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Biology subjects

Moore, G.

Publications and source records attributed to Moore, G..

At least 19 recordsLinked to original sources

Inference of admixture in dogs from whole genome sequences

BackgroundUnderstanding the genetic architecture of domestic dogs provides unique insights into the processes of domestication, breed formation, and the genetic basis of complex traits and diseases. Dog populations, characterized by their diverse morphologies and behaviors, also exhibit extensive evidence of historical and ongoing admixture. This widespread mixing, driven by both natural migration and selective breeding practices, has profoundly shaped the genomic landscape of modern dog breeds. Though global admixture has been extensively estimated in human population studies, where the number of subgroups is typically limited, there has been more limited analysis in canines, where there may be dozens of ancestral groups, or breeds. ResultsHere we present a procedure for estimating global admixture in dogs from whole genome sequence data using SCOPE. We created a reference population of 65 dog breeds that included 349 individuals, from which we determined breed-informative SNPs. We demonstrate that SCOPE can accurately infer breed composition in both simulated and real admixed samples, even at low sequencing depths. We also characterized the genetic similarity between our reference dog breeds and recovered previously reported relationships. ConclusionThis approach allows us to identify the strength of the genetic signature of breeds and place error bounds on admixture estimates. It also provides evidence that admixture can be accurately inferred in subjects that may originate from multiple ancestral populations.

genomics↗

A single BRCA2 BRC repeat supports viability while multiple repeats ensure resilience under stress

BRC repeats are integral to BRCA2 function and mediate RAD51 loading during homologous recombination (HR). Their number varies across species, but mammals, including mice and humans, harbor eight repeats. Prior studies have suggested functional redundancy among these repeats, but the biological significance of maintaining multiple repeats remains unresolved. Here, we demonstrate that the presence of a single BRC repeat, either BRC2 or BRC4, is sufficient for mouse embryonic stem cell (mESC) viability, RAD51 loading, PARP inhibitor resistance and protection of stalled replication forks. Consistent with these findings, we show that knock-in mice with a single BRC repeat 2 or 4 are viable and exhibit normal growth and fertility. In contrast, embryonic fibroblasts from these mice display genomic instability and impaired RAD51 recruitment. Notably, this defect is rescued under low oxygen culture conditions, which mimics physoxic levels, whereas exposure to oxidative stress impairs RAD51 recruitment in mESCs harboring a single BRC repeat. Together, our findings indicate that while a single BRC repeat is sufficient under physiological conditions, the evolutionary retention of multiple BRC repeats likely ensures robust genome stability under extreme oxidative stress.

genetics↗

Accumulation of ph1 (zip4-5B) and ph2 (msh7-3D) mutations fails to boost homoeologous recombination in hexaploid wheat

Diversification of the hexaploid (bread) wheat genetic pool using wild genetic resources relies on effective meiotic recombination (crossover) between wheat chromosomes and their counterparts from related species (homoeologues). However, crossover between homoeologues is normally suppressed by two major genes, ZIP4-5B (Ph1) and MSH7-3D (Ph2). We investigated the effect of introducing zip4-5B and/or msh7-3D mutations into interspecific hybrids derived from crosses between wheat and Aegilops variabilis. Single and double mutants were exploited in Chinese Spring (CS) and Cadenza (Cad) genetic backgrounds, as well as in a CS/Cad recombinant background. The number of univalents, bivalents and multivalents was scored from meiotic cells at metaphase I, from which numbers of chiasmata were deduced. We demonstrated a non-cumulative effect of simultaneous zip4-5B and msh7-3D mutations on homoeologous recombination, as homoeologous crossovers reached a maximum when ZIP4-5B alone was mutated. We also showed that hybrids carrying both the zip4-5B and msh7-3D mutations in the same genetic background exhibited more effective recombination compared to a double mutant in the CS/Cad recombinant background. The progression of meiosis was also monitored in the different interspecific hybrids mutants, revealing clear disruptions. Thus, our study significantly contributes to the optimization of the introgression of beneficial alleles from wild relatives into elite wheat germplasm; first by demonstrating the efficiency of ZIP4-5B and MSH7-3D mutations independently and in combination and second by elucidating the influence of the genetic background in which these mutations are present in an interspecific hybrid context.

genetics↗

A targeted cell lysis mechanism facilitates toxin release in Clostridioides difficile

