An Integrated Korean Biodiversity and Genetic Information Retrieval System

Background: On-line biodiversity information databases are growing quickly and being integrated into general bioinformatics systems due to the advances of fast gene sequencing technologies and the Internet. These can reduce the cost and effort of performing biodiversity surveys and genetic searches, which allows scientists to spend more time researching and less time collecting and maintaining data. This will cause an increased rate of knowledge build-up and improve conservations. The biodiversity databases in Korea have been scattered among several institutes and local natural history museums with incompatible data types. Therefore, a comprehensive database and a nation wide web portal for biodiversity information is necessary in order to integrate diverse information resources, including molecular and genomic databases. Results: The Korean Natural History Research Information System (NARIS) was built and serviced as the central biodiversity information system to collect and integrate the biodiversity data of various institutes and natural history museums in Korea. This database aims to be an integrated resource that contains additional biological information, such as genome sequences and molecular level diversity. Currently, twelve institutes and museums in Korea are integrated by the DiGIR (Distributed Generic Information Retrieval) protocol, with Darwin Core2.0 format as its metadata standard for data exchange. Data quality control and statistical analysis functions have been implemented. In particular, integrating molecular and genetic information from the National Center for Biotechnology Information (NCBI) databases with NARIS was recently accomplished. NARIS can also be extended to accommodate other institutes abroad, and the whole system can be exported to establish local biodiversity management servers. Conclusion: A Korean data portal, NARIS, has been developed to efficiently manage and utilize biodiversity data, which includes genetic resources. NARIS aims to be integral in maximizing biofrom resource utilization for conservation, management, research, education, industrial applications, and integration with other bioinformation data resources. It can be found at http://www.naris.go.krclose1

Laparoscopic Surgical Management and Clinical Characteristics of Ovarian Fibromas

Ovarian fibromas may be misdiagnosed as uterine myoma or ovarian malignant tumor. Laparoscopic examination appears to be an effective and safe surgical approach for managing ovarian fibromas

Numerical study on sequential period-doubling bifurcations of graphene wrinkles on a soft substrate

A compressed stiff film on a soft substrate may exhibit wrinkles and, under increased compressive strain, post-buckling instabilities as well. We numerically analyze wrinkling behaviors of graphene attached on a polydimethylsiloxane (PDMS) substrate under lateral compression. The finite element method is used to simulate the equilibrium shape of the wrinkles as a function of compressive strain. Two-dimensional stretching and bending properties of graphene are obtained by density functional theory analysis, which are then converted to equivalent elastic properties of a continuum film with finite effective thickness. The PDMS is described using an Ogden or a neo-Hookean material model. Wrinkles first appear at extremely small strain. As the lateral compression increases, due to the nonlinear elasticity of the PDMS, sequential period-doubling bifurcations of the wrinkle mode are activated until the bifurcation stops and the film folds. We show that the bifurcations are consequences of a delicate balance between the deformations of the film and the substrate to minimize the total energy.J.H.J., J.B., and J.I. were supported by the National Research Foundation of Korea through the MSIP Grant no. 2006-0093853 and the Korea Institute of Science and Technology. M.-W.M. was supported by the Korea Institute of Science and Technology (KIST), and K.-S.K. by the Institute for Molecular and Nanoscale Innovation (IMNI) at Brown University (GR260000.1001) and KIST (529243). Computations were performed through the support from the Korea Institute of Science and Technology Information

BioBarcode: a general DNA barcoding database and server platform for Asian biodiversity resources

<p>Abstract</p> <p>Background</p> <p>DNA barcoding provides a rapid, accurate, and standardized method for species-level identification using short DNA sequences. Such a standardized identification method is useful for mapping all the species on Earth, particularly when DNA sequencing technology is cheaply available. There are many nations in Asia with many biodiversity resources that need to be mapped and registered in databases.</p> <p>Results</p> <p>We have built a general DNA barcode data processing system, BioBarcode, with open source software - which is a general purpose database and server. It uses mySQL RDBMS 5.0, BLAST2, and Apache httpd server. An exemplary database of BioBarcode has around 11,300 specimen entries (including GenBank data) and registers the biological species to map their genetic relationships. The BioBarcode database contains a chromatogram viewer which improves the performance in DNA sequence analyses.</p> <p>Conclusion</p> <p>Asia has a very high degree of biodiversity and the BioBarcode database server system aims to provide an efficient bioinformatics protocol that can be freely used by Asian researchers and research organizations interested in DNA barcoding. The BioBarcode promotes the rapid acquisition of biological species DNA sequence data that meet global standards by providing specialized services, and provides useful tools that will make barcoding cheaper and faster in the biodiversity community such as standardization, depository, management, and analysis of DNA barcode data. The system can be downloaded upon request, and an exemplary server has been constructed with which to build an Asian biodiversity system <url>http://www.asianbarcode.org</url>.</p

Effect of Epigallocatechin-3-Gallate on PMA-Induced MUC5B Expression in Human Airway Epithelial Cells

