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Sample records for global phosphoproteomic effects

  1. Global Effects of Kinase Inhibitors on Signaling Networks Revealed by Quantitative Phosphoproteomics*

    PubMed Central

    Pan, Cuiping; Olsen, Jesper V.; Daub, Henrik; Mann, Matthias

    2009-01-01

    Aberrant signaling causes many diseases, and manipulating signaling pathways with kinase inhibitors has emerged as a promising area of drug research. Most kinase inhibitors target the conserved ATP-binding pocket; therefore specificity is a major concern. Proteomics has previously been used to identify the direct targets of kinase inhibitors upon affinity purification from cellular extracts. Here we introduce a complementary approach to evaluate the effects of kinase inhibitors on the entire cell signaling network. We used triple labeling SILAC (stable isotope labeling by amino acids in cell culture) to compare cellular phosphorylation levels for control, epidermal growth factor stimulus, and growth factor combined with kinase inhibitors. Of thousands of phosphopeptides, less than 10% had a response pattern indicative of targets of U0126 and SB202190, two widely used MAPK inhibitors. Interestingly, 83% of the growth factor-induced phosphorylation events were affected by either or both inhibitors, showing quantitatively that early signaling processes are predominantly transmitted through the MAPK cascades. In contrast to MAPK inhibitors, dasatinib, a clinical drug directed against BCR-ABL, which is the cause of chronic myelogenous leukemia, affected nearly 1,000 phosphopeptides. In addition to the proximal effects on ABL and its immediate targets, dasatinib broadly affected the downstream MAPK pathways. Pathway mapping of regulated sites implicated a variety of cellular functions, such as chromosome remodeling, RNA splicing, and cytoskeletal organization, some of which have been described in the literature before. Our assay is streamlined and generic and could become a useful tool in kinase drug development. PMID:19651622

  2. Sample Collection Method Bias Effects in Quantitative Phosphoproteomics.

    PubMed

    Kanshin, Evgeny; Tyers, Michael; Thibault, Pierre

    2015-07-01

    Current advances in selective enrichment, fractionation, and MS detection of phosphorylated peptides allowed identification and quantitation of tens of thousands phosphosites from minute amounts of biological material. One of the major challenges in the field is preserving the in vivo phosphorylation state of the proteins throughout the sample preparation workflow. This is typically achieved by using phosphatase inhibitors and denaturing conditions during cell lysis. Here we determine if the upstream cell collection techniques could introduce changes in protein phosphorylation. To evaluate the effect of sample collection protocols on the global phosphorylation status of the cell, we compared different sample workflows by metabolic labeling and quantitative mass spectrometry on Saccharomyces cerevisiae cell cultures. We identified highly similar phosphopeptides for cells harvested in ice cold isotonic phosphate buffer, cold ethanol, trichloroacetic acid, and liquid nitrogen. However, quantitative analyses revealed that the commonly used phosphate buffer unexpectedly activated signaling events. Such effects may introduce systematic bias in phosphoproteomics measurements and biochemical analysis. PMID:26040406

  3. Novel Host Proteins and Signaling Pathways in Enteropathogenic E. coli Pathogenesis Identified by Global Phosphoproteome Analysis.

    PubMed

    Scholz, Roland; Imami, Koshi; Scott, Nichollas E; Trimble, William S; Foster, Leonard J; Finlay, B Brett

    2015-07-01

    Enteropathogenic Escherichia coli (EPEC) uses a type III secretion system (T3SS) to directly translocate effector proteins into host cells where they play a pivotal role in subverting host cell signaling needed for disease. However, our knowledge of how EPEC affects host protein phosphorylation is limited to a few individual protein studies. We employed a quantitative proteomics approach to globally map alterations in the host phosphoproteome during EPEC infection. By characterizing host phosphorylation events at various time points throughout infection, we examined how EPEC dynamically impacts the host phosphoproteome over time. This experimental setup also enabled identification of T3SS-dependent and -independent changes in host phosphorylation. Specifically, T3SS-regulated events affected various cellular processes that are known EPEC targets, including cytoskeletal organization, immune signaling, and intracellular trafficking. However, the involvement of phosphorylation in these events has thus far been poorly studied. We confirmed the MAPK family as an established key host player, showed its central role in signal transduction during EPEC infection, and extended the repertoire of known signaling hubs with previously unrecognized proteins, including TPD52, CIN85, EPHA2, and HSP27. We identified altered phosphorylation of known EPEC targets, such as cofilin, where the involvement of phosphorylation has so far been undefined, thus providing novel mechanistic insights into the roles of these proteins in EPEC infection. An overlap of regulated proteins, especially those that are cytoskeleton-associated, was observed when compared with the phosphoproteome of Shigella-infected cells. We determined the biological relevance of the phosphorylation of a novel protein in EPEC pathogenesis, septin-9 (SEPT9). Both siRNA knockdown and a phosphorylation-impaired SEPT9 mutant decreased bacterial adherence and EPEC-mediated cell death. In contrast, a phosphorylation

  4. SELPHI: correlation-based identification of kinase-associated networks from global phospho-proteomics data sets

    PubMed Central

    Petsalaki, Evangelia; Helbig, Andreas O.; Gopal, Anjali; Pasculescu, Adrian; Roth, Frederick P.; Pawson, Tony

    2015-01-01

    While phospho-proteomics studies have shed light on the dynamics of cellular signaling, they mainly describe global effects and rarely explore mechanistic details, such as kinase/substrate relationships. Tools and databases, such as NetworKIN and PhosphoSitePlus, provide valuable regulatory details on signaling networks but rely on prior knowledge. They therefore provide limited information on less studied kinases and fewer unexpected relationships given that better studied signaling events can mask condition- or cell-specific ‘network wiring’. SELPHI is a web-based tool providing in-depth analysis of phospho-proteomics data that is intuitive and accessible to non-bioinformatics experts. It uses correlation analysis of phospho-sites to extract kinase/phosphatase and phospho-peptide associations, and highlights the potential flow of signaling in the system under study. We illustrate SELPHI via analysis of phospho-proteomics data acquired in the presence of erlotinib—a tyrosine kinase inhibitor (TKI)—in cancer cells expressing TKI-resistant and -sensitive variants of the Epidermal Growth Factor Receptor. In this data set, SELPHI revealed information overlooked by the reporting study, including the known role of MET and EPHA2 kinases in conferring resistance to erlotinib in TKI sensitive strains. SELPHI can significantly enhance the analysis of phospho-proteomics data contributing to improved understanding of sample-specific signaling networks. SELPHI is freely available via http://llama.mshri.on.ca/SELPHI. PMID:25948583

  5. SELPHI: correlation-based identification of kinase-associated networks from global phospho-proteomics data sets.

    PubMed

    Petsalaki, Evangelia; Helbig, Andreas O; Gopal, Anjali; Pasculescu, Adrian; Roth, Frederick P; Pawson, Tony

    2015-07-01

    While phospho-proteomics studies have shed light on the dynamics of cellular signaling, they mainly describe global effects and rarely explore mechanistic details, such as kinase/substrate relationships. Tools and databases, such as NetworKIN and PhosphoSitePlus, provide valuable regulatory details on signaling networks but rely on prior knowledge. They therefore provide limited information on less studied kinases and fewer unexpected relationships given that better studied signaling events can mask condition- or cell-specific 'network wiring'. SELPHI is a web-based tool providing in-depth analysis of phospho-proteomics data that is intuitive and accessible to non-bioinformatics experts. It uses correlation analysis of phospho-sites to extract kinase/phosphatase and phospho-peptide associations, and highlights the potential flow of signaling in the system under study. We illustrate SELPHI via analysis of phospho-proteomics data acquired in the presence of erlotinib-a tyrosine kinase inhibitor (TKI)-in cancer cells expressing TKI-resistant and -sensitive variants of the Epidermal Growth Factor Receptor. In this data set, SELPHI revealed information overlooked by the reporting study, including the known role of MET and EPHA2 kinases in conferring resistance to erlotinib in TKI sensitive strains. SELPHI can significantly enhance the analysis of phospho-proteomics data contributing to improved understanding of sample-specific signaling networks. SELPHI is freely available via http://llama.mshri.on.ca/SELPHI. PMID:25948583

  6. The Global Phosphoproteome of Chlamydomonas reinhardtii Reveals Complex Organellar Phosphorylation in the Flagella and Thylakoid Membrane *

    PubMed Central

    Wang, Hongxia; Gau, Brian; Slade, William O.; Juergens, Matthew; Li, Ping; Hicks, Leslie M.

    2014-01-01

    Chlamydomonas reinhardtii is the most intensively-studied and well-developed model for investigation of a wide-range of microalgal processes ranging from basic development through understanding triacylglycerol production. Although proteomic technologies permit interrogation of these processes at the protein level and efforts to date indicate phosphorylation-based regulation of proteins in C. reinhardtii is essential for its underlying biology, characterization of the C. reinhardtii phosphoproteome has been limited. Herein, we report the richest exploration of the C. reinhardtii proteome to date. Complementary enrichment strategies were used to detect 4588 phosphoproteins distributed among every cellular component in C. reinhardtii. Additionally, we report 18,160 unique phosphopeptides at <1% false discovery rate, which comprise 15,862 unique phosphosites - 98% of which are novel. Given that an estimated 30% of proteins in a eukaryotic cell are subject to phosphorylation, we report the majority of the phosphoproteome (23%) of C. reinhardtii. Proteins in key biological pathways were phosphorylated, including photosynthesis, pigment production, carbon assimilation, glycolysis, and protein and carbohydrate metabolism, and it is noteworthy that hyperphosphorylation was observed in flagellar proteins. This rich data set is available via ProteomeXchange (ID: PXD000783) and will significantly enhance understanding of a range of regulatory mechanisms controlling a variety of cellular process and will serve as a critical resource for the microalgal community. PMID:24917610

  7. Phosphoproteomics in Cancer

    PubMed Central

    Harsha, H. C.; Pandey, Akhilesh

    2010-01-01

    Reversible protein phosphorylation serves as a basis for regulating a number of cellular processes. Aberrant activation of kinase signaling pathways is commonly associated with several cancers. Recent developments in phosphoprotein/phosphopeptide enrichment strategies and quantitative mass spectrometry have resulted in robust pipelines for high-throughput characterization of phosphorylation in a global fashion. Today, it is possible to profile site-specific phosphorylation events on thousands of proteins in a single experiment. The potential of this approach is already being realized to characterize signaling pathways that govern oncogenesis. In addition, chemical proteomic strategies have been used to unravel targets of kinase inhibitors, which are otherwise difficult to characterize. This review summarizes various approaches used for analysis of the phosphoproteome in general, and protein kinases in particular, highlighting key cancer phosphoproteomic studies. PMID:20937571

  8. Human cytomegalovirus pUL97 kinase induces global changes in the infected cell phosphoproteome

    PubMed Central

    Oberstein, Adam; Perlman, David H.; Shenk, Thomas; Terry, Laura J.

    2015-01-01

    Replication of human cytomegalovirus is regulated in part by cellular kinases and the single viral Ser/Thr kinase, pUL97. The virus-coded kinase augments the replication of human cytomegalovirus (HCMV) by enabling nuclear egress and altering cell cycle progression. These roles are accomplished through direct phosphorylation of nuclear lamins and the retinoblastoma protein, respectively. In an effort to identify additional pUL97 substrates, we analyzed the phosphoproteome of SILAC-labeled human fibroblasts during infection with either wild-type HCMV or a pUL97 kinase-dead mutant virus. Phosphopeptides were enriched over a titanium dioxide matrix and analyzed by high resolution mass spectrometry. We identified 157 unambiguous phosphosites from 106 cellular and 17 viral proteins whose phosphorylation required UL97. Analysis of peptides containing these sites allowed the identification of several candidate pUL97 phosphorylation motifs, including a completely novel phosphorylation motif, LxSP. Substrates harboring the LxSP motif were enriched in nucleocytoplasmic transport functions, including a number of components of the nuclear pore complex. These results extend the known functions of pUL97 and suggest that modulation of nuclear pore function may be important during HCMV replication. PMID:25867546

  9. Global Phosphoproteomic Analysis of Human Skeletal Muscle Reveals a Network of Exercise-Regulated Kinases and AMPK Substrates.

    PubMed

    Hoffman, Nolan J; Parker, Benjamin L; Chaudhuri, Rima; Fisher-Wellman, Kelsey H; Kleinert, Maximilian; Humphrey, Sean J; Yang, Pengyi; Holliday, Mira; Trefely, Sophie; Fazakerley, Daniel J; Stöckli, Jacqueline; Burchfield, James G; Jensen, Thomas E; Jothi, Raja; Kiens, Bente; Wojtaszewski, Jørgen F P; Richter, Erik A; James, David E

    2015-11-01

    Exercise is essential in regulating energy metabolism and whole-body insulin sensitivity. To explore the exercise signaling network, we undertook a global analysis of protein phosphorylation in human skeletal muscle biopsies from untrained healthy males before and after a single high-intensity exercise bout, revealing 1,004 unique exercise-regulated phosphosites on 562 proteins. These included substrates of known exercise-regulated kinases (AMPK, PKA, CaMK, MAPK, mTOR), yet the majority of kinases and substrate phosphosites have not previously been implicated in exercise signaling. Given the importance of AMPK in exercise-regulated metabolism, we performed a targeted in vitro AMPK screen and employed machine learning to predict exercise-regulated AMPK substrates. We validated eight predicted AMPK substrates, including AKAP1, using targeted phosphoproteomics. Functional characterization revealed an undescribed role for AMPK-dependent phosphorylation of AKAP1 in mitochondrial respiration. These data expose the unexplored complexity of acute exercise signaling and provide insights into the role of AMPK in mitochondrial biochemistry. PMID:26437602

  10. Global analysis of phosphoproteome dynamics in embryonic development of zebrafish (Danio rerio).

    PubMed

    Kwon, Oh Kwang; Kim, Sun Ju; Lee, You-Mie; Lee, Young-Hoon; Bae, Young-Seuk; Kim, Jin Young; Peng, Xiaojun; Cheng, Zhongyi; Zhao, Yingming; Lee, Sangkyu

    2016-01-01

    The zebrafish (Danio rerio) is a popular animal model used for studies on vertebrate development and organogenesis. Recent research has shown a similarity of approximately 70% between the human and zebrafish genomes and about 84% of human disease-causing genes have common ancestry with that of the zebrafish genes. Zebrafish embryos have a number of desirable features, including transparency, a large size, and rapid embryogenesis. Protein phosphorylation is a well-known PTM, which can carry out various biological functions. Recent MS developments have enabled the study of global phosphorylation patterns by using MS-based proteomics coupled with titanium dioxide phosphopeptide enrichment. In the present study, we identified 3500 nonredundant phosphorylation sites on 2166 phosphoproteins and quantified 1564 phosphoproteins in developing embryos of zebrafish. The distribution of Ser/Thr/Tyr phosphorylation sites in zebrafish embryos was found to be 88.9, 10.2, and 0.9%, respectively. A potential kinase motif was predicted using Motif-X analysis, for 80% of the identified phosphorylation sites, with the proline-directed motif appearing most frequently, and 35 phosphorylation sites having the pSF motif. In addition, we created six phosphoprotein clusters based on their dynamic pattern during the development of zebrafish embryos. Here, we report the largest dataset of phosphoproteins in zebrafish embryos and our results can be used for further studies on phosphorylation sites or phosphoprotein dynamics in zebrafish embryos. PMID:26449285

  11. Identifying novel targets of oncogenic EGF receptor signaling in lung cancer through global phosphoproteomics.

    PubMed

    Zhang, Xu; Belkina, Natalya; Jacob, Harrys Kishore Charles; Maity, Tapan; Biswas, Romi; Venugopalan, Abhilash; Shaw, Patrick G; Kim, Min-Sik; Chaerkady, Raghothama; Pandey, Akhilesh; Guha, Udayan

    2015-01-01

    Mutations in the epidermal growth factor receptor (EGFR) kinase domain occur in 10-30% of lung adenocarcinoma and are associated with tyrosine kinase inhibitor (TKI) sensitivity. We sought to identify the immediate direct and indirect phosphorylation targets of mutant EGFRs in lung adenocarcinoma. We undertook SILAC strategy, phosphopeptide enrichment, and quantitative MS to identify dynamic changes of phosphorylation downstream of mutant EGFRs in lung adenocarcinoma cells harboring EGFR(L858R) and EGFR(L858R/T790M) , the TKI-sensitive, and TKI-resistant mutations, respectively. Top canonical pathways that were inhibited upon erlotinib treatment in sensitive cells, but not in the resistant cells include EGFR, insulin receptor, hepatocyte growth factor, mitogen-activated protein kinase, mechanistic target of rapamycin, ribosomal protein S6 kinase beta 1, and Janus kinase/signal transducer and activator of transcription signaling. We identified phosphosites in proteins of the autophagy network, such as ULK1 (S623) that is constitutively phosphorylated in these lung adenocarcinoma cells; phosphorylation is inhibited upon erlotinib treatment in sensitive cells, but not in resistant cells. Finally, kinase-substrate prediction analysis from our data indicated that substrates of basophilic kinases from, AGC and Calcium and calmodulin-dependent kinase groups, as well as STE group kinases were significantly enriched and those of proline-directed kinases from, CMGC and Casein kinase groups were significantly depleted among substrates that exhibited increased phosphorylation upon EGF stimulation and reduced phosphorylation upon TKI inhibition. This is the first study to date to examine global phosphorylation changes upon erlotinib treatment of lung adenocarcinoma cells and results from this study provide new insights into signaling downstream of mutant EGFRs in lung adenocarcinoma. All MS data have been deposited in the ProteomeXchange with identifier PXD001101 (http

  12. Global Phosphoproteome Profiling Reveals Unanticipated Networks Responsive to Cisplatin Treatment of Embryonic Stem Cells ▿ †

    PubMed Central

    Pines, Alex; Kelstrup, Christian D.; Vrouwe, Mischa G.; Puigvert, Jordi C.; Typas, Dimitris; Misovic, Branislav; de Groot, Anton; von Stechow, Louise; van de Water, Bob; Danen, Erik H. J.; Vrieling, Harry; Mullenders, Leon H. F.; Olsen, Jesper V.

    2011-01-01

    Cellular responses to DNA-damaging agents involve the activation of various DNA damage signaling and transduction pathways. Using quantitative and high-resolution tandem mass spectrometry, we determined global changes in protein level and phosphorylation site profiles following treatment of SILAC (stable isotope labeling by amino acids in cell culture)-labeled murine embryonic stem cells with the anticancer drug cisplatin. Network and pathway analyses indicated that processes related to the DNA damage response and cytoskeleton organization were significantly affected. Although the ATM (ataxia telangiectasia mutated) and ATR (ATM and Rad3-related) consensus sequence (S/T-Q motif) was significantly overrepresented among hyperphosphorylated peptides, about half of the >2-fold-upregulated phosphorylation sites based on the consensus sequence were not direct substrates of ATM and ATR. Eleven protein kinases mainly belonging to the mitogen-activated protein kinase (MAPK) family were identified as being regulated in their kinase domain activation loop. The biological importance of three of these kinases (cyclin-dependent kinase 7 [CDK7], Plk1, and KPCD1) in the protection against cisplatin-induced cytotoxicity was demonstrated by small interfering RNA (siRNA)-mediated knockdown. Our results indicate that the cellular response to cisplatin involves a variety of kinases and phosphatases not only acting in the nucleus but also regulating cytoplasmic targets, resulting in extensive cytoskeletal rearrangements. Integration of transcriptomic and proteomic data revealed a poor correlation between changes in the relative levels of transcripts and their corresponding proteins, but a large overlap in affected pathways at the levels of mRNA, protein, and phosphoprotein. This study provides an integrated view of pathways activated by genotoxic stress and deciphers kinases that play a pivotal role in regulating cellular processes other than the DNA damage response. PMID:22006019

  13. Unbiased phosphoproteomic method identifies the initial effects of a methacrylic acid copolymer on macrophages.

    PubMed

    Chamberlain, Michael Dean; Wells, Laura A; Lisovsky, Alexandra; Guo, Hongbo; Isserlin, Ruth; Talior-Volodarsky, Ilana; Mahou, Redouan; Emili, Andrew; Sefton, Michael V

    2015-08-25

    An unbiased phosphoproteomic method was used to identify biomaterial-associated changes in the phosphorylation patterns of macrophage-like cells. The phosphorylation differences between differentiated THP1 (dTHP1) cells treated for 10, 20, or 30 min with a vascular regenerative methacrylic acid (MAA) copolymer or a control methyl methacrylate (MM) copolymer were determined by MS. There were 1,470 peptides (corresponding to 729 proteins) that were differentially phosphorylated in dTHP1 cells treated with the two materials with a greater cellular response to MAA treatment. In addition to identifying pathways (such as integrin signaling and cytoskeletal arrangement) that are well known to change with cell-material interaction, previously unidentified pathways, such as apoptosis and mRNA splicing, were also discovered. PMID:26261332

  14. Unbiased phosphoproteomic method identifies the initial effects of a methacrylic acid copolymer on macrophages

    PubMed Central

    Chamberlain, Michael Dean; Wells, Laura A.; Lisovsky, Alexandra; Guo, Hongbo; Isserlin, Ruth; Talior-Volodarsky, Ilana; Mahou, Redouan; Emili, Andrew; Sefton, Michael V.

    2015-01-01

    An unbiased phosphoproteomic method was used to identify biomaterial-associated changes in the phosphorylation patterns of macrophage-like cells. The phosphorylation differences between differentiated THP1 (dTHP1) cells treated for 10, 20, or 30 min with a vascular regenerative methacrylic acid (MAA) copolymer or a control methyl methacrylate (MM) copolymer were determined by MS. There were 1,470 peptides (corresponding to 729 proteins) that were differentially phosphorylated in dTHP1 cells treated with the two materials with a greater cellular response to MAA treatment. In addition to identifying pathways (such as integrin signaling and cytoskeletal arrangement) that are well known to change with cell–material interaction, previously unidentified pathways, such as apoptosis and mRNA splicing, were also discovered. PMID:26261332

  15. Effects of MEK inhibitors GSK1120212 and PD0325901 in vivo using 10-plex quantitative proteomics and phosphoproteomics

    PubMed Central

    Paulo, Joao A.; McAllister, Fiona E.; Everley, Robert A.; Beausoleil, Sean A.; Banks, Alexander S.; Gygi, Steven P.

    2015-01-01

    Multiplexed isobaric tag-based quantitative proteomics and phosphoproteomics strategies can comprehensively analyze drug treatments effects on biological systems. Given the role of MEK signaling in cancer and MAPK-dependent diseases, we sought to determine if this pathway could be inhibited safely by examining the downstream molecular consequences. We used a series of TMT10-plex experiments to analyze the effect of two MEK inhibitors (GSK1120212 and PD0325901) on three tissues (kidney, liver, and pancreas) from nine mice. We quantified ~6000 proteins in each tissue, but significant protein level alterations were minimal with inhibitor treatment. Of particular interest was kidney tissue, as edema is an adverse effect of these inhibitors. From kidney tissue, we enriched phosphopeptides using titanium dioxide (TiO2) and quantified 10,562 phosphorylation events. Further analysis by phosphotyrosine (pY) peptide immunoprecipitation quantified an additional 592 phosphorylation events. Phosphorylation motif analysis revealed that the inhibitors decreased phosphorylation levels of PxSP and SP sites, consistent with ERK inhibition. The MEK inhibitors had the greatest decrease on the phosphorylation of two proteins, Barttin and Slc12a3, which have roles in ion transport and fluid balance. Further studies will provide insight into the effect of these MEK inhibitors with respect to edema and other adverse events in mouse models and human patients. PMID:25195567

  16. Rapid Phosphoproteomic Effects of Abscisic Acid (ABA) on Wild-Type and ABA Receptor-Deficient A. thaliana Mutants*

    PubMed Central

    Minkoff, Benjamin B.; Stecker, Kelly E.; Sussman, Michael R.

    2015-01-01

    Abscisic acid (ABA)1 is a plant hormone that controls many aspects of plant growth, including seed germination, stomatal aperture size, and cellular drought response. ABA interacts with a unique family of 14 receptor proteins. This interaction leads to the activation of a family of protein kinases, SnRK2s, which in turn phosphorylate substrates involved in many cellular processes. The family of receptors appears functionally redundant. To observe a measurable phenotype, four of the fourteen receptors have to be mutated to create a multilocus loss-of-function quadruple receptor (QR) mutant, which is much less sensitive to ABA than wild-type (WT) plants. Given these phenotypes, we asked whether or not a difference in ABA response between the WT and QR backgrounds would manifest on a phosphorylation level as well. We tested WT and QR mutant ABA response using isotope-assisted quantitative phosphoproteomics to determine what ABA-induced phosphorylation changes occur in WT plants within 5 min of ABA treatment and how that phosphorylation pattern is altered in the QR mutant. We found multiple ABA-induced phosphorylation changes that occur within 5 min of treatment, including three SnRK2 autophosphorylation events and phosphorylation on SnRK2 substrates. The majority of robust ABA-dependent phosphorylation changes observed were partially diminished in the QR mutant, whereas many smaller ABA-dependent phosphorylation changes observed in the WT were not responsive to ABA in the mutant. A single phosphorylation event was increased in response to ABA treatment in both the WT and QR mutant. A portion of the discovery data was validated using selected reaction monitoring-based targeted measurements on a triple quadrupole mass spectrometer. These data suggest that different subsets of phosphorylation events depend upon different subsets of the ABA receptor family to occur. Altogether, these data expand our understanding of the model by which the family of ABA receptors directs

  17. Enrichment Strategies in Phosphoproteomics.

    PubMed

    Leitner, Alexander

    2016-01-01

    The comprehensive study of the phosphoproteome is heavily dependent on appropriate enrichment strategies that are most often, but not exclusively, carried out on the peptide level. In this chapter, I give an overview of the most widely used techniques. In addition to dedicated antibodies, phosphopeptides are enriched by their selective interaction with metals in the form of chelated metal ions or metal oxides. The negative charge of the phosphate group is also exploited in a variety of chromatographic fractionation methods that include different types of ion exchange chromatography, hydrophilic interaction chromatography (HILIC), and electrostatic repulsion HILIC (ERLIC) chromatography. Selected examples from the literature will demonstrate how a combination of these techniques with current high-performance mass spectrometry enables the identification of thousands of phosphorylation sites from various sample types. PMID:26584921

  18. Challenges in plasma membrane phosphoproteomics

    PubMed Central

    Orsburn, Benjamin C; Stockwin, Luke H; Newton, Dianne L

    2011-01-01

    The response to extracellular stimuli often alters the phosphorylation state of plasma membrane-associated proteins. In this regard, generation of a comprehensive membrane phosphoproteome can significantly enhance signal transduction and drug mechanism studies. However, analysis of this subproteome is regarded as technically challenging, given the low abundance and insolubility of integral membrane proteins, combined with difficulties in isolating, ionizing and fragmenting phosphopeptides. In this article, we highlight recent advances in membrane and phosphoprotein enrichment techniques resulting in improved identification of these elusive peptides. We also describe the use of alternative fragmentation techniques, and assess their current and future value to the field of membrane phosphoproteomics. PMID:21819303

  19. A Phos-tag SDS-PAGE method that effectively uses phosphoproteomic data for profiling the phosphorylation dynamics of MEK1.

    PubMed

    Kinoshita, Eiji; Kinoshita-Kikuta, Emiko; Kubota, Yuji; Takekawa, Mutsuhiro; Koike, Tohru

    2016-07-01

    MEK1, an essential component of the mitogen-activated protein kinase (MAPK) pathway, is phosphorylated during activation of the pathway; 12 phosphorylation sites have been identified in human MEK1 by MS-based phosphoproteomic methods. By using Phos-tag SDS-PAGE, we found that multiple variants of MEK1 with different phosphorylation states are constitutively present in typical human cells. The Phos-tag-based strategy, which makes effective use of existing information on the location of phosphorylation sites, permits quantitative time-course profiling of MEK1 phosphospecies in their respective phosphorylation states. By subsequent immunoblotting with an anti-HaloTag antibody, we analyzed a HaloTag-fused MEK1 protein and 12 potential phosphorylation-site-directed mutants of the protein transiently expressed in HEK 293 cells. This strategy revealed that MEK1 is constitutively and mainly phosphorylated at the Thr-292, Ser-298, Thr-386, and Thr-388 residues in vivo, and that combinations of phosphorylations at these four residues produce at least six phosphorylated variants of MEK1. Like the levels of phosphorylation of the Ser-218 and Ser-222 residues by RAF1, which have been well studied, the phosphorylation statuses of Thr-292, Ser-298, Thr-386, and Thr-388 residues vary widely during activation and deactivation of the MAPK pathway. Furthermore, we demonstrated inhibitor-specific profiling of MEK1 phosphospecies by using three MEK inhibitors: TAK-733, PD98059, and U0126. PMID:27169363

  20. Phosphoproteomics and Lung Cancer Research

    PubMed Central

    López, Elena; Cho, William C. S.

    2012-01-01

    Massive evidence suggests that genetic abnormalities contribute to the development of lung cancer. These molecular abnormalities may serve as diagnostic, prognostic and predictive biomarkers for this deadly disease. It is imperative to search these biomarkers in different tumorigenesis pathways so as to provide the most appropriate therapy for each individual patient with lung malignancy. Phosphoproteomics is a promising technology for the identification of biomarkers and novel therapeutic targets for cancer. Thousands of proteins interact via physical and chemical association. Moreover, some proteins can covalently modify other proteins post-translationally. These post-translational modifications ultimately give rise to the emergent functions of cells in sequence, space and time. Phosphoproteomics clinical researches imply the comprehensive analysis of the proteins that are expressed in cells or tissues and can be employed at different stages. In addition, understanding the functions of phosphorylated proteins requires the study of proteomes as linked systems rather than collections of individual protein molecules. In fact, proteomics approaches coupled with affinity chromatography strategies followed by mass spectrometry have been used to elucidate relevant biological questions. This article will discuss the relevant clues of post-translational modifications, phosphorylated proteins, and useful proteomics approaches to identify molecular cancer signatures. The recent progress in phosphoproteomics research in lung cancer will be also discussed. PMID:23202899

  1. An Initial Characterization of the Serum Phosphoproteome

    PubMed Central

    Zhou, Weidong; Ross, Mark M.; Tessitore, Alessandra; Ornstein, David; VanMeter, Amy; Liotta, Lance A.; Petricoin, Emanuel F.

    2009-01-01

    Phosphorylation is a dynamic post-translational protein modification that is the basis of a general mechanism for maintaining and regulating protein structure and function, and of course underpins key cellular processes through signal transduction. In the last several years, many studies of large-scale profiling of phosphoproteins and mapping phosphorylation sites from cultured human cells or tissues by mass spectrometry technique have been published; however, there is little information on general (or global) phosphoproteomic characterization and description of the content of phosphoprotein analytes within the circulation. Circulating phosphoproteins and phosphopeptides could represent important disease biomarkers because of their well-known importance in cellular function, and these analytes frequently are mutated and activated in human diseases such as cancer. Here we report an initial attempt to characterize the phosphoprotein content of serum. To accomplish this, we developed a method in which phosphopeptides are enriched from digested serum proteins and analyzed by LC-MS/MS using LTQ-Orbitrap (CID) and LTQ-ETD mass spectrometers. Using this approach we identified ~100 unique phosphopeptides with stringent filtering criteria and a lower than 1% false discovery rate. PMID:19824718

  2. Phosphoproteomic Analyses Reveal Signaling Pathways That Facilitate Lytic Gammaherpesvirus Replication

    PubMed Central

    Stahl, James A.; Chavan, Shweta S.; Sifford, Jeffrey M.; MacLeod, Veronica; Voth, Daniel E.; Edmondson, Ricky D.; Forrest, J. Craig

    2013-01-01

    Lytic gammaherpesvirus (GHV) replication facilitates the establishment of lifelong latent infection, which places the infected host at risk for numerous cancers. As obligate intracellular parasites, GHVs must control and usurp cellular signaling pathways in order to successfully replicate, disseminate to stable latency reservoirs in the host, and prevent immune-mediated clearance. To facilitate a systems-level understanding of phosphorylation-dependent signaling events directed by GHVs during lytic replication, we utilized label-free quantitative mass spectrometry to interrogate the lytic replication cycle of murine gammaherpesvirus-68 (MHV68). Compared to controls, MHV68 infection regulated by 2-fold or greater ca. 86% of identified phosphopeptides – a regulatory scale not previously observed in phosphoproteomic evaluations of discrete signal-inducing stimuli. Network analyses demonstrated that the infection-associated induction or repression of specific cellular proteins globally altered the flow of information through the host phosphoprotein network, yielding major changes to functional protein clusters and ontologically associated proteins. A series of orthogonal bioinformatics analyses revealed that MAPK and CDK-related signaling events were overrepresented in the infection-associated phosphoproteome and identified 155 host proteins, such as the transcription factor c-Jun, as putative downstream targets. Importantly, functional tests of bioinformatics-based predictions confirmed ERK1/2 and CDK1/2 as kinases that facilitate MHV68 replication and also demonstrated the importance of c-Jun. Finally, a transposon-mutant virus screen identified the MHV68 cyclin D ortholog as a viral protein that contributes to the prominent MAPK/CDK signature of the infection-associated phosphoproteome. Together, these analyses enhance an understanding of how GHVs reorganize and usurp intracellular signaling networks to facilitate infection and replication. PMID:24068923

  3. Quantitative Phosphoproteomics Analysis of ERBB3/ERBB4 Signaling

    PubMed Central

    Jacobs, Kris; Klammer, Martin; Jordan, Nicole; Elschenbroich, Sarah; Parade, Marc; Jacoby, Edgar; Linders, Joannes T. M.; Brehmer, Dirk; Cools, Jan; Daub, Henrik

    2016-01-01

    The four members of the epidermal growth factor receptor (EGFR/ERBB) family form homo- and heterodimers which mediate ligand-specific regulation of many key cellular processes in normal and cancer tissues. While signaling through the EGFR has been extensively studied on the molecular level, signal transduction through ERBB3/ERBB4 heterodimers is less well understood. Here, we generated isogenic mouse Ba/F3 cells that express full-length and functional membrane-integrated ERBB3 and ERBB4 or ERBB4 alone, to serve as a defined cellular model for biological and phosphoproteomics analysis of ERBB3/ERBB4 signaling. ERBB3 co-expression significantly enhanced Ba/F3 cell proliferation upon neuregulin-1 (NRG1) treatment. For comprehensive signaling studies we performed quantitative mass spectrometry (MS) experiments to compare the basal ERBB3/ERBB4 cell phosphoproteome to NRG1 treatment of ERBB3/ERBB4 and ERBB4 cells. We employed a workflow comprising differential isotope labeling with mTRAQ reagents followed by chromatographic peptide separation and final phosphopeptide enrichment prior to MS analysis. Overall, we identified 9686 phosphorylation sites which could be confidently localized to specific residues. Statistical analysis of three replicate experiments revealed 492 phosphorylation sites which were significantly changed in NRG1-treated ERBB3/ERBB4 cells. Bioinformatics data analysis recapitulated regulation of mitogen-activated protein kinase and Akt pathways, but also indicated signaling links to cytoskeletal functions and nuclear biology. Comparative assessment of NRG1-stimulated ERBB4 Ba/F3 cells revealed that ERBB3 did not trigger defined signaling pathways but more broadly enhanced phosphoproteome regulation in cells expressing both receptors. In conclusion, our data provide the first global picture of ERBB3/ERBB4 signaling and provide numerous potential starting points for further mechanistic studies. PMID:26745281

  4. Phosphoproteomics in translational research: a sarcoma perspective.

    PubMed

    Noujaim, J; Payne, L S; Judson, I; Jones, R L; Huang, P H

    2016-05-01

    Phosphoproteomics has been extensively used as a preclinical research tool to characterize the phosphorylated components of the cancer proteome. Advances in the field have yielded insights into new drug targets, mechanisms of disease progression and drug resistance, and biomarker discovery. However, application of this technology to clinical research has been challenging because of practical issues relating to specimen integrity and tumour heterogeneity. Beyond these limitations, phosphoproteomics has the potential to play a pivotal role in translational studies and contribute to advances in different tumour groups, including rare disease sites like sarcoma. In this review, we propose that deploying phosphoproteomic technologies in translational research may facilitate the identification of better defined predictive biomarkers for patient stratification, inform drug selection in umbrella trials and identify new combinations to overcome drug resistance. We provide an overview of current phosphoproteomic technologies, such as affinity-based assays and mass spectrometry-based approaches, and discuss their advantages and limitations. We use sarcoma as an example to illustrate the current challenges in evaluating targeted kinase therapies in clinical trials. We then highlight useful lessons from preclinical studies in sarcoma biology to demonstrate how phosphoproteomics may address some of these challenges. Finally, we conclude by offering a perspective and list the key measures required to translate and benchmark a largely preclinical technology into a useful tool for translational research. PMID:26802162

  5. Wrangling Phosphoproteomic Data to Elucidate Cancer Signaling Pathways

    PubMed Central

    Grimes, Mark L.; Lee, Wan-Jui; van der Maaten, Laurens; Shannon, Paul

    2013-01-01

    The interpretation of biological data sets is essential for generating hypotheses that guide research, yet modern methods of global analysis challenge our ability to discern meaningful patterns and then convey results in a way that can be easily appreciated. Proteomic data is especially challenging because mass spectrometry detectors often miss peptides in complex samples, resulting in sparsely populated data sets. Using the R programming language and techniques from the field of pattern recognition, we have devised methods to resolve and evaluate clusters of proteins related by their pattern of expression in different samples in proteomic data sets. We examined tyrosine phosphoproteomic data from lung cancer samples. We calculated dissimilarities between the proteins based on Pearson or Spearman correlations and on Euclidean distances, whilst dealing with large amounts of missing data. The dissimilarities were then used as feature vectors in clustering and visualization algorithms. The quality of the clusterings and visualizations were evaluated internally based on the primary data and externally based on gene ontology and protein interaction networks. The results show that t-distributed stochastic neighbor embedding (t-SNE) followed by minimum spanning tree methods groups sparse proteomic data into meaningful clusters more effectively than other methods such as k-means and classical multidimensional scaling. Furthermore, our results show that using a combination of Spearman correlation and Euclidean distance as a dissimilarity representation increases the resolution of clusters. Our analyses show that many clusters contain one or more tyrosine kinases and include known effectors as well as proteins with no known interactions. Visualizing these clusters as networks elucidated previously unknown tyrosine kinase signal transduction pathways that drive cancer. Our approach can be applied to other data types, and can be easily adopted because open source software

  6. KinasePA: Phosphoproteomics data annotation using hypothesis driven kinase perturbation analysis.

    PubMed

    Yang, Pengyi; Patrick, Ellis; Humphrey, Sean J; Ghazanfar, Shila; James, David E; Jothi, Raja; Yang, Jean Yee Hwa

    2016-07-01

    Mass spectrometry (MS)-based quantitative phosphoproteomics has become a key approach for proteome-wide profiling of phosphorylation in tissues and cells. Traditional experimental design often compares a single treatment with a control, whereas increasingly more experiments are designed to compare multiple treatments with respect to a control. To this end, the development of bioinformatic tools that can integrate multiple treatments and visualise kinases and substrates under combinatorial perturbations is vital for dissecting concordant and/or independent effects of each treatment. Here, we propose a hypothesis driven kinase perturbation analysis (KinasePA) to annotate and visualise kinases and their substrates that are perturbed by various combinatorial effects of treatments in phosphoproteomics experiments. We demonstrate the utility of KinasePA through its application to two large-scale phosphoproteomics datasets and show its effectiveness in dissecting kinases and substrates within signalling pathways driven by unique combinations of cellular stimuli and inhibitors. We implemented and incorporated KinasePA as part of the "directPA" R package available from the comprehensive R archive network (CRAN). Furthermore, KinasePA also has an interactive web interface that can be readily applied to annotate user provided phosphoproteomics data (http://kinasepa.pengyiyang.org). PMID:27145998

  7. Phosphoproteomic Analysis Reveals the Effects of PilF Phosphorylation on Type IV Pilus and Biofilm Formation in Thermus thermophilus HB27*

    PubMed Central

    Wu, Wan-Ling; Liao, Jiahn-Haur; Lin, Guang-Huey; Lin, Miao-Hsia; Chang, Ying-Che; Liang, Suh-Yuen; Yang, Feng-Ling; Khoo, Kay-Hooi; Wu, Shih-Hsiung

    2013-01-01

    Thermus thermophilus HB27 is an extremely thermophilic eubacteria with a high frequency of natural competence. This organism is therefore often used as a thermophilic model to investigate the molecular basis of type IV pili–mediated functions, such as the uptake of free DNA, adhesion, twitching motility, and biofilm formation, in hot environments. In this study, the phosphoproteome of T. thermophilus HB27 was analyzed via a shotgun approach and high-accuracy mass spectrometry. Ninety-three unique phosphopeptides, including 67 in vivo phosphorylated sites on 53 phosphoproteins, were identified. The distribution of Ser/Thr/Tyr phosphorylation sites was 57%/36%/7%. The phosphoproteins were mostly involved in central metabolic pathways and protein/cell envelope biosynthesis. According to this analysis, the ATPase motor PilF, a type IV pili–related component, was first found to be phosphorylated on Thr-368 and Ser-372. Through the point mutation of PilF, mimic phosphorylated mutants T368D and S372E resulted in nonpiliated and nontwitching phenotypes, whereas nonphosphorylated mutants T368V and S372A displayed piliation and twitching motility. In addition, mimic phosphorylated mutants showed elevated biofilm-forming abilities with a higher initial attachment rate, caused by increasing exopolysaccharide production. In summary, the phosphorylation of PilF might regulate the pili and biofilm formation associated with exopolysaccharide production. PMID:23828892

  8. Computational phosphoproteomics: From identification to localization

    PubMed Central

    Lee, Dave C H; Jones, Andrew R; Hubbard, Simon J

    2015-01-01

    Analysis of the phosphoproteome by MS has become a key technology for the characterization of dynamic regulatory processes in the cell, since kinase and phosphatase action underlie many major biological functions. However, the addition of a phosphate group to a suitable side chain often confounds informatic analysis by generating product ion spectra that are more difficult to interpret (and consequently identify) relative to unmodified peptides. Collectively, these challenges have motivated bioinformaticians to create novel software tools and pipelines to assist in the identification of phosphopeptides in proteomic mixtures, and help pinpoint or “localize” the most likely site of modification in cases where there is ambiguity. Here we review the challenges to be met and the informatics solutions available to address them for phosphoproteomic analysis, as well as highlighting the difficulties associated with using them and the implications for data standards. PMID:25475148

  9. 15N labeled brain enables quantification of proteome and phosphoproteome in cultured primary neurons

    PubMed Central

    Liao, Lujian; Sando, Richard C.; Farnum, John B.; Vanderklish, Peter W.; Maximov, Anton; Yates, John R.

