De novo transcriptome analysis of high growth rate Pyropia yezoensis (Bangiales, Rhodophyta) mutant with high utilization of nitrogen

Pyropia yezoensis (Ueda) M.S.Hwang et H.G.Choi (Bangiales, Rhodophyta) has potentially high economic value. P. yezoensis has been used as food in East Asian countries for a long time, and, in addition to that its consumption is increasing worldwide owing to the growing interest in healthy seaweed food. A mutant (Py2K) with a high growth rate was developed using gamma rays to increase the production of P. yezoensis. De novo transcriptome analysis was performed to determine the mechanism underlying the high growth rate of this mutant. The transcriptomes from wild-type (PyWT) and mutant (Py2K) strains were assembled, and 167,165 genes were analyzed. A total of 15,979 genes were differentially expressed. Transcriptome analysis of nitrogen pathway revealed the increase in nitrogen availability through the upregulation of nitrate transporter gene (nrt) expression. Activation of nitrogen assimilation and re-assimilation and upregulation in alternative oxidase (aox) gene contributed to the increase in cellular nitrogen availability, thereby affecting the synthesis of phycobiliprotein. As a consequence, the efficiency of photosynthesis and the subsequent growth rate increased, which contributed to the color differences in thalli between PyWT and Py2K

Design of GPU Based Non-coherent Signal Tracking Module for Real-time GNSS SDR

In this paper, we design and implement GPU-based non-coherent GPS signal tracking module for real-time SDR. When using CPU and GPU simultaneously, the signal tracking module should be designed considering the memory bottleneck between the two processors. The basic non-coherent module, which accumulates the 1msec correlation value 20 times, is changed to accumulate M(20/N) times of Nmsec units. From the experiments using real GPS signals, the computational performance of N=20 is improved by 80% compared to N=1. Therefore, the implemented SDR using notebook computer can tracks more channels simultaneously in the real time

Forage Rye Cultivars for Animal Feed in Korea

Rye (Secale cereal L.) is well known for its overwintering ability and has the highest tolerance to cold temperature of the small grain cereals such as wheat, barley, and oat. Rye is used as livestock pasture and as green manure in Korea, and its cultivation area for fodder is about 50,000 ha in 2014. Most rye is grown as a fall-sown annual crop, generally called “winter rye”. In Korea, rye cultivation for whole crop silage (WCS) in the winter-season rice field can be considered as a promising way to enhance feed supply. The WCS production can be an efficient way to use farm products as livestock feed, and it can also contribute to increasing farm income. Although rye is inferior in several ways to the predominant cereal crops (wheat, rice, and maize), it will continue to be an important crop for farmers in Korea because of its winter hardiness and early harvesting by rapid growing ability

A genome-wide Asian genetic map and ethnic comparison: The GENDISCAN study

<p>Abstract</p> <p>Background</p> <p>Genetic maps provide specific positions of genetic markers, which are required for performing genetic studies. Linkage analyses of Asian families have been performed with Caucasian genetic maps, since appropriate genetic maps of Asians were not available. Different ethnic groups may have different recombination rates as a result of genomic variations, which would generate misspecification of the genetic map and reduce the power of linkage analyses.</p> <p>Results</p> <p>We constructed the genetic map of a Mongolian population in Asia with CRIMAP software. This new map, called the GENDISCAN map, is based on genotype data collected from 1026 individuals of 73 large Mongolian families, and includes 1790 total and 1500 observable meioses. The GENDISCAN map provides sex-averaged and sex-specific genetic positions of 1039 microsatellite markers in Kosambi centimorgans (cM) with physical positions. We also determined 95% confidence intervals of genetic distances of the adjacent marker intervals.</p> <p>Genetic lengths of the whole genome, chromosomes and adjacent marker intervals are compared with those of Rutgers Map v.2, which was constructed based on Caucasian populations (Centre d'Etudes du Polymorphisme Humain (CEPH) and Icelandic families) by mapping methods identical to those of the GENDISCAN map, CRIMAP software and the Kosambi map function. Mongolians showed approximately 1.9 fewer recombinations per meiosis than Caucasians. As a result, genetic lengths of the whole genome and chromosomes of the GENDISCAN map are shorter than those of Rutgers Map v.2. Thirty-eight marker intervals differed significantly between the Mongolian and Caucasian genetic maps.</p> <p>Conclusion</p> <p>The new GENDISCAN map is applicable to the genetic study of Asian populations. Differences in the genetic distances between the GENDISCAN and Caucasian maps could facilitate elucidation of genomic variations between different ethnic groups.</p

Korea's developmental program for superconductivity

Superconductivity research in Korea was firstly carried out in the late 70's by a research group in Seoul National University (SNU), who fabricated a small scale superconducting magnetic energy storage system under the financial support from Korea Electric Power Company (KEPCO). But a few researchers were involved in superconductivity research until the oxide high Tc superconductor was discovered by Bednorz and Mueller. After the discovery of YBaCuO superconductor operating above the boiling point of liquid nitrogen (77 K)(exp 2), Korean Ministry of Science and Technology (MOST) sponsored a special fund for the high Tc superconductivity research to universities and national research institutes by recognizing its importance. Scientists engaged in this project organized 'High Temperature Superconductivity Research Association (HITSRA)' for effective conducting of research. Its major functions are to coordinate research activities on high Tc superconductivity and organize the workshop for active exchange of information. During last seven years the major superconductivity research has been carried out through the coordination of HITSRA. The major parts of the Korea's superconductivity research program were related to high temperature superconductor and only a few groups were carrying out research on conventional superconductor technology, and Korea Atomic Energy Research Institute (KAERI) and Korea Electrotechnology Research Institute (KERI) have led this research. In this talk, the current status and future plans of superconductivity research in Korea will be reviewed based on the results presented in interim meeting of HITSRA, April 1-2, 1994. Taejeon, as well as the research activity of KAERI

