• Environmental Engineering Research
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• 제14권1호
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• pp.3-9
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• 2009

Microorganisms play an important role in the geochemical cycles, industry, environmental cleanup, and biotechnology among other fields. Given the high microbial diversity, identification of the microorganism is essential in understanding and managing the processes. One of the most popular and powerful method for microbial identification is comparative 16S rRNA gene analysis. Due to the highly conserved nature of this essential gene, sequencing and later comparison of it against known rRNA databases can provide assignment of the bacteria into the taxonomy, and the identity of its closest relatives. Isolation and sequencing of 16S rRNA genes directly from natural environments (either from DNA or RNA) can also be used to study the structure of the whole microbial community. Nowadays, novel sequencing technologies with massive outputs are giving researchers worldwide the chance to study the microbial world with a depth that was previously too expensive to achieve. In this article we describe commonly used research approaches for the study of individual microorganisms and microbial communities using the tools provided by Ribosomal Database Project website.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2018년도 춘계학술발표회
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• pp.5-5
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• 2018

Ginseng (Panax ginseng C.A. Meyer), one of the most widely used medicinal plants in traditional oriental medicine, is used for the treatment of various diseases. It has been classified according to its cultivation environment, such as field cultivated ginseng (FCG) and mountain cultivated ginseng (MCG). However, little is known about differences in gene expression in ginseng roots between field cultivated and mountain cultivated ginseng. In order to investigate the whole transcriptome landscape of ginseng, we employed High-Throughput sequencing technologies using the Illumina HiSeqTM2500 system, and generated a large amount of sequenced transcriptome from ginseng roots. Approximately 77 million and 87 million high-quality reads were produced in the FCG and MCG roots transcriptome analyses, respectively, and we obtained 256,032 assembled unigenes with an average length of 1,171 bp by de novo assembly methods. Functional annotations of the unigenes were performed using sequence similarity comparisons against the following databases: the non-redundant nucleotide database, the InterPro domains database, the Gene Ontology Consortium database, and the Kyoto Encyclopedia of Genes and Genomes pathway database. A total of 4,207 unigenes were assigned to specific metabolic pathways, and all of the known enzymes involved in starch and sucrose metabolism pathways were also identified in the KEGG library. This study indicated that alpha-glucan phosphorylase 1, putative pectinesterase/pectinesterase inhibitor 17, beta-amylase, and alpha-glucan phosphorylase isozyme H might be important factors involved in starch and sucrose metabolism between FCG and MCG in different environments.

• Biotechnology and Bioprocess Engineering:BBE
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• 제8권2호
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• pp.83-88
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• 2003

A cellulose-producing strain isolated from rotten apples was identified as Gluconacetobacter hansenii based on its physiological properties and the 16S rDNA complete sequencing method, and specifically named Gluconacetobacter hansenii PJK. The amount of bacterial cellulose (BC) produced by G. hansenii PJK in a shaking incubator was 1.5 times higher than that produced in a static culture. The addition of ethanol to the medium during cultivation enhanced the productivity of bacterial cellulose, plus the supplementation of 1% ethanol into the culture medium made the produced BC aggregate into a big lump and thus protected the bacterial-cellulose-producing G. hansenii PJK cells in the shear stress field from being converted into non-cellulose-producing (Cel) mutants. Cells subcultured three times in a medium containing ethanol retained their ability to produce BC without any loss in the production yield.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2014년도 제46회 동계 정기학술대회 초록집
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• pp.415.1-415.1
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• 2014

Carrying out first-principles calculations, we study N-doped capped carbon nanotube (CNT) electrodes applied to DNA sequencing. While we obtain for the face-on nucleobase junction configurations a conventional conductance ordering where the largest signal results from guanine according to its high highest occupied molecular orbital (HOMO) level, we extract for the edge-on counterparts a distinct conductance ordering where the low-HOMO thymine provides the largest signal. The edge-on mode is shown to operate based on a novel molecular sensing mechanism that reflects the chemical connectivity between N-doped CNT caps that can act both as electron donors and electron acceptors and DNA functional groups that include the hyperconjugated thymine methyl group[1].

• Journal of Microbiology
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• 제38권2호
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• pp.66-73
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• 2000

To investigate the genetic relationship among 12 species belonging to the Fusarium section Martiella, Dlaminia, Gibbosum, Arthrosporiella, Liseola and Elegans, the internal transcribed spacer(ITS) regions of ribosomal DNA (rDNA) were amplified with primer pITS1 and pITS4 using the polymerase chain reaction(PCR). After the amplified products were digested with 7 restriction enzymes, restriction fragment length polymorphism (RFLP) patterns were analyzed. The partial nucleotide sequences of the ITS region were determined and compared. Little variation was observed in the size of the amplified product having sizes of 550bp or 570bp. Based on the RFLP analysis, the 12 species studied were divided into 5 RFLP types. In particular, strains belonging to the section Martiella were separated into three RFLP types. Interestingly, the RFLP type of F. solani f. sp. piperis was identical with that of isolates belonging to the section Elegans. In the dendrogram derived from RFLP analysis of the ITS region, the Fusarium spp. examined were divided into two major groups. In general, section Martiella excluding F. solani f. sp. piperis showed relatively low similarity with the other section. The dendrogram based on the sequencing analysis of the ITS2 region also gave the same results as that of the RFLP analysis. As expected, 5.8S, a coding region, was highly conserved, whereas the ITS2 region was more variable and informative. The difference in the ITS2 region between the length of F. solani and its formae speciales excluding F. solani f. sp. piperis and that of other species was caused by the insertion/deletion of nucleotides in positions 143-148 and 179-192.

