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1

Quantitative phosphoproteomics in fatty acid stimulated Saccharomyces cerevisiae.  

PubMed

This protocol describes the growth and stimulation, with the fatty acid oleate, of isotopically heavy and light S. cerevisiae cells. Cells are ground using a cryolysis procedure in a ball mill grinder and the resulting grindate brought into solution by urea solubilization. This procedure allows for the lysis of the cells in a metabolically inactive state, preserving phosphorylation and preventing reorientation of the phosphoproteome during cell lysis. Following reduction, alkylation, trypsin digestion of the proteins, the samples are desalted on C18 columns and the sample complexity reduced by fractionation using hydrophilic interaction chromatography (HILIC). HILIC columns preferentially retain hydrophilic molecules which is well suited for phosphoproteomics. Phosphorylated peptides tend to elute later in the chromatographic profile than the non phosphorylated counterparts. After fractionation, phosphopeptides are enriched using immobilized metal chromatography, which relies on charge-based affinities for phosphopeptide enrichment. At the end of this procedure the samples are ready to be quantitatively analyzed by mass spectrometry. PMID:19823167

Saleem, Ramsey A; Aitchison, John D

2009-01-01

2

Quantitative Phosphoproteomics Reveals Extensive Cellular Reprogramming During HIV-1 Entry  

PubMed Central

SUMMARY Receptor engagement by HIV-1 during host cell entry activates signaling pathways that can reprogram the cell for optimal viral replication. To obtain a global view of the signaling events induced during HIV-1 entry, we conducted a quantitative phosphoproteomics screen of primary human CD4+ T cell after infection with an HIV-1 strain that engages the receptors CD4 and CXCR4. We quantified 1,757 phosphorylation sites with high stringency. The abundance of 239 phosphorylation sites from 175 genes, including several proteins in pathways known to be impacted by HIV-receptor binding, changed significantly within a minute after HIV-1 exposure. Several previously uncharacterized HIV-1 host factors were also identified and confirmed through RNAi depletion studies. Surprisingly, 5 serine/arginine-rich (SR)-proteins involved in mRNA splicing, including the splicing factor SRm300 (SRRM2) were differentially phosophorylated. Mechanistic studies with SRRM2 suggest that HIV-1 modulates host cell alternative splicing machinery during entry in order to facilitate virus replication and release.

Wojcechowskyj, Jason A.; Didigu, Chuka A.; Lee, Jessica Y.; Parrish, Nicholas F.; Sinha, Rohini; Hahn, Beatrice H.; Bushman, Frederic D.; Jensen, Shane T.; Seeholzer, Steven H.; Doms, Robert W.

2014-01-01

3

Quantitative Phosphoproteomics of Proteasome Inhibition in Multiple Myeloma Cells  

Microsoft Academic Search

BackgroundThe proteasome inhibitor bortezomib represents an important advance in the treatment of multiple myeloma (MM). Bortezomib inhibits the activity of the 26S proteasome and induces cell death in a variety of tumor cells; however, the mechanism of cytotoxicity is not well understood.Methodology\\/Principal FindingsWe investigated the differential phosphoproteome upon proteasome inhibition by using stable isotope labeling by amino acids in cell

Feng Ge; Chuan-Le Xiao; Li-Jun Bi; Sheng-Ce Tao; Sheng Xiong; Xin-Feng Yin; Li-Ping Li; Chun-Hua Lu; Hai-Tao Jia; Qing-Yu He

2010-01-01

4

Quantitative analysis of cell signaling and drug action via mass spectrometry-based systems level phosphoproteomics.  

PubMed

Protein phosphorylation is a primary form of information transfer in cell signaling pathways and plays a crucial role in regulating biological responses. Aberrant phosphorylation has been implicated in a number of diseases, and kinases and phosphatases, the cellular enzymes that control dynamic phosphorylation events, present attractive therapeutic targets. However, the innate complexity of signaling networks has presented many challenges to therapeutic target selection and successful drug development. Approaches in phosphoproteomics can contribute functional, systems-level datasets across signaling networks that can provide insight into suitable drug targets, more broadly profile compound activities, and identify key biomarkers to assess clinical outcomes. Advances in MS-based phosphoproteomics efforts now provide the ability to quantitate phosphorylation with throughput and sensitivity to sample a significant portion of the phosphoproteome in clinically relevant systems. This review will discuss recent work and examples of application data that demonstrate the utility of MS, with a particular focus on the use of quantitative phosphoproteomics and phosphotyrosine-directed signaling analyses to provide robust measurement for functional biological interpretation of drug action on signaling and phenotypic outcomes. PMID:19294625

Tedford, Nathan C; Hall, Amy B; Graham, James R; Murphy, Cheryl E; Gordon, Neal F; Radding, Jeffrey A

2009-03-01

5

Quantitative phosphoproteomic analysis of prion-infected neuronal cells  

PubMed Central

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 two-dimensional gel electrophoresis. To quantify phosphorylated proteins, we performed a SILAC (stable isotope labeling by amino acids in cell culture) analysis and identified 105 proteins, which showed a regulated phosphorylation upon PrPSc infection. Among those proteins, we validated the dephosphorylation of stathmin and Cdc2 and the induced phosphorylation of cofilin in PrPSc-infected N2a cells in Western blot analyses. Our analysis showed for the first time a differentially regulated phospho-proteome in PrPSc infection, which could contribute to the establishment of novel protein markers and to the development of novel therapeutic intervention strategies in targeting prion-associated disease.

2010-01-01

6

Quantitative Phosphoproteomics Applied to the Yeast Pheromone Signaling Pathway  

Microsoft Academic Search

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

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

2005-01-01

7

Quantitative Phosphoproteomics Analysis of Nitric Oxide-Responsive Phosphoproteins in Cotton Leaf  

PubMed Central

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

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

2014-01-01

8

Quantitative phosphoproteomics analysis of nitric oxide-responsive phosphoproteins in cotton leaf.  

PubMed

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

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

2014-01-01

9

Quantitative phospho-proteomic profiling of hepatocyte growth factor (HGF)-MET signaling in colorectal cancer.  

PubMed

Colorectal cancer (CRC) is the second leading cause of death from cancer. The MET receptor tyrosine kinase and/or its ligand HGF are frequently amplified or overexpressed in CRC. It is known that tyrosine phosphorylated proteins are involved in progression and metastasis of colorectal cancer; however, little is known about the MET phospho-proteome in CRC. High resolution mass spectrometry was used to characterize immunoaffinity-purified, phosphotyrosine (pY)-containing tryptic peptides of the MET-expressing CRC cell model, DLD1. A total of 266 unambiguously identified pY sites spanning 168 proteins were identified. Quantification of mass spectrometry ion currents identified 161 pY sites, including many not previously linked to MET signaling, that were modulated in abundance by HGF stimulation. Overlay of these data with protein-protein interaction data sets suggested that many of the identified HGF-modulated phospho-proteins may be directly or indirectly associated with MET. Analysis of pY sequence motifs indicated a prevalence of Src family kinase consensus sequences, and reciprocal signaling between Src and MET was confirmed by using selective small molecule inhibitors of these kinases. Therefore, using quantitative phospho-proteomics profiling, kinase modulation by ligand and inhibitors, and data integration, an outline of the MET signaling network was generated for the CRC model. PMID:21609022

Organ, Shawna L; Tong, Jiefei; Taylor, Paul; St-Germain, Jonathan R; Navab, Roya; Moran, Michael F; Tsao, Ming-Sound

2011-07-01

10

Quantitative phosphoproteomic profiling of PINK1-deficient cells identifies phosphorylation changes in nuclear proteins.  

PubMed

The Parkinson's disease (PD) associated gene PINK1 encodes a protein kinase that mediates the phosphorylation of multiple proteins involved in mitochondrial homeostasis. The broader downstream signaling events mediated by PINK1 kinase activity have not been well documented. We combine quantitative phosphoproteomic strategies with siRNA mediated PINK1 knock down in mammalian cells to identify alterations of phosphorylation events downstream of PINK1. Although down-regulation of PINK1 has no major effect on the proteome expression in these cells, phosphorylation of over one hundred proteins was reduced reflecting basal levels of phosphorylation signaling events downstream of PINK1. Motif analysis of the residues flanking the phosphorylation sites indicates proline-directed kinase specificity. Surprisingly, we found that the downstream signaling nodes included many transcription factors, as well as nuclear proteins involved in DNA and RNA metabolism. Thus, PINK1 dependent phosphorylation signaling may regulate nuclear activities. PMID:24626860

Qin, Xiaoyan; Zheng, Chaoya; Yates Iii, John R; Liao, Lujian

2014-07-01

11

A quantitative map of the liver mitochondrial phosphoproteome reveals post-translational control of ketogenesis  

PubMed Central

Summary Mitochondria are dynamic organelles that play a central role in a diverse array of metabolic processes. Elucidating mitochondrial adaptations to changing metabolic demands and the pathogenic alterations that underlie metabolic disorders represent principal challenges in cell biology. Here, we performed multiplexed quantitative mass spectrometry-based proteomics to chart the remodeling of the mouse liver mitochondrial proteome and phosphoproteome during both acute and chronic physiological transformations in more than 50 mice. Our analyses reveal that reversible phosphorylation is widespread in mitochondria, and is a key mechanism for regulating ketogenesis during the onset of obesity and type 2 diabetes. Specifically, we have demonstrated that phosphorylation of a conserved serine on Hmgcs2 (S456) significantly enhances its catalytic activity in response to increased ketogenic demand. Collectively, our work describes the plasticity of this organelle at high resolution and provides a framework for investigating the roles of proteome restructuring and reversible phosphorylation in mitochondrial adaptation.

Grimsrud, Paul A.; Carson, Joshua J.; Hebert, Alex S.; Hubler, Shane L.; Niemi, Natalie M.; Bailey, Derek J.; Jochem, Adam; Stapleton, Donald S.; Keller, Mark P.; Westphall, Michael S.; Yandell, Brian S.; Attie, Alan D.; Coon, Joshua J.; Pagliarini, David J.

2012-01-01

12

Quantitative phosphoproteomics analysis reveals broad regulatory role of heparan sulfate on endothelial signaling.  

PubMed

Heparan sulfate (HS) is a linear, abundant, highly sulfated polysaccharide that expresses in the vasculature. Recent genetic studies documented that HS critically modulates various endothelial cell functions. However, elucidation of the underlying molecular mechanism has been challenging because of the presence of a large number of HS-binding ligands found in the examined experimental conditions. In this report, we used quantitative phosphoproteomics to examine the global HS-dependent signaling by comparing wild type and HS-deficient endothelial cells that were cultured in a serum-containing medium. A total of 7222 phosphopeptides, corresponding to 1179 proteins, were identified. Functional correlation analysis identified 25 HS-dependent functional networks, and the top five are related to cell morphology, cellular assembly and organization, cellular function and maintenance, cell-to-cell communication, inflammatory response and disorder, cell growth and proliferation, cell movement, and cellular survival and death. This is consistent with cell function studies showing that HS deficiency altered endothelial cell growth and mobility. Mining for the underlying molecular mechanisms further revealed that HS modulates signaling pathways critically related to cell adhesion, migration, and coagulation, including ILK, integrin, actin cytoskeleton organization, tight junction and thrombin signaling. Intriguingly, this analysis unexpectedly determined that the top HS-dependent signaling is the IGF-1 signaling pathway, which has not been known to be modulated by HS. In-depth analysis of growth factor signaling identified 22 HS-dependent growth factor/cytokine/growth hormone signaling pathways, including those both previously known, such as HGF and VEGF, and those unknown, such as IGF-1, erythropoietin, angiopoietin/Tie, IL-17A and growth hormones. Twelve of the identified 22 growth factor/cytokine/growth hormone signaling pathways, including IGF-1 and angiopoietin/Tie signaling, were alternatively confirmed in phospho-receptor tyrosine kinase array analysis. In summary, our SILAC-based quantitative phosphoproteomic analysis confirmed previous findings and also uncovered novel HS-dependent functional networks and signaling, revealing a much broader regulatory role of HS on endothelial signaling. PMID:23649490

Qiu, Hong; Jiang, Jun-Lin; Liu, Miao; Huang, Xin; Ding, Shi-Jian; Wang, Lianchun

2013-08-01

13

Research Resource: Identification of Novel Growth Hormone-Regulated Phosphorylation Sites by Quantitative Phosphoproteomics  

PubMed Central

GH and GH receptors are expressed throughout life, and GH elicits a diverse range of responses, including growth and altered metabolism. It is therefore important to understand the full spectrum of GH signaling pathways and cellular responses. We applied mass spectrometry-based phosphoproteomics combined with stable isotope labeling with amino acids in cell culture to identify proteins rapidly phosphorylated in response to GH in 3T3-F442A preadipocytes. We identified 132 phosphosites in 95 proteins that exhibited rapid (5 or 15 min) GH-dependent statistically significant increases in phosphorylation by more than or equal to 50% and 96 phosphosites in 46 proteins that were down-regulated by GH by more than or equal to 30%. Several of the GH-stimulated phosphorylation sites were known (e.g. regulatory Thr/Tyr in Erks 1 and 2, Tyr in signal transducers and activators of transcription (Stat) 5a and 5b, Ser939 in tuberous sclerosis protein (TSC) 2 or tuberin). The remaining 126 GH-stimulated sites were not previously associated with GH. Kyoto Encyclopedia of Genes and Genomes pathway analysis of GH-stimulated sites indicated enrichment in proteins associated with the insulin and mammalian target of rapamycin (mTOR) pathways, regulation of the actin cytoskeleton, and focal adhesions. Akt/protein kinase A consensus sites (RXRXXS/T) were the most commonly phosphorylated consensus sites. Immunoblotting confirmed GH-stimulated phosphorylation of all seven novel GH-dependent sites tested [regulatory sites in proline-rich Akt substrate, 40 kDA (PRAS40), regulatory associated protein of mTOR, ATP-citrate lyase, Na+/H+ exchanger-1, N-myc downstream regulated gene 1, and Shc]). The immunoblot results suggest that many, if not most, of the GH-stimulated phosphosites identified in this large-scale quantitative phosphoproteomics analysis, including sites in multiple proteins in the Akt/ mTOR complex 1 pathway, are phosphorylated in response to GH. Their identification significantly broadens our thinking of GH-regulated cell functions.

Ray, Bridgette N.; Kweon, Hye Kyong; Argetsinger, Lawrence S.; Fingar, Diane C.; Andrews, Philip C.

2012-01-01

14

Quantitative phosphoproteomics identifies filaggrin and other targets of ionizing radiation in a human skin model.  

PubMed

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 signalling in a complex three-dimensional setting. Application of an isobaric labelling strategy using sham and three radiation doses (3, 10, 200 cGy) resulted in the identification of 1052 unique phosphopeptides. Statistical analyses identified 176 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, 2 and 3) had altered phosphorylation levels following exposure to both low and high doses of radiation. Altered phosphorylation of multiple sites in profilaggrin linker domains 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 both low and high doses of ionizing radiation involving multiple layers of the stratified epithelium that serve to maintain tissue integrity and mitigate effects of radiation exposure. PMID:22509832

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

2012-05-01

15

Quantitative phosphoproteome analysis unveils LAT as a modulator of CD3? and ZAP-70 tyrosine phosphorylation.  

PubMed

Signaling through the T cell receptor (TCR) initiates adaptive immunity and its perturbation may results in autoimmunity. The plasma membrane scaffolding protein LAT acts as a central organizer of the TCR signaling machinery to activate many functional pathways. LAT-deficient mice develop an autoimmune syndrome but the mechanism of this pathology is unknown. In this work we have compared global dynamics of TCR signaling by MS-based quantitative phosphoproteomics in LAT-sufficient and LAT-defective Jurkat T cells. Surprisingly, we found that many TCR-induced phosphorylation events persist in the absence of LAT, despite ERK and PLC?1 phosphorylation being repressed. Most importantly, the absence of LAT resulted in augmented and persistent tyrosine phosphorylation of CD3? and ZAP70. This indicates that LAT signaling hub is also implicated in negative feedback signals to modulate upstream phosphorylation events. Phosphorylation kinetics data resulting from this investigation is documented in a database (phosphoTCR) accessible online. The MS data have been deposited to the ProteomeXchange with identifier PXD000341. PMID:24204825

Salek, Mogjiborahman; McGowan, Simon; Trudgian, David C; Dushek, Omer; de Wet, Ben; Efstathiou, Georgios; Acuto, Oreste

2013-01-01

16

Quantitative phosphoproteomics identifies filaggrin and other targets of ionizing radiation in a human skin model  

PubMed Central

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 1052 unique phosphopeptides. Statistical analyses identified 176 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, 2 and 3) had altered phosphorylation levels following exposure to both low and high doses of radiation. Altered phosphorylation of multiple sites in profilaggrin linker domains 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 both low and high doses of ionizing radiation involving multiple layers of the stratified epithelium that serve to maintain tissue integrity and mitigate effects of radiation exposure.

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

2012-01-01

17

Urinary proteomic and non-prefractionation quantitative phosphoproteomic analysis during pregnancy and non-pregnancy  

PubMed Central

Background Progress in the fields of protein separation and identification technologies has accelerated research into biofluids proteomics for protein biomarker discovery. Urine has become an ideal and rich source of biomarkers in clinical proteomics. Here we performed a proteomic analysis of urine samples from pregnant and non-pregnant patients using gel electrophoresis and high-resolution mass spectrometry. Furthermore, we also apply a non-prefractionation quantitative phosphoproteomic approach using mTRAQ labeling to evaluate the expression of specific phosphoproteins during pregnancy comparison with non-pregnancy. Results In total, 2579 proteins (10429 unique peptides) were identified, including 1408 from the urine of pregnant volunteers and 1985 from the urine of non-pregnant volunteers. One thousand and twenty-three proteins were not reported in previous studies at the proteome level and were unique to our study. Furthermore, we obtained 237 phosphopeptides, representing 105 phosphoproteins. Among these phosphoproteins, 16 of them were found to be significantly differentially expressed, of which 14 were up-regulated and two were down-regulated in urine samples from women just before vaginal delivery. Conclusion Taken together, these results offer a comprehensive urinary proteomic profile of healthy women during before and after vaginal delivery and novel information on the phosphoproteins that are differentially regulated during the maintenance of normal pregnancy. Our results may provide a better understanding of the mechanisms of pregnancy maintenance, potentially leading to the development of biomarker-based sensitive assays for understanding pregnancy.

2013-01-01

18

Quantitative Phosphoproteomic Analysis of Soybean Root Hairs Inoculated with Bradyrhizobium japonicum  

SciTech Connect

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

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

2012-11-11

19

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

PubMed Central

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.

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; Pasa-Tolic, Ljiljana; Xu, Dong; Nguyen, Henry T.; Stacey, Gary

2012-01-01

20

Quantitative phosphoproteomic analysis reveals system-wide signaling pathways downstream of SDF-1/CXCR4 in breast cancer stem cells.  

PubMed

Breast cancer is the leading cause of cancer-related mortality in women worldwide, with an estimated 1.7 million new cases and 522,000 deaths around the world in 2012 alone. Cancer stem cells (CSCs) are essential for tumor reoccurrence and metastasis which is the major source of cancer lethality. G protein-coupled receptor chemokine (C-X-C motif) receptor 4 (CXCR4) is critical for tumor metastasis. However, stromal cell-derived factor 1 (SDF-1)/CXCR4-mediated signaling pathways in breast CSCs are largely unknown. Using isotope reductive dimethylation and large-scale MS-based quantitative phosphoproteome analysis, we examined protein phosphorylation induced by SDF-1/CXCR4 signaling in breast CSCs. We quantified more than 11,000 phosphorylation sites in 2,500 phosphoproteins. Of these phosphosites, 87% were statistically unchanged in abundance in response to SDF-1/CXCR4 stimulation. In contrast, 545 phosphosites in 266 phosphoproteins were significantly increased, whereas 113 phosphosites in 74 phosphoproteins were significantly decreased. SDF-1/CXCR4 increases phosphorylation in 60 cell migration- and invasion-related proteins, of them 43 (>70%) phosphoproteins are unrecognized. In addition, SDF-1/CXCR4 upregulates the phosphorylation of 44 previously uncharacterized kinases, 8 phosphatases, and 1 endogenous phosphatase inhibitor. Using computational approaches, we performed system-based analyses examining SDF-1/CXCR4-mediated phosphoproteome, including construction of kinase-substrate network and feedback regulation loops downstream of SDF-1/CXCR4 signaling in breast CSCs. We identified a previously unidentified SDF-1/CXCR4-PKA-MAP2K2-ERK signaling pathway and demonstrated the feedback regulation on MEK, ERK1/2, ?-catenin, and PPP1C? in SDF-1/CXCR4 signaling in breast CSCs. This study gives a system-wide view of phosphorylation events downstream of SDF-1/CXCR4 signaling in breast CSCs, providing a resource for the study of CSC-targeted cancer therapy. PMID:24782546

Yi, Tingfang; Zhai, Bo; Yu, Yonghao; Kiyotsugu, Yoshikawa; Raschle, Thomas; Etzkorn, Manuel; Seo, Hee-Chan; Nagiec, Michal; Luna, Rafael E; Reinherz, Ellis L; Blenis, John; Gygi, Steven P; Wagner, Gerhard

2014-05-27

21

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

PubMed

Vasopressin regulates transport across the collecting duct epithelium in part via effects on gene transcription. Transcriptional regulation occurs partially via changes in phosphorylation of transcription factors, transcriptional coactivators, and protein kinases in the nucleus. To test whether vasopressin alters the nuclear phosphoproteome of vasopressin-sensitive cultured mouse mpkCCD cells, we used stable isotope labeling and mass spectrometry to quantify thousands of phosphorylation sites in nuclear extracts and nuclear pellet fractions. Measurements were made in the presence and absence of the vasopressin analog dDAVP. Of the 1,251 sites quantified, 39 changed significantly in response to dDAVP. Network analysis of the regulated proteins revealed two major clusters ("cell-cell adhesion" and "transcriptional regulation") that were connected to known elements of the vasopressin signaling pathway. The hub proteins for these two clusters were the transcriptional coactivator ?-catenin and the transcription factor c-Jun. Phosphorylation of ?-catenin at Ser552 was increased by dDAVP [log(2)(dDAVP/vehicle) = 1.79], and phosphorylation of c-Jun at Ser73 was decreased [log(2)(dDAVP/vehicle) = -0.53]. The ?-catenin site is known to be targeted by either protein kinase A or Akt, both of which are activated in response to vasopressin. The c-Jun site is a canonical target for the MAP kinase Jnk2, which is downregulated in response to vasopressin in the collecting duct. The data support the idea that vasopressin-mediated control of transcription in collecting duct cells involves selective changes in the nuclear phosphoproteome. All data are available to users at http://helixweb.nih.gov/ESBL/Database/mNPPD/. PMID:22992673

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

2012-11-15

22

Quantitative comparison of the fasted and re-fed mouse liver phosphoproteomes using lower pH reductive dimethylation.  

PubMed

Phosphorylation is a common but crucial protein posttranslational modification occurring in virtually all known species. A successful technique for identifying phosphorylation sites is via liquid chromatography-tandem mass spectrometry (LC-MS/MS). In addition to identification, the introduction of stable isotopes allows for LC-MS based quantification of thousands of phosphorylation sites. Historically, stable isotope labeling by amino acids in cell culture (SILAC) has been the preferred method for introducing stable isotopes for quantification. SILAC is not well suited, however, for quantitative proteomics in larger animals. The introduction of stable isotope instead by reductive dimethylation is an alternative for performing quantitative proteomics in animal tissues. Here we present an improved reductive dimethylation protocol and demonstrate the application of this method in the analysis of the fasted vs. re-fed mouse liver phosphoproteome. In our analysis, greater than 8500 sites were identified from ?2700 phosphoproteins. Nearly 7400 phosphorylation events from ?2300 phosphoproteins were reliably quantified. Using a 2-fold change as a cutoff, 390 phosphorylation sites were found to change between fasted and re-fed mice, many of which may have interesting biological interpretations. PMID:23567750

Wilson-Grady, Joshua T; Haas, Wilhelm; Gygi, Steven P

2013-06-15

23

Dynamics of the G Protein-coupled Vasopressin V2 Receptor Signaling Network Revealed by Quantitative Phosphoproteomics*  

PubMed Central

G protein-coupled receptors (GPCRs) regulate diverse physiological processes, and many human diseases are due to defects in GPCR signaling. To identify the dynamic response of a signaling network downstream from a prototypical Gs-coupled GPCR, the vasopressin V2 receptor, we have carried out multireplicate, quantitative phosphoproteomics with iTRAQ labeling at four time points following vasopressin exposure at a physiological concentration in cells isolated from rat kidney. A total of 12,167 phosphopeptides were identified from 2,783 proteins, with 273 changing significantly in abundance with vasopressin. Two-dimensional clustering of phosphopeptide time courses and Gene Ontology terms revealed that ligand binding to the V2 receptor affects more than simply the canonical cyclic adenosine monophosphate-protein kinase A and arrestin pathways under physiological conditions. The regulated proteins included key components of actin cytoskeleton remodeling, cell-cell adhesion, mitogen-activated protein kinase signaling, Wnt/?-catenin signaling, and apoptosis pathways. These data suggest that vasopressin can regulate an array of cellular functions well beyond its classical role in regulating water and solute transport. These results greatly expand the current view of GPCR signaling in a physiological context and shed new light on potential roles for this signaling network in disorders such as polycystic kidney disease. Finally, we provide an online resource of physiologically regulated phosphorylation sites with dynamic quantitative data (http://helixweb.nih.gov/ESBL/Database/TiPD/index.html).

Hoffert, Jason D.; Pisitkun, Trairak; Saeed, Fahad; Song, Jae H.; Chou, Chung-Lin; Knepper, Mark A.

2012-01-01

24

Global Quantitative SILAC Phosphoproteomics Reveals Differential Phosphorylation Is Widespread between the Procyclic and Bloodstream Form Lifecycle Stages of Trypanosoma brucei  

PubMed Central

We report a global quantitative phosphoproteomic study of bloodstream and procyclic form Trypanosoma brucei using SILAC labeling of each lifecycle stage. Phosphopeptide enrichment by SCX and TiO2 led to the identification of a total of 10096 phosphorylation sites on 2551 protein groups and quantified the ratios of 8275 phosphorylation sites between the two lifecycle stages. More than 9300 of these sites (92%) have not previously been reported. Model-based gene enrichment analysis identified over representation of Gene Ontology terms relating to the flagella, protein kinase activity, and the regulation of gene expression. The quantitative data reveal that differential protein phosphorylation is widespread between bloodstream and procyclic form trypanosomes, with significant intraprotein differential phosphorylation. Despite a lack of dedicated tyrosine kinases, 234 phosphotyrosine residues were identified, and these were 3–4 fold over-represented among site changing >10-fold between the two lifecycle stages. A significant proportion of the T. brucei kinome was phosphorylated, with evidence that MAPK pathways are functional in both lifecycle stages. Regulation of gene expression in T. brucei is exclusively post-transcriptional, and the extensive phosphorylation of RNA binding proteins observed may be relevant to the control of mRNA stability in this organism.

2013-01-01

25

Quantitative analysis of castration resistant prostate cancer progression through phosphoproteome signaling  

PubMed Central

Background Although recent progress has been made in treating castration resistant prostate cancer, the interplay of signaling pathways which enable castration resistant growth is incompletely understood. A data driven, multivariate approach, was used in this study to predict prostate cancer cell survival based on the phosphorylation levels of key proteins in PC3, LNCaP, and MDA-PCa-2b cell lines in response to EGF, IGF1, IL6, TNF?, dihydrotestosterone, and docetaxel treatment. Methods The prostate cancer cell lines were treated with ligands or inhibitors, cell lyates were collected, and the amount of phosphoprotein quantified using 384 well ELISA assays. In separate experiments, relative cell viability was determined using an MTT assay. Normalized data was imported into Matlab where regression analysis was performed. Results Based on a linear model developed using partial least squares regression, p-Erk1/2 was found to correlate with castration resistant survival along with p-RPS6, and this model was determined to have a leave-one-out cross validated R2 value of 0.61. The effect of androgen on the phosphoproteome was examined, and increases in PI3K related phosphoproteins (p-Akt, p-RPS6, and p-GSK3) were observed which accounted for the majority of the significant increase in androgen-mediated cell survival. Simultaneous inhibition of the PI3K pathway and treatment with androgen resulted in a non-significant increase in survival. Given the strong effect of PI3K related signaling in enabling castration resistant survival, the specific effect of mTor versus complete inhibition was examined using targeted inhibitors. It was determine that mTor inhibition accounts for 52% of the effect of complete PI3K inhibition on cell survival. The differences in signaling between the cell lines were explored it was observed that MDA-PCa-2b exhibited far less activation of p-Erk in response to varying treatments, explaining one of the reasons for the lack of castration resistance. Conclusion In this work, regression analysis to the phosphoproteome was used to illustrate the sources of castration resistance between the cell lines including reduced p-Erk signaling in MDA-PCa-2b and variations in p-JNK across the cell lines, as well as studying the signaling pathways which androgen acts through, and determining the response to treatment with targeted inhibitors.

2014-01-01

26

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

PubMed Central

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.

2014-01-01

27

Quantitative phosphoproteomics revealed interplay between Syk and Lyn in the resistance to nilotinib in chronic myeloid leukemia cells.  

PubMed

In this study, we have addressed how Lyn kinase signaling mediates nilotinib-resistance by quantitative phospho-proteomics using Stable Isotope Labeling with Amino acid in Cell culture. We have found an increased tyrosine phosphorylation of 2 additional tyrosine kinases in nilotinib-resistant cells: the spleen tyrosine kinase Syk and the UFO family receptor tyrosine kinase Axl. This increased tyrosine phosphorylation involved an interaction of these tyrosine kinases with Lyn. Inhibition of Syk by the inhibitors R406 or BAY 61-3606 or by RNA interference restored the capacity of nilotinib to inhibit cell proliferation. Conversely, coexpression of Lyn and Syk were required to fully induce resistance to nilotinib in drug-sensitive cells. Surprisingly, the knockdown of Syk also strongly decreased tyrosine phosphorylation of Lyn and Axl, thus uncovering interplay between Syk and Lyn. We have shown the involvement of the adaptor protein CDCP-1 in resistance to nilotinib. Interestingly, the expression of Axl and CDCP1 were found increased both in a nilotinib-resistant cell line and in nilotinib-resistant CML patients. We conclude that an oncogenic signaling mediated by Lyn and Syk can bypass the need of Bcr-Abl in CML cells. Thus, targeting these kinases may be of therapeutic value to override imatinib or nilotinib resistance in CML. PMID:21730355

Gioia, Romain; Leroy, Cédric; Drullion, Claire; Lagarde, Valérie; Etienne, Gabriel; Dulucq, Stéphanie; Lippert, Eric; Roche, Serge; Mahon, François-Xavier; Pasquet, Jean-Max

2011-08-25

28

Quantitative phosphoproteomics of vasopressin-sensitive renal cells: regulation of aquaporin-2 phosphorylation at two sites.  

PubMed

Protein phosphorylation plays a key role in vasopressin signaling in the renal-collecting duct. Large-scale identification and quantification of phosphorylation events triggered by vasopressin is desirable to gain a comprehensive systems-level understanding of this process. We carried out phosphoproteomic analysis of rat inner medullary collecting duct cells by using a combination of phosphopeptide enrichment by immobilized metal affinity chromatography and phosphorylation site identification by liquid chromatography-mass spectrometry(n) neutral loss scanning. A total of 714 phosphorylation sites on 223 unique phosphoproteins were identified from inner medullary collecting duct samples treated short-term with either calyculin A or vasopressin. A number of proteins involved in cytoskeletal reorganization, vesicle trafficking, and transcriptional regulation were identified. Previously unidentified phosphorylation sites were found for membrane proteins essential to collecting duct physiology, including eight sites among aquaporin-2 (AQP2), aquaporin-4, and urea transporter isoforms A1 and A3. Through label-free quantification of phosphopeptides, we identified a number of proteins that significantly changed phosphorylation state in response to short-term vasopressin treatment: AQP2, Bclaf1, LRRC47, Rgl3, and SAFB2. In the presence of vasopressin, AQP2 monophosphorylated at S256 and diphosphorylated AQP2 (pS256/261) increased in abundance, whereas AQP2 monophosphorylated at S261 decreased, raising the possibility that both sites are involved in vasopressin-dependent AQP2 trafficking. This study reveals the practicality of liquid chromatography-mass spectrometry(n) neutral loss scanning for large-scale identification and quantification of protein phosphorylation in the analysis of cell signaling in a native mammalian system. PMID:16641100

Hoffert, Jason D; Pisitkun, Trairak; Wang, Guanghui; Shen, Rong-Fong; Knepper, Mark A

2006-05-01

29

Phosphoproteomics in Cancer  

PubMed Central

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

Harsha, H. C.; Pandey, Akhilesh

2010-01-01

30

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

PubMed Central

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.

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

31

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

PubMed

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

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

2014-05-01

32

Quantitative Phosphoproteomics Unravels Biased Phosphorylation of Serotonin 2A Receptor at Ser280 by Hallucinogenic versus Nonhallucinogenic Agonists*  

PubMed Central

The serotonin 5-HT2A 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-HT2A 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-HT2A receptor and exposed to either vehicle or the synthetic hallucinogen 1-[2,5-dimethoxy-4-iodophenyl]-2-aminopropane (DOI) or the nonhallucinogenic 5-HT2A 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 (Ser280) located in the third intracellular loop of the 5-HT2A receptor, a region important for its desensitization. The specific phosphorylation of Ser280 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-HT2A receptors at Ser280 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 Ser280 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-HT2A receptor in response to hallucinogenic versus nonhallucinogenic agonists, which underlies their distinct capacity to desensitize the receptor.

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

2014-01-01

33

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

PubMed Central

Summary 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 various cellular processes. Here we present an integrated quantitative phosphoproteomics approach and its application 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 LC-MS/MS analysis. LC separation and MS/MS are followed by neutral loss-dependent MS/MS/MS for phosphopeptide identification using a linear ion trap (LTQ)-FT mass spectrometer. A variety of phosphorylated proteins were identified and quantified including receptors, kinases, proteins associated with small GTPases, and cytoskeleton proteins. A number of hypothetical proteins were also identified as differentially expressed followed by LPA stimulation, and we have shown evidence of pseudopodia subcellular localization of one of these candidate proteins. These results demonstrate the efficiency of this quantitative phosphoproteomics approach and its application for rapid discovery of phosphorylation events associated with LPA gradient sensing and cell chemotaxis.

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

2009-01-01

34

Quantitative Phosphoproteome Analysis of Lysophosphatidic Acid Induced Chemotaxis applying Dual-step ¹?O Labeling Coupled with Immobilized Metal-ion Affinity Chromatography  

SciTech Connect

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.

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

35

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

PubMed Central

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

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

2012-01-01

36

Quantitative trait locus analysis of leaf dissection in tomato using Lycopersicon pennellii segmental introgression lines.  

PubMed Central

Leaves are one of the most conspicuous and important organs of all seed plants. A fundamental source of morphological diversity in leaves is the degree to which the leaf is dissected by lobes and leaflets. We used publicly available segmental introgression lines to describe the quantitative trait loci (QTL) controlling the difference in leaf dissection seen between two tomato species, Lycopersicon esculentum and L. pennellii. We define eight morphological characteristics that comprise the mature tomato leaf and describe loci that affect each of these characters. We found 30 QTL that contribute one or more of these characters. Of these 30 QTL, 22 primarily affect leaf dissection and 8 primarily affect leaf size. On the basis of which characters are affected, four classes of loci emerge that affect leaf dissection. The majority of the QTL produce phenotypes intermediate to the two parent lines, while 5 QTL result in transgression with drastically increased dissection relative to both parent lines.

Holtan, Hans E E; Hake, Sarah

2003-01-01

37

Quantitative trait locus analysis of leaf dissection in tomato using Lycopersicon pennellii segmental introgression lines.  

PubMed

Leaves are one of the most conspicuous and important organs of all seed plants. A fundamental source of morphological diversity in leaves is the degree to which the leaf is dissected by lobes and leaflets. We used publicly available segmental introgression lines to describe the quantitative trait loci (QTL) controlling the difference in leaf dissection seen between two tomato species, Lycopersicon esculentum and L. pennellii. We define eight morphological characteristics that comprise the mature tomato leaf and describe loci that affect each of these characters. We found 30 QTL that contribute one or more of these characters. Of these 30 QTL, 22 primarily affect leaf dissection and 8 primarily affect leaf size. On the basis of which characters are affected, four classes of loci emerge that affect leaf dissection. The majority of the QTL produce phenotypes intermediate to the two parent lines, while 5 QTL result in transgression with drastically increased dissection relative to both parent lines. PMID:14668401

Holtan, Hans E E; Hake, Sarah

2003-11-01

38

Synaptic transmission in neurological disorders dissected by a quantitative approach  

PubMed Central

Synaptic transmission depends on several molecular and geometric components, such as the location of vesicular release, the number of released neurotransmitter molecules, the number and type of receptors, as well as the synapse organization. Our goal here is to illustrate how synaptic modeling allows extracting quantitative information in the context of neurological diseases and associated therapies. Combining electrophysiology with simulation tools, we first evaluate the reduction in synaptically released glutamate molecules induced by a ketogenic diet. In a second part, because the scaffolding molecule Shank3 is disrupted at the postsynaptic density in Autism Spectral Disorders, we present a numerical simulation of the synaptic response where this disruption leads to an alteration of the excitatory AMPA receptor trafficking. The take home message is that combining recent experimental findings with modeling approaches allows obtaining precise quantitative properties of what was still unapproachable a decade ago.

Freche, Dominik; Lee, Chun-Yao; Rouach, Nathalie; Holcman, David

2012-01-01

39

Dissection Dissected.  

ERIC Educational Resources Information Center

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)

Berman, William

1984-01-01

40

Dissecting Dissection.  

ERIC Educational Resources Information Center

This journal features articles covering various aspects of dissection. "Biology--The Study of Life" (George Russell) offers students experiments that do not require using invasive procedures. "Animal Cruelty--Behind the Scenes" (Zoe Weil) describes sources of laboratory animals. "Doing without Dissection" (Juliana Texley) discusses objections over…

AV Magazine, 1996

1996-01-01

41

The Lottia gigantea shell matrix proteome: re-analysis including MaxQuant iBAQ quantitation and phosphoproteome analysis  

PubMed Central

Background Although the importance of proteins of the biomineral organic matrix and their posttranslational modifications for biomineralization is generally recognized, the number of published matrix proteomes is still small. This is mostly due to the lack of comprehensive sequence databases, usually derived from genomic sequencing projects. However, in-depth mass spectrometry-based proteomic analysis, which critically depends on high-quality sequence databases, is a very fast tool to identify candidates for functional biomineral matrix proteins and their posttranslational modifications. Identification of such candidate proteins is facilitated by at least approximate quantitation of the identified proteins, because the most abundant ones may also be the most interesting candidates for further functional analysis. Results Re-quantification of previously identified Lottia shell matrix proteins using the intensity-based absolute quantification (iBAQ) method as implemented in the MaxQuant identification and quantitation software showed that only 57 of the 382 accepted identifications constituted 98% of the total identified matrix proteome. This group of proteins did not contain obvious intracellular proteins, such as cytoskeletal components or ribosomal proteins, invariably identified as minor components of high-throughput biomineral matrix proteomes. Fourteen of these major proteins were phosphorylated to a variable extent. All together we identified 52 phospho sites in 20 of the 382 accepted proteins with high confidence. Conclusions We show that iBAQ quantitation may be a useful tool to narrow down the group of functional biomineral matrix protein candidates for further research in cell biology, genetics or materials research. Knowledge of posttranslational modifications in these major proteins could be a valuable addition to previously published proteomes. This is true especially for phosphorylation, because this modification was already shown to modify mineralization processes in some instances.

2014-01-01

42

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

PubMed Central

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.

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

2013-01-01

43

Quantitative mitochondrial phosphoproteomics using iTRAQ on an LTQ-Orbitrap with high energy collision dissociation.  

PubMed

With the use of iTRAQ labeling and mass spectrometry on an LTQ-Orbitrap with HCD capability, we assessed relative changes in protein phosphorylation in the mitochondria upon physiological perturbation. As a reference reaction, we monitored the well-characterized regulation of pyruvate dehydrogenase (PDH) activity via phosphorylation/dephosphorylation by pyruvate dehydrogenase kinase/pyruvate dehydrogenase phosphatase in response to dichloroacetate, de-energization and Ca2+. Relative quantification of phosphopeptides of PDH-E1alpha subunit from porcine heart revealed dephosphorylation at three serine sites (Ser231, Ser292 and Ser299). Dephosphorylation at Ser292 (i.e., the inhibitory site) with DCA correlated with an activation of PDH activity as previously reported, consistent with our de-energization data. Calcium also dephosphorylated (i.e., activated) PDH, thus, confirming calcium activation of PDP. With this approach, we successfully monitored other phosphorylation sites of mitochondrial proteins including adenine nucleotide translocase, malate dehydrogenase and mitochondrial creatine kinase. Among them, four proteins exhibited phosphorylation changes with these physiological stimuli: (1) BCKDH-E1alpha subunit increased phosphorylation at Ser337 with DCA and de-energization; (2) apoptosis-inducing factor phosphorylation was elevated at Ser345 with calcium; (3) ATP synthase F1 complex alpha subunit and (4) mitofilin dephosphorylated at Ser65 and Ser264 upon de-energization. This screening validated the iTRAQ/HCD technology as a method for functional quantitation of mitochondrial protein phosphorylation as well as providing insight into the regulation of mitochondria via phosphorylation. PMID:19694452

Boja, Emily S; Phillips, Darci; French, Stephanie A; Harris, Robert A; Balaban, Robert S

2009-10-01

44

Phosphoproteomics in drug discovery.  

