WorldWideScience

Sample records for portal protein diversity

  1. The Protein Model Portal.

    Science.gov (United States)

    Arnold, Konstantin; Kiefer, Florian; Kopp, Jürgen; Battey, James N D; Podvinec, Michael; Westbrook, John D; Berman, Helen M; Bordoli, Lorenza; Schwede, Torsten

    2009-03-01

    Structural Genomics has been successful in determining the structures of many unique proteins in a high throughput manner. Still, the number of known protein sequences is much larger than the number of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. Thereby, experimental structure determination efforts and homology modeling complement each other in the exploration of the protein structure space. One of the challenges in using model information effectively has been to access all models available for a specific protein in heterogeneous formats at different sites using various incompatible accession code systems. Often, structure models for hundreds of proteins can be derived from a given experimentally determined structure, using a variety of established methods. This has been done by all of the PSI centers, and by various independent modeling groups. The goal of the Protein Model Portal (PMP) is to provide a single portal which gives access to the various models that can be leveraged from PSI targets and other experimental protein structures. A single interface allows all existing pre-computed models across these various sites to be queried simultaneously, and provides links to interactive services for template selection, target-template alignment, model building, and quality assessment. The current release of the portal consists of 7.6 million model structures provided by different partner resources (CSMP, JCSG, MCSG, NESG, NYSGXRC, JCMM, ModBase, SWISS-MODEL Repository). The PMP is available at http://www.proteinmodelportal.org and from the PSI Structural Genomics Knowledgebase.

  2. The Protein Model Portal

    OpenAIRE

    Arnold, Konstantin; Kiefer, Florian; Kopp, J?rgen; Battey, James N. D.; Podvinec, Michael; Westbrook, John D.; Berman, Helen M.; Bordoli, Lorenza; Schwede, Torsten

    2008-01-01

    Structural Genomics has been successful in determining the structures of many unique proteins in a high throughput manner. Still, the number of known protein sequences is much larger than the number of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. Thereby, experimental structure determination efforts and homology modeling complement each other in the exploratio...

  3. The portal protein plays essential roles at different steps of the SPP1 DNA packaging process

    International Nuclear Information System (INIS)

    Isidro, Anabela; Henriques, Adriano O.; Tavares, Paulo

    2004-01-01

    A large number of viruses use a specialized portal for entry of DNA to the viral capsid and for its polarized exit at the beginning of infection. These families of viruses assemble an icosahedral procapsid containing a portal protein oligomer in one of its 12 vertices. The viral ATPase (terminase) interacts with the portal vertex to form a powerful molecular motor that translocates DNA to the procapsid interior against a steep concentration gradient. The portal protein is an essential component of this DNA packaging machine. Characterization of single amino acid substitutions in the portal protein gp6 of bacteriophage SPP1 that block DNA packaging identified sequential steps in the packaging mechanism that require its action. Gp6 is essential at early steps of DNA packaging and for DNA translocation to the capsid interior, it affects the efficiency of DNA packaging, it is a central component of the headful sensor that determines the size of the packaged DNA molecule, and is essential for closure of the portal pore by the head completion proteins to prevent exit of the DNA encapsidated. Functional regions of gp6 necessary at each step are identified within its primary structure. The similarity between the architecture of portal oligomers and between the DNA packaging strategies of viruses using portals strongly suggests that the portal protein plays the same roles in a large number of viruses

  4. Direct interaction of the bacteriophage SPP1 packaging ATPase with the portal protein.

    Science.gov (United States)

    Oliveira, Leonor; Cuervo, Ana; Tavares, Paulo

    2010-03-05

    DNA packaging in tailed bacteriophages and other viruses requires assembly of a complex molecular machine at a specific vertex of the procapsid. This machine is composed of the portal protein that provides a tunnel for DNA entry, an ATPase that fuels DNA translocation (large terminase subunit), and most frequently, a small terminase subunit. Here we characterized the interaction between the terminase ATPase subunit of bacteriophage SPP1 (gp2) and the procapsid portal vertex. We found, by affinity pulldown assays with purified proteins, that gp2 interacts with the portal protein, gp6, independently of the terminase small subunit gp1, DNA, or ATP. The gp2-procapsid interaction via the portal protein depends on gp2 concentration and requires the presence of divalent cations. Competition experiments showed that isolated gp6 can only inhibit gp2-procapsid interactions and DNA packaging at gp6:procapsid molar ratios above 10-fold. Assays with gp6 carrying mutations in distinct regions of its structure that affect the portal-induced stimulation of ATPase and DNA packaging revealed that none of these mutations impedes gp2-gp6 binding. Our results demonstrate that the SPP1 packaging ATPase binds directly to the portal and that the interaction is stronger with the portal embedded in procapsids. Identification of mutations in gp6 that allow for assembly of the ATPase-portal complex but impair DNA packaging support an intricate cross-talk between the two proteins for activity of the DNA translocation motor.

  5. Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal.

    Science.gov (United States)

    Bordoli, Lorenza; Schwede, Torsten

    2012-01-01

    Comparative protein structure modeling is a computational approach to build three-dimensional structural models for proteins using experimental structures of related protein family members as templates. Regular blind assessments of modeling accuracy have demonstrated that comparative protein structure modeling is currently the most reliable technique to model protein structures. Homology models are often sufficiently accurate to substitute for experimental structures in a wide variety of applications. Since the usefulness of a model for specific application is determined by its accuracy, model quality estimation is an essential component of protein structure prediction. Comparative protein modeling has become a routine approach in many areas of life science research since fully automated modeling systems allow also nonexperts to build reliable models. In this chapter, we describe practical approaches for automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal.

  6. The Protein Model Portal--a comprehensive resource for protein structure and model information.

    Science.gov (United States)

    Haas, Juergen; Roth, Steven; Arnold, Konstantin; Kiefer, Florian; Schmidt, Tobias; Bordoli, Lorenza; Schwede, Torsten

    2013-01-01

    The Protein Model Portal (PMP) has been developed to foster effective use of 3D molecular models in biomedical research by providing convenient and comprehensive access to structural information for proteins. Both experimental structures and theoretical models for a given protein can be searched simultaneously and analyzed for structural variability. By providing a comprehensive view on structural information, PMP offers the opportunity to apply consistent assessment and validation criteria to the complete set of structural models available for proteins. PMP is an open project so that new methods developed by the community can contribute to PMP, for example, new modeling servers for creating homology models and model quality estimation servers for model validation. The accuracy of participating modeling servers is continuously evaluated by the Continuous Automated Model EvaluatiOn (CAMEO) project. The PMP offers a unique interface to visualize structural coverage of a protein combining both theoretical models and experimental structures, allowing straightforward assessment of the model quality and hence their utility. The portal is updated regularly and actively developed to include latest methods in the field of computational structural biology. Database URL: http://www.proteinmodelportal.org.

  7. Effects of chronic portal hypertension on small heat-shock proteins in mesenteric arteries.

    Science.gov (United States)

    Chen, Xuesong; Zhang, Hai-Ying; Pavlish, Kristin; Benoit, Joseph N

    2005-04-01

    Previous studies have shown that impaired vasoconstrictor function in chronic portal hypertension is mediated via cAMP-dependent events. Recent data have implicated two small heat-shock proteins (HSP), namely HSP20 and HSP27, in the regulation of vascular tone. Phosphorylation of HSP20 is associated with vasorelaxation, whereas phosphorylation of HSP27 is associated with vasoconstriction. We hypothesized that alterations in the expression and/or phosphorylation of small HSPs may play a role in impaired vasoconstriction in portal hypertension. A rat model of prehepatic chronic portal hypertension was used. Studies were conducted in small mesenteric arteries isolated from normal and portal hypertensive rats. Protein levels of HSP20 and HSP27 were detected by Western blot analysis. Protein phosphorylation was analyzed by isoelectric focusing. HSP20 mRNA expression was determined by RT-PCR. To examine the role of cAMP in the regulation of small HSP phosphorylation and expression, we treated both normal and portal hypertensive vessels with a PKA inhibitor Rp-cAMPS. We found both an increased HSP20 phosphorylation and a decreased HPS20 protein level in portal hypertension, both of which were restored to normal by PKA inhibition. However, PKA did not change HSP20 mRNA expression. We conclude that decreased HSP20 protein level is mediated by cAMP-dependent pathway and that impaired vasoconstrictor function in portal hypertension may be partially explained by decreased expression of HSP20. We also suggest that the phosphorylation of HSP20 by PKA may alter HSP20 turnover.

