These are representative sample records from Science.gov related to your search topic.
For comprehensive and current results, perform a real-time search at Science.gov.
1

Simultaneous dissection and comparison of IL-2 and IL-15 signaling pathways by global quantitative phosphoproteomics.  

PubMed

Common ?-chain family of cytokines (IL-2, IL-4, IL-7, IL-9, IL-15, and IL-21, where IL stands for interleukin) are key regulators of the immune homeostasis that exhibit pleiotropic biological activities and even sometimes redundant roles as a result of the utilization of the same receptor subunit. However, they also exert distinct functions that make each of them to be indispensable. For instance, all family members can act as T-cell growth factors; however, we found that IL-15 but not IL-7 can replace IL-2 to promote and sustain the proliferation of Kit225T cells. In addition to the ?-chain, IL-2 and IL-15 share the ?-chain, which creates the paradox of how they can trigger diverse phenotypes despite signaling through the same receptors. To investigate this paradigm, we combined SILAC with enrichment of tyrosine-phosphorylated proteins and peptides followed by mass spectrometric analysis to quantitatively assess the signaling networks triggered downstream IL-2/IL-2R and IL-15/IL-15R. This study confirmed that the transduction pathways initiated by both cytokines are highly similar and revealed that the main signaling branches, JAK/STAT, RAS/MAPK and PI3K/AKT, were nearly equivalently activated in response to both ILs. Despite that, our study revealed that receptor internalization rates differ in IL-2- and IL-15-treated cells indicating a discrete modulation of cytokine signaling. All MS data have been deposited in the ProteomeXchange with identifier PXD001129 (http://proteomecentral.proteomexchange.org/dataset/PXD001129). PMID:25142963

Osinalde, Nerea; Sanchez-Quiles, Virginia; Akimov, Vyacheslav; Guerra, Barbara; Blagoev, Blagoy; Kratchmarova, Irina

2015-01-01

2

Quantitative Phosphoproteomics Reveals Extensive Cellular Reprogramming During HIV-1 Entry  

PubMed Central

SUMMARY Receptor engagement by HIV-1 during host cell entry activates signaling pathways that can reprogram the cell for optimal viral replication. To obtain a global view of the signaling events induced during HIV-1 entry, we conducted a quantitative phosphoproteomics screen of primary human CD4+ T cell after infection with an HIV-1 strain that engages the receptors CD4 and CXCR4. We quantified 1,757 phosphorylation sites with high stringency. The abundance of 239 phosphorylation sites from 175 genes, including several proteins in pathways known to be impacted by HIV-receptor binding, changed significantly within a minute after HIV-1 exposure. Several previously uncharacterized HIV-1 host factors were also identified and confirmed through RNAi depletion studies. Surprisingly, 5 serine/arginine-rich (SR)-proteins involved in mRNA splicing, including the splicing factor SRm300 (SRRM2) were differentially phosophorylated. Mechanistic studies with SRRM2 suggest that HIV-1 modulates host cell alternative splicing machinery during entry in order to facilitate virus replication and release. PMID:23684312

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

2014-01-01

3

Quantitative Phosphoproteomics of Proteasome Inhibition in Multiple Myeloma Cells  

Microsoft Academic Search

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

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

2010-01-01

4

Cost-effective isobaric tagging for quantitative phosphoproteomics using DiART reagents.  

PubMed

We describe the use of an isobaric tagging reagent, Deuterium isobaric Amine Reactive Tag (DiART), for quantitative phosphoproteomic experiments. Using DiART tagged custom mixtures of two phosphorylated peptides from alpha casein and their non-phosphorylated counterparts, we demonstrate the compatibility of DiART with TiO2 affinity purification of phosphorylated peptides. Comparison of theoretical vs. experimental reporter ion ratios reveals accurate quantification of phosphorylated peptides over a dynamic range of more than 15-fold. Using DiART labelling and TiO2 enrichment (DiART-TiO2) with large quantities of proteins (8 mg) from the cell lysate of model fungus Aspergillus nidulans, we quantified 744 unique phosphopeptides. Overlap of median values of TiO2 enriched phosphopeptides with theoretical values indicates accurate trends. Altogether these findings confirm the feasibility of performing quantitative phosphoproteomic experiments in a cost-effective manner using isobaric tagging reagents, DiART. PMID:24129742

Ramsubramaniam, Nikhil; Tao, Feng; Li, Shuwei; Marten, Mark R

2013-12-01

5

Quantitative phosphoproteomics of cytotoxic T cells to reveal protein kinase d 2 regulated networks.  

PubMed

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

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

2014-12-01

6

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

PubMed Central

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

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

2014-01-01

7

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

PubMed Central

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

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

2014-01-01

8

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

PubMed Central

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

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

2013-01-01

9

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

PubMed Central

GH and GH receptors are expressed throughout life, and GH elicits a diverse range of responses, including growth and altered metabolism. It is therefore important to understand the full spectrum of GH signaling pathways and cellular responses. We applied mass spectrometry-based phosphoproteomics combined with stable isotope labeling with amino acids in cell culture to identify proteins rapidly phosphorylated in response to GH in 3T3-F442A preadipocytes. We identified 132 phosphosites in 95 proteins that exhibited rapid (5 or 15 min) GH-dependent statistically significant increases in phosphorylation by more than or equal to 50% and 96 phosphosites in 46 proteins that were down-regulated by GH by more than or equal to 30%. Several of the GH-stimulated phosphorylation sites were known (e.g. regulatory Thr/Tyr in Erks 1 and 2, Tyr in signal transducers and activators of transcription (Stat) 5a and 5b, Ser939 in tuberous sclerosis protein (TSC) 2 or tuberin). The remaining 126 GH-stimulated sites were not previously associated with GH. Kyoto Encyclopedia of Genes and Genomes pathway analysis of GH-stimulated sites indicated enrichment in proteins associated with the insulin and mammalian target of rapamycin (mTOR) pathways, regulation of the actin cytoskeleton, and focal adhesions. Akt/protein kinase A consensus sites (RXRXXS/T) were the most commonly phosphorylated consensus sites. Immunoblotting confirmed GH-stimulated phosphorylation of all seven novel GH-dependent sites tested [regulatory sites in proline-rich Akt substrate, 40 kDA (PRAS40), regulatory associated protein of mTOR, ATP-citrate lyase, Na+/H+ exchanger-1, N-myc downstream regulated gene 1, and Shc]). The immunoblot results suggest that many, if not most, of the GH-stimulated phosphosites identified in this large-scale quantitative phosphoproteomics analysis, including sites in multiple proteins in the Akt/ mTOR complex 1 pathway, are phosphorylated in response to GH. Their identification significantly broadens our thinking of GH-regulated cell functions. PMID:22570334

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

2012-01-01

10

Global analysis of muscle-specific kinase signaling by quantitative phosphoproteomics.  

PubMed

The development of the neuromuscular synapse depends on signaling processes that involve protein phosphorylation as a crucial regulatory event. Muscle-specific kinase (MuSK) is the key signaling molecule at the neuromuscular synapse whose activity is required for the formation of a mature and functional synapse. However, the signaling cascade downstream of MuSK and the regulation of the different components are still poorly understood. In this study we used a quantitative phosphoproteomics approach to study the phosphorylation events and their temporal regulation downstream of MuSK. We identified a total of 10,183 phosphopeptides, of which 203 were significantly up- or down-regulated. Regulated phosphopeptides were classified into four different clusters according to their temporal profiles. Within these clusters we found an overrepresentation of specific protein classes associated with different cellular functions. In particular, we found an enrichment of regulated phosphoproteins involved in posttranscriptional mechanisms and in cytoskeletal organization. These findings provide novel insights into the complex signaling network downstream of MuSK and form the basis for future mechanistic studies. PMID:24899341

Dürnberger, Gerhard; Camurdanoglu, Bahar Z; Tomschik, Matthias; Schutzbier, Michael; Roitinger, Elisabeth; Hudecz, Otto; Mechtler, Karl; Herbst, Ruth

2014-08-01

11

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

PubMed Central

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

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

2012-01-01

12

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

PubMed

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

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

2015-01-01

13

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

PubMed

The modification of intracellular proteins by monosaccharides of O-linked ?-N-acetylglucosamine (O-GlcNAc) is an essential and dynamic PTM of metazoans. The addition and removal of O-GlcNAc is catalyzed by the O-GlcNAc transferase (OGT) and O-GlcNAcase, respectively. One mechanism by which O-GlcNAc is thought to mediate proteins is by regulating phosphorylation. To provide insight into the pathways regulated by O-GlcNAc, we have utilized SILAC-based quantitative proteomics to carry out comparisons of site-specific phosphorylation in OGT wild-type and Null cells. Quantitation of the phosphoproteome demonstrated that of 5529 phosphoserine, phosphothreonine, and phosphotyrosine sites, 232 phosphosites were upregulated and 133 downregulated in the absence of O-GlcNAc. Collectively, these data suggest that deletion of OGT has a profound effect on the phosphorylation of cell cycle and DNA damage response proteins. Key events were confirmed by biochemical analyses and demonstrate an increase in the activating autophosphorylation event on ATM (Ser1987) and on ATM's downstream targets p53, H2AX, and Chk2. Together, these data support widespread changes in the phosphoproteome upon removal of O-GlcNAc, suggesting that O-GlcNAc regulates processes such as the cell cycle, genomic stability, and lysosomal biogenesis. All MS data have been deposited in the ProteomeXchange with identifier PXD001153 (http://proteomecentral.proteomexchange.org/dataset/PXD001153). PMID:25263469

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

2015-01-01

14

Quantitative Phosphoproteomic Analysis of Soybean Root Hairs Inoculated with Bradyrhizobium japonicum  

SciTech Connect

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

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

2012-11-11

15

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

PubMed Central

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

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

2014-01-01

16

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

PubMed

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

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

2014-05-27

17

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

PubMed Central

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

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

2014-01-01

18

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

PubMed

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

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

2015-01-01

19

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

PubMed

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

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

2011-08-25

20

Quantitative phosphoproteomic analysis reveals cAMP/vasopressin-dependent signaling pathways in native renal thick ascending limb cells  

PubMed Central

Quantitative mass spectrometry was used to identify hormone-dependent signaling pathways in renal medullary thick ascending limb (mTAL) cells via phosphoproteomic analysis. Active transport of NaCl across the mTAL epithelium is accelerated by hormones that increase cAMP levels (vasopressin, glucagon, parathyroid hormone, and calcitonin). mTAL suspensions from rat kidneys were exposed (15 min) to a mixture of these four hormones. Tryptic phosphopeptides (immobilized metal affinity chromatography-enriched) were identified and quantified by mass spectrometry (LTQ-Orbitrap) using label-free methodology. We quantified a total of 654 phosphopeptides, of which 414 were quantified in three experimental pairs (hormone vs. vehicle). Of these phosphopeptides, 82% were statistically unchanged in abundance in response to the hormone mixture. In contrast, 48 phosphopeptides were significantly increased, whereas 28 were significantly decreased. The population of up-regulated phosphopeptides was highly enriched in basophilic kinase substrate motifs (AGC or calmodulin-sensitive kinase families), whereas the down-regulated sites were dominated by “proline-directed” motifs (cyclin-dependent or MAP kinase families). Bioinformatic classification uncovered overrepresentation of transmembrane transporters, protein phosphatase regulators, and cytoskeletal binding proteins among the regulated proteins. Immunoblotting with phospho-specific antibodies confirmed cAMP/vasopressin-dependent phosphorylation at Thr96, Ser126, and Ser874 of the Na+:K+:2Cl? cotransporter NKCC2, at Ser552 of the Na+:H+ exchanger NHE3, and at Ser552 of ?-catenin. Vasopressin also increased phosphorylation of NKCC2 at both Ser126 (more than fivefold) and Ser874 (more than threefold) in rats in vivo. Both sites were phosphorylated by purified protein kinase A during in vitro assays. These results support the view that, although protein kinase A plays a central role in mTAL signaling, additional kinases, including those that target proline-directed motifs, may be involved. PMID:20713729

Gunaratne, Ruwan; Braucht, Drew W. W.; Rinschen, Markus M.; Chou, Chung-Lin; Hoffert, Jason D.; Pisitkun, Trairak; Knepper, Mark A.

2010-01-01

21

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

PubMed

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

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

2014-05-01

22

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

PubMed Central

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

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

23

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

SciTech Connect

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

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

2008-10-01

24

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

PubMed Central

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

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

2012-01-01

25

Quantitative label-free phosphoproteomics of six different life stages of the late blight pathogen Phytophthora infestans reveals abundant phosphorylation of members of the CRN effector family.  

PubMed

The oomycete Phytophthora infestans is the causal agent of late blight in potato and tomato. Since the underlying processes that govern pathogenicity and development in P. infestans are largely unknown, we have performed a large-scale phosphoproteomics study of six different P. infestans life stages. We have obtained quantitative data for 2922 phosphopeptides and compared their abundance. Life-stage-specific phosphopeptides include ATP-binding cassette transporters and a kinase that only occurs in appressoria. In an extended data set, we identified 2179 phosphorylation sites and deduced 22 phosphomotifs. Several of the phosphomotifs matched consensus sequences of kinases that occur in P. infestans but not Arabidopsis. In addition, we detected tyrosine phosphopeptides that are potential targets of kinases resembling mammalian tyrosine kinases. Among the phosphorylated proteins are members of the RXLR and Crinkler effector families. The latter are phosphorylated in several life stages and at multiple positions, in sites that are conserved between different members of the Crinkler family. This indicates that proteins in the Crinkler family have functions beyond their putative role as (necrosis-inducing) effectors. This phosphoproteomics data will be instrumental for studies on oomycetes and host-oomycete interactions. The data sets have been deposited to ProteomeXchange (identifier PXD000433). PMID:24588563

Resjö, Svante; Ali, Ashfaq; Meijer, Harold J G; Seidl, Michael F; Snel, Berend; Sandin, Marianne; Levander, Fredrik; Govers, Francine; Andreasson, Erik

2014-04-01

26

Using Isotopic Tools to Dissect and Quantitate Parallel Metabolic Pathways  

PubMed Central

4-hydroxyacids are ubiquitous in human physiology. They are derived from the drugs of abuse ?-hydroxybutyrate (GHB), ?-hydroxypentanoate(GHP), in addition to the omnipresent lipid peroxidation product 4-Hydroxy-2-(E)-nonenal (4-HNE). Previously we reported that 4-hydroxyacids are catabolized through two parallel pathways. In this report we detail two isotopic tools that have allowed the dissection of this catabolic process, and illustrate how these tools can be used to quantify the relative flux down each pathway. We found that 4-hydroxynonanoate (a 4-hydroxyacid derived from 4-HNE) is primarly catabolized through a pathway that phosphorylates the C-4 hydroxyl and isomerizes it to a C-3 hydroxy compound, which is catabolized through ?-oxidation. PMID:20408520

Sadhukhan, Sushabhan; Han, Yong; Zhang, Guo-Fang; Brunengraber, Henri; Tochtrop, Gregory P

2010-01-01

27

Quantitative phosphoproteome analysis of bacillus subtilis reveals novel substrates of the kinase PrkC and phosphatase PrpC.  

PubMed

Reversible protein phosphorylation on serine, threonine, and tyrosine (Ser/Thr/Tyr) residues plays a critical role in regulation of vital processes in the cell. Despite of considerable progress in our understanding of the role of this modification in bacterial physiology, the dynamics of protein phosphorylation during bacterial growth has rarely been systematically addressed. In addition, little is known about in vivo substrates of bacterial Ser/Thr/Tyr kinases and phosphatases. An excellent candidate to study these questions is the Gram-positive bacterium Bacillus subtilis, one of the most intensively investigated bacterial model organism with both research and industrial applications. Here we employed gel-free phosphoproteomics combined with SILAC labeling and high resolution mass spectrometry to study the proteome and phosphoproteome dynamics during the batch growth of B. subtilis. We measured the dynamics of 1666 proteins and 64 phosphorylation sites in five distinct phases of growth. Enzymes of the central carbon metabolism and components of the translation machinery appear to be highly phosphorylated in the stationary phase, coinciding with stronger expression of Ser/Thr kinases. We further used the SILAC workflow to identify novel putative substrates of the Ser/Thr kinase PrkC and the phosphatase PrpC during stationary phase. The overall number of putative substrates was low, pointing to a high kinase and phosphatase specificity. One of the phosphorylation sites affected by both, PrkC and PrpC, was the Ser281 on the oxidoreductase YkwC. We showed that PrkC phosphorylates and PrpC dephosphorylates YkwC in vitro and that phosphorylation at Ser281 abolishes the oxidoreductase activity of YkwC in vitro and in vivo. Our results present the most detailed phosphoproteomic analysis of B. subtilis growth to date and provide the first global in vivo screen of PrkC and PrpC substrates. PMID:24390483

Ravikumar, Vaishnavi; Shi, Lei; Krug, Karsten; Derouiche, Abderahmane; Jers, Carsten; Cousin, Charlotte; Kobir, Ahasanul; Mijakovic, Ivan; Macek, Boris

2014-08-01

28

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

Microsoft Academic Search

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

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

2004-01-01

29

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

E-print Network

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

Boxer, Steven G.

30

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

PubMed Central

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

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

2013-01-01

31

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

PubMed

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

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

2014-09-01

32

Quantitative phosphoproteomic analysis of signaling downstream of the prostaglandin e2/g-protein coupled receptor in human synovial fibroblasts: potential antifibrotic networks.  

PubMed

The Prostaglandin E2 (PGE2) signaling mechanism within fibroblasts is of growing interest as it has been shown to prevent numerous fibrotic features of fibroblast activation with limited evidence of downstream pathways. To understand the mechanisms of fibroblasts producing tremendous amounts of PGE2 with autocrine effects, we apply a strategy of combining a wide-screening of PGE2-induced kinases with quantitative phosphoproteomics. Our large-scale proteomic approach identified a PKA signal transmitted through phosphorylation of its substrates harboring the R(R/X)X(S*/T*) motif. We documented 115 substrates, of which 72 had 89 sites with a 2.5-fold phosphorylation difference in PGE2-treated cells than in untreated cells, where approximately half of such sites were defined as being novel. They were compiled by networking software to focus on highlighted activities and to associate them with a functional readout of fibroblasts. The substrates were associated with a variety of cellular functions including cytoskeletal structures (migration/motility), regulators of G-protein coupled receptor function, protein kinases, and transcriptional/translational regulators. For the first time, we extended the PGE2 pathway into an elaborate network of interconnecting phosphoproteins, providing vital information to a once restricted signalosome. These data provide new insights into eicosanoid-initiated cell signaling with regards to the regulation of fibroblast activation and the identification of new targets for evidenced-based pharmacotherapy against fibrosis. PMID:25223752

Gerarduzzi, Casimiro; He, QingWen; Antoniou, John; Di Battista, John A

2014-11-01

33

Phosphoproteomics in photosynthetic organisms.  

PubMed

As primarily sessile organisms, photosynthetic species survive in dynamic environments by using elegant signaling pathways to manifest molecular responses to extracellular cues. These pathways exploit phosphorylation of specific amino acids (e.g. serine, threonine, tyrosine), which impact protein structure, function, and localization. Despite substantial progress in implementation of phosphoproteomics to understand photosynthetic organisms, researchers still struggle to translate a biological question into an experimental strategy and vice versa. This review evaluates the current status of phosphoproteomics in photosynthetic organisms and concludes with recommendations based on current knowledge. PMID:24825726

Slade, William O; Werth, Emily G; Chao, Alex; Hicks, Leslie M

2014-12-01

34

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

PubMed Central

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

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

2014-01-01

35

Dissection of a quantitative trait locus for genetic hypertension on rat chromosome 10.  

PubMed Central

We have previously identified a locus on rat chromosome 10 as carrying a major hypertension gene, BP/SP-1. The 100:1 odds support interval for this gene extended over a 35-centimorgan (cM) region of the chromosome that included the angiotensin I-converting enzyme (ACE) locus as demonstrated in a cross between the stroke-prone spontaneously hypertensive rat (SHRSPHD) and the normotensive Wistar-Kyoto (WKY-0HD) rat. Here we report on the further characterization of BP/SP-1, using a congenic strain, WKY-1HD. WKY-1HD animals carry a 6-cM chromosomal fragment genotypically identical with SHRSPHD on chromosome 10, 26 cM away from the ACE locus. Higher blood pressures in the WKY-1HD strain compared with the WKY-0HD strain, as well as absence of linkage of the chromosome 10 region to blood pressure in an F2 (WKY-1HD x SHRSPHD) population suggested the existence of a quantitative trait locus, termed BP/SP-1a, that lies within the SHRSP-congenic region in WKY-1HD. Linkage analysis in the F2 (WKY-0HD x SHRSPHD) cross revealed that BP/SP-1a is linked to basal blood pressure, whereas a second locus on chromosome 10, termed BP/SP-1b, that maps closer to the ACE locus cosegregates predominantly with blood pressure after exposure to excess dietary NaCl. Thus, we hypothesize that the previously reported effect of BP/SP-1 represents a composite phenotype that can be dissected into at least two specific components on the basis of linkage data and congenic experimentation. One of the loci identified, BP/SP-1a, represents the most precisely mapped locus affecting blood pressure that has so far been characterized by random-marker genome screening. Images Fig. 3 PMID:7568016

Kreutz, R; Hübner, N; James, M R; Bihoreau, M T; Gauguier, D; Lathrop, G M; Ganten, D; Lindpaintner, K

1995-01-01

36

Quantitative phosphoproteomics of tomato mounting a hypersensitive response reveals a swift suppression of photosynthetic activity and a differential role for hsp90 isoforms.  

PubMed

An important mechanism by which plants defend themselves against pathogens is the rapid execution of a hypersensitive response (HR). Tomato plants containing the Cf-4 resistance gene mount an HR that relies on the activation of phosphorylation cascades, when challenged with the Avr4 elicitor secreted by the pathogenic fungus Cladosporium fulvum. Phosphopeptides were isolated from tomato seedlings expressing both Cf-4 and Avr4 using titanium dioxide columns and LC-MS/MS analysis led to the identification of 50 phosphoproteins, most of which have not been described in tomato before. Phosphopeptides were quantified using a label-free approach based on the MS peak areas. We identified 12 phosphopeptides for which the abundance changed upon HR initiation, as compared to control seedlings. Our results suggest that photosynthetic activity is specifically suppressed in a phosphorylation-dependent way during the very early stages of HR development. In addition, phosphopeptides originating from four Hsp90 isoforms exhibited altered abundances in Cf-4/Avr4 seedlings compared to control seedlings, suggesting that the isoforms of this chaperone protein have a different function in defense signaling. We show that label-free relative quantification of the phosphoproteome of complex samples is feasible, allowing extension of our knowledge on the general physiology and defense signaling of plants mounting the HR. PMID:19178300

Stulemeijer, Iris J E; Joosten, Matthieu H A J; Jensen, Ole N

2009-03-01

37

Phosphoproteomics combined with quantitative 14-3-3-affinity capture identifies SIRT1 and RAI as novel regulators of cytosolic double-stranded RNA recognition pathway.  

PubMed

Viral double-stranded RNA (dsRNA) is the most important viral structure recognized by cytosolic pattern-recognition receptors of the innate immune system, and its recognition results in the activation of signaling cascades that stimulate the production of antiviral cytokines and apoptosis of infected cells. 14-3-3 proteins are ubiquitously expressed regulatory molecules that participate in a variety of cellular processes, and 14-3-3 protein-mediated signaling pathways are activated by cytoplasmic dsRNA in human keratinocytes. However, the functional role of 14-3-3 protein-mediated interactions during viral dsRNA stimulation has remained uncharacterized. Here, we used functional proteomics to identify proteins whose phosphorylation and interaction with 14-3-3 is modulated by dsRNA and to characterize the signaling pathways activated during cytosolic dsRNA-induced innate immune response in human HaCaT keratinocytes. Phosphoproteome analysis showed that several MAPK- and immune-response-related signaling pathways were activated after dsRNA stimulation. Interactome analysis identified RelA-associated inhibitor, high-mobility group proteins, and several proteins associated with host responses to viral infection as novel 14-3-3 target proteins. Functional studies showed that RelA-associated inhibitor regulated dsRNA-induced apoptosis and TNF production. Integrated network analyses of proteomic data revealed that sirtuin1 was a central molecule regulated by 14-3-3s during dsRNA stimulation. Further experiments showed that sirtuin 1 negatively regulated dsRNA-induced NF?B transcriptional activity, suppressed expression of antiviral cytokines, and protected cells from apoptosis in dsRNA-stimulated and encephalomyocarditis-virus-infected keratinocytes. In conclusion, our data highlight the importance of 14-3-3 proteins in antiviral responses and identify RelA-associated inhibitor and sirtuin 1 as novel regulators of antiviral innate immune responses. PMID:24997996

Öhman, Tiina; Söderholm, Sandra; Hintsanen, Petteri; Välimäki, Elina; Lietzén, Niina; MacKintosh, Carol; Aittokallio, Tero; Matikainen, Sampsa; Nyman, Tuula A

2014-10-01

38

Towards single-cell LC-MS phosphoproteomics.  

PubMed

Protein phosphorylation is a ubiquitous posttranslational modification, which is heavily involved in signal transduction. Misregulation of protein phosphorylation is often associated with a decrease in cell viability and complex diseases such as cancer. The dynamic and low abundant nature of phosphorylated proteins makes studying phosphoproteome a challenging task. In this review, we summarize state of the art proteomic techniques to study and quantify peptide phosphorylation in biological systems and discuss their limitations. Due to its short-lived nature, the phosphorylation event cannot be precisely traced in a heterogonous cell population, which highlights the importance of analyzing phosphorylation events at the single cell level. Mainly, we focus on the methodical and instrumental developments in proteomics and nanotechnology, which will help to build more accurate and robust systems for the feasibility of phosphorylation analysis at the single cell level. We propose that an automated and miniaturized construction of analytical systems holds the key to the future of phosphoproteomics; therefore, we highlight the benchmark studies in this direction. Having advanced and automated microfluidic chip LC systems will allow us to analyze single-cell phosphoproteomics and quantitatively compare it with others. The progress in the microfluidic chip LC systems and feasibility of the single-cell phosphoproteomics will be beneficial for early diagnosis and detection of the treatment response of many crucial diseases. PMID:25068147

Polat, Ayse Nur; Özlü, Nurhan

2014-10-01

39

Clinical and Technical Phosphoproteomic Research  

PubMed Central

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

2011-01-01

40

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

E-print Network

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

Wolf Yadlin, Alejandro

2007-01-01

41

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

PubMed

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

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

2014-02-01

42

Recent advances and challenges in plant phosphoproteomics.  

