• Journal of Microbiology and Biotechnology
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• v.27 no.7
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• pp.1266-1271
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• 2017

Lactobacillus fermentum strain JDFM216, isolated from a Korean infant feces sample, possesses the ability to enhance the longevity and immune response of a Caenorhabditis elegans host. To explore the characteristics of strain JDFM216 at the genetic level, we performed whole-genome sequencing using the PacBio system. The circular draft genome has a total length of 2,076,427 bp and a total of 2,682 encoding sequences were identified. Five phylogenetically featured genes possibly related to the longevity and immune response of the host were identified in L. fermentum strain JDFM216. These genes encode UDP-N-acetylglucosamine 1-carboxyvinyltransferase (E.C. 2.5.1.7), ErfK/YbiS/YcfS/YnhG family protein, site-specific recombinase XerD, homocysteine S-methyltransferase (E.C. 2.1.1.10), and aspartate-ammonia ligase (E.C. 6.3.1.1), which are involved in peptidoglycan synthesis and amino acid metabolism in the gut environment. Our findings on the genetic background of L. fermentum strain JDFM216 and its potential candidate genes for host longevity and immune response provide new insight for the application of this strain in the food industry as newly isolated functional probiotic.

• Journal of Microbiology and Biotechnology
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• v.28 no.6
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• pp.987-996
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• 2018

Bacterial programmed cell death is regulated by the toxin-antitoxin (TA) system. YhaV (toxin) and Pr1F (antitoxin) have been recently identified as a type II TA system in Escherichia coli. YhaV homologs have conserved active residues within the C-terminus, and to characterize the function of this region, we purified native YhaV protein (without denaturing) and constructed YhaV proteins of varying lengths. Here, we report a new low-temperature method of purifying native YhaV, which is notable given the existing challenges of purifying this highly toxic protein. The secondary structures and thermostability of the purified native protein were characterized and no significant structural destruction was observed, suggesting that the observed inhibition of cell growth in vivo was not the result of structural protein damage. However, it has been reported that excessive levels of protein expression may result in protein misfolding and changes in cell growth and mRNA stability. To exclude this possibility, we used an [$^{35}S$]-methionine prokaryotic cell-free protein synthesis system in vitro in the presence of purified YhaV, and two C-terminal truncated forms of this protein (YhaV-L and YhaV-S). Our results suggest that the YhaV C-terminal region is essential for mRNA interferase activity, and the W143 or H154 residues may play an analogous role to Y87 of RelE.

• Proceedings of the Korean Society of Sericultural Science Conference
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• 1997.06a
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• pp.73-101
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• 1997

Baculoviruses are characterized by large double-stranded circular DNA genomes and rod-shaped enveloped virions. Bombyx mori nucleopolyhedrovirus(BmNPV) is a major pathogen, which causes severe damage in sericulture. Currently, BmNPV is recogtnized as an improtant tool in molecular biology, especially for expression of useful genes in B.mori cells and silkworm larvae. Our laboratories have focused on the studies of the molecular mechanisms of BmNPV replication and the application of BmNPV to agriculture and medicine. The entire nucleotide sequence of the BmNPV genome has recently determined. The BmNPV genome possessed 135 putative genes and 7 homologous repeated sequence (hrs) regions. Relatively little space, a few to a few hundred base-pairs, was observed between the open reading frames and hrs. Termination codons often overlapped. These results showed a compactly packde BmNPV genome. Based on comparative sequence analyses, we speculated that the ancestor of BmNPV was a baculovirus similar to Autographa californica NPV(AcNPV). The function of the BmNPV genes were characterized by gene deletion analysis; p35 was found to be involved in blocking apoptosis and cysteine proteinase was found to be involved in horizontal virus transmission by degrading viral-infected larval host. By AcNPV and BmNPV coinfection experiments, we identified a BmNPV gene involved in expanding host specificity of AcNPV. The identified gene was likely encoded a DNA helicase based on the amino acid sequence analysis; a few amino acid substitutions in the putative DNA helicase gene resulted in the expansion of host range of AcNPV. These findings indicate that BmNPV evolved within a short period from an AcNPV-like ancestral virus due to rapid evolution including specific amino acid substitutions and gene deletions/insertions.