PubMed

Several important aspects of the drug discovery process, including target identification, mechanism of action determination and biomarker identification as well as drug repositioning, require complete understanding of the effects of drugs on protein phosphorylation in relevant biological systems. Novel high-throughput phosphoproteomic technologies can be employed to measure these phosphorylation events. In this review, we describe the advantages and limitations of state-of-the-art phosphoproteomic approaches such as mass spectrometry and antibody-based technologies in terms of sample and data throughput as well as data quality. We then discuss how datasets from each technology can be analyzed and how the results can be and have been applied to advance different aspects of the drug discovery process. PMID:24141136

Morris, Melody K; Chi, An; Melas, Ioannis N; Alexopoulos, Leonidas G

2014-04-01

45

Challenges in plasma membrane phosphoproteomics  

PubMed Central

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.

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

2011-01-01

46

Phosphoproteomics-based network medicine.  

PubMed

One of the major tasks of phosphoproteomics is providing potential biomarkers for either diagnosis or drug targets in medical applications. Because most complex diseases are due to the actions of multiple genes/proteins, the identification of complex phospho-signatures containing multiple phosphorylation events within phosphoproteomics-based networks generates more efficient and robust biomarkers than a single, differentially phosphorylated substrate or site. Here, we briefly summarize the current efforts and progress in this newly emerging field of phosphoproteomics-based network medicine by reviewing the computational (re)construction of phosphorylation-mediated signaling networks from unannotated phosphoproteomic data, the discovery of robust network phospho-signatures and the application of these signatures for classifying cancers and predicting drug responses. The challenges as well as the potential advantages are evaluated and discussed. Although the current techniques are at present far from mature, we believe that such a systematic approach as we describe can generate more useful and robust biomarkers for biomedical usage, even at the current stage of development. PMID:23751130

Liu, Zexian; Wang, Yongbo; Xue, Yu

2013-11-01

47

Maize association population: a high-resolution platform for quantitative trait locus dissection  

Microsoft Academic Search

Summary Crop improvement and the dissection of complex genetic traits require germplasm diversity. Although this necessary phenotypic variability exists in diverse maize, most research is conducted using a small subset of inbred lines. An association population of 302 lines is now available - a valuable research tool that captures a large proportion of the alleles in cultivated maize. Provided that

Sherry A. Flint-Garcia; Anne-Celine Thuillet; Jianming Yu; Gael Pressoir; Susan M. Romero; Sharon E. Mitchell; John Doebley; Stephen Kresovich; Major M. Goodman; Edward S. Buckler

2005-01-01

48

Phosphoproteomics and Lung Cancer Research  

PubMed Central

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.

Lopez, Elena; Cho, William C. S.

2012-01-01

49

Functional phosphoproteomic mass spectrometry-based approaches  

PubMed Central

Mass Spectrometry (MS)-based phosphoproteomics tools are crucial for understanding the structure and dynamics of signaling networks. Approaches such as affinity purification followed by MS have also been used to elucidate relevant biological questions in health and disease. The study of proteomes and phosphoproteomes as linked systems, rather than research studies of individual proteins, are necessary to understand the functions of phosphorylated and un-phosphorylated proteins under spatial and temporal conditions. Phosphoproteome studies also facilitate drug target protein identification which may be clinically useful in the near future. Here, we provide an overview of general principles of signaling pathways versus phosphorylation. Likewise, we detail chemical phosphoproteomic tools, including pros and cons with examples where these methods have been applied. In addition, basic clues of electrospray ionization and collision induced dissociation fragmentation are detailed in a simple manner for successful phosphoproteomic clinical studies.

2012-01-01

50

Functional phosphoproteomic mass spectrometry-based approaches.  

PubMed

Mass Spectrometry (MS)-based phosphoproteomics tools are crucial for understanding the structure and dynamics of signaling networks. Approaches such as affinity purification followed by MS have also been used to elucidate relevant biological questions in health and disease.The study of proteomes and phosphoproteomes as linked systems, rather than research studies of individual proteins, are necessary to understand the functions of phosphorylated and un-phosphorylated proteins under spatial and temporal conditions. Phosphoproteome studies also facilitate drug target protein identification which may be clinically useful in the near future.Here, we provide an overview of general principles of signaling pathways versus phosphorylation. Likewise, we detail chemical phosphoproteomic tools, including pros and cons with examples where these methods have been applied. In addition, basic clues of electrospray ionization and collision induced dissociation fragmentation are detailed in a simple manner for successful phosphoproteomic clinical studies. PMID:23369623

López, Elena; Wang, Xiangdong; Madero, Luis; López-Pascual, Juan; Latterich, Martin

2012-01-01

51

Impact of phosphoproteomics on studies of bacterial physiology.  

PubMed

Protein phosphorylation on serine, threonine and tyrosine is recognized as a major tool of signal transduction in bacteria. However, progress in the field has been hampered by the lack of global and site-specific data on bacterial phosphoproteomes. Recent advances in mass spectrometry-based proteomics have encouraged bacteriologists to start using powerful gel-free approaches for global detection of phosphorylated proteins. These studies have generated large data sets of proteins phosphorylated on serine, threonine and tyrosine, with identified phosphorylation sites which represent an excellent starting point for in-depth physiological characterization of kinases and their substrates. The list of phosphorylated proteins inspired a number of physiological studies in which the identity of the phosphorylation site facilitated the elucidation of molecular mechanisms of signaling and regulation. Bacterial phosphoproteomics also provided interesting insights into the evolutionary aspects of protein phosphorylation. The field is rapidly embracing quantitative mass spectrometry strategies, comparing phosphoproteome dynamics in changing conditions and aiming to reconstruct the entire regulatory networks by linking kinases to their physiological substrates. PMID:22091997

Mijakovic, Ivan; Macek, Boris

2012-07-01

52

Global dynamics of the Escherichia coli proteome and phosphoproteome during growth in minimal medium.  

PubMed

Recent phosphoproteomics studies have generated relatively large data sets of bacterial proteins phosphorylated on serine, threonine, and tyrosine, implicating this type of phosphorylation in the regulation of vital processes of a bacterial cell; however, most phosphoproteomics studies in bacteria were so far qualitative. Here we applied stable isotope labeling by amino acids in cell culture (SILAC) to perform a quantitative analysis of proteome and phosphoproteome dynamics of Escherichia coli during five distinct phases of growth in the minimal medium. Combining two triple-SILAC experiments, we detected a total of 2118 proteins and quantified relative dynamics of 1984 proteins in all measured phases of growth, including 570 proteins associated with cell wall and membrane. In the phosphoproteomic experiment, we detected 150 Ser/Thr/Tyr phosphorylation events, of which 108 were localized to a specific amino acid residue and 76 were quantified in all phases of growth. Clustering analysis of SILAC ratios revealed distinct sets of coregulated proteins for each analyzed phase of growth and overrepresentation of membrane proteins in transition between exponential and stationary phases. The proteomics data indicated that proteins related to stress response typically associated with the stationary phase, including RpoS-dependent proteins, had increasing levels already during earlier phases of growth. Application of SILAC enabled us to measure median occupancies of phosphorylation sites, which were generally low (<12%). Interestingly, the phosphoproteome analysis showed a global increase of protein phosphorylation levels in the late stationary phase, pointing to a likely role of this modification in later phases of growth. PMID:23590516

Soares, Nelson C; Spät, Philipp; Krug, Karsten; Macek, Boris

2013-06-01

53

The calcium-dependent protein kinase 3 of toxoplasma influences basal calcium levels and functions beyond egress as revealed by quantitative phosphoproteome analysis.  

PubMed

Calcium-dependent protein kinases (CDPKs) are conserved in plants and apicomplexan parasites. In Toxoplasma gondii, TgCDPK3 regulates parasite egress from the host cell in the presence of a calcium-ionophore. The targets and the pathways that the kinase controls, however, are not known. To identify pathways regulated by TgCDPK3, we measured relative phosphorylation site usage in wild type and TgCDPK3 mutant and knock-out parasites by quantitative mass-spectrometry using stable isotope-labeling with amino acids in cell culture (SILAC). This revealed known and novel phosphorylation events on proteins predicted to play a role in host-cell egress, but also a novel function of TgCDPK3 as an upstream regulator of other calcium-dependent signaling pathways, as we also identified proteins that are differentially phosphorylated prior to egress, including proteins important for ion-homeostasis and metabolism. This observation is supported by the observation that basal calcium levels are increased in parasites where TgCDPK3 has been inactivated. Most of the differential phosphorylation observed in CDPK3 mutants is rescued by complementation of the mutants with a wild type copy of TgCDPK3. Lastly, the TgCDPK3 mutants showed hyperphosphorylation of two targets of a related calcium-dependent kinase (TgCDPK1), as well as TgCDPK1 itself, indicating that this latter kinase appears to play a role downstream of TgCDPK3 function. Overexpression of TgCDPK1 partially rescues the egress phenotype of the TgCDPK3 mutants, reinforcing this conclusion. These results show that TgCDPK3 plays a pivotal role in regulating tachyzoite functions including, but not limited to, egress. PMID:24945436

Treeck, Moritz; Sanders, John L; Gaji, Rajshekhar Y; LaFavers, Kacie A; Child, Matthew A; Arrizabalaga, Gustavo; Elias, Joshua E; Boothroyd, John C

2014-06-01

54

The Calcium-Dependent Protein Kinase 3 of Toxoplasma Influences Basal Calcium Levels and Functions beyond Egress as Revealed by Quantitative Phosphoproteome Analysis  

PubMed Central

Calcium-dependent protein kinases (CDPKs) are conserved in plants and apicomplexan parasites. In Toxoplasma gondii, TgCDPK3 regulates parasite egress from the host cell in the presence of a calcium-ionophore. The targets and the pathways that the kinase controls, however, are not known. To identify pathways regulated by TgCDPK3, we measured relative phosphorylation site usage in wild type and TgCDPK3 mutant and knock-out parasites by quantitative mass-spectrometry using stable isotope-labeling with amino acids in cell culture (SILAC). This revealed known and novel phosphorylation events on proteins predicted to play a role in host-cell egress, but also a novel function of TgCDPK3 as an upstream regulator of other calcium-dependent signaling pathways, as we also identified proteins that are differentially phosphorylated prior to egress, including proteins important for ion-homeostasis and metabolism. This observation is supported by the observation that basal calcium levels are increased in parasites where TgCDPK3 has been inactivated. Most of the differential phosphorylation observed in CDPK3 mutants is rescued by complementation of the mutants with a wild type copy of TgCDPK3. Lastly, the TgCDPK3 mutants showed hyperphosphorylation of two targets of a related calcium-dependent kinase (TgCDPK1), as well as TgCDPK1 itself, indicating that this latter kinase appears to play a role downstream of TgCDPK3 function. Overexpression of TgCDPK1 partially rescues the egress phenotype of the TgCDPK3 mutants, reinforcing this conclusion. These results show that TgCDPK3 plays a pivotal role in regulating tachyzoite functions including, but not limited to, egress.

Treeck, Moritz; Sanders, John L.; Gaji, Rajshekhar Y.; LaFavers, Kacie A.; Child, Matthew A.; Arrizabalaga, Gustavo; Elias, Joshua E.; Boothroyd, John C.

2014-01-01

55

Dissecting Analogical Leveling Quantitatively: The Case of the Innovative Potential Suffix in Tokyo Japanese.  

ERIC Educational Resources Information Center

Analogical leveling in progress of a potential suffix in Tokyo Japanese is analyzed within a quantitative model. The phenomenon is shown to be controlled by five factors: sociological variable complex, verb stem length, verb conjugation pattern, the following inflectional form, and embeddedness of the clause containing the suffix. (Contains 70…

Matsuda, Kenjiro

1993-01-01

56

Chemical Visualization of Phosphoproteomes on Membrane*  

PubMed Central

With new discoveries of important roles of phosphorylation on a daily basis, phospho-specific antibodies, as the primary tool for on-membrane detection of phosphoproteins, face enormous challenges. To address an urgent need for convenient and reliable analysis of phosphorylation events, we report a novel strategy for sensitive phosphorylation analysis in the Western blotting format. The chemical reagent, which we termed pIMAGO, is based on a multifunctionalized soluble nanopolymer and is capable of selectively binding to phosphorylated residues independent of amino acid microenvironment, thus offering great promise as a universal tool in biological analyses where the site of phosphorylation is not known or its specific antibody is not available. The specificity and sensitivity of the approach was first examined using a mixture of standard proteins. The method was then applied to monitor phosphorylation changes in in vitro kinase and phosphatase assays. Finally, to demonstrate the unique ability of pIMAGO to measure endogenous phosphorylation, we used it to visualize and determine the differences in phosphorylated proteins that interact with wild-type and kinase dead mutant of Polo-like kinase 1 during mitosis, the results of which were further confirmed by a quantitative phosphoproteomics experiment.

Iliuk, Anton; Liu, X. Shawn; Xue, Liang; Liu, Xiaoqi; Tao, W. Andy

2012-01-01

57

Characterization of the Phosphoproteome in SLE Patients  

PubMed Central

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

Huang, Jianrong; Dai, Yong

2012-01-01

58

Genetic analysis and characterization of a new maize association mapping panel for quantitative trait loci dissection  

Microsoft Academic Search

Association mapping based on the linkage disequilibrium provides a promising tool to identify genes responsible for quantitative\\u000a variations underlying complex traits. Presented here is a maize association mapping panel consisting of 155 inbred lines with\\u000a mainly temperate germplasm, which was phenotyped for 34 traits and genotyped using 82 SSRs and 1,536 SNPs. Abundant phenotypic\\u000a and genetic diversities were observed within

Xiaohong YangJianbing; Jianbing Yan; Trushar Shah; Marilyn L. Warburton; Qing Li; Lin Li; Yufeng Gao; Yuchao Chai; Zhiyuan Fu; Yi Zhou; Shutu Xu; Guanghong Bai; Yijiang Meng; Yanping Zheng; Jiansheng Li

2010-01-01

59

Profiling the Trypanosoma cruzi phosphoproteome.  

PubMed

Protein phosphorylation is a reversible post-translational modification essential for the regulation of several signal transduction pathways and biological processes in the living cell. Therefore, the identification of protein phosphorylation sites is crucial to understand cell signaling control at the molecular level. Based on mass spectrometry, recent studies have reported the large-scale mapping of phosphorylation sites in various eukaryotes and prokaryotes. However, little is known about the impact of phosphorylation in protozoan parasites. To in depth characterize the phosphoproteome of Trypanosoma cruzi, a parasite of the Kinetoplastida class, protein samples from cells at different phases of the metacyclogenesis--differentiation process of the parasites from non-infective epimastigotes to infective metacyclic trypomastigotes--were enriched for phosphopeptides using TiO(2) chromatography and analyzed on an LTQ-Orbitrap mass spectrometer. In total, 1,671 proteins were identified, including 753 phosphoproteins, containing a total of 2,572 phosphorylation sites. The distribution of phosphorylated residues was 2,162 (84.1%) on serine, 384 (14.9%) on threonine and 26 (1.0%) on tyrosine. Here, we also report several consensus phosphorylation sequence motifs and as some of these conserved groups have enriched biological functions, we can infer the regulation by protein kinases of this functions. To our knowledge, our phosphoproteome is the most comprehensive dataset identified until now for Kinetoplastida species. Here we also were able to extract biological information and infer groups of sites phosphorylated by the same protein kinase. To make our data accessible to the scientific community, we uploaded our study to the data repositories PHOSIDA, Proteome Commons and TriTrypDB enabling researchers to access information about the phosphorylation sites identified here. PMID:21966514

Marchini, Fabricio K; de Godoy, Lyris M F; Rampazzo, Rita C P; Pavoni, Daniela P; Probst, Christian M; Gnad, Florian; Mann, Matthias; Krieger, Marco A

2011-01-01

60

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

NASA Astrophysics Data System (ADS)

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.

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

2012-07-01

61

Phosphoproteomic analyses reveal signaling pathways that facilitate lytic gammaherpesvirus replication.  

PubMed

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

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

2013-09-01

62

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

PubMed

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

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

2014-04-01

63

The interplay of light and oxygen in the reactive oxygen stress response of Chlamydomonas reinhardtii dissected by quantitative mass spectrometry.  

PubMed

Light and oxygen are factors that are very much entangled in the reactive oxygen species (ROS) stress response network in plants, algae and cyanobacteria. The first obligatory step in understanding the ROS network is to separate these responses. In this study, a LC-MS/MS based quantitative proteomic approach was used to dissect the responses of Chlamydomonas reinhardtii to ROS, light and oxygen employing an interlinked experimental setup. Application of novel bioinformatics tools allow high quality retention time alignment to be performed on all LC-MS/MS runs increasing confidence in protein quantification, overall sequence coverage and coverage of all treatments measured. Finally advanced hierarchical clustering yielded 30 communities of co-regulated proteins permitting separation of ROS related effects from pure light effects (induction and repression). A community termed redox(II) was identified that shows additive effects of light and oxygen with light as the first obligatory step. Another community termed 4-down was identified that shows repression as an effect of light but only in the absence of oxygen indicating ROS regulation, for example, possibly via product feedback inhibition because no ROS damage is occurring. In summary the data demonstrate the importance of separating light, O? and ROS responses to define marker genes for ROS responses. As revealed in this study, an excellent candidate is DHAR with strong ROS dependent induction profiles. PMID:24482124

Barth, Johannes; Bergner, Sonja Verena; Jaeger, Daniel; Niehues, Anna; Schulze, Stefan; Scholz, Martin; Fufezan, Christian

2014-04-01

64

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

PubMed Central

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.

2012-01-01

65

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site.  

PubMed

Hydrogen bond networks are key elements of protein structure and function but have been challenging to study within the complex protein environment. We have carried out in-depth interrogations of the proton transfer equilibrium within a hydrogen bond network formed to bound phenols in the active site of ketosteroid isomerase. We systematically varied the proton affinity of the phenol using differing electron-withdrawing substituents and incorporated site-specific NMR and IR probes to quantitatively map the proton and charge rearrangements within the network that accompany incremental increases in phenol proton affinity. The observed ionization changes were accurately described by a simple equilibrium proton transfer model that strongly suggests the intrinsic proton affinity of one of the Tyr residues in the network, Tyr16, does not remain constant but rather systematically increases due to weakening of the phenol-Tyr16 anion hydrogen bond with increasing phenol proton affinity. Using vibrational Stark spectroscopy, we quantified the electrostatic field changes within the surrounding active site that accompany these rearrangements within the network. We were able to model these changes accurately using continuum electrostatic calculations, suggesting a high degree of conformational restriction within the protein matrix. Our study affords direct insight into the physical and energetic properties of a hydrogen bond network within a protein interior and provides an example of a highly controlled system with minimal conformational rearrangements in which the observed physical changes can be accurately modeled by theoretical calculations. PMID:23798390

Sigala, Paul A; Fafarman, Aaron T; Schwans, Jason P; Fried, Stephen D; Fenn, Timothy D; Caaveiro, Jose M M; Pybus, Brandon; Ringe, Dagmar; Petsko, Gregory A; Boxer, Steven G; Herschlag, Daniel

2013-07-01

66

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site  

PubMed Central

Hydrogen bond networks are key elements of protein structure and function but have been challenging to study within the complex protein environment. We have carried out in-depth interrogations of the proton transfer equilibrium within a hydrogen bond network formed to bound phenols in the active site of ketosteroid isomerase. We systematically varied the proton affinity of the phenol using differing electron-withdrawing substituents and incorporated site-specific NMR and IR probes to quantitatively map the proton and charge rearrangements within the network that accompany incremental increases in phenol proton affinity. The observed ionization changes were accurately described by a simple equilibrium proton transfer model that strongly suggests the intrinsic proton affinity of one of the Tyr residues in the network, Tyr16, does not remain constant but rather systematically increases due to weakening of the phenol–Tyr16 anion hydrogen bond with increasing phenol proton affinity. Using vibrational Stark spectroscopy, we quantified the electrostatic field changes within the surrounding active site that accompany these rearrangements within the network. We were able to model these changes accurately using continuum electrostatic calculations, suggesting a high degree of conformational restriction within the protein matrix. Our study affords direct insight into the physical and energetic properties of a hydrogen bond network within a protein interior and provides an example of a highly controlled system with minimal conformational rearrangements in which the observed physical changes can be accurately modeled by theoretical calculations.

Sigala, Paul A.; Fafarman, Aaron T.; Schwans, Jason P.; Fried, Stephen D.; Fenn, Timothy D.; Caaveiro, Jose M. M.; Pybus, Brandon; Ringe, Dagmar; Petsko, Gregory A.; Boxer, Steven G.; Herschlag, Daniel

2013-01-01

67

Phosphoproteomic analysis: An emerging role in deciphering cellular signaling in human embryonic stem cells and their differentiated derivatives  

PubMed Central

Cellular signaling is largely controlled by protein phosphorylation. This post-translational modification (PTM) has been extensively analyzed when examining one or a few protein phosphorylation events that effect cell signaling. However, protein kinase-driven signaling networks, comprising total (phospho)proteomes, largely control cell fate. Therefore, large-scale analysis of differentially regulated protein phosphorylation is central to elucidating complex cellular events, including maintenance of pluripotency and differentiation of embryonic stem cells (ESCs). The current technology of choice for total phosphoproteome and combined total proteome plus total phosphoproteome (termed (phospho)proteome)1 analyses is multidimensional liquid chromatography- (MDLC) tandem mass spectrometry (MS/MS).Advances in the use of MDLC for separation of peptides comprising total (phospho)proteomes, phosphopeptide enrichment, separation of enriched fractions, and quantitative peptide identification by MS/MS have been rapid in recent years, as have improvements in the sensitivity, speed, and accuracy of mass spectrometers. Increasingly deep coverage of (phospho)proteomes is allowing an improved understanding of changes in protein phosphorylation networks as cells respond to stimuli and progress from one undifferentiated or differentiated state to another. Although MDLC-MS/MS studies are powerful, understanding the interpretation of the data is important, and targeted experimental pursuit of biological predictions provided by total (phospho)proteome analyses is needed.(Phospho)proteomic analyses of pluripotent stem cells are in their infancy at this time. However, such studies have already begun to contribute to an improved and accelerated understanding of basic pluripotent stem cell signaling and fate control, especially at the systems-biology level.

Tobe, Brian T.D.; Hou, Junjie; Crain, Andrew M.; Singec, Ilyas; Snyder, Evan Y.; Brill, Laurence M.

2013-01-01

68

Molecular Marker-Assisted Dissection of Quantitative Trait Loci for seven Morphological Traits in Rice ( Oryza Sativa L.)  

Microsoft Academic Search

Summary  The genetic dissection of morphological traits can helpful to evaluate their potential values as markers for rice genetic improvement. In this study, a RI population derived from a cross from Zhenshan97 and IRAT109 was used to dissect the genetic bases of seven morphological traits such as leaf sheath color (LSC), grain apiculus color (GAC), grain hairiness density (GHD), grain awn

Bing Yue; Kehui Cui; Shibin Yu; Weiya Xue; Lijun Luo; Yongzhong Xing

2006-01-01

69

Dissection of additive genetic variability for quantitative traits in chickens using SNP markers.  

PubMed

The aim of this study was to separate marked additive genetic variability for three quantitative traits in chickens into components associated with classes of minor allele frequency (MAF), individual chromosomes and marker density using the genomewide complex trait analysis (GCTA) approach. Data were from 1351 chickens measured for body weight (BW), ultrasound of breast muscle (BM) and hen house egg production (HHP), each bird with 354 364 SNP genotypes. Estimates of variance components show that SNPs on commercially available genotyping chips marked a large amount of genetic variability for all three traits. The estimated proportion of total variation tagged by all autosomal SNPs was 0.30 (SE 0.04) for BW, 0.33 (SE 0.04) for BM, and 0.19 (SE 0.05) for HHP. We found that a substantial proportion of this variation was explained by low frequency variants (MAF <0.20) for BW and BM, and variants with MAF 0.10-0.30 for HHP. The marked genetic variance explained by each chromosome was linearly related to its length (R(2)  = 0.60) for BW and BM. However, for HHP, there was no linear relationship between estimates of variance and length of the chromosome (R(2)  = 0.01). Our results suggest that the contribution of SNPs to marked additive genetic variability is dependent on the allele frequency spectrum. For the sample of birds analysed, it was found that increasing marker density beyond 100K SNPs did not capture additional additive genetic variance. PMID:24460953

Abdollahi-Arpanahi, R; Pakdel, A; Nejati-Javaremi, A; Moradi Shahrbabak, M; Morota, G; Valente, B D; Kranis, A; Rosa, G J M; Gianola, D

2014-06-01

70

Phosphoproteomics-Based Systems Analysis of Signal Transduction Networks  

PubMed Central

Signal transduction systems coordinate complex cellular information to regulate biological events such as cell proliferation and differentiation. Although the accumulating evidence on widespread association of signaling molecules has revealed essential contribution of phosphorylation-dependent interaction networks to cellular regulation, their dynamic behavior is mostly yet to be analyzed. Recent technological advances regarding mass spectrometry-based quantitative proteomics have enabled us to describe the comprehensive status of phosphorylated molecules in a time-resolved manner. Computational analyses based on the phosphoproteome dynamics accelerate generation of novel methodologies for mathematical analysis of cellular signaling. Phosphoproteomics-based numerical modeling can be used to evaluate regulatory network elements from a statistical point of view. Integration with transcriptome dynamics also uncovers regulatory hubs at the transcriptional level. These omics-based computational methodologies, which have firstly been applied to representative signaling systems such as the epidermal growth factor receptor pathway, have now opened up a gate for systems analysis of signaling networks involved in immune response and cancer.

Kozuka-Hata, Hiroko; Tasaki, Shinya; Oyama, Masaaki

2012-01-01

71

Temporal Dynamics of the Saccharopolyspora erythraea Phosphoproteome.  

PubMed

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

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

2014-05-01

72

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

PubMed Central

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.

2014-01-01

73

Identifying differentially regulated subnetworks from phosphoproteomic data  

PubMed Central

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 this manner may expose signal transduction pathways and, in the case of experiments with drug-treated cells, reveal the drug's mode of action. Results Here, we introduce SubExtractor, an algorithm that combines phosphoproteomic data with protein network information from STRING to identify differentially regulated subnetworks and individual proteins. The method is based on a Bayesian probabilistic model combined with a genetic algorithm and rigorous significance testing. The Bayesian model accounts for information about both differential regulation and network topology. The method was tested with artificial data and subsequently applied to a comprehensive phosphoproteomics study investigating the mode of action of sorafenib, a small molecule kinase inhibitor. Conclusions SubExtractor reliably identifies differentially regulated subnetworks from phosphoproteomic data by integrating protein networks. The method can also be applied to gene or protein expression data.

2010-01-01

74

TSLP signaling network revealed by SILAC-based phosphoproteomics.  

PubMed

Thymic stromal lymphopoietin (TSLP) is a cytokine that plays diverse roles in the regulation of immune responses. TSLP requires a heterodimeric receptor complex consisting of IL-7 receptor ? subunit and its unique TSLP receptor (gene symbol CRLF2) to transmit signals in cells. Abnormal TSLP signaling (e.g. overexpression of TSLP or its unique receptor TSLPR) contributes to the development of a number of diseases including asthma and leukemia. However, a detailed understanding of the signaling pathways activated by TSLP remains elusive. In this study, we performed a global quantitative phosphoproteomic analysis of the TSLP signaling network using stable isotope labeling by amino acids in cell culture. By employing titanium dioxide in addition to antiphosphotyrosine antibodies as enrichment methods, we identified 4164 phosphopeptides on 1670 phosphoproteins. Using stable isotope labeling by amino acids in cell culture-based quantitation, we determined that the phosphorylation status of 226 proteins was modulated by TSLP stimulation. Our analysis identified activation of several members of the Src and Tec families of kinases including Btk, Lyn, and Tec by TSLP for the first time. In addition, we report TSLP-induced phosphorylation of protein phosphatases such as Ptpn6 (SHP-1) and Ptpn11 (Shp2), which has also not been reported previously. Co-immunoprecipitation assays showed that Shp2 binds to the adapter protein Gab2 in a TSLP-dependent manner. This is the first demonstration of an inducible protein complex in TSLP signaling. A kinase inhibitor screen revealed that pharmacological inhibition of PI-3 kinase, Jak family kinases, Src family kinases or Btk suppressed TSLP-dependent cellular proliferation making them candidate therapeutic targets in diseases resulting from aberrant TSLP signaling. Our study is the first phosphoproteomic analysis of the TSLP signaling pathway that greatly expands our understanding of TSLP signaling and provides novel therapeutic targets for TSLP/TSLPR-associated diseases in humans. PMID:22345495

Zhong, Jun; Kim, Min-Sik; Chaerkady, Raghothama; Wu, Xinyan; Huang, Tai-Chung; Getnet, Derese; Mitchell, Christopher J; Palapetta, Shyam M; Sharma, Jyoti; O'Meally, Robert N; Cole, Robert N; Yoda, Akinori; Moritz, Albrecht; Loriaux, Marc M; Rush, John; Weinstock, David M; Tyner, Jeffrey W; Pandey, Akhilesh

2012-06-01

75

TSLP Signaling Network Revealed by SILAC-Based Phosphoproteomics*  

PubMed Central

Thymic stromal lymphopoietin (TSLP) is a cytokine that plays diverse roles in the regulation of immune responses. TSLP requires a heterodimeric receptor complex consisting of IL-7 receptor ? subunit and its unique TSLP receptor (gene symbol CRLF2) to transmit signals in cells. Abnormal TSLP signaling (e.g. overexpression of TSLP or its unique receptor TSLPR) contributes to the development of a number of diseases including asthma and leukemia. However, a detailed understanding of the signaling pathways activated by TSLP remains elusive. In this study, we performed a global quantitative phosphoproteomic analysis of the TSLP signaling network using stable isotope labeling by amino acids in cell culture. By employing titanium dioxide in addition to antiphosphotyrosine antibodies as enrichment methods, we identified 4164 phosphopeptides on 1670 phosphoproteins. Using stable isotope labeling by amino acids in cell culture-based quantitation, we determined that the phosphorylation status of 226 proteins was modulated by TSLP stimulation. Our analysis identified activation of several members of the Src and Tec families of kinases including Btk, Lyn, and Tec by TSLP for the first time. In addition, we report TSLP-induced phosphorylation of protein phosphatases such as Ptpn6 (SHP-1) and Ptpn11 (Shp2), which has also not been reported previously. Co-immunoprecipitation assays showed that Shp2 binds to the adapter protein Gab2 in a TSLP-dependent manner. This is the first demonstration of an inducible protein complex in TSLP signaling. A kinase inhibitor screen revealed that pharmacological inhibition of PI-3 kinase, Jak family kinases, Src family kinases or Btk suppressed TSLP-dependent cellular proliferation making them candidate therapeutic targets in diseases resulting from aberrant TSLP signaling. Our study is the first phosphoproteomic analysis of the TSLP signaling pathway that greatly expands our understanding of TSLP signaling and provides novel therapeutic targets for TSLP/TSLPR-associated diseases in humans.

Zhong, Jun; Kim, Min-Sik; Chaerkady, Raghothama; Wu, Xinyan; Huang, Tai-Chung; Getnet, Derese; Mitchell, Christopher J.; Palapetta, Shyam M.; Sharma, Jyoti; O'Meally, Robert N.; Cole, Robert N.; Yoda, Akinori; Moritz, Albrecht; Loriaux, Marc M.; Rush, John; Weinstock, David M.; Tyner, Jeffrey W.; Pandey, Akhilesh

2012-01-01

76

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

PubMed Central

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

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

2011-01-01

77

Comparison of SILAC and mTRAQ quantification for phosphoproteomics on a quadrupole orbitrap mass spectrometer.  

PubMed

Advances in mass spectrometric methodology and instrumentation have promoted a continuous increase in analytical performance in the field of phosphoproteomics. Here, we employed the recently introduced quadrupole Orbitrap (Q Exactive) mass spectrometer for quantitative signaling analysis to a depth of more than 15?000 phosphorylation sites. In parallel to the commonly used SILAC approach, we evaluated the nonisobaric chemical labeling reagent mTRAQ as an alternative quantification technique. Both enabled high phosphoproteome coverage in H3122 lung cancer cells. Replicate quantifications by mTRAQ identified almost as many significant phosphorylation changes upon treatment with ALK kinase inhibitor crizotinib as found by SILAC quantification. Overall, mTRAQ was slightly less precise than SILAC as evident from a somewhat higher variance of replicate phosphosite ratios. Direct comparison of SILAC- and mTRAQ-quantified phosphosites revealed that the majority of changes were detected by either quantification techniques, but also highlighted the aspect of false negative identifications in quantitative proteomics applications. Further inspection of crizotinib-regulated phosphorylation changes unveiled interference with multiple antioncogenic mechanisms downstream of ALK fusion kinase in H3122 cells. In conclusion, our results demonstrate a strong analytical performance of the Q Exactive in global phosphoproteomics, and establish mTRAQ quantification as a useful alternative to metabolic isotope labeling. PMID:23898821

Oppermann, Felix S; Klammer, Martin; Bobe, Caroline; Cox, Jürgen; Schaab, Christoph; Tebbe, Andreas; Daub, Henrik

2013-09-01

78

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

PubMed Central

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.

2013-01-01

79

Tissue reaction to three different types of tissue glues in an experimental aorta dissection model: a quantitative approach.  

PubMed

Tissue glues are used during surgical treatment of acute aorta dissection although some glues release toxic products and thus alter the histological structure of the vessel wall. The aim of our study was to use a porcine experimental model of infrarenal aorta dissection to compare histological changes of the vessel wall 1, 6 and 12 months after application of BioGlue, Gelatin-resorcin-formaldehyde (GRF) glue and Tissucol. For quantification, stereological methods were used. All types of glue caused stenosis, GRF most and Tissucol least severely. With increasing postoperative survival time, stenosis was again reduced. Elastine length density decreased with increasing survival time in Control as well as in all Experimental groups. The immunohistochemical phenotype of vascular smooth muscle cells was similar in Tissucol and Control samples. In GRF samples, actin, desmin and vimentin expression changed most severely. Similarly, number and distribution of vasa vasorum in the aortic wall was altered most severely in GRF samples. They tended to return to normal with increasing postoperative survival time, but at a slow rate in the GRF samples. It can be concluded that GRF causes the most severe histopathological changes within the treated aorta, which could be a reason for late failures of dissection surgery. However, glue handling and adhesive properties have to be taken into account, too, when certain glue is chosen for surgical intervention. Increased inflammation and vascularisation might even stabilise the aortic wall. Long-term experimental studies would be helpful to assess healing processes after initial disorganisation of the aortic wall structure. PMID:19902233

Witter, Kirsti; Tonar, Zbynek; Matejka, Vít Martin; Martinca, Tomás; Jonák, Michael; Rokosný, Slavomír; Pirk, Jan

2010-02-01

80

Phosphoproteomic Analysis Identifies Grb10 as an mTORC1 Substrate That Negatively Regulates Insulin Signaling  

Microsoft Academic Search

The evolutionarily conserved serine-threonine kinase mammalian target of rapamycin (mTOR) plays a critical role in regulating many pathophysiological processes. Functional characterization of the mTOR signaling pathways, however, has been hampered by the paucity of known substrates. We used large-scale quantitative phosphoproteomics experiments to define the signaling networks downstream of mTORC1 and mTORC2. Characterization of one mTORC1 substrate, the growth factor

Yonghao Yu; Sang-Oh Yoon; George Poulogiannis; Qian Yang; Xiaoju Max Ma; Judit Villén; Neil Kubica; Gregory R. Hoffman; Lewis C. Cantley; Steven P. Gygi; John Blenis

2011-01-01

81

Quahog Dissection  

NSDL National Science Digital Library

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.

Grant, Rhode I.

82

Paper dissection  

NSDL National Science Digital Library

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?

Varricchio, David

83

Phosphoproteomic studies of receptor tyrosine kinases: future perspectives.  

PubMed

In the last decade, large-scale mass spectrometry-based phosphoproteomic studies of receptor tyrosine kinases (RTKs) have generated a compendium of signalling networks that are activated downstream of these receptors. In this article, a brief summary of previous phosphoproteomic studies on epidermal growth factor receptor (EGFR) signalling will be presented together with a perspective on the importance for the field to keep pace with new advances in RTK biology. Using examples drawn primarily from studies on the EGFR, c-Met and Flt3 receptors, areas in RTK biology which will greatly benefit from the power of phosphoproteomics will be discussed, including (a) validating oncogenic RTK mutants identified in cancer genome sequencing efforts, (b) spatial RTK signalling networks and (c) understanding crosstalk and co-activation between members of the RTK superfamily. PMID:22134727

Huang, Paul H

2012-04-01

84

Specific visualization and identification of phosphoproteome in gels.  

PubMed

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

Wang, Linna; Pan, Li; Tao, W Andy

2014-07-15

85

Polyomino Dissections  

ERIC Educational Resources Information Center

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…

Hohn, Tiina; Liu, Andy

2012-01-01

86

Dissect It!  

NSDL National Science Digital Library

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).

Wood, Olga

2012-06-27

87

Global Screening of CK2 Kinase Substrates by an Integrated Phosphoproteomics Workflow  

PubMed Central

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.

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

2013-01-01

88

Global screening of CK2 kinase substrates by an integrated phosphoproteomics workflow.  

PubMed

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

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

2013-01-01

89

Dynamic Adipocyte Phosphoproteome Reveals that Akt Directly Regulates mTORC2  

PubMed Central

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

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

2013-01-01

90

Clam Dissection  

NSDL National Science Digital Library

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.

Plotnick, Roy

91

Evaluation and Properties of the Budding Yeast Phosphoproteome*  

PubMed Central

We have assembled a reliable phosphoproteomic data set for budding yeast Saccharomyces cerevisiae and have investigated its properties. Twelve publicly available phosphoproteome data sets were triaged to obtain a subset of high-confidence phosphorylation sites (p-sites), free of “noisy” phosphorylations. Analysis of this combined data set suggests that the inventory of phosphoproteins in yeast is close to completion, but that these proteins may have many undiscovered p-sites. Proteins involved in budding and protein kinase activity have high numbers of p-sites and are highly over-represented in the vast majority of the yeast phosphoproteome data sets. The yeast phosphoproteome is characterized by a few proteins with many p-sites and many proteins with a few p-sites. We confirm a tendency for p-sites to cluster together and find evidence that kinases may phosphorylate off-target amino acids that are within one or two residues of their cognate target. This suggests that the precise position of the phosphorylated amino acid is not a stringent requirement for regulatory fidelity. Compared with nonphosphorylated proteins, phosphoproteins are more ancient, more abundant, have longer unstructured regions, have more genetic interactions, more protein interactions, and are under tighter post-translational regulation. It appears that phosphoproteins constitute the raw material for pathway rewiring and adaptation at various evolutionary rates.

Amoutzias, Grigoris D.; He, Ying; Lilley, Kathryn S.; Van de Peer, Yves; Oliver, Stephen G.

2012-01-01

92

Dissection of a quantitative trait locus for PR interval duration identifies Tnni3k as a novel modulator of cardiac conduction.  

PubMed

Atrio-ventricular conduction disease is a common feature in Mendelian rhythm disorders associated with sudden cardiac death and is characterized by prolongation of the PR interval on the surface electrocardiogram (ECG). Prolongation of the PR interval is also a strong predictor of atrial fibrillation, the most prevalent sustained cardiac arrhythmia. Despite the significant genetic component in PR duration variability, the genes regulating PR interval duration remain largely elusive. We here aimed to dissect the quantitative trait locus (QTL) for PR interval duration that we previously mapped in murine F2 progeny of a sensitized 129P2 and FVBN/J cross. To determine the underlying gene responsible for this QTL, genome-wide transcriptional profiling was carried out on myocardial tissue from 109 F2 mice. Expression QTLs (eQTLs) were mapped and the PR interval QTL was inspected for the co-incidence of eQTLs. We further determined the correlation of each of these transcripts to the PR interval. Tnni3k was the only eQTL, mapping to the PR-QTL, with an established abundant cardiac-specific expression pattern and a significant correlation to PR interval duration. Genotype inspection in various inbred mouse strains revealed the presence of at least three independent haplotypes at the Tnni3k locus. Measurement of PR interval duration and Tnni3k mRNA expression levels in six inbred lines identified a positive correlation between the level of Tnni3k mRNA and PR interval duration. Furthermore, in DBA/2J mice overexpressing hTNNI3K, and in DBA.AKR.hrtfm2 congenic mice, which harbor the AKR/J "high-Tnni3k expression" haplotype in the DBA/2J genetic background, PR interval duration was prolonged as compared to DBA/2J wild-type mice ("low-Tnni3k expression" haplotype). Our data provide the first evidence for a role of Tnni3k in controlling the electrocardiographic PR interval indicating a function of Tnni3k in atrio-ventricular conduction. PMID:23236294

Lodder, Elisabeth M; Scicluna, Brendon P; Milano, Annalisa; Sun, Albert Y; Tang, Hao; Remme, Carol Ann; Moerland, Perry D; Tanck, Michael W T; Pitt, Geoffrey S; Marchuk, Douglas A; Bezzina, Connie R

2012-01-01

93

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

PubMed Central

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.

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

2012-01-01

94

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

PubMed Central

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.

2014-01-01

95

A shotgun phosphoproteomics analysis of embryos in germinated maize seeds  

Microsoft Academic Search

To better understand the role that reversible protein phosphorylation plays in seed germination, we initiated a phosphoproteomic\\u000a investigation of embryos of germinated maize seeds. A total of 776 proteins including 39 kinases, 16 phosphatases, and 33\\u000a phosphoproteins containing 36 precise in vivo phosphorylation sites were identified. All the phosphorylation sites identified,\\u000a with the exception of the phosphorylation site on HSP22,

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

2008-01-01

96

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

PubMed Central

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.

