• Title/Summary/Keyword: DNA contents

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Stream based DNA Read Deduplication Method (스트림 기반 DNA 리드 중복제거 방법)

  • Lee, Hyeon-byeong;Song, Seok-il;Yoo, Jaesoo
    • Proceedings of the Korea Contents Association Conference
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    • 2019.05a
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    • pp.9-10
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    • 2019
  • NGS 분석과정 중 증폭된 DNA 리드(Read)는 중복이 발생하여 이로 인해 다음 단계의 정확도 저하 등의 문제를 야기한다. 이 논문에서는 기존 DNA 리드 중복 제거 도구 중 하나인 Samblaster의 중복제거 알고리즘을 이용하여 분산 병렬 형태로 중복제거를 수행하는 방법을 제안한다. 제안하는 중복제거 방법은 중복제거 전단계인 정렬단계애서 정렬된 리드에 대해 중복제거 키를 생성하고 이를 스트림으로 전달하여 중복제거를 수행한다.

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Alterations in Mitochondrial DNA Copy Numbers and Mitochondrial Oxidative Phosphorylation (OXPHOS) Protein Levels in Gastric Cancer Tissues and Cell Lines (위암 조직과 세포주에서 mDNA와 OXPHOS 단백질 분석)

  • Siregar, Adrian;Hah, Young-Sool;Moon, Dong Kyu;Woo, Dong Kyun
    • Journal of Life Science
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    • v.31 no.12
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    • pp.1057-1065
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    • 2021
  • Alterations in mitochondrial DNA (mtDNA) copy numbers have been reported in patients with stomach cancer and suggested to play a role in gastric carcinogenesis or gastric cancer progression. However, changes in the levels of mitochondrial proteins or mtDNA-encoded oxidative phosphorylation (OXPHOS) proteins in gastric cancer remain unclear. In this study, we investigated mtDNA contents, mitochondrial protein levels, and mtDNA-encoded OXPHOS protein levels in gastric cancer tissues and cell lines. We correlated mtDNA copy numbers with clinicopathologic features of the gastric cancer samples used in this study and used quantitative PCR to analyze the mtDNA copy numbers of the gastric cancer tissues and cell lines. Western blot analysis was used for assessing the amounts of mitochondrial proteins and mtDNA-encoded OXPHOS proteins. Among the 27 gastric cancer samples, 22 showed a reduction in mtDNA copy numbers. The mtDNA content was increased in the other five samples relative to that in normal matched gastric tissues. Mitochondrial protein and OXPHOS protein levels were reduced in some gastric cancer tissues. However, mitochondrial protein and OXPHOS protein levels in gastric cancer cell lines were not always in line with their mtDNA contents. The mtDNA copy numbers were reduced in five gastric cancer cell lines tested in this study. In summary, this study reports a common reduction in mtDNA contents in gastric carcinoma tissues and cell lines, pointing to the possible involvement of mtDNA content alterations in tumorigenesis of the stomach.

The Effects of Temperature, Starvation, and Kind of Foods on Growth, RNA/DNA Ratios and Protein Contents during the Early Life Stages of Olive Flounder (Paralichthys olivaceus)

  • Gwak Woo-Seok;Tanaka Masaru
    • Fisheries and Aquatic Sciences
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    • v.7 no.4
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    • pp.192-203
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    • 2004
  • The effects of temperatures, starvation, and kind of foods on growth, RNA/DNA ratio and protein contents during metamorphosis and early juvenile stage of olive flounder (Paralichthys olivaceus) were examined. During metamorphosis, warm-acclimated fish showed higher RNA and DNA content than those of the cold-acclimated fish, excepting H stage (28 DAH) at which the ratio was higher at cold temperature. RNA/DNA ratio during metamorphosis showed similar values at two temperatures tested. However, after 42 DAH warm-acclimated juveniles had higher DNA content compared with cold-acclimated fish, resulted in marked decreases in RNA/DNA ratios. Higher RNA content at H stage of cold-acclimated fish was consistent with an increase in protein content. Growth of fish rearing at warm temperature was higher than those of fish at cold temperature during all experiments. In starvation experiment, contents of DNA, RNA and protein significantly decreased. Even though there were no significant differences in total length (TL) and body weight between the live mysid-fed and artificial pellet-fed fish at 35 mm TL, both RNA/DNA and protein/DNA ratios of the former group was significantly higher than those of the latter due primarily to lower DNA content of the live mysid-fed group. The results from this study suggest that temperature, starvation and kind of foods should be considered when RNA/DNA ratio applied to assessing the cultured larval and juvenile fish condition.

