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Simpson, David C.,Ahn, Seonghee,Pasa-Tolic, Ljiljana,Bogdanov, Bogdan,Mottaz, Heather M.,Vilkov, Andrey N.,Anderson, Gordon A.,Lipton, Mary S.,Smith, Richard D. WILEY-VCH Verlag 2006 Electrophoresis Vol.27 No.13
<P>Bottom-up proteomics (analyzing peptides that result from protein digestion) has demonstrated capability for broad proteome coverage and good throughput. However, due to incomplete sequence coverage, this approach is not ideally suited to the study of modified proteins. The modification complement of a protein can best be elucidated by analyzing the intact protein. 2-DE, typically coupled with the analysis of peptides that result from in-gel digestion, is the most frequently applied protein separation technique in MS-based proteomics. As an alternative, numerous column-based liquid phase techniques, which are generally more amenable to automation, are being investigated. In this work, the combination of size-exclusion chromatography (SEC) fractionation with RPLC-Fourier-transform ion cyclotron resonance (FTICR)-MS is compared with the combination of RPLC fractionation with CIEF-FTICR-MS for the analysis of the Shewanella oneidensis proteome. SEC-RPLC-FTICR-MS allowed the detection of 297 proteins, as opposed to 166 using RPLC-CIEF-FTICR-MS, indicating that approaches based on LC-MS provide better coverage. However, there were significant differences in the sets of proteins detected and both approaches provide a basis for accurately quantifying changes in protein and modified protein abundances.</P>
Body fluid proteomics: Prospects for biomarker discovery
Ahn, Sung-Min,Simpson, Richard J. WILEY-VCH Verlag 2007 PROTEOMICS CLINICAL APPLICATIONS Vol.1 No.9
<P>Many diseases are caused by perturbations of cellular signaling pathways and related pathway networks as a result of genetic aberrations. These perturbations are manifested by altered cellular protein profiles in the fluids bathing tissue/organs (i.e., the tissue interstitial fluid, TIF). A major challenge of clinical chemistry is to quantitatively map these perturbed protein profiles – the so-called “signatures of disease” – using modern proteomic technologies. This information can be utilized to design protein biomarkers for the early detection of disease, monitoring disease progression and efficacy of drug action. Here, we discuss the use of body fluids in the context of prospective biomarker discovery, and the marked 1000–1500-fold dilution of body fluid proteins, during their passage from TIF to the circulatory system. Further, we discuss proteomics strategies aimed at depleting major serum proteins, especially albumin, in order to focus on low-abundance protein/peptides in plasma. A major limitation of depletion strategies is the removal of low-molecular weight protein/peptides which specifically bind major plasma proteins. We present a prototype model, using albumin, for understanding the multifaceted nature of biomarker research, highlighting the involvement of albumin in Alzheimer's disease. This model underscores the need for a system-level understanding for biomarker research and personalized medicine.</P>
Genomics and proteomics in stem cell research
Sung-Min Ahn,Richard Simpson,Bonghee Lee 대한해부학회 2010 Anatomy & Cell Biology Vol.43 No.1
Stem cell research has been widely studied over the last few years and has attracted increasing attention from researchers in all fields of medicine due to its potential to treat many previously incurable diseases by replacing damaged cells or tissues. As illustrated by hematopoietic stem research, understanding stem cell differentiation at molecular levels is essential for both basic research and for clinical applications of stem cells. Although multiple integrative analyses, such as genomics, epigenomics, transcriptomics and proteomics, are required to understand stem cell biology, proteomics has a unique position in stem cell research. For example, several major breakthroughs in HSC research were due to the identification of proteins such as colony-stimulating factors (CSFs) and cell-surface CD molecules. In 2007, the Human Proteome Organization (HUPO) and the International Society for Stem Cell Research (ISSCR) launched the joint Proteome Biology of Stem Cells Initiative. A systematic proteomics approach to understanding stem cell differentiation will shed new light on stem cell biology and accelerate clinical applications of stem cells.
