• Title, Summary, Keyword: Genes

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RFLP Analysis of cry1 and cry2 Genes of Bacillus thuringiensis Isolates from India

  • Patel, Ketan D.;Ingle, Sanjay S.
    • Journal of Microbiology and Biotechnology
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    • v.22 no.6
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    • pp.729-735
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    • 2012
  • The PCR-RFLP method has been useful for detection of known genes and identification of novel genes. In the present study, degenerate primers were designed from five groups of cry1 genes for PCR-RFLP analysis. Bacillus thuringiensis (Bt) isolates from different regions were evaluated for PCR amplification of various cry1 genes using newly designed primers and cry2 genes using reported primers. PCR analysis showed an abundance of cry1A genes and especially cry1Ac genes in isolates from all regions. RFLP analysis revealed the presence of multiple cry1A genes in isolates from central and southern regions. Unique digestion patterns of cry1A genes were observed in isolates from each region. Few of the isolates represented a digestion pattern of cry1A genes that did match to any of the known cry1A genes. RFLP analysis suggested an abundance of cry2Ab along with a novel cry2 gene in Bt isolates from different regions of India. Sequence analysis of the novel cry2 gene revealed 95% sequence identity to cry2Ab and cry2Ah genes. Phylogenetic analysis revealed that the novel cry2 gene could have diverged earlier than the other cry2 genes. Our results encourage finding of more diverse cry2 genes in Bt isolates. Rarefaction analysis was used to compare cry1A gene diversity in isolates from different soil types. It showed a higher degree of cry1A gene diversity in isolates from central region. In the present study, we propose the use of novel degenerate primers for cry1 genes and the PCR-RFLP method using a single enzyme to distinguish multiple cry1A and cry2 genes as well as identify novel genes.

Alteration of chromosomal structure within .betha.-Tubulin and flagellar calmodulin genes during differentiation of naegleria gruberi amebae into flagellates

  • Bok, Jin-Woong;Lee, Joo-Hun
    • Journal of Microbiology
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    • v.33 no.3
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    • pp.222-227
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    • 1995
  • We have examined DNase I sensitivity of .betha.-tubulin and flagellar calmodulin genes which are transiently and coordinately activated differentiation of Naegleria gruberi amebae into flagellates. The DNase I sensitivity of .betha.-tubulin and flagellar calmodulin genes changed in parallel with the changes in transcriptional activity of the respective genes during differentiation. The two genes were resistant to DNase I inamebae stage when transcription of the two genes was inactive. Forthy minutes after initiation of differentiation, when the two genes were most actively being transcribed, the two genes showed the highest sensitsivity to DNase I. One hundred and twenty minutes after initiation, the differentiation was completed and transcriptional activity of the two genes decreased to a low level. At this stage, the two genes were resistant to DNase I treatment like the ones at the amebae stage. This change in the DNase I sensitivity of the two genes was not observed when transcription of the two genes was blocked by adding cycloheximide at the beginning of differentiation.

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Molecular Characterization of Plant Genes (식물 유전자의 구조와 특성)

  • 이종섭
    • Proceedings of the Botanical Society of Korea Conference
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    • pp.19-49
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    • 1987
  • Recent development of recombinant DNA techniques such as gene cloning and DNA sequencing has led to understanding of genetic information coded on plant genes and their application to crop improvements. Nuclear genes so far isolated and characterized at the molecular level from various plants are those involved mainly in photosynthesis, nitrogen fixation, seed development and defensive responses to environmental stresses. Most of plant genes contain intervening sequences (introns) flanked with GT and AG, as it typical of animal genes. The 5' flanking regions of plant gene revealed the presence of promoter elements such as TATAAA and CCAAT, which have been identified at animal genes to be involved in transcrip- tion initiation. The 3' untranslated regions include a sequence similar to AATAAA whcih functions as a polyadenylation signal in other eukaryotic genes. Furthermore, enhancer-type sequences were found at the 5' flanking regions of various plant genes. This indicates that the structure of plant genes is very similar to animal genes and mechanisms governing the synthesis and processing of mRNAs may be identical in higher eukaryotes. However, genes expression studies involving transformation revealed their differ ences within plants and between plant and animal systems.

