• Journal of fish pathology
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• v.18 no.2
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• pp.133-146
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• 2005

A bacteriological survey in maricultured fish farms was conducted in Korea from 2002 to 2004. A total number of 166 Vibrio isolates were collected from diseased fishes, including olive flounder (133 isolates), black rock fish (8 isolates), red sea bream (6 isolates), shrimp (5 isolates), black sea bream (4 isolates), abalone (3 isolates) and other fishes (7 isolates). All isolates were phenotypically characterized and then groups were obtained using the traditional biochemical test. Representative isolates of each group were genotypically characterized with sequencing the 16S rRNA genes or 16S-23S intergenic space genes. Above 14 species of Vibrio were identified as V. ichthyoenteri (45 strains), V. alginolyticus (34 strains), V. harveyi (32 strains), Ph. damselae subsp. damselae (Formerly V. damsela, 10 strains), V. campbellii (6 strains), V. costicola-like (6 strains), V. fisheri (5 stains), V. fluvialis (4 strains) and others Vibrio sp. (24 strains) by combining of biochemial and genetic characteristics.

• Journal of Microbiology and Biotechnology
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• v.29 no.6
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• pp.989-998
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• 2019

Autophagy is crucial for immune defense against Mycobacterium tuberculosis (Mtb) infection. Mtb can evade host immune attack and survival within macrophages by manipulating the autophagic process. MicroRNAs (miRNAs) are small, non-coding RNAs that are involved in regulating vital genes during Mtb infection. The precise role of miRNAs in autophagy with the exits of Mtb remains largely unknown. In this study, we found miR-1958, a new miRNA that could regulate autophagy by interacting with 3'UTR of autophagy-related gene 5 (Atg5). In addition, Mtb infection triggered miR-1958 expression in RAW264.7 cells. What's more, miR-1958 overexpression blocked autophagic flux by impairing the fusion of autophagosomes and lysosomes. Overexpression of miR-1958 reduced Atg5 expression and LC3 puncta while inhibition of miR-1958 brought an increase of Atg5 and LC3 puncta; the opposite results were observed in detection of p62. The survival of Mtb in RAW264.7 cells transfected with mimic of miR-1958 was enhanced. Taken together, our research demonstrated that a novel miR-1958 could inhibit autophagy by interacting with Atg5 and favored intracellular Mtb survival in RAW264.7 cells.

• Journal of Life Science
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• v.22 no.7
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• pp.912-919
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• 2012

A Bacillus sp. strain producing celluase and xylanase was isolated from environmental soil with LB agar plate containing carboxymethylcellulose (CM-cellulose) and beechwood xylan stained with trypan blue as substrates, respectively. Based on the 16S rRNA gene sequence and API 50 CHL test, the strain was identified as B. subtilis and named B. subtilis NC1. The cellulase and xylanase from B. subtilis NC1 exhibited the highest activities for CM-cellulose and beechwood xylan as substrate, respectively, and both enzymes showed the maximum activity at pH 5.0 and $50^{\circ}C$. We cloned and sequenced the genes for cellulase and xylanase from genomic DNA of the B. subtilis NC1 by the shot-gun cloning method. The cloned cellulase and xylanase genes consisted of a 1,500 bp open reading frame (ORF) encoding a 499 amino acid protein with a calculated molecular mass of 55,251 Da and a 1,269 bp ORF encoding a 422 amino acid protein with a calculated molecular mass of 47,423 Da, respectively. The deduced amino acid sequences from the genes of cellulase and xylanase showed high identity with glycosyl hydrolases family (GH) 5 and 30, respectively.

• Korean Journal of Microbiology
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• v.34 no.3
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• pp.132-136
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• 1998

Molecular analyses of natural microbial communities are often dependent upon the obtainments of pure nucleic acids. The four methods (elution after agarose gel electrophoresis, G-75 microspin columns, hydroxyapatite mi-crospin columns, and polyvinylpolypyrrolidone (PVPP) microspin columns) were compared for the removal of PCR-inhibitory humic substances from the crude DNA extracts of marine sediment samples. The PVPP microspin columns have shown superior removal of humic substances from the crude DNA extract of marine sediment samples, with yield of $4.8{\mu}g/g$ (dry weight of sediment). The purified DNA by this rapid method was pure enough to amplify 1.5 kb fragment corresponding almost full length of 16S rRNA genes.