Clostridioides difficile infection depends on the production of two large toxins, TcdA and TcdB, encoded within a pathogenicity locus alongside the phage-like holin TcdE. The mechanism of toxin secretion remains actively debated, with current models proposing either TcdE-dependent non-lytic secretion or TcdE-independent lytic release. Here, we provide evidence for a unifying model where TcdE drives lysis in a phenotypically distinct subpopulation of cells. We show that TcdE, TcdA, and TcdB expression is restricted to a small fraction of cells exhibiting markers of active lysis and establish this subpopulation as the driver of severe pathogenic outcomes in a mouse model of CDI. Overexpression of TcdR, the sigma factor regulating the pathogenicity locus, triggers TcdE-dependent lysis, even in strains previously reported to employ TcdE-independent secretion mechanisms. Correlative light and electron microscopy combined with cryo-ET reveal a distinctive ultrastructure in lytic cells. Membrane vesicles accumulate between a disrupted inner membrane and intact peptidoglycan, alongside electron-dense material containing TcdA. These observations reveal a population-level strategy in which a minority of bacteria sacrifice themselves through TcdE-mediated lysis to release toxins as a 'bet-hedging strategy'.

microbiology↗

PRIMPOL promotes replication fork progression but not double strand break formation in FBH1-deficient cells in response to hydroxyurea

In response to stress, stalled replication forks undergo fork reversal converting replication forks into a 4-way junction. FBH1 is a DNA helicase that promotes replication fork reversal. After prolonged replication stress, FBH1 promotes double strand break accumulation and cell death. One of the hallmarks of loss of fork reversal is unrestrained replication in the presence of DNA damage, but how FBH1 restrains replication at stalled forks is not known. Here, we show that FBH1 limits replication fork progression by PRIMPOL in response to hydroxyurea. However, PRIMPOL is not preventing double strand break formation in FBH1 knockout cells. Finally, we demonstrate that increased resistance of FBH1-deficient cells to hydroxyurea treatment is not due to unrestrained replication by PRIMPOL. Our results indicate FBH1 restrains PRIMPOL-mediated DNA synthesis at stalled replication forks and promoting double strand break accumulation occur by distinct mechanisms.

molecular biology↗

Overexpression of the NEk8 kinase inhibits homologous recombination

Homologous recombination maintains genome stability by repairing double strand breaks and protecting replication fork stability. Defects in homologous recombination results in cancer predisposition but can be exploited due to increased sensitivity to certain chemotherapeutics such as PARP inhibitors. The NEK8 kinase has roles in the replication response and homologous recombination. NEK8 is overexpressed in breast cancer, but the impact of NEK8 overexpression on homologous recombination has not been determined. Here, we demonstrate NEK8 overexpression inhibits RAD51 focus formation resulting in a defect in homologous recombination and degradation of stalled replication forks. Importantly, NEK8 overexpression sensitizes cells to the PARP inhibitor, Olaparib. Together, our results suggest NEK8 overexpressing tumors may be recombination-deficient and respond to chemotherapeutics that target defects in recombination such as Olaparib.

cell biology↗

Design and testing of a PCR assay to quantify coliform bacteria in drinking water

Here we present an enhanced lacZ qPCR assay targeting {beta}-galactosidase, encoded by lacZ, to assess coliforms in drinking water. Coliform bacteria are a diverse group of over 80 species, commonly found in enteric environments, and act as indicators of water supply contamination. Due to the significant variation among coliforms, and the size of the group designing a single target was challenging, as previous studies have demonstrated. To address this, a coliform lacZ sequence database was created, and the phylogeny of the group was reviewed. The degree of phylogenetic differences both between and among different coliform genera is indeed large, raising questions about their current definition. Using the database, current and new primer sets were tested for specificity and coverage both in silico and in vitro. The de novo primer set, LZ1, was found to be the most effective for qPCR. When compared directly with traditional culture-based methods and flow cytometry total cell counts, the LZ1 lacZ qPCR assay quantified E. coli in drinking water down to a concentration of 1.82 x 103 cfu/100mL, equivalent to 360 cfu per qPCR reaction. ImportanceColiform bacteria and E. coli are key indicators of faecal contamination in drinking water. Compliance with U.K., U.S.A., or European regulations requires that drinking water be free of these organisms. However, the culture-based methods used to quantify these bacteria have remained unchanged for over 100 years, relying on the culturability of the organisms, sampling only a small volume at a single time point, and lacking direct correlation to pathogenic microbes. There is a pressing need for a rapid, high-throughput analysis capable of detecting coliforms more representatively, without relying solely on culturability. By analysing larger volumes or more replicates, this qPCR assay could potentially be used to assess the risk of drinking water contamination over longer periods of time, offering a more comprehensive evaluation compared to traditional, culture-dependent methods.

