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Journal articles on the topic 'Gene fragment'

Author: Grafiati

Published: 28 May 2022

Last updated: 30 July 2025

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1

Lindley, Helen K., V. Jayne Deeble, Ursula Peschke, Mary O'Neill, Simon Baumberg, and Jonathan Cove. "Dependence on reporter gene of apparent activity in gene fusions of a Streptomyces griseus streptomycin biosynthesis promoter." Canadian Journal of Microbiology 41, no. 4-5 (1995): 407–17. http://dx.doi.org/10.1139/m95-054.

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The adjacent genes strR–strA–strB1 lie within the large cluster of genes of streptomycin biosynthesis and resistance in Streptomyces griseus. sirR encodes a pathway-specific activator StrR, suggested by previous work to be either an antiterminator or a conventional activator, binding to its DNA target via a helix-turn-helix motif. strB1 is transcribed in an StrR-dependent fashion from a promoter (PstrB1) that lies downstream from strA; between PstrB1 and sirB1 there is a 300-bp leader region containing numerous inverted repeats that could represent modulatable transcription termination sites.

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2

Sumie, Akihiro, Tetsu Yamashiro, Kazutoshi Nakashima, Masaru Nasu, Makoto Watanabe, and Akira Nishizono. "Comparison of Genomic Structures and Antigenic Reactivities of Orthologous 29-Kilodalton Outer Membrane Proteins ofHelicobacter pylori." Infection and Immunity 69, no. 11 (2001): 6846–52. http://dx.doi.org/10.1128/iai.69.11.6846-6852.2001.

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ABSTRACT We purified a 29-kDa Helicobacter pylori outer membrane protein (Omp29 protein) and cloned the gene encoding the protein from H. pylori strain ATCC 43504. The Omp29 gene corresponded to the reported JHP73 and the HP78–79 genes of H. pylori strains. A corresponding nucleotide fragment was detected in all 150 tested H. pylori clinical isolates by PCR or Southern blotting. The amplified Omp29-corresponding fragments were categorized into a ca. 770-bp-long group and a larger-fragment group. Sequence analysis indicated that the larger fragments were likely synthesized from the 770-bp fragm

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3

Barlow, J. W., L. E. Raggatt, C. C. Drinkwater, I. G. Lyons, and R. I. Richards. "Differential binding of thyroid hormone receptors to mouse glandular kallikrein gene promoters: evidence for multiple binding regions in the mGK-6 gene." Journal of Molecular Endocrinology 3, no. 2 (1989): 79–84. http://dx.doi.org/10.1677/jme.0.0030079.

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ABSTRACT We have used a DNA-cellulose competition assay to investigate the binding of thyroid hormone receptors to fragments of the mouse glandular kallikrein genes and the human and rat GH genes. Nuclear extracts from human lymphoblastoid IM-9 cells were incubated with [125I]tri-iodothyronine ([125I]T3) and DNA-cellulose. The ability of cloned gene fragments to compete for radiolabelled receptors bound to DNA-cellulose was compared with that of DNA from pBR322. As previously observed, a 900 bp fragment from the human GH gene showed preferential binding to the thyroid hormone receptor. High-af

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4

Inoue, Y., S. Kobayashi, K. Yoshikawa, LT Tran, and A. Kimura. "Lipid hydroperoxide‐resistance gene in Saccharomyces cerevisiae: utilization as a selectable marker gene for yeast transformation." Biotechnology and Applied Biochemistry 17, no. 3 (1993): 305–10. http://dx.doi.org/10.1111/j.1470-8744.1993.tb00246.x.

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Two kinds of DNA fragments concerned with resistance against lipid hydroperoxide were cloned from the yeast Saccharomyces cerevisiae. When the recombinant plasmid carrying the DNA fragment was introduced into the cells of S. cerevisiae which do not have an appropriate auxotrophic marker, the transformants could be selected by their resistance to t‐butyl hydroperoxide. By Southern hybridization analysis, such transformants were found to contain the recombinant plasmid, suggesting that the DNA fragment could be used as a selection marker for the transformation of S. cerevisiae.

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5

Messick, Joanne B., Geoffrey Smith, Linda Berent, and Sandra Cooper. "Genome size ofEperythrozoon suisand hybridization with 16S rRNA gene." Canadian Journal of Microbiology 46, no. 11 (2000): 1082–86. http://dx.doi.org/10.1139/w00-088.

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The genome size of Eperythrozoon suis, an unculturable haemotropic mycoplasma, was estimated using pulsed-field gel electrophoresis (PFGE). Gamma irradiation was used to introduce one (on the average) double-strand break in the E. suis Illinois chromosome. Restriction enzymes that cut infrequently were also used to analyze genome size. The size estimate for the full-length genome was 745 kilobases (kb), whereas the size estimates based on the summation of restriction fragments ranged from 730 to 770 kb. The 16S rRNA gene was located on the 120-kb MluI fragment, 128-kb NruI fragment, 25-kb SacI

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6

Djordjevic, G., B. Bojovic, N. Miladinov, and L. Topisirovic. "Cloning and molecular analysis of promoter-like sequences isolated from the chromosomal DNA ofLactobacillus acidophilusATCC 4356." Canadian Journal of Microbiology 43, no. 1 (1997): 61–69. http://dx.doi.org/10.1139/m97-009.