• Microbiology and Biotechnology Letters
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• v.47 no.1
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• pp.25-33
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• 2019

Lactobacillus rhamnosus BFE5264, isolated from a Maasai fermented milk product ("kule naoto"), was previously shown to exhibit bile acid resistance, cholesterol assimilation, and adhesion to HT29-MTX cells in vitro. In this study, we re-annotated and analyzed the previously reported complete genome sequence of strain BFE5264. The genome consists of a circular chromosome of 3,086,152 bp and a putative plasmid, which is the largest one identified among L. rhamnosus strains. Among the 2,883 predicted protein-coding genes, those with carbohydrate-related functions were the most abundant. Genome analysis of strain BFE5264 revealed two consecutive CRISPR regions and no known virulence factors or antimicrobial resistance genes. In addition, previously known highly variable regions in the genomes of L. rhamnosus strains were also evident in strain BFE5264. Pairwise comparison with the most studied probiotic strain L. rhamnosus GG revealed strain BFE5264-specific deletions, probably due to insertion sequence-mediated recombination. The latter was associated with loss of the spaCBA pilin gene cluster and exopolysaccharide biosynthetic genes. Comparative genomic analysis of the sequences from all available L. rhamnosus strains revealed that they were clustered into two groups, being within the same species boundary based on the average nucleotide identities. Strain BFE5264 had a sister group relationship with the group that contained strain GG, but neither ANI-based hierarchical clustering nor core-gene-based phylogenetic tree construction showed a clear distinctive pattern associated with the isolation source, implying that the genotype alone cannot account for their ecological niches. These results provide insights into the probiotic mechanisms of strain BFE5264 at the genomic level.

• The Korean Journal of Pesticide Science
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• v.18 no.3
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• pp.202-209
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• 2014

RNA interference (RNAi) is the method which controls phenotypes of gene in live cells. Chitinase is the enzyme helping digestion and absorption of old cuticles during the ecdysis of insects. In order to investigate molting-inhibition effect with the chitinase related gene in Spodoptera litura, RNA was extracted from the $5^{th}$ instars. cDNA was synthesized and then we obtained about 700 bp size chitinase. After PCR products were cloned into a pGEM T-easy vector, colonies were picked. DNA was extracted from the colony cultures. EcoR I enzyme was used to check whether PCR products were inserted or not. And then we confirmed vector band of about 3 kb and insert band of about 700 bp. To synthesize the dsRNA, each DNA was cut with Spe I and Nco I enzymes (Circular DNA became lineared DNA). After synthesis of dsRNA, approximately 5 ul dsRNA was injected into the $3^{rd}$ abdominal segment of S. litura $4^{th}$ larvae. The concentration of dsRNA was about $10{\mu}g/{\mu}l$. We confirmed larval-larval molting : there were phenotypically abnormal individuals - for instance malformation, molting inhibition and change of integument color. Pupaadult molting : there were phenotypically abnormal individuals - for instance molting inhibition, change of wings and malformation. Also we could investigate the pupation, emergence and variation about noninjection, treated with DW and dsRNA. Each pupation was non-injection 83.3%, DW 78.3% and dsRNA 66.7%. Each emergence was non-injection 90.0%, DW 72.3% and dsRNA 65.0%. So we considered that chitinase dsRNA induced molting inhibition effect. But each variation was non-injection 8.9%, DW 2.9% and dsRNA 19.2%. Therefore dsRNA group showed the highest variation value. When 18 hours after injecting dsRNA, we could obtain abnormal individual.

• Journal of Korean Society of Forest Science
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• v.17 no.1
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• pp.35-42
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• 1973

Deciduous trees grown naturally in the forest of Korea usually have an irregular Lee-form and their utility has been decreased. In Korea, most of the deciduous stands are distributed in the hinterland. A shortage of the total growing stock made utilization of them necessary in this country even though some difficulties to be cutted and transported are accompanied. Therefore, this study was conducted to select the suitable sampling method for surveying them. The results investigated are as follows. 1. Three locations being 10 hectares in each location for the plots were chosen and surveyed with six $20m{\times}50m$ rectangular sample plots by four types of sampling method below. And the result is shown in Table 1. A. Random sampling by grids B. Random sampling by co-ordinates C. Systematic line plot. D. Sub-sampling 2. One hundred and fifty hectares from all plots were sectioned through the application of aerial photography scaled of 1 : 15,000. The author divided forest types according to diameter class and crown density with mirror stereoscope. The forest types were divided into three classes. Seven sample plots from the area of 150 hectars are systematically arranged and the results investigated on the circular sample point of 0.1 hectare are shown in Table 4. 3. There were no significant differences between results by sampling method and by diameter measurement method (population mean) as shown in Table 3. 4. Random sampling by grid and systematic line plot are better than others. 5. There are more over-estimated values when the circular sample point is used than where the rectangular sample point. 6. As forest stands are irregular, smaller number of sample points will make many errors.

