• BMB Reports
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• v.43 no.11
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• pp.711-719
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• 2010

Kinomics is an emerging and promising approach for deciphering kinomes. Chemical kinomics is a discipline of chemical genomics that is also referred to as "chemogenomics", which is derived from chemistry and biology. Chemical kinomics has become a powerful approach to decipher complicated phosphorylation-based cellular signaling networks with the aid of small molecules that modulate kinase functions. Moreover, chemical kinomics has played a pivotal role in the field of kinase drug discovery as it enables identification of new molecular targets of small molecule kinase modulators and/or exploitation of novel functions of known kinases and has also provided novel chemical entities as hit/lead compounds. In this short review, contemporary chemical kinomics technologies such as activity-based protein profiling, T7 kinasetagged phages, kinobeads, three-hybrid systems, fluorescenttagged kinase binding assays, and chemical genomic profiling are discussed along with a novel allosteric Bcr-Abl kinase inhibitor (GNF-2/GNF-5) as a successful application of chemical kinomics approaches.

• Molecules and Cells
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• v.38 no.5
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• pp.390-395
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• 2015

Degradation of chlorophyll (Chl) by Chl catabolic enzymes (CCEs) causes the loss of green color that typically occurs during senescence of leaves. In addition to CCEs, STAYGREEN1 (SGR1) functions as a key regulator of Chl degradation. Although sgr1 mutants in many plant species exhibit a staygreen phenotype, the biochemical function of the SGR1 protein remains elusive. Many recent studies have examined the physiological and molecular roles of SGR1 and its homologs (SGR2 and SGR-LIKE) in Chl metabolism, finding that these proteins have different roles in different species. In this review, we summarize the recent studies on SGR and discuss the most likely functions of SGR homologs.

• Preventive Nutrition and Food Science
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• v.8 no.1
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• pp.105-112
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• 2003

Animals possess a highly sophisticated mechanism of storing energy in adipose tissue inside their bodies. However, in humans it has been clarified that adipocyte (fat cell), which composes the body fat (adipose) tissues, development and the extent of subsequent fat accumulation are closely associated with the occurrence and advancement of various common diseases (e.g., type-2 diabetes, coronary artery disease, and hypertension) resulting from obesity. Recent exciting progress in clinical and biochemical studies of adipocytes has rapidly clarified the functions of adipocytes and adipose tissue. Interesting findings are the function of white adipocytes as "secreting cells" and the molecular mechanism undelying adipocyte differentiation at the transcriptional level in relation to nuclear receptors. Consequently, the adipose tissue is being targeted for the prevention or treatment of many common diseases. In this review, I will focus on recent information on characteristics of adipocytes and the relationship between obesity and common obesity-related diseases. diseases.

• Bulletin of the Korean Chemical Society
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• v.4 no.2
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• pp.87-91
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• 1983

Molecular dynamic method has been applied to a single polymer chain immersed in a solvent. The interactions for the pairs, of two solvent molecules (SS), of a chain element and a solvent molecules (CS), and of two non-neighbor chain elements (CC) are given by the Lennard-Jones potential, and the interaction between two bonded chain elements is given by a harmonic potential. We changed the CS interaction parameter ${\varepsilon}_{CS}$ to 0.5, 1.0 and 2.0 times of the SS interaction ${\varepsilon}_{SS}$. We calculated the pair correlation functions for the SS, CS, and CC pairs, end-to-end distance and radius of gyration with the varying ${\varepsilon}_{CS}$ parameters. The results showed that a phase separation occurs between the polymer and solvent in the 0.5 system where ${\varepsilon}_{CS}$ = 0.5 {\varepsilon}_{SS}$. The autocorrelation functions for end-to-end distance and radius of gyration were also calculated.

