• Korean Journal of Microbiology
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• v.55 no.3
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• pp.289-292
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• 2019

Lachnospiraceae bacterium KGMB03038 (=KCTC 15821) belonging to the class Clostridia in phylum Firmicutes, was isolated from a stool sample of a healthy Korean. Herein, we report the complete genome sequence of strain KGMB03038 analyzed using the PacBio Sequel platform. The genome comprises of 3,334,474 bp with G + C content of 47.8%, which includes 3,099 predicted protein-coding genes, 12 ribosomal RNAs, 54 transfer RNAs, and 4 ncRNAs. Genome analysis revealed that strain KGMB03038 possesses a number of genes involved in hydrolysis of carbohydrates, including mono-, di-, and oligo-saccharides, and biosynthesis of various amino acids.

• Korean Journal of Microbiology
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• v.33 no.1
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• pp.31-37
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• 1997

Intergeneric hybrids between Aspergillus niger and Perricillium ch~y.sop~um(Tyr ), hyperlipolytic enzyne-producing fungi, were obtained by nuclear transfer technique:. Optimal conditions for formation of intergeneric hybrids were investigated. Maximum production of protoplasts were obtainrd by 1% Novozym 234 at $30^{\circ}C$ for 3 hrs and the most effective osmotic stabilizers for the isolation of protoplasts were 0.6 M KC]. Frequencies of hybrid formation by nuclear transfer were $1.3{\times}$10^{-3}$$ $-3.8{\times}$10^{-3}$$. From the chervation of genetic stability, conidial size, DNA content, ;md nuclear stain, it was suggested that their karyotypes are aneuploid. The hybrids showed 1.4-2.2 fold higher lipase activities than parental strains. It was strongly supported by results of this study that nuclear transfer technique is much more efficient in the formation of intergeneric hybrids than protoplast fusion and is very useful for the improvement of strains.

• Journal of the Korean Vacuum Society
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• v.22 no.2
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• pp.55-65
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• 2013

Sterilization of Neurospora crassa has been investigated in this research by using a surface air plasma with dielectric barrier discharged (DBD) structure under atmospheric pressure. The sinusoidal alternating current has been used in this experiment with discharge voltage of 1.4~2.3 kV. The phase difference between the voltage and current signals are found to be almost 80 degree due to the capacitive property of dielectric barrier. Temperature on the biomaterials has been minimized by radiating the heat with the air cooling system. It is noted that the substrate temperature remains under 37 degree for plasma exposure time of 10 minutes with operation of cooler system. It is found that the ozone, $O_3$, has been measured to be about 25~30 ppm within 1 cm region and to be about 5 ppm at the 150 cm downstream region away from the suface plasma. It is also noted that the nitric oxide, NO, and nitric dioxide, $NO_2$, are not nearly detected. Germination rate and mitochodrial activity of Neurospora crassa immersed in the deionized water have been found to be drastically decreased as the plasma treatment time and its electrical power are increased in this experiment. Here, the mitochondrial activity has been analyzed by MTT (3-(4,5-dimethy lthiazol-2yl)-2,5-diphenyl-2H-tetrazolium bromide) assay. However, sterilization of Neurospora crassa immersed in the Vogel's minimal media has been found to be low by plasma treatment, which is caused by surrounding background solution. This research shows the sterilization possibility of Neurospora crassa by using the noncontated surface DBD plasma, which is different from the plasma jet. This is mainly attibuted to the reactive species generated by the surface plasma, since they play a major role for inhibition of micobes such as Neurospora crassa.

• Korean Journal of Microbiology
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• v.42 no.2
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• pp.156-159
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• 2006

A base substitution was introduced at the position 789 in Escherichia coli 16S rRNA, which was previously identified as an invariant residue for ribosome function and the ability of the mutant ribosomes to translate chloramphenicol acetyltransfernse mRNA was measured by determining the degree of resistance to chloramphenicol of cells expressing these mutant ribosomes. As expected, mutant ribosomes containing a base sub-stitution at the position 789 showed significantly reduced protein-synthesis ability and to identify a functional role played by this residue in protein synthesis, we developed an efficient genetic method to select second-site revertants in 16S rRNA that restore protein-synthesis function to these mutant ribosomes.

