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Search Results: 1 - 10 of 4396 matches for " Kwang-Hyun Baek "
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Production of reactive oxygen species by freezing stress and the protective roles of antioxidant enzymes in plants  [PDF]
Kwang-Hyun Baek, Daniel Z. Skinner
Journal of Agricultural Chemistry and Environment (JACEN) , 2012, DOI: 10.4236/jacen.2012.11006
Abstract: As one of the most severe environmental stresses, freezing stress can determine native flora in nature and severely reduce crop production. Many mechanisms have been proposed to explain the damage induced by freezing-thawing cycle, and oxidative stress caused by uncontrollable production of harmful reactive oxygen species (ROS) are partially contributed to causing the injury. Plants in temperate regions have evolved a unique but effective metabolism of protecting themselves called cold acclimation. Cold-acclimating plants undergo a complex but orchestrated metabolic process to increase cold hardness triggered by exposure to low temperature and shortened photoperiod and achieve the maximum freezing tolerance by a concerted regulation and expression of a number of cold responsive genes. A complicated enzymatic system have been evolved in plants to scavenge the ROS to protect themselves from oxidative stress, therefore, cold-acclimating plants are expected to increase the de novo synthesis of the genes of antioxidant genes. Indeed, many antioxidant genes increase the expression levels in response to low temperature. Furthermore, the higher expression of many antioxidant enzymes are positively correlated to inducing higher tolerance levels against freezing. All the information summarized here can be applied for developing crop and horticultural plants to have more freezing tolerance for higher production with better quality. There have been extensive studies on the activities of antioxidant enzymes and the gene regulation, however, more researches will be required in near future to elucidate the most effective antioxidant enzymes to induce highest freezing tolerance in a crop plant in a transformation process or a breeding program.
Hydrogen Peroxide Alleviates Hypoxia during Imbibition and Germination of Bean Seeds (Phaseolus vulgaris L.)  [PDF]
C. B. Rajashekar, Kwang-Hyun Baek
American Journal of Plant Sciences (AJPS) , 2014, DOI: 10.4236/ajps.2014.524373
Abstract: Bean seeds (Phaseolus vulgaris L. cv. Tendergreen) were imbibed in water to examine the effects of hypoxia during imbibition and subsequent germination. Hypoxic conditions occurred when seeds were imbibed in water for 24 h or longer and resulted in severe reduction of hypocotyl elongation and stem growth during subsequent germination under non-limiting oxygen conditions. Under continued hypoxic conditions, bean seeds failed to germinate, however, this was reversed in the presence of hydrogen peroxide (20 mM) in the medium. Furthermore, imbibition of seeds in the presence of hydrogen peroxide overcame the adverse hypoxic effects on hypocotyl elongation and stem growth. Exogenous hydrogen peroxide increased the dissolved oxygen levels in the germinating medium, and catalase and transition metal ions such as Fe2+, Cu2+ and Mn2 helped to facilitate the production of oxygen from hydrogen peroxide. In these catalysts, catalase played a major role in the decomposition of hydrogen peroxide as demonstrated by the use of a catalase inhibitor, 3-amino-1, 2, 4-triazole, which reversed the positive effects produced by hydrogen peroxide on germination of seeds under hypoxic conditions. The results show that imbibition is sensitive to oxygen deficits which affect subsequent hypocotyl growth and seedling performance. The adverse effects of hypoxia on germination of bean seeds can be overcome by exogenous hydrogen peroxide.
Quantitative real-time PCR method to detect changes in specific transcript and total RNA amounts
Baek,Kwang-Hyun; Skinner,Daniel Z;
Electronic Journal of Biotechnology , 2004,
Abstract: quantitative real-time pcr (qrt-pcr), used in conjunction with reverse transcriptase, has been applied to the determination of the number of copies of a transcript per unit mass of rna, but did not indicate any change in the amount of total rna per mass of tissue. in the present work, we described a simple method to use qrt-pcr to estimate the change in the amount of total rna per unit mass of wheat (triticum aestivum l.) tissue in response to cold temperature. three qrt-pcr templates, i.e. control, cold-exposed, and one of rna extracted from a sample consisting of equal masses of control and cold-exposed tissue, were analyzed. the number of copies of target transcript per unit mass of rna was estimated from the three samples using standard qrt-pcr techniques. equations describing the number of copies of the target sequence in each of the tissue samples were solved simultaneously to describe the relative proportion of the target sequence that originated from each tissue sample in the mixture, thereby providing an estimate of relative amounts of total rna in the two tissues.
