• Korean Journal of Microbiology
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• v.50 no.1
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• pp.33-39
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• 2014

One hundred forty four bacterial colonies which were able to degrade crude oil were isolated from soil samples that were contaminated with oil in Daejeon area. Among them, one bacterial strain was selected for this study based on its emulsification activity, growth rate and surface tension activity, and this selected bacterial strain was identified as Pseudomonas sp. HN37 through physiological- biochemical tests and analysis of its 16S rRNA sequence. Pseudomonas sp. HN37 utilize the several aliphatic hydrocarbons, 3,5-dinitrosalicylic acid and 2,4-dichlorophooxyacetic acid as a sole carbon source. And this bacterial strain showed a high resistance to antibiotics such as ampicillin and chloramphenicol, as well as heavy metals such as Ba, Cr, Li and Mn. Also, it was found that the optimal pH and temperature for the cell growth, surface tension, and emulsification activity of Pseudomonas sp. HN37 were pH 6.0-9.0 and $30^{\circ}C$, respectively. The emulsification and surface tension activity was reached the maximum to 1% (V/V) crude oil and 1% (W/V) NaCl concentration. The surface tension of the culture broth was decreased from 62 to 27 dyne/cm after fifteen hours of inoculation in LB media.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.4
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• pp.460-466
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• 2004

This study was undertaken with the aim to establish a reliable radioimmunoassay (RIA) system for urinary pregnanediol glucuronide (PdG) and to employ it for monitoring the reproductive status of dairy cows. Urine and blood samples were collected from the Holstein cows both pregnant and non-pregnant. The samples were then investigated for evaluating the relationship between progesterone ($P_{4}$) in blood and PdG in urine adjusted with or without urinary creatinine basis. Biweekly urine collection was employed for three cows in estrous and those artificially inseminated, while urine from pregnant cows was collected on a monthly basis. P_{4}$ and PdG levels were measured by enzymeimmunoassay (EIA) and RIA techniques, respectively. Our results indicated the sensitivity of PdG for RIA being 35 pg/tube and the recovery rate of 100%. Urinary creatinine concentrations also fluctuated within a day, but change at midday was not noteworthy. Regardless of the time of urination the change in concentrations of PdG was relatively smaller and did not vary significantly. The urinary PdG concentration showed periodic changes as that with serum P_{4}$ levels during the cow's estrus cycle. The correlation coefficient rose when creatinine level in urine was adjusted but the change was also not significant. The concentrations of PdG during the luteal phase were detected between 8.2 and 17.4 ng/ml, three to five times higher than that in the follicular phase. The concentration of PdG from pregnant cows (21 days after conception) was three to four times higher than in the nonpregnant cows. Our finding suggests that the determination of urinary PdG could be reliably employed for early pregnancy detection. The urinary PdG level continued to raise until 30 days pre-partum while the concentration reached its peak at 30 ng/ml, after which it started to fall 18 to 30 days before parturition and finally fell to its nadir value one week after parturition. As the correlation coefficient between the urinary PdG and serum P_{4}$ was higher than that corrected by urinary creatinine it can be suggested that the adjustment is not needed. The concentrations of urinary PdG could be maintained stably for 2 days in urine samples stored at room temperature and extended to 8 days when the samples were pretreated by boiling for 30 minutes. In conclusion urinary PdG concentration even without the need for creatinine basis adjustment can be used directly for monitoring the reproductive status of dairy cows.

• Journal of Microbiology and Biotechnology
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• v.30 no.5
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• pp.668-680
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• 2020

