Sample records for quantitative phosphoproteomics dissection

  1. Dissection of the insulin signaling pathway via quantitative phosphoproteomics

    Microsoft Academic Search

    Marcus Krüger; Irina Kratchmarova; Blagoy Blagoev; Yu-Hua Tseng; C. Ronald Kahn; Matthias Mann

    2008-01-01

    The insulin signaling pathway is of pivotal importance in metabolic diseases, such as diabetes, and in cellular processes, such as aging. Insulin activates a tyrosine phosphorylation cascade that branches to create a complex network affecting multiple biological processes. To understand the full spectrum of the tyrosine phosphorylation cascade, we have defined the tyrosine-phosphoproteome of the insulin signaling pathway, using high

  2. Quantitative Plant Phosphoproteomics

    PubMed Central

    Kline, Kelli G.; Barrett-Wilt, Gregory A.; Sussman, Michael R.

    2011-01-01

    Protein phosphorylation is a major post-translational modification in plants crucial for the regulation of diverse cellular functions. In the early stages of this field, efforts focused on the qualitative detection, identification, and cataloging of in vivo protein phosphorylation sites. Recently these studies have advanced into utilizing quantitative mass spectrometric measurements, capable of dynamically monitoring changes in phosphorylation levels in response to genetic and environmental alterations. This review will highlight current untargeted and targeted mass spectral technologies used for quantitative phosphoproteome measurements in plants, and provide a discussion of these phosphorylation changes in relation to important biological events. PMID:21764629

  3. Global Quantitative SILAC Phosphoproteomics Reveals Differential Phosphorylation Is Widespread between the Procyclic and

    E-print Network

    Schnaufer, Achim

    Global Quantitative SILAC Phosphoproteomics Reveals Differential Phosphorylation Is Widespread in this organism. KEYWORDS: phosphorylation, SILAC, Trypanosoma brucei, quantitative proteomics, phosphoproteomics

  4. Robust, Quantitative, Labelfree Phosphoproteomics Platform: Automated Enrichment and 2DLC/MS/MS Brenna M. Richardson, Erik J. Soderblom, J. Will Thompson, M. Arthur Moseley

    E-print Network

    Richardson, David

    Robust, Quantitative, Labelfree Phosphoproteomics Platform: Automated Enrichment and 2DLC Traditionally, quantitative phosphoproteomics strategies were limited to the use of stableisotope labeled cell

  5. 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

  6. Quantitative phosphoproteomic analysis of IL-33-mediated signaling.

    PubMed

    Pinto, Sneha M; Nirujogi, Raja Sekhar; Rojas, Pamela Leal; Patil, Arun H; Manda, Srikanth S; Subbannayya, Yashwanth; Roa, Juan Carlos; Chatterjee, Aditi; Prasad, T S Keshava; Pandey, Akhilesh

    2015-01-01

    Interleukin-33 (IL-33) is a novel member of the IL-1 family of cytokines that plays diverse roles in the regulation of immune responses. IL-33 exerts its effects through a heterodimeric receptor complex resulting in the production and release of proinflammatory cytokines. A detailed understanding of the signaling pathways activated by IL-33 is still unclear. To gain insights into the IL-33-mediated signaling mechanisms, we carried out a SILAC-based global quantitative phosphoproteomic analysis that resulted in the identification of 7191 phosphorylation sites derived from 2746 proteins. We observed alterations in the level of phosphorylation in 1050 sites corresponding to 672 proteins upon IL-33 stimulation. We report, for the first time, phosphorylation of multiple protein kinases, including mitogen-activated protein kinase activated protein kinase 2 (Mapkapk2), receptor (TNFRSF) interacting serine-threonine kinase 1 (Ripk1), and NAD kinase (Nadk) that are induced by IL-33. In addition, we observed IL-33-induced phosphorylation of several protein phosphatases including protein tyrosine phosphatase, nonreceptor-type 12 (Ptpn12), and inositol polyphosphate-5-phosphatase D (Inpp5d), which have not been reported previously. Network analysis revealed an enrichment of actin binding and cytoskeleton reorganization that could be important in macrophage activation induced by IL-33. Our study is the first quantitative analysis of IL-33-regulated phosphoproteome. Our findings significantly expand the understanding of IL-33-mediated signaling events and have the potential to provide novel therapeutic targets pertaining to immune-related diseases such as asthma where dysregulation of IL-33 is observed. All MS data have been deposited in the ProteomeXchange with identifier PXD000984 (http://proteomecentral.proteomexchange.org/dataset/PXD000984). PMID:25367039

  7. Quantitative phosphoproteomic analysis of prion-infected neuronal cells

    Microsoft Academic Search

    Wibke Wagner; Paul Ajuh; Johannes Löwer; Silja Wessler

    2010-01-01

    Prion diseases or transmissible spongiform encephalopathies (TSEs) are fatal diseases associated with the conversion of the cellular prion protein (PrPC) to the abnormal prion protein (PrPSc). Since the molecular mechanisms in pathogenesis are widely unclear, we analyzed the global phospho-proteome and detected a differential pattern of tyrosine- and threonine phosphorylated proteins in PrPSc-replicating and pentosan polysulfate (PPS)-rescued N2a cells in

  8. Quantitative phosphoproteomics by mass spectrometry: Past, present, and future

    PubMed Central

    Nita-Lazar, Aleksandra; Saito-Benz, Hideshiro; White, Forest M.

    2009-01-01

    Protein phosphorylation-mediated signaling networks regulate much of the cellular response to external stimuli, and dysregulation in these networks has been linked to multiple disease states. Significant advancements have been made over the past decade to enable the analysis and quantification of cellular protein phosphorylation events, but comprehensive analysis of the phosphoproteome is still lacking, as is the ability to monitor signaling at the network level while comprehending the biological implications of each phosphorylation site. In this review we highlight many of the technological advances over the past decade and describe some of the latest applications of these tools to uncover signaling networks in a variety of biological settings. We finish with a concise discussion of the future of the field, including additional advances that are required to link protein phosphorylation analysis with biological insight. PMID:18846511

  9. Quantitative Phospho-proteomics to Investigate the Polo-like Kinase 1-Dependent Phospho-proteome*

    PubMed Central

    Grosstessner-Hain, Karin; Hegemann, Björn; Novatchkova, Maria; Rameseder, Jonathan; Joughin, Brian A.; Hudecz, Otto; Roitinger, Elisabeth; Pichler, Peter; Kraut, Norbert; Yaffe, Michael B.; Peters, Jan-Michael; Mechtler, Karl

    2011-01-01

    Polo-like kinase 1 (PLK1) is a key regulator of mitotic progression and cell division, and small molecule inhibitors of PLK1 are undergoing clinical trials to evaluate their utility in cancer therapy. Despite this importance, current knowledge about the identity of PLK1 substrates is limited. Here we present the results of a proteome-wide analysis of PLK1-regulated phosphorylation sites in mitotic human cells. We compared phosphorylation sites in HeLa cells that were or were not treated with the PLK1-inhibitor BI 4834, by labeling peptides via methyl esterification, fractionation of peptides by strong cation exchange chromatography, and phosphopeptide enrichment via immobilized metal affinity chromatography. Analysis by quantitative mass spectrometry identified 4070 unique mitotic phosphorylation sites on 2069 proteins. Of these, 401 proteins contained one or multiple phosphorylation sites whose abundance was decreased by PLK1 inhibition. These include proteins implicated in PLK1-regulated processes such as DNA damage, mitotic spindle formation, spindle assembly checkpoint signaling, and chromosome segregation, but also numerous proteins that were not suspected to be regulated by PLK1. Analysis of amino acid sequence motifs among phosphorylation sites down-regulated under PLK1 inhibition in this data set identified two potential novel variants of the PLK1 consensus motif. PMID:21857030

  10. Phosphoproteome Analysis

    Microsoft Academic Search

    Roberto Raggiaschi; Stefano Gotta; Georg C. Terstappen

    2005-01-01

    Protein phosphorylation is directly or indirectly involved in all important cellular events. The understanding of its regulatory role requires the discovery of the proteins involved in these processes and how, where and when protein phosphorylation takes place. Investigation of the phosphoproteome of a cell is becoming feasible today although it still represents a very difficult task especially if quantitative comparisons

  11. Quantitative Phosphoproteomics Applied to the Yeast Pheromone Signaling Pathway

    Microsoft Academic Search

    Albrecht Gruhler; Jesper V. Olsen; Shabaz Mohammed; Peter Mortensen; Nils J. Færgeman; Matthias Mann; Ole N. Jensen

    2005-01-01

    Cellular processes such as proliferation, differentiation, and adaptation to environmental changes are regulated by protein phosphorylation. Development of sensitive and comprehensive analytical methods for determination of protein phosphorylation is therefore a necessity in the pursuit of a detailed molecular view of complex biological processes. We present a quantitative modification-spe- cific proteomic approach that combines stable isotope labeling by amino acids

  12. Quantitative Measurement of Phosphoproteome Response to Osmotic Stress in Arabidopsis

    E-print Network

    Radivojac, Predrag

    can be achieved mainly by two major techniques, stable isotope labeling and label- free quantitation. Isotope labeling prior to liquid chromatog- raphy-mass spectrometry (LC-MS)1 has been widely used, including metabolic labeling such as stable isotope labeling by amino acids in cell culture (SILAC

  13. Developmentally-Dynamic Murine Brain Proteomes and Phosphoproteomes Revealed by Quantitative Proteomics

    PubMed Central

    Doubleday, Peter F.; Ballif, Bryan A.

    2014-01-01

    Developmental processes are governed by a diverse suite of signaling pathways employing reversible phosphorylation. Recent advances in large-scale phosphoproteomic methodologies have made possible the identification and quantification of hundreds to thousands of phosphorylation sites from primary tissues. Towards a global characterization of proteomic changes across brain development, we present the results of a large-scale quantitative mass spectrometry study comparing embryonic, newborn and adult murine brain. Using anti-phosphotyrosine immuno-affinity chromatography and strong cation exchange (SCX) chromatography, coupled to immobilized metal affinity chromatography (IMAC), we identified and quantified over 1,750 phosphorylation sites and over 1,300 proteins between three developmental states. Bioinformatic analyses highlight functions associated with the identified proteins and phosphoproteins and their enrichment at distinct developmental stages. These results serve as a primary reference resource and reveal dynamic developmental profiles of proteins and phosphoproteins from the developing murine brain. PMID:25177544

  14. Automated, reproducible, titania-based phosphopeptide enrichment strategy for label-free quantitative phosphoproteomics.

    PubMed

    Richardson, Brenna McJury; Soderblom, Erik J; Thompson, J Will; Moseley, M Arthur

    2013-04-01

    An automated phosphopeptide enrichment strategy is described using titanium dioxide (TiO2)-packed, fused silica capillaries for use with liquid chromatography (LC)-mass spectrometry (MS)/MS-based, label-free proteomics workflows. To correlate an optimum peptide:TiO2 loading ratio between different particle types, the ratio of phenyl phosphate-binding capacities was used. The optimum loading for the column was then verified through replicate enrichments of a range of quantities of digested rat brain tissue cell lysate. Fractions were taken during sample loading, multiple wash steps, and the elution steps and analyzed by LC-MS/MS to gauge the efficiency and reproducibility of the enrichment. Greater than 96% of the total phosphopeptides were detected in the elution fractions, indicating efficient trapping of the phosphopeptides on the first pass of enrichment. The quantitative reproducibility of the automated setup was also improved greatly with phosphopeptide intensities from replicate enrichments exhibiting a median coefficient of variation (CV) of 5.8%, and 80% of the identified phosphopeptides had CVs below 11.1%, while maintaining >85% specificity. By providing this high degree of analytical reproducibility, this method allows for label-free phosphoproteomics over large sample sets with complex experimental designs (multiple biological conditions, multiple biological replicates, multiple time-points, etc.), including large-scale clinical cohorts. PMID:23542237

  15. Quantitative Phosphoproteomics Identifies Filaggrin and other Targets of Ionizing Radiation in a Human Skin Model

    SciTech Connect

    Yang, Feng; Waters, Katrina M.; Webb-Robertson, Bobbie-Jo M.; Sowa, Marianne B.; Freiin von Neubeck, Claere H.; Aldrich, Joshua T.; Markillie, Lye Meng; Wirgau, Rachel M.; Gristenko, Marina A.; Zhao, Rui; Camp, David G.; Smith, Richard D.; Stenoien, David L.

    2012-04-17

    Our objective here was to perform a quantitative phosphoproteomic study on a reconstituted human skin tissue to identify low and high dose ionizing radiation dependent signaling in a complex 3-dimensional setting. Application of an isobaric labeling strategy using sham and 3 radiation doses (3, 10, 200 cGy) resulted in the identification of 1113 unique phosphopeptides. Statistical analyses identified 151 phosphopeptides showing significant changes in response to radiation and radiation dose. Proteins responsible for maintaining skin structural integrity including keratins and desmosomal proteins (desmoglein, desmoplakin, plakophilin 1 and 2,) had altered phosphorylation levels following exposure to both low and high doses of radiation. A phosphorylation site present in multiple copies in the linker regions of human profilaggrin underwent the largest fold change. Increased phosphorylation of these sites coincided with altered profilaggrin processing suggesting a role for linker phosphorylation in human profilaggrin regulation. These studies demonstrate that the reconstituted human skin system undergoes a coordinated response to ionizing radiation involving multiple layers of the stratified epithelium that serve to maintain skin barrier functions and minimize the damaging consequences of radiation exposure.

  16. Towards functional phosphoproteomics by mapping differential phosphorylation events in signaling networks

    E-print Network

    Hirt, Heribert

    REVIEW Towards functional phosphoproteomics by mapping differential phosphorylation events screening for potential cancer therapies and in-depth analysis of phosphoproteomes. In this review, we aim to describe current progress in quantitative phosphoproteomics. This emerging field has changed numerous

  17. Quantitative phosphoproteomics reveals crosstalk between phosphorylation and O-GlcNAc in the DNA damage response pathway.

    PubMed

    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 ?-N-acetylglucosamine (O-GlcNAc) is an essential and dynamic PTM 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 SILAC-based quantitative proteomics to carry out comparisons of site-specific phosphorylation in OGT wild-type and Null cells. Quantitation of the phosphoproteome demonstrated that of 5529 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 an 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. All MS data have been deposited in the ProteomeXchange with identifier PXD001153 (http://proteomecentral.proteomexchange.org/dataset/PXD001153). PMID:25263469

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

    PubMed Central

    Nguyen, Tran Hong Nha; Brechenmacher, Laurent; Aldrich, Joshua T.; Clauss, Therese R.; Gritsenko, Marina A.; Hixson, Kim K.; Libault, Marc; Tanaka, Kiwamu; Yang, Feng; Yao, Qiuming; Paša-Toli?, Ljiljana; Xu, Dong; Nguyen, Henry T.; Stacey, Gary

    2012-01-01

    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 eight-plex iTRAQ, enriched using Ni-NTA magnetic beads and subjected to nanoRPLC-MS/MS1 analysis using HCD and decision tree guided CID/ETD strategy. A total of 1625 unique phosphopeptides, spanning 1659 nonredundant phosphorylation sites, were detected from 1126 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. PMID:22843990

  19. Identification of novel signaling components in N,N’-Dinitrosopiperazine-mediated metastasis of nasopharyngeal Carcinoma by quantitative phosphoproteomics

    PubMed Central

    2014-01-01

    Background Nasopharyngeal carcinoma (NPC) is a highly invasive and metastatic cancer. N,N’-dinitrosopiperazine (DNP), a carcinogen with specificity for nasopharyngeal epithelium, facilitates NPC metastasis. However, the underlying mechanism is not known. Methods Quantitative phosphoproteomics, using stable isotope labeling of amino acids in cell cultures, was employed to identify phosphoproteins associated with NPC metastasis mediated by DNP. NPC cell line 6-10B, which is relatively less metastatic, was used to investigate DNP-mediated metastasis. Boyden chamber invasion assay was used to measure DNP-induced motility and invasion, and nude mice were used to verify DNP-mediated metastasis in vivo. Several different phosphoproteins detected by proteomics analysis were verified by immunoblotting. DNP-mediated metastasis facilitated by lysine-rich CEACAM1 co-isolated protein (LYRIC) phosphorylation at serine 568 was confirmed using mutations targeting the phosphorylation site of LYRIC. DNP-mediated metastasis through LYRIC phosphorylation was confirmed in the NPC cell line CNE1. DNP-mediated LYRIC phosphorylation at serine 568 was also verified in metastatic tumors of BABL/c nude mice. Results Boyden chamber invasion assay indicated that DNP mediated cell motility and invasion of NPC cell 6-10B in vitro, and experiments with nude mice indicated that DNP increased 6-10B metastasis in vivo. In the phosphoproteomics analysis, we detected 216 phosphorylation sites on 130 proteins; among these, 48 phosphorylation sites on 30 unique phosphopeptides were modulated by DNP by at least 1.5-fold. DNP mediated the expression of phosphorylated GTPase, ferritin, LYRIC, and RNA polymerase, and it decreased the expression of phosphorylated torsin-1A protein 1. Furthermore, DNP induced LYRIC phosphorylation at serine 568 to facilitate cell motility and invasion, whereas DNP-mediated motility and invasion was decreased when serine 568 in LYRIC was mutated. In another NPC cell line, CNE1, DNP also mediated cell motility and invasion followed by enhanced phosphorylation of LYRIC at serine 568. Finally, phosphorylated-LYRIC expression at serine 568 was significantly increased in metastatic tumors induced by DNP. Conclusion DNP regulates multiple signaling pathways through protein phosphorylation, including the phosphorylation of LYRIC at serine 568, and mediates NPC metastasis. These findings provide insights on the complexity and dynamics of DNP-facilitated metastasis, and may help to gain a better understanding of the mechanisms by clarifying NPC-induced metastasis. PMID:24708550

  20. Investigation of Receptor interacting protein (RIP3)-dependent Protein Phosphorylation by Quantitative Phosphoproteomics*

    PubMed Central

    Wu, Xiurong; Tian, Lili; Li, Jie; Zhang, Yingying; Han, Victor; Li, Yuanyue; Xu, Xiaozheng; Li, Hanjie; Chen, Xi; Chen, Jinan; Jin, Wenhai; Xie, Yongming; Han, Jiahuai; Zhong, Chuan-Qi

    2012-01-01

    Receptor interacting protein 3 (RIP3) is a protein kinase that plays a key role in programmed necrosis. Despite the importance of RIP3-dependent necrosis in many pathological processes, current knowledge on the function of RIP3 is very limited. Here we present the results of a proteome-wide analysis of RIP3-regulated phosphorylation sites using cells from wildtype (RIP3+/+) and RIP3 knockout (RIP3?/?) mice. Because the activation of RIP3 requires stimulation by certain extracellular stimuli such as ligands of death receptors or Toll-like receptors, we compared the phosphorylation sites of lipopolysaccharide (LPS)-treated peritoneal macrophages from RIP3+/+ and RIP3?/? mice and the phosphorylation sites of tumor necrosis factor (TNF)-treated RIP3+/+ and RIP3?/? mouse embryonic fibroblast (MEF) cells. Stable isotope labeling by amino acids in cell culture and spike-in stable isotope labeling by amino acids in cell culture were used in the analyses of the MEFs and macrophages, respectively. Proteomic analyses using stable isotope labeling by amino acids in cell culture coupled with immobilized metal affinity chromatography-hydrophilic interaction liquid chromatography fractionation and nanoLC MS/MS identified 14,057 phosphopeptides in 4306 proteins from the macrophages and 4732 phosphopeptides in 1785 proteins from the MEFs. Analysis of amino acid sequence motifs among the phosphopeptides identified a potential motif of RIP3 phosphorylation. Among the phosphopeptides identified, 73 were found exclusively in RIP3+/+ macrophages, 121 were detected exclusively from RIP3+/+ MEFs, 286 phosphopeptides were induced more in RIP3+/+ macrophages than in RIP3?/? macrophages and 26 phosphopeptides had higher induction in RIP3+/+ MEFs than in RIP3?/? cells. Many of the RIP3 regulated phosphoproteins from the macrophages and MEF cells are functionally associated with the cell cycle; the rest, however, appear to have diverse functions in that a number of metabolism related proteins were phosphorylated in macrophages and development related phosphoproteins were induced in MEFs. The results of our phosphoproteomic analysis suggest that RIP3 might function beyond necrosis and that cell type specific function of RIP3 exists. PMID:22942356

  1. Quantitative phosphoproteomics unravels biased phosphorylation of serotonin 2A receptor at Ser280 by hallucinogenic versus nonhallucinogenic agonists.

    PubMed

    Karaki, Samah; Becamel, Carine; Murat, Samy; Mannoury la Cour, Clotilde; Millan, Mark J; Prézeau, Laurent; Bockaert, Joël; Marin, Philippe; Vandermoere, Franck

    2014-05-01

    The serotonin 5-HT(2A) receptor is a primary target of psychedelic hallucinogens such as lysergic acid diethylamine, mescaline, and psilocybin, which reproduce some of the core symptoms of schizophrenia. An incompletely resolved paradox is that only some 5-HT(2A) receptor agonists exhibit hallucinogenic activity, whereas structurally related agonists with comparable affinity and activity lack such a psychoactive activity. Using a strategy combining stable isotope labeling by amino acids in cell culture with enrichment in phosphorylated peptides by means of hydrophilic interaction liquid chromatography followed by immobilized metal affinity chromatography, we compared the phosphoproteome in HEK-293 cells transiently expressing the 5-HT(2A) receptor and exposed to either vehicle or the synthetic hallucinogen 1-[2,5-dimethoxy-4-iodophenyl]-2-aminopropane (DOI) or the nonhallucinogenic 5-HT(2A) agonist lisuride. Among the 5995 identified phosphorylated peptides, 16 sites were differentially phosphorylated upon exposure of cells to DOI versus lisuride. These include a serine (Ser(280)) located in the third intracellular loop of the 5-HT(2A) receptor, a region important for its desensitization. The specific phosphorylation of Ser(280) by hallucinogens was further validated by quantitative mass spectrometry analysis of immunopurified receptor digests and by Western blotting using a phosphosite specific antibody. The administration of DOI, but not of lisuride, to mice, enhanced the phosphorylation of 5-HT(2A) receptors at Ser(280) in the prefrontal cortex. Moreover, hallucinogens induced a less pronounced desensitization of receptor-operated signaling in HEK-293 cells and neurons than did nonhallucinogenic agonists. The mutation of Ser(280) to aspartic acid (to mimic phosphorylation) reduced receptor desensitization by nonhallucinogenic agonists, whereas its mutation to alanine increased the ability of hallucinogens to desensitize the receptor. This study reveals a biased phosphorylation of the 5-HT(2A) receptor in response to hallucinogenic versus nonhallucinogenic agonists, which underlies their distinct capacity to desensitize the receptor. PMID:24637012

  2. Quantitative phosphoproteomics identifies SnRK2 protein kinase substrates and reveals the effectors of abscisic acid action

    PubMed Central

    Wang, Pengcheng; Xue, Liang; Batelli, Giorgia; Lee, Shinyoung; Hou, Yueh-Ju; Van Oosten, Michael J.; Zhang, Huiming; Tao, W. Andy; Zhu, Jian-Kang

    2013-01-01

    Sucrose nonfermenting 1 (SNF1)-related protein kinase 2s (SnRK2s) are central components of abscisic acid (ABA) signaling pathways. The snrk2.2/2.3/2.6 triple-mutant plants are nearly completely insensitive to ABA, suggesting that most of the molecular actions of ABA are triggered by the SnRK2s-mediated phosphorylation of substrate proteins. Only a few substrate proteins of the SnRK2s are known. To identify additional substrate proteins of the SnRK2s and provide insight into the molecular actions of ABA, we used quantitative phosphoproteomics to compare the global changes in phosphopeptides in WT and snrk2.2/2.3/2.6 triple mutant seedlings in response to ABA treatment. Among the 5,386 unique phosphorylated peptides identified in this study, we found that ABA can increase the phosphorylation of 166 peptides and decrease the phosphorylation of 117 peptides in WT seedlings. In the snrk2.2/2.3/2.6 triple mutant, 84 of the 166 peptides, representing 58 proteins, could not be phosphorylated, or phosphorylation was not increased under ABA treatment. In vitro kinase assays suggest that most of the 58 proteins can serve as substrates of the SnRK2s. The SnRK2 substrates include proteins involved in flowering time regulation, RNA and DNA binding, miRNA and epigenetic regulation, signal transduction, chloroplast function, and many other cellular processes. Consistent with the SnRK2 phosphorylation of flowering time regulators, the snrk2.2/2.3/2.6 triple mutant flowered significantly earlier than WT. These results shed new light on the role of the SnRK2 protein kinases and on the downstream effectors of ABA action, and improve our understanding of plant responses to adverse environments. PMID:23776212

  3. Quantitative Phosphoproteome Analysis of Lysophosphatidic Acid Induced Chemotaxis applying Dual-step ¹?O 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.

  4. Targeted quantitative phosphoproteomic analysis of erythrocyte membranes during blood bank storage.

    PubMed

    Rinalducci, Sara; Longo, Valentina; Ceci, Luigi R; Zolla, Lello

    2015-02-01

    One of the hallmarks of blood bank stored red blood cells (RBCs) is the irreversible transition from a discoid to a spherocyte-like morphology with membrane perturbation and cytoskeleton disorders. Therefore, identification of the storage-associated modifications in the protein-protein interactions between the cytoskeleton and the lipid bilayer may contribute to enlighten the molecular mechanisms involved in the alterations of mechanical properties of stored RBCs. Here we report the results obtained analyzing RBCs after 0, 21 and 35?days of storage under standard blood banking conditions by label free mass spectrometry (MS)-based experiments. We could quantitatively measure changes in the phosphorylation level of crucial phosphopeptides belonging to ?-spectrin, ankyrin-1, ?-adducin, dematin, glycophorin A and glycophorin C proteins. Data have been validated by both western blotting and pseudo-Multiple Reaction Monitoring (MRM). Although each phosphopeptide showed a distinctive trend, a sharp increase in the phosphorylation level during the storage duration was observed. Phosphopeptide mapping and structural modeling analysis indicated that the phosphorylated residues localize in protein functional domains fundamental for the maintenance of membrane structural integrity. Along with previous morphological evidence acquired by electron microscopy, our results seem to indicate that 21-day storage may represent a key point for the molecular processes leading to the erythrocyte deformability reduction observed during blood storage. These findings could therefore be helpful in understanding and preventing the morphology-linked mechanisms responsible for the post-transfusion survival of preserved RBCs. PMID:25800014

  5. In vivo quantitative phosphoproteomic profiling identifies novel regulators of castration-resistant prostate cancer growth.

    PubMed

    Jiang, N; Hjorth-Jensen, K; Hekmat, O; Iglesias-Gato, D; Kruse, T; Wang, C; Wei, W; Ke, B; Yan, B; Niu, Y; Olsen, J V; Flores-Morales, A

    2015-05-21

    Prostate cancer remains a leading cause of cancer-related mortality worldwide owing to our inability to treat effectively castration-resistant tumors. To understand the signaling mechanisms sustaining castration-resistant growth, we implemented a mass spectrometry-based quantitative proteomic approach and use it to compare protein phosphorylation in orthotopic xenograft tumors grown in either intact or castrated mice. This investigation identified changes in phosphorylation of signaling proteins such as MEK, LYN, PRAS40, YAP1 and PAK2, indicating the concomitant activation of several oncogenic pathways in castration-resistant tumors, a notion that was confirmed by tumor transcriptome analysis. Further analysis demonstrated that the activation of mTORC1, PAK2 and the increased levels of YAP1 in castration-resistant tumors can be explained by the loss of androgen inhibitory actions. The analysis of clinical samples demonstrated elevated levels of PAK2 and YAP1 in castration-resistant tumors, whereas knockdown experiments in androgen-independent cells demonstrated that both YAP1 and PAK2 regulate cell colony formation and cell invasion activity. PAK2 also influenced cell proliferation and mitotic timing. Interestingly, these phenotypic changes occur in the absence of obvious alterations in the activity of AKT, MAPK or mTORC1 pathways, suggesting that PAK2 and YAP1 may represent novel targets for the treatment of castration-resistant prostate cancer. Pharmacologic inhibitors of PAK2 (PF-3758309) and YAP1 (Verteporfin) were able to inhibit the growth of androgen-independent PC3 xenografts. This work demonstrates the power of applying high-resolution mass spectrometry in the proteomic profiling of tumors grown in vivo for the identification of novel and clinically relevant regulatory proteins. PMID:25065596

  6. iTRAQ Labeling is Superior to mTRAQ for Quantitative Global Proteomics and Phosphoproteomics*

    PubMed Central

    Mertins, Philipp; Udeshi, Namrata D.; Clauser, Karl R.; Mani, DR; Patel, Jinal; Ong, Shao-en; Jaffe, Jacob D.; Carr, Steven A.

    2012-01-01

    Labeling of primary amines on peptides with reagents containing stable isotopes is a commonly used technique in quantitative mass spectrometry. Isobaric labeling techniques such as iTRAQ™ or TMT™ allow for relative quantification of peptides based on ratios of reporter ions in the low m/z region of spectra produced by precursor ion fragmentation. In contrast, nonisobaric labeling with mTRAQ™ yields precursors with different masses that can be directly quantified in MS1 spectra. In this study, we compare iTRAQ- and mTRAQ-based quantification of peptides and phosphopeptides derived from EGF-stimulated HeLa cells. Both labels have identical chemical structures, therefore precursor ion- and fragment ion-based quantification can be directly compared. Our results indicate that iTRAQ labeling has an additive effect on precursor intensities, whereas mTRAQ labeling leads to more redundant MS2 scanning events caused by triggering on the same peptide with different mTRAQ labels. We found that iTRAQ labeling quantified nearly threefold more phosphopeptides (12,129 versus 4,448) and nearly twofold more proteins (2,699 versus 1,597) than mTRAQ labeling. Although most key proteins in the EGFR signaling network were quantified with both techniques, iTRAQ labeling allowed quantification of twice as many kinases. Accuracy of reporter ion quantification by iTRAQ is adversely affected by peptides that are cofragmented in the same precursor isolation window, dampening observed ratios toward unity. However, because of tighter overall iTRAQ ratio distributions, the percentage of statistically significantly regulated phosphopeptides and proteins detected by iTRAQ and mTRAQ was similar. We observed a linear correlation of logarithmic iTRAQ to mTRAQ ratios over two orders of magnitude, indicating a possibility to correct iTRAQ ratios by an average compression factor. Spike-in experiments using peptides of defined ratios in a background of nonregulated peptides show that iTRAQ quantification is less accurate but not as variable as mTRAQ quantification. PMID:22210691

  7. Cell Metabolism A Quantitative Map of the Liver Mitochondrial

    E-print Network

    Yandell, Brian S.

    Cell Metabolism Resource A Quantitative Map of the Liver Mitochondrial Phosphoproteome Reveals of the mouse liver mitochondrial proteome and phosphoproteome during both acute and chronic physiological

  8. Genetic dissection of a behavioral quantitative trait locus shows that Rgs2 modulates anxiety in mice

    Microsoft Academic Search

    Binnaz Yalcin; Saffron A G Willis-Owen; Jan Fullerton; Anjela Meesaq; Robert M Deacon; J Nicholas P Rawlins; Richard R Copley; Andrew P Morris; Jonathan Flint; Richard Mott

    2004-01-01

    Here we present a strategy to determine the genetic basis of variance in complex phenotypes that arise from natural, as opposed to induced, genetic variation in mice. We show that a commercially available strain of outbred mice, MF1, can be treated as an ultrafine mosaic of standard inbred strains and accordingly used to dissect a known quantitative trait locus influencing

  9. Dissection Dissected.

    ERIC Educational Resources Information Center

    Berman, William

    1984-01-01

    Discusses the role of dissection in science courses, examining essential lessons students can learn (such as developing an abiding respect for all forms of life, including the animal being dissected). Also presents a list of tips related to classroom dissection and comments on formaldehyde and formalin substitutes. (JN)

  10. Using Quantitative Redox Proteomics to Dissect the Yeast Redoxome*

    PubMed Central

    Brandes, Nicolas; Reichmann, Dana; Tienson, Heather; Leichert, Lars I.; Jakob, Ursula

    2011-01-01

    To understand and eventually predict the effects of changing redox conditions and oxidant levels on the physiology of an organism, it is essential to gain knowledge about its redoxome: the proteins whose activities are controlled by the oxidation status of their cysteine thiols. Here, we applied the quantitative redox proteomic method OxICAT to Saccharomyces cerevisiae and determined the in vivo thiol oxidation status of almost 300 different yeast proteins distributed among various cellular compartments. We found that a substantial number of cytosolic and mitochondrial proteins are partially oxidized during exponential growth. Our results suggest that prevailing redox conditions constantly control central cellular pathways by fine-tuning oxidation status and hence activity of these proteins. Treatment with sublethal H2O2 concentrations caused a subset of 41 proteins to undergo substantial thiol modifications, thereby affecting a variety of different cellular pathways, many of which are directly or indirectly involved in increasing oxidative stress resistance. Classification of the identified protein thiols according to their steady-state oxidation levels and sensitivity to peroxide treatment revealed that redox sensitivity of protein thiols does not predict peroxide sensitivity. Our studies provide experimental evidence that the ability of protein thiols to react to changing peroxide levels is likely governed by both thermodynamic and kinetic parameters, making predicting thiol modifications challenging and de novo identification of peroxide sensitive protein thiols indispensable. PMID:21976664

  11. Quantitative Phosphoproteomics after Auxin-stimulated Lateral Root Induction Identifies an SNX1 Protein Phosphorylation Site Required for Growth*

    PubMed Central

    Zhang, Hongtao; Zhou, Houjiang; Berke, Lidija; Heck, Albert J. R.; Mohammed, Shabaz; Scheres, Ben; Menke, Frank L. H.

    2013-01-01

    Protein phosphorylation is instrumental to early signaling events. Studying system-wide phosphorylation in relation to processes under investigation requires a quantitative proteomics approach. In Arabidopsis, auxin application can induce pericycle cell divisions and lateral root formation. Initiation of lateral root formation requires transcriptional reprogramming following auxin-mediated degradation of transcriptional repressors. The immediate early signaling events prior to this derepression are virtually uncharacterized. To identify the signal molecules responding to auxin application, we used a lateral root-inducible system that was previously developed to trigger synchronous division of pericycle cells. To identify and quantify the early signaling events following this induction, we combined 15N-based metabolic labeling and phosphopeptide enrichment and applied a mass spectrometry-based approach. In total, 3068 phosphopeptides were identified from auxin-treated root tissue. This root proteome dataset contains largely phosphopeptides not previously reported and represents one of the largest quantitative phosphoprotein datasets from Arabidopsis to date. Key proteins responding to auxin treatment included the multidrug resistance-like and PIN2 auxin carriers, AUXIN RESPONSE FACTOR2 (ARF2), SUPPRESSOR OF AUXIN RESISTANCE 3 (SAR3), and SORTING NEXIN1 (SNX1). Mutational analysis of serine 16 of SNX1 showed that overexpression of the mutated forms of SNX1 led to retarded growth and reduction of lateral root formation due to the reduced outgrowth of the primordium, showing proof of principle for our approach. PMID:23328941

  12. Phosphoproteomic approaches to elucidate cellular signaling networks

    E-print Network

    Phosphoproteomic approaches to elucidate cellular signaling networks Katrin Schmelzle and Forest M be complemented with a variety of recently developed and improved phosphoproteomic techniques. These include developmentshave occurrednotonly inMS,however, but also in various other phosphoproteomic technologies. Thus

  13. Databases for plant phosphoproteomics.

    PubMed

    Schulze, Waltraud X; Yao, Qiuming; Xu, Dong

    2015-01-01

    Phosphorylation is the most studied posttranslational modification involved in signal transduction in stress responses, development, and growth. In the recent years large-scale phosphoproteomic studies were carried out using various model plants and several growth and stress conditions. Here we present an overview of online resources for plant phosphoproteomic databases: PhosPhAt as a resource for Arabidopsis phosphoproteins, P3DB as a resource expanding to crop plants, and Medicago PhosphoProtein Database as a resource for the model plant Medicago trunculata. PMID:25930705

  14. Quantitative phosphoproteomic analysis of early alterations in protein phosphorylation by 2,3,7,8-tetrachlorodibenzo-p-dioxin.

    PubMed

    Schulz, Melanie; Brandner, Stefanie; Eberhagen, Carola; Eckardt-Schupp, Friederike; Larsen, Martin R; Andrae, Ulrich

    2013-02-01

    A comprehensive quantitative analysis of changes in protein phosphorylation preceding or accompanying transcriptional activation by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in 5L rat hepatoma cells was performed using the SILAC approach. Following exposure of the cells to DMSO or 1 nM TCDD for 0.5 to 2 h, 5648 phosphorylated peptides corresponding to 2156 phosphoproteins were identified. Eight peptides exhibited a statistically significantly altered phosphorylation because of TCDD exposure and 22 showed a regulation factor of ? 1.5 in one of the experiments per time point. The vast majority of the TCCD-induced phosphorylation changes had not been reported before. The transcription factor ARNT, the obligate partner for gene activation by the TCDD-bound Ah receptor, exhibited an up-regulation of its Ser77 phosphorylation, a modification known to control the differential binding of ARNT homodimers and heterodimers to different enhancers suggesting that this phosphorylation represents a novel mechanism contributing to the alteration of gene expression by TCDD. Other proteins with altered phosphorylation included, among others, various transcriptional coregulators previously unknown to participate in TCDD-induced gene activation, regulators of small GTPases of the Ras superfamily, UBX domain-containing proteins and the oncogenic protein LYRIC. The results open up new directions for research on the molecular mechanisms of dioxin action and toxicity. PMID:23298284

  15. Comprehensive Quantitative Comparison of the Membrane Proteome, Phosphoproteome, and Sialiome of Human Embryonic and Neural Stem Cells*

    PubMed Central

    Melo-Braga, Marcella Nunes; Schulz, Melanie; Liu, Qiuyue; Swistowski, Andrzej; Palmisano, Giuseppe; Engholm-Keller, Kasper; Jakobsen, Lene; Zeng, Xianmin; Larsen, Martin Røssel

    2014-01-01

    Human embryonic stem cells (hESCs) can differentiate into neural stem cells (NSCs), which can further be differentiated into neurons and glia cells. Therefore, these cells have huge potential as source for treatment of neurological diseases. Membrane-associated proteins are very important in cellular signaling and recognition, and their function and activity are frequently regulated by post-translational modifications such as phosphorylation and glycosylation. To obtain information about membrane-associated proteins and their modified amino acids potentially involved in changes of hESCs and NSCs as well as to investigate potential new markers for these two cell stages, we performed large-scale quantitative membrane-proteomic of hESCs and NSCs. This approach employed membrane purification followed by peptide dimethyl labeling and peptide enrichment to study the membrane subproteome as well as changes in phosphorylation and sialylation between hESCs and NSCs. Combining proteomics and modification specific proteomics we identified a total of 5105 proteins whereof 57% contained transmembrane domains or signal peptides. The enrichment strategy yielded a total of 10,087 phosphorylated peptides in which 78% of phosphopeptides were identified with ?99% confidence in site assignment and 1810 unique formerly sialylated N-linked glycopeptides. Several proteins were identified as significantly regulated in hESCs and NSC, including proteins involved in the early embryonic and neural development. In the latter group of proteins, we could identify potential NSC markers as Crumbs 2 and several novel proteins. A motif analysis of the altered phosphosites showed a sequence consensus motif (R-X-XpS/T) significantly up-regulated in NSC. This motif is among other kinases recognized by the calmodulin-dependent protein kinase-2, emphasizing a possible importance of this kinase for this cell stage. Collectively, this data represent the most diverse set of post-translational modifications reported for hESCs and NSCs. This study revealed potential markers to distinguish NSCs from hESCs and will contribute to improve our understanding on the differentiation process. PMID:24173317

  16. Phosphoproteomics in cereals.

    PubMed

    Yang, Pingfang

    2015-01-01

    Cereals are the most important crop plant supplying staple food throughout the world. The economic importance and continued breeding of crop plants such as rice, maize, wheat, or barley require a detailed scientific understanding of adaptive and developmental processes. Protein phosphorylation is one of the most important regulatory posttranslational modifications and its analysis allows deriving functional and regulatory principles in plants. This minireview summarizes the current knowledge of phosphoproteomic studies in cereals. PMID:25930692

  17. Reproducible isolation of distinct, overlapping segments of the phosphoproteome

    E-print Network

    Cai, Long

    Reproducible isolation of distinct, overlapping segments of the phosphoproteome Bernd Bodenmiller1 detect different, partially overlapping segments of the phosphoproteome and that, at present, no single method is sufficient for a comprehensive phosphoproteome analysis. Among the several hundred known

  18. Clinical and Technical Phosphoproteomic Research

    PubMed Central

    2011-01-01

    An encouraging approach for the diagnosis and effective therapy of immunological pathologies, which would include cancer, is the identification of proteins and phosphorylated proteins. Disease proteomics, in particular, is a potentially useful method for this purpose. A key role is played by protein phosphorylation in the regulation of normal immunology disorders and targets for several new cancer drugs and drug candidates are cancer cells and protein kinases. Protein phosphorylation is a highly dynamic process. The functioning of new drugs is of major importance as is the selection of those patients who would respond best to a specific treatment regime. In all major aspects of cellular life signalling networks are key elements which play a major role in inter- and intracellular communications. They are involved in diverse processes such as cell-cycle progression, cellular metabolism, cell-cell communication and appropriate response to the cellular environment. A whole range of networks that are involved in the regulation of cell development, differentiation, proliferation, apoptosis, and immunologic responses is contained in the latter. It is so necessary to understand and monitor kinase signalling pathways in order to understand many immunology pathologies. Enrichment of phosphorylated proteins or peptides from tissue or bodily fluid samples is required. The application of technologies such as immunoproteomic techniques, phosphoenrichments and mass spectrometry (MS) is crucial for the identification and quantification of protein phosphorylation sites in order to advance in clinical research. Pharmacodynamic readouts of disease states and cellular drug responses in tumour samples will be provided as the field develops. We aim to detail the current and most useful techniques with research examples to isolate and carry out clinical phosphoproteomic studies which may be helpful for immunology and cancer research. Different phosphopeptide enrichment and quantitative techniques need to be combined to achieve good phosphopeptide recovery and good up- and-down phospho-regulation protein studies. PMID:21635771

  19. The phosphoproteome of toll-like receptor-activated macrophages

    Microsoft Academic Search

    Gabriele Weintz; Jesper V Olsen; Katja Frühauf; Magdalena Niedzielska; Ido Amit; Jonathan Jantsch; Jörg Mages; Cornelie Frech; Lars Dölken; Matthias Mann; Roland Lang

    2010-01-01

    Recognition of microbial danger signals by toll-like receptors (TLR) causes re-programming of macrophages. To investigate kinase cascades triggered by the TLR4 ligand lipopolysaccharide (LPS) on systems level, we performed a global, quantitative and kinetic analysis of the phosphoproteome of primary macrophages using stable isotope labelling with amino acids in cell culture, phosphopeptide enrichment and high-resolution mass spectrometry. In parallel, nascent

  20. 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

  1. Development of mass spectrometry based technologies for quantitative cell signaling phosphoproteomics : the epidermal growth factor receptor family as a model system

    E-print Network

    Wolf Yadlin, Alejandro

    2007-01-01

    Ligand binding to cell surface receptors initiates a cascade of signaling events regulated by dynamic phosphorylation on a multitude of pathway proteins. Quantitative features, including intensity, timing, and duration of ...

  2. Dissecting Quantitative Trait Loci for Boron Efficiency across Multiple Environments in Brassica napus

    PubMed Central

    Zhao, Zunkang; Wu, Likun; Nian, Fuzhao; Ding, Guangda; Shi, Taoxiong; Zhang, Didi; Shi, Lei; Xu, Fangsen; Meng, Jinling

    2012-01-01

    High yield is the most important goal in crop breeding, and boron (B) is an essential micronutrient for plants. However, B deficiency, leading to yield decreases, is an agricultural problem worldwide. Brassica napus is one of the most sensitive crops to B deficiency, and considerable genotypic variation exists among different cultivars in response to B deficiency. To dissect the genetic basis of tolerance to B deficiency in B. napus, we carried out QTL analysis for seed yield and yield-related traits under low and normal B conditions using the double haploid population (TNDH) by two-year and the BQDH population by three-year field trials. In total, 80 putative QTLs and 42 epistatic interactions for seed yield, plant height, branch number, pod number, seed number, seed weight and B efficiency coefficient (BEC) were identified under low and normal B conditions, singly explaining 4.15–23.16% and 0.53–14.38% of the phenotypic variation. An additive effect of putative QTLs was a more important controlling factor than the additive-additive effect of epistatic interactions. Four QTL-by-environment interactions and 7 interactions between epistatic interactions and the environment contributed to 1.27–4.95% and 1.17–3.68% of the phenotypic variation, respectively. The chromosome region on A2 of SYLB-A2 for seed yield under low B condition and BEC-A2 for BEC in the two populations was equivalent to the region of a reported major QTL, BE1. The B. napus homologous genes of Bra020592 and Bra020595 mapped to the A2 region and were speculated to be candidate genes for B efficiency. These findings reveal the complex genetic basis of B efficiency in B. napus. They provide a basis for the fine mapping and cloning of the B efficiency genes and for breeding B-efficient cultivars by marker-assisted selection (MAS). PMID:23028855

  3. Dissecting eukaryotic cells by coherent phase microscopy: quantitative analysis of quiescent and activated T lymphocytes

    PubMed Central

    Tychinsky, Vladimir P.; Kretushev, Alexander V.; Vyshenskaya, Tatiana V.; Shtil, Alexander A.

    2012-01-01

    Abstract. We present a concept for quantitative characterization of a functional state of an individual eukaryotic cell based on interference imaging. The informative parameters of the phase images of quiescent and mitogen-activated T lymphocytes included the phase thickness, phase volume, the area, and the size of organelles. These parameters were obtained without a special hypothesis about cell structure. Combinations of these parameters generated a “phase portrait” of the cell. A simplified spherical multilayer optic model of a T lymphocyte was used to calculate the refractivity profile, to identify structural elements of the image with the organelles, and to interpret the parameters of the phase portrait. The values of phase image parameters underwent characteristic changes in the course of mitogenic stimulation of T cells; thereby, the functional state of individual cells can be described using these parameters. Because the values of the components of the phase portrait are measured in absolute units, it is possible to compare the parameters of images obtained with different interference microscopes. Thus, the analysis of phase portraits provides a new and perspective approach for quantitative, real-time analysis of subcellular structure and physiologic state of an individual cell. PMID:22894503

  4. Dissecting eukaryotic cells by coherent phase microscopy: quantitative analysis of quiescent and activated T lymphocytes

    NASA Astrophysics Data System (ADS)

    Tychinsky, Vladimir P.; Kretushev, Alexander V.; Vyshenskaya, Tatiana V.; Shtil, Alexander A.

    2012-07-01

    We present a concept for quantitative characterization of a functional state of an individual eukaryotic cell based on interference imaging. The informative parameters of the phase images of quiescent and mitogen-activated T lymphocytes included the phase thickness, phase volume, the area, and the size of organelles. These parameters were obtained without a special hypothesis about cell structure. Combinations of these parameters generated a ``phase portrait'' of the cell. A simplified spherical multilayer optic model of a T lymphocyte was used to calculate the refractivity profile, to identify structural elements of the image with the organelles, and to interpret the parameters of the phase portrait. The values of phase image parameters underwent characteristic changes in the course of mitogenic stimulation of T cells; thereby, the functional state of individual cells can be described using these parameters. Because the values of the components of the phase portrait are measured in absolute units, it is possible to compare the parameters of images obtained with different interference microscopes. Thus, the analysis of phase portraits provides a new and perspective approach for quantitative, real-time analysis of subcellular structure and physiologic state of an individual cell.

  5. Quantitative proteomic dissection of a native 14-3-3? interacting protein complex associated with hepatocellular carcinoma.

    PubMed

    Bai, Chen; Tang, Siwei; Bai, Chen; Chen, Xian

    2014-04-01

    The 14-3-3 proteins regulate diverse biological processes that are implicated in cancer development, and seven 14-3-3 isoforms were identified with isoform-specific roles in different human tumors. In our previous work, we dissected the interactome of 14-3-3? formed during the DNA damage response in a hepatocellular carcinoma (HCC) cell using an AACT/SILAC-based quantitative proteomic approach. In this study, we used a similar proteomic approach to profile/identify the 14-3-3? interactome formed in native HCC cells. Functional categorization and data-dependent network analysis of the native HCC-specific 14-3-3? interactome revealed that 14-3-3? is involved in the regulation of multiple biological processes (BPs)/pathways, including cell cycle control, apoptosis, signal transduction, transport, cell adhesion, carbohydrate metabolism, and nucleic acid metabolism. Biological validation further supports that 14-3-3?, via association with multiple BP/pathway-specific proteins, coordinates the regulation of proliferation, survival, and metastasis of HCC. The findings in this study, together with those of our previous study, provide an extensive profile of the 14-3-3? interaction network in HCC cells, which should be valuable for understanding the pathology of HCC and HCC therapy. PMID:24363202

  6. Phosphoproteomics: new insights into cellular signaling

    Microsoft Academic Search

    Marc Mumby; Deirdre Brekken

    2005-01-01

    Developments in the field of phosphoproteomics have been fueled by the need simultaneously to monitor many different phosphoproteins within the signaling networks that coordinate responses to changes in the cellular environment. This article presents a brief review of phosphoproteomics with an emphasis on the biological insights that have been derived so far.

  7. Integrating phosphoproteomics in systems biology.

    PubMed

    Liu, Yu; Chance, Mark R

    2014-07-01

    Phosphorylation of serine, threonine and tyrosine plays significant roles in cellular signal transduction and in modifying multiple protein functions. Phosphoproteins are coordinated and regulated by a network of kinases, phosphatases and phospho-binding proteins, which modify the phosphorylation states, recognize unique phosphopeptides, or target proteins for degradation. Detailed and complete information on the structure and dynamics of these networks is required to better understand fundamental mechanisms of cellular processes and diseases. High-throughput technologies have been developed to investigate phosphoproteomes in model organisms and human diseases. Among them, mass spectrometry (MS)-based technologies are the major platforms and have been widely applied, which has led to explosive growth of phosphoproteomic data in recent years. New bioinformatics tools are needed to analyze and make sense of these data. Moreover, most research has focused on individual phosphoproteins and kinases. To gain a more complete knowledge of cellular processes, systems biology approaches, including pathways and networks modeling, have to be applied to integrate all components of the phosphorylation machinery, including kinases, phosphatases, their substrates, and phospho-binding proteins. This review presents the latest developments of bioinformatics methods and attempts to apply systems biology to analyze phosphoproteomics data generated by MS-based technologies. Challenges and future directions in this field will be also discussed. PMID:25349677

  8. 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

  9. Dissecting genetic architecture of grape proanthocyanidin composition through quantitative trait locus mapping

    PubMed Central

    2012-01-01

    Background Proanthocyanidins (PAs), or condensed tannins, are flavonoid polymers, widespread throughout the plant kingdom, which provide protection against herbivores while conferring organoleptic and nutritive values to plant-derived foods, such as wine. However, the genetic basis of qualitative and quantitative PA composition variation is still poorly understood. To elucidate the genetic architecture of the complex grape PA composition, we first carried out quantitative trait locus (QTL) analysis on a 191-individual pseudo-F1 progeny. Three categories of PA variables were assessed: total content, percentages of constitutive subunits and composite ratio variables. For nine functional candidate genes, among which eight co-located with QTLs, we performed association analyses using a diversity panel of 141 grapevine cultivars in order to identify causal SNPs. Results Multiple QTL analysis revealed a total of 103 and 43 QTLs, respectively for seed and skin PA variables. Loci were mainly of additive effect while some loci were primarily of dominant effect. Results also showed a large involvement of pairwise epistatic interactions in shaping PA composition. QTLs for PA variables in skin and seeds differed in number, position, involvement of epistatic interaction and allelic effect, thus revealing different genetic determinisms for grape PA composition in seeds and skin. Association results were consistent with QTL analyses in most cases: four out of nine tested candidate genes (VvLAR1, VvMYBPA2, VvCHI1, VvMYBPA1) showed at least one significant association with PA variables, especially VvLAR1 revealed as of great interest for further functional investigation. Some SNP-phenotype associations were observed only in the diversity panel. Conclusions This study presents the first QTL analysis on grape berry PA composition with a comparison between skin and seeds, together with an association study. Our results suggest a complex genetic control for PA traits and different genetic architectures for grape PA composition between berry skin and seeds. This work also uncovers novel genomic regions for further investigation in order to increase our knowledge of the genetic basis of PA composition. PMID:22369244

  10. Computational analysis of phosphoproteomics: progresses and perspectives.

    PubMed

    Ren, Jian; Gao, Xinjiao; Liu, Zexian; Cao, Jun; Ma, Qian; Xue, Yu

    2011-11-01

    Phosphorylation is one of the most essential post-translational modifications (PTMs) of proteins, regulates a variety of cellular signaling pathways, and at least partially determines the biological diversity. Recent progresses in phosphoproteomics have identified more than 100,000 phosphorylation sites, while this number will easily exceed one million in the next decade. In this regard, how to extract useful information from flood of phosphoproteomics data has emerged as a great challenge. In this review, we summarized the leading edges on computational analysis of phosphoproteomics, including discovery of phosphorylation motifs from phosphoproteomics data, systematic modeling of phosphorylation network, analysis of genetic variation that influences phosphorylation, and phosphorylation evolution. Based on existed knowledge, we also raised several perspectives for further studies. We believe that integration of experimental and computational analyses will propel the phosphoproteomics research into a new phase. PMID:21827424

  11. Broader implications of SILAC-based proteomics for dissecting signaling dynamics in cancer.

    PubMed

    Zhang, Hua; Xu, Yichen; Papanastasopoulos, Panos; Stebbing, Justin; Giamas, Georgios

    2014-12-01

    Large-scale transcriptome and epigenome analyses have been widely utilized to discover gene alterations implicated in cancer development at the genetic level. However, mapping of signaling dynamics at the protein level is likely to be more insightful and needed to complement massive genomic data. Stable isotope labeling with amino acids in cell culture (SILAC)-based proteomic analysis represents one of the most promising comparative quantitative methods that has been extensively employed in proteomic research. This technology allows for global, robust and confident identification and quantification of signal perturbations important for the progress of human diseases, particularly malignancies. The present review summarizes the latest applications of in vitro and in vivo SILAC-based proteomics in identifying global proteome/phosphoproteome and genome-wide protein-protein interactions that contribute to oncogenesis, highlighting the recent advances in dissecting signaling dynamics in cancer. PMID:25345469

  12. Dissecting paclitaxel-microtubule association: quantitative assessment of the 2'-OH group.

    PubMed

    Sharma, Shubhada; Lagisetti, Chandraiah; Poliks, Barbara; Coates, Robert M; Kingston, David G I; Bane, Susan

    2013-04-01

    Paclitaxel (PTX) is a microtubule-stabilizing agent that is widely used in cancer chemotherapy. This structurally complex natural product acts by binding to ?-tubulin in assembled microtubules. The 2'-hydroxyl group in the flexible side chain of PTX is an absolute requirement for activity, but its precise role in the drug-receptor interaction has not been specifically investigated. The contribution of the 2'-OH group to the affinity and tubulin-assembly efficacy of PTX has been evaluated through quantitative analysis of PTX derivatives possessing side chain deletions: 2'-deoxy-PTX, N-debenzoyl-2'-deoxy-PTX, and baccatin III. The affinity of 2'-deoxy-PTX for stabilized microtubules was more than 100-fold lower than that of PTX and only ~3-fold greater than the microtubule affinity of baccatin III. No microtubule binding activity was detected for the analogue N-debenzoyl-2'-deoxy-PTX. The tubulin-assembly efficacy of each ligand was consistent with the microtubule binding affinity, as was the trend in cytotoxicities. Molecular dynamics simulations revealed that the 2'-OH group of PTX can form a persistent hydrogen bond with D26 within the microtubule binding site. The absence of this interaction between 2'-deoxy-PTX and the receptor can account for the difference in binding free energy. Computational analyses also provide a possible explanation for why N-debenzoyl-2'-deoxy-PTX is inactive, in spite of the fact that it is essentially a substituted baccatin III. We propose that the hydrogen bonding interaction between the 2'-OH group and D26 is the most important stabilizing interaction that PTX forms with tubulin in the region of the C-13 side chain. We further hypothesize that the substituents at the 3'-position function to orient the 2'-OH group for a productive hydrogen bonding interaction with the protein. PMID:23473345

  13. New Tools for Quantitative Phosphoproteome Analysis

    Microsoft Academic Search

    Thomas P. Conrads; Haleem J. Issaq; Timothy D. Veenstra

    2002-01-01

    Recent advances in analytical methods, particularly in the area of mass spectrometry, have brought the field of proteomics to the forefront in biological science. The ultimate goal of proteomics—to characterize proteins expressed within a cell under a specific set of conditions—is daunting due to the complexity and dynamic nature the of protein population within the cell. While much of the

  14. Using phosphoproteomics to reveal signalling dynamics in plants

    E-print Network

    Hirt, Heribert

    Using phosphoproteomics to reveal signalling dynamics in plants Sergio de la Fuente van Bentem1, in addition to kinase substrates. A combined phosphoproteomic approach of mass spectrometry and microarray

  15. Characterization of the Phosphoproteome in SLE Patients.

    PubMed

    Zhang, Xinzhou; Ma, Hualin; 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 TiO? 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

  16. Phosphoproteomics reveals extensive in vivo phosphorylation of Arabidopsis proteins involved

    E-print Network

    Hirt, Heribert

    Phosphoproteomics reveals extensive in vivo phosphorylation of Arabidopsis proteins involved in RNA a small and therefore easier analyzable component of the com- plex phosphoproteome. In contrast to the wealth of phosphoproteomic investi- gations performed on yeast and animal systems, only a few studies

  17. Phosphoproteomic analyses reveal signaling pathways that facilitate lytic gammaherpesvirus replication.

    PubMed

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

    2013-09-01

    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

  18. Clam Dissection

    NSDL National Science Digital Library

    Kelly Riedell

    This online slide presentation features an image rich overview of clam dissections. The 31 slides include images portraying step of a dissection as well as information about each structure and its function. This presentation may serve as an introduction to the laboratory procedure, student review, or virtual dissection.

  19. Novel Mouse Models in Biomedical Research: The Power of Dissecting Pathways by Quantitative Control of Gene Activities

    Microsoft Academic Search

    S. Berger; H. Bujard

    \\u000a The last decade has seen significant progress in the development and refinement of genetic approaches applicable to the mouse,\\u000a making this animal the prime organism for the study of mammalian genetics. Particularly, the potential to control individual\\u000a gene activities in a temporally defined and tissuespecific manner has allowed us to dissect gene functions and pathways in\\u000a vivo with unprecedented precision,

  20. 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

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

    PubMed

    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

  2. Phosphoproteomics in Phytophthora infestans Differences in life stages and comparative analysis

    E-print Network

    Utrecht, Universiteit

    Phosphoproteomics in Phytophthora infestans ­ Differences in life stages and comparative analysis posttranslational phosphorylation. Phosphoproteomics, the analysis of the set of phosphorylated proteins in the cell. infestans life cycle. We want to utilize primary data from experimental collaborators on the phosphoproteome

  3. Temporal Dynamics of the Saccharopolyspora erythraea Phosphoproteome*

    PubMed Central

    Licona-Cassani, Cuauhtemoc; Lim, SooA; Marcellin, Esteban; Nielsen, Lars K.