microbiology↗

Hierarchical Bayesian modeling of multi-region brain cell count data

We can now collect cell-count data across whole animal brains quantifying recent neuronal activity, gene expression, or anatomical connectivity. This is a powerful approach since it is a multi-region measurement, but because the imaging is done post-mortem, each animal only provides one set of counts. Experiments are expensive and since cells are counted by imaging and aligning a large number of brain sections, they are time-intensive. The resulting datasets tend to be under-sampled with fewer animals than brain regions. As a consequence, these data are a challenge for traditional statistical approaches. We present a standard partially-pooled Bayesian model for multi-region cell-count data and apply it to two example datasets. These examples demonstrate that hierarchical Bayesian methods are well suited to these data. In both cases the Bayesian model outperformed standard parallel t-tests. Overall, inference for cell-count data is substantially improved by the ability of the Bayesian approach to capture nested data and by its rigorous handling of uncertainty in under-sampled data.

neuroscience↗

An avidity-driven mechanism of extracellular BMP regulation by Twisted gastrulation

During dorsoventral patterning of bilaterian embryos, the conserved regulator Twisted gastrulation (Tsg) modulates BMP signalling by binding Chordin/Short gastrulation (Sog). Here we elucidate the mechanism by which Tsg interacts with Sog/Chordin to promote formation of the inhibitory Tsg-Sog/Chordin-BMP complex and regulate BMP signalling extracellularly. We identify and validate in vitro a hydrophobic interface in the Tsg C-terminal domain that binds Chordin. Mutation of this epitope in Drosophila Tsg (TsgL100A) results in an unexpectedly mild perturbation to embryonic BMP gradient formation. We show that a protosome-specific Tsg C-terminal extension also binds Sog, and the presence of this second binding site allows partial rescue of Sog interaction with TsgL100A in the presence of BMP. Consistent with this, a truncated Tsg protein lacking both Sog binding regions is unable to support BMP gradient formation in vivo. As our data show that disruption of either Sog binding site in Tsg, but not both, can be overcome by Tsg-BMP and Sog-BMP interactions, we present a new avidity-driven mechanism of BMP gradient formation that will be relevant to a broad range of developmental contexts. Summary statementIdentification and mutational analysis of the binding epitopes that mediate Twisted gastrulation interaction with Short gastrulation/Chordin reveals an avidity-based model of embryonic BMP gradient formation.

developmental biology↗

PARP1 condensates differentially partition DNA repair proteins and enhance DNA ligation

Poly(ADP-ribose) polymerase 1 (PARP1) is one of the first responders to DNA damage and plays crucial roles in recruiting DNA repair proteins through its activity - poly(ADP-ribosyl)ation (PARylation). The enrichment of DNA repair proteins at sites of DNA damage has been described as the formation of a biomolecular condensate. However, it is not understood how PARP1 and PARylation contribute to the formation and organization of DNA repair condensates. Using recombinant human PARP1 in vitro, we find that PARP1 readily forms viscous biomolecular condensates in a DNA-dependent manner and that this depends on its three zinc finger (ZnF) domains. PARylation enhances PARP1 condensation in a PAR chain-length dependent manner and increases the internal dynamics of PARP1 condensates. DNA and single-strand break repair proteins XRCC1, LigIII, Pol{beta}, and FUS partition in PARP1 condensates, although in different patterns. While Pol{beta} and FUS are both homogeneously mixed within PARP1 condensates, FUS enrichment is greatly enhanced upon PARylation whereas Pol{beta} partitioning is not. XRCC1 and LigIII display an inhomogeneous organization within PARP1 condensates; their enrichment in these multiphase condensates is enhanced by PARylation. Functionally, PARP1 condensates concentrate short DNA fragments and facilitate compaction of long DNA and bridge DNA ends. Furthermore, the presence of PARP1 condensates significantly promotes DNA ligation upon PARylation. These findings provide insight into how PARP1 condensation and PARylation regulate the assembly and biochemical activities in DNA repair foci, which may inform on how PARPs function in other PAR-driven condensates.

biochemistry↗

The type of inhibition provided by thalamic interneurons alters the input selectivity of thalamocortical neurons.

