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Search Results: 1 - 10 of 466769 matches for " Marina A Gritsenko "
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The cerebrospinal fluid proteome in HIV infection: change associated with disease severity
Thomas E Angel, Jon M Jacobs, Serena S Spudich, Marina A Gritsenko, Dietmar Fuchs, Teri Liegler, Henrik Zetterberg, David G Camp, Richard W Price, Richard D Smith
Clinical Proteomics , 2012, DOI: 10.1186/1559-0275-9-3
Abstract: After establishing an accurate mass and time (AMT) tag database containing 23,141 AMT tags for CSF peptides, we analyzed 91 CSF samples by LC-MS from 12 HIV-uninfected and 14 HIV-infected subjects studied in the context of initiation of antiretroviral therapy and correlated abundances of identified proteins a) within and between subjects, b) with all other proteins across the entire sample set, and c) with "external" CSF biomarkers of infection (HIV RNA), immune activation (neopterin) and neural injury (neurofilament light chain protein, NFL). We identified a mean of 2,333 +/- 328 (SD) peptides covering 307 +/-16 proteins in the 91 CSF sample set. Protein abundances differed both between and within subjects sampled at different time points and readily separated those with and without HIV infection. Proteins also showed inter-correlations across the sample set that were associated with biologically relevant dynamic processes. One-hundred and fifty proteins showed correlations with the external biomarkers. For example, using a threshold of cross correlation coefficient (Pearson's) ≤ -0.3 and ≥0.3 for potentially meaningful relationships, a total of 99 proteins correlated with CSF neopterin (43 negative and 56 positive correlations) and related principally to neuronal plasticity and survival and to innate immunity. Pathway analysis defined several networks connecting the identified proteins, including one with amyloid precursor protein as a central node.Advanced CSF proteomic analysis enabled the identification of an array of novel protein changes across the spectrum of CNS HIV infection and disease. This initial analysis clearly demonstrated the value of contemporary state-of-the-art proteomic CSF analysis as a discovery tool in HIV infection with likely similar application to other neurological inflammatory and degenerative diseases.While central nervous system (CNS) HIV infection is a nearly universal facet of systemic infection, its course and clinical manifestatio
Proteomic Profiling of Exosomes Leads to the Identification of Novel Biomarkers for Prostate Cancer
Diederick Duijvesz, Kristin E. Burnum-Johnson, Marina A. Gritsenko, A. Marije Hoogland, Mirella S. Vredenbregt-van den Berg, Rob Willemsen, Theo Luider, Ljiljana Pa?a-Toli?, Guido Jenster
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0082589
Abstract: Background Current markers for prostate cancer, such as PSA lack specificity. Therefore, novel biomarkers are needed. Unfortunately, the complexity of body fluids often hampers biomarker discovery. An attractive alternative approach is the isolation of small vesicles, i.e. exosomes, ~100 nm, which contain proteins that are specific to the tissue from which they are derived and therefore can be considered as treasure chests for disease-specific biomarker discovery. Materials and Methods Exosomes were isolated from 2 immortalized primary prostate epithelial cells (PNT2C2 and RWPE-1) and 2 PCa cell lines (PC346C and VCaP) by ultracentrifugation. After tryptic digestion, proteomic analyses utilized a nanoLC coupled with an LTQ-Orbitrap operated in tandem MS (MS/MS) mode. Accurate Mass and Time (AMT) tag approach was employed for peptide identification and quantitation. Candidate biomarkers were validated by Western blotting and Immunohistochemistry. Results Proteomic characterization resulted in the identification of 248, 233, 169, and 216 proteins by at least 2 peptides in exosomes from PNT2C2, RWPE-1, PC346C, and VCaP, respectively. Statistical analyses revealed 52 proteins differently abundant between PCa and control cells, 9 of which were more abundant in PCa. Validation by Western blotting confirmed a higher abundance of FASN, XPO1 and PDCD6IP (ALIX) in PCa exosomes. Conclusions Identification of exosomal proteins using high performance LC-FTMS resulted in the discovery of PDCD6IP, FASN, XPO1 and ENO1 as new candidate biomarkers for prostate cancer.