  8. Portal protein functions akin to a DNA-sensor that couples genome-packaging to icosahedral capsid maturation

    OpenAIRE

    Lokareddy, Ravi K.; Sankhala, Rajeshwer S.; Roy, Ankoor; Afonine, Pavel V.; Motwani, Tina; Teschke, Carolyn M.; Parent, Kristin N.; Cingolani, Gino

    2017-01-01

    Tailed bacteriophages and herpesviruses assemble infectious particles via an empty precursor capsid (or ?procapsid') built by multiple copies of coat and scaffolding protein and by one dodecameric portal protein. Genome packaging triggers rearrangement of the coat protein and release of scaffolding protein, resulting in dramatic procapsid lattice expansion. Here, we provide structural evidence that the portal protein of the bacteriophage P22 exists in two distinct dodecameric conformations: a...

  9. Novel serological neo-epitope markers of extracellular matrix proteins for the detection of portal hypertension

    DEFF Research Database (Denmark)

    Leeming, Diana Julie; Karsdal, M A; Byrjalsen, I

    2013-01-01

    The hepatic venous pressure gradient (HVPG) is an invasive, but important diagnostic and prognostic marker in cirrhosis with portal hypertension (PHT). During cirrhosis, remodelling of fibrotic tissue by matrix metalloproteinases (MMPs) is a permanent process generating small fragments of degrade...... extracellular matrix (ECM) proteins known as neoepitopes, which are then released into the circulation....

  10. Portal protein functions akin to a DNA-sensor that couples genome-packaging to icosahedral capsid maturation

    Science.gov (United States)

    Lokareddy, Ravi K.; Sankhala, Rajeshwer S.; Roy, Ankoor; Afonine, Pavel V.; Motwani, Tina; Teschke, Carolyn M.; Parent, Kristin N.; Cingolani, Gino

    2017-01-01

    Tailed bacteriophages and herpesviruses assemble infectious particles via an empty precursor capsid (or ‘procapsid') built by multiple copies of coat and scaffolding protein and by one dodecameric portal protein. Genome packaging triggers rearrangement of the coat protein and release of scaffolding protein, resulting in dramatic procapsid lattice expansion. Here, we provide structural evidence that the portal protein of the bacteriophage P22 exists in two distinct dodecameric conformations: an asymmetric assembly in the procapsid (PC-portal) that is competent for high affinity binding to the large terminase packaging protein, and a symmetric ring in the mature virion (MV-portal) that has negligible affinity for the packaging motor. Modelling studies indicate the structure of PC-portal is incompatible with DNA coaxially spooled around the portal vertex, suggesting that newly packaged DNA triggers the switch from PC- to MV-conformation. Thus, we propose the signal for termination of ‘Headful Packaging' is a DNA-dependent symmetrization of portal protein. PMID:28134243

  11. Portal protein functions akin to a DNA-sensor that couples genome-packaging to icosahedral capsid maturation

    Energy Technology Data Exchange (ETDEWEB)

    Lokareddy, Ravi K.; Sankhala, Rajeshwer S.; Roy, Ankoor; Afonine, Pavel V.; Motwani, Tina; Teschke, Carolyn M.; Parent, Kristin N.; Cingolani, Gino (Rutgers); (LBNL); (Connecticut); (TJU); (MSU)

    2017-01-30

    Tailed bacteriophages and herpesviruses assemble infectious particles via an empty precursor capsid (or ‘procapsid’) built by multiple copies of coat and scaffolding protein and by one dodecameric portal protein. Genome packaging triggers rearrangement of the coat protein and release of scaffolding protein, resulting in dramatic procapsid lattice expansion. Here, we provide structural evidence that the portal protein of the bacteriophage P22 exists in two distinct dodecameric conformations: an asymmetric assembly in the procapsid (PC-portal) that is competent for high affinity binding to the large terminase packaging protein, and a symmetric ring in the mature virion (MV-portal) that has negligible affinity for the packaging motor. Modelling studies indicate the structure of PC-portal is incompatible with DNA coaxially spooled around the portal vertex, suggesting that newly packaged DNA triggers the switch from PC- to MV-conformation. Thus, we propose the signal for termination of ‘Headful Packaging’ is a DNA-dependent symmetrization of portal protein.

  12. Amino acid metabolism conflicts with protein diversity

    OpenAIRE

    Krick, Teresa; Shub, David A.; Verstraete, Nina; Ferreiro, Diego U.; Alonso, Leonardo G.; Shub, Michael; Sanchez, Ignacio E.

    2014-01-01

    The 20 protein-coding amino acids are found in proteomes with different relative abundances. The most abundant amino acid, leucine, is nearly an order of magnitude more prevalent than the least abundant amino acid, cysteine. Amino acid metabolic costs differ similarly, constraining their incorporation into proteins. On the other hand, a diverse set of protein sequences is necessary to build functional proteomes. Here, we present a simple model for a cost-diversity trade-off postulating that n...

  13. Analysis of capsid portal protein and terminase functional domains: interaction sites required for DNA packaging in bacteriophage T4.

    Science.gov (United States)

    Lin, H; Rao, V B; Black, L W

    1999-06-04

    Bacteriophage DNA packaging results from an ATP-driven translocation of concatemeric DNA into the prohead by the phage terminase complexed with the portal vertex dodecamer of the prohead. Functional domains of the bacteriophage T4 terminase and portal gene 20 product (gp20) were determined by mutant analysis and sequence localization within the structural genes. Interaction regions of the portal vertex and large terminase subunit (gp17) were determined by genetic (terminase-portal intergenic suppressor mutations), biochemical (column retention of gp17 and inhibition of in vitro DNA packaging by gp20 peptides), and immunological (co-immunoprecipitation of polymerized gp20 peptide and gp17) studies. The specificity of the interaction was tested by means of a phage T4 HOC (highly antigenicoutercapsid protein) display system in which wild-type, cs20, and scrambled portal peptide sequences were displayed on the HOC protein of phage T4. Binding affinities of these recombinant phages as determined by the retention of these phages by a His-tag immobilized gp17 column, and by co-immunoprecipitation with purified terminase supported the specific nature of the portal protein and terminase interaction sites. In further support of specificity, a gp20 peptide corresponding to a portion of the identified site inhibited packaging whereas the scrambled sequence peptide did not block DNA packaging in vitro. The portal interaction site is localized to 28 residues in the central portion of the linear sequence of gp20 (524 residues). As judged by two pairs of intergenic portal-terminase suppressor mutations, two separate regions of the terminase large subunit gp17 (central and COOH-terminal) interact through hydrophobic contacts at the portal site. Although the terminase apparently interacts with this gp20 portal peptide, polyclonal antibody against the portal peptide appears unable to access it in the native structure, suggesting intimate association of gp20 and gp17 possibly

  14. Novel serological neo-epitope markers of extracellular matrix proteins for the detection of portal hypertension.

    Science.gov (United States)

    Leeming, D J; Karsdal, M A; Byrjalsen, I; Bendtsen, F; Trebicka, J; Nielsen, M J; Christiansen, C; Møller, S; Krag, A

    2013-11-01

    The hepatic venous pressure gradient (HVPG) is an invasive, but important diagnostic and prognostic marker in cirrhosis with portal hypertension (PHT). During cirrhosis, remodelling of fibrotic tissue by matrix metalloproteinases (MMPs) is a permanent process generating small fragments of degraded extracellular matrix (ECM) proteins known as neoepitopes, which are then released into the circulation. To investigate their potential as plasma markers for detection of PHT. Ninety-four patients with alcoholic cirrhosis and 20 liver-healthy controls were included. Clinical and laboratory data of the patients were collected. All patients received HVPG measurement with blood sampling. In these samples, the following degradation or formation markers were measured: C1M (type I-collagen), C3M and PRO-C3 (type III collagen), C4M and P4NP 7S (type IV collagen), C5M (type V collagen), C6M (type VI collagen), BGM (biglycan), ELM (elastin), CRPM (CRP). All ECM markers except for CRPM correlated significantly with HVPG. Interestingly, C4M, C5M and ELM levels were significantly higher in patients with HVPG >10 mmHg. Multiple regression analysis identified PRO-C3, C6M and ELM as significant determinants, while the models A and B including PRO-C3, ELM, C6M and model for end-stage liver disease (MELD) provided better description of PHT (r = 0.75, P models provided odds ratios of >100 for having clinical significant PHT. These novel non-invasive extracellular matrix markers reflect the degree of liver dysfunction. The different degrees of portal hypertension correlated with these circulating neoepitopes. Using a single blood sample, these neoepitopes in combination with MELD detect the level of portal hypertension. © 2013 The Authors. Alimentary Pharmacology and Therapeutics published by John Wiley & Sons Ltd.