Copy Number Variation of Age-Related Macular Degeneration Relevant Genes in the Korean Population

PURPOSE: Studies that analyzed single nucleotide polymorphisms (SNP) in various genes have shown that genetic factors are strongly associated with age-related macular degeneration (AMD) susceptibility. Copy number variation (CNV) may be an additional type of genetic variation that contributes to AMD pathogenesis. This study investigated CNV in 4 AMD-relevant genes in Korean AMD patients and control subjects. METHODS: Four CNV candidate regions located in AMD-relevant genes (VEGFA, ARMS2/HTRA1, CFH and VLDLR), were selected based on the outcomes of our previous study which elucidated common CNVs in the Asian populations. Real-time PCR based TaqMan Copy Number Assays were performed on CNV candidates in 273 AMD patients and 257 control subjects. RESULTS: The predicted copy number (PCN, 0, 1, 2 or 3+) of each region was called using the CopyCaller program. All candidate genes except ARMS2/HTRA1 showed CNV in at least one individual, in which losses of VEGFA and VLDLR represent novel findings in the Asian population. When the frequencies of PCN were compared, only the gain in VLDLR showed significant differences between AMD patients and control subjects (p = 0.025). Comparisons of the raw copy values (RCV) revealed that 3 of 4 candidate genes showed significant differences (2.03 vs. 1.92 for VEGFA, p<0.01; 2.01 vs. 1.97 for CFH, p<0.01; 1.97 vs. 2.01, p<0.01 for ARMS2/HTRA1). CONCLUSION: CNVs located in AMD-relevant genes may be associated with AMD susceptibility. Further investigations encompassing larger patient cohorts are needed to elucidate the role of CNV in AMD pathogenesis

PutidaNET: Interactome database service and network analysis of Pseudomonas putida KT2440

<p>Abstract</p> <p>Background</p> <p><it>Pseudomonas putida </it>KT2440 (<it>P. putida </it>KT2440) is a highly versatile saprophytic soil bacterium. It is a certified bio-safety host for transferring foreign genes. Therefore, the bacterium is used as a model organism for genetic and physiological studies and for the development of biotechnological applications. In order to provide a more systematic application of the organism, we have constructed a protein-protein interaction (PPI) network analysis system of <it>P. putida </it>KT2440.</p> <p>Results</p> <p>PutidaNET is a comprehensive interaction database and server of <it>P. putida </it>KT2440 which is generated from three protein-protein interaction (PPI) methods. We used PSIMAP (Protein Structural Interactome MAP), PEIMAP (Protein Experimental Interactome MAP), and Domain-domain interactions using iPfam. PutidaNET contains 3,254 proteins, and 82,019 possible interactions consisting of 61,011 (PSIMAP), 4,293 (PEIMAP), and 30,043 (iPfam) interaction pairs except for self interaction. Also, we performed a case study by integrating a protein interaction network and experimental 1-DE/MS-MS analysis data <it>P. putida</it>. We found that 1) major functional modules are involved in various metabolic pathways and ribosomes, and 2) existing PPI sub-networks that are specific to succinate or benzoate metabolism are not in the center as predicted.</p> <p>Conclusion</p> <p>We introduce the PutidaNET which provides predicted interaction partners and functional analyses such as physicochemical properties, KEGG pathway assignment, and Gene Ontology mapping of <it>P. putida </it>KT2440 PutidaNET is freely available at <url>http://sequenceome.kobic.kr/PutidaNET</url>.</p

Association of Epidermal Growth Factor Receptor Mutations with Metastatic Presentations in Non-Small Cell Lung Cancer

We performed this retrospective study to assess the association of epidermal growth factor receptor (EGFR) with metastatic presentations in advanced non-small cell lung cancer (NSCLC). The data from 125 patients with stage III or IV NSCLC were analyzed. We detected EGFR mutations in 36 NSCLC patients. EGFR mutations were predominant in never-smokers (P < .001), patients with adenocarcinomas (P < .001), and female patients (P < .001). When the metastatic sites were analyzed, pleural metastases were associated with a high incidence of EGFR mutations (P = .028). Particularly, pleural metastases with minimal effusion (PMME) were associated with EGFR mutational status (P = .001). Patients with N3 lesions were less likely to harbor EGFR mutations (P = .033). On multivariate analysis, N3 lesions (P = .017) and PMME (P < .001) remained significant factors for EGFR mutations. EGFR mutations may be associated with different presentations of pleural and N3 nodal metastases

Spontaneous Pharyngeal Perforation After Forceful Vomiting: The Difference from Classic Boerhaave's Syndrome

Boerhaave's syndrome is spontaneous transmural perforation of the esophagus, which occurs most often after forceful vomiting or retching. This commonly occurs in the lower third of the esophagus but spontaneous perforation of the pharynx or cervical esophagus is extremely rare. This case presented a 20-yr-old healthy man with spontaneous pharyngeal perforation after forceful vomiting who had no history of instrumentation, cervical trauma, or having eaten anything sharp. Cervical pain and crepitus were the early symptom and sign of pharyngeal perforation and the rupture was detected on gastrografin swallow and CT examinations. The rupture site was higher than the upper esophageal sphincter, differing from Boerhaave's syndrome. The patient was conservatively managed without significant morbidity and mortality. Although this may resolve without surgical intervention, the pharyngeal rupture should receive early detection and clinical attention for preventing potential morbidity by late diagnosis