• Title/Summary/Keyword: M-DNA

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Cloning, Expression, and Nucleotide Sequencing of the Gene Encoding Glucose Permease of Phosphotransferase System from Brevibacterium ammoniagenes

  • Yoon, Ki-Hong;Yim, Hyouk;Jung, Kyung-Hwa
    • Journal of Microbiology and Biotechnology
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    • v.8 no.3
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    • pp.214-221
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    • 1998
  • A Brevibacterium ammoniagenes gene coding for glucose/mannose-specific enzyme II ($EII^{Glc}$) of the phosphoenolpyruvate-dependent phosphotransferase system (PTS) was cloned by complementing an Escherichia coli mutation affecting a ptsG gene, and the complete DNA nucleotide sequence was determined. The cloned gene was identified to be a ptsG, which enables the E. coli transportment to use glucose more efficiently than mannose as the sole carbon source in an M9 minimal medium. The ptsG gene of B. ammoniagenes consists of an open reading frame of 1,983 nucleotides putatively encoding a polypeptide of 661 amino acid residues and a TAA stop codon. The deduced amino acid sequence of the B. ammoniagenes $EII^{Glc}$ shows, at $46\%$, the highest degree of sequence similarity with the Corynebacterium glutamicum EII specific for both glucose and mannose. In addition, the $EII^{Glc}$ shares approximately $30\%$ sequence similarities with sucrose-specific and ${\beta}$-glucoside-specific EIIs of the several bacteria belonging to the glucose-PTS class. The 161-amino-acid C-terminal sequence of $EII^{Glc}$ is also similar to that of E. coli enzyme $IIA^{Glc}$, specific for glucose ($EIIA^{Glc}$). The B. ammoniagenes $EII^{Glc}$ consists of three domains; a hydrophobic region (EIIC) and two hydrophilic regions (EIIA, EIIB). The arrangement of structural domains, IIBCA, of the $EII^{Glc}$ is identical to those of EIIs specific for sucrose or ${\beta}$-glucoside. While the domain IIA was removed from the B. ammoniagenes $EII^{Glc}$ the remaining domains IIBC were found to restore the glucose and mannose-utilizing capacity of E. coli mutant lacking $EII^{Glc}$ activity with $EIIA^{Glc}$ of the E. coli mutant. $EII^{Glc}$ contains a histidine residue and a cysteine residue which are putative phosphorylation sites for the protein.

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Identification of Single Nucleotide Polymorphisms (SNPs) of the Bovine Growth Hormone (bGH) Gene Associated with Growth and Carcass Traits in Hanwoo

  • Lee, Ji-Hong;Lee, Yun-Mi;Lee, Jea-Young;Oh, Dong-Yep;Jeong, Dae-Jin;Kim, Jong-Joo
    • Asian-Australasian Journal of Animal Sciences
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    • v.26 no.10
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    • pp.1359-1364
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    • 2013
  • The purpose of this study was to find any association of the bovine growth hormone (bGH) gene with growth and carcass quality traits in Korean native cattle, Hanwoo. Genomic DNA was extracted from 21 Hanwoo individuals, and the 47 to 2,528 bp region of the bGH 2,856 bp (GenBank accession number M57764) including the promoter and the five exons was sequenced. A total of ten bGH SNPs were confirmed, including four (253 C>T, 303 C>T, 502 C>T, and 559 G>A) in the promoter, one (679 C>T) in exon 1, one (1,692 T>C) in intron 3, and four (2141 C>G, 2258 C>T, 2277 C>T, and 2291 A>C) in exon 5. The ten bGH SNPs were genotyped for a sample of 242 Hanwoo steers and association tests were performed to find any significant SNP that was correlated with growth and carcass quality. Of the SNPs, the 303 C>T SNP in the promoter region was significantly associated with 6-month-old weight, the 559 G>A SNP with longissimus dorsi muscle area, the 2141 C>G SNP in exon 5 with daily weight gain, and the 2258 C>T SNP with daily weight gain and carcass weight (p<0.05). The significant SNPs need to be verified in other Hanwoo populations before considering implementation of marker-assisted selection for genetic improvement of growth and carcass quality in Hanwoo.