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Promoter-like sequences from the chromosomal DNA of thermophilic strain Lactobacillus acidophilus ATCC 4356 were cloned. Analysis of the three DNA fragments showing promoter activity, designated P3, P6, and P15, were performed in Lactobacillus reuteri, Lactococcus lactis, and E. coli. The reporter cat-86 gene was expressed in all three bacterial species under control of the fragments P3 and P6. Fragment P15 showed promoter activity only in Lactobacillus reuteri and E. coli but not in Lactococcus lactis. The three host-specific transcriptional start points (TSPs) were used when transcription of

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7

Li, Xiu-min, Xing-long Bai, and Guo-dong Ren. "A new species of the genus Blaptogonia from the Himalayas with four DNA markers (Coleoptera, Tenebrionidae, Blaptini)." ZooKeys 773 (July 9, 2018): 69–78. http://dx.doi.org/10.3897/zookeys.773.24656.

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A new species of the genus Blaptogonia Medvedev, 1998, B.zhentanga sp. n., is described from the southern Himalayas of China. Two fragments of mitochondrial protein-coding genes (COI, Cytb), one fragment of mitochondrial ribosomal RNA gene (16S), and one fragment of nuclear rRNA gene (28SD2) of the new species were obtained. A key to the known species of the genus is presented.

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8

Li, Xiu-Min, Xing-Long Bai, and Guo-Dong Ren. "A new species of the genus Blaptogonia from the Himalayas with four DNA markers (Coleoptera, Tenebrionidae, Blaptini)." ZooKeys 773 (July 9, 2018): 69–78. https://doi.org/10.3897/zookeys.773.24656.

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A new species of the genus Blaptogonia Medvedev, 1998, B. zhentanga sp. n., is described from the southern Himalayas of China. Two fragments of mitochondrial protein-coding genes (COI, Cytb), one fragment of mitochondrial ribosomal RNA gene (16S), and one fragment of nuclear rRNA gene (28SD2) of the new species were obtained. A key to the known species of the genus is presented.

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9

Shigematsu, Toru, Satoshi Hanada, Masahiro Eguchi, Yoichi Kamagata, Takahiro Kanagawa, and Ryuichiro Kurane. "Soluble Methane Monooxygenase Gene Clusters from Trichloroethylene-Degrading Methylomonas sp. Strains and Detection of Methanotrophs during In Situ Bioremediation." Applied and Environmental Microbiology 65, no. 12 (1999): 5198–206. http://dx.doi.org/10.1128/aem.65.12.5198-5206.1999.

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ABSTRACT The soluble MMO (sMMO) gene clusters from group I methanotrophs were characterized. An 8.1-kb KpnI fragment fromMethylomonas sp. strain KSWIII and a 7.5-kbSalI fragment from Methylomonas sp. strain KSPIII which contained the sMMO gene clusters were cloned and sequenced. The sequences of these two fragments were almost identical. The sMMO gene clusters in the fragment consisted of six open reading frames which were 52 to 79% similar to the corresponding genes of previously described sMMO gene clusters of the group II and group X methanotrophs. The phylogenetic analysis of the predicted

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10

Reid, L. H., E. G. Shesely, H. S. Kim, and O. Smithies. "Cotransformation and gene targeting in mouse embryonic stem cells." Molecular and Cellular Biology 11, no. 5 (1991): 2769–77. http://dx.doi.org/10.1128/mcb.11.5.2769-2777.1991.

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We have investigated cotransformation in mammalian cells and its potential for identifying cells that have been modified by gene targeting. Selectable genes on separate DNA fragments were simultaneously introduced into cells by coelectroporation. When the introduced fragments were scored for random integration, 75% of the transformed cells integrated both fragments within the genome of the same cell. When one of the cointroduced fragments was scored for integration at a specific locus by gene targeting, only 4% of the targeted cells cointegrated the second fragment. Apparently, cells that have

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11

Reid, L. H., E. G. Shesely, H. S. Kim, and O. Smithies. "Cotransformation and gene targeting in mouse embryonic stem cells." Molecular and Cellular Biology 11, no. 5 (1991): 2769–77. http://dx.doi.org/10.1128/mcb.11.5.2769.

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We have investigated cotransformation in mammalian cells and its potential for identifying cells that have been modified by gene targeting. Selectable genes on separate DNA fragments were simultaneously introduced into cells by coelectroporation. When the introduced fragments were scored for random integration, 75% of the transformed cells integrated both fragments within the genome of the same cell. When one of the cointroduced fragments was scored for integration at a specific locus by gene targeting, only 4% of the targeted cells cointegrated the second fragment. Apparently, cells that have

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12

He, Huoguang, Bin Wu, Min Xiong, Yang Li, Wenhua Wu, and Xingguo Wang. "Gene cloning, structural gene and promoter identification, and active assay of the phosphatidylcholine synthase of Pseudomonas sp. strain 593." Canadian Journal of Microbiology 57, no. 10 (2011): 785–94. http://dx.doi.org/10.1139/w11-073.

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Pseudomonas sp. strain 593, a soil bacterium, is able to use exogenous choline to synthesize phosphatidylcholine via phosphatidylcholine synthase (Pcs). A 2020 bp DNA fragment that hybridized to a Pcs probe was cloned. This fragment contained a large open reading frame (ORF) with two potential ATG start sites that would encode for 293 and 231 amino acid proteins. Fragments containing the two ORFs encoded Pcs when they were inserted into the expression vector pET23a and expressed under the control of the T7 promoter in Escherichia coli BL21(DE3) pLysS. However, when the two ORFs were inserted i

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13

Vohra, Vikas, Tarun Kumar Bhattacharya, Shanker Dayal, Pushpendra Kumar, and Arjava Sharma. "Genetic variants of beta-lactoglobulin gene and its association with milk composition traits in riverine buffalo." Journal of Dairy Research 73, no. 4 (2006): 499–503. http://dx.doi.org/10.1017/s0022029906002044.

