• Title/Summary/Keyword: genetic parameters

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A Study on the Genomic Patterns of SARS coronavirus using Bioinformtaics Techniques (바이오인포매틱스 기법을 활용한 SARS 코로나바이러스의 유전정보 연구)

  • Ahn, Insung;Jeong, Byeong-Jin;Son, Hyeon S.
    • Proceedings of the Korea Contents Association Conference
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    • 2007.11a
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    • pp.522-526
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    • 2007
  • Since newly emerged disease, the Severe Acute Respiratory Syndrome (SARS), spread from Asia to North America and Europe rapidly in 2003, many researchers have tried to determine where the virus came from. In the phylogenetic point of view, SARS virus has been known to be one of the genus Coronavirus, but, the overall conservation of SARS virus sequence was not highly similar to that of known coronaviruses. The natural reservoirs of SARS-CoV are not clearly determined, yet. In the present study, the genomic sequences of SARS-CoV were analyzed by bioinformatics techniques such as multiple sequence alignment and phylogenetic analysis methods as well multivariate statistical analysis. All the calculating processes, including calculations of the relative synonymous codon usage (RSCU) and other genomic parameters using 30,305 coding sequences from the two genera, Coronavirus, and Lentivirus, and one family, Orthomyxoviridae, were performed on SMP cluster in KISTI, Supercomputing Center. As a result, SARS_CoV showed very similar RSCU patterns with feline coronavirus on the both axes of the correspondence analysis, and this result showed more agreeable results with serological results for SARS_CoV than that of phylogenetic result itself. In addition, SARS_CoV, human immunodeficiency virus, and influenza A virus commonly showed the very low RSCU differences among each synonymous codon group, and this low RSCU bias might provide some advantages for them to be transmitted from other species into human beings more successfully. Large-scale genomic analysis using bioinformatics techniques may be useful in genetic epidemiology field effectively.

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Factors Affecting Prognosis in Metastatic Colorectal Cancer Patients

  • Eker, Baki;Ozaslan, Ersin;Karaca, Halit;Berk, Veli;Bozkurt, Oktay;Inanc, Mevlude;Duran, Ayse Ocak;Ozkan, Metin
    • Asian Pacific Journal of Cancer Prevention
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    • v.16 no.7
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    • pp.3015-3021
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    • 2015
  • Background: Colorectal cancer (CRC) is a major cause of mortality in developed countries, and it is the third most frequent malignancy in Turkey. There are many biological, genetic, molecular, and tissue-derived prognostic factors for CRCs. In this study, we evaluated prognostic factors in patients who were metastatic at diagnosis or progressed to metastatic disease during follow-up. Patients and Methods: This study included 116 patients with malignancies either in the colon or rectum. Of these, 65 had metastatic disease at diagnosis, and 51 progressed to metastatic disease during the course of the disease. The parameters evaluated were age, gender, comorbidity, performance status and stage of the disease at the beginning, localization, history of surgery, chemotherapy regimen, response to first-line treatment, K-RAS status, site and number of metastases, expression of tumor predictors (CEA, CA19-9), and survival times. A multivariate analysis conducted with factors that considered statistically significant in the univariate analysis. Findings: Median age was 56 (32-82) years and the male/female ratio was 80/36. Eleven patients were at stage II, 40 at stage III, and 65 at stage IV at diagnosis. Twenty three patients had tumor in the right colon, 48 in the left colon, and 45 in the rectum. Ninety seven patients were operated, and 27 had surgical metastasectomy. Ninety three patients received targeted therapy. At the end of follow-up, 61 patients had died, and 55 survived. Metastatic period survival times were longer in the adjuvant group, but the difference did not reach the level of statistical significance (adjuvant group: median 29 months, metastatic group: median 22 months; p=0.285). In the adjuvant group before the metastatic first-line therapy, CEA and CA 19-9 levels were significiantly lower compared to the metastatic group (p<0.005). We also found that patients with elevated tumor predictor (CEA, CA 19-9) levels before the first-line therapy had significiantly poorer prognosis and shorter survival time. Survival was significiantly better with the patients who were younger than 65 years of age, had better initial performance status, a history of primary surgery and metastatectomy, and single site of metastasis. Those who benefitted from the first-line therapy were K-RAS wild type and whose tumor markers (CEA, CA 19-9) were not elevated before the first line therapy. Conclusions: Among the patients with metastatic CRC, those who benefited from first-line therapy, had history of metastasectomy, were K-RAS wild type and had low CA 19-9 levels before the first-line therapy, showed better prognosis independent of other factors.

