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1

A New Approach for Quantitative Phosphoproteomic Dissection of Signaling Pathways Applied to T Cell Receptor Activation*  

PubMed Central

Reversible protein phosphorylation plays a pivotal role in the regulation of cellular signaling pathways. Current approaches in phosphoproteomics focus on analysis of the global phosphoproteome in a single cellular state or of receptor stimulation time course experiments, often with a restricted number of time points. Although these studies have provided some insights into newly discovered phosphorylation sites that may be involved in pathways, they alone do not provide enough information to make precise predictions of the placement of individual phosphorylation events within a signaling pathway. Protein disruption and site-directed mutagenesis are essential to clearly define the precise biological roles of the hundreds of newly discovered phosphorylation sites uncovered in modern proteomics experiments. We have combined genetic analysis with quantitative proteomic methods and recently developed visual analysis tools to dissect the tyrosine phosphoproteome of isogenic Zap-70 tyrosine kinase null and reconstituted Jurkat T cells. In our approach, label-free quantitation using normalization to copurified phosphopeptide standards is applied to assemble high density temporal data within a single cell type, either Zap-70 null or reconstituted cells, providing a list of candidate phosphorylation sites that change in abundance after T cell stimulation. Stable isotopic labeling of amino acids in cell culture (SILAC) ratios are then used to compare Zap-70 null and reconstituted cells across a time course of receptor stimulation, providing direct information about the placement of newly observed phosphorylation sites relative to Zap-70. These methods are adaptable to any cell culture signaling system in which isogenic wild type and mutant cells have been or can be derived using any available phosphopeptide enrichment strategy. PMID:19605366

Nguyen, Vinh; Cao, Lulu; Lin, Jonathan T.; Hung, Norris; Ritz, Anna; Yu, Kebing; Jianu, Radu; Ulin, Samuel P.; Raphael, Benjamin J.; Laidlaw, David H.; Brossay, Laurent; Salomon, Arthur R.

2009-01-01

2

Quantitative Phosphoproteomics Dissection of Seven-transmembrane Receptor Signaling Using Full and Biased Agonists*  

PubMed Central

Seven-transmembrane receptors (7TMRs) signal through the well described heterotrimeric G proteins but can also activate G protein-independent signaling pathways of which the impact and complexity are less understood. The angiotensin II type 1 receptor (AT1R) is a prototypical 7TMR and an important drug target in cardiovascular diseases. “Biased agonists” with intrinsic “functional selectivity” that simultaneously blocks G?q protein activity and activates G protein-independent pathways of the AT1R confer important perspectives in treatment of cardiovascular diseases. In this study, we performed a global quantitative phosphoproteomics analysis of the AT1R signaling network. We analyzed ligand-stimulated SILAC (stable isotope labeling by amino acids in cell culture) cells by high resolution (LTQ-Orbitrap) MS and compared the phosphoproteomes of the AT1R agonist angiotensin II and the biased agonist [Sar1,Ile4,Ile8]angiotensin II (SII angiotensin II), which only activates the G?q protein-independent signaling. We quantified more than 10,000 phosphorylation sites of which 1183 were regulated by angiotensin II or its analogue SII angiotensin II. 36% of the AT1R-regulated phosphorylations were regulated by SII angiotensin II. Analysis of phosphorylation site patterns showed a striking distinction between protein kinases activated by G?q protein-dependent and -independent mechanisms, and we now place protein kinase D as a key protein involved in both G?q-dependent and -independent AT1R signaling. This study provides substantial novel insight into angiotensin II signal transduction and is the first study dissecting the differences between a full agonist and a biased agonist from a 7TMR on a systems-wide scale. Importantly, it reveals a previously unappreciated diversity and quantity of G?q protein-independent signaling and uncovers novel signaling pathways. We foresee that the amount and diversity of G protein-independent signaling may be more pronounced than previously recognized for other 7TMRs as well. Quantitative mass spectrometry is a promising tool for evaluation of the signaling properties of biased agonists to other receptors in the future. PMID:20363803

Christensen, Gitte L.; Kelstrup, Christian D.; Lyngsø, Christina; Sarwar, Uzma; Bøgebo, Rikke; Sheikh, Søren P.; Gammeltoft, Steen; Olsen, Jesper V.; Hansen, Jakob L.

2010-01-01

3

Quantitative Phosphoproteomics of CXCL12 (SDF-1) Signaling  

PubMed Central

CXCL12 (SDF-1) is a chemokine that binds to and signals through the seven transmembrane receptor CXCR4. The CXCL12/CXCR4 signaling axis has been implicated in both cancer metastases and human immunodeficiency virus type 1 (HIV-1) infection and a more complete understanding of CXCL12/CXCR4 signaling pathways may support efforts to develop therapeutics for these diseases. Mass spectrometry-based phosphoproteomics has emerged as an important tool in studying signaling networks in an unbiased fashion. We employed stable isotope labeling with amino acids in cell culture (SILAC) quantitative phosphoproteomics to examine the CXCL12/CXCR4 signaling axis in the human lymphoblastic CEM cell line. We quantified 4,074 unique SILAC pairs from 1,673 proteins and 89 phosphopeptides were deemed CXCL12-responsive in biological replicates. Several well established CXCL12-responsive phosphosites such as AKT (pS473) and ERK2 (pY204) were confirmed in our study. We also validated two novel CXCL12-responsive phosphosites, stathmin (pS16) and AKT1S1 (pT246) by Western blot. Pathway analysis and comparisons with other phosphoproteomic datasets revealed that genes from CXCL12-responsive phosphosites are enriched for cellular pathways such as T cell activation, epidermal growth factor and mammalian target of rapamycin (mTOR) signaling, pathways which have previously been linked to CXCL12/CXCR4 signaling. Several of the novel CXCL12-responsive phosphoproteins from our study have also been implicated with cellular migration and HIV-1 infection, thus providing an attractive list of potential targets for the development of cancer metastasis and HIV-1 therapeutics and for furthering our understanding of chemokine signaling regulation by reversible phosphorylation. PMID:21949786

Wojcechowskyj, Jason A.; Lee, Jessica Y.; Seeholzer, Steven H.; Doms, Robert W.

2011-01-01

4

Quantitative phosphoproteomics of CXCL12 (SDF-1) signaling.  

PubMed

CXCL12 (SDF-1) is a chemokine that binds to and signals through the seven transmembrane receptor CXCR4. The CXCL12/CXCR4 signaling axis has been implicated in both cancer metastases and human immunodeficiency virus type 1 (HIV-1) infection and a more complete understanding of CXCL12/CXCR4 signaling pathways may support efforts to develop therapeutics for these diseases. Mass spectrometry-based phosphoproteomics has emerged as an important tool in studying signaling networks in an unbiased fashion. We employed stable isotope labeling with amino acids in cell culture (SILAC) quantitative phosphoproteomics to examine the CXCL12/CXCR4 signaling axis in the human lymphoblastic CEM cell line. We quantified 4,074 unique SILAC pairs from 1,673 proteins and 89 phosphopeptides were deemed CXCL12-responsive in biological replicates. Several well established CXCL12-responsive phosphosites such as AKT (pS473) and ERK2 (pY204) were confirmed in our study. We also validated two novel CXCL12-responsive phosphosites, stathmin (pS16) and AKT1S1 (pT246) by Western blot. Pathway analysis and comparisons with other phosphoproteomic datasets revealed that genes from CXCL12-responsive phosphosites are enriched for cellular pathways such as T cell activation, epidermal growth factor and mammalian target of rapamycin (mTOR) signaling, pathways which have previously been linked to CXCL12/CXCR4 signaling. Several of the novel CXCL12-responsive phosphoproteins from our study have also been implicated with cellular migration and HIV-1 infection, thus providing an attractive list of potential targets for the development of cancer metastasis and HIV-1 therapeutics and for furthering our understanding of chemokine signaling regulation by reversible phosphorylation. PMID:21949786

Wojcechowskyj, Jason A; Lee, Jessica Y; Seeholzer, Steven H; Doms, Robert W

2011-01-01

5

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. PMID:23684312

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

6

Quantitative phosphoproteomics reveals extensive cellular reprogramming during HIV-1 entry.  

PubMed

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 cells 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, five serine/arginine-rich (SR) proteins involved in messenger RNA 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. PMID:23684312

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

2013-05-15

7

Quantitative Phosphoproteomics of Cytotoxic T Cells to Reveal Protein Kinase D 2 Regulated Networks*  

PubMed Central

The focus of the present study was to characterize the phosphoproteome of cytotoxic T cells and to explore the role of the serine threonine kinase PKD2 (Protein Kinase D2) in the phosphorylation networks of this key lymphocyte population. We used Stable Isotope Labeling of Amino acids in Culture (SILAC) combined with phosphopeptide enrichment and quantitative mass-spectrometry to determine the impact of PKD2 loss on the cytotoxic T cells phosphoproteome. We identified 15,871 phosphorylations on 3505 proteins in cytotoxic T cells. 450 phosphosites on 281 proteins were down-regulated and 300 phosphosites on 196 proteins were up-regulated in PKD2 null cytotoxic T cells. These data give valuable new insights about the protein phosphorylation networks operational in effector T cells and reveal that PKD2 regulates directly and indirectly about 5% of the cytotoxic T-cell phosphoproteome. PKD2 candidate substrates identified in this study include proteins involved in two distinct biological functions: regulation of protein sorting and intracellular vesicle trafficking, and control of chromatin structure, transcription, and translation. In other cell types, PKD substrates include class II histone deacetylases such as HDAC7 and actin regulatory proteins such as Slingshot. The current data show these are not PKD substrates in primary T cells revealing that the functional role of PKD isoforms is different in different cell lineages. PMID:25266776

Navarro, María N.; Goebel, Juergen; Hukelmann, Jens L.; Cantrell, Doreen A.

2014-01-01

8

Quantitative Phosphoproteomics Identifies Substrates and Functional Modules of Aurora and Polo-Like Kinase Activities in Mitotic Cells  

PubMed Central

Mitosis is a process involving a complex series of events that require careful coordination. Protein phosphorylation by a small number of kinases, in particular Aurora A, Aurora B, the cyclin-dependent kinase–cyclin complex Cdk1/cyclinB, and Polo-like kinase 1 (Plk1), orchestrates almost every step of cell division, from entry into mitosis to cytokinesis. To discover more about the functions of Aurora A, Aurora B, and kinases of the Plk family, we mapped mitotic phosphorylation sites to these kinases through the combined use of quantitative phosphoproteomics and selective targeting of kinase activities by small-molecule inhibitors. Using this integrated approach, we connected 778 phosphorylation sites on 562 proteins with these enzymes in cells arrested in mitosis. By connecting the kinases to protein complexes, we associated these kinases with functional modules. In addition to predicting previously unknown functions, this work establishes additional substrate-recognition motifs for these kinases and provides an analytical template for further use in dissecting kinase signaling events in other areas of cellular signaling and systems biology. PMID:21712546

Kettenbach, Arminja N.; Schweppe, Devin K.; Faherty, Brendan K.; Pechenick, Dov; Pletnev, Alexandre A.; Gerber, Scott A.

2013-01-01

9

Quantitative analysis of the TNF-?-induced phosphoproteome reveals AEG-1/MTDH/LYRIC as an IKK? substrate  

PubMed Central

The inhibitor of the nuclear factor-?B (I?B) kinase (IKK) complex is a key regulator of the canonical NF-?B signalling cascade and is crucial for fundamental cellular functions, including stress and immune responses. The majority of IKK complex functions are attributed to NF-?B activation; however, there is increasing evidence for NF-?B pathway-independent signalling. Here we combine quantitative mass spectrometry with random forest bioinformatics to dissect the TNF-?-IKK?-induced phosphoproteome in MCF-7 breast cancer cells. In total, we identify over 20,000 phosphorylation sites, of which ?1% are regulated up on TNF-? stimulation. We identify various potential novel IKK? substrates including kinases and regulators of cellular trafficking. Moreover, we show that one of the candidates, AEG-1/MTDH/LYRIC, is directly phosphorylated by IKK? on serine 298. We provide evidence that IKK?-mediated AEG-1 phosphorylation is essential for I?B? degradation as well as NF-?B-dependent gene expression and cell proliferation, which correlate with cancer patient survival in vivo. PMID:25849741

Krishnan, Ramesh K.; Nolte, Hendrik; Sun, Tianliang; Kaur, Harmandeep; Sreenivasan, Krishnamoorthy; Looso, Mario; Offermanns, Stefan; Krüger, Marcus; Swiercz, Jakub M.

2015-01-01

10

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

11

Quantitative Time-Resolved Phosphoproteomic Analysis of Mast Cell Signaling  

PubMed Central

Mast cells play a central role in type I hypersensitivity reactions and allergic disorders such as anaphylaxis and asthma. Activation of mast cells, through a cascade of phosphorylation events, leads to the release of mediators of the early phase allergic response. Understanding the molecular architecture underlying mast cell signaling may provide possibilities for therapeutic intervention in asthma and other allergic diseases. Although many details of mast cell signaling have been described previously, a systematic, quantitative analysis of the global tyrosine phosphorylation events that are triggered by activation of the mast cell receptor is lacking. In many cases, the involvement of particular proteins in mast cell signaling has been established generally but the precise molecular mechanism of the interaction between known signaling proteins often mediated through phosphorylation is still obscure. Using recently advanced methodologies in mass spectrometry, including automation of phosphopeptide enrichments and detection, we have now substantially characterized, with temporal resolution as short as 10 s, the sites and levels of tyrosine phosphorylation across 10 min of Fc?RI-induced mast cell activation. These results reveal a far more extensive array of tyrosine phosphorylation events than previously known, including novel phosphorylation sites on canonical mast cell signaling molecules, as well as unexpected pathway components downstream of Fc?RI activation. Furthermore, our results, for the first time in mast cells, reveal the sequence of phosphorylation events for 171 modification sites across 121 proteins in the MCP5 mouse mast cell line and 179 modification sites on 117 proteins in mouse bone marrow-derived mast cells. PMID:17947660

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

2009-01-01

12

Quantitative Phosphoproteomics Analysis Reveals Broad Regulatory Role of Heparan Sulfate on Endothelial Signaling*  

PubMed Central

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

2013-01-01

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. PMID:22570334

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

2012-01-01

14

Quantitative Phosphoproteomics Reveals the Role of Protein Arginine Phosphorylation in the Bacterial Stress Response*  

PubMed Central

Arginine phosphorylation is an emerging protein modification implicated in the general stress response of Gram-positive bacteria. The modification is mediated by the arginine kinase McsB, which phosphorylates and inactivates the heat shock repressor CtsR. In this study, we developed a mass spectrometric approach accounting for the peculiar chemical properties of phosphoarginine. The improved methodology was used to analyze the dynamic changes in the Bacillus subtilis arginine phosphoproteome in response to different stress situations. Quantitative analysis showed that a B. subtilis mutant lacking the YwlE arginine phosphatase accumulated a strikingly large number of arginine phosphorylations (217 sites in 134 proteins), however only a minor fraction of these sites was increasingly modified during heat shock or oxidative stress. The main targets of McsB-mediated arginine phosphorylation comprise central factors of the stress response system including the CtsR and HrcA heat shock repressors, as well as major components of the protein quality control system such as the ClpCP protease and the GroEL chaperonine. These findings highlight the impact of arginine phosphorylation in orchestrating the bacterial stress response. PMID:24263382

Schmidt, Andreas; Trentini, Débora Broch; Spiess, Silvia; Fuhrmann, Jakob; Ammerer, Gustav; Mechtler, Karl; Clausen, Tim

2014-01-01

15

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. PMID:24215720

2013-01-01

16

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

SciTech Connect

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

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

2012-04-17

17

Quantitative phosphoproteomic analysis of T cell receptor signaling in diabetes prone and resistant mice.  

PubMed

Type 1 diabetes, in human patients and NOD mice, results from an immune attack on insulin-producing beta-cells of the pancreas by autoreactive T lymphocytes. In NOD mice, genetically controlled perturbations in the signaling pathways downstream of the antigen-specific T cell receptor (TCR) may be instrumental in the altered responses of T cells, manifest as inefficient induction of apoptosis after recognition of self-antigens in the thymus or as perturbed reactivity of mature T cells in peripheral organs. To map this signaling difference(s), we have used mass spectrometry-based quantitative phosphoproteomics to compare the activation of primary CD4(+) T cells of diabetes-prone NOD and -resistant B6.H2g7 mice. Immunoprecipitation and IMAC purification of tyrosine-phosphorylated peptides, combined with a stable-isotope iTRAQ labeling, enabled us to identify and quantify over 77 phosphorylation events in 54 different proteins downstream of TCR stimulation of primary CD4(+) T cells. This analysis showed a generally higher level of phosphotyrosine in activated NOD cells, as well as several phosphorylation sites that appeared to be differentially regulated in these two strains (involving TXK, CD5, PAG1, and ZAP-70). These data highlight the differences in signaling between CD4(+) T cell compartments of NOD and B6g7 mice and may underlie the dysregulation of T cells in NOD mice. PMID:20438120

Iwai, Leo K; Benoist, Christophe; Mathis, Diane; White, Forest M

2010-06-01

18

QUANTITATIVE PHOSPHOPROTEOMIC ANALYSIS OF T CELL RECEPTOR SIGNALING IN DIABETES PRONE AND RESISTANT MICE  

PubMed Central

Type 1 diabetes, in human patients and NOD mice, results from immune attack on insulin-producing beta-cells of the pancreas by autoreactive T lymphocytes. In NOD mice, genetically-controlled perturbations in the signaling pathways downstream of the antigen-specific T cell receptor (TCR) may be instrumental in the altered responses of T cells, manifest as inefficient induction of apoptosis after recognition of self-antigens in the thymus, or as perturbed reactivity of mature T cells in peripheral organs. To map this signaling difference(s), we have used mass spectrometry-based quantitative phosphoproteomics to compare the activation of primary CD4+ T cells of diabetes-prone NOD and -resistant B6.H2g7 mice. Immunoprecipitation and IMAC purification of tyrosine-phosphorylated peptides, combined with a stable-isotope iTRAQ labeling, enabled us to identify and quantify over 77 phosphorylation events in 54 different proteins downstream of TCR stimulation of primary CD4+ T cells. This analysis showed a generally higher level of phosphotyrosine in activated NOD cells, as well as several phosphorylation sites that appeared to be differentially regulated in these two strains (involving TXK, CD5, PAG1, and ZAP-70). These data highlight the differences in signaling between CD4+ T cell compartments of NOD and B6g7 mice, and may underlie the dysregulation of T cells in NOD mice. PMID:20438120

Iwai, Leo K.; Benoist, Christophe; Mathis, Diane; White, Forest M

2012-01-01

19

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. PMID:22509832

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

20

Quantitative Phosphoproteomic Profiling of Human Non-Small Cell Lung Cancer Tumors  

PubMed Central

Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related deaths worldwide. Within the molecular scope of NCSLC, a complex landscape of dysregulated cellular signaling has emerged, defined largely by mutations in select mediators of signal transduction, including the epidermal growth factor receptor (EGFR) and anaplastic lymphoma (ALK) kinases. Consequently, these mutant kinases become constitutively activated and targets for chemotherapeutic intervention. Encouragingly, small molecule inhibitors of these pathways have shown promise in clinical trials or are approved for clinical use. However, many protein kinases are dysregulated in NSCLC without genetic mutations. To quantify differences in tumor cell signaling that are transparent to genomic methods, we established a super-SILAC internal standard derived from NSCLC cell lines grown in vitro and labeled with heavy lysine and arginine, and deployed them in a phosphoproteomics workflow. We identified 9019 and 8753 phosphorylation sites in two separate tumors. Relative quantification of phosphopeptide abundance between tumor samples allowed for the determination of specific hubs and pathways differing between each tumor. Sites downstream of Ras showed decreased inhibitory phosphorylation (Raf/Mek) and increased activating phosphorylation (Erk1/2) in one tumor versus another. In this way, we were able to quantitatively access oncogenic kinase signaling in primary human tumors. PMID:23911959

Schweppe, Devin K.; Rigas, James R.; Gerber, Scott A.

2013-01-01

21

Integration of conventional quantitative and phospho-proteomics reveals new elements in activated Jurkat T-cell receptor pathway maintenance.  

PubMed

Recent years have seen a constant development of tools for the global assessment of phosphoproteins. Here, we outline a concept for integrating approaches for quantitative proteomics and phosphoproteomics. The strategy was applied to the analysis of changes in signalling and protein synthesis occurring after activation of the T-cell receptor (TCR) pathway in a T-cell line (Jurkat cells). For this purpose, peptides were obtained from four biological replicates of activated and control Jurkat T-cells and phosphopeptides enriched via a TiO2-based chromatographic step. Both phosphopeptide-enriched and flow-through fractions were analyzed by LC-MS. We observed 1314 phosphopeptides in the enriched fraction whereas 19 were detected in the flow-through, enabling the quantification of 414 and eight phosphoproteins in the respective fractions. Pathway analysis revealed the differential regulation of many metabolic pathways. Among the quantified proteins, 11 kinases with known TCR-related function were detected. A kinase-substrate database search for the phosphosites identified also confirmed the activity of a further ten kinases. In total, these two approaches provided evidence of 19 unique TCR-related kinases. The combination of phosphoproteomics and conventional quantitative shotgun analysis leads to a more comprehensive assessment of the signalling networks needed for the maintenance of the activated status of Jurkat T-cells. PMID:25348772

Jouy, Florent; Müller, Stephan A; Wagner, Juliane; Otto, Wolfgang; von Bergen, Martin; Tomm, Janina M

2015-01-01

22

Multidimensional electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) for quantitative analysis of the proteome and phosphoproteome in clinical and biomedical research.  

PubMed

Quantitative proteomics and phosphoproteomics have become key disciplines in understanding cellular processes. Fundamental research can be done using cell culture providing researchers with virtually infinite sample amounts. In contrast, clinical, pre-clinical and biomedical research is often restricted to minute sample amounts and requires an efficient analysis with only micrograms of protein. To address this issue, we generated a highly sensitive workflow for combined LC-MS-based quantitative proteomics and phosphoproteomics by refining an ERLIC-based 2D phosphoproteomics workflow into an ERLIC-based 3D workflow covering the global proteome as well. The resulting 3D strategy was successfully used for an in-depth quantitative analysis of both, the proteome and the phosphoproteome of murine cytomegalovirus-infected mouse fibroblasts, a model system for host cell manipulation by a virus. In a 2-plex SILAC experiment with 150?g of a tryptic digest per condition, the 3D strategy enabled the quantification of ~75% more proteins and even ~134% more peptides compared to the 2D strategy. Additionally, we could quantify ~50% more phosphoproteins by non-phosphorylated peptides, concurrently yielding insights into changes on the levels of protein expression and phosphorylation. Beside its sensitivity, our novel three-dimensional ERLIC-strategy has the potential for semi-automated sample processing rendering it a suitable future perspective for clinical, pre-clinical and biomedical research. PMID:25619855

Loroch, Stefan; Schommartz, Tim; Brune, Wolfram; Zahedi, René Peiman; Sickmann, Albert

2015-05-01

23

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

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. PMID:23485197

2013-01-01

25

Analysis of T4SS-induced signaling by H. pylori using quantitative phosphoproteomics  

PubMed Central

Helicobacter pylori is a Gram-negative bacterial pathogen colonizing the human stomach. Infection with H. pylori causes chronic inflammation of the gastric mucosa and may lead to peptic ulceration and/or gastric cancer. A major virulence determinant of H. pylori is the type IV secretion system (T4SS), which is used to inject the virulence factor CagA into the host cell, triggering a wide range of cellular signaling events. Here, we used a phosphoproteomic approach to investigate tyrosine signaling in response to host-pathogen interaction, using stable isotope labeling in cell culture (SILAC) of AGS cells to obtain a differential picture between multiple infection conditions. Cells were infected with wild type H. pylori P12, a P12? CagA deletion mutant, and a P12? PAI deletion mutant to compare signaling changes over time and in the absence of CagA or the T4SS. Tryptic peptides were enriched for tyrosine (Tyr) phosphopeptides and analyzed by nano-LC-Orbitrap MS. In total, 85 different phosphosites were found to be regulated following infection. The majority of phosphosites identified were kinases of the MAPK family. CagA and the T4SS were found to be key regulators of Tyr phosphosites. Our findings indicate that CagA primarily induces activation of ERK1 and integrin-linked factors, whereas the T4SS primarily modulates JNK and p38 activation. PMID:25101063

Glowinski, Frithjof; Holland, Carsten; Thiede, Bernd; Jungblut, Peter R.; Meyer, Thomas F.

2014-01-01

26

Quantitative analysis of a phosphoproteome readily altered by the protein kinase CK2 inhibitor quinalizarin in HEK-293T cells.  

PubMed

CK2 is an extremely pleiotropic Ser/Thr protein kinase, responsible for the generation of a large proportion of the human phosphoproteome and implicated in a wide variety of biological functions. CK2 plays a global role as an anti-apoptotic agent, a property which is believed to partially account for the addiction of many cancer cells to high CK2 levels. To gain information about the CK2 targets whose phosphorylation is primarily implicated in its pro-survival signaling advantage has been taken of quinalizarin (QZ) a cell permeable fairly specific CK2 inhibitor, previously shown to be able to block endogenous CK2 triggering an apoptotic response. HEK-293T cells either treated or not for 3h with 50?M QZ were exploited to perform a quantitative SILAC phosphoproteomic analysis of phosphosites readily responsive to QZ treatment. Our analysis led to the identification of 4883 phosphosites, belonging to 1693 phosphoproteins. 71 phosphosites (belonging to 47 proteins) underwent a 50% or more decreased occupancy upon QZ treatment. Almost 50% of these fulfilled the typical consensus sequence recognized by CK2 (S/T-x-x-E/D/pS) and in several cases were validated as bona fide substrates of CK2 either based on data in the literature or by performing in vitro phosphorylation experiments with purified proteins. The majority of the remaining phosphosites drastically decreased upon QZ treatment display the pS/T-P motif typical of proline directed protein kinases and a web logo extracted from them differentiates from the web logo extracted from all the proline directed phosphosites quantified during our analysis (1151 altogether). A paradoxical outcome of our study was the detection of 116 phosphosites (belonging to 92 proteins altogether) whose occupancy is substantially increased (50% or more), rather than decreased by QZ treatment: 40% of these display the typical motif recognized by proline directed kinases, while about 25% fulfill the CK2 consensus. Collectively taken our data on one side have led to the disclosure of a subset of CK2 targets which are likely to be implicated in the early steps of CK2 signaling counteracting apoptosis, on the other they provide evidence for the existence of side and off-target effects of the CK2 inhibitor quinalizarin, paving the road toward the detection of other kinases susceptible to this compound. This article is part of a Special Issue entitled: Medical Proteomics. PMID:25278378

Franchin, Cinzia; Cesaro, Luca; Salvi, Mauro; Millioni, Renato; Iori, Elisabetta; Cifani, Paolo; James, Peter; Arrigoni, Giorgio; Pinna, Lorenzo

2015-06-01

27

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. PMID:24708550

2014-01-01

28

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

PubMed

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

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

2014-10-01

29

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

30

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. PMID:24637012

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

2014-01-01

31

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

32

A comparative phosphoproteomic analysis of a human tumor metastasis model using a label free quantitative approach  

PubMed Central

Alterations in cellular phosphorylation patterns have been implicated in a number of diseases, including cancer, through multiple mechanisms. Herein we present a survey of the phosphorylation profiles of an isogenic pair of human cancer cell lines with opposite metastatic phenotype. Phosphopeptides were enriched from tumor cell lysates with titanium dioxide and zirconium dioxide, and identified with nano-LC-MS/MS using an automatic cross-validation of MS/MS and MS/MS/MS (MS2 + MS3) data-dependent neutral loss method. A spectral counting quantitative strategy was applied to the two cell line samples on the MS2-only scan which was implemented successively after each MS2 + MS3 scan in the same sample. For all regulated phosphopeptides reported by spectral counting analysis, sequence and phosphorylation site assignments were validated by a MS2 + MS3 data-dependent neutral loss method. With this approach, we identified over 70 phosphorylated sites on 27 phosphoproteins as being differentially expressed with respect to tumor cell phenotype. The altered expression levels of proteins identified by LC-MS/MS were validated using Western blotting. Using network pathway analysis, we observed that the majority of the differentially expressed proteins were highly interconnected and belong to two major intracellular signaling pathways. Our findings suggest that the phosphorylation of isoform A of lamin A/C and GTPase activating protein binding protein 1 is associated with metastatic propensity. The study demonstrates a quantitative and comparative proteomics strategy to identify differential phosphorylation patterns in complex biological samples. PMID:20446291

Xie, Xiaolei; Feng, Shun; Vuong, Huy; Liu, Yashu; Goodison, Steve; Lubman, David M

2010-01-01

33

Quantitative Measurement of Phosphoproteome Response to Osmotic Stress in Arabidopsis Based on Library-Assisted eXtracted Ion Chromatogram (LAXIC)*  

PubMed Central

Global phosphorylation changes in plants in response to environmental stress have been relatively poorly characterized to date. Here we introduce a novel mass spectrometry-based label-free quantitation method that facilitates systematic profiling plant phosphoproteome changes with high efficiency and accuracy. This method employs synthetic peptide libraries tailored specifically as internal standards for complex phosphopeptide samples and accordingly, a local normalization algorithm, LAXIC, which calculates phosphopeptide abundance normalized locally with co-eluting library peptides. Normalization was achieved in a small time frame centered to each phosphopeptide to compensate for the diverse ion suppression effect across retention time. The label-free LAXIC method was further treated with a linear regression function to accurately measure phosphoproteome responses to osmotic stress in Arabidopsis. Among 2027 unique phosphopeptides identified and 1850 quantified phosphopeptides in Arabidopsis samples, 468 regulated phosphopeptides representing 497 phosphosites have shown significant changes. Several known and novel components in the abiotic stress pathway were identified, illustrating the capability of this method to identify critical signaling events among dynamic and complex phosphorylation. Further assessment of those regulated proteins may help shed light on phosphorylation response to osmotic stress in plants. PMID:23660473

Xue, Liang; Wang, Pengcheng; Wang, Lianshui; Renzi, Emily; Radivojac, Predrag; Tang, Haixu; Arnold, Randy; Zhu, Jian-Kang; Tao, W. Andy

2013-01-01

34

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

PubMed

One of the hallmarks of blood bank stored red blood cells (RBCs) is the irreversible transition from a discoid to a spherocyte-like morphology with membrane perturbation and cytoskeleton disorders. Therefore, identification of the storage-associated modifications in the protein-protein interactions between the cytoskeleton and the lipid bilayer may contribute to enlighten the molecular mechanisms involved in the alterations of mechanical properties of stored RBCs. Here we report the results obtained analyzing RBCs after 0, 21 and 35?days of storage under standard blood banking conditions by label free mass spectrometry (MS)-based experiments. We could quantitatively measure changes in the phosphorylation level of crucial phosphopeptides belonging to ?-spectrin, ankyrin-1, ?-adducin, dematin, glycophorin A and glycophorin C proteins. Data have been validated by both western blotting and pseudo-Multiple Reaction Monitoring (MRM). Although each phosphopeptide showed a distinctive trend, a sharp increase in the phosphorylation level during the storage duration was observed. Phosphopeptide mapping and structural modeling analysis indicated that the phosphorylated residues localize in protein functional domains fundamental for the maintenance of membrane structural integrity. Along with previous morphological evidence acquired by electron microscopy, our results seem to indicate that 21-day storage may represent a key point for the molecular processes leading to the erythrocyte deformability reduction observed during blood storage. These findings could therefore be helpful in understanding and preventing the morphology-linked mechanisms responsible for the post-transfusion survival of preserved RBCs. Copyright © 2015 John Wiley & Sons, Ltd. PMID:25800014

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

2015-02-01

35

Quantitative Phosphoproteomics Reveals SLP-76 Dependent Regulation of PAG and Src Family Kinases in T Cells  

PubMed Central

The SH2-domain-containing leukocyte protein of 76 kDa (SLP-76) plays a critical scaffolding role in T cell receptor (TCR) signaling. As an adaptor protein that contains multiple protein-binding domains, SLP-76 interacts with many signaling molecules and links proximal receptor stimulation to downstream effectors. The function of SLP-76 in TCR signaling has been widely studied using the Jurkat human leukaemic T cell line through protein disruption or site-directed mutagenesis. However, a wide-scale characterization of SLP-76-dependant phosphorylation events is still lacking. Quantitative profiling of over a hundred tyrosine phosphorylation sites revealed new modes of regulation of phosphorylation of PAG, PI3K, and WASP while reconfirming previously established regulation of Itk, PLC?, and Erk phosphorylation by SLP-76. The absence of SLP-76 also perturbed the phosphorylation of Src family kinases (SFKs) Lck and Fyn, and subsequently a large number of SFK-regulated signaling molecules. Altogether our data suggests unique modes of regulation of positive and negative feedback pathways in T cells by SLP-76, reconfirming its central role in the pathway. PMID:23071622

Cao, Lulu; Ding, Yiyuan; Hung, Norris; Yu, Kebing; Ritz, Anna; Raphael, Benjamin J.; Salomon, Arthur R.

2012-01-01

36

Identification of Direct Tyrosine Kinase Substrates Based on Protein Kinase Assay-Linked Phosphoproteomics*  

PubMed Central

Protein kinases are implicated in multiple diseases such as cancer, diabetes, cardiovascular diseases, and central nervous system disorders. Identification of kinase substrates is critical to dissecting signaling pathways and to understanding disease pathologies. However, methods and techniques used to identify bona fide kinase substrates have remained elusive. Here we describe a proteomic strategy suitable for identifying kinase specificity and direct substrates in high throughput. This approach includes an in vitro kinase assay-based substrate screening and an endogenous kinase dependent phosphorylation profiling. In the in vitro kinase reaction route, a pool of formerly phosphorylated proteins is directly extracted from whole cell extracts, dephosphorylated by phosphatase treatment, after which the kinase of interest is added. Quantitative proteomics identifies the rephosphorylated proteins as direct substrates in vitro. In parallel, the in vivo quantitative phosphoproteomics is performed in which cells are treated with or without the kinase inhibitor. Together, proteins phosphorylated in vitro overlapping with the kinase-dependent phosphoproteome in vivo represents the physiological direct substrates in high confidence. The protein kinase assay-linked phosphoproteomics was applied to identify 25 candidate substrates of the protein-tyrosine kinase SYK, including a number of known substrates and many novel substrates in human B cells. These shed light on possible new roles for SYK in multiple important signaling pathways. The results demonstrate that this integrated proteomic approach can provide an efficient strategy to screen direct substrates for protein tyrosine kinases. PMID:23793017

Xue, Liang; Geahlen, Robert L.; Tao, W. Andy

2013-01-01

37

Quantitative Phosphoproteomics of the Ataxia Telangiectasia-Mutated (ATM) and Ataxia Telangiectasia-Mutated and Rad3-related (ATR) Dependent DNA Damage Response in Arabidopsis thaliana.  