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A study was carried out to determine genetic variants of β-lactoglobulin gene and to explore associations between these and milk composition traits in riverine buffalo. Single strand conformation polymorphism was employed to detect the genetic variants of the gene. Two fragments of this gene i.e. 119 bp of exon I and 400 bp spanning exon IV and intron IV were included in the study. For 119 bp fragment, three alleles namely, A, B and C were observed in all the buffalo breeds whereas four alleles (A, B, C and D) were detected for 400 bp fragment. The frequency distribution of alleles was differe

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14

Zhao, Qiao-Ling, Xing-Jia Shen, Liang-Jun Zhu, et al. "Characterization of CIb1 Gene Promoter from Silkworm, Bombyx mori." Zeitschrift für Naturforschung C 62, no. 11-12 (2007): 875–80. http://dx.doi.org/10.1515/znc-2007-11-1216.

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The hemolymph chymotrypsin inhibitor b1 (CIb1) of silkworm, Bombyx mori, plays an important role in innate immunity. In order to study its encoding gene CIb1, five heterogeneous promoter fragments of 844 bp, 682 bp, 516 bp, 312 bp and 82 bp in length were cloned from genomic DNA of the p50 silkworm strain. Characterization of the CIb1 promoter was performed in vitro using the firefly luciferase gene as reporter. The results showed that CIb1 promoter fragments have transcription activities in the B. mori ovary-derived BmN cell line. The 82 bp fragment (-72 to +10 nt) containing the eukaryotic c

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15

Raharjo, Tri Joko, Rosyida Azis Rizki, Stalis Norma Ethica, Elly Rustanti, and L. Hartanto Nugroho. "CHARACTERIZATION OF 0.58 kb DNA STILBENE SYNTHASE ENCODING GENE FRAGMENT FROM MELINJO PLANT (Gnetum gnemon)." Indonesian Journal of Chemistry 11, no. 3 (2011): 246–52. http://dx.doi.org/10.22146/ijc.21388.

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Resveratrol is a potent anticancer agent resulted as the main product of enzymatic reaction between common precursor in plants and Stilbene Synthase enzyme, which is expressed by sts gene. Characterization of internal fragment of Stilbene Synthase (STS) encoding gene from melinjo plant (Gnetum gnemon L.) has been carried out as part of a larger work to obtain a full length of Stilbene Synthase encoding gene of the plant. RT-PCR (Reverse Transcriptase Polymerase Chain Reaction) was performed using two degenerated primers to amplify the gene fragment. Ten published STS conserved amino acid seque

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16

Webb, G. C., and D. D. Chaplin. "Genetic variability at the human tumor necrosis factor loci." Journal of Immunology 145, no. 4 (1990): 1278–85. http://dx.doi.org/10.4049/jimmunol.145.4.1278.

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Abstract Variability in the structure of the human tumor necrosis factor (TNF-alpha) or lymphotoxin (TNF-beta) genes may contribute to the functional polymorphism of the HLA gene complex. We have characterized an allelic restriction fragment length polymorphism (RFLP) of the TNF-beta gene by using the restriction endonuclease NcoI. Digestion of genomic DNA with NcoI and Southern blotting by using TNF-alpha gene probes show 5.4-kb and 10.5-kb hybridizing fragments. In Caucasian populations, the 10.5-kb fragment is present in 64 to 72% of haplotypes. The polymorphic NcoI site is located within t

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17

Lamb, P., and L. Crawford. "Characterization of the human p53 gene." Molecular and Cellular Biology 6, no. 5 (1986): 1379–85. http://dx.doi.org/10.1128/mcb.6.5.1379-1385.1986.

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Cosmid and lambda clones containing the human p53 gene were isolated and characterized in detail. The gene is 20 kilobases (kb) long and has 11 exons, the first and second exons being separated by an intron of 10 kb. Restriction fragments upstream of sequences known to be within the first identified exon were tested for promoter activity by cloning them in front of the chloramphenicol acetyltransferase gene and transfecting the resulting constructs into HeLa cells. A 0.35-kb DNA fragment was identified that had promoter activity. Results of primer extension experiments indicated that the mRNA

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18

Lamb, P., and L. Crawford. "Characterization of the human p53 gene." Molecular and Cellular Biology 6, no. 5 (1986): 1379–85. http://dx.doi.org/10.1128/mcb.6.5.1379.

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Cosmid and lambda clones containing the human p53 gene were isolated and characterized in detail. The gene is 20 kilobases (kb) long and has 11 exons, the first and second exons being separated by an intron of 10 kb. Restriction fragments upstream of sequences known to be within the first identified exon were tested for promoter activity by cloning them in front of the chloramphenicol acetyltransferase gene and transfecting the resulting constructs into HeLa cells. A 0.35-kb DNA fragment was identified that had promoter activity. Results of primer extension experiments indicated that the mRNA

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19

Solís-Hernández, Wendy, and Eric-J. Fuchs. "Effective gene flow patterns across a fragmented landscape in southern Costa Rica for Symphonia globulifera (Clusiaceae); a species with mobile seed and pollen dispersers." Revista de Biología Tropical 67, no. 2SUPL (2019): S95—S111. http://dx.doi.org/10.15517/rbt.v67i2supl.37209.

