• Journal of Microbiology and Biotechnology
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• v.33 no.10
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• pp.1292-1298
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• 2023

PAMB 00755^T, a bacterial strain, was isolated from Korean fir leaves. The strain exhibits yellow colonies and consists of Gram-negative, non-motile, short rods or ovoid-shaped cells. It displays optimal growth conditions at 20℃, 0% NaCl, and pH 6.0. Results of 16S rRNA gene-based phylogenetic analyses showed that strain PAMB 00755^T was most closely related to Sphingomonas chungangi MAH-6^T (97.7%) and Sphingomonas polyaromaticivorans B2-7^T (97.4%), and ≤96.5% sequence similarity to other members of the genus Sphingomonas. The values of average nucleotide identity (79.9-81.3%), average amino acid identity (73.3-75.9%), and digital DNA-DNA hybridization (73.3-75.9%) were significantly lower than the threshold values for species boundaries; these overall genome-related indexes (OGRI) analyses indicated that the strain represents a novel species. Genomic analysis revealed that the strain has a 4.4-Mbp genome encoding 4,083 functional genes, while the DNA G+C content of the whole genome is 66.1%. The genome of strain PAMB 00755^T showed a putative carotenoid biosynthetic cluster responsible for its antioxidant activity. The respiratory quinone was identified as ubiquinone 10 (Q-10), while the major fatty acids in the profile were identified as C_18:1ω7c and/or C_18:1ω6c (summed feature 8). The major polar lipids of strain PAMB 00755^T were diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, and phosphatidylcholine. Based on a comprehensive analysis of genomic, phenotypic, and chemotaxonomic characteristics, we proposed the name Sphingomonas abietis sp. nov. for this novel species, with PAMB 00755^T as the type strain (= KCTC 92781^T = GDMCC 1.3779^T).

• The Korean Journal of Nuclear Medicine Technology
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• v.23 no.1
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• pp.69-74
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• 2019

Purpose $^{18}F$-FDOPA using amino acid is particularly attractive for imaging of brain tumors because of the high uptake in tumor tissue and the low uptake in normal brain tissue. But, on the other hand, $^{18}F$-FDG is highly uptake in both tumor tissue and normal brain tissue. The purpose of study is to evaluate comparison of contrasts in $^{18}F$-FDOPA Brain PET/CT and $^{18}F$-FDG Brain PET/CT and to find out optimal scan time by analysis of variation in SUV with the passage of uptake time. Materials and Methods A region of interest of approximately $350mm^2$ at the center of the tumor and cerebellum in 12 patients ($51.4{\pm}12.8yrs$) who $^{18}F$-FDG Brain PET/CT and $^{18}F$-FDOPA Brain PET/CT were examined more than once each. The $SUV_{max}$ was measured, and the $SUV_{max}$ ratio (T/C ratio) of the tumor cerebellum was calculated. In the analysis of SUV, T/C ratio was calculated for each frame after dividing into 15 frames of 2 minutes each using List mode data in 25 patients ($49.{\pm}10.3yrs$). SPSS 21 was used to compare T/C ratio of $^{18}F$-FDOPA and T/C ratio of $^{18}F$-FDG. Results The T/C ratio of $^{18}F$-FDOPA Brain PET/CT was higher than the T/C ratio of $^{18}F$-FDG Brain, and show a significant difference according to a paired t-test(t=-5.214, p=0.000). As a result of analyzing changes in $SUV_{max}$ and T/C ratio, the peak point of $SUV_{max}$ was $5.6{\pm}2.9$ and appeared in the fourth frame (6 to 8 minutes), and the peak of T/C ratio also appeared in the fourth frame (6 to 8 minutes). Taking this into consideration and comparing the existing 10 to 30 minutes image and 6 to 26 minutes image, the $SUV_{max}$ and T/C ratio increased by 0.2 and 0.1 each, compared to the 10 to 30 minutes image for 6 to 26 minutes image. Conclusion From this study, $^{18}F$-FDOPA Brain PET/CT is effective when reading the image, because the T/C ratio of $^{18}F$-FDOPA Brain PET/CT was higher than T/C ratio of $^{18}F$-FDG Brain PET/CT. In addition, in the case of $^{18}F$-FDOPA Brain PET/CT, there was no difference between the existing 10 to 30 minutes image and 6 to 26 minutes image. Through continuous research, we can find possibility of shortening examination time in $^{18}F$-FDOPA Brain PET/CT. Also, we can help physician to accurate reading using additional scan data.