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

97

Global Impact of Salmonella Pathogenicity Island 2-secreted Effectors on the Host Phosphoproteome*  

PubMed Central

During the late stages of infection, Salmonella secretes numerous effectors through a type III secretion system that is encoded within Salmonella pathogenicity island 2 (SPI2). Despite the importance of SPI2 as a major virulence factor leading to the systemic spread of the bacteria and diseases, a global view of its effects on host responses is still lacking. Here, we measured global impacts of SPI2 effectors on the host phosphorylation and protein expression levels in RAW264.7 and in HeLa cells, as macrophage and nonphagocytic models of infection. We observe that SPI2 effectors differentially modulate the host phosphoproteome and cellular processes (e.g. protein trafficking, cytoskeletal regulation, and immune signaling) in a host cell-dependent manner. Our unbiased approach reveals the involvement of many previously unrecognized proteins, including E3 ligases (HERC4, RanBP2, and RAD18), kinases (CDK, SIK3, and WNK1), and histones (H2B1F, H4, and H15), in late stages of Salmonella infection. Furthermore, from this phosphoproteome analysis and other quantitative screens, we identified HSP27 as a direct in vitro and in vivo molecular target of the only type III secreted kinase, SteC. Using biochemical and cell biological assays, we demonstrate that SteC phosphorylates multiple sites in HSP27 and induces actin rearrangement through this protein. Together, these results provide a broader landscape of host players contributing to specific processes/pathways mediated by SPI2 effectors than was previously appreciated.

Imami, Koshi; Bhavsar, Amit P.; Yu, Hongbing; Brown, Nat F.; Rogers, Lindsay D.; Finlay, B. Brett; Foster, Leonard J.

2013-01-01

98

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

PubMed Central

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.

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

2014-01-01

99

Characterization of the Phosphoproteome in Human Bronchoalveolar Lavage Fluid  

PubMed Central

Global-scale examination of protein phosphorylation in human biological fluids by phosphoproteomics approaches is an emerging area of research with potential for significant contributions towards discovery of novel biomarkers. In this pilot work, we analyzed the phosphoproteome in human bronchoalveolar lavage fluid (BAL) from nondiseased subjects. The main objectives were to assess the feasibility to probe phosphorylated proteins in human BAL and to obtain the initial catalog of BAL phosphoproteins, including protein identities and exact description of their phosphorylation sites. We used a gel-free bioanalytical workflow that included whole-proteome digestion of depleted BAL proteins, enrichment of phosphopeptides by immobilized metal ion affinity chromatography (IMAC), LC-MS/MS analyses with a linear ion trap mass spectrometer, and searches of a protein sequence database to generate a panel of BAL phosphoproteins and their sites of phosphorylation. Based on sequence-diagnostic MS/MS fragmentation patterns, we identified a collection of 36 phosphopeptides that contained 26 different phosphorylation sites. These phosphopeptides mapped to 21 phosphoproteins including, for example, vimentin, plastin-2, ferritin heavy chain, kininogen-1, and others. The characterized phosphoproteins have diverse characteristics in terms of cellular origin and biological function. To the best of our knowledge, results of this study represent the first description of the human BAL phosphoproteome.

Giorgianni, Francesco; Mileo, Valentina; Desiderio, Dominic M.; Catinella, Silvia; Beranova-Giorgianni, Sarka

2012-01-01

100

Characterization of the phosphoproteome in human bronchoalveolar lavage fluid.  

PubMed

Global-scale examination of protein phosphorylation in human biological fluids by phosphoproteomics approaches is an emerging area of research with potential for significant contributions towards discovery of novel biomarkers. In this pilot work, we analyzed the phosphoproteome in human bronchoalveolar lavage fluid (BAL) from nondiseased subjects. The main objectives were to assess the feasibility to probe phosphorylated proteins in human BAL and to obtain the initial catalog of BAL phosphoproteins, including protein identities and exact description of their phosphorylation sites. We used a gel-free bioanalytical workflow that included whole-proteome digestion of depleted BAL proteins, enrichment of phosphopeptides by immobilized metal ion affinity chromatography (IMAC), LC-MS/MS analyses with a linear ion trap mass spectrometer, and searches of a protein sequence database to generate a panel of BAL phosphoproteins and their sites of phosphorylation. Based on sequence-diagnostic MS/MS fragmentation patterns, we identified a collection of 36 phosphopeptides that contained 26 different phosphorylation sites. These phosphopeptides mapped to 21 phosphoproteins including, for example, vimentin, plastin-2, ferritin heavy chain, kininogen-1, and others. The characterized phosphoproteins have diverse characteristics in terms of cellular origin and biological function. To the best of our knowledge, results of this study represent the first description of the human BAL phosphoproteome. PMID:22997577

Giorgianni, Francesco; Mileo, Valentina; Desiderio, Dominic M; Catinella, Silvia; Beranova-Giorgianni, Sarka

2012-01-01

101

Concurrent Quantification of Proteome and Phosphoproteome to Reveal System-wide Association of Protein Phosphorylation and Gene Expression*  

PubMed Central

Reversible phosphorylation of proteins is an important process modulating cellular activities from upstream, which mainly involves sequential phosphorylation of signaling molecules, to downstream where phosphorylation of transcription factors regulates gene expression. In this study, we combined quantitative labeling with multidimensional liquid chromatography-mass spectrometry to monitor the proteome and phosphoproteome changes in the initial period of adipocyte differentiation. The phosphorylation level of a specific protein may be regulated by a kinase or phosphatase without involvement of gene expression or as a phenomenon that accompanies the alteration of its gene expression. Concurrent quantification of phosphopeptides and non-phosphorylated peptides makes it possible to differentiate cellular phosphorylation changes at these two levels. Furthermore, on the system level, certain proteins were predicted as the targeted gene products regulated by identified transcription factors. Among them, several proteins showed significant expression changes along with the phosphorylation alteration of their transcription factors. This is to date the first work to concurrently quantify proteome and phosphoproteome changes during the initial period of adipocyte differentiation, providing an approach to reveal the system-wide association of protein phosphorylation and gene expression.

Wu, Yi-Bo; Dai, Jie; Yang, Xing-Lin; Li, Su-Jun; Zhao, Shi-Lin; Sheng, Quan-Hu; Tang, Jia-Shu; Zheng, Guang-Yong; Li, Yi-Xue; Wu, Jia-Rui; Zeng, Rong

2009-01-01

102

Systematic Analysis of Protein Phosphorylation Networks From Phosphoproteomic Data*  

PubMed Central

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

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

2012-01-01

103

Phosphoproteomic analysis of chromoplasts from sweet orange during fruit ripening.  

PubMed

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

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

2014-02-01

104

Marquette University Neuroanatomical Dissection  

NSDL National Science Digital Library

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.

Marquette University (Marquette University)

2012-07-24

105

Dissecting Classroom Ethics.  

ERIC Educational Resources Information Center

Described are activities that lead to values clarification. Issues such as dissection, bioengineering, birth control, medical resources, and death are discussed. Included is a student questionnaire on the subject of dissection and the use of animals in laboratories. (KR)

Allchin, Douglas

1991-01-01

106

The Problems of Dissection.  

ERIC Educational Resources Information Center

Describes some problems of classroom dissection including the cruelty that animals destined for the laboratory suffer. Discusses the multilevel approach that the National Anti-Vivisection Society (NAVS) has developed to address the problems of animal dissection such as offering a dissection hotline, exhibiting at science teacher conferences, and…

Davis, Pat

1997-01-01

107

Integrative Features of the Yeast Phosphoproteome and Protein–Protein Interaction Map  

Microsoft Academic Search

Following recent advances in high-throughput mass spectrometry (MS)–based proteomics, the numbers of identified phosphoproteins and their phosphosites have greatly increased in a wide variety of organisms. Although a critical role of phosphorylation is control of protein signaling, our understanding of the phosphoproteome remains limited. Here, we report unexpected, large-scale connections revealed between the phosphoproteome and protein interactome by integrative data-mining

Nozomu Yachie; Rintaro Saito; Naoyuki Sugiyama; Masaru Tomita; Yasushi Ishihama

2011-01-01

108

Genetic dissection of tocopherol and phytosterol in recombinant inbred lines of sunflower through quantitative trait locus analysis and the candidate gene approach  

Microsoft Academic Search

Sunflower (Helianthus annuus L.) contains tocopherol, a non-enzymatic antioxidant known as lipid-soluble vitamin E, and phytosterol, with interesting\\u000a properties, which can result in decreased risk of chronic diseases in humans and with several beneficial effects in plants.\\u000a The genetic control of tocopherol and phytosterol content in a population of 123 recombinant inbred lines of sunflower was\\u000a studied through quantitative trait

P. Haddadi; A. Ebrahimi; N. B. Langlade; B. Yazdi-samadi; M. Berger; A. Calmon; M. R. Naghavi; P. Vincourt; A. Sarrafi

109

Genetic dissection of a genomic region for a quantitative trait locus, Hd3 , into two loci, Hd3a and Hd3b , controlling heading date in rice  

Microsoft Academic Search

The rice photoperiod sensitivity gene Hd3 was originally detected as a heading date-related quantitative trait locus localized on chromosome 6 of rice. High-resolution linkage mapping of Hd3 was performed using a large segregating population derived from advanced backcross progeny between a japonica variety, Nipponbare, and an indica variety, Kasalath. To determine the genotype of Hd3, we employed progeny testing under

L. Monna; H. Lin; S. Kojima; T. Sasaki; M. Yano

2002-01-01

110

Genetic dissection of collagen-induced arthritis in Chromosome 10 quantitative trait locus speed congenic rats: evidence for more than one regulatory locus and sex influences  

Microsoft Academic Search

Rat Chromosome 10 (RNO10) harbors Cia5, a non-MHC quantitative trait locus (QTL) that regulates the severity of type II collagen-induced arthritis (CIA) in DA2F344 and DA2BN F2 rats. CIA is an animal model with many features that resemble rheumatoid arthritis. To facilitate analysis of Cia5 independently of the other CIA regulatory loci on other chromosomes, DA recombinant QTL speed congenic

Bina Joe; Elaine F. Remmers; David E. Dobbins; Jennifer L. Salstrom; Takefumi Furuya; Svetlana Dracheva; Pércio S. Gulko; Grant W. Cannon; Marie M. Griffiths; Ronald L. Wilder

2000-01-01

111

Global phosphoproteomics of activated B cells using complementary metal ion functionalized soluble nanopolymers.  

PubMed

Engagement of the B cell receptor for antigen (BCR) leads to immune responses through a cascade of intracellular signaling events. Most studies to date have focused on the BCR and protein tyrosine phosphorylation. Because spleen tyrosine kinase, Syk, is an upstream kinase in multiple BCR-regulated signaling pathways, it also affects many downstream events that are modulated through the phosphorylation of proteins on serine and threonine residues. Here, we report a novel phosphopeptide enrichment strategy and its application to a comprehensive quantitative phosphoproteomics analysis of Syk-dependent downstream signaling events in B cells, focusing on serine and threonine phosphorylation. Using a combination of the Syk inhibitor piceatannol, SILAC quantification, peptide fractionation, and complementary PolyMAC-Ti and PolyMAC-Zr enrichment techniques, we analyzed changes in BCR-stimulated protein phosphorylation that were dependent on the activity of Syk. We identified and quantified over 13?000 unique phosphopeptides, with a large percentage dependent on Syk activity in BCR-stimulated B cells. Our results not only confirmed many known functions of Syk, but more importantly, suggested many novel roles, including in the ubiquitin proteasome pathway, that warrant further exploration. PMID:24905233

Jayasundera, Keerthi B; Iliuk, Anton B; Nguyen, Andrew; Higgins, Renee; Geahlen, Robert L; Tao, W Andy

2014-07-01

112

Phosphoproteome dynamics reveal heat-shock protein complexes specific to the Leishmania donovani infectious stage  

PubMed Central

Leishmania is exposed to a sudden increase in environmental temperature during the infectious cycle that triggers stage differentiation and adapts the parasite phenotype to intracellular survival in the mammalian host. The absence of classical promoter-dependent mechanisms of gene regulation and constitutive expression of most of the heat-shock proteins (HSPs) in these human pathogens raise important unresolved questions as to regulation of the heat-shock response and stage-specific functions of Leishmania HSPs. Here we used a gel-based quantitative approach to assess the Leishmania donovani phosphoproteome and revealed that 38% of the proteins showed significant stage-specific differences, with a strong focus of amastigote-specific phosphoproteins on chaperone function. We identified STI1/HOP-containing chaperone complexes that interact with ribosomal client proteins in an amastigote-specific manner. Genetic analysis of STI1/HOP phosphorylation sites in conditional sti1?/? null mutant parasites revealed two phosphoserine residues essential for parasite viability. Phosphorylation of the major Leishmania chaperones at the pathogenic stage suggests that these proteins may be promising drug targets via inhibition of their respective protein kinases.

Morales, Miguel A.; Watanabe, Reiko; Dacher, Mariko; Chafey, Philippe; Osorio y Fortea, Jose; Scott, David A.; Beverley, Stephen M.; Ommen, Gabi; Clos, Joachim; Hem, Sonia; Lenormand, Pascal; Rousselle, Jean-Claude; Namane, Abdelkader; Spath, Gerald F.

2010-01-01

113

Recurrent Spontaneous Esophageal Dissection  

PubMed Central

Introduction: Spontaneous esophageal dissection is a rare disorder of the esophagus. Case Description: We present what is believed to be the first reported case of recurrent esophageal dissection in a previously healthy 33-year-old man with chronic eosinophilic esophagitis. He had two episodes of spontaneous dissection of the midesophagus separated by a 5-month interval. Both episodes responded to treatment with endoscopic intervention. He has remained free of additional recurrences after definitive endoscopic therapy and oral steroid therapy. A complete description of the case, relevant radiologic imaging, and a review of the relevant literature are provided. Discussion: Endoscopic therapy is an option for the management of recurrent esophageal dissection.

Stephens, Nicholas A.; Walker, Peter A.; Jayanty, Vikram; Raijman, Isaac; Khalil, Kamal

2014-01-01

114

Proteome and phosphoproteome of Africanized and European honeybee venoms.  

PubMed

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

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

2013-09-01

115

A consensus map of rapeseed (Brassica napus L.) based on diversity array technology markers: applications in genetic dissection of qualitative and quantitative traits  

PubMed Central

Background Dense consensus genetic maps based on high-throughput genotyping platforms are valuable for making genetic gains in Brassica napus through quantitative trait locus identification, efficient predictive molecular breeding, and map-based gene cloning. This report describes the construction of the first B. napus consensus map consisting of a 1,359 anchored array based genotyping platform; Diversity Arrays Technology (DArT), and non-DArT markers from six populations originating from Australia, Canada, China and Europe. We aligned the B. napus DArT sequences with genomic scaffolds from Brassica rapa and Brassica oleracea, and identified DArT loci that showed linkage with qualitative and quantitative loci associated with agronomic traits. Results The integrated consensus map covered a total of 1,987.2?cM and represented all 19 chromosomes of the A and C genomes, with an average map density of one marker per 1.46?cM, corresponding to approximately 0.88 Mbp of the haploid genome. Through in silico physical mapping 2,457 out of 3,072 (80%) DArT clones were assigned to the genomic scaffolds of B. rapa (A genome) and B. oleracea (C genome). These were used to orientate the genetic consensus map with the chromosomal sequences. The DArT markers showed linkage with previously identified non-DArT markers associated with qualitative and quantitative trait loci for plant architecture, phenological components, seed and oil quality attributes, boron efficiency, sucrose transport, male sterility, and race-specific resistance to blackleg disease. Conclusions The DArT markers provide increased marker density across the B. napus genome. Most of the DArT markers represented on the current array were sequenced and aligned with the B. rapa and B. oleracea genomes, providing insight into the Brassica A and C genomes. This information can be utilised for comparative genomics and genomic evolution studies. In summary, this consensus map can be used to (i) integrate new generation markers such as SNP arrays and next generation sequencing data; (ii) anchor physical maps to facilitate assembly of B. napus genome sequences; and (iii) identify candidate genes underlying natural genetic variation for traits of interest.

2013-01-01

116

The Phosphoproteome of the Minimal Bacterium Mycoplasma pneumoniae  

PubMed Central

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.

Schmidl, Sebastian R.; Gronau, Katrin; Pietack, Nico; Hecker, Michael; Becher, Dorte; Stulke, Jorg

2010-01-01

117

Cellular Quantitative Structure-Activity Relationship (Cell-QSAR): Conceptual Dissection of Receptor Binding and Intracellular Disposition in Antifilarial Activities of Selwood Antimycins  

PubMed Central

We present the cellular quantitative structure–activity relationship (cell-QSAR) concept that adapts ligand-based and receptor-based 3D-QSAR methods for use with cell-level activities. The unknown intracellular drug disposition is accounted for by the disposition function (DF), a model-based, nonlinear function of a drug’s lipophilicity, acidity, and other properties. We conceptually combined the DF with our multispecies, multimode version of the frequently used ligand-based comparative molecular field analysis (CoMFA) method, forming a single correlation function for fitting the cell-level activities. The resulting cell-QSAR model was applied to the Selwood data on filaricidal activities of antimycin analogues. Their molecules are flexible, ionize under physiologic conditions, form different intramolecular H-bonds for neutral and ionized species, and cross several membranes to reach unknown receptors. The calibrated cell-QSAR model is significantly more predictive than other models lacking the disposition part and provides valuable structure optimization clues by factorizing the cell-level activity of each compound into the contributions of the receptor binding and disposition.

2012-01-01

118

Genetic dissection of a genomic region for a quantitative trait locus, Hd3, into two loci, Hd3a and Hd3b, controlling heading date in rice.  

PubMed

The rice photoperiod sensitivity gene Hd3 was originally detected as a heading date-related quantitative trait locus localized on chromosome 6 of rice. High-resolution linkage mapping of Hd3 was performed using a large segregating population derived from advanced backcross progeny between a japonica variety, Nipponbare, and an indica variety, Kasalath. To determine the genotype of Hd3, we employed progeny testing under natural field and short-day conditions. As a result, two tightly linked loci, Hd3a and Hd3b, were identified in the Hd3 region. Nearly-isogenic lines for Hd3a and Hd3b were selected from progeny using marker-assisted selection. The inheritance mode of both Hd3a and Hd3b was found to be additive. Analysis of daylength response in nearly-isogenic lines of Hd3a and Hd3b showed that the Kasalath allele at Hd3a promotes heading under short-day conditions while that at Hd3b causes late heading under long-day and natural field conditions. PMID:12582636

Monna, L.; Lin, X.; Kojima, S.; Sasaki, T.; Yano, M.

2002-04-01

119

Renal artery dissection.  

PubMed Central

Renal artery dissections are stenotic or occlusive lesions most often observed in hypertensive patients with underlying atherosclerosis or fibromuscular disease. Acute dissections may present spontaneously, as a complication of diagnostic or therapeutic angiography or as an agonal event associated with overwhelming systemic illness. Chronic dissections may produce renovascular hypertension or be entirely asymptomatic. Fourteen renal artery dissections have been encountered in nine patients treated at Vanderbilt University Medical Center during the past decade. Eleven dissections have been found in seven patients with renovascular hypertension. Seven of these dissections were chronic (six functional, one silent) and four acute (two spontaneous, two secondary to angiography). Three agonal dissections were found in two additional patients postmortem: one at autopsy and bilateral dissections found at the time of cadaveric donor nephrectomy. Ten bypass procedures, including five complex branch reconstructions of which three were performed ex vivo, have been performed with 100% immediate patency and maintenance or improvement of renal function. Long-term follow-up of these patients has shown sustained patency of the reconstructed renal arteries, excellent blood pressure control, and normal renal function in all. Nephrectomy has not been required and there have been no associated deaths. Seventy-seven additional renal artery dissections in 72 patients collected from previous reports have been analyzed. Patient survival (55/72, 76.4%) and preservation of the involved kidney in surviving patients (26/55, 47.3%) were low in these earlier series. In addition, renal failure was associated with 59% of the deaths. The lethality of renal artery dissections and the ease and success of revascularization, which preserves renal function and ameliorates associated renovascular hypertension, emphasize the need for an aggressive approach to the recognition and treatment of this entity. Therapy should be directed toward arterial reconstructions and the preservation of functioning renal tissue. Images FIG. 1A. FIG. 2A. FIG. 5. FIG. 6. FIG. 7. FIG. 9. FIG. 10. FIG. 11.

Smith, B M; Holcomb, G W; Richie, R E; Dean, R H

1984-01-01

120

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

PubMed Central

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.

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

2013-01-01

121

Introduction to Dissection  

NSDL National Science Digital Library

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.

Wineski, Lawrence

2007-11-20

122

[Lymphorrhea after neck dissection].  

PubMed

In this publication lymphorrhea was described as one of possible complications after the neck dissection surgery of Crile-Jawdy?ski procedurae. The matter of this complication is rise of pressure in lymph system. 4 women with this complication after neck dissection, the best treatment is drainage of the operated area. In one patient, because of the failure of conservative treatment, another surgical intervention was preformed. The full treatment of lymphorrhea was after 4-6 weeks. PMID:10481496

Nowaczyk, M T

1999-01-01

123

Postpartum coronary artery dissection.  

PubMed Central

A 27-year-old woman experienced anterior myocardial infarction three weeks after the delivery of her second child. Coronary arteriography subsequently showed primary dissection of the left coronary artery. This patient is believed to be the second reported survivor of angiographically proven peripartal left coronary artery dissection and the only such patient to achieve and maintain asymptomatic status for a prolonged period without operative intervention. Images

Shaver, P J; Carrig, T F; Baker, W P

1978-01-01

124

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

PubMed

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

Salovská, Barbora; Fabrik, Ivo; Durišová, Kamila; Link, Marek; Vávrová, Ji?ina; Rezá?ová, Martina; Tichý, Aleš

2014-01-01

125

Early phosphoproteomic changes in the mouse spleen during deoxynivalenol-induced ribotoxic stress.  

PubMed

The trichothecene mycotoxin deoxynivalenol (DON) targets the innate immune system and is of public health significance because of its frequent presence in human and animal food. DON-induced proinflammatory gene expression and apoptosis in the lymphoid tissue have been associated with a ribotoxic stress response (RSR) that involves rapid phosphorylation of mitogen-activated protein kinases (MAPKs). To better understand the relationship between protein phosphorylation and DON's immunotoxic effects, stable isotope dimethyl labeling-based proteomics in conjunction with titanium dioxide chromatography was employed to quantitatively profile the immediate (? 30min) phosphoproteome changes in the spleens of mice orally exposed to 5mg/kg body weight DON. A total of 90 phosphoproteins indicative of novel phosphorylation events were significantly modulated by DON. In addition to critical branches and scaffolds of MAPK signaling being affected, DON exposure also altered phosphorylation of proteins that mediate phosphatidylinositol 3-kinase/AKT pathways. Gene ontology analysis revealed that DON exposure affected biological processes such as cytoskeleton organization, regulation of apoptosis, and lymphocyte activation and development, which likely contribute to immune dysregulation associated with DON-induced RSR. Consistent with these findings, DON impacted phosphorylation of proteins within diverse immune cell populations, including monocytes, macrophages, T cells, B cells, dendritic cells, and mast cells. Fuzzy c-means clustering analysis further indicated that DON evoked several distinctive temporal profiles of regulated phosphopeptides. Overall, the findings from this investigation can serve as a template for future focused exploration and modeling of cellular responses associated with the immunotoxicity evoked by DON and other ribotoxins. PMID:23811945

Pan, Xiao; Whitten, Douglas A; Wu, Ming; Chan, Christina; Wilkerson, Curtis G; Pestka, James J

2013-09-01

126

Synaptic activity bidirectionally regulates a novel sequence-specific S-Q phosphoproteome in neurons.  

PubMed

Protein phosphorylation plays a critical role in neuronal transcription, translation, cell viability, and synaptic plasticity. In neurons, phospho-enzymes and specific substrates directly link glutamate release and post-synaptic depolarization to these cellular functions; however, many of these enzymes and their protein substrates remain uncharacterized or unidentified. In this article, we identify a novel, synaptically driven neuronal phosphoproteome characterized by a specific motif of serine/threonine-glutamine ([S/T]-Q, abbreviated as SQ). These SQ-containing substrates are predominantly localized to dendrites, synapses, the soma; and activation of this SQ phosphoproteome by bicuculline application is induced via calcium influx through L-type calcium channels. On the other hand, acute application of NMDA can inactivate this SQ phosphoproteome. We demonstrate that the SQ motif kinase Ataxia-telangiectasia mutated can also localize to dendrites and dendritic spines, in addition to other subcellular compartments, and is activated by bicuculline application. Pharmacology studies indicate that Ataxia-telangiectasia mutated and its sister kinase ataxia telangiectasia mutated and Rad3-related up-regulate these neuronal SQ substrates. Phosphoproteomics identified over 150 SQ-containing substrates whose phosphorylation is bidirectionally regulated by synaptic activity. PMID:24117848

Siddoway, Benjamin; Hou, Hailong; Yang, Hongtian; Petralia, Ronald; Xia, Houhui

2014-03-01

127

Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis.  

PubMed

Human Protein Reference Database (HPRD) is a rich resource of experimentally proven features of human proteins. Protein information in HPRD includes protein-protein interactions, post-translational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization of human proteins. Although, protein-protein interaction data from HPRD has been widely used by the scientific community, its phosphoproteome data has not been exploited to its full potential. HPRD is one of the largest documentations of human phosphoproteins in the public domain. Currently, phosphorylation data in HPRD comprises of 95,016 phosphosites mapped on to 13,041 proteins. Additionally, enzyme-substrate reactions responsible for 5930 phosphorylation events were also documented. Significant improvements in technologies and high-throughput platforms in biomedical investigations led to an exponential increase of biological data and phosphoproteomic data in recent years. Human Proteinpedia, a community annotation portal developed by us, has also contributed to the significant increase in phosphoproteomic data in HPRD. A large number of phosphorylation events have been mapped on to reference sequences available in HPRD and Human Proteinpedia along with associated protein features. This will provide a platform for systems biology approaches to determine the role of protein phosphorylation in protein function, cell signaling, biological processes and their implication in human diseases. This review aims to provide a composite view of phosphoproteomic data pertaining to human proteins in HPRD and Human Proteinpedia. PMID:22159132

Goel, Renu; Harsha, H C; Pandey, Akhilesh; Prasad, T S Keshava

2012-02-01

128

Human Protein Reference Database and Human Proteinpedia as Resources for Phosphoproteome Analysis  

PubMed Central

Human Protein Reference Database (HPRD) is a rich resource of diverse features of human proteins, which are experimentally proven. Protein information in HPRD includes protein–protein interactions, post-translational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization of human proteins. Although, protein-protein interaction data from HPRD has been widely used by scientific community, its phosphoproteome data has not been exploited up to the potential. HPRD is one of the largest documentation of human phosphoproteins in the public domain. Currently, phosphorylation data in HPRD comprises of 95,016 phosphosites mapped on to 13,041 proteins. Additionally, enzyme-substrate reactions responsible for 5,930 phosphorylation events were also curated. Significant improvements in technologies and high-throughput platforms in biomedical investigations, led to exponential increase of biological data and phosphoproteomic data in the recent years. Human Proteinpedia, a community annotation portal developed by us, has also led to significant increase in phosphoproteomic data in HPRD. A large number of phosphorylation events have been mapped on to reference sequences available in HPRD and Human Proteinpedia along with associated protein features. This will provide a platform for systems biology approaches to determine role of protein phosphorylation in protein function, cell signaling, biological processes and their implications in human diseases. This review aims to provide a composite view of phosphoproteomic data pertaining to human proteins in HPRD and Human Proteinpedia.

Goel, Renu; Harsha, H. C.; Pandey, Akhilesh; Keshava Prasad, T. S.

2013-01-01

129

Parametric binary dissection  

NASA Technical Reports Server (NTRS)

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.

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

1993-01-01

130

Wrangling Phosphoproteomic Data to Elucidate Cancer Signaling Pathways  

PubMed Central

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.

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

2013-01-01

131

Wrangling phosphoproteomic data to elucidate cancer signaling pathways.  

PubMed

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

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

2013-01-01

132

Relevant phosphoproteomic and mass spectrometry: approaches useful in clinical research  

PubMed Central

Background "It's not what we do, it's the way that we do it". Never has this maxim been truer in proteomics than now. Mass Spectrometry-based proteomics/phosphoproteomics tools are critical to understand the structure and dynamics (spatial and temporal) of signalling that engages and migrates through the entire proteome. Approaches such as affinity purification followed by Mass Spectrometry (MS) have been used to elucidate relevant biological questions disease vs. health. Thousands of proteins interact via physical and chemical association. Moreover, certain proteins can covalently modify other proteins post-translationally. These post-translational modifications (PTMs) ultimately give rise to the emergent functions of cells in sequence, space and time. Findings Understanding the functions of phosphorylated proteins thus requires one to study proteomes as linked-systems rather than collections of individual protein molecules. Indeed, the interacting proteome or protein-network knowledge has recently received much attention, as network-systems (signalling pathways) are effective snapshots in time, of the proteome as a whole. MS approaches are clearly essential, in spite of the difficulties of some low abundance proteins for future clinical advances. Conclusion Clinical proteomics-MS has come a long way in the past decade in terms of technology/platform development, protein chemistry, and together with bioinformatics and other OMICS tools to identify molecular signatures of diseases based on protein pathways and signalling cascades. Hence, there is great promise for disease diagnosis, prognosis, and prediction of therapeutic outcome on an individualized basis. However, and as a general rule, without correct study design, strategy and implementation of robust analytical methodologies, the efforts, efficiency and expectations to make biomarkers (especially phosphorylated kinases) a useful reality in the near future, can easily be hampered.

2012-01-01

133

Integrative features of the yeast phosphoproteome and protein-protein interaction map.  

PubMed

Following recent advances in high-throughput mass spectrometry (MS)-based proteomics, the numbers of identified phosphoproteins and their phosphosites have greatly increased in a wide variety of organisms. Although a critical role of phosphorylation is control of protein signaling, our understanding of the phosphoproteome remains limited. Here, we report unexpected, large-scale connections revealed between the phosphoproteome and protein interactome by integrative data-mining of yeast multi-omics data. First, new phosphoproteome data on yeast cells were obtained by MS-based proteomics and unified with publicly available yeast phosphoproteome data. This revealed that nearly 60% of ?6,000 yeast genes encode phosphoproteins. We mapped these unified phosphoproteome data on a yeast protein-protein interaction (PPI) network with other yeast multi-omics datasets containing information about proteome abundance, proteome disorders, literature-derived signaling reactomes, and in vitro substratomes of kinases. In the phospho-PPI, phosphoproteins had more interacting partners than nonphosphoproteins, implying that a large fraction of intracellular protein interaction patterns (including those of protein complex formation) is affected by reversible and alternative phosphorylation reactions. Although highly abundant or unstructured proteins have a high chance of both interacting with other proteins and being phosphorylated within cells, the difference between the number counts of interacting partners of phosphoproteins and nonphosphoproteins was significant independently of protein abundance and disorder level. Moreover, analysis of the phospho-PPI and yeast signaling reactome data suggested that co-phosphorylation of interacting proteins by single kinases is common within cells. These multi-omics analyses illuminate how wide-ranging intracellular phosphorylation events and the diversity of physical protein interactions are largely affected by each other. PMID:21298081

Yachie, Nozomu; Saito, Rintaro; Sugiyama, Naoyuki; Tomita, Masaru; Ishihama, Yasushi

2011-01-01

134

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.

135

Spontaneous coronary artery dissection.  

PubMed

Spontaneous coronary artery dissection (SCAD) is an infrequent condition that is underdiagnosed. There is a predilection for young women without traditional cardiovascular risk factors, and it is increasingly diagnosed in women who are not peripartum. We discovered an association between SCAD and fibromuscular dysplasia (FMD), in which most women with nonatherosclerotic SCAD were found to have FMD in another vascular territory. We suspect that these seemingly healthy patients have underlying coronary FMD that predisposed them to coronary dissection. Medical treatment of SCAD includes antiplatelet therapy and ?-blockade. Revascularization of SCAD patients might be challenging, and the recommendation for stenting or surgery depends on their clinical status and the dissected coronary anatomy. The long-term outcome of patients who survived their SCAD event is generally good, however, they are at risk for recurrent dissection and major cardiovascular events, and thus should be closely monitored by cardiovascular specialists. This review summarizes the epidemiology, associated etiology, diagnosis, management, and outcome of patients with SCAD. PMID:23498840

Saw, Jacqueline

2013-09-01

136

Interrogating cAMP-dependent kinase signaling in Jurkat T cells via a protein kinase A targeted immune-precipitation phosphoproteomics approach.  

PubMed

In the past decade, mass-spectrometry-based methods have emerged for the quantitative profiling of dynamic changes in protein phosphorylation, allowing the behavior of thousands of phosphorylation sites to be monitored in a single experiment. However, when one is interested in specific signaling pathways, such shotgun methodologies are not ideal because they lack selectivity and are not cost and time efficient with respect to instrument and data analysis time. Here we evaluate and explore a peptide-centric antibody generated to selectively enrich peptides containing the cAMP-dependent protein kinase (PKA) consensus motif. This targeted phosphoproteomic strategy is used to profile temporal quantitative changes of potential PKA substrates in Jurkat T lymphocytes upon prostaglandin E2 (PGE2) stimulation, which increases intracellular cAMP, activating PKA. Our method combines ultra-high-specificity motif-based immunoaffinity purification with cost-efficient stable isotope dimethyl labeling. We identified 655 phosphopeptides, of which 642 (i.e. 98%) contained the consensus motif [R/K][R/K/X]X[pS/pT]. When our data were compared with a large-scale Jurkat T-lymphocyte phosphoproteomics dataset containing more than 10,500 phosphosites, a minimal overlap of 0.2% was observed. This stresses the need for such targeted analyses when the interest is in a particular kinase. Our data provide a resource of likely substrates of PKA, and potentially some substrates of closely related kinases. Network analysis revealed that about half of the observed substrates have been implicated in cAMP-induced signaling. Still, the other half of the here-identified substrates have been less well characterized, representing a valuable resource for future research. PMID:23882029

Giansanti, Piero; Stokes, Matthew P; Silva, Jeffrey C; Scholten, Arjen; Heck, Albert J R

2013-11-01

137

Combination of Chemical Genetics and Phosphoproteomics for Kinase Signaling Analysis Enables Confident Identification of Cellular Downstream Targets*  

PubMed Central

Delineation of phosphorylation-based signaling networks requires reliable data about the underlying cellular kinase-substrate interactions. We report a chemical genetics and quantitative phosphoproteomics approach that encompasses cellular kinase activation in combination with comparative replicate mass spectrometry analyses of cells expressing either inhibitor-sensitive or resistant kinase variant. We applied this workflow to Plk1 (Polo-like kinase 1) in mitotic cells and induced cellular Plk1 activity by wash-out of the bulky kinase inhibitor 3-MB-PP1, which targets a mutant kinase version with an enlarged catalytic pocket while not interfering with wild-type Plk1. We quantified more than 20,000 distinct phosphorylation sites by SILAC, approximately half of which were measured in at least two independent experiments in cells expressing mutant and wild-type Plk1. Based on replicate phosphorylation site quantifications in both mutant and wild-type Plk1 cells, our chemical genetic proteomics concept enabled stringent comparative statistics by significance analysis of microarrays, which unveiled more than 350 cellular downstream targets of Plk1 validated by full concordance of both statistical and experimental data. Our data point to hitherto poorly characterized aspects in Plk1-controlled mitotic progression and provide a largely extended resource for functional studies. We anticipate the described strategies to be of general utility for systematic and confident identification of cellular protein kinase substrates.

Oppermann, Felix S.; Grundner-Culemann, Kathrin; Kumar, Chanchal; Gruss, Oliver J.; Jallepalli, Prasad V.; Daub, Henrik

2012-01-01

138

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

PubMed

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

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

2014-01-01

139

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

PubMed Central

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.

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

2014-01-01

140

Dudeney Dissection of Polygons  

Microsoft Academic Search

\\u000a Given an equilateral triangle A and A Square B of the same area, Henry E. Dudeney introduced A partition of A into parts that tan be reassembled in some way, without turning over the surfaces, to form B. An examination of Dudeney’s method of partition motivates us to introduce the notion of Dudeney dissections of various polygons\\u000a to other polygons.

Jin Akiyama; Gisaku Nakamura

1998-01-01

141

Sheep Brain Dissection  

NSDL National Science Digital Library

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.

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

2004-04-30

142

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.

2001-01-01

143

Aortic dissection during pregnancy.  

PubMed Central

Aortic dissection occurred in a nineteen year old woman during the thirty seventh week of pregnancy. Immediate elective delivery of a normal baby by caesarean section was followed by aortic root replacement 48 hours later. It was decided not to proceed immediately to operation on the aortic root because it was believed that the anticoagulation necessary for cardiopulmonary bypass might provoke dangerous haemorrhage from the raw placental site. Images Fig. 1 Fig. 2

Pumphrey, C W; Fay, T; Weir, I

1986-01-01

144

Phosphoproteome of Pristionchus pacificus Provides Insights into Architecture of Signaling Networks in Nematode Models*  

PubMed Central

Pristionchus pacificus is a nematode that is increasingly used as a model organism in evolutionary biology. The genome of P. pacificus differs markedly from that of C. elegans, with a high number of orphan genes that are restricted to P. pacificus and have no homologs in other species. To gain insight into the architecture of signal transduction networks in model nematodes, we performed a large-scale qualitative phosphoproteome analysis of P. pacificus. Using two-stage enrichment of phosphopeptides from a digest of P. pacificus proteins and their subsequent analysis via high accuracy MS, we detected and localized 6,809 phosphorylation events on 2,508 proteins. We compared the detected P. pacificus phosphoproteome to the recently published phosphoproteome of C. elegans. The overall numbers and functional classes of phosphoproteins were similar between the two organisms. Interestingly, the products of orphan genes were significantly underrepresented among the detected P. pacificus phosphoproteins. We defined the theoretical kinome of P. pacificus and compared it to that of C. elegans. While tyrosine kinases were slightly underrepresented in the kinome of P. pacificus, all major classes of kinases were present in both organisms. Application of our kinome annotation to a recent transcriptomic study of dauer and mixed stage populations showed that Ser/Thr and Tyr kinases show similar expression levels in P. pacificus but not in C. elegans. This study presents the first systematic comparison of phosphoproteomes and kinomes of two model nematodes and, as such, will be a useful resource for comparative studies of their signal transduction networks.

Borchert, Nadine; Krug, Karsten; Gnad, Florian; Sinha, Amit; Sommer, Ralf J.; Macek, Boris

2012-01-01

145

Phosphoproteome of Pristionchus pacificus provides insights into architecture of signaling networks in nematode models.  

PubMed

Pristionchus pacificus is a nematode that is increasingly used as a model organism in evolutionary biology. The genome of P. pacificus differs markedly from that of C. elegans, with a high number of orphan genes that are restricted to P. pacificus and have no homologs in other species. To gain insight into the architecture of signal transduction networks in model nematodes, we performed a large-scale qualitative phosphoproteome analysis of P. pacificus. Using two-stage enrichment of phosphopeptides from a digest of P. pacificus proteins and their subsequent analysis via high accuracy MS, we detected and localized 6,809 phosphorylation events on 2,508 proteins. We compared the detected P. pacificus phosphoproteome to the recently published phosphoproteome of C. elegans. The overall numbers and functional classes of phosphoproteins were similar between the two organisms. Interestingly, the products of orphan genes were significantly underrepresented among the detected P. pacificus phosphoproteins. We defined the theoretical kinome of P. pacificus and compared it to that of C. elegans. While tyrosine kinases were slightly underrepresented in the kinome of P. pacificus, all major classes of kinases were present in both organisms. Application of our kinome annotation to a recent transcriptomic study of dauer and mixed stage populations showed that Ser/Thr and Tyr kinases show similar expression levels in P. pacificus but not in C. elegans. This study presents the first systematic comparison of phosphoproteomes and kinomes of two model nematodes and, as such, will be a useful resource for comparative studies of their signal transduction networks. PMID:22923814

Borchert, Nadine; Krug, Karsten; Gnad, Florian; Sinha, Amit; Sommer, Ralf J; Macek, Boris

2012-12-01

146

Global phosphoproteomic profiling reveals distinct signatures in B-cell non-hodgkin lymphomas.  

PubMed

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

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

2014-05-01

147

Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data.  

PubMed

Construction of large and cell-specific signaling pathways is essential to understand information processing under normal and pathological conditions. On this front, gene-based approaches offer the advantage of large pathway exploration whereas phosphoproteomic approaches offer a more reliable view of pathway activities but are applicable to small pathway sizes. In this paper, we demonstrate an experimentally adaptive approach to construct large signaling pathways from phosphoproteomic data within a 3-day time frame. Our approach--taking advantage of the fast turnaround time of the xMAP technology--is carried out in four steps: (i) screen optimal pathway inducers, (ii) select the responsive ones, (iii) combine them in a combinatorial fashion to construct a phosphoproteomic dataset, and (iv) optimize a reduced generic pathway via an Integer Linear Programming formulation. As a case study, we uncover novel players and their corresponding pathways in primary human hepatocytes by interrogating the signal transduction downstream of 81 receptors of interest and constructing a detailed model for the responsive part of the network comprising 177 species (of which 14 are measured) and 365 interactions. PMID:22446821

Melas, Ioannis N; Mitsos, Alexander; Messinis, Dimitris E; Weiss, Thomas S; Rodriguez, Julio-Saez; Alexopoulos, Leonidas G

2012-04-01

148

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

PubMed

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

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

149

"Dissection" of a Hair Dryer  

ERIC Educational Resources Information Center

The electrical design of the common hair dryer is based almost entirely on relatively simple principles learned in introductory physics classes. Just as biology students dissect a frog to see the principles of anatomy in action, physics students can "dissect" a hair dryer to see how principles of electricity are used in a real system. They can…

Eisenstein, Stan; Simpson, Jeff

2008-01-01

150

Early cytokinin response proteins and phosphoproteins of Arabidopsis thaliana identified by proteome and phosphoproteome profiling.  

