• Journal of Microbiology and Biotechnology
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• v.26 no.2
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• pp.270-276
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• 2016

Extended-spectrum β-lactamases (ESBLs), particularly those of the CTX-M types, are the predominant resistance determinants of Escherichia coli that are rapidly spreading worldwide. To determine CTX-M types, E. coli isolates were collected from retail chickens (n = 390) and environmental samples from chicken farms (n = 32) and slaughterhouses (n = 67) in Korea. Fifteen strains harboring bla_CTX-M genes were isolated from 358 E. coli isolates. The most common CTX-M type was eight of CTX-M-15, followed by six of CTX-M-1 and one of CTX-M-14. The bla_CTX-M genes were identified in the isolates from retail chickens (n = 9), followed by feces, water pipes, floors, and walls. Conjugations confirmed the transferability of the plasmids carrying bla_CTX-M genes to the recipient E. coli J53 strain. Furthermore, eight addiction systems carried by the replicons in CTX-M types were confirmed. The dominant system was identified as ccdAB, vagCD, and pndAC in donor strains and transconjugants. The clonal relationship between the two strains carrying bla_CTX-M genes indicates that E. coli may transmit from the farm to retail chickens, suggesting a possible public health risk. Our findings demonstrate that the detection of CTX-M types in E. coli isolates is important for tracking ESBL production in animals, and suggest linkage of multiple addiction systems in plasmids bearing bla_CTX-M genes.

• Food Engineering Progress
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• v.21 no.1
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• pp.22-28
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• 2017

Ginger was steamed at $121^{\circ}C$ and $1.5lb/in^2$ for 30 min, dried at $60^{\circ}C$ for 12 h, and each step was repeated nine times. During processing, the lightness ($L^*$ value) and yellowness ($b^*$ value) decreased from $85.65{\pm}0.33$ and $26.99{\pm}0.20$ in the non-treated ginger to $56.91{\pm}0.25$ and $16.69{\pm}0.06$ in ginger treated for the ninth treatment. On the other hand, redness ($a^*$ value) increased from $-1.51{\pm}0.03$ to $7.34{\pm}0.08$ on the eight treatment and then decreased to $7.21{\pm}0.04$ on the ninth theatment. The contents of 6-gingerol decreased from $3.257{\pm}0.067mg/g$ in the non-treated ginger to $0.567{\pm}0.036mg/g$ on the theatment, whereas the contents of 6-shogaol increased from $1.299{\pm}0.050mg/g$ to $2.999{\pm}0.089mg/g$ on the sixth treatment and decreased to $2.099{\pm}0.039$ on the ninth treatment. The contents of 10-gingerol decreased slightly from $1.106{\pm}0.125mg/g$ to $0.806{\pm}0.026mg/g$. Unlike the 6- and 10-gingerol, the contents of 8-gingerol did not change greatly, with values between $0.916{\pm}0.005mg/g$ and $1.106{\pm}0.005mg/g$ being observed during processing. The tyrosinase inhibitory activities were increased from $43.42{\pm}11.45%$ in the non-treated ginger to 100% on the sixth treatment and then decreased to $51.98{\pm}7.36%$ on the theatment. The antioxidative activity was retained during processing.

• Microbiology and Biotechnology Letters
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• v.34 no.1
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• pp.1-6
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• 2006

Harmful algal blooms (HABs or red tides), caused by uncontrolled proliferation of marine phytoplankton, impose a severe environmental problem and occasionally threaten even public health. We sequenced the genome of an EPS-producing marine bacterium Hahella chejuensis that produces a red pigment with the lytic activity against red-tide dinoflagellates at parts per billion level. H. chejuensis is the first sequenced species among algicidal bacteria as well as in the order Oceanospirillales. Sequence analysis indicated a distant relationship to the Pseudomonas group. Its 7.2-megabase genome encodes basic metabolic functions and a large number of proteins involved in regulation or transport. One of the prominent features of the H. chejuensis genome is a multitude of genes of functional equivalence or of possible foreign origin. A significant proportion (${\sim}23%$) of the genome appears to be of foreign origin, i.e. genomic islands, which encode genes for biosynthesis of exopolysaccharides, toxins, polyketides or non-ribosomal peptides, iron utilization, motility, type III protein secretion and pigment production. Molecular structure of the algicidal pigment was determined to be prodigiosin by LC-ESI-MS/MS and NMR analyses. The genomics-based research on H. chejuensis opens a new possibility for controlling algal blooms by exploiting biotic interactions in the natural environment and provides a model in marine bioprospecting through genome research.