Analysis and Design Theory of Aperture-Coupled Cavity-Fed Back-to-Back Microstrip Directional Coupler (개구면 결합 공진기 급전 마이크로스트립 방향성결합기 해석 및 설계)

  • Nam, Sang-Ho;Jang, Guk-Hyun;Nam, Kyung-Min;Lee, Jang-Hwan;Kim, Chul-Un;Kim, Jeong-Phill
    • Journal of the Institute of Electronics Engineers of Korea TC
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    • v.44 no.3 s.357
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    • pp.7-17
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    • 2007
  • An analysis and design theory of an aperture-coupled cavity-fed back-to-back microstrip directional coupler is presented for the efficient and optimized design. For this purpose, an equivalent network is developed, and simple but accurate calculations of circuit element values are described. Design equations of the coupler are derived based on the equivalent circuit. In order to determine various structural design parameters, the evolutionary hybrid optimization method based on the genetic algorithm and Nelder-Mead method is invoked. As a validation check of the proposed theory and optimized design method, a 10 dB directional coupler was designed and fabricated. The measured coupling was 10.3 dB at 3 GHz, and the return loss and isolation were 31.8 dB and 30.5 dB, respectively. The directional coupler also showed very good quadrature phase characteristics. Good agreements between the measured and the design specifications fully validate the proposed network analysis and design procedure.

Effects of harvesting times on pasting properties of starch in colored rices

  • Kim, Sang Kuk;Song, Young Un;Shin, Jong Hee;Kim, Se Jong
    • Proceedings of the Korean Society of Crop Science Conference
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    • 2017.06a
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    • pp.329-329
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    • 2017
  • The study was conducted to investigate the effects of different harvesting time on pasting properties of starch in three colored rices. Seven major parameters of starch pasting properties, peak viscosity (PKV), hot pasting viscosity (HPV), cool pasting viscosity (CPV), setback (CPV minus PKV), breakdown (PKV minus HPV), peak time, and pasting time were determined by Rapid Visco Analyzer. The peak viscosity, hot viscosity, cool viscosity and peak time were influenced by different harvesting times. Pasting time was delayed slightly with prolonged harvesting time in all rice cultivars. Pasting temperature in each rice cultivar differed from each harvesting time, and pasting temperature of the two rice cultivars, Hongjinju and Joseongheugchal, showed the highest at the 40 days after heading and then it decreased at the final harvesting time. With the delay of the harvesting time, peak viscosity, hot viscosity, cool viscosity, setback value and pasting temperature did not exhibit a regular trend depending on their genetic characteristics. Branch chain length distribution of amylopectin was demonstrated a distinct difference among these colored rices. In changes of amylopectin branch chain-length distribution, the amylopectin structure of Hongjinju rice cultivar as affected by different harvesting time, the shortest chain length of amylopectin in rice starch harvested at 20 days after heading was characterized by the significant increase in A chains with $DP{\geq}12$ and remarked decrease in long chains $37{\leq}DP$ compared to that of 30, 40, and 50 days after heading. In particular, when harvesting time is delayed the distribution percentage of short chain (A chains with $DP{\geq}12$) was increased except for the rice which harvested 20 days after heading. The similar results were also observed in Sintoheugmi rice cultivar like that of Hongjinju rice cultivar. Otherwise, distribution percentage of the shortest chain length of amylopectin in rice starch harvested at 20 days after heading was characterized by the significant decrease in A chains with $DP{\geq}12$ and remarked increase in B chains $13{\leq}DP{\geq}24$ compared to that of 30, 40, and 50 days after heading.