    2011-01-01

    Terminally differentiated primary cells represent a valuable in vitro model to study signaling events associated within a specific tissue. Quantitative proteomic methods using metabolic labeling in primary cells encounter labeling efficiency issues hindering the use of these cells. Here we developed a method to quantify the proteome and phosphoproteome of cultured neurons using 15N labeled brain tissue as an internal standard, and applied this method to determine how an inhibitor of an excitatory neural transmitter receptor, phencyclidine (PCP), affects the global phosphoproteome of cortical neurons. We identified over 10,000 phosphopeptides and made accurate quantitative measurements of the neuronal phosphoproteome after neuronal inhibition. We show that short PCP treatments lead to changes in phosphorylation for 7% of neuronal phosphopeptides and that prolonged PCP treatment alters the total levels of several proteins essential for synaptic transmission and plasticity and leads to a massive reduction in the synaptic strength of inhibitory synapses. The results provide valuable insights into the dynamics of molecular networks implicated in PCP-mediated NMDA receptor inhibition and sensorimotor deficits. PMID:22070516

  10. Phosphoproteome of the cyanobacterium Synechocystis sp. PCC 6803 and its dynamics during nitrogen starvation

    PubMed Central

    Spät, Philipp; Maček, Boris; Forchhammer, Karl

    2015-01-01

    Cyanobacteria have shaped the earth's biosphere as the first oxygenic photoautotrophs and still play an important role in many ecosystems. The ability to adapt to changing environmental conditions is an essential characteristic in order to ensure survival. To this end, numerous studies have shown that bacteria use protein post-translational modifications such as Ser/Thr/Tyr phosphorylation in cell signaling, adaptation, and regulation. Nevertheless, our knowledge of cyanobacterial phosphoproteomes and their dynamic response to environmental stimuli is relatively limited. In this study, we applied gel-free methods and high accuracy mass spectrometry toward the detection of Ser/Thr/Tyr phosphorylation events in the model cyanobacterium Synechocystis sp. PCC 6803. We could identify over 300 phosphorylation events in cultures grown on nitrate as exclusive nitrogen source. Chemical dimethylation labeling was applied to investigate proteome and phosphoproteome dynamics during nitrogen starvation. Our dataset describes the most comprehensive (phospho)proteome of Synechocystis to date, identifying 2382 proteins and 183 phosphorylation events and quantifying 2111 proteins and 148 phosphorylation events during nitrogen starvation. Global protein phosphorylation levels were increased in response to nitrogen depletion after 24 h. Among the proteins with increased phosphorylation, the PII signaling protein showed the highest fold-change, serving as positive control. Other proteins with increased phosphorylation levels comprised functions in photosynthesis and in carbon and nitrogen metabolism. This study reveals dynamics of Synechocystis phosphoproteome in response to environmental stimuli and suggests an important role of protein Ser/Thr/Tyr phosphorylation in fundamental mechanisms of homeostatic control in cyanobacteria. PMID:25873915

  11. Identification of novel protein functions and signaling mechanisms by genetics and quantitative phosphoproteomics in Caenorhabditis elegans.

    PubMed

    Fredens, Julius; Engholm-Keller, Kasper; Møller-Jensen, Jakob; Larsen, Martin Røssel; Færgeman, Nils J

    2014-01-01

    Stable isotope labeling by amino acids combined with mass spectrometry is a widely used methodology for measuring relative changes in protein and phosphorylation levels at a global level. We have applied this method to the model organism Caenorhabditis elegans in combination with RNAi-mediated gene knockdown by feeding the nematode on pre-labeled lysine auxotroph Escherichia coli. In this chapter, we describe in details the generation of the E. coli strain, incorporation of heavy isotope-labeled lysine in C. elegans, and the procedure for a comprehensive global phosphoproteomic experiment. PMID:25059608

  12. The proteome and phosphoproteome of Neurospora crassa in response to cellulose, sucrose and carbon starvation.

    PubMed

    Xiong, Yi; Coradetti, Samuel T; Li, Xin; Gritsenko, Marina A; Clauss, Therese; Petyuk, Vlad; Camp, David; Smith, Richard; Cate, Jamie H D; Yang, Feng; Glass, N Louise

    2014-11-01

    Improving cellulolytic enzyme production by plant biomass degrading fungi holds great potential in reducing costs associated with production of next-generation biofuels generated from lignocellulose. How fungi sense cellulosic materials and respond by secreting enzymes has mainly been examined by assessing function of transcriptional regulators and via transcriptional profiling. Here, we obtained global proteomic and phosphoproteomic profiles of the plant biomass degrading filamentous fungus Neurospora crassa grown on different carbon sources, i.e. sucrose, no carbon, and cellulose, by performing isobaric tags for relative and absolute quantification (iTRAQ)-based LC-MS/MS analyses. A comparison between proteomes and transcriptomes under identical carbon conditions suggests that extensive post-transcriptional regulation occurs in N. crassa in response to exposure to cellulosic material. Several hundred amino acid residues with differential phosphorylation levels on crystalline cellulose (Avicel) or carbon-free medium vs sucrose medium were identified, including phosphorylation sites in a major transcriptional activator for cellulase genes, CLR1, as well as a cellobionic acid transporter, CBT1. Mutation of phosphorylation sites on CLR1 did not have a major effect on transactivation of cellulase production, while mutation of phosphorylation sites in CBT1 increased its transporting capacity. Our data provides rich information at both the protein and phosphorylation levels of the early cellular responses to carbon starvation and cellulosic induction and aids in a greater understanding of the underlying post-transcriptional regulatory mechanisms in filamentous fungi. PMID:24881580

  13. The proteome and phosphoproteome of Neurospora crassa in response to cellulose, sucrose and carbon starvation

    SciTech Connect

    Xiong, Yi; Coradetti, Samuel T.; Li, Xin; Gritsenko, Marina A.; Clauss, Therese; Petyuk, Vlad; Camp, David; Smith, Richard; Cate, Jamie H. D.; Yang, Feng; Glass, N. Louise

    2014-05-29

    Improving cellulolytic enzyme production by plant biomass degrading fungi holds great potential in reducing costs associated with production of next-generation biofuels generated from lignocellulose. How fungi sense cellulosic materials and respond by secreting enzymes has mainly been examined by assessing function of transcriptional regulators and via transcriptional profiling. Here, we obtained global proteomic and phosphoproteomic profiles of the plant biomass degrading filamentous fungus Neurospora crassa grown on different carbon sources, i.e. sucrose, no carbon, and cellulose, by performing isobaric tags for relative and absolute quantification (iTRAQ) -based LC-MS/MS analyses. A comparison between proteomes and transcriptomes under identical carbon conditions suggests that extensive post-transcriptional regulation occurs in N. crassa in response to exposure to cellulosic material. Several hundred amino acid residues with differential phosphorylation levels on crystalline cellulose (Avicel) or carbon-free medium versus sucrose medium were identified, including phosphorylation sites in a major transcriptional activator for cellulase genes, CLR1, as well as a cellobionic acid transporter, CBT1. Finally, we found mutation of phosphorylation sites on CLR1 did not have a major effect on transactivation of cellulase production, while mutation of phosphorylation sites in CBT1 increased its transporting capacity. Our data provides rich information at both the protein and phosphorylation levels of the early cellular responses to carbon starvation and cellulosic induction and aids in a greater understanding of the underlying post-transcriptional regulatory mechanisms in filamentous fungi.

  14. The proteome and phosphoproteome of Neurospora crassa in response to cellulose, sucrose and carbon starvation

    DOE PAGESBeta

    Xiong, Yi; Coradetti, Samuel T.; Li, Xin; Gritsenko, Marina A.; Clauss, Therese; Petyuk, Vlad; Camp, David; Smith, Richard; Cate, Jamie H. D.; Yang, Feng; et al

    2014-05-29

    Improving cellulolytic enzyme production by plant biomass degrading fungi holds great potential in reducing costs associated with production of next-generation biofuels generated from lignocellulose. How fungi sense cellulosic materials and respond by secreting enzymes has mainly been examined by assessing function of transcriptional regulators and via transcriptional profiling. Here, we obtained global proteomic and phosphoproteomic profiles of the plant biomass degrading filamentous fungus Neurospora crassa grown on different carbon sources, i.e. sucrose, no carbon, and cellulose, by performing isobaric tags for relative and absolute quantification (iTRAQ) -based LC-MS/MS analyses. A comparison between proteomes and transcriptomes under identical carbon conditions suggestsmore » that extensive post-transcriptional regulation occurs in N. crassa in response to exposure to cellulosic material. Several hundred amino acid residues with differential phosphorylation levels on crystalline cellulose (Avicel) or carbon-free medium versus sucrose medium were identified, including phosphorylation sites in a major transcriptional activator for cellulase genes, CLR1, as well as a cellobionic acid transporter, CBT1. Finally, we found mutation of phosphorylation sites on CLR1 did not have a major effect on transactivation of cellulase production, while mutation of phosphorylation sites in CBT1 increased its transporting capacity. Our data provides rich information at both the protein and phosphorylation levels of the early cellular responses to carbon starvation and cellulosic induction and aids in a greater understanding of the underlying post-transcriptional regulatory mechanisms in filamentous fungi.« less

  15. The proteome and phosphoproteome of Neurospora crassa in response to cellulose, sucrose and carbon starvation

    SciTech Connect

    Xiong, Yi; Coradetti, Samuel T.; Li, Xin; Gritsenko, Marina A.; Clauss, Therese RW; Petyuk, Vladislav A.; Camp, David G.; Smith, Richard D.; Cate, Jamie H.; Yang, Feng; Glass, Louise

    2014-11-01

    Improving cellulolytic enzyme production by plant biomass degrading fungi holds great potential in reducing costs associated with production of next-generation biofuels generated from lignocellulose. How fungi sense cellulosic materials and respond by secreting enzymes has mainly been examined by assessing function of transcriptional regulators and via transcriptional profiling. Here, we obtained global proteomic and phosphoproteomic profiles of the plant biomass degrading filamentous fungus Neurospora crassa grown on different carbon sources, i.e. sucrose, no carbon, and cellulose, by performing isobaric tags for relative and absolute quantification (iTRAQ) -based LC-MS/MS analyses. A comparison between proteomes and transcriptomes under identical carbon conditions suggests that extensive post-transcriptional regulation occurs in N. crassa in response to exposure to cellulosic material. Several hundred amino acid residues with differential phosphorylation levels on crystalline cellulose (Avicel) or carbon-free medium versus sucrose medium were identified, including phosphorylation sites in a major transcriptional activator for cellulase genes, CLR1, as well as a cellobionic acid transporter, CBT1. Mutation of phosphorylation sites on CLR1 did not have a major effect on transactivation of cellulase production, while mutation of phosphorylation sites in CBT1 increased its transporting capacity. Our data provides rich information at both the protein and phosphorylation levels of the early cellular responses to carbon starvation and cellulosic induction and aids in a greater understanding of the underlying post-transcriptional regulatory mechanisms in filamentous fungi.

  16. The proteome and phosphoproteome of Neurospora crassa in response to cellulose, sucrose and carbon starvation

    PubMed Central

    Xiong, Yi; Coradetti, Samuel T.; Li, Xin; Gritsenko, Marina A.; Clauss, Therese; Petyuk, Vlad; Camp, David; Smith, Richard; Cate, Jamie H.D.; Yang, Feng; Glass, N. Louise

    2014-01-01

    Improving cellulolytic enzyme production by plant biomass degrading fungi holds great potential in reducing costs associated with production of next-generation biofuels generated from lignocellulose. How fungi sense cellulosic materials and respond by secreting enzymes has mainly been examined by assessing function of transcriptional regulators and via transcriptional profiling. Here, we obtained global proteomic and phosphoproteomic profiles of the plant biomass degrading filamentous fungus Neurospora crassa grown on different carbon sources, i.e. sucrose, no carbon, and cellulose, by performing isobaric tags for relative and absolute quantification (iTRAQ)-based LC–MS/MS analyses. A comparison between proteomes and transcriptomes under identical carbon conditions suggests that extensive post-transcriptional regulation occurs in N. crassa in response to exposure to cellulosic material. Several hundred amino acid residues with differential phosphorylation levels on crystalline cellulose (Avicel) or carbon-free medium vs sucrose medium were identified, including phosphorylation sites in a major transcriptional activator for cellulase genes, CLR1, as well as a cellobionic acid transporter, CBT1. Mutation of phosphorylation sites on CLR1 did not have a major effect on transactivation of cellulase production, while mutation of phosphorylation sites in CBT1 increased its transporting capacity. Our data provides rich information at both the protein and phosphorylation levels of the early cellular responses to carbon starvation and cellulosic induction and aids in a greater understanding of the underlying post-transcriptional regulatory mechanisms in filamentous fungi. PMID:24881580

  17. Phosphoproteomics technologies and applications in plant biology research

    PubMed Central

    Li, Jinna; Silva-Sanchez, Cecilia; Zhang, Tong; Chen, Sixue; Li, Haiying

    2015-01-01

    Protein phosphorylation has long been recognized as an essential mechanism to regulate many important processes of plant life. However, studies on phosphorylation mediated signaling events in plants are challenged with low stoichiometry and dynamic nature of phosphorylated proteins. Significant advances in mass spectrometry based phosphoproteomics have taken place in recent decade, including phosphoprotein/phosphopeptide enrichment, detection and quantification, and phosphorylation site localization. This review describes a variety of separation and enrichment methods for phosphoproteins and phosphopeptides, the applications of technological innovations in plant phosphoproteomics, and highlights significant achievement of phosphoproteomics in the areas of plant signal transduction, growth and development. PMID:26136758

  18. Phosphoproteome of Human Glioblastoma Initiating Cells Reveals Novel Signaling Regulators Encoded by the Transcriptome

    PubMed Central

    Kozuka-Hata, Hiroko; Nasu-Nishimura, Yukiko; Koyama-Nasu, Ryo; Ao-Kondo, Hiroko; Tsumoto, Kouhei; Akiyama, Tetsu; Oyama, Masaaki

    2012-01-01

    Background Glioblastoma is one of the most aggressive tumors with poor prognosis. Although various studies have been performed so far, there are not effective treatments for patients with glioblastoma. Methodology/Principal Findings In order to systematically elucidate the aberrant signaling machinery activated in this malignant brain tumor, we investigated phosphoproteome dynamics of glioblastoma initiating cells using high-resolution nanoflow LC-MS/MS system in combination with SILAC technology. Through phosphopeptide enrichment by titanium dioxide beads, a total of 6,073 phosphopeptides from 2,282 phosphorylated proteins were identified based on the two peptide fragmentation methodologies of collision induced dissociation and higher-energy C-trap dissociation. The SILAC-based quantification described 516 up-regulated and 275 down-regulated phosphorylation sites upon epidermal growth factor stimulation, including the comprehensive status of the phosphorylation sites on stem cell markers such as nestin. Very intriguingly, our in-depth phosphoproteome analysis led to identification of novel phosphorylated molecules encoded by the undefined sequence regions of the human transcripts, one of which was regulated upon external stimulation in human glioblastoma initiating cells. Conclusions/Significance Our result unveils an expanded diversity of the regulatory phosphoproteome defined by the human transcriptome. PMID:22912867

  19. Toward defining the phosphoproteome of Xenopus laevis embryos

    PubMed Central

    McGivern, Jered V.; Swaney, Danielle L.; Coon, Joshua J.; Sheets, Michael D.

    2010-01-01

    Phosphorylation is universally used for controlling protein function, but knowledge of the phosphoproteome in vertebrate embryos has been limited. However, recent technical advances make it possible to define an organism's phosphoproteome at a more comprehensive level. Xenopus laevis offers established advantages for analyzing the regulation of protein function by phosphorylation. Functionally unbiased, comprehensive information about the Xenopus phosphoproteome would provide a powerful guide for future studies of phosphorylation in a developmental context. To this end, we performed a phosphoproteomic analysis of Xenopus oocytes, eggs, and embryos using recently developed mass spectrometry methods. We identified 1,441 phosphorylation sites present on 654 different Xenopus proteins, including hundreds of previously unknown phosphorylation sites. This approach identified several phosphorylation sites described in the literature and/or evolutionarily conserved in other organisms, validating the data's quality. These data will serve as a powerful resource for the exploration of phosphorylation and protein function within a developmental context. PMID:19384857

  20. Global anomalies and effective field theory

    NASA Astrophysics Data System (ADS)

    Golkar, Siavash; Sethi, Savdeep

    2016-05-01

    We show that matching anomalies under large gauge transformations and large diffeomorphisms can explain the appearance and non-renormalization of couplings in effective field theory. We focus on thermal effective field theory, where we argue that the appearance of certain unusual Chern-Simons couplings is a consequence of global anomalies. As an example, we show that a mixed global anomaly in four dimensions fixes the chiral vortical effect coefficient (up to an overall additive factor). This is an experimentally measurable prediction from a global anomaly. For certain situations, we propose a simpler method for calculating global anomalies which uses correlation functions rather than eta invariants.

  1. Global Cooling: Effect of Urban Albedo on Global Temperature

    SciTech Connect

    Akbari, Hashem; Menon, Surabi; Rosenfeld, Arthur

    2007-05-22

    In many urban areas, pavements and roofs constitute over 60% of urban surfaces (roof 20-25%, pavements about 40%). The roof and the pavement albedo can be increased by about 0.25 and 0.10, respectively, resulting in a net albedo increase for urban areas of about 0.1. Many studies have demonstrated building cooling-energy savings in excess of 20% upon raising roof reflectivity from an existing 10-20% to about 60%. We estimate U.S. potential savings in excess of $1 billion (B) per year in net annual energy bills. Increasing albedo of urban surfaces can reduce the summertime urban temperature and improve the urban air quality. Increasing the urban albedo has the added benefit of reflecting more of the incoming global solar radiation and countering the effect of global warming. We estimate that increasing albedo of urban areas by 0.1 results in an increase of 3 x 10{sup -4} in Earth albedo. Using a simple global model, the change in air temperature in lowest 1.8 km of the atmosphere is estimated at 0.01K. Modelers predict a warming of about 3K in the next 60 years (0.05K/year). Change of 0.1 in urban albedo will result in 0.01K global cooling, a delay of {approx}0.2 years in global warming. This 0.2 years delay in global warming is equivalent to 10 Gt reduction in CO2 emissions.

  2. Phosphoproteomic analysis of the response of maize leaves to drought, heat and their combination stress

    PubMed Central

    Hu, Xiuli; Wu, Liuji; Zhao, Feiyun; Zhang, Dayong; Li, Nana; Zhu, Guohui; Li, Chaohao; Wang, Wei

    2015-01-01

    Drought and heat stress, especially their combination, greatly affect crop production. Many studies have described transcriptome, proteome and phosphoproteome changes in response of plants to drought or heat stress. However, the study about the phosphoproteomic changes in response of crops to the combination stress is scare. To understand the mechanism of maize responses to the drought and heat combination stress, phosphoproteomic analysis was performed on maize leaves by using multiplex iTRAQ-based quantitative proteomic and LC-MS/MS methods. Five-leaf-stage maize was subjected to drought, heat or their combination, and the leaves were collected. Globally, heat, drought and the combined stress significantly changed the phosphorylation levels of 172, 149, and 144 phosphopeptides, respectively. These phosphopeptides corresponded to 282 proteins. Among them, 23 only responded to the combined stress and could not be predicted from their responses to single stressors; 30 and 75 only responded to drought and heat, respectively. Notably, 19 proteins were phosphorylated on different sites in response to the single and combination stresses. Of the seven significantly enriched phosphorylation motifs identified, two were common for all stresses, two were common for heat and the combined stress, and one was specific to the combined stress. The signaling pathways in which the phosphoproteins were involved clearly differed among the three stresses. Functional characterization of the phosphoproteins and the pathways identified here could lead to new targets for the enhancement of crop stress tolerance, which will be particularly important in the face of climate change and the increasing prevalence of abiotic stressors. PMID:25999967

  3. Climate Effects of Global Land Cover Change

    SciTech Connect

    Gibbard, S G; Caldeira, K; Bala, G; Phillips, T; Wickett, M

    2005-08-24

    There are two competing effects of global land cover change on climate: an albedo effect which leads to heating when changing from grass/croplands to forest, and an evapotranspiration effect which tends to produce cooling. It is not clear which effect would dominate in a global land cover change scenario. We have performed coupled land/ocean/atmosphere simulations of global land cover change using the NCAR CAM3 atmospheric general circulation model. We find that replacement of current vegetation by trees on a global basis would lead to a global annual mean warming of 1.6 C, nearly 75% of the warming produced under a doubled CO{sub 2} concentration, while global replacement by grasslands would result in a cooling of 0.4 C. These results suggest that more research is necessary before forest carbon storage should be deployed as a mitigation strategy for global warming. In particular, high latitude forests probably have a net warming effect on the Earth's climate.

  4. Ecological effects of global change

    NASA Astrophysics Data System (ADS)

    Menzel, A.

    2010-03-01

    Mankind actually puts manifolds loads on our earth including stratospheric ozone depletion, rising freshwater use, changes of land cover and land use. For several of these threats, critical loads and thresholds may be already exceeded, e.g. nitrogen input, climate change and biodiversity loss (Röckström et al. 2009). The working group on Impacts, Adaptation and Vulnerability of the last IPCC report (AR4, 2007) concluded that anthropogenic warming over the last three decades has had a discernible influence on many physical and biological systems, thus global fingerprint of anthropogenic climate change was detectable on all continents and almost all ocean areas (Rosenzweig et al. 2007, 2008). 90% of the significant temperature related changes in 29000 records analysed were consistent with climate warming, e.g. in warming climates earlier spring events, distributional shifts pole wards and to higher altitudes, or community changes with reduced cold adapted species were observed. These impacts, already visible and only related to less than 1°C global warming, allow a limited glance at future changes and pressures on our ecosystems, as the rate of warming may accelerate and will be linked to stronger and more frequent extreme events. Vegetation is an important component of the climate system, part of biogeochemical cycles and the lower boundary of GCMs characterised by certain albedo and roughness. Thus, climate change impacts on vegetation exert feedbacks. The most striking and challenging problems in analysing climate change impacts on ecosystems are related to cases where one would expect major changes due to warming however there is reduced, limited or no reaction in the observed systems. This feature is known as divergence problem in tree ring research, called resilience in ecosystem dynamics or might be simply a time-lag or environmental monitoring problem. However, there are various other pressures by global change, e.g. land use change or pollution, leading

  5. The use of elemental mass spectrometry in phosphoproteomic applications.

    PubMed

    Maes, Evelyne; Tirez, Kristof; Baggerman, Geert; Valkenborg, Dirk; Schoofs, Liliane; Encinar, Jorge Ruiz; Mertens, Inge

    2016-01-01

    Reversible phosphorylation is one of the most important post-translational modifications in mammalian cells. Because this molecular switch is an important mechanism that diversifies and regulates proteins in cellular processes, knowledge about the extent and quantity of phosphorylation is very important to understand the complex cellular interplay. Although phosphoproteomics strategies are applied worldwide, they mainly include only molecular mass spectrometry (like MALDI or ESI)-based experiments. Although identification and relative quantification of phosphopeptides is straightforward with these techniques, absolute quantification is more complex and usually requires for specific isotopically phosphopeptide standards. However, the use of elemental mass spectrometry, and in particular inductively coupled plasma mass spectrometry (ICP-MS), in phosphoproteomics-based experiments, allow one to absolutely quantify phosphopeptides. Here, these phosphoproteomic applications with ICP-MS as elemental detector are reviewed. Pioneering work and recent developments in the field are both described. Additionally, the advantage of the parallel use of molecular and elemental mass spectrometry is stressed. PMID:25139451

  6. Quantitative phosphoproteomics of murine Fmr1-KO cell lines provides new insights into FMRP-dependent signal transduction mechanisms.

    PubMed

    Matic, Katarina; Eninger, Timo; Bardoni, Barbara; Davidovic, Laetitia; Macek, Boris

    2014-10-01

    Fragile X mental retardation protein (FMRP) is an RNA-binding protein that has a major effect on neuronal protein synthesis. Transcriptional silencing of the FMR1 gene leads to loss of FMRP and development of Fragile X syndrome (FXS), the most common known hereditary cause of intellectual impairment and autism. Here we utilize SILAC-based quantitative phosphoproteomics to analyze murine FMR1(-) and FMR1(+) fibroblastic cell lines derived from FMR1-KO embryos to identify proteins and phosphorylation sites dysregulated as a consequence of FMRP loss. We quantify FMRP-related changes in the levels of 5,023 proteins and 6,133 phosphorylation events and map them onto major signal transduction pathways. Our study confirms global downregulation of the MAPK/ERK pathway and decrease in phosphorylation level of ERK1/2 in the absence of FMRP, which is connected to attenuation of long-term potentiation. We detect differential expression of several key proteins from the p53 pathway, pointing to the involvement of p53 signaling in dysregulated cell cycle control in FXS. Finally, we detect differential expression and phosphorylation of proteins involved in pre-mRNA processing and nuclear transport, as well as Wnt and calcium signaling, such as PLC, PKC, NFAT, and cPLA2. We postulate that calcium homeostasis is likely affected in molecular pathogenesis of FXS. PMID:25168779

  7. Phosphoproteomic analysis of Methanohalophilus portucalensis FDF1(T) identified the role of protein phosphorylation in methanogenesis and osmoregulation.

    PubMed

    Wu, Wan-Ling; Lai, Shu-Jung; Yang, Jhih-Tian; Chern, Jeffy; Liang, Suh-Yuen; Chou, Chi-Chi; Kuo, Chih-Horng; Lai, Mei-Chin; Wu, Shih-Hsiung

    2016-01-01

    Methanogens have gained much attention for their metabolic product, methane, which could be an energy substitute but also contributes to the greenhouse effect. One factor that controls methane emission, reversible protein phosphorylation, is a crucial signaling switch, and phosphoproteomics has become a powerful tool for large-scale surveying. Here, we conducted the first phosphorylation-mediated regulation study in halophilic Methanohalophilus portucalensis FDF1(T), a model strain for studying stress response mechanisms in osmoadaptation. A shotgun approach and MS-based analysis identified 149 unique phosphoproteins. Among them, 26% participated in methanogenesis and osmolytes biosynthesis pathways. Of note, we uncovered that protein phosphorylation might be a crucial factor to modulate the pyrrolysine (Pyl) incorporation and Pyl-mediated methylotrophic methanogenesis. Furthermore, heterologous expression of glycine sarcosine N-methyltransferase (GSMT) mutant derivatives in the osmosensitive Escherichia coli MKH13 revealed that the nonphosphorylated T68A mutant resulted in increased salt tolerance. In contrast, mimic phosphorylated mutant T68D proved defective in both enzymatic activity and salinity tolerance for growth. Our study provides new insights into phosphorylation modification as a crucial role of both methanogenesis and osmoadaptation in methanoarchaea, promoting biogas production or reducing future methane emission in response to global warming and climate change. PMID:27357474

  8. Phosphoproteomic analysis of Methanohalophilus portucalensis FDF1T identified the role of protein phosphorylation in methanogenesis and osmoregulation

    PubMed Central

    Wu, Wan-Ling; Lai, Shu-Jung; Yang, Jhih-Tian; Chern, Jeffy; Liang, Suh-Yuen; Chou, Chi-Chi; Kuo, Chih-Horng; Lai, Mei-Chin; Wu, Shih-Hsiung

    2016-01-01

    Methanogens have gained much attention for their metabolic product, methane, which could be an energy substitute but also contributes to the greenhouse effect. One factor that controls methane emission, reversible protein phosphorylation, is a crucial signaling switch, and phosphoproteomics has become a powerful tool for large-scale surveying. Here, we conducted the first phosphorylation-mediated regulation study in halophilic Methanohalophilus portucalensis FDF1T, a model strain for studying stress response mechanisms in osmoadaptation. A shotgun approach and MS-based analysis identified 149 unique phosphoproteins. Among them, 26% participated in methanogenesis and osmolytes biosynthesis pathways. Of note, we uncovered that protein phosphorylation might be a crucial factor to modulate the pyrrolysine (Pyl) incorporation and Pyl-mediated methylotrophic methanogenesis. Furthermore, heterologous expression of glycine sarcosine N-methyltransferase (GSMT) mutant derivatives in the osmosensitive Escherichia coli MKH13 revealed that the nonphosphorylated T68A mutant resulted in increased salt tolerance. In contrast, mimic phosphorylated mutant T68D proved defective in both enzymatic activity and salinity tolerance for growth. Our study provides new insights into phosphorylation modification as a crucial role of both methanogenesis and osmoadaptation in methanoarchaea, promoting biogas production or reducing future methane emission in response to global warming and climate change. PMID:27357474

  9. Quantitative analysis of changes in the phosphoproteome of maize induced by the plant hormone salicylic acid

    PubMed Central

    Wu, Liuji; Hu, Xiuli; Wang, Shunxi; Tian, Lei; Pang, Yanjie; Han, Zanping; Wu, Liancheng; Chen, Yanhui

    2015-01-01

    Phytohormone salicylic acid (SA) plays an important role in regulating various physiological and biochemical processes. Our previous study identified several protein kinases responsive to SA, suggesting that phosphorylation events play an important role in the plant response to SA. In this study, we characterized the phosphoproteome of maize in response to SA using isotope tags for relative and absolute quantification (iTRAQ) technology and TiO2 enrichment method. Based on LC-MS/MS analysis, we found a total of 858 phosphoproteins among 1495 phosphopeptides. Among them, 291 phosphopeptides corresponding to 244 phosphoproteins were found to be significantly changed after SA treatment. The phosphoproteins identified are involved in a wide range of biological processes, which indicate that the response to SA encompasses a reformatting of major cellular processes. Furthermore, some of the phosphoproteins which were not previously known to be involved with SA were found to have significantly changed phosphorylation levels. Many of these changes are phosphorylation decreases, indicating that other currently unknown SA signaling pathways that result in decreased phosphorylation of downstream targets must be involved. Our study represents the first attempt at global phosphoproteome profiling in response to SA, and provides a better understanding of the molecular mechanisms regulated by SA. PMID:26659305

  10. Identification of Putative Mek1 Substrates during Meiosis in Saccharomyces cerevisiae Using Quantitative Phosphoproteomics

    PubMed Central

    Suhandynata, Raymond T.; Wan, Lihong; Zhou, Huilin; Hollingsworth, Nancy M.

    2016-01-01

    Meiotic recombination plays a key role in sexual reproduction as it generates crossovers that, in combination with sister chromatid cohesion, physically connect homologous chromosomes, thereby promoting their proper segregation at the first meiotic division. Meiotic recombination is initiated by programmed double strand breaks (DSBs) catalyzed by the evolutionarily conserved, topoisomerase-like protein Spo11. Repair of these DSBs is highly regulated to create crossovers between homologs that are distributed throughout the genome. This repair requires the presence of the mitotic recombinase, Rad51, as well as the strand exchange activity of the meiosis-specific recombinase, Dmc1. A key regulator of meiotic DSB repair in Saccharomyces cerevisiae is the meiosis-specific kinase Mek1, which promotes interhomolog strand invasion and is required for the meiotic recombination checkpoint and the crossover/noncrossover decision. Understanding how Mek1 regulates meiotic recombination requires the identification of its substrates. Towards that end, an unbiased phosphoproteomic approach utilizing Stable Isotope Labeling by Amino Acids in Cells (SILAC) was utilized to generate a list of potential Mek1 substrates, as well as proteins containing consensus phosphorylation sites for cyclin-dependent kinase, the checkpoint kinases, Mec1/Tel1, and the polo-like kinase, Cdc5. These experiments represent the first global phosphoproteomic dataset for proteins in meiotic budding yeast. PMID:27214570

  11. Identification of Putative Mek1 Substrates during Meiosis in Saccharomyces cerevisiae Using Quantitative Phosphoproteomics.

    PubMed

    Suhandynata, Raymond T; Wan, Lihong; Zhou, Huilin; Hollingsworth, Nancy M

    2016-01-01

    Meiotic recombination plays a key role in sexual reproduction as it generates crossovers that, in combination with sister chromatid cohesion, physically connect homologous chromosomes, thereby promoting their proper segregation at the first meiotic division. Meiotic recombination is initiated by programmed double strand breaks (DSBs) catalyzed by the evolutionarily conserved, topoisomerase-like protein Spo11. Repair of these DSBs is highly regulated to create crossovers between homologs that are distributed throughout the genome. This repair requires the presence of the mitotic recombinase, Rad51, as well as the strand exchange activity of the meiosis-specific recombinase, Dmc1. A key regulator of meiotic DSB repair in Saccharomyces cerevisiae is the meiosis-specific kinase Mek1, which promotes interhomolog strand invasion and is required for the meiotic recombination checkpoint and the crossover/noncrossover decision. Understanding how Mek1 regulates meiotic recombination requires the identification of its substrates. Towards that end, an unbiased phosphoproteomic approach utilizing Stable Isotope Labeling by Amino Acids in Cells (SILAC) was utilized to generate a list of potential Mek1 substrates, as well as proteins containing consensus phosphorylation sites for cyclin-dependent kinase, the checkpoint kinases, Mec1/Tel1, and the polo-like kinase, Cdc5. These experiments represent the first global phosphoproteomic dataset for proteins in meiotic budding yeast. PMID:27214570

  12. Quantitative phosphoproteomic analysis of early seed development in rice (Oryza sativa L.).

    PubMed

    Qiu, Jiehua; Hou, Yuxuan; Tong, Xiaohong; Wang, Yifeng; Lin, Haiyan; Liu, Qing; Zhang, Wen; Li, Zhiyong; Nallamilli, Babi R; Zhang, Jian

    2016-02-01

    Rice (Oryza sativa L.) seed serves as a major food source for over half of the global population. Though it has been long recognized that phosphorylation plays an essential role in rice seed development, the phosphorylation events and dynamics in this process remain largely unknown so far. Here, we report the first large scale identification of rice seed phosphoproteins and phosphosites by using a quantitative phosphoproteomic approach. Thorough proteomic studies in pistils and seeds at 3, 7 days after pollination resulted in the successful identification of 3885, 4313 and 4135 phosphopeptides respectively. A total of 2487 proteins were differentially phosphorylated among the three stages, including Kip related protein 1, Rice basic leucine zipper factor 1, Rice prolamin box binding factor and numerous other master regulators of rice seed development. Moreover, differentially phosphorylated proteins may be extensively involved in the biosynthesis and signaling pathways of phytohormones such as auxin, gibberellin, abscisic acid and brassinosteroid. Our results strongly indicated that protein phosphorylation is a key mechanism regulating cell proliferation and enlargement, phytohormone biosynthesis and signaling, grain filling and grain quality during rice seed development. Overall, the current study enhanced our understanding of the rice phosphoproteome and shed novel insight into the regulatory mechanism of rice seed development. PMID:26613898

  13. Overview of global greenhouse effects

    SciTech Connect

    Reck, R.A.

    1993-09-01

    This report reviews the factors that influence the evolution of climate and climate change. Recent studies have confirmed that CO{sub 2}, O{sub 3}, N{sub 2}O, CH{sub 4}, and chlorofluorocarbos are increasing in abundance in the atmosphere and can alter the radiation balance by means of the so-called greenhouse effect. The greenhouse effect is as well-accepted phenomenon, but the prediction of its consequences is much less certain. Attempts to detect a human-caused temperature change are still inconclusive. This report presents a discussion of the scientific basis for the greenhouse effect, its relationship to the abundances of greenhouse gases, and the evidence confirming the increases in the abundances. The basis for climate modeling is presented together with an example of the model outputs from one of the most sophisticated modeling efforts. Uncertainties in the present understanding of climate are outlined.

  14. Sperm phosphoproteomics: historical perspectives and current methodologies

    PubMed Central

    Porambo, James R; Salicioni, Ana M; Visconti, Pablo E; Platt, Mark D

    2013-01-01

    Mammalian sperm are differentiated germ cells that transfer genetic material from the male to the female. Owing to this essential role in the reproductive process, an understanding of the complex mechanisms that underlie sperm function has implications ranging from the development of novel contraceptives to the treatment of male infertility. While the importance of phosphorylation in sperm differentiation, maturation and fertilization has been well established, the ability to directly determine the sites of phosphorylation within sperm proteins and to quantitate the extent of phosphorylation at these sites is a recent development that has relied almost exclusively on advances in the field of proteomics. This review will summarize the work that has been carried out to date on sperm phosphoproteomics and discuss how the resulting qualitative and quantitative information has been used to provide insight into the manner in which protein phosphorylation events modulate sperm function. The authors also present the proteomics process as it is most often utilized for the elucidation of protein expression, with a particular emphasis on the way in which the process has been modified for the analysis of protein phosphorylation in sperm. PMID:23194270

  15. Structural insight into effector proteins of Gram-negative bacterial pathogens that modulate the phosphoproteome of their host

    PubMed Central

    Grishin, Andrey M; Beyrakhova, Ksenia A; Cygler, Miroslaw

    2015-01-01

    Invading pathogens manipulate cellular process of the host cell to establish a safe replicative niche. To this end they secrete a spectrum of proteins called effectors that modify cellular environment through a variety of mechanisms. One of the most important mechanisms is the manipulation of cellular signaling through modifications of the cellular phosphoproteome. Phosphorylation/dephosphorylation plays a pivotal role in eukaryotic cell signaling, with ∼500 different kinases and ∼130 phosphatases in the human genome. Pathogens affect the phosphoproteome either directly through the action of bacterial effectors, and/or indirectly through downstream effects of host proteins modified by the effectors. Here we review the current knowledge of the structure, catalytic mechanism and function of bacterial effectors that modify directly the phosphorylation state of host proteins. These effectors belong to four enzyme classes: kinases, phosphatases, phospholyases and serine/threonine acetylases. PMID:25565677

  16. Potential effects on health of global warming

    SciTech Connect

    Haines, A. . Whittington Hospital); Parry, M. . Environmental Change Unit)

    1993-12-01

    Prediction of the impacts of global climate change on health is complicated by a number of factors. These include: the difficulty in predicting regional changes in climate, the capacity for adaptation to climate change, the interactions between the effects of global climate change and a number of other key determinants of health, including population growth and poverty, and the availability of adequate preventive and curative facilities for diseases that may be effected by climate change. Nevertheless, it is of importance to consider the potential health impacts of global climate change for a number of reasons. It is also important to monitor diseases which could be effected by climate change in order to detect changes in incidence as early as possible and study possible interactions with other factors. It seems likely that the possible impacts on health of climate change will be a major determinant of the degree to which policies aimed at reducing global warming are followed, as perceptions of the effect of climate change to human health and well-being are particularly likely to influence public opinion. The potential health impacts of climate change can be divided into direct (primary) and indirect (secondary and tertiary) effects. Primary effects are those related to the effect of temperature on human well-being and disease. Secondary effects include the impacts on health of changes in food production, availability of water and of sea level rise. A tertiary level of impacts can also be hypothesized.

  17. Phosphoproteomics Analysis of Endometrium in Women with or without Endometriosis

    PubMed Central

    Xu, Hong-Mei; Deng, Hai-Teng; Liu, Chong-Dong; Chen, Yu-Ling; Zhang, Zhen-Yu

    2015-01-01

    Background: The molecular mechanisms underlying the endometriosis are still not completely understood. In order to test the hypothesis that the approaches in phosphoproteomics might contribute to the identification of key biomarkers to assess disease pathogenesis and drug targets, we carried out a phosphoproteomics analysis of human endometrium. Methods: A large-scale differential phosphoproteome analysis, using peptide enrichment of titanium dioxide purify and sequential elution from immobilized metal affinity chromatography with linear trap quadrupole-tandem mass spectrometry, was performed in endometrium tissues from 8 women with or without endometriosis. Results: The phosphorylation profiling of endometrium from endometriosis patients had been obtained, and found that identified 516 proteins were modified at phosphorylation level during endometriosis. Gene ontology annotation analysis showed that these proteins were enriched in cellular processes of binding and catalytic activity. Further pathway analysis showed that ribosome pathway and focal adhesion pathway were the top two pathways, which might be deregulated during the development of endometriosis. Conclusions: That large-scale phosphoproteome quantification has been successfully identified in endometrium tissues of women with or without endometriosis will provide new insights to understand the molecular mechanisms of the development of endometriosis. PMID:26415800

  18. Characterization of the Phosphoproteome in SLE Patients

    PubMed Central

    Huang, Jianrong; Dai, Yong

    2012-01-01

    Protein phosphorylation is a complex regulatory event that is involved in the signaling networks that affect virtually every cellular process. The protein phosphorylation may be a novel source for discovering biomarkers and drug targets. However, a systematic analysis of the phosphoproteome in patients with SLE has not been performed. To clarify the pathogenesis of systemic lupus erythematosus (SLE), we compared phosphoprotein expression in PBMCs from SLE patients and normal subjects using proteomics analyses. Phosphopeptides were enriched using TiO2 from PBMCs isolated from 15 SLE patients and 15 healthy subjects and then analyzed by automated LC-MS/MS analysis. Phosphorylation sites were identified and quantitated by MASCOT and MaxQuant. A total of 1035 phosphorylation sites corresponding to 618 NCBI-annotated genes were identified in SLE patients compared with normal subjects. Differentially expressed proteins, peptides and phosphorylation sites were then subjected to bioinformatics analyses. Gene ontology(GO) and pathway analyses showed that nucleic acid metabolism, cellular component organization, transport and multicellular organismal development pathways made up the largest proportions of the differentially expressed genes. Pathway analyses showed that the mitogen-activated protein kinase (MAPK) signaling pathway and actin cytoskeleton regulators made up the largest proportions of the metabolic pathways. Network analysis showed that rous sarcoma oncogene (SRC), v-rel reticuloendotheliosis viral oncogene homolog A (RELA), histone deacetylase (HDA1C) and protein kinase C, delta (PRKCD) play important roles in the stability of the network. These data suggest that aberrant protein phosphorylation may contribute to SLE pathogenesis. PMID:23285258

  19. Managerial Effectiveness in a Global Context.

    ERIC Educational Resources Information Center

    Leslie, Jean Brittain; Dalton, Maxine; Ernst, Christopher; Deal, Jennifer

    This report investigates characteristics of managers who work across the borders of multiple countries simultaneously. Chapter 1 sets the stage by introducing the work of global managers--what they do and how it is different from managerial work in a domestic context. Chapter 2 investigates the relationship of personality to effectiveness in a…

  20. GLOBAL CHANGE EFFECTS ON CORAL REEF CONDITION

    EPA Science Inventory

    Fisher, W., W. Davis, J. Campbell, L. Courtney, P. Harris, B. Hemmer, M. Parsons, B. Quarles and D. Santavy. In press. Global Change Effects on Coral Reef Condition (Abstract). To be presented at the EPA Science Forum: Healthy Communities and Ecosystems, 1-3 June 2004, Washington...

