• Interdisciplinary Bio Central
• /
• v.5 no.1
• /
• pp.1.1-1.8
• /
• 2013

High quality publicly-available transcriptomic data representing relationships in gene expression across a diverse set of biological conditions is used as a context network to explore transcriptomics of the CNS. The context network, 18367Hu-matrix, contains pairwise Pearson correlations for 22,215 human genes across18,637 human tissue samples1. To do this, we compute a network derived from biological samples from CNS cells and tissues, calculate clusters of co-expressed genes from this network, and compare the significance of these to clusters derived from the larger 18367Hu-matrix network. Sorting and visualization uses the publicly available software, MetaOmGraph (http://www.metnetdb.org/MetNet_MetaOm-Graph.htm). This identifies genes that characterize particular disease conditions. Specifically, differences in gene expression within and between two designations of glial cancer, astrocytoma and glioblastoma, are evaluated in the context of the broader network. Such gene groups, which we term outlier-networks, tease out abnormally expressed genes and the samples in which this expression occurs. This approach distinguishes 48 subnetworks of outlier genes associated with astrocytoma and glioblastoma. As a case study, we investigate the relationships among the genes of a small astrocytoma-only subnetwork. This astrocytoma-only subnetwork consists of SVEP1, IGF1, CHRNA3, and SPAG6. All of these genes are highly coexpressed in a single sample of anaplastic astrocytoma tumor (grade III) and a sample of juvenile pilocytic astrocytoma. Three of these genes are also associated with nicotine. This data lead us to formulate a testable hypothesis that this astrocytoma outlier-network provides a link between some gliomas/astrocytomas and nicotine.

• Applied Biological Chemistry
• /
• v.28 no.4
• /
• pp.271-277
• /
• 1985

A polarograph with specially designed cell compartment usable in kinetic study of the mitochondrial respiration of a small sized sample was made, and its performance and experimental conditions were examined. An applied potential (ca-1.2V vs. SCE) which gives rise to the second step reduction of oxygen caused a considerable level of a residual current independent of oxygen, which is temporarily interpreted as the reduction current of the membrane-bound redox material(s) of mitochondria. A potential corresponding to the first slop reduction of oxygen (ca-0.4V vs SCE) did not produce the residual current. Thus, it is suggested that a measurement of oxygen concentration in a sample of mitochondria and submitochondrial particles by using dropping mercury electrode should be done with an applied potential of about -0.4V vs SCE. Consumption of oxygen by mitochondria was observed to follow practically zero order kinetics. Its rate constant exhibited the proportional relationship with the respiratory activity of mitochondria. Usefulness of tile instrument was properly demonstrated in the work on the temperature effect on the respiration of mitochondria isolated from several plant 4issues which were selected on the basis of chilling susceptivity.

• Korean Journal of Microbiology
• /
• v.41 no.4
• /
• pp.287-292
• /
• 2005

The cyanobacterial diversity was analyzed by restriction fragment length polymorphism (RFLP) of PCR-amplified rpcBA-Intergenic Spacer (IGS) genes and cpcBA-IGS gene sequencing with a sample collected at Chuso-ri in Daechung Reservoir on March 15, 2005, The Shannon-Weiner diversity index was 0.65, indicating that the cyanobacterial community structure was simple. PCR-RFLP profiles obtained were Phormidium spp. (58 clones), Anabaena spp. (14 clones), Microcystis spp. (4 clones), Spirulina sp. (1 clone) and uncultured cyanobacteria (2 clones). The PCR-RFLP of cpcBA-IGS revealed that Phormidium spp. and Anabaena spp. dominated in the invested sample. As a consequence, it seems that the analysis of functional genes such as cpcBA-IGS can be used for the species identification and community analysis of cyanobacteria.