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Effects of Incubation and Thawing Temperature on Frozen-thawed Stallion Epididymal Spermatozoa (말의 정소상체 정자의 동결 후 해동 온도 및 Incubation의 효과)

  • Kim, Keun-Jung;Lee, Kyung-Bon;Lee, Ji-Hye;Kim, Eun-Young;Han, Kil-Woo;Park, Kang-Sun;Kim, Min-Kyu
    • Journal of Embryo Transfer
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    • v.28 no.3
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    • pp.297-302
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    • 2013
  • Cryopreservation of epididymal spermatozoa offers a potential tool for rescuing genetic material from males of genetically elite populations. Castration, catastrophic injury, sudden death or any other event that makes semen collection or mating impossible may prematurely terminate a stallion reproduction. Stallion epididymal spermatozoa vary widely in the loss of progressive motility, acrosomal integrity, and viability during freezing and thawing. The objective of this work was to investigate the effect of (1) freezing package types on cryopreservation efficiency, (2) thawing temperatures (37, 56 or $70^{\circ}C$) on Computer Assisted Sperm Analysis (CASA) parameters and (3) post-thawing incubation time (0, 1, 2 or 4h) on castrated stallion epididymis. Post-thawed sperm motility ranged between 59.69% and 64.28% ($56^{\circ}C$ and $37^{\circ}C$) in various thawing temperatures. When stallion epididymis sperm was frozen, straw was better than freezing tube on VCL (Velocity of Curvilinear Line) and VAP (Velocity of Average Path) parameter. Higher percentage of motility was observed at $37^{\circ}C$ thawing temperature even though no significant difference was observed among various temperatures. The motility, VCL, ALH (Amplitude of Lateral Head displacement), VAP, BCF (Beat-Cross Frequency) and STR (Straightness index) parameter of post-thawed sperm were significantly decreased by increasing the incubation time for all thawing temperatures. The present study showed that type of freezing package (Straw vs. Freezing tube) was not significantly different on cryopreservation efficiency. Furthermore, stallion epididymal spermatozoa frozen-thawed at $37^{\circ}C$ for 1 min resulted the highest proportion of motility and velocity movement. In addition, motility and viability of frozen-thawed stallion epididymal spermatozoa were also decreased by incubation.

Genetic Analysis of Thiobencarb Tolerance in Rice(Oryza sativa L.) (제초제(除草劑) Thiobencarb에 대한 벼 내성(耐性)의 유전(遺傳))

  • Shin, D.H.;Moody, K.;Zapata, F.J.;Kim, K.U.
    • Korean Journal of Weed Science
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    • v.10 no.3
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    • pp.179-185
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    • 1990
  • Five parents which showed differential response to thiobencarb and their $F_1$ hybrids were treated with thiobencarb (S-[(4-chlorophenyl) methyl]diethylcarbamothioate) at 2 and 4 kg ai/ha in order to investigate the inheritance of rice (Oryza sativa L.) to the herbicide. In the analysis of diallel crosses for tolerance of rice cultivars to the herbicide, highly significant GCA (general combining ability) and SCA (specific combining ability) effects were observed at both herbicide rates using the parameters of plant height and dry weight ; the GCA effect being greater than the SCA effect. The additive effects appeared to be more prevalent than dominance effects, and partial dominance was recognized in relation to herbicide tolerance in the different rice cultivars. Higher heritabilities in the narrow and broad senses were observed at 4 kg ai/ha. The heritabilities in the narrow sense for plant height and dry weight were 0.726 and 0. 743, respectively. IR9660-50-3-1 which showed the highest GCA effects seemed to possess more dominant genes related to herbicide tolerance than the other rice cultivars tested.