Analysis of DNA Methylation Motif Patterns for Development Related Genes (발생 관련 유전자의 DNA 메틸화 모티프 패턴 분석)

  • Lee, Hyun jae;Ryu, Jea woon;Kim, Hak yong
    • Proceedings of the Korea Contents Association Conference
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    • 2012.05a
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    • pp.355-356
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    • 2012
  • 후성유전은 DNA 염기 서열이 변화하지 않고 DNA의 메틸화(methyaltion) 및 히스톤 단백질의 변형(modification)등의 후천적 과정에 의해 유전자 발현이 조절되는 현상이다. 특히 DNA 메틸화 정도에 대한 패턴 분석은 후성유전을 이해하는 중요한 접근방법중 하나이다. DNA 메틸화 패턴 분석을 위해 발생에 관련된 123개 유전자들의 -5000bp ~ +200bp사이에 있는 DNA 염기 서열 정보를 추출하였다. 추출한 염기 서열 정보를 기반으로 기존에 알려진 메틸화 경향성 모티프와 메틸화 저항성 모티프를 모니터링 함으로써 발생관련 유전자들의 메틸화 모티프 패턴을 분석하였다. 결과적으로 메틸화 저항 모티프만이 발견되었고 따라서 메틸화 저항 모티프 패턴과 발생관련 유전자들의 상관관계를 분석하였다.

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Analysis of DNA Methylation Motif for Immune Related Genes Based on Networks (네트워크 기반 면역관련 유전자의 DNA 메탈화 모티프 분석)

  • Lee, Jihoo;Ryu, Jea Woon;Kim, Hak Yong
    • Proceedings of the Korea Contents Association Conference
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    • 2012.05a
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    • pp.357-358
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    • 2012
  • 후성유전은 DNA 염기서열이 변화하지 않은 상태에서 특별한 후성적 조절 기전에 의해 유전자의 발현 양상이 변하는 현상이다. 후성적 조절 기전에는 DNA의 메틸화(methyaltion)와 히스톤 단백질의 변형(modification), non coding RNA에 의한 조절 등이 포함되는데, 이 중 DNA 메틸화 정도에 대한 패턴 분석은 후성유전을 이해하는 중요한 접근방법 중 하나이다. 네트워크와 DNA 메틸화 분석을 위하여 면역관련 264개 유전자들의 -2000bp ~ +200bp사이에 있는 DNA 염기 서열 정보를 추출하였다. 또한 면역관련 단백질들의 상호작용 정보를 이용하여 네트워크를 구축하고 여기에 메틸화 정보를 적용하여 상호작용과 메틸화 모티프와의 관계를 분석하였다. 메틸화 모티프 정보를 적용한 단백질 네트워크에서는 기존 단백질 네트워크보다 더 복잡한 구조를 이루고 있었다. 이러한 구조는 동일한 메틸화 모티프들이 여러 유전자들의 활성을 조절할 것으로 사료된다. 단백질 상호작용 네트워크에 모티프를 적용한 분석은 새로운 후성유전학적 연구를 위한 접근 방법으로 이용될 수 있을 것이다.

