• Genomics & Informatics
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• v.16 no.2
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• pp.22-29
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• 2018

Incorporation of unique barcodes into fission yeast gene deletion collections has enabled the identification of gene functions by growth fitness analysis. For fine tuning, it is important to examine barcode sequences, because mutations arise during strain construction. Out of 8,708 barcodes (4,354 strains) covering 88.5% of all 4,919 open reading frames, 7,734 barcodes (88.8%) were validated as high-fidelity to be inserted at the correct positions by Sanger sequencing. Sequence examination of the 7,734 high-fidelity barcodes revealed that 1,039 barcodes (13.4%) deviated from the original design. In total, 1,284 mutations (mutation rate of 16.6%) exist within the 1,039 mutated barcodes, which is comparable to budding yeast (18%). When the type of mutation was considered, substitutions accounted for 845 mutations (10.9%), deletions accounted for 319 mutations (4.1%), and insertions accounted for 121 mutations (1.6%). Peculiarly, the frequency of substitutions (67.6%) was unexpectedly higher than in budding yeast (~28%) and well above the predicted error of Sanger sequencing (~2%), which might have arisen during the solid-phase oligonucleotide synthesis and PCR amplification of the barcodes during strain construction. When the mutation rate was analyzed by position within 20-mer barcodes using the 1,284 mutations from the 7,734 sequenced barcodes, there was no significant difference between up-tags and down-tags at a given position. The mutation frequency at a given position was similar at most positions, ranging from 0.4% (32/7,734) to 1.1% (82/7,734), except at position 1, which was highest (3.1%), as in budding yeast. Together, well-defined barcode sequences, combined with the next-generation sequencing platform, promise to make the fission yeast gene deletion library a powerful tool for understanding gene function.

• Journal of Life Science
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• v.18 no.11
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• pp.1507-1512
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• 2008

In spite of long research period for Salmonella typhi, little information is known about the pathogenesis mechanism of human typhoid fever caused by S. typhi due to lack of infection model in animals. A wild-type of S. typhi Ty2 strain requires cysteine to grow on minimal media. We hypothesized that this cysteine requirement may restrict colonization of S. typhi in animals during infection process. Among the S. typhi strains carrying Salmonella typhimurium genomic library, we have isolated three S. typhi transformants growing on minimal media without cysteine. Although there were three ORFs in DNA of pBP71, the STM1490 ORF complemented cysteine auxotrophy of S. typhi. Analysis of the deduced amino acid sequence of the STM1490 homolog in S. typhi revealed that there are differences in two amino acids. Plasmids containing amino acid substitutions in STM1490 supported S. typhi growth on minimal media without cysteine, indicating irrelevance of these two amino acids to STM1490 function. These results tells us that there are other factors or systems involved in cysteine requirement of S. typhi.

• The Korean Journal of Mycology
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• v.36 no.2
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• pp.189-195
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• 2008

When a homothallic ascomycete Aspergillus nidulans is exposed to visible light, cleistothecial development is inhibited. The light response of development in A. nidulans implies the existence of delicate regulation process including reception and translocation of light signaling and determination of development. Previously, mutants that could develop cleistothecia even in the presence of relatively intensive visible light were isolated and several complementation groups were identified. A gene that was able to complement the silA98 mutation, which was responsible for preferred cleistothecia development under visible light, was isolated from AMA-NotI genomic library. The silA gene retained in the 4.3 kb recovered genomic library DNA has an open reading frame (ORF) consisted of 2,388 bp nucleotides, interrupted by 3 introns and consequently encoding 795 amino acids. The putative SilA carries a ${Zn_2}{Cys_6}$ binuclear cluster motif at N terminus and shows high amino acid sequence similarity to Aro80p of Saccharomyces cerevisiae. Deletion mutants of silA showed a strong induction of sexual development under visible light, indicating that SilA is involved in the negative regulation of sexual development in response to the light.

