• Journal of Microbiology and Biotechnology
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• v.33 no.6
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• pp.753-759
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• 2023

The genus Paenibacillus contains a variety of biologically active compounds that have potential applications in a range of fields, including medicine, agriculture, and livestock, playing an important role in the health and economy of society. Our study focused on the bacterium SS4^T (KCTC 43402^T = GDMCC 1.3498^T), which was characterized using a polyphasic taxonomic approach. This strain was analyzed using antiSMASH, BAGEL4, and PRISM to predict the secondary metabolites. Lassopeptide clusters were found using all three analysis methods, with the possibility of secretion. Additionally, PRISM found three biosynthetic gene clusters (BGC) and predicted the structure of the product. Genome analysis indicated that glucoamylase is present in SS4^T. 16S rRNA sequence analysis showed that strain SS4^T most closely resembled Paenibacillus marchantiophytorum DSM 29850^T (98.22%), Paenibacillus nebraskensis JJ-59^T (98.19%), and Paenibacillus aceris KCTC 13870^T (98.08%). Analysis of the 16S rRNA gene sequences and Type Strain Genome Server (TYGS) analysis revealed that SS4^T belongs to the genus Paenibacillus based on the results of the phylogenetic analysis. As a result of the matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) results, SS4^T was determined to belong to the genus Paenibacillus. Comparing P. marchantiophytorum DSM 29850^T with average nucleotide identity (ANI 78.97%) and digital DNA-DNA hybridization (dDDH 23%) revealed values that were all less than the threshold for bacterial species differentiation. The results of this study suggest that strain SS4^T can be classified as a Paenibacillus andongensis species and is a novel member of the genus Paenibacillus.

• The Korean Journal of Medicine
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• v.99 no.1
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• pp.50-56
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• 2024

Nocardiosis is uncommon. Immunocompromising conditions predispose individuals to pulmonary and disseminated nocardiosis of the brain, skin, and subcutaneous tissues. The most common pathogens are Nocardia cyriacigeorgica, Nocardia nova, and Nocardia farcinica. The speciation of Nocardia to determine antimicrobial susceptibility is difficult using traditional biochemical methods. Here, we report the case of a 73-year-old man with chronic obstructive lung disease who developed a rapidly progressing intramuscular abscess around the left hip and thigh. Within 3 days, the lesions progressed to an epidural abscess at the L4 to S1 level. Although he was treated with broad-spectrum antibiotics and extensive incision and drainage, he died of rapidly progressive respiratory failure. Nocardia abscessus (N. abscessus) was identified in pus samples using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). This case shows that the diagnosis of an intramuscular abscess caused by N. abscessus is challenging and that using MALDI-TOF MS may facilitate the diagnosis and ensure appropriate treatment.

• Development and Reproduction
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• v.8 no.1
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• pp.1-9
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• 2004

The potential importance of proteomic approaches has been clearly demonstrated in other fields of human medical research, including liver and heart disease and certain forms of cancer. However, reproductive researches have been applied to proteomics poorly. Proteomics can be defined as the systematic analysis of proteins for their identity, quantity, and function. It could increase the predictability of early drug development and identify non-invasive biomarkers of toxicity or efficacy. Proteome analysis is most commonly accomplished by the combination of two-dimensional gel electrophoresis(2DE) and MALDI-TOF(matrix-assisted laser desorption ionization-time of flight) MS(mass spectrometry) or protein chip array and SELDI-TOF(surface-enhanced laser desorption ionization-time of flight) MS. In addition understanding the possessing knowledge of the developing biomarkers used to assess reproductive biology will also be essential components relevant to the topic of reproduction. The continued integration of proteomic and genomic data will have a fundamental impact on our understanding of the normal functioning of cells and organisms and will give insights into complex cellular processes and disease and provides new opportunities for the development of diagnostics and therapeutics. The challenge to researchers in the field of reproduction is to harness this new technology as well as others that are available to a greater extent than at present as they have considerable potential to greatly improve our understanding of the molecular aspects of reproduction both in health and disease.