    2014-01-01

    Actinomycetes undergo a dramatic reorganization of metabolic and cellular machinery during a brief period of growth arrest (“metabolic switch”) preceding mycelia differentiation and the onset of secondary metabolite biosynthesis. This study explores the role of phosphorylation in coordinating the metabolic switch in the industrial actinomycete Saccharopolyspora erythraea. A total of 109 phosphopeptides from 88 proteins were detected across a 150-h fermentation using open-profile two-dimensional LC-MS proteomics and TiO2 enrichment. Quantitative analysis of the phosphopeptides and their unphosphorylated cognates was possible for 20 pairs that also displayed constant total protein expression. Enzymes from central carbon metabolism such as putative acetyl-coenzyme A carboxylase, isocitrate lyase, and 2-oxoglutarate dehydrogenase changed dramatically in the degree of phosphorylation during the stationary phase, suggesting metabolic rearrangement for the reutilization of substrates and the production of polyketide precursors. In addition, an enzyme involved in cellular response to environmental stress, trypsin-like serine protease (SACE_6340/NC_009142_6216), decreased in phosphorylation during the growth arrest stage. More important, enzymes related to the regulation of protein synthesis underwent rapid phosphorylation changes during this stage. Whereas the degree of phosphorylation of ribonuclease Rne/Rng (SACE_1406/NC_009142_1388) increased during the metabolic switch, that of two ribosomal proteins, S6 (SACE_7351/NC_009142_7233) and S32 (SACE_6101/NC_009142_5981), dramatically decreased during this stage of the fermentation, supporting the hypothesis that ribosome subpopulations differentially regulate translation before and after the metabolic switch. Overall, we show the great potential of phosphoproteomic studies to explain microbial physiology and specifically provide evidence of dynamic protein phosphorylation events across the developmental cycle of actinomycetes. PMID:24615062

  4. PhosFox: a bioinformatics tool for peptide-level processing of LC-MS/MS-based phosphoproteomic data

    PubMed Central

    2014-01-01

    Background It is possible to identify thousands of phosphopeptides and –proteins in a single experiment with mass spectrometry-based phosphoproteomics. However, a current bottleneck is the downstream data analysis which is often laborious and requires a number of manual steps. Results Toward automating the analysis steps, we have developed and implemented a software, PhosFox, which enables peptide-level processing of phosphoproteomic data generated by multiple protein identification search algorithms, including Mascot, Sequest, and Paragon, as well as cross-comparison of their identification results. The software supports both qualitative and quantitative phosphoproteomics studies, as well as multiple between-group comparisons. Importantly, PhosFox detects uniquely phosphorylated peptides and proteins in one sample compared to another. It also distinguishes differences in phosphorylation sites between phosphorylated proteins in different samples. Using two case study examples, a qualitative phosphoproteome dataset from human keratinocytes and a quantitative phosphoproteome dataset from rat kidney inner medulla, we demonstrate here how PhosFox facilitates an efficient and in-depth phosphoproteome data analysis. PhosFox was implemented in the Perl programming language and it can be run on most common operating systems. Due to its flexible interface and open source distribution, the users can easily incorporate the program into their MS data analysis workflows and extend the program with new features. PhosFox source code, implementation and user instructions are freely available from https://bitbucket.org/phintsan/phosfox. Conclusions PhosFox facilitates efficient and more in-depth comparisons between phosphoproteins in case–control settings. The open source implementation is easily extendable to accommodate additional features for widespread application use cases. PMID:25028575

  5. A phosphoproteomics approach to elucidate neuropeptide signal transduction controlling insect metamorphosis

    Microsoft Academic Search

    Kim F. Rewitz; Martin R. Larsen; Anders Lobner-Olesen; Robert Rybczynski; Michael B. O'Connor; Lawrence I. Gilbert

    2009-01-01

    In insects, the neuropeptide prothoracicotropic hormone (PTTH) stimulates production of ecdysone (E) in the prothoracic glands (PGs). E is the precursor of the principal steroid hormone, 20-hydroxyecdysone (20E), that is responsible for eliciting molting and metamorphosis. In this study, we used quantitative phosphoproteomics to investigate signal transduction events initiated by PTTH. We identified Spook (CYP307A1), a suspected rate-limiting enzyme for

  6. Identifying differentially regulated subnetworks from phosphoproteomic data

    Microsoft Academic Search

    Martin Klammer; Klaus Godl; Andreas Tebbe; Christoph Schaab

    2010-01-01

    BACKGROUND: Various high throughput methods are available for detecting regulations at the level of transcription, translation or posttranslation (e.g. phosphorylation). Integrating these data with protein networks should make it possible to identify subnetworks that are significantly regulated. Furthermore, such integration can support identification of regulated entities from often noisy high throughput data. In particular, processing mass spectrometry-based phosphoproteomic data in

  7. A QUANTITATIVE ULTRASOUND-BASED METHOD AND DEVICE FOR RELIABLY GUIDING PATHOLOGISTS TO METASTATIC REGIONS OF DISSECTED LYMPH NODES

    E-print Network

    Illinois at Urbana-Champaign, University of

    in freshly-excised lymph nodes of pa- tients with histologically-proven primary cancer. From a signal- structed a 3D cancer-likelihood map of a partially metastatic lymph node and compared that map requiring histological evaluation. Index Terms-- metastatic cancer, lymph nodes, quantitative ul- trasound

  8. Quahog Dissection

    NSDL National Science Digital Library

    Rhode Island Sea Grant

    This Rhode Island Sea Grant informational page presents a descriptive guide to Quahog (a type of hard-shell clam) dissections. The page accompanies students performing a Quahog dissection, using colorful images and highlighted vocabulary terms to illustrate special features. In addition to general anatomy, the reference includes informational sections about feeding & digestion and respiration & circulation. Linked terms direct users to related Sea Grant web pages.

  9. Mass Spectrometry-Based Quantitative Proteomics for Dissecting Multiplexed Redox Cysteine Modifications in Nitric Oxide-Protected Cardiomyocyte Under Hypoxia

    PubMed Central

    Pan, Kuan-Ting; Chen, Yi-Yun; Pu, Tsung-Hsien; Chao, Yu-Shu; Yang, Chun-Yi; Bomgarden, Ryan D.; Rogers, John C.

    2014-01-01

    Abstract Aims: Distinctive states of redox-dependent cysteine (Cys) modifications are known to regulate signaling homeostasis under various pathophysiological conditions, including myocardial injury or protection in response to ischemic stress. Recent evidence further implicates a dynamic interplay among these modified forms following changes in cellular redox environment. However, a precise delineation of multiplexed Cys modifications in a cellular context remains technically challenging. To this end, we have now developed a mass spectrometry (MS)-based quantitative approach using a set of novel iodoacetyl-based Cys-reactive isobaric tags (irreversible isobaric iodoacetyl Cys-reactive tandem mass tag [iodoTMT]) endowed with unique irreversible Cys-reactivities. Results: We have established a sequential iodoTMT-switch procedure coupled with efficient immunoenrichment and advanced shotgun liquid chromatography-MS/MS analysis. This workflow allows us to differentially quantify the multiple redox-modified forms of a Cys site in the original cellular context. In one single analysis, we have identified over 260 Cys sites showing quantitative differences in multiplexed redox modifications from the total lysates of H9c2 cardiomyocytes experiencing hypoxia in the absence and presence of S-nitrosoglutathione (GSNO), indicative of a distinct pattern of individual susceptibility to S-nitrosylation or S-glutathionylation. Among those most significantly affected are proteins functionally implicated in hypoxic damage from which we showed that GSNO would protect. Innovation: We demonstrate for the first time how quantitative analysis of various Cys-redox modifications occurring in biological samples can be performed precisely and simultaneously at proteomic levels. Conclusion: We have not only developed a new approach to map global Cys-redoxomic regulation in vivo, but also provided new evidences implicating Cys-redox modifications of key molecules in NO-mediated ischemic cardioprotection. Antioxid. Redox Signal. 20, 1365–1381. PMID:24152285

  10. Computational phosphoproteomics: from identification to localization.

    PubMed

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

    2015-03-01

    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

  11. 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

  12. Dynamic phosphoproteomics reveals TORC1-dependent regulation of yeast nucleotide and amino acid biosynthesis.

    PubMed

    Oliveira, Ana Paula; Ludwig, Christina; Zampieri, Mattia; Weisser, Hendrik; Aebersold, Ruedi; Sauer, Uwe

    2015-01-01

    Phosphoproteomics studies have unraveled the extent of protein phosphorylation as a key cellular regulation mechanism, but assigning functionality to specific phosphorylation events remains a major challenge. TORC1 (target of rapamycin complex 1) is a kinase-containing protein complex that transduces changes in nutrient availability into phosphorylation signaling events that alter cell growth and proliferation. To resolve the temporal sequence of phosphorylation responses to nutritionally and chemically induced changes in TORC1 signaling and to identify previously unknown kinase-substrate relationships in Saccharomyces cerevisiae, we performed quantitative mass spectrometry-based phosphoproteomic analyses after shifts in nitrogen sources and rapamycin treatment. From early phosphorylation events that were consistent over at least two experimental perturbations, we identified 51 candidate and 10 known proximal targets of TORC1 that were direct substrates of TORC1 or of one of its kinase or phosphatase substrates. By correlating these phosphoproteomics data with dynamic metabolomics data, we inferred the functional role of phosphorylation on the metabolic activity of 12 enzymes, including three candidate TORC1-proximal targets: Amd1, which is involved in nucleotide metabolism; Hom3, which is involved in amino acid metabolism; and Tsl1, which mediates carbohydrate storage. Finally, we identified the TORC1 substrates Sch9 and Atg1 as candidate kinases that phosphorylate Amd1 and Hom3, respectively. PMID:25921291

  13. Sample preparation for phosphoproteomic analysis of circadian time series in Arabidopsis thaliana.

    PubMed

    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

  14. 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

  15. Paper dissection

    NSDL National Science Digital Library

    David Varricchio

    Students are provided with a dinosaur article from a popular magazine (e.g. Discover or Natural History) or the journal Science. Their task is to dissect the article distinguishing evidence from interpretation. They need to recognize the various hypotheses presented and also evaluate the strength of these ideas. Then during classroom discussion, they explore the implications of their dissections. For example they would address some of the following questions: Are other interpretations possible? Where have the authors over interpreted the evidence? What are the strongest interpretations? How could the ideas be further tested? What type of evidence would be sufficient to falsify or further support the interpretations of the papers?

  16. Dissect It!

    NSDL National Science Digital Library

    Olga Wood

    2012-06-27

    After dissecting a flower(s), the students will be able to identify the parts necessary for pollination, or reproduction of flowering plants. They will also make comparisons and find patterns in nature, leading them to the understanding of the processes of sexual reproduction in flowering plants, including pollination and fertilization (seed production).

  17. Polyomino Dissections

    ERIC Educational Resources Information Center

    Hohn, Tiina; Liu, Andy

    2012-01-01

    One of Gardner's passions was to introduce puzzles into the classroom. From this point of view, polyomino dissections are an excellent topic. They require little background, provide training in geometric visualization, and mostly they are fun. In this article, we put together a large collection of such puzzles, introduce a new approach in solving…

  18. 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

  19. Towards a phosphoproteome map of Corynebacterium glutamicum.

    PubMed

    Bendt, Anne K; Burkovski, Andreas; Schaffer, Steffen; Bott, Michael; Farwick, Mike; Hermann, Thomas

    2003-08-01

    In this study, the phosphoproteome of Corynebacterium glutamicum, an industrially important soil bacterium of the Corynebacterium/Mycobacterium/Nocardia (CMN) group of Gram-positive bacteria, was investigated by two different detection methods: first, by in vivo radio-labeling using [(33)P]-phosphoric acid with subsequent autoradiography and second, by immunostaining with phosphoamino acid-specific monoclonal antibodies. After two-dimensional gel electrophoresis (2-DE), around 60 [(33)P]-labeled protein spots were visualized and around 90 antibody-decorated protein spots detected; 31 of the protein spots were detected with both methods. By peptide mass fingerprinting, 41 different proteins were identified, namely 5-enolpyruvylshikimate 3-phosphate synthase, aconitase, acyl-CoA carboxylase, acyl-CoA synthetase, ATP (synthase alpha- and beta-chain), carbamoyl-phosphate synthase, citrate synthase, cysteine synthase, DnaK, the elongation factors G, P, Ts and Tu, enolase, fructose bisphosphate aldolase, fumarase, Gap dehydrogenase, glutamine synthetase I, glycine hydroxymethyltransferase, GroEL2, GTPase, heat-inducible transcriptional repressor DnaJ2, inorganic pyrophosphatase, isocitrate dehydrogenase, ketol-acid reductoisomerase, lactate dehydrogenase, leucine-tRNA ligase, lipoamide dehydrogenase, methionine synthase, O-acetylhomoserine sulfhydrylase, pyruvate carboxylase, pyruvate kinase, pyruvate oxidase, ribosomal protein S1, RNA polymerase (beta-subunit), succinyl-CoA:CoA transferase, transketolase and UDP-N-acetylmuramoyl-L-alanine ligase, besides a hypothetical 35k protein and a hypothetical glucose kinase. Both detection techniques were used to create a phosphoproteome map. Additionally, the influence of nitrogen deprivation on the phosphoproteome of C. glutamicum was investigated. PMID:12923788

  20. Clam Dissection

    NSDL National Science Digital Library

    Roy Plotnick

    Students observe clams (Mercenaria) in a salt water aquarium, paying attention to siphons and any burrowing. They then remove the clams and describe the external morphology. The clams are then dissected, with special attention made to features (siphons, muscles) that leave observable marks on the shells. They are then provided the shells of a different genus (Mya) and asked to predict the soft tissue morphology and life mode.

  1. TiSH--a robust and sensitive global phosphoproteomics strategy employing a combination of TiO2, SIMAC, and HILIC.

    PubMed

    Engholm-Keller, Kasper; Birck, Pernille; Størling, Joachim; Pociot, Flemming; Mandrup-Poulsen, Thomas; Larsen, Martin R

    2012-10-22

    Large scale quantitative phosphoproteomics depends upon multidimensional strategies for peptide fractionation, phosphopeptide enrichment, and mass spectrometric analysis. Previously, most robust comprehensive large-scale phosphoproteomics strategies have relied on milligram amounts of protein. We have set up a multi-dimensional phosphoproteomics strategy combining a number of well-established enrichment and fraction methods: An initial TiO(2) phosphopeptide pre-enrichment step is followed by post-fractionation using sequential elution from IMAC (SIMAC) to separate multi- and mono-phosphorylated peptides, and hydrophilic interaction liquid chromatography (HILIC) of the mono-phosphorylated peptides (collectively abbreviated "TiSH"). The advantages of the strategy include a high specificity and sample preparation workload reduction due to the TiO(2) pre-enrichment step, as well as low adsorptive losses. We demonstrate the capability of this strategy by quantitative investigation of early interferon-? signaling in low quantities of insulinoma cells. We identified ~6600 unique phosphopeptides from 300 ?g of peptides/condition (22 unique phosphopeptides/?g) in a duplex dimethyl labeling experiment, with an enrichment specificity>94%. When doing network analysis of putative phosphorylation changes it could be noted that the identified protein interaction network centered upon proteins known to be affected by the interferon-? pathway, thereby supporting the utility of this global phosphoproteomics strategy. This strategy thus shows great potential for interrogating signaling networks from low amounts of sample with high sensitivity and specificity. PMID:22906719

  2. Dissected Plateau

    NASA Technical Reports Server (NTRS)

    2005-01-01

    [figure removed for brevity, see original site] Context image for PIA03193 Dissected Plateau

    This plateau borders Echus Chasma. The surface of the plateau has been dissected by shallow channels of unknown origin.

    Image information: VIS instrument. Latitude 0.2N, Longitude 279.1E. 17 meter/pixel resolution.

    Note: this THEMIS visual image has not been radiometrically nor geometrically calibrated for this preliminary release. An empirical correction has been performed to remove instrumental effects. A linear shift has been applied in the cross-track and down-track direction to approximate spacecraft and planetary motion. Fully calibrated and geometrically projected images will be released through the Planetary Data System in accordance with Project policies at a later time.

    NASA's Jet Propulsion Laboratory manages the 2001 Mars Odyssey mission for NASA's Office of Space Science, Washington, D.C. The Thermal Emission Imaging System (THEMIS) was developed by Arizona State University, Tempe, in collaboration with Raytheon Santa Barbara Remote Sensing. The THEMIS investigation is led by Dr. Philip Christensen at Arizona State University. Lockheed Martin Astronautics, Denver, is the prime contractor for the Odyssey project, and developed and built the orbiter. Mission operations are conducted jointly from Lockheed Martin and from JPL, a division of the California Institute of Technology in Pasadena.

  3. Dissected Surface

    NASA Technical Reports Server (NTRS)

    2005-01-01

    [figure removed for brevity, see original site] Context image for PIA03286 Dissected Surface

    Small channels dissect this region near Nectaris Fossae.

    Image information: VIS instrument. Latitude -22.9N, Longitude 17.4E. 17 meter/pixel resolution.

    Note: this THEMIS visual image has not been radiometrically nor geometrically calibrated for this preliminary release. An empirical correction has been performed to remove instrumental effects. A linear shift has been applied in the cross-track and down-track direction to approximate spacecraft and planetary motion. Fully calibrated and geometrically projected images will be released through the Planetary Data System in accordance with Project policies at a later time.

    NASA's Jet Propulsion Laboratory manages the 2001 Mars Odyssey mission for NASA's Office of Space Science, Washington, D.C. The Thermal Emission Imaging System (THEMIS) was developed by Arizona State University, Tempe, in collaboration with Raytheon Santa Barbara Remote Sensing. The THEMIS investigation is led by Dr. Philip Christensen at Arizona State University. Lockheed Martin Astronautics, Denver, is the prime contractor for the Odyssey project, and developed and built the orbiter. Mission operations are conducted jointly from Lockheed Martin and from JPL, a division of the California Institute of Technology in Pasadena.

  4. Surface Dissection

    NASA Technical Reports Server (NTRS)

    2006-01-01

    [figure removed for brevity, see original site] Context image for PIA03290 Surface Dissection

    At the southern end of Echus Cansma this dissected surface and mega-gullies occur.

    Image information: VIS instrument. Latitude -1.1N, Longitude 278.8E. 17 meter/pixel resolution.

    Note: this THEMIS visual image has not been radiometrically nor geometrically calibrated for this preliminary release. An empirical correction has been performed to remove instrumental effects. A linear shift has been applied in the cross-track and down-track direction to approximate spacecraft and planetary motion. Fully calibrated and geometrically projected images will be released through the Planetary Data System in accordance with Project policies at a later time.

    NASA's Jet Propulsion Laboratory manages the 2001 Mars Odyssey mission for NASA's Office of Space Science, Washington, D.C. The Thermal Emission Imaging System (THEMIS) was developed by Arizona State University, Tempe, in collaboration with Raytheon Santa Barbara Remote Sensing. The THEMIS investigation is led by Dr. Philip Christensen at Arizona State University. Lockheed Martin Astronautics, Denver, is the prime contractor for the Odyssey project, and developed and built the orbiter. Mission operations are conducted jointly from Lockheed Martin and from JPL, a division of the California Institute of Technology in Pasadena.

  5. Comparative phosphoproteome pro ling reveals a function of the STN8 kinase in ne-tuning

    E-print Network

    Halazonetis, Thanos

    Comparative phosphoproteome pro ling reveals a function of the STN8 kinase in ne-tuning of cyclic and regulatory functions. We performed an unbiased phosphoproteome-wide screen with Arabidopsis WT and stn8. phosphoproteomics | Arabidopsis thaliana In the eld of chloroplast biogenesis, interest in protein phos- phorylation

  6. Phosphoproteomics as a tool to unravel plant regulatory Sergio de la Fuente van Bentema

    E-print Network

    Hirt, Heribert

    REVIEW Phosphoproteomics as a tool to unravel plant regulatory mechanisms Sergio de la Fuente van on recent developments in the field of phosphoproteomics that are based on phosphopeptide isolation from at any time (Hubbard and Cohen 1993), indicating that the phosphoproteome of each multicel- lular

  7. 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

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

    PubMed

    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

  9. 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-mimicking SEPT9 mutant rescued these effects. Collectively, this study provides the first global analysis of phosphorylation-mediated processes during infection with an extracellular, diarrheagenic bacterial pathogen. PMID:25944883

  10. Is Phosphoproteomics Ready for Clinical Research?

    PubMed Central

    Iliuk, Anton B.; Tao, W. Andy

    2012-01-01

    Background For many diseases such as cancer where phosphorylation-dependent signaling is the foundation of disease onset and progression, single-gene testing and genomic profiling alone are not sufficient in providing most critical information. The reason for this is that in these activated pathways the signaling changes and drug resistance are often not directly correlated with changes in protein expression levels. In order to obtain the essential information needed to evaluate pathway activation or the effects of certain drugs and therapies on the molecular level, the analysis of changes in protein phosphorylation is critical. Methods Existing approaches do not differentiate clinical disease subtypes on the protein and signaling pathway level, and therefore hamper the predictive management of the disease and the selection of therapeutic targets. Conclusions The mini-review examines the impact of emerging systems biology tools and the possibility of applying phosphoproteomics to clinical research. PMID:23159844

  11. Phosphoproteomic analysis reveals compensatory effects in the piriform cortex of VX nerve agent exposed rats.

    PubMed

    Nirujogi, Raja Sekhar; Wright, James D; Manda, Srikanth S; Zhong, Jun; Na, Chan Hyun; Meyerhoff, James; Benton, Bernard; Jabbour, Rabih; Willis, Kristen; Kim, Min-Sik; Pandey, Akhilesh; Sekowski, Jennifer W

    2015-01-01

    To gain insights into the toxicity induced by the nerve agent VX, an MS-based phosphoproteomic analysis was carried out on the piriform cortex region of brains from VX-treated rats. Using isobaric tag based TMT labeling followed by titanium dioxide enrichment strategy, we identified 9975 unique phosphosites derived from 3287 phosphoproteins. Temporal changes in the phosphorylation status of peptides were observed over a time period of 24 h in rats exposed to a 1× LD50, intravenous (i.v.) dose with the most notable changes occurring at the 1 h postexposure time point. Five major functional classes of proteins exhibited changes in their phosphorylation status: (i) ion channels/transporters, including ATPases, (ii) kinases/phosphatases, (iii) GTPases, (iv) structural proteins, and (v) transcriptional regulatory proteins. This study is the first quantitative phosphoproteomic analysis of VX toxicity in the brain. Understanding the toxicity and compensatory signaling mechanisms will improve the understanding of the complex toxicity of VX in the brain and aid in the elucidation of novel molecular targets that would be important for development of improved countermeasures. All MS data have been deposited in the ProteomeXchange with identifier PXD001184 (http://proteomecentral.proteomexchange.org/dataset/PXD001184). PMID:25403869

  12. Global Screening of CK2 Kinase Substrates by an Integrated Phosphoproteomics Workflow

    PubMed Central

    Bian, Yangyang; Ye, Mingliang; Wang, Chunli; Cheng, Kai; Song, Chunxia; Dong, Mingming; Pan, Yanbo; Qin, Hongqiang; Zou, Hanfa

    2013-01-01

    Due to its constitutive activity and ubiquitous distribution, CK2 is the most pleiotropic kinase among the individual members of the protein kinase superfamily. Identification of CK2 substrates is vital to decipher its role in biological processes. However, only a limited number of CK2 substrates were identified so far. In this study, we developed an integrated phosphoproteomics workflow to identify the CK2 substrates in large scale. First, in vitro kinase reactions with immobilized proteomes were combined with quantitative phosphoproteomics to identify in vitro CK2 phosphorylation sites, which leaded to identification of 988 sites from 581 protein substrates. To reduce false positives, we proposed an approach by comparing these in vitro sites with the public databases that collect in vivo phosphorylation sites. After the removal of the sites that were excluded in the databases, 605 high confident CK2 sites corresponding to 356 proteins were retained. The CK2 substrates identified in this study were based on the discovery mode, in which an unbiased overview of CK2 substrates was provided. Our result revealed that CK2 substrates were significantly enriched in the spliceosomal proteins, indicating CK2 might regulate the functions of spliceosome. PMID:24322422

  13. Specific Visualization and Identification of Phosphoproteome in Gels

    PubMed Central

    2015-01-01

    The applicability of gel-based proteomic strategies in phosphoproteomics has been largely limited by the lack of technologies for specific detection of phosphoproteins in gels. Here for the first time we report a strategy for simultaneous visualization and identification of phosphoproteome in gels (VIPing) through coupling specific detection of phosphoproteins with protein identification and phosphorylation site mapping by tandem mass spectrometry. The core of the strategy is a novel compound multifunctionalized with a titanium ion(IV) for outstanding selectivity toward phosphorylated residues, a fluorophore for visualization, and a biotin group for phosphopeptide enrichment. The sensitivity and specificity of the VIPing strategy was demonstrated using standard protein mixtures and complex cell extracts, and the method was applied to study the phosphorylation changes of an essential tyrosine kinase Syk and interacting proteins upon B-cell stimulation. The novel technique provides a powerful platform for gel-based phosphoproteomic studies. PMID:24941108

  14. Quantitative phosphoproteome analysis of embryonic stem cell differentiation toward blood

    PubMed Central

    Piazzi, Manuela; Williamson, Andrew; Lee, Chia-Fang; Pearson, Stella; Lacaud, Georges; Kouskoff, Valerie; McCubrey, James A.; Cocco, Lucio; Whetton, Anthony D.

    2015-01-01

    Murine embryonic stem (ES) cells can differentiate in vitro into three germ layers (endodermic, mesodermic, ectodermic). Studies on the differentiation of these cells to specific early differentiation stages has been aided by an ES cell line carrying the Green Fluorescent Protein (GFP) targeted to the Brachyury (Bry) locus which marks mesoderm commitment. Furthermore, expression of the Vascular Endothelial Growth Factor receptor 2 (Flk1) along with Bry defines hemangioblast commitment. Isobaric-tag for relative and absolute quantification (iTRAQTM) and phosphopeptide enrichment coupled to liquid chromatography separation and mass spectrometry allow the study of phosphorylation changes occurring at different stages of ES cell development using Bry and Flk1 expression respectively. We identified and relatively quantified 37 phosphoentities which are modulated during mesoderm-induced ES cells differentiation, comparing epiblast-like, early mesoderm and hemangioblast-enriched cells. Among the proteins differentially phosphorylated toward mesoderm differentiation were: the epigenetic regulator Dnmt3b, the protein kinase GSK3b, the chromatin remodeling factor Smarcc1, the transcription factor Utf1; as well as protein specifically related to stem cell differentiation, as Eomes, Hmga2, Ints1 and Rif1. As most key factors regulating early hematopoietic development have also been implicated in various types of leukemia, understanding the post-translational modifications driving their regulation during normal development could result in a better comprehension of their roles during abnormal hematopoiesis in leukemia. PMID:25890499

  15. Quantitative phosphoproteome analysis of embryonic stem cell differentiation toward blood.

    PubMed

    Piazzi, Manuela; Williamson, Andrew; Lee, Chia-Fang; Pearson, Stella; Lacaud, Georges; Kouskoff, Valerie; McCubrey, James A; Cocco, Lucio; Whetton, Anthony D

    2015-05-10

    Murine embryonic stem (ES) cells can differentiate in vitro into three germ layers (endodermic, mesodermic, ectodermic). Studies on the differentiation of these cells to specific early differentiation stages has been aided by an ES cell line carrying the Green Fluorescent Protein (GFP) targeted to the Brachyury (Bry) locus which marks mesoderm commitment. Furthermore, expression of the Vascular Endothelial Growth Factor receptor 2 (Flk1) along with Bry defines hemangioblast commitment. Isobaric-tag for relative and absolute quantification (iTRAQTM) and phosphopeptide enrichment coupled to liquid chromatography separation and mass spectrometry allow the study of phosphorylation changes occurring at different stages of ES cell development using Bry and Flk1 expression respectively. We identified and relatively quantified 37 phosphoentities which are modulated during mesoderm-induced ES cells differentiation, comparing epiblast-like, early mesoderm and hemangioblast-enriched cells. Among the proteins differentially phosphorylated toward mesoderm differentiation were: the epigenetic regulator Dnmt3b, the protein kinase GSK3b, the chromatin remodeling factor Smarcc1, the transcription factor Utf1; as well as protein specifically related to stem cell differentiation, as Eomes, Hmga2, Ints1 and Rif1. As most key factors regulating early hematopoietic development have also been implicated in various types of leukemia, understanding the post-translational modifications driving their regulation during normal development could result in a better comprehension of their roles during abnormal hematopoiesis in leukemia. PMID:25890499

  16. Marquette University Neuroanatomical Dissection

    NSDL National Science Digital Library

    Marquette University (Marquette University)

    2012-07-24

    This website provides information regarding Marquette University' Neuroanatomical Dissection Summer Course. The focus of the course is an intensive review of the brain and spinal cord. Participants will spend a portion of the course dissecting a cadaver.

  17. Rapid Phosphoproteomic and Transcriptomic Changes in the Rhizobia-legume Symbiosis*

    PubMed Central

    Rose, Christopher M.; Venkateshwaran, Muthusubramanian; Volkening, Jeremy D.; Grimsrud, Paul A.; Maeda, Junko; Bailey, Derek J.; Park, Kwanghyun; Howes-Podoll, Maegen; den Os, Désirée; Yeun, Li Huey; Westphall, Michael S.; Sussman, Michael R.; Ané, Jean-Michel; Coon, Joshua J.

    2012-01-01

    Symbiotic associations between legumes and rhizobia usually commence with the perception of bacterial lipochitooligosaccharides, known as Nod factors (NF), which triggers rapid cellular and molecular responses in host plants. We report here deep untargeted tandem mass spectrometry-based measurements of rapid NF-induced changes in the phosphorylation status of 13,506 phosphosites in 7739 proteins from the model legume Medicago truncatula. To place these phosphorylation changes within a biological context, quantitative phosphoproteomic and RNA measurements in wild-type plants were compared with those observed in mutants, one defective in NF perception (nfp) and one defective in downstream signal transduction events (dmi3). Our study quantified the early phosphorylation and transcription dynamics that are specifically associated with NF-signaling, confirmed a dmi3-mediated feedback loop in the pathway, and suggested “cryptic” NF-signaling pathways, some of them being also involved in the response to symbiotic arbuscular mycorrhizal fungi. PMID:22683509

  18. Phosphoproteomics reveals distinct modes of Mec1/ATR signaling during DNA replication.

    PubMed

    Bastos de Oliveira, Francisco Meirelles; Kim, Dongsung; Cussiol, José Renato; Das, Jishnu; Jeong, Min Cheol; Doerfler, Lillian; Schmidt, Kristina Hildegard; Yu, Haiyuan; Smolka, Marcus Bustamante

    2015-03-19

    The Mec1/Tel1 kinases (human ATR/ATM) play numerous roles in the DNA replication stress response. Despite the multi-functionality of these kinases, studies of their in vivo action have mostly relied on a few well-established substrates. Here we employed a combined genetic-phosphoproteomic approach to monitor Mec1/Tel1 signaling in a systematic, unbiased, and quantitative manner. Unexpectedly, we find that Mec1 is highly active during normal DNA replication, at levels comparable or higher than Mec1's activation state induced by replication stress. This "replication-correlated" mode of Mec1 action requires the 9-1-1 clamp and the Dna2 lagging-strand factor and is distinguishable from Mec1's action in activating the downstream kinase Rad53. We propose that Mec1/ATR performs key functions during ongoing DNA synthesis that are distinct from their canonical checkpoint role during replication stress. PMID:25752575

  19. 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

  20. Battle through Signaling between Wheat and the Fungal Pathogen Septoria tritici Revealed by Proteomics and Phosphoproteomics*

    PubMed Central

    Yang, Fen; Melo-Braga, Marcella N.; Larsen, Martin R.; Jørgensen, Hans J. L.; Palmisano, Giuseppe

    2013-01-01

    The fungus Septoria tritici causes the disease septoria tritici blotch in wheat, one of the most economically devastating foliar diseases in this crop. To investigate signaling events and defense responses in the wheat–S. tritici interaction, we performed a time-course study of S. tritici infection in resistant and susceptible wheat using quantitative proteomics and phosphoproteomics, with special emphasis on the initial biotrophic phase of interactions. Our study revealed an accumulation of defense and stress-related proteins, suppression of photosynthesis, and changes in sugar metabolism during compatible and incompatible interactions. However, differential regulation of the phosphorylation status of signaling proteins, transcription and translation regulators, and membrane-associated proteins was observed between two interactions. The proteomic data were correlated with a more rapid or stronger accumulation of signal molecules, including calcium, H2O2, NO, and sugars, in the resistant than in the susceptible cultivar in response to the infection. Additionally, 31 proteins and 5 phosphoproteins from the pathogen were identified, including metabolic proteins and signaling proteins such as GTP-binding proteins, 14–3-3 proteins, and calcium-binding proteins. Quantitative PCR analysis showed the expression of fungal signaling genes and genes encoding a superoxide dismutase and cell-wall degrading enzymes. These results indicate roles of signaling, antioxidative stress mechanisms, and nutrient acquisition in facilitating the initial symptomless growth. Taken in its entirety, our dataset suggests interplay between the plant and S. tritici through complex signaling networks and downstream molecular events. Resistance is likely related to several rapidly and intensively triggered signal transduction cascades resulting in a multiple-level activation of transcription and translation processes of defense responses. Our sensitive approaches and model provide a comprehensive (phospho)proteomics resource for studying signaling from the point of view of both host and pathogen during a plant–pathogen interaction. PMID:23722186

  1. Phosphoproteomics Study Based on In Vivo Inhibition Reveals Sites of Calmodulin?Dependent Protein Kinase II Regulation in the Heart

    PubMed Central

    Scholten, Arjen; Preisinger, Christian; Corradini, Eleonora; Bourgonje, Vincent J.; Hennrich, Marco L.; van Veen, Toon A. B.; Swaminathan, Paari D.; Joiner, Mei?Ling; Vos, Marc A.; Anderson, Mark E.; Heck, Albert J. R.

    2013-01-01

    Background The multifunctional Ca2+? and calmodulin?dependent protein kinase II (CaMKII) is a crucial mediator of cardiac physiology and pathology. Increased expression and activation of CaMKII has been linked to elevated risk for arrhythmic events and is a hallmark of human heart failure. A useful approach to determining CaMKII's role therein is large?scale analysis of phosphorylation events by mass spectrometry. However, current large?scale phosphoproteomics approaches have proved inadequate for high?fidelity identification of kinase?specific roles. The purpose of this study was to develop a phosphoproteomics approach to specifically identify CaMKII's downstream effects in cardiac tissue. Methods and Results To identify putative downstream CaMKII targets in cardiac tissue, animals with myocardial?delimited expression of the specific peptide inhibitor of CaMKII (AC3?I) or an inactive control (AC3?C) were compared using quantitative phosphoproteomics. The hearts were isolated after isoproterenol injection to induce CaMKII activation downstream of ??adrenergic receptor agonist stimulation. Enriched phosphopeptides from AC3?I and AC3?C mice were differentially quantified using stable isotope dimethyl labeling, strong cation exchange chromatography and high?resolution LC?MS/MS. Phosphorylation levels of several hundred sites could be profiled, including 39 phosphoproteins noticeably affected by AC3?I?mediated CaMKII inhibition. Conclusions Our data set included known CaMKII substrates, as well as several new candidate proteins involved in functions not previously implicated in CaMKII signaling. PMID:23926118

  2. 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

  3. "Hands-Off" Dissection?

    ERIC Educational Resources Information Center

    Allchin, Douglas

    2005-01-01

    Computer programs and models are used to express respect for life by not sacrificing any animal but these alternatives might be deeply flawed. Alternatives to dissection are perverse alternatives that tend to preserve the features of inappropriate dissections like destructiveness, reductionism and objectification.

  4. Cervicocerebral arterial dissection.

    PubMed

    Jensen, Matt B; Chacon, Marcus R; Aleu, Aitziber

    2008-01-01

    Dissection of the cervicocerebral arteries is an infrequent occurrence but is a leading cause of stroke in young and otherwise healthy patients. A brief review of the history, pathogenesis, and management is presented. The proper management for stroke prevention in dissection is unclear as there have been no randomized, controlled trials performed; small trials are under way. PMID:18195650

  5. Flower Dissection Lab

    NSDL National Science Digital Library

    From Fairchild Tropical Botanic Garden, this site presents a simple Flower Dissection Lab using orchids and composite flowers. This pdf document contains the materials needed and instructions for the lab, as well as a worksheet for students to complete as they dissect their flower.

  6. Phosphoproteome Profiling of the Macrophage Response to Different Toll-Like Receptor Ligands Identifies Differences in Global Phosphorylation Dynamics

    PubMed Central

    2015-01-01

    Toll-like receptors (TLRs) are among the first sensors that detect infection and drive immune response. Macrophages encountering a pathogen are usually stimulated not by one TLR, but by a combination of TLRs engaged by distinct microbe ligands. To understand the integrated signaling under complex conditions, we investigated the differences in the phosphoprotein signaling cascades triggered by TLR2, TLR4, and TLR7 ligands using a single responding cell population. We performed a global, quantitative, early poststimulation kinetic analysis of the mouse macrophage phosphoproteome using stable isotope labeling with amino acids coupled to phosphopeptide enrichment and high-resolution mass spectrometry. For each TLR ligand, we found marked elevation of phosphorylation of cytoskeleton components, GTPases of the Rho family, and phospholipase C signaling pathway proteins. Phosphorylation of proteins involved in phagocytosis was only seen in response to TLR2 and TLR4 but not to TLR7 activation. Changes in the phosphorylation of proteins involved in endocytosis were delayed in response to TLR2 as compared to TLR4 ligands. These findings reveal that the phosphoproteomic response to stimulation of distinct TLRs varies both in the major modification targets and the phosphorylation dynamics. These results advance the understanding of how macrophages sense and respond to a diverse set of TLR stimuli. PMID:24941444

  7. Development of a tandem affinity phosphoproteomic method with motif selectivity and its application in analysis of signal transduction networks.

    PubMed

    Herring, Laura E; Grant, Kyle G; Blackburn, Kevin; Haugh, Jason M; Goshe, Michael B

    2015-04-15

    Phosphorylation is an important post-translational modification that is involved in regulating many signaling pathways. Of particular interest are the growth factor mediated Ras and phosphoinositide 3-kinase (PI3K) signaling pathways which, if misregulated, can contribute to the progression of cancer. Phosphoproteomic methods have been developed to study regulation of signaling pathways; however, due to the low stoichiometry of phosphorylation, understanding these pathways is still a challenge. In this study, we have developed a multi-dimensional method incorporating electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) with tandem IMAC/TiO2 enrichment for subsequent phosphopeptide identification by LC/MS/MS. We applied this method to PDGF-stimulated NIH 3T3 cells to provide over 11,000 unique phosphopeptide identifications. Upon motif analysis, IMAC was found to enrich for basophilic kinase substrates while the subsequent TiO2 step enriched for acidophilic kinase substrates, suggesting that both enrichment methods are necessary to capture the full complement of kinase substrates. Biological functions that were over-represented at each PDGF stimulation time point, together with the phosphorylation dynamics of several phosphopeptides containing known kinase phosphorylation sites, illustrate the feasibility of this approach in quantitative phosphoproteomic studies. PMID:25777480

  8. Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V.

    PubMed

    Achenbach, Ute; Paulo, Joao; Ilarionova, Evgenyia; Lübeck, Jens; Strahwald, Josef; Tacke, Eckhard; Hofferbert, Hans-Reinhard; Gebhardt, Christiane

    2009-02-01

    The damage caused by the parasitic root cyst nematode Globodera pallida is a major yield-limiting factor in potato cultivation . Breeding for resistance is facilitated by the PCR-based marker 'HC', which is diagnostic for an allele conferring high resistance against G. pallida pathotype Pa2/3 that has been introgressed from the wild potato species Solanum vernei into the Solanum tuberosum tetraploid breeding pool. The major quantitative trait locus (QTL) controlling this nematode resistance maps on potato chromosome V in a hot spot for resistance to various pathogens including nematodes and the oomycete Phytophthora infestans. An unstructured sample of 79 tetraploid, highly heterozygous varieties and breeding clones was selected based on presence (41 genotypes) or absence (38 genotypes) of the HC marker. Testing the clones for resistance to G. pallida confirmed the diagnostic power of the HC marker. The 79 individuals were genotyped for 100 single nucleotide polymorphisms (SNPs) at 10 loci distributed over 38 cM on chromosome V. Forty-five SNPs at six loci spanning 2 cM in the interval between markers GP21-GP179 were associated with resistance to G. pallida. Based on linkage disequilibrium (LD) between SNP markers, six LD groups comprising between 2 and 18 SNPs were identified. The LD groups indicated the existence of multiple alleles at a single resistance locus or at several, physically linked resistance loci. LD group C comprising 18 SNPs corresponded to the 'HC' marker. LD group E included 16 SNPs and showed an association peak, which positioned one nematode resistance locus physically close to the R1 gene family. PMID:19020852

  9. Introduction to Dissection

    NSDL National Science Digital Library

    Wineski, Lawrence

    Many health science students do not enroll in undergraduate dissection-based anatomy courses during their pre-professional education. As a result, they are not familiar with dissection instruments and the mechanics of dissection, and are poorly prepared for medical, dental, and allied health science anatomy courses. Thus, the first dissections are very challenging and require extensive help from instructors. This program is designed to alleviate those deficits. It serves as an introduction to dissection in a human gross anatomy course for first-year medical and other health science students. It can be used either as a component of a structured classroom session, or, independently by individual students. The content is presented in a series of video clips arranged in two sections, each containing multiple chapters. Section #1 is a guide to the selection of proper dissection instruments. Section #2 is an overview of how to begin the first dissection in the course, including the use of dissection tools. The program is menu-driven, allowing viewing of the entire content in sequence, or, selected chapters in any order. Student and faculty surveys indicate the program prepares students well for and improves time management during the first dissections. It is available as a web-based download and as a CD-ROM. This work was supported in part by NIH P03 1B040107 and G12-RR 03034. Note: The files must be downloaded, unzipped, extracted, and saved to your local system. Download a stand-alone Flash player from Adobe.com.

  10. Genetic Dissection of Quantitative Trait Loci for Hemostasis and Thrombosis on Mouse Chromosomes 11 and 5 Using Congenic and Subcongenic Strains

    PubMed Central

    Hoover-Plow, Jane; Sa, Qila; Huang, Menggui; Grondolsky, Jessica

    2013-01-01

    Susceptibility to thrombosis varies in human populations as well as many inbred mouse strains. Only a small portion of this variation has been identified, suggesting that there are unknown modifier genes. The objective of this study was to narrow the quantitative trait locus (QTL) intervals previously identified for hemostasis and thrombosis on mouse distal chromosome 11 (Hmtb6) and on chromosome 5 (Hmtb4 and Hmtb5). In a tail bleeding/rebleeding assay, a reporter assay for hemostasis and thrombosis, subcongenic strain (6A-2) had longer clot stability time than did C57BL/6J (B6) mice but a similar time to the B6-Chr11A/J consomic mice, confirming the Hmtb6 phenotype. Six congenic and subcongenic strains were constructed for chromosome 5, and the congenic strain, 2A-1, containing the shortest A/J interval (16.6 cM, 26.6 Mbp) in the Hmtb4 region, had prolonged clot stability time compared to B6 mice. In the 3A-2 and CSS-5 mice bleeding time was shorter than for B6, mice confirming the Hmtb5 QTL. An increase in bleeding time was identified in another congenic strain (3A-1) with A/J interval (24.8 cM, 32.9 Mbp) in the proximal region of chromosome 5, confirming a QTL for bleeding previously mapped to that region and designated as Hmtb10. The subcongenic strain 4A-2 with the A/J fragment in the proximal region had a long occlusion time of the carotid artery after ferric chloride injury and reduced dilation after injury to the abdominal aorta compared to B6 mice, suggesting an additional locus in the proximal region, which was designated Hmtb11 (5 cM, 21.4 Mbp). CSS-17 mice crossed with congenic strains, 3A-1 and 3A-2, modified tail bleeding. Using congenic and subcongenic analysis, candidate genes previously identified and novel genes were identified as modifiers of hemostasis and thrombosis in each of the loci Hmtb6, Hmtb4, Hmtb10, and Hmtb11. PMID:24147020

  11. Neck dissections: radical to conservative

    Microsoft Academic Search

    K Harish; M. S. Ramaiah

    2005-01-01

    BACKGROUND: Neck dissection is an important surgical procedure for the management of metastatic nodal disease in the neck. The gold standard of neck nodal management has been the radical neck dissection. Any modification in the neck dissection is always compared with this standard. Over the last few decades, in order to alleviate the morbidity of radical neck dissection, several modifications

  12. Phosphoproteomic analysis of chromoplasts from sweet orange during fruit ripening.

    PubMed

    Zeng, Yunliu; Pan, Zhiyong; Wang, Lun; Ding, Yuduan; Xu, Qiang; Xiao, Shunyuan; Deng, Xiuxin

    2014-02-01

    Like other types of plastids, chromoplasts have essential biosynthetic and metabolic activities which may be regulated via post-translational modifications, such as phosphorylation, of their resident proteins. We here report a proteome-wide mapping of in vivo phosphorylation sites in chromoplast-enriched samples prepared from sweet orange [Citrus sinensis (L.) Osbeck] at different ripening stages by titanium dioxide-based affinity chromatography for phosphoprotein enrichment with LC-MS/MS. A total of 109 plastid-localized phosphoprotein candidates were identified that correspond to 179 unique phosphorylation sites in 135 phosphopeptides. On the basis of Motif-X analysis, two distinct types of phosphorylation sites, one as proline-directed phosphorylation motif and the other as casein kinase II motif, can be generalized from these identified phosphopeptides. While most identified phosphoproteins show high homology to those already identified in plastids, approximately 22% of them are novel based on BLAST search using the public databases PhosPhAt and P(3) DB. A close comparative analysis showed that approximately 50% of the phosphoproteins identified in citrus chromoplasts find obvious counterparts in the chloroplast phosphoproteome, suggesting a rather high-level of conservation in basic metabolic activities in these two types of plastids. Not surprisingly, the phosphoproteome of citrus chromoplasts is also characterized by the lack of phosphoproteins involved in photosynthesis and by the presence of more phosphoproteins implicated in stress/redox responses. This study presents the first comprehensive phosphoproteomic analysis of chromoplasts and may help to understand how phosphorylation regulates differentiation of citrus chromoplasts during fruit ripening. PMID:23786612

  13. Phosphoproteome Dynamics Upon Changes in Plant Water Status Reveal Early Events Associated With Rapid Growth Adjustment in Maize Leaves*

    PubMed Central

    Bonhomme, Ludovic; Valot, Benoît; Tardieu, François; Zivy, Michel

    2012-01-01

    Plant growth adjustment during water deficit is a crucial adaptive response. The rapid fine-tuned control achieved at the post-translational level is believed to be of considerable importance for regulating early changes in plant growth reprogramming. Aiming at a better understanding of early responses to contrasting plant water statuses, we carried out a survey of the protein phosphorylation events in the growing zone of maize leaves upon a range of water regimes. In this study, the impact of mild and severe water deficits were evaluated in comparison with constant optimal watering and with recovery periods lasting 5, 10, 20, 30, 45, and 60 min. Using four biological replicates per treatment and a robust quantitative phosphoproteomic methodology based on stable-isotope labeling, we identified 3664 unique phosphorylation sites on 2496 proteins. The abundance of nearly 1250 phosphorylated peptides was reproducibly quantified and profiled with high confidence among treatments. A total of 138 phosphopeptides displayed highly significant changes according to water regimes and enabled to identify specific patterns of response to changing plant water statuses. Further quantification of protein amounts emphasized that most phosphorylation changes did not reflect protein abundance variation. During water deficit and recovery, extensive changes in phosphorylation status occurred in critical regulators directly or indirectly involved in plant growth and development. These included proteins influencing epigenetic control, gene expression, cell cycle-dependent processes and phytohormone-mediated responses. Some of the changes depended on stress intensity whereas others depended on rehydration duration, including rapid recoveries that occurred as early as 5 or 10 mins after rewatering. By combining a physiological approach and a quantitative phosphoproteomic analysis, this work provides new insights into the in vivo early phosphorylation events triggered by rapid changes in plant water status, and their possible involvement in plant growth-related processes. PMID:22787273

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

    PubMed

    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

  15. 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

  16. 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

  17. ATM-dependent and -independent dynamics of the nuclear phosphoproteome after DNA damage.

    PubMed

    Bensimon, Ariel; Schmidt, Alexander; Ziv, Yael; Elkon, Ran; Wang, Shih-Ya; Chen, David J; Aebersold, Ruedi; Shiloh, Yosef

    2010-01-01

    The double-strand break (DSB) is a cytotoxic DNA lesion caused by oxygen radicals, ionizing radiation, and radiomimetic chemicals. Cells cope with DNA damage by activating the DNA damage response (DDR), which leads either to damage repair and cellular survival or to programmed cell death. The main transducer of the DSB response is the nuclear protein kinase ataxia telangiectasia mutated (ATM). We applied label-free quantitative mass spectrometry to follow the dynamics of DSB-induced phosphoproteome in nuclear fractions of the human melanoma G361 cells after radiomimetic treatment. We found that these dynamics are complex, including both phosphorylation and dephosphorylation events. In addition to identifying previously unknown ATM-dependent phosphorylation and dephosphorylation events, we found that about 40% of DSB-induced phosphorylations were ATM-independent and that several other kinases are potentially involved. Sustained activity of ATM was required to maintain many ATM-dependent phosphorylations. We identified an ATM-dependent phosphorylation site on ATM itself that played a role in its retention on damaged chromatin. By connecting many of the phosphorylated and dephosphorylated proteins into functional networks, we highlight putative cross talks between proteins pertaining to several cellular biological processes. Our study expands the DDR phosphorylation landscape and identifies previously unknown ATM-dependent and -independent branches. It reveals insights into the breadth and complexity of the cellular responses involved in the coordination of many DDR pathways, which is in line with the critical importance of genomic stability in maintenance of cellular homeostasis. PMID:21139141

  18. Targeted phosphoproteomics of insulin signaling using data-independent acquisition mass spectrometry.

    PubMed

    Parker, Benjamin L; Yang, Guang; Humphrey, Sean J; Chaudhuri, Rima; Ma, Xiuquan; Peterman, Scott; James, David E

    2015-01-01

    A major goal in signaling biology is the establishment of high-throughput quantitative methods for measuring changes in protein phosphorylation of entire signal transduction pathways across many different samples comprising temporal or dose data or patient samples. Data-independent acquisition (DIA) mass spectrometry (MS) methods, which involve tandem MS scans that are collected independently of precursor ion information and then are followed by targeted searching for known peptides, may achieve this goal. We applied DIA-MS to systematically quantify phosphorylation of components in the insulin signaling network in response to insulin as well as in stimulated cells exposed to a panel of kinase inhibitors targeting key downstream effectors in the network. We accurately quantified the effect of insulin on phosphorylation of 86 protein targets in the insulin signaling network using either stable isotope standards (SIS) or label-free quantification (LFQ) and mapped signal transmission through this network. By matching kinases to specific phosphorylation events (based on linear consensus motifs and temporal phosphorylation) to the quantitative phosphoproteomic data from cells exposed to inhibitors, we investigated predicted kinase-substrate relationships of AKT and mTOR in a targeted fashion. Furthermore, we applied this approach to show that AKT2-dependent phosphorylation of GAB2 promoted insulin signaling but inhibited epidermal growth factor (EGF) signaling in a manner dependent on 14-3-3 binding. Because DIA-MS can increase throughput and improve the reproducibility of peptide detection across multiple samples, this approach should facilitate more accurate, comprehensive, and quantitative assessment of signaling networks under various experimental conditions than are possible using other MS proteomic methods. PMID:26060331

  19. Virtual Pig Dissection

    NSDL National Science Digital Library

    Fleck, Earl W.

    Dissection can be an aspect of scientific education that can make some parties queasy, but it is a fascinating way to learn more about the different body systems, their operations, and basic animal anatomy. Entering the world of pig dissection can make budding scientists even more squeamish, but they need never fear, as this site allows these individuals the opportunity to engage in a bit of virtual pig dissection. Originally created by Professor Earl W. Fleck of Whitman Collegeâ??s biology department, the site lets users go inside the pig to learn about its various systems, via a set of high-quality color photographs, which can be viewed at different angles and perspectives. Of course, what would a lab be without a quiz? Rounding out the site, visitors can take short quizzes on the pigâ??s anatomy and such.

  20. Parametric binary dissection

    NASA Technical Reports Server (NTRS)

    Bokhari, Shahid H.; Crockett, Thomas W.; Nicol, David M.

    1993-01-01

    Binary dissection is widely used to partition non-uniform domains over parallel computers. This algorithm does not consider the perimeter, surface area, or aspect ratio of the regions being generated and can yield decompositions that have poor communication to computation ratio. Parametric Binary Dissection (PBD) is a new algorithm in which each cut is chosen to minimize load + lambda x(shape). In a 2 (or 3) dimensional problem, load is the amount of computation to be performed in a subregion and shape could refer to the perimeter (respectively surface) of that subregion. Shape is a measure of communication overhead and the parameter permits us to trade off load imbalance against communication overhead. When A is zero, the algorithm reduces to plain binary dissection. This algorithm can be used to partition graphs embedded in 2 or 3-d. Load is the number of nodes in a subregion, shape the number of edges that leave that subregion, and lambda the ratio of time to communicate over an edge to the time to compute at a node. An algorithm is presented that finds the depth d parametric dissection of an embedded graph with n vertices and e edges in O(max(n log n, de)) time, which is an improvement over the O(dn log n) time of plain binary dissection. Parallel versions of this algorithm are also presented; the best of these requires O((n/p) log(sup 3)p) time on a p processor hypercube, assuming graphs of bounded degree. How PBD is applied to 3-d unstructured meshes and yields partitions that are better than those obtained by plain dissection is described. Its application to the color image quantization problem is also discussed, in which samples in a high-resolution color space are mapped onto a lower resolution space in a way that minimizes the color error.

  1. Endoluminal treatment of aortic dissection

    Microsoft Academic Search

    Ajay Chavan; Joachim Lotz; Frank Oelert; Michael Galanski; Axel Haverich; Matthias Karck

    2003-01-01

    Aortic dissection is most often a catastrophic medical emergency which, if untreated, can be potentially fatal. The intention of therapy in patients with aortic dissection is to prevent aortic rupture or aneurysm formation as well as to relieve branch vessel ischaemia. Patients with aortic dissection are often poor candidates for anaesthesia and surgery and the surgical procedure itself is challenging

  2. Video Gallery: Shark Dissection

    NSDL National Science Digital Library

    This video gallery is from the Museum's Seminars on Science, a series of distance-learning courses designed to help educators meet the new national science standards. There are 16 videos each covering dissection of a different part of the dogfish shark. There is a downloadable pdf for each video.

  3. Proteome and phosphoproteome of Africanized and European honeybee venoms.

    PubMed

    Resende, Virgínia Maria Ferreira; Vasilj, Andrej; Santos, Keity Souza; Palma, Mario Sergio; Shevchenko, Andrej

    2013-09-01

    Honey bee venom toxins trigger immunological, physiological, and neurological responses within victims. The high occurrence of bee attacks involving potentially fatal toxic and allergic reactions in humans and the prospect of developing novel pharmaceuticals make honey bee venom an attractive target for proteomic studies. Using label-free quantification, we compared the proteome and phosphoproteome of the venom of Africanized honeybees with that of two European subspecies, namely Apis mellifera ligustica and A. m. carnica. From the total of 51 proteins, 42 were common to all three subspecies. Remarkably, the toxins melittin and icarapin were phosphorylated. In all venoms, icarapin was phosphorylated at the (205) Ser residue, which is located in close proximity to its known antigenic site. Melittin, the major toxin of honeybee venoms, was phosphorylated in all venoms at the (10) Thr and (18) Ser residues. (18) Ser phosphorylated melittin-the major of its two phosphorylated forms-was less toxic compared to the native peptide. PMID:23798553

  4. The Phosphoproteome of the Minimal Bacterium Mycoplasma pneumoniae

    PubMed Central

    Schmidl, Sebastian R.; Gronau, Katrin; Pietack, Nico; Hecker, Michael; Becher, Dörte; Stülke, Jörg

    2010-01-01

    Mycoplasma pneumoniae belongs to the Mollicutes, the group of organisms with the smallest genomes that are capable of host-independent life. These bacteria show little regulation in gene expression, suggesting an important role for the control of protein activities. We have studied protein phosphorylation in M. pneumoniae to identify phosphorylated proteins. Two-dimensional gel electrophoresis and mass spectrometry allowed the detection of 63 phosphorylated proteins, many of them enzymes of central carbon metabolism and proteins related to host cell adhesion. We identified 16 phosphorylation sites, among them 8 serine and 8 threonine residues, respectively. A phosphoproteome analysis with mutants affected in the two annotated protein kinase genes or in the single known protein phosphatase gene suggested that only one protein (HPr) is phosphorylated by the HPr kinase, HPrK, whereas four adhesion-related or surface proteins were targets of the protein kinase C, PrkC. A comparison with the phosphoproteomes of other bacteria revealed that protein phosphorylation is evolutionarily only poorly conserved. Only one single protein with an identified phosphorylation site, a phosphosugar mutase (ManB in M. pneumoniae), is phosphorylated on a conserved serine residue in all studied organisms from archaea and bacteria to man. We demonstrate that this protein undergoes autophosphorylation. This explains the strong conservation of this phosphorylation event. For most other proteins, even if they are phosphorylated in different species, the actual phosphorylation sites are different. This suggests that protein phosphorylation is a form of adaptation of the bacteria to the specific needs of their particular ecological niche. PMID:20097688

  5. SIMAC (Sequential Elution from IMAC), a Phosphoproteomics Strategy for the Rapid Separation of Monophosphorylated from Multiply Phosphorylated Peptides

    Microsoft Academic Search

    Tine E. Thingholm; Ole N. Jensen; Phillip J. Robinson; Martin R. Larsen

    2007-01-01

    The complete analysis of phosphoproteomes has been hampered by the lack of methods for efficient purification, detection, and characterization of phosphorylated pep- tides from complex biological samples. Despite several strategies for affinity enrichment of phosphorylated pep- tides prior to mass spectrometric analysis, such as im- mobilized metal affinity chromatography or titanium diox- ide, the coverage of the phosphoproteome of a

  6. Neck dissections: radical to conservative

    PubMed Central

    Harish, K

    2005-01-01

    Background Neck dissection is an important surgical procedure for the management of metastatic nodal disease in the neck. The gold standard of neck nodal management has been the radical neck dissection. Any modification in the neck dissection is always compared with this standard. Over the last few decades, in order to alleviate the morbidity of radical neck dissection, several modifications and conservative procedures have been advocated. These procedures retain certain lymphatic or non-lymphatic structures and have been shown not to compromise oncological safety. Methods A literature search of the Medline was carried out for all articles on neck dissections. The articles were systematically reviewed to analyze and trace the evolution of neck dissection. These were then categorized to address the nomenclature, management of node positive and node negative neck including those who had received chemoradiation. Results The present article discusses the neck nodal nomenclature, the radical neck dissection, its modifications and migration to more conservative procedures and possible advances in the near future. Conclusion Radical neck dissection is now replaced with modified radical neck dissections in most situations. Attempts are being made to replace modified radical neck dissections with selective neck dissections for early node positivity. Sentinel node biopsy is being studied to address the issue of node negative neck. More conservative surgeries are likely to replace the 'radical' surgeries of bygone era. This process is facilitated by earlier detection of the disease and better understanding of cancer biology. PMID:15836786

  7. Sheep Brain Dissection

    NSDL National Science Digital Library

    Science NetLinks (The museum of science, art and human perception at the Palace of Fine Arts; )

    2004-04-30

    A sheep brain is used to teach about memory and where it takes place because its brain structure and functions are similar to the human brain. Students will be exposed briefly to the fact that electrochemical connections made between brain cells help us remember the thoughts, skills, experiences, and knowledge that make each of us unique. Through dissections, students will learn about the cortex, brain cells, and where the three main subdivisions of memory (working, long-term, and skill memory) take place.