  15. Plasma ADAMTS-13 protein is not associated with portal hypertension or hemodynamic changes in patients with cirrhosis

    DEFF Research Database (Denmark)

    Wiese, Signe; Timm, Annette; Nielsen, Lars B

    2016-01-01

    BACKGROUND: Activated hepatic stellate cells synthesize the matrix metalloprotease ADAMTS13, which may be involved in the development of liver cirrhosis and portal hypertension. Plasma ADAMTS13 activity has been reported as both increased and decreased in cirrhosis, but ADAMTS13 protein has...... in cirrhosis. However, ADAMTS13 was unrelated to portal hypertension and systemic hemodynamics. In conclusion, ADAMTS13 does not appear to be associated to disease severity or the hemodynamic derangement in patients with cirrhosis....... not previously been examined. AIM: To evaluate ADAMTS13 protein in the hepatic circulation and the relation to disease severity, portal pressure, and systemic hemodynamics in cirrhotic patients. METHODS: Sixty-one cirrhotic patients (Child class: A=22; B=21; C=18) and nine healthy controls underwent a liver vein...

  16. [Characteristics of sublingual vein and expressions of vascular endothelial growth factor and hypoxia-inducible factor 1alpha proteins in sublingual tissues of Beagle dogs with portal hypertension].

    Science.gov (United States)

    Li, Bai-yu; Wang, Li-na; Yue, Xiao-qiang; Li, Bai

    2009-05-01

    To observe sublingual vein characteristics and the expressions of vascular endothelial growth factor (VEGF) and hypoxia-inducible factor 1alpha (HIF-1alpha) proteins in sublingual tissues of Beagle dogs with cirrhotic portal hypertension. Twelve Beagle dogs were randomly divided into normal control group and cirrhotic portal hypertension group. There were 6 dogs in each group. A canine model of cirrhosis portal hypertension was established by injecting dimethylnitrosamine (DMN) into portal vein once a week for 7 weeks. The characteristics of sublingual vein were observed. Portal venous pressure was measured by using bioelectric recording techniques. The expressions of VEGF and HIF-1alpha proteins in sublingual vein were detected by immunohistochemical method. The shape and color of sublingual vein in beagle dogs in the cirrhotic portal hypertension group changed obviously as compared with the normal control group. Immunohistochemical results showed that there were almost no expressions of VEGF and HIF-1alpha proteins in sublingual tissues in the normal control group; however, the expressions of VEGF and HIF-1alpha proteins in sublingual tissues in the cirrhotic portal hypertension group significantly increased. Changes of portal pressure may lead to the formation of the abnormal sublingual vein by increasing the expressions of VEGF and HIF-1alpha proteins in sublingual tissues in Beagle dogs with portal hypertension.

  17. Mobile Portal Implementation Strategy

    DEFF Research Database (Denmark)

    Gao, Ping; Damsgaard, Jan

    2005-01-01

    Mobile portal plays an important role in mobile commerce market. Current literature focuses on static analysis on the value chain of mobile portals. This article provides a dynamic perspective on mobile portal strategy. Drawing upon network economics, we describe mobile portal implementation...... as a fourphase process. In different phase, a portal provider has various challenges to overcome and adopt diverse strategies, and correspondingly the regulator has different foci. The conceptual framework proposed in this article offers a basis for further analyses on the market dynamics of mobile commerce......, and can be generalized to studying other networked technologies...

  18. Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal

    OpenAIRE

    Bordoli, Lorenza; Schwede, Torsten

    2012-01-01

    Comparative protein structure modeling is a computational approach to build three-dimensional structural models for proteins using experimental structures of related protein family members as templates. Regular blind assessments of modeling accuracy have demonstrated that comparative protein structure modeling is currently the most reliable technique to model protein structures. Homology models are often sufficiently accurate to substitute for experimental structures in a wide variety of appl...

  19. Diversity and evolution of coral fluorescent proteins.

    Directory of Open Access Journals (Sweden)

    Naila O Alieva

    2008-07-01

    Full Text Available GFP-like fluorescent proteins (FPs are the key color determinants in reef-building corals (class Anthozoa, order Scleractinia and are of considerable interest as potential genetically encoded fluorescent labels. Here we report 40 additional members of the GFP family from corals. There are three major paralogous lineages of coral FPs. One of them is retained in all sampled coral families and is responsible for the non-fluorescent purple-blue color, while each of the other two evolved a full complement of typical coral fluorescent colors (cyan, green, and red and underwent sorting between coral groups. Among the newly cloned proteins are a "chromo-red" color type from Echinopora forskaliana (family Faviidae and pink chromoprotein from Stylophora pistillata (Pocilloporidae, both evolving independently from the rest of coral chromoproteins. There are several cyan FPs that possess a novel kind of excitation spectrum indicating a neutral chromophore ground state, for which the residue E167 is responsible (numeration according to GFP from A. victoria. The chromoprotein from Acropora millepora is an unusual blue instead of purple, which is due to two mutations: S64C and S183T. We applied a novel probabilistic sampling approach to recreate the common ancestor of all coral FPs as well as the more derived common ancestor of three main fluorescent colors of the Faviina suborder. Both proteins were green such as found elsewhere outside class Anthozoa. Interestingly, a substantial fraction of the all-coral ancestral protein had a chromohore apparently locked in a non-fluorescent neutral state, which may reflect the transitional stage that enabled rapid color diversification early in the history of coral FPs. Our results highlight the extent of convergent or parallel evolution of the color diversity in corals, provide the foundation for experimental studies of evolutionary processes that led to color diversification, and enable a comparative analysis of

  20. Treatment of chronic portal--systemic encephalopathy with vegetable and animal protein diets. A controlled crossover study.

    Science.gov (United States)

    Uribe, M; Márquez, M A; Garcia Ramos, G; Ramos-Uribe, M H; Vargas, F; Villalobos, A; Ramos, C

    1982-12-01

    A controlled crossover clinical comparison of 40-g/day and 80-g/day vegetable protein diets vs a 40-g/day meat protein diet plus neomycin-milk of magnesia (as control therapy) was performed on 10 cirrhotic patients with mild chronic portal-systemic encephalopathy. The 40-g vegetable protein diet had a high fiber volume and contained low methionine and low aromatic amino acids. The 80-g vegetable protein diet was rich in branched-chain amino acids and fiber, with a similar content of sulfur-containing amino acids as compared to the 40-g meat protein diet. Serial semiquantitative assessments were done, including mental state, asterixis, number connection tests, electroencephalograms and blood ammonia levels. No patient developed deep coma while ingesting either vegetable protein diet or neomycin-milk of magnesia plus 40-g meat protein diet. A significant improvement in the number connection test times was observed during the 40-g vegetable protein diet (P less than 0.05) and during the 80-g vegetable protein diet (P less than 0.05) as compared to their previous 40-g meat protein--neomycin periods. In addition, during the period of 80-g vegetable protein diet, the patients showed a significant improvement in their electroencephalograms (P less than 0.05). The frequency of bowel movements significantly increased (P less than 0.05) during the 80-g vegetable protein diet period. During the 40-g vegetable protein diet, two cirrhotic--diabetic patients experienced hypoglycemia. Three patients complained of the voluminous 80-g vegetable protein diet. Patients with mild portal--systemic encephalopathy may be adequately controlled with vegetable protein diets as a single therapy.

  1. Human extrahepatic portal vein obstruction correlates with decreased factor VII and protein C transcription but increased hepatocyte proliferation.

    Science.gov (United States)

    Chiu, Bill; Melin-Aldana, Hector; Superina, Riccardo A

    2007-10-01

    A 3-year-old girl developed extrahepatic portal vein obstruction (EHPVO) after a liver transplant. She had sequelae of portal hypertension that required another transplantation. The circumstances allowed for comparison of liver-dependent coagulation factor production between the second donor liver and the explanted liver with EHPVO. Liver samples from the explanted first graft and the second transplant were obtained. Fresh tissue was used to perform reverse transcription-polymerase chain reaction with primers against factors V, VII, as well as VIII, protein C, and paraffin-embedded sections for hepatocyte proliferation using Ki-67 antibody as well as for apoptosis using TUNEL assay. The transcription of factor VII and that of protein C were decreased in the explant as compared with the newly transplanted liver (factor VII, 77% of the donor; protein C, 88% of the donor). The transcription of factor V and that of factor VIII were unchanged. The explant had a greater percentage of proliferating hepatocytes than the new organ (0.85% +/- 0.75% vs 0.11% +/- 0.21%). The percentage of apoptotic cells was similar between the 2 livers (0.09% +/- 0.13% vs 0.09% +/- 0.13%). Idiopathic EHPVO is associated with a reduction in liver-dependent coagulation factor transcription and an increase in hepatocyte proliferation. Portal blood flow deprivation alters hepatic homeostasis and initiates mechanisms that attempt to restore liver-dependent coagulation factors.

  2. Portal Hypertension

    Science.gov (United States)

    ... Overview of Gallbladder Cancer Additional Content Medical News Portal Hypertension By Steven K. Herrine, MD, Professor of Medicine, ... Liver Hepatic Encephalopathy Jaundice in Adults Liver Failure Portal Hypertension Portal hypertension is abnormally high blood pressure in ...

