LONGITUDINAL STUDY OF RPE65-ASSOCIATED INHERITED RETINAL DEGENERATIONS

PURPOSE: To study the disease course of RPE65-associated inherited retinal degenerations (IRDs) as a function of the genotype, define a critical age for blindness, and identify potential modifiers. METHODS: Forty-five patients with IRD from 33 families with biallelic RPE65 mutations, 28 stemming from a genetic isolate. We collected retrospective data from medical charts. Coexisting variants in 108 IRD-associated genes were identified with Molecular Inversion Probe analysis. RESULTS: Most patients were diagnosed within the first years of life. Daytime visual function ranged from near-normal to blindness in the first four decades and met WHO criteria for blindness for visual acuity and visual field in the fifth decade. p.(Thr368His) was the most common variant (54%). Intrafamilial variability and interfamilial variability in disease severity and progression were observed. Molecular Inversion Probe analysis confirmed all RPE65 variants and identified one additional variant in LRAT and one in EYS in two separate patients. CONCLUSION: All patients with RPE65-associated IRDs developed symptoms within the first year of life. Visual function in childhood and adolescence varied but deteriorated inevitably toward blindness after age 40. In this study, genotype was not predictive of clinical course. The variance in severity of disease could not be explained by double hits in other IRD genes

RANTES/CCL5 and risk for coronary events: Results from the MONICA/KORA Augsburg case-cohort, Athero-express and CARDIoGRAM studies

Background: The chemokine RANTES (regulated on activation, normal T-cell expressed and secreted)/CCL5 is involved in the pathogenesis of cardiovascular disease in mice, whereas less is known in humans. We hypothesised that its relevance for atherosclerosis should be reflected by associations between CCL5 gene variants, RANTES serum concentrations and protein levels in atherosclerotic plaques and risk for coronary events. Methods and Findings: We conducted a case-cohort study within the population-based MONICA/KORA Augsburg studies. Baseline RANTES serum levels were measured in 363 individuals with incident coronary events and 1,908 non-cases (mean follow-up: 10.2±

Expanding the clinical phenotype of individuals with a 3-bp in-frame deletion of the NF1 gene (c.2970_2972del): an update of genotype–phenotype correlation

Purpose: Neurofibromatosis type 1 (NF1) is characterized by a highly variable clinical presentation, but almost all NF1-affected adults present with cutaneous and/or subcutaneous neurofibromas. Exceptions are individuals heterozygous for the NF1 in-frame deletion, c.2970_2972del (p.Met992del), associated with a mild phenotype without any externally visible tumors. Methods: A total of 135 individuals from 103 unrelated families, all carrying the constitutional NF1 p.Met992del pathogenic variant and clinically assessed using the same standardized phenotypic checklist form, were included in this study. Results: None of the individuals had externally visible plexiform or histopathologically confirmed cutaneous or subcutaneous neurofibromas. We did not identify any complications, such as symptomatic optic pathway gliomas (OPGs) or symptomatic spinal neurofibromas; however, 4.8% of individuals had nonoptic brain tumors, mostly low-grade and asymptomatic, and 38.8% had cognitive impairment/learning disabilities. In an individual with the NF1 constitutional c.2970_2972del and three astrocytomas, we provided proof that all were NF1-associated tumors given loss of heterozygosity at three intragenic NF1 microsatellite markers and c.2970_297

Detectable clonal mosaicism and its relationship to aging and cancer

In an analysis of 31,717 cancer cases and 26,136 cancer-free controls from 13 genome-wide association studies, we observed large chromosomal abnormalities in a subset of clones in DNA obtained from blood or buccal samples. We observed mosaic abnormalities, either aneuploidy or copy-neutral loss of heterozygosity, of >2 Mb in size in autosomes of 517 individuals (0.89%), with abnormal cell proportions of between 7% and 95%. In cancer-free individuals, frequency increased with age, from 0.23% under 50 years to 1.91% between 75 and 79 years (P = 4.8 × 10(-8)). Mosaic abnormalities were more frequent in individuals with solid tumors (0.97% versus 0.74% in cancer-free individuals; odds ratio (OR) = 1.25; P = 0.016), with stronger association with cases who had DNA collected before diagnosis or treatment (OR = 1.45; P = 0.0005). Detectable mosaicism was also more common in individuals for whom DNA was collected at least 1 year before diagnosis with leukemia compared to cancer-free individuals (OR = 35.4; P = 3.8 × 10(-11)). These findings underscore the time-dependent nature of somatic events in the etiology of cancer and potentially other late-onset diseases

Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome

To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected 124 mosaic X events42Mb in 97 (0.25%) women. Here we show rates for X-chromosome mosaicism are four times higher than mean autosomal rates; X mosaic events more often include the entire chromosome and participants with X events more likely harbour autosomal mosaic events. X mosaicism frequency increases with age (0.11% in 50-year olds; 0.45% in 75-year olds), as reported for Y and autosomes. Methylation array analyses of 33 women with X mosaicism indicate events preferentially involve the inactive X chromosome. Our results provide further evidence that the sex chromosomes undergo mosaic events more frequently than autosomes, which could have implications for understanding the underlying mechanisms of mosaic events and their possible contribution to risk for chronic diseases

Assessment of genetic diversity of rice in registered cultivars and farmers' fields in Burkina Faso

The genetic diversity of cultivated rice in farmers' fields remains understudied in West Africa despite the importance of rice for food security in this region. In this study, we genotyped rice samples from Burkina Faso using the C6AIR SNP (Single Nucleotide Polymorphism) array (IRRI), including 27 registered cultivars and 50 rice samples collected in rice fields from three geographical zones in western Burkina Faso. Most of the registered cultivars clustered with the indica genetic group, except seven assigned to japonica and one admix. All but one of the rice samples from farmers' fields belonged to the indica group. The other field sample, which unexpectedly clustered with the Aus genetic group, originated from a rainfed lowland site known to differ in terms of agronomic practices, and which revealed to be highly differentiated from the five other sites. Apart from this peculiar site, the rice grown in irrigated areas did not differ from rice sampled in rainfed lowlands. Finally, obtained genetic data confirmed the high frequency of one cultivar, in congruence with farmers' interviews. We argue on the importance to document and preserve the high agro-biodiversity observed in rice from Burkina Faso as a prerequisite to face the current challenges of growing rice demand and global change

Genesis, design and methods of the Beef CRC Maternal Productivity Project

Australian seedstock cattle breeders have expressed concerns that while there has been genetic improvement in feedlot and abattoir performance of cows, it could have led to a decline in maternal productivity, especially under variable nutritional conditions. This paper describes a substantial project with two components designed to address these issues. The first sub-project was to monitor bodyweight and composition of 7760 young Angus and Hereford cows as they experience variable physiological states (pregnancy and lactation) and seasons. This was conducted on large numbers in seedstock herds. The second sub-project was to monitor more regularly bodyweight, body composition, and calf rearing performance of 500 Angus cows that are genetically divergent for either fat or residual feed intake at two research centres. This also included two levels of nutrition and recording of weekly feed intake of small groups of cows for at least three parities to allow reporting of genotype × nutrition effects on maternal productivity and efficiency. Results from the project are reported in a series of papers with each one having a defined focus

Invited review: Current enteric methane mitigation options

peer-reviewedRuminant livestock are an important source of anthropogenic methane (CH4). Decreasing the emissions of enteric CH4 from ruminant production is strategic to limit the global temperature increase to 1.5°C by 2050. Research in the area of enteric CH4 mitigation has grown exponentially in the last 2 decades, with various strategies for enteric CH4 abatement being investigated: production intensification, dietary manipulation (including supplementation and processing of concentrates and lipids, and management of forage and pastures), rumen manipulation (supplementation of ionophores, 3-nitrooxypropanol, macroalgae, alternative electron acceptors, and phytochemicals), and selection of low-CH4-producing animals. Other enteric CH4 mitigation strategies are at earlier stages of research but rapidly developing. Herein, we discuss and analyze the current status of available enteric CH4 mitigation strategies with an emphasis on opportunities and barriers to their implementation in confined and partial grazing production systems, and in extensive and fully grazing production systems. For each enteric CH4 mitigation strategy, we discuss its effectiveness to decrease total CH4 emissions and emissions on a per animal product basis, safety issues, impacts on the emissions of other greenhouse gases, as well as other economic, regulatory, and societal aspects that are key to implementation. Most research has been conducted with confined animals, and considerably more research is needed to develop, adapt, and evaluate antimethanogenic strategies for grazing systems. In general, few options are currently available for extensive production systems without feed supplementation. Continuous research and development are needed to develop enteric CH4 mitigation strategies that are locally applicable. Information is needed to calculate carbon footprints of interventions on a regional basis to evaluate the impact of mitigation strategies on net greenhouse gas emissions. Economically affordable enteric CH4 mitigation solutions are urgently needed. Successful implementation of safe and effective antimethanogenic strategies will also require delivery mechanisms and adequate technical support for producers, as well as consumer involvement and acceptance. The most appropriate metrics should be used in quantifying the overall climate outcomes associated with mitigation of enteric CH4 emissions. A holistic approach is required, and buy-in is needed at all levels of the supply chain