PubMed

Cytokinins are plant hormones involved in regulation of diverse developmental and physiological processes in plants whose molecular mechanisms of action are being intensely researched. However, most rapid responses to cytokinin signals at the proteomic and phosphoproteomic levels are unknown. Early cytokinin responses were investigated through proteome-wide expression profiling based on image and mass spectrometric analysis of two-dimensionally separated proteins and phosphoproteins. The effects of 15 min treatments of 7-day-old Arabidopsis thaliana seedlings with four main cytokinins representing hydroxyisopentenyl, isopentenyl, aromatic, and urea-derived type cytokinins were compared to help elucidate their common and specific function(s) in regulating plant development. In proteome and phosphoproteome maps, significant differences were reproducibly observed for 53 and 31 protein spots, respectively. In these spots, 96 proteins were identified by matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF MS), providing a snapshot of early links in cytokinin-regulated signalling circuits and cellular processes, including light signalling and photosynthesis, nitrogen metabolism, the CLAVATA pathway, and protein and gene expression regulation, in accordance with previously described cytokinin functions. Furthermore, they indicate novel links between temperature and cytokinin signalling, and an involvement of calcium ions in cytokinin signalling. Most of the differentially regulated proteins and phosphoproteins are located in chloroplasts, suggesting an as yet uncharacterized direct signalling chain responsible for cytokinin action in chloroplasts. Finally, first insights into the degree of specificity of cytokinin receptors on phosphoproteomic effects were obtained from analyses of cytokinin action in a set of cytokinin receptor double mutants. PMID:20974740

Cerny, Martin; Dycka, Filip; Bobál'ová, Janette; Brzobohaty, Bretislav

2011-01-01

151

Early cytokinin response proteins and phosphoproteins of Arabidopsis thaliana identified by proteome and phosphoproteome profiling  

PubMed Central

Cytokinins are plant hormones involved in regulation of diverse developmental and physiological processes in plants whose molecular mechanisms of action are being intensely researched. However, most rapid responses to cytokinin signals at the proteomic and phosphoproteomic levels are unknown. Early cytokinin responses were investigated through proteome-wide expression profiling based on image and mass spectrometric analysis of two-dimensionally separated proteins and phosphoproteins. The effects of 15?min treatments of 7-day-old Arabidopsis thaliana seedlings with four main cytokinins representing hydroxyisopentenyl, isopentenyl, aromatic, and urea-derived type cytokinins were compared to help elucidate their common and specific function(s) in regulating plant development. In proteome and phosphoproteome maps, significant differences were reproducibly observed for 53 and 31 protein spots, respectively. In these spots, 96 proteins were identified by matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF MS), providing a snapshot of early links in cytokinin-regulated signalling circuits and cellular processes, including light signalling and photosynthesis, nitrogen metabolism, the CLAVATA pathway, and protein and gene expression regulation, in accordance with previously described cytokinin functions. Furthermore, they indicate novel links between temperature and cytokinin signalling, and an involvement of calcium ions in cytokinin signalling. Most of the differentially regulated proteins and phosphoproteins are located in chloroplasts, suggesting an as yet uncharacterized direct signalling chain responsible for cytokinin action in chloroplasts. Finally, first insights into the degree of specificity of cytokinin receptors on phosphoproteomic effects were obtained from analyses of cytokinin action in a set of cytokinin receptor double mutants.

Cerny, Martin; Dycka, Filip; Bobal'ova, Janette; Brzobohaty, Bretislav

2011-01-01

152

Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome  

Microsoft Academic Search

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

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

2002-01-01

153

Computational Fluid Dynamics Analysis of Thoracic Aortic Dissection  

NASA Astrophysics Data System (ADS)

Thoracic Aortic Dissection (TAD) is a cardiovascular disease with high mortality. An aortic dissection is formed when blood infiltrates the layers of the vascular wall, and a new artificial channel, the false lumen, is created. The expansion of the blood vessel due to the weakened wall enhances the risk of rupture. Computational fluid dynamics analysis is performed to study the hemodynamics of this pathological condition. Both idealized geometry and realistic patient configurations from computed tomography (CT) images are investigated. Physiological boundary conditions from in vivo measurements are employed. Flow configuration and biomechanical forces are studied. Quantitative analysis allows clinicians to assess the risk of rupture in making decision regarding surgical intervention.

Sau Tang, Yik; Fan, Yi; Wing Keung Cheng, Stephen; Wing Chow, Kwok

2011-11-01

154

Traumatic internal carotid artery dissection.  

PubMed

Traumatic internal carotid artery dissection is a serious condition that may cause ischemic stroke in young patients. It has been under-diagnosed in the past. We present three cases of traumatic internal carotid artery dissection. The clinical manifestations include hemicrania, hemiparesis, partial Horner's syndrome and cranial nerve palsy. Diagnosis is with carotid color Doppler ultrasound, CT angiography of the neck and conventional angiography. The outcome may be poor with hemiparesis, persistent vegetative state and death. We review the literature and discuss the clinical presentation, diagnosis, grading and treatment choices for traumatic internal carotid artery dissection and stroke. PMID:16410213

Yang, Shun-Tai; Huang, Yin-Cheng; Chuang, Chi-Cheng; Hsu, Peng-Wei

2006-01-01

155

Biomedicine: an ontological dissection.  

PubMed

Though ubiquitous across the medical social sciences literature, the term "biomedicine" as an analytical concept remains remarkably slippery. It is argued here that this imprecision is due in part to the fact that biomedicine is comprised of three interrelated ontological spheres, each of which frames biomedicine as a distinct subject of investigation. This suggests that, depending upon one's ontological commitment, the meaning of biomedicine will shift. From an empirical perspective, biomedicine takes on the appearance of a scientific enterprise and is defined as a derivative category of Western science more generally. From an interpretive perspective, biomedicine represents a symbolic-cultural expression whose adherence to the principles of scientific objectivity conceals an ideological agenda. From a conceptual perspective, biomedicine represents an expression of social power that reflects structures of power and privilege within capitalist society. No one perspective exists in isolation and so the image of biomedicine from any one presents an incomplete understanding. It is the mutually-conditioning interrelations between these ontological spheres that account for biomedicine's ongoing development. Thus, the ontological dissection of biomedicine that follows, with particular emphasis on the period of its formal crystallization in the latter nineteenth and early twentieth century, is intended to deepen our understanding of biomedicine as an analytical concept across the medical social sciences literature. PMID:18802784

Baronov, David

2008-01-01

156

Genetic Dissection of SLE  

PubMed Central

Genetic dissection of lupus pathogenesis in the NZM2410 strain has recently revealed that Sle1 is a potent locus that triggers the formation of IgG anti-histone/DNA antibodies, when expressed on the B6 background as a congenic interval. B6.lpr mice, in contrast, exhibit distinctly different cellular and serological phenotypes. Both strains, however, do not usually exhibit pathogenic autoantibodies, or succumb to lupus nephritis. In this study, we show that the epistatic interaction of Sle1 (in particular, Sle1/Sle1) with FASlpr leads to massive lymphosplenomegaly (with elevated numbers of activated CD4 T cells, CD4?CD8? double negative (DN) T cells, and B1a cells), high levels of IgG and IgM antinuclear (including anti-ssDNA, anti-dsDNA, and anti-histone/DNA), and antiglomerular autoantibodies, histological, and clinical evidence of glomerulonephritis, and >80% mortality by 5–6 mo of age. Whereas FASlpr functions as a recessive gene, Sle1 exhibits a gene dosage effect. These studies indicate that Sle1 and FASlpr must be impacting alternate pathways leading to lymphoproliferative autoimmunity.

Shi, Xiaoyan; Xie, Chun; Kreska, Desi; Richardson, James A.; Mohan, Chandra

2002-01-01

157

Experience with parametric binary dissection  

NASA Technical Reports Server (NTRS)

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.

Bokhari, Shahid H.

1993-01-01

158

Phosphoproteomic analysis of Rhodopseudomonas palustris reveals the role of pyruvate phosphate dikinase phosphorylation in lipid production.  

PubMed

Rhodopseudomonas palustris (R. palustris) is a purple nonsulfur anoxygenic phototrophic bacterium with metabolic versatility and is able to grow under photoheterotrophic and chemoheterotrophic states. It has uses in carbon management, carbon recycling, hydrogen generation, and lipid production; therefore, it has the potential for bioenergy production and biodegradation. This study is the first to identify the phosphoproteome of R. palustris including 100 phosphopeptides from 54 phosphoproteins and 74 phosphopeptides from 42 phosphoproteins in chemoheterotrophic and photoheterotrophic growth conditions, respectively. In the identified phosphoproteome, phosphorylation at the threonine residue, Thr487, of pyruvate phosphate dikinase (PPDK, RPA1051) was found to participate in the regulation of carbon metabolism. Here, we show that PPDK enzyme activity is higher in photoheterotrophic growth, with Thr487 phosphorylation as a possible mediator. Under the same photoheterotrophic conditions, R. palustris with overexpressed wild-type PPDK showed an enhanced accumulation of total lipids than those with mutant PPDK (T487V) form. This study reveals the role of the PPDK in the production of biodiesel material, lipid content, with threonyl-phosphorylation as one of the possible regulatory events during photoheterotrophic growth in R. palustris. PMID:23030682

Hu, Chia-Wei; Lin, Miao-Hsia; Huang, Hsuan-Cheng; Ku, Wei-Chi; Yi, Tsun-Hsuan; Tsai, Chia-Feng; Chen, Yu-Ju; Sugiyama, Naoyuki; Ishihama, Yasushi; Juan, Hsueh-Fen; Wu, Shih-Hsiung

2012-11-01

159

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

PubMed Central

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.

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

2014-01-01

160

Characterization of the human cerebrospinal fluid phosphoproteome by titanium dioxide affinity chromatography and mass spectrometry.  

PubMed

Biomarkers in the cerebrospinal fluid (CSF) may be important for the diagnosis of chronic degenerative disorders in the central nervous system including dementia. Existing CSF biomarkers for dementia, however, are relatively nonspecific. More specific markers may be found by targeting investigations based on knowledge of the molecular pathology of the disease in question. In Alzheimer's disease, hyperphosphorylation of the tau protein is a characteristic feature and thus a comprehensive characterization of the phosphoproteome of the CSF may be pursued to obtain a complete picture of phosphorylation aberrations in health and disease. Toward that goal we here describe a method for a comprehensive isolation and identification of phosphorylated tryptic peptides derived from CSF proteins using a simple sample preparation step and titanium dioxide-affinity chromatography followed by MALDI-TOF or LC-MS/MS linear ion-trap-FT mass spectrometry. Whereas not all previously reported phosphoproteins were found in normal CSF, we detected 56 putative novel phosphorylation sites in 38 proteins in addition to known sites. The approach seems to be a promising foundation for the discovery of new biomarkers embedded in the CSF phosphoproteome. PMID:18702456

Bahl, Justyna Maria Czarna; Jensen, Søren Skov; Larsen, Martin R; Heegaard, Niels H H

2008-08-15

161

Large scale phosphoproteome analysis of LNCaP human prostate cancer cells  

PubMed Central

Prostate cancer is the most frequently diagnosed cancer among men in the western world. The androgen receptor, a phosphoprotein, is suspected to be involved in all stages of the prostate cancer. Androgen receptor activity can be modulated by various kinases such as PKA, MAPK, AKT, and Src. Phosphorylation is an important post-translational modification and serves as a molecular on/off switch to regulate signaling. Disruptions of cellular phosphorylation are associated with various diseases such as cancer and kinases provide important drug targets. Here we present an analysis of the phosphoproteome in LNCaP human prostate cancer cells. The analytical strategy employed used proteomics based methodologies with a combination of detergent and chaotropic reagent during trypsin digestion followed by titanium dioxide enrichment of phosphopeptides. Over the course of multiple analyses by mass spectrometry we identified a total of 746 phosphorylation sites in 540 phosphopeptides corresponding to 116 phosphoproteins, of which 56 have not been previously reported. Phosphoproteins identified included transcription factors, co-regulators of the androgen receptor, and cancer-related proteins that include ?-catenin, USP10, and histone deacetylase-2. The information of signaling pathways, motifs of phosphorylated peptides, biological processes, molecular functions, cellular components, and protein interactions from the identified phosphoproteins established a map of phosphoproteome and signaling pathways in LNCaP cells.

Myung, Jae-Kyung; Sadar, Marianne D

2012-01-01

162

Changes of proteome and phosphoproteome trigger embryo-larva transition of honeybee worker (Apis mellifera ligustica).  

PubMed

The development of the last day embryo to the first instar larva is an essential process in the honeybee life cycle. However, the molecular mechanism of this life transition is still unknown. The proteome and phosphoproteome of last day embryos (72 h) and first instar larvae (24h, post hatching) were analyzed using 2-DE, multiplex fluorescent staining, mass spectrometry, bioinformatics, and qRT-PCR. Sixty-five proteins and 34 phosphoproteins changed their expression across the shift of embryos to larvae. The embryo stronger expression of proteins related to energy metabolism, development and amino acid metabolism suggests its high metabolic energy demand during active embryogenesis. While, the newly hatched larvae escalated the expression of proteins related to cytoskeleton, biosynthesis, protein folding, fatty acid and oxidative metabolism, particularly the higher phosphorylation of cytoskeleton and biosynthesis indicates their roles to ensure the fast growing larvae. These differences in protein expression level illustrate that specific protein functions are restricted to particular developmental stage. Our data suggest the essential changes of proteome and phosphoproteome to trigger the transition of embryo to larvae. This unravels the molecular event behind the first life cycle transition of honeybees and is potentially helpful for future reverse genetic studies in this model insect. PMID:23088927

Gala, Alemayehu; Fang, Yu; Woltedji, Dereje; Zhang, Lan; Han, Bin; Feng, Mao; Li, Jianke

2013-01-14

163

Comprehensive phosphoproteome analysis of INS-1 pancreatic ?-cells using various digestion strategies coupled with liquid chromatography-tandem mass spectrometry.  

PubMed

Type 2 diabetes results from aberrant regulation of the phosphorylation cascade in beta-cells. Phosphorylation in pancreatic beta-cells has not been examined extensively, except with regard to subcellular phosphoproteomes using mitochondria. Thus, robust, comprehensive analytical strategies are needed to characterize the many phosphorylated proteins that exist, because of their low abundance, the low stoichiometry of phosphorylation, and the dynamic regulation of phosphoproteins. In this study, we attempted to generate data on a large-scale phosphoproteome from the INS-1 rat pancreatic beta-cell line using linear ion trap MS/MS. To profile the phosphoproteome in-depth, we used comprehensive phosphoproteomic strategies, including detergent-based protein extraction (SDS and SDC), differential sample preparation (in-gel, in-solution digestion, and FASP), TiO2 enrichment, and MS replicate analyses (MS2-only and multiple-stage activation). All spectra were processed and validated by stringent multiple filtering using target and decoy databases. We identified 2467 distinct phosphorylation sites on 1419 phosphoproteins using 4 mg of INS-1 cell lysate in 24 LC-MS/MS runs, of which 683 (27.7%) were considered novel phosphorylation sites that have not been characterized in human, mouse, or rat homologues. Our informatics data constitute a rich bioinformatics resource for investigating the function of reversible phosphorylation in pancreatic beta-cells. In particular, novel phosphorylation sites on proteins that mediate the pathology of type 2 diabetes, such as Pdx-1, Nkx.2, and Srebf1, will be valuable targets in ongoing phosphoproteomics studies. PMID:22276854

Han, Dohyun; Moon, Sungyoon; Kim, Yikwon; Ho, Won-Kyung; Kim, Kyunggon; Kang, Yup; Jun, Heesook; Kim, Youngsoo

2012-04-01

164

Aortic Dissection in Turner Syndrome  

PubMed Central

Purpose of review Turner syndrome (TS) is a relatively common disorder of female development with cardinal features of short stature and congenital cardiovascular defects (CHD). TS is the most common established cause of aortic dissection in young women, but has received little attention outside of pediatric literature. This review focuses on emerging knowledge of the characteristics of aortic disease in TS in comparison with Marfan-like syndromes and isolated aortic valve disease. Recent findings The incidence of aortic dissection is significantly increased in individuals with TS at all ages, highest during young adult years and in pregnancy. Pediatric patients with dissection have known CHD, but adults often have aortic valve and arch abnormalities detected only by screening cardiac MR (CMR). Thoracic aortic dilation in TS must be evaluated in relation to body surface area (BSA). Dilation is most prominent at the ascending aorta similar to the pattern seen in non-syndromic bicuspid aortic valve (BAV), is equally prevalent (20-30%) in children and adults, and does not seem to be rapidly progressive. Cardiovascular anomalies and risk for aortic dissection in TS are strongly linked to a history of fetal lymphedema, evidenced by the presence of neck webbing and shield chest. Summary Risk for acute aortic dissection is increased by more than 100-fold in young and middle-aged women with TS. Monitoring frequency and treatment modalities are decided on an individual basis until more information on outcomes becomes available.

Bondy, Carolyn A.

2009-01-01

165

[Neurological signs in aortic dissection].  

PubMed

A substantial number of patients suffering from aortic dissection will show neurological signs. These can dominate the clinical picture and hinder an accurate diagnosis of this life-threatening disease. We present a case of lower extremity pain and a case of transient global amnesia caused by aortic dissection. A third patient suffered from acute cerebral ischemia accompanied by hypotension and back pain, suggestive of aortic dissection. In this third case, aortic dissection was excluded before systemic thrombolytic therapy was administered, for the patient could have suffered disastrous complications caused by this emergency stroke therapy. Clinicians should be aware that a wide range of cerebral, spinal and peripheral neurological signs can be caused by aortic dissection. An unusual combination of symptoms can be a clue for underlying aortic disease. High-risk clinical features are predisposing factors in medical history, typical acute onset back or chest pain, and pulse deficit, blood pressure asymmetry or a new cardiac murmur on physical examination. These features should be explicitly evaluated in patients with an acute neurological deficit. If neurological symptoms and a high-risk clinical feature are present, immediate aortic imaging should be considered since early detection can be life saving. PMID:24330794

Walma, Rinske A; Vermeij, Frederique H; Bakker, Stef L M

2013-01-01

166

Osteogenesis imperfecta and aortic dissection.  

PubMed

Osteogenesis imperfecta (OI) is a group of autosomal dominant disorders affecting Type I collagen synthesis with the predominant clinical manifestations in skeleton, skin, eyes, and teeth. Valvular cardiac manifestations and aortic root changes have long been reported. However, aortic dissection and repair were not described until 1993, with only 3 more proximal aortic dissections and repair noted. We report a fifth case and the first distal dissection. Surgeons performing vascular operations will in all probability never have encountered vascular repair in those with OI. The reports and this case are strong evidence that special efforts are required because of the fragility of tissues and propensity for bleeding. Reinforcement of any vascular suture line should be considered to reduce failure and bleeding. PMID:18626241

Byra, Paul; Chillag, Shawn; Petit, Scott

2008-07-01

167

Asymptomatic spontaneous coronary artery dissection.  

PubMed

Spontaneous coronary artery dissection (SCAD) is a rare cause of myocardial ischemia that could present as angina, acute myocardial infarction, or even sudden death. It occurs more commonly in women and it has been associated with autoimmune and collagen vascular diseases. The management and prognosis in these patients depend on the initial clinical presentation and the extent of dissection. In this article, we report 2 cases of asymptomatic SCAD that were diagnosed on routine preoperative evaluation. The management options and clinical implications are discussed. PMID:20641110

Dakik, Habib A; Nader, Gilbert Abou; Arja, Wajih A; Sawaya, Jaber; Gharzuddine, Walid

2010-07-01

168

``Dissection'' of a Hair Dryer  

NASA Astrophysics Data System (ADS)

The electrical design of the common hair dryer is based almost entirely on relatively simple principles learned in introductory physics classes. Just as biology students dissect a frog to see the principles of anatomy in action, physics students can ``dissect'' a hair dryer to see how principles of electricity are used in a real system. They can discover how engineers solve problems such as how to vary between low and high heat and fan speed by simply moving the position of a single switch. Principles of alternating versus direct current, series and parallel circuits, electrical safety, voltage dividing, ac rectification, power, and measurement of resistance and continuity all come in to play.

Eisenstein, Stan; Simpson, Jeff

2008-12-01

169

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

PubMed Central

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.

Rampitsch, Christof; Bykova, Natalia V.

2012-01-01

170

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

SciTech Connect

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.

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

171

Dissect Your Squid and Eat It Too!  

ERIC Educational Resources Information Center

Introduces a science lab activity in which students dissect fresh squids in groups of four and observe the anatomy. Parent volunteers cook the squid mantle for kids to taste. Includes directions for squid dissection. (YDS)

McGinnis, Patricia

2001-01-01

172

Phosphoproteome Profiling of Human Skin Fibroplast Cells in Response to Low- and High-Dose Irradiation  

SciTech Connect

The biological effect of low-dose radiation is currently not well understood. A hallmark of the response to radiation is the phosphorylation of proteins involved in DNA repair, DNA damage signaling, and cell cycle checkpoint control, which is important in prompt cellular response. The objective of the work presented here was to explore the phosphoproteome of normal human skin fibroblast (HSF) cells to reveal differences between low- and high-dose irradiation responses at the protein phosphorylation level. Several techniques —Trizol extract of proteins, methylation of the enzyme digest (peptides), enrichment of phosphopeptides with immobilized metal affinity chromatography (IMAC), nanoflow reversed-phase HPLC (nano-LC)/electrospray ionization, and tandem mass spectrometry— were combined for analysis of the HSF cell phosphoproteome following low- and high-doses of irradiation. More than 95% of the peptides identified after IMAC enrichment were phosphopeptides. Among the 493 unique phosphopeptides, 232 were singly phosphorylated, 220 were doubly phosphorylated, and 41 were triply phosphorylated, indicating the overall effectiveness of the IMAC technique to enrich both singly and multiple phosphorylated peptides. Over 700 phosphorylation sites were assigned to a total of 346 proteins, many of which are known or proposed to be highly relevant to a plethora of fundamental biological processes. The profile for proteins identified from the low-dose (2cGy) irradiated HSF cells was shown to be different from the profile obtained for proteins irradiated at the high-dose (4 Gy). This type of fundamental information regarding radiation-response to cellular events at the molecular level provides a mechanistic basis for identifying relevant molecular markers that can be used in future to better evaluate human health risks at low doses of irradiation and to develop low dose radiation counter measurements.

Yang, Feng; Stenoien, David L.; Strittmatter, Eric F.; Wang, Jeng-Han; Ding, Lianghao; Lipton, Mary S.; Monroe, Matthew E.; Nicora, Carrie D.; Gritsenko, Marina A.; Tang, Keqi; Fang, Ruihua; Adkins, Joshua N.; Camp, David G.; Chen, David J.; Smith, Richard D.

2006-05-01

173

Robust phosphoproteome enrichment using monodisperse microsphere-based immobilized titanium (IV) ion affinity chromatography.  

PubMed

Mass spectrometry (MS)-based proteomics has become the preferred tool for the analysis of protein phosphorylation. To be successful at such an endeavor, there is a requirement for an efficient enrichment of phosphopeptides. This is necessary because of the substoichiometric nature of phosphorylation at a given site and the complexity of the cell. Recently, new alternative materials have emerged that allow excellent and robust enrichment of phosphopeptides. These monodisperse microsphere-based immobilized metal ion affinity chromatography (IMAC) resins incorporate a flexible linker terminated with phosphonate groups that chelate either zirconium or titanium ions. The chelated zirconium or titanium ions bind specifically to phosphopeptides, with an affinity that is similar to that of other widely used metal oxide affinity chromatography materials (typically TiO(2)). Here we present a detailed protocol for the preparation of monodisperse microsphere-based Ti(4+)-IMAC adsorbents and the subsequent enrichment process. Furthermore, we discuss general pitfalls and crucial steps in the preparation of phosphoproteomics samples before enrichment and, just as importantly, in the subsequent mass spectrometric analysis. Key points such as lysis, preparation of the chromatographic system for analysis and the most appropriate methods for sequencing phosphopeptides are discussed. Bioinformatics analysis specifically relating to site localization is also addressed. Finally, we demonstrate how the protocols provided are appropriate for both single-protein analysis and the screening of entire phosphoproteomes. It takes ?2 weeks to complete the protocol: 1 week to prepare the Ti(4+)-IMAC material, 2 d for sample preparation, 3 d for MS analysis of the enriched sample and 2 d for data analysis. PMID:23391890

Zhou, Houjiang; Ye, Mingliang; Dong, Jing; Corradini, Eleonora; Cristobal, Alba; Heck, Albert J R; Zou, Hanfa; Mohammed, Shabaz

2013-03-01

174

Dissection & Science Fairs. [Information Packet.  

ERIC Educational Resources Information Center

This collection of pamphlets and articles reprinted from other National Anti-Vivisection Society (NAVS) publications was compiled to address the issues of classroom laboratory dissection and the use of animals in science fair projects. Three of the pamphlets contained in this packet are student handbooks designed to help students of elementary,…

National Anti-Vivisection Society, Chicago, IL.

175

Animal Rights Activism Threatens Dissection.  

ERIC Educational Resources Information Center

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)

Holden, Constance

1990-01-01

176

Insights into acute aortic dissection  

Microsoft Academic Search

Aortic dissection represents one of the most catastrophic and complex cardiovascular diseases. Its origin is related to an intimal tear with course of blood flow into the aortic wall and division of the aortic lumen into two different lumens, defined as the true and false lumen, separated by a septum or intimal flap. Based on the location of the entry

S. Trimarchi

2012-01-01

177

Traumatic bilateral vertebral artery dissection.  

PubMed

Traumatic vertebral artery dissection is not often seen by forensic pathologists, and cases investigated are scarce in the forensic literature. We present the case of a 40-year-old woman cyclist who was struck by a car while wearing a helmet, and was neurologically near normal immediately thereafter at Emergency. She presented 48 h later with acute right hemiparesis, decreasing level of consciousness, and unsteadiness. CT revealed massive cerebellar infarction. CT angiography was normal. The patient died in coma 7 days after injury and autopsy revealed bilateral edematous cerebellar infarction and bilateral vertebral artery dissection. Rotational neck injury and mural tear in the wall of the Atlantic parts of both vertebral arteries is suggested as the possible mechanism of the arterial injury. Head and neck injuries are reported as a precipitating cause of vertebral artery injury. The possible influence of trauma may be further underestimated if longer intervals between vessel dissection and ischemia occur. The current case illustrates that "talk-and-die" syndrome may be due to occult vertebral artery dissection, possibly bilateral. In forensic cases of delayed death after mild trauma to the head and neck, the vertebral arteries should be examined for the cause of death. PMID:21798679

Galtés, Ignasi; Borondo, Juan Carlos; Cos, Mònica; Subirana, Mercè; Martin-Fumadó, Carles; Martín, Carles; Castellà, Josep; Medallo, Jordi

2012-01-10

178

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

PubMed Central

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.

He, Yikun

2014-01-01

179

Hi-Tech Alternatives to Dissection.  

ERIC Educational Resources Information Center

The debate on the educational value of dissection versus the value of animal life is examined. Interactive videodisc (IVD) technology is described in light of its potential for laboratory simulations. The design of the IVD-based dissection simulation, The Interactive Frog Dissection, is presented. (KR)

Strauss, Richard T.; Kinzie, Mable B.

1991-01-01

180

Isolated dissection of the superior mesenteric artery  

Microsoft Academic Search

Dissection of the superior mesenteric artery (SMA) not associated with aortic dissection is rare. The purpose of this study is to describe the computed tomographic (CT) findings of this condition. We studied the CT findings of six patients with isolated dissection of the SMA. CT demonstrated thrombosis of the false lumen or intramural hematoma ( n = 4) and\\/or intimal

S. Suzuki; S. Furui; H. Kohtake; T. Sakamoto; M. Yamasaki; A. Furukawa; K. Murata; R. Takei

2004-01-01

181

Spontaneous Dissection of the Superior Mesenteric Artery  

Microsoft Academic Search

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

Patrick J. Sheldon; James B. Esther; Elana L. Sheldon; Steven R. Sparks; David P. Brophy; Steven B. Oglevie

2001-01-01

182

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

PubMed Central

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.

Horst, Walter Johannes

2013-01-01

183

Spontaneous Dissection of the Superior Mesenteric Artery  

SciTech Connect

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.

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

184

Spontaneous dissection of the superior mesenteric artery.  

PubMed

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. PMID:11815839

Sheldon, P J; Esther, J B; Sheldon, E L; Sparks, S R; Brophy, D P; Oglevie, S B

2001-01-01

185

Netfrog: The Interactive Frog Dissection  

NSDL National Science Digital Library

This tutorial on frog dissection contains an introduction and sections on preparation, skin incisions, muscle incisions, and internal organs. The purpose of this lab activity is to help students learn the anatomy of a frog and provide them with a better understanding of the anatomy of vertebrate animals in general, including humans. This site provides still and motion visuals of preserved and pithed (severed spinal cord) frogs to demonstrate incisions, in addition to text.

Kinzie, Mable

186

[Paraplegia associated with acute aortic dissection complicated with pulmonary embolism and re-dissection].  

PubMed

Paraplegia associated with acute aortic dissection is one of the most serious complications. We experienced a case of Stanford type A acute aortic dissection with paraplegia and cardiac tamponade because the dissection was already thrombosed, conservative therapy was chosen. After drainage of pericardial effusion, a spinal drainage tube was inserted. Eleven days later, pulmonary embolism and re-dissection occurred, and an emergency operation was performed. Although the operation was successful, paraplegia did not improve. Even if type A acute aortic dissection is complicated with paraplegia, early surgical repair of aortic dissection should be considered, when paraplegia does not improve rapidly in spite of treatment. PMID:19999086

Murakami, H; Makuuchi, H; Chikada, M; Kobayashi, T; Suzuki, T; Ando, T; Oono, M; Ono, H; Chiba, K; Nagata, T

2009-12-01

187

[Isolated spontaneous dissection of visceral arteries].  

PubMed

We present the cases of two men with isolated spontaneous dissection of visceral arteries diagnosed by multidetector CT. In the first patient, dissection of the celiac trunk was associated with periarterial changes. In the second patient, dissection of the superior mesenteric artery was associated with stenosis at the root of the celiac trunk. Both patients presented with acute pain, which was more intense and longer lasting in the first patient. Aortic dissection was suspected clinically in both patients. Both dissections were short and had patent saccular false lumens and reduced caliber of the true lumens. This morphological type is one of the most uncommon within this rare entity. However, in recent years, the number of cases published is rising. This suggests that this entity may have been underdiagnosed before the widespread use of multidetector CT. We discuss the two morphological classifications of dissection of the visceral arteries and the need to adapt therapeutic management to the particular circumstances of each case. PMID:21724211

Corral, M A; Encinas, J; Fernández-Pérez, G C

2014-01-01

188

Vertebral artery dissection associated with sildenafil abuse.  

PubMed

We present a 49-year-old male who suffered a cerebellar infarction due to a vertebral artery dissection. The patient had taken sildenafil daily for at least 2 years for sexual enhancement. There was no sexual intercourse or traumatic event prior to symptom onset. Sildenafil intake has been associated with aortic dissection and, in the light of this report, we suggest that chronic sildenafil intake could be a risk factor for arterial dissection. PMID:23454143

Dersch, Rick; Anastasopoulos, Constantin; Hader, Claudia; Stich, Oliver

2013-05-01

189

Spontaneous Dissection of the Superior Mesenteric Artery  

Microsoft Academic Search

Spontaneous dissection of the superior mesenteric artery (SMA) is a rare occurrence, especially when not associated with aortic\\u000a dissection [1]. Currently, only 28 cases appear to have been reported. Due to the scarcity of cases in the literature, the\\u000a natural history of isolated, spontaneous SMA dissection is unclear. CT has been reported to be useful for the initial diagnosis\\u000a of

Patrick J. Sheldon; James B. Esther; Elana L. Sheldon; Steven R. Sparks; David P. Brophy; Steven B. Oglevie

2001-01-01

190

Phosphoproteomics of collagen receptor networks reveals SHP-2 phosphorylation downstream of wild-type DDR2 and its lung cancer mutants.  

PubMed

Collagen is an important extracellular matrix component that directs many fundamental cellular processes including differentiation, proliferation and motility. The signalling networks driving these processes are propagated by collagen receptors such as the ?1 integrins and the DDRs (discoidin domain receptors). To gain an insight into the molecular mechanisms of collagen receptor signalling, we have performed a quantitative analysis of the phosphorylation networks downstream of collagen activation of integrins and DDR2. Temporal analysis over seven time points identified 424 phosphorylated proteins. Distinct DDR2 tyrosine phosphorylation sites displayed unique temporal activation profiles in agreement with in vitro kinase data. Multiple clustering analysis of the phosphoproteomic data revealed several DDR2 candidate downstream signalling nodes, including SHP-2 (Src homology 2 domain-containing protein tyrosine phosphatase 2), NCK1 (non-catalytic region of tyrosine kinase adaptor protein 1), LYN, SHIP-2 [SH2 (Src homology 2)-domain-containing inositol phosphatase 2], PIK3C2A (phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2?) and PLCL2 (phospholipase C-like 2). Biochemical validation showed that SHP-2 tyrosine phosphorylation is dependent on DDR2 kinase activity. Targeted proteomic profiling of a panel of lung SCC (squamous cell carcinoma) DDR2 mutants demonstrated that SHP-2 is tyrosine-phosphorylated by the L63V and G505S mutants. In contrast, the I638F kinase domain mutant exhibited diminished DDR2 and SHP-2 tyrosine phosphorylation levels which have an inverse relationship with clonogenic potential. Taken together, the results of the present study indicate that SHP-2 is a key signalling node downstream of the DDR2 receptor which may have therapeutic implications in a subset of DDR2 mutations recently uncovered in genome-wide lung SCC sequencing screens. PMID:23822953

Iwai, Leo K; Payne, Leo S; Luczynski, Maciej T; Chang, Francis; Xu, Huifang; Clinton, Ryan W; Paul, Angela; Esposito, Edward A; Gridley, Scott; Leitinger, Birgit; Naegle, Kristen M; Huang, Paul H

2013-09-15

191

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

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.

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

192

Phosphoproteomic evaluation of pharmacological inhibition of leucine-rich repeat kinase 2 reveals significant off-target effects of LRRK-2-IN-1.  

PubMed

Genetic mutations in leucine-rich repeat kinase 2 (LRRK2) have been linked to autosomal dominant Parkinson's disease. The most prevalent mutation, G2019S, results in enhanced LRRK2 kinase activity that potentially contributes to the etiology of Parkinson's disease. Consequently, disease progression is potentially mediated by poorly characterized phosphorylation-dependent LRRK2 substrate pathways. To address this gap in knowledge, we transduced SH-SY5Y neuroblastoma cells with LRRK2 G2019S via adenovirus, then determined quantitative changes in the phosphoproteome upon LRRK2 kinase inhibition (LRRK2-IN-1 treatment) using stable isotope labeling of amino acids in culture combined with phosphopeptide enrichment and LC-MS/MS analysis. We identified 776 phosphorylation sites that were increased or decreased at least 50% in response to LRRK2-IN-1 treatment, including sites on proteins previously known to associate with LRRK2. Bioinformatic analysis of those phosphoproteins suggested a potential role for LRRK2 kinase activity in regulating pro-inflammatory responses and neurite morphology, among other pathways. In follow-up experiments, LRRK2-IN-1 inhibited lipopolysaccharide-induced tumor necrosis factor alpha (TNF?) and C-X-C motif chemokine 10 (CXCL10) levels in astrocytes and also enhanced multiple neurite characteristics in primary neuronal cultures. However, LRRK2-IN-1 had almost identical effects in primary glial and neuronal cultures from LRRK2 knockout mice. These data suggest LRRK2-IN-1 may inhibit pathways of perceived LRRK2 pathophysiological function independently of LRRK2 highlighting the need to use multiple pharmacological tools and genetic approaches in studies determining LRRK2 function. PMID:24117733

Luerman, Gregory C; Nguyen, Chuong; Samaroo, Harry; Loos, Paula; Xi, Hualin; Hurtado-Lorenzo, Andres; Needle, Elie; Stephen Noell, G; Galatsis, Paul; Dunlop, John; Geoghegan, Kieran F; Hirst, Warren D

2014-02-01

193

Phosphoproteomics of collagen receptor networks reveals SHP-2 phosphorylation downstream of wild-type DDR2 and its lung cancer mutants  

PubMed Central

Collagen is an important extracellular matrix component that directs many fundamental cellular processes including differentiation, proliferation and motility. The signalling networks driving these processes are propagated by collagen receptors such as the ?1 integrins and the DDRs (discoidin domain receptors). To gain an insight into the molecular mechanisms of collagen receptor signalling, we have performed a quantitative analysis of the phosphorylation networks downstream of collagen activation of integrins and DDR2. Temporal analysis over seven time points identified 424 phosphorylated proteins. Distinct DDR2 tyrosine phosphorylation sites displayed unique temporal activation profiles in agreement with in vitro kinase data. Multiple clustering analysis of the phosphoproteomic data revealed several DDR2 candidate downstream signalling nodes, including SHP-2 (Src homology 2 domain-containing protein tyrosine phosphatase 2), NCK1 (non-catalytic region of tyrosine kinase adaptor protein 1), LYN, SHIP-2 [SH2 (Src homology 2)-domain-containing inositol phosphatase 2], PIK3C2A (phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2?) and PLCL2 (phospholipase C-like 2). Biochemical validation showed that SHP-2 tyrosine phosphorylation is dependent on DDR2 kinase activity. Targeted proteomic profiling of a panel of lung SCC (squamous cell carcinoma) DDR2 mutants demonstrated that SHP-2 is tyrosine-phosphorylated by the L63V and G505S mutants. In contrast, the I638F kinase domain mutant exhibited diminished DDR2 and SHP-2 tyrosine phosphorylation levels which have an inverse relationship with clonogenic potential. Taken together, the results of the present study indicate that SHP-2 is a key signalling node downstream of the DDR2 receptor which may have therapeutic implications in a subset of DDR2 mutations recently uncovered in genome-wide lung SCC sequencing screens.

Iwai, Leo K.; Payne, Leo S.; Luczynski, Maciej T.; Chang, Francis; Xu, Huifang; Clinton, Ryan W.; Paul, Angela; Esposito, Edward A.; Gridley, Scott; Leitinger, Birgit; Naegle, Kristen M.; Huang, Paul H.

2013-01-01

194

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

PubMed Central

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.

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

195

Visualization and Biochemical Analyses of the Emerging Mammalian 14-3-3-Phosphoproteome*  

PubMed Central

Hundreds of candidate 14-3-3-binding (phospho)proteins have been reported in publications that describe one interaction at a time, as well as high-throughput 14-3-3-affinity and mass spectrometry-based studies. Here, we transcribed these data into a common format, deposited the collated data from low-throughput studies in MINT (http://mint.bio.uniroma2.it/mint), and compared the low- and high-throughput data in VisANT graphs that are easy to analyze and extend. Exploring the graphs prompted questions about technical and biological specificity, which were addressed experimentally, resulting in identification of phosphorylated 14-3-3-binding sites in the mitochondrial import sequence of the iron-sulfur cluster assembly enzyme (ISCU), cytoplasmic domains of the mitochondrial fission factor (MFF), and endoplasmic reticulum-tethered receptor expression-enhancing protein 4 (REEP4), RNA regulator SMAUG2, and cytoskeletal regulatory proteins, namely debrin-like protein (DBNL) and kinesin light chain (KLC) isoforms. Therefore, 14-3-3s undergo physiological interactions with proteins that are destined for diverse subcellular locations. Graphing and validating interactions underpins efforts to use 14-3-3-phosphoproteomics to identify mechanisms and biomarkers for signaling pathways in health and disease.

Johnson, Catherine; Tinti, Michele; Wood, Nicola T.; Campbell, David G.; Toth, Rachel; Dubois, Fanny; Geraghty, Kathryn M.; Wong, Barry H. C.; Brown, Laura J.; Tyler, Jennifer; Gernez, Aurelie; Chen, Shuai; Synowsky, Silvia; MacKintosh, Carol

2011-01-01

196

Phosphoproteomics identifies driver tyrosine kinases in sarcoma cell lines and tumors.  

PubMed

Driver tyrosine kinase mutations are rare in sarcomas, and patterns of tyrosine phosphorylation are poorly understood. To better understand the signaling pathways active in sarcoma, we examined global tyrosine phosphorylation in sarcoma cell lines and human tumor samples. Anti-phosphotyrosine antibodies were used to purify tyrosine phosphorylated peptides, which were then identified by liquid chromatography and tandem mass spectrometry. The findings were validated with RNA interference, rescue, and small-molecule tyrosine kinase inhibitors. We identified 1,936 unique tyrosine phosphorylated peptides, corresponding to 844 unique phosphotyrosine proteins. In sarcoma cells alone, peptides corresponding to 39 tyrosine kinases were found. Four of 10 cell lines showed dependence on tyrosine kinases for growth and/or survival, including platelet-derived growth factor receptor (PDGFR)?, MET, insulin receptor/insulin-like growth factor receptor signaling, and SRC family kinase signaling. Rhabdomyosarcoma samples showed overexpression of PDGFR? in 13% of examined cases, and sarcomas showed abundant tyrosine phosphorylation and expression of a number of tyrosine phosphorylated tyrosine kinases, including DDR2, EphB4, TYR2, AXL, SRC, LYN, and FAK. Together, our findings suggest that integrating global phosphoproteomics with functional analyses with kinase inhibitors can identify drivers of sarcoma growth and survival. PMID:22461510

Bai, Yun; Li, Jiannong; Fang, Bin; Edwards, Arthur; Zhang, Guolin; Bui, Marilyn; Eschrich, Steven; Altiok, Soner; Koomen, John; Haura, Eric B

2012-05-15

197

Rapid combinatorial ERLIC-SCX solid-phase extraction for in-depth phosphoproteome analysis.  