  3. Protein landmarks for diversity assessment in wheat genotypes ...

    African Journals Online (AJOL)

    Grain proteins from 20 Indian wheat genotypes were evaluated for diversity assessment based seed storage protein profiling on sodium dodecylsulphate polyacrylamide gel electrophoresis (SDS-PAGE). Genetic diversity was evaluated using Nei's index, Shannon index and Unweighted pair group method with arithmetic ...

  4. Effect of antithrombin, protein C and protein S on portal vein thrombosis in liver cirrhosis: a meta-analysis.

    Science.gov (United States)

    Qi, Xingshun; Chen, Hui; Han, Guohong

    2013-07-01

    The effects of antithrombin (AT), protein C (PC) and protein S (PS) on the pathogenesis of portal vein thrombosis (PVT) in liver cirrhosis remain controversial in different studies. In this study, a systematic review and meta-analysis to examine this issue were performed. PubMed database was employed to identify all studies in which AT, PC and PS concentrations were measured in both cirrhotic patients with and without PVT. A standardized mean difference (SMD) with 95% confidence interval (CI) was calculated to evaluate the effect of AT, PC and PS on PVT. Data were pooled using both fixed-effect and random-effect models. Only the pooled data using random-effect model were considered appropriate, when significant heterogeneity was observed. Nine studies involving 160 cirrhotic patients with PVT and 428 cirrhotic patients without PVT were eligible. AT and PC concentrations were similar between PVT and non-PVT groups (AT: SMD = -0.21, 95% CI = -0.56 to 0.14, P = 0.24; PC: SMD = -0.23, 95% CI = -0.55 to 0.09, P = 0.16). But PS concentration was significantly lower in the PVT group than in the non-PVT group (SMD = -0.29, 95% CI = -0.49 to -0.08, P = 0.006). Subgroup analyses were further conducted in 4 studies in which baseline liver function was similar between cirrhotic patients with and without PVT, showing similar AT, PC and PS concentrations between the 2 groups (AT: SMD = -0.10, 95% CI = -0.36 to 0.16, P = 0.57; PC: SMD = -0.18, 95% CI = -0.62 to 0.25, P = 0.41; PS: SMD = -0.10, 95% CI = -0.59 to 0.39, P = 0.69). AT, PC and PS concentrations might not be associated with the pathogenesis of PVT in liver cirrhosis, especially when the impact of liver function was excluded.

  5. Diverse role of CBL-interacting protein kinases in plant

    Indian Academy of Sciences (India)

    admin

    Diverse role of CBL-interacting protein kinases in plant. Most of the extracellular and ... to their role in stress signalling. Their role in transport of plant hormone auxin and mechanism of action in stress response shed new light on diverse role of.

  6. Diversity in protein glycosylation among insect species.

    Directory of Open Access Journals (Sweden)

    Gianni Vandenborre

    Full Text Available BACKGROUND: A very common protein modification in multicellular organisms is protein glycosylation or the addition of carbohydrate structures to the peptide backbone. Although the Class of the Insecta is the largest animal taxon on Earth, almost all information concerning glycosylation in insects is derived from studies with only one species, namely the fruit fly Drosophila melanogaster. METHODOLOGY/PRINCIPAL FINDINGS: In this report, the differences in glycoproteomes between insects belonging to several economically important insect orders were studied. Using GNA (Galanthus nivalis agglutinin affinity chromatography, different sets of glycoproteins with mannosyl-containing glycan structures were purified from the flour beetle (Tribolium castaneum, the silkworm (Bombyx mori, the honeybee (Apis mellifera, the fruit fly (D. melanogaster and the pea aphid (Acyrthosiphon pisum. To identify and characterize the purified glycoproteins, LC-MS/MS analysis was performed. For all insect species, it was demonstrated that glycoproteins were related to a broad range of biological processes and molecular functions. Moreover, the majority of glycoproteins retained on the GNA column were unique to one particular insect species and only a few glycoproteins were present in the five different glycoprotein sets. Furthermore, these data support the hypothesis that insect glycoproteins can be decorated with mannosylated O-glycans. CONCLUSIONS/SIGNIFICANCE: The results presented here demonstrate that oligomannose N-glycosylation events are highly specific depending on the insect species. In addition, we also demonstrated that protein O-mannosylation in insect species may occur more frequently than currently believed.

  7. Trombosis portal y mesentérica asociada al déficit de la proteína S Portal and mesenteric thrombosis associated with protein S deficiency

    Directory of Open Access Journals (Sweden)

    J. A. Chirinos Vega

    2008-02-01

    Full Text Available Introducción: la causa más frecuente de trombosis portal (TP es la cirrosis hepática, mientras que los estados hipercoagulables son raramente identificados como etiología de la TP. Presentamos un caso de TP y mesentérica secundaria al déficit de la proteína S (pS. Caso clínico: paciente mujer de 74 años, que debuta con dolor abdominal difuso de 2 semanas de evolución y hemorragia digestiva alta tipo melena secundaria a varices esofágicas. En el estudio se objetiva un hígado heterogéneo, esplenomegalia y ascitis, así como una trombosis portal completa no oclusiva del hilio hepático y de sus ramas y de la vena mesentérica superior con circulación colateral. El estudio etiológico de hepatopatía fue negativo, incluyendo una biopsia hepática que mostraba cambios arquitecturales secundarios al flujo hemático disminuido compatible con hipertensión portal no cirrótica. El estudio de hipercoagulabilidad fue positivo para un déficit de proteína S. pS libre 56%, pS total 107%. Desde entonces se inició tratamiento anticoagulante sin presentar descompensaciones posteriores. Discusión: la trombosis portal suele manifestarse con síntomas inespecíficos, siendo la forma de presentación más frecuente la hemorragia digestiva alta como el caso que nos ocupa. La cirrosis es una de las causas más frecuentes de trombosis portal, sin embargo existe hasta un 65% de estos pacientes que tienen una enfermedad protrombótica asociada, como es el déficit de proteína S. Nuestro caso remarca la importancia de realizar estudios de factores trombogénicos en pacientes con TP, incluso cuando la etiología se puede atribuir a una cirrosis.Introduction: liver cirrhosis is the main cause of portal thrombosis (PT, while hypercoagulability syndromes are rarely found as the etiology of PT. We report a case of portal and mesenteric thrombosis secondary to protein S deficiency. Case report: a 74-year-old woman was admitted with melena secondary to upper

  8. Detection of a Bacteriophage Gene Encoding a Mu-like Portal Protein in Haemophilus parasuis Reference Strains and Field Isolates by Nested Polymerase Chain Reaction

    Science.gov (United States)

    A nested PCR assay was developed to determine the presence of a gene encoding a bacteriophage Mu-like portal protein, gp29, in 15 reference strains and 31 field isolates of Haemophilus parasuis. Specific primers, based on the gene’s sequence, were utilized. A majority of the virulent reference strai...

  9. Expression of vasoactive proteins in gastric antral mucosa reflects vascular dysfunction in patients with cirrhosis and portal hypertension.

    Science.gov (United States)

    Trebicka, Jonel; Wix, Cyrus; von Heydebrand, Matthias; Hittatiya, Kanishka; Reiberger, Thomas; Klein, Sabine; Schierwagen, Robert; Kristiansen, Glen; Peck-Radosavljevic, Markus; Fischer, Hans-Peter; Møller, Søren; Bendtsen, Flemming; Krag, Aleksander; Sauerbruch, Tilman

    2015-04-01

    Patients with cirrhosis display hypocontractility of splanchnic vessels because of dysregulation of vasoactive proteins, such as decreased effect of RhoA/ROCK and increased activity of β-Arrestin-2 and eNOS. However, it is unknown whether the dysregulation of vasoactive proteins is displayed in other vessels. We investigated whether expression of vasoactive proteins can be evaluated in gastric mucosa vessels. Biopsies from the gastric mucosa of 111 patients with cirrhosis were collected at three different centres and from 13 controls. Forty-nine patients had received TIPS. Portal pressure gradient was measured in 49 patients with TIPS and in 16 patients without TIPS. Biopsies from the antrum were conserved in formaldehyde for immunohistochemistry or shock-frozen for PCR and Western blot. The mucosal transcription of vascular markers (αSMA, CD31) was higher in cirrhotic patients than controls, which was confirmed by immunohistochemistry. On average, relative mucosal levels of RhoA and ROCK were lower, while β-Arrestin-2 levels were higher in cirrhotic patients compared to controls. Transcriptional levels of eNOS increased with presence of ascites and grade of oesophageal varices. Patients with TIPS showed less pronounced markers of vascular dysfunction in gastric mucosa. This is the first evidence that the expression of vasoactive proteins in mucosa from the gastric antrum of patients with cirrhosis reflects their vascular dysfunction and possibly changes after therapeutic interventions. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  10. A new model for portal protein profile analysis in course of ileal intraluminal bile acid infusion using an in situ perfused rat intestine.

