Science.gov

Sample records for quantitative phosphoproteomics dissection

  1. Peptide Labeling Using Isobaric Tagging Reagents for Quantitative Phosphoproteomics.

    PubMed

    Cheng, Lei; Pisitkun, Trairak; Knepper, Mark A; Hoffert, Jason D

    2016-01-01

    Isobaric tagging reagents have become an invaluable tool for multiplexed quantitative proteomic analysis. These reagents can label multiple, distinct peptide samples from virtually any source material (e.g., tissue, cell line, purified proteins), allowing users the opportunity to assess changes in peptide abundances across many different time points or experimental conditions. Here, we describe the application of isobaric peptide labeling, specifically 8plex isobaric tags for relative and absolute quantitation (8plex iTRAQ), for quantitative phosphoproteomic analysis of cultured cells or tissue suspensions. For this particular protocol, labeled samples are pooled, fractionated by strong cation exchange chromatography, enriched for phosphopeptides, and analyzed by tandem mass spectrometry (LC-MS/MS) for both peptide identification and quantitation. PMID:26584918

  2. Quantitative Phosphoproteomics Reveals Extensive Cellular Reprogramming During HIV-1 Entry

    PubMed Central

    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

    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

  3. Quantitative Proteomic and Phosphoproteomic Analysis of Trypanosoma cruzi Amastigogenesis*

    PubMed Central

    Queiroz, Rayner M. L.; Charneau, Sébastien; Mandacaru, Samuel C.; Schwämmle, Veit; Lima, Beatriz D.; Roepstorff, Peter; Ricart, Carlos A. O.

    2014-01-01

    Chagas disease is a tropical neglected disease endemic in Latin America caused by the protozoan Trypanosoma cruzi. The parasite has four major life stages: epimastigote, metacyclic trypomastigote, bloodstream trypomastigote, and amastigote. The differentiation from infective trypomastigotes into replicative amastigotes, called amastigogenesis, takes place in vivo inside mammalian host cells after a period of incubation in an acidic phagolysosome. This differentiation process can be mimicked in vitro by incubating tissue-culture-derived trypomastigotes in acidic DMEM. Here we used this well-established differentiation protocol to perform a comprehensive quantitative proteomic and phosphoproteomic analysis of T. cruzi amastigogenesis. Samples from fully differentiated forms and two biologically relevant intermediate time points were Lys-C/trypsin digested, iTRAQ-labeled, and multiplexed. Subsequently, phosphopeptides were enriched using a TiO2 matrix. Non-phosphorylated peptides were fractionated via hydrophilic interaction liquid chromatography prior to LC-MS/MS analysis. LC-MS/MS and bioinformatics procedures were used for protein and phosphopeptide quantitation, identification, and phosphorylation site assignment. We were able to identify regulated proteins and pathways involved in coordinating amastigogenesis. We also observed that a significant proportion of the regulated proteins were membrane proteins. Modulated phosphorylation events coordinated by protein kinases and phosphatases that are part of the signaling cascade induced by incubation in acidic medium were also evinced. To our knowledge, this work is the most comprehensive quantitative proteomics study of T. cruzi amastigogenesis, and these data will serve as a trustworthy basis for future studies, and possibly for new potential drug targets. PMID:25225356

  4. Quantitative proteomic and phosphoproteomic analysis of Trypanosoma cruzi amastigogenesis.

    PubMed

    Queiroz, Rayner M L; Charneau, Sébastien; Mandacaru, Samuel C; Schwämmle, Veit; Lima, Beatriz D; Roepstorff, Peter; Ricart, Carlos A O

    2014-12-01

    Chagas disease is a tropical neglected disease endemic in Latin America caused by the protozoan Trypanosoma cruzi. The parasite has four major life stages: epimastigote, metacyclic trypomastigote, bloodstream trypomastigote, and amastigote. The differentiation from infective trypomastigotes into replicative amastigotes, called amastigogenesis, takes place in vivo inside mammalian host cells after a period of incubation in an acidic phagolysosome. This differentiation process can be mimicked in vitro by incubating tissue-culture-derived trypomastigotes in acidic DMEM. Here we used this well-established differentiation protocol to perform a comprehensive quantitative proteomic and phosphoproteomic analysis of T. cruzi amastigogenesis. Samples from fully differentiated forms and two biologically relevant intermediate time points were Lys-C/trypsin digested, iTRAQ-labeled, and multiplexed. Subsequently, phosphopeptides were enriched using a TiO2 matrix. Non-phosphorylated peptides were fractionated via hydrophilic interaction liquid chromatography prior to LC-MS/MS analysis. LC-MS/MS and bioinformatics procedures were used for protein and phosphopeptide quantitation, identification, and phosphorylation site assignment. We were able to identify regulated proteins and pathways involved in coordinating amastigogenesis. We also observed that a significant proportion of the regulated proteins were membrane proteins. Modulated phosphorylation events coordinated by protein kinases and phosphatases that are part of the signaling cascade induced by incubation in acidic medium were also evinced. To our knowledge, this work is the most comprehensive quantitative proteomics study of T. cruzi amastigogenesis, and these data will serve as a trustworthy basis for future studies, and possibly for new potential drug targets. PMID:25225356

  5. In situ sample processing approach (iSPA) for comprehensive quantitative phosphoproteome analysis.

    PubMed

    Huang, Junfeng; Qin, Hongqiang; Dong, Jing; Song, Chunxia; Bian, Yangyang; Dong, Mingming; Cheng, Kai; Wang, Fangjun; Sun, Deguang; Wang, Liming; Ye, Mingliang; Zou, Hanfa

    2014-09-01

    Current sample preparation protocols for quantitative phosphoproteome analysis are tedious and time-consuming. Here, a facile in situ sample processing approach (iSPA) is developed by using macroporous Ti(IV)-IMAC microspheres as the preparation "beds", where all sample preparation procedures including the enrichment of phosphoproteins, tryptic digestion of proteins, enrichment, and isotope labeling of phosphopeptides are performed in situ sequentially. As a result of the in situ processing design and the seamless procedures, extra steps for desalting and buffer exchanging, which are always required in conventional approaches, are avoided, and the sample loss and contamination could be greatly reduced. Thus, better sensitivity and accuracy for the quantitative phosphoproteome analysis were obtained. This strategy was further applied to differential phosphoproteome analysis of human liver tissues with or without hepatocellular carcinoma (HCC). In total, 8548 phosphorylation sites were confidently quantified from three replicate analyses of 0.5 mg of human liver protein extracts. PMID:25072903

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

    PubMed

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

    2015-11-01

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

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

    PubMed Central

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

    2014-01-01

    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

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

    PubMed Central

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

    2015-01-01

    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

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

    PubMed Central

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

    2012-01-01

    Summary Mitochondria are dynamic organelles that play a central role in a diverse array of metabolic processes. Elucidating mitochondrial adaptations to changing metabolic demands and the pathogenic alterations that underlie metabolic disorders represent principal challenges in cell biology. Here, we performed multiplexed quantitative mass spectrometry-based proteomics to chart the remodeling of the mouse liver mitochondrial proteome and phosphoproteome during both acute and chronic physiological transformations in more than 50 mice. Our analyses reveal that reversible phosphorylation is widespread in mitochondria, and is a key mechanism for regulating ketogenesis during the onset of obesity and type 2 diabetes. Specifically, we have demonstrated that phosphorylation of a conserved serine on Hmgcs2 (S456) significantly enhances its catalytic activity in response to increased ketogenic demand. Collectively, our work describes the plasticity of this organelle at high resolution and provides a framework for investigating the roles of proteome restructuring and reversible phosphorylation in mitochondrial adaptation. PMID:23140645

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

    SciTech Connect

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

    2012-04-17

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

  11. Quantitative phosphoproteomics reveals the role of protein arginine phosphorylation in the bacterial stress response.

    PubMed

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

    2014-02-01

    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

  12. Quantitative Phosphoproteome Profiling of Iron-Deficient Arabidopsis Roots1[C][W

    PubMed Central

    Lan, Ping; Li, Wenfeng; Wen, Tuan-Nan; Schmidt, Wolfgang

    2012-01-01

    Iron (Fe) is an essential mineral nutrient for plants, but often it is not available in sufficient quantities to sustain optimal growth. To gain insights into adaptive processes to low Fe availability at the posttranslational level, we conducted a quantitative analysis of Fe deficiency-induced changes in the phosphoproteome profile of Arabidopsis (Arabidopsis thaliana) roots. Isobaric tags for relative and absolute quantitation-labeled phosphopeptides were analyzed by liquid chromatography-tandem mass spectrometry on an LTQ-Orbitrap with collision-induced dissociation and high-energy collision dissociation capabilities. Using a combination of titanium dioxide and immobilized metal affinity chromatography to enrich phosphopeptides, we extracted 849 uniquely identified phosphopeptides corresponding to 425 proteins and identified several not previously described phosphorylation motifs. A subset of 45 phosphoproteins was defined as being significantly changed in abundance upon Fe deficiency. Kinase motifs in Fe-responsive proteins matched to protein kinase A/calcium calmodulin-dependent kinase II, casein kinase II, and proline-directed kinase, indicating a possible critical function of these kinase classes in Fe homeostasis. To validate our analysis, we conducted site-directed mutagenesis on IAA-CONJUGATE-RESISTANT4 (IAR4), a protein putatively functioning in auxin homeostasis. iar4 mutants showed compromised root hair formation and developed shorter primary roots. Changing serine-296 in IAR4 to alanine resulted in a phenotype intermediate between mutant and wild type, whereas acidic substitution to aspartate to mimic phosphorylation was either lethal or caused an extreme dwarf phenotype, supporting the critical importance of this residue in Fe homeostasis. Our analyses further disclose substantial changes in the abundance of phosphoproteins involved in primary carbohydrate metabolism upon Fe deficiency, complementing the picture derived from previous proteomic and transcriptomic profiling studies. PMID:22438062

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

    E-print Network

    Richardson, David

    Robust, Quantitative, Labelfree Phosphoproteomics Platform: Automated Enrichment and 2DLC/MS/MS normalization of identified phosphopeptides from four replicated enrichment analyzed by LC/MS/MS on a Waters to the LC/MS/MS analysis of enriched samples. This strategy employs the high/low pH separation

  14. Quantitative Label-Free Phosphoproteomics Reveals Differentially Regulated Protein Phosphorylation Involved in West Nile Virus-Induced Host Inflammatory Response.

    PubMed

    Zhang, Hao; Sun, Jun; Ye, Jing; Ashraf, Usama; Chen, Zheng; Zhu, Bibo; He, Wen; Xu, Qiuping; Wei, Yanming; Chen, Huanchun; Fu, Zhen F; Liu, Rong; Cao, Shengbo

    2015-12-01

    West Nile virus (WNV) can cause neuro-invasive and febrile illness that may be fatal to humans. The production of inflammatory cytokines is key to mediating WNV-induced immunopathology in the central nervous system. Elucidating the host factors utilized by WNV for productive infection would provide valuable insights into the evasion strategies used by this virus. Although attempts have been made to determine these host factors, proteomic data depicting WNV-host protein interactions are limited. We applied liquid chromatography-tandem mass spectrometry for label-free, quantitative phosphoproteomics to systematically investigate the global phosphorylation events induced by WNV infection. Quantifiable changes to 1,657 phosphoproteins were found; of these, 626 were significantly upregulated and 227 were downregulated at 12 h postinfection. The phosphoproteomic data were subjected to gene ontology enrichment analysis, which returned the inflammation-related spliceosome, ErbB, mitogen-activated protein kinase, nuclear factor kappa B, and mechanistic target of rapamycin signaling pathways. We used short interfering RNAs to decrease the levels of glycogen synthase kinase-3 beta, bifunctional polynucleotide phosphatase/kinase, and retinoblastoma 1 and found that the activity of nuclear factor kappa B (p65) is significantly decreased in WNV-infected U251 cells, which in turn led to markedly reduced inflammatory cytokine production. Our results provide a better understanding of the host response to WNV infection and highlight multiple targets for the development of antiviral and anti-inflammatory therapies. PMID:26485063

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

    PubMed

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

    2015-05-01

    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

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

    SciTech Connect

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

    2012-11-11

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2012-01-01

    G protein-coupled receptors (GPCRs) regulate diverse physiological processes, and many human diseases are due to defects in GPCR signaling. To identify the dynamic response of a signaling network downstream from a prototypical Gs-coupled GPCR, the vasopressin V2 receptor, we have carried out multireplicate, quantitative phosphoproteomics with iTRAQ labeling at four time points following vasopressin exposure at a physiological concentration in cells isolated from rat kidney. A total of 12,167 phosphopeptides were identified from 2,783 proteins, with 273 changing significantly in abundance with vasopressin. Two-dimensional clustering of phosphopeptide time courses and Gene Ontology terms revealed that ligand binding to the V2 receptor affects more than simply the canonical cyclic adenosine monophosphate-protein kinase A and arrestin pathways under physiological conditions. The regulated proteins included key components of actin cytoskeleton remodeling, cell-cell adhesion, mitogen-activated protein kinase signaling, Wnt/?-catenin signaling, and apoptosis pathways. These data suggest that vasopressin can regulate an array of cellular functions well beyond its classical role in regulating water and solute transport. These results greatly expand the current view of GPCR signaling in a physiological context and shed new light on potential roles for this signaling network in disorders such as polycystic kidney disease. Finally, we provide an online resource of physiologically regulated phosphorylation sites with dynamic quantitative data (http://helixweb.nih.gov/ESBL/Database/TiPD/index.html). PMID:22108457

  1. Quantitative Phosphoproteomic Analyses of the Inferior Parietal Lobule from Three Different Pathological Stages of Alzheimer's Disease.

    PubMed

    Triplett, Judy C; Swomley, Aaron M; Cai, Jian; Klein, Jon B; Butterfield, D Allan

    2015-09-22

    Alzheimer's disease (AD), the most common age-related neurodegenerative disorder, is clinically characterized by progressive neuronal loss resulting in loss of memory and dementia. AD is histopathologically characterized by the extensive distribution of senile plaques and neurofibrillary tangles, and synapse loss. Amnestic mild cognitive impairment (MCI) is generally accepted to be an early stage of AD. MCI subjects have pathology and symptoms that fall on the scale intermediately between 'normal' cognition with little or no pathology and AD. A rare number of individuals, who exhibit normal cognition on psychometric tests but whose brains show widespread postmortem AD pathology, are classified as 'asymptomatic' or 'preclinical' AD (PCAD). In this study, we evaluated changes in protein phosphorylation states in the inferior parietal lobule of subjects with AD, MCI, PCAD, and control brain using a 2-D PAGE proteomics approach in conjunction with Pro-Q Diamond phosphoprotein staining. Statistically significant changes in phosphorylation levels were found in 19 proteins involved in energy metabolism, neuronal plasticity, signal transduction, and oxidative stress response. Changes in the disease state phosphoproteome may provide insights into underlying mechanisms for the preservation of memory with expansive AD pathology in PCAD and the progressive memory loss in amnestic MCI that escalates to the dementia and the characteristic pathology of AD brain. PMID:26444780

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

    PubMed

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

    2014-10-01

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

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

    PubMed

    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

    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

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

    PubMed Central

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

    2013-01-01

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

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

    SciTech Connect

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

    2008-10-01

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

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

    PubMed Central

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

    2010-01-01

    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

  7. Quantitative Genetic Dissection of Shoot Architecture Traits in Maize: Towards a Functional Genomics Approach

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Quantitative trait loci (QTL) affecting the total number of leaves (TNOL) made prior to flowering and the number of leaves below the ear (NLBE) were mapped and characterized in order to dissect the genetic regulatory components of these agronomically important traits of corn. The full set of interm...

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

    PubMed Central

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

    2015-01-01

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

  9. Quantitative dissection of the simple repression input–output function

    PubMed Central

    Garcia, Hernan G.; Phillips, Rob

    2011-01-01

    We present a quantitative case study of transcriptional regulation in which we carry out a systematic dialogue between theory and measurement for an important and ubiquitous regulatory motif in bacteria, namely, that of simple repression. This architecture is realized by a single repressor binding site overlapping the promoter. From the theory point of view, this motif is described by a single gene regulation function based upon only a few parameters that are convenient theoretically and accessible experimentally. The usual approach is turned on its side by using the mathematical description of these regulatory motifs as a predictive tool to determine the number of repressors in a collection of strains with a large variation in repressor copy number. The predictions and corresponding measurements are carried out over a large dynamic range in both expression fold change (spanning nearly four orders of magnitude) and repressor copy number (spanning about two orders of magnitude). The predictions are tested by measuring the resulting level of gene expression and are then validated by using quantitative immunoblots. The key outcomes of this study include a systematic quantitative analysis of the limits and validity of the input–output relation for simple repression, a precise determination of the in vivo binding energies for DNA–repressor interactions for several distinct repressor binding sites, and a repressor census for Lac repressor in Escherichia coli. PMID:21730194

  10. Quantitative and Functional Phosphoproteomic Analysis Reveals that Ethylene Regulates Water Transport via the C-Terminal Phosphorylation of Aquaporin PIP2;1 in Arabidopsis.

    PubMed

    Qing, Dongjin; Yang, Zhu; Li, Mingzhe; Wong, Wai Shing; Guo, Guangyu; Liu, Shichang; Guo, Hongwei; Li, Ning

    2016-01-01

    Ethylene participates in the regulation of numerous cellular events and biological processes, including water loss, during leaf and flower petal wilting. The diverse ethylene responses may be regulated via dynamic interplays between protein phosphorylation/dephosphorylation and ubiquitin/26S proteasome-mediated protein degradation and protease cleavage. To address how ethylene alters protein phosphorylation through multi-furcated signaling pathways, we performed a (15)N stable isotope labelling-based, differential, and quantitative phosphoproteomics study on air- and ethylene-treated ethylene-insensitive Arabidopsis double loss-of-function mutant ein3-1/eil1-1. Among 535 non-redundant phosphopeptides identified, two and four phosphopeptides were up- and downregulated by ethylene, respectively. Ethylene-regulated phosphorylation of aquaporin PIP2;1 is positively correlated with the water flux rate and water loss in leaf. Genetic studies in combination with quantitative proteomics, immunoblot analysis, protoplast swelling/shrinking experiments, and leaf water loss assays on the transgenic plants expressing both the wild-type and S280A/S283A-mutated PIP2;1 in the both Col-0 and ein3eil1 genetic backgrounds suggest that ethylene increases water transport rate in Arabidopsis cells by enhancing S280/S283 phosphorylation at the C terminus of PIP2;1. Unknown kinase and/or phosphatase activities may participate in the initial up-regulation independent of the cellular functions of EIN3/EIL1. This finding contributes to our understanding of ethylene-regulated leaf wilting that is commonly observed during post-harvest storage of plant organs. PMID:26476206

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

    SciTech Connect

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

    2012-10-19

    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.

  12. Quantitative- and Phospho-Proteomic Analysis of the Yeast Response to the Tyrosine Kinase Inhibitor Imatinib to Pharmacoproteomics-Guided Drug Line Extension

    PubMed Central

    dos Santos, Sandra C.; Mira, Nuno P.; Moreira, Ana S.

    2012-01-01

    Abstract Imatinib mesylate (IM) is a potent tyrosine kinase inhibitor used as front-line therapy in chronic myeloid leukemia, a disease caused by the oncogenic kinase Bcr-Abl. Although the clinical success of IM set a new paradigm in molecular-targeted therapy, the emergence of IM resistance is a clinically significant problem. In an effort to obtain new insights into the mechanisms of adaptation and tolerance to IM, as well as the signaling pathways potentially affected by this drug, we performed a two-dimensional electrophoresis-based quantitative- and phospho-proteomic analysis in the eukaryotic model Saccharomyces cerevisiae. We singled out proteins that were either differentially expressed or differentially phosphorylated in response to IM, using the phosphoselective dye Pro-Q® Diamond, and identified 18 proteins in total. Ten were altered only at the content level (mostly decreased), while the remaining 8 possessed IM-repressed phosphorylation. These 18 proteins are mainly involved in cellular carbohydrate processes (glycolysis/gluconeogenesis), translation, protein folding, ion homeostasis, and nucleotide and amino acid metabolism. Remarkably, all 18 proteins have human functional homologs. A role for HSP70 proteins in the response to IM, as well as decreased glycolysis as a metabolic marker of IM action are suggested, consistent with findings from studies in human cell lines. The previously-proposed effect of IM as an inhibitor of vacuolar H+-ATPase function was supported by the identification of an underexpressed protein subunit of this complex. Taken together, these findings reinforce the role of yeast as a valuable eukaryotic model for pharmacological studies and identification of new drug targets, with potential clinical implications in drug reassignment or line extension under a personalized medicine perspective. PMID:22775238

  13. Quantitative phosphoproteomic analysis reveals ?-bisabolene inducing p53-mediated apoptosis of human oral squamous cell carcinoma via HDAC2 inhibition and ERK1/2 activation.

    PubMed

    Jou, Yu-Jen; Chen, Chao-Jung; Liu, Yu-Ching; Way, Tzong-Der; Lai, Chih-Ho; Hua, Chun-Hung; Wang, Ching-Ying; Huang, Su-Hua; Kao, Jung-Yie; Lin, Cheng-Wen

    2015-10-01

    ?-Bisabolene, one of main components in cardamom, showed potent in vitro and in vivo anti-proliferative activities against human oral squamous cell carcinoma (OSCC). ?-Bisabolene activated caspases-3/9 and decreased mitochondrial memebrane potential, leading to apoptosis of OSCC cell lines (Ca9-22 and SAS), but not normal oral fibroblast cells. Phosphoproteome profiling of OSCC cells treated with ?-bisabolene was identified using TiO2-PDMS plate and LC-MS/MS, then confirmed using Western blotting and real-time RT-PCR assays. Phosphoproteome profiling revealed that ?-bisabolene increased the phosphorylation of ERK1/2, protein phosphatases 1 (PP1), and p53, as well as decreased the phosphorylation of histone deacetylase 2 (HDAC2) in the process of apoptosis induction. Protein-protein interaction network analysis proposed the involvement of PP1-HDAC2-p53 and ERK1/2-p53 pathways in ?-bisabolene-induced apoptosis. Subsequent assays indicated ?-bisabolene eliciting p53 acetylation that enhanced the expression of p53-regulated apoptotic genes. PP1 inhibitor-2 restored the status of HDAC2 phosphorylation, reducing p53 acetylation and PUMA mRNA expression in ?-bisabolene-treated Ca9-22 and SAS cells. Meanwhile, MEK and ERK inhibitors significantly decreased ?-bisabolene-induced PUMA expression in both cancer cell lines. Notably, the results ascertained the involvement of PP1-HDAC2-p53 and ERK1/2-p53 pathways in mitochondria-mediated apoptosis of ?-bisabolene-treated cells. This study demonstrated ?-bisabolene displaying potent anti-proliferative and apoptosis-inducing activities against OSCC in vitro and in vivo, elucidating molecular mechanisms of ?-bisabolene-induced apoptosis. The novel insight could be useful for developing anti-cancer drugs. PMID:26194454

  14. Stable Isotope Metabolic Labeling-based Quantitative Phosphoproteomic Analysis of Arabidopsis Mutants Reveals Ethylene-regulated Time-dependent Phosphoproteins and Putative Substrates of Constitutive Triple Response 1 Kinase*

    PubMed Central

    Yang, Zhu; Guo, Guangyu; Zhang, Manyu; Liu, Claire Y.; Hu, Qin; Lam, Henry; Cheng, Han; Xue, Yu; Li, Jiayang; Li, Ning

    2013-01-01

    Ethylene is an important plant hormone that regulates numerous cellular processes and stress responses. The mode of action of ethylene is both dose- and time-dependent. Protein phosphorylation plays a key role in ethylene signaling, which is mediated by the activities of ethylene receptors, constitutive triple response 1 (CTR1) kinase, and phosphatase. To address how ethylene alters the cellular protein phosphorylation profile in a time-dependent manner, differential and quantitative phosphoproteomics based on 15N stable isotope labeling in Arabidopsis was performed on both one-minute ethylene-treated Arabidopsis ethylene-overly-sensitive loss-of-function mutant rcn1-1, deficient in PP2A phosphatase activity, and a pair of long-term ethylene-treated wild-type and loss-of-function ethylene signaling ctr1-1 mutants, deficient in mitogen-activated kinase kinase kinase activity. In total, 1079 phosphopeptides were identified, among which 44 were novel. Several one-minute ethylene-regulated phosphoproteins were found from the rcn1-1. Bioinformatic analysis of the rcn1-1 phosphoproteome predicted nine phosphoproteins as the putative substrates for PP2A phosphatase. In addition, from CTR1 kinase-enhanced phosphosites, we also found putative CTR1 kinase substrates including plastid transcriptionally active protein and calcium-sensing receptor. These regulatory proteins are phosphorylated in the presence of ethylene. Analysis of ethylene-regulated phosphosites using the group-based prediction system with a protein–protein interaction filter revealed a total of 14 kinase–substrate relationships that may function in both CTR1 kinase- and PP2A phosphatase-mediated phosphor-relay pathways. Finally, several ethylene-regulated post-translational modification network models have been built using molecular systems biology tools. It is proposed that ethylene regulates the phosphorylation of arginine/serine-rich splicing factor 41, plasma membrane intrinsic protein 2A, light harvesting chlorophyll A/B binding protein 1.1, and flowering bHLH 3 proteins in a dual-and-opposing fashion. PMID:24043427

  15. Clinical and Technical Phosphoproteomic Research

    PubMed Central

    2011-01-01

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

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

    E-print Network

    Wolf Yadlin, Alejandro

    2007-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-07-01

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

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

    PubMed

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

    2014-04-01

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

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

    PubMed Central

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

    2014-01-01

    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

  20. Combining Quantitative Genetics Approaches with Regulatory Network Analysis to Dissect the Complex Metabolism of the Maize Kernel.

    PubMed

    Wen, Weiwei; Liu, Haijun; Zhou, Yang; Jin, Min; Yang, Ning; Li, Dong; Luo, Jie; Xiao, Yingjie; Pan, Qingchun; Tohge, Takayuki; Fernie, Alisdair R; Yan, Jianbing

    2016-01-01

    Metabolic quantitative trait locus (QTL) studies have allowed us to better understand the genetic architecture underlying naturally occurring plant metabolic variance. Here, we use two recombinant inbred line (RIL) populations to dissect the genetic architecture of natural variation of 155 metabolites measured in the mature maize (Zea mays) kernel. Overall, linkage mapping identified 882 metabolic QTLs in both RIL populations across two environments, with an average of 2.1 QTLs per metabolite. A large number of metabolic QTLs (more than 65%) were identified with moderate effects (r(2) = 2.1%-10%), while a small portion (less than 35%) showed major effects (r(2) > 10%). Epistatic interactions between these identified loci were detected for more than 30% of metabolites (with the proportion of phenotypic variance ranging from 1.6% to 37.8%), implying that genetic epistasis is not negligible in determining metabolic variation. In total, 57 QTLs were validated by our previous genome-wide association study on the same metabolites that provided clues for exploring the underlying genes. A gene regulatory network associated with the flavonoid metabolic pathway was constructed based on the transcriptional variations of 28,769 genes in kernels (15 d after pollination) of 368 maize inbred lines. A large number of genes (34 of 58) in this network overlapped with previously defined genes controlled by maize PERICARP COLOR1, while three of them were identified here within QTL intervals for multiple flavonoids. The deeply characterized RIL populations, elucidation of metabolic phenotypes, and identification of candidate genes lay the foundation for maize quality improvement. PMID:26556794

  1. Influence of sample preparation and reliability of automated numerical refocusing in stain-free analysis of dissected tissues with quantitative phase digital holographic microscopy

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

    Digital holographic microscopy (DHM) has been demonstrated to be a versatile tool for high resolution non-destructive quantitative phase imaging of surfaces and multi-modal minimally-invasive monitoring of living cell cultures in-vitro. DHM provides quantitative monitoring of physiological processes through functional imaging and structural analysis which, for example, gives new insight into signalling of cellular water permeability and cell morphology changes due to toxins and infections. Also the analysis of dissected tissues quantitative DHM phase contrast prospects application fields by stain-free imaging and the quantification of tissue density changes. We show that DHM allows imaging of different tissue layers with high contrast in unstained tissue sections. As the investigation of fixed samples represents a very important application field in pathology, we also analyzed the influence of the sample preparation. The retrieved data demonstrate that the quality of quantitative DHM phase images of dissected tissues depends strongly on the fixing method and common staining agents. As in DHM the reconstruction is performed numerically, multi-focus imaging is achieved from a single digital hologram. Thus, we evaluated the automated refocussing feature of DHM for application on different types of dissected tissues and revealed that on moderately stained samples highly reproducible holographic autofocussing can be achieved. Finally, it is demonstrated that alterations of the spatial refractive index distribution in murine and human tissue samples represent a reliable absolute parameter that is related of different degrees of inflammation in experimental colitis and Crohn's disease. This paves the way towards the usage of DHM in digital pathology for automated histological examinations and further studies to elucidate the translational potential of quantitative phase microscopy for the clinical management of patients, e.g., with inflammatory bowel disease.

  2. Identification of Direct Kinase Substrates via Kinase Assay-Linked Phosphoproteomics.

    PubMed

    Xue, Liang; Arrington, Justine V; Tao, W Andy

    2016-01-01

    Protein phosphorylation plays an essential role in the regulation of various cellular functions. Dysregulation of phosphorylation is implicated in the pathogenesis of certain cancers, diabetes, cardiovascular diseases, and central nervous system disorders. As a result, protein kinases have become potential drug targets for treating a wide variety of diseases. Identification of kinase substrates is vital not only for dissecting signaling pathways, but also for understanding disease pathologies and identifying novel therapeutic targets. However, identification of bona fide kinase substrates has remained challenging, necessitating the development of new methods and techniques. The kinase assay linked phosphoproteomics (KALIP) approach integrates in vitro kinase assays with global phosphoproteomics experiments to identify the direct substrates of protein kinases. This strategy has demonstrated outstanding sensitivity and a low false-positive rate for kinase substrate screening. PMID:26584932

  3. Profiling the Trypanosoma cruzi Phosphoproteome

    PubMed Central

    Rampazzo, Rita C. P.; Pavoni, Daniela P.; Probst, Christian M.; Gnad, Florian; Mann, Matthias; Krieger, Marco A.

    2011-01-01

    Protein phosphorylation is a reversible post-translational modification essential for the regulation of several signal transduction pathways and biological processes in the living cell. Therefore, the identification of protein phosphorylation sites is crucial to understand cell signaling control at the molecular level. Based on mass spectrometry, recent studies have reported the large-scale mapping of phosphorylation sites in various eukaryotes and prokaryotes. However, little is known about the impact of phosphorylation in protozoan parasites. To in depth characterize the phosphoproteome of Trypanosoma cruzi, a parasite of the Kinetoplastida class, protein samples from cells at different phases of the metacyclogenesis – differentiation process of the parasites from non-infective epimastigotes to infective metacyclic trypomastigotes - were enriched for phosphopeptides using TiO2 chromatography and analyzed on an LTQ-Orbitrap mass spectrometer. In total, 1,671 proteins were identified, including 753 phosphoproteins, containing a total of 2,572 phosphorylation sites. The distribution of phosphorylated residues was 2,162 (84.1%) on serine, 384 (14.9%) on threonine and 26 (1.0%) on tyrosine. Here, we also report several consensus phosphorylation sequence motifs and as some of these conserved groups have enriched biological functions, we can infer the regulation by protein kinases of this functions. To our knowledge, our phosphoproteome is the most comprehensive dataset identified until now for Kinetoplastida species. Here we also were able to extract biological information and infer groups of sites phosphorylated by the same protein kinase. To make our data accessible to the scientific community, we uploaded our study to the data repositories PHOSIDA, Proteome Commons and TriTrypDB enabling researchers to access information about the phosphorylation sites identified here. PMID:21966514

  4. Phosphoproteomic Analysis of Aurora Kinase Inhibition in Monopolar Cytokinesis.

    PubMed

    Polat, Ayse Nur; Karayel, Özge; Giese, Sven H; Harmanda, Bü?ra; Sanal, Erdem; Hu, Chi-Kuo; Renard, Bernhard Y; Özlü, Nurhan

    2015-09-01

    Cytokinesis is the last step of the cell cycle that requires coordinated activities of the microtubule cytoskeleton, actin cytoskeleton, and membrane compartments. Aurora B kinase is one of the master regulatory kinases that orchestrate multiple events during cytokinesis. To reveal targets of the Aurora B kinase, we combined quantitative mass spectrometry with chemical genetics. Using the quantitative proteomic approach, SILAC (stable isotope labeling with amino acids in cell culture), we analyzed the phosphoproteome of monopolar cytokinesis upon VX680- or AZD1152-mediated aurora kinase inhibition. In total, our analysis quantified over 20?000 phosphopeptides in response to the Aurora-B kinase inhibition; 246 unique phosphopeptides were significantly down-regulated and 74 were up-regulated. Our data provide a broad analysis of downstream effectors of Aurora kinase and offer insights into how Aurora kinase regulates cytokinesis. PMID:26270265

  5. Temporal dynamics of the Saccharopolyspora erythraea phosphoproteome.

    PubMed

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

    2014-05-01

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

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

    E-print Network

    Illinois at Urbana-Champaign, University of

    -frequency ultra- sound (HFU) and 3D quantitative ultrasound (QUS) to help pathol- ogists detect micrometastases. Using our database of 134 abdominal cancer-free nodes and 26 fully cancerous abdominal nodes

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

    PubMed Central

    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

    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

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

    PubMed

    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

    2015-03-01

    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

  9. Quantitative dissection and modeling of the NF-?B p100-p105 module reveals interdependent precursor proteolysis.

    PubMed

    Y?lmaz, Zekiye Buket; Kofahl, Bente; Beaudette, Patrick; Baum, Katharina; Ipenberg, Inbal; Weih, Falk; Wolf, Jana; Dittmar, Gunnar; Scheidereit, Claus

    2014-12-11

    The mechanisms that govern proteolytic maturation or complete destruction of the precursor proteins p100 and p105 are fundamental to homeostasis and activation of NF-?B; however, they remain poorly understood. Using mass-spectrometry-based quantitative analysis of noncanonical LT?R-induced signaling, we demonstrate that stimulation induces simultaneous processing of both p100 and p105. The precursors not only form hetero-oligomers but also interact with the ATPase VCP/p97, and their induced proteolysis strictly depends on the signal response domain (SRD) of p100, suggesting that the SRD-targeting proteolytic machinery acts in cis and in trans. Separation of cellular pools by isotope labeling revealed synchronous dynamics of p105 and p100 proteolysis. The generation of p50 and p52 from their precursors depends on functional VCP/p97. We have developed quantitative mathematical models that describe the dynamics of the system and predict that p100-p105 complexes are signal responsive. PMID:25482563

  10. Computational phosphoproteomics: From identification to localization

    PubMed Central

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

    2015-01-01

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

  11. Systems Analysis for Interpretation of Phosphoproteomics Data.

    PubMed

    Munk, Stephanie; Refsgaard, Jan C; Olsen, Jesper V

    2016-01-01

    Global phosphoproteomics investigations yield overwhelming datasets with up to tens of thousands of quantified phosphosites. The main challenge after acquiring such large-scale data is to extract the biological meaning and relate this to the experimental question at hand. Systems level analysis provides the best means for extracting functional insights from such types of datasets, and this has primed a rapid development of bioinformatics tools and resources over the last decade. Many of these tools are specialized databases that can be mined for annotation and pathway enrichment, whereas others provide a platform to generate functional protein networks and explore the relations between proteins of interest. The use of these tools requires careful consideration with regard to the input data, and the interpretation demands a critical approach. This chapter provides a summary of the most appropriate tools for systems analysis of phosphoproteomics datasets, and the considerations that are critical for acquiring meaningful output. PMID:26584937

  12. Dissecting quantitative trait variation in the resequencing era: complementarity of bi-parental, multi-parental and association panels.

    PubMed

    Pascual, Laura; Albert, Elise; Sauvage, Christopher; Duangjit, Janejira; Bouchet, Jean-Paul; Bitton, Frédérique; Desplat, Nelly; Brunel, Dominique; Le Paslier, Marie-Christine; Ranc, Nicolas; Bruguier, Laure; Chauchard, Betty; Verschave, Philippe; Causse, Mathilde

    2016-01-01

    Quantitative trait loci (QTL) have been identified using traditional linkage mapping and positional cloning identified several QTLs. However linkage mapping is limited to the analysis of traits differing between two lines and the impact of the genetic background on QTL effect has been underlined. Genome-wide association studies (GWAs) were proposed to circumvent these limitations. In tomato, we have shown that GWAs is possible, using the admixed nature of cherry tomato genomes that reduces the impact of population structure. Nevertheless, GWAs success might be limited due to the low decay of linkage disequilibrium, which varies along the genome in this species. Multi-parent advanced generation intercross (MAGIC) populations offer an alternative to traditional linkage and GWAs by increasing the precision of QTL mapping. We have developed a MAGIC population by crossing eight tomato lines whose genomes were resequenced. We showed the potential of the MAGIC population when coupled with whole genome sequencing to detect candidate single nucleotide polymorphisms (SNPs) underlying the QTLs. QTLs for fruit quality traits were mapped and related to the variations detected at the genome sequence and expression levels. The advantages and limitations of the three types of population, in the context of the available genome sequence and resequencing facilities, are discussed. PMID:26566830

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

    PubMed Central

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

    2015-01-01

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

  14. Polyomino Dissections

    ERIC Educational Resources Information Center

    Hohn, Tiina; Liu, Andy

    2012-01-01

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

  15. Genetic dissection of milk yield traits and mastitis resistance quantitative trait loci on chromosome 20 in dairy cattle.

    PubMed

    Kadri, Naveen K; Guldbrandtsen, Bernt; Lund, Mogens S; Sahana, Goutam

    2015-12-01

    Intense selection to increase milk yield has had negative consequences for mastitis incidence in dairy cattle. Due to low heritability of mastitis resistance and an unfavorable genetic correlation with milk yield, a reduction in mastitis through traditional breeding has been difficult to achieve. Here, we examined quantitative trait loci (QTL) that segregate for clinical mastitis and milk yield on Bos taurus autosome 20 (BTA20) to determine whether both traits are affected by a single polymorphism (pleiotropy) or by multiple closely linked polymorphisms. In the latter but not the former situation, undesirable genetic correlation could potentially be broken by selecting animals that have favorable variants for both traits. First, we performed a within-breed association study using a haplotype-based method in Danish Holstein cattle (HOL). Next, we analyzed Nordic Red dairy cattle (RDC) and Danish Jersey cattle (JER) with the goal of determining whether these QTL identified in Holsteins were segregating across breeds. Genotypes for 12,566 animals (5,966 HOL, 5,458 RDC, and 1,142 JER) were determined by using the Illumina Bovine SNP50 BeadChip (50K; Illumina, San Diego, CA), which identifies 1,568 single nucleotide polymorphisms on BTA20. Data were combined, phased, and clustered into haplotype states, followed by within- and across-breed haplotype-based association analyses using a linear mixed model. Association signals for both clinical mastitis and milk yield peaked in the 26- to 40-Mb region on BTA20 in HOL. Single-variant association analyses were carried out in the QTL region using whole sequence level variants imputed from references of 2,036 HD genotypes (BovineHD BeadChip; Illumina) and 242 whole-genome sequences. The milk QTL were also segregating in RDC and JER on the BTA20-targeted region; however, an indication of differences in the causal factor(s) was observed across breeds. A previously reported F279Y mutation (rs385640152) within the growth hormone receptor gene showed strong association with milk, fat, and protein yields. In HOL, the highest peaks for milk yield and susceptibility to mastitis were separated by over 3.5 Mb (3.8 Mb by haplotype analysis, 3.6 Mb by single nucleotide polymorphism analysis), suggesting separate genetic variants for the traits. Further analysis yielded 2 candidate mutations for the mastitis QTL, at 33,642,072 bp (rs378947583) in an intronic region of the caspase recruitment domain protein 6 gene and 35,969,994 bp (rs133596506) in an intronic region of the leukemia-inhibitory factor receptor gene. These findings suggest that it may be possible to separate these beneficial and detrimental genetic factors through targeted selective breeding. PMID:26409972

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

    NASA Astrophysics Data System (ADS)

    Milano, Regina Nicole

    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.

  17. Two Birds with One Stone: Parallel Quantification of Proteome and Phosphoproteome Using iTRAQ.

    PubMed

    Solari, Fiorella A; Kollipara, Laxmikanth; Sickmann, Albert; Zahedi, René P

    2016-01-01

    Altered and abnormal levels of proteins and their phosphorylation states are associated with many disorders. Detection and quantification of such perturbations may provide a better understanding of pathological conditions and help finding candidates for treatment or biomarkers. Over the years, isobaric mass tags for relative quantification of proteins and protein phosphorylation by mass spectrometry have become increasingly popular. One of the most commonly used isobaric chemical tags is iTRAQ (isobaric tag for relative and absolute quantitation). In a typical iTRAQ-8plex experiment, a multiplexed sample amounts for up to 800 ?g of peptides. Using state-of-the-art LC-MS approaches, only a fraction (~5 %) of such a sample is required to generate comprehensive quantitative data on the global proteome level, so that the bulk of the sample can be simultaneously used for quantitative phosphoproteomics. Here, we provide a simple and straightforward protocol to perform quantitative analyses of both proteome and phosphoproteome from the same sample using iTRAQ. PMID:26700039

  18. Analysis of the Candida albicans Phosphoproteome

    PubMed Central

    Willger, S. D.; Liu, Z.; Olarte, R. A.; Adamo, M. E.; Myers, L. C.; Kettenbach, A. N.

    2015-01-01

    Candida albicans is an important human fungal pathogen in both immunocompetent and immunocompromised individuals. C. albicans regulation has been studied in many contexts, including morphological transitions, mating competence, biofilm formation, stress resistance, and cell wall synthesis. Analysis of kinase- and phosphatase-deficient mutants has made it clear that protein phosphorylation plays an important role in the regulation of these pathways. In this study, to further our understanding of phosphorylation in C. albicans regulation, we performed a deep analysis of the phosphoproteome in C. albicans. We identified 19,590 unique peptides that corresponded to 15,906 unique phosphosites on 2,896 proteins. The ratios of serine, threonine, and tyrosine phosphosites were 80.01%, 18.11%, and 1.81%, respectively. The majority of proteins (2,111) contained at least two detected phosphorylation sites. Consistent with findings in other fungi, cytoskeletal proteins were among the most highly phosphorylated proteins, and there were differences in Gene Ontology (GO) terms for proteins with serine and threonine versus tyrosine phosphorylation sites. This large-scale analysis identified phosphosites in protein components of Mediator, an important transcriptional coregulatory protein complex. A targeted analysis of the phosphosites in Mediator complex proteins confirmed the large-scale studies, and further in vitro assays identified a subset of these phosphorylations that were catalyzed by Cdk8 (Ssn3), a kinase within the Mediator complex. These data represent the deepest single analysis of a fungal phosphoproteome and lay the groundwork for future analyses of the C. albicans phosphoproteome and specific phosphoproteins. PMID:25750214

  19. Phosphoproteomics technologies and applications in plant biology research

    PubMed Central

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

    2015-01-01

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

  20. Variable Digestion Strategies for Phosphoproteomics Analysis.

    PubMed

    Gonczarowska-Jorge, Humberto; Dell'Aica, Margherita; Dickhut, Clarissa; Zahedi, René P

    2016-01-01

    In recent years, mass spectrometry-based phosphoproteomics has propelled our knowledge about the regulation of cellular pathways. Nevertheless, typically applied bottom-up strategies have several limitations. Trypsin, the preferentially used proteolytic enzyme shows impaired cleavage efficiency in the vicinity of phosphorylation sites. Moreover, depending on the frequency and distribution of tryptic cleavage sites (Arg/Lys), generated peptides can be either too short or too long for confident identification using standard LC-MS approaches. To overcome these limitations, we introduce an alternative and simple approach based on the usage of the nonspecific serine protease subtilisin, which enables a fast and reproducible digestion and provides access to "hidden" areas of the proteome. Thus, in a single LC-MS experiment >1800 phosphopeptides were confidently identified and localized from 125 ?g of HeLa digest, compared to >2100 sites after tryptic digestion. While the overlap was less than 20 %, subtilisin allowed the identification of many phosphorylation sites that are theoretically not accessible via tryptic digestion, thus considerably increasing the coverage of the phosphoproteome. PMID:26584929

  1. Toward defining the phosphoproteome of Xenopus laevis embryos

    PubMed Central

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

    2010-01-01

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

  2. Quantitative phosphoproteome profiling of Wnt3a-mediated signaling network: indicating the involvement of ribonucleoside-diphosphate reductase M2 subunit phosphorylation at residue serine 20 in canonical Wnt signal transduction.