• Journal of Microbiology and Biotechnology
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• v.30 no.8
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• pp.1142-1148
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• 2020

Mitochondria play a vital role in iron uptake and metabolism in pathogenic fungi, and also influence virulence and drug tolerance. However, the regulation of iron transport within the mitochondria of Cryptococcus neoformans, a causative agent of fungal meningoencephalitis in immunocompromised individuals, remains largely uncharacterized. In this study, we identified and functionally characterized Mrs3/4, a homolog of the Saccharomyces cerevisiae mitochondrial iron transporter, in C. neoformans var. grubii. A strain expressing an Mrs3/4-GFP fusion protein was generated, and the mitochondrial localization of the fusion protein was confirmed. Moreover, a mutant lacking the MRS3/4 gene was constructed; this mutant displayed significantly reduced mitochondrial iron and cellular heme accumulation. In addition, impaired mitochondrial iron-sulfur cluster metabolism and altered expression of genes required for iron uptake at the plasma membrane were observed in the mrs3/4 mutant, suggesting that Mrs3/4 is involved in iron import and metabolism in the mitochondria of C. neoformans. Using a murine model of cryptococcosis, we demonstrated that an mrs3/4 mutant is defective in survival and virulence. Taken together, our study suggests that Mrs3/4 is responsible for iron import in mitochondria and reveals a link between mitochondrial iron metabolism and the virulence of C. neoformans.

• Journal of the Korean Magnetic Resonance Society
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• v.15 no.2
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• pp.137-145
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• 2011

Hsp33, a prokaryotic molecular chaperone, exerts holdase activity in response to oxidative stress. In this study, the stepwise conformational change of Hsp33 upon oxidation was monitored by NMR. In order to overcome its high molecular weight (33 kDa as a monomer and 66 kDa as a dimer), spectra were simplified using a selectively [$^{15}N$]His-labeled protein. All of the eight histidines were observed in the TROSY spectrum of the reduced Hsp33. Among them, three peaks showed dramatic resonance shifts dependent on the stepwise oxidation, indicating a remarkable conformational change. The results suggest that unfolding of the linker domain is associated with dimerization, but not entire region of the linker domain is unfolded.

• Journal of Microbiology and Biotechnology
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• v.19 no.7
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• pp.635-646
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• 2009

Rapid and accurate diagnosis of diseases is very important for appropriate treatment of patients. Recent advances in molecular-level interaction and detection technologies are upgrading the clinical diagnostics by providing new ways of diagnosis, with higher speed and accuracy. In particular, DNA microarrays can be efficiently used in clinical diagnostics which span from discovery of diseaserelevant genes to diagnosis using its biomarkers. Diagnostic DNA microarrays have been used for genotyping and determination of disease-relevant genes or agents causing diseases, mutation analysis, screening of single nucleotide polymorphisms (SNPs), detection of chromosome abnormalities, and global determination of posttranslational modification. The performance of DNA-microarray-based diagnosis is continuously improving by the integration of other tools. Thus, DNA microarrays will play a central role in clinical diagnostics and will become a gold standard method for disease diagnosis. In this paper, various applications of DNA microarrays in disease diagnosis are reviewed. Special effort was made to cover the information disclosed in the patents so that recent trends and missing applications can be revealed.

• Journal of Microbiology and Biotechnology
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• v.30 no.10
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• pp.1583-1591
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• 2020

CRISPR/Cpf1 has emerged as a new CRISPR-based genome editing tool because, in comparison with CRIPSR/Cas9, it has a different T-rich PAM sequence to expand the target DNA sequence. Single-base editing in the microbial genome can be facilitated by oligonucleotide-directed mutagenesis (ODM) followed by negative selection with the CRISPR/Cpf1 system. However, single point mutations aided by Cpf1 negative selection have been rarely reported in Corynebacterium glutamicum. This study aimed to introduce an amber stop codon in crtEb encoding lycopene hydratase, through ODM and Cpf1-mediated negative selection; deficiency of this enzyme causes pink coloration due to lycopene accumulation in C. glutamicum. Consequently, on using double-, triple-, and quadruple-base-mutagenic oligonucleotides, 91.5-95.3% pink cells were obtained among the total live C. glutamicum cells. However, among the negatively selected live cells, 0.6% pink cells were obtained using single-base-mutagenic oligonucleotides, indicating that very few single-base mutations were introduced, possibly owing to mismatch tolerance. This led to the consideration of various target-mismatched crRNAs to prevent the death of single-base-edited cells. Consequently, we obtained 99.7% pink colonies after CRISPR/Cpf1-mediated negative selection using an appropriate single-mismatched crRNA. Furthermore, Sanger sequencing revealed that single-base mutations were successfully edited in the 99.7% of pink cells, while only two of nine among 0.6% of pink cells were correctly edited. The results indicate that the target-mismatched Cpf1 negative selection can assist in efficient and accurate single-base genome editing methods in C. glutamicum.