A fundamental problem in neuroscience is how neurons select for their many inputs. A common assumption is that a neurons selectivity is largely explained by differences in excitatory synaptic input weightings. Here we describe another solution to this important problem. We show that within the first order visual thalamus, the type of inhibition provided by thalamic interneurons has the potential to alter the input selectivity of thalamocortical neurons. To do this, we developed conductance injection protocols to compare how different types of synchronous and asynchronous GABA release influence thalamocortical excitability in response to realistic patterns of retinal ganglion cell input. We show that the asynchronous GABA release associated with tonic inhibition is particularly efficient at maintaining information content, ensuring that thalamocortical neurons can distinguish between their inputs. We propose a model where alterations in GABA release properties results in rapid changes in input selectivity without requiring structural changes in the network.

neuroscience↗

A workflow for the detection of antibiotic residues, measurement of water chemistry and preservation of hospital sink drain samples for metagenomic sequencing

Structured summaryO_ST_ABSBackgroundC_ST_ABSHospital sinks are environmental reservoirs that harbour healthcare-associated (HCA) pathogens. Selective pressures in sink environments, such as antibiotic residues, nutrient waste and hardness ions, may promote antibiotic resistance gene (ARG) exchange between bacteria. However, cheap and accurate sampling methods to characterise these factors are lacking. AimTo validate a workflow to detect antibiotic residues and evaluate water chemistry using dipsticks. Secondarily, to validate boric acid to preserve the taxonomic and ARG ("resistome") composition of sink trap samples for metagenomic sequencing. MethodsAntibiotic residue dipsticks were validated against serial dilutions of ampicillin, doxycycline, sulfamethoxazole and ciprofloxacin, and water chemistry dipsticks against serial dilutions of chemical calibration standards. Sink trap aspirates were used for a "real-world" pilot evaluation of dipsticks. To assess boric acid as a preservative of microbial diversity, the impact of incubation with and without boric acid at [~]22{degrees}C on metagenomic sequencing outputs was evaluated at Day 2 and Day 5 compared with baseline (Day 0). FindingsThe limits of detection for each antibiotic were: 3{micro}g/L (ampicillin), 10{micro}g/L (doxycycline), 20{micro}g/L (sulfamethoxazole) and 8{micro}g/L (ciprofloxacin). The best performing water chemistry dipstick correctly characterised 34/40 (85%) standards in a concentration-dependent manner. One trap sample tested positive for the presence of tetracyclines and sulfonamides. Taxonomic and resistome composition were largely maintained after storage with boric acid at [~]22{degrees}C for up to five days. ConclusionsDipsticks can be used to detect antibiotic residues and characterise water chemistry in sink trap samples. Boric acid was an effective preservative of trap sample composition, representing a low-cost alternative to cold-chain transport.

microbiology↗

DMC1 stabilizes synapsis and crossover at high and low temperatures during wheat meiosis