Bacillus velezensis is an important plant growth-promoting rhizobacterium with immense potential in agriculture development. In the present study, Bacillus velezensis Lle-9 was isolated from the bulbs of Lilium leucanthum. The isolated strain showed antifungal activities against plant pathogens like Botryosphaeria dothidea, Fusarium oxysporum, Botrytis cinerea and Fusarium fujikuroi. The highest percentage of growth inhibition i.e., 68.56±2.35% was observed against Fusarium oxysporum followed by 63.12 ± 2.83%, 61.67 ± 3.39% and 55.82 ± 2.76% against Botrytis cinerea, Botryosphaeria dothidea, and Fusarium fujikuroi, respectively. The ethyl acetate fraction revealed a number of bioactive compounds and several were identified as antimicrobial agents such as diketopiperazines, cyclo-peptides, linear peptides, latrunculin A, 5α-hydroxy-6-ketocholesterol, (R)-S-lactoylglutathione, triamterene, rubiadin, moxifloxacin, 9-hydroxy-5Z,7E,11Z,14Z-eicosatetraenoic acid, D-erythro-C18-Sphingosine, citrinin, and 2-arachidonoyllysophosphatidylcholine. The presence of these antimicrobial compounds in the bacterial culture might have contributed to the antifungal activities of the isolated B. velezensis Lle-9. The strain showed plant growth-promoting traits such as production of organic acids, ACC deaminase, indole-3-acetic acid (IAA), siderophores, and nitrogen fixation and phosphate solubilization. IAA production was accelerated with application of exogenous tryptophan concentrations in the medium. Further, the lily plants upon inoculation with Lle-9 exhibited improved vegetative growth, more flowering shoots and longer roots than control plants under greenhouse condition. The isolated B. velezensis strain Lle-9 possessed broad-spectrum antifungal activities and multiple plant growth-promoting traits and thus may play an important role in promoting sustainable agriculture. This strain could be developed and applied in field experiments in order to promote plant growth and control disease pathogens.

• Parasites, Hosts and Diseases
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• v.53 no.4
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• pp.403-411
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• 2015

Plasmodium falciparum can invade all stages of red blood cells, while Plasmodium vivax can invade only reticulocytes. Although many P. vivax proteins have been discovered, their functions are largely unknown. Among them, P. vivax reticulocyte binding proteins (PvRBP1 and PvRBP2) recognize and bind to reticulocytes. Both proteins possess a C-terminal hydrophobic transmembrane domain, which drives adhesion to reticulocytes. PvRBP1 and PvRBP2 are large (>326 kDa), which hinders identification of the functional domains. In this study, the complete genome information of the P. vivax RBP family was thoroughly analyzed using a prediction server with bioinformatics data to predict B-cell epitope domains. Eleven pvrbp family genes that included 2 pseudogenes and 9 full or partial length genes were selected and used to express recombinant proteins in a wheat germ cell-free system. The expressed proteins were used to evaluate the humoral immune response with vivax malaria patients and healthy individual serum samples by protein microarray. The recombinant fragments of 9 PvRBP proteins were successfully expressed; the soluble proteins ranged in molecular weight from 16 to 34 kDa. Evaluation of the humoral immune response to each recombinant PvRBP protein indicated a high antigenicity, with 38-88% sensitivity and 100% specificity. Of them, N-terminal parts of PvRBP2c (PVX_090325-1) and PvRBP2 like partial A (PVX_090330-1) elicited high antigenicity. In addition, the PvRBP2-like homologue B (PVX_116930) fragment was newly identified as high antigenicity and may be exploited as a potential antigenic candidate among the PvRBP family. The functional activity of the PvRBP family on merozoite invasion remains unknown.

• Biomolecules & Therapeutics
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• v.21 no.1
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• pp.29-34
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• 2013

The tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) is a member of the tumor necrosis factor family of cytokines. TRAIL selectively induces apoptotic cell death in various tumors and cancer cells, but it has little or no toxicity in normal cells. Agonism of TRAIL receptors has been considered to be a valuable cancer-therapeutic strategy. However, more than 85% of primary tumors are resistant to TRAIL, emphasizing the importance of investigating how to overcome TRAIL resistance. In this report, we have found that nemadipine-A, a cell-permeable L-type calcium channel inhibitor, sensitizes TRAIL-resistant cancer cells to this ligand. Combination treatments using TRAIL with nemadipine-A synergistically induced both the caspase cascade and apoptotic cell death, which were blocked by a pan caspase inhibitor (zVAD) but not by autophagy or a necrosis inhibitor. We further found that nemadipine-A, either alone or in combination with TRAIL, notably reduced the expression of survivin, an inhibitor of the apoptosis protein (IAP) family of proteins. Depletion of survivin by small RNA interference (siRNA) resulted in increased cell death and caspase activation by TRAIL treatment. These results suggest that nemadipine-A potentiates TRAIL-induced apoptosis by down-regulation of survivin expression in TRAIL resistant cells. Thus, combination of TRAIL with nemadipine-A may serve a new therapeutic scheme for the treatment of TRAIL resistant cancer cells, suggesting that a detailed study of this combination would be useful.

