• 대한환경공학회지
• /
• 제28권10호
• /
• pp.1055-1064
• /
• 2006

본 연구소에서는 혐기성 입상슬러지를 충진한 UASB 반응기와 탄소섬유를 충진한 배양기를 조합하여 아주 느린 성장특성을 가진 혐기성 암모늄 산화균의 배양을 시도하였다. 연속배양 180일 이후, 유입질소부하가 0.6 kg $N/m^3-d$였을 때, 평균 질소전환율은 0.54 kg $N/m^3-d$로 나타났다. 검은 혐기성 입상슬러지는 연속배양시간이 지남에 따라 갈색과 붉은 색으로 변화되었으며, anammox 반응기는 붉은색 입상슬러지가 많을수록 높은 활성도를 나타내었다. 따라서, 붉은색 입상슬러지를 채취하여 분자생물학적 방법을 이용하여 미생물 군집구조를 분석하였다. 클로닝 및 계통분류학적 분지도 작성 결과, anammox UASB 반응조의 붉은색 입상슬러지에서 발견된 미생물 종류는 anammox 미생물과 더불어 문단위의 4가지 다른 미생물, Proteobacteria, Acidobacteria, Chlorobi와 Chloroflexi로 나타났다. Anammox UASB 반응조내의 붉은색 입상슬러지에서는 clone의 개수를 기준으로 anammox 미생물이 약 25%가 존재하였고 $\beta$-proteobacteria가 우점하고 있는 양상을 보여주었으며, 본 연구의 클로닝 정보와 AMX368 FISH 탐침자를 이용해 in silico 실험을 수행한 결과 AMX368과 정확히 들어맞는 anammox 미생물 clone 하나와 하나의 염기서열이 변이를 일으킨 11개의 anammox 미생물 clone을 확인할 수 있었다. 사상균 형태의 Chloroflexi는 혐기조건 입상 슬러지의 형성과 관련이 있는 것으로 판단되었다. FISH 수행결과, anammox 미생물은 붉은색 입상 슬러지에 우점하고 있는 것으로 나타났다.

• International Journal of Industrial Entomology and Biomaterials
• /
• 제15권2호
• /
• pp.115-122
• /
• 2007

As the genome of B.mori is available in GenBank and the EST database of B.mori is expanding, identification of novel genes of B.mori is conceivable by data-mining techniques. We used the in silico cloning method to get the vacuolar-type $H^+-ATP$ synthetase (V-ATPase) c subunit (16 kDa proteolipid subunit) gene of B.mori and analysed with bioinformatics tools. The result was confirmed by RT-PCR and sequencing. The V-ATPase c subunit cDNA contains a 468 bp ORF. The ORF encoded a 155-residue protein that showed extensive homology with V-ATPase c subunits from other 15 species and contained four membrane-spanning helices. Tissue expression pattern analysis revealed that V-ATPase c expressed strongly in Malpighian tubules, not in fat body. This gene has been registered in GenBank under the accession number EU082222.

• International Journal of Industrial Entomology and Biomaterials
• /
• 제14권2호
• /
• pp.69-74
• /
• 2007

As the genome of B. mori is available in GenBank and the EST database of B. mori is expanding, identification of novel genes of B. mori was conceivable by datamining techniques and bioinformatics tools. In this study, we used the in silico cloning method to get the 6-Phosphogluconolactonase (6PGL) gene of B. mori and analysed with bioinformatics tools. The result was confirmed by RT-PCR and prokaryotic expression. The 6PGL cDNA comtains a 702 bp ORF. The deduced protein has 233 amino acid residues, with the predicted molecular weight of 25946. 72 Da, isoelectric point of 5.41, and contains conserved NagB domains. This gene has been registered in GenBank under the accession number EF198104.

