Biology subjects

Johnson, S. D.

Publications and source records attributed to Johnson, S. D..

6 recordsLinked to original sources

bioRxiv2026

VigExp: A functionally verified platform for aiding cowpea (Vigna unguiculata) and related legume crop improvement

Legumes include some of the worlds most significant crop species, such as cowpea (Vigna unguiculata), a subsistence crop widely grown in sub-Saharan Africa. Despite their importance, legume crop improvement is hindered by a lack of high-resolution expression data, particularly for reproductive tissues and cell types. Here, we report on VigExp, a tool for visualising cowpea gene expression datasets. We demonstrate its utility across a range of vegetative and reproductive cell types of varieties IT97K-499-35 and IT86D-1010, which exhibit 93.75% protein sequence conservation and are amenable to stable transformation. This includes previously published transcriptomes of vegetative, floral and seed tissues, combined with developmentally staged male and female reproductive tissues. Also integrated are novel transcriptomes of laser-captured cell types covering reproductive development from meiosis to early embryo formation post-fertilisation. Spatial expression patterns and transcript levels can be visualised through an electronic fluorescent pictograph (eFP) browser. Validated by RT-qPCR, in situ hybridisation, transgenic, and CRISPR gene editing analyses, the predictive accuracy of VigExp matches prior cowpea functional study observations. Critical genes for nodule development and regulation were also identified and their expression patterns established in cowpea. Novel reference genes, constitutively expressed gene promoters for visualisation markers/gene-editing, and tissue- and cell-specific gene promoters for targeting these regions, were identified. The A-type cyclin, VuTAM2, was also identified, with a critical role in male meiosis established. Collectively, VigExp represents an adaptable and updatable resource to support crop improvement in cowpea and other legumes, which are often highly syntenic with respect to genome composition.

plant biology↗

bioRxiv2026

BABYBOOM-like expression in the cowpea egg and central cellenables parthenogenesis, endosperm development, and viable haploid seed formation

Introductory Paragraph (Nature Plants format)Parthenogenesis or fertilization-independent embryogenesis occurs at low frequency in sexual plants. Expression of BABYBOOM-like (BBML) and PARTHENOGENESIS (PAR) genes in the egg cell of several diploid dicot crops induce parthenogenesis at varying frequency; however, recovery of viable haploid seeds has rarely been reported, perhaps due to a lack of viable endosperm formation. In the legume cowpea (Vigna unguiculata L. Walp), ectopic egg cell expression of the endogenous BBML homolog (VuBBML1) and PAR from Taraxacum officinale induces parthenogenesis; however, seeds abort as endosperm formation is blocked following self-pollination. Expression of VuBBML1 in both the egg cell and central cell, together with central cell fertilization following self-pollination, results in viable seeds that germinate and give rise to haploid plants. VuBBML1 has a functional role in the formation of cowpea embryo and endosperm seed compartments. This finding opens possibilities for establishing double haploid production during homozygous parental breeding, and asexual seed induction for fixing hybrid vigor in cowpea.

plant biology↗

bioRxiv2026

Intranasal Delivery of HIV/SIV Antigens with NE/AS01B Adjuvants Enhances Cellular Immunity and Reduces Viral Loads in SHIV-Challenged Macaques

The primary route of HIV transmission is across mucosal tissues; therefore, developing a protective mucosal vaccine is a top priority. In a pilot study, using a macaque model, we delivered HIV gp140 envelope glycoprotein and SIVmac239 P55 Gag and Nef antigens using heterologous prime/boost via the intranasal route with a soybean oil-based nanoemulsion (NE) adjuvant and through the intramuscular route with the AS01B adjuvant system to generate enhanced cell-mediated immunity. We used a NE adjuvant to promote gut-homing cell-mediated immunity and the AS01B system to enhance humoral immune responses. Following intrarectal challenge with SHIV 4MTF.tHy, vaccinated macaques acquired the virus but experienced lower viral loads in plasma (P=0.003) and CSF (P=0.001), and potent polyfunctional gag-specific (CD107a+, IFN{gamma}, TNF+) responses across diverse lymph nodes. Significant antibody-dependent complement deposition (ADCD) and antibody-dependent cellular phagocytosis (ADCP) responses were induced, and gut-microbiome crosstalk could be modulated and showing reduced SHIV-dysbiosis. Notably, vaccination preserved mucosal all-trans retinoic acid levels (atRA) (p<0.05). However, no significant differences were observed for antibody responses between vaccinated and unvaccinated macaques. In summary, the induced gut-homing properties by the NE adjuvant are effective at generating cell-mediated immunity and reducing viral set points and warrant further investigations as a mucosal adjuvant in HIV vaccine design. ImportanceThree major non-mucosal vaccine trials (RV144, HVTN702, and 706) failed to reduce HIV infection rates. Therefore, new approaches in developing a mucosal vaccine remain an effective strategy to attempt to control HIV infection. Coherent vaccine approaches against HIV were focused on immune correlates related to viral loads, persistent reservoirs, and antibody responses. As a proof-of-principle, we developed a vaccine regimen consisting of AS01B and an adjuvanted oil-in-water NE cleaved HIV clade C gp140 protein and non-cleaved Gag, and nef particles administered through intranasal, subcutaneous, and intramuscular routes, followed by intrarectal challenge with clade C SHIV. This vaccine elicited strong ADCD and ADCP responses, modulated immune-microbiome crosstalk, and reduced susceptibility to SHIV-infection-associated dysbiosis. Additionally, it preserved mucosal all trans retinoic acid (atRA) levels, suggesting a potential role for this approach in HIV vaccine development.