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In tropical trees, forest fragmentation has been shown to affect mating and gene flow patterns. Mobile dispersal vectors should be less sensitive to fragmented landscapes and may ameliorate the genetic effects of forest fragmentation on plant populations. To test this hypothesis, we analyzed gene flow patterns in Symphonia globulifera, a tropical tree species with highly mobile pollinators and seed dispersers in the Osa Peninsula in southern Costa Rica. We used microsatellites to study genetic diversity and realized gene flow patterns between a continuous forest and a forest fragment. We found

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20

Kemp, P. R., J. K. Osbourn, D. J. Grainger та J. C. Metcalfe. "Cloning and analysis of the promoter region of the rat SM22α gene". Biochemical Journal 310, № 3 (1995): 1037–43. http://dx.doi.org/10.1042/bj3101037.

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We have cloned and sequenced a 1.9 kb fragment of the 5′-upstream sequence of the smooth-muscle-specific gene SM22 alpha. The region cloned consisted of the SM22 alpha promoter, a 65 bp exon containing most of the 5′-untranslated region and 307 bp of the first intron. A 1.5 kb fragment at the 5′ end of this sequence was able to drive the expression of a reporter chloramphenicol acetyltransferase (CAT) gene in both vascular smooth-muscle cells and Rat-1 fibroblasts. This promoter region did not contain a consensus TATAA box but contained the sequence TTTAAA 25 bp from the major start site ident

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21

DWIVANY, FENNY MARTHA, KRISTI LENCI PATTY, and CINDY NOVIANTI. "ISOLATION AND CHARACTERIZATION OF PISANG TONGKAT LANGIT (Musa troglodytarum L.) ACS1 AND ACO1 GENE EXPRESSION DURING FRUIT RIPENING PROCESS." Malaysian Applied Biology 49, no. 2 (2021): 81–92. http://dx.doi.org/10.55230/mabjournal.v49i2.1527.

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Pisang tongkat langit (Musa troglodytarum L.) is a banana cultivar originated from Eastern Indonesia. Previous studies showed that ACS1 and ACO1 are genes that play an important role in banana ethylene biosynthesis. However, characterization and analysis of M. troglodytarum ACS1 and ACO1 genes have not been reported. This study aims to isolate and characterize the ACS1 and ACO1 gene expression profile during fruit ripening process. Gene fragment isolation was performed using PCR based method. Results showed that the isolated genomic fragments of ACS1 was 400 bp and ACO1 was 500 bp. cDNA fragme

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Manggabarani, Andi Madihah, Ria Reinnata Juliandari, Elhah Nailul Khasna, Shelly Zairina, Eko Sri Sulasmi, and Dwi Listyorini. "ISOLATION OF UPSTREAM AND DOWNSTREAM FRAGMENT OF ACYLTRANSFERASE (AT3) GENE FROM Capsicum frutescens L. CV. CAKRAHIJAU." KnE Life Sciences 2, no. 1 (2015): 21. http://dx.doi.org/10.18502/kls.v2i1.111.

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Capsicum frutescens cv. CakraHijau is a local cultivar that has been widely cultivated in Indonesia due to its several advantages, including its pungency. Pungent taste of Capsicum is generated by capsaicin compound encoded by AT3 gene. Recently, 404 bp fragment of AT3 gene had been isolated. This research aimed to isolate upstream and downstream fragments of AT3 gene. PCR method used two pairs of primers: F2/R2 (F2 5’-TCT CCA TGC TGA CAA CAA CA-3’, and R2 5’-CGA TGA AAG ATA GCT TGT G-3’) and F3/R3 (F3 5’-GCA TCT CTT GCA GAG AGC ATA G-3’, and R3 5’-TGT ACG CAC TCG TTG AGA CT-3’). F2/R2 primers

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23

Lin, Y., K. L. Larson, R. Dorer, and G. R. Smith. "Meiotically induced rec7 and rec8 genes of Schizosaccharomyces pombe." Genetics 132, no. 1 (1992): 75–85. http://dx.doi.org/10.1093/genetics/132.1.75.

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Abstract The Schizosaccharomyces pombe rec7 and rec8 genes, which are required for meiotic intragenic recombination but not for mitotic recombination, have been cloned and their DNA sequences determined. Genetic and physical analyses demonstrated that the cloned fragments contained the rec genes rather than rec mutation suppressors. A 1.6-kb DNA fragment contained a functional rec7 gene, and a 2.1-kb fragment contained a functional rec8 gene. The nucleotide sequences of these fragments revealed open reading frames predicting 249 amino acids for the rec7 gene product and 393 amino acids for the

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24

Devchand, Medhavinee R., and M. Kapoor. "Binding of a 30-kDa protein to the pyruvate kinase gene of Neurospora crassa." Biochemistry and Cell Biology 66, no. 9 (1988): 958–66. http://dx.doi.org/10.1139/o88-110.

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Extracts of a wild-type strain of Neurospora crassa, electrophoresed on SDS–polyacrylamide gels and electroblotted onto nitrocellulose sheets, were hybridized to an end-labelled pyruvate kinase (PK) gene fragment containing the 5′ noncoding sequence and a large part of the coding region. A 30-kDa protein was found to bind strongly to the PK gene DNA, while binding weakly to plasmid pUC12 DNA and to total N. crassa DNA. Probing of blots with individual restriction fragments derived from the PK gene showed that the protein binding occurred primarily to the 5′ noncoding region. Nonspecific DNA fr

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25

Yan, Fan, Shaokang Di, and Ryoji Takahashi. "CACTA-superfamily transposable element is inserted in MYB transcription factor gene of soybean line producing variegated seeds." Genome 58, no. 8 (2015): 365–74. http://dx.doi.org/10.1139/gen-2015-0054.