    Science.gov (United States)

    Montagnani, Marco; Tsivian, Matvey; Neri, Flavia; Zvi, Ido Ben; Mantovani, Irina; Nanni, Paolo; Benevento, Marco; Simoni, Patrizia; Marangoni, Antonella; Pariali, Milena; Fato, Romana; Bergamini, Christian; Leoni, Serena; Azzaroli, Francesco; Mazzella, Giuseppe; Nardo, Bruno; Roda, Enrico; Aldini, Rita

    2011-07-01

    Due to the importance of intestinal transport in pharmacological studies and the emerging role of intestinal signaling activity in the gut-liver axis, we have developed a new method to investigate intestinal transport and liver signaling using cell and serum free mesenteric perfusion system in the rat. The method regarding bile acid active absorption was validated, then, the portal venous content was examined for fibroblast growth factor 15(FGF15), a putative signaling protein produced by the ileal enterocytes following bile acid absorption. After isolation and cannulation of the relevant vessels (abdominal aorta and portal vein), the abdominal aorta and the terminal ileum were infused with respectively Krebs-Ringer solution and tauroursodeoxycholate (TUDCA) and the absorption was assessed by its recovery in the portal vein. After immunoblot, liquid chromatography and mass spectrometry analysis were performed both on gel bands digestion products and on portal outflow samples in order to evaluate if negligible amounts of FGF15 were present in the portal circulation. TUDCA absorption was efficient, intestinal morphology and oxygen consumption were normal. Despite accurate analysis, we could not find FGF15. Our method proved to be reliable for studying the active bile acid absorption. It is also suitable to identify molecules produced by enterocytes and transferred to the portal circulation in response to absorption of different substances such as nutrients or drugs. Since FGF15 was not recovered we suggest the possibilities that this protein is produced in very little amounts, poorly transferred outside the cell, or that it is extremely unstable and rapidly degraded.

  11. The Phyre2 web portal for protein modeling, prediction and analysis.

    Science.gov (United States)

    Kelley, Lawrence A; Mezulis, Stefans; Yates, Christopher M; Wass, Mark N; Sternberg, Michael J E

    2015-06-01

    Phyre2 is a suite of tools available on the web to predict and analyze protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a paper in Nature Protocols. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants (e.g., nonsynonymous SNPs (nsSNPs)) for a user's protein sequence. Users are guided through results by a simple interface at a level of detail they determine. This protocol will guide users from submitting a protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for proteins that are difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2. A typical structure prediction will be returned between 30 min and 2 h after submission.

  12. Protein chimerism: novel source of protein diversity in humans adds complexity to bottom-up proteomics.

    Science.gov (United States)

    Casado-Vela, Juan; Lacal, Juan Carlos; Elortza, Felix

    2013-01-01

    Three main molecular mechanisms are considered to contribute expanding the repertoire and diversity of proteins present in living organisms: first, at DNA level (gene polymorphisms and single nucleotide polymorphisms); second, at messenger RNA (pre-mRNA and mRNA) level including alternative splicing (also termed differential splicing or cis-splicing); finally, at the protein level mainly driven through PTM and specific proteolytic cleavages. Chimeric mRNAs constitute an alternative source of protein diversity, which can be generated either by chromosomal translocations or by trans-splicing events. The occurrence of chimeric mRNAs and proteins is a frequent event in cells from the immune system and cancer cells, mainly as a consequence of gene rearrangements. Recent reports support that chimeric proteins may also be expressed at low levels under normal physiological circumstances, thus, representing a novel source of protein diversity. Notably, recent publications demonstrate that chimeric protein products can be successfully identified through bottom-up proteomic analyses. Several questions remain unsolved, such as the physiological role and impact of such chimeric proteins or the potential occurrence of chimeric proteins in higher eukaryotic organisms different from humans. The occurrence of chimeric proteins certainly seems to be another unforeseen source of complexity for the proteome. It may be a process to take in mind not only when performing bottom-up proteomic analyses in cancer studies but also in general bottom-up proteomics experiments. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. GEO portal

    Data.gov (United States)

    US Agency for International Development — The USAID GeoPortal is a new application that groups web-based capabilities for on-demand discovery of and access to geospatial content, services, expertise, and...

  14. Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data

    Science.gov (United States)

    Koleti, Amar; Terryn, Raymond; Stathias, Vasileios; Chung, Caty; Cooper, Daniel J; Turner, John P; Vidović, Dušica; Forlin, Michele; Kelley, Tanya T; D’Urso, Alessandro; Allen, Bryce K; Torre, Denis; Jagodnik, Kathleen M; Wang, Lily; Jenkins, Sherry L; Mader, Christopher; Niu, Wen; Fazel, Mehdi; Mahi, Naim; Pilarczyk, Marcin; Clark, Nicholas; Shamsaei, Behrouz; Meller, Jarek; Vasiliauskas, Juozas; Reichard, John; Medvedovic, Mario; Ma’ayan, Avi; Pillai, Ajay

    2018-01-01

    Abstract The Library of Integrated Network-based Cellular Signatures (LINCS) program is a national consortium funded by the NIH to generate a diverse and extensive reference library of cell-based perturbation-response signatures, along with novel data analytics tools to improve our understanding of human diseases at the systems level. In contrast to other large-scale data generation efforts, LINCS Data and Signature Generation Centers (DSGCs) employ a wide range of assay technologies cataloging diverse cellular responses. Integration of, and unified access to LINCS data has therefore been particularly challenging. The Big Data to Knowledge (BD2K) LINCS Data Coordination and Integration Center (DCIC) has developed data standards specifications, data processing pipelines, and a suite of end-user software tools to integrate and annotate LINCS-generated data, to make LINCS signatures searchable and usable for different types of users. Here, we describe the LINCS Data Portal (LDP) (http://lincsportal.ccs.miami.edu/), a unified web interface to access datasets generated by the LINCS DSGCs, and its underlying database, LINCS Data Registry (LDR). LINCS data served on the LDP contains extensive metadata and curated annotations. We highlight the features of the LDP user interface that is designed to enable search, browsing, exploration, download and analysis of LINCS data and related curated content. PMID:29140462

  15. Diversity and functions of protein glycosylation in insects.

    Science.gov (United States)

    Walski, Tomasz; De Schutter, Kristof; Van Damme, Els J M; Smagghe, Guy

    2017-04-01

    The majority of proteins is modified with carbohydrate structures. This modification, called glycosylation, was shown to be crucial for protein folding, stability and subcellular location, as well as protein-protein interactions, recognition and signaling. Protein glycosylation is involved in multiple physiological processes, including embryonic development, growth, circadian rhythms, cell attachment as well as maintenance of organ structure, immunity and fertility. Although the general principles of glycosylation are similar among eukaryotic organisms, insects synthesize a distinct repertoire of glycan structures compared to plants and vertebrates. Consequently, a number of unique insect glycans mediate functions specific to this class of invertebrates. For instance, the core α1,3-fucosylation of N-glycans is absent in vertebrates, while in insects this modification is crucial for the development of wings and the nervous system. At present, most of the data on insect glycobiology comes from research in Drosophila. Yet, progressively more information on the glycan structures and the importance of glycosylation in other insects like beetles, caterpillars, aphids and bees is becoming available. This review gives a summary of the current knowledge and recent progress related to glycan diversity and function(s) of protein glycosylation in insects. We focus on N- and O-glycosylation, their synthesis, physiological role(s), as well as the molecular and biochemical basis of these processes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. ASH External Web Portal (External Portal) -

    Data.gov (United States)

    Department of Transportation — The ASH External Web Portal is a web-based portal that provides single sign-on functionality, making the web portal a single location from which to be authenticated...

  17. Portal Vein Thrombosis

    Directory of Open Access Journals (Sweden)

    Hakan Demirci

    2016-01-01

    Full Text Available Portal vein thrombosis is an important cause of presinusoidal portal hypertension. Portal vein thrombosis commonly occurs in patient with cirrhosis, malignancy and prothrombotic states. Patients with acute portal vein thrombosis have immediate onset. Patients with chronic portal vein thrombosis have developed portal hypertension and cavernous portal transformation. Portal vein thrombosis is diagnosed with doppler ultrasound, computed tomography and magnetic resonance imaging. Therapy with low molecular weight heparin achieves recanalization in more than half of acute cases.

  18. Diabetes diminishes the portal-systemic collateral vascular response to vasopressin via vasopressin receptor and Gα proteins regulations in cirrhotic rats.

