Genomes and Genes
Experts and Doctors on proteome in Seoul, South Korea
Locale: Seoul, South Korea
- Ju J, Joo H, Lee M, Cho S, Cheun H, Kim J, et al. Identification of a serodiagnostic antigen, legumain, by immunoproteomic analysis of excretory-secretory products of Clonorchis sinensis adult worms. Proteomics. 2009;9:3066-78 pubmed publisher..Our results illustrate the validity of immuno-proteomic approaches in the identification of serodiagnostic antigens in the parasites. ..
- Paik Y, Omenn G, Uhlen M, Hanash S, Marko Varga G, Aebersold R, et al. Standard guidelines for the chromosome-centric human proteome project. J Proteome Res. 2012;11:2005-13 pubmed publisher..hupo.org/research). The common application of these guidelines in the participating laboratories is expected to facilitate the goal of a comprehensive analysis of the human proteome. ..
- Hong I, Kang T, Yoo Y, Park R, Lee J, Lee S, et al. Quantitative proteomic analysis of the hippocampus in the 5XFAD mouse model at early stages of Alzheimer's disease pathology. J Alzheimers Dis. 2013;36:321-34 pubmed publisher..Together with a recent study on the transcriptome of 5XFAD mice, our study allows a comprehensive understanding of the molecular events occurring in 5XFAD mice during the early stages of AD pathology. ..
- Cho S, Seo M, Ko J, Shim J, Yoo J, Kim J, et al. Up-regulation of Idh3alpha causes reduction of neuronal differentiation in PC12 cells. BMB Rep. 2010;43:369-74 pubmed..As a result, we proved that up-regulation of Idh3alpha causes reduction in neural differentiation of PC12 cells. Based on these data, we suggest that Idh3alpha plays a role to the neuronal differentiation. ..
- Kim S, Jin J, Kim Y, Kim Y, Yu H. Retinal proteome analysis in a mouse model of oxygen-induced retinopathy. J Proteome Res. 2012;11:5186-203 pubmed publisher..These proteins, including ORP150, are potential novel therapeutic targets for the treatment of proliferative ischemic retinopathy. ..
- Lee H, Jeong S, Na K, Lee M, Lee S, Lim J, et al. Comprehensive genome-wide proteomic analysis of human placental tissue for the Chromosome-Centric Human Proteome Project. J Proteome Res. 2013;12:2458-66 pubmed publisher..As far as we know, this work produced the highest number of proteins identified in the placenta and will be useful for annotating and mapping all proteins encoded in the human genome. ..
- Choi Y, Kang S, Hong S, Xie X, Cho N. Proteomic analysis of progressive factors in uterine cervical cancer. Proteomics. 2005;5:1481-93 pubmed
- Han D, Moon S, Kim Y, Kim J, Jin J, Kim Y. In-depth proteomic analysis of mouse microglia using a combination of FASP and StageTip-based, high pH, reversed-phase fractionation. Proteomics. 2013;13:2984-8 pubmed publisher..All MS data have been deposited in the ProteomeXchange with identifier PXD000168. ..
- Poulsen E, Nielsen N, Jensen M, Nielsen E, Hjortdal J, Kim E, et al. LASIK surgery of granular corneal dystrophy type 2 patients leads to accumulation and differential proteolytic processing of transforming growth factor beta-induced protein (TGFBIp). Proteomics. 2016;16:539-43 pubmed publisher..Lastly, 2DE also revealed differential processing between GCD2 patients with a history of LASIK surgery when compared to healthy individuals. ..
- Park S, Yoon W, Song J, Jung H, Kim C, Oh S, et al. Proteome analysis of human amnion and amniotic fluid by two-dimensional electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Proteomics. 2006;6:349-63 pubmed
- Lee J, Kim S, Lee J, Yoo E, Cho M, Cho M, et al. A differentially expressed proteomic analysis in placental tissues in relation to pungency during the pepper fruit development. Proteomics. 2006;6:5248-59 pubmed
- Park S, Lee J, Yeom C. A proteomic approach to the identification of early molecular targets changed by L-ascorbic acid in NB4 human leukemia cells. J Cell Biochem. 2006;99:1628-41 pubmed..These results suggest that LAA oxidizes intracellular reduced glutathione and modulates disulfide bond formation in proteins. ..
- Park D, Lee K, Baek C, Kim I, Kwon J, Lee W, et al. Cyclo(Phe-Pro) modulates the expression of ompU in Vibrio spp. J Bacteriol. 2006;188:2214-21 pubmed..cholerae of the ctx genes, which are known to be regulated by ToxR. Our results suggest that cFP is a signal molecule controlling the expression of genes important for the pathogenicity of Vibrio spp. ..
