Biology subjects

Kay, A.

Publications and source records attributed to Kay, A..

7 recordsLinked to original sources

bioRxiv2026

Generalisation of training-induced recovery in occipital stroke: neurochemical and fMRI correlates

BACKGROUNDDamage to the early visual cortex after an occipital stroke typically results in the loss of conscious vision in the contralateral hemifield. Nonetheless, extensive perceptual training can restore visual motion discrimination in the blind-field. Here, we assessed, in a cohort study, whether improvements transferred to an untrained Gabor detection task and whether awareness within the blind field increased. We then explored the neural underpinnings of these changes. METHODSEighteen participants (6 female; aged 24-74 years; >6 months post-stroke) completed at least six months of visual rehabilitation in their blind field. Rehabilitation consisted of participants practicing a two-alternative, forced-choice, motion discrimination task using random dot stimuli, five days/week, at home, at one or two non-overlapping, locations in their blind-field. Each participant also completed two in-lab visits: one pre- and one post-training. A subset returned to the lab for a follow-up visit three months later to assess persistence of recovery. In addition to the trained task, an untrained, drifting-Gabor detection task was used to measure transfer of learning and changes in visual awareness at the trained locations. To investigate neural mechanisms underlying generalisation of improvements, participants completed MRI scanning at each lab visit. Magnetic resonance spectroscopy (MRS) was used to quantify GABA and glutamate concentrations in the ipsilesional motion sensitive area, hMT+, and a control voxel in the sensorimotor cortex. Functional MRI was conducted to assess BOLD signal changes in hMT+ and across the rest of the brain during passive viewing of high contrast Gabor stimuli in the blind field. RESULTSParticipants showed significant improvements in motion direction discrimination (trained task) between pre- and post-training in-lab visits, which generalised to improvements in Gabor detection and awareness (untrained task). Reduced GABA and glutamate in ipsilesional hMT+ was linked to improved Gabor detection, but not awareness. Increased BOLD signals in hMT+ and dorsolateral prefrontal cortex also correlated with improved Gabor detection, while awareness changes were linked to higher-level areas associated with visual attention in the contralesional prefrontal cortex (area 46) and inferior parietal lobule. CONCLUSIONSLong-term visual rehabilitation using a global motion discrimination task generalised to enhance both detection and awareness of moving Gabors within the blind field of occipital stroke survivors. Improvements were supported by selective changes in brain regions known to be involved in motion perception and attention respectively, suggesting that a broad network supports recovery, which could be targeted to enhance outcomes.

neuroscience↗

bioRxiv2026

The distribution of fitness effects of new mutations in regulatory regions of the D. melanogaster genome

Although non-coding regions play important roles in gene regulation and contribute to individual fitness, the precise distribution of fitness effects (DFE) of new mutations in these regions remains poorly understood. Here, we carefully compile experimentally validated regulatory regions in non-coding regions in the Drosophila melanogaster genome and identify putatively neutral sites near them. Incorporating a realistic genomic architecture that mimics the placement of the regulatory and coding regions, as well as a realistic heterogeneity in recombination and mutation rates across the genome, we use forward-in-time simulations to assess the power and accuracy of population genetics approaches that infer the DFE of new mutations in these regions. While the parameters of DFEs primarily comprising moderately and strongly deleterious mutations are estimated accurately, those of a DFE comprising mostly mildly deleterious mutations are misinferred. Applying these insights to three African D. melanogaster populations, we find that a large fraction of new mutations in functionally important non-coding regions are moderately deleterious, as opposed to strongly deleterious in coding regions. While the fraction of beneficial substitutions in regulatory regions (0.25-0.45) was also lower in coding regions ([~]0.5), our results suggest that non-coding regions contribute a majority of new deleterious mutations and beneficial substitutions in D. melanogaster populations. By incorporating both the genomic distribution and the inferred DFE of non-coding regions, we demonstrate that the effects of background selection across the genome are more accurately captured than with coding regions alone, highlighting the importance of considering selection on non-coding regions when interpreting patterns of genomic variation.