    PubMed

    Tang, Liu-Ya; Deng, Ning; Wang, Lian-Shui; Dai, Jie; Wang, Zheng-Long; Jiang, Xiao-Sheng; Li, Su-Jun; Li, Long; Sheng, Quan-Hu; Wu, Dian-Qing; Li, Lin; Zeng, Rong

    2007-11-01

    The complexity of canonical Wnt signaling comes not only from the numerous components but also from multiple post-translational modifications. Protein phosphorylation is one of the most common modifications that propagates signals from extracellular stimuli to downstream effectors. To investigate the global phosphorylation regulation and uncover novel phosphoproteins at the early stages of canonical Wnt signaling, HEK293 cells were metabolically labeled with two stable isotopic forms of lysine and were stimulated for 0, 1, or 30 min with purified Wnt3a. After phosphoprotein enrichment and LC-MS/MS analysis, 1057 proteins were identified in all three time points. In total 287 proteins showed a 1.5-fold or greater change in at least one time point. In addition to many known Wnt signaling transducers, other phosphoproteins were identified and quantitated, implicating their involvement in canonical Wnt signaling. k-Means clustering analysis showed dynamic patterns for the differential phosphoproteins. Profile pattern and interaction network analysis of the differential phosphoproteins implicated the possible roles for those unreported components in Wnt signaling. Moreover 100 unique phosphorylation sites were identified, and 54 of them were quantitated in the three time points. Site-specific phosphopeptide quantitation revealed that Ser-20 phosphorylation on RRM2 increased upon 30-min Wnt3a stimulation. Further studies with mutagenesis, the Wnt reporter gene assay, and RNA interference indicated that RRM2 functioned downstream of beta-catenin as an inhibitor of Wnt signaling and that Ser-20 phosphorylation of RRM2 counteracted its inhibition effect. Our systematic profiling of dynamic phosphorylation changes responding to Wnt3a stimulation not only presented a comprehensive phosphorylation network regulated by canonical Wnt signaling but also found novel molecules and phosphorylation involved in Wnt signaling. PMID:17693683

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-07-01

    Enteropathogenic Escherichia coli (EPEC) uses a type III secretion system (T3SS) to directly translocate effector proteins into host cells where they play a pivotal role in subverting host cell signaling needed for disease. However, our knowledge of how EPEC affects host protein phosphorylation is limited to a few individual protein studies. We employed a quantitative proteomics approach to globally map alterations in the host phosphoproteome during EPEC infection. By characterizing host phosphorylation events at various time points throughout infection, we examined how EPEC dynamically impacts the host phosphoproteome over time. This experimental setup also enabled identification of T3SS-dependent and -independent changes in host phosphorylation. Specifically, T3SS-regulated events affected various cellular processes that are known EPEC targets, including cytoskeletal organization, immune signaling, and intracellular trafficking. However, the involvement of phosphorylation in these events has thus far been poorly studied. We confirmed the MAPK family as an established key host player, showed its central role in signal transduction during EPEC infection, and extended the repertoire of known signaling hubs with previously unrecognized proteins, including TPD52, CIN85, EPHA2, and HSP27. We identified altered phosphorylation of known EPEC targets, such as cofilin, where the involvement of phosphorylation has so far been undefined, thus providing novel mechanistic insights into the roles of these proteins in EPEC infection. An overlap of regulated proteins, especially those that are cytoskeleton-associated, was observed when compared with the phosphoproteome of Shigella-infected cells. We determined the biological relevance of the phosphorylation of a novel protein in EPEC pathogenesis, septin-9 (SEPT9). Both siRNA knockdown and a phosphorylation-impaired SEPT9 mutant decreased bacterial adherence and EPEC-mediated cell death. In contrast, a phosphorylation-mimicking SEPT9 mutant rescued these effects. Collectively, this study provides the first global analysis of phosphorylation-mediated processes during infection with an extracellular, diarrheagenic bacterial pathogen. PMID:25944883

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

    PubMed Central

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

    2015-01-01

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

  6. The phosphoproteome of human Jurkat T cell clones upon costimulation with anti-CD3/anti-CD28 antibodies.

    PubMed

    Nguyen, Tien Dung; Carrascal, Montserrat; Vidal-Cortes, Oriol; Gallardo, Oscar; Casas, Vanessa; Gay, Marina; Phan, Van Chi; Abian, Joaquin

    2016-01-10

    Phosphorylation is a reversible post-translational modification, playing a vital role in protein function. In T cells, protein phosphorylation is the key mechanism regulating T cell receptor-driven signaling pathways. In order to gain insights into the phosphoproteome evolution of T cell activation, we performed a large-scale quantitative phosphoproteomics study of Jurkat E6.1 (wild type) and Jurkat gamma1 (Phospholipase gamma1 null) cell clones upon costimulation with anti-CD3 and anti-CD28 antibodies at times ranging from 15min to as long as 120min. In total, we identified 5585 phosphopeptides belonging to 2008 phosphoproteins from both cell clones. We detected 130 and 114 novel phosphopeptides in Jurkat E6.1 and Jurkat gamma1 clones, respectively. A significantly lower number of proteins containing regulated phosphorylation sites were identified in Jurkat gamma1 in comparison to Jurkat E6.1, reflecting the vital role of Phospholipase gamma1 in T cell signaling. Several new phosphorylation sites from lymphocyte-specific protein tyrosine kinase (Lck) were identified. Of these, serine-121 showed significant changes in JE6.1 while only small changes in the Jgamma1 clone. Our data may contribute to the current human T cell phosphoproteome and provide a better understanding on T cell receptor signaling. Data are available via ProteomeXchange with identifier PXD002871. PMID:26546556

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

    PubMed Central

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

    2013-01-01

    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

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

    PubMed

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

    2015-05-10

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

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

    PubMed Central

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

    2015-01-01

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

  10. Dissecting Classroom Ethics.

    ERIC Educational Resources Information Center

    Allchin, Douglas

    1991-01-01

    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)

  11. The Problems of Dissection.

    ERIC Educational Resources Information Center

    Davis, Pat

    1997-01-01

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

  12. Proteome, Phosphoproteome, and Hydroxyproteome of Liver Mitochondria in

    E-print Network

    Tian, Weidong

    and ectopic fat storage in liver (5). The dysfunction of mitochondria damages the pancreatic -cellsProteome, Phosphoproteome, and Hydroxyproteome of Liver Mitochondria in Diabetic Rats at Early mechanisms, we performed a mul- tiplexed proteomics study on liver mitochondria isolated from a spontaneous

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

    PubMed Central

    2014-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  15. Dissecting heart failure.

    PubMed

    Verma, Sameer; Gupta, Sameer; Guglin, Maya

    2014-06-01

    Dissection of ascending aorta is a medical emergency typically presenting with acute chest or back pain and hemodynamic instability. We are reporting a very unusual case of dissection of a large ascending aortic aneurysm presenting as a new onset heart failure. A 46-year-old man presented with gradually increasing dyspnea and orthopnea. His physical examination and laboratory findings were consistent with heart failure. The only unusual feature was a diastolic murmur, which prompted echocardiographic evaluation. Besides left ventricular dilatation, hypertrophy, and severe global hypokinesis, which were expected, we also found severely dilated aortic root with aortic regurgitation and a 8.6×9.7 cm ascending aortic aneurysm with dissection. The patient had a brother who died several years earlier from aortic dissection. Surgical treatment was successful. Type A aortic dissection may rarely present as heart failure. Aortic dissection at young age should prompt screening of first-degree relatives because genetic nature of the disease is very likely. PMID:24418447

  16. Global impact of Salmonella pathogenicity island 2-secreted effectors on the host phosphoproteome.

    PubMed

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

    2013-06-01

    During the late stages of infection, Salmonella secretes numerous effectors through a type III secretion system that is encoded within Salmonella pathogenicity island 2 (SPI2). Despite the importance of SPI2 as a major virulence factor leading to the systemic spread of the bacteria and diseases, a global view of its effects on host responses is still lacking. Here, we measured global impacts of SPI2 effectors on the host phosphorylation and protein expression levels in RAW264.7 and in HeLa cells, as macrophage and nonphagocytic models of infection. We observe that SPI2 effectors differentially modulate the host phosphoproteome and cellular processes (e.g. protein trafficking, cytoskeletal regulation, and immune signaling) in a host cell-dependent manner. Our unbiased approach reveals the involvement of many previously unrecognized proteins, including E3 ligases (HERC4, RanBP2, and RAD18), kinases (CDK, SIK3, and WNK1), and histones (H2B1F, H4, and H15), in late stages of Salmonella infection. Furthermore, from this phosphoproteome analysis and other quantitative screens, we identified HSP27 as a direct in vitro and in vivo molecular target of the only type III secreted kinase, SteC. Using biochemical and cell biological assays, we demonstrate that SteC phosphorylates multiple sites in HSP27 and induces actin rearrangement through this protein. Together, these results provide a broader landscape of host players contributing to specific processes/pathways mediated by SPI2 effectors than was previously appreciated. PMID:23459991

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

    PubMed Central

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

    2014-01-01

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

  18. Phosphoproteomic Analyses Reveal Early Signaling Events in the Osmotic Stress Response.

    PubMed

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

    2014-05-01

    Elucidating how plants sense and respond to water loss is important for identifying genetic and chemical interventions that may help sustain crop yields in water-limiting environments. Currently, the molecular mechanisms involved in the initial perception and response to dehydration are not well understood. Modern mass spectrometric methods for quantifying changes in the phosphoproteome provide an opportunity to identify key phosphorylation events involved in this process. Here, we have used both untargeted and targeted isotope-assisted mass spectrometric methods of phosphopeptide quantitation to characterize proteins in Arabidopsis (Arabidopsis thaliana) whose degree of phosphorylation is rapidly altered by hyperosmotic treatment. Thus, protein phosphorylation events responsive to 5 min of 0.3 m mannitol treatment were first identified using (15)N 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

  19. Proteomics and Phosphoproteomics Analysis of Human Lens Fiber Cell Membranes

    PubMed Central

    Wang, Zhen; Han, Jun; David, Larry L.; Schey, Kevin L.

    2013-01-01

    Purpose. The human lens fiber cell insoluble membrane fraction contains important membrane proteins, cytoskeletal proteins, and cytosolic proteins that are strongly associated with the membrane. The purpose of this study was to characterize the lens fiber cell membrane proteome and phosphoproteome from human lenses. Methods. HPLC-mass spectrometry–based multidimensional protein identification technology (MudPIT), without or with phosphopeptide enrichment, was applied to study the proteome and phosphoproteome of lens fiber cell membranes, respectively. Results. In total, 951 proteins were identified, including 379 integral membrane and membrane-associated proteins. Enriched gene categories and pathways based on the proteomic analysis include carbohydrate metabolism (glycolysis/gluconeogenesis, pentose phosphate pathway, pyruvate metabolism), proteasome, cell-cell signaling and communication (GTP binding, gap junction, focal adhesion), glutathione metabolism, and actin regulation. The combination of TiO2 phosphopeptide enrichment and MudPIT analysis revealed 855 phosphorylation sites on 271 proteins, including 455 phosphorylation sites that have not been previously identified. PKA, PKC, CKII, p38MAPK, and RSK are predicted as the major kinases for phosphorylation on the sites identified in the human lens membrane fraction. Conclusions. The results presented herein significantly expand the characterized proteome and phosphoproteome of the human lens fiber cell and provide a valuable reference for future research in studies of lens development and disease. PMID:23349431

  20. Quantitative Analysis of Tissue Samples by Combining iTRAQ Isobaric Labeling with Selected/Multiple Reaction Monitoring (SRM/MRM).

    PubMed

    Narumi, Ryohei; Tomonaga, Takeshi

    2016-01-01

    Mass spectrometry-based phosphoproteomics is an indispensible technique used in the discovery and quantification of phosphorylation events on proteins in biological samples. The application of this technique to tissue samples is especially useful for the discovery of biomarkers as well as biological studies. We herein describe the application of a large-scale phosphoproteome analysis and SRM/MRM-based quantitation to develop a strategy for the systematic discovery and validation of biomarkers using tissue samples. PMID:26584920

  1. Mass spectrometry-driven phosphoproteomics: patterning the systems biology mosaic.

    PubMed

    Jünger, Martin A; Aebersold, Ruedi

    2014-01-01

    Protein phosphorylation is the best-studied posttranslational modification and plays a role in virtually every biological process. Phosphoproteomics is the analysis of protein phosphorylation on a proteome-wide scale, and mainly uses the same instrumentation and analogous strategies as conventional mass spectrometry (MS)-based proteomics. Measurements can be performed either in a discovery-type, also known as shotgun mode, or in a targeted manner which monitors a set of a priori known phosphopeptides, such as members of a signal transduction pathway, across biological samples. Here, we delineate the different experimental levels at which measures can be taken to optimize the scope, reliability, and information content of phosphoproteomic analyses. Various chromatographic and chemical protocols exist to physically enrich phosphopeptides from proteolytic digests of biological samples. Subsequent mass spectrometric analysis revolves around peptide ion fragmentation to generate sequence information and identify the backbone sequence of phosphopeptides as well as the phosphate group attachment site(s), and different modes of fragmentation like collision-induced dissociation (CID), electron transfer dissociation (ETD), and higher energy collisional dissociation (HCD) have been established for phosphopeptide analysis. Computational tools are important for the identification and quantification of phosphopeptides and mapping of phosphorylation sites, the deposition of large-scale phosphoproteome datasets in public databases, and the extraction of biologically meaningful information by data mining, integration with other data types, and descriptive or predictive modeling. Finally, we discuss how orthogonal experimental approaches can be employed to validate newly identified phosphorylation sites on a biochemical, mechanistic, and physiological level. PMID:24902836

  2. Search Databases and Statistics: Pitfalls and Best Practices in Phosphoproteomics.

    PubMed

    Refsgaard, Jan C; Munk, Stephanie; Jensen, Lars J

    2016-01-01

    Advances in mass spectrometric instrumentation in the past 15 years have resulted in an explosion in the raw data yield from typical phosphoproteomics workflows. This poses the challenge of confidently identifying peptide sequences, localizing phosphosites to proteins and quantifying these from the vast amounts of raw data. This task is tackled by computational tools implementing algorithms that match the experimental data to databases, providing the user with lists for downstream analysis. Several platforms for such automated interpretation of mass spectrometric data have been developed, each having strengths and weaknesses that must be considered for the individual needs. These are reviewed in this chapter. Equally critical for generating highly confident output datasets is the application of sound statistical criteria to limit the inclusion of incorrect peptide identifications from database searches. Additionally, careful filtering and use of appropriate statistical tests on the output datasets affects the quality of all downstream analyses and interpretation of the data. Our considerations and general practices on these aspects of phosphoproteomics data processing are presented here. PMID:26584936

  3. Two Dimensional Gel Electrophoresis-Based Plant Phosphoproteomics.

    PubMed

    Han, Chao; Yang, Pingfang

    2016-01-01

    Phosphorylation is one of the most important reversible protein modifications and is involved in regulating signal transduction, subcellular localization and enzyme activity of target proteins. Phosphorylation or dephosphorylation of proteins is directly reflected in changed ratios of phosphoprotein abundance and total protein abundance. Two-dimensional gel electrophoresis (2-DE)-based proteomics allow quantification of both total protein abundance by Coomassie Brilliant Blue (CBB) staining and phosphoprotein abundance by fluorescence-based staining. Pro-Q diamond phosphoprotein stain (Pro-Q DPS) can bind to the phosphate moiety of the phospho-amino acid directly, regardless of the nature of the phospho-amino acid. Phosphoproteins can thus be detected using proper excitation light, quantified using image analysis software and subsequently be subjected to analysis by mass spectrometry. Here, we describe a protein phosphorylation status analysis method combining both CBB and Pro-Q DPS staining based on 2-DE gel-based phosphoproteomics, which has been widely applied to plant phosphoproteomics studies. PMID:26584928

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

    Cancer.gov

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

  5. A unifying experimental design for dissecting tree genomes.

    PubMed

    Sun, Lidan; Zhu, Xuli; Zhang, Qixiang; Wu, Rongling

    2015-08-01

    Linkage mapping and association mapping are adopted as an approach of choice for dissecting complex traits, but each shows a limitation when used alone. We propose an open-pollinated (OP) family design to integrate these two approaches into an organizing framework. The design unifies the strengths of population and quantitative genetic studies for evolutionary inference and high-resolution gene mapping. It particularly suits genome dissection of forest trees given their extant populations that are mostly undomesticated. PMID:26094003

  6. Postpartum vertebral artery dissection.

    PubMed

    Finley, Amanda; Rogers, Brenton; Richards, Theodore; Vogel, Heather

    2015-01-01

    We report a case of a right vertebral artery dissection in a 35-year-old woman, 3?weeks post partum, with manifestations of vertebrobasilar disease. She was 3?weeks out from the uneventful delivery of her fourth child, with presentation of acute neurological symptoms, predominantly intractable vertigo. Vertigo can have many non-specific generalised symptoms and clinical findings. Postpartum women have a lengthy list of possible aetiologies of vertigo not limited to our initially suspected preeclampsia, dural venous thrombosis and vertebral dissection. PMID:26604230

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

    PubMed

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

    2014-12-01

    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

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

    PubMed

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

    2016-01-01

    Understanding molecular mechanisms underlying plant salinity tolerance provides valuable knowledgebase for effective crop improvement through genetic engineering. Current proteomic technologies, which support reliable and high-throughput analyses, have been broadly used for exploring sophisticated molecular networks in plants. In the current study, we compared phosphoproteomic and proteomic changes in roots of different soybean seedlings of a salt-tolerant cultivar (Wenfeng07) and a salt-sensitive cultivar (Union85140) induced by salt stress. The root samples of Wenfeng07 and Union85140 at three-trifoliate stage were collected at 0 h, 0.5 h, 1 h, 4 h, 12 h, 24 h, and 48 h after been treated with 150 mm NaCl. LC-MS/MS based phosphoproteomic analysis of these samples identified a total of 2692 phosphoproteins and 5509 phosphorylation sites. Of these, 2344 phosphoproteins containing 3744 phosphorylation sites were quantitatively analyzed. Our results showed that 1163 phosphorylation sites were differentially phosphorylated in the two compared cultivars. Among them, 10 MYB/MYB transcription factor like proteins were identified with fluctuating phosphorylation modifications at different time points, indicating that their crucial roles in regulating flavonol accumulation might be mediated by phosphorylated modifications. In addition, the protein expression profiles of these two cultivars were compared using LC MS/MS based shotgun proteomic analysis, and expression pattern of all the 89 differentially expressed proteins were independently confirmed by qRT-PCR. Interestingly, the enzymes involved in chalcone metabolic pathway exhibited positive correlations with salt tolerance. We confirmed the functional relevance of chalcone synthase, chalcone isomerase, and cytochrome P450 monooxygenase genes using soybean composites and Arabidopsis thaliana mutants, and found that their salt tolerance were positively regulated by chalcone synthase, but was negatively regulated by chalcone isomerase and cytochrome P450 monooxygenase. A novel salt tolerance pathway involving chalcone metabolism, mostly mediated by phosphorylated MYB transcription factors, was proposed based on our findings. (The mass spectrometry raw data are available via ProteomeXchange with identifier PXD002856). PMID:26407991

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

    PubMed Central

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

    2015-01-01

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

  10. Phosphoproteomics Identifies CK2 as a Negative Regulator of Beige Adipocyte Thermogenesis and Energy Expenditure.

    PubMed

    Shinoda, Kosaku; Ohyama, Kana; Hasegawa, Yutaka; Chang, Hsin-Yi; Ogura, Mayu; Sato, Ayaka; Hong, Haemin; Hosono, Takashi; Sharp, Louis Z; Scheel, David W; Graham, Mark; Ishihama, Yasushi; Kajimura, Shingo

    2015-12-01

    Catecholamines promote lipolysis both in brown and white adipocytes, whereas the same stimuli preferentially activate thermogenesis in brown adipocytes. Molecular mechanisms for the adipose-selective activation of thermogenesis remain poorly understood. Here, we employed quantitative phosphoproteomics to map global and temporal phosphorylation profiles in brown, beige, and white adipocytes under ?3-adrenenoceptor activation and identified kinases responsible for the adipose-selective phosphorylation profiles. We found that casein kinase2 (CK2) activity is preferentially higher in white adipocytes than brown/beige adipocytes. Genetic or pharmacological blockade of CK2 in white adipocytes activates the thermogenic program in response to cAMP stimuli. Such activation is largely through reduced CK2-mediated phosphorylation of class I HDACs. Notably, inhibition of CK2 promotes beige adipocyte biogenesis and leads to an increase in whole-body energy expenditure and ameliorates diet-induced obesity and insulin resistance. These results indicate that CK2 is a plausible target to rewire the ?3-adrenenoceptor signaling cascade that promotes thermogenesis in adipocytes. PMID:26525534

  11. Phosphoproteome dynamics reveal novel ERK1/2 MAP kinase substrates with broad spectrum of functions

    PubMed Central

    Courcelles, Mathieu; Frémin, Christophe; Voisin, Laure; Lemieux, Sébastien; Meloche, Sylvain; Thibault, Pierre

    2013-01-01

    The ERK1/2 MAP kinase pathway is an evolutionarily conserved signaling module that controls many fundamental physiological processes. Deregulated activity of ERK1/2 MAP kinases is associated with developmental syndromes and several human diseases. Despite the importance of this pathway, a comprehensive picture of the natural substrate repertoire and biochemical mechanisms regulated by ERK1/2 is still lacking. In this study, we used large-scale quantitative phosphoproteomics and bioinformatics analyses to identify novel candidate ERK1/2 substrates based on their phosphorylation signature and kinetic profiles in epithelial cells. We identified a total of 7936 phosphorylation sites within 1861 proteins, of which 155 classify as candidate ERK1/2 substrates, including 128 new targets. Candidate ERK1/2 substrates are involved in diverse cellular processes including transcriptional regulation, chromatin remodeling, RNA splicing, cytoskeleton dynamics, cellular junctions and cell signaling. Detailed characterization of one newly identified substrate, the transcriptional regulator JunB, revealed that ERK1/2 phosphorylate JunB on a serine adjacent to the DNA-binding domain, resulting in increased DNA-binding affinity and transcriptional activity. Our study expands the spectrum of cellular functions controlled by ERK1/2 kinases. PMID:23712012

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

    PubMed Central

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

    2015-01-01

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

  13. Alternatives To Dissection. Second Edition.

    ERIC Educational Resources Information Center

    DeRosa, Bill, Ed.; Winiarskyj, Lesia, Ed.

    This packet attempts to provide educationally sound alternatives to dissection in the classroom, thereby making it possible for teachers to eliminate dissection from the curriculum. This packet can also be used by educators who include dissection in their curricula but consider it important to respect the expression of students' ethical, moral, or…

  14. Dissecting Diversity Part II

    ERIC Educational Resources Information Center

    Matthews, Frank

    2005-01-01

    This article presents "Dissecting Diversity, Part II," the conclusion of a wide-ranging two-part roundtable discussion on diversity in higher education. The participants were as follows: Lezli Baskerville, J.D., President and CEO of the National Association for Equal Opportunity (NAFEO); Dr. Gerald E. Gipp, Executive Director of the American…

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

    PubMed

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

    2013-09-01

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

  16. Temporal Phosphoproteome Dynamics Induced by an ATP Synthase Inhibitor Citreoviridin.

    PubMed

    Hu, Chia-Wei; Hsu, Chia-Lang; Wang, Yu-Chao; Ishihama, Yasushi; Ku, Wei-Chi; Huang, Hsuan-Cheng; Juan, Hsueh-Fen

    2015-12-01

    Citreoviridin, one of toxic mycotoxins derived from fungal species, can suppress lung cancer cell growth by inhibiting the activity of ectopic ATP synthase, but has limited effect on normal cells. However, the mechanism of citreoviridin triggering dynamic molecular responses in cancer cells remains unclear. Here, we performed temporal phosphoproteomics to elucidate the dynamic changes after citreoviridin treatment in cells and xenograft model. We identified a total of 829 phosphoproteins and demonstrated that citreoviridin treatment affects protein folding, cell cycle, and cytoskeleton function. Furthermore, response network constructed by mathematical modeling shows the relationship between the phosphorylated heat shock protein 90 ? and mitogen-activated protein kinase signaling pathway. This work describes that citreoviridin suppresses cancer cell growth and mitogen-activated protein kinase/extracellular signal-regulated kinase signaling by site-specific dephosphorylation of HSP90AB1 on Serine 255 and provides perspectives in cancer therapeutic strategies. PMID:26503892

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

    PubMed

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

    2015-05-01

    Abscisic acid (ABA)ą is a plant hormone that controls many aspects of plant growth, including seed germination, stomatal aperture size, and cellular drought response. ABA interacts with a unique family of 14 receptor proteins. This interaction leads to the activation of a family of protein kinases, SnRK2s, which in turn phosphorylate substrates involved in many cellular processes. The family of receptors appears functionally redundant. To observe a measurable phenotype, four of the fourteen receptors have to be mutated to create a multilocus loss-of-function quadruple receptor (QR) mutant, which is much less sensitive to ABA than wild-type (WT) plants. Given these phenotypes, we asked whether or not a difference in ABA response between the WT and QR backgrounds would manifest on a phosphorylation level as well. We tested WT and QR mutant ABA response using isotope-assisted quantitative phosphoproteomics to determine what ABA-induced phosphorylation changes occur in WT plants within 5 min of ABA treatment and how that phosphorylation pattern is altered in the QR mutant. We found multiple ABA-induced phosphorylation changes that occur within 5 min of treatment, including three SnRK2 autophosphorylation events and phosphorylation on SnRK2 substrates. The majority of robust ABA-dependent phosphorylation changes observed were partially diminished in the QR mutant, whereas many smaller ABA-dependent phosphorylation changes observed in the WT were not responsive to ABA in the mutant. A single phosphorylation event was increased in response to ABA treatment in both the WT and QR mutant. A portion of the discovery data was validated using selected reaction monitoring-based targeted measurements on a triple quadrupole mass spectrometer. These data suggest that different subsets of phosphorylation events depend upon different subsets of the ABA receptor family to occur. Altogether, these data expand our understanding of the model by which the family of ABA receptors directs rapid phosphoproteomic changes. PMID:25693798

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

    PubMed

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

    2014-01-01

    Within the past two decades, the biological application of mass spectrometric technology has seen great advances in terms of innovations in hardware, software, and reagents. Concurrently, the burgeoning field of proteomics has followed closely (Yates et al., Annu Rev Biomed Eng 11:49-79, 2009)-and with it, importantly, the ability to globally assay altered levels of posttranslational modifications in response to a variety of stimuli. Though many posttranslational modifications have been described, a major focus of these efforts has been protein-level phosphorylation of serine, threonine, and tyrosine residues (Schreiber et al., Proteomics 8:4416-4432, 2008). The desire to examine changes across signal transduction cascades and networks in their entirety using a single mass spectrometric analysis accounts for this push-namely, preservation and enrichment of the transient yet informative phosphoryl side group. Analyzing global changes in phosphorylation allows inferences surrounding cascades/networks as a whole to be made. Towards this same end, much work has explored ways to permit quantitation and combine experimental samples such that more than one replicate or experimental condition can be identically processed and analyzed, cutting down on experimental and instrument variability, in addition to instrument run time. One such technique that has emerged is metabolic labeling (Gouw et al., Mol Cell Proteomics 9:11-24, 2010), wherein biological samples are labeled in living cells with nonradioactive heavy isotopes such as (15)N or (13)C. Since metabolic labeling in living organisms allows one to combine the material to be processed at the earliest possible step, before the tissue is homogenized, it provides a unique and excellent method for comparing experimental samples in a high-throughput, reproducible fashion with minimal technical variability. This chapter describes a pipeline used for labeling living Arabidopsis thaliana plants with nitrogen-15 ((15)N) and how this can be used, in conjunction with a technique for enrichment of phosphorylated peptides (phosphopeptides), to determine changes in A. thaliana's phosphoproteome on an untargeted, global scale. PMID:24057376

  19. "Dissection" of a Hair Dryer

    ERIC Educational Resources Information Center

    Eisenstein, Stan; Simpson, Jeff

    2008-01-01

    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…

  20. Automatic Dissection Of Plantlets

    NASA Astrophysics Data System (ADS)

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

    1989-03-01

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

  1. Immobilized zirconium ion affinity chromatography for specific enrichment of phosphopeptides in phosphoproteome analysis.

    PubMed

    Feng, Shun; Ye, Mingliang; Zhou, Houjiang; Jiang, Xiaogang; Jiang, Xingning; Zou, Hanfa; Gong, Bolin

    2007-09-01

    Large scale characterization of phosphoproteins requires highly specific methods for purification of phosphopeptides because of the low abundance of phosphoproteins and substoichiometry of phosphorylation. Enrichment of phosphopeptides from complex peptide mixtures by IMAC is a popular way to perform phosphoproteome analysis. However, conventional IMAC adsorbents with iminodiacetic acid as the chelating group to immobilize Fe(3+) lack enough specificity for efficient phosphoproteome analysis. Here we report a novel IMAC adsorbent through Zr(4+) chelation to the phosphonate-modified poly(glycidyl methacrylate-co-ethylene dimethacrylate) polymer beads. The high specificity of Zr(4+)-IMAC adsorbent was demonstrated by effectively enriching phosphopeptides from the digest mixture of phosphoprotein (alpha- or beta-casein) and bovine serum albumin with molar ratio at 1:100. Zr(4+)-IMAC adsorbent was also successfully applied for the analysis of mouse liver phosphoproteome, resulting in the identification of 153 phosphopeptides (163 phosphorylation sites) from 133 proteins in mouse liver lysate. Significantly more phosphopeptides were identified than by the conventional Fe(3+)-IMAC approach, indicating the excellent performance of the Zr(4+)-IMAC approach. The high specificity of Zr(4+)-IMAC adsorbent was found to mainly result from the strong interaction between chelating Zr(4+) and phosphate group on phosphopeptides. Enrichment of phosphopeptides by Zr(4+)-IMAC provides a powerful approach for large scale phosphoproteome analysis. PMID:17575324

  2. Highly sensitive phosphoproteomics by tailoring solid-phase extraction to electrostatic repulsion-hydrophilic interaction chromatography.

    PubMed

    Loroch, Stefan; Zahedi, René Peiman; Sickmann, Albert

    2015-02-01

    In the past decade, several strategies for comprehensive phosphoproteome analysis have been introduced. Most of them combine different phosphopeptide enrichment techniques and require starting material in the milligram range, as a consequence of their insufficient sensitivity. This limitation impairs the applicability of phosphoproteomics to a wide variety of clinical research, where sample material is highly limited. Here we introduce a highly sensitive and easy-to-establish 2D bottom-up strategy for microgram-scale phosphoproteomics, based on electrostatic repulsion-hydrophilic interaction chromatography (ERLIC), a simple solid-phase extraction step by strong cation exchange (SCX) or reversed phase (RP), and LC-MS analysis. With only 100 ?g of tryptic digested, nonstimulated HeLa protein and 45 h of LC-MS analysis time, we identified ?7500 nonredundant and highly confident phosphorylation sites (per replicate). We assigned all phosphorylation sites to 3013 phosphoproteins, covering the entire dynamic range from 10(7) down to a few copies per cell. Compared to affinity-based-enrichment methods using Ti(4+), our ERLIC-based strategy enriched considerably longer and more acidic phosphopeptides and consequently, we identified 327 phosphorylated C-terminal peptides. The simplicity and high sensitivity of ERLIC-SCX/RP-LC-MS render its future promising for microgram-scale-phosphoproteomics in biological, biomedical, and clinical research. PMID:25405705

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

    PubMed Central

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

    2014-01-01

    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

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

    PubMed

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

    2015-12-01

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

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

    PubMed Central

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

    2013-01-01

    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

  6. Experience with parametric binary dissection

    NASA Technical Reports Server (NTRS)

    Bokhari, Shahid H.

    1993-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  8. Phosphoproteomic Analysis Identifies Focal Adhesion Kinase 2 (FAK2) as a Potential Therapeutic Target for Tamoxifen Resistance in Breast Cancer.

    PubMed

    Wu, Xinyan; Zahari, Muhammad Saddiq; Renuse, Santosh; Nirujogi, Raja Sekhar; Kim, Min-Sik; Manda, Srikanth S; Stearns, Vered; Gabrielson, Edward; Sukumar, Saraswati; Pandey, Akhilesh

    2015-11-01

    Tamoxifen, an estrogen receptor-? (ER) antagonist, is an important agent for the treatment of breast cancer. However, this therapy is complicated by the fact that a substantial number of patients exhibit either de novo or acquired resistance. To characterize the signaling mechanisms underlying this resistance, we treated the MCF7 breast cancer cell line with tamoxifen for over six months and showed that this cell line acquired resistance to tamoxifen in vitro and in vivo. We performed SILAC-based quantitative phosphoproteomic profiling on the tamoxifen resistant and vehicle-treated sensitive cell lines to quantify the phosphorylation alterations associated with tamoxifen resistance. From >5600 unique phosphopeptides identified, 1529 peptides exhibited hyperphosphorylation and 409 peptides showed hypophosphorylation in the tamoxifen resistant cells. Gene set enrichment analysis revealed that focal adhesion pathway was one of the most enriched signaling pathways activated in tamoxifen resistant cells. Significantly, we showed that the focal adhesion kinase FAK2 was not only hyperphosphorylated but also transcriptionally up-regulated in tamoxifen resistant cells. FAK2 suppression by specific siRNA knockdown or a small molecule inhibitor repressed cellular proliferation in vitro and tumor formation in vivo. More importantly, our survival analysis revealed that high expression of FAK2 is significantly associated with shorter metastasis-free survival in estrogen receptor-positive breast cancer patients treated with tamoxifen. Our studies suggest that FAK2 is a potential therapeutic target for the management of hormone-refractory breast cancers. PMID:26330541

  9. Early history of neck dissection.

    PubMed

    Rinaldo, Alessandra; Ferlito, Alfio; Silver, Carl E

    2008-12-01

    With the exception of distant metastases, the presence of lymph node metastasis in the neck is accepted as the single most important adverse independent prognostic factor and an indicator of survival in squamous carcinoma of the head and neck. Neck dissection in its various forms is the standard surgical treatment for clinical, subclinical and subpathologic metastatic cancer to the neck. The pertinent literature from the beginning of the nineteenth century to the middle of the twentieth century was reviewed. The four giants of late nineteenth century surgery: von Langenbeck, Billroth, von Volkmann and Kocher developed and reported the early cases of different types of neck dissection. Butlin, in England, conceived and developed the concept of elective neck dissection. In 1888, the Polish surgeon Jawdy?sky reported and described in detail the first successful extended en bloc neck dissection. Crile, in 1905 and 1906, reported the first significant series of radical en bloc neck dissections, bringing this procedure to the attention of the medical world as an effective operation with reproducible technique and results. The greatest impetus to the status of this surgical procedure came from Martin and colleagues, who published a monumental report in 1951 of 1,450 cases that established the place and technique of radical neck dissection in the modern treatment of head and neck cancer. Neck dissection, for treatment of cervical lymph node metastases in head and neck cancer, was conceived and attempted in the nineteenth century, with some limited success reported by the end of that era. An effective operation was described and reported in the early twentieth century and evolved by the mid century into a fundamental tool in the management of patients with head and neck cancer. PMID:18488240

  10. Phosphoproteomic screening identifies Rab GTPases as novel downstream targets of PINK1.

    PubMed

    Lai, Yu-Chiang; Kondapalli, Chandana; Lehneck, Ronny; Procter, James B; Dill, Brian D; Woodroof, Helen I; Gourlay, Robert; Peggie, Mark; Macartney, Thomas J; Corti, Olga; Corvol, Jean-Christophe; Campbell, David G; Itzen, Aymelt; Trost, Matthias; Muqit, Miratul Mk

    2015-11-12

    Mutations in the PTEN-induced kinase 1 (PINK1) are causative of autosomal recessive Parkinson's disease (PD). We have previously reported that PINK1 is activated by mitochondrial depolarisation and phosphorylates serine 65 (Ser(65)) of the ubiquitin ligase Parkin and ubiquitin to stimulate Parkin E3 ligase activity. Here, we have employed quantitative phosphoproteomics to search for novel PINK1-dependent phosphorylation targets in HEK (human embryonic kidney) 293 cells stimulated by mitochondrial depolarisation. This led to the identification of 14,213 phosphosites from 4,499 gene products. Whilst most phosphosites were unaffected, we strikingly observed three members of a sub-family of Rab GTPases namely Rab8A, 8B and 13 that are all phosphorylated at the highly conserved residue of serine 111 (Ser(111)) in response to PINK1 activation. Using phospho-specific antibodies raised against Ser(111) of each of the Rabs, we demonstrate that Rab Ser(111) phosphorylation occurs specifically in response to PINK1 activation and is abolished in HeLa PINK1 knockout cells and mutant PINK1 PD patient-derived fibroblasts stimulated by mitochondrial depolarisation. We provide evidence that Rab8A GTPase Ser(111) phosphorylation is not directly regulated by PINK1 in vitro and demonstrate in cells the time course of Ser(111) phosphorylation of Rab8A, 8B and 13 is markedly delayed compared to phosphorylation of Parkin at Ser(65). We further show mechanistically that phosphorylation at Ser(111) significantly impairs Rab8A activation by its cognate guanine nucleotide exchange factor (GEF), Rabin8 (by using the Ser111Glu phosphorylation mimic). These findings provide the first evidence that PINK1 is able to regulate the phosphorylation of Rab GTPases and indicate that monitoring phosphorylation of Rab8A/8B/13 at Ser(111) may represent novel biomarkers of PINK1 activity in vivo. Our findings also suggest that disruption of Rab GTPase-mediated signalling may represent a major mechanism in the neurodegenerative cascade of Parkinson's disease. PMID:26471730

  11. Phosphoproteomic screening identifies Rab GTPases as novel downstream targets of PINK1

    PubMed Central

    Lai, Yu-Chiang; Kondapalli, Chandana; Lehneck, Ronny; Procter, James B; Dill, Brian D; Woodroof, Helen I; Gourlay, Robert; Peggie, Mark; Macartney, Thomas J; Corti, Olga; Corvol, Jean-Christophe; Campbell, David G; Itzen, Aymelt; Trost, Matthias; Muqit, Miratul MK

    2015-01-01

    Mutations in the PTEN-induced kinase 1 (PINK1) are causative of autosomal recessive Parkinson's disease (PD). We have previously reported that PINK1 is activated by mitochondrial depolarisation and phosphorylates serine 65 (Ser65) of the ubiquitin ligase Parkin and ubiquitin to stimulate Parkin E3 ligase activity. Here, we have employed quantitative phosphoproteomics to search for novel PINK1-dependent phosphorylation targets in HEK (human embryonic kidney) 293 cells stimulated by mitochondrial depolarisation. This led to the identification of 14,213 phosphosites from 4,499 gene products. Whilst most phosphosites were unaffected, we strikingly observed three members of a sub-family of Rab GTPases namely Rab8A, 8B and 13 that are all phosphorylated at the highly conserved residue of serine 111 (Ser111) in response to PINK1 activation. Using phospho-specific antibodies raised against Ser111 of each of the Rabs, we demonstrate that Rab Ser111 phosphorylation occurs specifically in response to PINK1 activation and is abolished in HeLa PINK1 knockout cells and mutant PINK1 PD patient-derived fibroblasts stimulated by mitochondrial depolarisation. We provide evidence that Rab8A GTPase Ser111 phosphorylation is not directly regulated by PINK1 in vitro and demonstrate in cells the time course of Ser111 phosphorylation of Rab8A, 8B and 13 is markedly delayed compared to phosphorylation of Parkin at Ser65. We further show mechanistically that phosphorylation at Ser111 significantly impairs Rab8A activation by its cognate guanine nucleotide exchange factor (GEF), Rabin8 (by using the Ser111Glu phosphorylation mimic). These findings provide the first evidence that PINK1 is able to regulate the phosphorylation of Rab GTPases and indicate that monitoring phosphorylation of Rab8A/8B/13 at Ser111 may represent novel biomarkers of PINK1 activity in vivo. Our findings also suggest that disruption of Rab GTPase-mediated signalling may represent a major mechanism in the neurodegenerative cascade of Parkinson's disease. PMID:26471730

  12. Simple and Reproducible Sample Preparation for Single-Shot Phosphoproteomics with High Sensitivity.

    PubMed

    Jersie-Christensen, Rosa R; Sultan, Abida; Olsen, Jesper V

    2016-01-01

    The traditional sample preparation workflow for mass spectrometry (MS)-based phosphoproteomics is time consuming and usually requires multiple steps, e.g., lysis, protein precipitation, reduction, alkylation, digestion, fractionation, and phosphopeptide enrichment. Each step can introduce chemical artifacts, in vitro protein and peptide modifications, and contaminations. Those often result in sample loss and affect the sensitivity, dynamic range and accuracy of the mass spectrometric analysis. Here we describe a simple and reproducible phosphoproteomics protocol, where lysis, denaturation, reduction, and alkylation are performed in a single step, thus reducing sample loss and increasing reproducibility. Moreover, unlike standard cell lysis procedures the cell harvesting is performed at high temperatures (99 °C) and without detergents and subsequent need for protein precipitation. Phosphopeptides are enriched using TiO2 beads and the orbitrap mass spectrometer is operated in a sensitive mode with higher energy collisional dissociation (HCD). PMID:26584931

  13. [Pregnancy and coronary artery dissection].

    PubMed

    Martínez-Quintana, Efrén; Rodríguez-González, Fayna

    2015-01-01

    Acute myocardial infarction during pregnancy is associated with high maternal and fetal mortality. Coronary atherosclerosis is the most common cause due to an increase in the age of the patients and the association with cardiovascular risk factors such as smoking, hypertension, diabetes mellitus, preeclampsia, and the existence of family history of coronary disease. However, thrombosis, coronary dissection or coronary vasospasms are other causes that may justify it. We report the case of a 33 weeks pregnant first-time mother, without cardiovascular risk factors, who presented an acute coronary event in the context of atherosclerotic disease and coronary dissection after percutaneous coronary intervention. PMID:25795261

  14. [Tonsillar microsurgery by bipolar dissection].

    PubMed

    Sánchez del Hoyo, A; Lacosta Nicolás, J L; Má Salóm, J; Martínez Torre, I; Fernández Martín, M J

    1995-01-01

    The 66 amygdalectomies done by the AA. under general anesthesia and tracheal intubation are considered in two groups. The first one was composed by 32 patients operated following a dissection and coagulation procedure with the aid of a bipolar forceps and under microscopical magnification. The second group, 34 cases, underwent the classical procedure with ligature of the bleeding vessels. The usage of the bipolar forceps procure lesser loss of blood as compared with the dissection-ligature procedure. On the contrary, the bipolar clip method showed and increased postoperative pain and also the lagging of the swallow function. Both techniques presented with very similar complications (bleeding, edema, loca infection). PMID:7573857

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2012-01-01

    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

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

    PubMed Central

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

    2012-01-01

    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

  19. Large-Scale Comparative Phosphoproteomics Identifies Conserved Phosphorylation Sites in Plants1[W][OA

    PubMed Central

    Nakagami, Hirofumi; Sugiyama, Naoyuki; Mochida, Keiichi; Daudi, Arsalan; Yoshida, Yuko; Toyoda, Tetsuro; Tomita, Masaru; Ishihama, Yasushi; Shirasu, Ken

    2010-01-01

    Knowledge of phosphorylation events and their regulation is crucial to understand the functional biology of plants. Here, we report a large-scale phosphoproteome analysis in the model monocot rice (Oryza sativa japonica ‘Nipponbare’), an economically important crop. Using unfractionated whole-cell lysates of rice cells, we identified 6,919 phosphopeptides from 3,393 proteins. To investigate the conservation of phosphoproteomes between plant species, we developed a novel phosphorylation-site evaluation method and performed a comparative analysis of rice and Arabidopsis (Arabidopsis thaliana). The ratio of tyrosine phosphorylation in the phosphoresidues of rice was equivalent to those in Arabidopsis and human. Furthermore, despite the phylogenetic distance and the use of different cell types, more than 50% of the phosphoproteins identified in rice and Arabidopsis, which possessed ortholog(s), had an orthologous phosphoprotein in the other species. Moreover, nearly half of the phosphorylated orthologous pairs were phosphorylated at equivalent sites. Further comparative analyses against the Medicago phosphoproteome also showed similar results. These data provide direct evidence for conserved regulatory mechanisms based on phosphorylation in plants. We also assessed the phosphorylation sites on nucleotide-binding leucine-rich repeat proteins and identified novel conserved phosphorylation sites that may regulate this class of proteins. PMID:20466843

  20. Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data

    PubMed Central

    Terfve, Camille D. A.; Wilkes, Edmund H.; Casado, Pedro; Cutillas, Pedro R.; Saez-Rodriguez, Julio

    2015-01-01

    Mass spectrometry is widely used to probe the proteome and its modifications in an untargeted manner, with unrivalled coverage. Applied to phosphoproteomics, it has tremendous potential to interrogate phospho-signalling and its therapeutic implications. However, this task is complicated by issues of undersampling of the phosphoproteome and challenges stemming from its high-content but low-sample-throughput nature. Hence, methods using such data to reconstruct signalling networks have been limited to restricted data sets and insights (for example, groups of kinases likely to be active in a sample). We propose a new method to handle high-content discovery phosphoproteomics data on perturbation by putting it in the context of kinase/phosphatase-substrate knowledge, from which we derive and train logic models. We show, on a data set obtained through perturbations of cancer cells with small-molecule inhibitors, that this method can study the targets and effects of kinase inhibitors, and reconcile insights obtained from multiple data sets, a common issue with these data. PMID:26354681

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

    PubMed Central

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

    2014-01-01

    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

  2. Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data.

    PubMed

    Terfve, Camille D A; Wilkes, Edmund H; Casado, Pedro; Cutillas, Pedro R; Saez-Rodriguez, Julio

    2015-01-01

    Mass spectrometry is widely used to probe the proteome and its modifications in an untargeted manner, with unrivalled coverage. Applied to phosphoproteomics, it has tremendous potential to interrogate phospho-signalling and its therapeutic implications. However, this task is complicated by issues of undersampling of the phosphoproteome and challenges stemming from its high-content but low-sample-throughput nature. Hence, methods using such data to reconstruct signalling networks have been limited to restricted data sets and insights (for example, groups of kinases likely to be active in a sample). We propose a new method to handle high-content discovery phosphoproteomics data on perturbation by putting it in the context of kinase/phosphatase-substrate knowledge, from which we derive and train logic models. We show, on a data set obtained through perturbations of cancer cells with small-molecule inhibitors, that this method can study the targets and effects of kinase inhibitors, and reconcile insights obtained from multiple data sets, a common issue with these data. PMID:26354681

  3. Dissect Your Squid and Eat It Too!

    ERIC Educational Resources Information Center

    McGinnis, Patricia

    2001-01-01

    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)

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

    E-print Network

    Schnaufer, Achim

    Trypanosoma brucei using SILAC labeling of each lifecycle stage. Phos- phopeptide enrichment by SCX and TiO2-cation exchange (SCX) and TiO2 enrichment of phosphopeptides derived from the cytosolic fraction of bloodstream for

  5. Nested Dissection: A survey and comparison of various nested dissection algorithms

    E-print Network

    Miller, Gary L.

    Nested Dissection: A survey and comparison of various nested dissection algorithms Manpreet S on gaussian elimination. This report discusses one such direct method namely Nested dissection. Nested. This report is a survey of some of the work in the area of nested dissection and attempts to put it together

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

  7. Animal Rights Activism Threatens Dissection.

    ERIC Educational Resources Information Center

    Holden, Constance

    1990-01-01

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

  8. Dissection & Science Fairs. [Information Packet.

    ERIC Educational Resources Information Center

    National Anti-Vivisection Society, Chicago, IL.

    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,…

  9. Detection and characterisation of quantitative trait loci affecting muscle and growth phenotypes in sheep 

    E-print Network

    Hadjipavlou, Georgia

    2010-01-01

    This thesis addresses the dissection and characterisation of quantitative trait loci (QTL) affecting production traits in sheep. Firstly, the association between specific genetic polymorphisms and complex variation in ...

  10. Dissection of the barley 2L1.0 region carrying the 'Laevigatum' quantitative resistance gene to leaf rust using near-isogenic lines (NIL) and subNIL.

    PubMed

    Marcel, Thierry C; Aghnoum, Reza; Durand, Jérôme; Varshney, Rajeev K; Niks, Rients E

    2007-12-01

    Partial resistance to leaf rust (Puccinia hordei G. H. Otth) in barley is a quantitative resistance that is not based on hypersensitivity. This resistance hampers haustorium formation, resulting in a long latency period in greenhouse tests. The three most consistent quantitative trait loci (QTL) uncovered in the L94 x 'Vada' mapping population were introgressed by marker-assisted backcrossing into the susceptible L94 background to obtain near-isogenic lines (NIL). We also developed the reciprocal Vada-NIL for the susceptibility alleles of those QTL. The QTL Rphq2 affected latency period of P. hordei more than the QTL Rphq3 and Rphq4. The NIL confirmed the contribution of Rphq2 to partial resistance by prolonging the latency period by 28 h on L94-Rphq2 and shortening the latency period by 23 h on Vada-rphq2. On the basis of flanking restriction fragment length polymorphism-based markers, Rphq2 appeared to be located near the telomeric end of the long arm of chromosome 2H, in a physical region of high recombination, making it the target QTL for map-based cloning. Microscopic observations on the NIL confirmed the nonhypersensitive nature of the resistance conferred by Rphq2. A high-resolution genetic map of the Rphq2 region was constructed using a population of 38 subNIL with overlapping L94 introgressions in Vada background across the region. Rphq2 mapped approximately 2 centimorgans (cM) proximal from the MlLa locus. By bulked segregant analysis and use of synteny with rice, we developed additional markers and fine-mapped Rphq2 to a genetic interval of 0.11 cM that corresponds to a stretch of sequence of, at most, 70 kb in rice. Analysis of this rice sequence revealed predicted genes encoding two proteins with unknown function, retrotransposon proteins, peroxidase proteins, and a protein similar to a mitogen-activated protein kinase kinase kinase (MAP3K). Possible homologs of those peroxidases and MAP3K in barley are candidates for the gene that contributes to partial resistance to P. hordei. PMID:17990968

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

    PubMed Central

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

    2010-01-01

    Background High doses of ionizing radiation result in biological damage; however, the precise relationships between long-term health effects, including cancer, and low-dose exposures remain poorly understood and are currently extrapolated using high-dose exposure data. Identifying the signaling pathways and individual proteins affected at the post-translational level by radiation should shed valuable insight into the molecular mechanisms that regulate dose-dependent responses to radiation. Principal Findings We have identified 7117 unique phosphopeptides (2566 phosphoproteins) from control and irradiated (2 and 50 cGy) primary human skin fibroblasts 1 h post-exposure. Semi-quantitative label-free analyses were performed to identify phosphopeptides that are apparently altered by radiation exposure. This screen identified phosphorylation sites on proteins with known roles in radiation responses including TP53BP1 as well as previously unidentified radiation-responsive proteins such as the candidate tumor suppressor SASH1. Bioinformatic analyses suggest that low and high doses of radiation affect both overlapping and unique biological processes and suggest a role for MAP kinase and protein kinase A (PKA) signaling in the radiation response as well as differential regulation of p53 networks at low and high doses of radiation. Conclusions Our results represent the most comprehensive analysis of the phosphoproteomes of human primary fibroblasts exposed to multiple doses of ionizing radiation published to date and provide a basis for the systems-level identification of biological processes, molecular pathways and individual proteins regulated in a dose dependent manner by ionizing radiation. Further study of these modified proteins and affected networks should help to define the molecular mechanisms that regulate biological responses to radiation at different radiation doses and elucidate the impact of low-dose radiation exposure on human health. PMID:21152398

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

    PubMed Central

    2013-01-01

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

  13. [Isolated spontaneous dissection of visceral arteries].