- Lek M, Karczewski K, Minikel E, Samocha K, Banks E, Fennell T, et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016;536:285-91 pubmed publisher..Finally, we demonstrate that these data can be used for the efficient filtering of candidate disease-causing variants, and for the discovery of human 'knockout' variants in protein-coding genes. ..
- Park S, Ahn E, Lee S, Jung M, Park J, Yi S, et al. Proteomic analysis reveals upregulation of RKIP in S-180 implanted BALB/C mouse after treatment with ascorbic acid. J Cell Biochem. 2009;106:1136-45 pubmed publisher..Our results suggest a possibility that these proteins are related to the ascorbic acid-mediated suppression of tumor formation. ..
- Kim J, Bae S, Sung M, Lee K, Park S. Comparative proteomic analysis of trophozoites versus cysts of Giardia lamblia. Parasitol Res. 2009;104:475-9 pubmed publisher..Interestingly, genes encoding two heat shock proteins (Hsp70 and Hsp90) showed increased expression during encystation, suggesting that this differentiation process accompanies a cellular response to stress in G. lamblia...
- Nam J, Moon J, Kim I, Lee M, Hong S, Ahn J, et al. Free radicals enzymatically triggered by Clonorchis sinensis excretory-secretory products cause NF-?B-mediated inflammation in human cholangiocarcinoma cells. Int J Parasitol. 2012;42:103-13 pubmed publisher..These findings provide new insights into the pathophysiological role of C. sinensis excretory-secretory products in host chronic inflammatory processes, which are initial events in hepatobiliary diseases...
- Kim H, Kim K, Yu S, Jang E, Yu J, Cho G, et al. Development of biomarkers for screening hepatocellular carcinoma using global data mining and multiple reaction monitoring. PLoS ONE. 2013;8:e63468 pubmed publisher..This efficacious integrative strategy is applicable to the development of markers for cancer and other diseases. ..
- Choi D, Hwang B. Proteomics and functional analyses of pepper abscisic acid-responsive 1 (ABR1), which is involved in cell death and defense signaling. Plant Cell. 2011;23:823-42 pubmed publisher..Together, these results reveal ABR1 as a novel negative regulator of ABA signaling and suggest that the nuclear ABR1 pool is essential for the cell death induction associated with ABA-SA antagonism. ..
- Nam S, Kim S, Kim J, Lim M, Elenitoba Johnson K, Kim C, et al. Aberrant expression of napsin A in a subset of malignant lymphomas. Histol Histopathol. 2016;31:213-21 pubmed publisher..These results demonstrated that napsin A is aberrantly expressed in a subset of lymphomas. The biological significance of napsin A in lymphomas warrants further study. ..
- Lee S, Yoon T, Yoo Y, Bang Y, Kim H, Jeoung D, et al. Analysis of spinal cord proteome in the rats with mechanical allodynia after the spinal nerve injury. Biotechnol Lett. 2003;25:2071-8 pubmed..Therefore, a lower creatine kinase B expression level may be important in the development and maintenance of neuropathic pain...
- Cho W, Lee K, Yu J, Son M, Kim K. Insight into mycoviruses infecting Fusarium species. Adv Virus Res. 2013;86:273-88 pubmed publisher..Research is now needed on the molecular biology of mycovirus life cycles and mycovirus-host interactions. This research will be facilitated by the further development of omics technologies. ..
- Lim S, Park S, Kim W, Park S, Kim H, Kim Y, et al. Proteome analysis of hepatocellular carcinoma. Biochem Biophys Res Commun. 2002;291:1031-7 pubmed..The proteins revealed in this experiment can be used in the future for studies pertaining to hepatocarcinogenesis, or as diagnostic markers and therapeutic targets for HCC. ..
- Ahn Y, Hwang C, Lee S, Kwon K, Lee C. The tumour suppressor PTEN mediates a negative regulation of the E3 ubiquitin-protein ligase Nedd4. Biochem J. 2008;412:331-8 pubmed publisher..Thus our results have important implications regarding the roles of PTEN upon the E3 ubquitin ligase Nedd4 as a negative feedback regulator as well as a substrate. ..
- Kim K, Moon M. High speed two-dimensional protein separation without gel by isoelectric focusing-asymmetrical flow field flow fractionation: application to urinary proteome. J Proteome Res. 2009;8:4272-8 pubmed publisher..Our experiments also showed a higher efficiency in the identification of urine proteins using ampholyte solution in the narrower pH range. ..