PubMed

Protein phosphorylation is an important mechanism of cellular signaling, and many proteins are precisely regulated through the interplay of stimulatory and inhibitory phosphorylation sites. Phosphoproteomics offers great opportunities to unravel this complex interplay, generating a mechanistic understanding of vital cellular processes. However, protein phosphorylation is substoichiometric and, in particular, peptides carrying multiple phosphorylation sites are extremely difficult to detect in a highly complex mixture of abundant nonphosphorylated peptides. Chromatographic methods are employed to reduce sample complexity and thereby significantly increase the number of phosphopeptide identifications. We previously demonstrated that combinatorial strong cation exchange-electrostatic repulsion-hydrophilic interaction chromatography yields a surplus in overall identifications of phosphopeptides compared with single chromatographic approaches. Here we present a simple and rapid strategy implemented as solid-phase extraction not requiring specific instrumentation such as off-line HPLC systems. It is inexpensive, adaptable for high and low amounts of starting material, and saves time by allowing multiplexed sample preparation without any carry-over problem. PMID:24144214

Zarei, Mostafa; Sprenger, Adrian; Gretzmeier, Christine; Dengjel, Joern

2013-12-01

198

Phosphoproteomic analysis of cells treated with longevity-related autophagy inducers.  

PubMed

Macroautophagy is a self-cannibalistic process that enables cells to adapt to various stresses and maintain energy homeostasis. Additionally, autophagy is an important route for turnover of misfolded proteins and damaged organelles, with important implications in cancer, neurodegenerative diseases and aging. Resveratrol and spermidine are able to induce autophagy by affecting deacetylases and acetylases, respectively, and have been found to extend the life-span of model organisms. With the aim to reveal the signaling networks involved in this drug-induced autophagic response, we quantified resveratrol and spermidine-induced changes in the phosphoproteome using SILAC and mass spectrometry. The data were subsequently analyzed using the NetworKIN algorithm to extract key features of the autophagy-responsive kinase-substrate network. We found that two distinct sequence motifs were highly responsive to resveratrol and spermidine and that key proteins modulating the acetylation, phosphorylation, methylation and ubiquitination status were affected by changes in phosphorylation during the autophagic response. Essential parts of the apoptotic signaling network were subjected to post-translational modifications during the drug-induced autophagy response, suggesting potential crosstalk and balancing between autophagy and apoptosis. Additionally, we predicted cellular signaling networks affected by resveratrol and spermidine using a computational framework. Altogether, these results point to a profound crosstalk between distinct networks of post-translational modifications and provide a resource for future analysis of autophagy and cell death. PMID:22517431

Bennetzen, Martin V; Mariño, Guillermo; Pultz, Dennis; Morselli, Eugenia; Færgeman, Nils J; Kroemer, Guido; Andersen, Jens S

2012-05-01

199

Phosphoproteomic dynamics of chickpea (Cicer arietinum L.) reveals shared and distinct components of dehydration response.  

PubMed

Reversible protein phosphorylation is a ubiquitous regulatory mechanism that plays critical roles in transducing stress signals to bring about coordinated intracellular responses. To gain better understanding of dehydration response in plants, we have developed a differential phosphoproteome in a food legume, chickpea (Cicer arietinum L.). Three-week-old chickpea seedlings were subjected to progressive dehydration by withdrawing water, and the changes in the phosphorylation status of a large repertoire of proteins were monitored. The proteins were resolved by 2-DE and stained with phosphospecific fluorescent Pro-Q Diamond dye. Mass spectrometric analysis led to the identification of 91 putative phosphoproteins, presumably involved in a variety of functions including cell defense and rescue, photosynthesis and photorespiration, molecular chaperones, and ion transport, among others. Multiple sites of phosphorylation were predicted on several key elements, which include both the regulatory as well as the functional proteins. A critical survey of the phosphorylome revealed a DREPP (developmentally regulated plasma membrane protein) plasma membrane polypeptide family protein, henceforth designated CaDREPP1. The transcripts of CaDREPP1 were found to be differentially regulated under dehydration stress, further corroborating the proteomic results. This work provides new insights into the possible phosphorylation events triggered by the conditions of progressive water-deficit in plants. PMID:24083463

Subba, Pratigya; Barua, Pragya; Kumar, Rajiv; Datta, Asis; Soni, Kamlesh Kumar; Chakraborty, Subhra; Chakraborty, Niranjan

2013-11-01

200

Phosphoproteomics Identifies Oncogenic Ras Signaling Targets and Their Involvement in Lung Adenocarcinomas  

PubMed Central

Background Ras is frequently mutated in a variety of human cancers, including lung cancer, leading to constitutive activation of MAPK signaling. Despite decades of research focused on the Ras oncogene, Ras-targeted phosphorylation events and signaling pathways have not been described on a proteome-wide scale. Methodology/Principal Findings By functional phosphoproteomics, we studied the molecular mechanics of oncogenic Ras signaling using a pathway-based approach. We identified Ras-regulated phosphorylation events (n?=?77) using label-free comparative proteomics analysis of immortalized human bronchial epithelial cells with and without the expression of oncogenic Ras. Many were newly identified as potential targets of the Ras signaling pathway. A majority (?60%) of the Ras-targeted events consisted of a [pSer/Thr]-Pro motif, indicating the involvement of proline-directed kinases. By integrating the phosphorylated signatures into the Pathway Interaction Database, we further inferred Ras-regulated pathways, including MAPK signaling and other novel cascades, in governing diverse functions such as gene expression, apoptosis, cell growth, and RNA processing. Comparisons of Ras-regulated phosphorylation events, pathways, and related kinases in lung cancer-derived cells supported a role of oncogenic Ras signaling in lung adenocarcinoma A549 and H322 cells, but not in large cell carcinoma H1299 cells. Conclusions/Significance This study reveals phosphorylation events, signaling networks, and molecular functions that are regulated by oncogenic Ras. The results observed in this study may aid to extend our knowledge on Ras signaling in lung cancer.

Sudhir, Putty-Reddy; Hsu, Chia-Lang; Wang, Mei-Jung; Wang, Yi-Ting; Chen, Yu-Ju; Sung, Ting-Yi; Hsu, Wen-Lian; Yang, Ueng-Cheng; Chen, Jeou-Yuan

2011-01-01

201

A solid phase extraction-based platform for rapid phosphoproteomic analysis  

PubMed Central

Protein phosphorylation is among the most common and intensely studied post-translational protein modification. It plays crucial roles in virtually all cellular processes and has been implicated in numerous human diseases, including cancer. Traditional biochemical and genetic methods for identifying and monitoring sites of phosphorylation are laborious and slow and in recent years have largely been replaced by mass spectrometric analysis. Improved methods for phosphopeptide enrichment coupled with faster and more sensitive mass spectrometers have led to an explosion in the size of phosphoproteomic datasets. However, wider application of these methods is limited by equipment costs and the resultant high demand for instrument time as well as by a technology gap between biologists and mass spectrometrists. Here we describe a modified two-step enrichment strategy that employs lysC digestion and step elution from self-packed strong cation exchange (SCX) solid phase extraction (SPE) columns followed by immobilized metal ion affinity chromatography (IMAC) and LC-MS/MS analysis using a hybrid LTQ Orbitrap Velos mass spectrometer. The SCX procedure does not require an HPLC system, demands little expertise, and because multiple samples can be processed in parallel, can provide a large savings of time and labor. We demonstrate this method in conjunction with stable isotope labeling to quantify peptides harboring >8,000 unique phosphorylation sites in yeast in 12 hours of instrument analysis time and examine the impact of enzyme choice and instrument platform.

Dephoure, Noah; Gygi, Steven P.

2011-01-01

202

Towards the identification of late-embryogenic-abundant phosphoproteome in Arabidopsis by 2-DE and MS.  

PubMed

Late-embryogenesis-abundant (LEA) proteins accumulate as plant seeds desiccate and also in vegetative organs during periods of stress. They are predicted to play a role in plant stress tolerance. In the present study, we have initiated the characterization of phosphorylated LEA proteins present in the Arabidopsis seed, using a strategy that combines the thermostability (solubility upon heating) of many LEA-type proteins with the use of phosphoaffinity chromatography to obtain an enriched subpopulation of phosphoproteins. The specificity and efficiency of the procedure was assessed by alkaline phosphatase treatment and by a specific stain for phosphoproteins, in addition to the immunodetection of AtRab18, a phosphorylated LEA protein present in the mature dry seed. The phosphoproteins were identified by MS either by PMF using MALDI-TOF MS after 2-DE separation, or by peptide sequencing using both capillary LC MS/MS (LC muESI-ITMS/MS) and nanoLC coupled to nanoESI-MS/MS (LC-nanoESI-Q-TOF-MS/MS). Several LEA-type and storage-like proteins were identified as components of the phosphoproteome of the Arabidopsis seed. PMID:16511814

Irar, Sami; Oliveira, Eliandre; Pagès, Montserrat; Goday, Adela

2006-04-01

203

Dissection of Floral Pollination Syndromes in Petunia  

PubMed Central

Animal-mediated pollination is essential in the reproductive biology of many flowering plants and tends to be associated with pollination syndromes, sets of floral traits that are adapted to particular groups of pollinators. The complexity and functional convergence of various traits within pollination syndromes are outstanding examples of biological adaptation, raising questions about their mechanisms and origins. In the genus Petunia, complex pollination syndromes are found for nocturnal hawkmoths (P. axillaris) and diurnal bees (P. integrifolia), with characteristic differences in petal color, corolla shape, reproductive organ morphology, nectar quantity, nectar quality, and fragrance. We dissected the Petunia syndromes into their most important phenotypic and genetic components. They appear to include several distinct differences, such as cell-growth and cell-division patterns in the basal third of the petals, elongation of the ventral stamens, nectar secretion and nectar sugar metabolism, and enzymatic differentiation in the phenylpropanoid pathway. In backcross-inbred lines of species-derived chromosome segments in a transposon tagging strain of P. hybrida, one to five quantitative trait loci were identified for each syndrome component. Two loci for stamen elongation and nectar volume were confirmed in introgression lines and showed large allelic differences. The combined data provide a framework for a detailed understanding of floral syndromes from their developmental and molecular basis to their impact on animal behavior. With its molecular genetic tools, this Petunia system provides a novel venue for a pattern of adaptive radiation that is among the most characteristic of flowering plants.

Stuurman, Jeroen; Hoballah, Maria Elena; Broger, Larissa; Moore, James; Basten, Christopher; Kuhlemeier, Cris

2004-01-01

204

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

PubMed Central

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.

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

205

Spontaneous Cervical Artery Dissection: The Borgess Classification  

PubMed Central

Background and Purpose: The pathogenesis of spontaneous cervical artery dissections (sCAD) and its best medical treatment are debated. This may be due to a lack of clear classification of sCAD. We propose the new Borgess classification of sCAD, based on the presence or absence of intimal tear as depicted on imaging studies and effect on blood flow. Materials and Methods: This is a single-center investigator-initiated registry on consecutive patients treated for sCAD. In the Borgess classification, type I dissections have intact intima and type II dissections have an intimal tear. Results: Forty-four patients and 52 dissected arteries were found. Forty-nine of 52 dissections (93%) were treated with dual anti-platelet therapy. Twenty-one of 52 dissections were type I; 31 were type II. Type I dissections were more likely to present with ischemic symptoms [stroke, transient ischemic attack (TIA)] (p?=?0.001). More type I dissections occurred in the vertebral artery, while more type II dissections occurred in the internal carotid artery (p?dissections were more likely to heal than type II (p?dissection types in the Borgess classification appear to relate to clinical presentation and rate of healing, making the classification useful in clinical management. Dual anti-platelet therapy for sCAD seems to have a very low risk of subsequent stroke; however, a large prospective study is needed to investigate the best treatment.

Al-Ali, Firas; Perry, Brandon C.

2013-01-01

206

Aortic arch dissection: a controversy of classification.  

PubMed

Aortic dissections originating in the ascending aorta and descending aorta have been classified as type A and type B dissections, respectively. However, dissections with intimal flap extension into the aortic arch between the innominate and left subclavian arteries are not accounted for adequately in the widely used Stanford classification. This gap has been the subject of controversy in the medical and surgical literature, and there is a tendency among many radiologists to categorize such arch dissections as type A lesions, thus making them an indication for surgery. However, the radiologic perspective is not supported by either standard dissection classification or current clinical management. In this special report, the origin of dissection classification and its evolution into current radiologic interpretation and surgical practice are reviewed. The cause for the widespread misconception about classification and treatment algorithms is identified. Institutional review board approval and waiver of informed consent were obtained as part of this HIPAA-compliant retrospective study to assess all aortic dissection studies performed at the University of Maryland Medical Center, Baltimore between 2010 and 2012 to determine the prevalence of arch dissections. Finally, a unified classification system that reconciles imaging interpretation and management implementation is proposed. © RSNA, 2014. PMID:24617732

Lempel, Jason K; Frazier, Aletta Ann; Jeudy, Jean; Kligerman, Seth J; Schultz, Randall; Ninalowo, Hammed A; Gozansky, Elliott K; Griffith, Bartley; White, Charles S

2014-06-01

207

Objecting To Dissection: A College Student's Handbook.  

ERIC Educational Resources Information Center

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…

National Anti-Vivisection Society, Chicago, IL.

208

Modeling the propagation of arterial dissection  

Microsoft Academic Search

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

T. Christian Gasser; Gerhard A. Holzapfel

2006-01-01

209

Beyond Dissection: Innovative Tools for Biology Education.  

ERIC Educational Resources Information Center

This catalog lists resources available for classroom use in teaching about anatomy and physiology which are alternatives to dissection. The entries are provided under three main categories: (1) Whole Animal Dissection/Vivisection; (2) Animal Organ or System Anatomy and Physiology; and (3) Other, including animal behavior, biotechnology,…

Larson, Sandra, Ed.

210

Virtual temporal bone dissection: a case study  

Microsoft Academic Search

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

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

2001-01-01

211

Quick Dissection of the Segmental Bronchi  

ERIC Educational Resources Information Center

Knowledge of the three-dimensional anatomy of the bronchopulmonary segments is essential for respiratory medicine. This report describes a quick guide for dissecting the segmental bronchi in formaldehyde-fixed human material. All segmental bronchi are easy to dissect, and thus, this exercise will help medical students to better understand the…

Nakajima, Yuji

2010-01-01

212

[Isolated dissection of the superior mesenteric artery].  

PubMed

Isolated spontaneous dissection of the superior mesenteric artery is uncommon. We report a case complicated by arterial rupture and discuss diagnostic imaging work-up. Diagnosis is usually made by conventional arteriography. But, dissection can also be diagnosed noninvasively by computed tomography angiography and ultrasound. PMID:12910178

Gomez, M-A; Tchokonte, M; Delhommais, A; Bretagnol, F; Bleuet, F; Besson, M; Roger, R; Alison, D

2003-06-01

213

Spontaneous bilateral internal carotid artery dissection  

PubMed Central

Spontaneous internal carotid artery dissection is not an uncommon cause of ischaemic stroke in younger patients, but multiple cervical arterial dissections at presentation are uncommon. Recurrence of dissection in a previously normal artery is common. In this case report we review the history, clinical findings and management of a 42-year-old woman who presented with stroke and Horner syndrome and was found to have spontaneous bilateral internal carotid artery dissection. She was not anticoagulated due to concerns relating to the size of her infarct. She was treated with a combination of aspirin and clopidogrel. We use dual antiplatelets for the management of cervical dissections as a part of the CADISS trial. The patient made good progress with the multidisciplinary team and was discharged on day 22 with support from the community stroke team.

Ardhalapudi, Srujan; Addy, Victoria; Da Costa, David

2009-01-01

214

The design and synthesis of a hydrophilic core-shell-shell structured magnetic metal-organic framework as a novel immobilized metal ion affinity platform for phosphoproteome research.  

PubMed

In this work, polydopamine (PDA)-coated magnetic microspheres with surface modification of zirconium-based MOFs were synthesized for the first time. The as-synthesized Fe3O4@PDA@Zr-MOF composites were successfully applied as a novel immobilized metal ion affinity platform for phosphoproteome research. PMID:24789051

Zhao, Man; Deng, Chunhui; Zhang, Xiangmin

2014-06-14

215

Use of 32P to Study Dynamics of the Mitochondrial Phosphoproteome  

PubMed Central

Protein phosphorylation is a well characterized regulatory mechanism in the cytosol, but remains poorly defined in the mitochondrion. In this study, we characterized the use of 32P-labeling to monitor the turnover of protein phosphorylation in the heart and liver mitochondria matrix. The 32P labeling technique was compared and contrasted to Phos-tag protein phosphorylation fluorescent stain and 2D isoelectric focusing. Of the 64 proteins identified by MS spectroscopy in the Phos-Tag gels, over 20 proteins were correlated with 32P labeling. The high sensitivity of 32P incorporation detected proteins well below the mass spectrometry and even 2D gel protein detection limits. Phosphate-chase experiments revealed both turnover and phosphate associated protein pool size alterations dependent on initial incubation conditions. Extensive weak phosphate/phosphate metabolite interactions were observed using non-disruptive native gels, providing a novel approach to screen for potential allosteric interactions of phosphate metabolites with matrix proteins. We confirmed the phosphate associations in Complexes V and I due to their critical role in oxidative phosphorylation and to validate the 2D methods. These complexes were isolated by immunocapture, after 32P labeling in the intact mitochondria, and revealed 32P-incorporation for the ?, ?, ?, OSCP, and d subunits in Complex V and the 75kDa, 51kDa, 42kDa, 23kDa, and 13a kDa subunits in Complex I. These results demonstrate that a dynamic and extensive mitochondrial matrix phosphoproteome exists in heart and liver.

Aponte, Angel M.; Phillips, Darci; Hopper, Rachel K.; Johnson, D. Thor; Harris, Robert A.; Blinova, Ksenia; Boja, Emily S.; French, Stephanie; Balaban, Robert S.

2009-01-01

216

Salt-Induced Changes in Cardiac Phosphoproteome in a Rat Model of Chronic Renal Failure  

PubMed Central

Heart damage is widely present in patients with chronic kidney disease. Salt diet is the most important environmental factor affecting development of chronic renal failure and cardiovascular diseases. The proteins involved in chronic kidney disease -induced heart damage, especially their posttranslational modifications, remain largely unknown to date. Sprague-Dawley rats underwent 5/6 nephrectomy (chronic renal failure model) or sham operation were treated for 2 weeks with a normal-(0.4% NaCl), or high-salt (4% NaCl) diet. We employed TiO2 enrichment, iTRAQ labeling and liquid-chromatography tandem mass spectrometry strategy for phosphoproteomic profiling of left ventricular free walls in these animals. A total of 1724 unique phosphopeptides representing 2551 non-redundant phosphorylation sites corresponding to 763 phosphoproteins were identified. During normal salt feeding, 89 (54%) phosphopeptides upregulated and 76 (46%) phosphopeptides downregulated in chronic renal failure rats relative to sham rats. In chronic renal failure rats, high salt intake induced upregulation of 84 (49%) phosphopeptides and downregulation of 88 (51%) phosphopeptides. Database searches revealed that most of the identified phospholproteins were important signaling molecules such as protein kinases, receptors and phosphatases. These phospholproteins were involved in energy metabolism, cell communication, cell differentiation, cell death and other biological processes. The Search Tool for the Retrieval of Interacting Genes analysis revealed functional links among 15 significantly regulated phosphoproteins in chronic renal failure rats compared to sham group, and 23 altered phosphoproteins induced by high salt intake. The altered phosphorylation levels of two proteins involved in heart damage, lamin A and phospholamban were validated. Expression of the downstream genes of these two proteins, desmin and SERCA2a, were also analyzed.

Su, Zhengxiu; Zhu, Hongguo; Zhang, Menghuan; Wang, Liangliang; He, Hanchang; Jiang, Shaoling; Hou, Fan Fan; Li, Aiqing

2014-01-01

217

Ultra-low flow electrospray ionization-mass spectrometry for improved ionization efficiency in phosphoproteomics.  

PubMed

The potential benefits of ultra-low flow electrospray ionization (ESI) for the analysis of phosphopeptides in proteomics was investigated. First, the relative flow dependent ionization efficiency of nonphosphorylated vs multiplyphosphorylated peptides was characterized by infusion of a five synthetic peptide mix with zero to four phophorylation sites at flow rates ranging from 4.5 to 500 nL/min. Most importantly, similar to what was found earlier by Schmidt et al., it has been verified that at flow rates below 20 nL/min the relative peak intensities for the various peptides show a trend toward an equimolar response, which would be highly beneficial in phosphoproteomic analysis. As the technology to achieve liquid chromatography separation at flow rates below 20 nL/min is not readily available, a sheathless capillary electrophoresis-electrospray ionization-mass spectrometry (CE-ESI-MS) strategy based on the use of a neutrally coated separation capillary was used to develop an analytical strategy at flow rates as low as 6.6 nL/min. An in-line preconcentration technique, namely, transient isotachophoresis (t-ITP), to achieve efficient separation while using larger volume injections (37% of capillary thus 250 nL) was incorporated to achieve even greater sample concentration sensitivities. The developed t-ITP-ESI-MS strategy was then used in a direct comparison with nano-LC-MS for the detection of phosphopeptides. The comparison showed significantly improved phosphopeptide sensitivity in equal sample load and equal sample concentration conditions for CE-MS while providing complementary data to LC-MS, demonstrating the potential of ultra-low flow ESI for the analysis of phosphopeptides in liquid based separation techniques. PMID:22494114

Heemskerk, Anthonius A M; Busnel, Jean-Marc; Schoenmaker, Bart; Derks, Rico J E; Klychnikov, Oleg; Hensbergen, Paul J; Deelder, André M; Mayboroda, Oleg A

2012-05-15

218

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

SciTech Connect

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.

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

219

Phosphoproteomic analysis of the non-seed vascular plant model Selaginella moellendorffii  

PubMed Central

Background Selaginella (Selaginella moellendorffii) is a lycophyte which diverged from other vascular plants approximately 410 million years ago. As the first reported non-seed vascular plant genome, Selaginella genome data allow comparative analysis of genetic changes that may be associated with land plant evolution. Proteomics investigations on this lycophyte model have not been extensively reported. Phosphorylation represents the most common post-translational modifications and it is a ubiquitous regulatory mechanism controlling the functional expression of proteins inside living organisms. Results In this study, polyethylene glycol fractionation and immobilized metal ion affinity chromatography were employed to isolate phosphopeptides from wild-growing Selaginella. Using liquid chromatography-tandem mass spectrometry analysis, 1593 unique phosphopeptides spanning 1104 non-redundant phosphosites with confirmed localization on 716 phosphoproteins were identified. Analysis of the Selaginella dataset revealed features that are consistent with other plant phosphoproteomes, such as the relative proportions of phosphorylated Ser, Thr, and Tyr residues, the highest occurrence of phosphosites in the C-terminal regions of proteins, and the localization of phosphorylation events outside protein domains. In addition, a total of 97 highly conserved phosphosites in evolutionary conserved proteins were identified, indicating the conservation of phosphorylation-dependent regulatory mechanisms in phylogenetically distinct plant species. On the other hand, close examination of proteins involved in photosynthesis revealed phosphorylation events which may be unique to Selaginella evolution. Furthermore, phosphorylation motif analyses identified Pro-directed, acidic, and basic signatures which are recognized by typical protein kinases in plants. A group of Selaginella-specific phosphoproteins were found to be enriched in the Pro-directed motif class. Conclusions Our work provides the first large-scale atlas of phosphoproteins in Selaginella which occupies a unique position in the evolution of terrestrial plants. Future research into the functional roles of Selaginella-specific phosphorylation events in photosynthesis and other processes may offer insight into the molecular mechanisms leading to the distinct evolution of lycophytes.

2014-01-01

220

Proteome and phosphoproteome analysis of starch granule-associated proteins from normal maize and mutants affected in starch biosynthesis  

PubMed Central

In addition to the exclusively granule-bound starch synthase GBSSI, starch granules also bind significant proportions of other starch biosynthetic enzymes, particularly starch synthases (SS) SSI and SSIIa, and starch branching enzyme (BE) BEIIb. Whether this association is a functional aspect of starch biosynthesis, or results from non-specific entrapment during amylopectin crystallization, is not known. This study utilized genetic, immunological, and proteomic approaches to investigate comprehensively the proteome and phosphoproteome of Zea mays endosperm starch granules. SSIII, BEI, BEIIa, and starch phosphorylase were identified as internal granule-associated proteins in maize endosperm, along with the previously identified proteins GBSS, SSI, SSIIa, and BEIIb. Genetic analyses revealed three instances in which granule association of one protein is affected by the absence of another biosynthetic enzyme. First, eliminating SSIIa caused reduced granule association of SSI and BEIIb, without affecting GBSS abundance. Second, eliminating SSIII caused the appearance of two distinct electrophoretic mobility forms of BEIIb, whereas only a single migration form of BEIIb was observed in wild type or any other mutant granules examined. Third, eliminating BEIIb caused significant increases in the abundance of BEI, BEIIa, SSIII, and starch phosphorylase in the granule, without affecting SSI or SSIIa. Analysis of the granule phosphoproteome with a phosphorylation-specific dye indicated that GBSS, BEIIb, and starch phosphorylase are all phosphorylated as they occur in the granule. These results suggest the possibility that starch metabolic enzymes located in granules are regulated by post-translational modification and/or protein–protein interactions.

Grimaud, Florent; Rogniaux, Helene; James, Martha G.; Myers, Alan M.; Planchot, Veronique

2008-01-01

221

Quantitative Phosphoproteomic Analysis Identifies Activation of the RET and IGF-1R/IR Signaling Pathways in Neuroblastoma  

PubMed Central

Neuroblastoma is an embryonal tumor of childhood with a heterogenous clinical presentation that reflects differences in activation of complex biological signaling pathways. Protein phosphorylation is a key component of cellular signal transduction and plays a critical role in processes that control cancer cell growth and survival. We used shotgun LC/MS to compare phosphorylation between a human MYCN amplified neuroblastoma cell line (NB10), modeling a resistant tumor, and a human neural precursor cell line (NPC), modeling a normal baseline neural crest cell. 2181 unique phosphorylation sites representing 1171 proteins and 2598 phosphopeptides were found. Protein kinases accounted for 6% of the proteome, with a predominance of tyrosine kinases, supporting their prominent role in oncogenic signaling pathways. Highly abundant receptor tyrosine kinase (RTK) phosphopeptides in the NB10 cell line relative to the NPC cell line included RET, insulin-like growth factor 1 receptor/insulin receptor (IGF-1R/IR), and fibroblast growth factor receptor 1 (FGFR1). Multiple phosphorylated peptides from downstream mediators of the PI3K/AKT/mTOR and RAS pathways were also highly abundant in NB10 relative to NPC. Our analysis highlights the importance of RET, IGF-1R/IR and FGFR1 as RTKs in neuroblastoma and suggests a methodology that can be used to identify potential novel biological therapeutic targets. Furthermore, application of this previously unexploited technology in the clinic opens the possibility of providing a new wide-scale molecular signature to assess disease progression and prognosis.

DeNardo, Bradley D.; Holloway, Michael P.; Ji, Qinqin; Nguyen, Kevin T.; Cheng, Yan; Valentine, Marcus B.; Salomon, Arthur; Altura, Rachel A.

2013-01-01

222

Isolated dissection of superior mesenteric artery.  

PubMed

Isolated dissection of the superior mesenteric artery is a rare occurrence with a hitherto unknown exact etiology. Patients may present with abdominal symptoms or hemodynamic instability.We herein present a case of spontaneous isolated superior mesenteric artery dissection in a 48-year-old man, who was admitted with epigastric pain. Due to an undiagnosed paced rhythm on the electrocardiogram, he was given fibrinolysis treatment for acute myocardial infarction. On further evaluation, angiography revealed that the cause of pain was the dissection of the superior mesenteric artery. The patient's symptoms were diminished with conservative management, obviating the need for the angioplasty of the superior mesenteric artery. PMID:23304184

Taherkhani, Maryam; Hashemi, Seyyed Reza; Nikpoor, Shahryar

2012-08-01

223

Isolated Dissection of Superior Mesenteric Artery  

PubMed Central

Isolated dissection of the superior mesenteric artery is a rare occurrence with a hitherto unknown exact etiology. Patients may present with abdominal symptoms or hemodynamic instability. We herein present a case of spontaneous isolated superior mesenteric artery dissection in a 48-year-old man, who was admitted with epigastric pain. Due to an undiagnosed paced rhythm on the electrocardiogram, he was given fibrinolysis treatment for acute myocardial infarction. On further evaluation, angiography revealed that the cause of pain was the dissection of the superior mesenteric artery. The patient’s symptoms were diminished with conservative management, obviating the need for the angioplasty of the superior mesenteric artery.

Taherkhani, Maryam; Hashemi, Seyyed Reza; Nikpoor, Shahryar

2012-01-01

224

Training in endoscopic submucosal dissection.  

PubMed

Endoscopic submucosal dissection (ESD) represents an important advancement in the therapy of early neoplastic gastrointestinal lesions by providing higher en-bloc curative resection rate with lower recurrence compared to endoscopic mucosal resection (EMR) and by sparing the involved organ and protecting patient's quality of life. Despite these advantages ESD is associated with long procedure times and a higher rate of complications, making ESD a challenging procedure which requires advanced endoscopic skills. Thus, there has been a recognized need for structured training system for ESD to enhance trainee experience and, to reduce the risks of complications and inadequate treatment. ESD has a very flat learning curve. However, we do not have uniformly accepted benchmarks for competency. Nevertheless, it appears that, in Japan, more than 30 supervised gastric ESD procedures are required to achieve technical proficiency and minimize complications. A number of training algorithms have been proposed in Japan with the aim to standardize ESD training. These algorithms cannot be directly applied in the West due to substantial differences including the availability of highly qualified mentors, the type of pathology seen, choice of devices, and trainee's background. We propose a training algorithm for Western physicians which integrates both hands-on training courses, animal model work as well as visits to expert centers. No specific preceptor training programs have been yet developed but there is a consensus that these programs are important for permeation of ESD worldwide. PMID:23951392

Coman, Roxana M; Gotoda, Takuji; Draganov, Peter V

2013-08-16

225

A New Idea for Dissecting Tray  

ERIC Educational Resources Information Center

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)

Branham, Arthur

1976-01-01

226

Animal Rights Groups Target High School Dissection.  

ERIC Educational Resources Information Center

Two groups leading the charge against dissection are People for the Ethical Treatment of Animals (PETA) and the Student Action Corps for Animals (SACA). Protests by student and community members remain the movement's strongest weapon. (MLF)

Trotter, Andrew

1992-01-01

227

Eyelid lymphedema following neck dissection and radiotherapy.  

PubMed

Chronic eyelid lymphedema following neck dissection and radiotherapy is rare with 1 report in the literature. The authors report 3 cases and review the literature. Two cases had bilateral neck dissection and developed bilateral eyelid lymphedema and 1 case had unilateral neck dissection (left side) and developed ipsilateral lymphedema. Two patients underwent surgical debulking of lymphedema with significant improvement in symptoms. One patient declined surgical intervention, and the lymphedema remained unchanged. Chronic eyelid lymphedema following neck dissection and radiotherapy occurs where predominant lymphatic drainage to the submandibular and deep cervical lymph node basin is removed. Lymphedema tends to persist when it occurs and in selected cases appearance can be effectively improved by debulking and excision of festoons. PMID:23446298

Sagili, Suresh; Selva, Dinesh; Malhotra, Raman

2013-01-01

228

Incomplete nested dissection for solving n by n grid problems  

NASA Technical Reports Server (NTRS)

Nested dissection orderings are known to be very effective for solving sparse positive definite linear systems which arise from n by n grid problems. In this paper we consider incomplete nested dissection, an ordering which corresponds to the premature termination of nested dissection. Analyses of the arithmetic and storage requirements for incomplete nested dissection are given and the ordering is shown to be competitive with nested dissection with regard to arithmetic operations and superior to that ordering in storage requirements.

George, A.; Poole, W. G., Jr.; Voigt, R. G.

1978-01-01

229

The Phosphoproteomes of Plasmodium falciparum and Toxoplasma gondii reveal unusual adaptations within and beyond the parasites' boundaries  

PubMed Central

Summary Plasmodium falciparum and Toxoplasma gondii are obligate intracellular apicomplexan parasites that rapidly invade and extensively modify host cells. Protein phosphorylation is one mechanism by which these parasites can control such processes. Here we present a phosphoproteome analysis of peptides enriched from schizont stage P. falciparum and T. gondii tachyzoites that are either “intracellular” or purified away from host material. Using liquid chromatography and tandem mass-spectrometry we identified over 5,000 and 10,000 previously unknown phosphorylation sites in P. falciparum and T. gondii respectively, revealing that protein phosphorylation is an extensively used regulation mechanism both within and beyond parasite boundaries. Unexpectedly both parasites have phosphorylated tyrosines and P. falciparum has unusual phosphorylation motifs that are apparently shaped by its A:T-rich genome. This dataset provides important information on the role of phosphorylation in the host-pathogen interaction, and clues to the evolutionary forces operating on protein phosphorylation motifs in both parasites.

Treeck, Moritz; Sanders, John L.; Elias, Joshua E.; Boothroyd, John C.

2012-01-01

230

Student injuries in the dissecting room.  

PubMed

Cadaver dissection is the first opportunity for many students to practice handling human tissue and is their first exposure to the occupational hazards involved with this task. Few studies examine dissection room injuries to ascertain the dangers associated with dissecting. We performed a retrospective cohort analysis of dissection room injuries from four student cohorts over an eleven-year period (2001-2011), including second-year medical students, third-year medical students, second-year dental students, and third-year science students. Injury data included activity causing injury, object responsible, and injury site. A total of 163 injuries during 70,039 hours of dissection were recorded, with 66 in third-year medical students, 42 in second-year medical students, 36 in third-year science students, and 16 in second-year dental students. The overall rate was 2.87 injuries per 1,000 dissection hours, with second-year medical students most frequently injured (5.5 injuries per 1,000 hours); third-year medical students were least frequently injured (1.3 injuries per 1,000 hours). A significant difference in injury rates between student groups indicated a higher than expected injury rate to second-year medical students and lower than expected rates to third-year medical students. Injury rates increased for most groups between 2001-2006 and 2007-2011 periods. Most injuries (79%) were from scalpel cuts to the finger or thumb. This study provides injury rates for dissection room injuries to students, indicating differences in injury frequency between cohorts and an increase in injury rate over time. As scalpel cuts were the most likely injury mechanism, targeting scalpel handling with preventative strategies may reduce future injury risk. PMID:23536433

Cornwall, Jon; Davies, Tilman M; Lees, David

2013-01-01

231

Science Teachers and the Dissection Debate: Perspectives on Animal Dissection and Alternatives  

ERIC Educational Resources Information Center

This study investigated Ontario science and biology teachers' practices and attitudes toward animal dissection and dissection alternatives. The data was collected through a mixed methods approach involving online surveys (n = 153) and subsequent telephone interviews (n = 9) with secondary school science and biology teachers. The findings indicate…

Oakley, Jan

2012-01-01

232

Proteome and Phosphoproteome Characterization Reveals New Response and Defense Mechanisms of Brachypodium distachyon Leaves under Salt Stress*  

PubMed Central

Salinity is a major abiotic stress affecting plant growth and development. Understanding the molecular mechanisms of salt response and defense in plants will help in efforts to improve the salt tolerance of crops. Brachypodium distachyon is a new model plant for wheat, barley, and several potential biofuel grasses. In the current study, proteome and phosphoproteome changes induced by salt stress were the focus. The Bd21 leaves were initially treated with salt in concentrations ranging from 80 to 320 mm and then underwent a recovery process prior to proteome analysis. A total of 80 differentially expressed protein spots corresponding to 60 unique proteins were identified. The sample treated with a median salt level of 240 mm and the control were selected for phosphopeptide purification using TiO2 microcolumns and LC-MS/MS for phosphoproteome analysis to identify the phosphorylation sites and phosphoproteins. A total of 1509 phosphoproteins and 2839 phosphorylation sites were identified. Among them, 468 phosphoproteins containing 496 phosphorylation sites demonstrated significant changes at the phosphorylation level. Nine phosphorylation motifs were extracted from the 496 phosphorylation sites. Of the 60 unique differentially expressed proteins, 14 were also identified as phosphoproteins. Many proteins and phosphoproteins, as well as potential signal pathways associated with salt response and defense, were found, including three 14-3-3s (GF14A, GF14B, and 14-3-3A) for signal transduction and several ABA signal-associated proteins such as ABF2, TRAB1, and SAPK8. Finally, a schematic salt response and defense mechanism in B. distachyon was proposed.

Lv, Dong-Wen; Subburaj, Saminathan; Cao, Min; Yan, Xing; Li, Xiaohui; Appels, Rudi; Sun, Dong-Fa; Ma, Wujun; Yan, Yue-Ming

2014-01-01

233

Dynamic changes in ribosome-associated proteome and phosphoproteome during deoxynivalenol-induced translation inhibition and ribotoxic stress.  

PubMed

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 (? 30 min) 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 (250 ng/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

Pan, Xiao; Whitten, Douglas A; Wilkerson, Curtis G; Pestka, James J

2014-03-01

234

Dissecting aneurysm of the hepatic artery caused by an isolated spontaneous celiac trunk dissection.  

PubMed

Dissecting hepatic artery aneurysm caused by an isolated spontaneous celiac artery dissection is a life-threatening condition with only 5 cases reported previously. We report a successful resection and revascularization of all affected arteries with an inferior mesenteric vein graft in a 59-year-old asymptomatic man with a large dissecting common and proper hepatic artery aneurysm (diameter, 4.2 cm) due to a spontaneous dissection from the celiac trunk to the proximal splenic artery and the right hepatic artery. Our case suggests that intervention should not be delayed in cases of hepatic aneurysm and a long dissection extending to the proper hepatic artery because of the difficulty in restoring hepatic circulation and preventing rupture. PMID:24365084

Higashiyama, Hiroshi; Ishii, Masayuki; Fujimoto, Koji; Oka, Yurika; Uehara, Tetsuya; Kumada, Kaoru; Yamamoto, Masayuki

2014-07-01

235

Recurrent cotyledonoid dissecting leiomyoma of the uterus.  

PubMed

Cotyledonoid dissecting leiomyoma is a benign smooth muscle neoplasm with an unusual growth pattern that is characterized by intramural dissection within the uterine corpus and often a placental-like appearance macroscopically in its extrauterine component that may be alarming to the surgeon. All cases reported to date have been nonaggressive. We report a case in a 33-yr-old woman who had a history of prolonged uterine bleeding. She was operated upon for uterine leiomyomas, and the diagnosis of cotyledonoid dissecting leiomyoma was made at the time of intraoperative consultation. To maintain fertility, the intrauterine tumor was resected by myomectomy and the extrauterine tumor by excision. However, persistent uterine bleeding that eventually became intractable and continued growth of the neoplasm in the uterus necessitated hysterectomy 5 yr later. She was living and well 2.5 yr after hysterectomy with no evidence of disease. PMID:23370645

Roth, Lawrence Max; Kirker, James A; Insull, Mark; Whittaker, John

2013-03-01

236

[Minocycline sclerotherapy for lymphorrhea following neck dissection].  

PubMed

Postoperative cervical lymphorrhea is a complication uncommonly encountered following neck dissection for which several treatment modalities have been described in the literature. We managed 8 cases of lymphorrhea after neck dissection by injecting Minocycline through a drainage tube. We attempted this procedure for lymph discharge that had continued despite pressure dressing and systemic management with nutritional modification for about 1 week. This treatment rapidly resolved lymph discharge in 6 of the 8 cases. No patient required surgical intervention. Minocycline sclerotherapy has typically been used to treat pleural effusion, ascites, pneumothorax, and other cystic diseases of the liver, pancreas, and kidney. In many cases, this therapy brings rapid resolution. This inefficiency is due to the acidity and toxicity of Minocycline. No major adverse effects have been reported. We believe that Minocycline sclerotherapy is effective for rapidly resolving lymphorrhea following neck dissection and use of this therapy should be attempted before surgical intervention. PMID:12692958

Koda, Hiroko; Gotsu, Kazuo; Sugimoto, Taro; Ishikawa, Norihiko; Kishimoto, Seiji

2003-02-01

237

Spontaneous celiac artery dissection and its management.  

PubMed

Spontaneous visceral artery dissection is an uncommon event with an unpredictable natural history with superior mesenteric artery being the most common affected artery. It is most often asymptomatic and usually diagnosed at autopsy. Pre-disposing factors are not specific but have been suggested to be pre-existing vascular disease, hypertension and pregnancy. Spontaneous resolution, definitive occlusion of the artery, and formation of an aneurysm with associated complications are some other possible outcomes. Isolated dissection of the celiac artery (CA) is rare and there are only a few cases reported in the literature. We present a case of a 65 year old male with spontaneous celiac artery dissection and provide a review of the current literature about imaging findings and management of this entity. PMID:22470724

Vaidya, Sandeep; Dighe, Manjiri

2010-01-01

238

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

PubMed Central

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.

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

2012-01-01

239

The nature of dissection: Exploring student conceptions  

NASA Astrophysics Data System (ADS)

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.

York, Katharine

240

[An efficient way in mouse brain dissection].  

PubMed

Laboratory mice are common experimental animals in biological, medical, pharmacological and psychological researches primarily because they are easy to maintain and reproduce quickly. The protection of the welfare of experimental animals is gaining greater attention during the application of a large number of mice. It's therefore essential to consider how to reduce the unnecessary use of animals and fully exploit each experimental animal. We report, in this article, an efficient way to dissect various brain regions from a mouse for protein immunoblot and/or neuronal culture, providing technical reference information for minimizing the number of animals used in projects, and refining methods and procedures to quick brain dissection. PMID:24777412

Wang, Jin-Zhao; Long, Cheng; Yang, Li

2014-04-25

241

Genetic dissection of ``OLETF'', a rat model for non-insulin-dependent diabetes mellitus  

Microsoft Academic Search

.   To elucidate the genetic factors underlying non-insulin-dependent diabetes mellitus (NIDDM), we performed genome-wide quantitative\\u000a trait locus (QTL) analysis, using the Otsuka Long-Evans Tokushima Fatty (OLETF) rat. The OLETF rat is an excellent animal\\u000a model of NIDDM because the features of the disease closely resemble human NIDDM. Genetic dissection with two kinds of F2 intercross\\u000a progeny, from matings between the

Naohide Kanemoto; Haretsugu Hishigaki; Ayako Miyakita; Keiko Oga; Shiro Okuno; Atsushi Tsuji; Toshihisa Takagi; Ei-ichi Takahashi; Yusuke Nakamura; Takeshi K. Watanabe

1998-01-01

242

Stenting for vertebrobasilar dissection: a possible treatment option for nonhemorrhagic vertebrobasilar dissection  

Microsoft Academic Search

Introduction  It has been reported that stent placement may improve compromised blood flow resulting from vertebrobasilar dissection. In\\u000a this study the technical feasibility, safety, as well as short-term outcome of stent placement for the treatment of nonhemorrhagic\\u000a vertebrobasilar dissection was retrospectively investigated.\\u000a \\u000a \\u000a \\u000a Methods  Ten patients (eight men, two women; age range 36 to 45 years) with nonhemorrhagic vertebrobasilar dissection were treated\\u000a by stenting.

