• BMB Reports
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• v.57 no.1
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• pp.30-39
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• 2024

Directed evolution (DE) of desired locus by targeted random mutagenesis (TRM) tools is a powerful approach for generating genetic variations with novel or improved functions, particularly in complex genomes. TRM-based DE involves developing a mutant library of targeted DNA sequences and screening the variants for the desired properties. However, DE methods have for a long time been confined to bacteria and yeasts. Lately, CRISPR/Cas and DNA deaminase-based tools that circumvent enduring barriers such as longer life cycle, small library sizes, and low mutation rates have been developed to facilitate DE in native genetic environments of multicellular organisms. Notably, deaminase-based base editing-TRM (BE-TRM) tools have greatly expanded the scope and efficiency of DE schemes by enabling base substitutions and randomization of targeted DNA sequences. BE-TRM tools provide a robust platform for the continuous molecular evolution of desired proteins, metabolic pathway engineering, creation of a mutant library of desired locus to evolve novel functions, and other applications, such as predicting mutants conferring antibiotic resistance. This review provides timely updates on the recent advances in BE-TRM tools for DE, their applications in biology, and future directions for further improvements.

• Journal of Microbiology and Biotechnology
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• v.34 no.9
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• pp.1867-1875
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• 2024

Identification of the biochemical metabolic pathway for lignin decomposition and the responsible degradative enzymes is needed for the effective biotechnological valorization of lignin to renewable chemical products. In this study, we investigated the decomposition of kraft lignin by the soil bacterium Pseudomonas kribbensis CHA-19, a strain that can utilize kraft lignin and its main degradation metabolite, vanillic acid, as growth substrates. Gel permeation chromatography revealed that CHA-19 decomposed polymeric lignin and degraded dehydrodivanillin (a representative lignin model compound); however, the degradative enzyme(s) and mechanism were not identified. Quantitative polymerase chain reaction with mRNAs from CHA-19 cells induced in the presence of lignin showed that the putative genes coding for two laccase-like multicopper oxidases (LMCOs) and three dye-decolorizing peroxidases (DyPs) were upregulated by 2.0- to 7.9-fold compared with glucose-induced cells, which indicates possible cooperation with multiple enzymes for lignin decomposition. Computational homology analysis of the protein sequences of LMCOs and DyPs also predicted their roles in lignin decomposition. Based on the above data, CHA-19 appears to initiate oxidative lignin decomposition using multifunctional LMCOs and DyPs, producing smaller metabolites such as vanillic acid, which is further degraded via ortho- and meta-ring cleavage pathways. This study not only helps to better understand the role of bacteria in lignin decomposition and thus in terrestrial ecosystems, but also expands the biocatalytic toolbox with new bacterial cells and their degradative enzymes for lignin valorization.

• Korean Journal of Veterinary Research
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• v.32 no.1
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• pp.35-39
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• 1992

SMZ is one of the most widely used antibacterial agents in veterinary medicine. It is also used as a growth promotant in many species of domestic animals There are marked species differences in its metabolism and pharmacokinetics. However, its pharmacokinetic and metabolism in rabbits. which are ragarded not only as good laboratorty animals hut also as good economical animals in its own, are lacking. Sex-differences in drug metabolism are well recognized in wide range of animal species including rats. Males are known to he more active than females. It is also know that there are Significant differences in the direction of metabolic pathways. But recently, female goats are reported to be more active in the metabolie capacity of SMZ than the other sex by Dutch researchers at Utrecht. Therefore, it is not easy to make general conclusicn of having higher SMZ metal-die capacity in the male compared to the opposite sex in every animal species. In this regard, the study on metabolic pattern of SMZ in rabbits, which are regarded as hervivorous, is of interest because the dietary habbits of rabbit are comparable to thai of goal, NEW Zealand White rabbits of each sex were given SMZ(35mg/kg) as a bolus injection into the marginalean, vein in order to study its pharmacokinetic profiles(using plasma) anc metabolic pattem(24h urine) as specified in the methods anc materials. 1. In the rabbit, the major metabolic pathway of SMZ was the acetylation(the formation of $N_4AcSMZ$). There were hydroxylation pathways(50HSMZ, $6CH_2OHSMZ$) as well, in the metabolism of SMZ in the rabbit, but minor pathways. 2. No sex differences in the metabolic direction of SMZ and its metabolites formation were found from the urinary excreted metabolites of SMZ out of 24h collected urine. 3. The concentration-time curves of SMZ(35mg/kg, iv) in the plasma compartment were fitted to a one-compartment open model when using a computer program(NONLIN). There was also no difference in the pharmacokinetic pattem of SMZ between two sexes. 4. The emergence of $N_4AcSMZ$ metabolized from SMZ was very fast in the plasma of the rabbit The elimination of $N_4AcSMZ$ was prolonged as compared to that of the parent drug Vie found no sex difference in the elimination pattern of $N_4AcSMZ$ in the rabbit.

