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Jiyeong Lee,EunJeong Joo,HeeJoung Lim,JongMoon Park,KyuYoung Lee,Arum Park,AeEun Seok,HooKeun Lee,HeeGyoo Kang 대한신경정신의학회 2015 PSYCHIATRY INVESTIGATION Vol.12 No.2
Objective-Currently, there are a few biological markers to aid in the diagnosis and treatment of depression. However, it is not sufficient for diagnosis. We attempted to identify differentially expressed proteins during depressive moods as putative diagnostic biomarkers by using quantitative proteomic analysis of serum. Methods-Blood samples were collected twice from five patients with major depressive disorder (MDD) at depressive status before treatment and at remission status during treatment. Samples were individually analyzed by liquid chromatography-tandem mass spectrometry for protein profiling. Differentially expressed proteins were analyzed by label-free quantification. Enzyme-linked immunosorbent assay (ELISA) results and receiver-operating characteristic (ROC) curves were used to validate the differentially expressed proteins. For validation, 8 patients with MDD including 3 additional patients and 8 matched normal controls were analyzed. Results-The quantitative proteomic studies identified 10 proteins that were consistently upregulated or downregulated in 5 MDD patients. ELISA yielded results consistent with the proteomic analysis for 3 proteins. Expression levels were significantly different between normal controls and MDD patients. The 3 proteins were ceruloplasmin, inter-alpha-trypsin inhibitor heavy chain H4 and complement component 1qC, which were upregulated during the depressive status. The depressive status could be distinguished from the euthymic status from the ROC curves for these proteins, and this discrimination was enhanced when all 3 proteins were analyzed together. Conclusion-This is the first proteomic study in MDD patients to compare intra-individual differences dependent on mood. This technique could be a useful approach to identify MDD biomarkers, but requires additional proteomic studies for validation.
Tran, Trang Huyen,Park, SunYoung,Lee, Hyunjin,Park, Sungsuk,Kim, Bora,Kim, Ok-Hee,Oh, Byung-chul,Lee, Dongil,Lee, Hookeun The Royal Society of Chemistry 2012 The Analyst Vol.137 No.4
<P>In recent years, gold nanoparticles have been increasingly utilized as a promising material for biomedical analysis. We report here for the first time the synthesis of ultrasmall gold nanoparticles with core diameter of 1.2 nm functionalized with hydrazide groups and their use in isolation/enrichment of N-glycosylated peptides. Hydrazide-functionalized gold nanoparticles showed excellent stability in biological samples and exhibited a large capacity for peptide capturing. The captured peptides from tested standard glycoproteins were found to be highly specific as determined by Agilent HPLC chip and quadrupole time-of-flight (Q-TOF) mass spectrometer. The hydrazide-functionalized gold nanoparticles were successfully utilized in the isolation of a real proteome complex, which showed that more than 90% of captured product was glycopeptide. These results demonstrate that the ultrasmall gold nanoparticles can be used for a high-throughput analysis platform of glycoproteins.</P> <P>Graphic Abstract</P><P>Glycopeptide capturing using novel hydrazide-functionalization of glutathione-protected Au<SUB>25</SUB> ultrasmall nanoparticle is developed and demonstrated in tissue proteome analysis. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c1an15810d'> </P>
Zahra, Zahra,Kim, Seok-Young,Kim, Hye-Youn,Lee, Hwanhui,Lee, Heayyean,Jeon, Jun-Yeong,Kim, Dong-Min,Kim, Dong-Myung,Hong, Seong-Joo,Cho, Byung-Kwan,Lee, Hookeun,Lee, Choul-Gyun,Arshad, Muhammad,Choi, American Chemical Society 2018 Journal of agricultural and food chemistry Vol.66 No.32