• Korean Journal of Biological Psychiatry
• /
• v.29 no.2
• /
• pp.33-39
• /
• 2022

Objectives The early growth response 3 (EGR3) gene located in chromosome 8p21.3 is one of the susceptibility loci in many psychiatric disorders. EGR3 gene plays critical roles in signal transduction in the brain, which is involved in neuronal plasticity, neuronal development, learning, memory, and circadian rhythms. Recent studies have suggested EGR3 as a potential susceptibility gene for bipolar disorder (BPD). However, this requires further replication with an independent sample set. Methods To investigate the genetic role of EGR3 in Korean patients, we genotyped six single-nucleotide polymorphisms (SNPs) in the chromosome region of EGR3 in 1076 Korean BPD patients and 773 healthy control subjects. Results Among the six examined SNPs of EGR3 (rs17088531, rs1996147, rs3750192, rs35201266, rs7009708, rs1008949), SNP rs35201266, rs7009708, rs1008949 showed a significant association with BPD (p = 0.0041 for rs35201266 and BPD2, p = 0.0074 for rs1008949 and BPD, p = 0.0052 for rs1008949 and BPD1), which withstand multiple testing correction. In addition, the 'G-C-C-C' and 'G-C-G-C' haplotypes of EGR3 were overrepresented in the patients with BPD (p = 0.0055, < 0.0001, respectively) and the 'G-T-G-C' haplotype of EGR3 was underrepresented in patients with BPD (p = 0.0040). Conclusions In summary, our study supports the association of EGR3 with BPD in Korean population sample, and EGR3 could be suggested as a compelling susceptibility gene in BPD.

• Journal of Microbiology and Biotechnology
• /
• v.22 no.9
• /
• pp.1193-1201
• /
• 2012

The analysis and quantification of ammonia-oxidizing bacteria (AOB) is crucial, as they initiate the biological removal of ammonia-nitrogen from sewage. Previous methods for analyzing the microbial community structure, which involve the plating of samples or culture media over agar plates, have been inadequate because many microorganisms found in a sewage plant are unculturable. In this study, to exclusively detect AOB, the analysis was carried out via denaturing gradient gel electrophoresis using a primer specific to the amoA gene, which is one of the functional genes known as ammonia monooxygenase. An AOB consortium (S1 sample) that could oxidize an unprecedented 100% of ammonia in 24 h was obtained from sewage sludge. In addition, real-time PCR was used to quantify the AOB. Results of the microbial community analysis in terms of carbon utilization ability of samples showed that the aeration tank water sample (S2), influent water sample (S3), and effluent water sample (S4) used all the 31 substrates considered, whereas the AOB consortium (S1) used only Tween 80, D-galacturonic acid, itaconic acid, D-malic acid, and $_L$-serine after 192 h. The largest concentration of AOB was detected in S1 ($7.6{\times}10^6copies/{\mu}l$), followed by S2 ($3.2{\times}10^6copies/{\mu}l$), S4 ($2.8{\times}10^6copies/{\mu}l$), and S3 ($2.4{\times}10^6copies/{\mu}l$).

• Journal of Biomedical Engineering Research
• /
• v.39 no.6
• /
• pp.250-255
• /
• 2018

Accurate blood typing is the crucial factor for safe and successful blood transfusion and plays a very important role in organ transplantation and genetic information of forensic medicine. Microfluidic devices have been developed to overcome the limitations of the conventional blood typing methods. In this study, we demonstrate a Lamb wave-based device for simple blood typing in a sample droplet and we propose new indices for quantitative and accurate blood typing. Using Lamb wave-induced acoustic streaming in the droplet, the blood sample and the reagent can be mixed rapidly and red blood cells start to form clumps, which is agglutination. Based on the recorded image and video, the intensity of transmitted light through the sample droplet is evaluated to determine the blood type. Effect of the concentration of suspended red blood cells was evaluated and we found that 10% concentration of suspended red blood cells was suitable to observe the difference between aggregated and non-aggregated samples. Finally, sample with blood type A could be determined using anti-A reagent in our Lamb wave-based device. Our device enables simple and accurate blood typing, which can be applied to resource-limited environments.