  1. Cloud effects on middle ultraviolet global radiation

    NASA Technical Reports Server (NTRS)

    Borkowski, J.; Chai, A.-T.; Mo, T.; Green, A. E. O.

    1977-01-01

    An Eppley radiometer and a Robertson-Berger sunburn meter are employed along with an all-sky camera setup to study cloud effects on middle ultraviolet global radiation at the ground level. Semiempirical equations to allow for cloud effects presented in previous work are compared with the experimental data. The study suggests a means of defining eigenvectors of cloud patterns and correlating them with the radiation at the ground level.

  2. HOPE-fixation of lung tissue allows retrospective proteome and phosphoproteome studies.

    PubMed

    Shevchuk, Olga; Abidi, Nada; Klawonn, Frank; Wissing, Josef; Nimtz, Manfred; Kugler, Christian; Steinert, Michael; Goldmann, Torsten; Jänsch, Lothar

    2014-11-01

    Hepes-glutamic acid buffer-mediated organic solvent protection effect (HOPE)-fixation has been introduced as an alternative to formalin fixation of clinical samples. Beyond preservation of morphological structures for histology, HOPE-fixation was demonstrated to be compatible with recent methods for RNA and DNA sequencing. However, the suitability of HOPE-fixed materials for the inspection of proteomes by mass spectrometry so far remained undefined. This is of particular interest, since proteins constitute a prime resource for drug research and can give valuable insights into the activity status of signaling pathways. In this study, we extracted proteins from human lung tissue and tested HOPE-treated and snap-frozen tissues comparatively by proteome and phosphoproteome analyses. High confident data from accurate mass spectrometry allowed the identification of 2603 proteins and 3036 phosphorylation sites. HOPE-fixation did not hinder the representative extraction of proteins, and investigating their biochemical properties, covered subcellular localizations, and cellular processes revealed no bias caused by the type of fixation. In conclusion, proteome as well as phosphoproteome data of HOPE lung samples were qualitatively equivalent to results obtained from snap-frozen tissues. Thus, HOPE-treated tissues match clinical demands in both histology and retrospective proteome analyses of patient samples by proteomics. PMID:24702127

  3. The G Protein-Coupled Estrogen Receptor Agonist G-1 Inhibits Nuclear Estrogen Receptor Activity and Stimulates Novel Phosphoproteomic Signatures.

    PubMed

    Smith, L Cody; Ralston-Hooper, Kimberly J; Ferguson, P Lee; Sabo-Attwood, Tara

    2016-06-01

    Estrogen exerts cellular effects through both nuclear (ESR1 and ESR2) and membrane-bound estrogen receptors (G-protein coupled estrogen receptor, GPER); however, it is unclear if they act independently or engage in crosstalk to influence hormonal responses. To investigate each receptor's role in proliferation, transcriptional activation, and protein phosphorylation in breast cancer cells (MCF-7), we employed selective agonists for ESR1 propyl-pyrazole-triol (PPT), ESR2 diarylpropionitrile (DPN), and GPER (G-1) and also determined the impact of xenoestrogens bisphenol-A (BPA) and genistein on these effects. As anticipated, 17β-estradiol (E2), PPT, DPN, BPA, and genistein each enhanced proliferation and activation of an ERE-driven reporter gene whereas G-1 had no significant impact. However, G-1 significantly reduced E2-, PPT-, DPN-, BPA-, and genistein-induced proliferation and ERE activation at doses greater than 500 nM indicating that G-1 mediated inhibition is not ESR isotype specific. As membrane receptors initiate cascades of phosphorylation events, we performed a global phosphoproteomic analysis on cells exposed to E2 or G-1 to identify potential targets of receptor crosstalk via downstream protein phosphorylation targets. Of the 211 phosphorylated proteins identified, 40 and 13 phosphoproteins were specifically modified by E2 and G-1, respectively. Subnetwork enrichment analysis revealed several processes related to cell cycle were specifically enriched by G-1 compared with E2. Further there existed a number of newly identified proteins that were specifically phosphorylated by G-1. These phosphorylation networks highlight specific proteins that may modulate the inhibitory effects of G-1 and suggest a novel role for interference with nuclear receptor activity driven by E2 and xenoestrogens. PMID:27026707

  4. Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer.

    PubMed

    Drake, Justin M; Paull, Evan O; Graham, Nicholas A; Lee, John K; Smith, Bryan A; Titz, Bjoern; Stoyanova, Tanya; Faltermeier, Claire M; Uzunangelov, Vladislav; Carlin, Daniel E; Fleming, Daniel Teo; Wong, Christopher K; Newton, Yulia; Sudha, Sud; Vashisht, Ajay A; Huang, Jiaoti; Wohlschlegel, James A; Graeber, Thomas G; Witte, Owen N; Stuart, Joshua M

    2016-08-11

    We used clinical tissue from lethal metastatic castration-resistant prostate cancer (CRPC) patients obtained at rapid autopsy to evaluate diverse genomic, transcriptomic, and phosphoproteomic datasets for pathway analysis. Using Tied Diffusion through Interacting Events (TieDIE), we integrated differentially expressed master transcriptional regulators, functionally mutated genes, and differentially activated kinases in CRPC tissues to synthesize a robust signaling network consisting of druggable kinase pathways. Using MSigDB hallmark gene sets, six major signaling pathways with phosphorylation of several key residues were significantly enriched in CRPC tumors after incorporation of phosphoproteomic data. Individual autopsy profiles developed using these hallmarks revealed clinically relevant pathway information potentially suitable for patient stratification and targeted therapies in late stage prostate cancer. Here, we describe phosphorylation-based cancer hallmarks using integrated personalized signatures (pCHIPS) that shed light on the diversity of activated signaling pathways in metastatic CRPC while providing an integrative, pathway-based reference for drug prioritization in individual patients. PMID:27499020

  5. Identification of kinase inhibitor targets in the lung cancer microenvironment by chemical and phosphoproteomics

    PubMed Central

    Gridling, Manuela; Ficarro, Scott B.; Breitwieser, Florian P.; Song, Lanxi; Parapatics, Katja; Colinge, Jacques; Haura, Eric B.; Marto, Jarrod A.; Superti-Furga, Giulio; Bennett, Keiryn L.; Rix, Uwe

    2014-01-01

    A growing number of gene mutations, which are recognized as cancer drivers, can be successfully targeted with drugs. The redundant and dynamic nature of oncogenic signaling networks and complex interactions between cancer cells and the microenvironment, however, can cause drug resistance. Whereas these challenges can be addressed by developing drug combinations or polypharmacology drugs, this benefits greatly from a detailed understanding of the proteome-wide target profiles. Using mass spectrometry-based chemical proteomics, we report the comprehensive characterization of the drug-protein interaction networks for the multikinase inhibitors dasatinib and sunitinib in primary lung cancer tissue specimens derived from patients. We observed in excess of 100 protein kinase targets plus various protein complexes involving, for instance, AMPK, TBK1 (sunitinib) and ILK (dasatinib). Importantly, comparison with lung cancer cell lines and mouse xenografts thereof showed that most targets were shared between cell lines and tissues. Several targets, however, were only present in tumor tissues. In xenografts, most of these proteins were of mouse origin suggesting that they originate from the tumor microenvironment. Furthermore, intersection with subsequent global phosphoproteomic analysis identified several activated signaling pathways. These included MAPK, immune and integrin signaling, which were affected by these drugs in both cancer cells and the microenvironment. Thus, the combination of chemical and phosphoproteomics can generate a systems view of proteins, complexes and signaling pathways that are simultaneously engaged by multi-targeted drugs in cancer cells and the tumor microenvironment. This may allow for the design of novel anticancer therapies that concurrently target multiple tumor compartments. PMID:25189542

  6. Phosphoproteomics analysis of a clinical Mycobacterium tuberculosis Beijing isolate: expanding the mycobacterial phosphoproteome catalog

    PubMed Central

    Fortuin, Suereta; Tomazella, Gisele G.; Nagaraj, Nagarjuna; Sampson, Samantha L.; Gey van Pittius, Nicolaas C.; Soares, Nelson C.; Wiker, Harald G.; de Souza, Gustavo A.; Warren, Robin M.

    2015-01-01

    Reversible protein phosphorylation, regulated by protein kinases and phosphatases, mediates a switch between protein activity and cellular pathways that contribute to a large number of cellular processes. The Mycobacterium tuberculosis genome encodes 11 Serine/Threonine kinases (STPKs) which show close homology to eukaryotic kinases. This study aimed to elucidate the phosphoproteomic landscape of a clinical isolate of M. tuberculosis. We performed a high throughput mass spectrometric analysis of proteins extracted from an early-logarithmic phase culture. Whole cell lysate proteins were processed using the filter-aided sample preparation method, followed by phosphopeptide enrichment of tryptic peptides by strong cation exchange (SCX) and Titanium dioxide (TiO2) chromatography. The MaxQuant quantitative proteomics software package was used for protein identification. Our analysis identified 414 serine/threonine/tyrosine phosphorylated sites, with a distribution of S/T/Y sites; 38% on serine, 59% on threonine and 3% on tyrosine; present on 303 unique peptides mapping to 214 M. tuberculosis proteins. Only 45 of the S/T/Y phosphorylated proteins identified in our study had been previously described in the laboratory strain H37Rv, confirming previous reports. The remaining 169 phosphorylated proteins were newly identified in this clinical M. tuberculosis Beijing strain. We identified 5 novel tyrosine phosphorylated proteins. These findings not only expand upon our current understanding of the protein phosphorylation network in clinical M. tuberculosis but the data set also further extends and complements previous knowledge regarding phosphorylated peptides and phosphorylation sites in M. tuberculosis. PMID:25713560

  7. Global charts of ocean tide loading effects

    SciTech Connect

    Francis, O.; Mazzega, P. )

    1990-07-15

    Global ocean tide loading charts of the radial displacement, the potential divided by g (gravity acceleration), and the gravity effect have been computed using the 11 constituents M{sub 2}, S{sub 2}, N{sub 2}, K{sub 2}K{sub 1}, O{sub 1}, P{sub 1}, Q{sub 1}, M{sub f}, M{sub m}, S{sub s a} of Schwiderski's tidal model. These new charts have a resolution of 1{degree}{times}1{degree} on the continents as well as on the oceanic area. A description of Farrell's convolution method to compute the loading effects is given, and an estimate of the numerical errors leads to the conclusion that these global charts have a precision better than 2.5% independent of the accuracy of Schwiderski's maps. The current approximation of the loading effects by a proportionality relation with the local oceanic tides is also compared with Farrell's convolution method. Departures of several centimeters systematically appear, in particular over the continental shelves. The authors then show that the maps of the oceanic tides deduced from satellite altimetry could be corrected for the loading effect by an iterative computational procedure based on their algorithm of Farrell's convolution.

  8. Global alliances effect in coalition forming

    NASA Astrophysics Data System (ADS)

    Vinogradova, Galina; Galam, Serge

    2014-11-01

    Coalition forming is investigated among countries, which are coupled with short range interactions, under the influence of externally-set opposing global alliances. The model extends a recent Natural Model of coalition forming inspired from Statistical Physics, where instabilities are a consequence of decentralized maximization of the individual benefits of actors. In contrast to physics where spins can only evaluate the immediate cost/benefit of a flip of orientation, countries have a long horizon of rationality, which associates with the ability to envision a way up to a better configuration even at the cost of passing through intermediate loosing states. The stabilizing effect is produced through polarization by the global alliances of either a particular unique global interest factor or multiple simultaneous ones. This model provides a versatile theoretical tool for the analysis of real cases and design of novel strategies. Such analysis is provided for several real cases including the Eurozone. The results shed a new light on the understanding of the complex phenomena of planned stabilization in the coalition forming.

  9. Effects of Global Warming on Vibrio Ecology.

    PubMed

    Vezzulli, Luigi; Pezzati, Elisabetta; Brettar, Ingrid; Höfle, Manfred; Pruzzo, Carla

    2015-06-01

    Vibrio-related infections are increasing worldwide both in humans and aquatic animals. Rise in global sea surface temperature (SST), which is approximately 1 °C higher now than 140 years ago and is one of the primary physical impacts of global warming, has been linked to such increases. In this chapter, major known effects of increasing SST on the biology and ecology of vibrios are described. They include the effects on bacterial growth rate, both in the field and in laboratory, culturability, expression of pathogenicity traits, and interactions with aquatic organisms and abiotic surfaces. Special emphasis is given to the effect of ocean warming on Vibrio interactions with zooplankters, which represent one of the most important aquatic reservoirs for these bacteria. The reported findings highlight the biocomplexity of the interactions between vibrios and their natural environment in a climate change scenario, posing the need for interdisciplinary studies to properly understand the connection between ocean warming and persistence and spread of vibrios in sea waters and the epidemiology of the diseases they cause. PMID:26185070

  10. Microscale Effects from Global Hot Plasma Imagery

    NASA Technical Reports Server (NTRS)

    Moore, T. E.; Fok, M.-C.; Perez, J. D.; Keady, J. P.

    1995-01-01

    We have used a three-dimensional model of recovery phase storm hot plasmas to explore the signatures of pitch angle distributions (PADS) in global fast atom imagery of the magnetosphere. The model computes mass, energy, and position-dependent PADs based on drift effects, charge exchange losses, and Coulomb drag. The hot plasma PAD strongly influences both the storm current system carried by the hot plasma and its time evolution. In turn, the PAD is strongly influenced by plasma waves through pitch angle diffusion, a microscale effect. We report the first simulated neutral atom images that account for anisotropic PADs within the hot plasma. They exhibit spatial distribution features that correspond directly to the PADs along the lines of sight. We investigate the use of image brightness distributions along tangent-shell field lines to infer equatorial PADS. In tangent-shell regions with minimal spatial gradients, reasonably accurate PADs are inferred from simulated images. They demonstrate the importance of modeling PADs for image inversion and show that comparisons of models with real storm plasma images will reveal the global effects of these microscale processes.

  11. Integrative Network Analysis Combined with Quantitative Phosphoproteomics Reveals Transforming Growth Factor-beta Receptor type-2 (TGFBR2) as a Novel Regulator of Glioblastoma Stem Cell Properties.

    PubMed

    Narushima, Yuta; Kozuka-Hata, Hiroko; Koyama-Nasu, Ryo; Tsumoto, Kouhei; Inoue, Jun-ichiro; Akiyama, Tetsu; Oyama, Masaaki

    2016-03-01

    Glioblastoma is one of the most malignant brain tumors with poor prognosis and their development and progression are known to be driven by glioblastoma stem cells. Although glioblastoma stem cells lose their cancer stem cell properties during cultivation in serum-containing medium, little is known about the molecular mechanisms regulating signaling alteration in relation to reduction of stem cell-like characteristics. To elucidate the global phosphorylation-related signaling events, we performed a SILAC-based quantitative phosphoproteome analysis of serum-induced dynamics in glioblastoma stem cells established from the tumor tissues of the patient. Among a total of 2876 phosphorylation sites on 1584 proteins identified in our analysis, 732 phosphorylation sites on 419 proteins were regulated through the alteration of stem cell-like characteristics. The integrative computational analyses based on the quantified phosphoproteome data revealed the relevant changes of phosphorylation levels regarding the proteins associated with cytoskeleton reorganization such as Rho family GTPase and Intermediate filament signaling, in addition to transforming growth factor-β receptor type-2 (TGFBR2) as a prominent upstream regulator involved in the serum-induced phosphoproteome regulation. The functional association of transforming growth factor-β receptor type-2 with stem cell-like properties was experimentally validated through signaling perturbation using the corresponding inhibitors, which indicated that transforming growth factor-β receptor type-2 could play an important role as a novel cell fate determinant in glioblastoma stem cell regulation. PMID:26670566

  12. Comparative Ser/Thr/Tyr phosphoproteomics between two mycobacterial species: the fast growing Mycobacterium smegmatis and the slow growing Mycobacterium bovis BCG

    PubMed Central

    Nakedi, Kehilwe C.; Nel, Andrew J. M.; Garnett, Shaun; Blackburn, Jonathan M.; Soares, Nelson C.

    2015-01-01

    Ser/Thr/Tyr protein phosphorylation plays a critical role in regulating mycobacterial growth and development. Understanding the mechanistic link between protein phosphorylation signaling network and mycobacterial growth rate requires a global view of the phosphorylation events taking place at a given time under defined conditions. In the present study we employed a phosphopeptide enrichment and high throughput mass spectrometry-based strategy to investigate and qualitatively compare the phosphoproteome of two mycobacterial model organisms: the fast growing Mycobacterium smegmatis and the slow growing Mycobacterium bovis BCG. Cells were harvested during exponential phase and our analysis detected a total of 185 phospho-sites in M. smegmatis, of which 106 were confidently localized [localization probability (LP) = 0.75; PEP = 0.01]. By contrast, in M. bovis BCG the phosphoproteome comprised 442 phospho-sites, of which 289 were confidently localized. The percentage distribution of Ser/Thr/Tyr phosphorylation was 39.47, 57.02, and 3.51% for M. smegmatis and 35, 61.6, and 3.1% for M. bovis BCG. Moreover, our study identified a number of conserved Ser/Thr phosphorylated sites and conserved Tyr phosphorylated sites across different mycobacterial species. Overall a qualitative comparison of the fast and slow growing mycobacteria suggests that the phosphoproteome of M. smegmatis is a simpler version of that of M. bovis BCG. In particular, M. bovis BCG exponential cells exhibited a much more complex and sophisticated protein phosphorylation network regulating important cellular cycle events such as cell wall biosynthesis, elongation, cell division including immediately response to stress. The differences in the two phosphoproteomes are discussed in light of different mycobacterial growth rates. PMID:25904896

  13. Comparative Ser/Thr/Tyr phosphoproteomics between two mycobacterial species: the fast growing Mycobacterium smegmatis and the slow growing Mycobacterium bovis BCG.

    PubMed

    Nakedi, Kehilwe C; Nel, Andrew J M; Garnett, Shaun; Blackburn, Jonathan M; Soares, Nelson C

    2015-01-01

    Ser/Thr/Tyr protein phosphorylation plays a critical role in regulating mycobacterial growth and development. Understanding the mechanistic link between protein phosphorylation signaling network and mycobacterial growth rate requires a global view of the phosphorylation events taking place at a given time under defined conditions. In the present study we employed a phosphopeptide enrichment and high throughput mass spectrometry-based strategy to investigate and qualitatively compare the phosphoproteome of two mycobacterial model organisms: the fast growing Mycobacterium smegmatis and the slow growing Mycobacterium bovis BCG. Cells were harvested during exponential phase and our analysis detected a total of 185 phospho-sites in M. smegmatis, of which 106 were confidently localized [localization probability (LP) = 0.75; PEP = 0.01]. By contrast, in M. bovis BCG the phosphoproteome comprised 442 phospho-sites, of which 289 were confidently localized. The percentage distribution of Ser/Thr/Tyr phosphorylation was 39.47, 57.02, and 3.51% for M. smegmatis and 35, 61.6, and 3.1% for M. bovis BCG. Moreover, our study identified a number of conserved Ser/Thr phosphorylated sites and conserved Tyr phosphorylated sites across different mycobacterial species. Overall a qualitative comparison of the fast and slow growing mycobacteria suggests that the phosphoproteome of M. smegmatis is a simpler version of that of M. bovis BCG. In particular, M. bovis BCG exponential cells exhibited a much more complex and sophisticated protein phosphorylation network regulating important cellular cycle events such as cell wall biosynthesis, elongation, cell division including immediately response to stress. The differences in the two phosphoproteomes are discussed in light of different mycobacterial growth rates. PMID:25904896

  14. Kinetic effects on global Alfven waves

    SciTech Connect

    Betti, R.

    1992-01-01

    A theoretical investigation is carried out on the effects of the kinetic particle response on global type shear-Alfven waves in tokamaks. Two kinds of wave-particle interactions have been identified: (1) resonant interaction between energetic circulating particles and high frequency Alfven waves, (2) nonresonant interaction between trapped particles and low frequency modes. The author focuses on gap modes which are discrete modes whose real frequency lies in gas of the Alfven continuum induced by geometrical effects. A new gap mode, the Ellipticity Induced Alfven Eigenmode (EAE), is induced by the ellipticity of the plasma cross section that couples the m and m + 2 poloidal harmonics. This mode is of the general class as the Toroidicity Induced Alfven Eigenmode (TAE). In configurations with finite ellipticity, the EAE (n; m, m + 2) has a global structure centered about the q = (m + 1)/n surface. In the presence of an energetic ion species any Alfven wave can be destabilized via transit resonance with circulating particles. A sufficient stability criterion is derived for energetic particle-Alfven mode. To include the stabilizing effects of the electron and ion Landau damping a general treatment using a newly derived drift kinetic description of each species is carried out. The analysis has been restricted to Alfven gap modes. Low frequency modes have been investigated using the new drift kinetic model. Focusing on the internal kink mode, the main kinetic contributions arises from trapped particles which process in the toroidal direction. The trapped bulk ions can destabilize the high frequency branch of the internal kink. The numerical solution of the dispersion relation shows that a sharp threshold in [beta][sub p] exists for the instability to grow and that stabilizing effects come from the trapped electron response.

  15. Label-free quantitative phosphoproteomic analysis reveals differentially regulated proteins and pathway in PRRSV-infected pulmonary alveolar macrophages.

    PubMed

    Luo, Rui; Fang, Liurong; Jin, Hui; Wang, Dang; An, Kang; Xu, Ningzhi; Chen, Huanchun; Xiao, Shaobo

    2014-03-01

    Porcine reproductive and respiratory syndrome virus (PRRSV) is an important pathogen of swine worldwide and causes significant economic losses. Through regulating the host proteins phosphorylation, PRRSV was found to manipulate the activities of several signaling molecules to regulate innate immune responses. However, the role of protein phosphorylation during PRRSV infection and the signal pathways responsible for it are relatively unknown. Here liquid chromatography-tandem mass spectrometry for label-free quantitative phosphoproteomics was applied to systematically investigate the global phosphorylation events in PRRSV-infected pulmonary alveolar macrophages. In total, we identified 2125 unique phosphosites, of which the phosphorylation level of 292 phosphosites on 242 proteins and 373 phosphosites on 249 proteins was significantly altered at 12 and 36 h pi, respectively. The phosphoproteomics data were analyzed using ingenuity pathways analysis to identify defined canonical pathways and functional networks. Pathway analysis revealed that PRRSV-induced inflammatory cytokines production was probably due to the activation of mitogen-activated protein kinase and NF-κB signal pathway, which were regulated by several protein kinases during virus infection. Interacting network analysis indicated that altered phosphoproteins were involved in cellular assembly and organization, protein synthesis, molecular transport, and signal transduction in PRRSV infected cells. These pathways and functional networks analysis could provide direct insights into the biological significance of phosphorylation events modulated by PRRSV and may help us elucidate the pathogenic mechanisms of PRRSV infection. PMID:24533505

  16. Development of the affinity materials for phosphorylated proteins/peptides enrichment in phosphoproteomics analysis.

    PubMed

    Wang, Zhi-Gang; Lv, Nan; Bi, Wen-Zhi; Zhang, Ji-Lin; Ni, Jia-Zuan

    2015-04-29

    Reversible protein phosphorylation is a key event in numerous biological processes. Mass spectrometry (MS) is the most powerful analysis tool in modern phosphoproteomics. However, the direct MS analysis of phosphorylated proteins/peptides is still a big challenge because of the low abundance and insufficient ionization of phosphorylated proteins/peptides as well as the suppression effects of nontargets. Enrichment of phosphorylated proteins/peptides by affinity materials from complex biosamples is the most widely used strategy to enhance the MS detection. The demand of efficiently enriching phosphorylated proteins/peptides has spawned diverse affinity materials based on different enrichment principles (e.g., electronic attraction, chelating). In this review, we summarize the recent development of various affinity materials for phosphorylated proteins/peptides enrichment. We will highlight the design and fabrication of these affinity materials, discuss the enrichment mechanisms involved in different affinity materials, and suggest the future challenges and research directions in this field. PMID:25845677

  17. Automated Immobilized Metal Affinity Chromatography System for Enrichment of Escherichia coli Phosphoproteome

    SciTech Connect

    Qu, Yi; Wu, Si; Zhao, Rui; Zink, Erika M.; Orton, Daniel J.; Moore, Ronald J.; Meng, Da; Clauss, Therese RW; Aldrich, Joshua T.; Lipton, Mary S.; Pasa-Tolic, Ljiljana

    2013-06-05

    Enrichment of bacterial phosphopeptides is an essential step prior to bottom-up mass spectrometry-based analysis of the phosphoproteome, which is fundamental to understanding the role of phosphoproteins in cell signaling and regulation of protein activity. We developed an automated IMAC system to enrich strong cation exchange-fractionated phosphopeptides from the soluble proteome of Escherichia coli MG1655 grown on minimal medium. Initial demonstration of the system resulted in identification of 75 phosphopeptides covering 52 phosphoproteins. Consistent with previous studies, many of these phosphoproteins are involved in the carbohydrate portion of central metabolism. The automated system utilizes a large capacity IMAC column that can effectively enrich phosphopeptides from a bacterial sample by increasing peptide loading and reducing the wash time. An additional benefit of the automated IMAC system is reduced labor and associated costs.

  18. Systematic Analysis of Protein Phosphorylation Networks From Phosphoproteomic Data*

    PubMed Central

    Song, Chunxia; Ye, Mingliang; Liu, Zexian; Cheng, Han; Jiang, Xinning; Han, Guanghui; Songyang, Zhou; Tan, Yexiong; Wang, Hongyang; Ren, Jian; Xue, Yu; Zou, Hanfa

    2012-01-01

    In eukaryotes, hundreds of protein kinases (PKs) specifically and precisely modify thousands of substrates at specific amino acid residues to faithfully orchestrate numerous biological processes, and reversibly determine the cellular dynamics and plasticity. Although over 100,000 phosphorylation sites (p-sites) have been experimentally identified from phosphoproteomic studies, the regulatory PKs for most of these sites still remain to be characterized. Here, we present a novel software package of iGPS for the prediction of in vivo site-specific kinase-substrate relations mainly from the phosphoproteomic data. By critical evaluations and comparisons, the performance of iGPS is satisfying and better than other existed tools. Based on the prediction results, we modeled protein phosphorylation networks and observed that the eukaryotic phospho-regulation is poorly conserved at the site and substrate levels. With an integrative procedure, we conducted a large-scale phosphorylation analysis of human liver and experimentally identified 9719 p-sites in 2998 proteins. Using iGPS, we predicted a human liver protein phosphorylation networks containing 12,819 potential site-specific kinase-substrate relations among 350 PKs and 962 substrates for 2633 p-sites. Further statistical analysis and comparison revealed that 127 PKs significantly modify more or fewer p-sites in the liver protein phosphorylation networks against the whole human protein phosphorylation network. The largest data set of the human liver phosphoproteome together with computational analyses can be useful for further experimental consideration. This work contributes to the understanding of phosphorylation mechanisms at the systemic level, and provides a powerful methodology for the general analysis of in vivo post-translational modifications regulating sub-proteomes. PMID:22798277

  19. Targeted Phosphoproteome Analysis Using Selected/Multiple Reaction Monitoring (SRM/MRM).

    PubMed

    Adachi, Jun; Narumi, Ryohei; Tomonaga, Takeshi

    2016-01-01

    Mass spectrometry-based phosphoproteomics has been rapidly spread based on the advancement of mass spectrometry and development of efficient enrichment techniques for phosphorylated proteins or peptides. Non-targeted approach has been employed in most of the studies for phosphoproteome analysis. However, targeted approach using selected/multiple reaction monitoring (SRM/MRM) is an indispensible technique used for the quantitation of known targets especially when we have many samples to quantitate phosphorylation events on proteins in biological or clinical samples. We herein describe the application of a large-scale phosphoproteome analysis and SRM-based quantitation for the systematic discovery and validation of biomarkers. PMID:26700043

  20. Brief Isoflurane Anesthesia Produces Prominent Phosphoproteomic Changes in the Adult Mouse Hippocampus.

    PubMed

    Kohtala, Samuel; Theilmann, Wiebke; Suomi, Tomi; Wigren, Henna-Kaisa; Porkka-Heiskanen, Tarja; Elo, Laura L; Rokka, Anne; Rantamäki, Tomi

    2016-06-15

    Anesthetics are widely used in medical practice and experimental research, yet the neurobiological basis governing their effects remains obscure. We have here used quantitative phosphoproteomics to investigate the protein phosphorylation changes produced by a 30 min isoflurane anesthesia in the adult mouse hippocampus. Altogether 318 phosphorylation alterations in total of 237 proteins between sham and isoflurane anesthesia were identified. Many of the hit proteins represent primary pharmacological targets of anesthetics. However, findings also enlighten the role of several other proteins-implicated in various biological processes including neuronal excitability, brain energy homeostasis, synaptic plasticity and transmission, and microtubule function-as putative (secondary) targets of anesthetics. In particular, isoflurane increases glycogen synthase kinase-3β (GSK3β) phosphorylation at the inhibitory Ser(9) residue and regulates the phosphorylation of multiple proteins downstream and upstream of this promiscuous kinase that regulate diverse biological functions. Along with confirmatory Western blot data for GSK3β and p44/42-MAPK (mitogen-activated protein kinase; reduced phosphorylation of the activation loop), we observed increased phosphorylation of microtubule-associated protein 2 (MAP2) on residues (Thr(1620,1623)) that have been shown to render its dissociation from microtubules and alterations in microtubule stability. We further demonstrate that diverse anesthetics (sevoflurane, urethane, ketamine) produce essentially similar phosphorylation changes on GSK3β, p44/p42-MAPK, and MAP2 as observed with isoflurane. Altogether our study demonstrates the potential of quantitative phosphoproteomics to study the mechanisms of anesthetics (and other drugs) in the mammalian brain and reveals how already a relatively brief anesthesia produces pronounced phosphorylation changes in multiple proteins in the central nervous system. PMID:27074656

  1. Quantitative phosphoproteomics in nuclei of vasopressin-sensitive renal collecting duct cells

    PubMed Central

    Bolger, Steven J.; Hurtado, Patricia A. Gonzales; Hoffert, Jason D.; Saeed, Fahad; Pisitkun, Trairak

    2012-01-01

    Vasopressin regulates transport across the collecting duct epithelium in part via effects on gene transcription. Transcriptional regulation occurs partially via changes in phosphorylation of transcription factors, transcriptional coactivators, and protein kinases in the nucleus. To test whether vasopressin alters the nuclear phosphoproteome of vasopressin-sensitive cultured mouse mpkCCD cells, we used stable isotope labeling and mass spectrometry to quantify thousands of phosphorylation sites in nuclear extracts and nuclear pellet fractions. Measurements were made in the presence and absence of the vasopressin analog dDAVP. Of the 1,251 sites quantified, 39 changed significantly in response to dDAVP. Network analysis of the regulated proteins revealed two major clusters (“cell-cell adhesion” and “transcriptional regulation”) that were connected to known elements of the vasopressin signaling pathway. The hub proteins for these two clusters were the transcriptional coactivator β-catenin and the transcription factor c-Jun. Phosphorylation of β-catenin at Ser552 was increased by dDAVP [log2(dDAVP/vehicle) = 1.79], and phosphorylation of c-Jun at Ser73 was decreased [log2(dDAVP/vehicle) = −0.53]. The β-catenin site is known to be targeted by either protein kinase A or Akt, both of which are activated in response to vasopressin. The c-Jun site is a canonical target for the MAP kinase Jnk2, which is downregulated in response to vasopressin in the collecting duct. The data support the idea that vasopressin-mediated control of transcription in collecting duct cells involves selective changes in the nuclear phosphoproteome. All data are available to users at http://helixweb.nih.gov/ESBL/Database/mNPPD/. PMID:22992673

  2. Acceptance Effects in the Hyperons Global Polarization Measurement

    SciTech Connect

    Selyuzhenkov, Ilya

    2006-11-17

    The possible sources of systematic uncertainties in the hyperons global polarization measurement are discussed. The equation with detector acceptance effects taken into account is provided. Contribution of the hyperons directed flow into the hyperons global polarization measurement is shown. The systematic uncertainties of the {lambda} hyperons global polarization measurement in Au+Au collisions with the STAR detector at RHIC are calculated.

  3. Radiative effects of global MODIS cloud regimes

    NASA Astrophysics Data System (ADS)

    Oreopoulos, Lazaros; Cho, Nayeong; Lee, Dongmin; Kato, Seiji

    2016-03-01

    We update previously published Moderate Resolution Imaging Spectroradiometer (MODIS) global cloud regimes (CRs) using the latest MODIS cloud retrievals in the Collection 6 data set. We implement a slightly different derivation method, investigate the composition of the regimes, and then proceed to examine several aspects of CR radiative appearance with the aid of various radiative flux data sets. Our results clearly show that the CRs are radiatively distinct in terms of shortwave, longwave, and their combined (total) cloud radiative effect. We show that we can clearly distinguish regimes based on whether they radiatively cool or warm the atmosphere, and thanks to radiative heating profiles, to discern the vertical distribution of cooling and warming. Terra and Aqua comparisons provide information about the degree to which morning and afternoon occurrences of regimes affect the symmetry of CR radiative contribution. We examine how the radiative discrepancies among multiple irradiance data sets suffering from imperfect spatiotemporal matching depend on CR and whether they are therefore related to the complexity of cloud structure, its interpretation by different observational systems, and its subsequent representation in radiative transfer calculations.

  4. A shotgun phosphoproteomics analysis of embryos in germinated maize seeds.

    PubMed

    Lu, Tian-Cong; Meng, Ling-Bo; Yang, Chuan-Ping; Liu, Gui-Feng; Liu, Guan-Jun; Ma, Wei; Wang, Bai-Chen

    2008-11-01

    To better understand the role that reversible protein phosphorylation plays in seed germination, we initiated a phosphoproteomic investigation of embryos of germinated maize seeds. A total of 776 proteins including 39 kinases, 16 phosphatases, and 33 phosphoproteins containing 36 precise in vivo phosphorylation sites were identified. All the phosphorylation sites identified, with the exception of the phosphorylation site on HSP22, have not been reported previously (Lund et al. in J Biol Chem, 276, 29924-29929, 2001). Assayed with QRT-PCR, the transcripts of ten kinase genes were found to be dramatically up-regulated during seed germination and those of four phosphatase genes were up-regulated after germination, which indicated that reversible protein phosphorylation occurred and complex regulating networks were activated during this period. At least one-third of these phosphoproteins are key components involved in biological processes which relate to seed germination, such as DNA repair, gene transcription, RNA splicing and protein translation, suggesting that protein phosphorylation plays an important role in seed germination. As far as we know, this is the first phosphoproteomic study on a monocot and it will lay a solid foundation for further study of the molecular mechanisms of seed germination and seedling development. PMID:18726113

  5. Phosphopeptide enrichment using offline titanium dioxide columns for phosphoproteomics.

    PubMed

    Yu, Li-Rong; Veenstra, Timothy

    2013-01-01

    Identification of phosphoproteins or phosphopeptides as cancer biomarkers is an emerging field in phosphoproteomics. Owing to the low stoichiometric nature of protein phosphorylation, phosphoproteins or phosphopeptides must be enriched prior to downstream mass spectrometry analysis. Titanium dioxide (TiO2) has been prevalently used to enrich phosphopeptides from complex proteome samples due to its high affinity for phosphopeptides, and the method is straightforward. In this protocol, an offline phosphopeptide enrichment procedure using TiO2 columns is described. Peptides from a proteome lysate are loaded onto a TiO2 column in an acidic environment, followed by column washing with aqueous, organic, and ammonium glutamate (NH4Glu) buffers at acidic conditions. Phosphopeptides are eluted using an ammonia solution at high pH. Use of NH4Glu significantly reduces nonspecific bindings while a high recovery rate (84 %) of phosphopeptides is retained. The method is optimized for large-scale phosphoproteomic analysis and phosphoprotein biomarker discovery starting from sub-milligram or milligrams of proteome samples. PMID:23625397

  6. Technical phosphoproteomic and bioinformatic tools useful in cancer research.

    PubMed

    López, Elena; Wesselink, Jan-Jaap; López, Isabel; Mendieta, Jesús; Gómez-Puertas, Paulino; Muñoz, Sarbelio Rodríguez

    2011-01-01

    Reversible protein phosphorylation is one of the most important forms of cellular regulation. Thus, phosphoproteomic analysis of protein phosphorylation in cells is a powerful tool to evaluate cell functional status. The importance of protein kinase-regulated signal transduction pathways in human cancer has led to the development of drugs that inhibit protein kinases at the apex or intermediary levels of these pathways. Phosphoproteomic analysis of these signalling pathways will provide important insights for operation and connectivity of these pathways to facilitate identification of the best targets for cancer therapies. Enrichment of phosphorylated proteins or peptides from tissue or bodily fluid samples is required. The application of technologies such as phosphoenrichments, mass spectrometry (MS) coupled to bioinformatics tools is crucial for the identification and quantification of protein phosphorylation sites for advancing in such relevant clinical research. A combination of different phosphopeptide enrichments, quantitative techniques and bioinformatic tools is necessary to achieve good phospho-regulation data and good structural analysis of protein studies. The current and most useful proteomics and bioinformatics techniques will be explained with research examples. Our aim in this article is to be helpful for cancer research via detailing proteomics and bioinformatic tools. PMID:21967744

  7. Technical phosphoproteomic and bioinformatic tools useful in cancer research

    PubMed Central

    2011-01-01

    Reversible protein phosphorylation is one of the most important forms of cellular regulation. Thus, phosphoproteomic analysis of protein phosphorylation in cells is a powerful tool to evaluate cell functional status. The importance of protein kinase-regulated signal transduction pathways in human cancer has led to the development of drugs that inhibit protein kinases at the apex or intermediary levels of these pathways. Phosphoproteomic analysis of these signalling pathways will provide important insights for operation and connectivity of these pathways to facilitate identification of the best targets for cancer therapies. Enrichment of phosphorylated proteins or peptides from tissue or bodily fluid samples is required. The application of technologies such as phosphoenrichments, mass spectrometry (MS) coupled to bioinformatics tools is crucial for the identification and quantification of protein phosphorylation sites for advancing in such relevant clinical research. A combination of different phosphopeptide enrichments, quantitative techniques and bioinformatic tools is necessary to achieve good phospho-regulation data and good structural analysis of protein studies. The current and most useful proteomics and bioinformatics techniques will be explained with research examples. Our aim in this article is to be helpful for cancer research via detailing proteomics and bioinformatic tools. PMID:21967744

  8. Comparative phosphoproteome analysis of the developing grains in bread wheat (Triticum aestivum L.) under well-watered and water-deficit conditions.

    PubMed

    Zhang, Ming; Ma, Cao-Ying; Lv, Dong-Wen; Zhen, Shou-Min; Li, Xiao-Hui; Yan, Yue-Ming

    2014-10-01

    Wheat (Triticum aestivum), one of the most important cereal crops, is often threatened by drought. In this study, water deficit significantly reduced the height of plants and yield of grains. To explore further the effect of drought stress on the development and yield of grains, we first performed a large scale phosphoproteome analysis of developing grains in wheat. A total of 590 unique phosphopeptides, representing 471 phosphoproteins, were identified under well-watered conditions. Motif-X analysis showed that four motifs were enriched, including [sP], [Rxxs], [sDxE], and [sxD]. Through comparative phosphoproteome analysis between well-watered and water-deficit conditions, we found that 63 unique phosphopeptides, corresponding to 61 phosphoproteins, showed significant changes in phosphorylation level (≥2-fold intensities). Functional analysis suggested that some of these proteins may be involved in signal transduction, embryo and endosperm development of grains, and drought response and defense under water-deficit conditions. Moreover, we also found that some chaperones may play important roles in protein refolding or degradation when the plant is subjected to water stress. These results provide a detailed insight into the stress response and defense mechanisms of developmental grains at the phosphoproteome level. They also suggested some potential candidates for further study of transgenosis and drought stress as well as incorporation into molecular breeding for drought resistance. PMID:25145454

  9. Breast Cancer Proteomic and Phosphoproteomic Data Released - Office of Cancer Clinical Proteomics Research

    Cancer.gov

    National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) scientists have released a dataset of proteins and phophorylated phosphopeptides identified through deep proteomic and phosphoproteomic analysis of breast tumor samples, previously genomically analyzed by The Cancer Genome Atlas (TCGA).