PubMed

Plants are sessile organisms that need to respond to environmental changes quickly and efficiently. They can accomplish this by triggering specialized signaling pathways often mediated by protein phosphorylation and dephosphorylation. Phosphorylation is a fast response that can switch on or off a myriad of biological pathways and processes. Proteomics and mass spectrometry (MS) are the main tools employed in the study of protein phosphorylation. Advances in the technologies allow simultaneous identification and quantification of thousands of phosphopeptides and proteins that are essential to understanding the sophisticated biological systems and regulations. In this review we summarize the advances in phosphopeptide enrichment and quantitation, MS for phosphorylation site mapping and new data acquisition methods, databases and informatics, interpretation of biological insights and crosstalk with other PTMs, as well as future directions and challenges in the field of phosphoproteomics. This article is protected by copyright. All rights reserved. PMID:25429768

Silva-Sanchez, Cecilia; Li, Haiying; Chen, Sixue

2014-11-28

43

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

NASA Astrophysics Data System (ADS)

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

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

2012-07-01

44

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

PubMed

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

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

2014-04-01

45

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

PubMed

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

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

2012-05-01

46

Dissecting the Paclitaxel-Microtubule Association: Quantitative Assessment of the 2?-OH Group†  

PubMed Central

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

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

2013-01-01

47

Integrating phosphoproteomics in systems biology  

PubMed Central

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

Liu, Yu; Chance, Mark R.

2014-01-01

48

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

PubMed Central

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

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

2014-01-01

49

Sperm phosphoproteomics: historical perspectives and current methodologies  

PubMed Central

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

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

2013-01-01

50

Data analysis techniques in phosphoproteomics.  

PubMed

The interpretation of phosphoproteomics data sets is crucial for generating hypotheses that guide therapeutic solutions, yet not many techniques have been applied to this type of analysis. This paper intends to give an overview about the two main standard techniques that can be applied to the analysis of these large scale data sets. These are data-driven or exploratory techniques based on a statistical model and topology-driven methods that analyze the signaling network from a dynamical standpoint. While employing different paradigms, these algorithms will detect unique "fingerprints" by revealing the intricate interactions at the proteome level and will support the experimental environment for novel therapeutics for many diseases. PMID:25311575

Meyer-Baese, Anke; Wildberger, Joachim; Meyer-Baese, Uwe; Nilsson, Carol L

2014-12-01

51

The role of periosteum and different dissection types on callus formation: quantitative analyses with scintigraphy in a rabbit mandible model.  

PubMed

In this experimental study, the effects of different dissection types and the role of the periosteum on callus formation were investigated. Forty-five rabbits were divided into three groups of 15 rabbits. In the first group, a classic subperiosteal dissection was performed to reach the mandible. In the second group, the dissection was done extraperiosteally between the periosteum and the muscle. In the third group, the periosteum at the osteotomy line was stripped out bilaterally both on the lingual and the buccal sides (1.5 cm wide on each side). In all groups, linear vertical osteotomy was performed using an oscillating saw, and fracture fragments were fixed with surgical wire. The animals were evaluated using biomechanical (traction test), histological, and scintigraphic methods. The most durable callus in the traction test and, scintigraphically, the most rapid remodeling were seen in the second group. The histological study performed during week 3 revealed immature callus formation in the first and second groups, and no such formation in the third group. At week 8 the callus was mature in the first two groups and in the third group it was seen but not mature. PMID:10917098

Bilkay, U; Celik, N; Bilkay, U; Görken, C; Alper, M; Songür, E; Ca?da?, A

2000-07-01

52

Clam Dissection  

NSDL National Science Digital Library

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

Kelly Riedell

53

Phosphoproteomic analyses reveal signaling pathways that facilitate lytic gammaherpesvirus replication.  

PubMed

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

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

2013-09-01

54

Phosphoproteomic Analyses Reveal Signaling Pathways That Facilitate Lytic Gammaherpesvirus Replication  

PubMed Central

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

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

2013-01-01

55

Technical phosphoproteomic and bioinformatic tools useful in cancer research  

PubMed Central

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

2011-01-01

56

Characterization of the Phosphoproteome in SLE Patients  

PubMed Central

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

Huang, Jianrong; Dai, Yong

2012-01-01

57

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

PubMed Central

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

2014-01-01

58

Identifying differentially regulated subnetworks from phosphoproteomic data  

Microsoft Academic Search

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

Martin Klammer; Klaus Godl; Andreas Tebbe; Christoph Schaab

2010-01-01

59

TSLP Signaling Network Revealed by SILAC-Based Phosphoproteomics*  

PubMed Central

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

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

2012-01-01

60

Quahog Dissection  

NSDL National Science Digital Library

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

Rhode Island Sea Grant

61

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

PubMed Central

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

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

2014-01-01

62

Identification of Targets of c-Src Tyrosine Kinase by Chemical Complementation and Phosphoproteomics*  

PubMed Central

The cellular proto-oncogene c-Src is a nonreceptor tyrosine kinase involved in cell growth and cytoskeletal regulation. Despite being dysregulated in a variety of human cancers, its precise functions are not fully understood. Identification of the substrates of c-Src remains a major challenge, because there is no simple way to directly stimulate its activity. Here we combine the chemical rescue of mutant c-Src and global quantitative phosphoproteomics to obtain the first high resolution snapshot of the range of tyrosine phosphorylation events that occur in the cell immediately after specific c-Src stimulation. After enrichment by anti-phosphotyrosine antibodies, we identified 29 potential novel c-Src substrate proteins. Tyrosine phosphopeptide mapping allowed the identification of 382 nonredundant tyrosine phosphopeptides on 213 phosphoproteins. Stable isotope labeling of amino acids in cell culture-based quantitation allowed the detection of 97 nonredundant tyrosine phosphopeptides whose level of phosphorylation is increased by c-Src. A large number of previously uncharacterized c-Src putative protein targets and phosphorylation sites are presented here, a majority of which play key roles in signaling and cytoskeletal networks, particularly in cell adhesion. Integrin signaling and focal adhesion kinase signaling pathway are two of the most altered pathways upon c-Src activation through chemical rescue. In this context, our study revealed the temporal connection between c-Src activation and the GTPase Rap1, known to stimulate integrin-dependent adhesion. Chemical rescue of c-Src provided a tool to dissect the spatiotemporal mechanism of activation of the Rap1 guanine exchange factor, C3G, one of the identified potential c-Src substrates that plays a role in focal adhesion signaling. In addition to unveiling the role of c-Src in the cell and, specifically, in the Crk-C3G-Rap1 pathway, these results exemplify a strategy for obtaining a comprehensive understanding of the functions of nonreceptor tyrosine kinases with high specificity and kinetic resolution. PMID:22499769

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

2012-01-01

63

Quantitative Dissection and Modeling of the NF-?B p100-p105 Module Reveals Interdependent Precursor Proteolysis.  

PubMed

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

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

2014-12-11

64

Computional phosphoproteomics: From identification to localisation.  

PubMed

Analysis of the phosphoproteome by mass spectrometry has become a key technology for the characterisation 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 sidechain 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 'localise' 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. This article is protected by copyright. All rights reserved. PMID:25475148

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

2014-12-01

65

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

PubMed Central

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

2013-01-01

66

Phosphoproteomic Analysis of Human Embryonic Stem Cells  

PubMed Central

SUMMARY Protein phosphorylation, while critical to cellular behavior, has been under-characterized in pluripotent cells. Therefore, we performed phosphoproteomic analyses of human embryonic stem cells (hESCs) and their differentiated derivatives. 2546 phosphorylation sites were identified on 1602 phosphoproteins; 389 proteins contained more phosphorylation site identifications in undifferentiated hESCs, whereas 540 contained more such identifications in differentiated derivatives. Phosphoproteins in receptor tyrosine kinase (RTK) signaling pathways were numerous in undifferentiated hESCs. Cellular assays corroborated this observation by showing that multiple RTKs cooperatively supported undifferentiated hESCs. In addition to bFGF, EGFR, VEGFR and PDGFR activation was critical to the undifferentiated state of hESCs. PDGF-AA complemented a sub-threshold bFGF concentration to maintain undifferentiated hESCs. Also consistent with phosphoproteomics, JNK activity participated in maintenance of undifferentiated hESCs. These results support the utility of phosphoproteomic data, provide guidance for investigating known and novel proteins in hESCs, and complement transcriptomics/epigenetics for broadening our understanding of hESC fate determination. PMID:19664994

Brill, Laurence M.; Xiong, Wen; Lee, Ki-Bum; Ficarro, Scott B.; Crain, Andrew; Xu, Yue; Terskikh, Alexey; Snyder, Evan Y.; Ding, Sheng

2009-01-01

67

Polyomino Dissections  

ERIC Educational Resources Information Center

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

Hohn, Tiina; Liu, Andy

2012-01-01

68

Dissect It!  

NSDL National Science Digital Library

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

Olga Wood

2012-06-27

69

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

NASA Astrophysics Data System (ADS)

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

Milano, Regina Nicole

70

Clam Dissection  

NSDL National Science Digital Library

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

Roy Plotnick

71

Investigation of phosphoproteome in RAGE signaling.  

PubMed

The receptor for advanced glycation end products (RAGE) is one of the most important proteins implicated in diabetes, cardiovascular diseases, neurodegenerative diseases, and cancer. It is a pattern recognition receptor by virtue of its ability to interact with multiple ligands, RAGE activates several signal transduction pathways through involvement of various kinases that phosphorylate their respective substrates. Only few substrates have been known to be phosphorylated in response to activation by RAGE (e.g., nuclear factor kappa B); however, it is possible that these kinases can phosphorylate multiple substrates depending upon their expression and localization, leading to altered cellular responses in different cell types and conditions. One such example is, glycogen synthase kinase 3 beta which is known to phosphorylate glycogen synthase, acts downstream to RAGE, and hyperphosphorylates microtubule-associated protein tau causing neuronal damage. Thus, it is important to understand the role of various RAGE-activated kinases and their substrates. Therefore, we have reviewed here the details of RAGE-activated kinases in response to different ligands and their respective phosphoproteome. Furthermore, we discuss the analysis of the data mined for known substrates of these kinases from the PhosphoSitePlus (http://www.phosphosite.org) database, and the role of some of the important substrates involved in cancer, diabetes, cardiovascular diseases, and neurodegenerative diseases. In summary, this review provides information on RAGE-activated kinases and their phosphoproteome, which will be helpful in understanding the possible role of RAGE and its ligands in progression of diseases. PMID:25315903

Batkulwar, Kedar B; Bansode, Sneha B; Patil, Gouri V; Godbole, Rashmi K; Kazi, Rubina S; Chinnathambi, Subashchandrabose; Shanmugam, Dhanasekaran; Kulkarni, Mahesh J

2015-01-01

72

Phosphoproteomic analysis of apoptotic hematopoietic stem cells from hemoglobin E/?-thalassemia  

PubMed Central

Background Hemoglobin E/?-thalassemia is particularly common in Southeast Asia and has variable symptoms ranging from mild to severe anemia. Previous investigations demonstrated the remarkable symptoms of ?-thalassemia in terms of the acceleration of apoptotic cell death. Ineffective erythropoiesis has been studied in human hematopoietic stem cells, however the distinct apoptotic mechanism was unclear. Methods The phosphoproteome of bone marrow HSCs/CD34+ cells from HbE/?-thalassemic patients was analyzed using IMAC phosphoprotein isolation followed by LC-MS/MS detection. Decyder MS software was used to quantitate differentially expressed proteins in 3 patients and 2 normal donors. The differentially expressed proteins from HSCs/CD34+ cells were compared with HbE/?-thalassemia and normal HSCs. Results A significant change in abundance of 229 phosphoproteins was demonstrated. Importantly, the analysis of the candidate proteins revealed a high abundance of proteins that are commonly found in apoptotic cells including cytochrome C, caspase 6 and apoptosis inducing factors. Moreover, in the HSCs patients a significant increase was observed in a specific type of phosphoserine/threonine binding protein, which is known to act as an important signal mediator for the regulation of cell survival and apoptosis in HbE/?-thalassemia. Conclusions Our study used a novel method to investigate proteins that influence a particular pathway in a given disease or physiological condition. Ultimately, phosphoproteome profiling in HbE/?-thalassemic stem cells is an effective method to further investigate the cell death mechanism of ineffective erythropoiesis in ?-thalassemia. Our report provides a comprehensive phosphoproteome, an important resource for the study of ineffective erythropoiesis and developing therapies for HbE/?-thalassemia. PMID:21702968

2011-01-01

73

Dynamic Adipocyte Phosphoproteome Reveals that Akt Directly Regulates mTORC2  

PubMed Central

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

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

2013-01-01

74

Dynamic adipocyte phosphoproteome reveals that Akt directly regulates mTORC2.  

PubMed

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

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

2013-06-01

75

Specific visualization and identification of phosphoproteome in gels.  

PubMed

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

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

2014-07-15

76

Evidence for a Minimal Eukaryotic Phosphoproteome?  

PubMed Central

Background Reversible phosphorylation catalysed by kinases is probably the most important regulatory mechanism in eukaryotes. Methodology/Principal Findings We studied the in vitro phosphorylation of peptide arrays exhibiting the majority of PhosphoBase-deposited protein sequences, by factors in cell lysates from representatives of various branches of the eukaryotic species. We derived a set of substrates from the PhosphoBase whose phosphorylation by cellular extracts is common to the divergent members of different kingdoms and thus may be considered a minimal eukaryotic phosphoproteome. The protein kinases (or kinome) responsible for phosphorylation of these substrates are involved in a variety of processes such as transcription, translation, and cytoskeletal reorganisation. Conclusions/Significance These results indicate that the divergence in eukaryotic kinases is not reflected at the level of substrate phosphorylation, revealing the presence of a limited common substrate space for kinases in eukaryotes and suggests the presence of a set of kinase substrates and regulatory mechanisms in an ancestral eukaryote that has since remained constant in eukaryotic life. PMID:17712425

Diks, Sander H.; Parikh, Kaushal; van der Sijde, Marijke; Joore, Jos; Ritsema, Tita; Peppelenbosch, Maikel P.

2007-01-01

77

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

PubMed Central

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

2014-01-01

78

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

PubMed Central

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

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

2012-01-01

79

Battle through signaling between wheat and the fungal pathogen Septoria tritici revealed by proteomics and phosphoproteomics.  

PubMed

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

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

2013-09-01

80

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

PubMed Central

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

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

2013-01-01

81

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

Microsoft Academic Search

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

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

2002-01-01

82

Interactive Frog Dissection  

NSDL National Science Digital Library

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

83

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

PubMed Central

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

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

2013-01-01

84

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

PubMed Central

Background Dense consensus genetic maps based on high-throughput genotyping platforms are valuable for making genetic gains in Brassica napus through quantitative trait locus identification, efficient predictive molecular breeding, and map-based gene cloning. This report describes the construction of the first B. napus consensus map consisting of a 1,359 anchored array based genotyping platform; Diversity Arrays Technology (DArT), and non-DArT markers from six populations originating from Australia, Canada, China and Europe. We aligned the B. napus DArT sequences with genomic scaffolds from Brassica rapa and Brassica oleracea, and identified DArT loci that showed linkage with qualitative and quantitative loci associated with agronomic traits. Results The integrated consensus map covered a total of 1,987.2?cM and represented all 19 chromosomes of the A and C genomes, with an average map density of one marker per 1.46?cM, corresponding to approximately 0.88 Mbp of the haploid genome. Through in silico physical mapping 2,457 out of 3,072 (80%) DArT clones were assigned to the genomic scaffolds of B. rapa (A genome) and B. oleracea (C genome). These were used to orientate the genetic consensus map with the chromosomal sequences. The DArT markers showed linkage with previously identified non-DArT markers associated with qualitative and quantitative trait loci for plant architecture, phenological components, seed and oil quality attributes, boron efficiency, sucrose transport, male sterility, and race-specific resistance to blackleg disease. Conclusions The DArT markers provide increased marker density across the B. napus genome. Most of the DArT markers represented on the current array were sequenced and aligned with the B. rapa and B. oleracea genomes, providing insight into the Brassica A and C genomes. This information can be utilised for comparative genomics and genomic evolution studies. In summary, this consensus map can be used to (i) integrate new generation markers such as SNP arrays and next generation sequencing data; (ii) anchor physical maps to facilitate assembly of B. napus genome sequences; and (iii) identify candidate genes underlying natural genetic variation for traits of interest. PMID:23617817

2013-01-01

85

Advances in Phos-tag-based methodologies for separation and detection of the phosphoproteome.  

PubMed

This review article describes analytical techniques based on the phosphate-binding tag molecule "Phos-tag", which is an alkoxide-bridged dinuclear metal complex with 1,3-bis(pyridin-2-ylmethylamino)propan-2-olate, for studying the protein phosphorylome. The dinuclear zinc(II) complex forms a stable 1:1 complex with a phosphate monoester dianion in an aqueous solution under conditions of neutral pH. By using a series of functional Phos-tag derivatives, our group has developed novel techniques that are useful in studies on kinomics and phosphoproteomics. Among the derivatives, a series of biotinylated Phos-tag derivatives have been used as molecular tools in applications such as Western blotting for comprehensive detection of phosphorylated proteins and in highly sensitive peptide microarray-based techniques for the detection of kinase activities in biological samples. The review also gives an outline of phosphate affinity electrophoresis, in which immobilized Phos-tag molecules in a general polyacrylamide gel are used to separate proteins and detect differences in their phosphorylation status. This technique permits quantitative analyses of multiple phosphorylation statuses of individual cellular proteins and their time-dependent changes. Conventional mass spectrometry-based shotgun techniques used in phosphoproteomics detect the phosphorylation modification of proteins in peptide fragments, whereas the Phos-tag electrophoresis technique permits the direct analysis of the phosphorylation status of full-length proteins. The technique therefore provides a greater understanding of the detailed properties of particular proteins involved in specific physiological and pathological events. This article is part of a Special Issue entitled: Medical Proteomics. PMID:25315852

Kinoshita, Eiji; Kinoshita-Kikuta, Emiko; Koike, Tohru

2014-10-12

86

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

PubMed Central

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

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

2013-01-01

87

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

PubMed Central

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

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

2014-01-01

88

A shotgun phosphoproteomics analysis of embryos in germinated maize seeds  

Microsoft Academic Search

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

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

2008-01-01

89

"Hands-Off" Dissection?  

ERIC Educational Resources Information Center

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

Allchin, Douglas

2005-01-01

90

Flower Dissection Lab  

NSDL National Science Digital Library

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

2007-12-27

91

Proteomics and Phosphoproteomics Analysis of Human Lens Fiber Cell Membranes  

PubMed Central

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

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

2013-01-01

92

The use of elemental mass spectrometry in phosphoproteomic applications.  

PubMed

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

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

2014-08-19

93

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

PubMed Central

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

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

2013-01-01

94

Phosphoproteome profiling of the macrophage response to different toll-like receptor ligands identifies differences in global phosphorylation dynamics.  

PubMed

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

Sjoelund, Virginie; Smelkinson, Margery; Nita-Lazar, Aleksandra

2014-11-01

95

Spontaneous coronary artery dissection.  

PubMed

Spontaneous coronary artery dissection is a rarely identified entity whose exact incidence, etiology, pathogenesis, medium-term evolution, and optimal treatment have not yet been firmly established. This article describes five new cases with additional specific characteristics. Five of 2,241 coronary arteriograms taken between September 1989 and November 1992 showed angiographic signs of coronary dissection. Three of the patients were treated pharmacologically, and two were operated on. All were evaluated angiographically 10-18 months after diagnosis and followed up clinically for > or = 20 months. Three patients exhibited acute myocardial infarction, one showed effort angina and the fifth unstable angina. In four cases, coronary dissection was associated with coronary atherosclerosis, but in the fifth the coronary tree was apparently healthy except for the dissection. Dissection affected the right coronary artery in three cases and the left in two. Angiographic evolution varied among the five and was uncorrelated with treatment. Dissection disappeared in three; it persisted, with total obstruction of the artery in the middle of the dissected segment in one case; and advanced to affect the whole left coronary tree in the fifth. After an 18-month follow-up, none of the five patients experienced symptoms. These cases provide a good illustration of the variability of spontaneous coronary dissection as regards etiology, clinical presentation, treatment, and evolution. Coronary dissection is always caused by hemorrhage in the media of the arterial wall; its variability in evolution and in optimal treatment may be derived from the cause of the hemorrage, which possibly was not the same in all cases. PMID:8039214

Pasalodos Pita, J; Vazquez Gonzalez, N; Perez Alvarez, L; Vazquez Rodriguez, J M; Castro Beiras, A

1994-05-01

96

Global analysis of phosphoproteome regulation by the Ser/Thr phosphatase Ppt1 in Saccharomyces cerevisiae.  

PubMed

Even though protein phosphatases are key regulators of signal transduction, their cellular mechanisms of action are poorly understood. Here, we undertook a large-scale proteomics survey to identify cellular protein targets of a serine/threonine phosphatase. We used SILAC-based quantitative MS to measure differences in protein expression and phosphorylation upon ablation of the serine/threonine phosphatase Ppt1 in Saccharomyces cerevisiae. Phosphopeptide fractionation by strong cation exchange chromatography combined with immobilized metal affinity chromatography (IMAC) enrichment enabled quantification of more than 8000 distinct phosphorylation sites in Ppt1 wild-type versus Ppt1-deficient yeast cells. We further quantified the relative expression of 1897 yeast proteins and detected no major protein changes accompanying Ppt1 deficiency. Notably, we found 33 phosphorylation sites to be significantly and reproducibly up-regulated while no phosphorylation events were repressed in cells lacking Ppt1. Ppt1 acted on its cellular target proteins in a sequence- and site-specific fashion. Several of the regulated phosphoproteins were involved in the response to heat stress in agreement with known Ppt1 functions. Additionally, biosynthetic enzymes were particularly prominent among Ppt1-regulated phosphoproteins, pointing to unappreciated roles of Ppt1 in the control of various metabolic functions. These results demonstrate the utility of large-scale and quantitative phosphoproteomics to identify cellular sites of serine/threonine phosphatase action in an unbiased manner. PMID:22369663

Schreiber, Thiemo B; Mäusbacher, Nina; Soroka, Joanna; Wandinger, Sebastian K; Buchner, Johannes; Daub, Henrik

2012-04-01

97

Discovery of O-GlcNAc-6-phosphate modified proteins in large-scale phosphoproteomics data.  

PubMed

Phosphorylated O-GlcNAc is a novel post-translational modification that has so far only been found on the neuronal protein AP180 from the rat (Graham et al., J. Proteome Res. 2011, 10, 2725-2733). Upon collision induced dissociation, the modification generates a highly mass deficient fragment ion (m/z 284.0530) that can be used as a reporter for the identification of phosphorylated O-GlcNAc. Using a publically available mouse brain phosphoproteome data set, we employed our recently developed Oscore software to re-evaluate high resolution/high accuracy tandem mass spectra and discovered the modification on 23 peptides corresponding to 11 mouse proteins. The systematic analysis of 220 candidate phosphoGlcNAc tandem mass spectra as well as a synthetic standard enabled the dissection of the major phosphoGlcNAc fragmentation pathways, suggesting that the modification is O-GlcNAc-6-phosphate. We find that the classical O-GlcNAc modification often exists on the same peptides indicating that O-GlcNAc-6-phosphate may biosynthetically arise in two steps involving the O-GlcNAc transferase and a currently unknown kinase. Many of the identified proteins are involved in synaptic transmission and for Ca(2+)/calmodulin kinase IV, the O-GlcNAc-6-phosphate modification was found in the vicinity of two autophosphorylation sites required for full activation of the kinase suggesting a potential regulatory role for O-GlcNAc-6-phosphate. By re-analyzing mass spectrometric data from human embryonic and induced pluripotent stem cells, our study also identified Zinc finger protein 462 (ZNF462) as the first human O-GlcNAc-6-phosphate modified protein. Collectively, the data suggests that O-GlcNAc-6-phosphate is a general post-translation modification of mammalian proteins with a variety of possible cellular functions. PMID:22826440

Hahne, Hannes; Kuster, Bernhard

2012-10-01

98

Phosphoproteomic analysis of chromoplasts from sweet orange during fruit ripening.  

PubMed

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

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

2014-02-01

99

Virtual Pig Dissection  

NSDL National Science Digital Library

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

Fleck, Earl W.

