Biology subjects

Smith, J. M.

Publications and source records attributed to Smith, J. M..

16 recordsLinked to original sources

bioRxiv2026

Single-cell roadmap of bovine oogenesis and somatic niche interactions during fetal ovarian development

The major events of female germline establishment, from primordial germ cell (PGC) specification to assembly of primordial follicles, occur during embryonic/fetal development. This study presents a single-cell RNA-sequencing atlas of the bovine fetal ovary at four gestational timepoints: estimated day 50, and timed pregnancies at days 70, 90, and 120, capturing the progression of PGCs through commitment, meiotic entry, and early oocyte growth. Fourteen transcriptionally distinct cell populations were identified, including stromal, epithelial, endothelial, immune, somatic support cell, and germ cell lineages. Sub-clustering of the germ cell population resolved six developmental stages (PGCs, transitioning oogonia, proliferative oogonia, committed oogonia, meiotic prophase I oogonia, and oocytes), while that of the somatic support cell compartment revealed five granulosa cell subtypes (steroidogenic, pre-granulosa 1, pre-granulosa 2, pre-granulosa 3, and epithelial cells). Trajectory analysis reconstructed the developmental path of PGCs to oocytes, with sequential activation of meiotic and oocyte-specific gene programs. Representation of all six germ cell stages at day 120 pointed to asynchronous oogenesis in the fetal ovary, which was validated and shown to be region-specific by protein immunolocalization. Intercellular signaling networks between germ cells and the somatic niche were mapped, revealing strong interactions through BMP, KIT, IGF, IGFBP, WNT, and MDK pathways with temporal specificity across gestational ages. The bovine germ cell and pre-granulosa cell subtypes demonstrate significant transcriptional parallels with similarly-staged cells from human fetal ovaries, establishing the cow as a reliable model for human germ cell and ovarian development. Collectively, these data provide a developmental roadmap for bovine oogenesis at the single-cell resolution that advances fundamental understanding of gametogenesis and informs strategies for advanced assisted reproduction.

developmental biology↗

bioRxiv2026

Genome-wide cell type-specific and sex-specific transcriptional dysregulation in the islet of Langerhans underlies islet dysfunction in Down syndrome-related diabetes

Individuals with Down syndrome (trisomy of human chromosome 21) are at a significantly higher risk of developing type 2 diabetes (T2D) than the general population. Systemic metabolic defects in Down syndrome have been linked to gene expression dysregulation in peripheral tissues like the liver, muscle, brain, and adipose. However, the contribution of gene expression dysregulation in the islets of Langerhans to the increased risk of T2D in Down syndrome has not been explored. Here we show that trisomic Ts65Dn mice, a common Down syndrome mouse model, are glucose intolerant and display reduced {beta}-to- cell ratio compared to disomic controls. Using single cell RNA sequencing on islets from Ts65Dn mice we found genome-wide, cell type-specific, and sex-specific transcriptional dysregulation in trisomic islets compared to controls. The Down syndrome-associated transcriptional signature revealed important islet defects, both at the cell autonomous level and at the whole-islet level, increasing T2D susceptibility. Our results put forth innate islet defects as a central underlying cause of Down syndrome-related T2D, warranting additional studies.

developmental biology↗

bioRxiv2025

Molecular profiling of bovine primordial germ cell specification and migration onset reveals a conserved program in bilaminar disc embryos

The goal of this study was to establish the timing and location of bovine primordial germ cell (PGC) specification, as well as the molecular characteristics that differentiate early PGCs from other cells in the embryo. A founder population of PGCs was identified via protein immunolocalization in the posterior epiblast (TBXT+) region at E16, by the unique co-expression of OCT4, SOX17, PRDM1, and TFAP2C with absent SOX2. At E20, PGCs were spread along the allantois and hindgut endoderm, indicative of migration onset. Single-cell RNA-sequencing at E20-22 revealed ten PGCs that were subset using the above markers. Further analysis of this population uncovered conserved and novel markers of the early germline and gave numerous insights into their developmental status, including markers associated with pluripotency maintenance, cell migration, repression of the somatic program, and initiation of epigenetic remodeling. This work establishes the region and transcription factor network of bovine PGC specification at day 16 of embryonic development and the first transcriptomic profile of migratory PGCs in cattle, demonstrating a conserved program with other species that form as a bilaminar embryonic disc leading to gastrulation.

