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Search Results: 1 - 10 of 117548 matches for " Samuel O. Purvine "
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Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium
Charles Ansong, Nikola Toli？, Samuel O Purvine, Steffen Porwollik, Marcus Jones, Hyunjin Yoon, Samuel H Payne, Jessica L Martin, Meagan C Burnet, Matthew E Monroe, Pratap Venepally, Richard D Smith, Scott N Peterson, Fred Heffron, Michael McClelland, Joshua N Adkins
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-433
Abstract: We experimentally annotated the bacterial pathogen Salmonella Typhimurium 14028, using "shotgun" proteomics to accurately uncover the translational landscape and post-translational features. The data provide protein-level experimental validation for approximately half of the predicted protein-coding genes in Salmonella and suggest revisions to several genes that appear to have incorrectly assigned translational start sites, including a potential novel alternate start codon. Additionally, we uncovered 12 non-annotated genes missed by gene prediction programs, as well as evidence suggesting a role for one of these novel ORFs in Salmonella pathogenesis. We also characterized post-translational features in the Salmonella genome, including chemical modifications and proteolytic cleavages. We find that bacteria have a much larger and more complex repertoire of chemical modifications than previously thought including several novel modifications. Our in vivo proteolysis data identified more than 130 signal peptide and N-terminal methionine cleavage events critical for protein function.This work highlights several ways in which application of proteomics data can improve the quality of genome annotations to facilitate novel biological insights and provides a comprehensive proteome map of Salmonella as a resource for systems analysis.Many aspects of modern biological research are dependent on accurate identification of the protein-coding genes in each genome, as well as the nature of the mature functional protein products, a process commonly referred to as genome annotation. With the exponential increase in the number of sequenced prokaryotic genomes afforded by advances in genome sequencing technologies over the last decade, present day prokaryotic genome annotation is essentially an automated high-throughput process that relies heavily on de novo gene prediction programs [1-3].While de novo gene prediction programs have significantly improved for prokaryotic genomes consider
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.
Establishing the Proteome of Normal Human Cerebrospinal Fluid
Steven E. Schutzer,Tao Liu,Benjamin H. Natelson,Thomas E. Angel,Athena A. Schepmoes,Samuel O. Purvine,Kim K. Hixson,Mary S. Lipton,David G. Camp II,Patricia K. Coyle,Richard D. Smith,Jonas Bergquist
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0010980
Abstract: Knowledge of the entire protein content, the proteome, of normal human cerebrospinal fluid (CSF) would enable insights into neurologic and psychiatric disorders. Until now technologic hurdles and access to true normal samples hindered attaining this goal.
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.
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
Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae
Alexandra C. Schrimpe-Rutledge, Marcus B. Jones, Sadhana Chauhan, Samuel O. Purvine, James A. Sanford, Matthew E. Monroe, Heather M. Brewer, Samuel H. Payne, Charles Ansong, Bryan C. Frank, Richard D. Smith, Scott N. Peterson, Vladimir L. Motin, Joshua N. Adkins
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0033903
Abstract: Genome sequencing continues to be a rapidly evolving technology, yet most downstream aspects of genome annotation pipelines remain relatively stable or are even being abandoned. The annotation process is now performed almost exclusively in an automated fashion to balance the large number of sequences generated. One possible way of reducing errors inherent to automated computational annotations is to apply data from omics measurements (i.e. transcriptional and proteomic) to the un-annotated genome with a proteogenomic-based approach. Here, the concept of annotation refinement has been extended to include a comparative assessment of genomes across closely related species. Transcriptomic and proteomic data derived from highly similar pathogenic Yersiniae (Y. pestis CO92, Y. pestis Pestoides F, and Y. pseudotuberculosis PB1/+) was used to demonstrate a comprehensive comparative omic-based annotation methodology. Peptide and oligo measurements experimentally validated the expression of nearly 40% of each strain's predicted proteome and revealed the identification of 28 novel and 68 incorrect (i.e., observed frameshifts, extended start sites, and translated pseudogenes) protein-coding sequences within the three current genome annotations. Gene loss is presumed to play a major role in Y. pestis acquiring its niche as a virulent pathogen, thus the discovery of many translated pseudogenes, including the insertion-ablated argD, underscores a need for functional analyses to investigate hypotheses related to divergence. Refinements included the discovery of a seemingly essential ribosomal protein, several virulence-associated factors, a transcriptional regulator, and many hypothetical proteins that were missed during annotation.
