Extensive Structural Variations Between Mitochondrial Genomes of CMS and Normal Peppers (Capsicum Annuum L.) Revealed by Complete Nucleotide Sequencing

Cytoplasmic male sterility (CMS) is an inability to produce functional pollen that is caused by mutation of the mitochondrial genome. Comparative analyses of mitochondrial genomes of lines with and without CMS in several species have revealed structural differences between genomes, including extensive rearrangements caused by recombination. However, the mitochondrial genome structure and the DNA rearrangements that may be related to CMS have not been characterized in Capsicum spp. Results: We obtained the complete mitochondrial genome sequences of the pepper CMS line FS4401 (507,452 bp) and the fertile line Jeju (511,530 bp). Comparative analysis between mitochondrial genomes of peppers and tobacco that are included in Solanaceae revealed extensive DNA rearrangements and poor conservation in non-coding DNA. In comparison between pepper lines, FS4401 and Jeju mitochondrial DNAs contained the same complement of protein coding genes except for one additional copy of an atp6 gene (psi atp6-2) in FS4401. In terms of genome structure, we found eighteen syntenic blocks in the two mitochondrial genomes, which have been rearranged in each genome. By contrast, sequences between syntenic blocks, which were specific to each line, accounted for 30,380 and 17,847 bp in FS4401 and Jeju, respectively. The previously-reported CMS candidate genes, orf507 and psi atp6-2, were located on the edges of the largest sequence segments that were specific to FS4401. In this region, large number of small sequence segments which were absent or found on different locations in Jeju mitochondrial genome were combined together. The incorporation of repeats and overlapping of connected sequence segments by a few nucleotides implied that extensive rearrangements by homologous recombination might be involved in evolution of this region. Further analysis using mtDNA pairs from other plant species revealed common features of DNA regions around CMS-associated genes. Conclusions: Although large portion of sequence context was shared by mitochondrial genomes of CMS and male-fertile pepper lines, extensive genome rearrangements were detected. CMS candidate genes located on the edges of highly-rearranged CMS-specific DNA regions and near to repeat sequences. These characteristics were detected among CMS-associated genes in other species, implying a common mechanism might be involved in the evolution of CMS-associated genes.Golden Seed ProjectMinistry of Agriculture, Food and Rural Affairs (MAFRA)Ministry of Oceans and Fisheries (MOF)Rural Development Administration (RDA)Korea Forest Service (KFS)Vegetable Breeding Research Center through the R&D Convergence Center Support Program, Ministry of Agriculture, Food and Rural Affairs (MAFRA) Republic of Korea 710001-07Molecular Bioscience

Optimization of isoprene production using a metabolically engineered Escherichia Coli

The volatile C5 hydrocarbon, isoprene is an important platform chemical, which has been used in the manufacture of synthetic rubber for tires and also has the potential for various other applications such as elastomers and adhesives. Moreover, isoprene is convertible to biofuel blend stocks such as C10 gasoline, C15 diesel, and jet fuels because of its higher energy content than other biofuels. Although isoprene is currently derived from petroleum, its sustainable supply has been suffered from price fluctuation of crude oil, high refining cost and energy consumption, and low recovery yield of pure isoprene. As an alternative, the biologically produced isoprene (bio-isoprene) has been developed rapidly for the last decade. Bio-isoprene is synthesized from dimethylallyl diphosphate (DMAPP), which is derived from mevalonate (MVA) pathway or the methylerythritol phosphate (MEP) pathway, by isoprene synthase. In this study, metabolic engineering for enhanced production of bio-isoprene was performed by deletion of relevant genes and optimization of culture condition. In comparison of isoprene production between E.coli DH5α and MG1655, lower isoprene production was observed in MG1655. The lower isoprene production in E. coli MG1655 was ascribed to the presence of recA gene which is absent in the DH5α strain. The deletion of recA gene in E.coli MG1655 allows higher isoprene production than E. coli DH5α. Moreover, the optimized expression of isoprene synthesis pathway with 0.03mM IPTG induction enhanced the isoprene production up to 2,850 mg/L. Overall, isoprene production through the optimization was improved by 28.5-fold compared to the initial production of MG1655 strain. Please click Additional Files below to see the full abstract

Gene-based copy number variation study reveals a microdeletion at 12q24 that influences height in the Korean population

AbstractHeight is a classic polygenic trait with high heritability (h2=0.8). Recent genome-wide association studies have revealed many independent loci associated with human height. In addition, although many studies have reported an association between copy number variation (CNV) and complex diseases, few have explored the relationship between CNV and height. Recent studies reported that single nucleotide polymorphisms (SNPs) are highly correlated with common CNVs, suggesting that it is warranted to survey CNVs to identify additional genetic factors affecting heritable traits such as height.This study tested the hypothesis that there would be CNV regions (CNVRs) associated with height nearby genes from the GWASs known to affect height. We identified regions containing >1% copy number deletion frequency from 3667 population-based cohort samples using the Illumina HumanOmni1-Quad BeadChip. Among the identified CNVRs, we selected 15 candidate regions that were located within 1Mb of 283 previously reported genes. To assess the effect of these CNVRs on height, statistical analyses were conducted with samples from a case group of 370 taller (upper 10%) individuals and a control group of 1828 individuals (lower 50%).We found that a newly identified 17.7kb deletion at chromosomal position 12q24.33, approximately 171.6kb downstream of GPR133, significantly correlated with height; this finding was validated using quantitative PCR. These results suggest that CNVs are potentially important in determining height and may contribute to height variation in human populations