    Directory of Open Access Journals (Sweden)

    Jing-Yi Lee

    Full Text Available Liver cirrhosis may lead to portal-systemic collateral formation and bleeding. The hemostatic effect is influenced by the response of collateral vessels to vasoconstrictors. Diabetes and glucose also influence vasoresponsiveness, but their net effect on collaterals remains unexplored. This study investigated the impact of diabetes or glucose application on portal-systemic collateral vasoresponsiveness to arginine vasopressin (AVP in cirrhosis. Spraque-Dawley rats with bile duct ligation (BDL-induced cirrhosis received vehicle (citrate buffer or streptozotocin (diabetic, BDL/STZ. The in situ collateral perfusion was done after hemodynamic measurements: Both were perfused with Krebs solution, D-glucose, or D-glucose and NaF, with additional OPC-31260 for the BDL/STZ group. Splenorenal shunt vasopressin receptors and Gα proteins mRNA expressions were evaluated. The survival rate of cirrhotic rats was decreased by STZ injection. The collateral perfusion pressure changes to AVP were lower in STZ-injected groups, which were reversed by OPC-31260 (a V2R antagonist and overcome by NaF (a G protein activator. The splenorenal shunt V2R mRNA expression was increased while Gα proteins mRNA expressions were decreased in BDL/STZ rats compared to BDL rats. The Gαq and Gα11 mRNA expressions also correlated with the maximal perfusion pressure changes to AVP. Diabetes diminished the portal-systemic collateral vascular response to AVP in rats with BDL-induced cirrhosis, probably via V2 receptor up-regulation and Gα proteins down-regulation.

  19. Portal manga

    OpenAIRE

    Temprano Hernandez, Joan

    2011-01-01

    El projecte Portal Manga pretén construir una aplicació web que ha de permetre a una empresa anunciar els seus productes a la web, disposar de una botiga virtual en la que es puguin adquirir aquests productes en format digital i finalment un lector web que en permeti la lectura online.

  20. Expression of vasoactive proteins in gastric antral mucosa reflects vascular dysfunction in patients with cirrhosis and portal hypertension

    DEFF Research Database (Denmark)

    Trebicka, Jonel; Wix, Cyrus; von Heydebrand, Matthias

    2015-01-01

    . Portal pressure gradient was measured in 49 patients with TIPS and in 16 patients without TIPS. Biopsies from the antrum were conserved in formaldehyde for immunohistochemistry or shock-frozen for PCR and Western blot. RESULTS: The mucosal transcription of vascular markers (αSMA, CD31) was higher...

  1. Electronic portal imaging devices

    International Nuclear Information System (INIS)

    Lief, Eugene

    2008-01-01

    The topics discussed include, among others, the following: Role of portal imaging; Port films vs. EPID; Image guidance: Elekta volume view; Delivery verification; Automation tasks of portal imaging; Types of portal imaging (Fluorescent screen, mirror, and CCD camera-based imaging; Liquid ion chamber imaging; Amorpho-silicon portal imagers; Fluoroscopic portal imaging; Kodak CR reader; and Other types of portal imaging devices); QA of EPID; and Portal dosimetry (P.A.)

  2. Diversity of T cell epitopes in Plasmodium falciparum circumsporozoite protein likely due to protein-protein interactions.

    Directory of Open Access Journals (Sweden)

    Nagesh R Aragam

    Full Text Available Circumsporozoite protein (CS is a leading vaccine antigen for falciparum malaria, but is highly polymorphic in natural parasite populations. The factors driving this diversity are unclear, but non-random assortment of the T cell epitopes TH2 and TH3 has been observed in a Kenyan parasite population. The recent publication of the crystal structure of the variable C terminal region of the protein allows the assessment of the impact of diversity on protein structure and T cell epitope assortment. Using data from the Gambia (55 isolates and Malawi (235 isolates, we evaluated the patterns of diversity within and between epitopes in these two distantly-separated populations. Only non-synonymous mutations were observed with the vast majority in both populations at similar frequencies suggesting strong selection on this region. A non-random pattern of T cell epitope assortment was seen in Malawi and in the Gambia, but structural analysis indicates no intramolecular spatial interactions. Using the information from these parasite populations, structural analysis reveals that polymorphic amino acids within TH2 and TH3 colocalize to one side of the protein, surround, but do not involve, the hydrophobic pocket in CS, and predominately involve charge switches. In addition, free energy analysis suggests residues forming and behind the novel pocket within CS are tightly constrained and well conserved in all alleles. In addition, free energy analysis shows polymorphic residues tend to be populated by energetically unfavorable amino acids. In combination, these findings suggest the diversity of T cell epitopes in CS may be primarily an evolutionary response to intermolecular interactions at the surface of the protein potentially counteracting antibody-mediated immune recognition or evolving host receptor diversity.

  3. Exploring the diversity of protein modifications: special bacterial phosphorylation systems

    DEFF Research Database (Denmark)

    Mijakovic, Ivan; Grangeasse, Christophe; Turgay, Kürşad

    2016-01-01

    Protein modifications not only affect protein homeostasis but can also establish new cellular protein functions and are important components of complex cellular signal sensing and transduction networks. Among these post-translational modifications, protein phosphorylation represents the one that ...

  4. Protein landmarks for diversity assessment in wheat genotypes

    African Journals Online (AJOL)

    jai ganesha

    2013-07-17

    Jul 17, 2013 ... of genetic diversity in wheat has been on differences in morphological and ... glutenins, are the main components of gluten, which is the main contributor to the .... However, there was no within variety diversity observed as a ...

  5. Diversity and evolution of ABC proteins in basidiomycetes.

    Science.gov (United States)

    Kovalchuk, Andriy; Lee, Yong-Hwan; Asiegbu, Fred O

    2013-01-01

    ABC proteins constitute one of the largest families of proteins. They are implicated in wide variety of cellular processes ranging from ribosome biogenesis to multidrug resistance. With the advance of fungal genomics, the number of known fungal ABC proteins increases rapidly but the information on their biological functions remains scarce. In this work we extended the previous analysis of fungal ABC proteins to include recently sequenced species of basidiomycetes. We performed an identification and initial cataloging of ABC proteins from 23 fungal species representing 10 orders within class Agaricomycotina. We identified more than 1000 genes coding for ABC proteins. Comparison of sets of ABC proteins present in basidiomycetes and ascomycetes revealed the existence of two groups of ABC proteins specific for basidiomycetes. Results of survey should contribute to the better understanding of evolution of ABC proteins in fungi and support further experimental work on their characterization.

  6. Noncirrotisk intrahepatisk portal hypertension

    DEFF Research Database (Denmark)

    Dam Fialla, Annette; Havelund, Troels

    2007-01-01

    Non-cirrhotic intrahepatic portal hypertension is characterized by portal hypertension in the absence of liver cirrhosis or portal vein thrombosis. The disease is common in the East and rarely seen in the West. Two cases with oesophageal varices are described. The histopathology is heterogeneous...... but includes vascular lesions and portal fibrosis. Patient management follows the current recommendations for variceal bleeding....

  7. Diversity, classification and function of the plant protein kinase superfamily

    OpenAIRE

    Lehti-Shiu, Melissa D.; Shiu, Shin-Han

    2012-01-01

    Eukaryotic protein kinases belong to a large superfamily with hundreds to thousands of copies and are components of essentially all cellular functions. The goals of this study are to classify protein kinases from 25 plant species and to assess their evolutionary history in conjunction with consideration of their molecular functions. The protein kinase superfamily has expanded in the flowering plant lineage, in part through recent duplications. As a result, the flowering plant protein kinase r...

  8. Diversity and subcellular distribution of archaeal secreted proteins.

    Science.gov (United States)

    Szabo, Zalan; Pohlschroder, Mechthild

    2012-01-01

    Secreted proteins make up a significant percentage of a prokaryotic proteome and play critical roles in important cellular processes such as polymer degradation, nutrient uptake, signal transduction, cell wall biosynthesis, and motility. The majority of archaeal proteins are believed to be secreted either in an unfolded conformation via the universally conserved Sec pathway or in a folded conformation via the Twin arginine transport (Tat) pathway. Extensive in vivo and in silico analyses of N-terminal signal peptides that target proteins to these pathways have led to the development of computational tools that not only predict Sec and Tat substrates with high accuracy but also provide information about signal peptide processing and targeting. Predictions therefore include indications as to whether a substrate is a soluble secreted protein, a membrane or cell wall anchored protein, or a surface structure subunit, and whether it is targeted for post-translational modification such as glycosylation or the addition of a lipid. The use of these in silico tools, in combination with biochemical and genetic analyses of transport pathways and their substrates, has resulted in improved predictions of the subcellular localization of archaeal secreted proteins, allowing for a more accurate annotation of archaeal proteomes, and has led to the identification of potential adaptations to extreme environments, as well as phyla-specific pathways among the archaea. A more comprehensive understanding of the transport pathways used and post-translational modifications of secreted archaeal proteins will also facilitate the identification and heterologous expression of commercially valuable archaeal enzymes.