ObjectivesAmong the inflammatory mediators, phorbol 12-myristate 13-acetate (PMA) is associated with the regulation of MUC5B expression in the airway epithelial cells. Epigallocatechin-3-gallate (EGCG) is the major component of green tea extract. The biological activity of EGCG includes reduction of cholesterol and antioxidant activity, as well as anti-inflammatory effect. However, the precise action mechanism of anti-inflammatory effect of EGCG in the airway epithelial cells has not been fully defined. This study investigates the effect and the brief signaling pathway of EGCG on PMA-induced MUC5B expression in the airway epithelial cells.MethodsIn NCI-H292 airway epithelial cells, the effect and signaling pathway of EGCG on MUC5B expression were investigated using real-time polymerase chain reaction analysis, enzyme immunoassay, immunohistochemical analysis, gelatin zymography assay, and immunoblot analysis.ResultsIn NCI-H292 airway epithelial cells, PMA induced MUC5B expression, phosphorylation of p38 mitogen-activated protein kinase (MAPK), and matrix metalloproteinase-9 (MMP-9) expression and protein activity. EGCG significantly decreased PMA-induced MUC5B expression, phosphorylation of p38 MAPK, and MMP-9 expression and protein activity. SB203580 (p38 MAPK inhibitor) significantly decreased PMA-induced MMP-9 expression. In addition, SB203580 and MMP-9 I (MMP-9 inhibitor) significantly decreased PMA-induced MUC5B expression.ConclusionThese results suggest that EGCG down-regulates PMA-induced MUC5B expression through the p38 MAPK dependent MMP-9 signaling pathway in human airway epithelial cells

Transparent, low resistance, and flexible amorphous ZnO-doped In2O3 Anode Grown on a PES Substrate

Transparent and low resistance amorphous ZnO-doped In2O3 (IZO) anode films were grown by radio-frequency (rf) sputtering on an organic passivated polyethersulfone (PES) substrate for use in flexible organic light-emitting diodes (OLEDs). Under optimized growth conditions, a sheet resistance of 15.2 /, average transmittance above 89% in the green range, and a root mean square roughness of 0.375 nm were obtained, even for the IZO anode film grown in a pure Ar ambient without the addition of oxygen as a reactive gas. All of the IZO anode films had an amorphous structure regardless of the rf power and the working pressure due to the low substrate temperature of 50°C and the structural stability of the amorphous IZO films. In addition, an X-ray photoelectron spectroscopy depth profile obtained for the IZO/PES showed no obvious evidence of interfacial reactions between the IZO anode and the PES substrate, except for some indiffusion of oxygen atoms from the IZO anode. Furthermore, the current-voltage-luminance of the flexible OLEDs fabricated on IZO anode was found to be critically dependent on the sheet resistance of the IZO anode.This work was supported by a Korea Research Foundation grant funded by the Korean Government (MOEHRD: Basic Research Promotion Fund)(KRF-2006-003-D00243) and the Ministry of Commerce, Industry and Energy

Identification of Factors that Influence Conscious Sedation in Gastrointestinal Endoscopy

Although several studies examined factors that influence conscious sedation, investigation was limited into the gender and age. The aim of this prospective study is to identify the clinical variables of successful conscious sedation during gastrointestinal endoscopy. A total of 300 subjects who underwent gastrointestinal endoscopy were enrolled in a prospective fashion. They completed a questionnaire to assess height, weight, drinking, smoking, education level, recent medication, past medical history, previous experience of conscious sedation, preprocedural anxiety, and apprehension about the procedure. Efficacy of sedation and amnesia were evaluated by the subject and the endoscopist. Amnesic and sedative effects were proportionally related with age (p<0.0001). Preprocedural anxiety level was higher in women (p=0.0062), younger subjects (p=0.035), slender subjects (p=0.041), and in those without previous experience of conscious sedation (p=0.0034). This anxiety level was also related to increased pain (p=0.0026) and alertness (p=0.0003) during the procedure. Lower dose of midazolam is needed for sedation in older subjects. Subjects with a high level of preprocedural anxiety such as women, younger subjects, slender subjects, and those without previous experience of conscious sedation should be sedated with great caution because generally, they complain of much more severe pain and alertness during the procedure

Impact of the Metabolic Syndrome on the Clinical Outcome of Patients with Acute ST-Elevation Myocardial Infarction

We sought to determine the prevalence of metabolic syndrome (MS) in patients with acute myocardial infarction and its effect on clinical outcomes. Employing data from the Korea Acute Myocardial Infarction Registry, a total of 1,990 patients suffered from acute ST-elevation myocardial infarction (STEMI) between November 2005 and December 2006 were categorized according to the National Cholesterol Education Program-Adult Treatment Panel III criteria of MS. Primary study outcomes included major adverse cardiac events (MACE) during one-year follow-up. Patients were grouped based on existence of MS: group I: MS (n=1,182, 777 men, 62.8±12.3 yr); group II: Non-MS (n=808, 675 men, 64.2±13.1 yr). Group I showed lower left ventricular ejection fraction (LVEF) (P=0.005). There were no differences between two groups in the coronary angiographic findings except for multivessel involvement (P=0.01). The incidence of in-hospital death was higher in group I than in group II (P=0.047), but the rates of composite MACE during one-year clinical follow-up showed no significant differences. Multivariate analysis showed that low LVEF, old age, MS, low high density lipoprotein cholesterol and multivessel involvement were associated with high in-hospital death rate. In conclusion, MS is an important predictor for in-hospital death in patients with STEMI