Effective chromosome synapsis and crossover during meiosis are essential for fertility, especially in grain crops such as wheat. These processes function most efficiently in wheat at temperatures between 17-23 {degrees}C, although the genetic mechanisms for such temperature dependence are unknown. In a previously identified mutant of the hexaploid wheat reference variety Chinese Spring lacking the long arm of chromosome 5D, exposure to low temperatures during meiosis resulted in asynapsis and crossover failure. In a second mutant (ttmei1), containing a 4 Mb deletion in chromosome 5DL, exposure to 13 {degrees}C led to similarly high levels of asynapsis and univalence. Moreover, exposure to 30 {degrees}C led to a significant, but less extreme effect on crossover. Previously, we proposed that, of 41 genes deleted in this 4 Mb region, the major meiotic gene TaDMC1-D1 was the most likely candidate for preservation of synapsis and crossover at low (and possibly high) temperatures. In the current study, using RNA-guided Cas9, we developed a new Chinese Spring CRISPR mutant, containing a 39 bp deletion in the 5D copy of DMC1, representing the first reported CRISPR-Cas9 targeted mutagenesis in Chinese Spring, and the first CRISPR mutant for DMC1 in wheat. In controlled environment experiments, wild-type Chinese Spring, CRISPR dmc1-D1 and backcrossed ttmei1 mutants were exposed to either high or low temperatures during the temperature-sensitive period from premeiotic interphase to early meiosis I. After 6-7 days at 13 {degrees}C, crossover decreased by over 95% in the dmc1-D1 mutants, when compared with wild-type plants grown under the same conditions. After 24 hours at 30 {degrees}C, dmc1-D1 mutants exhibited a reduced number of crossovers and increased univalence, although these differences were less marked than at 13 {degrees}C. Similar results were obtained for ttmei1 mutants, although their scores were more variable, possibly reflecting higher levels of background mutation. These experiments confirm our previous hypothesis that DMC1-D1 is responsible for preservation of normal synapsis and crossover at low and, to a certain extent, high temperatures. Given that reductions in crossover have significant effects on grain yield, these results have important implications for wheat breeding, particularly in the face of climate change. Key messageThe meiotic recombination gene DMC1 on wheat chromosome 5D preserves normal chromosome synapsis and crossover during periods of high and low temperature.

molecular biology↗

ZIP4 is required for normal progression of synapsis and for over 95% of crossovers in wheat meiosis.

Tetraploid and hexaploid wheat have multiple genomes, with successful meiosis and preservation of fertility relying on synapsis and crossover only taking place between homologous chromosomes. In hexaploid wheat, the major meiotic gene TaZIP4-B2 (Ph1) on chromosome 5B, promotes crossover between homologous chromosomes, whilst suppressing crossover between homeologous (related) chromosomes. Tetraploid wheat has three ZIP4 copies: TtZIP4-A1 on chromosome 3A, TtZIP4-B1 on 3B and TtZIP4-B2 on 5B. Previous studies showed that ZIP4 mutations eliminate approximately 85% of crossovers, consistent with loss of the class I crossover pathway. Here, we show that disruption of two ZIP4 gene copies in Ttzip4-A1B1 double mutants, results in a 76-78% reduction in crossovers when compared to wild-type plants. Moreover, when all three copies are disrupted in Ttzip4-A1B1B2 triple mutants, crossover is reduced by over 95%, suggesting that the TtZIP4-B2 copy is also affecting class II crossovers. This implies that, in wheat, the class I and class II crossover pathways may be interlinked. When ZIP4 duplicated and diverged from chromosome 3B on wheat polyploidization, the new 5B copy, TaZIP4-B2, may have acquired an additional function to stabilize both crossover pathways. In plants deficient in all three ZIP4 copies, synapsis is delayed and does not complete, consistent with our previous studies in hexaploid wheat, when a similar delay in synapsis was observed in a 59.3Mb deletion mutant, ph1b, encompassing the TaZIP4-B2 gene on chromosome 5B. These findings confirm the requirement of ZIP4-B2 for efficient synapsis, and suggest that TtZIP4 genes have a stronger effect on synapsis than previously described in Arabidopsis and rice. Thus, ZIP4-B2 accounts for the two major phenotypes reported for Ph1, promotion of homologous synapsis and suppression of homeologous crossover. Key messageIn tetraploid wheat, ZIP4 is required for efficient chromosome synapsis and for over 95% of crossovers, involving both the class I and class II crossover pathways. Author contribution statementTD grew and maintained the plants, made the crosses, carried out the KASP genotyping and sequencing, carried out the meiotic metaphase I studies and produced the corresponding figure, and wrote the manuscript. M-DR scored chromosome crossover, performed the statistical analysis and produced the graphs. AM selected the TILLING mutant, carried out the immunolocalization and FISH experiments and produced the immunolocalization figure; SH and MS developed the Ttzip4-B2 CRISPR mutant in Kronos using RNA-guided Cas9 and produced the CRISPR Ttzip4-B2 sequence figure; AKA designed the KASP primers; AM and GM provided the concept, provided thoughts and guidance, and revised and edited the manuscript. Conflict of interestThe authors declare that they have no conflict of interest.

cell biology↗

Laboratory evaluation of a quaternary ammonium compound (QAC)-based antimicrobial coating used in public transport during the COVID-19 pandemic