• Bioinformatics and Biosystems
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• v.1 no.2
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• pp.99-102
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• 2006

The Basic Local Alignment Search Tool (BLAST) is one of the most established software in bioinformatics research and it compares a query sequence against the libraries of known sequences in order to investigate sequence similarity. Expressed Sequence Tags (ESTs) are single-pass sequence reads from mRNA (or cDNA) and represent the expression for a given cDNA library and the snapshot of genes expressed in a given tissue and/or at a given developmental stage. Therefore, ESTs can be very valuable information for functional genomics and bioinformatics researches. Although major bio database (DB) websites including NCBI are providing BLAST services and EST data, local DB and search system is demanding for better performance and security issue. Here we present animal EST DBs and local BLAST search system. The animal ESTs DB in NCBI Genbank were divided by animal species using the Perl script we developed. and we also built the new extended DB search systems fur the new data (Local Animal BLAST Search System: http://bioinfo.kohost.net), which was constructed on the high-capacity PC Cluster system fur the best performance. The new local DB contains 650,046 sequences for Bos taurus(cattle), 368,120 sequences for Sus scrofa (pig), 693,005 sequences for Gallus gallus (fowl), respectively.

• Korean Journal of Biological Psychiatry
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• v.6 no.2
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• pp.170-175
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• 1999

Until recently, the etiology of schizophrenia was generally attributed to abnormalities in dopaminergic neurotransmission. Specifically, an excess of dopaminergic activity in the mesolimbic system has been postulated to produce the positive symptoms, while decreased dopaminergic activity in the mesocortical system has been suggested to cause negative symptoms. Accordingly, we performed an association study of schizophrenia with TH gene. Three hundred and seventy four biologically unrelated schizophrenic patients meeting DSM-III-R criteria from Kangnam St. Mary's Hospital affiliated with Catholic university of Korea were recruited for our study. The 393 healthy controls were volunteers for DNA library of Kangnam St. Mary's Hospital without personal or family history of psychiatric and neurologic illness. DNA was extracted from peripheral mononuclear cells and polymorphic region was amplified by polymerase chain reaction. TH intron 1 VNTR polymorphism was typed by silver staining. The allele distributions of TH gene were not different between schizophrenics and controls. However, the frequency of allele A was significantly higher in positive group than that of negative group of schizophrenics. These findings suggest that poitive schizophrenia may be associated with allele A of TH gene.

• Journal of Plant Biotechnology
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• v.44 no.4
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• pp.372-378
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• 2017

For comparison of the transcription profiles in apple (Malus domestica L.) cultivars differing in flesh color expression, two cDNA libraries were constructed. Differences in gene expression between red flesh apple cultivar, 'Redfield' and white flesh apple cultivar, 'Granny Smith' were investigated by next-generation sequencing (NGS). Expressed sequence tag (EST) of clones from the red flesh apple cultivar and white flesh apple cultivar were selected for nucleotide sequence determination and homology searches. High resolution melting (HRM) technique measures temperature induced strand separation of short PCR amplicons, and is able to detect variation as small as one base difference between red flesh apple cultivars and white flesh apple cultivars. We applied high resolution melting (HRM) analysis to discover single nucleotide polymorphisms (SNP) based on the predicted SNP information derived from the apple EST database. All 103 pairs of SNPs were discriminated, and the HRM profiles of amplicons were established. Putative SNPs were screened from the apple EST contigs by HRM analysis displayed specific difference between 10 red flesh apple cultivars and 11 white flesh apple cultivars. In this study, we report an efficient method to develop SNP markers from an EST database with HRM analysis in apple. These SNP markers could be useful for apple marker assisted breeding and provide a good reference for relevant research on molecular mechanisms of color variation in apple cultivars.

