Biology subjects

Griffiths, C.

Publications and source records attributed to Griffiths, C..

10 recordsLinked to original sources

bioRxiv2025

Natural variation in an NLR pair confers thermostable resistance to a devastating bacterial pathogen

Climate change reshapes host-pathogen interactions by increasing pathogen aggressiveness and weakening plant immune responses, particularly under heat stress. Nucleotide-binding leucine-rich repeat (NLR) immune receptors, key players in pathogen recognition, are altered under elevated temperatures in both plants and mammals, posing a major challenge to disease resistance. In Arabidopsis thaliana, the well-described RPS4/RRS1 NLR pair confers resistance to the worldwide devastating phytopathogenic Ralstonia pseudosolanacearum. Here, by combining the exploration of natural genetic variation with genetic mapping, polymorphism analysis, structural modeling, and functional complementation, we demonstrated that the paucity of full thermostable resistance is primarily associated with a unique RPS4/RRS1 haplotype carrying key substitutions in leucine-rich repeat domains. These findings reveal natural genetic diversity as a source of thermostable resistance, highlighting promising opportunities to engineer climate-resilient plants.

plant biology↗

bioRxiv2025

Non-catalytic and catalytic TREHALOSE-6-PHOSPHATE SYNTHASES interact with RAMOSA3 to control maize development.

Trehalose-6-phosphate (Tre6P) is the intermediate in the two-step pathway of trehalose biosynthesis mediated by Tre6P-synthases (TPSs) and Tre6P-phosphatases (TPPs). Plants harbor small families of TPS and TPP genes, however most plant TPSs lack enzymatic activity, suggesting they have regulatory functions. The classical mutant ramosa3 (ra3) increases inflorescence branching in maize, and RA3 encodes a catalytic TPP. We found that RA3 interacts with maize ZmTPS1, a non-catalytic TPS. Mutants in ZmTPS1 and its close paralog ZmTPS12 enhance ra3 phenotypes, suggesting their physical interaction is biologically significant. ZmTPS1 also interacts with the two catalytically active maize TPSs, ZmTPS11 and ZmTPS14, however zmtps11;zmtps14 double mutants fail to complete embryogenesis, suggesting that they are essential, as in arabidopsis. Interestingly, the non-catalytic ZmTPS1 protein stimulated the coupled activity of RA3 and ZmTPS14, suggesting that RA3, ZmTPS1, and ZmTPS14 form a complex, and we confirmed this by expressing and purifying the three proteins and by Alphafold predictions. Our results suggest that non-catalytic TPSs form a complex with catalytic TPSs and TPPs to stimulate catalytic activity and regulate plant development.

plant biology↗

bioRxiv2023

The penetration of sunflower root tissues by the parasitic plant Orobanche cumana Wallr. is intracellular

O_LIParasitic plants cause yield losses for important crops. Among these, Orobanche cumana Wallr, sunflower broomrape, is one of the major pests for sunflower. Previous studies stated that in most cases, the haustorium, a specific parasitic plant organ, penetrates host roots intercellularly. However, host cellular mechanisms involved during the parasitic cells penetration remained poorly described. C_LIO_LIWe investigated sunflower root cellular behavior during haustorium penetration using various microscopy approaches including live cell imaging of inoculated transgenic fluorescent sunflower roots. C_LIO_LIWe showed that the haustorium of O. cumana penetrated living sunflower root tissues, as a result of the degradation of the host cell wall and the formation of a new host trans-cellular apoplastic compartment for haustorium accommodation. Moreover, broomrape induced cell divisions in outer root tissues at very early stages of the interaction, leading to localized hypertrophy at the site of broomrape attachments. C_LIO_LIThese findings are a change of paradigm in the research field of parasitic plants. They extend host root intracellular accommodation mechanisms initially shown for symbiotic and pathogenic biotrophic fungi to parasitic plants. It paves the way for future understanding and development of resistance to parasitic plants. C_LI Key messageCombination of in vivo confocal, large field and transmission electron microscopy approaches revealed how intimate the relationship between the parasitic plant broomrape (Orobanche cumana Wallr.) and its sunflower host (Helianthus annus L.) is at very early stages of their interaction.

plant biology↗

bioRxiv2023

Delayed development of basal spikelets in wheat explains their increased floret abortion and rudimentary nature