• The Korean Journal of Physiology
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• v.2 no.1
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• pp.23-30
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• 1968

Tissue homogenates of 12 kinds of human cancer tissues were incubated separately in medium containing $C^{14}-1-glucose$ and $C^{14}-6-glucose$ as a substrate in order to observe the oxidative pathway of glucose in the tumor tissues. At the end of 3 hours incubation in the Dubnuff metabolic shaking incubator, respiratory $CO_2$ samples trapped by alkaling which was placed in the center well of incubation flask were analysed for total $CO_2$ production rates and their radioactivities. The tissue homogenate samples after incubation were analyzed for their concentrations of glucose, lactate and pyruvate. Calculations were made on the glucose consumption rate and accumulation rates of lactate and pyruvate. Fractionation of oxidative pathway of glucose was carried out by calculating $C^{14}O_2 yields from C-1 and C-6 carbon of glucose. The following results were obtained. 1. In 12 kinds of human cancer, total $CO_2$ production rates were less than $8{\mu}M/gm$ except 2 cases. These lower values impressed that oxidative metabolism in the tumor tissues generally inhibited as compared with that in normal tissues. On the other hand, fractions of $CO_2$ derived from glucose to total $CO_2$ production rates (RSA) were less than 10% in every case. These facts showed that oxidation of glucose into $CO_2$ was remarkably inhibited in the tumor tissues. 2. Factions of glucose disappeared into $CO_2\;(RGD_{CO_2})$, lactate $(RGD_L)$, pyruvate $(RGD_P)$ to glucose consumption rates were as follows. $RGD_{CO_2}$ were less than 2% in cases of in this experiment and $RGD_L$ showed more than 5% except in 2 cases. These facts showed that anaerobic degradation of glucose into 3 carbon compounds was easily proceeded but further degradation into $CO_2$ via the TCA cycle was greatly inhibited resulting in accumulation of lactate. There are large variation in values of $RGD_P$ in different kinds of tumor tissue but relatively higher values in $RGD_{CO_2}$ were obtained in the tumor tissues as compared with those of normal tissues. 3. The oxidative pathway of glucose in tumor tissues were analyzed from the values of RSA which were obtained in $C^{14}-1\;and\;C^{14}-6-glucose$ incubation experiments. It was found that 3% of $CO_2$ derived from glucose were oxidized via the principal EMP-TCA cycle and the remainder were via alternate pathway such as HMP in the liver cancer and values in other cancer tissues were as follows; 4% in the tongue cancer, 6% in the colon cancer, 6% in the lung cancer, 9% in the stomach cancer, 11% in the ovarian cancer, 12% in the neck tumor, 22% in the uterine cancer, 22% in the bladder tumor, 32% in the spindle cell sarcoma and 65% in the brain tumor. These values except later 2 cases showed less than 30% which is the lowest value among the normal tissues. Even in the brain tumor in which showed highest value in the tumor group. It is reasonable to suppose that this fraction was remarkably decreased because values in normal brain tissue was more than 90%. From the above data, it was concluded that in tumor tissues, oxidation of glucose via TCA cycle was greatly inhibited but correlation between degree of inhibited oxidation of glucose via TCA cycle and malignancy of tumor were not clarified in this experiments.

