Biology subjects

Garcia, J.

Publications and source records attributed to Garcia, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Arthroscopic Raman Probe Provides Biomarkers of TMJ Tissue Composition that Account for Tissue Function

Background: Temporomandibular joint (TMJ) disorders affect up to 25% of the population and may require diverse surgical interventions. However, intraoperative decision-making relies largely on visual assessment, which does not quantitatively characterize tissue composition or mechanical function. Raman spectroscopy offers a nondestructive approach to molecular-level tissue characterization, but its application to TMJ tissues remains unvalidated. Methods: An arthroscopy-compatible Raman probe was used to characterize mandibular condyles (n=15 porcine, n=11 human) and human articular discs (n=7). Raman-derived biomarkers associated with glycosaminoglycans (GAG), collagen (COL), water (H2O), and hydroxyapatite (HA) were evaluated against condylar indentation modulus and disc tensile modulus. Arthroscopic measurements in cadaveric TMJs assessed technical feasibility, while hyperspectral Raman imaging characterized spatial compositional distributions. Results: For condylar cartilage, combined GAG and H2O biomarkers accounted for 86% of the variation in indentation modulus (R2=0.86), compared with 4% for Outerbridge grading (R2=0.04). For articular discs, combined proline and water-associated biomarkers accounted for 88% of the variation in tensile modulus (R2=0.88). Raman spectra acquired in situ under simulated arthroscopic conditions were comparable in quality to ex vivo measurements. Raman imaging revealed distinct compositional patterns in healthy and degenerated tissues, including GAG depletion and cartilage thinning in degenerated condylar cartilage. Conclusions: Raman-derived biomarkers are strongly associated with TMJ cartilage and disc mechanical properties and outperform Outerbridge grading in explaining variation in condylar indentation modulus. Arthroscopic Raman spectroscopy is technically feasible and may complement visual assessment by providing objective compositional information to support future development of tissue-informed surgical decision-making.

pathology↗

bioRxiv2026

Choline Kinase Alpha Inhibition is a Mutation Agnostic Therapeutic Vulnerability in Clonal Hematopoiesis

Clonal Hematopoiesis (CH) affects the aging population and is associated with increased risk of hematological malignancy, cardiovascular disease, and all-cause mortality. Therapeutic options for CH remain limited. Using hematopoietic stem and progenitor cell (HSPC) color barcoding and mosaic mutagenesis in zebrafish, we identified perturbed choline metabolism and increased phosphatidylcholine (PC) biosynthesis via choline kinase alpha (CHKA) in asxl1-mutant HSPCs. Suppressing CHKA-dependent choline flux reduced ASXL1-driven clonal expansion. This effect was conserved in a murine DNMT3A and human TET2 model. Mechanistically, CHKA- dependent choline flux controls phosphatidylcholine production that supports platelet activating factor (PAF) production. Exogenous PAF overcomes the suppressive effect of CHKA inhibition in ASXL1 and TET2 models. We isolated primary, human HSPCs from the peripheral blood of patients with endogenous ASXL1 mutations and demonstrated that perturbing PAF signaling reduces their competitive potential in an ex vivo clonal competition assay. This CHKA/PAF axis is conserved in TET2-mutant HSPCs. Together, these findings identify a mutation agnostic metabolic dependency across the three most common CH genotypes and demonstrate that targeting the CHKA-dependent choline flux suppresses clonal expansion.

cancer biology↗

bioRxiv2026

BUDDY: An interactive web platform to accelerate the functional modeling of human missense variants using Saccharomyces cerevisiae orthologs