- Kim H, Kang H, Lee H, Lee S, Yu M, Kim H, et al. Identification of S100A8 and S100A9 as serological markers for colorectal cancer. J Proteome Res. 2009;8:1368-79 pubmed publisher..Therefore, we suggest S100A8 and S100A9 as candidates for serological biomarkers in combination with other serum markers that aid CRC diagnosis. ..
- Jin J, Park J, Kim K, Kang Y, Park S, Kim J, et al. Detection of differential proteomes of human beta-cells during islet-like differentiation using iTRAQ labeling. J Proteome Res. 2009;8:1393-403 pubmed publisher..Our analysis of differential proteomic and mRNA expression has resulted in a greater understanding of the molecular functions that are involved in beta-cell differentiation and insulin synthesis and release. ..
- Han K, Park J, Seo H, Ahn K, Lee J. Multiple stressor-induced proteome responses of Escherichia coli BL21(DE3). J Proteome Res. 2008;7:1891-903 pubmed publisher..The quantitative and systematic proteome analyses that we have performed provide more detailed information on E. coli BL21(DE3), a widely used host strain for recombinant protein overexpression. ..
- Lee K, Kim Y, Park C, Kim H. Proteomic identification of differentially expressed proteins in Arabidopsis mutant ntm1-D with disturbed cell division. Mol Cells. 2008;25:70-7 pubmed..These observations suggest that the reduced growth observed in the ntm1-D mutant is caused by enhancement of its stress responses, possibly resulting in a cost in fitness. ..
- Kim D, Chae J, Kim J, Pak J, Koo D, Bahk Y, et al. Proteomic analysis of apoptosis related proteins regulated by proto-oncogene protein DEK. J Cell Biochem. 2009;106:1048-59 pubmed publisher..Using immunoblotting analysis, we have demonstrated the modulation of other caspase-dependent apoptosis related proteins by DEK knock-down and further implicate its role in apoptosis pathway. ..
- Han K, Seo H, Song J, Ahn K, Park J, Lee J. Transport proteins PotD and Crr of Escherichia coli, novel fusion partners for heterologous protein expression. Biochim Biophys Acta. 2007;1774:1536-43 pubmed..Both the stress-induced proteins were well suited for the production of a biologically active fusion mutant of P. putida cutinase that can be expected to be of biotechnological and commercial interest. ..
- Han K, Song J, Ahn K, Park J, Seo H, Lee J. Solubilization of aggregation-prone heterologous proteins by covalent fusion of stress-responsive Escherichia coli protein, SlyD. Protein Eng Des Sel. 2007;20:543-9 pubmed..SlyD was also shown to be suitable for the production of a biologically active fusion mutant of Pseudomonas putida cutinase that is of considerable biotechnological and commercial interest. ..
- Seo P, Kim M, Ryu J, Jeong E, Park C. Two splice variants of the IDD14 transcription factor competitively form nonfunctional heterodimers which may regulate starch metabolism. Nat Commun. 2011;2:303 pubmed publisher..Notably, IDD14? overproduction rescued the 35S:IDD14? phenotypes. We propose that alternative splicing of the IDD14 gene generates a self-controlled regulatory loop that may modulate starch accumulation in response to cold. ..
- Kim H, Kang H, You K, Kim S, Lee K, Kim T, et al. Suppression of human selenium-binding protein 1 is a late event in colorectal carcinogenesis and is associated with poor survival. Proteomics. 2006;6:3466-76 pubmed..Our findings indicate that suppression of SELENBP1 is a frequent and late event in colorectal carcinogenesis, and may contribute to the rapid progression of colorectal carcinoma. ..
- Han I, Jeong S, Lee H, Koh W, Lee H, Lee E, et al. Proteomic analysis of mesenchymal stem-like cells derived from ovarian teratoma: potential role of glutathione S-transferase M2 in ovarian teratoma. Proteomics. 2011;11:352-60 pubmed publisher..Taken together, these findings suggest that that ovarian teratoma MSCLCs have a higher potency for proliferation and angiogenesis and GSTM2 appears to be involved in the regulation of other survival genes. ..
- Kim Y, Park J, Cho J, Cho K, Park Y, Lee J. Proteomic response analysis of a threonine-overproducing mutant of Escherichia coli. Biochem J. 2004;381:823-9 pubmed..coli mutant. ..