  8. Shark Dissection Webcast

    NSDL National Science Digital Library

    View this Webcast dissection of four shark species conducted last August at the Birch Aquarium and narrated by Dr. Jeffrey Graham of the Scripps Institution of Oceanography. This is a rare opportunity to learn from a marine biologist as he examines the internal organs of these sharks for the audience. The site also has several short text sections offering life history and behavioral information for those users interested in learning more about sharks in general.

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

    PubMed Central

    Šalovská, Barbora; Fabrik, Ivo; ?urišová, Kamila; Link, Marek; Vávrová, Ji?ina; ?ezá?ová, 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. Radiosensitization of human leukemic HL-60 cells by ATR kinase inhibitor (VE-821): phosphoproteomic analysis.

    PubMed

    Šalovská, Barbora; Fabrik, Ivo; ?urišová, Kamila; Link, Marek; Vávrová, Ji?ina; ?ezá?ová, 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

  11. A Single Kinase Generates the Majority of the Secreted Phosphoproteome.

    PubMed

    Tagliabracci, Vincent S; Wiley, Sandra E; Guo, Xiao; Kinch, Lisa N; Durrant, Eric; Wen, Jianzhong; Xiao, Junyu; Cui, Jixin; Nguyen, Kim B; Engel, James L; Coon, Joshua J; Grishin, Nick; Pinna, Lorenzo A; Pagliarini, David J; Dixon, Jack E

    2015-06-18

    The existence of extracellular phosphoproteins has been acknowledged for over a century. However, research in this area has been undeveloped largely because the kinases that phosphorylate secreted proteins have escaped identification. Fam20C is a kinase that phosphorylates S-x-E/pS motifs on proteins in milk and in the extracellular matrix of bones and teeth. Here, we show that Fam20C generates the majority of the extracellular phosphoproteome. Using CRISPR/Cas9 genome editing, mass spectrometry, and biochemistry, we identify more than 100 secreted phosphoproteins as genuine Fam20C substrates. Further, we show that Fam20C exhibits broader substrate specificity than previously appreciated. Functional annotations of Fam20C substrates suggest roles for the kinase beyond biomineralization, including lipid homeostasis, wound healing, and cell migration and adhesion. Our results establish Fam20C as the major secretory pathway protein kinase and serve as a foundation for new areas of investigation into the role of secreted protein phosphorylation in human biology and disease. PMID:26091039

  12. Application of molecular technologies for phosphoproteomic analysis of clinical samples.

    PubMed

    Pierobon, M; Wulfkuhle, J; Liotta, L; Petricoin, E

    2015-02-12

    The integration of small kinase inhibitors and monoclonal antibodies into oncological practice has opened a new paradigm for treating cancer patients. As proteins are the direct targets of the new generations of targeted therapeutics, many of which are kinase/enzymatic inhibitors, there is an increasing interest in developing technologies capable of monitoring post-translational changes of the human proteome for the identification of new predictive, prognostic and therapeutic biomarkers. It is well known that the vast majority of the activation/deactivation of these drug targets is driven by phosphorylation. This review provides a description of the main proteomic platforms (planar and bead array, reverse phase protein microarray, phosphoflow, AQUA and mass spectrometry) that have successfully been used for measuring changes in phosphorylation level of drug targets and downstream substrates using clinical specimens. Major emphasis was given to the strengths and weaknesses of the different platforms and to the major barriers that are associated with the analysis of the phosphoproteome. Finally, a number of examples of application of the above-mentioned technologies in the clinical setting are reported. PMID:24608425

  13. Dissecting the unspeakable: a fatal case of aortic dissection.

    PubMed

    Dherange, Parinita A; Patel, Sarah; Singh, Nirmal; Suryanarayana, Prakash

    2015-01-01

    A 47-year-old man with diabetes and hypertension presented with sudden onset of chest pain and subsequently developed expressive aphasia. Brain imaging revealed multiple areas of ischaemic infarcts. Transoesophageal echocardiogram revealed aortic dissection with a free-floating thrombus on the dissection flap, which was the source of emboli. Given the poor prognosis, surgical intervention was not pursued and artificial support was withdrawn. Aortic dissection is a highly fatal condition with varied presentation including heart failure, myocardial infarction, neurological deficits, abdominal pain or acute renal failure. Aortic dissection is a relatively uncommon but catastrophic condition. A high degree of clinical suspicion is required for early and accurate diagnosis since mortality is high and increases by the hour. The mechanism for stroke in our case was due to an artery-to-artery embolism from a thrombus, which developed on the intimal surface of the dissected artery. This is an infrequent complication with a very unique mechanism. PMID:26077807

  14. Aortic Dissection Mimicking Subarachnoidal Hemorrhage

    Microsoft Academic Search

    Ulrike Ernemann; Gunnar Tepe; Rainer Ritz; Dorothee Bail

    2005-01-01

    Inthisreportwedescribeacomatosepatientwithprox- imal aortic dissection who presented with the signs of subarachnoidalhemorrhage.Shortlybeforelosingcon- sciousness, the patient complained of an excruciating headache. Upon initial examination, neck stiffness and opisthotonos were present. The cardiovascular exami- nation, chest radiograph, and cerebral computed to- mography were normal. Eight hours later, the aortic dissection was verified by a thoracic computed tomog- raphy. This case shows that aortic

  15. Thoracic aortic aneurysm and dissection.

    PubMed

    Goldfinger, Judith Z; Halperin, Jonathan L; Marin, Michael L; Stewart, Allan S; Eagle, Kim A; Fuster, Valentin

    2014-10-21

    Aortic dissection is the most devastating complication of thoracic aortic disease. In the more than 250 years since thoracic aortic dissection was first described, much has been learned about diseases of the thoracic aorta. In this review, we describe normal thoracic aortic size; risk factors for dissection, including genetic and inflammatory conditions; the underpinnings of genetic diseases associated with aneurysm and dissection, including Marfan syndrome and the role of transforming growth factor beta signaling; data on the role for medical therapies in aneurysmal disease, including beta-blockers, angiotensin receptor blockers, and angiotensin-converting enzyme inhibitors; prophylactic surgery for aneurysm; surgical techniques for the aortic root; and surgical and endovascular management of aneurysm and dissection for different aortic segments. PMID:25323262

  16. Analytical challenges translating mass spectrometry-based phosphoproteomics from discovery to clinical applications

    PubMed Central

    Iliuk, Anton B.; Arrington, Justine V.; Tao, Weiguo Andy

    2014-01-01

    Phosphoproteomics is the systematic study of one of the most common protein modifications in high throughput with the aim of providing detailed information of the control, response, and communication of biological systems in health and disease. Advances in analytical technologies and strategies, in particular the contributions of high-resolution mass spectrometers, efficient enrichments of phosphopeptides, and fast data acquisition and annotation, have catalyzed dramatic expansion of signaling landscapes in multiple systems during the past decade. While phosphoproteomics is an essential inquiry to map high-resolution signaling networks and to find relevant events among the apparently ubiquitous and widespread modifications of proteome, it presents tremendous challenges in separation sciences to translate it from discovery to clinical practice. In this mini-review, we summarize the analytical tools currently utilized for phosphoproteomic analysis (with focus on MS), progresses made on deciphering clinically relevant kinase-substrate networks, MS uses for biomarker discovery and validation, and the potential of phosphoproteomics for disease diagnostics and personalized medicine. PMID:24890697

  17. Analytical challenges translating mass spectrometry-based phosphoproteomics from discovery to clinical applications.

    PubMed

    Iliuk, Anton B; Arrington, Justine V; Tao, Weiguo Andy

    2014-12-01

    Phosphoproteomics is the systematic study of one of the most common protein modifications in high throughput with the aim of providing detailed information of the control, response, and communication of biological systems in health and disease. Advances in analytical technologies and strategies, in particular the contributions of high-resolution mass spectrometers, efficient enrichments of phosphopeptides, and fast data acquisition and annotation, have catalyzed dramatic expansion of signaling landscapes in multiple systems during the past decade. While phosphoproteomics is an essential inquiry to map high-resolution signaling networks and to find relevant events among the apparently ubiquitous and widespread modifications of proteome, it presents tremendous challenges in separation sciences to translate it from discovery to clinical practice. In this mini-review, we summarize the analytical tools currently utilized for phosphoproteomic analysis (with focus on MS), progresses made on deciphering clinically relevant kinase-substrate networks, MS uses for biomarker discovery and validation, and the potential of phosphoproteomics for disease diagnostics and personalized medicine. PMID:24890697

  18. Automatic Dissection Of Plantlets

    NASA Astrophysics Data System (ADS)

    Batchelor, B. G.; Harris, I. P.; Marchant, J. A.; Tillett, R. D.

    1989-03-01

    Micropropagation is a technique used in horticulture for generating a monoclonal colony of plants. A tiny plantlet is cut into several parts, each of which is then replanted. At the moment, the cutting is performed manually. Automating this task would have significant economic benefits. A robot designed to dissect plants would need to be equipped with intelligent visual sensing. This article is concerned with the image acquisition and processing techniques which such a machine might use. A program, which can calculate where to cut a plant with an "open" structure, is presented. This is expressed in the ProVision language, which is described in another article presented at this conference. (Article 1002-65)

  19. 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 packages are employed. PMID:23300999

  20. Aortic dissection mimicking subarachnoidal hemorrhage.

    PubMed

    Nohé, Boris; Ernemann, Ulrike; Tepe, Gunnar; Ritz, Rainer; Bail, Dorothee

    2005-07-01

    In this report we describe a comatose patient with proximal aortic dissection who presented with the signs of subarachnoidal hemorrhage. Shortly before losing consciousness, the patient complained of an excruciating headache. Upon initial examination, neck stiffness and opisthotonos were present. The cardiovascular examination, chest radiograph, and cerebral computed tomography were normal. Eight hours later, the aortic dissection was verified by a thoracic computed tomography. This case shows that aortic dissection, which causes severe pain and possibly transient malperfusion of the carotid arteries, may present with the misleading signs of subarachnoidal hemorrhage but without classical symptoms of aortic syndromes. PMID:15976237

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

    PubMed

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

    2015-06-01

    Inhibitors of oncogenic B-RAF(V600E) and MKK1/2 have yielded remarkable responses in B-RAF(V600E)-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-RAF(V600E) and MKK1/2 inhibitors has been shown to improve both response rates and progression-free survival in B-RAF(V600E) 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-RAF(V600E) 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 MKK1/2 inhibitors in human cell lines, revealing unexpected cell specificity in the molecular responses to pathway activation. PMID:25850435

  2. The rapamycin-sensitive phosphoproteome reveals that TOR controls protein kinase A toward some but not all substrates.

    PubMed

    Soulard, Alexandre; Cremonesi, Alessio; Moes, Suzette; Schütz, Frédéric; Jenö, Paul; Hall, Michael N

    2010-10-01

    Regulation of cell growth requires extensive coordination of several processes including transcription, ribosome biogenesis, translation, nutrient metabolism, and autophagy. In yeast, the protein kinases Target of Rapamycin (TOR) and protein kinase A (PKA) regulate these processes and are thereby the main activators of cell growth in response to nutrients. How TOR, PKA, and their corresponding signaling pathways are coordinated to control the same cellular processes is not understood. Quantitative analysis of the rapamycin-sensitive phosphoproteome combined with targeted analysis of PKA substrates suggests that TOR complex 1 (TORC1) activates PKA but only toward a subset of substrates. Furthermore, we show that TORC1 signaling impinges on BCY1, the negative regulatory subunit of PKA. Inhibition of TORC1 with rapamycin leads to BCY1 phosphorylation on several sites including T129. Phosphorylation of BCY1 T129 results in BCY1 activation and inhibition of PKA. TORC1 inhibits BCY1 T129 phosphorylation by phosphorylating and activating the S6K homolog SCH9 that in turn inhibits the MAP kinase MPK1. MPK1 phosphorylates BCY1 T129 directly. Thus, TORC1 activates PKA toward some substrates by preventing MPK1-mediated activation of BCY1. PMID:20702584

  3. The Rapamycin-sensitive Phosphoproteome Reveals That TOR Controls Protein Kinase A Toward Some But Not All Substrates

    PubMed Central

    Soulard, Alexandre; Cremonesi, Alessio; Moes, Suzette; Schütz, Frédéric; Jenö, Paul

    2010-01-01

    Regulation of cell growth requires extensive coordination of several processes including transcription, ribosome biogenesis, translation, nutrient metabolism, and autophagy. In yeast, the protein kinases Target of Rapamycin (TOR) and protein kinase A (PKA) regulate these processes and are thereby the main activators of cell growth in response to nutrients. How TOR, PKA, and their corresponding signaling pathways are coordinated to control the same cellular processes is not understood. Quantitative analysis of the rapamycin-sensitive phosphoproteome combined with targeted analysis of PKA substrates suggests that TOR complex 1 (TORC1) activates PKA but only toward a subset of substrates. Furthermore, we show that TORC1 signaling impinges on BCY1, the negative regulatory subunit of PKA. Inhibition of TORC1 with rapamycin leads to BCY1 phosphorylation on several sites including T129. Phosphorylation of BCY1 T129 results in BCY1 activation and inhibition of PKA. TORC1 inhibits BCY1 T129 phosphorylation by phosphorylating and activating the S6K homolog SCH9 that in turn inhibits the MAP kinase MPK1. MPK1 phosphorylates BCY1 T129 directly. Thus, TORC1 activates PKA toward some substrates by preventing MPK1-mediated activation of BCY1. PMID:20702584

  4. Phosphoproteomic analysis identifies the tumor suppressor PDCD4 as a RSK substrate negatively regulated by 14-3-3

    PubMed Central

    Galan, Jacob A.; Geraghty, Kathryn M.; Lavoie, Geneviève; Kanshin, Evgeny; Tcherkezian, Joseph; Calabrese, Viviane; Jeschke, Grace R.; Turk, Benjamin E.; Ballif, Bryan A.; Blenis, John; Thibault, Pierre; Roux, Philippe P.

    2014-01-01

    The Ras/MAPK signaling cascade regulates various biological functions, including cell growth and proliferation. As such, this pathway is frequently deregulated in several types of cancer, including most cases of melanoma. RSK (p90 ribosomal S6 kinase) is a MAPK-activated protein kinase required for melanoma growth and proliferation, but relatively little is known about its exact function and the nature of its substrates. Herein, we used a quantitative phosphoproteomics approach to define the signaling networks regulated by RSK in melanoma. To more accurately predict direct phosphorylation substrates, we defined the RSK consensus phosphorylation motif and found significant overlap with the binding consensus of 14-3-3 proteins. We thus characterized the phospho-dependent 14-3-3 interactome in melanoma cells and found that a large proportion of 14-3-3 binding proteins are also potential RSK substrates. Our results show that RSK phosphorylates the tumor suppressor PDCD4 (programmed cell death protein 4) on two serine residues (Ser76 and Ser457) that regulate its subcellular localization and interaction with 14-3-3 proteins. We found that 14-3-3 binding promotes PDCD4 degradation, suggesting an important role for RSK in the inactivation of PDCD4 in melanoma. In addition to this tumor suppressor, our results suggest the involvement of RSK in a vast array of unexplored biological functions with relevance in oncogenesis. PMID:25002506

  5. Decreased expression of fibulin-4 in aortic wall of aortic dissection.

    PubMed

    Huawei, P; Qian, C; Chuan, T; Lei, L; Laing, W; Wenlong, X; Wenzhi, L

    2014-02-01

    In this research, we will examine the expression of Fibulin-4 in aortic wall to find out its role in aortic dissection development. The samples of aortic wall were obtained from 10 patients operated for acute ascending aortic dissection and five patients for chronic ascending aortic dissection. Another 15 pieces of samples from patients who had coronary artery bypass were as controls. The aortic samples were stained with aldehyde magenta dyeing to evaluate the arrangement of elastic fibers. The Fibulin-4 protein and mRNA expression were both determined by Western blot and realtime quantitative polymerase chain reaction. Compared with the control group, both in acute and chronic ascending aortic dissection, elastic fiber fragments increased and the expression of fibulin-4 protein significantly decreased (P= 0.045 < 0.05). The level of fibulin-4 mRNA decreased in acute ascending aortic dissection (P= 0.034 < 0.05), while it increased in chronic ascending aortic dissection (P=0.004 < 0.05). The increased amounts of elastic fiber fragments were negatively correlated with the expression of fibulin-4 mRNA in acute ascending aortic dissection. In conclusion, in aortic wall of ascending aortic dissection, the expression of fibulin-4 protein decreased and the expression of fibulin-4 mRNA was abnormal. Fibulin-4 may play an important role in the pathogenesis of aortic dissection. PMID:23518852

  6. Experience with parametric binary dissection

    NASA Technical Reports Server (NTRS)

    Bokhari, Shahid H.

    1993-01-01

    Parametric Binary Dissection (PBD) is a new algorithm that can be used for partitioning graphs embedded in 2- or 3-dimensional space. It partitions explicitly on the basis of nodes + (lambda)x(edges cut), where lambda is the ratio of time to communicate over an edge to the time to compute at a node. The new algorithm is faster than the original binary dissection algorithm and attempts to obtain better partitions than the older algorithm, which only takes nodes into account. The performance of parametric dissection with plain binary dissection on 3 large unstructured 3-d meshes obtained from computational fluid dynamics and on 2 random graphs were compared. It was showm that the new algorithm can usually yield partitions that are substantially superior, but that its performance is heavily dependent on the input data.

  7. Confident and sensitive phosphoproteomics using combinations of collision induced dissociation and electron transfer dissociation?

    PubMed Central

    Collins, Mark O.; Wright, James C.; Jones, Matthew; Rayner, Julian C.; Choudhary, Jyoti S.

    2014-01-01

    We present a workflow using an ETD-optimised version of Mascot Percolator and a modified version of SLoMo (turbo-SLoMo) for analysis of phosphoproteomic data. We have benchmarked this against several database searching algorithms and phosphorylation site localisation tools and show that it offers highly sensitive and confident phosphopeptide identification and site assignment with PSM-level statistics, enabling rigorous comparison of data acquisition methods. We analysed the Plasmodium falciparum schizont phosphoproteome using for the first time, a data-dependent neutral loss-triggered-ETD (DDNL) strategy and a conventional decision-tree method. At a posterior error probability threshold of 0.01, similar numbers of PSMs were identified using both methods with a 73% overlap in phosphopeptide identifications. The false discovery rate associated with spectral pairs where DDNL CID/ETD identified the same phosphopeptide was < 1%. 72% of phosphorylation site assignments using turbo-SLoMo without any score filtering, were identical and 99.8% of these cases are associated with a false localisation rate of < 5%. We show that DDNL acquisition is a useful approach for phosphoproteomics and results in an increased confidence in phosphopeptide identification without compromising sensitivity or duty cycle. Furthermore, the combination of Mascot Percolator and turbo-SLoMo represents a robust workflow for phosphoproteomic data analysis using CID and ETD fragmentation. Biological significance Protein phosphorylation is a ubiquitous post-translational modification that regulates protein function. Mass spectrometry-based approaches have revolutionised its analysis on a large-scale but phosphorylation sites are often identified by single phosphopeptides and therefore require more rigorous data analysis to unsure that sites are identified with high confidence for follow-up experiments to investigate their biological significance. The coverage and confidence of phosphoproteomic experiments can be enhanced by the use of multiple complementary fragmentation methods. Here we have benchmarked a data analysis pipeline for analysis of phosphoproteomic data generated using CID and ETD fragmentation and used it to demonstrate the utility of a data-dependent neutral loss triggered ETD fragmentation strategy for high confidence phosphopeptide identification and phosphorylation site localisation. PMID:24657495

  8. Searching for Novel Cdk5 Substrates in Brain by Comparative Phosphoproteomics of Wild Type and Cdk5?/? Mice

    PubMed Central

    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

  9. Human Embryonic Stem Cell Phosphoproteome Revealed by Electron Transfer Dissociation Tandem Mass Spectrometry

    Microsoft Academic Search

    Danielle L. Swaney; Craig D. Wenger; James A. Thomson; Joshua J. Coon

    2009-01-01

    Protein phosphorylation is central to the understanding of cellular signaling, and cellular signaling is suggested to play a major role in the regulation of human embryonic stem (ES) cell pluripotency. Here, we describe the use of conventional tandem mass spectrometry-based sequencing technology--collision-activated dissociation (CAD)--and the more recently developed method electron transfer dissociation (ETD) to characterize the human ES cell phosphoproteome.

  10. Phosphoproteome Analysis Links Protein Phosphorylation to Cellular Remodeling and Metabolic Adaptation during Magnaporthe oryzae Appressorium Development.

    PubMed

    Franck, William L; Gokce, Emine; Randall, Shan M; Oh, Yeonyee; Eyre, Alex; Muddiman, David C; Dean, Ralph A

    2015-06-01

    The rice pathogen, Magnaporthe oryzae, undergoes a complex developmental process leading to formation of an appressorium prior to plant infection. In an effort to better understand phosphoregulation during appressorium development, a mass spectrometry based phosphoproteomics study was undertaken. A total of 2924 class I phosphosites were identified from 1514 phosphoproteins from mycelia, conidia, germlings, and appressoria of the wild type and a protein kinase A (PKA) mutant. Phosphoregulation during appressorium development was observed for 448 phosphosites on 320 phosphoproteins. In addition, a set of candidate PKA targets was identified encompassing 253 phosphosites on 227 phosphoproteins. Network analysis incorporating regulation from transcriptomic, proteomic, and phosphoproteomic data revealed new insights into the regulation of the metabolism of conidial storage reserves and phospholipids, autophagy, actin dynamics, and cell wall metabolism during appressorium formation. In particular, protein phosphorylation appears to play a central role in the regulation of autophagic recycling and actin dynamics during appressorium formation. Changes in phosphorylation were observed in multiple components of the cell wall integrity pathway providing evidence that this pathway is highly active during appressorium development. Several transcription factors were phosphoregulated during appressorium formation including the bHLH domain transcription factor MGG_05709. Functional analysis of MGG_05709 provided further evidence for the role of protein phosphorylation in regulation of glycerol metabolism and the metabolic reprogramming characteristic of appressorium formation. The data presented here represent a comprehensive investigation of the M. oryzae phosphoproteome and provide key insights on the role of protein phosphorylation during infection-related development. PMID:25926025

  11. Global Phosphoproteomic Profiling Reveals Distinct Signatures in B-Cell Non-Hodgkin Lymphomas

    PubMed Central

    Rolland, Delphine; Basrur, Venkatesha; Conlon, Kevin; Wolfe, Thomas; Fermin, Damian; Nesvizhskii, Alexey I.; Lim, Megan S.; Elenitoba-Johnson, Kojo S.J.

    2015-01-01

    Deregulation of signaling pathways controlled by protein phosphorylation underlies the pathogenesis of hematological malignancies; however, the extent to which deregulated phosphorylation may be involved in B-cell non-Hodgkin lymphoma (B-NHL) pathogenesis is largely unknown. To identify phosphorylation events important in B-NHLs, we performed mass spectrometry–based, label-free, semiquantitative phosphoproteomic profiling of 11 cell lines derived from three B-NHL categories: Burkitt lymphoma, follicular lymphoma, and mantle-cell lymphoma. In all, 6579 unique phosphopeptides, corresponding to 1701 unique phosphorylated proteins, were identified and quantified. The data are available via ProteomeXchange with identifier PXD000658. Hierarchical clustering highlighted distinct phosphoproteomic signatures associated with each lymphoma subtype. Interestingly, germinal center–derived B-NHL cell lines were characterized by phosphorylation of proteins involved in the B-cell receptor signaling. Of these proteins, phosphoprotein associated with glycosphingolipid-enriched microdomains 1 (PAG1) was identified with the most phosphorylated tyrosine peptides in Burkitt lymphoma and follicular lymphoma. PAG1 knockdown resulted in perturbation of the tyrosine phosphosignature of B-cell receptor signaling components. Significantly, PAG1 knockdown increased cell proliferation and response to antigen stimulation of these germinal center–derived B-NHLs. These data provide a detailed annotation of phosphorylated proteins in human lymphoid cancer. Overall, our study revealed the utility of unbiased phosphoproteome interrogation in characterizing signaling networks that may provide insights into pathogenesis mechanisms in B-cell lymphomas. PMID:24667141

  12. Morphological Variation in Leaf Dissection of Rheum palmatum Complex (Polygonaceae)

    PubMed Central

    Wang, Xu-Mei; Hou, Xiao-Qi; Zhang, Yu-Qu; Li, Yan

    2014-01-01

    Aims Rheum palmatum complex comprises all taxa within section Palmata in the genus Rheum, including R. officinale, R. palmatum, R. tanguticum, R. tanguticum var. liupanshanense and R. laciniatum. The identification of the taxa in section Palmata is based primarily on the degree of leaf blade dissection and the shape of the lobes; however, difficulties in species identification may arise from their significant variation. The aim of this study is to analyze the patterns of variation in leaf blade characteristics within and among populations through population-based sampling covering the entire distribution range of R. palmatum complex. Methods Samples were taken from 2340 leaves from 780 individuals and 44 populations representing the four species, and the degree of leaf blade dissection and the shape of the lobe were measured to yield a set of quantitative data. Furthermore, those data were statistically analyzed. Important Findings The statistical analysis showed that the degree of leaf blade dissection is continuous from lobed to parted, and the shape of the lobe is also continuous from broadly triangular to lanceolate both within and between populations. We suggested that taxa in section Palmata should be considered as one species. Based on the research on the R. palmatum complex, we considered that the quantitative characteristics were greatly influenced by the environment. Therefore, it is not reliable to delimitate the species according to the continuously quantitative vegetative characteristics. PMID:25349989

  13. Quantitative Time-Resolved Phosphoproteomic Analysis of Mast Cell Signaling1

    Microsoft Academic Search

    Lulu Cao; Kebing Yu; Cindy Banh; Vinh Nguyen; Anna Ritz; Benjamin J. Raphael; Yuko Kawakami; Toshiaki Kawakami; Arthur R. Salomon

    Mast cells play a central role in type I hypersensitivity reactions and allergic disorders such as anaphylaxis and asthma. Activation of mast cells, through a cascade of phosphorylation events, leads to the release of mediators of the early phase allergic response. Understanding the molecular architecture underlying mast cell signaling may provide possibilities for therapeutic intervention in asthma and other allergic

  14. Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry

    Microsoft Academic Search

    W Andy Tao; Bernd Wollscheid; Robert O'Brien; Jimmy K Eng; Xiao-jun Li; Bernd Bodenmiller; Julian D Watts; Leroy Hood; Ruedi Aebersold

    2005-01-01

    We present a robust and general method for the identification and relative quantification of phosphorylation sites in complex protein mixtures. It is based on a new chemical derivatization strategy using a dendrimer as a soluble polymer support and tandem mass spectrometry (MS\\/MS). In a single step, phosphorylated peptides are covalently conjugated to a dendrimer in a reaction catalyzed by carbodiimide

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

    Microsoft Academic Search

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

    2009-01-01

    Aberrant signaling causes many diseases, and manipu- lating signaling pathways with kinase inhibitors has emerged as a promising area of drug research. Most kinase inhibitors target the conserved ATP-binding pock- et; 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

  16. Running, ischaemic stroke and carotid artery dissection

    E-print Network

    Evans, N. R.; Harper, V.; Scoffings, D. J.; Warburton, E. A.

    2015-05-13

    demonstrated bilateral dissection of the internal carotid arteries (figure 1). The patient was started on longterm aspirin (75mg daily) and atorvastatin (80mg daily) with advice against participating in activities associated with carotid dissection...

  17. Evaluation of Educator & Student Use of & Attitudes toward Dissection & Dissection Alternatives

    ERIC Educational Resources Information Center

    Osenkowski, Pamela; Green, Che; Tjaden, Anne; Cunniff, Peggy

    2015-01-01

    Animal dissection has been routinely practiced in American biology classrooms for decades. With technological advancements, more states adopting student choice measures, and increased awareness about ethical concerns surrounding dissection, many useful dissection alternatives have been developed. To understand the current use of animal dissection

  18. Animal Rights Activism Threatens Dissection.

    ERIC Educational Resources Information Center

    Holden, Constance

    1990-01-01

    Discussed is the movement against the use of dissections in science laboratories. Examples of protests across the United States are included. Compared is the plight of using animals in a biology classroom and the demise of the teaching of evolution in some areas. (KR)

  19. Expressive Aphasia and Carotid Dissection

    E-print Network

    Simmons, Joshua R; Laselle, Brooks T; Della-Giustina, David A.

    2010-01-01

    Figure 2. Color Doppler ultrasound (CDUS) showing aliasing,Doppler techniques may require specialized training, they are not beyond the scope of emergency ultrasound.ultrasound can identify up to 72% of dissections and an additional 10% can be identified with use of color Doppler,

  20. Phosphoproteomics Profiling of Human Skin Fibroblast Cells Reveals Pathways and Proteins Affected by Low Doses of Ionizing Radiation

    PubMed Central

    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.

    2010-01-01

    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. Principal Findings We have identified 7117 unique phosphopeptides (2566 phosphoproteins) from control and irradiated (2 and 50 cGy) primary human skin fibroblasts 1 h post-exposure. Semi-quantitative label-free analyses were performed to identify phosphopeptides that are apparently altered by radiation exposure. 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. Bioinformatic analyses suggest that low and high doses of radiation affect both overlapping and unique biological processes and suggest a role for 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. Conclusions 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 provide 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 different radiation doses and elucidate the impact of low-dose radiation exposure on human health. PMID:21152398

  1. Spontaneous Dissection of the Superior Mesenteric Artery

    SciTech Connect

    Sheldon, Patrick J. [Department of Radiology, University of California San Diego Medical Center, 200 West Arbor Drive, San Diego, CA 92103 (United States); Esther, James B. [Department of Radiology, Beth Israel Deaconess Medical Center, Harvard Medical School, West Campus, CC308E, One Deaconess Road, Boston, MA 02215 (United States); Sheldon, Elana L. [Department of Medicine, University of California San Diego Medical Center, 200 West Arbor Drive, San Diego, CA 92103 (United States); Sparks, Steven R. [Department of Surgery, University of California San Diego Medical Center, 200 West Arbor Drive, San Diego, CA 92103 (United States); Brophy, David P. [Department of Radiology, Beth Israel Deaconess Medical Center, Harvard Medical School, West Campus, CC308E, One Deaconess Road, Boston, MA 02215 (United States); Oglevie, Steven B. [Department of Radiology, University of California San Diego Medical Center, 200 West Arbor Drive, San Diego, CA 92103 (United States)

    2001-09-15

    Spontaneous dissection of the superior mesenteric artery (SMA) is a rare occurrence, especially when not associated with aortic dissection [1]. Currently, only 28 cases appear to have been reported. Due to the scarcity of cases in the literature, the natural history of isolated, spontaneous SMA dissection is unclear. CT has been reported to be useful for the initial diagnosis of SMA dissection [2-5]. We present two recent cases of spontaneous SMA dissection in which enhanced spiral CT was instrumental in following the disease process and guiding clinical decision making.

  2. Reproducible isolation of distinct, overlapping segments of the phosphoproteome

    Microsoft Academic Search

    Bernd Bodenmiller; Lukas N Mueller; Markus Mueller; Bruno Domon; Ruedi Aebersold

    2007-01-01

    The ability to routinely analyze and quantitatively measure changes in protein phosphorylation on a proteome-wide scale is essential for biological and clinical research. We assessed the ability of three common phosphopeptide isolation methods (phosphoramidate chemistry (PAC), immobilized metal affinity chromatography (IMAC) and titanium dioxide) to reproducibly, specifically and comprehensively isolate phosphopeptides from complex mixtures. Phosphopeptides were isolated from aliquots of

  3. Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome

    Microsoft Academic Search

    Matthias Mann; Shao-En Ong; Mads Grønborg; Hanno Steen; Ole N. Jensen; Akhilesh Pandey

    2002-01-01

    In signal transduction in eukaryotes, protein phosphorylation is a key event. To understand signaling processes, we must first acquire an inventory of phosphoproteins and their phosphorylation sites under different conditions. Because phosphorylation is a dynamic process, elucidation of signaling networks also requires quantitation of these phosphorylation events. In this article, we outline several methods for enrichment of phosphorylated proteins and

  4. A mill based instrument and software system for dissecting slide-mounted tissue that provides digital guidance and documentation

    PubMed Central

    2013-01-01

    Background Dissection of specific Areas Of Interest (AOIs) of slide-mounted tumor samples is often used to enrich for cancer cells in order to generate better signal to noise ratios in subsequent biochemical characterization. Most clinical laboratories utilize manual dissection for practical reasons and to avoid the expense and difficulties of laser microdissection systems. Unfortunately, manual methods often lack resolution and process documentation. The goal of this project was to design a dissection system for slide-mounted tissue with better precision than manual methods that also provides digital image guidance and electronic process documentation. Methods An instrument that is essentially a micro tissue mill was developed. It employs a specialized disposable mill bit that simultaneously dispenses liquid, cuts tissue from the slide surface, and aspirates the liquid along with the displaced tissue fragments. A software package was also developed that is capable of transferring digitally annotated AOIs between images of serially cut tissue sections to guide dissection and generate an electronic record of the process. Results The performance of this “meso” dissection system was tested using post dissection visual examination for resolution and accuracy, fluorescence based DNA quantitation for recovery efficiency, and dissection of closely situated mouse-human tissue sections followed by PCR amplification for purity determination. The minimum resolution is a dissected circle smaller than 200 microns in diameter, edge dissection accuracy is tighter than 100 microns, recovery efficiency appears greater than 95%, and recovery purity is greater than 99% relative to a different tissue located 100 microns from the dissection boundary. The system can dissect from both paraffinized and deparaffinized FFPE tissue sections that are mounted on plain glass slides, and it is compatible with DNA, RNA, and protein isolation. Conclusions The mesodissection system is an effective alternative to manual dissection methods and is applicable for biomarker analysis of anatomical pathology samples, where enrichment of AOIs from the tissue section is helpful, but pure cell populations are not required. PMID:24188417

  5. Phosphoproteomic analysis of Her2\\/neu signaling and inhibition

    Microsoft Academic Search

    R. Bose; Henrik Molina; A. Scott Patterson; John K. Bitok

    2007-01-01

    Full Text ABSTRACT Her2\\/neu (Her2) is a tyrosine kinase belonging to the EGF receptor (EGFR)\\/ErbB family and is overexpressed in 20-30% of human breast cancers. We sought to characterize Her2 signal transduction pathways further by using MS-based quantitative proteomics. Stably transfected cell lines overexpressing Her2 or empty vector were generated, and the effect of an EGFR and Her2 selective tyrosine

  6. Phosphoproteomic analysis of Her2\\/neu signaling and inhibition

    Microsoft Academic Search

    Ron Bose; Henrik Molina; A. Scott Patterson; John K. Bitok; Balamurugan Periaswamy; Joel S. Bader; Akhilesh Pandey; Philip A. Cole

    2006-01-01

    Her2\\/neu (Her2) is a tyrosine kinase belonging to the EGF receptor (EGFR)\\/ErbB family and is overexpressed in 20-30% of human breast cancers. We sought to characterize Her2 signal transduction pathways further by using MS-based quantitative proteomics. Stably transfected cell lines overexpressing Her2 or empty vector were generated, and the effect of an EGFR and Her2 selective tyrosine kinase inhibitor, PD168393,

  7. Enabling Population and Quantitative Genomics

    Microsoft Academic Search

    GREG GIBSON; TRUDY F. C. MACKAY

    2002-01-01

    Summary Dissection of quantitative traits to the nucleotide level requires phenotypic and genotypic analysis of traits on a genome scale. Here we discuss the set of community-wide genetic and molecular resources, including panels of specific types of inbred lines and high density resequencing and SNP detection, that will facilitate such studies. 1. Background

  8. 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

  9. 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

  10. Cardiac Phosphoproteomics during Remote Ischemic Preconditioning: A Role for the Sarcomeric Z-Disk Proteins

    PubMed Central

    Abdul-Ghani, Safa; Heesom, Kate J.; Angelini, Gianni D.; Suleiman, M-Saadeh

    2014-01-01

    Remote ischemic preconditioning (RIPC) induced by brief ischemia/reperfusion cycles of remote organ (e.g., limb) is cardioprotective. The myocardial cellular changes during RIPC responsible for this phenomenon are not currently known. The aim of this work was to identify the activation by phosphorylation of cardiac proteins following RIPC. To achieve our aim we used isobaric tandem mass tagging (TMT) and reverse phase nanoliquid chromatography tandem spectrometry using a Linear Trap Quadropole (LTQ) Orbitrap Velos mass spectrometer. Male C57/Bl6 mice were anesthetized by an intraperitoneal injection of Tribromoethanol. A cuff was placed around the hind limb and inflated at 200?mmHg to prevent blood flow as confirmed by Laser Doppler Flowmetry. RIPC was induced by 4 cycles of 5?min of limb ischemia followed by 5?min of reperfusion. Hearts were extracted for phosphoproteomics. We identified approximately 30 phosphoproteins that were differentially expressed in response to RIPC protocol. The levels of several phosphoproteins in the Z-disk of the sarcomere including phospho-myozenin-2 were significantly higher than control. This study describes and validates a novel approach to monitor the changes in the cardiac phosphoproteome following the cardioprotective intervention of RIPC and prior to index ischemia. The increased level of phosphorylated sarcomeric proteins suggests they may have a role in cardiac signaling during RIPC. PMID:24795895

  11. Cardiac phosphoproteomics during remote ischemic preconditioning: a role for the sarcomeric Z-disk proteins.

    PubMed

    Abdul-Ghani, Safa; Heesom, Kate J; Angelini, Gianni D; Suleiman, M-Saadeh

    2014-01-01

    Remote ischemic preconditioning (RIPC) induced by brief ischemia/reperfusion cycles of remote organ (e.g., limb) is cardioprotective. The myocardial cellular changes during RIPC responsible for this phenomenon are not currently known. The aim of this work was to identify the activation by phosphorylation of cardiac proteins following RIPC. To achieve our aim we used isobaric tandem mass tagging (TMT) and reverse phase nanoliquid chromatography tandem spectrometry using a Linear Trap Quadropole (LTQ) Orbitrap Velos mass spectrometer. Male C57/Bl6 mice were anesthetized by an intraperitoneal injection of Tribromoethanol. A cuff was placed around the hind limb and inflated at 200?mmHg to prevent blood flow as confirmed by Laser Doppler Flowmetry. RIPC was induced by 4 cycles of 5?min of limb ischemia followed by 5?min of reperfusion. Hearts were extracted for phosphoproteomics. We identified approximately 30 phosphoproteins that were differentially expressed in response to RIPC protocol. The levels of several phosphoproteins in the Z-disk of the sarcomere including phospho-myozenin-2 were significantly higher than control. This study describes and validates a novel approach to monitor the changes in the cardiac phosphoproteome following the cardioprotective intervention of RIPC and prior to index ischemia. The increased level of phosphorylated sarcomeric proteins suggests they may have a role in cardiac signaling during RIPC. PMID:24795895

  12. Phosphoproteomic analysis of electroacupuncture analgesia in an inflammatory pain rat model.

    PubMed

    Lee, Si-Hyoung; Kim, Sun-Young; Kim, Ji-Hwan; Jung, Hye-Yun; Moon, Jeong-Hee; Bae, Kwang-Hee; Choi, Byung-Tae

    2012-07-01

    The phosphorylation changes of nociceptive signaling proteins in the spinal cord dorsal horn (SCDH) are important in creating exaggerated pain following peripheral inflammation. Electroacupuncture (EA) has been widely used to relieve acute and chronic inflammatory pain in human and experimental pain models. In the present study, we performed a phosphoproteomic analysis to investigate whether EA alters protein phosphorylation in SCDH to attenuate pain development. Inflammatory hyperalgesia was induced by intraplantar injection of complete Freund's adjuvant (CFA) into the rat hind paw. EA treatment at ST36 and SP6 acupoints alleviated thermal hyperalgesia of the CFA-induced inflammatory pain model rats. The SCDH proteins from the control, inflammatory pain model and EA treatment rats were separated by 2-dimensional gel electrophoresis and the alterations in phosphoproteins were detected by Pro-Q Diamond staining. Eight proteins were differentially phosphorylated following EA treatment in the inflammatory pain model. Aldolase C, nascent polypeptide-associated complex ?, stress-induced phosphoprotein 1 and heat shock protein 90 were identified as phosphoproteins whose expression was increased, whereas GDP dissociation inhibitor 1, thiamine triphosphatase, phosphoglycerate kinase 1 and 14-3-3 ? were phosphoproteins whose expression was decreased. This is the first phosphoproteomic screening study to elucidate the working mechanisms of EA analgesia. The results suggest that the regulation of cellular pathways in which the identified proteins are involved may be associated with an EA analgesic mechanism. PMID:22576741

  13. The global phosphoproteome of Chlamydomonas reinhardtii reveals complex organellar phosphorylation in the flagella and thylakoid membrane.

    PubMed

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

    2014-09-01

    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

  14. Phosphoproteome dynamics in onset and maintenance of oncogene-induced senescence.

    PubMed

    de Graaf, Erik L; Kaplon, Joanna; Zhou, Houjiang; Heck, Albert J R; Peeper, Daniel S; Altelaar, A F Maarten

    2014-08-01

    Expression of the BRAF(V600E) oncoprotein is known to cause benign lesions, such as melanocytic nevi (moles). Despite the oncogenic function of mutant BRAF, these lesions are arrested by a cell-autonomous mechanism called oncogene-induced senescence. Infrequently, nevi can progress to malignant melanoma, through mechanisms that are incompletely understood. To gain more insight into this vital tumor-suppression mechanism, we performed a mass-spectrometry-based screening of the proteome and phosphoproteome in cycling and senescent cells and in cells with abrogated senescence. Proteome analysis of senescent cells revealed the up-regulation of established senescence biomarkers, including specific cytokines, but also several proteins not previously associated with senescence, including extracellular matrix-interacting. Using both general and targeted phosphopeptide enrichment by Ti(4+)-IMAC and phosphotyrosine antibody enrichment, we identified over 15,000 phosphorylation sites. Among the regulated phosphorylation sites we encountered components of the interleukin, BRAF/MAPK, and CDK-retinoblastoma pathways and several other factors. The extensive proteome and phosphoproteome dataset of BRAF(V600E)-expressing senescent cells provides molecular clues as to how oncogene-induced senescence is initiated, maintained, or evaded, serving as a comprehensive proteomic basis for functional validation. PMID:24961811

  15. Meta-Analysis of Arabidopsis thaliana Phospho-Proteomics Data Reveals Compartmentalization of Phosphorylation Motifs.

    PubMed

    van Wijk, Klaas J; Friso, Giulia; Walther, Dirk; Schulze, Waltraud X

    2014-06-01

    Protein (de)phosphorylation plays an important role in plants. To provide a robust foundation for subcellular phosphorylation signaling network analysis and kinase-substrate relationships, we performed a meta-analysis of 27 published and unpublished in-house mass spectrometry-based phospho-proteome data sets for Arabidopsis thaliana covering a range of processes, (non)photosynthetic tissue types, and cell cultures. This resulted in an assembly of 60,366 phospho-peptides matching to 8141 nonredundant proteins. Filtering the data for quality and consistency generated a set of medium and a set of high confidence phospho-proteins and their assigned phospho-sites. The relation between single and multiphosphorylated peptides is discussed. The distribution of p-proteins across cellular functions and subcellular compartments was determined and showed overrepresentation of protein kinases. Extensive differences in frequency of pY were found between individual studies due to proteomics and mass spectrometry workflows. Interestingly, pY was underrepresented in peroxisomes but overrepresented in mitochondria. Using motif-finding algorithms motif-x and MMFPh at high stringency, we identified compartmentalization of phosphorylation motifs likely reflecting localized kinase activity. The filtering of the data assembly improved signal/noise ratio for such motifs. Identified motifs were linked to kinases through (bioinformatic) enrichment analysis. This study also provides insight into the challenges/pitfalls of using large-scale phospho-proteomic data sets to nonexperts. PMID:24894044

  16. Pancreatitis Secondary to Celiac Trunk Dissection

    PubMed Central

    Obando, Jorge V.; Burbridge, Rebecca A.

    2014-01-01

    Dissection of the visceral arteries happens infrequently, with the superior mesenteric artery being the most commonly affected. Isolated dissection of the celiac trunk is rare, and only a few cases have been reported in the medical literature. We report the case of a 51-year-old male who presented with abdominal pain and was subsequently diagnosed with a celiac trunk dissection with secondary pancreatitis and pancreatic infarction. The patient's symptoms improved with conservative medical management. We review the current literature involving celiac trunk dissection and its management, and provide discussion regarding this unrecognized complication of pancreatitis.

  17. Molecular Dissection of Developmental Behavior of Plant Height in Rice (Oryza sativa L.)

    Microsoft Academic Search

    Juqiang Yan; Jun Zhu; Cixin He; Mebrouk Benmoussa; Ping Wu

    A doubled haploid population of 123 lines from IR64\\/Azucena was used to dissect the developmental behavior and genotype by environment interaction for plant height by conditional and unconditional quantitative trait loci (QTL) mapping methods in rice. It was shown that the number of QTL detected was different at various measuring stages. Some QTL could be detected at all stages and

  18. Novel aspects of grapevine response to phytoplasma infection investigated by a proteomic and phospho-proteomic approach with data integration into functional networks

    PubMed Central

    2013-01-01

    Background Translational and post-translational protein modifications play a key role in the response of plants to pathogen infection. Among the latter, phosphorylation is critical in modulating protein structure, localization and interaction with other partners. In this work, we used a multiplex staining approach with 2D gels to study quantitative changes in the proteome and phosphoproteome of Flavescence dorée-affected and recovered ‘Barbera’ grapevines, compared to healthy plants. Results We identified 48 proteins that differentially changed in abundance, phosphorylation, or both in response to Flavescence dorée phytoplasma infection. Most of them did not show any significant difference in recovered plants, which, by contrast, were characterized by changes in abundance, phosphorylation, or both for 17 proteins not detected in infected plants. Some enzymes involved in the antioxidant response that were up-regulated in infected plants, such as isocitrate dehydrogenase and glutathione S-transferase, returned to healthy-state levels in recovered plants. Others belonging to the same functional category were even down-regulated in recovered plants (oxidoreductase GLYR1 and ascorbate peroxidase). Our proteomic approach thus agreed with previously published biochemical and RT-qPCR data which reported down-regulation of scavenging enzymes and accumulation of H2O2 in recovered plants, possibly suggesting a role for this molecule in remission from infection. Fifteen differentially phosphorylated proteins (| ratio |?>?2, p?phosphoproteome changes during pathogen infection in this host. PMID:23327683

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

    PubMed

    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(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 ? were further confirmed by Mn(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. PMID:25448045

  20. Virtual temporal bone dissection: a case study

    Microsoft Academic Search

    Jason Bryan; Don Stredney; Gregory J. Wiet; Dennis Sessanna

    2001-01-01

    The Temporal Bone Dissection Simulator is an ongoing research project for the construction of a synthetic environment suitable for virtual dissection of human temporal bone and related anatomy. Funded by the National Institute on Deafness and Other Communication Disorders (NIDCD), the primary goal of this project is to provide a safe, robust, and cost-effective virtual environment for learning the anatomy

  1. Modeling the propagation of arterial dissection

    Microsoft Academic Search

    T. Christian Gasser; Gerhard A. Holzapfel

    2006-01-01

    Arterial dissections are frequently observed in clinical practice and during road traffic accidents. In particular, the lamellarly arrangement of elastin, collagen, in addition to smooth muscle cells in the middle arterial layer, the media, favors dissection failure. Experimental studies and related biomechanical models are rare in the literature. Finite strain kinematics is employed, and the discontinuity in the displacement field

  2. Keeping Dissection Alive for Medical Students

    ERIC Educational Resources Information Center

    Chambers, James; Emlyn-Jones, Daniel

    2009-01-01

    Traditional dissection teaching is being reduced in a number of medical schools, particularly in the United Kingdom. In response to this, 12 medical students from Warwick University, UK, traveled to the Island of Grenada for an intensive extracurricular dissection course at St. George's University. This course not only benefited the host…

  3. Objecting To Dissection: A College Student's Handbook.

    ERIC Educational Resources Information Center

    National Anti-Vivisection Society, Chicago, IL.

    In a number of states, students from kindergarten through high school have won the right to refuse to dissect or kill animals and the right to substitute an alternative project. This booklet was designed to help college science students take an ethical stand by refusing to participate in dissection exercises. The booklet begins with an overview of…

  4. Neck Dissection Through a Facelift Incision

    PubMed Central

    Melvin, Thuy-Anh N.; Eliades, Steven J.; Ha, Patrick K.; Fakhry, Carole; Saunders, John M.; Califano, Joseph A.; Blanco, Ray G. F.

    2013-01-01

    Obectives/Hypothesis To determine the feasibility and safety of neck dissection through a facelift incision. Study Design Prospective case series. Methods Cadavers and live subjects underwent neck dissection using a facelift incision with and without endoscopic assistance. In the live facelift neck dissection (FLND), the preoperative surgical indications, staging, adjuvant therapy, intraoperative technical procedure, pathology reports on lymph nodes, and short-term outcomes were reviewed. Results FLND was successfully performed in four cadavers and four live subjects, including selective (less than five neck levels removed) and comprehensive (levels I–V removed) neck dissections. All levels were accessible through this approach, with additional retraction required for levels I and IV. Endoscopic assistance was required in one neck dissection for adequate visualization. Short-term complications and number of excised lymph nodes were comparable to those from traditional neck dissection approaches. Conclusions Open neck dissection through a facelift incision is feasible and offers an alternate approach to traditional incisions. This can be performed without requiring robotic assistance and with endoscopic assistance only in certain cases. Endoscopic assistance can offer enhanced visualization of the surgical field and complement open direct approaches in neck dissection. Although FLND offers improved cosmetic outcomes when compared to those of traditional neck incisions, further study is required to determine its efficacy and indications. PMID:23023877

  5. Application of metal-chelate affinity chromatography to the study of the phosphoproteome.

    PubMed

    Imam-Sghiouar, N; Joubert-Caron, R; Caron, M

    2005-02-01

    With the increasing importance of proteome analysis, studying the phosphoproteome is a priority for functional studies. Therefore, a rational approach to simplifying the proteome is needed. In this work, we examined the use of immobilized metal affinity chromatography (IMAC) using ferric ions-chelated column for enriching crude cell extracts in phosphoproteins. The adsorption of the proteins on Fe(3+) was obtained at an acidic pH 5.6, and their elution at a more basic pH in Tris buffer. To evaluate the separation, western blots were performed with either anti-phosphotyrosine or anti-phosphoserine/threonine. The analysis of the eluates demonstrated the selectivity of the separation, particularly for proteins phosphorylated on serine or threonine. In conclusion, the advantages and the limits of this approach are discussed. PMID:15645166

  6. Contribution of phosphoproteomics in understanding SRC signaling in normal and tumor cells.

    PubMed

    Sirvent, Audrey; Urbach, Serge; Roche, Serge

    2015-01-01

    The membrane-anchored, non-receptor tyrosine kinase (non-RTK) SRC is a critical regulator of signal transduction induced by a large variety of cell-surface receptors, including RTKs that bind to growth factors to control cell growth and migration. When deregulated, SRC shows strong oncogenic activity, probably because of its capacity to promote RTK-mediated downstream signaling even in the absence of extracellular stimuli. Accordingly, SRC is frequently deregulated in human cancer and is thought to play important roles during tumorigenesis. However, our knowledge on the molecular mechanism by which SRC controls signaling is incomplete due to the limited number of key substrates identified so far. Here, we review how phosphoproteomic methods have changed our understanding of the mechanisms underlying SRC signaling in normal and tumor cells and discuss how these novel findings can be used to improve therapeutic strategies aimed at targeting SRC signaling in human cancer. PMID:25403792

  7. 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

  8. 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.

  9. Phosphoproteomics as an emerging weapon to develop new antibiotics against carbapenem resistant strain of Acinetobacter baumannii.

    PubMed

    Tiwari, Vishvanath; Tiwari, Monalisa

    2015-01-01

    Acinetobacter baumannii causes pneumonia, bloodstream infections, urinary tract infections, respiratory infections and meningitis. A. baumannii has developed resistance against most of the antibiotics including carbapenem. Therefore, to battle carbapenem resistance, there is a need to develop antimicrobial drugs with new modes of action. Phosphoproteomics will help identify the differentially phosphorylated protein and its crucial phosphosites which facilitate the elucidation of molecular mechanism of signaling and regulation of carbapenem resistant strain of A. baumannii as compared to carbapenem sensitive strain. This understanding might be useful for the development of new antibiotics against kinases involved in the phosphorylation of identified phosphosites in carbapenem resistant strain of A. baumannii. The proposed antibiotics selectively inhibit carbapenem resistant strain which further avoids its excessive use against carbapenem sensitive strain and thereafter reduces emergence of resistance. PMID:25252118

  10. Plasma phosphoproteome and differential plasma phosphoproteins with opisthorchis viverrini-related cholangiocarcinoma.

    PubMed

    Kotawong, Kanawut; Thitapakorn, Veerachai; Roytrakul, Sittiruk; Phaonakrop, Narumon; Viyanant, Vithoon; Na-Bangchang, Kesara

    2015-01-01

    This study was conducted to investigate the plasma phosphoproteome and differential plasma phosphoproteins in cases of of Opisthorchis viverrini (OV)-related cholangiocarcinoma (CCA). Plasma phosphoproteomes from CCA patients (10) and non-CCA subjects (5 each for healthy subjects and OV infection) were investigated using gel-based and solution-based LC-MS/MS. Phosphoproteins in plasma samples were enriched and analyzed by LC-MS/MS. STRAP, PANTHER, iPath, and MeV programs were applied for the identification of their functions, signaling and metabolic pathways; and for the discrimination of potential biomarkers in CCA patients and non-CCA subjects, respectively. A total of 90 and 60 plasma phosphoproteins were identified by gel-based and solution-based LC-MS/MS, respectively. Most of the phosphoproteins were cytosol proteins which play roles in several cellular processes, signaling pathways, and metabolic pathways (STRAP, PANTHER, and iPath analysis). The absence of serine/arginine repetitive matrix protein 3 (A6NNA2), tubulin tyrosine ligase-like family, member 6, and biorientation of chromosomes in cell division protein 1-like (Q8NFC6) in plasma phosphoprotein were identified as potential biomarkers for the differentiation of healthy subjects from patients with CCA and OV infection. To differentiate CCA from OV infection, the absence of both serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform and coiled-coil domain-containing protein 126 precursor (Q96EE4) were then applied. A combination of 5 phosphoproteins may new alternative choices for CCA diagnosis. PMID:25735322

  11. Phosphatase of regenerating liver 3 (PRL3) provokes a tyrosine phosphoproteome to drive prometastatic signal transduction.

    PubMed

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

    2013-12-01

    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(?/?)-, Eph (A2/B3/B4)-, and Integrin (?1/?5)-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

  12. Large-scale phosphoproteomic analysis of membrane proteins in renal proximal and distal tubule

    PubMed Central

    Feric, Marina; Zhao, Boyang; Hoffert, Jason D.; Pisitkun, Trairak

    2011-01-01

    Recent advances in mass spectrometry (MS) have provided means for large-scale phosphoproteomic profiling of specific tissues. Here, we report results from large-scale tandem MS [liquid chromatography (LC)-MS/MS]-based phosphoproteomic profiling of biochemically isolated membranes from the renal cortex, with focus on transporters and regulatory proteins. Data sets were filtered (by target-decoy analysis) to limit false-positive identifications to <2%. A total of 7,125 unique nonphosphorylated and 743 unique phosphorylated peptides were identified. Among the phosphopeptides identified were sites on transporter proteins, i.e., solute carrier (Slc, n = 63), ATP-binding cassette (Abc, n = 4), and aquaporin (Aqp, n = 3) family proteins. Database searches reveal that a majority of the phosphorylation sites identified in transporter proteins were previously unreported. Most of the Slc family proteins are apical or basolateral transporters expressed in proximal tubule cells, including proteins known to mediate transport of glucose, amino acids, organic ions, and inorganic ions. In addition, we identified potentially important phosphorylation sites for transport proteins from distal nephron segments, including the bumetanide-sensitive Na-K-2Cl cotransporter (Slc12a1 or NKCC2) at Ser87, Thr101, and Ser126 and the thiazide-sensitive Na-Cl cotransporter (Slc12a3 or NCC) at Ser71 and Ser124. A subset of phosphorylation sites in regulatory proteins coincided with known functional motifs, suggesting specific regulatory roles. An online database from this study (http://dir.nhlbi.nih.gov/papers/lkem/rcmpd/) provides a resource for future studies of transporter regulation. PMID:21209370

  13. Phosphoproteomic Profiling of Human Myocardial Tissues Distinguishes Ischemic from Non-Ischemic End Stage Heart Failure

    PubMed Central

    Njoroge, Linda W.; Thompson, J. Will; Soderblom, Erik J.; Feger, Bryan J.; Troupes, Constantine D.; Hershberger, Kathleen A.; Ilkayeva, Olga R.; Nagel, Whitney L.; Landinez, Gina P.; Shah, Kishan M.; Burns, Virginia A.; Santacruz, Lucia; Hirschey, Matthew D.; Foster, Matthew W.; Milano, Carmelo A.; Moseley, M. Arthur; Piacentino, Valentino; Bowles, Dawn E.

    2014-01-01

    The molecular differences between ischemic (IF) and non-ischemic (NIF) heart failure are poorly defined. A better understanding of the molecular differences between these two heart failure etiologies may lead to the development of more effective heart failure therapeutics. In this study extensive proteomic and phosphoproteomic profiles of myocardial tissue from patients diagnosed with IF or NIF were assembled and compared. Proteins extracted from left ventricular sections were proteolyzed and phosphopeptides were enriched using titanium dioxide resin. Gel- and label-free nanoscale capillary liquid chromatography coupled to high resolution accuracy mass tandem mass spectrometry allowed for the quantification of 4,436 peptides (corresponding to 450 proteins) and 823 phosphopeptides (corresponding to 400 proteins) from the unenriched and phospho-enriched fractions, respectively. Protein abundance did not distinguish NIF from IF. In contrast, 37 peptides (corresponding to 26 proteins) exhibited a ?2-fold alteration in phosphorylation state (p<0.05) when comparing IF and NIF. The degree of protein phosphorylation at these 37 sites was specifically dependent upon the heart failure etiology examined. Proteins exhibiting phosphorylation alterations were grouped into functional categories: transcriptional activation/RNA processing; cytoskeleton structure/function; molecular chaperones; cell adhesion/signaling; apoptosis; and energetic/metabolism. Phosphoproteomic analysis demonstrated profound post-translational differences in proteins that are involved in multiple cellular processes between different heart failure phenotypes. Understanding the roles these phosphorylation alterations play in the development of NIF and IF has the potential to generate etiology-specific heart failure therapeutics, which could be more effective than current therapeutics in addressing the growing concern of heart failure. PMID:25117565

  14. Direct evidence of phosphorylated neuronal intermediate filament proteins in neurofibrillary tangles (NFTs): phosphoproteomics of Alzheimer's NFTs

    PubMed Central

    Rudrabhatla, Parvathi; Jaffe, Howard; Pant, Harish C.

