• Title, Summary, Keyword: Phenotype

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Amino acid substitutions conferring cold-sensitive phenotype on the yeast MTF1 gene

  • Jang, Sei-Heon
    • Journal of Microbiology
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    • v.35 no.3
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    • pp.228-233
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    • 1997
  • The MTF1 gene of Saccharomyces cerevisiae encodes a 43 kDa MITOCHONDRIAL RNA polymerase specificity factor which recognizes mitochondrial promoters to initiate correct transcription. To better understand structure-function of the MTF1 gene as well as the transcription mechanism of mitochondrial RNA polymerase, two cold-sensitive alleles of the MTF1 mutation were isolated by plasmid shuffling method after PCR-based random mutagenesis of the MTF1 gene. The mutation sites were analyzed by nucleotide sequencing. These cs phenotype mtf1 mutants were respiration competent on the nonfermentible glycerol medium at the permissive temperature, but incompetent at 13.deg.C. The cs phenotype allele of the MTF1, yJH147, encoded an L146P replacement. The other cs allele, yJH148, contained K179E and K214M double replacements. Mutations in both alleles were in a region of Mtflp which is located between domains with amino acid sequence similarities to conserved regions 2 and 3 of bacterial s factors.

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KRDD: Korean Rice Ds-tagging Lines Database for Rice (Oryza sativa L. Dongjin)

  • Kim, Chang-Kug;Lee, Myung-Chul;Ahn, Byung-Ohg;Yun, Doh-Won;Yoon, Ung-Han;Suh, Seok-Cheol;Eun, Moo-Young;Hahn, Jang-Ho
    • Genomics & Informatics
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    • v.6 no.2
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    • pp.64-67
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    • 2008
  • The Korean Rice Ds-tagging lines Database (KRDD) is designed to provide information about Ac/Ds insertion lines and activation tagging lines using japonica rice. This database has provided information on 18,158 Ds lines, which includes the ID, description, photo image, sequence information, and gene characteristics. The KRDD is visualized using a web-based graphical view, and anonymous users can query and browse the data using the search function. It has four major menus of web pages: (i) a Blast Search menu of a mutant line; Blast from rice Ds-tagging mutant lines; (ii) a primer design tool to identify genotypes of Ds insertion lines; (iii) a Phenotype menu for Ds lines, searching by identification name and phenotype characteristics; and (iv) a Management menu for Ds lines.

Allelic Frequencies of 20 Visible Phenotype Variants in the Korean Population

  • Lim, Ji Eun;Oh, Bermseok
    • Genomics & Informatics
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    • v.11 no.2
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    • pp.93-96
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    • 2013
  • The prediction of externally visible characteristics from DNA has been studied for forensic genetics over the last few years. Externally visible characteristics include hair, skin, and eye color, height, and facial morphology, which have high heritability. Recent studies using genome-wide association analysis have identified genes and variations that correlate with human visible phenotypes and developed phenotype prediction programs. However, most prediction models were constructed and validated based on genotype and phenotype information on Europeans. Therefore, we need to validate prediction models in diverse ethnic populations. In this study, we selected potentially useful variations for forensic science that are associated with hair and eye color, iris pattern, and facial morphology, based on previous studies, and analyzed their frequencies in 1,920 Koreans. Among 20 single nucleotide polymorphisms (SNPs), 10 SNPs were polymorphic, 6 SNPs were very rare (minor allele frequency < 0.005), and 4 SNPs were monomorphic in the Korean population. Even though the usability of these SNPs should be verified by an association study in Koreans, this study provides 10 potential SNP markers for forensic science for externally visible characteristics in the Korean population.