• Industrial Engineering and Management Systems
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• 제1권1호
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• pp.10-18
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• 2002

A more comprehensive analytical framework for examining the relative merits of alternative dispatching process policies for nurseries is developed in this paper. The efficiency of the dispatch process of plants in a nursery is analysed using a vehicle routing model. The problem then involves determining in what order each vehicle should visit its locations. The problem is NP-hard. Several heuristic techniques are used to solve a real life nursery sequencing problem. The results obtained by these heuristic techniques are compared with each other and the current sequencing of orders. The model with some minor alterations can be also used to minimise the dispatching and collecting process in different agricultural plants.

• 한국식품영양학회지
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• 제8권1호
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• pp.37-42
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• 1995

The amino acid sequence of basic isozyme 55 of Horseradish Peroxidase (HRP E5) was determined by protein sequencing. HRP E5 consisted about 300 residues, and has a molecular weight of approximately 36,000 $\pm$ 500 dalton. The protein was rich In aspartic acid (14%), arginine(13%), and leucine(11%). The primary structure of HRP E5 was established by sequencing its tryptic (T1-T19) and lysylendopeptic (Al-A3) peptides. The sequence homology between HRP E5 and HRP C (neutral isozyme of horseradish peroxidase) is found to be more than 66%. The highest concentration of identical residues are found on residues 29~56, 90~123, and 155~173, but relatively low on 174~271.

• Journal of Animal Science and Technology
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• 제63권6호
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• pp.1464-1467
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• 2021

Bacillus coagulans CACC 834 was isolated from canine feces, and its potential probiotic properties were characterized by functional genome analysis. Whole-genome sequencing of B. coagulans CACC 834 was performed using the PacBio RSII platforms. The complete genome assembly consisted of one circular chromosome (3.1 Mb) with guanine (G) + cytosine (C) content of 47.1%. Annotation revealed 3,181 protein-coding sequences (CDSs), 30 rRNAs, and 83 tRNAs. Gene associated 11% of the genes were involved in replication, recombination, and repair. We also annotated various stress-related, acid resistance, bile salt resistance and adhesion-related domains in this strain, which likely provide support in exerting probiotic action by survival under gastrointestinal tract. These results add to our comprehensive understanding of B. coagulans and suggest potential mammal-related industrial applications.

• Genomics & Informatics
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• 제21권3호
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• pp.34.1-34.10
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• 2023

Nosocomial infections, commonly referred to as healthcare-associated infections, are illnesses that patients get while hospitalized and are typically either not yet manifest or may develop. One of the most prevalent nosocomial diseases in hospitalized patients is pneumonia, among the leading causes of mortality and morbidity. Viral, bacterial, and fungal pathogens cause pneumonia. More severe introductions commonly included Staphylococcus aureus, which is at the top of bacterial infections, per World Health Organization reports. The staphylococci, S. aureus, strain RMI-014804, mesophile, on-sporulating, and non-motile bacterium, was isolated from the sputum of a pulmonary patient in Pakistan. Many characteristics of S. aureus strain RMI-014804 have been revealed in this paper, with complete genome sequence and annotation. Our findings indicate that the genome is a single circular 2.82 Mbp long genome with 1,962 protein-coding genes, 15 rRNA, 49 tRNA, 62 pseudogenes, and a GC content of 28.76%. As a result of this genome sequencing analysis, researchers will fully understand the genetic and molecular basis of the virulence of the S. aureus bacteria, which could help prevent the spread of nosocomial infections like pneumonia. Genome analysis of this strain was necessary to identify the specific genes and molecular mechanisms that contribute to its pathogenicity, antibiotic resistance, and genetic diversity, allowing for a more in-depth investigation of its pathogenesis to develop new treatments and preventive measures against infections caused by this bacterium.

• Journal of Veterinary Science
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• 제22권4호
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• pp.55.1-55.17
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• 2021

Background: Naringenin and its glycoside naringin are well known citrus flavonoids with several therapeutic benefits. Although the anti-adipogenic effects of naringenin and naringin have been reported previously, the detailed mechanism underlying their anti-adipogenesis effects is poorly understood. Objectives: This study examined the anti-adipogenic effects of naringenin and naringin by determining differential gene expression patterns in these flavonoids-treated 3T3-L1 adipocytes. Methods: Lipid accumulation and triglyceride (TG) content were determined by Oil red O staining and TG assay. Glucose uptake was measured using a 2-[N-(7-Nitrobenz-2-oxa-1,3-diazol-4-yl)amino]-2-deoxy-d-glucose fluorescent d-glucose analog. The phosphorylation levels of AMP-activated protein kinase (AMPK) and acetyl Co-A carboxylase (ACC) were observed via Western blot analysis. Differential gene expressions in 3T3-L1 adipocytes were evaluated via RNA sequencing analysis. Results: Naringenin and naringin inhibited both lipid accumulation and TG content, increased phosphorylation levels of both AMPK and ACC and decreased the expression level of 3-hydroxy-3-methylglutaryl CoA reductase (HMGCR) in 3T3-L1 adipocytes. RNA sequencing analysis revealed that 32 up-regulated (> 2-fold) and 17 down-regulated (< 0.6-fold) genes related to lipid metabolism, including Acaca, Fasn, Scd1, Mogat1, Dgat, Lipin1, Cpt1a, and Lepr, were normalized to the control level in naringenin-treated adipocytes. In addition, 25 up-regulated (> 2-fold) and 25 down-regulated (< 0.6-fold) genes related to lipid metabolism, including Acaca, Fasn, Fabp5, Scd1, Srebf1, Hmgcs1, Cpt1c, Lepr, and Lrp1, were normalized to the control level by naringin. Conclusions: The results indicate that naringenin and naringin have anti-adipogenic potentials that are achieved by normalizing the expression levels of lipid metabolism-related genes that were perturbed in differentiated 3T3-L1 cells.