• Journal of Microbiology and Biotechnology
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• v.21 no.4
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• pp.333-340
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• 2011

Herbicide-tolerant Zoysia grass has been previously developed through Agrobacterium-mediated transformation. We investigated the effects of genetically modified (GM) Zoysia grass and the associated herbicide application on bacterial community structure by using culture-independent approaches. To assess the possible horizontal gene transfer (HGT) of transgenic DNA to soil microorganisms, total soil DNAs were amplified by PCR with two primer sets for the bar and hpt genes, which were introduced into the GM Zoysia grass by a callus-type transformation. The transgenic genes were not detected from the total genomic DNAs extracted from 1.5 g of each rhizosphere soils of GM and non-GM Zoysia grasses. The structures and diversities of the bacterial communities in rhizosphere soils of GM and non-GM Zoysia grasses were investigated by constructing 16S rDNA clone libraries. Classifier, provided in the RDP II, assigned 100 clones in the 16S rRNA gene sequences library into 11 bacterial phyla. The most abundant phyla in both clone libraries were Acidobacteria and Proteobacteria. The bacterial diversity of the GM clone library was lower than that of the non- GM library. The former contained four phyla, whereas the latter had seven phyla. Phylogenetic trees were constructed to confirm these results. Phylogenetic analyses of the two clone libraries revealed considerable difference from each other. The significance of difference between clone libraries was examined with LIBSHUFF statistics. LIBSHUFF analysis revealed that the two clone libraries differed significantly (P<0.025), suggesting alterations in the composition of the microbial community associated with GM Zoysia grass.

• Korean Journal of Microbiology
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• v.55 no.3
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• pp.313-315
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• 2019

An anaerobic bacterial strain WCF-2 was isolated from cow dung in finding cellulose-degrading bacteria for use as silage additives. Strain WCF-2 showed a higher cellulolytic activity than Cellulosilyticum lentocellum DSM $5427^T$, the closest relative of strain WCF-2 (98.2% of 16S rRNA gene sequence similarity). We sequenced the complete genome of strain WCF-2 and compared it with that of C. lentocellum DSM $5427^T$. The OrthoANI value between the two strains was 97.9% thus strain WCF-2 was identified as C. lentocellum. The genome size of strain WCF-2 was 4,779,774 bp with a G + C content of 34.4%, 4,154 coding genes (CDS), 54 pseudo genes, and 142 RNA genes. Strain WCF-2 harbored seven cellulase genes, five of which showed low similarities with those of C. lentocellum DSM $5427^T$.

• Journal of the Korean Institute of Intelligent Systems
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• v.14 no.5
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• pp.545-550
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• 2004

The study of available genotypes (biodiversity analysis) in bacterial communities is of growing importance in several fields such as ecology, environmental technology, clinical diagnostics, etc. These culture-independent genotyping techniques, especially amplifying 16S rRNA genes, attempt to overcome some shortcomings of conventional cultivation method. Biodiversity analysis based on molecular technique were laborious for base-calling chromatogram, trimming primer sites, correcting strand directions, electing representative operation taxonomic units (OTU), etc. Also, biologists wanted intuitively to confirm results of the above processes. For making up these demands, we developed the web application based on Folder-Process-Filter (FPF) modeling with correspondence to classical Model-View-Controller model. The model of web application leads to keep virtues of simplicity and directness for development and management of the stepwise web interfaces. The web application was developed in Perl and CGI on Linux workstation. It can be freely accessed from http://home.pusan.ac.kr/～genome/tools/rat.htm.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.2
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• pp.179-186
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• 2014

