• Korean Journal of Microbiology
• /
• v.45 no.2
• /
• pp.155-162
• /
• 2009

A cultivation-based approach was employed to compare the culturable bacterial diversity associated with two phylogenetically closely related marine sponges, Spirastrella abata and Spirastrella panis, which have geologically overlapping distribution patterns. The bacteria associated with sponge were cultivated using MA medium supplemented with 3% sponge extracts. Community structures of the culturable bacteria of the two sponge species were analyzed with PCR-RFLP (restriction fragment length polymorphism) based on 16S rDNA sequences. The RFLP fingerprinting of 16S rDNA digested with HaeIII and MspI, revealed 24 independent RFLP types, in which 1-5 representative strains from each type were partially sequenced. The sequence analysis showed >98.4% similarity to known bacterial species in public databases. Overall, the microbial populations of two sponges investigated were found to be the members of the classes; Alphaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria. The Alphaproteobacteria were predominant in the bacterial communities of the two sponges. Gammaproteobacteria represented 38.5% of bacterial community in S. abata. Whereas only 1.6% of this class was present in S. panis. Bacillus species were dominat in S. panis. Bacillus species were found to be 44.3% of bacterial species in S. panis, while they were only 9.7% in S. abata. It is interesting to note that Planococcus maritimus (8.1%, phylum Firmicutes) and Psychrobacter nivimaris (28.9%, phylum Gammaproteobacteria) were found only in S. abata. This result revealed that profiles of bacterial communities from the sponges with a close phylogenetic relationship were highly species-specific.

• Journal of Mushroom
• /
• v.18 no.1
• /
• pp.100-106
• /
• 2020

Eight morel mushroom species were collected from Korea and other countries. The culture characteristics, genetic relationships, and beta-glucan content of the strains were analyzed. The mycelia of Morchella species exhibited optimal growth when cultured in dark at 25 ℃ in media with pH 7. The mycelia had a distinctive mycelial scent and characteristically changed color, being white initially, and then turning dark yellow to dark brown as it grew. The mycelia were classified into five types based on morphology. The isolates were identified as Morchella conica, two M. sextelata, M. importuna, M. esculenta, and three M. crassipes, based on ITS-rDNA sequences. PCR polymorphisms were variably produced within Morchella spp. using Universal Fungal Fingerprinting Primers (UFPF) and classified into four groups at the intra and inter species level. The strains, KMCC04971 and KMCC04407, showed the same banding pattern as M. conica and M. sextelata, respectively; however, these results were different from those of ITS analysis. Glucan content analysis by strain showed that the KMCC 04973 strain of M. importuna had the highest alpha- and beta-glucan content, at 16.4 g and 33.1 g per 100 g, respectively.

• Journal of Plant Biotechnology
• /
• v.37 no.1
• /
• pp.12-24
• /
• 2010

Plant metabolomics is a research field for identifying all of the metabolites found in a certain plant cell, tissue, organ, or whole plant in a given time and conditions and for studying changes in metabolic profiling as time goes or conditions change. Metabolomics is one of the most recently developed omics for holistic approach to biology and is a kind of systems biology. Metabolomics or metabolite fingerprinting techniques usually involves collecting spectra of crude solvent extracts without purification and separation of pure compounds or not in standardized conditions. Therefore, that requires a high degree of reproducibility, which can be achieved by using a standardized method for sample preparation and data acquisition and analysis. In plant biology, metabolomics is applied for various research fields including rapid discrimination between plant species, cultivar and GM plants, metabolic evaluation of commercial food stocks and medicinal herbs, understanding various physiological, stress responses, and determination of gene functions. Recently, plant metabolomics is applied for characterization of gene function often in combination with transcriptomics by analyzing tagged mutants of the model plants of Arabidopsis and rice. The use of plant metabolomics combined by transcriptomics in functional genomics will be the challenge for the coming year. This review paper attempted to introduce current status and prospects of plant metabolomics research.