Molecular cloning and expression analysis of annexin A2 gene in sika deer antler tip

  • Xia, Yanling;Qu, Haomiao;Lu, Binshan;Zhang, Qiang;Li, Heping
    • Asian-Australasian Journal of Animal Sciences
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    • v.31 no.4
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    • pp.467-472
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    • 2018
  • Objective: Molecular cloning and bioinformatics analysis of annexin A2 (ANXA2) gene in sika deer antler tip were conducted. The role of ANXA2 gene in the growth and development of the antler were analyzed initially. Methods: The reverse transcriptase polymerase chain reaction (RT-PCR) was used to clone the cDNA sequence of the ANXA2 gene from antler tip of sika deer (Cervus Nippon hortulorum) and the bioinformatics methods were applied to analyze the amino acid sequence of Anxa2 protein. The mRNA expression levels of the ANXA2 gene in different growth stages were examined by real time reverse transcriptase polymerase chain reaction (real time RT-PCR). Results: The nucleotide sequence analysis revealed an open reading frame of 1,020 bp encoding 339 amino acids long protein of calculated molecular weight 38.6 kDa and isoelectric point 6.09. Homologous sequence alignment and phylogenetic analysis indicated that the Anxa2 mature protein of sika deer had the closest genetic distance with Cervus elaphus and Bos mutus. Real time RT-PCR results showed that the gene had differential expression levels in different growth stages, and the expression level of the ANXA2 gene was the highest at metaphase (rapid growing period). Conclusion: ANXA2 gene may promote the cell proliferation, and the finding suggested Anxa2 as an important candidate for regulating the growth and development of deer antler.

Opportunistic Screening for Cervical Cancer in a Tertiary Hospital in Karnataka, India

  • Kulkarni, Padmaja Ramesh;Rani, Hephzibah;Vimalambike, Manjunath Gubbanna;Ravishankar, Sunila
    • Asian Pacific Journal of Cancer Prevention
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    • v.14 no.9
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    • pp.5101-5105
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    • 2013
  • The incidence and mortality of cervical cancer remains high in India even after sixty years of introduction of the Pap smear (cervical cytology) which is an effective means of identifying preinvasive lesions of carcinoma cervix. The morbidity and mortality due to cervical cancer has come down drastically in countries with well established screening programmes at national level. This study aims at screening women for cervical cancer opportunistically during their visit to hospital and to study various types of neoplastic and non-neoplastic lesions of the cervix by cervical smear study (Pap smear study). In the present study, a total of 350 cervical smears were studied. The age of patients ranged from 19 years to 80 years with mean age being 37.5 years. Out of 350 cases, the diagnosis of neoplasia was given in 43 cases and 258 cases were diagnosed as inflammatory smears. Forty-cases were normal and 9 cases were inadequate to evaluate. Forty-three patients who were found to have neoplastic lesions on cytology were referred for further investigations like colposcopy and biopsy to confirm the diagnosis and avail proper treatment. Limitation of the present study was small sample size as all female patients aged between 20 and 60 years visiting hospital were not included in the screening, other screening tests like VIA (visual inspection with acetic acid test) and HPV DNA (human papilloma virus) tests were not done. Until the time centrally organised screening programmes for cervical cancer are established in India, arrangements should be made for hospital based opportunistic screening for all women attending hospital. The cost effectiveness of different screening tests for cervical cancer should be evaluated.

Cloning and Characterization of the HSP70 Gene, and Its Expression in Response to Diapauses and Thermal Stress in the Onion Maggot, Delia antiqua

  • Chen, Bin;Kayukawa, Takumi;Monteiro, Antonia;Ishikawa, Yukio
    • BMB Reports
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    • v.39 no.6
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    • pp.749-758
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    • 2006
  • The cytosolic members of the HSP70 family of proteins play key roles in the molecular chaperone machinery of the cell. In the study we cloned and sequenced the full-length cDNA of Delia antiqua HSP70 gene, which is 2461 bp long and encodes 643 a.a. with a calculated molecular mass of 70,787 Da. We investigated gene copies of cytosolic HSP70 members of 4 insect species with complete genome available, and found that they are quite variable with species. In order to characterize this protein we carried out an alignment and a phylogenetic analysis with 41 complete protein sequences from insects. The analysis divided the cytosolic members of the family into two classes, HSP70 and HSC70, distinguishable on the basis of 15 residues. HSP70 class members were slightly shorter in length and smaller in molecular mass relative to the HSC70 class members, and the conservative and functional regions in these sequences were documented. Mainly, we investigated the expression of Delia antiqua HSP70 gene, in response to diapauses and thermal stresses. Both summer and winter diapauses elevated HSP70 transcript levels. Cold-stress led to increased HSP70 expression levels in summer- and winter-diapausing pupae, but heat-stress elevated the levels only in the winter-diapausing pupae. In all cases, the expression levels, after being elevated, gradually decreased with time. HSP70 expression was low in non-diapausing pupae but was up-regulated following cold- and heat-stresses. Heat-stress gradually increased the mRNA level with time whereas cold-stress gradually decreased levels after an initial increase.