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    E-print Network

    Yang, Sichun

    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

  16. An optimized platform for hydrophilic interaction chromatography-immobilized metal affinity chromatography enables deep coverage of the rat liver phosphoproteome.

    PubMed

    Zappacosta, Francesca; Scott, Gilbert F; Huddleston, Michael J; Annan, Roland S

    2015-02-01

    While analysis of the phosphoproteome has become an important component of understanding how cells function, it remains a nontrivial task in terms of the number of sample preparation steps and instrument time needed to achieve sufficient depth of coverage to produce meaningful results. We previously described a multidimensional method that uses hydrophilic interaction chromatography (HILIC) followed by Fe(3+) immobilized metal affinity chromatography (IMAC) to reduce complexity, improve selectivity, and increase phosphopeptide identifications. Here we present refinements to our overall protocol that make it simpler and more efficient, while they provide greater coverage of the phosphoproteome. We introduce filter-aided sample prep (FASP) for cell lysis and trypsin digestion. Following HILIC separation, fractions are IMAC enriched using a 96-well filter plate. Finally, enriched samples are analyzed using an LC-MS strategy optimized for the fractionation scheme. The optimized protocol improves protein recovery, simplifies phosphopeptide enrichment, and optimizes instrument time, while it maintains deep coverage of the phosphoproteome. By using the refined protocol, we identified more than 16,000 unique phosphosites from rat liver in a single experiment, which used approximately 1 day of instrument time. All together, we present evidence for 24,485 rat liver phosphosites that represents the deepest coverage of a tissue phosphoproteome to date. PMID:25575281

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

    PubMed

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

    2013-01-14

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

  18. Phosphoproteomic Analysis of Protein Phosphorylation Networks in the Hypopharyngeal Gland of Honeybee Workers (Apis mellifera ligustica).

    PubMed

    Qi, Yuping; Fan, Pei; Hao, Yue; Han, Bin; Fang, Yu; Feng, Mao; Cui, Ziyou; Li, Jianke

    2015-11-01

    The hypopharyngeal gland (HG) in honeybee workers changes functions according to physiological age in the bee colony from producing royal jelly (RJ) in nurse bees to digestive enzymes in foragers. The same set of secretory cells expresses different genes or proteins to create these age-dependent changes; however, it is unknown precisely how the phosphorylation network regulates physiological differences across the development of the adult worker HG. We employed high-accuracy mass-spectrometry-based proteomics to survey phosphoproteome changes in the newly emerged, nurse, and forager bees. Overall, 941, 1322, and 1196 phosphorylation sites matching 1007, 1353, and 1199 phosphopeptides from 549, 720, and 698 phosphoproteins were identified in the three ages of the HG, respectively. Specialized, interconnected phosphorylation networks within each age were found by comparing protein abundance and phosphorylation levels. This illustrates that many proteins are regulated by phosphorylation independent of their expression levels. Furthermore, proteins in key biological processes and pathways were dynamically phosphorylated with age development, including the centrosome cycle, mitotic spindle elongation, macromolecular complex disassembly, and ribosome, indicating that phosphorylation tunes protein activity to optimize cellular behavior of the HG over time. Moreover, complementary protein and phosphoprotein expression is required to support the unique physiology of secretory activity in the HG. This reported data set of the honeybee phosphoproteome significantly improves our understanding of a range of regulatory mechanisms controlling a variety of cellular processes and will serve as a valuable resource for those studying the honeybee and other insects. PMID:26384081

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

    PubMed Central

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

    2006-01-01

    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

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

    PubMed

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

    2006-03-01

    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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-11-01

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

  3. NeuCode Labeling in Nematodes: Proteomic and Phosphoproteomic Impact of Ascaroside Treatment in Caenorhabditis elegans.

    PubMed

    Rhoads, Timothy W; Prasad, Aman; Kwiecien, Nicholas W; Merrill, Anna E; Zawack, Kelson; Westphall, Michael S; Schroeder, Frank C; Kimble, Judith; Coon, Joshua J

    2015-11-01

    The nematode Caenorhabditis elegans is an important model organism for biomedical research. We previously described NeuCode stable isotope labeling by amino acids in cell culture (SILAC), a method for accurate proteome quantification with potential for multiplexing beyond the limits of traditional stable isotope labeling by amino acids in cell culture. Here we apply NeuCode SILAC to profile the proteomic and phosphoproteomic response of C. elegans to two potent members of the ascaroside family of nematode pheromones. By consuming labeled E. coli as part of their diet, C. elegans nematodes quickly and easily incorporate the NeuCode heavy lysine isotopologues by the young adult stage. Using this approach, we report, at high confidence, one of the largest proteomic and phosphoproteomic data sets to date in C. elegans: 6596 proteins at a false discovery rate ? 1% and 6620 phosphorylation isoforms with localization probability ?75%. Our data reveal a post-translational signature of pheromone sensing that includes many conserved proteins implicated in longevity and response to stress. PMID:26392051

  4. Quick Dissection of the Segmental Bronchi

    ERIC Educational Resources Information Center

    Nakajima, Yuji

    2010-01-01

    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…

  5. Keeping Dissection Alive for Medical Students

    ERIC Educational Resources Information Center

    Chambers, James; Emlyn-Jones, Daniel

    2009-01-01

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

  6. Beyond Dissection: Innovative Tools for Biology Education.

    ERIC Educational Resources Information Center

    Larson, Sandra, Ed.

    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,…

  7. Analysis of the Rana catesbeiana tadpole tail fin proteome and phosphoproteome during T3-induced apoptosis: identification of a novel type I keratin

    PubMed Central

    Domanski, Dominik; Helbing, Caren C

    2007-01-01

    Background Thyroid hormones (THs) are vital in the maintenance of homeostasis and in the control of development. One postembryonic developmental process that is principally regulated by THs is amphibian metamorphosis. This process has been intensively studied at the genomic level yet very little information at the proteomic level exists. In addition, there is increasing evidence that changes in the phosphoproteome influence TH action. Results Here we identify components of the proteome and phosphoproteome in the tail fin that changed within 48 h of exposure of premetamorphic Rana catesbeiana tadpoles to 10 nM 3,5,3'-triiodothyronine (T3). To this end, we developed a cell and protein fractionation method combined with two-dimensional gel electrophoresis and phosphoprotein-specific staining. Altered proteins were identified using mass spectrometry (MS). We identified and cloned a novel Rana larval type I keratin, RLK I, which may be a target for caspase-mediated proteolysis upon exposure to T3. In addition, the RLK I transcript is reduced during T3-induced and natural metamorphosis which is consistent with a larval keratin. Furthermore, GILT, a protein involved in the immune system, is changed in phosphorylation state which is linked to its activation. Using a complementary MS technique for the analysis of differentially-expressed proteins, isobaric tags for relative and absolute quantitation (iTRAQ) revealed 15 additional proteins whose levels were altered upon T3 treatment. The success of identifying proteins whose levels changed upon T3 treatment with iTRAQ was enhanced through de novo sequencing of MS data and homology database searching. These proteins are involved in apoptosis, extracellular matrix structure, immune system, metabolism, mechanical function, and oxygen transport. Conclusion We have demonstrated the ability to derive proteomics-based information from a model species for postembryonic development for which no genome information is currently available. The present study identifies proteins whose levels and/or phosphorylation states are altered within 48 h of the induction of tadpole tail regression prior to overt remodeling of the tail. In particular, we have identified a novel keratin that is a target for T3-mediated changes in the tail that can serve as an indicator of early response to this hormone. PMID:17683616

  8. Spontaneous Coronary Artery Dissection with Cardiac Tamponade

    PubMed Central

    Lundstrom, Robert J.

    2015-01-01

    Spontaneous coronary artery dissection is a rare cause of acute coronary syndrome. Clinical presentation ranges from chest pain alone to ST-segment-elevation myocardial infarction, ventricular fibrillation, and sudden death. The treatment of patients with spontaneous coronary artery dissection is challenging because the disease pathophysiology is unclear, optimal treatment is unknown, and short- and long-term prognostic data are minimal. We report the case of a 70-year-old woman who presented with an acute ST-segment-elevation myocardial infarction secondary to a spontaneous dissection of the left anterior descending coronary artery. She was treated conservatively. Cardiac tamponade developed 16 hours after presentation. Repeat coronary angiography revealed extension of the dissection. Medical therapy was continued after the hemopericardium was aspirated. The patient remained asymptomatic 3 years after hospital discharge. To our knowledge, this is the first reported case of spontaneous coronary artery dissection in association with cardiac tamponade that was treated conservatively and had a successful outcome. PMID:26504447

  9. Dissecting Genetic Networks Underlying Complex Phenotypes: The Theoretical Framework

    PubMed Central

    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

    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

  10. Offline High pH Reversed-Phase Peptide Fractionation for Deep Phosphoproteome Coverage.

    PubMed

    Batth, Tanveer S; Olsen, Jesper V

    2016-01-01

    Protein phosphorylation, a process in which kinases modify serines, threonines, and tyrosines with phosphoryl groups is of major importance in eukaryotic biology. Protein phosphorylation events are key initiators of signaling responses which determine cellular outcomes after environmental and metabolic stimuli, and are thus highly regulated. Therefore, studying the mechanism of regulation by phosphorylation, and pinpointing the exact site of phosphorylation on proteins is of high importance. This protocol describes in detail a phosphoproteomics workflow for ultra-deep coverage by fractionating peptide mixtures based on high pH (basic) reversed-phase chromatography prior to phosphopeptide enrichment and mass spectrometric analysis. Peptides are separated on a C18 reversed-phase column under basic conditions and fractions collected in timed intervals followed by concatenation of the fractions. Each Fraction is subsequently enriched for phosphopeptides using TiO2 followed by LC/MS analysis. PMID:26584926

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

    SciTech Connect

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

    2013-06-05

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

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

    PubMed

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

    2015-09-15

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

  13. Phosphoproteome Analysis Reveals Regulatory Sites in Major Pathways of Cardiac Mitochondria*

    PubMed Central

    Deng, Ning; Zhang, Jun; Zong, Chenggong; Wang, Yueju; Lu, Haojie; Yang, Pengyuan; Wang, Wenhai; Young, Glen W.; Wang, Yibin; Korge, Paavo; Lotz, Christopher; Doran, Philip; Liem, David A.; Apweiler, Rolf; Weiss, James N.; Duan, Huilong; Ping, Peipei

    2011-01-01

    Mitochondrial functions are dynamically regulated in the heart. In particular, protein phosphorylation has been shown to be a key mechanism modulating mitochondrial function in diverse cardiovascular phenotypes. However, site-specific phosphorylation information remains scarce for this organ. Accordingly, we performed a comprehensive characterization of murine cardiac mitochondrial phosphoproteome in the context of mitochondrial functional pathways. A platform using the complementary fragmentation technologies of collision-induced dissociation (CID) and electron transfer dissociation (ETD) demonstrated successful identification of a total of 236 phosphorylation sites in the murine heart; 210 of these sites were novel. These 236 sites were mapped to 181 phosphoproteins and 203 phosphopeptides. Among those identified, 45 phosphorylation sites were captured only by CID, whereas 185 phosphorylation sites, including a novel modification on ubiquinol-cytochrome c reductase protein 1 (Ser-212), were identified only by ETD, underscoring the advantage of a combined CID and ETD approach. The biological significance of the cardiac mitochondrial phosphoproteome was evaluated. Our investigations illustrated key regulatory sites in murine cardiac mitochondrial pathways as targets of phosphorylation regulation, including components of the electron transport chain (ETC) complexes and enzymes involved in metabolic pathways (e.g. tricarboxylic acid cycle). Furthermore, calcium overload injured cardiac mitochondrial ETC function, whereas enhanced phosphorylation of ETC via application of phosphatase inhibitors restored calcium-attenuated ETC complex I and complex III activities, demonstrating positive regulation of ETC function by phosphorylation. Moreover, in silico analyses of the identified phosphopeptide motifs illuminated the molecular nature of participating kinases, which included several known mitochondrial kinases (e.g. pyruvate dehydrogenase kinase) as well as kinases whose mitochondrial location was not previously appreciated (e.g. Src). In conclusion, the phosphorylation events defined herein advance our understanding of cardiac mitochondrial biology, facilitating the integration of the still fragmentary knowledge about mitochondrial signaling networks, metabolic pathways, and intrinsic mechanisms of functional regulation in the heart. PMID:20495213

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

    PubMed Central

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

    2013-01-01

    Phosphatase of regenerating liver 3 (PRL3) is suspected to be a causative factor toward cellular metastasis when in excess. To date, the molecular basis for PRL3 function remains an enigma, making efforts at distilling a concerted mechanism for PRL3-mediated metastatic dissemination very difficult. We previously discovered that PRL3 expressing cells exhibit a pronounced increase in protein tyrosine phosphorylation. Here we take an unbiased mass spectrometry-based approach toward identifying the phosphoproteins exhibiting enhanced levels of tyrosine phosphorylation with a goal to define the “PRL3-mediated signaling network.” Phosphoproteomic data support intracellular activation of an extensive signaling network normally governed by extracellular ligand-activated transmembrane growth factor, cytokine, and integrin receptors in the PRL3 cells. Additionally, data implicate the Src tyrosine kinase as the major intracellular kinase responsible for “hijacking” this network and provide strong evidence that aberrant Src activation is a major consequence of PRL3 overexpression. Importantly, the data support a PDGF(?/?)-, Eph (A2/B3/B4)-, and Integrin (?1/?5)-receptor array as being the predominant network coordinator in the PRL3 cells, corroborating a PRL3-induced mesenchymal-state. Within this network, we find that tyrosine phosphorylation is increased on a multitude of signaling effectors responsible for Rho-family GTPase, PI3K-Akt, STAT, and ERK activation, linking observations made by the field as a whole under Src as a primary signal transducer. Our phosphoproteomic data paint the most comprehensive picture to date of how PRL3 drives prometastatic molecular events through Src activation. PMID:24030100

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-09-01

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

  17. Animal Rights Groups Target High School Dissection.

    ERIC Educational Resources Information Center

    Trotter, Andrew

    1992-01-01

    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)

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

    NASA Video Gallery

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

  19. Running, ischaemic stroke and carotid artery dissection

    E-print Network

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

    2015-05-13

    (figure 1). The patient was started on longterm aspirin (75mg daily) and atorvastatin (80mg daily) with advice against participating in activities associated with carotid dissection. The residual deficits two days post-presentation were mild loss of fine...

  20. Dissecting genetic interactions in complex traits 

    E-print Network

    Hemani, Gibran

    2012-06-30

    Of central importance in the dissection of the components that govern complex traits is understanding the architecture of natural genetic variation. Genetic interaction, or epistasis, constitutes one aspect of this, but ...

  1. Peripartum presentation of an acute aortic dissection.

    PubMed

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

    2005-04-01

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

  2. Postoperative hypertension after radical neck dissection.

    PubMed

    Celikkanat, S; Akyol, M U; Koç, C; Olçer, S; Ensari, S; Turgut, S; Ozdem, C

    1997-07-01

    Postoperative hypertension after radical neck dissection was detected in 20.2% of 109 neck dissections in our department between 1989 and 1993. It was probably caused by carotid sinus denervation and appeared after the vasodilation generated by anesthesia had subsided. If postoperative hypertension was encountered after the first operation, the risk of such hypertension after surgery on the contralateral side significantly increased. PMID:9230330

  3. Pulmonary artery dissection: echocardiographic findings and diagnosis.

    PubMed

    Areco, Daniel; Pizzano, Nelson

    2003-05-01

    Pulmonary artery dissection is a rare but life-threatening event, predisposing to sudden cardiac death or cardiogenic shock. It is often associated with underlying congenital disorders predisposing to pulmonary hypertension. Rarely, it is diagnosed by echocardiography or other image techniques. We present a case report of a pulmonary artery dissection, diagnosed primarily by echocardiography. The patient died soon after refusing any interventional approach after a short period under medication. PMID:12848882

  4. Spontaneous Mirror Dissections of Cervicocephalic Arteries

    PubMed Central

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

    2006-01-01

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

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

    PubMed Central

    Horst, Walter Johannes

    2013-01-01

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

  6. Evaluating dissection in the gross anatomy course: Correlation between quality of laboratory dissection and students outcomes.

    PubMed

    Nwachukwu, Chika; Lachman, Nirusha; Pawlina, Wojciech

    2015-01-01

    Anatomy learned by active exploration through dissection has many proven benefits including improvement of anatomic knowledge. Decreased laboratory time may affect the quality of dissection and ultimately lower student performance in anatomy translating to lower knowledge acquisition. The aim of this study was to determine whether the quality of students' dissection in teams correlates with their performance in the gross anatomy course. Quality of dissections for each team enrolled in a gross anatomy course at Mayo Medical School was evaluated biweekly using a five-point rubric based on course learning objectives. Assessment of anatomic knowledge was based on sequential laboratory practice practical examination scores, achievements on daily audience response system (ARS) quizzes, and final practical, written, and National Board of Medical Examiners(®) (NBME(®) ) Gross Anatomy and Embryology Subject Examinations. Twelve teams comprising 48 students were included in the study. There was a positive correlation between dissection quality and practice practical examination score (R = 0.83) and a negative correlation between dissection quality and ARS quizzes (R = -0.985). Dissection teams with a passing score on their dissection evaluations (>70%) performed better on their final examinations. Based on an end of course survey, students agreed that dissection evaluations should continue to be a part of the course. This study showed that better quality of dissection was associated with higher scores on practice practical examinations, final practical, written, and NBME examinations. The study demonstrated a positive correlation between dissection evaluations, accompanied by formative feedback during the course, and higher scores on final course assessments. PMID:24799441

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

    ERIC Educational Resources Information Center

    Oakley, Jan

    2012-01-01

    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…

  8. Student injuries in the dissecting room.

    PubMed

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

    2013-01-01

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

  9. Preventable Sternocleidomastoid Muscular Atrophy after Neck Dissection

    PubMed Central

    Yamamoto, Nao; Sawai, Natsuko Yoshimura; Ishimoto, Shunsuke; Ogura, Hide; Aikawa, Tomonao; Kogo, Mikihiko

    2015-01-01

    Background: Modified radical neck dissection (mRND) [preserving the sternocleidomastoid muscle (SCM) and the spinal accessory nerve] and supraomohyoid neck dissection have become common surgical procedures for treating head and neck cancer. Postoperative severe asymmetry of the neck and severe atrophy of the SCM, however, have been demonstrated. Methods: Using computed tomographic images, cross-sectional areas of the SCMs were measured in 99 patients with carcinoma of the oral cavity who underwent unilateral mRND or supraomohyoid neck dissection. An asymmetry index was used. Results: Innervation to the SCM was preserved in 91 patients. The spinal accessory nerve and the innervation were sacrificed in 3 patients; the innervation was repaired in 5 patients. Sacrifice of innervation to the SCM resulted in extremely severe asymmetry. Repair of the innervation prevented severe asymmetry in 40%. Preservation of the innervation prevented severe asymmetry in 75% at the middle portion of the neck and in 56% at the lower portion after mRND. Conclusion: Preserving innervation to the SCM and gentle handling of the nerve during neck dissection could prevent severe asymmetry after neck dissection. PMID:26495217

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

    PubMed

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

    2014-01-01

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

  11. Improving the Phosphoproteome Coverage for Limited Sample Amounts Using TiO2-SIMAC-HILIC (TiSH) Phosphopeptide Enrichment and Fractionation.

    PubMed

    Engholm-Keller, Kasper; Larsen, Martin R

    2016-01-01

    Obtaining high phosphoproteome coverage requires specific enrichment of phosphorylated peptides from the often extremely complex peptide mixtures generated by proteolytic digestion of biological samples, as well as extensive chromatographic fractionation prior to liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Due to the sample loss resulting from fractionation, this procedure is mainly performed when large quantities of sample are available. To make large-scale phosphoproteomics applicable to smaller amounts of protein we have recently combined highly specific TiO2-based phosphopeptide enrichment with sequential elution from immobilized metal affinity chromatography (SIMAC) for fractionation of mono- and multi-phosphorylated peptides prior to capillary scale hydrophilic interaction liquid chromatography (HILIC) based fractionation of monophosphorylated peptides. In the following protocol we describe the procedure step by step to allow for comprehensive coverage of the phosphoproteome utilizing only a few hundred micrograms of protein. PMID:26584925

  12. Changes in the Phosphoproteome and Metabolome Link Early Signaling Events to Rearrangement of Photosynthesis and Central Metabolism in Salinity and Oxidative Stress Response in Arabidopsis.

    PubMed

    Chen, Yanmei; Hoehenwarter, Wolfgang

    2015-12-01

    Salinity and oxidative stress are major factors affecting and limiting the productivity of agricultural crops. The molecular and biochemical processes governing the plant response to abiotic stress have often been researched in a reductionist manner. Here, we report a systemic approach combining metabolic labeling and phosphoproteomics to capture early signaling events with quantitative metabolome analysis and enzyme activity assays to determine the effects of salt and oxidative stress on plant physiology. K(+) and Na(+) transporters showed coordinated changes in their phosphorylation pattern, indicating the importance of dynamic ion homeostasis for adaptation to salt stress. Unique phosphorylation sites were found for Arabidopsis (Arabidopsis thaliana) SNF1 kinase homolog10 and 11, indicating their central roles in the stress-regulated responses. Seven Sucrose Non-fermenting1-Related Protein Kinase2 kinases showed varying levels of phosphorylation at multiple serine/threonine residues in their kinase domain upon stress, showing temporally distinct modulation of the various isoforms. Salinity and oxidative stress also lead to changes in protein phosphorylation of proteins central to photosynthesis, in particular the kinase State Transition Protein7 required for state transition and light-harvesting II complex proteins. Furthermore, stress-induced changes of the phosphorylation of enzymes of central metabolism were observed. The phosphorylation patterns of these proteins were concurrent with changes in enzyme activity. This was reflected by altered levels of metabolites, such as the sugars sucrose and fructose, glycolysis intermediates, and amino acids. Together, our study provides evidence for a link between early signaling in the salt and oxidative stress response that regulates the state transition of photosynthesis and the rearrangement of primary metabolism. PMID:26471895

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

    SciTech Connect

    Matsumura, Takayuki; Department of Life Science and Medical Bio-Science, Waseda University, Shinjuku-ku, Tokyo 162-8480 ; Oyama, Masaaki; Kozuka-Hata, Hiroko; Ishikawa, Kosuke; Inoue, Takafumi; Department of Life Science and Medical Bio-Science, Waseda University, Shinjuku-ku, Tokyo 162-8480 ; Muta, Tatsushi; Semba, Kentaro; Department of Life Science and Medical Bio-Science, Waseda University, Shinjuku-ku, Tokyo 162-8480 ; Inoue, Jun-ichiro; Division of Cellular and Molecular Biology, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639

    2010-09-17

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

  14. Bowel "dissection" in microvillus inclusion disease.

    PubMed

    Chiang, Ming-Chou; Hsu, Jen-Fu; Hsueh, Chuen; Chao, Hsun-Chin; Wang, Tzu-Hao; Chen, Chih-Ping; Lai, Ming-Wei

    2015-04-01

    A preterm male neonate was diagnosed as having microvillus inclusion disease based on the characteristics of histological and ultrastructural findings. The peripheral blood sample also revealed MYO5B mutation. He had been on long-term parenteral nutrition. However, a bowel segment was seen in the baby's diaper during hospitalization when he was 5 months old. Serial abdominal ultrasound demonstrated progressive dissection of the bowel wall with detached mucosa in real-time. Small intestinal epithelia were seen on the histology of the detached bowel segment. He died 2 weeks after the episode; postmortem autopsy showed diffuse detachment of mucosa of small bowels without perforation. This is the first report of an infant with microvillus inclusion disease that presented with bowel "dissection". Weakened adhesion and integrity of intestinal epithelial cells caused by MYO5B mutation was speculated to result in the dissection and detachment of the epithelia of the gastrointestinal tract. PMID:23608388

  15. The nature of dissection: Exploring student conceptions

    NASA Astrophysics Data System (ADS)

    York, Katharine

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

  16. Preservation of the optic radiations based on comparative analysis of diffusion tensor imaging tractography and anatomical dissection

    PubMed Central

    Nooij, Roland P.; Hoving, Eelco W.; van Hulzen, Arjen L. J.; Cornelissen, Frans W.; Renken, Remco J.

    2015-01-01

    Background: Visualization of the precise course of the visual pathways is relevant to prevent damage that may inflict visual field deficits during neurosurgical resections. In particular the optic radiations (OR) are susceptible to such damage during neurosurgery. Cortical pathways can be mapped in vivo, by using Diffusion Tensor Imaging (DTI). Visualization of these pathways would be potentially helpful to prevent neurosurgical visual morbidity. In this study an anatomical dissection of the visual pathways was compared to DTI fiber tractography (DTI-FT) data of four human brains. The feasibility of a definition of a Safety Zone is investigated. Methods: Four adult brains were dissected using Klingler's fiber dissection method, which allowed preparation of the OR. Measurements before and after dissection were used to establish distances from the cortex to the OR. DTI-scans were also obtained from these brains to determine the same distances. Results: Measurements from specific landmark points on the cortex to the lateral border of the OR were performed in four brains. Analysis through DTI tractography corresponded with the dissection results. Based on the combined results of both dissection and DTI-FT, we defined a quantitative surgical Safety Zone with respect to various anatomical landmarks (in particular the ventricle system). Conclusion: We conclude that there is a good correlation between the visualizations of the optic pathways based on dissection and DTI. Furthermore, we conclude that defining a neurosurgical Safety Zone which could preserve the integrity of the OR during surgery, based on the combination of DTI-FT images and dissection is feasible. PMID:26300739

  17. 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 ...

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  20. FAIMS and Phosphoproteomics of Fibroblast Growth Factor Signaling: Enhanced Identification of Multiply Phosphorylated Peptides.

    PubMed

    Zhao, Hongyan; Cunningham, Debbie L; Creese, Andrew J; Heath, John K; Cooper, Helen J

    2015-12-01

    We have applied liquid chromatography high-field asymmetric waveform ion mobility spectrometry tandem mass spectrometry (LC-FAIMS-MS/MS) and liquid chromatography tandem mass spectrometry (LC-MS/MS) to the investigation of site-specific phosphorylation in fibroblast growth factor (FGF) signaling. We have combined a SILAC approach with chemical inhibition by SU5402 (an FGF receptor tyrosine kinase inhibitor) and dasatinib (a Src family kinase inhibitor). The results show that incorporation of FAIMS within the workflow results in (a) an increase in the relative proportion of phosphothreonine and phosphotyrosine sites identified, (b) an increase in phosphopeptide identifications from precursors with charge states ? +3 (with an associated increase in peptide length), and (c) an increase in the identification of multiply phosphorylated peptides. Approximately 20% of the phosphorylation sites identified via the FAIMS workflow had not been reported previously, and over 80% of those were from multiply phosphorylated peptides. Moreover, FAIMS provided access to a distinct set of phosphorylation sites regulated in response to SU5402 and dasatinib. The enhanced identification of multiply phosphorylated peptides was particularly striking in the case of sites regulated by SU5402. In addition to providing a compelling example of the complementarity of FAIMS in phosphoproteomics, the results provide a valuable resource of phosphorylation sites for further investigation of FGF signaling and trafficking. PMID:26503514

  1. Site-Specific Ser/Thr/Tyr Phosphoproteome of Sinorhizobium meliloti at Stationary Phase

    PubMed Central

    Liu, Tao; Tian, Chang Fu; Chen, Wen Xin

    2015-01-01

    Sinorhizobium meliloti, a facultative microsymbiont of alfalfa, should fine-tune its cellular processes to live saprophytically in soils characterized with limited nutrients and diverse stresses. In this study, TiO2 enrichment and LC-MS/MS were used to uncover the site-specific Ser/Thr/Tyr phosphoproteome of S. meliloti in minimum medium at stationary phase. There are a total of 96 unique phosphorylated sites, with a Ser/Thr/Tyr distribution of 63:28:5, in 77 proteins. Phosphoproteins identified in S. meliloti showed a wide distribution pattern regarding to functional categories, such as replication, transcription, translation, posttranslational modification, transport and metabolism of amino acids, carbohydrate, inorganic ion, succinoglycan etc. Ser/Thr/Tyr phosphosites identified within the conserved motif in proteins of key cellular function indicate a crucial role of phosphorylation in modulating cellular physiology. Moreover, phosphorylation in proteins involved in processes related to rhizobial adaptation was also discussed, such as those identified in SMa0114 and PhaP2 (polyhydroxybutyrate synthesis), ActR (pH stress and microaerobic adaption), SupA (potassium stress), chaperonin GroEL2 (viability and potentially symbiosis), and ExoP (succinoglycan synthesis and secretion). These Ser/Thr/Tyr phosphosites identified herein would be helpful for our further investigation and understanding of the role of phosphorylation in rhizobial physiology. PMID:26401955

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

    SciTech Connect

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

    2014-11-01

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

  3. Tyrosine phosphoproteomics of fibroblast growth factor signaling: a role for insulin receptor substrate-4.

    PubMed

    Hinsby, Anders M; Olsen, Jesper V; Mann, Matthias

    2004-11-01

    Signal transduction by receptor tyrosine kinases is initiated by recruitment of a variety of signaling proteins to tyrosine-phosphorylated motifs in the activated receptors. Several signaling pathways are thus activated in parallel, the combination of which decides the cellular response. Here, we present a dual strategy for extensive mapping of tyrosine-phosphorylated proteins and probing of signal-dependent protein interactions of a signaling cascade. The approach relies on labeling of cells with "heavy" and "light" isotopic forms of Arg to distinguish two cell populations. First, tyrosine-phosphorylated proteins from stimulated ("heavy"-labeled) and control samples ("normal"-labeled) are isolated and subjected to high sensitivity Fourier transform ion cyclotron resonance mass spectrometry analysis. Next, phosphopeptides corresponding to tyrosine phosphorylation sites identified during the tyrosine phosphoproteomic analysis are used as baits to isolate phosphospecific protein binding partners, which are subsequently identified by mass spectrometry. We used this approach to identify 28 components of the signaling cascade induced by stimulation with the basic fibroblast growth factor. Insulin receptor substrate-4 was identified as a novel candidate in fibroblast growth factor receptor signaling, and we defined phosphorylation-dependent interactions with other components, such as adaptor protein Grb2, of the signaling cascade. Finally, we present evidence for a complex containing insulin receptor substrate-4 and ShcA in signaling by the fibroblast growth factor receptor. PMID:15316024

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

    PubMed

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

    2010-04-01

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

  5. Hinged Dissection of Polypolyhedra Erik D. Demaine1

    E-print Network

    Demaine, Erik

    family of 3D hinged dissections for polypolyhedra, i.e., connected 3D solids formed by joining several for reflectionally symmetric faces.) Each hinged dissection consists of a linear number of solid polyhedral pieces from 2D [7]. Along the way, we present hinged dissections for polyplatonics (where P is a platonic

  6. Squid Dissection: From Pen to Ink.

    ERIC Educational Resources Information Center

    Brown, Cindy; Kisiel, Jim

    2003-01-01

    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)

  7. The etiology of cervical artery dissection

    PubMed Central

    Haneline, Michael T.; Rosner, Anthony L.

    2007-01-01

    Abstract The etiology of cervical artery dissection (CAD) is unclear, although a number of risk factors have been reported to be associated with the condition. On rare occasions, patients experience CAD after cervical spine manipulation, making knowledge about the cervical arteries, the predisposing factors, and the pathogenesis of the condition of interest to chiropractors. This commentary reports on the relevant anatomy of the cervical arteries, developmental features of CAD, epidemiology of the condition, and mechanisms of dissection. The analysis of CAD risk factors is confusing, however, because many people are exposed to mechanical events and known pathophysiological associations without ever experiencing dissection. No cause-and-effect relationship has been established between cervical spine manipulation and CAD, but it seems that cervical manipulation may be capable of triggering dissection in a susceptible patient or contributing to the evolution of an already existing CAD. Despite the many risk factors that have been proposed as possible causes of CAD, it is still unknown which of them actually predispose patients to CAD after cervical spine manipulation. PMID:19674705

  8. Global Distribution of Dissected Duricrust on Mars

    NASA Technical Reports Server (NTRS)

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

    2000-01-01

    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.

  9. Hinged Dissection of Polypolyhedra Erik D. Demaine

    E-print Network

    Demaine, Erik

    interior to the face or on its boundary). For platonic solids, these hinges will be edges of the polyhedron. Souvaine 1 Introduction. A dissection of two figures (solid 2D or 3D shapes, e.g., polygons or polyhedra with labeled faces, a polypoly- hedron of type P is an interior-connected non-self- intersecting solid formed

  10. Intraoperative aortic dissection in pediatric heart surgery.

    PubMed

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

    2006-06-01

    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

  11. Cow's Eye Dissection in the Physics Lab.

    ERIC Educational Resources Information Center

    Lapp, David R.; Keenan, James E.

    1991-01-01

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

  12. 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

  13. 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

  14. Sporulation and Dissection From Kristina Schmidt, USF

    E-print Network

    Aris, John P.

    fresh sporulation media. Tetrad Dissection 1. Transfer 500 µl of sporulation culture to a sterile 1.5 ml medium. Grow 24 hours in drum rotator at 30°C. 3. Transfer 250 µl of culture to a sterile 1.5 ml tube for later use. 7. Transfer to sterile GLASS test tube containing 4.75 ml of sporulation medium. 8. Incubate

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

    PubMed Central

    2014-01-01

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

  16. Which Comes First: The Use of Computer Simulation of Frog Dissection or Conventional Dissection as Academic Exercise?

    ERIC Educational Resources Information Center

    Akpan, Joseph; Strayer, Jeremy

    2010-01-01

    Science educators and school administrators are reexamining the educational value of animal dissection in the nation's schools and are focusing on simulation as an instructional alternative. One implication of the debate is that simulations can lead to equivalent learning to hands-on dissection. The second implication is whether dissection is…

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

    PubMed

    Zhao, Man; Deng, Chunhui; Zhang, Xiangmin

    2014-06-14

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

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

    PubMed

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

    2014-12-01

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

  19. A case of carotid artery dissection after surgical repair of aortic dissection successfully treated with endovascular therapy using intravascular ultrasound.

    PubMed

    Katoh, Hiromasa; Nozue, Tsuyoshi; Nagamine, Hiroshi; Kawase, Yushi; Michishita, Ichiro

    2014-07-01

    A 71-year-old woman developed the dissection from right brachiocephalic trunk (BCT) to internal carotid artery 6 days after the operation of ascending aortic dissection. Since no improvement of symptoms was observed despite conservative therapy, we performed endovascular therapy (EVT). Although a balloon-expandable stent was implanted in the BCT to seal the entry point of the dissection, the true lumen of the carotid artery was still compressed. Thus, we covered the dissected lesion completely with multiple stents, and her neurological findings improved. This case demonstrates that EVT using multiple stents is an effective strategy to manage dissection of supra-aortic branches. PMID:24142487

  20. Comparative Phosphoproteomics Reveals Components of Host Cell Invasion and Post-transcriptional Regulation During Francisella Infection*

    PubMed Central

    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

    2013-01-01

    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 with 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, 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 tristetraprolin, leading to the production of cytokines such as IL-1beta and TNF-alpha that 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 control infection by this pathogen. PMID:23970565

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

    SciTech Connect

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

    2013-09-22

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

  2. Phosphoproteomic Approach to Characterize Protein Mono- and Poly(ADP-ribosyl)ation Sites from Cells

    PubMed Central

    2015-01-01

    Poly(ADP-ribose), or PAR, is a cellular polymer implicated in DNA/RNA metabolism, cell death, and cellular stress response via its role as a post-translational modification, signaling molecule, and scaffolding element. PAR is synthesized by a family of proteins known as poly(ADP-ribose) polymerases, or PARPs, which attach PAR polymers to various amino acids of substrate proteins. The nature of these polymers (large, charged, heterogeneous, base-labile) has made these attachment sites difficult to study by mass spectrometry. Here we propose a new pipeline that allows for the identification of mono(ADP-ribosyl)ation and poly(ADP-ribosyl)ation sites via the enzymatic product of phosphodiesterase-treated ADP-ribose, or phospho(ribose). The power of this method lies in the enrichment potential of phospho(ribose), which we show to be enriched by phosphoproteomic techniques when a neutral buffer, which allows for retention of the base-labile attachment site, is used for elution. Through the identification of PARP-1 in vitro automodification sites as well as endogenous ADP-ribosylation sites from whole cells, we have shown that ADP-ribose can exist on adjacent amino acid residues as well as both lysine and arginine in addition to known acidic modification sites. The universality of this technique has allowed us to show that enrichment of ADP-ribosylated proteins by macrodomain leads to a bias against ADP-ribose modifications conjugated to glutamic acids, suggesting that the macrodomain is either removing or selecting against these distinct protein attachments. Ultimately, the enrichment pipeline presented here offers a universal approach for characterizing the mono- and poly(ADP-ribosyl)ated proteome. PMID:24920161

  3. Investigating the role of FGF-2 in stem cell maintenance by global phosphoproteomics profiling.

    PubMed

    Zoumaro-Djayoon, Adja D; Ding, Vanessa; Foong, Leong-Yan; Choo, Andre; Heck, Albert J R; Muńoz, Javier

    2011-10-01

    Human embryonic stem cells (hESCs) are of immense interest for regenerative medicine as a source of tissue replacement. Expansion of hESCs as a pluripotent population requires a balance between survival, proliferation and self-renewal signals. One of the key growth factors that maintains this balance is fibroblast growth factor-2 (FGF-2). However, the underlying molecular mechanisms are poorly understood. We recently profiled specifically tyrosine phosphorylation events that occur during FGF-2 stimulation of hESCs (Ding et al., J. Cell. Physiol. 2010, 225, 417-428). Here, we complement this phosphoproteome profiling by analyzing temporal dynamics of mostly serine and threonine protein phosphorylation events. Our multi-dimensional strategy combines strong cation exchange chromatography to reduce the sample complexity followed by titanium dioxide off-line for the enrichment of phosphopeptides and dimethylation-based stable isotope labeling for quantification. This approach allowed us to identify and quantify 3261 unique proteins from which 1064 proteins were found to be phosphorylated in one or more residues (representing 1653 unique phosphopeptides). Approximately 40% of the proteins (553 unique phosphopeptides) showed differential phosphorylation upon FGF-2 treatment. Among those are several members of the canonical pathways involved in pluripotency and self-renewal (e.g. Wnt and PI3K/AKT), hESC-associated proteins such as SOX2, RIF1, SALL4, DPPA4, DNMT3B and 53 proteins that are target genes of the pluripotency transcription factors SOX2, OCT4 and NANOG. These findings complement existing pluripotency analyses and provide new insights into how FGF-2 assists in maintaining the undifferentiated state of hESCs. PMID:21761559

  4. Proteomic and phosphoproteomic analyses reveal extensive phosphorylation of regulatory proteins in developing rice anthers.

    PubMed

    Ye, Juanying; Zhang, Zaibao; Long, Haifei; Zhang, Zhimin; Hong, Yue; Zhang, Xumin; You, Chenjiang; Liang, Wanqi; Ma, Hong; Lu, Pingli

    2015-11-01

    Anther development, particularly around the time of meiosis, is extremely crucial for plant sexual reproduction. Meanwhile, cell-to-cell communication between somatic (especial tapetum) cells and meiocytes are important for both somatic anther development and meiosis. To investigate possible molecular mechanisms modulating protein activities during anther development, we applied high-resolution mass spectrometry-based proteomic and phosphoproteomic analyses for developing rice (Oryza sativa) anthers around the time of meiosis (RAM). In total, we identified 4984 proteins and 3203 phosphoproteins with 8973 unique phosphorylation sites (p-sites). Among those detected here, 1544 phosphoproteins are currently absent in the Plant Protein Phosphorylation DataBase (P(3) DB), substantially enriching plant phosphorylation information. Mapman enrichment analysis showed that 'DNA repair','transcription regulation' and 'signaling' related proteins were overrepresented in the phosphorylated proteins. Ten genetically identified rice meiotic proteins were detected to be phosphorylated at a total of 25 p-sites; moreover more than 400 meiotically expressed proteins were revealed to be phosphorylated and their phosphorylation sites were precisely assigned. 163 putative secretory proteins, possibly functioning in cell-to-cell communication, are also phosphorylated. Furthermore, we showed that DNA synthesis, RNA splicing and RNA-directed DNA methylation pathways are extensively affected by phosphorylation. In addition, our data support 46 kinase-substrate pairs predicted by the rice Kinase-Protein Interaction Map, with SnRK1 substrates highly enriched. Taken together, our data revealed extensive protein phosphorylation during anther development, suggesting an important post-translational modification affecting protein activity. PMID:26360816

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

    PubMed Central

    Hřjlund, 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

    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

  6. Spontaneous Coronary Artery Dissection: A Case Report

    PubMed Central

    Mokhberi, Vahid; Bagheri, Babak; Navidi, Seyfollah; Amini, Seyed Mohammad

    2015-01-01

    Spontaneous coronary artery dissection (SCAD) is a rare and important cause of acute coronary syndrome and sudden cardiac death. Various etiologies are thought to be responsible for this condition, among which underlying atherosclerosis seems to be the most common. SCAD is predominant in women and is usually diagnosed via coronary artery angiography. Therapeutic interventions include medical therapy, percutaneous coronary artery intervention, and surgery based on lesion characteristics. We describe a 36-year-old woman with SCAD presenting with acute chest pain to Fatemeh-Zahra Hospital, Sari, Iran. The patient had no current atherosclerosis risk factors and had given birth 6 months previously. Coronary angiography was performed due to the persistence of the chest pain after initial management, and a spontaneous dissection of the left anterior descending artery was observed. She underwent coronary artery bypass graft and was discharged in good condition. PMID:26697091

  7. Therapeutic node dissections in malignant melanoma.

    PubMed

    Karakousis, C P

    1998-06-01

    In the absence of distant disease, therapeutic node dissections in malignant melanoma, i.e., dissections of regional nodal basins for palpable suspicious or biopsy-proven positive nodes, offer the chance of cure. The 5-year survival rates after therapeutic lymphadenectomy closely correlate with expected cure rates. Although they varied greatly in the literature, from 19% to 38%, the currently obtainable survival rates are in the upper ranges of this spectrum because patients now are closely followed-up and operated for early palpable nodal disease. Properly done, these procedures carry a low morbidity, but they should be done thoroughly to completely eradicate regional disease and avoid recurrences in the same nodal basin to achieve the maximum survival that is surgically attainable. PMID:9588722

  8. Recurrent tamponade and aortic dissection in syphilis.

    PubMed

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

    2013-11-01

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

  9. Future directions of duodenal endoscopic submucosal dissection

    PubMed Central

    Matsumoto, Satohiro; Miyatani, Hiroyuki; Yoshida, Yukio

    2015-01-01

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

  10. Peer-Assisted Learning in a Gross Anatomy Dissection Course

    PubMed Central

    Han, Eui-Ryoung; Chung, Eun-Kyung; Nam, Kwang-Il

    2015-01-01

    Peer-assisted learning encourages students to participate more actively in the dissection process and promotes thoughtful dissection. We implemented peer-assisted dissection in 2012 and compared its effects on students’ self-assessments of learning and their academic achievement with those of faculty-led dissection. All subjects performed dissections after a lecture about upper-limb gross anatomy. Experimental group (n = 134) dissected a cadaver while guided by peer tutors who had prepared for the dissection in advance, and control group (n = 71) dissected a cadaver after the introduction by a faculty via prosection. Self-assessment scores regarding the learning objectives related to upper limbs were significantly higher in experimental group than in control group. Additionally, experimental group received significantly higher academic scores than did control group. The students in peer-assisted learning perceived themselves as having a better understanding of course content and achieved better academic results compared with those who participated in faculty-led dissection. Peer-assisted dissection contributed to self-perception and to the ability to retain and explain anatomical knowledge. PMID:26565616

  11. Peer-Assisted Learning in a Gross Anatomy Dissection Course.

    PubMed

    Han, Eui-Ryoung; Chung, Eun-Kyung; Nam, Kwang-Il

    2015-01-01

    Peer-assisted learning encourages students to participate more actively in the dissection process and promotes thoughtful dissection. We implemented peer-assisted dissection in 2012 and compared its effects on students' self-assessments of learning and their academic achievement with those of faculty-led dissection. All subjects performed dissections after a lecture about upper-limb gross anatomy. Experimental group (n = 134) dissected a cadaver while guided by peer tutors who had prepared for the dissection in advance, and control group (n = 71) dissected a cadaver after the introduction by a faculty via prosection. Self-assessment scores regarding the learning objectives related to upper limbs were significantly higher in experimental group than in control group. Additionally, experimental group received significantly higher academic scores than did control group. The students in peer-assisted learning perceived themselves as having a better understanding of course content and achieved better academic results compared with those who participated in faculty-led dissection. Peer-assisted dissection contributed to self-perception and to the ability to retain and explain anatomical knowledge. PMID:26565616

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

    PubMed

    Anyanwu, Emeka G

    2015-06-01

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

  13. Cadaver Dissection and the Ritual Transformation of Medical Students

    E-print Network

    Laudermilk, Ryan

    2011-12-31

    to prompts such as “Tell me about your first experience dissecting a cadaver...” before being asked scripted questions and follow-up questions based on their answers: 1. What qualities are important for competent dissection? 2. Do you remember your first... cadavers to living patients? 10. Do you think cadaver dissection was beneficial for learning anatomy? Essential? Was it a positive or negative experience over-all? Do you think you could get the same level of instruction without the use of cadavers...

