miTarget: microRNA target gene prediction using a support vector machine

BACKGROUND: MicroRNAs (miRNAs) are small noncoding RNAs, which play significant roles as posttranscriptional regulators. The functions of animal miRNAs are generally based on complementarity for their 5' components. Although several computational miRNA target-gene prediction methods have been proposed, they still have limitations in revealing actual target genes. RESULTS: We implemented miTarget, a support vector machine (SVM) classifier for miRNA target gene prediction. It uses a radial basis function kernel as a similarity measure for SVM features, categorized by structural, thermodynamic, and position-based features. The latter features are introduced in this study for the first time and reflect the mechanism of miRNA binding. The SVM classifier produces high performance with a biologically relevant data set obtained from the literature, compared with previous tools. We predicted significant functions for human miR-1, miR-124a, and miR-373 using Gene Ontology (GO) analysis and revealed the importance of pairing at positions 4, 5, and 6 in the 5' region of a miRNA from a feature selection experiment. We also provide a web interface for the program. CONCLUSION: miTarget is a reliable miRNA target gene prediction tool and is a successful application of an SVM classifier. Compared with previous tools, its predictions are meaningful by GO analysis and its performance can be improved given more training examples

Crystal structure of hyperthermophilic esterase EstE1 and the relationship between its dimerization and thermostability properties

<p>Abstract</p> <p>Background</p> <p>EstE1 is a hyperthermophilic esterase belonging to the hormone-sensitive lipase family and was originally isolated by functional screening of a metagenomic library constructed from a thermal environmental sample. Dimers and oligomers may have been evolutionally selected in thermophiles because intersubunit interactions can confer thermostability on the proteins. The molecular mechanisms of thermostabilization of this extremely thermostable esterase are not well understood due to the lack of structural information.</p> <p>Results</p> <p>Here we report for the first time the 2.1-Å resolution crystal structure of EstE1. The three-dimensional structure of EstE1 exhibits a classic α/β hydrolase fold with a central parallel-stranded beta sheet surrounded by alpha helices on both sides. The residues Ser154, Asp251, and His281 form the catalytic triad motif commonly found in other α/β hydrolases. EstE1 exists as a dimer that is formed by hydrophobic interactions and salt bridges. Circular dichroism spectroscopy and heat inactivation kinetic analysis of EstE1 mutants, which were generated by structure-based site-directed mutagenesis of amino acid residues participating in EstE1 dimerization, revealed that hydrophobic interactions through Val274 and Phe276 on the β8 strand of each monomer play a major role in the dimerization of EstE1. In contrast, the intermolecular salt bridges contribute less significantly to the dimerization and thermostability of EstE1.</p> <p>Conclusion</p> <p>Our results suggest that intermolecular hydrophobic interactions are essential for the hyperthermostability of EstE1. The molecular mechanism that allows EstE1 to endure high temperature will provide guideline for rational design of a thermostable esterase/lipase using the lipolytic enzymes showing structural similarity to EstE1.</p

Organosilicate Spin-on Glasses II. Effect of Physical Modification on Mechanical Properties

Porous copolymer films were synthesized from a methylsilsequioxane:1,2-bis(trimethoxysilyl)ethane (MSSQ:BTMSE) matrix and either an aromatic-core or aliphatic-core porogen at 10, 20, or 30 wt % porogen loading. Films were characterized using scanning electron microscopy (SEM), IR spectroscopy, and ellipsometry. Depth-sensing indentation experiments were performed to measure apparent film modulus, E, and hardness, H. Indentation load-displacement traces and SEM images were used to determine the threshold load for cracking, Pc. The aliphatic-core porogen produced a greater porosity film than the aromatic-core porogen for 10 wt % loading and smaller porosity films for 20 and 30 wt % loadings. IR spectra, normalized for film thickness and density, indicated decreased O-Si-O networking in porous MSSQ:BTMSE films. The combination of increased porosity and decreased O-Si-O networking led to a decreased apparent E and H relative to the unmodified MSSQ:BTMSE film. However, low-porosity (approximately 7%), aliphatic-porogen MSSQ:BTMSE films are optimized relative to unmodified MSSQ with smaller dielectric constant and greater E and H.This work is supported by the Korean Collaborative Project for Excellence in Basic System IC Technology (System IC 2010: 98- B4-C0-00-01-00-02). Financial support from the Ministry of Science and Technology (MOST) and the Korean Ministry of Education through the National Research Laboratory Fund and the Brain Korea 21 Program, respectively, is also greatly acknowledged