• Journal of Oriental Neuropsychiatry
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• v.26 no.1
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• pp.63-78
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• 2015

Objectives: Pinelliae Rhizoma has traditionally been used as an anti-depressant in oriental medicine. This study is to investigate the effect of Pinelliae Rhizoma extract (PRe) on psychological stress in genome wild expression of mice. Methods: After giving physical stress to mice, PRe was orally administered with 100 mg/kg/day for five days. After extracting whole brain tissue from the mice, their genome changes were observed by micorarray analysis method. The genome changes were analyzed by IMAGENE 4.0, TREEVIEW, FatiGo algorithems, BOND database, cytoscape program, etc. Results: 1. PRe administered group were remained at normal level; 60% of increase was shown in expressed genes by physical stress, and 65% of decrease was shown in expressed genes by psychological stress. 2. Genes with increased expression in control group that remained at a normal state in PRe administered group were involved with the gene of a cellular metabolic process on biological process, protein binding on molecular function, and cell part on cell composition. The pathway was found to be cytokin-cytokin receptor interaction. 3. Genes with decreased expression in control group that remained at a normal state in PRe administered group were involved with the gene of a cellular metabolic process on biologiacl detail and coupled ATPaes activity on molecular function. This gene related path was Ubiquintin mediated proteolysis etc. 4. Core node genes analyzed by protein interaction network were Vinculin, Cell sdivision cycle 42 homolog (S. cerevisiae) etc. They played an important role in maintaining cytoskeleton and controlling cell cycle. Conclusions: Several genes were up-regulated and down-regulated in response to psychological stress. The expression of most of the genes that were altered in response to psychological stress was restored to normal levels in PRe treated mice. When the interaction network information was analyzed, the recovery of the core node genes in PRe treated mice indicates that this final set of genes may be the effective target of PRe.

• 한국생물공학회:학술대회논문집
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• 2000.04a
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• pp.53-56
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• 2000

Two-stage fed-batch culture was peformed to improve the volumetric productivity of erythritol. In the growth phase dissolved oxygen was maintained to 20% and the feed medium was automatically supplied to the fermenter by pH-stat mode. The cell yield was 0.76 g-cell/g-glucose. In two-stage fed-batch culture, 41% of total erythritol conversion yield with 187 g/L of erythritol concentration and 2.79 g/L-h of maximum erythritol Productivity were obtained when 400 g/L of glucose was directly added in the form of non-sterile powder at production phase. The erythritol productivity increased in parallel with cell mass. The metabolic shift in the biosynthetic pathway of erythritol was caused by dissolved oxygen concentration. The production of gluconic acid was observed when the dissolved oxygen in the medium was maintained over 40% during the production phase, whereas the dissolved oxygen concentration lower than 40% caused the production of citric acid. But the butyric acid was produced independently with dissolved oxygen concentration in the medium. The production of organic acids such as gluconic acid, citric acid, and butyric acid was decreased by addition of mineral salts.

• Journal of Life Science
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• v.24 no.10
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• pp.1055-1062
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• 2014

We investigated the expression of cucumber genes involved in lipid mobilization and metabolism during cotyledon development to compare gene activity and to study the direction of carbon (acetyl unit) transport between glyoxysomes and mitochondria. The core metabolic pathway involving 10 genes was examined in four intracellular compartments: glyoxysomes (peroxisomes), mitochondria, chloroplasts, and cytosol. Additionally, we tested the early germination response of dark-grown seedlings and the immediate light response for a further 3 days. According to the reverse transcription polymerase chain reaction (RT-PCR), 3-L-ketoacyl-CoA thiolase 2 (Thio2), isocitrate lyase (ICL), and malate synthase (MS), the genes involved in storage lipid mobilization showed a similar and consistent pattern of gene expression in seedling development. Furthermore, coordinate expression of the A BOUT DE SOUFFLE (BOU) gene with ICL and MS during seedling emergence pointed to a possible secondary route of acetyl unit (acetyl-CoA) transport between peroxisomes and mitochondria in cucumber. The expression of the BOU gene was light dependent, as shown by BOU activity in Arabidopsis, suggesting that the dark condition also results in weak membrane biogenesis. In addition, several genes were active throughout the development of the green cotyledon, even during senescence. In conclusion, this study summarizes oil-seed germination and gene expression during cucumber cotyledon development and proposes an additional route for acetyl unit transport.