• Korean Journal of Clinical Laboratory Science
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• v.52 no.1
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• pp.18-27
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• 2020

The correct distinction of carbapenem-resistant Enterobacteriaceae (CRE) and ccarbapenemase producing Enterobacteriaceae (CPE) and the rapid detection of CPE are important for instituting the correct treatment and management of clinical infections. Screening protocols are mainly based on cultures of rectal swab specimens on selective media followed by phenotypic tests to confirm a carbapenem-hydrolyzing activity, the rapid carbapenem inactivation method, lateral flow immunoassay, the matrix-assisted laser desorption ionization-time-of-flight test and molecular methods. The CPE is accurate for detection, and is essential for the clinical treatment and prevention of infections. A variety of phenotypic methods and gene-based methods are available for the rapid detection of carbapenemases, and these are expected to be routinely used in clinical microbiology laboratories. Therefore, to control the spread of carbapenemase, many laboratories around the world will need to use reliable, fast, high efficiency, simple and low cost methods. Optimal effects in patient applications would require rapid testing of CRE to provide reproducible support for antimicrobial management interventions or the treatment by various types of clinicians. For the optimal test method, it is necessary to combine complementary test methods to discriminate between various resistant bacterial species and to discover the genetic diversity of various types of carbapenemase for arriving at the best infection control strategy.

• The Journal of the Petrological Society of Korea
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• v.24 no.2
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• pp.141-147
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• 2015

Using laser-ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), we evaluated the reliability of trace element abundance data measured from the silicate rock references of JR-3, JG-3, JGb-1 and JB-1b using glass discs made by alkali fusion. For 28 elements including rare earth elements, relative standard deviations (RSD) are better than 7% in case when the concentrations of the elements in the rock samples are greater than 10 ppm. However, RSD shows somewhat increased values for the concentrations less than 10 ppm, but never exceeds 25%. Compared with previously reported averages of the compiled abundance data, our data display satisfactory results for the most cases with differences less than 10%. We suggest that LA-ICP-MS analysis using fused glass beads is a reliable, precise and time-saving method of trace element analysis for the silicate rocks spanning from mafic to felsic compositions.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.59 no.3
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• pp.252-262
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• 2014

Sorghum seed is traditionally used as secondary food sources in addition to rice in Korea. While the hypoglycemia regulating phytochemicals have been found in sorghum seed, peptides related with hypoglycemia never been studied before. To obtain the peptide characteristics and the specifically high-expressed peptides in hypoglycemic sorghum seed, peptide profiles of seven hypoglycemic and five non-hypoglycemic sorghum lines bred in RDA were determined using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS). The twelve sorghum lines exhibited 104 peptides on CM10 protein chip array (weak cation exchange) and 95 peptides on Q10 (weak cation exchange) in the molecular mass range from 2,000 to 20,000 Da. Heat map via supervised hierarchical clustering of the significantly different peptides (p < 0.01) in peak intensity among the 12 lines effectively revealed the specifically upregulated peptides in each line and distinguished between 7 hypoglycemic and 5 non-hypoglycemic lines. Through the comparison with hypoglycemic and non-hypoglycemic lines, 10 peptides including 2231.6, 2845.4, 2907.9, 3063.5, 3132.6, 3520.8, 4078.8, 5066.2, 5296.5, 5375.5 Da were specifically high-expressed in hypoglycemic lines at p < 0.00001. This study characterized seed peptides of 12 sorghums and found ten peptides highly expressed for hypoglycemic sorghum lines, which could be used as peptide biomarkers for identification of hypoglycemic sorghum.

• Journal of The Korean Society of Grassland and Forage Science
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• v.25 no.4
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• pp.287-296
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• 2005

To investigation protein expression pattern in rice leaves exposed to cold stress, the soluble proteins extracted from leaf tissue were fractionated with $15\%$ PEG and separated by two-dimensional polyacrylamide gel electrophoresis (2-DE). Differentially expressed proteins were identified by peptide mass fingerprinting using matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). Eight proteins up-regulated and 10 down-regulated were found in $15\%$ PEG supernatant fraction. In addition, 13 proteins up-regulated and 14 down-regulated were found in $15\%$ PEG pellet fraction. It was identified the differentially expressed proteins in $15\%$ PEG supernatant fraction as pimerase/dehydratase fructokinase, ribose-5-phosphate isomerase (Rpi), chaperonin 21 precursor, probable photosystem II oxygen-envolving complex (PS II OEC) protein 2 precursor and thioredoxin h-type (Trx-h) and those in $15\%$ PEG pellet fraction as OSINBb0059K02.15, hypothetical protein, putative mitogen-activated protein kinase kinase (MAPKK), beta 7 subunit of 205 proteasome, ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco) small subunit. These proteins are involved in metabolism, energy, protein synthesis, disease/defense and signal transduction-related proteins.

