Canalization of the Polygenic Risk for Common Diseases and Traits in the UK Biobank Cohort

Since organisms develop and thrive in the face of constant perturbations due to environmental and genetic variation, species may evolve resilient genetic architectures. We sought evidence for this process, known as canalization, through a comparison of the prevalence of phenotypes as a function of the polygenic score (PGS) across environments in the UK Biobank cohort study. Contrasting seven diseases and three categorical phenotypes with respect to 151 exposures in 408,925 people, the deviation between the prevalence–risk curves was observed to increase monotonically with the PGS percentile in one-fifth of the comparisons, suggesting extensive PGS-by-Environment (PGS×E) interaction. After adjustment for the dependency of allelic effect sizes on increased prevalence in the perturbing environment, cases where polygenic influences are greater or lesser than expected are seen to be particularly pervasive for educational attainment, obesity, and metabolic condition type-2 diabetes. Inflammatory bowel disease analysis shows fewer interactions but confirms that smoking and some aspects of diet influence risk. Notably, body mass index has more evidence for decanalization (increased genetic influence at the extremes of polygenic risk), whereas the waist-to-hip ratio shows canalization, reflecting different evolutionary pressures on the architectures of these weight-related traits. An additional 10 % of comparisons showed evidence for an additive shift of prevalence independent of PGS between exposures. These results provide the first widespread evidence for canalization protecting against disease in humans and have implications for personalized medicine as well as understanding the evolution of complex traits. The findings can be explored through an R shiny app at https://canalization-gibsonlab.shinyapps.io/rshiny/.     

The Relative Importance of Seed-borne Inoculum to Common Scab Disease of Potato and the Efficacy of Seed Tuber and Soil Treatments for Disease Control

The importance of both seed and soil-borne inoculum in the epidemiology of common scab disease under Australian conditions was clearly demonstrated. In field trials the severity of disease in harvested potatoes was directly related to the severity of disease on the planted seed tubers. Chemical seed dressing treatments were assessed for common scab disease control under field conditions in four trials over 5 years. Where seed treatments were applied to both diseased and visibly clean seed pieces significantly more disease was found in tubers harvested from diseased seed than the corresponding clean seed treatment. In all but one trial, the treatments applied to diseased seed significantly reduced the incidence of common scab. Fluazinam, flusulfamide (at elevated rates), fenpiclonil, pentachloronitrobezene and mancozeb seed treatments were particularly effective as seed dressing treatments. Applications to visibly clean seed failed to significantly diminish disease levels below that found on untreated seed. Preliminary investigations of some chemical soil treatments gave disappointing levels of control.     

解放军疾控所SPF动物房的工艺设计

解放军疾病预防控制所,为履行职能和任务,在业务办公大楼12层建设了SPF动物实验设施,面积约240 m^2。文章介绍了作者的设计思路和建设方案。同时还介绍了SPF动物房的建设经验。     

On the Stability of Messenger RNA and Ribosomal RNA in the Brains of Control Human Subjects and Patients with Alzheimer''s Disease

The levels of the mRNAs encoding the G protein subunits GS alpha, G beta 1, and G beta 2 were measured by northern blotting in the frontal cortex and hippocampus of control subjects and of patients with a clinical and histopathological diagnosis of dementia of the Alzheimer type (DAT). There was no significant difference, in either brain region, between the control and DAT groups for any of the G protein mRNAs measured. The degree of intersubject variability was very high, e.g., GS alpha mRNA in the frontal cortex (mean optical density +/- SD) was 405 +/- 342 in the control group versus 305 +/- 207 in the DAT group. The extent of generalised RNA degradation was assessed by detecting the breakdown products of 28S rRNA. RNA degradation was present in tissue samples from every human subject studied. The extent of 28S rRNA degradation in each subject was found to be related to the levels of G protein mRNA detected. The degree of RNA degradation in human subjects was found to be very variable and unaffected by the presence of DAT. RNA degradation correlated poorly with postmortem interval and this was confirmed by a controlled study of postmortem degradation in rat tissue. The possibility that the relative hypoxia and ischaemia in patients immediately before death could influence RNA degradation is discussed. The variable extent of RNA degradation means that great care must be taken to ensure the validity of RNA analyses undertaken in human postmortem brain, particularly when techniques are employed (such as in situ hybridisation) that themselves give no indication of RNA integrity.     

The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease

The Human Phenotype Ontology (HPO) is widely used in the rare disease community for differential diagnostics, phenotype-driven analysis of next-generation sequence-variation data, and translational research, but a comparable resource has not been available for common disease. Here, we have developed a concept-recognition procedure that analyzes the frequencies of HPO disease annotations as identified in over five million PubMed abstracts by employing an iterative procedure to optimize precision and recall of the identified terms. We derived disease models for 3,145 common human diseases comprising a total of 132,006 HPO annotations. The HPO now comprises over 250,000 phenotypic annotations for over 10,000 rare and common diseases and can be used for examining the phenotypic overlap among common diseases that share risk alleles, as well as between Mendelian diseases and common diseases linked by genomic location. The annotations, as well as the HPO itself, are freely available.     