• Microbiology and Biotechnology Letters
• /
• v.44 no.4
• /
• pp.512-521
• /
• 2016

A bacterial strain was isolated from a soil sample collected on Jeju Island, Korea. The strain, designated WJ-2, exhibited a high xylanase activity, whereas cellulase activity was not detected. The 16S rRNA gene sequence of WJ-2 was highly similar to type strains of the genus Streptomyces. A neighbor-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain WJ-2 is phylogenetically related to Streptomyces atrovirens. Furthermore, DNA-DNA hybridization analysis confirmed that strain WJ-2 is a novel subspecies of Streptomyces atrovirens. The genomic DNA G+C content was 73.98 mol% and the major fatty acid present was anteiso-C15:0 (36.19%). The growth and xylanase production of strain WJ-2 were significantly enhanced by using soytone and xylan as nitrogen and carbon sources, respectively. Crude enzyme preparations from the culture broth of strain WJ-2 exhibited maximal total xylanase activities at pH 7.0 and $55^{\circ}C$. Thin-layer chromatography analysis revealed that the crude enzyme degrades beechwood xylan to yield xylobiose and xylotriose as the principal hydrolyzed end products.

• Journal of Environmental Science International
• /
• v.21 no.8
• /
• pp.989-996
• /
• 2012

Nitrate contamination of water environments can create serious problems such as eutrophication of rivers. Conventional biological processes for nitrate removal by heterotrophic denitrification often need additional organic substrates as carbon sources and electron donors. We tried to accelerate biological denitrification by using bioelectrochemical reactor (BER) in which electrode works as an electron donor. Denitrification activity of 8 environmental samples from various sediments, soils, groundwaters, and sludges were tested to establish an efficient enrichment culture for BER. The established enrichment culture from a soil sample showed stable denitrification activity without any nitrite accumulation. Microbial community analysis by using PCR-DGGE method revealed that dominant denitrifiers in the enrichment culture were Pantoea sp., Cronobacter sakazakii, and Castellaniella defragrans. Denitrification rate ($0.08kg/m^3{\cdot}day$) of the enrichment culture in BER with electrode poised at -0.5 V (vs Ag/AgCl) was higher than that ($2.1{\times}10^{-2}kg/m^3{\cdot}day$) of BER without any poised potential. This results suggested that biological denitrification would be improved by supplying potential throughout electrode in BER. Further research using BER without any organic substrate addition is needed to apply this system for bioremediation of water and wastewater contaminated by nitrate.

• Ocean and Polar Research
• /
• v.29 no.3
• /
• pp.205-216
• /
• 2007

The purpose of this study was to investigate effects of large scale marine sand mining on the marine ecological community. For the study, four stations along the coast were selected and monitored in 1998 and 2001 at mining areas and non-mining areas about the Gyeonggi Bay. The result revealed that in 1998, 9 species of fishes, 16 species of crustaceans, and 6 species of mollusks were collected where as in 2001, 11 species of fishes, 5 species of crustaceans, and 2 species of mollusks were collected, uncovering the fact that fishes have diversified while crustaceans and mollusks have reduced on a grand scale. Also, there were two key characteristics regarding the changes of biological communities in mining and nonmining areas. The first was the dwindling of crustaceans inhabiting the sand area. This outcome may be accounted for by the facts that physical removal of seabed sediments and re-sediment due to expansion of floating particles cause direct influence on the ocean floor ecosystem and have continuous effect on the communities of crustaceans which feed on them. Secondly, the newly arrived species and their population during spring and summer seasons have increased in the non-mining areas and have decreased in the mining area. It can be concluded that highly nomadic fish species migrate toward areas with less disturbance or destruction of ecosystem from marine sand mining, and consequently, the communities of fishes change in the sea area. Setting aside the characteristics of the investigated sea areas where the arriving conditions of species vary by seasons, the clear differences of population of organisms in those areas are due to environmental alterations owing to the marine sand mining ; if those large-scale marine sand mining activities continue in the Gyeonggi Bay, their effects on biological communities in the areas will only grow.

• Analytical Science and Technology
• /
• v.18 no.1
• /
• pp.23-26
• /
• 2005

Se is well known as an anti-oxidant trace element and many customers are interested in an analysis and contents of Se in the various foodstuff samples. This study was aimed at establishig and comparing an analytical method for the determination of the Se in biological samples by neutron activation analysis using two nuclides, $^{75}Se$ and $^{77m}Se$. Keeping this objective, three NIST biological standard reference materials were chosen and the concentrations of the Se were determined under the prefixed analytical conditions such as the irradiation, decay and measurement time. The measured values by both analytical methods were evaluated with certified values. In addition, the detection limits and measurement uncertainty for the analytical results using $^{75}Se$ and $^{77m}Se$ were compared with each other.