• Interdisciplinary Bio Central
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• v.4 no.4
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• pp.14.1-14.6
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• 2012

Splice site prediction in DNA sequence is a basic search problem for finding exon/intron and intron/exon boundaries. Removing introns and then joining the exons together forms the mRNA sequence. These sequences are the input of the translation process. It is a necessary step in the central dogma of molecular biology. The main task of splice site prediction is to find out the exact GT and AG ended sequences. Then it identifies the true and false GT and AG ended sequences among those candidate sequences. In this paper, we survey research works on splice site prediction based on support vector machine (SVM). The basic difference between these research works is nucleotide encoding technique and SVM kernel selection. Some methods encode the DNA sequence in a sparse way whereas others encode in a probabilistic manner. The encoded sequences serve as input of SVM. The task of SVM is to classify them using its learning model. The accuracy of classification largely depends on the proper kernel selection for sequence data as well as a selection of kernel parameter. We observe each encoding technique and classify them according to their similarity. Then we discuss about kernel and their parameter selection. Our survey paper provides a basic understanding of encoding approaches and proper kernel selection of SVM for splice site prediction.

• Proceedings of the KSAR Conference
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• 2002.06a
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• pp.92-92
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• 2002

The neuropeptide vasopressin (VP) is a nine- amino acid hormone synthesized as preprohormone in the cell bodies of hypothalamic magnocellular neurons. The tumor in magnocellular neurons of the hypothalamus is associated with disfunctions of the cell bodies, leading to the diabetes insipidus. In order to produce the disease models with a defect in VP synthesis and its secretion, we have produced the transgenic mice regulated by VP constructs containing 3.8 kbp of the 5'flanking region and all the exons and introns in the mouse VP gene, which was fused at the end of exon 3 to a SV40 Tag. The two VP-transgene constructs differed by the lengths of their VP gene 3' flanking regions (2.1 versus 3.6 kbp). (omitted)

• Journal of fish pathology
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• v.19 no.3
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• pp.227-233
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• 2006

Olive flounder immunoreceptor DAP10 homologue cDNA was cloned from a peripheral blood lymphocytes (PBLs) cDNA library. The length of the olive flounder DAP10 cDNA is 473bp and it contains an open reading frame of 234bp. The predicted polypeptide sequence is 78 amino acids, consisting of a 22-amino acid leader, an 11-amino acid extracellular domain, a 21-amino acid transmembrane segment, and a 24-amino acid cytoplasmic domain. The amino acid sequence of olive flounder DAP10 has 56%, 50%, 32%, 31%, and 31% sequence identity with zebrafish DAP10, catfish DAP10, cattle DAP10, rat DAP10 and Monkey DAP10, respectively. Olive flounder DAP10 has a conserved aspartic acid in the transmembrane domain and a phophatidylinositol-3 kinase-binding site (YxxM/V) in the cytoplasmic region. Genomic organization reveals that olive flounder DAP10 comprises five exons and four introns. A phylogenetic analysis based on the deduced amino acid sequence grouped the olive flounder DAP10 with other species DAP10. In RT-PCR analysis, DAP10 transcripts were detected predominantly in PBLs, kidney, spleen and intestine.

• Fisheries and Aquatic Sciences
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• v.12 no.2
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• pp.90-97
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• 2009

The cytoskeletal $\beta$-actin gene and its 5'-upstream region were isolated and characterized in the rockbream (Oplegnathus fasciatus). Complementary DNA of the rockbream $\beta$-actin represented a 1,125 bp of an open reading frame encoding 375 amino acids, and the rockbream $\beta$-actin cDNA and deduced amino acid sequences were highly homologous to those of other vertebrate orthologs. At the genomic level, the $\beta$-actin gene also exhibited an organization typical of vertebrate cytoskeletal actin genes (2,159 bp composed of five translated exons interrupted by four introns) with a conserved GT/AG exon-intron splicing rule. The putative non-translated exon predicted in the rockbream $\beta$-actin gene was much more homologous with those of teleostean $\beta$-actin genes than those of mammals. The 5'-upstream regulatory region isolated by genome walking displayed conserved and essential elements such as TATA, CArG and CAAT boxes in its proximal part, while several other immune- or stress-related motifs such as those for NF-kappa B, USF, HNF, AP-1 and C/EBP were in the distal part. Semi-quantitative RT-PCR assay results demonstrated that the rockbream $\beta$-actin transcripts were ubiquitously but different-tially expressed across the tissues of juveniles.

