• Journal of Life Science
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• v.12 no.6
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• pp.821-834
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• 2002

In order to measure the inter- and intraspecific genetic divergences within the genus Alexandrium, the variations within the internal transcribed spacer (ITS1 and ITS2) regions and 5.85 ribosomal RNA gene of eight Alexandrium species were examined for 33 strains from diverse geographical locations by direct sequencing. Five isolates of A. tamarense (AT-2, AT-6, AT-10, AT-A and AT-B) from Jinhae Bay, Korea were found to be completely identical to a Japanese strain OFX151-A. The length of the amplified ITSI-5.85-ITS2 region varied from 481 nucleotides (in A. margalefi) to 528 nucleotides (in A. affine CU1-1). ITS1 and ITS2 nucleotide lengths were negatively correlated, whereas a positive correlation was found between their G＋C content. The degree of sequence divergence ranged from 0.3% (1 bp) to a maximum of 53% (305 Up). Pairwise sequence comparisons revealed a small degree of divergence between A. tamarense and A. Pundyense isolates (1.2 - 2.3% ＝ 6-12 bp), but a high degree of divergence between A. tamarense and A. catenella (19.8% ＝ 102 bp), and between A. catenella and A. Pundyense (19.7%). Although most nodes were weakly supported by bootstrap values, some types tend to form independent molecular groups. A. catenella isolates also formed an independent molecular sub-group, with relaticula strong bootstrap values (94% or 85% and 79% or 98%, respectively in PAUP and NJ trees). Interestingly, A. cohorticula and A. frateculus always clustered within the same sub-group, this result being supported by strong bootstrap values. Our results indicate that the ITS regions provide useful informations on hierarchical population genetic structure and a high phylogenetic resolution in intraspecific and interspecific Alexandrium population.

• Journal of Plant Biotechnology
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• v.44 no.4
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• pp.372-378
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• 2017

For comparison of the transcription profiles in apple (Malus domestica L.) cultivars differing in flesh color expression, two cDNA libraries were constructed. Differences in gene expression between red flesh apple cultivar, 'Redfield' and white flesh apple cultivar, 'Granny Smith' were investigated by next-generation sequencing (NGS). Expressed sequence tag (EST) of clones from the red flesh apple cultivar and white flesh apple cultivar were selected for nucleotide sequence determination and homology searches. High resolution melting (HRM) technique measures temperature induced strand separation of short PCR amplicons, and is able to detect variation as small as one base difference between red flesh apple cultivars and white flesh apple cultivars. We applied high resolution melting (HRM) analysis to discover single nucleotide polymorphisms (SNP) based on the predicted SNP information derived from the apple EST database. All 103 pairs of SNPs were discriminated, and the HRM profiles of amplicons were established. Putative SNPs were screened from the apple EST contigs by HRM analysis displayed specific difference between 10 red flesh apple cultivars and 11 white flesh apple cultivars. In this study, we report an efficient method to develop SNP markers from an EST database with HRM analysis in apple. These SNP markers could be useful for apple marker assisted breeding and provide a good reference for relevant research on molecular mechanisms of color variation in apple cultivars.

• Korean Journal of Microbiology
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• v.50 no.1
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• pp.73-83
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• 2014

The objective of the this study was to investigate the binding capacity and removal ability of lactic acid bacterial strains obtained from Korean soybean paste for mutagenic heterocyclic amines (HCAs) formed during cooking of protein-rich food at high temperature. Among 19 strains identified by carbohydrate fermentation and 16S rRNA sequencing, the live cell or cell-free culture supernatant of Lactobacillus acidophilus D11, Enterococcus faecium D12, Pediococcus acidilactici D19, L. acidophilus D38, Lactobacillus sakei D44, Enterococcus faecalis D66, and Lactobacillus plantarum D70 inhibited the mutagenesis caused by either 3-amino-1,4-dimethyl-5H-pyrido[4,3-b] indole (Trp-P-1) or 3-amino-1-methyl-5H-pyrido[4,3-b] indole (Trp-P-2) in Salmonella typhimurium TA98 and TA100. The bacterial cells of the isolated strains showed greater binding activity than the pure cell wall, exopolysaccharide, and pepetidoglycan. The carbohydrate moieties of the cell wall or protein molecules on the cell surface have a significant role in binding Trp-P-1 and Trp-P-2, since protease, heating, sodium metaperiodate, or acidic pH treatments significantly (P<0.05) reduced the binding efficacy of the tested bacteria. Addition of metal ions or sodium dodecyl sulfate decreased the binding ability of E. faecium D12, L. acidophilus D38, and E. faecalis D66. Therefore, the binding mechanisms of these strains may consist of ion-exchange and hydrophobic bonds. Especially, the high mutagen binding by L. acidophilus D38 and L. plantarum D70 may reduce the accumulation or absorption of Trp-P-1 and Trp-P-2 in the small intestine via increased excretion of a mutagen-bacteria complex.