PubMed

The reversible phosphorylation of proteins on serine, threonine, and tyrosine residues is an important biological regulatory mechanism. In the context of genome integrity, signaling cascades driven by phosphorylation are crucial for the coordination and regulation of DNA repair. The two serine/threonine protein kinases ataxia telangiectasia-mutated (ATM) and Ataxia telangiectasia-mutated and Rad3-related (ATR) are key factors in this process, each specific for different kinds of DNA lesions. They are conserved across eukaryotes, mediating the activation of cell-cycle checkpoints, chromatin modifications, and regulation of DNA repair proteins. We designed a novel mass spectrometry-based phosphoproteomics approach to study DNA damage repair in Arabidopsis thaliana. The protocol combines filter aided sample preparation, immobilized metal affinity chromatography, metal oxide affinity chromatography, and strong cation exchange chromatography for phosphopeptide generation, enrichment, and separation. Isobaric labeling employing iTRAQ (isobaric tags for relative and absolute quantitation) was used for profiling the phosphoproteome of atm atr double mutants and wild type plants under either regular growth conditions or challenged by irradiation. A total of 10,831 proteins were identified and 15,445 unique phosphopeptides were quantified, containing 134 up- and 38 down-regulated ATM/ATR dependent phosphopeptides. We identified known and novel ATM/ATR targets such as LIG4 and MRE11 (needed for resistance against ionizing radiation), PIE1 and SDG26 (implicated in chromatin remodeling), PCNA1, WAPL, and PDS5 (implicated in DNA replication), and ASK1 and HTA10 (involved in meiosis). PMID:25561503

Roitinger, Elisabeth; Hofer, Manuel; Köcher, Thomas; Pichler, Peter; Novatchkova, Maria; Yang, Jianhua; Schlögelhofer, Peter; Mechtler, Karl

2015-03-01

38

Quantitative Phosphoproteomics of the Ataxia Telangiectasia-Mutated (ATM) and Ataxia Telangiectasia-Mutated and Rad3-related (ATR) Dependent DNA Damage Response in Arabidopsis thaliana*  

PubMed Central

The reversible phosphorylation of proteins on serine, threonine, and tyrosine residues is an important biological regulatory mechanism. In the context of genome integrity, signaling cascades driven by phosphorylation are crucial for the coordination and regulation of DNA repair. The two serine/threonine protein kinases ataxia telangiectasia-mutated (ATM) and Ataxia telangiectasia-mutated and Rad3-related (ATR) are key factors in this process, each specific for different kinds of DNA lesions. They are conserved across eukaryotes, mediating the activation of cell-cycle checkpoints, chromatin modifications, and regulation of DNA repair proteins. We designed a novel mass spectrometry-based phosphoproteomics approach to study DNA damage repair in Arabidopsis thaliana. The protocol combines filter aided sample preparation, immobilized metal affinity chromatography, metal oxide affinity chromatography, and strong cation exchange chromatography for phosphopeptide generation, enrichment, and separation. Isobaric labeling employing iTRAQ (isobaric tags for relative and absolute quantitation) was used for profiling the phosphoproteome of atm atr double mutants and wild type plants under either regular growth conditions or challenged by irradiation. A total of 10,831 proteins were identified and 15,445 unique phosphopeptides were quantified, containing 134 up- and 38 down-regulated ATM/ATR dependent phosphopeptides. We identified known and novel ATM/ATR targets such as LIG4 and MRE11 (needed for resistance against ionizing radiation), PIE1 and SDG26 (implicated in chromatin remodeling), PCNA1, WAPL, and PDS5 (implicated in DNA replication), and ASK1 and HTA10 (involved in meiosis). PMID:25561503

Roitinger, Elisabeth; Hofer, Manuel; Köcher, Thomas; Pichler, Peter; Novatchkova, Maria; Yang, Jianhua; Schlögelhofer, Peter; Mechtler, Karl

2015-01-01

39

Quantitative expression proteomics and phosphoproteomics profile of brain from PINK1 knockout mice: insights into mechanisms of familial Parkinson's disease.  

PubMed

Parkinson's disease (PD) is an age-related, neurodegenerative motor disorder characterized by progressive degeneration of dopaminergic neurons in the substantia nigra pars compacta and presence of ?-synuclein-containing protein aggregates. Mutations in the mitochondrial Ser/Thr kinase PTEN-induced kinase 1 (PINK1) are associated with an autosomal recessive familial form of early-onset PD. Recent studies have suggested that PINK1 plays important neuroprotective roles against mitochondrial dysfunction by phosphorylating and recruiting Parkin, a cytosolic E3 ubiquitin ligase, to facilitate elimination of damaged mitochondria via autophagy-lysosomal pathways. Loss of PINK1 in cells and animals leads to various mitochondrial impairments and oxidative stress, culminating in dopaminergic neuronal death in humans. Using a 2-D polyacrylamide gel electrophoresis proteomics approach, the differences in expressed brain proteome and phosphoproteome between 6-month-old PINK1-deficient mice and wild-type mice were identified. The observed changes in the brain proteome and phosphoproteome of mice lacking PINK1 suggest that defects in signaling networks, energy metabolism, cellular proteostasis, and neuronal structure and plasticity are involved in the pathogenesis of familial PD. Mutations in PINK1 are associated with an early-onset form of Parkinson's disease (PD). This study examines changes in the proteome and phosphoproteome of the PINK1 knockout mouse brain. Alterations were noted in several key proteins associated with: increased oxidative stress, aberrant cellular signaling, altered neuronal structure, decreased synaptic plasticity, reduced neurotransmission, diminished proteostasis networks, and altered metabolism. 14-3-3?, 14-3-3 protein epsilon; 3-PGDH, phosphoglycerate dehydrogenase; ALDOA, aldolase A; APT1, acyl-protein thioesterase 1; CaM, calmodulin; CBR3, carbonyl reductase [NADPH] 3; ENO2, gamma-enolase; HPRT, hypoxanthine-guanine phosphoribosyltransferase; HSP70, heat-shock-related 70 kDa protein 2; IDHc, cytoplasmic isocitrate dehydrogenase [NADP+]; MAPK1, mitogen-activated protein kinase 1; MEK1, MAP kinase kinase 1; MDHc, cytoplasmic malate dehydrogenase; NFM, neurofilament medium polypeptide; NSF, N-ethylmaleimide-sensitive fusion protein; PHB, prohibitin; PINK1, PTEN-induced putative kinase 1; PPIaseA, peptidyl-prolyl cis-trans isomerase A; PSA2, proteasome subunit alpha type-2; TK, transketolase; VDAC-2, voltage-dependent anion-selective channel protein 2. PMID:25626353

Triplett, Judy C; Zhang, Zhaoshu; Sultana, Rukhsana; Cai, Jian; Klein, Jon B; Büeler, Hansruedi; Butterfield, David Allan

2015-06-01

40

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

E-print Network

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase and Chemistry and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454 for review February 1, 2013) Hydrogen bond networks are key elements of protein structure and function

Boxer, Steven G.

41

Quantitative phosphoproteomics reveals the protein tyrosine kinase Pyk2 as a central effector of olfactory receptor signaling in prostate cancer cells.  

PubMed

The prostate-specific G-protein-coupled receptor 1 (PSGR1) is an olfactory receptor specifically expressed in the prostate gland. PSGR1 expression is elevated both in benign prostatic hyperplasia tissue and in prostate cancer. Stimulation of PSGR1 by the odorant ?-ionone leads to an increase in the intracellular Ca(2+) concentration, activation of mitogen-activated protein (MAP) kinases and a decrease in prostate cancer cell proliferation. To further extend our knowledge about PSGR1 signaling in prostate cancer cells, we performed a quantitative phosphoproteomics study using stable isotope labeling by amino acids in cell culture and mass spectrometry. We report 51 differentially regulated phosphorylation sites in 24 proteins with functions in cytoskeletal remodeling, signaling and ion transport. Activation of PSGR1 evoked an increase in intracellular pH mediated by the sodium/hydrogen exchanger NHE1. Furthermore, we report the protein tyrosine kinase Pyk2 as a central effector of PSGR1 signaling cascades in LNCaP cells. Our data show that phosphorylation of p38 MAP kinase is triggered by Pyk2. In addition, we confirmed dephosphorylation of the tumor suppressor protein N-myc downstream regulated gene 1 (NDRG1) at Ser330 downstream of Pyk2. Since NDRG1 impacts oncogenic signaling pathways interfering with tumor progression, we suggest that the Pyk2-NDRG1 axis is possibly involved in conveying the anti-proliferative effect of ?-ionone in prostate cancer cells. This article is part of a Special Issue entitled: Medical Proteomics. PMID:25219547

Wiese, Heike; Gelis, Lian; Wiese, Sebastian; Reichenbach, Christa; Jovancevic, Nikolina; Osterloh, Markus; Meyer, Helmut E; Neuhaus, Eva M; Hatt, Hanns H; Radziwill, Gerald; Warscheid, Bettina

2015-06-01

42

Exploiting induced variation to dissect quantitative traits in barley.  

PubMed

The identification of genes underlying complex quantitative traits such as grain yield by means of conventional genetic analysis (positional cloning) requires the development of several large mapping populations. However, it is possible that phenotypically related, but more extreme, allelic variants generated by mutational studies could provide a means for more efficient cloning of QTLs (quantitative trait loci). In barley (Hordeum vulgare), with the development of high-throughput genome analysis tools, efficient genome-wide identification of genetic loci harbouring mutant alleles has recently become possible. Genotypic data from NILs (near-isogenic lines) that carry induced or natural variants of genes that control aspects of plant development can be compared with the location of QTLs to potentially identify candidate genes for development--related traits such as grain yield. As yield itself can be divided into a number of allometric component traits such as tillers per plant, kernels per spike and kernel size, mutant alleles that both affect these traits and are located within the confidence intervals for major yield QTLs may represent extreme variants of the underlying genes. In addition, the development of detailed comparative genomic models based on the alignment of a high-density barley gene map with the rice and sorghum physical maps, has enabled an informed prioritization of 'known function' genes as candidates for both QTLs and induced mutant genes. PMID:20298243

Druka, Arnis; Franckowiak, Jerome; Lundqvist, Udda; Bonar, Nicola; Alexander, Jill; Guzy-Wrobelska, Justyna; Ramsay, Luke; Druka, Ilze; Grant, Iain; Macaulay, Malcolm; Vendramin, Vera; Shahinnia, Fahimeh; Radovic, Slobodanka; Houston, Kelly; Harrap, David; Cardle, Linda; Marshall, David; Morgante, Michele; Stein, Nils; Waugh, Robbie

2010-04-01

43

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. PMID:25018669

2014-01-01

44

Quantitative Tools for Dissection of Hydrogen-Producing Metabolic Networks-Final Report  

SciTech Connect

During this project we have pioneered the development of integrated experimental-computational technologies for the quantitative dissection of metabolism in hydrogen and biofuel producing microorganisms (i.e. C. acetobutylicum and various cyanobacteria species). The application of these new methodologies resulted in many significant advances in the understanding of the metabolic networks and metabolism of these organisms, and has provided new strategies to enhance their hydrogen or biofuel producing capabilities. As an example, using mass spectrometry, isotope tracers, and quantitative flux-modeling we mapped the metabolic network structure in C. acetobutylicum. This resulted in a comprehensive and quantitative understanding of central carbon metabolism that could not have been obtained using genomic data alone. We discovered that biofuel production in this bacterium, which only occurs during stationary phase, requires a global remodeling of central metabolism (involving large changes in metabolite concentrations and fluxes) that has the effect of redirecting resources (carbon and reducing power) from biomass production into solvent production. This new holistic, quantitative understanding of metabolism is now being used as the basis for metabolic engineering strategies to improve solvent production in this bacterium. In another example, making use of newly developed technologies for monitoring hydrogen and NAD(P)H levels in vivo, we dissected the metabolic pathways for photobiological hydrogen production by cyanobacteria Cyanothece sp. This investigation led to the identification of multiple targets for improving hydrogen production. Importantly, the quantitative tools and approaches that we have developed are broadly applicable and we are now using them to investigate other important biofuel producers, such as cellulolytic bacteria.

Rabinowitz, Joshua D.; Dismukes, G.Charles.; Rabitz, Herschel A.; Amador-Noguez, Daniel

2012-10-19

45

Integrated genomics and molecular breeding approaches for dissecting the complex quantitative traits in crop plants.  

PubMed

The enormous population growth, climate change and global warming are now considered major threats to agriculture and world's food security. To improve the productivity and sustainability of agriculture, the development of highyielding and durable abiotic and biotic stress-tolerant cultivars and/climate resilient crops is essential. Henceforth, understanding the molecular mechanism and dissection of complex quantitative yield and stress tolerance traits is the prime objective in current agricultural biotechnology research. In recent years, tremendous progress has been made in plant genomics and molecular breeding research pertaining to conventional and next-generation whole genome, transcriptome and epigenome sequencing efforts, generation of huge genomic, transcriptomic and epigenomic resources and development of modern genomics-assisted breeding approaches in diverse crop genotypes with contrasting yield and abiotic stress tolerance traits. Unfortunately, the detailed molecular mechanism and gene regulatory networks controlling such complex quantitative traits is not yet well understood in crop plants. Therefore, we propose an integrated strategies involving available enormous and diverse traditional and modern -omics (structural, functional, comparative and epigenomics) approaches/resources and genomics-assisted breeding methods which agricultural biotechnologist can adopt/utilize to dissect and decode the molecular and gene regulatory networks involved in the complex quantitative yield and stress tolerance traits in crop plants. This would provide clues and much needed inputs for rapid selection of novel functionally relevant molecular tags regulating such complex traits to expedite traditional and modern marker-assisted genetic enhancement studies in target crop species for developing high-yielding stress-tolerant varieties. PMID:24296899

Kujur, Alice; Saxena, Maneesha S; Bajaj, Deepak; Laxmi; Parida, Swarup K

2013-12-01

46

Phosphoproteome analysis of formalin-fixed and paraffin-embedded tissue sections mounted on microscope slides.  

PubMed

Formalin-fixed and paraffin-embedded (FFPE) sections mounted on microscope slides are one of the largest available resources for retrospective research on various diseases, but quantitative phosphoproteome analysis of FFPE sections has never been achieved because of the extreme difficulty of procuring sufficient phosphopeptides from the limited amounts of proteins on the slides. Here, we present the first protocol for quantitative phosphoproteome analysis of FFPE sections by utilizing phase-transfer surfactant-aided extraction/tryptic digestion of FFPE proteins followed by high-recovery phosphopeptide enrichment via lactic acid-modified titania chromatography. We established that FFPE sections retain a similar phosphoproteome to fresh tissue specimens during storage for at least 9 months, confirming the utility of our method for evaluating phosphorylation profiles in various diseases. We also verified that chemical labeling based on reductive dimethylation of amino groups was feasible for quantitative phosphoproteome analysis of FFPE samples on slides. Furthermore, we improved the LC-MS sensitivity by miniaturizing nanoLC columns to 25 ?m inner diameter. With this system, we could identify 1090 phosphopeptides from a single FFPE section obtained from a microscope slide, containing 25.2 ± 5.4 ?g of proteins. This protocol should be useful for large-scale phosphoproteome analysis of archival FFPE slides, especially scarce samples from patients with rare diseases. PMID:24328109

Wakabayashi, Masaki; Yoshihara, Hiroki; Masuda, Takeshi; Tsukahara, Mai; Sugiyama, Naoyuki; Ishihama, Yasushi

2014-02-01

47

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

E-print Network

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

Wolf Yadlin, Alejandro

2007-01-01

48

Dissecting the heterogeneity of rheumatoid arthritis through linkage analysis of quantitative traits  

Microsoft Academic Search

Objective. To dissect the heterogeneity of rheuma- toid arthritis (RA) through linkage analysis of quanti- tative traits, specifically, IgM rheumatoid factor (IgM- RF) and anti-cyclic citrullinated peptide (anti-CCP) autoantibody titers. Methods. Subjects, 1,002 RA patients from 491 multiplex families recruited by the North American RA Consortium, were typed for 379 microsatellite markers. Anti-CCP titers were determined based on a second-

Lindsey A. Criswell; Wei V. Chen; Damini Jawaheer; Raymond F. Lum; Mark H. Wener; Xiangjun Gu; Peter K. Gregersen; Christopher I. Amos

2007-01-01

49

Integrating phosphoproteomics in systems biology  

PubMed Central

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

Liu, Yu; Chance, Mark R.

2014-01-01

50

Neck dissection  

MedlinePLUS

... dissection; Modified radical neck dissection; Selective neck dissection; Lymph node removal - neck ... dissection is a major surgery done to remove lymph nodes that have cancer. It is done in the ...

51

Phosphoproteomics for the masses  

PubMed Central

Protein phosphorylation serves as a primary mechanism of signal transduction in the cells of biological organisms. Technical advancements over the last several years in mass spectrometry now allow for the large-scale identification and quantitation of in vivo phosphorylation at unprecedented levels. These developments have occurred in the areas of sample preparation, instrumentation, quantitative methodology, and informatics so that today, ten to twenty thousand phosphorylation sites can be identified and quantified within a few weeks. With the rapid development and widespread availability of such data, its translation into biological insight and knowledge is a current obstacle. Here we present an overview of how this technology came to be and is currently applied, as well as future challenges for the field. PMID:20047291

Grimsrud, Paul A.; Swaney, Danielle L.; Wenger, Craig D.; Beauchene, Nicole A.; Coon, Joshua J.

2010-01-01

52

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

PubMed Central

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

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

2012-01-01

53

Molecular genetic dissection of quantitative trait loci regulating rice grain size.  

PubMed

Grain size is one of the most important factors determining rice yield. As a quantitative trait, grain size is predominantly and tightly controlled by genetic factors. Several quantitative trait loci (QTLs) for grain size have been molecularly identified and characterized. These QTLs may act in independent genetic pathways and, along with other identified genes for grain size, are mainly involved in the signaling pathways mediated by proteasomal degradation, phytohormones, and G proteins to regulate cell proliferation and cell elongation. Many of these QTLs and genes have been strongly selected for enhanced rice productivity during domestication and breeding. These findings have paved new ways for understanding the molecular basis of grain size and have substantial implications for genetic improvement of crops. PMID:25149369

Zuo, Jianru; Li, Jiayang

2014-01-01

54

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

PubMed

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

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

2014-12-01

55

The Interplay of Light and Oxygen in the Reactive Oxygen Stress Response of Chlamydomonas reinhardtii Dissected by Quantitative Mass Spectrometry*  

PubMed Central

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 redoxII 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, O2 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

2014-01-01

56

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

57

Dissection of genotype-phenotype associations in rice grains using metabolome quantitative trait loci analysis.  

PubMed

A comprehensive and large-scale metabolome quantitative trait loci (mQTL) analysis was performed to investigate the genetic backgrounds associated with metabolic phenotypes in rice grains. The metabolome dataset consisted of 759?metabolite signals obtained from the grains of 85 lines of rice (Oryza sativa, Sasanishiki?×?Habataki back-crossed inbred lines). Metabolome analysis was performed using four mass spectrometry pipelines to enhance detection of different classes of metabolites. This mQTL analysis of a wide range of metabolites highlighted an uneven distribution of 802 mQTLs on the rice genome, as well as different modes of metabolic trait (m-trait) control among various types of metabolites. The levels of most metabolites within rice grains were highly sensitive to environmental factors, but only weakly associated with mQTLs. Coordinated control was observed for several groups of metabolites, such as amino acids linked to the mQTL hotspot on chromosome?3. For flavonoids, m-trait variation among the experimental lines was tightly governed by genetic factors that alter the glycosylation of flavones. Many loci affecting levels of metabolites were detected by QTL analysis, and plausible gene candidates were evaluated by in silico analysis. Several mQTLs profoundly influenced metabolite levels, providing insight into the control of rice metabolism. The genomic region and genes potentially responsible for the biosynthesis of apigenin-6,8-di-C-?-l-arabinoside are presented as an example of a critical mQTL identified by the analysis. PMID:22229385

Matsuda, Fumio; Okazaki, Yozo; Oikawa, Akira; Kusano, Miyako; Nakabayashi, Ryo; Kikuchi, Jun; Yonemaru, Jun-Ichi; Ebana, Kaworu; Yano, Masahiro; Saito, Kazuki

2012-05-01

58

Natural variation for carbohydrate content in Arabidopsis. Interaction with complex traits dissected by quantitative genetics.  

PubMed

Besides being a metabolic fuel, carbohydrates play important roles in plant growth and development, in stress responses, and as signal molecules. We exploited natural variation in Arabidopsis (Arabidopsis thaliana) to decipher the genetic architecture determining carbohydrate content. A quantitative trait locus (QTL) approach in the Bay-0 x Shahdara progeny grown in two contrasting nitrogen environments led to the identification of 39 QTLs for starch, glucose, fructose, and sucrose contents representing at least 14 distinct polymorphic loci. A major QTL for fructose content (FR3.4) and a QTL for starch content (ST3.4) were confirmed in heterogeneous inbred families. Several genes associated with carbon (C) metabolism colocalize with the identified QTL. QTLs for senescence-related traits, and for flowering time, water status, and nitrogen-related traits, previously detected with the same genetic material, colocalize with C-related QTLs. These colocalizations reflect the complex interactions of C metabolism with other physiological processes. QTL fine-mapping and cloning could thus lead soon to the identification of genes potentially involved in the control of different connected physiological processes. PMID:16798941

Calenge, Fanny; Saliba-Colombani, Véra; Mahieu, Stéphanie; Loudet, Olivier; Daniel-Vedele, Françoise; Krapp, Anne

2006-08-01

59

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. 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

2013-01-01

60

Quantitative trait loci mapping and genetic dissection for lint percentage in upland cotton (Gossypium hirsutum).  

PubMed

Lint percentage is an important character of cotton yield components and it is also correlated with cotton fibre development. In this study, we used a high lint percentage variety, Baimian1, and a low lint percentage, TM-1 genetic standard for Gossypium hirsutum, as parents to construct a mapping populations in upland cotton (G. hirsutum). A quantitative trait locus/loci (QTL) analysis of lint percentage was performed by using two mapping procedures; composite interval mapping (CIM), inclusive composite interval mapping (ICIM) and the F2:3 populations in 2 years. Six main-effect QTL (M-QTL) for lint percentage (four significant and two suggestive) were detected in both years by CIM, and were located on chr. 3, chr. 19, chr. 26 and chr. 5/chr. 19. Of the six QTL, marker intervals and favourable gene sources of the significant M-QTL, qLP-3(2010) and qLP-3(2011) were consistent. These QTL were also detected by ICIM, and therefore, should preferentially be used for markerassisted selection (MAS) of lint percentage. Another M-QTL, qLP-19(2010), was detected by two mapping procedures, and it could also be a candidate for MAS. We detected the interaction between two M-QTL and environment, and 11 epistatic QTL (E-QTL) and their interaction with environment by using ICIM. The study also found two EST-SSRs, NAU1187 and NAU1255, linked to M-QTL for lint percentage that could be candidate markers affecting cotton fibre development. PMID:25189232

Wang, Min; Li, Chengqi; Wang, Qinglian

2014-08-01

61

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

Microsoft Academic Search

Tissue glues are used during surgical treatment of acute aorta dissection although some glues release toxic products and thus\\u000a alter the histological structure of the vessel wall. The aim of our study was to use a porcine experimental model of infrarenal\\u000a aorta dissection to compare histological changes of the vessel wall 1, 6 and 12 months after application of BioGlue, Gelatin-resorcin-formaldehyde

Kirsti Witter; Zbyn?k Tonar; Vít Martin Mat?jka; Tomáš Martin?a; Michael Jonák; Slavomír Rokošný; Jan Pirk

2010-01-01

62

Refined phosphopeptide enrichment by phosphate additive and the analysis of human brain phosphoproteome.  

PubMed

Alzheimer's disease (AD) is the most common form of dementia, characterized by progressive loss of cognitive function. One of the pathological hallmarks of AD is the formation of neurofibrillary tangles composed of abnormally hyperphosphorylated tau protein, but global deregulation of protein phosphorylation in AD is not well analyzed. Here, we report a pilot investigation of AD phosphoproteome by titanium dioxide enrichment coupled with high resolution LC-MS/MS. During the optimization of the enrichment method, we found that phosphate ion at a low concentration (e.g. 1 mM) worked efficiently as a nonphosphopeptide competitor to reduce background. The procedure was further tuned with respect to peptide-to-bead ratio, phosphopeptide recovery, and purity. Using this refined method and 9 h LC-MS/MS, we analyzed phosphoproteome in one milligram of digested AD brain lysate, identifying 5243 phosphopeptides containing 3715 nonredundant phosphosites on 1455 proteins, including 31 phosphosites on the tau protein. This modified enrichment method is simple and highly efficient. The AD case study demonstrates its feasibility of dissecting phosphoproteome in a limited amount of postmortem human brain. All MS data have been deposited in the ProteomeXchange with identifier PXD001180 (http://proteomecentral.proteomexchange.org/dataset/PXD001180). PMID:25307156

Tan, Haiyan; Wu, Zhiping; Wang, Hong; Bai, Bing; Li, Yuxin; Wang, Xusheng; Zhai, Bo; Beach, Thomas G; Peng, Junmin

2015-01-01

63

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. PMID:22291655

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

2012-01-01

64

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. PMID:25028575

2014-01-01

65

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

PubMed Central

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

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

2015-01-01

66

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

67

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. 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

2012-01-01

68

Clam Dissection  

NSDL National Science Digital Library

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

Kelly Riedell

69

Computational phosphoproteomics: From identification to localization  

PubMed Central

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

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

2015-01-01

70

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. PMID:23628362

2013-01-01

71

Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea  

PubMed Central

Phylogenetic footprinting identified 666 genome-wide paralogous and orthologous CNMS (conserved non-coding microsatellite) markers from 5?-untranslated and regulatory regions (URRs) of 603 protein-coding chickpea genes. The (CT)n and (GA)n CNMS carrying CTRMCAMV35S and GAGA8BKN3 regulatory elements, respectively, are abundant in the chickpea genome. The mapped genic CNMS markers with robust amplification efficiencies (94.7%) detected higher intraspecific polymorphic potential (37.6%) among genotypes, implying their immense utility in chickpea breeding and genetic analyses. Seventeen differentially expressed CNMS marker-associated genes showing strong preferential and seed tissue/developmental stage-specific expression in contrasting genotypes were selected to narrow down the gene targets underlying seed weight quantitative trait loci (QTLs)/eQTLs (expression QTLs) through integrative genetical genomics. The integration of transcript profiling with seed weight QTL/eQTL mapping, molecular haplotyping, and association analyses identified potential molecular tags (GAGA8BKN3 and RAV1AAT regulatory elements and alleles/haplotypes) in the LOB-domain-containing protein- and KANADI protein-encoding transcription factor genes controlling the cis-regulated expression for seed weight in the chickpea. This emphasizes the potential of CNMS marker-based integrative genetical genomics for the quantitative genetic dissection of complex seed weight in chickpea. PMID:25504138

Bajaj, Deepak; Saxena, Maneesha S.; Kujur, Alice; Das, Shouvik; Badoni, Saurabh; Tripathi, Shailesh; Upadhyaya, Hari D.; Gowda, C. L. L.; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K.; Parida, Swarup K.

2015-01-01

72

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.

Rhode Island Sea Grant

73

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

PubMed Central

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

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

2014-01-01

74

Toward defining the phosphoproteome of Xenopus laevis embryos  

PubMed Central

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

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

2010-01-01

75

Integrating Phosphoproteome and Transcriptome Reveals New Determinants of Macrophage Multinucleation*  

PubMed Central

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

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

2015-01-01

76

Integrating phosphoproteome and transcriptome reveals new determinants of macrophage multinucleation.  

PubMed

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

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

2015-03-01

77

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

PubMed

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

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

2012-10-22

78

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?

David Varricchio

79

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).

Olga Wood

2012-06-27

80

Biology teachers' dissection practices and the influences that lead to their adoption: An exploratory research  

NASA Astrophysics Data System (ADS)

The lack of resolution in the on-going animal dissection debate inspired this mixed methods study to identify Connecticut secondary biology teachers' dissection practices and the influences that lead to their adoption. Qualitative findings indicate past experiences, managing objections to dissection, school culture, goals of biology teaching and ethics as major influences on dissection practices with 58.4% (n=7) of the sample dissecting and 41.6% not dissecting (n=5). Quantitative findings reveal gender, standards and curriculum, advantages of dissection and experiences as a student as major influences on dissection practices with 71.9% (n=92) of the sample dissecting and 28.1% (n=36) not dissecting. The study concludes that dissection policies are necessary and imminent in Connecticut school districts. Furthermore, it advises teacher-initiated, qualitative and quantitative assessments to expose disparities between student dissection perspectives and their own, prior to conducting dissection. Finally, it provides suggestions for addressing potential differences including administrative involvement.

Milano, Regina Nicole

81

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.

Roy Plotnick

82

System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.  

PubMed

To elucidate cellular events underlying the pluripotency of human embryonic stem cells (hESCs), we performed parallel quantitative proteomic and phosphoproteomic analyses of hESCs during differentiation initiated by a diacylglycerol analog or transfer to media that had not been conditioned by feeder cells. We profiled 6521 proteins and 23,522 phosphorylation sites, of which almost 50% displayed dynamic changes in phosphorylation status during 24 hours of differentiation. These data are a resource for studies of the events associated with the maintenance of hESC pluripotency and those accompanying their differentiation. From these data, we identified a core hESC phosphoproteome of sites with similar robust changes in response to the two distinct treatments. These sites exhibited distinct dynamic phosphorylation patterns, which were linked to known or predicted kinases on the basis of the matching sequence motif. In addition to identifying previously unknown phosphorylation sites on factors associated with differentiation, such as kinases and transcription factors, we observed dynamic phosphorylation of DNA methyltransferases (DNMTs). We found a specific interaction of DNMTs during early differentiation with the PAF1 (polymerase-associated factor 1) transcriptional elongation complex, which binds to promoters of the pluripotency and known DNMT target genes encoding OCT4 and NANOG, thereby providing a possible molecular link for the silencing of these genes during differentiation. PMID:21406692

Rigbolt, Kristoffer T G; Prokhorova, Tatyana A; Akimov, Vyacheslav; Henningsen, Jeanette; Johansen, Pia T; Kratchmarova, Irina; Kassem, Moustapha; Mann, Matthias; Olsen, Jesper V; Blagoev, Blagoy

2011-01-01

83

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

PubMed

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

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

2015-01-01

84

Parallel Proteomic and Phosphoproteomic Analyses of Successive Stages of Maize Leaf Development[C][W][OPEN  

PubMed Central

We performed large-scale, quantitative analyses of the maize (Zea mays) leaf proteome and phosphoproteome at four developmental stages. Exploiting the developmental gradient of maize leaves, we analyzed protein and phosphoprotein abundance as maize leaves transition from proliferative cell division to differentiation to cell expansion and compared these developing zones to one another and the mature leaf blade. Comparison of the proteomes and phosphoproteomes suggests a key role for posttranslational regulation in developmental transitions. Analysis of proteins with cell wall– and hormone-related functions illustrates the utility of the data set and provides further insight into maize leaf development. We compare phosphorylation sites identified here to those previously identified in Arabidopsis thaliana. We also discuss instances where comparison of phosphorylated and unmodified peptides from a particular protein indicates tissue-specific phosphorylation. For example, comparison of unmodified and phosphorylated forms of PINFORMED1 (PIN1) suggests a tissue-specific difference in phosphorylation, which correlates with changes in PIN1 polarization in epidermal cells during development. Together, our data provide insights into regulatory processes underlying maize leaf development and provide a community resource cataloging the abundance and phosphorylation status of thousands of maize proteins at four leaf developmental stages. PMID:23933881

Facette, Michelle R.; Shen, Zhouxin; Björnsdóttir, Fjola R.; Briggs, Steven P.; Smith, Laurie G.

2013-01-01

85

Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem  

E-print Network

, Julian D Watts2, Leroy Hood2 & Ruedi Aebersold2­4 We present a robust and general method in a reaction catalyzed by carbodiimide and imidazole. Modified phosphopeptides are released from the dendrimer

Cai, Long

86

A chemical and phosphoproteomic characterization of dasatinib action in lung cancer  

PubMed Central

We describe a strategy to comprehend signaling pathways active in lung cancer cells and targeted by dasatinib employing chemical proteomics to identify direct interacting proteins combined with immunoaffinity purification of tyrosine phosphorylated peptides corresponding to activated tyrosine kinases. We identified nearly 40 different kinase targets of dasatinib. These include SFK members (LYN, SRC, FYN, LCK, YES), non-receptor tyrosine kinases (FRK, BRK, ACK), and receptor tyrosine kinases (Ephrin receptors, DDR1, EGFR). Using quantitative phosphoproteomics we identified peptides corresponding to autophosphorylation sites of these tyrosine kinases that are inhibited in a concentration-dependent manner by dasatinib. Using drug resistant gatekeeper mutants, we show that SFK kinases, particularly SRC and FYN, as well as EGFR are relevant targets for dasatinib action. The combined mass spectrometry based approach described here provides a system-level view of dasatinib action in cancer cells and suggests both functional targets and rationale combinatorial therapeutic strategies. PMID:20190765

Li, Jiannong; Rix, Uwe; Fang, Bin; Bai, Yun; Edwards, Arthur; Colinge, Jacques; Bennett, Keiryn L.; Gao, Jingchun; Song, Lanxi; Eschrich, Steven; Superti-Furga, Giulio; Koomen, John; Haura, Eric B.

2010-01-01

87

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. PMID:22683509

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

2012-01-01

88

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. PMID:23926118

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

89

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. PMID:24808101

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

2014-01-01

90

Phosphoproteomic analysis of seed maturation in Arabidopsis, rapeseed, and soybean.  

PubMed

To characterize protein phosphorylation in developing seed, a large-scale, mass spectrometry-based phosphoproteomic study was performed on whole seeds at five sequential stages of development in soybean (Glycine max), rapeseed (Brassica napus), and Arabidopsis (Arabidopsis thaliana). Phosphopeptides were enriched from 0.5 mg of total peptides using a combined strategy of immobilized metal affinity and metal oxide affinity chromatography. Enriched phosphopeptides were analyzed by Orbitrap tandem mass spectrometry and mass spectra mined against cognate genome or cDNA databases in both forward and randomized orientations, the latter to calculate false discovery rate. We identified a total of 2,001 phosphopeptides containing 1,026 unambiguous phosphorylation sites from 956 proteins, with an average false discovery rate of 0.78% for the entire study. The entire data set was uploaded into the Plant Protein Phosphorylation Database (www.p3db.org), including all meta-data and annotated spectra. The Plant Protein Phosphorylation Database is a portal for all plant phosphorylation data and allows for homology-based querying of experimentally determined phosphosites. Comparisons with other large-scale phosphoproteomic studies determined that 652 of the phosphoproteins are novel to this study. The unique proteins fall into several Gene Ontology categories, some of which are overrepresented in our study as well as other large-scale phosphoproteomic studies, including metabolic process and RNA binding; other categories are only overrepresented in our study, like embryonic development. This investigation shows the importance of analyzing multiple plants and plant organs to comprehensively map the complete plant phosphoproteome. PMID:22440515

Meyer, Louis J; Gao, Jianjiong; Xu, Dong; Thelen, Jay J

2012-05-01

91

The use of elemental mass spectrometry in phosphoproteomic applications.  