• Molecules and Cells
• /
• v.23 no.2
• /
• pp.145-153
• /
• 2007

Elucidation of the roles of circadian associated factors requires a better understanding of the molecular mechanisms of circadian rhythms, control of flowering time through photoperiodic pathways, and photosensory signal transduction. In Arabidopsis, the APRR1 quintet, APRRs 1, 3, 5, 7, and 9, are known as central oscillator genes. Other plants may share the molecular mechanism underlying the circadian rhythm. To identify and characterize these circadian response genes in Brassica crops whose genome was triplicated after divergence from Arabidopsis, we identified B. rapa BAC clones containing these genes by BLAST analysis of B. rapa BAC end sequences against the five corresponding Arabidopsis regions. Subsequent fingerprinting, Southern hybridization, and PCR allowed identification of five BAC clones, one for each of the five circadian-related genes. By draft shotgun sequencing of the BAC clones, we identified the complete gene sequences and cloned the five expressed B. rapa circadian-associated gene members, BrPRRs 1, 3, 5, 7, and 9. Phylogenetic analysis revealed that each BrPRR was orthologous to the corresponding APRR at the sequence level. Northern hybridization revealed that the five genes were transcribed at distinct points in the 24 hour period, and Southern hybridization revealed that they are present in 2, 1, 2, 2, and 1 copies, respectively in the B. rapa genome, which was triplicated and then diploidized during the last 15 million years.

• Journal of the Korean Society of Marine Environment & Safety
• /
• v.30 no.1
• /
• pp.58-64
• /
• 2024

Approximately 250 marine oil spill accidents have occurred in Korea, with profound impact on local communities and the environment. The restoration process necessitates significant resources and costs to return affected areas to their pre-accident state. In accordance with the polluter pays principle, compensation is demanded from polluter, as stipulated in both international conventions and national laws. Consequently, investigations are conducted to determine civil and criminal liability. As the importance of investigation actors in oil spill accidents increases, standards such as CEN 15522-2 and ASTM D 3248 are employed to determine the similarity between the spilled oil and the oil of the suspected ship. Among these standards, CEN 15522-2, the most actively used European standard, underwent its third revision and is now known as EN 15522-2, as of 2023. This study used EN 15522-2 to analyze samples from marine oil spill accidents that occurred in Korea. The results indicated that, considering the characteristics of domestic spills where light fuel oil spills account for more than 40%, the application of EN 15522-2, which includes low-boiling point substances such as Adamantanes, was confirmed to be highly effective.

• Journal of Plant Biotechnology
• /
• v.29 no.3
• /
• pp.161-170
• /
• 2002

For the hairy root of Panax ginseng, we have got mass spectrums from MALDI/TOF/MS analysis and Tandem mass spectrums from ESI/Q-TOF/MS analysis. While mass spectrum provides the molecular weights of peptide fragments digested by protease such as trypsin, tandem mass spectrum produces amino acid sequence of digested peptides. Each amino acid sequences can be a query sequence in BLAST search to identify proteins. For the specimens of animals or plants of which genome sequences were known, we can easily identify expressed proteins from mass spectrums with high accuracy. However, for the other specimens such as ginseng, it is difficult to identify proteins with accuracy since all the protein sequences are not available yet. Here we compared the mass spectrums and the peptide amino acid sequences with ginseng expressed sequence tag (EST) DB. The matched EST sequence was used as a query in BLAST search for protein identification. They could offer the correct protein information by the sequence alignment with EST sequences. 90% of peptide sequences of ESI/Q-TOF/MS are matched with EST sequences. Comparing 68% matches of the same sequences with the nr database of NCBI, we got more matches by 22% from ginseng EST sequence search. In case of peptide mass fingerprinting from MALDI/TOF/MS, only about 19% (9 proteins of 47 spots) among peptide matches from nr DB were correlated with ginseng EST DB. From these results, we suggest that amino acid sequencing using tandem mass spectrum analysis may be necessary for protein identification in ginseng proteome analysis.

• Korean Journal of Microbiology
• /
• v.53 no.3
• /
• pp.163-169
• /
• 2017

Strains D4 and D5 were isolated from peach-rotten soil during the peach harvest season. The isolates were identified based on morphological and biochemical characterization, and identification was determined by 16S rRNA gene sequencing. Results showed that D4 has high similarity to Lactobacillus plantarum ATCC $14917^T$ and Lactobacillus pentosus ATCC $8041^T$ at 99.05% and 98.98%, respectively. D5 was also similar to Lactobacillus pentosus ATCC $8041^T$ and Lactobacillus plantarum ATCC $14917^T$ at 98.71% and 98.64%, respectively. In contrast, isolates showed differences in carbohydrate utilization in comparison to Lactobacillus plantarum ATCC $14917^T$ and Lactobacillus pentosus ATCC $8041^T$. In view of this we performed VITEK MS matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis, multiplex PCR fingerprinting, and random amplified polymorphic DNA (RAPD)-PCR to further confirm the identification of D4 and D5. The results of these analyses showed that both strains were most similar to Lactobacillus plantarum.