The advent of next-generation sequencing has transformed clinical genetics, accelerating the identification of human genetic variants. However, the labor-intensive process of functional validation of Variants of Uncertain Significance (VUS) remains a significant diagnostic barrier. While expressing humanized genes in Saccharomyces cerevisiae is a common approach for modeling missense variants with functional assays, using native yeast orthologs provides a more streamlined approach that preserves species-specific interactions within multisubunit complexes. However, taking this approach relies on a fragmented workflow that requires bioinformatic experience. To address this issue, we developed the Bioinformatic Utility for Diagnostic Discovery in Yeast (BUDDY), an integrated web platform designed to streamline variant analysis by connecting bioinformatic tools and databases including ClinVar. Features include amino acid alignments, a protein structure viewer that displays a superposition of yeast and human proteins, pathogenicity prediction data, CRISPR-Cas9 reagent design, and yeast phenotypes to provide potential functional assays. The platform also contains an artificial intelligence (AI)-assisted experimental design feature that evaluates the utility of modeling specific variant and gene combinations in yeast and can assist with phenotype selection. BUDDY significantly accelerated the bioinformatic preparation time needed for ortholog variant modeling by an experienced biologist. Additionally, without prior bioinformatics training, a first-year medical student used BUDDY to develop a self-directed project and proposed a study of five Lynch syndrome-associated VUS using a forward mutation rate assay. BUDDY is designed to accelerate the investigation of human variants in yeast and has a high potential utility for use in resource-constrained settings such as course-based undergraduate research experiences (CUREs).

bioinformatics↗

bioRxiv2026

TGFB1-Engineered Induced Mesenchymal Stromal Cells Exhibit High Immunomodulatory Potency and Durably Reprogram Synovial Macrophages in Osteoarthritis

Clinical translation of mesenchymal stromal cell (MSC) therapies derived from primary tissue sources is limited by manufacturing inconsistencies driven by donor-to-donor variability, which reduces predictability of clinical response. Induced pluripotent stem cell (iPSC)-derived MSCs (iMSCs) offer a promising donor-independent, clonal alternative strategy that is also more amenable to engineering, but whether engineered iMSCs reproduce the potency attributes of primary MSCs remains unclear. Here, we benchmarked a doxycycline-inducible, hTERT-immortalized iMSC line engineered to overexpress TGFB1 (TGFB1-iMSCs), a key regulator of macrophage polarization, against multiple adipose tissue-derived MSC (MSC(AT)) donors across predefined immunomodulatory and angiogenic potency attributes. TGFB1-iMSCs were smaller and more circular with comparable or higher proliferative rates than primary MSC(AT) donors. Interestingly, they had a distinct angiogenic signature (EDIL3, EDN1, PDGFA), and nine differentially expressed microRNAs were predicted to target secretory trafficking and growth factor receptor signalling. Functionally, however, TGFB1-iMSCs secreted less VEGF and showed intermediate HUVEC tube formation, but matched or exceeded all primary MSC(AT) donors in a monocyte-macrophage transwell immunomodulatory assay. Notably, in a murine destabilization of the medial meniscus (DMM) model of post-traumatic osteoarthritis, a single intra-articular injection of TGFB1-iMSCs, but not MSC(AT), reduced total synovial macrophage numbers and lowered the MHCII/CD206 ratio at eight weeks, although it did not reduce cartilage degeneration, synovitis, or fibrosis. Together, these findings show that TGFB1-engineered iMSCs have a macrophage-directed potency profile distinct from that of primary MSC(AT). Immortalized iMSCs therefore provide a reproducible platform for mechanistically dissecting engineered MSC potency and its effects on the immune environment.

immunology↗

bioRxiv2026

Identification of soil microbes associated with real-time plastic degradation using in situ conductivity sensors

Microbial-mediated plastic degradation has the potential to address the persistent global problems of plastic waste and pollution. Previous work has shown that soils can harbour microbes capable of plastic degradation, but we expect there is a broader diversity of soil microbes capable of metabolizing plastics than identified to date using more traditional cultivation-based screening methods. Here we demonstrate a novel approach to identify putative plastic degrading microbes in soil. We paired in situ, real-time measurements of microbial plastic degradation on conductive sensors with subsequent microbial community profiling of the sensor-associated biofilms exhibiting appreciable degradation. To illustrate the utility of our approach, we focus on microbial degradation of the bioplastic polymer PHBV, poly(3-hydroxybutuyrate-co-3-hydroxyvalerate). We screened a range of soils with the in situ sensors to identify a subset of five soils with high PHBV degradation rates, and confirmed that PHBV degradation was due to microbial activity. We then extracted DNA directly from sensors placed in soils with high measured rates of PHBV degradation and used marker gene sequencing to identify the bacterial and fungal taxa associated with the observed PHBV degradation. We confirmed via in vitro culturing that microbes isolated from the sensors have a demonstrated capacity for PHBV metabolism. Together, these results highlight the benefit and feasibility of using low-cost, in-soil sensors to simultaneously collect real-time data on plastic degradation rates in soil and identify previously unrecognized microbial taxa capable of degrading and metabolizing plastic polymers in situ.