PubMed

Reversible phosphorylation is one of the most important post-translational modifications in mammalian cells. Because this molecular switch is an important mechanism that diversifies and regulates proteins in cellular processes, knowledge about the extent and quantity of phosphorylation is very important to understand the complex cellular interplay. Although phosphoproteomics strategies are applied worldwide, they mainly include only molecular mass spectrometry (like MALDI or ESI)-based experiments. Although identification and relative quantification of phosphopeptides is straightforward with these techniques, absolute quantification is more complex and usually requires for specific isotopically phosphopeptide standards. However, the use of elemental mass spectrometry, and in particular inductively coupled plasma mass spectrometry (ICP-MS), in phosphoproteomics-based experiments, allow one to absolutely quantify phosphopeptides. Here, these phosphoproteomic applications with ICP-MS as elemental detector are reviewed. Pioneering work and recent developments in the field are both described. Additionally, the advantage of the parallel use of molecular and elemental mass spectrometry is stressed. © 2014 Wiley Periodicals, Inc. Mass Spec Rev. PMID:25139451

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

2014-08-19

92

Dissection of TBK1 signaling via phosphoproteomics in lung cancer cells  

PubMed Central

TANK-binding kinase 1 (TBK1) has emerged as a novel therapeutic target for unspecified subset of lung cancers. TBK1 reportedly mediates prosurvival signaling by activating NF-?B and AKT. However, we observed that TBK1 knockdown also decreased viability of cells expressing constitutively active NF-?B and interferon regulatory factor 3. Basal phospho-AKT level was not reduced after TBK1 knockdown in TBK1-sensitive lung cancer cells, implicating that TBK1 mediates unknown survival mechanisms. To gain better insight into TBK1 survival signaling, we searched for altered phosphoproteins using mass spectrometry following RNAi-mediated TBK1 knockdown. In total, we identified 2,080 phosphoproteins (4,621 peptides), of which 385 proteins (477 peptides) were affected after TBK1 knockdown. A view of the altered network identified a central role of Polo-like kinase 1 (PLK1) and known PLK1 targets. We found that TBK1 directly phosphorylated PLK1 in vitro. TBK1 phosphorylation was induced at mitosis, and loss of TBK1 impaired mitotic phosphorylation of PLK1 in TBK1-sensitive lung cancer cells. Furthermore, lung cancer cell sensitivity to TBK1 was highly correlated with sensitivity to pharmacological PLK inhibition. We additionally found that TBK1 knockdown decreased metadherin phosphorylation at Ser-568. Metadherin was associated with poor outcome in lung cancer, and loss of metadherin caused growth inhibition and apoptosis in TBK1-sensitive lung cancer cells. These results collectively revealed TBK1 as a mitosis regulator through activation of PLK1 and also suggested metadherin as a putative TBK1 downstream effector involved in lung cancer cell survival. PMID:23836654

Kim, Jae-Young; Welsh, Eric A.; Oguz, Umut; Fang, Bin; Bai, Yun; Kinose, Fumi; Bronk, Crystina; Remsing Rix, Lily L.; Beg, Amer A.; Rix, Uwe; Eschrich, Steven A.; Koomen, John M.; Haura, Eric B.

2013-01-01

93

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

94

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

95

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

PubMed

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

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

2015-04-15

96

Validation and dissection of quantitative trait loci for leaf traits in interval RM4923-RM402 on the short arm of rice chromosome 6.  

PubMed

Validation and dissection of a QTL region for leaf traits in rice which has been reported in a number of independent studies were conducted. Three sets of near isogenic lines (NILs) were originated from a residual heterozygous line derived the indica cross Zhenshan 97B/Milyang 46. They were overlapping and totally covered a 4.2-Mb heterogenous region extending from RM4923 to RM402 on the short arm of rice chromosome 6. Each NIL set consisted of 10 maternal lines and 10 paternal lines. They were measured for the length, width, perimeter and area of the top three leaves and the number of spikelets per panicle, number of grains per panicle and grain weight per panicle. In NIL sets 6-4 and 6-7, differing in intervals RM4923-RM225 and RM19410-RM6119, respectively, significant variations with the enhancing alleles from the female parent ZS97 were shown for the length, perimeter and area except for the area of the third leaf from top in 6-4, but the effects were lower in 6-4 than in 6-7. No significant effects were detected for the three traits in the remaining NIL set. It was shown that flag leaf length (FLL) is the primary target of the QTLs detected. Two QTLs for FLL linked in repulsion phase were resolved, of which qFLL6.2 located in the 1.19-Mb interval RM3414-RM6917 had a major effect with the enhancing allele from Zhenshan 97B, and qFLL6.1 located in the 946.8-kb interval RM19350-RM19410 had a smaller effect with the enhancing allele from Milyang 46. The two QTLs also exerted pleiotropic effects on the yield traits. PMID:21677387

Shen, Bo; Yu, Wei-Dong; Du, Jing-Hong; Fan, Ye-Yang; Wu, Ji-Rong; Zhuang, Jie-Yun

2011-04-01

97

In vivo SILAC-based proteomics reveals phosphoproteome changes during mouse skin carcinogenesis.  

PubMed

Cancer progresses through distinct stages, and mouse models recapitulating traits of this progression are frequently used to explore genetic, morphological, and pharmacological aspects of tumor development. To complement genomic investigations of this process, we here quantify phosphoproteomic changes in skin cancer development using the SILAC mouse technology coupled to high-resolution mass spectrometry. We distill protein expression signatures from our data that distinguish between skin cancer stages. A distinct phosphoproteome of the two stages of cancer progression is identified that correlates with perturbed cell growth and implicates cell adhesion as a major driver of malignancy. Importantly, integrated analysis of phosphoproteomic data and prediction of kinase activity revealed PAK4-PKC/SRC network to be highly deregulated in SCC but not in papilloma. This detailed molecular picture, both at the proteome and phosphoproteome level, will prove useful for the study of mechanisms of tumor progression. PMID:23375375

Zanivan, Sara; Meves, Alexander; Behrendt, Kristina; Schoof, Erwin M; Neilson, Lisa J; Cox, Jürgen; Tang, Hao R; Kalna, Gabriela; van Ree, Janine H; van Deursen, Jan M; Trempus, Carol S; Machesky, Laura M; Linding, Rune; Wickström, Sara A; Fässler, Reinhard; Mann, Matthias

2013-02-21

98

Aortic Dissection: Clinical Presentation  

Microsoft Academic Search

More ink than blood has been split on the subject of aortic dissections, beginning with the first well-documented case of\\u000a aortic dissection—George II of England, who died while straining on the commode. Morgagni first described aortic dissection\\u000a more than 200 years ago. The advent and adoption of modern cardiac surgical procedures have dramatically altered the outcome\\u000a what was once a

Ragavendra R. Baliga; Jai Raman; Kim Eagle

99

Interactive Frog Dissection  

NSDL National Science Digital Library

University of Virginia Curry School of Education's Instructional Technology Program has announced Interactive Frog Dissection. The tutorial combines text with 60 in-line color images and 17 QuickTime movies illustrating dissection procedures and internal organs. Numerous clickable image maps provide interactive practice. Research with pre-Web versions of the program suggests it is a valuable preparation tool or even a useful substitute for laboratory dissection.

100

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. PMID:23617817

2013-01-01

101

In-depth phosphoproteomic analysis of royal jelly derived from western and eastern honeybee species.  

PubMed

The proteins in royal jelly (RJ) play a pivotal role in the nutrition, immune defense, and cast determination of honeybee larvae and have a wide range of pharmacological and health-promoting functions for humans as well. Although the importance of post-translational modifications (PTMs) in protein function is known, investigation of protein phosphorylation of RJ proteins is still very limited. To this end, two complementary phosphopeptide enrichment materials (Ti(4+)-IMAC and TiO2) and high-sensitivity mass spectrometry were applied to establish a detailed phosphoproteome map and to qualitatively and quantitatively compare the phosphoproteomes of RJ produced by Apis mellifera ligustica (Aml) and Apis cerana cerana (Acc). In total, 16 phosphoproteins carrying 67 phosphorylation sites were identified in RJ derived from western bees, and nine proteins phosphorylated on 71 sites were found in RJ produced by eastern honeybees. Of which, eight phosphorylated proteins were common to both RJ samples, and the same motif ([S-x-E]) was extracted, suggesting that the function of major RJ proteins as nutrients and immune agents is evolutionary preserved in both of these honeybee species. All eight overlapping phosphoproteins showed significantly higher abundance in Acc-RJ than in Aml-RJ, and the phosphorylation of Jelleine-II (an antimicrobial peptide, TPFKLSLHL) at S(6) in Acc-RJ had stronger antimicrobial properties than that at T(1) in Aml-RJ even though the overall antimicrobial activity of Jelleine-II was found to decrease after phosphorylation. The differences in phosphosites, peptide abundance, and antimicrobial activity of the phosphorylated RJ proteins indicate that the two major honeybee species employ distinct phosphorylation strategies that align with their different biological characteristics shaped by evolution. The phosphorylation of RJ proteins are potentially driven by the activity of extracellular serine/threonine protein kinase FAM20C-like protein (FAM20C-like) through the [S-x-E] motif, which is supported by evidence that mRNA and protein expression of FAM20C-like protein kinase are both found in the highest level in the hypopharyngeal gland of nurse bees. Our data represent the first comprehensive RJ phosphorylation atlas, recording patterns of phosphorylated RJ protein abundance and antibacterial activity of some RJ proteins in two major managed honeybee species. These data constitute a firm basis for future research to better understand the biological roles of each RJ protein for honeybee biology and human health care. PMID:25265229

Han, Bin; Fang, Yu; Feng, Mao; Lu, Xiaoshan; Huo, Xinmei; Meng, Lifeng; Wu, Bin; Li, Jianke

2014-12-01

102

Delayed times to tissue fixation result in unpredictable global phosphoproteome changes.  

PubMed

Protein phosphorylation controls the activity of signal transduction pathways regulated by kinases and phosphatases. Little is known, however, about the impact of preanalytical factors, for example, delayed times to tissue fixation, on global phosphoprotein levels in tissues. The aim of this study was to characterize the potential effects of delayed tissue preservation (cold ischemia) on the levels of phosphoproteins using targeted and nontargeted proteomic approaches. Rat and murine liver samples were exposed to different cold ischemic conditions ranging from 10 to 360 min prior to cryopreservation. The phosphoproteome was analyzed using reverse phase protein array (RPPA) technology and phosphoprotein-enriched quantitative tandem mass spectrometry (LC-MS/MS). RPPA analysis of rat liver tissues with long (up to 360 min) cold ischemia times did not reveal statistically significant alterations of specific phosphoproteins even though nonphosphorylated cytokeratin 18 (CK18) showed increased levels after 360 min of delay to freezing. Keeping the samples on ice prior to cryopreservation prevented this effect. LC-MS/MS-based quantification of 1684 phosphorylation sites in rat liver tissues showed broadening of their distribution compared to time point zero, but without reaching statistical significance for individual phosphosites. Similarly, RPPA analysis of mouse liver tissues with short (<60 min) cold ischemia times did not reveal directed or predictable changes of protein and phosphoprotein levels. Using LC-MS/MS and quantification of 791 phosphorylation sites, we found that the distribution of ratios compared to time point zero broadens with prolonged ischemia times, but these were rather undirected and diffuse changes, as we could not detect significant alterations of individual phosphosites. On the basis of our results from RPPA and LC-MS/MS analysis of rat and mouse liver tissues, we conclude that prolonged cold ischemia results in unspecific phosphoproteome changes that can be neither predicted nor assigned to individual proteins. On the other hand, we identified a number of phosphosites which were extraordinarily stable even after 360 min of cold ischemia and, therefore, may be used as general reference markers for future companion diagnostics for kinase inhibitors. PMID:23984901

Gündisch, Sibylle; Grundner-Culemann, Kathrin; Wolff, Claudia; Schott, Christina; Reischauer, Bilge; Machatti, Manuela; Groelz, Daniel; Schaab, Christoph; Tebbe, Andreas; Becker, Karl-Friedrich

2013-10-01

103

Flower Dissection Lab  

NSDL National Science Digital Library

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

104

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. PMID:22468611

2012-01-01

105

Reliable PCR quantitation of estrogen, progesterone and ERBB2 receptor mRNA from formalin-fixed, paraffin-embedded tissue is independent of prior macro-dissection.  

PubMed

Gene expression analysis on messenger RNA (mRNA) purified from formalin-fixed, paraffin-embedded tissue is increasingly used for research purposes. Tissue heterogeneity may question specificity and interpretation of results from mRNA isolated from a whole slide section, and thresholds for minimal tumor content in the paraffin block or macrodissection are used to avoid contamination from non-neoplastic tissue. The aim was to test if mRNA from tissue surrounding breast cancer affected quantification of estrogen receptor ? (ESR1), progesterone receptor (PGR) and human epidermal growth factor receptor 2 (ERBB2), by comparing gene expression from whole slide and tumor-enriched sections, and correlating gene expression from whole slide sections with corresponding immunohistochemistry. Gene expression, based on mRNA extracted from a training set (36 paraffin blocks) and two validation sets (133 + 1,083 blocks), were determined by quantitative reverse transcription polymerase chain reaction for all samples, as well as by microarray for 133 validation samples. In the training set, agreement between high vs. low mRNA expression from whole slide and tumor-enriched sections was absolute for ESR1 and ERBB2, and 83 % for PGR. Overall agreements, when comparing mRNA expression to immunohistochemistry, were 100 % (ERBB2), 89 % (ESR1) and 83 % (PGR), which was confirmed in the validation sets. Percentage of tumor in the sections did not influence the results. In conclusion, reliable quantification of ESR1, PGR and ERBB2 mRNA expression can be obtained from a whole slide section, and correlates well with immunohistochemistry. Prior removal of surrounding tissue was found to be unnecessary even with minimal tumor content in the section. PMID:24100522

Tramm, Trine; Hennig, Guido; Kyndi, Marianne; Alsner, Jan; Sørensen, Flemming Brandt; Myhre, Simen; Sørlie, Therese; Overgaard, Jens

2013-12-01

106

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

PubMed

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

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

2009-02-01

107

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

108

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. PMID:24147020

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

2013-01-01

109

Functional Divergence and Evolutionary Turnover in Mammalian Phosphoproteomes  

PubMed Central

Protein phosphorylation is a key mechanism to regulate protein functions. However, the contribution of this protein modification to species divergence is still largely unknown. Here, we studied the evolution of mammalian phosphoregulation by comparing the human and mouse phosphoproteomes. We found that 84% of the positions that are phosphorylated in one species or the other are conserved at the residue level. Twenty percent of these conserved sites are phosphorylated in both species. This proportion is 2.5 times more than expected by chance alone, suggesting that purifying selection is preserving phosphoregulation. However, we show that the majority of the sites that are conserved at the residue level are differentially phosphorylated between species. These sites likely result from false-negative identifications due to incomplete experimental coverage, false-positive identifications and non-functional sites. In addition, our results suggest that at least 5% of them are likely to be true differentially phosphorylated sites and may thus contribute to the divergence in phosphorylation networks between mouse and humans and this, despite residue conservation between orthologous proteins. We also showed that evolutionary turnover of phosphosites at adjacent positions (in a distance range of up to 40 amino acids) in human or mouse leads to an over estimation of the divergence in phosphoregulation between these two species. These sites tend to be phosphorylated by the same kinases, supporting the hypothesis that they are functionally redundant. Our results support the hypothesis that the evolutionary turnover of phosphorylation sites contributes to the divergence in phosphorylation profiles while preserving phosphoregulation. Overall, our study provides advanced analyses of mammalian phosphoproteomes and a framework for the study of their contribution to phenotypic evolution. PMID:24465218

Freschi, Luca; Osseni, Mazid; Landry, Christian R.

2014-01-01

110

Dissection efficiency during laparoscopic oesophageal dissection.  

PubMed

Advanced techniques in laparoscopic surgery have led to an increased need for appropriate training in instrument handling and dissection. Recent developments in computer video technology have facilitated critical analysis of surgical technique. Video deconstruction of oesophageal hiatal dissection during six laparoscopic fundoplication procedures was undertaken. The procedures were performed by surgeons with a wide range of surgical experience, and the investigators analysing performance were blinded to their level of training. Sequential five-second video segments were analysed in detail by 3 investigators. A taxonomy list was developed to describe individual types of movement. The number and time per movement was assessed and a degree of efficiency was assigned. An efficient movement was defined as one that advances the dissection towards a recognised goal. The total oesophageal dissection time varied from 10 minutes (min) to 25 min (mean 16 min). The mean number of actions performed was 173 (range 120-272). A mean of 7 min was spent separating tissues (range 5-13), with 6 min spent grasping and positioning tissue (range 3-8). The amount of time spent in inefficient movement varied from 3 to 14 min (mean 7 min). The greatest variation between operators was seen in the efficiency of tissue separation when using dissecting instruments. Inexperienced operators spent a lot more time performing additional movements such as scope cleaning, observation and instrument exchange. This technique of video deconstruction can identify key areas for improvement. This could be used for trainee assessment and to provide constructive feedback. Future development in this area could enhance training in advanced laparoscopic techniques. PMID:16754147

Leeder, P C; Patkin, M; Stoddard, J; Watson, D I

2005-01-01

111

Inducing autophagy: a comparative phosphoproteomic study of the cellular response to ammonia and rapamycin.  

PubMed

Autophagy is a lysosomal-mediated catabolic process, which through degradation of different cytoplasmic components aids in maintaining cellular homeostasis and survival during exposure to extra- or intracellular stresses. Ammonia is a potential toxic and stress-inducing byproduct of glutamine catabolism, which has recently been found to induce autophagy in an MTOR independent way and support cancer cell survival. In this study, quantitative phosphoproteomics was applied to investigate the initial signaling events linking ammonia to the induction of autophagy. The MTOR inhibitor rapamycin was used as a reference treatment to emphasize the differences between an MTOR-dependent and -independent autophagy-induction. By this means 5901 phosphosites were identified of which 626 were treatment-specific regulated and 175 were coregulated. Investigation of the ammonia-specific regulated sites supported that MTOR activity was not affected, but indicated increased MAPK3 activity, regulation of proteins involved in Rho signal transduction, and a novel phosphorylation motif, serine-proline-threonine (SPT), which could be linked to cytoskeleton-associated proteins. MAPK3 could not be identified as the primary driver of ammonia-induced autophagy but instead the data suggested an upregulation of AMPK and the unfolded protein response (UPR), which might link ammonia to autophagy induction. Support of UPR induction was further obtained from the finding of increased protein levels of the ER stress markers DDIT3/CHOP and HSPA5 during ammonia treatment. The large-scale data set presented here comprises extensive high-quality quantitative information on phosphoprotein regulation in response to 2 very different autophagy inducers and should therefore be considered a general resource for the community. PMID:24300666

Harder, Lea M; Bunkenborg, Jakob; Andersen, Jens S

2014-02-01

112

Early Phosphoproteomic Changes in the Mouse Spleen During Deoxynivalenol-Induced Ribotoxic Stress  

PubMed Central

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

Pestka, James J.

2013-01-01

113

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

PubMed Central

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

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

2014-01-01

114

Phosphoproteomic analysis of primary human multiple myeloma cells.  

PubMed

Multiple myeloma (MM) is a malignant disorder of differentiated B cells. Clonal expansion of the tumor results in the excessive production of monoclonal immunoglobulin (Ig) which is a diagnostic feature of this disease. Previous investigations have demonstrated the alteration of the ERK, jun kinase, STAT, and AKT kinase signaling cascades in MM cells, suggesting that deregulated phosphorylation may contribute to MM pathogenesis. However, systematic analysis of the phosphoproteome in MM cells has not been reported. Here, we described a large-scale phosphorylation analysis of primary MM cells. Using a separation strategy involving immunomagnetic bead-positive selection of MM cells, preparative SDS-PAGE for prefractionation, in-gel digestion with trypsin, and titanium dioxide enrichment of phosphopeptides, followed by LC-MS/MS analysis employing a hybrid LTQ-Orbitrap mass spectrometer, we were able to catalog a substantial portion of the phosphoproteins present in primary MM cells. This analysis led to the identification of 530 phosphorylation sites from 325 unique phosphopeptides corresponding to 260 proteins at false positive rate (FPR) of 1.3%. This dataset provides an important resource for future studies on phosphorylation and carcinogenesis analysis of multiple myeloma. PMID:20230923

Ge, Feng; Xiao, Chuan-Le; Yin, Xing-Feng; Lu, Chun-Hua; Zeng, Hui-Lan; He, Qing-Yu

2010-05-01

115

Virtual Pig Dissection  

NSDL National Science Digital Library

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

Fleck, Earl W.

116

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

117

Is dissection humane?  

PubMed Central

Dissection is being jeopardized in the modern medical education. It has unrelentingly faced the lashes of time and has been the scapegoat for numerous convenient curricula reforms and subjective biases. The cadaver is unparallel in establishing core knowledge among the medical community and it needs to be appreciated in a new light in the “cyber anatomy” realm of today. This article elucidates the medical and ethical validity of continuing human body dissection in medicine which outweighs all the prejudices associated with it. PMID:23908746

Hasan, Tabinda

2011-01-01

118

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.

119

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

PubMed Central

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 (ATM) can also localize to dendrites and dendritic spines, in addition to other subcellular compartments, and is activated by bicuculline application. Pharmacology studies indicate that ATM and its sister kinase ATR 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

2013-01-01

120

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

PubMed Central

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

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

2014-01-01

121

Phosphoproteomic profiling of selenate-treated Alzheimer's disease model cells.  

PubMed

The reversible phosphorylation of proteins regulates most biological processes, while abnormal phosphorylation is a cause or consequence of many diseases including Alzheimer's disease (AD). One of the hallmarks of AD is the formation of neurofibrillary tangles (NFTs), which is composed of hyperphosphorylated tau proteins. Sodium selenate has been recently found to reduce tau hyperphosphorylation and NFTs formation, and to improve spatial learning and motor performance in AD mice. In the current study, the phosphoproteomics of N2aSW cells treated with selenate were investigated. To avoid missing low-abundance phosphoproteins, both the total proteins of cells and the phosphor-enriched proteins were extracted and subjected to the two-dimensional gel electrophoresis with Pro-Q diamond staining and then LC-MS/MS analysis. A total of 65 proteins were altered in phosphorylation level, of which 39 were up-regulated and 26 were down-regulated. All identified phosphoproteins were bioinformatically annotated according to their physiochemical features, subcellular location, and biological function. Most of these significantly changed phosphoproteins are involved in crucial neural processes such as protesome activity, oxidative stress, cysteine and methionine metabolism, and energy metabolism. Furthermore, decreases were found in homocysteine, phosphor-tau and amyloid ? upon selenate treatment. Our results suggest that selenate may intervene in the pathological process of AD by altering the phosphorylation of some key proteins involved in oxidative stress, energy metabolism and protein degradation, thus play important roles in maintaining redox homeostasis, generating ATP, and clearing misfolded proteins and aggregates. The present paper provides some new clues to the mechanism of selenate in AD prevention. PMID:25485856

Chen, Ping; Wang, Lixiang; Wang, Yong; Li, Shuiming; Shen, Liming; Liu, Qiong; Ni, Jiazuan

2014-01-01

122

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

123

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. PMID:23300999

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

2013-01-01

124

Phosphoproteomic Profiling of Selenate-Treated Alzheimer's Disease Model Cells  

PubMed Central

The reversible phosphorylation of proteins regulates most biological processes, while abnormal phosphorylation is a cause or consequence of many diseases including Alzheimer's disease (AD). One of the hallmarks of AD is the formation of neurofibrillary tangles (NFTs), which is composed of hyperphosphorylated tau proteins. Sodium selenate has been recently found to reduce tau hyperphosphorylation and NFTs formation, and to improve spatial learning and motor performance in AD mice. In the current study, the phosphoproteomics of N2aSW cells treated with selenate were investigated. To avoid missing low-abundance phosphoproteins, both the total proteins of cells and the phosphor-enriched proteins were extracted and subjected to the two-dimensional gel electrophoresis with Pro-Q diamond staining and then LC-MS/MS analysis. A total of 65 proteins were altered in phosphorylation level, of which 39 were up-regulated and 26 were down-regulated. All identified phosphoproteins were bioinformatically annotated according to their physiochemical features, subcellular location, and biological function. Most of these significantly changed phosphoproteins are involved in crucial neural processes such as protesome activity, oxidative stress, cysteine and methionine metabolism, and energy metabolism. Furthermore, decreases were found in homocysteine, phosphor-tau and amyloid ? upon selenate treatment. Our results suggest that selenate may intervene in the pathological process of AD by altering the phosphorylation of some key proteins involved in oxidative stress, energy metabolism and protein degradation, thus play important roles in maintaining redox homeostasis, generating ATP, and clearing misfolded proteins and aggregates. The present paper provides some new clues to the mechanism of selenate in AD prevention. PMID:25485856

Wang, Yong; Li, Shuiming; Shen, Liming; Liu, Qiong; Ni, Jiazuan

2014-01-01

125

Interrogating cAMP-dependent Kinase Signaling in Jurkat T Cells via a Protein Kinase A Targeted Immune-precipitation Phosphoproteomics Approach*  

PubMed Central

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.

2013-01-01

126

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

127

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.

128

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

PubMed Central

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

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

2014-01-01

129

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

130

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. PMID:24657495

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

2014-01-01

131

Aortic dissection and dissecting aortic aneurysms.  

PubMed Central

Operation was employed in the treatment of 546 patients for complications of aortic dissection during the 32-year period of 1956-1988. Current concepts and operative techniques evolved during this period. Fortunately, about half the patients were treated during the latter 4 years, as modern therapy became standardized. The cumulative survival rate was 86% for all patients and 94% for those treated during recent years. Pathologic processes and requirements of operation became clearer by treating 174 patients who had had 198 previous operations by the time of referral. Reoperation was required for complications of operations now considered outdated, heart operations in patients with ascending aortic dilatation, and progressive dilatation of residual segments of the aorta. The 546 patients were followed, and a total of 838 operations were finally employed, resulting in total aortic replacement in 18, near total replacement in 41, entire thoracic aorta in 22, near total thoracic aorta in 33, and the entire thoracoabdominal aorta in 148 patients. Long-term survival in 439 patients after final operation was 66% and 44% at 5 and 10 years, respectively, despite the fact that the median age at first admission was 59. Operative treatment appears to be well-established for this disease. Images Figs. 12A-C. Figs. 12A-C. Figs. 1A and B. Figs. 2A and B. Fig. 3. Figs. 4A-D. Figs. 5A-C. Figs. 5A-C. Figs. 6A and B. Figs. 7A and B. Figs. 8A and B. Figs. 9A and B. Figs. 10A and B.,Figs. 11A and B. PMID:3421752

Crawford, E S; Svensson, L G; Coselli, J S; Safi, H J; Hess, K R

1988-01-01

132

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

PubMed Central

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

Spät, Philipp; Ma?ek, Boris; Forchhammer, Karl

2015-01-01

133

Phosphoproteomic Analysis of Seed Maturation in Arabidopsis, Rapeseed, and Soybean1[C][W][OA  

PubMed Central

To characterize protein phosphorylation in developing seed, a large-scale, mass spectrometry-based phosphoproteomic study was performed on whole seeds at five sequential stages of development in soybean (Glycine max), rapeseed (Brassica napus), and Arabidopsis (Arabidopsis thaliana). Phosphopeptides were enriched from 0.5 mg of total peptides using a combined strategy of immobilized metal affinity and metal oxide affinity chromatography. Enriched phosphopeptides were analyzed by Orbitrap tandem mass spectrometry and mass spectra mined against cognate genome or cDNA databases in both forward and randomized orientations, the latter to calculate false discovery rate. We identified a total of 2,001 phosphopeptides containing 1,026 unambiguous phosphorylation sites from 956 proteins, with an average false discovery rate of 0.78% for the entire study. The entire data set was uploaded into the Plant Protein Phosphorylation Database (www.p3db.org), including all meta-data and annotated spectra. The Plant Protein Phosphorylation Database is a portal for all plant phosphorylation data and allows for homology-based querying of experimentally determined phosphosites. Comparisons with other large-scale phosphoproteomic studies determined that 652 of the phosphoproteins are novel to this study. The unique proteins fall into several Gene Ontology categories, some of which are overrepresented in our study as well as other large-scale phosphoproteomic studies, including metabolic process and RNA binding; other categories are only overrepresented in our study, like embryonic development. This investigation shows the importance of analyzing multiple plants and plant organs to comprehensively map the complete plant phosphoproteome. PMID:22440515

Meyer, Louis J.; Gao, Jianjiong; Xu, Dong; Thelen, Jay J.

2012-01-01

134

Identification of the PLK2-Dependent Phosphopeptidome by Quantitative Proteomics  

PubMed Central

Polo-like kinase 2 (PLK2) has been recently recognized as the major enzyme responsible for phosphorylation of ?-synuclein at S129 in vitro and in vivo, suggesting that this kinase may play a key role in the pathogenesis of Parkinson's disease and other synucleinopathies. Moreover PLK2 seems to be implicated in cell division, oncogenesis, and synaptic regulation of the brain. However little is known about the phosphoproteome generated by PLK2 and, consequently the overall impact of PLK2 on cellular signaling. To fill this gap we exploited an approach based on in vitro kinase assay and quantitative phosphoproteomics. A proteome-derived peptide library obtained by digestion of undifferentiated human neuroblastoma cell line was exhaustively dephosphorylated by lambda phosphatase followed by incubation with or without PLK2 recombinant kinase. Stable isotope labeling based quantitative phosphoproteomics was applied to identify the phosphosites generated by PLK2. A total of 98 unique PLK2-dependent phosphosites from 89 proteins were identified by LC-MS/MS. Analysis of the primary structure of the identified phosphosites allowed the detailed definition of the kinase specificity and the compilation of a list of potential PLK2 targets among those retrieved in PhosphositePlus, a curated database of in cell/vivo phosphorylation sites. PMID:25338102

Franchin, Cinzia; Cesaro, Luca; Pinna, Lorenzo A.; Arrigoni, Giorgio; Salvi, Mauro

2014-01-01

135

Phosphoproteomics-Based Modeling Defines the Regulatory Mechanism Underlying Aberrant EGFR Signaling  

PubMed Central

Background Mutation of the epidermal growth factor receptor (EGFR) results in a discordant cell signaling, leading to the development of various diseases. However, the mechanism underlying the alteration of downstream signaling due to such mutation has not yet been completely understood at the system level. Here, we report a phosphoproteomics-based methodology for characterizing the regulatory mechanism underlying aberrant EGFR signaling using computational network modeling. Methodology/Principal Findings Our phosphoproteomic analysis of the mutation at tyrosine 992 (Y992), one of the multifunctional docking sites of EGFR, revealed network-wide effects of the mutation on EGF signaling in a time-resolved manner. Computational modeling based on the temporal activation profiles enabled us to not only rediscover already-known protein interactions with Y992 and internalization property of mutated EGFR but also further gain model-driven insights into the effect of cellular content and the regulation of EGFR degradation. Our kinetic model also suggested critical reactions facilitating the reconstruction of the diverse effects of the mutation on phosphoproteome dynamics. Conclusions/Significance Our integrative approach provided a mechanistic description of the disorders of mutated EGFR signaling networks, which could facilitate the development of a systematic strategy toward controlling disease-related cell signaling. PMID:21085658

Tasaki, Shinya; Nagasaki, Masao; Kozuka-Hata, Hiroko; Semba, Kentaro; Gotoh, Noriko; Hattori, Seisuke; Inoue, Jun-ichiro; Yamamoto, Tadashi; Miyano, Satoru; Sugano, Sumio; Oyama, Masaaki

2010-01-01

136

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

PubMed Central

Specific oxidized phospholipids (oxPCCD36) promote platelet hyper-reactivity and thrombosis in hyperlipidemia via the scavenger receptor CD36, however the signaling pathway(s) induced in platelets by oxPCCD36 are not well defined. We have employed mass spectrometry-based tyrosine, serine, and threonine phosphoproteomics for the unbiased analysis of platelet signaling pathways induced by oxPCCD36 as well as by the strong physiological agonist thrombin. oxPCCD36 and thrombin induced differential phosphorylation of 115 proteins (162 phosphorylation sites) and 181 proteins (334 phosphorylation sites) respectively. Most of the phosphoproteome changes induced by either agonist have never been reported in platelets; thus they provide candidates in the study of platelet signaling. Bioinformatic analyses of protein phosphorylation dependent responses were used to categorize preferential motifs for (de)phosphorylation, predict pathways and kinase activity, and construct a phosphoproteome network regulating integrin activation. A putative signaling pathway involving Src-family kinases, SYK, and PLC?2 was identified in platelets activated by oxPCCD36. Subsequent ex vivo studies in human platelets demonstrated that this pathway is downstream of the scavenger receptor CD36 and is critical for platelet activation by oxPCCD36. Our results provide multiple insights into the mechanism of platelet activation and specifically in platelet regulation by oxPCCD36. PMID:24400094

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

2014-01-01

137

Phosphoproteomic Analysis of Protein Phosphorylation Networks in Tetrahymena thermophila, a Model Single-celled Organism*  

PubMed Central

Tetrahymena thermophila is a widely used unicellular eukaryotic model organism in biological research and contains more than 1000 protein kinases and phosphatases with specificity for Ser/Thr/Tyr residues. However, only a few dozen phosphorylation sites in T. thermophila are known, presenting a major obstacle to further understanding of the regulatory roles of reversible phosphorylation in this organism. In this study, we used high-accuracy mass-spectrometry-based proteomics to conduct global and site-specific phosphoproteome profiling of T. thermophila. In total, 1384 phosphopeptides and 2238 phosphorylation sites from 1008 T. thermophila proteins were identified through the combined use of peptide prefractionation, TiO2 enrichment, and two-dimensional LC-MS/MS analysis. The identified phosphoproteins are implicated in the regulation of various biological processes such as transport, gene expression, and mRNA metabolic process. Moreover, integrated analysis of the T. thermophila phosphoproteome and gene network revealed the potential biological functions of many previously unannotated proteins and predicted some putative kinase–substrate pairs. Our data provide the first global survey of phosphorylation in T. thermophila using a phosphoproteomic approach and suggest a wide-ranging regulatory scope of this modification. The provided dataset is a valuable resource for the future understanding of signaling pathways in this important model organism. PMID:24200585

Tian, Miao; Chen, Xiulan; Xiong, Qian; Xiong, Jie; Xiao, Chuanle; Ge, Feng; Yang, Fuquan; Miao, Wei

2014-01-01

138

Application of Phosphoproteomics to Find Targets of Casein Kinase 1 in the Flagellum of Chlamydomonas  

PubMed Central

The green biflagellate alga Chlamydomonas reinhardtii serves as model for studying structural and functional features of flagella. The axoneme of C. reinhardtii anchors a network of kinases and phosphatases that control motility. One of them, Casein Kinase 1 (CK1), is known to phosphorylate the Inner Dynein Arm I1 Intermediate Chain 138 (IC138), thereby regulating motility. CK1 is also involved in regulating the circadian rhythm of phototaxis and is relevant for the formation of flagella. By a comparative phosphoproteome approach, we determined phosphoproteins in the flagellum that are targets of CK1. Thereby, we applied the specific CK1 inhibitor CKI-7 that causes significant changes in the flagellum phosphoproteome and reduces the swimming velocity of the cells. In the CKI-7-treated cells, 14 phosphoproteins were missing compared to the phosphoproteome of untreated cells, including IC138, and four additional phosphoproteins had a reduced number of phosphorylation sites. Notably, inhibition of CK1 causes also novel phosphorylation events, indicating that it is part of a kinase network. Among them, Glycogen Synthase Kinase 3 is of special interest, because it is involved in the phosphorylation of key clock components in flies and mammals and in parallel plays an important role in the regulation of assembly in the flagellum. PMID:23316220

Boesger, Jens; Wagner, Volker; Weisheit, Wolfram; Mittag, Maria

2012-01-01

139

Application of phosphoproteomics to find targets of casein kinase 1 in the flagellum of chlamydomonas.  