• Journal of Plant Biotechnology
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• v.40 no.2
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• pp.59-64
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• 2013

Auxin is a key plant hormone which regulates overall plant growth development. A number of researches to investigate auxin signaling identified three major classes of early auxin response genes: AUX/IAA, GH3 and SMALL AUXIN UP RNA (SAUR). Among these genes, in planta functions of SAUR gene family are largely ambiguous, while both AUX/IAA and GH3 genes are analyzed to mediate negative feedback on auxin response. SAUR genes encode small plant-specific proteins. SAUR gene products are highly unstable and transiently expressed in the tissue- and developmental-specific manners in response to auxin and various environmental stimuli. In the decades, molecular and genetic approaches to elucidate in planta functions of SAURs have been hampered by several factors such as the unstable molecular features and functional redundancy among them. However, a series of recent studies focusing on several subgroups of SAUR gene family made significant progress in our understanding of its biochemical and physiological functions. These works suggest that many SAUR proteins mainly regulate auxin-related cell expansion and auxin transport. In this review, the recent progress in SAUR research and prospects for crop improvement through its genetic manipulation are discussed.

• Bulletin of the Korean Chemical Society
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• v.20 no.8
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• pp.897-904
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• 1999

We have presented the thermodynamic, structural and dynamic properties of liquid pentane isomers - normal pentane, isopentane, and neopentane - using an expanded collapsed atomic model. The thermodynamic properties show that the intermolecular interactions become weaker as the molecular shape becomes more nearly spherical and the surface area decreases with branching. The structural properties are well predicted from the site-site radial, the average end-to-end distance, and the root-mean-squared radius of gyration distribution func-tions. The dynamic properties are obtained from the time correlation functions - the mean square displacement (MSD), the velocity auto-correlation (VAC), the cosine (CAC), the stress (SAC), the pressure (PAC), and the heat flux auto-correlation (HFAC) functions - of liquid pentane isomers. Two self-diffusion coefficients of liquid pentane isomers calculated from the MSD's via the Einstein equation and the VAC's via the Green-Kubo relation show the same trend but do not coincide with the branching effect on self-diffusion. The rotational re-laxation time of liquid pentane isomers obtained from the CAC's decreases monotonously as branching increases. Two kinds of viscosities of liquid pentane isomers calculated from the SAC and PAC functions via the Green-Kubo relation have the same trend compared with the experimental results. The thermal conductivity calculated from the HFAC increases as branching increases.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.1
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• pp.131-138
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• 2009

Among rumen microbes, bacteria play important roles in the biological degradation of plant fiber due to their large biomass and high activity. To maximize the utilization of fiber components such as cellulose and hemicellulose by ruminant animals, the ecology and functions of rumen bacteria should be understood in detail. Recent genome sequencing analyses of representative fibrolytic bacterial species revealed that the number and variety of enzymes for plant fiber digestion clearly differ between Fibrobacter succinogenes and Ruminococcus flavefaciens. Therefore, the mechanism of plant fiber digestion is also thought to differ between these two species. Ecology of individual fibrolytic bacterial species has been investigated using pure cultures and electron microscopy. Recent advances in molecular biology techniques complement the disadvantages of conventional techniques and allow accurate evaluation of the ecology of specific bacteria in mixed culture, even in situ and in vivo. Molecular monitoring of fibrolytic bacterial species in the rumen indicated the predominance of F. succinogenes. Nutritive interactions between fibrolytic and non-fibrolytic bacteria are important in maintaining and promoting fibrolytic activity, mainly in terms of crossfeeding of metabolites. Recent 16S rDNA-based analyses suggest that presently recognized fibrolytic species such as F. succinogenes and two Ruminococcus species with fibrolytic activity may represent only a small proportion of the total fibrolytic population and that uncultured bacteria may be responsible for fiber digestion in the rumen. Therefore, characterization of these unidentified bacteria is important to fully understand the physiology and ecology of fiber digestion. To achieve this, a combination of conventional and modern techniques could be useful.