Miniaturized asymmetrical flow field-flow fractionation: Application to biological vesicles
Oh, Sunok,Kang, Dukjin,Ahn, Sung-Min,Simpson, Richard J.,Lee, Bong-Hee,Moon, Myeong Hee Wiley - VCH Verlag GmbH & Co. KGaA 2007 Journal of Separation Science Vol.30 No.7
<P>Asymmetrical flow field-flow fractionation (AFlFFF) has been carried out in a miniaturized channel by reducing the channel dimensions. Performance of the miniaturized AFlFFF (mAFlFFF) channel was evaluated with standard proteins and polystyrene latex spheres from nanometer to micrometer size. By reducing the channel dimension, proteins or particulate materials can be separated within a few minutes without a significant loss in resolution. The mAFlFFF channel was applied for the separation of exosomes harvested from immortalized human mesenchymal stem cell line. It shows a potential to fractionate exosome vesicles according to sizes which can be useful for proteomic studies in relation to immunotherapeutic applications.</P>
Park, Jung Wook,Kim, Seyoon,Lim, Kook Jin,Simpson, Richard J.,Kim, Yu Sam,Bahk, Young Yil WILEY-VCH Verlag 2006 Proteomics Vol.6 No.4
<P>To elucidate the oncogenic H-Ras network, we have established various stable and inducible oncogenic H-Ras-expressing NIH/3T3 mouse embryonic fibroblast cell clones, which express G12V H-Ras and G12R H-Ras proteins under the influence of a strong cytomegalovirus promoter and under the tight control of expression by an antibiotic, doxycycline, respectively. Here we provide a catalogue of proteome profiles in total cell lysates derived from oncogenic H-Ras-expressing NIH/3T3 cells. In this biological context, we compared total proteome changes by the combined methods of 2-DE, quantitative image analysis and MALDI-TOF MS analysis using both a stable expression system as well as an inducible expression system. There were a large number of common targets for oncogenic H-Ras, which were identified in both cell lines and consisted of 64 proteins (36 up-regulated and 28 down-regulated). Differentially regulated expression was further confirmed for some subsets of candidates by Western blot analysis using specific antibodies. Taken together, the results presented here show that comparative analysis of the proteome from the oncogenic H-Ras-expressing cells yielded interpretable data to elucidate protein networks directly and/or indirectly.</P>
Gorantla, Vasavi R.,Bond, Vernon Jr.,Dorsey, James,Tedesco, Sarah,Kaur, Tanisha,Simpson, Matthew,Pemminati, Sudhakar,Millis, Richard M. KOREAN PHARMACOPUNCTURE INSTITUTE 2019 Journal of pharmacopuncture Vol.22 No.3
Objectives: Attentional and memory functions are important aspects of neural plasticity that, theoretically, should be amenable to pharmacopuncture treatments. A previous study from our laboratory suggested that quantitative electroencephalographic (qEEG) measurements of theta/beta ratio (TBR), an index of attentional control, may be indicative of academic performance in a first-semester medical school course. The present study expands our prior report by extracting and analyzing data on frontal theta and beta asymmetries. We test the hypothesis that the amount of frontal theta and beta asymmetries (fTA, fBA), are correlated with TBR and academic performance, thereby providing novel targets for pharmacopuncture treatments to improve cognitive performance. Methods: Ten healthy male volunteers were subjected to 5-10 min of qEEG measurements under eyes-closed conditions. The qEEG measurements were performed 3 days before each of first two block examinations in anatomy-physiology, separated by five weeks. Amplitudes of the theta and beta waveforms, expressed in ${\mu}V$, were used to compute TBR, fTA and fBA. Significance of changes in theta and beta EEG wave amplitude was assessed by ANOVA with post-hoc t-testing. Correlations between TBR, fTA, fBA and the raw examination scores were evaluated by Pearson's product-moment coefficients and linear regression analysis. Results: fTA and fBA were found to be negatively correlated with TBR (P<0.03, P<0.05, respectively) and were positively correlated with the second examination score (P<0.03, P=0.1, respectively). Conclusion: Smaller fTA and fBA were associated with lower academic performance in the second of two first-semester medical school anatomy-physiology block examination. Future studies should determine whether these qEEG metrics are useful for monitoring changes associated with the brain's cognitive adaptations to academic challenges, for predicting academic performance and for targeting phamacopuncture treatments to improve cognitive performance.
Vasavi R Gorantla,Vernon Bond Jr,James Dorsey,Sarah Tedesco,Tanisha Kaur,Matthew Simpson,Sudhakar Pemminati,Richard M. Millis 대한약침학회 2019 Journal of pharmacopuncture Vol.22 No.3
Objectives: Attentional and memory functions are important aspects of neural plasticity that, theoretically, should be amenable to pharmacopuncture treatments. A previous study from our laboratory suggested that quantitative electroencephalographic (qEEG) measurements of theta/beta ratio (TBR), an index of attentional control, may be indicative of academic performance in a first-semester medical school course. The present study expands our prior report by extracting and analyzing data on frontal theta and beta asymmetries. We test the hypothesis that the amount of frontal theta and beta asymmetries (fTA, fBA), are correlated with TBR and academic performance, thereby providing novel targets for pharmacopuncture treatments to improve cognitive performance. Methods: Ten healthy male volunteers were subjected to 5-10 min of qEEG measurements under eyes-closed conditions. The qEEG measurements were performed 3 days before each of first two block examinations in anatomy-physiology, separated by five weeks. Amplitudes of the theta and beta waveforms, expressed in μV, were used to compute TBR, fTA and fBA. Significance of changes in theta and beta EEG wave amplitude was assessed by ANOVA with post-hoc t-testing. Correlations between TBR, fTA, fBA and the raw examination scores were evaluated by Pearson’s product-moment coefficients and linear regression analysis. Results: fTA and fBA were found to be negatively correlated with TBR (P<0.03, P<0.05, respectively) and were positively correlated with the second examination score (P<0.03, P=0.1, respectively). Conclusion: Smaller fTA and fBA were associated with lower academic performance in the second of two first-semester medical school anatomy-physiology block examination. Future studies should determine whether these qEEG metrics are useful for monitoring changes associated with the brain’s cognitive adaptations to academic challenges, for predicting academic performance and for targeting phamacopuncture treatments to improve cognitive performance.