microbiology↗

bioRxiv2025

Electrochemical guided mode resonance biosensor for simultaneous refractive index and electrochemical measurements

A comprehensive miniaturised biosensing platform needs to detect multiple analytes, which often rely on different transduction mechanisms for their detection and quantification. This necessitates the development of multimodal sensors capable of simultaneous measurements without interference between measurement modalities. Guided mode resonance (GMR) biosensors are highly sensitive to refractive index changes and well suited to out-of-plane optical coupling, but have not previously been implemented in a multimodal configuration. Here, we present the electrochemical guided mode resonance (EC-GMR) sensor, a Si3N4 GMR photonic grating integrated with an indium tin oxide (ITO) electrode that enables concurrent optical and electrochemical sensing. Finite difference time domain (FDTD) simulations show that the resonance wavelength of the GMR shifts as a function of ITO thickness and applied bias. These findings are validated experimentally using EC-GMR devices fabricated with a range of ITO thicknesses. We demonstrate that the EC-GMR achieves a refractive index sensitivity of 84.4 nm/RIU while simultaneously measuring the double-layer capacitance. To highlight its multimodal capability, we characterise the optical and electrochemical responses of methylene blue, a widely used redox reporter in biosensing. By integrating photonic and electrochemical modalities in a compact format, the EC-GMR platform provides critical analytical information beyond that which could be obtained from a traditional single-modality sensor. This approach extends the analytical utility of GMR sensors and represents a robust, adaptable solution for diverse biosensing applications, from clinical diagnostics to environmental monitoring.

biophysics↗

bioRxiv2024

TISSUE-SPECIFIC METABOLOMIC REPROGRAMMING DETERMINES THE DISEASE PATHOPHYSIOLOGY OF SARS-COV-2 VARIANTS IN HAMSTER MODEL

Despite significant effort, a clear understanding of host tissue-specific responses and their implications for immunopathogenicity against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant infection has remained poorly defined. To shed light on the interaction between organs and specific SARS-CoV-2 variants, we sought to characterize the complex relationship among acute multisystem manifestations, dysbiosis of the gut microbiota, and the resulting implications for SARS-CoV-2 variant-specific immunopathogenesis in the Golden Syrian Hamster (GSH) model using multi-omics approaches. Our investigation revealed increased viremia in diverse tissues of delta-infected GSH compared to the omicron variant. Multi-omics analyses uncovered distinctive metabolic responses between the delta and omicron variants, with the former demonstrating dysregulation in synaptic transmission proteins associated with neurocognitive disorders. Additionally, delta-infected GSH exhibited an altered fecal microbiota composition, marked by increased inflammation-associated taxa and reduced commensal bacteria compared to the omicron variant. These findings underscore the SARS-CoV-2-mediated tissue insult, characterized by modified host metabolites, neurological protein dysregulation, and gut dysbiosis, highlighting the compromised gut-lung-brain axis during acute infection. TeaserIn hamsters at acute infection, SARS-CoV-2 variant-specific metabolic responses and gut dysbiosis dysregulate synaptic transmission proteins.

systems biology↗

bioRxiv2020

Gene expression in reproductive cell-types isolated in temporal sequence from meiosis to early seed initiation in cowpea (Vigna unguiculata L. Walp)

Molecular knowledge of pathways regulating seed formation in legumes, remains scarce. Thirteen isolated cell-type transcriptomes were developed, spanning temporal events of male and female gametogenesis and seed initiation, to examine pathways involved in cowpea seed formation. In situ hybridization confirmed localization of in silico identified cell-specific genes, verifying transcriptome utility. Cowpea and Arabidopsis reproductive cells showed some conservation in regulators enabling cell-type expression as some cowpea cell-specific genes promoters and their Arabidopsis homologs directed expression to identical reproductive cell-types in transgenic plants. In silico analyses revealed gene expression similarities and differences with genes in pathways regulating reproductive events in other plants. Meiosis-related genes were expressed at mitotic stages of gametogenesis and during sporophytic development in cowpea. Plant hormone pathways showing preferential expression at particular reproductive stages were identified. Expression of epigenetic pathways, resembling those found in Arabidopsis, including microRNA mediated gene silencing, RNA directed DNA methylation and histone modification were associated with particular stages of male and female gametophyte development, suggesting roles in gametogenic cell specification and elaboration. Analyses of cell-cycle related gene expression in mature cowpea female gametophytes, indicated that the egg and central cell were arrested at the G1/S and G2/M cell cycle phases, respectively, prior to fertilization. Pre-fertilization female gametophyte arrest was characterized by barely detectable auxin biosynthesis gene expression levels, and elevated expression of genes involved in RNA-mediated gene silencing and histone modification. These transcriptomes provide a useful resource for additional interrogation to support functional analyses for development of higher yielding cowpea and syntenic legume crops. One sentence summaryAnalyses of laser capture derived cell-type transcriptomes spanning meiosis to seed initiation revealed gene expression profiles during cell specification and reproductive development in cowpea.

plant biology↗