Biology subjects

Short, M.

Publications and source records attributed to Short, M..

6 recordsLinked to original sources

bioRxiv2026

Development of a Staining-based Electrophoretic Mobility Shift Assay for Analyzing Pbx1, DNA and HoxA9 Interactions

Transcription factors (TFs) are master regulators of gene expression and control a wide range of cellular functions including embryonic development, signaling pathways, immune response, and differentiation. A tight regulation of gene expression is crucial during all stages of life and changes in the TF function can lead to developmental abnormalities, diseases such as cancer, or resistance to treatment. Therefore, TFs are a promising class of drug targets, and the techniques that would contribute to the development of TF modulators are critical. Electrophoretic Mobility Shift Assay (EMSA) has been a primary tool to verify protein-DNA interactions, where a fluorescent, biotin, or isotope end-labelled DNA probe is used to quantify binding. Such labeling techniques, however, can be costly, time consuming, possess safety hazard risks and require capital equipment for imaging. Here, we optimized a label-free, staining-based EMSA to characterize a potential drug target, homeodomain (HD) TF Pre-B-cell leukemia homeobox-1 (Pbx1) and its binding partner Homeobox A9 (HoxA9). Staining the polyacrylamide EMSA gel with a DNA intercalating green cyanine dye - SYBR safe - allowed the visualization of Pbx1 homeodomain interactions with DNA at nanomolar concentrations and enabled quantitative determination of protein-DNA apparent binding affinity in the sub-micromolar range. Furthermore, a ternary complex of homeodomains of Pbx1 with HoxA9 and the DNA was also visible in the assay. We have shown that the staining-based EMSA can be used to evaluate inhibitors of Pbx1 that block the interaction with DNA. We have further validated the data from our assay with fluorophore labeling-based EMSA. Overall, using HD transcription factors Pbx1 and HoxA9 as a model, we have optimized a reliable and cost-effective staining-based EMSA that enables the high-sensitivity visualization and quantitative evaluation of transcription factor-DNA complexes without the need for end-labeled DNA probes. The streamlined workflow could be readily adapted to other DNA-binding proteins to study their interactions with the DNA, inhibitors, and other proteins.

biochemistry↗

bioRxiv2026

Modelling Anaerobic Co-Digestion with Agricultural Feedstock: Model Validation and Cross-Reactor Verification

As the United Kingdom (UK) targets net-zero emissions by 2050, anaerobic digestion (AD) has become a cornerstone of renewable energy infrastructure. However, mathematical models, such as the Anaerobic Digestion Model No. 1 (ADM1), often struggle with high-solids agricultural feedstocks because they rely on Chemical Oxygen Demand (COD), a metric that introduces significant experimental error. To overcome this, this study applies an established mass-based ADM1 framework tailored for the co-digestion of maize silage and cow manure sourced from a UK AD site. This study uses a parallel reactor framework, using two identical laboratory-scale reactors to physically replicate the dynamic conditions of the full-scale site. A Global Sensitivity Analysis was first conducted, identifying biomass decay and carbohydrate breakdown rates as the most influential factors affecting system stability and model accuracy. The model was calibrated using data from the first reactor and then tested against an independent second reactor subjected to significant organic loading stress. Results show high predictive capabilities, with the model achieving a R2 of 0.81 for biogas production during calibration. The model maintained high predictive accuracy during the validation test of the second physical twin, achieving an R2 of 0.85, proving that the framework is robust and not overfitted to a single dataset. While predicting rapid fluctuations in pH and alkalinity remains challenging, the mass-based approach effectively forecasts gas yields and process stability. This methodology provides a reliable foundation for robust process modelling, offering a scalable tool for the UK biogas sector to optimise AD. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/721061v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@92c7e2org.highwire.dtl.DTLVardef@80d723org.highwire.dtl.DTLVardef@ac3d24org.highwire.dtl.DTLVardef@1e21a51_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

A Novel Bioprocess Control Strategy Under Uncertainty via Operational Space Identification

Bioprocesses are critical for sustainable industrial development but face challenges from their inherent uncertainties that affect efficiency and scalability. This study in-troduces a worst-case operational space design framework, integrating symbolic optimization with scenario-based validation, to preemptively mitigate uncertainties so that key performance indicators are consistently satisfied even under adverse conditions. The methodology is demonstrated through two case studies: a lab-scale fermentation for astaxanthin production and a site-scale anaerobic digestion for biogas production. Process uncertainty is quantified through model parameter variations (2% - 13%) to reflect real-world scenarios. The results indicate that highly flexible operational spaces are identified in both case studies, with control variables able to vary by up to 25% and 15% in the respective systems, while consistently adhering to system constraints. Validation over 10,000 scenarios confirmed 0 violation per case study. The proposed framework delivers validated operational flexibility with modest computational requirements, making it practical for lab-to-site deployment.