developmental biology↗

bioRxiv2024

Primed bovine embryonic stem cell lines can be derived at diverse stages of blastocyst development with similar efficiency and molecular characteristics

In this study, we established bovine embryonic stem cell (bESC) lines from early (eBL) and full (BL) blastocysts to determine the efficiency of bESC derivation from an earlier embryonic stage and compare the characteristics of the resulting lines. Using established medium and protocols for derivation of primed bESCs from expanded blastocysts, we derived bESC lines from eBLs and BLs with the same efficiency (4/12 each, 33%). Regardless of original blastocyst stage, bESC lines had a similar phenotype, including differentiation capacity, stable karyotype, and pluripotency marker expression over feeder-free transition and long-term culture. Transcriptome and functional analyses indicated that eBL- and BL-derived lines were in primed pluripotency. We additionally compared RNA-sequencing data from our lines to bovine embryos and stem cells from other recent reports, finding that base medium was the predominant source of variation among cell lines. In conclusion, our results show that indistinguishable bESC lines can be readily derived from eBL and BL, widening the pool of embryos available for bESC establishment. Finally, our investigation points to sources of variation in cell phenotype among recently reported bESC conditions, opening the door to future studies investigating the impact of factors aside from signaling molecules on ESC derivation, maintenance, and performance. SUMMARY STATEMENTPrimed bovine embryonic stem cell lines can be readily established from early blastocysts and are indistinguishable from full blastocyst-derived lines, widening the pool of embryos available for stem cell derivation.

cell biology↗

bioRxiv2024

Passive accumulation of alkaloids in putatively non-toxic frogs challenges paradigms of the origins of acquired chemical defenses

Understanding the origins of novel, complex phenotypes is a major goal in evolutionary biology. Poison frogs of the family Dendrobatidae have evolved the novel ability to acquire alkaloids from their diet for chemical defense at least three times. However, taxon sampling for alkaloids has been biased towards colorful species, without similar attention paid to inconspicuous ones that are often assumed to be undefended. As a result, our understanding of how chemical defense evolved in this group is incomplete. Here we provide new data showing that, in contrast to previous studies, species from each undefended poison frog clade have measurable yet low amounts of alkaloids. We confirm that undefended dendrobatids regularly consume mites and ants, which are known sources of alkaloids. Thus, our data suggest that diet is insufficient to explain the defended phenotype. Our data support the existence of a phenotypic intermediate between toxin consumption and sequestration -- passive accumulation -- that differs from sequestration in that it involves no derived forms of transport and storage mechanisms yet results in low levels of toxin accumulation. We discuss the concept of passive accumulation and its potential role in the origin of chemical defenses in poison frogs and other toxin-sequestering organisms. In light of ideas from pharmacokinetics we incorporate new and old data from poison frogs into an evolutionary model that could help explain the origins of acquired chemical defenses in animals and provide insight into the molecular processes that govern the fate of ingested toxins. ResumenComprender los origenes de fenotipos novedosos y complejos es un objetivo central en biologia evolutiva. Las ranas venenosas de la familia Dendrobatidae han desarrollado una novedosa habilidad para adquirir alcaloides de su dieta como defensas quimicas, al menos tres veces. Sin embargo, el muestreo de taxones en busca de alcaloides ha estado sesgado hacia las especies coloridas, sin prestar atencion similar a las poco conspicuas que a menudo se presume, no tienen defensas. Como resultado, nuestra comprension de como evolucionan las defensas quimicas en este grupo es incompleta. Aqui, proporcionamos nuevos datos que muestran que, en contraste con estudios anteriores, las especies de cada clado de ranas venenosas no defendidas tienen cantidades bajas pero cuantificables de alcaloides. Confirmamos que los dendrobatidos no defendidos consumen regularmente acaros y hormigas, que son fuentes conocidas de alcaloides. Por lo tanto, nuestros datos sugieren que la dieta es insuficiente para explicar el fenotipo defendido. Nuestros datos respaldan la existencia de un fenotipo intermedio entre consumo y secuestro de toxinas (acumulacion pasiva), que difiere del secuestro en que no implica formas derivadas de mecanismos de transporte y almacenamiento, pero da lugar a bajos niveles de acumulacion de toxinas. Discutimos el concepto de acumulacion pasiva y su potencial rol en el origen de defensas quimicas en ranas venenosas y otros organismos que secuestran toxinas. Considerando ideas de farmacocinetica, incorporamos datos nuevos y antiguos de ranas venenosas dentro de un modelo evolutivo que podria ayudar a explicar los origenes de defensas quimicas adquiridas en animales, y proporcionar una vision de los procesos moleculares que regulan el destino de las toxinas ingeridas.