Longitudinal relationship between depression and antisocial behaviors in Korean adolescents

BackgroundIt is well known that depression and delinquency in adolescents are highly correlated, but longitudinal studies on the causal relationship between them are not active in East Asia compared to in Western culture. In addition, even the results of research on causal models and sex differences are inconsistent.ObjectivesThis study examines the longitudinal reciprocal effects between depression and delinquent behavior in Korean adolescents based on sex differences.MethodsWe conducted multiple-group analysis by using an autoregressive cross-lagged model (ACLM). Longitudinal data from 2,075 individuals (2011–2013) were used for analysis. The longitudinal data are from the Korean Children and Youth Panel Survey (KCYPS), and data were used beginning with students at 14 years old (in the second grade of middle school) and tracked them until they were 16 (in the first grade of high school).ResultsBoys’ delinquent behaviors at 15 years (the third grade of middle school) affected their depression at 16 years (the first grade of high school). In contrast, girls’ depression at 15 years (the third grade of middle school) influenced their delinquent behaviors at 16 years (the first grade of high school).DiscussionThe findings support the failure model (FM) among adolescent boys and the acting-out model (ACM) among girls. The results imply that strategies to effectively prevent and treat delinquency and depression in adolescents must consider sex effects

Data of methylome and transcriptome derived from human dilated cardiomyopathy

AbstractAlterations in DNA methylation and gene expression have been implicated in the development of human dilated cardiomyopathy (DCM). Differentially methylated probes (DMPs) and differentially expressed genes (DEGs) were identified between the left ventricle (LV, a pathological locus for DCM) and the right ventricle (RV, a proxy for normal hearts). The data in this DiB are for supporting our report entitled “Methylome analysis reveals alterations in DNA methylation in the regulatory regions of left ventricle development genes in human dilated cardiomyopathy” (Bong-Seok Jo, In-Uk Koh, Jae-Bum Bae, Ho-Yeong Yu, Eun-Seok Jeon, Hae-Young Lee, Jae-Joong Kim, Murim Choi, Sun Shim Choi, 2016) [1]

Investigation of the mechanism of the anomalous Hall effects in Cr2Te3/(BiSb)2(TeSe)3 heterostructure

The interplay between ferromagnetism and the non-trivial topology has unveiled intriguing phases in the transport of charges and spins. For example, it is consistently observed the so-called topological Hall effect (THE) featuring a hump structure in the curve of the Hall resistance (Rxy) vs. a magnetic field (H) of a heterostructure consisting of a ferromagnet (FM) and a topological insulator (TI). The origin of the hump structure is still controversial between the topological Hall effect model and the multi-component anomalous Hall effect (AHE) model. In this work, we have investigated a heterostructure consisting of BixSb2-xTeySe3-y (BSTS) and Cr2Te3 (CT), which are well-known TI and two-dimensional FM, respectively. By using the so-called minor-loop measurement, we have found that the hump structure observed in the CT/BSTS is more likely to originate from two AHE channels. Moreover, by analyzing the scaling behavior of each amplitude of two AHE with the longitudinal resistivities of CT and BSTS, we have found that one AHE is attributed to the extrinsic contribution of CT while the other is due to the intrinsic contribution of BSTS. It implies that the proximity-induced ferromagnetic layer inside BSTS serves as a source of the intrinsic AHE, resulting in the hump structure explained by the two AHE model

Identification of a Copy Number Variation on Chromosome 20q13.12 Associated with Osteoporotic Fractures in the Korean Population

Osteoporotic fractures (OFs) are critical hard outcomes of osteoporosis and are characterized by decreased bone strength induced by low bone density and microarchitectural deterioration in bone tissue. Most OFs cause acute pain, hospitalization, immobilization, and slow recovery in patients and are associated with increased mortality. A variety of genetic studies have suggested associations of genetic variants with the risk of OF. Genome-wide association studies have reported various single-nucleotide polymorphisms and copy number variations (CNVs) in European and Asian populations. To identify CNV regions associated with OF risk, we conducted a genome-wide CNV study in a Korean population. We performed logistic regression analyses in 1,537 Korean subjects (299 OF cases and 1,238 healthy controls) and identified a total of 8 CNV regions significantly associated with OF (p < 0.05). Then, one CNV region located on chromosome 20q13.12 was selected for experimental validation. The selected CNV region was experimentally validated by quantitative polymerase chain reaction. The CNV region of chromosome 20q13.12 is positioned upstream of a family of long non-coding RNAs, LINC01260. Our findings could provide new information on the genetic factors associated with the risk of OF