• Korean Journal of Environmental Biology
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• v.37 no.4
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• pp.493-502
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• 2019

Maize (Zea mays L.) is a C4-plant and one of the three major crops grown worldwide. Because of its high productivity, maize is considered as one of the most important food and feed stocks in the world. Recently, bioethanol from maize was predominantly generated in the USA and Brazil. Infection of maize by several diseases resulted in a huge disaster and prevented maize production. Downy mildew, caused by Peronosclerospora sorghi, is one of the most serious diseases of maize. Despite efforts to develop downy mildew-resistant cultivars or seed treatment with metalaxyl, downy mildew persists as a serious pathogen and is still prevalent in specific geographical locations. Analysis of soils infected with downy mildew and investigation of candidates associated with downy mildew resistance is an attractive method to overcome downy mildew damage in maize. In a previous study, we reported that maize chromosome 6 carries a possible candidate gene for downy mildew resistance. Using bioinformatics tools and RT-PCR analysis, five novel genes including bZIP, OFP transcription factor, and Ppr were identified as candidate genes associated with downy mildew resistance.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.8
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• pp.1366-1372
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• 2018

Objective: A disintegrin and metallopeptidase with thrombospondin motifs type 8 (ADAMTS8) is crucial for diverse physiological processes, such as inflammation, tissue morphogenesis, and tumorigenesis. The chicken ADAMTS8 (chADAMTS8) gene was differentially expressed in the kidney following exposure to different calcium concentrations, suggesting a pathological role of this protein in metabolic diseases. We aimed to examine the molecular characteristics of chADAMTS8 and analyze the gene-expression differences in response to toll-like receptor 3 (TLR3) stimulation. Methods: The ADAMTS8 mRNA and amino acid sequences of various species (chicken, duck, cow, mouse, rat, human, chimpanzee, pig, and horse) were retrieved from the Ensembl database and subjected to bioinformatics analyses. Reverse-transcription polymerase chain reaction (RT-PCR) and quantitative PCR (qPCR) experiments were performed with various chicken tissues and the chicken fibroblast DF-1 cell line, which was stimulated with polyinosinic-polycytidylic acid (poly[I:C]; a TLR3 ligand). Results: The chADAMTS8 gene was predicted to contain three thrombospondin type 1 (TSP1) domains, whose amino acid sequences shared homology among the different species, whereas sequences outside the TSP1 domains (especially the amino-terminal region) were very dif­ferent. Phylogenetic analysis revealed that chADAMTS8 is evolutionarily clustered in the same clade with that of the duck. chADAMTS8 mRNA was broadly expressed in chicken tissues, and the expression was significantly up-regulated in the DF-1 cells in response to poly(I:C) stimulation (p<0.05). These results showed that chADAMTS8 may be a target gene for TLR3 signaling. Conclusion: In this report, the genetic information of chADAMTS8 gene, its expression in chicken tissues, and chicken DF-1 cells under the stimulation of TLR3 were shown. The result suggests that chADAMTS8 expression may be induced by viral infection and correlated with TLR3-mediated signaling pathway. Further study of the function of chADAMTS8 during TLR3-dependent inflammation (which represents RNA viral infection) is needed and it will also be important to examine the molecular mechanisms during different regulation, depending on innate immune receptor activation.

