Biology subjects

Thomas, J. E.

Publications and source records attributed to Thomas, J. E..

9 recordsLinked to original sources

bioRxiv2026

Biophysical and enzymatic comparison of Bacillus safensis and Bacillus subtilis malate dehydrogenase (MDH) enzymes

Species of Bacillus bacteria including Bacillus safensis and Bacillus subtilis are finding increasing uses in biotechnology and bioremediation, thanks in part to their metabolic robustness. Malate dehydrogenase (MDH) is at the heart of central metabolism and thus a better understanding of Bacillus MDH proteins could aid in the optimization of these applications. MDH of Bacillus spp. belong to the lactate dehydrogenase (LDH)-like class of MDHs, otherwise known as the MDH3 class. Despite wide prevalence in nature among prokaryotes and archaea, this typically homotetrameric class is understudied compared to the MDH1 and MDH2 classes found in eukaryotes. We therefore recombinantly expressed and purified MDH proteins from two societally relevant Bacillus spp.-B. safensis and B. subtilis-and characterized them biophysically (via Size Exclusion Chromatography-Small Angle X-ray Scattering (SEC-SAXS) and Differential Scanning Fluorimetry (DSF)) and enzymatically (via spectroscopic activity assays). As expected based on their high sequence identity, the two MDH orthologs had similar properties in most regards, including a tetrameric structure and high susceptibility to substrate inhibition. However, we uncovered differences in conditional thermal stability, in addition to subtle differences in enzymatic activity that offer insight into the workings of LDH-like MDH. Summary statementMalate dehydrogenase (MDH) is a fundamental metabolic enzyme, from microbes to mammals, yet comparably little is known about microbial MDH, especially MDH of the tetrameric MDH3 class. We compare the biophysical and enzymatic properties of two such enzymes from the societally relevant bacterial species Bacillus subtilis and Bacillus safensis, offering useful insight with potential biotechnological implications.

biochemistry↗

bioRxiv2026

Sustaining smallholder banana production in Banana Bunchy Top Disease endemic landscapes: integrating clean seed, roguing, and farmer training

Banana bunchy top virus (BBTV) continues to threaten smallholder livelihoods and food security across sub-Saharan Africa. While clean-seed programmes are widely promoted, their long-term effectiveness is often compromised by rapid reinfection in endemic landscapes. We developed an integrated framework combining spatially explicit, stochastic epidemiological modelling with additional cost-benefit analysis and use of socio-behavioural data to evaluate strategies for stabilising production. Our results demonstrate that frequent monthly inspections and accurate symptom detection are essential for disease suppression. Crucially, the economic analysis reveals that prioritizing diagnostic competence as an economic asset is necessary: improving detection efficiency can more than double farmer net revenue under realistic market conditions. Socio-behavioural findings further confirm that a farmers ability to correctly recognise symptoms is the strongest predictor of roguing adoption, far outweighing demographic characteristics. These results provide quantifiable guidance for disease management and highlight that the sustainability of clean-seed interventions hinges on shifting policy from simple seed replacement to investing in farmer diagnostic capacity. Strengthening this local surveillance capability transforms informal seed systems into resilient, durable tools for safeguarding household nutrition and regional food security.

plant biology↗

bioRxiv2025

Parameterisation of epidemiological models from small field experiments: a case study of banana bunchy top virus transmission

Accurate estimation of epidemiological parameters from limited field data remains a major challenge in plant disease modeling. We present a novel data-augmented adaptive multiple importance sampling (DA-AMIS) framework that integrates Bayesian inference with stochastic epidemic modeling to estimate key transmission parameters from small field experiments. Using detailed individual-level observations from a 24-plant experiment on the natural spread of banana bunchy top virus (BBTV) in Benin, we jointly inferred infection timing, dispersal characteristics, and transmission rates for both primary and secondary infections. Model validation against independent datasets from BBTV field trials in Burundi and Malawi showed close correspondence between simulated and observed prevalence dynamics, confirming the generality of parameter estimates across regions. The inferred 12% infection rate of replanting suckers underscores the risk of disease introduction through planting material, while simulations identified April as the period of peak infection, providing actionable insights for surveillance timing.

plant biology↗

bioRxiv2025

Controlling Banana Bunchy Top Disease in Benin: crop protection strategies with socioeconomic perspectives