microbiology↗

bioRxiv2026

Range wide analysis of genetic diversity and structure gives insights into Rosa gallica L. evolutionary history

Rosa gallica L., the French rose, is a perennial, tetraploid, heterozygous species that naturally propagates by seed and sucker. It occurs in the wild, primarily in Europe, and also exists as cultivated varieties. R. gallica cultivars were extensively bred and cultivated in France at the beginning of the 19th century. Although several hypotheses have been proposed regarding the species expansion based on historical records, none have been assessed using molecular data. Indeed, its genetic diversity has so far been investigated only at local or regional scales, hindering the identification of the evolutionary factors shaping its present-day distribution. Using 29 sequenced microsatellites, we genotyped a comprehensive sample of 1618 individuals, including wild R. gallica from 219 sites across the species range, rose cultivars, and specimens from other Rosa species. We then detected clonal lineages and characterized the range-wide genetic diversity and structure, aiming to disentangle the roles of natural and human factors in shaping the distribution of R. gallica, with particular focus on France. French diversity appears particularly structured compared to the rest of the range, suggesting multiple origins within France. Populations in South Alps, Central Eastern Europe, and Eastern France appear to have recolonized naturally from a single southern glacial refugium. In contrast, populations in the western part of France likely resulted from more recent natural or human-mediated dispersal. Finally, clonal lineages containing both wild and cultivated individuals were predominantly found in France, highlighting the role of human-mediated dispersal in 28 of the 98 French sites studied. These findings show that the present-day natural range of R. gallica was shaped primarily by post-glacial recolonization, but also reveal a contribution of human activities to its recent dispersal, particularly in France, where cultivated varieties were intensively bred and exchanged.

genetics↗

bioRxiv2026

A p53-ΔNp73 signaling axis drives selective motor neuron degeneration in spinal muscular atrophy

Selective neuronal vulnerability is a hallmark of many neurodegenerative diseases, yet how ubiquitous genetic insults cause highly selective neuronal loss remains poorly understood. In spinal muscular atrophy (SMA), reduced SMN levels trigger degeneration of specific motor neuron pools. Although non-apoptotic, p53-mediated death pathways have been implicated, p53 is expressed in both vulnerable and resistant neurons, leaving the downstream determinants of selective vulnerability unresolved. Here, we identify a p53-{Delta}Np73 signaling axis as a previously unrecognized execution pathway driving motor neuron degeneration. Using differential transcriptional profiling of SMA motor neurons following pharmacological modulation of p53 activity, we uncover p73 as a critical downstream mediator of neuronal death. Notably, SMN deficiency induces cell-autonomous, p53-dependent expression of the {Delta}Np73 isoform selectively in vulnerable, but not resistant, motor neurons. {Delta}Np73 induction precisely parallels the spatial and temporal pattern of degeneration in mouse models and is also detected in motor neurons from SMA patients. Strikingly, despite its established role as a pro-survival antagonist of p53, depletion of {Delta}Np73 improves motor neuron survival and partially preserves neuromuscular junction integrity in SMA mice. These findings reveal a context-dependent, isoform-specific functional switch in p53 family signaling that redirects a canonical survival factor into a driver of neurodegeneration, identifying a novel molecular mechanism underlying selective neuronal vulnerability in SMA and a potential therapeutic target for neuroprotection.

neuroscience↗

bioRxiv2026

Ryanodine receptor 1 ( RYR1 ) patient-derived muscle cells recapitulate disease phenotypes in 2D and 3D culture models

