• Interdisciplinary Bio Central
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• 제5권1호
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• pp.1.1-1.8
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• 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
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• 제28권4호
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• pp.271-277
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• 1985

소량의 시료로서 미토콘드리아 및 SMP호흡의 속도론적 연구에 이용할 수 있는 적하수은전극 polarograph를 제작하여 그 성능, 실험조건 및 응용성을 검토하였다. 산소의 제 2단계환원이 일어나는 전위 (약 -1.2 vs SCE)는 막에 결합된 환원성물질의 환원전류로 해석되는 상당한 크기의 잔존전류를 일으키기 때문에 부적절한 것으로 판단되었다. 그러나 산소의 제 1단계환원이 일어나는 -0.4V(vs SCE)하에서는 잔존전류가 관찰되지 않았으며 산소농도의 변화는 정량적으로 추적되었다. 호흡기질의 농도를 충분히 크게 유지하는한 호흡에 의한 용존산소 소모는 O차반응의 처리가 가능하였으며, 그속도 상수와 미토콘드리아 호흡활성간에는 비례관계가 성립되었다. 내냉성이 서로 다른 몇가지 식물조직으로부터 분리한 미토콘드리아의 호흡활성에 미치는 온도효과를 조사하고 호흡활성전이온도를 측정하므로서 제작한 장치의 효용성을 확인하였다.

• 미생물학회지
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• 제41권4호
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• pp.287-292
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• 2005

대청호에서 수화 발생이 빈번한 추소리 수역에서 2005년 3월 15일에 채취한 시료를 대상으로 유전자 분식에 의한 cyanobacteria의 다양성을 조사하였다. rpcBA-Intergenic Spacer (IGS)는 cyanobacteria에 특징적 색소인 phycocyanin을 합성하는 유전자와 유전자 사이의 부분으로, 환경시료에서 cyanobacteria의 다양성을 조사하기에 매우 유용한 기능 유전자이다. cpcBA-IGS를 이용하여 restriction fragment length polymorphism (RELP)으로 cyanobacteria의 다양성을 분석한 결과 Phomidium 속은 58 clones, Anabaena 속은 14 clones, Microcyxtis 속은 4 clones, Spirulina 속은 1 clone 그리고 uncultured cyanobacteria 2 clones가 존재하였다. 전반적으로 Phormidium 속이 우점하였으며, 여름철에 수화를 일으키는 Anabaena 속과 Microcystis 속도 많이 분포하였다. 따라서 cyanobacteria는 cpcBA-IGS와 같은 기능 유전자에 의한 종 동정 및 군집분석이 가능함을 보였다.

• 생물정신의학
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• 제29권2호
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• pp.33-39
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• 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
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• 제22권9호
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• pp.1193-1201
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• 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 ($2.4{\times}10^6copies/{\mu}l$).

• 대한의용생체공학회:의공학회지
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• 제39권6호
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• pp.250-255
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• 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.

• 한국미생물·생명공학회지
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• 제44권4호
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• pp.512-521
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• 2016

제주도에서 채집된 토양시료로부터 xylanase 활성을 나타내는 균주를 분리하여 WJ-2로 명명하였다. 균주 WJ-2의 16S rRNA 유전자 염기서열을 결정하여 이를 토대로 상동성을 검색한 결과, Streptomyces 속의 균주들과 높은 염기서열 상동성을 보였다. 16S rRNA 유전자 염기서열을 토대로하는 neighbor-joining 계통수를 제작하여 Streptomyces atrovirens와 가장 높은 계통발생적 연관성이 갖고 있는 것을 밝혔다. 또한 DNA-DNA hybridization 분석을 통하여 Streptomyces atrovirens의 신규한 아종임을 증명하였다. 균주 WJ-의 게놈내 GC 농도는 73.98 mol%이었으며, 주요 세포벽 지방산으로 anteiso-$C_{15:0}$ (36.19%)을 함유하고 있었다. 균주 WJ-2의 성장 및 xylanase 생산은 배지내에 질소원으로 soytone과 탄소원으로 xylan을 첨가하였을 때 급격히 증가되는 것을 확인하였다. 액체배양액으로부터 준비된 조효소의 xylanase 활성은 pH 7.0과 $55^{\circ}C$에서 가장 높게 나타났다. Thin layer chromatography (TLC) 분석을 통하여 균주 WJ-2의 조효소는 xylan을 분해하여 최종분해산물로서 xylobiose와 xylotriose 생산하는 효소임을 확인하였다.

• 한국환경과학회지
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• 제21권8호
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• pp.989-996
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• 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
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• 제29권3호
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• pp.205-216
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• 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.

• 분석과학
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• 제18권1호
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• pp.23-26
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• 2005

셀렌은 항산화 작용을 하는 미량 원소로 잘 알려져 있으며 많은 고객들은 다양한 식품시료중의 셀렌의 농도 및 정량에 관심을 갖고 있다. 본 연구에서는 $^{75}Se$과 $^{77m}Se$ 핵종을 이용한 중성자 방사화 분석법에 의한 생물시료중의 셀렌 분석법을 확립하고 비교하고자 하였다. 이를 위하여 미국표준연구원의 3종의 인증 표준물질을 선택하여 미리 설정된 분석조건 (조사, 냉각 및 측정시간) 하에서 셀렌의 농도를 결정하였다. 두 가지 분석방법에 의한 측정값을 인증값과 평가하였으며 $^{75}Se$과 $^{77m}Se$의 측정값에 대한 검출한계와 불확도를 서로 비교 하였다.