  14. Endovascular repair of a double-lumen dissecting aneurysm

    PubMed Central

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

    2013-01-01

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

  15. Isolated brachiocephalic artery dissection presenting as acute stroke.

    PubMed

    Mani, Hariharasudan; Ahluwalia, Sharat

    2015-01-01

    Isolated brachiocephalic artery dissection is an extremely rare condition. Its presentation as an acute stroke can pose a significant diagnostic challenge in patients because of its rarity. We present a case of isolated spontaneous brachiocephalic artery dissection presenting as acute cerebrovascular accident. This case also illustrates the treatment dilemma brachiocephalic artery dissection can present, whether to choose antithrombotic/anticoagulation therapy and/or surgery, and also the dilemma in blood pressure management. PMID:26315357

  16. Chronic pulmonary artery dissection associated with pulmonary arterial hypertension

    PubMed Central

    2013-01-01

    Abstract Pulmonary artery dissection is a complication associated with pulmonary arterial hypertension. This complication is described as acute in onset and is frequently fatal without intervention. We describe a patient with idiopathic pulmonary arterial hypertension and chest pain found to have an unsuspected chronic pulmonary artery dissection on postmortem examination. Chronic pulmonary artery dissection should be considered in patients with chest pain and worsening dyspnea, as the frequency this condition may be underestimated. PMID:24618553

  17. Aortic dissection after superior mesenteric artery percutaneous stenting. Case report.

    PubMed

    Socrate, A M; Locati, P; Marchetti, G

    2000-03-01

    We report an unusual case of aortic dissection after superior mesenteric artery percutaneous stenting. A 44-year-old patient, who suffered from back pain and fever, was diagnosed as having an aortic dissection. Aortic dissection, extending from the aortic arch (just after left subclavian artery origin) to the aortic carrefour, was successfully diagnosed by means of Duplex scan and CT scan examination. Two pathogenetic hypotheses, malformative and iatrogenic, were discussed. PMID:10838838

  18. Spontaneous Coronary Dissection Masquerading as Benign Fascicular Ventricular Tachycardia.

    PubMed

    Ho, Sara Wei-Fen; Lin, Weiqin; Chan, Koo Hui; Seow, Swee-Chong

    2016-01-01

    Spontaneous coronary artery dissection is an uncommon cause of acute coronary syndrome. Diagnosis of coronary artery dissection is made on coronary angiogram and prompt revascularisation is the key in management. We present a case of coronary artery dissection with an atypical presentation of cardiac arrhythmia mimicking benign fascicular ventricular tachycardia. A high index of suspicion and early coronary angiogram allowed us to diagnose and treat this potentially life-threatening disease. PMID:26475648

  19. Acute aortic dissection diagnosed after embalming: macroscopic and microscopic findings.

    PubMed

    Savall, Frédéric; Dedouit, Fabrice; Piercecchi-Marti, Marie-Dominique; Leonetti, Georges; Rougé, Daniel; Telmon, Norbert

    2014-09-01

    A 58-year-old man died suddenly in Madagascar and poisoning was suspected. The body was embalmed after death and the general state of preservation was good. We found a major aortic dissection with a large false lumen from the aortic root to the common iliac arteries and a hemopericardium with formalinized blood clot. The intimal tear was on the ascending aorta, and an intramural hemorrhage was noted at the right coronary artery, attesting to a retrograde dissection. Microscopic studies confirmed aortic dissection with extensive intramural hemorrhage and also confirmed the retrograde dissection to the right coronary artery with a reduction of 90% of the true lumen. Classically, aortic dissection occurs in individuals with hypertension and individuals with genetic disorders of collagen formation. The diagnosis is often first established at the postmortem examination. Aortic dissection is therefore dealt with largely in necropsy studies. The usual cause of death is rupture into the pericardial sac. One case of bloodless dissection has been reported but the sudden death was explained by acute myocardial ischemia secondary to dissection of the left coronary artery. In our case, we found major hemopericardium and also intramural hemorrhage at the right coronary artery. We were able to make the diagnosis of aortic dissection and exclude the suspicion of homicide 15 days after death and after embalming. PMID:24684562

  20. Spontaneous coronary artery dissection—A review

    PubMed Central

    Yip, Amelia

    2015-01-01

    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

  1. Background Music in the Dissection Laboratory: Impact on Stress Associated with the Dissection Experience

    ERIC Educational Resources Information Center

    Anyanwu, Emeka G.

    2015-01-01

    Notable challenges, such as mental distress, boredom, negative moods, and attitudes, have been associated with learning in the cadaver dissection laboratory (CDL). The ability of background music (BM) to enhance the cognitive abilities of students is well documented. The present study was designed to investigate the impact of BM in the CDL and on…

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

    ERIC Educational Resources Information Center

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

    2013-01-01

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

  3. Functional dissection of Odorant binding protein genes in Drosophila melanogaster.

    PubMed

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

    2011-08-01

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

  4. Dissection of miRNA pathways using arabidopsis mesophyll protoplasts.

    PubMed

    Martinho, Cláudia; Confraria, Ana; Elias, Carlos Alexandre; Crozet, Pierre; Rubio-Somoza, Ignacio; Weigel, Detlef; Baena-González, Elena

    2015-02-01

    MicroRNAs (miRNAs) control gene expression mostly post-transcriptionally by guiding transcript cleavage and/or translational repression of complementary mRNA targets, thereby regulating developmental processes and stress responses. Despite the remarkable expansion of the field, the mechanisms underlying miRNA activity are not fully understood. In this article, we describe a transient expression system in Arabidopsis mesophyll protoplasts, which is highly amenable for the dissection of miRNA pathways. We show that by transiently overexpressing primary miRNAs and target mimics, we can manipulate miRNA levels and consequently impact on their targets. Furthermore, we developed a set of luciferase-based sensors for quantifying miRNA activity that respond specifically to both endogenous and overexpressed miRNAs and target mimics. We demonstrate that these miRNA sensors can be used to test the impact of putative components of the miRNA pathway on miRNA activity, as well as the impact of specific mutations, by either overexpression or the use of protoplasts from the corresponding mutants. We further show that our miRNA sensors can be used for investigating the effect of chemicals on miRNA activity. Our cell-based transient expression system is fast and easy to set up, and generates quantitative results, being a powerful tool for assaying miRNA activity in vivo. PMID:25680775

  5. Dissection of miRNA pathways using Arabidopsis mesophyll protoplasts.

    PubMed

    Martinho, Cláudia; Confraria, Ana; Elias, Carlos Alexandre; Crozet, Pierre; Rubio-Somoza, Ignacio; Weigel, Detlef; Baena-González, Elena

    2014-10-24

    microRNAs (miRNAs) control gene expression mostly post-transcriptionally by guiding transcript cleavage and/or translational repression of complementary mRNA targets, thereby regulating developmental processes and stress responses. Despite the remarkable expansion of the field, the mechanisms underlying miRNA activity are not fully understood. In this paper, we describe a transient expression system in Arabidopsis mesophyll protoplasts that is highly amenable for the dissection of miRNA pathways. We show that by transiently overexpressing primary miRNAs and target mimics, we can manipulate miRNA levels and consequently impact on their targets. Furthermore, we developed a set of luciferase-based sensors for quantifying miRNA activity that respond specifically to both endogenous and overexpressed miRNAs and target mimics. We demonstrate that these miRNA sensors can be used to test the impact of putative components of the miRNA pathway on miRNA activity, as well as the impact of specific mutations, either by overexpression or by the use of protoplasts from the corresponding mutants. We further show that our miRNA sensors can be used for investigating the effect of chemicals on miRNA activity. Our cell-based transient expression system is fast and easy to set up and generates quantitative results, being a powerful tool for assaying miRNA activity in vivo. PMID:25343984

  6. Diagnosis of Aortic Dissection in Emergency Department Patients is Rare

    PubMed Central

    Alter, Scott M.; Eskin, Barnet; Allegra, John R.

    2015-01-01

    Introduction Aortic dissection is a rare event. While the most frequent symptom is chest pain, that is a common emergency department (ED) chief complaint and other diseases causing chest pain occur much more often. Furthermore, 20% of dissections are without chest pain and 6% are painless. For these reasons, diagnosing dissections may be challenging. Our goal was to determine the number of total ED and atraumatic chest pain patients for every aortic dissection diagnosed by emergency physicians. Methods Design: Retrospective cohort. Setting: 33 suburban and urban New York and New Jersey EDs with annual visits between 8,000 and 80,000. Participants: Consecutive patients seen by emergency physicians from 1-1-1996 through 12-31-2010. Observations: We identified aortic dissection and atraumatic chest pain patients using the International Classification of Diseases 9th Revision and Clinical Modification codes. We then calculated the number of total ED and atraumatic chest pain patients for every aortic dissection, along with 95% confidence intervals (CIs). Results From a database of 9.5 million ED visits, we identified 782 aortic dissections or one for every 12,200 (95% CI [11,400–13,100]) visits. The mean age of dissection patients was 66±16 years and 38% were female. There were 763,000 (8%) with atraumatic chest pain diagnoses. Thus, there is one dissection for every 980 (95% CI [910–1,050]) atraumatic chest pain patients. Conclusion The diagnosis of aortic dissections by emergency physicians is rare and challenging. An emergency physician seeing 3,000 to 4,000 patients a year would diagnose an aortic dissection approximately every three to four years. PMID:26587083

  7. Phosphoproteomes of Strongylocentrotus purpuratus shell and tooth matrix: identification of a major acidic sea urchin tooth phosphoprotein, phosphodontin

    PubMed Central

    2010-01-01

    Background Sea urchin is a major model organism for developmental biology and biomineralization research. However, identification of proteins involved in larval skeleton formation and mineralization processes in the embryo and adult, and the molecular characterization of such proteins, has just gained momentum with the sequencing of the Strongylocentrotus purpuratus genome and the introduction of high-throughput proteomics into the field. Results The present report contains the determination of test (shell) and tooth organic matrix phosphoproteomes. Altogether 34 phosphoproteins were identified in the biomineral organic matrices. Most phosphoproteins were specific for one compartment, only two were identified in both matrices. The sea urchin phosphoproteomes contained several obvious orthologs of mammalian proteins, such as a Src family tyrosine kinase, protein kinase C-delta 1, Dickkopf-1 and other signal transduction components, or nucleobindin. In most cases phosphorylation sites were conserved between sea urchin and mammalian proteins. However, the majority of phosphoproteins had no mammalian counterpart. The most interesting of the sea urchin-specific phosphoproteins, from the perspective of biomineralization research, was an abundant highly phosphorylated and very acidic tooth matrix protein composed of 35 very similar short sequence repeats, a predicted N-terminal secretion signal sequence, and an Asp-rich C-terminal motif, contained in [Glean3:18919]. Conclusions The 64 phosphorylation sites determined represent the most comprehensive list of experimentally identified sea urchin protein phosphorylation sites at present and are an important addition to the recently analyzed Strongylocentrotus purpuratus shell and tooth proteomes. The identified phosphoproteins included a major, highly phosphorylated protein, [Glean3:18919], for which we suggest the name phosphodontin. Although not sequence-related to such highly phosphorylated acidic mammalian dental phosphoproteins as phosphoryn or dentin matrix protein-1, phosphodontin may perform similar functions in the sea urchin tooth. More than half of the detected proteins were not previously identified at the protein level, thus confirming the existence of proteins only known as genomic sequences previously. PMID:20181113

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

    PubMed Central

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

    2014-01-01

    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

  9. The Effect of a Prior Dissection Simulation on Middle School Students' Dissection Performance and Understanding of the Anatomy and Morphology of the Frog.

    ERIC Educational Resources Information Center

    Akpan, Joseph Paul; Andre, Thomas

    1999-01-01

    Reports on a study that examined the prior use of simulation on frog dissection in improving students' actual dissection performance and learning of frog anatomy and morphology. Finds that students who performed the simulation before dissection performed significantly better than students who performed dissection before using the simulation or…

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

    ERIC Educational Resources Information Center

    Franklin, Sue; Peat, Mary; Lewis, Alison

    2002-01-01

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

  11. Antiplatelet treatment compared with anticoagulation treatment for cervical artery dissection (CADISS): a randomised trial

    E-print Network

    CADISS trial investigators

    2015-02-12

    common alternative diagnoses were atherosclerosis, an atretic rather than dissected vertebral artery, a narrowed artery without any defi nite evidence of dissection and, in one case, adherent thrombus without clear evidence of dissection. Several...

  12. 78 FR 6838 - Certain Balloon Dissection Devices and Products Containing Same; Institution of Investigation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-31

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

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

    PubMed Central

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

    2015-01-01

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

  14. Coronary artery dissection following blunt chest trauma: a case report

    PubMed Central

    Swinkels, B.M.; Hoedemaker, G.; Peters, R.H.J.

    2005-01-01

    Coronary artery dissection following blunt chest trauma is rare. We report the case of a 43-year-old woman who was admitted with a subacute inferior myocardial infarction due to dissection of the right coronary artery. Ten days earlier, she had sustained a minimal chest trauma. The literature is reviewed and management is discussed. ImagesFigure 1Figure 2 PMID:25696487

  15. Dissecting the transcription networks of a cell using computational genomics

    E-print Network

    Babu, M. Madan

    Dissecting the transcription networks of a cell using computational genomics Hao LiĂ and Wei Wangy to systematically dissect transcriptional regulatory networks. Effective algorithms have been developed to predict cis-regulatory elements in a genome, to identify the target genes of transcription factors, to infer

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

    ERIC Educational Resources Information Center

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

    2011-01-01

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

  17. A Modified Dissection Method to Preserve Neck Structures

    ERIC Educational Resources Information Center

    Hankin, Mark H.; Stoller, Jeremy L.

    2009-01-01

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

  18. Isolated Superior Mesenteric Artery Dissection with Small Intestine Ischemia

    PubMed Central

    Aimi, Masahito; Amano, Chika; Yoshida, Rika; Matsubara, Takeshi; Mikami, Hironobu; Izumi, Daisuke; Okimoto, Eiko; Ishimura, Norihisa; Ishihara, Shunji; Kinoshita, Yoshikazu

    2015-01-01

    Superior mesenteric artery (SMA) dissection without aortic dissection is a rare condition, and its diagnosis is considered to be difficult. Intestinal infarction is a severe complication of the disease, which may require resection of the intestine. We present a case of isolated SMA dissection. A 53-year-old man experienced sudden pain in the abdomen while playing Japanese pinball and was admitted to our hospital due to acute abdominal symptoms of uncertain cause. Enhanced CT revealed a defect of the root of the SMA, while angiography and intravascular ultrasound findings showed dissection of the SMA wall. Conservative treatment was chosen at the time, while a part of the small intestine was eventually resected because of progressive ischemia. Although SMA dissection is a rare occurrence in cases with acute abdominal symptoms, awareness of the condition is important for differential diagnosis.

  19. 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

    Kariuki, Patrick; Paulson, Ronda

    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…

  20. Structural Dissection for Controlling Complex Networks

    E-print Network

    Wang, Wen-Xu; Zhao, Chen; Liu, Yang-Yu; Lai, Ying-Cheng

    2015-01-01

    Controlling complex networked systems has been a central goal in different fields and understanding controllability of complex networks has been at the forefront of contemporary science. Despite the recent progress in the development of controllability theories for complex networks, we continue to lack efficient tools to fully understand the effect of network topology and interaction strengths among nodes on controllability. Here we establish a framework to discern the significance of links and nodes for controlling general complex networks in a simple way based on local information. A dissection process is offered by the framework to probe and classify nodes and links completely, giving rise to a criterion for strong structural controllability. Analytical results indicate phase transitions associated with link and node categories, and strong structural controllability. Applying the tools to real networks demonstrate that real technological networks are strong structurally controllable, whereas most of real s...

  1. Cervical Artery Dissection: Emerging Risk Factors

    PubMed Central

    Micheli, S; Paciaroni, M; Corea, F; Agnelli, G; Zampolini, M; Caso, V

    2010-01-01

    Cervical artery dissection (CAD) represents an increasingly recognized cause of stroke and the most common cause of ischemic stroke in young adults. Many factors have been identified in association with CAD such as primary disease of arterial wall (fibrodysplasia) and other non-specific diseases related to CAD like Ehlers Danlos-syndrome IV, Marfan’s syndrome, vessel tortuosity. Moreover, an underlying arteriopathy which could be in part genetically determined, has been suspected. The rule of emerging risk factors for CAD such as recent respiratory tract infection, migraine and hyperhomocysteinemia are still a matter of research. Other known risks factors for CAD are major head/neck trauma like chiropractic maneuver, coughing or hyperextension injury associated to car. We examined emerging risks factors for CAD detected in the last years, as CAD pathogenesis is still not completely understood and needs further investigations. PMID:21270941

  2. Dissecting the iTRAQ Data Analysis.

    PubMed

    Aggarwal, Suruchi; Yadav, Amit Kumar

    2016-01-01

    In the era of large-scale quantitative biology, mass spectrometry-based quantitative proteomics is progressively becoming indispensable for gaining insights into the biological systems at molecular level. Various quantitative study designs rely on chemical tagging approaches to study disease, stress, or drug response and temporal studies aiming at disease/developmental progression in a biological system. Isobaric tags for relative and absolute quantitation (iTRAQ) is one of the most popular chemical labeling techniques which allows four, six, or eight samples to be multiplexed in a single run. As the iTRAQ tag has a balancer group to equalize all states of a labeled peptide to same mass, the differentially labeled iTRAQ peptides are mixed before chromatography and elute as a single combined peak in MS. This enhances the peptide signal and quantitation is performed during MS/MS along with sequencing, where reporter ions of different masses are released to give relative quantitation. Known amount of a spiked-in protein can also help in absolute quantitation of the proteins in a sample. PMID:26519184

  3. Sequential multiple visceral arteries dissections without aortic involvement.

    PubMed

    Bonardelli, Stefano; Battaglia, Giuseppe; Zanotti, Camilla; Cervi, Edoardo; Guadrini, Cristina; Giulini, Stefano M

    2013-05-01

    Isolated dissection of visceral arteries without associated aortic pathology is very rare. Risk factors, etiology, and natural history of this pathology continue to be unclear, and the guidelines for clinical management remain to be defined. We present a case not described previously, with sequential dissections of the celiac trunk, superior mesenteric artery, and renal arteries without aortic involvement. The patient presented with severe back thoracic and abdominal pain and without evidence of peritonitis. An abdominal angio-CT scan showed dissection of the superior mesenteric artery (SMA), with partial thrombosis of the false lumen and subsequent stenosis of around 60%. Conservative treatment with anticoagulants seemed to be appropriate in the beginning, because the patient became asymptomatic spontaneously within a few hours and angio-CT showed dissection but no ischemic lesions. On day 10 after onset, however, he again indicated severe back thoracic and abdominal pain. Emergent CT was performed. The prior SMA dissection appeared to be worse due to increased size of the false lumen, followed by SMA stenosis (about 75?80%). In addition, dissection of the celiac artery and both renal arteries could be seen. The patient underwent angiography and stenting of the main trunk of the SMA, with good clinical and radiologic outcome. Double oral antiplatelet therapy was then introduced. An angio-MRI scan 6 months later showed stability of the multiple dissections. PMID:23522441

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

    PubMed

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

    2015-04-01

    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

  5. Multiplex staining of 2-DE gels for an initial phosphoproteome analysis of germinating seeds and early grown seedlings from a non-orthodox specie: Quercus ilex L. subsp. ballota [Desf.] Samp.

    PubMed Central

    Romero-Rodríguez, M. Cristina; Abril, Nieves; Sánchez-Lucas, Rosa; Jorrín-Novo, Jesús V.

    2015-01-01

    As a preliminary step in the phosphoproteome analysis of germinating seeds (0 and 24 h after seed imbibition) and early grown seedlings (216 h after seed imbibition) from a non-orthodox sp. Quercus ilex, a multiplex (SYPRO-Ruby and Pro-Q DPS) staining of high-resolution 2-DE gels was used. By using this protocol it was possible to detect changes in protein-abundance and/or phosphorylation status. This simple approach could be a good complementary alternative to the enrichment protocols used in the search for phosphoprotein candidates. While 482 spots were visualized with SYPRO-Ruby, 222 were with Pro-Q DPS. Statistically significant differences in spot intensity were observed among samples, these corresponding to 85 SYPRO-Ruby-, 20 Pro-Q-DPS-, and 35 SYPRO-Ruby and Pro-Q-DPS-stained spots. Fifty-five phosphoprotein candidates showing qualitative or quantitative differences between samples were subjected to MALDI-TOF-TOF MS analysis, with 20 of them being identified. Identified proteins belonged to five different functional categories, namely: carbohydrate and amino acid metabolism, defense, protein folding, and oxidation-reduction processes. With the exception of a putative cyclase, the other 19 proteins had at least one orthologous phosphoprotein in Arabidopsis thaliana, Medicago truncatula, N. tabacum, and Glycine max. Out of the 20 identified, seven showed differences in intensity in Pro-Q-DPS but not in SYPRO-Ruby-stained gels, including enzymes of the glycolysis and amino acid metabolism. This bears out that theory the regulation of these enzymes occurs at the post-translational level by phosphorylation with no changes at the transcriptional or translational level. This is different from the mechanism reported in orthodox seeds, in which concomitant changes in abundance and phosphorylation status have been observed for these enzymes. PMID:26322061

  6. Blindness after bilateral neck dissection: case report and review.

    PubMed

    Pazos, G A; Leonard, D W; Blice, J; Thompson, D H

    1999-01-01

    The primary objective of this review of the literature is to identify the probable causes of blindness after bilateral radical neck dissections. This case report and literature review also discusses possible preventive measures that may avert this catastrophic outcome. Cases of blindness after bilateral radical neck dissection were identified by an electronic literature search, as well as cross-checking all references of the above-identified papers. Eleven previous cases of blindness after bilateral neck dissection were identified. The most common cause was posterior ischemic optic neuropathy (PION), which was permanent. We present the only case in the literature in which blindness occurred after radical neck dissections separated by a span of 9 years. The cause of blindness in our patient was posterior ischemic optic neuropathy. Contributing factors included anemia, hypotension, and disruption of collateral venous return from the neck. PMID:10512147

  7. SMAD2 Mutations Are Associated with Arterial Aneurysms and Dissections.

    PubMed

    Micha, Dimitra; Guo, Dong-Chuan; Hilhorst-Hofstee, Yvonne; van Kooten, Fop; Atmaja, Dian; Overwater, Eline; Cayami, Ferdy K; Regalado, Ellen S; van Uffelen, René; Venselaar, Hanka; Faradz, Sultana M H; Vriend, Gerrit; Weiss, Marjan M; Sistermans, Erik A; Maugeri, Alessandra; Milewicz, Dianna M; Pals, Gerard; van Dijk, Fleur S

    2015-12-01

    We report three families with arterial aneurysms and dissections in which variants predicted to be pathogenic were identified in SMAD2. Moreover, one variant occurred de novo in a proband with unaffected parents. SMAD2 is a strong candidate gene for arterial aneurysms and dissections given its role in the TGF-? signaling pathway. Furthermore, although SMAD2 and SMAD3 probably have functionally distinct roles in cell signaling, they are structurally very similar. Our findings indicate that SMAD2 mutations are associated with arterial aneurysms and dissections and are in accordance with the observation that patients with pathogenic variants in genes encoding proteins involved in the TGF-? signaling pathway exhibit arterial aneurysms and dissections as key features. PMID:26247899

  8. Combining Genomic Tools to Dissect Multifactorial Virulence in Pseudomonas

    E-print Network

    Ausubel, Frederick M.

    Combining Genomic Tools to Dissect Multifactorial Virulence in Pseudomonas aeruginosa Daniel G. Lee- ronmental bacterium and important opportunistic human pathogen, Pseudomonas aeruginosa. By comparing PA14 Introduction The growing number of sequenced bacterial genomes, including those of important pathogenic

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

    MedlinePLUS

    ... Stroke More Coronary Artery Dissection: Not Just a Heart Attack Updated:Sep 3,2015 Sometimes a heart attack ... Disease Go Red For Women Types of aneurysms Heart Attack • Home • About Heart Attacks • Warning Signs of a ...

  10. Dissecting intramyocardial hematoma after robotic mitral valve repair.

    PubMed

    McGrath, Tory; Ushukumari, Deepu; Canale, Leonardo; Gillinov, Marc

    2015-03-01

    We report the first case of a dissecting intramyocardial hematoma discovered intraoperatively after robotic mitral valve repair, potential etiologies relevant to robotic surgery, and its successful management. PMID:25742825

  11. Chemistry & Biology Structure-Based Dissection of the Natural Product

    E-print Network

    van Aalten, Daan

    Chemistry & Biology Article Structure-Based Dissection of the Natural Product Cyclopentapeptide chemotherapeutic potential as fungicides, pesticides, and antiasthmatics. Argifin, a natural product extensive substrate mim- icry. In an attempt to map the active fragments of this large natural product

  12. The risk for type B aortic dissection in Marfan syndrome.

    PubMed

    Setacci, C; Galzerano, G; Setacci, F; Mazzitelli, G; de Donato, G; Ricci, C

    2015-12-01

    Marfan syndrome is the most prevalent connective tissue disorder, with an autosomal dominant inheritance with variable penetrance. This paper aims to summarize epidemiology and treatment for type B dissection in Marfan patients. PMID:26350976

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

    SciTech Connect

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

    1982-01-01

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

  14. Robotic transaxillary central neck dissection: video description of the technique.

    PubMed

    Agcaoglu, Orhan; Aliyev, Shamil; Siperstein, Allan; Berber, Eren

    2012-08-01

    Although various groups have described their experiences with robotic transaxillary thyroidectomy, to our knowledge, robotic central neck dissection has not been described in the North American literature. We here demonstrate the technique of robotic central neck dissection at the time of transaxillary total thyroidectomy. The procedure was performed under general anesthesia through a 6-cm right axillary incision. The robotic camera and 2 working robotic arms were used for the procedure. PMID:22874698

  15. Radical lymph node dissection for cancer of the thoracic esophagus.

    PubMed Central

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

    1994-01-01

    OBJECTIVE: The authors documented the localization and frequency of lymphatic spread in squamous cell carcinoma of the thoracic esophagus and evaluated the influence of radical systematic lymph node dissection on patient survival. SUMMARY BACKGROUND DATA: From accumulated surgical experience, it was suggested that some of the patients with lymph nodal involvement from cancer could be cured by its clearance. However, it is only recently that cancer of the esophagus has been evaluated in terms of analyzing lymphatic spread and results of lymphadenectomy. METHODS: Among 1298 patients admitted to the Toranomon Hospital between 1973 and 1993, 913 (70.3%) had resections, including curative and palliative procedures. For this study, 717 patients with TNM RO (resection with no residual tumor at operation in TNM classification) were analyzed. Survival was compared between groups of patients with less extensive thoracoabdominal (two-field) dissections and extensive collothoracoabdominal (three-field) dissections. RESULTS: Comparative study revealed that 5-year survival rate for TNM RO patients after free-field dissection (55.0%) was significantly better (log rank test, p = 0.0013) than the rate after two-field dissection (38.3%). The results were particularly significant in subgroups with stage III and IV (because of nodal factor). Overall 5-year survival rate after all resections was 42.4%. CONCLUSIONS: The role of radical lymph node dissection in cancer of the thoracic esophagus evaluated. Long-term survival was compared between two groups with two- and three-field dissection. It was concluded that survival rate was significantly better in patients with extensive three-field dissection. PMID:8092902

  16. Isolated Spontaneous Renal Artery Dissection Presented with Flank Pain

    PubMed Central

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

    2015-01-01

    Spontaneous renal artery dissection is a rare but important cause of flank pain. We report a case of isolated spontaneous renal artery dissection in 56-year-old man complicated by renal infarction presented with flank pain. Doppler study pointed towards vascular pathology. Computed tomography (CT) angiography was used to make final diagnosis which demonstrated intimal flap in main renal artery with renal infarction. PMID:26090259

  17. Dissecting innate immunity by germline mutagenesis

    PubMed Central

    Rutschmann, Sophie; Hoebe, Kasper

    2008-01-01

    The innate arm of our immune system is the first line of defence against infections. In addition, it is believed to drive adaptive immune responses, which help fight pathogens and provide long-term memory. As such, the innate immune system is instrumental for protection against pathogens that would otherwise destroy their host. Although our understanding of the innate immune components involved in pathogen sensing and fighting is improving, it is still limited. This is particularly exemplified by increased documentation of innate immune deficiencies in humans that often result in high and recurrent susceptibility to infections or even death, without the genetic cause being evident. To provide further insight into the mechanisms by which pathogen sensing and eradication occur, several strategies can be used. The current review focuses on the forward genetic approaches that have been used to dissect innate immunity in the fruit fly and the mouse. For both animal models, forward genetics has been instrumental in the deciphering of innate immunity and has greatly improved our understanding of how we respond to invading pathogens. PMID:18205789

  18. Endoscopic Submucosal Dissection (ESD) in Colorectal Tumors

    PubMed Central

    Dumoulin, Franz Ludwig; Sido, Bernd; Bollmann, Reinhard; Sauer, Malte

    2014-01-01

    Summary Background Endoscopic submucosal dissection (ESD) – initially developed for the treatment of early gastric cancer in Japan – is an attractive option for en bloc resection of larger sessile or flat colorectal neoplasia. Methods A review of the current literature on colorectal ESD was carried out. Results In contrast to conventional endoscopic mucosal resection (EMR), ESD for larger colorectal neoplasia yields high en bloc resection rates and very low recurrence rates. The frequency of delayed bleeding is similar for EMR and ESD. Higher perforation rates during ESD are mostly due to microperforations identified and treated during the intervention, and are therefore of minor clinical relevance. A major disadvantage of ESD is the necessity for high-level endoscopic skills and long procedure times. ESD also has the potential to replace laparoscopic surgery or transanal endoscopic microsurgery mainly due to its lower complication rates. Conclusion ESD for the resection of larger flat or sessile colorectal lesions has potential advantages over conventional EMR or minimally invasive surgery. Due to the low incidence of early gastric cancer, experience with ESD will remain limited in Western countries. The spread of colorectal ESD will depend on adequate training opportunities and also on modifications yielding a reduction in procedure time. PMID:26288580

  19. [Esophagectomy after endoscopic submucosal dissection (ESD)].

    PubMed

    Nako, Yoshito; Shiozaki, Atushi; Fujiwara, Hitoshi; Konishi, Hirotaka; Kosuga, Toshiyuki; Morimura, Ryo; Murayama, Yasutoshi; Komatsu, Shuhei; Ikoma, Hisashi; Kuriu, Yoshiaki; Nakanishi, Masayoshi; Ichikawa, Daisuke; Okamoto, Kazuma; Sakakura, Chouhei; Otsuji, Eigo

    2014-11-01

    Herein, we report 9 patients who underwent esophagectomy after endoscopic submucosal dissection (ESD) between April 2003 and December 2013. All patients were men, with a mean age of 65 years. En bloc ESD was performed, and no complications arose in any patient. The mean surgical time of esophagectomy was 323 minutes, and mean blood loss was 295 mL. Postoperative complications were present in 5 patients(anastomotic leakage in 3, pulmonary complications in 2, and recurrent laryngeal nerve palsy in 1). In a patient diagnosed with pT1b-SM1 disease after ESD, a residual tumor(pT1a-MM, N0) was detected after esophagectomy. In another patient diagnosed with pT1b-SM2 disease, lymph node metastasis was detected after esophagectomy. In all patients, curative resection was performed, and no recurrences have been observed to date. This highlights the importance of additional esophagectomy after ESD for patients with pT1b disease. Esophagectomy after ESD can be considered a valid treatment because it provides high curative rates with acceptable safety. PMID:25731401

  20. Optogenetic dissection of medial prefrontal cortex circuitry

    PubMed Central

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

    2014-01-01

    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

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

    PubMed

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

    2015-11-01

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

  2. The Tec Kinase-Regulated Phosphoproteome Reveals a Mechanism for the Regulation of Inhibitory Signals in Murine Macrophages.

    PubMed

    Tampella, Giacomo; Kerns, Hannah M; Niu, Deqiang; Singh, Swati; Khim, Socheath; Bosch, Katherine A; Garrett, Meghan E; Moguche, Albanus; Evans, Erica; Browning, Beth; Jahan, Tahmina A; Nacht, Mariana; Wolf-Yadlin, Alejandro; Plebani, Alessandro; Hamerman, Jessica A; Rawlings, David J; James, Richard G

    2015-07-01

    Previous work has shown conflicting roles for Tec family kinases in regulation of TLR-dependent signaling in myeloid cells. In the present study, we performed a detailed investigation of the role of the Tec kinases Btk and Tec kinases in regulating TLR signaling in several types of primary murine macrophages. We demonstrate that primary resident peritoneal macrophages deficient for Btk and Tec secrete less proinflammatory cytokines in response to TLR stimulation than do wild-type cells. In contrast, we found that bone marrow-derived and thioglycollate-elicited peritoneal macrophages deficient for Btk and Tec secrete more proinflammatory cytokines than do wild-type cells. We then compared the phosphoproteome regulated by Tec kinases and LPS in primary peritoneal and bone marrow-derived macrophages. From this analysis we determined that Tec kinases regulate different signaling programs in these cell types. In additional studies using bone marrow-derived macrophages, we found that Tec and Btk promote phosphorylation events necessary for immunoreceptor-mediated inhibition of TLR signaling. Taken together, our results are consistent with a model where Tec kinases (Btk, Tec, Bmx) are required for TLR-dependent signaling in many types of myeloid cells. However, our data also support a cell type-specific TLR inhibitory role for Btk and Tec that is mediated by immunoreceptor activation and signaling via PI3K. PMID:26026062

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

    PubMed Central

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

    2011-01-01

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

  4. Comparative proteomic and phosphoproteomic analysis of the silkworm (Bombyx mori) posterior silk gland under high temperature treatment.

    PubMed

    Li, Jisheng; Ye, Lupeng; Lan, Tianyun; Yu, Meilan; Liang, Jianshe; Zhong, Boxiong

    2012-08-01

    The proteins from the posterior silk gland of silkworm hybrids and their parents reared under high temperatures were studied by using comparative proteomic and phosphoproteomic analysis. A total of 82.07, 6.17 and 11.76 % protein spots showed additivity, overdominance and underdominance patterns, respectively. Fifteen differentially expressed protein spots were identified by peptide mass fingerprinting. Among these, four spots, including sHSPs and prohibitin protein that were directly relevant to heat response, were identified. Eleven protein spots were found to play an important role in silk synthesis, and nine protein spots expressed phosphorylation states. According to Gene ontology and KEGG pathway analysis, these nine spots played an important role in stress-induced signal transduction. Expression of most silk synthesis-related proteins was reduced, whereas stress-responsive proteins increased with heat exposure time in three breeds. Furthermore, most proteins showed under- or overdominance in the hybrids compared to the parents. The results suggested that high temperature could alter the expression of proteins related to silk synthesis and heat response in silkworm. Moreover, differentially expressed proteins occurring in the hybrid and its parents may be the main explanation of the observed heterosis. PMID:22707192

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

    PubMed Central

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

    2013-01-01

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

  6. Integrated analysis of global proteome, phosphoproteome, and glycoproteome enables complementary interpretation of disease-related protein networks.

    PubMed

    Park, Jong-Moon; Park, Ji-Hwan; Mun, Dong-Gi; Bae, Jingi; Jung, Jae Hun; Back, Seunghoon; Lee, Hangyeore; Kim, Hokeun; Jung, Hee-Jung; Kim, Hark Kyun; Lee, Hookeun; Kim, Kwang Pyo; Hwang, Daehee; Lee, Sang-Won

    2015-01-01

    Multi-dimensional proteomic analyses provide different layers of protein information, including protein abundance and post-translational modifications. Here, we report an integrated analysis of protein expression, phosphorylation, and N-glycosylation by serial enrichments of phosphorylation and N-glycosylation (SEPG) from the same tissue samples. On average, the SEPG identified 142,106 unmodified peptides of 8,625 protein groups, 18,846 phosphopeptides (15,647 phosphosites), and 4,019 N-glycopeptides (2,634 N-glycosites) in tumor and adjacent normal tissues from three gastric cancer patients. The combined analysis of these data showed that the integrated analysis additively improved the coverages of gastric cancer-related protein networks; phosphoproteome and N-glycoproteome captured predominantly low abundant signal proteins, and membranous or secreted proteins, respectively, while global proteome provided abundances for general population of the proteome. Therefore, our results demonstrate that the SEPG can serve as an effective approach for multi-dimensional proteome analyses, and the holistic profiles of protein expression and PTMs enabled improved interpretation of disease-related networks by providing complementary information. PMID:26657352

  7. Phosphoproteomics Reveals Resveratrol-Dependent Inhibition of Akt/mTORC1/S6K1 Signaling

    PubMed Central

    2015-01-01

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

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

    PubMed Central

    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

    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

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

    PubMed Central

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

    2015-01-01

    Basal and kinase inhibitor-driven adaptive signaling has been examined in a panel of melanoma cell lines using phosphoproteomics in conjunction with pathway analysis. A considerable divergence in the spectrum of tyrosine-phosphorylated peptides was noted at the cell line level. The unification of genotype-specific cell line data revealed the enrichment for the tyrosine-phosphorylated cytoskeletal proteins to be associated with the presence of a BRAF mutation and oncogenic NRAS to be associated with increased receptor tyrosine kinase phosphorylation. A number of proteins including cell cycle regulators (CDK1, CDK2 and CDK3), MAPK pathway components (ERK1 and ERK2), interferon regulators (TYK2), GTPase regulators (RIN1) and controllers of protein tyrosine phosphorylation (DYR1A and PTPRA) were common to all genotypes. Treatment of a BRAF-mutant/PTEN-null melanoma cell line with vemurafenib led to decreased phosphorylation of ERK, phospholipase C1 and ?-catenin with increases in RTK phosphorylation, STAT3 and GSK3? noted. In NRAS-mutant melanoma, MEK inhibition led to increased phosphorylation of EGFR signaling pathway components, Src family kinases and PKC? with decreased phosphorylation seen in STAT3 and ERK1/2. Together these data present the first systems level view of adaptive and basal phosphotyrosine signaling in BRAF- and NRAS-mutant melanoma. PMID:25339196

  10. Integrated analysis of global proteome, phosphoproteome, and glycoproteome enables complementary interpretation of disease-related protein networks

    PubMed Central

    Park, Jong-Moon; Park, Ji-Hwan; Mun, Dong-Gi; Bae, Jingi; Jung, Jae Hun; Back, Seunghoon; Lee, Hangyeore; Kim, Hokeun; Jung, Hee-Jung; Kim, Hark Kyun; Lee, Hookeun; Kim, Kwang Pyo; Hwang, Daehee; Lee, Sang-Won

    2015-01-01

    Multi-dimensional proteomic analyses provide different layers of protein information, including protein abundance and post-translational modifications. Here, we report an integrated analysis of protein expression, phosphorylation, and N-glycosylation by serial enrichments of phosphorylation and N-glycosylation (SEPG) from the same tissue samples. On average, the SEPG identified 142,106 unmodified peptides of 8,625 protein groups, 18,846 phosphopeptides (15,647 phosphosites), and 4,019 N-glycopeptides (2,634 N-glycosites) in tumor and adjacent normal tissues from three gastric cancer patients. The combined analysis of these data showed that the integrated analysis additively improved the coverages of gastric cancer-related protein networks; phosphoproteome and N-glycoproteome captured predominantly low abundant signal proteins, and membranous or secreted proteins, respectively, while global proteome provided abundances for general population of the proteome. Therefore, our results demonstrate that the SEPG can serve as an effective approach for multi-dimensional proteome analyses, and the holistic profiles of protein expression and PTMs enabled improved interpretation of disease-related networks by providing complementary information. PMID:26657352

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

    PubMed Central

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

    2015-01-01

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

  12. Case Misclassification in Studies of Spinal Manipulation and Arterial Dissection

    PubMed Central

    Cai, Xuemei; Razmara, Ali; Paulus, Jessica K; Switkowski, Karen; Fariborz, Pari J; Goryachev, Sergey D; D’Avolio, Leonard; Feldmann, Edward; Thaler, David E

    2014-01-01

    Goals Spinal manipulation has been associated with cervical arterial dissection and stroke but a causal relationship has been questioned by population-based studies. Earlier studies identified cases using International Classification of Diseases-9 codes specific to anatomical stroke location rather than stroke etiology. We hypothesize that case misclassification occurred in these previous studies and an underestimation of the strength of the association. We also predicted that case misclassification would differ by patient age. Materials and methods We identified cases in the Veterans Health Administration database using the same strategy as the prior studies. The electronic medical record was then screened for the word “dissection.” The presence of atraumatic dissection was determined by medical record review by a neurologist. Findings Of 3690 patients found by International Classification of Diseases-9 codes over a 30-month period, 414 (11.2%) had confirmed cervical artery dissection with a positive predictive value of 10.5% (95% CI 9.6–11.5%). The positive predictive value was higher in patients <45 versus ?45 years (41% vs. 9%, p<0.001). We reanalyzed a previous study which reported no association between spinal manipulation and cervical artery dissection (OR=1.12, 95% CI 0.77–1.63), and re-calculated an odds ratio of 2.15 (95% CI 0.98–4.69). For patients under age 45, the OR was 6.91 (95% CI 2.59–13.74). Conclusions Prior studies grossly misclassified cases of cervical dissection and mistakenly dismissed a causal association with manipulation. Our study indicates that the odds ratio for spinal manipulation exposure in cervical artery dissection is higher than previously reported. PMID:25085345

  13. 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.

  14. Dissecting the impact of matrix anchorage and elasticity in cell adhesion.

    PubMed

    Pompe, Tilo; Glorius, Stefan; Bischoff, Thomas; Uhlmann, Ina; Kaufmann, Martin; Brenner, Sebastian; Werner, Carsten

    2009-10-21

    Extracellular matrices determine cellular fate decisions through the regulation of intracellular force and stress. Previous studies suggest that matrix stiffness and ligand anchorage cause distinct signaling effects. We show herein how defined noncovalent anchorage of adhesion ligands to elastic substrates allows for dissection of intracellular adhesion signaling pathways related to matrix stiffness and receptor forces. Quantitative analysis of the mechanical balance in cell adhesion using traction force microscopy revealed distinct scalings of the strain energy imparted by the cells on the substrates dependent either on matrix stiffness or on receptor force. Those scalings suggested the applicability of a linear elastic theoretical framework for the description of cell adhesion in a certain parameter range, which is cell-type-dependent. Besides the deconvolution of biophysical adhesion signaling, site-specific phosphorylation of focal adhesion kinase, dependent either on matrix stiffness or on receptor force, also demonstrated the dissection of biochemical signaling events in our approach. Moreover, the net contractile moment of the adherent cells and their strain energy exerted on the elastic substrate was found to be a robust measure of cell adhesion with a unifying power-law scaling exponent of 1.5 independent of matrix stiffness. PMID:19843448

  15. 3D segmentation of the true and false lumens on CT aortic dissection images

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

    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.

  16. On Quantitizing

    ERIC Educational Resources Information Center

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

    2009-01-01

    "Quantitizing", commonly understood to refer to the numerical translation, transformation, or conversion of qualitative data, has become a staple of mixed methods research. Typically glossed are the foundational assumptions, judgments, and compromises involved in converting disparate data sets into each other and whether such conversions advance…

  17. Unraveling pancreatic islet biology by quantitative proteomics

    SciTech Connect

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

    2011-08-01

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

  18. Snack Cake 'Dissection': A Flipped Classroom Exercise to Engage Undergraduates With Basic Neuroanatomy.

    PubMed

    Watson, Todd D

    2015-01-01

    This report describes a brief classroom activity for introducing basic neuroanatomical terminology and concepts to undergraduates in a survey-level course. Prior to completing the activity, students watched a short online lecture discussing the relevant material. During class, students worked in groups to 'dissect' snack cakes using the information they learned in the video and then reported and shared their 'results' using anatomical terminology. Quantitative feedback suggests that students found that the exercise was useful practice, that it helped increase their confidence in their ability to learn neuroanatomy, and that it helped increase their interest in the material generally. Data from an online anatomy quiz further supports the exercise's efficacy. Overall, the data suggest that this exercise may be a worthwhile addition to courses that introduce neuroanatomy to undergraduates. PMID:26557799

  19. Neurocognitive Phenotypes and Genetic Dissection of Disorders of Brain and Behavior

    PubMed Central

    Congdon, Eliza; Poldrack, Russell A.; Freimer, Nelson B.

    2014-01-01

    Summary Elucidating the molecular mechanisms underlying quantitative neurocognitive phenotypes will further our understanding of the brain’s structural and functional architecture and advance the diagnosis and treatment of the psychiatric disorders that these traits underlie. Although many neurocognitive traits are highly heritable, little progress has been made in identifying genetic variants unequivocally associated with these phenotypes. A major obstacle to such progress is the difficulty in identifying heritable neurocognitive measures which are precisely defined, systematically assessed and represent unambiguous mental constructs, yet are amenable to the high-throughput phenotyping necessary to obtain adequate power for genetic association studies. In this perspective we compare the current status of genetic investigations of neurocognitive phenotypes to that of other categories of biomedically relevant traits and suggest strategies for genetically dissecting traits that may underlie disorders of brain and behavior. PMID:20955930

  20. Snack Cake ‘Dissection’: A Flipped Classroom Exercise to Engage Undergraduates With Basic Neuroanatomy

    PubMed Central

    Watson, Todd D.

    2015-01-01

    This report describes a brief classroom activity for introducing basic neuroanatomical terminology and concepts to undergraduates in a survey-level course. Prior to completing the activity, students watched a short online lecture discussing the relevant material. During class, students worked in groups to ‘dissect’ snack cakes using the information they learned in the video and then reported and shared their ‘results’ using anatomical terminology. Quantitative feedback suggests that students found that the exercise was useful practice, that it helped increase their confidence in their ability to learn neuroanatomy, and that it helped increase their interest in the material generally. Data from an online anatomy quiz further supports the exercise’s efficacy. Overall, the data suggest that this exercise may be a worthwhile addition to courses that introduce neuroanatomy to undergraduates. PMID:26557799

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

    PubMed Central

    2013-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    SciTech Connect

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

    2010-11-30

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

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

    PubMed

    Chung, Beom Sun; Chung, Min Suk

    2015-06-01

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

  5. Digital dissection system for medical school anatomy training

    NASA Astrophysics Data System (ADS)

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

    2003-05-01

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

  6. Ischemia-reperfusion injury in an aortic dissection patient.

    PubMed

    Yin, Zhuo; Yang, J R; Wei, Y S; Liang, B L; Wei, Y B; Zhou, K Q; Wang, Z; Yan, B; Gao, Y L

    2015-07-01

    Aortic dissection is a life-threatening emergency. Well-established risk factors include systemic hypertension, hereditary connective tissue diseases (Marfan syndrome and Ehlers-Danlos syndrome), coarctation of the aorta, bicuspid aortic valve, aortitis, and arch hypoplasia. Ischemia of the viscera, the kidneys, the spinal cord, or the lower extremities due to malperfusion constitutes life-threatening complications that have to be considered in the treatment strategy.We report a rare case of symptomatic ischemia of the lower extremities due to aortic dissection. This case demonstrates that the treating physician needs to be vigilant for ischemia reperfusion injuries such as osteofascial compartment syndrome and acute renal failure in aortic dissection. PMID:25667158

  7. A Comparison of the Chicken and Turkey Proteomes and Phosphoproteomes in the Development of Poultry-Specific Immuno-Metabolism Kinome Peptide Arrays

    PubMed Central

    Arsenault, Ryan J.; Trost, Brett; Kogut, Michael H.