The Ryanodine Receptor 1 (RyR1) is the major Ca2+ release channel in skeletal muscle and plays a crucial role in excitation-contraction coupling. Pathogenic variants in RYR1 are the most common cause of congenital myopathy, for which there are no approved treatments. Patient-centric disease models may help to facilitate the design and screening of novel therapeutics in a human genomic context. In this report, we describe the differentiation of five dominant RYR1-related myopathy patient-derived induced pluripotent stem cell (iPSC) lines into muscle progenitor cells (MPCs), and subsequently into multinucleated myotubes in 2- and 3- Dimensional (D) culture models. In 2D, we show significantly reduced Ca2+ release in a patient line compared to a healthy control following stimulation with caffeine. In 3D engineered muscle tissues (EMTs), patient-relevant phenotypes including reduced twitch amplitude, delayed relaxation and altered force-frequency relationships were observed in a patient line compared to two healthy controls. We also show that the 2D cultures are a suitable platform for screening the efficacy and cellular toxicity of antisense oligonucleotide therapeutics. Together, these results suggest that iPSC-derived skeletal muscle cultures are useful models for understanding the pathobiology of RYR1-related myopathies and as a testbed for emerging treatments.

Cell Biology↗

bioRxiv2026

Genome-wide characterization of extant clonal diversity in Chilean Carmenere

Carmenere is a widely cultivated and internationally recognized grapevine cultivar in Chile, yet genetic variation among its clones remains poorly characterized. Early studies based on SSR and AFLP markers detected limited polymorphism, but these approaches interrogate only a small fraction of the genome, leaving the extent of clonal diversity unresolved. Here, we generated an improved chromosome-scale diploid genome assembly of Carmenere FPS clone 02 and characterized clonal genomic diversity by sequencing 36 biological replicates representing 12 clones maintained in Chile, including heritage selections rescued from old producer vineyards by Vina Santa Carolina as part of its Bloque Herencia conservation program, and commercial nursery-derived clones. Focusing on low-frequency variants and using replicate-aware consensus calling, we identified more than 9,000 private single nucleotide variants (SNVs) and small indels per clone, providing high-resolution markers for clonal identification. Although most variants were located in repetitive or intergenic regions, a subset affected coding sequences, with genes involved in plant-pathogen interactions, transport, and secondary metabolism most frequently impacted. While variant-affected genes associated with wine anthocyanin content, TA, pH, and alcohol percentage were identified, broader phenotypic characterization will be required to assess their biological significance. Overall, this study provides a genome-wide characterization of extant clonal diversity in Carmenere, with implications for clonal selection and genetic resource conservation.

genomics↗

bioRxiv2026

Patient-derived organoids from malignant pleural effusion to explore for alternative therapies in thoracic tumors

Thoracic malignancies, including lung adenocarcinoma (ADC) and malignant pleural mesothelioma (MPM), remain associated with poor prognosis and limited durable therapeutic responses in advanced stages. Although targeted therapies and immunotherapy have improved outcomes in selected patients, systemic chemotherapy continues to play a central role in routine clinical practice. However, treatment response is highly heterogeneous, and reliable predictive biomarkers of chemotherapy sensitivity are lacking. Both ADC and MPM frequently involve the pleural cavity and are commonly associated with malignant pleural effusion (MPE), which contributes to symptoms such as dyspnea and chest pain and requires therapeutic drainage. Importantly, MPE represents a clinically accessible source of viable tumor cells obtained through minimally invasive procedures. In this study, we established patient-derived organoids (PDOs) from malignant pleural effusion samples obtained from five patients with advanced lung adenocarcinoma and, as an exploratory extension, from one patient with malignant pleural mesothelioma. Organoids were characterized by immunohistochemistry and subjected to systematic chemotherapy drug screening. Inter-model variability in treatment response was assessed, and selected drug sensitivities were further validated through dose-response assays. Pleural effusion-derived organoids successfully recapitulated tumor-specific phenotypic features and revealed marked heterogeneity in chemotherapy sensitivity across models. Secondary validation confirmed the reproducibility of selected responses. Our findings support the feasibility of generating functional organoid models from malignant pleural effusions and highlight their potential as translational platforms for individualized chemotherapy profiling in advanced thoracic malignancies.