• Journal of the Korea Organic Resources Recycling Association
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• v.28 no.1
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• pp.65-72
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• 2020

The aims of this study were to compare the biomethanation of CO₂ through specific methanogenic activity (SMA) test which was inoculated with four different types of mixed microbial culture obtained from full-scale anaerobic digestion (AD) plants. The experimental results showed that CH₄ conversion was the highest in the samples inoculated by seed sludge taken from ADs of food waste and brewery; under this condition, the produced biomethane contains 89.3-91.9% of CH₄. Meanwhile, the lowest level was obtained in the sample from sewage sludge. The measured ratio of CH₄ production rate to CO₂ consumption rate in all reactors was higher than the theoretical value (1) in the middle of the period and soon dropped to 0.7-0.8. It might be due to changed metabolic pathways in the reactor by the degradation of residual organic matter and the increased activity of homoacetogenic bacteria.

• KSBB Journal
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• v.29 no.6
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• pp.443-447
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• 2014

Biosynthesis of lactate-containing polyhydroxyalkanoates (PHAs) was examined in recombinant Escherichia coli W strain from sucrose. The Pseudomonas sp. MBEL 6-19 phaC1437 gene and the Clostridium propionicum pct540 gene, which encode engineered Pseudomonas sp. MBEL 6-19 PHA synthase 1 ($PhaC1_{Ps6-19}$) and engineered C. propionicum propionyl-CoA transferase ($Pct_{Cp}$), respectively, were expressed in E. coli W to construct key metabolic pathway to produce poly(3-hydroxybutyrate-co-lactate) [P(3HB-co-LA)]. The recombinant E. coli W expressing the phaC1437 gene and the pct540 gene could synthesize P(3HB-co-13mol%LA) up to the polymer content of 31.3 wt% when it was cultured in chemically defined MR medium containing 20 g/L of sucrose and 2 g/L of sodium 3-hydroxybutyrate. When Ralstonia eutropha phaAB genes were additionally expressed to provide 3-hydroxybutyrate-CoA (3HB-CoA) from sucrose, P(3HB-co-16mol%LA) could be synthesized from sucrose as a sole carbon source without supplement of sodium 3-hydroxybutyrate in culture medium, but the PHA content was decreased to 12.2 wt%. The molecular weight of P(3HB-co-16 mol%LA) synthesized in E. coli W using sucrose as carbon source were $1.53{\times}10^4$ ($M_n$) and $2.78{\times}10^4$ ($M_w$), respectively, which are not different from those that have previously been reported by other recombinant E. coli strains. Engineered E. coli strains developed in this study should be useful for the production of lactate-containing PHAs from sucrose, one of the most abundant and least expensive carbon sources.

• The Korean Journal of Nuclear Medicine
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• v.26 no.2
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• pp.257-264
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• 1992

Diagnostic approaches such as angiography, ultrasound, computed tomography and nuclear magnetic resonance have limitation for contributing to the early clinical diagnosis of atherosclerosis. Recently, $^{99m}Tc-labelled$ low density lipoprotein was developed to detect early atherosclerotic lesion by external imaging with gamma camera. To determine whether $^{99m}Tc-LDL$ scintigraphy can visualize the active atherosclerotic lesion, rabbits were injected with $^{99m}Tc-LDL$, 3 months after feeding dietary fat (lanolin) and we obtained following results. 1) Labelling efficiency of $^{99m}Tc-LDL$ was $79\sim88%$. 2) Biodistribution study of normal rabbits with $^{99m}Tc-LDL$ revealed the high activities in spleen, adrenal gland, liver, kidney which are major organs of high metabolic rate of LDL. 3) Three months after feeding lanolin, serum cholesterol was markedly increased from $74{\pm}17mg/dl$ to $979{\pm}153mg/dl$ and histologic study of aorta after sacrificing the rabbit demonstrated marked atherosclerotic changes. 4) Atherosclerotic lesion of abdominal aorta which was confirmed with histologic study could be demonstrated in $^{99m}Tc-LDL$ scintigraphy after feeding lanolin for 3 months. In conclusion, the results of this preliminary investigation suggest that it may be possible to image active atheromatous lesion with $^{99m}Tc-LDL$. It is anticipated that this promising agent may allow the in vivo monitoring of preclinical atherosclerotic lesions and may be useful to evaluate the metabolic pathway of LDL in humans.