• Journal of Microbiology and Biotechnology
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• v.26 no.1
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• pp.207-212
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• 2016

PacBio's long-read sequencing technologies can be successfully used for a complete bacterial genome assembly using recently developed non-hybrid assemblers in the absence of second-generation, high-quality short reads. However, standardized procedures that take into account multiple pre-existing second-generation sequencing platforms are scarce. In addition to Illumina HiSeq and Ion Torrent PGM-based genome sequencing results derived from previous studies, we generated further sequencing data, including from the PacBio RS II platform, and applied various bioinformatics tools to obtain complete genome assemblies for five bacterial strains. Our approach revealed that the hierarchical genome assembly process (HGAP) non-hybrid assembler resulted in nearly complete assemblies at a moderate coverage of ~75x, but that different versions produced non-compatible results requiring post processing. The other two platforms further improved the PacBio assembly through scaffolding and a final error correction.

• Journal of Korean Society of Environmental Engineers
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• v.36 no.2
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• pp.96-102
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• 2014

To meet the reinforced discharge standards, effect of coagulant PAC (Poly aluminium chloride, 10.4% as $Al_2O_3$) on phosphorous removal in advanced wastewater treatment process (a modified $A^2$/O). 15 mg/L of PAC determined by jar-test was added to influent of settling basin in a modified $A^2$/O consists of anaerobic, anoxic, and oxic chamber which contains Bio-clod and porous polyurethane media. Performance of PAC was tested by supernatant after settling. The removal efficiencies of BOD, COD, TP (total phosphorus) and SP (soluble phosphorus) on biological process with PAC were 96.1%, 88.8%, 97.0% and 98.6%, compared with those on biological process without PAC were 95.4%, 72.4%, 71.6% and 59.5% respectively. 18.4% of TP and 39.1% of SP removal efficiency was increased, although increase of BOD and COD removal rate was not significant. Only PAC addition to influent of settling basin in $A^2O$ process can help total phosphorus removal to 0.13 mg/L with following discharge standard.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.253-253
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• 2022

Codonopsis lanceolata (C. lanceolata) has been widely used in East Asia as a traditional medicine to treat various diseases such as bronchitis, convulsions, cough, obesity, and hepatitis. C. lanceolata belonging to Campanulaceae contains bioactive compounds such as polyphenols, saponins, and steroids. However, despite the pharmacological significance of C. lanceolata, the genetic information of this plant is limited and there are few studies of its transcriptome. In this study, we constructed a unigene set of C. lanceolata using Pac-Bio sequencing. Furthermore, the reads generated from Pac-bio and Illumina sequencing were mixed and assembled using rnaSPAdes. All genes involved in the triterpenoid pathway, a major bioactive compounds of C. lanceolata, were searched from the two unigene sets and the expression profiles of these genes were analyzed. The results showed that lupeol, beta-amyrin, and dammarenediol synthesis genes were activated in the leaves and roots of C. lanceolata. In particular, the expression of genes related to lupeol synthesis was relatively high, suggesting that the main triterpenoid of C. lanceolata is lupeol. Transcriptome studies related to lupeol synthesis in C. lanceolata have been rarely reported. Lupeol has been reported to have pharmacological effects such as anti-inflammatory, anti-cancer, and anti-bacterial. This study suggests the importance of C. lanceolata as a lupeol producing plant.

• Korean Journal of Microbiology
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• v.54 no.1
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• pp.84-86
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• 2018

Cells of Deinococcus puniceus $DY1^T$ are Gram-positive, coccus-shaped, and crimson color-pigmented. Strain $DY1^T$ was isolated from soil irradiated with 5 kGy gamma radiation and showed resistance to UVC and gamma radiation. In this study, we report the complete genome sequence of a bacterium Deinococcus puniceus $DY1^T$ is consist of circular chromosome comprised of 2,971,983 bp, with the G + C content of 62.5%. The complete genome sequence was obtained using the PacBio RS II platform, it included 2,617 coding sequences (CDs), 2,762 genes, and 88 pseudogene.

• Journal of Korean Society of Water and Wastewater
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• v.22 no.1
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• pp.141-148
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• 2008

This study was conducted to evaluate the effect of PAC(Powder Activated Carbon) retention time on stable operation of high concentration powered activated carbon(HCPAC-MBR) in the treatment of secondary domestic wastewater. The pilot scale HCPAC-MBR system was operated at two different SRTs, 25 days and 100 days. The main drawback of HCPAC-MBR system was the rapid increase of trans-membrane pressure. The increase rate of trans-membrane pressure was proportional to SRT value at constant flux. This result seemed to be caused by reduced amount of EPS adsorbed on the PAC in the reactor by decreasing the SRT of the PAC. The particle size of the PAC was also influenced by SRT. The PAC size was decreased as SRT was increased. The change of particle size could be one reason for the change of trans-membrane pressure. The pore volume in the cake-layer formed on the membrane surface became to be increased by reducing SRT, because the cake-layer was highly composed of the PAC. Therefore, increased pore volume might play a role to reduce the trans-membrane pressure. The removal rate of E260 and TOC was also inversely proportional to SRT value.