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The R gene of soybean, presumably encoding a MYB transcription factor, controls seed coat color. The gene consists of multiple alleles, R (black), r-m (black spots and (or) concentric streaks on brown seed), and r (brown seed). This study was conducted to determine the structure of the MYB transcription factor gene in a near-isogenic line (NIL) having r-m allele. PCR amplification of a fragment of the candidate gene Glyma.09G235100 generated a fragment of about 1 kb in the soybean cultivar Clark, whereas a fragment of about 14 kb in addition to fragments of 1 and 1.4 kb were produced in L72-20

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26

Wilson, J. G., E. E. Murphy, W. W. Wong, L. B. Klickstein, J. H. Weis, and D. T. Fearon. "Identification of a restriction fragment length polymorphism by a CR1 cDNA that correlates with the number of CR1 on erythrocytes." Journal of Experimental Medicine 164, no. 1 (1986): 50–59. http://dx.doi.org/10.1084/jem.164.1.50.

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A genetic basis for the regulation of the number of CR1 on E of different normal individuals was investigated by probing Southern blots of their genomic DNA with a 0.75-kb fragment of CR1 cDNA. Using Hind III, we observed a RFLP involving fragments of 7.4 kb and 6.9 kb that correlated with the number of CR1 on E. 32 individuals having only the 7.4-kb restriction fragment had a mean of 661 +/- 33 (SEM) CR1/E, 11 donors having both restriction fragments had a mean of 455 +/- 52 CR1/E, and 7 individuals having only the 6.9-kb fragment had a mean of 156 +/- 13 CR1/E, all means being significantly

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Kostia, Silja, Jukka Palo, and Sirkka-Liisa Varvio. "DNA sequences of RAPD fragments in artiodactyls." Genome 39, no. 2 (1996): 456–58. http://dx.doi.org/10.1139/g96-057.

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A bovine RAPD profile, generated by a 10-mer primer, was analysed by sequencing the major fragments. Three of four different fragments showed homologies to previously characterized mammalian sequences. One was 61–66% identical to LINE sequences and another was 78.5% identical to a human chromosome 2 sequence tagged site. The third fragment was 93.1% identical to the human type 2 inositol 1,4,5-trisphosphate receptor gene. This fragment had counterparts in white-tailed deer and reindeer; fragments of slightly different size in these species showed high sequence similarity and the size differenc

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28

Tsivitse, Maryanne, and Michael D. P. Boyle. "Evidence for independent binding domains within a group A streptococcal type IIo IgG-binding protein." Canadian Journal of Microbiology 42, no. 11 (1996): 1172–75. http://dx.doi.org/10.1139/m96-149.

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The gene for a type IIo IgG-binding protein has previously been cloned and sequenced. The ~60 000 Mrrecombinant gene product binds all four human IgG subclasses and fibrinogen. Treatment of this recombinant protein with CNBr results in generation of a series of fragments. One fragment, an ~32 000 Mrpolypeptide, binds IgG1, IgG2, and IgG4but neither IgG3nor fibrinogen. N-terminal amino sequencing of this fragment indicated that this was an internal fragment of the protein starting at amino acid 186 of the mature protein. These findings provide evidence for two distinct domains for binding IgG1,

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29

Wiharyani, Risma, Dudi Hardianto, Hermin Pancasakti Kusumaningrum, and Anto Budiharjo. "Kloning Gen pcbC dari Penicillium chrysogenum ke dalam Plasmid pPICZA untuk Pengembangan Produksi Penisilin G." Bioma : Berkala Ilmiah Biologi 16, no. 1 (2014): 33. http://dx.doi.org/10.14710/bioma.16.1.33-38.

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Availability of drugs in Indonesia is still limited by the high prices of drugs due to on the imported raw materials that reaches 95%. Developing antibiotic raw materials can be achieved by increasing of penicillin G production, which is the raw material for the formation of semisynthetic penicillin derivatives through the production of 6-aminopenisillanic acid (6-APA). One of the important enzyme in the penicillin G biosynthesis is Isopenisilin N Synthase (IPNS) that encodes by pcbC gene on Penicillium chrysogenum. This study aimed to obtain a recombinant of pcbC gene fragments that is insert

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Kobielak, K., A. Kobielak, J. Limon, and W. H. Trzeciak. "Mutation in the regulatory region of the EDA gene coincides with the symptoms of anhidrotic ectodermal dysplasia." Acta Biochimica Polonica 45, no. 1 (1998): 245–50. http://dx.doi.org/10.18388/abp.1998_4307.

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We have investigated a fragment of the regulatory region of the EDA gene in a patient with clinical symptoms of anhidrotic ectodermal dysplasia (EDA), whose DNA sequence of exon 1 was normal. The single-strand conformation polymorphism (SSCP) analysis of PCR-amplified fragments of the regulatory region of the EDA gene suggested a mutation localized within the fragment extending from nucleotide -571 to -182 upstream of the 5' end of the cDNA. Sequence analysis of this fragment documented an additional adenine in position -452, located 32 nucleotides upstream from the response element HK-1, a ta

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31

Miller, B. L., K. Y. Miller, and W. E. Timberlake. "Direct and indirect gene replacements in Aspergillus nidulans." Molecular and Cellular Biology 5, no. 7 (1985): 1714–21. http://dx.doi.org/10.1128/mcb.5.7.1714-1721.1985.