Wheat (Triticum aestivum L.) breeding efforts have increased grain yield predominantly by raising grain numbers per spikelet, rather than grain weight or spikelet number. However, across a single spike large differences exist in the number of grains per spikelet. The central spikelets produce the highest number of grains in any given genotype while apical and basal spikelets are less productive. Basal spikelets are delayed in development just after initiation and are smaller and less advanced than central spikelets already by the glume primordium stage. However, basal spikelets continue to develop and produce florets until much later in the wheat growth cycle. The precise timings or the cause of their growth cessation, and subsequent abortion, is largely unknown. In this study we investigated the underlying causes of rudimentary basal spikelet abortion. We investigated basal spikelet development in four UK winter wheat varieties as well as a set of near-isogenic lines for VRT-A2 (VEGETATIVE TO REPRODUCTIVE TRANSITION 2) using shading applications in the field. We propose that basal spikelet abortion is likely the consequence of complete floret abortion as both occur at the same time and have the same response to shading treatments. Furthermore, we found that the developmental age of florets pre-abortion is an important factor for their likelihood to survive and develop viable seed. Previously, it had been proposed that reduced assimilate availability in the base of the spike leads to increased abortion. Re-analysis of published data alongside data presented here, however, does not support this model. We found that rather than assimilate availability, it is the reduced developmental age of basal florets before abortion that correlates with increased abortion. Using the floret Waddington developmental stage pre-abortion, we were able to predict final grain set per spikelet across the spike, alongside the characteristic gradient in number of grains from basal to central spikelets. We found that advancing past Waddington stage 5.5 seems to be important for floret survival and that most florets in basal spikelets had not reached this stage at the onset of floret abortion. The abortion of all florets could therefore be the reason for their rudimentary appearance in the mature spike, suggesting that basal spikelet abortion is simply the consequence of all florets inside the spikelet being aborted and thus all other spikelet structures (e.g., lemma, rachilla, glume) also ceasing to develop. Future efforts to improve spikelet homogeneity across the spike could thus focus on improving basal spikelet establishment and increasing floret development rates pre-abortion.

plant biology↗

bioRxiv2022

Overconfidence undermines global wildlife abundance trends

In the face of rapid global change and an uncertain fate for biodiversity, it is vital to quantify trends in wild populations. These trends are typically estimated from abundance time series for suites of species across large geographic and temporal scales. Such data implicitly contain phylogenetic, spatial, and temporal structure which, if not properly accounted for, may obscure the true magnitude and direction of biodiversity change. Here, using a novel statistical framework to simultaneously account for all three of these structures, we show that the majority of current abundance trends estimates among 10 high-profile datasets, representing millions of abundance observations, are likely unreliable or incorrect. Our new approach suggests that previous models are too simplistic, incorrectly estimating global abundance trends and often dramatically underestimating uncertainty, an aspect that is critical when translating global assessments into policy outcomes. Further, our approach also results in substantial improvements in abundance forecasting accuracy. Whilst our results do not improve the outlook for biodiversity, our framework does allow us to make more robust estimates of global wildlife abundance trends, which is critical for developing policy to protect our biosphere.

ecology↗

bioRxiv2020

Predicting and validating protein degradation in proteomes using deep learning

Age, disease, and exposure to environmental factors can induce tissue remodelling and alterations in protein structure and abundance. In the case of human skin, ultraviolet radiation (UVR)-induced photo-ageing has a profound effect on dermal extracellular matrix (ECM) proteins. We have previously shown that ECM proteins rich in UV-chromophore amino acids are differentially susceptible to UVR. However, this UVR-mediated mechanism alone does not explain the loss of UV-chromophore-poor assemblies such as collagen. Here, we aim to develop novel bioinformatics tools to predict the relative susceptibility of human skin proteins to not only UVR and photodynamically produced ROS but also to endogenous proteases. We test the validity of these protease cleavage site predictions against experimental datasets (both previously published and our own, derived by exposure of either purified ECM proteins or a complex cell-derived proteome, to matrix metalloproteinase [MMP]-9). Our deep Bidirectional Recurrent Neural Network (BRNN) models for cleavage site prediction in nine MMPs, four cathepsins, elastase-2, and granzyme-B perform better than existing models when validated against both simple and complex protein mixtures. We have combined our new BRNN protease cleavage prediction models with predictions of relative UVR/ROS susceptibility (based on amino acid composition) into the Manchester Proteome Susceptibility Calculator (MPSC) webapp http://www.manchesterproteome.manchester.ac.uk/#/MPSC (or http://130.88.96.141/#/MPSC). Application of the MPSC to the dermal proteome suggests that fibrillar collagens and elastic fibres will be preferentially degraded by proteases alone and by UVR/ROS and protease in combination, respectively. We also identify novel targets of oxidative damage and protease activity including dermatopontin (DPT), fibulins (EFEMP-1,-2, FBLN-1,-2,-5), defensins (DEFB1, DEFA3, DEFA1B, DEFB4B), proteases and protease inhibitors themselves (CTSA, CTSB, CTSZ, CTSD, TIMPs-1,-2,-3, SPINK6, CST6, PI3, SERPINF1, SERPINA-1,-3,-12). The MPSC webapp has the potential to identify novel protein biomarkers of tissue damage and to aid the characterisation of protease degradomics leading to improved identification of novel therapeutic targets.