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Classification and Expression Profiling of Putative R2R3 MYB Genes in Rice

  • Kim, Bong-Gyu;Ko, Jae-Hyung;Min, Shin-Young;Ahn, Joong-Hoon
    • Journal of Applied Biological Chemistry
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    • v.48 no.3
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    • pp.127-132
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    • 2005
  • MYB genes, comprising group of related genes found in animal, plant, and fungal genomes, encode common DNA-binding domains composed of one to four repeat motifs. MYB genes containing two repeats (R2R3) constitute largest MYB gene family in plants. R2R3 MYB genes play important roles in regulation of secondary metabolism, control of cell shape, disease resistance, and hormone response. Eight-four R2R3 MYB genes were retrieved from rice genome for functional characterization of MYB genes. Analysis of MYB domains revealed each MYB domain contains three ${\alpha}$-helices with regularly spaced tryptophan residues. R2R3 MYB genes were divided into four subfamilies based on phylogenic analysis result. Real-time PCR analysis of 34 MYB genes revealed 12 MYB genes were highly expressed in seeds than in leaves, whereas 4 genes were highly expressed in leaves.

Identification and Characterization of Human Genes Targeted by Natural Selection

  • Ryu, Ha-Jung;Kim, Young-Joo;Park, Young-Kyu;Kim, Jae-Jung;Park, Mi-Young;Seo, Eul-Ju;Yoo, Han-Wook;Park, In-Sook;Oh, Berm-Seok;Lee, Jong-Keuk
    • Genomics & Informatics
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    • v.6 no.4
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    • pp.173-180
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    • 2008
  • The human genome has evolved as a consequence of evolutionary forces, such as natural selection. In this study, we investigated natural selection on the human genes by comparing the numbers of nonsynonymous (NS) and synonymous (S) mutations in individual genes. We initially collected all coding SNP data of all human genes from the public dbSNP. Among the human genes, we selected 3 different selection groups of genes: positively selected genes (NS/S${\geq}$3), negatively selected genes (NS/S${\leq}$1/3) and neutral selection genes (0.9

Genes expression monitoring using cDNA microarray: Protocol and Application

  • Muramatsu Masa-aki
    • Proceedings of the Korean Society of Toxicology Conference
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    • pp.31-41
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    • 2000
  • The major issue in the post genome sequencing era is determination of gene expression patterns in variety of biological systems. A microarray system is a powerful technology for analyzing the expression profile of thousands of genes at one experiment. In this study, we constructed cDNA microarray which carries 2,304 cDNAS derived from oligo-capped mouse cDNA library. Using this hand-made microarray we determined gene expression in various biological systems. To determine tissue specific genes, we compared Nine genes were highly-expressed in adult mouse brain compared to kidney, liver, and skeletal muscle. Tissue distribution analysis using DNA microarray extracted 9 genes that were predominantly expressed in the brain. A database search showed that five of the 9 genes, MBP, SC1, HiAT3, S100 protein-beta, and SNAP25, were previously known to be expressed at high level in the brain and in the nervous system. One gene was highly sequence similar to rat S-Rex-s/human NSP-C, suggesting that the gene is a mouse homologue. The remaining three genes did not match to known genes in the GenBank/EMBL database, indicating that these are novel genes highly-expressed in the brain. Our DNA microarray was also used to detect differentiation specific genes, hormone dependent genes, and transcription-factor-induced genes. We conclude that DNA microarray is an excellent tool for identifying differentially expressed genes.

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Identification of Novel Universal Housekeeping Genes by Statistical Analysis of Microarray Data

  • Lee, Se-Ram;Jo, Min-Joung;Lee, Jung-Eun;Koh, Sang-Seok;Kim, So-Youn
    • BMB Reports
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    • v.40 no.2
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    • pp.226-231
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    • 2007
  • Housekeeping genes are widely used as internal controls in a variety of study types, including real time RT-PCR, microarrays, Northern analysis and RNase protection assays. However, even commonly used housekeeping genes may vary in stability depending on the cell type or disease being studied. Thus, it is necessary to identify additional housekeeping-type genes that show sample-independent stability. Here, we used statistical analysis to examine a large human microarray database, seeking genes that were stably expressed in various tissues, disease states and cell lines. We further selected genes that were expressed at different levels, because reference and target genes should be present in similar copy numbers to achieve reliable quantitative results. Real time RT-PCR amplification of three newly identified reference genes, CGI-119, CTBP1 and GOLGAl, alongside three well-known housekeeping genes, B2M, GAPD, and TUBB, confirmed that the newly identified genes were more stably expressed in individual samples with similar ranges. These results collectively suggest that statistical analysis of microarray data can be used to identify new candidate housekeeping genes showing consistent expression across tissues and diseases. Our analysis identified three novel candidate housekeeping genes (CGI-119, GOLGA1, and CTBP1) that could prove useful for normalization across a variety of RNA-based techniques.

