• Journal of Information Processing Systems
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• v.12 no.1
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• pp.1-34
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• 2016

Gene identification is at the center of genomic studies. Although the first phase of the Encyclopedia of DNA Elements (ENCODE) project has been claimed to be complete, the annotation of the functional elements is far from being so. Computational methods in gene identification continue to play important roles in this area and other relevant issues. So far, a lot of work has been performed on this area, and a plethora of computational methods and avenues have been developed. Many review papers have summarized these methods and other related work. However, most of them focus on the methodologies from a particular aspect or perspective. Different from these existing bodies of research, this paper aims to comprehensively summarize the mainstream computational methods in gene identification and tries to provide a short but concise technical reference for future studies. Moreover, this review sheds light on the emerging trends and cutting-edge techniques that are believed to be capable of leading the research on this field in the future.

• Proceedings of the Korean Society of Developmental Biology Conference
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• 2003.10a
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• pp.94-94
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• 2003

Rotavirus는 유아나 어린아이들에게 가장 일반적으로 나타나는 심한 위장염의 원인자이며 설사로 인한 심한 탈수 증세를 일으켜 급속히 성장하는 유아의 균형적인 영양 공급을 방해함으로써 유아들의 발육과 성장 그리고 심하면 생명에 커다란 영향을 미치게 된다. 한편 모유로 키운 유아들은 설사병의 낮은 발병율과 연관이 있었다. 특히 모유의 뮤신 복합체는 rotavirus에 특이적으로 결합하여 항 바이러스활동을 보여주는 것으로 나타났다. 이러한 배경에서 본 연구는 human breast tissue로부터 lactadherin의 cloning 및 sequence 분석을 통하여 유전자의 다양성을 조사하기로 하였다. 한국 여성 9명의 유두 근처 조직에서 lactadherin을 cloning하여 그 sequence를 보고 된 서양여성의 염기서열과 비교 분석결과 여러 곳에서 single nucleotide variation이 발견되었고 본 연구에서 클론한 lactadherin(31bp-1518bp)의 염기서열과 보고된 서양여성 lactadherin gene의 SNP와 비교하였을 때 8개의 SNP중 3부분만이 일치한다는 것을 확인하였다. 또한 같은 조직중 정상 조직과 암 조직 부분에서 각각 lactadherin을 클론하여 염기서열을 비교 분석하였는데 정상 조직에서 2곳의 silent mutation있었고 암조직에서 2곳의 mutation과 1곳의 silent mutation을 발견하였으며 전체 적으로 정상조직과 암 조직 부분에서 lactadherin을 clone하여 염기서열을 분석해본 결과 암조직일수록 유전자의 변이 비율이 높다는 것을 알 수 있었다. 그리고 동일한 염기서열 상에서 많은 변이가 일어났는데 286dp(A->C), 1418dp(G->C)은 mutation이었고 327dp (A->G), 454(C->T)은 silent mutation이었다. 그 외 DNA상에서 여러 부근에 변이가 존재하였는데 이 결과로 보아 coding region에 위치한 cSNP 중 amino acid 변화를 일으켜 protein structure 또는 function에 영향을 줄 수 있는 non-synonymous cSNP 일 것으로 예상되어지며 natural selection의 영향을 받고 있음을 암시하고 있다. 본 연구에서 관찰되어진 각각의 염기 서열의 변이는 한국 사람이 가지는 lactadherin gene의 cSNP의 일부라고 판단하였다.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.127.1-127
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• 2003

We describe two new Trichoderma species associated with oyster mushroom in Korea. Trichoderma green mould has been one of the most serious diseases of oyster mushroom in Korea. Of these the predominant species are two unrecorded species. We designed as Trichoderma sp. Korean type 1 (Th K1) and Trichoderma sp. Korean type 2 (Th K2), respectively. Th K1 and Th K2 can be distinguished from previously reported Trichoderma species as well as each other in morphological characteristics including growth rate at 35$^{\circ}C$, colony morphology, conidia shape and branch pattern of phialides. Sequence of the ITS region of rDNA, the protein coding translation elongation factor gene(EF-1${\alpha}$), and RNA polymeraseII (RPB2) not only clearly separated Trichoderma sp. Korean types from their closely related T. harzianum biotype but also distinguished them from each other. Analyses of the EF-1${\alpha}$ and RPB2 sequences were found to be more useful for establishing systematic relationships among Trichoderma isolates than those of the ITS sequence. Based on the results of morphological and molecular characteristics. We propose the two Trichoderma sp. Korean types as the new species

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.76.2-77
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• 2003

The complete nucleotide sequences of genomic RNA of an isolate of soybean mosaic virus (SMV-CN18), which has ability to overcome Rsv resistance of soybean, have been determined. A large open reading frame encodes a polyprotein of 3068 amino acids with a predicted Mr of 350 kDa. Based on comparison with the proposed cleavage site of other potyviral polyproteins, nine mature proteins are predicted as a following order, P1, HC-Pro, P3, CI, 6K, VPg, NIa, NIb and coat protein (CP). The mature proteins of the strain share various amino acid identity with known SMV-G2, -G7 and -N strain, with the greatest variability occurring in the P1 (91 ％, 88 ％, 96％)and the lowest variability in the CP (100 ％, 99 ％, 100 ％). In addition, 5' untranslated region determined by 5' RACE is much more various than any coding regions. Difference in amino acid sequences throughout the genome is discussed in relation to resistance and susceptibility of soybean cultivars to SMV-CNl8.