Diurnal Rhythms Result in Significant Changes in the Cellular Protein Complement in the Cyanobacterium Cyanothece 51142
Jana St?ckel,Jon M. Jacobs,Thanura R. Elvitigala,Michelle Liberton,Eric A. Welsh,Ashoka D. Polpitiya,Marina A. Gritsenko,Carrie D. Nicora,David W. Koppenaal,Richard D. Smith,Himadri B. Pakrasi
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0016680
Abstract: Cyanothece sp. ATCC 51142 is a diazotrophic cyanobacterium notable for its ability to perform oxygenic photosynthesis and dinitrogen fixation in the same single cell. Previous transcriptional analysis revealed that the existence of these incompatible cellular processes largely depends on tightly synchronized expression programs involving ~30% of genes in the genome. To expand upon current knowledge, we have utilized sensitive proteomic approaches to examine the impact of diurnal rhythms on the protein complement in Cyanothece 51142. We found that 250 proteins accounting for ~5% of the predicted ORFs from the Cyanothece 51142 genome and 20% of proteins detected under alternating light/dark conditions exhibited periodic oscillations in their abundances. Our results suggest that altered enzyme activities at different phases during the diurnal cycle can be attributed to changes in the abundance of related proteins and key compounds. The integration of global proteomics and transcriptomic data further revealed that post-transcriptional events are important for temporal regulation of processes such as photosynthesis in Cyanothece 51142. This analysis is the first comprehensive report on global quantitative proteomics in a unicellular diazotrophic cyanobacterium and uncovers novel findings about diurnal rhythms.
Phosphoproteomics Profiling of Human Skin Fibroblast Cells Reveals Pathways and Proteins Affected by Low Doses of Ionizing Radiation
Feng Yang,Katrina M. Waters,John H. Miller,Marina A. Gritsenko,Rui Zhao,Xiuxia Du,Eric A. Livesay,Samuel O. Purvine,Matthew E. Monroe,Yingchun Wang,David G. Camp II,Richard D. Smith,David L. Stenoien
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0014152
Abstract: High doses of ionizing radiation result in biological damage; however, the precise relationships between long-term health effects, including cancer, and low-dose exposures remain poorly understood and are currently extrapolated using high-dose exposure data. Identifying the signaling pathways and individual proteins affected at the post-translational level by radiation should shed valuable insight into the molecular mechanisms that regulate dose-dependent responses to radiation.
Blood Peptidome-Degradome Profile of Breast Cancer
Yufeng Shen,Nikola Toli?,Tao Liu,Rui Zhao,Brianne O. Petritis,Marina A. Gritsenko,David G. Camp,Ronald J. Moore,Samuel O. Purvine,Francisco J. Esteva,Richard D. Smith
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0013133
Abstract: Cancer invasion and metastasis are closely associated with activities within the degradome; however, little is known about whether these activities can be detected in the blood of cancer patients.
Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles
Uma K Aryal, Jana St?ckel, Ravi K Krovvidi, Marina A Gritsenko, Matthew E Monroe, Ronald J Moore, David W Koppenaal, Richard D Smith, Himadri B Pakrasi, Jon M Jacobs
BMC Systems Biology , 2011, DOI: 10.1186/1752-0509-5-194
Abstract: To expand upon the current knowledge of protein expression patterns in Cyanothece ATCC51142, we performed quantitative proteomic analysis using partial ("unsaturated") metabolic labeling and high mass accuracy LC-MS analysis. This dynamic proteomic profiling identified 721 actively synthesized proteins with significant temporal changes in expression throughout the light-dark cycles, of which 425 proteins matched with previously characterized cycling transcripts. The remaining 296 proteins contained a cluster of proteins uniquely involved in DNA replication and repair, protein degradation, tRNA synthesis and modification, transport and binding, and regulatory functions. Functional classification of labeled proteins suggested that proteins involved in respiration and glycogen metabolism showed increased expression in the dark cycle together with nitrogenase, suggesting that N2-fixation is mediated by higher respiration and glycogen metabolism. Results indicated that Cyanothece ATCC51142 might utilize alternative pathways for carbon (C) and nitrogen (N) acquisition, particularly, aspartic acid and glutamate as substrates of C and N, respectively. Utilization of phosphoketolase (PHK) pathway for the conversion of xylulose-5P to pyruvate and acetyl-P likely constitutes an alternative strategy to compensate higher ATP and NADPH demand.This study provides a deeper systems level insight into how Cyanothece ATCC51142 modulates cellular functions to accommodate photosynthesis and N2-fixation within the single cell.Oxygenic photosynthetic cyanobacteria are widely recognized for their important role in the global carbon cycle [1], and have generated significant interest as a potential solution for carbon-neutral energy production and carbon (C) sequestration [2]. Some unicellular cyanobacteria such as Cyanothece and Crocosphaera are also capable of biological N2-fixation (diazotrophic) [3], and play a significant role in marine nitrogen (N) cycle [4]. One of the most important