WTO, an ontology for wheat traits and phenotypes in scientific publications

  • Nedellec, Claire;Ibanescu, Liliana;Bossy, Robert;Sourdille, Pierre
    • Genomics & Informatics
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    • v.18 no.2
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    • pp.14.1-14.11
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    • 2020
  • Phenotyping is a major issue for wheat agriculture to meet the challenges of adaptation of wheat varieties to climate change and chemical input reduction in crop. The need to improve the reuse of observations and experimental data has led to the creation of reference ontologies to standardize descriptions of phenotypes and to facilitate their comparison. The scientific literature is largely under-exploited, although extremely rich in phenotype descriptions associated with cultivars and genetic information. In this paper we propose the Wheat Trait Ontology (WTO) that is suitable for the extraction and management of scientific information from scientific papers, and its combination with data from genomic and experimental databases. We describe the principles of WTO construction and show examples of WTO use for the extraction and management of phenotype descriptions obtained from scientific documents.

Regulation of vascular smooth muscle phenotype by cross-regulation of krüppel-like factors

  • Ha, Jung Min;Yun, Sung Ji;Jin, Seo Yeon;Lee, Hye Sun;Kim, Sun Ja;Shin, Hwa Kyoung;Bae, Sun Sik
    • The Korean Journal of Physiology and Pharmacology
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    • v.21 no.1
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    • pp.37-44
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    • 2017
  • Regulation of vascular smooth muscle cell (VSMC) phenotype plays an essential role in many cardiovascular diseases. In the present study, we provide evidence that $kr{\ddot{u}}ppel$-like factor 8 (KLF8) is essential for tumor necrosis factor ${\alpha}$ ($TNF{\alpha}$)-induced phenotypic conversion of VSMC obtained from thoracic aorta from 4-week-old SD rats. Stimulation of the contractile phenotype of VSMCs with $TNF{\alpha}$ significantly reduced the VSMC marker gene expression and KLF8. The gene expression of KLF8 was blocked by $TNF{\alpha}$ stimulation in an ERK-dependent manner. The promoter region of KLF8 contained putative Sp1, KLF4, and $NF{\kappa}B$ binding sites. Myocardin significantly enhanced the promoter activity of KLF4 and KLF8. The ectopic expression of KLF4 strongly enhanced the promoter activity of KLF8. Moreover, silencing of Akt1 significantly attenuated the promoter activity of KLF8; conversely, the overexpression of Akt1 significantly enhanced the promoter activity of KLF8. The promoter activity of SMA, $SM22{\alpha}$, and KLF8 was significantly elevated in the contractile phenotype of VSMCs. The ectopic expression of KLF8 markedly enhanced the expression of SMA and $SM22{\alpha}$ concomitant with morphological changes. The overexpression of KLF8 stimulated the promoter activity of SMA. Stimulation of VSMCs with $TNF{\alpha}$ enhanced the expression of KLF5, and the promoter activity of KLF5 was markedly suppressed by KLF8 ectopic expression. Finally, the overexpression of KLF5 suppressed the promoter activity of SMA and $SM22{\alpha}$, thereby reduced the contractility in response to the stimulation of angiotensin II. These results suggest that cross-regulation of KLF family of transcription factors plays an essential role in the VSMC phenotype.

Correlation between Karyotype and Phenotype in Turner Syndrome (터너증후군의 핵형과 표현형간의 연관성)