PubMed

The green biflagellate alga Chlamydomonas reinhardtii serves as model for studying structural and functional features of flagella. The axoneme of C. reinhardtii anchors a network of kinases and phosphatases that control motility. One of them, Casein Kinase 1 (CK1), is known to phosphorylate the Inner Dynein Arm I1 Intermediate Chain 138 (IC138), thereby regulating motility. CK1 is also involved in regulating the circadian rhythm of phototaxis and is relevant for the formation of flagella. By a comparative phosphoproteome approach, we determined phosphoproteins in the flagellum that are targets of CK1. Thereby, we applied the specific CK1 inhibitor CKI-7 that causes significant changes in the flagellum phosphoproteome and reduces the swimming velocity of the cells. In the CKI-7-treated cells, 14 phosphoproteins were missing compared to the phosphoproteome of untreated cells, including IC138, and four additional phosphoproteins had a reduced number of phosphorylation sites. Notably, inhibition of CK1 causes also novel phosphorylation events, indicating that it is part of a kinase network. Among them, Glycogen Synthase Kinase 3 is of special interest, because it is involved in the phosphorylation of key clock components in flies and mammals and in parallel plays an important role in the regulation of assembly in the flagellum. PMID:23316220

Boesger, Jens; Wagner, Volker; Weisheit, Wolfram; Mittag, Maria

2012-01-01

140

Dissections of a metal rectangle  

E-print Network

In the present popular science paper the following geometric questions are answered: - Which rectangles can be dissected into squares? - When a square can be dissected into rectangles similar to a given rectangle? The proofs are based on a physical interpretation using electrical networks. Only secondary school background is assumed in the paper.

Prasolov, Maxim

2010-01-01

141

"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

142

Spontaneous coronary artery dissection.  

PubMed

Spontaneous coronary artery dissection (SCAD) is a relatively rare and unexplored type of coronary disease. Although atherosclerosis, hormonal changes during pregnancy and connective tissue disorders might represent a sufficiently convincing explanation for some patients with SCAD, the many remaining cases display only a weak relationship with these causes. While on one side the clinical heterogeneity of SCAD masks a full understanding of their underlying pathophysiologic process, on the other side paucity of data and misleading presentations hamper the quick diagnosis and optimal management of this condition. A definite diagnosis of SCAD can be significantly facilitated by endovascular imaging techniques. In fact, intravascular ultrasound (IVUS) and optical coherence tomography (OCT) overcome the limitations of coronary angiography providing detailed endovascular morphologic information. In contrast, optimal treatment strategies for SCAD still represent a burning controversial question. Herein, we review the published data examining possible causes and investigating the best therapy for SCAD in different clinical scenarios. PMID:24861255

Giacoppo, Daniele; Capodanno, Davide; Dangas, George; Tamburino, Corrado

2014-07-15

143

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

144

Quantitative Phosphoproteomics of Alzheimer's Disease Reveals Crosstalk between Kinases and Small Heat Shock Proteins  

PubMed Central

Abnormal phosphorylation contributes to the formation of neurofibrillary tangles in Alzheimer Disease (AD), but may play other signaling roles during AD pathogenesis. In this study, we employed immobilized metal affinity chromatography (IMAC) followed by liquid chromatography-tandem mass spectrometry to identify phosphopeptides from 8 individual AD and 8 age-matched control postmortem human brain tissues. Using this approach, we identified 5,569 phosphopeptides in frontal cortex across all 16 cases in which phosphopeptides represented 80 percent of all peptide spectral counts collected following IMAC enrichment. Marker selection identified 253 significantly altered phosphopeptides by precursor intensity, changed by at least 1.75 fold relative to controls, with an empirical false discovery rate below 7 percent. Approximately 21 percent of all significantly altered phosphopeptides in AD tissue were derived from tau. Of the other 142 proteins hyperphosphorylated in AD, membrane, synapse, cell junction, and alternatively spliced proteins were overrepresented. Of these, we validated differential phosphorylation of heat-shock protein-beta-1 (HSPB1) and crystallin-alpha-B (CRYAB) as hyperphosphorylated by western blotting. We further identified a network of phosphorylated kinases, which co-enriched with phosphorylated small heat shock proteins. This supports a hypothesis that a number of kinases are regulating and/or regulated by the small heat shock protein folding network. PMID:25332170

Duong, Duc M.; Gearing, Marla; Lah, James J.; Levey, Allan I.; Seyfried, Nicholas T

2015-01-01

145

Quantitative phosphoproteomics unveils temporal dynamics of thrombin signaling in human endothelial cells  

PubMed Central

Thrombin is the key serine protease of the coagulation cascade and a potent trigger of protease-activated receptor 1 (PAR1)-mediated platelet aggregation. In recent years, PAR1 has become an appealing target for anticoagulant therapies. However, the inhibitors that have been developed so far increase bleeding risk in patients, likely because they interfere with endogenous PAR1 signaling in the endothelium. Because of its complexity, thrombin-induced signaling in endothelial cells has remained incompletely understood. Here, we have combined stable isotope amino acids in cell culture, affinity-based phosphopeptide enrichment, and high-resolution mass spectrometry and performed a time-resolved analysis of the thrombin-induced signaling in human primary endothelial cells. We identified 2224 thrombin-regulated phosphorylation sites, the majority of which have not been previously related to thrombin. Those sites were localized on proteins that are novel to thrombin signaling, but also on well-known players such as PAR1, Rho-associated kinase 2, phospholipase C, and proteins related to actin cytoskeleton, cell-cell junctions, and Weibel-Palade body release. Our study provides a unique resource of phosphoproteins and phosphorylation sites that may generate novel insights into an intimate understanding of thrombin-mediated PAR signaling and the development of improved PAR1 antagonists that affect platelet but not endothelial cell function. PMID:24501219

van den Biggelaar, Maartje; Hernández-Fernaud, Juan Ramon; van den Eshof, Bart L.; Neilson, Lisa J.; Meijer, Alexander B.; Mertens, Koen

2014-01-01

146

[Dissection techniques in liver surgery].  

PubMed

The first liver resection was performed in 1888. Since then a wide variety of dissection techniques have been introduced. The blunt dissection was replaced by novel methods, i.e. the CUSA technique and the Jet Cutter for major liver resections. These methods represent selective dissection techniques; whereas non-selective methods include the scalpel, scissors, linear stapling cutter, high-frequency coagulation, and the laser technique. The aim of this review article is the comparison of the different resection techniques in liver surgery, focussing on blood loss and resection time. PMID:11253668

Rau, H G; Schauer, R; Pickelmann, S; Beyer, B C; Angele, M K; Zimmermann, A; Meimarakis, G; Heizmann, O; Schildberg, F W

2001-02-01

147

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

148

Spontaneous coronary artery dissection.  

PubMed

Spontaneous coronary artery dissection (SCAD) is a rare but challenging clinical entity of unknown etiology. From a pathophysiological standpoint, SCAD may occur in patients with a coronary intimal tear (presenting with the classic angiographic "flap" and multiple lumens), but also in patients without an intimal rupture (presenting as an intramural hematoma). Until now, available information on SCAD was largely based on multiple, small case-series studies but, recently, data from relatively large registries have cast a new light on this disease. Classically, SCAD was thought to present in young females without traditional atherosclerotic risk factors but recent reports suggest a broader clinical spectrum encompassing older patients with associated coronary artery disease. In this review, we concentrate on 3 main aspects of this unique disease: (1) the value of intracoronary diagnostic techniques (intravascular ultrasound and optical coherence tomography) to complement coronary angiography and to provide novel diagnostic insights on this elusive clinical condition; (2) the growing clinical evidence suggesting an association and potential causation between fibromuscular dysplasia and SCAD; and (3) the challenges of coronary revascularization in this adverse anatomic setting, together with recent data suggesting that a initial, conservative medical management may be preferable for the majority of patients with SCAD. PMID:25131524

Alfonso, Fernando; Bastante, Teresa; Rivero, Fernando; Cuesta, Javier; Benedicto, Amparo; Saw, Jacqueline; Gulati, Rajiv

2014-01-01

149

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

150

Ethylenediaminetetraacetic acid increases identification rate of phosphoproteomics in real biological samples.  

PubMed

We have developed a novel approach to enhance phosphopeptide identification in liquid chromatography/mass spectrometry (LC/MS)-based phosphoproteomics. After enrichment of phosphopeptides with immobilized metal affinity chromatography (IMAC) and titanium dioxide (TiO(2)) microcolumns, samples were coinjected with ethylenediaminetetraacetic acid (EDTA) into LC/MS. This procedure decreased the MS peak intensity of nonphosphorylated peptides, but not that of phosphopeptides, and as a result, the number of identified phosphopeptides was increased. EDTA appeared to have no effect on liquid chromatographic separation of phosphorylated and nonphosphorylated peptides. Although the mechanism of the positive effect of EDTA on identification of phosphopeptides is unknown, and we have never observed metal ion adduct peaks in LC/MS spectra, coinjection of EDTA seemed to enhance phosphopeptide recovery from the LC/MS system. This simple technique was successfully applied to the identification of phosphopeptides in mouse brain (2938 phosphopeptides), human plasma (127 phosphopetides), and human cerebrospinal fluid (CSF) (123 phosphopeptides). We also identified nonphosphopeptides in the same samples using a two-dimensional (2D) LC/MS-based shotgun approach. The results overall indicated that 20-25% of brain proteins were phosphorylated, while only 1-2% of proteins in plasma and CSF were phosphorylated. These ratios were almost constant throughout the range of protein expression levels. In addition, EDTA-enhanced phosphoproteomics could identify low-abundance proteins in the samples, because nonphosphoproteins corresponding to more than one-third of the identified phosphoproteins could not be identified by 2D-LC/MS. Finally, we were able to find that the newly developed approach was very effective for the phosphoproteome analysis in Alzheimer disease model mice brain. PMID:20099890

Nakamura, Tatsuji; Myint, Khin Than; Oda, Yoshiya

2010-03-01

151

Phosphoproteomic and Bioinformatic Characterization of the Signaling Alterations in Response to a PP2A Activator in Lung Cancer  

E-print Network

to a PP2A Activator in Lung Cancer Danica Wiredja1, Yu Liu1, Giridharan Gokulrangan1, Daniela Schlatzer1 cell lung cancer involves the coordinate activation of multiple oncogenic pathways, including the MAPK, the spectrum of perturbations in the phosphoproteome of cancer cells induced by these compounds is unknown

Yang, Sichun

152

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

PubMed

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

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

2014-11-01

153

Analysis of the Phosphoproteome of Chlamydomonas reinhardtii Provides New Insights into Various Cellular Pathways†  

PubMed Central

The unicellular flagellated green alga Chlamydomonas reinhardtii has emerged as a model organism for the study of a variety of cellular processes. Posttranslational control via protein phosphorylation plays a key role in signal transduction, regulation of gene expression, and control of metabolism. Thus, analysis of the phosphoproteome of C. reinhardtii can significantly enhance our understanding of various regulatory pathways. In this study, we have grown C. reinhardtii cultures in the presence of an inhibitor of Ser/Thr phosphatases to increase the phosphoprotein pool. Phosphopeptides from these cells were enriched by immobilized metal-ion affinity chromatography and analyzed by nano-liquid chromatography-electrospray ionization-mass spectrometry (MS) with MS-MS as well as neutral-loss-triggered MS-MS-MS spectra. In this way, we were able to identify 360 phosphopeptides from 328 different phosphoproteins of C. reinhardtii, thus providing new insights into a variety of cellular processes, including metabolic and signaling pathways. Comparative analysis of the phosphoproteome also yielded new functional information on proteins controlled by redox regulation (thioredoxin target proteins) and proteins of the chloroplast 70S ribosome, the centriole, and especially the flagella, for which 32 phosphoproteins were identified. The high yield of phosphoproteins of the latter correlates well with the presence of several flagellar kinases and indicates that phosphorylation/dephosphorylation represents one of the key regulatory mechanisms of eukaryotic cilia. Our data also provide new insights into certain cilium-related mammalian diseases. PMID:16524901

Wagner, Volker; Geßner, Gunther; Heiland, Ines; Kaminski, Marc; Hawat, Susan; Scheffler, Kai; Mittag, Maria

2006-01-01

154

Analysis of the phosphoproteome of Chlamydomonas reinhardtii provides new insights into various cellular pathways.  

PubMed

The unicellular flagellated green alga Chlamydomonas reinhardtii has emerged as a model organism for the study of a variety of cellular processes. Posttranslational control via protein phosphorylation plays a key role in signal transduction, regulation of gene expression, and control of metabolism. Thus, analysis of the phosphoproteome of C. reinhardtii can significantly enhance our understanding of various regulatory pathways. In this study, we have grown C. reinhardtii cultures in the presence of an inhibitor of Ser/Thr phosphatases to increase the phosphoprotein pool. Phosphopeptides from these cells were enriched by immobilized metal-ion affinity chromatography and analyzed by nano-liquid chromatography-electrospray ionization-mass spectrometry (MS) with MS-MS as well as neutral-loss-triggered MS-MS-MS spectra. In this way, we were able to identify 360 phosphopeptides from 328 different phosphoproteins of C. reinhardtii, thus providing new insights into a variety of cellular processes, including metabolic and signaling pathways. Comparative analysis of the phosphoproteome also yielded new functional information on proteins controlled by redox regulation (thioredoxin target proteins) and proteins of the chloroplast 70S ribosome, the centriole, and especially the flagella, for which 32 phosphoproteins were identified. The high yield of phosphoproteins of the latter correlates well with the presence of several flagellar kinases and indicates that phosphorylation/dephosphorylation represents one of the key regulatory mechanisms of eukaryotic cilia. Our data also provide new insights into certain cilium-related mammalian diseases. PMID:16524901

Wagner, Volker; Gessner, Gunther; Heiland, Ines; Kaminski, Marc; Hawat, Susan; Scheffler, Kai; Mittag, Maria

2006-03-01

155

Hippocampal phosphoproteomics of F344 rats exposed to 1-bromopropane.  

PubMed

1-Bromopropane (1-BP) is neurotoxic in both experimental animals and human. To identify phosphorylated modification on the unrecognized post-translational modifications of proteins and investigate their role in 1-BP-induced neurotoxicity, changes in hippocampal phosphoprotein expression levels were analyzed quantitatively in male F344 rats exposed to 1-BP inhalation at 0, 400, or 1000 ppm for 8 h/day for 1 or 4 weeks. Hippocampal protein extracts were analyzed qualitatively and quantitatively by Pro-Q Diamond gel staining and SYPRO Ruby staining coupled with two-dimensional difference in gel electrophoresis (2D-DIGE), respectively, as well as by matrix-assisted laser-desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) to identify phosphoproteins. Changes in selected proteins were further confirmed by Manganese II (Mn(2+))-Phos-tag SDS-polyacrylamide gel electrophoresis (SDS-PAGE). Bax and cytochrome c protein levels were determined by western blotting. Pro-Q Diamond gel staining combined with 2D-DIGE identified 26 phosphoprotein spots (p<0.05), and MALDI-TOF/MS identified 18 up-regulated proteins and 8 down-regulated proteins. These proteins are involved in the biological process of response to stimuli, metabolic processes, and apoptosis signaling. Changes in the expression of phosphorylated 14-3-3 ? were further confirmed by Mn(2+)-Phos-tag SDS-PAGE. Western blotting showed overexpression of Bax protein in the mitochondria with down-regulation in the cytoplasm, whereas cytochrome c expression was high in the cytoplasm but low in the mitochondria after 1-BP exposure. Our results suggest that the pathogenesis of 1-BP-induced hippocampal damage involves inhibition of antiapoptosis process. Phosphoproteins identified in this study can potentially serve as biomarkers for 1-BP-induced neurotoxicity. PMID:25448045

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

2015-01-15

156

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

157

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.

158

[Acute non-opacified dissection of the ascending thoracic aorta--significance of retrograde dissection and re-dissection].  

PubMed

Thirteen cases of acute aortic dissection with non-opacified false lumen of the ascending aorta were examined by CT and other imaging modalities. On the basis of the initial CT findings, these cases were classified into two types; one was pure non-opacified dissection not associated with opacified false lumen (Type N, n = 7), the other was non-opacified dissection of the ascending aorta associated with opacified false lumen of the following aorta (Type N+O, n = 6). On examining the relation between the entry site and the false lumen in Type N+O, the dissection of the ascending aorta was considered to be retrograde. Retrograde dissection seemed to be an important factor in the development of the non-opacified dissection of the ascending aorta. During the follow-up period, re-dissection in the ascending aorta occurred in four of the 13 cases (Type N = 3, Type N+O = 1). The re-dissection occurred within the first four weeks in all of them, and the diagnosis of re-dissection was possible at its early stage. In one case, ulcerlike projection (ULP) was detected by aortography. In another case, ULP was identified by cine-MR imaging. Contrast CT also revealed enlargement and small opacification of the false lumen. In two other cases, similar CT findings were observed. Three of the four patients recovered by surgical treatment. One died the day after the diagnosis of re-dissection. Early diagnosis and earliest possible surgical intervention for re-dissection were considered necessary to save the patients with re-dissected false lumen in the ascending aorta. Close observations with several imaging modalities, mainly CT examination, should be paid in the patients with non-opacified dissection of the ascending aorta for at least four weeks after the onset of dissection. PMID:1508658

Matsuoka, Y

1992-07-25

159

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

160

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

PubMed Central

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

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

2014-01-01

161

Phosphoproteomic Analysis of the Highly-Metastatic Hepatocellular Carcinoma Cell Line, MHCC97-H.  

PubMed

Invasion and metastasis of hepatocellular carcinoma (HCC) is a major cause for lethal liver cancer. Signaling pathways associated with cancer progression are frequently reconfigured by aberrant phosphorylation of key proteins. To capture the key phosphorylation events in HCC metastasis, we established a methodology by an off-line high-pH HPLC separation strategy combined with multi-step IMAC and LC-MS/MS to study the phosphoproteome of a metastatic HCC cell line, MHCC97-H (high metastasis). In total, 6593 phosphopeptides with 6420 phosphorylation sites (p-sites) of 2930 phosphoproteins were identified. Statistical analysis of gene ontology (GO) categories for the identified phosphoproteins showed that several of the biological processes, such as transcriptional regulation, mRNA processing and RNA splicing, were over-represented. Further analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations demonstrated that phosphoproteins in multiple pathways, such as spliceosome, the insulin signaling pathway and the cell cycle, were significantly enriched. In particular, we compared our dataset with a previously published phosphoproteome in a normal liver sample, and the results revealed that a number of proteins in the spliceosome pathway, such as U2 small nuclear RNA Auxiliary Factor 2 (U2AF2), Eukaryotic Initiation Factor 4A-III (EIF4A3), Cell Division Cycle 5-Like (CDC5L) and Survival Motor Neuron Domain Containing 1 (SMNDC1), were exclusively identified as phosphoproteins only in the MHCC97-H cell line. These results indicated that the phosphorylation of spliceosome proteins may participate in the metastasis of HCC by regulating mRNA processing and RNA splicing. PMID:25690035

Tian, Miaomiao; Cheng, Han; Wang, Zhiqiang; Su, Na; Liu, Zexian; Sun, Changqing; Zhen, Bei; Hong, Xuechuan; Xue, Yu; Xu, Ping

2015-01-01

162

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

PubMed

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

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

2015-01-01

163

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

PubMed Central

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

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

2014-01-01

164

Phosphoproteomic Analysis of the Highly-Metastatic Hepatocellular Carcinoma Cell Line, MHCC97-H  

PubMed Central

Invasion and metastasis of hepatocellular carcinoma (HCC) is a major cause for lethal liver cancer. Signaling pathways associated with cancer progression are frequently reconfigured by aberrant phosphorylation of key proteins. To capture the key phosphorylation events in HCC metastasis, we established a methodology by an off-line high-pH HPLC separation strategy combined with multi-step IMAC and LC–MS/MS to study the phosphoproteome of a metastatic HCC cell line, MHCC97-H (high metastasis). In total, 6593 phosphopeptides with 6420 phosphorylation sites (p-sites) of 2930 phosphoproteins were identified. Statistical analysis of gene ontology (GO) categories for the identified phosphoproteins showed that several of the biological processes, such as transcriptional regulation, mRNA processing and RNA splicing, were over-represented. Further analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations demonstrated that phosphoproteins in multiple pathways, such as spliceosome, the insulin signaling pathway and the cell cycle, were significantly enriched. In particular, we compared our dataset with a previously published phosphoproteome in a normal liver sample, and the results revealed that a number of proteins in the spliceosome pathway, such as U2 small nuclear RNA Auxiliary Factor 2 (U2AF2), Eukaryotic Initiation Factor 4A-III (EIF4A3), Cell Division Cycle 5-Like (CDC5L) and Survival Motor Neuron Domain Containing 1 (SMNDC1), were exclusively identified as phosphoproteins only in the MHCC97-H cell line. These results indicated that the phosphorylation of spliceosome proteins may participate in the metastasis of HCC by regulating mRNA processing and RNA splicing. PMID:25690035

Tian, Miaomiao; Cheng, Han; Wang, Zhiqiang; Su, Na; Liu, Zexian; Sun, Changqing; Zhen, Bei; Hong, Xuechuan; Xue, Yu; Xu, Ping

2015-01-01

165

Phosphoproteomic analysis reveals an intrinsic pathway for histone deacetylase 7 regulation that controls cytotoxic T lymphocyte function  

PubMed Central

The present study reports an unbiased analysis of cytotoxic T cell serine-threonine phosphoproteome using high resolution mass spectrometry. Approximately 2,000 phosphorylations were identified in CTLs of which approximately 450 were controlled by TCR signaling. A significantly overrepresented group of molecules identified were transcription activators, co-repressors and chromatin regulators. A focus on chromatin regulators revealed that CTLs have high expression of histone deacetylase HDAC7 but continually phosphorylate and export this transcriptional repressor from the nucleus. HDAC7 dephosphorylation results in its nuclear accumulation and suppressed expression of genes encoding key cytokines, cytokine receptors and adhesion molecules that determine CTL function. The screening of CTL phosphoproteome thus reveals intrinsic pathways of serine-threonine phosphorylation that target chromatin regulators and determine the CTL functional program. PMID:21399638

Navarro, Maria N.; Goebel, Jurgen; Feijoo-Carnero, Carmen; Morrice, Nick; Cantrell, Doreen A.

2011-01-01

166

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

PubMed

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

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

2014-05-01

167

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. PMID:24700621

He, Yikun

2014-01-01

168

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.

Mable Kinzie

169

Phosphoproteomic analysis reveals major default phosphorylation sites outside long intrinsically disordered regions of Arabidopsis plasma membrane proteins  

PubMed Central

Background Genome-wide statistics established that long intrinsically disordered regions (over 30 residues) are predicted in a large part of proteins in all eukaryotes, with a higher ratio in trans-membrane proteins. At functional level, such unstructured and flexible regions were suggested for years to favour phosphorylation events. In plants, despite increasing evidence of the regulation of transport and signalling processes by phosphorylation events, only few data are available without specific information regarding plasma membrane proteins, especially at proteome scale. Results Using a dedicated phosphoproteomic workflow, 75 novel and unambiguous phosphorylation sites were identified in Arabidopsis plasma membrane. Bioinformatics analysis showed that this new dataset concerned mostly integral proteins involved in key functions of the plasma membrane (such as transport and signal transduction, including protein phosphorylation). It thus expanded by 15% the directory of phosphosites previously characterized in signalling and transport proteins. Unexpectedly, 66% of phosphorylation sites were predicted to be located outside long intrinsically disordered regions. This result was further corroborated by analysis of publicly available data for the plasma membrane. Conclusions The new phosphoproteomics data presented here, with published datasets and functional annotation, suggest a previously unexpected topology of phosphorylation in the plant plasma membrane proteins. The significance of these new insights into the so far overlooked properties of the plant plasma membrane phosphoproteome and the long disordered regions is discussed. PMID:23110452

2012-01-01

170

Genetic dissection of neurodegeneration and CNS inflammation.  

PubMed

Inflammation and neurodegeneration characterize multiple sclerosis, as well as many other diseases of the central nervous system (CNS). The understanding of the molecular pathways that regulate these processes is of fundamental importance for the development of new therapies. Nerve lesions paradigms in animals can serve as important tools to dissect central features of human CNS disease and by using these models certain key regulators have also been identified. However, our knowledge of how aspects of neurodegeneration and CNS inflammation are regulated on a genomic level is very limited. Such knowledge may help to unravel disease mechanisms. By using a standardized nerve trauma model, ventral root avulsion (VRA), in a series of inbred rat strains we here demonstrate a potent genetic regulation of the degree of neuron death and glial activation. Genome wide mapping of these phenotypes in experimental rat strain crosses identifies several quantitative trait loci (QTLs) controlling nerve lesion-induced nerve cell death, local T cell accumulation and expression of MHC class II on microglia. This approach may lead to the identification of evolutionary conserved genetic polymorphisms in key controlling genes, which can serve as prime candidates for association studies in several human CNS diseases. PMID:15894332

Olsson, Tomas; Piehl, Fredrik; Swanberg, Maria; Lidman, Olle

2005-06-15

171

Elucidating the CXCL12/CXCR4 Signaling Network in Chronic Lymphocytic Leukemia through Phosphoproteomics Analysis  

PubMed Central

Background Chronic Lymphocytic Leukemia (CLL) pathogenesis has been linked to the prolonged survival and/or apoptotic resistance of leukemic B cells in vivo, and is thought to be due to enhanced survival signaling responses to environmental factors that protect CLL cells from spontaneous and chemotherapy-induced death. Although normally associated with cell migration, the chemokine, CXCL12, is one of the factors known to support the survival of CLL cells. Thus, the signaling pathways activated by CXCL12 and its receptor, CXCR4, were investigated as components of these pathways and may represent targets that if inhibited, could render resistant CLL cells more susceptible to chemotherapy. Methodology/Principal Findings To determine the downstream signaling targets that contribute to the survival effects of CXCL12 in CLL, we took a phosphoproteomics approach to identify and compare phosphopeptides in unstimulated and CXCL12-stimulated primary CLL cells. While some of the survival pathways activated by CXCL12 in CLL are known, including Akt and ERK1/2, this approach enabled the identification of additional signaling targets and novel phosphoproteins that could have implications in CLL disease and therapy. In addition to the phosphoproteomics results, we provide evidence from western blot validation that the tumor suppressor, programmed cell death factor 4 (PDCD4), is a previously unidentified phosphorylation target of CXCL12 signaling in all CLL cells probed. Additionally, heat shock protein 27 (HSP27), which mediates anti-apoptotic signaling and has previously been linked to chemotherapeutic resistance, was detected in a subset (?25%) of CLL patients cells examined. Conclusions/Significance Since PDCD4 and HSP27 have previously been associated with cancer and regulation of cell growth and apoptosis, these proteins may have novel implications in CLL cell survival and represent potential therapeutic targets. PDCD4 also represents a previously unknown signaling target of chemokine receptors; therefore, these observations increase our understanding of alternative pathways to migration that may be activated or inhibited by chemokines in the context of cancer cell survival. PMID:20661426

O'Hayre, Morgan; Salanga, Catherina L.; Kipps, Thomas J.; Messmer, Davorka; Dorrestein, Pieter C.; Handel, Tracy M.

2010-01-01

172

Aortic dissection in the elderly.  

PubMed

To analyze the characteristics of aortic dissection in the elderly, we reviewed 168 cases from January 1999 to September 2005 in a medical center in Taiwan. Fifty-six cases were suitable for enrollment in our study. Of these, 44 (79%) were male and 12 (21%) were female; ages ranged from 29 to 92 years, with a mean of 61 +/- 11.75 years. We defined elderly as age >/= 65 years. There was no obvious discrepancy between age and types of aortic dissections involved (p = 0.726). The elderly had the lower mean systolic blood pressure (166.4 mm Hg) upon arrival at the Emergency Department (p = 0.002). Presentation to the Emergency Department with chest pain or chest tightness was more commonly seen in the elderly (66.7%) (p = 0.042). The mean hospital stay was 12.6 +/- 0.5 days, and it was longer in the elderly group (12.96 days) (p = 0.009). Otherwise, the mortality rate was 6.7% +/- 3.6%. We found a lower mortality rate in the elderly than in the younger group (4% vs. 9%, respectively; p = 0.008). PMID:17976820

Su, Yu-Jang; Chang, Wen-Han; Chang, Kuo-Song; Tsai, Cheng-Ho

2008-08-01

173

Keeping Dissection Alive for Medical Students  

ERIC Educational Resources Information Center

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

Chambers, James; Emlyn-Jones, Daniel

2009-01-01

174

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

175

Aortic Dissection Type A in Alpine Skiers  

PubMed Central

Patients and Methods. 140 patients with aortic dissection type A were admitted for cardiac surgery. Seventy-seven patients experienced their dissection in the winter season (from November to April). We analyzed cases of ascending aortic dissection associated with alpine skiing. Results. In 17 patients we found skiing-related aortic dissections. Skiers were taller (180 (172–200)?cm versus 175 (157–191)?cm, P = 0.008) and heavier (90 (68–125)?kg versus 80 (45–110)?kg, P = 0.002) than nonskiers. An extension of aortic dissection into the aortic arch, the descending thoracic aorta, and the abdominal aorta was found in 91%, 74%, and 69%, respectively, with no significant difference between skiers and nonskiers. Skiers experienced RCA ostium dissection requiring CABG in 17.6% while this was true for 5% of nonskiers (P = 0.086). Hospital mortality of skiers was 6% versus 13% in nonskiers (P = 0.399). The skiers live at an altitude of 170 (0–853) m.a.s.l. and experience their dissection at 1602 (1185–3105; P < 0.001) m.a.s.l. In 82% symptom start was during recreational skiing without any trauma. Conclusion. Skiing associated aortic dissection type A is usually nontraumatic. The persons affected live at low altitudes and practice an outdoor sport at unusual high altitude at cold temperatures. Postoperative outcome is good. PMID:23971024

Schachner, Thomas; Fischler, Nikolaus; Dumfarth, Julia; Bonaros, Nikolaos; Krapf, Christoph; Schobersberger, Wolfgang; Grimm, Michael

2013-01-01

176

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.

177

[Dissection is still important when learning anatomy].  

PubMed

Dissection and prosection require a donation programme of cadavers for education and research. The importance of maintaining the donation programme and the significance of dissection as a teaching method when learning anatomic structures and obtaining surgical skills are evaluated. PMID:23697565

Knudsen, Britt Mejer; Søe, Niels H; Jensen, Nina Vendel; Langebæk, Rikke; Dahlin, Lars B

2013-05-20

178

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

179

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

180

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. 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.

2013-01-01

181

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. PMID:24392096

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

182

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

PubMed Central

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

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

2014-01-01

183

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

PubMed Central

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

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

2015-01-01

184

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

PubMed

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

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

2015-01-01

185

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

PubMed Central

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

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

2014-01-01

186

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

PubMed

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

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

2014-11-01

187

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

PubMed Central

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

2014-01-01

188

Dissecting Genetic Networks Underlying Complex Phenotypes: The Theoretical Framework  

PubMed Central

Great progress has been made in genetic dissection of quantitative trait variation during the past two decades, but many studies still reveal only a small fraction of quantitative trait loci (QTLs), and epistasis remains elusive. We integrate contemporary knowledge of signal transduction pathways with principles of quantitative and population genetics to characterize genetic networks underlying complex traits, using a model founded upon one-way functional dependency of downstream genes on upstream regulators (the principle of hierarchy) and mutual functional dependency among related genes (functional genetic units, FGU). Both simulated and real data suggest that complementary epistasis contributes greatly to quantitative trait variation, and obscures the phenotypic effects of many ‘downstream’ loci in pathways. The mathematical relationships between the main effects and epistatic effects of genes acting at different levels of signaling pathways were established using the quantitative and population genetic parameters. Both loss of function and “co-adapted” gene complexes formed by multiple alleles with differentiated functions (effects) are predicted to be frequent types of allelic diversity at loci that contribute to the genetic variation of complex traits in populations. Downstream FGUs appear to be more vulnerable to loss of function than their upstream regulators, but this vulnerability is apparently compensated by different FGUs of similar functions. Other predictions from the model may account for puzzling results regarding responses to selection, genotype by environment interaction, and the genetic basis of heterosis. PMID:21283795

Zhang, Fan; Zhai, Hu-Qu; Paterson, Andrew H.; Xu, Jian-Long; Gao, Yong-Ming; Zheng, Tian-Qing; Wu, Rong-Ling; Fu, Bin-Ying; Ali, Jauhar; Li, Zhi-Kang

2011-01-01

189

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. PMID:23304184

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

2012-01-01

190

Quantitative phosphoproteomics reveals a cluster of tyrosine kinases that mediates Src invasive activity in advanced colon carcinoma cells.  

E-print Network

/or activated in human colon carcinoma (CRC) and its increased activity has been associated with a poor clinical activity in advanced colon carcinoma cells. Cédric Leroy1 , Camille Fialin1 , Audrey Sirvent1 , Valérie-mail: Serge.Roche@crbm.cnrs.fr Running title: Src oncogenic signaling in colon carcinoma cells Abbreviations

Boyer, Edmond

191

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. PMID:24349301

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

2013-01-01

192

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

PubMed

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

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

2014-09-01

193

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

194

Postoperative adjuvant chemoradiotherapy in D2-dissected gastric cancer: is radiotherapy necessary after D2-dissection?  

PubMed

Studies from the Far East have demonstrated that D2-dissection is superior to D0/1-dissection. The effect of postoperative chemoradiotherapy (CRT) after D2-dissection has not been accepted due to the lack of D2-dissection in Western countries, as well as the potential harmful effect of radiotherapy. In the current NCCN guideline, adjuvant chemotherapy alone is recommended in D2-dissected patients. However, three recent prospective randomized controlled trials in South Korea and China (ARTIST, NCC and Multicenter IMRT Trials) demonstrated that adjuvant CRT can be safely administered to D2-dissected patients with notable benefits. To identify the role of radiotherapy (RT) in the D2-dissected postoperative setting, clinical research attempts should include (1) identification of high-risk patients for loco-regional recurrence who might benefit from CRT; (2) modification of RT target volume based on the findings that failure patterns should be different after D1- and D2-dissection; and (3) integration of new RT techniques to decrease treatment-related toxicity. The present paper is a review of recent studies addressing these fields. Well-designed prospective randomized studies are needed to clearly define the role of adjuvant CRT in D2-dissected gastric cancer, however, future clinical studies should also focus on answering these questions. PMID:25278687

Chang, Jee Suk; Koom, Woong Sub; Lee, Youngin; Yoon, Hong In; Lee, Hyung Sik

2014-09-28

195

Postoperative adjuvant chemoradiotherapy in D2-dissected gastric cancer: Is radiotherapy necessary after D2-dissection?  

PubMed Central

Studies from the Far East have demonstrated that D2-dissection is superior to D0/1-dissection. The effect of postoperative chemoradiotherapy (CRT) after D2-dissection has not been accepted due to the lack of D2-dissection in Western countries, as well as the potential harmful effect of radiotherapy. In the current NCCN guideline, adjuvant chemotherapy alone is recommended in D2-dissected patients. However, three recent prospective randomized controlled trials in South Korea and China (ARTIST, NCC and Multicenter IMRT Trials) demonstrated that adjuvant CRT can be safely administered to D2-dissected patients with notable benefits. To identify the role of radiotherapy (RT) in the D2-dissected postoperative setting, clinical research attempts should include (1) identification of high-risk patients for loco-regional recurrence who might benefit from CRT; (2) modification of RT target volume based on the findings that failure patterns should be different after D1- and D2-dissection; and (3) integration of new RT techniques to decrease treatment-related toxicity. The present paper is a review of recent studies addressing these fields. Well-designed prospective randomized studies are needed to clearly define the role of adjuvant CRT in D2-dissected gastric cancer, however, future clinical studies should also focus on answering these questions. PMID:25278687

Chang, Jee Suk; Koom, Woong Sub; Lee, Youngin; Yoon, Hong In; Lee, Hyung Sik

2014-01-01

196

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. PMID:19351177

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

197

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. PMID:21637843

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

198

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. PMID:24628833

2014-01-01

199

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

200

Spontaneous coronary dissection in polycystic kidney disease.  