- Shin J, Kim G, Lee J, Lee J, Kim Y, Yu J, et al. Identification of ganglioside GM2 activator playing a role in cancer cell migration through proteomic analysis of breast cancer secretomes. Cancer Sci. 2016;107:828-35 pubmed publisher..Although GM2A as a diagnostic and prognostic marker in BC should be carefully verified further, this study has established the potential role of GM2A in BC progression. ..
- Shigeoka T, Jung H, Jung J, Turner Bridger B, Ohk J, Lin J, et al. Dynamic Axonal Translation in Developing and Mature Visual Circuits. Cell. 2016;166:181-92 pubmed publisher..Our results indicate that intricate regulation of compartment-specific mRNA translation in mammalian CNS axons supports the formation and maintenance of neural circuits in vivo. ..
- Shin M, Lee D, Wohlgemuth G, Choi I, Fiehn O, Kim K. Global metabolite profiling of agarose degradation by Saccharophagus degradans 2-40. N Biotechnol. 2010;27:156-68 pubmed publisher..The use of polysaccharides such as agarose or cellulose led to the increased abundances of amino acids and intermediates of nucleotide biosynthesis...
- Lee B, Kwon S, Kim S, Kim K, Park C, Kim Y, et al. Functional study of hot pepper 26S proteasome subunit RPN7 induced by Tobacco mosaic virus from nuclear proteome analysis. Biochem Biophys Res Commun. 2006;351:405-11 pubmed..Thus, this report presents that the TMV-induced CaRPN7 may be involved in programmed cell death (PCD) in the hot pepper plant. ..
- Kim C, Yun N, Lee Y, Jeong J, Baek J, Song H, et al. Gel-based protease proteomics for identifying the novel calpain substrates in dopaminergic neuronal cell. J Biol Chem. 2013;288:36717-32 pubmed publisher..Moreover, the results described here will help us decipher the molecular mechanisms underlying the progression of neurodegenerative disorders where protease activation is critically involved. ..
- Shim Y, Paik Y. Caenorhabditis elegans proteomics comes of age. Proteomics. 2010;10:846-57 pubmed publisher..Thus, C. elegans proteomics, in combination of other molecular, biological and genetic techniques, would provide a versatile new tool box for the systematic analysis of gene functions throughout the entire life cycle of this nematode. ..
- Cho B, Cho N, Min C, Kim S, Yang J, Lee J, et al. Global gene expression profile of Orientia tsutsugamushi. Proteomics. 2010;10:1699-715 pubmed publisher..Some major changes were the downregulation of genes involved in translation, protein processing and secretion, which correlated with the reduction in bacterial translation rates and growth within macrophages...
- Seo H, Hirano M, Shibato J, Rakwal R, Hwang I, Masuo Y. Effects of coffee bean aroma on the rat brain stressed by sleep deprivation: a selected transcript- and 2D gel-based proteome analysis. J Agric Food Chem. 2008;56:4665-73 pubmed publisher..In conclusion, the roasted coffee bean aroma changes the mRNA and protein expression levels of the rat brain, providing for the first time clues to the potential antioxidant or stress relaxation activities of the coffee bean aroma. ..
- Lee J, Kim Y, Yun H, Kim J, Oh S, Kim S. Genetic and proteomic analysis of factors affecting serum cholesterol reduction by Lactobacillus acidophilus A4. Appl Environ Microbiol. 2010;76:4829-35 pubmed publisher..acidophilus showed only an approximately 10% reduction in cholesterol. These results provide important insights into the mechanism by which these lactic acid bacteria reduce cholesterol...
- Lee S, Joung M, Nam T, Park W, Ji Y, Yu J. Cryptosporidium parvum: radiation-induced alteration of the oocyst proteome. Exp Parasitol. 2011;127:25-30 pubmed publisher..The roles of these two upregulated proteins as related to the radioresistance of C. parvum remain to be evaluated. ..
- Shin S, Bae I, Kim J, Jeong S, Yong D, Kim J, et al. Resistance to carbapenems in sequence type 11 Klebsiella pneumoniae is related to DHA-1 and loss of OmpK35 and/or OmpK36. J Med Microbiol. 2012;61:239-45 pubmed publisher..The crude mortality rate of infected patients was 81.8 %. Carbapenem resistance was mainly due to a combination of DHA-1 AmpC ?-lactamase coupled with the loss of OmpK35 and/or OmpK36 and was associated with poor clinical outcome...
- Yoo K, Kim Y, Lee M, Seong J, Park J. Identification of apolipoproteinA1 reduction in the polycystic kidney by proteomics analysis of the Mxi1-deficient mouse. Proteomics. 2009;9:3824-32 pubmed publisher..These results indicate that expression of proteins related with inflammation and renal fibrosis changes by Mxi1 inactivation in polycystic kidney. ..
