Genome-wide analysis of copy number variations reveals that aging processes influence body fat distribution in Korea Associated Resource (KARE) cohorts

Bioactive composition, free radical scavenging and fatty acid profile of Ximenia americana grown in Ethiopia

Ximenia americana is among wild edible fruit indigenous to Ethiopia. The fruit reported as indispensable source of phytochemicals and health imparting components. However, the phytochemicals constituents, antioxidant activities and fatty acid profile of Ethiopian X. americana cultivar studies are still scarce. This research aimed at evaluation of flesh and seed of Ethiopian X. americana yellow and red colored cultivars for bioactive component, antioxidant activities, fatty acid profiles and physicochemical characteristics. The red fruit flesh had higher total phenol (3292.60 mg GAE/100 g) while yellow fruit flesh showed higher total flavonoid (173.95 mg quercetin/100g). The higher DPPH∗ radical scavenging activity (97%) was observed in red fruit flesh due to its higher phenolic content. The yellow X. americana seed (90.69 mg QE/100g) had higher total flavonoid contents than the red seed (18.64 mg QE/100g). The dominant unsaturated fatty acid found in red X. americana flesh was oleic acid (26.29%), and the main saturated fatty acid detected was palmitic acid (29.78%). The seed also had high unsaturated fatty acid which was elaidic acid, (84.32%). Ximeninic acid (12.78%) which is expected to be detected in Ximenia americana seed oil was also observed. The highest content of fat (52.23%) and protein (16.59%) was obtained in yellow fruit seed and the lowest fat content observed in yellow flesh (7.25%). Most abundant minerals were calcium (42.45–49.55 mg/100g) and manganese (26.73–33.92 mg/100g) in seeds. Whereas, fleshs displayed higher magnesium (76.3–98.27 mg/100g) and copper (1.35–1.52 mg/100g) contents. The Ethiopian X. americana fruit cultivars represent high nutritional and medicinal values despite variation related to genetic variability.

In vivo and in vitro ageing results in accumulation of de novo copy number variations in bulls

We have identified de novo copy number variations (CNVs) generated in bulls as they age. Blood samples from eight bulls were collected and SNP arrayed in a prospective design over 30 months allowing us to differentiate de novo CNVs from constant CNVs that are present throughout the sampling period. Quite remarkably, the total number of CNVs doubled over the 30-month period, as we observed an almost equal number of de novo and constant CNVs (107 and 111, respectively, i.e. 49% and 51%). Twice as many de novo CNVs emerged during the second half of the sampling schedule as in the first part. It suggests a dynamic generation of de novo CNVs in the bovine genome that becomes more frequent as the age of the animal progresses. In a second experiment de novo CNVs were detected through in vitro ageing of bovine fibroblasts by sampling passage #5, #15 and #25. De novo CNVs also became more frequent, but the proportion of them was only ~25% of the total number of CNVs (21 out of 85). Temporal generation of de novo CNVs resulted in increasing genome coverage. Genes and quantitative trait loci overlapping de novo CNVs were further investigated for ageing related functions.

Effective population size of korean populations

Recently, new methods have been developed for estimating the current and recent changes in effective population sizes. Based on the methods, the effective population sizes of Korean populations were estimated using data from the Korean Association Resource (KARE) project. The overall changes in the population sizes of the total populations were similar to CHB (Han Chinese in Beijing, China) and JPT (Japanese in Tokyo, Japan) of the HapMap project. There were no differences in past changes in population sizes with a comparison between an urban area and a rural area. Age-dependent current and recent effective population sizes represent the modern history of Korean populations, including the effects of World War II, the Korean War, and urbanization. The oldest age group showed that the population growth of Koreans had already been substantial at least since the end of the 19th century.

Pathway Analysis of Metabolic Syndrome Using a Genome-Wide Association Study of Korea Associated Resource (KARE) Cohorts

Metabolic syndrome (MetS) is a complex disorder related to insulin resistance, obesity, and inflammation. Genetic and environmental factors also contribute to the development of MetS, and through genome-wide association studies (GWASs), important susceptibility loci have been identified. However, GWASs focus more on individual single-nucleotide polymorphisms (SNPs), explaining only a small portion of genetic heritability. To overcome this limitation, pathway analyses are being applied to GWAS datasets. The aim of this study is to elucidate the biological pathways involved in the pathogenesis of MetS through pathway analysis. Cohort data from the Korea Associated Resource (KARE) was used for analysis, which include 8,842 individuals (age, 52.2 ± 8.9 years; body mass index, 24.6 ± 3.2 kg/m(2)). A total of 312,121 autosomal SNPs were obtained after quality control. Pathway analysis was conducted using Meta-analysis Gene-Set Enrichment of Variant Associations (MAGENTA) to discover the biological pathways associated with MetS. In the discovery phase, SNPs from chromosome 12, including rs11066280, rs2074356, and rs12229654, were associated with MetS (p < 5 × 10(-6)), and rs11066280 satisfied the Bonferroni-corrected cutoff (unadjusted p < 1.38 × 10(-7), Bonferroni-adjusted p < 0.05). Through pathway analysis, biological pathways, including electron carrier activity, signaling by platelet-derived growth factor (PDGF), the mitogen-activated protein kinase kinase kinase cascade, PDGF binding, peroxisome proliferator-activated receptor (PPAR) signaling, and DNA repair, were associated with MetS. Through pathway analysis of MetS, pathways related with PDGF, mitogen-activated protein kinase, and PPAR signaling, as well as nucleic acid binding, protein secretion, and DNA repair, were identified. Further studies will be needed to clarify the genetic pathogenesis leading to MetS.

Metallothionein polymorphisms in pathological processes

Metallothioneins (MTs) are a class of metal-binding proteins characterized by a high cysteine content and low molecular weight. MTs play an important role in metal metabolism and protect cells against the toxic effects of radiation, alkylating agents and oxygen free radicals. The evidence that individual genetic characteristics of MTs play an important role in physiological and pathological processes associated with antioxidant defense and detoxification inspired targeted studies of genetic polymorphisms in a clinical context. In recent years, common MT polymorphisms were identified and associated with, particularly, western lifestyle diseases such as cancer, complications of atherosclerosis, and type 2 diabetes mellitus along with related complications. This review summarizes all evidence regarding MT polymorphisms of major human MTs (MT1, MT2, MT3 and MT4), their relation to pathological processes, and outlines specific applications of MTs as a set of genetic markers for certain pathologies.