• Proceedings of the Korean Information Science Society Conference
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• 2011.06a
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• pp.37-40
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• 2011

선택 스플라이싱 (alternative splicing)은 mRNA (messenger RNA)의 전구체인 pre-mRNA가 mRNA로 전사될 때 pre-mRNA의 엑손 영역들 (exons)이 여러 가지 유형 (pattern)으로 다시 연결되는 과정을 말한다. 선택 스플라이싱에 의해 하나의 유전자로부터 서로 다른 mRNA가 만들어 지고 서로 다른 이소형의 단백질 (protein isoforms)이 생성된다. 현재까지 알려진 선택 스플라이싱의 유형은 약 7가지 종류가 있으며, 유전자의 돌연변이 및 질병과 밀접한 연관성을 가지고 있는 것으로 알려져 있다. 본 연구에서는 차세대 시퀀싱 (Next Generation Sequencing : NGS) 기술로 생성된 RNA-Seq 데이터로부터 각 유전자 영역에 대한 선택 스플라이싱 유형을 분류/추출하는 새로운 알고리즘을 제안한다. 제안된 알고리즘에서는 RNA-Seq 데이터를 DNA 시퀀스와 mRNA 트랜스크립트 시퀀스에 동시 매핑하고, 각 엑손 영역에 정렬된 RNA-Seq 데이터의 커버리지 정보 및 엑손의 접합 (junction) 정보를 이용하여 발현된 트랜스크립트 (transcript)의 종류와 양을 측정한다. 알고리즘의 유효성을 보이기 위하여 시뮬레이션 데이터를 이용한 인간 유전자 영역에서의 선택 스플라이싱 유형 추출 실험을 수행하였으며, 검증된 선택 스플라이싱 DB와 비교, 검증하였다.

• Current Research on Agriculture and Life Sciences
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• v.30 no.1
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• pp.1-11
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• 2012

We identified cdf based on screening of the Arabidopsis cDNA library for functional suppressors of the AtBI-1 (a gene described to suppress the cell death induced by Bax gene expression in yeast). The cdf was located on Chr. V and was composed of 5 exons and 4 introns. It encodes a protein of 258 amino acid residues with a molecular weight of 28.8 kDa. The protein has 3 transmembrane domains in the C-terminal region. The cdf has one homologue, named cdf2, which was found in Arabidopsis. Like cdf, cdf2 also induced growth defect in yeast. The effect of the cell growth defect factor was somewhat lower than Bax. cdf could arrest the growth of yeast. Its localization to the nucleus was essential for the suppression of yeast cell proliferation. Morphological abnormality of intracellular network, which is a hallmark of AtBI-1, was attenuated by expression of cdf.

• 한국약용작물학회:학술대회논문집
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• 2006.11a
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• pp.103-115
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• 2006

[ ${\beta}-Glucan$ ] is a glucose polymer that has linkage of ${\beta}-(1,3)$, -(1,4) and -(1,6). As exclusively found in fungal and bacterial cell wall, not in animal, ${\beta}-glucans$ are recognized by innate immune system. Dendritic cells (DC) or macrophages possesses pattern recognition molecule (PRM) for binding ${\beta}-glucans$ as pathogen-associated molecular pattern (PAMP). Recently ${\beta}-glucans$ receptor was cloned from DC and named as dectin-l which belongs to type II C-type lectin family. Human dectin-l is consisted of 7 exons and 6 introns. The polypeptide of dectin-l has 247 amino acids and has cytoplasmic, transmembrane, stalk and carbohydrate recognition domains. Dectin-l could recognize variety of beta-l,3 and/or beta-l,6 glucan linkages, but not alpha-glucans. In our macrophage cell line culture system, dectin-l mRNA was detected in RA W264.7 cells by reverse transcription-polymerase chain reaction (RT-PCR). Dectin-l was also detected in the murine organs of spleen, thymus, lung and intestines. Treatment of RA W264.7 cells with ${\beta}-glucans$ of Ganoderma lucidum (GLG) resulted in increased expression of IL-6 and $TNF-{\alpha}$ in the presence of LPS. However, GLG alone did not increase IL-6 nor $TNF-{\alpha}$ These results suggest that receptor dectin-l cooperate with CD14 to activate signal transduction that is very critical in immunoresponse.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.1
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• pp.15-20
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• 2013