  10. Global aerosol effects on convective clouds

    NASA Astrophysics Data System (ADS)

    Wagner, Till; Stier, Philip

    2013-04-01

    Atmospheric aerosols affect cloud properties, and thereby the radiation balance of the planet and the water cycle. The influence of aerosols on clouds is dominated by increase of cloud droplet and ice crystal numbers (CDNC/ICNC) due to enhanced aerosols acting as cloud condensation and ice nuclei. In deep convective clouds this increase in CDNC/ICNC is hypothesised to increase precipitation because of cloud invigoration through enhanced freezing and associated increased latent heat release caused by delayed warm rain formation. Satellite studies robustly show an increase of cloud top height (CTH) and precipitation with increasing aerosol optical depth (AOD, as proxy for aerosol amount). To represent aerosol effects and study their influence on convective clouds in the global climate aerosol model ECHAM-HAM, we substitute the standard convection parameterisation, which uses one mean convective cloud for each grid column, with the convective cloud field model (CCFM), which simulates a spectrum of convective clouds, each with distinct values of radius, mixing ratios, vertical velocity, height and en/detrainment. Aerosol activation and droplet nucleation in convective updrafts at cloud base is the primary driver for microphysical aerosol effects. To produce realistic estimates for vertical velocity at cloud base we use an entraining dry parcel sub cloud model which is triggered by perturbations of sensible and latent heat at the surface. Aerosol activation at cloud base is modelled with a mechanistic, Köhler theory based, scheme, which couples the aerosols to the convective microphysics. Comparison of relationships between CTH and AOD, and precipitation and AOD produced by this novel model and satellite based estimates show general agreement. Through model experiments and analysis of the model cloud processes we are able to investigate the main drivers for the relationship between CTH / precipitation and AOD.

  11. Effect of global climate on termites population. Effect of termites population on global climate

    NASA Astrophysics Data System (ADS)

    Sapunov, Valentin

    2010-05-01

    The global climate is under control of factors having both earth and space origin. Global warming took place from XVII century till 1997. Then global cold snap began. This dynamics had effect on global distribution of some animals including termites. Direct human effect on climate is not significant. At the same time man plays role of trigger switching on significant biosphere processes controlling climate. The transformation of marginal lands, development of industry and building, stimulated increase of termite niche and population. Termite role in green house gases production increases too. It may have regular effect on world climate. The dry wood is substrate for metabolism of termites living under symbiosis with bacteria Hypermastigina (Flagellata). The use of dry wood by humanity increased from 18 *108 ton in XVIII to 9*109 to the middle of XX century. Then use of wood decreased because of a new technology development. Hence termite population is controlled by microevolution depending on dry wood and climate dynamics. Producing by them green house gases had reciprocal effect on world climate. It is possible to describe and predict dynamic of termite population using methods of mathematical ecology and analogs with other well studied insects (Colorado potatoes beetle, Chrisomelid beetle Zygogramma and so on). Reclamation of new ecological niche for such insects as termites needs 70 - 75 years. That is delay of population dynamics in relation to dynamics of dry wood production. General principles of population growth were described by G.Gause (1934) and some authors of the end of XX century. This works and analogs with other insects suggest model of termite distribution during XXI century. The extremum of population and its green house gases production would be gotten during 8 - 10 years. Then the number of specimens and sum biological mass would be stabilized and decreased. Termite gas production is not priority for climate regulation, but it has importance as

  12. Plug-and-play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry.

    PubMed

    Lawrence, Robert T; Searle, Brian C; Llovet, Ariadna; Villén, Judit

    2016-05-01

    Systematic approaches to studying cellular signaling require phosphoproteomic techniques that reproducibly measure the same phosphopeptides across multiple replicates, conditions, and time points. Here we present a method to mine information from large-scale, heterogeneous phosphoproteomics data sets to rapidly generate robust targeted mass spectrometry (MS) assays. We demonstrate the performance of our method by interrogating the IGF-1/AKT signaling pathway, showing that even rarely observed phosphorylation events can be consistently detected and precisely quantified. PMID:27018578

  13. Quantitative Phosphoproteomics Reveals Crosstalk Between Phosphorylation and O-GlcNAc in the DNA Damage Response Pathway

    PubMed Central

    Zhong, Jun; Martinez, Marissa; Sengupta, Srona; Lee, Albert; Wu, Xinyan; Chaerkady, Raghothama; Chatterjee, Aditi; O’Meally, Robert N.; Cole, Robert N.; Pandey, Akhilesh; Zachara, Natasha E.

    2015-01-01

    The modification of intracellular proteins by monosaccharides of O-linked β-N-acetylglucosamine (O-GlcNAc) is an essential and dynamic post-translational modification of metazoans. The addition and removal of O-GlcNAc is catalyzed by the O-GlcNAc transferase (OGT) and O-GlcNAcase, respectively. One mechanism by which O-GlcNAc is thought to mediate proteins is by regulating phosphorylation. To provide insight into the pathways regulated by O-GlcNAc, we have utilized stable isotope labeling of amino acids in cell culture (SILAC)-based quantitative proteomics to carry out comparisons of site-specific phosphorylation in OGT wild-type (WT) and Null cells. Quantitation of the phosphoproteome demonstrated that out of 5,529 phosphoserine, phosphothreonine and phosphotyrosine sites, 232 phosphosites were upregulated and 133 downregulated in the absence of O-GlcNAc. Collectively, these data suggest that deletion of OGT has a profound effect on the phosphorylation of cell cycle and DNA damage response proteins. Key events were confirmed by biochemical analyses and demonstrate a increase in the activating autophosphorylation event on ATM (Ser1987) and on ATM’s downstream targets p53, H2AX and Chk2. Together, these data support widespread changes in the phosphoproteome upon removal of O-GlcNAc, suggesting that O-GlcNAc regulates processes such as the cell cycle, genomic stability, and lysosomal biogenesis. PMID:25263469

  14. Label-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergistic RAS and CIP2A signaling

    PubMed Central

    Kauko, Otto; Laajala, Teemu Daniel; Jumppanen, Mikael; Hintsanen, Petteri; Suni, Veronika; Haapaniemi, Pekka; Corthals, Garry; Aittokallio, Tero; Westermarck, Jukka; Imanishi, Susumu Y.

    2015-01-01

    Hyperactivated RAS drives progression of many human malignancies. However, oncogenic activity of RAS is dependent on simultaneous inactivation of protein phosphatase 2A (PP2A) activity. Although PP2A is known to regulate some of the RAS effector pathways, it has not been systematically assessed how these proteins functionally interact. Here we have analyzed phosphoproteomes regulated by either RAS or PP2A, by phosphopeptide enrichment followed by mass-spectrometry-based label-free quantification. To allow data normalization in situations where depletion of RAS or PP2A inhibitor CIP2A causes a large uni-directional change in the phosphopeptide abundance, we developed a novel normalization strategy, named pairwise normalization. This normalization is based on adjusting phosphopeptide abundances measured before and after the enrichment. The superior performance of the pairwise normalization was verified by various independent methods. Additionally, we demonstrate how the selected normalization method influences the downstream analyses and interpretation of pathway activities. Consequently, bioinformatics analysis of RAS and CIP2A regulated phosphoproteomes revealed a significant overlap in their functional pathways. This is most likely biologically meaningful as we observed a synergistic survival effect between CIP2A and RAS expression as well as KRAS activating mutations in TCGA pan-cancer data set, and synergistic relationship between CIP2A and KRAS depletion in colony growth assays. PMID:26278961

  15. Phosphoproteomics reveals malaria parasite Protein Kinase G as a signalling hub regulating egress and invasion

    PubMed Central

    Alam, Mahmood M.; Solyakov, Lev; Bottrill, Andrew R.; Flueck, Christian; Siddiqui, Faiza A.; Singh, Shailja; Mistry, Sharad; Viskaduraki, Maria; Lee, Kate; Hopp, Christine S.; Chitnis, Chetan E.; Doerig, Christian; Moon, Robert W.; Green, Judith L.; Holder, Anthony A.; Baker, David A.; Tobin, Andrew B.

    2015-01-01

    Our understanding of the key phosphorylation-dependent signalling pathways in the human malaria parasite, Plasmodium falciparum, remains rudimentary. Here we address this issue for the essential cGMP-dependent protein kinase, PfPKG. By employing chemical and genetic tools in combination with quantitative global phosphoproteomics, we identify the phosphorylation sites on 69 proteins that are direct or indirect cellular targets for PfPKG. These PfPKG targets include proteins involved in cell signalling, proteolysis, gene regulation, protein export and ion and protein transport, indicating that cGMP/PfPKG acts as a signalling hub that plays a central role in a number of core parasite processes. We also show that PfPKG activity is required for parasite invasion. This correlates with the finding that the calcium-dependent protein kinase, PfCDPK1, is phosphorylated by PfPKG, as are components of the actomyosin complex, providing mechanistic insight into the essential role of PfPKG in parasite egress and invasion. PMID:26149123

  16. Phosphoproteomics reveals malaria parasite Protein Kinase G as a signalling hub regulating egress and invasion.

    PubMed

    Alam, Mahmood M; Solyakov, Lev; Bottrill, Andrew R; Flueck, Christian; Siddiqui, Faiza A; Singh, Shailja; Mistry, Sharad; Viskaduraki, Maria; Lee, Kate; Hopp, Christine S; Chitnis, Chetan E; Doerig, Christian; Moon, Robert W; Green, Judith L; Holder, Anthony A; Baker, David A; Tobin, Andrew B

    2015-01-01

    Our understanding of the key phosphorylation-dependent signalling pathways in the human malaria parasite, Plasmodium falciparum, remains rudimentary. Here we address this issue for the essential cGMP-dependent protein kinase, PfPKG. By employing chemical and genetic tools in combination with quantitative global phosphoproteomics, we identify the phosphorylation sites on 69 proteins that are direct or indirect cellular targets for PfPKG. These PfPKG targets include proteins involved in cell signalling, proteolysis, gene regulation, protein export and ion and protein transport, indicating that cGMP/PfPKG acts as a signalling hub that plays a central role in a number of core parasite processes. We also show that PfPKG activity is required for parasite invasion. This correlates with the finding that the calcium-dependent protein kinase, PfCDPK1, is phosphorylated by PfPKG, as are components of the actomyosin complex, providing mechanistic insight into the essential role of PfPKG in parasite egress and invasion. PMID:26149123

  17. Phosphoproteomic network analysis in the sea urchin Strongylocentrotus purpuratus reveals new candidates in egg activation.

    PubMed

    Guo, Hongbo; Garcia-Vedrenne, Ana Elisa; Isserlin, Ruth; Lugowski, Andrew; Morada, Anthony; Sun, Alex; Miao, Yishen; Kuzmanov, Uros; Wan, Cuihong; Ma, Hongyue; Foltz, Kathy; Emili, Andrew

    2015-12-01

    Fertilization triggers a dynamic symphony of molecular transformations induced by a rapid rise in intracellular calcium. Most prominent are surface alterations, metabolic activation, cytoskeletal reorganization, and cell-cycle reentry. While the activation process appears to be broadly evolutionarily conserved, and protein phosphorylation is known to play a key role, the signaling networks mediating the response to fertilization are not well described. To address this gap, we performed a time course phosphoproteomic analysis of egg activation in the sea urchin Strongylocentrotus purpuratus, a system that offers biochemical tractability coupled with exquisite synchronicity. By coupling large-scale phosphopeptide enrichment with unbiased quantitative MS, we identified striking changes in global phosphoprotein patterns at 2- and 5-min postfertilization as compared to unfertilized eggs. Overall, we mapped 8796 distinct phosphosite modifications on 2833 phosphoproteins, of which 15% were differentially regulated in early egg activation. Activated kinases were identified by phosphosite mapping, while enrichment analyses revealed conserved signaling cascades not previously associated with egg activation. This work represents the most comprehensive study of signaling associated with egg activation to date, suggesting novel mechanisms that can be experimentally tested and providing a valuable resource for the broader research community. All MS data have been deposited in the ProteomeXchange with identifier PXD002239 (http://proteomecentral.proteomexchange.org/dataset/PXD002239). PMID:26227301

  18. Phosphoproteome dynamics of Saccharomyces cerevisiae under heat shock and cold stress

    PubMed Central

    Kanshin, Evgeny; Kubiniok, Peter; Thattikota, Yogitha; D'Amours, Damien; Thibault, Pierre

    2015-01-01

    The ability of cells and organisms to survive and function through changes in temperature evolved from their specific adaptations to nonoptimal growth conditions. Responses to elevated temperatures have been studied in yeast and other model organisms using transcriptome profiling and provided valuable biological insights on molecular mechanisms involved in stress tolerance and adaptation to adverse environment. In contrast, little is known about rapid signaling events associated with changes in temperature. To gain a better understanding of global changes in protein phosphorylation in response to heat and cold, we developed a high temporal resolution phosphoproteomics protocol to study cell signaling in Saccharomyces cerevisiae. The method allowed for quantitative analysis of phosphodynamics on 2,777 phosphosites from 1,228 proteins. The correlation of kinetic profiles between kinases and their substrates provided a predictive tool to identify new putative substrates for kinases such as Cdc28 and PKA. Cell cycle analyses revealed that the increased phosphorylation of Cdc28 at its inhibitory site Y19 during heat shock is an adaptive response that delays cell cycle progression under stress conditions. The cellular responses to heat and cold were associated with extensive changes in phosphorylation on proteins implicated in transcription, protein folding and degradation, cell cycle regulation and morphogenesis. PMID:26040289

  19. Plasmodiumfalciparum infection induces dynamic changes in the erythrocyte phospho-proteome.

    PubMed

    Bouyer, Guillaume; Reininger, Luc; Ramdani, Ghania; D Phillips, Lee; Sharma, Vikram; Egee, Stephane; Langsley, Gordon; Lasonder, Edwin

    2016-05-01

    The phosphorylation status of red blood cell proteins is strongly altered during the infection by the malaria parasite Plasmodium falciparum. We identify the key phosphorylation events that occur in the erythrocyte membrane and cytoskeleton during infection, by a comparative analysis of global phospho-proteome screens between infected (obtained at schizont stage) and uninfected RBCs. The meta-analysis of reported mass spectrometry studies revealed a novel compendium of 495 phosphorylation sites in 182 human proteins with regulatory roles in red cell morphology and stability, with about 25% of these sites specific to infected cells. A phosphorylation motif analysis detected 7 unique motifs that were largely mapped to kinase consensus sequences of casein kinase II and of protein kinase A/protein kinase C. This analysis highlighted prominent roles for PKA/PKC involving 78 phosphorylation sites. We then compared the phosphorylation status of PKA (PKC) specific sites in adducin, dematin, Band 3 and GLUT-1 in uninfected RBC stimulated or not by cAMP to their phosphorylation status in iRBC. We showed cAMP-induced phosphorylation of adducin S59 by immunoblotting and we were able to demonstrate parasite-induced phosphorylation for adducin S726, Band 3 and GLUT-1, corroborating the protein phosphorylation status in our erythrocyte phosphorylation site compendium. PMID:27067487

  20. Global effects in quaternionic quantum field theory

    NASA Astrophysics Data System (ADS)

    Brumby, S. P.; Joshi, G. C.

    1996-12-01

    We present some striking global consequences of a model quaternionic quantum field theory which is locally complex. We show how making the quaternionic structure a dynamical quantity naturally leads to the prediction of cosmic strings and nonbaryonic hot dark matter candidates.

  1. A pipeline for 15N metabolic labeling and phosphoproteome analysis in Arabidopsis thaliana.

    PubMed

    Minkoff, Benjamin B; Burch, Heather L; Sussman, Michael R

    2014-01-01

    this can be used, in conjunction with a technique for enrichment of phosphorylated peptides (phosphopeptides), to determine changes in A. thaliana's phosphoproteome on an untargeted, global scale. PMID:24057376

  2. Discovery of Mouse Spleen Signaling Responses to Anthrax using Label-Free Quantitative Phosphoproteomics via Mass Spectrometry*

    PubMed Central

    Manes, Nathan P.; Dong, Li; Zhou, Weidong; Du, Xiuxia; Reghu, Nikitha; Kool, Arjan C.; Choi, Dahan; Bailey, Charles L.; Petricoin, Emanuel F.; Liotta, Lance A.; Popov, Serguei G.

    2011-01-01

    Inhalational anthrax is caused by spores of the bacterium Bacillus anthracis (B. anthracis), and is an extremely dangerous disease that can kill unvaccinated victims within 2 weeks. Modern antibiotic-based therapy can increase the survival rate to ∼50%, but only if administered presymptomatically (within 24–48 h of exposure). To discover host signaling responses to presymptomatic anthrax, label-free quantitative phosphoproteomics via liquid chromatography coupled to mass spectrometry was used to compare spleens from uninfected and spore-challenged mice over a 72 h time-course. Spleen proteins were denatured using urea, reduced using dithiothreitol, alkylated using iodoacetamide, and digested into peptides using trypsin, and the resulting phosphopeptides were enriched using titanium dioxide solid-phase extraction and analyzed by nano-liquid chromatography-Linear Trap Quadrupole-Orbitrap-MS(/MS). The fragment ion spectra were processed using DeconMSn and searched using both Mascot and SEQUEST resulting in 252,626 confident identifications of 6248 phosphopeptides (corresponding to 5782 phosphorylation sites). The precursor ion spectra were deisotoped using Decon2LS and aligned using MultiAlign resulting in the confident quantitation of 3265 of the identified phosphopeptides. ANOVAs were used to produce a q-value ranked list of host signaling responses. Late-stage (48–72 h postchallenge) Sterne strain (lethal) infections resulted in global alterations to the spleen phosphoproteome. In contrast, ΔSterne strain (asymptomatic; missing the anthrax toxin) infections resulted in 188 (5.8%) significantly altered (q<0.05) phosphopeptides. Twenty-six highly tentative phosphorylation responses to early-stage (24 h postchallenge) anthrax were discovered (q<0.5), and ten of these originated from eight proteins that have known roles in the host immune response. These tentative early-anthrax host response signaling events within mouse spleens may translate into presymptomatic

  3. Global climatic effects of a nuclear war: An interdisciplinary problem

    SciTech Connect

    Ghan, S.J.

    1988-05-01

    In summary, an elucidation of the global-scale response to a nuclear war is a problem of great breadth, involving many of the sub-disciplines of aerosol physics, meteorology, oceanography, atmospheric chemistry and ecology. As diverse as these fields are, communication between the sub-disciplines has been remarkably effective, with two major interdisciplinary reports published in the last few years. It is my belief that, in addition to addressing the global-scale implications of a nuclear war, the global effects effort also serves as an excellent example of an interdisciplinary research program. 23 refs.

  4. Mechanisms of Soybean Roots' Tolerances to Salinity Revealed by Proteomic and Phosphoproteomic Comparisons Between Two Cultivars.

    PubMed

    Pi, Erxu; Qu, Liqun; Hu, Jianwen; Huang, Yingying; Qiu, Lijuan; Lu, Hongfei; Jiang, Bo; Liu, Cong; Peng, Tingting; Zhao, Ying; Wang, Huizhong; Tsai, Sau-Na; Ngai, Saiming; Du, Liqun

    2016-01-01

    Understanding molecular mechanisms underlying plant salinity tolerance provides valuable knowledgebase for effective crop improvement through genetic engineering. Current proteomic technologies, which support reliable and high-throughput analyses, have been broadly used for exploring sophisticated molecular networks in plants. In the current study, we compared phosphoproteomic and proteomic changes in roots of different soybean seedlings of a salt-tolerant cultivar (Wenfeng07) and a salt-sensitive cultivar (Union85140) induced by salt stress. The root samples of Wenfeng07 and Union85140 at three-trifoliate stage were collected at 0 h, 0.5 h, 1 h, 4 h, 12 h, 24 h, and 48 h after been treated with 150 mm NaCl. LC-MS/MS based phosphoproteomic analysis of these samples identified a total of 2692 phosphoproteins and 5509 phosphorylation sites. Of these, 2344 phosphoproteins containing 3744 phosphorylation sites were quantitatively analyzed. Our results showed that 1163 phosphorylation sites were differentially phosphorylated in the two compared cultivars. Among them, 10 MYB/MYB transcription factor like proteins were identified with fluctuating phosphorylation modifications at different time points, indicating that their crucial roles in regulating flavonol accumulation might be mediated by phosphorylated modifications. In addition, the protein expression profiles of these two cultivars were compared using LC MS/MS based shotgun proteomic analysis, and expression pattern of all the 89 differentially expressed proteins were independently confirmed by qRT-PCR. Interestingly, the enzymes involved in chalcone metabolic pathway exhibited positive correlations with salt tolerance. We confirmed the functional relevance of chalcone synthase, chalcone isomerase, and cytochrome P450 monooxygenase genes using soybean composites and Arabidopsis thaliana mutants, and found that their salt tolerance were positively regulated by chalcone synthase, but was negatively regulated by

  5. The effect of global warming on infectious diseases.

    PubMed

    Kurane, Ichiro

    2010-12-01

    Global warming has various effects on human health. The main indirect effects are on infectious diseases. Although the effects on infectious diseases will be detected worldwide, the degree and types of the effect are different, depending on the location of the respective countries and socioeconomical situations. Among infectious diseases, water- and foodborne infectious diseases and vector-borne infectious diseases are two main categories that are forecasted to be most affected. The effect on vector-borne infectious diseases such as malaria and dengue fever is mainly because of the expansion of the infested areas of vector mosquitoes and increase in the number and feeding activity of infected mosquitoes. There will be increase in the number of cases with water- and foodborne diarrhoeal diseases. Even with the strongest mitigation procedures, global warming cannot be avoided for decades. Therefore, implementation of adaptation measures to the effect of global warming is the most practical action we can take. It is generally accepted that the impacts of global warming on infectious diseases have not been apparent at this point yet in East Asia. However, these impacts will appear in one form or another if global warming continues to progress in future. Further research on the impacts of global warming on infectious diseases and on future prospects should be conducted. PMID:24159433

  6. The effects of variable biome distribution on global climate

    SciTech Connect

    Noever, D.A.; Brittain, A.; Matsos, H.C.; Baskaran, S.; Obenhuber, D.

    1996-12-31

    In projecting climatic adjustments to anthropogenically elevated atmospheric carbon dioxide, most global climate models fix biome distribution to current geographic conditions. The authors develop a model that examines the albedo-related effects of biome distribution on global temperature. The model was tested on historical biome changes since 1860 and the results fit both the observed trend and order of magnitude change in global temperature. Once backtested in this way on historical data, the model is then used to generate an optimized future biome distribution which minimizes projected greenhouse effects on global temperature. Because of the complexity of this combinatorial search an artificial intelligence method, the genetic algorithm, was employed. The genetic algorithm assigns various biome distributions to the planet, then adjusts their percentage area and albedo effects to regulate or moderate temperature changes.

  7. A Simple Model of Global Aerosol Indirect Effects

    SciTech Connect

    Ghan, Steven J.; Smith, Steven J.; Wang, Minghuai; Zhang, Kai; Pringle, K. J.; Carslaw, K. S.; Pierce, Jeffrey; Bauer, Susanne E.; Adams, P. J.

    2013-06-28

    Most estimates of the global mean indirect effect of anthropogenic aerosol on the Earth’s energy balance are from simulations by global models of the aerosol lifecycle coupled with global models of clouds and the hydrologic cycle. Extremely simple models have been developed for integrated assessment models, but lack the flexibility to distinguish between primary and secondary sources of aerosol. Here a simple but more physically-based model expresses the aerosol indirect effect using analytic representations of droplet nucleation, cloud and aerosol vertical structure, and horizontal variability in cloud water and aerosol concentration. Although the simple model is able to produce estimates of aerosol indirect effects that are comparable to those from some global aerosol models using the same global mean aerosol properties, the estimates are found to be sensitive to several uncertain parameters, including the preindustrial cloud condensation nuclei concentration, primary and secondary anthropogenic emissions, the size of the primary particles, the fraction of the secondary anthropogenic emissions that accumulates on the coarse mode, the fraction of the secondary mass that forms new particles, and the sensitivity of liquid water path to droplet number concentration. Aerosol indirect effects are surprisingly linear in emissions. This simple model provides a much stronger physical basis for representing aerosol indirect effects than previous representations in integrated assessment models designed to quickly explore the parameter space of emissions-climate interactions. The model also produces estimates that depend on parameter values in ways that are consistent with results from detailed global aerosol-climate simulation models.

  8. Phosphoproteome and Transcriptome of RA-Responsive and RA-Resistant Breast Cancer Cell Lines

    PubMed Central

    Carrier, Marilyn; Joint, Mathilde; Lutzing, Régis; Page, Adeline; Rochette-Egly, Cécile

    2016-01-01

    Retinoic acid (RA), the main active vitamin A metabolite, controls multiple biological processes such as cell proliferation and differentiation through genomic programs and kinase cascades activation. Due to these properties, RA has proven anti-cancer capacity. Several breast cancer cells respond to the antiproliferative effects of RA, while others are RA-resistant. However, the overall signaling and transcriptional pathways that are altered in such cells have not been elucidated. Here, in a large-scale analysis of the phosphoproteins and in a genome-wide analysis of the RA-regulated genes, we compared two human breast cancer cell lines, a RA-responsive one, the MCF7 cell line, and a RA-resistant one, the BT474 cell line, which depicts several alterations of the “kinome”. Using high-resolution nano-LC-LTQ-Orbitrap mass spectrometry associated to phosphopeptide enrichment, we found that several proteins involved in signaling and in transcription, are differentially phosphorylated before and after RA addition. The paradigm of these proteins is the RA receptor α (RARα), which was phosphorylated in MCF7 cells but not in BT474 cells after RA addition. The panel of the RA-regulated genes was also different. Overall our results indicate that RA resistance might correlate with the deregulation of the phosphoproteome with consequences on gene expression. PMID:27362937

  9. Quantitative proteomics and phosphoproteomics on serial tumor biopsies from a sorafenib-treated HCC patient.

    PubMed

    Dazert, Eva; Colombi, Marco; Boldanova, Tujana; Moes, Suzette; Adametz, David; Quagliata, Luca; Roth, Volker; Terracciano, Luigi; Heim, Markus H; Jenoe, Paul; Hall, Michael N

    2016-02-01

    Compensatory signaling pathways in tumors confer resistance to targeted therapy, but the pathways and their mechanisms of activation remain largely unknown. We describe a procedure for quantitative proteomics and phosphoproteomics on snap-frozen biopsies of hepatocellular carcinoma (HCC) and matched nontumor liver tissue. We applied this procedure to monitor signaling pathways in serial biopsies taken from an HCC patient before and during treatment with the multikinase inhibitor sorafenib. At diagnosis, the patient had an advanced HCC. At the time of the second biopsy, abdominal imaging revealed progressive disease despite sorafenib treatment. Sorafenib was confirmed to inhibit MAPK signaling in the tumor, as measured by reduced ribosomal protein S6 kinase phosphorylation. Hierarchical clustering and enrichment analysis revealed pathways broadly implicated in tumor progression and resistance, such as epithelial-to-mesenchymal transition and cell adhesion pathways. Thus, we describe a protocol for quantitative analysis of oncogenic pathways in HCC biopsies and obtained first insights into the effect of sorafenib in vivo. This protocol will allow elucidation of mechanisms of resistance and enable precision medicine. PMID:26787912

  10. Quantitative proteomics and phosphoproteomics on serial tumor biopsies from a sorafenib-treated HCC patient

    PubMed Central

    Dazert, Eva; Colombi, Marco; Boldanova, Tujana; Moes, Suzette; Adametz, David; Quagliata, Luca; Roth, Volker; Terracciano, Luigi; Heim, Markus H.; Jenoe, Paul; Hall, Michael N.

    2016-01-01

    Compensatory signaling pathways in tumors confer resistance to targeted therapy, but the pathways and their mechanisms of activation remain largely unknown. We describe a procedure for quantitative proteomics and phosphoproteomics on snap-frozen biopsies of hepatocellular carcinoma (HCC) and matched nontumor liver tissue. We applied this procedure to monitor signaling pathways in serial biopsies taken from an HCC patient before and during treatment with the multikinase inhibitor sorafenib. At diagnosis, the patient had an advanced HCC. At the time of the second biopsy, abdominal imaging revealed progressive disease despite sorafenib treatment. Sorafenib was confirmed to inhibit MAPK signaling in the tumor, as measured by reduced ribosomal protein S6 kinase phosphorylation. Hierarchical clustering and enrichment analysis revealed pathways broadly implicated in tumor progression and resistance, such as epithelial-to-mesenchymal transition and cell adhesion pathways. Thus, we describe a protocol for quantitative analysis of oncogenic pathways in HCC biopsies and obtained first insights into the effect of sorafenib in vivo. This protocol will allow elucidation of mechanisms of resistance and enable precision medicine. PMID:26787912

  11. Quantitative Phosphoproteomic Analysis Reveals a Role for Serine and Threonine Kinases in the Cytoskeletal Reorganization in Early T Cell Receptor Activation in Human Primary T Cells*

    PubMed Central

    Ruperez, Patricia; Gago-Martinez, Ana; Burlingame, A. L.; Oses-Prieto, Juan A.

    2012-01-01

    Protein phosphorylation-dephosphorylation events play a primary role in regulation of almost all aspects of cell function including signal transduction, cell cycle, or apoptosis. Thus far, T cell phosphoproteomics have focused on analysis of phosphotyrosine residues, and little is known about the role of serine/threonine phosphorylation in early activation of the T cell receptor (TCR). Therefore, we performed a quantitative mass spectrometry-based analysis of the global phosphoproteome of human primary T cells in response to 5 min of TCR activation with anti-CD3 antibody. Combining immunoprecipitation with an antiphosphotyrosine antibody, titanium dioxide phosphopeptide enrichment, isobaric tag for the relative and absolute quantitation methodology, and strong cation exchange separation, we were able to identify 2814 phosphopeptides. These unique sites were employed to investigate the site-specific phosphorylation dynamics. Five hundred and seventeen phosphorylation sites showed TCR-responsive changes. We found that upon 5 min of stimulation of the TCR, specific serine and threonine kinase motifs are overrepresented in the set of responsive phosphorylation sites. These phosphorylation events targeted proteins with many different activities and are present in different subcellular locations. Many of these proteins are involved in intracellular signaling cascades related mainly to cytoskeletal reorganization and regulation of small GTPase-mediated signal transduction, probably involved in the formation of the immune synapse. PMID:22499768

  12. Recent advances in enrichment and separation strategies for mass spectrometry-based phosphoproteomics

    PubMed Central

    Yang, Chenxi; Zhong, Xuefei; Li, Lingjun

    2016-01-01

    Due to the significance of protein phosphorylation in various biological processes and signaling events, new analytical techniques for enhanced phosphoproteomics have been rapidly introduced in recent years. The combinatorial use of the phospho-specific enrichment techniques and prefractionation methods prior to MS analysis enables comprehensive profiling of the phosphoproteome and facilitates deciphering the critical roles that phosphorylation plays in signaling pathways in various biological systems. This review places special emphasis on the recent five-year (2009–2013) advances for enrichment and separation techniques that have been utilized for phosphopeptides prior to MS analysis. PMID:24687451

  13. Integrating Phosphoproteome and Transcriptome Reveals New Determinants of Macrophage Multinucleation*

    PubMed Central

    Rotival, Maxime; Ko, Jeong-Hun; Srivastava, Prashant K.; Kerloc'h, Audrey; Montoya, Alex; Mauro, Claudio; Faull, Peter; Cutillas, Pedro R.; Petretto, Enrico; Behmoaras, Jacques

    2015-01-01

    Macrophage multinucleation (MM) is essential for various biological processes such as osteoclast-mediated bone resorption and multinucleated giant cell-associated inflammatory reactions. Here we study the molecular pathways underlying multinucleation in the rat through an integrative approach combining MS-based quantitative phosphoproteomics (LC-MS/MS) and transcriptome (high-throughput RNA-sequencing) to identify new regulators of MM. We show that a strong metabolic shift toward HIF1-mediated glycolysis occurs at transcriptomic level during MM, together with modifications in phosphorylation of over 50 proteins including several ARF GTPase activators and polyphosphate inositol phosphatases. We use shortest-path analysis to link differential phosphorylation with the transcriptomic reprogramming of macrophages and identify LRRFIP1, SMARCA4, and DNMT1 as novel regulators of MM. We experimentally validate these predictions by showing that knock-down of these latter reduce macrophage multinucleation. These results provide a new framework for the combined analysis of transcriptional and post-translational changes during macrophage multinucleation, prioritizing essential genes, and revealing the sequential events leading to the multinucleation of macrophages. PMID:25532521

  14. The Effects of Global Change upon United States Air Quality

    EPA Science Inventory

    To understand more fully the effects of global changes on ambient concentrations of ozone and particulate matter with aerodynamic diameter smaller than 2.5 μm (PM2.5) in the US, we conducted a comprehensive modeling effort to evaluate explicitly the effects of change...

  15. Energetic particle effects on global MHD modes

    SciTech Connect

    Cheng, C.Z.

    1990-01-01

    The effects of energetic particles on MHD type modes are studied by analytical theories and the nonvariational kinetic-MHD stability code (NOVA-K). In particular we address the problems of (1) the stabilization of ideal MHD internal kink modes and the excitation of resonant fishbone'' internal modes and (2) the alpha particle destabilization of toroidicity-induced Alfven eigenmodes (TAE) via transit resonances. Analytical theories are presented to help explain the NOVA-K results. For energetic trapped particles generated by neutral-beam injection (NBI) or ion cyclotron resonant heating (ICRH), a stability window for the n=1 internal kink mode in the hot particle beat space exists even in the absence of core ion finite Larmor radius effect (finite {omega}{sub *i}). On the other hand, the trapped alpha particles are found to resonantly excite instability of the n=1 internal mode and can lower the critical beta threshold. The circulating alpha particles can strongly destabilize TAE modes via inverse Landau damping associated with the spatial gradient of the alpha particle pressure. 23 refs., 5 figs.

  16. A Simple Model of Global Aerosol Indirect Effects

    NASA Technical Reports Server (NTRS)

    Ghan, Steven J.; Smith, Steven J.; Wang, Minghuai; Zhang, Kai; Pringle, Kirsty; Carslaw, Kenneth; Pierce, Jeffrey; Bauer, Susanne; Adams, Peter

    2013-01-01

    Most estimates of the global mean indirect effect of anthropogenic aerosol on the Earth's energy balance are from simulations by global models of the aerosol lifecycle coupled with global models of clouds and the hydrologic cycle. Extremely simple models have been developed for integrated assessment models, but lack the flexibility to distinguish between primary and secondary sources of aerosol. Here a simple but more physically based model expresses the aerosol indirect effect (AIE) using analytic representations of cloud and aerosol distributions and processes. Although the simple model is able to produce estimates of AIEs that are comparable to those from some global aerosol models using the same global mean aerosol properties, the estimates by the simple model are sensitive to preindustrial cloud condensation nuclei concentration, preindustrial accumulation mode radius, width of the accumulation mode, size of primary particles, cloud thickness, primary and secondary anthropogenic emissions, the fraction of the secondary anthropogenic emissions that accumulates on the coarse mode, the fraction of the secondary mass that forms new particles, and the sensitivity of liquid water path to droplet number concentration. Estimates of present-day AIEs as low as 5 W/sq m and as high as 0.3 W/sq m are obtained for plausible sets of parameter values. Estimates are surprisingly linear in emissions. The estimates depend on parameter values in ways that are consistent with results from detailed global aerosol-climate simulation models, which adds to understanding of the dependence on AIE uncertainty on uncertainty in parameter values.

  17. Global factors generate the McCollough effect.

    PubMed

    Dodwell, P C; O'Shea, R P

    1987-01-01

    It has recently been demonstrated that certain globally orthogonal pattern pairs derived from Hoffman's Lie Transformation Group Model of Neuropsychology (LTG/NP) are sufficient to generate McCollough effects (pattern-contingent colour aftereffects: PCCAES). We now provide evidence that the global factors postulated to generate these particular PCCAEs are also necessary. In Experiment 1 observers made controlled eye movements over the induction patterns and subsequently showed PCCAEs which were as strong as those obtained under central fixation. The induction process therefore did not depend on selectively adapting local oriented and colour-specific edge detectors. The global structure of the inducing patterns appears to be a necessary component of the generation of such aftereffects. In Experiment 2, a number of pattern pairs having various degrees of global organization were used as induction patterns, but in every case there was an equal degree of local orthogonality. Local orthogonality was shown not to be sufficient to induce PCCAEs, but global orthogonality was. These results lend strong support to the notion that McCollough-type PCCAEs are generated in a structure of the visual system somewhat above the level of strictly local operations, whether defined as edge and bar detectors or, equivalently, as units selectively tuned to different spatial frequencies and orientations. The global nature of the effects, and the particular pattern structures involved, lead us to suggest that Hoffman's LTG/NP provides a sound basis for explaining our findings. PMID:3660619

  18. Organizing for Effective Global Environmental Governance

    NASA Astrophysics Data System (ADS)

    Fontaine, K. S.; Ryan, B. J.

    2012-12-01

    Environmental governance organizations strive to address problems that benefit society across local, national, and regional scales. While some of these problems may be best understood from a physical science perspective, some solutions may be best implemented using a social science approach. In the world of international organizations, many groups address various pieces of the environmental governance puzzle. None, however, addressed it from the aspect of voluntary governance until 2003, when the Group on Earth Observations (GEO) was established. In any organization, a number of factors including, but not limited to, organizational dynamics and governance, resources and leadership play a vital role in ensuring solutions are found and implemented successfully, and GEO is no exception. One characteristic, however, of GEO that both complements and complicates effective environmental governance is its voluntary nature. This paper will discuss the characteristics of GEO, lessons learned from its various organizational structures over time, and ways in which social science disciplines can help advance the goals of GEO.

  19. Global non-linear effect of temperature on economic production

    NASA Astrophysics Data System (ADS)

    Burke, Marshall; Hsiang, Solomon M.; Miguel, Edward

    2015-11-01

    Growing evidence demonstrates that climatic conditions can have a profound impact on the functioning of modern human societies, but effects on economic activity appear inconsistent. Fundamental productive elements of modern economies, such as workers and crops, exhibit highly non-linear responses to local temperature even in wealthy countries. In contrast, aggregate macroeconomic productivity of entire wealthy countries is reported not to respond to temperature, while poor countries respond only linearly. Resolving this conflict between micro and macro observations is critical to understanding the role of wealth in coupled human-natural systems and to anticipating the global impact of climate change. Here we unify these seemingly contradictory results by accounting for non-linearity at the macro scale. We show that overall economic productivity is non-linear in temperature for all countries, with productivity peaking at an annual average temperature of 13 °C and declining strongly at higher temperatures. The relationship is globally generalizable, unchanged since 1960, and apparent for agricultural and non-agricultural activity in both rich and poor countries. These results provide the first evidence that economic activity in all regions is coupled to the global climate and establish a new empirical foundation for modelling economic loss in response to climate change, with important implications. If future adaptation mimics past adaptation, unmitigated warming is expected to reshape the global economy by reducing average global incomes roughly 23% by 2100 and widening global income inequality, relative to scenarios without climate change. In contrast to prior estimates, expected global losses are approximately linear in global mean temperature, with median losses many times larger than leading models indicate.

  20. Global non-linear effect of temperature on economic production.

    PubMed

    Burke, Marshall; Hsiang, Solomon M; Miguel, Edward

    2015-11-12

    Growing evidence demonstrates that climatic conditions can have a profound impact on the functioning of modern human societies, but effects on economic activity appear inconsistent. Fundamental productive elements of modern economies, such as workers and crops, exhibit highly non-linear responses to local temperature even in wealthy countries. In contrast, aggregate macroeconomic productivity of entire wealthy countries is reported not to respond to temperature, while poor countries respond only linearly. Resolving this conflict between micro and macro observations is critical to understanding the role of wealth in coupled human-natural systems and to anticipating the global impact of climate change. Here we unify these seemingly contradictory results by accounting for non-linearity at the macro scale. We show that overall economic productivity is non-linear in temperature for all countries, with productivity peaking at an annual average temperature of 13 °C and declining strongly at higher temperatures. The relationship is globally generalizable, unchanged since 1960, and apparent for agricultural and non-agricultural activity in both rich and poor countries. These results provide the first evidence that economic activity in all regions is coupled to the global climate and establish a new empirical foundation for modelling economic loss in response to climate change, with important implications. If future adaptation mimics past adaptation, unmitigated warming is expected to reshape the global economy by reducing average global incomes roughly 23% by 2100 and widening global income inequality, relative to scenarios without climate change. In contrast to prior estimates, expected global losses are approximately linear in global mean temperature, with median losses many times larger than leading models indicate. PMID:26503051

  1. The temporal dynamics of the distractor in the global effect.

    PubMed

    Choi, Woo Young; Viswanathan, Jayalakshmi; Barton, Jason J S

    2016-09-01

    In the global effect, saccades are displaced towards a distractor if the latter is near to the target, an effect thought to reflect spatial averaging in neurons of the superior colliculus. The temporal dynamics of the global effect have not been well studied, however. We had twelve subjects perform horizontal saccades to a target in trials in which there were either no distractor or a distractor stimulus located 20° above or below the target. The distractor appeared either simultaneously with the target or preceded it by an interval of between 100 and 800 ms, and was either flashed for only 100 ms or remained visible until the subject responded with a saccade. Both flashed and persistent distractors reduced saccadic latency if they preceded target onset, indicating that subjects could use this cue to prepare saccades in advance. Saccadic endpoint was displaced towards a flashed distractor only if it was simultaneous with the target. However, persistent distractors produced a global effect for both simultaneous presentation and distractor-target intervals of 100 ms, but not for longer intervals. We conclude that the global effect requires of the distractor both a recent onset and persistence of the distractor, and that distractor-related activity decays rapidly within 300 ms. PMID:27086262

  2. [The influences of laterality on global precedence: interference effects].