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Analysis of DNA Methylation Motif for Aging Related Genes Based on Networks (네트워크 기반 노화 관련 유전자의 DNA 메틸화 모티프 분석)

  • Cho, sung-jin;Ryu, jea-woon;Kim, hak-yong
    • Proceedings of the Korea Contents Association Conference
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    • 2012.05a
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    • pp.133-134
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    • 2012
  • 후성유전은 DNA 염기서열이 변화하지 않고 DNA의 메틸화(methylation)및 히스톤 단백질의 변형(modification)등의 후천적 과정에 의해 유전자 발현이 조절되는 현상이다. 특히 DNA 메틸화 정도에 대한 분석은 후성유전을 이해하는 중요한 접근방법 중 하나이다. DNA 메틸화 패턴 분석을 위하여 노화관련 109개 유전자들의 단백질 상호작용 네트워크를 구축하였으며 -3000bp ~ +200bp 사이에 있는 DNA 염기서열 정보를 추출하여 기존에 알려진 메틸화 저항성 (Methylation resistant) 모티프를 네트워크로 구축하였다. 메틸화 모티프기반 단백질 네트워크에서는 기존 단백질 네트워크보다 더 복잡한 구조를 이루고 있었다. 이러한 구조는 동일한 메틸화 모티프들이 여러 유전자들의 활성을 조절할 것으로 추측되며 복잡한 모티프들을 분석하기 위한 방법으로 이용될 수 있을 것이다.

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Cereal Resources in National BioResource Project of Japan

  • Sato, Kazuhiro;Endo, Takashi R.;Kurata, Nori
    • Interdisciplinary Bio Central
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    • v.2 no.4
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    • pp.13.1-13.8
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    • 2010
  • The National BioResource Project of Japan is a governmental project to promote domestic/international research activities using biological resources. The project has 27 biological resources including three cereal resources. The core center and sub-center which historically collected the cereal resources were selected for each cereal program. These resources are categorized into several different types in the project; germplasm, genetic stocks, genome resources and database information. Contents of rice resources are wild species, local varieties in East and Southwest Asia & wild relatives, MNU-induced chemical mutant lines, marker tester lines, chromosome substitution lines and other experimental lines. Contents of wheat resources are wild strains, cultivated strains, experimental lines, rye wild and cultivated strains; EST clones and full-length cDNA clones. Contents of barley resources are cultivar and experimental lines, core collection, EST/cDNA clones, BAC clones, their filters and superpool DNA. Each resource is accessible from the online database to see the contents and information about the resources. Links to the genome information and genomic tools are also important function of each database. The major contents and some examples are presented here.

Selection of optimal protein domains for DNA repair inhibition in cancer cells based on bioinformatics (생물정보학 기반 암세포 내 DNA 복구 저해를 위한 최적 단백질 도메인 선정)

  • Jo, Si Hyang;Kim, Hak Yong
    • Proceedings of the Korea Contents Association Conference
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    • 2016.05a
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    • pp.185-186
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    • 2016
  • 최근 DNA 복구 기작 저해가 암 전이를 억제한다는 연구결과가 발표되었다. 이번 연구에서는 DNA 복구 기작을 효율적으로 저해시킬 수 있는 단백질을 선정하고자 했다. 먼저 HPRD에서 59개의 DNA repair 단백질 정보를 얻고 각각의 도메인 정보를 추출하였다. 이 단백질과 상호작용하는 단백질을 KEGG로 부터 추출하고 추출한 단백질의 도메인 정보는 HPRD에서 얻었다. Cytoscape를 통하여 DNA 복구 단백질-상호작용 단백질-도메인의 네트워크를 시각화하였다. 네트워크 상에서 보존적이며 핵심적인 단백질 후보 및 도메인 후보를 선정 하였다. KEGG에서 제공하는 암의 경로(pathways in cancer)을 이용하여 후보의 적용 가능성을 확인하였다. 선정한 최종 후보들은 향후 암 전이 억제에 사용될 수 있는 타깃이 될 수 있을 것으로 기대한다.