• Journal of the Society of Cosmetic Scientists of Korea
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• v.41 no.4
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• pp.375-382
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• 2015

Ginsenosides (ginseng saponin) as the one of important pharmaceutical compounds of ginseng and is responsible for the pharmacological and biological activities. These ginsenoside produces diverse small molecules ginsenoside which have more pharmacological activities including anti-wrinkle, anti-cancer and anti-oxidant effects. In the present study, we isolated bacteria using esculin agar, to produce ${\beta}$-glucosidase, and we focused on the bio-transformation of ginsenoside. Phylogenetic tree analysis was performed by comparing the 16S rRNA sequences; we identified the strain as Stenotrophomonas rhizopilae strain GFC09. In order to determine the optimal conditions for enzyme activity, the crude enzyme was incubated with 1 mM ginsenoside $Rb_1$. Bioconversion of ginsenoside $Rb_1$ were analyzed using TLC and HPLC. The crude enzyme hydrolyzed the ginsenoside $Rb_1$ along the following pathway: LB: $Rb_1{\rightarrow}Rd{\rightarrow}F_2$ into compound K, TSB: $Rb_1{\rightarrow}Rd{\rightarrow}F_2$. The structure of the hydrolyzed metabolites were identified by NMR. The activity screening tests showed that the conversion product induced the production of type I procollagen in a dose-dependent manner. These results suggested that hydrolyzed ginseng product containing the ginsenoside $F_2$ and compound K could be useful as an active ingredient for wrinkle-care cosmetics.

• Parasites, Hosts and Diseases
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• v.58 no.5
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• pp.551-558
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• 2020

The flaviviruses are small single-stranded RNA viruses that are typically transmitted by mosquitoes or tick vectors and are etiological agents of acute zoonotic infections. The viruses are found around the world and account for significant cases of human diseases. We investigated population of culicine mosquitoes in central region of Korean Peninsula, Incheon Metropolitan City and Hwaseong-si. Aedes vexans nipponii was the most frequently collected mosquitoes (56.5%), followed by Ochlerotatus dorsalis (23.6%), Anopheles spp. (10.9%), and Culex pipiens complex (5.9%). In rural regions of Hwaseong, Aedes vexans nipponii was the highest population (62.9%), followed by Ochlerotatus dorsalis (23.9%) and Anopheles spp. (12.0%). In another rural region of Incheon (habitat of migratory birds), Culex pipiens complex was the highest population (31.4%), followed by Ochlerotatus dorsalis (30.5%), and Aedes vexans vexans (27.5%). Culex pipiens complex was the predominant species in the urban region (84.7%). Culicine mosquitoes were identified at the species level, pooled up to 30 mosquitoes each, and tested for flaviviral RNA using the SYBR Green-based RT-PCR and confirmed by cDNA sequencing. Three of the assayed 2,683 pools (989 pools without Anopheles spp.) were positive for Culex flaviviruses, an insect-specific virus, from Culex pipiens pallens collected at the habitats for migratory birds in Incheon. The maximum likelihood estimation (the estimated number) for Culex pipiens pallens positive for Culex flavivirus was 25. Although viruses responsible for mosquito-borne diseases were not identified, we encourage intensified monitoring and long-term surveillance of both vector and viruses in the interest of global public health.

• Journal of Microbiology and Biotechnology
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• v.32 no.4
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• pp.405-418
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• 2022

Simotang oral liquid (SMT) is a traditional Chinese medicine (TCM) consisting of four natural plants and is used to alleviate gastrointestinal side effects after chemotherapy and functional dyspepsia (FD). However, the mechanism by which SMT helps cure these gastrointestinal diseases is still unknown. Here, we discovered that SMT could alleviate gastrointestinal side effects after chemotherapy by altering gut microbiota. C57BL/6J mice were treated with cisplatin (DDP) and SMT, and biological samples were collected. Pathological changes in the small intestine were observed, and the intestinal injury score was assessed. The expression levels of the inflammatory factors IL-1β and IL-6 and the adhesive factors Occludin and ZO-1 in mouse blood or small intestine tissue were also detected. Moreover, the gut microbiota was analyzed by high-throughput sequencing of 16S rRNA amplicons. SMT was found to effectively reduce gastrointestinal mucositis after DDP injection, which lowered inflammation and tightened the intestinal epithelial cells. Gut microbiota analysis showed that the abundance of the anti-inflammatory microbiota was downregulated and that the inflammatory microbiota was upregulated in DDP-treated mice. SMT upregulated anti-inflammatory and anticancer microbiota abundance, while the inflammatory microbiota was downregulated. An antibiotic cocktail (ABX) was also used to delete mice gut microbiota to test the importance of gut microbiota, and we found that SMT could not alleviate gastrointestinal mucositis after DDP injection, showing that gut microbiota might be an important mediator of SMT treatment. Our study provides evidence that SMT might moderate gastrointestinal mucositis after chemotherapy by altering gut microbiota.