evolutionary biology↗

bioRxiv2026

Production benefits of community-created vermicompost and worm juice in a South African township

As urbanization increases globally, many residents of cities face challenges from food insecurity and general poverty. In sub-Saharan Africa (SSA), many migrants to cities come from rural, agricultural backgrounds and may be eager to farm in community or kitchen gardens for nutritional, economic, and social benefits. However, soil nutrient deficiencies and other constraints on production limit potential gains from urban agriculture. As a result, low-cost innovations to increase production could provide important community benefits. Here, we report on results from an experiment to assess the production value of worm-generated, food-waste compost created by a community initiative in Khayelitsha, South Africa, one of the largest and fastest growing urban settlements in South Africa. We first describe a community-embedded program for generating worm-based compost ("vermicompost") and "worm juice" (liquid extracts from the composting process). We then describe an experiment conducted in the community in which we field tested the effects of vermicompost and worm juice addition on the growth of Swiss chard, a common winter crop at this location. We grew plants in one of three levels of vermicompost addition (0%, 10%, 20%) either with or without worm juice in a fully factorial design. We found that 10% and 20% vermicompost significantly (P < 0.0001) increased chard yield (by [~]51% and [~]59% respectively), and worm juice also significantly increased yield (p = 0.024). Soil analyses indicated that vermicompost addition reduced soil pH and increased soil P levels. These results suggest that a community-embedded, grassroots vermicomposting operation can substantially increase yields for urban farmers, thereby increasing the economic and social benefits that emerge from community and kitchen gardens in marginalized urban areas.

ecology↗

bioRxiv2019

Persistent DNA Hyper-methylation Dampens Host Anti-Mycobacterial Immunity

Mycobacterium tuberculosis (Mtb) has co-evolved with humans for millennia and developed multiple mechanisms to evade host immunity. Restoring host immunity in order to shorten existing therapy and improve outcomes will require identifying the full complement by which host immunity is inhibited. Perturbing host DNA methylation is a mechanism induced by chronic infections such as HIV, HPV, LCMV and schistosomiasis to evade host immunity. Here, we evaluated the DNA methylation status of TB patients and their asymptomatic household contacts demonstrating that TB patients have DNA hyper-methylation of the IL-2-STAT5, TNF-NF-{varkappa}B and IFN-{gamma} signaling pathways. By MSRE-qPCR, multiple genes of the IL-12-IFN-{gamma} signaling pathway (IL12B, IL12RB2, TYK2, IFNGR1, JAK1 and JAK2) were hyper-methylated in TB patients. The DNA hyper-methylation of these pathways is associated with decreased immune responsiveness with decreased mitogen induced upregulation of IFN-{gamma}, TNF, IL-6 and IL-1{beta} production. The DNA hyper-methylation of the IL-12-IFN-{gamma} pathway was associated with decreased IFN-{gamma} induced gene expression and decreased IL-12 inducible up-regulation of IFN-{gamma}. This work demonstrates that immune cells from TB patients are characterized by DNA hyper-methylation of genes critical to mycobacterial immunity resulting in decreased mycobacteria-specific and non-specific immune responsiveness.

immunology↗

bioRxiv2018

CD38 is a key regulator of enhanced NK cell immune responses during pregnancy through its role in immune synapse formation

Natural killer (NK) cells use a diverse array of activating and inhibitory surface receptors to detect threats and provide an early line of defense against viral infections and cancer. Here, we demonstrate that the cell surface protein CD38 is a key human NK cell functional receptor through a role in immune synapse formation. CD38 expression marks a mature subset of human NK cells with a high functional capacity. NK cells expressing high levels of CD38 display enhanced killing and IFN-{gamma} secretion in response to influenza virus-infected and tumor cells. Inhibition of CD38 enzymatic activity does not influence NK cell function, but blockade of CD38 and its ligand CD31 abrogates killing and IFN-{gamma} expression in response to influenza-infected cells. Blockade of CD38 on NK cells similarly inhibits killing of tumor cells. CD38 localizes and accumulates at the immune synapse between NK cells and their targets, and blocking CD38 severely abrogates the ability of NK cells to form conjugates and immune synapses with target cells. Thus, CD38 plays a critical role in NK cell immune synapse formation. These findings open new avenues in immunotherapeutic development for cancer and infection by revealing a critical role for CD38 in NK cell function.