100

Parametric binary dissection  

NASA Technical Reports Server (NTRS)

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

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

1993-01-01

101

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

PubMed

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

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

2014-12-01

102

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

PubMed

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

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

2014-07-01

103

Large Scale Phosphoproteome Profiles Comprehensive Features of Mouse Embryonic Stem Cells*  

PubMed Central

Embryonic stem cells are pluripotent and capable of unlimited self-renewal. Elucidation of the underlying molecular mechanism may contribute to the advancement of cell-based regenerative medicine. In the present work, we performed a large scale analysis of the phosphoproteome in mouse embryonic stem (mES) cells. Using multiplex strategies, we detected 4581 proteins and 3970 high confidence distinct phosphosites in 1642 phosphoproteins. Notably, 22 prominent phosphorylated stem cell marker proteins with 39 novel phosphosites were identified for the first time by mass spectrometry, including phosphorylation sites in NANOG (Ser-65) and RE1 silencing transcription factor (Ser-950 and Thr-953). Quantitative profiles of NANOG peptides obtained during the differentiation of mES cells revealed that the abundance of phosphopeptides and non-phosphopeptides decreased with different trends. To our knowledge, this study presents the largest global characterization of phosphorylation in mES cells. Compared with a study of ultimately differentiated tissue cells, a bioinformatics analysis of the phosphorylation data set revealed a consistent phosphorylation motif in human and mouse ES cells. Moreover, investigations into phosphorylation conservation suggested that phosphoproteins were more conserved in the undifferentiated ES cell state than in the ultimately differentiated tissue cell state. However, the opposite conclusion was drawn from this conservation comparison with phosphosites. Overall, this work provides an overview of phosphorylation in mES cells and is a valuable resource for the future understanding of basic biology in mES cells. PMID:21149613

Li, Qing-Run; Xing, Xiao-Bin; Chen, Tao-Tao; Li, Rong-Xia; Dai, Jie; Sheng, Quan-Hu; Xin, Shun-Mei; Zhu, Li-Li; Jin, Ying; Pei, Gang; Kang, Jiu-Hong; Li, Yi-Xue; Zeng, Rong

2011-01-01

104

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

PubMed Central

Leishmania is exposed to a sudden increase in environmental temperature during the infectious cycle that triggers stage differentiation and adapts the parasite phenotype to intracellular survival in the mammalian host. The absence of classical promoter-dependent mechanisms of gene regulation and constitutive expression of most of the heat-shock proteins (HSPs) in these human pathogens raise important unresolved questions as to regulation of the heat-shock response and stage-specific functions of Leishmania HSPs. Here we used a gel-based quantitative approach to assess the Leishmania donovani phosphoproteome and revealed that 38% of the proteins showed significant stage-specific differences, with a strong focus of amastigote-specific phosphoproteins on chaperone function. We identified STI1/HOP-containing chaperone complexes that interact with ribosomal client proteins in an amastigote-specific manner. Genetic analysis of STI1/HOP phosphorylation sites in conditional sti1?/? null mutant parasites revealed two phosphoserine residues essential for parasite viability. Phosphorylation of the major Leishmania chaperones at the pathogenic stage suggests that these proteins may be promising drug targets via inhibition of their respective protein kinases. PMID:20404152

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

2010-01-01

105

Alternative surgical dissection techniques.  

PubMed

The bipolar scissors, coblator, harmonic scalpel, and somnoplasty techniques are widely available and offer new choices for the operating arena. There are advantages and disadvantages to all four techniques. With time, these dissection methods will prove their lasting power. Otolaryngologists have already begun to expand their applications and will surely play a role in their use and development. PMID:15823600

Carroll, Thomas; Ladner, Keith; Meyers, Arlen D

2005-04-01

106

Video Gallery: Shark Dissection  

NSDL National Science Digital Library

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

107

Doing without Dissection.  

ERIC Educational Resources Information Center

Both the National Science Teachers Association (NSTA) and the National Association of Biology Teachers (NABT) have issued position statements on the use of animals in the classroom. Dissection has not become extinct, but its role is far smaller than it used to be. (MLF)

Texley, Juliana

1992-01-01

108

Single-step enrichment by Ti4+-IMAC and label-free quantitation enables in-depth monitoring of phosphorylation dynamics with high reproducibility and temporal resolution.  

PubMed

Quantitative phosphoproteomics workflows traditionally involve additional sample labeling and fractionation steps for accurate and in-depth analysis. Here we report a high-throughput, straightforward, and comprehensive label-free phosphoproteomics approach using the highly selective, reproducible, and sensitive Ti(4+)-IMAC phosphopeptide enrichment method. We demonstrate the applicability of this approach by monitoring the phosphoproteome dynamics of Jurkat T cells stimulated by prostaglandin E2 (PGE2) over six different time points, measuring in total 108 snapshots of the phosphoproteome. In total, we quantitatively monitored 12,799 unique phosphosites over all time points with very high quantitative reproducibility (average r > 0.9 over 100 measurements and a median cv < 0.2). PGE2 is known to increase cellular cAMP levels, thereby activating PKA. The in-depth analysis revealed temporal regulation of a wide variety of phosphosites associated not only with PKA, but also with a variety of other classes of kinases. Following PGE2 stimulation, several pathways became only transiently activated, revealing that in-depth dynamic profiling requires techniques with high temporal resolution. Moreover, the large publicly available dataset provides a valuable resource for downstream PGE2 signaling dynamics in T cells, and cAMP-mediated signaling in particular. More generally, our method enables in-depth, quantitative, high-throughput phosphoproteome screening on any system, requiring very little sample, sample preparation, and analysis time. PMID:24850871

de Graaf, Erik L; Giansanti, Piero; Altelaar, A F Maarten; Heck, Albert J R

2014-09-01

109

Neck dissections: radical to conservative  

PubMed Central

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

Harish, K

2005-01-01

110

Proteome and phosphoproteome of Africanized and European honeybee venoms.  

PubMed

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

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

2013-09-01

111

Functional Divergence and Evolutionary Turnover in Mammalian Phosphoproteomes  

PubMed Central

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

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

2014-01-01

112

Sheep Brain Dissection  

NSDL National Science Digital Library

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

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

2004-04-30

113

Radiosensitization of human leukemic HL-60 cells by ATR kinase inhibitor (VE-821): phosphoproteomic analysis.  

PubMed

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

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

2014-01-01

114

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

PubMed

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

Yang, Chenxi; Zhong, Xuefei; Li, Lingjun

2014-12-01

115

"Dissection" of a Hair Dryer  

ERIC Educational Resources Information Center

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

Eisenstein, Stan; Simpson, Jeff

2008-01-01

116

Thoracic aortic aneurysm and dissection.  

PubMed

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

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

2014-10-21

117

The biguanide metformin alters phosphoproteomic profiling in mouse brain.  

PubMed

Metformin, a potent antihyperglycemic agent is recommended as the first-line oral therapy for type 2 diabetes (T2D). Recently, metformin has been reported to be beneficial to neurodegenerative disease models. However, the putative mechanisms underlying the neuroprotective effects of metformin in disease models are unknown. Thus, we applied LC-MS/MS-based pattern analysis and two-dimensional electrophoresis (2DE)-based proteomic approach to understand the global phosphoproteomic alteration in the brain of metformin-administrated mice. Collectively, LC-MS/MS-based pattern analysis reveals that 41 phosphoproteins were upregulated and 22 phosphoproteins were downregulated in the brain of metformin-administrated mice. In addition, 5 differentially expressed phosphoproteins were identified upon metformin administration by 2DE coupled with mass spectrometry. The phosphorylation status of metabolic enzymes was decreased while that of mitochondrial proteins was increased by metformin. Interestingly, phosphorylated ?-synuclein was significantly decreased by metformin administration. Taken together, our results might provide potential pathways to understand the pharmacological effect of metformin on neuroprotection. PMID:25067825

Khang, Rin; Park, ChiHu; Shin, Joo-Ho

2014-09-01

118

Large-Scale Proteomics and Phosphoproteomics of Urinary Exosomes  

PubMed Central

Normal human urine contains large numbers of exosomes, which are 40- to 100-nm vesicles that originate as the internal vesicles in multivesicular bodies from every renal epithelial cell type facing the urinary space. Here, we used LC-MS/MS to profile the proteome of human urinary exosomes. Overall, the analysis identified 1132 proteins unambiguously, including 177 that are represented on the Online Mendelian Inheritance in Man database of disease-related genes, suggesting that exosome analysis is a potential approach to discover urinary biomarkers. We extended the proteomic analysis to phosphoproteomic profiling using neutral loss scanning, and this yielded multiple novel phosphorylation sites, including serine-811 in the thiazide-sensitive Na-Cl co-transporter, NCC. To demonstrate the potential use of exosome analysis to identify a genetic renal disease, we carried out immunoblotting of exosomes from urine samples of patients with a clinical diagnosis of Bartter syndrome type I, showing an absence of the sodium-potassium-chloride co-transporter 2, NKCC2. The proteomic data are publicly accessible at http://dir.nhlbi.nih.gov/papers/lkem/exosome/. PMID:19056867

Gonzales, Patricia A.; Pisitkun, Trairak; Hoffert, Jason D.; Tchapyjnikov, Dmitry; Star, Robert A.; Kleta, Robert; Wang, Nam Sun; Knepper, Mark A.

2009-01-01

119

Automatic Dissection Of Plantlets  

NASA Astrophysics Data System (ADS)

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)

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

1989-03-01

120

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

PubMed

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

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

2014-12-01

121

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

PubMed

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

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

2015-02-01

122

Alternative synthetic tools to phospho-specific antibodies for phosphoproteome analysis: progress and prospects.  

PubMed

Signal transduction cascades in living systems are often controlled via post-translational phosphorylation and dephosphorylation of proteins. These processes are catalyzed in vivo by kinase and phosphatase enzymes, which consequently play an important role in many disease states, including cancer and immune system disorders. Current techniques for studying the phosphoproteome (isotopic labeling, chromatographic techniques, and phosphospecific antibodies), although undoubtedly very powerful, have yet to provide a generic tool for phosphoproteomic analysis despite the widespread utility such a technique would have. The use of small molecule organic catalysts that can promote selective phosphate esterification could provide a useful alternative to current state-of-the-art techniques for use in, e.g., the labeling and pull-down of phosphorylated proteins. This report reviews current techniques used for phosphoproteomic analysis and the recent use of small molecule peptide-based catalysts in phosphorylation reactions, indicating possible future applications for this type of catalyst as synthetic alternatives to phosphospecific antibodies for phosphoproteome analysis. PMID:24432133

Murray, James I; Spivey, Alan C; Woscholski, Rudiger

2013-07-01

123

MMFPh: a maximal motif finder for phosphoproteomics datasets  

PubMed Central

Motivation: Protein phosphorylation, driven by specific recognition of substrates by kinases and phosphatases, plays central roles in a variety of important cellular processes such as signaling and enzyme activation. Mass spectrometry enables the determination of phosphorylated peptides (and thereby proteins) in scenarios ranging from targeted in vitro studies to in vivo cell lysates under particular conditions. The characterization of commonalities among identified phosphopeptides provides insights into the specificities of the kinases involved in a study. Several algorithms have been developed to uncover linear motifs representing position-specific amino acid patterns in sets of phosphopeptides. To more fully capture the available information, reduce sensitivity to both parameter choices and natural experimental variation, and develop more precise characterizations of kinase specificities, it is necessary to determine all statistically significant motifs represented in a dataset. Results: We have developed MMFPh (Maximal Motif Finder for Phosphoproteomics datasets), which extends the approach of the popular phosphorylation motif software Motif-X (Schwartz and Gygi, 2005) to identify all statistically significant motifs and return the maximal ones (those not subsumed by motifs with more fixed amino acids). In tests with both synthetic and experimental data, we show that MMFPh finds important motifs missed by the greedy approach of Motif-X, while also finding more motifs that are more characteristic of the dataset relative to the background proteome. Thus MMFPh is in some sense both more sensitive and more specific in characterizing the involved kinases. We also show that MMFPh compares favorably to other recent methods for finding phosphorylation motifs. Furthermore, MMFPh is less dependent on parameter choices. We support this powerful new approach with a web interface so that it may become a useful tool for studies of kinase specificity and phosphorylation site prediction. Availability: A web server is at www.cs.dartmouth.edu/~cbk/ Contact: cbk@cs.dartmouth.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22531218

Wang, Tuobin; Kettenbach, Arminja N.; Gerber, Scott A.; Bailey-Kellogg, Chris

2012-01-01

124

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

PubMed Central

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

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

2014-01-01

125

Identification of the PLK2-Dependent Phosphopeptidome by Quantitative Proteomics  

PubMed Central

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

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

2014-01-01

126

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

PubMed

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

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

2014-07-22

127

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

PubMed Central

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

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

2014-01-01

128

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

PubMed Central

Delineation of phosphorylation-based signaling networks requires reliable data about the underlying cellular kinase-substrate interactions. We report a chemical genetics and quantitative phosphoproteomics approach that encompasses cellular kinase activation in combination with comparative replicate mass spectrometry analyses of cells expressing either inhibitor-sensitive or resistant kinase variant. We applied this workflow to Plk1 (Polo-like kinase 1) in mitotic cells and induced cellular Plk1 activity by wash-out of the bulky kinase inhibitor 3-MB-PP1, which targets a mutant kinase version with an enlarged catalytic pocket while not interfering with wild-type Plk1. We quantified more than 20,000 distinct phosphorylation sites by SILAC, approximately half of which were measured in at least two independent experiments in cells expressing mutant and wild-type Plk1. Based on replicate phosphorylation site quantifications in both mutant and wild-type Plk1 cells, our chemical genetic proteomics concept enabled stringent comparative statistics by significance analysis of microarrays, which unveiled more than 350 cellular downstream targets of Plk1 validated by full concordance of both statistical and experimental data. Our data point to hitherto poorly characterized aspects in Plk1-controlled mitotic progression and provide a largely extended resource for functional studies. We anticipate the described strategies to be of general utility for systematic and confident identification of cellular protein kinase substrates. PMID:22199227

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

2012-01-01

129

Phosphoproteomic analysis identifies activated MET-axis PI3K/AKT and MAPK/ERK in lapatinib-resistant cancer cell line  

PubMed Central

Lapatinib, a dual inhibitor of epidermal growth factor receptor (EGFR) and human epidermal growth factor receptor 2 (HER2) tyrosine kinases, has shown promising results as a growth inhibitor of HER2-positive cancer cells in vitro. However, similar to other EGFR-targeting drugs, acquired resistance to lapatinib by HER2-positive cancer cells remains a major clinical challenge. To elucidate resistance mechanisms to EGFR/HER2-targeting agents, we performed a systematic quantitative comparison of the phosphoproteome of lapatinib-resistant (LR) human gastric cancer cells (SNU216-LR) versus parental cells (SNU216) using a titanium dioxide (TiO2) phosphopeptide enrichment method and analysis with a Q-Exactive hybrid quadrupole-Orbitrap mass spectrometer. Biological network analysis of differentially expressed phosphoproteins revealed apparent constitutive activation of the MET-axis phosphatidylinositide 3-kinase (PI3K)/?-serine/threonine-protein kinase (AKT) and mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) signaling pathways in SNU216-LR. Inhibition of the PI3K/AKT and MAPK/ERK signaling pathways in SNU216-LR also leads to cell cycle arrest, confirming the biological network analysis. Lapatinib sensitivity was restored when cells were treated with several molecular targeting agents in combination with lapatinib. Thus, by integrating phosphoproteomic data, protein networks and effects of signaling pathway modulation on cell proliferation, we found that SNU216-LR maintains constitutive activation of the PI3K/AKT and MAPK/ERK pathways in a MET-dependent manner. These findings suggest that pathway activation is a key compensatory intracellular phospho-signaling event that may govern gastric cancer cell resistance to drug treatment. PMID:24263233

Lee, Yong Yook; Kim, Hwang-Phill; Kang, Min Jueng; Cho, Byoung-Kyu; Han, Sae-Won; Kim, Tae-You; Yi, Eugene C

2013-01-01

130

Dissecting aortic aneurysm in computed tomography.  

PubMed

The dissecting aortic aneurysm (DAA) is an emergency, and because of that it requires urgent diagnosis and treatment. Many methods may by used to diagnose dissection, including aortography, CT, MRI, traditional and transesophageal ultrasonography. The computed tomography is often used in diagnostic of DAA, thus the knowledge of morphological characteristic of dissection is very important. The most important features of dissection in CT are presence of dissection of intima and two lumens, true and false. Nevertheless, the CT pictures of dissection not always appears like this, and sometimes the two lumens are identified only by their different rates of opacification with contrast material. PMID:15314960

Pas?awski, Marek; Z?omaniec, Janusz; Ruci?ska, Eulalia; Horbaczewska, Anna

2003-01-01

131

Cutting Edge Controversy: The Politics of Animal Dissection and Responses to Student Objection  

NASA Astrophysics Data System (ADS)

This mixed methods study investigated the experiences and perspectives of former Ontario high school students and current Ontario science and biology teachers toward animal dissection, objection to dissection, and choice policies that grant students the right to opt out of dissection and use an alternative instead. Data was collected via a student questionnaire (n=311), a teacher questionnaire (n=153), and interviews with eight students and nine teachers. Quantitative and qualitative data analyses and reporting techniques were employed within a humane education and critical pedagogy framework to explore the experiences and perspectives of both groups.

Oakley, Jan

2011-12-01

132

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

PubMed Central

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

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

2012-01-01

133

The role of phosphoproteomics in the development of personalized cancer therapies.  

PubMed

Cell signalling pathways driven by protein and lipid kinases contribute to the onset and progression of virtually all cancer types. Consequently, several inhibitors against these enzymes have clinical utility for the treatment of different forms of cancer. A problem that hampers further development is that not all patients respond equally well to kinase inhibitors and a significant proportion of those that initially respond eventually develop resistance. This review considers how an integrative analysis of kinase signalling may be used to address this issue. Advances in the biophysics of mass spectrometry, in biochemical procedures for phosphopeptide enrichment, and in computational approaches for label-free quantification have contributed to the development of phosphoproteomics workflows compatible with the analysis of clinical material. These developments, together with new bioinformatics tools to derive information on signalling circuitry from phosphoproteomics data, allow investigating kinase networks with unprecedented depth. Phosphoproteomics technology is starting to be used in translational research and, with further developments, such methods may also be able to measure the circuitry of cancer signalling networks in routine clinical assays. This review reflects on how this information could be used to accurately predict the best kinase inhibitor for each individual cancer patient. This article is protected by copyright. All rights reserved. PMID:25488289

Cutillas, Pedro R

2014-12-01

134

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

PubMed Central

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

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

2010-01-01

135

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

PubMed Central

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

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

2010-01-01

136

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

PubMed

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

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

2014-05-01

137

Predicting Kinase Activity in Angiotensin Receptor Phosphoproteomes Based on Sequence-Motifs and Interactions  

PubMed Central

Recent progress in the understanding of seven-transmembrane receptor (7TMR) signalling has promoted the development of a new generation of pathway selective ligands. The angiotensin II type I receptor (AT1aR) is one of the most studied 7TMRs with respect to selective activation of the ?-arrestin dependent signalling. Two complimentary global phosphoproteomics studies have analyzed the complex signalling induced by the AT1aR. Here we integrate the data sets from these studies and perform a joint analysis using a novel method for prediction of differential kinase activity from phosphoproteomics data. The method builds upon NetworKIN, which applies sophisticated linear motif analysis in combination with contextual network modelling to predict kinase-substrate associations with high accuracy and sensitivity. These predictions form the basis for subsequently nonparametric statistical analysis to identify likely activated kinases. This suggested that AT1aR-dependent signalling activates 48 of the 285 kinases detected in HEK293 cells. Of these, Aurora B, CLK3 and PKG1 have not previously been described in the pathway whereas others, such as PKA, PKB and PKC, are well known. In summary, we have developed a new method for kinase-centric analysis of phosphoproteomes to pinpoint differential kinase activity in large-scale data sets. PMID:24722691

Bøgebo, Rikke; Horn, Heiko; Olsen, Jesper V.; Gammeltoft, Steen; Jensen, Lars J.; Hansen, Jakob L.; Christensen, Gitte L.

2014-01-01

138

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

PubMed Central

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

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

2014-01-01

139

Quantitative phosphoproteomics of Alzheimer's disease reveals cross-talk between kinases and small heat shock proteins.  

PubMed

Abnormal phosphorylation contributes to the formation of neurofibrillary tangles in Alzheimer's disease (AD), but may play other signaling roles during AD pathogenesis. In this study, we employed IMAC followed by LC-MS/MS to identify phosphopeptides from eight individual AD and eight age-matched control postmortem human brain tissues. Using this approach, we identified 5569 phosphopeptides in frontal cortex across all 16 cases in which phosphopeptides represented 80% of all peptide spectral counts collected following IMAC enrichment. Marker selection identified 253 significantly altered phosphopeptides by precursor intensity, changed by at least 1.75-fold relative to controls, with an empirical false discovery rate below 7%. Approximately 21% of all significantly altered phosphopeptides in AD tissue were derived from tau. Of the other 142 proteins hyperphosphorylated in AD, membrane, synapse, cell junction, and alternatively spliced proteins were overrepresented. Of these, we validated differential phosphorylation of HSP 27 (HSPB1) and crystallin-alpha-B (CRYAB) as hyperphosphorylated by Western blotting. We further identified a network of phosphorylated kinases, which coenriched with phosphorylated small HSPs. This supports a hypothesis that a number of kinases are regulating and/or regulated by the small HSP folding network. PMID:25332170

Dammer, Eric B; Lee, Andrew K; Duong, Duc M; Gearing, Marla; Lah, James J; Levey, Allan I; Seyfried, Nicholas T

2015-01-01

140

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

PubMed Central

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

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

2014-01-01

141

Dissect Your Squid and Eat It Too!  

ERIC Educational Resources Information Center

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

McGinnis, Patricia

2001-01-01

142

Surgery for three-channeled aortic dissection  

Microsoft Academic Search

Among aortic dissections, three-channeled aortic dissection, in which two parallel false lumens are present, is relatively rare. We surgically treated 26 patients with this type of dissection, they accounted for 7.4% of all 349 patients with aortic dissection surgically treated between 1978 and May 1997. Their ages ranged from 24 to 77 years (mean 45 years). The male\\/female ratio was

Motomi Ando; Shinichi Takamoto; Yutaka Okita; Tetsuro Moroto

1998-01-01

143

Dissection & Science Fairs. [Information Packet.  

ERIC Educational Resources Information Center

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

National Anti-Vivisection Society, Chicago, IL.

144

Animal Rights Activism Threatens Dissection.  

ERIC Educational Resources Information Center

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

Holden, Constance

1990-01-01

145

Netfrog: The Interactive Frog Dissection  

NSDL National Science Digital Library

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

Kinzie, Mable

146

Aortic dissection presenting as pleural effusion  

PubMed Central

Aortic dissection is a life threatening emergency. This case illustrates the unusual way an aortic dissection can present. This patient presented with sharp, left interscapular pain, which subsided after a while and left-sided pleural effusion. Further investigations revealed that this was a case of thoracic aortic dissection with a leak into pleural space. She underwent thoracic endovascular aortic repair with stent graft insertion. PMID:22692486

Somasamudra, Pramod; Smith, Ed; Tandan, Ronja

2011-01-01

147

Integration of cell lysis, protein extraction, and digestion into one step for ultrafast sample preparation for phosphoproteome analysis.  

PubMed

Conventional sample preparation protocols for phosphoproteome analysis require multiple time-consuming and labor-intensive steps, including cell lysis, protein extraction, protein digestion, and phosphopeptide enrichment. In this study, we found that the presence of a large amount of trypsin in the sample did not interfere with phosphopeptide enrichment and subsequent LC-MS/MS analysis. Taking advantage of fast digestion achieved with high trypsin-to-protein ratio, we developed a novel concurrent lysis-digestion method for phosphoproteome analysis. In this method, the harvested cells were first placed in a lysis buffer containing a huge amount of trypsin. After ultrasonication, the cells were lysed and the proteins were efficiently digested into peptides within one step. Thereafter, tryptic digest was subjected to phosphopeptide enrichment, in which unphosphorylated peptides, trypsin, and other components incompatible with LC-MS/MS analysis were removed. Compared with conventional methods, better phosphoproteome coverage was achieved in this new one-step method. Because protein solubilization and cell lysis were facilitated by fast protein digestion, the complete transformation of cell pellets into the peptide mixture could be finished within 25 min, while it would take at least 16 h for conventional methods. Hence, our method, which integrated cell lysis, protein extraction, and protein digestion into one step, is rapid and convenient. It is expected to have broad applications in phosphoproteomics analysis. PMID:24958348

Liu, Fangjie; Ye, Mingliang; Pan, Yanbo; Zhang, Yi; Bian, Yangyang; Sun, Zhen; Zhu, Jun; Cheng, Kai; Zou, Hanfa

2014-07-15

148

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

E-print Network

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

Yang, Sichun

149

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

PubMed

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

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

2015-02-01

150

An integrated comparative phosphoproteomic and bioinformatic approach reveals a novel class of MPM-2 motifs upregulated in EGFRvIII-expressing Glioblastoma Cells  

E-print Network

Glioblastoma (GBM, WHO grade IV) is an aggressively proliferative and invasive brain tumor that carries a poor clinical prognosis with a median survival of 9 to 12 months. In a prior phosphoproteomic study performed in the ...

Joughin, Brian A.

151

Proteomic and phosphoproteomic analyses of chromatin-associated proteins from Arabidopsis thaliana.  

PubMed

The nucleus is the organelle where basically all DNA-related processes take place in eukaryotes, such as replication, transcription, and splicing as well as epigenetic regulation. The identification and description of the nuclear proteins is one of the requisites toward a comprehensive understanding of the biological functions accomplished in the nucleus. Many of the regulatory mechanisms of protein functions rely on their PTMs among which phosphorylation is probably one of the most important properties affecting enzymatic activity, interaction with other molecules, localization, or stability. So far, the nuclear and subnuclear proteome and phosphoproteome of the model plant Arabidopsis thaliana have been the subject of very few studies. In this work, we developed a purification protocol of Arabidopsis chromatin-associated proteins and performed proteomic and phosphoproteomic analyses identifying a total of 879 proteins of which 198 were phosphoproteins that were mainly involved in chromatin remodeling, transcriptional regulation, and RNA processing. From 230 precisely localized phosphorylation sites (phosphosites), 52 correspond to hitherto unidentified sites. This protocol and data thereby obtained should be a valuable resource for many domains of plant research. PMID:24889360

Bigeard, Jean; Rayapuram, Naganand; Bonhomme, Ludovic; Hirt, Heribert; Pflieger, Delphine

2014-10-01

152

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

PubMed Central

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

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

2014-01-01

153

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

PubMed

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

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

2014-09-01

154

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

PubMed Central

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

2013-01-01

155

Aortic arch dissection: a controversy of classification.  

PubMed

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

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

2014-06-01

156

Aortic Dissection Type A in Alpine Skiers  

PubMed Central

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

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

2013-01-01

157

Beyond Dissection: Innovative Tools for Biology Education.  

ERIC Educational Resources Information Center

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

Larson, Sandra, Ed.

158

Objecting To Dissection: A College Student's Handbook.  

