets. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/642351v1_ufig1.gif" ALT="Figure 1"> View larger version (159K): org.highwire.dtl.DTLVardef@c1f975org.highwire.dtl.DTLVardef@e076deorg.highwire.dtl.DTLVardef@9bf280org.highwire.dtl.DTLVardef@4dd9d1_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

A cell atlas of human and mouse synovium from early and advanced stages of knee osteoarthritis: BHLHE40 regulates fibroblast activation

Osteoarthritis (OA) is a destructive joint disease affecting multiple tissues, including synovium. Previous studies have identified some distinct fibroblast subtypes within synovium; however, the characterization of fibroblast subsets during distinct stages of knee (K)OA disease, and their contributions to the endogenous mechanisms that drive synovial fibrosis during KOA, are not well characterized. Here we profile synovium from early- (KL I) and advanced- (KL III/IV) stages of radiographic KOA. First, bulk-RNA sequencing of early- and advanced-staged KOA synovial tissue revealed transcriptomic differences between the two disease stages. Using single-nuclei RNA sequencing (snRNA-seq) and flow cytometry, we identified distinct fibroblast subsets and uncovered an endotypic shift in fibroblast subsets during KOA pathogenesis, transitioning from DPP4+ in early-stage to ITGB8+ in advanced-stages. SnRNA-seq of synovium from mice with experimental KOA revealed analogous populations of Dpp4+ and Itgb8+ fibroblasts in tissue from early and advanced model stages. Human advanced-stage KOA synovial tissue had stronger expression of matrisome-annotated genes compared to early-stage tissue. BHLHE40, a crucial transcriptional regulator of ECM related genes, was identified as upregulated in ITGB8+ fibroblasts compared to DPP4+ fibroblasts. Using primary human OA fibroblasts in vitro, and conditional knock out mice in vivo, we found that fibroblast-intrinsic loss of BHLHE40 increased fibrosis-related gene expression, enhanced fibroblast activation and induced severe synovial fibrosis in vivo. In contrast, overexpression of BHLHE40 in vitro was able to suppress TGF-{beta}-induced fibroblast activation. Overall, this study provides a comprehensive cellular atlas of KOA synovium and has identified BHLHE40 as a crucial regulator of fibroblast-mediated synovial fibrosis.

molecular biology↗

bioRxiv2024

Notch signaling maintains a progenitor-like subclass of hepatocellular carcinoma

Hepatocellular carcinomas (HCCs) constitute one of the few cancer indications for which mortality rates continue to rise. While Notch signaling dictates a key progenitor lineage choice during development, its role in HCC has remained controversial. Using therapeutic antibodies targeting Notch ligands and receptors to screen over 40 patient-derived xenograft models, we here identify progenitor-like HCCs that crucially depend on a tumor-intrinsic JAG1-NOTCH2 signal. Inhibiting this signal induces tumor regressions by triggering progenitor-to-hepatocyte differentiation, the same cell fate-switch that Notch controls during development. Transcriptomic analysis places the responsive tumors within the well-characterized progenitor subclass, a poor prognostic group of highly proliferative tumors, providing a diagnostic method to enrich for Notch-dependent HCCs. Furthermore, single-cell RNA sequencing uncovers a heterogeneous population of tumor cells and reveals how Notch inhibition shifts cells from a mixed cholangiocyte-hepatocyte lineage to one resembling mature hepatocytes. Analyzing the underlying transcriptional programs brings molecular detail to this process by showing that Notch inhibition de-represses expression of CEBPA, which enables the activity of HNF4, a hepatocyte lineage factor that is otherwise quiescent. We thus describe a compelling and targetable dependency in a poor-prognosis class of HCCs.

cancer biology↗

bioRxiv2024

Quantifying the influence of biophysical factors in shaping brain communication through remnant functional networks

Functional connectivity (FC) reflects brain-wide communication essential for cognition, yet the role of underlying biophysical factors in shaping FC remains unclear. We quantify the influence of physical factors--structural connectivity (SC) and Euclidean distance (DC), which capture anatomical wiring and regional distance--and molecular factors--gene expression similarity (GC) and neuroreceptor congruence (RC), representing neurobiological similarity--on resting- state FC. We assess how these factors impact graph-theoretic and gradient features, capturing pairwise and higher-order interactions. By generating remnant functional networks after selectively removing connections tied to specific factors, we show that molecular factors, particularly RC, dominate graph-theoretic features, while gradient features are shaped by a mix of molecular and physical factors, especially GC and DC. SC has a surprisingly minor role. We also link FC alterations to biophysical factors in schizophrenia, bipolar disorder, and ADHD, with physical factors differentiating these groups. These insights are key for understanding FC across various applications, including task performance, development, and clinical conditions.

neuroscience↗

bioRxiv2024

Putting computational models of immunity to the test - an invited challenge to predict B. pertussis vaccination outcomes