Yong Sam Shin; Ho Sung Kim; Sun Yong Kim

2007-01-01

243

In vitro atherosclerotic plaque and calcium quantitation by intravascular ultrasound and electron-beam computed tomography  

Microsoft Academic Search

The purpose of this investigation was to compare the accuracy of intravascular ultrasound (IVUS) and electron-beam computed tomography (EBCT) in quantitating human atherosclerotic plaque and calcium. In experiment 1, 12 human atherosclerotic arterial segments were obtained at autopsy and imaged by using IVUS and EBCT. The plaque from each arterial segment was dissected and a volume measurement of the dissected

Dan E. Gutfinger; Cyril Y. Leung; Takafumi Hiro; Bavani Maheswaran; Shigeru Nakamura; Robert Detrano; Xingping Kang; Weiyi Tang; Jonathan M. Tobis

1996-01-01

244

Do frogs have to croak? Comparing academic performance of students in traditional dissection labs on campus with students using virtual simulations via distance education  

Microsoft Academic Search

This quantitative study was designed to determine whether there were any significant differences in students and their understanding of animal anatomy and basic physiology in introductory biology and anatomy courses when instructed using self-directed, virtual simulation dissections in a distance-learning format rather than by teacher-directed, hands-on dissections in traditional on-campus classes. Two different courses at Snead State Community College, a

Susie Annette Humphries

2007-01-01

245

Acute dissecting aortic aneurysm: community hospital experience in 20 cases.  

PubMed

Of 20 patients with dissecting aortic aneurysm managed at our community hospital, 16 had type A (ascending) dissection and four had type B (descending) dissection. Twelve of the patients with type A dissection were operated on; six of them survived and six died postoperatively. The remaining four patients with type A dissection had cardiopulmonary arrest and died before surgical intervention was attempted. All four patients with type B dissection were treated medically and all survived. Although acute aortic dissection is not commonly seen at community hospitals, expedient management of such patients can have a major impact on their survival. Patients at extreme risk are those with type A dissection, particularly those with cardiopulmonary arrest. PMID:2371604

Salem, B I; Selke, K; Gowda, S; Haikal, M; Coordes, C; Leidenfrost, R

1990-07-01

246

Conservative Management of Chronic Aortic Dissection with Underlying Aortic Aneurysm  

PubMed Central

Aortic dissection is one of the most common aortic emergencies affecting around 2000 Americans each year. It usually presents in the acute state but in a small percentage of patients aortic dissections go unnoticed and these patients survive without any adequate therapy. With recent advances in medical care and diagnostic technologies, aortic dissection can be successfully managed through surgical or medical options, consequently increasing the related survival rate. However, little is known about the optimal long-term management of patients suffering from chronic aortic dissection. The purpose of the present report is to review aortic dissection, namely its pathology and the current diagnostic tools available, and to discuss the management options for chronic aortic dissection. We report a patient in which chronic aortic dissection presented with recurring episodes of vomiting and also discuss the management plan of our patient who had a chronic aortic dissection as well as an underlying aortic aneurysm.

Yusuf Beebeejaun, Mohammad; Malec, Aleksandra; Gupta, Ravi

2013-01-01

247

Genetics Home Reference: Familial thoracic aortic aneurysm and dissection  

MedlinePLUS

... literature OMIM Genetic disorder catalog Conditions > Familial thoracic aortic aneurysm and dissection (often shortened to familial TAAD ) On ... February 2011 What is familial TAAD? Familial thoracic aortic aneurysm and dissection (familial TAAD) is a disorder that ...

248

Carotid artery dissection causing hypoglossal nerve palsy  

PubMed Central

A 45-year-old man was admitted with a 4 day history of right facial pain and on examination, there was atrophy of the right side of the tongue. Magnetic resonance angiography demonstrated carotid artery dissection and aspirin was commenced.

Epstein, Elliot; Khan, Muhammed Azeem; Francis, David; Sada, Priyo; Thuse, Makarand

2012-01-01

249

Pythagoras and the Dissection of Polygons.  

ERIC Educational Resources Information Center

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)

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

1984-01-01

250

[Arteriovenous dissection for branch retinal vein occlusion].  

PubMed

Arteriovenous dissection (AVD) is a surgical maneuver to separate the retinal artery and vein at the crossing site in patients with branch retinal vein occlusion (BRVO). The published studies showed an evidence level 3. AVD seems to be maintainable in patients with recent onset of BRVO and decimal visual acuity < or =0.4. PMID:18317778

Feltgen, N; Hattenbach, L-O; Mirshahi, A; Hansen, L

2008-04-01

251

Microvascular Reconstruction After Previous Neck Dissection  

Microsoft Academic Search

Background: Microvascular reconstruction of defects in the head and neck is more challenging in patients who have undergone a previous neck dissection, owing to prior resection of potential cervical recipient blood vessels used for free flap perfusion. Objective: To evaluate the reliability and safety of free flap reconstruction in patients with previous neck dis- section. Patients and Methods: Sixty free

Christian Head; Joel A. Sercarz; Elliot Abemayor; Thomas C. Calcaterra; Jeffrey D. Rawnsley; Keith E. Blackwell

2002-01-01

252

Spontaneous isolated dissection of the abdominal aorta.  

PubMed

Isolated spontaneous dissection of the abdominal aorta is such a rare entity and there are only a few cases reported in literature up to date. A 42-year old male was admitted to the hospital with mild pain in the lower abdomen and back that had began seven days prior to admission together with the sudden onset of the ischemic symptoms of the left leg (ischemic ulcers of the calf gangrenous toe and pallor foot). Patient denied any trauma, hypertension history was negative, while he was active cigarette smoker. MSCT and digital subtracted angiography have shown a dissection of the abdominal aorta approximately two centimeters below the origin of the inferior mesenteric artery extending in the left common iliac artery, with no sign of the aneurysmatic dilatation of the abdominal aorta. Emergent surgery was performed with aorto-biiliacal bypass graft interposition, amputation of the left toe and necrectomy of the left calf Postoperative follow up and local vascular condition were satisfied. Even though is rare entity, isolated abdominal aorta dissection accounts for approximately 2-4% of all aortic dissection. Nowadays therapeutic regimen includes endovascular, open surgery or conservative treatment. PMID:24611358

Ivkosi?, Ante; Budincevi?, Hrvoje; Krstonijevi?, Zoran; Bari?, Marko; Lojo, Nermin; Trajbar, Dubravka; Gorski, Dinko; Suknai?, Slaven; Suci?, Tena

2013-12-01

253

Squid Dissection: From Pen to Ink.  

ERIC Educational Resources Information Center

Introduces students to dissection, which is an important part of scientific discovery. Students not only gain an understanding of the anatomy of a squid, but also develop a sense of responsibility and respect for the animal that they are using as a learning tool. (Author/SOE)

Brown, Cindy; Kisiel, Jim

2003-01-01

254

Postpartum Four-Vessel Cervical Artery Dissection  

PubMed Central

A postpartum four-vessel cervical artery dissection with no stroke is reported. This transient vasculopathy took place in the autoimmune context of the HELLP syndrome combined with the reversible posterior leucoencephalopathy syndrome. Correlations between the clinical, radiological and biological entities are discussed.

Barroso, Bruno; Demasles, Stephanie

2013-01-01

255

Cow's Eye Dissection in the Physics Lab.  

ERIC Educational Resources Information Center

Proposes the science demonstration of dissecting a cow's eye to integrate biology and physics in the study of optics and lenses. Reviews the anatomy of the eye, describes the visual process and covers topics as index of refraction of the cornea, microscopic receptors, the lens, and the retina. (MDH)

Lapp, David R.; Keenan, James E.

1991-01-01

256

The etiology of cervical artery dissection  

PubMed Central

Abstract The etiology of cervical artery dissection (CAD) is unclear, although a number of risk factors have been reported to be associated with the condition. On rare occasions, patients experience CAD after cervical spine manipulation, making knowledge about the cervical arteries, the predisposing factors, and the pathogenesis of the condition of interest to chiropractors. This commentary reports on the relevant anatomy of the cervical arteries, developmental features of CAD, epidemiology of the condition, and mechanisms of dissection. The analysis of CAD risk factors is confusing, however, because many people are exposed to mechanical events and known pathophysiological associations without ever experiencing dissection. No cause-and-effect relationship has been established between cervical spine manipulation and CAD, but it seems that cervical manipulation may be capable of triggering dissection in a susceptible patient or contributing to the evolution of an already existing CAD. Despite the many risk factors that have been proposed as possible causes of CAD, it is still unknown which of them actually predispose patients to CAD after cervical spine manipulation.

Haneline, Michael T.; Rosner, Anthony L.

2007-01-01

257

Superior mesenteric artery dissection: Case report  

Microsoft Academic Search

Spontaneous dissections of the superior mesenteric artery are exceptional events because only 26 reports have been published. We present a new case, revealed with an acute abdominal syndrome. Computed tomographic angiography and arteriography allowed a rapid diagnosis and urgent surgical intervention. Progress in imagery makes diagnosis and follow-up examination easier. Surgery is indicated for acute symptomatic forms with suspicion of

Yann Gouëffic; Alain Costargent; Marie-Françoise Heymann; Philippe Chaillou; Philippe Patra

2002-01-01

258

Spontaneous dissection of the hepatic artery  

Microsoft Academic Search

Two cases of spontaneous dissection of hepatic arteries are described. Presentation and management of these two patients are distinctly different. The first patient presented with mild back pain and mild abnormal liver function tests and was treated conservatively. The second patient presented with hemoperitoneum and shock and was treated surgically.

M. F. Miiller; D. Kim

1995-01-01

259

Spontaneous dissection of the splanchnic arteries.  

PubMed

Three patients had severe abdominal pain of sudden onset. Computed tomography showed localized dissection in the superior mesenteric artery in two patients and in the celiac artery in one. With conservative therapy abdominal symptoms were self-remitted. All patients were successfully treated with medication and have been doing well during follow-up. PMID:20071446

Ozaki, Nobuchika; Wakita, Noboru; Yamada, Akitoshi; Tanaka, Yosuke

2010-04-01

260

Unusual Manifestations of Bilateral Carotid Artery Dissection: Dysphagia and Hoarseness  

Microsoft Academic Search

Dissection of the carotid artery can occur intracranially or extracranially, although dissections tend to affect extracranial\\u000a segments of the arteries much more commonly than intracranial segments. Carotid artery dissection (CAD) is most common in\\u000a middle-aged women. Although not completely known, the main risk factors related to carotid artery dissection are genetic and\\u000a environmental factors, traumatic events, cervical manipulation, migraine, recent

Huseyin Isildak; Emin Karaman; Ahmet Ozdogan; Metin Ibrahimov; Mehmet Yilmaz

2010-01-01

261

Spontaneous isolated superior mesenteric artery dissection - Report of two cases.  

PubMed

Two cases of isolated superior mesenteric artery dissection diagnosed by contrast enhanced 64 slice CT are reported. In both, the dissection was seen extending along the entire length of the artery with one of them showing partially thrombosed false lumen. One case was associated with dissection of left renal artery with consequent renal infarcts. Although superior mesenteric artery dissection is a rare phenomenon, it should be considered in the differential diagnosis of abdominal angina. PMID:22470682

Srinivasan, Kaliappan Gurusamy; Srividya, Saravanan; Ushanandhini, Premnath; Ramprabananth, Sivanandan

2009-01-01

262

Pediatric tonsillectomy: post-operative morbidity comparing microsurgical bipolar dissection versus cold sharp dissection  

Microsoft Academic Search

A prospective single-blinded study was conducted to compare pediatric tonsillectomy using the traditional cold sharp dissection with ligation for securing hemostasis (CSDL) versus microsurgical bipolar dissection technique (MBCT). Sixty children aged between 2 and 14 years were sequentially assigned to each group. Blood loss and postoperative pain in the first hour were markedly decreased in the MBCT group (P<0.0001 and

Luis Lassaletta; Gonzalo Mart??n; Miguel Angel Villafruela; Caridad Bolaños; Juan José Álvarez-Vicent

1997-01-01

263

Osteogenesis Imperfecta, Multiple Intra-Abdominal Arterial Dissections and a Ruptured Dissecting-Type Intracranial Aneurysm  

PubMed Central

Summary We describe an adult patient with a ruptured dissecting-type superior cerebellar artery aneurysm and known osteogenesis imperfecta. He was successfully treated with coil embolization and intentional parent vessel sacrifice. During his hospital admission, he also suffered from abdominal distension. An incidental note was made of multiple intra-abdominal arterial dissections. These were managed conservatively. We review the rare association of osteogenesis imperfecta and intracranial aneurysms, as well as discuss management implications.

Matouk, C.C.; Hanbidge, A.; Mandell, D.M.; Terbrugge, K.G.; Agid, R.

2011-01-01

264

A case report on asymptomatic ascending aortic dissection  

PubMed Central

Aortic dissection is a relatively rare but dreadful illness, often presenting with tearing chest pain and acute hemodynamic compromise. Early and accurate diagnosis and treatment are essential for survival. In the present review, a rare case of an asymptomatic ascending aortic dissection is reported. The general clinical manifestations, diagnosis and management of aortic dissection will also be reviewed.

Cohen, Ronny; Mena, Derrick; Carbajal-Mendoza, Roger; Arole, Olugbenga; Mejia, Jose O

2008-01-01

265

Tricuspid regurgitation resulting from acute type a aortic dissection.  

PubMed

Proximal extension of acute type A aortic dissection can affect the aortic valve but seldom affects the tricuspid valve. We report the case of an octogenarian who underwent successful surgical repair of an aortic dissection that was accompanied by tricuspid regurgitation. We believe that the tricuspid regurgitation was attributable to displacement of the valve resulting from aortic dissection. PMID:24996748

Kurisu, Kazuhiro; Baba, Hironori; Nakashima, Hidehiko; Kajiwara, Takashi; Hisahara, Manabu; Joo, Kunihiko; Ochiai, Yoshie

2014-07-01

266

Weight Lifting and Aortic Dissection: More Evidence for a Connection  

Microsoft Academic Search

Background\\/Aims: In 2003, we reported on a small number of patients in whom acute aortic dissection appeared to be causally related to intense weight lifting. If additional cases could be identified, the phenomenon of weight lifting induced aortic dissection would be further substantiated. We now report a substantially larger number of cases in which aortic dissection is associated with intense

I. Hatzaras; M. Tranquilli; M. Coady; P. M. Barrett; J. Bible; J. A. Elefteriades

2007-01-01

267

[Open submucosal dissection: first case described].  

PubMed

Endoscopic submucosal dissection is a new treatment, basically for the management of early gastric cancer, it is also a good option for large benign lesions if a "una pieza" resection needs to be performed. However this technique requires not only gastroenterologist with proven technical skill, but also some special devices not necessarily disposables in our country. The present paper describes the case of a patient with a large hyperplastic polyp located in the upper third of the stomach who underwent an open endoscopic submucosal dissection to resect the lesion owing to its size and characteristics. According our knowledge this is the first case in the medical literature describing the use of this technique during an open surgery. PMID:18183281

Portanova, Michel; Vesco, Eduardo; Morales, Domingo

2007-01-01

268

Management of Posterior Fossa Dissecting Aneurysms  

PubMed Central

Summary Treatment and prognosis of 14 patients of posterior fossa arterial dissections (AD) and dissecting aneurysms (DA) in one institution was reviewed. Internal trapping of aneurysm was performed for six patients presenting with SAH (three Vertebral, one posterior cerebral, one posterior inferior cerebellar, one anterior inferior cerebellar DA). The patency of the parent arteries was preserved in four DA patients with SAH (two Vertebral, two Basilar DA), 1 incidental vertebral DA, and one DA patient with brainstem infarction using stents and coils (four patients) or coils only (two patient). Proximal occlusion of parent artery was performed in a vertebral DA with SAH. One patient with a superior cerebellar DA presented with a midbrain infarct developed SAH with spontaneous occlusion of the aneurysm two weeks later. Of the 14 cases, ten were angiographically stable or cured during a follow up period of four to 70 months. one spontaneously resolved and two recurred. There was one death.

Winston Chong, W. K.

2008-01-01

269

Dissecting aortic aneurysm manifesting as acute pericarditis.  

PubMed

Two patients with coarctation of the aorta initially had acute idiopathic pericarditis with anterior pleuritic chest pain as the chief complaint. A pericardial friction rub was present in both patients. Both patients died suddenly. At autopsy, they were found to have a dissecting aneurysm of the ascending aorta with extension into the pericardial space; acute pericardial tamponade was the cause of death. We recommend that when a patient with coarctation of the aorta is admitted with pericarditis, aortic dissection should be considered and appropriate diagnostic procedures undertaken. In all young patients with acute pericarditis there should be careful palpation of the femoral pulses and review of the chest x-ray film for rib notching. PMID:760674

Greenberg, D I; Davia, J E; Fenoglio, J; McAllister, H A; Cheitlin, M D

1979-01-01

270

Thoracic aortic dissection associated with cocaine abuse.  

PubMed

Cardiovascular complications of cocaine abuse include myocardial ischemia and infarction, dysrhythmias, cardiomyopathies and aortic dissection. The case in point pertains to a 26-year-old, Caucasian male, substance abuser who suffered a thoracic aortic dissection following the use of crack cocaine. The autopsy and histological findings showed a connective tissue abnormality including a focal microcystic medial necrosis and a fragmentation of the elastic fibers in the arterial walls. Blood concentrations of cocaine and benzoylecgonine, taken individually, were considered to be within a potentially toxic range. Blood concentrations of methadone also indicated use of this drug at the same time. The small amounts of morphine found in the blood and urine were compatible with heroine or morphine use more than 24 h before death. PMID:15062953

Palmiere, Cristian; Burkhardt, Sandra; Staub, Christian; Hallenbarter, Myriam; Paolo Pizzolato, Gian; Dettmeyer, Reinhard; La Harpe, Romano

2004-05-10

271

Phosphoproteome profiles of the phytopathogenic fungi Alternaria brassicicola and Botrytis cinerea during exponential growth in axenic cultures.  

PubMed

This study describes the gel-free phosphoproteomic analysis of the phytopathogenic fungi Alternaria brassicicola and Botrytis cinerea grown in vitro under nonlimiting conditions. Using a combination of strong cation exchange and IMAC prior to LC-MS, we identified over 1350 phosphopeptides per fungus representing over 800 phosphoproteins. The preferred phosphorylation sites were found on serine (>80%) and threonine (>15%), whereas phosphorylated tyrosine residues were found at less than 1% in A. brassicicola and at a slightly higher ratio in B. cinerea (1.5%). Biological processes represented principally among the phoshoproteins were those involved in response and transduction of stimuli as well as in regulation of cellular and metabolic processes. Most known elements of signal transduction were found in the datasets of both fungi. This study also revealed unexpected phosphorylation sites in histidine kinases, a category overrepresented in filamentous ascomycetes compared to yeast. The data have been deposited to the ProteomeXchange database with identifier PXD000817 (http://proteomecentral.proteomexchange.org/dataset/PXD000817). PMID:24825570

Davanture, Marlène; Dumur, Jérôme; Bataillé-Simoneau, Nelly; Campion, Claire; Valot, Benoît; Zivy, Michel; Simoneau, Philippe; Fillinger, Sabine

2014-07-01

272

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

PubMed Central

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.

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

2013-01-01

273

Optimization of enrichment conditions on TiO2 chromatography using glycerol as an additive reagent for effective phosphoproteomic analysis.  

PubMed

Metal oxide affinity chromatography (MOAC) represented by titanium dioxide (TiO2) chromatography has been used for phosphopeptide enrichment from cell lysate digests prior to mass spectrometry. For in-depth phosphoproteomic analysis, it is important for MOAC to achieve high phosphopeptide enrichment efficiency by optimizing purification conditions. However, there are some differences in phosphopeptide selectivity and specificity enriched by various TiO2 materials and procedures. Here, we report that binding/wash buffers containing polyhydric alcohols, such as glycerol, markedly improve phosphopeptide selectivity from complex peptide mixtures. In addition, the elution conditions combined with secondary amines, such as bis-Tris propane, made it possible to recover phosphopeptides with highly hydrophobic properties and/or longer peptide lengths. To assess the practical applicability of our improved method, we confirmed using PC3 prostate cancer cells. By combining the hydrophilic interaction chromatography (HILIC) with the optimized TiO2 enrichment method prior to LC-MS/MS analysis, over 8300 phosphorylation sites and 2600 phosphoproteins were identified. Additionally, some dephosphorylations of those were identified by treatment with dasatinib for a kinase inhibitor. These results indicate that our method is applicable to understanding the profiling of kinase inhibitors such as anticancer compounds, which will be useful for drug discovery and development. PMID:24245541

Fukuda, Isao; Hirabayashi-Ishioka, Yoshino; Sakikawa, Ikue; Ota, Takeshi; Yokoyama, Mari; Uchiumi, Takaoki; Morita, Atsushi

2013-12-01

274

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

PubMed

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

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

2011-08-01

275

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

PubMed Central

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.

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

276

Using multiplex-staining to study changes in the maize leaf phosphoproteome in response to mechanical wounding.  

PubMed

Mechanical wounding of 2-week-old maize (Zea mays L.) leaves, one of the first steps in both pathogen infection and herbivore attack, stimulates metabolism and activates signal transduction pathways dedicated to defense and recovery. The signaling pathways include reversible protein phosphorylation which can modulate protein activities, and transmit signals within cellular pathways and networks. We have used multiplex-staining of high-resolution 2D gels for protein (Sypro Ruby) and phosphorylation (Pro-Q Diamond) as a strategy for quantifying changes in the stoichiometry of phosphorylation after wounding for 270 protein spots. Rigorous statistical analysis of the time-index data allowed us to accept patterns of change in 125 of the spots as non-random, and these patterns were assigned to five clusters. A reliable identity was assigned to 21 selected proteins, most of which have been previously described as phospho-proteins. The results suggest that analysis of protein spots from high-resolution 2D gels by multiplex-staining for protein plus phosphorylation is a strategy that can be broadly useful for study of how the phospho-proteome responds to abiotic stress. PMID:21334701

Lewandowska-Gnatowska, El?bieta; Johnston, Mark L; Antoine, Wesner; Szczegielniak, Jadwiga; Muszy?ska, Gra?yna; Miernyk, Ján A

2011-07-01

277

Donors' attitudes towards body donation for dissection  

Microsoft Academic Search

SummaryWe report a survey in the UK of potential whole-body donors for dissection. 218 people (age range 19-97 years) answered a postal questionnaire, giving information about themselves, their reasons for donation, attitudes towards the dead body, funeral preferences and medical giving and receiving. In addition to altruism, motives included the wish to avoid funeral ceremonies, to avoid waste, and in

R Richardson; B Hurwitz

1995-01-01

278

Aortic dissection: the flood tide sign.  

PubMed

Aortic dissection is a challenging medical and surgical problem. Its evolution depends on size and location of its intimal tears. We describe a case of contrast enhanced MD-CT with low out flow of the false lumen for an unbalanced between the entry and the reentry tears. This determined a delayed filling up of the false lumen on the arterial phase that was complete on the venous one. PMID:24268122

Rossi, Umberto G; Seitun, Sara; Cariati, Maurizio

2013-01-01

279

Recurrent tamponade and aortic dissection in syphilis.  

PubMed

Syphilitic cardiovascular disease has been described since the 19th century, mainly on autopsy series. Major clinical manifestations are aortic aneurysm, aortic insufficiency, and coronary ostial stenosis. The diagnosis of syphilitic cardiovascular disease is based mainly on positive serologic tests and overt clinical manifestations. We present here a rare and unusual clinical presentation of a tertiary syphilis with recurrent tamponade and type B aortic dissection, whose positive diagnosis was made by polymerase chain reaction on pericardial fluid analysis. PMID:24182507

Stansal, Audrey; Mirault, Tristan; Rossi, Aude; Dupin, Nicolas; Bruneval, Patrick; Bel, Alain; Azarine, Arshid; Minozzi, Catherine; Deman, Anne Laure; Messas, Emmanuel

2013-11-01

280

Laparoscopic Retroperitoneal Lymph Node Dissection: Extraperitoneal Approach  

Microsoft Academic Search

We review our early experience with laparoscopic retroperitoneal lymph node dissection (RPLND) via extraperitoneal approach\\u000a to assess the precise pathological status of retroperitoneal lymph nodes in early-stage testicular cancer. A total of 32 patients\\u000a (23 with stage I, 4 with stage IIa, and 5 with stage IIb) with testicular cancer underwent extraperitoneal laparoscopic RPLND\\u000a in the supine position. After developing

Makoto Satoh; Akihiro Ito; Yoichi Arai

281

Molecular Dissection of a Bifidobacterial Replicon  

Microsoft Academic Search

The 2.1-kb cryptic plasmid pCIBAO89 from Bifidobacterium asteroides harbors a 1.4-kb segment which is sufficient for its autonomous replication. The segment is divided into two parts, the presumed replication origin, ori89, and the rep gene encoding the putative 41-kDa Rep89 replication initiation protein. This minimal replication region of pCIBAO89 was functionally dissected by transcriptional analyses as well as by DNA-

Michelle Cronin; Moritz Knobel; Mary O'Connell-Motherway; Gerald F. Fitzgerald; Douwe van Sinderen

2007-01-01

282

Spontaneous dissection of the superior mesenteric artery.  

PubMed

We describe a case of spontaneous dissection and thrombosis of the superior mesenteric artery in a 54-year-old man who presented with new onset of hypertension and epigastric pain. Initial unsuccessful treatment with catheter-directed thrombolysis was followed by surgical intervention. In cases in which an extensive intimectomy is performed, early institution of antiplatelet therapy or anticoagulation may be necessary to preserve vessel patency due to the presence of a prothrombotic surface and compromised outflow. PMID:20142003

Hwang, Christopher K; Wang, Jeffrey Y; Chaikof, Elliot L

2010-02-01

283

Superior mesenteric artery dissection: case report.  

PubMed

Spontaneous dissections of the superior mesenteric artery are exceptional events because only 26 reports have been published. We present a new case, revealed with an acute abdominal syndrome. Computed tomographic angiography and arteriography allowed a rapid diagnosis and urgent surgical intervention. Progress in imagery makes diagnosis and follow-up examination easier. Surgery is indicated for acute symptomatic forms with suspicion of mesenteric ischemia. In the other cases, a simple follow-up examination may be appropriate. PMID:12021719

Gouëffic, Yann; Costargent, Alain; Dupas, Benoît; Heymann, Marie-Françoise; Chaillou, Philippe; Patra, Philippe

2002-05-01

284

Advanced endoscopic submucosal dissection with traction  

PubMed Central

Endoscopic submucosal dissection (ESD) has been established as a standard treatment for early stage gastric cancer (EGC) in Japan and has spread worldwide. ESD has been used not only for EGC but also for early esophageal and colonic cancers. However, ESD is associated with several adverse events, such as bleeding and perforation, which requires more skill. Adequate tissue tension and clear visibility of the tissue to be dissected are important for effective and safe dissection. Many ESD methods using traction have been developed, such as clip-with-line method, percutaneous traction method, sinker-assisted method, magnetic anchor method, external forceps method, internal-traction method, double-channel-scope method, outerroute method, double-scope method, endoscopic-surgical-platform, and robot-assisted method. Each method has both advantages and disadvantages. Robotic endoscopy, enabling ESD with a traction method, will become more common due to advances in technology. In the near future, simple, noninvasive, and effective ESD using traction is expected to be developed and become established as a worldwide standard treatment for superficial gastrointestinal neoplasias.

Imaeda, Hiroyuki; Hosoe, Naoki; Kashiwagi, Kazuhiro; Ohmori, Tai; Yahagi, Naohisa; Kanai, Takanori; Ogata, Haruhiko

2014-01-01

285

Endoscopic submucosal dissection of gastric ectopic pancreas  

PubMed Central

Patients with gastric tumors usually present with symptoms of discomfort or pain in the epigastrium, regurgitations, nausea, vomiting or melena. Treatment options include open and laparoscopic total or partial gastrectomy and recently endoscopic mucosal resection. A case of successful endoscopic submucosal dissection is described with the unusual pathological finding of heterotopic pancreatic tissue forming a gastric tumor. The 67-year-old male patient was operated on due to the initial diagnosis of gastro-intestinal stromal tumor of the gastric trunk. Two intra-operative biopsies were negative for cancer cells. Submucosal endoscopic dissection was performed with IT and Hook knives (Olympus). A literature review was performed. The operative time was 180 min with hospital stay of 6 days. During the injection of the carmine dye and the air insufflation pneumoperitoneum occurred and remained clinically silent during the observation period. The pathology result showed a heterotopic pancreatic tissue type 2 according to Heinrich's classification with microfoci of intestinal metaplasia. Preoperative diagnostics of gastric masses might be misleading and such tumors not necessarily should be excised. There are several surgical options with endoscopic submucosal dissection being probably the safest one and a non-disabling approach. Patients tolerate that kind of surgery well with good postoperative functional outcomes.

Makarewicz, Wojciech; Dubowik, Michal; Kosinski, Adam; Jastrzebski, Tomasz; Jaskiewicz, Janusz

2013-01-01

286

"Ostrich sign" indicates bilateral vertebral artery dissection.  

PubMed

Vertebral artery dissections (VADs) comprise about 2% of ischemic strokes and can be associated with trauma, chiropractic manipulation, motor vehicle collisions, whiplash, amusement park rides, golfing, and other motion-induced injuries to the neck. We present a case of bilateral extracranial VAD as a complication of conducting an orchestra. To our knowledge, this has not been documented in the literature. Conceivably, vigorous neck twisting in an inexperienced, amateur conductor may place excessive rotational forces upon mobile portions of the verterbral arteries, tear the intima, deposit subintimal blood that extends longitudinally, and cause neck pain and/or posterior fossa ischemic symptoms. Magnetic resonance angiography examinations of axially oriented slices of bilateral VADs resemble the face of an ostrich. This observation is similar to the "puppy sign," in which bilateral internal carotid artery dissections resemble the face of a dog. Craniocervical dissections of either the carotid or vertebral arteries have the potential to form an aneurysm, cause artery-to-artery embolism, or completely occlude the parent artery, resulting in an ischemic stroke. Because bilateral VADs in axial magnetic resonance angiographic sections stand out like the eyes of an ostrich, and because the fast identification of VADs is so critical, we eponymize this image the "ostrich sign." PMID:21440457

Rose, David Z; Husain, M Rizwan

2012-11-01

287

Advanced endoscopic submucosal dissection with traction.  

PubMed

Endoscopic submucosal dissection (ESD) has been established as a standard treatment for early stage gastric cancer (EGC) in Japan and has spread worldwide. ESD has been used not only for EGC but also for early esophageal and colonic cancers. However, ESD is associated with several adverse events, such as bleeding and perforation, which requires more skill. Adequate tissue tension and clear visibility of the tissue to be dissected are important for effective and safe dissection. Many ESD methods using traction have been developed, such as clip-with-line method, percutaneous traction method, sinker-assisted method, magnetic anchor method, external forceps method, internal-traction method, double-channel-scope method, outerroute method, double-scope method, endoscopic-surgical-platform, and robot-assisted method. Each method has both advantages and disadvantages. Robotic endoscopy, enabling ESD with a traction method, will become more common due to advances in technology. In the near future, simple, noninvasive, and effective ESD using traction is expected to be developed and become established as a worldwide standard treatment for superficial gastrointestinal neoplasias. PMID:25031787

Imaeda, Hiroyuki; Hosoe, Naoki; Kashiwagi, Kazuhiro; Ohmori, Tai; Yahagi, Naohisa; Kanai, Takanori; Ogata, Haruhiko

2014-07-16

288

Central compartment dissection in laryngeal cancer.  

PubMed

We report here a review of the literature intended to clarify the nomenclature and boundaries of the nodes in the "central compartment" of the neck, the frequency with which tumors from the different laryngeal sites metastasize to these nodes, and the indications for central compartment node dissection in the treatment of cancers of the larynx. From this review, we conclude that, until consensus is reached about grouping of the lymph nodes in this area, it is best to refer to these nodes by their anatomic location, ie, prelaryngeal, pretracheal, or paratracheal lymph nodes. It is also advisable to describe dissection of these nodes as selective neck dissection (SND) with an annotation about the specific lymph node groups removed. Metastases in prelaryngeal and paratracheal lymph nodes in patients with squamous cell carcinoma of the larynx are associated with increased tumor recurrence, more frequent metastases in lymph nodes of the lateral compartment of the neck, and decreased survival. If untreated, they may lead to the development of peristomal recurrence. Therefore, elective treatment of level VI nodes is recommended in patients with squamous cell carcinomas of the subglottic region, advanced glottis carcinomas with subglottic extension, and in certain advanced carcinomas of the supraglottic region. PMID:20652888

Medina, Jesus E; Ferlito, Alfio; Robbins, K Thomas; Silver, Carl E; Rodrigo, Juan P; de Bree, Remco; Rinaldo, Alessandra; Elsheikh, Mohamed N; Weber, Randal S; Werner, Jochen A

2011-05-01

289

Endoscopic submucosal dissection of gastric ectopic pancreas.  

PubMed

Patients with gastric tumors usually present with symptoms of discomfort or pain in the epigastrium, regurgitations, nausea, vomiting or melena. Treatment options include open and laparoscopic total or partial gastrectomy and recently endoscopic mucosal resection. A case of successful endoscopic submucosal dissection is described with the unusual pathological finding of heterotopic pancreatic tissue forming a gastric tumor. The 67-year-old male patient was operated on due to the initial diagnosis of gastro-intestinal stromal tumor of the gastric trunk. Two intra-operative biopsies were negative for cancer cells. Submucosal endoscopic dissection was performed with IT and Hook knives (Olympus). A literature review was performed. The operative time was 180 min with hospital stay of 6 days. During the injection of the carmine dye and the air insufflation pneumoperitoneum occurred and remained clinically silent during the observation period. The pathology result showed a heterotopic pancreatic tissue type 2 according to Heinrich's classification with microfoci of intestinal metaplasia. Preoperative diagnostics of gastric masses might be misleading and such tumors not necessarily should be excised. There are several surgical options with endoscopic submucosal dissection being probably the safest one and a non-disabling approach. Patients tolerate that kind of surgery well with good postoperative functional outcomes. PMID:24130642

Makarewicz, Wojciech; Bobowicz, Maciej; Dubowik, Michal; Kosinski, Adam; Jastrzebski, Tomasz; Jaskiewicz, Janusz

2013-09-01

290

Student attitudes to whole body donation are influenced by dissection.  

PubMed

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 dissection and again after 9 weeks of anatomical dissection. Analysis of student responses to the idea of whole body donation by an unrelated stranger, a family member, or by the respondent showed that a priori attitudes to donation by a stranger did not change with exposure to dissection. However, student opposition to donation by a family member was evident immediately after the initial dissection and was sustained throughout the duration of this study. Support for the idea of donating their bodies to medical science decreased significantly among respondents after exposure to dissection (31.5% before dissection, 19.6% after dissecting for 9 weeks) but not to levels reported in the general population in other studies. This study demonstrates that where dissection forms a part of anatomy teaching, students expect to learn anatomy by dissecting donors whom they do not know. As a potential donor population, students are reluctant to become emotionally involved in the donation process and are unwilling to become donors themselves. PMID:19177413

Cahill, Kevin C; Ettarh, Raj R

2008-01-01

291

Application of electrostatic repulsion hydrophilic interaction chromatography to the characterization of proteome, glycoproteome, and phosphoproteome using nano LC-MS/MS.  

PubMed

In shotgun proteomics, peptide fractionation is essential for in-depth characterization of proteomes and the mapping of protein posttranslational modifications. Recently, a mix-mode chromatography [i.e., electrostatic repulsion hydrophilic interaction chromatography (ERLIC)] has been developed and found to be a versatile method in proteome characterization. Here, we use ERLIC to characterize the glycoproteome and phosphoproteome simultaneously. We also demonstrate that the ERLIC can be an alternative to the commonly used strong cation exchange chromatography for higher recovery of proteins during whole proteome analysis. These protocols can be easily adopted in most proteomics laboratories. PMID:21948424

Hao, Piliang; Zhang, Huoming; Sze, Siu Kwan

2011-01-01

292

Principles of Quality Controlled Endoscopic Submucosal Dissection with Appropriate Dissection Level and High Quality Resected Specimen  

PubMed Central

Endoscopic submucosal dissection (ESD) has enabled en bloc resection of early stage gastrointestinal tumors with negligible risk of lymph node metastasis, regardless of tumor size, location, and shape. However, ESD is a relatively difficult technique compared with conventional endoscopic mucosal resection, requiring a longer procedure time and potentially causing more complications. For safe and reproducible procedure of ESD, the appropriate dissection of the ramified vascular network in the level of middle submucosal layer is required to reach the avascular stratum just above the muscle layer. The horizontal approach to maintain the appropriate depth for dissection beneath the vascular network enables treatment of difficult cases with large vessels and severe fibrosis. The most important aspect of ESD is the precise evaluation of curability. This approach can also secure the quality of the resected specimen with enough depth of the submucosal layer.

Nishino, Eisei; Man-i, Mariko; East, James E.; Azuma, Takeshi

2012-01-01

293

Effectiveness of a new inflatable balloon device for gluing dissected layers in an experimental model of aortic dissection  

PubMed Central

OBJECTIVES: In the surgical treatment of acute aortic dissection, tissue glues are widely used to reinforce the adhesion between the dissected aortic layers. A new inflatable balloon device was developed to compress the dissected aortic wall during gluing to increase adhesion between the dissected layers. The present study used an ex vivo experimental animal model to test the hypothesis that this device is effective when gluing the true and false channels of dissected aortas. METHODS: In the ex vivo experimental model, aortic dissection was simulated surgically on 12 fresh bovine aorta samples. In six samples (group I), the inflatable balloon device was inserted into the aorta to reinforce and fuse the dissected layers during gluing. The other six fresh bovine aortic samples (group II) were compressed between the surgeon’s fingers during gluing. Aortic samples were evaluated and compared macroscopically and histologically. RESULTS: In group I, adhesion between the dissected layers was easily achieved during gluing. All false cavities were perfectly closed, with no deleterious effects related to the device. In group II, the adhesion between the dissected layers was not complete and some false cavities remained patent. CONCLUSIONS: The inflatable balloon device can increase the adhesive effect of tissue glues via homogenous compression of the dissected aortic layers. In addition, the balloon can prevent distal embolization of the glue.

Colak, Necmettin; Nazli, Yunus; Alpay, Mehmet Fatih; Akkaya, Ismail Olgun; Aksoy, Omer Nuri; Akgedik, Sukran; Cakir, Omer

2013-01-01

294

Spontaneous Coronary Artery Dissection following Topical Hormone Replacement Therapy  

PubMed Central

Spontaneous coronary artery dissection is a rare condition, usually presenting as an acute coronary syndrome, and is often seen in states associated with high systemic estrogen levels such as pregnancy or oral contraceptive use. While topical hormonal replacement therapy may result in increased estrogen levels similar to those documented with oral contraceptive use, there are no reported cases of spontaneous coronary dissection with topical hormonal replacement therapy. We describe a 53-year-old female who developed two spontaneous coronary dissections while on topical hormonal replacement therapy. The patient had no other risk factors for coronary dissection. After withdrawal from topical hormonal therapy, our patient has done well and has not had recurrent coronary artery dissections over a one-year follow-up period. The potential contributory role of topical hormonal therapy as a cause of spontaneous coronary dissection should be recognized.

Pan, Alexander L.; Fergusson, David; Hong, Robert; Badawi, Ramy A.

2012-01-01

295

Quantitative radiography  

Microsoft Academic Search

We have developed a system of quantitative radiography in order to produce quantitative images displaying homogeneity of parts. The materials that we characterize are synthetic composites and may contain important subtle density variations not discernable by examining a raw film x-radiograph. In order to quantitatively interpret film radiographs, it is necessary to digitize, interpret, and display the images. Our integrated

C. M. Logan; J. M. Hernandez; G. J. Devine

1991-01-01

296

Chronic pulmonary artery dissection associated with pulmonary arterial hypertension  

PubMed Central

Abstract Pulmonary artery dissection is a complication associated with pulmonary arterial hypertension. This complication is described as acute in onset and is frequently fatal without intervention. We describe a patient with idiopathic pulmonary arterial hypertension and chest pain found to have an unsuspected chronic pulmonary artery dissection on postmortem examination. Chronic pulmonary artery dissection should be considered in patients with chest pain and worsening dyspnea, as the frequency this condition may be underestimated.

2013-01-01

297

Seeing the invisible: painless aortic dissection in the emergency setting.  

PubMed

Acute dissection of the aorta can be one of the most dramatic cardiovascular emergencies. Classically, aortic dissection presents as sudden, severe chest, back, or abdominal pain that is characterised as ripping or tearing in nature. However, a timely diagnosis can be elusive in the event of an atypical presentation. In this report, the authors present two patients with painless aortic dissection who were misdiagnosed during their initial evaluation in the emergency department. PMID:16498148

Ayrik, C; Cece, H; Aslan, O; Karcioglu, O; Yilmaz, E

2006-03-01

298

Seeing the invisible: painless aortic dissection in the emergency setting  

PubMed Central

Acute dissection of the aorta can be one of the most dramatic cardiovascular emergencies. Classically, aortic dissection presents as sudden, severe chest, back, or abdominal pain that is characterised as ripping or tearing in nature. However, a timely diagnosis can be elusive in the event of an atypical presentation. In this report, the authors present two patients with painless aortic dissection who were misdiagnosed during their initial evaluation in the emergency department.