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We performed three sets of experiments to determine whether cloned DNA fragments can be substituted for homologous regions of the Aspergillus nidulans genome by DNA-mediated transformation. A linear DNA fragment containing a heteromorphic trpC+ allele was used to transform a trpC- strain to trpC+. Blot analysis of DNA from the transformants showed that the heteromorphic allele had replaced the trpC- allele in a minority of the strains. An A. nidulans trpC+ gene was inserted into the argB+ gene, and a linear DNA fragment containing the resultant null argB allele was used to transform a trpC- ar

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Miller, B. L., K. Y. Miller, and W. E. Timberlake. "Direct and indirect gene replacements in Aspergillus nidulans." Molecular and Cellular Biology 5, no. 7 (1985): 1714–21. http://dx.doi.org/10.1128/mcb.5.7.1714.

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We performed three sets of experiments to determine whether cloned DNA fragments can be substituted for homologous regions of the Aspergillus nidulans genome by DNA-mediated transformation. A linear DNA fragment containing a heteromorphic trpC+ allele was used to transform a trpC- strain to trpC+. Blot analysis of DNA from the transformants showed that the heteromorphic allele had replaced the trpC- allele in a minority of the strains. An A. nidulans trpC+ gene was inserted into the argB+ gene, and a linear DNA fragment containing the resultant null argB allele was used to transform a trpC- ar

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Deng, Pan, Yuehan Liu, Jingwen Wu, Shuyue Zhang, Piwu Li, and Junqing Wang. "Seamless gene knockout of malate synthetase gene improves the yield of pullulan of Aureobasidium pullulans." Advances in Engineering Technology Research 12, no. 1 (2024): 1032. https://doi.org/10.56028/aetr.12.1.1032.2024.

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Pullulan is a linear extracellular polysaccharide produced by yeast like fungus Aureobasidium pullulans through fermentation. Due to its high safety, strong stability, good film-forming property and strong oxygen resistance, there is great market potential in the fields of medicine, food additives, cosmetics, etc. This study constructed a seamless recombinant knockout plasmid pUC57-PMA-ms with a hygromycin resistance gene as a screening marker. The plasmid contains a PMA-ms gene fragment, the upstream and downstream homologous arm fragments of the gene, as well as the hygromycin resistance gen

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McMillin, David E., Lycurgus L. Muldrow, and Shwanda J. Laggette. "Simultaneous detection of toxin A and toxin B genetic determinants of Clostridium difficile using the multiplex polymerase chain reaction." Canadian Journal of Microbiology 38, no. 1 (1992): 81–83. http://dx.doi.org/10.1139/m92-013.

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A multiplex polymerase chain reaction was developed to simultaneously detect the presence of toxin A and toxin B genes of Clostridium difficile. A 1050-bp fragment of the toxin B gene and a 1217-bp fragment of the toxin A gene were amplified from 42 toxic strains of C. difficile; however, from 10 nontoxic strains the toxin gene fragments were not amplified; these data demonstrate that this multiplex polymerase chain reaction procedure can be used to differentiate between toxic and nontoxic strains. This sensitive and specific multiplex polymerase chain reaction for C. difficile toxins may prov

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Wu, Yanduo, Yongshuang Xiao, Zhizhong Xiao, Yuting Ma, Haixia Zhao, and Jun Li. "Identification of Male-Specific Molecular Markers by Recombination of RhoGEF10 Gene in Spotted Knifejaw (Oplegnathus punctatus)." Genes 13, no. 7 (2022): 1262. http://dx.doi.org/10.3390/genes13071262.

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The spotted knifejaw (Oplegnathus punctatus) is a marine economic fish with high ecological value, food value, and fishing value, and its growth has obvious sex dimorphism. The rapid identification of its sex is beneficial to the development of sex determination and breeding. In this study, the method of comparative genomics and PCR amplification was used to further establish a rapid detection method for the recombinant RhoGEF10 gene in O. punctatus, which can quickly, accurately, and efficiently identify the sex of the O. punctatus to be tested. The homologous comparison results of male and f

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WU, Z., I. NAGANO, E. POZIO, and Y. TAKAHASHI. "Polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) for the identification of Trichinella isolates." Parasitology 118, no. 2 (1999): 211–18. http://dx.doi.org/10.1017/s0031182098003679.

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In the present study, polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis was developed to identify 5 species (Trichinella spiralis, Trichinella britovi, Trichinella nativa, Trichinella nelsoni and Trichinella pseudospiralis) and 3 phenotypes of uncertain taxonomic status (Trichinella T5, T6, and T8). Eleven restriction endonucleases were used to restrict 3 DNA fragments (1) a 2800 bp fragment of the 43 kDa excretory–secretory (E–S) protein gene, (2) a 1250 bp fragment amplified with the primer pair SB147A and (3) a 372 bp fragment amplified with the primer p

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Daxhelet, Guy, Philippe Gilot, and Philippe Hoet. "Cloning and characterization of transcriptional promoters fromBacillus subtilisphage 2C." Canadian Journal of Microbiology 42, no. 9 (1996): 919–26. http://dx.doi.org/10.1139/m96-118.

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Phage 2C is a Bacillus subtilis lytic phage, whose genome contains hydroxymethyluracil in place of thymine. To isolate promoters of early phage genes involved in the take-over of cellular metabolism, 2C DNA libraries were constructed in promoter-probe plasmids replicating in Escherichia coli and B. subtilis. Four different 2C DNA fragments strongly expressed reporter genes in E. coli but not in B. subtilis. All fragments originated from unique sequences of the genome and not from its terminal redundancies. One fragment was sequenced. Despite the presence of an σA-RNA polymerase binding site up

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Gorski, Lisa, та Dale Kaiser. "Targeted Mutagenesis of ς54 Activator Proteins in Myxococcus xanthus". Journal of Bacteriology 180, № 22 (1998): 5896–905. http://dx.doi.org/10.1128/jb.180.22.5896-5905.1998.