• Journal of the Korean Society of International Agriculture
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• v.31 no.4
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• pp.378-383
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• 2019

To determine whether FT-IR spectral analysis based on multivariate analysis for whole cell extracts can be used to discriminate papaya at metabolic level. FT-IR spectral data from leaves were analyzed by principal component analysis (PCA), partial least square discriminant analysis (PLS-DA) and hierarchical clustering analysis (HCA). FT-IR spectra confirmed typical spectral differences between the frequency regions of 1,700-1,500, 1,500-1,300 and 1,100-950 cm^-1, respectively. These spectral regions were reflecting the quantitative and qualitative variations of amide I, II from amino acids and proteins (1,700-1,500 cm^-1), phosphodiester groups from nucleic acid and phospholipid (1,500-1,300 cm^-1) and carbohydrate compounds (1,100-950 cm^-1). The result of PCA analysis showed that papaya leaves could be separated into clusters depending on different growth temperature. In this case, showed discrimination confirmed according to metabolite content of growth condition from papaya. And PLS-DA analysis also showed more clear discrimination pattern than PCA result. Furthermore, these metabolic discrimination systems could be applied for rapid selection and classification of useful papaya cultivars.

• Journal of Animal Science and Technology
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• v.49 no.5
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• pp.549-558
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• 2007

C4B and BAT2, assigned to the SLA class III region, were recently reported on relation with human diseases. The primers for RT-PCR and RACE-PCR for CDS analysis of these genes of pig were designed by aligning the CDSs of humans and mice from GenBank. After we amplified and sequenced with these primers and cDNAs, the full-length CDSs of pig were determined. The CDS lengths of C4B and BAT2 were shown as 5226 bp and 6501 bp. In addition, the identities of nucleotide sequences with human and mouse were 76% to 87%, and the identities of amino acids were 72% to 90%. After we carried out the alignment with determined CDSs in this study and pig genomic sequences from GenBank, the primers for cSNP detection in genome were designed in intron regions that flanked one or more exons. Then, we amplified and directly sequenced with genomic DNAs of six pig breeds. Four cSNPs from C4B and three 3 cSNPs from BAT2 were identified. In addition, amino acid substitution occurred in six cSNP positions except for C4248T of C4B. By the Multiplex-ARMS method, we genotyped seven cSNPs with DNA samples used for direct sequencing. We verified that this result was the same as that analyzed using direct sequencing. To demonstrate recrudescence, we performed both direct sequencing and Multiplex-ARMS on two randomly selected DNA samples. The genotype of each sample showed the same result from both methods. Therefore, seven cSNPs were identified from C4B and BAT2 and could be used as the basic data for haplotype analysis of SLA class III region. Moreover, the Multiplex-ARMS method should be powerful for genotyping of genes assigned to the whole SLA region for the xenograft study.

• Journal of Plant Biotechnology
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• v.32 no.3
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• pp.167-173
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• 2005

Three different cDNAS for cinnamate 4-hydroxylase (C4H) which are involved in the second step of the general phenylpropanoid pathway were isolated and designated as pc4h1 (1,755 bp), pc4h2 (1,655 bp), and pc4h3 (1,316 bp), respectively. The nucleotide sequence analysis revealed that both pc4h1 and pc4h2 clones encode polypeptides of 505 amino acids frame but pc4h3 clone was truncated at the 5'-end of coding region. The alignment of the deduced amino acid sequences showed that PC4H1 and PC4H2 are highly homologous (95.8% identical) with each other and contain three conserved domains which are typical in cytochrome P450 monooxygenase: proline-rich region, threonine-containing binding pocket for the oxygen molecule, and heme binding region. In addition, result of the phylogenic tree analysis revealed that both pepper C4Hs belong to Class 1. pc4h2 transcription was strongly induced in wounded fruit (400%) and root (200%) relative to its very low basal level but not in leaf or stem tissue. In case of pc4h1, the basal level of transcription was higher than pc4h2 but induction by wounding was lower in fruit and root while leaf and stem tissues did not respond to wounding. The basal level of pc4h3 transcripts was not, if any, detectable and response to wounding was not observed.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.15 no.1
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• pp.1-8
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• 2015