evolutionary biology↗

bioRxiv2022

Engineering cellular communication between light-activated synthetic cells and bacteria

Gene-expressing compartments assembled from simple, modular parts, are a versatile platform for creating minimal synthetic cells. In a manner synonymous with natural cells, these life-like assemblies utilise information encoded in DNA within the compartments interior to dictate which proteins are expressed and consequently the overall function of the synthetic cell. Hence, by incorporating gene regulatory motifs into the DNA templates, in situ gene expression can be controlled according to specific stimuli. In this work, cell-free protein synthesis within synthetic cells was controlled using light by encoding genes of interest on light-activated DNA templates. Light-activated DNA contained a photocleavable blockade within the T7 promoter region that tightly repressed transcription until the blocking groups were removed with UV light. In this way, synthetic cells were activated remotely, in a spatiotemporally controlled manner. By applying this strategy to the expression of an acyl homo-serine lactone synthetase, BjaI, quorum-sensing based communication between synthetic cells and bacteria was controlled with light. This work provides a framework for the remote-controlled production and delivery of small molecules from non-living matter to living matter, with applications in biology and medicine.

synthetic biology↗

bioRxiv2022

A SARS-CoV-2 Spike Ferritin Nanoparticle Vaccine is Protective and Promotes a Strong Immunological Response in the Cynomolgus Macaque Coronavirus Disease 2019 (COVID-19) Model

The COVID-19 pandemic has had a staggering impact on social, economic, and public health systems worldwide. Vaccine development and mobilization against SARS-CoV-2 (the etiologic agent of COVID-19) has been rapid. However, novel strategies are still necessary to slow the pandemic, and this includes new approaches to vaccine development and/or delivery, which improve vaccination compliance and demonstrate efficacy against emerging variants. Here we report on the immunogenicity and efficacy of a SARS-CoV-2 vaccine comprised of stabilized, pre-fusion Spike protein trimers displayed on a ferritin nanoparticle (SpFN) adjuvanted with either conventional aluminum hydroxide or the Army Liposomal Formulation QS-21 (ALFQ) in a cynomolgus macaque COVID-19 model. Vaccination resulted in robust cell-mediated and humoral responses and a significant reduction of lung lesions following SARS-CoV-2 infection. The strength of the immune response suggests that dose sparing through reduced or single dosing in primates may be possible with this vaccine. Overall, the data support further evaluation of SpFN as a SARS-CoV-2 protein-based vaccine candidate with attention to fractional dosing and schedule optimization.

microbiology↗

bioRxiv2021

Aerosol Exposure of Cynomolgus Macaques to SARS-CoV-2 Results in More Severe Pathology than Existing Models

The emergence of SARS-CoV-2 pandemic has highlighted the need for animal models that faithfully recapitulate the salient features of COVID-19 disease in humans; these models are necessary for the rapid down-selection, testing, and evaluation of medical countermeasures. Here we performed a direct comparison of two distinct routes of SARS-CoV-2 exposure, combined intratracheal/intranasal and small particle aerosol, in two nonhuman primate species: rhesus and cynomolgus macaques. While all four experimental groups displayed very few outward clinical signs, evidence of mild to moderate respiratory disease was present on radiographs and at the time of necropsy. Cynomolgus macaques exposed via the aerosol route also developed the most consistent fever responses and had the most severe respiratory disease and pathology. This study demonstrates that while all four models were suitable representations of mild COVID-like illness, aerosol exposure of cynomolgus macaques to SARS-CoV-2 produced the most severe disease, which may provide additional clinical endpoints for evaluating therapeutics and vaccines.