<P>This study aimed to improve the production of phycobiliproteins using TiO<SUB>2</SUB> nanoparticles (NPs) in <I>Synechocystis</I> sp. PCC 6803. The growth characteristics of <I>Synechocystis</I> cells were not affected by TiO<SUB>2</SUB> NPs treatment, but this treatment increased the chlorophyll content significantly by 62.2% (14.6 mg/L) compared to that of control (9.0 mg/L) on day 16. Phycocyanin production was increased by 33.8% (29.3 g/L) compared to that of control (21.9 g/L) on day 8. Allophycocyanin production was increased by 55.0% (6.2 g/L) compared to that of control (4.0 g/L) on day 8, and by 22.4% (16.4 g/L) compared to that of control (13.4 g/L) on day 16. Direct infusion mass spectrometry revealed that TiO<SUB>2</SUB> NPs treatment significantly increased the levels of major thylakoid membranes of monogalactosyldiacylglycerols (18:2/18:3, 18:2/18:2, 18:1/18:2), phosphatidylglycerol (16:0/16:1), and sulfoquinovosyldiacylglycerols (16:0/16:1, 16:0:18:4) on day 8. These findings indicate that TiO<SUB>2</SUB> NPs have potential for commercial applications in <I>Synechocystis</I> species or other microalgal strains.</P> [FIG OMISSION]</BR>
HIF-1-Dependent Induction of Jumonji Domain-Containing Protein (JMJD) 3 under Hypoxic Conditions
Lee, Ho-Youl,Choi, Kang,Oh, Hookeun,Park, Young-Kwon,Park, Hyunsung Korean Society for Molecular and Cellular Biology 2014 Molecules and cells Vol.37 No.1
Jumonji domain-containing proteins (JMJD) catalyze the oxidative demethylation of a methylated lysine residue of histones by using $O_2$, ${\alpha}$-ketoglutarate, vitamin C, and Fe(II). Several JMJDs are induced by hypoxic stress to compensate their presumed reduction in catalytic activity under hypoxia. In this study, we showed that an H3K27me3 specific histone demethylase, JMJD3 was induced by hypoxia-inducible factor (HIF)-$1{\alpha}/{\beta}$ under hypoxia and that treatment with Clioquinol, a HIF-$1{\alpha}$ activator, increased JMJD3 expression even under normoxia. Chromatin immunoprecipitation (ChIP) analyses showed that both HIF-$1{\alpha}$ and its dimerization partner HIF-$1{\beta}$/Arnt occupied the first intron region of the mouse JMJD3 gene, whereas the HIF-$1{\alpha}/{\beta}$ heterodimer bound to the upstream region of the human JMJD3, indicating that human and mouse JMJD3 have hypoxia-responsive regulatory regions in different locations. This study shows that both mouse and human JMJD3 are induced by HIF-1.
Jang, Inae,Lee, Sun Young,Hwangbo, Song,Kang, Dukjin,Lee, Hookeun,Kim, Hugh I.,Moon, Bongjin,Oh, Han Bin Springer US 2017 Journal of the American Society for Mass Spectrome Vol.28 No.1
<P>The present study demonstrates that one-step peptide backbone fragmentations can be achieved using the TEMPO [2-(2,2,6,6-tetramethyl piperidine-1-oxyl)]-assisted free radical-initiated peptide sequencing (FRIPS) mass spectrometry in a hybrid quadrupole time-of-flight (Q-TOF) mass spectrometer and a Q-Exactive Orbitrap instrument in positive ion mode, in contrast to two-step peptide fragmentation in an ion-trap mass spectrometer (reference Anal. Chem. <B>85</B>, 7044-7051 ((30))). In the hybrid Q-TOF and Q-Exactive instruments, higher collisional energies can be applied to the target peptides, compared with the low collisional energies applied by the ion-trap instrument. The higher energy deposition and the additional multiple collisions in the collision cell in both instruments appear to result in one-step peptide backbone dissociations in positive ion mode. This new finding clearly demonstrates that the TEMPO-assisted FRIPS approach is a very useful tool in peptide mass spectrometry research.</P> [FIG OMISSION]</BR>
HIF-1-Dependent Induction of Jumonji Domain-Containing Protein (JMJD) 3 under Hypoxic Conditions
Ho-Youl Lee,Kang Choi,Hookeun Oh,박영권,박현성 한국분자세포생물학회 2014 Molecules and cells Vol.37 No.1
Jumonji domain-containing proteins (JMJD) catalyze the oxidative demethylation of a methylated lysine residue of histones by using O2, a-ketoglutarate, vitamin C, and Fe(II). Several JMJDs are induced by hypoxic stress to compensate their presumed reduction in catalytic activity under hypoxia. In this study, we showed that an H3K27me3 specific histone demethylase, JMJD3 was induced by hypoxia-inducible factor (HIF)-1a/b under hypoxia and that treatment with Clioquinol, a HIF-1a activator, increased JMJD3 expression even under normoxia. Chromatin immunoprecipitation (ChIP) analyses showed that both HIF-1a and its dimerization partner HIF-1b/Arnt occu-pied the first intron region of the mouse JMJD3 gene, whereas the HIF-1a/b heterodimer bound to the upstream region of the human JMJD3, indicating that human and mouse JMJD3 have hypoxia-responsive regulatory regions in different locations. This study shows that both mouse and human JMJD3 are induced by HIF-1.