    2014-01-01

    The use of species-specific peptide arrays for the study of animal kinomes has a proven track record of success. This technique has been used in a variety of species for the study of host–pathogen interactions and metabolism. Species-specific peptide arrays have been designed previously for use with chicken but a turkey array has never been attempted. In addition, arrays designed around individual cellular functions have been designed and utilized, but cross-function immuno-metabolic arrays have not been considered previously. Antecedent to designing separate chicken and turkey immuno-metabolic kinome peptide arrays, we show that while the chicken and turkey genomes are quite similar, the two species are much more distinct at the proteome and phosphoproteome levels. Despite a genome identity of approximately 90%, we observe that only 83% of chicken and turkey orthologous proteins display sequence matches between the two species. Further, less than 70% of kinase recognition target sequences are exact matches between chicken and turkey. Thus, our analysis shows that, at the proteome and kinome level, these two species must be considered separately in the design of novel peptide arrays. Our ultimate array design covers numerous immune and metabolic processes including innate and adaptive immunity, inflammatory responses, carbohydrate, protein, and fat metabolism, and response to hormones. We have shown the proteomic and phosphoproteomic diversity of chicken and turkey and have designed a valuable research tool for the study of immuno-metabolism within these two species. PMID:26664921

  8. Role of cadaveric dissections in modern medical curricula: a study on student perceptions

    PubMed Central

    Nirthanan, Selvanayagam N.; Khoo, Tien K.; Tedman, Raymond

    2015-01-01

    The shift from traditional medical curricula to newer teaching and learning approaches such as problem-based learning has often resulted in omission or significant reduction of cadaveric dissections as a method of learning anatomy. The objective of this study was to evaluate students' perception of dissection in a graduate-entry, problem-based learning-based medical curriculum. At the end of the musculoskeletal dissection program in second year, a Likert-type questionnaire was used to explore medical student perceptions of the perceived advantages and challenges of cadaveric dissections in comparison with other anatomy teaching methods. Overall, a majority of students had a positive perception of dissections. Students who attended dissections regularly had significantly more positive perceptions about their experience and were in agreement with statements such as "dissections make learning more interesting" and "I would be disadvantaged if I did not attend dissection classes." Non-regular attendance was associated with statements about dissections such as "I do not like the smell," "time consuming," and "bored with the way it is carried-out." A follow-up study after completion of the medical program revealed a significant improvement of positive perception about dissection. Student perceptions appear to favour a role for cadaveric dissection in learning anatomy in modern medical curricula. However, optimal and effective integration of dissections is important, with consideration given to its structure and extent of content weighed against logistics and availability of resources; while addressing negative perceptions of dissection-based teaching. PMID:26417481

  9. Quantitative radiography

    SciTech Connect

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

    1991-02-01

    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.

  10. What is happening in our anatomical dissection rooms?

    PubMed

    Hildebrandt, Sabine

    2014-09-01

    A recent student article relates disrespectful and traumatizing events in a modern dissection room. This comment serves to remind anatomical educators' of their duties toward the medical students. It is the anatomical educators' duty to help students not only to become familiar with the structure of the human body but also with the emotional repertoire available when dealing with the living and the dead. And it is the educators' duty to accompany students through the dissection course experience in a manner that keeps them safe from emotional harm. PMID:24648394

  11. Basic dissecting techniques in ultrasound-guided surgery

    PubMed Central

    Koczy, Bogdan; Mielnik, Micha?; Pilecki, Grzegorz; Dzielicki, Józef; Jakubowski, Wies?aw

    2014-01-01

    Ultrasound-guided surgery is an area of minimally-invasive surgery where surgical procedures are performed with the aid of ultrasound imaging throghout the operation. This requires the operator to posses a certain degree of experience in endoscopic procedures, and to be adeptly skillfull in conducting US examinations. It is combining and finely tuning together these two elements that allows to perform efficiently an ultrasound-guided surgical procedure. Accessing an affected site correctly is of utmost importance in surgery, being oftentimes decisive in terms of the procedure's final outcome. In ultrasound-guided procedures, the operative site is accessed percutaneously, with a single point incision, yet tissues situated deeper within are dissected with dissecting techniques in a fluid evironment, typical for this area of surgery. Dissecting techniques in ultrasound-guided surgery are currently divided into basic ones which employ either a hydrodissection needle, surgical instruments, electrosurgical instruments, a thread, or a combination thereof, and advanced ones where either a balloon, a hook dissection technique, or a hybrid one is used. Hydrodissection with a needle was devised based on the rule of complementarity, and is the most frequently applied technique in ultrasound-guided surgery. The immense possibilities that go along with this modality will be of huge benefit to any surgeon, regardless of their field. Dissection with a variety of surgical instruments and electrosurgery instruments is a standard practice in all surgery areas, yet the method of imaging we employ in ultrasound-guided surgery results in certain modifications of these techniques. It is, however, learning the thread technique that facilitates a precise and oftentimes extensive dissection. This technique is successfully applied for dissecting muscle, ligament, tendon, vascular and other structures. Having mastered dissecting techniques allows to perform any minimally-invasive procedure efficiently, be they ultrasound-guided, artroscopic, or endoscopic ones. Various surgical techniques are bridged, resulting in applying the so-called hybrid ones. Their strength lies in excellent imaging results allowing to conduct a surgical procedure both in a body cavity and within a parenchymal organ. PMID:26674391

  12. Dissecting cellular biomechanics with a laser

    NASA Astrophysics Data System (ADS)

    Hutson, M. Shane

    2011-10-01

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

  13. 78 FR 17429 - Certain Balloon Dissection Devices and Products Containing Same; Commission Determination Not To...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-21

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

  14. Internal carotid artery dissection following chiropractic treatment in a pregnant woman with Systemic Lupus Erythematosus

    PubMed Central

    2012-01-01

    A case of internal carotid artery dissection in a pregnant woman with Systemic Lupus Erythematosus (SLE) immediately following chiropractic treatment is presented. The literature regarding complications of neck manipulation during pregnancy, spontaneous dissection of craniocervical arteries in pregnancy and the postpartum period, and dissection of craniocervical arteries in SLE are reviewed. To the best of the author’s knowledge, this is the first case of carotid artery dissection following chiropractic treatment in a pregnant woman published in the literature. PMID:23254252

  15. Genetic dissection of NK cell responses

    PubMed Central

    Moussa, Peter; Marton, Jennifer; Vidal, Silvia M.; Fodil-Cornu, Nassima

    2012-01-01

    The association of Natural Killer (NK) cell deficiencies with disease susceptibility has established a central role for NK cells in host defence. In this context, genetic approaches have been pivotal in elucidating and characterizing the molecular mechanisms underlying NK cell function. To this end, homozygosity mapping and linkage analysis in humans have identified mutations that impact NK cell function and cause life-threatening diseases. However, several critical restrictions accompany genetic studies in humans. Studying NK cell pathophysiology in a mouse model has therefore proven a useful tool. The relevance of the mouse model is underscored by the similarities that exist between cell-structure-sensing receptors and the downstream signaling that leads to NK cell activation. In this review, we provide an overview of how human and mouse quantitative trait locis (QTLs) have facilitated the identification of genes that modulate NK cell development, recognition, and killing of target cells. PMID:23346087

  16. Dissecting cell death with proteomic scalpels.

    PubMed

    Wang, Li-Shun; Xia, Li; Shen, Shao-Min; Zheng, Ying; Yu, Yun; Chen, Guo-Qiang

    2012-02-01

    Programmed cell deaths (PCD), including apoptosis, autophagy and programmed necrosis, are genetically determined, complex processes in multi-cellular organisms. Problems with the regulation of PCD have been implicated in a number of diseases including myocardial infarction, cancer and autoimmune disease. As a result, the investigation on PCD regulation has stirred considerable interest. In the past decades, many PCD-involved proteins had been identified as being modulated by post-translational mechanisms, including post-translational modification, protein-protein interactions and protein cleavage, which fall precisely within the range of proteomic analysis. Contemporary quantitative proteomics, interactomics, PTMomics, degradomics, chemical proteomics and pharmacoproteomics have been quickly applied in the field of PCD research, and possess the potential to be the driving forces of the field. This review attempts to highlight some of the major achievements in the application of proteomics in PCD research to trigger further thinking and application. PMID:22247084

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  18. Oregon Sea Grant Marine Education Program at Hatfield Marine Science Center Squid Dissection

    E-print Network

    Wright, Dawn Jeannine

    Oregon Sea Grant Marine Education Program at Hatfield Marine Science Center Squid Dissection The Squid Dissection program at Hatfield Marine Science Center is designed to be a 50- minute lab the directions of their marine educator, to systematically dissect a thawed squid and explore the many

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

    ERIC Educational Resources Information Center

    Milano, Regina Nicole

    2010-01-01

    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…

  20. Hinged Dissection of Polypolyhedra Erik D. Demaine 1# , Martin L. Demaine 1 ,

    E-print Network

    Demaine, Erik

    a general family of 3D hinged dissections for polypolyhedra, i.e., connected 3D solids formed by joining for reflectionally symmetric faces.) Each hinged dissection consists of a linear number of solid polyhedral pieces from 2D [7]. Along the way, we present hinged dissections for polyplatonics (where P is a platonic

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

    ERIC Educational Resources Information Center

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

    2010-01-01

    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…

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

    ERIC Educational Resources Information Center

    De Villiers, Rian; Monk, Martin

    2005-01-01

    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…

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

    ERIC Educational Resources Information Center

    Carlin, Joel L.

    2010-01-01

    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…

  4. A Computational Algorithm for Creating Geometric Dissection Puzzles Yahan Zhou Rui Wang

    E-print Network

    Massachusetts at Amherst, University of

    polygons, the challenge is to find a solution with as few pieces as possible. In this paper, we present show 2D dissections ­ the first is a 4- piece dissection, and the second is a 5-piece dissection of a rectan- gle with a rasterized octagon. The bottom two rows show 3D dissec- tions ­ the first is a 6-piece

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

    ERIC Educational Resources Information Center

    Fancovicova, Jana; Prokop, Pavol; Leskova, Andrea

    2013-01-01

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

  6. Dissecting eukaryotic translation and its control by ribosome density mapping

    E-print Network

    Herschlag, Dan

    Dissecting eukaryotic translation and its control by ribosome density mapping Yoav Arava, F. Edward of these steps determine both the number and position of ribosomes along the mRNA, but tra- ditional velocity sedimentation assays for the trans- lational status of mRNA determine only the number of bound ribosomes. We

  7. Gastric Wall Dissection as a Complication of Percutaneous Gastrostomy

    SciTech Connect

    Reimer, Wolfgang; Farres, Maria Teresa; Lammer, Johannes

    1996-04-15

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

  8. Using a Dissecting Microscope in Teaching Introductory Chemistry.

    ERIC Educational Resources Information Center

    Winokur, Robert; Monroe, Manus

    1985-01-01

    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…

  9. A sinister cause of anterograde amnesia: painless aortic dissection.

    PubMed

    April, Michael D; Fossum, Kurt; Hounshell, Charles; Stolper, Katherine; Spear, Leigh; Semelrath, Kevin

    2015-07-01

    Aortic dissection is a frequently devastating diagnosis classically associated with severe chest pain.We present a case of painless aortic dissection with anterograde amnesia. An 84-year-old man was brought to the emergency department by ambulance, when his wife noted that he developed acute onset complete loss of short-term memory. Medical history was notable for a 4.5-cm fusiform thoracic aortic root aneurysm. On arrival,he denied pain or syncope.On examination, he was mildly hypotensive(110/59 mm Hg); and there were no murmurs, pulse deficits, or focal neurologic deficits. During his stay, he developed left flank pain. Chest radiography demonstrated subtle mediastinal widening and obscuration of the aortic knob compared with previous films. Computed tomography revealed an extensive intimal flap consistent with an aortic dissection involving the sinus of Valsalva and left renal artery. The patient subsequently developed acute onset chest pain after which he became unresponsive. Echocardiography demonstrated tamponade physiology.The family decided to transition to comfort care measures, and the patient died soon after.We identified 7 other cases in the literature of aortic dissection cases with presentations consistent with transient global amnesia,5 of which without neurologic deficits and 3 of which without pain. This case highlights the imperative of a thorough history and high index of suspicion for this catastrophic diagnosis in patients with transient global amnesia who otherwise might be expected to have an excellent prognosis and little need for diagnostic work-up. PMID:25649752

  10. Exploring Dissections of Rectangles into Right-Angled Triangles

    ERIC Educational Resources Information Center

    Griffiths, Martin

    2013-01-01

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

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

    ERIC Educational Resources Information Center

    Cahill, Kevin C.; Ettarh, Raj R.

    2008-01-01

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

  12. Three cases of cervicocephalic artery dissection in an amusement park.

    PubMed

    Kurita, Naohide; Ueno, Yuji; Watanabe, Masao; Miyamoto, Nobukazu; Shimura, Hideki; Nonaka, Senshu; Tsutsumi, Satoshi; Yasumoto, Yukimasa; Hattori, Nobutaka; Urabe, Takao

    2014-01-01

    About 20 cases of cerebrovascular accidents in amusement parks have been documented. However, only a few cases of amusement park stroke (APS) after roller coaster rides have been reported. Here, we present triggers of stroke, clinical characteristics, and the angiographic appearance of 3 consecutive patients of APS. Their clinical characteristics included young age, absence of atherosclerotic risk factors, and severe injuries. Serial changes in angiographic appearance led to the diagnosis of cervicocephalic artery dissection (CAD). Patients A and B were diagnosed with isolated middle cerebral artery (MCA) dissection, and patient C was diagnosed with internal carotid artery dissection involving MCA dissection. Running excitedly toward an attraction in patient A, a go-kart ride in patient B, and riding in an enhanced motion vehicle in patient C were considered as the likely triggers for APS. We had specific cases with APS associated with CAD, which can occur under diverse contexts other than roller coaster rides at amusement parks. Our findings suggest that the variable directions of the high gravitational forces induced by vehicle riding or running excitedly might injure the MCA or internal carotid artery, and thereby cause CAD in the amusement park. PMID:25263648

  13. MBE Supplementary Material Dissecting Linkage Disequilibrium in African American

    E-print Network

    Xu, Shuhua

    S 1 MBE Supplementary Material Dissecting Linkage Disequilibrium in African American: Roles the data and hence was chosen for further analyses. Under the assumption that African and European were either the African cluster or the European cluster. The natural logarithms of the probability ratio (Ln

  14. Hinged Dissection of Polypolyhedra Erik D. Demaine # Martin L. Demaine #

    E-print Network

    Demaine, Erik

    that lies on the face (either interior to the face or on its boundary). For platonic solids, these hinges. Souvaine # 1 Introduction. A dissection of two figures (solid 2D or 3D shapes, e.g., polygons or polyhedra with labeled faces, a polypoly­ hedron of type P is an interior­connected non­self­ intersecting solid formed

  15. Prototyping Dissection Puzzles with Layered Manufacturing Carlo H. Squin

    E-print Network

    O'Brien, James F.

    typically show them some Hamiltonian dissections of the Platonic solids (Fig.1). In these Hamiltonian used as class exercises in a graduate course on computer-aided solid modeling: Helicoidal sectioning concerned with modeling of solid shapes (CS285). Before we give the students their own assignments, we

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

    ERIC Educational Resources Information Center

    Lee, Yeung Chung

    2004-01-01

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

  17. Refractory dissecting Cellulitis of the Scalp Successfully controlled with Adalimumab.

    PubMed

    Martin-García, Rafael F; Rullán, Jennifer M

    2015-06-01

    Dissecting cellulitis of the scalp (DCS) is an uncommon inflammatory disease that often results in scarring alopecia. Numerous therapies have either proved ineffective or only temporarily effective in the management of this condition. Recent reports show adequate responses to tumor necrosis factor (TNF) inhibitors in cases of DCS. We report a case of severe recalcitrant DCS successfully treated with adalimumab. PMID:26061062

  18. 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.01.023 SUMMARY The RB protein family (RB, p107, and p130) has overlapping and compensatory functions in cell-cycle control. However, cancer-associated mutations are almost exclusively found in RB, implying that RB has

  19. Dissection and immunostaining of imaginal discs from Drosophila melanogaster.

    PubMed

    Spratford, Carrie M; Kumar, Justin P

    2014-01-01

    A significant portion of post-embryonic development in the fruit fly, Drosophila melanogaster, takes place within a set of sac-like structures called imaginal discs. These discs give rise to a high percentage of adult structures that are found within the adult fly. Here we describe a protocol that has been optimized to recover these discs and prepare them for analysis with antibodies, transcriptional reporters and protein traps. This procedure is best suited for thin tissues like imaginal discs, but can be easily modified for use with thicker tissues such as the larval brain and adult ovary. The written protocol and accompanying video will guide the reader/viewer through the dissection of third instar larvae, fixation of tissue, and treatment of imaginal discs with antibodies. The protocol can be used to dissect imaginal discs from younger first and second instar larvae as well. The advantage of this protocol is that it is relatively short and it has been optimized for the high quality preservation of the dissected tissue. Another advantage is that the fixation procedure that is employed works well with the overwhelming number of antibodies that recognize Drosophila proteins. In our experience, there is a very small number of sensitive antibodies that do not work well with this procedure. In these situations, the remedy appears to be to use an alternate fixation cocktail while continuing to follow the guidelines that we have set forth for the dissection steps and antibody incubations. PMID:25285379

  20. Dissecting Darknets: Measurement and Performance Analysis Xiaowen Chu, Xiaowei Chen

    E-print Network

    Chu, Xiaowen

    Dissecting Darknets: Measurement and Performance Analysis Xiaowen Chu, Xiaowei Chen Hong Kong-rider problem, Darknets are becoming increasingly popular, which use Sharing Ratio Enforcement to increase their efficiency. We crawled and traced 17 Darknets from September 2009 to Feb 2011, and obtained data sets about

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

    ERIC Educational Resources Information Center

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

    2009-01-01

    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…

  2. The Influence of Emotion on Students' Performance in Dissection Exercises

    ERIC Educational Resources Information Center

    Holstermann, Nina; Grube, Dietmar; Bogeholz, Susanne

    2009-01-01

    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'…

  3. General Dissection of Female Ant Reproductive System and Brain

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dissection of the reproductive system of ant workers and queens can be useful for answering many questions. Observations of ovarian status in both female castes can be used to identify relationships between other factors and the ovaries, determine whether an individual has laid eggs, and, with more ...

  4. Standard methods for Apis mellifera anatomy and dissection

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  5. Fatal dissecting aneurysm of the aorta in a diver.

    PubMed

    James, R; Hayman, J A

    1986-07-01

    A 20-yr-old trained sports diver developed severe chest pain shortly after decompressing from a 40 m repetitive freshwater sinkhole dive, and died 6 h later. An autopsy examination showed a dissecting aneurysm of the aorta with rupture into the left pleural cavity. The relationship between the fatal event and the diving is discussed. PMID:3785985

  6. INVESTIGATION Genetic Dissection of a Major Anthocyanin QTL

    E-print Network

    Bradshaw, Toby

    INVESTIGATION Genetic Dissection of a Major Anthocyanin QTL Contributing to Pollinator in sympatry. Flower color differences resulting from both carotenoid and anthocyanin pigments contribute on anthocyanin concentration and that cis-regulatory change rather than coding DNA mutations cause the allelic

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

    E-print Network

    Govindjee

    11CHAPTER Dissecting Oxygenic Photosynthesis: The Evolution of the "Z"-Scheme for Thylakoid provide here a summary and the evolution of the so-called "Z" scheme for the electron flow from water that this scheme has been proven to be wrong. For the description and historical evaluation of this early

  8. INVESTIGATION Genetic Dissection of a Key Reproductive Barrier

    E-print Network

    Payseur, Bret

    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

  9. Advanced endovascular techniques for thoracic and abdominal aortic dissections.

    PubMed

    Kölbel, T; Diener, H; Larena-Avellaneda, A; Debus, S

    2013-02-01

    Endovascular treatment of aortic dissection is still in its infancy and consists usually of implantation of thoracic tubular stent-grafts to cover the proximal entry tear and redirect flow into the true lumen. Large registries comparing endovascular treatment by thoracic endovascular aortic repair (TEVAR) with open surgery for aortic dissection of the descending aorta have demonstrated a clear benefit for endovascular treatment with lower mortality and morbidity rates turning TEVAR into the standard treatment for complicated type B aortic dissection. With this momentum of success endovascular techniques continue to challenge open surgical techniques also in the aortic arch and the ascending aorta. TEVAR for aortic dissection has become more complex requiring an individualized treatment strategy as endovascular techniques have developed with the advent of new devices and increased experience of the operators. In many cases straight implantation of a thoracic tubular stent-graft is sufficient. But as rerouting of the blood flow can also change perfusion of vital side-branches the endovascular operator needs to have a large armamentarium of techniques and adjunctive procedures in order to sufficiently address the individual patient morphology. This chapter reviews a variety of endovascular techniques including access techniques, proximal sealing, the Petticoat-technique, false lumen deployment, fenestration techniques, branch vessel stenting and false lumen obstruction by various techniques. PMID:23443592

  10. Dissection of a Novel Autocrine Signaling Pathway via Quantitative Secretome and Interactome Mapping

    E-print Network

    Trinkle-Mulcahy, Laura

    ) is a previously unknown player in this regulatory axis, promoting an increase in proliferation of HaCaT human dermatitis, psoriasis, and cancer.1 Development begins with commitment of a single layer of multipotent

  11. 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...

  12. 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...

  13. Activating Mutations in PIK3CA Lead to Widespread Modulation of the Tyrosine Phosphoproteome.

    PubMed

    Zahari, Muhammad Saddiq; Wu, Xinyan; Blair, Brian G; Pinto, Sneha M; Nirujogi, Raja S; Jelinek, Christine A; Malhotra, Radhika; Kim, Min-Sik; Park, Ben Ho; Pandey, Akhilesh

    2015-09-01

    The human oncogene PIK3CA is frequently mutated in human cancers. Two hotspot mutations in PIK3CA, E545K and H1047R, have been shown to regulate widespread signaling events downstream of AKT, leading to increased cell proliferation, growth, survival, and motility. We used quantitative mass spectrometry to profile the global phosphotyrosine proteome of isogenic knock-in cell lines containing these activating mutations, where we identified 824 unique phosphopeptides. Although it is well understood that these mutations result in hyperactivation of the serine/threonine kinase AKT, we found a surprisingly widespread modulation of tyrosine phosphorylation levels of proteins in the mutant cells. In the tyrosine kinome alone, 29 tyrosine kinases were altered in their phosphorylation status. Many of the regulated phosphosites that we identified were located in the kinase domain or the canonical activation sites, indicating that these kinases and their downstream signaling pathways were activated. Our study demonstrates that there is frequent and unexpected cross-talk that occurs between tyrosine signaling pathways and serine/threonine signaling pathways activated by the canonical PI3K-AKT axis. PMID:26267517

  14. Activating Mutations in PIK3CA Lead to Widespread Modulation of the Tyrosine Phosphoproteome

    PubMed Central

    Blair, Brian G.; Pinto, Sneha M.; Nirujogi, Raja S.; Jelinek, Christine A.; Malhotra, Radhika; Kim, Min-Sik; Park, Ben Ho; Pandey, Akhilesh

    2015-01-01

    The human oncogene PIK3CA is frequently mutated in human cancers. Two hotspot mutations in PIK3CA, E545K and H1047R, have been shown to regulate widespread signaling events downstream of AKT, leading to increased cell proliferation, growth, survival, and motility. We used quantitative mass spectrometry to profile the global phosphotyrosine proteome of isogenic knock-in cell lines containing these activating mutations, where we identified 824 unique phosphopeptides. Although it is well understood that these mutations result in hyperactivation of the serine/threonine kinase AKT, we found a surprisingly widespread modulation of tyrosine phosphorylation levels of proteins in the mutant cells. In the tyrosine kinome alone, 29 tyrosine kinases were altered in their phosphorylation status. Many of the regulated phosphosites that we identified were located in the kinase domain or the canonical activation sites, indicating that these kinases and their downstream signaling pathways were activated. Our study demonstrates that there is frequent and unexpected cross-talk that occurs between tyrosine signaling pathways and serine/threonine signaling pathways activated by the canonical PI3K-AKT axis. PMID:26267517

  15. The Institute of Surgery and Innovation Trunk Flap Dissection Course.

    PubMed

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

    2015-11-01

    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

  16. Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding

    SciTech Connect

    Lipfert, Jan; Sim, Adelene Y.L.; Herschlag, Daniel; Doniach, Sebastian

    2010-09-17

    Riboswitches are gene-regulating RNAs that are usually found in the 5{prime}-untranslated regions of messenger RNA. As the sugar-phosphate backbone of RNA is highly negatively charged, the folding and ligand-binding interactions of riboswitches are strongly dependent on the presence of cations. Using small angle X-ray scattering (SAXS) and hydroxyl radical footprinting, we examined the cation dependence of the different folding stages of the glycine-binding riboswitch from Vibrio cholerae. We found that the partial folding of the tandem aptamer of this riboswitch in the absence of glycine is supported by all tested mono- and divalent ions, suggesting that this transition is mediated by nonspecific electrostatic screening. Poisson-Boltzmann calculations using SAXS-derived low-resolution structural models allowed us to perform an energetic dissection of this process. The results showed that a model with a constant favorable contribution to folding that is opposed by an unfavorable electrostatic term that varies with ion concentration and valency provides a reasonable quantitative description of the observed folding behavior. Glycine binding, on the other hand, requires specific divalent ions binding based on the observation that Mg{sup 2+}, Ca{sup 2+}, and Mn{sup 2+} facilitated glycine binding, whereas other divalent cations did not. The results provide a case study of how ion-dependent electrostatic relaxation, specific ion binding, and ligand binding can be coupled to shape the energetic landscape of a riboswitch and can begin to be quantitatively dissected.

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

    PubMed Central

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

    2011-01-01

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

  18. Automated Quantitative Phosphopeptide Enrichment using Titania-packed Capillary Columns and Its Application to Human Tissues for Label-Free Phosphoproteomics

    E-print Network

    Richardson, David

    . For this reason, there has been a rapid increase in the used of TiO2 materials to enrich for phosphorylated species. o Our laboratory previously developed a enrichment protocol using TiO2 particles in a spin column, 83( 10), 3758-3764. Evaluation of TiO2 materials and Capillary Column Enrichment Application

  19. Bare Stent Implantation in Iatrogenic Dissecting Pseudoaneurysm of the Superior Mesenteric Artery

    SciTech Connect

    Kutlu, Ramazan Ara, Cengiz; Sarac, Kaya

    2007-02-15

    Iatrogenic arterial dissection leading to the development of dissecting pseudoaneurysms of the superior mesenteric artery (SMA) is a rare complication of angiography. Surgical and endovascular treatment options exist for this important condition. We report a case of bare stent implantation in dissecting pseudoaneurysm of the SMA that developed after angiography in a patient with acute mesenteric ischemia. Although it is rarely published, iatrogenic arterial dissection causing pseudoaneurysm can occur after diagnostic and interventional angiography. Bare stent implantation in dissecting pseudoaneurysm of the SMA could be an advantageous endovascular treatment option in selected cases due its to potential preservation of important side branches of the SMA.

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

    NASA Astrophysics Data System (ADS)

    Allspaw, Kathleen M.

    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.

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

    NASA Astrophysics Data System (ADS)

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

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

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

    ERIC Educational Resources Information Center

    Kotze, Sanet Henriet; Mole, Calvin Gerald

    2013-01-01

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

  3. Comparative Phosphoproteomics Reveals the Role of AmpC ?-lactamase Phosphorylation in the Clinical Imipenem-resistant Strain Acinetobacter baumannii SK17.

    PubMed

    Lai, Juo-Hsin; Yang, Jhih-Tian; Chern, Jeffy; Chen, Te-Li; Wu, Wan-Ling; Liao, Jiahn-Haur; Tsai, Shih-Feng; Liang, Suh-Yuen; Chou, Chi-Chi; Wu, Shih-Hsiung

    2016-01-01

    Nosocomial infectious outbreaks caused by multidrug-resistant Acinetobacter baumannii have emerged as a serious threat to human health. Phosphoproteomics of pathogenic bacteria has been used to identify the mechanisms of bacterial virulence and antimicrobial resistance. In this study, we used a shotgun strategy combined with high-accuracy mass spectrometry to analyze the phosphoproteomics of the imipenem-susceptible strain SK17-S and -resistant strain SK17-R. We identified 410 phosphosites on 248 unique phosphoproteins in SK17-S and 285 phosphosites on 211 unique phosphoproteins in SK17-R. The distributions of the Ser/Thr/Tyr/Asp/His phosphosites in SK17-S and SK17-R were 47.0%/27.6%/12.4%/8.0%/4.9% versus 41.4%/29.5%/17.5%/6.7%/4.9%, respectively. The Ser-90 phosphosite, located on the catalytic motif S(88)VS(90)K of the AmpC ?-lactamase, was first identified in SK17-S. Based on site-directed mutagenesis, the nonphosphorylatable mutant S90A was found to be more resistant to imipenem, whereas the phosphorylation-simulated mutant S90D was sensitive to imipenem. Additionally, the S90A mutant protein exhibited higher ?-lactamase activity and conferred greater bacterial protection against imipenem in SK17-S compared with the wild-type. In sum, our results revealed that in A. baumannii, Ser-90 phosphorylation of AmpC negatively regulates both ?-lactamase activity and the ability to counteract the antibiotic effects of imipenem. These findings highlight the impact of phosphorylation-mediated regulation in antibiotic-resistant bacteria on future drug design and new therapies. PMID:26499836

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

    PubMed

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

    2014-03-01

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

  5. [Neonatal cervical artery dissection secondary to birth trauma].

    PubMed

    Hamida, N; Hakim, A; Fourati, H; Ben Thabet, A; Walha, L; Bouraoui, A; Mnif, Z; Gargouri, A

    2014-02-01

    Cervical artery dissection is rare in the neonatal period and is most often caused by birth injury during dystocic labor. The severity of this pathology is due to the possibility of serious neurological complications. We report a case of a male newborn who was born vaginally after shoulder dystocia. The extraction was difficult, resulting in a fracture of the right humerus. On the second day of life, the child presented generalized clonic convulsions. Computed tomography of the brain showed an ischemic stroke in the territory of the right middle cerebral artery, the territory of the right posterior cerebral artery, and the right lenticulostriate and capsular regions. Doppler ultrasonography and magnetic resonance angiography showed bilateral carotid artery thrombosis and dissection at the left common carotid artery and its two branches and the right vertebral artery. We discuss the mechanisms of this pathology and we emphasize preventive measures. PMID:24290182

  6. Management of Acute Aortic Syndrome and Chronic Aortic Dissection

    SciTech Connect

    Nordon, Ian M. Hinchliffe, Robert J.; Loftus, Ian M.; Morgan, Robert A.; Thompson, Matt M.

    2011-10-15

    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.

  7. Femtosecond laser dissection in C. elegans neural circuits

    NASA Astrophysics Data System (ADS)

    Samuel, Aravinthan D. T.; Chung, Samuel H.; Clark, Damon A.; Gabel, Christopher V.; Chang, Chieh; Murthy, Venkatesh; Mazur, Eric

    2006-02-01

    The nematode C. elegans, a millimeter-long roundworm, is a well-established model organism for studies of neural development and behavior, however physiological methods to manipulate and monitor the activity of its neural network have lagged behind the development of powerful methods in genetics and molecular biology. The small size and transparency of C. elegans make the worm an ideal test-bed for the development of physiological methods derived from optics and microscopy. We present the development and application of a new physiological tool: femtosecond laser dissection, which allows us to selectively ablate segments of individual neural fibers within live C. elegans. Femtosecond laser dissection provides a scalpel with submicrometer resolution, and we discuss its application in studies of neural growth, regenerative growth, and the neural basis of behavior.

  8. Acute aortic dissection: typical and atypical imaging features.

    PubMed

    Fisher, E R; Stern, E J; Godwin, J D; Otto, C M; Johnson, J A

    1994-11-01

    Acute aortic dissection (AAD) is the most common emergency affecting the aorta. Noninvasive imaging allows prompt and reliable diagnosis of AAD and has largely supplanted aortography. However, atypical imaging features and diagnostic pitfalls can delay lifesaving therapy. An intimal flap is the characteristic feature of AAD. If there is flow within both lumina, typical imaging features are probably present. If the false lumen is thrombosed or there is no intimal tear to permit flow through the false lumen, a distinct intimal flap may not be present. Secondary signs of AAD include an intramural or periaortic acute thrombus, which manifests as a high-attenuation cuff or crescent on unenhanced computed tomographic scans. Other conditions that can reduce the conspicuity of the intimal flap include atypical configurations of the flap, such as seen with short dissections or with multiple false channels, in which case the flaps are complex. Finally, aortic anomalies may cause confusion. PMID:7855340

  9. A sneeze: an unusual trigger for aortic dissection

    PubMed Central

    Upadhyaya, Subramanya G N; Large, A

    2013-01-01

    We describe a rare case of type B thoracic aortic dissection resulting from a forceful sneeze in a 57-year-old man. The presenting clinical features were not typical and consisted of pleuritic chest pain and breathlessness following a forceful sneeze. There was no haemodynamic compromise. The diagnosis was made incidentally when he underwent a CT pulmonary angiography as part of pulmonary embolism work-up. PMID:24302662

  10. Saphenous Vein Sparing Superficial Inguinal Dissection in Lower Extremity Melanoma

    PubMed Central

    Öztürk, Muhammed Be?ir; Akan, Arzu; Özkaya, Özay; Egemen, Onur; Örero?lu, Ali R?za; Akan, Mithat

    2014-01-01

    Aim. The classic inguinal lymph node dissection is the main step for the regional control of the lower extremity melanoma, but this surgical procedure is associated with significant postoperative morbidity. The permanent lymphedema is the most devastating long-term complication leading to a significant decrease in the patient's quality of life. In this study we present our experience with modified, saphenous vein sparing, inguinal lymph node dissections for patients with melanoma of the lower extremity. Methods. Twenty one patients (10 women, 11 men) who underwent saphenous vein sparing superficial inguinal lymph node dissection for the melanoma of lower extremity were included in this study. The effects of saphenous vein sparing on postoperative complications were evaluated. Results. We have observed the decreased rate of long-term lymphedema in patients undergoing inguinal lymphadenectomy for the lower extremity melanoma. Conclusion. The inguinal lymphadenectomy with saphenous vein preservation in lower extremity melanoma patients seems to be an oncologically safe procedure and it may offer reduced long-term morbidity. PMID:25126426

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

    ERIC Educational Resources Information Center

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

    2014-01-01

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

  12. 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

    Bernstein, Penny L.

    2000-01-01

    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)

  13. Human cadaveric dissection: a historical account from ancient Greece to the modern era

    PubMed Central

    2015-01-01

    The review article attempts to focus on the practice of human cadaveric dissection during its inception in ancient Greece in 3rd century BC, revival in medieval Italy at the beginning of 14th century and subsequent evolution in Europe and the United States of America over the centuries. The article highlights on the gradual change in attitude of religious authorities towards human dissection, the shift in the practice of human dissection being performed by barber surgeons to the anatomist himself dissecting the human body and the enactment of prominent legislations which proved to be crucial milestones during the course of the history of human cadaveric dissection. It particularly emphasizes on the different means of procuring human bodies which changed over the centuries in accordance with the increasing demand due to the rise in popularity of human dissection as a tool for teaching anatomy. Finally, it documents the rise of body donation programs as the source of human cadavers for anatomical dissection from the second half of the 20th century. Presently innovative measures are being introduced within the body donation programs by medical schools across the world to sensitize medical students such that they maintain a respectful, compassionate and empathetic attitude towards the human cadaver while dissecting the same. Human dissection is indispensable for a sound knowledge in anatomy which can ensure safe as well as efficient clinical practice and the human dissection lab could possibly be the ideal place to cultivate humanistic qualities among future physicians in the 21st century. PMID:26417475

  14. Human cadaveric dissection: a historical account from ancient Greece to the modern era.

    PubMed

    Ghosh, Sanjib Kumar

    2015-09-01

    The review article attempts to focus on the practice of human cadaveric dissection during its inception in ancient Greece in 3rd century BC, revival in medieval Italy at the beginning of 14th century and subsequent evolution in Europe and the United States of America over the centuries. The article highlights on the gradual change in attitude of religious authorities towards human dissection, the shift in the practice of human dissection being performed by barber surgeons to the anatomist himself dissecting the human body and the enactment of prominent legislations which proved to be crucial milestones during the course of the history of human cadaveric dissection. It particularly emphasizes on the different means of procuring human bodies which changed over the centuries in accordance with the increasing demand due to the rise in popularity of human dissection as a tool for teaching anatomy. Finally, it documents the rise of body donation programs as the source of human cadavers for anatomical dissection from the second half of the 20th century. Presently innovative measures are being introduced within the body donation programs by medical schools across the world to sensitize medical students such that they maintain a respectful, compassionate and empathetic attitude towards the human cadaver while dissecting the same. Human dissection is indispensable for a sound knowledge in anatomy which can ensure safe as well as efficient clinical practice and the human dissection lab could possibly be the ideal place to cultivate humanistic qualities among future physicians in the 21st century. PMID:26417475

  15. Dissecting repulsion linkage in the dwarfing gene Dw3 region for sorghum plant height provides insights into heterosis.

    PubMed

    Li, Xin; Li, Xianran; Fridman, Eyal; Tesso, Tesfaye T; Yu, Jianming

    2015-09-22

    Heterosis is a main contributor to yield increase in many crop species. Different mechanisms have been proposed for heterosis: dominance, overdominance, epistasis, epigenetics, and protein metabolite changes. However, only limited examples of molecular dissection and validation of these mechanisms are available. Here, we present an example of discovery and validation of heterosis generated by a combination of repulsion linkage and dominance. Using a recombinant inbred line population, a separate quantitative trait locus (QTL) for plant height (qHT7.1) was identified near the genomic region harboring the known auxin transporter Dw3 gene. With two loci having repulsion linkage between two inbreds, heterosis in the hybrid can appear as a single locus with an overdominance mode of inheritance (i.e., pseudo-overdominance). Individually, alleles conferring taller plant height exhibited complete dominance over alleles conferring shorter height. Detailed analyses of different height components demonstrated that qHT7.1 affects both the upper and lower parts of the plant, whereas Dw3 affects only the part below the flag leaf. Computer simulations show that repulsion linkage could influence QTL detection and estimation of effect in segregating populations. Guided by findings in linkage mapping, a genome-wide association study of plant height with a sorghum diversity panel pinpointed genomic regions underlying the trait variation, including Dw1, Dw2, Dw3, Dw4, and qHT7.1. Multilocus mixed model analysis confirmed the advantage of complex trait dissection using an integrated approach. Besides identifying a specific genetic example of heterosis, our research indicated that integrated molecular dissection of complex traits in different population types can enable plant breeders to fine tune the breeding process for crop production. PMID:26351684

  16. Spontaneous Isolated Celiac Artery and Superior Mesenteric Artery Dissections: A Rare Case

    PubMed Central

    Aydin, Sonay; Ergun, Elif; Fatihoglu, Erdem; Durhan, Gamze; Kosar, Pinar Nercis

    2015-01-01

    Summary Background Arterial dissection is defined as the cleavage of the arterial wall by an intramural hematoma. Reports of dissection of the celiac and/or superior mesenteric artery are rare; as far as we know, only 24 cases of spontaneous isolated celiac trunk dissection, and 71 cases of spontaneous isolated superior mesenteric artery dissection have been reported. Case Report The case presents a 48-year-old male with a sudden-onset epigastric pain. A Computed Tomography Angiography of the thoracoabdominal aorta was applied and dissections of both the celiac artery and SMA were determined. A conservative therapeutic approach was preferred and the patient was discharged with anticoagulant and antihypertensive therapy. Conclusions Although rare, spontaneous isolated celiac artery and superior mesenteric artery dissections must be kept in mind in the differential diagnosis of the epigastric pain in the emergency room. Contrast-enhanced Computed Tomography Angiography examination is the method of choice in the diagnosis. PMID:26543511

  17. Dissection of the ascending thoracic aorta as a complication of percutaneous coronary intervention

    PubMed Central

    Uyan, Cihangir; Arinc, Huseyin; Gunduz, Huseyin; Akdemir, Ramazan

    2008-01-01

    Acute aortic dissection is a medical emergency with high morbidity and mortality requiring emergent diagnosis and therapy. A 79-year-old woman with acute aortic dissection due to percutaneous coronary intervention was presented. Aortic dissection is an uncommon but potentially lethal illness that can present in an occult manner making the initial diagnosis difficult. Aggressive medical management is mandatory, as well as urgent diagnostic testing and cardiothoracic consultation. PMID:18629358

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

    SciTech Connect

    Papadopoulos, Dimitris P. Moyssakis, Ioannis; Perakis, Alexandros; Athanasiou, Andreas; Anagnostopoulou, Sophia; Benos, Ioannis; Votteas, Vassilios E.

    2004-09-15

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

  19. Pregnancy after a previous gestation complicated by an acute aortic dissection.

    PubMed

    Rodrigues, Cátia; Pinto, Luísa; Clode, Nuno; Almeida, Ana G; Cardoso, Conceiçăo; Graça, Luís M

    2009-10-01

    Acute aortic dissection is a rare life-threatening event. No further pregnancies in women who had a previous acute aortic dissection have been reported. We present the case of a chronic hypertensive woman, who in her previous gestation was submitted to an acute aortic dissection repair at 28 weeks of gestation with cesarean delivery at the same operative procedure. The index pregnancy was uneventful. An elective cesarean was performed at 33 weeks' gestation. Aneurysm expansion, rupture or redissections are potential complications of operated aortic dissection. Normal blood pressure values and close cardiologic and obstetrical follow-up are essential to obtain a favourable outcome. PMID:19488938

  20. Stent implantation for treatment of symptomatic spontaneous cervical internal carotid artery dissecting aneurysm. A case report.

    PubMed

    Briganti, F; Tortora, F; Volpe, A; Elefante, A; De Notaris, M; Panagiotopoulos, K

    2005-10-01

    Cervical internal carotid dissections are rare. Approximately one third of the cases are associated with pseudoaneurysm. The first-choice management of cervical carotid dissecting aneurysms consists in anticoagulation or antiplatelet therapy. Surgery is typically indicated in cases of failure of conservative therapy with recurrent cerebral ischemic attacks. In recent years, stent implantation has been also employed for the management of patients with carotid dissecting aneurysms whose neurological conditions were refractory to medical treatment. In the present case we describe the treatment of a patient with a carotid dissecting aneurysm, by means of endovascular stent application and provide angiographic control 24 months after the intervention. PMID:16320195

  1. Preauricular transparotid approach to mandibular condylar fractures without dissecting facial nerves.

    PubMed

    Yabe, Tetsuji; Tsuda, Tomoyuki; Hirose, Shunsuke; Ozawa, Toshiyuki

    2013-07-01

    Preauricular transparotid approach without dissecting the facial nerve was used for surgical treatment of 15 condylar fractures in 14 patients. The parotid fascia was opened just above the fracture site, and by dissecting the parotid gland and masseter muscle, the fracture was directly exposed. The facial nerve itself was not dissected expressly. All fractures could be reduced accurately and fixed firmly with miniplates. A direct approach just above the fracture site provided good vision of the fracture, avoiding facial nerve palsy caused by strong retraction. Moreover, by not dissecting the facial nerve, the operation time was shortened. This approach was useful for surgical treatment of both condylar neck and subcondylar fractures. PMID:23851809

  2. Cervical Artery Dissection: A Review of the Epidemiology, Pathophysiology, Treatment, and Outcome

    PubMed Central

    Blum, Christina A.; Yaghi, Shadi

    2015-01-01

    Context Cervical artery dissection (CAD) is a common cause of stroke in young adults. There is controversy over whether anticoagulation is superior to antiplatelet therapy in preventing stroke in patients with CAD, although meta-analyses to date have not shown any difference between the two treatments. Evidence acquisition We performed a PubMed search using each of the keywords: “Cervical artery dissection”, “Dissection”, “Carotid dissection”, and “Vertebral dissection” between January 1st, 1990 and July 1st 2015. We identified evidence-based peer-reviewed articles, including randomized trials, case series and reports, and retrospective reviews that encompass the epidemiology, clinical manifestations, pathophysiology, treatment, and outcome of cervical artery dissection. Results This paper highlights the mechanisms of cervical artery dissection and stroke in patients with dissection as well as the natural history and treatment. Conclusion Given the relatively rare incidence of this disease, multicenter studies with collaborative effort among stroke centers worldwide should be considered to enroll patients with cervical artery dissection in a randomized trial comparing the two treatments. PMID:26478890

  3. Application of blunt dissection in ESD of a gastric submucosal tumor.

    PubMed

    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

    2014-06-01

    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

  4. Application of blunt dissection in ESD of a gastric submucosal tumor

    PubMed Central

    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

    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

  5. Cell-type Specific Optogenetic Mice for Dissecting Neural Circuitry Function

    E-print Network

    Zhao, Shengli

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

  6. Revisiting the Timing of Action of the PAG Adaptor Using Quantitative Proteomics Analysis of Primary T Cells.

    PubMed

    Reginald, Kavita; Chaoui, Karima; Roncagalli, Romain; Beau, Mathilde; Goncalves Menoita, Marisa; Monsarrat, Bernard; Burlet-Schiltz, Odile; Malissen, Marie; Gonzalez de Peredo, Anne; Malissen, Bernard

    2015-12-01

    The protein tyrosine kinase LCK plays a key role in TCR signaling, and its activity is dynamically controlled by the tyrosine kinase C-terminal Src kinase (CSK) and the tyrosine phosphatase CD45. CSK is brought in contiguity to LCK via binding to a transmembrane adaptor known as phosphoprotein associated with glycosphingolipid-enriched microdomains (PAG). The lack of a blatant phenotype in PAG-deficient mice has impeded our understanding of the mechanisms through which PAG exerts its negative-regulatory role in TCR signaling. We used quantitative mass spectrometry and both thymocytes and CD4(+) T cells from mice in which a tag for affinity purification was knocked in the gene coding for PAG to determine the composition and dynamics of the multiprotein complexes that are found around PAG over 5 min of activation. Most of the high-confidence interactions that we observed were previously unknown. Using phosphoproteomic analysis, PAG showed low levels of tyrosine phosphorylation in resting primary mouse CD4(+) T cells; the levels of tyrosine phosphorylation increased and reached a maximum 2 min after stimulation. Analysis of the dynamics of association of the protein tyrosine phosphatase PTPN22 and lipid phosphatase SHIP-1 with PAG following T cell activation suggests that both cooperate with CSK to terminate T cell activation. Our findings provide a model of the role for PAG in mouse primary CD4(+) T cells that is consistent with recent phosphoproteomic studies of the Jurkat T cell line but difficult to reconcile with former biochemical studies indicating that PAG is constitutively phosphorylated in resting T cells and rapidly dephosphorylated once the TCR is engaged. PMID:26512138

  7. Theoretical and Experimental Dissection of DNA Loop-Mediated Repression

    NASA Astrophysics Data System (ADS)

    Boedicker, James Q.; Garcia, Hernan G.; Phillips, Rob

    2013-01-01

    Transcriptional networks across all domains of life feature a wide range of regulatory architectures. Theoretical models now make clear predictions about how key parameters describing those architectures modulate gene expression, and the ability to construct genetic circuits with tunable parameters enables precise tests of such models. We dissect gene regulation through DNA looping by tuning network parameters such as repressor copy number, DNA binding strengths, and loop length in both thermodynamic models and experiments. Our results help clarify the short-length mechanical properties of DNA.