• Journal of Plant Biotechnology
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• v.36 no.2
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• pp.137-143
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• 2009

An efficient system for high frequency plant regeneration was established through investigating various factors such as plant growth regulator combinations, explant types and ages, and addition of $AgNO_3$ influenced on shoot regeneration in Brassica juncea L. cv. BARI sarisha-10. Murashige and Skoog (MS) medium supplemented with 0.1 mg/L NAA (1-naphthaleneacetic acid) and 1 mg/L BA (6-benzyladenine) showed the maximum shoot regeneration frequency (56.67%) among the different combinations of NAA and BA. Explant type, explant age, and addition of $AgNO_3$ also significantly affected shoot regeneration. Of the four type of explants (cotyledon, hypocotyl, root, and leaf explants)- cotyledon explants produced the highest shoot regeneration frequency and hypocotyls explants produced the highest number of shoots per explant, whereas root explants did not produce any shoot. The cotyledonary explants from Four-day-old seedlings showed the maximum shoot regeneration frequency and number of shoots per explant. Shoot regeneration frequency increased significantly by adding $AgNO_3$ to the medium. Two mg/L $AgNO_3$ appeared to be the best for shoot regeneration with the highest shoot regeneration frequency (86.67%) and number of shoots per explant (7.5 shoots). Considerable variation in shoot regeneration from cotyledonay explants was observed within the B. juncea L. genotypes. The shoot regeneration frequency ranged from 47.78% for cv. Shambol to 91.11% for cv. Rai-5. In terms of the number of shoots produced per explant, B. juncea L. cv. Daulot showed the maximum efficiency. MS medium supplemented with 0.1 mg/L NAA showed the highest frequency of rooting. The regenerated plantlets were transferred to pot soil and grown to maturity in the greenhouse. All plants were fertile and morphologically identical with the source plants.

• Journal of Species Research
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• v.7 no.1
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• pp.50-59
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• 2018

During the course of investigation of indigenous prokaryotic species in Korea, a total of 30 bacterial strains belonging to the phylum Firmicutes were isolated from diverse environmental sites such as soil, avian feces, wastewater treatment plants, fermented vegetables, seawater, algae, sea cucumber, octopus and tidal flat sediment. Phylogenetic analysis based on 16S rRNA gene sequences revealed that each strain showed high sequence similarity (${\geq}98.7%$) to the closest type strain and formed a robust phylogenetic clade with the most closely related species in the phylum Firmicutes. To date, there is no official record of these 30 species in Korea. Therefore, we report 26 species of 12 genera in the order Bacillales and 4 species of 4 genera in the order Lactobacillales which have not been reported in Korea. Morphological and biochemical characteristics, isolation sources and NIBR deposit numbers are described in the species descriptions.

• Journal of Plant Biotechnology
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• v.38 no.1
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• pp.9-14
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• 2011

To determine whether pattern recognition based on metabolite fingerprinting for whole cell extracts can be used to discriminate cultivars metabolically, leaves of nine commercial Orostachys plants were subjected to Fourier transform infrared spectroscopy (FT-IR). FT-IR spectral data from leaves were analyzed by principal component analysis (PCA) and Partial least square discriminant analysis (PLS-DA). The dendrogram based on hierarchical clustering analysis of these PLS-DA data separated the nine Orostachys species into five major groups. The first group consisted of O. iwarenge 'Yimge', 'Jeju', 'Jeongsun' and O. margaritifolius 'Jinju' whereas in the second group, 'Sacheon' was clustered with 'Busan,' both of which belong to O. malacophylla species. However, 'Samchuk', belong to O. malacophylla was not clustered with the other O. malacophylla species. In addition, O. minuta and O. japonica were separated to the other Orostachys plants. Thus we suggested that the hierarchical dendrogram based on PLS-DA of FT-IR spectral data from leaves represented the most probable chemotaxonomical relationship between commercial Orostachys plants. Furthermore these metabolic discrimination systems could be applied for reestablishment of precise taxonomic classification of commercial Orostachys plants.