Molecular cloning, expression and characterization of a novel feruloyl esterase enzyme from the symbionts of termite (Coptotermes formosanus) gut

  • Chandrasekharaiah, Matam;Thulasi, Appoothy;Bagath, M.;Kumar, Duvvuri Prasanna;Santosh, Sunil Singh;Palanivel, Chenniappan;Jose, Vazhakkala Lyju;Sampath, K.T.
    • BMB Reports
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    • v.44 no.1
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    • pp.52-57
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    • 2011
  • Termites play an important role in the degradation of dead plant materials and have acquired endogenous and symbiotic cellulose digestion capabilities. The feruloyl esterase enzyme (FAE) gene amplified from the metagenomic DNA of Coptotermes formosanus gut was cloned in the TA cloning vector and subcloned into a pET32a expression vector. The Ft3-7 gene has 84% sequence identity with Clostridium saccharolyticum and shows amino acid sequence identity with predicted xylanase/chitin deacetylase and endo-1,4-beta-xylanase. The sequence analysis reveals that probably Ft3-7 could be a new gene and that its molecular mass was 18.5 kDa. The activity of the recombinant enzyme (Ft3-7) produced in Escherichia coli (E.coli) was 21.4 U with substrate ethyl ferulate and its specific activity was 24.6 U/mg protein. The optimum pH and temperature for enzyme activity were 7.0 and $37^{\circ}C$, respectively. The substrate utilization preferences and sequence similarity of the Ft3-7 place it in the type-D sub-class of FAE.

Production of Invertase from Newly Isolated Strain Bacilus flexus (토양에서 분리한 Bacilus flexus로부터 Invertase의 생산)

  • Oh, Tae-Seok;Yun, Hee;Sim, Ye-Ji;Kim, Jin-Woo;Choi, Min-Ji;Yun, Jong-Won
    • KSBB Journal
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    • v.25 no.1
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    • pp.79-84
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    • 2010
  • In the present study, we isolated a new bacterial strain producing invertase (EC 3.2.1.26) and determined optimized culture condition in flask culture. The strain was identified as Bacilus flexus determined by the 16S rDNA sequencing method. The invertase was produced only in the sucrose medium as the sole carbon source. Potassium nitrate was an adequate nitrogen source for enzyme production, whereas meat peptone showed the highest bacterial growth. Enzyme production was increased about 2-fold when $MgSO_4\cdot7H_2O$ was supplemented to the growth media. The optimum temperature was found to be $30^{\circ}C$ for both enzyme production and bacterial growth. Invertase exhibited pH optima in the range 5.0-6.0 and have a temperature optimum at $40^{\circ}C$, similarly to other invertases found from different microbial sources. Several mineral ions (K and Fe) stimulated the invertase activity, whereas some bioelements (Ag, Mg, and Mn) inhibited enzyme activity. Under the optimized culture condition, the maximum enzyme production (over 250 units/mL) was achieved at 20 h. To the best of our knowledge, this is the first time to report on invertase production by Bacilus flexus.

Simultaneous and Systemic Knock-down of Big Defensin 1 and 2 gene Expression in the Pacific Oyster Crassostrea gigas using Long Double-stranded RNA-mediated RNA Interference

  • Jee, Bo Young;Kim, Min Sun;Cho, Mi Young;Lee, Soon Jeong;Park, Myung Ae;Kim, Jin Woo;Choi, Seung Hyuk;Jeong, Hyun Do;Kim, Ki Hong
    • Fisheries and Aquatic Sciences
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    • v.17 no.3
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    • pp.377-380
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    • 2014
  • RNA interference (RNAi)-mediated transcriptional knock-down of Crassostrea gigas big defensin 1 and 2 genes (Cg-BigDef1 and Cg-BigDef2) was investigated. The cDNA sequences of Cg-BigDef1 and Cg-BigDef2 were identical, excluding an additional fragment of 20 nucleotides in Cg-BigDef1; thus, a long double-stranded RNA (dsRNA) targeting the mRNA of Cg-BigDef2 effectively downregulated both Cg-BigDef2 and Cg-BigDef1. In addition, long dsRNA targeting green fluorescent protein (GFP) did not affect transcription of the two big defensin genes. These results suggest that the transcriptional downregulation of Cg-BigDef1 and Cg-BigDef2 was mediated by sequence-specific RNA interference (RNAi). Despite injection of long dsRNA targeting Cg-BigDef2 into only the adductor muscle, knock-down of Cg-BigDef1 and Cg-BigDef2 was observed in the adductor muscle, hemocytes, mantle, and gills, suggestive of systemic spread of RNAi in C. gigas. Furthermore, the inhibitory effect of dsRNA persisted until 72 h post-injection, indicative of a long-lasting RNAi-mediated knock-down of target genes.