    PubMed

    Kimura, Jun

    2008-02-01

    This study aimed to clarify the influence of laterality on interference effects for global precedence, and to examine the mechanism of these effects. In most previous studies, the neutral condition was excluded from the consistency factor and the difference of latencies between the consistent and inconsistent conditions was regarded as the interference score, which may not be accurate. In this study, the difference of latencies between the neutral and the inconsistent condition was regarded as the interference score. The results of the analysis of variance (ANOVA) for latencies showed that interference effects influenced only right visual field-left hemisphere (RVF-LH), and facilitation effects influenced only left visual field-right hemisphere (LVF-RH) in the local condition. These findings indicate that it does not matter how optimal processing influenced interference effects on suboptimal processing in each hemisphere, for example how global processing influenced local processing in the right hemisphere, but rather how each hemisphere controlled optimal processing. PMID:18402064

  3. Effects of Information Capitalism and Globalization on Teaching and Learning

    ERIC Educational Resources Information Center

    Adeoye, Blessing F., Ed.; Tomei, Lawrence, Ed.

    2014-01-01

    As computers and Internet connections become widely available in schools and classrooms, it is critical to examine cross-cultural issues in the utilization of information and communication technologies. "Effects of Information Capitalism and Globalization on Teaching and Learning" examines issues concerning emerging multimedia…

  4. Effects of Globalization on Careers. Myths and Realities.

    ERIC Educational Resources Information Center

    Brown, Bettina Lankard

    Is the positive potential of globalization being realized? Are transnational careers becoming a reality? What effects are uncertainty and continuous change having on career development? There is evidence that a growing number of companies are exporting both blue- and white-collar jobs overseas, although some contend that it is new technologies…

  5. Monitoring the Effects of the Global Crisis on Education Provision

    ERIC Educational Resources Information Center

    Chang, Gwang-Chol

    2010-01-01

    This paper summarizes the experience and findings from the monitoring work carried out by UNESCO throughout 2009 to examine and assess the possible effects of the global financial and economic crisis on education provision in its Member States. The findings showed that although it was too early to ascertain the full extent of the impact of the…

  6. Comprehensive Analysis of in Vivo Phosphoproteome of Mouse Liver Microsomes.

    PubMed

    Kwon, Oh Kwang; Sim, JuHee; Kim, Sun Ju; Sung, Eunji; Kim, Jin Young; Jeong, Tae Cheon; Lee, Sangkyu

    2015-12-01

    Protein phosphorylation at serine, threonine, and tyrosine residues are some of the most widespread reversible post-translational modifications. Microsomes are vesicle-like bodies, not ordinarily present within living cells, which form from pieces of the endoplasmic reticulum (ER), plasma membrane, mitochondria, or Golgi apparatus of broken eukaryotic cells. Here we investigated the total phosphoproteome of mouse liver microsomes (MLMs) using TiO2 enrichment of phosphopeptides coupled to on-line 2D-LC-MS/MS. In total, 699 phosphorylation sites in 527 proteins were identified in MLMs. When compared with the current phosphoSitePlus database, 155 novel phosphoproteins were identified in MLM. The distributions of phosphosites were 89.4, 8.0, and 2.6% for phosphoserine, phosphotheronine, and phosphotyrosine, respectively. By Motif-X analysis, eight Ser motifs and one Thr motif were found, and five acidic, two basophilic-, and two proline-directed motifs were assigned. The potential functions of phosphoproteins in MLM were assigned by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. In GO annotation, phosphorylated microsomal proteins were involved in mRNA processing, mRNA metabolic processes, and RNA splicing. In the KEGG pathway analysis, phosphorylated microsomal proteins were highly enriched in ribosome protein processing in ER and ribosomes and in RNA transport. Furthermore, we determined that 52 and 23 phosphoproteins were potential substrates of cAMP-dependent protein kinase A and casein kinase II, respectively, many of which are 40S/60S ribosomal proteins. Overall, our results provide an overview of features of protein phosphorylation in MLMs that should be a valuable resource for the future understanding of protein synthesis or translation involving phosphorylation. PMID:26487105

  7. The effects of missing data on global ozone estimates

    NASA Technical Reports Server (NTRS)

    Drewry, J. W.; Robbins, J. L.

    1981-01-01

    The effects of missing data and model truncation on estimates of the global mean, zonal distribution, and global distribution of ozone are considered. It is shown that missing data can introduce biased estimates with errors that are not accounted for in the accuracy calculations of empirical modeling techniques. Data-fill techniques are introduced and used for evaluating error bounds and constraining the estimate in areas of sparse and missing data. It is found that the accuracy of the global mean estimate is more dependent on data distribution than model size. Zonal features can be accurately described by 7th order models over regions of adequate data distribution. Data variance accounted for by higher order models appears to represent climatological features of columnar ozone rather than pure error. Data-fill techniques can prevent artificial feature generation in regions of sparse or missing data without degrading high order estimates over dense data regions.

  8. The local and global effects of African deforestation

    NASA Astrophysics Data System (ADS)

    Werth, David; Avissar, Roni

    2005-06-01

    Using a global climate model (GCM), we simulate the effects of the total deforestation of equatorial Africa, looking specifically at the local and remote precipitation changes caused by such a land-use change. We observe a strong local effect, with a large reduction in African precipitation during the dry season, and little change during either of the two rainy seasons. The effects of African deforestation extend throughout the Tropics and also reach into the midlatitudes. The remote effect is caused by the African geopotential changes being spread beyond the deforested area by the large-scale winds.

  9. Radiosensitization of Human Leukemic HL-60 Cells by ATR Kinase Inhibitor (VE-821): Phosphoproteomic Analysis

    PubMed Central

    Šalovská, Barbora; Fabrik, Ivo; Ďurišová, Kamila; Link, Marek; Vávrová, Jiřina; Řezáčová, Martina; Tichý, Aleš

    2014-01-01

    DNA damaging agents such as ionizing radiation or chemotherapy are frequently used in oncology. DNA damage response (DDR)—triggered by radiation-induced double strand breaks—is orchestrated mainly by three Phosphatidylinositol 3-kinase-related kinases (PIKKs): Ataxia teleangiectasia mutated (ATM), DNA-dependent protein kinase (DNA-PK) and ATM and Rad3-related kinase (ATR). Their activation promotes cell-cycle arrest and facilitates DNA damage repair, resulting in radioresistance. Recently developed specific ATR inhibitor, VE-821 (3-amino-6-(4-(methylsulfonyl)phenyl)-N-phenylpyrazine-2-carboxamide), has been reported to have a significant radio- and chemo-sensitizing effect delimited to cancer cells (largely p53-deficient) without affecting normal cells. In this study, we employed SILAC-based quantitative phosphoproteomics to describe the mechanism of the radiosensitizing effect of VE-821 in human promyelocytic leukemic cells HL-60 (p53-negative). Hydrophilic interaction liquid chromatography (HILIC)-prefractionation with TiO2-enrichment and nano-liquid chromatography—tandem mass spectrometry (LC-MS/MS) analysis revealed 9834 phosphorylation sites. Proteins with differentially up-/down-regulated phosphorylation were mostly localized in the nucleus and were involved in cellular processes such as DDR, all phases of the cell cycle, and cell division. Moreover, sequence motif analysis revealed significant changes in the activities of kinases involved in these processes. Taken together, our data indicates that ATR kinase has multiple roles in response to DNA damage throughout the cell cycle and that its inhibitor VE-821 is a potent radiosensitizing agent for p53-negative HL-60 cells. PMID:25003641

  10. The Effect of Subducting Slabs in Global Shear Wave Tomography

    NASA Astrophysics Data System (ADS)

    Lu, Chang; Grand, Stephen P.

    2016-03-01

    Subducting slabs create strong short wavelength seismic anomalies in the upper mantle where much of Earth's seismicity is located. As such, they have the potential to bias longer wavelength seismic tomography models. To evaluate the effect of subducting slabs in global tomography, we performed a series of inversions using a global synthetic shear wave travel time dataset for a theoretical slab model based on predicted thermal anomalies within slabs. The spectral element method was applied to predict the travel time anomalies produced by the 3D slab model for paths corresponding to our current data used in actual tomography models. Inversion tests have been conducted first using the raw travel time anomalies to check how well the slabs can be imaged in global tomography without the effect of earthquake mislocation. Our results indicate that most of the slabs can be identified in the inversion result but with smoothed and reduced amplitude. The recovery of the total mass anomaly in slab regions is about 88%. We then performed another inversion test to investigate the effect of mislocation caused by subducting slabs. We found that source mislocation largely removes slab signal and significantly degrades the imaging of subducting slabs - potentially reducing the recovery of mass anomalies in slab regions to only 41%. We tested two source relocation procedures - an iterative relocation inversion and joint relocation inversion. Both methods partially recover the true source locations and improve the inversion results, but the joint inversion method worked significantly better than the iterative method. In all of our inversion tests, the amplitude of artifact structures in the lower mantle caused by the incorrect imaging of slabs (up to ˜0.5% S velocity anomalies) are comparable to some large scale lower mantle heterogeneities seen in global tomography studies. Based on our inversion tests, we suggest including a-priori subducting slabs in the starting models in global

  11. The effect of subducting slabs in global shear wave tomography

    NASA Astrophysics Data System (ADS)

    Lu, Chang; Grand, Stephen P.

    2016-05-01

    Subducting slabs create strong short wavelength seismic anomalies in the upper mantle where much of Earth's seismicity is located. As such, they have the potential to bias longer wavelength seismic tomography models. To evaluate the effect of subducting slabs in global tomography, we performed a series of inversions using a global synthetic shear wave traveltime data set for a theoretical slab model based on predicted thermal anomalies within slabs. The spectral element method was applied to predict the traveltime anomalies produced by the 3-D slab model for paths corresponding to our current data used in actual tomography models. Inversion tests have been conducted first using the raw traveltime anomalies to check how well the slabs can be imaged in global tomography without the effect of earthquake mislocation. Our results indicate that most of the slabs can be identified in the inversion result but with smoothed and reduced amplitude. The recovery of the total mass anomaly in slab regions is about 88 per cent. We then performed another inversion test to investigate the effect of mislocation caused by subducting slabs. We found that source mislocation largely removes slab signal and significantly degrades the imaging of subducting slabs-potentially reducing the recovery of mass anomalies in slab regions to only 41 per cent. We tested two source relocation procedures-an iterative relocation inversion and joint relocation inversion. Both methods partially recover the true source locations and improve the inversion results, but the joint inversion method worked significantly better than the iterative method. In all of our inversion tests, the amplitudes of artefact structures in the lower mantle caused by the incorrect imaging of slabs (up to ˜0.5 per cent S velocity anomalies) are comparable to some large-scale lower-mantle heterogeneities seen in global tomography studies. Based on our inversion tests, we suggest including a-priori subducting slabs in the

  12. Quantitative Phosphoproteome Analysis of Lysophosphatidic Acid Induced Chemotaxis applying Dual-step ¹⁸O Labeling Coupled with Immobilized Metal-ion Affinity Chromatography

    SciTech Connect

    Ding, Shi-Jian; Wang, Yingchun; Jacobs, Jon M.; Qian, Weijun; Yang, Feng; Tolmachev, Aleksey V.; Du, Xiuxia; Wang, Wei; Moore, Ronald J.; Monroe, Matthew E.; Purvine, Samuel O.; Waters, Katrina M.; Heibeck, Tyler H.; Adkins, Joshua N.; Camp, David G.; Klemke, Richard L.; Smith, Richard D.

    2008-10-01

    Reversible protein phosphorylation is a central cellular regulatory mechanism in modulating protein activity and propagating signals within cellular pathways and networks. Development of more effective methods for the simultaneous identification of phosphorylation sites and quantification of temporal changes in protein phosphorylation could provide important insights into molecular signaling mechanisms in a variety of different cellular processes. Here we present an integrated quantitative phosphoproteomics approach and its applications for comparative analysis of Cos-7 cells in response to lysophosphatidic acid (LPA) gradient stimulation. The approach combines trypsin-catalyzed 16O/18O labeling plus 16O/18O-methanol esterification labeling for quantitation, a macro- Immobilized Metal-ion Affinity Chromatography trap for phosphopeptide enrichment, and a monolithic capillary column with integrated electrospray emitter. LC separation and MS/MS is followed by neutral loss-dependent MS/MS/MS for phosphopeptide identification using a linear ion trap (LTQ)-FT mass spectrometer and complementary searching algorithms for interpreting MS/MS spectra. Protein phosphorylation involved in various signaling pathways of cell migration were identified and quantified, such as mitogen-activated protein kinase 1, dual-specificity mitogen-activated protein kinase kinase 2, and dual-specificity tyrosine-phosphorylation regulated kinase 1b, and a number of Rho GTPase-activating proteins. These results demonstrate the efficiency of this quantitative phosphoproteomics approach and its application for rapid discovery of phosphorylation events associated with gradient sensing and cell chemotaxis.

  13. Quantitative Phosphoproteomics Reveals Wee1 Kinase as a Therapeutic Target in a Model of Proneural Glioblastoma.

    PubMed

    Lescarbeau, Rebecca S; Lei, Liang; Bakken, Katrina K; Sims, Peter A; Sarkaria, Jann N; Canoll, Peter; White, Forest M

    2016-06-01

    Glioblastoma (GBM) is the most common malignant primary brain cancer. With a median survival of about a year, new approaches to treating this disease are necessary. To identify signaling molecules regulating GBM progression in a genetically engineered murine model of proneural GBM, we quantified phosphotyrosine-mediated signaling using mass spectrometry. Oncogenic signals, including phosphorylated ERK MAPK, PI3K, and PDGFR, were found to be increased in the murine tumors relative to brain. Phosphorylation of CDK1 pY15, associated with the G2 arrest checkpoint, was identified as the most differentially phosphorylated site, with a 14-fold increase in phosphorylation in the tumors. To assess the role of this checkpoint as a potential therapeutic target, syngeneic primary cell lines derived from these tumors were treated with MK-1775, an inhibitor of Wee1, the kinase responsible for CDK1 Y15 phosphorylation. MK-1775 treatment led to mitotic catastrophe, as defined by increased DNA damage and cell death by apoptosis. To assess the extensibility of targeting Wee1/CDK1 in GBM, patient-derived xenograft (PDX) cell lines were also treated with MK-1775. Although the response was more heterogeneous, on-target Wee1 inhibition led to decreased CDK1 Y15 phosphorylation and increased DNA damage and apoptosis in each line. These results were also validated in vivo, where single-agent MK-1775 demonstrated an antitumor effect on a flank PDX tumor model, increasing mouse survival by 1.74-fold. This study highlights the ability of unbiased quantitative phosphoproteomics to reveal therapeutic targets in tumor models, and the potential for Wee1 inhibition as a treatment approach in preclinical models of GBM. Mol Cancer Ther; 15(6); 1332-43. ©2016 AACR. PMID:27196784

  14. Reactive Oxygen Species (ROS)-Activated ATM-Dependent Phosphorylation of Cytoplasmic Substrates Identified by Large-Scale Phosphoproteomics Screen.

    PubMed

    Kozlov, Sergei V; Waardenberg, Ashley J; Engholm-Keller, Kasper; Arthur, Jonathan W; Graham, Mark E; Lavin, Martin

    2016-03-01

    Ataxia-telangiectasia, mutated (ATM) protein plays a central role in phosphorylating a network of proteins in response to DNA damage. These proteins function in signaling pathways designed to maintain the stability of the genome and minimize the risk of disease by controlling cell cycle checkpoints, initiating DNA repair, and regulating gene expression. ATM kinase can be activated by a variety of stimuli, including oxidative stress. Here, we confirmed activation of cytoplasmic ATM by autophosphorylation at multiple sites. Then we employed a global quantitative phosphoproteomics approach to identify cytoplasmic proteins altered in their phosphorylation state in control and ataxia-telangiectasia (A-T) cells in response to oxidative damage. We demonstrated that ATM was activated by oxidative damage in the cytoplasm as well as in the nucleus and identified a total of 9,833 phosphorylation sites, including 6,686 high-confidence sites mapping to 2,536 unique proteins. A total of 62 differentially phosphorylated peptides were identified; of these, 43 were phosphorylated in control but not in A-T cells, and 19 varied in their level of phosphorylation. Motif enrichment analysis of phosphopeptides revealed that consensus ATM serine glutamine sites were overrepresented. When considering phosphorylation events, only observed in control cells (not observed in A-T cells), with predicted ATM sites phosphoSerine/phosphoThreonine glutamine, we narrowed this list to 11 candidate ATM-dependent cytoplasmic proteins. Two of these 11 were previously described as ATM substrates (HMGA1 and UIMCI/RAP80), another five were identified in a whole cell extract phosphoproteomic screens, and the remaining four proteins had not been identified previously in DNA damage response screens. We validated the phosphorylation of three of these proteins (oxidative stress responsive 1 (OSR1), HDGF, and ccdc82) as ATM dependent after H2O2 exposure, and another protein (S100A11) demonstrated ATM

  15. Health effects of global warming: Problems in assessment

    SciTech Connect

    Longstreth, J.

    1993-06-01

    Global warming is likely to result in a variety of environmental effects ranging from impacts on species diversity, changes in population size in flora and fauna, increases in sea level and possible impacts on the primary productivity of the sea. Potential impacts on human health and welfare have included possible increases in heat related mortality, changes in the distribution of disease vectors, and possible impacts on respiratory diseases including hayfever and asthma. Most of the focus thus far is on effects which are directly related to increases in temperature, e.g., heat stress or perhaps one step removed, e.g., changes in vector distribution. Some of the more severe impacts are likely to be much less direct, e.g., increases in migration due to agricultural failure following prolonged droughts. This paper discusses two possible approaches to the study of these less-direct impacts of global warming and presents information from on-going research using each of these approaches.

  16. Effect of heterogeneousatmospheric CO2 on simulated global carbon budget

    USGS Publications Warehouse

    Zhang, Zhen; Jiang, Hong; Liu, Jinxun; Ju, Weimin; Zhang, Xiuying

    2013-01-01

    The effects of rising atmospheric carbon dioxide (CO2) on terrestrial carbon (C) sequestration have been a key focus in global change studies. As anthropological CO2 emissions substantially increase, the spatial variability of atmospheric CO2 should be considered to reduce the potential bias on C source and sink estimations. In this study, the global spatial–temporal patterns of near surface CO2 concentrations for the period 2003-2009 were established using the SCIAMACHY satellite observations and the GLOBALVIEW-CO2 field observations. With this CO2 data and the Integrated Biosphere Simulator (IBIS), our estimation of the global mean annual NPP and NEP was 0.5% and 7% respectively which differs from the traditional C sequestration assessments. The Amazon, Southeast Asia, and Tropical Africa showed higher C sequestration than the traditional assessment, and the rest of the areas around the world showed slightly lower C sequestration than the traditional assessment. We find that the variability of NEP is less intense under heterogeneous CO2 pattern on a global scale. Further studies of the cause of CO2 variation and the interactions between natural and anthropogenic processes of C sequestration are needed.

  17. Hippocampal phosphoproteomics of F344 rats exposed to 1-bromopropane

    SciTech Connect

    Huang, Zhenlie; Ichihara, Sahoko; Oikawa, Shinji; Chang, Jie; Zhang, Lingyi; Hu, Shijie; Huang, Hanlin; Ichihara, Gaku

    2015-01-15

    1-Bromopropane (1-BP) is neurotoxic in both experimental animals and human. To identify phosphorylated modification on the unrecognized post-translational modifications of proteins and investigate their role in 1-BP-induced neurotoxicity, changes in hippocampal phosphoprotein expression levels were analyzed quantitatively in male F344 rats exposed to 1-BP inhalation at 0, 400, or 1000 ppm for 8 h/day for 1 or 4 weeks. Hippocampal protein extracts were analyzed qualitatively and quantitatively by Pro-Q Diamond gel staining and SYPRO Ruby staining coupled with two-dimensional difference in gel electrophoresis (2D-DIGE), respectively, as well as by matrix-assisted laser-desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) to identify phosphoproteins. Changes in selected proteins were further confirmed by Manganese II (Mn{sup 2+})-Phos-tag SDS-polyacrylamide gel electrophoresis (SDS-PAGE). Bax and cytochrome c protein levels were determined by western blotting. Pro-Q Diamond gel staining combined with 2D-DIGE identified 26 phosphoprotein spots (p < 0.05), and MALDI-TOF/MS identified 18 up-regulated proteins and 8 down-regulated proteins. These proteins are involved in the biological process of response to stimuli, metabolic processes, and apoptosis signaling. Changes in the expression of phosphorylated 14-3-3 θ were further confirmed by Mn{sup 2+}-Phos-tag SDS-PAGE. Western blotting showed overexpression of Bax protein in the mitochondria with down-regulation in the cytoplasm, whereas cytochrome c expression was high in the cytoplasm but low in the mitochondria after 1-BP exposure. Our results suggest that the pathogenesis of 1-BP-induced hippocampal damage involves inhibition of antiapoptosis process. Phosphoproteins identified in this study can potentially serve as biomarkers for 1-BP-induced neurotoxicity. - Highlights: • 1-BP modified hippocampal phosphoproteome in rat and 23 altered proteins were identified. • 1-BP changed phosphorylation

  18. Phosphoproteomic profiling identifies focal adhesion kinase as a mediator of docetaxel resistance in castrate-resistant prostate cancer.

    PubMed

    Lee, Brian Y; Hochgräfe, Falko; Lin, Hui-Ming; Castillo, Lesley; Wu, Jianmin; Raftery, Mark J; Martin Shreeve, S; Horvath, Lisa G; Daly, Roger J

    2014-01-01

    Docetaxel remains the standard-of-care for men diagnosed with metastatic castrate-resistant prostate cancer (CRPC). However, only approximately 50% of patients benefit from treatment and all develop docetaxel-resistant disease. Here, we characterize global perturbations in tyrosine kinase signaling associated with docetaxel resistance and thereby develop a potential therapeutic strategy to reverse this phenotype. Using quantitative mass spectrometry-based phosphoproteomics, we identified that metastatic docetaxel-resistant prostate cancer cell lines (DU145-Rx and PC3-Rx) exhibit increased phosphorylation of focal adhesion kinase (FAK) on Y397 and Y576, in comparison with parental controls (DU145 and PC3, respectively). Bioinformatic analyses identified perturbations in pathways regulating focal adhesions and the actin cytoskeleton and in protein-protein interaction networks related to these pathways in docetaxel-resistant cells. Treatment with the FAK tyrosine kinase inhibitor (TKI) PF-00562271 reduced FAK phosphorylation in the resistant cells, but did not affect cell viability or Akt phosphorylation. Docetaxel administration reduced FAK and Akt phosphorylation, whereas cotreatment with PF-00562271 and docetaxel resulted in an additive attenuation of FAK and Akt phosphorylation and overcame the chemoresistant phenotype. The enhanced efficacy of cotreatment was due to increased autophagic cell death, rather than apoptosis. These data strongly support that enhanced FAK activation mediates chemoresistance in CRPC, and identify a potential clinical niche for FAK TKIs, where coadministration with docetaxel may be used in patients with CRPC to overcome chemoresistance. PMID:24194567

  19. Label-free quantitative analysis of the casein kinase 2-responsive phosphoproteome of the marine minimal model species Ostreococcus tauri.

    PubMed

    Le Bihan, Thierry; Hindle, Matthew; Martin, Sarah F; Barrios-Llerena, Martin E; Krahmer, Johanna; Kis, Katalin; Millar, Andrew J; van Ooijen, Gerben

    2015-12-01

    Casein kinase 2 (CK2) is a protein kinase that phosphorylates a plethora of cellular target proteins involved in processes including DNA repair, cell cycle control, and circadian timekeeping. CK2 is functionally conserved across eukaryotes, although the substrate proteins identified in a range of complex tissues are often different. The marine alga Ostreococcus tauri is a unicellular eukaryotic model organism ideally suited to efficiently study generic roles of CK2 in the cellular circadian clock. Overexpression of CK2 leads to a slow circadian rhythm, verifying functional conservation of CK2 in timekeeping. The proteome was analysed in wild-type and CK2-overexpressing algae at dawn and dusk, revealing that differential abundance of the global proteome across the day is largely unaffected by overexpression. However, CK2 activity contributed more strongly to timekeeping at dusk than at dawn. The phosphoproteome of a CK2 overexpression line and cells treated with CK2 inhibitor was therefore analysed and compared to control cells at dusk. We report an extensive catalogue of 447 unique CK2-responsive differential phosphopeptide motifs to inform future studies into CK2 activity in the circadian clock of more complex tissues. All MS data have been deposited in the ProteomeXchange with identifier PXD000975 (http://proteomecentral.proteomexchange.org/dataset/PXD000975). PMID:25930153

  20. Fast and easy phosphopeptide fractionation by combinatorial ERLIC-SCX solid-phase extraction for in-depth phosphoproteome analysis.

    PubMed

    Zarei, Mostafa; Sprenger, Adrian; Rackiewicz, Michal; Dengjel, Joern

    2016-01-01

    Mass spectrometry-based phosphoproteomic analysis is a powerful method for gaining a global, unbiased understanding of cellular signaling. Its accuracy and comprehensiveness stands or falls with the quality and choice of the applied phosphopeptide prefractionation strategy. This protocol covers a powerful but simple and rapid strategy for phosphopeptide prefractionation. The combinatorial use of two distinct chromatographic techniques that address the inverse physicochemical properties of peptides allows for superior fractionation efficiency of multiple phosphorylated peptides. In the first step, multiphosphorylated peptides are separated according to the number of negatively charged phosphosites by electrostatic repulsion-hydrophilic interaction chromatography (ERLIC). A subsequent strong cation exchange (SCX) step separates mostly singly phosphorylated peptides in the ERLIC flow-through according to their positive charge. The presented strategy is inexpensive and adaptable to large and small amounts of starting material, and it allows highly multiplexed sample preparation. Because of its implementation as solid-phase extraction, the entire workflow takes only 2 h to complete. PMID:26633130

  1. The effects of global change upon United States air quality

    NASA Astrophysics Data System (ADS)

    Gonzalez-Abraham, R.; Chung, S. H.; Avise, J.; Lamb, B.; Salathé, E. P., Jr.; Nolte, C. G.; Loughlin, D.; Guenther, A.; Wiedinmyer, C.; Duhl, T.; Zhang, Y.; Streets, D. G.

    2015-11-01

    To understand more fully the effects of global changes on ambient concentrations of ozone and particulate matter with aerodynamic diameter smaller than 2.5 μm (PM2.5) in the United States (US), we conducted a comprehensive modeling effort to evaluate explicitly the effects of changes in climate, biogenic emissions, land use and global/regional anthropogenic emissions on ozone and PM2.5 concentrations and composition. Results from the ECHAM5 global climate model driven with the A1B emission scenario from the Intergovernmental Panel on Climate Change (IPCC) were downscaled using the Weather Research and Forecasting (WRF) model to provide regional meteorological fields. We developed air quality simulations using the Community Multiscale Air Quality Model (CMAQ) chemical transport model for two nested domains with 220 and 36 km horizontal grid cell resolution for a semi-hemispheric domain and a continental United States (US) domain, respectively. The semi-hemispheric domain was used to evaluate the impact of projected global emissions changes on US air quality. WRF meteorological fields were used to calculate current (2000s) and future (2050s) biogenic emissions using the Model of Emissions of Gases and Aerosols from Nature (MEGAN). For the semi-hemispheric domain CMAQ simulations, present-day global emissions inventories were used and projected to the 2050s based on the IPCC A1B scenario. Regional anthropogenic emissions were obtained from the US Environmental Protection Agency National Emission Inventory 2002 (EPA NEI2002) and projected to the future using the MARKet ALlocation (MARKAL) energy system model assuming a business as usual scenario that extends current decade emission regulations through 2050. Our results suggest that daily maximum 8 h average ozone (DM8O) concentrations will increase in a range between 2 to 12 parts per billion (ppb) across most of the continental US. The highest increase occurs in the South, Central and Midwest regions of the US due to

  2. Identification of targets of c-Src tyrosine kinase by chemical complementation and phosphoproteomics.

    PubMed

    Ferrando, Isabel Martinez; Chaerkady, Raghothama; Zhong, Jun; Molina, Henrik; Jacob, Harrys K C; Herbst-Robinson, Katie; Dancy, Beverley M; Katju, Vikram; Bose, Ron; Zhang, Jin; Pandey, Akhilesh; Cole, Philip A

    2012-08-01

    The cellular proto-oncogene c-Src is a nonreceptor tyrosine kinase involved in cell growth and cytoskeletal regulation. Despite being dysregulated in a variety of human cancers, its precise functions are not fully understood. Identification of the substrates of c-Src remains a major challenge, because there is no simple way to directly stimulate its activity. Here we combine the chemical rescue of mutant c-Src and global quantitative phosphoproteomics to obtain the first high resolution snapshot of the range of tyrosine phosphorylation events that occur in the cell immediately after specific c-Src stimulation. After enrichment by anti-phosphotyrosine antibodies, we identified 29 potential novel c-Src substrate proteins. Tyrosine phosphopeptide mapping allowed the identification of 382 nonredundant tyrosine phosphopeptides on 213 phosphoproteins. Stable isotope labeling of amino acids in cell culture-based quantitation allowed the detection of 97 nonredundant tyrosine phosphopeptides whose level of phosphorylation is increased by c-Src. A large number of previously uncharacterized c-Src putative protein targets and phosphorylation sites are presented here, a majority of which play key roles in signaling and cytoskeletal networks, particularly in cell adhesion. Integrin signaling and focal adhesion kinase signaling pathway are two of the most altered pathways upon c-Src activation through chemical rescue. In this context, our study revealed the temporal connection between c-Src activation and the GTPase Rap1, known to stimulate integrin-dependent adhesion. Chemical rescue of c-Src provided a tool to dissect the spatiotemporal mechanism of activation of the Rap1 guanine exchange factor, C3G, one of the identified potential c-Src substrates that plays a role in focal adhesion signaling. In addition to unveiling the role of c-Src in the cell and, specifically, in the Crk-C3G-Rap1 pathway, these results exemplify a strategy for obtaining a comprehensive understanding of

  3. Weak ergodicity breaking induced by global memory effects

    NASA Astrophysics Data System (ADS)

    Budini, Adrián A.

    2016-08-01

    We study the phenomenon of weak ergodicity breaking for a class of globally correlated random walk dynamics defined over a finite set of states. The persistence in a given state or the transition to another one depends on the whole previous temporal history of the system. A set of waiting time distributions, associated to each state, sets the random times between consecutive steps. Their mean value is finite for all states. The probability density of time-averaged observables is obtained for different memory mechanisms. This statistical object explicitly shows departures between time and ensemble averages. While the residence time in each state may have a divergent mean value, we demonstrate that this condition is in general not necessary for breaking ergodicity. Hence, we conclude that global memory effects are an alternative mechanism able to induce ergodicity breaking without involving power-law statistics. Analytical and numerical calculations support these results.

  4. The effect of eurasian snow cover on global climate.

    PubMed

    Barnett, T P; Dümenil, L; Schlese, U; Roeckner, E

    1988-01-29

    Numerical simulations with a global atmospheric circulation model suggest that largescale variations in the amount of snowfall over Eurasia in the springtime are linked to the subsequent strength of the Asian summer monsoon. Large-scale changes in Eurasian snow cover are coupled to larger scale changes in the global climate system. There is a large, strong teleconnection to the atmospheric field over North America. The model results also show snow cover effects to subsequently alter other climatic fields known to be intimately associated with the El Niño-Southern Oscillation (ENSO) phenomenon. Thus the model results seem to challenge the current dogma that the ENSO phenomenon is solely the result of close coupling between the atmosphere and ocean by suggesting that processes over continental land masses may also have to be considered. PMID:17838886

  5. GIS applications to evaluate public health effects of global warming

    SciTech Connect

    Regens, J.L.; Hodges, D.G.

    1996-12-31

    Modeling projections of future climatic conditions suggest changes in temperature and precipitation patterns that might induce direct adverse effects on human health by altering the extent and severity of infectious and vector-borne diseases. The incidence of mosquito-borne diseases, for example, could increase substantially in areas where temperature and relative humidity rise. The application of Geographic Information Systems (GIS) offers new methodologies to evaluate the impact of global warming on changes in the incidence of infectious and vector-borne diseases. This research illustrates the potential analytical and communication uses of GIS for monitoring historical patterns of climate and human health variables and for projecting changes in these health variables with global warming.

  6. Weak ergodicity breaking induced by global memory effects.

    PubMed

    Budini, Adrián A

    2016-08-01

    We study the phenomenon of weak ergodicity breaking for a class of globally correlated random walk dynamics defined over a finite set of states. The persistence in a given state or the transition to another one depends on the whole previous temporal history of the system. A set of waiting time distributions, associated to each state, sets the random times between consecutive steps. Their mean value is finite for all states. The probability density of time-averaged observables is obtained for different memory mechanisms. This statistical object explicitly shows departures between time and ensemble averages. While the residence time in each state may have a divergent mean value, we demonstrate that this condition is in general not necessary for breaking ergodicity. Hence, we conclude that global memory effects are an alternative mechanism able to induce ergodicity breaking without involving power-law statistics. Analytical and numerical calculations support these results. PMID:27627247

  7. Phosphoproteomic Analysis of Cell-Based Resistance to BRAF Inhibitor Therapy in Melanoma

    PubMed Central

    Parker, Robert; Vella, Laura J.; Xavier, Dylan; Amirkhani, Ardeshir; Parker, Jimmy; Cebon, Jonathan; Molloy, Mark P.

    2015-01-01

    The treatment of melanoma by targeted inhibition of the mutated kinase BRAF with small molecules only temporarily suppresses metastatic disease. In the face of chemical inhibition tumor plasticity, both innate and adaptive, promotes survival through the biochemical and genetic reconfiguration of cellular pathways that can engage proliferative and migratory systems. To investigate this process, high-resolution mass spectrometry was used to characterize the phosphoproteome of this transition in vitro. A simple and accurate, label-free quantitative method was used to localize and quantitate thousands of phosphorylation events. We also correlated changes in the phosphoproteome with the proteome to more accurately determine changes in the activity of regulatory kinases determined by kinase landscape profiling. The abundance of phosphopeptides with sites that function in cytoskeletal regulation, GTP/GDP exchange, protein kinase C, IGF signaling, and melanosome maturation were highly divergent after transition to a drug resistant phenotype. PMID:26029660

  8. Biogeophysical effects of CO2 fertilization on global climate

    NASA Astrophysics Data System (ADS)

    Bala, G.; Caldeira, K.; Mirin, A.; Wickett, M.; Delire, C.; Phillips, T. J.

    2006-11-01

    CO2 fertilization affects plant growth, which modifies surface physical properties, altering the surface albedo, and fluxes of sensible and latent heat. We investigate how such CO2-fertilization effects on vegetation and surface properties would affect the climate system. Using a global three-dimensional climate-carbon model that simulates vegetation dynamics, we compare two multicentury simulations: a `Control' simulation with no emissions and a `Physiol-noGHG' simulation where physiological changes occur as a result of prescribed CO2 emissions, but where CO2-induced greenhouse warming is not included. In our simulations, CO2 fertilization produces warming; we obtain an annual- and global-mean warming of about 0.65 K (and land-only warming of 1.4 K) after 430 yr. This century-scale warming is mostly due to a decreased surface albedo associated with the expansion of the Northern Hemisphere boreal forests. On decadal timescales, the CO2 uptake by afforestation should produce a cooling effect that exceeds this albedo-based warming; but if the forests remain in place, the CO2-enhanced-greenhouse effect would diminish as the ocean equilibrates with the atmosphere, whereas the albedo effect would persist. Thus, on century timescales, there is the prospect for net warming from CO2 fertilization of the land biosphere. Further study is needed to confirm and better quantify our results.

  9. Biogeophysical effects of CO2-fertilization on global climate

    SciTech Connect

    Bala, G; Caldeira, K; Mirin, A; Wickett, M; Delire, C; Phillips, T J

    2006-04-26

    CO{sub 2}-fertilization affects plant growth, which modifies surface physical properties, altering the surface albedo, and fluxes of sensible and latent heat. We investigate how such CO{sub 2}-fertilization effects on vegetation and surface properties would affect the climate system. Using a global three-dimensional climate-carbon model that simulates vegetation dynamics, we compare two multi-century simulations: a ''Control'' simulation with no emissions, and a ''Physiol-noGHG'' simulation where physiological changes occur as a result of prescribed CO{sub 2} emissions, but where CO{sub 2}-induced greenhouse warming is not included. In our simulations, CO{sub 2}-fertilization produces warming; we obtain an annual- and global-mean warming of about 0.65 K (and land-only warming of 1.4 K) after 430 years. This century-scale warming is mostly due to a decreased surface albedo associated with the expansion of the Northern Hemisphere boreal forests. On decadal time scales, the CO{sub 2} uptake by afforestation should produce a cooling effect that exceeds this albedo-based warming; but if the forests remain in place, the CO{sub 2}-enhanced-greenhouse effect would diminish as the ocean equilibrates with the atmosphere, whereas the albedo effect would persist. Thus, on century time scales, there is the prospect for net warming from CO{sub 2}-fertilization of the land biosphere. Further study is needed to confirm and better quantify our results.

  10. Quantifying the Intercontinental and Global Reach and Effects of Pollution

    NASA Technical Reports Server (NTRS)

    Chatfield, Robert B.; Guo, Zitan

    2000-01-01

    The Atmospheric Chemistry Modeling Group is participating in an international effort to explore the projected interactions of the atmosphere with biota, human activity, and the natural environment over the next three decades. The group uses computer simulations and statistical analyses to compare theory and observations of the composition of the lower atmosphere. This study of global habitability change is part of a more ambitious activity to understand global habitability. This broad planetary understanding is central to planetary habitability, biomarker detection, and similar aspects of Astrobiology. The group has made highly detailed studies of immense intercontinental plumes that affect the chemistry of the global atmosphere, especially the region below the ozone (O3) layer whose chemical composition defines the conditions for healthy humans and the biosphere. For some decades there has been concern about the pollution from cities and industrial burning and its possible effect in increasing smog ozone, not only in continental regions, but also in plumes that spread downwind. Recently, there has been new concern about another kind of pollution plume. Projections for a greatly expanded aircraft fleet imply that there will be plumes of nitrogen oxides (NO(x)) from jet exhaust in the Northern Hemisphere downwind of major air traffic routes. Both of these are tied to large-scale O3 in the troposphere, where it is toxic to humans and plant tissues.

  11. Global versus local effects on climate change in Asia

    NASA Astrophysics Data System (ADS)

    Paeth, Heiko; Müller, Markus; Mannig, Birgit

    2015-10-01

    Regional climate change arises from two processes which, in the real climate system, cannot be separated from each other: local radiative forcing and advection of air masses from regions which themselves have been subject to climate change. In this study, we present an experimental design based on a regional climate model allowing for the assessment of global and local effects on future climate change in Asia. We carry out two runs which are characterized by increasing greenhouse gas concentrations within the model domain, but one (the control run) is one-way nested into a global control run at the lateral and oceanic boundaries while the other (the forced run) is one-way nested into a consistently forced global simulation. The aim is to improve our understanding of the mechanisms of climate change in a regional context. It turns out that temperature and precipitation changes in Asia are indeed mostly related to changes in the advected air masses which enter along the lateral boundaries. Regionally confined greenhouse forcing only affects the atmospheric heating rate while precipitation and atmospheric circulation features remain more or less unchanged. Temperature changes in the forced experiment are partly governed by warmer air masses penetrating the lateral boundaries and partly by a modification of atmospheric circulation processes, including a tendency towards a double-trough structure over Central Asia and changing temperature advection. The trend pattern of precipitation is much more heterogeneous in space but can partly be attributed to changes in horizontal wind divergence and vertical velocity.

  12. An effective way to address global environmental and energy problems

    NASA Astrophysics Data System (ADS)

    Andrienko, O.; Garelina, S.; Gysev, A.; Zakharyan, R.; Kazaryan, M.; Sachkov, V.

    2015-12-01

    This work scales the present globalism of ecological and energetic problems. The ecological problem is connected with environment pollution by polymeric waste. The energetic problem - with traditional approaches of modern energetic, in particular, use of fossil fuel for energy production and concentration of capacities for ensuring overall performance of global power supply systems that doesn't guarantee a sustainable development of power for long prospect, doesn't provide power safety of the country. The second part of work is devoted to a choice of the most effective solutions of the present global problems. The authors have proposed the plasma-chemical method of the polymer waste processing and developed a schematic diagram of the reactor. The paper contains the results of the theoretical calculation of the polymer waste processing products. The reagents, allowing to obtain hydrogen and other liquid products from polymer waste are selected. It is proposed to use rare elements for increasing the efficiency of hydrogen production from polymer waste. The results of the calculation of the efficiency of hydrogen production from polymer waste using molybdenum are revealed in the paper.