Purpose: 3-methylcrotonyl CoA carboxylase deficiency (3MCCD) is leucine metabolic disorder caused by mutation in MCCC1 or MCCC2 gene. Clinical manifestations are variable, ranging from fatal neonatal onset to asymptomatic individuals. There is no retrospective study of Korean patients undergoing long-term treatment for 3MCCD. We reported this study to find out clinical symptoms and gene analysis of 3MCCD patients. Methods: This study was based on data of patients diagnosed with 3MCCD in Soonchunhyang university hospital between April 2009 and September 2013. We report clinical, enzymatic and mutation data of 3MCCD patients found by newborn screening. Results: In tandem mass spectrometry, 3-OH-isovalerylcarnitine (C5OH) of all patients increased. And all 7 patients were elevated 3-methylcrotonylglycine (3MCG) and 3-hydroxyisovaleric acid (3HIVA) in urine. MCCC mutation was identified in 2 patients and MCCC2 was mutated in 5 patients. We found mutation occurred in 8 different parts of nucleotide and such mutation caused 7 different types of changes in amino acid. All patients are on medication of L-carnitine and L-glycine. 4 patients are taking biotin. And 4 patients are eating leucine free formula. After starting treatment, there were no significant changes of urine 3MCG and 3HIVA levels. Conclusions: According to our data, MCCC2 gene mutation was more common than MCCC1 gene mutation. But the level of 3HIVA or 3MCG in urine has no correlation with phenotype. All patients has no symptoms and are shown normal development.

• Journal of Life Science
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• v.30 no.12
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• pp.1109-1117
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• 2020

In order to verify whether Zophobas atratus is an edible insect, the nutrients and harmful substances of Z. atratus larvae reared with an artificial diet (AD) and wheat bran (WB) were compared and analyzed. Based on dry weight, the crude protein content of Z. atratus larvae reared with an AD was 62.4%, 1.4 times higher than that of those reared with WB (45.2%). The crude fat content was 20.5% in the AD group, 2.3 times less than in the WB group (46.3%). The leucine content was 1.4 times higher in the AD group (4.2%) than in the WB group (3.0%). The glutamic acid content of nonessential amino acids was 1.3 times higher in the AD group (7.0%) than in the WB group (5.3%). The oleic acid content was 1.4 times higher in the WB group (37.0%) than in the AD group (26.7%). The potassium content was 1.1 times higher in the AD group (975.9 mg/100 g) than in the WB group (872.9 mg/100 g). According to the results of the toxic substances analysis, the lead and cadmium levels of the WB and AD groups were standard for edible insects. Pathogenic microorganisms, such as E. coli and salmonella, were not detected in either group. According to the results of the present analysis of nutrition and harmful substances, Z. atratus larvae raised on an AD are safe and contain various nutrients. Therefore, such larvae could be useful sources of food and feed.

• Microbiology and Biotechnology Letters
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• v.39 no.1
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• pp.9-19
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• 2011

The Bacillus subtilis pyrimidine biosynthetic (pyr) operon encodes all of the enzymes for the de novo biosynthesis of Uridine monophosphate (UMP) and additional cistrones encoding a uracil permease and the regulatory protein PyrR. The PyrR is a bifunctional protein with pyr mRNA-binding regulatory funtion and uracil phosphoribosyltransferase activity. To study the global regulation by the pyrR deletion, the proteome comparison between Bacillus subtilis DB104 and Bacillus subtilis DB104 ${\Delta}$pyrR in the minimal medium without pyrimidines was employed. Proteome analysis of the cytosolic proteins from both strains by 2D-gel electrophoresis showed the variations in levels of protein expression. On the silver stained 2D-gel with an isoelectric point (pI) between 4 and 10, about 1,300 spots were detected and 172 spots showed quantitative variations in which 42 high quantitatively variant proteins were identified. The results showed that production of the pyrimidine biosynthetic enzymes (PyrAA, PyrAB, PyrB, PyrC, PyrD, and PyrF) were significantly increased in B. subtilis DB104 ${\Delta}$pyrR. Besides, proteins associated carbohydrate metabolism, elongation protein synthesis, metabolism of cofactors and vitamins, motility, tRNA synthetase, catalase, ATP-binding protein, and cell division protein FtsZ were overproduced in the PyrR-deficient mutant. Based on analytic results, the PyrR might be involved a number of other metabolisms or various phenomena in the bacterial cell besides the pyrimidine biosynthesis.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.11
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• pp.1655-1661
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• 2007