PubMed

We report a case of a 46-year-old woman with hypertension and autosomal dominant polycystic kidney disease who presented with chest pain and was found to have spontaneous coronary artery dissection (SCAD) on diagnostic catheterization. We review the pathogenesis, management and prognosis of SCAD. We conclude that in patients with polycystic kidney disease who present with angina pectoris and positive cardiac biomarkers, coronary artery dissection should be considered. PMID:24303518

Afari, Maxwell E; Quddus, Abdullah; Bhattarai, Manoj; John, Amrita R; Broderick, Ryan J

2013-12-01

201

Managing Dissections of the Thoracic Aorta  

PubMed Central

Thoracic aortic dissection is associated with substantial morbidity and mortality, and it requires timely and accurate diagnosis and treatment. Long-term antihypertensive therapy remains critical for the treatment of this disease. Surgical intervention, although still a formidable undertaking, has evolved to better address both acute and chronic dissection, and the results have improved. Basic and clinical research, as well as technological advances, have increased our understanding of this challenging disease state. PMID:18481490

WONG, DANIEL R.; LEMAIRE, SCOTT A.; COSELLI, JOSEPH S.

2010-01-01

202

Peripartum presentation of an acute aortic dissection.  

PubMed

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

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

2005-04-01

203

In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution.  

PubMed

Recent phosphoproteome analyses using mass spectrometry-based technologies have provided new insights into the extensive presence of protein phosphorylation in various species and have raised the interesting question of how this protein modification was gained evolutionarily on such a large scale. We investigated this issue by using human and mouse phosphoproteome data. We initially found that phosphoproteins followed a power-law distribution with regard to their number of phosphosites: most of the proteins included only a few phosphosites, but some included dozens of phosphosites. The power-law distribution, unlike more commonly observed distributions such as normal and log-normal distributions, is considered by the field of complex systems science to be produced by a specific rich-get-richer process called preferential attachment growth. Therefore, we explored the factors that may have promoted the rich-get-richer process during phosphosite evolution. We conducted a bioinformatics analysis to evaluate the relationship of amino acid sequences of phosphoproteins with the positions of phosphosites and found an overconcentration of phosphosites in specific regions of protein surfaces and implications that in many phosphoproteins these clusters of phosphosites are activated simultaneously. Multiple phosphosites concentrated in limited spaces on phosphoprotein surfaces may therefore function biologically as cooperative modules that are resistant to selective pressures during phosphoprotein evolution. We therefore proposed a hypothetical model by which the modularization of multiple phosphosites has been resistant to natural selection and has driven the rich-get-richer process of the evolutionary growth of phosphosite numbers. PMID:19136663

Yachie, Nozomu; Saito, Rintaro; Sugahara, Junichi; Tomita, Masaru; Ishihama, Yasushi

2009-05-01

204

In vivo Phosphoproteome of Human Skeletal Muscle Revealed by Phosphopeptide Enrichment and HPLC-ESI-MS/MS  

PubMed Central

Protein phosphorylation plays an essential role in signal transduction pathways that regulate substrate and energy metabolism, contractile function, and muscle mass in human skeletal muscle. Abnormal phosphorylation of signaling enzymes has been identified in insulin resistant muscle using phosphoepitope-specific antibodies, but its role in other skeletal muscle disorders remains largely unknown. This may be in part due to insufficient knowledge of relevant targets. Here, we therefore present the first large-scale in vivo phosphoproteomic study of human skeletal muscle from 3 lean, healthy volunteers. Trypsin digestion of 3-5 mg human skeletal muscle protein was followed by phosphopeptide enrichment using SCX and TiO2. The resulting phosphopeptides were analyzed by HPLC-ESI-MS/MS. Using this unbiased approach, we identified 306 distinct in vivo phosphorylation sites in 127 proteins, including 240 phosphoserines, 53 phosphothreonines and 13 phosphotyrosines in at least 2 out of 3 subjects. In addition, 61 ambiguous phosphorylation sites were identified in at least 2 out of 3 subjects. The majority of phosphoproteins detected are involved in sarcomeric function, excitation-contraction coupling (the Ca2+-cycle), glycolysis and glycogen metabolism. Of particular interest, we identified multiple novel phosphorylation sites on several sarcomeric Z-disc proteins known to be involved in signaling and muscle disorders. These results provide numerous new targets for the investigation of human skeletal muscle phosphoproteins in health and disease and demonstrate feasibility of phosphoproteomics research of human skeletal muscle in vivo. PMID:19764811

Højlund, Kurt; Bowen, Benjamin P.; Hwang, Hyonson; Flynn, Charles R.; Madireddy, Lohith; Thangiah, Geetha; Langlais, Paul; Meyer, Christian; Mandarino, Lawrence J.; Yi, Zhengping

2009-01-01

205

The Effect of Animal Dissections on Student Acquisition of Knowledge of and Attitudes toward the Animals Dissected.  

ERIC Educational Resources Information Center

A conflict exists over the use of animals in the classroom. One aspect of this use involved the dissection of animals. Animal protection advocates report that dissections constitute abuse of the animals dissected. The advocates state that what is learned by dissection could be more effectively learned by other means. Some science educators state…

McCollum, Terry L.

206

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

207

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

208

Dissection of QTLs for Yield Traits on the Short Arm of Rice Chromosome 6  

Microsoft Academic Search

This study was undertaken to dissect quantitative trait loci (QTLs) controlling yield traits on the short arm of rice chromosome 6. A residual heterozygous line that carries a heterozygous segment extending from RM587 to RM19784 on the short arm of rice chromosome 6 was selected from an F7 population of the indica rice cross Zhenshan 97B\\/Milyang 46. An F2:3 population

Jing-hong DU; Ye-yang FAN; Ji-rong WU; Jie-yun ZHUANG

2008-01-01

209

[Pelvic lymph node dissection. Complication management].  

PubMed

Extended pelvic lymph node dissection allows exact lymph node staging and has the potential to improve prognosis. In addition to these advantages, there are some perioperative and postoperative complications. In case of transection of the obturator nerve, a microsurgical end-to-end anastomosis should be performed. The most frequent postoperative complication is (symptomatic) lymphocele which is predominantly diagnosed after extraperitoneal surgery. Meticulous lymph node dissection with clipping of lymphatic vessels, sparing the lateral wall of the external iliac artery from dissection, sufficient postoperative drainage, and application of low molecular weight heparin in the upper arm may reduce their incidence. Instillation of sclerosing agents and sufficient drainage are normally successful. If not, laparoscopic fenestration of lymphocele should be performed. Regular ultrasound examinations are necessary to diagnose and treat postoperative lymphocele in a timely manner. PMID:24705476

Weckermann, D

2014-07-01

210

Prevention of complications in neck dissection  

PubMed Central

Background The neck dissection has remained a pivotal aspect of head and neck cancer management for over a century. During this time its role has expanded from a purely therapeutic option into an elective setting, in part promoted by efforts to reduce its morbidity. Objectives This review will consider the potential complications of neck dissection and on the basis of the available evidence describe both their management and prevention. Conclusion Although the neck dissection continues to provide clinicians with a method of addressing cervical disease, its reliability and safety can only be assured if surgeons remain cognisant of the potential complications and aim to minimise such morbidity by appropriate management in the peri-operative period. PMID:19822010

Kerawala, Cyrus J; Heliotos, Manolis

2009-01-01

211

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

212

Lebensbedrohliche und letale Komplikationen der Neck dissection  

Microsoft Academic Search

Zusammenfassung  \\u000a \\u000a Hintergrund. Von 1990–1999 wurden 395 Neck dissections bei 357 Patienten durchgeführt: 195 links, davon 105 radikal, 200 rechts, davon\\u000a 107 radikal. In 4 Fällen traten lebensbedrohliche Komplikationen auf, woran 2 Patienten verstarben.\\u000a \\u000a \\u000a \\u000a \\u000a Kasuistik. Im 1. Fall kam es nach radikaler Neck dissection links mit Chylusfistel zu einem Chylothorax, der trotz Drainage und Thorakotomie\\u000a nicht beherrschbar war, sodass die 75-jährige

H. Eufinger; J. Lehmbrock

2001-01-01

213

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. PMID:24335353

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

2014-01-01

214

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

PubMed Central

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

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

2011-01-01

215

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 ... January 2015 What is familial TAAD? Familial thoracic aortic aneurysm and dissection (familial TAAD) involves problems with the ...

216

ForPeerReview Dissecting the Uncinate Fasciculus: Disorders,  

E-print Network

ForPeerReview Dissecting the Uncinate Fasciculus: Disorders, Controversies, and a Hypothesis: Uncinate Fasciculus Page 1 Dissecting the Uncinate Fasciculus: Disorders, Controversies, and a Hypothesis the Uncinate Fasciculus: Disorders, Controversies, and a Hypothesis 1. Introduction The uncinate fasciculus (UF

Olson, Ingrid

217

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

PubMed Central

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

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

2015-01-01

218

Global Distribution of Dissected Duricrust on Mars  

NASA Technical Reports Server (NTRS)

Evidence for dissected duricrust was identified in high resolution MOC images. Analysis of all available images was used to map the global distribution of this terrain. It is apparently restricted to two latitude bands: 30-60 deg. N and 30-60 deg. S.

Mustard, J. F.; Cooper, C. D.

2000-01-01

219

A COMPARATIVE PRIMATE ANATOMY Dissection Manual  

E-print Network

is used as a reference species against which we compared the anatomy of the non-human primates. It alsoA COMPARATIVE PRIMATE ANATOMY Dissection Manual Edited by: Rebecca Rogers Ackermann Version 1 Anatomy taught jointly by Professors J Cheverud, G Conroy, and J Phillips-Conroy, at Washington University

Ackermann, Rebecca Rogers

220

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

221

Dissecting the pressure field in tidal flow  

E-print Network

Dissecting the pressure field in tidal flow past a headland: When is form drag "real?" Sally Warner of oscillating flow H L HL velocity form drag power average power floodslack work done on system #12;0 0 0 0 90 180 270 360 90 180 270 360 0 degrees Drag of oscillating flow H L HL velocity form drag power average

Warner, Sally

222

Dissecting the pressure field in tidal flow  

E-print Network

amplitude [N x 107 ] phase relative to the velocity [deg] power [W x107 ] 1 2 3 4 tidal excursion parameterDissecting the pressure field in tidal flow past a headland: When is form drag "real?" Sally Warner waves eddies H L LHH H L L LH #12;Numerical model Gaussian-shaped headland Barotropic tidal velocity D L

Warner, Sally

223

Genetic dissection of neurodegeneration and CNS inflammation  

Microsoft Academic Search

Inflammation and neurodegeneration characterize multiple sclerosis, as well as many other diseases of the central nervous system (CNS). The understanding of the molecular pathways that regulate these processes is of fundamental importance for the development of new therapies. Nerve lesions paradigms in animals can serve as important tools to dissect central features of human CNS disease and by using these

Tomas Olsson; Fredrik Piehl; Maria Swanberg; Olle Lidman

2005-01-01

224

Dissecting spider embryos for light microscopy.  

PubMed

INTRODUCTIONThe spider Cupiennius salei, commonly known as the American wandering spider, is a particularly useful laboratory model for embryological studies because of the availability of tools to study and manipulate its embryonic development. Cupiennius is used to study axis formation, segmentation, appendage development, neurogenesis, and silk production. These studies contribute to our understanding of the evolution of these processes, but they also help us to understand the origin and diversification of evolutionary novelties. Comparisons between spiders and insects can show the degree of conservation and divergence of developmental mechanisms during arthropod evolution. Any embryological feature conserved between spiders and insects is likely to represent an ancestral feature for arthropods. Comparative molecular embryological work in insects and spiders should eventually allow us to define a molecular archetype for the phylum Arthropoda. This in itself will be a necessary cornerstone for comparing the different metazoan phyla, including chordates. Spider embryos can be studied as whole mounts under the dissection microscope. Alternatively, the embryos can be dissected and observed under the compound microscope. Preparing and dissecting spider embryos for compound microscopy is difficult due to the high amount of yolk, which makes the embryos very fragile. The following protocol describes how to make the necessary tools, then use them to obtain good preparations. Not all embryonic stages can be dissected and prepared; very young stages can only be examined as whole mounts. PMID:21356703

Prpic, Nikola-Michael; Schoppmeier, Michael; Damen, Wim G M

2008-01-01

225

Intraoperative aortic dissection in pediatric heart surgery.  

PubMed

Intraoperative aortic dissection occurred in a 3-year-old-boy undergoing repair of an atrial septal defect. Transesophageal echocardiography was useful for the diagnosis, and conservative medical treatment under close observation was feasible in this case which involved a limited intimal tear. PMID:16714685

Hibino, Narutoshi; Harada, Yorikazu; Hiramatsu, Takeshi; Yasukochi, Satoshi; Satomi, Gengi

2006-06-01

226

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

227

Endoscopic microsurgical dissection of the esophagus  

Microsoft Academic Search

Blunt dissection of the esophagus is considered the least invasive technique in the treatment of either benign or malignant diseases of the esophagus. Its disadvantage is that it has to be carried out blindly. The results may be uncontrollable hemorrhage, unrecognized injuries to the trachea, and damage to the recurrent laryngeal nerve. In order to reduce the degree of invasivness

K. Kipfmüller; M. Naruhn; A. Melzer; S. Kessler; G. Bueß

1989-01-01

228

Hand Related Disorders Following Axillary Dissection for Breast Cancer  

Microsoft Academic Search

Lymphedema is the most common complication of an axillary dissection with lymph node examination. A retrospective chart review and a detailed questionnaire were used to evaluate the prevalence of hand disorders in patients following breast surgery with an axillary dissection. The questionnaire was sent to 250 patients who had undergone an axillary dissection for breast can- cer. 143 patients returned

DAVID J. BOZENTKA; PEDRO K. BEREDJIKLIAN; PETER S. H. CHAN; STEVEN SCHMIDT; GORDON P. BUZBY; FIONA BORA

2001-01-01

229

A Novel Approach to the Dissection of the Human Knee  

NSDL National Science Digital Library

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

Michael Schumaker (Youngstown Orthopedics)

2009-02-01

230

Detection of basilar artery dissection by ultrasound.  

PubMed

We report a case of a 45-year-old woman with unusual headache 1 week before admission. After cerebrovascular ultrasound, a basilar artery dissection was supposed despite the normal neurologic, cerebrospinal fluid, and computed tomography findings. On a follow-up color-coded duplex sonography (1 month after the onset), reperfusion was detected in the vertebral and basilar arteries, but residual high-grade stenosis of the basilar artery was also present. PMID:25817628

Vassileva, Evguenia; Getsov, Plamen; Vavrek, Evgenii; Daskalov, Marin

2015-05-01

231

Hybrid Strategy for Residual Arch and Thoracic Aortic Dissection following Acute Type A Aortic Dissection Repair  

PubMed Central

Progressive dilatation of the false lumen in the arch and descending aorta has been encountered in one-third of survivors as a late sequelae following repair of ascending aortic dissection. Conventional treatment for the same requiring cardiopulmonary bypass and deep hypothermic circulatory arrest is associated with high morbidity and mortality especially in the elderly cohort of patients. Herein we report a case of symptomatic progressive aneurysmal dilatation of residual arch and descending thoracic aortic dissection following repair of type A aortic dissection, successfully treated by total arch debranching and ascending aortic prosthesis to bicarotid and left subclavian bypass followed by staged retrograde aortic stent-graft deployment. This case report with relevant review of the literature highlights this clinical entity and the present evidence on its appropriate management strategies. Close surveillance is mandatory following surgical repair of type A aortic dissection and hybrid endovascular procedures seem to be the most dependable modality for salvage of patients detected to have progression of residual arch dissection. PMID:24716088

Agrawal, Vivek; Parameshwarappa, Shashidhar Kallappa; Savlania, Ajay; Kumar, Santhosh; Madathipat, Unnikrishnan

2014-01-01

232

Future directions of duodenal endoscopic submucosal dissection  

PubMed Central

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

Matsumoto, Satohiro; Miyatani, Hiroyuki; Yoshida, Yukio

2015-01-01

233

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. PMID:25031787

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

2014-01-01

234

Evaluation of Quantitative Performance of Sequential Immobilized Metal Affinity Chromatographic Enrichment for Phosphopeptides  

PubMed Central

We evaluated a sequential elution protocol from immobilized metal affinity chromatography (SIMAC) employing gallium-based immobilized metal affinity chromatography (IMAC) in conjunction with titanium-dioxide-based metal oxide affinity chromatography (MOAC). The quantitative performance of this SIMAC enrichment approach, assessed in terms of repeatability, dynamic range, and linearity, was evaluated using a mixture composed of tryptic peptides from caseins, bovine serum albumin, and phosphopeptide standards. While our data demonstrate the overall consistent performance of the SIMAC approach under various loading conditions, the results also revealed that the method had limited repeatability and linearity for most phosphopeptides tested, and different phosphopeptides were found to have different linear ranges. These data suggest that, unless additional strategies are used, SIMAC should be regarded as a semi-quantitative method when used in large-scale phosphoproteomics studies in complex backgrounds. PMID:24096195

Sun, Zeyu; Hamilton, Karyn L.; Reardon, Kenneth F.

2014-01-01

235

[Selective neck dissection in head and neck cancer].  

PubMed

While (modified) radical neck dissection was seen formerly as an essential measure for securing local tumor control and improvement of the prognosis for head and neck cancer patients, this procedure is nowadays often replaced by selective neck dissection. Selective neck dissection is associated with a comparably low morbidity and acceptable functional results without having a negative impact on the prognosis of the patients. As staging procedure, neck dissection is currently the gold standard, so that selective neck dissection is an approved part of the therapy of the clinical N0 neck and is recommended as salvage therapy of the neck after radiochemotherapy. There are also aspects supporting the performance of selective neck dis-section in selected patients with N + neck. PMID:23996554

Teymoortash, A; Werner, J A

2013-09-01

236

Large-Scale Phosphoproteome of Human Whole Saliva Using Disulphide-Thiol-Interchange Covalent Chromatography and Mass Spectrometry  

PubMed Central

Thus far only a handful of phosphoproteins with important biological functions have been identified and characterized in oral fluids and these include some of the abundant protein constituents of saliva. Whole saliva (WS) samples were trypsin digested followed by chemical derivatization using dithiothreitol (DTT) of the phospho-serine/threonine containing peptides. The DTT-phosphopeptides were enriched by covalent disulphide-thiol-interchange chromatography and analysis by nano-flow LC-ESI-MS/MS. The specificity of DTT chemical derivatization was evaluated separately under different base-catalyzed conditions with NaOH and Ba(OH)2, blocking cysteine residues by iodoacetamide and enzymatic O-deglycosylation prior to DTT reaction. Further analysis of WS samples which were subjected to either of these conditions provided supporting evidence for phosphoprotein identifications. The combined chemical strategies and mass spectrometric analyses identified 65 phosphoproteins in WS of which 28 were based on two or more peptide identification criteria with high confidence, and 37 were based on a single phosphopeptide identification. Most of the identified proteins, ~80%, were hitherto unknown phosphoprotein components. This study represents the first large-scale documentation of phosphoproteins of WS. The origins and identity of WS phosphoproteome suggest significant implications for both basic science and the development of novel biomarkers/diagnostic tools for both systemic and oral disease states. PMID:20659418

Salih, Erdjan; Siqueira, Walter L.; Helmerhorst, Eva J.; Oppenheim, Frank G.

2010-01-01

237

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

PubMed Central

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

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

2015-01-01

238

Proteomic and Phospho-Proteomic Profile of Human Platelets in Basal, Resting State: Insights into Integrin Signaling  

PubMed Central

During atherogenesis and vascular inflammation quiescent platelets are activated to increase the surface expression and ligand affinity of the integrin ?IIb?3 via inside-out signaling. Diverse signals such as thrombin, ADP and epinephrine transduce signals through their respective GPCRs to activate protein kinases that ultimately lead to the phosphorylation of the cytoplasmic tail of the integrin ?IIb?3 and augment its function. The signaling pathways that transmit signals from the GPCR to the cytosolic domain of the integrin are not well defined. In an effort to better understand these pathways, we employed a combination of proteomic profiling and computational analyses of isolated human platelets. We analyzed ten independent human samples and identified a total of 1507 unique proteins in platelets. This is the most comprehensive platelet proteome assembled to date and includes 190 membrane-associated and 262 phosphorylated proteins, which were identified via independent proteomic and phospho-proteomic profiling. We used this proteomic dataset to create a platelet protein-protein interaction (PPI) network and applied novel contextual information about the phosphorylation step to introduce limited directionality in the PPI graph. This newly developed contextual PPI network computationally recapitulated an integrin signaling pathway. Most importantly, our approach not only provided insights into the mechanism of integrin ?IIb?3 activation in resting platelets but also provides an improved model for analysis and discovery of PPI dynamics and signaling pathways in the future. PMID:19859549

Maiguel, Dony; Faridi, Mohd Hafeez; Barth, Constantinos J.; Salem, Saeed M.; Singhal, Mudita; Stoub, Darren; Krastins, Bryan; Ogihara, Mitsunori; Zaki, Mohammed J.; Gupta, Vineet

2009-01-01

239

Vertebral and carotid artery dissection following chiropractic cervical manipulation  

Microsoft Academic Search

A 50-year-old woman presented a sudden left occipital headache and a posterior circulation stroke after cervical manipulation\\u000a for neck pain. Magnetic resonance imaging documented a left intracranial vertebral artery occlusive dissection associated\\u000a with an ipsilateral internal carotid artery dissection with vessel stenosis in its prepetrous tract. This is the first reported\\u000a case showing an associate vertebral and carotid artery dissection

Giuliano Parenti; Giovanni Orlandi; Mariacristina Bianchi; Maria Renna; Antonio Martini; Luigi Murri

1999-01-01

240

Multiple hereditary exostoses and stroke due to vertebral artery dissection.  

PubMed Central

Vascular complications related to multiple hereditary exostoses are uncommon. We present a 39-year-old male patient with multiple exostoses in the upper and lower limbs with an associated positive familial history of such lesions. He experienced a sudden onset of left-side ataxia and hypoesthesia secondary to a left lateral medullary infarction, which was due to a stenotic-pattern vertebral artery dissection (V1-V4). This complication is very rare as a differential diagnosis in the vertebro-basilar dissection spectrum, and a nonspecific relation has been found. Abbreviations MHE Multiple hereditary exostoses AT angiotomography VAD vertebral artery dissection CAD cervical artery dissection OI osteogenesis imperfecta PMID:25825632

Arauz, Antonio; Hernández-Curiel, Bernardo; Colin-Luna, Jonathan; Dávila-Ortiz de Montellano, David J.; Barboza, Miguel A.

2015-01-01

241

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.

242

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. PMID:24058442

von Schönfels, 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; Röcken, Christoph; Rimbach, Gerald; Becker, Thomas

2013-01-01

243

Harnessing Natural Sequence Variation to Dissect Posttranscriptional Regulatory Networks in Yeast  

PubMed Central

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

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

2014-01-01

244

Spontaneous coronary artery dissection-A review.  

PubMed

Spontaneous coronary artery dissection (SCAD) is an infrequent and often missed diagnosis among patients presenting with acute coronary syndrome (ACS). Unfortunately, SCAD can result in significant morbidities such as myocardial ischemia and infarction, ventricular arrhythmias and sudden cardiac death. Lack of angiographic recognition from clinicians is a major factor of under-diagnosis. With the advent of new imaging modalities, particularly with intracoronary imaging, there has been improved diagnosis of SCAD. The aim of this paper is to review the epidemiology, etiology, presentation, diagnosis and management of SCAD. PMID:25774346

Yip, Amelia; Saw, Jacqueline

2015-02-01

245

Spontaneous coronary artery dissection—A review  

PubMed Central

Spontaneous coronary artery dissection (SCAD) is an infrequent and often missed diagnosis among patients presenting with acute coronary syndrome (ACS). Unfortunately, SCAD can result in significant morbidities such as myocardial ischemia and infarction, ventricular arrhythmias and sudden cardiac death. Lack of angiographic recognition from clinicians is a major factor of under-diagnosis. With the advent of new imaging modalities, particularly with intracoronary imaging, there has been improved diagnosis of SCAD. The aim of this paper is to review the epidemiology, etiology, presentation, diagnosis and management of SCAD.

Yip, Amelia

2015-01-01

246

Genetic dissection of agronomic traits in Capsicum baccatum var. pendulum.  

PubMed

Genetic mapping is very useful for dissecting complex agronomic traits. Genetic mapping allows for identification of quantitative trait loci (QTL), provide knowledge on a gene position and its adjacent region, and enable prediction of evolutionary mechanisms, in addition to contributing to synteny studies. The aim of this study was to predict genetic values associated with different agronomic traits evaluated in an F2 population of Capsicum baccatum var. pendulum. Previously, a reference genetic map for C. baccatum was constructed, which included 183 markers (42 microsatellite, 85 inter-simple sequence repeat, and 56 random amplification of polymorphic DNA) arranged in 16 linkage groups. The map was used to identify QTL associated with 11 agronomic traits, including plant height, crown diameter, number of days to flowering, days to fruiting, number of fruits per plant, average fruit weight, fruit length, fruit diameter, fruit pulp thickness, soluble solids, and fruit dry weight. QTL mapping was performed by standard interval mapping. The number of small QTL effects ranged from 3-11, with a total of 61 QTL detected in 9 linkage groups. This is the first report involving QTL analysis for C. baccatum species. PMID:25867359

Moulin, M M; Rodrigues, R; Bento, C S; Gonçalves, L S A; Santos, J O; Sudré, C P; Viana, A P

2015-01-01

247

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

248

[Common carotid artery dissection propagated from acute aortic dissection: a case successfully treated by PTA].  

PubMed

We reported a rare case, which was successfully treated by PTA, of right common carotid artery dissection propagated from acute aortic dissection (AAD) type A. A 45-year-old male with a past history of hypertension and an artificial graft replacement of the abdominal aorta due to AAD type B, 7 years ago, was brought into our hospital by ambulance 30 minutes after an attack of fainting and left hemiparesis. On admission, the patient complained not of chest pain or left hemiparesis, but nausea. At that time his consciousness level was JCS 1. During examinations, he had the same attack twice and his consciousness level deteriorated to JCS 2. Brain MRI showed no abnormality, but cervical MRA did not visualize the right carotid artery and thoracic CT depicted acute aortic dissection including branches of the aorta. Emergent angiography disclosed that the dissecting 99% stenosis of the right common carotid artery had developed from AAD type A with poor collateral blood flow. PTA was carried out 8 times and reduced the residual stenosis to about 50% with shortened circulation time. The patient's consciousness disturbance improved. After the replacement of the whole aortic arch in an artificial graft, the residual stenosis disappeared. The patient recovered without neurological deficit but right frontal silent embolic infarction caused by the artificial graft replacement was detected. AAD is a catastrophic illness and sometimes accompanied by devastating ischemic cerebral disease (ICD) because of propagation of dissecting to extracranial vessels. This is the first report that shows the efficacy of PTA for treatment of ICD associated with AAD. PMID:11127587

Kubota, T; Niwa, J; Chiba, M; Mikami, T; Oka, S

2000-11-01

249

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

Cancer.gov

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

250

Management of isolated superior mesenteric artery dissection  

PubMed Central

AIM: To evaluate our experience of the clinical management of spontaneous isolated superior mesenteric artery dissection (ISMAD). METHODS: From January 2008 to July 2013, 18 patients with ISMAD were retrospectively analyzed, including 7 patients who received conservative therapy, 9 patients who received reconstruction with bare stents, and 2 patients who underwent surgical treatment. The decision to intervene was based on anatomic suitability, patient comorbidities and symptoms. RESULTS: Intestinal ischemia-related symptoms completely resolved in 7 patients who received conservative therapy. Stent placement was successful in 9 patients. Of the 9 patients who received endovascular stenting, abdominal pain was alleviated after the procedure and gradually disappeared within 3 d. Follow-up computed tomography and computed tomography angiography were available in all patients during the first month and the first year after the procedure, which revealed patent stent and patent involved superior mesenteric artery branches with complete obliteration of the dissection lesion. In the 2 patients who underwent surgical treatment, good clinical efficacy was also observed. CONCLUSION: ISMAD may be managed successfully in a variety of ways based on the clinical symptoms. ISMAD should be treated by conservative management as the ?rst-line option, however, in those with bowel necrosis or imminent arterial rupture during conservative therapy, endovascular or surgical therapy is indicated. PMID:25493033

Lv, Peng-Hua; Zhang, Xi-Cheng; Wang, Li-Fu; Chen, Zhao-Lei; Shi, Hai-Bin

2014-01-01

251

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

Federal Register 2010, 2011, 2012, 2013, 2014

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

2013-01-31

252

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

253

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

PubMed Central

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

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

2014-01-01

254

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

255

Predicting death in patients with acute type A aortic dissection  

Microsoft Academic Search

Background—Given the high mortality rates in patients with type A aortic dissection, predictive tools to identify patients at increased risk of death are needed to assist clinicians for optimal treatment. Methods and Results—Accordingly, we evaluated 547 patients with this diagnosis enrolled in the International Registry of Acute Aortic Dissection (IRAD) between January 1996 and December 1999. Univariate testing followed by

Rajendra H. Mehta; Toru Suzuki; Peter G. Hagan

2002-01-01

256

Real-time thermography during energized vessel sealing and dissection  

Microsoft Academic Search

Background: Energized dissection systems facilitate laparoscopic dissection and hemostasis and reduce instrument traffic. However, they can introduce undesirable thermal collateral\\/proximity damage to adjacent structures mainly by heat conduction, although other mechanisms may be involved. The latest generation devices have the potential to reduce the incidence of such problems through use of active feedback control over the power output. This effectively

P. A. Campbell; A. B. Cresswell; T. G. Frank; A. Cuschieri

2003-01-01

257

Spontaneous coronary artery dissection and pseudoaneurysm: a case report.  

PubMed

Spontaneous coronary artery dissection (SCAD) is a very rare but potentially fatal condition, which often causes acute myocardial infarction and sudden cardiac death. Spontaneous coronary artery dissection associated with pseudoaneurysm has been rarely reported mostly managed with coronary artery bypass grafting. We report a female patient with SCAD and pseudoaneurysm who was treated by successful percutaneous coronary intervention. PMID:24176591

Nie, Jun-Gang; Dong, Jian-Zeng

2014-02-01

258

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

259

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

260

Is there a relationship between weather conditions and aortic dissection?  

Microsoft Academic Search

BACKGROUND: Bleeding and rupture of blood vessels has been correlated with weather conditions in the past. This is the first study in the world literature with the aim of investigating the relationship between atmospheric pressure and temperature with the presentation of aortic dissection. METHODS: The dates of all emergency aortic dissection repairs from 1996–2002 in a regional cardiothoracic unit at

Costa Repanos; Neil K Chadha

2005-01-01

261

ASSOCIATION OF INTERNAL CAROTID ARTERY DISSECTION AND CHIROPRACTIC MANIPULATION  

Microsoft Academic Search

BACKGROUND- To determine the relationship between chiropractic manipulative therapy (CMT) and internal carotid artery dissection (ICAD), a MEDLINE literature search was performed for the years 1966 through 2000 using the terms internal carotid dissection. Literature that included information concerning causation of ICAD, as well as all case studies and series, was selected for review. REVIEW SUMMARY- In reviewing the cases

Michael T. Haneline; Arthur C. Croft; Benjamin M. Frishberg

2003-01-01

262

Outcome of extensive coronary artery dissection during coronary angioplasty  

Microsoft Academic Search

A total of 32 (3.6%) patients of 880 undergoing coronary angioplasty during a nine year period at one hospital had extensive dissection (defined as a dissection extending beyond the limits of the dilated angioplasty balloon) in the coronary artery in which the angioplasty procedure was performed. Two (6.25%) of the 32 patients (both of whom were undergoing angioplasty because of

T R Cripps; J M Morgan; A F Rickards

1991-01-01

263

Dissection Videos Do Not Improve Anatomy Examination Scores  

ERIC Educational Resources Information Center

In this quasi-experimental study, we describe the effect of showing dissection videos on first-year medical students' performance in terms of test scores during a gross anatomy course. We also surveyed students' perception regarding the showing of dissection videos. Two hundred eighty-seven first-year medical students at Rawalpindi Medical College…

Mahmud, Waqas; Hyder, Omar; Butt, Jamaal; Aftab, Arsalan

2011-01-01

264

Predictive factors for postoperative wound complications after neck dissection.  

PubMed

The objective of this retrospective study was to evaluate risk factors for wound complications after neck dissection. One hundred and nineteen patients were treated with neck dissection for squamous-cell carcinoma of the upper aerodigestive tract at the National Cancer Institute in Rome between 2006 and 2009. Postoperative wound complications were divided into major or minor and were related to different variables to identify risk factors. Postoperative wound complications were found in 20.2% of patients with an individual patient probability for different risk factors ranging from 2% to 34.1%. Preoperative chemoradiation therapy (CRT) and the type of neck dissection were associated with a higher risk of major complications (p ? 0.05). Previous CRT and radical neck dissection/modified radical neck dissection are risk factors for major wound complications in patients with head and neck squamous cell carcinoma undergoing neck dissection. Patients requiring neck dissection after CRT should be informed about the increased risk of the procedure, and selective neck dissection, if oncologically appropriate, should be considered to reduce complications. PMID:23620635

Pellini, R; Mercante, G; Marchese, C; Terenzi, V; Sperduti, I; Manciocco, V; Ruscito, P; Cristalli, G; Marchesi, P; Pichi, B; Spriano, G

2013-02-01

265

Value of systematic mediastinal lymph node dissection during pulmonary metastasectomy  

Microsoft Academic Search

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

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

2001-01-01

266

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

PubMed

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

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

2012-03-01

267

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. PMID:24199871

2013-01-01

268

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

PubMed

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

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

2015-04-01

269

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

270

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

PubMed Central

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

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

2015-01-01

271

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

PubMed

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

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

2015-01-01

272

Quantitative analysis of global phosphorylation changes with high-resolution tandem mass spectrometry and stable isotopic labeling  

PubMed Central

Quantitative measurement of specific protein phosphorylation sites is a primary interest of biologists, as site-specific phosphorylation information provides insights into cell signaling networks and cellular dynamics at a system level. Over the last decade, selective phosphopeptide enrichment methods including IMAC and metal oxides (TiO2 and ZrO2) have been developed and greatly facilitate large scale phosphoproteome analysis of various cells, tissues and living organisms, in combination with modern mass spectrometers featuring high mass accuracy and high mass resolution. Various quantification strategies have been applied to detecting relative changes in expression of proteins, peptides, and specific modifications between samples. The combination of mass spectrometry-based phosphoproteome analysis with quantification strategies provides a straightforward and unbiased method to identify and quantify site-specific phosphorylation. We describe common strategies for mass spectrometric analysis of stable isotope labeled samples, as well as two widely applied phosphopeptide enrichment methods based on IMAC(NTA-Fe3+) and metal oxide (ZrO2). Instrumental configurations for on-line LC-tandem mass spectrometric analysis and parameters of conventional bioinformatic analysis of large data sets are also considered for confident identification, localization, and reliable quantification of site-specific phosphorylation. PMID:23611819

Kweon, Hye Kyong; Andrews, Philip C.