microbiology↗

bioRxiv2026

Genetic Modifiers of Cognitive Function: Novel Genetic Associations with Memory, Executive Function, and Attention in the Long Life Family Study

Cognitive performance is central to health and quality of life. Studying the factors that sustain performance may offer insights into maintaining cognitive function into advanced ages and may inform strategies to promote healthy cognitive aging. To identify single nucleotide polymorphisms (SNPs) underlying cognitive function, we performed genome-wide association studies (GWAS) of nine neuropsychological test scores capturing performance in three cognitive domains in 2,455 participants of the Long Life Family Study (LLFS). We identified 12 variants in seven tests and three domains that reached genome-wide significance (p < 5x10-). Three rare (minor allele frequency, European population MAF<0.01) protective, intronic variants, rs190287985 (CCSER1), rs75730801 (FHOD3), and rs552842447 (LINC00508), were uniquely associated with semantic fluency, phonemic fluency and number span forward, respectively. Two rare deleterious variants, rs556333682 and rs188304645, were associated with performance on the Hopkins Verbal Learning Test-Revised (HVLT-R) learning trials and lie in ischemia-related genes SH3TC1 and RPH3A. Another variant, rs180691759, associated with HVLT-R delayed recall, was proximal to RSPO3 and linked to decreased ECHDC1 expression, implicating ischemic and unexplained Ethylmalonic acid (EMA) pathways. We compared the results with GWASs of a general cognitive factor (GCF) and reaction time (RT) in the UK Biobank and meta-analysis results of the UK Biobank, CHARGE and COGENT by Davies et al. We found that rs535509651 associates with HVLT-R delayed recall in the LLFS and nominally associates (p<0.05) with GCF, and that rs10424537 associates with Immediate Logical Memory in the LLFS and nominally associates with RT. Furthermore, we identified 5 genome-wide significant loci in Davies et al. that reached loci adjusted significance in the LLFS (GCF p<0.05/128 and RT p<0.05/39). Each locus was associated with a single cognitive domain in the LLFS. We annotated the genome-wide significant results with quantitative trait loci (QTL) analyses of whole blood transcriptomic, serum metabolomic data, and gene set enrichment analyses (GSEA) using all nominally significant transcripts (p < 0.05/12). QTL analyses discovered 1 SNP-transcript (ECHDC1, p < 3 x 10-6), no SNP-lipid (p < 2 x 10-4), and no SNP-polar metabolite (p < 2 x 10-4) associations. Gene set enrichment analyses identified three pathways at FDR < 0.05. Our findings provide insight into the domain-specific genetic architecture of cognitive function.

genetics↗

bioRxiv2025

Robust Serum Proteomic Signatures of APOE2

We previously identified a signature of 16 serum proteins that highlighted a role of the e2 allele of APOE in lipid regulation via apolipoprotein B (APOB) and apolipoprotein E (APOE), and in inflammation. The serum proteins were profiled using the aptamer-based Somalogic technology. Here, we validate and expand the serum protein signature of APOE using a combination of mass-spectrometry, ELISA, Luminex, antibody-based Olink proteomics, and blood transcriptomics. We replicate the association between APOB and the e2 allele of APOE, we correct the pattern of association between APOE genotypes and serum level of APOE, and we detect new associations between APOE genotypes and the complex of apolipoproteins APOC1, APOC4, APOC2, APOC3, APOE, APOF and APOL1. In addition, we discover 13 new proteins that correlate with APOE genotypes. This extended signature includes granule proteins CAMP, CTSG, DEFA3, and MPO secreted from neutrophils and points to olfactomedin 4 (OLFM4) as a new target for the prevention of Alzheimers disease.

genetics↗

bioRxiv2022

Genetic exchange in Leishmania is facilitated by IgM natural antibodies

Host factors mediating Leishmania genetic exchange are not well defined. Here, we demonstrate that IgM antibodies, but not IgG or IgA, facilitate parasite genetic hybridization in vitro and in vivo. IgM induces the gradual and transient formation of a structured parasite clump in a process essential for L. major and L. tropica hybridization in vitro. Parasite hybrids and 3-nucleated parasites were observed inside this structure, named the Leishmania mating clump. IgM was also required for or significantly increased Leishmania hybrid formation in vivo. At minimum, we observed a 12-fold increase in the proportion of hybrids recovered from sand flies provided a second blood meal containing IgM compared to controls. Notably, genetic backcross events in sand flies were only observed in the presence of IgM, and were reproducibly recovered, reinforcing the relevance of IgM for Leishmania genetic exchange in vivo. The in vitro and in vivo Leishmania crosses from these studies resulted in full genome hybrids. Leishmania co-option of a host antibody to facilitate mating in the insect vector establishes a new paradigm of parasite-host-vector coevolution that promotes parasite diversity and fitness through genetic exchange.

microbiology↗