Coupled transcriptome and proteome analysis of human lymphotropic tumor viruses: insights on the detection and discovery of viral genes
Lindsay R Dresang, Jeremy R Teuton, Huichen Feng, Jon M Jacobs, David G Camp, Samuel O Purvine, Marina A Gritsenko, Zhihua Li, Richard D Smith, Bill Sugden, Patrick S Moore, Yuan Chang
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-625
Abstract: The majority of viral genes were efficiently detected at the transcript and/or protein level on manipulating the viral life cycle. Overall the correlation of expressed viral proteins and transcripts was highly complementary in both validating and providing orthogonal data with latent/lytic viral gene expression. Our approach also identified novel viral genes in both KSHV and EBV, and extends viral genome annotation. Several previously uncharacterized genes were validated at both transcript and protein levels.This systems biology approach coupling proteome and transcriptome measurements provides a comprehensive view of viral gene expression that could not have been attained using each methodology independently. Detection of viral proteins in combination with viral transcripts is a potentially powerful method for establishing virus-disease relationships.Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV) are related gamma-herpesviruses that cause a variety of human B cell and non-B cell malignancies. EBV was identified in 1964 as the etiological agent of Burkitt's lymphoma (BL) [1], and is detected in the majority of African endemic BL [2-4]. KSHV was identified in 1994 as the etiological agent of Kaposi's sarcoma [5], and later detected in all cases of primary effusion lymphoma (PEL) [6,7]. In a unique example of co-infection, 60-90% of PEL cases carry EBV in addition to KSHV (reviewed in [8]). Both KSHV and EBV encode genes that promote proliferation, enhance survival, and inhibit host immune responses (reviewed in [9-11]). Unfortunately, the expression of these genes also contributes to viral malignancies if the host's immune system is compromised.Preliminary annotation of viral genes is typically based on sequence homology to related viruses and in silico prediction of open reading frames (ORFs) typically defined by a minimum of 100 amino acids with a preceding start methionine [12,13]. New viral genes can also be proposed using computer-ba
Distribution of secretory inhibitor of platelet microbicidal protein among anaerobic bacteria isolated from stool of children with diarrhea
Iuri B Ivanov, Viktor A Gritsenko
World Journal of Gastroenterology , 2008,
Abstract: AIM: To study the secretory inhibitor of platelet microbicidal protein (SIPMP) phenotypes of faecal anaerobic isolates from patients with diarrhea.METHODS: Faecal isolates of anaerobic bacteria (B. fragilis, n = 42; B. longum, n = 70; A. israelii, n = 21; E. lentum, n = 12) from children with diarrhea were tested. SIPMP production was tested by inhibition of platelet microbicidal protein (PMP) bioactivity against B. subtilis and was expressed as percentage of inhibition of PMP bactericidal activity.RESULTS: Among anaerobic isolates 80% of B. longum strains, 85.7% of A. israelii strains, 50% of E. lentum strains and 92.86% of B. fragilis strains were SIPMP-positive. The isolated anaerobic organisms demonstrated SIPMP production at a mean level of 13.8% ± 0.7%, 14.7% ± 1.8%, 3.9% ± 0.9% (P < 0.05) and 26.8% ± 7.5% (P < 0.05) for bifidobacteria, A. israelii, E. lentum and B. fragilis, respectively.CONCLUSION: Data from the present study may have significant implications in understanding the pathogenesis of microecological disorders in the intestine, as well as for future improvement in the prevention and therapy of anaerobe-associated infections.
Ternary Goldbach's Problem Involving Primes of a Special Type
Sergey A. Gritsenko,Natalya N. Motkina
Mathematics , 2008,
Abstract: Let $\eta$ be a quadratic irrationality. The variant of a ternary problem of Goldbach involving primes such that $a<\{\eta p\}
Hua Loo Keng's Problem Involving Primes of a Special Type
Sergey A. Gritsenko,Natalya N. Motkina
Mathematics , 2008,
Abstract: Let $\eta$ be a quadratic irrationality. The variant of Hua Loo Keng's problem involving primes such that $a<\{\eta p^2\}
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