  13. Sensitive kinase assay linked with phosphoproteomics for identifying direct kinase substrates.

    PubMed

    Xue, Liang; Wang, Wen-Horng; Iliuk, Anton; Hu, Lianghai; Galan, Jacob A; Yu, Shuai; Hans, Michael; Geahlen, Robert L; Tao, W Andy

    2012-04-10

    Our understanding of the molecular control of many disease pathologies requires the identification of direct substrates targeted by specific protein kinases. Here we describe an integrated proteomic strategy, termed kinase assay linked with phosphoproteomics, which combines a sensitive kinase reaction with endogenous kinase-dependent phosphoproteomics to identify direct substrates of protein kinases. The unique in vitro kinase reaction is carried out in a highly efficient manner using a pool of peptides derived directly from cellular kinase substrates and then dephosphorylated as substrate candidates. The resulting newly phosphorylated peptides are then isolated and identified by mass spectrometry. A further comparison of these in vitro phosphorylated peptides with phosphopeptides derived from endogenous proteins isolated from cells in which the kinase is either active or inhibited reveals new candidate protein substrates. The kinase assay linked with phosphoproteomics strategy was applied to identify unique substrates of spleen tyrosine kinase (Syk), a protein-tyrosine kinase with duel properties of an oncogene and a tumor suppressor in distinctive cell types. We identified 64 and 23 direct substrates of Syk specific to B cells and breast cancer cells, respectively. Both known and unique substrates, including multiple centrosomal substrates for Syk, were identified, supporting a unique mechanism that Syk negatively affects cell division through its centrosomal kinase activity. PMID:22451900

  14. Quantitative Phosphoproteomics Revealed Glucose-Stimulated Responses of Islet Associated with Insulin Secretion.

    PubMed

    Li, Jiaming; Li, Qingrun; Tang, Jiashu; Xia, Fangying; Wu, Jiarui; Zeng, Rong

    2015-11-01

    As central tissue of glucose homeostasis, islet has been an important focus of diabetes research. Phosphorylation plays pivotal roles in islet function, especially in islet glucose-stimulated insulin secretion. A systematic view on how phosphorylation networks were coordinately regulated in this process remains lacking, partially due to the limited amount of islets from an individual for a phosphoproteomic analysis. Here we optimized the in-tip and best-ratio phosphopeptide enrichment strategy and a SILAC-based workflow for processing rat islet samples. With limited islet lysates from each individual rat (20-47 μg), we identified 8539 phosphosites on 2487 proteins. Subsequent quantitative analyses uncovered that short-term (30 min) high glucose stimulation induced coordinate responses of islet phosphoproteome on multiple biological levels, including insulin secretion related pathways, cytoskeleton dynamics, protein processing in ER and Golgi, transcription and translation, and so on. Furthermore, three glucose-responsive phosphosites (Prkar1a pT75pS77 and Tagln2 pS163) from the data set were proved to be correlated with insulin secretion. Overall, we initially gave an in-depth map of islet phosphoproteome regulated by glucose on individual rat level. This was a significant addition to our knowledge about how phosphorylation networks responded in insulin secretion. Also, the list of changed phosphosites was a valuable resource for molecular researchers in diabetes field. PMID:26437020

  15. Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors

    PubMed Central

    2013-01-01

    Background Tumor classification based on their predicted responses to kinase inhibitors is a major goal for advancing targeted personalized therapies. Here, we used a phosphoproteomic approach to investigate biological heterogeneity across hematological cancer cell lines including acute myeloid leukemia, lymphoma, and multiple myeloma. Results Mass spectrometry was used to quantify 2,000 phosphorylation sites across three acute myeloid leukemia, three lymphoma, and three multiple myeloma cell lines in six biological replicates. The intensities of the phosphorylation sites grouped these cancer cell lines according to their tumor type. In addition, a phosphoproteomic analysis of seven acute myeloid leukemia cell lines revealed a battery of phosphorylation sites whose combined intensities correlated with the growth-inhibitory responses to three kinase inhibitors with remarkable correlation coefficients and fold changes (> 100 between the most resistant and sensitive cells). Modeling based on regression analysis indicated that a subset of phosphorylation sites could be used to predict response to the tested drugs. Quantitative analysis of phosphorylation motifs indicated that resistant and sensitive cells differed in their patterns of kinase activities, but, interestingly, phosphorylations correlating with responses were not on members of the pathway being targeted; instead, these mainly were on parallel kinase pathways. Conclusion This study reveals that the information on kinase activation encoded in phosphoproteomics data correlates remarkably well with the phenotypic responses of cancer cells to compounds that target kinase signaling and could be useful for the identification of novel markers of resistance or sensitivity to drugs that target the signaling network. PMID:23628362

  16. Phosphoproteomic Analysis of Platelets Activated by Pro-Thrombotic Oxidized Phospholipids and Thrombin

    PubMed Central

    Zimman, Alejandro; Titz, Bjoern; Komisopoulou, Evangelia; Biswas, Sudipta; Graeber, Thomas G.; Podrez, Eugene A.

    2014-01-01

    Specific oxidized phospholipids (oxPCCD36) promote platelet hyper-reactivity and thrombosis in hyperlipidemia via the scavenger receptor CD36, however the signaling pathway(s) induced in platelets by oxPCCD36 are not well defined. We have employed mass spectrometry-based tyrosine, serine, and threonine phosphoproteomics for the unbiased analysis of platelet signaling pathways induced by oxPCCD36 as well as by the strong physiological agonist thrombin. oxPCCD36 and thrombin induced differential phosphorylation of 115 proteins (162 phosphorylation sites) and 181 proteins (334 phosphorylation sites) respectively. Most of the phosphoproteome changes induced by either agonist have never been reported in platelets; thus they provide candidates in the study of platelet signaling. Bioinformatic analyses of protein phosphorylation dependent responses were used to categorize preferential motifs for (de)phosphorylation, predict pathways and kinase activity, and construct a phosphoproteome network regulating integrin activation. A putative signaling pathway involving Src-family kinases, SYK, and PLCγ2 was identified in platelets activated by oxPCCD36. Subsequent ex vivo studies in human platelets demonstrated that this pathway is downstream of the scavenger receptor CD36 and is critical for platelet activation by oxPCCD36. Our results provide multiple insights into the mechanism of platelet activation and specifically in platelet regulation by oxPCCD36. PMID:24400094

  17. Sample Preparation for Phosphoproteomic Analysis of Circadian Time Series in Arabidopsis thaliana

    PubMed Central

    Krahmer, Johanna; Hindle, Matthew M.; Martin, Sarah F.; Le Bihan, Thierry; Millar, Andrew J.

    2015-01-01

    Systems biological approaches to study the Arabidopsis thaliana circadian clock have mainly focused on transcriptomics while little is known about the proteome, and even less about posttranslational modifications. Evidence has emerged that posttranslational protein modifications, in particular phosphorylation, play an important role for the clock and its output. Phosphoproteomics is the method of choice for a large-scale approach to gain more knowledge about rhythmic protein phosphorylation. Recent plant phosphoproteomics publications have identified several thousand phosphopeptides. However, the methods used in these studies are very labor-intensive and therefore not suitable to apply to a well-replicated circadian time series. To address this issue, we present and compare different strategies for sample preparation for phosphoproteomics that are compatible with large numbers of samples. Methods are compared regarding number of identifications, variability of quantitation, and functional categorization. We focus on the type of detergent used for protein extraction as well as methods for its removal. We also test a simple two-fraction separation of the protein extract. PMID:25662467

  18. OVERVIEW OF GLOBAL RESEARCH WITHIN THE EPA NATIONAL HEALTH AND ENVIRONMENTAL EFFECTS RESEARCH LABORATORY (NHEERL)

    EPA Science Inventory

    The National Health and Environmental Effects Research Laboratory (NHEERL) is one of the laboratories in EPA's Office of Research and Development contributing the Global Change Research Program. NHEERL is studying the potential effects of global change on vulnerable ecosystems. ...

  19. A Grounded Theory Study of Effective Global Leadership Development Strategies: Perspectives from Brazil, India, and Nigeria

    ERIC Educational Resources Information Center

    Lokkesmoe, Karen Jane

    2009-01-01

    This qualitative, grounded theory study focuses on global leadership and global leadership development strategies from the perspective of people from three developing countries, Brazil, India, and Nigeria. The study explores conceptualizations of global leadership, the skills required to lead effectively in global contexts, and recommended…

  20. The effects of global change upon United States air quality

    NASA Astrophysics Data System (ADS)

    Gonzalez-Abraham, R.; Avise, J.; Chung, S. H.; Lamb, B.; Salathé, E. P., Jr.; Nolte, C. G.; Loughlin, D.; Guenther, A.; Wiedinmyer, C.; Duhl, T.; Zhang, Y.; Streets, D. G.

    2014-12-01

    To understand more fully the effects of global changes on ambient concentrations of ozone and particulate matter with aerodynamic diameter smaller than 2.5 μm (PM2.5) in the US, we conducted a comprehensive modeling effort to evaluate explicitly the effects of changes in climate, biogenic emissions, land use, and global/regional anthropogenic emissions on ozone and PM2.5 concentrations and composition. Results from the ECHAM5 global climate model driven with the A1B emission scenario from the Intergovernmental Panel on Climate Change (IPCC) were downscaled using the Weather Research and Forecasting (WRF) model to provide regional meteorological fields. We developed air quality simulations using the Community Multiscale Air Quality Model (CMAQ) chemical transport model for two nested domains with 220 and 36 km horizontal grid cell resolution for a semi-hemispheric domain and a continental United States (US) domain, respectively. The semi-hemispheric domain was used to evaluate the impact of projected Asian emissions changes on US air quality. WRF meteorological fields were used to calculate current (2000s) and future (2050s) biogenic emissions using the Model of Emissions of Gases and Aerosols from Nature (MEGAN). For the semi-hemispheric domain CMAQ simulations, present-day global emissions inventories were used and projected to the 2050s based on the IPCC A1B scenario. Regional anthropogenic emissions were obtained from the US Environmental Protection Agency National Emission Inventory 2002 (EPA NEI2002) and projected to the future using the MARKet ALlocation (MARKAL) energy system model assuming a business as usual scenario that extends current decade emission regulations through 2050. Our results suggest that daily maximum 8 h average ozone (DM8O) concentrations will increase in a range between 2 to 12 ppb across most of the continental US, with the highest increase in the South, Central, and Midwest regions of the US, due to increases in temperature, enhanced

  1. Agricultural ecosystem effects on trace gases and global climate change

    SciTech Connect

    Not Available

    1993-01-01

    Global climate change is an issue that has been thrust to the forefront of scientific, political, and general community interest. In the span of this human generation, the earth's climate is expected to change more rapidly than it has over any comparable period of recorded history. Some of the changes will result from natural processes, beyond human control, but much of this change is subject to anthropogenic influence arising from processes that are only beginning to be understood. Increasing concentrations of atmospheric radiatively active trace gases are being inadvertently affected by fossil fuel combustion; but other activities of industry, agriculture, forestry, changing land-use practices, waste disposal, and transportation also affect the chemical composition of the atmosphere. The measured and projected changes of the atmospheric concentrations of radiatively active trace gases have been modeled and estimated to predict changes in the global climate. Accuracy and reliability of these predictions are the subject of considerable debate among scientists and other concerned individuals, groups, and governmental agencies throughout the world. The objective of this book is to provide a review of current knowledge on the measurement of radiatively active trace gases in agricultural ecosystems and the effect of agriculture on the atmospheric concentrations of these gases. This book is compiled from written papers presented at a symposium entitled, Agroecosystem Effects on Radiatively Important Trace Gases and Global Climate Change, held at the American Society of Agronomy Meetings in Denver, CO, 27 Oct.-1 Nov. 1991. Fourteen chapters have been processed separately for inclusion in the appropriate data bases.

  2. Global model for the lithospheric strength and effective elastic thickness

    NASA Astrophysics Data System (ADS)

    Tesauro, Magdala; Kaban, Mikhail K.; Cloetingh, Sierd A. P. L.

    2013-08-01

    Global distribution of the strength and effective elastic thickness (Te) of the lithosphere are estimated using physical parameters from recent crustal and lithospheric models. For the Te estimation we apply a new approach, which provides a possibility to take into account variations of Young modulus (E) within the lithosphere. In view of the large uncertainties affecting strength estimates, we evaluate global strength and Te distributions for possible end-member 'hard' (HRM) and a 'soft' (SRM) rheology models of the continental crust. Temperature within the lithosphere has been estimated using a recent tomography model of Ritsema et al. (2011), which has much higher horizontal resolution than previous global models. Most of the strength is localized in the crust for the HRM and in the mantle for the SRM. These results contribute to the long debates on applicability of the "crème brulée" or "jelly-sandwich" model for the lithosphere structure. Changing from the SRM to HRM turns most of the continental areas from the totally decoupled mode to the fully coupled mode of the lithospheric layers. However, in the areas characterized by a high thermal regime and thick crust, the layers remain decoupled even for the HRM. At the same time, for the inner part of the cratons the lithospheric layers are coupled in both models. Therefore, rheological variations lead to large changes in the integrated strength and Te distribution in the regions characterized by intermediate thermal conditions. In these areas temperature uncertainties have a greater effect, since this parameter principally determines rheological behavior. Comparison of the Te estimates for both models with those determined from the flexural loading and spectral analysis shows that the 'hard' rheology is likely applicable for cratonic areas, whereas the 'soft' rheology is more representative for young orogens.

  3. A Phosphoproteomic Comparison of B-RAFV600E and MKK1/2 Inhibitors in Melanoma Cells*

    PubMed Central

    Stuart, Scott A.; Houel, Stephane; Lee, Thomas; Wang, Nan; Old, William M.; Ahn, Natalie G.

    2015-01-01

    Inhibitors of oncogenic B-RAFV600E and MKK1/2 have yielded remarkable responses in B-RAFV600E-positive melanoma patients. However, the efficacy of these inhibitors is limited by the inevitable onset of resistance. Despite the fact that these inhibitors target the same pathway, combination treatment with B-RAFV600E and MKK1/2 inhibitors has been shown to improve both response rates and progression-free survival in B-RAFV600E melanoma patients. To provide insight into the molecular nature of the combinatorial response, we used quantitative mass spectrometry to characterize the inhibitor-dependent phosphoproteome of human melanoma cells treated with the B-RAFV600E inhibitor PLX4032 (vemurafenib) or the MKK1/2 inhibitor AZD6244 (selumetinib). In three replicate experiments, we quantified changes at a total of 23,986 phosphosites on 4784 proteins. This included 1317 phosphosites that reproducibly decreased in response to at least one inhibitor. Phosphosites that responded to both inhibitors grouped into networks that included the nuclear pore complex, growth factor signaling, and transcriptional regulators. Although the majority of phosphosites were responsive to both inhibitors, we identified 16 sites that decreased only in response to PLX4032, suggesting rare instances where oncogenic B-RAF signaling occurs in an MKK1/2-independent manner. Only two phosphosites were identified that appeared to be uniquely responsive to AZD6244. When cells were treated with the combination of AZD6244 and PLX4032 at subsaturating concentrations (30 nm), responses at nearly all phosphosites were additive. We conclude that AZD6244 does not substantially widen the range of phosphosites inhibited by PLX4032 and that the benefit of the drug combination is best explained by their additive effects on suppressing ERK1/2 signaling. Comparison of our results to another recent ERK1/2 phosphoproteomics study revealed a surprising degree of variability in the sensitivity of phosphosites to MKK1

  4. Direct Physical Effects of CO2-Fertilization on Global Climate

    NASA Astrophysics Data System (ADS)

    Govindasamy, B.; Caldeira, K.; Mirin, A.; Wickett, M.

    2005-12-01

    CO2-fertilization affects plant growth, which modifies surface physical properties, altering the surface albedo and latent heat fluxes. Here we investigate how such changes to surface properties via CO2-fertilization, including changes in vegetation distribution, would directly affect the physical climate system. We know of no previous study that has investigated this question. Using a global three-dimensional climate-carbon model that simulates vegetation dynamics, we compare two multi-century simulations: a "Control" simulation with no emissions, and a "Fertilization-noGHG" simulation where the land biosphere is fertilized as a result of prescribed CO2 emissions, but where the climate model sees no additional greenhouse gas forcing. Our simulations indicate that the direct physical effect of CO2-fertilization could be warming over a timescale of a few centuries; we obtain an annual- and global-mean warming of about 0.65 K over 430 years in our model. The average land warming is 1.4 K. We find that this warming is mostly due to the albedo decrease in the Northern Hemisphere boreal forest regions. This albedo-based warming could partially offset the century-scale cooling effect of additional CO2 uptake due to CO2-fertilization. Further study is needed to confirm and better quantify our results.

  5. Mercury as a Global Pollutant: Sources, Pathways, and Effects

    PubMed Central

    2013-01-01

    Mercury (Hg) is a global pollutant that affects human and ecosystem health. We synthesize understanding of sources, atmosphere-land-ocean Hg dynamics and health effects, and consider the implications of Hg-control policies. Primary anthropogenic Hg emissions greatly exceed natural geogenic sources, resulting in increases in Hg reservoirs and subsequent secondary Hg emissions that facilitate its global distribution. The ultimate fate of emitted Hg is primarily recalcitrant soil pools and deep ocean waters and sediments. Transfers of Hg emissions to largely unavailable reservoirs occur over the time scale of centuries, and are primarily mediated through atmospheric exchanges of wet/dry deposition and evasion from vegetation, soil organic matter and ocean surfaces. A key link between inorganic Hg inputs and exposure of humans and wildlife is the net production of methylmercury, which occurs mainly in reducing zones in freshwater, terrestrial, and coastal environments, and the subsurface ocean. Elevated human exposure to methylmercury primarily results from consumption of estuarine and marine fish. Developing fetuses are most at risk from this neurotoxin but health effects of highly exposed populations and wildlife are also a concern. Integration of Hg science with national and international policy efforts is needed to target efforts and evaluate efficacy. PMID:23590191

  6. Stormtime Ionospheric Outflow Effects in Global Multi-Fluid MHD

    NASA Astrophysics Data System (ADS)

    Garcia-Sage, K.; Moore, T. E.; Eccles, V.; Merkin, V. G.; Welling, D. T.; Schunk, R. W.; Barakat, A. R.

    2015-12-01

    We present work detailing the effects of ionospheric outflow in the magnetosphere during the Sept 27- Oct 4, 2002 and Oct 22- Oct 29, 2002 GEM storms. The Multi-Fluid LFM global MHD code is driven by OMNI solar wind and IMF data and by outflow from the Generalized Polar Wind (GPW) model. The GPW input results in a realistic and dynamic, although not self-consistent, outflow of O+, H+, and He+ from the ionosphere. The validity of this outflow and its entry into the magnetosphere is tested through comparisons to Cluster and geosynchronous spacecraft observations. We show the access of these various populations to the magnetosphere, and we examine their effects on plasma sheet structure and storm time dynamics.

  7. Global inospheric effects of the October 1989 geomagnetic storm

    SciTech Connect

    Yeh, K.C.; Lin, K.H.; Ma, S.Y.

    1994-04-01

    Based on a large data base from 40 ionosonde stations distributed worldwide and 12 total electron content stations, a case study is made on the global behavior of ionospheric responses to the great magnetic storm of October 1989. The magnetic storm was triggered by a solar flare with the largest class of X13/4B and started with a sudden storm commencement (ssc) at 0917 UT on October 20. After the initial phase the storm underwent two periods of maximum activities in the following 2 days. Low-latitude auroras were sighted and reported in widely separated areas in both northern and southern hemispheres. In response to these magnetic and auroral activities the ionosphere showed remarkable effects. Depending on the local time of ssc occurrence, the ionospheric response differed appreciably. Impressive changes were long-lasting, large-scale effects, such as the severe depressions of foF2 at higher latitudes, the temporary suppression of the equatorial anomaly and large horizontal gradients at certain latitudes. Also observed were positive storm effects of short duration during the post-sunset period in response to the onset of both ssc and main phase of the magnetic storm. These two positive storm effects showed different patterns suggesting different casual mechanisms. In addition, global propagation of large-scale traveling ionospheric disturbances (TIDs) was seen during 2 nights, identified by dramatic rises of h{prime}F with periodic fluctuations. The equatorward propagation velocities of the TIDs varied between 330 m/s and 680 m/s for the east Asia region. 33 refs., 16 figs., 1 tab.

  8. Hydrophilic polydopamine-coated graphene for metal ion immobilization as a novel immobilized metal ion affinity chromatography platform for phosphoproteome analysis.

    PubMed

    Yan, Yinghua; Zheng, Zhifang; Deng, Chunhui; Li, Yan; Zhang, Xiangmin; Yang, Pengyuan

    2013-09-17

    To discover trace phosphorylated proteins or peptides with great biological significance for in-depth phosphoproteome analysis, it is urgent to develop a novel technique for highly selective and effective enrichment of phosphopeptides. In this work, an IMAC (immobilized metal ion affinity chromatography) material with polydopamine coated on the surface of graphene and functionalized with titanium ions (denoted as Ti(4+)-G@PD) was initially designed and synthesized. The newly prepared Ti(4+)-G@PD with enhanced hydrophilicity and biological compatibility was characterized using scanning electron microscopy (SEM), transmission electron microscopy (TEM), and infrared (IR), and its performance for selective and effective enrichment of phosphopeptide was evaluated with both standard peptide mixtures and human serum. PMID:23941301

  9. A novel double-component MOAC honeycomb composite with pollen grains as a template for phosphoproteomics research.

    PubMed

    Wang, Jiaxi; Li, Jie; Wang, Yanan; Gao, Mingxia; Zhang, Xiangmin; Deng, Chunhui

    2016-07-01

    The enrichment and separation of phosphopeptides from mixed biological samples is a technologically very significance, but highly challenging work. Current designed materials are mainly based on the broad and effective adsorptive character of metal oxide affinity chromatography (MOAC). Though significant progress has been made in the enrichment of phosphopeptides with MOAC material, there are chances for further development. In this study, a novel pollen-based MOAC honeycomb material was firstly explored in which the suitable hydrophilic channels preferentially enrich much more endogenous phosphopeptides than nonphosphopeptides or proteins while doping binary metal oxides at the atomic level and the ultra-high specific surface area have further allowed it to possess more effective active sites. Based on these unique features, the pollen-based material exhibited high selectivity for β-casein (mass ratio of β-casein/BSA, 1:1500), ultra-low detection limit (0.1fmol), desirable reusability. Moreover, the bionics MOAC composites were investigated in the enrichment of phosphopeptides from nonfat milk, human serum (male and female at the same age) and mice liver, results of which indicate the great potential of the composite for the phosphoproteome analysis of complex biological samples through the cheap and environmentally friendly process. PMID:27154659

  10. Modeling plasma pressure anisotropy's effect on Saturn's global magnetospheric dynamics

    NASA Astrophysics Data System (ADS)

    Tilley, M.; Harnett, E. M.; Winglee, R.

    2014-12-01

    A 3D multi-fluid, multi-scale plasma model with a complete treatment of plasma pressure anisotropy is employed to study global magnetospheric dynamics at Saturn. Cassini has observed anisotropies in the Saturnian magnetosphere, and analyses have showed correlations between anisotropy and plasma convection, ring current structure and intensity, confinement of plasma to the equatorial plane, as well as mass transport to the outer magnetosphere. The energization and transport of plasma within Saturn's magnetosphere is impactful upon the induced magnetic environments and atmospheres of potentially habitable satellites such as Enceladus and Titan. Recent efforts to couple pressure anisotropy with 3D multi-fluid plasma modeling have shown a significant move towards matching observations for simulations of Earth's magnetosphere. Our approach is used to study the effects of plasma pressure anisotropy on global processes of the Saturnian magnetosphere such as identifying the effect of pressure anisotropy on the centrifugal interchange instability. Previous simulation results have not completely replicated all aspects of the structure and formation of the interchange 'fingers' measured by Cassini at Saturn. The related effects of anisotropy, in addition to those mentioned above, include contribution to formation of MHD waves (e.g. reduction of Alfvén wave speed) and formation of firehose and mirror instabilities. An accurate understanding of processes such as the interchange instability is required if a complete picture of mass and energy transport at Saturn is to be realized. The results presented here will detail how the inclusion of a full treatment of pressure anisotropy for idealized solar wind conditions modifies the interchange structure and shape of the tail current sheet. Simulation results are compared to observations made by Cassini.

  11. Reviewing Biosphere Reserves globally: effective conservation action or bureaucratic label?

    PubMed

    Coetzer, Kaera L; Witkowski, Edward T F; Erasmus, Barend F N

    2014-02-01

    The Biosphere Reserve (BR) model of UNESCO's Man and the Biosphere Programme reflects a shift towards more accountable conservation. Biosphere Reserves attempt to reconcile environmental protection with sustainable development; they explicitly acknowledge humans, and human interests in the conservation landscape while still maintaining the ecological values of existing protected areas. Conceptually, this model is attractive, with 610 sites currently designated globally. Yet the practical reality of implementing dual 'conservation' and 'development' goals is challenging, with few examples successfully conforming to the model's full criteria. Here, we review the history of Biosphere Reserves from first inception in 1974 to the current status quo, and examine the suitability of the designation as an effective conservation model. We track the spatial expansion of Biosphere Reserves globally, assessing the influence of the Statutory Framework of the World Network of Biosphere Reserves and Seville strategy in 1995, when the BR concept refocused its core objectives on sustainable development. We use a comprehensive range of case studies to discuss conformity to the Programme, the social and ecological consequences associated with implementation of the designation, and challenges in aligning conservation and development. Given that the 'Biosphere Reserve' label is a relatively unknown designation in the public arena, this review also provides details on popularising the Biosphere Reserve brand, as well as prospects for further research, currently unexploited, but implicit in the designation. PMID:23701641

  12. Prospects for a Globally Effective HIV-1 Vaccine.

    PubMed

    Excler, Jean-Louis; Robb, Merlin L; Kim, Jerome H

    2015-12-01

    A globally effective vaccine strategy must cope with the broad genetic diversity of HIV and contend with multiple transmission modalities. Understanding correlates of protection and the role of diversity in limiting protective vaccines with those correlates is key. RV144 was the first HIV-1 vaccine trial to demonstrate efficacy against HIV-1 infection. A correlates analysis comparing vaccine-induced immune responses in vaccinated-infected and vaccinated-uninfected volunteers suggested that IgG specific for the V1V2 region of gp120 was associated with reduced risk of HIV-1 infection and that plasma Env IgA was directly correlated with infection risk. RV144 and recent non-human primate (NHP) challenge studies suggest that Env is essential and perhaps sufficient to induce protective antibody responses against mucosally acquired HIV-1. Whether RV144 immune correlates can apply to different HIV vaccines, to populations with different modes and intensity of transmission, or to divergent HIV-1 subtypes remains unknown. Newer prime-boost mosaic and conserved sequence immunization strategies aiming at inducing immune responses of greater breadth and depth as well as the development of immunogens inducing broadly neutralizing antibodies should be actively pursued. Efficacy trials are now planned in heterosexual populations in southern Africa and men who have sex with men in Thailand. Although NHP challenge studies may guide vaccine development, human efficacy trials remain key to answer the critical questions leading to the development of a global HIV-1 vaccine for licensure. PMID:26590431

  13. Prospects for a globally effective HIV-1 vaccine.

    PubMed

    Excler, Jean-Louis; Robb, Merlin L; Kim, Jerome H

    2015-11-27

    A globally effective vaccine strategy must cope with the broad genetic diversity of HIV and contend with multiple transmission modalities. Understanding correlates of protection and the role of diversity in limiting protective vaccines with those correlates is key. RV144 was the first HIV-1 vaccine trial to demonstrate efficacy against HIV-1 infection. A correlates analysis compared vaccine-induced immune responses in vaccinated-infected and vaccinated-uninfected volunteers suggested that IgG specific for the V1V2 region of gp120 was associated with reduced risk of HIV-1 infection and that plasma Env IgA was directly correlated with infection risk. RV144 and recent NHP challenge studies suggest that Env is essential and perhaps sufficient to induce protective antibody responses against mucosally acquired HIV-1. Whether RV144 immune correlates can apply to different HIV vaccines, to populations with different modes and intensity of transmission, or to divergent HIV-1 subtypes remains unknown. Newer prime-boost mosaic and conserved sequence immunization strategies aiming at inducing immune responses of greater breadth and depth as well as the development of immunogens inducing broadly neutralizing antibodies should be actively pursued. Efficacy trials are now planned in heterosexual populations in southern Africa and MSM in Thailand. Although NHP challenge studies may guide vaccine development, human efficacy trials remain key to answer the critical questions leading to the development of a global HIV-1 vaccine for licensure. PMID:26100921

  14. Health Promotion: An Effective Tool for Global Health

    PubMed Central

    Kumar, Sanjiv; Preetha, GS

    2012-01-01

    Health promotion is very relevant today. There is a global acceptance that health and social wellbeing are determined by many factors outside the health system which include socioeconomic conditions, patterns of consumption associated with food and communication, demographic patterns, learning environments, family patterns, the cultural and social fabric of societies; sociopolitical and economic changes, including commercialization and trade and global environmental change. In such a situation, health issues can be effectively addressed by adopting a holistic approach by empowering individuals and communities to take action for their health, fostering leadership for public health, promoting intersectoral action to build healthy public policies in all sectors and creating sustainable health systems. Although, not a new concept, health promotion received an impetus following Alma Ata declaration. Recently it has evolved through a series of international conferences, with the first conference in Canada producing the famous Ottawa charter. Efforts at promoting health encompassing actions at individual and community levels, health system strengthening and multi sectoral partnership can be directed at specific health conditions. It should also include settings-based approach to promote health in specific settings such as schools, hospitals, workplaces, residential areas etc. Health promotion needs to be built into all the policies and if utilized efficiently will lead to positive health outcomes. PMID:22529532

  15. Global Warming: Understanding and Teaching the Forecast. Part A The Greenhouse Effect.

    ERIC Educational Resources Information Center

    Andrews, Bill

    1993-01-01

    Provides information necessary for an interdisciplinary analysis of the greenhouse effect, enhanced greenhouse effect, global warming, global climate change, greenhouse gases, carbon dioxide, and scientific study of global warming for students grades 4-12. Several activity ideas accompany the information. (LZ)

  16. Plant functional traits have globally consistent effects on competition.

    PubMed

    Kunstler, Georges; Falster, Daniel; Coomes, David A; Hui, Francis; Kooyman, Robert M; Laughlin, Daniel C; Poorter, Lourens; Vanderwel, Mark; Vieilledent, Ghislain; Wright, S Joseph; Aiba, Masahiro; Baraloto, Christopher; Caspersen, John; Cornelissen, J Hans C; Gourlet-Fleury, Sylvie; Hanewinkel, Marc; Herault, Bruno; Kattge, Jens; Kurokawa, Hiroko; Onoda, Yusuke; Peñuelas, Josep; Poorter, Hendrik; Uriarte, Maria; Richardson, Sarah; Ruiz-Benito, Paloma; Sun, I-Fang; Ståhl, Göran; Swenson, Nathan G; Thompson, Jill; Westerlund, Bertil; Wirth, Christian; Zavala, Miguel A; Zeng, Hongcheng; Zimmerman, Jess K; Zimmermann, Niklaus E; Westoby, Mark

    2016-01-14

    Phenotypic traits and their associated trade-offs have been shown to have globally consistent effects on individual plant physiological functions, but how these effects scale up to influence competition, a key driver of community assembly in terrestrial vegetation, has remained unclear. Here we use growth data from more than 3 million trees in over 140,000 plots across the world to show how three key functional traits--wood density, specific leaf area and maximum height--consistently influence competitive interactions. Fast maximum growth of a species was correlated negatively with its wood density in all biomes, and positively with its specific leaf area in most biomes. Low wood density was also correlated with a low ability to tolerate competition and a low competitive effect on neighbours, while high specific leaf area was correlated with a low competitive effect. Thus, traits generate trade-offs between performance with competition versus performance without competition, a fundamental ingredient in the classical hypothesis that the coexistence of plant species is enabled via differentiation in their successional strategies. Competition within species was stronger than between species, but an increase in trait dissimilarity between species had little influence in weakening competition. No benefit of dissimilarity was detected for specific leaf area or wood density, and only a weak benefit for maximum height. Our trait-based approach to modelling competition makes generalization possible across the forest ecosystems of the world and their highly diverse species composition. PMID:26700807

  17. Effects of local and global network connectivity on synergistic epidemics

    NASA Astrophysics Data System (ADS)

    Broder-Rodgers, David; Pérez-Reche, Francisco J.; Taraskin, Sergei N.

    2015-12-01

    Epidemics in networks can be affected by cooperation in transmission of infection and also connectivity between nodes. An interplay between these two properties and their influence on epidemic spread are addressed in the paper. A particular type of cooperative effects (called synergy effects) is considered, where the transmission rate between a pair of nodes depends on the number of infected neighbors. The connectivity effects are studied by constructing networks of different topology, starting with lattices with only local connectivity and then with networks that have both local and global connectivity obtained by random bond-rewiring to nodes within a certain distance. The susceptible-infected-removed epidemics were found to exhibit several interesting effects: (i) for epidemics with strong constructive synergy spreading in networks with high local connectivity, the bond rewiring has a negative role in epidemic spread, i.e., it reduces invasion probability; (ii) in contrast, for epidemics with destructive or weak constructive synergy spreading on networks of arbitrary local connectivity, rewiring helps epidemics to spread; (iii) and, finally, rewiring always enhances the spread of epidemics, independent of synergy, if the local connectivity is low.

  18. Comparative Phosphoproteomics Analysis of VEGF and Angiopoietin-1 Signaling Reveals ZO-1 as a Critical Regulator of Endothelial Cell Proliferation.

    PubMed

    Chidiac, Rony; Zhang, Ying; Tessier, Sylvain; Faubert, Denis; Delisle, Chantal; Gratton, Jean-Philippe

    2016-05-01

    VEGF and angiopoietin-1 (Ang-1) are essential factors to promote angiogenesis through regulation of a plethora of signaling events in endothelial cells (ECs). Although pathways activated by VEGF and Ang-1 are being established, the unique signaling nodes conferring specific responses to each factor remain poorly defined. Thus, we conducted a large-scale comparative phosphoproteomic analysis of signaling pathways activated by VEGF and Ang-1 in ECs using mass spectrometry. Analysis of VEGF and Ang-1 networks of regulated phosphoproteins revealed that the junctional proteins ZO-1, ZO-2, JUP and p120-catenin are part of a cluster of proteins phosphorylated following VEGF stimulation that are linked to MAPK1 activation. Down-regulation of these junctional proteins led to MAPK1 activation and accordingly, increased proliferation of ECs stimulated specifically by VEGF, but not by Ang-1. We identified ZO-1 as the central regulator of this effect and showed that modulation of cellular ZO-1 levels is necessary for EC proliferation during vascular development of the mouse postnatal retina. In conclusion, we uncovered ZO-1 as part of a signaling node activated by VEGF, but not Ang-1, that specifically modulates EC proliferation during angiogenesis. PMID:26846344

  19. Phosphoproteomic profiling of tumor tissues identifies HSP27 Ser82 phosphorylation as a robust marker of early ischemia

    PubMed Central

    Zahari, Muhammad Saddiq; Wu, Xinyan; Pinto, Sneha M.; Nirujogi, Raja Sekhar; Kim, Min-Sik; Fetics, Barry; Philip, Mathew; Barnes, Sheri R.; Godfrey, Beverly; Gabrielson, Edward; Nevo, Erez; Pandey, Akhilesh

    2015-01-01

    Delays between tissue collection and tissue fixation result in ischemia and ischemia-associated changes in protein phosphorylation levels, which can misguide the examination of signaling pathway status. To identify a biomarker that serves as a reliable indicator of ischemic changes that tumor tissues undergo, we subjected harvested xenograft tumors to room temperature for 0, 2, 10 and 30 minutes before freezing in liquid nitrogen. Multiplex TMT-labeling was conducted to achieve precise quantitation, followed by TiO2 phosphopeptide enrichment and high resolution mass spectrometry profiling. LC-MS/MS analyses revealed phosphorylation level changes of a number of phosphosites in the ischemic samples. The phosphorylation of one of these sites, S82 of the heat shock protein 27 kDa (HSP27), was especially abundant and consistently upregulated in tissues with delays in freezing as short as 2 minutes. In order to eliminate effects of ischemia, we employed a novel cryogenic biopsy device which begins freezing tissues in situ before they are excised. Using this device, we showed that the upregulation of phosphorylation of S82 on HSP27 was abrogated. We thus demonstrate that our cryogenic biopsy device can eliminate ischemia-induced phosphoproteome alterations, and measurements of S82 on HSP27 can be used as a robust marker of ischemia in tissues. PMID:26329039

  20. Phosphoproteome analysis demonstrates the potential role of THRAP3 phosphorylation in androgen-independent prostate cancer cell growth.

    PubMed

    Ino, Yoko; Arakawa, Noriaki; Ishiguro, Hitoshi; Uemura, Hiroji; Kubota, Yoshinobu; Hirano, Hisashi; Toda, Tosifusa

    2016-04-01

    Elucidating the androgen-independent growth mechanism is critical for developing effective treatment strategies to combat androgen-independent prostate cancer. We performed a comparative phosphoproteome analysis using a prostate cancer cell line, LNCaP, and an LNCaP-derived androgen-independent cell line, LNCaP-AI, to identify phosphoproteins involved in this mechanism. We performed quantitative comparisons of the phosphopeptide levels in tryptic digests of protein extracts from these cell lines using MS. We found that the levels of 69 phosphopeptides in 66 proteins significantly differed between LNCaP and LNCaP-AI. In particular, we focused on thyroid hormone receptor associated protein 3 (THRAP3), which is a known transcriptional coactivator of the androgen receptor. The phosphorylation level of THRAP3 was significantly lower at S248 and S253 in LNCaP-AI cells. Furthermore, pull-down assays showed that 32 proteins uniquely bound to the nonphosphorylatable mutant form of THRAP3, whereas 31 other proteins uniquely bound to the phosphorylation-mimic form. Many of the differentially interacting proteins were identified as being involved with RNA splicing and processing. These results suggest that the phosphorylation state of THRAP3 at S248 and S253 might be involved in the mechanism of androgen-independent prostate cancer cell growth by changing the interaction partners. PMID:26841317

  1. Stereoscopic augmented reality with pseudo-realistic global illumination effects

    NASA Astrophysics Data System (ADS)

    de Sorbier, Francois; Saito, Hideo

    2014-03-01

    Recently, augmented reality has become very popular and has appeared in our daily life with gaming, guiding systems or mobile phone applications. However, inserting object in such a way their appearance seems natural is still an issue, especially in an unknown environment. This paper presents a framework that demonstrates the capabilities of Kinect for convincing augmented reality in an unknown environment. Rather than pre-computing a reconstruction of the scene like proposed by most of the previous method, we propose a dynamic capture of the scene that allows adapting to live changes of the environment. Our approach, based on the update of an environment map, can also detect the position of the light sources. Combining information from the environment map, the light sources and the camera tracking, we can display virtual objects using stereoscopic devices with global illumination effects such as diffuse and mirror reflections, refractions and shadows in real time.

  2. Effects of Drake Passage on a strongly eddying global ocean

    NASA Astrophysics Data System (ADS)

    Viebahn, Jan; von der Heydt, Anna S.; Dijkstra, Henk A.

    2015-04-01

    During the past 65 Million (Ma) years, Earth's climate has undergone a major change from warm 'greenhouse' to colder 'icehouse' conditions with extensive ice sheets in the polar regions of both hemispheres. The Eocene-Oligocene (~34 Ma) and Oligocene-Miocene (~23 Ma) boundaries reflect major transitions in Cenozoic global climate change. Proposed mechanisms of these transitions include reorganization of ocean circulation due to critical gateway opening/deepening, changes in atmospheric CO2-concentration, and feedback mechanisms related to land-ice formation. Drake Passage (DP) is an intensively studied gateway because it plays a central role in closing the transport pathways of heat and chemicals in the ocean. The climate response to a closed DP has been explored with a variety of general circulation models, however, all of these models employ low model-grid resolutions such that the effects of subgrid-scale fluctuations ('eddies') are parameterized. We present results of the first high-resolution (0.1° horizontally) realistic global ocean model simulation with a closed DP in which the eddy field is largely resolved. The simulation extends over more than 200 years such that the strong transient adjustment process is passed and a near-equilibrium ocean state is reached. The effects of DP are diagnosed by comparing with both an open DP high-resolution control simulation (of same length) and corresponding low-resolution simulations. By focussing on the heat/tracer transports we demonstrate that the results are twofold: Considering spatially integrated transports the overall response to a closed DP is well captured by low-resolution simulations. However, looking at the actual spatial distributions drastic differences appear between far-scattered high-resolution and laminar-uniform low-resolution fields. We conclude that sparse and highly localized tracer proxy observations have to be interpreted carefully with the help of high-resolution model simulations.

  3. Atmospheric pressure loading effects on Global Positioning System coordinate determinations

    NASA Technical Reports Server (NTRS)

    Vandam, Tonie M.; Blewitt, Geoffrey; Heflin, Michael B.

    1994-01-01

    Earth deformation signals caused by atmospheric pressure loading are detected in vertical position estimates at Global Positioning System (GPS) stations. Surface displacements due to changes in atmospheric pressure account for up to 24% of the total variance in the GPS height estimates. The detected loading signals are larger at higher latitudes where pressure variations are greatest; the largest effect is observed at Fairbanks, Alaska (latitude 65 deg), with a signal root mean square (RMS) of 5 mm. Out of 19 continuously operating GPS sites (with a mean of 281 daily solutions per site), 18 show a positive correlation between the GPS vertical estimates and the modeled loading displacements. Accounting for loading reduces the variance of the vertical station positions on 12 of the 19 sites investigated. Removing the modeled pressure loading from GPS determinations of baseline length for baselines longer than 6000 km reduces the variance on 73 of the 117 baselines investigated. The slight increase in variance for some of the sites and baselines is consistent with expected statistical fluctuations. The results from most stations are consistent with approximately 65% of the modeled pressure load being found in the GPS vertical position measurements. Removing an annual signal from both the measured heights and the modeled load time series leaves this value unchanged. The source of the remaining discrepancy between the modeled and observed loading signal may be the result of (1) anisotropic effects in the Earth's loading response, (2) errors in GPS estimates of tropospheric delay, (3) errors in the surface pressure data, or (4) annual signals in the time series of loading and station heights. In addition, we find that using site dependent coefficients, determined by fitting local pressure to the modeled radial displacements, reduces the variance of the measured station heights as well as or better than using the global convolution sum.

  4. Effects of mineral dust on global atmospheric nitrate concentrations

    NASA Astrophysics Data System (ADS)

    Karydis, V. A.; Tsimpidi, A. P.; Pozzer, A.; Astitha, M.; Lelieveld, J.