  8. [Microbiological monitoring of embalmed cadavera during dissection courses (author's transl)].

    PubMed

    Wewalka, G; Lischka, M F; Krammer, E B; Stanek, G

    1979-01-01

    Microbiological monitoring of normal anatomical specimens was done in order to evaluate results which were obtained in a investigation of decay of embalmed cadavera. The process of decay was characterized by massive colonisation with enterobacteria and aerobic sporeformers. Under normal conditions mainly germs from skin and air are cultivated from surfaces of anatomical specimens, but only in small numbers. The number of germs is increased after periods of intensive preparative work. The results show that the main criterion for the microbiological quality of embalmed cadavera is resistency against external germs during course work. This is to be achieved by consequent preventive measures in the dissection laboratory. PMID:543566

  9. Dissecting inhibitory brain circuits with genetically-targeted technologies

    PubMed Central

    Murphey, Dona K.; Herman, Alexander M.; Arenkiel, Benjamin R.

    2014-01-01

    The evolution of genetically targeted tools has begun to allow us to dissect anatomically and functionally heterogeneous interneurons, and to probe circuit function from synapses to behavior. Over the last decade, these tools have been used widely to visualize neurons in a cell type-specific manner, and engage them to activate and inactivate with exquisite precision. In this process, we have expanded our understanding of interneuron diversity, their functional connectivity, and how selective inhibitory circuits contribute to behavior. Here we discuss the relative assets of genetically encoded fluorescent proteins (FPs), viral tracing methods, optogenetics, chemical genetics, and biosensors in the study of inhibitory interneurons and their respective circuits. PMID:25368555

  10. Endoscopic submucosal dissection (ESD) versus simplified/hybrid ESD.

    PubMed

    Toyonaga, Takashi; Man-I, Mariko; Morita, Yoshinori; Azuma, Takeshi

    2014-04-01

    The development of endoscopic submucosal dissection (ESD) has enabled en bloc resection of lesions regardless of size and shape. However, ESD of colorectal tumors is technically difficult. Early stage colorectal tumors can be removed by endoscopic mucosal resection (EMR) but larger tumors may require piecemeal resection. Therefore, ESD with snaring has been proposed for more reliable EMR and easier ESD. This is a good option to fill the gap between EMR and ESD, and a good step to the introduction of full ESD. PMID:24679231

  11. Herophilus and Erasistratus, pioneers of human anatomical dissection.

    PubMed

    Reverón, Rafael Romero

    2014-01-01

    Herophilus (c335 - c280 B.C.) was the founder of the school of anatomy of Alexandria, and was among the first physicians to conduct anatomical dissections in public. He made extraordinary anatomical discoveries and developed standards for measuring the flow of blood from the heart through the arteries. Erasistratus (c310- c250 B.C.) was a disciple and collaborator of Herophilus. He made important contributions in the study and teaching of human anatomy and carried out research at the Museum of Alexandria. PMID:25181783

  12. Genetic Dissection of Learning and Memory in Mice

    PubMed Central

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

    2004-01-01

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

  13. Characterization of residual stresses by WEDM-assisted dissectioning

    NASA Astrophysics Data System (ADS)

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

    2010-06-01

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

  14. Quantitative Analysis of Signaling Networks across Differentially Embedded Tumors Highlights Interpatient Heterogeneity in Human Glioblastoma

    PubMed Central

    2015-01-01

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

  15. Dissecting the complex molecular evolution and expression of polygalacturonase gene family in Brassica rapa ssp. chinensis.

    PubMed

    Liang, Ying; Yu, Youjian; Shen, Xiuping; Dong, Heng; Lyu, Meiling; Xu, Liai; Ma, Zhiming; Liu, Tingting; Cao, Jiashu

    2015-12-01

    Polygalacturonases (PGs) participate in pectin disassembly of cell wall and belong to one of the largest hydrolase families in plants. In this study, we identified 99 PG genes in Brassica rapa. Comprehensive analysis of phylogeny, gene structures, physico-chemical properties and coding sequence evolution demonstrated that plant PGs should be classified into seven divergent clades and each clade's members had specific sequence and structure characteristics, and/or were under specific selection pressures. Genomic distribution and retention rate analysis implied duplication events and biased retention contributed to PG family's expansion. Promoter divergence analysis using "shared motif method" revealed a significant correlation between regulatory and coding sequence evolution of PGs, and proved Clades A and E were of ancient origin. Quantitative real-time PCR analysis showed that expression patterns of PGs displayed group specificities in B. rapa. Particularly, nearly half of PG family members, especially those of Clades C, D and F, closely relates to reproductive development. Most duplicates showed similar expression profiles, suggesting dosage constraints accounted for preservation after duplication. Promoter-GUS assay further indicated PGs' extensive roles and possible redundancy during reproductive development. This work can provide a scientific classification of plant PGs, dissect the internal relationships between their evolution and expressions, and promote functional researches. PMID:26506823

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

    PubMed

    Kamphuis, Lars G; Lichtenzveig, Judith; Peng, Kefan; Guo, Su-Min; Klingler, John P; Siddique, Kadambot H M; Gao, Ling-Ling; Singh, Karam B

    2013-11-01

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

  17. An integrated bioinformatics analysis to dissect kinase dependency in triple negative breast cancer

    PubMed Central

    2015-01-01

    Background Triple-Negative Breast Cancer (TNBC) is an aggressive disease with a poor prognosis. Clinically, TNBC patients have limited treatment options besides chemotherapy. The goal of this study was to determine the kinase dependency in TNBC cell lines and to predict compounds that could inhibit these kinases using integrative bioinformatics analysis. Results We integrated publicly available gene expression data, high-throughput pharmacological profiling data, and quantitative in vitro kinase binding data to determine the kinase dependency in 12 TNBC cell lines. We employed Kinase Addiction Ranker (KAR), a novel bioinformatics approach, which integrated these data sources to dissect kinase dependency in TNBC cell lines. We then used the kinase dependency predicted by KAR for each TNBC cell line to query K-Map for compounds targeting these kinases. Wevalidated our predictions using published and new experimental data. Conclusions In summary, we implemented an integrative bioinformatics analysis that determines kinase dependency in TNBC. Our analysis revealed candidate kinases as potential targets in TNBC for further pharmacological and biological studies. PMID:26681397

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

    PubMed Central

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

    2013-01-01

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

  19. Towards a fast implementation of spectral nested dissection

    NASA Technical Reports Server (NTRS)

    Pothen, Alex; Simon, Horst D.; Wang, Lie; Barnard, Stephen T.

    1992-01-01

    We describe the spectral nested dissection (SND) algorithm, a new algorithm for computing orderings appropriate for parallel factorization of sparse, symmetric matrices. The algorithm makes use of spectral properties of the Laplacian matrix associated with the given matrix to compute separators. We evaluate the quality of the spectral orderings with respect to several measures: fill, elimination tree height, height and weight balances of elimination trees, and clique tree heights. We use some very large structural analysis problems as test cases and demonstrate on these real applications (such as the Space Shuttle Solid Rocket Booster) that spectral orderings compare quite favorably with commonly used orderings, outperforming them by a wide margin for some of these measures. The only disadvantage of SND is its relatively long execution time. We will present some recent efforts to improve the execution time using both a multilevel and a hybrid approach. We use SND in computing a multifrontal numerical factorization with the different orderings on an eight processor Cray Y-MP and show its effectiveness. We believe that spectral nested dissection is a major breakthrough in terms of generating efficient sparse orderings for parallel machines.

  20. Cadaveric Temporal Bone Dissection: Is It Obsolete Today?

    PubMed Central

    Naik, Sulabha M.; Naik, Mahendra S.; Bains, Nainjot Kaur

    2013-01-01

    Introduction?Traditionally, surgical training in otology, is imparted by dissecting harvested human cadaveric temporal bones. However, maintenance of a cadaveric temporal bone laboratory is expensive and carries risk of exposure to infection. In recent times, other modalities of training are gaining ground and are likely to eventually replace cadaveric temporal bone dissection altogether. Objectives?Other alternative methods of training are emerging. New technology like simulation and virtual reality as high-fidelity, safer alternatives, are making rapid strides as teaching tools. Other options are the use of animal temporal bones as teaching tools. The advantages of these are compared. Data Synthesis?None of these modalities can replicate the innumerable anatomical variations which are a characteristic feature of the human temporal bone. A novice surgeon not only needs exposure to surgical anatomy and it's variations but also needs to develop hand-eye coordination skills to gain expertise. Conclusion?Deliberate practice on human cadaveric temporal bones only, will confer both mastery in anatomy and surgical technique. The human cadaveric temporal bone is ideal simulator for training in otology. PMID:25992066

  1. How to establish endoscopic submucosal dissection in Western countries

    PubMed Central

    Oyama, Tsuneo; Yahagi, Naohisa; Ponchon, Thierry; Kiesslich, Tobias; Berr, Frieder

    2015-01-01

    Endoscopic submucosal dissection (ESD) has been invented in Japan to provide resection for cure of early cancer in the gastrointestinal tract. Professional level of ESD requires excellent staging of early neoplasias with image enhanced endoscopy (IEE) to make correct indications for ESD, and high skills in endoscopic electrosurgical dissection. In Japan, endodiagnostic and endosurgical excellence spread through personal tutoring of skilled endoscopists by the inventors and experts in IEE and ESD. To translocate this expertise to other continents must overcome two fundamental obstacles: (1) inadequate expectations as to the complexity of IEE and ESD; and (2) lack of suitable lesions and master-mentors for ESD trainees. Leading endoscopic mucosal resection-proficient endoscopists must pioneer themselves through the long learning curve to proficient ESD experts. Major referral centers for ESD must arise in Western countries on comparable professional level as in Japan. In the second stage, the upcoming Western experts must commit themselves to teach skilled endoscopists from other referral centers, in order to spread ESD in Western countries. Respect for patients with early gastrointestinal cancer asks for best efforts to learn endoscopic categorization of early neoplasias and skills for ESD based on sustained cooperation with the masters in Japan. The strategy is discussed here. PMID:26523097

  2. Virtual Temporal Bone Dissection System: Development and Testing

    PubMed Central

    Wiet, Gregory J.; Stredney, Don; Kerwin, Thomas; Hittle, Bradley; Fernandez, Soledad A.; Welling, D. Bradley

    2012-01-01

    Objectives/Hypothesis The objective of this project was to develop a virtual temporal bone dissection system that would provide an enhanced educational experience for the training of otologic surgeons. Study Design A randomized, controlled, multi-institutional single blinded validation study. Methods The project encompassed 4 areas of emphasis: structural data acquisition, integration of the system, dissemination of the system, and validation. Results Structural acquisition was performed on multiple imaging platforms. Integration achieved a cost effective system. Dissemination was achieved on different levels including casual interest, downloading of software, and full involvement in development and validation studies. A validation study was performed at 8 different training institutions across the country using a two arm, randomized trial where study subjects were randomized to a two-week practice session using either the virtual temporal bone or standard cadaveric temporal bones. Eighty subjects were enrolled and randomized to one of the two treatment arms, 65 completed the study. There was no difference between the two groups using a blinded rating tool to assess performance after training. Conclusions 1. A virtual temporal bone dissection system has been developed and compared to cadaveric temporal bones for practice using a multi-center trial. 2. There is no statistical difference seen between practice on the current simulator when compared to practice on human cadaveric temporal bones. 3. Further refinements in structural acquisition and interface design have been identified which can be implemented prior to full incorporation into training programs and use for objective skills assessment. PMID:22294268

  3. Dissecting neural differentiation regulatory networks through epigenetic footprinting

    PubMed Central

    Yaffe, Yakey; Donaghey, Julie; Pop, Ramona; Mallard, William; Issner, Robbyn; Gifford, Casey A.; Goren, Alon; Xing, Jeff; Gu, Hongcang; Cachiarelli, Davide; Tsankov, Alexander; Epstein, Chuck; Rinn, John R.; Mikkelsen, Tarjei S.; Kohlbacher, Oliver; Gnirke, Andreas; Bernstein, Bradley E.

    2014-01-01

    Human pluripotent stem cell derived models that accurately recapitulate neural development in vitro and allow for the generation of specific neuronal subtypes are of major interest to the stem cell and biomedical community. Notch signaling, particularly through the Notch effector HES5, is a major pathway critical for the onset and maintenance of neural progenitor cells (NPCs) in the embryonic and adult nervous system1-3. This can be exploited to isolate distinct populations of human embryonic stem (ES) cell derived NPCs4. Here, we report the transcriptional and epigenomic analysis of six consecutive stages derived from a HES5-GFP reporter ES cell line5 differentiated along the neural trajectory aimed at modeling key cell fate decisions including specification, expansion and patterning during the ontogeny of cortical neural stem and progenitor cells. In order to dissect the regulatory mechanisms that orchestrate the stage-specific differentiation process, we developed a computational framework to infer key regulators of each cell state transition based on the progressive remodeling of the epigenetic landscape and then validated these through a pooled shRNA screen. We were also able to refine our previous observations on epigenetic priming at transcription factor binding sites and show here that they are mediated by combinations of core and stage- specific factors. Taken together, we demonstrate the utility of our system and outline a general framework, not limited to the context of the neural lineage, to dissect regulatory circuits of differentiation. PMID:25533951

  4. How to establish endoscopic submucosal dissection in Western countries.

    PubMed

    Oyama, Tsuneo; Yahagi, Naohisa; Ponchon, Thierry; Kiesslich, Tobias; Berr, Frieder

    2015-10-28

    Endoscopic submucosal dissection (ESD) has been invented in Japan to provide resection for cure of early cancer in the gastrointestinal tract. Professional level of ESD requires excellent staging of early neoplasias with image enhanced endoscopy (IEE) to make correct indications for ESD, and high skills in endoscopic electrosurgical dissection. In Japan, endodiagnostic and endosurgical excellence spread through personal tutoring of skilled endoscopists by the inventors and experts in IEE and ESD. To translocate this expertise to other continents must overcome two fundamental obstacles: (1) inadequate expectations as to the complexity of IEE and ESD; and (2) lack of suitable lesions and master-mentors for ESD trainees. Leading endoscopic mucosal resection-proficient endoscopists must pioneer themselves through the long learning curve to proficient ESD experts. Major referral centers for ESD must arise in Western countries on comparable professional level as in Japan. In the second stage, the upcoming Western experts must commit themselves to teach skilled endoscopists from other referral centers, in order to spread ESD in Western countries. Respect for patients with early gastrointestinal cancer asks for best efforts to learn endoscopic categorization of early neoplasias and skills for ESD based on sustained cooperation with the masters in Japan. The strategy is discussed here. PMID:26523097

  5. SILAC-based quantification of changes in protein tyrosine phosphorylation induced by Interleukin-2 (IL-2) and IL-15 in T-lymphocytes.

    PubMed

    Osinalde, Nerea; Sánchez-Quiles, Virginia; Akimov, Vyacheslav; Blagoev, Blagoy; Kratchmarova, Irina

    2015-12-01

    This data article presents the first large-scale quantitative phosphoproteomics dataset generated to decipher the signaling networks initiated by IL-2 and IL-15 in T-lymphocytes. Data was collected by combining immunoprecipitation of tyrosine phosphorylated proteins and TiO2-based phosphopeptide enrichment with SILAC-based quantitative mass spectrometry. We report all the proteins and phosphotyrosine-containing peptides identified and quantified in IL-2- and IL-15-stimulated T-lymphocytes. The gene ontology analysis of IL-2 and IL-15 effector proteins detected in the present work is also included. The data supplied in this article is related to the research work entitled "Simultaneous dissection and comparison of IL-2 and IL-15 signaling pathways by global quantitative phosphoproteomics" [1]. All mass spectrometry data have been deposited in the ProteomeXchange with the identifier PXD001129. PMID:26425665

  6. SILAC-based quantification of changes in protein tyrosine phosphorylation induced by Interleukin-2 (IL-2) and IL-15 in T-lymphocytes

    PubMed Central

    Osinalde, Nerea; Sánchez-Quiles, Virginia; Akimov, Vyacheslav; Blagoev, Blagoy; Kratchmarova, Irina

    2015-01-01

    This data article presents the first large-scale quantitative phosphoproteomics dataset generated to decipher the signaling networks initiated by IL-2 and IL-15 in T-lymphocytes. Data was collected by combining immunoprecipitation of tyrosine phosphorylated proteins and TiO2-based phosphopeptide enrichment with SILAC-based quantitative mass spectrometry. We report all the proteins and phosphotyrosine-containing peptides identified and quantified in IL-2- and IL-15-stimulated T-lymphocytes. The gene ontology analysis of IL-2 and IL-15 effector proteins detected in the present work is also included. The data supplied in this article is related to the research work entitled “Simultaneous dissection and comparison of IL-2 and IL-15 signaling pathways by global quantitative phosphoproteomics” [1]. All mass spectrometry data have been deposited in the ProteomeXchange with the identifier PXD001129. PMID:26425665

  7. The Use of Specially Designed Tasks to Enhance Student Interest in the Cadaver Dissection Laboratory

    ERIC Educational Resources Information Center

    Kang, Seok Hoon; Shin, Jwa-Seop; Hwang, Young-il

    2012-01-01

    Cadaver dissection is a key component of anatomy education. Unfortunately, students sometimes regard the process of dissection as uninteresting or stressful. To make laboratory time more interesting and to encourage discussion and collaborative learning among medical students, specially designed tasks were assigned to students throughout…

  8. Isolated Spontaneous Dissection of the Common Iliac Artery: Percutaneous Stent Placement in Two Patients

    SciTech Connect

    Kwak, Hyo-Sung; Han, Young-Min Chung, Gyung-Ho; Yu, Hee Chul; Jeong, Yeon-Jun

    2006-10-15

    Isolated spontaneous dissection of the common iliac artery (CIA) is a rare entity. Two patients with this condition were successfully treated by percutaneous stent placement. We emphasize the feasibility of nonsurgical management by percutaneous stent placement for isolated spontaneous dissection of the CIA.

  9. 78 FR 17429 - Certain Balloon Dissection Devices and Products Containing Same; Commission Determination Not To...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-21

    ... (``Covidien'') on December 21, 2012. 78 FR 6838 (January 31, 2013). The complaint alleged violations of... Certain Balloon Dissection Devices and Products Containing Same; Commission Determination Not To Review an... importation, or sale in the United States after importation of certain balloon dissection devices and...

  10. Students' Physical and Psychological Reactions to Forensic Dissection: Are There Risk Factors?

    ERIC Educational Resources Information Center

    Sergentanis, Theodoros N.; Papadodima, Stavroula A.; Evaggelakos, Christos I.; Mytilinaios, Dimitrios G.; Goutas, Nikolaos D.; Spiliopoulou, Chara A.

    2010-01-01

    The reactions of students to forensic dissection encompass psychologico-emotional and physical components. This exploratory study aimed to determine risk factors for students' adverse physical and psychological reactions to forensic dissection. All sixth-year medical students (n = 304) attending the compulsory practical course in forensic medicine…

  11. [Acute coronary syndrome during dissection of left main as a complication of radiofrequency ablation].

    PubMed

    Kulawik, Tomasz; Ka?u?a, Bernadetta; Ku?nierz, Jacek

    2012-01-01

    We present a case of 44 year-old female who was admitted to the hospital due to performed radio frequency ablation because of VF during WPW syndrome, which was complicated by dissection of left main. The dissection was treated with success by primary percutaneous coronary intervention with two metal stents. PMID:22427091

  12. The discovery of the body: human dissection and its cultural contexts in ancient Greece.

    PubMed Central

    von Staden, H.

    1992-01-01

    In the first half of the third century B.C, two Greeks, Herophilus of Chalcedon and his younger contemporary Erasistratus of Ceos, became the first and last ancient scientists to perform systematic dissections of human cadavers. In all probability, they also conducted vivisections of condemned criminals. Their anatomical and physiological discoveries were extraordinary. The uniqueness of these events presents an intriguing historical puzzle. Animals had been dissected by Aristotle in the preceding century (and partly dissected by other Greeks in earlier centuries), and, later, Galen (second century A.D.) and others again systematically dissected numerous animals. But no ancient scientists ever seem to have resumed systematic human dissection. This paper explores, first, the cultural factors--including traditional Greek attitudes to the corpse and to the skin, also as manifested in Greek sacred laws--that may have prevented systematic human dissection during almost all of Greek antiquity, from the Pre-Socratic philosopher-scientists of the sixth and fifth centuries B.C. to distinguished Greek physicians of the later Roman Empire. Second, the exceptional constellation of cultural, political, and social circumstances in early Alexandria that might have emboldened Herophilus to overcome the pressures of cultural traditions and to initiate systematic human dissection, is analyzed. Finally, the paper explores possible reasons for the mysteriously abrupt disappearance of systematic human dissection from Greek science after the death of Erasistratus and Herophilus. PMID:1285450

  13. An Algorithm for Creating Geometric Dissection Puzzles Yahan Zhou, yhzhou@cs.umass.edu

    E-print Network

    Massachusetts at Amherst, University of

    - ational math and art [4,7]. In its basic form, the dissection question asks whether any two shapes by the ancient Greeks. One of the earliest examples is a visual proof of the Pythagorean theorem. In Arabic-Islamic mathematics and art, dissection figures are frequently used to construct intriguing patterns ornamenting

  14. GCSE Students' Attitudes to Dissection and Using Animals in Research and Product Testing.

    ERIC Educational Resources Information Center

    Lock, Roger

    1995-01-01

    Questionnaires from students passing the General Certificate of Secondary Education (GCSE) that explored attitudes to dissection and using animals in product testing administered to (n=469) students ages 14-15 showed a high level of support for peers who object to dissection, although objectors are likely to be met with derogatory comments,…

  15. 78 FR 6838 - Certain Balloon Dissection Devices and Products Containing Same; Institution of Investigation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-31

    ... COMMISSION Certain Balloon Dissection Devices and Products Containing Same; Institution of Investigation... dissection balloons and products containing the same by reason of infringement of certain claims of U.S... desist orders. ADDRESSES: The complaint, except for any confidential information contained therein,...

  16. Science Laboratory Depth of Learning: Interactive Multimedia Simulation and Virtual Dissection Software

    ERIC Educational Resources Information Center

    Yuza, Steve C.

    2010-01-01

    The purpose of this study was to determine the effects of interactive multimedia simulations and virtual dissection software on depth of learning among students participating in biology and chemistry laboratory courses. By understanding more about how simulation and virtual dissection software changes depth of learning, educators will have the…

  17. Dissecting the Dissectors: Knowledge, Attitude, and Practice of Body Bequests by Nigerian Anatomists

    ERIC Educational Resources Information Center

    Anyanwu, Emeka G.; Obikili, Emmanuel N.

    2012-01-01

    Anatomy education in most African countries is limited by an insufficient number of cadavers for students to undertake dissection. This already significant shortage is exacerbated by an increasing number of medical schools and students. Virtual dissections are impractical in alleviating such a shortfall in African anatomy education, and further…

  18. Medical Students' Reactions to Anatomic Dissection and the Phenomenon of Cadaver Naming

    ERIC Educational Resources Information Center

    Williams, Austin D.; Greenwald, Emily E.; Soricelli, Rhonda L.; DePace, Dennis M.

    2014-01-01

    The teaching of gross anatomy has, for centuries, relied on the dissection of human cadavers, and this formative experience is known to evoke strong emotional responses. The authors hypothesized that the phenomenon of cadaver naming is a coping mechanism used by medical students and that it correlates with other attitudes about dissection and body…

  19. Oregon Sea Grant Marine Education Program at Hatfield Marine Science Center Fish Dissection

    E-print Network

    Wright, Dawn Jeannine

    Oregon Sea Grant Marine Education Program at Hatfield Marine Science Center Fish Dissection The Fish Dissection program at Hatfield Marine Science Center is a 50-minute hands-on program for 4th through 12th grade students. Students will work in small groups as they examine a variety of fish, study

  20. EBprot: Statistical analysis of labeling-based quantitative proteomics data.

    PubMed

    Koh, Hiromi W L; Swa, Hannah L F; Fermin, Damian; Ler, Siok Ghee; Gunaratne, Jayantha; Choi, Hyungwon

    2015-08-01

    Labeling-based proteomics is a powerful method for detection of differentially expressed proteins (DEPs). The current data analysis platform typically relies on protein-level ratios, which is obtained by summarizing peptide-level ratios for each protein. In shotgun proteomics, however, some proteins are quantified with more peptides than others, and this reproducibility information is not incorporated into the differential expression (DE) analysis. Here, we propose a novel probabilistic framework EBprot that directly models the peptide-protein hierarchy and rewards the proteins with reproducible evidence of DE over multiple peptides. To evaluate its performance with known DE states, we conducted a simulation study to show that the peptide-level analysis of EBprot provides better receiver-operating characteristic and more accurate estimation of the false discovery rates than the methods based on protein-level ratios. We also demonstrate superior classification performance of peptide-level EBprot analysis in a spike-in dataset. To illustrate the wide applicability of EBprot in different experimental designs, we applied EBprot to a dataset for lung cancer subtype analysis with biological replicates and another dataset for time course phosphoproteome analysis of EGF-stimulated HeLa cells with multiplexed labeling. Through these examples, we show that the peptide-level analysis of EBprot is a robust alternative to the existing statistical methods for the DE analysis of labeling-based quantitative datasets. The software suite is freely available on the Sourceforge website http://ebprot.sourceforge.net/. All MS data have been deposited in the ProteomeXchange with identifier PXD001426 (http://proteomecentral.proteomexchange.org/dataset/PXD001426/). PMID:25913743

  1. Selective Neck Dissection (IIa, III): A Rational Replacement for Extended Supraomohyoid Neck Dissection in Patients with N0 Supraglottic and Glottic Squamous Cell Carcinoma

    PubMed Central

    Zohdi, Ismail; El Sharkawy, Louay S; El Bestar, Mahmoud F; Abdel Tawab, Hazem M; Hamela, Mo’men AA; Hareedy, Amal A

    2015-01-01

    OBJECTIVES To evaluate the effectiveness of selective neck dissection of sublevel IIa and level III in cases of glottis and supraglottic laryngeal carcinoma in the absence of lymph node metastasis and to show if there is value in dissecting the sublevel IIb or level IV in these cases. PATIENTS AND METHODS Twenty-five patients with N0 glottic or supraglottic cancer were subjected to unilateral or bilateral selective neck dissection according to the site and the extent of the tumor, and the specimens were histopathologically examined for metastasis. RESULTS Twenty-five patients (23 males and 2 females) with mean age of 55.72 years were included in the study. Lymph node metastasis to sublevel IIa and level III was found in 6/25 (24%) cases with glottic or supraglottic carcinoma, while to sublevel IIb and level IV was found in 1/25 (4%) with P-value of 0.05, which is statistically significant. CONCLUSION Selective neck dissection of level IIb is not required in cases of the supraglottic laryngeal cancer. Dissection of sublevel IIa and level III takes less time and is effective. Dissection of level IV is not needed in the case of supraglottic cancer. PMID:25733946

  2. Identification of Extracellular Signal-regulated Kinase 1 (ERK1) Direct Substrates using Stable Isotope Labeled Kinase Assay-Linked Phosphoproteomics*

    PubMed Central

    Xue, Liang; Wang, Pengcheng; Cao, Pianpian; Zhu, Jian-kang; Tao, W. Andy

    2014-01-01

    Kinase mediated phosphorylation signaling is extensively involved in cellular functions and human diseases, and unraveling phosphorylation networks requires the identification of substrates targeted by kinases, which has remained challenging. We report here a novel proteomic strategy to identify the specificity and direct substrates of kinases by coupling phosphoproteomics with a sensitive stable isotope labeled kinase reaction. A whole cell extract was moderately dephosphorylated and subjected to in vitro kinase reaction under the condition in which 18O-ATP is the phosphate donor. The phosphorylated proteins are then isolated and identified by mass spectrometry, in which the heavy phosphate (+85.979 Da) labeled phosphopeptides reveal the kinase specificity. The in vitro phosphorylated proteins with heavy phosphates are further overlapped with in vivo kinase-dependent phosphoproteins for the identification of direct substrates with high confidence. The strategy allowed us to identify 46 phosphorylation sites on 38 direct substrates of extracellular signal-regulated kinase 1, including multiple known substrates and novel substrates, highlighting the ability of this high throughput method for direct kinase substrate screening. PMID:25022875

  3. Classic Ras Proteins Promote Proliferation and Survival via Distinct Phosphoproteome Alterations in Neurofibromin-Null Malignant Peripheral Nerve Sheath Tumor Cells.

    PubMed

    Brossier, Nicole M; Prechtl, Amanda M; Longo, Jody Fromm; Barnes, Stephen; Wilson, Landon S; Byer, Stephanie J; Brosius, Stephanie N; Carroll, Steven L

    2015-06-01

    Neurofibromin, the tumor suppressor encoded by the neurofibromatosis type 1 (NF1) gene, potentially suppresses the activation of H-Ras, N-Ras, and K-Ras. However, it is not known whether these classic Ras proteins are hyperactivated in NF1-null nerve sheath tumors, how they contribute to tumorigenesis, and what signaling pathways mediate their effects. Here we show that H-Ras, N-Ras, and K-Ras are coexpressed with their activators (guanine nucleotide exchange factors) in neurofibromin-null malignant peripheral nerve sheath tumor (MPNST) cells, and that all 3 Ras proteins are activated. Dominant negative (DN) H-Ras, a pan-inhibitor of the classic Ras family, inhibited MPNST proliferation and survival, but not migration. However, NF1-null MPNST cells were variably dependent on individual Ras proteins. In some lines, ablation of H-Ras, N-Ras, and/or K-Ras inhibited mitogenesis. In others, ablation of a single Ras protein had no effect on proliferation; in these lines, ablation of a single Ras protein resulted in compensatory increases in the activation and/or expression of other Ras proteins. Using mass spectrometry-based phosphoproteomics, we identified 7 signaling networks affecting morphology, proliferation, and survival that are regulated by DN H-Ras. Thus, neurofibromin loss activates multiple classic Ras proteins that promote proliferation and survival by regulating several distinct signaling cascades. PMID:25946318

  4. A High-Resolution Tissue-Specific Proteome and Phosphoproteome Atlas of Maize Primary Roots Reveals Functional Gradients along the Root Axes1[OPEN

    PubMed Central

    Malik, Waqas Ahmed; Shen, Zhouxin; Paschold, Anja

    2015-01-01

    A high-resolution proteome and phosphoproteome atlas of four maize (Zea mays) primary root tissues, the cortex, stele, meristematic zone, and elongation zone, was generated. High-performance liquid chromatography coupled with tandem mass spectrometry identified 11,552 distinct nonmodified and 2,852 phosphorylated proteins across the four root tissues. Two gradients reflecting the abundance of functional protein classes along the longitudinal root axis were observed. While the classes RNA, DNA, and protein peaked in the meristematic zone, cell wall, lipid metabolism, stress, transport, and secondary metabolism culminated in the differentiation zone. Functional specialization of tissues is underscored by six of 10 cortex-specific proteins involved in flavonoid biosynthesis. Comparison of this data set with high-resolution seed and leaf proteome studies revealed 13% (1,504/11,552) root-specific proteins. While only 23% of the 1,504 root-specific proteins accumulated in all four root tissues, 61% of all 11,552 identified proteins accumulated in all four root tissues. This suggests a much higher degree of tissue-specific functionalization of root-specific proteins. In summary, these data illustrate the remarkable plasticity of the proteomic landscape of maize primary roots and thus provide a starting point for gaining a better understanding of their tissue-specific functions. PMID:25780097

  5. Near-peer driven dissection selective: A primer to the medical school anatomy course.

    PubMed

    Cantwell, Sean; Bonadurer, George F; Pawlina, Wojciech; Lachman, Nirusha

    2015-11-01

    In the anatomy laboratory, skill remains a critical component to unlocking the true value of learning from cadaveric dissection. However, there is little if any room for provision of instruction in proper dissection technique. We describe how near-peer instructors designed a supplemental learning activity to enhance the dissection experience for first-year medical students. This study aimed to evaluate the efficacy of this curriculum in improving participants' understanding of dissection technique and its impact on perceived challenges associated with the anatomy course. Curriculum was designed under faculty guidance and included didactic sessions, low-fidelity models, dissection, student presentations, and clinical correlations. Participants' (n?=?13) knowledge of basic dissection techniques and concepts were assessed before the selective, and both participants' and nonparticipants' (n?=?39) knowledge was assessed at the end of week one and week seven of the anatomy course. Scores were compared using repeated measures ANOVA followed by post hoc t-tests. Thirteen deidentified reflective essays were reviewed by four independent reviewers for themes that aligned with learning objectives. Participants in the selective course scored higher on assessment of dissection techniques and concepts one week after the selective compared to both nonparticipants and their own baseline scores before the selective. Analysis of student reflections resulted in four themes: confidence with dissection skill, sharing resources and transfer of knowledge, learning environment, and psychological impact of perceived challenges of the anatomy course. Near-peer driven supplemental exercises are effective in facilitating dissection skills. This dissection primer increases student confidence and alleviates apprehension associated with anatomy courses. Clin. Anat. 28:985-993, 2015. © 2015 Wiley Periodicals, Inc. PMID:26375596

  6. Toward a Genetic Dissection of Cortical Circuits in the Mouse

    PubMed Central

    Huang, Z. Josh

    2014-01-01

    The mammalian neocortex gives rise to a wide range of mental activities and consists of a constellation of interconnected areas that are built from a set of basic circuit templates. Major obstacles to understanding cortical architecture include the diversity of cell types, their highly recurrent local and global connectivity, dynamic circuit operations, and a convoluted developmental assembly process rooted in the genome. With our increasing knowledge of gene expression and developmental genetic principles, it is now feasible to launch a program of genetic dissection of cortical circuits through systematic targeting of cell types and fate-mapping of neural progenitors. Strategic design of even a modest number of mouse driver lines will facilitate efforts to compile a cell type parts list, build a Cortical Cell Atlas, establish experimental access to modern tools, and provide coordinates for tracing developmental trajectory from circuit assembly to functional operation. PMID:25233312

  7. Vertebral artery dissection after a chiropractor neck manipulation.

    PubMed

    Jones, Jeremy; Jones, Catherine; Nugent, Kenneth

    2015-01-01

    The differential diagnosis for ischemic central nervous system infarcts in young patients includes paradoxic emboli through cardiac shunts, vasculitis, and vascular trauma. We report a young woman who developed headache, vomiting, diplopia, dizziness, and ataxia following neck manipulation by her chiropractor. A computed tomography scan of the head revealed an infarct in the inferior half of the left cerebellar hemisphere and compression of the fourth ventricle causing moderate acute obstructive hydrocephalus. Magnetic resonance angiography revealed severe narrowing and low flow in the intracranial segment of the left distal vertebral artery. The patient was treated with mannitol and a ventriculostomy and had an excellent functional recovery. This report illustrates the potential hazards associated with neck trauma, including chiropractic manipulation. The vertebral arteries are at risk for aneurysm formation and/or dissection, which can cause acute stroke. PMID:25552813

  8. Vertebral artery dissection and cerebellar infarction following chiropractic manipulation

    PubMed Central

    Chen, W?L; Chern, C?H; Wu, Y?L; Lee, C?H

    2006-01-01

    Vertebral artery dissection (VAD) associated with chiropractic cervical manipulation is a rare but potentially disabling condition. In this report, we present a young patient manifesting with repeated vertigo. Owing to the initial misdiagnosis, the patient later developed cerebellar stroke with inability to stand or walk. Vertigo and disequilibrium are the usual presenting symptoms of this condition, which can result from inner ear or vestibular nerve dysfunction, vertebrobasilar insufficiency, and even lethal cerebellar infarction or haemorrhage; these last two, although rarely seen in young adults, can be caused by traumatic or spontaneous arterial injury, including injury secondary to chiropractic cervical manipulation. A number of cases of VAD associated with chiropractic cervical manipulation have been reported, but rarely in the emergency medicine literature. We present a case of this rare occurrence, and discuss the diagnostic pitfalls. PMID:16373786

  9. Vertebral artery dissection after a chiropractor neck manipulation

    PubMed Central

    Jones, Jeremy; Nugent, Kenneth

    2015-01-01

    The differential diagnosis for ischemic central nervous system infarcts in young patients includes paradoxic emboli through cardiac shunts, vasculitis, and vascular trauma. We report a young woman who developed headache, vomiting, diplopia, dizziness, and ataxia following neck manipulation by her chiropractor. A computed tomography scan of the head revealed an infarct in the inferior half of the left cerebellar hemisphere and compression of the fourth ventricle causing moderate acute obstructive hydrocephalus. Magnetic resonance angiography revealed severe narrowing and low flow in the intracranial segment of the left distal vertebral artery. The patient was treated with mannitol and a ventriculostomy and had an excellent functional recovery. This report illustrates the potential hazards associated with neck trauma, including chiropractic manipulation. The vertebral arteries are at risk for aneurysm formation and/or dissection, which can cause acute stroke. PMID:25552813

  10. Vertebral artery dissection in evolution found during chiropractic examination.

    PubMed

    Futch, Dan; Schneider, Michael J; Murphy, Donald; Grayev, Allison

    2015-01-01

    A 30-year-old woman presented to an emergency department with sudden onset of transient loss of left peripheral vision. Owing to a history of migraine headaches, she was released with a diagnosis of ocular migraine. Two days later, she sought chiropractic care for the chief symptom of severe neck pain. The chiropractor suspected the possibility of vertebral artery dissection (VAD). No manipulation was performed; instead, MR angiography (MRA) of the neck was obtained, which revealed an acute left VAD with early thrombus formation. The patient was placed on aspirin therapy. Repeat MRA of the neck 3?months later revealed resolution of the thrombus, without progression to stroke. This case illustrates the importance for all healthcare providers who see patients with neck pain and headache to be attentive to the symptomatic presentation of possible VAD in progress. PMID:26564115

  11. Esophageal diverticulum exposed during endoscopic submucosal dissection of superficial cancer

    PubMed Central

    Tanaka, Shinwa; Toyonaga, Takashi; Ohara, Yoshiko; Yoshizaki, Tetsuya; Kawara, Fumiaki; Ishida, Tsukasa; Hoshi, Namiko; Morita, Yoshinori; Azuma, Takeshi

    2015-01-01

    Endoscopic submucosal dissection (ESD) is now widely accepted as a strategy to treat superficial esophageal neoplasms. The rate of adverse events, such as perforation, has been decreasing with the improvement of devices and techniques. In this paper, we report a case of esophageal cancer that had a diverticulum under cancerous epithelium. The diverticulum was not detected during preoperative examination, and led to perforation during the ESD procedure. Our case shows that, although rare, some diverticula can exist underneath the mucosal surface without obvious depression. If there is any sign of hidden diverticula during ESD, surgeons should proceed with caution or, depending on the case, the procedure should be discontinued to avoid adverse events. PMID:25780314

  12. Induced pluripotent stem cell technology for dissecting the cancer epigenome

    PubMed Central

    Semi, Katsunori; Yamada, Yasuhiro

    2015-01-01

    Cancer arises through the accumulation of both genetic and epigenetic alterations. Although the causal role of genetic mutations on cancer development has been established in vivo, similar evidence for epigenetic alterations is limited. Moreover, mutual interactions between genetic mutations and epigenetic alterations remain unclear. Cellular reprogramming technology can be used to actively modify the epigenome without affecting the underlying genomic sequences. Here we introduce recent studies that have utilized this property for cancer research. We propose that just as it has potential for regenerative medicine and disease modeling, cell reprogramming could also be a powerful tool for dissecting the role of the cancer epigenome in the development and maintenance of cancer cells. PMID:26224327

  13. From microscopes to microarrays: dissecting recurrent chromosomal rearrangements

    PubMed Central

    Emanuel, Beverly S.; Saitta, Sulagna C.

    2010-01-01

    Submicroscopic chromosomal rearrangements that lead to copy-number changes have been shown to underlie distinctive and recognizable clinical phenotypes. The sensitivity to detect copy-number variation has escalated with the advent of array comparative genomic hybridization (CGH), including BAC and oligonucleotide-based platforms. Coupled with improved assemblies and annotation of genome sequence data, these technologies are facilitating the identification of new syndromes that are associated with submicroscopic genomic changes. Their characterization reveals the role of genome architecture in the aetiology of many clinical disorders. We review a group of genomic disorders that are mediated by segmental duplications, emphasizing the impact that high-throughput detection methods and the availability of the human genome sequence have had on their dissection and diagnosis. PMID:17943194

  14. Dissecting Alzheimer disease in Down syndrome using mouse models

    PubMed Central

    Choong, Xun Yu; Tosh, Justin L.; Pulford, Laura J.; Fisher, Elizabeth M. C.

    2015-01-01

    Down syndrome (DS) is a common genetic condition caused by the presence of three copies of chromosome 21 (trisomy 21). This greatly increases the risk of Alzheimer disease (AD), but although virtually all people with DS have AD neuropathology by 40 years of age, not all develop dementia. To dissect the genetic contribution of trisomy 21 to DS phenotypes including those relevant to AD, a range of DS mouse models has been generated which are trisomic for chromosome segments syntenic to human chromosome 21. Here, we consider key characteristics of human AD in DS (AD-DS), and our current state of knowledge on related phenotypes in AD and DS mouse models. We go on to review important features needed in future models of AD-DS, to understand this type of dementia and so highlight pathogenic mechanisms relevant to all populations at risk of AD. PMID:26528151

  15. Dissecting the hypothalamic pathways that underlie innate behaviors.

    PubMed

    Zha, Xi; Xu, Xiaohong

    2015-12-01

    Many complex behaviors that do not require learning are displayed and are termed innate. Although traditionally the subject matter of ethology, innate behaviors offer a unique entry point for neuroscientists to dissect the physiological mechanisms governing complex behaviors. Since the last century, converging evidence has implicated the hypothalamus as the central brain area that controls innate behaviors. Recent studies using cutting-edge tools have revealed that genetically-defined populations of neurons residing in distinct hypothalamic nuclei and their associated neural pathways regulate the initiation and maintenance of diverse behaviors including feeding, sleep, aggression, and parental care. Here, we review the newly-defined hypothalamic pathways that regulate each innate behavior. In addition, emerging general principles of the neural control of complex behaviors are discussed. PMID:26552801

  16. Dissection of C. elegans behavioral genetics in 3-D environments

    PubMed Central

    Kwon, Namseop; Hwang, Ara B.; You, Young-Jai; V. Lee, Seung-Jae; Ho Je, Jung

    2015-01-01

    The nematode Caenorhabditis elegans is a widely used model for genetic dissection of animal behaviors. Despite extensive technical advances in imaging methods, it remains challenging to visualize and quantify C. elegans behaviors in three-dimensional (3-D) natural environments. Here we developed an innovative 3-D imaging method that enables quantification of C. elegans behavior in 3-D environments. Furthermore, for the first time, we characterized 3-D-specific behavioral phenotypes of mutant worms that have defects in head movement or mechanosensation. This approach allowed us to reveal previously unknown functions of genes in behavioral regulation. We expect that our 3-D imaging method will facilitate new investigations into genetic basis of animal behaviors in natural 3-D environments. PMID:25955271

  17. Epidemiology and Medication Utilization Pattern of Aortic Dissection in Taiwan

    PubMed Central

    Yeh, Ting-Yu; Chen, Chung-Yu; Huang, Jiann-Woei; Chiu, Chaw-Chi; Lai, Wen-Ter; Huang, Yaw-Bin

    2015-01-01

    Abstract Acute aortic dissection (AD) is a catastrophic condition associated with a high rate of mortality. However, current epidemiological information regarding AD remains sparse. The objective of the present study was to investigate the current epidemiological profile and medication utilization patterns associated with aortic dissection in Taiwan. In this population-based study, we identified cases of AD diagnosed during 2005 to 2012 in the complete Taiwan National Health Insurance (NHI) Research Database. Patients with AD were identified using the International Classification of Disease, Ninth Revision (ICD-9) code 441.0, and surgical interventions were defined using NHI procedure codes. A total of 9092 individuals with a mean age of 64.4?±?15.1 years were identified. The cases were divided into 3 groups: Group A included 2340 patients (25.74%) treated surgically for type A AD; Group B included 1144 patients (12.58%) treated surgically for type B AD, and Group C included 5608 patients (61.68%) with any type of AD treated with medical therapy only. The average annual incidence of AD was 5.6 per 100,000 persons, and the average prevalence was 19.9 per 100,000 persons. Hypertension was the most common risk factor, followed by coronary artery disease and chronic obstructive pulmonary disease. Within 1 year of AD diagnosis, 92% of patients were taking antihypertensive medication. Calcium channel blockers were the most frequently prescribed antihypertensive medication for long-term observation in Taiwan. The annual trends revealed statistically significant increases in the numbers and percentages of prevalence, incidence, and mortality. Changes in patients’ drug utilization in patterns were observed after AD diagnosis. Our study provides a local profile that supports further in-depth analyses in AD-affected populations. PMID:26356726

  18. Students as teachers in an anatomy dissection course.

    PubMed

    Salomäki, Tiina; Laakkonen, Juha; Ruohoniemi, Mirja

    2014-01-01

    One way to improve students' learning outcomes and well-being is to change teaching practices to allow students to become more active participants. We used an anatomy dissection course to test a cooperative group work method in which first-year veterinary students took turns leading their peer group and were each responsible for teaching the anatomy of a particular topographic region. The important blood vessels, lymphatic system, and nerves of each region of the body were covered. Students felt that exploration of the entire topographic region helped them to acquire a comprehensive understanding of the respiratory apparatus and the cardiovascular and nervous systems. Assigning individual tasks to each group member resulted in sharing the workload equally. Open-ended comments revealed that support from other group members was important for the students' learning experience, but the results also offered insight into a lack of constructive criticism. While teaching was considered challenging, and even a stress factor that hindered learning for some students, group work was generally held to be supportive of learning. The results suggest that more thorough instruction of students in their group work and in their individual tasks is required. Some students experienced difficulty in expressing their concerns openly and in seeking guidance from teachers, demonstrating the need for further investigation regarding students' self-regulation skills. Comments from the open-ended responses suggest that use of a cooperative learning method in anatomy dissection courses not only deepens student understanding of a subject but also offers first-year students an opportunity to practice the generic skills that will be needed in their future profession. PMID:24219999

  19. Quantitative photoacoustic assessment of ex-vivo lymph nodes of colorectal cancer patients

    NASA Astrophysics Data System (ADS)

    Sampathkumar, Ashwin; Mamou, Jonathan; Saegusa-Beercroft, Emi; Chitnis, Parag V.; Machi, Junji; Feleppa, Ernest J.

    2015-03-01

    Staging of cancers and selection of appropriate treatment requires histological examination of multiple dissected lymph nodes (LNs) per patient, so that a staggering number of nodes require histopathological examination, and the finite resources of pathology facilities create a severe processing bottleneck. Histologically examining the entire 3D volume of every dissected node is not feasible, and therefore, only the central region of each node is examined histologically, which results in severe sampling limitations. In this work, we assess the feasibility of using quantitative photoacoustics (QPA) to overcome the limitations imposed by current procedures and eliminate the resulting under sampling in node assessments. QPA is emerging as a new hybrid modality that assesses tissue properties and classifies tissue type based on multiple estimates derived from spectrum analysis of photoacoustic (PA) radiofrequency (RF) data and from statistical analysis of envelope-signal data derived from the RF signals. Our study seeks to use QPA to distinguish cancerous from non-cancerous regions of dissected LNs and hence serve as a reliable means of imaging and detecting small but clinically significant cancerous foci that would be missed by current methods. Dissected lymph nodes were placed in a water bath and PA signals were generated using a wavelength-tunable (680-950 nm) laser. A 26-MHz, f-2 transducer was used to sense the PA signals. We present an overview of our experimental setup; provide a statistical analysis of multi-wavelength classification parameters (mid-band fit, slope, intercept) obtained from the PA signal spectrum generated in the LNs; and compare QPA performance with our established quantitative ultrasound (QUS) techniques in distinguishing metastatic from non-cancerous tissue in dissected LNs. QPA-QUS methods offer a novel general means of tissue typing and evaluation in a broad range of disease-assessment applications, e.g., cardiac, intravascular, musculoskeletal, endocrine-gland, etc.