• BMB Reports
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• v.36 no.6
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• pp.565-571
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• 2003

The locomotor responses of human peripheral blood neutrophils and lymphocytes were measured by the change from spherical to polarized shapes in the presence of endotoxins (lipopolysaccharide, LPS) of enteric pathogens: S. dysenteriae type 1, V. cholerae Inaba 569B, S. typhimurium, and K. pneumoniae. We reported earlier that these endotoxins are chemotactic factors for the neutrophils since they stimulated cell polarization within a few minutes of incubation. Endotoxins had an inhibitory effect upon neutrophil phagocytosis of opsonized yeast and the cells engulfed fewer yeasts. Interestingly, endotoxins increased neutrophil adhesion to clean glass surfaces, but stimulated the cells to exhibit increased random locomotion (chemokinesis) through cellulose nitrate filters and show an enhanced ability to reduce nitroblue tetrazolium (NBT) dye. Unlike neutrophils, lymphocytes direct from blood do not show polarized morphology towards chemotactic factors but the cells acquire locomotor capacity during 24-72 h culture with mitogens such as phytohemagglutinin (PHA), phorbol myristate acetate or concanavalin A. Stimulation of blood lymphocytes with endotoxins did not induce cell polarization in short-term but long-term culture resulted in an increase in the proportion of polarized cells that acquired locomotor morphologies. The majority of these cells were identified as esterase negative B-lymphocytes that migrated through filters. Despite the optimum time of incubation for each of these cell types being different, we found that lymphocytes respond to much lower concentrations of endotoxins than the neutrophils. These findings suggest that endotoxins of enteric pathogens modulate the functions of human blood neutrophils and lymphocytes.

• Journal of the Korean Society of Food Science and Nutrition
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• v.34 no.10
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• pp.1642-1654
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• 2005

With the decoding of human genome in 2004 and the recent development in nutritional science there has been an integration of molecular biology and nutrition. As a consequenc a now word ' molecular nutrition ' has been formed and recently the word 'nutrigenomics' is coined and widely being used. The field of science that showed the most positive result from grafting the science of nutrition and nutrigenomics is obesity. In 1994, Jeffrey Friedman from Rockeffeler University announced that ob gene and obesity has a close relationship and since then there's been a huge research done on genes related to obesity from the molecular nutrition's Point of view. Even now there are many genes presented which are supposed to be related to obesity and big efforts are put into finding what exactly those genes do. Moreover studying only in the context of genes was not enough so functional genomics, which is the study of the functions of cells and the functions and effects between genes and Protein Products, is being studied. This review article discusses the relationship between nutrition and genes and the general idea of nutrigenomics. The article also discusses about the current research status on these subjects.

• Animal cells and systems
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• v.7 no.3
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• pp.207-211
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• 2003

Caveolin-1 is a principal protein in the plasma membrane microdomains called caveolae. Caveolae play an important role in the transcytosis and pinocytosis. Therefore, caveolin-1 is most likely to work for the membrane dynamic events. In addition, caveolin-1 interacts with various signaling molecules. Although caveolin-1 possesses a variety of physiological functions, its structural properties were little construed. Here we analyzed the structural dynamics of the N-terminal caveolin-1 (residues 1-101), in order to better understand the structural properties in terms of its versatile functionality. We first analyzed its oligomeric form using GST-fused N-terminal domain, revealing that it equilibrates between a dimer and monomers in av concentration-dependent manner. The N-terminal domain of caveolin-1 was previously found to form a heptamer, so that our data suggest the dimeric form as an intermediate structure for the heptamer formation. Then, we obtained the folding profile, which indicated that $\DeltaG_{H2O}\;is\;about\;0.5\;\pm0.03$ kcal/mol. The stability of N-terminal domain is relatively low, indicating that N-terminal domain may not be crystalline. Conclusively, the dynamic and flexible structure of N-terminal domain appears more favorable to maintain the versatile functions of caveolin-1.