microbiology↗

bioRxiv2020

Scalable Analysis of Multi-Modal Biomedical Data

Targeted diagnosis and treatment options are dependent on insights drawn from multi-modal analysis of large-scale biomedical datasets. Advances in genomics sequencing, image processing, and medical data management have supported data collection and management within medical institutions. These efforts have produced large-scale datasets and have enabled integrative analyses that provide a more thorough look of the impact of a disease on the underlying system. The integration of large-scale biomedical data commonly involves several complex data transformation steps, such as combining datasets to build feature vectors for learning analysis. Thus, scalable data integration solutions play a key role in the future of targeted medicine. Though large-scale data processing frameworks have shown promising performance for many domains, they fail to support scalable processing of complex datatypes. To address these issues and achieve scalable processing of multi-modal biomedical data, we present TraNCE, a framework that automates the difficulties of designing distributed analyses with complex biomedical data types. We outline research and clinical applications for the platform, including data integration support for building feature sets for classification. We show that the system is capable of outperforming the common alternative, based on "flattening" complex data structures, and runs efficiently when alternative approaches are unable to perform at all. Key PointsO_LIModern biomedical analyses are integrated pipelines of data access mechanisms and analysis components that operate on and produce datasets in a variety of complex, domain specific formats. C_LIO_LIScalable data integration and aggregation solutions that support joint inference on such large-scale datasets play a key role advancing biomedical analysis. C_LIO_LIQuery compilation techniques that optimize nested data processing are essential for scaling multi-modal, biomedical analysis. C_LI

bioinformatics↗

bioRxiv2020

Protective efficacy of a SARS-CoV-2 DNA Vaccine in wild-type and immunosuppressed Syrian hamsters

A worldwide effort to counter the COVID-19 pandemic has resulted in hundreds of candidate vaccines moving through various stages of research and development, including several vaccines in phase 1, 2 and 3 clinical trials. A relatively small number of these vaccines have been evaluated in SARS-CoV-2 disease models, and fewer in a severe disease model. Here, a SARS-CoV-2 DNA targeting the spike protein and delivered by jet injection, nCoV-S(JET), elicited neutralizing antibodies in hamsters and was protective in both wild-type and transiently immunosuppressed hamster models. This study highlights the DNA vaccine, nCoV-S(JET), we developed has a great potential to move to next stage of preclinical studies, and it also demonstrates that the transiently-immunosuppressed Syrian hamsters, which recapitulate severe and prolonged COVID-19 disease, can be used for preclinical evaluation of the protective efficacy of spike-based COVID-19 vaccine.

microbiology↗

bioRxiv2020

The soybean Rhg1 amino acid transporter protein becomes abundant along the SCN penetration path and impacts ROS generation

Rhg1 mediates soybean resistance to soybean cyst nematode. Glyma.18G022400, one of three resistance-conferring genes at the complex Rhg1 locus, encodes the putative amino acid transporter AATRhg1 whose mode of action is largely unknown. We discovered that AATRhg1 protein abundance increases 7- to 15-fold throughout root cells penetrated by SCN. These root cells develop increased abundance of vesicles and larger vesicle-like bodies. AATRhg1 was often associated with these vesicles. AATRhg1 abundance remained low in syncytia (plant reprogrammed feeding cells), unlike the Rhg1 -SNAP protein whose abundance was previously shown to increase in syncytia. In N. benthamiana, if soybean AATRhg1 was present, oxidative stress promoted formation of larger macrovesicles and they contained AATRhg1. AATRhg1 was found to interact with GmRBOHC2, a soybean ortholog of Arabidopsis RBOHD previously found to exhibit upregulated expression upon SCN infection. Reactive oxygen species (ROS) generation was more elevated when AATRhg1 and GmRBOHC2 abundance were co-expressed. These findings suggest that AATRhg1 contributes to SCN resistance along the penetration path as SCN invades the plant, and does so at least in part by interactions with GmRBOHC2 that increase ROS production. The study also shows that Rhg1 resistance functions via at least two spatially and temporally separate modes of action.