• Journal of Korean Society on Water Environment
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• v.22 no.6
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• pp.996-1003
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• 2006

The absorption characteristics of powdered activated carbon doped by transition-metal nanoparticles were investigated to enhance the remove efficiencies of $TCOD_{Mn}$ and Color from the flexo-inks wastewater. According to the adsorption dynamics of PAC and MPAC, the optimal dosage of activated-carbon adsorbents was 3 g/L under the reaction conditions of pH6.0, 30 mill of reaction time, 240 rpm of mixing intensity. The removal efficiencies by the optimal dosages were maximized as 19% $TCOD_{Mn}$, 57% Color for PAC and 88% $TCOD_{Mn}$, 95% Color for MPAC. Freundlich indexes of isotherm absorption were estimated as follows: i) For PAC, k=-8.11, 1/n=2.98, r=0.91 in the raw water, and k=0.14, b/n=0.75, r=0.96 in the biological treatment water, ii) For MPAC, k=2.69, 1/n=0.21, r=0.80 in the raw water, and k=0.74, 1/n=1.17, r=0.95 in the biological treatment water. MPAC (Powdered activated carbon doped by transition-metal nanoaprticles) was very effective in the removal of organics from the raw water and biological treatment water, as Freundlich indexes of 1/n for both types of water were estimated less than 2.0.

• Korean Journal of Microbiology
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• v.55 no.3
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• pp.309-312
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• 2019

Comamonas sp. NLF-7-7 was isolated from biofilter of wastewater treatment plant. The whole-genome sequence of Comamonas sp. NLF-7-7 was analyzed using the PacBio RS II and Illumina HiSeqXten platform. The genome comprises a 3,333,437 bp chromosome with a G + C content of 68.04%, 3,197 total genes, 9 rRNA genes, and 49 tRNA genes. This genome contained pollutants degradation and floc forming genes such as sulfur oxidization pathway (SoxY, SoxZ, SoxA, and SoxB) and floc forming pathway (EpsG, EpsE, EpsF, EpsG, EpsL, and glycosyltransferase), respectively. The Comamonas sp. NLF-7-7 can be used to the purification of wastewater.

• Korean Journal of Microbiology
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• v.53 no.3
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• pp.227-229
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• 2017

Spirosoma rigui KCTC $12531^T$ was isolated from fresh water from the Woopo wetland, Korea. In this study, we report the complete genome sequence of a bacterium Spirosoma rigui KCTC $12531^T$, its complete genome sequence was obtained using the PacBio RS II platform. The genome comprised of 5,828,404 bp with the G + C content of 54.4%, the genome included 4,774 genes were predicted, among them, 4,647 genes are protein-coding genes.

• Korean Journal of Microbiology
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• v.53 no.3
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• pp.230-232
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• 2017

A Gram-stain-negative, yellow-pigmented bacterial strain, designated Spirosoma aerolatum KACC $17939^T$, was isolated from a biofilm of car air conditioner collected in Republic of Korea. In this study, we report the complete genome sequence of a bacterium Spirosoma aerolatum KACC $17939^T$ obtained using the PacBio RS II platform. The genome comprised of 7,959,595 bp with the G + C content of 48.3%, the genome included 6,640 genes were predicted, among them, 6,471 genes are protein-coding genes.

• Journal of Biomedical Engineering Research
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• v.38 no.1
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• pp.16-24
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• 2017

For the development of feasible retinal prosthesis, one of the important elements is acquiring proper judging tool if electrical stimulus leads to patient's visual perception. If evoked potential to electrical stimulus is recorded in primary visual (V1) cortex, it means that the stimulus effectively evokes visual perception. Therefore, in this study, we established VEP recording system on V1 cortex using BioPAC modules as the judging tool. And the measuring system was evaluated by recording VEP of mice. After anesthesia, normal mice (C57BL/6J strain; n = 6) were secured to stereotaxic apparatus (Harvard Apparatus, USA). For the recording of VEP, the stainless steel needle electrode (impedance: $2-5k{\Omega}$) was positioned on the surface of the cortex through the burr hole at 2.5 mm lateral and 4.6 mm caudal to bregma. DA 100C and EEG 100C BioPAC modules were used for the trigger signal and VEP recording, respectively. When left eye was blocked by black cover and right eye was stimulated by flash light using HMsERG (RetVet Corp, USA), VEP response at left V1 cortex was detected, but there was no response at right V1 cortex. Amplitudes and latencies of P2, N3 peaks of VEP recording varied according to the depths of the electrodes on V1 cortex. From the surface upto $600{\mu}m$ depth, amplitudes of P2 and N3 increased, while deeper than $600{\mu}m$, those amplitudes decreased. The deeper the insertion depth of the electrode, the latency of N1 peaks tends to be delayed. However, there was no statistically significant difference among the latencies of P2 and N3 peaks (P > 0.05, ANOVA). Our VEP recording data such as the insertion depth and the latency and amplitudes of peaks might be used as guidelines for electrically-evoked potential (EEP) recording experiment in near future.