Urinary bladder squamous cell carcinoma (SCC), one of the most common neoplasms in Egypt, is attributed to chronic urinary infection with Schistosoma haematobium (Schistosomiasis). The proto-oncogene c-KIT, encoding a tyrosine kinase receptor and implicated in the development of a number of human malignancies, has not been studied so far in schistosomal urinary bladder SCCs. We therefore determined immunohistochemical (IHC) expression of c-KIT in paraffin sections from 120 radical cystectomies of SCCs originally obtained from the Pathology Department of Suez Canal University (Ismailia, Egypt). Each slide was evaluated for staining intensity where the staining extent of >10% of cells was considered positive. c-KIT overexpression was detected in 78.3% (94/120) of the patients, the staining extents in the tumor cells were 11-50% and >50% in 40 (42.6%) and 54 (57.4%) respectively. The positive cases had 14.9%, 63.8%, 21.3% as weak, moderate and strong intensity respectively. Patients with positive bilharzial ova had significantly higher c-KIT expression than patients without (95.2% vs. 38.9%, P=0.000). Mutation analysis of exons 9-13 was negative in thirty KIT positive cases. The high rate of positivity in SBSCC was one of the striking findings; However, CD117 may be a potential target for site specific immunotherapy to improve the outcome of this tumor.

• BMB Reports
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• v.41 no.4
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• pp.334-337
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• 2008

MCL1 expression has been found to be up-regulated during infection with virulent Mycobacterium tuberculosis. We investigated the genetic polymorphisms in MCL1 as potential candidate gene for a host genetic study of clinical TB infection. We have sequenced exons and their boundaries of MCL1, including the 1.5 kb promoter region, to identify polymorphisms, and eight polymorphisms were identified. The genetic associations of polymorphisms in MCL1 with clinical TB patients (n=486) and normal controls (n=370) were analyzed. Using statistical analyses, one common promoter polymorphism (MCL1-324C>A) which is absolutely linked with three other SNPs in the promoter and 3'UTR regions, were found to be significantly associated with increased risk of clinical TB disease. The frequency of the A-bearing genotype of -324C>A was higher in clinical TB patients than in normal controls (P=0.0008, OR=1.68). Our findings suggest that polymorphisms in MCL1 might be one of genetic factors for the risk of clinical tuberculosis development.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.4
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• pp.1599-1603
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• 2012

Objectives: Since methylenetetrahydrofolate reductase (MTHFR) maintains the balance of circulating folate and methionine and blocks the formation of homocysteine, its regulation in relation to different cancers has extensively been studied in different populations. However, information on Pakistani breast cancer patients is lacking. The MTHFR gene has two most common mutations that are single nucleotide additions which result in change of amino acids C677T to Ala222val and A1298C to Glu429Ala. Methodology: 110 sporadic breast patients with no prior family history of cancer or any other type of genetic disorders along with 110 normal individuals were screened for mutations in exons 1 to exon 9 using single strand conformational polymorphism, RFLP and sequencing analyzer. Results: The p values for the 677CC, 677CT, and 677TT genotypes were 0.223, 0.006, and 0.077, respectively. Those for the 1298AA, 1298AC, and 1298CC genotypes were 0.555, 0.009, and 0.003, respectively. Conclusions: We found an overall a significant, weak inverse association between breast cancer risk and the 677TT genotype and an inverse association with the 1298C variant. These results for MTHFR polymorphism might be population specific in sporadic breast cancer affected patients but many other factors need to be excluded before making final conclusions including folate intake, population and disease heterogeneity.