plant biology↗

bioRxiv2020

Animal Model Prescreening: Pre-exposure to SARS-CoV-2 impacts responses in the NHP model

COVID-19 presents herculean challenges to research and scientific communities for producing diagnostic and treatment solutions. Any return to normalcy requires rapid development of countermeasures, with animal models serving as a critical tool in testing vaccines and therapeutics. Animal disease status and potential COVID-19 exposure prior to study execution may severely bias efficacy testing. We developed a toolbox of immunological and molecular tests to monitor countermeasure impact on disease outcome and evaluate pre-challenge COVID-19 status. Assay application showed critical necessity for animal pre-screening. Specifically, real-time PCR results documented pre-exposure of an African Green Monkey prior to SARS-CoV-2 challenge with sequence confirmation as a community-acquired exposure. Longitudinal monitoring of nasopharyngeal swabs and serum showed pre-exposure impacted both viral disease course and resulting immunological response. This study demonstrates utility in a comprehensive pre-screening strategy for animal models, which captured the first documented case of community-acquired, non-human primate infection. One Sentence SummaryPre-exposure to SARS-CoV-2 affects biomarker responses in animal models, highlighting a need for robust pre-screening protocols prior to medical countermeasure studies.

immunology↗

bioRxiv2020

Measuring the accuracy of gridded human population density surfaces: a case study in Bioko Island, Equatorial Guinea

Geospatial datasets of population are becoming more common in models used for health policy. Publicly-available maps of human population in sub-Saharan Africa make a consistent picture from inconsistent census data, and the techniques they use to impute data makes each population map unique. Each mapping model explains its methods, but it can be difficult to know which map is appropriate for which policy work. Gold-standard census datasets, where available, are a unique opportunity to characterize maps by comparing them with truth. We use census data from Bioko Island, in Equatorial Guinea, to evaluate LandScan (LS), WorldPop (WP), and the High-Resolution Settlement Layer (HRSL). Each layer is compared to the gold-standard using statistical measures to evaluate distribution, error, and bias. We investigated how map choice affects burden estimates from a malaria prevalence model. Specific population layers were able to match the gold-standard distribution at different population densities. LandScan was able to most accurately capture highly urban distribution, HRSL matched best at all other lower population densities and WorldPop performed poorly everywhere. Correctly capturing empty pixels is key, and smaller pixel sizes (100 m vs 1 km) improve this. Normalizing areas based on known district populations increased performance. The use of differing population layers in a malaria model showed a disparity in results around transition points between endemicity levels. The metrics in this paper, some of them novel in this context, characterize how these population maps differ from the gold standard census and from each other. We show that the metrics help understand the performance of a population map within a malaria model. The closest match to the census data would combine LandScan within urban areas and the HRSL for rural areas. Researchers should prefer particular maps if health calculations have a strong dependency on knowing where people are not, or if it is important to categorize variation in density within a city.

ecology↗

bioRxiv2020

Plasticity of behavioural variability reflects conflicting selection in group-living and solitary desert locusts

Animals living in groups tend to express less variable behaviour than animals living alone. It is widely assumed that this difference reflects, at least in part, an adaptive response to contrasting selection pressures: group-living should favour the evolution of more uniform behaviour whereas lone-living should favour behaviour that is less predictable. Empirical evidence linking these contrasting selection pressures to intrinsic differences in behavioural variability is, however, largely lacking. The desert locust, Schistocerca gregaria, manifests in two very distinct eco-phenotypes, a lone-living cryptic "solitarious phase" and a swarming "gregarious phase" that aggregates into very large and dense groups. This "phase polyphenism" has evolved in response to contrasting selection pressures that change rapidly and unpredictably. Phase differences in mean behaviour are well-characterised, but no previous study has considered differences in variability. Here we used locust phase polyphenism to test the hypothesis that group living leads to the evolution of reduced intrinsic variability in behaviour. We measured two behaviours in both phenotypes: locomotor activity in the presence of conspecifics, and locomotor hesitation in approaching food when alone. We assayed each individual repeatedly and estimated variability relative to the mean in log-normal mixed-effects models that explicitly account for the means-variance dependency in the behavioural measures. Our results demonstrate that relative behavioural variability differs between the two phases in line with predictions from ecological theory: both within-individual and between-individual variability were lower in the group-living gregarious phenotype. This contrasts with previous studies on social niche construction in spiders and crickets, and highlights the importance of social ecology: in animals that form non-social collectives, such as locusts, reduced individual behavioural variability is key for coherent collective behaviour. The differences in variability persisted when gregarious locusts were tested in isolation and solitarious locusts were tested in groups, indicating that they arise not simply as flexible reactions to different social contexts, but are intrinsic to the individual animals of each phase. This "variance polyphenism" in locusts provides empirical evidence that evolutionary adaptation for group living has driven a reduction in within- and between-individual behavioural variability.