Round-robin test on thermal conductivity measurement of ZnO nanofluids and comparison of experimental results with theoretical bounds

Ethylene glycol (EG)-based zinc oxide (ZnO) nanofluids containing no surfactant have been manufactured by one-step pulsed wire evaporation (PWE) method. Round-robin tests on thermal conductivity measurements of three samples of EG-based ZnO nanofluids have been conducted by five participating labs, four using accurate measurement apparatuses developed in house and one using a commercial device. The results have been compared with several theoretical bounds on the effective thermal conductivity of heterogeneous systems. This study convincingly demonstrates that the large enhancements in the thermal conductivities of EG-based ZnO nanofluids tested are beyond the lower and upper bounds calculated using the models of the Maxwell and Nan et al. with and without the interfacial thermal resistance

Development of a Rating System for Digestive System Impairments: Korean Academy of Medical Sciences Guideline

A systematic and effective welfare system for people with digestive system impairments is required. In Korea, an objective and scientific rating guideline does not exist to judge the digestive system impairments. Whether the impairments exist or not and the degree of it need to be examined. Thus, with these considerations we need a scientific rating guideline for digestive system impairments to fit our cultural and social background. In 2007, a research team, for the development of rating impairment guidelines, was organized under the supervision of Korean Academy of Medical Sciences. The rating guidelines for digestive system impairments was classified into upper and lower gastrointestinal tracts impairments and liver impairment. We developed objective rating guidelines for the upper gastrointestinal tract, the impairment generated after surgery for the stomach, duodenum, esophagus, and for the lower gastrointestinal tract, the impairment generated after construction and surgery for colon, rectum, anus, and intestinal stomas. We tried to make the rating impairment guidelines to include science, objectivity, convenience, rationality, and actuality. We especially emphasized objectivity as the most important value. We worked to make it easy and convenient to use for both the subjects who received the impairment ratings and the doctors who will give the ratings

Yoga Training Improves Metabolic Parameters in Obese Boys

Yoga has been known to have stimulatory or inhibitory effects on the metabolic parameters and to be uncomplicated therapy for obesity. The purpose of the present study was to test the effect of an 8-week of yoga-asana training on body composition, lipid profile, and insulin resistance (IR) in obese adolescent boys. Twenty volunteers with body mass index (BMI) greater than the 95th percentile were randomly assigned to yoga (age 14.7±0.5 years, n=10) and control groups (age 14.6±1.0 years, n=10). The yoga group performed exercises three times per week at 40~60% of heart-rate reserve (HRR) for 8 weeks. IR was determined with the homeostasis model assessment of insulin resistance (HOMA-IR). After yoga training, body weight, BMI, fat mass (FM), and body fat % (BF %) were significantly decreased, and fat-free mass and basal metabolic rate were significantly increased than baseline values. FM and BF % were significantly improved in the yoga group compared with the control group (p\u3c0.05). Total cholesterol (TC) was significantly decreased in the yoga group (p\u3c0.01). HDL-cholesterol was decreased in both groups (p\u3c0.05). No significant changes were observed between or within groups for triglycerides, LDL-cholesterol, glucose, insulin, and HOMA-IR. Our findings show that an 8-week of yoga training improves body composition and TC levels in obese adolescent boys, suggesting that yoga training may be effective in controlling some metabolic syndrome factors in obese adolescent boys

Serosurveillance for Japanese encephalitis, Akabane, and Aino viruses for Thoroughbred horses in Korea

Recent global warming trends may have a significant impact on vector-borne viral diseases, possibly affecting vector population dynamics and disease transmission. This study measured levels of hemagglutination-inhibition (HI) antibodies against Japanese encephalitis virus (JEV) and neutralizing antibodies against Akabane virus (AKAV) and Aino virus (AINV) for Thoroughbred horses in Korea. Blood samples were collected from 989 racehorses in several provinces, between October 2005 and March 2007. Sera were tested using either an HI assay or a virus neutralization test. Approximately half (49.7%; 492/989) of the horses tested were antibody-positive for JEV. The HI titer against JEV was significantly correlated with racehorse age (p < 0.05). Horses with an HI antibody titer of 1:160 or higher accounted for 3.9% of the animals tested, indicating that vectors transmitting arthropod-borne viruses bit relatively few horses. In contrast, 3.8% (19/497) and 19.5% (97/497) of horse sera collected in March 2007 were positive against AKAV and AINV, respectively. The presence of antibodies against AKAV and AINV may indicate the multiplication of AKAV and AINV in these horses