Biology subjects

Lord, J.

Publications and source records attributed to Lord, J..

13 recordsLinked to original sources

bioRxiv2025

Risk factors, patterns and seropositivity of inter-epizootic Rift Valley fever virus of cattle in northern Tanzania.

1.1BackgroundRift Valley Fever (RVF) is a zoonotic viral disease affecting both animals and humans, with significant public health and economic implications. In Tanzania, a series of RVF outbreaks in livestock have been reported. The epidemiological information about hosts exposures status, time, location and risk factors that contribute to virus maintenance between one epizootic and the other, is important for preparedness and intervention plans. This study investigated the seroprevalence and potential determinants of RVFV exposure in cattle in Babati, Hai, and Moshi Districts between the last RVF outbreak in 2007 and the anticipated El Nino rains of 2024, which could precipitate the next outbreak. MethodsA total of 1,627 cattle serum samples (790 from Babati, 518 from Moshi, and 319 from Hai), were collected between August and October 2023 from both urban and rural areas, were analyzed using a competitive ELISA to detect RVFV-specific antibodies. Data on cattle biodata, management practices, environmental factors, were obtained through structured questionnaires and field records. Sero-prevalence was determined by descriptive statistics, while risk factors were quantified by multivariable logistic regression and RVF seropositivity was plotted on administrative boundaries of Babati, Moshi, and Hai districts by using QGIS. ResultsThe overall RVFV seroprevalence was 15.0% (95% CI: 13.26 - 16.73). Seropositivity was 22.2% (95% CI: 18.62-25.78) in Moshi, 12.2% (95% CI: 8.63-15.82) in Hai and 11.4% (95% CI 9.18-13.61) in Babati. Age (OR = 1.22, 95% CI: 1.15-1.3, p<0.001), sex (OR = 0.53, 95% CI: 0.36-0.79, p = 0.0017), herd size (OR=0.2201; 95% CI: 0.095-0.5101; p=0.0004), water access along irrigated crop fields (OR=3.7181; 95% CI: 1.5868-8.7121; p=0.0025), and geographical location (OR = 2.23, 95% CI: 1.63-3.06, p < 0.001) were significant predictors of seropositivity. Spatial visualization revealed clustering of seropositive herds in villages near lake Manyara and Tarangire National parks in Manyara region, also seropositive clusters in villages near irrigated areas, Nyumba ya Mungu dam and floodplains in lower Moshi. ConclusionThis study highlights ongoing inter-epizootic exposure of cattle to RVFV in northern Tanzania. The RVFV is not randomly distributed during inter-epizootic periods, but rather forms seropositive clusters. Most significant determinants of seropositivity includes age, sex, herd size, water access along irrigated crop fields and geographical location Moshi showing higher seropositivity.

ecology↗

bioRxiv2025

Cell type-specific intronic RNAs shape genome architecture during neuronal lineage specification

Cell differentiation towards neurons is accompanied by widespread changes in three-dimensional (3D) genome organization and gene expression. Chromatin-associated RNAs have been proposed to be important regulators of such changes; however, the type, abundance, and role of these RNAs during neuronal differentiation remain largely unexplored. Here, we integrate multi-omic data generated in the frame of the Functional ANnoTation Of the Mammalian genome (FANTOM6) to chart 3D genome, RNA-DNA contactome, and transcriptome changes occurring during in vitro differentiation of human induced pluripotent stem cells to neural stem cells and neurons. We reveal a previously unreported phenomenon, in which intronic RNAs engage in long-distance contacts with DNA loci distributed all over the genome. These trans-contacting intronic RNAs (TIRs) are produced from exceptionally long (mean length: 750 kilobases, kb) protein-coding genes that carry ultra-long introns and are selectively expressed in neurons. We show that TIRs do not undergo rapid co-transcriptional degradation but rather accumulate in the nucleus of neuronal cells, forming large dot clouds around their source loci and spreading across the nucleus, as visualized by single-molecule RNA fluorescence in situ hybridization. TIRs engage in contacts with a set of genomic regions (TIR-contacted regions or TIRCs) that carry much shorter (mean length: [~]30 kb) neuronally expressed genes forming high-connectivity hubs. We also show that the expression of genes within TIRCs contacted by the same set of TIRs is highly co-varied, and that TIR source genes, especially their introns, are enriched in genetic risk loci for neurodevelopmental and neuropsychiatric disorders. Our findings point to a functional role of the persistence of long intronic RNAs in the nucleus of neuronal cells and might contribute to explain why neurons uniquely express many ultra-long genes. We propose a model in which TIRs form pan-nuclear scaffolds--which we propose to name introsomes--that constitute a dynamically self-renewing regulatory layer, where transcription itself continuously regenerates the very scaffold that organizes genome function in neurons, and that might be involved in the pathogenesis of neurodevelopmental and neuropsychiatric disorders.