• Korean Journal of Ecology and Environment
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• v.56 no.1
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• pp.36-44
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• 2023

Environmental DNA (eDNA) can exist in both intracellular and extracellular forms in natural ecosystems. When targeting harmful cyanobacteria, extracellular eDNA indicates the presence of traces of cyanobacteria, while intracellular eDNA indicates the potential for cyanobacteria to occur. However, identifying the "actual" potential for harmful cyanobacteria to occur is difficult using the existing sediment eDNA analysis method, which uses silica beads and cannot distinguish between these two forms of eDNA. This study analyzes the applicability of a density gradient centrifugation method (Ludox method) that can selectively analyze intracellular eDNA in sediment to overcome the limitations of conventional sediment eDNA analysis. PCR was used to amplify the extracted eDNA based on the two different methods, and the relative amount of gene amplification was compared using electrophoresis and Image J application. While the conventional bead beating method uses sediment as it is to extract eDNA, it is unknown whether the mic gene amplified from eDNA exists in the cyanobacterial cell or only outside of the cell. However, since the Ludox method concentrates the intracellular eDNA of the sediment through filtration and density gradient, only the mic gene present in the cyanobacteria cells could be amplified. Furthermore, the bead beating method can analyze up to 1 g of sediment at a time, whereas the Ludox method can analyze 5 g to 30 g at a time. This gram of sediments makes it possible to search for even a small amount of mic gene that cannot be searched by conventional bead beating method. In this study, the Ludox method secured sufficient intracellular gene concentration and clearly distinguished intracellular and extracellular eDNA, enabling more accurate and detailed potential analysis. By using the Ludox method for environmental RNA expression and next-generation sequencing (NGS) of harmful cyanobacteria in the sediment, it will be possible to analyze the potential more realistically.

• Journal of Life Science
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• v.17 no.8 s.88
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• pp.1082-1089
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• 2007

Serological anlysis of recombinant cDNA expression libraries (SEREX) has led to identification of several categories of new antigens recognized by the immune system of cancer patients, which are referred to as the cancer immunome. We analyzed normal testis cDNA expression libraries with serumobtained from non-small lung cancer patient and isolated 40 distinct antigen designated KP-LuT-1 through KP-LuT-40. Among these antigens 20 antigens were previously identified by SEREX analysis of other tumor types, and 20 out of 40 antigens (50%) did not match entries in Cancer Immunome Database and were considered newly identified antigens. Sequencing analysis showed that the anti-gens comprised 26 functional known proteins and 14 noble/uncharacterized gene products. Of these, the hypothetical protein KP-LuT-6 was shown tissue-restricted. RT-PCR showed it to be expressed strongly only in normal testis. In addition to normal tissues-restricted expression, KP-LuT-6 mRNA was detected in lung tumor samples(3/l0), stomach tumor samples(3/l0), and breast tumor samples(l/5), whereas not detected in colon tumor samples(O/I2). These data suggest that KP-LuT-6 is a cancer/testis (CT)-like antigen as a potential target for cancer immunotherapies.

• KSBB Journal
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• v.24 no.2
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• pp.149-155
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• 2009

19 strains, which could be identified as Lactobacillus sp. were isolated. The Cucurbita maxima has been known as a traditional healthy food and variable positive effects on the human body were already reported. In this study we tried to develop a production process for a healthy fermented drink with Cucurbita maxima and strains originated from Kimchi. Many kinds of lacctobacci species existed in the fermented food cannot survive in the acidic conditions in the stomach. So we tried to search and select a strain, which can arrive to the small intestine. A species of a Lactobacillus named as C332 was identifed as Lactobacillus plantarum and selected for the fermentation process. With the treatment with artificial gastric juice and artificial bile the survival rate of the cells could be calculated. The physiological characteristics at the variable conditions have been tested. After fermentation process the sensoric tests on the product with panels were tried. The most of the cells could survive in the acidic conditions and falcultive anaerobe. Especially some antibacterial effects aganinst E.coli were also found. With all kinds of the results from our research the fermented Cucurbita maxima drink can be a successful item in the market.

• Korean Journal of Poultry Science
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• v.51 no.2
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• pp.73-82
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• 2024

The gut microbiome of broilers is a critical factor in overall health and productivity. However, high summer temperatures and high stocking density (conventional farm condition) may cause stress to broilers, resulting in an imbalance in the gut microbiome. This study was conducted to compare the gut microbiome of broilers between spring and summer in welfare (Bosung, Jeollanam-do, South Korea) and conventional farms (Jangsu, Jeollabuk-do, South Korea). A total of 31 broilers were assigned to the following groups: conventional farm in spring (n = 8); conventional farm in summer (n = 8); welfare farm in spring (n = 7); welfare farm in summer (n = 8). Cecal digesta were collected from eight broilers from each farm, and microbiome analysis was performed using 16S rRNA gene sequencing. Beta diversity analysis indicated clear differences in cecal microbiome composition between spring and summerin both welfare and conventional farm. At the phylum level, analysis of conventional farm revealed a higher proportion of Bacteroidetes in spring than in summer. At the genus level, broilers exhibited a higher abundance of Bacteroides and Alistipesin spring compared to summer. In contrast, the difference in microbial flora composition observed in welfare farm was relatively small compared to conventional farm. In conclusion, the results of this study suggest that heat stress can negatively affect the caecum microbiome of broilers. However, improvements in the housing environment can mitigate the effects of heat stress.