• Journal of Life Science
• /
• v.24 no.4
• /
• pp.393-402
• /
• 2014

Culture-dependent and culture-independent denaturing gradient gel electrophoresis (DGGE) analyses were employed to investigate the bacterial community associated with a natural dye wastewater treatment facility. A total of 104 (influent water, 48 strains; aeration tank, 25; settling tank, 31) bacterial strains were isolated. Based on the 16S rRNA gene sequences comparison analysis, the isolates belonged to four phyla: Proteobacteria, Actinobacteria, Firmicutes, and Bacteriodetes. Seventeen DGGE bands representing dominant taxa in each sample were cloned and partially sequenced. The same four phyla were detected by DGGE fingerprinting. The most dominant taxon retrieved by both methods was the member of the phylum Proteobacteria with Alphaproteobacteria as the predominant class. The bacterial community associated with the natural dye wastewater treatment facility is composed of parasites of animals and plants, decomposers of polysaccharides and dyes, and producers of extracellular polysaccharides.

• KOREAN JOURNAL OF CROP SCIENCE
• /
• v.55 no.3
• /
• pp.253-258
• /
• 2010

In this study, a total of 25 lines consisting of five native ginseng collections from Poonggi area, five lines from Geumsam area and 15 varieties were analyzed and clustered for the selection of Poonggi native ginseng in Korea using DNA markers. The results indicated that the long cluster distance were observed between the collections of 331002, 331004, 331005, 331007 and 331026 from Poonggi area, and the collections of 332009, 332021, 332046, 332050 and 332066 from Geumsan area because of the sensible differences on the number of leaves per stem, stem color and petiole color. Thus, the collections from Poonggi area with specific characters consisting of one stem per plant, five leaves per stem and broad elliptic leaflet shape were finely classified using nine primers including OPD05, OPD20, OPG17, OPH05 and so on. In this study, the collection of 331007 from Poonggi area was considered as the respective collection with above characters. Thus, the nine primers such as OPD05 and so on, will be used to select the Poonggi ginseng in the future studies.

• Journal of Microbiology and Biotechnology
• /
• v.27 no.2
• /
• pp.321-334
• /
• 2017

Process surveillance within agricultural biogas plants (BGPs) was concurrently studied by high-throughput 16S rRNA gene amplicon sequencing and an optimized quantitative microscopic fingerprinting (QMF) technique. In contrast to 16S rRNA gene amplicons, digitalized microscopy is a rapid and cost-effective method that facilitates enumeration and morphological differentiation of the most significant groups of methanogens regarding their shape and characteristic autofluorescent factor 420. Moreover, the fluorescence signal mirrors cell vitality. In this study, four different BGPs were investigated. The results indicated stable process performance in the mesophilic BGPs and in the thermophilic reactor. Bacterial subcommunity characterization revealed significant differences between the four BGPs. Most remarkably, the genera Defluviitoga and Halocella dominated the thermophilic bacterial subcommunity, whereas members of another taxon, Syntrophaceticus, were found to be abundant in the mesophilic BGP. The domain Archaea was dominated by the genus Methanoculleus in all four BGPs, followed by Methanosaeta in BGP1 and BGP3. In contrast, Methanothermobacter members were highly abundant in the thermophilic BGP4. Furthermore, a high consistency between the sequencing approach and the QMF method was shown, especially for the thermophilic BGP. The differences elucidated that using this biphasic approach for mesophilic BGPs provided novel insights regarding disaggregated single cells of Methanosarcina and Methanosaeta species. Both dominated the archaeal subcommunity and replaced coccoid Methanoculleus members belonging to the same group of Methanomicrobiales that have been frequently observed in similar BGPs. This work demonstrates that combining QMF and 16S rRNA gene amplicon sequencing is a complementary strategy to describe archaeal community structures within biogas processes.