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Effect of Ginseng on Visceral Nucleic Acid Content of Rats (고려인삼이 흰쥐의 장기조직 핵산 함유량에 미치는 영향)

  • Kim, Chul;Choi, Hyun;Kim, Chung-Chin;Kim, Jong-Kyu;Kim, Myung-Suk;Huh, Man-Kyung
    • The Korean Journal of Physiology
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    • v.5 no.1
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    • pp.23-42
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    • 1971
  • I. Chemical analysis A study was planned to see if administration of ginseng extract has any influence upon the adrenal, the hepatic, the splenic, and the pancreatic nucleic acid contents of rats, and to estimate the effect of ACTH administration as a substitute for stress reaction upon these nucleic acid contents of rats previously primed with ginseng. Ninety male rats$(body\;weight:\;150{\sim}200gm)$ were divided into the ginseng, the saline, and the normal control groups, which received for 5 days 0.5ml/100 gm body weight of ginseng extract solution (4 mg of ginseng alcohol extract in 1 ml of saline), same amount of saline, or no medication, respectively. On the 5th experimental day, each of the 3 groups was further divided into 2 subgroups yielding the ginseng, the ginseng-ACTIT, the saline, the saline-ACTH, the normal control, and the normal-ACTH subgroups. The ginseng, the saline, and the normal control subgroups were sacrificed 3 hours after the last medication, while the ginseng-ACTH, the saline·ACTH, and the normal-ACTH subgroups received ACTH(0.1 unit/subject) 1 hour after the last medication and were sacrificed after 1 more hour. The adrenal gland, the liver, the spleen and the pancreas of each rat were measured for RNA and DNA contents using the chemical method of Schmidt-Thannhauser-Schneider. Following results were obtained: 1. Adrenal RNA and DNA contents and RNA/DNA ratio were all significantly higher in the ginseng group compared with the values obtained from the normal control and the saline groups. Generally administration of ACTH reduced nucleic acid contents of the viscera examined. However, in the ginseng group the rate of decrease [(value of ginseng-ACTH subgroup-value of ginseng subgroup) x100/value of ginseng subgroup)] in adrenal RNA and DNA contents and in RNA/DNA ratio were more conspicuous than they were in the normal control and the saline groups. 2. Hepatic RNA and DNA contents and RNA/DNA ratio were all significantly less in the ginseng group than in the normal control and the saline groups. After ACTH, the rate of decrease in hepatic RNA, DNA, and RNA/DNA ratio of the ginseng· group was less conspicuous than those of the other 2 groups. 3. With regard to the splenic nucleic acid contents, the RNA and the RNA/DNA values of the ginseng group were higher than those of the normal control group but lower than those of the saline group, while the DNA value of the ginseng group was lower than that of the normal control group but higher than that of the saline group. Following administration of ACTH, the rate of decrease in RNA and DNA contents and in RNA/DNA ratio of the ginseng group was more conspicuous than that of the normal control group but less remarkable than that of the saline group. 4. Pancreatic RNA and DNA contents were notably lower in the ginseng group than in the normal control and the saline groups. However, the RNA/DNA ratio of the ginseng group was higher than that of the normal control and the saline groups.'After ACTH, the rate of decrease in pancreatic RNA and RNA/DNA ratio of the ginseng group was less than that of the normal. control group but more than that of the saline group, while the DNA content was actually increased in the ginseng group though it decreased in the normal control and the saline groups. Although the results are not clear enough for an accurate interpretation, they seem to indicate that ginseng exerts notable influence upon the RNA and DNA contents and the RNA/DNA ratio of the viscera stodied. On the whole the drug tends to increase the RNA and DNA contents and RNA/DNA ratio of the adrenal gland but seems to diminish the values of the other 3 viscera. In the early period following ACTH, ginseng facilitates the fall in RNA and DNA contents and RNA/DNA ratio of the adrenal gland, while it tends to reduce the fall in the values of the other viscera studied. II. Autoradiographic and histochemical analysis It was planned autoradiographically and histochemically to affirm and extend the results obtained in part I with regard to the chemically assessed change in the adrenal, the pancreatic, the hepatic and the splenic DNA and RNA contents under the influence of ginseng and ACTH. Fourty male mice (body weight: $18{\sim}20gm$) and 20 male rats were used. Each animal species was divided into the saline, the ginseng, the saline-ACTH, and the ginseng-ACTH groups according to the administered drugs. In the mice, the adrenal, the pancreatic, the splenic and the hepatic DNA-synthetic activity was assessed autoradiographically after administration of $^3H$-thymidine. In the rats, the RNA content of the above 4 organs was assessed histochemically after staining them with methylgreen pyronine. Following results were obtained: 1. Labeled cells were significantly more numerous in the adrenal cortex, the spleen and the liver of the ginseng group than in those of the saline group, although they were less numerous in the pancreas of the ginseng group than in the pancreas of the saline group. The adrenocortical, the pancreatic, the splenic and the hepatic tissues were stained with methylgreen pyronine more deeply in the ginseng group than in the saline group. 2. The adrenocortical, the pancreatic, the splenic and the hepatic tissues contained labeled cells less numerously in the saline-ACTH and the ginseng-ACTH group than in the saline and the ginseng groups. All these tissues were also stained with methylgreen pyronine less deeply in the saline-ACTH and the ginseng-ACTH groups than in the saline and the ginseng groups. 3. However, the adrenal cortex, the spleen, the pancreas, and the liver contained labeled cells more numerously in the ginseng-ACTH group than in the saline-ACTH group. the 4 tissues were stained with methylgreen pyronine more deeply in the ginseng-ACTH group than in the saline-ACTH group. It is inferred from the above results that though with exception, the ginseng mostly facilitates cellular synthesis of nucleic acids and mitigates reduction in nucleic acid content of tissues after administration of ACTH.