ERIC Educational Resources Information Center

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

National Anti-Vivisection Society, Chicago, IL.

159

Quick Dissection of the Segmental Bronchi  

ERIC Educational Resources Information Center

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

Nakajima, Yuji

2010-01-01

160

Surgery for Three-Channeled Aortic Dissection.  

PubMed

Among aortic dissections, three-channeled aortic dissection, in which two parallel false lumens are present, is relatively rare. We surgically treated 26 patients with this type of dissection, they accounted for 7.4% of all 349 patients with aortic dissection surgically treated between 1978 and May 1997. Their ages ranged from 24 to 77 years (mean 45 years). The male/female ratio was 1:1. Marfan's syndrome was present in 15 patients and Bentall's-type operation had been performed in 12 patients. Pain at different times was observed in 19 patients. For preoperative diagnosis, computed tomography (CT) and magnetic resonance imaging (MRI) were useful. The morphology of the 1st and 2nd false lumens was Stanford type A + type B in 11 patients, type B + type B in 12, type A + type A in 2, and localized abdominal dissection in 1. Reentry of the second false lumen was observed in only 3 patients. Descending aortic replacement was performed in 13 patients, thoracoabdominal aortic replacement in 6, ascending aortic replacement in 3, and others in 4. Seven patients died in the hospital. There were 4 late deaths during follow-up for 10-158 months (mean, 58 months). When pain recurred in patients with aortic dissection, three-channeled dissection should be suspected. The incidence of this dissection is high in patients with Marfan's syndrome. PMID:9716796

Ando; Takamoto; Okita; Moroto

1998-08-01

161

Hippocampal phosphoproteomics of F344 rats exposed to 1-bromopropane.  

PubMed

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

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

2014-10-29

162

Spontaneous bilateral internal carotid artery dissection.  

PubMed

Spontaneous internal carotid artery dissection is not an uncommon cause of ischaemic stroke in younger patients, but multiple cervical arterial dissections at presentation are uncommon. Recurrence of dissection in a previously normal artery is common. In this case report we review the history, clinical findings and management of a 42-year-old woman who presented with stroke and Horner syndrome and was found to have spontaneous bilateral internal carotid artery dissection. She was not anticoagulated due to concerns relating to the size of her infarct. She was treated with a combination of aspirin and clopidogrel. We use dual antiplatelets for the management of cervical dissections as a part of the CADISS trial. The patient made good progress with the multidisciplinary team and was discharged on day 22 with support from the community stroke team. PMID:22110554

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

2009-01-01

163

Left atrial dissection: an almost unknown entity.  

PubMed

Left atrial dissection is an exceedingly rare but potentially fatal complication of cardiac surgery. It is most commonly associated with mitral valve surgery, including both replacement and repair, with a reported incidence rate of 0.16%. However, other cardiac surgical or catheter-based interventional procedures are also known as potential predisposing factors. The time of presentation from the cause of dissection varies extremely, ranging from immediate occurrence up to 20 years later. The dissection forms a large cavity between the endocardium and epicardium of the left atrium, causing obliteration of the left atrial cavity and resultant haemodynamic compromise, which almost always requires immediate surgical intervention. In contrast, left atrial dissection without haemodynamic instability can often be managed non-operatively with satisfactory outcomes. This article reviews this rare but relevant clinical entity to further elucidate the incidence, pathogenesis, clinical course, management and outcome of left atrial dissection. PMID:25260895

Fukuhara, Shinichi; Dimitrova, Kamellia R; Geller, Charles M; Hoffman, Darryl M; Tranbaugh, Robert F

2015-01-01

164

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

PubMed

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

Sirvent, Audrey; Urbach, Serge; Roche, Serge

2015-01-01

165

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

SciTech Connect

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

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

2013-06-05

166

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

PubMed

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

Rampitsch, Christof; Bykova, Natalia V

2012-01-01

167

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

PubMed

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

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

2014-11-01

168

Phosphoproteomic profiling of human myocardial tissues distinguishes ischemic from non-ischemic end stage heart failure.  

PubMed

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

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

2014-01-01

169

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

PubMed Central

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

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

170

Systematic analysis of the phosphoproteome and kinase-substrate networks in the mouse testis.  

PubMed

Spermatogenesis is a complex process closely associated with the phosphorylation-orchestrated cell cycle. Elucidating the phosphorylation-based regulations should advance our understanding of the underlying molecular mechanisms. Here we present an integrative study of phosphorylation events in the testis. Large-scale phosphoproteome profiling in the adult mouse testis identified 17,829 phosphorylation sites in 3955 phosphoproteins. Although only approximately half of the phosphorylation sites enriched by IMAC were also captured by TiO2, both the phosphoprotein data sets identified by the two methods significantly enriched the functional annotation of spermatogenesis. Thus, the phosphoproteome profiled in this study is a highly useful snapshot of the phosphorylation events in spermatogenesis. To further understand phosphoregulation in the testis, the site-specific kinase-substrate relations were computationally predicted for reconstructing kinase-substrate phosphorylation networks. A core sub-kinase-substrate phosphorylation networks among the spermatogenesis-related proteins was retrieved and analyzed to explore the phosphoregulation during spermatogenesis. Moreover, network-based analyses demonstrated that a number of protein kinases such as MAPKs, CDK2, and CDC2 with statistically more site-specific kinase-substrate relations might have significantly higher activities and play an essential role in spermatogenesis, and the predictions were consistent with previous studies on the regulatory roles of these kinases. In particular, the analyses proposed that the activities of POLO-like kinases (PLKs) might be dramatically higher, while the prediction was experimentally validated by detecting and comparing the phosphorylation levels of pT210, an indicator of PLK1 activation, in testis and other tissues. Further experiments showed that the inhibition of POLO-like kinases decreases cell proliferation by inducing G2/M cell cycle arrest. Taken together, this systematic study provides a global landscape of phosphoregulation in the testis, and should prove to be of value in future studies of spermatogenesis. PMID:25293948

Qi, Lin; Liu, Zexian; Wang, Jing; Cui, Yiqiang; Guo, Yueshuai; Zhou, Tao; Zhou, Zuomin; Guo, Xuejiang; Xue, Yu; Sha, Jiahao

2014-12-01

171

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

PubMed

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

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

2015-01-01

172

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

PubMed Central

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

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

2013-01-01

173

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

PubMed

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

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

2014-05-01

174

Animal Rights Groups Target High School Dissection.  

ERIC Educational Resources Information Center

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

Trotter, Andrew

1992-01-01

175

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

PubMed Central

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

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

2014-01-01

176

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

PubMed

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

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

2014-09-28

177

Carotid artery dissection: a challenging diagnosis.  

PubMed

Spontaneous extracranial internal carotid artery dissection (ICAD) is a rare vascular event. Even in the presence of existing signs and symptoms, the diagnosis can be missed by experienced clinicians of all specialties. This is a report of a patient who presented with symptomatic bilateral dissection manifested as partial Horner's syndrome. The diagnosis was made after several clinical evaluations with the use of duplex ultrasound and angiography. PMID:9949691

Aburahma, A F; Burns, W; Mullins, D A

1999-01-01

178

Peripartum presentation of an acute aortic dissection.  

PubMed

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

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

2005-04-01

179

Pulmonary hypertension and pulmonary artery dissection  

PubMed Central

Pulmonary artery dissection is a fatal complication of long-standing pulmonary hypertension, manifesting as acute, stabbing chest pain, progressive dyspnea, cardiogenic shock, or sudden death. Its incidence has been underestimated, and therapeutic options are still scarce. In patients with pulmonary hypertension, new chest pain, acute chest pain, or cardiogenic shock should raise the suspicion of pulmonary artery dissection, which can result in sudden death. PMID:23670510

Corrêa, Ricardo de Amorim; Silva, Luciana Cristina dos Santos; Rezende, Cláudia Juliana; Bernardes, Rodrigo Castro; Prata, Tarciane Aline; Silva, Henrique Lima

2013-01-01

180

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

PubMed Central

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

Horst, Walter Johannes

2013-01-01

181

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

PubMed

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. Anat Sci Educ 8: 45-52. © 2014 American Association of Anatomists. PMID:24799441

Nwachukwu, Chika; Lachman, Nirusha; Pawlina, Wojciech

2015-01-01

182

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

PubMed

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

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

2014-01-01

183

Prevention of complications in neck dissection  

PubMed Central

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

Kerawala, Cyrus J; Heliotos, Manolis

2009-01-01

184

Surgical treatment of acute ascending aortic dissection.  

PubMed Central

Since adopting a policy of immediate operation on patients with acute dissection of the ascending aorta, 42 men and 6 women (ages 18-67 years) have been managed surgically. Thirty-two patients had graft replacement of the ascending aorta and resuspension of the incompetent aortic valve. One of these had a coronary graft. There were five deaths in this group. Eight patients required aortic valve replacement because of a diseased aortic valve as well as grafting of the ascending aorta, with one death. Three patients had resuspension of the aortic valve and primary repair of their dissection without mortality. Two patients were managed successfully with an intraluminal prosthesis and resuspension of the aortic valve. Another patient had successful repair with a valved conduit and reimplantation of the coronaries. Two patients dissected 4 and 6 years after aortic valve replacement and neither survived operative repair. Of the surviving patients, one required dialysis, one a femoral-femoral bypass graft, and one an axillo-femoral bypass graft. One patient required a pacemaker for heart block, and two underwent successful repair of suture line aneurysms, both occurring three years after operation. On the basis of this experience, prompt surgical intervention for acute ascending aortic dissection is the treatment of choice. A variety of techniques are available to repair the dissected aorta. Long-term results for resuspension of the aortic valve in acute ascending aortic dissection have been excellent and emphasize that valve replacement should be reserved for those patients found at operation to have a primary abnormality of the aortic valve. PMID:6222709

Wolfe, W G; Oldham, H N; Rankin, J S; Moran, J F

1983-01-01

185

The nature of dissection: Exploring student conceptions  

NASA Astrophysics Data System (ADS)

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

York, Katharine

186

[Surgery of aortic dissection: for which patient?].  

PubMed

In the acute stage (less than two weeks), surgery is indicated for Stanford type A aortic dissections. With respect to the initial work-up, surgery consists in replacing the ascending aorta, sometimes the aortic arch (with supra aortic vessels reimplantation), and aortic valve replacement (valve replacement, Bentall valved tube or valve sparing Tyron David technique). Ischemic visceral complications must be searched for and treated by endovascular techniques or surgery. Aneurismal evolution of chronic dissections must be treated surgically. Replacement can encompass the entire aorta. PMID:21146353

Verhoye, Jean-Philippe; Abouliatim, Issam; Larralde, Antoine; Beneux, Xavier; Heautot, Jean-François

2011-01-01

187

Intracranial Vertebral Artery Dissections: Evolving Perspectives  

PubMed Central

Summary Intracranial vertebral artery dissection (VAD) represents the underlying etiology in a significant percentage of posterior circulation ischemic strokes and subarachnoid hemorrhages. These lesions are particularly challenging in their diagnosis, management, and in the prediction of long-term outcome. Advances in the understanding of underlying processes leading to dissection, as well as the evolution of modern imaging techniques are discussed. The data pertaining to medical management of intracranial VADs, with emphasis on anticoagulants and antiplatelet agents, is reviewed. Surgical intervention is discussed, including, the selection of operative candidates, open and endovascular procedures, and potential complications. The evolution of endovascular technology and techniques is highlighted. PMID:23217643

Ali, M.S.; Amenta, P.S.; Starke, R.M.; Jabbour, P.M.; Gonzalez, L.F.; Tjoumakaris, S.I.; Flanders, A.E.; Rosenwasser, R.H.; Dumont, A.S.

2012-01-01

188

Politics & Prejudice: Dissection in Biology Education. Part II.  

ERIC Educational Resources Information Center

The issues, roles, dynamics, rationales and events embroiled in the dissection controversy are discussed. Insights into where the politics of biology education without speciesism or dissection are likely to take science education in the future are provided. (KR)

Gilmore, David R.

1991-01-01

189

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

PubMed Central

Hundreds of candidate 14-3-3-binding (phospho)proteins have been reported in publications that describe one interaction at a time, as well as high-throughput 14-3-3-affinity and mass spectrometry-based studies. Here, we transcribed these data into a common format, deposited the collated data from low-throughput studies in MINT (http://mint.bio.uniroma2.it/mint), and compared the low- and high-throughput data in VisANT graphs that are easy to analyze and extend. Exploring the graphs prompted questions about technical and biological specificity, which were addressed experimentally, resulting in identification of phosphorylated 14-3-3-binding sites in the mitochondrial import sequence of the iron-sulfur cluster assembly enzyme (ISCU), cytoplasmic domains of the mitochondrial fission factor (MFF), and endoplasmic reticulum-tethered receptor expression-enhancing protein 4 (REEP4), RNA regulator SMAUG2, and cytoskeletal regulatory proteins, namely debrin-like protein (DBNL) and kinesin light chain (KLC) isoforms. Therefore, 14-3-3s undergo physiological interactions with proteins that are destined for diverse subcellular locations. Graphing and validating interactions underpins efforts to use 14-3-3-phosphoproteomics to identify mechanisms and biomarkers for signaling pathways in health and disease. PMID:21725060

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

2011-01-01

190

The differential hippocampal phosphoproteome of Apodemus sylvaticus paralleling spatial memory retrieval in the Barnes maze.  

PubMed

Protein phosphorylation is a well-known and well-documented mechanism in memory processes. Although a large series of protein kinases involved in memory processes have been reported, information on phosphoproteins is limited. It was therefore the aim of the study to determine a partial and differential phosphoproteome along with the corresponding network in hippocampus of a wild caught mouse strain with excellent performance in several paradigms of spatial memory. Apodemus sylvaticus mice were trained in the Barnes maze, a non-invasive test system for spatial memory and untrained mice served as controls. Animals were sacrificed 6h following memory retrieval, hippocampi were taken, proteins extracted and in-solution digestion was carried out with subsequent iTRAQ double labelling. Phosphopeptides were enriched by a TiO2-based method and semi-quantified using two fragmentation principles on the LTQ-orbitrap Velos. In hippocampi of trained animals phosphopeptide levels representing signalling, neuronal, synaptosomal, cytoskeletal and metabolism proteins were at least twofold reduced or increased. Furthermore, a network revealing a link to pathways of ubiquitination, the androgen receptor, small GTPase Rab5 and MAPK signaling as well as synucleins was constructed. This work is relevant for interpretation of previous work and the design of future studies on protein phosphorylation in spatial memory. PMID:24509310

Li, Lin; Csaszar, Edina; Szodorai, Edit; Patil, Sudarshan; Pollak, Arnold; Lubec, Gert

2014-05-01

191

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

PubMed Central

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

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

2014-01-01

192

The Plasmodium falciparum schizont phosphoproteome reveals extensive phosphatidylinositol and cAMP-protein kinase A signaling.  

PubMed

The asexual blood stages of Plasmodium falciparum cause the most lethal form of human malaria. During growth within an infected red blood cell, parasite multiplication and formation of invasive merozoites is called schizogony. Here, we present a detailed analysis of the phosphoproteome of P. falciparum schizonts revealing 2541 unique phosphorylation sites, including 871 novel sites. Prominent roles for cAMP-dependent protein kinase A- and phosphatidylinositol-signaling were identified following analysis by functional enrichment, phosphoprotein interaction network clustering and phospho-motif identification tools. We observed that most key enzymes in the inositol pathway are phosphorylated, which strongly suggests additional levels of regulation and crosstalk with other protein kinases that coregulate different biological processes. A distinct pattern of phosphorylation of proteins involved in merozoite egress and red blood cell invasion was noted. The analyses also revealed that cAMP-PKA signaling is implicated in a wide variety of processes including motility. We verified this finding experimentally using an in vitro kinase assay and identified three novel PKA substrates associated with the glideosome motor complex: myosin A, GAP45 and CDPK1. Therefore, in addition to an established role for CDPK1 in the motor complex, this study reveals the coinvolvement of PKA, further implicating cAMP as an important regulator of host cell invasion. PMID:23025827

Lasonder, Edwin; Green, Judith L; Camarda, Grazia; Talabani, Hana; Holder, Anthony A; Langsley, Gordon; Alano, Pietro

2012-11-01

193

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

PubMed

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

Han, Chao; Wang, Kun; Yang, Pingfang

2014-08-01

194

Global Distribution of Dissected Duricrust on Mars  

NASA Technical Reports Server (NTRS)

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

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

2000-01-01

195

Dissecting the pressure field in tidal flow  

E-print Network

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

Warner, Sally

196

Dissecting the pressure field in tidal flow  

E-print Network

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

Warner, Sally

197

Physical injuries in the dissecting room.  

PubMed

Dissection of human cadavers remains an important element of learning anatomy in many medical and dental schools. During this activity, students are introduced to the safe handling of surgical instruments. The frequency, type, and mechanism of associated injuries are unknown. We undertook a retrospective cohort analysis of dissecting-room accidents during a 6-year period (2001-2006). Injury rates were adjusted to account for exposure risk. A total of 55 injuries, all minor, were recorded in 53 students, representing an overall injury rate of less than 4 injuries per 1,000 hr of dissection. Twenty-four injuries were documented in third-year medical students, 13 in second-year medical students, 10 in second-year dental students, and 8 in third-year science students. There was a statistically significant difference in injury rates between the groups due to a higher than expected rate among second-year medical students and a lower than expected rate among third-year medical students (P < 0.01). At least 38 (69%) injuries were from a scalpel blade. A further three injuries were from bone spicules. All except two injuries affected the hand. In conclusion, it is unusual for students to injure themselves in the dissecting room. Injuries tend to be minor and largely related to scalpel blades. A greater awareness of hazards due to sharps and safe handling techniques may reduce the risks of minor injury and better prepare students for future clinical practice. PMID:18058901

Cornwall, Jon; Stringer, Mark D

2008-01-01

198

A COMPARATIVE PRIMATE ANATOMY Dissection Manual  

E-print Network

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

Ackermann, Rebecca Rogers

199

Pythagoras and the Dissection of Polygons.  

ERIC Educational Resources Information Center

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

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

1984-01-01

200

Ownership and control: dissecting the pyramid  

Microsoft Academic Search

Pyramids, cross-ownership, rings and other complex features are frequent in the European and Japanese industrial world. The dissection of these structures requires a proper measurement of indirect shareholdings. While some authors use the (generally overestimated) data coming from legal ownership declarations, Ellerman (1991) and Flath (1992), Baldone et al. (1997) use the input-output matrix technology applied to raw ownership data.

Ariane Chapelle; Ariane Szafarz

2002-01-01

201

Dissection of the Mammalian Midbody Proteome Reveals  

E-print Network

, and chromosome segregation (6­9). Mammalian midbody isolation. We iso- lated midbodies from Chinese hamster ovaryDissection of the Mammalian Midbody Proteome Reveals Conserved Cytokinesis Mechanisms Ahna R. Skop is the essential process that partitions cellular contents into daugh- ter cells. To identify and characterize

Meyer, Barbara

202

Intraoperative aortic dissection in pediatric heart surgery.  

PubMed

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

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

2006-06-01

203

Cow's Eye Dissection in the Physics Lab.  

ERIC Educational Resources Information Center

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

Lapp, David R.; Keenan, James E.

1991-01-01

204

Squid Dissection: From Pen to Ink.  

ERIC Educational Resources Information Center

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

Brown, Cindy; Kisiel, Jim

2003-01-01

205

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

PubMed

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

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

2010-12-01

206

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

PubMed Central

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

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

2011-01-01

207

Quantitative phosphoproteomic analysis identifies activation of the RET and IGF-1R/IR signaling pathways in neuroblastoma.  

PubMed

Neuroblastoma is an embryonal tumor of childhood with a heterogenous clinical presentation that reflects differences in activation of complex biological signaling pathways. Protein phosphorylation is a key component of cellular signal transduction and plays a critical role in processes that control cancer cell growth and survival. We used shotgun LC/MS to compare phosphorylation between a human MYCN amplified neuroblastoma cell line (NB10), modeling a resistant tumor, and a human neural precursor cell line (NPC), modeling a normal baseline neural crest cell. 2181 unique phosphorylation sites representing 1171 proteins and 2598 phosphopeptides were found. Protein kinases accounted for 6% of the proteome, with a predominance of tyrosine kinases, supporting their prominent role in oncogenic signaling pathways. Highly abundant receptor tyrosine kinase (RTK) phosphopeptides in the NB10 cell line relative to the NPC cell line included RET, insulin-like growth factor 1 receptor/insulin receptor (IGF-1R/IR), and fibroblast growth factor receptor 1 (FGFR1). Multiple phosphorylated peptides from downstream mediators of the PI3K/AKT/mTOR and RAS pathways were also highly abundant in NB10 relative to NPC. Our analysis highlights the importance of RET, IGF-1R/IR and FGFR1 as RTKs in neuroblastoma and suggests a methodology that can be used to identify potential novel biological therapeutic targets. Furthermore, application of this previously unexploited technology in the clinic opens the possibility of providing a new wide-scale molecular signature to assess disease progression and prognosis. PMID:24349301

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

2013-01-01

208

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

PubMed Central

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

2014-01-01

209

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

ERIC Educational Resources Information Center

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…

Akpan, Joseph; Strayer, Jeremy

2010-01-01

210

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

PubMed

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

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

2014-12-01

211

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

PubMed

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

Zhao, Man; Deng, Chunhui; Zhang, Xiangmin

2014-06-14

212

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

PubMed Central

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

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

2014-01-01

213

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

Microsoft Academic Search

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

Dominik Domanski; Caren C Helbing

2007-01-01

214

Current evidence for thoracic aorta type B dissection management.  

PubMed

Aortic dissection is a devastating cardiovascular condition and represents the most common aortic emergency. Outcome is determined by the type and extent of dissection and the presence of associated complications requiring early diagnosis and treatment. Aortic dissection is defined as acute within 14 days from onset and chronic after that time period. The natural course of type B dissection is determined by 2 elements, early and chronic complications. An uncomplicated acute type B dissection is less frequently lethal but it is not totally benign. Some peculiar issues must be taken into account, such as the high probability of complications development in a dissected aorta and the poor long-term prognosis on medical treatment alone. Then, it would be helpful to identify which patients with uncomplicated type B dissection will have a poorest aortic prognosis over time in order to apply an early intervention. PMID:24043474

Capoccia, Laura; Riambau, Vicente

2014-12-01

215

Temporal phosphoproteomics to investigate the mechanotransduction of vascular smooth muscle cells in response to cyclic stretch.  

PubMed

Vascular smooth muscle cells (VSMCs) are exposed to mechanical cyclic stretch in vivo, which play important roles in maintenance of vascular homeostasis and regulation of pathological vascular remodeling. Reversible protein phosphorylation is crucial for intracellular signaling transduction. However, the dynamic phosphorylated profile induced by cyclic stretch in VSMCs is still unclear. Using the stable isotope labeling by amino acid in cell culture, VSMCs were labeled and exposed to 10% physiological cyclic stretch in vitro at 1.25Hz for 0min, 15min, 30min, 1h and 6h, respectively. Using TiO2 beads and liquid chromatography tandem mass spectrometry, the temporal phosphoproteomic profiles in response to cyclic stretch were then detected. Bioinformatics analysis including fuzzy c-means clustering, functional classifications, and Ingenuity Pathway Analysis were applied to further reveal the potential mechanotranduction networks. The results indicated that protein kinase C (PKCs) family, Rho-associated coiled-coil containing protein kinase 1 (ROCK1) and Akt may participate in cyclic-stretch induced VSMC functions. Cyclic stretch repressed the expression of ROCK1, while it had no significant effect on the phosphorylation of PKC?/?II, PKC?/? and PKC?/?. PKC? was activated first at short time-phase (15min and 30min), and again at long time-phase (6h, 12h and 24h). The activation of p-PKC? was immediate and short-term, similar to p-Akt. Our present in vitro work hence revealed that cyclic stretch activates complex mechanotransduction networks, suggesting that novel mechanoresponsive molecules, i.e., PKC?, PKC?, and ROCK1, may participate in the mechanotransduction and modulation VSMC functions. PMID:25458152

Yang, Yu-Chen; Wang, Xiao-Dong; Huang, Kai; Wang, Lu; Jiang, Zong-Lai; Qi, Ying-Xin

2014-10-16

216

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

PubMed Central

Background Selaginella (Selaginella moellendorffii) is a lycophyte which diverged from other vascular plants approximately 410 million years ago. As the first reported non-seed vascular plant genome, Selaginella genome data allow comparative analysis of genetic changes that may be associated with land plant evolution. Proteomics investigations on this lycophyte model have not been extensively reported. Phosphorylation represents the most common post-translational modifications and it is a ubiquitous regulatory mechanism controlling the functional expression of proteins inside living organisms. Results In this study, polyethylene glycol fractionation and immobilized metal ion affinity chromatography were employed to isolate phosphopeptides from wild-growing Selaginella. Using liquid chromatography-tandem mass spectrometry analysis, 1593 unique phosphopeptides spanning 1104 non-redundant phosphosites with confirmed localization on 716 phosphoproteins were identified. Analysis of the Selaginella dataset revealed features that are consistent with other plant phosphoproteomes, such as the relative proportions of phosphorylated Ser, Thr, and Tyr residues, the highest occurrence of phosphosites in the C-terminal regions of proteins, and the localization of phosphorylation events outside protein domains. In addition, a total of 97 highly conserved phosphosites in evolutionary conserved proteins were identified, indicating the conservation of phosphorylation-dependent regulatory mechanisms in phylogenetically distinct plant species. On the other hand, close examination of proteins involved in photosynthesis revealed phosphorylation events which may be unique to Selaginella evolution. Furthermore, phosphorylation motif analyses identified Pro-directed, acidic, and basic signatures which are recognized by typical protein kinases in plants. A group of Selaginella-specific phosphoproteins were found to be enriched in the Pro-directed motif class. Conclusions Our work provides the first large-scale atlas of phosphoproteins in Selaginella which occupies a unique position in the evolution of terrestrial plants. Future research into the functional roles of Selaginella-specific phosphorylation events in photosynthesis and other processes may offer insight into the molecular mechanisms leading to the distinct evolution of lycophytes. PMID:24628833

2014-01-01

217

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

SciTech Connect

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

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

2013-09-22

218

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

PubMed Central

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

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

2009-01-01

219

Recurrent tamponade and aortic dissection in syphilis.  