cancer biology↗

bioRxiv2026

Immune checkpoint inhibitors amplify type 2 immune mediated repair bypro-regenerative scaffolds

Extracellular matrix (ECM) scaffolds induce type 2 immunity to promote repair. Here, we show that immune cells recruited to ECM-treated murine muscle injuries and clinical soft tissue defects express immune checkpoints. Specifically, TH2 cells and regulatory T cells (Tregs) increase LAG3 expression, while macrophages express PDL2. TCR analysis and a triple-reporter strain for interleukin (IL)-13 and Treg fate-mapping suggest that Tregs in ECM-treated wounds transition into TH2-like exTregs that express LAG3. Immune checkpoint inhibition (ICI) significantly stimulated type 2 immunity in ECM-treated wounds, including increased TH2 cells, Treg transition to TH2-like exTregs, and pro-regenerative macrophages. Moreover, ICI enhanced muscle repair and reduced fibrosis in ECM-treated wounds. Collectively, these findings show Treg/TH2 plasticity in wound healing and introduce a novel ICI application to enhance immune-mediated regeneration.

bioengineering↗

bioRxiv2026

Synthetic Hybrid Receptors for Safer and Programmable T Cell Therapy

Engineered T cell therapies have achieved significant clinical success in hematological malignancies but remain largely ineffective in solid tumors. Overcoming this limitation requires strategies that enhance T cell function while avoiding systemic immune toxicities and pathological T cell states. Existing approaches typically rely on constitutive gene overexpression or suppression to augment potency or remodel the tumor microenvironment, but these strategies frequently lead to dysregulated immune activation and dose-limiting toxicity. Here, we present Hybrid Receptors (Hybrid-Rs), a modular receptor platform that integrates features of chimeric antigen receptors (CARs) and SyNthetic Intramembrane Proteolysis Receptors (SNIPRs) to couple antigen-dependent T cell activation with programmable gene regulation. Hybrid-Rs enable precise, context-dependent control of T cell potency, differentiation states, and conditional expression of secreted immunotherapeutic payloads with otherwise prohibitive toxicity. Hybrid-Rs are readily humanized and compatible with precision genome editing in primary human T cells, providing a direct and practical path to clinical translation.

bioengineering↗

bioRxiv2026

p21(CIP1/WAF1)-mediated partial senescence supports steroidogenesis and therapy resistance in primary prostate cancer cultures

BackgroundProgression of prostate cancer to castration-resistant disease is driven by early adaptive mechanisms that remain poorly defined. Increasing evidence suggests that senescence-associated programs and intratumoral steroidogenesis may contribute to therapeutic resistance, but their functional interplay in hormone-naive disease is unclear. MethodsHormone-naive primary prostate cancer cultures (hnPCs) were established from diagnostic biopsies and characterized for proliferation, therapeutic response, senescence markers, and steroidogenic gene expression. Functional relevance of CDKN1A was assessed by knockdown experiments. Public transcriptomic datasets from ETS fusion-negative, AR signaling inhibitor-naive metastatic castration-resistant prostate cancer (mCRPC) were interrogated for clinical validation. ResultshnPCs exhibited low proliferative capacity yet intrinsic resistance to androgen deprivation therapy and docetaxel. Most cultures displayed coordinated overexpression of CDKN1A/p21CIP1 together with steroidogenic enzymes, particularly AKR1C3, alongside p16INK4a expression and SA-{beta}-galactosidase activity, consistent with a partial senescence-like state. CDKN1A depletion selectively reduced AKR1C3 expression and increased proliferation in a subset of cultures, indicating that p21 maintains specific senescence-associated features while permitting adaptive plasticity. Analysis of ETS fusion-negative, ARSI-naive mCRPC tumors revealed positive correlations between CDKN1A and steroidogenic genes, supporting the translational relevance of this program. ConclusionsThese findings identify a previously underrecognized CDKN1A-associated partial senescence program that supports steroidogenic reprogramming, survival, and early therapeutic resistance in aggressive prostate cancer. This adaptive state may predispose tumors to progression toward castration resistance and represents a potential biomarker and therapeutic vulnerability in high-risk, ETS-negative disease.