bioinformatics↗

bioRxiv2019

Single cell and single nucleus RNA-Seq reveal cellular heterogeneity and homeostatic regulatory networks in adult mouse stria vascularis

The stria vascularis (SV) generates the endocochlear potential (EP) in the inner ear and is necessary for proper hair cell mechanotransduction and hearing. While channels belonging to SV cell types are known to play crucial roles in EP generation, relatively little is known about gene regulatory networks that underlie the ability of the SV to generate and maintain the EP. Using single cell and single nucleus RNA-sequencing, we identify and validate known and rare cell populations in the SV. Furthermore, we establish a basis for understanding molecular mechanisms underlying SV function by identifying potential gene regulatory networks as well as druggable gene targets. Finally, we associate known deafness genes with adult SV cell types. This work establishes a basis for dissecting the genetic mechanisms underlying the role of the SV in hearing and will serve as a basis for designing therapeutic approaches to hearing loss related to SV dysfunction.

genomics↗

bioRxiv2019

Deep phenotyping of a healthy human HAO1 knockout informs therapeutic development for primary hyperoxaluria type 1.

Primary Hyperoxaluria Type 1 (PH1) is a rare autosomal recessive metabolic disorder of oxalate metabolism leading to kidney failure as well as multi-organ damage. Overproduction of oxalate occurs in the liver due to an inherited genetic defect in the enzyme alanine-glyoxylate aminotransferase (AGXT), causing pathology due to the insolubility of calcium oxalate crystals in body fluids. The main current therapy is dual liver-kidney transplant, which incurs high morbidity and has poor availability in some health systems where PH1 is more prevalent. One approach currently in active clinical investigation targets HAO1 (hydroxyacid oxidase 1), encoding glycolate oxidase, to reduce substrate levels for oxalate production. To inform drug development, we sought individuals with reduced HAO1 function due to naturally occurring genetic variation.\n\nAnalysis of loss of function variants in 141,456 sequenced individuals suggested individuals with complete HAO1 knockout would only be observed in 1 in 30 million outbred people. However in a large sequencing and health records program (Genes & Health), in populations with substantial autozygosity, we identified a healthy adult individual predicted to have complete knockout of HAO1 due to an ultra rare homozygous frameshift variant (rs1186715161, ENSP00000368066.3:p.Leu333SerfsTer4). Primary care and hospital health records confirmed no apparently related clinical phenotype. At recall, urine and plasma oxalate levels were normal, however plasma glycolate levels (171 nmol/mL) were 12 times the upper limit of normal in healthy, reference individuals (mean+2sd=14 nmol/mL, n=67) while her urinary glycolate levels were 6 times the upper limit of normal. Comparison with preclinical and phase 1 clinical trial data of an RNAi therapeutic targeting HAO1 (lumasiran) suggests the individual likely retains <2% residual glycolate oxidase activity.\n\nThese results provide important data to support the safety of HAO1 inhibition as a potential chronic therapy for a devastating metabolic disease (PH1). We also suggest that the effect of glycolate oxidase suppression in any potential other roles in humans beyond glycolate oxidation do not lead to clinical phenotypes, at least in this specific individual. This demonstrates the value of studying the lifelong complete knockdown of a target protein in a living human to aid development of a potential therapeutic, both in de-risking the approach and providing potential hypotheses to optimize its development. Furthermore, therapy for PH1 is likely to be required lifelong, in contrast to data from chronicity studies in non-human species or relatively short-term therapeutic studies in people. Our approach demonstrates the potential for improved drug discovery through unlocking relevant evidence hiding in the diversity of human genetic variation.

genetics↗

bioRxiv2018

Cohort Profile: East London Genes & Health (ELGH), a community based population genomics and health study in people of British-Bangladeshi and -Pakistani heritage.