ecology↗

bioRxiv2019

Advancing clinical cohort selection with genomics analysis on a distributed platform

BackgroundThe affordability of next-generation genomic sequencing and the improvement of medical data management have contributed largely to the evolution of biological analysis from both a clinical and research perspective. Precision medicine is a response to these advancements that places individuals into better-defined subsets based on shared clinical and genetic features. The identification of personalized diagnosis and treatment options is dependent on the ability to draw insights from large-scale, multi-modal analysis of biomedical datasets. Driven by a real use case, we premise that platforms that support precision medicine analysis should maintain data in their optimal data stores, should support distributed storage and query mechanisms, and should scale as more samples are added to the system. ResultsWe extended a genomics-based columnar data store, GenomicsDB, for ease of use within a distributed analytics platform for clinical and genomic data integration, known as the ODA framework. The framework supports interaction from an i2b2 plugin as well as a notebook environment. We show that the ODA framework exhibits worst-case linear scaling for array size (storage), import time (data construction), and query time for an increasing number of samples. We go on to show worst-case linear time for both import of clinical data and aggregate query execution time within a distributed environment. ConclusionsThis work highlights the integration of a distributed genomic database with a distributed compute environment to support scalable and efficient precision medicine queries from a HIPAA-compliant, cohort system in a real-world setting. The ODA framework is currently deployed in production to support precision medicine exploration and analysis from clinicians and researchers at UCLA David Geffen School of Medicine.

bioinformatics↗

bioRxiv2018

Strong hybrid male incompatibilities impede the spread of a selfish chromosome between populations of a fly.

Meiotically driving sex chromosomes manipulate gametogenesis to increase their transmission at a cost to the rest of the genome. The intragenomic conflicts they produce have major impacts on the ecology and evolution of their host species. However their ecological dynamics remain poorly understood. Simple population genetic models predict meiotic drivers will rapidly reach fixation in a population and spread across a landscape. In contrast, natural populations commonly show spatial variation in the frequency of drivers, with drive present in clines or mosaics across species ranges. For example, Drosophila subobscura harbours a Sex Ratio distorting drive chromosome (\"SRs\") at 15-25% frequency in North Africa, present at less than 2% frequency in adjacent Southern Spain and absent in other European populations. Here, we investigate the forces preventing the spread of the driver northward. We show that SRs has remained at a constant frequency in North Africa, and failed to spread in Spain. We find strong evidence in favour of our first hypothesis, genetic incompatibility between SRs and Spanish autosomal background. When we cross SRs from North Africa onto Spanish genetic backgrounds we observe strong SRs specific incompatibilities in hybrids. The incompatibilities increase in severity in F2 male hybrids, leading to almost complete infertility. We find no evidence supporting a second hypothesis, that there is resistance to drive in Spanish populations. We conclude that the source of the stepped frequency variation is genetic incompatibility between the SRs chromosome and the genetic backgrounds of the adjacent population, preventing SRs spreading northward. The low frequency of SRs in South Spain is consistent with recurrent gene flow across the Strait of Gibraltar combined with selection against the SRs element through genetic incompatibility. This demonstrates that incompatibilities between drive chromosomes and naive populations can prevent the spread of drive between populations, at a continental scale.

evolutionary biology↗