    2015-04-01

    This study provides an assessment of the chemical composition and global aerosol load of the major inorganic aerosol components and determines the effect of mineral dust on their formation, focusing on aerosol nitrate. To account for this effect, the mineral dust aerosol components (i.e., Ca2+, Mg2+, K+, Na+) and their emissions are added to the ECHAM5/MESSy Atmospheric Chemistry model (EMAC). Gas/aerosol partitioning is simulated using the ISORROPIA-II thermodynamic equilibrium model that considers the interactions of K+-Ca2+-Mg2+-NH4+-Na+-SO42--NO3--Cl--H2O aerosol components. Emissions of mineral dust aerosol components (K+-Ca2+-Mg2+-Na+) are calculated online by taking into account the soil particle size distribution and chemical composition of different deserts worldwide. The presence of the metallic ions on the simulated suite of components can substantially affect the nitrate partitioning into the aerosol phase due to thermodynamic interactions. The updated model improved the nitrate predictions over remote areas and found that the fine aerosol nitrate concentration is highest over urban and industrialized areas (1-3 μg m-3), while coarse aerosol nitrate is highest close to deserts (1-4 μg m-3). The contribution of mineral dust components to nitrate formation is large in areas with high dust concentrations with impacts that can extend across southern Europe, western USA and northeastern China. The tropospheric burden of aerosol nitrate increases by 44% by considering the interactions of nitrate with mineral dust cations. The calculated global average nitrate aerosol concentration near the surface increases by 36% while the coarse and fine mode concentrations of nitrate increase by 53 and 21%, respectively. Sensitivity tests show that nitrate aerosol formation is most sensitive to the chemical composition of the emitted mineral dust, followed by the soil size distribution of dust particles, the magnitude of the mineral dust emissions, and the aerosol state

  5. The effects of urbanization on global Plasmodium vivax malaria transmission

    PubMed Central

    2012-01-01

    Background Many recent studies have examined the impact of urbanization on Plasmodium falciparum malaria endemicity and found a general trend of reduced transmission in urban areas. However, none has examined the effect of urbanization on Plasmodium vivax malaria, which is the most widely distributed malaria species and can also cause severe clinical syndromes in humans. In this study, a set of 10,003 community-based P. vivax parasite rate (PvPR) surveys are used to explore the relationships between PvPR in urban and rural settings. Methods The PvPR surveys were overlaid onto a map of global urban extents to derive an urban/rural assignment. The differences in PvPR values between urban and rural areas were then examined. Groups of PvPR surveys inside individual city extents (urban) and surrounding areas (rural) were identified to examine the local variations in PvPR values. Finally, the relationships of PvPR between urban and rural areas within the ranges of 41 dominant Anopheles vectors were examined. Results Significantly higher PvPR values in rural areas were found globally. The relationship was consistent at continental scales when focusing on Africa and Asia only, but in the Americas, significantly lower values of PvPR in rural areas were found, though the numbers of surveys were small. Moreover, except for the countries in the Americas, the same trends were found at national scales in African and Asian countries, with significantly lower values of PvPR in urban areas. However, the patterns at city scales among 20 specific cities where sufficient data were available were less clear, with seven cities having significantly lower PvPR values in urban areas and two cities showing significantly lower PvPR in rural areas. The urban–rural PvPR differences within the ranges of the dominant Anopheles vectors were generally, in agreement with the regional patterns found. Conclusions Except for the Americas, the patterns of significantly lower P. vivax transmission in

  6. The proteome and phosphoproteome of maize pollen uncovers fertility candidate proteins.

    PubMed

    Chao, Qing; Gao, Zhi-Fang; Wang, Yue-Feng; Li, Zhe; Huang, Xia-He; Wang, Ying-Chun; Mei, Ying-Chang; Zhao, Biligen-Gaowa; Li, Liang; Jiang, Yu-Bo; Wang, Bai-Chen

    2016-06-01

    Maize is unique since it is both monoecious and diclinous (separate male and female flowers on the same plant). We investigated the proteome and phosphoproteome of maize pollen containing modified proteins and here we provide a comprehensive pollen proteome and phosphoproteome which contain 100,990 peptides from 6750 proteins and 5292 phosphorylated sites corresponding to 2257 maize phosphoproteins, respectively. Interestingly, among the total 27 overrepresented phosphosite motifs we identified here, 11 were novel motifs, which suggested different modification mechanisms in plants compared to those of animals. Enrichment analysis of pollen phosphoproteins showed that pathways including DNA synthesis/chromatin structure, regulation of RNA transcription, protein modification, cell organization, signal transduction, cell cycle, vesicle transport, transport of ions and metabolisms, which were involved in pollen development, the following germination and pollen tube growth, were regulated by phosphorylation. In this study, we also found 430 kinases and 105 phosphatases in the maize pollen phosphoproteome, among which calcium dependent protein kinases (CDPKs), leucine rich repeat kinase, SNF1 related protein kinases and MAPK family proteins were heavily enriched and further analyzed. From our research, we also uncovered hundreds of male sterility-associated proteins and phosphoproteins that might influence maize productivity and serve as targets for hybrid maize seed production. At last, a putative complex signaling pathway involving CDPKs, MAPKs, ubiquitin ligases and multiple fertility proteins was constructed. Overall, our data provides new insight for further investigation of protein phosphorylation status in mature maize pollen and construction of maize male sterile mutants in the future. PMID:26969016

  7. Phosphoproteomic analysis of the Chlamydia caviae elementary body and reticulate body forms

    PubMed Central

    Adams, Nancy E.; Maurelli, Anthony T.

    2015-01-01

    Chlamydia are Gram-negative, obligate intracellular bacteria responsible for significant diseases in humans and economically important domestic animals. These pathogens undergo a unique biphasic developmental cycle transitioning between the environmentally stable elementary body (EB) and the replicative intracellular reticulate body (RB), a conversion that appears to require extensive regulation of protein synthesis and function. However, Chlamydia possess a limited number of canonical mechanisms of transcriptional regulation. Ser/Thr/Tyr phosphorylation of proteins in bacteria has been increasingly recognized as an important mechanism of post-translational control of protein function. We utilized 2D gel electrophoresis coupled with phosphoprotein staining and MALDI-TOF/TOF analysis to map the phosphoproteome of the EB and RB forms of Chlamydia caviae. Forty-two non-redundant phosphorylated proteins were identified (some proteins were present in multiple locations within the gels). Thirty-four phosphorylated proteins were identified in EBs, including proteins found in central metabolism and protein synthesis, Chlamydia-specific hypothetical proteins and virulence-related proteins. Eleven phosphorylated proteins were identified in RBs, mostly involved in protein synthesis and folding and a single virulence-related protein. Only three phosphoproteins were found in both EB and RB phosphoproteomes. Collectively, 41 of 42 C. caviae phosphoproteins were present across Chlamydia species, consistent with the existence of a conserved chlamydial phosphoproteome. The abundance of stage-specific phosphoproteins suggests that protein phosphorylation may play a role in regulating the function of developmental-stage-specific proteins and/or may function in concert with other factors in directing EB–RB transitions. PMID:25998263

  8. Quantitative Phosphoproteomic Analysis of Soybean Root Hairs Inoculated with Bradyrhizobium japonicum

    SciTech Connect

    Nguyen, Tran H.; Brechenmacher, Laurent; Aldrich, Joshua T.; Clauss, Therese RW; Gritsenko, Marina A.; Hixson, Kim K.; Libault, Marc; Tanaka, Kiwamu; Yang, Feng; Yao, Qiuming; Pasa-Tolic, Ljiljana; Xu, Dong; Nguyen, Henry T.; Stacey, Gary

    2012-11-11

    Root hairs are single hair-forming cells on roots that function to increase root surface area, enhancing water and nutrient uptake. In leguminous plants, root hairs also play a critical role as the site of infection by symbiotic nitrogen fixing rhizobia, leading to the formation of a novel organ, the nodule. The initial steps in the rhizobia-root hair infection process are known to involve specific receptor kinases and subsequent kinase cascades. Here, we characterize the phosphoproteome of the root hairs and the corresponding stripped roots (i.e., roots from which root hairs were removed) during rhizobial colonization and infection to gain insight into the molecular mechanism of root hair cell biology. We chose soybean (Glycine max L.), one of the most important crop plants in the legume family, for this study because of its larger root size, which permits isolation of sufficient root hair material for phosphoproteomic analysis. Phosphopeptides derived from root hairs and stripped roots, mock inoculated or inoculated with the soybean-specific rhizobium Bradyrhizobium japonicum, were labeled with the isobaric tag 8-plex ITRAQ, enriched using Ni-NTA magnetic beads and subjected to nRPLC-MS/MS analysis using HCD and decision tree guided CID/ETD strategy. A total of 1,625 unique phosphopeptides, spanning 1,659 non-redundant phosphorylation sites, were detected from 1,126 soybean phosphoproteins. Among them, 273 phosphopeptides corresponding to 240 phosphoproteins were found to be significantly regulated (>1.5 fold abundance change) in response to inoculation with B. japonicum. The data reveal unique features of the soybean root hair phosphoproteome, including root hair and stripped root-specific phosphorylation suggesting a complex network of kinase-substrate and phosphatase-substrate interactions in response to rhizobial inoculation.

  9. Langmuir mixing effects on global climate: WAVEWATCH III in CESM

    NASA Astrophysics Data System (ADS)

    Li, Qing; Webb, Adrean; Fox-Kemper, Baylor; Craig, Anthony; Danabasoglu, Gokhan; Large, William G.; Vertenstein, Mariana

    2016-07-01

    Large-Eddy Simulations (LES) have shown the effects of ocean surface gravity waves in enhancing the ocean boundary layer mixing through Langmuir turbulence. Neglecting this Langmuir mixing process may contribute to the common shallow bias in mixed layer depth in regions of the Southern Ocean and the Northern Atlantic in most state-of-the-art climate models. In this study, a third generation wave model, WAVEWATCH III, has been incorporated as a component of the Community Earth System Model, version 1.2 (CESM1.2). In particular, the wave model is now coupled with the ocean model through a modified version of the K-Profile Parameterization (KPP) to approximate the influence of Langmuir mixing. Unlike past studies, the wind-wave misalignment and the effects of Stokes drift penetration depth are considered through empirical scalings based on the rate of mixing in LES. Wave-Ocean only experiments show substantial improvements in the shallow biases of mixed layer depth in the Southern Ocean. Ventilation is enhanced and low concentration biases of pCFC-11 are reduced in the Southern Hemisphere. A majority of the improvements persist in the presence of other climate feedbacks in the fully coupled experiments. In addition, warming of the subsurface water over the majority of global ocean is observed in the fully coupled experiments with waves, and the cold subsurface ocean temperature biases are reduced.

  10. Picking the right tool for the job--Phosphoproteomics of egg activation.

    PubMed

    Wessel, Gary M

    2015-12-01

    Eggs are the rarest cell in the human body, yet their study is essential for the fields of fertility, reproduction, and fetal health. Guo et al. (Proteomics 2015, 15, 4080-4095) use a "surrogate" animal to discover the phosphoproteomic pathways involved in egg activation. With datasets of several thousand phosphosites on 2500 different proteins, these investigators have defined new pathways, connections to pathways, and priorities in searches for how eggs are activated at fertilization. These results in a sea urchin are now transposable to mammals for testing on a per candidate strategy. PMID:26573262

  11. Dataset from the global phosphoproteomic mapping of early mitotic exit in human cells.

    PubMed

    Rogers, Samuel; McCloy, Rachael A; Parker, Benjamin L; Chaudhuri, Rima; Gayevskiy, Velimir; Hoffman, Nolan J; Watkins, D Neil; Daly, Roger J; James, David E; Burgess, Andrew

    2015-12-01

    The presence or absence of a phosphorylation on a substrate at any particular point in time is a functional readout of the balance in activity between the regulatory kinase and the counteracting phosphatase. Understanding how stable or short-lived a phosphorylation site is required for fully appreciating the biological consequences of the phosphorylation. Our current understanding of kinases and their substrates is well established; however, the role phosphatases play is less understood. Therefore, we utilized a phosphatase dependent model of mitotic exit to identify potential substrates that are preferentially dephosphorylated. Using this method, we identified >16,000 phosphosites on >3300 unique proteins, and quantified the temporal phosphorylation changes that occur during early mitotic exit (McCloy et al., 2015 [1]). Furthermore, we annotated the majority of these phosphorylation sites with a high confidence upstream kinase using published, motif and prediction based methods. The results from this study have been deposited into the ProteomeXchange repository with identifier PXD001559. Here we provide additional analysis of this dataset; for each of the major mitotic kinases we identified motifs that correlated strongly with phosphorylation status. These motifs could be used to predict the stability of phosphorylated residues in proteins of interest, and help infer potential functional roles for uncharacterized phosphorylations. In addition, we provide validation at the single cell level that serine residues phosphorylated by Cdk are stable during phosphatase dependent mitotic exit. In summary, this unique dataset contains information on the temporal mitotic stability of thousands of phosphorylation sites regulated by dozens of kinases, and information on the potential preference that phosphatases have at both the protein and individual phosphosite level. The compellation of this data provides an invaluable resource for the wider research community. PMID:26425664

  12. The Effects of Globalization Phenomena on Educational Concepts

    ERIC Educational Resources Information Center

    Schrottner, Barbara Theresia

    2010-01-01

    It is becoming more and more apparent that globalization processes represent, theoretically as well as practically, a challenge for educational sciences and therefore, it must be addressed within the sphere of education. Accordingly, educational conceptions have to adapt to globalization phenomena and focus more on alternative and innovative…

  13. No globally consistent effect of ectomycorrhizal status on foliar traits.

    PubMed

    Koele, Nina; Dickie, Ian A; Oleksyn, Jacek; Richardson, Sarah J; Reich, Peter B

    2012-11-01

    The concept that ectomycorrhizal plants have a particular foliar trait suite characterized by low foliar nutrients and high leaf mass per unit area (LMA) is widely accepted, but whether this trait suite can be generalized to all ectomycorrhizal clades is unclear. We identified 19 evolutionary clades of ectomycorrhizal plants and used a global leaf traits dataset comprising 11,466 samples across c. 3000 species to test whether there were consistent shifts in leaf nutrients or LMA with the evolution of ectomycorrhiza. There were no consistent effects of ectomycorrhizal status on foliar nutrients or LMA in the 17 ectomycorrhizal/non-ectomycorrhizal pairs for which we had sufficient data, with some ectomycorrhizal groups having higher and other groups lower nutrient status than non-ectomycorrhizal contrasts. Controlling for the woodiness of host species did not alter the results. Our findings suggest that the concepts of ectomycorrhizal plant trait suites should be re-examined to ensure that they are broadly reflective of mycorrhizal status across all evolutionary clades, rather than reflecting the traits of a few commonly studied groups, such as the Pinaceae and Fagales. PMID:22966750

  14. Potential effects of global warming on calving caribou

    SciTech Connect

    Eastland, W.G.; White, R.G.

    1992-03-01

    Calving grounds of barren-ground caribou (Rangifer tarandus) are often in the portion of their range that remains covered by snow late into spring. The authors propose that global warming would alter the duration of snow cover on the calving grounds and the rate of snowmelt, and thus affect caribou population dynamics. The rationale for this hypothesis is based upon the following arguments. For females of the Porcupine Herd, one of the few forages available before and during early calving are the inflorescences of cotton grass (Eriophorum vaginatum), which are very digestible, high in nitrogen and phosphorus, and low in phenols and acid-detergent fiber. The nutritional levels of the inflorescences are highest in the early stages of phenology and decline rapidly until they are lowest at seed set, about 2 weeks after being exposed from snow cover. The high nutritional level of cotton grass inflorescences is important to post-paturient caribou attempting to meet nutritional requirements of lactation while minimizing associated weight loss. The pattern of weight regain in summer is important to herd productivity as female body weight at mating influences conception in late summer and calving success in spring. Therefore, temporal changes in snowmelt may have major effects on nutritional regimes of the female.

  15. Global priorities for an effective information basis of biodiversity distributions.

    PubMed

    Meyer, Carsten; Kreft, Holger; Guralnick, Robert; Jetz, Walter

    2015-01-01

    Gaps in digital accessible information (DAI) on species distributions hamper prospects of safeguarding biodiversity and ecosystem services, and addressing central ecological and evolutionary questions. Achieving international targets on biodiversity knowledge requires that information gaps be identified and actions prioritized. Integrating 157 million point records and distribution maps for 21,170 terrestrial vertebrate species, we find that outside a few well-sampled regions, DAI on point occurrences provides very limited and spatially biased inventories of species. Surprisingly, many large, emerging economies are even more under-represented in global DAI than species-rich, developing countries in the tropics. Multi-model inference reveals that completeness is mainly limited by distance to researchers, locally available research funding and participation in data-sharing networks, rather than transportation infrastructure, or size and funding of Western data contributors as often assumed. Our results highlight the urgent need for integrating non-Western data sources and intensifying cooperation to more effectively address societal biodiversity information needs. PMID:26348291

  16. Global priorities for an effective information basis of biodiversity distributions

    PubMed Central

    Meyer, Carsten; Kreft, Holger; Guralnick, Robert; Jetz, Walter

    2015-01-01

    Gaps in digital accessible information (DAI) on species distributions hamper prospects of safeguarding biodiversity and ecosystem services, and addressing central ecological and evolutionary questions. Achieving international targets on biodiversity knowledge requires that information gaps be identified and actions prioritized. Integrating 157 million point records and distribution maps for 21,170 terrestrial vertebrate species, we find that outside a few well-sampled regions, DAI on point occurrences provides very limited and spatially biased inventories of species. Surprisingly, many large, emerging economies are even more under-represented in global DAI than species-rich, developing countries in the tropics. Multi-model inference reveals that completeness is mainly limited by distance to researchers, locally available research funding and participation in data-sharing networks, rather than transportation infrastructure, or size and funding of Western data contributors as often assumed. Our results highlight the urgent need for integrating non-Western data sources and intensifying cooperation to more effectively address societal biodiversity information needs. PMID:26348291

  17. Towards More Efficient and Effective Global Sensitivity Analysis

    NASA Astrophysics Data System (ADS)

    Razavi, Saman; Gupta, Hoshin

    2014-05-01

    Sensitivity analysis (SA) is an important paradigm in the context of model development and application. There are a variety of approaches towards sensitivity analysis that formally describe different "intuitive" understandings of the sensitivity of a single or multiple model responses to different factors such as model parameters or forcings. These approaches are based on different philosophies and theoretical definitions of sensitivity and range from simple local derivatives to rigorous Sobol-type analysis-of-variance approaches. In general, different SA methods focus and identify different properties of the model response and may lead to different, sometimes even conflicting conclusions about the underlying sensitivities. This presentation revisits the theoretical basis for sensitivity analysis, critically evaluates the existing approaches in the literature, and demonstrates their shortcomings through simple examples. Important properties of response surfaces that are associated with the understanding and interpretation of sensitivities are outlined. A new approach towards global sensitivity analysis is developed that attempts to encompass the important, sensitivity-related properties of response surfaces. Preliminary results show that the new approach is superior to the standard approaches in the literature in terms of effectiveness and efficiency.

  18. Kicking Genomic Profiling to the Curb: How Re-wiring the Phosphoproteome Can Explain Treatment Resistance in Glioma.

    PubMed

    Lam, Fred C; Yaffe, Michael B

    2016-04-11

    In this issue of Cancer Cell, Wei et al. (2016) identify adaptive re-wiring of signaling nodes in glioma as major mechanisms of treatment resistance without genome-wide mutations. Targeting these nodes before treatment blocks resistance and underscores the importance of single-cell phosphoproteomics and network re-wiring in predicting cancer treatment responses. PMID:27070697

  19. Finite frequency effects on global S diffracted traveltimes

    NASA Astrophysics Data System (ADS)

    To, Akiko; Romanowicz, Barbara

    2009-12-01

    Many seismic observations have shown that strong heterogeneities exist in the bottom few hundreds kilometres of the mantle. Among different seismic phases, this region, that is, the D'' layer, can be most globally sampled by diffracted waves along the core mantle boundary. Here, we assess the amplitude and distribution of S-wave velocity variations in the D'' layer of an existing tomographic model. We compare observed SHdiff traveltime anomalies to synthetic ones obtained using (1) the coupled spectral element method (CSEM), which is our reference exact method, (2) non-linear asymptotic coupling theory (NACT) and (3) 1-D ray theory. Synthetic waveforms are calculated down to 0.057 Hz with a corner frequency at 0.026 Hz. In the first part of this paper, we compare the traveltime anomaly predictions from the three different methods. The anomalies from CSEM and NACT are obtained by taking cross-correlations of the 3-D and 1-D synthetic waveforms. Both NACT and standard ray theory, which are used in other recent tomographic models, suffer from biases in traveltime predictions for vertically varying structure near the core-mantle boundary: NACT suffers from saturation of traveltimes, due to the portion in the kernel calculation that is based on the reference 1-D model, while ray theory suffers from wave front healing effects in the vertical plane, exacerbated in the presence of thin low velocity layers. In the second part, we compare observed traveltime anomalies and predictions from CSEM. The data consists of 506 Sdiff traveltime anomalies from 15 events, obtained form global seismograph network records. The tomographic model does a good job at predicting traveltimes of Sdiff phases especially when the path mostly samples fast S velocity regions at the base of the mantle, such as beneath India, China, North America and Northern Pacific. The underprediction of the positive observed traveltime anomalies seems to occur in regions where the paths sample close to the border

  20. Phosphorylation-Specific MS/MS Scoring for Rapid and Accurate Phosphoproteome Analysis

    PubMed Central

    Payne, Samuel H.; Yau, Margaret; Smolka, Marcus B.; Tanner, Stephen; Zhou, Huilin; Bafna, Vineet

    2008-01-01

    The promise of mass spectrometry as a tool for probing signal-transduction is predicated on reliable identification of post-translational modifications. Phosphorylations are key mediators of cellular signaling, yet are hard to detect, partly because of unusual fragmentation patterns of phosphopeptides. In addition to being accurate, MS/MS identification software must be robust and efficient to deal with increasingly large spectral data sets. Here, we present a new scoring function for the Inspect software for phosphorylated peptide tandem mass spectra for ion-trap instruments, without the need for manual validation. The scoring function was modeled by learning fragmentation patterns from 7677 validated phosphopeptide spectra. We compare our algorithm against SEQUEST and X!Tandem on testing and training data sets. At a 1% false positive rate, Inspect identified the greatest total number of phosphorylated spectra, 13% more than SEQUEST and 39% more than X!Tandem. Spectra identified by Inspect tended to score better in several spectral quality measures. Furthermore, Inspect runs much faster than either SEQUEST or X!Tandem, making desktop phosphoproteomics feasible. Finally, we used our new models to reanalyze a corpus of 423 000 LTQ spectra acquired for a phosphoproteome analysis of Saccharomyces cerevisiae DNA damage and repair pathways and discovered 43% more phosphopeptides than the previous study. PMID:18563926

  1. Phosphoproteome mapping of cardiomyocyte mitochondria in a rat model of heart failure.

    PubMed

    Giorgianni, Francesco; Usman Khan, M; Weber, Karl T; Gerling, Ivan C; Beranova-Giorgianni, Sarka

    2014-04-01

    Mitochondria are complex organelles essential to cardiomyocyte survival. Protein phosphorylation is emerging as a key regulator of mitochondrial function. In the study reported here, we analyzed subsarcolemmal (SSM) mitochondria harvested from rats who have received 4 weeks of aldosterone/salt treatment to simulate the neurohormonal profile of human congestive heart failure. Our objective was to obtain an initial qualitative inventory of the phosphoproteins in this biologic system. SSM mitochondria were harvested, and the phosphoproteome was analyzed with a gel-free bioanalytical platform. Mitochondrial proteins were digested with trypsin, and the digests were enriched for phosphopeptides with immobilized metal ion affinity chromatography. The phosphopeptides were analyzed by ion trap liquid chromatography-tandem mass spectrometry, and the phosphoproteins identified via database searches. Based on MS/MS and MS(3) data, we characterized a set of 42 phosphopeptides that encompassed 39 phosphorylation sites. These peptides mapped to 26 proteins, for example, long-chain specific acyl-CoA dehydrogenase, Complex III subunit 6, and mitochondrial import receptor TOM70. Collectively, the characterized phosphoproteins belong to diverse functional modules, including bioenergetic pathways, protein import machinery, and calcium handling. The phosphoprotein panel discovered in this study provides a foundation for future differential phosphoproteome profiling toward an integrated understanding of the role of mitochondrial phosphorylation in heart failure. PMID:24395194

  2. Quantitative Phosphoproteomics Analysis of Nitric Oxide–Responsive Phosphoproteins in Cotton Leaf

    PubMed Central

    Song, Meizhen; Pang, Chaoyou; Wei, Hengling; Liu, Ji; Zhan, Xianjin; Lan, Jiayang; Feng, Changhui; Zhang, Shengxi; Yu, Shuxun

    2014-01-01

    Knowledge of phosphorylation events and their regulation is crucial to understanding the functional biology of plant proteins, but very little is currently known about nitric oxide–responsive phosphorylation in plants. Here, we report the first large-scale, quantitative phosphoproteome analysis of cotton (Gossypium hirsutum) treated with sodium nitroprusside (nitric oxide donor) by utilizing the isobaric tag for relative and absolute quantitation (iTRAQ) method. A total of 1315 unique phosphopeptides, spanning 1528 non-redundant phosphorylation sites, were detected from 1020 cotton phosphoproteins. Among them, 183 phosphopeptides corresponding to 167 phosphoproteins were found to be differentially phosphorylated in response to sodium nitroprusside. Several of the phosphorylation sites that we identified, including RQxS, DSxE, TxxxxSP and SPxT, have not, to our knowledge, been reported to be protein kinase sites in other species. The phosphoproteins identified are involved in a wide range of cellular processes, including signal transduction, RNA metabolism, intracellular transport and so on. This study reveals unique features of the cotton phosphoproteome and provides new insight into the biochemical pathways that are regulated by nitric oxide. PMID:24714030

  3. Dynamic Adipocyte Phosphoproteome Reveals that Akt Directly Regulates mTORC2

    PubMed Central

    Humphrey, Sean J.; Yang, Guang; Yang, Pengyi; Fazakerley, Daniel J.; Stöckli, Jacqueline; Yang, Jean Y.; James, David E.

    2013-01-01

    Summary A major challenge of the post-genomics era is to define the connectivity of protein phosphorylation networks. Here, we quantitatively delineate the insulin signaling network in adipocytes by high-resolution mass spectrometry-based proteomics. These data reveal the complexity of intracellular protein phosphorylation. We identified 37,248 phosphorylation sites on 5,705 proteins in this single-cell type, with approximately 15% responding to insulin. We integrated these large-scale phosphoproteomics data using a machine learning approach to predict physiological substrates of several diverse insulin-regulated kinases. This led to the identification of an Akt substrate, SIN1, a core component of the mTORC2 complex. The phosphorylation of SIN1 by Akt was found to regulate mTORC2 activity in response to growth factors, revealing topological insights into the Akt/mTOR signaling network. The dynamic phosphoproteome described here contains numerous phosphorylation sites on proteins involved in diverse molecular functions and should serve as a useful functional resource for cell biologists. PMID:23684622

  4. Quantitative Phosphoproteomics Reveals Signaling Mechanisms Associated with Rapid Cold Hardening in a Chill-Tolerant Fly.

    PubMed

    Teets, Nicholas M; Denlinger, David L

    2016-08-01

    Rapid cold hardening (RCH) is a physiological adaptation in which brief chilling (minutes to hours) significantly enhances the cold tolerance of insects. RCH allows insects to cope with sudden cold snaps and diurnal variation in temperature, but the mechanistic basis of this rapid stress response is poorly understood. Here, we used phosphoproteomics to identify phosphorylation-mediated signaling events that are regulated by chilling that induces RCH. Phosphoproteomic changes were measured in both brain and fat bodies, two tissues that are essential for sensing cold and coordinating RCH at the organismal level. Tissues were chilled ex vivo, and changes in phosphoprotein abundance were measured using 2D electrophoresis coupled with Pro-Q diamond labeling of phosphoproteins followed by protein identification via LC-MS/MS. In both tissues, we observed an abundance of protein phosphorylation events in response to chilling. Some of the proteins regulated by RCH-inducing chilling include proteins involved in cytoskeletal reorganization, heat shock proteins, and proteins involved in the degradation of damaged cellular components via the proteasome and autophagosome. Our results suggest that phosphorylation-mediated signaling cascades are major drivers of RCH and enhance our mechanistic understanding of this complex phenotype. PMID:27362561

  5. Comprehensive Analysis of the Membrane Phosphoproteome Regulated by Oligogalacturonides in Arabidopsis thaliana.

    PubMed

    Mattei, Benedetta; Spinelli, Francesco; Pontiggia, Daniela; De Lorenzo, Giulia

    2016-01-01

    Early changes in the Arabidopsis thaliana membrane phosphoproteome in response to oligogalacturonides (OGs), a class of plant damage-associated molecular patterns (DAMPs), were analyzed by two complementary proteomic approaches. Differentially phosphorylated sites were determined through phosphopeptide enrichment followed by LC-MS/MS using label-free quantification; differentially phosphorylated proteins were identified by 2D-DIGE combined with phospho-specific fluorescent staining (phospho-DIGE). This large-scale phosphoproteome analysis of early OG-signaling enabled us to determine 100 regulated phosphosites using LC-MS/MS and 46 differential spots corresponding to 34 pdhosphoproteins using phospho-DIGE. Functional classification showed that the OG-responsive phosphoproteins include kinases, phosphatases and receptor-like kinases, heat shock proteins (HSPs), reactive oxygen species (ROS) scavenging enzymes, proteins related to cellular trafficking, transport, defense and signaling as well as novel candidates for a role in immunity, for which elicitor-induced phosphorylation changes have not been shown before. A comparison with previously identified elicitor-regulated phosphosites shows only a very limited overlap, uncovering the immune-related regulation of 70 phosphorylation sites and revealing novel potential players in the regulation of elicitor-dependent immunity. PMID:27532006

  6. Comprehensive Analysis of the Membrane Phosphoproteome Regulated by Oligogalacturonides in Arabidopsis thaliana

    PubMed Central

    Mattei, Benedetta; Spinelli, Francesco; Pontiggia, Daniela; De Lorenzo, Giulia

    2016-01-01

    Early changes in the Arabidopsis thaliana membrane phosphoproteome in response to oligogalacturonides (OGs), a class of plant damage-associated molecular patterns (DAMPs), were analyzed by two complementary proteomic approaches. Differentially phosphorylated sites were determined through phosphopeptide enrichment followed by LC-MS/MS using label-free quantification; differentially phosphorylated proteins were identified by 2D-DIGE combined with phospho-specific fluorescent staining (phospho-DIGE). This large-scale phosphoproteome analysis of early OG-signaling enabled us to determine 100 regulated phosphosites using LC-MS/MS and 46 differential spots corresponding to 34 pdhosphoproteins using phospho-DIGE. Functional classification showed that the OG-responsive phosphoproteins include kinases, phosphatases and receptor-like kinases, heat shock proteins (HSPs), reactive oxygen species (ROS) scavenging enzymes, proteins related to cellular trafficking, transport, defense and signaling as well as novel candidates for a role in immunity, for which elicitor-induced phosphorylation changes have not been shown before. A comparison with previously identified elicitor-regulated phosphosites shows only a very limited overlap, uncovering the immune-related regulation of 70 phosphorylation sites and revealing novel potential players in the regulation of elicitor-dependent immunity. PMID:27532006

  7. Off-line high-pH reversed-phase fractionation for in-depth phosphoproteomics.

    PubMed

    Batth, Tanveer S; Francavilla, Chiara; Olsen, Jesper V

    2014-12-01

    Protein phosphorylation is an important post-translational modification (PTM) involved in embryonic development, adult homeostasis, and disease. Over the past decade, several advances have been made in liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based technologies to identify thousands of phosphorylation sites. However, in-depth phosphoproteomics often require off-line enrichment and fractionation techniques. In this study, we provide a detailed analysis of the physicochemical characteristics of phosphopeptides, which have been fractionated by off-line high-pH chromatography (HpH) before subsequent titanium dioxide (TiO2) enrichment and LC-MS/MS analysis. Our results demonstrate that HpH is superior to standard strong-cation exchange (SCX) fractionation in the total number of phosphopeptides detected when analyzing the same number of fractions by identical LC-MS/MS gradients. From 14 HpH fractions, we routinely identified over 30,000 unique phosphopeptide variants, which is more than twice the number of that obtained from SCX fractionation. HpH chromatography displayed an exceptional ability to fractionate singly phosphorylated peptides, with minor benefits for doubly phosphorylated peptides over that with SCX. Further optimizations in the pooling and concatenation strategy increased the total number of multiphosphorylated peptides detected after HpH fractionation. In conclusion, we provide a basic framework and resource for performing in-depth phosphoproteome studies utilizing off-line basic reversed-phased fractionation. Raw data is available at ProteomeXchange (PXD001404). PMID:25338131

  8. Phosphoproteome mapping of cardiomyocyte mitochondria in a rat model of heart failure

    PubMed Central

    Giorgianni, Francesco; Khan, M. Usman; Weber, Karl T.; Gerling, Ivan C.; Beranova-Giorgianni, Sarka

    2014-01-01

    Mitochondria are complex organelles essential to cardiomyocyte survival. Protein phosphorylation is emerging as a key regulator of mitochondrial function. In the study reported here, we analyzed subsarcolemmal mitochondria harvested from rats who have received 4 weeks of aldosterone/salt treatment to simulate the neurohormonal profile of human congestive heart failure. Our objective was to obtain an initial qualitative inventory of the phosphoproteins in this biological system. Subsarcolemmal mitochondria were harvested and the phosphoproteome was analyzed with a gel-free bioanalytical platform. Mitochondrial proteins were digested with trypsin, and the digests were enriched for phosphopeptides with Immobilized Metal Ion Affinity Chromatography (IMAC). The phosphopeptides were analyzed by ion trap LC-MS/MS, and the phosphoproteins identified via database searches. Based on MS/MS and MS3 data, we characterized a set of 42 phosphopeptides that encompassed 39 phosphorylation sites. These peptides mapped to 26 proteins, for example long-chain specific acyl-CoA dehydrogenase (LCAD), Complex III subunit 6, and mitochondrial import receptor TOM70. Collectively, the characterized phosphoproteins belong to diverse functional modules, including bioenergetic pathways, protein import machinery, and calcium handling. The phosphoprotein panel discovered in this study provides a foundation for future differential phosphoproteome profiling towards an integrated understanding of the role of mitochondrial phosphorylation in heart failure. PMID:24395194

  9. Understanding the Development and Perception of Global Health for More Effective Student Education

    PubMed Central

    Chen, Xinguang

    2014-01-01

    The concept of “global health” that led to the establishment of the World Health Organization in the 1940s is still promoting a global health movement 70 years later. Today’s global health acts first as a guiding principle for our effort to improve people’s health across the globe. Furthermore, global health has become a branch of science, “global health science,” supporting institutionalized education. Lastly, as a discipline, global health should focus on medical and health issues that: 1) are determined primarily by factors with a cross-cultural, cross-national, cross-regional, or global scope; 2) are local but have global significance if not appropriately managed; and 3) can only be efficiently managed through international or global efforts. Therefore, effective global health education must train students 1) to understand global health status; 2) to investigate both global and local health issues with a global perspective; and 3) to devise interventions to deal with these issues. PMID:25191139

  10. Auditory global-local processing: effects of attention and musical experience.

    PubMed

    Ouimet, Tia; Foster, Nicholas E V; Hyde, Krista L

    2012-10-01

    In vision, global (whole) features are typically processed before local (detail) features ("global precedence effect"). However, the distinction between global and local processing is less clear in the auditory domain. The aims of the present study were to investigate: (i) the effects of directed versus divided attention, and (ii) the effect musical training on auditory global-local processing in 16 adult musicians and 16 non-musicians. Participants were presented with short nine-tone melodies, each comprised of three triplet sequences (three-tone units). In a "directed attention" task, participants were asked to focus on either the global or local pitch pattern and had to determine if the pitch pattern went up or down. In a "divided attention" task, participants judged whether the target pattern (up or down) was present or absent. Overall, global structure was perceived faster and more accurately than local structure. The global precedence effect was observed regardless of whether attention was directed to a specific level or divided between levels. Musicians performed more accurately than non-musicians overall, but non-musicians showed a more pronounced global advantage. This study provides evidence for an auditory global precedence effect across attention tasks, and for differences in auditory global-local processing associated with musical experience. PMID:23039447

  11. Effects of climate variability on global scale flood risk

    NASA Astrophysics Data System (ADS)

    Ward, P.; Dettinger, M. D.; Kummu, M.; Jongman, B.; Sperna Weiland, F.; Winsemius, H.

    2013-12-01

    In this contribution we demonstrate the influence of climate variability on flood risk. Globally, flooding is one of the worst natural hazards in terms of economic damages; Munich Re estimates global losses in the last decade to be in excess of $240 billion. As a result, scientifically sound estimates of flood risk at the largest scales are increasingly needed by industry (including multinational companies and the insurance industry) and policy communities. Several assessments of global scale flood risk under current and conditions have recently become available, and this year has seen the first studies assessing how flood risk may change in the future due to global change. However, the influence of climate variability on flood risk has as yet hardly been studied, despite the fact that: (a) in other fields (drought, hurricane damage, food production) this variability is as important for policy and practice as long term change; and (b) climate variability has a strong influence in peak riverflows around the world. To address this issue, this contribution illustrates the influence of ENSO-driven climate variability on flood risk, at both the globally aggregated scale and the scale of countries and large river basins. Although it exerts significant and widespread influences on flood peak discharges in many parts of the world, we show that ENSO does not have a statistically significant influence on flood risk once aggregated to global totals. At the scale of individual countries, though, strong relationships exist over large parts of the Earth's surface. For example, we find particularly strong anomalies of flood risk in El Niño or La Niña years (compared to all years) in southern Africa, parts of western Africa, Australia, parts of Central Eurasia (especially for El Niño), the western USA (especially for La Niña), and parts of South America. These findings have large implications for both decadal climate-risk projections and long-term future climate change

  12. Exploratory investigation on nitro- and phospho-proteome cerebellum changes in hyperammonemia and hepatic encephalopathy rat models.

    PubMed

    Brunelli, Laura; Campagna, Roberta; Airoldi, Luisa; Cauli, Omar; Llansola, Marta; Boix, Jordi; Felipo, Vicente; Pastorelli, Roberta

    2012-03-01

    Hepatic encephalopathy (HE) is a neurological disease associated with hepatic dysfunction. Current knowledge suggests that hyperammonemia, related to liver failure, is a main factor contributing to the cerebral alterations in HE and that hyperammonemia might impair signal transduction associated with post-translational modification of proteins such as tyrosine-nitration and phosphorylation. However, the molecular bases of the HE remain unclear and very little is known about the occurrence of post-translational modification on in vivo proteins. In this exploratory study we look for evidence of post-translation modifications of proteins in the cerebellum of experimental HE rat models using a proteomic approach. For the first time we showed that hyperammonemia without liver failure (HA rats) and experimental HE with liver failure due to portacaval shunt (PCS rats) lead to a reduced protein nitration in rat cerebellum, where the undernitrated proteins were involved in energy metabolism and cytoskeleton remodelling. Moreover we showed that tyrosine nitration loss of these proteins was not necessarily associated to a change in their phosphorylation state as result of the disease. Interestingly the rat cerebellum phosphoproteome was mainly perturbed in PCS rats, whereas HA rats did not shown appreciable changes in their phosphoprotein profile. Since the protein nitration level decreased similarly in the cerebellum of both HA and PCS rats, this implies that the two disease models share common effects but also present some differential signalling effects in the cerebellum of the same animals. This study highlights the interest for studying the concerted action of multiple signalling pathways in HE development. PMID:22083566

  13. Using Interactive Technology to Support Students' Understanding of the Greenhouse Effect and Global Warming

    ERIC Educational Resources Information Center

    Varma, Keisha; Linn, Marcia C.

    2012-01-01

    In this work, we examine middle school students' understanding of the greenhouse effect and global warming. We designed and refined a technology-enhanced curriculum module called "Global Warming: Virtual Earth". In the module activities, students conduct virtual experiments with a visualization of the greenhouse effect. They analyze data and draw…

  14. Commercial Complexity and Local and Global Involvement in Programs: Effects on Viewer Responses.

    ERIC Educational Resources Information Center

    Oberman, Heiko; Thorson, Esther

    A study investigated the effects of local (momentary) and global (whole program) involvement in program context and the effects of message complexity on the retention of television commercials. Sixteen commercials, categorized as simple video/simple audio through complex video/complex audio were edited into two globally high- and two globally…

  15. Effects of mountain uplift on global monsoon precipitation

    NASA Astrophysics Data System (ADS)

    Lee, June-Yi; Wang, Bin; Seo, Kyong-Hwan; Ha, Kyung-Ja; Kitoh, Akio; Liu, Jian

    2015-08-01

    This study explores the role of the global mountain uplift (MU), which occurred during the middle and late Cenozoic, in modulating global monsoon precipitation using the Meteorological Research Institute atmosphere-ocean coupled model experiments. First, the MU causes changes in the annual mean of major monsoon precipitation. Although the annual mean precipitation over the entire globe remains about the same from the no-mountain experiment (MU0) to the realistic MU (MU1), that over the Asian-Australian monsoon region and Americas increases by about 16% and 9%, respectively. Second, the MU plays an essential role in advancing seasonal march, and summer-monsoon onset, especially in the Northern Hemisphere, by shaping pre-monsoon circulation. The rainy seasons are lengthened as a result of the earlier onset of the summer monsoon since the monsoon retreat is not sensitive to the MU. The East Asian monsoon is a unique consequence of the MU, while other monsoons are attributed primarily to land-sea distribution. Third, the strength of the global monsoon is shown to be substantially affected by the MU. In particular, the second annual cycle (AC) mode of global precipitation (the spring-autumn asymmetry mode) is more sensitive to the progressive MU than the first mode of the AC (the solstice mode), suggesting that the MU may have a greater impact during transition seasons than solstice seasons. Finally, the MU strongly modulates interannual variation in global monsoon precipitation in relation to El Niño and Southern Oscillation (ENSO). The Progressive MU changes not only the spatial distribution but also the periodicity of the first and second AC mode of global precipitation on interannual timescale.

  16. Studying mechanisms of cAMP and cyclic nucleotide phosphodiesterase signaling in Leydig cell function with phosphoproteomics.