genomics↗

bioRxiv2025

FUS post-transcriptional splicing is autoregulated via RNA condensation with therapeutic potential for ALS-FUS

Mutations in the FUS gene cause aggressive and often juvenile forms of amyotrophic lateral sclerosis (ALS-FUS). In addition to mRNA, the FUS gene gives rise to a partially processed RNA with retained introns 6 and 7. We demonstrate that these FUSint6&7-RNAs form nuclear condensates scaffolded by the highly structured intron 7 and associated with nuclear speckles. Using hybridization-proximity labelling proteomics, we show that the FUSint6&7-RNA condensates are enriched in splicing factors and the m6A reader YTHDC1. These ribonucleoprotein structures facilitate post-transcriptional FUS splicing and depend on m6A/YTHDC1 for their maintenance. FUSint6&7-RNAs become hypermethylated in cells expressing mutant FUS, leading to their enhanced condensation and consequently, splicing. We further demonstrate that FUS protein is repelled by m6A. Thus, ALS-FUS mutations may cause an abnormal activation of FUS post-transcriptional splicing via altered RNA methylation. Strikingly, ectopic expression of FUS intron 6&7 sequences dissolves the endogenous FUSint6&7-RNA condensates, downregulating FUS mRNA and protein. Overall, we describe an RNA condensation-dependent mechanism regulating FUS splicing that can be harnessed for developing new therapies.

cell biology↗

bioRxiv2024

Cellular heterogeneity in hypertrophic burn scars in response to carbon dioxide laser therapy

Fractional carbon dioxide (AFCO2) laser therapy is used for treating pathological scarring, but the clinical outcomes are variable and the mechanisms of scar reduction poorly understood. We investigated the mechanisms underpinning efficacy of AFCO2 laser therapy, performing single-cell RNA sequencing in skin biopsies from patients with hypertrophic scars after AFCO2 laser therapy. Patients with younger scars (Good Responder, GR, <6 years from healing) had better scar reduction than patients with older scars (Poor Responder, PR, >6 years from healing) by various measures of scarring. scRNAseq analysis revealed that genes enriched in GR were associated with extracellular matrix and structure organisation (COL14A1, POSTN, SPARC); whereas genes enriched in PR were related to enhanced immune responses (IL-12, MSTN, HLA-DQA). The groups had distinct intercellular communication networks and differentiation trajectories after AFCO2, with regenerative Mesenchymal fibroblasts associated with a good response and inflammatory Secretory Papillary and Inflammatory Fibroblasts with a poor response.

cell biology↗

bioRxiv2023

Insights into Trypanosomiasis Transmission: Age, Infection Rates and Bloodmeal Analysis of Glossina fuscipes fuscipes in N.W. Uganda