The impact of freeze-drying on the glycoproteomic profiles of human milk
Won-Ho Hahn,Seong Phil Bae,Hookeun Lee,Jong-Moon Park,Suyeon Park,이주현,강남미 한국분석과학회 2020 분석과학 Vol.33 No.4
Human milk (HM) glycoproteins play important roles protecting infants against various pathogens. Recently, freezing HM is reported to affect some glycoproteins and freeze-drying is suggested as an alternative method. However, the effects of freeze-drying on HM glycoproteins were not evaluated yet. Six fresh HM samples were collected from three healthy mothers at 15 and 60th days of lactation from each mother. Each sample was divided into frozen and freeze-dried subgroups yielding totally 12 samples, and the glycoproteomic analysis was performed by liquid chromatography mass spectrometry. The results were compared between samples of 15 and 60th days of lactation, and before and after the freeze-drying. Totally, 203 glycoproteins were detected. The glycoprotein levels were not different between two groups of 15/60th day of lactation and before/after freeze-drying groups (P > 0.050). In addition, significant correlation of glycoprotein levels was found between the different lactation stages (r = 0.897, P < 0.001) and the status of freeze-drying (r = 0.887, P < 0.001) in a partial correlation analysis. As no significant change of HM glycoproteins was not found after the freezedrying, we hope that introducing freeze-drying to HM banks is supported by the present study. This work was supported by the National Research Foundation (NRF) of Korea grant funded by the Korea government (MSIP) (No.2017R1D1A1B03034270; No.2020R1A2C1005082).
An Automated High Throughput Proteolysis and Desalting Platform for Quantitative Proteomic Analysis
Arul, Albert-Baskar,Han, Na-Young,Lee, Hookeun Korean Society for Mass Spectrometry 2013 Mass spectrometry letters Vol.4 No.2
Proteomics for biomarker validation needs high throughput instrumentation to analyze huge set of clinical samples for quantitative and reproducible analysis at a minimum time without manual experimental errors. Sample preparation, a vital step in proteomics plays a major role in identification and quantification of proteins from biological samples. Tryptic digestion a major check point in sample preparation for mass spectrometry based proteomics needs to be more accurate with rapid processing time. The present study focuses on establishing a high throughput automated online system for proteolytic digestion and desalting of proteins from biological samples quantitatively and qualitatively in a reproducible manner. The present study compares online protein digestion and desalting of BSA with conventional off-line (in-solution) method and validated for real time sample for reproducibility. Proteins were identified using SEQUEST data base search engine and the data were quantified using IDEALQ software. The present study shows that the online system capable of handling high throughput samples in 96 well formats carries out protein digestion and peptide desalting efficiently in a reproducible and quantitative manner. Label free quantification showed clear increase of peptide quantities with increase in concentration with much linearity compared to off line method. Hence we would like to suggest that inclusion of this online system in proteomic pipeline will be effective in quantification of proteins in comparative proteomics were the quantification is really very crucial.