  20. Stent-assisted coil embolization for anterior cerebral artery dissection presented with cerebral infarction

    PubMed Central

    Iwasaki, Mitsuhiro; Hattori, Itaro; Sasaki, Makoto; Ishimori, Hisatsugu; Nemoto, Akihiro; Hikita, Chiyoe; Sato, Junko; Fukuta, Shinya; Morimoto, Masafumi

    2015-01-01

    Background: Compared to those found in the vertebrobasilar system, intracranial dissection in the anterior circulation is relatively rare, especially in the anterior cerebral artery (ACA). Moreover, only several cases of ACA dissection that underwent endovascular treatment have been reported. Here we present a rare case of gradually developing ACA dissecting aneurysm causing cerebral infarction, successfully treated by stent-assisted coil embolization. Case Description: A 36-year-old man was admitted with sudden right hemiparesis. Diffusion-weighted magnetic resonance (MR) imaging showed cerebral infarction in the left ACA territory, and MR angiography showed segmental stenosis at the A2 portion of the left ACA. Three-dimensional digital subtraction angiogram showed segmental dilatation and stenosis at the left A2 portion. We diagnosed ACA dissection causing acute cerebral infarction and treated the patient conservatively. Five months after the onset, the dissecting artery at the left A2 portion formed a gradually dilating aneurysm, suggesting increased risk for aneurysmal rupture. We attempted endovascular treatment entailing coil embolization of an aneurysm while preserving the left A2 with stent assistance. The patient remained neurologically stable 6 months after the procedure. Conclusions: Although there are few reported cases of ACA dissection where endovascular treatment was attempted, we consider stent-assisted embolization for gradually developing ACA dissecting aneurysm as an alternative method to prevent bleeding and recurrent infarction. PMID:26677416

  1. Complications of neck dissection at a tertiary level hospital: study of 30 cases.

    PubMed

    Masud, M K; Ahmad, S M; Karim, M A; Ferdouse, F; Fakir, A Y; Hanif, M A; Abdullah, M; Roy, A S

    2014-10-01

    Metastatic dissemination into lymph nodes of neck occurs frequently in head neck cancers which down grade the patient's curability and survival. Neck dissection is a curable option for its management. To evaluate the complications following different types of neck dissection. This cross sectional study was conducted among patients undergone different types of neck dissection due to cervical nodal metastasis and attended follow up during July 2010 to June 2011 in Department of ENTs and Head-Neck surgery Dhaka Medical College Hospital, Dhaka, Bangladesh. Among 30 selected patient, 23 were male (76.67%) and 7 were female (23.33%), age ranged from 31-72 years (Mean=59.1±5.44). In different modalities of neck dissection 11 were modified neck dissection (36.67%) and 10(33.33%) were radical neck dissection. Common indication was carcinoma of unknown origin (66.67%). Involved neck nodes were commonly level II-IV (69.99%). Nodal stage was N2(50%) and N3 (40%).Common immediate complications were bleeding 03(10%), facial oedema 02 (6.67%) and thoracic duct injury 02(6.67%). Intermediate complications were seroma 05(16.67%), wound infection 04(13.33%) and chylous fistula 02(6.67%), Late Complications were hypertrophic scar 07(23.33%) and shoulder syndrome 06(20%). Proper indications, skilled surgery along with early recognize and treatment in both early and late manifestations of neck dissection preventing its grave sequence. PMID:25481582

  2. A rare complication of pre-Eisenmenger patent ductus arteriosus: Pulmonary artery dissection

    PubMed Central

    Ay, Yasin; Ay, Nuray Kahraman; Aydin, Cemalettin; Kara, Ibrahim; Zeybek, Rahmi

    2013-01-01

    INTRODUCTION Pulmonary artery dissection associated with patent ductus arteriosus is usually seen in patients with pulmonary hypertension and Eisenmenger's syndrome. This paper presents a case with pre-Eisenmenger patent ductus arteriosus complicated by pulmonary artery dissection, and explains how she was surgically treated. PRESENTATION OF CASE The transthoracic echocardiography of a 21-year-old woman complaining of effort dyspnea revealed patent ductus arteriosus. Contrast-enhanced thoracic computed tomography scan showed patent ductus arteriosus and dissection in the main pulmonary artery extending from the edge of the patent ductus arteriosus orifice to the pulmonary valve. The patent ductus arteriosus was divided with pledgeted prolene suture and the dissected aneurysmal portion of the pulmonary artery was resected by surgery. Dacron graft interposition was applied to the main pulmonary artery. DISCUSSION Because rupture causes cardiogenic shock and sudden death, diagnosis is rare in the living subject and pulmonary artery dissection is frequently detected in autopsy. A case with pulmonary artery dissection as a result of patent ductus arteriosus has been reported in the literature, but the patient died in the preoperative period. In our study, the patient was not diagnosed to have Eisenmenger's syndrome, but had pulmonary artery dissection, a complication arising from patent ductus arteriosus. The patient underwent curative surgery that included pulmonary artery dissection repair and closure of the patent ductus arteriosus. CONCLUSION In addition to pulmonary artery aneurysm, pulmonary artery dissection must also be considered as a complication in cases of patent ductus arteriosus with high pulmonary artery pressure diagnosed in adulthood. PMID:23562897

  3. Unexpected Delayed Colon Perforation after the Endoscopic Submucosal Dissection with Snaring of a Laterally Spreading Tumor

    PubMed Central

    Ko, Young Bo; Lee, Jeong-Mi; Kim, Wan Soo; Kwak, Min Seob; Lee, Ji Wan; Shin, Dong Yeol; Yang, Dong-Hoon; Byeon, Jeong-Sik

    2015-01-01

    Colonic perforation may occur as a complication of diagnostic and therapeutic colonoscopy. The risk factors for perforation after colorectal endoscopic submucosal dissection (ESD) include an inexperienced endoscopist, a large tumor size, and submucosal fibrosis. The mechanisms of perforation include unintended endoscopic resection/dissection and severe thermal injury. Here, we report a case of colon perforation that occurred after ESD with snaring of a laterally spreading tumor. The perforation was completely unexpected because there were no colorectal ESD-associated risk factors for perforation, deep dissection, or severe coagulation injury in our patient. PMID:26668808

  4. Sensitivity of partial carcass dissection for assessment of porcine cysticercosis at necropsy.

    PubMed

    Lightowlers, M W; Assana, E; Jayashi, C M; Gauci, C G; Donadeu, M

    2015-11-01

    Many interventions against Taenia solium are evaluated by assessing changes in the prevalence of porcine cysticercosis ascertained by carcass dissection. Financial and logistical difficulties often prohibit dissection of entire pig carcasses. We assessed 209 pigs from rural areas of Cameroon and Peru for the presence of T. solium cysticerci and determined the distribution of parasites within the musculature of infected animals. Considering the presence of cysts in the tongue, masticatory muscles and heart, 31 of the 38 (81%) naturally infected animals were identified as having cysts. Dissection of only the tongue, masticatory muscles and heart provides a relatively sensitive and highly specific method for diagnosis of porcine cysticercosis. PMID:26385439

  5. Delayed Intestinal Ischemia after Surgery for Type A Acute Aortic Dissection

    PubMed Central

    Kato, Yasuyuki; Motoki, Manabu; Takahashi, Yosuke; Nishimura, Shinsuke; Shibata, Toshihiko

    2015-01-01

    We report a rare case of delayed intestinal ischemia after total arch replacement for type A acute aortic dissection. At the onset of acute aortic dissection, computed tomography (CT) angiography revealed celiac trunk occlusion and progressive dissection into the superior mesenteric artery without stenosis. However, following total arch replacement, visceral malperfusion was not detected by exploratory laparotomy. On postoperative day 12, the patient developed paralytic ileus without an elevated lactate level. CT angiography revealed new superior mesenteric artery stenosis by a thrombosed false lumen with persistent celiac trunk occlusion. Endovascular treatment including stent implantation resolved intestinal ischemia. PMID:26421078

  6. [Traumatic dissection of the carotid artery: challenges for diagnostics and therapy illustrated by a case example].

    PubMed

    Jansen, G; Popp, J; Dietrich, U; Mertzlufft, F; Bach, F

    2013-10-01

    Traumatic dissection of the carotid artery is an easily overlooked consequence of trauma with notable morbidity and mortality which can be observed in up to 4% of cases involving multiple trauma. Certain mechanisms and patterns of injury as well as specific symptoms should serve as indicators of a dissection and should therefore result in further diagnostic measures. An early diagnosis is of major relevance. This report describes the case of a 45-year-old victim of a traffic accident who showed symptoms of a dissection which had initially not been diagnosed. PMID:24057761

  7. Sensitivity of partial carcass dissection for assessment of porcine cysticercosis at necropsy

    PubMed Central

    Lightowlers, M.W.; Assana, E.; Jayashi, C.M.; Gauci, C.G.; Donadeu, M.

    2015-01-01

    Many interventions against Taenia solium are evaluated by assessing changes in the prevalence of porcine cysticercosis ascertained by carcass dissection. Financial and logistical difficulties often prohibit dissection of entire pig carcasses. We assessed 209 pigs from rural areas of Cameroon and Peru for the presence of T. solium cysticerci and determined the distribution of parasites within the musculature of infected animals. Considering the presence of cysts in the tongue, masticatory muscles and heart, 31 of the 38 (81%) naturally infected animals were identified as having cysts. Dissection of only the tongue, masticatory muscles and heart provides a relatively sensitive and highly specific method for diagnosis of porcine cysticercosis. PMID:26385439

  8. Delayed Intestinal Ischemia after Surgery for Type A Acute Aortic Dissection.

    PubMed

    Morisaki, Akimasa; Kato, Yasuyuki; Motoki, Manabu; Takahashi, Yosuke; Nishimura, Shinsuke; Shibata, Toshihiko

    2015-01-01

    We report a rare case of delayed intestinal ischemia after total arch replacement for type A acute aortic dissection. At the onset of acute aortic dissection, computed tomography (CT) angiography revealed celiac trunk occlusion and progressive dissection into the superior mesenteric artery without stenosis. However, following total arch replacement, visceral malperfusion was not detected by exploratory laparotomy. On postoperative day 12, the patient developed paralytic ileus without an elevated lactate level. CT angiography revealed new superior mesenteric artery stenosis by a thrombosed false lumen with persistent celiac trunk occlusion. Endovascular treatment including stent implantation resolved intestinal ischemia. PMID:26421078

  9. Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways.

    PubMed

    Mitsos, Alexander; Melas, Ioannis N; Morris, Melody K; Saez-Rodriguez, Julio; Lauffenburger, Douglas A; Alexopoulos, Leonidas G

    2012-01-01

    Modeling of signal transduction pathways plays a major role in understanding cells' function and predicting cellular response. Mathematical formalisms based on a logic formalism are relatively simple but can describe how signals propagate from one protein to the next and have led to the construction of models that simulate the cells response to environmental or other perturbations. Constrained fuzzy logic was recently introduced to train models to cell specific data to result in quantitative pathway models of the specific cellular behavior. There are two major issues in this pathway optimization: i) excessive CPU time requirements and ii) loosely constrained optimization problem due to lack of data with respect to large signaling pathways. Herein, we address both issues: the former by reformulating the pathway optimization as a regular nonlinear optimization problem; and the latter by enhanced algorithms to pre/post-process the signaling network to remove parts that cannot be identified given the experimental conditions. As a case study, we tackle the construction of cell type specific pathways in normal and transformed hepatocytes using medium and large-scale functional phosphoproteomic datasets. The proposed Non Linear Programming (NLP) formulation allows for fast optimization of signaling topologies by combining the versatile nature of logic modeling with state of the art optimization algorithms. PMID:23226239

  10. Non Linear Programming (NLP) Formulation for Quantitative Modeling of Protein Signal Transduction Pathways

    PubMed Central

    Morris, Melody K.; Saez-Rodriguez, Julio; Lauffenburger, Douglas A.; Alexopoulos, Leonidas G.

    2012-01-01

    Modeling of signal transduction pathways plays a major role in understanding cells' function and predicting cellular response. Mathematical formalisms based on a logic formalism are relatively simple but can describe how signals propagate from one protein to the next and have led to the construction of models that simulate the cells response to environmental or other perturbations. Constrained fuzzy logic was recently introduced to train models to cell specific data to result in quantitative pathway models of the specific cellular behavior. There are two major issues in this pathway optimization: i) excessive CPU time requirements and ii) loosely constrained optimization problem due to lack of data with respect to large signaling pathways. Herein, we address both issues: the former by reformulating the pathway optimization as a regular nonlinear optimization problem; and the latter by enhanced algorithms to pre/post-process the signaling network to remove parts that cannot be identified given the experimental conditions. As a case study, we tackle the construction of cell type specific pathways in normal and transformed hepatocytes using medium and large-scale functional phosphoproteomic datasets. The proposed Non Linear Programming (NLP) formulation allows for fast optimization of signaling topologies by combining the versatile nature of logic modeling with state of the art optimization algorithms. PMID:23226239

  11. Direct thrombus aspiration using the Penumbra system for the treatment of pediatric intracranial dissection.

    PubMed

    Fujimoto, Motoaki; Tateshima, Satoshi; Ali, Latisha; Raychev, Radoslav; Vinuela, Fernando

    2013-11-01

    We describe a case of a 15-year-old girl who developed a spontaneous intracranial arterial dissection with distal middle cerebral artery (MCA) occlusions. From the digital subtraction angiography provided, the dissection flap appeared to originate at the internal carotid artery terminus with extension into the right M1 segment and occluding the right anterior cerebral artery, A1 segment. CT perfusion study showed salvageable tissue in the posterior MCA territory, including the motor cortex. In order to avoid further injury to the dissection, clot retrieval systems were not a treatment option. We therefore performed selective thrombus aspiration with the Penumbra system for the occluded central and precentral arteries distal to the non-occlusive dissecting lesion. Sufficient recanalization was achieved and the patient made a marked recovery. Although mechanical thrombectomy with the use of retrieval intracranial stent systems has demonstrated satisfactory recanalization rates, the aspiration methodology remains useful for patients with an accompanying proximal vascular lesion. PMID:23188785

  12. Fatal Delayed Esophageal Rupture Following Aortic Clamping for Treatment of Stanford Type B Dissection

    SciTech Connect

    Ito, Hisao; Yamada, Takayuki; Ishibashi, Tadashi; Akiyama, Masatoshi; Nakame, Takahiko; Ito, Yasuhiro; Konnai, Toshiaki

    2003-11-15

    A 65-year-old man underwent a thromboexclusionoperation for management of chronic Stanford type B dissecting aneurysmin 1991. However, long-term follow-up CT scans after the operation revealed that the ascending aorta gradually enlarged and was eventually complicated by recurrent aortic dissection. The patient complained of frequent bloody sputum, whereas chest roentogenography showed no pulmonary abnormalities. Subsequent swallow esophagogram demonstrated that the upper esophagus was deviated to the right and the middle esophagus was greatly compressed by the aortic clamp. Esophageal endoscopy showed a bloody inner surface and marked swelling of the middle esophagus. The patient eventually died of massive hematemesis in 2001. We describe the imaging features of unanticipated complications such as recurrent dissecting aneurysm or impending esophageal rupture.Furthermore, we discuss the cause of hematemesis and document that the aortic clamp migrated and resulted in development of a recurrent aneurysmal dissection, which in turn resulted in esophageal rupture with aneurysmal disruption.

  13. J Physiol 580.3 (2007) pp 961975 961 Pharmacological dissection of the human gastro-

    E-print Network

    Brasseur, James G.

    2007-01-01

    J Physiol 580.3 (2007) pp 961­975 961 Pharmacological dissection of the human gastro- oesophageal and quantify in vivo the skeletal and smooth muscle sphincteric components pharmacologically and clarify

  14. Direct thrombus aspiration using the Penumbra system for the treatment of pediatric intracranial dissection.

    PubMed

    Fujimoto, Motoaki; Tateshima, Satoshi; Ali, Latisha; Raychev, Radoslav; Vinuela, Fernando

    2012-01-01

    We describe a case of a 15-year-old girl who developed a spontaneous intracranial arterial dissection with distal middle cerebral artery (MCA) occlusions. From the digital subtraction angiography provided, the dissection flap appeared to originate at the internal carotid artery terminus with extension into the right M1 segment and occluding the right anterior cerebral artery, A1 segment. CT perfusion study showed salvageable tissue in the posterior MCA territory, including the motor cortex. In order to avoid further injury to the dissection, clot retrieval systems were not a treatment option. We therefore performed selective thrombus aspiration with the Penumbra system for the occluded central and precentral arteries distal to the non-occlusive dissecting lesion. Sufficient recanalization was achieved and the patient made a marked recovery. Although mechanical thrombectomy with the use of retrieval intracranial stent systems has demonstrated satisfactory recanalization rates, the aspiration methodology remains useful for patients with an accompanying proximal vascular lesion. PMID:23162036

  15. Temporary Strecker Stent for Management of Acute Dissection in Popliteal and Crural Arteries

    SciTech Connect

    Manke, Christoph; Geissler, Angela; Seitz, Johannes; Lenhart, Markus; Kasprzak, Piotr; Gmeinwieser, Josef; Feuerbach, Stefan

    1999-03-15

    Stent placement is a widely used bail-out treatment for dissection of peripheral arteries. Below the level of the superficial femoral artery permanent stenting is complicated by a high incidence of subacute thrombosis and restenosis. We present two cases of arterial occlusion due to acute iatrogenic dissection of the popliteal and distal fibular arteries. Successful treatment was achieved with a new bail-out procedure. Strecker stents were implanted to seal off the dissection flap. Stents were retrieved easily after 24 hr using a myocardial biopsy forceps. After stent retrieval the temporarily stented segments were patent and showed a larger lumen compared with segments treated by balloon dilatation alone. Temporary stenting is a simple and safe procedure and offers the advantage of tacking up dissection membranes and preventing recoil. Persistent presence of a metallic implant as a source of continued injury and stimulus for intimal proliferation is avoided.

  16. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

    E-print Network

    Kheradpour, Pouya

    Genome-wide chromatin annotations have permitted the mapping of putative regulatory elements across multiple human cell types. However, their experimental dissection by directed regulatory motif disruption has remained ...

  17. A historical perspective: infection from cadaveric dissection from the 18th to 20th centuries.

    PubMed

    Shoja, Mohammadali M; Benninger, Brion; Agutter, Paul; Loukas, Marios; Tubbs, R Shane

    2013-03-01

    Today, the study of human anatomy utilizing the ultimate study guide, the cadaver, is relatively safe. In the past, however, human dissection was dangerous. Prior to the germ theory, antibiotics, and the use of gloves, cadavers were often life threatening to dissectors including both the teacher and the student. Medical students who graduated in the United States before 1880 were unlikely to practice antisepsis in the dissecting room. In the present article, we review human cadaveric dissection in Europe and the United States primarily from the 1700s to the early 1900s in regard to its potential for transmission of infection to the dissector. A brief account of the infectious hazards of human cadavers in general and those of cadavers used for dissection in particular is given. PMID:23037893

  18. A case of anterior cerebral artery dissection caused by scuba diving.

    PubMed

    Fukuoka, Takuya; Kato, Yuji; Ohe, Yasuko; Deguchi, Ichiro; Maruyama, Hajime; Hayashi, Takeshi; Tanahashi, Norio

    2014-08-01

    A 51-year-old man was admitted with right hemiparesis during scuba diving, without headache. Brain magnetic resonance (MR) imaging depicted high-intensity areas in the left superior frontal and cingulate gyri on diffusion-weighted imaging. Dissection of the anterior cerebral artery (ACA) was detected using axial MR angiography and 3-dimensional MR cisternography. Dissection of the ACA during and after scuba diving has not been reported before. Dissection of the arteries should be included in the differential diagnosis when neurologic symptoms occur both during and after scuba diving, even if the patient does not experience headache. Furthermore, the combination of MR cisternography and MR angiography is useful to detect ACA dissection. PMID:24784014

  19. Cell type–specific channelrhodopsin-2 transgenic mice for optogenetic dissection of neural circuitry function

    E-print Network

    Zhao, Shengli

    Optogenetic methods have emerged as powerful tools for dissecting neural circuit connectivity, function and dysfunction. We used a bacterial artificial chromosome (BAC) transgenic strategy to express the H134R variant of ...

  20. Dissecting biological ``dark matter'' with single-cell genetic analysis of rare and uncultivated TM7

    E-print Network

    Quake, Stephen R.

    Dissecting biological ``dark matter'' with single-cell genetic analysis of rare and uncultivated TM of a microbial community. environmental microbiology metagenomics microfluidics single-cell analysis The earth

  1. Values, dissection, and school science: An inquiry into students' construction of meaning

    NASA Astrophysics Data System (ADS)

    Doster, Elizabeth Christina Tsamas

    The purpose of this study is to question how the values found in the secondary science curriculum, specifically those which are inherent in the dissection experience, relate to the personal values of individual students. Additionally, by exploring the human connection between science and science learning, the study questions the implications of this value relationship in students' assignment of meaning to the science. Participants were selected from four basic and intermediate level high school biology classrooms. The data collection methods include participant observation, in-depth student interviews, and videotaping. Analysis of data followed a constant-comparative methodology. Findings indicate students' perception of the dissection experience were contingent on the consistency (or lack thereof) of their personal value systems with the underlying factors found in each of four dimensions of dissection. These dimensions affect students to varying degrees, and many times their influences are overlapping. Taken together, the four dimensions create a multifaceted tool for viewing the dissection phenomenon. The first dimension concerns the moral issues prevalent in the minds of students as they reflect on dissection. The second dimension explores epistemological issues associated with dissection. The third explores the phenomenon of physical aversion to the dissection experience. The fourth dimension focuses on the issue of familiarity as it relates to dissection. Embedded in these four dimensions are degrees of agreement with seven beliefs inherent in the practice of dissection as an aspect of the biology curriculum: (1) killing of animals for the purpose of learning is a justifiable and acceptable behavior; (2) touching the dead body of an animal is a socially and culturally acceptable behavior; (3) the greater the similarity between the body of the animal and the human body, the greater the gains in understanding of human anatomy; (4) cutting apart, probing, and pinning is acceptable treatment of a dead animal's body; (5) the interaction of the students with dissection specimens will result in their gaining understanding of the structure and function of the animal's internal anatomical structures; (6) touching, seeing, or smelling the dead body of an animal is not offensive enough to prevent students from learning from it; and (7) dissection as an activity is independent of the experiences the students are familiar with, and how they interpret those experiences.

  2. Renal Infarction Caused by Spontaneous Renal Artery Dissection: Treatment with Catheter-Directed Thrombolysis and Stenting

    SciTech Connect

    Jeon, Yong Sun Cho, Soon Gu; Hong, Ki Cheon

    2009-03-15

    Spontaneous renal artery dissection (SRAD) is rare and presents a diagnostic and therapeutic challenge. We report a case of a 36-year-old man who had an SRAD-complicated renal infarction. The patient experienced severe unilateral flank pain. Enhanced abdominal computed axial tomography scan showed renal infarction, and urinalysis showed no hematuria. Selective renal angiography was essential to evaluate the extent of dissection and suitability for repair. The patient was treated with catheter-directed thrombolysis and frenal artery stenting.

  3. Prediction of Neck Dissection Requirement After Definitive Radiotherapy for Head-and-Neck Squamous Cell Carcinoma

    SciTech Connect

    Thariat, Juliette; Ahamad, Anesa; Williams, Michelle D.; Myers, Jeffrey N.; El-Naggar, Adel K.; Ginsberg, Lawrence E.; Rosenthal, David I.; Glisson, Bonnie S.; Weber, Randal S.; Garden, Adam S.

    2012-03-01

    Background: This analysis was undertaken to assess the need for planned neck dissection in patients with a complete response (CR) of involved nodes after irradiation and to determine the benefit of a neck dissection in those with less than CR by tumor site. Methods: Our cohort included 880 patients with T1-4, N1-3M0 squamous cell carcinoma of the oropharynx, larynx, or hypopharynx who received treatment between 1994 and 2004. Survival curves were calculated by the Kaplan-Meier Method, comparisons of rates with the log-rank test and prognostic factors by Cox's proportional hazard model. Results: Nodal CR occurred in 377 (43%) patients, of whom 365 patients did not undergo nodal dissection. The 5-year actuarial regional control rate of patients with CR was 92%. Two hundred sixty-eight of the remaining patients (53%) underwent neck dissections. The 5-year actuarial regional control rate for patients without a CR was 84%. Those who had a neck dissection fared better with 5-year actuarial regional control rates of 90% and 76% for those operated and those not operated (p < 0.001). Variables associated with poorer regional control rates included higher T and N stage, non-oropharynx cancers, non-CR, both clinical and pathological. Conclusions: With 92% 5-year neck control rate without neck dissection after CR, there is little justification for systematic neck dissection. The addition of a neck dissection resulted in higher neck control after partial response though patients with viable tumor on pathology specimens had poorer outcomes. The identification of that subgroup that benefits from additional treatment remains a challenge.

  4. Treatment of acute cervical internal carotid artery dissection using the Solitaire FR revascularization device.

    PubMed

    To, Chiu Yuen; Badr, Yaser; Richards, Boyd

    2012-01-01

    During treatment of a right internal carotid artery terminus aneurysm, an acute iatrogenic flow limiting dissection was caused in the cervical internal carotid. The true lumen was catheterized using a Mirage 0.008 microwire over an Excelsior SL-10 microcatheter, which was exchanged for a Marksman microcatheter. A 6 mm×30 mm Solitaire FR revascularization device was then deployed across the dissection as a salvage technique. PMID:23257942

  5. Treatment of acute cervical internal carotid artery dissection using the Solitaire FR revascularization device.

    PubMed

    To, Chiu Yuen; Badr, Yaser; Richards, Boyd

    2013-11-01

    During treatment of a right internal carotid artery terminus aneurysm, an acute iatrogenic flow limiting dissection was caused in the cervical internal carotid. The true lumen was catheterized using a Mirage 0.008 microwire over an Excelsior SL-10 microcatheter, which was exchanged for a Marksman microcatheter. A 6 mm × 30 mm Solitaire FR revascularization device was then deployed across the dissection as a salvage technique. PMID:23299103

  6. Prediction of Neck Dissection Requirement After Definitive Radiotherapy for Head and Neck Squamous Cell Carcinoma

    PubMed Central

    Thariat, Juliette; Ang, K. Kian; Allen, Pamela K.; Ahamad, Anesa; Williams, Michelle D.; Myers, Jeffrey N.; El-Naggar, Adel K.; Ginsberg, Lawrence E.; Rosenthal, David I.; Glisson, Bonnie S.; Morrison, William H.; Weber, Randal S.; Garden, Adam S.

    2014-01-01

    BACKGROUND This analysis was undertaken to assess the need for planned neck dissection in patients with a complete response (CR) of involved nodes after irradiation, and to determine the benefit of a neck dissection in those with less than CR by tumor site. METHODS Our cohort included 880 patients with T1-4, N1-3M0 squamous cell carcinoma of the oropharynx, larynx or hypopharynx who received treatment between 1994 and 2004. Survival curves were calculated by the Kaplan-Meier Method, comparisons of rates with the log-rank test and prognostic factors by Cox analyses. RESULTS Nodal CR occurred in 377 (43%) patients of whom 365 patients did not undergo nodal dissection. The 5-year actuarial regional control rate of patients with CR was 92%. Two hundred sixty-eight of the remaining patients (53%) underwent neck dissections. The 5-year actuarial regional control rate for patients without a CR was 84%. Those who had a neck dissection fared better with 5-year actuarial regional control rates of 90% and 76% for those operated and those not operated (p <.001). Variables associated with poorer regional control rates included higher T and N stage, non-oropharynx cancers, non-CR, both clinical and pathological. CONCLUSIONS With 92% 5-year neck control rate without neck dissection after CR, there is little justification for systematic neck dissection. The addition of a neck dissection resulted in higher neck control after partial response though patients with viable tumor on pathology specimens had poorer outcomes. The identification of that subgroup that benefits from additional treatment remains a challenge. PMID:22284033

  7. Ascending Aortic False Aneurysm Formation Associated with Rupture of Acute Type A Aortic Dissection

    PubMed Central

    Mukai, Shogo; Morimoto, Hironobu; Okubo, Shuhei

    2015-01-01

    A 63-year-old man with ruptured acute type A aortic dissection was referred to our hospital. Computed tomography showed a false aneurysm arising from the false lumen located beside the ascending aorta. His hemodynamic status was stable inspite of the ruptured acute aortic dissection. We consider that the containment of the false aneurysm by thin mediastinal structures prevented worsening of his hemodynamic status, and this is extremely rare. PMID:25848434

  8. A Population-Based Study of 30-day Incidence of Ischemic Stroke Following Surgical Neck Dissection

    PubMed Central

    MacNeil, S. Danielle; Liu, Kuan; Garg, Amit X.; Tam, Samantha; Palma, David; Thind, Amardeep; Winquist, Eric; Yoo, John; Nichols, Anthony; Fung, Kevin; Hall, Stephen; Shariff, Salimah Z.

    2015-01-01

    Abstract The objective of this study was to determine the 30-day incidence of ischemic stroke following neck dissection compared to matched patients undergoing non-head and neck surgeries. A surgical dissection of the neck is a common procedure performed for many types of cancer. Whether such dissections increase the risk of ischemic stroke is uncertain. A retrospective cohort study using data from linked administrative and registry databases (1995–2012) in the province of Ontario, Canada was performed. Patients were matched 1-to-1 on age, sex, date of surgery, and comorbidities to patients undergoing non-head and neck surgeries. The primary outcome was ischemic stroke assessed in hospitalized patients using validated database codes. A total of 14,837 patients underwent surgical neck dissection. The 30-day incidence of ischemic stroke following the dissection was 0.7%. This incidence decreased in recent years (1.1% in 1995 to 2000; 0.8% in 2001 to 2006; 0.3% in 2007 to 2012; P for trend <0.0001). The 30-day incidence of ischemic stroke in patients undergoing neck dissection is similar to matched patients undergoing thoracic surgery (0.5%, P?=?0.26) and colectomy (0.5%, P?=?0.1). Factors independently associated with a higher risk of stroke in 30 days following neck dissection surgery were of age ?75 years (odds ratio (OR) 1.63, 95% confidence interval (CI) 1.05–2.53), and a history of diabetes (OR 1.60, 95% CI 1.02–2.49), hypertension (OR 2.64, 95% CI 1.64–4.25), or prior stroke (OR 4.06, 95% CI 2.29–7.18). Less than 1% of patients undergoing surgical neck dissection will experience an ischemic stroke in the following 30 days. This incidence of stroke is similar to thoracic surgery and colectomy. PMID:26287406

  9. Malignant Middle Cerebral Artery Infarction Resulting from Dissection of Middle Cerebral Artery.

    PubMed

    Sakuta, Kenichi; Sengoku, Renpei; Mitsumura, Hidetaka; Kono, Yu; Kan, Issei; Kaku, Shogo; Iguchi, Yasuyuki

    2015-10-01

    A 30-year-old man presented with headache, left hemiparesis, and uncal herniation. Magnetic resonance imaging showed acute infarction in the right middle cerebral artery (MCA). Lifesaving craniotomy proceeded because of the uncal herniation. Assessment of brain tissue led to a diagnosis of MCA dissection. His skin biopsy showed ultrastructural abnormalities of dermal connective tissue. This is the unique case that dissection was diagnosed from both a biopsy specimen of the MCA and the dermal connective tissue. PMID:26279098

  10. Targeting cancer by binding iron: Dissecting cellular signaling pathways.

    PubMed

    Lui, Goldie Y L; Kovacevic, Zaklina; Richardson, Vera; Merlot, Angelica M; Kalinowski, Danuta S; Richardson, Des R

    2015-08-01

    Newer and more potent therapies are urgently needed to effectively treat advanced cancers that have developed resistance and metastasized. One such strategy is to target cancer cell iron metabolism, which is altered compared to normal cells and may facilitate their rapid proliferation. This is supported by studies reporting the anti-neoplastic activities of the clinically available iron chelators, desferrioxamine and deferasirox. More recently, ligands of the di-2-pyridylketone thiosemicarbazone (DpT) class have demonstrated potent and selective anti-proliferative activity across multiple cancer-types in vivo, fueling studies aimed at dissecting their molecular mechanisms of action. In the past five years alone, significant advances have been made in understanding how chelators not only modulate cellular iron metabolism, but also multiple signaling pathways implicated in tumor progression and metastasis. Herein, we discuss recent research on the targeting of iron in cancer cells, with a focus on the novel and potent DpT ligands. Several key studies have revealed that iron chelation can target the AKT, ERK, JNK, p38, STAT3, TGF-?, Wnt and autophagic pathways to subsequently inhibit cellular proliferation, the epithelial-mesenchymal transition (EMT) and metastasis. These developments emphasize that these novel therapies could be utilized clinically to effectively target cancer. PMID:26125440

  11. Genetic dissection of meiotic cytokinesis in Drosophila males.

    PubMed

    Giansanti, Maria Grazia; Farkas, Rebecca M; Bonaccorsi, Silvia; Lindsley, Dan L; Wakimoto, Barbara T; Fuller, Margaret T; Gatti, Maurizio

    2004-05-01

    We have used Drosophila male meiosis as a model system for genetic dissection of the cytokinesis mechanism. Drosophila mutants defective in meiotic cytokinesis can be easily identified by their multinucleate spermatids. Moreover, the large size of meiotic spindles allows characterization of mutant phenotypes with exquisite cytological resolution. We have screened a collection of 1955 homozygous mutant male sterile lines for those with multinucleate spermatids, and thereby identified mutations in 19 genes required for cytokinesis. These include 16 novel loci and three genes, diaphanous, four wheel drive, and pebble, already known to be involved in Drosophila cytokinesis. To define the primary defects leading to failure of cytokinesis, we analyzed meiotic divisions in male mutants for each of these 19 genes. Examination of preparations stained for tubulin, anillin, KLP3A, and F-actin revealed discrete defects in the components of the cytokinetic apparatus, suggesting that these genes act at four major points in a stepwise pathway for cytokinesis. Our results also indicated that the central spindle and the contractile ring are interdependent structures that interact throughout cytokinesis. Moreover, our genetic and cytological analyses provide further evidence for a cell type-specific control of Drosophila cytokinesis, suggesting that several genes required for meiotic cytokinesis in males are not required for mitotic cytokinesis. PMID:15004238

  12. DISSECTING OCD CIRCUITS: FROM ANIMAL MODELS TO TARGETED TREATMENTS.

    PubMed

    Ahmari, Susanne E; Dougherty, Darin D

    2015-08-01

    Obsessive-compulsive disorder (OCD) is a chronic, severe mental illness with up to 2-3% prevalence worldwide. In fact, OCD has been classified as one of the world's 10 leading causes of illness-related disability according to the World Health Organization, largely because of the chronic nature of disabling symptoms.([1]) Despite the severity and high prevalence of this chronic and disabling disorder, there is still relatively limited understanding of its pathophysiology. However, this is now rapidly changing due to development of powerful technologies that can be used to dissect the neural circuits underlying pathologic behaviors. In this article, we describe recent technical advances that have allowed neuroscientists to start identifying the circuits underlying complex repetitive behaviors using animal model systems. In addition, we review current surgical and stimulation-based treatments for OCD that target circuit dysfunction. Finally, we discuss how findings from animal models may be applied in the clinical arena to help inform and refine targeted brain stimulation-based treatment approaches. PMID:25952989

  13. Dissecting the matrilineal components of Tongjiang cattle from southwest China.

    PubMed

    Chen, Shi-Yi; Liu, Yi-Ping; Wang, Wei; Gao, Cheng-Zhong; Yao, Yong-Gang; Lai, Song-Jia

    2008-04-01

    Tongjiang cattle are a local cattle population of Sichuan Province, China, numbering approximately half a million in 2005. They have long been grouped into the Bashan breed, although they have a unique breeding history and phenotypic characteristics, as well as a restricted geographic distribution. Morphologically, they can be divided into two groups based on the basic coat color (black and russet). In order to dissect the matrilineal components of Tongjiang cattle and to compare the body size traits of the two morphological groups, we measured five body size traits among 59 Tongjiang cattle samples and further sequenced the mtDNA D-loop sequence of 54 individuals. Among the 54 mtDNAs, 37 (68.5%) were Bos taurus types and 17 (31.5%) were Bos indicus types. Four known B. taurus haplogroups (T1-T4) and one B. indicus haplogroup (I1) were detected in these samples. Two body size traits differed significantly (P < 0.05) between the black group and the russet group, although the two groups possessed similar matrilineal genetic structure. This is the first report to identify all four B. taurus haplogroups in one local Chinese cattle population. Our results suggest that the contribution of different matrilineal lineages to Chinese cattle might be more complex than we originally thought. PMID:18246422

  14. Dissecting the role of infections in atopic dermatitis.

    PubMed

    Biedermann, Tilo

    2006-01-01

    In patients with atopic dermatitis the skin is highly susceptible to infection by bacteria, fungi and viruses. Increasing knowledge about the complex immune network that regulates anti-microbial responses has helped to dissect further the role of infections in atopic dermatitis. Conserved patterns of microbes are recognized by the innate immune system, which mediates microbicidal activity, either directly or through inflammatory responses. New evidence suggests that components of the innate immune system, such as anti-microbial peptides, humoural lectins, nucleotide-binding oligomerization domain-containing (NOD) proteins, and Toll-like receptors not only protect from microbial invasion, but contribute to skin inflammation in atopic dermatitis. In addition, atopic patients tend to develop Th2-dominated immune responses that weaken anti-microbial immunity. This impairment of an appropriate anti-microbial defence compounded by amplified microbe-driven innate and adaptive immune responses leads to the vicious circle of skin inflammation. New microbial management in atopic dermatitis will foster a well-balanced microbial flora, which establishes natural defence mechanisms to maintain immuno-surveillance of the skin. In addition to anti-microbial therapies, other innate immune stimuli may suppress pro-inflammatory signals and help to break the vicious circle of cutaneous inflammation. To elucidate further these different interactions of the skin immune system and microbes in atopic dermatitis, clinical studies and further efforts in basic research are needed. PMID:16648910

  15. Targeting cancer by binding iron: Dissecting cellular signaling pathways

    PubMed Central

    Lui, Goldie Y.L.; Kovacevic, Zaklina; Richardson, Vera; Merlot, Angelica M.; Kalinowski, Danuta S.; Richardson, Des R.

    2015-01-01

    Newer and more potent therapies are urgently needed to effectively treat advanced cancers that have developed resistance and metastasized. One such strategy is to target cancer cell iron metabolism, which is altered compared to normal cells and may facilitate their rapid proliferation. This is supported by studies reporting the anti-neoplastic activities of the clinically available iron chelators, desferrioxamine and deferasirox. More recently, ligands of the di-2-pyridylketone thiosemicarbazone (DpT) class have demonstrated potent and selective anti-proliferative activity across multiple cancer-types in vivo, fueling studies aimed at dissecting their molecular mechanisms of action. In the past five years alone, significant advances have been made in understanding how chelators not only modulate cellular iron metabolism, but also multiple signaling pathways implicated in tumor progression and metastasis. Herein, we discuss recent research on the targeting of iron in cancer cells, with a focus on the novel and potent DpT ligands. Several key studies have revealed that iron chelation can target the AKT, ERK, JNK, p38, STAT3, TGF-?, Wnt and autophagic pathways to subsequently inhibit cellular proliferation, the epithelial-mesenchymal transition (EMT) and metastasis. These developments emphasize that these novel therapies could be utilized clinically to effectively target cancer. PMID:26125440

  16. Genetic Dissection of the Function of Hindbrain Axonal Commissures

    PubMed Central

    Renier, Nicolas; Schonewille, Martijn; Giraudet, Fabrice; Badura, Aleksandra; Tessier-Lavigne, Marc; Avan, Paul; De Zeeuw, Chris I.; Chédotal, Alain

    2010-01-01

    In Bilateria, many axons cross the midline of the central nervous system, forming well-defined commissures. Whereas in mammals the functions of commissures in the forebrain and in the visual system are well established, functions at other axial levels are less clearly understood. Here, we have dissected the function of several hindbrain commissures using genetic methods. By taking advantage of multiple Cre transgenic lines, we have induced site-specific deletions of the Robo3 receptor. These lines developed with the disruption of specific commissures in the sensory, motor, and sensorimotor systems, resulting in severe and permanent functional deficits. We show that mice with severely reduced commissures in rhombomeres 5 and 3 have abnormal lateral eye movements and auditory brainstem responses, respectively, whereas mice with a primarily uncrossed climbing fiber/Purkinje cell projection are strongly ataxic. Surprisingly, although rerouted axons remain ipsilateral, they still project to their appropriate neuronal targets. Moreover, some Cre;Robo3 lines represent potential models that can be used to study human syndromes, including horizontal gaze palsy with progressive scoliosis (HGPPS). To our knowledge, this study is one of the first to link defects in commissural axon guidance with specific cellular and behavioral phenotypes. PMID:20231872

  17. Dissecting Impulsivity and its Relationships to Drug Addictions

    PubMed Central

    Ashenhurst, James R.; Cervantes, M. Catalina; James, Alexander S.; Groman, Stephanie M.; Pennington, Zachary T.

    2015-01-01

    Addictions are often characterized as forms of impulsive behavior. That said, it is often noted that impulsivity is a multidimensional construct, spanning several psychological domains. This review describes the relationship between varieties of impulsivity and addiction-related behaviors, the nature of the causal relationship between the two and the underlying neurobiological mechanisms that promote impulsive behaviors. We conclude that the available data strongly supports the notion that impulsivity is both a risk factor for, and a consequence of, drug and alcohol consumption. While the evidence indicating that subtypes of impulsive behavior are uniquely informative – either biologically or with respect to their relationships to addictions – is convincing, multiple lines of study link “distinct” subtypes of impulsivity to low dopamine D2 receptor function and perturbed serotonergic transmission, revealing shared mechanisms between the subtypes. Therefore, a common biological framework involving monoaminergic transmitters in key frontostriatal circuits may link multiple forms of impulsivity to drug self-administration and addiction-related behaviors. Further dissection of these relationships is needed before the next phase of genetic and genomic discovery will be able to reveal the biological sources of the vulnerability for addiction indexed by impulsivity. PMID:24654857

  18. Polypoid leiomyosarcoma of the esophagus treated by endoscopic submucosal dissection.

    PubMed

    Yamamoto, Yoshinobu; Nishisaki, Hogara; Koma, Yu-ichiro; Sawai, Hiroaki; Sakai, Aya; Mimura, Takuya; Kushida, Saeko; Tsumura, Hidetaka; Sakamoto, Takeshi; Tobimatsu, Kazutoshi; Miki, Ikuya; Sakuma, Toshiko; Tsuda, Masahiro; Mano, Masayuki; Hirose, Takanori; Inokuchi, Hideto

    2015-09-01

    We report a rare case of polypoid leiomyosarcoma of the esophagus that was treated by endoscopic submucosal dissection (ESD). A 63-year-old man with complaints of progressive dysphagia was referred to Hyogo Cancer Center for treatment of esophageal tumor. Esophagoscopy revealed a polypoid tumor 25 mm in diameter on the left side of the upper esophagus. Despite several biopsy specimens, the diagnosis could not be confirmed. Computed tomography showed a protruded, homogeneously enhancing mass in the upper esophagus, but no lymph node enlargement or metastasis. After 1.5 months, the esophagogram showed a filling defect 47 mm in diameter in the upper esophagus. Given this rapid tumor growth, en bloc resection was done by ESD for therapeutic diagnosis. After this treatment, the tumor seemed to grow larger, showing a short stalk and occupying the esophageal lumen. Histopathologically, the tumor comprised pleomorphic spindle cells with mitosis. Tumor invasion involved the lumina propria mucosae and contact with the muscularis mucosae, but not involving the submucosa. Immunohistochemical examination showed positive staining for smooth muscle actin and HHF35, but negative for desmin, caldesmon, CD34, c-kit, DOG1, ALK, S-100 protein and cytokeratin. These histopathological findings were compatible with a diagnosis of esophageal leiomyosarcoma derived from the muscularis mucosae. PMID:25597630

  19. Prevention of esophageal strictures after endoscopic submucosal dissection

    PubMed Central

    Kobayashi, Shinichiro; Kanai, Nobuo; Ohki, Takeshi; Takagi, Ryo; Yamaguchi, Naoyuki; Isomoto, Hajime; Kasai, Yoshiyuki; Hosoi, Takahiro; Nakao, Kazuhiko; Eguchi, Susumu; Yamamoto, Masakazu; Yamato, Masayuki; Okano, Teruo

    2014-01-01

    Endoscopic mucosal resection (EMR) and endoscopic submucosal dissection (ESD) have recently been accepted as less invasive methods for treating patients with early esophageal cancers such as squamous cell carcinoma and dysplasia of Barrett’s esophagus. However, the large defects in the esophageal mucosa often cause severe esophageal strictures, which dramatically reduce the patient’s quality of life. Although preventive endoscopic balloon dilatation can reduce dysphagia and the frequency of dilatation, other approaches are necessary to prevent esophageal strictures after ESD. This review describes several strategies for preventing esophageal strictures after ESD, with a particular focus on anti-inflammatory and tissue engineering approaches. The local injection of triamcinolone acetonide and other systemic steroid therapies are frequently used to prevent esophageal strictures after ESD. Tissue engineering approaches for preventing esophageal strictures have recently been applied in basic research studies. Scaffolds with temporary stents have been applied in five cases, and this technique has been shown to be safe and is anticipated to prevent esophageal strictures. Fabricated autologous oral mucosal epithelial cell sheets to cover the defective mucosa similarly to how commercially available skin products fabricated from epidermal cells are used for skin defects or in cases of intractable ulcers. Fabricated autologous oral-mucosal-epithelial cell sheets have already been shown to be safe. PMID:25386058

  20. Interpolations of groundwater table elevation in dissected uplands.

    PubMed

    Chung, Jae-won; Rogers, J David

    2012-01-01

    The variable elevation of the groundwater table in the St. Louis area was estimated using multiple linear regression (MLR), ordinary kriging, and cokriging as part of a regional program seeking to assess liquefaction potential. Surface water features were used to determine the minimum water table for MLR and supplement the principal variables for ordinary kriging and cokriging. By evaluating the known depth to the water and the minimum water table elevation, the MLR analysis approximates the groundwater elevation for a contiguous hydrologic system. Ordinary kriging and cokriging estimate values in unsampled areas by calculating the spatial relationships between the unsampled and sampled locations. In this study, ordinary kriging did not incorporate topographic variations as an independent variable, while cokriging included topography as a supporting covariable. Cross validation suggests that cokriging provides a more reliable estimate at known data points with less uncertainty than the other methods. Profiles extending through the dissected uplands terrain suggest that: (1) the groundwater table generated by MLR mimics the ground surface and elicits a exaggerated interpolation of groundwater elevation; (2) the groundwater table estimated by ordinary kriging tends to ignore local topography and exhibits oversmoothing of the actual undulations in the water table; and (3) cokriging appears to give the realistic water surface, which rises and falls in proportion to the overlying topography. The authors concluded that cokriging provided the most realistic estimate of the groundwater surface, which is the key variable in assessing soil liquefaction potential in unconsolidated sediments. PMID:22107357

  1. Role of antisecretory agents for gastric endoscopic submucosal dissection.

    PubMed

    Fujishiro, Mitsuhiro; Chiu, Philip W Y; Wang, Hsui-Po

    2013-03-01

    Gastric endoscopic submucosal dissection (ESD) causes artificial gastric ulcers and there is no consensus regarding the optimal perioperative management in terms of prevention of intra- or postoperative bleeding and promotion of healing. Traditionally, 8-week administration of proton pump inhibitors (PPI) and mucosal protective agents were used in the same way as for peptic ulcer management. However, recent studies have revealed that prior use of PPI might reduce intraoperative bleeding or early-phase postoperative bleeding, and combination of histamine-2 receptor antagonist (H2RA), and second-look endoscopy might have a similar effect on postoperative bleeding to PPI. Additionally, the advantage of PPI over H2RA is not proven and the optimal duration of PPI may be shortened until 2 weeks when the deteriorating factors for ESD ulcer are excluded. Furthermore, mucosal protective agents may facilitate ulcer healing. Further studies are needed to determine the optimal treatment protocol before and after ESD for both prevention of bleeding complication and promotion of ulcer healing, by using available antisecretory agents and mucosal protective agents. PMID:23368844

  2. Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates

    PubMed Central

    Skerker, Jeffrey M; Leon, Dacia; Price, Morgan N; Mar, Jordan S; Tarjan, Daniel R; Wetmore, Kelly M; Deutschbauer, Adam M; Baumohl, Jason K; Bauer, Stefan; Ibáńez, Ana B; Mitchell, Valerie D; Wu, Cindy H; Hu, Ping; Hazen, Terry; Arkin, Adam P

    2013-01-01

    The efficient production of biofuels from cellulosic feedstocks will require the efficient fermentation of the sugars in hydrolyzed plant material. Unfortunately, plant hydrolysates also contain many compounds that inhibit microbial growth and fermentation. We used DNA-barcoded mutant libraries to identify genes that are important for hydrolysate tolerance in both Zymomonas mobilis (44 genes) and Saccharomyces cerevisiae (99 genes). Overexpression of a Z. mobilis tolerance gene of unknown function (ZMO1875) improved its specific ethanol productivity 2.4-fold in the presence of miscanthus hydrolysate. However, a mixture of 37 hydrolysate-derived inhibitors was not sufficient to explain the fitness profile of plant hydrolysate. To deconstruct the fitness profile of hydrolysate, we profiled the 37 inhibitors against a library of Z. mobilis mutants and we modeled fitness in hydrolysate as a mixture of fitness in its components. By examining outliers in this model, we identified methylglyoxal as a previously unknown component of hydrolysate. Our work provides a general strategy to dissect how microbes respond to a complex chemical stress and should enable further engineering of hydrolysate tolerance. PMID:23774757

  3. Dissecting ribosome assembly and transport in budding yeast.

    PubMed

    Altvater, Martin; Schütz, Sabina; Chang, Yiming; Panse, Vikram Govind

    2014-01-01

    Construction of the eukaryotic ribosome begins in the nucleolus and requires >300 evolutionarily conserved nonribosomal trans-acting factors, which transiently associate with preribosomal subunits at distinct assembly stages. A subset of trans-acting and transport factors passage assembled preribosomal subunits in a functionally inactive state through the nuclear pore complexes (NPC) into the cytoplasm, where they undergo final maturation before initiating translation. Here, we summarize the repertoire of tools developed in the model organism budding yeast that are spearheading the functional analyses of trans-acting factors involved in the assembly and intracellular transport of preribosomal subunits. We elaborate on different GFP-tagged ribosomal protein reporters and a pre-rRNA reporter that reliably monitors the movement of preribosomal particles from the nucleolus to cytoplasm. We discuss the powerful yeast heterokaryon assay, which can be employed to uncover shuttling trans-acting factors that need to accompany preribosomal subunits to the cytoplasm to be released prior to initiating translation. Moreover, we present two biochemical approaches, namely sucrose gradient analyses and tandem affinity purification, that are rapidly facilitating the uncovering of regulatory processes that control the compositional dynamics of trans-acting factors on maturing preribosomal particles. Altogether, these approaches when combined with traditional analytical biochemistry, targeted proteomics and structural methodologies, will contribute to the dissection of the assembly and intracellular transport of preribosomal subunits, as well as other macromolecular assemblies that influence diverse biological pathways. PMID:24857742

  4. Pulse energy dependence of subcellular dissection by femtosecond laser pulses

    NASA Technical Reports Server (NTRS)

    Heisterkamp, A.; Maxwell, I. Z.; Mazur, E.; Underwood, J. M.; Nickerson, J. A.; Kumar, S.; Ingber, D. E.