• Journal of The Korean Society of Grassland and Forage Science
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• v.31 no.2
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• pp.99-106
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• 2011

In order to investigate rice stem proteome in response to heat stress, rice plants were subjected to heat treatment at 42$^{\circ}C$ and total soluble proteins were extracted from stem tissues, and were fractionated with 15% PEG (poly ethylene glycol) and separated by two-dimensional polyacrylamide gel electrophoresis (2-DE). After staining of 2-DE gels, 46 of differentially expressed proteins were extracted, digested by trypsin, and subjected to matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis. Proteins were identified through database search by using peptide mass fingerprints. Among them, 10 proteins were successfully identified. Seven proteins were up- and 3 proteins were down-regulated, respectively. These proteins are involved in energy and metabolism, redox homeostasis, and mitochondrial small heat shock proteins. The identification of some novel proteins in the heat stress response provides new insights that can lead to a better understanding of the molecular basis of heat-sensitivity in plants, and also useful to molecular breeding of thermotolerant forage crops.

• Economic and Environmental Geology
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• v.51 no.4
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• pp.323-343
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• 2018

This study defines the mineralogical, micro-textural and geochemical characteristics for the carbonate rocks and discusses the fluids that have affected the depositional environment of the Lower Makgol Formation in Seokgaejae section. Based on analysis of X-ray Diffraction (XRD), Scanning Electron Microscope-Energy Dispersive X-ray Spectrometry (SEM-EDS), Electron Probe Micro Analyzer-Wavelength Dispersive X-ray Spectrometry (EPMA-WDS) and Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry (LA-ICP-MS), carbonate miorofacies in the basal and the lower members of the Makgol Formation are distinguished and classified into four types. Type 1 dolomite (xenotopic interlocking texture) and Type 2 dolomite (idiotopic interlocking texture) have relatively high Mg/Ca ratio, flat REE pattern, low Fe and Mn. Extensively interlocking textures in these dolomites indicate constant supply of Mg ion from hypersaline brine. Type 3 and Type 4 dolomite (scattered and loosely-aggregated texture) have relatively moderate Mg/Ca ratio, MREE enriched pattern, low to high Fe and Mn. These partial dolomitization indicate limited supply of Mg ion under the influx of meteoric water with seawater. Also, the evidence of Fe-bearing minerals, recrystallization and relatively high Fe and Mn in Type 4 indicates the influence of secondary diagenetic fluids under suboxic conditions. Integrating geochemical data with mineralogical and micro-textural evidence, the discrepancy between the basal and the lower members of the Makgol Formation indicates different sedimentary environment. It suggest that hypersaline brine have an influence on the basal member, while mixing meteoric water with seawater have an effect on the lower member of the Makgol Formation.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.64 no.4
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• pp.422-431
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• 2019

Severe droughts in spring have occurred frequently in Korea in recent years, exerting a critical impact on corn yield. Therefore, it is necessary to find physiological and/or molecular indicators of the response to drought stress in maize plants. In this study, we investigated the effects of water-deficit stress on two Korean elite F₁ maize hybrids, Ilmichal and Gwangpyeongok, by withholding water for 10 days at tassel initiation. The water deficit drastically reduced the relative leaf water content, leaf number, leaf area, and stem length, leading to dry matter reduction. Moreover, it reduced the SPAD values and stomatal conductance of leaves in drought-stressed plants of both hybrids. Importantly, the number of leaves and SPAD value were non-destructive and easy to investigate in response to water-deficit stress, suggesting that they may be useful indicators for screening drought-tolerant genetic resources. We detected more than 100 spots that were differentially accumulated under drought stress. Of these spots, a total of 21 protein spots (≥1.5-fold) from drought-exposed maize leaves were successfully analyzed by MALDI-TOF-TOF mass spectrometry. Functional annotation using Gene Ontology analysis revealed that most of the identified proteins were involved in carbohydrate metabolism, stress response fatty acid catabolism, photosynthesis, energy metabolism, and transport. The protein expression levels were increased in both Ilmichal and Gwangpyeongok, except for triosephosphate isomerase, fructose-bisphosphate aldolase, and an uncharacterized protein. The lactoylglutathione lyase delta (3,5)-delta (2,4)-dienoyl-CoA isomerase was overexpressed in Gwangpyeongok only. The results obtained from this study suggest that the drought-specific genes may be useful as molecular markers for screening drought-tolerant maize genotypes.