• Journal of Korean Society of Forest Science
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• v.42 no.1
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• pp.67-73
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• 1979

In order to observe the anatomical phenomena of root formation in the hypocotyl cuttings of maples, the hypocotyls of Acer palmatum. Acer micro-sieboldianum, and Acer saccharinum were used as the materials. The rooted portions were sectioned by a microtom and doubly stained by safranin and fast green. The results obtained are summarized as follows; 1. A cross section structure of hypocotyl cuttings of Acer sp. is consist of epidermis, cortex, vascular bundle and pith from the outside. The vascular bundle makes circular shape forming polyarch in A. saccharinum and tetrarch in both A. palmatum and A. micro-sieboldianum. 2. An adventitious root of A. saccharinum originated in phloem parenchyma, while that of A. palmatum and A. micro-sieboldianum originated in interfascicular parenchyma related with phloem cells. 3. The hypocotyl cuttings of Acer sp. is commonly composed of parenchyma tissue having vigorous differentiation capability. Therefore, the originated root grow easily through the cortex and epidermis breaking their tissues.

• Research in Plant Disease
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• v.12 no.3
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• pp.189-196
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• 2006

Crown gall on lower stem of weeping fig(Ficus benjamina Roxb.) was first observed at Daejon in 2003. Tumors were about 15 cm in size and semi-round with rough surface texture of dark brown color. Two virulent isolates among ten bacteria isolated from the tumor tissues were characterized. Their colonies were convex, glistening, circular with an entire edge, and white or tannish cream in color on potato dextrose agar supplemented with 0.5% $CaCO_3$. They were rod shape with peritrichous flagellae, gram-negative, aerobic growth, oxidase-positive, and grew on D1M agar. The isolates were identified as Agrobacterium larrymoorei and A. tumefaciens based on biochemical and physiological characteristics, fatty acid profiles and substrate utilization patterns. Seedlings of some host plants excepting grapevine produced typical galls two to three weeks after inoculation with cell suspensions of the virulent strains. This is the first report on crown gall of weeping fig in Korea.

• Research in Plant Disease
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• v.12 no.3
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• pp.197-204
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• 2006

Crown gall on lower stem and root of chrysanthemum(Dendranthema grandiflorum Kitamura) was observed at Hwasung and Gumi in 2001 and 2004, respectively. Tumors were semi-round with rough surface texture of dark brown color. Nine isolates inducing gall formation on lower stem of chrysanthemum among twenty isolates from the tumor tissues were characterized. Their colonies were convex, glistening, circular with an entire edge and whitish or tannish cream in color on potato dextrose agar supplemented with 0.5% $CaCO_3$. The virulent isolates were rod-shaped with peritrichous flagellae, gram negative, aerobic and growing on D1M agar. Among nine virulent isolates, one isolate was identified as Agrobacterium rubi and eight isolates were A. tumefaciens based on biochemical and physiological characteristics, fatty acid profiles and substrate utilization patterns. A. tumefaciens had strong pathogenicity and broad host range compared with A. rubi. This is the first report on crown gall of chrysanthemum in Korea. To our knowledge, crown gall of chrysanthemum caused by A. rubi is first report in this study worldwide.

• Weed & Turfgrass Science
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• v.5 no.2
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• pp.101-104
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• 2016

Curvularia leaf blight of creeping bentgrass (Agrostis stolonifera) putting green by caused Curvularia trifolii was observed in Hapcheon, Korea. In July to September 2014, curvularia leaf blight developed on leaf blades of creeping bentgrass as small water-soaked lesions that subsequently turned into dark-colored, necrotic spots. The spots were expanded and became gray, grayish-brown, or light brown, circular to oblong lesions with purple to dark brown borders that often were surrounded by a yellow halo. The necrotic lesions coalesced, became irregular in shape and caused tip or complete blighting of the leaves. Blighted leaf blades appeared grayish-white to tan. The fungus was identified by morphological characters and 16S rDNA sequencing as C. trifolii. Conidia of the pathogen were short, with predominantly 3-septa, straight or often curved, with end cells frequently paler than intermediate cells. Size of the 3-septate conidia in culture are $26{\sim}28{\times}11{\sim}12{\mu}m$. Pathogenicity of the fungus was proved by artificial inoculation on the host. This is the first report of C. trifolii causing leaf blight on creeping bentgrass in Korea.