    2005-01-01

    Precise dissection of cells with ultrashort laser pulses requires a clear understanding of how the onset and extent of ablation (i.e., the removal of material) depends on pulse energy. We carried out a systematic study of the energy dependence of the plasma-mediated ablation of fluorescently-labeled subcellular structures in the cytoskeleton and nuclei of fixed endothelial cells using femtosecond, near-infrared laser pulses focused through a high-numerical aperture objective lens (1.4 NA). We find that the energy threshold for photobleaching lies between 0.9 and 1.7 nJ. By comparing the changes in fluorescence with the actual material loss determined by electron microscopy, we find that the threshold for true material ablation is about 20% higher than the photobleaching threshold. This information makes it possible to use the fluorescence to determine the onset of true material ablation without resorting to electron microscopy. We confirm the precision of this technique by severing a single microtubule without disrupting the neighboring microtubules, less than 1 micrometer away. c2005 Optical Society of America.

  5. Spontaneous coronary artery dissection: a case series and literature review

    PubMed Central

    Garcia, Nelson A. Telles; Khan, Abul N.; Boppana, Ratna C.; Smith, Hayden L.

    2014-01-01

    Spontaneous coronary artery dissection (SCAD) is a rare and often lethal cause of acute coronary syndrome, which typically affects young women and otherwise healthy individuals. SCAD can be diagnosed in patients undergoing coronary angiography and can be underestimated. Special techniques such as optical coherence tomography (OCT) and intravascular ultrasound should be used when there is suspicion of the condition. In the majority of cases, the left anterior descending (LAD) artery is involved; however, a few cases of the right coronary artery (RCA) involvement have been reported. This article describes three cases of SCAD in women of different ages, all presenting with chest pain. Coronary angiography in conjunction with OCT was used for diagnosis in two of the cases. One of the patients had involvement of the proximal RCA and underwent percutaneous coronary intervention, whereas the other two patients had mid-LAD disease and were treated conservatively with medical therapy. Presently, there are no specific guidelines for the treatment of SCAD, and therapy is individualized according to extent and severity of the condition. PMID:25317273

  6. Spontaneous isolated dissection at renal upper abdominal aortic: a rare case report

    PubMed Central

    Liu, Jian-Ping; Liu, Feng-En; Duan, Qing; Ye, Rong; Xiao, Jun-Qi

    2015-01-01

    Arterial dissection is defined as a cleavage of the arterial wall caused by intramural hematoma. Isolated extra-aortic arterial dissection has been reported in renal and carotid arteries in few literatures but suprarenal aorta dissection associated with retrograde formation of a giant descending thoracic aneurysm is considered very rare. We present a quite unusual case of suprarenal aorta dissection associated with retrograde formation of a giant descending thoracic aneurysm sparing both renal and mesenteric vessels, without any branch vessel involvement or visceral damage. Because of the patient’s persistent epigastric pain, endovascular celiac artery stent implantation was performed with 3 multiple overlapping uncovered stents. Twelve months after the procedure, computed tomographic angiography (CTA) of the abdomen showed patency of both celiac stents with thrombus formation in the retrograde dissection sac, and the patient remained asymptomatic. This case and others in the medical literature suggest that endovascular treatment can be feasible in symptomatic patients with spontaneous isolated dissection at renal upper abdominal aortic. PMID:26221391

  7. Indication of endovascular treatment of type B aortic dissection--literature review.

    PubMed

    Duarte, Joăo Jackson; Pontes, José Carlos Dorsa Vieira; Benfatti, Ricardo Adala; Ferrachini, Adriana Lugo; Karakhanian, Walter Kegham; Razuk Filho, Alvaro

    2014-01-01

    Aortic dissection is a cardiovascular event of high mortality if not early diagnosed and properly treated. In Stanford type A aortic dissection, there is the involvement of the ascending aorta, whereas in type B the ascending aorta is not affected. The treatment of type A aortic dissection is mainly surgical. The hospital mortality of type B aortic dissection surgical treatment is approximately 20%, while medical therapy is 10%. However, half the patients who are discharged from hospital after medical treatment, progress to aortic complications in the following years, and the mortality in three to five years may reach 25-50%. In addition, the surgical treatment of aortic complications after medical treatment, has also a significant mortality. This way, the endovascular treatment comes up as an interesting alternative of a less invasive treatment for this disease. They presented a mortality rate lower than 10% with more than 80% success rate of occlusion and thrombosis of the false lumen. The INSTEAD TRIAL, which randomized patients with uncomplicated type B aortic dissection for optimal medical therapy and endovascular treatment in addition to optimal medical therapy, showed that after three years of follow up, patients who underwent endovascular treatment had lower mortality and aorta-related complications. Therefore, there is a current tendency to recommend the endovascular treatment as a standard for the treatment of type B aortic dissection. PMID:25372915

  8. Indication of endovascular treatment of type B aortic dissection - Literature review

    PubMed Central

    Duarte, Joăo Jackson; Pontes, José Carlos Dorsa Vieira; Benfatti, Ricardo Adala; Ferrachini, Adriana Lugo; Karakhanian, Walter Kegham; Razuk Filho, Álvaro

    2014-01-01

    Aortic dissection is a cardiovascular event of high mortality if not early diagnosed and properly treated. In Stanford type A aortic dissection, there is the involvement of the ascending aorta, whereas in type B the ascending aorta is not affected. The treatment of type A aortic dissection is mainly surgical. The hospital mortality of type B aortic dissection surgical treatment is approximately 20%, while medical therapy is 10%. However, half the patients who are discharged from hospital after medical treatment, progress to aortic complications in the following years, and the mortality in three to five years may reach 25-50%. In addition, the surgical treatment of aortic complications after medical treatment, has also a significant mortality. This way, the endovascular treatment comes up as an interesting alternative of a less invasive treatment for this disease. They presented a mortality rate lower than 10% with more than 80% success rate of occlusion and thrombosis of the false lumen. The INSTEAD TRIAL, which randomized patients with uncomplicated type B aortic dissection for optimal medical therapy and endovascular treatment in addition to optimal medical therapy, showed that after three years of follow up, patients who underwent endovascular treatment had lower mortality and aorta-related complications. Therefore, there is a current tendency to recommend the endovascular treatment as a standard for the treatment of type B aortic dissection PMID:25372915

  9. Efficacy and Optimal Timing of Endovascular Treatment for Type B Aortic Dissection

    PubMed Central

    Kinoshita, Hajime; Fujimoto, Eiki; Arase, Hiroki; Kurobe, Hirotsugu; Chikugo, Fumio; Sogabe, Hitoshi; Kitaichi, Takashi

    2015-01-01

    Objectives: To determine the efficacy and the optimal timing of thoracic endovascular aortic repair (TEVAR) for closing the primary entry in uncomplicated patients with chronic type B aortic dissection and a patent false lumen (FL). Methods: Thirteen patients underwent TEVAR for aortic dissection between 2008 and 2012. These patients had chronic dissection with a patent FL and expansion of the aorta. Early TEVAR was performed for five patients within 1–7 months from the index dissection (TEVAR-EC group) and delayed TEVAR was performed for eight patients within 1–16 years (TEVAR-DC group). Changes in the diameters and volumes of the true lumen (TL) and FL and the aortic remodeling were assessed by multidetector computed tomography for 3 years after TEVAR. Results: The reduction rate of FL in the thoracic aorta was notably higher in the TEVAR-EC group than in the TEVAR-DC group regardless of the presence or absence of distal retrograde flow. There was a significant TL expansion despite different timings of TEVAR. Conclusions: Early TEVAR resulted in good prognosis and preferable aortic remodeling in uncomplicated patients with chronic type B aortic dissection and a patent FL, and we recommend early TEVAR within seven months after the index dissection.

  10. Quantitative Finance CONTACT INFORMATION

    E-print Network

    Arnold, Elizabeth A.

    Quantitative Finance CONTACT INFORMATION Pamela Peterson Drake, PhD Department Head, Finance of Finance College of Business ZSH 325 (540) 568-8107 finkjd@jmu.edu Michelle Duncan, Advisor Academic Services Center College of Business ZSH 205 (540) 568-3078 duncanml@jmu.edu What is a quantitative finance

  11. Dissecting gene expression at the blood-brain barrier

    PubMed Central

    Huntley, Melanie A.; Bien-Ly, Nga; Daneman, Richard; Watts, Ryan J.

    2014-01-01

    The availability of genome-wide expression data for the blood-brain barrier is an invaluable resource that has recently enabled the discovery of several genes and pathways involved in the development and maintenance of the blood-brain barrier, particularly in rodent models. The broad distribution of published data sets represents a viable starting point for the molecular dissection of the blood-brain barrier and will further direct the discovery of novel mechanisms of blood-brain barrier formation and function. Technical advances in purifying brain endothelial cells, the key cell that forms the critical barrier, have allowed for greater specificity in gene expression comparisons with other central nervous system cell types, and more systematic characterizations of the molecular composition of the blood-brain barrier. Nevertheless, our understanding of how the blood-brain barrier changes during aging and disease is underrepresented. Blood-brain barrier data sets from a wider range of experimental paradigms and species, including invertebrates and primates, would be invaluable for investigating the function and evolution of the blood-brain barrier. Newer technologies in gene expression profiling, such as RNA-sequencing, now allow for finer resolution of transcriptomic changes, including isoform specificity and RNA-editing. As our field continues to utilize more advanced expression profiling in its ongoing efforts to elucidate the blood-brain barrier, including in disease and drug delivery, we will continue to see rapid advances in our understanding of the molecular mediators of barrier biology. We predict that the recently published data sets, combined with forthcoming genomic and proteomic blood-brain barrier data sets, will continue to fuel the molecular genetic revolution of blood-brain barrier biology. PMID:25414634

  12. Genetic dissection of the Down syndrome critical region.

    PubMed

    Jiang, Xiaoling; Liu, Chunhong; Yu, Tao; Zhang, Li; Meng, Kai; Xing, Zhuo; Belichenko, Pavel V; Kleschevnikov, Alexander M; Pao, Annie; Peresie, Jennifer; Wie, Sarah; Mobley, William C; Yu, Y Eugene

    2015-11-15

    Down syndrome (DS), caused by trisomy 21, is the most common chromosomal disorder associated with developmental cognitive deficits. Despite intensive efforts, the genetic mechanisms underlying developmental cognitive deficits remain poorly understood, and no treatment has been proven effective. The previous mouse-based experiments suggest that the so-called Down syndrome critical region of human chromosome 21 is an important region for this phenotype, which is demarcated by Setd4/Cbr1 and Fam3b/Mx2. We first confirmed the importance of the Cbr1-Fam3b region using compound mutant mice, which carry a duplication spanning the entire human chromosome 21 orthologous region on mouse chromosome 16 [Dp(16)1Yey] and Ms1Rhr. By dividing the Setd4-Mx2 region into complementary Setd4-Kcnj6 and Kcnj15-Mx2 intervals, we started an unbiased dissection through generating and analyzing Dp(16)1Yey/Df(16Setd4-Kcnj6)Yey and Dp(16)1Yey/Df(16Kcnj15-Mx2)Yey mice. Surprisingly, the Dp(16)1Yey-associated cognitive phenotypes were not rescued by either deletion in the compound mutants, suggesting the possible presence of at least one causative gene in each of the two regions. The partial rescue by a Dyrk1a mutation in a compound mutant carrying Dp(16)1Yey and the Dyrk1a mutation confirmed the causative role of Dyrk1a, whereas the absence of a similar rescue by Df(16Dyrk1a-Kcnj6)Yey in Dp(16)1Yey/Df(16Dyrk1a-Kcnj6)Yey mice demonstrated the importance of Kcnj6. Our results revealed the high levels of complexities of gene actions and interactions associated with the Setd4/Cbr1-Fam3b/Mx2 region as well as their relationship with developmental cognitive deficits in DS. PMID:26374847

  13. Dissecting the Transcriptional Response to Elicitors in Vitis vinifera Cells

    PubMed Central

    Belchí-Navarro, Sarai; Bru, Roque; Martínez-Zapater, José M.; Lijavetzky, Diego; Pedreńo, María A.

    2014-01-01

    The high effectiveness of cyclic oligosaccharides like cyclodextrins in the production of trans-resveratrol in Vitis vinifera cell cultures is enhanced in the presence of methyl jasmonate. In order to dissect the basis of the interactions among the elicitation responses triggered by these two compounds, a transcriptional analysis of grapevine cell cultures treated with cyclodextrins and methyl jasmonate separately or in combination was carried out. The results showed that the activation of genes encoding enzymes from phenylpropanoid and stilbene biosynthesis induced by cyclodextrins alone was partially enhanced in the presence of methyl jasmonate, which correlated with their effects on trans-resveratrol production. In addition, protein translation and cell cycle regulation were more highly repressed in cells treated with cyclodextrins than in those treated with methyl jasmonate, and this response was enhanced in the combined treatment. Ethylene signalling was activated by all treatments, while jasmonate signalling and salicylic acid conjugation were activated only in the presence of methyl jasmonate and cyclodextrins, respectively. Moreover, the combined treatment resulted in a crosstalk between the signalling cascades activated by cyclodextrins and methyl jasmonate, which, in turn, provoked the activation of additional regulatory pathways involving the up-regulation of MYB15, NAC and WRKY transcription factors, protein kinases and calcium signal transducers. All these results suggest that both elicitors cause an activation of the secondary metabolism in detriment of basic cell processes like the primary metabolism or cell division. Crosstalk between cyclodextrins and methyl jasmonate-induced signalling provokes an intensification of these responses resulting in a greater trans-resveratrol production. PMID:25314001

  14. Advances in sentinel node dissection in prostate cancer from a technical perspective.

    PubMed

    Acar, Cenk; Kleinjan, Gijs H; van den Berg, Nynke S; Wit, Esther Mk; van Leeuwen, Fijs Wb; van der Poel, Henk G

    2015-10-01

    The most important feature of sentinel node biopsy for prostate cancer procedure is that staging can be improved. Sentinel nodes might be found outside the extended pelvic lymph node dissection template what renders the sentinel node additive of extended pelvic lymph node dissection. At the same time, staging within the template can be further refined. We reviewed the literature regarding the sentinel node biopsy procedure for prostate cancer. PubMed and Embase were searched for all English-language publications from January 1999 to September 2014 by using the keywords as "prostate cancer" and "sentinel lymph node" plus "biopsy" "dissection" and/or "procedure." The present review discusses step-by-step sentinel node biopsy for prostate cancer. Topics of discussion are: (i) preoperative sentinel node mapping (tracers and imaging); (ii) intraoperative sentinel node identification (surgical procedure and outcome); and (iii) novelties to improve sentinel node identification (pre- and intraoperative approaches). Conventional sentinel node mapping is carried out after the injection of a (99m) Tc-based tracer and subsequent preoperative imaging; for example, lymphoscintigraphy and single-photon emission computed tomography/computed tomography. This approach allowed the detection of sentinel nodes outside the extended lymph node dissection template in 3.6-36% of men with intermediate- and high-risk prostate cancer. Hereby, an overall false negative rate of sentinel nodes was reported between 0% and 24.4%. To further refine the intraoperative sampling procedure, novel imaging methods such as fluorescence imaging have been introduced. Prospective randomized comparison studies are required to confirm the added benefit of sentinel template directed nodal dissection. A proper and obtainable end-point of such a study could be the number of removed positive nodes for carrying out nodal dissection with or without sentinel template directed dissection. Similarly, the clinical impact of novel imaging technologies requires further investigation. PMID:26173593

  15. Is Planned Neck Dissection Necessary for Head and Neck Cancer After Intensity-Modulated Radiotherapy?

    SciTech Connect

    Yao Min |. E-mail: min-yao@uiowa.edu; Hoffman, Henry T.; Funk, Gerry F. |; Chang, Kristi; Smith, Russell B. |; Tan Huaming; Clamon, Gerald H.; Dornfeld, Ken |; Buatti, John M. |

    2007-07-01

    Purpose: The objective of this study was to determine regional control of local regional advanced head and neck squamous cell carcinoma (HNSCC) treated with intensity-modulated radiotherapy (IMRT), along with the role and selection criteria for neck dissection after IMRT. Methods and Materials: A total of 90 patients with stage N2A or greater HNSCC were treated with definitive IMRT from December 1999 to July 2005. Three clinical target volumes were defined and were treated to 70 to 74 Gy, 60 Gy, and 54 Gy, respectively. Neck dissection was performed for selected patients after IMRT. Selection criteria evolved during this period with emphasis on post-IMRT [{sup 18}F] fluorodeoxyglucose positron emission tomography in recent years. Results: Median follow-up for all patients was 29 months (range, 0.2-74 months). All living patients were followed at least 9 months after completing treatment. Thirteen patients underwent neck dissection after IMRT because of residual lymphadenopathy. Of these, 6 contained residual viable tumor. Three patients with persistent adenopathy did not undergo neck dissection: 2 refused and 1 had lung metastasis. Among the remaining 74 patients who were observed without neck dissection, there was only 1 case of regional failure. Among all 90 patients in this study, the 3-year local and regional control was 96.3% and 95.4%, respectively. Conclusions: Appropriately delivered IMRT has excellent dose coverage for cervical lymph nodes. A high radiation dose can be safely delivered to the abnormal lymph nodes. There is a high complete response rate. Routine planned neck dissection for patients with N2A and higher stage after IMRT is not necessary. Post-IMRT [{sup 18}F] fluorodeoxyglucose positron emission tomography is a useful tool in selecting patients appropriate for neck dissection.

  16. Aortic dissection presenting as acute subtotal left main coronary artery occlusion: a case approach and review of the literature.

    PubMed

    Ruisi, Michael; Fallahi, Arzhang; Lala, Moinakhtar; Kanei, Yumiko

    2015-05-01

    Aortic dissection is the most common fatal condition of the aorta, yet it is often missed on initial clinical presentation. Aortic dissection associated with acute coronary syndrome (ACS) is relatively rare, but if it occurs, it can be diagnostically challenging, and the condition can be fatal. Here we describe a case of aortic dissection presenting as ST-segment elevation myocardial infarction (STEMI) managed via the transradial approach. We describe the current literature on the subject. PMID:25780485

  17. Aortic Dissection Presenting as Acute Subtotal Left Main Coronary Artery Occlusion: A Case Approach and Review of the Literature

    PubMed Central

    Ruisi, Michael; Fallahi, Arzhang; Lala, Moinakhtar; Kanei, Yumiko

    2015-01-01

    Aortic dissection is the most common fatal condition of the aorta, yet it is often missed on initial clinical presentation. Aortic dissection associated with acute coronary syndrome (ACS) is relatively rare, but if it occurs, it can be diagnostically challenging, and the condition can be fatal. Here we describe a case of aortic dissection presenting as ST-segment elevation myocardial infarction (STEMI) managed via the transradial approach. We describe the current literature on the subject. PMID:25780485

  18. Quantitative RT-PCR gene expression analysis of laser microdissected tissue samples

    PubMed Central

    Erickson, Heidi S.; Albert, Paul S.; Gillespie, John W.; Rodriguez-Canales, Jaime; Linehan, W. Marston; Pinto, Peter A.; Chuaqui, Rodrigo F.; Emmert-Buck, Michael R.

    2009-01-01

    Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a valuable tool for measuring gene expression in biological samples. However, unique challenges are encountered when studies are performed on cells microdissected from tissues derived from animal models or the clinic, including specimen related issues, variability of RNA template quality and quantity, and normalization. qRT-PCR using small amounts of mRNA derived from dissected cell populations requires adaptation of standard methods to allow meaningful comparisons across sample sets. The protocol described here presents the rationale, technical steps, normalization strategy, and data analysis necessary to generate reliable gene expression measurements of transcripts from dissected samples. The entire protocol from tissue microdissection through qRT-PCR analysis requires approximately 16 hours. PMID:19478806

  19. Endovascular coil trapping of a ruptured dissecting aneurysm of the vertebral artery using detachable coils and micro-tornado® coils.

    PubMed

    Kim, Myeong-Soo

    2013-06-01

    We experienced a patient with a ruptured dissecting aneurysm of the vertebral artery who was treated by trapping of the lesion using Guglielmi detachable coils (GDCs) with micro-tornado® coils (MTCs). An 80-year-old male was transferred with a ruptured left vertebral artery dissecting aneurysm (VADA). The dissected portion of the vertebral artery was effectively trapped using GDCs and MTCs. The MTCs used for neurointervention were comprised of various types of coils and we successfully placed them into the parent artery of the dissected segment. The author suggests that this case demonstrates the usefulness of endovascular coil trapping of VADAs using MTCs in achievement of embolization. PMID:23844353

  20. Phosphoproteomic Profiling Reveals Epstein-Barr Virus Protein Kinase Integration of DNA Damage Response and Mitotic Signaling.

    PubMed

    Li, Renfeng; Liao, Gangling; Nirujogi, Raja Sekhar; Pinto, Sneha M; Shaw, Patrick G; Huang, Tai-Chung; Wan, Jun; Qian, Jiang; Gowda, Harsha; Wu, Xinyan; Lv, Dong-Wen; Zhang, Kun; Manda, Srikanth S; Pandey, Akhilesh; Hayward, S Diane

    2015-12-01

    Epstein-Barr virus (EBV) is etiologically linked to infectious mononucleosis and several human cancers. EBV encodes a conserved protein kinase BGLF4 that plays a key role in the viral life cycle. To provide new insight into the host proteins regulated by BGLF4, we utilized stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics to compare site-specific phosphorylation in BGLF4-expressing Akata B cells. Our analysis revealed BGLF4-mediated hyperphosphorylation of 3,046 unique sites corresponding to 1,328 proteins. Frequency analysis of these phosphosites revealed a proline-rich motif signature downstream of BGLF4, indicating a broader substrate recognition for BGLF4 than its cellular ortholog cyclin-dependent kinase 1 (CDK1). Further, motif analysis of the hyperphosphorylated sites revealed enrichment in ATM, ATR and Aurora kinase substrates while functional analyses revealed significant enrichment of pathways related to the DNA damage response (DDR), mitosis and cell cycle. Phosphorylation of proteins associated with the mitotic spindle assembly checkpoint (SAC) indicated checkpoint activation, an event that inactivates the anaphase promoting complex/cyclosome, APC/C. Furthermore, we demonstrated that BGLF4 binds to and directly phosphorylates the key cellular proteins PP1, MPS1 and CDC20 that lie upstream of SAC activation and APC/C inhibition. Consistent with APC/C inactivation, we found that BGLF4 stabilizes the expression of many known APC/C substrates. We also noted hyperphosphorylation of 22 proteins associated the nuclear pore complex, which may contribute to nuclear pore disassembly and SAC activation. A drug that inhibits mitotic checkpoint activation also suppressed the accumulation of extracellular EBV virus. Taken together, our data reveal that, in addition to the DDR, manipulation of mitotic kinase signaling and SAC activation are mechanisms associated with lytic EBV replication. All MS data have been deposited in the ProteomeXchange with identifier PXD002411 (http://proteomecentral.proteomexchange.org/dataset/PXD002411). PMID:26714015

  1. Sources of Technical Variability in Quantitative LC-MS Proteomics: Human Brain Tissue Sample Analysis.

    SciTech Connect

    Piehowski, Paul D.; Petyuk, Vladislav A.; Orton, Daniel J.; Xie, Fang; Moore, Ronald J.; Ramirez Restrepo, Manuel; Engel, Anzhelika; Lieberman, Andrew P.; Albin, Roger L.; Camp, David G.; Smith, Richard D.; Myers, Amanda J.

    2013-05-03

    To design a robust quantitative proteomics study, an understanding of both the inherent heterogeneity of the biological samples being studied as well as the technical variability of the proteomics methods and platform is needed. Additionally, accurately identifying the technical steps associated with the largest variability would provide valuable information for the improvement and design of future processing pipelines. We present an experimental strategy that allows for a detailed examination of the variability of the quantitative LC-MS proteomics measurements. By replicating analyses at different stages of processing, various technical components can be estimated and their individual contribution to technical variability can be dissected. This design can be easily adapted to other quantitative proteomics pipelines. Herein, we applied this methodology to our label-free workflow for the processing of human brain tissue. For this application, the pipeline was divided into four critical components: Tissue dissection and homogenization (extraction), protein denaturation followed by trypsin digestion and SPE clean-up (digestion), short-term run-to-run instrumental response fluctuation (instrumental variance), and long-term drift of the quantitative response of the LC-MS/MS platform over the 2 week period of continuous analysis (instrumental stability). From this analysis, we found the following contributions to variability: extraction (72%) >> instrumental variance (16%) > instrumental stability (8.4%) > digestion (3.1%). Furthermore, the stability of the platform and its’ suitability for discovery proteomics studies is demonstrated.

  2. The Quantitative Methods Boot Camp: Teaching Quantitative Thinking and

    E-print Network

    Born, Richard

    biological systems. The boot camp teaches basic programming using biological examples from statistics, image processing, and data analysis. This integrative approach to teaching programming and quantitative reasoningEDUCATION The Quantitative Methods Boot Camp: Teaching Quantitative Thinking and Computing Skills

  3. Outcome of Frozen Elephant Trunk Technique for Acute Type A Aortic Dissection

    PubMed Central

    Lin, Hui-Han; Liao, Shou-Fu; Wu, Ching-Feng; Li, Ping-Chun; Li, Ming-Li

    2015-01-01

    Abstract Acute aortic dissections of Stanford type A require emergency surgery repair and present challenges to surgeons. The frozen elephant technique is one of several approaches used to treat aortic arch dissection. The purpose of this meta-analysis was to investigate the clinical effectiveness of the frozen elephant technique for treating acute type A aortic dissection. Medline, Cochrane, Google Scholar, and ClinicalTrials.gov databases were searched up to March 31, 2014, for studies that assessed the use of frozen elephant trunk technique for treating acute type A aortic dissection. The primary outcome was in-hospital mortality. Secondary outcomes included rate of stroke, spinal cord injury, renal failure, and reoperations for bleeding. Eleven studies were included in the analysis that encompassed 881 patients. The mean age ranged from 45.4 to 66.8 years, and the proportion of the population that was male ranged from 45 to 85%. The overall in-hospital mortality rate was 8%. The rate of stroke, spinal cord injury, renal failure, and frequency of reoperations for bleeding were 3, 4, 5, and 5, respectively. Sensitivity analysis indicates that the findings are robust and there was no publication bias. These findings indicate that the frozen elephant techniques does not bring unacceptable mortality or morbidity risk for treating acute type A aortic dissection. PMID:25906096

  4. Dissecting the mechanisms of squirrel monkey (Saimiri boliviensis) social learning

    PubMed Central

    Holmes, AN; Williams, LE; Brosnan, SF

    2013-01-01

    Although the social learning abilities of monkeys have been well documented, this research has only focused on a few species. Furthermore, of those that also incorporated dissections of social learning mechanisms, the majority studied either capuchins (Cebus apella) or marmosets (Callithrix jacchus). To gain a broader understanding of how monkeys gain new skills, we tested squirrel monkeys (Saimiri boliviensis) which have never been studied in tests of social learning mechanisms. To determine whether S. boliviensis can socially learn, we ran “open diffusion” tests with monkeys housed in two social groups (N = 23). Over the course of 10 20-min sessions, the monkeys in each group observed a trained group member retrieving a mealworm from a bidirectional task (the “Slide-box”). Two thirds (67%) of these monkeys both learned how to operate the Slide-box and they also moved the door significantly more times in the direction modeled by the trained demonstrator than the alternative direction. To tease apart the underlying social learning mechanisms we ran a series of three control conditions with 35 squirrel monkeys that had no previous experience with the Slide-box. The first replicated the experimental open diffusion sessions but without the inclusion of a trained model, the second was a no-information control with dyads of monkeys, and the third was a ‘ghost’ display shown to individual monkeys. The first two controls tested for the importance of social support (mere presence effect) and the ghost display showed the affordances of the task to the monkeys. The monkeys showed a certain level of success in the group control (54% of subjects solved the task on one or more occasions) and paired controls (28% were successful) but none were successful in the ghost control. We propose that the squirrel monkeys’ learning, observed in the experimental open diffusion tests, can be best described by a combination of social learning mechanisms in concert; in this case, those mechanisms are most likely object movement reenactment and social facilitation. We discuss the interplay of these mechanisms and how they related to learning shown by other primate species. PMID:23638347

  5. On Quantitative Rorschach Scales.

    ERIC Educational Resources Information Center

    Haggard, Ernest A.

    1978-01-01

    Two types of quantitative Rorschach scales are discussed: first, those based on the response categories of content, location, and the determinants, and second, global scales based on the subject's responses to all ten stimulus cards. (Author/JKS)

  6. Quantitative film radiography

    SciTech Connect

    Devine, G.; Dobie, D.; Fugina, J.; Hernandez, J.; Logan, C.; Mohr, P.; Moss, R.; Schumacher, B.; Updike, E.; Weirup, D.

    1991-02-26

    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 discernible 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 pseudo-color images in units of density. We characterize approximately 10,000 parts per year in hundreds of different configurations and compositions with this system. This report discusses: the method; film processor monitoring and control; verifying film and processor performance; and correction of scatter effects.

  7. Quantitative Imaging Network

    Cancer.gov

    The QIN Imaging Network is designed to promote research and development of quantitative imaging methods for the measurement of tumor response to therapies in clinical trial settings, with the overall goal of facilitating clinical decision-making. The

  8. Quantitative receptor autoradiography

    SciTech Connect

    Boast, C.A.; Snowhill, E.W.; Altar, C.A.

    1986-01-01

    Quantitative receptor autoradiography addresses the topic of technical and scientific advances in the sphere of quantitative autoradiography. The volume opens with a overview of the field from a historical and critical perspective. Following is a detailed discussion of in vitro data obtained from a variety of neurotransmitter systems. The next section explores applications of autoradiography, and the final two chapters consider experimental models. Methodological considerations are emphasized, including the use of computers for image analysis.

  9. Quantitative enantioselective Raman spectroscopy.

    PubMed

    Kiefer, J

    2015-08-01

    Analytical methods for quantitative enantioselective measurements are highly desirable in the life sciences. Existing technologies have disadvantages such as limited temporal resolution, the need for molecular labeling, or high experimental complexity. To overcome these limitations, this work presents a method based on conventional Raman spectroscopy. A systematic investigation of the key parameters is carried out. It is demonstrated that their careful choice provides an opportunity for enantioselective and quantitative analysis of enantiopure systems as well as enantiomer mixtures. PMID:26066374

  10. QTL Dissection of Lag Phase in Wine Fermentation Reveals a New Translocation Responsible for Saccharomyces cerevisiae Adaptation to Sulfite

    PubMed Central

    Zimmer, Adrien; Durand, Cécile; Loira, Nicolás; Durrens, Pascal; Sherman, David James; Marullo, Philippe

    2014-01-01

    Quantitative genetics and QTL mapping are efficient strategies for deciphering the genetic polymorphisms that explain the phenotypic differences of individuals within the same species. Since a decade, this approach has been applied to eukaryotic microbes such as Saccharomyces cerevisiae in order to find natural genetic variations conferring adaptation of individuals to their environment. In this work, a QTL responsible for lag phase duration in the alcoholic fermentation of grape juice was dissected by reciprocal hemizygosity analysis. After invalidating the effect of some candidate genes, a chromosomal translocation affecting the lag phase was brought to light using de novo assembly of parental genomes. This newly described translocation (XV-t-XVI) involves the promoter region of ADH1 and the gene SSU1 and confers an increased expression of the sulfite pump during the first hours of alcoholic fermentation. This translocation constitutes another adaptation route of wine yeast to sulfites in addition to the translocation VIII-t-XVI previously described. A population survey of both translocation forms in a panel of domesticated yeast strains suggests that the translocation XV-t-XVI has been empirically selected by human activity. PMID:24489712

  11. Correction method of bending loss in the hollow optical fiber for endoscopic submucosal dissection using carbon dioxide laser

    NASA Astrophysics Data System (ADS)

    Kusakari, Daisuke; Hazama, Hisanao; Awazu, Kunio

    2015-03-01

    Endoscopic submucosal dissection using carbon dioxide laser is a promising treatment of early digestive cancer because it can avoid the risk of perforation. Although a hollow optical fiber transmitting mid-infrared light has been used, it was observed that the irradiation effect was influenced by bending a gastrointestinal gastrointestinal endoscope due to the change in transmittance by the bending loss. Therefore, we quantitatively evaluated the change in the irradiation effect by bending the hollow optical fiber in the gastrointestinal endoscope and proposed a correction method to stabilize the irradiation effect. First, the relationship between the irradiated laser energy density and the incision depth for porcine stomach was measured by bending the head of the gastrointestinal endoscope. Next, the relationship between the bending angle of the head of the gastrointestinal endoscope and the temperature rise of the hollow optical fiber in the head of the gastrointestinal endoscope was measured during the laser irradiation. As a result, the laser energy density and the incision depth decreased as the bending angle increased, and linear correlation between the laser energy density and the incision depth was observed. It was found that the bending angle can be estimated by the ratio of the setting laser power to time derivative of the temporal profile of the temperature of the hollow optical fiber. In conclusion, it is suggested that the correction of the laser energy density and stabilization of the incision capability is possible by measuring the temporal profile of the temperature of the hollow optical fiber.

  12. Dissecting apple tree architecture into genetic, ontogenetic and environmental effects: mixed linear modelling of repeated spatial and temporal measures.

    PubMed

    Segura, Vincent; Cilas, Christian; Costes, Evelyne

    2008-01-01

    The present study aimed to dissect tree architectural plasticity into genetic, ontogenetic and environmental effects over the first 4 yr of growth of an apple (Malus x domestica) F1 progeny by means of mixed linear modelling of repeated data. Traits related to both growth and branching processes were annually assessed on different axes of the trees planted in a staggered-start design. Both spatial repetitions, (i.e. different axis types) and temporal repetitions (i.e. successive ages of trees) were considered in a mixed linear model of repeated data. A significant genotype effect was found for most studied traits and interactions between genotype and year and/or age were also detected. The analysis of repeated temporal measures highlighted that the magnitude of the decrease in primary growth is mainly determined by the first year of growth, and the decrease in bottom diameter increment is concomitant with the first fruiting occurrence. This approach allowed us to distinguish among the traits that were under genetic control, those for which this control is exerted differentially throughout tree life or depending on climatic conditions or an axis type. Mapping quantitative trait loci (QTL) that are specific to these different effects will constitute the next step in the research. PMID:18248585

  13. Reversible cerebral vasoconstriction syndrome with multivessel cervical artery dissections and a double aortic arch.

    PubMed

    Nouh, Amre; Ruland, Sean; Schneck, Michael J; Pasquale, David; Biller, José

    2014-02-01

    Reversible cerebral vasoconstriction syndrome (RCVS) has been associated with exposure to vasoactive substances and few reports with cervical arterial dissections (CADs). We evaluated a 32-year-old woman with history of depression, migraines without aura, and cannabis use who presented with a thunderclap headache unresponsive to triptans. She was found to have bilateral occipital infarcts, bilateral extracranial vertebral artery dissections, bilateral internal carotid artery dissecting aneurysms, and extensive distal multifocal segmental narrowing of the anterior and posterior intracranial circulation with a "sausage on a string-like appearance" suggestive of RCVS. Subsequently, she was found to have a distal thrombus of the basilar artery, was anticoagulated, and discharged home with no residual deficits. We highlight the potential association of CADs and RCVS. The association of RCVS and a double aortic arch has not been previously reported. PMID:24103665

  14. Internal carotid artery dissection in stroke from SCUBA diving: a case report.

    PubMed

    Gibbs, J W; Piantadosi, C A; Massey, E W

    2002-01-01

    Although diving with compressed air is generally safe, neurological problems resulting from infarction in SCUBA diving are well known, including arterial gas embolism and decompression sickness (caisson's disease, bends) involving the brain and spinal cord. While air gas embolism forms the overwhelming majority of causes for stroke in divers, internal carotid artery (ICA) dissection is another potential mechanism for central nervous system infarction in the setting of SCUBA diving. A 38 year-old female, who presented with complaints of headache, nausea, vomiting, and left sided hemiparesis after rapid ascent to the surface from a depth of 120 feet of seawater was initially treated for decompression illness in a hyperbaric chamber. Further neurological workup revealed a right ICA dissection. This case demonstrates the dangers of ICA dissection following rapid ascent to the surface from underwater and emphasizes an interesting presentation of stroke associated with SCUBA diving. PMID:12670119

  15. [Dissecting aneurysm of the thoracic aorta--the value of computed tomography].

    PubMed

    Schurawitzki, H; Imhof, H; Gritzmann, N

    1986-06-01

    For the detection and classification of dissection of the thoracic aorta, in cases where a corresponding tentative diagnosis is made on the basis of clinical and plain thorax radiographs with intravenous contrast medium, computed tomography is the method of choice. In cases in which, primarily, a Type A dissection is suspected, catheter angiography is to be preferred to CT, in spite of being the more invasive method, because it is the only method capable of supplying the information necessary for surgery. In all other cases of dissection of the thoracic aorta computed tomography has the highest clinical-diagnostic value. It furnishes an initial finding on the basis of which the course may be monitored without difficulty where there is a corresponding clinical indication. It is as yet impossible to judge how far routine magnetic resonance imaging will supplant or complement CT in making the initial clinical diagnosis. PMID:3731694

  16. Spontaneous coronary artery dissection in a parturient with Nail-Patella syndrome.

    PubMed

    Nizamuddin, S L; Broderick, D K; Minehart, R D; Kamdar, B B

    2015-02-01

    Spontaneous coronary artery dissection is an uncommon cause of acute coronary syndrome, occurring predominantly in women during and immediately after pregnancy; it carries a mortality rate of greater than 50%. While the exact etiology is unknown, possible contributing factors include pregnancy-related hormonal, connective tissue and hemodynamic changes. We present a case of a 35-year-old multigravid woman with Nail-Patella syndrome who developed an acute myocardial infarction secondary to spontaneous coronary artery dissection during labor which was not diagnosed until after delivery. We hypothesize that abnormal collagen fiber formation found in Nail-Patella syndrome may have put her at an increased risk of coronary dissection and myocardial infarction. Regardless of etiology, a delay in diagnosis of myocardial ischemia can lead to significant morbidity and mortality. In light of the increasing burden of cardiac disease in the obstetric population, clinicians should remain vigilant for signs of myocardial infarction and prepare for definitive diagnosis and treatment. PMID:25433575

  17. Acute fatal coronary artery dissection following exercise-related blunt chest trauma.

    PubMed

    Barbesier, Marie; Boval, Catherine; Desfeux, Jacques; Lebreton, Catherine; Léonetti, Georges; Piercecchi, Marie-Dominique

    2015-01-01

    Coronary artery injury such as acute coronary dissection is an uncommon and potentially life-threatening complication after blunt chest trauma. The authors report an unusual autopsy case of a 43-year-old healthy man who suddenly collapsed after receiving a punch to the chest during the practice of kung fu. The occurrence of the punch was supported by the presence of one recent contusion on the left lateral chest area at the external examination and by areas of hemorrhage next to the left lateral intercostal spaces at the internal examination. The histological examination revealed the presence of an acute dissection of the proximal segment of the left anterior descending coronary artery. Only few cases of coronary artery dissection have been reported due to trauma during sports activities such as rugby and soccer games, but never during the practice of martial arts, sports usually considered as safe and responsible for only minor trauma. PMID:25066483

  18. Anatomists' views on human body dissection and donation: an international survey.

    PubMed

    Arráez-Aybar, Luis-Alfonso; Bueno-López, José Luis; Moxham, Bernard John

    2014-12-01

    A survey was conducted to test three hypotheses: anatomists believe that dissection by students conveys not just anatomical knowledge but also essential skills and attitudes, including professionalism; anatomists approve of the donation of their own bodies or body parts/organs for medical/health-care training and research; attitudes towards body dissection and donation are not dependent upon gender or upon the extent of teaching experience, but are related to transcendental convictions relating to beliefs in the afterlife. Eighty-one anatomists, from 29 countries responded to the survey; 80% indicated that they required medical/health-care students to dissect human cadavers (60% females-86% males, p=0.02). Most teachers recorded that dissection was an instrument for training undergraduate students, an instrument for the development of professional skills, and an instrument to help to control emotions in the future doctor rather than being only a means of teaching/learning anatomy facts. Males were more receptive to the concept that dissection helps to control emotions in the future doctor (p=0.02). Most teachers (75%) said they were willing to donate their bodies, 41% saying they would donate body organs only, 9% would donate their entire bodies only, 25% would separately donate organs and also the entire body. The willingness to donate increased significantly with the years of teaching experience (p=0.04). Teachers who were not believers in the afterlife were more likely to donate their organs/bodies than were believers (p=0.03). Our findings showed that anatomists' attitudes towards body dissection and donation are dependent upon gender, upon the extent of teaching experience, and upon transcendental convictions. PMID:25048843

  19. Percutaneous balloon fenestration and stent placement for lower limb ischemia complicated with type B aortic dissection.

    PubMed

    Yamaguchi, Masato; Sugimoto, Koji; Tsuji, Yoshihiko; Ozaki, Nobuchika; Tsurusaki, Masakatsu; Taniguchi, Takanori; Zamora, Carlos Armando; Okita, Yutaka; Sugimura, Kazuro

    2006-04-01

    We report a case of lower limb ischemia secondary to type B aortic dissection, which was successfully treated with endovascular aortic fenestration and stent placement. In this case, we were not able to restore adequate flow to the ischemic limb by means of aortic balloon fenestration alone, so additional stent placement was required to buttress the true lumen and fenestra. There was no recurrence of lower limb ischemia complications during the follow-up period. Aortic balloon fenestration with stent placement seems to be a safe and effective technique to salvage an ischemic lower limb complicated by acute aortic dissection. PMID:16875314

  20. Hybrid endovascular treatment of an anomalous right subclavian artery dissection in a patient with Marfan syndrome.

    PubMed

    Stanley, Gregory A; Arko, Frank R; Foteh, Mazin I; Jessen, Michael E; DiMaio, J Michael

    2012-08-01

    We report the case of a 26-year-old female patient with Marfan syndrome and an aberrant right subclavian artery (ARSA) with associated Kommerell diverticulum. The patient presented with spontaneous acute dissection of the ARSA that showed fusiform dilation to 4 cm in diameter. Definitive treatment was performed using a two-stage hybrid endovascular technique, including extrathoracic bilateral upper extremity bypass and thoracic endovascular aortic repair with debranching of the right and left subclavian arteries. This was followed by coil and plug embolization to exclude the dissection and prevent subsequent endoleak. PMID:22579900