2013-01-01

273

Endoscopic submucosal dissection for malignant esophageal lesions.  

PubMed

The incidence of esophageal cancer has been increasing while the prognosis remains very poor. Endoscopic submucosal dissection (ESD) was developed in Japan for en bloc resection of early gastric cancer with excellent results. The use of ESD in early squamous cell cancer (SCC) of the esophagus in Japan has been increasing with long-term results comparable to those in early gastric cancer. The use of ESD in Barrett's neoplasia in western countries has been challenged by the low complete resection rates and the risk of metachronous lesions from surrounding non-dysplastic Barrett's epithelium. Efforts to combine ESD with other treatment modalities such as radiofrequency ablation in Barrett's neoplasia and chemoradiation in SCC appear to be promising. The use of steroid therapy (local or systemic) has been demonstrated to prevent post-ESD stenosis, which is the most common complication after esophageal ESD. PMID:24659252

Hammad, Hazem; Kaltenbach, Tonya; Soetikno, Roy

2014-01-01

274

Endoscopic submucosal dissection for colorectal neoplasms  

PubMed Central

Endoscopic submucosal dissection (ESD) is an established therapeutic technique for the treatment of gastrointestinal neoplasms. Because it is typically completed as en bloc resection, this technique provides a complete specimen for precise pathological evaluation. On the other hand, ESD is not as widely applied in treating colorectal neoplasms as with gastric cancers, due to its technical difficulty, longer procedure time, and increased risk of perforation. However, some devices that facilitate ESD and improve the safety of the procedure have been recently reported, and the use of the technique has gradually spread worldwide. Endoscopists who begin to perform ESD need to recognize the indications of ESD, the technical issue involved in this procedure, and its associated complications. This review outlines the methods and certain types of devices used for colorectal ESD. PMID:25333002

Takamaru, Hiroyuki; Mori, Genki; Yamada, Masayoshi; Kinjo, Yuzuru; So, Eriko; Abe, Seiichiro; Otake, Yosuke; Nakajima, Takeshi; Matsuda, Takahisa; Saito, Yutaka

2014-01-01

275

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

276

Dissection and Downstream Analysis of Zebra Finch Embryos at Early Stages of Development  

PubMed Central

The zebra finch (Taeniopygiaguttata) has become an increasingly important model organism in many areas of research including toxicology1,2, behavior3, and memory and learning4,5,6. As the only songbird with a sequenced genome, the zebra finch has great potential for use in developmental studies; however, the early stages of zebra finch development have not been well studied. Lack of research in zebra finch development can be attributed to the difficulty of dissecting the small egg and embryo. The following dissection method minimizes embryonic tissue damage, which allows for investigation of morphology and gene expression at all stages of embryonic development. This permits both bright field and fluorescence quality imaging of embryos, use in molecular procedures such as in situ hybridization (ISH), cell proliferation assays, and RNA extraction for quantitative assays such as quantitative real-time PCR (qtRT-PCR). This technique allows investigators to study early stages of development that were previously difficult to access. PMID:24999108

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

2014-01-01

277

Proteomic and phosphoproteomic comparison of human ES and iPS cells  

PubMed Central

Combining high mass accuracy mass spectrometry, isobaric tagging, and novel software for multiplexed, large-scale protein quantification, we report deep proteomic coverage across multiple biological replicates and cell lines. We applied this method to study four human embryonic stem cell and four induced pluripotent stem cell lines in biological triplicate, a 24-sample comparison resulting in the largest set of identified proteins and phosphorylation sites in pluripotent cells to date. The statistical analysis afforded by this approach revealed, for the first time, subtle but reproducible differences in protein and protein phosphorylation between embryonic stem cells and induced pluripotent cells. Merging these results with RNA-seq analyses, we found functionally related differences across each tier of regulation. Finally, we introduce the Stem Cell–Omics Repository (SCOR), a resource that collates and displays 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.

2012-01-01

278

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

279

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.

280

Spontaneous coronary artery dissection of all major coronary arteries  

PubMed Central

Spontaneous coronary artery dissection is a rare cause of myocardial infarction and sudden cardiac death. A 32-year-old man presented with effort angina. He had a positive treadmill exercise electrocardiogram test, and coronary angiography showed that he had dissection of all major coronary vessels. The left anterior descending coronary artery was completely blocked, probably secondary to dissection and subsequent occlusion. He was advised to undergo coronary artery bypass surgery, to which he did not agree; instead, he was treated by medication and followed up. PMID:17380226

Harikrishnan, S; Ajithkumar, VK; Tharakan, JM

2007-01-01

281

Iatrogenic aortic dissection during right coronary artery stenting.  

PubMed

Aortic dissection limited to one sinus of Valsalva has been observed as an iatrogenic complication during coronary intervention. We report on a 65-year-old female patient who had a diagnosis of acute inferior myocardial infarction and experienced type A aortic dissection during stenting of the right coronary artery (RCA). Dissection was seen during aortic injection. There were no associated diseases in the sinuses of Valsalva or the aortic valve. An opening was seen intraoperatively in the right sinus of Valsalva. The opening was immediately and successfully sutured. The RCA was bypassed. PMID:18583289

Cebi, Niyazi; Tanriverdi, Süleyman; Karabulut, Ahmet

2008-01-01

282

Neck dissection with cervical sensory preservation in thyroid cancer.  

PubMed

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. PMID:25083485

Xue, Shuai; Wang, Peisong; Chen, Guang

2013-11-01

283

Chronic type B aortic dissection: indications and strategies for treatment.  

PubMed

Chronic type B aortic dissection is a distinctive condition that needs individual treatment strategies and different considerations than in therapy of acute or subacute type B aortic dissection. The most common indication for treatment of this complex disease is aneurysmal dilatation of the dissected aortic segment. While open repair of the enlarged dissected aorta remains the best option for good-risk patients and patients with connective tissue disorders in high-volume centers with respective expertise, endovascular management of chronic type B aortic dissection with postdissection aneurysms has significantly gained ground in the past years. But the concept of TEVAR with implantation of a tubular stent-graft into the thoracic aorta to seal the proximal entry tear and reroute the blood flow into the true lumen alone, is not associated with satisfactory results. This is mainly due to the sparse remodeling capacity of the aortic tissue compared to earlier stages of the disease as the aortic wall and the dissection membrane are thickened and more rigid. On the other hand, it is restricted by the most limiting factor for endovascular success in chronic type B aortic dissection: persistent false lumen perfusion. This problem also affects patients with residual dissection after surgical repair of a DeBakey type I aortic dissection or dissection after ascending aortic repair for other pathologies. Hence, it is evident that strategies to achieve endovascular false lumen occlusion are of increasing importance and novel techniques have been introduced to solve the problem of persisting false lumen flow. Thus, the evolution of a large variety of techniques to address the false lumen perfusion issue indicates that complicated chronic type B dissection involves a high diversity in clinical presentation and morphology. A large armamentarium of catheter skills as well as critical individualized treatment strategies are required to address the heterogenous morphological disease pattern for each individual patient. The rapid development in endovascular techniques gives new directions for treatment indications and strategies in chronic aortic dissection and enables new insights into this old disease. PMID:25604323

Rohlffs, F; Tsilimparis, N; Diener, H; Larena-Avellaneda, A; Von Kodolitsch, Y; Wipper, S; Debus, E S; Kölbel, T

2015-04-01

284

Global Phosphoproteomics Reveals Crosstalk between Bcr-Abl and Negative Feedback Mechanisms Controlling Src Signaling  

PubMed Central

In subtypes and late stages of leukemias driven by the tyrosine kinase fusion protein Bcr-Abl, Src signaling critically contributes to the leukemic phenotype. We performed global tyrosine phosphoprofiling using quantitative mass spectrometry of Bcr-Abl transformed cells in which the activities of the Src family kinases (SFKs) were perturbed to build a detailed context-dependent network of cancer signaling. Perturbation of the SFKs Lyn and Hck with genetics or inhibitors revealed Bcr-Abl downstream phosphorylation events either mediated by or independent of SFKs. We identified multiple negative feedback mechanisms within the network of signaling events affected by Bcr-Abl and SFKs, and found that Bcr-Abl attenuated these inhibitory mechanisms. The Csk binding protein Pag1 (also known as Cbp) and the tyrosine phosphatase Ptpn18 both mediated negative feedback to SFKs. We observed Bcr-Abl-mediated phosphorylation of the phosphatase Shp2 (Ptpn11) and this may contribute to the suppression of these negative feedback mechanisms to promote Bcr-Abl-activated SFK signaling. Csk and a kinase-deficient Csk mutant both produced similar globally repressive signaling consequences, suggesting a critical role for the adaptor protein function of Csk in its inhibition of Bcr-Abl and SFK signaling. The identified Bcr-Abl-activated SFK regulatory mechanisms are candidates for dysregulation during leukemia progression and acquisition of SFK-mediated drug resistance. PMID:21447799

Brown, Lauren; Galvan, Erica; Komisopoulou, Evangelia; Chen, Sharon S.; Low, Tracey; Tahmasian, Martik; Skaggs, Brian; Müschen, Markus; Pellegrini, Matteo; Graeber, Thomas G.

2014-01-01

285

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

286

VIRTUAL FETAL PIG DISSECTION AS AN AGENT OF KNOWLEDGE ACQUISITION FOR FEMALE HIGH SCHOOL BIOLOGY STUDENTS  

Microsoft Academic Search

This study attempted to determine if a virtual fetal pig dissection can be used as a viable alternative for an actual dissection for females enrolled in high school biology classes by comparing the knowledge acquisition between the experimental (virtual dissection) and control (actual dissection) groups. Two hundred and twenty four students enrolled in biology classes in a suburban all-girl parochial

Rebecca S. Maloney

287

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. PMID:24890864

2014-01-01

288

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

289

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)

2011-01-03

290

GPM Dissects Typhoon Hagupit - Duration: 0:38.  

NASA Video Gallery

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

291

Laser Ablation-ICP-MS Analysis of Dissected Tissue: A  

E-print Network

Laser Ablation-ICP-MS Analysis of Dissected Tissue: A Conservation-Minded Approach to Assessing the animal. In this paper, we report on the application of laser ablation-ICP-MS (LA- ICP-MS) for sampling

Hopkins, William A.

292

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. PMID:18669070

Di Rienzo Businco, L; Coen Tirelli, G

2008-01-01

293

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

PubMed

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. PMID:18669070

Di Rienzo Businco, L; Coen Tirelli, G

2008-04-01

294

Unusual vascular complications of dissecting thoracic aortic aneurysms  

Microsoft Academic Search

Nondissecting, chronic, thoracic aortic aneurysms (TAA) may be associated with such vascular complications as aorto-cardiac,\\u000a aorto-superior vena caval (SVC) and aorto-pulmonary arterial (PA) fistula formation, and\\/or SVC or PA compression. Dissecting\\u000a TAA have been associated with these lesions far less often. This report summarizes the occurrence and outcome of the following\\u000a complications of dissecting TAA: (1) SVC obstruction; (2) aortoright

A. L. Morris; J. Barwinsky

1978-01-01

295

[Postoperative acute aortic dissection. Apropos of two cases].  

PubMed

Aortic dissection after cardiac surgery is a rare complication. The prognosis is often poor: 33-78% of mortality. The study of two cases out of 2100 patients operated upon during the last three years, and the review of the literature, allows to recall the mechanism, the anatomic origin and the different surgical techniques. Early diagnosis is essential. Some preventive techniques may reduce the incidence of the iatrogenic dissections. PMID:1285610

Kreitmann, P; Popoff, G; Diaz, F; Declemy, S; Sciotti, G

1992-01-01

296

Dissecting the Milky Way disk with LAMOST  

NASA Astrophysics Data System (ADS)

The Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) survey has obtained over 3 million stellar spectra through its first two years of operations. This vast ensemble of bright star spectra is an unprecedented resource for detailed kinematical studies of the nearby Galactic disk. We detail recent results from LAMOST that uncover asymmetries in the vertical and radial (Galactocentric) velocity components of Milky Way disk stars. Using effective temperature as a proxy for stellar age, we have found that cooler stars in the extended Solar neighborhood appear to be in equilibrium, and that the velocity substructure is mostly present among warmer -- and thus younger -- stars. We detail our continued efforts to improve estimates of stellar distances and proper motions, which are vital to the process of disentangling complicated disk kinematics. With the huge number of spectra observed by LAMOST covering large contiguous sky areas, it is becoming possible to dissect the kinematical structure of the local disk in minute detail, while also reconstructing the larger-scale dynamics of the disk. This research was supported by NSF grants AST 09-37523 and AST 14-09421.

Carlin, Jeffrey L.; Newberg, Heidi Jo; Liu, Chao; Beers, Timothy C.; Chen, Xuelei; Grabowski, Kathleen; Guhathakurta, Puragra; Lepine, Sebastien; Liu, Xiaowei; Luo, A.-Li; Tian, Hai-Jun; Yanny, Brian; Yuan, Haibo; Zhang, Haotong; Zhao, Gang; Zhao, Yongheng; Zheng, Zheng

2015-01-01

297

Optogenetic dissection of medial prefrontal cortex circuitry  

PubMed Central

The medial prefrontal cortex (mPFC) is critically involved in numerous cognitive functions, including attention, inhibitory control, habit formation, working memory and long-term memory. Moreover, through its dense interconnectivity with subcortical regions (e.g., thalamus, striatum, amygdala and hippocampus), the mPFC is thought to exert top-down executive control over the processing of aversive and appetitive stimuli. Because the mPFC has been implicated in the processing of a wide range of cognitive and emotional stimuli, it is thought to function as a central hub in the brain circuitry mediating symptoms of psychiatric disorders. New optogenetics technology enables anatomical and functional dissection of mPFC circuitry with unprecedented spatial and temporal resolution. This provides important novel insights in the contribution of specific neuronal subpopulations and their connectivity to mPFC function in health and disease states. In this review, we present the current knowledge obtained with optogenetic methods concerning mPFC function and dysfunction and integrate this with findings from traditional intervention approaches used to investigate the mPFC circuitry in animal models of cognitive processing and psychiatric disorders. PMID:25538574

Riga, Danai; Matos, Mariana R.; Glas, Annet; Smit, August B.; Spijker, Sabine; Van den Oever, Michel C.

2014-01-01

298

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. PMID:18625253

Wheeler, Robert A.; Carelli, Regina M.

2009-01-01

299

Genetic dissection of drug resistance in trypanosomes.  

PubMed

The trypanosomes cause two neglected tropical diseases, Chagas disease in the Americas and African trypanosomiasis in sub-Saharan Africa. Over recent years a raft of molecular tools have been developed enabling the genetic dissection of many aspects of trypanosome biology, including the mechanisms underlying resistance to some of the current clinical and veterinary drugs. This has led to the identification and characterization of key resistance determinants, including transporters for the anti-Trypanosoma brucei drugs, melarsoprol, pentamidine and eflornithine, and the activator of nifurtimox-benznidazole, the anti-Trypanosoma cruzi drugs. More recently, advances in sequencing technology, combined with the development of RNA interference libraries in the clinically relevant bloodstream form of T. brucei have led to an exponential increase in the number of proteins known to interact either directly or indirectly with the anti-trypanosomal drugs. In this review, we discuss these findings and the technological developments that are set to further revolutionise our understanding of drug-trypanosome interactions. The new knowledge gained should inform the development of novel interventions against the devastating diseases caused by these parasites. PMID:23552488

Alsford, Sam; Kelly, John M; Baker, Nicola; Horn, David

2013-10-01

300

Quantitative habitability.  

PubMed

A framework is proposed for a quantitative approach to studying habitability. Considerations of environmental supply and organismal demand of energy lead to the conclusions that power units are most appropriate and that the units for habitability become watts per organism. Extreme and plush environments are revealed to be on a habitability continuum, and extreme environments can be quantified as those where power supply only barely exceeds demand. Strategies for laboratory and field experiments are outlined that would quantify power supplies, power demands, and habitability. An example involving a comparison of various metabolisms pursued by halophiles is shown to be well on the way to a quantitative habitability analysis. PMID:18163866

Shock, Everett L; Holland, Melanie E

2007-12-01

301

Early and late management of type B aortic dissection.  

PubMed

The management of type B aortic dissection is undergoing profound changes with timely TEVAR accepted as first-line strategy in the setting of complicated dissection; with recent technological advances and in experienced hands this intervention is considered safe and life-saving. With the ability to remodel the dissected aorta as a result of scaffolding even pre-emptive endovascular treatment is being considered and supported by long-term stability and often prevention of aneurysmal expansion. This insight and a growing number of silent risk conditions (resistant hypertension, partial false lumen thrombosis) may lower the threshold for TEVAR in asymptomatic patients in the subacute phase. In the chronic phase of a type B dissection patients are usually free of symptoms, however, with the expanding false lumen at risk of rupture. Advanced TEVAR options (including branches and fenestrations) are likely to be used more often than open surgical replacement of such aneurysmatic segment of the dissected aorta in that chronic phase. All dissection patients should be offered lifelong surveillance. PMID:25092877

Nienaber, Christoph A; Divchev, Dimitar; Palisch, Holger; Clough, Rachel E; Richartz, Barbara

2014-10-01

302

Axillary dissection for breast carcinoma. The myth of skip metastasis.  

PubMed

The question of what constitutes an adequate axillary dissection for breast cancer remains open for debate. Central to this controversy is whether axillary nodal metastasis occurs in a stepwise fashion or spreads sporadically, creating skip metastases. The therapeutic aim of axillary dissection also must be considered. To resolve this controversy, a prospective study involving 129 patients who underwent complete axillary dissection for breast carcinoma was performed. The tissue from the axillary dissections was divided intraoperatively and sent to the pathologist as two specimens. The first specimen contained all nodes lateral to the pectoralis minor muscle (Level I), whereas the second contained all nodes beneath and medial to the pectoralis minor (Levels II and III). The tissue was analyzed to determine the frequency of skip metastasis. Only two patients, 1.6 per cent of the total group or 3.2 per cent of the positive node group, were found to have a positive node in Level II-III with no metastasis in Level I. A thorough dissection of Level I alone is sufficient to detect more than 98 per cent of all axillary lymph node metastases from breast cancer. Thus, proper staging of the disease can be obtained. When Level I contained positive nodes, the probability of metastatic disease to higher levels was significant (45%), indicating further treatment is necessary in incomplete axillary dissections. PMID:2729776

Lloyd, L R; Waits, R K; Schroder, D; Hawasli, A; Rizzo, P; Rizzo, J

1989-06-01

303

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. PMID:24260401

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

2013-01-01

304

On Quantitizing  

ERIC Educational Resources Information Center

"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…

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

2009-01-01

305

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 ...

306

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

307

A comparison of retention of anatomical knowledge in an introductory college biology course: Traditional dissection vs. virtual dissection  

NASA Astrophysics Data System (ADS)

Dissection has always played a crucial role in biology and anatomy courses at all levels of education. However, in recent years, ethical concerns, as well as improved technology, have brought to the forefront the issue of whether virtual dissection is as effective or whether it is more effective than traditional dissection. Most prior research indicated the two methods produced equal results. However, none of those studies examined retention of information past the initial test of knowledge. Two groups of college students currently enrolled in an introductory level college biology course were given one hour to complete a frog dissection. One group performed a traditional frog dissection, making cuts in an actual preserved frog specimen with scalpels and scissors. The other group performed a virtual frog dissection, using "The Digital Frog 2" software. Immediately after the dissections were completed, each group was given an examination consisting of questions on actual specimens, pictures generated from the computer software, and illustrations that neither group had seen. Two weeks later, unannounced, the groups took the same exam in order to test retention. The traditional dissection group scored significantly higher on two of the three sections, as well as the total score on the initial exam. However, with the exception of specimen questions (on which the traditional group retained significantly more information), there was no significant difference in the retention from exam 1 to exam 2 between the two groups. These results, along with the majority of prior studies, show that the two methods produce, for the most part, the same end results. Therefore, the decision of which method to employ should be based on the goals and preferences of the instructor(s) and the department. If that department's goals include: Being at the forefront of new technology, increasing time management, increasing student: teacher ratio for economic reasons, and/or ethical issues, then the choice should be the use of computer software. If the goals include: Students gaining a 3-dimensional feel for the location and relationship of parts to one another, students being able to see various naturally occurring anomalies, and increased experience with manipulation of dissection tools, then the choice should be dissection of actual specimens. It is important to note, however, that regardless of which method is chosen, the effectiveness of that method is very much dependent on the skill and enthusiasm of the instructor.

Taeger, Kelli Rae

308

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

309

Quantitative radiography  

SciTech Connect

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 system of quantitative radiography displays accurate, high-resolution pseudocolor images in units of density. We characterize approximately 10,000 parts per year in hundreds of different configurations and compositions with this system. Images are captured using DuPont NDT55 industrial x-ray film in Daypack{trademark} packages. X-ray cabinets are of custom design, with helium flight path and a filter wheel for positioning filters if desired. The cabinets contain baffles to reduce scattered radiation and are equipped with drawer for rapid load/unload of parts. Separate units with tungsten-anode or copper-anode tubes are available. The usual operating voltage is 15 to 35 kVp. Fixturing provides for rough part positioning and precise alignment with respect to the x-ray source. Areal density standards are placed at several locations on each film. In interpreting the image, we use the standards nearest the image of the part being quantified. Because of this, small variations in x-ray flux uniformity (heel effects) are unimportant. The usual standard is a step wedge of aluminum containing 13 steps. Films are permanently labeled by imaging a perforated metal numbering strip. Data such as part number, step wedge identification, etc. are read from barcode labels and transferred to a data base for later retrieval and use in quantifying the image.

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

1991-02-01

310

Congenital Incomplete Fusion of Superior Mesenteric Artery Mimicking Dissection  

PubMed Central

Patient: Male, 62 Final Diagnosis: Superior mesenteric artery anatomic variant Symptoms: Abdominal pain • diarrhea • transcient ischemic attacks Medication: — Clinical Procedure: CT of abdomen and pelvis Specialty: Surgery Objective: Congenital defects/diseases Background: Both spontaneous SMA dissection and anatomical variants of GIT vasculature are well known entities. We present a case initially diagnosed as an SMA dissection on CT, but upon detailed review of the imaging findings was considered to be incompletely fused ventral segmental arteries – a rare anatomic variant not well described before. This finding is clinically significant, as it can mimic a vascular dissection and such a wrong diagnosis will lead to unnecessary investigation and intervention. Case Report: A 62-year-old male patient presented with abdominal pain of uncertain etiology. The initial CT revealed an abnormal appearance of the superior mesenteric artery (SMA) which was diagnosed as SMA dissection. However, the appearance of this ‘dissection’ was unusual and there was a mismatch between the clinical presentation and radiological findings. The scan was reviewed and a 3D reconstruction of the abdominal aortal and visceral arteries was performed. The abnormal appearance of the SMA was deemed to be from a congenital anatomical variant. A review of the embryological origin of gut vasculature provides a likely explanation for this appearance. Conclusions: Ours is an unusual case of a developmental variant that has not been well described hitherto. Attention to the ancillary radiological signs and understanding the embryological origin of the abdominal vasculature is important to distinguish such variants from pathology. PMID:25623118

Sharma, Vasu Keshav; H’ng, Martin Weng Chin

2015-01-01

311

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. PMID:24955061

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

2014-01-01

312

Methodological aspects of the genetic dissection of gene expression  

SciTech Connect

Motivation: Dissection of the genetics underlying gene expression utilizes techniques from microarray analyses as well as quantitative trait loci (QTL) mapping. Available QTL mapping methods are not tailored for the highly automated analyses required to deal with the thousands of gene transcripts encountered in the mapping of QTL affecting gene expression (sometimes referred to as eQTL). This report focuses on the adaptation of QTL mapping methodology to perform automated mapping of QTL affecting gene expression. Results: The analyses of expression data on>12 000 gene transcripts in BXD recombinant inbred mice found, on average, 629 QTL exceeding the genome-wide 5% threshold. Using additional information on trait repeatabilities and QTL location, 168 of these were classified as high confidence QTL. Current sample sizes of genetical genomics studies make it possible to detect a reasonable number of QTL using simple genetic models, but considerably larger studies are needed to evaluate more complex genetic models. After extensive analyses of real data and additional simulated data (altogether >300 000 genome scans) we make the following recommendations for detection of QTL for gene expression: (1) For populations with an unbalanced number of replicates on each genotype, weighted least squares should be preferred above ordinary least squares. Weights can be based on the repeatability of the trait and the number of replicates. (2) A genome scan based on multiple marker information but analysing only at marker locations is a good approximation to a full interval mapping procedure. (3) Significance testing should be based on empirical genome-wide significance thresholds that are derived for each trait separately. (4) The significant QTL can be separated into high and low confidence QTL using a false discovery rate that incorporates prior information such as transcript repeatabilities and co-localization of gene- ranscripts and QTL. (5) Including observations on the founder lines in the QTL analysis should be avoided as it inflates the test statistic and increases the Type I error. (6) To increase the computational efficiency of the study, use of parallel computing is advised. These recommendations are summarized in a possible strategy for mapping of QTL in a least squares framework.

Carlborg, O [University of Tennessee Health Science Center, Memphis; DeKoning, D [University of Tennessee Health Science Center, Memphis; Manly, Kenneth [University of Tennessee Health Science Center, Memphis; Chesler, Elissa J [ORNL; Williams, Robert [University of Tennessee Health Science Center, Memphis; Haley, C [University of Tennessee Health Science Center, Memphis

2004-01-01

313

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. PMID:21211047

2011-01-01

314

Spontaneous coronary artery dissection in a patient with bacterial meningitis.  

PubMed

A 40-year-old man was admitted to our hospital because of the acute onset of fever and headache, which were attributed to bacterial meningitis. Antibiotic treatment was initiated and his condition gradually improved. On day 5 after admission, immediately after masturbation, he developed abrupt onset of severe chest pain and cold sweat and the ECG suggested acute anterior myocardial infarction. Immediate coronary angiography revealed spontaneous dissection of the left anterior descending artery. After conservative management, his cardiac function improved. Acute coronary syndrome may be rarely caused by spontaneous coronary artery dissection. Sepsis was considered as a probable trigger for spontaneous coronary artery dissection, possibly through vascular damage from increased nitric oxide and sympathetic nervous over-activation. PMID:24194165

Kinoshita, Kensuke; Tsunoda, Yoshiya; Watanabe, Shigeyuki; Tokuda, Yasuharu

2013-01-01

315

Digital dissection system for medical school anatomy training  

NASA Astrophysics Data System (ADS)

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

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

2003-05-01

316

Giant Dissecting Aortic Aneurysm in an Asymptomatic Young Male  

PubMed Central

Giant aortic aneurysm is defined as aneurysm in the aorta greater than 10?cm in diameter. It is a rare finding since most patients will present with complications of dissection or rupture before the size of aneurysm reaches that magnitude. Etiological factors include atherosclerosis, Marfan's syndrome, giant cell arteritis, tuberculosis, syphilis, HIV-associated vasculitis, hereditary hemorrhagic telangiectasia, and medial agenesis. Once diagnosed, prompt surgical intervention is the treatment of choice. Although asymptomatic unruptured giant aortic aneurysm has been reported in the literature, there has not been any case of asymptomatic giant dissecting aortic aneurysm reported in the literature thus far. We report a case of giant dissecting ascending aortic aneurysm in an asymptomatic young male who was referred to our institution for abnormal findings on physical exam.

Shah, Priyank; Gupta, Nishant; Goldfarb, Irvin; Shamoon, Fayez

2015-01-01

317

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 PMID:8680278

Lukács, L; Kassai, I; Lengyel, M

1996-01-01

318

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

PubMed

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

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

2012-08-01

319

Blunt dissection for the treatment of plantar verrucae.  

PubMed

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

Baruch, K

1990-08-01

320

Endoscopic subfascial dissection of the perforating veins: treatment results.  

PubMed

Before introduction of endoscopic subfascial dissection, surgical treatment of the perforating veins was a neglected topic. High error rates in the preoperatively marked perforating veins, wound-healing problems due to the incision in trophically disturbed areas, and leg ulcers prevented correct surgical treatment. Endoscopic subfascial dissection allows the accurate elimination of all clinically relevant, insufficient perforating veins in the lower leg. Therefore, it has become an accepted, improved treatment concept in the surgical therapy of primary varicosis in all three stages of chronic venous insufficiency. This experience is demonstrated based on a prospective study of the patients treated in the year 2000. PMID:12931302

Jugenheimer, Michael; Mayer, Wolfgang; Uckele, Matthias

2003-01-01

321

Infective Left Atrial Dissecting Flap after Cardiac Surgery  

PubMed Central

Left atrial dissection (LatD), defined as the forced separation of the left atrial (LA) wall layers by blood, is a rare and severe complication of cardiac surgery. It is most frequently associated with atrioventricular junction injuries. We report a case of infected LatD after coronary artery bypass graft, mitral valve replacement, aortic valve replacement and ascending aortic root replacement. The patient was presented with septicemia and disseminated intravascular coagulation. To the best of our knowledge, this is the first case report of LA dissecting flap concomitant with attached infective vegetations identified by transesophageal echocardiography. PMID:25309695

Tabiban, Sasan; Ghaemian, Ali; Bagheri, Babak; Shokri, Mojtaba

2014-01-01

322

Radiological pitfalls of a large intracranial dissecting aneurysm.  

PubMed

We report the case of a large dissecting aneurysm of the anterior cerebral artery revealed by cerebral infarction in 38-year-old man. The volume and aspect of the aneurysm initially led us to the diagnosis of saccular aneurysm. Given the complete thrombosis, the risk of bleeding was low and antithrombotic therapy was started. Surgery could be discussed later. However radiological monitoring by MRI (magnetic resonance imaging) showed a rapid decrease in volume of the aneurysm. The final angiography found an aspect of stenosis followed by a little arterial dilatation. The diagnosis of dissecting anterior cerebral aneurysm was a posteriori established. PMID:25640563

Aboukais, Rabih; Zairi, Fahed; Bourgeois, Philippe; Thines, Laurent; Lejeune, Jean-Paul

2015-01-01

323

Gene expression levels assessed by CA1 pyramidal neuron and regional hippocampal dissections in Alzheimer’s disease  

PubMed Central

To evaluate molecular signatures of an individual cell type in comparison to the associated region relevant towards understanding the pathogenesis of Alzheimer’s disease (AD), CA1 pyramidal neurons and the surrounding hippocampal formation were microaspirated via laser capture microdissection (LCM) from neuropathologically confirmed AD and age-matched control (CTR) subjects as well as from wild type mouse brain using single population RNA amplification methodology coupled with custom-designed microarray analysis with real-time quantitative polymerase-chain reaction (qPCR) validation. CA1 pyramidal neurons predominantly displayed downregulation of classes of transcripts related to synaptic transmission in AD versus CTR. Regional hippocampal dissections displayed downregulation of several overlapping genes found in the CA1 neuronal population related to neuronal expression, as well as upregulation of select transcripts indicative of admixed cell types including glial-associated markers and immediate-early and cell death genes. Gene level distributions observed in CA1 neurons and regional hippocampal dissections in wild type mice paralleled expression mosaics seen in postmortem human tissue. Microarray analysis was validated in qPCR studies using human postmortem brain tissue and CA1 sector and regional hippocampal dissections obtained from a mouse model of AD/Down syndrome (Ts65Dn mice) and normal disomic (2N) littermates. Classes of transcripts that have a greater percentage of the overall hybridization signal intensity within single neurons tended to be genes related to neuronal communication. The converse was also found, as classes of transcripts such as glial-associated markers were under represented in CA1 pyramidal neuron expression profiles relative to regional hippocampal dissections. These observations highlight a dilution effect that is likely to occur in conventional regional microarray and qPCR studies. Thus, single population studies of specific neurons and intrinsic circuits will likely yield informative gene expression profile data that may be subthreshold and/or under represented in regional studies with an admixture of cell types. PMID:21821124

Ginsberg, Stephen D.; Alldred, Melissa J.; Che, Shaoli

2011-01-01

324

From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions  

E-print Network

of thousands of genetic interactions (GIs) in Saccharomyces cerevisiae. The interpretation of these data synthetic lethality, has first been performed in Saccharomyces cerevisiae using the SGA (Tong et al, 2004

Shamir, Ron

325

Dissecting sources of quantitative gene expression pattern divergence between Drosophila species  

PubMed Central

Gene expression patterns can diverge between species due to changes in a gene's regulatory DNA or changes in the proteins, e.g., transcription factors (TFs), that regulate the gene. We developed a modeling framework to uncover the sources of expression differences in blastoderm embryos of three Drosophila species, focusing on the regulatory circuit controlling expression of the hunchback (hb) posterior stripe. Using this framework and cellular-resolution expression measurements of hb and its regulating TFs, we found that changes in the expression patterns of hb's TFs account for much of the expression divergence. We confirmed our predictions using transgenic D. melanogaster lines, which demonstrate that this set of orthologous cis-regulatory elements (CREs) direct similar, but not identical, expression patterns. We related expression pattern differences to sequence changes in the CRE using a calculation of the CRE's TF binding site content. By applying this calculation in both the transgenic and endogenous contexts, we found that changes in binding site content affect sensitivity to regulating TFs and that compensatory evolution may occur in circuit components other than the CRE. PMID:22893002

Wunderlich, Zeba; Bragdon, Meghan D; Eckenrode, Kelly B; Lydiard-Martin, Tara; Pearl-Waserman, Sivanne; DePace, Angela H

2012-01-01

326

Dissecting Quantitative Trait Loci for Head Rot Tolerance in Two Sunflower Lines with Partial Tolerance  

Technology Transfer Automated Retrieval System (TEKTRAN)

One hundred and twenty-three F3 lines derived from a cross between HA 441 and RHA 439 were used for the current study. Both parental lines showed partial tolerance to Sclerotinia head rot caused by Sclerotinia sclerotiorum. A genetic map with 236 TRAP, 11 SSR, and 2 morphological markers was constru...

327

DISSECTION OF QUANTITATIVE TRAIT LOCI (QTL) ASSOCIATED WITH GRAY LEAF SPOT RESISTANCE AND MATURITY IN MAIZE  

Technology Transfer Automated Retrieval System (TEKTRAN)

Abstract Gray Leaf Spot (GLS) is recognized as one of the most significant yield-limiting diseases of maize worldwide and has the potential to threaten maize production. Breeding for resistance provides the best preventive measure against the disease. However, associations between GLS and maturity c...

328

Genome-wide association mapping of quantitative resistance to sudden death syndrome in soybean  

Technology Transfer Automated Retrieval System (TEKTRAN)

Sudden death syndrome (SDS) is a serious threat to soybean production that can be controlled by host plant resistance. To dissect the genetic architecture of quantitative resistance to the disease in soybean, two independent association panels of soybean elite cultivar, consisting of 392 and 300 uni...

329

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

Microsoft Academic Search

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

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

1994-01-01

330

Quantitative Measurement of the Choline Acetyltransferase Activity of the Mauthner Cell Axon  

Microsoft Academic Search

To examine the possible cholinergic nature of the Mauthner cell, freeze-dried sections of goldfish spinal cord were prepared, enabling access to the Mauthner axons. Profiles of the Mauthner axons were dissected out, weighed, and quantitatively assayed for activity of choline acetyltransferase. The Mauthner axon was shown to contain significantly less activity than surrounding tissue containing motor neurons, which are likely

Penny L. Eddy; Donald A. Godfrey; Judy A. Parli; C. David Ross

1989-01-01

331

Carotid artery dissection following minimal postural trauma in a firefighter  

Microsoft Academic Search

Carotid artery dissections (CAD) are uncommon, but not rare, and are increasingly recognized as a cause of morbidity. A case of CAD following minimal sustained postural trauma is described. The causes and outcomes of CAD are discussed, with particular reference to risks that might be found in the workplace.