A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection
Brooke L. Deatherage Kaiser, Jie Li, James A. Sanford, Young-Mo Kim, Scott R. Kronewitter, Marcus B. Jones, Christine T. Peterson, Scott N. Peterson, Bryan C. Frank, Samuel O. Purvine, Joseph N. Brown, Thomas O. Metz, Richard D. Smith, Fred Heffron, Joshua N. Adkins
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0067155
Abstract: The potential for commensal microorganisms indigenous to a host (the ‘microbiome’ or ‘microbiota’) to alter infection outcome by influencing host-pathogen interplay is largely unknown. We used a multi-omics “systems” approach, incorporating proteomics, metabolomics, glycomics, and metagenomics, to explore the molecular interplay between the murine host, the pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium), and commensal gut microorganisms during intestinal infection with S. Typhimurium. We find proteomic evidence that S. Typhimurium thrives within the infected 129/SvJ mouse gut without antibiotic pre-treatment, inducing inflammation and disrupting the intestinal microbiome (e.g., suppressing Bacteroidetes and Firmicutes while promoting growth of Salmonella and Enterococcus). Alteration of the host microbiome population structure was highly correlated with gut environmental changes, including the accumulation of metabolites normally consumed by commensal microbiota. Finally, the less characterized phase of S. Typhimurium’s lifecycle was investigated, and both proteomic and glycomic evidence suggests S. Typhimurium may take advantage of increased fucose moieties to metabolize fucose while growing in the gut. The application of multiple omics measurements to Salmonella-induced intestinal inflammation provides insights into complex molecular strategies employed during pathogenesis between host, pathogen, and the microbiome.
A Comparative Assessment of the Physico-Chemical and Microbial Trends in Njaba River, Niger Delta Basin, Southeastern Nigeria  [PDF]
Cosmas Ahamefula Ahiarakwem, Samuel O. Onyekuru
Journal of Water Resource and Protection (JWARP) , 2011, DOI: 10.4236/jwarp.2011.39079
Abstract: Water quality monitoring at five (5) different gauge stations on the course of Njaba River was undertaken to understand the variability of the physico-chemical and microbial contents of the river water within a specified period of time (2003-2008). Collected water samples were analyzed using Atomic Absorption Spectrophotometer (AAS), Digital Meters and Standard Plate Counts. Results of the analyses indicated that average pH, electrical conductivity and the Total Dissolved Solids (TDS) of the Njaba River in 2003 were 6.3, 22 µS/cm and 13.5 mg/l, respectively. Mean values in 2008 for the same parameters were 6.4, 24.4µS/cm and 14.7 mg/l, respectively. Mean concentrations of analyzed cations (Ca2+, Mg2+, Na+ and K+) in 2003 were 4.10, 0.15, 5.00 and 1.20 mg/l, respectively, and that obtained for same parameters in 2008 were 4.40, 0.18, 6.40 and 1.30 mg/l, respectively. The mean concentrations of analyzed anions (HCO3 - , SO4 2-, Cl- and NO3 - ) in 2003 were 20.0, 4.0, 1.30 and 0.20 mg/l, respectively and in 2008 the mean concentrations were 24.5, 4.20, 1.60 and 0.22 mg/l, respectively. Characterization of the river water followed the trend: Na+ > Ca2+ > K+ > Mg2+ (for the cations) and HCO3 - > SO4 2- > Cl- > NO3 - (for anions), showing the Njaba River is NaHCO3 water. Mean concentrations of Dissolved Oxygen (DO) and Biochemical Oxygen Demand (BOD) of the river water were 7.2 and 2.2 mg/l, respectively in 2003, and 8.0 and 4.0 mg/l respectively, in 2008. Total Coliform Counts of the river water in 2003 ranged from 70 - 90 cfu/100ml with a mean value of 80 cfu/100ml, while the counts in 2008 ranged from 100 - 120 cfu/100ml with a mean value of 110 cfu/100 ml. Calculated Pollution Index (PI) slightly increased from 0.72 in 2003 to 0.73 in 2008. These water quality determinants revealed gradual rise in the concentrations of the respective physico-chemical parameters and bacteriological constituents of the Njaba River water. Sodium Adsorption Ratio (SAR) of 1.37 in 2003 and 1.54 in 2008, however, indicated