    2011-01-01

    Alzheimer's disease (AD) is a neurodegenerative disorder characterized by brain pathology of intracellular neurofibrillary tangles (NFTs) and extracellular amyloid plaques. NFTs contain aberrantly hyperphosphorylated Tau as paired helical filaments (PHFs). Although NFs have been shown immunohistologically to be part of NFTs, there has been debate that the identity of NF proteins in NFTs is due to the cross-reactivity of phosphorylated NF antibodies with phospho-Tau. Here, we provide direct evidence on the identity of NFs in NFTs by immunochemical and mass spectrometric analysis. We have purified sarkosyl-insoluble NFTs and performed liquid chromatography/tandem mass spectrometry of NFT tryptic digests. The phosphoproteomics of NFTs clearly identified NF-M phosphopeptides SPVPKS*PVEEAK, corresponding to Ser685, and KAES*PVKEEAVAEVVTITK, corresponding to Ser736, and an NF-H phosphopeptide, EPDDAKAKEPS*KP, corresponding to Ser942. Western blotting of purified tangles with SMI31 showed a 150-kDa band corresponding to phospho-NF-M, while RT97 antibodies detected phospho-NF-H. The proteomics analysis also identified an NF-L peptide (ALYEQEIR, EAEEEKKVEGAGEEQAAAK) and another intermediate filament protein, vimentin (FADLSEAANR). Mass spectrometry revealed Tau phosphopeptides corresponding to Thr231, Ser235, Thr181, Ser184, Ser185, Thr212, Thr217, Ser396, and Ser403. And finally, phosphopeptides corresponding to MAP1B (corresponding to Ser1270, Ser1274, and Ser1779) and MAP2 (corresponding to Thr350, Ser1702, and Ser1706) were identified. In corresponding matched control preparations of PHF/NFTs, none of these phosphorylated neuronal cytoskeletal proteins were found. These studies independently demonstrate that NF proteins are an integral part of NFTs in AD brains.—Rudrabhatla, P., Jaffe, H., Pant, H. C. Direct evidence of phosphorylated neuronal intermediate filament proteins in neurofibrillary tangles (NFTs): phosphoproteomics of Alzheimer's NFTs. PMID:21828286

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

    PubMed

    Wang, Xiaoqin; Qi, Meiyan; Li, Jingyun; Ji, Zhongzhong; Hu, Yong; Bao, Fang; Mahalingam, Ramamurthy; He, Yikun

    2014-05-01

    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

  16. 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

  17. 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

  18. Predicting flow in aortic dissection: comparison of computational model with PC-MRI velocity measurements.

    PubMed

    Cheng, Z; Juli, C; Wood, N B; Gibbs, R G J; Xu, X Y

    2014-09-01

    Aortic dissection is a life-threatening process in which the weakened wall develops a tear, causing separation of wall layers. The dissected layers separate the original true aortic lumen and a newly created false lumen. If untreated, the condition can be fatal. Flow rate in the false lumen is a key feature for false lumen patency, which has been regarded as one of the most important predictors of adverse early and later outcomes. Detailed flow analysis in the dissected aorta may assist vascular surgeons in making treatment decisions, but computational models to simulate flow in aortic dissections often involve several assumptions. The purpose of this study is to assess the computational models adopted in previous studies by comparison with in vivo velocity data obtained by means of phase-contrast magnetic resonance imaging (PC-MRI). Aortic dissection geometry was reconstructed from computed tomography (CT) images, while PC-MRI velocity data were used to define inflow conditions and to provide distal velocity components for comparison with the simulation results. The computational fluid dynamics (CFD) simulation incorporated a laminar-turbulent transition model, which is necessary for adequate flow simulation in aortic conditions. Velocity contours from PC-MRI and CFD in the two lumens at the distal plane were compared at four representative time points in the pulse cycle. The computational model successfully captured the complex regions of flow reversal and recirculation qualitatively, although quantitative differences exist. With a rigid wall assumption and exclusion of arch branches, the CFD model over-predicted the false lumen flow rate by 25% at peak systole. Nevertheless, an overall good agreement was achieved, confirming the physiological relevance and validity of the computational model for type B aortic dissection with a relatively stiff dissection flap. PMID:25070022

  19. A New Idea for Dissecting Tray

    ERIC Educational Resources Information Center

    Branham, Arthur

    1976-01-01

    A method of preparing a special dissecting tray to be used with transmitted light as well as reflected light is presented. It may also be used with an overhead projector to illustrate some skeletal structures in vertebrates. (Author/EB)

  20. GPM Dissects Typhoon Hagupit - Duration: 38 seconds.

    NASA Video Gallery

    NASA/JAXA's GPM Dissects Typhoon Hagupit Animation revealing a swath of NASA/JAXA's Global Precipitation Measurement (GPM) mission's Core Observatory GMI precipitation rates over Typhoon Hagupit. A...

  1. [Cervical, inguinal and abdominal lymphnode dissection].

    PubMed

    Kraus, T W; Suna, K; Berkhoff, S; Jäger, E; Kraus-Tiefenbacher, U

    2013-07-01

    Diagnostic lymph node dissections can be defined as a form of oncological service surgery. These procedures aim at clarification of differential diagnoses of local or systemic lymph node pathologies or contribute to tumor staging. Procedure implementation can either involve incisional biopsy, selective lymph node extirpation or regional systematic lymph node dissection. Sentinel lymph node lymphadenectomy is a focused form of selective lymphadenectomy. Both surgeon and oncologist must have a preoperative consensus and mutual understanding about the detailed purpose of the procedure in the individual patient setting. Terminology conventions must be considered in communication. Potential reasons to extend surgery should be strategically reflected prior to surgery. Interventional techniques and minimally invasive forms of surgical lymph node dissection must be technically taken into account in order to reduce procedural morbidity. Clinically indicative scenarios, pathophysiological concepts and technical options of surgical lymph node dissection are described and discussed for various anatomical regions. PMID:23719728

  2. Neck dissection: current concepts and future directions.

    PubMed

    Rigual, Nestor R; Wiseman, Sam M

    2004-01-01

    For individuals diagnosed with head and neck cancer, neck dissection may be performed for therapy or disease staging. The classification of neck dissection and the definition of precise anatomic landmarks have allowed for this operation, and its many variations, to become standardized world-wide. SLNBX shows promise in its ability to accurately stage NO head and neck cancer and may allow patients with no micro metastatic disease to avoid neck dissection. Before this technique becomes adopted into routine clinical practice, however, it must first be prospectively scrutinized in large patient populations. Regardless of the future role of SLNBX in the management of head and neck cancer, currently it is only through a complete understanding of the clinical, theoretic, and technical aspects of neck dis-section that surgeons may benefit individual patients and the head and neck cancer patient population as a whole. PMID:15062367

  3. Treatment of spontaneous intradural vertebral artery dissections.

    PubMed

    Nakazawa, T; Takeichi, Y; Yokoi, T; Fukami, T; Jito, J; Nitta, N; Takagi, K; Nozaki, K

    2011-10-31

    Spontaneous intradural vertebral artery dissections may cause subarachnoid hemorrhage and often result in devastating damage. Increased use of noninvasive imaging studies has allowed larger numbers of patients to be diagnosed. In addition, intracranial vertebral artery dissection tends to induce multiple lesions affecting both intracranial vertebral arteries recurrently. Although unruptured dissections in this area usually have a benign nature, some authors have reported on the incidence of rupture from this lesion. Once hemorrhage from a dissecting vessel wall has occurred, it needs to be treated in the acute phase because of the high risk of rebleeding resulting in high morbidity and mortality. From December 2004 to July 2010, we managed 47 patients with spontaneous vertebral artery dissection, 31 patients were ruptured and 16 were unruptured. All patients who suffered from subarachnoid hemorrhage were treated with endovascular procedures. Most of the patients with unruptured dissection received medical therapy, but if the aneurysmal dilatation persisted or grew, surgical interventions were performed. Stenting with or without coils was deployed for 13 patients with posterior inferior cerebellar artery involvement at the site of dissection and/or were affected on the dominant side. In some patients, stenting was performed even if they were in the acute phase. For other ruptured patients, internal coil trappings were performed. Six patients died due to severe initial subarachnoid hemorrhage and one patient, who underwent stent deployment with coils for the dominant vertebral artery, with bilateral dissection continuing to the basilar artery died due to rerupture while the next additional coiling was planning. There were two cases of complications related to the intervention. During the follow-up period no bleeding occurred in any of the patients except for the previously mentioned patient. In conclusion, internal coil trapping or stent placement with or without coils was effective in preventing rebleeding of ruptured vertebral artery dissection. If the dissection is unruptured, it is necessary to detect the risk of bleeding with careful watching and when progress appears to be made, patients should be treated promptly. Stent-assisted therapy for preserving the patency of the parent artery and major branches is a promising treatment for vertebral artery dissection, even in the acute stage of subarachnoid hemorrhage. However, the risk of acute rerupture and recurrence remains even with the porous stent placement with or without coils. PMID:24059764

  4. Peripartum presentation of an acute aortic dissection.

    PubMed

    Lewis, S; Ryder, I; Lovell, A T

    2005-04-01

    We report the case of an acute type A aortic dissection occurring in a 35-year-old parturient. The initial diagnosis was missed; a subsequent emergency Caesarean section 3 weeks after presentation was followed by the development of left ventricular failure and pulmonary oedema in the early postoperative period. Echocardiography confirmed the diagnosis of aortic dissection and the patient underwent a successful surgical repair. PMID:15640303

  5. Cancer borealis stomatogastric nervous system dissection.

    PubMed

    Gutierrez, Gabrielle J; Grashow, Rachel G

    2009-01-01

    The stomatogastric ganglion (STG) is an excellent model for studying cellular and network interactions because it contains a relatively small number of cells (approximately 25 in C. borealis) which are well characterized. The cells in the STG exhibit a broad range of outputs and are responsible for the motor actions of the stomach. The stomach contains the gastric mill which breaks down food with three internal teeth, and the pylorus which filters the food before it reaches the midgut. The STG produces two rhythmic outputs to control the gastric mill and pylorus known as central pattern generators (CPGs). Each cell in the STG can participate in one or both of these rhythms. These CPGs allow for the study of neuromodulation, homeostasis, cellular and network variability, network development, and network recovery. The dissection of the stomatogastric nervous system (STNS) from the Jonah crab (Cancer borealis) is done in two parts; the gross and fine dissection. In the gross dissection the entire stomach is dissected from the crab. During the fine dissection the STNS is extracted from the stomach using a dissection microscope and micro-dissection tools (see figure 1). The STNS includes the STG, the oesophageal ganglion (OG), and the commissural ganglia (CoG) as well as the nerves that innervate the stomach muscles. Here, we show how to perform a complete dissection of the STNS in preparation for an electrophysiology experiment where the cells in the STG would be recorded from intracellularly and the peripheral nerves would be used for extracellular recordings. The proper technique for finding the desired nerves is shown as well as our technique of desheathing the ganglion to reveal the somata and neuropil. PMID:19308017

  6. Bilateral spontaneous dissection of extracranial vertebral arteries

    Microsoft Academic Search

    D. Leys; F. Lesoin; J. P. Pruvo; G. Gozet; M. Jomin; H. Petit

    1987-01-01

    A previously healthy 35-year-old man suddenly developed vertebrobasilar ischaemia while playing tennis. Cerebral arteriography revealed a dissecting aneurysm of the cervical portion of both vertebral arteries. The neurological deficit and the angiographic features resolved with anticoagulant treatment alone. Only 15 patients with non-traumatic extracranial vertebral artery dissection have been previously reported. It is necessary to recognize the condition very quickly,

  7. Spontaneous Mirror Dissections of Cervicocephalic Arteries

    PubMed Central

    Zhao, W.Y.; Krings, T.; Alvarez, H.; Ozanne, A.; Holmin, S.; Lasjaunias, P.L.

    2006-01-01

    Summary While so-called twin or mirror aneurysms constitute an established subgroup of multiple aneurysms, simultaneous spontaneous mirror dissections of cervicocephalic artery have not yet been reported as a particular entity. Among the patients treated at our institution since 1989, we identified 74 patients with spontaneous, nontraumatic dissections. Six of these cases presented with simultaneous bilateral dissections and four of the six patients had mirror dissections. Acute or chronic headache was present in all four cases. Additional clinical presentations consisted of impaired consciousness, cranial nerve palsy, and tinnitus. Angiography revealed irregular stenosis, dilatation or aneurysms located in the cervical ICA (internal carotid artery), VA (vertebral artery), or MCA (middle cerebral artery) without evident location bias. Although mirror dissections seems to be an exceptional finding, they may shed light on the vulnerability of different arterial segments to specific diseases. Similar to arterial aneurysm formation, pathogenesis of mirror dissection may involve an underlying "shared defect" in the endothelial cells, since these cells demonstrate a bilateral distribution during embryological development. This particular distribution therefore also provides a chronicle trail of the first trigger striking during embryonic development and demonstrates the segmental vulnerability to highly specific triggers. PMID:20569557

  8. Molecular Dissection of Phage Endolysin

    PubMed Central

    Pohane, Amol Arunrao; Joshi, Himanshu; Jain, Vikas

    2014-01-01

    Mycobacterium tuberculosis has always been recognized as one of the most successful pathogens. Bacteriophages that attack and kill mycobacteria offer an alternate mechanism for the curtailment of this bacterium. Upon infection, mycobacteriophages produce lysins that catalyze cell wall peptidoglycan hydrolysis and mycolic acid layer breakdown of the host resulting in bacterial cell rupture and virus release. The ability to lyse bacterial cells make lysins extremely significant. We report here a detailed molecular dissection of the function and regulation of mycobacteriophage D29 Lysin A. Several truncated versions of Lysin A were constructed, and their activities were analyzed by zymography and by expressing them in both Escherichia coli and Mycobacterium smegmatis. Our experiments establish that Lysin A harbors two catalytically active domains, both of which show E. coli cell lysis upon their expression exclusively in the periplasmic space. However, the expression of only one of these domains and the full-length Lysin A caused M. smegmatis cell lysis. Interestingly, full-length protein remained inactive in E. coli periplasm. Our data suggest that the inactivity is ensued by a C-terminal domain that interacts with the N-terminal domain. This interaction was affirmed by surface plasmon resonance. Our experiments also demonstrate that the C-terminal domain of Lysin A selectively binds to M. tuberculosis and M. smegmatis peptidoglycans. Our methodology of studying E. coli cell lysis by Lysin A and its truncations after expressing these proteins in the bacterial periplasm with the help of signal peptide paves the way for a large scale identification and analysis of such proteins obtained from other bacteriophages. PMID:24627486

  9. Identification of BCAP-{sub L} as a negative regulator of the TLR signaling-induced production of IL-6 and IL-10 in macrophages by tyrosine phosphoproteomics

    SciTech Connect

    Matsumura, Takayuki [Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, Shinjuku-ku, Tokyo 162-0041 (Japan) [Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, Shinjuku-ku, Tokyo 162-0041 (Japan); Department of Life Science and Medical Bio-Science, Waseda University, Shinjuku-ku, Tokyo 162-8480 (Japan); Oyama, Masaaki; Kozuka-Hata, Hiroko [Medical Proteomics Laboratory, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639 (Japan)] [Medical Proteomics Laboratory, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639 (Japan); Ishikawa, Kosuke; Inoue, Takafumi [Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, Shinjuku-ku, Tokyo 162-0041 (Japan) [Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, Shinjuku-ku, Tokyo 162-0041 (Japan); Department of Life Science and Medical Bio-Science, Waseda University, Shinjuku-ku, Tokyo 162-8480 (Japan); Muta, Tatsushi [Laboratory of Cell Recognition and Response, Graduate School of Life Sciences, Tohoku University, Sendai 980-8578 (Japan)] [Laboratory of Cell Recognition and Response, Graduate School of Life Sciences, Tohoku University, Sendai 980-8578 (Japan); Semba, Kentaro, E-mail: ksemba@waseda.jp [Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, Shinjuku-ku, Tokyo 162-0041 (Japan) [Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, Shinjuku-ku, Tokyo 162-0041 (Japan); Department of Life Science and Medical Bio-Science, Waseda University, Shinjuku-ku, Tokyo 162-8480 (Japan); Inoue, Jun-ichiro, E-mail: jun-i@ims.u-tokyo.ac.jp [Medical Proteomics Laboratory, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639 (Japan) [Medical Proteomics Laboratory, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639 (Japan); Division of Cellular and Molecular Biology, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639 (Japan)

    2010-09-17

    Research highlights: {yields} Twenty five tyrosine-phosphorylated proteins in LPS-stimulated macrophages were determined. {yields} BCAP is a novel tyrosine-phosphorylated protein in LPS-stimulated macrophages. {yields} BCAP-{sub L} inhibits IL-6 and IL-10 production in LPS-stimulated macrophages. -- Abstract: Toll-like receptor (TLR) signaling in macrophages is essential for anti-pathogen responses such as cytokine production and antigen presentation. Although numerous reports suggest that protein tyrosine kinases (PTKs) are involved in cytokine induction in response to lipopolysaccharides (LPS; TLR4 ligand) in macrophages, the PTK-mediated signal transduction pathway has yet to be analyzed in detail. Here, we carried out a comprehensive and quantitative dynamic tyrosine phosphoproteomic analysis on the TLR4-mediated host defense system in RAW264.7 macrophages using stable isotope labeling by amino acids in cell culture (SILAC). We determined the temporal profiles of 25 proteins based on SILAC-encoded peptide(s). Of these, we focused on the tyrosine phosphorylation of B-cell adaptor for phosphatidylinositol 3-kinase (BCAP) because the function of BCAP remains unknown in TLR signaling in macrophages. Furthermore, Bcap has two distinct transcripts, a full-length (Bcap-{sub L}) and an alternatively initiated or spliced (Bcap-{sub S}) mRNA, and little is known about the differential functions of the BCAP-{sub L} and BCAP-{sub S} proteins. Our study showed, for the first time, that RNAi-mediated selective depletion of BCAP-{sub L} enhanced IL-6 and IL-10 production but not TNF-{alpha} production in TLR ligand-stimulated macrophages. We propose that BCAP-{sub L} (but not BCAP-{sub S}) is a negative regulator of the TLR-mediated host defense system in macrophages.

  10. Dissection and downstream analysis of zebra finch embryos at early stages of development.

    PubMed

    Murray, Jessica R; Stanciauskas, Monika E; Aralere, Tejas S; Saha, Margaret S

    2014-01-01

    The zebra finch (Taeniopygiaguttata) has become an increasingly important model organism in many areas of research including toxicology, behavior, and memory and learning. As the only songbird with a sequenced genome, the zebra finch has great potential for use in developmental studies; however, the early stages of zebra finch development have not been well studied. Lack of research in zebra finch development can be attributed to the difficulty of dissecting the small egg and embryo. The following dissection method minimizes embryonic tissue damage, which allows for investigation of morphology and gene expression at all stages of embryonic development. This permits both bright field and fluorescence quality imaging of embryos, use in molecular procedures such as in situ hybridization (ISH), cell proliferation assays, and RNA extraction for quantitative assays such as quantitative real-time PCR (qtRT-PCR). This technique allows investigators to study early stages of development that were previously difficult to access. PMID:24999108

  11. Scope on Safety: Dissection--Don't cut out safety

    NSDL National Science Digital Library

    Ken Roy

    2007-02-01

    In June 2005, the NSTA Board of Directors adopted a revised position statement, Responsible Use of Live Animals and Dissection in the Science Classroom. Under the "Dissection" section, NSTA calls for more research to determine the effectiveness of animal dissection activities and alternatives, and the extent to which these activities should be integrated into the science curriculum. Until research indicates the effectiveness of alternatives to dissection, many teachers will continue including dissections in their classrooms. Those that do need to make sure they are addressing related safety issues to ensure a successful learning experience. This month's Scope on Safety features NSTA's safety recommendations for safe and ethical dissection practices.

  12. Dissecting apple tree architecture into genetic, ontogenetic and environmental effects: QTL mapping

    Microsoft Academic Search

    Vincent Segura; Charles-Eric Durel; Evelyne Costes

    2009-01-01

    The present study aimed to dissect tree architectural plasticity into genetic, ontogenetic and environmental effects over\\u000a the first 4 years of growth of an apple F1 progeny by means of quantitative traits loci (QTL) mapping. Both growth and branching\\u000a processes were phenotyped on the consecutive annual shoots of different axes within a tree. For each studied trait, predicted\\u000a values (best linear

  13. Dissection of the aorta in Turner's syndrome.

    PubMed Central

    Price, W H; Wilson, J

    1983-01-01

    Three deaths from dissection of the aorta in a series of 157 adult women with Turner's syndrome are reported. These are greatly in excess of the numbers expected. None of the three patients had a coarctation of the aorta. One had aortic regurgitation but there was no reason to believe that the aorta in the other two patients had been subjected to unusual haemodynamic stresses. Cystic medial necrosis of the aorta was described in two patients on whom necropsies were carried out. It is concluded that there is probably a greatly increased risk of dissection of the aorta in Turner's syndrome even in the absence of any other abnormality of the aorta and aortic valve. Previously reported cases of aortic dissection in Turner's syndrome are discussed. PMID:6842536

  14. Aortic dissection after ingestion of "ecstasy" (MDMA).

    PubMed

    Duflou, J; Mark, A

    2000-09-01

    The authors report a case of aortic dissection and cardiac tamponade in a 29-year-old man after ingestion of ecstasy (methylenedioxymethamphetamine, MDMA) at a "rave" party. There was no history of hypertension, myxoid heart disease, or other risk factors for aortic dissection in the deceased, although a minor degree of cystic medial necrosis was noted on histologic examination of the aorta. Autopsy toxicology revealed low residual levels of MDMA in the blood about 48 hours after ingestion of the drug. This case report describes a probable association between MDMA ingestion and aortic dissection in a previously well young adult. The likely mechanisms are discussed, and the difficulties in diagnosing this complication are highlighted. PMID:10990289

  15. Proteomic and phosphoproteomic profiling during diapause entrance in the flesh fly, Sarcophaga crassipalpis.

    PubMed

    Pavlides, Savvas C; Pavlides, Sheri A; Tammariello, Steven P

    2011-05-01

    Diapause is an alternate developmental pathway that is regulated by the neuroendocrine system in insects. To date, much of the information that has been published regarding the possible molecular events associated with diapause have been at the level of transcription. However, since transcription and translation are not linked in eukaryotic systems, a proteomics approach may represent a better tool to identify the gene products that regulate this period of developmental arrest. In this study, we performed gel-based proteomic and phospho-proteomic analyses to identify proteins that are differentially expressed or differentially phosphorylated in the brain during the initiation of pupal diapause in the flesh fly, Sarcophaga crassipalpis. A total of 27 proteins and phosphoproteins were identified by LC-MS/MS, including 16 that were either upregulated or phosphorylated during diapause, including proteins that function in cellular defense, cell cycle inhibition and neuronal protection. Of equal importance, 11 proteins were identified that were either downregulated at the total protein level, or from nuclear fractions. These included proteins involved in cell proliferation, adult development and aging. These data provide potentially valuable insight into the regulation of insect dormancy as well as the general phenomenon of aging in eukaryotic systems. PMID:21501620

  16. Defining the phospho-adhesome through the phosphoproteomic analysis of integrin signalling

    PubMed Central

    Robertson, Joseph; Jacquemet, Guillaume; Byron, Adam; Jones, Matthew C.; Warwood, Stacey; Selley, Julian N.; Knight, David; Humphries, Jonathan D.; Humphries, Martin J.

    2015-01-01

    Cell–extracellular matrix (ECM) adhesion is a fundamental requirement for multicellular existence due to roles in positioning, proliferation and differentiation. Phosphorylation plays a major role in adhesion signalling; however, a full understanding of the phosphorylation events that occur at sites of adhesion is lacking. Here we report a proteomic and phosphoproteomic analysis of adhesion complexes isolated from cells spread on fibronectin. We identify 1,174 proteins, 499 of which are phosphorylated (1,109 phosphorylation sites), including both well-characterized and novel adhesion-regulated phosphorylation events. Immunoblotting suggests that two classes of phosphorylated residues are found at adhesion sites—those induced by adhesion and those constitutively phosphorylated but recruited in response to adhesion. Kinase prediction analysis identifies novel kinases with putative roles in adhesion signalling including CDK1, inhibition of which reduces adhesion complex formation. This phospho-adhesome data set constitutes a valuable resource to improve our understanding of the signalling mechanisms through which cell–ECM interactions control cell behaviour. PMID:25677187

  17. 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.

  18. 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

  19. Gel-based comparative phosphoproteomic analysis on rice embryo during germination.

    PubMed

    Han, Chao; Wang, Kun; Yang, Pingfang

    2014-08-01

    Seed germination is a well regulated process, which incorporates many events including signal transduction, mobilization of reserves, reactive oxygen species scavenging and cell division. Although many transcriptomic and proteomic studies have been conducted on this process, regulation of protein modification has not been studied. To better understand the mechanism, a gel-based comparative phosphoproteomic study was performed on rice embryo during the germination process. In total, 168 protein spots exhibited significantly changed Pro-Q staining intensity during germination. Using matrix-assisted laser deionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF MS) analysis, 193 proteins were identified. By combining Pro-Q and Coomassie brilliant blue stain intensity analyses, 109 proteins were verified to be phosphorylation regulation proteins. Functional analyses indicated that phosphorylation of proteins involved in stress response and storage was gradually enhanced. Phosphorylation of signal transduction proteins was mainly activated during the early stage of germination, while stress response and storage protein phosphorylation were enhanced at the late stage. Enzyme assays proved that the phosphorylation of fructokinase, pyruvate kinase, malate dehydrogenase, GDP-mannose 3,5-epimerase1, ascorbate peroxidase and glutathione S-transferase could consistently enhance their activity. This study showed the dynamic changes of protein phosphorylation status in rice embryo during germination and provided new insight into understanding the mechanism underlying this process. PMID:24793751

  20. Phosphoproteomic analysis of the resistant and susceptible genotypes of maize infected with sugarcane mosaic virus.

    PubMed

    Wu, Liuji; Wang, Shunxi; Wu, Jianyu; Han, Zanping; Wang, Rui; Wu, Liancheng; Zhang, Huimin; Chen, Yanhui; Hu, Xiuli

    2015-03-01

    Protein phosphorylation plays a pivotal role in the regulation of many cellular events. No information is yet available, however, on protein phosphorylation in plants in response to virus infection. In this study, we characterized phosphoproteomes of resistant and susceptible genotypes of maize (Zea mays L.) in response to Sugarcane mosaic virus (SCMV) infection. Based on isotope tags for relative and absolute quantification technology, TiO2 enrichment method and LC-MS/MS analysis, we identified 65 and 59 phosphoproteins respectively, whose phosphorylation level regulated significantly in susceptible and resistant plants. Some identified phosphoproteins were shared by both genotypes, suggesting a partial overlapping of the responsive pathways to virus infection. While several phosphoproteins are well-known pathogen response phosphoproteins, virus infection differentially regulates most other phosphoproteins, which has not been reported in literature. Changes in protein phosphorylation status indicated that response to SCMV infection encompass a reformatting of major cellular processes. Our data provide new valuable insights into plant-virus interactions. PMID:25488425

  1. Defining the phospho-adhesome through the phosphoproteomic analysis of integrin signalling.

    PubMed

    Robertson, Joseph; Jacquemet, Guillaume; Byron, Adam; Jones, Matthew C; Warwood, Stacey; Selley, Julian N; Knight, David; Humphries, Jonathan D; Humphries, Martin J

    2015-01-01

    Cell-extracellular matrix (ECM) adhesion is a fundamental requirement for multicellular existence due to roles in positioning, proliferation and differentiation. Phosphorylation plays a major role in adhesion signalling; however, a full understanding of the phosphorylation events that occur at sites of adhesion is lacking. Here we report a proteomic and phosphoproteomic analysis of adhesion complexes isolated from cells spread on fibronectin. We identify 1,174 proteins, 499 of which are phosphorylated (1,109 phosphorylation sites), including both well-characterized and novel adhesion-regulated phosphorylation events. Immunoblotting suggests that two classes of phosphorylated residues are found at adhesion sites-those induced by adhesion and those constitutively phosphorylated but recruited in response to adhesion. Kinase prediction analysis identifies novel kinases with putative roles in adhesion signalling including CDK1, inhibition of which reduces adhesion complex formation. This phospho-adhesome data set constitutes a valuable resource to improve our understanding of the signalling mechanisms through which cell-ECM interactions control cell behaviour. PMID:25677187

  2. 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

  3. Phosphoproteome characterization reveals that Sendai virus infection activates mTOR signaling in human epithelial cells.

    PubMed

    Öhman, Tiina; Söderholm, Sandra; Paidikondala, Maruthibabu; Lietzén, Niina; Matikainen, Sampsa; Nyman, Tuula A

    2015-06-01

    Sendai virus (SeV) is a common respiratory pathogen in mice, rats, and hamsters. Host cell recognition of SeV is mediated by pathogen recognition receptors, which recognize viral components and induce intracellular signal transduction pathways that activate the antiviral innate immune response. Viruses use host proteins to control the activities of signaling proteins and their downstream targets, and one of the most important host protein modifications regulated by viral infection is phosphorylation. In this study, we used phosphoproteomics combined with bioinformatics to get a global view of the signaling pathways activated during SeV infection in human lung epithelial cells. We identified altogether 1347 phosphoproteins, and our data shows that SeV infection induces major changes in protein phosphorylation affecting the phosphorylation of almost one thousand host proteins. Bioinformatics analysis showed that SeV infection activates known pathways including MAPK signaling, as well as signaling pathways previously not linked to SeV infection including Rho family of GTPases, HIPPO signaling, and mammalian target of rapamycin (mTOR)-signaling pathway. Further, we performed functional studies with mTOR inhibitors and siRNA approach, which revealed that mTOR signaling is needed for both the host IFN response as well as viral protein synthesis in SeV-infected human lung epithelial cells. PMID:25764225

  4. Phosphoproteomics screen reveals Akt isoform-specific signals linking RNA processing to lung cancer

    PubMed Central

    Sanidas, Ioannis; Polytarchou, Christos; Hatziapostolou, Maria; Ezell, Scott A.; Kottakis, Filippos; Hu, Lan; Guo, Ailan; Xie, Jianxin; Comb, Michael J.; Iliopoulos, Dimitrios; Tsichlis, Philip N.

    2014-01-01

    The three Akt isoforms are functionally distinct. Here we show that their phosphoproteomes also differ, suggesting that their functional differences are due to differences in target specificity. One of the top cellular functions differentially-regulated by Akt isoforms is RNA processing. IWS1, an RNA processing regulator, is phosphorylated by Akt3 and Akt1 at Ser720/Thr721. The latter is required for the recruitment of SETD2 to the RNA Pol II complex. SETD2 trimethylates histone H3 at K36 during transcription, creating a docking site for MRG15 and PTB. H3K36me3-bound MRG15 and PTB regulate FGFR-2 splicing, which controls tumor growth and invasiveness downstream of IWS1 phosphorylation. 21/24 non-small-cell-lung carcinomas we analyzed, express IWS1. More important, the stoichiometry of IWS1 phosphorylation in these tumors correlates with the FGFR-2 splicing pattern, and with Akt phosphorylation and Akt3 expression. These data identify a novel Akt isoform-dependent regulatory mechanism for RNA processing and demonstrate its role in lung cancer. PMID:24462114

  5. Probing the phosphoproteome of HeLa cells using nanocast metal oxide microspheres for phosphopeptide enrichment.

    PubMed

    Leitner, Alexander; Sturm, Martin; Hudecz, Otto; Mazanek, Michael; Smått, Jan-Henrik; Lindén, Mika; Lindner, Wolfgang; Mechtler, Karl

    2010-04-01

    Metal oxide affinity chromatography (MOAC) has become a prominent method to enrich phosphopeptides prior to their analysis by liquid chromatography-mass spectrometry. To overcome limitations in material design, we have previously reported the use of nanocasting as a means to generate metal oxide spheres with tailored properties. Here, we report on the application of two oxides, tin dioxide (stannia) and titanium dioxide (titania), for the analysis of the HeLa phosphoproteome. In combination with nanoflow LC-MS/MS analysis on a linear ion trap-Fourier transform ion cyclotron resonance instrument, we identified 619 phosphopeptides using the new stannia material, and 896 phosphopeptides using titania prepared in house. We also compared the newly developed materials to commercial titania material using an established enrichment protocol. Both titania materials yielded a comparable total number of phosphopeptides, but the overlap of the two data sets was less than one-third. Although fewer peptides were identified using stannia, the complementarity of SnO(2)-based MOAC could be shown as more than 140 phosphopeptides were exclusively identified by this material. PMID:20201521

  6. Phosphoproteomics and Bioinformatics Analyses of Spinal Cord Proteins in Rats with Morphine Tolerance

    PubMed Central

    Liaw, Wen-Jinn; Tsao, Cheng-Ming; Huang, Go-Shine; Wu, Chin-Chen; Ho, Shung-Tai; Wang, Jhi-Joung; Tao, Yuan-Xiang; Shui, Hao-Ai

    2014-01-01

    Introduction Morphine is the most effective pain-relieving drug, but it can cause unwanted side effects. Direct neuraxial administration of morphine to spinal cord not only can provide effective, reliable pain relief but also can prevent the development of supraspinal side effects. However, repeated neuraxial administration of morphine may still lead to morphine tolerance. Methods To better understand the mechanism that causes morphine tolerance, we induced tolerance in rats at the spinal cord level by giving them twice-daily injections of morphine (20 µg/10 µL) for 4 days. We confirmed tolerance by measuring paw withdrawal latencies and maximal possible analgesic effect of morphine on day 5. We then carried out phosphoproteomic analysis to investigate the global phosphorylation of spinal proteins associated with morphine tolerance. Finally, pull-down assays were used to identify phosphorylated types and sites of 14-3-3 proteins, and bioinformatics was applied to predict biological networks impacted by the morphine-regulated proteins. Results Our proteomics data showed that repeated morphine treatment altered phosphorylation of 10 proteins in the spinal cord. Pull-down assays identified 2 serine/threonine phosphorylated sites in 14-3-3 proteins. Bioinformatics further revealed that morphine impacted on cytoskeletal reorganization, neuroplasticity, protein folding and modulation, signal transduction and biomolecular metabolism. Conclusions Repeated morphine administration may affect multiple biological networks by altering protein phosphorylation. These data may provide insight into the mechanism that underlies the development of morphine tolerance. PMID:24392096

  7. Phosphoproteomic analysis of kinase-deficient mice reveals multiple TAK1 targets in osteoclast differentiation.

    PubMed

    Sumiya, Eriko; Negishi-Koga, Takako; Nagai, Yusuke; Suematsu, Ayako; Suda, Tomomi; Shinohara, Masahiro; Sato, Kojiro; Sanjo, Hideki; Akira, Shizuo; Takayanagi, Hiroshi

    2015-08-01

    TAK1 (encoded by Map3k7) is a mitogen-activated protein kinase kinase kinase (MAP3K), which activates the transcription factors AP-1 and NF-?B in response to receptor activator of NF-?B ligand (RANKL) stimulation, thus constituting a key regulator of osteoclast differentiation. Here we report the functional relevance of the kinase activity of TAK1 in the late stage of osteoclast differentiation in vivo using Ctsk-Cre mice and TAK1 mutant mice in which the TAK1 kinase domain was flanked by loxP. The Map3k7(flox/kd)Ctsk(Cre/+) mice displayed a severe osteopetrotic phenotype due to a marked decrease in osteoclast number. RANKL-induced activation of MAPK and NF-?B was impaired in the late stage of osteoclast differentiation. The absence of suppressive effect of an administered NF-?B inhibitor on the late stage of osteoclastogenesis led us to investigate unknown TAK1 targets in osteoclast differentiation. We performed a phosphoproteomic analysis of RANKL-stimulated osteoclast precursor cells from Map3k7(flox/kd)Ctsk(Cre/+) mice, revealing multiple targets regulated by TAK1 during osteoclastogenesis. Thus, TAK1 functions as a critical regulator of the phosophorylation status of various cellular proteins that govern osteoclastogenesis. PMID:26102028

  8. The phosphoproteome of Arabidopsis plants lacking the oxidative signal-inducible1 (OXI1) protein kinase.

    PubMed

    Howden, Andrew J M; Salek, Mogjiborahman; Miguet, Laurent; Pullen, Margaret; Thomas, Benjamin; Knight, Marc R; Sweetlove, Lee J

    2011-04-01

    The AGC protein kinase OXI1 is a key protein in plant responses to oxidative signals, and is important for two oxidative burst-mediated processes: basal resistance to microbial pathogens and root hair growth. To identify possible components of the OXI1 signalling pathway, phosphoproteomic techniques were used to detect alterations in the abundance of phosphorylated proteins and peptides in an oxi1 null mutant of Arabidopsis thaliana. The relative abundance of phosphorylated proteins was assessed either using two-dimensional gel electrophoresis and staining with the phosphoprotein stain Pro-Q Diamond or by the identification and quantification, by mass spectrometry, of stable-isotope labelled phosphopeptides. A number of proteins show altered phosphorylation in the oxi1 mutant. Five proteins, including a putative F-box and 3-phosphoinositide-dependent kinase 1, show reduced phosphorylation in the oxi1 mutant, and may be direct or indirect targets of OXI1. Four proteins, including ethylene insensitive 2 and phospholipase d-gamma, show increased phosphorylation in the oxi1 mutant. This study has identified a range of candidate proteins from the OXI1 signalling pathway. The diverse activities of these proteins, including protein degradation and hormone signalling, may suggest crosstalk between OXI1 and other signal transduction cascades. PMID:21175636

  9. Phosphoproteomic Analysis of Gossypol-Induced Apoptosis in Ovarian Cancer Cell Line, HOC1a

    PubMed Central

    Jin, Lixu; Chen, Yuling; Mu, Xinlin; Lian, Qingquan; Deng, Haiyun; Ge, Renshan

    2014-01-01

    Ovarian cancer is a major cause for death of gynecological cancer patients. The efficacy of traditional surgery and chemotherapy is rather compromised and platinum-resistant cancer recurs. Finding new therapeutic targets is urgently needed to increase the survival rate and to improve life quality of patients with ovarian cancer. In the present work, phosphoproteomic analysis was carried out on untreated and gossypol-treated ovarian cancer cell line, HOC1a. We identified approximately 9750 phosphopeptides from 3030 phosphoproteins, which are involved in diverse cellular processes including cytoskeletal organization, RNA and nucleotide binding, and cell cycle regulation. Upon gossypol treatment, changes in phosphorylation of twenty-nine proteins including YAP1 and AKAP12 were characterized. Western blotting and qPCR analysis were used to determine expression levels of proteins in YAP1-related Hippo pathway showing that gossypol induced upregulation of LATS1, which phosphorylates YAP1 at Ser 61. Furthermore, our data showed that gossypol targets the actin cytoskeletal organization through mediating phosphorylation states of actin-binding proteins. Taken together, our data provide valuable information to understand effects of gossypol on protein phosphorylation and apoptosis of ovarian cancer cells. PMID:25180175

  10. The nature of dissection: Exploring student conceptions

    NASA Astrophysics Data System (ADS)

    York, Katharine

    The model of conceptual change in science describes the process of learning as a complete restructuring of knowledge, when learners discover or are shown more plausible, intelligent alternatives to existing conceptions. Emotions have been acknowledged as part of a learner's conceptual ecology, but the effects of emotions on learning have yet to be described. This research was conducted to examine the role that emotions have on learning for thirteen high school students, as they dissected cats in a Human Anatomy and Physiology class. The project also investigated whether a student's emotional reactions may be used to develop a sense of connectedness with the nonhuman world, which is defined as ecological literacy. This study utilized a grounded theory approach, in which student responses to interviews were the primary source of data. Interviews were transcribed, and responses were coded according to a constant comparative method of analysis. Responses were compared with the four conditions necessary for conceptual change to occur, and also to five principles of ecological literacy. Students who had negative reactions to dissection participated less in the activity, and demonstrated less conceptual change. Two female students showed the strongest emotional reactions to dissection, and also the lowest amount of conceptual change. One male student also had strong negative reactions to death, and showed no conceptual change. The dissection experiences of the students in this study did not generally reflect ecological principles. The two students whose emotional reactions to dissection were the most negative demonstrated the highest degree of ecological literacy. These results provide empirical evidence of the effects that emotions have on learning, and also supports the opinions of educators who do not favor dissection, because it does not teach students to respect all forms of life.

  11. Phosphoproteome Analysis of Functional Mitochondria Isolated from Resting Human Muscle Reveals Extensive Phosphorylation of Inner Membrane Protein Complexes and Enzymes*

    PubMed Central

    Zhao, Xiaolu; León, Ileana R.; Bak, Steffen; Mogensen, Martin; Wrzesinski, Krzysztof; Højlund, Kurt; Jensen, Ole Nørregaard

    2011-01-01

    Mitochondria play a central role in energy metabolism and cellular survival, and consequently mitochondrial dysfunction is associated with a number of human pathologies. Reversible protein phosphorylation emerges as a central mechanism in the regulation of several mitochondrial processes. In skeletal muscle, mitochondrial dysfunction is linked to insulin resistance in humans with obesity and type 2 diabetes. We performed a phosphoproteomics study of functional mitochondria isolated from human muscle biopsies with the aim to obtain a comprehensive overview of mitochondrial phosphoproteins. Combining an efficient mitochondrial isolation protocol with several different phosphopeptide enrichment techniques and LC-MS/MS, we identified 155 distinct phosphorylation sites in 77 mitochondrial phosphoproteins, including 116 phosphoserine, 23 phosphothreonine, and 16 phosphotyrosine residues. The relatively high number of phosphotyrosine residues suggests an important role for tyrosine phosphorylation in mitochondrial signaling. Many of the mitochondrial phosphoproteins are involved in oxidative phosphorylation, tricarboxylic acid cycle, and lipid metabolism, i.e. processes proposed to be involved in insulin resistance. We also assigned phosphorylation sites in mitochondrial proteins involved in amino acid degradation, importers and transporters, calcium homeostasis, and apoptosis. Bioinformatics analysis of kinase motifs revealed that many of these mitochondrial phosphoproteins are substrates for protein kinase A, protein kinase C, casein kinase II, and DNA-dependent protein kinase. Our results demonstrate the feasibility of performing phosphoproteome analysis of organelles isolated from human tissue and provide novel targets for functional studies of reversible phosphorylation in mitochondria. Future comparative phosphoproteome analysis of mitochondria from healthy and diseased individuals will provide insights into the role of abnormal phosphorylation in pathologies, such as type 2 diabetes. PMID:20833797

  12. Phosphoproteomic analysis reveals site-specific changes in GFAP and NDRG2 phosphorylation in frontotemporal lobar degeneration

    PubMed Central

    Herskowitz, Jeremy H.; Seyfried, Nicholas T.; Duong, Duc M.; Xia, Qiangwei; Rees, Howard D.; Gearing, Marla; Peng, Junmin; Lah, James J.; Levey, Allan I.

    2010-01-01

    Frontotemporal lobar degeneration (FTLD) is a progressive neurodegenerative disease characterized by behavioral abnormalities, personality changes, language dysfunction, and can co-occur with the development of motor neuron disease. One major pathological form of FTLD is characterized by intracellular deposition of ubiquitinated and phosphorylated TAR DNA binding protein-43 (TDP-43), suggesting that dysregulation in phosphorylation events may contribute to disease progression. However, to date systematic analysis of the phosphoproteome in FTLD brains has not been reported. In this study we employed immobilized metal affinity chromatography (IMAC) followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify phosphopeptides from FTLD and age-matched control postmortem human brain tissue. Using this approach we identified 786 phosphopeptides in frontal cortex (control and FTLD), in which the population of phosphopeptides represented approximately 50% of the total peptides analyzed. Label free quantification using spectral counts revealed six proteins with significant changes in the FTLD phosphoproteome. N-myc-downstream regulated gene 2 (NDRG2) and glial fibrillary acidic protein (GFAP) had an increased number of phosphospectra in FTLD, whereas microtubule associated protein 1A (MAP1A), reticulon 4 (RTN4; also referred to as neurite outgrowth inhibitor (Nogo)), protein kinase C gamma (PRKCG), and heat shock protein 90kDa alpha, class A member 1(HSP90AA1) had significantly fewer phosphospectra compared to control brain. To validate these differences, we examined NDRG2 phosphorylation in FTLD brain by immunoblot analyses, and using a phosphoserine-13 (pSer13) GFAP monoclonal antibody we show an increase in pSer13 GFAP levels by immunoblot concomitant with increased overall GFAP levels in FTLD cases. These data highlight the utility of combining proteomic and phosphoproteomic strategies to characterize postmortem human brain tissue. PMID:20886841

  13. iPhos: a toolkit to streamline the alkaline phosphatase-assisted comprehensive LC-MS phosphoproteome investigation

    PubMed Central

    2014-01-01

    Background Comprehensive characterization of the phosphoproteome in living cells is critical in signal transduction research. But the low abundance of phosphopeptides among the total proteome in cells remains an obstacle in mass spectrometry-based proteomic analysis. To provide a solution, an alternative analytic strategy to confidently identify phosphorylated peptides by using the alkaline phosphatase (AP) treatment combined with high-resolution mass spectrometry was provided. While the process is applicable, the key integration along the pipeline was mostly done by tedious manual work. Results We developed a software toolkit, iPhos, to facilitate and streamline the work-flow of AP-assisted phosphoproteome characterization. The iPhos tookit includes one assister and three modules. The iPhos Peak Extraction Assister automates the batch mode peak extraction for multiple liquid chromatography mass spectrometry (LC-MS) runs. iPhos Module-1 can process the peak lists extracted from the LC-MS analyses derived from the original and dephosphorylated samples to mine out potential phosphorylated peptide signals based on mass shift caused by the loss of some multiples of phosphate groups. And iPhos Module-2 provides customized inclusion lists with peak retention time windows for subsequent targeted LC-MS/MS experiments. Finally, iPhos Module-3 facilitates to link the peptide identifications from protein search engines to the quantification results from pattern-based label-free quantification tools. We further demonstrated the utility of the iPhos toolkit on the data of human metastatic lung cancer cells (CL1-5). Conclusions In the comparison study of the control group of CL1-5 cell lysates and the treatment group of dasatinib-treated CL1-5 cell lysates, we demonstrated the applicability of the iPhos toolkit and reported the experimental results based on the iPhos-facilitated phosphoproteome investigation. And further, we also compared the strategy with pure DDA-based LC-MS/MS phosphoproteome investigation. The results of iPhos-facilitated targeted LC-MS/MS analysis convey more thorough and confident phosphopeptide identification than the results of pure DDA-based analysis. PMID:25521246

  14. A Novel Approach to the Dissection of the Human Knee

    NSDL National Science Digital Library

    Michael Schumaker (Youngstown Orthopedics)

    2009-02-01

    This article describes an alternate technique to dissecting the human knee in a cadaver lab. The purpose behind the procedure is to allow for maximal visualization of intra-articular structures that are typically removed early in dissection. This technique modernizes the dissection to allow for students to visualize structures that they would see during a knee replacement surgery.

  15. Triangular dissections, aperiodic tilings and Jones algebras

    E-print Network

    R. Coquereaux

    1995-03-27

    The Brattelli diagram associated with a given bicolored Dynkin-Coxeter graph of type $A_n$ determines planar fractal sets obtained by infinite dissections of a given triangle. All triangles appearing in the dissection process have angles that are multiples of $\\pi/ (n+1).$ There are usually several possible infinite dissections compatible with a given $n$ but a given one makes use of $n/2$ triangle types if $n$ is even. Jones algebra with index $[ 4 \\ \\cos^2{\\pi \\over n+1}]^{-1}$ (values of the discrete range) act naturally on vector spaces associated with those fractal sets. Triangles of a given type are always congruent at each step of the dissection process. In the particular case $n=4$, there are isometric and the whole structure lead, after proper inflation, to aperiodic Penrose tilings. The ``tilings'' associated with other values of the index are discussed and shown to be encoded by equivalence classes of infinite sequences (with appropriate constraints) using $n/2$ digits (if $n$ is even) and generalizing the Fibonacci numbers.

  16. Gastric mucosa under the dissecting microscope

    Microsoft Academic Search

    S. N. Salem

    1965-01-01

    D ISSECTING-MICROSCOPY~ EXAMINATION of the small-intestinal mucosa has become an important part of biopsy study in diseases affecting the small intestine, particularly tile condition known as idiopathic steatorrhea (nontropical sprue). Examination of the biopsy specimen with the dissecting microscope provides immediate diagnosis in that condition. Rubin et at. 1 showed that in nontropical sprue, the appearance of the jejunal biopsy

  17. Pythagoras and the Dissection of Polygons.

    ERIC Educational Resources Information Center

    Mortimer, M. E.; Ball, R. W.

    1984-01-01

    Provides examples of proofs of the Pythagorean result. These proofs fall into three categories: using ratios, using dissection, and using other forms of transformation. Shows that polygons of equal area are equidecomposable and that the approach taken (via squares) is a new approach. (JN)

  18. Tissue phosphoproteomics with PolyMAC identifies potential therapeutic targets in a transgenic mouse model of HER2 positive breast cancer.

    PubMed

    Searleman, Adam C; Iliuk, Anton B; Collier, Timothy S; Chodosh, Lewis A; Tao, W Andy; Bose, Ron

    2014-12-01

    Altered protein phosphorylation is a feature of many human cancers that can be targeted therapeutically. Phosphopeptide enrichment is a critical step for maximizing the depth of phosphoproteome coverage by MS, but remains challenging for tissue specimens because of their high complexity. We describe the first analysis of a tissue phosphoproteome using polymer-based metal ion affinity capture (PolyMAC), a nanopolymer that has excellent yield and specificity for phosphopeptide enrichment, on a transgenic mouse model of HER2-driven breast cancer. By combining phosphotyrosine immunoprecipitation with PolyMAC, 411 unique peptides with 139 phosphotyrosine, 45 phosphoserine, and 29 phosphothreonine sites were identified from five LC-MS/MS runs. Combining reverse phase liquid chromatography fractionation at pH 8.0 with PolyMAC identified 1571 unique peptides with 1279 phosphoserine, 213 phosphothreonine, and 21 phosphotyrosine sites from eight LC-MS/MS runs. Linear motif analysis indicated that many of the phosphosites correspond to well-known phosphorylation motifs. Analysis of the tyrosine phosphoproteome with the Drug Gene Interaction database uncovered a network of potential therapeutic targets centered on Src family kinases with inhibitors that are either FDA-approved or in clinical development. These results demonstrate that PolyMAC is well suited for phosphoproteomic analysis of tissue specimens. PMID:24723360

  19. Multidimensional strategy for sensitive phosphoproteomics incorporating protein prefractionation combined with SIMAC, HILIC, and TiO(2) chromatography applied to proximal EGF signaling.

    PubMed

    Engholm-Keller, Kasper; Hansen, Thomas Aarup; Palmisano, Giuseppe; Larsen, Martin R

    2011-12-01

    Comprehensive enrichment and fractionation is essential to obtain a broad coverage of the phosphoproteome. This inevitably leads to sample loss, and thus, phosphoproteomics studies are usually only performed on highly abundant samples. Here, we present a comprehensive phosphoproteomics strategy applied to 400 ?g of protein from EGF-stimulated HeLa cells. The proteins are separated into membrane and cytoplasmic fractions using sodium carbonate combined with ultracentrifugation. The phosphopeptides were separated into monophosphorylated and multiphosphorylated pools using sequential elution from IMAC (SIMAC) followed by hydrophilic interaction liquid chromatography of the mono- and nonphosphorylated peptides and subsequent titanium dioxide chromatography of the HILIC fractions. This strategy facilitated the identification of >4700 unique phosphopeptides, while 636 phosphosites were changing following short-term EGF stimulation, many of which were not previously known to be involved in EGFR signaling. We further compared three different data processing programs and found large differences in their peptide identification rates due to different implementations of recalibration and filtering. Manually validating a subset of low-scoring peptides exclusively identified using the MaxQuant software revealed a large percentage of false positive identifications. This indicates that, despite having highly accurate precursor mass determination, peptides with low fragment ion scores should not automatically be reported in phosphoproteomics studies. PMID:21955146

  20. Comparative phosphoproteomics reveals components of host cell invasion and post-transcriptional regulation during Francisella infection

    SciTech Connect

    Nakayasu, Ernesto S.; Tempel, Rebecca; Cambronne, Xiaolu A.; Petyuk, Vladislav A.; Jones, Marcus B.; Gritsenko, Marina A.; Monroe, Matthew E.; Yang, Feng; Smith, Richard D.; Adkins, Joshua N.; Heffron, Fred

    2013-09-22

    Francisella tularensis is a facultative intracellular bacterium that causes the deadly disease tularemia. Most evidence suggests that Francisella is not well recognized by the innate immune system that normally leads to cytokine expression and cell death. In previous work, we identified new bacterial factors that were hyper-cytotoxic to macrophages. Four of the identified hyper-cytotoxic strains (lpcC, manB, manC and kdtA) had an impaired lipopolysaccharide (LPS) synthesis and produced an exposed lipid A lacking the O-antigen. These mutants were not only hyper-cytotoxic but also were phagocytosed at much higher rates compared to the wild type parent strain. To elucidate the cellular signaling underlying this enhanced phagocytosis and cell death, we performed a large-scale comparative phosphoproteomic analysis of cells infected with wild-type and delta-lpcC F. novicida. Our data suggest that not only actin but also intermediate filaments and microtubules are important for F. novicida entry into the host cells. In addition, we observed differential phosphorylation of tristetraprolin (TTP), a key component of the mRNA-degrading machinery that controls the expression of a variety of genes including many cytokines. Infection with the delta-lpcC mutant induced the hyper-phosphorylation and inhibition of TTP, leading to the production of cytokines such as IL-1beta and TNF-alpha which may kill the host cells by triggering apoptosis. Together, our data provide new insights for Francisella invasion and a post-transcriptional mechanism that prevents the expression of host immune response factors that controls infection by this pathogen.

  1. Phosphoproteomics reveals the effect of ethylene in soybean root under flooding stress.

    PubMed

    Yin, Xiaojian; Sakata, Katsumi; Komatsu, Setsuko

    2014-12-01

    Flooding has severe negative effects on soybean growth. To explore the flooding-responsive mechanisms in early-stage soybean, a phosphoproteomic approach was used. Two-day-old soybean plants were treated without or with flooding for 3, 6, 12, and 24 h, and root tip proteins were then extracted and analyzed at each time point. After 3 h of flooding exposure, the fresh weight of soybeans increased, whereas the ATP content of soybean root tips decreased. Using a gel-free proteomic technique, a total of 114 phosphoproteins were identified in the root tip samples, and 34 of the phosphoproteins were significantly changed with respect to phosphorylation status after 3 h of flooding stress. Among these phosphoproteins, eukaryotic translation initiation factors were dephosphorylated, whereas several protein synthesis-related proteins were phosphorylated. The mRNA expression levels of sucrose phosphate synthase 1F and eukaryotic translation initiation factor 4 G were down-regulated, whereas UDP-glucose 6-dehydrogenase mRNA expression was up-regulated during growth but down-regulated under flooding stress. Furthermore, bioinformatic protein interaction analysis of flooding-responsive proteins based on temporal phosphorylation patterns indicated that eukaryotic translation initiation factor 4 G was located in the center of the network during flooding. Soybean eukaryotic translation initiation factor 4 G has homology to programmed cell death 4 protein and is implicated in ethylene signaling. The weight of soybeans was increased with treatment by an ethylene-releasing agent under flooding condition, but it was decreased when plants were exposed to an ethylene receptor antagonist. These results suggest that the ethylene signaling pathway plays an important role, via the protein phosphorylation, in mechanisms of plant tolerance to the initial stages of flooding stress in soybean root tips. PMID:25316100

  2. Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data.