Ayrik, C; Cece, H; Aslan, O; Karcioglu, O; Yilmaz, E

2006-01-01

299

TEVAR for type B aortic dissection in Japan.  

PubMed

TEVAR is a new strategy for treating both acute and chronic type B aortic dissection. The JSC guidelines classify TEVAR as a Class I recommendation for cases of complicated acute type B dissection and a Class IIa recommendation for cases of chronic type B aortic dissection. While TEVAR has been primarily applied to treat complicated acute type B aortic dissection in Europe and the USA, the procedure remains an off-label treatment strategy for aortic dissection in Japan. The current state of TEVAR for type B aortic dissection in Japan from 2001 to 2011 is estimated in the annual reports of the Japanese Association for Thoracic Surgery. The number of acute type B aortic dissection patients treated with transluminal stent grafting increased rapidly after 2008, from 10 cases in 2001 to 76 cases in 2010. Meanwhile, the number acute type B aortic dissection patients treated with any type of surgery has increased gradually, from 100 cases in 2001 to 194 cases in 2009. The number of chronic type B aortic dissection patients treated with transluminal stent grafting increased abruptly in 2010, reaching 346 cases, which accounted for one-third of all surgical procedures for chronic type B aortic dissection. Furthermore, the number of open surgeries for chronic type B aortic dissection has also increased gradually, from 401 cases in 2001 to 947 cases in 2011. At present, open surgery, TEVAR and hybrid procedures are available to treat patients with type B aortic dissection. The use of a multidisciplinary team approach is mandatory when selecting the appropriate surgical strategy. PMID:24317874

Usui, Akihiko

2014-05-01

300

Iatrogenic left main artery dissection: A catastrophic complication.  

PubMed

Iatrogenic left main artery (LM) dissection is a catastrophic complication of coronary angiography and angioplasty that requires prompt management using stenting. Although LM dissection can be prevented, it cannot always be avoided and has a reported incidence rate of 0.02%. In the present report, a case of iatrogenic LM dissection that was successfully treated with multiple stents is presented and followed by a brief review of the literature. PMID:23592948

Namazi, Mohammad Hassan; Rostami, Reza Tajik; Mohammadi, Afsaneh; Amini, Abdol Latifi; Safi, Morteza; Saadat, Habibollah; Vakili, Hosein; Motamedi, Mohammad Reza; Movahed, Mohammad Reza

2012-01-01

301

Iatrogenic left main artery dissection: A catastrophic complication  

PubMed Central

Iatrogenic left main artery (LM) dissection is a catastrophic complication of coronary angiography and angioplasty that requires prompt management using stenting. Although LM dissection can be prevented, it cannot always be avoided and has a reported incidence rate of 0.02%. In the present report, a case of iatrogenic LM dissection that was successfully treated with multiple stents is presented and followed by a brief review of the literature.

Namazi, Mohammad Hassan; Rostami, Reza Tajik; Mohammadi, Afsaneh; Amini, Abdol Latifi; Safi, Morteza; Saadat, Habibollah; Vakili, Hosein; Motamedi, Mohammad Reza; Movahed, Mohammad Reza

2012-01-01

302

Metabolic Signature of Electrosurgical Liver Dissection  

PubMed Central

Background and Aims High frequency electrosurgery has a key role in the broadening application of liver surgery. Its molecular signature, i.e. the metabolites evolving from electrocauterization which may inhibit hepatic wound healing, have not been systematically studied. Methods Human liver samples were thus obtained during surgery before and after electrosurgical dissection and subjected to a two-stage metabolomic screening experiment (discovery sample: N?=?18, replication sample: N?=?20) using gas chromatography/mass spectrometry. Results In a set of 208 chemically defined metabolites, electrosurgical dissection lead to a distinct metabolic signature resulting in a separation in the first two dimensions of a principal components analysis. Six metabolites including glycolic acid, azelaic acid, 2-n-pentylfuran, dihydroactinidiolide, 2-butenal and n-pentanal were consistently increased after electrosurgery meeting the discovery (p<2.0×10?4) and the replication thresholds (p<3.5×10?3). Azelaic acid, a lipid peroxidation product from the fragmentation of abundant sn-2 linoleoyl residues, was most abundant and increased 8.1-fold after electrosurgical liver dissection (preplication?=?1.6×10?4). The corresponding phospholipid hexadecyl azelaoyl glycerophosphocholine inhibited wound healing and tissue remodelling in scratch- and proliferation assays of hepatic stellate cells and cholangiocytes, and caused apoptosis dose-dependently in vitro, which may explain in part the tissue damage due to electrosurgery. Conclusion Hepatic electrosurgery generates a metabolic signature with characteristic lipid peroxidation products. Among these, azelaic acid shows a dose-dependent toxicity in liver cells and inhibits wound healing. These observations potentially pave the way for pharmacological intervention prior liver surgery to modify the metabolic response and prevent postoperative complications.

von Schonfels, Witigo; von Kampen, Oliver; Patsenker, Eleonora; Stickel, Felix; Schniewind, Bodo; Hinz, Sebastian; Ahrens, Markus; Balschun, Katharina; Egberts, Jan-Hendrik; Richter, Klaus; Landrock, Andreas; Sipos, Bence; Will, Olga; Huebbe, Patrizia; Schreiber, Stefan; Nothnagel, Michael; Rocken, Christoph; Rimbach, Gerald; Becker, Thomas

2013-01-01

303

Contemporary inguinal lymph node dissection: minimizing complications  

Microsoft Academic Search

Objectives  This review describes the morbidity of inguinal lymph node dissection (ILND) performed as part of the management of penile\\u000a cancer as well as recent modifications that may reduce the incidence of complications.\\u000a \\u000a \\u000a \\u000a Methods  A review of the literature was conducted using Pubmed© for studies reporting complication outcomes of ILND for penile cancer. Furthermore, our contemporary results and patient\\u000a related morbidity associated

Philippe E. Spiess; Mike S. Hernandez; Curtis A. Pettaway

2009-01-01

304

Molecular Dissection of a Bifidobacterial Replicon? †  

PubMed Central

The 2.1-kb cryptic plasmid pCIBAO89 from Bifidobacterium asteroides harbors a 1.4-kb segment which is sufficient for its autonomous replication. The segment is divided into two parts, the presumed replication origin, ori89, and the rep gene encoding the putative 41-kDa Rep89 replication initiation protein. This minimal replication region of pCIBAO89 was functionally dissected by transcriptional analyses as well as by DNA-binding studies, and the information obtained was exploited to create a number of Escherichia coli-Bifidobacterium shuttle vectors capable of transforming various bifidobacteria with an efficiency of up to 106 transformants/?g DNA.

Cronin, Michelle; Knobel, Moritz; O'Connell-Motherway, Mary; Fitzgerald, Gerald F.; van Sinderen, Douwe

2007-01-01

305

Intramural esophageal dissection associated with esophageal perforation.  

PubMed

Intramural esophageal dissection (IED) is a rare clinical entity involving a mucosal injury and creation of a true and false lumen within the esophagus. We report on a case of IED caused by repeated vomiting due to a small bowel obstruction associated with a small amount of pneumomediastinum on CT. IED has traditionally been believed not to be associated with esophageal perforation. Our case adds to the few reported instances where IED has been associated with extraluminal air leakage, the mildest form of esophageal perforation and demonstrates imaging not previously published in the radiology literature. Our case was successfully managed conservatively. PMID:23819141

Monu, Nicholas C; Murphy, Brian L

2013-01-01

306

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.

307

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

PubMed Central

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.

2013-01-01

308

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

SciTech Connect

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.

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

309

The Effects of Interactive Dissection Simulation on the Performance and Achievement of High School Biology Students.  

ERIC Educational Resources Information Center

A study of 61 high school biology students found that Interactive Video Disk (IVD) simulation was as effective as actual frog dissection in promoting student learning of frog anatomy and dissection procedures. When used as a preparation for dissection, IVD simulation helped students perform better dissections and learn more from doing dissections.…

Kinzie, Mable B.; And Others

1993-01-01

310

Functional dissection of Odorant binding protein genes in Drosophila melanogaster.  

PubMed

Most organisms rely on olfaction for survival and reproduction. The olfactory system of Drosophila melanogaster is one of the best characterized chemosensory systems and serves as a prototype for understanding insect olfaction. Olfaction in Drosophila is mediated by multigene families of odorant receptors and odorant binding proteins (OBPs). Although molecular response profiles of odorant receptors have been well documented, the contributions of OBPs to olfactory behavior remain largely unknown. Here, we used RNAi-mediated suppression of Obp gene expression and measurements of behavioral responses to 16 ecologically relevant odorants to systematically dissect the functions of 17 OBPs. We quantified the effectiveness of RNAi-mediated suppression by quantitative real-time polymerase chain reaction and used a proteomic liquid chromatography and tandem mass spectrometry procedure to show target-specific suppression of OBPs expressed in the antennae. Flies in which expression of a specific OBP is suppressed often show altered behavioral responses to more than one, but not all, odorants, in a sex-dependent manner. Similarly, responses to a specific odorant are frequently affected by suppression of expression of multiple, but not all, OBPs. These results show that OBPs are essential for mediating olfactory behavioral responses and suggest that OBP-dependent odorant recognition is combinatorial. PMID:21605338

Swarup, S; Williams, T I; Anholt, R R H

2011-08-01

311

Dissecting specific and global transcriptional regulation of bacterial gene expression  

PubMed Central

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.

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

2013-01-01

312

Dissection of Organs from the Adult Zebrafish  

PubMed Central

Over the last 20 years, the zebrafish has become a powerful model organism for understanding vertebrate development and disease. Although experimental analysis of the embryo and larva is extensive and the morphology has been well documented, descriptions of adult zebrafish anatomy and studies of development of the adult structures and organs, together with techniques for working with adults are lacking. The organs of the larva undergo significant changes in their overall structure, morphology, and anatomical location during the larval to adult transition. Externally, the transparent larva develops its characteristic adult striped pigment pattern and paired pelvic fins, while internally, the organs undergo massive growth and remodeling. In addition, the bipotential gonad primordium develops into either testis or ovary. This protocol identifies many of the organs of the adult and demonstrates methods for dissection of the brain, gonads, gastrointestinal system, heart, and kidney of the adult zebrafish. The dissected organs can be used for in situ hybridization, immunohistochemistry, histology, RNA extraction, protein analysis, and other molecular techniques. This protocol will assist in the broadening of studies in the zebrafish to include the remodeling of larval organs, the morphogenesis of organs specific to the adult and other investigations of the adult organ systems.

Gupta, Tripti; Mullins, Mary C.

2010-01-01

313

Molecular mechanisms of thoracic aortic dissection.  

PubMed

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

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

2013-10-01

314

Extracranial carotid and vertebral artery dissection: a review.  

PubMed

Dissection of the extracranial carotid and vertebral arteries is increasingly recognized as a cause of transient ischemic attacks and stroke. The annual incidence of spontaneous carotid artery dissection is 2.5 to 3 per 100,000, while the annual incidence of spontaneous vertebral artery dissection is 1 to 1.5 per 100,000. Traumatic dissection occurs in approximately 1% of all patients with blunt injury mechanisms, and is frequently initially unrecognized. Overall, dissections are estimated to account for only 2% of all ischemic strokes, but they are an important factor in the young, and account for approximately 20% of strokes in patients less than 45 years of age. Arterial dissection can cause ischemic stroke either by thromboemboli forming at the site of injury or as a result of hemodynamic insufficiency due to severe stenosis or occlusion. Available evidence strongly favors embolism as the most common cause. Both anticoagulation and antiplatelet agents have been advocated as treatment methods, but there is limited evidence on which to base these recommendations. A Cochrane review on the topic of antithrombotic drugs for carotid dissection did not identify any randomized trials, and did not find that anticoagulants were superior to antiplatelet agents for the primary outcomes of death and disability. Healing of arterial dissections occurs within three to six months, with resolution of stenosis seen in 90%, and recanalization of occlusions in as many as 50%. Dissecting aneurysms resolve on follow-up imaging in 5-40%,decrease in size in 15-30%, and remain unchanged in 50-65%. Resolution is more common in vertebral dissections than in carotid dissections. Aneurysm enlargement occurs rarely. The uncommon patient presenting with acute hemodynamic insufficiency should be managed with measures to increase cerebral blood flow, and in this setting emergency stent placement to restore cerebral perfusion may be considered, provided that irreversible infarction has not already occurred. PMID:18574926

Redekop, Gary John

2008-05-01

315

Functional neck dissection: an evaluation and review of 843 cases.  

PubMed

After briefly reviewing the principles, indications, and merits of functional neck dissection, the results of 1200 neck dissections performed on 843 patients in the period 1961-1979 are presented. They compare very favorably with those reported for classic (radical) neck dissection by other leading authors; however, a retrospective analysis of data derived from material of different origin is hardly possible and has a disputable value. Therefore, we decided to compare our data on functional neck dissections (FND) with those of classic neck dissections (CND) performed by the same surgical team at the same clinic in the period 1948-1960. The clinical material was largely the same in both cases, and the data were collected and analyzed using the same criteria. In both series, neck dissections were divided into elective and curative. It could be demonstrated that the number of neck recurrences observed in the dissected necks is the same for FND and CND in curative dissections, while it is considerably lower for FND in elective neck dissections. This of course does not prove improved radicality in FND, but only proves that a systematic bilateral elective neck dissection in N0 cases affords improved cancerological safety. This radical bilateral approach to regional lymph nodes is made possible routinely by FND which avoids the problems of unnecessary mutilation. The figures produced speak in favor of a wider adoption of FND especially for expanding the indications to elective treatment of regional lymph nodes in cancer of the head and neck. Elective neck dissection is made practically harmless by this newer technique and averts the dreadful appearance of late metastases in N0 cases. PMID:6738274

Bocca, E; Pignataro, O; Oldini, C; Cappa, C

1984-07-01

316

Negative results - Vascular thoracic Retrograde aortic dissection after a stent graft repair of a type B dissection: how to improve the endovascular technique  

Microsoft Academic Search

To date, endovascular repair of thoracic dissections is a reality, associated with acceptable morbidity and mortality. We present the case of a 72-year-old woman presenting a retrograde aortic dissection at the postoperative day 12, after an endovascular repair for a 60-mm thoracic dissecting aneurysm. Two years earlier, she had presented an uncomplicated thoracoabdominal type B aortic dissection between the isthmic

Sylvain Rubin; Aurelie Bayle; Anne Poncet; Bernard Baehrel

317

Proteomic and phosphoproteomic comparison of human ES and iPS cells.  

PubMed

Combining high-mass-accuracy mass spectrometry, isobaric tagging and software for multiplexed, large-scale protein quantification, we report deep proteomic coverage of four human embryonic stem cell and four induced pluripotent stem cell lines in biological triplicate. This 24-sample comparison resulted in a very large set of identified proteins and phosphorylation sites in pluripotent cells. The statistical analysis afforded by our approach revealed subtle but reproducible differences in protein expression and protein phosphorylation between embryonic stem cells and induced pluripotent cells. Merging these results with RNA-seq analysis data, we found functionally related differences across each tier of regulation. We also introduce the Stem Cell-Omics Repository (SCOR), a resource to collate and display quantitative information across multiple planes of measurement, including mRNA, protein and post-translational modifications. PMID:21983960

Phanstiel, Douglas H; Brumbaugh, Justin; Wenger, Craig D; Tian, Shulan; Probasco, Mitchell D; Bailey, Derek J; Swaney, Danielle L; Tervo, Mark A; Bolin, Jennifer M; Ruotti, Victor; Stewart, Ron; Thomson, James A; Coon, Joshua J

2011-01-01

318

Quantitative analysis  

PubMed Central

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.

Nevin, John A.

1984-01-01

319

Student Attitudes toward Cadaveric Dissection at a UK Medical School  

ERIC Educational Resources Information Center

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…

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

2011-01-01

320

Student Attitudes Toward Cadaveric Dissection at a UK Medical School  

NSDL National Science Digital Library

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.

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

2011-06-08

321

A Modified Dissection Method to Preserve Neck Structures  

ERIC Educational Resources Information Center

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…

Hankin, Mark H.; Stoller, Jeremy L.

2009-01-01

322

An alternate dissection approach to the female urogenital triangle.  

PubMed

Traditional dissections of the female urogenital (UG) triangle can lead to early destruction of the erectile tissues, associated musculature, and neurovascular structures. Here, we present an alternate dissection of the female UG triangle. Rather than begin the female UG triangle dissection with the fatty tissue of the labia majora, we utilize an early identification of the suspensory ligament of the clitoris to organize the dissection. The suspensory ligament leads to the body of the clitoris, which can be palpated from distal to proximal to find the crura of the clitoris with overlying ischiocavernosus muscles. Once the crura have been defined, the bulbs of the vestibule with overlying bulbospongiosus muscles can be palpated medially and posteriorly. This dissection approach results in a clean dissection that well demonstrates homologies between male and female external genitalia. Through the use of this method, most student dissection attempts are able to demonstrate the erectile tissues and associated musculature that comprise the female UG triangle. This technique can also be used for male UG triangle dissections, encouraging identification of male and female homologies. PMID:23825011

Hall, Margaret I; Walters, Linda M

2013-09-01

323

Traumatic internal carotid artery dissections caused by blunt softball injuries  

Microsoft Academic Search

This report describes recently treated patients with carotid artery dissection caused by blunt softball injuries, as well as the results of a study of carotid artery trauma in a community. Data obtained through the medical records linkage system used for epidemiologic studies in Olmsted County, MN were used to identify all cases of traumatic internal carotid artery dissection diagnosed from

Wouter I Schievink; John L. D Atkinson; J. D Bartleson; Jack P Whisnant

1998-01-01

324

Traumatic Axillary Artery Dissection with Radial Artery Embolism  

SciTech Connect

This report describes a case of pathologically proven traumatic arterial dissection, presenting as complete occlusion of the axillary artery with radial artery embolism. Occlusion of the axillary artery by traumatic dissection mimicked transection and radial artery embolism mimicked congenital absence of the radial artery on the initial angiogram, but these were correctly diagnosed with the following sonogram.

Chung, Hwan-Hoon; Cha, Sang Hoon, E-mail: shcha123@naver.com; Cho, Sung Bum; Kim, Jung Hyuck; Lee, Seung Hwa [Ansan Hospital, Korea University College of Medicine, Department of Radiology (Korea, Republic of); Shin, Jae Seung [Ansan Hospital, Korea University College of Medicine, Department of Thoracic and Cardiovascular Surgery (Korea, Republic of); Park, Sang Woo [KonKuk University Hospital, Department of Radiology (Korea, Republic of)

2006-04-15

325

Justifying the Dissection of Animals in Biology Teaching.  

ERIC Educational Resources Information Center

Presents the idea that several points should be considered in animal dissection: (1) ethics; (2) the animal's position; (3) the law; and (4) the actual benefits to society. Recommends that students be carefully prepared for animal dissection. Contains 21 references. (DDR)

Wheeler, Anthony G.

1993-01-01

326

Aortic Valve Conservation in Acute Type A Dissection  

Microsoft Academic Search

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

Stephen Westaby; Takahiro Katsumata; Edward Freitas

1997-01-01

327

Virtual temporal bone dissection: An interactive surgical simulator  

Microsoft Academic Search

Objective: Our goal was to integrate current and emerging technology in virtual systems to provide a temporal bone dissection simulator that allows the user interactivity and realism similar to the cadaver laboratory. Study Design: Iterative design and validation of a virtual environment for simulating temporal bone dissection. Setting: University otolaryngology training program with interdisciplinary interaction in a high-performance computer facility.

Gregory J. Wiet; Don Stredney; Dennis Sessanna; Jason A. Bryan; D. Bradley Welling; Petra Schmalbrock

2002-01-01

328

Therapy Insight: aortic aneurysm and dissection in Marfan's syndrome  

Microsoft Academic Search

Aortic dissection and aneurysm are common clinical problems with life-threatening consequences; they are also the hallmark of several genetic diseases, including Marfan's syndrome (MFS). In spite of clinical and surgical advances that have increased life expectancy for affected patients, cardiovascular manifestations remain significant contributors to morbidity and mortality in MFS. Dissecting aortic aneurysm in this disorder is accounted for by

Harry C Dietz; Francesco Ramirez

2004-01-01

329

Surgical treatment of 50 carotid dissections: Indications and results  

Microsoft Academic Search

Purpose: This article analyzes the course of 48 patients with 49 chronic carotid dissections (who were treated surgically at our institution after a median anticoagulation period of 9 months because of a persistent high-grade stenosis or an aneurysm) and the course of one additional patient with acute carotid dissection (who underwent early operative reconstruction 12 hours after onset because of

Barbara Theresia Müller; Bernd Luther; Waldemar Hort; Tobias Neumann-Haefelin; Albrecht Aulich; Wilhelm Sandmann

2000-01-01

330

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

ERIC Educational Resources Information Center

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)

Franklin, Sue; Peat, Mary; Lewis, Alison

2002-01-01

331

Dissection of the adult zebrafish kidney.  

PubMed

Researchers working in the burgeoning field of adult stem cell biology seek to understand the signals that regulate the behavior and function of stem cells during normal homeostasis and disease states. The understanding of adult stem cells has broad reaching implications for the future of regenerative medicine. For example, better knowledge about adult stem cell biology can facilitate the design of therapeutic strategies in which organs are triggered to heal themselves or even the creation of methods for growing organs in vitro that can be transplanted into humans. The zebrafish has become a powerful animal model for the study of vertebrate cell biology. There has been extensive documentation and analysis of embryonic development in the zebrafish. Only recently have scientists sought to document adult anatomy and surgical dissection techniques, as there has been a progressive movement within the zebrafish community to broaden the applications of this research organism to adult studies. For example, there are expanding interests in using zebrafish to investigate the biology of adult stem cell populations and make sophisticated adult models of diseases such as cancer. Historically, isolation of the zebrafish adult kidney has been instrumental for studying hematopoiesis, as the kidney is the anatomical location of blood cell production in fish. The kidney is composed of nephron functional units found in arborized arrangements, surrounded by hematopoietic tissue that is dispersed throughout the intervening spaces. The hematopoietic component consists of hematopoietic stem cells (HSCs) and their progeny that inhabit the kidney until they terminally differentiate. In addition, it is now appreciated that a group of renal stem/progenitor cells (RPCs) also inhabit the zebrafish kidney organ and enable both kidney regeneration and growth, as observed in other fish species. In light of this new discovery, the zebrafish kidney is one organ that houses the location of two exciting opportunities for adult stem cell biology studies. It is clear that many outstanding questions could be well served with this experimental system. To encourage expansion of this field, it is beneficial to document detailed methods of visualizing and then isolating the adult zebrafish kidney organ. This protocol details our procedure for dissection of the adult kidney from both unfixed and fixed animals. Dissection of the kidney organ can be used to isolate and characterize hematopoietic and renal stem cells and their offspring using established techniques such as histology, fluorescence activated cell sorting (FACS), expression profiling, and transplantation. We hope that dissemination of this protocol will provide researchers with the knowledge to implement broader use of zebrafish studies that ultimately can be translated for human application. PMID:21897357

Gerlach, Gary F; Schrader, Lauran N; Wingert, Rebecca A

2011-01-01

332

Analysis of quantitative trait loci that influence animal behavior  

Microsoft Academic Search

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

Jonathan Flint

2003-01-01

333

Controlled ultrasonic micro-dissection of thin tissue sections.  

PubMed

In order to obtain sufficient quantities of pure populations of cells or a single cell from surrounding tissue for analytical investigation, we have developed an ultrasonic microdissection system. The system utilizes a vision-based method for detecting the contact between the microdissection needle tip and a target surface. A multilayer stack piezoelectric actuator is employed to generate ultrasonic vibrations for histological isolation. Automated micro-dissection is also realized using visual feedback and vision-based control. Experimental results on tumor tissue sections show that the system has a high dissection accuracy and efficiency and is able to realize dissecting arbitrary shapes in specified locations on a tissue sample. Furthermore, effects in variations of vibration amplitude and frequency of ultrasonic micro-dissection as well as needle insertion depths on micro-dissection accuracy and speed were evaluated. PMID:24718707

Ru, Changhai; Liu, Jun; Pang, Ming; Sun, Yu

2014-08-01

334

A variant of nested dissection for solving n by n grid problems  

NASA Technical Reports Server (NTRS)

Nested dissection orderings are known to be very effective for solving the sparse positive definite linear systems which arise from n by n grid problems. In this paper nested dissection is shown to be the final step of incomplete nested dissection, an ordering which corresponds to the premature termination of dissection. Analyses of the arithmetic and storage requirements for incomplete nested dissection are given, and the ordering is shown to be competitive with nested dissection under certain conditions.

George, A.; Poole, W. G., Jr.; Voigt, R. G.

1976-01-01

335

Dissecting Lagrangian Velocities and Ramp Waves  

NASA Astrophysics Data System (ADS)

Lagrangian velocities are typically the observational quantity for compression wave experiments that probe material response at high-pressure. Depending on the experimental compression methodology (high-explosive to laser), a wide range of strain rates are possible from 10^3 to 10^8 s-1 yielding unique insight into non-linear wave propagation. We have been developing a method to understand the thermodynamic response of a material subjected to these high-pressure, compression waves. As part of that effort, we have found that the relationship between Lagrangian acceleration and the velocity offers insight into the material response and helps to dissect the velocity for subsequent analysis related to equation of state and non-elastic response mechanisms. We shall discuss this methodology and provide several examples.

Orlikowski, Daniel; Minich, Roger

2011-06-01

336

PBS Learning Media: Cow's Eye Dissection  

NSDL National Science Digital Library

This video-based interactive activity gives users a close-up and fascinating view of the anatomy of a real cow eye as it is dissected by a teenage narrator. You'll get a view of the cornea, watch light refract through the extracted lens, see the retina from the inside, and more. The Flash movies are divided into 12 segments which may be stopped/started interactively. Each segment contains text information with vocabulary definitions in hover-over format. The resource also provides a diagram of the eye and detailed illustrations of how the eye refracts light and sends messages to the optic nerve. PBS Learning Media is a growing collection of 10,000+ free educational resources compiled by researchers and experienced teachers to promote the use of digital resources in the classroom.

2009-06-12

337

Quantitative Easing  

Microsoft Academic Search

Central banks around the world have moved to cut interest rates to record lows, with many in advanced economies going further and embracing full quantitative easing – creating new money to inject into the economy. This paper examines why quantitative easing has been necessary, and whether it is likely to result in higher demand or instead show up in higher

Colin Ellis

2009-01-01

338

The Effects of Computer Animated Dissection versus Preserved Animal Dissection on the Student Achievement in a High School Biology Class.  

ERIC Educational Resources Information Center

The purpose of this study was to examine the effectiveness of computer-animated dissection techniques versus the effectiveness of traditional dissection techniques as related to student achievement. The sample used was 104 general biology students from a small, rural high school in Northeast Tennessee. Random selection was used to separate the…

Kariuki, Patrick; Paulson, Ronda

339

Diamondiferous Peridotite Tomography: Precursor to Xenolith Dissections.  

NASA Astrophysics Data System (ADS)

Three-dimensional, high-resolution computed X-ray tomography (HRCXT) of diamondiferous peridotite xenoliths from Siberia has successfully imaged diamonds and their textural relationships with co-existing minerals. This is an extension to the tomography and xenolith dissections performed previously on diamondiferous eclogites (e.g., Taylor et al., 2000, Int'l Geol Rev 42; Anand et al., 2003, 8th Int'l Kimb Conf). Spatial relationships between diamonds and their surroundings provide clues to the processes that control diamond crystallization. These relationships can be determined by rotating and viewing the 3-D model at different perspectives and orientations to look for specific associations/alignments. It is possible to render some of the phases transparent and display only one or two minerals at a time. Then by rotating the model, it is possible to look for spatial relationships between different crystals of the same mineral or different minerals. The maps obtained from the tomography form the basis for the delicate dissections of the xenoliths, revealing the diamonds as they formed in their mantle host rocks. Diamondiferous peridotites appear to be sparse carriers of diamonds compared to eclogites, where one unusual eclogite of 65 g contained 74 macro-diamonds. Although kimberlites always contain considerably more peridotite xenoliths than eclogites, the diamond population may actually be more indicative of eclogitic origin. The diamonds appear to be preferentially located in zones with a prominent sub-planar fabric of secondary mineralization - i.e., zones of increased permeability. Diamond was never observed in direct contact with any fresh, primary minerals. Also, there is insufficient sulfide mineralization to call upon an immiscible-sulfide melt as the diamond-forming medium. The association of the diamonds with secondary minerals strongly suggests that the diamonds formed after the initial host peridotite or eclogite, perhaps in conjunction with introduction of metasomatic fluids.

Taylor, L. A.; Taylor, D. S.; Anand, M.; Ketcham, R.; Carlson, W.; Sobolev, N. V.; Pokhilenko, N.

2003-12-01

340

Immunostaining of dissected zebrafish embryonic heart.  

PubMed

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

Yang, Jingchun; Xu, Xiaolei

2012-01-01

341

Immunostaining of Dissected Zebrafish Embryonic Heart  

PubMed Central

Zebrafish embryo becomes a popular in vivo vertebrate model for studying cardiac development and human heart diseases due to its advantageous embryology and genetics 1,2. 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 3. The expression of any gene can be manipulated via morpholino technology or RNA injection 4. Moreover, forward genetic screens have already generated a list of mutants that affect different perspectives of cardiogenesis 5. Whole mount immunostaining is an important technique in this animal model to reveal the expression pattern of the targeted protein to a particular tissue 6. 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.

Yang, Jingchun; Xu, Xiaolei

2012-01-01

342

Isolated dissections and dissecting aneurysms of the posterior inferior cerebellar artery: topic and literature review.  

PubMed

Isolated dissections of the posterior inferior cerebellar artery (PICA) are rare. Thus, no large series of cases have been reported in the literature. Due to limited knowledge regarding the natural history of these lesions and the lack of high-quality evidence supporting various treatment options, management is controversial and practice parameters are ill defined. In order to offer a comprehensive reference for the diagnosis and management of isolated PICA dissections, the authors reviewed the National Library of Medicine from 1966 to October 2001. Twenty-seven patients averaging 43.6 years of age and including 14 males and 13 females were reported. Subarachnoid hemorrhage occurred in 20 patients, and two died. Dissections were located in the proximal PICA in 22 patients and were three times more common on the left side (left:right=3:1). Six patients were managed conservatively, and four with endovascular techniques. Seventeen had open surgery: five underwent resection, two went through trapping, and two had proximal clipping. Wrapping with muscle was performed in two patients, encasement with Sundt clips in two, and four had occipital artery (OA)-PICA bypass surgery. A meticulous analysis of reported cases with regard to clinical and pathological features, management strategies, and outcomes is presented. PMID:12845546

Tawk, Rabih G; Bendok, Bernard R; Qureshi, Adnan I; Getch, Christopher C; Srinivasan, Jayashree; Alberts, Mark; Russell, Eric J; Batjer, H Hunt

2003-07-01

343

Global Phosphoproteome Profiling Reveals Unanticipated Networks Responsive to Cisplatin Treatment of Embryonic Stem Cells ? †  

PubMed Central

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.

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

2011-01-01

344

Acute aortic dissection in a patient receiving gemcitabine and cisplatin.  

PubMed

Acute aortic dissection is often a fatal condition with in-hospital mortality rates of 27%. The incidence of acute aortic dissection is low at around 3 cases per 100,000 person-years. There is a strong relationship between hypertension and aortic dissection. 72% of patients in the International Registry of Acute Aortic Dissection had a history of hypertension. The inciting event is an intimal tear extending into the media with resultant dissection of blood along the laminar planes of the media. Cisplatin, a commonly used platinum-based chemotherapy drug, is associated with the development of hypertension on long-term follow up studies. This knowledge should prompt clinicians to screen for the development of hypertension and to be aware of its potential complications in patients treated with cisplatin-containing chemotherapy. Despite the known vascular complications of chemotherapy, there is a paucity of data on the association of aortic dissection with active cancer or chemotherapy. We present an unusual case of an extensive, acute aortic dissection in a relatively young male patient receiving gemcitabine and cisplatin for advanced metastatic pancreatic adenocarcinoma. PMID:23344098

Madden, George W; Ishaq, Muhammad K; Gupta, Raghav

2014-01-01

345

Isolated dissection of the celiac artery--a case report.  

PubMed

Isolated arterial dissection, which occurs with the absence of aortic dissection, has been reported in carotid and renal arteries but rarely in visceral arteries. A case of isolated celiac artery dissection is reported here. A healthy 58-year-old man experienced sudden upper abdominal pain, which continued for several days. A body computed tomogram (CT) showed a multiple low-density wedge-shaped area in the spleen, which was diagnosed as splenic infarction, and an aneurysm with thrombus in the celiac artery. A selective angiogram showed dilatation of the celiac artery with wall irregularity, and proximal occlusion of the hepatic artery. The distal hepatic artery was fed by collateral arteries from the superior mesenteric artery. Splenic infarction was probably due to the embolism from the thrombus in the dissected celiac artery. The absence of other vascular lesions and causes or risks for the arterial dissection would suggest the occurrence of spontaneous dissection. The dissection of visceral arteries should be considered in diagnosing acute abdominal pain. PMID:10917586

Matsuo, R; Ohta, Y; Ohya, Y; Kitazono, T; Irie, H; Shikata, T; Abe, I; Fujishima, M

2000-07-01

346

Endovascular management of chronic post-dissection aneurysms.  

PubMed

Open repair is still the gold standard in acute type A dissection. Endovascular repair is advocated for complicated acute type B dissections. Recent evidence also supports the role of endovascular repair in a larger proportion of uncomplicated acute type B dissections. The role of endovascular repair in chronic post-dissection aneurysms, however, is still unclear. Most commonly, post-dissection aneurysms involve the thoracoabdominal aorta, making the use of fenestrated/branched stent-grafts to achieve complete aneurysm exclusion mandatory. These fenestrated/branched stent-grafts have been used with success in atherosclerotic thoracoabdominal aortic aneurysms (TAAAs). In chronic post-dissection aneurysms, however, additional technical challenges arise. The usually narrow true lumen makes the use of branches more tedious and overall planning difficult. A second technical challenge relates to the fact that visceral branches can also originate from the false lumen. In such cases, perforation of the stiff chronic dissection flap is required to obtain access to the vessel. During the period January 2010 to November 2013, 17 patients (13 males, mean age 65±7.8 years) with chronic thoracoabdominal aneurismal degeneration following acute dissection were treated in our department with the use of fenestrated/branched stent-grafts. Technical success was achieved in all cases (100%). Perioperative mortality was two (11.8%) patients. One patient died due to multiple organ failure and one due to cardiac failure. No case of paraplegia was observed. During a 12-month median follow-up (range, 4-28 months) no aneurysm-related deaths were observed. Reintervention was required in three cases to repair a type Ib endoleak from a side branch. Endovascular treatment with fenestrated/branched stent-grafts is feasible for chronic post-dissection aneurysms. Standard thoracic stent-grafting is an option in a minority of patients, when the aneurysm is limited to the thoracic segment. Fenestrated and branched devices can successfully be used for aneurysms extending to the thoracoabdominal aorta. PMID:24967171

Oikonomou, Kyriakos; Katsargyris, Athanasios; Ritter, Wolfgang; Spinelli, Domenico; Seto, Yuki; Verhoeven, Eric L

2014-05-01

347

Endovascular management of chronic post-dissection aneurysms  

PubMed Central

Open repair is still the gold standard in acute type A dissection. Endovascular repair is advocated for complicated acute type B dissections. Recent evidence also supports the role of endovascular repair in a larger proportion of uncomplicated acute type B dissections. The role of endovascular repair in chronic post-dissection aneurysms, however, is still unclear. Most commonly, post-dissection aneurysms involve the thoracoabdominal aorta, making the use of fenestrated/branched stent-grafts to achieve complete aneurysm exclusion mandatory. These fenestrated/branched stent-grafts have been used with success in atherosclerotic thoracoabdominal aortic aneurysms (TAAAs). In chronic post-dissection aneurysms, however, additional technical challenges arise. The usually narrow true lumen makes the use of branches more tedious and overall planning difficult. A second technical challenge relates to the fact that visceral branches can also originate from the false lumen. In such cases, perforation of the stiff chronic dissection flap is required to obtain access to the vessel. During the period January 2010 to November 2013, 17 patients (13 males, mean age 65±7.8 years) with chronic thoracoabdominal aneurismal degeneration following acute dissection were treated in our department with the use of fenestrated/branched stent-grafts. Technical success was achieved in all cases (100%). Perioperative mortality was two (11.8%) patients. One patient died due to multiple organ failure and one due to cardiac failure. No case of paraplegia was observed. During a 12-month median follow-up (range, 4-28 months) no aneurysm-related deaths were observed. Reintervention was required in three cases to repair a type Ib endoleak from a side branch. Endovascular treatment with fenestrated/branched stent-grafts is feasible for chronic post-dissection aneurysms. Standard thoracic stent-grafting is an option in a minority of patients, when the aneurysm is limited to the thoracic segment. Fenestrated and branched devices can successfully be used for aneurysms extending to the thoracoabdominal aorta.

Oikonomou, Kyriakos; Katsargyris, Athanasios; Ritter, Wolfgang; Spinelli, Domenico; Seto, Yuki

2014-01-01

348

Quantitative NMR  

NSDL National Science Digital Library

This site features a learning module focused on principles and practice of NMR for quantitative analysis, an application less commonly associated with the technique than is structure determination. Links to simulation packages are included.

Korir, Albert K.; Larive, Cynthia K.

2011-07-18

349

On Quantitizing  

PubMed Central

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.

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

2009-01-01

350

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

PubMed Central

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.

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

2013-01-01

351

Neck dissection with cervical sensory preservation in thyroid cancer  

PubMed Central

Thyroid cancer is the most common endocrine malignancy. Recently, controversy has focused on the management of lymph node metastases, which represent approximately 90% of disease recurrences and may require considerable time, effort, and resources to diagnose and treat. Neck dissections play an essential role in the management of head and neck cancer. A modified radical neck dissection (MND) refers to resection of the lymph nodes in levels II through V and often including the central nodes in level VI. When performing modified neck dissection, we recommend to protect more reserved cervical plexus. The purpose is to better protect patient’s neck skin feeling.

Xue, Shuai; Wang, Peisong

2013-01-01

352

Pseudo-dissection of ascending aorta in inferior myocardial infarction  

PubMed Central

Acute aortic dissection is a cardiac emergency which can present as inferior myocardial infarction. It has high morbidity and mortality requiring prompt diagnosis and treatment. Rapid advances in non-invasive imaging have facilitated the early diagnosis of this condition and in ruling out this potentially catastrophic illness. We report an interesting case of a 57-year old man who presented with inferior myocardial infarction requiring thrombolysis and temporary pacing wire for complete heart block. An echocardiogram was highly suspicious of aortic dissection. CT scan confirmed that the malposition of the temporary pacing wire through the aorta mimicked aortic dissection.

Attar, Muhammad Nadeem; Elmahy, Hossam; Goode, Grahame K.

2011-01-01

353

Pulmonary multislice computed tomography findings in acute aortic dissection  

PubMed Central

Objective To document the type and incidence of pulmonary multislice computed tomography (CT) findings at presentation in patients with acute aortic dissection. Materials and methods Multidetector CT scans of 36 patients with a diagnosis of acute aortic dissection or intramural hematoma were retrospectively reviewed. Results Pleural effusion, dependent stasis, mosaic attenuation, interlobular septal thickening, thickening of the peribronchovascular interstitium, vascular enlargement, compression atelectasis were common findings. Additionally air trapping, emphysema, consolidation, nodules, bronchiectasis or scarring were also noted. Conclusions Various pulmonary imaging findings may accompany acute aortic dissection. These findings and their clinical significance should be further investigated.

Okur, Aysegul; Sahin, Sinan

2012-01-01

354

Severe Orthostatic Hypotension due to Unilateral Carotid Artery Dissection  

PubMed Central

A 46-year-old woman was admitted to our hospital with mild right-sided hemiparesis and orthostatic hypotension. Magnetic resonance angiography of the neck showed stenosis of the left distal carotid sinus surrounded by intraluminal hyperintensities on both T1-weighted and T2-weighted images, representing a periluminal hematoma secondary to carotid artery dissection. The dissection hyper-extended the carotid artery wall and stimulated baroreceptors in the carotid sinus. The stimulated baroreceptors induced carotid sinus hypersensitivity, which may have been related to her orthostatic hypotension. Post-stroke orthostatic hypotension should prompt consideration of carotid artery dissection.

Ishii, Nobuyuki; Mochizuki, Hitoshi; Taniguchi, Akitoshi; Shiomi, Kazutaka; Nakazato, Masamitsu

2014-01-01

355

Intimal intussusception in aortic dissection and coexisting coronary artery disease.  