BackgroundTsetse flies (Glossina) transmit species of Trypanosoma which cause human African trypanosomiasis (HAT) and animal African trypanosomiasis (AAT). Measuring the infection status of wild-caught tsetse is an important part of operations to control HAT. In north-west Uganda, we conducted field studies over a 15-month period to compare classical, microscope-based, and PCR-based methods of detecting trypanosomes in tsetse. We also quantified the age structure and host preferences of tsetse. MethodsUsing Pyramidal traps placed along the Kochi River, in Koboko district, 12512 G. fuscipes fuscipes were caught. A subset of females ({not}n= 5051) and males (n= 1221) underwent dissection wherein mouthparts, midguts and salivary glands were screened for trypanosomes. Additionally, the age of the females was estimated using ovarian ageing and the trypanosome-positive status of 1931 females and 438 males was investigated by ITS PCR. Further the bloodmeal sources of 131 tsetse were identified using vertebrate cytochrome b PCR. ResultsInfection rates estimated were significantly greater (1.9-9.3 times) using the PCR-based method compared to the classical dissection-based method. Positive rates for T. brucei sl, T. congolense and T. vivax were 1.6% (1.32-2.24), 2.4% (1.83-3.11and 2.0% (1.46-2.63), respectively by PCR. The abundance and age structure of tsetse populations were relatively stable and the slight seasonal four-fold variation in abundance appeared to be correlated with rainfall. Analyses of age structure suggests a low natural daily mortality of 1.75% (1.62-1.88). The majority of bloodmeals were identified as cattle (39%, 30.5-47.8) and human (37% of meals, 28.4-45.6). ConclusionPCR provides a more sensitive and specific method of estimating the infection rates of all pathogenic species of trypanosome circulating in Koboko. The seasonally stable abundance, low mortality rate and high proportion of bloodmeals from humans may explain, in part, why this district has historically been a focus of sleeping sickness. Author summaryTsetse flies (Glossina) transmit African trypanosomiasis in humans ( sleeping sickness) and livestock ( nagana). Identifying trypanosome species and quantifying infection rates in tsetse is important in understanding and controlling trypanosomiasis. Traditionally this relied on microscopic examination of tsetse, however, this method is unable to reliably identify different species of trypanosome. We compared microscopy and PCR, trypanosome-detection methods, using G. fuscipes fuscipes collected from traps deployed in Koboko district, in North-West Uganda. Our results show that the PCR-based method was 1.9-9.3 times more sensitive than the classical approach and able to identify different species of Trypanosoma, including mixed infections. In collecting tsetse we also obtained data on the seasonal abundance, age and diet of the tsetse population. Analyses of these results showed that natural mortality was low (1.75%/day) among adult females and only a slight seasonal variation in abundance and age structure occurred. The most important hosts were cattle and humans, providing 39% and 37% of bloodmeals, respectively. The PCR method provided a sensitive means of identifying trypanosomes to the species level. The longevity and diet of tsetse in Koboko may explain, why this district was a persistent focus of disease prior to the deployment of Tiny Targets to control tsetse.

ecology↗

bioRxiv2023

Predicting the impact of rare variants on RNA splicing in CAGI6

BackgroundVariants which disrupt splicing are a frequent cause of rare disease that have been under-ascertained clinically. Accurate and efficient methods to predict a variants impact on splicing are needed to interpret the growing number of variants of unknown significance (VUS) identified by exome and genome sequencing. Here we present the results of the CAGI6 Splicing VUS challenge, which invited predictions of the splicing impact of 56 variants ascertained clinically and functionally validated to determine splicing impact. ResultsThe performance of 12 prediction methods, along with SpliceAI and CADD, was compared on the 56 functionally validated variants. The maximum overall accuracy achieved was 82% from two different approaches, one weighting SpliceAI scores by minor allele frequency, and one applying the recently published Splicing Prediction Pipeline (SPiP). SPiP performed optimally in terms of sensitivity, while an ensemble method combining multiple prediction tools and information from databases exceeded all others for specificity. ConclusionsSeveral challenge methods equalled or exceeded the performance of SpliceAI, with ultimate choice of prediction method likely to depend on experimental or clinical aims. One quarter of the variants were incorrectly predicted by at least 50% of the methods, highlighting the need for further improvements to splicing prediction methods for successful clinical application.

bioinformatics↗

bioRxiv2020

Autophagy in T cells from aged donors is maintained by spermidine, and correlates with function and vaccine responses

Older adults are at high risk for infectious diseases such as the recent COVID-19 and vaccination seems to be the only long-term solution to the pandemic. While most vaccines are less efficacious in older adults, little is known about the molecular mechanisms that underpin this. Autophagy, a major degradation pathway and one of the few processes known to prevent aging, is critical for the maintenance of immune memory in mice. Here, we show induction of autophagy is specifically induced in human vaccine-induced antigen-specific T cells in vivo. Reduced IFN{gamma} secretion by vaccine-induced T cells in older vaccinees correlates with low autophagy. We demonstrate in human cohorts that levels of the endogenous autophagy-inducing metabolite spermidine, fall with age and supplementing it in vitro recovers autophagy and T cell function. Finally, our data show that endogenous spermidine maintains autophagy via the translation factor eIF5A and transcription factor TFEB. With these findings we have uncovered novel targets and biomarkers for the development of anti-aging drugs for human T cells, providing evidence for the use of spermidine in improving vaccine immunogenicity in the aged human population.

