Biology subjects

Taylor, G.

Publications and source records attributed to Taylor, G..

32 records · Page 2Linked to original sources

bioRxiv2023

Granulins rescue inflammation, lysosome dysfunction, and neuropathology in a mouse model of progranulin deficiency.

Progranulin (PGRN) deficiency is linked to neurodegenerative diseases including frontotemporal dementia, Alzheimers disease, Parkinsons disease, and neuronal ceroid lipofuscinosis. Proper PGRN levels are critical to maintain brain health and neuronal survival, however the function of PGRN is not well understood. PGRN is composed of 7.5 tandem repeat domains, called granulins, and is proteolytically processed into individual granulins inside the lysosome. The neuroprotective effects of full-length PGRN are well-documented, but the role of granulins is still unclear. Here we report, for the first time, that expression of single granulins is sufficient to rescue the full spectrum of disease pathology in mice with complete PGRN deficiency (Grn-/-). Specifically, rAAV delivery of either human granulin-2 or granulin-4 to Grn-/- mouse brain ameliorates lysosome dysfunction, lipid dysregulation, microgliosis, and lipofuscinosis similar to full-length PGRN. These findings support the idea that individual granulins are the functional units of PGRN, likely mediate neuroprotection within the lysosome, and highlight their importance for developing therapeutics to treat FTD-GRN and other neurodegenerative diseases.

neuroscience↗

bioRxiv2022

Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin

Secondary metabolites play essential roles in ecological interactions and nutrient acquisition, and are of interest for their potential uses in medicine and biotechnology. Under laboratory conditions the discovery of new compounds is hindered by low production, high rediscovery rates, and detection evasion. Genome mining for biosynthetic gene clusters (BGCs) is a popular approach to address these limitations, thereby uncovering often cryptic secondary metabolic potential. Marine systems are often underrepresented in bulk genome mining efforts; and habitats with unique physicochemical characteristics such as oxygen-depleted and anoxic water columns remain virtually unexplored regarding BGCs. Here, we use genome mining and differential gene expression analyses to show that redox potential and particle-associated vs. free-living lifestyles both influence the composition and production of secondary metabolites through the stratified water column of the Cariaco Basin, Venezuela. Microbiota, including understudied clades, such as Planctomycetota, encode and express a wide range of secondary metabolites in these anoxic/euxinic waters.

bioinformatics↗

bioRxiv2022

Chromatin remodeller Chd7 is developmentally regulated in the neural crest by tissue-specific transcription factors

Neurocristopathies such as CHARGE syndrome result from aberrant neural crest development. A large proportion of CHARGE cases are attributed to mutations in the gene encoding CHD7, chromodomain helicase DNA binding protein 7, which remodels chromatin. While the role for CHD7 in neural crest development is well documented, it remains elusive how this seemingly ubiquitous factor is specifically upregulated in neural crest cells. Here, we use epigenomic profiling of chick neural crest to identify a cohort of enhancers regulating Chd7 expression in neural crest cells and other tissues. We functionally validate upstream transcription factor binding at candidate enhancers, revealing novel epistatic relationships between neural crest master regulators and Chd7. To our knowledge, this is the first report of tissue-specific regulation of a chromatin remodeller. Furthermore, we find conserved enhancer features in human embryonic epigenomic data and validate the activity of the human equivalent CHD7 enhancers in the chick embryo. Collectively our findings embed Chd7 in the neural crest gene regulatory network and offer potentially clinically relevant elements for interpreting CHARGE syndrome cases without causative allocation.

developmental biology↗

bioRxiv2022

The identification of a gene expression signature of primordial follicle activation in mouse pregranulosa cells

Primordial follicles are quiescent ovarian structures comprised of a single oocyte surrounded by a layer of somatic supporting pregranulosa cells. Primordial follicle activation is the first step towards oocyte maturation and, ultimately, ovulation. As the number of quiescent primordial follicles is finite, their rate of activation is a critical parameter of the duration of the female reproductive lifespan. Activation status is established by the presence of cuboidal and proliferative granulosa cells in primary follicles, rather than squamous and quiescent pregranulosa cells in primordial follicles. Here, using a continuous Entropy Sort Feature Weighting approach on single-cell RNA sequencing data, we identify a distinct transcriptomic signature of activating pregranulosa cells in neonatal wildtype mice. This signature contains several genes previously linked with mature granulosa cells as well several novel candidates: Slc18a2, Tnni3, Fam13a and Myo1e. We confirm expression of Slc18a2 and TNNI3 in the granulosa cells of activating follicles in embryonic, neonatal and adult mouse ovaries. Perturbation of cell cycle inhibitor p27kip1 in Cdkn1b-/- mice results in complete activation of all primordial follicles during this neonatal period. Contrary to previous reports on this established mouse model, we find substantial transcriptomic changes in embryonic Cdkn1b-/- ovaries. Upon loss of cell-cycle inhibition, we find increased expression of our signature of pregranulosa cell activation, particularly that of cardiac troponin I (Tnni3). We conclude that pregranulosa cells engage a distinct transcriptional programme prior to cell-cycle dependent primordial follicle activation.