cancer biology↗

bioRxiv2026

Distinctive spore architecture and developmental biology of Turicibacter sanguinis reveal unexpected diversity among gut spore formers

Sporulation is a widespread but incompletely characterized trait among gut commensals, where it underpins microbial persistence, transmission, and ecological resilience. Most insights into spore biology derive from Bacilli and Clostridia, yet little is known about sporulation in phylogenetically distant gut-associated lineages. Turicibacter sanguinis, a strict anaerobe linked to host serotonin metabolism, lipid homeostasis, and neurodegenerative disease, represents one such understudied taxon. Here, we integrate ultrastructural, physiological, and comparative genomic analyses to define the sporulation and germination program of T. sanguinis. We show that T. sanguinis forms heat-resistant spores with a canonical core-cortex-coat architecture but displays previously undescribed features including a dual-layered outer envelope and bimodal electron-dense coat morphotypes. Developmental stages of sporulation follow canonical stages of Bacillus- and Clostridium-like sporulation while genomic analyses reveal a hybrid regulatory architecture combining Clostridial-type Spo0A initiation with Bacillus-like late-stage sigma factor control. Germination assays and genomic signatures further indicate a nutrient-responsive, Bacillus-like pathway involving Ger-family receptors, SpoVA-mediated Ca-DPA release, and CwlJ- and SleM-type cortex hydrolases. Together, these findings identify T. sanguinis as a distinct spore-forming lineage within the human gut microbiota and expand the known diversity of sporulation strategies across the Firmicutes.

microbiology↗

bioRxiv2025

Wearable Focused Ultrasound Neuromodulation and Electrophysiological Recording Patch for REM Sleep Enhancement

The rise in sleep disease affecting the general population globally in the past decade has been detrimental to individually and socioeconomically. As of now, approaches often are temporary through medication, permanently using invasive implants with surgical complications or neuromodulation therapy. However, non-invasive, state-dependent neuromodulation during sleep is technically challenging, especially with the lack of flexibility, comfortability and robustness for sleep conditions. Here, we introduce a Non-invasive Electrophysiological Recording and Ultrasound Neuromodulation Sleep Patch (NEUSLeeP) in delivering focused ultrasound stimulation to the subthalamic nucleus (STN) overnight with simultaneous stable polysomnography recording. Our sleep patch integrates a custom eight-channel concentric ring transducer array with real-time electroencephalography (EEG), electrooculography (EOG), electromyography (EMG) recording, and individualized line-of-sight targeting to sonicate deep brain areas while preserving mobility. Our platform operated safely and comfortably across the two-nights sleep study. Stimulation of the left STN was delivered every 90 minutes throughout the night and was associated with a 25% increase in REM (Rapid Eye Movement) sleep duration and a 43 minutes reduction in REM sleep latency compared to a sham night in a study of 26 subjects. Blood Oxygen Level Dependent (BOLD) signal attenuation in functional Magnetic Resonance Imaging (fMRI) was localized primarily to a left ipsilateral basal-ganglia-midbrain-temporal circuit, consistent with selective network modulation rather than global arousal changes. Overall, NEUSLeeP demonstrates feasibility by (i) a light weight and wearable ultrasound neuromodulation and sleep recording during natural sleep; (ii) establishing a potential mechanism relating targeted ultrasound stimulation of STN/sleep networks to REM enhancement.

bioengineering↗

bioRxiv2025

Ascending propriospinal modulation of thoracic sympathetic preganglionic neurons during lumbar locomotor activity