• Asian-Australasian Journal of Animal Sciences
• /
• 제20권10호
• /
• pp.1473-1477
• /
• 2007

Four-and-a-half LIM-only protein 3 (FHL3) is a member of the LIM protein superfamily and can participate in mediating protein-protein interaction by binding one another through their LIM domains. In this study, the 5'- and 3'- cDNA ends were characterized by RACE (Rapid Amplification of the cDNA Ends) methodology in combination with in silico cloning based on the partial cDNA sequence obtained. Bioinformatics analysis showed FHL3 protein contained four LIM domains and four LIM zinc-binding domains. In silico mapping assigned this gene to the gene cluster MTF1-INPP5B-SF3A3-FHL3-CGI-94 on pig chromosome 6 where several QTL affecting intramuscular fat and eye muscle area had previously been identified. Transcription of the FHL3 gene was detected in spleen, liver, kidney, small intestine, skeletal muscle, fat and stomach, with the greatest expression in skeletal muscle. The A/G polymorphism in exon II was significantly associated with birth weight, average daily gain before weaning, drip loss rate, water holding capacity and intramuscular fat in a Landrace-derived pig population. Together, the present study provided the useful information for further studies to determine the roles of FHL3 gene in the regulation of skeletal muscle cell growth and differentiation in pigs.

• International Journal of Oral Biology
• /
• 제42권2호
• /
• pp.63-70
• /
• 2017

Selecting an appropriate antigen with optimal immunogenicity and physicochemical properties is a pivotal factor to develop a protein based subunit vaccine. Despite rapid progress in modern molecular cloning and recombinant protein technology, there remains a huge challenge for purifying and using protein antigens rich in hydrophobic domains, such as membrane associated proteins. To overcome current limitations using hydrophobic proteins as vaccine antigens, we adopted in silico analyses which included bioinformatic prediction and sequence-based protein 3D structure modeling, to develop a novel periodontitis subunit vaccine against the outer membrane protein FomA of Fusobacterium nucleatum. To generate an optimal antigen candidate, we predicted hydrophilicity and B cell epitope parameter by querying to web-based databases, and designed a truncated FomA (tFomA) candidate with better solubility and preserved B cell epitopes. The truncated recombinant protein was engineered to expose epitopes on the surface through simulating amino acid sequence-based 3D folding in aqueous environment. The recombinant tFomA was further expressed and purified, and its immunological properties were evaluated. In the mice intranasal vaccination study, tFomA significantly induced antigen-specific IgG and sIgA responses in both systemic and oral-mucosal compartments, respectively. Our results testify that intelligent in silico designing of antigens provide amenable vaccine epitopes from hard-to-manufacture hydrophobic domain rich microbial antigens.

• 대한의생명과학회지
• /
• 제14권1호
• /
• pp.47-53
• /
• 2008

Hox genes are known to be transcription factors controlling vertebrate pattern formation along the anteroposterior body axis by regulating many target gene expressions during vertebrate embryogenesis. In order to isolate in vivo Hox responsive target genes, ChIP-cloning technique has been applied using Hoxc8 antibody. Here murine embryo of day 11.5 post coitum (E11.5) highly expressing Hoxc8 gene was used after removing head and tail portions where Hoxc8 is rarely expressing. After fixation with formaldehyde, the chromatin DNAs harboring bound proteins were isolated. After sonication, about 0.5- to 1 Kb chromatin DNAs were immunoprecipitated with anti Hoxc8 antibody. After removing the bound proteins with proteinase K, DNAs were isolated, cloned into the pBluescsript II SK vector, and then sequenced. Total 33 random clones sequenced were anlalyzed to be located at 12 different genomic regions. Among these, 8 turned out to be introns and 4 were intergenic regions localized in random chromosomes. The base composition of total cloned genomic sequences (6608 bp) were AT-rich, i.e., 40% GC. When the Hoxc8 core binding sites, such as TAAT, ATTA, TTAT, and ATAA were analyzed total number of 55, 45, 54, and 55 were found, respectively, which are than twice as many as expected number of 26. Although this in silico analysis does not mean that the ChIP-cloned sequence is real Hoxc8 regulatory element in vivo, these results strongly imply that the DNA fragments cloned through chromatin immunoprecipitation could be very much likely the putative Hoxc8 downstream target genes.