  • Shim, Ye-Jee;Hwang, Young-Ju;Lee, Kun-Soo
    • Journal of Genetic Medicine
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    • v.6 no.1
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    • pp.67-73
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    • 2009
  • Purpose : In spite of the karyotype and phenotype diversity in Turner syndrome patients, there are few reports about such differences in Korea. We reviewed the data of chromosome abnormalities, clinical manifestations, and comorbidities of Turner syndrome patients in Kyungpook National University Hospital to compare them to the recent hypotheses about sex chromosome gene loci related to Turner symptoms. Materials and Methods : We identified the cytologic findings of 92 patients with Turner syndrome and the clinical findings of 62 patients among them. Results : 54.3 percent of patients had 45,X while 45.7 percent showed other karyotype combinations (45,X/46,XX, 45,X/46,XX/47,XXX, 46,X,del(Xp), 46,X,del(Xq), 45,X/46,X,del(Xq), 46,X,i(Xq), 45,X/46,X,i (Xq)). The Turner symptoms found included short neck, high arched palate, broad chest, Madelung deformity, short metacarpals, scoliosis, cubitus valgus, low hair line, webbed neck, edematous extremities, pigmented nevus, and sexual infantilism. The specific diseases associated Turner syndrome included renal abnormalities, congenital heart disease, hearing defects, diabetes mellitus, hyperlipidemia, and decreased bone density. The phenotype of the mosaicism group was milder than that of the monosomy group. In the case of 46,X,del(Xp) and 45,X/46,X,del(Xq) groups, all had skeletal abnormalities, but the 46,X,del(Xq) group had none. In the case of 46,X,del(Xp) group, all showed short statures and skeletal abnormalities, but no sexual infantilism was observed. In the case of 46,X,i(Xq) and 45,X/46,X,i(Xq) groups, they all showed delayed puberty and had primary amenorrhea. Conclusion : It is important to study karyotype-phenotype correlations in patients with Turner syndrome to obtain interesting information about the genotype-phenotype correlations related to the X chromosome.

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TGF-$\beta$ INDUCES INVASIVE PHENOTYPE OF MCF10A HUMAN BREAST EPITHELIAL CELLS

  • Kim, Mi-Sung;Aree Moon
    • Proceedings of the Korean Society of Toxicology Conference
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    • pp.141-141
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    • 2002
  • Transforming growth factor-${\beta}$ (TGF-${\beta}$), a hormonally active polypeptide found in normal and transformed tissues, regulates cellular growth and phenotyphic plasticity. We have previously shown that H-ras, but not N-ras, induces invasive phenotype in MCF10A human breast epithelial cells.(omitted)

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Roles of Phosphatidylinositol 3-Kinase(PI3K) and Rac1

  • Shin, Il-Chung;Kim, Seon-Hoe;Moon, A-Ree
    • Proceedings of the PSK Conference
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    • pp.223.1-223
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    • 2003
  • Many studies have identified the phosphatidylinositol 3-kinase (PI3K) as a key regulator for various cellular functions including cell survival, growth and motility. We have previously shown that H-ras, but not N-ras. induces invasiveness and motility in human breast epithelial cells (MCF10A), while both H-ras and N-ras induce transformed phenotype. In the present study, we wished to investigate the functional role of PI3K pathway in H-ra-induced invasive phenotype and motility of MCF10A cells. (omitted)

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Dermatomyositis sine dermatitis, a rare phenotype of idiopathic inflammatory myopathy

  • Park, Jin-Sung;Park, Ji-Young
    • Yeungnam University Journal of Medicine
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    • v.34 no.1
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    • pp.137-139
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    • 2017
  • Dermatomyositis (DM) is characterized by progressive proximal limb weakness and typical skin manifestations. The histological findings that show perifascicular atrophy and deposition of membrane attack complex are pathognomic features of DM. Dermatomyositis is categorized into classical DM and non-classical DM, which includes amyopathic DM and DM sine dermatitis. DM sine dermatitis is seldom described because of its rarity, making the diagnosis more challenging. We report a case of DM sine dermatitis, a rare phenotype of DM.

Simulation study on the estimation of multinomial proportions

  • Kim, Dae-Hak
    • Journal of the Korean Data and Information Science Society
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    • v.23 no.2
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    • pp.411-417
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    • 2012
  • In this paper, we consider the estimation of multinomial proportions. Multinomial distribution is the most important multivaritate distribution. Estimation of multinomial parameters for multinomial distribution is widely applicable to many practical research areas including genetics. We investigated the properties of several frequency substitution estimates and derived the maximum likelihood estimate of multinomial proportions of Hardy Weinberg proportions. Phenotype and genotype frequencies of allele are used to the estimation of multinomial proportions. These estimates are then analyzed via numerical data. Small sample Monte Carlo simulation is conducted to compare considered estimates of multinomial proportions.