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Analysis of Stomach Contents of Marine Orgnaisms in Gwangyang Bay and Yeosu Fish Market Using DNA Metabarcoding (DNA 메타바코딩을 이용한 광양만 및 어시장 해양 생물 위 내용물 분석)

  • Gun Hee Oh;Yong Jun Kim;Won-Seok Kim;Cheol Hong;Chang Woo Ji;Ihn-Sil Kwak
    • Korean Journal of Ecology and Environment
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    • v.55 no.4
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    • pp.368-375
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    • 2022
  • Gut contents analysis is essential to predict the impact of organisms on food source changes due to variations of the habitat environment. Previous studies of gut content analysis have been conducted using traditional methods, such as visual observation. However, these studies are limited in analyzing food sources because of the digestive process in gut organ. DNA metabarcoding analysis is a useful method to analyze food sources by supplementing these limitations. We sampled marine fish of Pennahia argentata, Larimichthys polyactis, Crangon affinis, Loligo beka and Sepia officinalis from Gwangyang Bay and Yeosu fisheries market for analyzing gut contents by applying DNA metabarcoding analysis. 18S rRNA v9 primer was used for analyzing food source by DNA metabarcoding. Network and two-way clustering analyses characterized the relationship between organisms and food sources. As a result of comparing metabarcoding of gut contents for P. argentata between sampled from Gwangyang Bay and the fisheries market, fish and Copepoda were analyzed as common food sources. In addition, Decapoda and Copepoda were analyzed as common food sources for L. polyactis and C. affinis, respectively. Copepoda was analyzed as the primary food source for L. beka and S. officinalis. These study results demonstrated that gut contents analysis using DNA metabarcoding reflects diverse and detailed information of biological food sources in the aquatic environment. In addition, it will be possible to provide biological information in the gut to identify key food sources by applying it to the research on the food web in the ecosystem.