The promoter -1031(T/C) polymorphism in tumor necrosis factor-alpha associated with polycystic ovary syndrome
Ji-Hyun Yun, Jin-Woo Choi, Kyung-Ju Lee, Joong-Sik Shin, Kwang-Hyun Baek
Reproductive Biology and Endocrinology , 2011, DOI: 10.1186/1477-7827-9-131
Abstract: The -1031(T/C) polymorphism of TNF-alpha gene was analyzed by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) in a total of 217 PCOS patients and 144 matched female controls of healthy women. And statistical analysis was performed using HapAnalyzer. X2 test and logistic regression were utilized analyze the association between two groups. A p-value under 0.05 was considered statistically significant.The genotype and allelic frequencies were in Hardy-Weinberg equilibrium (HWE). There was strong association between the -1031(T/C) polymorphism in the promoter region of TNF-alpha gene and PCOS (p-value = 0.0003, odd ratio (OR) = 2.53). In addition, the frequency of C allele was significantly higher in PCOS patients compared with controls. Sequence analyses also showed the -1031(T/C) polymorphism of TNF-alpha gene.This is the first study on the -1031(T/C) polymorphism of TNF-alpha gene in PCOS. We concluded that the -1031(T/C) polymorphism of TNF-alpha gene is associated with PCOS in a Korean population. Therefore, it is possible that it may be considered as a clinical biomarker to diagnose for PCOS, and is helpful in understanding the etiology for the pathogenesis of PCOS.Polycystic ovary syndrome (PCOS) is one the most common gynecological disorder and affects up to 5% women in reproductive ages [1-4]. Generally, PCOS patients show the symptoms of obesity, increased risk of type 2 diabetes mellitus, menstrual irregularity, and anovulation [5-9]. A number of groups focused on the studies for single nucleotide polymorphisms and expected that could be associated with PCOS. However, its etiology is still not fully identified [10,11].Up to now, several association studies were reported that the some of polymorphisms of tumor necrosis factor-α (TNF-α) are related with gynecological diseases including pre-eclampsia, endometriosis [12]. It is a multifunctional proinflammation cytokine and has a significant source of genetic variability [13,14]. Man
Hyaluronan Binding Motifs of USP17 and SDS3 Exhibit Anti-Tumor Activity
Suresh Ramakrishna, Bharathi Suresh, Su-Mi Bae, Woong-Shick Ahn, Key-Hwan Lim, Kwang-Hyun Baek
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0037772
Abstract: Background We previously reported that the USP17 deubiquitinating enzyme having hyaluronan binding motifs (HABMs) interacts with human SDS3 (suppressor of defective silencing 3) and specifically deubiquitinates Lys-63 branched polyubiquitination of SDS3 resulting in negative regulation of histone deacetylase (HDAC) activity in cancer cells. Furthermore, USP17 and SDS3 mutually interact with each other to block cell proliferation in HeLa cells but the mechanism for this inhibition in cell proliferation is not known. We wished to investigate whether the HABMs of USP17 were responsible for tumor suppression activity. Methodology/Principal Findings Similarly to USP17, we have identified that SDS3 also has three consecutive HABMs and shows direct binding with hyaluronan (HA) using cetylpyridinium chloride (CPC) assay. Additionally, HA oligosaccharides (6-18 sugar units) competitively block binding of endogenous HA polymer to HA binding proteins. Thus, administration of HA oligosaccharides antagonizes the interaction between HA and USP17 or SDS3. Interestingly, HABMs deleted USP17 showed lesser interaction with SDS3 but retain its deubiquitinating activity towards SDS3. The deletion of HABMs of USP17 could not alter its functional regulation on SDS3-associated HDAC activity. Furthermore, to explore whether HABMs in USP17 and SDS3 are responsible for the inhibition of cell proliferation, we investigated the effect of USP17 and SDS3-lacking HABMs on cell proliferation by soft agar, apoptosis, cell migration and cell proliferation assays. Conclusions Our results have demonstrated that these HABMs in USP17 and its substrate SDS3 are mainly involved in the inhibition of anchorage-independent tumor growth.