Systems vaccinology studies have been used to build computational models that predict individual vaccine responses and identify the factors contributing to differences in outcome. Comparing such models is challenging due to variability in study designs. To address this, we established a community resource to compare models predicting B. pertussis booster responses and generate experimental data for the explicit purpose of model evaluation. We here describe our second computational prediction challenge using this resource, where we benchmarked 49 algorithms from 53 scientists. We found that the most successful models stood out in their handling of nonlinearities, reducing large feature sets to representative subsets, and advanced data preprocessing. In contrast, we found that models adopted from literature that were developed to predict vaccine antibody responses in other settings performed poorly, reinforcing the need for purpose-built models. Overall, this demonstrates the value of purpose-generated datasets for rigorous and open model evaluations to identify features that improve the reliability and applicability of computational models in vaccine response prediction.

immunology↗

bioRxiv2024

PCM1 conveys centrosome asymmetry to polarized endosome dynamics in regulating daughter cell fate

Vertebrate radial glia progenitors (RGPs), the principal neural stem cells, balance self-renewal and differentiation through asymmetric cell division (ACD), during which unequal inheritance of centrosomes is observed. Mechanistically, how centrosome asymmetry leads to distinct daughter cell fate remains largely unknown. Here we find that the centrosome protein Pericentriolar Material 1 (Pcm1), asymmetrically distributed at the centrosomes, regulates polarized endosome dynamics and RGP fate. In vivo time-lapse imaging and nanoscale-resolution expansion microscopy of zebrafish embryonic RGPs detect Pcm1 on Notch ligand-containing endosomes, in a complex with the polarity regulator Par-3 and dynein motor. Loss of pcm1 disrupts endosome dynamics, with clonal analysis uncovering increased neuronal production at the expense of progenitors. Pcm1 facilitates an exchange of Rab5b (early) for Rab11a (recycling) endosome markers and promotes the formation of Par-3 and dynein macromolecular complexes on recycling endosomes. Finally, in human-induced pluripotent stem cell-derived brain organoids, PCM1 shows asymmetry and co-localization with PARD3 and RAB11A in mitotic neural progenitors. Our data reveal a new mechanism by which centrosome asymmetry is conveyed by Pcm1 to polarize endosome dynamics and Notch signaling in regulating ACD and progenitor fate.

cell biology↗

bioRxiv2024

Deconvoluted methylation profiles discriminate between closely related melanocytic nevi

Congenital melanocytic nevi (CMN) and common acquired melanocytic nevi (AMN) are melanoma-predisposing skin conditions presenting excessive numbers of melanocytes but arising at different times in life. Appropriately weighted whole-genome methylation analysis can be used as a basis for further research in dermatopathology and as applied here provides new insights into nevus biology.

cancer biology↗

bioRxiv2024

Conformational switching of Arp5 subunit differentially regulates INO80 chromatin remodeling

The INO80 chromatin remodeler is a versatile enzyme capable of several functions, including spacing nucleosomes equal distances apart, precise positioning of nucleosomes based on DNA shape/sequence and exchanging histone dimers. Within INO80, the Arp5 subunit plays a central role in INO80 remodeling, evidenced by its interactions with the histone octamer, nucleosomal and extranucleosomal DNA, and its necessity in linking INO80s ATPase activity to nucleosome movement. Our investigation reveals that the grappler domain of Arp5 interacts with the acidic pocket of nucleosomes through two distinct mechanisms: an arginine anchor or a hydrophobic/acidic patch. These two modes of binding serve distinct functions within INO80 as shown in vivo by mutations in these regions resulting in varying phenotypes and in vitro by diverse effects on nucleosome mobilization. Our findings suggest that the hydrophobic/acidic patch of Arp5 is likely important for dimer exchange by INO80, while the arginine anchor is crucial for mobilizing nucleosomes.

biochemistry↗

bioRxiv2024

Puberty Blocker and Aging Impact on Testicular Cell States and Function

Spermatogonial stem cell (SSC) acquisition of meiotogenetic state during puberty to produce genetically diverse gametes is blocked by drugs collectively referred as puberty blocker (PB). Investigating the impact of PB on juvenile SSC state and function is challenging due to limited tissue access and clinical data. Herein, we report largest clinically annotated juvenile testicular biorepository with all children with gender dysphoria on chronic PB treatment highlighting shift in pediatric patient demography in US. At the tissue level, we report mild-to-severe sex gland atrophy in PB treated children. We developed most extensive integrated single-cell RNA dataset to date (>100K single cells; 25 patients), merging both public and novel (52 month PB-treated) datasets, alongside innovative computational approach tailed for germ cells and evaluated the impact of PB and aging on SSC. We report novel constitutional ranges for each testicular cell type across the entire age spectrum, distinct effects of treatments on prepubertal vs adult SSC, presence of spermatogenic epithelial cells exhibiting post-meiotic-state, irrespective of age, puberty status, or PB treatment. Further, we defined distinct effects of PB and aging on testicular cell lineage composition, and SSC meiotogenetic state and function. Using single cell data from prepubertal and young adult, we were able to accurately predict sexual maturity based both on overall cell type proportions, as well as on gene expression patterns within each major cell type. Applying these models to a PB-treated patient that they appeared pre-pubertal across the entire tissue. This combined with the noted gland atrophy and abnormalities from the histology data raise a potential concern regarding the complete reversibility and reproductive fitness of SSC. The biorepository, data, and research approach presented in this study provide unique opportunity to explore the impact of PB on testicular reproductive health.