    PubMed

    Mitsos, Alexander; Melas, Ioannis N; Siminelakis, Paraskeuas; Chairakaki, Aikaterini D; Saez-Rodriguez, Julio; Alexopoulos, Leonidas G

    2009-12-01

    Understanding the mechanisms of cell function and drug action is a major endeavor in the pharmaceutical industry. Drug effects are governed by the intrinsic properties of the drug (i.e., selectivity and potency) and the specific signaling transduction network of the host (i.e., normal vs. diseased cells). Here, we describe an unbiased, phosphoproteomic-based approach to identify drug effects by monitoring drug-induced topology alterations. With our proposed method, drug effects are investigated under diverse stimulations of the signaling network. Starting with a generic pathway made of logical gates, we build a cell-type specific map by constraining it to fit 13 key phopshoprotein signals under 55 experimental conditions. Fitting is performed via an Integer Linear Program (ILP) formulation and solution by standard ILP solvers; a procedure that drastically outperforms previous fitting schemes. Then, knowing the cell's topology, we monitor the same key phosphoprotein signals under the presence of drug and we re-optimize the specific map to reveal drug-induced topology alterations. To prove our case, we make a topology for the hepatocytic cell-line HepG2 and we evaluate the effects of 4 drugs: 3 selective inhibitors for the Epidermal Growth Factor Receptor (EGFR) and a non-selective drug. We confirm effects easily predictable from the drugs' main target (i.e., EGFR inhibitors blocks the EGFR pathway) but we also uncover unanticipated effects due to either drug promiscuity or the cell's specific topology. An interesting finding is that the selective EGFR inhibitor Gefitinib inhibits signaling downstream the Interleukin-1alpha (IL1alpha) pathway; an effect that cannot be extracted from binding affinity-based approaches. Our method represents an unbiased approach to identify drug effects on small to medium size pathways which is scalable to larger topologies with any type of signaling interventions (small molecules, RNAi, etc). The method can reveal drug effects on pathways, the cornerstone for identifying mechanisms of drug's efficacy. PMID:19997482

  3. Lymph node dissection for lung cancer: past, present, and future.

    PubMed

    Watanabe, Shun-ichi

    2014-07-01

    In 1978, Naruke et al. proposed an anatomical map that included numbered lymph node stations, which then became widely used for nodal dissection. In 1997, Mountain and Dresler published a new map, which is now favored by the American Thoracic Society and the European Respiratory Society. Using these maps, regional nodal dissection has been universally performed in lung cancer surgery. Clear evidence regarding the survival benefit of lymph node dissection for lung cancer is lacking. However, lobectomy with lymph node dissection continues to be a standard surgical procedure for lung cancer because lymph node dissection is an important investigative process in staging patients. Over the last decade, the extent of nodal dissection for lung cancer has changed due to the increasing number of early detected lung cancers made possible by the recent development of the CT scanner. This manuscript describes the history, present strategy, and future perspectives of lymph node dissection for lung cancer. PMID:24823489

  4. Quantitative Proteomics Reveals That Hsp90 Inhibition Preferentially Targets Kinases and the DNA Damage Response*

    PubMed Central

    Sharma, Kirti; Vabulas, R. Martin; Macek, Boris; Pinkert, Stefan; Cox, Jürgen; Mann, Matthias; Hartl, F. Ulrich

    2012-01-01

    Despite the increasing importance of heat shock protein 90 (Hsp90) inhibitors as chemotherapeutic agents in diseases such as cancer, their global effects on the proteome remain largely unknown. Here we use high resolution, quantitative mass spectrometry to map protein expression changes associated with the application of the Hsp90 inhibitor, 17-(dimethylaminoethylamino)-17-demethoxygeldanamycin (17-DMAG). In depth data obtained from five replicate SILAC experiments enabled accurate quantification of about 6,000 proteins in HeLa cells. As expected, we observed activation of a heat shock response with induced expression of molecular chaperones, which refold misfolded proteins, and proteases, which degrade irreparably damaged polypeptides. Despite the broad range of known Hsp90 substrates, bioinformatics analysis revealed that particular protein classes were preferentially affected. These prominently included proteins involved in the DNA damage response, as well as protein kinases and especially tyrosine kinases. We followed up on this observation with a quantitative phosphoproteomic analysis of about 4,000 sites, which revealed that Hsp90 inhibition leads to much more down- than up-regulation of the phosphoproteome (34% down versus 6% up). This study defines the cellular response to Hsp90 inhibition at the proteome level and sheds light on the mechanisms by which it can be used to target cancer cells. PMID:22167270

  5. The Harmonic Scalpel versus Conventional Hemostasis for Neck Dissection: A Meta-Analysis of the Randomized Controlled Trials

    PubMed Central

    Ren, Zhen-Hu; Xu, Jian-Lin; Fan, Teng-Fei; Ji, Tong; Wu, Han-Jiang; Zhang, Chen-Ping

    2015-01-01

    Objective Neck dissection is the most definitive and effective treatment for head and neck cancer. This systematic review aims to compare the efficacy and surgical outcomes of neck dissection between the harmonic scalpel and conventional surgical techniques and conduct a quantitative meta-analysis of the randomized trials. Methods Randomized controlled trials (RCTs) were identified from the major electronic databases (MEDLINE, EMBASE and Cochrane Library) using the keywords ‘‘harmonic scalpel’’ and ‘‘neck dissection,’’ and a quantitative meta-analysis was conducted. The operative time and intraoperative bleeding were the primary outcome measures, and other parameters assessed included the drainage fluid volume and length of hospital stay. Results Seven trials that met the inclusion criteria included 406 neck dissection cases (201 in the harmonic scalpel group). Compared with conventional surgical techniques, the HS group had an operative time that was significantly reduced by 29.3 minutes [mean difference: -29.29; 95% CI = (-44.26, -14.32); P=0.0001], a reduction in intraoperative bleeding by 141.1 milliliters [mean difference: -141.13; 95% CI = (-314.99, 32.73); P=0.11], and a reduction in drainage fluid volume by 64.9 milliliters [mean difference: -64.86; 95% CI = (-110.40, -19.32); P=0.005] , but it is not significant after removal of studies driving heterogeneity. There was no significant difference in the length of the hospital stay [mean difference: -0.21; 95% CI = (-0.48, 0.07); P=0.14]. Conclusion This systematic review showed that using the harmonic scalpel for neck dissection significantly reduces the operative time and drainage fluid volume and that it is not associated with an increased length of hospital stay or perioperative complications. Therefore, the harmonic scalpel method is safe and effective for neck dissection. However, the statistical heterogeneity was high. Further studies are required to substantiate our findings. PMID:26161897

  6. Renal artery dissection associated with Gz acceleration.

    PubMed

    Beyer, Reinaldo W; Daily, Pat O

    2004-03-01

    A 55-yr-old male presented with flank pain and nausea minutes after intensive aerobatic flight maneuvers. An initial diagnosis of acute appendicitis was made. Computed axial tomography and renal arteriography showed a right kidney with two renal arteries, a right upper pole infarction, and a dissection in the upper renal artery which had a more vertical trajectory than the usual main renal artery. No signs of diseases known to be associated with renal artery dissection were present. The patient recovered without residual hypertension. Heavy positive G loads may have potential to cause renal arterial injury, particularly when renal vascular anatomical variations exist. The postulated mechanism is similar to fall injuries in which the subjects landed on their feet, with inertia causing caudal renal dislodgement and stretch of the renal vessels. PMID:15018300

  7. Managing aortic aneurysms and dissections during pregnancy.

    PubMed

    Muiño Mosquera, Laura; De Backer, Julie

    2015-06-01

    Cardiovascular diseases during pregnancy account for significant morbidity and mortality, with aortic aneurysms, complicated by aortic dissection or rupture, being high on the list of underlying causes in this category. Correct knowledge of the diagnosis, risks and treatment is mandatory to improve the outcome and save lives. In this article, the authors aim to provide an overview of the underlying causes and risk factors for aortic aneurysms and dissections during pregnancy, while presenting the ways of preventing and treating these conditions. Although an important focus lies on the proximal part of the aorta due to it bearing the greatest risk for complications and being more frequently implicated in aortic disease in younger subjects, many aspects on the etiology and underlying diseases also apply to the other parts of the vessel. PMID:26000563

  8. Recanalization of Spontaneous Carotid Artery Dissection

    Microsoft Academic Search

    Krassen Nedeltchev; Stefan Bickel; Marcel Arnold; Hakan Sarikaya; Dimitrios Georgiadis; Matthias Sturzenegger; Heinrich P. Mattle; Ralf W. Baumgartner

    Background and Purpose—We set out to investigate the predictors and time course for recanalization of spontaneous dissection of the cervical internal carotid artery (SICAD). Methods—We prospectively included 249 consecutive patients (mean age, 4511 years) with 268 SICAD. Ultrasound examinations were performed at presentation, during the first month, and then at 3, 6, and 12 months, and clinical follow-ups after 3,

  9. Geometric dissections now swing and twist

    Microsoft Academic Search

    Greg N. Frederickson

    2001-01-01

    Conclusion  With their visual and kinetic appeal, hinged dissections and their design techniques will continue to play a role in mathematical\\u000a recreation and education. They also invite substantive research in mathematics and computer science. Hinges are the simplest\\u000a of linkages, permitting only relative rotation between connected pieces; with hingeability we address issues of transformation\\u000a of objects which have wider relevance. In

  10. Future directions of duodenal endoscopic submucosal dissection

    PubMed Central

    Matsumoto, Satohiro; Miyatani, Hiroyuki; Yoshida, Yukio

    2015-01-01

    Endoscopic therapies for lesions of the duodenum are technically more difficult than those for lesions of the other parts of the gastrointestinal tract due to the anatomical features of the duodenum, and the incidence rate of complications such as perforation and bleeding is also higher. These aforementioned trends were especially noticeable for the case of duodenal endoscopic submucosal dissection (ESD). The indication for ESD of duodenal tumors should be determined by assessment of the histopathology, macroscopic morphology, and diameter of the tumors. The three types of candidate lesions for endoscopic therapy are adenoma, carcinoma, and neuroendocrine tumors. For applying endoscopic therapies to duodenal lesions, accurate preoperative histopathological diagnosis is necessary. The most important technical issue in duodenal ESD is the submucosal dissection process. In duodenal ESD, a short needle-type knife is suitable for the mucosal incision and submucosal dissection processes, and the Small-caliber-tip Transparent hood is an important tool. After endoscopic therapies, the wound should be closed by clipping in order to prevent complications such as secondary hemorrhage and delayed perforation. At present, the criteria for selection between ESD and EMR vary among institutions. The indications for ESD should be carefully considered. Duodenal ESD should have limitations, such as the need for its being performed by experts with abundant experience in performing the procedure. PMID:25901218

  11. Whole Vitreous Humor Dissection for Vitreodynamic Analysis.

    PubMed

    Murali, Karthik; Kashani, Amir H; Humayun, Mark S

    2015-01-01

    The authors propose an effective technique to isolate whole, intact vitreous core and cortex from post mortem enucleated porcine eyes. While previous studies have shown the results of such dissections, the detailed steps have not been described, precluding researchers outside the field from replicating their methods. Other studies harvest vitreous either through aspiration, which does not maintain the vitreous structure anatomy, or through partial dissection, which only isolates the vitreous core. The proposed method isolates the whole vitreous body, with the vitreous core and cortex intact, while maintaining vitreous anatomy and structural integrity. In this method, a full thickness scleral flap in an enucleated porcine eye is first created and through this, the choroid tissue can be separated from the sclera. The scleral flap is then expanded and the choroid is completely separated from the sclera. Finally the choroid-retina tissue is peeled off the vitreous to leave an isolated intact vitreous body. The proposed vitreous dissection technique can be used to study physical properties of the vitreous humor. In particular, this method has significance for experimental studies involving drug delivery, vitreo-retinal oxygen transport, and intraocular convection. PMID:26065393

  12. Future directions of duodenal endoscopic submucosal dissection.

    PubMed

    Matsumoto, Satohiro; Miyatani, Hiroyuki; Yoshida, Yukio

    2015-04-16

    Endoscopic therapies for lesions of the duodenum are technically more difficult than those for lesions of the other parts of the gastrointestinal tract due to the anatomical features of the duodenum, and the incidence rate of complications such as perforation and bleeding is also higher. These aforementioned trends were especially noticeable for the case of duodenal endoscopic submucosal dissection (ESD). The indication for ESD of duodenal tumors should be determined by assessment of the histopathology, macroscopic morphology, and diameter of the tumors. The three types of candidate lesions for endoscopic therapy are adenoma, carcinoma, and neuroendocrine tumors. For applying endoscopic therapies to duodenal lesions, accurate preoperative histopathological diagnosis is necessary. The most important technical issue in duodenal ESD is the submucosal dissection process. In duodenal ESD, a short needle-type knife is suitable for the mucosal incision and submucosal dissection processes, and the Small-caliber-tip Transparent hood is an important tool. After endoscopic therapies, the wound should be closed by clipping in order to prevent complications such as secondary hemorrhage and delayed perforation. At present, the criteria for selection between ESD and EMR vary among institutions. The indications for ESD should be carefully considered. Duodenal ESD should have limitations, such as the need for its being performed by experts with abundant experience in performing the procedure. PMID:25901218

  13. Background music in the dissection laboratory: impact on stress associated with the dissection experience.

    PubMed

    Anyanwu, Emeka G

    2015-06-01

    Notable challenges, such as mental distress, boredom, negative moods, and attitudes, have been associated with learning in the cadaver dissection laboratory (CDL). The ability of background music (BM) to enhance the cognitive abilities of students is well documented. The present study was designed to investigate the impact of BM in the CDL and on stress associated with the dissection experience. After 8 wk of normal dissection without BM, various genres of BM were introduced into the cadaver dissection sessions of 260 medical and dental students for 3 wk. Feedback on the impact of BM on students in the CDL and students' attitude were accessed using a questionnaire. Psychological stress assessment was done using Psychological Stress Measure 9. Two batches of 30 students each were made to dissect same areas of the body for 2 h, one batch with BM playing and the other batch without. The same examination was given to both groups at the end. Over 90% of the participants expressed a desire to incorporate BM into the CDL; 87% of the sampled population that expressed love for music also reported BM to be a very useful tool that could be used to enhance learning conditions in the CDL. A strong positive relationship was established between love for music and its perception as a tool for learning in the CDL (P < 0.001). Students that studied under the influence of BM had significantly higher scores (P < 0.001) in the overall examination result. BM reduced the level of stress associated with the dissection experience by ?33%. PMID:26031725

  14. Endovascular repair of a double-lumen dissecting aneurysm

    PubMed Central

    Johnson, Andrew Kelly; Gerard, Carter S; Lopes, Demetrius Klee

    2013-01-01

    Treating dissections and dissecting aneurysms requires maintenance of flow through the true lumen and exclusion of the false lumen from the circulation. A dissecting aneurysm of the vertebral artery presented with both a true and false lumen within the aneurysmal sac. Stenting of the true lumen followed by coil embolization of both lumens was performed. Management options and decision-making are discussed for this unique situation. PMID:23737597

  15. Biomechanical Properties of Human Ascending Thoracic Aortic Dissections.

    PubMed

    Babu, Anju R; Byju, Achu G; Gundiah, Namrata

    2015-08-01

    Thoracic aortic dissections are associated with a significant risk of morbidity and mortality, and currently challenge our understanding of the biomechanical factors leading to their initiation and propagation. We quantified the biaxial mechanical properties of human type A dissections (n?=?16) and modeled the stress-strain data using a microstructurally motivated form of strain energy function. Our results show significantly higher stiffness for dissected tissues as compared to control aorta without arterial disease. Higher stiffness of dissected tissues did not, however, correlate with greater aortic diameter measured prior to surgery nor were there any age dependent differences in the tissue properties. PMID:26043270

  16. A Comparative Approach To Animal Dissections (A Phylogenic Study)

    NSDL National Science Digital Library

    In this biology inquiry lab, students study evolutionary relationships by making observations of preserved animal specimens, developing a question, then investigating by dissecting the specimens provided.

  17. Phosphoproteomic Profiling of In Vivo Signaling in Liver by the Mammalian Target of Rapamycin Complex 1 (mTORC1)

    PubMed Central

    Demirkan, Gokhan; Yu, Kebing; Boylan, Joan M.; Salomon, Arthur R.; Gruppuso, Philip A.

    2011-01-01

    Background Our understanding of signal transduction networks in the physiological context of an organism remains limited, partly due to the technical challenge of identifying serine/threonine phosphorylated peptides from complex tissue samples. In the present study, we focused on signaling through the mammalian target of rapamycin (mTOR) complex 1 (mTORC1), which is at the center of a nutrient- and growth factor-responsive cell signaling network. Though studied extensively, the mechanisms involved in many mTORC1 biological functions remain poorly understood. Methodology/Principal Findings We developed a phosphoproteomic strategy to purify, enrich and identify phosphopeptides from rat liver homogenates. Using the anticancer drug rapamycin, the only known target of which is mTORC1, we characterized signaling in liver from rats in which the complex was maximally activated by refeeding following 48 hr of starvation. Using protein and peptide fractionation methods, TiO2 affinity purification of phosphopeptides and mass spectrometry, we reproducibly identified and quantified over four thousand phosphopeptides. Along with 5 known rapamycin-sensitive phosphorylation events, we identified 62 new rapamycin-responsive candidate phosphorylation sites. Among these were PRAS40, gephyrin, and AMP kinase 2. We observed similar proportions of increased and reduced phosphorylation in response to rapamycin. Gene ontology analysis revealed over-representation of mTOR pathway components among rapamycin-sensitive phosphopeptide candidates. Conclusions/Significance In addition to identifying potential new mTORC1-mediated phosphorylation events, and providing information relevant to the biology of this signaling network, our experimental and analytical approaches indicate the feasibility of large-scale phosphoproteomic profiling of tissue samples to study physiological signaling events in vivo. PMID:21738781

  18. Dynamic Changes in Ribosome-Associated Proteome and Phosphoproteome During Deoxynivalenol-Induced Translation Inhibition and Ribotoxic Stress

    PubMed Central

    Pestka, James J.

    2014-01-01

    Deoxynivalenol (DON), a trichothecene mycotoxin produced by Fusarium that commonly contaminates cereal-based food, interacts with the ribosome to cause translation inhibition and activate stress kinases in mononuclear phagocytes via the ribotoxic stress response (RSR). The goal of this study was to test the hypothesis that the ribosome functions as a platform for spatiotemporal regulation of translation inhibition and RSR. Specifically, we employed stable isotope labeling of amino acids in cell culture (SILAC)-based proteomics to quantify the early (?30min) DON-induced changes in ribosome-associated proteins in RAW 264.7 murine macrophage. Changes in the proteome and phosphoproteome were determined using off-gel isoelectric focusing and titanium dioxide chromatography, respectively, in conjunction with LC-MS/MS. Following exposure of RAW 264.7 to a toxicologically relevant concentration of DON (250ng/ml), we observed an overall decrease in translation-related proteins interacting with the ribosome, concurrently with a compensatory increase in proteins that mediate protein folding, biosynthesis, and cellular organization. Alterations in the ribosome-associated phosphoproteome reflected proteins that modulate translational and transcriptional regulation, and others that converged with signaling pathways known to overlap with phosphorylation changes characterized previously in intact RAW 264.7 cells. These results suggest that the ribosome plays a central role as a hub for association and phosphorylation of proteins involved in the coordination of early translation inhibition as well as recruitment and maintenance of stress-related proteins—both of which enable cells to adapt and respond to ribotoxin exposure. This study provides a template for elucidating the molecular mechanisms of DON and other ribosome-targeting agents. PMID:24284785

  19. Harnessing Natural Sequence Variation to Dissect Posttranscriptional Regulatory Networks in Yeast

    PubMed Central

    Fazlollahi, Mina; Lee, Eunjee; Muroff, Ivor; Lu, Xiang-Jun; Gomez-Alcala, Pilar; Causton, Helen C.; Bussemaker, Harmen J.

    2014-01-01

    Understanding how genomic variation influences phenotypic variation through the molecular networks of the cell is one of the central challenges of biology. Transcriptional regulation has received much attention, but equally important is the posttranscriptional regulation of mRNA stability. Here we applied a systems genetics approach to dissect posttranscriptional regulatory networks in the budding yeast Saccharomyces cerevisiae. Quantitative sequence-to-affinity models were built from high-throughput in vivo RNA binding protein (RBP) binding data for 15 yeast RBPs. Integration of these models with genome-wide mRNA expression data allowed us to estimate protein-level RBP regulatory activity for individual segregants from a genetic cross between two yeast strains. Treating these activities as a quantitative trait, we mapped trans-acting loci (activity quantitative trait loci, or aQTLs) that act via posttranscriptional regulation of transcript stability. We predicted and experimentally confirmed that a coding polymorphism at the IRA2 locus modulates Puf4p activity. Our results also indicate that Puf3p activity is modulated by distinct loci, depending on whether it acts via the 5? or the 3? untranslated region of its target mRNAs. Together, our results validate a general strategy for dissecting the connectivity between posttranscriptional regulators and their upstream signaling pathways. PMID:24938291

  20. Quantitation, networking, and function of protein phosphorylation in plant cell

    PubMed Central

    Zhu, Lin; Li, Ning

    2013-01-01

    Protein phosphorylation is one of the most important post-translational modifications (PTMs) as it participates in regulating various cellular processes and biological functions. It is therefore crucial to identify phosphorylated proteins to construct a phosphor-relay network, and eventually to understand the underlying molecular regulatory mechanism in response to both internal and external stimuli. The changes in phosphorylation status at these novel phosphosites can be accurately measured using a 15N-stable isotopic labeling in Arabidopsis (SILIA) quantitative proteomic approach in a high-throughput manner. One of the unique characteristics of the SILIA quantitative phosphoproteomic approach is the preservation of native PTM status on protein during the entire peptide preparation procedure. Evolved from SILIA is another quantitative PTM proteomic approach, AQUIP (absolute quantitation of isoforms of post-translationally modified proteins), which was developed by combining the advantages of targeted proteomics with SILIA. Bioinformatics-based phosphorylation site prediction coupled with an MS-based in vitro kinase assay is an additional way to extend the capability of phosphosite identification from the total cellular protein. The combined use of SILIA and AQUIP provides a novel strategy for molecular systems biological study and for investigation of in vivo biological functions of these phosphoprotein isoforms and combinatorial codes of PTMs. PMID:23316209

  1. Diagnosis and treatment of cervical artery dissection.

    PubMed

    Engelter, Stefan T; Traenka, Christopher; Von Hessling, Alexander; Lyrer, Philippe A

    2015-05-01

    Cervical artery dissection (CAD) is a major cause of stroke in the young. A mural hematoma is detected in most CAD patients. The intramural blood accumulation should not be considered a reason to withhold intravenous thrombolysis in patients with CAD-related stroke. Because intravenous-thrombolyzed CAD patients might not recover as well as other stroke patients, acute endovascular treatment is an alternative. Regarding the choice of antithrombotic agents, this article discusses the findings of 4 meta-analyses across observational data, the current status of 3 randomized controlled trials, and arguments and counterarguments favoring anticoagulants over antiplatelets. Furthermore, the role of stenting and surgery is addressed. PMID:25907914

  2. Prognostic biological features in neck dissection specimens.

    PubMed

    Woolgar, Julia A; Triantafyllou, Asterios; Lewis, James S; Hunt, Jennifer; Williams, Michelle D; Takes, Robert P; Thompson, Lester D R; Slootweg, Pieter J; Devaney, Kenneth O; Ferlito, Alfio

    2013-05-01

    The superior prognostic value offered by routine histopathological staging of neck dissections, as compared to clinical staging using palpation and modern imaging techniques, is well established in the literature concerning the management of squamous cell carcinoma of the head and neck. In this review, we discuss the definitions and criteria used in standardised routine histopathological reporting and explore additional potential nodal prognostic features. In addition, we critically appraise the value of immunohistochemistry, histochemistry, molecular and other non-morphological techniques and suggest tumour and host features that merit further investigations. PMID:22983222

  3. Doing Dissections Differently: A Structured, Peer-Assisted Learning Approach to Maximizing Learning in Dissections

    ERIC Educational Resources Information Center

    Hall, Emma R.; Davis, Rachel C.; Weller, Renate; Powney, Sonya; Williams, Sarah B.

    2013-01-01

    Areas of difficulty faced by our veterinary medicine students, with respect to their learning in dissection classes, were identified. These challenges were both general adult-learning related and specific to the discipline of anatomy. Our aim was to design, implement, and evaluate a modified reciprocal peer-assisted/team-based learning…

  4. 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

  5. Dissecting specific and global transcriptional regulation of bacterial gene expression

    PubMed Central

    Gerosa, Luca; Kochanowski, Karl; Heinemann, Matthias; Sauer, Uwe

    2013-01-01

    Gene expression is regulated by specific transcriptional circuits but also by the global expression machinery as a function of growth. Simultaneous specific and global regulation thus constitutes an additional—but often neglected—layer of complexity in gene expression. Here, we develop an experimental-computational approach to dissect specific and global regulation in the bacterium Escherichia coli. By using fluorescent promoter reporters, we show that global regulation is growth rate dependent not only during steady state but also during dynamic changes in growth rate and can be quantified through two promoter-specific parameters. By applying our approach to arginine biosynthesis, we obtain a quantitative understanding of both specific and global regulation that allows accurate prediction of the temporal response to simultaneous perturbations in arginine availability and growth rate. We thereby uncover two principles of joint regulation: (i) specific regulation by repression dominates the transcriptional response during metabolic steady states, largely repressing the biosynthesis genes even when biosynthesis is required and (ii) global regulation sets the maximum promoter activity that is exploited during the transition between steady states. PMID:23591774

  6. Displacement of N/Q-rich peptides on TiO2 beads enhances the depth and coverage of yeast phosphoproteome analyses.

    PubMed

    Kanshin, Evgeny; Michnick, Stephen W; Thibault, Pierre

    2013-06-01

    Phosphorylation is a reversible protein modification that regulates major cellular processes such as cell division, growth, and differentiation through highly dynamic and complex signaling pathways. Large-scale phosphoproteomics analyses have been greatly facilitated using affinity chromatography such as metal oxide affinity chromatography (e.g., TiO2), which in combination with mass spectrometry has enabled unbiased detection and quantification of thousands of phosphorylation sites in a single experiment. However, global phosphoproteome analyses do not provide comparable enrichment yields for different model organisms. While the proportion of phosphopeptides exceed 90% in mammalian cells using TiO2, similar levels have been notoriously difficult to achieve for yeast or dictylostelium cells. In a systematic study of TiO2 using cell extracts from different organisms, we determined that phosphopeptides are coenriched with peptides containing repetitive stretches of glutamine and asparagine residues. The proportion of these nonspecific binders can reach up to 50% in cell extracts from budding yeast and thus limit the depth and comprehensiveness of phosphoproteomics analyses. To address this limitation, we developed an effective method that used decoy amino acids to reduce the extent of nonspecific peptide binding and improve the recovery and detection of low abundance phosphopeptides that remained undetected by conventional TiO2 enrichment protocols. PMID:23607784

  7. A comprehensive proteomic and phosphoproteomic analysis of yeast deletion mutants of 14-3-3 orthologs and associated effects of rapamycin.

    PubMed

    Paulo, Joao A; Gygi, Steven P

    2015-01-01

    We applied a multiplexed, MS-based strategy to interrogate the proteome and phosphoproteome of three yeast strains under two growth conditions in triplicate. The yeast proteins brain modulosignalin homologue (Bmh)1 and Bmh2, analogs to the 14-3-3 protein family, have a wide array of cellular functions including the regulation of phosphorylation events. Moreover, rapamycin is a drug that can regulate phosphorylation events. By performing a series of tandem mass tag 10-plex experiments, we investigated the alterations in the proteome and phosphoproteome of wildtype and two deletion strains (bmh1? and bmh2?) of Saccharomyces cerevisiae treated with rapamycin and DMSO as a control. Our 3 × 3 + 1 strategy allowed for triplicate analysis of each of the three strains, plus an additional sample consisting of an equal mix of all samples. We quantified over 4000 proteins and 20,000 phosphorylation events. Of these, we quantified over 3700 proteins across all 20 samples and over 14,300 phosphorylation events within each drug treatment. In total, data collected from four tandem mass tag 10-plex experiments required approximately 1 week of data collection on the mass spectrometer. This study underscores the complex cellular roles of Bmh1 and Bmh2 coupled with response to rapamycin treatment and emphasizes the utility of multiplexed proteomic techniques to elucidate comprehensive proteomes and phosphoproteomes. PMID:25315811

  8. Traditional versus Computer-Based Dissections in Enhancing Learning in a Tertiary Setting: A Student Perspective.

    ERIC Educational Resources Information Center

    Franklin, Sue; Peat, Mary; Lewis, Alison

    2002-01-01

    Describes a study that investigates both the use and usefulness of laboratory dissections and computer-based dissections in a tertiary, first-year human biology course. Explores attitudes toward dissection. (DDR)

  9. 78 FR 6838 - Certain Balloon Dissection Devices and Products Containing Same; Institution of Investigation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-31

    ...337-TA-865] Certain Balloon Dissection Devices and Products...importation of certain dissection balloons and products containing the...importation of certain dissection balloons and products containing the...Geisingen, Germany; Pajunk Medical Systems L.P., 6611...

  10. Molecular Mechanisms of Thoracic Aortic Dissection

    PubMed Central

    Wu, Darrell; Shen, Ying H.; Russell, Ludivine; Coselli, Joseph S.; LeMaire, Scott A.

    2013-01-01

    Thoracic aortic dissection (TAD) is a highly lethal vascular disease. In many patients with TAD, the aorta progressively dilates and ultimately ruptures. Dissection formation, progression, and rupture cannot be reliably prevented pharmacologically because the molecular mechanisms of aortic wall degeneration are poorly understood. The key histopathologic feature of TAD is medial degeneration, a process characterized by smooth muscle cell depletion and extracellular matrix degradation. These structural changes have a profound impact on the functional properties of the aortic wall and can result from excessive protease-mediated destruction of the extracellular matrix, altered signaling pathways, and altered gene expression. Review of the literature reveals differences in the processes that lead to ascending versus descending and sporadic versus hereditary TAD. These differences add to the complexity of this disease. Although tremendous progress has been made in diagnosing and treating TAD, a better understanding of the molecular, cellular, and genetic mechanisms that cause this disease is necessary to developing more effective preventative and therapeutic treatment strategies. PMID:23856125

  11. Analysis of quantitative trait loci that influence animal behavior

    Microsoft Academic Search

    Jonathan Flint

    2003-01-01

    Behavioral differences between in- bred strains of mice and rats have a genetic basis that can now be dissected using quantitative trait locus (QTL) analysis. Over the last 10 years, a large number of genetic loci that influence behavior have been mapped. In this article I review what that information has revealed about the genetic architecture of behavior. I show

  12. Open surgical repair for chronic type B aortic dissection: a systematic review

    PubMed Central

    Tian, David H.; De Silva, Ramesh P.; Wang, Tom

    2014-01-01

    Background The treatment of chronic type B aortic dissection (CBAD) remains complicated. Thoracic endovascular aortic repair (TEVAR) has supplanted open surgical repair (OSR) as the preferred surgical treatment for CBAD. Despite TEVAR’s superior short-term results, much less is understood about its long-term outcomes. As much of the understanding of OSR originates from historical report, contemporary series, with modern surgical techniques and technologies, may present an alternative to TEVAR. The present systematic review will assess the short- and long-term outcomes of historic and contemporary series of OSR for CBAD. Methods Electronic searches were performed using six databases from their inception to March 2014. Relevant studies with OSRs for chronic type B dissection were identified. Data were extracted by two independent reviewers and analyzed according to predefined clinical endpoints. Studies were sub-classified into the pre-endovascular (historic series) and endovascular era (contemporary series) depending on whether the majority of cases were performed after 1999. Results Nineteen studies were identified for inclusion for quantitative analysis. Pooled short-term mortality was 11.1% overall, and 7.5% in the nine contemporary studies. Stroke, spinal cord ischemia, renal dysfunction, and reoperation for bleeding were 5.9%, 4.9%, 8.1%, and 8.1%, respectively, for the contemporary series. Absolute late reintervention was identified in 13.3% of patients overall, and in 11.3% of patients in the contemporary series. Aggregated survival at 1-, 3-, 5-, and 10-years of all patients were 82.1%, 74.1%, 66.3%, and 50.8%, respectively. Conclusions OSR for chronic type B dissection in the contemporary era offers acceptable results. Management approaches should be considered carefully, taking into account both short-term and long-term complications. More research is required to clarify specific indications for OSR and TEVAR in chronic type B dissections. PMID:25133097

  13. Six Cases of Chylous Leakage after Axillary Lymph Node Dissection

    Microsoft Academic Search

    Ming-hua Cong; Qi Liu; Wen-hong Zhou; Jian Zhu; Chen-xin Song; Xing-song Tian

    2008-01-01

    Summary Background: Chylous leakage has been described after several surgical procedures, especially in the region of the neck and thorax. However, it has rarely been reported after axillary lymph node dissection. Patients and Methods: We encountered 6 cases of chylous leakage after axillary lymph node dissection out of a total of 882 breast cancer patients between July 2005 and June

  14. A Modified Dissection Method to Preserve Neck Structures

    ERIC Educational Resources Information Center

    Hankin, Mark H.; Stoller, Jeremy L.

    2009-01-01

    The neck is not only one of the more challenging anatomical regions to dissect but also has important application to clinical conditions, diseases, and procedures. In this study, we describe two simple modifications for dissection of the neck that (1) aid in the identification and preservation of the cutaneous branches of the cervical plexus and…

  15. Value of systematic mediastinal lymph node dissection during pulmonary metastasectomy

    Microsoft Academic Search

    Florian Loehe; Sonja Kobinger; Rudolf A Hatz; Thomas Helmberger; Udo Loehrs; Heinrich Fuerst

    2001-01-01

    Background. Systematic mediastinal lymph node dissection is the accepted standard when curative resection of bronchial carcinoma is performed. However, mediastinal lymph node dissection is not routinely performed with pulmonary metastasectomy, in which only enlarged or suspicious lymph nodes are removed. The incidence of malignant infiltration of mediastinal lymph nodes in patients with pulmonary metastases is not known.Methods. Sixty-three patients who

  16. Choosing the correct treatment for acute aortic type B dissection.

    PubMed

    Singh, M; Hager, E; Avgerinos, E; Genovese, E; Mapara, K; Makaroun, M

    2015-04-01

    Acute type B aortic dissection is a life threatening disease process, which remains a clinical dilemma despite advances in technology, surgical technique and postoperative management. The variability of presenting symptoms, lack of a consensus on indications for treatment and differing opinions about the optimal timing for repair have added to the management confusion. Medical management has been the standard of care for acute uncomplicated type B dissection. Surgical repair and endovascular intervention are reserved for those who present with, or subsequently develop, dissection-related complications. Complicated dissections occur in 25% of cases and may include organ malperfusion, aortic rupture, periaortic hematoma, and uncontrolled hypertension. In the past decade thoracic endovascular aortic repair (TEVAR) has gained widespread acceptance as the modality of choice for the treatment of complicated type B dissection. This transition is representative of advances in technology, physician experience with aortic endografts and lower morbidity and mortality rates associated with TEVAR. The best medical therapy remains the standard of care for uncomplicated dissection, however this strategy fails to prevent long-term aortic-related morbidity and mortality. Recent data suggest that early TEVAR lowers aortic-related events and improves long-term aortic specific survival by covering the entry tear, promoting false lumen thrombosis and inducing aortic wall remodeling. The paucity of supporting data has created controversy surrounding the optimal treatment strategy for acute type B dissection. Nonetheless, recent healthcare trends show a paradigm shift towards the utilization of early TEVAR in acute type B dissection. PMID:25644833

  17. Geographic Dissection of the Twitter Network Juhi Kulshrestha Farshad Kooti

    E-print Network

    Gummadi, Krishna P.

    Geographic Dissection of the Twitter Network Juhi Kulshrestha Farshad Kooti Max Planck Institute interactions occur online via social net- working sites like Twitter and Facebook, users can in- teract in online social networks? In this paper, we attempt to address this question by dissecting the Twitter so

  18. Aortic Valve Conservation in Acute Type A Dissection

    Microsoft Academic Search

    Stephen Westaby; Takahiro Katsumata; Edward Freitas

    1997-01-01

    Background. We consider operative survival as the primary objective in acute type A dissection and believe that virtually all native aortic valves can be conserved. We sought to answer the question: “Does glue repair improve the long-term stability of proximal aortic repair?”Methods. We retrospectively studied 64 patients with an acute type A dissection, an ascending aortic tear, and aortic regurgitation

  19. Isolated Spontaneous Renal Artery Dissection Presented with Flank Pain

    PubMed Central

    Gandhi, Shruti P.; Patel, Kajal; Pal, Bipin C.

    2015-01-01

    Spontaneous renal artery dissection is a rare but important cause of flank pain. We report a case of isolated spontaneous renal artery dissection in 56-year-old man complicated by renal infarction presented with flank pain. Doppler study pointed towards vascular pathology. Computed tomography (CT) angiography was used to make final diagnosis which demonstrated intimal flap in main renal artery with renal infarction.

  20. Late Sequelae of Whiplash Injury with Dissection of Cervical Arteries

    Microsoft Academic Search

    Vital Hauser; Peter Zangger; Yaroslav Winter; Wolfgang Oertel; Jürg Kesselring

    2010-01-01

    Background\\/Aims: The objective of our study was to estimate the incidence of posttraumatic dissections of cervical arteries in patients with whiplash injury acquired in a car accident. Methods and Patients: We performed a retrospective analysis of medical records of 500 patients with whiplash injury acquired in car accidents between 1996 and 2005 and searched for dissections of cervical arteries occurring

  1. Active inflammatory bowel disease and coronary artery dissection

    PubMed Central

    Srinivas, M; Basumani, P; Muthusamy, R; Wheeldon, N

    2005-01-01

    The case of a young woman with flare-up of Crohn's disease, who had an acute myocardial infarction due to the spontaneous dissection of the left anterior descending coronary artery, is reported. The literature on this rare condition is reviewed and a mechanism postulated for spontaneous coronary artery dissection in inflammatory bowel disease. PMID:15640436

  2. Student Attitudes Toward Cadaveric Dissection at a UK Medical School

    NSDL National Science Digital Library

    Thelma Quince (University of Cambridge Department of Public Health and Primary Care)

    2011-06-08

    This article describes a survey conducted among first year medical students examining two main questions. One, attitudes toward the process of dissection and the personhood of the cadaver Two, the extent to which gender, anxiety, exposure to dissection, bereavement and prior experience of a dead body influenced these attitudes. Outcomes and suggestions on how to respond to first year dissectors are provided.

  3. Student Attitudes toward Cadaveric Dissection at a UK Medical School

    ERIC Educational Resources Information Center

    Quince, Thelma A.; Barclay, Stephen I. G.; Spear, Michelle; Parker, Richard A.; Wood, Diana F.

    2011-01-01

    A more humanistic approach toward dissection has emerged. However, student attitudes toward this approach are unknown and the influences on such attitudes are little understood. One hundred and fifty-six first-year medical students participated in a study examining firstly, attitudes toward the process of dissection and the personhood of the…

  4. Pancreatic dissection in the procedure of pancreaticoduodenectomy (with videos).

    PubMed

    Yamaue, Hiroki; Tani, Masaji; Kawai, Manabu; Hirono, Seiko; Okada, Ken-ichi; Miyazawa, Motoki

    2012-03-01

    The procedure of pancreaticoduodenectomy consists of three parts: resection, lymph node dissection, and reconstruction. A transection of the pancreas is commonly performed after a maneuver of the pancreatic head, exposing of the portal vein or lymph node dissection, and it should be confirmed as a safe method for pancreatic transection for decreasing the incidence of pancreatic fistula. However, there are only a few clinical trials with high levels of evidence for pancreatic surgery. In this report, we discuss the following issues: dissection of peripancreatic tissue, exposing the portal vein, pancreatic transection, dissection of the right hemicircle of the peri-superior mesenteric artery including plexus and lymph nodes, and dissection of the pancreatic parenchyma. PMID:22076671

  5. Quantitative analysis

    PubMed Central

    Nevin, John A.

    1984-01-01

    Quantitative analysis permits the isolation of invariant relations in the study of behavior. The parameters of these relations can serve as higher-order dependent variables in more extensive analyses. These points are illustrated by reference to quantitative descriptions of performance maintained by concurrent schedules, multiple schedules, and signal-detection procedures. Such quantitative descriptions of empirical data may be derived from mathematical theories, which in turn can lead to novel empirical analyses so long as their terms refer to behavioral and environmental events. Thus, quantitative analysis is an integral aspect of the experimental analysis of behavior. PMID:16812400

  6. Spontaneous renal artery dissection with renal infarction

    PubMed Central

    Leray-Moraguès, Hélène; Chenine, Leila; Vernhet-Kovacsik, Hélène

    2012-01-01

    Spontaneous renal artery dissection (SRAD) is a rare entity, which often presents diagnostic difficulties because of its non-specific clinical presentation. We report six cases complicated with renal infarction, occurring in middle-aged male patients without risk factors, illustrating the difficulty and delay for diagnosing SRAD. Ultrasound and Doppler imaging were not sensitive enough to confirm the diagnosis, and contrast-enhanced abdominal computed tomography was used to correct the diagnosis and allow the clinicians to propose appropriate treatment. We conclude that considering the urgency in diagnosing and treating SRAD, contrast enhanced abdominal tomography and/or abdominal magnetic resonance imaging should be proposed as soon as a suspicion of SRAD is evoked by the clinical presentation.

  7. Nanoscale scraping and dissection of collagen fibrils.

    PubMed

    Wenger, M P E; Horton, M A; Mesquida, P

    2008-09-24

    The main function of collagen is mechanical, hence there is a fundamental scientific interest in experimentally investigating the mechanical and structural properties of collagen fibrils on the nanometre scale. Here, we present a novel atomic force microscopy (AFM) based scraping technique that can dissect the outer layer of a biological specimen. Applied to individual collagen fibrils, the technique was successfully used to expose the fibril core and reveal the presence of a D-banding-like structure. AFM nanoindentation measurements of fibril shell and core indicated no significant differences in mechanical properties such as stiffness (reduced modulus), hardness, adhesion and adhesion work. This suggests that collagen fibrils are mechanically homogeneous structures. The scraping technique can be applied to other biological specimens, as demonstrated on the example of bacteria. PMID:21832566

  8. Immunostaining of dissected zebrafish embryonic heart.

    PubMed

    Yang, Jingchun; Xu, Xiaolei

    2012-01-01

    Zebrafish embryo becomes a popular in vivo vertebrate model for studying cardiac development and human heart diseases due to its advantageous embryology and genetics. About 100-200 embryos are readily available every week from a single pair of adult fish. The transparent embryos that develop ex utero make them ideal for assessing cardiac defects. The expression of any gene can be manipulated via morpholino technology or RNA injection. Moreover, forward genetic screens have already generated a list of mutants that affect different perspectives of cardiogenesis. Whole mount immunostaining is an important technique in this animal model to reveal the expression pattern of the targeted protein to a particular tissue. However, high resolution images that can reveal cellular or subcellular structures have been difficult, mainly due to the physical location of the heart and the poor penetration of the antibodies. Here, we present a method to address these bottlenecks by dissecting heart first and then conducting the staining process on the surface of a microscope slide. To prevent the loss of small heart samples and to facilitate solution handling, we restricted the heart samples within a circle on the surface of the microscope slides drawn by an immEdge pen. After the staining, the fluorescence signals can be directly observed by a compound microscope. Our new method significantly improves the penetration for antibodies, since a heart from an embryonic fish only consists of few cell layers. High quality images from intact hearts can be obtained within a much reduced procession time for zebrafish embryos aged from day 2 to day 6. Our method can be potentially extended to stain other organs dissected from either zebrafish or other small animals. PMID:22258109

  9. Pediatric traumatic carotid, vertebral and cerebral artery dissections: a review.

    PubMed

    Mortazavi, Martin M; Verma, Ketan; Tubbs, R Shane; Harrigan, Mark

    2011-12-01

    Traumatic cerebral dissections are rare but potentially dangerous conditions that through improved diagnostics have recently gained increased interest. However, there is still a significant lack of knowledge on the natural history, as well as on the best treatment options. Most of the literature on this topic consists of case reports and retrospective studies with no prospective randomized controlled studies. In our review, we highlight the fact that there is no level 1 evidence for the natural history of cerebral dissections or for the best treatment. We present 26 case studies derived from 70 pediatric patients affected by dissections, occlusions, and pseudoaneurysms. PMID:21318614

  10. Differential Phosphoproteome Regulation of Nucleus Accumbens in Environmentally Enriched and Isolated Rats in Response to Acute Stress

    PubMed Central

    Fan, Xiuzhen; Li, Dingge; Zhang, Yafang; Green, Thomas A.

    2013-01-01

    Increasing evidence shows that stress contributes to the pathogenesis of major depressive disorder which is a severe neuropsychiatric disorder and influences over 10% of the world's population. Our previous studies revealed that rats reared in an enriched environment display less depression-related behavior compared to rats raised in an isolated environment, which implies that environmental enrichment produces an antidepressant-like behavioral phenotype. However, the molecular mechanisms are not fully understood. Protein phosphorylation rapidly changes signaling pathway function and alters the function of proteins associated with the stress-induced depressive disorder. Thus, in this study, a phosphoproteomic approach was used to uncover differential phosphoprotein regulation in rat nucleus accumbens between isolated (IC) and enriched environmental conditions (EC) under basal conditions, and in response to acute stress. We found 23 phosphoproteins were regulated in EC vs. IC rats under basal conditions; 10 phosphoproteins regulated by stress in IC rats; and 15 regulated by stress in EC rats. Among all significantly regulated phosphoproteins, 11 of them were represented in at least two conditions. The regulated phosphoproteins represent signaling pathway proteins (including ERK2), enzymes, transcriptional regulators, protein translation regulators, transporters, chaperones and cytoskeletal proteins. These findings provide a global view for further understanding the contribution of protein phosphorylation in depression pathogenesis and antidepressant action. PMID:24278208

  11. A phosphoproteomic screen demonstrates differential dependence on HER3 for MAP kinase pathway activation by distinct PIK3CA mutations.

    PubMed

    Blair, Brian G; Wu, Xinyan; Zahari, Muhammad Saddiq; Mohseni, Morassa; Cidado, Justin; Wong, Hong Yuen; Beaver, Julia A; Cochran, Rory L; Zabransky, Daniel J; Croessmann, Sarah; Chu, David; Toro, Patricia Valda; Cravero, Karen; Pandey, Akhilesh; Park, Ben Ho

    2015-01-01

    The PIK3CA gene encodes for the p110 alpha isoform of PI3 kinase and is one of the most frequently mutated oncogenes in human cancers. However, the mechanisms by which PIK3CA mutations activate cell signaling are not fully understood. Here we used a phosphoproteomic approach to compare differential phosphorylation patterns between human breast epithelial cells and two isogenic somatic cell knock in derivatives, each harboring a distinct PIK3CA mutation. We demonstrated differential phosphorylation patterns between isogenic cell lines containing a PIK3CA helical domain mutation (E545K) compared to cells with a PIK3CA kinase domain mutation (H1047R). In particular, the receptor tyrosine kinase, HER3, showed increased phosphorylation at tyrosine 1328 in H1047R cells versus E545K cells. Genetic studies using shRNA demonstrated that H1047R cells have a profound decrease in growth factor independent proliferation upon HER3 knock down, but this effect was attenuated in E545K cells. In addition, HER3 knock down led to reductions in both PI3 kinase and MAP kinase pathway activation in H1047R cells, but in E545K cells only PI3 kinase pathway diminution was observed. These studies demonstrate the power of using paired isogenic cell lines for proteomic analysis to gain new insights into oncogenic signal transduction pathways. PMID:25367220

  12. Phosphoproteomics reveals resveratrol-dependent inhibition of Akt/mTORC1/S6K1 signaling.

    PubMed

    Alayev, Anya; Doubleday, Peter F; Berger, Sara Malka; Ballif, Bryan A; Holz, Marina K

    2014-12-01

    Resveratrol, a plant-derived polyphenol, regulates many cellular processes, including cell proliferation, aging and autophagy. However, the molecular mechanisms of resveratrol action in cells are not completely understood. Intriguingly, resveratrol treatment of cells growing in nutrient-rich conditions induces autophagy, while acute resveratrol treatment of cells in a serum-deprived state inhibits autophagy. In this study, we performed a phosphoproteomic analysis after applying resveratrol to serum-starved cells with the goal of identifying the acute signaling events initiated by resveratrol in a serum-deprived state. We determined that resveratrol in serum-starved conditions reduces the phosphorylation of several proteins belonging to the mTORC1 signaling pathway, most significantly, PRAS40 at T246 and S183. Under these same conditions, we also found that resveratrol altered the phosphorylation of several proteins involved in various biological processes, most notably transcriptional modulators, represented by p53, FOXA1, and AATF. Together these data provide a more comprehensive view of both the spectrum of phosphoproteins upon which resveratrol acts as well as the potential mechanisms by which it inhibits autophagy in serum-deprived cells. PMID:25311616

  13. Comparative phosphoproteome profiling reveals a function of the STN8 kinase in fine-tuning of cyclic electron flow (CEF)

    PubMed Central

    Reiland, Sonja; Finazzi, Giovanni; Endler, Anne; Willig, Adrian; Baerenfaller, Katja; Grossmann, Jonas; Gerrits, Bertran; Rutishauser, Dorothea; Gruissem, Wilhelm; Rochaix, Jean-David; Baginsky, Sacha

    2011-01-01

    Important aspects of photosynthetic electron transport efficiency in chloroplasts are controlled by protein phosphorylation. Two thylakoid-associated kinases, STN7 and STN8, have distinct roles in short- and long-term photosynthetic acclimation to changes in light quality and quantity. Although some substrates of STN7 and STN8 are known, the complexity of this regulatory kinase system implies that currently unknown substrates connect photosynthetic performance with the regulation of metabolic and regulatory functions. We performed an unbiased phosphoproteome-wide screen with Arabidopsis WT and stn8 mutant plants to identify unique STN8 targets. The phosphorylation status of STN7 was not affected in stn8, indicating that kinases other than STN8 phosphorylate STN7 under standard growth conditions. Among several putative STN8 substrates, PGRL1-A is of particular importance because of its possible role in the modulation of cyclic electron transfer. The STN8 phosphorylation site on PGRL1-A is absent in both monocotyledonous plants and algae. In dicots, spectroscopic measurements with Arabidopsis WT, stn7, stn8, and stn7/stn8 double-mutant plants indicate a STN8-mediated slowing down of the transition from cyclic to linear electron flow at the onset of illumination. This finding suggests a possible link between protein phosphorylation by STN8 and fine-tuning of cyclic electron flow during this critical step of photosynthesis, when the carbon assimilation is not commensurate to the electron flow capacity of the chloroplast. PMID:21768351

  14. Applications of quantitative whole body autoradiographic technique in radiopharmaceutical research

    SciTech Connect

    Som, P.; Oster, Z.H.; Yonekura, Y.; Meyer, M.A.; Fand, I.; Brill, A.B.

    1982-01-01

    The routine evaluation of radiopharmaceuticals involves dissecting tissue distribution studies (DTDS) and gamma or positron imaging. DTDS have the following disadvantages: since not all tissues can always be sampled, sites of radiopharmaceutical uptake may be missed and because the procedure involves weighing of dissected tissue samples, the spatial resolution of this method is low and determined by the smallest amount that can be weighed accurately. Gamma camera imaging and positron emission tomography though more comprehensive in evaluating the global distribution of a compound, have relative low spatial resolution. Whole body autoradiography of small animals has a much higher spatial resolution as compared to the above and depicts the global distribution of radiopharmaceuticals. A computer-assisted quantification method of WBARG applied to positron, beta, and gamma emitters will complement the method by producing quantitative values comparable to those obtained by dissection and direct tissue counting, with the advantages of depicting the global distribution at high spatial resolution.

  15. Dissection of the Hyperadhesive Phenotype of Airway Eosinophils in Asthma

    E-print Network

    Mosher, Deane F.

    Dissection of the Hyperadhesive Phenotype of Airway Eosinophils in Asthma Steven R. Barthel, Nizar, and Department of Medicine, University of Wisconsin­Madison, Madison, Wisconsin Asthma is characterized. Keywords: adhesion molecules; cell trafficking; eosinophils; human Asthma is an inflammatory syndrome

  16. Spontaneous Coronary Artery Dissection: Not Just a Heart Attack

    MedlinePLUS

    Spontaneous Coronary Artery Dissection: Not Just a Heart Attack Updated:May 15,2015 Sometimes a heart attack is not just a ... the result of spontaneous tearing in the coronary artery wall. The artery wall has three layers and ...

  17. Cadaver Dissection and the Ritual Transformation of Medical Students

    E-print Network

    Laudermilk, Ryan

    2011-12-31

    Human cadaver dissection is a common component of Western medical education. While most students react emotionally to the presence of such a deeply-held symbol of death, the expression of emotion is often seen as unprofessional, ...

  18. On Quantitizing

    PubMed Central

    Sandelowski, Margarete; Voils, Corrine I.; Knafl, George

    2009-01-01

    Quantitizing, commonly understood to refer to the numerical translation, transformation, or conversion of qualitative data, has become a staple of mixed methods research. Typically glossed are the foundational assumptions, judgments, and compromises involved in converting disparate data sets into each other and whether such conversions advance inquiry. Among these assumptions are that qualitative and quantitative data constitute two kinds of data, that quantitizing constitutes a unidirectional process essentially different from qualitizing, and that counting is an unambiguous process. Among the judgments are deciding what and how to count. Among the compromises are balancing numerical precision with narrative complexity. The standpoints of “conditional complementarity,” “critical remediation,” and “analytic alternation” clarify the added value of converting qualitative data into quantitative form. PMID:19865603

  19. Peripartum acute aortic dissection: A case report & review of literature.

    PubMed

    Aziz, Fahad; Penupolu, Sudheer; Alok, Anshu; Doddi, Sujatha; Abed, Mary

    2011-03-01

    Acute aortic dissection is a rare clinical entity that mainly affects patients older than 50 years. It is unusual in younger patients and its presence has been traditionally associated with trauma, Marfan syndrome, bicuspid aortic valve and pregnancy. We present here, a case of a 30 year old pregnant female with acute aortic dissection type A (De Bakey II), without family history of connective tissue diseases and signs of Marfan syndrome. PMID:22263062

  20. Emergency stent grafting of type B aortic dissection: technical considerations

    Microsoft Academic Search

    Tommaso Lupattelli; Francesco Giuseppe Garaci; Antonio Basile; Andrea Casini; Ilias Dalainas; Daniela Paola Minnella; Roberto Iezzi

    2008-01-01

    Type B aortic dissection is an uncommon yet potentially catastrophic clinical event that mandates prompt recognition and expeditious\\u000a treatment. Patient survival depends on early and accurate diagnosis and prompt medical or surgical treatment. Unfortunately,\\u000a when type B aortic dissection is associated with end-organ ischemia, medical treatment may not prove beneficial, with patients\\u000a addressed to surgery; recently, either percutaneous fenestration or

  1. Stroke prevention and treatment in patients with spontaneous carotid dissection

    Microsoft Academic Search

    Ralf W. Baumgartner

    This review on spontaneous dissection of the internal carotid artery (sICAD) will discuss in the first part stroke prevention\\u000a and focus on vascular risk factors, antithrombotic therapy, and treatment of severe stenosis or occlusion, and dissecting\\u000a aneurysm. The second part of the review will summarize the treatment of acute ischemic stroke due to sICAD.

  2. Vertebral artery stenting in an aneurysm after dissection

    Microsoft Academic Search

    B. Griewing; F. Brassel; V. Schminke

    2000-01-01

    Purpose: Traumatic and spontaneous dissections of brain-supplying arteries are the cause of approximately 5% of cerebral infarctions in young adults. They are localized more often in the carotid, and less frequently in vertebral arteries. Aneurysms following dissections, which can develop as a possible embolic source, are generally treated with endovascular surgery.Methods: We describe the case of a 42-year-old man who

  3. Primary headaches and painful spontaneous cervical artery dissection

    Microsoft Academic Search

    Cynthia R. Campos; Marcelo Calderaro; Milberto Scaff; Adriana B. Conforto

    2007-01-01

    The relation between primary headaches (PH) and pain related to spontaneous cervical artery dissection (SCAD) is still unclear,\\u000a as well as the progress of PH after dissection. To investigate this relation, the characteristics of pain related to SCAD\\u000a and changes in PH patterns after SCAD, we evaluated 54 consecutive patients. Thirty-five (65%) had previous PH. Painful SCAD\\u000a occurred in 39

  4. A Modified Dissection Method to Preserve Neck Structures

    NSDL National Science Digital Library

    Mark Hankin (Toledo Neurosciences)

    2009-07-27

    This article provides two simple modifications for dissection of the neck that (1) aid in the identification and preservation of the cutaneous branches of the cervical plexus and the accessory nerve, and (2) provide wide exposure of the root of the neck. These modified procedures can be readily performed by first-year medical students and integrate well with methods described in widely used anatomy dissection manuals.

  5. “Curettage and aspiration dissection technique” using PMOD for liver resection

    PubMed Central

    Peng, S. Y.

    2008-01-01

    Background and aims. To introduce a special dissection technique named “Curettage and Aspiration Dissection Technique” (CADT) using a versatile instrument called Peng's Multifunction Operative Dissector (PMOD) for liver resection. PMOD is an electrosurgical pencil with an inline suction, bearing four functions: electric cutting, coagulation, aspiration and dissection, The above-mentioned functions can be achieved simultaneously or sequentially during liver resection. The purpose of this study was to evaluate this technique and the special electrosurgical device in hepatic surgery. Patients and methods. From June 2005 to December 2006, 70 consecutive patients with segmentectomy or major hepatectomy were performed with this dissection technique by the same surgeon. Peri-operative data and the technical aspect of this device and dissection technique for various types of liver resection were summarised. Results. Forty-nine of 70 cases with various degrees of cirrhosis. Median blood loss were 470 ml (100–2400 ml), the bleeding and mortality within one month postoperatively was zero. There were postoperative complications in 20 patients: bile leak occurred in five cases, nine cases with right pleural effusion and six with ascites. No relative complications with this method were found. Conclusion. The CADT and PMOD can achieve better dissection and hemostasis. It possible is a much more valuable alternative to other devices currently used for liver surgery. PMID:18773106

  6. Large-scale determination of absolute phosphorylation stoichiometries in human cells by motif-targeting quantitative proteomics.

    PubMed

    Tsai, Chia-Feng; Wang, Yi-Ting; Yen, Hsin-Yung; Tsou, Chih-Chiang; Ku, Wei-Chi; Lin, Pei-Yi; Chen, Hsuan-Yu; Nesvizhskii, Alexey I; Ishihama, Yasushi; Chen, Yu-Ju

    2015-01-01

    Our ability to model the dynamics of signal transduction networks will depend on accurate methods to quantify levels of protein phosphorylation on a global scale. Here we describe a motif-targeting quantitation method for phosphorylation stoichiometry typing. Proteome-wide phosphorylation stoichiometry can be obtained by a simple phosphoproteomic workflow integrating dephosphorylation and isotope tagging with enzymatic kinase reaction. Proof-of-concept experiments using CK2-, MAPK- and EGFR-targeting assays in lung cancer cells demonstrate the advantage of kinase-targeted complexity reduction, resulting in deeper phosphoproteome quantification. We measure the phosphorylation stoichiometry of >1,000 phosphorylation sites including 366 low-abundance tyrosine phosphorylation sites, with high reproducibility and using small sample sizes. Comparing drug-resistant and sensitive lung cancer cells, we reveal that post-translational phosphorylation changes are significantly more dramatic than those at the protein and messenger RNA levels, and suggest potential drug targets within the kinase-substrate network associated with acquired drug resistance. PMID:25814448

  7. Open Retrograde Endovascular Stenting for Left Common Carotid Artery Dissection Secondary to Surgical Repair of Acute Aortic Dissection: A Case Report and Review of the Literature.

    PubMed

    Gao, Peng; Wang, Yabing; Chen, Yanfei; Jiao, Liqun

    2015-07-01

    A 30-year-old male presented with an acute aortic artery dissection (Stanford type A) and underwent total arch replacement using a stented elephant trunk technique. One month later, the patient developed dissections in the innominate and left common carotid artery (CCA). The innominate artery dissection caused occlusion in the right internal carotid artery (ICA) and a major stroke. Dissection of the left CCA progressed and extended to the bifurcation site. Antegrade access for a left carotid intervention was deemed as difficult because of the previously implanted stent and the additional risks of embolic events and dissection enlargement. Hybrid procedures combining left carotid bifurcation exposure and retrograde endovascular stenting were successfully completed. This report is a rare case of retrograde endovascular reconstruction for the left CCA dissection following surgical repair of an aortic artery dissection. Here, we also review previous cases of iatrogenic carotid dissections following surgical intervention. PMID:25765635

  8. AACR 2015: Proteogenomics and Phosphoproteomics in Cancer: Analysis of the TCGA Tumor Samples

    Cancer.gov

    The Cancer Genome Atlas has provided an important foundation for understanding the scope and relationships of genomic alterations in human cancers. The National Cancer Institute recognized that global proteomic characterization of genomically annotated TCGA samples, leveraging recent dramatic improvements in the depth and quantitative capability of mass spectrometry-based proteomics, could provide complementary as well as unique information about cancer biology and signaling that cannot be inferred from genomic analyses alone.