Although the autonomic sympathetic system is activated in parallel with locomotion, the underlying neural mechanisms mediating this coordination are not completely understood. Descending exercise or central command signals from hypothalamic and brainstem regions are thought to activate thoracic spinal sympathetic neurons in parallel with descending locomotor commands. In turn, subsets of thoracic sympathetic preganglionic neurons (SPNs) then increase activation of a constellation of tissues and organs that provide homeostatic and metabolic support during movement and exercise. It is known that neurons within the spinal cord (propriospinal networks) can generate well-coordinated and sustained locomotor activity but whether these propriospinal networks contribute to coordination between locomotor and autonomic systems is unknown. To investigate this, we applied neurochemicals to elicit whole-cord or lumbar-evoked locomotor activity in an in vitro spinal cord preparation, simultaneously recording lumbar ventral root (VR) activity and changes in calcium fluorescence of pre-labelled SPNs in thoracic segments. Using whole-bath drug application to elicit hindlimb locomotor activity, recorded SPN responses were increased in rostral (T4 - T7) compared to caudal (T8 - T11) segments. When locomotor-inducing neurochemicals were applied only to the lumbar region using a split-bath configuration, SPN population responses were increased in rostral (T4-7) but not caudal (T8-9) segments during both tonic and rhythmic VR activity. In both approaches, the greatest numbers of SPNs with increased fluorescence during rhythmic activity were in T6/7, whereas the greatest numbers with unchanged or decreased fluorescence were in caudal segments (T8-T11). Together these findings reveal a strong ascending lumbar to thoracic integrating communication pathway and may represent a key feature of spinal neural network function normally. Such communication pathways should be further investigated for targeted autonomic function(s) activation and therapeutic benefit after spinal cord injury.

neuroscience↗

bioRxiv2025

GCAD: a Computational Framework for Mammalian Genetic Program Computer-Aided Design

Genetic programs can direct living systems to perform diverse, pre-specified functions. As the library of parts available for building such programs continues to expand, computation-guided design is increasingly helpful and necessary. Predictive models aid the challenging design process, but iterative simulation and experimentation are intractable for complex functions. Computer-aided design accelerates this process, but existing tools do not yet capture the behavior of mammalian-specific parts and population-level effects needed for mammalian synthetic biologists. To address these needs, we developed a framework for mammalian genetic program computer-aided design. Starting with a user-defined design specification to quantify circuit performance, the framework uses a genetic algorithm to search through possible designs. Circuit space is defined by a library of experimentally characterized parts and dynamical systems models for gene expression in a heterogeneous cell population. We developed this genetic algorithm using a directed graph-based formulation with biologically constrained rules to explore regulatory connections and parts. We evaluated the framework for design problems of varying complexity, including programs we describe as an amplifier, signal conditioner, and pulse generator, demonstrating that the algorithm can successfully find optimal circuit designs. Finally, we experimentally evaluated selected circuits, demonstrating the path from a predicted circuit design to experimental testing and highlighting the importance of characterization for enabling predictive design. Overall, this framework establishes general approaches that can be refined and expanded, accelerating the design and implementation of mammalian genetic programs.

synthetic biology↗

bioRxiv2025

Dual single-nucleus gene expression atlas of grapevine and Erysiphe necator during early powdery mildew infection

We applied dual-organism single-nucleus transcriptomics to study the interaction between grapevine leaves and Erysiphe necator, the causal agent of powdery mildew, at one and five days post-infection, including controls and three biological replicates. We generated a grapevine leaf atlas encompassing over 100,000 nuclei, and a pathogen atlas of more than 3,000 nuclei. We successfully annotated all major grapevine cell types, including mesophyll, epidermis, phloem and xylem parenchyma, companion cells, and guard cells. We identified key E. necator structures, including appressoria, haustoria, and hyphae, and provided a list of novel cell type markers for both species. We reveal structure-specific gene expression programs in E. necator laying a foundation for future studies of fungal development and virulence mechanisms. In the host, we identified spatially distinct expression patterns of defense-related genes. As the infection progressed, we observed the activation of a coordinated immune response involving multiple cell types, mainly epidermal and mesophyll cells. High-dimensional weighted gene co-expression network analysis identified key hubs and networks associated with cell type-specific signaling and defense response. We describe a spatial separation of pattern- and effector-triggered immunity, supporting a model in which pattern-triggered immunity is activated at the site of pathogen contact and effector-triggered immunity is induced in surrounding tissue.

plant biology↗