SummaryO_LIThis study combines satellite mapping, field surveillance, farmer surveys, and disease modelling to assess BBTV dynamics across Benin. It provides the first national-scale map of banana cultivation in Benin and identifies high-risk areas for targeted intervention. C_LIO_LIThe study highlights the dominance of informal networks for exchange of planting material ([~]80% of farmers), limited farmer awareness of BBTV ([~]60% unaware), and low recognition of symptoms or transmission routes, all of which contribute to the spread and persistence of disease. C_LIO_LIAlthough women represented only a quarter of respondents, they demonstrated comparable levels of market orientation and access to planting materials and land. The findings call for spatially targeted, socially informed BBTV management strategies that integrate clean planting material systems, farmer education, and accessible control methods. C_LIO_LIBBTV was detected in 140 out of 747 fields surveyed, with the highest prevalence in the humid southern regions. No cases were found in the northern Sudanian zone, reflecting known agroecological patterns of disease distribution. C_LIO_LIModelling of three control strategies - decapitation, uprooting, and injection - revealed injection as most effective nationally (70% reduction in disease incidence), while uprooting was most effective in vulnerable communities with high disease pressure. C_LIO_LIThe study reveals an interconnected system in which socioeconomic vulnerability, informal seed networks, limited disease awareness, and spatial clustering of banana cultivation collectively drive BBTV dynamics in Benin, highlighting the need for epidemiologically effective, socially informed, and spatially targeted interventions. C_LI Societal Impact StatementBanana and plantain are critical for food security and income generation in West Africa, particularly for smallholder farmers in countries such as Benin. However, banana bunchy top virus (BBTV) poses a major threat to sustainable production. This study integrates high-resolution remote sensing, field epidemiology, mathematical modelling, and socioeconomic analysis to improve understanding of the spread of BBTV and to evaluate the effectiveness of different disease control strategies. Our findings reveal that BBTV risk is highest in southern Benin, where socioeconomic vulnerability is also greatest. Low disease awareness, limited adoption of effective control methods and informal exchange of planting material exacerbate this risk. By identifying priority areas and strategies tailored to local social, economic, and agroecological contexts, this research offers a roadmap for designing targeted, sustainable BBTV management programs. These insights can support smallholder resilience, reduce disease burden, and safeguard banana-based livelihoods across sub-Saharan Africa.

plant biology↗

bioRxiv2025

Identification of QTLs linked to partial resistance to foot and root rot caused by Fusarium avenaceum and Fusarium oxysporum in faba bean (Vicia faba)

Foot and root rot, caused by a complex of soil-borne fungal and oomycete pathogens, including several Fusarium spp., can cause serious yield losses in faba bean. Current control strategies rely largely on agronomic practices and limited varietal resistance. Identifying novel sources of genetic resistance is of great potential value for breeding elite varieties with improved foot rot resistance. A partially resistant Vicia faba accession ig124213 (NV490) was crossed with a moderately susceptible ig124301 (NV512) and a mapping population comprising 198 F3 families was developed. This was screened for resistance to a mixture of seven UK field isolates of Fusarium avenaceum and Fusarium oxysporum under glasshouse conditions. Several F3 families with moderate to high levels of resistance to both Fusarium species were identified, and a high-density linkage map of the V. faba genome including 6755 SNP-markers in seven linkage groups (LG) was generated using the Vfaba_v2 Axiom SNP array. Quantitative trait loci associated with improved resistance to Fusarium foot and root rot were identified, including one major QTL on LG4, corresponding to the chromosome 4 of V. faba. Key messageThe first QTL associated with partial resistance to Fusarium foot and root rot has been identified using a biparental mapping population of Vicia faba.

plant biology↗

bioRxiv2024

Peripheral mutations underlie promiscuous transport of quaternary ammonium antiseptics by Small Multidrug Resistance transporters

The mechanistic basis of transport promiscuity in multidrug exporters is not well understood. We examine this question using the Small Multidrug Resistance (SMR) transporters. We engineer a selective SMR protein to promiscuously export quaternary ammonium antiseptics, similar to multidrug exporters in this family. Using combinatorial mutagenesis and deep sequencing, we identify the necessary and sufficient molecular determinants of this new activity. Using x-ray crystallography, electrophysiology, and a novel proteoliposome-based antiseptic transport assay, we tease apart the mechanistic roles that these residues play in transport polyspecificity. We find that substrate preference changes not through modification of the residues that directly interact with the substrate, but through mutations peripheral to the binding pocket. Our new molecular insights into substrate promiscuity among the SMRs can be applied to understand multidrug export and the evolution of novel transport functions more generally.

