Biology subjects

Perry, J.

Publications and source records attributed to Perry, J..

27 records · Page 2Linked to original sources

bioRxiv2020

Simple fence modification increases floodplain land movement prospects for freshwater turtles

Feral pigs predate on freshwater turtles and damage wetland habitats in the process. Installing fences successfully averts access and damage, however, they become a barrier for freshwater turtles requiring land access during migration. We collected 161 turtles (Chelodina rugosa, Emydura subglobosa worrelli, Myuchelys latisternum) from twenty floodplain and riverine wetlands during post-wet (June-August) and late-dry season (November-December) surveys (2015-2018) in northern Australia. Wetlands were either fenced (150 x 150mm square, 1.05m high wire mesh) or not around the wet perimeter. Nine-seven percent of individuals caught in either fenced or unfenced wetlands had a shell carapace width greater than mesh width, of these 44 (46%) were captured inside fenced wetlands, while 50 were caught in unfenced wetlands. The remaining 35 were smaller than 150mm and would easily pass through fence mesh. Sixty-five turtles partook in a fencing manipulative experiment. Turtles with carapace widths wider than mesh often successfully escaped through fences by lifting one side of their shell and passing diagonally. In a second experiment where a piece of vertical wire (1500mmx300mm) was removed, turtles located gates after prospecting and trying to fit through meshing areas that were too small to pass through. Nine-two percent of turtles were able to locate and pass through gates, while 8% failed to locate a gate after 2 hours. Three turtles that did not use gates, and seemed to give up and dug into the grass. Gates applied every 4m showed an 83% passage rate, every 2m was 91%, and while every 1m was 100%. Combing field and manipulative experiments revealed that large turtles will prospect and move along a fence until they find suitable passage. Applying turtle gates every 1-4m allows almost 100% passage, and if strategically applied in travel corridors, would minimize the need for large-scale clipping efforts around entire wetlands.

ecology↗

bioRxiv2020

cDC1 Coordinate Innate and Adaptive Responses in the Omentum required for T cell Priming and Memory

The omentum in the peritoneal cavity contains fat associated lymphoid clusters (FALCs) whose role in the response to microbial challenge are poorly understood. After intraperitoneal immunization with Toxoplasma gondii, type I dendritic cells (cDC1) were critical to induce innate sources of IFN-{gamma} required to recruit monocytes to the FALCs. The migration of infected peritoneal macrophages into T and B cell rich areas of the FALCs allowed the TCR-induced activation of parasite-specific T cells. Unexpectedly, cDC1 were not required for T cell priming but rather supported the expansion of parasite-specific CD8+ T cells. An agent-based mathematical model predicted that the lack of cDC1 would impact the early proliferative burst, and we confirmed that cDC1 were required for optimal T cell expression of nutrient uptake receptors and cell survival. These studies highlight that cDC1 in the FALCs have distinct roles in the co-ordination of the innate and adaptive responses to microbial challenge.

immunology↗

bioRxiv2020

Genome-wide analysis identifies genetic effects on reproductive success and ongoing natural selection at the FADS locus.

Identifying genetic determinants of reproductive success may highlight mechanisms underlying fertility and also identify alleles under present-day selection. Using data in 785,604 individuals of European ancestry, we identify 43 genomic loci associated with either number of children ever born (NEB) or childlessness. These loci span diverse aspects of reproductive biology across the life course, including puberty timing, age at first birth, sex hormone regulation and age at menopause. Missense alleles in ARHGAP27 were associated with increased NEB but reduced reproductive lifespan, suggesting a trade-off between reproductive ageing and intensity. As NEB is one component of evolutionary fitness, our identified associations indicate loci under present-day natural selection. Accordingly, we find that NEB-increasing alleles have increased in frequency over the past two generations. Furthermore, integration with data from ancient selection scans identifies a unique example of an allele--FADS1/2 gene locus--that has been under selection for thousands of years and remains under selection today. Collectively, our findings demonstrate that diverse biological mechanisms contribute to reproductive success, implicating both neuro-endocrine and behavioural influences.

genetics↗

bioRxiv2020

Genetic analyses identify widespread sex-differential participation bias

Genetic association results are often interpreted with the assumption that study participation does not affect downstream analyses. Understanding the genetic basis of this participation bias is challenging as it requires the genotypes of unseen individuals. However, we demonstrate that it is possible to estimate comparative biases by performing GWAS contrasting one subgroup versus another. For example, we show that sex exhibits autosomal heritability in the presence of sex-differential participation bias. By performing a GWAS of sex in ~3.3 million males and females, we identify over 158 autosomal loci significantly associated with sex and highlight complex traits underpinning differences in study participation between sexes. For example, the body mass index (BMI) increasing allele at the FTO locus was observed at higher frequency in males compared to females (OR 1.02 [1.02-1.03], P=4.4x10-36). Finally, we demonstrate how these biases can potentially lead to incorrect inferences in downstream analyses and propose a conceptual framework for addressing such biases. Our findings highlight a new challenge that genetic studies may face as sample sizes continue to grow.

genetics↗

bioRxiv2019

Using genetics to disentangle the complex relationship between food choices and health status