• International Journal of Industrial Entomology and Biomaterials
• /
• 제15권2호
• /
• pp.137-143
• /
• 2007

Lactate dehydrogenase (LDH) is a ubiquitous enzyme that plays a significant role in the clinical diagnosis of pathologic processes. Discovery of the LDH (BmLDH) gene in B. mori may shed light on its role in the biology of Lepidoptera species, and afford further understanding of the function of the enzyme. In this study, we used the bioinformatics tools to identify LDH gene in B. mori. Sequence analysis showed that BmLDH cDNA contains a 996 bp open reading frame, encoding 331 AA proteins, with seven introns. Compared with hHLDH (human heart LDH), BmLDH contained the same key active sites. Domain search and protein fold recognition analyses provide compelling evidences that the deduced protein is a LDH. Using the computer program MEGA3, we conducted a search for homologs of BmLDH among many eukaryotic species and confirmed that the BmLDH was conserved in all organisms investigated. This gene has been registered in GenBank under the accession number EU000385.

• 대한약학회:학술대회논문집
• /
• 대한약학회 2003년도 Proceedings of the Convention of the Pharmaceutical Society of Korea Vol.1
• /
• pp.192.2-193
• /
• 2003

Capsaicin, a pungent ingredient in chili pepper, is known to excite sensory neurons that mediate pain sensation. This effect of capsaicin is determined by unique receptors and the capsaicin receptor (transient receptor potential subfamily V, member 1 (TRPV1)) was cloned recently. TRPV1 contains six transmembrane domains and three ankyrin repeats at N-terminal. This characteristic architecture is common in other ion channel in TRPV families. (omitted)

• 한국정보처리학회:학술대회논문집
• /
• 한국정보처리학회 2001년도 추계학술발표논문집 (상)
• /
• pp.105-108
• /
• 2001

cDNA(complementary DNA)를 복제(cloneing)하여 염기 서열화 한 EST(Expressed Sequence Tag) 데이터는 여러 생물체들의 염기서열 정보들과 비교를 통해 유사점을 찾거나 기능적 부위 검색을 통해 유전자 기능을 추정한 수 있어 기능 유전체 연구에 많이 사용되고 있다. EST 데이터를 식물은 특정종(Species)별로, 동물의 경우 종의 조직별로 클러스터링 함으로써 아직 알려지지 않은 종의 유전자를 밝혀낼 수 있음은 물론 유전자의 발현에 따른 단백질의 기능도 알아낼 수 있다. 따라서 이 논문에서는 NCBI에서 flatfile 형태로 제공하는 EST 데이터를 분석하여 관계형 데이터베이스로 모델링하고 구축하였다. 또한 EST 데이터의 효율적인 사용을 위하여 데이터를 특정 종의 조직별로 클러스터링하여 제공하는 시스템을 설계하고 구현하였다.

• Asian-Australasian Journal of Animal Sciences
• /
• 제18권9호
• /
• pp.1237-1241
• /
• 2005

Mannose-P-dolichol utilization defect 1 (MPDU1) gene is required for utilization of the mannose donor MPD in synthesis of both lipid-linked oligosaccharides (LLOs) and glycosylphosphatidylinositols (GPI) which are important for functions such as protein folding and membrane anchoring. The full length cDNA of the porcine MPDU1 was determined by in silico cloning and rapid amplification of cDNA ends (RACE). The deduced amino acid showed 91% identity to the corresponding human sequence with five predicted transmembrane regions. RT-PCR was performed to detect its expression pattern in five tissues and results showed that it is expressed ubiquitously among the tissues checked. A single nucleotide substitution resulting in the amino acid change (137 Tyr-137 His) was detected within exon 5. Allele frequencies in six pig breeds showed distinctive differences between those Chinese indigenous pigs breeds and European pigs. Using the pig/rodent somatic cell hybrid panel (SCHP), we mapped the porcine MPDU1 gene to SSC12, which is consistent with the comparative mapping result as conservative syntenic groups presented between human chromosome 17 and pig chromosome 12.