developmental biology↗

bioRxiv2024

Seasonal behavioral patterns of the Caqueta titi monkey (Plecturocebus caquetensis)

The Caqueta titi monkey (Plecturocebus caquetensis) is Critically Endangered (CR) due to habitat destruction associated with extensive livestock ranching and farming. But unfortunately, information on the ecology and behavior of the species is scarce. Here we describe seasonal behavioral patterns and home range size of P. caquetensis in a 23-ha forest fragment in Colombia. In 2013, we collected focal animal behavioral data of a group of seven individuals of P. caquetensis. Overall, titi monkeys spent 33% of their time feeding, 4% locomotion, 42% resting, and 21% engaging in social interactions, such as grooming and vocalizations. However, the activity budgets differed substantially between seasons. In the dry season titi monkeys invested significantly more time feeding than in the rainy season, when they spent more time moving. They invested a similar amount of time in social interactions in both seasons. Home range size was larger during the rainy season; but the core areas of the home ranges had a similar size and they overlapped across seasons, suggesting the overall importance of this area for titi monkeys. These findings constitute the first study on the seasonal ecology and home range of this Critically Endangered species, and it identifies a priority local conservation area.

ecology↗

bioRxiv2023

Perpetual bioplastic production by a cyanobacteria-dominated microbiome

Departing from the conventional axenic and heterotrophic cultures, our research ventures into unexplored territory by investigating the potential of photosynthetic microbiomes for polyhydroxybutyrate (PHB) synthesis, a biodegradable polyester that presents a sustainable alternative to conventional plastics. Our investigation focused on a cyanobacteria-enriched microbiome, dominated by Synechocystis sp. and Synechococcus sp., cultivated in a 3 L photobioreactor under non-sterile conditions, achieving significant PHB production--up to 28% dry cell weight (dcw) over a span of 108 days through alternating cycles of growth and accumulation. Nile Blue staining and Transmission Electron Microscope visualization allowed to successfully confirm the presence of PHB granules within cyanobacteria cells. Furthermore, the overexpression of PHA synthase during the accumulation phase directly correlated with the increased PHB production. Also, gene expression changes revealed glycogen as the primary storage compound, but under prolonged macronutrient stress, there was a shift of the carbon flux towards favoring PHB synthesis. Finally, analysis through proton Nuclear Magnetic Resonance further validated the extracted polymer as PHB. Overall, it was demonstrated for the first time the feasibility of using phototrophic microbiomes to continuous production of PHB in a non-sterile system. This study also offers valuable insights into the metabolic pathways involved.

bioengineering↗

bioRxiv2023

Antidiabetic Drugs May Prevent Kidney Damage

IntroductionSodium-glucose cotransporter 2 inhibitors (SGLT2i) are a class of drugs that act as glucose reducers in patients with type 2 diabetes mellitus. Recent meta-analyses have shown that SGLT2i also prevent acute kidney injury (AKI) in diabetic patients. The aim of this study was to investigate the protective effect of canagliflozin an SGLT2i on AKI due to ischemia and reperfusion (I/R) in non-diabetic rats. MethodsMale Wistar rats weighing 250-300 g were divided into four groups: Control; SHAM (rats submitted to surgical simulation of renal ischemia); I/R: rats submitted to renal ischemia (bilateral clamping of the renal hilum for 30 minutes); CANA+I/R: I/R rats that received canagliflozin (30mg/kg, oral, gavage; 5 days before I/R). Renal function parameters were evaluated (serum creatinine [CrS], inulin clearance [Clin]; renal hemodynamics mean arterial pressure [MAP], renal blood flow [RBF], renal vascular resistance [RVR]); oxidative profile (urinary peroxides - FOX, lipid peroxidation - TBARS, urinary nitrate- NO) and thiols in renal tissue and expression of nuclear factor-erythroid 2 related factor 2 [Nrf2] protein. ResultsThe I/R group showed an increase in CrS and a reduction in inulin clearance, while the CANA+I/R group showed a reduction in serum creatinine and an increase in inulin clearance compared to the I/R group. In addition, the CANA+I/R group showed a decrease in oxidative metabolites (FOX and TBARS) and an increase in Nrf2 compared to the I/R group. ConclusionCanagliflozin treatment prevented the reduction in renal function induced by ischemia and reperfusion. In addition, there was a reduction in oxidative activity due to a decrease in oxidative metabolites and urinary peroxides and an increase in renal tissue thiols and Nrf-2, which is responsible for transcribing antioxidant activity. Therefore, the current study confirmed a relevant renoprotective effect of canagliflozin in the presence of renal ischemia.

physiology↗