developmental biology↗

bioRxiv2021

Good and bad lettuce leaf microbes? Unravelling the genetic architecture of the microbiome to inform plant breeding for enhanced food safety and reduced food waste

Lettuce is a high value food crop, consumed raw around the world. Engineering of the leaf microbiome could provide significant benefits for enhanced crop yield and stress resistance and help to reduce food waste caused by microbial spoilage. Lettuce leaves also act as a vector for human pathogens, implicated in several high-profile food-borne disease outbreaks. Since host genotype helps determine microbiome composition, we hypothesize that leaf surface traits can be defined that associate with good bacterial microbiomes providing benefits to the crop and that bad microbiomes, where spoilage organisms and human pathogens are abundant, can also be associated to underlying leaf genetics, providing key targets for future crop breeding. Using a Recombinant Inbred Line (RIL) population, we show that cultivated and wild parental genotypes differ with reduced bacterial diversity, larger leaves and fewer, larger stomata, smaller epidermal cells and more hydrophilic leaf surfaces found in the cultivated compared to wild lettuce. Functional analysis of the associated microbiome revealed increased abundance of genes associated with disease virulence for the cultivated lettuce genotype, suggesting domestication has had broad impacts on leaf and associated bacterial microbiome traits. We defined the core lettuce bacterial microbiome from 171 RILs, comprised of 45 taxa in the phyla Proteobacteria, Actinobacteria, Firmicutes, Chloroflexi and Deinococcus-Thermus. Leaf surface characteristics important in influencing bacterial diversity and abundance were identified as stomatal size (length and width), epidermal cell area and number and leaf surface hydrophobicity of the abaxial leaf surface. Quantitative trait loci (QTL) for leaf surface traits, frequently mapped alongside those for the extended phenotype of bacterial taxa abundance, including for human pathogens Campylobacter spp., Escherichia-Shigella spp., Clostridium spp. (LG 4, 5 and 6) and spoilage bacteria, Pseudomonas spp. (LG 1, 3, 4, 6 and 9). Candidate genes underlying these QTL were enriched in GO terms for cell wall assembly and modification, defence response, hormone-mediated signalling and biosynthesis and anatomical structure development. This work provides the first insight into the genetic architecture of host surface traits in a leafy crop alongside the mapped genetic architecture of bacterial communities and has identified areas of the lettuce genome as important targets for future microbiome engineering.

plant biology↗

bioRxiv2021

Land-use change from food to energy: meta-analysis unravels effects of bioenergy on biodiversity and amenity

Most decarbonization scenarios of energy systems necessitate more than 500 Mha of land converted to non-food bioenergy crops to provide both energy substitutes for fossil fuels and negative emissions through bioenergy with carbon capture and storage (BECCS). Understanding the environmental and societal impact of this significant land-use change (LUC) is important in determining where and how bioenergy crops should be deployed, and the trade-offs and co-benefits to the environment and society. Here, we use two systematic reviews and a meta-analysis to assess the existing literature on impacts that are likely to have an important effect on public perceptions of the acceptability of such land use change: biodiversity and amenity value. We focus on the impact of LUC to non-food bioenergy crops on agricultural landscapes, where large-scale bioenergy planting may be required. Our meta-analysis finds strong benefits for biodiversity overall (up 75 % {+/-} 13 %), with particular benefits for bird abundance (+ 81 % {+/-} 32 %), bird species richness (+ 100 % {+/-} 31 %), arthropod abundance (+ 52 % {+/-} 36 %), microbial biomass (+ 77 % {+/-} 24 %), and plant species richness (+ 25 % {+/-} 22 %), when land moves out of either arable crops or grassland to bioenergy production. Conversions from arable land to energy trees led to particularly strong benefits, providing an insight into how future LUC to bioenergy crops could support biodiversity. There were inadequate data to complete a meta-analysis on the effects of bioenergy crops on landscape amenity value, and few generalizable conclusions from a systematic review of the literature, however, findings highlight the importance of landscape context and planting strategies in determining amenity values. Our findings demonstrate improved farm-scale biodiversity on agricultural land with bioenergy crops, but also limited knowledge concerning public response to this land use change which could prove crucial to the effective deployment of bioenergy crops for BECCS.

ecology↗

bioRxiv2021

Proximity-based labeling reveals DNA damage-induced N-terminal phosphorylation of fused in sarcoma (FUS) leads to distinct changes in the FUS protein interactome.