  9. A Second-Generation Device for Automated Training and Quantitative Behavior Analyses of Molecularly-Tractable Model Organisms

    Microsoft Academic Search

    Douglas Blackiston; Tal Shomrat; Cindy L. Nicolas; Christopher Granata; Michael Levin

    2010-01-01

    A deep understanding of cognitive processes requires functional, quantitative analyses of the steps leading from genetics and the development of nervous system structure to behavior. Molecularly-tractable model systems such as Xenopus laevis and planaria offer an unprecedented opportunity to dissect the mechanisms determining the complex structure of the brain and CNS. A standardized platform that facilitated quantitative analysis of behavior

  10. Spontaneous vertebral dissection: Clinical, conventional angiographic, CT, and MR findings

    SciTech Connect

    Provenzale, J.M.; Morgenlander, J.C. [Duke Univ. Medical Center, Durham, NC (United States)] [Duke Univ. Medical Center, Durham, NC (United States); Gress, D. [Univ. of California, San Francisco, CA (United States)] [Univ. of California, San Francisco, CA (United States)

    1996-03-01

    The purpose of this study was to determine if typical clinical and neuroradiologic patterns exist in patients with spontaneous vertebral artery (VA) dissection. The medical records and neuroradiologic examinations of 14 patients with spontaneous VA dissection were reviewed. The medical records were examined to exclude patients with a history of trauma and to record evidence of a nontratimatic precipitating event ({open_quotes}trivial trauma{close_quotes}) and presence of possible risk factors such as hypertension. All patients under-went conventional angiography, 13 either CT or MRI (II both CT and MRI), and 3 MRA. Conventional arteriograrris were evaluated for dissection site, evidence of fibromuscular dysplasia, luminal stenosis or occlusion, and pseudoaneurysm formation, CT examinations for the presence of infarction or subarachnoid hemorrhage, MR examinations for the presence of infarction or arterial signal abnormality, and MR angiograms for abnormality of the arterial signal column. Seven patients had precipitating events within 24 h of onset of symptoms that may have been causative of dissection and five had hypertension. At catheter angiography, two patients had dissections in two arteries (both VAs in one patient, VA and internal carotid artery in one patient), giving a total of 15 VAs with dissection. Dissection sites included V1 in four patients, V2 in one patient, V3 in three patients, V4 in six patients, and both V3 and V4 in one patient. Luminal stenosis was present in 13 VAs, occlusion in 2, pseudoaneurysm in 1, and evidence of fibromuscular dysplasia in 1. Posterior circulation infarcts were found on CT or MR in five patients. Subarachnoid hemorrhage was found on CT in two patients and by lumbar puncture alone in two patients. Abnormal periarterial signal on MRI was seen in three patients. MRA demonstrated absent VA signal in one patient, pseudoaneurysm in one, and a false-negative examination in one.

  11. Unraveling pancreatic islet biology by quantitative proteomics

    SciTech Connect

    Zhou, Jianying; Dann, Geoffrey P.; Liew, Chong W.; Smith, Richard D.; Kulkarni, Rohit N.; Qian, Weijun

    2011-08-01

    The pancreatic islets of Langerhans play a critical role in maintaining blood glucose homeostasis by secreting insulin and several other important peptide hormones. Impaired insulin secretion due to islet dysfunction is linked to the pathogenesis underlying both Type 1 and Type 2 diabetes. Over the past 5 years, emerging proteomic technologies have been applied to dissect the signaling pathways that regulate islet functions and gain an understanding of the mechanisms of islet dysfunction relevant to diabetes. Herein, we briefly review some of the recent quantitative proteomic studies involving pancreatic islets geared towards gaining a better understanding of islet biology relevant to metabolic diseases.

  12. Proteome and phosphoproteome analysis of honeybee (Apis mellifera) venom collected from electrical stimulation and manual extraction of the venom gland

    PubMed Central

    2013-01-01

    Background Honeybee venom is a complicated defensive toxin that has a wide range of pharmacologically active compounds. Some of these compounds are useful for human therapeutics. There are two major forms of honeybee venom used in pharmacological applications: manually (or reservoir disrupting) extracted glandular venom (GV), and venom extracted through the use of electrical stimulation (ESV). A proteome comparison of these two venom forms and an understanding of the phosphorylation status of ESV, are still very limited. Here, the proteomes of GV and ESV were compared using both gel-based and gel-free proteomics approaches and the phosphoproteome of ESV was determined through the use of TiO2 enrichment. Results Of the 43 proteins identified in GV, < 40% were venom toxins, and >?60% of the proteins were non-toxic proteins resulting from contamination by gland tissue damage during extraction and bee death. Of the 17 proteins identified in ESV, 14 proteins (>80%) were venom toxic proteins and most of them were found in higher abundance than in GV. Moreover, two novel proteins (dehydrogenase/reductase SDR family member 11-like and histone H2B.3-like) and three novel phosphorylation sites (icarapin (S43), phospholipase A-2 (T145), and apamin (T23)) were identified. Conclusions Our data demonstrate that venom extracted manually is different from venom extracted using ESV, and these differences may be important in their use as pharmacological agents. ESV may be more efficient than GV as a potential pharmacological source because of its higher venom protein content, production efficiency, and without the need to kill honeybee. The three newly identified phosphorylated venom proteins in ESV may elicit a different immune response through the specific recognition of antigenic determinants. The two novel venom proteins extend our proteome coverage of honeybee venom. PMID:24199871

  13. Phosphoproteomic analysis of basal and therapy-induced adaptive signaling networks in BRAF and NRAS mutant melanoma.

    PubMed

    Fedorenko, Inna V; Fang, Bin; Munko, Ana Cecelia; Gibney, Geoffrey T; Koomen, John M; Smalley, Keiran S M

    2015-01-01

    Basal and kinase inhibitor driven adaptive signaling has been examined in a panel of melanoma cell lines using phosphoproteomics in conjunction with pathway analysis. A considerable divergence in the spectrum of tyrosine-phosphorylated peptides was noted at the cell line level. The unification of genotype-specific cell line data revealed the enrichment for the tyrosine-phosphorylated cytoskeletal proteins to be associated with the presence of a BRAF mutation and oncogenic NRAS to be associated with increased receptor tyrosine kinase phosphorylation. A number of proteins including cell cycle regulators (cyclin dependent kinase 1, cyclin dependent kinase 2, and cyclin dependent kinase 3), MAPK pathway components (Extracellular signal regulated kinase 1 and Extracellular signal regulated kinase 2), interferon regulators (tyrosine kinase-2), GTPase regulators (Ras-Rasb interactor 1), and controllers of protein tyrosine phosphorylation (dual specificity tyrosine (Y) phosphorylation regulated kinase 1A and protein tyrosine phosphatase receptor type A) were common to all genotypes. Treatment of a BRAF-mutant/phosphatase and tensin homologue (PTEN) null melanoma cell line with vemurafenib led to decreased phosphorylation of ERK, phospholipase C1, and ?-catenin with increases in receptor tyrosine kinase phosphorylation, signal transduction and activator of signaling 3, and glycogen synthase kinase 3? noted. In NRAS-mutant melanoma, MEK inhibition led to increased phosphorylation of epidermal growth factor receptor signaling pathway components, Src family kinases, and protein kinase C? with decreased phosphorylation seen in STAT3 and ERK1/2. Together these data present the first systems level view of adaptive and basal phosphotyrosine signaling in BRAF- and NRAS-mutant melanoma. PMID:25339196

  14. Phosphoproteomic Analysis of KSHV-Infected Cells Reveals Roles of ORF45-Activated RSK during Lytic Replication

    PubMed Central

    Avey, Denis; Tepper, Sarah; Li, Wenwei; Turpin, Zachary; Zhu, Fanxiu

    2015-01-01

    Kaposi’s Sarcoma-Associated Herpesvirus (KSHV) is an oncogenic virus which has adapted unique mechanisms to modulate the cellular microenvironment of its human host. The pathogenesis of KSHV is intimately linked to its manipulation of cellular signaling pathways, including the extracellular signal-regulated kinase (ERK) mitogen-activated protein kinase (MAPK) pathway. We have previously shown that KSHV ORF45 contributes to the sustained activation of both ERK and p90 ribosomal S6 kinase (RSK, a major functional mediator of ERK/MAPK signaling) during KSHV lytic replication. ORF45-activated RSK is required for optimal KSHV lytic gene expression and progeny virion production, though the underlying mechanisms downstream of this activation are still unclear. We hypothesized that the activation of RSK by ORF45 causes differential phosphorylation of cellular and viral substrates, affecting biological processes essential for efficient KSHV lytic replication. Accordingly, we observed widespread and significant differences in protein phosphorylation upon induction of lytic replication. Mass-spectrometry-based phosphoproteomic screening identified putative substrates of ORF45-activated RSK in KSHV-infected cells. Bioinformatic analyses revealed that nuclear proteins, including several transcriptional regulators, were overrepresented among these candidates. We validated the ORF45/RSK-dependent phosphorylation of several putative substrates by employing KSHV BAC mutagenesis, kinase inhibitor treatments, and/or CRISPR-mediated knockout of RSK in KSHV-infected cells. Furthermore, we assessed the consequences of knocking out these substrates on ORF45/RSK-dependent regulation of gene expression and KSHV progeny virion production. Finally, we show data to support that ORF45 regulates the translational efficiency of a subset of viral/cellular genes with complex secondary structure in their 5’ UTR. Altogether, these data shed light on the mechanisms by which KSHV ORF45 manipulates components of the host cell machinery via modulation of RSK activity. Thus, this study has important implications for the pathobiology of KSHV and other diseases in which RSK activity is dysregulated. PMID:26133373

  15. 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 different radiation doses and elucidate the impact of low dose radiation exposure on human health.

  16. Phosphoproteomic analysis of mouse thymoma cells treated with tributyltin oxide: TBTO affects proliferation and energy sensing pathways.

    PubMed

    Osman, Ahmed M; van Loveren, Henk

    2012-03-01

    We report the results of phosphoproteomic analysis of mouse thymoma cells treated with tributyltin oxide (TBTO), an immunotoxic compound. After cell lysis, phosphoproteins were isolated using Phosphoprotein Purification Kit, separated by SDS-PAGE and subsequently digested with trypsin. Phosphopeptides were enriched employing titanium dioxide, and the obtained fractions were analyzed by nano-LC-MS/MS. A total of 160 phosphoproteins and 328 phosphorylation sites were identified in thymoma cells. Among the differentially phosphorylated proteins identified in TBTO-treated cells were key enzymes, which catalyze rate-limiting steps in pathways that are sensitive to cellular energy status. These proteins included acetyl-CoA carboxylase isoform 1, which catalyzes the rate-limiting step of fatty acid synthesis. Another enzyme was glutamine: fructose-6-phosphate amidotransferase, GFAT1, the first and rate-limiting enzyme for the hexoamine synthesis pathway. Pyruvate dehydrogenase (PDH), a multicomplex enzyme that catalyzes the rate-limiting step of aerobic oxidation of fuel carbohydrates, was identified in both TBTO-treated and control cells; however, phosphorylation at residue S293, known to inhibit PDH activity, was identified only in control cells. A lower expression level of ribosomal protein S6 kinase 1, a downstream kinase of the mammalian target of rapamycin signaling pathway implicated in protein synthesis through phosphorylation of 40 ribosomal S6, was observed in the treated cells. Giant kinases like AMP-activated protein kinase (AMPK) and cAMP-dependent protein kinase (PKAR1A), which are known to mediate the phosphorylation of these enzymes, were identified in TBTO-treated cells. Downregulation of proteins, such as MAPK, matrin-3 and ribonucleotide reductase, subunit RRM2, which are implicated in cell proliferation, was also observed in TBTO-treated cells. Together, the results show that TBTO affects proliferation and energy sensor pathways. PMID:22174045

  17. Comparative phosphoproteomic analysis of mammalian glomeruli reveals conserved podocin C-terminal phosphorylation as a determinant of slit diaphragm complex architecture.

    PubMed

    Rinschen, Markus M; Pahmeyer, Caroline; Pisitkun, Trairak; Schnell, Nicole; Wu, Xiongwu; Maaß, Martina; Bartram, Malte P; Lamkemeyer, Tobias; Schermer, Bernhard; Benzing, Thomas; Brinkkoetter, Paul T

    2015-04-01

    Glomerular biology is dependent on tightly controlled signal transduction networks that control phosphorylation of signaling proteins such as cytoskeletal regulators or slit diaphragm proteins of kidney podocytes. Cross-species comparison of phosphorylation events is a powerful mean to functionally prioritize and identify physiologically meaningful phosphorylation sites. Here, we present the result of phosphoproteomic analyses of cow and rat glomeruli to allow cross-species comparisons. We discovered several phosphorylation sites with potentially high biological relevance, e.g. tyrosine phosphorylation of the cytoskeletal regulator synaptopodin and the slit diaphragm protein neph-1 (Kirrel). Moreover, cross-species comparisons revealed conserved phosphorylation of the slit diaphragm protein nephrin on an acidic cluster at the intracellular terminus and conserved podocin phosphorylation on the very carboxyl terminus of the protein. We studied a highly conserved podocin phosphorylation site in greater detail and show that phosphorylation regulates affinity of the interaction with nephrin and CD2AP. Taken together, these results suggest that species comparisons of phosphoproteomic data may reveal regulatory principles in glomerular biology. All MS data have been deposited in the ProteomeXchange with identifier PXD001005 (http://proteomecentral.proteomexchange.org/dataset/PXD001005). PMID:25420462

  18. Proximity injury by the ultrasonically activated scalpel during dissection.

    PubMed

    Kadesky, K M; Schopf, B; Magee, J F; Blair, G K

    1997-06-01

    The ultrasonically activated scalpel is a high-frequency oscillating instrument that is reported to have a decreased dispersion of energy to surrounding tissues during use. To determine if this effect is beneficial and safe to surrounding tissue, it was used on anesthetized adolescent swine to dissect the portal vein from the pancreas, the renal artery and vein from the renal hilum, the ureter from the retroperitoneum, the aorta from the inferior vena cava and the common bile duct from surrounding tissue. Three-second contact to intestine and nerve roots was also performed. Wedge biopsy specimens of liver and spleen were performed. Dissection technique used was as described by the company. Structures were dissected with electrocautery using similar techniques for comparison. Tissues were harvested and placed in formalin for histological analysis. Dissection with the ultrasonically activated scalpel was simple, achieved excellent hemostasis, and did not appear to damage adjacent tissue. Microscopic analysis showed adventicial and media injury to vascular structures. The ureter and common bile duct demonstrated marked injury with regions of transmural coagulation. Nerve and small bowel did not appear to have much injury from the 3-second contact with the instrument. This study indicated that although the ultrasonically activated scalpel can ease dissection with good hemostasis, care must be taken to avoid injury to adjacent structures. Although its lateral energy dispersion may be less than that of cautery, it can still cause transmural necrosis to major structures. PMID:9200091

  19. Aortic Dissection in Young Adults Who Abuse Amphetamines

    PubMed Central

    Westover, Arthur N.; Nakonezny, Paul A.

    2010-01-01

    Background Case reports suggest a relationship between amphetamine abuse/dependence and aortic dissection, but no population-based epidemiologic studies have examined this link. Our objective was to test the hypothesis that young adults with a diagnosis of amphetamine abuse or dependence would be at higher risk for aortic dissection, after accounting for known risk factors. Methods In this population-based case control study of 30,922,098 discharges from the Healthcare Cost and Utilization Project (HCUP) Nationwide Inpatient Sample (NIS) from 1995 to 2007, among persons aged 18 to 49 years, we identified 3,116 thoracic and thoracoabdominal aortic dissections using ICD-9-CM codes 441.01 and 441.03. The SURVEYLOGISTIC procedure in SAS 9.2 was used to account for the NIS sampling methodology. Results In a multiple logistic regression analysis, while controlling for known risk factors, amphetamine abuse/dependence was significantly associated with aortic dissection (adjusted odds ratio = 3.33; 95% CI=2.37—4.69, p < 0.0001). Conclusions This statistically significant association suggests that amphetamine abuse/dependence may play a role in aortic dissection in young adults in the United States. PMID:20691838

  20. A Simple Emergency Prediction Tool for Acute Aortic Dissection

    PubMed Central

    Peng, Wen; Zhu, Qing-yi; Zhou, Xiang-hong; Chai, Xiang-ping

    2013-01-01

    Abstract Background A simple emergency risk prediction tool should be developed for clinicians to quickly identify the prognosis of patients with acute aortic dissection. Methods We enrolled 280 patients with acute aortic dissection admitted to emergency department between May 2010 and February 2013. Multivariate logistic regression analysis was performed to identify independent predictors of in-hospital death. Results The in-hospital mortality of our patients with acute aortic dissection was 32.5%, in-hospital deaths with surgery less than the survived (34.1% VS 54.5%). Multivariate analysis identified that age (?65 years old), Type A, blood pressure (mean systolic blood pressure ? 90 mmHg), neutrophil percentage (? 80%) and serum D-dimer (? 5.0 mg/L) were significant predictors of death. With the simple emergency risk prediction tool, scores of all in-hospital deaths were ? 3, whereas almost all of the survivors (97.9%) had scores < 15. A score of 10 offered the best threshold value, with the highest sensitivity (81.3%) and specificity (86.8%). Conclusions The in-hospital mortality rate of patients with acute aortic dissection is high and can be predicted. Early surgery would be beneficial for in-hospital survive. This tool should be available for clinicians in the emergency department to quickly identify the prognosis of patients with acute aortic dissection.

  1. Molecular dissection of phenotypic variation between Gossypium hirsutum and Gossypium barbadense (cotton) by a backcross-self approach: III. Fiber length

    Microsoft Academic Search

    Peng W. Chee; Xavier Draye; Chun-Xiao Jiang; Laura Decanini; Terrie A. Delmonte; Robert Bredhauer; C. Wayne Smith; Andrew H. Paterson

    2005-01-01

    A backcross-self population from a cross between Gossypium hirsutum and G. barbadense was used to dissect the molecular basis of genetic variation governing 15 parameters that reflect fiber length. Applying a detailed restriction fragment length polymorphism (RFLP) map to 3,662 BC3F2 plants from 24 independently derived BC3 families, we detected 28, nine, and eight quantitative trait loci (QTLs) for fiber

  2. Second Harmonic Generation, Sum Frequency Generation, and ?(3): Dissecting Environmental Interfaces with a Nonlinear Optical Swiss Army Knife

    NASA Astrophysics Data System (ADS)

    Geiger, Franz M.

    2009-05-01

    This review discusses recent advances in the nonlinear optics of environmental interfaces. We discuss the quantitative aspects of the label-free approaches presented here and demonstrate that nonlinear optics has now assumed the role of a Swiss Army knife that can be used to dissect, with molecular detail, the fundamental and practical aspects of environmental interfaces and heterogeneous geochemical environments. In this work, nonlinear optical methods are applied to complex organic molecules, such as veterinary antibiotics, and to small inorganic anions and cations, such as nitrate and chromate, or cadmium, zinc, and manganese. The environmental implications of the thermodynamic, kinetic, spectroscopic, structural, and electrochemical data are discussed.

  3. A standardized surgical technique for mastoscopic axillary lymph node dissection.

    PubMed

    Chengyu, Luo; Yongqiao, Zhou; Hua, Lin; Xiaoxin, Ji; Chen, Guan; Jing, Li; Jian, Zhang

    2005-06-01

    To standardize the surgical technique for mastoscopic axillary lymph node dissection (MALND). Mastoscopic lymph node dissection was performed consistently by a group of surgeons in 316 cases of breast cancer. The mean operation time was 46.7 minutes with minimal bleeding, and the median number of lymph nodes dissected at each operation was 17.0. There were no operative complications in any case, nor did trocar implantation or tumor diffusion occurring during the mean follow-up time of 15.1 months. MALND is distinctive and practicable in operative anatomy as well as safe and convenient. The location of critical anatomy such as the intercostobrachial nerve, lateral thoracic artery, medial thoracic nerve, and thoracoepigastric vein should be clearly identified to avoid damage to them, so that is the great advantage of MALND. PMID:15956900

  4. Free manual of cadaver dissection modifiable by other anatomists.

    PubMed

    Chung, Beom Sun; Chung, Min Suk

    2015-06-01

    Even in the rapidly changing field of cadaver dissection, published guide books still play an important role in the anatomy lab. However, commercial manuals with lengthy volumes and inflexible copyrights have several limitations which can be complemented by open-source manuals. Recently, the authors have manufactured and distributed a free electronic dissection manual (anatomy.co.kr), where descriptions are written concisely and images are drawn schematically. Moreover, simplified signs are employed to represent the cadaver viewing angles and manner of dissection. Based on the original files of this manual, other anatomists can revise and utilize the descriptions and figures. We expect many updated versions of our manual to be shared between students all over the world. PMID:25577205

  5. Biostatistical basis of elective node dissection for malignant melanoma.

    PubMed Central

    Fortner, J G; Woodruff, J; Schottenfeld, D; Maclean, B

    1977-01-01

    During the years 1954 through 1964, 259 individuals with primary malignant melanoma had an elective node dissection. Microscopic metastases were found in 15% of these patients. The presence of only a microscopic focus of involvement gave a 10-year cure rate of 67%; metastasis larger than a microscopic focus in a single node, 50%; and more than one node, 15%. One hundred forty-five individuals were treated by wide excision alone with 18% subsequently requiring a therapeutic lymphadenectomy with a ten-year cure of only 6%. A prospective study was then initiated which was concerned with efficacy of selection of patients for elective node dissection. Clark's level of invasion was determined for 258 patients treated since January 1972. The depth of invasion of the primary lesion was found to correlate directly with the absence of lymph node metastases, extent of nodal involvement, and rate of recurrence. It is concluded that the concept of elective node dissection is valid. PMID:879870

  6. Digital dissection system for medical school anatomy training

    NASA Astrophysics Data System (ADS)

    Augustine, Kurt E.; Pawlina, Wojciech; Carmichael, Stephen W.; Korinek, Mark J.; Schroeder, Kathryn K.; Segovis, Colin M.; Robb, Richard A.

    2003-05-01

    As technology advances, new and innovative ways of viewing and visualizing the human body are developed. Medicine has benefited greatly from imaging modalities that provide ways for us to visualize anatomy that cannot be seen without invasive procedures. As long as medical procedures include invasive operations, students of anatomy will benefit from the cadaveric dissection experience. Teaching proper technique for dissection of human cadavers is a challenging task for anatomy educators. Traditional methods, which have not changed significantly for centuries, include the use of textbooks and pictures to show students what a particular dissection specimen should look like. The ability to properly carry out such highly visual and interactive procedures is significantly constrained by these methods. The student receives a single view and has no idea how the procedure was carried out. The Department of Anatomy at Mayo Medical School recently built a new, state-of-the-art teaching laboratory, including data ports and power sources above each dissection table. This feature allows students to access the Mayo intranet from a computer mounted on each table. The vision of the Department of Anatomy is to replace all paper-based resources in the laboratory (dissection manuals, anatomic atlases, etc.) with a more dynamic medium that will direct students in dissection and in learning human anatomy. Part of that vision includes the use of interactive 3-D visualization technology. The Biomedical Imaging Resource (BIR) at Mayo Clinic has developed, in collaboration with the Department of Anatomy, a system for the control and capture of high resolution digital photographic sequences which can be used to create 3-D interactive visualizations of specimen dissections. The primary components of the system include a Kodak DC290 digital camera, a motorized controller rig from Kaidan, a PC, and custom software to synchronize and control the components. For each dissection procedure, the images are captured automatically, and then processed to generate a Quicktime VR sequence, which permits users to view an object from multiple angles by rotating it on the screen. This provides 3-D visualizations of anatomy for students without the need for special '3-D glasses' that would be impractical to use in a laboratory setting. In addition, a digital video camera may be mounted on the rig for capturing video recordings of selected dissection procedures being carried out by expert anatomists for playback by the students. Anatomists from the Department of Anatomy at Mayo have captured several sets of dissection sequences and processed them into Quicktime VR sequences. The students are able to look at these specimens from multiple angles using this VR technology. In addition, the student may zoom in to obtain high-resolution close-up views of the specimen. They may interactively view the specimen at varying stages of dissection, providing a way to quickly and intuitively navigate through the layers of tissue. Electronic media has begun to impact all areas of education, but a 3-D interactive visualization of specimen dissections in the laboratory environment is a unique and powerful means of teaching anatomy. When fully implemented, anatomy education will be enhanced significantly by comparison to traditional methods.

  7. Advanced, recurrent mesothelioma growth mimicking an aortic dissection

    PubMed Central

    Pankhania, Miran; Hardiment, Kate; Marathe, Mandar

    2011-01-01

    In the emergency setting, a cold, clammy, dyspnoeic patient presenting with interscapular chest pain and unequal blood pressures suggests an acute aortic dissection until proven otherwise. By means of a case report, the authors detail one such patient who presented identically to one having an acute aortic dissection. Initial assessment showed unequal blood pressures in left and right arms, a resting tachycardia and indistinct heart sounds. Fluid resuscitation failed to improve the patient's physiological parameters and they rapidly deteriorated. The medical history included mesothelioma and atrial fibrillation. Existing investigations were reviewed and after thorough consideration of the patient's premorbid state and likely prognosis, the decision was made to palliate. The patient died shortly after being transferred to the oncology ward. Imaging is therefore integral to the assessment and management of a patient in whom an aortic dissection is feared. PMID:22714611

  8. Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource

    PubMed Central

    King, Elizabeth G.; Merkes, Chris M.; McNeil, Casey L.; Hoofer, Steven R.; Sen, Saunak; Broman, Karl W.; Long, Anthony D.; Macdonald, Stuart J.

    2012-01-01

    Genetic dissection of complex, polygenic trait variation is a key goal of medical and evolutionary genetics. Attempts to identify genetic variants underlying complex traits have been plagued by low mapping resolution in traditional linkage studies, and an inability to identify variants that cumulatively explain the bulk of standing genetic variation in genome-wide association studies (GWAS). Thus, much of the heritability remains unexplained for most complex traits. Here we describe a novel, freely available resource for the Drosophila community consisting of two sets of recombinant inbred lines (RILs), each derived from an advanced generation cross between a different set of eight highly inbred, completely resequenced founders. The Drosophila Synthetic Population Resource (DSPR) has been designed to combine the high mapping resolution offered by multiple generations of recombination, with the high statistical power afforded by a linkage-based design. Here, we detail the properties of the mapping panel of >1600 genotyped RILs, and provide an empirical demonstration of the utility of the approach by genetically dissecting alcohol dehydrogenase (ADH) enzyme activity. We confirm that a large fraction of the variation in this classic quantitative trait is due to allelic variation at the Adh locus, and additionally identify several previously unknown modest-effect trans-acting QTL (quantitative trait loci). Using a unique property of multiparental linkage mapping designs, for each QTL we highlight a relatively small set of candidate causative variants for follow-up work. The DSPR represents an important step toward the ultimate goal of a complete understanding of the genetics of complex traits in the Drosophila model system. PMID:22496517

  9. How can we deal with mental distress in the dissection room?-An evaluation of the need for psychological support.

    PubMed

    Boeckers, Anja; Brinkmann, Anke; Jerg-Bretzke, Lucia; Lamp, Christoph; Traue, Harald C; Boeckers, Tobias M

    2010-12-20

    The dissection course (DC) is an essential part of the preclinical medical curriculum that mediates professionalism. The process of dissecting, however, has an inherent additional stress potential. Our study determined student mental stress, their need of psychological support and factors influencing this need. A quantitative longitudinal query before, during and after the DC was performed including the Brief Symptom Inventory (BSI) as well as self-formulated questions used a 5-point Likert scale. Half of the students who anticipated dissection to be a stress factor reported that this declined significantly over time. Instead, student fear of not being able to cope with the work load increased significantly. As many as 64% of the students favored psychological support on the first course day, while 75% rejected this during the period of dissection and 39% appreciated this after the course. Moreover, 42% emphasized the importance of the funeral ceremony. Additionally, 75% documented their need for support in coping with stress and learning strategies. Gender, previous medical training, and BSI levels were identified as psychosocial influence factors. A majority of students named friends, members of their family or workmates as partners with whom they could talk about mental stress. Our results document the need to develop an optimum support during the DC taking into account the ascertained indicators. Exemplarily the Institute of Anatomy and Cell Biology at Ulm University suggests several options like a step by step approach for optimization. These measures reduce mental stress and help students to cope with it by the development of "detached concern" towards their "first patient" as this will decisively influence their future professional behavior. PMID:20846838

  10. Concomitant Reconstruction of Arch Vessels during Repair of Aortic Dissection

    PubMed Central

    Nezic, Dusko; Vukovic, Petar; Jovanovic, Marko; Lozuk, Branko; Jagodic, Sinisa; Djukanovic, Bosko

    2014-01-01

    Surgery for acute aortic dissection is challenging, especially in cases of cerebral malperfusion. Should we perform only the aortic repair, or should we also reconstruct the arch vessels when they are severely affected by the disease process? Here we present a case of acute aortic dissection with multiple tears that involved the brachiocephalic artery and caused cerebral and right upper-extremity malperfusion. The patient successfully underwent complete replacement of the brachiocephalic artery and the aortic arch during deep hypothermic circulatory arrest, with antegrade cerebral protection. We have found this technique to be safe and reproducible for use in this group of patients. PMID:25120398

  11. Concomitant reconstruction of arch vessels during repair of aortic dissection.

    PubMed

    Micovic, Slobodan; Nezic, Dusko; Vukovic, Petar; Jovanovic, Marko; Lozuk, Branko; Jagodic, Sinisa; Djukanovic, Bosko

    2014-08-01

    Surgery for acute aortic dissection is challenging, especially in cases of cerebral malperfusion. Should we perform only the aortic repair, or should we also reconstruct the arch vessels when they are severely affected by the disease process? Here we present a case of acute aortic dissection with multiple tears that involved the brachiocephalic artery and caused cerebral and right upper-extremity malperfusion. The patient successfully underwent complete replacement of the brachiocephalic artery and the aortic arch during deep hypothermic circulatory arrest, with antegrade cerebral protection. We have found this technique to be safe and reproducible for use in this group of patients. PMID:25120398

  12. Spontaneous coronary artery dissection in polycystic kidney disease

    PubMed Central

    Limburg, Sander; Boereboom, Frans

    2012-01-01

    Little is known about the association between autosomal-dominant polycystic kidney disease (ADPKD) and coronary artery dissection (CAD). We suggest that the genetic disorder in ADPKD is the main cause of instable artery vasculature. Our case also shows that CAD can be missed in the acute phase. Therefore, we recommend additional investigation in patients with ADPKD presenting with acute chest pain. We report a case of a patient who developed a myocardial infarction due to a spontaneous dissection of the left anterior descending coronary artery. ADPKD was diagnosed during the additional investigation. The patient received medical management.

  13. Blunt dissection for the treatment of plantar verrucae.

    PubMed

    Baruch, K

    1990-08-01

    The treatment of plantar verrucae has always been a challenging and perplexing problem to physicians. Due to the inherent nature of verrucae, response to various forms of treatment has been extremely unpredictable. It is believed that hyperhidrosis and abnormal pressure to the plantar aspects of the feet are contributing factors predisposing one to developing verrucae. This article describes a painless and effective approach to the treatment of plantar verruca through the use of blunt dissection. Following anesthesia obtained with a posterior tibial nerve block, the plantar verruca can be successfully dissected with an 80 percent cure rate. PMID:2209078

  14. Dissecting Single-Molecule Signal Transduction in Carbon Nanotube Circuits with Protein Engineering

    E-print Network

    Weiss, Gregory A.

    Dissecting Single-Molecule Signal Transduction in Carbon Nanotube Circuits with Protein Engineering dissected using eight di erent lysozyme variants synthesized by protein engineering. The data prove that e

  15. 78 FR 17429 - Certain Balloon Dissection Devices and Products Containing Same; Commission Determination Not To...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-21

    ...337-TA-865] Certain Balloon Dissection Devices and Products...after importation of certain balloon dissection devices and products...Geisingen, Germany; and Pajunk Medical Systems LP of Norcross, Georgia...Medizintechnologie and Pajunk Medical Systems LP filed a motion...

  16. Analysis of dissected tissues with digital holographic microscopy: quantification of inflammation mediated tissue alteration, influence of sample preparation, and reliability of numerical autofocusing

    NASA Astrophysics Data System (ADS)

    Kemper, Björn; Lenz, Philipp; Bettenworth, Dominik; Krausewitz, Philipp; Domagk, Dirk; Ketelhut, Steffi

    2015-03-01

    Quantitative phase imaging with digital holographic microscopy (DHM) allows label-free imaging of tissue sections and quantification of the spatial refractive index distribution, which is of interest for applications in digital pathology. We show that DHM allows quantitative imaging of different layers in unstained tissue samples by detection of refractive index changes. In addition, we evaluate the automated refocussing feature of DHM for application on dissected tissues and could achieve highly reproducible holographic autofocusing for unstained and moderately stained samples. Finally, it is demonstrated that in human ulcerative colitis patients the average tissue refractive index is reduced significantly in all parts of the inflamed colonic wall in comparison to patients in remission.

  17. Circumferential intramural esophageal dissection successfully treated by endoscopic procedure and metal stent insertion

    Microsoft Academic Search

    Seong Hun Kim; Seung-Ok Lee

    2005-01-01

    Spontaneous intramural esophageal dissection is a rare disorder characterized by a lengthy laceration between the mucosal\\u000a and submucosal layers of the esophageal wall, without perforation. The majority of previously reported cases of spontaneous\\u000a intramural esophageal dissection were partial, and the circumferential type of intramural esophageal dissection has not been\\u000a reported previously. Most spontaneous intramural esophageal dissection responds to conservative management,

  18. Mapping Quantitative Trait Loci in Crosses Between Outbred Lines Using Least Squares

    Microsoft Academic Search

    Chris S. Haley; Sara A. Knott; Jean-Michel Elsen

    1994-01-01

    The use of genetic maps based upon molecular markers has allowed the dissection of some of the factors underlying quantitative variation in crosses between inbred lines. For many species crossing inbred lines is not a practical proposition, although crosses between genetically very different outbred lines are pos- sible. Here we develop a least squares method for the analysis of crosses

  19. Residual dissection of the brachiocephalic arteries: Significance, management, and long-term outcome

    Microsoft Academic Search

    Eugenio Neri; Guido Sani; Massimo Massetti; Giacomo Frati; Dimitrios Buklas; Rossana Tassi; Michele Giubbolini; Antonio Benvenuti; Carlo Sassi

    2004-01-01

    ObjectivesResidual dissection of the brachiocephalic arteries after operations for acute type A dissection is considered a benign condition that does not expose patients to late neurologic events. This retrospective study, conducted on an outpatient clinic basis between June 1995 and May 2003, had the objectives of evaluating the consequences of residual dissection of the brachiocephalic arteries, investigating the long-term outcomes

  20. Changes in Inflammatory Response after Endovascular Treatment for Type B Aortic Dissection

    Microsoft Academic Search

    Bernice L. Y. Cheuk; Y. C. Chan; Stephen W. K. Cheng

    2012-01-01

    This present study aims to investigate the changes in the inflammatory markers after elective endovascular treatment of Type B aortic dissection with aneurysm, as related to different anatomical features of the dissection flap in the paravisceral perfusion. Consecutive patients with type B aortic dissections with elective endovascular stent graft repair were recruited and categorized into different groups. Serial plasma levels

  1. Perceived Disgust and Personal Experiences are Associated with Acceptance of Dissections in Schools

    ERIC Educational Resources Information Center

    Fancovicova, Jana; Prokop, Pavol; Leskova, Andrea

    2013-01-01

    Animal dissections are essential parts of anatomy/zoology courses, but their effectiveness is influenced by student attitudes and emotions. Here we examined attitudes toward dissections in 397 prospective biology teachers enrolling two Slovak universities. Perceived disgust of dissections negatively correlated with other attitudes toward…

  2. Acute complicated and uncomplicated Type III Aortic Dissection: An endovascular perspective

    PubMed Central

    Bhamidipati, Castigliano; Ailawadi, Gorav

    2010-01-01

    Type III aortic dissection is associated with high morbidity and mortality. There is a shifting paradigm in the treatment of complicated and uncomplicated acute Type III aortic dissection towards earlier endovascular repair. In this review, the authors present the current perspective on the endovascular management of acute complicated and uncomplicated Type III aortic dissection. PMID:20226352

  3. The use of gelatin-resorcin-formalin glue in acute aortic dissection type A

    Microsoft Academic Search

    Suhji Fukunaga; Matthias Karck; Wolfgang Harringer; Joachim Cremer; Christine Rhein; Axel Haverich

    1999-01-01

    Objectives: The Gelatin-resorcin-formalin (GRF) glue is widely used in the surgical treatment of dissecting aneurysms. This paper is focused on our experience with the GRF glue in cases, operated for acute aortic dissection type A. Methods: Between September 1990 and December 1997, 164 patients were operated on for acute aortic dissection type A. In 148 patients GRF was used to

  4. Increased Carotid Artery Stiffness Without Atherosclerotic Change in Patients With Aortic Dissection

    Microsoft Academic Search

    Shinji Makita; Atsushi Ohira; Yujiro Naganuma; Yoshiteru Moriai; Hiroyuki Niinuma; Akihiko Abiko; Katsuhiko Hiramori

    2006-01-01

    The arterial properties and pathogenesis of aortic dissection remain obscure. To examine the arterial properties of patients with aortic dissection, the authors studied the ultrasonographic characteristics of the carotid artery in patients with an aortic dissection (AD, n=86), and compared these findings with data of patients suffering from arteriosclerosis obliterans (ASO, n=151), coronary artery disease (CAD, n=163), and with healthy

  5. Appropriate lymph node dissection for early gastric cancer based on lymph node metastases

    Microsoft Academic Search

    Chikara Kunisaki; Hiroshi Shimada; Masato Nomura; Hirotoshi Akiyama

    2001-01-01

    Background. Lymph node dissection in patients with early gastric cancer is controversial because lymph node metastases are much less common than in advanced cancer. Therefore, routine extensive lymph node dissection with wide resection of the stomach may be excessive, and an appropriate lymph node dissection procedure in patients with early gastric cancer should be established. Methods. Retrospectively, 588 consecutive patients

  6. Dissection of epistasis in oligogenic Bardet-Biedl syndrome

    Microsoft Academic Search

    Jose L. Badano; Carmen C. Leitch; Stephen J. Ansley; Helen May-Simera; Shaneka Lawson; Richard Alan Lewis; Philip L. Beales; Harry C. Dietz; Shannon Fisher; Nicholas Katsanis

    2006-01-01

    Epistatic interactions have an important role in phenotypic variability, yet the genetic dissection of such phenomena remains challenging. Here we report the identification of a novel locus, MGC1203, that contributes epistatic alleles to Bardet-Biedl syndrome (BBS), a pleiotropic, oligogenic disorder. MGC1203 encodes a pericentriolar protein that interacts and colocalizes with the BBS proteins. Sequencing of two independent BBS cohorts revealed

  7. Dissecting the Molecular Basis of the Mechanics of Living Cells

    E-print Network

    Kumar, Sanjay

    , and differentiation. For example, the differentiation trajectory of mesenchymal stem cells (MSCs) may be controlled-induced osteogenic differentiation of MSCs may be blocked by inhibiting Rho GTPase-dependent cell contractility [1Dissecting the Molecular Basis of the Mechanics of Living Cells S. Kumar & P.R. LeDuc Received: 29

  8. Parent Vessel Occlusion for Vertebrobasilar Fusiform and Dissecting Aneurysms

    Microsoft Academic Search

    R. Leibowitz; M. L. Marcellus; S. D. Chang; G. K. Steinberg; M. P. Marks

    BACKGROUND AND PURPOSE: Previous reports of outcome with permanent vessel occlu- sion (PVO) for large, giant, or fusiform aneurysms in the posterior circulation have been limited. We undertook this study to evaluate the perioperative (within 30 days) and follow-up outcomes for patients treated with permanent occlusion of the vertebral artery for vertebro- basilar fusiform and dissecting aneurysms. METHODS: Thirteen consecutive

  9. Delayed left atrial wall dissection after mitral valve replacement.

    PubMed

    Idir, M; Deville, C; Roudaut, R

    2000-04-01

    We report two unusual cases of left atrial wall dissection creating a left atrial pseudoaneurysm associated with regurgitation a few months after mitral valve replacement. We emphasize the important role of transesophageal echocardiography in the diagnosis. The two patients successfully underwent surgery. PMID:10978990

  10. Constant Weight Codes: A Geometric Approach Based on Dissections

    E-print Network

    Fisher, Kathleen

    -rectangle and a polytope in this Euclidean space. An inductive dissection algorithm is developed for constructing. Our technique is based on embedding the codebook in a Euclidean space of dimension equal to the weight such a bijection. We prove that the algorithm is correct and then analyze its complexity. The complexity depends

  11. Gastric Wall Dissection as a Complication of Percutaneous Gastrostomy

    SciTech Connect

    Reimer, Wolfgang; Farres, Maria Teresa; Lammer, Johannes [Department of Radiology, Division of Angiography and Interventional Radiology, University of Vienna, AKH, Waehringer Guertel 18-20, A-1090 Vienna (Austria)

    1996-04-15

    A percutaneous gastrostomy (PG) was complicated by gastric wall dissection and partial tube malposition. It occurred after tangential puncture along the greater curvature of the stomach which was performed in order to avoid an enlarged left lobe of the liver. To prevent this complication we recommend not using hydrophilic guidewires during PG.

  12. Exploring Dissections of Rectangles into Right-Angled Triangles

    ERIC Educational Resources Information Center

    Griffiths, Martin

    2013-01-01

    In this article we highlight how a simple classroom activity associated with the dissection of rectangles into right-angled triangles can lead on to a number of interesting explorations for students following a post-16 mathematics course. Several results connected with this construction are obtained, and some of the educational benefits of…

  13. Standard methods for Apis mellifera anatomy and dissection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An understanding of the anatomy and functions of internal and external structures are fundamental to many studies on the honey bee Apis mellifera. Similarly, proficiency in dissection techniques is vital for many more complex procedures. In this paper, which is a prelude to the other papers of the C...

  14. Emergent endovascular treatment of ruptured vertebral artery dissecting aneurysms

    Microsoft Academic Search

    K. Sugiu; K. Tokunaga; K. Watanabe; W. Sasahara; S. Ono; T. Tamiya; I. Date

    2005-01-01

    The goal of this study was to evaluate the results of endovascular and surgical treatments for ruptured vertebral artery dissecting aneurysms (VADAs) to determine which treatment is preferable. We evaluated the cases of 25 consecutive patients with ruptured VADAs treated in our institution. From 1992 to 1997, five patients were treated surgically. Since 1998, 20 patients with VADAs have been

  15. Mutations in Myosin Light Chain Kinase Cause Familial Aortic Dissections

    PubMed Central

    Wang, Li; Guo, Dong-chuan; Cao, Jiumei; Gong, Limin; Kamm, Kristine E.; Regalado, Ellen; Li, Li; Shete, Sanjay; He, Wei-Qi; Zhu, Min-Sheng; Offermanns, Stephan; Gilchrist, Dawna; Elefteriades, John; Stull, James T.; Milewicz, Dianna M.

    2010-01-01

    Mutations in smooth muscle cell (SMC)-specific isoforms of ?-actin and ?-myosin heavy chain, two major components of the SMC contractile unit, cause familial thoracic aortic aneurysms leading to acute aortic dissections (FTAAD). To investigate whether mutations in the kinase that controls SMC contractile function (myosin light chain kinase [MYLK]) cause FTAAD, we sequenced MYLK by using DNA from 193 affected probands from unrelated FTAAD families. One nonsense and four missense variants were identified in MYLK and were not present in matched controls. Two variants, p.R1480X (c.4438C>T) and p.S1759P (c.5275T>C), segregated with aortic dissections in two families with a maximum LOD score of 2.1, providing evidence of linkage of these rare variants to the disease (p = 0.0009). Both families demonstrated a similar phenotype characterized by presentation with an acute aortic dissection with little to no enlargement of the aorta. The p.R1480X mutation leads to a truncated protein lacking the kinase and calmodulin binding domains, and p.S1759P alters amino acids in the ?-helix of the calmodulin binding sequence, which disrupts kinase binding to calmodulin and reduces kinase activity in vitro. Furthermore, mice with SMC-specific knockdown of Mylk demonstrate altered gene expression and pathology consistent with medial degeneration of the aorta. Thus, genetic and functional studies support the conclusion that heterozygous loss-of-function mutations in MYLK are associated with aortic dissections. PMID:21055718

  16. Effect of Skeletonizing Dissection on the Internal Thoracic Artery

    Microsoft Academic Search

    Tadahiro Sasajima; Moses Hong-De Wu; Qun Shi; Naoki Hayashida; Lester R. Sauvage

    1998-01-01

    Background. Skeletonization of the internal thoracic artery (ITA) produces greater length for coronary bypass grafting. We studied the effect of skeletonization on the morphology, histology, and tissue viability of the ITA wall.Methods. Six mongrel dogs underwent unilateral ITA dissection; the contralateral ITA was the control. Study periods were 3 weeks (n = 3) and 12 weeks (n = 3). At

  17. Student Attitudes to Whole Body Donation Are Influenced by Dissection

    ERIC Educational Resources Information Center

    Cahill, Kevin C.; Ettarh, Raj R.

    2008-01-01

    Given the important role that anatomical dissection plays in the shaping of medical student attitudes to life and death, these attitudes have not been evaluated in the context of whole body donation for medical science. First year students of anatomy in an Irish university medical school were surveyed by questionnaire before and after the initial…

  18. Molecular and Functional Dissection of the Maize B Chromosome Centromere

    E-print Network

    Molecular and Functional Dissection of the Maize B Chromosome Centromere Weiwei Jin,a Jonathan C, Georgia 30602 The centromere of the maize (Zea mays) B chromosome contains several megabases of a B-specific repeat (ZmBs), a 156-bp satellite repeat (CentC), and centromere-specific retrotransposons (CRM elements

  19. Student Attitudes to Whole Body Donation are Influenced by Dissection

    NSDL National Science Digital Library

    2008-09-01

    This article describes a pre-post survey given to medical students in a gross anatomy course addressing the attitudes toward becoming cadaver donators. Outcomes discuss the influence of actively dissecting a cadaver and how that shifts students away from donating one's body.

  20. Lymph node dissection – understanding the immunological function of lymph nodes

    PubMed Central

    Buettner, M; Bode, U

    2012-01-01

    Lymph nodes (LN) are one of the important sites in the body where immune responses to pathogenic antigens are initiated. This immunological function induced by cells within the LN is an extensive area of research. To clarify the general function of LN, to identify cell populations within the lymphatic system and to describe the regeneration of the lymph vessels, the experimental surgical technique of LN dissection has been established in various animal models. In this review different research areas in which LN dissection is used as an experimental tool will be highlighted. These include regeneration studies, immunological analysis and studies with clinical questions. LN were dissected in order to analyse the different cell subsets of the incoming lymph in detail. Furthermore, LN were identified as the place where the induction of an antigen-specific response occurs and, more significantly, where this immune response is regulated. During bacterial infection LN, as a filter of the lymph system, play a life-saving role. In addition, LN are essential for the induction of tolerance against harmless antigens, because tolerance could not be induced in LN-resected animals. Thus, the technique of LN dissection is an excellent and simple method to identify the important role of LN in immune responses, tolerance and infection. PMID:22861359

  1. Dissection of Conformational Conversion Events during Prion Amyloid Fibril

    E-print Network

    Dissection of Conformational Conversion Events during Prion Amyloid Fibril Formation Using Hydrogen A molecular understanding of prion diseases requires an understanding of the mechanism of amyloid fibril formation by the prion protein. In particular, it is necessary to define the sequence of the structural

  2. Blood Vessels of the Fetal Pig Dissection Posterior Vessels Protocol

    E-print Network

    Loughry, Jim

    Blood Vessels of the Fetal Pig Dissection Posterior Vessels Protocol: 1. The blood vessels membrane is the peritoneum, the blood vessels are said to be retroperitoneal). In order to see the blood that supplies the stomach, liver and spleen with blood. This is the celiac artery. c. Just below where

  3. Dissecting BitTorrent: Five Months in a Torrent's Lifetime

    E-print Network

    Rivière, Etienne

    Dissecting BitTorrent: Five Months in a Torrent's Lifetime M. Izal, G. Urvoy-Keller, E.W. Biersack as clients and servers. In this paper, we study BitTorrent, a new and already very popular peer- to-peer application that allows distribution of very large contents to a large set of hosts. Our analysis of BitTorrent

  4. There Is More to the Dissection of a Pig's Heart

    ERIC Educational Resources Information Center

    Lee, Yeung Chung

    2004-01-01

    The dissection of the mammalian heart in secondary biology classes need not be restricted to revealing the internal structure of the heart and its function. It could also be used to demonstrate other important aspects of blood circulation, including the blood supply to the heart itself as well as the causes and effects of coronary heart disease.…

  5. INVESTIGATION Genetic Dissection of a Key Reproductive Barrier

    E-print Network

    Nachman, Michael

    diverged subspecies, house mice provide a powerful system for understanding the genetics of reproductive responsible for the initial development of reproductive isolation. House mice provide a powerful systemINVESTIGATION Genetic Dissection of a Key Reproductive Barrier Between Nascent Species of House

  6. Dissection of midgut and salivary glands from Ae. aegypti mosquitoes.

    PubMed

    Coleman, Judy; Juhn, Jennifer; James, Anthony A A

    2007-01-01

    The mosquito midgut and salivary glands are key entry and exit points for pathogens such as Plasmodium parasites and Dengue viruses. This video protocol demonstrates dissection techniques for removal of the midgut and salivary glands from Aedes aegypti mosquitoes. PMID:18979026

  7. Functional Dissection of IME1 Transcription Using Quantitative Promoter–Reporter Screening

    PubMed Central

    Kahana, Smadar; Pnueli, Lilach; Kainth, Pinay; Sassi, Holly E.; Andrews, Brenda; Kassir, Yona

    2010-01-01

    Transcriptional regulation is a key mechanism that controls the fate and response of cells to diverse signals. Therefore, the identification of the DNA-binding proteins, which mediate these signals, is a crucial step in elucidating how cell fate is regulated. In this report, we applied both bioinformatics and functional genomic approaches to scrutinize the unusually large promoter of the IME1 gene in budding yeast. Using a recently described fluorescent protein-based reporter screen, reporter-synthetic genetic array (R-SGA), we assessed the effect of viable deletion mutants on transcription of various IME1 promoter–reporter genes. We discovered potential transcription factors, many of which have no perfect consensus site within the IME1 promoter. Moreover, most of the cis-regulatory sequences with perfect homology to known transcription factor (TF) consensus were found to be nonfunctional in the R-SGA analysis. In addition, our results suggest that lack of conservation may not discriminate against a TF regulatory role at a specific promoter. We demonstrate that Sum1 and Sok2, which regulate IME1, bind to nonperfect consensuses within nonconserved regions in the sensu stricto Saccharomyces strains. Our analysis supports the view that although comparative analysis can provide a useful guide, functional assays are required for accurate identification of TF-binding site interactions in complex promoters. PMID:20739709

  8. Functional dissection of IME1 transcription using quantitative promoter-reporter screening.

    PubMed

    Kahana, Smadar; Pnueli, Lilach; Kainth, Pinay; Sassi, Holly E; Andrews, Brenda; Kassir, Yona

    2010-11-01

    Transcriptional regulation is a key mechanism that controls the fate and response of cells to diverse signals. Therefore, the identification of the DNA-binding proteins, which mediate these signals, is a crucial step in elucidating how cell fate is regulated. In this report, we applied both bioinformatics and functional genomic approaches to scrutinize the unusually large promoter of the IME1 gene in budding yeast. Using a recently described fluorescent protein-based reporter screen, reporter-synthetic genetic array (R-SGA), we assessed the effect of viable deletion mutants on transcription of various IME1 promoter-reporter genes. We discovered potential transcription factors, many of which have no perfect consensus site within the IME1 promoter. Moreover, most of the cis-regulatory sequences with perfect homology to known transcription factor (TF) consensus were found to be nonfunctional in the R-SGA analysis. In addition, our results suggest that lack of conservation may not discriminate against a TF regulatory role at a specific promoter. We demonstrate that Sum1 and Sok2, which regulate IME1, bind to nonperfect consensuses within nonconserved regions in the sensu stricto Saccharomyces strains. Our analysis supports the view that although comparative analysis can provide a useful guide, functional assays are required for accurate identification of TF-binding site interactions in complex promoters. PMID:20739709

  9. 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://proteomecentral.proteomexchange.org/dataset/PXD001101). PMID:25404012

  10. Global phosphoproteome profiling reveals unanticipated networks responsive to cisplatin treatment of embryonic stem cells.

    PubMed

    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

    2011-12-01

    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

  11. Comparative N-Glycoproteomic and Phosphoproteomic Profiling of Human Placental Plasma Membrane between Normal and Preeclampsia Pregnancies with High-Resolution Mass Spectrometry

    PubMed Central

    Wang, Fuqiang; Wang, Ling; Shi, Zhonghua; Liang, Gaolin

    2013-01-01

    Preeclampsia is a serious complication of pregnancy, which affects 2–8% of all pregnancies and is one of the leading causes of maternal and perinatal mortality and morbidity worldwide. To better understand the molecular mechanisms involved in pathological development of placenta in preeclampsia, we used high-resolution LC-MS/MS technologies to construct a comparative N-glycoproteomic and phosphoproteomic profiling of human placental plasma membrane in normal and preeclamptic pregnancies. A total of 1027 N-glyco- and 2094 phospho- sites were detected in human placental plasma membrane, and 5 N-glyco- and 38 phospho- proteins, respectively, with differentially expression were definitively identified between control and preeclamptic placental plasma membrane. Further bioinformatics analysis indicated that these differentially expressed proteins correlate with several specific cellular processes occurring during pathological changes of preeclamptic placental plasma membrane. PMID:24260401

  12. Quantitative Analysen

    NASA Astrophysics Data System (ADS)

    Hübner, Philipp

    Der heilige Gral jeglicher Analytik ist, den wahren Wert bestimmen zu können. Dies bedingt quantitative Messmethoden, welche in der molekularen Analytik nun seit einiger Zeit zur Verfügung stehen. Das generelle Problem bei der Quantifizierung ist, dass wir meistens den wahren Wert weder kennen noch bestimmen können! Aus diesem Grund behelfen wir uns mit Annäherungen an den wahren Wert, indem wir aus Laborvergleichsuntersuchungen den Median oder den (robusten) Mittelwert berechnen oder indem wir einen Erwartungswert (expected value) aufgrund der Herstellung des Probenmaterials berechnen. Bei diesen Versuchen der Annäherung an den wahren Wert findet beabsichtigterweise eine Normierung der Analytik statt, entweder nach dem demokratischen Prinzip, dass die Mehrheit bestimmt oder durch zur Verfügungsstellung von geeignetem zertifiziertem Referenzmaterial. Wir müssen uns folglich bewusst sein, dass durch dieses Vorgehen zwar garantiert wird, dass die Mehrheit der Analysenlaboratorien gleich misst, wir jedoch dabei nicht wissen, ob alle gleich gut oder allenfalls gleich schlecht messen.

  13. Ultrasonic Detection of Metastases in Dissected Lymph Nodes of Cancer Patients

    NASA Astrophysics Data System (ADS)

    Feleppa, E. J.; Mamou, J.; Machi, J.; Hata, M.; Coron, A.; Yanagihara, E.; Laugier, P.

    Current histological methods can miss micrometastases (< 2.0 mm) in dissected lymph nodes because nodes are cut into sections that are at least 2-mm thick for examination, and the entire node volume cannot be evaluated microscopically. In this study, high-frequency, quantitative ultrasound (HFU, QUS) methods were applied to freshly dissected lymph nodes to detect micrometastases based on their microstructural properties. 3-D ultrasound data were acquired from 40 nodes from 22, colorectal-cancer patients using a single-element, 25 MHz transducer. Significant cancer was detected subsequently in 7 of the 40 nodes. Node images were segmented semi-automatically in 3-D, and echo signals were processed to yield basic spectral parameters (slope, intercept, and midband) values plus QUS estimates associated with tissue microstructural properties (scatterer size and acoustic concentration). Images were formed by expressing local QUS estimates as color-encoded pixels and overlaying the color on conventional, gray-scale ultrasound images. Linear discriminant analysis classified nodes based on intercept, midband, size, and acoustic concentration. ROC methods assessed classification performance. 3-D QUS images interactively displayed spectral-parameter and QUS values. Linear-discriminant methods produced an area under the ROC curve of 1.000 based on size and intercept; interestingly, the areas for size alone and for intercept alone were 0.986. These initial results appear to validate spectrum-analysis-based QUS methods for distinguishing cancerous from non-cancerous tissue in lymph nodes. The Areas under the ROC curves suggest that this approach can be valuable clinically to identify nodal micrometastases that current histologic methods can miss.

  14. Medical Student Dissection of Cadavers Improves Performance on Practical Exams but not on the NBME Anatomy Subject Exam

    Microsoft Academic Search

    Jones LS; Paulman LE; Leslie Sargent Jones; Lance E. Paulman; Raj Thadani; Louis Terracio

    We have examined whether cadaver dissection by first year medical students ( MIs) affected their performance in two test measures: the NBME Gross Anatomy and Embryology Subject Exam (dissection-relevant questions only), and practical exams given at the end of each major section within the course. The dissections for the entire course were divided into 18 regional dissection units and each

  15. Talking about Death: Implementing Peer Discussion as a Coping Mechanism to Overcome Fears about Dissection, Death, and Dying

    ERIC Educational Resources Information Center

    Kotze, Sanet Henriet; Mole, Calvin Gerald

    2013-01-01

    Many studies have reported on the perceptions of medical students toward dissection. It is important to understand the feelings and symptoms experienced during dissection so that they can be adequately handled. Prior to dissection, first year students are given lectures on aspects of dissection, death and dying, and death rituals in various…

  16. Are all hands-on activities equally effective? Effect of using plastic models, organ dissections, and virtual dissections on student learning and perceptions.

    PubMed

    Lombardi, Sara A; Hicks, Reimi E; Thompson, Katerina V; Marbach-Ad, Gili

    2014-03-01

    This study investigated the impact of three commonly used cardiovascular model-assisted activities on student learning and student attitudes and perspectives about science. College students enrolled in a Human Anatomy and Physiology course were randomly assigned to one of three experimental groups (organ dissections, virtual dissections, or plastic models). Each group received a 15-min lecture followed by a 45-min activity with one of the treatments. Immediately after the lesson and then 2 mo later, students were tested on anatomy and physiology knowledge and completed an attitude survey. Students who used plastic models achieved significantly higher overall scores on both the initial and followup exams than students who performed organ or virtual dissections. On the initial exam, students in the plastic model and organ dissection treatments scored higher on anatomy questions than students who performed virtual dissections. Students in the plastic model group scored higher than students who performed organ dissections on physiology questions. On the followup exam, when asked anatomy questions, students in the plastic model group scored higher than dissection students and virtual dissection students. On attitude surveys, organ dissections had higher perceived value and were requested for inclusion in curricula twice as often as any other activity. Students who performed organ dissections were more likely than the other treatment groups to agree with the statement that "science is fun," suggesting that organ dissections may promote positive attitudes toward science. The findings of this study provide evidence for the importance of multiple types of hands-on activities in anatomy laboratory courses. PMID:24585474

  17. [Stagewise surgical treatment in type III B chronic aortic dissection].

    PubMed

    Ignat'ev, I M; Generalov, M I; A?riian, N E; Volodiukhin, M Iu; Zanochkin, A V

    2012-01-01

    Presented herein is a clinical case report of successful surgical treatment (open and endovascular operation) of a patient with DeBakey type III B chronic aortic dissection. The diagnosis was verified by contrast-enhanced multispiral computed tomography (MSCT). The first stage consisted in operation of carotid-subclavian bypass grafting and aortomy with dissection of the internal membrane of the abdominal aorta, dividing the false and true channels. The second stage included endovascular prosthetic repair of the thoracic aorta with the Relay stent graft. The course of the postoperative period was uneventful. According to the MSCT findings 2 months after the intervention, the endograft was patent, with neither shift nor endoleack. The false channel along the descending thoracic aorta is thrombosed. The maximal diameter of the abdominal aorta does not exceed 4 cm. According to the findings of duplex scanning, the carotid-subclavian bypass is functioning. The patient's condition is satisfactory. PMID:23059612

  18. The role of imaging in aortic dissection and related syndromes.

    PubMed

    Baliga, Ragavendra R; Nienaber, Christoph A; Bossone, Eduardo; Oh, Jae K; Isselbacher, Eric M; Sechtem, Udo; Fattori, Rossella; Raman, Subha V; Eagle, Kim A

    2014-04-01

    Aortic aneurysm and acute aortic syndrome are not uncommon conditions. Management of acute aortic dissection and related syndromes requires a multidisciplinary approach with input from the patient, clinician, imager, surgeon, and anesthesiologist. This requires an integrated evaluation of pathophysiology, anatomy, and severity to enable appropriate therapy. This review includes discussion of essential anatomy of the aortic valve and the aorta that determines the candidacy for surgical repair. It also includes discussion of various imaging modalities, particularly echocardiography, cardiac computed tomography, and cardiac magnetic resonance angiography. The relative benefits and demerits of each of these techniques are reviewed. This paper is intended to help guide management decisions for patients with acute aortic dissection and related syndromes. PMID:24742892

  19. A quantum informational approach for dissecting chemical reactions

    NASA Astrophysics Data System (ADS)

    Duperrouzel, Corinne; Tecmer, Pawe?; Boguslawski, Katharina; Barcza, Gergely; Legeza, Örs; Ayers, Paul W.