Cohort profile in a nutshellO_LIEast London Genes & Health (ELGH) is a large scale, community genomics and health study (to date >34,000 volunteers; target 100,000 volunteers). C_LIO_LIELGH was set up in 2015 to gain deeper understanding of health and disease, and underlying genetic influences, in British-Bangladeshi and British-Pakistani people living in east London. C_LIO_LIELGH prioritises studies in areas important to, and identified by, the community it represents. Current priorities include cardiometabolic diseases and mental illness, these being of notably high prevalence and severity. However studies in any scientific area are possible, subject to community advisory group and ethical approval. C_LIO_LIELGH combines health data science (using linked UK National Health Service (NHS) electronic health record data) with exome sequencing and SNP array genotyping to elucidate the genetic influence on health and disease, including the contribution from high rates of parental relatedness on rare genetic variation and homozygosity (autozygosity), in two understudied ethnic groups. Linkage to longitudinal health record data enables both retrospective and prospective analyses. C_LIO_LIThrough Stage 2 studies, ELGH offers researchers the opportunity to undertake recall-by-genotype and/or recall-by-phenotype studies on volunteers. Sub-cohort, trial-within-cohort, and other study designs are possible. C_LIO_LIELGH is a fully collaborative, open access resource, open to academic and life sciences industry scientific research partners. C_LI

genomics↗

bioRxiv2018

A novel bioreactor technology for modelling fibrosis in human and rodent precision-cut liver slices.

Summary boxO_LIWhat is already known about this subject?\nO_LICurrently there are no effective anti-fibrotic drugs to treat liver fibrosis and there is an urgent unmet need to increase our knowledge of the disease process and develop better tools for anti-fibrotic drug discovery.\nC_LIO_LIPreclinical in vitro cell cultures and animal models are widely used to study liver fibrosis and test anti-fibrotic drugs, but have shortfalls; cell culture models lack the relevant complex cell-cell interactions of the liver and animal models only reproduce some features of human disease.\nC_LIO_LIPrecision Cut Liver Slices (PCLS) are structurally representative of the liver and can be used to model liver fibrosis and test anti-fibrotic drugs. However, PCLS are typically cultured in elevated, non-physiological oxygen levels and only have a healthy lifespan of 48h.\nC_LI\nC_LIO_LIWhat are the new findings?\nO_LIWe have developed a novel bioreactor culture system that increases the longevity of functional PCLS to up to 6 days under normoxic conditions.\nC_LIO_LIBioreactor cultured PCLS can be used to model fibrogenesis in both normal and fibrotic PCLS using a combination of biochemical and histological outputs.\nC_LIO_LIAdministration of an Alk5 inhibitor effectively limits fibrogenesis in normal rodent and human PCLS and in rodent PCLS with established fibrosis.\nC_LI\nC_LIO_LIHow might it impact on clinical practice in the foreseeable future?\nO_LIThe extended longevity of bioreactor cultured PCLS represent a novel pre-clinical tool to investigate the cellular and molecular mechanisms of liver fibrosis.\nC_LIO_LIBioreactor cultured human PCLS offer a clinically relevant system to test efficacy of anti-fibrotic drugs.\nC_LI\nC_LI\n\nAbstractO_ST_ABSObjectiveC_ST_ABSPrecision cut liver slices (PCLS) retain the structure and cellular composition of the native liver and represent an improved system to study liver fibrosis compared to two-dimensional mono or co-cultures. The objective of this study was to develop a bioreactor system to increase the healthy lifespan of PCLS and model fibrogenesis.\n\nDesignPCLS were generated from normal rat or human liver, or 4-week carbon tetrachloride-fibrotic rat liver and cultured in our patented bioreactor. PCLS function was quantified by albumin ELISA. Fibrosis was induced in PCLS by TGF{beta}1 and PDGF{beta}{beta} stimulation. Alk5 inhibitor therapy was used. Fibrosis was assessed by fibrogenic gene expression, Picrosirius Red and Smooth Muscle Actin staining, hydroxyproline assay and collagen 1a1, fibronectin and hyaluronic acid ELISA.\n\nResultsBioreactor cultured PCLS are viable, maintaining tissue structure and stable albumin secretion for up to 6 days under normoxic culture conditions. Conversely, standard static transwell cultured PCLS rapidly deteriorate and albumin secretion is significantly impaired by 48 hours. TGF{beta}1 and PDGF{beta}{beta} stimulation of rat or human PCLS induced fibrogenic gene expression, release of extracellular matrix proteins, activation of hepatic myofibroblasts and histological fibrosis. Fibrogenesis slowly progresses over 6-days in cultured fibrotic rat PCLS without exogenous challenge. Alk5 inhibitor limited fibrogenesis in both TGF{beta}1 and PDGF{beta}{beta} stimulated PCLS and fibrotic PCLS.\n\nConclusionWe describe a new bioreactor technology which maintains functional PCLS cultures for 6 days. Bioreactor cultured PCLS can be successfully used to model fibrogenesis and demonstrate efficacy of an anti-fibrotic therapy.

cell biology↗