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ABSTRACT Myxococcus xanthus DNA segments related to the highly conserved central sequence of ς54 activator proteins have been investigated. A genetic technique designed to inactivate a gene that encodes such an activator by inserting a plasmid-borne internal fragment of the putative gene has been tested. When the internal fragment inserted by homologous recombination into the corresponding chromosomal locus, the expected duplication of the gene was observed by Southern hybridization. The single restriction fragment characteristic of each segment was replaced in the insertion strains by two hyb

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Sumida, Takeshi, Hiroshi Yanagawa, and Nobuhide Doi. "In VitroSelection of Fab Fragments by mRNA Display and Gene-Linking Emulsion PCR." Journal of Nucleic Acids 2012 (2012): 1–9. http://dx.doi.org/10.1155/2012/371379.

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In vitroselection by display methods has been an effective tool for engineering recombinant antibodies. mRNA display based on a cell-free translation system has the advantages of larger library sizes and quicker selection procedures compared with cell-based display methods such as phage display. However, mRNA display has been limited to select single-chain polypeptides such as scFvs due to its characteristic of linking a nascent polypeptide with its encoding mRNA on the ribosome. Here we demonstrated a new way of selecting heterodimeric Fab fragments by using mRNA display combined with emulsio

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Sadeghi, S., A. Hajihosseinlo, and M. Bohlouli. "Haplotype association of ovine leptin gene on breeding value of body measurements in Makooei sheep breed." Biotehnologija u stocarstvu 30, no. 2 (2014): 233–42. http://dx.doi.org/10.2298/bah1402233s.

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The research was undertaken to find association of genetic variation in the exon 3 of the leptin gene and breeding value of body weight traits in Makooei sheep breed using single strand conformation polymorphism (SSCP). The PCR product was obtained to encompass exon 3 of leptin gene corresponding to ovine leptin gene. The PCR fragments were subjected to electrophoresis to reveal the SSCP patterns. Among the total of 130 sheep, five SSCP patterns (haplotypes) were identified for amplified fragment. The frequencies of SSCP patterns of polymorphic fragment were 0.09, 0.17, 0.37, 0.14 and 0.23.The

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Samuelsson, T., P. Elias, F. Lustig, and Y. S. Guindy. "Cloning and nucleotide sequence analysis of transfer RNA genes from Mycoplasma mycoides." Biochemical Journal 232, no. 1 (1985): 223–28. http://dx.doi.org/10.1042/bj2320223.

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As part of an investigation of the tRNA genes of Mycoplasma mycoides, two HindIII fragments of mycoplasma DNA comprising 0.4 and 2.5 kilobases (kb), respectively, were cloned in pBR322 and their nucleotide sequences determined. Only one tRNA gene was found in the 0.4 kb fragment, the gene for tRNAArg with the anticodon TCT, while the 2.5 kb fragment contained nine different tRNA genes arranged in a cluster which presumably constitutes a transcriptional unit. The clustered tRNA genes, with their respective anticodons, were as follows: Arg (ACG), Pro (TGG), Ala (TGC), Met (CAT), Ile (CAT), Ser (

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Mulligan, P. K., J. D. Mohler, and L. J. Kalfayan. "Molecular localization and developmental expression of the otu locus of Drosophila melanogaster." Molecular and Cellular Biology 8, no. 4 (1988): 1481–88. http://dx.doi.org/10.1128/mcb.8.4.1481-1488.1988.

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The female-sterile ovarian tumor gene, otu, is located in cytological region 7F1 on the Drosophila melanogaster chromosome map. We have mapped the gene at the molecular level by using four dysgenic alleles and two revertant derivatives of these alleles as well as an ethyl methanesulfonate-induced allele. The insertional (dysgenic) changes were all associated with one restriction fragment, and its size was restored after phenotypic reversion. One ethyl methanesulfonate-induced allele had a deletion in the restriction fragment adjacent (distal) to the fragment altered in the insertional alleles.

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Mulligan, P. K., J. D. Mohler, and L. J. Kalfayan. "Molecular localization and developmental expression of the otu locus of Drosophila melanogaster." Molecular and Cellular Biology 8, no. 4 (1988): 1481–88. http://dx.doi.org/10.1128/mcb.8.4.1481.

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The female-sterile ovarian tumor gene, otu, is located in cytological region 7F1 on the Drosophila melanogaster chromosome map. We have mapped the gene at the molecular level by using four dysgenic alleles and two revertant derivatives of these alleles as well as an ethyl methanesulfonate-induced allele. The insertional (dysgenic) changes were all associated with one restriction fragment, and its size was restored after phenotypic reversion. One ethyl methanesulfonate-induced allele had a deletion in the restriction fragment adjacent (distal) to the fragment altered in the insertional alleles.

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Liu, Brian Sun, Mengran Zhang, Takeshi Sugio, and Mohammad Shahrokh Esfahani. "Abstract 6243: Mathematical modeling of cell-free DNA fragmentation to map chromatin landscapes in health and cancer." Cancer Research 85, no. 8_Supplement_1 (2025): 6243. https://doi.org/10.1158/1538-7445.am2025-6243.