Cytoplasmic accumulation of the RNA/DNA binding protein, fused in sarcoma (FUS), into inclusions is a common hallmark of frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS) pathology. We have previously shown that DNA damage can trigger the cytoplasmic accumulation of an N-terminally phosphorylated FUS. However, the functional consequences of N-terminal FUS phosphorylation are unknown. To gain insight into this question, we utilized proximity-dependent biotin labeling via ascorbate peroxidase 2 (APEX2) paired with mass-spectrometry (MS) to investigate whether N-terminal phosphorylation shifts the FUS protein-protein interaction network (interactome), and subsequently, its function. We report the first comparative analysis of the interactomes for three FUS variants: homeostatic wild-type FUS (FUS WT), a phosphomimetic variant of FUS (a proxy for N-terminally phosphorylated FUS, FUS PM), and a toxic FUS P525L mutant (a mutation that causes juvenile ALS, FUS P525L). Data are available via ProteomeXchange with identifier PXD026578. We demonstrate that compared to FUS WT and FUS P525L, the FUS PM interactome uniquely enriches for a set of cytoplasmic proteins that mediate mRNA metabolism and translation and nuclear proteins involved in spliceosome and DNA repair functions, respectively. We further identify and validate three proteins, VPS35, MOV10, and CLTA, as novel interacting partners of all three FUS variants. Lastly, we provide functional evidence that N-terminally phosphorylated FUS may disrupt homeostatic translation and steady state levels of specific mRNA transcripts. Taken together, these results highlight phosphorylation as a unique modulator of the FUS interactome and function.

neuroscience↗

bioRxiv2020

Primary sex determination in chickens depends on DMRT1 dosage, but gonadal sex does not determine secondary sexual characteristics in adult birds

In birds, males are the homogametic sex (ZZ) and females the heterogametic sex (ZW), and primary sex determination is thought to depend on a sex chromosome gene dosage mechanism. Previous studies have suggested that the most likely sex-determinant is the Z chromosome gene DMRT1 (Doublesex and Mab-3 Related Transcription factor 1). To clarify this issue, we used a CRISPR-Cas9 based mono-allelic targeting approach and sterile surrogate hosts to generate birds with targeted mutations in the DMRT1 gene. The resulting chromosomally male (ZZ) chicken with a single functional copy of DMRT1 developed ovaries in place of testes, demonstrating the avian sex determining mechanism is based on DMRT1 dosage. These ZZ ovaries expressed typical female markers and showed clear evidence of follicular development. However, these ZZ adult birds with an ovary in place of testes were indistinguishable in appearance to wild type adult males, supporting the concept of cell-autonomous sex identity (CASI) in birds. In experiments where oestrogen synthesis was blocked in control ZW embryos, the resulting gonads developed as testes. In contrast, if oestrogen synthesis was blocked in ZW embryos that lacked DMRT1, the gonads invariably adopted an ovarian fate. Our analysis shows that DMRT1 is the key sex determination switch in birds and that it is essential for testis development, but that production of oestrogen is also a key factor in primary sex determination in chickens, and that this production is linked to DMRT1 expression.

developmental biology↗

bioRxiv2020

Dynamin-related Irgm proteins modulate LPS-induced caspase-4 activation and septic shock

Inflammation associated with gram-negative bacterial infections is often instigated by the bacterial cell wall component lipopolysaccharide (LPS). LPS-induced inflammation and resulting life-threatening sepsis are mediated by the two distinct LPS receptors TLR4 and caspase-4. Whereas the regulation of TLR4 activation by extracellular and phago-endosomal LPS has been studied in great detail, auxiliary host factors that specifically modulate recognition of cytosolic LPS by caspase-4 are largely unknown. This study identifies dynamin-related membrane remodeling proteins belonging to the family of Immunity related GTPases M clade (IRGM) as negative regulators of caspase-4 activation in macrophages. Phagocytes lacking expression of mouse isoform Irgm2 aberrantly activate caspase-4-dependent inflammatory responses when exposed to extracellular LPS, bacterial outer membrane vesicles or gram-negative bacteria. Consequently, Irgm2-deficient mice display increased susceptibility to caspase-4-mediated septic shock in vivo. This Irgm2 phenotype is partly reversed by the simultaneous genetic deletion of the two additional Irgm paralogs Irgm1 and Irgm3, indicating that dysregulated Irgm isoform expression disrupts intracellular LPS processing pathways that limit LPS availability for caspase-4 activation.