• Korean Journal of Microbiology
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• v.53 no.1
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• pp.64-66
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• 2017

Caballeronia sordidicola strain PAMC 26592 was isolated from Umbilicaria sp., a lichen material collected from Svalbard Archipelago in the Arctic Ocean. We report the draft genome sequence of the strain PAMC 26592, a metabolic generalist. As we have observed in previous genomic studies in the genus Caballeronia draft genomic sequences of PAMC 26592 had an assortment of genes of ecological importance and of bio-technical potentials, which include diverse metabolic genes for carbohydrates, aromatic compounds, amino acids, and vitamins, and genes for nitrogen / sulfur metabolisms, stress responses, membrane transporters, antibiotic resistance, and heavy metal resistance.

• Korean Journal of Microbiology
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• v.53 no.4
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• pp.340-341
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• 2017

Acidovorax citrulli is a causal agent for bacterial fruit blotch on watermelon. Here, we report the complete genome sequence of A. citrulli strain KACC17005. The genome contains 5,349,924 bp with G + C contents of 68.54%, including 4,520 protein coding genes in a circular chromosome. It also possesses at least 15 genes encoding putative type III effector proteins, which may contribute to promoting virulence in susceptible hosts or triggering immune responses in resistant hosts.

• Korean Journal of Microbiology
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• v.54 no.4
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• pp.442-444
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• 2018

Recently, we isolated a multidrug-resistant Escherichia coli strain KBN10P04869 from a patient with acute myeloid leukemia. We report the complete genome of this strain which consists of 5,104,264 bp with 4,457 protein-coding genes, 88 tRNAs, and 22 rRNAs, and the co-occurrence of multidrug- resistant genes including $^{bla}CMY-2$, $^{bla}TEM-1$, $^{bla}CTX-M-15$, $^{bla}NDM-5$, and $^{bla}OXA-18$.

• 축산식품과학과 산업
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• v.9 no.2
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• pp.26-35
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• 2020

• Journal of Life Science
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• v.31 no.12
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• pp.1079-1087
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• 2021

To analyze gut microbiota of livestock in Korea and compare taxonomic differences, we conducted 16S rRNA metagenomic analysis through next-generation sequencing. Fecal samples from broiler chickens, pigs, and cattle were collected from domestic feedlots randomly. α-diversity results showed that significant differences in estimated species richness estimates (Chao1 and ACE, Abundance-based coverage estimators) and species richness index (OUTs, Operational taxonomic units) were identified among the three groups. However, NPShannon, Shannon, and Simpson indices revealed that abundance and evenness of the species were statistically significant only for poultry (broiler chickens) and mammals (pigs and cattle). Firmicutes was the most predominant phylum in the three groups of fecal samples. Linear discriminant (LDA) effect size (LEfSe) analysis was conducted to reveal the ranking order of abundant taxa in each of the fecal samples. A size-effect over 2.0 on the logarithmic LDA score was used as a discriminative functional biomarker. As shown by the fecal analysis at the genus level, broiler chickens were characterized by the presence of Weissella and Lactobacillus, as well as pigs were characterized by the presence of provetella and cattele were characterized by the presence of Acinetobacter. A permutational multivariate analysis of variance (PERMANOVA) showed that differences of microbial clusters among three groups were significant at the confidence level. (p=0.001). This study provides basic data that could be useful in future research on microorganisms associated with performance growth, as well as in studies on the livestock gut microbiome to increase productivity in the domestic livestock industry.

• KIPS Transactions on Software and Data Engineering
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• v.2 no.2
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• pp.113-118
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• 2013

The current GPU virtualization techniques incur large overheads when executing application programs mainly due to the fine-grain time-sharing scheduling of the GPU among multiple Virtual Machines (VMs). Besides, the current techniques lack of portability, because they include the APIs for the GPU computations in the VM monitor. In this paper, we propose a low overhead and high performance GPU virtualization approach on a heterogeneous HPC system based on the open-source Xen. Our proposed techniques are tailored to the bio applications. In our virtualization framework, we allow a VM to solely occupy a GPU once the VM is assigned a GPU instead of relying on the time-sharing the GPU. This improves the performance of the applications and the utilization of the GPUs. Our techniques also allow a direct pass-through to the GPU by using the IOMMU virtualization features embedded in the hardware for the high portability. Experimental studies using microbiology genome analysis applications show that our proposed techniques based on the direct pass-through significantly reduce the overheads compared with the previous Domain0 based approaches. Furthermore, our approach closely matches the performance for the applications to the bare machine or rather improves the performance.