    PubMed

    Golkowski, Martin; Shimizu-Albergine, Masami; Suh, Hyong Won; Beavo, Joseph A; Ong, Shao-En

    2016-07-01

    Many cellular processes are modulated by cyclic AMP and nucleotide phosphodiesterases (PDEs) regulate this second messenger by catalyzing its breakdown. The major unique function of testicular Leydig cells is to produce testosterone in response to luteinizing hormone (LH). Treatment of Leydig cells with PDE inhibitors increases cAMP levels and the activity of its downstream effector, cAMP-dependent protein kinase (PKA), leading to a series of kinase-dependent signaling and transcription events that ultimately increase testosterone release. We have recently shown that PDE4B and PDE4C as well as PDE8A and PDE8B are expressed in rodent Leydig cells and that combined inhibition of PDE4 and PDE8 leads to dramatically increased steroid biosynthesis. Here we investigated the effect of PDE4 and PDE8 inhibition on the molecular mechanisms of cAMP actions in a mouse MA10 Leydig cell line model with SILAC mass spectrometry-based phosphoproteomics. We treated MA10 cells either with PDE4 family specific inhibitor (Rolipram) and PDE8 family specific inhibitor (PF-04957325) alone or in combination and quantified the resulting phosphorylation changes at five different time points between 0 and 180min. We identified 28,336 phosphosites from 4837 proteins and observed significant regulation of 749 sites in response to PDE4 and PDE8 inhibitor treatment. Of these, 132 phosphosites were consensus PKA sites. Our data strongly suggest that PDE4 and PDE8 inhibitors synergistically regulate phosphorylation of proteins required for many different cellular processes, including cell cycle progression, lipid and glucose metabolism, transcription, endocytosis and vesicle transport. Our data suggests that cAMP, PDE4 and PDE8 coordinate steroidogenesis by acting on not one rate-limiting step but rather multiple pathways. Moreover, the pools of cAMP controlled by these PDEs also coordinate many other metabolic processes that may be regulated to assure timely and sufficient testosterone secretion

  17. Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation

    SciTech Connect

    Yang, Feng; Waters, Katrina M.; Miller, John H.; Gritsenko, Marina A.; Zhao, Rui; Du, Xiuxia; Livesay, Eric A.; Purvine, Samuel O.; Monroe, Matthew E.; Wang, Yingchun; Camp, David G.; Smith, Richard D.; Stenoien, David L.

    2010-11-30

    Background: 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. Principle Findings: We have identified 6845 unique phosphopeptides (2566 phosphoproteins) from control and irradiated (2 and 50 cGy) primary human skin fibroblasts one hour post-exposure. Dual statistical analyses based on spectral counts and peak intensities identified 287 phosphopeptides (from 231 proteins) and 244 phosphopeptides (from 182 proteins) that varied significantly following exposure to 2 and 50 cGy respectively. This screen identified phosphorylation sites on proteins with known roles in radiation responses including TP53BP1 as well as previously unidentified radiation responsive proteins such as the candidate tumor suppressor SASH1. Bioinformatics analyses suggest that low and high doses of radiation affect both overlapping and unique biological processes and suggest a role of MAP kinase and protein kinase A (PKA) signaling in the radiation response as well as differential regulation of p53 networks at low and high doses of radiation. Conlcusions: Our results represent the most comprehensive analysis of the phosphoproteomes of human primary fibroblasts exposed to multiple doses of ionizing radiation published to date and provides a basis for the systems level identification of biological processes, molecular pathways and individual proteins regulated in a dose dependent manner by ionizing radiation. Further study of these modified proteins and affected networks should help to define the molecular mechanisms that regulate biological responses to radiation at

  18. Searching for novel Cdk5 substrates in brain by comparative phosphoproteomics of wild type and Cdk5-/- mice.

    PubMed

    Contreras-Vallejos, Erick; Utreras, Elías; Bórquez, Daniel A; Prochazkova, Michaela; Terse, Anita; Jaffe, Howard; Toledo, Andrea; Arruti, Cristina; Pant, Harish C; Kulkarni, Ashok B; González-Billault, Christian

    2014-01-01

    Protein phosphorylation is the most common post-translational modification that regulates several pivotal functions in cells. Cyclin-dependent kinase 5 (Cdk5) is a proline-directed serine/threonine kinase which is mostly active in the nervous system. It regulates several biological processes such as neuronal migration, cytoskeletal dynamics, axonal guidance and synaptic plasticity among others. In search for novel substrates of Cdk5 in the brain we performed quantitative phosphoproteomics analysis, isolating phosphoproteins from whole brain derived from E18.5 Cdk5+/+ and Cdk5-/- embryos, using an Immobilized Metal-Ion Affinity Chromatography (IMAC), which specifically binds to phosphorylated proteins. The isolated phosphoproteins were eluted and isotopically labeled for relative and absolute quantitation (iTRAQ) and mass spectrometry identification. We found 40 proteins that showed decreased phosphorylation at Cdk5-/- brains. In addition, out of these 40 hypophosphorylated proteins we characterized two proteins, :MARCKS (Myristoylated Alanine-Rich protein Kinase C substrate) and Grin1 (G protein regulated inducer of neurite outgrowth 1). MARCKS is known to be phosphorylated by Cdk5 in chick neural cells while Grin1 has not been reported to be phosphorylated by Cdk5. When these proteins were overexpressed in N2A neuroblastoma cell line along with p35, serine phosphorylation in their Cdk5 motifs was found to be increased. In contrast, treatments with roscovitine, the Cdk5 inhibitor, resulted in an opposite effect on serine phosphorylation in N2A cells and primary hippocampal neurons transfected with MARCKS. In summary, the results presented here identify Grin 1 as novel Cdk5 substrate and confirm previously identified MARCKS as a a bona fide Cdk5 substrate. PMID:24658276

  19. EFFECTS OF GLOBAL CHANGE ON CORAL REEF ECOSYSTEMS

    EPA Science Inventory

    Corals and coral reefs of the Caribbean and through the world are deteriorating at an accelerated rate. Several stressors are believed to contrbute to this decline, including global changes in atmospheric gases and land use patterns. In particular, warmer water temperatures and...

  20. Global efforts for effective training in fistula surgery.

    PubMed

    Elneil, Sohier

    2015-10-01

    Obstetric fistulas continue to be a problem in low- and middle-income nations, affecting women of childbearing age during pregnancy and labor and resulting in debilitating urinary and/or fecal incontinence. Historically, this predicament also affected women in high-income nations until the middle of the last century. This is not a "new world" crisis therefore, but simply one of economic and health development. In the last two decades, new global initiatives have been instituted to improve training and education in preventative and curative fistula treatment by developing a unified and competency-based learning tool by surgeons in the field in partnership with FIGO and its global partners. This modern approach to the management of a devastating condition can only serve to achieve the WHO objective of health security for women throughout their life span. PMID:26433511

  1. Global effects of land use on local terrestrial biodiversity.

    PubMed

    Newbold, Tim; Hudson, Lawrence N; Hill, Samantha L L; Contu, Sara; Lysenko, Igor; Senior, Rebecca A; Börger, Luca; Bennett, Dominic J; Choimes, Argyrios; Collen, Ben; Day, Julie; De Palma, Adriana; Díaz, Sandra; Echeverria-Londoño, Susy; Edgar, Melanie J; Feldman, Anat; Garon, Morgan; Harrison, Michelle L K; Alhusseini, Tamera; Ingram, Daniel J; Itescu, Yuval; Kattge, Jens; Kemp, Victoria; Kirkpatrick, Lucinda; Kleyer, Michael; Correia, David Laginha Pinto; Martin, Callum D; Meiri, Shai; Novosolov, Maria; Pan, Yuan; Phillips, Helen R P; Purves, Drew W; Robinson, Alexandra; Simpson, Jake; Tuck, Sean L; Weiher, Evan; White, Hannah J; Ewers, Robert M; Mace, Georgina M; Scharlemann, Jörn P W; Purvis, Andy

    2015-04-01

    Human activities, especially conversion and degradation of habitats, are causing global biodiversity declines. How local ecological assemblages are responding is less clear--a concern given their importance for many ecosystem functions and services. We analysed a terrestrial assemblage database of unprecedented geographic and taxonomic coverage to quantify local biodiversity responses to land use and related changes. Here we show that in the worst-affected habitats, these pressures reduce within-sample species richness by an average of 76.5%, total abundance by 39.5% and rarefaction-based richness by 40.3%. We estimate that, globally, these pressures have already slightly reduced average within-sample richness (by 13.6%), total abundance (10.7%) and rarefaction-based richness (8.1%), with changes showing marked spatial variation. Rapid further losses are predicted under a business-as-usual land-use scenario; within-sample richness is projected to fall by a further 3.4% globally by 2100, with losses concentrated in biodiverse but economically poor countries. Strong mitigation can deliver much more positive biodiversity changes (up to a 1.9% average increase) that are less strongly related to countries' socioeconomic status. PMID:25832402

  2. Direct health effects of global warming in Japan and China

    SciTech Connect

    Ando, M.; Yamamoto, S.; Tamura, K.

    1997-12-31

    Combustion of fossil fuels and industrial and agricultural activities are resulting in greater emissions of some greenhouse gases such as carbon dioxide and methane into the atmosphere, therefore contributing to global warming. Using general circulation models, it is estimated that surface temperatures in temperate regions will rise 1 to 3 degrees C during the next 100 years. Because global warming may increase the frequency and length of high temperatures during hot summer months, various health risks caused by heat stress have been studied. According to our epidemiological survey, the incidence of heat-related illness was significantly correlated to hot environments in Tokyo, Japan and in Nanjing and Wuhan, China. The epidemiological results also showed that the incidence of heat-related morbidity and mortality in the elderly increased very rapidly in summer. The regression analysis on these data showed that the number of heat stroke patients increased exponentially when the mean daily temperature and maximum daily temperature exceeded 27C and 32C in Tokyo and 31C and 36C in Wuhan and Nanjing, respectively. Since the incidence of heat-related morbidity and mortality has been shown to increase as a result of exposure to long periods of hot summer temperatures, it is important to determine to what extent the incidence of heat stress-related morbidity and mortality will be affected as a result of global warming.

  3. Global effects of land use on local terrestrial biodiversity

    NASA Astrophysics Data System (ADS)

    Newbold, Tim; Hudson, Lawrence N.; Hill, Samantha L. L.; Contu, Sara; Lysenko, Igor; Senior, Rebecca A.; Börger, Luca; Bennett, Dominic J.; Choimes, Argyrios; Collen, Ben; Day, Julie; de Palma, Adriana; Díaz, Sandra; Echeverria-Londoño, Susy; Edgar, Melanie J.; Feldman, Anat; Garon, Morgan; Harrison, Michelle L. K.; Alhusseini, Tamera; Ingram, Daniel J.; Itescu, Yuval; Kattge, Jens; Kemp, Victoria; Kirkpatrick, Lucinda; Kleyer, Michael; Correia, David Laginha Pinto; Martin, Callum D.; Meiri, Shai; Novosolov, Maria; Pan, Yuan; Phillips, Helen R. P.; Purves, Drew W.; Robinson, Alexandra; Simpson, Jake; Tuck, Sean L.; Weiher, Evan; White, Hannah J.; Ewers, Robert M.; Mace, Georgina M.; Scharlemann, Jörn P. W.; Purvis, Andy

    2015-04-01

    Human activities, especially conversion and degradation of habitats, are causing global biodiversity declines. How local ecological assemblages are responding is less clear--a concern given their importance for many ecosystem functions and services. We analysed a terrestrial assemblage database of unprecedented geographic and taxonomic coverage to quantify local biodiversity responses to land use and related changes. Here we show that in the worst-affected habitats, these pressures reduce within-sample species richness by an average of 76.5%, total abundance by 39.5% and rarefaction-based richness by 40.3%. We estimate that, globally, these pressures have already slightly reduced average within-sample richness (by 13.6%), total abundance (10.7%) and rarefaction-based richness (8.1%), with changes showing marked spatial variation. Rapid further losses are predicted under a business-as-usual land-use scenario; within-sample richness is projected to fall by a further 3.4% globally by 2100, with losses concentrated in biodiverse but economically poor countries. Strong mitigation can deliver much more positive biodiversity changes (up to a 1.9% average increase) that are less strongly related to countries' socioeconomic status.

  4. Effects of boreal forest vegetation on global climate

    NASA Astrophysics Data System (ADS)

    Bonan, Gordon B.; Pollard, David; Thompson, Starley L.

    1992-10-01

    TERRESTRIAL ecosystems are thought to play an important role in determining regional and global climate1-6 one example of this is in Amazonia, where destruction of the tropical rainforest leads to warmer and drier conditions4-6. Boreal forest ecosystems may also affect climate. As temperatures rise, the amount of continental and oceanic snow and ice is reduced, so the land and ocean surfaces absorb greater amounts of solar radiation, reinforcing the warming in a 'snow/ice/albedo' feedback which results in large climate sensitivity to radiative forcings7-9. This sensitivity is moderated, however, by the presence of trees in northern latitudes, which mask the high reflectance of snow10,11, leading to warmer winter temperatures than if trees were not present12-14. Here we present results from a global climate model which show that the boreal forest warms both winter and summer air temperatures, relative to simulations in which the forest is replaced with bare ground or tundra vegetation. Our results suggest that future redistributions of boreal forest and tundra vegetation (due, for example, to extensive logging, or the influence of global warming) could initiate important climate feedbacks, which could also extend to lower latitudes.

  5. Recent findings and technological advances in phosphoproteomics for cells and tissues

    PubMed Central

    von Stechow, Louise; Francavilla, Chiara; Olsen, Jesper V

    2015-01-01

    Site-specific phosphorylation is a fast and reversible covalent post-translational modification that is tightly regulated in cells. The cellular machinery of enzymes that write, erase and read these modifications (kinases, phosphatases and phospho-binding proteins) is frequently deregulated in different diseases, including cancer. Large-scale studies of phosphoproteins – termed phosphoproteomics – strongly rely on the use of high-performance mass spectrometric instrumentation. This powerful technology has been applied to study a great number of phosphorylation-based phenotypes. Nevertheless, many technical and biological challenges have to be overcome to identify biologically relevant phosphorylation sites in cells and tissues. This review describes different technological strategies to identify and quantify phosphorylation sites with high accuracy, without significant loss of analysis speed and reproducibility in tissues and cells. Moreover, computational tools for analysis, integration and biological interpretation of phosphorylation events are discussed. PMID:26400465

  6. Spatial proteomic and phospho-proteomic organization in three prototypical cell migration modes

    PubMed Central

    2014-01-01

    Background Tight spatio-temporal signaling of cytoskeletal and adhesion dynamics is required for localized membrane protrusion that drives directed cell migration. Different ensembles of proteins are therefore likely to get recruited and phosphorylated in membrane protrusions in response to specific cues. Results Here, we use an assay that allows to biochemically purify extending protrusions of cells migrating in response to three prototypical receptors: integrins, recepor tyrosine kinases and G-coupled protein receptors. Using quantitative proteomics and phospho-proteomics approaches, we provide evidence for the existence of cue-specific, spatially distinct protein networks in the different cell migration modes. Conclusions The integrated analysis of the large-scale experimental data with protein information from databases allows us to understand some emergent properties of spatial regulation of signaling during cell migration. This provides the cell migration community with a large-scale view of the distribution of proteins and phospho-proteins regulating directed cell migration. PMID:24987309

  7. Single-Cell Phosphoproteomics Resolves Adaptive Signaling Dynamics and Informs Targeted Combination Therapy in Glioblastoma.

    PubMed

    Wei, Wei; Shin, Young Shik; Xue, Min; Matsutani, Tomoo; Masui, Kenta; Yang, Huijun; Ikegami, Shiro; Gu, Yuchao; Herrmann, Ken; Johnson, Dazy; Ding, Xiangming; Hwang, Kiwook; Kim, Jungwoo; Zhou, Jian; Su, Yapeng; Li, Xinmin; Bonetti, Bruno; Chopra, Rajesh; James, C David; Cavenee, Webster K; Cloughesy, Timothy F; Mischel, Paul S; Heath, James R; Gini, Beatrice

    2016-04-11

    Intratumoral heterogeneity of signaling networks may contribute to targeted cancer therapy resistance, including in the highly lethal brain cancer glioblastoma (GBM). We performed single-cell phosphoproteomics on a patient-derived in vivo GBM model of mTOR kinase inhibitor resistance and coupled it to an analytical approach for detecting changes in signaling coordination. Alterations in the protein signaling coordination were resolved as early as 2.5 days after treatment, anticipating drug resistance long before it was clinically manifest. Combination therapies were identified that resulted in complete and sustained tumor suppression in vivo. This approach may identify actionable alterations in signal coordination that underlie adaptive resistance, which can be suppressed through combination drug therapy, including non-obvious drug combinations. PMID:27070703

  8. Quantitative phosphoproteomic analysis of the PI3K-regulated signaling network.

    PubMed

    Gnad, Florian; Wallin, Jeffrey; Edgar, Kyle; Doll, Sophia; Arnott, David; Robillard, Liliane; Kirkpatrick, Donald S; Stokes, Matthew P; Vijapurkar, Ulka; Hatzivassiliou, Georgia; Friedman, Lori S; Belvin, Marcia

    2016-07-01

    The PI3K pathway is commonly activated in cancer. Only a few studies have attempted to explore the spectrum of phosphorylation signaling downstream of the PI3K cascade. Such insight, however, is imperative to understand the mechanisms responsible for oncogenic phenotypes. By applying MS-based phosphoproteomics, we mapped 2509 phosphorylation sites on 1096 proteins, and quantified their responses to activation or inhibition of PIK3CA using isogenic knock-in derivatives and a series of targeted inhibitors. We uncovered phosphorylation changes in a wide variety of proteins involved in cell growth and proliferation, many of which have not been previously associated with PI3K signaling. A significant update of the posttranslational modification database PHOSIDA (http://www.phosida.com) allows efficient use of the data. All MS data have been deposited in the ProteomeXchange with identifier PXD003899 (http://proteomecentral.proteomexchange.org/dataset/PXD003899). PMID:27282143

  9. Systematic profiling of the bacterial phosphoproteome reveals bacterium-specific features of phosphorylation.

    PubMed

    Lin, Miao-Hsia; Sugiyama, Naoyuki; Ishihama, Yasushi

    2015-09-15

    Protein phosphorylation is a crucial posttranslational modification for regulating cellular processes in bacteria; however, it has not been extensively studied because of technical difficulties in the enrichment of phosphopeptides. We devised an enrichment protocol that enabled the identification of >1000 phosphopeptides from a single bacterial sample. We discovered three high-confidence serine and threonine phosphorylation motifs, as well as 29 other motifs at various levels of confidence, from three distinct bacterial phosphoproteomes. We found that the proline-directed and basophilic phosphorylation motifs that are commonly enriched in eukaryotes were not observed in bacteria. Unlike eukaryotes, bacteria had a low occurrence of both phosphorylation and acetylation in N-terminal phosphopeptides. Because infection of host cells by bacterial pathogens is often accompanied by kinase-mediated phosphorylation events, the differences in phosphorylation preferences between bacteria and eukaryotes revealed by this study could be useful in identifying bacterial-specific targets for future therapies. PMID:26373674

  10. Characterization of the human plasma phosphoproteome using linear ion trap mass spectrometry and multiple search engines.

    PubMed

    Carrascal, Montserrat; Gay, Marina; Ovelleiro, David; Casas, Vanessa; Gelpí, Emilio; Abian, Joaquin

    2010-02-01

    Major plasma protein families play different roles in blood physiology and hemostasis and in immunodefense. Other proteins in plasma can be involved in signaling as chemical messengers or constitute biological markers of the status of distant tissues. In this respect, the plasma phosphoproteome holds potentially relevant information on the mechanisms modulating these processes through the regulation of protein activity. In this work we describe for the first time a collection of phosphopeptides identified in human plasma using immunoaffinity separation of the seven major serum protein families from other plasma proteins, SCX fractionation, and TiO(2) purification prior to LC-MS/MS analysis. One-hundred and twenty-seven phosphosites in 138 phosphopeptides mapping 70 phosphoproteins were identified with FDR < 1%. A high-confidence collection of phosphosites was obtained using a combined search with the OMSSA, SEQUEST, and Phenyx search engines. PMID:19941383

  11. The beginnings of crop phosphoproteomics: exploring early warning systems of stress

    PubMed Central

    Rampitsch, Christof; Bykova, Natalia V.

    2012-01-01

    This review examines why a knowledge of plant protein phosphorylation events is important in devising strategies to protect crops from both biotic and abiotic stresses, and why proteomics should be included when studying stress pathways. Most of the achievements in elucidating phospho-signaling pathways in biotic and abiotic stress are reported from model systems: while these are discussed, this review attempts mainly to focus on work done with crops, with examples of achievements reported from rice, maize, wheat, grape, Brassica, tomato, and soy bean after cold acclimation, hormonal and oxidative hydrogen peroxide treatment, salt stress, mechanical wounding, or pathogen challenge. The challenges that remain to transfer this information into a format that can be used to protect crops against biotic and abiotic stresses are enormous. The tremendous increase in the speed and ease of DNA sequencing is poised to reveal the whole genomes of many crop species in the near future, which will facilitate phosphoproteomics and phosphogenomics research. PMID:22783265

  12. Global Warming Responses at the Primary Secondary Interface: 2. Potential Effectiveness of Education

    ERIC Educational Resources Information Center

    Skamp, Keith; Boyes, Eddie; Stannistreet, Martin

    2009-01-01

    In an earlier paper (Skamp, Boyes, & Stanisstreet, 2009b), students' beliefs and willingness to act in relation to 16 specific actions related to global warming were compared across the primary secondary interface. More primary students believed in the effectiveness of most actions to reduce global warming and were willing to take those actions.…

  13. Age and Gender Effects on Global Self-Esteem and Physical Self-Perception in Adolescents

    ERIC Educational Resources Information Center

    Maiano, Christophe; Ninot, Gregory; Bilard, Jean

    2004-01-01

    This study measured the effects of gender, age and their interaction on global self-esteem and physical self-perceptions (physical self-worth, PSW; physical condition, PC; physical strength, PS; attractive body, AB; sport competence, SC) of French adolescents. Global self-esteem (GSE) and physical self-perceptions were measured by the Physical…

  14. Phosphoproteomic Analyses Reveal Early Signaling Events in the Osmotic Stress Response1[W][OPEN

    PubMed Central

    E. Stecker, Kelly; Minkoff, Benjamin B.; Sussman, Michael R.

    2014-01-01

    Elucidating how plants sense and respond to water loss is important for identifying genetic and chemical interventions that may help sustain crop yields in water-limiting environments. Currently, the molecular mechanisms involved in the initial perception and response to dehydration are not well understood. Modern mass spectrometric methods for quantifying changes in the phosphoproteome provide an opportunity to identify key phosphorylation events involved in this process. Here, we have used both untargeted and targeted isotope-assisted mass spectrometric methods of phosphopeptide quantitation to characterize proteins in Arabidopsis (Arabidopsis thaliana) whose degree of phosphorylation is rapidly altered by hyperosmotic treatment. Thus, protein phosphorylation events responsive to 5 min of 0.3 m mannitol treatment were first identified using 15N metabolic labeling and untargeted mass spectrometry with a high-resolution ion-trap instrument. The results from these discovery experiments were then validated using targeted Selected Reaction Monitoring mass spectrometry with a triple quadrupole. Targeted Selected Reaction Monitoring experiments were conducted with plants treated under nine different environmental perturbations to determine whether the phosphorylation changes were specific for osmosignaling or involved cross talk with other signaling pathways. The results indicate that regulatory proteins such as members of the mitogen-activated protein kinase family are specifically phosphorylated in response to osmotic stress. Proteins involved in 5′ messenger RNA decapping and phosphatidylinositol 3,5-bisphosphate synthesis were also identified as targets of dehydration-induced phosphoregulation. The results of these experiments demonstrate the utility of targeted phosphoproteomic analysis in understanding protein regulation networks and provide new insight into cellular processes involved in the osmotic stress response. PMID:24808101

  15. Phosphatase of Regenerating Liver 3 (PRL3) Provokes a Tyrosine Phosphoproteome to Drive Prometastatic Signal Transduction*

    PubMed Central

    Walls, Chad D.; Iliuk, Anton; Bai, Yunpeng; Wang, Mu; Tao, W. Andy; Zhang, Zhong-Yin

    2013-01-01

    Phosphatase of regenerating liver 3 (PRL3) is suspected to be a causative factor toward cellular metastasis when in excess. To date, the molecular basis for PRL3 function remains an enigma, making efforts at distilling a concerted mechanism for PRL3-mediated metastatic dissemination very difficult. We previously discovered that PRL3 expressing cells exhibit a pronounced increase in protein tyrosine phosphorylation. Here we take an unbiased mass spectrometry-based approach toward identifying the phosphoproteins exhibiting enhanced levels of tyrosine phosphorylation with a goal to define the “PRL3-mediated signaling network.” Phosphoproteomic data support intracellular activation of an extensive signaling network normally governed by extracellular ligand-activated transmembrane growth factor, cytokine, and integrin receptors in the PRL3 cells. Additionally, data implicate the Src tyrosine kinase as the major intracellular kinase responsible for “hijacking” this network and provide strong evidence that aberrant Src activation is a major consequence of PRL3 overexpression. Importantly, the data support a PDGF(α/β)-, Eph (A2/B3/B4)-, and Integrin (β1/β5)-receptor array as being the predominant network coordinator in the PRL3 cells, corroborating a PRL3-induced mesenchymal-state. Within this network, we find that tyrosine phosphorylation is increased on a multitude of signaling effectors responsible for Rho-family GTPase, PI3K-Akt, STAT, and ERK activation, linking observations made by the field as a whole under Src as a primary signal transducer. Our phosphoproteomic data paint the most comprehensive picture to date of how PRL3 drives prometastatic molecular events through Src activation. PMID:24030100

  16. Multiplexed Detection of O-GlcNAcome, Phosphoproteome, and Whole Proteome within the Same Gel

    PubMed Central

    Cieniewski-Bernard, Caroline; Dupont, Erwan; Deracinois, Barbara; Lambert, Matthias; Bastide, Bruno

    2014-01-01

    The cellular diversity of proteins results in part from their post-translational modifications. Among all of them, the O-GlcNAcylation is an atypical glycosylation, more similar to phosphorylation than classical glycosylations. Highly dynamic, reversible, and exclusively localized on cytosolic, nuclear, and mitochondrial proteins, O-GlcNAcylation is known to regulate almost all if not all cellular processes. Fundamental for the cell life, O-GlcNAcylation abnormalities are involved in the etiology of several inherited diseases. Assessing to O-GlcNAcylation pattern will permit to get relevant data about the role of O-GlcNAcylation in cell physiology. To get understanding about the role of O-GlcNAcylation, as also considering its interplay with phosphorylation, the O-GlcNAc profiling remains a real challenge for the community of proteomists/glycoproteomists. The development of multiplexed proteomics based on fluorescent detection of proteins permits to go further in the understanding of the proteome complexity. We propose herein a multiplexed proteomic strategy to detect O-GlcNAcylated proteins, phosphoproteins, and the whole proteome within the same bidimensional gel. In particular, we investigated the phosphoproteome through the ProQ Diamond staining, while the whole proteome was visualized through Sypro Ruby staining, or after the labeling of proteins with a T-Dye fluorophore. The O-GlcNAcome was revealed by the way of the Click chemistry and the azide–alkyne cycloaddition of a fluorophore on GlcNAc moieties. This method permits, after sequential image acquisition, the direct in-gel detection of O-GlcNAcome, phosphoproteome, and whole proteome. PMID:25389416

  17. The effect of global warming on lightning frequencies

    NASA Technical Reports Server (NTRS)

    Price, Colin; Rind, David

    1990-01-01

    The first attempt to model global lightning distributions by using the Goddard Institute for Space Studies (GISS) GCM is reported. Three sets of observations showing the relationship between lightning frequency and cloud top height are shown. Zonally averaged lightning frequency observed by satellite are compared with those calculated using the GISS GCM, and fair agreement is found. The change in lightning frequency for a double CO2 climate is calculated and found to be nearly 2.23 x 10 exp 6 extra lightning flashes per day.

  18. Multipath effects in a Global Positioning Satellite system receiver

    NASA Technical Reports Server (NTRS)

    Mcdonald, Malcolm W.

    1992-01-01

    This study, as a part of a large continuing investigation being conducted by the Communications Systems Branch of the Information and Electronic Systems Laboratory at the Marshall Space Flight Center, was undertaken to explore the multipath response characteristics of a particular Global Positioning Satellite (GPS) receiver which was available in the laboratory at the beginning and throughout the entirety of the study, and to develop a suitable regime of experimental procedure which can be applied to other state-of-the-art GPS receivers in the larger investigation.

  19. The phosphoproteome in regenerating protoplasts from Physcomitrella patens protonemata shows changes paralleling postembryonic development in higher plants

    PubMed Central

    He, Yikun

    2014-01-01

    The moss Physcomitrella patens is an ideal model plant to study plant developmental processes. To better understand the mechanism of protoplast regeneration, a phosphoproteome analysis was performed. Protoplasts were prepared from protonemata. By 4 d of protoplast regeneration, the first cell divisions had ensued. Through a highly selective titanium dioxide (TiO2)-based phosphopeptide enrichment method and mass spectrometric technology, more than 300 phosphoproteins were identified as protoplast regeneration responsive. Of these, 108 phosphoproteins were present on day 4 but not in fresh protoplasts or those cultured for 2 d. These proteins are catalogued here. They were involved in cell-wall metabolism, transcription, signal transduction, cell growth/division, and cell structure. These protein functions are related to cell morphogenesis, organogenesis, and development adjustment. This study presents a comprehensive analysis of phosphoproteome involved in protoplast regeneration and indicates that the mechanism of plant protoplast regeneration is similar to that of postembryonic development. PMID:24700621

  20. A simple global carbon and energy coupled cycle model for global warming simulation: sensitivity to the light saturation effect

    NASA Astrophysics Data System (ADS)

    Ichii, Kazuhito; Matsui, Yohei; Murakami, Kazutaka; Mukai, Toshikazu; Yamaguchi, Yasushi; Ogawa, Katsuro

    2003-04-01

    A simple Earth system model, the Four-Spheres Cycle of Energy and Mass (4-SCEM) model, has been developed to simulate global warming due to anthropogenic CO2 emission. The model consists of the Atmosphere-Earth Heat Cycle (AEHC) model, the Four Spheres Carbon Cycle (4-SCC) model, and their feedback processes. The AEHC model is a one-dimensional radiative convective model, which includes the greenhouse effect of CO2 and H2O, and one cloud layer. The 4-SCC model is a box-type carbon cycle model, which includes biospheric CO2 fertilization, vegetation area variation, the vegetation light saturation effect and the HILDA oceanic carbon cycle model. The feedback processes between carbon cycle and climate considered in the model are temperature dependencies of water vapor content, soil decomposition and ocean surface chemistry. The future status of the global carbon cycle and climate was simulated up to the year 2100 based on the "business as usual" (IS92a) emission scenario, followed by a linear decline in emissions to zero in the year 2200. The atmospheric CO2 concentration reaches 645 ppmv in 2100 and a peak of 760 ppmv approximately in the year 2170, and becomes a steady state with 600 ppmv. The projected CO2 concentration was lower than those of the past carbon cycle studies, because we included the light saturation effect of vegetation. The sensitivity analysis showed that uncertainties derived from the light saturation effect of vegetation and land use CO2 emissions were the primary cause of uncertainties in projecting future CO2 concentrations. The climate feedback effects showed rather small sensitivities compared with the impacts of those two effects. Satellite-based net primary production trends analyses can somewhat decrease the uncertainty in quantifying CO2 emissions due to land use changes. On the other hand, as the estimated parameter in vegetation light saturation was poorly constrained, we have to quantify and constrain the effect more accurately.

  1. Globalization's effects on world agricultural trade, 1960-2050.

    PubMed

    Anderson, Kym

    2010-09-27

    Recent globalization has been characterized by a decline in the costs of cross-border trade in farm and other products. It has been driven primarily by the information and communication technology revolution and-in the case of farm products-by reductions in governmental distortions to agricultural production, consumption and trade. Both have boosted economic growth and reduced poverty globally, especially in Asia. The first but maybe not the second of these drivers will continue in coming decades. World food prices will depend also on whether (and if so by how much) farm productivity growth continues to outpace demand growth and to what extent diets in emerging economies move towards livestock and horticultural products at the expense of staples. Demand in turn will be driven not only by population and income growth, but also by crude oil prices if they remain at current historically high levels, since that will affect biofuel demand. Climate change mitigation policies and adaptation, water market developments and market access standards particularly for transgenic foods will add to future production, price and trade uncertainties. PMID:20713399

  2. Globalization's effects on world agricultural trade, 1960–2050

    PubMed Central

    Anderson, Kym

    2010-01-01

    Recent globalization has been characterized by a decline in the costs of cross-border trade in farm and other products. It has been driven primarily by the information and communication technology revolution and—in the case of farm products—by reductions in governmental distortions to agricultural production, consumption and trade. Both have boosted economic growth and reduced poverty globally, especially in Asia. The first but maybe not the second of these drivers will continue in coming decades. World food prices will depend also on whether (and if so by how much) farm productivity growth continues to outpace demand growth and to what extent diets in emerging economies move towards livestock and horticultural products at the expense of staples. Demand in turn will be driven not only by population and income growth, but also by crude oil prices if they remain at current historically high levels, since that will affect biofuel demand. Climate change mitigation policies and adaptation, water market developments and market access standards particularly for transgenic foods will add to future production, price and trade uncertainties. PMID:20713399

  3. System-wide effects of Global Fund investments in Nepal.

    PubMed

    Trägård, Anna; Shrestha, Ishwar Bahadur

    2010-11-01

    Nepal, with a concentrated HIV epidemic and high burden of tuberculosis (TB) and malaria, was perceived to have immensely benefited from grants by the Global Fund to Fight AIDS, Tuberculosis and Malaria in addressing the three diseases, amounting to total approved funding of US$80 million. This paper looks at the interaction and integration of Global Fund-supported programmes and national health systems. A mixed method 'case study' approach based on the Systemic Rapid Assessment Toolkit (SYSRA) was used to systematically analyse across the main health systems functional domains. The Country Coordinating Mechanism has been credited with providing the stewardship in attracting additional resources and providing oversight. The involvement of civil society for delivering key HIV and malaria interventions targeting high-risk groups was perceived to be highly beneficial. TB and malaria services were found to be well integrated into the public health care delivery system, while HIV services targeting at-risk groups were often delivered using parallel structures. Political instability, absence of continuity in leadership and sub-optimal investments in health were together perceived to have led to fragmentation of financing and planning activities, especially in HIV the programme. The demand for timely programmatic and financial reporting for donor-supported programmes has contributed to the creation of parallel monitoring and evaluation structures, with missed opportunities for strengthening and utilizing the national health management information systems. PMID:20966112

  4. Global Biomass Variation and its Geodynamic Effects, 1982-1998

    NASA Technical Reports Server (NTRS)

    Rodell, M.; Chao, B. F.; Au, A. Y.; Kimball, J. S.; McDonald, K. C.

    2005-01-01

    Redistribution of mass near Earth's surface alters its rotation, gravity field, and geocenter location. Advanced techniques for measuring these geodetic variations now exist, but the ability to attribute the observed modes to individual Earth system processes has been hampered by a shortage of reliable global data on such processes, especially hydrospheric processes. To address one aspect of this deficiency, 17 yrs of monthly, global maps of vegetation biomass were produced by applying field-based relationships to satellite-derived vegetation type and leaf area index. The seasonal variability of biomass was estimated to be as large as 5 kg m(exp -2). Of this amount, approximately 4 kg m(exp -2) is due to vegetation water storage variations. The time series of maps was used to compute geodetic anomalies, which were then compared with existing geodetic observations as well as the estimated measurement sensitivity of the Gravity Recovery and Climate Experiment (GRACE). For gravity, the seasonal amplitude of biomass variations may be just within GRACE'S limits of detectability, but it is still an order of magnitude smaller than current observation uncertainty using the satellite-laser-ranging technique. The contribution of total biomass variations to seasonal polar motion amplitude is detectable in today's measurement, but it is obscured by contributions from various other sources, some of which are two orders of magnitude larger. The influence on the length of day is below current limits of detectability. Although the nonseasonal geodynamic signals show clear interannual variability, they are too small to be detected.

  5. Advancing Intervention Science through Effectiveness Research: A Global Perspective

    ERIC Educational Resources Information Center

    Ferrer-Wreder, Laura; Adamson, Lena; Kumpfer, Karol L.; Eichas, Kyle

    2012-01-01

    Background: Effectiveness research is maturing as a field within intervention and prevention science. Effectiveness research involves the implementation and evaluation of the effectiveness of the dissemination of evidence-based interventions in everyday circumstances (i.e., type 2 translational research). Effectiveness research is characterized by…

  6. Proteomic and phosphoproteomic analysis of polyethylene glycol-induced osmotic stress in root tips of common bean (Phaseolus vulgaris L.)

    PubMed Central

    Horst, Walter Johannes

    2013-01-01

    Previous studies have shown that polyethylene glycol (PEG)-induced osmotic stress (OS) reduces cell-wall (CW) porosity and limits aluminium (Al) uptake by root tips of common bean (Phaseolus vulgaris L.). A subsequent transcriptomic study suggested that genes related to CW processes are involved in adjustment to OS. In this study, a proteomic and phosphoproteomic approach was applied to identify OS-induced protein regulation to further improve our understanding of how OS affects Al accumulation. Analysis of total soluble proteins in root tips indicated that, in total, 22 proteins were differentially regulated by OS; these proteins were functionally categorized. Seventy-seven per- cent of the total expressed proteins were involved in metabolic pathways, particularly of carbohydrate and amino acid metabolism. An analysis of the apoplastic proteome revealed that OS reduced the level of five proteins and increased that of seven proteins. Investigation of the total soluble phosphoproteome suggested that dehydrin responded to OS with an enhanced phosphorylation state without a change in abundance. A cellular immunolocalization analysis indicated that dehydrin was localized mainly in the CW. This suggests that dehydrin may play a major protective role in the OS-induced physical breakdown of the CW structure and thus maintenance of the reversibility of CW extensibility during recovery from OS. The proteomic and phosphoproteomic analyses provided novel insights into the complex mechanisms of OS-induced reduction of Al accumulation in the root tips of common bean and highlight a key role for modification of CW structure. PMID:24123251

  7. Integrated approach using multistep enzyme digestion, TiO2 enrichment, and database search for in-depth phosphoproteomic profiling.

    PubMed

    Han, Dohyun; Jin, Jonghwa; Yu, Jiyoung; Kim, Kyunggon; Kim, Youngsoo

    2015-01-01

    Protein phosphorylation is a major PTM that regulates important cell signaling mechanisms. In-depth phosphoproteomic analysis provides a method of examining this complex interplay, yielding a mechanistic understanding of the cellular processes and pathogenesis of various diseases. However, the analysis of protein phosphorylation is challenging, due to the low concentration of phosphoproteins in highly complex mixtures and the high variability of phosphorylation sites. Thus, typical phosphoproteome studies that are based on MS require large amounts of starting material and extensive fractionation steps to reduce the sample complexity. To this end, we present a simple strategy (integrated multistep enzyme digestion, enrichment, database search-iMEED) to improve coverage of the phosphoproteome from lower sample amounts which is faster than other commonly used approaches. It is inexpensive and adaptable to low sample amounts and saves time and effort with regard to sample preparation and mass spectrometric analysis, allowing samples to be prepared without prefractionation or specific instruments, such as HPLC. All MS data have been deposited in the ProteomeXchange with identifier PXD001033 (http://proteomecentral.proteomexchange.org/dataset/PXD001033). PMID:25159016

  8. In-depth Analyses of Kinase-dependent Tyrosine Phosphoproteomes Based on Metal Ion-functionalized Soluble Nanopolymers*

    PubMed Central

    Iliuk, Anton B.; Martin, Victoria A.; Alicie, Bethany M.; Geahlen, Robert L.; Tao, W. Andy

    2010-01-01

    The ability to obtain in-depth understanding of signaling networks in cells is a key objective of systems biology research. Such ability depends largely on unbiased and reproducible analysis of phosphoproteomes. We present here a novel proteomics tool, polymer-based metal ion affinity capture (PolyMAC), for the highly efficient isolation of phosphopeptides to facilitate comprehensive phosphoproteome analyses. This approach uses polyamidoamine dendrimers multifunctionalized with titanium ions and aldehyde groups to allow the chelation and subsequent isolation of phosphopeptides in a homogeneous environment. Compared with current strategies based on solid phase micro- and nanoparticles, PolyMAC demonstrated outstanding reproducibility, exceptional selectivity, fast chelation times, and high phosphopeptide recovery from complex mixtures. Using the PolyMAC method combined with antibody enrichment, we identified 794 unique sites of tyrosine phosphorylation in malignant breast cancer cells, 514 of which are dependent on the expression of Syk, a protein-tyrosine kinase with unusual properties of a tumor suppressor. The superior sensitivity of PolyMAC allowed us to identify novel components in a variety of major signaling networks, including cell migration and apoptosis. PolyMAC offers a powerful and widely applicable tool for phosphoproteomics and molecular signaling. PMID:20562096

  9. IMPACT OF GLOBAL CHANGE OF TERRESTRIAL ECOSYSTEMS: FRAMEWORKS FOR EVALUATING AGROECOSYSTEM AND FOREST ECOSYSTEM EFFECTS

    EPA Science Inventory

    The United States Environmental Protection Agency's (EPA) Global Climate Research Program (GCRP) is determining the effects of climate change on terrestrial ecosystems. his paper describes a general ecological risk assessment model as well as specific conceptual models for urrent...

  10. Existence and global attractivity of periodic solution for an impulsive delay differential equation with Allee effect

    NASA Astrophysics Data System (ADS)

    Yan, Jurang; Zhao, Aimin; Yan, Weiping

    2005-09-01

    Sufficient conditions are obtained for the existence and global attractivity of positive periodic solution of an impulsive delay differential equation with Allee effect. The results of this paper improve and generalize noticeably the known theorems in the literature.