Stewart Lloyd

332

Dissecting Oxygenic Photosynthesis: The Evolution of the "Z"-Scheme  

E-print Network

11CHAPTER Dissecting Oxygenic Photosynthesis: The Evolution of the "Z"-Scheme for Thylakoid and two photosystems are involved in oxygenic photosynthesis. This is then followed by the discovery Drop in Photosynthesis; Two Light Reactions; Two Photosystems; Z-Scheme of Photosynthesis #12

Govindjee

333

The Influence of Emotion on Students' Performance in Dissection Exercises  

ERIC Educational Resources Information Center

This paper investigates the issue of how emotions such as disgust influence students' self-efficacy belief in terms of mastering a dissection task and also how these affect their interest in the biology of the heart. Following models of intrinsic motivation and the development of motivation, we expected disgust to negatively impact on students'…

Holstermann, Nina; Grube, Dietmar; Bogeholz, Susanne

2009-01-01

334

Dissection of the Hyperadhesive Phenotype of Airway Eosinophils in Asthma  

E-print Network

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

Mosher, Deane F.

335

Outcomes following conservative management of spontaneous coronary artery dissection.  

PubMed

Spontaneous coronary artery dissection (SCAD) is a rare but a serious cause of myocardial ischaemia and infarction that occurs most frequently in younger female patients. The management of this rare condition remains controversial. In this case series we describe the spectrum of outcomes observed following conservative management. PMID:24996390

Shah, Nadim; Michel, Jonathan; Aitken, S Andrew; Harding, Scott A

2014-10-01

336

INVESTIGATION Genetic Dissection of a Key Reproductive Barrier  

E-print Network

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

Nachman, Michael

337

Functional dissection and module swapping of fungal cyclooligomer depsipeptide synthetases.  

PubMed

BbBSLS and BbBEAS were dissected and reconstituted in Saccharomyces cerevisiae. The intermodular linker is essential for the reconstitution of the separate modules. Module 1 can be swapped between BbBEAS and BbBSLS, while modules 2 and 3 control the product profiles. BbBSLS is a flexible enzyme that also synthesizes beauvericins. PMID:23727842

Yu, Dayu; Xu, Fuchao; Gage, David; Zhan, Jixun

2013-07-14

338

Rectilinear Glass-Cut Dissections of Rectangles to Squares  

E-print Network

Rectilinear Glass-Cut Dissections of Rectangles to Squares Jurek Czyzowicz§ czyzowic is made using only rectilinear glass-cuts, i.e., vertical or horizontal straight-line cuts separating pieces into two. 1 Introduction A glass-cut of a rectangle is a cut by a straight-line segment

Urrutia, Jorge

339

Gastric Wall Dissection as a Complication of Percutaneous Gastrostomy  

SciTech Connect

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

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

1996-04-15

340

Unnecessary axillary node dissections in the sentinel lymph node era  

Microsoft Academic Search

In the sentinel lymph node era, axillary lymph node dissection (ALND) for uninvolved axillary lymph nodes should be considered unnecessary and inappropriate. Between January 2000 and August 2005, 3487 out of 10,031 invasive breast cancer patients consecutively operated at the European Institute of Oncology were considered not suitable for sentinel lymph node biopsy (SNB) and were directly submitted to ALND

Mattia Intra; Nicole Rotmensz; Denise Mattar; Oreste D. Gentilini; Annarita Vento; Paolo Veronesi; Marco Colleoni; Concetta De Cicco; Enrico Cassano; Alberto Luini; Umberto Veronesi

2007-01-01

341

Dissecting SMS Malwares in Android Anoop Joseph Babu, Rahul Raveendranath,  

E-print Network

Terms--Android; Security threats; Countermeasures; SMS Malware; Permissions. I. INTRODUCTION Smartphones SMS malware. We demonstrate how android-based smartphones can be exploited by deploying a malwareDissecting SMS Malwares in Android Anoop Joseph Babu, Rahul Raveendranath, Venkiteswaran Rajamani

Gesbert, David

342

Marquette University Gross Dissection Workshop - Upper & Lower Extremity  

NSDL National Science Digital Library

This website provides information regarding Marquette University's Gross Dissection of the Extremities workshop. The focus of the course is an intensive anatomy and kinesiology review. Even years this course focus on the lower extremity and the odd years the focus is on the upper extremity.

Marquette University (Marquette University)

2012-07-24

343

Exploring Dissections of Rectangles into Right-Angled Triangles  

ERIC Educational Resources Information Center

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

Griffiths, Martin

2013-01-01

344

SUPPORTING INFORMATION Dissecting the Kinetic Process of Amyloid Fiber Formation  

E-print Network

SUPPORTING INFORMATION Dissecting the Kinetic Process of Amyloid Fiber Formation through Asymptotic is still valid as long as enough unfolded monomers can be provided for fiber elongation process (the red eight Type-I amyloid proteins (the yeast prion Sup35 NW region, Csg Btrunc, Ure2 protein, 2

Zhang, Yang

345

Blood Vessels of the Fetal Pig Dissection Posterior Vessels Protocol  

E-print Network

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

Loughry, Jim

346

Neurovascular bundle decompression without excessive dissection for tarsal tunnel syndrome.  

PubMed

Tarsal tunnel syndrome (TTS) is an entrapment neuropathy of the posterior tibial nerve and its branches in the tarsal tunnel. We present our less invasive surgical treatment of TTS in 69 patients (116 feet) and their clinical outcomes. The mean follow-up period was 64.6 months. With the patient under local anesthesia we use a microscope to perform sharp dissection of the flexor retinaculum and remove the connective tissues surrounding the posterior tibial nerve and vessels. To prevent postoperative adhesion and delayed neuropathy, decompression is performed to achieve symptom improvement without excessive dissection. Decompression is considered complete when the patient reports intraoperative symptom abatement and arterial pulsation is sufficient. The sensation of numbness and/or pain and of foreign substance adhesion was reduced in 92% and 95% of our patients, respectively. In self-assessments, 47 patients (68%) reported the treatment outcome as satisfactory, 15 (22%) as acceptable, and 7 (10%) were dissatisfied. Of 116 feet, 4 (3%) required re-operation, initial decompression was insufficient in 2 feet and further decompression was performed; in the other 2 feet improvement was achieved by decompression of the distal tarsal tunnel. Our surgical method involves neurovascular bundle decompression to obtain sufficient arterial pulsation. As we use local anesthesia, we can confirm symptom improvement intraoperatively, thereby avoiding unnecessary excessive dissection. Our method is simple, safe, and without detailed nerve dissection and it prevents postoperative adhesion. PMID:25367582

Kim, Kyongsong; Isu, Toyohiko; Morimoto, Daijiro; Sasamori, Toru; Sugawara, Atsushi; Chiba, Yasuhiro; Isobe, Masahiro; Kobayashi, Shiro; Morita, Akio

2014-01-01

347

Dissection of Midgut and Salivary Glands from Ae. aegypti Mosquitoes  

PubMed Central

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

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

2007-01-01

348

Dissection of epistasis in oligogenic Bardet-Biedl syndrome  

Microsoft Academic Search

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

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

2006-01-01

349

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

ERIC Educational Resources Information Center

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

Lee, Yeung Chung

2004-01-01

350

Kendall Hunt Dissection of a Squid: Part 2  

NSDL National Science Digital Library

The purpose of this 9-minute video is to illustrate notable anatomical structures of the market squid (Loligo opalescens) to prepare teachers to lead a dissection of this species; however, this video is not meant to be viewed by students. Presented as a workshop at the NMEA Annual Conference, July 2010.

2012-01-01

351

High definition video teaching module for learning neck dissection  

PubMed Central

Introduction Video teaching modules are proven effective tools for enhancing student competencies and technical skills in the operating room. Integration into post-graduate surgical curricula, however, continues to pose a challenge in modern surgical education. To date, video teaching modules for neck dissection have yet to be described in the literature. Purpose To develop and validate an HD video-based teaching module (HDVM) to help instruct post-graduate otolaryngology trainees in performing neck dissection. Methods This prospective study included 6 intermediate to senior otolaryngology residents. All consented subjects first performed a control selective neck dissection. Subjects were then exposed to the video teaching module. Following a washout period, a repeat procedure was performed. Recordings of the both sets of neck dissections were de-identified and reviewed by an independent evaluator and scored using the Observational Clinical Human Reliability Assessment (OCHRA) system. Results In total 91 surgical errors were made prior to the HDVM and 41 after exposure, representing a 55% decrease in error occurrence. The two groups were found to be significantly different. Similarly, 66 and 24 staff takeover events occurred pre and post HDVM exposure, respectively, representing a statistically significant 64% decrease. Conclusion HDVM is a useful adjunct to classical surgical training. Residents performed significantly less errors following exposure to the HD-video module. Similarly, significantly less staff takeover events occurred following exposure to the HDVM. PMID:24666440

2014-01-01

352

Cancer Cell Dissecting the Unique Role of the Retinoblastoma  

E-print Network

Cancer Cell Article Dissecting the Unique Role of the Retinoblastoma Tumor Suppressor during-cycle control. However, cancer-associated mutations are almost exclusively found in RB, implying that RB has for cancer development; hence, the roles and regulation of RB have been intensively studied (reviewed

353

A Novel Approach to the Dissection of the Human Knee  

ERIC Educational Resources Information Center

The knee is one of the most frequently injured joints of the human body with injuries affecting the general population and the athletic population of many age groups. Dissection procedures for the knee joint typically do not allow unobstructed visualization of the anterior cruciate or posterior cruciate ligaments without sacrificing the collateral…

Clemente, F. Richard; Fabrizio, Philip A.; Shumaker, Michael

2009-01-01

354

Using a Dissecting Microscope in Teaching Introductory Chemistry.  

ERIC Educational Resources Information Center

To have students develop observational skills and acquire an excitement about chemistry, stereoscopic dissecting microscopes are used to observe the physical characteristics and chemical reactions of various substances. Several of these reactions (including dissolving potassium permanganate in deionized water and reactions between copper metal and…

Winokur, Robert; Monroe, Manus

1985-01-01

355

Timing formulas for dissection algorithms on vector computers  

NASA Technical Reports Server (NTRS)

The use of the finite element and finite difference methods often leads to the problem of solving large, sparse, positive definite systems of linear equations. MACSYMA plays a major role in the generation of formulas representing the time required for execution of the dissection algorithms. The use of MACSYMA in the generation of those formulas is described.

Poole, W. G., Jr.

1977-01-01

356

Dissections aiguës de l'aorte : physiopathologie et diagnostic  

Microsoft Academic Search

Acute dissection of the aorta is defined by the sudden irruption of a pressurized blood flow trough a tear into the internal part of the aortic wall, resulting into longitudinal separation of the wall along its weakest constituent, and leading to the formation of two circulating channels. It represents the worst catastrophe affecting the human vascular network. Its spontaneous mortality,

J. Bachet

2004-01-01

357

Value of Systematic Mediastinal Lymph Node Dissection During Pulmonary Metastasectomy  

Microsoft Academic Search

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

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

2010-01-01

358

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

ERIC Educational Resources Information Center

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

Fancovicova, Jana; Prokop, Pavol; Leskova, Andrea

2013-01-01

359

Cervical artery dissection—clinicalfeatures, risk factors, therapy and outcome in 126patients  

Microsoft Academic Search

The highly variable clinical course of cervical artery dissections still poses a major challenge to the treating physician. This study was conducted (1) to describe the differences in clinical and angiographic presentation of patients with carotid and vertebral artery dissections (CAD, VAD), (2) to define the circumstances that are related to bilateral arterial dissections, and (3) to determine factors that

Rainer Dziewas; Carsten Konrad; Bianca Dräger; Stefan Evers; Michael Besselmann; Peter Lüdemann; Gregor Kuhlenbäumer; Florian Stögbauer; E. Bernd Ringelstein

2003-01-01

360

Biology Teachers' Dissection Practices and the Influences that Lead to Their Adoption: An Exploratory Research  

ERIC Educational Resources Information Center

The lack of resolution in the on-going animal dissection debate inspired this mixed methods study to identify Connecticut secondary biology teachers' dissection practices and the influences that lead to their adoption. Qualitative findings indicate past experiences, managing objections to dissection, school culture, goals of biology teaching and…

Milano, Regina Nicole

2010-01-01

361

The First Cut Is the Deepest: Reflections on the State of Animal Dissection in Biology Education  

ERIC Educational Resources Information Center

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…

De Villiers, Rian; Monk, Martin

2005-01-01

362

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

PubMed Central

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

Bhamidipati, Castigliano; Ailawadi, Gorav

2010-01-01

363

An Investigative Alternative to Single-Species Dissection in the Introductory Biology Laboratory  

ERIC Educational Resources Information Center

Dissections of single species (e.g., fetal pig) are a common student learning activity in introductory biology courses. Such dissections demonstrate location of anatomical parts and provide dissection practice but provide less opportunity for student critical thinking, numeracy and demonstration of the scientific method. A comparative anatomy lab…

Carlin, Joel L.

2010-01-01

364

Acute type A aortic dissection surgery impeded by substernal colon interposition.  

PubMed

A 54-year old female patient presented with acute aortic dissection, Stanford type A, and a past history of oesophageal resection with substernal colon interposition. Preoperative computer tomography confirmed the aortic dissection and revealed a colonic graft that was adherent to the sternum. We report the first successful surgical treatment of aortic dissection in this challenging patient. PMID:25312995

Vondran, Maximilian; Bakhtiary, Farhad; Borger, Michael Andrew; Mohr, Friedrich Wilhelm

2015-01-01

365

A Comparison of V-Frog[C] to Physical Frog Dissection  

ERIC Educational Resources Information Center

The purpose of the present study was to examine and compare the effectiveness of virtual frog dissection using V-Frog[C] and physical frog dissection on learning, retention, and affect. Subjects were secondary students enrolled in year-long life science classes in a suburban high school (N=102). Virtual dissections were done with V-Frog[C], a…

Lalley, James P.; Piotrowski, Phillip S.; Battaglia, Barbara; Brophy, Keith; Chugh, Kevin

2010-01-01

366

How we do it: a method of neck dissection for histopathological analysis  

Microsoft Academic Search

BACKGROUND: Dissection of the lymphatic structures in the neck is an integral part of the management of many head and neck cancers. We describe a technique of surgical dissection, preparing the tissue for more precise histological analysis while also reducing operative time and complexity. METHODS: When dissected, each level is excised between lymph nodes groups and put into a separate

Tahwinder Upile; Waseem Jerjes; Seyed Ahmad Reza Nouraei; Sandeep Singh; Peter Clarke; Peter Rhys-Evans; Colin Hopper; David Howard; Anthony Wright; Holger Sudhoff; Cyril Fisher; Ann Sandison

2007-01-01

367

Tissue Quality Assessment Using a Novel Direct Elasticity Assessment Device (The E-Finger): A Cadaveric Study of Prostatectomy Dissection  

PubMed Central

Introduction Minimally invasive radical prostatectomy (RP) (robotic and laparoscopic), have brought improvements in the outcomes of RP due to improved views and increased degrees of freedom of surgical devices. Robotic and laparoscopic surgeries do not incorporate haptic feedback, which may result in complications secondary to inadequate tissue dissection (causing positive surgical margins, rhabdosphincter damage, etc). We developed a micro-engineered device (6 mm2 sized) [E-finger]) capable of quantitative elasticity assessment, with amplitude ratio, mean ratio and phase lag representing this. The aim was to assess the utility of the device in differentiating peri-prostatic tissue types in order to guide prostate dissection. Material and Methods Two embalmed and 2 fresh frozen cadavers were used in the study. Baseline elasticity values were assessed in bladder, prostate and rhabdosphincter of pre-dissected embalmed cadavers using the micro-engineered device. A measurement grid was created to span from the bladder, across the prostate and onto the rhabdosphincter of fresh frozen cadavers to enable a systematic quantitative elasticity assessment of the entire area by 2 independent assessors. Tissue was sectioned along each row of elasticity measurement points, and stained with haematoxylin and eosin (H&E). Image analysis was performed with Image Pro Premier to determine the histology at each measurement point. Results Statistically significant differences in elasticity were identified between bladder, prostate and sphincter in both embalmed and fresh frozen cadavers (p?=?<0.001). Intra-class correlation (ICC) reliability tests showed good reliability (average ICC?=?0.851). Sensitivity and specificity for tissue identification was 77% and 70% respectively to a resolution of 6 mm2. Conclusions This cadaveric study has evaluated the ability of our elasticity assessment device to differentiate bladder, prostate and rhabdosphincter to a resolution of 6 mm2. The results provide useful data for which to continue to examine the use of elasticity assessment devices for tissue quality assessment with the aim of giving haptic feedback to surgeons performing complex surgery. PMID:25384014

Good, Daniel W.; Khan, Ashfaq; Hammer, Steven; Scanlan, Paul; Shu, Wenmiao; Phipps, Simon; Parson, Simon H.; Stewart, Grant D.; Reuben, Robert; McNeill, S. Alan

2014-01-01

368

Water-jet dissection for parenchymal division during hepatectomy1  

PubMed Central

Background. High-pressure water-jet dissection was originally developed for industry where ultra-precise cutting and engraving were desirable. This technology has been adapted for medical applications with favorable results, but little is understood about its performance in hepatic resections. Blood loss may be limited by the thin laminar liquid-jet effect that provides precise, controllable, tissue-selective dissection with excellent visualization and minimal trauma to surrounding fibrous structures. Patients and methods. The efficacy of the Water-jet system for hepatic parenchymal dissection was examined in a consecutive case series of 101 hepatic resections (including 22 living donor transplantation resections) performed over 11 months. Perioperative outcomes, including blood loss, transfusion requirements, complications, and length of stay (LOS), were assessed. Results. Three-quarters of the cases were major hepatectomies and 22% were cirrhotic. Malignancy was the most common indication (77%). Median operative time was 289 min. Median estimated blood loss (EBL) was 900 ml for all cases, and only 14% of patients had >2000 ml EBL. Furthermore, EBL was 1000 ml for major resections, 775 ml for living donor resections, 600 ml in cirrhotic patients, and 1950 ml for steatotic livers. In all, 14% of patients received heterologous packed red blood cell (PRBC) transfusions for an average of 0.59 units per case. Median LOS was 7 days. EBL, transfusion requirements, and LOS were slightly increased in the major resection cohort. There was one mortality (1%) overall. These results are equivalent to, or better than, those from our contemporary series of resections performed with ultrasonic dissection. Conclusion. Water-jet dissection minimizes large blood volume loss, requirements for transfusion, and complications. This initial experience suggests that this precision tool is safe and effective for hepatic division, and compares favorably to other established methods for hepatic parenchymal transection. PMID:18333091

Dixon, Elijah; Sahajpal, Ajay; Cattral, Mark S.; Grant, David R.; Gallinger, Steven; Taylor, Bryce R.; Greig, Paul D.

2006-01-01

369

The Institute of Surgery and Innovation Trunk Flap Dissection Course.  

PubMed

The Institute of Surgery and Innovation Trunk Flap Dissection Course is a biannual two day course, which covers dissection of flaps in the anterior and posterior trunk on fresh-frozen cadavers. The event is run by the Institute of Surgery and Innovation, and it was held for the first time in November 2013, at the Nottingham City Hospital Training Centre. The course was taught in English by senior faculty from the Department of Plastic Surgery of Nottingham University.The first day was dedicated to raising 8 flaps in the anterior chest and abdomen, while the second day was dedicated to 6 flaps in the posterior trunk and buttocks.There were 3 participants per dissection table and the faculty to participant ratio was 2:1, allowing close supervision and one-on-one teaching. Each flap was briefly introduced by a 10-minute presentation, followed by a live demonstration of how to raise the flap by one of the faculty. The main advantage of this course is that the focus is on practical dissection, rather than lectures. The presentations that were given had a very personal feel, describing real cases encountered in the faculty's previous experience. This served as a platform to discuss dissection tips, tricks, and common pitfalls. Flaps represent the basis of reconstructive surgery; however, they are often taught late in the professional course of a residency as they are technically challenging. This course offers the opportunity to practice skills and receive very comprehensive feedback from experienced faculty.The event is open to trainees of all levels, and it attracted very junior as well as senior trainees from across Europe, thus offering an international prospective.The course's affordability is a luring feature and the excellent content and quality of teaching makes it a highly valuable experience, which I would widely recommend to trainees of all levels. PMID:25003434

Rossi, Sabrina Helena; Mestak, Ondrej; Stampolidis, Nektarios; Vasconcelos, Inês

2014-07-01

370

Possible extracardiac predictors of aortic dissection in Marfan syndrome  

PubMed Central

Background According to previous studies, aortic diameter alone seems to be insufficient to predict the event of aortic dissection in Marfan syndrome (MFS). Determining the optimal schedule for preventive aortic root replacement (ARR) aortic growth rate is of importance, as well as family history, however, none of them appear to be decisive. Thus, the aim of this study was to search for potential predictors of aortic dissection in MFS. Methods A Marfan Biobank consisting of 79 MFS patients was established. Thirty-nine MFS patients who underwent ARR were assigned into three groups based on the indication for surgery (dissection, annuloaortic ectasia and prophylactic surgery). The prophylactic surgery group was excluded from the study. Transforming growth factor-? (TGF-?) serum levels were measured by ELISA, relative expression of c-Fos, matrix metalloproteinase 3 and 9 (MMP-3 and ?9) were assessed by RT-PCR. Clinical parameters, including anthropometric variables - based on the original Ghent criteria were also analyzed. Results Among patients with aortic dissection, TGF-? serum level was elevated (43.78?±?6.51 vs. 31.64?±?4.99 ng/l, p?dissection in MFS. Based on these findings a new classification of MFS, that is benign or malignant is also proposed, which could be taken into consideration in determining the timing of prophylactic ARR. PMID:24720641

2014-01-01

371

Traumatic vertebral artery dissection in an adult with brachial plexus injury and cervical spinal fractures.  

PubMed

We present a case of a 32 year-old right-hand dominant woman who sustained a right brachial plexus injury, ipsilateral fractures of the cervical spine transverse processes, and vertebral artery dissection. She presented to us four days following the initiating accident. Magnetic Resonance Imaging showed normal brachial plexus along with vertebral artery dissection with intramural thrombus and vascular lumen occlusion. The dissection was managed conservatively. A repeat CAT-SCAN Angiography three months later showed healing of the dissection plus vascular lumen re-canalization. There were no sequelae due to the dissection. The details of the case are discussed in this report. PMID:17822530

Motsitsi, Silas N S; Steyn, Rian R

2007-01-01

372

Secondary science classroom dissections: Informing policy by evaluating cognitive outcomes and exploring affective outcomes  

NASA Astrophysics Data System (ADS)

Animal protection organizations claim that dissection is pedagogically unsound and that it will cause students to lose respect for non-human animals. Science teacher organizations support curricula that teach respect for animal life and include dissection. Prior research compared dissection to dissection alternatives. Four of the six studies revealed no difference between groups on tests of cognitive outcomes. One study revealed that dissection was superior, and one revealed that the alternative was superior. No differences in attitudes toward science, dissection or school were found. Attitudes toward non-human animals were not measured. This study focused on the dissections of earthworms and frogs in middle and high school classrooms. Pre and post-tests of conceptual understanding revealed failing scores and no significant pre/post differences. Because these tests required critical thinking skills, and the dissection activities did not, it is difficult to determine if the poor performance on these tests indicates the inability of the students to think critically, and/or if it indicates the ineffectiveness of dissection. Further studies of dissections that focus on critical thinking would be necessary to make this distinction. Classroom observations, student written narratives, and student and adult interviews revealed mixed attitudes toward non-human animals. Student behaviors during dissection were similar to those behaviors exhibited during non-dissection activities. Most students and adults readily supported worm dissections while they expressed some trepidation about frog dissections. Students and adults universally expressed affection for their pets and opposed the use of their own pets for dissection/research. There was slight support for the use of dogs and cats for dissection/research, but only those students who expressed hate for cats said that they could dissect cats. None of the students or adults expressed a willingness to dissect dogs. Some students abandoned plans for life science careers because they did not want to do further dissections. Students and adults often expressed confliction about the use of animals for food and/or research. Students and adults employed psychological mechanisms including dissociation, conflict reduction and viewing animals as an "outgroup" to rationalize their support for the use of animals for food, dissection and research.

Allspaw, Kathleen M.

373

Facile synthesis of Fe3O4@mesoporous TiO2 microspheres for selective enrichment of phosphopeptides for phosphoproteomics analysis.  

PubMed

Protein phosphorylation is one of the most important post-translational modifications. Due to the dynamic nature and low stoichiometry of the protein phosphorylation, enrichment of phosphopeptides from proteolytic mixtures is necessary prior to their characterization by mass spectrometry. In this work, we synthesized Fe3O4@mesoporous TiO2 magnetic microspheres with core-shell structure and large surface area for selective enrichment of phosphopeptides. To demonstrate its ability for selective enrichment of phosphopeptides, we applied Fe3O4@mesoporous TiO2 magnetic microspheres to isolation and enrichment of the phosphopeptides from tryptic digestion of standard proteins and real samples, and then the enriched peptides were analyzed by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) or liquid chromatography coupled to electrospray ionization mass spectrometry (LC-ESI-MS). Due to that the as-made Fe3O4@mesoporous TiO2 microspheres have large surface area, good dispersivity and biocompatibility, they have been demonstrated as a powerful tool for phosphoproteomics research. PMID:23597982

Lu, Jin; Wang, Mengyi; Deng, Chunhui; Zhang, Xiangmin

2013-02-15

374

Sequential enrichment with titania-coated magnetic mesoporous hollow silica microspheres and zirconium arsenate-modified magnetic nanoparticles for the study of phosphoproteome of HL60 cells.  

PubMed

As one of the most important types of post-translational modifications, reversible phosphorylation of proteins plays crucial roles in a large number of biological processes. However, owing to the relatively low abundance and dynamic nature of phosphorylation and the presence of the unphosphorylated peptides in large excess, phosphopeptide enrichment is indispensable in large-scale phosphoproteomic analysis. Metal oxides including titanium dioxide have become prominent affinity materials to enrich phosphopeptides prior to their analysis using liquid chromatography-mass spectrometry (LC-MS). In the current study, we established a novel strategy, which encompassed strong cation exchange chromatography, sequential enrichment of phosphopeptides using titania-coated magnetic mesoporous hollow silica microspheres (TiO2/MHMSS) and zirconium arsenate-modified magnetic nanoparticles (ZrAs-Fe3O4@SiO2), and LC-MS/MS analysis, for the proteome-wide identification of phosphosites of proteins in HL60 cells. In total, we were able to identify 11,579 unique phosphorylation sites in 3432 unique proteins. Additionally, our results suggested that TiO2/MHMSS and ZrAs-Fe3O4@SiO2 are complementary in phosphopeptide enrichment, where the two types of materials displayed preferential binding of peptides carrying multiple and single phosphorylation sites, respectively. PMID:25262027

Yu, Qiong-Wei; Li, Xiao-Shui; Xiao, Yongsheng; Guo, Lei; Zhang, Fan; Cai, Qian; Feng, Yu-Qi; Yuan, Bi-Feng; Wang, Yinsheng

2014-10-24

375

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

PubMed

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

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

2014-03-01

376

Quantitative analysis of signaling networks across differentially embedded tumors highlights interpatient heterogeneity in human glioblastoma.  

PubMed

Glioblastoma multiforme (GBM) is the most aggressive malignant primary brain tumor, with a dismal mean survival even with the current standard of care. Although in vitro cell systems can provide mechanistic insight into the regulatory networks governing GBM cell proliferation and migration, clinical samples provide a more physiologically relevant view of oncogenic signaling networks. However, clinical samples are not widely available and may be embedded for histopathologic analysis. With the goal of accurately identifying activated signaling networks in GBM tumor samples, we investigated the impact of embedding in optimal cutting temperature (OCT) compound followed by flash freezing in LN2 vs immediate flash freezing (iFF) in LN2 on protein expression and phosphorylation-mediated signaling networks. Quantitative proteomic and phosphoproteomic analysis of 8 pairs of tumor specimens revealed minimal impact of the different sample processing strategies and highlighted the large interpatient heterogeneity present in these tumors. Correlation analyses of the differentially processed tumor sections identified activated signaling networks present in selected tumors and revealed the differential expression of transcription, translation, and degradation associated proteins. This study demonstrates the capability of quantitative mass spectrometry for identification of in vivo oncogenic signaling networks from human tumor specimens that were either OCT-embedded or immediately flash-frozen. PMID:24927040

Johnson, Hannah; White, Forest M

2014-11-01

377

Proteomic and phosphoproteomic analysis of cellular responses in medaka fish (Oryzias latipes) following oral gavage with microcystin-LR.  

PubMed

Chronic and subchronic toxicity resulting from exposure to microcystins (MCs) receives increasing attention due to the risk of bioaccumulation of these toxins by aquatic animals, including fish. The mechanisms of action of MCs that target the liver, involve modifications of protein phosphorylation resulting from phosphatases 1 and 2A inhibition. Therefore, studying phosphoprotein modifications by using a specific phosphoprotein stain Pro-Q Diamond in fish liver contaminated with MC-leucine-arginine (MC-LR), the most toxic MC, should help dissecting disturbed signaling and metabolic networks. We have recently used this technology to identify several proteins that are modulated either in expression or phosphorylation in the liver of medaka following short-term exposure to MC-LR by balneation. In the present study, we have decided to use an alternative way of introducing the toxin into fish; that is by gavage (force-feeding). This was first achieved using tritiated MC-LR and allowed us to quantify the quantity of toxin incorporated into fish and to demonstrate that the toxin is mainly accumulated in liver. Afterwards a proteomics study limited to liver cytosolic proteins of contaminated animals showed that several proteins were up or down regulated either in quantity or in phosphorylation or both. Some of them had been previously detected as modified in balneation experiments but new molecules were identified as involved in signal transduction pathways activated by the toxin. In addition, in the conditions used (5 microg toxin/g body weight) anatomopathological studies supported a process of apoptonecrosis established after 24h, which was suggested to proceed by the evolution of some of the proteins after 2h contamination. PMID:18471846

Mezhoud, K; Bauchet, A L; Château-Joubert, S; Praseuth, D; Marie, A; François, J C; Fontaine, J J; Jaeg, J P; Cravedi, J P; Puiseux-Dao, S; Edery, M

2008-06-15

378

Management of Acute Aortic Syndrome and Chronic Aortic Dissection  

SciTech Connect

Acute aortic syndrome (AAS) describes several life-threatening aortic pathologies. These include intramural hematoma, penetrating aortic ulcer, and acute aortic dissection (AAD). Advances in both imaging and endovascular treatment have led to an increase in diagnosis and improved management of these often catastrophic pathologies. Patients, who were previously consigned to medical management or high-risk open surgical repair, can now be offered minimally invasive solutions with reduced morbidity and mortality. Information from the International Registry of Acute Aortic Dissection (IRAD) database demonstrates how in selected patients with complicated AAD the 30-day mortality from open surgery is 17% and endovascular stenting is 6%. Despite these improvements in perioperative deaths, the risks of stroke and paraplegia remain with endovascular treatment (combined outcome risk 4%). The pathophysiology of each aspect of AAS is described. The best imaging techniques and the evolving role of endovascular techniques in the definitive management of AAS are discussed incorporating strategies to reduce perioperative morbidity.

Nordon, Ian M., E-mail: inordon@sgul.ac.uk; Hinchliffe, Robert J.; Loftus, Ian M.; Morgan, Robert A.; Thompson, Matt M. [St George's Hospital, St. George's Vascular Institute, St. James' Wing (United Kingdom)

2011-10-15

379

Description, dissection, and subsampling of Apollo 14 core sample 14230  

NASA Technical Reports Server (NTRS)

Core sample 14230, collected at Triplet Crater near the Fra Mauro landing site of the Apollo 14 mission, was dissected in greater detail than any previous core. Sediment from the actual lunar surface was missing, and 6.7 grams of sediment were removed from the base of the core for a portion of the biotest prime sample. Upper and lower portions of the original 70.7-gram core (12.5 centimeters long) were fractured excessively but not mixed stratigraphically. Three major morphologic units and 11 subdivisions were recognized. Dissection provided 55 subsamples in addition to three others made by removing longitudinal sections of the core impregnated with n-butyl methacrylate for use as a permanent documentary record and for studies requiring particles of known orientation.

Fryxell, R.; Heiken, G.

1971-01-01

380

A novel ultrasonic micro-dissection technique for biomedicine.  

PubMed

Molecular techniques are transforming our understanding of cellular function and disease. However, accurate molecular analysis methods will be limited if the input DNA, RNA, or protein is not derived from pure population of cells or is contaminated by the wrong cells. A novel Ultrasonic Vibration Micro-dissection (UVM) method was proposed to procure pure population of targeted cells from tissue sections for subsequent analysis. The principle of the ultrasonic vibration cutting is analyzed, and a novel micro-tool is designed. A multilayer piezoelectric actuator is used to actuate a sharp needle vibrating with high frequency and low amplitude (approx. 16-50 kHz, and 0-3 microm) to cut the tissue. Contrast experiment was done to test the feasibility of UVM method. Experimental results show that the embedded tissue can be quickly and precisely cut with the ultrasonic vibration micro-dissection method. PMID:16844160

Sun, Lining; Wang, Huixiang; Chen, Liguo; Liu, Yaxin

2006-12-22

381

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

Microsoft Academic Search

Traumatic cerebral dissections are rare but potentially dangerous conditions that through improved diagnostics have recently\\u000a gained increased interest. However, there is still a significant lack of knowledge on the natural history, as well as on the\\u000a best treatment options. Most of the literature on this topic consists of case reports and retrospective studies with no prospective\\u000a randomized controlled studies. In

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

382

Spontaneous multivessel coronary artery dissection with anomalous coronary artery  

PubMed Central

Spontaneous coronary artery dissection (SCAD) is one of the rare causes of acute coronary syndrome in young healthy individuals especially women without having any conventional risk factors for coronary artery disease. We describe a case of 34-year-old healthy man with diffuse multiple SCADs who presented with acute coronary syndrome and was managed conservatively with an uneventful course on long-term follow-up. PMID:23595252

Mahadevappa, Nagesh; Singh, Bhupinder; Bhairappa, Shivakumar; Nanjappa, Manjunath

2013-01-01

383

Coronary angiogram classification of spontaneous coronary artery dissection.  

PubMed

Spontaneous coronary artery dissection (SCAD) is under-diagnosed and the true prevalence is underestimated. Unfortunately, SCAD is frequently missed on coronary angiogram since the arterial wall is not imaged with this test. Optical coherence tomography or intravascular ultrasound should be the true gold-standard to diagnose SCAD. Given the elusive angiographic diagnosis of SCAD and the lack of familiarity with angiographic variants of SCAD, a diagnostic algorithm and angiographic classification for SCAD is proposed in this article. PMID:24227590

Saw, Jacqueline

2014-12-01

384

Acute aortic dissection type A discloses Corpus alienum  

PubMed Central

We report an unusual case of an aortic type A dissection with a corpus alienum which compresses the right ventricle. The patient successfully underwent an aortic root replacement in deep hypothermia with re-implantation of the coronary arteries using a modified Bentall procedure and the resection of the corpus alienum. Intraoperative finding reveals 3 greatly adhered gauze compresses, which were most likely forgotten in the operation 34 years ago. PMID:19121214

Popov, Aron Frederik; Baryalei, Mersa Mohammed; Schmitto, Jan Dieter; Hinz, Jose; Wiese, Christoph Hermann; Raab, Björn; Kolat, Philipp; Schoendube, Friedrich Albert; Seipelt, Ralf

2009-01-01

385

Chronic type A dissection in a pulmonary autograft.  