• Journal of Microbiology and Biotechnology
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• v.11 no.6
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• pp.994-1001
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• 2001

An easier way of understanding the BNR system was proposed from the study on substrate, nutrient removal tendency, microbial community and its metabolic function by applying the municipal settled sewage. During the anaerobic period, the phosphorus release rate per VFACOD we varied depending on the phosphorus content in the sludge. When the phosphorus content in the sludge was $6\%$ VSS, according to influent VFACOD, the phosphorus release rate and PHA production were $0.35 gPO_4P/gVFACOD$ and 1.0 gPHA/gVFACOD, respectively. The $NO_3N$ requirement for the phosphorus uptake as an electron acceptor was about $0.5 gNO_3N/gPO_4P_{uptake}$ based on the proposed equation with PHA, biomass, production, and the concentration of phosphorus release/uptake. Bacterial-community analysis of the sludge, as determined by FISH and 16SrDNA characterization FISH, revealed that the beta-subclass proteobacteria were the most abundant group ($27.9\%$ of the proteobacteria-specific probe EUB338), and it was likely that representative of the beta-subclass played key roles in activated sludge. The next dominant group found was the gamma-protebacteria ($15.4\%$ of probe EUB338). 16S rDNA clone library analysis showed that the members of${\beta}$- and ${\gamma}$-proteobacteria were also the most abundant groups, and $21.5\%$ (PN2 and PN4) and $15.4\%$ (PN1 and PN5) of total clones were the genera of denitrifying bacteria and PAO, respectively. Prediction of the microbial community composition was made with phosphorus content (Pv, $\%$ P/VSS) in wasted sludge and profiles of COD, PHA, $PO_4P,\;and\;NO_3N$ in an anaerobic-anoxic SBR unit. Generally, the predicted microbial composition based upon metabolic function, i.e., as measured by stoichiometry, is fairly similar to that measure by the unculturable dependent method. In this study, a proposal was made on he microbial community composition that was more easily approached to analyze the reactor behavior.

• Proceedings of the KSAR Conference
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• 2001.03a
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• pp.58-58
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• 2001

본 연구는 섬유소 분해효소 유전자 Cel D(Cellulase Digestion)가 도입된 형질전환 돼지 생산을 통하여 섬유소 함유 사료의 이용 효율을 증대시키고, 나아가 장기이식동물 및 고가의 의료용 단백질 생산가축을 개발하기 위한 원천기술 확보에 있다. 섬유소분해 유전자의 크로닝 및 조직 특이적 발현벡터를 개발하기 위하여, 우선 소의 위중 제4위 내의 미생물로부터 전체 유전자를 분리하였고, 이렇게 작성된 DNA library에서 섬유소분해 관련 유전자인 약 2.0 kb의 Cel D유전자를 크로닝하였으며, 췌장 특이적 발현 프로모터(rat elastase I: 약 200bp)를 크로닝한 후, 미세주입용 형질전환 재조합 벡터를 구축하기 위하여 rElastase I 프로모터 하류에 섬유소 분해 유전자(Cel D)를 연결하여 약 3.0 kb 크기의 재조합 벡터를 준비하였으며, 재조합 유전자를 1세포기 수정란 전핵내에 미세주입 하기 위해 Sal I과 BglII를 이용 유전자 단편을 만들었다. 구축된 유전자를 미세주입하기 위한 수정란을 회수하기위해 총68두의 돼지를 4-5두씩 분리사육하면서 발정동기화 및 과배란 유기를 위해 PG600, Altrenogest, FSH, hCG를 투여하였으며 hCG투여후 약54시간에 외과적 방법에 의해 총 1,359개의 수정란을 회수하였고, 이중 미세주입가능한 1세포기 수정란은 1,296개로 두당 평균 15.9개 였다. 1,296개의 1세포기 수정란 중에서 재조합 유전자(rE I-CelD)가 미세주입된 660개의 수정란을 32두의 수란돈에 외과적 방법에 의해 이식하였으며, 이식되어진 모돈 13두가 분만하여 40.6%의 임신율을 나타내었다. 이렇게 분만된 13두에서 총 65두(암:33두, 수:32두)의 자돈이 생산되었으며, 형질전환 여부를 판명하기 위해 자돈의 꼬리조직으로 부터 genomic DNA를 추출하고 PCR 검정을 실시하였다. PCR 검정 결과, 섬유소 분해 유전자가 도입된 자돈은 5두 이었으며, 그 결과를 Table에 나타내었다.(Table Omitted) Table 1 에서와 같이 섬유소 분해효소유전자가 형질전환된 자돈은 65마리 중 5마리로 7.69%의 형질전환율을 나타내었으며, 5마리의 자돈중 2두(암:1두, 수:1두)는 분만 후 즉시 폐사되었으며 2두(암:1두, 수:1두)는 86일령 그리고 14일령에 폐사하여 현재 1두(암)가 생존하여 섬유소 분해 사양 실험 중에 있다.