This study aimed to investigate the diversity of the Butyrivibrio group bacteria in goat rumen and its response to garlic oil (GO) supplementation as revealed by molecular analysis of cloned 16S rRNA genes. Six wethers fitted with ruminal fistulas were assigned to two groups for a cross-over design with 28-d experimental period and 14-d interval. Goats were fed a basal diet without (control) or with GO ruminal infusion (0.8 g/d). Ruminal contents were used for DNA extraction collected before morning feeding on d 28. A total bacterial clone library was firstly constructed by nearly full-length 16S rRNA gene cloned sequences using universal primers. The resulting plasmids selected by Butyrivibrio-specific primers were used to construct a Butyrivibrio group-specific bacterial clone library. Butyrivibrio group represented 12.98% and 10.95% of total bacteria in control and GO group, respectively. In libraries, clones were classified to the genus Pseudobutyrivibrio, Butyrivibrio and others within the family Lachnospiraceae. Additionally, some specific clones were observed in GO group, being classified to the genus Ruminococcus and others within the family Ruminococcaceae. Based on the criterion that the similarity was 97% or greater with database sequences, there were 29.73% and 18.42% of clones identified as known isolates (i.e. B. proteoclasticus and Ps. ruminis) in control and GO groups, respectively. Further clones identified as B. fibrisolvens (5.41%) and R. flavefaciens (7.89%) were specifically found in control and GO groups, respectively. The majority of clones resembled Ps. ruminis (98% to 99% similarity), except for Lachnospiraceae bacteria (87% to 92% similarity) in the two libraries. The two clone libraries also appeared different in Shannon diversity index (control 2.47 and GO group 2.91). Our results indicated that the Butyrivibrio group bacteria had a complex community with considerable unknown species in the goat rumen.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.30 no.1
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• pp.46-54
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• 1997

Sporulation in the fission yeast Schizosaccharomyces pombe has been regarded as an important model of cellular development and differentiation. S. pombe cells proliferate by mitosis and binary fission on growth medium. Deprivation of nutrients especially nitrogen sources, causes the cessation of mitosis and initiates sexual reproduction by malting between two sexually compatible cell types. Meiosis is then followed in a diploid cell in the absence of nitrogen source. DNA fragment complemented with the mutations of sporulation gene was isolated from the S. pombe gene library constructed in the vector, pDB 248' and designated as pDB (spo 5)1. We futher analyzed six recombinant plasmids, pDB (spo 5)2, pDB(spo 5)3, pDB(spo 5)4, pDB(spo 5)5, pDB(spo 5)6, pDB(spo 5)7, and found each plasmids is able to rescue the spo 5-2, spo 5-3, spo 5-4, spo 5-5, spo 5-6, spo 5-7, mutations, respectively. Mapping of the integrated plasmid into the homologous site of the S. pombe chromosomes demonstrated that pDB (spo 5)1, and pDB (spo 5)R1 contained the spo 5 gene. Transcipts of spo 5 gene were analyzed by Northern hybridization. Two transcripts of 3.2 kb and 25 kb were detected with 5 kb Hind III fragment containing a part of the spo 5 gene as a probe. The small mRNA (2.5 kb) appeared only when a wild-type strain was cultured in the absence of nitrogen source in which condition the large mRNA (3.2 kb) was produced constitutively. Appearance of a 2.5 kb spo 5-mRNA depends upon the function of the mei1, mei2 and mei3 genes.

• Parasites, Hosts and Diseases
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• v.54 no.5
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• pp.631-636
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• 2016

This study aimed to develop a multiplex-touchdown PCR method to simultaneously detect 3 species of protozoan parasites, i.e., Cryptosporidium parvum, Giardia lamblia, and Cyclospora cayetanensis, the major causes of traveler's diarrhea and are resistant to standard antimicrobial treatments. The target genes included the Cryptosporidium oocyst wall protein for C. parvum, Glutamate dehydrogenase for G. lamblia, and 18S ribosomal RNA (18S rRNA) for C. cayetanensis. The sizes of the amplified fragments were 555, 188, and 400 bps, respectively. The multiplex-touchdown PCR protocol using a primer mixture simultaneously detected protozoa in human stools, and the amplified gene was detected in > $1{\times}10^3$ oocysts for C. parvum, > $1{\times}10^4$ cysts for G. lamblia, and > 1 copy of the 18S rRNA gene for C. cayetanensis. Taken together, our protocol convincingly demonstrated the ability to simultaneously detect C. parvum, G. lamblia, and C. cayetanenesis in stool samples.