- Lee Y, Kim B, Kim J, Yoon W, Bang S, Park Y. CadC has a global translational effect during acid adaptation in Salmonella enterica serovar Typhimurium. J Bacteriol. 2007;189:2417-25 pubmed publisher..Taken together, our findings strongly suggest that CadC may be a global regulator involved in the OmpR regulatory system during acid adaptation...
- Lee S, Park J, Choi Y, Cho S, Ahn J, Kwon D, et al. Comparative proteomic analysis associated with term placental insufficiency in cloned pig. Proteomics. 2007;7:1303-15 pubmed..They also indicate that proteomic maps represent an important tool for future studies of placental insufficiency and pathology. ..
- Kim T, Kang J, Ahn J, Lee E, Cho K, Han B, et al. Proteomic analysis of the aqueous humor in age-related macular degeneration (AMD) patients. J Proteome Res. 2012;11:4034-43 pubmed publisher..This study demonstrates that integrated proteomic technologies can yield novel biomarkers to detect exudative AMD...
- Lee S, Kim G, Roh S, Song J, Kim H, Hong S, et al. Proteome changes related to the anti-cancer activity of HT29 cells by the treatment of ginsenoside Rd. Pharmazie. 2009;64:242-7 pubmed..It was supposed that ginsenoside Rd contributed to induce anti-cancer activity by complementary functions of these proteins in colon cancer cells. ..
- Jung J, Noh J, Park W. Physiological and metabolic responses for hexadecane degradation in Acinetobacter oleivorans DR1. J Microbiol. 2011;49:208-15 pubmed publisher..These results suggested that biofilm formation and oxidative stress defense are important physiological responses for hexadecane degradation along with metabolic switch to glyoxylate pathway in strain DR1...
- Jeong M, Lim D. A proteomic approach to study msDNA function in Escherichia coli. J Microbiol. 2004;42:200-4 pubmed..The molecular mechanism underlying the elevated mutation in msDNA-producing cell still remains elusive. ..
- Choi H, Kim N, Lee Y, Hwang B. The pepper extracellular xyloglucan-specific endo-?-1,4-glucanase inhibitor protein gene, CaXEGIP1, is required for plant cell death and defense responses. Plant Physiol. 2013;161:384-96 pubmed publisher..This response was also accompanied by cell wall thickening and darkening. Together, these results suggest that pathogen-inducible CaXEGIP1 positively regulates cell death-mediated defense responses in plants...
- Kang U, Ahn Y, Lee J, Kim Y, Kim J, Yu M, et al. Differential profiling of breast cancer plasma proteome by isotope-coded affinity tagging method reveals biotinidase as a breast cancer biomarker. BMC Cancer. 2010;10:114 pubmed publisher..78. Estrogen receptor status (p = 0.940) and progesterone receptor status (p = 0.440) were not associated with the plasma BTD levels. Our study suggests that BTD is a potential serological biomarker for the detection of breast cancer. ..
- Singh R, Lee M, Lee J, Choi J, Park J, Kim E, et al. Rice mitogen-activated protein kinase interactome analysis using the yeast two-hybrid system. Plant Physiol. 2012;160:477-87 pubmed publisher..Together, the results obtained essentially enhance our knowledge of the MAPK-interacting protein network and provide a valuable research resource for developing a nearly complete map of the rice MAPK interactome. ..
- Koh J, Lee Y, Kim Y, Park S, Lee S, Kim H, et al. Heat shock protein 60 causes osteoclastic bone resorption via toll-like receptor-2 in estrogen deficiency. Bone. 2009;45:650-60 pubmed publisher..In conclusion, HSP60 and TLR-2 are novel mediators of estrogen-deficiency-induced bone loss. ..
- Kennedy J, Abbatiello S, Kim K, Yan P, Whiteaker J, Lin C, et al. Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Nat Methods. 2014;11:149-55 pubmed publisher..These results establish the feasibility of a large-scale effort to develop an MRM assay resource. ..
- Lee Y, Choi I, Sheen Y, Park S, Kwon H. Identification of EBP50 as a specific biomarker for carcinogens via the analysis of mouse lymphoma cellular proteome. Mol Cells. 2012;33:309-16 pubmed publisher..Further, the expression level of EBP50 was increased in cells treated with seven additional carcinogens, verifying that EBP50 could serve as a specific biomarker for carcinogens. ..