immunology↗

bioRxiv2019

Irgm1-deficiency leads to myeloid dysfunction in colon lamina propria and susceptibility to the intestinal pathogen Citrobacter rodentium

IRGM and its mouse orthologue Irgm1 are dynamin-like proteins that regulate vesicular remodeling, intracellular microbial killing, and pathogen immunity. IRGM dysfunction is linked to inflammatory bowel disease (IBD), and while it is thought that defective intracellular killing of microbes underscores IBD susceptibility, studies have yet to address how IRGM/Irgm1 regulates immunity to microbes relevant to intestinal inflammation. Here we find that loss of Irgm1 confers marked susceptibility to Citrobacter rodentium, a noninvasive intestinal pathogen that models inflammatory responses to intestinal bacteria. Irgm1-deficient mice fail to control C. rodentium outgrowth in the intestine, leading to systemic pathogen spread and host mortality. Surprisingly, susceptibility due to loss of Irgm1 function was not linked to defective intracellular killing of C. rodentium or exaggerated inflammation, but was instead linked to failure to remodel specific colon lamina propria (C-LP) myeloid cells that expand in response to C. rodentium infection and are essential for C. rodentium immunity. Defective immune remodeling was most striking in C-LP monocytes, which were successfully recruited to the infected C-LP, but subsequently underwent apoptosis. Apoptotic susceptibility was induced by C. rodentium infection and was specific to this setting of pathogen infection, and was not apparent in other settings of intestinal inflammation. These studies reveal a novel role for Irgm1 in host defense and suggest that deficiencies in survival and remodeling of C-LP myeloid cells that control inflammatory intestinal bacteria may underpin IBD pathogenesis linked to IRGM dysfunction.\n\nAuthor SummaryIntestinal macrophages are seeded by peripheral monocytes that enter the intestine and mature into an essential component of immune defense. While this process is shaped by intestinal bacteria, the mechanisms that regulate the process, and their roles in host defense to enteric pathogens are poorly defined. We find that Irgm1 - the orthologue of the human Crohns disease resistance gene, IRGM - is required for monocyte/macrophage remodeling in response to the gram-negative enteric pathogen Citrobacter rodentium, with absence of Irgm1 leading to systemic spread of the bacterium and host mortality. Failure to remodel colonic monocytes/macrophages was due to a key requirement for Irgm1 in colon-infiltrating monocytes, which underwent dramatically high rates of cell death, specifically during the setting of enteric bacterial infection. While Irgm1/IRGM proteins are well appreciated for their role in regulating intracellular bacterial killing, our results expand the paradigm for Irgm1/IRGM-mediated host defense by demonstrating an essential function for Irgm1/IRGM to control the survival and population remodeling of monocytes and macrophages that expand during enteric infection and defend against pathogenic bacteria. These findings have significant implications for the genesis of Crohns disease in individuals that carry IRGM variants.

immunology↗

bioRxiv2018

Using micro-CT techniques to explore the role of sex and hair in the functional morphology of bumblebee (Bombus terrestris) ocelli

Many insects have triplets of camera type eyes, called ocelli, whose function remains unclear for most species. Here, we investigate the ocelli of the bumblebee, Bombus terrestris, using reconstructed 3D data from X-ray micro computed-tomography scans combined with computational ray-tracing simulations. This method enables us, not only to predict the visual fields of the ocelli, but to explore for the first time the effect that hair has on them as well as the difference between worker female and male ocelli.\n\nWe find that bumblebee ocellar fields of view are directed forward and dorsally, incorporating the horizon as well as the sky. There is substantial binocular overlap between the median and lateral ocelli, but no overlap between the two lateral ocelli. Hairs in both workers and males occlude the ocellar field of view, mostly laterally in the worker median ocellus and dorsally in the lateral ocelli. There is little to no sexual dimorphism in the ocellar visual field, suggesting that in B. terrestris they confer no advantage to mating strategies.\n\nWe compare our results with published observations for the visual fields of compound eyes in the same species as well as with the ocellar vision of other bee and insect species.

physiology↗

bioRxiv2018

Can Drosophila melanogaster tell who’s who?