Cloning, Expression, and Characterization of a Cold-Adapted Lipase Gene from an Antarctic Deep-Sea Psychrotrophic Bacterium, Psychrobacter sp. 7195

  • Zhang, Jinwei;Lin, Shu;Zeng, Runying
    • Journal of Microbiology and Biotechnology
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    • v.17 no.4
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    • pp.604-610
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    • 2007
  • A psychrotrophic strain 7195 showing extracellular lipolytic activity towards tributyrin was isolated from deep-sea sediment of Prydz Bay and identified as a Psychrobacter species. By screening a genomic DNA library of Psychrobacter sp. 7195, an open reading frame of 954 bp coding for a lipase gene, lipA1, was identified, cloned, and sequenced. The deduced LipA1 consisted of 317 amino acids with a molecular mass of 35,210 kDa. It had one consensus motif, G-N-S-M-G (GXSXG), containing the putative active-site serine, which was conserved in other cold-adapted lipolytic enzymes. The recombinant LipA1 was purified by column chromatography with DEAE Sepharose CL-4B, and Sephadex G-75, and preparative polyacrylamide gel electrophoresis, in sequence. The purified enzyme showed highest activity at $30^{\circ}C$, and was unstable at temperatures higher than $30^{\circ}C$, indicating that it was a typical cold-adapted enzyme. The optimal pH for activity was 9.0, and the enzyme was stable between pH 7.0-10.0 after 24h incubation at $4^{\circ}C$. The addition of $Ca^{2+}\;and\;Mg^{2+}$ enhanced the enzyme activity of LipA1, whereas the $Cd^{2+},\;Zn^{2+},\;CO^{2+},\;Fe^{3+},\;Hg^{2+},\;Fe^{2+},\;Rb^{2+}$, and EDTA strongly inhibited the activity. The LipA1 was activated by various detergents, such as Triton X-100, Tween 80, Tween 40, Span 60, Span 40, CHAPS, and SDS, and showed better resistance towards them. Substrate specificity analysis showed that there was a preference for trimyristin and p-nitrophenyl myristate $(C_{14}\;acyl\; groups)$.

Biochemical and Molecular Characterization of High Population Density Bacteria Isolated from Sunflower

  • Goes, Kelly Campos Guerra Pinheiro De;Fisher, Maria Luisa De Castro;Cattelan, Alexandre Jose;Nogueira, Marco Antonio;Carvalho, Claudio Guilherme Portela De;Oliveira, Andre Luiz Martinez De
    • Journal of Microbiology and Biotechnology
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    • v.22 no.4
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    • pp.437-447
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    • 2012
  • Natural and beneficial associations between plants and bacteria have demonstrated potential commercial application for several agricultural crops. The sunflower has acquired increasing importance in Brazilian agribusiness owing to its agronomic characteristics such as the tolerance to edaphoclimatic variations, resistance to pests and diseases, and adaptation to the implements commonly used for maize and soybean, as well as the versatility of the products and by-products obtained from its cultivation. A study of the cultivable bacteria associated with two sunflower cultivars, using classical microbiological methods, successfully obtained isolates from different plant tissues (roots, stems, florets, and rhizosphere). Out of 57 plant-growth-promoting isolates obtained, 45 were identified at the genus level and phylogenetically positioned based on 16S rRNA gene sequencing: 42 Bacillus (B. subtilis, B. cereus, B. thuringiensis, B. pumilus, B. megaterium, and Bacillus sp.) and 3 Methylobacterium komagatae. Random amplified polymorphic DNA (RAPD) analysis showed a broad diversity among the Bacillus isolates, which clustered into 2 groups with 75% similarity and 13 subgroups with 85% similarity, suggesting that the genetic distance correlated with the source of isolation. The isolates were also analyzed for certain growth-promoting activities. Auxin synthesis was widely distributed among the isolates, with values ranging from 93.34 to 1653.37 ${\mu}M$ auxin per ${\mu}g$ of protein. The phosphate solubilization index ranged from 1.25 to 3.89, and siderophore index varied from 1.15 to 5.25. From a total of 57 isolates, 3 showed an ability to biologically fix atmospheric nitrogen, and 7 showed antagonism against the pathogen Sclerotinia sclerotiorum. The results of biochemical characterization allowed identification of potential candidates for the development of biofertilizers targeted to the sunflower crop.