PubMed

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

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

2013-11-01

220

Central compartment dissection in laryngeal cancer.  

PubMed

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

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

2011-05-01

221

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

PubMed Central

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

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

2014-01-01

222

Undergraduate Quantitative  

E-print Network

Undergraduate Quantitative Research Methods with: Childhood Studies | Geography | Politics | Social.ac.uk/study The University of Bristol is introducing a new quantitative research methods pathway to a range of social science new courses, work placements and pathways to Why enhance your degree with quantitative research

Bristol, University of

223

Vertebral and carotid artery dissection following chiropractic cervical manipulation  

Microsoft Academic Search

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

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

1999-01-01

224

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

PubMed

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

Zhu, Lin; Li, Ning

2012-01-01

225

Metabolic Signature of Electrosurgical Liver Dissection  

PubMed Central

Background and Aims High frequency electrosurgery has a key role in the broadening application of liver surgery. Its molecular signature, i.e. the metabolites evolving from electrocauterization which may inhibit hepatic wound healing, have not been systematically studied. Methods Human liver samples were thus obtained during surgery before and after electrosurgical dissection and subjected to a two-stage metabolomic screening experiment (discovery sample: N?=?18, replication sample: N?=?20) using gas chromatography/mass spectrometry. Results In a set of 208 chemically defined metabolites, electrosurgical dissection lead to a distinct metabolic signature resulting in a separation in the first two dimensions of a principal components analysis. Six metabolites including glycolic acid, azelaic acid, 2-n-pentylfuran, dihydroactinidiolide, 2-butenal and n-pentanal were consistently increased after electrosurgery meeting the discovery (p<2.0×10?4) and the replication thresholds (p<3.5×10?3). Azelaic acid, a lipid peroxidation product from the fragmentation of abundant sn-2 linoleoyl residues, was most abundant and increased 8.1-fold after electrosurgical liver dissection (preplication?=?1.6×10?4). The corresponding phospholipid hexadecyl azelaoyl glycerophosphocholine inhibited wound healing and tissue remodelling in scratch- and proliferation assays of hepatic stellate cells and cholangiocytes, and caused apoptosis dose-dependently in vitro, which may explain in part the tissue damage due to electrosurgery. Conclusion Hepatic electrosurgery generates a metabolic signature with characteristic lipid peroxidation products. Among these, azelaic acid shows a dose-dependent toxicity in liver cells and inhibits wound healing. These observations potentially pave the way for pharmacological intervention prior liver surgery to modify the metabolic response and prevent postoperative complications. PMID:24058442

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

2013-01-01

226

Harnessing Natural Sequence Variation to Dissect Posttranscriptional Regulatory Networks in Yeast  

PubMed Central

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

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

2014-01-01

227

Contemporary inguinal lymph node dissection: minimizing complications  

Microsoft Academic Search

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

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

2009-01-01

228

[Bilateral cervical arterial dissection as a sign of proximal aortic dissection: a rare cause of recidivating TIA].  

PubMed

Proximal aortic dissection is a life-threatening disease. In addition to other complications, involvement of the brain-supplying arteries can lead to acute cerebral ischemia. In the presented case, only the patient's clinical course and duplex sonography, which showed bilateral cervical arterial dissections, led to the diagnosis of aortic dissection. This case emphasizes that early ultrasound examination is crucial in patients with suspected cerebral ischemia. PMID:16897049

Grabowski, A

2006-10-01

229

Dissecting specific and global transcriptional regulation of bacterial gene expression  

PubMed Central

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

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

2013-01-01

230

Dissection of miRNA pathways using Arabidopsis mesophyll protoplasts.  

PubMed

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

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

2014-10-24

231

Dissection of miRNA Pathways Using Arabidopsis Mesophyll Protoplasts.  

PubMed

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

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

2015-02-01

232

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

PubMed Central

Summary Plasmodium falciparum and Toxoplasma gondii are obligate intracellular apicomplexan parasites that rapidly invade and extensively modify host cells. Protein phosphorylation is one mechanism by which these parasites can control such processes. Here we present a phosphoproteome analysis of peptides enriched from schizont stage P. falciparum and T. gondii tachyzoites that are either “intracellular” or purified away from host material. Using liquid chromatography and tandem mass-spectrometry we identified over 5,000 and 10,000 previously unknown phosphorylation sites in P. falciparum and T. gondii respectively, revealing that protein phosphorylation is an extensively used regulation mechanism both within and beyond parasite boundaries. Unexpectedly both parasites have phosphorylated tyrosines and P. falciparum has unusual phosphorylation motifs that are apparently shaped by its A:T-rich genome. This dataset provides important information on the role of phosphorylation in the host-pathogen interaction, and clues to the evolutionary forces operating on protein phosphorylation motifs in both parasites. PMID:22018241

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

2012-01-01

233

Analysis of quantitative trait loci that influence animal behavior  

Microsoft Academic Search

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

Jonathan Flint

2003-01-01

234

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

PubMed Central

Salinity is a major abiotic stress affecting plant growth and development. Understanding the molecular mechanisms of salt response and defense in plants will help in efforts to improve the salt tolerance of crops. Brachypodium distachyon is a new model plant for wheat, barley, and several potential biofuel grasses. In the current study, proteome and phosphoproteome changes induced by salt stress were the focus. The Bd21 leaves were initially treated with salt in concentrations ranging from 80 to 320 mm and then underwent a recovery process prior to proteome analysis. A total of 80 differentially expressed protein spots corresponding to 60 unique proteins were identified. The sample treated with a median salt level of 240 mm and the control were selected for phosphopeptide purification using TiO2 microcolumns and LC-MS/MS for phosphoproteome analysis to identify the phosphorylation sites and phosphoproteins. A total of 1509 phosphoproteins and 2839 phosphorylation sites were identified. Among them, 468 phosphoproteins containing 496 phosphorylation sites demonstrated significant changes at the phosphorylation level. Nine phosphorylation motifs were extracted from the 496 phosphorylation sites. Of the 60 unique differentially expressed proteins, 14 were also identified as phosphoproteins. Many proteins and phosphoproteins, as well as potential signal pathways associated with salt response and defense, were found, including three 14-3-3s (GF14A, GF14B, and 14-3-3A) for signal transduction and several ABA signal-associated proteins such as ABF2, TRAB1, and SAPK8. Finally, a schematic salt response and defense mechanism in B. distachyon was proposed. PMID:24335353

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

2014-01-01

235

Management of isolated superior mesenteric artery dissection  

PubMed Central

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

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

2014-01-01

236

Molecular Mechanisms of Thoracic Aortic Dissection  

PubMed Central

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

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

2013-01-01

237

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

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…

Akpan, Joseph Paul; Andre, Thomas

1999-01-01

238

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

Federal Register 2010, 2011, 2012, 2013, 2014

...Investigation No. 337-TA-865] Certain Balloon Dissection Devices and Products Containing...after importation of certain dissection balloons and products containing the same by reason...after importation of certain dissection balloons and products containing the same...

2013-01-31

239

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

PubMed

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

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

2012-01-01

240

Lateral lymph node dissection for lower rectal cancer.  

PubMed

The mainstay of surgical therapy for rectal cancer is colectomy (including lesions) with lymph node dissection. The lymphatic spread of rectal cancer can proceed in two directions: medially toward the origin of the inferior mesenteric artery or laterally toward the pelvis aslong the internal iliac artery. To prevent postoperative recurrence, lymph nodes situated along these two axes should be adequately dissected, leaving no residual cancer cells. In Japan, the standard procedure for advanced lower rectal cancer is mesorectal excision and lateral lymph node dissection with autonomic nerve preservation. In Europe and North America, lateral lymph node dissection used to be performed, but it led to increased blood loss, complications, and dysfunction, with no improvement in survival. Lateral lymph node dissection is thus no longer performed. Instead, multidisciplinary therapy combining mesorectal excision with preoperative chemoradiotherapy is now the standard treatment for advanced rectal cancer. Although lateral lymph node dissection decreases the rate of local recurrence similar to preoperative chemoradiotherapy, whether it contributes to improved survival remains unclear. In addition, it is unlikely that prophylactic lateral lymph node dissection is required in all patients with rectal cancer. Definition of the indications for lateral lymph node dissection is thus an important concern. PMID:23703637

Nakamura, T; Watanabe, M

2013-08-01

241

Surgical Delay for Acute Type A Dissection With Malperfusion  

Microsoft Academic Search

Background. An acute type A aortic dissection is considered a surgical emergency. Review of the risk factors for a type A dissection showed that preoperative malperfusion was associated with a 22% (2\\/9) intraoperative mortality and an 89% (8\\/9) hospital mortality. Intraoperative deaths were secondary to pulmonary failure resulting from capillary leak; the remaining patients died of multiorgan failure resulting from

G. Michael Deeb; David M Williams; Steven F Bolling; Leslie E Quint; Hilary Monaghan; Jennifer Sievers; Dean Karavite; Michael Shea

1997-01-01

242

Choosing the correct treatment for acute aortic type B dissection.  

PubMed

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

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

2015-04-01

243

Dissection Videos Do Not Improve Anatomy Examination Scores  

ERIC Educational Resources Information Center

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

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

2011-01-01

244

A Modified Dissection Method to Preserve Neck Structures  

ERIC Educational Resources Information Center

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

Hankin, Mark H.; Stoller, Jeremy L.

2009-01-01

245

Cardiac tamponade – presentation of type A aortic dissection  

PubMed Central

Acute aortic dissection usually presents with severe chest and/or back pain but may have a varied presentation ranging from syncope, stroke, and heart failure to shock or tamponade. We present classic chest computed tomography images of a case of type A aortic dissection presenting with cardiac tamponade. PMID:25432649

Fadahunsi, Opeyemi; Romeo, Michael

2014-01-01

246

Axillary artery cannulation in type a aortic dissection operations  

Microsoft Academic Search

Background: Femoral arteries are the preferred site of peripheral cannulation for arterial inflow in type A aortic dissection operations. The presence of aortoiliac aneurysms, severe peripheral occlusive disease, atherosclerosis of the femoral vessels, and distal extension of the aortic dissection may preclude their utilization. Axillary artery cannulation may represent a valid alternative in these circumstances. Methods: Between January 15, 1989,

Eugenio Neri; Massimo Massetti; Gianni Capannini; Enrico Carone; Enrico Tucci; Francesco Diciolla; Edvin Prifti; Carlo Sassi

1999-01-01

247

ASSOCIATION OF INTERNAL CAROTID ARTERY DISSECTION AND CHIROPRACTIC MANIPULATION  

Microsoft Academic Search

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

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

2003-01-01

248

Alternatives To Animal Dissection in School Science Classes. ERIC Digest.  

ERIC Educational Resources Information Center

Until recently, one of the most expected and accepted experiences among students in biology classrooms of the United States has been the dissection of vertebrate animals, from frogs and mice to cats and fetal pigs. However, resistance to animal dissection has grown during the past decade with concerns ranging from inhumane treatment of animals by…

Haury, David L.

249

Controlled ultrasonic micro-dissection of thin tissue sections.  

PubMed

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

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

2014-08-01

250

Management and long-term outcome of aortic dissection.  

PubMed Central

All 163 patients admitted to one institution between 1975 and 1988 with aortic dissection were reviewed. Type I and type II patients received grafting of the ascending aorta, with an intraoperative mortality rate of 11%. For type III dissection, management was medical in 53 patients, while 19 required surgery for aortic rupture or expansion, with an intraoperative mortality rate of 11%. The 9- or 10-year survival rates were 29%, 46%, and 29% for types I, II, and III respectively. Of 135 patients with primary aortic dissection, 17 (13%) required subsequent aortic surgery. Cause of late death was other cardiovascular disease in 38%, rupture of another aortic segment in 18%, sudden death in 24%, and other medical conditions in 21%. Although operative therapy for types I and II dissections and reserving operation for selected type III dissections provides acceptable long-term survival, careful follow-up is necessary due to concurrent cardiovascular disease and residual aortic disease. Images Fig. 3. PMID:2064469

Glower, D D; Speier, R H; White, W D; Smith, L R; Rankin, J S; Wolfe, W G

1991-01-01

251

Evaluating multiplexed quantitative phosphopeptide analysis on a hybrid quadrupole mass filter/linear ion trap/orbitrap mass spectrometer.  

PubMed

As a driver for many biological processes, phosphorylation remains an area of intense research interest. Advances in multiplexed quantitation utilizing isobaric tags (e.g., TMT and iTRAQ) have the potential to create a new paradigm in quantitative proteomics. New instrumentation and software are propelling these multiplexed workflows forward, which results in more accurate, sensitive, and reproducible quantitation across tens of thousands of phosphopeptides. This study assesses the performance of multiplexed quantitative phosphoproteomics on the Orbitrap Fusion mass spectrometer. Utilizing a two-phosphoproteome model of precursor ion interference, we assessed the accuracy of phosphopeptide quantitation across a variety of experimental approaches. These methods included the use of synchronous precursor selection (SPS) to enhance TMT reporter ion intensity and accuracy. We found that (i) ratio distortion remained a problem for phosphopeptide analysis in multiplexed quantitative workflows, (ii) ratio distortion can be overcome by the use of an SPS-MS3 scan, (iii) interfering ions generally possessed a different charge state than the target precursor, and (iv) selecting only the phosphate neutral loss peak (single notch) for the MS3 scan still provided accurate ratio measurements. Remarkably, these data suggest that the underlying cause of interference may not be due to coeluting and cofragmented peptides but instead from consistent, low level background fragmentation. Finally, as a proof-of-concept 10-plex experiment, we compared phosphopeptide levels from five murine brains to five livers. In total, the SPS-MS3 method quantified 38?247 phosphopeptides, corresponding to 11?000 phosphorylation sites. With 10 measurements recorded for each phosphopeptide, this equates to more than 628?000 binary comparisons collected in less than 48 h. PMID:25521595

Erickson, Brian K; Jedrychowski, Mark P; McAlister, Graeme C; Everley, Robert A; Kunz, Ryan; Gygi, Steven P

2015-01-20

252

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

ERIC Educational Resources Information Center

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

Kariuki, Patrick; Paulson, Ronda

253

Cervical Artery Dissection: Emerging Risk Factors  

PubMed Central

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

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

2010-01-01

254

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

PubMed

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

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

2003-07-01

255

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

PubMed Central

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

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

2014-01-01

256

Ascending aortic dissection without intimal tear: a case report.  

PubMed

Aortic dissection may occur without the presence of intimal tear, and it may occur with medial dissection and intramural hematoma. We report a case in which mediastinal enlargement was found in the chest x-ray of a 79-year-old patient with chest and back pain that had started suddenly 1 week before. The patient had a decrease in hematocrit, and transthoracic echocardiography revealed around the heart pericardial fluid 5 cm thick. The ascending aorta could not be evaluated because of the presence of this fluid. The preoperative diagnosis, based on the computerized tomography findings (dissection of ascending aorta and pericardial fluid), was ruptured dissection of the ascending aorta. The patient underwent an emergency operation. Two liters of hemorrhagic fluid was aspirated from the pericardium during the operation. The ascending aorta was opened, but there was no intimal tear. Medial dissection and intramural hemorrhage were seen. The ascending aorta was replaced with a tube graft. Cases such as this, of medial dissection and intramural hematoma in which intimal integrity is preserved, should be approached in the same manner as classical dissections with intimal tear. PMID:12538130

Kaplan, Mehmet; Yapici, Fikri; Erkan, Murat; Sargin, Murat; Demirtas, Mahmut Murat

2002-01-01

257

Sequential multiple visceral arteries dissections without aortic involvement.  

PubMed

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

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

2013-05-01

258

Quantitative NMR  

NSDL National Science Digital Library

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

Korir, Albert K.; Larive, Cynthia K.

2011-07-18

259

Neck dissection with cervical sensory preservation in thyroid cancer  

PubMed Central

Thyroid cancer is the most common endocrine malignancy. Recently, controversy has focused on the management of lymph node metastases, which represent approximately 90% of disease recurrences and may require considerable time, effort, and resources to diagnose and treat. Neck dissections play an essential role in the management of head and neck cancer. A modified radical neck dissection (MND) refers to resection of the lymph nodes in levels II through V and often including the central nodes in level VI. When performing modified neck dissection, we recommend to protect more reserved cervical plexus. The purpose is to better protect patient’s neck skin feeling. PMID:25083485

Xue, Shuai; Wang, Peisong

2013-01-01

260

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

Microsoft Academic Search

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

Rian De Villiers; Martin Monk

2005-01-01

261

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

Microsoft Academic Search

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

Kathleen M. Allspaw

2008-01-01

262

Vertebral Artery Dissection as a Cause of Cervical Radiculopathy  

PubMed Central

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

Khangure, Mark; Silbert, Peter Linton

2013-01-01

263

GPM Dissects Typhoon Hagupit - Duration: 0:38.  

NASA Video Gallery

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

264

[Malperfusion in aortic dissection: diagnostic problems and therapeutic procedures].  

PubMed

Malperfusion of the thoracoabdominal aorta and its side branches is a common complication of aortic dissection, often proving fatal. Vital organ malperfusion accompanying acute aortic dissection is a major cause of mortality and morbidity and requires timely reperfusion of the ischemic organs as well as adequate management of the aortic dissection. Ischemic damage to vital organs supplied by the thoracoabdominal aorta greatly increases the overall risk of aortic dissection. As initial symptoms may be subtle, malperfusion tends to be recognized late, and therefore accounts for a considerable percentage of fatalities.Effective reperfusion is not readily achieved by central aortic surgery alone in a certain number of patients. Various strategies have been used, including entry closure by central aortic surgery or stent grafting, surgical or catheter fenestration, bypass grafting and percutaneous stenting.Endovascular bare-metal stent placement is an attractive and promising treatment option since it is readily available, is less invasive and presents fewer risks to the patient. PMID:21858546

Jánosi, R A; Böse, D; Konorza, T; Eggebrecht, H; Tsagakis, K; Jakob, H; Erbel, R

2011-09-01

265

Dissection Videos Do Not Improve Anatomy Examination Scores  

NSDL National Science Digital Library

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

Waqas Mahmud (Rawalpindi Medical College Anatomy)

2011-01-03

266

Spontaneous Coronary Artery Dissection: Not Just a Heart Attack  

MedlinePLUS

Spontaneous Coronary Artery Dissection: Not Just a Heart Attack Updated:Jun 19,2014 Sometimes a heart attack is not just a ... the result of spontaneous tearing in the coronary artery wall. The artery wall has three layers and ...

267

[Postoperative dissection of the vertebral artery in two steps].  

PubMed

The diagnosis of perioperative vertebral artery dissection can be difficult because of non-specific clinical signs. We report a case revealed by a tegmento-thalamic stroke after an abdominal second surgical look. The interest of this observation is related to a particular evolution in two steps separated by a 2-month-interval and an intercurrent cervical manipulation. After the second anesthesia, neck pain associated with a third cranial nerve palsy and a supranuclear ophtalmoplegia revealed a tegmento-thalamic ischemic stroke due to vertebral artery dissection. We discuss here the different factors possibly involved in the pathophysiology of postoperative vertebral artery dissection: positioning, cervical manipulation, subclavian central venous access and cisplatin toxicity. Vertebral artery dissection should be discussed in case of postoperative neck pain, especially with non-typical symptomatology. PMID:25447780

Bien, J-Y; Morel, J; Demasles, S; Abboud, K; Molliex, S

2014-12-01

268

Endovascular Treatment of Acute Type B Dissection Complicating Aortic Coarctation  

PubMed Central

Surgical treatment poses a high risk to patients with concomitant aortic coarctation and dissection, and an interventional approach could be an alternative. We describe the case of a 52-year-old man with a long history of untreated hypertension and aortic coarctation who emergently presented at our institution with an acute Stanford type B dissection. The patient's elevated serum creatinine level, perfusion deficit in the right lower limb, and hypertension did not respond to medical therapy, and he did not consent to surgery. By endovascular means, we used a self-expandable stent-graft to cover the entry point of the dissection; then, we deployed a balloon-expandable bare-metal stent to correct residual stenosis. To our knowledge, this is the first report of the endovascular treatment of aortic coarctation complicated by type B dissection. PMID:23678217

Kassaian, Seyed Ebrahim; Abbasi, Kyomars; Mousavi, Mehdi; Sahebjam, Mohammad

2013-01-01

269

Optogenetic dissection of medial prefrontal cortex circuitry  

PubMed Central

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

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

2014-01-01

270

Genetic dissection of drug resistance in trypanosomes.  

PubMed

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

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

2013-10-01

271

Dissecting the Milky Way disk with LAMOST  

NASA Astrophysics Data System (ADS)

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

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

2015-01-01

272

Multiple idiopathic arterial aneurysms masquerading as aortic dissection  

PubMed Central

We report the case of a 58-year-old lady who presented with abdominal pain and backache. Although initial evaluation was strongly suggestive of abdominal aortic dissection, she was ultimately found to have multiple arterial aneurysms. Work-up for underlying vasculitis was negative. Surgical repair was planned and the patient was referred to a cardiovascular surgeon. This case highlights the importance of careful radiological assessment in patients with suspected aortic dissection. PMID:23420724

Naha, Kushal; Vivek, G; Shetty, Ranjan K; Dias, Lorraine Simone

2013-01-01

273

Improved results for dissecting aneurysms. Intraluminal sutureless prosthesis.  

PubMed

Surgical therapy for dissection of the thoracic aorta has had a high mortality. One contributing factor has been hemorrhage from the prosthesis and the suture lines. A method of treatment with an intraluminal prosthesis that requires no end-to-end anastomosis has been developed. We have used this method in 14 patients, of whom eight had acute thoracic aortic dissections and six had chronic dissections. We assembled our own prosthesis in the first five cases but, more recently, we have utilized an intraluminal prosthesis provided by USCI. Eight of the patients had type 1 dissection, of whom five required concomitant aortic valve replacement and three coronary artery bypass grafting; one had a type II dissection and five had type III dissections. The age range was 31 to 71 years with a mean of 58. There were 12 men and 2 women. There were no intraoperative deaths, but one patient died 10 days postoperatively of a perforated ulcer and another died at 6 months of empyema. Follow-up has been from 9 to 51 months with a mean of 22 months. There has been no evidence of compromise of the aortic lumen and no prosthetic problems, such as erosion, migration, or thrombosis. This technique provides a safe and simple way to repair dissecting aneurysms of the thoracic aorta and has provided long-term reliability. We have subsequently used this graft for 11 patients with aneurysm of the aorta with favorable results. We presently recommend this technique for dissecting, atherosclerotic, and Marfanoid aneurysms of the thoracic aorta. PMID:6977074

Lemole, G M; Strong, M D; Spagna, P M; Karmilowicz, N P

1982-02-01

274

Stroke prevention and treatment in patients with spontaneous carotid dissection  

Microsoft Academic Search

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

Ralf W. Baumgartner

275

Cadaver Dissection and the Ritual Transformation of Medical Students  

E-print Network

the cultural aspects of healing: birthing suites are becoming more comfortable and social, and prayer circles are increasingly part of the prescribed treatment for some disease in many communities. Increased understanding of the power of the placebo effect... badly, or of contracting diseases. Many physicians recall their cadaver dissection 3 sessions as significant life events, in addition to acknowledging their importance in knowledge acquisition (Lempp 2005, p. 319). Cadaver dissection can be viewed...

Laudermilk, Ryan

2011-12-31

276

Planned neck dissection following chemo-radiotherapy in advanced HNSCC  

PubMed Central

Background Neck dissection has traditionally played an important role in the management of patients with regionally advanced head and neck squamous cell carcinoma (HNSCC) treated with radical radiotherapy alone. However, with the incorporation of chemotherapy in the therapeutic strategy for advanced HNSCC and resultant improvement in outcome the routine use of post chemo-radiotherapy neck dissection is being questioned. Methods Published data for this review was identified by systematically searching MEDLINE, CANCERLIT & EMBASE databases from 1995 until date with restriction to the English language. Results There is lack of high quality evidence on the role of planned neck dissection in advanced HNSCC treated with chemo-radiotherapy. A systematic literature search could identify only one small randomized controlled trial (Level I evidence) addressing this issue, albeit with major limitations. Upfront neck dissection followed by chemo-radiotherapy resulted in better disease-specific survival as compared to chemoradiation only. Several single arm prospective and retrospective reports were also identified with significant heterogeneity and often-contradictory conclusions. Conclusions Planned neck dissection after radical chemo-radiotherapy achieves a high level of regional control, but its ultimate benefit is limited to a small subset of patients only. Unless there are better non-invasive ways to identify residual viable disease, the role of such neck dissection shall remain debatable. A large randomized controlled trial addressing this issue is needed to clarify its role and provide evidence-based answers. PMID:15377383

Gupta, Tejpal; Agarwal, Jai Prakash

2004-01-01

277

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

PubMed

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

Baumann, F; Makaloski, V; Diehm, N

2013-05-01

278

Evaluation of quantitative performance of sequential immobilized metal affinity chromatographic enrichment for phosphopeptides.  

PubMed

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

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

2014-01-15

279

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

PubMed

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

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

2014-12-01

280

2D gel-based proteome and phosphoproteome analysis during larval metamorphosis in two major marine biofouling invertebrates.  