PubMed

Intimal tear is rarely circumferential in aortic dissection. In such an instance, intimal intussusception may occur. This exposes the patient to the additional risk of severe aortic regurgitation, blockage of the left main coronary artery ostium, or both in proximal intimal intussusception in ascending aortic dissection. Here we present a 61-year-old patient with ascending aortic dissection, aortic regurgitation caused by an intussuscepted proximal intimal flap, and coexisting coronary artery disease. The presenting symptoms and electrocardiographic findings simulated an acute coronary syndrome. Among other diagnostic measures, only transesophageal echocardiography clearly defined the pathologic condition. The patient underwent a successful aortic root replacement and coronary artery bypass grafting. PMID:24484815

K?z?ltan, H Tar?k; T?ra?, Münir; Idem, Asl?; Camsar?, Rahime; Tokta?, Sebahattin; Bozkurt, Abdi

2014-02-01

356

Quantitative Research  

Microsoft Academic Search

\\u000a By means of the previously introduced Research Pyramid this chapter provides a concise overview of the quantitative research\\u000a approach. The essence of quantitative research is to use a ‘theory’ to frame and thus understand the problem at hand. Its\\u000a starting point if not focus can be to contribute to the development of theory. It is grounded in the basic attitude

Jan Jonker; Bartjan W. Pennink

357

Dissecting Motivational Circuitry to Understand Substance Abuse  

PubMed Central

Summary An important goal of cocaine addiction research is to understand the neurobiological mechanisms underlying this disease state. Here, we review studies from our laboratory that examined nucleus accumbens (NAc) cell firing and rapid dopamine signaling using electrophysiological and electrochemical recordings in behaving rodents. A major advantage of these techniques is that they allow for the characterization of NAc activity and rapid dopamine release during specific phases of motivated behavior. Moreover, each approach enables an examination of the dynamic nature of NAc signaling as a function of factors such as hedonics and associative learning. We show that NAc neurons differentially respond to rewarding and aversive stimuli and their predictors in a bivalent manner. This differential responding is modifiable and can be altered by the presentation of other natural rewards or cocaine. Likewise, the dynamic nature of NAc cell firing is also reflected in the differential activation of distinct populations of NAc neurons during goal-directed behaviors for natural versus drug rewards, and the heightened activation of some NAc neurons following cocaine abstinence. Our electrochemical data also show that rapid dopamine signaling in the NAc reflects primary rewards and their predictors and appears to modulate specific NAc neuronal responses. In some cases, these influences are observed in a regionally specific manner that matches previous pharmacological manipulations. Collectively, these findings provide critical insight into the functional organization of the NAc that can be used to guide additional studies aimed at dissecting the neural code underlying compulsive drug-seeking behavior.

Wheeler, Robert A.; Carelli, Regina M.

2009-01-01

358

Dissecting soil moisture-precipitation coupling  

NASA Astrophysics Data System (ADS)

The ability of soil moisture to affect precipitation (SM-P) can be dissected into the ability of soil moisture to affect evapotranspiration (ET; SM-ET) and the ability of ET to affect precipitation (ET-P). SM-ET is a local process that is relatively easy to quantify, but ET-P includes nonlocal atmospheric processes and is more complex. Here, ET-P is quantified both locally and remotely with a back-trajectory method for water vapor transport, using corrected reanalysis data. It is found that, for SM-P and ET-P, local impact is greater than that from remote for most land areas with significant local impacts. By examining the responses of the three metrics (SM-ET, ET-P, and SM-P) to climate variations over different climate regimes, we show that SM-ET is the principal factor that determines the spatial pattern and variation of SM-P. For climatologically wet regions, SM-ET and SM-P are higher during dry periods, and vice versa for climatologically dry regions. All three metrics show highest values over the transitional zones.

Wei, Jiangfeng; Dirmeyer, Paul A.

2012-10-01

359

Paediatric tonsillectomy: radiofrequency-based plasma dissection compared to cold dissection with sutures  

PubMed Central

Summary Aim of this study was to compare post-operative recovery over 14 days in children submitted to tonsillectomy using a bipolar radiofrequency-based plasma device (Coblation®, Evac 70, ArthroCare Corp, Sunnyvale, CA, USA) to cold dissection. Paediatric patients (n = 42) aged 5-16 years old with chronic tonsillitis underwent tonsillectomy using cold dissection with suture ligatures or a plasma device (Evac 70, ArthroCare Corp, Sunnyvale, CA, USA). Pain intensity on the first day, use of analgesics, type of diet, and days of pain, fever, nausea, and absence from school were determined. Groups were compared using time-to-event (Kaplan-Meier) curves and statistically evaluated using the Breslow (generalized Wilcoxon) test. Children undergoing plasma tonsillectomy reported significantly less pain on the first post-operative day (1.2 ± 0.9 vs. 3.5 ± 1.5, p < 0.001), fewer days of pain (4.8 ± 1.5 vs. 9.4 ± 1.2, p < 0.001), pain medication withdrawal (2.6 ± 1.3 vs. 4.5 ± 1.3, p < 0.001) and earlier use of liquid diet (5.1 ± 1.4 vs. 8.5 ± 2.1, p < 0.001), and fewer school days lost (5.3 ± 1.7 vs. 8.9 ± 1.5, p < 0.001). After completing this study, plasma tonsillectomy was adopted for the majority of cases. Benefits of the plasma device include the possibility both to excise tissue and coagulate bleeding vessels using the same device whilst improving quality of post-operative recovery over cold dissection with suture ligatures.

Di Rienzo Businco, L; Coen Tirelli, G

2008-01-01

360

Radical lymph node dissection for gallbladder cancer: indications and limitations.  

PubMed

Radical lymph node dissection provides survival benefit for patients with pT2 or more advanced gallbladder carcinoma tumors only if potentially curative resection is feasible; it must always be considered when planning a resection or re-resection for robust patients with pT2 or more advanced gallbladder carcinoma tumors. The degree of radical lymphadenectomy depends on clinically assessed nodal status: portal lymph node dissection is limited to cN0 disease; extended portal nodal dissection is indicated for cN0 and a modest degree of cN1 disease; peripancreatic lymph node dissection with pancreaticoduodenectomy is indicated for selected cases of evident peripancreatic nodal disease and/or direct organ involvement. Extended resection with extensive lymphadenectomy should be limited to expert surgeons because it may cause serious morbidity and mortality. PMID:17336245

Shirai, Yoshio; Wakai, Toshifumi; Hatakeyama, Katsuyoshi

2007-01-01

361

Vertebral artery dissection as a cause of cervical radiculopathy.  

PubMed

The acute onset of neck pain and arm weakness is most commonly due to cervical radiculopathy or inflammatory brachial plexopathy. Rarely, extracranial vertebral artery dissection may cause radiculopathy in the absence of brainstem ischemia. We describe a case of vertebral artery dissection presenting as cervical radiculopathy in a previously healthy 43-year-old woman who presented with proximal left arm weakness and neck pain aggravated by movement. Cervical magnetic resonance imaging (MRI) and angiography revealed dissection of the left vertebral artery with an intramural hematoma compressing the left C5 and C6 nerve roots. Antiplatelet treatment was commenced, and full power returned after 2 months. Recognition of vertebral artery dissection on cervical MRI as a possible cause of cervical radiculopathy is important to avoid interventions within the intervertebral foramen such as surgery or nerve root sleeve injection. Treatment with antithrombotic agents is important to prevent secondary ischemic events. PMID:24353851

Silbert, Benjamin Isaac; Khangure, Mark; Silbert, Peter Linton

2013-12-01

362

Complicated Postpartum Type B Aortic Dissection and Endovascular Repair  

PubMed Central

BACKGROUND Fifty percent of aortic dissections in women younger than 40 years occur in association with pregnancy. Of these, half of type B dissections occur in the postpartum period. CASE A 30-year-old woman was status post spontaneous vaginal delivery at 30 weeks of gestation for fetal death, complicated by an eclamptic seizure. On post-partum day 4, she suffered an acute, complicated type B aortic dissection treated with endovascular stent graft placement. CONCLUSION Endovascular repair may be an attractive option for the treatment of complicated type B aortic dissections in pregnancy and the peripartum period, with reduced maternal and fetal mortality. This may allow the fetus to remain in situ and avoid the risks of surgery and possible cardiopulmonary bypass, with little radiation risk to the fetus.

Rosenberger, Laura H.; Adams, Joshua D.; Kern, John A.; Tracci, Margaret C.; Angle, J. Fritz; Cherry, Kenneth J.

2012-01-01

363

Dissection Videos Do Not Improve Anatomy Examination Scores  

NSDL National Science Digital Library

This article describes the effect and student perception of showing dissection videos on first-year medical students' performance in terms of test scores during a gross anatomy course. The article describes the methods and outcomes.

Waqas Mahmud (Rawalpindi Medical College Anatomy); Omar Hyder (Rawalpindi Medical College Obstetrics and Gynecology); Jamaal Butt (Rawalpindi Medical College Anatomy); Arsalan Aftab (Rawalpindi Medical College Anatomy)

2011-01-03

364

Dissection of cranial arteries in the neck: correlation of MRI and arteriography  

Microsoft Academic Search

Retrospective correlation of MRI and angiographic findings in nine patients with suspected cervical vascular dissections revealed MRI evidence of vessel abnormalities in eight patients, seven of whom proved to have arterial dissections. One patient whose MRI showed no abnormalities also proved to have a dissection, shown by angiography. Two patients had associated pseudoaneurysms not demonstrated by MRI. Five dissections involved

D. E. Sue; M. N. Brant-Zawadzki; J. Chance

1992-01-01

365

The first cut is the deepest: reflections on the state of animal dissection in biology education  

Microsoft Academic Search

In biology education, the study of structure has traditionally involved the use of dissection. Animal?rights campaigners have caused biology educators and learners to question the necessity of dissections. This study reviews the research evidence for the efficacy of alternatives to dissection and then turns to research evidence on attitudes to dissection. It suggests that the place, practice, and purpose of

Rian De Villiers; Martin Monk

2005-01-01

366

Three-Dimensional CT in Isolated Dissecting Aneurysm of the Superior Mesenteric Artery: A Case Report  

Microsoft Academic Search

Isolated dissecting aneurysm of the superior mesenteric artery (SMA) without aortic dissection is a rare condition. We report a case of isolated dissecting aneurysm of the SMA incidentally detected by postcontrast abdominal computed tomography (CT). Three-dimensional CT using helical scanning was helpful for the evaluation of dissecting aneurysmal structures such as the intimal flap, true lumen, and false lumen with

Takao Sagiuchi; Yuuji Asano; Hisashi Yanaihara; Yuki Aoki; Reiko Woodhams; Kazushige Hayakawa

367

Flip-flop phenomenon and dissection of extracranial carotid artery  

SciTech Connect

A case of extracranial carotid artery dissection investigated both by conventional brain imaging and by arteriography is presented. The radionuclide angiogram showed a flip-flop phenomenon on the left hemisphere. The implications, including clinical features, pathogenesis, diagnosis, and treatment are discussed. Dissection of extracranial carotid artery is a cause of carotid hypoactivity, and this phenomenon is associated directly with a flip-flop phenomenon on brain imaging.

Verreault, J.; Cote, C.

1986-04-01

368

Radical lymph node dissection for cancer of the thoracic esophagus.  

PubMed Central

OBJECTIVE: The authors documented the localization and frequency of lymphatic spread in squamous cell carcinoma of the thoracic esophagus and evaluated the influence of radical systematic lymph node dissection on patient survival. SUMMARY BACKGROUND DATA: From accumulated surgical experience, it was suggested that some of the patients with lymph nodal involvement from cancer could be cured by its clearance. However, it is only recently that cancer of the esophagus has been evaluated in terms of analyzing lymphatic spread and results of lymphadenectomy. METHODS: Among 1298 patients admitted to the Toranomon Hospital between 1973 and 1993, 913 (70.3%) had resections, including curative and palliative procedures. For this study, 717 patients with TNM RO (resection with no residual tumor at operation in TNM classification) were analyzed. Survival was compared between groups of patients with less extensive thoracoabdominal (two-field) dissections and extensive collothoracoabdominal (three-field) dissections. RESULTS: Comparative study revealed that 5-year survival rate for TNM RO patients after free-field dissection (55.0%) was significantly better (log rank test, p = 0.0013) than the rate after two-field dissection (38.3%). The results were particularly significant in subgroups with stage III and IV (because of nodal factor). Overall 5-year survival rate after all resections was 42.4%. CONCLUSIONS: The role of radical lymph node dissection in cancer of the thoracic esophagus evaluated. Long-term survival was compared between two groups with two- and three-field dissection. It was concluded that survival rate was significantly better in patients with extensive three-field dissection.

Akiyama, H; Tsurumaru, M; Udagawa, H; Kajiyama, Y

1994-01-01

369

Delayed aortic dissection after transcatheter aortic valve implantation.  

PubMed

In selected high-risk patients with aortic stenosis, transcatheter aortic valve implantation (TAVI) can provide comparable functional improvement and early survival after surgical aortic valve replacement. However, the long-term outcome after TAVI is still to be determined and the occurrence of aortic dissection has not been systematically reported. Herein, a case is presented of delayed aortic dissection and rupture several months after an uneventful TAVI in a patient with bicuspid aortic valve stenosis. PMID:24383384

Al-Attar, Nawwar; Himbert, Dominique; Barbier, François; Vahanian, Alec; Nataf, Patrick

2013-09-01

370

FBN1 Mutations in Patients With Descending Thoracic Aortic Dissections  

PubMed Central

Aortic aneurysm and dissection cause significant morbidity and mortality. There are several known single gene disorders that predispose to isolated aortic disease and eventually aneurysm and dissection. FBN1 mutations are associated with multiple clinical phenotypes, including Marfan syndrome (MFS), MASS phenotype, and familial ectopia lentis, but rarely with isolated aortic aneurysm and dissection. In this report, we describe three patients who presented with primary descending thoracic aortic dissection and who were found to have an FBN1 mutation. None of the patients fulfilled clinical criteria for the diagnosis of MFS, and all had few or none of the skeletal features typical of the condition. Two patients had a history of long-term hypertension, and such a history was suspected in the third patient. These observations suggest that some individuals with FBN1 mutations have significant aortic disease involvement of other systems that is typical of FBN1 mutation-related syndromes. Superimposed risk factors, such as hypertension, may weaken the aortic wall and eventually lead to aortic dissection. Given that the cost continues to decrease, we suggest that diagnostic DNA sequencing for FBN1 mutations in patients with thoracic aortic aneurysms and dissection may be a practical clinical step in evaluating such patients and at-risk family members.

Brautbar, Ariel; LeMaire, Scott A.; Franco, Luis M.; Coselli, Joseph S.; Milewicz, Dianna M.; Belmont, John W.

2013-01-01

371

[Aortic aneurysms and aortic dissection: epidemiology, pathophysiology and diagnostics].  

PubMed

Aortic aneurysms and aortic dissection represent a significant health risk due to the demographic developments and current life styles. The mortality of ruptured aortic aneurysms is up to 80 % and the prevalence of aneurysms varies depending on the localization (thoracic or abdominal). Most commonly affected is the infrarenal abdominal aorta; however, there is evidence that the prevalence is diminishing but in contrast the incidence of thoracic aortic aneurysms is increasing. Aortic dissection is often fatal and is the most common acute aortic disease but the incidence is presumed to be underestimated. The pathogenesis of aortic aneurysms is manifold and is based on an interplay between degenerative, proteolytic and inflammatory processes. An aortic dissection arises from a tear in the intima which results in a separation of the aortic wall layers with infiltration of bleeding and the danger of aortic rupture. Various genetic disorders of connective tissue promote degeneration of the aortic media, most notably Marfan syndrome. Risk factors for aortic aneurysms and aortic dissection are nicotine abuse, arterial hypertension, age and male gender. Aortic aneurysms initially have an uneventful course and as a consequence are mostly discovered incidentally. The clinical course and symptoms of aortic dissection are very much dependent on the section of the aorta affected and the manifestations are manifold. Acute aortic dissection is in 80 % of cases first manifested as sudden extremely severe pain. The diagnostics and subsequent course control can be achieved by a variety of imaging procedures but the modality of choice is computed tomography. PMID:23558776

Baumann, F; Makaloski, V; Diehm, N

2013-05-01

372

Applications of quantitative whole body autoradiographic technique in radiopharmaceutical research  

SciTech Connect

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.

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

1982-01-01

373

On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation  

PubMed Central

Background Protein sequence similarities to any types of non-globular segments (coiled coils, low complexity regions, transmembrane regions, long loops, etc. where either positional sequence conservation is the result of a very simple, physically induced pattern or rather integral sequence properties are critical) are pertinent sources for mistaken homologies. Regretfully, these considerations regularly escape attention in large-scale annotation studies since, often, there is no substitute to manual handling of these cases. Quantitative criteria are required to suppress events of function annotation transfer as a result of false homology assignments. Results The sequence homology concept is based on the similarity comparison between the structural elements, the basic building blocks for conferring the overall fold of a protein. We propose to dissect the total similarity score into fold-critical and other, remaining contributions and suggest that, for a valid homology statement, the fold-relevant score contribution should at least be significant on its own. As part of the article, we provide the DissectHMMER software program for dissecting HMMER2/3 scores into segment-specific contributions. We show that DissectHMMER reproduces HMMER2/3 scores with sufficient accuracy and that it is useful in automated decisions about homology for instructive sequence examples. To generalize the dissection concept for cases without 3D structural information, we find that a dissection based on alignment quality is an appropriate surrogate. The approach was applied to a large-scale study of SMART and PFAM domains in the space of seed sequences and in the space of UniProt/SwissProt. Conclusions Sequence similarity core dissection with regard to fold-critical and other contributions systematically suppresses false hits and, additionally, recovers previously obscured homology relationships such as the one between aquaporins and formate/nitrite transporters that, so far, was only supported by structure comparison.

2014-01-01

374

Pediatric tonsillectomy: post-operative morbidity comparing microsurgical bipolar dissection versus cold sharp dissection.  

PubMed

A prospective single-blinded study was conducted to compare pediatric tonsillectomy using the traditional cold sharp dissection with ligation for securing hemostasis (CSDL) versus microsurgical bipolar dissection technique (MBCT). Sixty children aged between 2 and 14 years were sequentially assigned to each group. Blood loss and postoperative pain in the first hour were markedly decreased in the MBCT group (P < 0.0001 and P < 0.05, respectively). Average surgical time was slightly decreased in diathermy tonsillectomy (15'30") compared with the cold technique (16'30"). Return to normal diet was significantly earlier in the CSDL group (P < 0.05). Late postoperative pain measured on the tenth day showed a moderate increase in children who underwent MBCT. There was no difference between the two techniques in the incidence of postoperative hemorrhage. No major complications occurred. We believe MBCT is a fast and safe technique which may be useful in children with known bleeding disorders. However, it increases late postoperative pain and, therefore, delay in patients' return to normal activities. Consequently, it does not represent a significant advantage over the traditional CSDL procedure. PMID:9350490

Lassaletta, L; Martín, G; Villafruela, M A; Bolaños, C; Alvarez-Vicent, J J

1997-09-18

375

Rapidly Aggravated Dissecting Flap by Angiography during Percutaneous Stent Placement for Acute Isolated Superior Mesenteric Artery Dissection  

PubMed Central

Acutely aggravated dissecting flap and consequent occlusion of the superior mesenteric artery (SMA) by simple contrast passage during initial angiography for percutaneous stent placement is a uncommon event, which usually is not reported. After analysis of many factors that underlie development of such complications, we present herein one case of successful treatment of isolated SMA dissection and its complications with favorable outcomes during 25 months follow-up after percutaneous stent placement.

Yang, Hye Jin; Son, Tae Jun; Jung, Yoon Young; Choi, Seung A; Lee, Suk Hoon

2011-01-01

376

Gastric obstruction after endoscopic submucosal dissection  

PubMed Central

Background Bleeding and perforation are two major complications of gastric endoscopic submucosal dissection (ESD). There are only a few reports concerning gastric obstruction related to ESD in the stomach. Objective The aim of this study was to clarify the clinicopathological features of patients who experienced gastric obstruction after gastric ESD. Methods Clinicopathological data of 1878 patients who underwent gastric ESD from September 2002 to December 2010 were retrospectively reviewed. Data of lesion location, circumference, circumferential extent of ESD ulcer, specimen diameter, depth of cancer, ulcer findings within the lesion, curability of ESD, number of simultaneous lesions, and occurrence of post-operative bleeding and perforation were collected. The risk of gastric obstruction regarding lesion and procedure related factors were assessed, and treatment for these patients was studied. Results Gastric obstruction was observed in 2.5% of the patients (47/1878). Symptoms occurred in a median of 24 days after ESD. The incidence among patients with lesions in the upper part of the stomach was 4.7% (17/316), 0.36% (3/818) in the middle, and 3.8% (27/699) in the lower part. In relation to the circumferential extent, the incidence was 50% (33/66) among patients with a resection of >75% of the circumference. Stenosis was observed in 87% (41/47) of patients with gastric obstruction. Endoscopic balloon dilation was performed in 45 patients. Perforation due to EBD occurred in four patients; one was referred to surgery. Conclusions Patients with a wide resection of >75% of the circumference should be considered for early repeat endoscopy after ESD, and dilation should be performed with caution if found to have stenosis.

Tanaka, Masaki; Sawai, Hiroaki; Imai, Kenichiro; Kawata, Noboru; Hagiwara, Tomoko; Takao, Toshitatsu; Hotta, Kinichi; Yamaguchi, Yuichiro; Takizawa, Kohei; Matsubayashi, Hiroyuki; Ono, Hiroyuki

2013-01-01

377

QUANTITATIVE MORPHOLOGY  

EPA Science Inventory

Abstract: In toxicology, the role of quantitative assessment of brain morphology can be understood in the context of two types of treatment-related alterations. One type of alteration is specifically associated with treatment and is not observed in control animals. Measurement ...

378

Combining Quantitative Trait Loci Analysis and an Ecophysiological Model to Analyze the Genetic Variability of the Responses of Maize Leaf Growth to Temperature and Water Deficit  

Microsoft Academic Search

Ecophysiological models predict quantitative traits of one genotype in any environment, whereas quantitative trait locus (QTL) models predict the contribution of alleles to quantitative traits under a limited number of environments. We have combined both approaches by dissecting into effects of QTLs the parameters of a model of maize (Zea mays) leaf elongation rate (LER; H. Ben Haj Salah, F.

Matthieu Reymond; Bertrand Muller; Agnes Leonardi; Alain Charcosset; Francois Tardieu

2003-01-01

379

Intravascular stenting of acute experimental type B dissections.  

PubMed

To evaluate the efficacy of intravascular stenting for acute aortic dissection, 12 dogs underwent surgical creation of an acute type B dissection. Intravascular ultrasound evaluated luminal diameter, distal propagation, and branch involvement. Three animals underwent no further treatment (control). In 9 dogs, balloon-expandable intravascular stents (15-20 mm) were placed proximally to compress the intimal flap. One dog with a small dissection had complete obliteration of the false lumen after initial stent placement. Six dogs with extension below the diaphragm were initially stented proximally to restore flow; 3 were left with a residual distal false lumen, while 3 had additional stents placed to obliterate their entire false lumen. In the final 2 dogs, proximal stenting resulted only in partial compression of the false lumen. Two animals died within 24 hr due to prolonged hemodynamic instability and aortic rupture at the intimal flap, respectively. Six weeks later, radiologic and histologic evaluation was performed on the 10 surviving animals. All stented true lumens were patent without thrombus formation, and stents were covered by neointima. In dogs with stenting of the entire dissection, the aortic wall had healed and no false lumen was present. However, in all dogs with only proximal obliteration, 1/2 with partial compression, and 2/3 controls, a patent false channel was present indicative of a chronic dissection. Thus, we found that intravascular stents can restore true lumen flow and obliterate the false lumen in experimental dissections; however, stenting limited to the proximal dissection does not prevent formation of a chronic residual patent false lumen. PMID:8331933

Moon, M R; Dake, M D; Pelc, L R; Liddell, R; Castro, L J; Mitchell, R S; Miller, D C

1993-04-01

380

3D segmentation of the true and false lumens on CT aortic dissection images  

NASA Astrophysics Data System (ADS)

Our works are related to aortic dissections which are a medical emergency and can quickly lead to death. In this paper, we want to retrieve in CT images the false and the true lumens which are aortic dissection features. Our aim is to provide a 3D view of the lumens that we can difficultly obtain either by volume rendering or by another visualization tool which only directly gives the outer contour of the aorta; or by other segmentation methods because they mainly directly segment either only the outer contour of the aorta or other connected arteries and organs both. In our work, we need to segment the two lumens separately; this segmentation will allow us to: distinguish them automatically, facilitate the landing of the aortic prosthesis, propose a virtual 3d navigation and do quantitative analysis. We chose to segment these data by using a deformable model based on the fast marching method. In the classical fast marching approach, a speed function is used to control the front propagation of a deforming curve. The speed function is only based on the image gradient. In our CT images, due to the low resolution, with the fast marching the front propagates from a lumen to the other; therefore, the gradient data is insufficient to have accurate segmentation results. In the paper, we have adapted the fast marching method more particularly by modifying the speed function and we succeed in segmenting the two lumens separately.

Fetnaci, Nawel; ?ubniewski, Pawe?; Miguel, Bruno; Lohou, Christophe

2013-03-01

381

Traumatic internal carotid artery dissections caused by blunt softball injuries.  

PubMed

This report describes recently treated patients with carotid artery dissection caused by blunt softball injuries, as well as the results of a study of carotid artery trauma in a community. Data obtained through the medical records linkage system used for epidemiologic studies in Olmsted County, MN were used to identify all cases of traumatic internal carotid artery dissection diagnosed from 1987 through 1994. Four patients with traumatic internal carotid artery dissections were identified during the 8-year period under study. In two patients (50%) the carotid dissection was a result of the direct impact of a softball. A 39-year-old-man, who developed transient cerebral ischemic symptoms, and a 35-year-old woman, who developed a painful Horner's syndrome, were struck by a softball on the anterolateral aspect of the neck. Both patients had a low carotid bifurcation. These data suggest that internal carotid artery dissections may be underrecognized sequelae of direct softball injuries to the anterolateral neck. A low carotid bifurcation may be a risk factor for such injuries. PMID:9517699

Schievink, W I; Atkinson, J L; Bartleson, J D; Whisnant, J P

1998-03-01

382

Central neck dissection in differentiated thyroid cancer: technical notes.  

PubMed

Differentiated thyroid cancers may be associated with regional lymph node metastases in 20-50% of cases. The central compartment (VIupper VII levels) is considered to be the first echelon of nodal metastases in all differentiated thyroid carcinomas. The indication for central neck dissection is still debated especially in patients with cN0 disease. For some authors, central neck dissection is recommended for lymph nodes that are suspect preoperatively (either clinically or with ultrasound) and/or for lymph node metastases detected intra-operatively with a positive frozen section. In need of a better definition, we divided the dissection in four different areas to map localization of metastases. In this study, we present the rationale for central neck dissection in the management of differentiated thyroid carcinoma, providing some anatomical reflections on surgical technique, oncological considerations and analysis of complications. Central neck dissection may be limited to the compartments that describe a predictable territory of regional recurrences in order to reduce associated morbidities. PMID:24711677

Giugliano, G; Proh, M; Gibelli, B; Grosso, E; Tagliabue, M; De Fiori, E; Maffini, F; Chiesa, F; Ansarin, M

2014-02-01

383

Computed Tomography of Aortic Wall Calcifications in Aortic Dissection Patients  

PubMed Central

Objectives To investigate the frequency of aortic calcifications at the outer edge of the false lumen and the frequency of fully circular aortic calcifications in a consecutive series of patients with aortic dissection who underwent contrast-enhanced CT. Methods The study population compromised of 69 consecutive subjects aged 60 years and older with a contrast-enhanced CT scan demonstrating an aortic dissection. All CT scans were evaluated for the frequency of aortic calcifications at the outer edge of the false lumen and the frequency of fully circular aortic calcifications by two experienced observers. Between observer reliability was evaluated by using Cohen’s Kappa. Differences between groups were tested using unpaired T test and Chi-square test. Results Presumed media calcifications were observed in 22 (32%) patients of 60 years and older and were found more frequently in chronic aortic dissection (N?=?12/23, 52%) than in acute aortic dissection (N?=?10/46, 22%). Conclusion As the intima has been torn away by the aortic dissection it is highly likely that CT scans can visualize the calcifications in the tunica media of the aorta.

de Jong, Pim A.; Hellings, Willem E.; Takx, Richard A. P.; Isgum, Ivana; van Herwaarden, Joost A.; Mali, Willem P. Th. M.

2014-01-01

384

Unraveling pancreatic islet biology by quantitative proteomics  

PubMed Central

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.

Zhou, Jian-Ying; Dann, Geoffrey P; Liew, Chong Wee; Smith, Richard D; Kulkarni, Rohit N; Qian, Wei-Jun

2011-01-01

385

Unraveling pancreatic islet biology by quantitative proteomics  

SciTech Connect

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.

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

2011-08-01

386

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

Microsoft Academic Search

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

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

2010-01-01

387

Genetic dissection of maize phenology using an intraspecific introgression library  

PubMed Central

Background Collections of nearly isogenic lines where each line carries a delimited portion of a donor source genome into a common recipient genetic background are known as introgression libraries and have already shown to be instrumental for the dissection of quantitative traits. By means of marker-assisted backcrossing, we have produced an introgression library using the extremely early-flowering maize (Zea mays L.) variety Gaspé Flint and the elite line B73 as donor and recipient genotypes, respectively, and utilized this collection to investigate the genetic basis of flowering time and related traits of adaptive and agronomic importance in maize. Results The collection includes 75 lines with an average Gaspé Flint introgression length of 43.1 cM. The collection was evaluated for flowering time, internode length, number of ears, number of nodes (phytomeres), number of nodes above the ear, number and proportion of nodes below the ear and plant height. Five QTLs for flowering time were mapped, all corresponding to major QTLs for number of nodes. Three additional QTLs for number of nodes were mapped. Besides flowering time, the QTLs for number of nodes drove phenotypic variation for plant height and number of nodes below and above the top ear, but not for internode length. A number of apparently Mendelian-inherited phenotypes were also observed. Conclusions While the inheritance of flowering time was dominated by the well-known QTL Vgt1, a number of other important flowering time QTLs were identified and, thanks to the type of plant material here utilized, immediately isogenized and made available for fine mapping. At each flowering time QTL, early flowering correlated with fewer vegetative phytomeres, indicating the latter as a key developmental strategy to adapt the maize crop from the original tropical environment to the northern border of the temperate zone (southern Canada), where Gaspé Flint was originally cultivated. Because of the trait differences between the two parental genotypes, this collection will serve as a permanent source of nearly isogenic materials for multiple studies of QTL analysis and cloning.

2011-01-01

388

Dissecting cellular biomechanics with a laser  

NASA Astrophysics Data System (ADS)

The biological tissues of a developing organism are built and reshaped by the mechanical behavior of individual cells. We probe the relevant cellular mechanics in vivo using laser-microsurgery -- both qualitatively, to assess whether removal of specific cells alters the dynamics of tissue reshaping, and quantitatively, to measure sub-cellular mechanical properties and stresses. I will detail two quantitative microsurgical measurements. The first uses a laser to drill a sub-cellular hole in a sheet of cells. The subsequent retraction of surrounding cells allows one to infer the local mechanical stress. The second uses a laser to isolate a single cell from the rest of a cell sheet. Isolation is accomplished on a microsecond time scale by holographically shaping a single laser pulse. The subsequent retraction (or expansion) of the isolated cell allows one to separate and quantify the effects of internal and external stresses in the determination of cell shape. I will discuss application of these techniques to the time-dependent biomechanics of epithelial tissues during early fruit fly embryogenesis -- specifically during the processes of germband retraction and dorsal closure.

Hutson, M. Shane

2011-10-01

389

Dissection of the atrial wall after mitral valve replacement.  

PubMed Central

We describe an unusual sequela of mitral valve replacement in a 50-year-old woman who had undergone a closed mitral commissurotomy in 1975. She was admitted to our hospital because of mitral restenosis in November 1993, at which time her mitral valve was replaced with a mechanical prosthesis. On the 8th postoperative day, the patient developed symptoms of heart failure; transesophageal echocardiography revealed dissection and rupture of the left atrial wall. At prompt reoperation, we found an interlayer dissection and rupture of the atrial wall into the left atrium. We repaired the ruptured atrial wall with a prosthetic patch. The postoperative course was uneventful, and postoperative transesophageal echocardiography showed normal prosthetic valve function and no dissection. Images

Lukacs, L; Kassai, I; Lengyel, M

1996-01-01

390

Modified prone position to dissect the popliteal fossa  

PubMed Central

Introduction Traditionally, the prone position is used for dissecting the popliteal fossa, which requires endotracheal intubation. Access to the airway in this position is limited, hence the complications. It is not surprising that the prone position is not favoured by the anaesthetists, especially in patients with a high body mass index. We describe a safe and novel alternative to the prone position. Methods The modified prone position (MPP) is described as an alternative position that facilitates access to the airway. Results Between October 2007 and May 2010, 12 patients underwent popliteal fossa dissection using the MPP. All patients had general anaesthesia using a laryngeal mask airway with the exception of one, who had an epidural anaesthesia. There were no airway or haemodynamic complications. The surgical access to the popliteal fossa was as good as with the traditional prone position. Conclusions The MPP was satisfactory for both the surgeon and the anaesthetists. The authors now use this position routinely for dissecting the popliteal fossa.

Boulemden, A; Ritzmann, T; Liptrot, S; Abbas, A

2013-01-01

391

Subareolar dissection for duct ectasia and periareolar sepsis.  

PubMed

Excision of the major duct system of the breast for symptoms owing to mammary duct ectasia may be curative, but recent reports have been less optimistic. A retrospective study (1978-1990) of 46 women (median age 38 years, range 18-78 years) who underwent subareolar dissection with antibiotic cover for symptoms associated with duct ectasia is presented. Thirty-three women presented without symptoms of overt sepsis (periareolar lump, nipple discharge or nipple retraction). Following subareolar dissection, six developed recurrent symptoms and five required further surgery. Thirteen women presented initially with abscesses. Eight abscesses recurred following incision and drainage, and one developed a mammillary fistula. Following subareolar dissection, six developed recurrent sepsis requiring further surgery. PMID:1958981

Hartley, M N; Stewart, J; Benson, E A

1991-10-01

392

Completely thoracoscopic right upper lobectomy and mediastinal lymph node dissection.  

PubMed

Video-assisted thoracoscopic surgery (VATS) has been constantly used in the diagnosis and treatment of intrathoracic disease. The focus of VATS is primarily concerned with the completeness of mediastinal lymph node dissection for lung cancer and the safety of surgery. Here we discuss the feasibility of VATS right upper lobectomy and systematic lymph node dissection, for a 60-year-old woman who was admitted for tumor of the right upper lobe, and describe this treatment method and the major indications. The technique of single-direction lobectomy and mediastinal lymph node dissection is a safe and feasible completely thoracoscopic lobectomy in minimally invasive approach. Single-direction lobectomy can shorten the operation time and reduce the difficulty and complexity of the procedure. The video demonstrates the manipulation of arterial and venous bleeding in thoracoscopic surgery and the skill of single-direction operation. PMID:24409365

Fan, Ping-Ming; Zheng, Wu-Ping; Zheng, Li-Ping; Gao, Bing-Yu; Chen, Guo-Ping; Liu, Yu

2013-12-01

393

Proteomic approaches to dissect platelet function: half the story  

PubMed Central

Platelets play critical roles in diverse hemostatic and pathologic disorders and are broadly implicated in various biological processes that include inflammation, wound healing, and thrombosis. Recent progress in high-throughput mRNA and protein profiling techniques has advanced our understanding of the biological functions of platelets. Platelet proteomics has been adopted to decode the complex processes that underlie platelet function by identifying novel platelet-expressed proteins, dissecting mechanisms of signal or metabolic pathways, and analyzing functional changes of the platelet proteome in normal and pathologic states. The integration of transcriptomics and proteomics, coupled with progress in bioinformatics, provides novel tools for dissecting platelet biology. In this review, we focus on current advances in platelet proteomic studies, with emphasis on the importance of parallel transcriptomic studies to optimally dissect platelet function. Applications of these global profiling approaches to investigate platelet genetic diseases and platelet-related disorders are also addressed.

Gnatenko, Dmitri V.; Perrotta, Peter L.; Bahou, Wadie F.

2006-01-01

394

Spontaneous Dissection of Internal Carotid Artery Masquerading as Angioedema  

PubMed Central

Spontaneous dissection of the internal carotid artery usually presents with stroke-like symptoms secondary to ischemia in its vascular territory, as well as local signs and symptoms, which may include head, face or neck pain, Horner’s syndrome, pulsatile tinnitus, and cranial nerve palsies. We report a case of a 44-year-old healthy white male who presented with tongue swelling mimicking angioedema as an unusual manifestation of spontaneous dissection of the internal carotid artery. Two weeks after the initial presentation, the patient returned with similar symptoms and slurred speech. Upon physical examination, he was noted to have isolated left-sided hypoglossal nerve palsy. Subsequent diagnostic imaging revealed segmental narrowing of the left internal carotid artery. The appearance was consistent with the presence of a spontaneous internal carotid artery dissection with associated pseudoaneurysm formation.

Abhishek, Kumar; Sofi, Umar

2008-01-01

395

Bilateral chylothorax following neck dissection: a case report  

PubMed Central

Background Chylothorax is an extremely rare but potentially life-threatening complication after radical neck dissection. We report the case of a bilateral chylothorax after total thyroidectomy and cervico-central and cervico-lateral lymphadenectomy for thyroid carcinoma. Case presentation A 40-year-old European woman underwent total thyroidectomy and neck dissection for papillary thyroid carcinoma. Postoperatively she developed dyspnoea and pleural effusion. A chylothorax was found and the initial conservative therapy was not successful. She had to be operated on again and the thoracic duct was legated. Conclusion The case presentation reports a very rare complication after total thyroidectomy and neck dissection, but it has to be kept in mind to prevent dangerous complications.

2014-01-01

396

Spontaneous Celiac Artery Dissection Case Report and Literature Review  

PubMed Central

Symptomatic spontaneous celiac artery dissection is a rare condition that is being detected more often with the use of advanced imaging techniques. There is no consensus as to whether surgical or endovascular treatment is more appropriate. We describe the case of a 41-year-old hypertensive woman who presented with the sudden onset of sharp, persistent, right-upper-quadrant abdominal and epigastric pain. Magnetic resonance angiography of the abdomen revealed celiac artery dissection, with a flap compressing the lumen approximately 17 mm from the artery's origin at the aorta. Because of the patient's persistent epigastric pain, endovascular celiac artery stent implantation was performed with the use of 2 overlapping balloon-expandable stents. Twelve months after the procedure, the patient remained asymptomatic, and the stents were patent. This case and others in the medical literature suggest that endovascular treatment can be feasible in symptomatic patients with isolated spontaneous celiac artery dissection.

Obon-Dent, Mauricio; Shabaneh, Bahaeddin; Dougherty, Kathryn G.; Strickman, Neil E.

2012-01-01

397

Completely thoracoscopic right upper lobectomy and mediastinal lymph node dissection  

PubMed Central

Video-assisted thoracoscopic surgery (VATS) has been constantly used in the diagnosis and treatment of intrathoracic disease. The focus of VATS is primarily concerned with the completeness of mediastinal lymph node dissection for lung cancer and the safety of surgery. Here we discuss the feasibility of VATS right upper lobectomy and systematic lymph node dissection, for a 60-year-old woman who was admitted for tumor of the right upper lobe, and describe this treatment method and the major indications. The technique of single-direction lobectomy and mediastinal lymph node dissection is a safe and feasible completely thoracoscopic lobectomy in minimally invasive approach. Single-direction lobectomy can shorten the operation time and reduce the difficulty and complexity of the procedure. The video demonstrates the manipulation of arterial and venous bleeding in thoracoscopic surgery and the skill of single-direction operation.

Fan, Ping-Ming; Zheng, Li-Ping; Gao, Bing-Yu; Chen, Guo-Ping; Liu, Yu

2013-01-01

398

Isolated Spontaneous Celiac Artery Dissection in a 47-Year-Old Man with von Willebrand Disease  

PubMed Central

Isolated spontaneous dissection of the celiac artery is rare, and its occurrence without aortic dissection is even rarer. The typical symptom of this dissection is acute-onset abdominal pain. Complications of the condition include aneurysm formation, rupture, and abdominal-organ ischemia or infarction, especially in the liver or spleen. We report the case of a 47-year-old man with von Willebrand disease who had an isolated spontaneous dissection of the celiac artery. We used computed tomography and computed tomographic angiography in the diagnosis and characterization of the dissection. To our knowledge, this is the first report of celiac artery dissection in a patient with von Willebrand disease.

Rehman, Aziz Ur; Nadella, Srikanth; Sohail, Umair

2014-01-01

399

Isolated spontaneous celiac artery dissection in a 47-year-old man with von Willebrand disease.  

PubMed

Isolated spontaneous dissection of the celiac artery is rare, and its occurrence without aortic dissection is even rarer. The typical symptom of this dissection is acute-onset abdominal pain. Complications of the condition include aneurysm formation, rupture, and abdominal-organ ischemia or infarction, especially in the liver or spleen. We report the case of a 47-year-old man with von Willebrand disease who had an isolated spontaneous dissection of the celiac artery. We used computed tomography and computed tomographic angiography in the diagnosis and characterization of the dissection. To our knowledge, this is the first report of celiac artery dissection in a patient with von Willebrand disease. PMID:24955061

Rehman, Aziz Ur; Almanfi, Abdelkader; Nadella, Srikanth; Sohail, Umair

2014-06-01

400

Determining cell division symmetry through the dissection of dividing cells using single-cell expression analysis.  

PubMed

Symmetric cell divisions give rise to two sister cells that are identical to each other, whereas asymmetric divisions produce two sister cells with distinctive phenotypes. Although cell division symmetry is usually determined on the basis of a few markers or biological functions, the overall similarity between sister cells has not been thoroughly examined at a molecular level. Here we provide a protocol to separate sister embryonic stem cells (ESCs) and to conduct multiplexed gene expression analyses at the single-cell level by using 48 ESC genes. The procedure includes the dissection of dividing, paired sister cells by micromanipulation, followed by cell lysis, reverse transcription, gene-specific cDNA amplification and multiplexed quantitative PCR analyses. This protocol can be completed in 10 d, and it can be readily adapted to other cell types that are able to grow in suspension culture. PMID:24504476

Jasnos, Lukasz; Sawado, Tomoyuki

2014-03-01

401

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

NASA Astrophysics Data System (ADS)

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.

Geiger, Franz M.

2009-05-01

402

Carotid artery dissection secondary to seatbelt trauma: case report.  

PubMed

A postmortem report of a patient with traumatic internal carotid artery dissection, along with evidence strongly suggestive of a car seatbelt as a causative factor, is presented. In this 5-foot subject, the shoulder harness could have been high, over the anterior cervical area. The authors feel this mechanism deserves consideration as one of the important causes of traumatic carotid dissection. If supported by further studies, remedial measures in the form of changes in seatbelt design, or the use of alternate protective measures may be warranted. PMID:2342151