    2015-02-01

    We present a conceptionally different approach to dissect bond-formation processes in metal-driven catalysis using concepts from quantum information theory. Our method uses the entanglement and correlation among molecular orbitals to analyze changes in electronic structure that accompany chemical processes. As a proof-of-principle example, the evolution of nickel-ethene bond-formation is dissected, which allows us to monitor the interplay of back-bonding and ?-donation along the reaction coordinate. Furthermore, the reaction pathway of nickel-ethene complexation is analyzed using quantum chemistry methods, revealing the presence of a transition state. Our study supports the crucial role of metal-to-ligand back-donation in the bond-forming process of nickel-ethene.

  20. SLE 1, 2, 3…Genetic Dissection of Lupus

    Microsoft Academic Search

    Jiankun Zhu; Chandra Mohan

    \\u000a Systemic lupus erythematosus (SLE) is a chronic and complex autoimmune disease of unknown etiology, characterized by the presence\\u000a of widespread immunological abnormalities and multiorgan injury. An important advance over the past decade has been our understanding\\u000a of how different genetic loci (or genes) may dictate specific immune abnormalities in lupus. “Genetic dissection” has unveiled\\u000a some of the mystery enshrouding lupus

  1. Spontaneous hemomediastinum and hemothorax after dissecting bronchial artery aneurysm.

    PubMed

    Quero-Valenzuela, Florencio; Piedra-Fernández, Inmaculada; Sevilla-López, Sebastián; Cueto-Ladrón de Guevara, Antonio

    2011-04-01

    Spontaneous hemomediastinum is a rare pathological event due to bleeding disorders, mediastinal organ hemorrhage or idiopathic causes. It usually presents with chest pain and dyspnea, which can lead to confusion with other clinical conditions. The election diagnostic method is computed tomography and treatment depends on underlying etiology, aimed on controlling hemorrhages, if present. In this paper, we present a case of spontaneous hemomediastinum and hemothorax after bronchial artery aneurysm dissection treated with endovascular embolization and chest drainage. PMID:21228046

  2. Robotic thyroidectomy and neck dissection: past, present, and future.

    PubMed

    Lee, Jandee; Chung, Woong Youn

    2013-01-01

    The advantages of endoscopic thyroidectomy and neck dissection include reduced hyperesthesia or paresthesia in the neck and favorable cosmetic outcomes. However, endoscopic thyroidectomy with neck dissection has a long learning curve, as well as technical limitations associated with a 2-dimensional view and a reduced dexterity of movement, particularly when operating in deep and narrow spaces such as the neck area. A robotic approach has been developed to overcome these limitations, facilitating manipulation and shortening the learning curve. This system enables the surgeon to control the 3-dimensional high-definition camera, reducing physiological tremors and enabling free dexterity of movement using articulated instruments. Therefore, robotic surgery has been found to eliminate many problems encountered with conventional endoscopic techniques.Recently, robotic thyroidectomy with neck dissection via a gasless transaxillary approach was shown to yield similar oncologic outcomes as conventional open procedures, as determined by postoperative radioactive iodine scans, serum thyroglobulin concentrations, and number of retrieved cervical lymph nodes. We also found that the robotic technique was safe and feasible in thyroid cancer patients, yielding excellent cosmetic results, reduced pain, improved sensory changes and decreased postoperative voice changes and swallowing discomfort. For surgeons, the use of a robot offers a shorter operation time and the need for a shorter learning curve than conventional endoscopic thyroidectomy. Robotic thyroidectomy also causes less musculoskeletal discomfort to surgeons than open or endoscopic thyroidectomy. The advantages of robotic surgery over open or endoscopic surgery suggest that robotic thyroidectomy with neck dissection may become the preferred surgical option for patients with thyroid cancer. Further analyses of surgeons' experience, assessments of long-term outcomes, and randomized controlled trials remain important. PMID:23528724

  3. A study of sternocleidomastoid muscular atrophy after modified neck dissection

    Microsoft Academic Search

    Takahiro Ohtawa; Makoto Katagiri; Tanekazu Harada

    1998-01-01

    To elucidate the conditions of atrophy in the sternocleidomastoid muscle (SCM) after modified neck dissection (MND), we tried\\u000a to scrutizine the atrophic regions in the SCM and determine the cause of atrophy, by electromyography in 40 patients with\\u000a SCM atrophy following MND. We also examined the detailed anatomy of the SCM in 40 cadavers. Atrophy was observed in the caudal

  4. Compartment-mediated dissection for papillary thyroid cancer

    Microsoft Academic Search

    Jeffrey F. Moley; Samuel A. Wells

    1999-01-01

    There is considerable controversy surrounding the appropriate treatment of papillary thyroid carcinoma (PTC), most of which\\u000a centers around the extent of thyroidectomy. Despite the advocation of less than total thyroidectomy by many surgeons, there\\u000a is a renewed interest by others, mainly in Europe and Japan, in the performance of routine total thyroidectomy and extensive\\u000a lymph-node dissection for PTC. This has

  5. Pediatric traumatic carotid, vertebral and cerebral artery dissections: a review

    Microsoft Academic Search

    Martin M. Mortazavi; Ketan Verma; R. Shane Tubbs; Mark Harrigan

    Traumatic cerebral dissections are rare but potentially dangerous conditions that through improved diagnostics have recently\\u000a gained increased interest. However, there is still a significant lack of knowledge on the natural history, as well as on the\\u000a best treatment options. Most of the literature on this topic consists of case reports and retrospective studies with no prospective\\u000a randomized controlled studies. In

  6. Resection of the sternocleidomastoid muscle during radical neck dissection

    Microsoft Academic Search

    M. Jaehne; Jürgen Ußmüller; Wolfgang Kehrl

    2001-01-01

    Background: Surgical therapy of lymph node metastasis is based on accessibility for en bloc resection. First described as “radical neck\\u000a dissection”, this original approach has since undergone various modifications. This has produced controversy about the particular\\u000a indications for the individual techniques. The aim of this study was to evaluate whether intraoperative macroscopic inspection\\u000a of the sternocleidomastoid muscle (SCM) in regard

  7. Debranching Solutions in Endografting for Complex Thoracic Aortic Dissections

    PubMed Central

    Goksel, Onur Selcuk; Guven, Koray; Karatepe, Celalettin; Gok, Emre; Acunas, Bulent; Cinar, Bayer; Alpagut, Ufuk

    2014-01-01

    Background Conventional surgical repair of thoracic aortic dissections is a challenge due to mortality and morbidity risks. Objectives We analyzed our experience in hybrid aortic arch repair for complex dissections of the aortic arch. Methods Between 2009 and 2013, 18 patients (the mean age of 67 ± 8 years-old) underwent hybrid aortic arch repair. The procedural strategy was determined on the individual patient. Results Thirteen patients had type I repair using trifurcation and another patient with bifurcation graft. Two patients had type II repair with replacement of the ascending aorta. Two patients received extra-anatomic bypass grafting to left carotid artery allowing covering of zone 1. Stent graft deployment rate was 100%. No patients experienced stroke. One patient with total debranching of the aortic arch following an acute dissection of the proximal arch expired 3 months after TEVAR due to heart failure. There were no early to midterm endoleaks. The median follow-up was 20 ± 8 months with patency rate of 100%. Conclusion Various debranching solutions for different complex scenarios of the aortic arch serve as less invasive procedures than conventional open surgery enabling safe and effective treatment of this highly selected subgroup of patients with complex aortic pathologies. PMID:25211314

  8. The zygorbicular dissection in composite rhytidectomy: an ideal midface plane.

    PubMed

    Hamra, S T

    1998-10-01

    Composite rhytidectomy added the repositioning of the orbicularis oculi muscle to the deep plane face lift to achieve a more harmonious appearance of the face by adding periorbital rejuvenation. By not separating the orbicularis oculi from the zygomaticus minor and by extending the dissection under medial portions of the zygomaticus major and minor muscles, a more significant improvement in composite rhytidectomy can now be achieved. A thin nonrestrictive mesentery between the deep plane face lift dissection and the zygorbicular dissection still allows vertical movement of the composite face lift flap without interrupting the intimate relationship between the platysma, cheek fat, and orbicularis oculi muscle. This modification eliminates the occasional prolonged edema and occasional temporary dystonia previously observed. It allows the continuation of the use of the arcus marginalis release, which has also been modified by resetting the septum orbitale over the orbital rim. These two modifications allow a more predictable and impressive result. They reinforce the concept of periorbital rejuvenation as an integral part of facial rejuvenation, which not only produces a more harmonious immediate result but prevents the possible unfavorable sequelae of conventional rhytidectomy and lower blepharoplasty. PMID:9774027

  9. Left anterior descending coronary artery dissection after blunt chest trauma.

    PubMed

    Sadr-Ameli, Mohammad Ali; Amiri, Elaheh; Pouraliakbar, Hamidreza; Heidarali, Mona

    2014-01-01

    Coronary artery dissection is a well-known albeit unusual complication of blunt chest trauma. It is also an uncommon cause of myocardial infarction. Only a few such cases have been reported, probably due to the high rate of sudden death. We report a case of left anterior descending (LAD) coronary artery dissection in a healthy 38-year-old female caused by blunt chest trauma. The patient was referred to our hospital with a complaint of chest pain. Electrocardiography showed T-wave inversion, echocardiography a revealed circumferential pericardial effusion, and the coronary angiogram demonstrated a thrombotic dissection of the LAD.  Troponin I was the only biomarker with elevated level. CT coronary angiography was performed using the subtotal occlusion of the LAD and illustrated a relatively good LAD run-off, and thallium scintigraphy displayed viable myocardium in this territory. Despite the total occlusion of the LAD in our case, myocardial injury was not significant due to the relatively good LAD run-off. She underwent coronary artery bypass graft surgery with an excellent result. PMID:24444069

  10. Are All Hands-On Activities Equally Effective? Effect of Using Plastic Models, Organ Dissections, and Virtual Dissections on Student Learning and Perceptions

    ERIC Educational Resources Information Center

    Lombardi, Sara A.; Hicks, Reimi E.; Thompson, Katerina V.; Marbach-Ad, Gili

    2014-01-01

    This study investigated the impact of three commonly used cardiovascular model-assisted activities on student learning and student attitudes and perspectives about science. College students enrolled in a Human Anatomy and Physiology course were randomly assigned to one of three experimental groups (organ dissections, virtual dissections, or…

  11. Recurrent aortic dissection presenting with repeated transient ischemic attacks: a novel pathophysiology and successful endovascular treatment.

    PubMed

    Elshikh, S; Schumacher, M; Dohmen, A; Weber, J

    2013-12-01

    Aortic dissection is the most common and the most lethal event that can involve the aorta. Typically, aortic dissection presents with sharp, tearing, or ripping pain. Alternatively, the patients may suffer from possible extension of the dissecting aneurysm into the supra-aortic vessels resulting in syncope in 9.4 % of patients cerebrovascular accidents in 4.7 %. We present a case of recurrent aortic dissection, which presented with recurrent transient ischemic attacks (TIAs). The etiology of the neurological symptoms was attributed to a steal phenomenon. The right subclavian artery was supplied by retrograde flow from the right internal carotid artery through the false lumen of the dissection. To prevent further hemodynamic TIAs, we successfully occluded the proximal part of the false lumen of the dissection responsible for the steal phenomenon. PMID:23307261

  12. Spontaneous type B aortic dissection in antepartum gemellary pregnancy and endovascular repair

    PubMed Central

    Gu, Xudong; Liu, Hongmei; Li, Yusheng; Fei, Libo; Shao, Danbing; Mao, Jianhua; Nie, Shinan

    2014-01-01

    Background: It has been found that 50% of all aortic dissections can be attributable to pregnancy in women younger than 45 years of age. An estimated 30% of cases are type B, with half occurring in the antepartum period. To date type B aortic dissection has rarely been reported in gemellary pregnancies. Case: A 24-year-old primigravida at 36 weeks of gemellary gestation presented symptoms of severe and persistent chest pain for 1 day, before suffering the acute type B aortic dissection. The primigravida was treated with immediate cesarean section and endovacular stent graft placement. Conclusion: Aortic dissection is a rare complication of pregnancy, especially in gemellary pregnancies. Pregnancy is considered an independent risk factor for aortic dissection and endovascular repair may be an ideal option for the treatment of complicated type B aortic dissection during pregnancy, with reduced maternal and fetal mortality. PMID:25550939

  13. Pinpointing genes underlying the quantitative trait loci for root-knot nematode resistance in palaeopolyploid soybean by whole genome resequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to utilize next-generation sequencing (NGS) technologies to dissect quantitative trait loci (QTL) for southern root-knot nematode (RKN) resistance into individual genes in soybean. Two-hundred forty-six recombinant inbred lines (RIL) derived from a cross between Mage...

  14. Dissection of the ascending thoracic aorta as a complication of percutaneous coronary intervention

    PubMed Central

    Uyan, Cihangir; Arinc, Huseyin; Gunduz, Huseyin; Akdemir, Ramazan

    2008-01-01

    Acute aortic dissection is a medical emergency with high morbidity and mortality requiring emergent diagnosis and therapy. A 79-year-old woman with acute aortic dissection due to percutaneous coronary intervention was presented. Aortic dissection is an uncommon but potentially lethal illness that can present in an occult manner making the initial diagnosis difficult. Aggressive medical management is mandatory, as well as urgent diagnostic testing and cardiothoracic consultation. PMID:18629358

  15. Acute Myocardial Infarction Due to Spontaneous Dissection of the Right Coronary Artery in a Young Male

    SciTech Connect

    Papadopoulos, Dimitris P., E-mail: jimpapdoc@yahoo.com; Moyssakis, Ioannis; Perakis, Alexandros; Athanasiou, Andreas [Department of Cardiology (Greece); Anagnostopoulou, Sophia [University of Athens Medical School, Department of Anatomy (Greece); Benos, Ioannis; Votteas, Vassilios E. [Department of Cardiology (Greece)

    2004-09-15

    Spontaneous coronary artery dissection is a rare cause of acute myocardial infarction. We report a case of a 33-year-old male who presented with an acute inferior myocardial infarction. Coronary arteriography performed 3 hours after the episode revealed a dissection involving the middle segment of right coronary artery. Because of a spiral form of dissection and the TIMI 3 flow grade, our patient was treated medically and repeat coronary angiography 6 months later was decided.

  16. Quantitative Analysis of Signaling Networks across Differentially Embedded Tumors Highlights Interpatient Heterogeneity in Human Glioblastoma

    PubMed Central

    2015-01-01

    Glioblastoma multiforme (GBM) is the most aggressive malignant primary brain tumor, with a dismal mean survival even with the current standard of care. Although in vitro cell systems can provide mechanistic insight into the regulatory networks governing GBM cell proliferation and migration, clinical samples provide a more physiologically relevant view of oncogenic signaling networks. However, clinical samples are not widely available and may be embedded for histopathologic analysis. With the goal of accurately identifying activated signaling networks in GBM tumor samples, we investigated the impact of embedding in optimal cutting temperature (OCT) compound followed by flash freezing in LN2 vs immediate flash freezing (iFF) in LN2 on protein expression and phosphorylation-mediated signaling networks. Quantitative proteomic and phosphoproteomic analysis of 8 pairs of tumor specimens revealed minimal impact of the different sample processing strategies and highlighted the large interpatient heterogeneity present in these tumors. Correlation analyses of the differentially processed tumor sections identified activated signaling networks present in selected tumors and revealed the differential expression of transcription, translation, and degradation associated proteins. This study demonstrates the capability of quantitative mass spectrometry for identification of in vivo oncogenic signaling networks from human tumor specimens that were either OCT-embedded or immediately flash-frozen. PMID:24927040

  17. Nanometer-Scale Dissection of Chromosomes by Atomic Force Microscopy Combined with Heat-Denaturing Treatment

    NASA Astrophysics Data System (ADS)

    Tsukamoto, Kazumi; Kuwazaki, Seigo; Yamamoto, Kimiko; Shichiri, Motoharu; Yoshino, Tomoyuki; Ohtani, Toshio; Sugiyama, Shigeru

    2006-03-01

    We have developed a method for dissecting chromosome fragments with a size of a few hundred nanometers by atomic force microscopy (AFM). By using this method, we demonstrated reproducible dissections of silkworm chromosomes in the pachytene phase. The dissected fragments were successfully recovered on the cantilever tips, as confirmed by fluorescent microscopy using fluorescent stained chromosomes. To recover dissected chromosome fragments from a larger chromosome, such as the human metaphase chromosome of a somatic cell, heat denaturation was found to be effective. Further improvements in this method may lead to a novel tool for isolating valuable genes and/or investigating local genome structures in the near future.

  18. Cell-type Specific Optogenetic Mice for Dissecting Neural Circuitry Function

    E-print Network

    Zhao, Shengli

    Optogenetic methods have emerged as powerful tools for dissecting neural circuit connectivity, function, and dysfunction. We used a Bacterial Artificial Chromosome (BAC) transgenic strategy to express Channelrhodopsin2 ...

  19. Successful angioplasty of three cases of coronary artery dissections using hydrophilic wires

    PubMed Central

    Menon, Rajeev; Kapadia, Anuj

    2014-01-01

    Three cases of successful angioplasty of high-grade coronary dissections using hydrophilic wires were reported. Our first case had edge dissection after a stent deployed in the left anterior descending artery, after which we found it impossible to track the second stent over the regular wires, and which was successful when we tried with a stiffer hydrophilic wire. The second had spontaneous coronary artery dissections (SCAD), and the third case was a complicated plaque with multiple stenotic and ectatic segments along with dissection and successful angioplasty carried out using the same wires and without additional hardware. These wires also provided adequate support in tracking the required balloons and stents PMID:25489325

  20. Quantitative proteomics to decipher ubiquitin signaling

    PubMed Central

    Chen, Ping-Chung; Peng, Junmin

    2012-01-01

    Ubiquitin signaling plays an essential role in controlling cellular processes in eukaryotes, and the impairment of ubiquitin regulation contributes to the pathogenesis of a wide range of human diseases. During the last decade, mass spectrometry–based proteomics has emerged as an indispensable approach for identifying ubiquitinated proteins, ubiquitin modification sites, the structure of complex ubiquitin chains, as well as the interactome of ubiquitin enzymes. In particular, implementation of quantitative strategies allows the detection of dynamic changes in the ubiquitinated proteome, enhancing the ability to differentiate between function-relevant protein targets and false positives arising from biological and experimental variations. The profiling of total cell lysate and ubiquitinated proteome in the same sets of samples has become a powerful tool, revealing a subset of substrates that are modulated by specific physiological and pathological conditions, such as gene mutations in ubiquitin signaling. This strategy is equally useful for dissecting the pathways of ubiquitin-like proteins. PMID:22821265

  1. Dissecting inhibitory brain circuits with genetically-targeted technologies

    PubMed Central

    Murphey, Dona K.; Herman, Alexander M.; Arenkiel, Benjamin R.

    2014-01-01

    The evolution of genetically targeted tools has begun to allow us to dissect anatomically and functionally heterogeneous interneurons, and to probe circuit function from synapses to behavior. Over the last decade, these tools have been used widely to visualize neurons in a cell type-specific manner, and engage them to activate and inactivate with exquisite precision. In this process, we have expanded our understanding of interneuron diversity, their functional connectivity, and how selective inhibitory circuits contribute to behavior. Here we discuss the relative assets of genetically encoded fluorescent proteins (FPs), viral tracing methods, optogenetics, chemical genetics, and biosensors in the study of inhibitory interneurons and their respective circuits. PMID:25368555

  2. Characterization of residual stresses by WEDM-assisted dissectioning

    NASA Astrophysics Data System (ADS)

    Regener, B.; Krempaszky, C.; Werner, E.; Berhuber, E.; Stockinger, M.

    2010-06-01

    Within the scope of this contribution a wire electric discharge machining assisted dissectioning method is presented, which combines high precision cutting, minimum generation of additional residual stresses during the cutting process and high precision measurement of the resulting distortion. As an example a forged component made of the titanium alloy Ti6Al4V is investigated in a multiple cut procedure. A finite element based mechanical model for the estimation of the residual stress distribution in the component from the distortion data is introduced and discussed.

  3. Genetic Dissection of Learning and Memory in Mice

    PubMed Central

    Mineur, Yann S.; Crusio, Wim E.; Sluyter, Frans

    2004-01-01

    In this minireview, we discuss different strategies to dissect genetically the keystones of learning and memory. First, we broadly sketch the neurogenetic analysis of complex traits in mice. We then discuss two general strategies to find genes affecting learning and memory: candidate gene studies and whole genome searches. Next, we briefly review more recently developed techniques, such as microarrays and RNA interference. In addition, we focus on gene-environment interactions and endophenotypes. All sections are illustrated with examples from the learning and memory field, including a table summarizing the latest information about genes that have been shown to have effects on learning and memory. PMID:15656270

  4. Genetic dissection of partial resistance to race 6 of Venturia inaequalis in apple.

    PubMed

    Durel, C E; Parisi, L; Laurens, F; Van de Weg, W E; Liebhard, R; Jourjon, M F

    2003-04-01

    Scab, caused by the fungus Venturia inaequalis, is one of the most important diseases of apple (Malus x domestica). The major resistance gene, Vf, has been widely used in apple breeding programs, but two new races of the fungus (races 6 and 7) are able to overcome this gene. A mapped F1 progeny derived from a cross between the cultivars Prima and Fiesta has bee n inoculated with two monoconidial strains of race 6. These strains originated from sporulating leaves of 'Prima' and a descendant of 'Prima' that were grown in an orchard in northern Germany. 'Prima' carries the Vf resistance gene, whereas 'Fiesta' lacks Vf. A large variation in resistance and (or) susceptibility was observed among the individuals of the progeny. Several quantitative trait loci (QTLs) for resistance were identified that mapped on four genomic regions. One of them was located in the very close vicinity of the Vf resistance gene on linkage group LG-1 of the 'Prima' genetic map. This QTL is isolate specific because it was only detected with one of the two isolates. Two out of the three other genomic regions were identified with both isolates (LG-11 and LG-17). On LG-11, a QTL effect was detected in both parents. The genetic dissection of this QTL indicated a favourable intra-locus interaction between some parental alleles. PMID:12723038

  5. Characterization and genetic dissection of resistance to spotted alfalfa aphid (Therioaphis trifolii) in Medicago truncatula

    PubMed Central

    Kamphuis, Lars G.; Lichtenzveig, Judith; Peng, Kefan; Guo, Su-Min; Klingler, John P.

    2013-01-01

    Aphids cause significant yield losses in agricultural crops worldwide. Medicago truncatula, a model legume, cultivated pasture species in Australia and close relative of alfalfa (Medicago sativa), was used to study the defence response against Therioaphis trifolii f. maculate [spotted alfalfa aphid (SAA)]. Aphid performance and plant damage were compared among three accessions. A20 is highly susceptible, A17 has moderate resistance, and Jester is strongly resistant. Subsequent analyses using A17 and A20, reciprocal F1s and an A17×A20 recombinant inbred line (RIL) population revealed that this moderate resistance is phloem mediated and involves antibiosis and tolerance but not antixenosis. Electrical penetration graph analysis also identified a novel waveform termed extended potential drop, which occurred following SAA infestation of M. truncatula. Genetic dissection using the RIL population revealed three quantitative trait loci on chromosomes 3, 6, and 7 involved in distinct modes of aphid defence including antibiosis and tolerance. An antibiosis locus resides on linkage group 3 (LG3) and is derived from A17, whereas a plant tolerance and antibiosis locus resides on LG6 and is derived from A20, which exhibits strong temporary tolerance. The loci identified reside in regions harbouring classical resistance genes, and introgression of these loci in current medic cultivars may help provide durable resistance to SAA, while elucidation of their molecular mechanisms may provide valuable insight into other aphid–plant interactions. PMID:24058162

  6. Digital PCR and Quantitation

    E-print Network

    Perkins, Richard A.

    Applied Genetics Digital PCR and Quantitation Ross Haynes Research Biologist, Applied Genetics Group Forensics@NIST 2012 Meeting Gaithersburg, MD November 28, 2012 #12;Applied Genetics Agenda · Why quantitate with qPCR? · How digital PCR Will Help Quantitation · Quantitative PCR versus Digital PCR

  7. Dissection of epistasis in oligogenic Bardet-Biedl syndrome.

    PubMed

    Badano, Jose L; Leitch, Carmen C; Ansley, Stephen J; May-Simera, Helen; Lawson, Shaneka; Lewis, Richard Alan; Beales, Philip L; Dietz, Harry C; Fisher, Shannon; Katsanis, Nicholas

    2006-01-19

    Epistatic interactions have an important role in phenotypic variability, yet the genetic dissection of such phenomena remains challenging. Here we report the identification of a novel locus, MGC1203, that contributes epistatic alleles to Bardet-Biedl syndrome (BBS), a pleiotropic, oligogenic disorder. MGC1203 encodes a pericentriolar protein that interacts and colocalizes with the BBS proteins. Sequencing of two independent BBS cohorts revealed a significant enrichment of a heterozygous C430T mutation in patients, and a transmission disequilibrium test (TDT) showed strong over-transmission of this variant. Further analyses showed that the 430T allele enhances the use of a cryptic splice acceptor site, causing the introduction of a premature termination codon (PTC) and the reduction of steady-state MGC1203 messenger RNA levels. Finally, recapitulation of the human genotypes in zebrafish shows that modest suppression of mgc1203 exerts an epistatic effect on the developmental phenotype of BBS morphants. Our data demonstrate how the combined use of biochemical, genetic and in vivo tools can facilitate the dissection of epistatic phenomena, and enhance our appreciation of the genetic basis of phenotypic variability. PMID:16327777

  8. [Aortic dissection induced by symmetry aortic connector system].

    PubMed

    Ito, Yutaka; Okamoto, H; Niimi, T; Tamenishi, A

    2005-05-01

    A 74-year-old male with severe triple vessel disease underwent off-pump coronary artery bypass grafting (OPCAB). Preoperative computed tomography (CT) showed severely calcified ascending aorta. We revasculize the left coronary arteries with in situ internal thoracic artery (ITA) graft and the right coronary artery with a saphenous vein graft, which was attached to the disease-free portion of the aortic root, using Symmetry aortic connector system (ACS). Although the operation was uncomplicated, and postoperative course was uneventful until the 5th postoperative day when acute type A aortic dissection occurred. The patient died of aortic rupture on the 7th postoperative day. Necropsy disclosed that the entry located just on the proximal anastomotic site of the vein graft. It is possible placement of ACS device would trigger the dissecting process. With regard to the use of these one-shot devices for diseased aorta, its safety needs further investigation, even though it might be placed on an apparently intact portion. PMID:15881233

  9. Virtual Temporal Bone Dissection System: Development and Testing

    PubMed Central

    Wiet, Gregory J.; Stredney, Don; Kerwin, Thomas; Hittle, Bradley; Fernandez, Soledad A.; Welling, D. Bradley

    2012-01-01

    Objectives/Hypothesis The objective of this project was to develop a virtual temporal bone dissection system that would provide an enhanced educational experience for the training of otologic surgeons. Study Design A randomized, controlled, multi-institutional single blinded validation study. Methods The project encompassed 4 areas of emphasis: structural data acquisition, integration of the system, dissemination of the system, and validation. Results Structural acquisition was performed on multiple imaging platforms. Integration achieved a cost effective system. Dissemination was achieved on different levels including casual interest, downloading of software, and full involvement in development and validation studies. A validation study was performed at 8 different training institutions across the country using a two arm, randomized trial where study subjects were randomized to a two-week practice session using either the virtual temporal bone or standard cadaveric temporal bones. Eighty subjects were enrolled and randomized to one of the two treatment arms, 65 completed the study. There was no difference between the two groups using a blinded rating tool to assess performance after training. Conclusions 1. A virtual temporal bone dissection system has been developed and compared to cadaveric temporal bones for practice using a multi-center trial. 2. There is no statistical difference seen between practice on the current simulator when compared to practice on human cadaveric temporal bones. 3. Further refinements in structural acquisition and interface design have been identified which can be implemented prior to full incorporation into training programs and use for objective skills assessment. PMID:22294268

  10. Popliteal lymph node dissection for metastases of cutaneous malignant melanoma

    PubMed Central

    2014-01-01

    Popliteal lymph node dissection is performed when grossly metastatic nodal disease is encountered in the popliteal fossa or after microscopic metastasis is found in interval sentinel nodes during clinical staging of cutaneous malignant melanoma. Initially, an S-shaped incision is made to gain access to the popliteal fossa. A careful en bloc removal of fat tissue and lymph nodes is made to preserve and avoid the injury of peroneal and tibial nerves as well as popliteal vessels, following the previous recommendations. This rare surgical procedure was successfully employed in a patient with cutaneous malignant melanoma and nodal metastases at the popliteal fossa. The technique described by Karakousis was reproduced in a step-by-step fashion to allow anatomical identification of the neurovascular structures and radical resection with no post-operative morbidity and prompt recovery. Popliteal lymph node dissection is a rarely performed operative procedure. Following a lymphoscintigraphic examination of the popliteal nodal station, surgeons can be asked to explore the popliteal fossa. Detailed familiarity of the operative procedure is necessary, however, to avoid complications. PMID:24886058

  11. Retroperitoneal lymph node dissection for metastatic germ cell tumours

    PubMed Central

    Haldipur, N; Devaraj, S; Shehata, A; Lewis, AK; Smith, MO; Hatton, M; Nassef, A; Beard, JD

    2011-01-01

    INTRODUCTION In the North Trent Cancer Network (NTCN) patients requiring retroperitoneal lymphadenectomy for metastatic testicular cancer have been treated by vascular service since 1990. This paper reviews our experience and considers the case for involvement of vascular surgeons in the management of these tumours. PATIENTS AND METHODS Patients referred by the NTCN to the vascular service for retroperitoneal lymphadenectomy between 1990 and 2009 were identified through a germ cell database. Data were supplemented by a review of case notes to record histology, intraoperative and postoperative details. RESULTS A total of 64 patients were referred to the vascular service for retroperitoneal lymph node dissection, with a median age of 29 years (16–63 years) and a median follow-up of 4.9 years. Ten patients died: eight from tumour recurrence, one from septicaemia during chemotherapy and one by suicide. Of the 54 who survived, 7 were alive with residual masses and 47 patients were disease-free at the last follow-up. Sixteen patients required vascular procedures: four had aortic repair (fascia), three had aortic replacement (spiral graft), four had inferior vena cava resection, two had iliac artery replacement and two had iliac vein resection. CONCLUSIONS Retroperitoneal lymph node dissection often involves mobilisation and/or the resection/replacement of major vessels. We recommend that a vascular surgeon should be a part of testicular germ cell multidisciplinary team. PMID:21944797

  12. Combined subgaleal/myocutaneous technique for temporalis muscle dissection.

    PubMed

    Youssef, A Samy; Ahmadian, Amir; Ramos, Edwin; Vale, Fernando; van Loveren, Harry R

    2012-12-01

    Background?The frontal branch of the facial nerve (FBFN) is the most susceptible neural structure to injury during frontotemporal craniotomies. The balance between adequate temporalis muscle mobilization and frontal branch protection with minimal anatomical alteration is the philosophy behind our approach to temporalis muscle dissection. Objective?To describe a combined subgaleal/myocutaneous technique for dissection and mobilization of the temporalis muscle in anterolateral cranial approaches. Methods?Interdisciplinary literature review of the anatomical course of the FBFN was performed. Retrospective analysis of anterolateral craniotomies performed at our institution in which the combined subgaleal/myocutaneous (CSGMC) technique was performed. Results?A total of 71 cases of anterolateral craniotomies (excluding full variant orbitozygomatic) were performed with the successful application of a CSGMC technique (36 pterional, 31 orbitopterional, and 4 fronto-orbital). Partial frontalis weakness was transient in one case. Conclusion?The CSGMC technique provides sufficient protection for the FBFN and allows for adequate mobilization for a variety of skull base exposures while minimally violating myofascial anatomy. This is the first reported technique that allows both adequate temporalis muscle mobilization with performance of the one-piece orbitofrontal and orbitopterional approaches, without disruption of the superficial/deep temporalis fascia and fat-pad complex. PMID:24294555

  13. Combined Subgaleal/Myocutaneous Technique for Temporalis Muscle Dissection

    PubMed Central

    Youssef, A. Samy; Ahmadian, Amir; Ramos, Edwin; Vale, Fernando; van Loveren, Harry R.

    2012-01-01

    Background?The frontal branch of the facial nerve (FBFN) is the most susceptible neural structure to injury during frontotemporal craniotomies. The balance between adequate temporalis muscle mobilization and frontal branch protection with minimal anatomical alteration is the philosophy behind our approach to temporalis muscle dissection. Objective?To describe a combined subgaleal/myocutaneous technique for dissection and mobilization of the temporalis muscle in anterolateral cranial approaches. Methods?Interdisciplinary literature review of the anatomical course of the FBFN was performed. Retrospective analysis of anterolateral craniotomies performed at our institution in which the combined subgaleal/myocutaneous (CSGMC) technique was performed. Results?A total of 71 cases of anterolateral craniotomies (excluding full variant orbitozygomatic) were performed with the successful application of a CSGMC technique (36 pterional, 31 orbitopterional, and 4 fronto-orbital). Partial frontalis weakness was transient in one case. Conclusion?The CSGMC technique provides sufficient protection for the FBFN and allows for adequate mobilization for a variety of skull base exposures while minimally violating myofascial anatomy. This is the first reported technique that allows both adequate temporalis muscle mobilization with performance of the one-piece orbitofrontal and orbitopterional approaches, without disruption of the superficial/deep temporalis fascia and fat-pad complex. PMID:24294555

  14. 10 20 30 40 50 60 70 80 90 100 CV% (Bins of 10%)

    E-print Network

    Richardson, David

    of a Label-Free Quantitative Phosphoproteomics Platform Applicable to Non-Cell Culture Biological Matrices employed LC-MS based approaches for quantitative phosphoproteomics include stable-isotope labeled-Free Quantitative Phosphoproteomics Workflow TiO2 Enrichment Optimization Application to evaluate ENO treated LPS

  15. Approach to systematic analysis of serine/threonine phosphoproteome using Beta elimination and subsequent side effects: intramolecular linkage and/or racemisation.

    PubMed

    Tinette, Sylvette; Feyereisen, René; Robichon, Alain

    2007-03-01

    Complete analysis of the phosphorylation of serine and threonine residues directly from biological extracts is still at an early stage and will remain a challenging goal for many years. Analysis of phosphorylated proteins and identification of the phosphorylated sites in a crude biological extract is a major topic in proteomics, since phosphorylation plays a dominant role in post-translational protein modification. Beta elimination of the serine/threonine-bound phosphate by alkali action generates (methyl)dehydroalanine. The reactivity of this group susceptible of nucleophilic attacks might be used as a tool for phosphoproteome analysis. Most of the known serine/threonine kinases recognize motifs in protein targets that are rich in lysine(s) and/or arginine(s). The (methyl)dehydroalanine resulting from beta elimination of the serine/threonine-bound phosphate by alkali action is likely to react with the amino groups of these neighboring amino acids. Furthermore, the addition reaction of dehydroalanine-peptides with a nucleophilic group more likely generates diastereoisomers derivatives. The internal cyclic bonds and/or the stereoisomer peptide derivatives thus generated confer resistance to trypsin cleavage and/or constitute stop signals for exopeptidases such as carboxypeptidase. This might form the basis of a method to facilitate the systematic identification of phosphorylated peptides. PMID:17115411

  16. A High-Resolution Tissue-Specific Proteome and Phosphoproteome Atlas of Maize Primary Roots Reveals Functional Gradients along the Root Axes1[OPEN

    PubMed Central

    Malik, Waqas Ahmed; Shen, Zhouxin; Paschold, Anja

    2015-01-01

    A high-resolution proteome and phosphoproteome atlas of four maize (Zea mays) primary root tissues, the cortex, stele, meristematic zone, and elongation zone, was generated. High-performance liquid chromatography coupled with tandem mass spectrometry identified 11,552 distinct nonmodified and 2,852 phosphorylated proteins across the four root tissues. Two gradients reflecting the abundance of functional protein classes along the longitudinal root axis were observed. While the classes RNA, DNA, and protein peaked in the meristematic zone, cell wall, lipid metabolism, stress, transport, and secondary metabolism culminated in the differentiation zone. Functional specialization of tissues is underscored by six of 10 cortex-specific proteins involved in flavonoid biosynthesis. Comparison of this data set with high-resolution seed and leaf proteome studies revealed 13% (1,504/11,552) root-specific proteins. While only 23% of the 1,504 root-specific proteins accumulated in all four root tissues, 61% of all 11,552 identified proteins accumulated in all four root tissues. This suggests a much higher degree of tissue-specific functionalization of root-specific proteins. In summary, these data illustrate the remarkable plasticity of the proteomic landscape of maize primary roots and thus provide a starting point for gaining a better understanding of their tissue-specific functions. PMID:25780097

  17. Classic Ras Proteins Promote Proliferation and Survival via Distinct Phosphoproteome Alterations in Neurofibromin-Null Malignant Peripheral Nerve Sheath Tumor Cells.

    PubMed

    Brossier, Nicole M; Prechtl, Amanda M; Longo, Jody Fromm; Barnes, Stephen; Wilson, Landon S; Byer, Stephanie J; Brosius, Stephanie N; Carroll, Steven L

    2015-06-01

    Neurofibromin, the tumor suppressor encoded by the neurofibromatosis type 1 (NF1) gene, potentially suppresses the activation of H-Ras, N-Ras, and K-Ras. However, it is not known whether these classic Ras proteins are hyperactivated in NF1-null nerve sheath tumors, how they contribute to tumorigenesis, and what signaling pathways mediate their effects. Here we show that H-Ras, N-Ras, and K-Ras are coexpressed with their activators (guanine nucleotide exchange factors) in neurofibromin-null malignant peripheral nerve sheath tumor (MPNST) cells, and that all 3 Ras proteins are activated. Dominant negative (DN) H-Ras, a pan-inhibitor of the classic Ras family, inhibited MPNST proliferation and survival, but not migration. However, NF1-null MPNST cells were variably dependent on individual Ras proteins. In some lines, ablation of H-Ras, N-Ras, and/or K-Ras inhibited mitogenesis. In others, ablation of a single Ras protein had no effect on proliferation; in these lines, ablation of a single Ras protein resulted in compensatory increases in the activation and/or expression of other Ras proteins. Using mass spectrometry-based phosphoproteomics, we identified 7 signaling networks affecting morphology, proliferation, and survival that are regulated by DN H-Ras. Thus, neurofibromin loss activates multiple classic Ras proteins that promote proliferation and survival by regulating several distinct signaling cascades. PMID:25946318

  18. Sequential enrichment with titania-coated magnetic mesoporous hollow silica microspheres and zirconium arsenate-modified magnetic nanoparticles for the study of phosphoproteome of HL60 cells.

    PubMed

    Yu, Qiong-Wei; Li, Xiao-Shui; Xiao, Yongsheng; Guo, Lei; Zhang, Fan; Cai, Qian; Feng, Yu-Qi; Yuan, Bi-Feng; Wang, Yinsheng

    2014-10-24

    As one of the most important types of post-translational modifications, reversible phosphorylation of proteins plays crucial roles in a large number of biological processes. However, owing to the relatively low abundance and dynamic nature of phosphorylation and the presence of the unphosphorylated peptides in large excess, phosphopeptide enrichment is indispensable in large-scale phosphoproteomic analysis. Metal oxides including titanium dioxide have become prominent affinity materials to enrich phosphopeptides prior to their analysis using liquid chromatography-mass spectrometry (LC-MS). In the current study, we established a novel strategy, which encompassed strong cation exchange chromatography, sequential enrichment of phosphopeptides using titania-coated magnetic mesoporous hollow silica microspheres (TiO2/MHMSS) and zirconium arsenate-modified magnetic nanoparticles (ZrAs-Fe3O4@SiO2), and LC-MS/MS analysis, for the proteome-wide identification of phosphosites of proteins in HL60 cells. In total, we were able to identify 11,579 unique phosphorylation sites in 3432 unique proteins. Additionally, our results suggested that TiO2/MHMSS and ZrAs-Fe3O4@SiO2 are complementary in phosphopeptide enrichment, where the two types of materials displayed preferential binding of peptides carrying multiple and single phosphorylation sites, respectively. PMID:25262027

  19. Endoscopic axillary lymph node dissection: an experimental study in human cadavers

    Microsoft Academic Search

    L. Michael Brunt; Daniel B. Jones; Justin S. Wu; Elizabeth M. Brunt; Diane M. Radford

    1998-01-01

    Background: The role of axillary lymph node dissection in the staging of patients with breast carcinoma is currently under evaluation. As a result of recent advances in minimally invasive techniques, an endoscopic approach to axillary lymph node dissection may be an attractive alternative to lymphadenectomy performed via a standard “open” axillary incision. The purpose of the present study was to

  20. Dissecting Aneurysm of the Superior Mesenteric Artery Successfully Treated by Endovascular Stent-Graft Placement

    SciTech Connect

    Ishida, Masaki, E-mail: mishida@clin.medic.mie-u.ac.jp; Kato, Noriyuki [MieUniversity Hospital, 2-174 Edobashi Tsu, Mie 514-8507, Department of Radiology (Japan); Hirano, Tadanori [Mie University Hospital, Mie, Department ofThoracic and Cardiovascular Surgery (Japan); Suzuki, Tomoaki; Shomura, Yu; Yada, Isao [Matsusaka General Hospital, Matsusaka, Department ofRadiology (Japan); Takeda, Kan [MieUniversity Hospital, 2-174 Edobashi Tsu, Mie 514-8507, Department of Radiology (Japan)

    2003-08-15

    Spontaneous and isolated dissecting aneurysm of the superior mesenteric artery is a rare event that has been successfully treated by surgery in several reported cases. To our knowledge, we present the first case of a patient with spontaneous and isolated dissecting aneurysm of the superior mesenteric artery that was successfully treated by endovascular stent-graft placement.

  1. Symptomatic Internal Carotid Artery Dissecting Pseudoaneurysm: Endovascular Treatment by Stent-Graft

    SciTech Connect

    Heye, Sam, E-mail: sam.heye@uz.kuleuven.ac.be; Maleux, Geert [University Hospitals Gasthuisberg, Department of Radiology (Belgium); Vandenberghe, Rik [University Hospitals Gasthuisberg, Department of Neurology (Belgium); Wilms, Guido [University Hospitals Gasthuisberg, Department of Radiology (Belgium)

    2005-05-15

    Dissecting pseudoaneurysm of the extracranial portion of the internal carotid artery (ICA) is a usually benign complication of spontaneous ICA dissection. We report a case in which pseudoaneurysm volume enlarged progressively and new clinical symptoms developed 9 months following disease onset. Placement of a coronary stent-graft resulted in immediate complete resolution of clinical symptoms and radiologic restoration of normal flow.

  2. Spontaneous coronary artery dissection: a neglected cause of acute myocardial ischaemia and sudden death

    Microsoft Academic Search

    C. Basso; G. L. Morgagni; G. Thiene

    1996-01-01

    Spontaneous coronary artery dissection is a rare cause of acute myocardial ischaemia. Eight consecutive fatal cases which occurred in women aged 34-54 years (mean 43) are described. The dissection involved the left anterior descending coronary artery in four, the left main trunk in two, the right coronary artery in one, and both left anterior descending and circumflex arteries in one.

  3. Traumatic dissection of the internal carotid artery: simultaneous infarct of optic nerve and brain

    PubMed Central

    Correa, Edgar; Martinez, Braulio

    2014-01-01

    Key Clinical Message Traumatic intracranial internal carotid artery dissection is a rare but significant cause of stroke in patients in their forties, leading to high morbidity and mortality. Simultaneous ischemic stroke and optic nerve infarction can occur. Clinical suspicion of dissection is determining in the acute management. PMID:25356244

  4. Extracranial internal carotid and vertebral artery dissections: angiographic spectrum, course and prognosis

    Microsoft Academic Search

    O. Pelkonen; T. Tikkakoski; S. Leinonen; J. Pyhtinen; M. Lepojärvi; K. Sotaniemi

    2003-01-01

    We reviewed the clinical and radiological findings of 93 consecutive patients with 111 extracranial internal carotid (ICAD) and vertebral artery (VAD) dissections and one concomitant intracranial VAD; 83% of the patients had unilateral and 17% multiple vessel dissections. The diagnosis was made by intra-arterial digital subtraction angiography in 92 patients and MR angiography in one. Follow-up angiography was performed in

  5. Dissection Reconsidered: A Reaction to de Villiers and Monk's "The First Cut Is the Deepest"

    ERIC Educational Resources Information Center

    Hug, Barbara

    2005-01-01

    Educators need to think about pedagogical as well as ethical issues when asking if dissection has a role in contemporary K-12 science education. I consider some arguments for and against dissection as a way to teach students the biological concepts of form and function.

  6. Science Laboratory Depth of Learning: Interactive Multimedia Simulation and Virtual Dissection Software

    ERIC Educational Resources Information Center

    Yuza, Steve C.

    2010-01-01

    The purpose of this study was to determine the effects of interactive multimedia simulations and virtual dissection software on depth of learning among students participating in biology and chemistry laboratory courses. By understanding more about how simulation and virtual dissection software changes depth of learning, educators will have the…

  7. Dissecting the Dissectors: Knowledge, Attitude, and Practice of Body Bequests by Nigerian Anatomists

    ERIC Educational Resources Information Center

    Anyanwu, Emeka G.; Obikili, Emmanuel N.

    2012-01-01

    Anatomy education in most African countries is limited by an insufficient number of cadavers for students to undertake dissection. This already significant shortage is exacerbated by an increasing number of medical schools and students. Virtual dissections are impractical in alleviating such a shortfall in African anatomy education, and further…

  8. Acute Basilar Artery Dissection Treated by Emergency Stenting in a 13YearOld Boy

    Microsoft Academic Search

    Masaki Komiyama; Masaki Yoshimura; Yuji Honnda; Yasuhiro Matsusaka; Toshihiro Yasui

    2005-01-01

    We report a 13-year-old boy who presented with acute basilar artery occlusion due to traumatic arterial dissection. Because a grave prognosis was expected if left untreated, and the chance of neurological recovery was believed to be unlikely but not zero, given that emergency stenting for the dissection was performed within 6 h of ictus. Recanalization of the basilar artery with

  9. Medical Students' Reactions to Anatomic Dissection and the Phenomenon of Cadaver Naming

    ERIC Educational Resources Information Center

    Williams, Austin D.; Greenwald, Emily E.; Soricelli, Rhonda L.; DePace, Dennis M.

    2014-01-01

    The teaching of gross anatomy has, for centuries, relied on the dissection of human cadavers, and this formative experience is known to evoke strong emotional responses. The authors hypothesized that the phenomenon of cadaver naming is a coping mechanism used by medical students and that it correlates with other attitudes about dissection and body…

  10. Stent Placement for Acute Superior Mesenteric Artery Occlusion Associated with Type B Aortic Dissection

    PubMed Central

    Suzuki, Kazushi; Shimohira, Masashi

    2015-01-01

    A 50-year-old man had a mesenteric ischemia related to superior mesenteric artery (SMA) occlusion associated with a type B aortic dissection. We decided to perform stent placement for the SMA and could avoid mesenteric ischemia. We think the stent placement in the SMA might be an option for the treatment of mesenteric ischemia caused by aortic dissection.

  11. Association of Left Ventricular Hypertrophy and Aortic Dilation in Patients with Acute Thoracic Aortic Dissection

    Microsoft Academic Search

    Diana Iarussi; Aurelio Caruso; Maurizio Galderisi; Franco Enrico Covino; Giovanni Dialetto; Eduardo Bossone; Oreste de Divitiis; Maurizio Cotrufo

    2001-01-01

    This study was designed to evaluate the impact of left ventricular mass on aortic diameters in patients who presented with acute thoracic aortic dissection where aortic dilation is common. Retrospective review of transthoracic and transesophageal echocardiograms was conducted for 63 patients treated for acute thoracic aortic dissection and for 16 normal subjects who were comparable for gender prevalence, age, heart

  12. Minimally invasive video-assisted functional lateral neck dissection for metastatic papillary thyroid carcinoma

    Microsoft Academic Search

    Celestino Pio Lombardi; Marco Raffaelli; Pietro Princi; Carmela De Crea; Rocco Bellantone

    2007-01-01

    Functional lateral neck dissection requires a large incision providing adequate exposure of the surgical field. We evaluated the feasibility of minimally invasive video-assisted functional lateral neck dissection (VALNED) in patients with papillary thyroid carcinoma (PTC). Low-risk PTC patients with lateral neck metastases

  13. The Specific Relationship between Disgust and Interest: Relevance during Biology Class Dissections and Gender Differences

    ERIC Educational Resources Information Center

    Holstermann, Nina; Ainley, Mary; Grube, Dietmar; Roick, Thorsten; Bogeholz, Susanne

    2012-01-01

    This investigation examined trajectories of interest and disgust related to a biology dissection class. Three hundred and two secondary students completed ratings of disgust sensitivity and individual interest in the topic of the heart approximately one week before a dissection class. States of disgust and interest were recorded before, during,…

  14. Students' Physical and Psychological Reactions to Forensic Dissection: Are There Risk Factors?

    ERIC Educational Resources Information Center

    Sergentanis, Theodoros N.; Papadodima, Stavroula A.; Evaggelakos, Christos I.; Mytilinaios, Dimitrios G.; Goutas, Nikolaos D.; Spiliopoulou, Chara A.

    2010-01-01

    The reactions of students to forensic dissection encompass psychologico-emotional and physical components. This exploratory study aimed to determine risk factors for students' adverse physical and psychological reactions to forensic dissection. All sixth-year medical students (n = 304) attending the compulsory practical course in forensic medicine…

  15. Postpartum multivessel spontaneous coronary artery dissection confirmed by coronary CT angiography

    PubMed Central

    Schroder, Catherine; Stoler, Robert C.; Branning, George B.

    2006-01-01

    Spontaneous coronary artery dissection is a rare but potentially life-threatening event associated with the peripartum period. We present a case of postpartum multivessel spontaneous coronary artery dissection diagnosed by conventional angiography and monitored with computed tomographic coronary angiography. The patient was initially managed medically and later received a coronary stent. PMID:17106495

  16. Aortic tear and dissection related to connective tissues abnormalities resembling Marfan syndrome in a Great Dane.

    PubMed

    Lenz, Jennifer A; Bach, Jonathan F; Bell, Cynthia M; Stepien, Rebecca L

    2015-06-01

    Aortic tears and acute aortic dissection are rarely reported in dogs. This report describes a case of aortic dissection and probable sinus of Valsalva rupture in a young Great Dane with associated histopathologic findings suggestive of a connective tissue abnormality. PMID:25890485

  17. Acute Aortic Dissections with Pregnancy in Women with ACTA2 Mutations

    PubMed Central

    Regalado, Ellen S.; Guo, Dong-chuan; Estrera, Anthony L.; Buja, L. Maximilian; Milewicz, Dianna M.

    2014-01-01

    Mutations in ACTA2 predispose to thoracic aortic aneurysms and dissections as well as coronary artery and cerebrovascular disease. Here we examined the risk of aortic dissections, stroke and myocardial infarct with pregnancy in women with ACTA2 mutations. Of the 53 women who had a total of 137 pregnancies, eight had aortic dissections in the third trimester or the postpartum period (6% of pregnancies). One woman also had a myocardial infarct that occurred during pregnancy that was independent of her aortic dissection. Compared to the population-based frequency of peripartum aortic dissections of 0.6%, the rate of peripartum aortic dissections in women with ACTA2 mutations is much higher (8 out of 39; 20%). Six of these dissections initiated in the ascending aorta (Stanford type A), three of which were fatal. Three women had ascending aortic dissections at diameters less that 5.0 cm (range 3.8 to 4.7 cm). Aortic pathology showed mild to moderate medial degeneration of the aorta in three women. Of note, five of the women had hypertension either during or before the pregnancy. In summary, the majority of women with ACTA2 mutations did not have aortic or other vascular complications with pregnancy. However, these findings show that pregnancy is associated with significant risk for aortic dissections in women in whom diagnosis of ACTA2 mutation has not been made. Women with ACTA2 mutations who are planning to get pregnant should be counseled about this risk of aortic dissections, and proper clinical management should be initiated to reduce this risk. PMID:24243736

  18. Simultaneous bilateral internal carotid and vertebral artery dissection following chiropractic manipulation: case report and review of the literature

    Microsoft Academic Search

    R. N. Nadgir; L. A. Loevner; T. Ahmed; G. Moonis; J. Chalela; K. Slawek; S. Imbesi

    2003-01-01

    Single-vessel cervical arterial dissections typically occur in young adults and are a common cause of cerebral ischemia and stroke. Although the pathogenesis of multivessel dissection is unclear, it is thought to be a consequence of underlying collagen vascular disease. We present a 34-year-old previously healthy man who developed bilateral internal carotid and vertebral artery dissection following chiropractic manipulation.

  19. Defense response genes co-localize with quantitative disease resistance loci in pepper

    Microsoft Academic Search

    S. Pflieger; A. Palloix; C. Caranta; A. Blattes; V. Lefebvre

    2001-01-01

    Functional bases of polygenically inherited disease resistance are still unknown. In recent years, molecular dissection of\\u000a polygenic resistance has led to the identification and location of quantitative trait loci (QTLs) on many plant genetic linkage\\u000a maps. This process is a pre-requisite for resistance QTL characterization at a molecular and functional level. Here, we report\\u000a the use of a candidate gene

  20. Genetic Dissection of Rhythmic Motor Networks in Mice

    PubMed Central

    Grossmann, Katja S.; Giraudin, Aurore; Britz, Olivier; Zhang, Jingming; Goulding, Martyn

    2011-01-01

    Simple motor behaviors such as locomotion and respiration involve rhythmic and coordinated muscle movements that are generated by central pattern generator (CPG) networks in the spinal cord and hindbrain. These CPG networks produce measurable behavioral outputs, and thus represent ideal model systems for studying the operational principles that the nervous system uses to produce specific behaviors. Recent advances in our understanding of the transcriptional code that controls neuronal development have provided an entry point into identifying and targeting distinct neuronal populations that make up locomotor CPG networks in the spinal cord. This has spurred the development of new genetic approaches to dissect and manipulate neuronal networks both in the spinal cord and hindbrain. Here we discuss how the advent of molecular genetics together with anatomical and physiological methods has begun to revolutionize studies of the neuronal networks controlling rhythmic motor behaviors in mice. PMID:21111198

  1. Open fenestration for complicated acute aortic B dissection

    PubMed Central

    Segreti, Sara; Grassi, Viviana; Lomazzi, Chiara; Cova, Marta; Piffaretti, Gabriele; Rampoldi, Vincenzo

    2014-01-01

    Acute type B aortic dissection (ABAD) is a serious cardiovascular emergency in which morbidity and mortality are often related to the presence of complications at clinical presentation. Visceral, renal, and limb ischemia occur in up to 30% of patients with ABAD and are associated with higher in-hospital mortality. The aim of the open fenestration is to resolve the malperfusion by creating a single aortic lumen at the suprarenal or infrarenal level. This surgical procedure is less invasive than total aortic replacement, thus not requiring extracorporeal support and allowing preservation of the intercostal arteries, which results in decreased risk of paraplegia. Surgical aortic fenestration represents an effective and durable option for treating ischemic complications of ABAD, particularly for patients with no aortic dilatation. In the current endovascular era, this open technique serves as an alternative option in case of contraindications or failure of endovascular management of complicated ABAD. PMID:25133107

  2. Genetic dissection of rhythmic motor networks in mice.

    PubMed

    Grossmann, Katja S; Giraudin, Aurore; Britz, Olivier; Zhang, Jingming; Goulding, Martyn

    2010-01-01

    Simple motor behaviors such as locomotion and respiration involve rhythmic and coordinated muscle movements that are generated by central pattern generator (CPG) networks in the spinal cord and hindbrain. These CPG networks produce measurable behavioral outputs and thus represent ideal model systems for studying the operational principles that the nervous system uses to produce specific behaviors. Recent advances in our understanding of the transcriptional code that controls neuronal development have provided an entry point into identifying and targeting distinct neuronal populations that make up locomotor CPG networks in the spinal cord. This has spurred the development of new genetic approaches to dissect and manipulate neuronal networks both in the spinal cord and hindbrain. Here we discuss how the advent of molecular genetics together with anatomical and physiological methods has begun to revolutionize studies of the neuronal networks controlling rhythmic motor behaviors in mice. PMID:21111198

  3. Dissecting Arabidopsis G? signal transduction on the protein surface.

    PubMed

    Jiang, Kun; Frick-Cheng, Arwen; Trusov, Yuri; Delgado-Cerezo, Magdalena; Rosenthal, David M; Lorek, Justine; Panstruga, Ralph; Booker, Fitzgerald L; Botella, José Ramón; Molina, Antonio; Ort, Donald R; Jones, Alan M

    2012-07-01

    The heterotrimeric G-protein complex provides signal amplification and target specificity. The Arabidopsis (Arabidopsis thaliana) G?-subunit of this complex (AGB1) interacts with and modulates the activity of target cytoplasmic proteins. This specificity resides in the structure of the interface between AGB1 and its targets. Important surface residues of AGB1, which were deduced from a comparative evolutionary approach, were mutated to dissect AGB1-dependent physiological functions. Analysis of the capacity of these mutants to complement well-established phenotypes of G?-null mutants revealed AGB1 residues critical for specific AGB1-mediated biological processes, including growth architecture, pathogen resistance, stomata-mediated leaf-air gas exchange, and possibly photosynthesis. These findings provide promising new avenues to direct the finely tuned engineering of crop yield and traits. PMID:22570469

  4. From microscopes to microarrays: dissecting recurrent chromosomal rearrangements

    PubMed Central

    Emanuel, Beverly S.; Saitta, Sulagna C.