PubMed

Larvae of some benthic invertebrates respond (metamorphose or not) to chemical cues within minutes or hours and often without excessive transcription or translation. Although protein phosphorylation is one of the most important molecular switching mechanisms that govern variety of rapid cellular responses in higher organisms, this is the first study to analyze the global protein expression and protein phosphorylation status during larval metamorphosis in two major marine biofouling invertebrates (a bryozoan Bugula neritina and a barnacle Balanus amphitrite). Results indicate that larval proteomic response to metamorphosis (inhibiton or induction) involves substantial change in the phosphorylation status of proteins rather than de novo protein synthesis. An abundantly expressed and an unnamed phosphoprotein that appears to play key regulatory role in larval metamorphosis was identified. When larvae of bryozoan and barnacle were challenged with a metamorphosis (and kinase) inhibitor, the genistein, the number of phosphoproteins in bryozoan were substantially reduced but drastically increased in barnacle. Taken together, this is the first time that the usefulness of employing 2DE-based proteomic and phosphoproteomic approaches was demonstrated for us to understand the molecular mechanisms of larval metamorphosis and to study the mode-of-action of chemical cues in marine organisms. PMID:19341272

Thiyagarajan, Vengatesen; Wong, Tim; Qian, Pei-Yuan

2009-06-01

281

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

PubMed

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

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

2011-08-01

282

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

PubMed Central

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

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

2013-01-01

283

Comprehensive phosphoproteome analysis unravels the core signaling network that initiates the earliest synapse pathology in preclinical Alzheimer's disease brain.  

PubMed

Using a high-end mass spectrometry, we screened phosphoproteins and phosphopeptides in four types of Alzheimer's disease (AD) mouse models and human AD postmortem brains. We identified commonly changed phosphoproteins in multiple models and also determined phosphoproteins related to initiation of amyloid beta (A?) deposition in the mouse brain. After confirming these proteins were also changed in and human AD brains, we put the proteins on experimentally verified protein-protein interaction databases. Surprisingly, most of the core phosphoproteins were directly connected, and they formed a functional network linked to synaptic spine formation. The change of the core network started at a preclinical stage even before histological A? deposition. Systems biology analyses suggested that phosphorylation of myristoylated alanine-rich C-kinase substrate (MARCKS) by overactivated kinases including protein kinases C and calmodulin-dependent kinases initiates synapse pathology. Two-photon microscopic observation revealed recovery of abnormal spine formation in the AD model mice by targeting a core protein MARCKS or by inhibiting candidate kinases, supporting our hypothesis formulated based on phosphoproteome analysis. PMID:25231903

Tagawa, Kazuhiko; Homma, Hidenori; Saito, Ayumu; Fujita, Kyota; Chen, Xigui; Imoto, Seiya; Oka, Tsutomu; Ito, Hikaru; Motoki, Kazumi; Yoshida, Chisato; Hatsuta, Hiroyuki; Murayama, Shigeo; Iwatsubo, Takeshi; Miyano, Satoru; Okazawa, Hitoshi

2015-01-15

284

Quantitative Thinking.  

ERIC Educational Resources Information Center

An appeal for more research to determine how to educate children as effectively as possible is made. Mathematics teachers can readily examine the educational problems of today in their classrooms since learning progress in mathematics can easily be measured and evaluated. Since mathematics teachers have learned to think in quantitative terms and…

DuBridge, Lee A.

285

Proteome, Phosphoproteome, and Hydroxyproteome of Liver Mitochondria in Diabetic Rats at Early Pathogenic Stages*  

PubMed Central

It has been proposed that mitochondrial dysfunction is involved in the pathogenesis of type 2 diabetes (T2D). To dissect the underlying mechanisms, we performed a multiplexed proteomics study on liver mitochondria isolated from a spontaneous diabetic rat model before/after they were rendered diabetic. Altogether, we identified 1091 mitochondrial proteins, 228 phosphoproteins, and 355 hydroxyproteins. Mitochondrial proteins were found to undergo expression changes in a highly correlated fashion during T2D development. For example, proteins involved in ?-oxidation, the tricarboxylic acid cycle, oxidative phosphorylation, and other bioenergetic processes were coordinately up-regulated, indicating that liver cells confronted T2D by increasing energy expenditure and activating pathways that rid themselves of the constitutively increased flux of glucose and lipid. Notably, activation of oxidative phosphorylation was immediately related to the overproduction of reactive oxygen species, which caused oxidative stress within the cells. Increased oxidative stress was also evidenced by our post-translational modification profiles such that mitochondrial proteins were more heavily hydroxylated during T2D development. Moreover, we observed a distinct depression of antiapoptosis and antioxidative stress proteins that might reflect a higher apoptotic index under the diabetic stage. We suggest that such changes in systematic metabolism were causally linked to the development of T2D. Comparing proteomics data against microarray data, we demonstrated that many T2D-related alterations were unidentifiable by either proteomics or genomics approaches alone, underscoring the importance of integrating different approaches. Our compendium could help to unveil pathogenic events in mitochondria leading to T2D and be useful for the discovery of diagnosis biomarker and therapeutic targets of T2D. PMID:19700791

Deng, Wen-Jun; Nie, Song; Dai, Jie; Wu, Jia-Rui; Zeng, Rong

2010-01-01

286

Unraveling pancreatic islet biology by quantitative proteomics  

SciTech Connect

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

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

2011-08-01

287

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

SciTech Connect

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

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

1996-03-01

288

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

NASA Astrophysics Data System (ADS)

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

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

2013-03-01

289

Dissecting the Impact of Matrix Anchorage and Elasticity in Cell Adhesion  

PubMed Central

Abstract 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

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

2009-01-01

290

Treatment of ruptured intracranial dissecting aneurysms in Hong Kong  

PubMed Central

Background: Data suggests that hemorrhagic presentations occur in 20% of internal carotid artery dissections and 50% of vertebral artery dissections. A Finnish study has reported favorable outcomes in only 32% of patients. We aimed to review the epidemiology and management outcomes in a Chinese population. Methods: We reviewed the aneurysmal subarachnoid hemorrhage registry of patients who presented with intracranial dissecting aneurysms at a neurosurgical center in Hong Kong over a five-year period. Results: A total of 23 patients with intracranial dissecting aneurysms were identified, accounting for 8% of all spontaneous subarachnoid hemorrhage patients. Forty-eight percent of the patients identified were treated by main trunk occlusion and 39% were treated by embolization or stent-assisted embolization or stent alone. Thirteen percent were managed by craniotomy and trapping or wrapping. Favorable outcomes at six months were achieved in 67%. Conclusions: Patients with intracranial dissecting aneurysms account for a significant proportion of the cases of spontaneous subarachnoid hemorrhage in our population. Carefully selected endovascular and microsurgical treatments can lead to management outcomes similar to patients with saccular aneurysms. PMID:21206536

Wong, George Kwok Chu; Tang, Hoi Bun; Poon, Wai Sang; Yu, Simon Chun Ho

2010-01-01

291

Congenital Incomplete Fusion of Superior Mesenteric Artery Mimicking Dissection  

PubMed Central

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

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

2015-01-01

292

Methodological aspects of the genetic dissection of gene expression  

SciTech Connect

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

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

2004-01-01

293

Second harmonic generation, sum frequency generation, and chi(3): dissecting environmental interfaces with a nonlinear optical Swiss Army knife.  

PubMed

This review discusses recent advances in the nonlinear optics of environmental interfaces. We discuss the quantitative aspects of the label-free approaches presented here and demonstrate that nonlinear optics has now assumed the role of a Swiss Army knife that can be used to dissect, with molecular detail, the fundamental and practical aspects of environmental interfaces and heterogeneous geochemical environments. In this work, nonlinear optical methods are applied to complex organic molecules, such as veterinary antibiotics, and to small inorganic anions and cations, such as nitrate and chromate, or cadmium, zinc, and manganese. The environmental implications of the thermodynamic, kinetic, spectroscopic, structural, and electrochemical data are discussed. PMID:18851705

Geiger, Franz M

2009-01-01

294

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

NASA Astrophysics Data System (ADS)

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

Geiger, Franz M.

2009-05-01

295

Morphological analysis of the proximal femur using quantitative computed tomography  

Microsoft Academic Search

The anatomy of the proximal femur was studied in 35 specimens using quantitative computed tomography (QCT) and compared with\\u000a anatomical sections studied by plane radiography and gross dissection. We found the primary supporting structure of the femoral\\u000a head to be the primary compressive strut, which is a dense column of trabecular bone projecting from the pressure buttress\\u000a of the medial

James B. Stiehl; Donald Jacobson; Guilermo Carrera

2007-01-01

296

Bilateral chylothorax following neck dissection: a case report  

PubMed Central

Background Chylothorax is an extremely rare but potentially life-threatening complication after radical neck dissection. We report the case of a bilateral chylothorax after total thyroidectomy and cervico-central and cervico-lateral lymphadenectomy for thyroid carcinoma. Case presentation A 40-year-old European woman underwent total thyroidectomy and neck dissection for papillary thyroid carcinoma. Postoperatively she developed dyspnoea and pleural effusion. A chylothorax was found and the initial conservative therapy was not successful. She had to be operated on again and the thoracic duct was legated. Conclusion The case presentation reports a very rare complication after total thyroidectomy and neck dissection, but it has to be kept in mind to prevent dangerous complications. PMID:24885488

2014-01-01

297

Digital dissection system for medical school anatomy training  

NASA Astrophysics Data System (ADS)

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

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

2003-05-01

298

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

PubMed

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

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

2015-01-01

299

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

PubMed

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

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

2014-11-25

300

Novel Fe3O4@TiO2 core-shell microspheres for selective enrichment of phosphopeptides in phosphoproteome analysis.  

PubMed

Due to the dynamic nature and low stoichiometry of protein phosphorylation, enrichment of phosphorylated peptides from proteolytic mixtures is often necessary prior to their characterization by mass spectrometry. Immobilized metal affinity chromatography (IMAC) is a popular way to enrich phosphopeptides; however, conventional IMAC lacks enough specificity for efficient phosphoproteome analysis. In this study, novel Fe 3O 4@TiO 2 microspheres with well-defined core-shell structure were prepared and developed for highly specific purification of phosphopeptides from complex peptide mixtures. The enrichment conditions were optimized using tryptic digests of beta-casein, and the high specificity of the Fe 3O 4@TiO 2 core-shell microspheres was demonstrated by effectively enriching phosphopeptides from the digest mixture of alpha-casein and beta-casein, as well as a five-protein mixture containing nonphosphoproteins (bovine serum albumin (BSA), myoglobin, cytochrome c) and phosphoproteins (ovalbumin and beta-casein). The Fe 3O 4@TiO 2 core-shell microspheres were further successfully applied for the nano-LC-MS/MS analysis of rat liver phosphoproteome, which resulted in identification of 56 phosphopeptides (65 phosphorylation sites) in mouse liver lysate in a single run, indicating the excellent performance of the Fe 3O 4@TiO 2 core-shell microspheres. PMID:18473453

Li, Yan; Xu, Xiuqing; Qi, Dawei; Deng, Chunhui; Yang, Pengyuan; Zhang, Xiangmin

2008-06-01

301

Isolated Unilateral Hypoglossal Nerve Palsy Due to Vertebral Artery Dissection  

PubMed Central

We report the case of a patient with unilateral tongue weakness secondary to an isolated lower motor neuron hypoglossal nerve palsy that was caused by a right vertebral artery dissection in the lower neck. The patient had a boggy tongue with a deviation to the right side but an otherwise normal neurological examination. Magnetic resonance angiography showed a narrow lumen of the right vertebral artery in the neck. After initially treating the patient with aspirin in the emergency room and later with warfarin for three months, there was complete recanalization of the right vertebral artery. Only one other case of vertebral artery dissection and twelfth nerve palsy has been reported before. PMID:22031481

Mahadevappa, Karthik; Chacko, Thomas; Nair, Anil K.

2012-01-01

302

Infective Left Atrial Dissecting Flap after Cardiac Surgery  

PubMed Central

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

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

2014-01-01

303

Concomitant Reconstruction of Arch Vessels during Repair of Aortic Dissection  

PubMed Central

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

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

2014-01-01

304

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

PubMed Central

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

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

2011-01-01

305

Adult-onset dysphagia lusoria secondary to a dissecting aberrant right subclavian artery associated with type B acute aortic dissection  

PubMed Central

The case of a 78-year-old African American woman who presented at the Mount Sinai Medical Center (Chicago, USA) with excruciating backache is presented. Computed tomography of the chest at the time of admission showed dissection of the aortic arch, descending aorta and dissection of an aberrant right subclavian artery. She was managed medically for Stanford type B acute aortic dissection. The patient was asymptomatic at presentation, but started complaining of new-onset dysphagia during her stay in the hospital. An esophagogram was performed and suggested posterior impingement of the esophagus, a classic sign of an aberrant right subclavian artery. Because the patient had multiple underlying comorbidities and the dysphagia was mild and intermittent, surgery was deferred. The patient was discharged home after complete stabilization and was scheduled for a follow-up appointment. PMID:18209773

Singh, Sarabjeet; Grewal, Puneet Dhillon; Symons, John; Ahmed, Aziz; Khosla, Sandeep; Arora, Rohit

2008-01-01

306

Extent of lymph node dissection: common hepatic artery lymph node dissection can be omitted for esophageal squamous cell carcinoma  

PubMed Central

Objectives Controversy persists regarding the adequate extent of lymph node (LN) dissection in thoracic esophageal cancer (EC) surgery. Oncologic efficacy should be balanced with the increased risk of postoperative complications after aggressive radical LN dissection. Here, we evaluate the effectiveness of common hepatic artery LN dissection in surgery for thoracic esophageal squamous cell carcinoma. Patients and methods Among a total of 1,563 EC patients who underwent surgery from May 2005 to December 2012 at the Fudan University Shanghai Cancer Center, 1,248 thoracic esophageal squamous cell carcinoma were selected for this study, including 682 patients who underwent esophagectomy with common hepatic artery LN dissection and 566 patients who underwent esophagectomy without common hepatic artery LN dissection. The clinical data of patients were retrospectively analyzed. In addition, the locoregional LN metastasis, relationship between metastatic rates of common hepatic artery LN and clinicopathological factors were analyzed. A propensity score match analysis were performed to control for potential differences in the characteristics of patients with EC cell carcinoma, and postoperative complications were analyzed after propensity score-matching. Results The metastatic rate of common hepatic LN was 3.5%. Logistic regression analysis revealed tumor diameter, N classification and pTNM stage were risk factors for common hepatic LN metastasis. Matching based on propensity scores produced 361 patients in each group. The overall incidence of postoperative complications was 32.70% and 35.45%, respectively, no significant difference was found (P=0.432). Conclusions The metastatic rate of common hepatic artery LN is low. For patients who undergo resection for Stage I thoracic esophageal squamous cell carcinoma, the dissection of common hepatic artery LN may be safely omitted. PMID:24876938

Ma, Xiao; Li, Bin; Yang, Su; Guo, Wei; Zhu, Xiaoli; Xiang, Jiaqing; Zhang, Yawei

2014-01-01

307

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

Federal Register 2010, 2011, 2012, 2013, 2014

...TRADE COMMISSION [Investigation No. 337-TA-865] Certain Balloon Dissection Devices and Products Containing Same; Commission...or sale in the United States after importation of certain balloon dissection devices and products containing same by reason...

2013-03-21

308

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...

309

Functional dissection and module swapping of fungal cyclooligomer depsipeptide synthetases.  

PubMed

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

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

2013-07-14

310

Dissecting BitTorrent: Five Months in a Torrent's Lifetime  

E-print Network

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

Rivière, Etienne

311

Blood Vessels of the Fetal Pig Dissection Posterior Vessels Protocol  

E-print Network

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

Loughry, Jim

312

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...

313

The Influence of Emotion on Students' Performance in Dissection Exercises  

ERIC Educational Resources Information Center

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

Holstermann, Nina; Grube, Dietmar; Bogeholz, Susanne

2009-01-01

314

Vertebral Artery Dissection in Children: A Comprehensive Review  

Microsoft Academic Search

Vertebral artery dissection (VAD) has been infrequently recognized in children. The authors have reviewed 68 reported cases of VAD in children in the existing literature. An association between routine types of neck movement in sports and the evolution of VAD was recognized in half of the reported cases. Boys outnumbered girls by a ratio of 6.6 to 1, in contrast

Izhar Hasan; Simon Wapnick; Michael S. Tenner; William T. Couldwell

2002-01-01

315

Familial Cervical Artery Dissections Clinical, Morphologic, and Genetic Studies  

Microsoft Academic Search

Background and Purpose—Genetic risk factors are thought to play a role in the etiology of spontaneous cervical artery dissections (CAD). However, familial CAD is extremely rare. In this study we analyzed patients with familial CAD and asked the question whether familial CAD has particular features. Methods—Seven families with 15 CAD patients were recruited. All patients were carefully investigated by a

Juan Jose Martin; Ingrid Hausser; Philippe Lyrer; Otto Busse; Ralf Schwarz; Rolf Schneider; Tobias Brandt; Manja Kloss; Markus Schwaninger; Stefan Engelter; Caspar Grond-Ginsbach

2010-01-01

316

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

ERIC Educational Resources Information Center

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

Lee, Yeung Chung

2004-01-01

317

INVESTIGATION Genetic Dissection of a Major Anthocyanin QTL  

E-print Network

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

Bradshaw, Toby

318

Exploring Dissections of Rectangles into Right-Angled Triangles  

ERIC Educational Resources Information Center

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

Griffiths, Martin

2013-01-01

319

Cancer Cell Dissecting the Unique Role of the Retinoblastoma  

E-print Network

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

320

Dissection of epistasis in oligogenic Bardet-Biedl syndrome  

Microsoft Academic Search

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

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

2006-01-01

321

Bilateral renal artery dissections: unusual complication of polyarteritis nodosa.  

PubMed

A case of polyarteritis nodosa with the acute complications of multiple bilateral real artery dissection, perirenal haemorrhage and kidney infarction is described. The diagnosis of polyarteritis nodosa was established on the basis of angiographical and clinical findings. Follow-up arteriograms and CT-findings after prednisone therapy are discussed. PMID:6144545

Hekali, P E; Pajari, R I; Kivisaari, M L; Haapanen, E J; Leirisalo, M

1984-02-01

322

Delayed left atrial wall dissection after mitral valve replacement.  

PubMed

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

Idir, M; Deville, C; Roudaut, R

2000-04-01

323

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

E-print Network

Dissecting SMS Malwares in Android Anoop Joseph Babu, Rahul Raveendranath, Venkiteswaran Rajamani of concept SMS malware is presented to analyze the working of most threatening SMS malwares in the wild Terms--Android; Security threats; Countermeasures; SMS Malware; Permissions. I. INTRODUCTION Smartphones

Gesbert, David

324

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

E-print Network

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

Govindjee

325

Lymph node dissection – understanding the immunological function of lymph nodes  

PubMed Central

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

Buettner, M; Bode, U

2012-01-01

326

Dissection of Conformational Conversion Events during Prion Amyloid Fibril  

E-print Network

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

327

Genetic Dissection of Behavioural and Autonomic Effects of D9  

E-print Network

Genetic Dissection of Behavioural and Autonomic Effects of D9 -Tetrahydrocannabinol in Mice Marijuana and its main psychotropic ingredient D9 -tetrahydrocannabinol (THC) exert a plethora -tetrahydrocannabinol in mice. PLoS Biol 5(10): e269. doi:10.1371/journal.pbio.0050269 Introduction Cannabinoids

Paris-Sud XI, Université de

328

Dissection of the Hyperadhesive Phenotype of Airway Eosinophils in Asthma  

E-print Network

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

Mosher, Deane F.

329

Kendall Hunt Dissection of a Squid: Part 2  

NSDL National Science Digital Library

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

2012-01-01

330

Clinical presentation and surgical management of dissecting posterior inferior cerebellar artery aneurysms: 2 case reports  

Microsoft Academic Search

Intracranial dissection presenting with subarachnoid hemorrhage (SAH) most commonly involves the vertebral artery. The natural history of this lesion suggests frequent early rehemorrhage and need for urgent treatment. Isolated dissection of the posterior inferior cerebellar artery (PICA) is very rare.We present 2 cases of isolated PICA dissections presenting with SAH. Both patients were middle-aged men who presented with transient loss

Nicholas M. Wetjen; Michael J. Link; Ronald Reimer; Douglas A. Nichols; Caterina Giannini

2005-01-01

331

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

Microsoft Academic Search

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

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

1999-01-01

332

Conservative treatment of iatrogenic left main coronary artery dissection: report of two cases  

PubMed Central

Revascularization treatment is mostly recommended for iatrogenic left main coronary artery dissection because of potential for catastrophic sequel, even in case of initial TIMI 3 flow and hemodynamic stability. However, conservative treatment seems to be feasible in asymptomatic and hemodinamically stable patient with low-grade dissection. We report two cases of iatrogenic left main coronary dissection managed conservatively. PMID:24400208

Yuksel, Uygar Cagdas; Yalcinkaya, Emre; Gokoglan, Yalcin; Iyisoy, Atila

2013-01-01

333

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

ERIC Educational Resources Information Center

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

De Villiers, Rian; Monk, Martin

2005-01-01

334

Spontaneous esophageal mucosal dissection in a patient with upper digestive bleeding and esophageal varices.  

PubMed

We present a case of mucosal esophageal dissection in a 44-year-old patient with alcoholic cirrhosis admitted for upper digestive bleeding. The endoscopic aspect was of chronic mucosal dissection in the esophagus and 3rd degree esophageal varices with red signs. To our knowledge, it is the only case with spontaneous esophageal mucosal dissection and portal hypertension with esophageal varices. PMID:21776303

Negreanu, L; Tribus, L C; Purcarea, M; Fierbinteanu Braticevici, C

2011-05-15

335

Spontaneous esophageal mucosal dissection in a patient with upper digestive bleeding and esophageal varices  

PubMed Central

We present a case of mucosal esophageal dissection in a 44–year–old patient with alcoholic cirrhosis admitted for upper digestive bleeding. The endoscopic aspect was of chronic mucosal dissection in the esophagus and 3rd degree esophageal varices with red signs. To our knowledge, it is the only case with spontaneous esophageal mucosal dissection and portal hypertension with esophageal varices. PMID:21776303

Tribus, LC; Purcarea, M; Fierbinteanu Braticevici, C

2011-01-01

336

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

ERIC Educational Resources Information Center

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

Carlin, Joel L.

2010-01-01

337

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

ERIC Educational Resources Information Center

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

Fancovicova, Jana; Prokop, Pavol; Leskova, Andrea

2013-01-01

338

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

ERIC Educational Resources Information Center

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

Milano, Regina Nicole

2010-01-01

339

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

ERIC Educational Resources Information Center

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

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

2010-01-01

340

Outcomes of a rotational dissection system in gross anatomy.  

PubMed

At the University of Texas Houston Medical School, a rotational dissection system was introduced to improve coordination between the Gross Anatomy and the Introduction to Clinical Medicine (ICM) courses. Six students were assigned to each cadaver and divided into two teams. For each laboratory, one team was assigned to dissect and the other to attend ICM or study independently. For the next laboratory, the assignments were reversed. At the start of the session, the team that had dissected previously spent 30 minutes teaching the other team. In 2012, the students were given three traditional practical examinations with 50 questions drawn equally from each laboratory. Students also completed three mid-course evaluations. There were no significant differences in overall performance between the two teams. Nevertheless, we wanted to determine how well individual students identified structures they had dissected compared with those they had not. For dissected structures, the mean percent correct was 80.0?±?13.0 (mean?±?standard deviation), and for undissected structures, it was 78.3?±?14.1. The difference was small, but statistically significant (P?=?0.0007). Although this result validated the concerns expressed by some students, it did not appear that a change in the system was justified. Students were generally enthusiastic about the opportunity to learn clinical skills in the first semester of medical school, and 91-96% of the students agreed that learning anatomy at the same time helped them understand the physical examination exercises in ICM. Anat Sci Educ. © 2014 American Association of Anatomists. PMID:25358463

Marshak, David W; Oakes, Joanne; Hsieh, Pei-Hsuan; Chuang, Alice Z; Cleary, Leonard J

2014-10-30

341

Possible extracardiac predictors of aortic dissection in Marfan syndrome  

PubMed Central

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

2014-01-01

342

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

NASA Astrophysics Data System (ADS)

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

Allspaw, Kathleen M.

343

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

PubMed Central

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

2007-01-01

344

[Neck dissection for Head and Neck cancers: state of the art and classification].  

PubMed

The purposes of this article are to review the history and evolution of neck dissections, including an update on node levels and their anatomical landmark. A number of classification systems were proposed and subsequently established for neck dissection procedures. The system most often employed was published in 1991 by the American Head and Neck Society and American Academy of Otolaryngology- Head and Neck Surgery and revised in 2002 and 2008. According to this classification, neck dissections are grouped into four broad categories: radical neck dissection (RND), modified radical neck dissection (MRND), selective neck dissection (SND) and extended neck dissection (ERND). The choice between different surgeries depends on type and site of head and neck tumor as well nodal involvement. PMID:21453600

Pezzullo, L; Chiofalo, M G; Di Cecilia, M L; Marone, U

2011-03-01

345

Giant, Dissecting, High-Pressure Pulmonary Artery Aneurysm  

PubMed Central

We report the rare subchronic clinical course of a giant, dissecting pulmonary artery aneurysm in an oligosymptomatic middle-aged woman who had idiopathic pulmonary hypertension. Diagnosis was simple with the use of echocardiography and multislice computed tomography. Conversely, deciding on the treatment was difficult, because prominent surgeons declined to perform surgical repair of the aneurysm and recommended heart–lung transplantation. Therefore, we were forced to treat our patient medically. She survived for 1 year, including 8 months of treatment with sildenafil, and then died suddenly while awaiting transplantation. Our patient, who had a dissecting, high-pressure pulmonary artery aneurysm, had an unexpectedly stable and uneventful clinical course for 1 year, which, under more favorable circumstances, might have provided enough time for heart–lung transplantation to be performed. PMID:16429912

Smalcelj, Anton; Brida, Vojtjeh; Samarzija, Miroslav; Matana, Ante; Margetic, Eduard; Drinkovic, Niksa

2005-01-01

346

Management of Acute Aortic Syndrome and Chronic Aortic Dissection  

SciTech Connect

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

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

2011-10-15

347

Femtosecond laser dissection in C. elegans neural circuits  

NASA Astrophysics Data System (ADS)

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.

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

2006-02-01

348

The role of imaging in aortic dissection and related syndromes.  