Hyaluronan- and RNA-binding deubiquitinating enzymes of USP17 family members associated with cell viability
Ju-Mi Shin, Kyong-Jai Yoo, Myung-Sun Kim, Dongku Kim, Kwang-Hyun Baek
BMC Genomics , 2006, DOI: 10.1186/1471-2164-7-292
Abstract: While identifying putative ubiquitin specific protease (USP) enzymes that contain a conserved Asp (I) domain in humans, 4 USP17 subfamily members, highly homologous to DUB-3, have been found (USP17K, USP17L, USP17M, and USP17N), from human chorionic villi. Expression analysis showed that USP17 transcripts are highly expressed in the heart, liver, and pancreas and are expressed moderately in various human cancerous cell lines. Amino acid sequence analysis revealed that they contain the highly conserved Cys, His, and Asp domains which are responsible for the deubiquitinating activity. Biochemical enzyme assays indicated that they have deubiquitinating activity. Interestingly, the sequence analysis showed that these proteins, with exception of USP17N, contain the putative hyaluronan/RNA binding motifs, and cetylpyridinium chloride (CPC)-precipitation analysis confirmed the association between these proteins and intracellular hyaluronan and RNA.Here, we report that the overexpression of these proteins, with exception of USP17N, leads to apoptosis, suggesting that the hyaluronan and RNA binding motifs in these enzymes play an important role in regulating signal transduction involved in cell death.The post-translational modification by ubiquitin (Ub) plays an essential role for numerous cellular functions such as protein degradation, cell cycle control, transcriptional regulation, immune response, apoptosis, oncogenesis, pre-implantation, and intracellular signaling pathways [1-6]. Conjugation of ubiquitin to a target protein is achieved by the sequential enzymatic actions via ubiquitin-activating enzymes (E1), ubiquitin-conjugating enzymes (E2), and ubiquitin ligases (E3). A novel ubiquitination factor (E4) required for efficient multiubiquitination has been identified in yeast [7]. Proteins modified with a polyubiquitin chain are then unfolded and degraded by the 26S proteasome [1,4,5]. Deubiquitination, a removal of ubiquitin from ubiquitin-conjugated protein substrate
Pepper EST database: comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum) transcriptome
Hyun-Jin Kim, Kwang-Hyun Baek, Seung-Won Lee, JungEun Kim, Bong-Woo Lee, Hye-Sun Cho, Woo Taek Kim, Doil Choi, Cheol-Goo Hur
BMC Plant Biology , 2008, DOI: 10.1186/1471-2229-8-101
Abstract: We built the Pepper EST database to mine the complexity of chili pepper ESTs. The database was built on 122,582 sequenced ESTs and 116,412 refined ESTs from 21 pepper EST libraries. The ESTs were clustered and assembled into virtual consensus cDNAs and the cDNAs were assigned to metabolic pathway, Gene Ontology (GO), and MIPS Functional Catalogue (FunCat). The Pepper EST database is designed to provide a workbench for (i) identifying unigenes in pepper plants, (ii) analyzing expression patterns in different developmental tissues and under conditions of stress, and (iii) comparing the ESTs with those of other members of the Solanaceae family. The Pepper EST database is freely available at http://genepool.kribb.re.kr/pepper/ webcite.The Pepper EST database is expected to provide a high-quality resource, which will contribute to gaining a systemic understanding of plant diseases and facilitate genetics-based population studies. The database is also expected to contribute to analysis of gene synteny as part of the chili pepper sequencing project by mapping ESTs to the genome.Pepper is a member of the family Solanaceae, which is one of the largest families in the plant kingdom and includes more than 3,000 species [1]. The Solanaceae family includes important crops, such as pepper, tomato, tobacco, potato, and eggplant and has been highly cultivated over the years for human nutrition and health. Capsicum species are consumed worldwide and are valued because of their unique color, pungency, and aroma. Capsicum peppers include C. annuum, C. chinense, C. baccatum, C. frutescens, and C. pubescens and are cultivated in different parts of the world. Of these, the varieties of the chili pepper plant species C. annuum, having a modest-sized diploid genome (2n = 24), are the most heavily consumed due to their nutritional value and spicy taste [2]. The chemical that is primarily responsible for the pungency of C. annuum has been identified as capsaicin [3], which elicits numerous b
Embryonic Demise Caused by Targeted Disruption of a Cysteine Protease Dub-2
Kwang-Hyun Baek, Heyjin Lee, Sunmee Yang, Soo-Bin Lim, Wonwoo Lee, Jeoung Eun Lee, Jung-Jin Lim, Kisun Jun, Dong-Ryul Lee, Young Chung
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0044223