Factorial Designs Application to Study Enhanced Bioremediation of Soil Artificially Contaminated with Weathered Bonny Light Crude Oil through Biostimulation and Bioaugmentation Strategy  [PDF]
Samuel E. Agarry, Oladipupo O. Ogunleye
Journal of Environmental Protection (JEP) , 2012, DOI: 10.4236/jep.2012.38089
Abstract: The objective of this study was designed to evaluate the effects of biostimulation and bioaugmentation amendment agents (NPK fertilizer, Tween 80 and mixed culture) on the bioremediation of tropical soil samples artificially contaminated with Weathered Bonny Light Crude Oil (WBLCO). Response Surface Methodology (RSM) with Box Behnken Design (BBD) was used with three levels and three factors of NPK fertilizer (2 - 6 g), Tween 80 (5 - 15 mg/l) and mixed culture (0.5 - 1.5 g/l) as independent variables and WBLCO removal as dependent variable (response) in a six weeks remediation period. The results showed that the rate of WBLCO removal generally increased with increase in the amount of NPK fertilizer, Tween 80 and mixed culture (biomass), respectively. A statistically significant (P < 0.0001) second-order quadratic regression model for WBLCO removal (using design-expert statistical program (v. 6.0.8)) with a coefficient of determination, R (=0.9996) was obtained. Numerical optimization technique based on desirability function was carried out to optimize the bioremediation process. The optimum values for biostimulation and bioaugmentation amendment agents to achieve a predicted maximum WBLCO removal of 84.88 percent were found to be: NPK fertilizer, 4.25 g; Tween 80, 10.22 mg/l and mixed culture, 0.46 g/l. At this optimum point, the observed WBLCO removal was found to be 83.79 percent. The statistical analyses and the closeness of the experimental results and model predictions show the reliability of the regression model and thus, biostimulation and bioaugmentation of indigenous microbial density and activity can reduce remediation period of petroleum hydrocarbon contaminated environment and subsequently the cost of remediation.
Proteomic Detection of Non-Annotated Protein-Coding Genes in Pseudomonas fluorescens Pf0-1
Wook Kim,Mark W. Silby,Sam O. Purvine,Julie S. Nicoll,Kim K. Hixson,Matt Monroe,Carrie D. Nicora,Mary S. Lipton,Stuart B. Levy
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0008455
Abstract: Genome sequences are annotated by computational prediction of coding sequences, followed by similarity searches such as BLAST, which provide a layer of possible functional information. While the existence of processes such as alternative splicing complicates matters for eukaryote genomes, the view of bacterial genomes as a linear series of closely spaced genes leads to the assumption that computational annotations that predict such arrangements completely describe the coding capacity of bacterial genomes. We undertook a proteomic study to identify proteins expressed by Pseudomonas fluorescens Pf0-1 from genes that were not predicted during the genome annotation. Mapping peptides to the Pf0-1 genome sequence identified sixteen non-annotated protein-coding regions, of which nine were antisense to predicted genes, six were intergenic, and one read in the same direction as an annotated gene but in a different frame. The expression of all but one of the newly discovered genes was verified by RT-PCR. Few clues as to the function of the new genes were gleaned from informatic analyses, but potential orthologs in other Pseudomonas genomes were identified for eight of the new genes. The 16 newly identified genes improve the quality of the Pf0-1 genome annotation, and the detection of antisense protein-coding genes indicates the under-appreciated complexity of bacterial genome organization.
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