Evidence for STAT4 as a Common Autoimmune Gene: rs7574865 Is Associated with Colonic Crohn's Disease and Early Disease Onset

Background

Recent studies demonstrated an association of STAT4 variants with systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA), indicating that multiple autoimmune diseases share common susceptibility genes. We therefore investigated the influence of STAT4 variants on the susceptibility and phenotype of inflammatory bowel diseases (IBD) in a large patient and control cohort.

Methodology/Principal Findings

Genomic DNA from 2704 individuals of Caucasian origin including 857 patients with Crohn''s disease (CD), 464 patients with ulcerative colitis (UC), and 1383 healthy, unrelated controls was analyzed for seven SNPs in the STAT4 gene (rs11889341, rs7574865, rs7568275, rs8179673, rs10181656, rs7582694, rs10174238). In addition, a detailed genotype-phenotype analysis was performed. Our analysis revealed an association of the STAT4 SNP rs7574865 with overall decreased susceptibility to CD (p = 0.047, OR 0.86 [95% CI 0.74–0.99]). However, compared to CD patients carrying the wild type genotype, the STAT4 SNP rs7574865 was significantly associated with early CD onset (p = 0.021) and colonic CD (p = 0.008; OR = 4.60, 95% CI 1.63–12.96). For two other STAT4 variants, there was a trend towards protection against CD susceptibility (rs7568275, p = 0.058, OR 0.86 [95% CI 0.74–1.00]; rs10174238, p = 0.057, OR 0.86 [95% CI 0.75–1.00]). In contrast, we did not observe any association with UC susceptibility. Evidence for weak gene-gene interaction of STAT4 with the IL23R SNP rs11209026 was lost after Bonferroni correction.

Conclusions/Significance

Our results identified the STAT4 SNP rs7574865 as a disease-modifying gene variant in colonic CD. However, in contrast to SLE and RA, the effect of rs7574865 on CD susceptibility is only weak.     

Control of Plant Architecture: The Role of Phyllotaxy and Plastochron

Plants display a wide variety of three dimensional forms, or architectures, that are critical for their survival in competitive environments or, in the case of crops, for their productivity. Architecture is generated after embryogenesis through the activities of shoot apical meristems and root apical meristems. Leaves are the principal lateral organ that determines the plant shoot morphology, and they normally develop in very regular patterns in time and space. The spatial pattern of leaf arrangement is called phyllotaxy, and the temporal pattern is determined by the plastochron, which is the time between successive leaf initiation events. Both programs involve many gene activities as well as the hormones auxin and cytokinin. Apparently, the mechanisms controlling phyllotaxy and plastochron share some regulatory components. In this review, the molecular mechanisms for both patterning programs will be discussed.     

Immunocytochemical Quantification of Tyrosine Hydroxylase at a Cellular Level in the Mesencephalon of Control Subjects and Patients with Parkinson's and Alzheimer's Disease

Abstract: Parkinson's disease is characterized by massive degeneration of the melanized dopaminergic neurons in the substantia nigra. The functional capacity of the surviving nigral neurons is affected, as indicated by the subnormal levels of tyrosine hydroxylase (TH) mRNA in these neurons and the presence in the parkinsonian mesencephalon of melanized neurons lacking TH immunoreactivity. This is apparently in contradiction with the known overactivity of dopamine synthesis and release that occurs in the remaining dopaminergic terminals. To test the ability of the surviving neurons to express TH protein, a semiquantitative immunocytochemical method was developed. The relative amounts of TH were estimated with a computer-assisted image analysis system in the dopaminergic neurons of representative mesencephalic sections of control and parkinsonian brains and for comparison in brains from patients with Alzheimer's disease. In control brains, the mean TH content per neuron differed from one subject to another and between the different dopaminergic cell groups of the mesencephalon in the same subject. Within a given dopaminergic region, the level of TH was variable among neurons. In patients with Parkinson's disease, the ratio of TH protein content per neuron in the substantia nigra by reference to that of the central gray substance was reduced. In patients with Alzheimer's disease, the amount of TH was selectively reduced in the remaining dopaminergic neurons of the ventral tegmental area, a region characterized by a loss in dopaminergic neurons. The decrease in cellular TH content might therefore be related to the presence of the neurodegenerative process in the area considered. In patients with Parkinson's disease, the incapacity of the surviving neurons to express normal TH levels may reduce the efficiency of the hyperactivity mechanisms that develop in the remaining striatal dopaminergic terminals.     

Flaxseed Oil for Control of Peanut Rust and Its Disease Control Mechanism

Severity of peanut rust caused by Puccinia arachidis was reduced by 15 edible oils tested. Flaxseed oil was the best suppressing the disease completely. Peanut oil, wheat germ oil, brown rice oil, aloe oil, olive oil and corn germ oil also caused more than 75% reduction in disease incidence. Flaxseed oil reduced the rust to a negligible level in the greenhouse and was nearly as effective as the fungicide chlorothalonil in peanut field trials. The control of peanut rust by flaxseed oil did not result from activation of the host defence mechanisms. Flaxseed oil did not affect urediniospore germination, but reduced the germ tube length and completely suppressed appressorium formation which is essential for the pathogen to form an infection peg to pass through the stomatal aperture and infect the host tissue. Although the pathogen had penetrated, flaxseed oil still exerted some inhibitory effect against the growth of the pathogen. The advantages of using flaxseed oil to control peanut rust are that it is relatively inexpensive, easy to prepare, and friendly to the environment and human health.