    2010-01-01

    Submicroscopic chromosomal rearrangements that lead to copy-number changes have been shown to underlie distinctive and recognizable clinical phenotypes. The sensitivity to detect copy-number variation has escalated with the advent of array comparative genomic hybridization (CGH), including BAC and oligonucleotide-based platforms. Coupled with improved assemblies and annotation of genome sequence data, these technologies are facilitating the identification of new syndromes that are associated with submicroscopic genomic changes. Their characterization reveals the role of genome architecture in the aetiology of many clinical disorders. We review a group of genomic disorders that are mediated by segmental duplications, emphasizing the impact that high-throughput detection methods and the availability of the human genome sequence have had on their dissection and diagnosis. PMID:17943194

  5. Mid-arm lymph nodes dissection for melanoma.

    PubMed

    Fujiwara, Masao; Suzuki, Ayano; Mizukami, Takahide; Nagata, Takeshi; Ito, Taisuke; Fukamizu, Hidekazu

    2010-09-01

    An interval node in the upper limb termed the mid-arm node was recently identified. However, its surgical anatomy remains unclear. We report a patient with metastatic melanoma of the mid-arm node and the epitrochlear node at 10 years after removal of the primary tumour from the forearm and therapeutic axillary lymph node dissection. The mid-arm node is located halfway up the upper arm on the medial intermuscular septum, at the site where the brachial vessels, the median nerve and the ulnar nerve run adjacent to each other. The mid-arm node lies adjacent to the basilic vein where lymphatic vessels ascend and converge. This is the first report regarding the surgical anatomy of the mid-arm node. PMID:20227935

  6. Brain virtual dissection and white matter 3D visualization.

    PubMed

    Serres, Barthélemy; Zemmoura, Ilyess; Andersson, Frédéric; Tauber, Clovis; Destrieux, Christophe; Venturini, Gilles

    2013-01-01

    This paper presents an immersive visualization tool that helps anatomists to establish a ground truth for brain white matter fiber bundles. Each step of a progressive anatomical dissection of human brain hemisphere is acquired using a high resolution 3D laser scanner and a photographic device. Each resulting surface is textured with a high resolution image and registered into a common 3D space using fiducial landmarks. Surfaces can be visualized using stereoscopic hardware and are interactively selectable. The tool allows the user to identify specific fiber bundle parts. Extracted fiber bundles are stacked together and rendered in stereoscopy with the corresponding MR volume. Surgeons have validated this tool for creating ground truth in medical imaging with the perspective of validating tractography algorithms. PMID:23400190

  7. Mesenteric malperfusion complicated with type A acute aortic dissection.

    PubMed

    Takagi, H; Watanabe, T; Umemoto, T

    2015-10-01

    Type A acute aortic dissection (AAAD), involving the ascending aorta, is one of life-threatening disorders. Emergent surgery, such as graft replacement of the aortic root, ascending aorta, aortic arch, or these combinations, is routinely performed to avoid sudden death due to free rupture, cardiac tamponade, or coronary obstruction. Even though appropriate surgery is immediately completed, however, operative mortality remains high, between 15% and 30%. Furthermore, mesenteric malperfusion, bringing about enteric ischemia, occurs unusually in AAAD with far and away higher mortality. In the present article, we reviewed contemporary evidence regarding incidence, mortality, and treatment of mesenteric malperfusion complicated with AAAD. The incidence and early mortality rate of mesenteric malperfusion complicated with AAAD was 4% and 68%, respectively. Patients with mesenteric malperfusion had a 9.7-fold risk of mortality relative to those without it. Evidence regarding optimal treatment of mesenteric malperfusion complicated with AAAD is very limited. PMID:25077517

  8. In vivo dissection of the chromosome condensation machinery

    PubMed Central

    Lavoie, Brigitte D.; Hogan, Eileen; Koshland, Douglas

    2002-01-01

    The machinery mediating chromosome condensation is poorly understood. To begin to dissect the in vivo function(s) of individual components, we monitored mitotic chromosome structure in mutants of condensin, cohesin, histone H3, and topoisomerase II (topo II). In budding yeast, both condensation establishment and maintenance require all of the condensin subunits, but not topo II activity or phospho-histone H3. Structural maintenance of chromosome (SMC) protein 2, as well as each of the three non-SMC proteins (Ycg1p, Ycs4p, and Brn1p), was required for chromatin binding of the condensin complex in vivo. Using reversible condensin alleles, we show that chromosome condensation does not involve an irreversible modification of condensin or chromosomes. Finally, we provide the first evidence of a mechanistic link between condensin and cohesin function. A model discussing the functional interplay between cohesin and condensin is presented. PMID:11864994

  9. Multivessel spontaneous coronary artery dissection in an unlikely patient.

    PubMed

    Jehangir, Waqas; Aly, Tarek; Bedran, Kebir H; Yousif, Abdalla; Niemiera, Mark L

    2015-01-01

    When approaching the symptom of acute onset chest pain in a previously healthy 26-year-old male, anchoring heuristic presents a challenge to healthcare workers. This diagnostic error is the healthcare professional's tendency to rely on a previous diagnosis, and, in situations where a set of symptoms might mask a rare and deadly condition, this error can prove fatal for the patient. One such condition, Spontaneous Coronary Artery Dissection (SCAD), is an uncommon and malefic presentation of coronary artery disease that can lead to myocardial infarction and sudden death. We present a case of SCAD in an otherwise healthy 26 year-old male who had been experiencing chest pain during and after sports activity. In the young, athletic male with SCAD, the danger of diagnostic error was a reality due to the broad symptomatology and the betraying demographics. PMID:25945264

  10. Early recognition of acute thoracic aortic dissection and aneurysm

    PubMed Central

    2013-01-01

    Background Thoracic aortic dissection (TAD) and aneurysm (TAA) are rare but catastrophic. Prompt recognition of TAD/TAA and differentiation from acute coronary syndrome (ACS) is difficult yet crucial. Earlier identification of TAA/TAD based upon routine emergency department screening is necessary. Methods A retrospective analysis of patients that presented with acute thoracic complaints to the ED from January 2007 through June 2012 was performed. Cases of TAA/TAD were compared to an equal number of controls which consisted of patients with the diagnosis of ACS. Demographics, physical findings, EKG, and the results of laboratory and radiological imaging were compared. P-value of?>?0.05 was considered statistically significant. Results In total, 136 patients were identified with TAA/TAD, 0.36% of patients that presented with chest complaints. Compared to ACS patients, TAA/TAD group was older (68.9 vs. 63.2 years), less likely to be diabetic (13% vs 32%), less likely to complain of chest pain (47% vs 85%) and head and neck pain (4% vs 17%). The pain for the TAA/TAD group was less likely characterized as tight/heavy in nature (5% vs 37%). TAA/TAD patients were also less likely to experience shortness of breath (42% vs. 51%), palpitations (2% vs 9%) and dizziness (2% vs 13%) and had a greater incidence of focal lower extremity neurological deficits (6% vs 1%), bradycardia (15% vs. 5%) and tachypnea (53% vs. 22%). On multivariate analysis, increasing heart rate, chest pain, diabetes, head & neck pain, dizziness, and history of myocardial infarction were independent predictors of ACS. Conclusions Increasing heart rate, chest pain, diabetes, head & neck pain, dizziness, and history of myocardial infarction can be used to differentiate acute coronary syndromes from thoracic aortic dissections/aneurysms. PMID:24499618

  11. Quantitative photoacoustic assessment of ex-vivo lymph nodes of colorectal cancer patients

    NASA Astrophysics Data System (ADS)

    Sampathkumar, Ashwin; Mamou, Jonathan; Saegusa-Beercroft, Emi; Chitnis, Parag V.; Machi, Junji; Feleppa, Ernest J.

    2015-03-01

    Staging of cancers and selection of appropriate treatment requires histological examination of multiple dissected lymph nodes (LNs) per patient, so that a staggering number of nodes require histopathological examination, and the finite resources of pathology facilities create a severe processing bottleneck. Histologically examining the entire 3D volume of every dissected node is not feasible, and therefore, only the central region of each node is examined histologically, which results in severe sampling limitations. In this work, we assess the feasibility of using quantitative photoacoustics (QPA) to overcome the limitations imposed by current procedures and eliminate the resulting under sampling in node assessments. QPA is emerging as a new hybrid modality that assesses tissue properties and classifies tissue type based on multiple estimates derived from spectrum analysis of photoacoustic (PA) radiofrequency (RF) data and from statistical analysis of envelope-signal data derived from the RF signals. Our study seeks to use QPA to distinguish cancerous from non-cancerous regions of dissected LNs and hence serve as a reliable means of imaging and detecting small but clinically significant cancerous foci that would be missed by current methods. Dissected lymph nodes were placed in a water bath and PA signals were generated using a wavelength-tunable (680-950 nm) laser. A 26-MHz, f-2 transducer was used to sense the PA signals. We present an overview of our experimental setup; provide a statistical analysis of multi-wavelength classification parameters (mid-band fit, slope, intercept) obtained from the PA signal spectrum generated in the LNs; and compare QPA performance with our established quantitative ultrasound (QUS) techniques in distinguishing metastatic from non-cancerous tissue in dissected LNs. QPA-QUS methods offer a novel general means of tissue typing and evaluation in a broad range of disease-assessment applications, e.g., cardiac, intravascular, musculoskeletal, endocrine-gland, etc.

  12. A case of Marfan’s syndrome with multi-level aortic dissections

    PubMed Central

    Khosravi, Alireza; Behjati, Mohaddeseh; Nilforoush, Peyman; Saieedi, Mahmoud; Balouchi, Abbas

    2014-01-01

    BACKGROUND Although Marfan’s syndrome is a disease with various phenotypes, but the major mechanism of death is cardiovascular complication. Aortic dissection is a major cause of death in Marfan syndrome. CASE REPORT A 30-year-old man with severe refractory chest and left flank pain and history of previously surgically repaired Type A aortic dissection was referred to the hospital. His typical manifestations of Marfan’s syndrome were identified. Cardiovascular imaging showed an acute spiral dissection in the descending aorta extending to the left renal and femoral arteries with no evidence of thrombosis in its huge false lumen (8 cm). By the diagnosis of acute, expanded, spiral, Type B aortic dissection, he underwent the stent grafting of dissected aorta. He discharged without any complication. On follow-up cardiovascular imaging, thrombosed false lumen in stented aorta from descending aorta to the proximal abdominal aorta was seen. CONCLUSION Endovascular treatment of Type B dissection is an effective treatment in Type B dissection, even in patients with Marfan syndrome. PMID:25815023

  13. Management of symptomatic spontaneous isolated visceral artery dissection: is emergent intervention mandatory?

    PubMed

    Zhang, Wayne W; Killeen, J David; Chiriano, Jason; Bianchi, Christian; Teruya, Theodore H; Abou-Zamzam, Ahmed M

    2009-01-01

    Spontaneous dissection of a visceral artery without associated aortic dissection is rare, although more cases have recently been reported because of the advancement of diagnostic techniques. The risk factors, causes, and natural history of spontaneous isolated visceral artery dissection are unclear. Treatment with open surgery, endovascular stenting, or anticoagulation therapy has been proposed; however, there is no consensus on the optimal management. We present three cases of spontaneous and isolated dissection of visceral arteries. Dissection involved the superior mesenteric artery in one and the celiac artery in two. All three patients presented with acute abdominal pain but lacked any peritoneal irritation. The patients were treated nonoperatively with anticoagulants or antiplatelets. No surgical or endovascular intervention was performed. Follow-up imaging studies demonstrated improvement of the dissection in two patients and no change in one patient. All patients were symptom-free over a mean follow-up of 17 months. Nonoperative treatment with close observation is an acceptable strategy in the management of spontaneous isolated dissection of visceral arteries. Emergent intervention is not mandatory in symptomatic patients without evidence of acute bowel ischemia or hemorrhage. PMID:18774686

  14. Students' physical and psychological reactions to forensic dissection: Are there risk factors?

    PubMed

    Sergentanis, Theodoros N; Papadodima, Stavroula A; Evaggelakos, Christos I; Mytilinaios, Dimitrios G; Goutas, Nikolaos D; Spiliopoulou, Chara A

    2010-01-01

    The reactions of students to forensic dissection encompass psychologico-emotional and physical components. This exploratory study aimed to determine risk factors for students' adverse physical and psychological reactions to forensic dissection. All sixth-year medical students (n = 304) attending the compulsory practical course in forensic medicine in the 2005-2006 academic year were asked to complete a questionnaire at the conclusion of the five-day course. The questionnaire surveyed physical and psychological reactions (outcomes) and 47 student traits, beliefs, and behaviors (risk factors) that might predispose to adverse reactions. Multivariate ordinal logistic regression yielded five independent risk factors for negative psychological reactions: female gender, stereotypic beliefs about forensic pathologists, a less cognitive and more emotional frame of mind relative to forensic dissection, more passive coping strategies, and greater fear of death. The sole independent risk factor for physical symptoms was a less cognitive/more emotional approach to dissection. Students' reactions to forensic dissection integrate a host of inherent and dissection-related risk factors, and future interventions to improve this aspect of medical education will need to take into account the complexities underlying students' experiences with dissection. PMID:21046569

  15. Use of covered stent devices for false lumen embolization in chronic dissection: a novel approach.

    PubMed

    Roselli, Eric E; Idrees, Jahanzaib; Reside, Joshua; Shafii, Susan

    2014-08-01

    Thoracic endovascular aortic repair (TEVAR) is effective in treating acute complicated dissection, but in the chronic state it is frequently complicated by persistent retrograde false lumen perfusion that results in treatment failure. We describe a novel endovascular technique and present an illustrative case of a patient with chronic dissection for which covered stent devices were used as an adjunct to TEVAR to occlude the distal thoracic false lumen and interrupt retrograde perfusion. The case demonstrates that this strategy promotes remodeling when used in addition to stent grafting the true lumen for chronic dissection. PMID:25087811

  16. Aortic dissection presenting as acute myocardial infarction: potential harm of antithrombin and antiplatelet therapy

    PubMed Central

    Gu, Y.L.; van den Heuvel, A.F.M.; Erasmus, M.E.; Zijlstra, F.

    2006-01-01

    In the treatment of acute myocardial infarction, antithrombin and antiplatelet therapy are indicated according to the current guidelines. When a patient presents with symptoms and signs of acute myocardial infarction, an extensive list of diagnoses should be considered. Because of the nonspecific symptoms of aortic dissection, the disease may be easily misdiagnosed. A high clinical suspicion of aortic dissection is therefore required. Once aortic dissection has been diagnosed, surgical intervention provides the only definitive treatment for these patients, regardless of antithrombin and antiplatelet therapy. ImagesFigure 1Figure 2 PMID:25696613

  17. Polyethylene glycol submucosal irrigation: a novel approach to improve visibility during endoscopic submucosal dissection

    PubMed Central

    Arantes, Vitor; Toyonaga, Takashi; Piñeros, Elias Alfonso Forero

    2014-01-01

    In order to expand the availability of endoscopic submucosal dissection (ESD), measures to facilitate the procedure are necessary. When bleeding occurs, the examiner’s field of vision is critically impaired, and ESD becomes less efficient and more hazardous because of the presence of submucosal hematoma and covered blood clot. We propose the use of polyethylene glycol (PEG) irrigation as a simple and effective measure to improve visibility during submucosal dissection, particularly when bleeding occurs. PEG irrigation facilitates further dissection by allowing a better recognition of the submucosal fibers and muscularis propria layer.

  18. Iatrogenic Aortic Dissection During Left Subclavian Artery Stenting: Immediate Detection by Calcium Sign Under Fluoroscope

    SciTech Connect

    Wang, Yi-Chih, E-mail: med011@seed.net.tw; Hwang, Juey-Jen; Lai, Ling-Ping; Tseng, Chuen-Den, E-mail: cdtseng@ha.mc.ntu.edu.tw [National Taiwan University Hospital, Department of Internal Medicine, Taiwan (China)

    2011-02-15

    Calcified aorta with acute iatrogenic aortic dissection is a potential but rarely reported complication of subclavian or innominate artery intervention. We report a patient who developed aortic dissection during stenting for left subclavian artery. A newly developed 'calcium sign,' signifying displacement of the intimal calcification from the outer soft-tissue margin and which is traditionally recognized on chest radiograph, was detected by real-time fluoroscopy and served as the diagnostic clue. Type B aortic dissection was further confirmed by chest computed tomography.

  19. Ischemic gall bladder perforation: a complication of type A aortic dissection.

    PubMed

    Jha, Neerod K; Kumar, Rajappan A; Ayman, Moataz; Khan, Javed A; Cristaldi, Massimo; Ahene, Charles; Augustin, Norbert

    2013-06-01

    Malperfusion of end organs occurs in 20% to 40% patients with acute type A aortic dissection. Because irreversible ischemia is a time-dependent event, expedient diagnosis and treatment are necessary. We herein report successful surgical management of a patient with acute type A aortic dissection causing transient gut ischemia and a rare gall bladder perforation. We implemented one-stage surgical and laparoscopic management approach for the diagnosis and treatment. Increased awareness of this complication and appropriate use of available diagnostic tools may improve the outcome in similar patients. Patients with aortic dissection complicated by visceral ischemia require a prompt sequential and rational multidisciplinary approach for successful management. PMID:23706468

  20. Spontaneous coronary artery dissection in a young woman precipitated by retching.

    PubMed

    Velusamy, Muthu; Fisherkeller, Mark; Keenan, Michael E; Kiernan, Francis J; Fram, Daniel B

    2002-04-01

    Spontaneous coronary artery dissection as a cause of acute myocardial ischemia is a rare entity that has been associated with several different clinical profiles and precipitating events. The recognition of this entity as the cause of acute ischemia is important because the therapeutic considerations may be different than that for ischemia due to a ruptured atherosclerotic plaque. We report a case of spontaneous coronary artery dissection in a 31-year-old female that was induced by prolonged, forceful retching. To our knowledge, this is the first reported case of such an association. Prolonged retching should be added to the list of causes of spontaneous coronary artery dissection. PMID:11923575

  1. A new order of D2 lymphadenectomy in laparoscopic gastrectomy for cancer: live anatomy-based dissection.

    PubMed

    Li, Guo-Xin; Zhang, Ce; Yu, Jiang; Wang, Ya-Nan; Hu, Yan-Feng

    2010-12-01

    It was the aim of this study to develop a methodology for dissection in laparoscopic distal gastrectomy with D2 lymphadenectomy (D2 LDG) for gastric cancer. One-hundred and thirty-two patients with distal gastric cancer underwent D2 LDG with a novel sequence of lymph node dissection between August 2004 and June 2008. Live anatomy in each step was observed simultaneously to ensure and confirm the newly developed methodology. Dissections in LDG were standardized as sequential steps: Dividing the gastrocolic ligament and getting access to the prepancreatic space--lymph node dissection in the lower left area--lymph node dissection in the lower right area--lymph node dissection in the upper right area--lymph nodes dissection centrally--lymph node dissection between liver and stomach. All dissections were successfully performed in peripancreatic spaces and their extensions. Gastric vessels were located by special landmarks, traced along vascular trunks and bifurcations, and identified by fine dissection technique in vaginavasorum. Sequential dissection around the pancreas was an effective method for D2 LDG. It was ensured by anatomical knowledge in each step: Vessels and fascial spaces around a central landmark, the pancreas. PMID:21091070

  2. nature methods | VOL.5 NO.10 | OCTOBER 2008 | 859 research highlights

    E-print Network

    Cravatt, Benjamin

    in the phosphoproteomics field, however, is how can we identify every phosphopeptide, and how do we know when this has been al. Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell

  3. Dissecting biological ``dark matter'' with single-cell genetic analysis of rare and uncultivated TM7

    E-print Network

    Quake, Stephen R.

    Dissecting biological ``dark matter'' with single-cell genetic analysis of rare and uncultivated TM include cultivated representatives (1). This can be viewed as biology's ``dark matter'' problem: just

  4. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

    E-print Network

    Kheradpour, Pouya

    Genome-wide chromatin annotations have permitted the mapping of putative regulatory elements across multiple human cell types. However, their experimental dissection by directed regulatory motif disruption has remained ...

  5. Cell type–specific channelrhodopsin-2 transgenic mice for optogenetic dissection of neural circuitry function

    E-print Network

    Zhao, Shengli

    Optogenetic methods have emerged as powerful tools for dissecting neural circuit connectivity, function and dysfunction. We used a bacterial artificial chromosome (BAC) transgenic strategy to express the H134R variant of ...

  6. J Physiol 580.3 (2007) pp 961975 961 Pharmacological dissection of the human gastro-

    E-print Network

    Brasseur, James G.

    2007-01-01

    J Physiol 580.3 (2007) pp 961­975 961 Pharmacological dissection of the human gastro- oesophageal and quantify in vivo the skeletal and smooth muscle sphincteric components pharmacologically and clarify

  7. Biomechanical roles of medial pooling of glycosaminoglycans in thoracic aortic dissection

    PubMed Central

    Roccabianca, Sara; Ateshian, Gerard A.; Humphrey, Jay D.

    2013-01-01

    Spontaneous dissection of the human thoracic aorta is responsible for significant morbidity and mortality, yet this devastating biomechanical failure process remains poorly understood. In this paper, we present finite element simulations that support a new hypothesis for the initiation of aortic dissections that is motivated by extensive histopathological observations. Specifically, our parametric simulations show that the pooling of glycosaminoglycans/proteoglycans that is singularly characteristic of the compromised thoracic aorta in aneurysms and dissections can lead to significant stress concentrations and intra-lamellar Donnan swelling pressures. We submit that these localized increases in intramural stress may be sufficient both to disrupt the normal cell-matrix interactions that are fundamental to aortic homeostasis and to delaminate the layered microstructure of the aortic wall and thereby initiate dissection. Hence, pathologic pooling of glycosaminoglycans/proteoglycans within the medial layer of the thoracic aortic should be considered as a possible target for clinical intervention. PMID:23494585

  8. Temporoparietal Headache as the Initial Presenting Symptom of a Massive Aortic Dissection

    PubMed Central

    Parikh, Manan; Thyagarajan, Braghadheeswar; Alagusundaramoorthy, Sayee Sundar; Martin, James

    2015-01-01

    Aortic dissection is a life-threatening medical emergency often presenting with severe chest pain and acute hemodynamic compromise. The presentation of aortic dissection can sometimes be different thus leading to a challenge in prompt diagnosis and treatment as demonstrated by the following presentation and discussion. We present a case of a 71-year-old male who presented to the emergency department with complaints of left sided temporoparietal headache and was eventually diagnosed with a thoracic aortic dissection involving the ascending aorta and descending aorta, with an intramural hematoma in the descending aorta. This case illustrates the importance of keeping in mind aortic dissection as a differential diagnosis in patients with acute onset headaches in which any intracranial source of headache is not found.

  9. Monotherapy with stenting in subarachnoid hemorrhage (SAH) after middle cerebral artery dissection.

    PubMed

    Puri, Ajit S; Gounis, Matthew J; Massari, Francesco; Howk, Mary; Weaver, John; Wakhloo, Ajay K

    2015-01-01

    Isolated middle cerebral artery dissection is a rare clinical entity, with descriptions limited to a few case reports and case series. Symptomatic dissection in the anterior circulation can present as an ischemic stroke in a young population; however, it is rarely associated with subarachnoid hemorrhage. We describe a young patient who presented with acute headache from a subarachnoid hemorrhage that was ultimately determined to be due to a vascular dissection in the middle cerebral artery. The initial angiogram showed vascular irregularities in this area with stenosis. Repeat imaging 4?days after presentation identified a pseudoaneurysm proximal to the stenosis. The patient was successfully treated with a self-expanding nitinol stent and followed up with serial angiography during postoperative recovery in the hospital; additional angiograms were performed approximately 1 and 6?months after treatment. Serial angiograms demonstrated incremental healing of the dissection. The patient was discharged and remains neurologically intact at the 6-month follow-up. PMID:25833904

  10. Oregon Sea Grant Marine Education Program at Hatfield Marine Science Center Squid Dissection

    E-print Network

    Wright, Dawn Jeannine

    in oceanic food webs. There is also a large commercial fishery for squid as they are highly prized by humans The Squid Dissection program at Hatfield Marine Science Center is designed to be a 50- minute lab

  11. The AFM as a tool for chromosomal dissection - the influence of physical parameters

    NASA Astrophysics Data System (ADS)

    Stark, R. W.; Thalhammer, S.; Wienberg, J.; Heckl, W. M.

    Human metaphase chromosomes were dissected using an atomic force microscope (AFM) in ambient conditions and in buffer. Cutting with z-modulation in air yielded precise cuts at loading forces F>17 ?N with a full width at maximum depth of 90 nm. After dissection, the chromosomal material adhered to the tip to be used for further biochemical processing. In liquids, we measured the effects of different types of buffer solution on swelling of the chromosomes and their elastic behaviour.

  12. Sentinel Lymph Node Biopsy in Patients with Previous Ipsilateral Complete Axillary Lymph Node Dissection

    Microsoft Academic Search

    Paramjeet Kaur; John V. Kiluk; Tammi Meade; Daniel Ramos; William Koeppel; Julia Jara; Jeff King; Charles E. Cox

    2011-01-01

    Background  Prior ipsilateral completion axillary lymph node dissection (CALND) may be considered a contraindication to performing a sentinel\\u000a lymph node (SLN) mapping in a patient with recurrent breast carcinoma. However, reoperative SLN biopsy following axillary\\u000a dissection would determine if alternative lymphatic drainage pathways exist. If nodes were found to contain metastatic disease,\\u000a staging and locoregional control of the disease could be

  13. Recurrent spontaneous coronary artery dissection in a woman with fibromuscular dysplasia.

    PubMed

    Khosla, Amit; Saw, Jacqueline

    2015-06-01

    We report a case of five recurrent myocardial infarctions due to repeat spontaneous coronary artery dissection (SCAD) in a woman with underlying fibromuscular dysplasia. Her angiographic SCADs were missed on two occasions. Patients with a history of SCAD are at risk for recurrent dissections. This case also highlights the angiographic variants of SCAD, and the utility of intracoronary imaging in diagnosing suspected SCAD. PMID:26028659

  14. Unusual cause of acute back pain mimicking aortic dissection: a case report.

    PubMed

    Czesla, Markus; Karnari, Olga; Götte, Julia; Schulte, Bernhard; Pfeilsticker, Ulrich; Narr, Anita; Doll, Nicolas

    2012-12-01

    We report the case of a 62-year-old woman who initially presented with symptoms suggesting acute type A aortic dissection. Imaging studies revealed hemorrhagic pericardial fluid without the evidence of dissection. Foreign body material was noted floating in the inferior vena cava (IVC) and also piercing the right ventricular wall. Upon surgical exploration, the extracted material could be identified to be acrylic bone cement (palacos). The patient had reported a history of kyphoplasty in 2008. PMID:22207371

  15. Superior mesenteric artery plasty for type A acute aortic dissection with visceral ischemia.

    PubMed

    Kato, Wataru; Fujita, Takashi; Uchida, Kenichiro; Munakata, Hisaaki; Hibino, Makoto; Fujii, Kei; Tanaka, Keisuke; Sakai, Yoshimasa; Tajima, Kazuyoshi

    2014-11-18

    Treatment of visceral ischemia complicated with acute type A aortic dissection is controversial. We had two cases of acute type A aortic dissection complicated by superior mesenteric artery (SMA) ischemia and successfully treated them with direct SMA perfusion during central aortic repair followed by SMA plasty. The presented procedures can be an option to treat visceral ischemia with a standard operative theater and equipment. PMID:25403999

  16. Extent of Routine Central Lymph Node Dissection With Small Papillary Thyroid Carcinoma

    Microsoft Academic Search

    Yong Sang Lee; Seok Won Kim; Sun Wook Kim; Seok Ki Kim; Han-Sung Kang; Eun Sook Lee; Ki-Wook Chung

    2007-01-01

    The indications for and extent of routine lymph node dissection in patients with papillary thyroid carcinoma (PTC) are unclear.\\u000a The aim of this study was to investigate the association between the extent of central lymph node dissection (CLND) and the\\u000a therapeutic effects and potential risks in patients with a small PTC. A total of 103 patients with a PTC <2 cm

  17. Carotid and vertebral artery dissections: clinical aspects, imaging features and endovascular treatment

    Microsoft Academic Search

    Christine M. Flis; H. Rolf Jäger; Paul S. Sidhu

    2007-01-01

    Extracranial arterial dissections are a recognised cause of stroke, particularly in young adults. Clinical diagnosis may be\\u000a difficult, and the classical triad of symptoms is uncommon. Imaging plays a pivotal role in the diagnosis of extracranial\\u000a arterial dissections, and this review provides a detailed discussion of the relative merits and limitations of currently available\\u000a imaging modalities. Conventional arteriography has been

  18. Renal Infarction Caused by Spontaneous Renal Artery Dissection: Treatment with Catheter-Directed Thrombolysis and Stenting

    SciTech Connect

    Jeon, Yong Sun, E-mail: radjeon@korea.com; Cho, Soon Gu [Inha University College of Medicine, Department of Radiology (Korea, Republic of); Hong, Ki Cheon [Inha University College of Medicine, Department of Surgery (Korea, Republic of)

    2009-03-15

    Spontaneous renal artery dissection (SRAD) is rare and presents a diagnostic and therapeutic challenge. We report a case of a 36-year-old man who had an SRAD-complicated renal infarction. The patient experienced severe unilateral flank pain. Enhanced abdominal computed axial tomography scan showed renal infarction, and urinalysis showed no hematuria. Selective renal angiography was essential to evaluate the extent of dissection and suitability for repair. The patient was treated with catheter-directed thrombolysis and frenal artery stenting.

  19. Successful Treatment of Isolated Spontaneous Superior Mesenteric Artery Dissection with Stent Placement

    SciTech Connect

    Yoon, Young-Won; Choi, Donghoon; Cho, Seung-Yun [Yonsei Cardiovascular Hospital, Yonsei Cardiovascular Research Institute, Yonsei University College of Medicine, 134 Shinchon-dong, Seodaemun-Ku, 120-752 Seoul, Cardiology Division (Korea, Republic of); Lee, Do Yun [Yonsei Cardiovascular Hospital, Yonsei Cardiovascular Research Institute, Yonsei University College of Medicine, 134 Shinchon-dong, Seodaemun-Ku, 120-752 Seoul, Division of Diagnostic Radiology (Korea, Republic of)

    2003-09-15

    Isolated dissection of superior mesenteric artery is a rare condition and is usually treated surgically. We treated a patient with severe abdominal pain who was angiographically confirmed to have superior mesenteric artery thrombosis associated with isolated spontaneous dissection. He was treated initially by thrombolysis and oral anticoagulation, but recurrent symptoms developed with radiologic evidence of disease progression. We performed superior mesenteric artery stenting and recovery was uneventful.

  20. Three-Dimensional Computed Tomographic Angiography in Four Patients with Dissecting Aneurysms of the Vertebrobasilar System

    Microsoft Academic Search

    M. Nakatsuka; S. Mizuno

    2000-01-01

    Summary  ¶?Background. Recently, three-dimensional computed tomographic angiography (CTA) has been used for the diagnosis and treatment planning\\u000a of cerebral aneurysm presenting with or without subarachnoid haemorrhage, but the diagnostic value of CTA has not been established.\\u000a This study evaluated the usefulness of CTA in patients with dissecting aneurysms of the vertebrobasilar system.\\u000a \\u000a ?Method. Four patients with acute dissecting aneurysms were examined

  1. Prediction of Neck Dissection Requirement After Definitive Radiotherapy for Head and Neck Squamous Cell Carcinoma

    PubMed Central

    Thariat, Juliette; Ang, K. Kian; Allen, Pamela K.; Ahamad, Anesa; Williams, Michelle D.; Myers, Jeffrey N.; El-Naggar, Adel K.; Ginsberg, Lawrence E.; Rosenthal, David I.; Glisson, Bonnie S.; Morrison, William H.; Weber, Randal S.; Garden, Adam S.

    2014-01-01

    BACKGROUND This analysis was undertaken to assess the need for planned neck dissection in patients with a complete response (CR) of involved nodes after irradiation, and to determine the benefit of a neck dissection in those with less than CR by tumor site. METHODS Our cohort included 880 patients with T1-4, N1-3M0 squamous cell carcinoma of the oropharynx, larynx or hypopharynx who received treatment between 1994 and 2004. Survival curves were calculated by the Kaplan-Meier Method, comparisons of rates with the log-rank test and prognostic factors by Cox analyses. RESULTS Nodal CR occurred in 377 (43%) patients of whom 365 patients did not undergo nodal dissection. The 5-year actuarial regional control rate of patients with CR was 92%. Two hundred sixty-eight of the remaining patients (53%) underwent neck dissections. The 5-year actuarial regional control rate for patients without a CR was 84%. Those who had a neck dissection fared better with 5-year actuarial regional control rates of 90% and 76% for those operated and those not operated (p <.001). Variables associated with poorer regional control rates included higher T and N stage, non-oropharynx cancers, non-CR, both clinical and pathological. CONCLUSIONS With 92% 5-year neck control rate without neck dissection after CR, there is little justification for systematic neck dissection. The addition of a neck dissection resulted in higher neck control after partial response though patients with viable tumor on pathology specimens had poorer outcomes. The identification of that subgroup that benefits from additional treatment remains a challenge. PMID:22284033

  2. DISSECTING OCD CIRCUITS: FROM ANIMAL MODELS TO TARGETED TREATMENTS.

    PubMed

    Ahmari, Susanne E; Dougherty, Darin D

    2015-08-01

    Obsessive-compulsive disorder (OCD) is a chronic, severe mental illness with up to 2-3% prevalence worldwide. In fact, OCD has been classified as one of the world's 10 leading causes of illness-related disability according to the World Health Organization, largely because of the chronic nature of disabling symptoms.([1]) Despite the severity and high prevalence of this chronic and disabling disorder, there is still relatively limited understanding of its pathophysiology. However, this is now rapidly changing due to development of powerful technologies that can be used to dissect the neural circuits underlying pathologic behaviors. In this article, we describe recent technical advances that have allowed neuroscientists to start identifying the circuits underlying complex repetitive behaviors using animal model systems. In addition, we review current surgical and stimulation-based treatments for OCD that target circuit dysfunction. Finally, we discuss how findings from animal models may be applied in the clinical arena to help inform and refine targeted brain stimulation-based treatment approaches. PMID:25952989

  3. Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates

    PubMed Central

    Skerker, Jeffrey M; Leon, Dacia; Price, Morgan N; Mar, Jordan S; Tarjan, Daniel R; Wetmore, Kelly M; Deutschbauer, Adam M; Baumohl, Jason K; Bauer, Stefan; Ibáñez, Ana B; Mitchell, Valerie D; Wu, Cindy H; Hu, Ping; Hazen, Terry; Arkin, Adam P

    2013-01-01

    The efficient production of biofuels from cellulosic feedstocks will require the efficient fermentation of the sugars in hydrolyzed plant material. Unfortunately, plant hydrolysates also contain many compounds that inhibit microbial growth and fermentation. We used DNA-barcoded mutant libraries to identify genes that are important for hydrolysate tolerance in both Zymomonas mobilis (44 genes) and Saccharomyces cerevisiae (99 genes). Overexpression of a Z. mobilis tolerance gene of unknown function (ZMO1875) improved its specific ethanol productivity 2.4-fold in the presence of miscanthus hydrolysate. However, a mixture of 37 hydrolysate-derived inhibitors was not sufficient to explain the fitness profile of plant hydrolysate. To deconstruct the fitness profile of hydrolysate, we profiled the 37 inhibitors against a library of Z. mobilis mutants and we modeled fitness in hydrolysate as a mixture of fitness in its components. By examining outliers in this model, we identified methylglyoxal as a previously unknown component of hydrolysate. Our work provides a general strategy to dissect how microbes respond to a complex chemical stress and should enable further engineering of hydrolysate tolerance. PMID:23774757

  4. Cervical-artery dissections: predisposing factors, diagnosis, and outcome.

    PubMed

    Debette, Stéphanie; Leys, Didier

    2009-07-01

    Cervical-artery dissection (CAD) is a major cause of cerebral ischaemia in young adults and can lead to various clinical symptoms, some of which are benign (eg, headache, neck pain, Horner's syndrome, and cranial-nerve palsy), but most patients have a stroke or transient ischaemic attack. In addition to trauma to the neck, other risk factors have been suggested, such as infection, migraine, hyperhomocysteinaemia, and the 677TT genotype of the 5,10-methylenetetrahydrofolate reductase gene (MTHFR 677TT), although evidence is sparse. An underlying arteriopathy, which could in part be genetically determined, is believed to have a role in the development of CAD. Importantly, both research on and optimum management of CAD strongly rely on diagnostic accuracy. Although the functional outcome of CAD is good in most patients, socioprofessional effects can be important. Incidence of the disorder in the general population is underestimated. Mortality and short-term recurrence rates are low but possibly also underestimated. Further research is warranted to improve our understanding of the underlying pathophysiology, to assess the long-term outcome, and ultimately to provide treatment and prevention strategies. PMID:19539238

  5. Role of antisecretory agents for gastric endoscopic submucosal dissection.

    PubMed

    Fujishiro, Mitsuhiro; Chiu, Philip W Y; Wang, Hsui-Po

    2013-03-01

    Gastric endoscopic submucosal dissection (ESD) causes artificial gastric ulcers and there is no consensus regarding the optimal perioperative management in terms of prevention of intra- or postoperative bleeding and promotion of healing. Traditionally, 8-week administration of proton pump inhibitors (PPI) and mucosal protective agents were used in the same way as for peptic ulcer management. However, recent studies have revealed that prior use of PPI might reduce intraoperative bleeding or early-phase postoperative bleeding, and combination of histamine-2 receptor antagonist (H2RA), and second-look endoscopy might have a similar effect on postoperative bleeding to PPI. Additionally, the advantage of PPI over H2RA is not proven and the optimal duration of PPI may be shortened until 2 weeks when the deteriorating factors for ESD ulcer are excluded. Furthermore, mucosal protective agents may facilitate ulcer healing. Further studies are needed to determine the optimal treatment protocol before and after ESD for both prevention of bleeding complication and promotion of ulcer healing, by using available antisecretory agents and mucosal protective agents. PMID:23368844

  6. Molecular Dissection of the Checkpoint Kinase Hsl1p

    PubMed Central

    Crutchley, John; King, Kindra M.; Keaton, Mignon A.; Szkotnicki, Lee; Orlando, David A.; Zyla, Trevin R.; Bardes, Elaine S.G.

    2009-01-01

    Cell shape can influence cell behavior. In Saccharomyces cerevisiae, bud emergence can influence cell cycle progression via the morphogenesis checkpoint. This surveillance pathway ensures that mitosis always follows bud formation by linking degradation of the mitosis-inhibitory kinase Swe1p (Wee1) to successful bud emergence. A crucial component of this pathway is the checkpoint kinase Hsl1p, which is activated upon bud emergence and promotes Swe1p degradation. We have dissected the large nonkinase domain of Hsl1p by using evolutionary conservation as a guide, identifying regions important for Hsl1p localization, function, and regulation. An autoinhibitory motif restrains Hsl1p activity when it is not properly localized to the mother-bud neck. Hsl1p lacking this motif is active as a kinase regardless of the assembly state of cytoskeletal septin filaments. However, the active but delocalized Hsl1p cannot promote Swe1p down-regulation, indicating that localization is required for Hsl1p function as well as Hsl1p activation. We also show that the septin-mediated Hsl1p regulation via the novel motif operates in parallel to a previously identified Hsl1p activation pathway involving phosphorylation of the Hsl1p kinase domain. We suggest that Hsl1p responds to alterations in septin organization, which themselves occur in response to the local geometry of the cell cortex. PMID:19211841

  7. Zebrafish as a novel vertebrate model to dissect enterococcal pathogenesis.

    PubMed

    Prajsnar, Tomasz K; Renshaw, Stephen A; Ogryzko, Nikolay V; Foster, Simon J; Serror, Pascale; Mesnage, Stéphane

    2013-11-01

    Enterococcus faecalis is an opportunistic pathogen responsible for a wide range of life-threatening nosocomial infections, such as septicemia, peritonitis, and endocarditis. E. faecalis infections are associated with a high mortality and substantial health care costs and cause therapeutic problems due to the intrinsic resistance of this bacterium to antibiotics. Several factors contributing to E. faecalis virulence have been identified. Due to the variety of infections caused by this organism, numerous animal models have been used to mimic E. faecalis infections, but none of them is considered ideal for monitoring pathogenesis. Here, we studied for the first time E. faecalis pathogenesis in zebrafish larvae. Using model strains, chosen isogenic mutants, and fluorescent derivatives expressing green fluorescent protein (GFP), we analyzed both lethality and bacterial dissemination in infected larvae. Genetically engineered immunocompromised zebrafish allowed the identification of two critical steps for successful establishment of disease: (i) host phagocytosis evasion mediated by the Epa rhamnopolysaccharide and (ii) tissue damage mediated by the quorum-sensing Fsr regulon. Our results reveal that the zebrafish is a novel, powerful model for studying E. faecalis pathogenesis, enabling us to dissect the mechanism of enterococcal virulence. PMID:24002065

  8. Pulse energy dependence of subcellular dissection by femtosecond laser pulses

    NASA Technical Reports Server (NTRS)

    Heisterkamp, A.; Maxwell, I. Z.; Mazur, E.; Underwood, J. M.; Nickerson, J. A.; Kumar, S.; Ingber, D. E.

    2005-01-01

    Precise dissection of cells with ultrashort laser pulses requires a clear understanding of how the onset and extent of ablation (i.e., the removal of material) depends on pulse energy. We carried out a systematic study of the energy dependence of the plasma-mediated ablation of fluorescently-labeled subcellular structures in the cytoskeleton and nuclei of fixed endothelial cells using femtosecond, near-infrared laser pulses focused through a high-numerical aperture objective lens (1.4 NA). We find that the energy threshold for photobleaching lies between 0.9 and 1.7 nJ. By comparing the changes in fluorescence with the actual material loss determined by electron microscopy, we find that the threshold for true material ablation is about 20% higher than the photobleaching threshold. This information makes it possible to use the fluorescence to determine the onset of true material ablation without resorting to electron microscopy. We confirm the precision of this technique by severing a single microtubule without disrupting the neighboring microtubules, less than 1 micrometer away. c2005 Optical Society of America.

  9. Dissection of complex protein dynamics in human thioredoxin

    PubMed Central

    Qiu, Weihong; Wang, Lijuan; Lu, Wenyun; Boechler, Amanda; Sanders, David A. R.; Zhong, Dongping

    2007-01-01

    We report our direct study of complex protein dynamics in human thioredoxin by dissecting into elementary processes and determining their relevant time scales. By combining site-directed mutagenesis with femtosecond spectroscopy, we have distinguished four partly time-overlapped dynamical processes at the active site of thioredoxin. Using intrinsic tryptophan as a molecular probe and from mutation studies, we ascertained the negligible contribution to solvation by protein sidechains and observed that the hydration dynamics at the active site occur in 0.47–0.67 and 10.8–13.2 ps. With reduced and oxidized states, we determined the electron-transfer quenching dynamics between excited tryptophan and a nearby disulfide bond in 10–17.5 ps for three mutants. A robust dynamical process in 95–114 ps, present in both redox states and all mutants regardless of neighboring charged, polar, and hydrophobic residues around the probe, is attributed to the charge transfer reaction with its adjacent peptide bond. Site-directed mutations also revealed the electronic quenching dynamics by an aspartate residue at a hydrogen bond distance in 275–615 ps. The local rotational dynamics determined by the measurement of anisotropy changes with time unraveled a relatively rigid local configuration but implies that the protein fluctuates on the time scale of longer than nanoseconds. These results elucidate the temporal evolution of hydrating water motions, electron-transfer reactions, and local protein fluctuations at the active site, and show continuously synergistic dynamics of biological function over wide time scales. PMID:17369362

  10. Dissecting the role of endothelial SURVIVIN ?Ex3 in angiogenesis

    PubMed Central

    Caldas, Hugo; Fangusaro, Jason R.; Boué, Daniel R.; Holloway, Michael P.; Altura, Rachel A.

    2007-01-01

    The identification of alternative splice variants of Survivin that possess distinct functions from those originally identified for the main Survivin isoform has greatly increased the complexity of our understanding of the role of Survivin in different cells. Previous functional studies of the Survivin splice variants have been performed almost exclusively in cancer cells. However, Survivin has increasingly been implicated in other normal physiologic and pathophysiologic processes, including angiogenesis. In this study, we dissect the involvement of Survivin ?Ex3 in angiogenesis. We show by confocal microscopy that a pool of endothelial Survivin ?Ex3 is localized to membrane ruffles. We also demonstrate that Survivin ?Ex3 is the Survivin splice variant responsible for modulating angiogenesis in vitro, in tube formation assays, and in vivo, in an in vivo angiogenesis assay. Our data indicate that Survivin ?Ex3 may regulate angiogenesis via several mechanisms including cell invasion, migration, and Rac1 activation. Our findings identify a novel pathway regulating angiogenesis through Survivin ?Ex3 and a novel mechanism for Rac1 activation during angiogenesis. In conclusion, our results provide new insights into the regulation of endothelial cell homeostasis and angiogenesis by the Survivin proteins. PMID:17038538

  11. Genetic dissection of the function of hindbrain axonal commissures.

    PubMed

    Renier, Nicolas; Schonewille, Martijn; Giraudet, Fabrice; Badura, Aleksandra; Tessier-Lavigne, Marc; Avan, Paul; De Zeeuw, Chris I; Chédotal, Alain

    2010-03-01

    In Bilateria, many axons cross the midline of the central nervous system, forming well-defined commissures. Whereas in mammals the functions of commissures in the forebrain and in the visual system are well established, functions at other axial levels are less clearly understood. Here, we have dissected the function of several hindbrain commissures using genetic methods. By taking advantage of multiple Cre transgenic lines, we have induced site-specific deletions of the Robo3 receptor. These lines developed with the disruption of specific commissures in the sensory, motor, and sensorimotor systems, resulting in severe and permanent functional deficits. We show that mice with severely reduced commissures in rhombomeres 5 and 3 have abnormal lateral eye movements and auditory brainstem responses, respectively, whereas mice with a primarily uncrossed climbing fiber/Purkinje cell projection are strongly ataxic. Surprisingly, although rerouted axons remain ipsilateral, they still project to their appropriate neuronal targets. Moreover, some Cre;Robo3 lines represent potential models that can be used to study human syndromes, including horizontal gaze palsy with progressive scoliosis (HGPPS). To our knowledge, this study is one of the first to link defects in commissural axon guidance with specific cellular and behavioral phenotypes. PMID:20231872

  12. Isolated regional lymph node dissection: morbidity, mortality and economic considerations.

    PubMed Central

    Bland, K I; Klamer, T W; Polk, H C; Knutson, C O

    1981-01-01

    Between 1971-1979, 330 consecutive isolated regional lymph node dissections (RLNDs) were performed as therapeutic procedures for metastatic disease, at the University of Louisville Affiliated Hospitals and the Ellis-Fischel State Cancer Hospital in Columbia, Missouri. This retrospective analysis includes 133 radical neck RLNDs, 87 axillary RLNDs, and 110 superficial groin RLNDs. All accessioned cases were elective and were performed as isolated procedures, discrete from resection of contiguous or remote organs. No patients received preoperative irradiation, chemotherapy or immunotherapy. Forty-eight per cent of the 330 RLND procedures resulted in some form of postoperative complication. However, 91% of the incurred morbidity was localized to the operative site and was related to serum collection and/or flap necrosis. The occurrence of postoperative complications for each RLND site resulted in a prolongation of the patients' hospital stays by a mean of 9 days, and was most extended for the superficial groin RLND by a mean of 11 days. Nine patients (3%) died. These data for morbidity and mortality rates, as well as the implicit economic impact, represent substantial factors in the utilization of elective RLND. PMID:7212799

  13. Dissecting the role of infections in atopic dermatitis.

    PubMed

    Biedermann, Tilo

    2006-01-01

    In patients with atopic dermatitis the skin is highly susceptible to infection by bacteria, fungi and viruses. Increasing knowledge about the complex immune network that regulates anti-microbial responses has helped to dissect further the role of infections in atopic dermatitis. Conserved patterns of microbes are recognized by the innate immune system, which mediates microbicidal activity, either directly or through inflammatory responses. New evidence suggests that components of the innate immune system, such as anti-microbial peptides, humoural lectins, nucleotide-binding oligomerization domain-containing (NOD) proteins, and Toll-like receptors not only protect from microbial invasion, but contribute to skin inflammation in atopic dermatitis. In addition, atopic patients tend to develop Th2-dominated immune responses that weaken anti-microbial immunity. This impairment of an appropriate anti-microbial defence compounded by amplified microbe-driven innate and adaptive immune responses leads to the vicious circle of skin inflammation. New microbial management in atopic dermatitis will foster a well-balanced microbial flora, which establishes natural defence mechanisms to maintain immuno-surveillance of the skin. In addition to anti-microbial therapies, other innate immune stimuli may suppress pro-inflammatory signals and help to break the vicious circle of cutaneous inflammation. To elucidate further these different interactions of the skin immune system and microbes in atopic dermatitis, clinical studies and further efforts in basic research are needed. PMID:16648910

  14. Dissecting Social Cell Biology and Tumors Using Drosophila Genetics

    PubMed Central

    Pastor-Pareja, José Carlos; Xu, Tian

    2014-01-01

    Cancer was seen for a long time as a strictly cell-autonomous process in which oncogenes and tumor-suppressor mutations drive clonal cell expansions. Research in the past decade, however, paints a more integrative picture of communication and interplay between neighboring cells in tissues. It is increasingly clear as well that tumors, far from being homogenous lumps of cells, consist of different cell types that function together as complex tissue-level communities. The repertoire of interactive cell behaviors and the quantity of cellular players involved call for a social cell biology that investigates these interactions. Research into this social cell biology is critical for understanding development of normal and tumoral tissues. Such complex social cell biology interactions can be parsed in Drosophila. Techniques in Drosophila for analysis of gene function and clonal behavior allow us to generate tumors and dissect their complex interactive biology with cellular resolution. Here, we review recent Drosophila research aimed at understanding tissue-level biology and social cell interactions in tumors, highlighting the principles these studies reveal. PMID:23988119

  15. Posterior subscapular dissection: An improved approach to the brachial plexus for human anatomy students.

    PubMed

    Hager, Shaun; Backus, Timothy Charles; Futterman, Bennett; Solounias, Nikos; Mihlbachler, Matthew C

    2014-05-01

    Students of human anatomy are required to understand the brachial plexus, from the proximal roots extending from spinal nerves C5 through T1, to the distal-most branches that innervate the shoulder and upper limb. However, in human cadaver dissection labs, students are often instructed to dissect the brachial plexus using an antero-axillary approach that incompletely exposes the brachial plexus. This approach readily exposes the distal segments of the brachial plexus but exposure of proximal and posterior segments require extensive dissection of neck and shoulder structures. Therefore, the proximal and posterior segments of the brachial plexus, including the roots, trunks, divisions, posterior cord and proximally branching peripheral nerves often remain unobserved during study of the cadaveric shoulder and brachial plexus. Here we introduce a subscapular approach that exposes the entire brachial plexus, with minimal amount of dissection or destruction of surrounding structures. Lateral retraction of the scapula reveals the entire length of the brachial plexus in the subscapular space, exposing the brachial plexus roots and other proximal segments. Combining the subscapular approach with the traditional antero-axillary approach allows students to observe the cadaveric brachial plexus in its entirety. Exposure of the brachial dissection in the subscapular space requires little time and is easily incorporated into a preexisting anatomy lab curriculum without scheduling additional time for dissection. PMID:24698357

  16. Treatment of Intra- and Extracranial Arterial Dissections Using Stents and Embolization

    SciTech Connect

    Joo, Jin Yang [Yonsei University College of Medicine, Department of Neurosurgery (Korea, Republic of); Ahn, Jung Yong, E-mail: jyahn@cha.ac.kr; Chung, Young Sun; Han, In Bo; Chung, Sang Sup [Pochon CHA Medical University, Department of Neurosurgery (Korea, Republic of); Yoon, Pyeong Ho; Kim, Sang Heum [Pochon CHA Medical University, Department of Radiology (Korea, Republic of); Choi, Eun Wan [National Police Hospital, Department of Radiology (Korea, Republic of)

    2005-06-15

    Purpose. To evaluate the safety and efficacy of stent placement for extracranial and intracranial arterial dissections. Methods. Eighteen patients underwent endovascular treatment of carotid and vertebral dissections using intraluminal stent placement. Five patients with arterial dissection were treated, 2 using one insertion of a single stent and 3 using placement of two stents. Patients with a dissecting aneurysm were treated as follows: 7 patients with insertion of one stent, 4 with placement of two stents, and 2 by stent-assisted Guglielmi detachable coil embolization. In the 18 patients in whom stenting was attempted, the overall success in reaching the target lesion was 94.4%. Of the 17 patients treated with stents, stent release and positioning were considered optimal in 16 (94%) and suboptimal in one (6%). In patients who underwent a successful procedure, all parent arteries were preserved. There were no instances of postprocedural ischemic attacks, new neurologic deficits, or new minor or major strokes prior to patient discharge. In follow up, all patients were assessed, using the modified Rankin scale, as functionally improved or of stable clinical status. The reduction in dissection-induced stenosis or pseudoaneurysm, the patency rate obtained at follow-up, and the lack of strokes (ischemic or hemorrhagic) suggest that stent placement offers a viable alternative to complex surgical bypass or reconstructive procedures. The long-term efficacy and durability of stent placement for arterial dissection remain to be determined in a larger series.

  17. Thoracic endovascular aortic repair versus open surgery for type-B chronic dissection.

    PubMed

    Roselli, Eric E

    2015-02-01

    An aging population, increased awareness, high-resolution imaging, and improving access to care all mean that more people are being diagnosed with acute aortic dissection. A better understanding of the role of initial medical therapy, improved surgical techniques, and the addition of endovascular approaches to the treatment algorithm, have resulted in more patients surviving the acute phase of disease. During the chronic phase, patients with residual dissection are challenged by the competing risks of reoperation or death. Open repair for chronic type-B dissection can be performed safely but is a relatively morbid operation. For this reason, surgery is often postponed until patients develop very late complications. Despite encouraging results for thoracic endovascular aortic repair of acute type-B dissection, chronic type-B dissection poses unique challenges that make application of endovascular technology more difficult. As our understanding of the disease and its natural history evolves, the ways in which these 2 methods of treatment complement each other need to be better understood. The benefits and limitations of each therapy, and how and when to apply each in the setting of chronic distal dissection, are discussed. PMID:25726076

  18. Dissecting the Machinery That Introduces Disulfide Bonds in Pseudomonas aeruginosa

    PubMed Central

    Arts, Isabelle S.; Ball, Geneviève; Leverrier, Pauline; Garvis, Steven; Nicolaes, Valérie; Vertommen, Didier; Ize, Bérengère; Tamu Dufe, Veronica; Messens, Joris; Voulhoux, Romé; Collet, Jean-François

    2013-01-01

    ABSTRACT Disulfide bond formation is required for the folding of many bacterial virulence factors. However, whereas the Escherichia coli disulfide bond-forming system is well characterized, not much is known on the pathways that oxidatively fold proteins in pathogenic bacteria. Here, we report the detailed unraveling of the pathway that introduces disulfide bonds in the periplasm of the human pathogen Pseudomonas aeruginosa. The genome of P. aeruginosa uniquely encodes two DsbA proteins (P. aeruginosa DsbA1 [PaDsbA1] and PaDsbA2) and two DsbB proteins (PaDsbB1 and PaDsbB2). We found that PaDsbA1, the primary donor of disulfide bonds to secreted proteins, is maintained oxidized in vivo by both PaDsbB1 and PaDsbB2. In vitro reconstitution of the pathway confirms that both PaDsbB1 and PaDsbB2 shuttle electrons from PaDsbA1 to membrane-bound quinones. Accordingly, deletion of both P. aeruginosa dsbB1 (PadsbB1) and PadsbB2 is required to prevent the folding of several P. aeruginosa virulence factors and to lead to a significant decrease in pathogenicity. Using a high-throughput proteomic approach, we also analyzed the impact of PadsbA1 deletion on the global periplasmic proteome of P. aeruginosa, which allowed us to identify more than 20 new potential substrates of this major oxidoreductase. Finally, we report the biochemical and structural characterization of PaDsbA2, a highly oxidizing oxidoreductase, which seems to be expressed under specific conditions. By fully dissecting the machinery that introduces disulfide bonds in P. aeruginosa, our work opens the way to the design of novel antibacterial molecules able to disarm this pathogen by preventing the proper assembly of its arsenal of virulence factors. PMID:24327342

  19. Building a virtual reality temporal bone dissection simulator.

    PubMed

    Kuppersmith, R B; Johnston, R; Moreau, D; Loftin, R B; Jenkins, H

    1997-01-01

    The temporal bone is one of seven bones that comprise the human skull, and has an intimate relationship with many vital structures. Anatomically, its three-dimensional relationships make it one of the most challenging areas for surgeons to understand and master. In addition, the temporal bone contains minute structures that are among the most sophisticated and delicate in the human body. These structures include the cochlea and vestibular organs, which are responsible for hearing and balance; the middle ear, including the ossicles, which conduct acoustic energy to the cochlea; and the facial nerve, which is responsible for controlling the muscles of facial expression, and contributes to the sensation of taste. Additionally, the temporal bone forms a major portion of the skull base, and has intimate relationships to vital structures including the carotid artery, jugular vein, cerebral cortex, brainstem, and cranial nerves. Surgical procedures performed on the temporal bone include: procedures to eradicate chronic and acute infections; procedures to remove malignant and benign tumors within the temporal bone, from the skull base, or from the posterior cranial fossa; procedures to restore the hearing mechanism; procedures to eliminate balance disorders; and procedures to correct congenital anomalies. For surgeons-in-training, and even surgeons-in-practice, mastery of the anatomy of the temporal bone and the many complex approaches necessary to treat patients takes years of focused endeavor. This is typically accomplished through the dissection of human cadaver temporal bones, which are scarce, and require a dedicated laboratory facility. Efforts are currently underway to develop a realistic simulator for temporal bone procedures. Users immersed in the simulator will interact with a three-dimensional temporal bone, derived from patient-specific data, using a haptic interface to simulate traditional surgical procedures. Feedback from experts in otologic surgery will be built into the system for additional instruction. This presentation will include an overview of the application being developed, a report of its current state of development, and plans for the future. PMID:10168915

  20. Dissecting structural and electronic effects in inducible nitric oxide synthase.

    PubMed

    Hannibal, Luciana; Page, Richard C; Haque, Mohammad Mahfuzul; Bolisetty, Karthik; Yu, Zhihao; Misra, Saurav; Stuehr, Dennis J

    2015-04-01

    Nitric oxide synthases (NOSs) are haem-thiolate enzymes that catalyse the conversion of L-arginine (L-Arg) into NO and citrulline. Inducible NOS (iNOS) is responsible for delivery of NO in response to stressors during inflammation. The catalytic performance of iNOS is proposed to rely mainly on the haem midpoint potential and the ability of the substrate L-Arg to provide a hydrogen bond for oxygen activation (O-O scission). We present a study of native iNOS compared with iNOS-mesohaem, and investigate the formation of a low-spin ferric haem-aquo or -hydroxo species (P) in iNOS mutant W188H substituted with mesohaem. iNOS-mesohaem and W188H-mesohaem were stable and dimeric, and presented substrate-binding affinities comparable to those of their native counterparts. Single turnover reactions catalysed by iNOSoxy with L-Arg (first reaction step) or N-hydroxy-L-arginine (second reaction step) showed that mesohaem substitution triggered higher rates of Fe(II)O? conversion and altered other key kinetic parameters. We elucidated the first crystal structure of a NOS substituted with mesohaem and found essentially identical features compared with the structure of iNOS carrying native haem. This facilitated the dissection of structural and electronic effects. Mesohaem substitution substantially reduced the build-up of species P in W188H iNOS during catalysis, thus increasing its proficiency towards NO synthesis. The marked structural similarities of iNOSoxy containing native haem or mesohaem indicate that the kinetic behaviour observed in mesohaem-substituted iNOS is most heavily influenced by electronic effects rather than structural alterations. PMID:25608846