Despite food choices being one of the most important factors influencing health, efforts to identify individual food groups and dietary patterns that cause disease have been challenging, with traditional nutritional epidemiological approaches plagued by biases and confounding. After identifying 302 individual genetic determinants of dietary intake in 445,779 individuals in the UK Biobank study, we develop a statistical genetics framework that enables us, to directly assess the impact of food choices on health outcomes. We show that the biases which affect observational studies extend also to GWAS, genetic correlations and causal inference through genetics, which can be corrected by applying our methods. Finally, by applying Mendelian Randomization approaches to the corrected results we identify some of the first robust causal associations between eating patterns and cancer, heart disease, obesity, and several other health related risk factors, distinguishing between the effects of specific foods or dietary patterns.

genetics↗

bioRxiv2019

Genetic and functional evidence relates a missense variant in B4GALT1 to lower LDL-C and fibrinogen

Increased LDL-cholesterol (LDL-C) and fibrinogen are independent risk factors for cardiovascular disease (CVD). We identified novel associations between an Amish-enriched missense variant (p.Asn352Ser) in a functional domain of beta-1,4-galactosyltransferase 1 (B4GALT1) and 13.5 mg/dl lower LDL-C (p=1.6E-15), and 26 mg/dl lower plasma fibrinogen (p= 9.8E-05). N-linked glycan profiling found p.Asn352Ser to be associated (p-values from 1.4E-06 to 1.0E-17) with decreased glycosylation of glycoproteins including: fibrinogen, ApoB100, immunoglobulin G (IgG), and transferrin. In vitro assays found that the mutant (352Ser) protein had 50% lower galactosyltransferase activity compared to wild type (352Asn) protein. Knockdown of b4galt1 in zebrafish embryos resulted in significantly lower LDL-C compared to control, which was fully rescued by co-expression of 352Asn human B4GALT1 mRNA but only partially rescued by co-expression of 352Ser human B4GALT1 mRNA. Our findings establish B4GALT1 as a novel gene associated with lower LDL-C and fibrinogen and suggest that targeted modulation of protein glycosylation may represent a therapeutic approach to decrease CVD risk.

genetics↗

bioRxiv2018

Glycan cross-feeding drives mutualism between Fusobacterium and the vaginal microbiota

Dysbiosis of the vaginal microbiome is associated with vaginal colonization by potential pathogens including Fusobacterium nucleatum, a bacterium linked with intrauterine infection and preterm birth. However, mechanisms by which such pathogens gain a foothold in the dysbiotic vagina remain obscure. Here we demonstrate that sialidase activity, a biochemical marker of vaginal dysbiosis, promoted F. nucleatum foraging on mammalian sialoglycans, an otherwise inaccessible resource. In mice with sialidase-positive vaginal microbiomes, mutant F. nucleatum unable to consume sialic acids displayed impaired colonization. Furthermore, community- and co-culture experiments showed that F. nucleatum did not simply take advantage of sialidase-positive bacteria, but also \"gave back\" to the community, supporting robust outgrowth of sialidase-producers, including Gardnerella vaginalis. These results illustrate that mutualistic relationships between vaginal bacteria support pathogen colonization and reinforce dysbiosis, adding complexity to the simplistic dogma that the mere absence of \"healthy\" lactobacilli is what creates a permissive environment for pathogens during dysbiosis.

microbiology↗

bioRxiv2017

Elucidating the genetic architecture of reproductive ageing in the Japanese population

Population studies over the past decade have successfully elucidated the genetic architecture of reproductive ageing. However, those studies were largely limited to European ancestries, restricting the generalizability of the findings and overlooking possible key genes poorly captured by common European genetic variation. Here, in up to 67,029 women of Japanese ancestry, we report 26 loci (all P<5x10{macron}8) for puberty timing or age at menopause, representing the first loci for reproductive ageing in any non-European population. Highlighted genes for menopause include GNRH1, which supports a primary, rather than passive, role for hypothalamic-pituitary GnRH signalling in the timing of menopause. For puberty timing, we demonstrate an aetiological role for receptor-like protein tyrosine phosphatases by combining evidence across population genetics and pre- and peri-pubertal changes in hypothalamic gene expression in rodent and primate models. Furthermore, our findings demonstrate widespread differences in allele frequencies and effect estimates between Japanese and European populations, highlighting the benefits and challenges of large-scale trans-ethnic approaches.

genetics↗

bioRxiv2017

Replication and characterization of CADM2 and MSRA genes on human behavior

Progress identifying the genetic determinants of personality has historically been slow, with candidate gene studies and small-scale genome-wide association studies yielding few reproducible results. In the UK Biobank study, genetic variants in CADM2 and MSRA were recently shown to influence risk taking behavior and irritability respectively, representing some of the first genomic loci to be associated with aspects of personality. We extend this observation by performing a personality \"phenome-scan\" across 16 traits in up to 140,487 participants from 23andMe for these two genes. Heritability estimates for these traits ranged from 5-19%, with both CADM2 and MSRA demonstrating significant effects on multiple personality types. These associations covered all aspects of the big five personality domains, including specific facet traits such as compliance, altruism, anxiety and activity / energy. This study both confirms and extends the original observations, highlighting the role of genetics in aspects of mental health and behavior.

genetics↗