• Journal of Animal Science and Technology
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• v.45 no.2
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• pp.169-182
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• 2003

To understand the structure and regulation of bovine ADRP (Adipocyte Differentiation Related Protein) gene, we have isolated the genomic clone of bovine ADRP and determined its sequence. A genomic Southern blot analysis confirmed that ADRP gene is present as a single copy in bovine genome and the ADRP gene spans 12 kb. Bovine ADRP genomic clone, HwADRPg-1, had 8 exons and 7 introns, and all splicing sites conformed to the GT/AG rule with the exon-intron boundaries located exactly. Analysis of the upstream 649 bp of the sequence of HwADRPg-1 showed that it does not contain any canonical TATAA boxes; however Sp1 binding sites and CAAT boxes are found. The promoter contained potential binding sites for AP-1, AP-2 and several putative transcription factor binding sites. The 5'-flanking region of HwADRPg-1 contained muscle specific transcription activator Myo G and C/EBP (CCAAT/ enhancer binding protein) recognizing site. These results suppose that the Myo G transcription activator regulate the transcription of bovine ADRP gene in muscular tissue and its transcriptional activity was triggered by degree of muscular development. Our results provide the necessary analysis for other flanking sequences are needed in addition to the proximal cis elements of this promoter to confer adipocyte differentiation-dependent or growth-dependent transcriptional control.

• Clinical and Experimental Reproductive Medicine
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• v.33 no.4
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• pp.253-263
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• 2006

Objective: Identification of the regulatory mechanism for arrest and initiation of primordial follicular growth is crucial for female fertility. Previously, we found 15 expressed sequence tags (ESTs) that were specifically abundant in the day-S-subtracted cDNA library and that the B357 clone was novel. The present study was conducted to obtain the whole sequence of the novel gene including B357 and to characterize its mRNA and protein expression in mouse ovary and testis. Methods: The extended sequence of the 2,965-bp cDNA fragment for the clone B357 was named ${\underline{5}}-{\underline{d}}ay-{\underline{o}}vary-{\underline{s}}pecific\;gene-{\underline{1}}$ (5DOS1) and submitted to GenBank (accession number ${\underline{AY751521}}$). Expression of 5DOS1 was characterized in both female and male gonads at various developmental stages by Northern blotting, real-time RT-PCR, in situ hybridization, Western blotting, and immunohistochemistry. Results: The 5DOS1 transcript was highly expressed in the adult testis, brain, and muscle as compared to the other tissues. In the ovary, the 5DOS1 transcript was detected in all oocytes from primordial to antral follicles, and highly expressed at day 5 after birth and decreased thereafter. In contrast, expression of 5DOS1 showed a gradual increase during testicular development and its expression was limited to various stages of male germ cells except spermatogonia. Conclusions: This is the first report on the expression and characterization of the 5DOS1 gene in the mouse gonads. Further functional analysis of the 5DOS1 protein will be required to predict its role in gametogenesis.