physiology↗

bioRxiv2020

Integrated lipidomics and proteomics network analysis highlights lipid and immunity pathways associated with Alzheimer's disease

INTRODUCTIONThere is an urgent need to understand the molecular mechanisms underlying Alzheimers Disease (AD) to enable early diagnosis and develop effective treatments. Here we aim to investigate Alzheimers dementia using an unsupervised lipid, protein and gene multi-omic integrative approach. METHODSA lipidomics dataset (185 AD, 40 MCI and 185 controls) and a proteomics dataset (201 AD patients, 104 MCI individuals and 97 controls) were utilised for weighted gene co-expression network analyses (WGCNA). An additional proteomics dataset (94 AD, 55 MCI and 100 controls) was included for external proteomics validation. Modules created within each modality were correlated with clinical AD diagnosis, brain atrophy measures and disease progression, as well as with each other. Gene Ontology (GO) enrichment analysis was employed to examine the biological processes and molecular and cellular functions for protein modules associated with AD phenotypes. Lipid species were annotated in the lipid modules associated with AD phenotypes. Associations between established AD risk loci and lipid/protein modules that showed high correlation with AD phenotypes were also explored. RESULTSFive of the 20 identified lipid modules and five of the 17 identified protein modules were correlated with AD phenotypes. Lipid modules comprising of phospholipids, triglycerides, sphingolipids and cholesterol esters, correlated with AD risk loci involved in immune response and lipid metabolism. Five protein modules involved in positive regulation of cytokine production, neutrophil mediated immunity, humoral immune responses were correlated with AD risk loci involved in immune and complement systems. DISCUSSIONWe have shown the first multi-omic study linking genes, proteins and lipids to study pathway dysregulation in AD. Results identified modules of tightly regulated lipids and proteins that were strongly associated with AD phenotypes and could be pathology drivers in lipid homeostasis and innate immunity. Research in ContextO_LILipid and protein modules were preserved amongst Alzheimers disease (AD) patients, participants with mild cognitive impairment (MCI) and controls. Protein modules were also externally validated. C_LIO_LIFive lipid and five protein modules out of a total of thirty-seven correlated with clinical AD diagnosis, brain atrophy measurements and the rate of cognitive decline in AD. C_LIO_LILipid and protein modules associated with AD phenotypes showed associations with established AD risk loci involved in lipid and immune pathways. C_LI

neuroscience↗

bioRxiv2019

Integrating healthcare and research genetic data empowers the discovery of 49 novel developmental disorders

De novo mutations (DNMs) in protein-coding genes are a well-established cause of developmental disorders (DD). However, known DD-associated genes only account for a minority of the observed excess of such DNMs. To identify novel DD-associated genes, we integrated healthcare and research exome sequences on 31,058 DD parent-offspring trios, and developed a simulation-based statistical test to identify gene-specific enrichments of DNMs. We identified 285 significantly DD-associated genes, including 28 not previously robustly associated with DDs. Despite detecting more DD-associated genes than in any previous study, much of the excess of DNMs of protein-coding genes remains unaccounted for. Modelling suggests that over 1,000 novel DD-associated genes await discovery, many of which are likely to be less penetrant than the currently known genes. Research access to clinical diagnostic datasets will be critical for completing the map of dominant DDs.

genomics↗

bioRxiv2019

Microglia are necessary for normal functional development of adult-born neurons in the olfactory bulb

Microglia play key roles in regulating synapse development and refinement in the developing brain, but it is unknown whether they are similarly involved during adult neurogenesis. By transiently ablating microglia from the healthy adult mouse brain, we show that microglia are necessary for the normal functional development of adult-born granule cells (abGCs) in the olfactory bulb. Microglia ablation reduces the odor responses of developing, but not preexisting GCs in vivo in both awake and anesthetized mice. Microglia preferentially target their motile processes to interact with mushroom spines on abGCs, and when microglia are absent, abGCs develop smaller spines and receive weaker excitatory synaptic inputs. These results suggest that microglia promote the development of excitatory synapses onto developing abGCs, which may impact the function of these cells in the olfactory circuit.