• Journal of Life Science
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• v.30 no.11
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• pp.1012-1020
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• 2020

Remicade is a therapeutic biosimilar natural antibody in which the mouse variable domain has been linked to the human constant domain. It is a chimeric monoclonal antibody specific to tumor necrosis factor-alpha (TNF-α) and has been developed for the treatment of rheumatoid arthritis. To investigate the biological activity of the Remicade antibody, we carried out a bioinformatics study using a protein data bank to characterize the TNF-α antigen binding mechanism of the Remicade natural antibody. Because the production of the Remicade antibody is often limited by genetic instability of the natural antibody-producing cell, we generated a Remicade single-chain variable domain fragment antibody (Remicade) in which a heavy chain variable domain (VH) is joined with a light chain variable domain (VL) by a polypeptide linker. Furthermore, Remicade was fused to a leucine zipper (RemicadeScZip) for higher production and higher antigen-binding activity than Remicade. The Remicade and Remicade ScZip were expressed in Escherichia coli and purified by a Ni⁺-NTA-agarose column. As expected, the purified proteins had migrated as 28.80 kDa and 33.96 kDa in sodium dodecyl sulfate-polyacrylamide electrophoresis. The TNF-α antigen binding activity of Remicade was not observed by ELISA and western blot. In contrast, RemicadeScZip showed antigen-binding activity. Additional bio-layer interferometry analysis confirmed the antigen-binding activity of RemicadeScZip, suggesting that the leucine zipper stabilized the folding of RemicadeScZip in a denatured condition and improved the TNF-α antigenbinding activity.

• Korean Chemical Engineering Research
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• v.49 no.6
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• pp.840-845
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• 2011

Degradation products of agarose are biologically active and thus used as an ingredient in pharmaceuticals or functional cosmetics. Furthermore, it has been strongly considered as a substrate for bio-ethanol fermentation. Recently, we isolated new agarase-producing microorganism, Pseudoalteromonas sp. from south sea of Korea. In this study, we aimed to separate and purify the agarase from culture broth of this strain. Separation of agarase was performed by ion- exchange chromatography on DEAE-Sepharose resin. Equilibrium pH and volume ratio of resin to the amount of protein were optimized for the efficient adsorption of protein. 410 ${\mu}g$ of protein was completely adsorbed to 3 mL of resin at pH 7.5. The total amount of eluted protein increased as NaCl concentration increased to 400 mM at isocratic elution. Agarase was separated by linear gradient elution of NaCl (0~1,000 mM). Three major protein peaks were observed and the presence or absence of agarase in these eluted proteins was measured by Lugol's staining technique. Only six eluted protein fractions showed strong agarase activity.

• Interdisciplinary Bio Central
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• v.4 no.3
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• pp.10.1-10.12
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• 2012

Introduction: We investigated frameshift suppressor tRNAs previously reported to use five-base anticodon-codon interactions in order to provide a collection of frameshift suppressor tRNAs to the synthetic biology community and to develop modular frameshift suppressor logic devices for use in synthetic biology applications. Results and Discussion: We adapted eleven previously described frameshift suppressor tRNAs to the BioBrick cloning format, and built three genetic logic circuits to detect frameshift suppression. The three circuits employed three different mechanisms: direct frameshift suppression of reporter gene mutations, frameshift suppression leading to positive feedback via quorum sensing, and enzymatic amplification of frameshift suppression signals. In the course of testing frameshift suppressor logic, we uncovered unexpected behavior in the frameshift suppressor tRNAs. The results led us to posit a four-base binding hypothesis for the frameshift suppressor tRNA interactions with mRNA as an alternative to the published five-base binding model. Conclusion and Prospects: The published five-base anticodon/codon rule explained only 17 of the 58 frameshift suppression experiments we conducted. Our deduced four-base binding rule successfully explained 56 out of our 58 frameshift suppression results. In the process of applying biological knowledge about frameshift suppressor tRNAs to the engineering application of frameshift suppressor logic, we discovered new biological knowledge. This knowledge leads to a redesign of the original engineering application and encourages new ones. Our study reinforces the concept that synthetic biology is often a winding path from science to engineering and back again; scientific investigations spark engineering applications, the implementation of which suggests new scientific investigations.