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Evaluation of DNA Double Strand Breaks in Human and Mouse Lymphocyte Following ${\gamma}-Irradiation$ (${\gamma}-Ray$ 조사에 따른 사람의 정상임파구와 마우스 정상임파구의 DNA Double Strand Break 발생율에 대한 비교분석)

  • Kim Tae Hwan;Kim Sung Ho;Chung In Yong;Cho Chul Koo;Ko Kyung Hwan;Yoo Seong Yul
    • Radiation Oncology Journal
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    • v.11 no.2
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    • pp.219-225
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    • 1993
  • The evaluation of radiation-induced DNA double strand breaks (DSB) was made following irradiation of human lymphocytes, murine lymphocytes and EL-4 leukemia cells over a wide dose range of $^{60}Co\;{gamma}-rays.$ In lipopolysaccharide (LPS) or phytohemagglutinin (PHA)-stimulated murine lymphocytes, the slopes of the stand scission factor (SSF) revealed that lymphocytes with LPS increased DNA DSB formation by a factor of 1.432 (p<0.005). Furthermore, strand break production was relatively inefficient in the T lymphocytes compared to the B lymuhocytes. And EL-4 leukemia cells were found to form significantly more DNA DSB to a greater extent than normal lymphocytes (p<0.005). The in vitro studies of the intrinsic radiosensitivity between human lymphocytes and murine lymphocytes showed similar phasic kinetics. However, murine lymphocytes were lower in DNA DSB formation and higher in the relative radiation dose of 10 percent DNA strand breaks at 3.5 hours following ${gamma}-irradiation$ than human lymphocytes. Though it is difficult to interpret these results, these differences may be result from environmental and genetic factors. From our data, if complementary explanations for this difference will be proposed, the differences in the dose-effect relationship for the induction of DSB between humans and mice must be related to interspecies variations in the physiological condition of the peripheral blood in vitro and not to differences in the intrinsic radiation sensitivity of the lymphocytes. These results can be estimated on the basis of dose-effect correlation enabling the interpretation of clinical response and the radiobiological parameters of cytometrical assessment.

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Physiological responses to drought stress of transgenic Chinese cabbage expressing Arabidopsis H+-pyrophosphatase (애기장대 H+-pyrophosphatase 발현 형질전환 배추의 건조스트레스에 대한 생리적 반응)

  • Jeong, Mihye;Kang, In-Kyu;Kim, Chang Kil;Park, Kyung Il;Choi, Cheol;Han, Jeung-Sul
    • Journal of Plant Biotechnology
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    • v.40 no.3
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    • pp.156-162
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    • 2013
  • Plant tolerance to drought is a beneficial trait for stabilizing crop productivity under water deficits. Here we report that genetically engineered Chinese cabbage expressing Arabidopsis $H^+$-pyrophosphatase (AVP1) shows enhanced physiological parameters related to drought tolerance. In comparison with wild type plants under soil water deficit stress created by cessation of irrigation, soil water potential in pot with AVP1-expressing plants was more rapidly decreased that might lead to increased relative water content in leaves, while both genotypes had indistinguishable wilting phenotypes. Transgenic plants subjected to drought treatment also exhibited higher photosystem II quantum yield in addition to lower electrolyte leakage and $H_2O_2-3,3^{\prime}$-diaminobenzidine content when compared to wild type plants.