Abstract: Background A plethora of biological metabolisms are regulated by the mechanisms of ubiquitination, wherein this process is balanced with the action of deubiquitination system. Dub-2 is an IL-2-inducible, immediate-early gene that encodes a deubiquitinating enzyme with growth regulatory activity. DUB-2 presumably removes ubiquitin from ubiquitin-conjugated target proteins regulating ubiquitin-mediated proteolysis, but its specific target proteins are unknown yet. Methodology/Principal Findings To elucidate the functional role of Dub-2, we generated genetically modified mice by introducing neo cassette into the second exon of Dub-2 and then homologous recombination was done to completely abrogate the activity of DUB-2 proteins. We generated Dub-2+/? heterozygous mice showing a normal phenotype and are fertile, whereas new born mouse of Dub-2?/? homozygous alleles could not survive. In addition, Dub-2?/? embryo could not be seen between E6.5 and E12.5 stages. Furthermore, the number of embryos showing normal embryonic development for further stages is decreased in heterozygotes. Even embryonic stem cells from inner cell mass of Dub-2?/? embryos could not be established. Conclusions Our study suggests that the targeted disruption of Dub-2 may cause embryonic lethality during early gestation, possibly due to the failure of cell proliferation during hatching process.
Production of taxadiene from cultured ginseng roots transformed with taxadiene synthase gene
Mijeong Cha1, Sang Hee Shim1, Sung Hong Kim2, Ok Tae Kim3, Se-Weon Lee4, Suk-Yoon Kwon5 & Kwang-Hyun Baek1,*
BMB Reports , 2012,
Abstract: Paclitaxel is produced by various species of yew trees and hasbeen extensively used to treat tumors. In our research, ataxadiene synthase (TS) gene from Taxus brevifolia was used totransform the roots of cultured ginseng (Panax ginseng C.A.Meyer) to produce taxadiene, the unique skeletal precursor totaxol. The TS gene was successfully introduced into theginseng genome, and the de novo formation of taxadiene wasidentified by mass spectroscopy profiling. Without any changein phenotypes or growth difference in a TS-transgenic ginsengline, the transgenic TSS3-2 line accumulated 9.1 μg taxadieneper gram of dry weight. In response to the treatment of methyljasmonate for 3 or 6 days, the accumulation was 14.6 and15.9 μg per g of dry weight, respectively. This is the first reportof the production of taxadiene by engineering ginseng rootswith a taxadiene synthase gene.
Analysis of feedback loops and robustness in network evolution based on Boolean models
Yung-Keun Kwon, Kwang-Hyun Cho
BMC Bioinformatics , 2007, DOI: 10.1186/1471-2105-8-430
Abstract: In this paper, we focus on the robustness of a network that is acquired during its evolutionary process. Through simulations using Boolean network models, we found that preferential attachment increases the number of coupled feedback loops in the course of network evolution. Whereas, if networks evolve to have more coupled feedback loops rather than following preferential attachment, the resulting networks are more robust than those obtained through preferential attachment, although both of them have similar degree distributions.The presented analysis demonstrates that coupled feedback loops may play an important role in network evolution to acquire robustness. The result also provides a hint as to why various biological networks have evolved to contain a number of coupled feedback loops.There is a growing interest in understanding the principle of biological network evolution and many network growth models have been proposed to investigate this issue. For example, the duplication-mutation models suggest that network growth occurs through the duplication of an existing node and mutation of links by deleting an existing link or adding a new link [1,2]. In addition, other models such as random static network models where links are randomly connected [3,4], aging vertex network models where the probability of producing new edges decreases with the age of a network node [5], and small-world network models based on an interpolation between regular ring lattices and randomly connected graphs [6], have been introduced. Meanwhile, there have been various studies on the topological properties of biological networks, and one prominent result is about the scale-free property indicating the power-law distribution in the number of connections (degree) per network node [7]. In this regard, finding a network growth model that can produce a scale-free network has become an issue. Preferential attachment, a way of adding new interactions to a network node in proportion to the connec
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