The virucidal activity of a quaternary ammonium compound (QAC)-based antimicrobial coating used by the UK rail industry during the COVID-19 pandemic was evaluated using the bacteriophage {phi}6 as a surrogate for SARS-CoV-2. Immediately after application and in the absence of interfering substance, the product showed efficacy (>3 log10 reduction) on some materials typically used in rail carriages (stainless steel, high pressure laminate and plastic), variable efficacy on glass and no efficacy (<3 log10 reduction) on a train armrest made of Terluran 22. If, after application of the product, the surfaces remained undisturbed, the antimicrobial coating retained its efficacy for at least 28 days on all materials where it was effective immediately after application. However, regardless of the material coated or time since application, the presence of organic debris (fetal bovine serum) significantly reduced the viricidal activity of the coating. Wiping the surface with a wetted cloth after organic debris deposition was not sufficient to restore efficacy. We conclude that the product is likely to be of limited effectiveness in a busy multi-user environment such as public transport. ImportanceThis study evaluated the performance of a commercially available antimicrobial coating used by the transport industry in the UK during the COVID-19 pandemic. While the product initially showed efficacy against {phi}6 when applied to some materials, when organic debris was subsequently deposited, the efficacy was severely diminished and could not be recovered through wiping (cleaning) the surface. This highlights the importance of including relevant materials and conditions when evaluating antimicrobial coatings in the laboratory. Further efforts are required to identify suitable infection prevention and control practices for the transport industry.

microbiology↗

Bromodomain factor 5 is an essential transcriptional regulator of the Leishmania genome.

Leishmania are unicellular parasites that cause human and animal disease. Alongside other organisms in kinetoplastida, they have evolved an unusual genome architecture that requires all RNA polymerase II transcribed genes to be expressed constitutively, with transcriptional start regions denoted by histone variants and histone lysine acetylation. However, the way these chromatin marks are interpreted by the cell is not understood. Seven predicted bromodomain factors (BDF1-7), the reader modules for acetyl-lysine, were identified across Leishmania genomes. Using L. mexicana as a model, Cas9-driven gene deletions indicate that BDF1-5 are essential for promastigote survival, whilst DiCre inducible gene deletion of the dual bromodomain factor BDF5 identified it to be essential for both promastigotes and amastigotes. ChIP-seq assessment of BDF5s genomic distribution revealed it as highly enriched at transcriptional start sites. Using an optimised proximity proteomic and phosphoproteomic technique, XL-BioID, we defined the BDF5-proximal environment to be enriched for other bromodomain factors, histone acetyltransferase 2, and proteins essential for transcriptional activity and RNA processing. Inducible deletion of BDF5, led to a disruption of pol II transcriptional activity and global defects in gene expression. Our results indicate the requirement of Leishmania to interpret histone acetylation marks for normal levels of gene expression and thus cellular viability.

cell biology↗

A separation-of-function ZIP4 wheat mutant allows crossover between related chromosomes and is meiotically stable

Many species, including most flowering plants, are polyploid, possessing multiple genomes. During polyploidisation, fertility is preserved via the evolution of mechanisms to control the behaviour of these multiple genomes during meiosis. On the polyploidisation of wheat, the major meiotic gene ZIP4 duplicated and diverged, with the resulting new gene TaZIP4-B2 being inserted into chromosome 5B. Previous studies showed that this TaZIP4-B2 promotes pairing and synapsis between wheat homologous chromosomes, whilst suppressing crossover between related (homoeologous) chromosomes. Moreover, in wheat, the presence of TaZIP4-B2 preserves up to 50% of grain number. The present study exploits a separation-of-function wheat Tazip4-B2 mutant named zip4-ph1d, in which the Tazip4-B2 copy still promotes correct pairing and synapsis between homologues (resulting in the same pollen profile and fertility normally found in wild type wheat), but which also allows crossover between the related chromosomes in wheat haploids of this mutant. This suggests an improved utility for the new zip4-ph1d mutant line during wheat breeding exploitation, compared to the previously described CRISPR Tazip4-B2 and ph1 mutant lines. The results also reveal that loss of suppression of homoeologous crossover between wheat chromosomes does not in itself reduce wheat fertility when promotion of homologous pairing and synapsis by TaZIP4-B2 is preserved.

genetics↗