Optimization of Mannitol Fermentation by Leuconostoc mesenteroides sp. strain JFY (Leuconostoc mesenteroides sp. strain JFY 균주에 의한 만니톨 발효 조건의 최적화)

  • Yoo Sun Kyun;Hur Sang Sun;Song Suckhwan;Kim Kyung Min;Whang Kyung Sook
    • Journal of Life Science
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    • v.15 no.3 s.70
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    • pp.374-381
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    • 2005
  • The production of functional foods providing health benefit is one of the fast growing fields in the food industry. Mannitol as GRAS (generally recognized as safe) is a functional food. Mannitol is about $70\%$ as sweet as sucrose and slowly and incompletely absorbed from the intestine, suppling only about one-half energy value of glucose. Commercially, the mannitol is synthesized by catalytic or electrochemical reduction of glucose. However, as strong demand for natural products increased, biological techniques have been developed for mannitol production. The object of this study was to determine the optimum conditions of mannitol fermentation by Leuconostoc mesenteroides sp. strain JFY isolated from fermented vegetables. The processes parameters such as pH, temperature, yeast extract concentration, and fructose concentration were optimized. The chosen ranges were 4.5 to 7.5 for pH, 22 to $34^{\circ}C$ for temperature, 0.05 to $2.0\%$ for yeast extract. and 5 to 350 g/L for fructose. The mineral medium used consisted of 3.0g $KH_2PO_4,\;0.01g\;FeSO_4{\cdot}H_2O,\;0.01g\;MnSO_4{\cdot}4H_2O,\;0.2g\; MgSO_4{\cdot}7H_2O,\;0.01g\;NaCl,\;and\;0.05g\;CaCl_2$ per 1 liter of deionized water. The optimum values of pH, temperature, yeast extract, and fructose concentration were obtained at about pH 6.5, temperature $28^{\circ}C$, yeast extract $0.5\%$ and fructose 30g/L. At optimum condition, the production of mannitol amounted to 31.6g/l. We hope that these findings are of particular importance for industrial application of mannitol production.

Luteinizing hormone beta gene polymorphism and its effect on semen quality traits and luteinizing hormone concentrations in Murrah buffalo bulls

  • Reen, Jagish Kour;Kerekoppa, Ramesha;Deginal, Revanasiddu;Ahirwar, Maneesh Kumar;Kannegundla, Uday;Chandra, Satish;Palat, Divya;Das, Dayal Nitai;Kataktalware, Mukund Amritrao;Jeyakumar, Sakthivel;Isloor, Shri krishna
    • Asian-Australasian Journal of Animal Sciences
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    • v.31 no.8
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    • pp.1119-1126
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    • 2018
  • Objective: Present investigation was aimed to study the Single Nucleotide Variants of the luteinizing hormone beta ($LH{\beta}$) gene and to analyze their association with the semen quality (fresh and post-thawed frozen semen) and luteinizing hormone (LH) concentrations in Murrah buffalo bulls. Methods: Polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) and Sanger sequencing method is used to study genetic variability in $LH{\beta}$ gene. LH assay was carried out using enzyme-linked immunosorbent assay method. A fixed general linear model was used to analyze association of single nucleotide polymorphism (SNP) of $LH{\beta}$ gene with semen quality in 109 and LH concentrations in 80 Murrah bulls. Results: $LH{\beta}$ gene was found to be polymorphic. Total six SNPs were identified in $LH{\beta}$ gene g C356090A, g C356113T, g A356701G, g G355869A, g G356330C, and g G356606T. Single Stranded Conformational Polymorphism variants of pattern 2 of exon 1+pattern 2 of exon 2+pattern 1 of exon 3 had highly significant (p<0.01) effect on sperm concentration (million/mL), percent mass motility, acrosome integrity and membrane integrity in fresh and frozen semen whereas significant (p<0.05) effect was observed on percent live spermatozoa. SSCP variants of pattern 2 of exon 1+pattern 2 of exon 2+pattern 1 of exon 3 had highly significant (p<0.01) effect on luteinizing hormone concentrations too. Conclusion: The observed association between SSCP variants of $LH{\beta}$ gene with semen quality parameters and LH concentrations indicated the possibilities of using $LH{\beta}$ as a candidate gene for identification of markers for semen quality traits and LH concentrations in Murrah buffaloes.