  9. Role of microProteins in controlling diverse biological pathways

    DEFF Research Database (Denmark)

    Dolde, Ulla Margrit

    MicroProteins are small, single-domain proteins that dimerize with larger multi-domain proteins and prevent them from forming functional complexes. To date, 22 microProteins have been identified in plants that regulate their target by sequestering them into non-productive protein complexes. The two......Proteins that regulate their target by forming a higher order protein complex. They form an at least trimeric complex with CO and the transcriptional repressor TOPLESS (TPL). Ectopic expression of miP1a or miP1b in plants causes a late flowering phenotype, due to the failure in COdependent activation of FLOWERING LOCUS...... T (FT) expression. In agreement with the late flowering of overexpression plants, loss-of-function mutants of both miP1a and miP1b, generated using CRISPR/Cas9 genome engineering, showed also a slightly early flowering phenotype. In a forward genetic screen using transgenic plants overexpressing mi...

  10. Idiopathic portal hypertension

    International Nuclear Information System (INIS)

    Han, Tae Kyun; Ryu, Dae Sik; Kim, Heung Chul; Hur, Hun; Eom, Kyeung Tae; Namkung, Sook; Park, Man Soo; Hwang, Woo Chul; Lee, Kwan Seop

    1996-01-01

    To describe the radiologic findings of idiopathic portal hypertension and to find the points of differentiation between idiopathic portal hypertension and liver cirrhosis. Four portograms in five patients who for four years had suffered from pathologically confirmed idiopathic portal hypertension were retrospectively analyzed and compared with a portogram obtained from a control subject with liver cirrhosis. Portographic finding s of idiopathic portal hypertension were paucity of medium-sized portal branches, irregular and obtuse-angled division of peripheral branches, abrupt interruption and an avascular area beneath the liver margin. A portogram of idiopathic portal hypertension may be useful in differentiation this and liver cirrhosis

  11. Rare Disease Video Portal

    OpenAIRE

    Sánchez Bocanegra, Carlos Luis

    2011-01-01

    Rare Disease Video Portal (RD Video) is a portal web where contains videos from Youtube including all details from 12 channels of Youtube. Rare Disease Video Portal (RD Video) es un portal web que contiene los vídeos de Youtube incluyendo todos los detalles de 12 canales de Youtube. Rare Disease Video Portal (RD Video) és un portal web que conté els vídeos de Youtube i que inclou tots els detalls de 12 Canals de Youtube.

  12. Using Gel Electrophoresis To Illustrate Protein Diversity and Isoelectric Point.

    Science.gov (United States)

    Browning, Mark; Vanable, Joseph

    2002-01-01

    Demonstrates the differences in protein structures by focusing on isoelectric point with an experiment that is observable under certain pH levels in gel electrophoresis. Explains the electrophoresis procedure and reports results of the experiments. (YDS)

  13. Diversity and subcellular distribution of archaeal secreted proteins

    Directory of Open Access Journals (Sweden)

    Mechthild ePohlschroder

    2012-07-01

    Full Text Available Secreted proteins make up a significant percentage of a prokaryotic proteome and play critical roles in important cellular processes such as polymer degradation, nutrient uptake, signal transduction, cell wall biosynthesis and motility. The majority of archaeal proteins are believed to be secreted either in an unfolded conformation via the universally conserved Sec pathway or in a folded conformation via the Twin arginine transport (Tat pathway. Extensive in vivo and in silico analyses of N-terminal signal peptides that target proteins to these pathways have led to the development of computational tools that not only predict Sec and Tat substrates with high accuracy but also provide information about signal peptide processing and targeting. Predictions therefore include indications as to whether a substrate is a soluble secreted protein, a membrane or cell-wall anchored protein, or a surface structure subunit, and whether it is targeted for post-translational modification such as glycosylation or the addition of a lipid. The use of these in silico tools, in combination with biochemical and genetic analyses of transport pathways and their substrates, has resulted in improved predictions of the subcellular localization of archaeal secreted proteins, allowing for a more accurate annotation of archaeal proteomes, and has led to the identification of potential adaptations to extreme environments, as well as archaeal kingdom-specific pathways. A more comprehensive understanding of the transport pathways and post-translational modifications of secreted archaeal proteins will also generate invaluable insights that will facilitate the identification of commercially valuable archaeal enzymes and the development of heterologous systems in which to efficiently express them.

  14. The Knowledge Portal

    Data.gov (United States)

    Office of Personnel Management — Information on various courses, as well as personal data of employees and training records from The Knowledge Portal (TKP), a web-based training portal used for the...

  15. Structure, diversity and evolution of protein toxins from spore-forming entomopathogenic bacteria

    NARCIS (Netherlands)

    Maagd, de R.A.; Bravo, A.; Berry, C.; Crickmore, N.; Schnepf, H.E.

    2003-01-01

    Gram-positive spore-forming entomopathogenic bacteria can utilize a large variety of protein toxins to help them invade, infect, and finally kill their hosts, through their action on the insect midgut. These toxins belong to a number of homology groups containing a diversity of protein structures

  16. Diversity

    Science.gov (United States)

    Portraits In Courage Vol. VIII Portraits In Courage Vol. IX Portraits In Courage Vol. X AF Sites Social -Wide Initiative to Promote Diversity and Inclusion in the Federal Workforce Executive Order 13548 : Virtual Diversity Conference Air Force Diversity & Inclusion Air Force Diversity Graphic There is no

  17. Molecular and clinical diversity in paraneoplastic immunity to Ma proteins.

    Science.gov (United States)

    Rosenfeld, M R; Eichen, J G; Wade, D F; Posner, J B; Dalmau, J

    2001-09-01

    Antibodies to Ma1 and Ma2 proteins identify a paraneoplastic disorder that affects the limbic system, brain stem, and cerebellum. Preliminary studies suggested the existence of other Ma proteins and different patterns of immune response associated with distinct neurologic symptoms and cancers. In this study, our aim was to isolate the full-length sequence of Ma2 and new family members, identify the major autoantigen of the disorder, and extend the dinical-immunological analysis to 29 patients. Sera from selected patients were used to probe a brainstem cDNA library and isolate the entire Ma2 gene and a new family member, Ma3. Ma3 mRNA is ubiquitously expressed in brain, testis, and several systemic tissues. The variable cellular expression of Ma proteins and analysis of protein motifs suggest that these proteins play roles in the biogenesis of mRNA. Immunoblot studies identify Ma2 as the major autoantigen with unique epitopes recognized by all patients' sera. Eighteen patients had antibodies limited to Ma2: they developed limbic, hypothalamic, and brainstem encephalitis, and 78% had germ-cell tumors of the testis. Eleven patients had antibodies to Ma2 and additional antibodies to Ma1 and/or Ma3; they usually developed additional cerebellar symptoms and more intense brainstem dysfunction, and 82% of these patients had tumors other than germ-cell neoplasms. Overall, 17 of 24 patients (71%) with brain magnetic resonance imaging studies had abnormalities within or outside the temporal lobes, some as contrast-enhancing nodular lesions. A remarkable finding of immunity to Ma proteins is that neurologic symptoms may improve or resolve. This improvement segregated to a group of patients with antibodies limited to Ma2.

  18. Customizable scientific web portal for fusion research

    International Nuclear Information System (INIS)

    Abla, G.; Kim, E.N.; Schissel, D.P.; Flanagan, S.M.

    2010-01-01

    Web browsers have become a major application interface for participating in scientific experiments such as those in magnetic fusion. The recent advances in web technologies motivated the deployment of interactive web applications with rich features. In the scientific world, web applications have been deployed in portal environments. When used in a scientific research environment, such as fusion experiments, web portals can present diverse sources of information in a unified interface. However, the design and development of a scientific web portal has its own challenges. One such challenge is that a web portal needs to be fast and interactive despite the high volume of information and number of tools it presents. Another challenge is that the visual output of the web portal must not be overwhelming to the end users, despite the high volume of data generated by fusion experiments. Therefore, the applications and information should be customizable depending on the needs of end users. In order to meet these challenges, the design and implementation of a web portal needs to support high interactivity and user customization. A web portal has been designed to support the experimental activities of DIII-D researchers worldwide by providing multiple services, such as real-time experiment status monitoring, diagnostic data access and interactive data visualization. The web portal also supports interactive collaborations by providing a collaborative logbook, shared visualization and online instant messaging services. The portal's design utilizes the multi-tier software architecture and has been implemented utilizing web 2.0 technologies, such as AJAX, Django, and Memcached, to develop a highly interactive and customizable user interface. It offers a customizable interface with personalized page layouts and list of services, which allows users to create a unique, personalized working environment to fit their own needs and interests. This paper describes the software

  19. Customizable scientific web portal for fusion research

    Energy Technology Data Exchange (ETDEWEB)

    Abla, G., E-mail: abla@fusion.gat.co [General Atomics, P.O. Box 85608, San Diego, CA (United States); Kim, E.N.; Schissel, D.P.; Flanagan, S.M. [General Atomics, P.O. Box 85608, San Diego, CA (United States)