PubMed

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

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

2014-04-01

349

Patterns of brain infarctions in internal carotid artery dissections  

Microsoft Academic Search

In 15 patients with internal carotid artery (ICA) dissections, patterns of brain infarctions visible on CT were categorized according to a pathogenetically oriented classification system. This differentiated ischemic brain damage due to low flow from thromboembolic infarctions. Simultaneously, cerebral hemodynamic reserve was evaluated by means of both CO2-dependent vasomotor reactivity and HMPAO- and 99 mTc-RBC-SPECT. Six out of 11 patients

Cornelius Weiller; Wolfgang Müllges; E. Bernd Ringelstein; Udalrich Buell; Werner Reiche

1991-01-01

350

Aortoesophageal fistula secondary to aortic dissection: case report and review.  

PubMed

Aortoesophageal fistula (AEF) formation nearly always results in catastrophic consequences. As a result of its development being extremely rare, many may never consider it in their differential. Although prognosis is extremely grim, early diagnosis and intervention is considered the optimal means to enhance one's prognosis. We present a case of AEF formation secondary to a Stanford B aortic dissection, along with a review of literature and terminology involved in describing such pathology. PMID:21560995

Miller, Tara Nikole; Miller, Ross Allen; Ziebarth, Joel

2011-04-01

351

Science Sampler: Frog dissection--An alternative model  

NSDL National Science Digital Library

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

Sanders, June

2007-02-01

352

Thymectomy in central lymph node dissection for papillary thyroid cancer  

PubMed Central

Background: Central lymph node dissection (CND) has been proposed in the treatment of patients affected by papillary thyroid cancer (PTC) with clinically negative neck lymph nodes. The procedure allows pathologic staging of lymph nodes of the central compartment and treatment of the micrometastases. By comparing bilateral and unilateral thymectomy during total thyroidectomy with central lymph node dissection for postoperative complications in sonographically node-negative papillary thyroid carcinomas, we aimed to determine the optimal extent of prophylactic central lymph node dissection. Methods: Patients were divided into two study groups: Group 1, total thyroidectomy plus unilateral thymectomy during the CND; Group 2, total thyroidectomy associated with bilateral thymectomy (both upper poles) during the CND. Primary endpoints of the study were evaluated by comparing the postoperative complications between the two groups. Results: The only significant result found when comparing the two groups was the rate of transient hypocalcemia. (Group 1: 13.7%, Group 2: 52.4%, p<0.01). A total of five cases of papillary thymic metastases were found in this study. And final pathology confirmed that all cases of thymic metastases were lymph node micrometastases of PTC, only situated in the ipsilateral thymus upper pole. Conclusions: Bilateral thymectomy during the CND did not provide a better carcinologic resection, as no contralateral thymic metastases were found. The unilateral thymectomy with total thyroidectomy during the CND may represent an effective strategy for reducing the rate of postoperative hypocalcemia. PMID:24955195

Huang, Du-Ping; Ye, Xiao-He; Xiang, You-Qun; Zhang, Xiao-Hua

2014-01-01

353

What Lies behind the Ischemic Stroke: Aortic Dissection?  

PubMed Central

Introduction. Some cases with aortic dissection (AD) could present with various complaints other than pain, especially neurological and cardiovascular manifestations. AD involving the carotid arteries could be associated with many clinical presentations, ranging from stroke to nonspecific headache. Case Report. A 71-year-old woman was admitted to emergency department with vertigo which started within the previous one hour and progressed with deterioration of consciousness following speech disorder. On arrival, she was disoriented and uncooperative. Diffusion magnetic resonance imaging (MRI) of brain was consistent with acute ischemia in the cerebral hemisphere. Fibrinolytic treatment has been planned since symptoms started within two hours. Echocardiography has shown the dilatation of ascending aorta with a suspicion of flap. Computed tomography (CT) angiography has been applied and intimal flap has been detected which was consistent with aortic dissection, intramural hematoma of which was reaching from aortic arch to bilateral common carotid artery. Thereafter, treatment strategy has completely changed and surgical invention has been done. Conclusion. In patients who are admitted to the emergency department with the loss of consciousness and stroke, inadequacy of anamnesis and carotid artery involvement of aortic dissection should be kept in mind.

Deniz, Turgut; Dag, Ersel; Tulmac, Murat; Azapoglu, Burcu; Alp, Caglar

2014-01-01

354

Saphenous Vein Sparing Superficial Inguinal Dissection in Lower Extremity Melanoma  

PubMed Central

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

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

2014-01-01

355

Quantitative Languages KRISHNENDU CHATTERJEE  

E-print Network

Quantitative Languages KRISHNENDU CHATTERJEE IST Austria (Institute of Science and Technology of Science and Technology Austria) and EPFL, Switzerland Quantitative generalizations of classical languages) to define several natural classes of quantitative languages over finite and infinite words; in particular

Doyen, Laurent

356

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

ERIC Educational Resources Information Center

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

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

2014-01-01

357

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

ERIC Educational Resources Information Center

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

Bernstein, Penny L.

2000-01-01

358

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

NASA Astrophysics Data System (ADS)

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

Youngblut, Christine

359

Use of endovascular stents for acute aortic dissection: an experimental study.  

PubMed

This study was designed to evaluate the potential obliteration of an experimental aortic dissection using an intravascular stent introduced via the femoral artery. Twenty-two adult dogs were divided into four groups: in group A (n = 6) a thoracoabdominal aortic dissection was surgically created to observe the natural course of this lesion; in group B (n = 6) a nitinol coil graft was introduced into the aorta via the femoral artery; in group C (n = 3) a nitinol coil graft was introduced via the femoral artery into a dissected aorta in an attempt to obliterate the dissection; and in group D (n = 7) an expandable intraluminal vascular graft (Palmaz stent) was introduced via the femoral artery into a dissected aorta in an attempt to obliterate the dissection. Arteriographic evaluation was performed postoperatively and again 6 weeks later before the aortas were explanted. Gross and light microscopic examinations were performed on all explanted aortas. In group A dissection was achieved and a postoperative aortogram demonstrated evidence of aortic dissection in all animals. Autopsy revealed persistence of dissection with a reentry tear near the celiac axis in five animals. In group B there was incomplete expansion of the nitinol coil graft in five dogs, resulting in aortic thrombosis in one. In group C the nitinol coil graft failed to obliterate the aortic dissection in all animals and resulted in aortic thrombosis in two. In group D placement of a balloon-expandable intraluminal stent solely at entry and reentry sites resulted in only partial obliteration of the dissection (n = 3), but when the entire length of the dissected aorta was treated, the dissection was completely obliterated (n = 3). PMID:7811581

Marty-Ané, C; Serres-Cousiné, O; Laborde, J C; Costes, V; Alauzen, M; Mary, H

1994-09-01

360

Combination of water-jet dissection and needle-knife as a hybrid knife simplifies endoscopic submucosal dissection  

Microsoft Academic Search

Background  The safety and efficacy of endoscopic submucosal dissection (ESD) is very dependent on an effective injection beneath the\\u000a submucosal lamina and on a controlled cutting technique. After our study group demonstrated the efficacy of the HydroJet in\\u000a needleless submucosal injections under various physical conditions to create a submucosal fluid cushion (Selective tissue\\u000a elevation by pressure = STEP technique), the next step was

Tobias Lingenfelder; Klaus Fischer; Moritz G. Sold; Stefan Post; Markus D. Enderle; Georg F. B. A. Kaehler

2009-01-01

361

Digital holographic microscopy for quantitative cell dynamic evaluation during laser microsurgery.  

PubMed

Digital holographic microscopy allows determination of dynamic changes in the optical thickness profile of a transparent object with sub-wavelength accuracy. Here, we report a quantitative phase laser microsurgery system for evaluation of cellular/ sub-cellular dynamic changes during laser micro-dissection. The proposed method takes advantage of the precise optical manipulation by the laser microbeam and quantitative phase imaging by digital holographic microscopy with high spatial and temporal resolution. This system will permit quantitative evaluation of the damage and/or the repair of the cell or cell organelles in real time. PMID:19582118

Yu, Lingfeng; Mohanty, Samarendra; Zhang, Jun; Genc, Suzanne; Kim, Myung K; Berns, Michael W; Chen, Zhongping

2009-07-01

362

Digital holographic microscopy for quantitative cell dynamic evaluation during laser microsurgery  

PubMed Central

Digital holographic microscopy allows determination of dynamic changes in the optical thickness profile of a transparent object with subwavelength accuracy. Here, we report a quantitative phase laser microsurgery system for evaluation of cellular/ sub-cellular dynamic changes during laser micro-dissection. The proposed method takes advantage of the precise optical manipulation by the laser microbeam and quantitative phase imaging by digital holographic microscopy with high spatial and temporal resolution. This system will permit quantitative evaluation of the damage and/or the repair of the cell or cell organelles in real time. PMID:19582118

Yu, Lingfeng; Mohanty, Samarendra; Zhang, Jun; Genc, Suzanne; Kim, Myung K.; Berns, Michael W.; Chen, Zhongping

2010-01-01

363

Spontaneous type B aortic dissection in antepartum gemellary pregnancy and endovascular repair  

PubMed Central

Background: It has been found that 50% of all aortic dissections can be attributable to pregnancy in women younger than 45 years of age. An estimated 30% of cases are type B, with half occurring in the antepartum period. To date type B aortic dissection has rarely been reported in gemellary pregnancies. Case: A 24-year-old primigravida at 36 weeks of gemellary gestation presented symptoms of severe and persistent chest pain for 1 day, before suffering the acute type B aortic dissection. The primigravida was treated with immediate cesarean section and endovacular stent graft placement. Conclusion: Aortic dissection is a rare complication of pregnancy, especially in gemellary pregnancies. Pregnancy is considered an independent risk factor for aortic dissection and endovascular repair may be an ideal option for the treatment of complicated type B aortic dissection during pregnancy, with reduced maternal and fetal mortality.

Gu, Xudong; Liu, Hongmei; Li, Yusheng; Fei, Libo; Shao, Danbing; Mao, Jianhua; Nie, Shinan

2014-01-01

364

True-false lumen segmentation of aortic dissection using multi-scale wavelet analysis and generative-discriminative model matching  

NASA Astrophysics Data System (ADS)

Computer aided diagnosis in the medical image domain requires sophisticated probabilistic models to formulate quantitative behavior in image space. In the diagnostic process detailed knowledge of model performance with respect to accuracy, variability, and uncertainty is crucial. This challenge has lead to the fusion of two successful learning schools namely generative and discriminative learning. In this paper, we propose a generative-discriminative learning approach to predict object boundaries in medical image datasets. In our approach, we perform probabilistic model matching of both modeling domains to fuse into the prediction step appearance and structural information of the object of interest while exploiting the strength of both learning paradigms. In particular, we apply our method to the task of true-false lumen segmentation of aortic dissections an acute disease that requires automated quantification for assisted medical diagnosis. We report empirical results for true-false lumen discrimination of aortic dissection segmentation showing superior behavior of the hybrid generative-discriminative approach over their non hybrid generative counterpart.

Lee, Noah; Tek, Huseyin; Laine, Andrew F.

2008-03-01

365

An electrical dissecting method of AC branch with FACTS for ancillary service assessment  

Microsoft Academic Search

This paper presents a new electrical dissecting method of AC branch installed with phase-shifter, which satisfies basic principles and laws of electric power network. With this method, the deep-seated electrical information between sources and flows, such as the contribution information of sources and flows, can be obtained. The dissected sub-branches are equivalent to the initial branch, and the dissecting procedure

Tang Yi; Yu Ji-Lai; Liu Xian Linz

2004-01-01

366

Cell-type Specific Optogenetic Mice for Dissecting Neural Circuitry Function  

E-print Network

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

Zhao, Shengli

367

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

PubMed Central

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

Menon, Rajeev; Kapadia, Anuj

2014-01-01

368

Multidetector computed tomography angiography: Application in vertebral artery dissection  

PubMed Central

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

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

2011-01-01

369

Rapid retraction of a post-infarction intramyocardial dissecting hematoma.  

PubMed

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

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

2014-06-01

370

Clinical Characteristics of Symptomatic Vertebral Artery Dissection. A Systematic Review  

PubMed Central

Background Vertebral artery dissection (VAD) is an important cause of stroke in the young. It can present nonspecifically and may be misdiagnosed with adverse consequences. We assessed the frequency of head/neck pain, other neurological symptoms, and cerebrovascular events in symptomatic VAD. Methods We conducted a systematic review of observational studies, searching electronic databases (MEDLINE, EMBASE) for English-language manuscripts with >5 subjects with clinical or radiological features of VAD. Two independent reviewers selected studies for inclusion; a third adjudicated differences. Studies were assessed for methodological quality and clinical data were abstracted. Pooled proportions were calculated. Results Of 3996 citations, we screened 511manuscripts and selected 75 studies describing 1,972 VAD patients. The most common symptoms were dizziness/vertigo (58%), headache (51%) and neck pain (46%). Stroke was common (63%), especially with extracranial dissections (66% vs. 32%, p<0.0001), while TIA (14%) and subarachnoid hemorrhage (SAH) (10%) were uncommon. SAH was seen only with intracranial dissections (57% vs. 0%, p=0.003). Fewer than half of the patients had obvious trauma, and only 7.9% had a known connective tissue disease. Outcome was good (modified Rankin scale (mRS) 0-1) in 67% and poor (mRS 5-6) in 10%. Conclusion VAD is associated with nonspecific symptoms such as dizziness, vertigo, headache, or neck pain. Ischemic stroke is the most common reported cerebrovascular complication. VAD should be considered in the diagnostic assessment of patients presenting with dizziness or craniocervical pain, even in the absence of other risk factors. Future studies should compare clinical findings as predictors in well-defined, undifferentiated populations of clinical VAD suspects. PMID:22931728

Gottesman, Rebecca F.; Sharma, Priti; Robinson, Karen A.; Arnan, Martinson; Tsui, Megan; Ladha, Karim; Newman-Toker, David E.

2013-01-01

371

In utero release of constriction amniotic bands via blunt dissection.  

PubMed

Therapeutic techniques for in utero release of amniotic bands have relied on transecting instruments. We present an additional technique, blunt dissection, to release a constriction band in utero. The lower extremity that had detectable abnormalities during prenatal ultrasound had improved outcome after blunt in utero release of the amniotic band compared to the contralateral (control) leg. These findings support two conjectures: first, the degree of band adherence to the fetus is an important factor influencing the surgical approach to in utero lysis of the bands; second, that in utero release of constriction bands can result in improvement in outcome. PMID:22017664

Assaf, Raymen; Llanes, Arlyn; Chmait, Ramen

2012-02-01

372

Aortoesophageal fistula after repair of descending aortic dissection.  

PubMed

The development of aortoesophageal fistula after aortic repair is rare. We describe a patient who presented with hematemesis 4 months after emergent repair of a descending thoracic aortic dissection using a prosthetic graft. Diagnosis was supported by computed tomographic, angiographic, and endoscopic findings. Resection of the involved graft was performed through a left thoracotomy after placement of an ascending aorta-to-abdominal aorta conduit through an anterior approach. The patient died of uncontrollable bleeding a few hours after the procedure. Surgical intervention offers the potential for cure in this otherwise uniformly fatal condition. But like medical therapy, operative management has thus far been associated with 100% mortality. PMID:8694638

Wong, R S; Champlin, A; Temes, R T; Wernly, J A

1996-08-01

373

Improving the run time and quality of nested dissection ordering  

SciTech Connect

When performing sparse matrix factorization, the ordering of matrix rows and columns has a dramatic impact on the factorization time. This paper describes an approach to the reordering problem that produces significantly better orderings than prior methods. The algorithm is a hybrid of nested dissection and minimum degree ordering, and combines an assortment of different algorithmic advances. New or improved algorithms are described for graph compression, multilevel partitioning, and separator improvement. When these techniques are combined, the resulting orderings average 39% better than minimum degree over a suite of test matrices, while requiring roughly 2.7 times the run time of Liu`s multiple minimum degree.

Hendrickson, B. [Sandia National Labs., Albuquerque, NM (United States)] [Sandia National Labs., Albuquerque, NM (United States); Rothberg, E. [Silicon Graphics, Inc., Mountain View, CA (United States)] [Silicon Graphics, Inc., Mountain View, CA (United States)

1998-09-01

374

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

PubMed

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

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

2015-03-01

375

Dissection of human vitreous body elements for proteomic analysis.  

PubMed

The vitreous is an optically clear, collagenous extracellular matrix that fills the inside of the eye and overlies the retina. (1,2) Abnormal interactions between vitreous substructures and the retina underlie several vitreoretinal diseases, including retinal tear and detachment, macular pucker, macular hole, age-related macular degeneration, vitreomacular traction, proliferative vitreoretinopathy, proliferative diabetic retinopathy, and inherited vitreoretinopathies. (1,2) The molecular composition of the vitreous substructures is not known. Since the vitreous body is transparent with limited surgical access, it has been difficult to study its substructures at the molecular level. We developed a method to separate and preserve these tissues for proteomic and biochemical analysis. The dissection technique in this experimental video shows how to isolate vitreous base, anterior hyaloid, vitreous core, and vitreous cortex from postmortem human eyes. One-dimensional SDS-PAGE analyses of each vitreous component showed that our dissection technique resulted in four unique protein profiles corresponding to each substructure of the human vitreous body. Identification of differentially compartmentalized proteins will reveal candidate molecules underlying various vitreoretinal diseases. PMID:21304469

Skeie, Jessica M; Mahajan, Vinit B

2011-01-01

376

Popliteal lymph node dissection for metastases of cutaneous malignant melanoma  

PubMed Central

Popliteal lymph node dissection is performed when grossly metastatic nodal disease is encountered in the popliteal fossa or after microscopic metastasis is found in interval sentinel nodes during clinical staging of cutaneous malignant melanoma. Initially, an S-shaped incision is made to gain access to the popliteal fossa. A careful en bloc removal of fat tissue and lymph nodes is made to preserve and avoid the injury of peroneal and tibial nerves as well as popliteal vessels, following the previous recommendations. This rare surgical procedure was successfully employed in a patient with cutaneous malignant melanoma and nodal metastases at the popliteal fossa. The technique described by Karakousis was reproduced in a step-by-step fashion to allow anatomical identification of the neurovascular structures and radical resection with no post-operative morbidity and prompt recovery. Popliteal lymph node dissection is a rarely performed operative procedure. Following a lymphoscintigraphic examination of the popliteal nodal station, surgeons can be asked to explore the popliteal fossa. Detailed familiarity of the operative procedure is necessary, however, to avoid complications. PMID:24886058

2014-01-01

377

Anesthesia Management in Aortic Dissection in Patients Undergoing Kidney Transplant.  

PubMed

Kidney transplant is a last resort to increase the life expectancy and quality of life in patients with renal failure. Aortic dissection is a disease that requires emergency intervention; it is characterized by sudden life-threatening back or abdominal pain. In the case described, constant chest pain that increased with respiration was present on examination of a 28-year-old man (85 kg, 173 cm) who presented at our emergency department complaining of severe back pain. He had undergone a kidney transplant in 2004 from his mother (live donor). He was diagnosed with acute Type II aortic dissection and was scheduled for emergent surgery. Because there were no surgical or anesthetic complications, the patient with 79 and 89 minutes aortic cross-clamping and cardiopulmonary bypass durations was sent, intubated, to intensive care unit. When nephrotoxic agents are avoided and blood flow is stabilized, cardiovascular surgery with cardio-pulmonary bypass may be performed seamlessly in patients who have undergone a kidney transplant. PMID:25375956

Ucar, Muharrem; Erdil, Feray; Sanl?, Mukadder; Aydogan, Mustafa Said; Durmus, Mahmut

2014-11-01

378

Fetal Pig Digestive System Dissection 1. Begin by placing the fetal pig on its side in your dissecting tray. Peel the skin back from the  

E-print Network

Fetal Pig Digestive System Dissection Protocol: 1. Begin by placing the fetal pig on its side of the digestive tract. First, locate the esophagus, the collapsible tube lying underneath the trachea. 10. Trace

Loughry, Jim

379

Students' Physical and Psychological Reactions to Forensic Dissection: Are There Risk Factors?  

ERIC Educational Resources Information Center

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…

Sergentanis, Theodoros N.; Papadodima, Stavroula A.; Evaggelakos, Christos I.; Mytilinaios, Dimitrios G.; Goutas, Nikolaos D.; Spiliopoulou, Chara A.

2010-01-01

380

Can the principles of evidence-based medicine be applied to the treatment of aortic dissections?  

Microsoft Academic Search

Surgical treatment of patients with acute type A aortic dissections has improved early survival from 10–20 to approximately 80%. Data supporting several other treatment recommendations in patients with aortic dissection, however, are less convincing. We hypothesized that applying strict principles of evidence-based medicine would invalidate most of the recommendations in these published papers. We conducted a literature search asking three

Truls Myrmel; David T. M. Lai; D. Craig Miller

2004-01-01

381

Preservation of the aortic valve in acute type A dissection complicated by aortic regurgitation  

Microsoft Academic Search

Background. The aim of the present study was to verify the efficacy of preserving the aortic valve in patients with acute type A aortic dissection complicated by significant aortic regurgitation.Methods. From January 1979 to December 1996, 178 patients (125 males; mean age 57 ± 9 years) underwent emergency surgery for acute type A aortic dissection, with an overall operative mortality

Renzo Pessotto; Francesco Santini; Peppino Pugliese; Giuseppe Montalbano; Giovanni Battista Luciani; Giuseppe Faggian; Paolo Bertolini; Alessandro Mazzucco

1999-01-01

382

GCSE Students' Attitudes to Dissection and Using Animals in Research and Product Testing.  

ERIC Educational Resources Information Center

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,…

Lock, Roger

1995-01-01

383

Platelet dysfunction in acute type A aortic dissection evaluated by the laser light-scattering method  

Microsoft Academic Search

ObjectivesPlatelet dysfunction contributes to bleeding tendency in acute type A aortic dissection. Particle counting by new laser light-scattering methods more accurately quantifies changes in the number of different-sized platelet aggregates than do conventional optical density methods. We studied platelet aggregation kinetics and patterns of aggregation deficiency in acute-phase aortic dissection with laser light scattering.

Masashi Tanaka; Koji Kawahito; Hideo Adachi; Takashi Ino

2003-01-01

384

[Acute coronary syndrome during dissection of left main as a complication of radiofrequency ablation].  

PubMed

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

Kulawik, Tomasz; Ka?u?a, Bernadetta; Ku?nierz, Jacek

2012-01-01

385

The discovery of the body: human dissection and its cultural contexts in ancient Greece.  

PubMed Central

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

von Staden, H.

1992-01-01

386

Aortoesophageal fistula as a late complication of type B aortic dissection.  

PubMed

We present a patient with aortoesophageal fistula that occurred years after an acute type B aortic dissection that was treated medically. This patient developed aneurysmal dilatation of the chronically dissected aorta, which finally eroded into the esophagus. Endovascular management with the placement of a stent graft was performed, but the patient ultimately died of multiorgan failure and possible myocardial infarction. PMID:21489929

Vasquez, Julio C; Delarosa, Jacob; Leon, Juan J

2011-02-01

387

Association of Cervical Artery Dissection with Connective Tissue Abnormalities in Skin and Arteries  

Microsoft Academic Search

Spontaneous cervical artery dissections (sCAD) often occur in otherwise healthy individuals without known risk factors for stroke and frequently develop spontaneously without relevant trauma. An underlying arteriopathy leading to a so-called ’weakness of the vessel wall’ and predisposing certain individuals to dissection has often been postulated. Therefore, the morphology of connective tissue, a main component of vessel wall and environment,

T. Brandt; M. Morcher; I. Hausser

2005-01-01

388

Endovascular Aortic Repair Of A Post-Dissecting1 Thoracoabdominal Aneurysm Using Intraoperative2  

E-print Network

1 Endovascular Aortic Repair Of A Post-Dissecting1 Thoracoabdominal Aneurysm Using Intraoperative2 of "Fusion Imaging" to facilitate the treatment of a post-dissection6 thoracoabdominal aneurysm The endovascular aortic repair of complex aortic aneurysms with fenestrated or branched2 grafts requires accurate

Paris-Sud XI, Université de

389

The dead center of the dental curriculum: changing attitudes of dental students during dissection.  

PubMed

The purpose of this study was to investigate changes in dental students' perceptions of professionalism, knowledge, and emotion over the period of dissection in a human anatomy course. Whether human dissection needs to be a part of the modern dental curriculum is often called into question, particularly with the plethora of electronic and other aids available to support the learning of anatomy. The influence of the dissection process on development of professional attitudes and emotional maturity has been studied in medical students, but how dental students react to this part of their education is less well known. To investigate this question, a survey was administered before and after the dissection course to two sequential year groups of dental students. It was found that these students had high levels of understanding of professional values before commencing dissection and continued to value the role of teamwork in aiding their learning over the survey period. The majority of students coped well with the assimilation of knowledge and developed coping mechanisms to handle the emotional aspects of dissection. The students remained excited by and interested in dissection, and the majority valued it as the most positive aspect of their anatomy course. The students increasingly valued the use of prosected specimens as an aid to learning. This study confirmed that significant changes occur in dental students' attitudes during the period of dissection, which we believe contribute to the development of more empathetic and caring practitioners. PMID:22012777

Redwood, Christopher J; Townsend, Grant C

2011-10-01

390

Vertigo as Manifestation of Vertebral Artery Dissection after Chiropractic Neck Manipulations  

Microsoft Academic Search

We recently observed a case of vertebral artery (VA) dissection following chiropractic neck manipulations. The first manifestation was unusual; in the form of vertigo. Therefore, the patient was referred to the otoneurologist. A VA dissection should be suspected in a case of vertigo following chiropractic neck manipulations, and vestibular tests should be done carefully, avoiding Rose’s positions. In our case,

Dominique Vibert; Josette Rohr-Le Floch; Gèrard Gauthier

1993-01-01

391

Aortic dissection presenting an acute onset of neuroradicular syndrome complicated by coeliac and superior mesenteric artery embolism.  