biochemistry↗

bioRxiv2022

Resistance of Musa balbisiana accessions of the Philippines to banana bunchy top virus

Mitigation of banana bunchy top disease (BBTD) is still a challenge worldwide. BBTD is caused by banana bunchy top virus (BBTV), the most important virus affecting banana. Currently, no cultivar or accession of banana has complete resistance to BBTD. A total of 36 wild Musa spp. accessions, including 34 Musabalbisiana and two M. acuminata subsp. errans ( Agutay), were screened for resistance against BBTV. In greenhouse tests using viruliferous banana aphids (Pentalonia nigronervosa), all M. balbisiana accessions remained symptomless and BBTV was not detected in any of these plants by PCR at three- and six-months post inoculation. In contrast, 100% disease incidence was recorded in M. acuminata subsp. errans and in cv. Lakatan susceptible control plants. The PCR-negative M.balbisiana plants were then transferred to a field with high BBTV inoculum pressure where they remained symptomless and PCR-negative for up to five years, while all cv. Lakatan developed BBTD. This study confirmed the resistance of wild M.balbisiana accessions to BBTV. It is therefore expected to provide a resource for conventional and marker assisted breeding.

pathology↗

bioRxiv2021

Environment, rather than Hematodinium parasitization, determines collateral disease contraction in a crustacean host

Host, pathogen, and environment are determinants of the disease triangle, the latter being a key driver of disease outcomes and persistence within a community. The dinoflagellate genus Hematodinium is detrimental to crustaceans globally - considered to suppress the innate defences of hosts, making them more susceptible to co-infections. Evidence supporting immune-suppression is largely anecdotal and sourced from diffuse accounts of compromised decapods. We used a population of shore crabs (Carcinus maenas), where Hematodinium sp. is endemic, to determine the extent of collateral infections across two distinct environments (open water, semi- closed dock). Using a multi-resource approach (PCR, histology, haematology, population genetics, eDNA), we identified 162 Hematodinium-positive crabs and size/sex-matched these to 162 Hematodinium-free crabs out of 1,191 analysed. Crabs were interrogated for additional disease-causing agents; haplosporidians, microsporidians, mikrocytids, Vibrio spp., fungi, Sacculina, trematodes, and haemolymph bacterial loads. We found no significant differences in occurrence, severity or composition of collateral infections between Hematodinium-positive and Hematodinium-free crabs at either site, but crucially, we recorded site-restricted blends of pathogens. We found no gross signs of host cell immune reactivity toward Hematodinium in the presence or absence of other pathogens. We contend Hematodinium sp. is an immune-evader rather than immune-suppressor, which suggests an evolutionary drive toward latency in this environmentally plastic host.

immunology↗

bioRxiv2021

Genetic Structure and Diversity of Banana Bunchy Top Virus (BBTV) in the Philippines

Banana bunchy top virus (BBTV) is an important disease of banana in the Philippines and in other banana-producing countries. This study was conducted to investigate the genetic structure and diversity of Philippine BBTV isolates which remain unexplored in the country. BBTV-infected plant tissues were sampled from banana-growing provinces (i.e., Cagayan, Isabela, Quirino, Batangas, Laguna, Rizal, Quezon, Palawan, Cebu, Leyte, and Davao del Sur) and the partial DNA-R gene of BBTV was sequenced. Analysis of all local BBTV isolates showed a nucleotide diversity ({pi}) of 0.00721, average number of nucleotide differences (k) of 5.51984, and haplotype diversity (hd) of 0.971. Neutrality tests using Fus Fs and Tajimas D showed significant and highly negative values which suggest an excess number of rare alleles due to recent population expansion or from genetic hitchhiking. Haplotype network and phylogenetic analyses revealed that the local BBTV isolates were closely related to Southeast Asian (SEA) group and exhibited a monophyletic clade with distinct haplotype grouping from other SEA sequences. However, some Indonesian and Indian reference sequences were also clustered within the Philippine BBTV group suggesting sequence homology. Results also showed that the local BBTV isolates may be categorized into three major haplotype groups (HA, HB, and HC) but only the HC group remained distinct upon comparison with other Philippine and SEA reference sequences. BBTV isolates from Quezon were the most diverse while isolates from Palawan displayed low genetic diversity indices and belonged only in the HC group. The assessment of the degree of variability among Philippine BBTV isolates will provide a reference towards the development of high-throughput BBTV detection systems as well as enable to devise plant breeding strategies to manage the current BBTV spread and variations.

genetics↗