Differential Gene Expression in the Pathogenic Strains of Actinobacillus pleuropneumoniae Serotypes 1 and 3

  • Xie, Fang;Zhang, Mingjun;Li, Shuqing;Du, Chongtao;Sun, Changjiang;Han, Wenyu;Zhou, Liang;Lei, Liancheng
    • Journal of Microbiology and Biotechnology
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    • v.20 no.4
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    • pp.789-797
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    • 2010
  • The limited information on differential gene expression in the different serotypes of Actinobacillus pleuropneumoniae has significantly hampered the research on the pathogenic mechanisms of this organism and the development of multivalent vaccines against A. pleuropneumoniae infection. To compare the gene expressions in the A. pleuropneumoniae strains CVCC259 (serotype 1) and CVCC261 (serotype 3), we screened the differentially expressed genes in the two strains by performing representational difference analysis (RDA). Northern blot analyses were used to confirm the results of RDA. We identified 22 differentially expressed genes in the CVCC259 strain and 20 differentially expressed genes in the CVCC261 strain, and these genes were classified into 11 groups: (1) genes encoding APX toxins; (2) genes encoding transferrin-binding protein; (3) genes involved in lipopolysaccharide (LPS) biosynthesis; (4) genes encoding autotransporter adhesin; (5) genes involved in metabolism; (6) genes involved in the ATP-binding cassette (ABC) transporter system; (7) genes encoding molecular chaperones; (8) genes involved in bacterial transcription and nucleic acid metabolism; (9) a gene encoding protease; (10) genes encoding lipoprotein/membrane protein; and (11) genes encoding various hypothetical proteins. This is the first report on the systematic application of RDA for the analysis of differential gene expression in A. pleuropneumoniae serotypes 1 and 3. The determination of these differentially expressed genes will serve as an indicator for future research on the pathogenic mechanisms of A. pleuropneumoniae and the development of a multivalent vaccine against A. pleuropneumoniae infection.

Screening of Essential Genes in Staphylococcus aureus N315 Using Comparative Genomics and Allelic Replacement Mutagenesis

  • Ko Kwan-Soo;Lee Ji-Young;Song Jae-Hoon;Baek Jin-Yang;Oh Won-Sup;Chun Jong-Sik;Yoon Ha-Sik
    • Journal of Microbiology and Biotechnology
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    • v.16 no.4
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    • pp.623-632
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    • 2006
  • To find potential targets of novel antimicrobial agents, we identified essential genes of Staphylococcus aureus N315 by using comparative genomics and allele replacement mutagenesis. By comparing the genome of S. aureus N315 with those of Bacillus subtilis, Enterococcus faecalis, Escherichia coli, Pseudomonas aeruginosa, and Streptococcus pneumoniae, a total of 481 candidate target genes with similar amino acid sequences with at least three other species by >40% sequence identity were selected. of 481 disrupted candidate genes, 122 genes were identified as essential genes for growth of S. aureus N315. Of these, 51 essential genes were those not identified in any bacterial species, and 24 genes encode proteins of unknown function. Seventeen genes were determined as non-essential although they were identified as essential genes in other strain of S. aureus and other species. We found no significant difference among essential genes between Streptococcus pneumoniae and S. aureus with regard to cellular function.

Screening of Specific Genes Expressed in the Swine Tissues and Development of a Functional cDNA Chip

  • Kim, Chul Wook;Chang, Kyu Tae;Hong, Yeon Hee;Kwon, Eun Jung;Jung, Won Yong;Cho, Kwang Keun;Chung, Ki Hwa;Kim, Byeong Woo;Lee, Jung Gyu;Yeo, Jung-Sou;Kang, Yang Su;Joo, Young Kuk
    • Asian-Australasian Journal of Animal Sciences
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    • v.18 no.7
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    • pp.933-941
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    • 2005
  • To develop a functional cDNA chip, specific genes expressed in the tissues of swine Kagoshima Berkshire were screened. A total of 4,434 ESTs were obtained by constructing a cDNA library from total RNA isolated from the muscle and fat tissues, affirming their functions by investigating similarity of nucleotide sequences with the database at the NCBI. Among them, 1,230 ESTs were confirmed as novel genes, which, to date, have not been identified. Attaching the genes to a cDNA microarray slide revealed expression patterns of genes in muscle and fat according to the growth stages of swine. As specific genes expressed in the muscle tissues of swine with body weight of 30 kg, 60 genes including actin, myosin, tropomysin, transfer RNA-trp synthetase, Kel-like protein 23, KIAA0182 and COI, Foocen-m, etc were obtained. In addition, 18 novel genes were obtained. As specific genes expressed in fat tissues of swine with body weight of 30 kg, 47 genes including annexin II, Collagen, Fibronectin, Pleckstrin homology domain, serine protease, etc were obtained. 21 novel genes were also obtained. The genes specifically expressed in the muscle and fat tissues of swine affect contraction and relaxation of the muscle and the fat. However, studies on the expression mechanisms of the genes are insufficient. To reveal species of structural genes in swine muscle and fat tissue, interrelation studies in expression and function of genes by using the cDNA chip should be conducted.