PubMed

Aortic dissection is a catastrophic medical emergency with complex and changeable clinical presentations. We report a case of aortic dissection complicated by coeliac and superior mesenteric artery embolism, which is hardly been reported till date. PMID:25358642

Zeng, Lixiong; Yuan, Hong; Jiang, Weihong; Yang, Kan; Zhang, Zhihui

2014-12-01

392

Extensive bilateral vertebral artery remodeling following treatment of dissection using pipeline embolic device  

PubMed Central

Background Cerebral artery dissection remains a significant cause of stroke, and the mainstay of treatment has been medical management with anticoagulation, although flow-diverting stents have been used in some cases of arterial dissection resistant to medical management. Methods We present a case report of bilateral vertebral artery stenting using pipeline embolic device flow-diverting stents, after failed medical management of the dissection. Results This case demonstrated substantial subsequent vertebral arterial remodeling and good clinical outcome with maintenance of posterior circulation. The patient did not suffer any further strokes or posterior circulation symptoms following vertebral artery remodeling. Conclusion In cases where traditional management of arterial dissection has not been efficacious, flow-diverting stents may be useful in treating dissections of the posterior cerebral circulation, even with bilateral involvement.

Mitchell, Bartley; Momin, Eric; Jou, Liang-Der; Shaltoni, Hashem; Morsi, Hesham; Mawad, Michel

2014-01-01

393

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

PubMed

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

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

2014-10-24

394

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

PubMed Central

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

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

2013-01-01

395

Defense response genes co-localize with quantitative disease resistance loci in pepper  

Microsoft Academic Search

Functional bases of polygenically inherited disease resistance are still unknown. In recent years, molecular dissection of\\u000a polygenic resistance has led to the identification and location of quantitative trait loci (QTLs) on many plant genetic linkage\\u000a maps. This process is a pre-requisite for resistance QTL characterization at a molecular and functional level. Here, we report\\u000a the use of a candidate gene

S. Pflieger; A. Palloix; C. Caranta; A. Blattes; V. Lefebvre

2001-01-01

396

Management Strategy of Isolated Spontaneous Dissection of the Superior Mesenteric Artery  

PubMed Central

Objective: Isolated spontaneous dissection of the superior mesenteric artery (SMA) is very rare among of the visceral artery dissection and its treatment is not established. In this paper we present our experiences and consider the treatment of isolated SMA dissection. Methods: A retrospective review of our cases from 2005 was performed. Clinical symptoms, radiologic findings and results were evaluated. There were 14 cases of visceral artery dissection, in which all cases were with SMA dissection. There were 12 males and 2 females with a mean age of 57 years (range 41–78 years). Results: We categorized SMA dissection into the six types according to the Sakamoto’s and Zerbib’s classification. One patient with type VI underwent emergent endovascular surgery with stent. One patient with type VI received thrombectomy and intimectomy with open surgery. One patient with type II underwent aneurysmectomy due to enlarged dissected SMA 3 months later from onset. The other eleven patients were managed conservatively. At follow-up, the diameter of SMA did not enlarged and the length of the dissection significantly decreased to 20.7 ± 15.7 mm from 38.0 ± 15.1 mm at onset (p <0.01). After treatment, imaging indicated the following changes in classification: type I, one patient; type II, 4 patients; type IV, 4 patients; complete remodeling, one patient, all without any event during the follow-up period of 5–82 months. Conclusion: Most patients with isolated visceral artery dissection occurred in superior mesenteric artery and can be treated conservatively; however, endovascular or surgical procedures including laparotomy are indicated when there is suspicion of severe mesenteric ischemia. Because the dissection configuration will change, long term follow-up is necessary. (*English translation of Jpn J Vasc Surg 2013; 22: 695-701) PMID:25298823

Takase, Shinya; Seto, Yuki; Yokoyama, Hitoshi; Gotoh, Mitsukazu; Kogure, Michihiko; Midorikawa, Hirofumi; Saito, Tomiyoshi; Maehara, Kazuhira

2014-01-01

397

Transoesophageal echocardiography as the sole diagnostic investigation in patients with suspected thoracic aortic dissection.  

PubMed Central

OBJECTIVES--To assess the value and limitations of using transoesophageal echocardiography as the sole diagnostic test in patients with suspected thoracic aortic dissection. DESIGN--Retrospective data review over a two year period. SETTING--A regional cardiothoracic centre. PATIENTS--Data were compiled from admission records, surgical records, and lists of patients undergoing diagnostic investigations in the hospital. Patient's notes were used to identify presentation, management, and outcome. INTERVENTIONS--Patients were managed according to the policy of our unit, which is to treat patients with dissection affecting the ascending aorta by an operation. Patients with uncomplicated dissection sparing the ascending aorta are initially managed medically. MAIN OUTCOME MEASURES--In hospital and two year follow-up of patients who were investigated by transoesophageal echocardiography alone. RESULTS--Of 48 patients referred, 45 underwent transoesophageal echocardiography. Dissection was confirmed in 22 patients. Transoesophageal echocardiography showed the proximal extent of the dissection in 21/22 (96%) and only one patient required a further diagnostic investigation. Ten patients with dissection of the ascending aorta underwent graft replacement of the ascending aorta; operative mortality was 10% and their two year survival was 80%. Of the eight patients with dissection of the descending aorta, six were discharged home, and five were alive at two years. No patient without evidence of dissection on their initial transoesophageal echocardiographic examination required re-investigation into possible dissection in the two years after discharge. CONCLUSIONS--In patients with suspected thoracic dissection transoesophageal echocardiography rapidly and safely gives all the necessary diagnostic information. Further investigations, including coronary angiography, before surgery are unnecessary. Images PMID:7818964

Banning, A P; Masani, N D; Ikram, S; Fraser, A G; Hall, R J

1994-01-01

398

Spontaneous coronary artery dissection as a cause of myocardial infarction.  

PubMed

Spontaneous coronary artery dissection (SCAD) is a rare disease that is usually seen in young women in left descending coronary artery and result in events like sudden cardiac death and acute myocardial infarction. A 70-year-old man was admitted to the emergency department with chest pain which started 1 h ago during a relative's funeral. The initial electrocardiography demonstrated 2 mm ST-segment depression in leads V1-V3 and the patient underwent emergent coronary angiography. SCAD simultaneously in two different coronary arteries [left anterior descending (LAD) artery and left circumflex (LCx)] artery was detected and SCAD in LCx artery was causing total occlusion which resulted in acute myocardial infarction. Successful stenting was performed thereafter for both lesions. In addition to the existence of SCAD simultaneously in two different coronary arteries, the presence of muscular bridge and SCAD together at the same site of the LAD artery was another interesting point which made us report this case. PMID:25548620

Aksakal, Aytekin; Arslan, U?ur; Yaman, Mehmet; Urumda?, Mehmet; Ate?, Ahmet Hakan

2014-12-26

399

Complications Related to Gastric Endoscopic Submucosal Dissection and Their Managements  

PubMed Central

Endoscopic submucosal dissection (ESD) for early gastric cancer is a well-established procedure with the advantage of resection in an en bloc fashion, regardless of the size, shape, coexisting ulcer, and location of the lesion. However, gastric ESD is a more difficult and meticulous technique, and also requires a longer procedure time, than conventional endoscopic mucosal resection. These factors naturally increase the risk of various complications. The two most common complications accompanying gastric ESD are bleeding and perforation. These complications are known to occur both intraoperatively and postoperatively. However, there are other rare but serious complications related to gastric ESD, including aspiration pneumonia, stenosis, venous thromboembolism, and air embolism. Endoscopists should have sufficient knowledge about such complications and be prepared to deal with them appropriately, as successful management of complications is necessary for the successful completion of the entire ESD procedure. PMID:25324997

Saito, Itaru; Tsuji, Yosuke; Sakaguchi, Yoshiki; Niimi, Keiko; Ono, Satoshi; Kodashima, Shinya; Yamamichi, Nobutake; Koike, Kazuhiko

2014-01-01

400

Unilateral shunt formation with thoracic aortic dissection in a whippet.  

PubMed

A three-year-old neutered male whippet was presented with intermittent, exercise-induced paraparesis. Femoral pulses were bilaterally absent. Neurologic examination was suggestive of a thoracolumbar myelopathy. Blood pressure measurements revealed hypotension in both pelvic limbs, hypertension in the right thoracic limb and it was immeasurable in the left thoracic limb. Echocardiography was within reference limits. A clear vascular pulsation was palpable on the right ventral abdominal wall. Computed tomographic angiography revealed a dissection of the aortic wall between the left subclavian artery and the brachiocephalic trunk with subsequent thrombus formation. A shunt between the right internal thoracic, cranial and caudal epigastric arteries to preserve blood flow to the pelvic limbs was visualized. Necropsy was declined by the owner. This is the first case report describing the formation of a unilateral vascular shunt following a thoracic aortic occlusion, which presented as exercise-induced paraparesis. PMID:24602076

Cornelis, I; Bosmans, T; Doom, M; Binst, D; Van der Vekens, E; Kromhout, K; Cornillie, P; Van Ham, L

2014-06-01

401

Dissecting functional connectivity of neuronal microcircuits: experimental and theoretical insights.  

PubMed

Structure-function studies of neuronal networks have recently benefited from considerable progress in different areas of investigation. Advances in molecular genetics and imaging have allowed for the dissection of neuronal connectivity with unprecedented detail whereas in vivo recordings are providing much needed clues as to how sensory, motor and cognitive function is encoded in neuronal firing. However, bridging the gap between the cellular and behavioral levels will ultimately require an understanding of the functional organization of the underlying neuronal circuits. One way to unravel the complexity of neuronal networks is to understand how their connectivity emerges during brain maturation. In this review, we will describe how graph theory provides experimentalists with novel concepts that can be used to describe and interpret these developing connectivity schemes. PMID:21459463

Feldt, Sarah; Bonifazi, Paolo; Cossart, Rosa

2011-05-01

402

Recommended sedation and intraprocedural monitoring for gastric endoscopic submucosal dissection.  

PubMed

Endoscopic submucosal dissection is associated with a longer treatment time and a higher risk of patient discomfort than conventional procedures. Adequate, safe sedation is therefore essential. Sedation can cause adverse effects such as hypoxemia and hypotension, requiring continuous intraoperative and postoperative monitoring of blood pressure, use of the electrocardiogram, and arterial blood oxygen saturation by pulse oximetry. A physician and a nurse solely responsible for sedating and monitoring the patient should be present during treatment.A combination of benzodiazepines and analgesics are generally used for sedation, but new sedatives such as propofol and dexmedetomidine hydrochloride are expected to be useful agents. Endoscopists should become more familiar with sedatives, analgesics, and emergency procedures in the future. PMID:23406354

Sasaki, Tohru; Tanabe, Satoshi; Ishido, Kenji; Azuma, Mizutomo; Katada, Chikatoshi; Higuchi, Katsuhiko; Koizumi, Wasaburo

2013-03-01

403

Open fenestration for complicated acute aortic B dissection.  

PubMed

Acute type B aortic dissection (ABAD) is a serious cardiovascular emergency in which morbidity and mortality are often related to the presence of complications at clinical presentation. Visceral, renal, and limb ischemia occur in up to 30% of patients with ABAD and are associated with higher in-hospital mortality. The aim of the open fenestration is to resolve the malperfusion by creating a single aortic lumen at the suprarenal or infrarenal level. This surgical procedure is less invasive than total aortic replacement, thus not requiring extracorporeal support and allowing preservation of the intercostal arteries, which results in decreased risk of paraplegia. Surgical aortic fenestration represents an effective and durable option for treating ischemic complications of ABAD, particularly for patients with no aortic dilatation. In the current endovascular era, this open technique serves as an alternative option in case of contraindications or failure of endovascular management of complicated ABAD. PMID:25133107

Trimarchi, Santi; Segreti, Sara; Grassi, Viviana; Lomazzi, Chiara; Cova, Marta; Piffaretti, Gabriele; Rampoldi, Vincenzo

2014-07-01

404

Open fenestration for complicated acute aortic B dissection  

PubMed Central

Acute type B aortic dissection (ABAD) is a serious cardiovascular emergency in which morbidity and mortality are often related to the presence of complications at clinical presentation. Visceral, renal, and limb ischemia occur in up to 30% of patients with ABAD and are associated with higher in-hospital mortality. The aim of the open fenestration is to resolve the malperfusion by creating a single aortic lumen at the suprarenal or infrarenal level. This surgical procedure is less invasive than total aortic replacement, thus not requiring extracorporeal support and allowing preservation of the intercostal arteries, which results in decreased risk of paraplegia. Surgical aortic fenestration represents an effective and durable option for treating ischemic complications of ABAD, particularly for patients with no aortic dilatation. In the current endovascular era, this open technique serves as an alternative option in case of contraindications or failure of endovascular management of complicated ABAD. PMID:25133107

Segreti, Sara; Grassi, Viviana; Lomazzi, Chiara; Cova, Marta; Piffaretti, Gabriele; Rampoldi, Vincenzo

2014-01-01

405

Desirable training of endoscopic submucosal dissection: further spread worldwide  

PubMed Central

Endoscopic submucosal dissection (ESD) is an excellent treatment because of its high curative resection rate and low local recurrence rate. However, its technical difficulty prevents from its permeation worldwide. For further permeation of ESD, the establishment of an appropriate training system is essential. In Japan, trainee endoscopists who have had prerequisites for ESD, that is to say, basic knowledge and skills, start ESD in accordance with a stepwise training system under close supervision by experts. The trainers select an appropriate lesion in human for each step of developments in ESD techniques. In Western countries there are few ESD experts at present, so an ex vivo animal model training must play a major role in the training system. It is desirable that these training systems should be constructed by some authorized organizations such as Japan Gastroenterological Endoscopy Society (JGES). PMID:25333003

Fujishiro, Mitsuhiro; Kodashima, Shinya; Niimi, Keiko; Ono, Satoshi; Yamamichi, Nobutake; Koike, Kazuhiko

2014-01-01

406

Tenascin C protects aorta from acute dissection in mice  

NASA Astrophysics Data System (ADS)

Acute aortic dissection (AAD) is caused by the disruption of intimomedial layer of the aortic walls, which is immediately life-threatening. Although recent studies indicate the importance of proinflammatory response in pathogenesis of AAD, the mechanism to keep the destructive inflammatory response in check is unknown. Here, we report that induction of tenascin-C (TNC) is a stress-evoked protective mechanism against the acute hemodynamic and humoral stress in aorta. Periaortic application of CaCl2 caused stiffening of abdominal aorta, which augmented the hemodynamic stress and TNC induction in suprarenal aorta by angiotensin II infusion. Deletion of Tnc gene rendered mice susceptible to AAD development upon the aortic stress, which was accompanied by impaired TGF? signaling, insufficient induction of extracellular matrix proteins and exaggerated proinflammatory response. Thus, TNC works as a stress-evoked molecular damper to maintain the aortic integrity under the acute stress.

Kimura, Taizo; Shiraishi, Kozoh; Furusho, Aya; Ito, Sohei; Hirakata, Saki; Nishida, Norifumi; Yoshimura, Koichi; Imanaka-Yoshida, Kyoko; Yoshida, Toshimichi; Ikeda, Yasuhiro; Miyamoto, Takanobu; Ueno, Takafumi; Hamano, Kimikazu; Hiroe, Michiaki; Aonuma, Kazutaka; Matsuzaki, Masunori; Imaizumi, Tsutomu; Aoki, Hiroki

2014-02-01

407

Spontaneous coronary artery dissection as a cause of myocardial infarction  

PubMed Central

Spontaneous coronary artery dissection (SCAD) is a rare disease that is usually seen in young women in left descending coronary artery and result in events like sudden cardiac death and acute myocardial infarction. A 70-year-old man was admitted to the emergency department with chest pain which started 1 h ago during a relative’s funeral. The initial electrocardiography demonstrated 2 mm ST-segment depression in leads V1-V3 and the patient underwent emergent coronary angiography. SCAD simultaneously in two different coronary arteries [left anterior descending (LAD) artery and left circumflex (LCx)] artery was detected and SCAD in LCx artery was causing total occlusion which resulted in acute myocardial infarction. Successful stenting was performed thereafter for both lesions. In addition to the existence of SCAD simultaneously in two different coronary arteries, the presence of muscular bridge and SCAD together at the same site of the LAD artery was another interesting point which made us report this case.

Aksakal, Aytekin; Arslan, U?ur; Yaman, Mehmet; Urumda?, Mehmet; Ate?, Ahmet Hakan

2014-01-01

408

Vertebral artery dissection after a chiropractor neck manipulation.  

PubMed

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

Jones, Jeremy; Jones, Catherine; Nugent, Kenneth

2015-01-01

409

Vertebral artery dissection after a chiropractor neck manipulation  

PubMed Central

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

Jones, Jeremy; Nugent, Kenneth

2015-01-01

410

Simultaneous bilateral internal carotid and vertebral artery dissection following chiropractic manipulation: case report and review of the literature  

Microsoft Academic Search

Single-vessel cervical arterial dissections typically occur in young adults and are a common cause of cerebral ischemia and stroke. Although the pathogenesis of multivessel dissection is unclear, it is thought to be a consequence of underlying collagen vascular disease. We present a 34-year-old previously healthy man who developed bilateral internal carotid and vertebral artery dissection following chiropractic manipulation.

R. N. Nadgir; L. A. Loevner; T. Ahmed; G. Moonis; J. Chalela; K. Slawek; S. Imbesi

2003-01-01

411

Murine Model of Surgically Induced Acute Aortic Dissection Type A  

PubMed Central

Objectives This study aimed at developing a murine model of surgically induced acute aortic dissection type A (AAD) for investigation of the formation and progression of AAD, and to test whether this system could be used for biomarker discovery. Methods Adult fibrillin-1 deficient, Fbn1C1039G/+ mice and wild-type mice were anesthetized, ventilated and the ascending aorta exposed via hemisternotomy. We hypothesized that AAD could be induced either by injecting autologous blood into the aortic wall or by injury to the wall with aortic clamping. Echocardiography was done preoperatively, and serum samples collected before and 30 minutes after surgery, and analyzed by ELISA. Results Echocardiography revealed larger aortic root diameters in Fbn1C1039G/+ compared with wild-type mice (P=0.001). Histology showed that aortic clamp injury but not injection of blood leads to large intimal tears, disruption of aortic wall structures and localized dissection of the aortic media in Fbn1C1039G/+ mice. AAD developed in 4 out of 5 Fbn1C1039G/+ mice versus 0 out of 5 wild-type mice after aortic clamping (P<0.01). Elastin staining showed higher elastic fiber fragmentation and disarray in Fbn1C1039G/+ compared with wild-type mice. ELISA analysis revealed elevated circulating TGF?1 concentrations after inducing AAD in Fbn1C1039G/+ mice (P=0.02, 150±61 ng/ml vs. 456±97 ng/ml), but not in wild-type or sham-operated mice. Conclusions Aortic clamp injury can induce AAD in Fbn1C1039G/+, but not in wild-type mice. This murine model of surgically induced AAD is highly reproducible and non-lethal in the short-term. Using this system, we revealed that circulating TGF?1 is a promising biomarker for AAD. PMID:19910001

Matt, Peter; Huso, David L.; Habashi, Jennifer; Holm, Tammy; Doyle, Jeff; Schoenhoff, Florian; Liu, Guosheng; Black, James; Van Eyk, Jennifer E.; Dietz, Harry C.

2010-01-01

412

Virtual, on-line, frog dissection vs. conventional laboratory dissection: A comparison of student achievement and teacher perceptions among honors, general ability, and foundations-level high school biology classes  

NASA Astrophysics Data System (ADS)

Dissecting animal specimens has long been a tradition in biology classes. Objections by students, based on religious or ethical grounds, have been raised regarding the dissections of animals in classroom laboratories. A number of states now have legal proceedings or statewide policies requiring that alternatives to the actual dissection of laboratory animal specimens be permitted in their school districts. Alternatives to actual dissections have been developed in recent years. For a variety of reasons, performing an actual or conventional animal dissection may not be a desirable option. The purpose of this study was to investigate how a virtual On-line frog dissection compares with an actual laboratory dissection. What were the perceptions of the teacher's using it? How does student achievement compare among three the different ability levels on a pre and posttest regarding basic frog anatomy? Is a virtual On-line dissection a suitable alternative for students who, for whatever reason, do not participate in the actual laboratory experience? The subjects consisted of 218 biology students among three different ability levels, in a Northeastern suburban high school. Approximately half of the student groups participated in a virtual On-line dissection, the other half in an actual laboratory dissection. A pretest of basic frog anatomy was administered to the students two days before and the posttest one day after their dissection experience. Data were analyzed using matched pairs t-Tests, Analysis of Variance, Tukey HSD, and Squared Curvilinear Coefficients. Survey questionnaires were administered to the teachers after the dissection experiences were completed. There were no significant differences found in achievement between the virtual and conventional dissection groups. There were significant differences found in achievement score means among the three ability levels. There was no significant interaction between gender and achievement. Perceptions of the teacher's facilitating the two instructional methods varied. The main area of agreement among them was that a virtual On-line frog dissection was a viable alternative for students who objected to doing a conventional dissection.

Kopec, Ronald H.

2002-09-01

413

Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways.  

PubMed

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

Mitsos, Alexander; Melas, Ioannis N; Morris, Melody K; Saez-Rodriguez, Julio; Lauffenburger, Douglas A; Alexopoulos, Leonidas G

2012-01-01

414

Aortic Dissection and Renal Failure in a Patient with Severe Hypothyroidism  

PubMed Central

Acute aortic dissection (AAD) is a life-threatening condition associated with high morbidity and mortality. The most important recognized acquired cause that leads to dissection is chronic arterial hypertension. With respect to the anuria and renal failure, aortic dissection is not something that is always considered and is still not a very common presentation unless both renal arteries come off the false lumen of the dissection. However, when present, preoperative renal failure in patients with acute type B dissection has been noted to be an independent predictor of mortality. Early recognition and diagnosis is the key and as noted by previous studies as well, almost a third of these patients are initially worked up for other causes until later when they are diagnosed with aortic dissection. Here we present a case of a patient presenting with severe hypothyroidism, long-standing hypertension, and anuria. Through the case, we highlight the importance of having aortic dissection as an important differential in patients presenting with anuria who have a long standing history of uncontrolled hypertension. Pathophysiology relating to severe hypothyroidism-induced renal dysfunction is also discussed. PMID:22829842

Brooke, Valerie; Goswami, Sangeeta; Mohanty, Arpan; Kasi, Pashtoon Murtaza

2012-01-01

415

A genome scan for quantitative trait loci affecting growth-related traits in an F1 family of Asian seabass (Lates calcarifer)  

Microsoft Academic Search

BACKGROUND: Body weight and length are economically important traits in foodfish species influenced by quantitative trait loci (QTL) and environmental factors. It is usually difficult to dissect the genetic and environmental effects. Asian seabass (Lates calcarifer) is an important marine foodfish species with a compact genome (~700 Mb). The recent construction of a first generation linkage map of Asian seabass

Chun Ming Wang; Loong Chueng Lo; Ze Yuan Zhu; Gen Hua Yue

2006-01-01

416

Endovascular treatment of spontaneous isolated common and external iliac artery dissections with preservation of pelvic blood flow.  

PubMed

Spontaneous isolated dissection of iliac arteries is very rare, with few reports in the literature. Medical, surgical, and endovascular treatment modalities have all been used to manage iliac artery dissections. We report a case of symptomatic, isolated, spontaneous dissection of the common iliac and external iliac arteries. Both dissections were successfully treated by separate percutaneous stent-graft placement, preserving hypogastric artery flow. This technique is interesting because it provides adequate sealing of proximal and distal dissection sites while preserving hypogastric artery and pelvic flow. PMID:25305424

Yoshida, Ricardo de Alvarenga; Kolvenbach, Ralf; Vieira, Paulo Roberto Bahdur; Moura, Regina; Jaldin, Rodrigo Gibin; Yoshida, Winston Bonetti

2015-01-01

417

Reversible cerebral vasoconstriction syndrome and bilateral vertebral artery dissection presenting in a patient after cesarean section  

PubMed Central

Reversible cerebral vasoconstriction syndrome (RCVS) is characterized by sudden-onset thunderclap headache and focal neurologic deficits. Once thought to be a rare syndrome, more advanced non-invasive imaging has led to an increase in RCVS diagnosis. Unilateral vertebral artery dissection has been described in fewer than 40% of cases of RCVS. Bilateral vertebral artery dissection has rarely been reported. We describe the case of a patient with RCVS and bilateral vertebral artery dissection presenting with an intramedullary infarct treated successfully with medical management and careful close follow-up. This rare coexistence should be recognized as the treatment differs. PMID:23354867

Mitchell, Lex A; Santarelli, Justin G; Singh, Inder Paul; Do, Huy M

2013-01-01

418

Probing cell mechanics with subcellular laser dissection of actomyosin networks in the early developing Drosophila embryo.  

PubMed

Laser dissection is a useful tool in developmental biology to probe mechanical forces from the subcellular to the tissue/embryo scale. During tissue morphogenesis, cells are equipped with networks of actomyosin that generate forces. Here we present a technique based on near-infrared (NIR) femtosecond (fs) pulsed laser dissection that allows subcellular ablation of actomyosin networks. This technique allows to selectively ablate actomyosin networks while preserving cell plasma membrane. The resulting relaxation of the remaining network after laser dissection is imaged and analyzed to deduce local forces responsible for tissue morphogenesis in the developing Drosophila embryo. PMID:25245696

Rauzi, M; Lenne, P-F

2015-01-01

419

Endovascular Stent Graft for Treatment of Complicated Spontaneous Dissection of Celiac Artery: Report of Two Cases  

PubMed Central

We report 2 cases of complicated spontaneous dissection of the celiac artery, which were successfully treated by a stent graft. The first patient was a 47-year-old man who presented with acute abdominal pain. CT scan showed ruptured saccular aneurysm with surrounding retroperitoneal hematoma. The second patient was a 57-year-old man with progressive dissecting aneurysm. Endovascular stent graft was placed in the celiac trunk to control bleeding, and to prevent rupture in each patient. Follow-up CT scans showed complete obliteration of a dissecting aneurysm. PMID:23690714

Kang, Ung Rae; Lee, Young-Hwan

2013-01-01