immunology↗

bioRxiv2018

Schistosomiasis Induces Persistent DNA Methylation and Tuberculosis-specific Immune Changes

Epigenetic mechanisms, like DNA methylation, determine immune cell phenotype. To understand the epigenetic alterations induced by helminth co-infections, we evaluated the longitudinal effect of ascariasis and schistosomiasis infection on CD4+ T cell DNA methylation and the downstream tuberculosis (TB)-specific and BCG-induced immune phenotype. All experiments were performed on human primary immune cells from a longitudinal cohort of recently TB-exposed children. Compared to age-matched uninfected controls, children with active Schistosoma haematobium and Ascaris lumbricoides infection had 751 differentially DNA methylated genes with 72% hyper-methylated. Gene ontology pathway analysis identified inhibition of IFN-{gamma} signaling, cellular proliferation, and the Th1 pathway. Targeted RT-PCR after methyl-specific endonuclease digestion confirmed DNA hyper-methylation of the transcription factors BATF3, ID2, STAT5A, IRF5, PPARg, RUNX2, IRF4 and NFATC1 and cytokines or cytokine receptors IFNGR1, TNFS11, RELT (TNF receptor), IL12RB2 and IL12B (p< 0.001; Sidak-Bonferroni). Functional blockage of the IFN-{gamma} signaling pathway was confirmed with helminth-infected individuals having decreased up-regulation of IFN-{gamma}-inducible genes (Mann-Whitney p < 0.05). Hypo-methylation of the IL-4 pathway and DNA hyper-methylation of the Th1 pathway was confirmed by antigen-specific multidimensional flow cytometry demonstrating decreased TB-specific IFN-{gamma} and TNF and increased IL-4 production by CD4+ T cells (Wilcoxon signed rank P <0.05). In S.haematobium infected individuals, these DNA methylation and immune phenotypic changes persisted at least six months after successful deworming. This work demonstrates that helminth infection induces DNA methylation and immune perturbations that inhibit TB-specific immune control and that the duration of these changes are helminth-specific.

immunology↗

bioRxiv2017

Decoupled Maternal and Zygotic Genetic Effects Shape the Evolution of Development

Many animals develop indirectly via a larval stage that is morphologically and ecologically distinct from its adult form. Hundreds of lineages across animal phylogeny have secondarily lost larval forms, instead producing offspring that directly develop into adult form without a distinct larval ecological niche1-7. Indirect development in the sea is typically planktotrophic: females produce large numbers of small offspring that require exogenous planktonic food to develop before metamorphosing into benthic juveniles. Direct development is typically lecithotrophic: females produce a smaller number of larger eggs, each developing into a juvenile without the need for larval feeding, provisioned by yolk. Evolutionary theory suggests that these alternative developmental strategies represent stable alternative fitness peaks, while intermediate states are disfavored4,8-11. Transitions from planktotrophy to lecithotrophy thus require crossing a fitness valley and represent radical and coordinated transformations of life-history, fecundity, ecology, dispersal, and development7,12-16. Here we dissect this transition in Streblospio benedicti, the sole genetically tractable species that harbors both states as heritable variation17-19. We identify large-effect loci that act maternally to influence larval size and independent, unlinked large-effect loci that act zygotically to affect discrete aspects of larval morphology. Because lecithotrophs and planktotrophs differ in both size and morphology, the genetic basis of larval form exhibits strong maternal-by-zygotic epistasis for fitness20. The fitness of zygotic alleles depends on their maternal background, creating a positive frequency-dependence that may homogenize local populations. Developmental and population genetics interact to shape larval evolution.

evolutionary biology↗