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Abstract Background: Cell-free DNA (cfDNA) fragments are shed into bodily fluids as a result of apoptosis and necrosis. Profiling plasma cfDNA has emerged as a powerful tool in cancer diagnostics and research, through circulating tumor DNA (ctDNA) fragments that enable genotyping of many tumors, and epigenetic analysis of cfDNA, including fragmentomics. Fragmentomics encompasses the analysis of fragment lengths, end motifs, and central dyads, which reflect epigenetic patterns, to identify the cell of origin for each fragment. We previously showed that fragment size diversity is strongly correl

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Sivolodskii, E. P., and O. A. Freylikhman. "Genetic and phenotypic characteristics of Klebsiella michiganensis isolates." Russian Journal of Infection and Immunity 9, no. 5-6 (2020): 648–54. http://dx.doi.org/10.15789/2220-7619-2019-5-6-648-654.

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The aim of the study was to identify an optimal research target for detection of Klebsiella michiganensis isolates, determine their genetic and phenotypic characteristics necessary for identification. Here, we examined 11 Klebsiella oxytoca strains, lacking (atypical, negative) a marker 5-aminosalicylate decarboxylase (detected by the chromogenic reaction by 5-aminosalicylic acid) unique for the genus Klebsiella bacteria. They were selected for genetic analysis subsequent to a phenotypic characterization of K. oxytoca clinical isolates, collected in within 2015–2018 period in medical instituti

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Gao, M. H., and P. B. Kavathas. "Functional importance of the cyclic AMP response element-like decamer motif in the CD8 alpha promoter." Journal of Immunology 150, no. 10 (1993): 4376–85. http://dx.doi.org/10.4049/jimmunol.150.10.4376.

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Abstract Expression of the CD8 gene is highly regulated during lymphocyte differentiation and in a tissue-specific manner. We characterized the human CD8 alpha promoter region to determine whether tissue specificity resides within the promoter and to define important regulatory elements. A set of six fragments 5' of the CD8 alpha gene were linked to a luciferase reporter gene. The luciferase activity was then measured in a transient transfection assay. We found that CD8 alpha promoter activity can be detected from a 146-bp fragment upstream of the translation start site, but not from a 133-bp

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Maansson, Christoffer Trier, Louise Skov Thomsen, Peter Meldgaard, Anders Lade Nielsen, and Boe Sandahl Sorensen. "Integration of Cell-Free DNA End Motifs and Fragment Lengths Can Identify Active Genes in Liquid Biopsies." International Journal of Molecular Sciences 25, no. 2 (2024): 1243. http://dx.doi.org/10.3390/ijms25021243.

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Multiple studies have shown that cell-free DNA (cfDNA) from cancer patients differ in both fragment length and fragment end motif (FEM) from healthy individuals, yet there is a lack of understanding of how the two factors combined are associated with cancer and gene transcription. In this study, we conducted cfDNA fragmentomics evaluations using plasma from lung cancer patients (n = 12) and healthy individuals (n = 7). A personal gene expression profile was established from plasma using H3K36me3 cell-free chromatin immunoprecipitation sequencing (cfChIP-seq). The genes with the highest express

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K, LENIN, and UDAYASURIYAN V. "Cloning of cry 2 Aa gene from an indigenous isolate of Bacillus thuringiensis." Madras Agricultural Journal 88, june (2001): 198–202. http://dx.doi.org/10.29321/maj.10.a00318.

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By using the cry24a operon specific primers, DNA fragments of about 4.0 kb were amplified at 55°C annealing temperature without any non-specific amplification from a new Bt strain 47-8 and cloned in pGEM-T(3.0 kb) vector. Double digestion with Sall and Sphl enzymes showed fragments of expected size (3, 4kb) in recombinant clones and one of the positive clones is designated as pTN2A (7.0 kb). Nucleotide sequencing of Bt DNA fragment cloned in pTN2A was carried out with M13F and M13R primers. Totally 983 bases have been sequenced in the insert DNA of pTN2A. Comparison of sequence data obtained f

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Nakao, M., H. Nomiyama, and K. Shimada. "Structures of human genes coding for cytokine LD78 and their expression." Molecular and Cellular Biology 10, no. 7 (1990): 3646–58. http://dx.doi.org/10.1128/mcb.10.7.3646-3658.1990.

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LD78 is a member of a newly identified superfamily of small inducible proteins involved in inflammatory responses, wound healing, and tumorigenesis. Southern blot analysis of the EcoRI-digested human genomic DNAs, using previously isolated LD78 cDNA as a probe, showed that in each individual there are 4.2- and 4.8-kilobase-pair (kb) fragments and that some have an additional 6.5-kb fragment. The 4.2-kb fragment contained genomic DNA sequences corresponding to the LD78 cDNA and was named the LD78 alpha gene. The 4.8-kb fragment contained similar sequences, showing 94% homology to the LD78 alpha

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50

Nakao, M., H. Nomiyama, and K. Shimada. "Structures of human genes coding for cytokine LD78 and their expression." Molecular and Cellular Biology 10, no. 7 (1990): 3646–58. http://dx.doi.org/10.1128/mcb.10.7.3646.

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LD78 is a member of a newly identified superfamily of small inducible proteins involved in inflammatory responses, wound healing, and tumorigenesis. Southern blot analysis of the EcoRI-digested human genomic DNAs, using previously isolated LD78 cDNA as a probe, showed that in each individual there are 4.2- and 4.8-kilobase-pair (kb) fragments and that some have an additional 6.5-kb fragment. The 4.2-kb fragment contained genomic DNA sequences corresponding to the LD78 cDNA and was named the LD78 alpha gene. The 4.8-kb fragment contained similar sequences, showing 94% homology to the LD78 alpha

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