Prolyl 4-hydroxylase (P4H) plays a central role in collagen synthesis by catalyzing the hydroxylation of the proline residue in the X-Pro-Gly amino acid sequence, and controls the biosynthesis of collagen that influences overall meat quality. In order to verify expression level of the catalytic ${\alpha}$ subunit of P4H, a 2.7 kb clone of the ${\alpha}$ subunit gene for P4H was selected from a cDNA library prepared from the muscular tissue of Sancheong berkshire pigs, and the whole gene sequence was determined. As expression level of the ${\alpha}$ subunit of P4H differed between tissues of pigs, we intended to assess more precisely the level of ${\alpha}$-subunit expression between tissues of Sancheong Berkshire pigs by using RT-PCR. Muscular and adipose tissues were taken from each pig grouped by growth stage (weighing 60, 80, and 110 kg) of Yorkshire and Sancheong Berkshire pigs, and the expression levels of the ${\alpha}$-subunit of P4H were examined. Since there were significant differences in the expression level with respect to variation in growth stage (p<0.01), an attempt was made to identify any influences of pig species and tissue variation. The muscular and adipose tissues of pigs weighing 110 kg showed higher expression levels than pigs weighing 60 kg and 80 kg. In general, significantly higher expression levels were found in muscular than in adipose tissue. The expression levels in Sancheong Berkshire were significantly higher than in Yorkshire pigs (p<0.01 or p<0.05). Since expression level of the ${\alpha}$-subunit of P4H affects the activity of P4H and is connected to the biosynthesis of collagen and increased collagen can improve meat texture, this finding may explain why meat quality of the Sancheong Berkshire pig is acclaimed in Korea. Given the higher expression levels of the ${\alpha}$-subunit gene in adipose than in muscular tissue, and also in the heavier pigs, more intensive studies are required to assess the correlation between expression level of the ${\alpha}$ subunit gene and overall meat quality.

• IMMUNE NETWORK
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• v.2 no.3
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• pp.175-181
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• 2002

Background: S100A6 is a calcium-binding protein overexpressed in several tumor cell lines including melanoma with high metastatic activity and involved in various cellular processes such as cell division and differentiation. To detect S100A6 protein in patient' samples (ex, blood or tissue), it is essential to produce a monoclonal antibody specific to the protein. Methods: First, cDNA coding for ORF region of human S100A6 gene was amplified and cloned into the expression vector for GST fusion protein. We have produced recombinant S100A6 protein and subsequently, monoclonal antibodies to the protein. The specificity of anti-S100A6 monoclonal antibody was confirmed using recombinant S100A recombinant proteins of other S100A family (GST-S100A1, GST-S100A2 and GST-S100A4) and the cell lysates of several human cell lines. Also, to identify the specific recognition site of the monoclonal antibody, we have performed the immunoblot analysis with serially deleted S100A6 recombinant proteins. Results: GST-S100A6 recombinant protein was induced and purified. And then S100A6 protein excluding GST protein was obtained and monoclonal antibody to the protein was produced. Monoclonal antibody (K02C12-1; patent number, 330311) has no cross-reaction to several other S100 family proteins. It appears that anti-S100A6 monoclonal antibody reacts with the region containing the amino acid sequence from 46 to 61 of S100A6 protein. Conclusion: These data suggest that anti-S100A6 monoclonal antibody produced can be very useful in development of diagnostic system for S100A6 protein.