Drosophila melanogaster are known to live in a social but cryptic world of touch and odours, but the extent to which they can perceive and integrate visual information is a hotly debated topic. Some researchers fixate on the limited resolution of D. melanogasters optics, others on their seemingly identical appearance; yet there is evidence of individual recognition and surprising visual learning in flies. Here, we apply machine learning and show that individual D. melanogaster are visually distinct. We also use the striking similarity of Drosophilas visual system to current convolutional neural networks to theoretically investigate D. melanogasters capacity for visual understanding. We find that, despite their limited optical resolution, D. melanogasters neuronal architecture has the capability to extract and encode a rich feature set that allows flies to re-identify individual conspecifics with surprising accuracy. These experiments provide a proof of principle that Drosophila inhabit in a much more complex visual world than previously appreciated.\n\nAuthor summaryIn this paper, we determine a proof of principle for inter-individual recognition in two parts; is there enough information contained in low resolution pictures for inter-fly discrimination, and if so does Drosophilas visual system have enough capacity to use it. We show that the information contained in a 29x29 pixel image (number of ommatidia in a fly eye) is sufficient to achieve 94% accuracy in fly re-identification. Further, we show that the fly eye has the theoretical capacity to identify another fly with about 75% accuracy. Although it is unlikely that flies use the exact algorithm we tested, our results show that, in principle, flies may be using visual perception in ways that are not usually appreciated.

animal behavior and cognition↗

bioRxiv2017

Temporal differentiation of bovine airway epithelial cells grown at an air-liquid interface

The respiratory epithelium is exposed to assault by toxins and pathogens through the process of inhalation, which has numerous implications on both human and animal health. As such, there is a need to develop and characterise an in vitro model of the airway epithelium to study respiratory pathologies during infection or toxicology experiments. This has been achieved by growing airway epithelial cells at an air-liquid interface (ALI). Characterisation of ALI models are not well-defined for airway epithelial cells derived from non-human species. In this study we have fully characterised a bovine airway epithelial cell models (AECM) grown at an ALI in relation to ex vivo tissue. The morphology of the model was monitored at three day intervals, to identify the time-period at which the culture was optimally differentiated. The model was shown to be fully-differentiated by day 21 post-ALI. The culture formed a stereotypical pseudostratified, columnar epithelium containing the major cell types of the bronchial epithelium (ciliated-, goblet- and basal cells). Once fully differentiated the bovine AECM displayed both barrier function, through the formation of tight-junctions, and active mucociliary clearance, important properties of the mucosal barrier. The bovine bronchial epithelial cells remained stable for three weeks, with no evidence of deterioration or dedifferentiation. The window in which the model displayed full differentiation was determined to be between day 21-42 post-ALI. Through comparison with ex vivo tissue derived from donor animals, our bovine AECM was shown to be highly representative of the in vivo bovine bronchial epithelium and can be utilised in the study of respiratory pathologies.

microbiology↗

bioRxiv2017

Interactions of pathogenic and commensal strains of Mannheimia haemolytica with differentiated bovine airway epithelial cells grown at an air-liquid interface

Mannheimia haemolytica serotype A2 is a common commensal species present in the nasopharynx of healthy cattle. However, prior to the onset of bovine pneumonic pasteurellosis, there is sudden increase in M. haemolytica serotype A1 within the upper respiratory tract. The events during this selective proliferation of serotype A1 strains are poorly characterised. In this investigation, a differentiated bovine airway epithelial cell culture was used to study the interactions of A1 and A2 bovine isolates with the respiratory epithelium. This model reproduced the key defences of the airway epithelium, including tight junctions and mucociliary clearance. Although initial adherence of the serotype A1 strains was low, by 12 hours post-infection the bacteria was able to traverse the tight junctions to form foci of infection below the apical surface. The size, density and number of these foci increased with time, as did the cytopathic effects observed in the bovine bronchial epithelial cells. Penetration of M. haemolytica A1 into the sub-apical epithelium was shown to be through transcytosis but not paracytosis. Commensal A2 bovine isolates however were not capable of colonising the model to a high degree, and did not penetrate the epithelium following initial adherence at the apical surface. This difference in their ability to colonise the respiratory epithelium may account for the sudden proliferation of serotype A1 in the onset of pneumonia pasteurellosis. The pathogenesis observed was replicated by virulent A2 ovine isolates; however colonisation was 10-fold lower in comparison to bovine A1 strains. This investigation provides new insight into the interactions of M. haemolytica with bovine airway epithelial cells which are occurring in vivo during pneumonia pasteurellosis.

microbiology↗