PubMed

A 37-year-old patient presented with severe aortic valve insufficiency due to massive dilatation of the neo-aortic root (77 mm diameter) 14 years after a Ross procedure. Intraoperatively, the dilatation appeared to be caused by a localized chronic dissection of the pulmonary autograft. Surgery consisted of a modified Bentall procedure with a mechanical composite valve, with an uncomplicated postoperative course. PMID:17484466

Kaya, Abdullah; Heijmen, Robin H; Vreuls, Willem; Seldenrijk, Cornelis A; Schepens, Marc A

2007-03-01

386

Stanford type A acute dissection developing acute myocardial infarction  

Microsoft Academic Search

A 75-year-old female, exhibiting epigastric pain and vomiting, underwent treatment for acute gastritis. She also experienced\\u000a incontinence of urine and chest pain. A diagnosis of acute myocardial infarction was made upon examination of electrocardiographic\\u000a findings and the patient was transferred to our hospital. Diffuse infarction of the left ventricle and acute aortic dissection\\u000a (Stanford type A) were diagnosed by electrocardiographic

Norifumi Ohtani; Keiko Kiyokawa; Hidenori Asada; Toshiaki Kawakami

2000-01-01

387

Science Sampler: Frog dissection--An alternative model  

NSDL National Science Digital Library

Local dollar stores can be a treasure-trove of inexpensive items that are ideal for hands-on activities in the science classroom. This article describes one such activity in which a model frog that costs less than a dollar was used to allow students to perform a simulated dissection. It was designed as a teacher-directed activity in order for students to practice reading, following complex directions, and using critical-thinking skills.

June Sanders

2007-02-01

388

Spontaneous Coronary Artery Dissection: Once is Never Enough.  

PubMed

Spontaneous Coronary Artery Dissection (SCAD) is a rare and potentially life threatening cause of Acute Coronary Syndrome. Recurrence of SCAD in patients, other than peripartum women, has been discussed infrequently in the literature. We report a case of patient who suffered recurrent SCAD in different coronary arteries. Her history was significant for a likely SCAD five years earlier. We briefly review the literature on SCAD and its recurrence. PMID:25529838

Majeed, K; Glenie, T J

2015-04-01

389

SLE 1, 2, 3…Genetic Dissection of Lupus  

Microsoft Academic Search

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

Jiankun Zhu; Chandra Mohan

390

Endovascular Treatment of Iatrogenic and Traumatic Carotid Artery Dissection  

SciTech Connect

This paper reports on the early and midterm results of endovascular treatment of acute carotid artery dissections, its specific problems, and its limitations. We encountered seven patients with symptomatic extracranial carotid artery dissection, three cases of which occurred after carotid endarterectomy, two after carotid angioplasty and stenting, and two after trauma. Balloon-expandable and self-expanding stents were placed using a transfemoral approach. Success in restoring the carotid lumen was achieved in all patients. No procedure-related complications occurred. All patients experienced significant clinical improvement while in the hospital and achieved complete long-term recovery. At follow-up (mean, 22.4 months), good luminal patency of the stented segments was observed. In conclusion, in this small series, primary stent-supported angioplasty seems to be a safe and effective strategy in the treatment of selected patients having acute traumatic extracranial carotid artery dissection, with excellent early and midterm results. Larger series and longer-term follow-up are required before definitive recommendations can be made.

Schulte, Stefan; Donas, Konstantinos P., E-mail: k.donas@gmx.at; Pitoulias, Georgios A.; Horsch, Svante [Hospital Porz am Rhein, Academic Teaching Hospital of the University of Cologne, Department of Vascular Surgery (Germany)

2008-09-15

391

Are All Hands-On Activities Equally Effective? Effect of Using Plastic Models, Organ Dissections, and Virtual Dissections on Student Learning and Perceptions  

ERIC Educational Resources Information Center

This study investigated the impact of three commonly used cardiovascular model-assisted activities on student learning and student attitudes and perspectives about science. College students enrolled in a Human Anatomy and Physiology course were randomly assigned to one of three experimental groups (organ dissections, virtual dissections, or…

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

2014-01-01

392

Dissection as Inquiry: Using the "Peanut Observation" Activity to Promote a Revised Paradigm of Dissection and Facilitate Student Involvement and Understanding.  

ERIC Educational Resources Information Center

Introduces the peanut observation activity to teach about the pros and cons of dissection. As an inquiry-based approach, dissection is one way to teach process skills. Lists the progression of the activity as observation, questioning and finding the answer, challenge, discussion, and further examination. (Contains 12 references.) (YDS)

Bernstein, Penny L.

2000-01-01

393

Use of multimedia technology to provide solutions to existing curriculum problems: Virtual frog dissection  

NASA Astrophysics Data System (ADS)

The objective of this research was to determine whether currently available multimedia technology can resolve existing problems in the K--12 science curriculum. There are several practical and ethical problems relating to the classroom use of animal dissection and this led to the selection of hands-on frog dissection as the curriculum activity where the use of multimedia was investigated. The major finding was that multimedia-based virtual dissection was more effective than hands-on dissection in helping students learn about frog anatomy. Moreover, this result was achieved when the time available for the virtual dissection was approximately 44% less than that available for hands-on dissection. Examination of possible relationships between student characteristics and achievement revealed that students' attitudes to educational uses of animal dissection and their computer experience were positively correlated with their achievement scores. No relationships were found between either student gender or dissection experience and achievement test outcomes. Students rated virtual dissection as the easier of the two types of dissection, though they gave equivalent ratings for their enjoyment of virtual and hands-on dissection. Despite favorable feedback on the virtual dissection, a significant majority of students stated that they felt they would be "missing-out" on a valuable experience if they were not given the opportunity to perform a hands-on frog dissection. Comparing how students spent their time during each type of dissection showed that students spent a significantly larger proportion of their time On-Task when using the multimedia-based virtual dissection. In particular, the average increase in the proportion of time spent on activities directly related to the subject matter was over 36%. Time spent On-Task had a significant positive relationship with achievement for hands-on dissection. It may play a similar role for achievement with virtual dissection, but the small deviation in time On-Task data for virtual dissection prevented confirming this intuition. The teacher who participated in the research found that the use of a multimedia, inquiry-based computer application did limit his insight into students' classroom progress. However, he did not feel this to be a problem, nor did it in any way reduce his control over class activities.

Youngblut, Christine

394

The extent of lateral lymph node dissection in differentiated thyroid cancer in the N+ neck.  

PubMed

The management of the lateral neck in metastatic differentiated thyroid cancer (DTC) varies widely. Most groups advocate dissection of nodal levels II-IV but many perform a more extensive dissection. We aimed to asses whether there was any evidence for a modified radical neck dissection over a selective neck dissection by looking at the extent to which DTC metastases to levels I and V. We performed a review of the current literature including adult and paediatric patients who underwent a lateral neck dissection for metastatic DTC. The primary endpoint was histological confirmation of metastases in nodal levels I and V. 650 abstracts were identified and reviewed. 23 papers were included in the study. The incidence of level V metastases during routine level V dissection in patients with DTC is 20 % and the incidence of level I metastases during routine level I dissection in patients with DTC is 8 %. Histologically proven metastases were found in 22.5 % of level V neck dissection of which 2.5 % were pre-operatively suspected of metastases. 20 % had histologically proven metastases to level I of which 12 % were pre-operatively suspected of metastases. Our study has shown a 20 % incidence of level V metastases in the N+ neck suggesting that level V should be part of a planned neck dissection. Evidence is lacking for routine dissection of level I. A future prospective study is required to asses the question of risk factors for lateral nodal metastases, recurrence and survival. PMID:23519682

Kumar, S; Burgess, C; Moorthy, R

2013-11-01

395

Combined Pulsed-Q dissociation and electron transfer dissociation for identification and quantitation of iTRAQ–labeled phosphopeptides  

SciTech Connect

Multiplex isobaric tags for relative and absolute quantification (iTRAQ) enable high-throughput quantification of peptides via reporter ion signals in the low mass range of tandem mass spectra. A challenging but highly promising application is to analyze iTRAQ-labeled peptides using a sensitive linear ion trap mass spectrometer (LTQ-MS) and pulsed Q dissociation (PQD), a form of ion trap collision activated dissociation (CAD) designed to allow detection of low mass-to-charge fragment ions. Electron dissociation transfer (ETD), on the other hand, is complementary to PQD and is especially useful for sequencing peptides containing post-translational modifications (PTMs). Here, we developed an integrated workflow for robust and accurate quantitative identification of iTRAQ labeled phosphopeptides that integrates the PQD and ETD fragmentation methods together with PQD optimization, data management and bioinformatics tools. Analysis of the phosphoproteome of human fibroblast cells demonstrated that this hybrid mode is superior to either PQD or ETD alone for phosphopeptide identification and quantitation. The combined PQD/ETD approach can qualitatively identify additional phosphopeptides than ETD alone and PQD information can provide better quantitation of ETD identified iTRAQ-labeled phosphopeptides.

Yang, Feng; Wu, Si; Stenoien, David L.; Zhao, Rui; Monroe, Matthew E.; Gritsenko, Marina A.; Purvine, Samuel O.; Polpitiya, Ashoka D.; Tolic, Nikola; Zhang, Qibin; Norbeck, Angela D.; Orton, Daniel J.; Moore, Ronald J.; Tang, Keqi; Anderson, Gordon A.; Pasa-Tolic, Ljiljana; Camp, David G.; Smith, Richard D.

2009-05-15

396

Phosphoproteome and proteome analyses reveal low-phosphate mediated plasticity of root developmental and metabolic regulation in maize (Zea mays L.).  

PubMed

Phosphate (Pi) deficiency has become a significant challenge to worldwide agriculture due to the depletion of accessible rock phosphate that is the major source of cheap Pi fertilizers. Previous research has identified a number of diverse adaptive responses to Pi starvation in the roots of higher plants. In this study, we found that accelerated axile root elongation of Pi-deprived maize plants resulted from enhanced cell proliferation. Comparative phosphoproteome and proteome profiles of maize axile roots were conducted in four stages in response to Pi deficiency by multiplex staining of high-resolution two dimensional gel separated proteins. Pro-Q DPS stained gels revealed that 6% of phosphoprotein spots displayed changes in phosphorylation state following low-Pi treatment. These proteins were involved in a large number of metabolic and cellular pathways including carbon metabolism and signal transduction. Changes in protein abundance of a number of enzymes indicated that low-Pi induced a number of carbon flux modifications in metabolic processes including sucrose breakdown and other downstream sugar metabolic pathways. A few key metabolic enzymes, including sucrose synthase (EC 2.4.1.13) and malate dehydrogenase (EC 1.1.1.37), and several signaling components involved in protein kinase or phosphatase cascades, auxin signaling and 14-3-3 proteins displayed low-Pi responsive changes in phosphorylation state or protein abundance. A variety of key enzymes and signaling components identified as potential targets for phosphorylation provide novel clues for comprehensive understanding of Pi regulation in plants. Protein phosphorylation, coordinating with changes in protein abundance, is required for maize root metabolic regulation and developmental acclimation to Pi starvation. PMID:25190054

Li, Kunpeng; Xu, Changzheng; Fan, Wenming; Zhang, Hongli; Hou, Jiajia; Yang, Aifang; Zhang, Kewei

2014-10-01

397

Large airway obstruction by a chronic dissecting aortic aneurysm in the Marfan syndrome.  

PubMed Central

We describe a patient with the Marfan syndrome who presented with an acute aortic dissection. She underwent composite graft replacement of the aortic root. She returned two years later with dyspnoea and stridor due to tracheal compression by a large chronic dissection of the thoracic aorta. Marfan patients are at risk of chronic dissection involving the remaining distal aorta and require regular noninvasive assessment following surgery. Images Figure 1 PMID:9519188

Hargreaves, M. R.; Gilbert, T. J.; Pillai, R.; Hart, G.

1997-01-01

398

Acute Myocardial Infarction Due to Spontaneous Dissection of the Right Coronary Artery in a Young Male  

SciTech Connect

Spontaneous coronary artery dissection is a rare cause of acute myocardial infarction. We report a case of a 33-year-old male who presented with an acute inferior myocardial infarction. Coronary arteriography performed 3 hours after the episode revealed a dissection involving the middle segment of right coronary artery. Because of a spiral form of dissection and the TIMI 3 flow grade, our patient was treated medically and repeat coronary angiography 6 months later was decided.

Papadopoulos, Dimitris P., E-mail: jimpapdoc@yahoo.com; Moyssakis, Ioannis; Perakis, Alexandros; Athanasiou, Andreas [Department of Cardiology (Greece); Anagnostopoulou, Sophia [University of Athens Medical School, Department of Anatomy (Greece); Benos, Ioannis; Votteas, Vassilios E. [Department of Cardiology (Greece)

2004-09-15

399

Transcervical videoscopic esophageal dissection during two-field minimally invasive esophagectomy: early patient experience  

Microsoft Academic Search

Background  Transhiatal (two-field) esophagectomy reduces cardiopulmonary complications by avoiding thoracic access, but requires blind\\u000a mediastinal dissection. The authors developed a minimally invasive esophagectomy (MIE) technique applying single-incision\\u000a laparoscopy technology to better visualize the thoracic esophageal dissection. This is performed using laparoscopy and simultaneous\\u000a transcervical videoscopic esophageal dissection (TVED). Our aim is to demonstrate feasibility of two-field MIE with TVED and\\u000a improve

Michael Parker; Steven P. Bowers; Ross F. Goldberg; Jason M. Pfluke; John A. Stauffer; Horacio J. Asbun; C. Daniel Smith

400

Successful angioplasty of three cases of coronary artery dissections using hydrophilic wires.  

PubMed

Three cases of successful angioplasty of high-grade coronary dissections using hydrophilic wires were reported. Our first case had edge dissection after a stent deployed in the left anterior descending artery, after which we found it impossible to track the second stent over the regular wires, and which was successful when we tried with a stiffer hydrophilic wire. The second had spontaneous coronary artery dissections (SCAD), and the third case was a complicated plaque with multiple stenotic and ectatic segments along with dissection and successful angioplasty carried out using the same wires and without additional hardware. These wires also provided adequate support in tracking the required balloons and stents. PMID:25489325

Prashant Ponangi, Udaya; Menon, Rajeev; Kapadia, Anuj

2014-01-01

401

Cell-type Specific Optogenetic Mice for Dissecting Neural Circuitry Function  

E-print Network

Optogenetic methods have emerged as powerful tools for dissecting neural circuit connectivity, function, and dysfunction. We used a Bacterial Artificial Chromosome (BAC) transgenic strategy to express Channelrhodopsin2 ...

Zhao, Shengli

402

Application of blunt dissection in ESD of a gastric submucosal tumor  

PubMed Central

We performed endoscopic submucosal dissection of a gastric fundus tumor. It was difficult to strip the tumor completely due to space limitation, and we used blunt dissection to remove the tumor quickly and safely. Firstly, the basal area of the 2.5 cm submucosal tumor located in the gastric fundus was cut open, and the mucosa was dissected. The tumor was difficult to peel, therefore, a snare was used and the tumor was pulled and tightened slightly. Short electronic coagulation was used during the procedure. The tumor was then bluntly dissected. This method ensured rapid and complete removal of the tumor. PMID:24914398

Wen, Zong-Quan; Wu, Guang-Yao; Yu, Shao-Ping; Lin, Xiao-Dong; Li, Song-Hu; Huang, Xian-Guang; Zhang, Fu; Zeng, Xiao-Yu; Huang, Hai-Yan; Li, Ai-Mei

2014-01-01

403

Intravascular ultrasound detected classification of coronary lesions as a predictor of dissections after balloon angioplasty.  

PubMed

Dissection after balloon angioplasty of coronary arteries may give rise to an unfavourable early outcome. Compared with coronary angiography, intravascular ultrasound (IVUS) allows more detailed characterisation of dissections. We investigated the incidence and type of dissections after balloon angioplasty in calcified coronary lesions. IVUS was performed in 43 patients with 48 lesions before and after percutaneous balloon angioplasty. Significant calcification was defined as an arc of more than 90 degrees with typical acoustic shadowing. Dissections were classified as type A when the media was not involved by the dissection and as type B when media involvement had occurred. In the group with significant calcification dissection was observed in 79% of the cases vs 38% in the control group (p < 0.03). Type B dissection was present in 71% of the dissections in the calcified lesions vs. 15% in the control group (p < 0.02). The balloon diameter and the ratio of balloon area to vessel area was not different in both groups but the required pressure for the first complete balloon inflation was significantly greater in the group with calcified lesions (9.46 +/- 3.6 atm vs. 6.65 +/- 2.6 atm; p < 0.001). Thus balloon angioplasty in calcified coronary lesions is more likely to lead to dissection with frequency involve the media. PMID:8915718

Voigtländer, T; Rupprecht, H J; Scharhag, J; Kearney, P; Nowak, B; Stähr, P; Brennecke, R; Meyer, J

1996-09-01

404

Spontaneous resolution of isolated dissecting aneurysm on the posterior inferior cerebellar artery.  

PubMed

The authors report a rare example of an isolated dissecting posterior inferior cerebellar artery (PICA) aneurysm with spontaneous resolution. A 41 year-old male suffered sudden dizziness, nausea and vomiting. An angiogram and magnetic resonance imaging (MRI) detected an isolated PICA dissection. The patient was treated conservatively and recovered without any apparent neurological deficit. MRI detected the self-resolution of the dissecting aneurysm. Dissecting PICA aneurysms, especially non-haemorrhagic lesions, have the possibility of spontaneous resolution resulting in a favorable outcome. The treatment strategy for this vascular lesion may be decided based upon neuroradiological changes on careful follow-up. PMID:18058059

Korematsu, K; Yoshioka, S; Abe, E; Nagai, Y; Kai, Y; Morioka, M; Kuratsu, J

2008-01-01

405

Successful angioplasty of three cases of coronary artery dissections using hydrophilic wires  

PubMed Central

Three cases of successful angioplasty of high-grade coronary dissections using hydrophilic wires were reported. Our first case had edge dissection after a stent deployed in the left anterior descending artery, after which we found it impossible to track the second stent over the regular wires, and which was successful when we tried with a stiffer hydrophilic wire. The second had spontaneous coronary artery dissections (SCAD), and the third case was a complicated plaque with multiple stenotic and ectatic segments along with dissection and successful angioplasty carried out using the same wires and without additional hardware. These wires also provided adequate support in tracking the required balloons and stents PMID:25489325

Menon, Rajeev; Kapadia, Anuj

2014-01-01

406

Multidetector computed tomography angiography: Application in vertebral artery dissection  

PubMed Central

Background and Purpose: Multidetector computed tomography angiography (MDCTA) is a minimally invasive radiological technique providing high-resolution images of the arterial wall and angiographic images of the lumen. We studied the radiological features of vertebral artery dissection (VAD) in a consecutive series of patients investigated for acute stroke and subarachnoid hemorrhage (SAH) in order to confirm and define the diagnostic features of VAD on MDCTA. Patients and Methods: Review of patients identified prospectively over a 4-year period with VAD assessed by MDCTA was conducted. Radiological features of VAD on MDCTA were reanalyzed utilising previously reported criteria for VAD. Results: Thirty-five patients (25 males, mean age 49.6 years) with a total of 45 dissected vertebral arteries were reviewed. MDCTA features of VAD included increased wall thickness in 44/45 (97.7%) arteries and increased total vessel diameter in 42/45 arteries (93.3%). All dissected arteries had either lumen stenosis (21/45) or associated segmental occlusion (24/45). An intimal flap was detected in 6/45 (13.3 %) vessels. Twenty-five patients had follow-up imaging, 14/32 vessels returned to normal, 4 showed improvement in stenosis but did not return to normal and 14 demonstrated no change. The majority of non-occluded vessels became normal or displayed improved patency. Only 4/17 occluded arteries demonstrated re-establishment of flow. No adverse effects were recorded. Conclusions: MDCTA is a safe and reliable technique for the diagnosis of VAD. Increased wall thickness (97.7%) and increased vessel wall diameter (93.3%) were the most frequently observed features. PMID:21633613

Teasdale, Evelyn; Zampakis, Peter; Santosh, Celestine; Razvi, Saif

2011-01-01

407

Laparoscopic Myomectomy With Lateral Dissection of the Uterine Artery  

PubMed Central

Background: We assessed the results and impact of lateral uterine artery dissection on clinical outcome following laparoscopic myomectomy. Methods: We retrospectively analyzed the clinical data for 27 laparoscopic myomectomy cases (Group I) and 54 laparoscopic myomectomy cases combined with lateral uterine artery dissection (Group II) between January 2001 and August 2004 in one center. Only 81 patients who had dominant fibroids between 4 cm and 10 cm in diameter were included in the study. We assessed the clinical outcomes: perioperative blood loss, operating time, hospital stay, complications, hemoglobin decrease, inflammatory response, and tissue markers (C-reactive protein, white blood cells, creatinine kinase) changes. Results: The mean operating time was 70.37 minutes in group I and 78.61 minutes in group II. The mean length of hospital stay was 2.7 days versus 2.2 days, respectively (P>0.05). The difference in intraoperative blood loss was 70.1 mL (147.7 mL vs 77.3 mL, Group I) and 33.9 mL (105 mL vs 71.1 mL, Group II); estimated postoperative blood loss was statistically significant (P<0.001, P<0.05, respectively). Group 2 demonstrated a less intense stress response in C-reactive protein (P<0.001) and white blood cell count (P<0.05). Conclusion: The dissection of the uterine artery in laparoscopic myomectomy is a feasible operative procedure with a low rate of complications. The procedure reduced perioperative blood loss and resulted in significant improvement in fibroid-related symptoms. PMID:16381365

Jabor, Antonin; Lukac, Jan; Kliment, Lev; Urbanek, Stepan

2005-01-01

408

Rapid retraction of a post-infarction intramyocardial dissecting hematoma.  

PubMed

A 60-year-old male with a recent anterior myocardial infarction (MI) was referred to our hospital for implantable cardioverter defibrillator (ICD) implantation. He was on the 42nd day of MI and clinically stable on admission. Electrocardiography showed right bundle branch block with QS pattern on anterior leads. Transthoracic echocardiographic examination revealed an ejection fraction of 25% with akinesis of the apex and mid-apical segments of anterior and septal walls. In the apical-septal region, a pulsatile cavity with systolic expansion surrounded by a thin endomyocardial border was visualized. Color-Doppler interrogation did not demonstrate any flow within that structure. These findings suggested an intramyocardial dissecting hemorrhage formed after MI. Cardiac magnetic resonance imaging also confirmed an intramyocardial hematoma in the mid-apical anteroseptal region. A conservative approach was assumed as the patient was hemodynamically stable. The planned ICD implantation was postponed due to the high risk of perforation. Subsequently, oral anticoagulant therapy with warfarin was initiated against risk of intracardiac thrombus formation. The existing dual antiplatelet therapy was also continued. One week after hospital discharge, he was rehospitalized due to a very high INR of 6.3. The repeated transthoracic echocardiography revealed an almost complete resolution of the intramyocardial dissecting hematoma and adhesion of the surrounding myocardial layers. Oral anticoagulant therapy was discontinued. Echocardiographic examinations showed no change compared to the last examination during hospitalization. This case illustrates a conservatively managed intramyocardial dissecting hematoma case, in which anticoagulant and antiaggregant therapy yielded a rapid retraction without any complication. PMID:24899483

Özpelit, Ebru; Badak, Özer; Özpelit, Mehmet Emre; Kozan, Ömer

2014-06-01

409

Genetic Dissection of Learning and Memory in Mice  

PubMed Central

In this minireview, we discuss different strategies to dissect genetically the keystones of learning and memory. First, we broadly sketch the neurogenetic analysis of complex traits in mice. We then discuss two general strategies to find genes affecting learning and memory: candidate gene studies and whole genome searches. Next, we briefly review more recently developed techniques, such as microarrays and RNA interference. In addition, we focus on gene-environment interactions and endophenotypes. All sections are illustrated with examples from the learning and memory field, including a table summarizing the latest information about genes that have been shown to have effects on learning and memory. PMID:15656270

Mineur, Yann S.; Crusio, Wim E.; Sluyter, Frans

2004-01-01

410

Ruptured Valsalva Sinus Aneurysm to Pericardium Simulated Aortic Root Dissection  

PubMed Central

Ruptured valsalva sinus aneurysm to pericardium is a rare condition. Here, we described a case presented with tamponade. Initially, hemopericardium was partially drained and then, imaging evaluations were done. Transesophageal echocardiography showed limited dissection of aortic sinus and CT angiography of the ascending aorta showed deformed dilated right coronary sinus. Besides, surgery showed that windsock tract of the right coronary sinus had ruptured into the pericardium with avulsed right coronary aortic cusp. This case indicated a rare cause of cardiac tamponade and insufficiency of imaging modalities for making an accurate diagnosis. PMID:24936486

Davarpasand, Tahereh; Hosseinsabet, Ali; Abassi, Kumars; Arzhan, Sorya

2014-01-01

411

Characterization of residual stresses by WEDM-assisted dissectioning  

NASA Astrophysics Data System (ADS)

Within the scope of this contribution a wire electric discharge machining assisted dissectioning method is presented, which combines high precision cutting, minimum generation of additional residual stresses during the cutting process and high precision measurement of the resulting distortion. As an example a forged component made of the titanium alloy Ti6Al4V is investigated in a multiple cut procedure. A finite element based mechanical model for the estimation of the residual stress distribution in the component from the distortion data is introduced and discussed.

Regener, B.; Krempaszky, C.; Werner, E.; Berhuber, E.; Stockinger, M.

2010-06-01

412

Expression of matrix metalloproteinase-12 in aortic dissection  

PubMed Central

Background Aortic dissection(AD) is an acute process of large blood vessels characterized by dangerous pathogenic conditions and high disability and high mortality. The pathogenesis of AD remains debated. Matrix metalloproteinase-12 (MMP-12) participates in many pathological processes such as abdominal aortic aneurysm, atherosclerosis, emphysema and cancer. However, this elastase has rarely been assessed in the presence of AD. The aim of the present study was to investigate the expression of MMP-12 in aortic tissue so as to offer a better understanding of the possible mechanisms of AD. Methods The protein expression levels of MMP-12 were analyzed and compared in aorta tissue and the blood serum samples by reverse transcription polymerase chain reaction(RT-PCR), Western blotting, immuno-histochemistry, fluorescence resonance energy transfer ( FRET ) activity assay and enzyme-linked immuno sorbent assay ( ELISA ), respectively. Ascending aorta tissue specimens were obtained from 12 patients with an acute Stanford A-dissection at the time of aortic replacement, and from 4 patients with coronary artery disease (CAD) undergoing coronary artery bypass surgery. Meanwhile, serum samples were harvested from 15 patients with an acute Stanford A-dissection and 10 healthy individuals who served as the control group. Results MMP-12 activity could be detected in both AD and CAD groups, but the level in the AD group was higher than those in the CAD group (P < 0.05). MMP-12 proteolysis existed in both serum samples of the AD and healthy groups, and the activity level in the AD group was clearly higher than in the healthy group (P < 0.05). For AD patients, MMP-12 activity in serum was higher than in the aorta wall (P < 0.05). MMP-12 activity in the aortic wall tissue can be inhibited by MMP inhibitor v (P < 0.05). Conclusion The present study directly demonstrates that MMP-12 proteolytic activity exists within the aorta specimens and blood samples from aortic dissection patients. MMP-12 might be of potential relevance as a clinically diagnostic tool and therapeutic target in vascular injury and repair. PMID:23642232

2013-01-01

413

Genetic dissection of an elite rice hybrid revealed that heterozygotes are not always advantageous for performance.  

PubMed Central

We introduced an experimental design that produced an "immortalized F(2)" population allowing for complete dissection of genetic components underlying quantitative traits. Data for yield and three component traits of the immortalized F(2) were collected from replicated field trials over 2 years. Using 231 marker loci, we resolved the genetic effects into individual components and assessed relative performance of all the genotypes at both single- and two-locus levels. Single-locus analysis detected 40 QTL for the four traits. Dominance effects for about one-half of the QTL were negative, resulting in little "net" positive dominance effect. Correlation between genotype heterozygosity and trait performance was low. Large numbers of digenic interactions, including AA, AD, and DD, were detected for all the traits, with AA as the most prevalent interaction. Complementary two-locus homozygotes frequently performed the best among the nine genotypes of many two-locus combinations. While cumulative small advantages over two-locus combinations may partly explain the genetic basis of heterosis of the hybrid as double heterozygotes frequently demonstrated marginal advantages, double heterozygotes were never the best genotypes in any of the two-locus combinations. It was concluded that heterozygotes were not necessarily advantageous for trait performance even among genotypes derived from such a highly heterotic hybrid. PMID:12524357

Hua, J P; Xing, Y Z; Xu, C G; Sun, X L; Yu, S B; Zhang, Qifa

2002-01-01

414

Dissection of a Krox20 positive feedback loop driving cell fate choices in hindbrain patterning  

PubMed Central

Although feedback loops are essential in development, their molecular implementation and precise functions remain elusive. Using enhancer knockout in mice, we demonstrate that a direct, positive autoregulatory loop amplifies and maintains the expression of Krox20, a transcription factor governing vertebrate hindbrain segmentation. By combining quantitative data collected in the zebrafish with biophysical modelling that accounts for the intrinsic stochastic molecular dynamics, we dissect the loop at the molecular level. We find that it underpins a bistable switch that turns a transient input signal into cell fate commitment, as we observe in single cell analyses. The stochasticity of the activation process leads to a graded input–output response until saturation is reached. Consequently, the duration and strength of the input signal controls the size of the hindbrain segments by modulating the distribution between the two cell fates. Moreover, segment formation is buffered from severe variations in input level. Finally, the progressive extinction of Krox20 expression involves a destabilization of the loop by repressor molecules. These mechanisms are of general significance for cell type specification and tissue patterning. PMID:24061538

Bouchoucha, Yassine X; Reingruber, Jürgen; Labalette, Charlotte; Wassef, Michel A; Thierion, Elodie; Desmarquet-Trin Dinh, Carole; Holcman, David; Gilardi-Hebenstreit, Pascale; Charnay, Patrick

2013-01-01

415

Characterization and genetic dissection of resistance to spotted alfalfa aphid (Therioaphis trifolii) in Medicago truncatula  

PubMed Central

Aphids cause significant yield losses in agricultural crops worldwide. Medicago truncatula, a model legume, cultivated pasture species in Australia and close relative of alfalfa (Medicago sativa), was used to study the defence response against Therioaphis trifolii f. maculate [spotted alfalfa aphid (SAA)]. Aphid performance and plant damage were compared among three accessions. A20 is highly susceptible, A17 has moderate resistance, and Jester is strongly resistant. Subsequent analyses using A17 and A20, reciprocal F1s and an A17×A20 recombinant inbred line (RIL) population revealed that this moderate resistance is phloem mediated and involves antibiosis and tolerance but not antixenosis. Electrical penetration graph analysis also identified a novel waveform termed extended potential drop, which occurred following SAA infestation of M. truncatula. Genetic dissection using the RIL population revealed three quantitative trait loci on chromosomes 3, 6, and 7 involved in distinct modes of aphid defence including antibiosis and tolerance. An antibiosis locus resides on linkage group 3 (LG3) and is derived from A17, whereas a plant tolerance and antibiosis locus resides on LG6 and is derived from A20, which exhibits strong temporary tolerance. The loci identified reside in regions harbouring classical resistance genes, and introgression of these loci in current medic cultivars may help provide durable resistance to SAA, while elucidation of their molecular mechanisms may provide valuable insight into other aphid–plant interactions. PMID:24058162

Kamphuis, Lars G.; Lichtenzveig, Judith; Peng, Kefan; Guo, Su-Min; Klingler, John P.

2013-01-01

416

Virtual dissection and comparative connectivity of the superior longitudinal fasciculus in chimpanzees and humans.  

PubMed

Many of the behavioral capacities that distinguish humans from other primates rely on fronto-parietal circuits. The superior longitudinal fasciculus (SLF) is the primary white matter tract connecting lateral frontal with lateral parietal regions; it is distinct from the arcuate fasciculus, which interconnects the frontal and temporal lobes. Here we report a direct, quantitative comparison of SLF connectivity using virtual in vivo dissection of the SLF in chimpanzees and humans. SLF I, the superior-most branch of the SLF, showed similar patterns of connectivity between humans and chimpanzees, and was proportionally volumetrically larger in chimpanzees. SLF II, the middle branch, and SLF III, the inferior-most branch, showed species differences in frontal connectivity. In humans, SLF II showed greater connectivity with dorsolateral prefrontal cortex, whereas in chimps SLF II showed greater connectivity with the inferior frontal gyrus. SLF III was right-lateralized and proportionally volumetrically larger in humans, and human SLF III showed relatively reduced connectivity with dorsal premotor cortex and greater extension into the anterior inferior frontal gyrus, especially in the right hemisphere. These results have implications for the evolution of fronto-parietal functions including spatial attention to observed actions, social learning, and tool use, and are in line with previous research suggesting a unique role for the right anterior inferior frontal gyrus in the evolution of human fronto-parietal network architecture. PMID:25534109

Hecht, Erin E; Gutman, David A; Bradley, Bruce A; Preuss, Todd M; Stout, Dietrich

2015-03-01

417

Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences  

PubMed Central

The growing world population and shrinkage of arable land demand yield improvement of rice, one of the most important staple crops. To elucidate the genetic basis of yield and uncover its associated loci in rice, we resequenced the core recombinant inbred lines of Liang–You–Pei–Jiu, the widely cultivated super hybrid rice, and constructed a high-resolution linkage map. We detected 43 yield-associated quantitative trait loci, of which 20 are unique. Based on the high-density physical map, the genome sequences of paternal variety 93–11 and maternal cultivar PA64s of Liang–You–Pei–Jiu were significantly improved. The large recombinant inbred line population combined with plentiful high-quality single nucleotide polymorphisms and insertions/deletions between parental genomes allowed us to fine-map two quantitative trait loci, qSN8 and qSPB1, and to identify days to heading8 and lax panicle1 as candidate genes, respectively. The quantitative trait locus qSN8 was further confirmed to be days to heading8 by a complementation test. Our study provided an ideal platform for molecular breeding by targeting and dissecting yield-associated loci in rice. PMID:23940322

Gao, Zhen-Yu; Zhao, Shan-Cen; He, Wei-Ming; Guo, Long-Biao; Peng, You-Lin; Wang, Jin-Jin; Guo, Xiao-Sen; Zhang, Xue-Mei; Rao, Yu-Chun; Zhang, Chi; Dong, Guo-Jun; Zheng, Feng-Ya; Lu, Chang-Xin; Hu, Jiang; Zhou, Qing; Liu, Hui-Juan; Wu, Hai-Yang; Xu, Jie; Ni, Pei-Xiang; Zeng, Da-Li; Liu, Deng-Hui; Tian, Peng; Gong, Li-Hui; Ye, Chen; Zhang, Guang-Heng; Wang, Jian; Tian, Fu-Kuan; Xue, Da-Wei; Liao, Yi; Zhu, Li; Chen, Ming-Sheng; Li, Jia-Yang; Cheng, Shi-Hua; Zhang, Geng-Yun; Wang, Jun; Qian, Qian

2013-01-01