• BMB Reports
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• v.28 no.5
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• pp.458-463
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• 1995

Two apparent rho-independent transcription terminator structures within the coding sequence of aceK have been destroyed to access their roles in the differential expression between aceA and aceK in the glyoxylate bypass operon of E. coli. The effect of mutations on the expression of aceK was evaluated in two different ways: one by maxicell labeling and the other by lacZ fusion gene construction. The maxicell labeling experiment with the mutant operon clones has failed, like that of the wild type operon clone, to visibly show isocitrate dehrogenase (IDH) kinase/phosphatase, the product of aceK, on the autoradiogram of a protein gel. When the same mutations were introduced into an aceK::lacZ fusion gene to quantitatively evaluate the mutational effect, the activity of ${\beta}-galactosidase$ in neither of the mutant versions of the fusion gene was elevated significantly enough to explain the degree of polarity observed in this region. Thus, we conclude that neither of these intragenic, apparent rho-independent transcription terminator structures, which have long been suspected as a major determinant in the down regulation of aceK, really act as a premature transcriptional terminator.

• Journal of Microbiology and Biotechnology
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• v.13 no.6
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• pp.949-954
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• 2003

The argG gene of Corynebacterium glutamicum encoding argininosuccinate synthetase (EC6345) was cloned and sequenced. The gene was cloned by heterologous complementation of an Escherichia coli arginine auxotrophic mutant (argG/sup -/). The cloned DNA fragment also complements E. coli argD, argF, and argH mutants, suggesting a clustered organization of the genes in the chromosome. The coding region of the argG gene is 1,206 nucleotides long with a deduced molecular weight of about 44 kDa, comparable with the predicted size of the expressed protein on the SDS-PAGE. Computer analysis revealed that the amino acid sequence of the argG gene product had a high similarity to that of Mycobacterium tuberculosis and Streptomyces clavuligerus. Two conserved sequence motifs within the ArgG appear to be ATP-binding sites which correspond to 2 of the 3 conserved regions found in sequences of all known argininosuccinate synthetases.

• Journal of Sericultural and Entomological Science
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• v.38 no.2
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• pp.144-149
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• 1996

To develope the baculovirus expression vector system (BEVS) using Spodoptera exigua nuclear polyhedrosis virus (SeNPV), we characterized the polyhedrin of SeNPV. The SeNPV polyhedra was irregular and composed of the major protein molecular weight of 30 kDa determined by electronmicroscopy and SDS-AGE analysis, respectively. The nucleotid suquences of 876 bases including the coding region of polyhedrin gene was determined and it was revealed that the polyhedrin gene is located within Xho I 3.0Kb and Nco I 6.0 Kb by Southern blot analysis, respectively. Also, the Xho I 3.0 Kb and the Nco I 6.0 Kb fragments were cloned and restriction enzyme map of these clones were determined.

• Korean Journal of Plant Resources
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• v.23 no.6
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• pp.535-540
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• 2010

Phenylalanine ammonia-lyase (PAL), a key enzyme of the phenylpropanoid biosynthesis pathway, is activated by a number of developmental and environmental cues. The coding region of the NtPAL4 gene was 2,154 bp in length, and its deduced protein was composed of 717 amino acids. Sequence analysis of NtPAL4 cDNA from tobacco (Nicotiana tabacum L.) revealed high structural similarity to PAL genes of other plant species. The NtPAL4 gene exists as a single copy in the tobacco plant, and its transcripts were strongly expressed in flowers and leaves. NtPAL4 expression was significantly induced in response to NaCl, mannitol, and cold treatments, but it was not induced by abscisic acid (ABA). NtPAL4 expression decreased gradually after treatment with ABA and $H_2O_2$; however, NtPAL4 transcripts accumulated after treatment with methyl viologen (MV). Our results suggest that the NtPAL4 gene may function in response to abiotic stresses.

• BMB Reports
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• v.28 no.1
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• pp.51-56
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• 1995

Thioredoxin is a small redox protein with an active-site disulfide/dithiol, and is ubiquitous in bacteria, plants, and animals. To investigate the structure-function relationship of thioredoxin, the genes encoding Escherichia coli thioredoxin and Corynebacterium nephridii thioredoxin C3 were fused via a common restriction site in the nucleotide sequence coding for the active site of the proteins to generate two chimeric thioredoxins, designated E-C3(N to C-terminal) and C3-E. The hybrid thioredoxin genes were put under the T7 promoter and their productions were confirmed. The two hybrid thioredoxins complemented phenotypes of a thioredoxin-deficient E. coli strain. A strain containing the C3-E hybrid thioredoxin supported growth of the T7 phage, whereas a strain expressing the E-C3 hybrid thioredoxin did not. However, both hybrids supported growth of M13 phages. The two hybrid thioredoxins were also characterized in other aspects. Differences in activity between the hybrid thioredoxins were attributed to altered interactions of the N- and C-terminal domains of the molecule, which produced changes in the three-dimensional structure of the active site region.

• Journal of Plant Biotechnology
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• v.43 no.1
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• pp.1-11
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• 2016

Single nucleotide polymorphism (SNP) is an abundant form of genetic variation within individuals of species. DNA polymorphism can arise throughout the whole genome at different frequencies in different species. SNP may cause phenotypic diversity among individuals, such as individuals with different color of plants or fruits, fruit size, ripening, flowering time adaptation, quality of crops, grain yields, or tolerance to various abiotic and biotic factors. SNP may result in changes in amino acids in the exon of a gene (asynonymous). SNP can also be silent (present in coding region but synonymous). It may simply occur in the noncoding regions without having any effect. SNP may influence the promoter activity for gene expression and finally produce functional protein through transcription. Therefore, the identification of functional SNP in genes and analysis of their effects on phenotype may lead to better understanding of their impact on gene function for varietal improvement. In this mini-review, we focused on evidences revealing the role of functional SNPs in genes and their phenotypic effects for the purpose of crop improvements.