neuroscience↗

bioRxiv2019

The Endocrine and Metabolic Response in Male Survivors of Major Trauma

ContextSurvival rates after severe injury are improving, but complication rates and outcomes are variable. ObjectiveThis cohort study addressed the lack of longitudinal data on the steroid response to major trauma and during recovery. DesignWe undertook a prospective, observational cohort study from time of injury to six months post-injury at a major UK trauma centre and a military rehabilitation unit, studying patients within 24 hours of major trauma (estimated New Injury Severity Score (NISS) >15). Main outcome measuresWe measured adrenal and gonadal steroids in serum and 24-h urine by mass spectrometry, assessed muscle loss by ultrasound and nitrogen excretion, and recorded clinical outcomes (ventilator days, length of hospital stay, opioid use, incidence of organ dysfunction and sepsis); results were analysed by generalized mixed-effect linear models. FindingsWe screened 996 multiple injured adults, approached 106, and recruited 95 eligible patients; 87 survived. We analysed all male survivors <50 years not treated with steroids (N=60; median age 27 [interquartile range 24-31] years; median NISS 34 [29-44]). Urinary nitrogen excretion and muscle loss peaked after one and six weeks, respectively. Serum testosterone, dehydroepiandrosterone and dehydroepiandrosterone sulfate decreased immediately after trauma and took two, four and more than six months, respectively, to recover; opioid treatment delayed dehydroepiandrosterone recovery in a dose-dependent fashion. Androgens and precursors correlated with SOFA score and probability of sepsis. ConclusionThe catabolic response to severe injury was accompanied by acute and sustained androgen suppression. Whether androgen supplementation improves health outcomes after major trauma requires further investigation. PrecisA cohort study in male survivors of major trauma revealed acute and sustained androgen suppression and protein catabolism including muscle loss. Serum androgens correlated with probability of sepsis.

physiology↗

bioRxiv2018

Speed breeding in growth chambers and glasshouses for crop breeding and model plant research

1.To meet the challenge of feeding a growing population, breeders and scientists are continuously looking for ways to increase genetic gain in crop breeding. One way this can be achieved is through \"speed breeding\" (SB), which shortens the breeding cycle and accelerates research studies through rapid generation advancement. The SB method can be carried out in a number of ways, one of which involves extending the duration of a plants daily exposure to light (photoperiod) combined with early seed harvest in order to cycle quickly from seed to seed, thereby reducing the generation times for some long-day (LD) or day-neutral crops. Here we present glasshouse and growth chamber-based SB protocols with supporting data from experimentation with several crop species. These protocols describe the growing conditions, including soil media composition, lighting, temperature and spacing, which promote rapid growth of spring and winter bread wheat, durum wheat, barley, oat, various members of the Brassica family, chickpea, pea, grasspea, quinoa and the model grass Brachypodium distachyon. Points of flexibility within the protocols are highlighted, including how plant density can be increased to efficiently scale-up plant numbers for single seed descent (SSD) purposes. Conversely, instructions on how to perform SB on a small-scale by creating a benchtop SB growth cabinet that enables optimization of parameters at a low cost are provided. We also outline the procedure for harvesting and germinating premature wheat, barley and pea seed to reduce generation time. Finally, we provide troubleshooting suggestions to avoid potential pitfalls.

plant biology↗

bioRxiv2018

The contribution of non-canonical splicing mutations to severe dominant developmental disorders

Mutations which perturb normal pre-mRNA splicing are significant contributors to human disease. We used exome sequencing data from 7,833 probands with developmental disorders (DD) and their unaffected parents, as well as >60,000 aggregated exomes from the Exome Aggregation Consortium, to investigate selection around the splice site, and quantify the contribution of splicing mutations to DDs. Patterns of purifying selection, a deficit of variants in highly constrained genes in healthy subjects and excess de novo mutations in patients highlighted particular positions within and around the consensus splice site of greater functional relevance. Using mutational burden analyses in this large cohort of proband-parent trios, we could estimate in an unbiased manner the relative contributions of mutations at canonical dinucleotides (73%) and flanking non-canonical positions (27%), and calculated the positive predictive value of pathogenicity for different classes of mutations. We identified 18 patients with likely diagnostic de novo mutations in dominant DD-associated genes at non-canonical positions in splice sites. We estimate 35-40% of pathogenic variants in non-canonical splice site positions are missing from public databases.

genetics↗