    2010-07-15

    Web browsers have become a major application interface for participating in scientific experiments such as those in magnetic fusion. The recent advances in web technologies motivated the deployment of interactive web applications with rich features. In the scientific world, web applications have been deployed in portal environments. When used in a scientific research environment, such as fusion experiments, web portals can present diverse sources of information in a unified interface. However, the design and development of a scientific web portal has its own challenges. One such challenge is that a web portal needs to be fast and interactive despite the high volume of information and number of tools it presents. Another challenge is that the visual output of the web portal must not be overwhelming to the end users, despite the high volume of data generated by fusion experiments. Therefore, the applications and information should be customizable depending on the needs of end users. In order to meet these challenges, the design and implementation of a web portal needs to support high interactivity and user customization. A web portal has been designed to support the experimental activities of DIII-D researchers worldwide by providing multiple services, such as real-time experiment status monitoring, diagnostic data access and interactive data visualization. The web portal also supports interactive collaborations by providing a collaborative logbook, shared visualization and online instant messaging services. The portal's design utilizes the multi-tier software architecture and has been implemented utilizing web 2.0 technologies, such as AJAX, Django, and Memcached, to develop a highly interactive and customizable user interface. It offers a customizable interface with personalized page layouts and list of services, which allows users to create a unique, personalized working environment to fit their own needs and interests. This paper describes the software

  20. Customizable Scientific Web Portal for Fusion Research

    Energy Technology Data Exchange (ETDEWEB)

    Abla, G; Kim, E; Schissel, D; Flannagan, S [General Atomics, San Diego (United States)

    2009-07-01

    The Web browser has become one of the major application interfaces for remotely participating in magnetic fusion experiments. Recently in other areas, web portals have begun to be deployed. These portals are used to present very diverse sources of information in a unified way. While a web portal has several benefits over other software interfaces, such as providing single point of access for multiple computational services, and eliminating the need for client software installation, the design and development of a web portal has unique challenges. One of the challenges is that a web portal needs to be fast and interactive despite a high volume of tools and information that it presents. Another challenge is the visual output on the web portal often is overwhelming due to the high volume of data generated by complex scientific instruments and experiments; therefore the applications and information should be customizable depending on the needs of users. An appropriate software architecture and web technologies can meet these problems. A web-portal has been designed to support the experimental activities of DIII-D researchers worldwide. It utilizes a multi-tier software architecture, and web 2.0 technologies, such as AJAX, Django, and Memcached, to develop a highly interactive and customizable user interface. It offers a customizable interface with personalized page layouts and list of services for users to select. The users can create a unique personalized working environment to fit their own needs and interests. Customizable services are: real-time experiment status monitoring, diagnostic data access, interactive data visualization. The web-portal also supports interactive collaborations by providing collaborative logbook, shared visualization and online instant message services. Furthermore, the web portal will provide a mechanism to allow users to create their own applications on the web portal as well as bridging capabilities to external applications such as

  1. Customisable Scientific Web Portal for Fusion Research

    Energy Technology Data Exchange (ETDEWEB)

    Abla, G; Kim, E; Schissel, D; Flannagan, S [General Atomics, San Diego (United States)

    2009-07-01

    The Web browser has become one of the major application interfaces for remotely participating in magnetic fusion. Web portals are used to present very diverse sources of information in a unified way. While a web portal has several benefits over other software interfaces, such as providing single point of access for multiple computational services, and eliminating the need for client software installation, the design and development of a web portal has unique challenges. One of the challenges is that a web portal needs to be fast and interactive despite a high volume of tools and information that it presents. Another challenge is the visual output on the web portal often is overwhelming due to the high volume of data generated by complex scientific instruments and experiments; therefore the applications and information should be customizable depending on the needs of users. An appropriate software architecture and web technologies can meet these problems. A web-portal has been designed to support the experimental activities of DIII-D researchers worldwide. It utilizes a multi-tier software architecture, and web 2.0 technologies, such as AJAX, Django, and Memcached, to develop a highly interactive and customizable user interface. It offers a customizable interface with personalized page layouts and list of services for users to select. Customizable services are: real-time experiment status monitoring, diagnostic data access, interactive data visualization. The web-portal also supports interactive collaborations by providing collaborative logbook, shared visualization and online instant message services. Furthermore, the web portal will provide a mechanism to allow users to create their own applications on the web portal as well as bridging capabilities to external applications such as Twitter and other social networks. In this series of slides, we describe the software architecture of this scientific web portal and our experiences in utilizing web 2.0 technologies. A

  2. Protein landmarks for diversity assessment in wheat genotypes

    African Journals Online (AJOL)

    STORAGESEVER

    2009-05-04

    May 4, 2009 ... agronomic performance, biochemical and molecular. (DNA-based) data ... analysis of storage protein variation in wheat has proved to be a useful tool ... concentration: 0.5 M Tris-HCl (pH 6.8), 2.5% SDS, 10 % glycerol and 5% ...

  3. BRICHOS - a superfamily of multidomain proteins with diverse functions

    Directory of Open Access Journals (Sweden)

    Johansson Jan

    2009-09-01

    Full Text Available Abstract Background The BRICHOS domain has been found in 8 protein families with a wide range of functions and a variety of disease associations, such as respiratory distress syndrome, dementia and cancer. The domain itself is thought to have a chaperone function, and indeed three of the families are associated with amyloid formation, but its structure and many of its functional properties are still unknown. Findings The proteins in the BRICHOS superfamily have four regions with distinct properties. We have analysed the BRICHOS proteins focusing on sequence conservation, amino acid residue properties, native disorder and secondary structure predictions. Residue conservation shows large variations between the regions, and the spread of residue conservation between different families can vary greatly within the regions. The secondary structure predictions for the BRICHOS proteins show remarkable coherence even where sequence conservation is low, and there seems to be little native disorder. Conclusions The greatly variant rates of conservation indicates different functional constraints among the regions and among the families. We present three previously unknown BRICHOS families; group A, which may be ancestral to the ITM2 families; group B, which is a close relative to the gastrokine families, and group C, which appears to be a truly novel, disjoint BRICHOS family. The C-terminal region of group C has nearly identical sequences in all species ranging from fish to man and is seemingly unique to this family, indicating critical functional or structural properties.

  4. Bacterial flagellar capping proteins adopt diverse oligomeric states

    Energy Technology Data Exchange (ETDEWEB)

    Postel, Sandra; Deredge, Daniel; Bonsor, Daniel A.; Yu, Xiong; Diederichs, Kay; Helmsing, Saskia; Vromen, Aviv; Friedler, Assaf; Hust, Michael; Egelman, Edward H.; Beckett, Dorothy; Wintrode, Patrick L.; Sundberg, Eric J. (UV); (Braunschweig); (Maryland-MED); (Konstanz); (Maryland); (Hebrew)

    2016-09-24

    Flagella are crucial for bacterial motility and pathogenesis. The flagellar capping protein (FliD) regulates filament assembly by chaperoning and sorting flagellin (FliC) proteins after they traverse the hollow filament and exit the growing flagellum tip. In the absence of FliD, flagella are not formed, resulting in impaired motility and infectivity. Here, we report the 2.2 Å resolution X-ray crystal structure of FliD fromPseudomonas aeruginosa, the first high-resolution structure of any FliD protein from any bacterium. Using this evidence in combination with a multitude of biophysical and functional analyses, we find thatPseudomonasFliD exhibits unexpected structural similarity to other flagellar proteins at the domain level, adopts a unique hexameric oligomeric state, and depends on flexible determinants for oligomerization. Considering that the flagellin filaments on which FliD oligomers are affixed vary in protofilament number between bacteria, our results suggest that FliD oligomer stoichiometries vary across bacteria to complement their filament assemblies.

  5. Usability of Discovery Portals

    NARCIS (Netherlands)

    Bulens, J.D.; Vullings, L.A.E.; Houtkamp, J.M.; Vanmeulebrouk, B.

    2013-01-01

    As INSPIRE progresses to be implemented in the EU, many new discovery portals are built to facilitate finding spatial data. Currently the structure of the discovery portals is determined by the way spatial data experts like to work. However, we argue that the main target group for discovery portals

  6. Portals people, processes, technology

    CERN Document Server

    Cox, Andrew

    2006-01-01

    First applied to internet gateways such as Yahoo, the concept of the ""portal"" has evolved in a number of directions. How can information services best take advantage of internet portals to improve access to resources? This collection seeks answers to such questions, providing an overview of how portals are being used.

  7. The Emerging and Diverse Roles of Src-Like Adaptor Proteins in Health and Disease

    Directory of Open Access Journals (Sweden)

    Nikolett Marton

    2015-01-01

    Full Text Available Although Src-like adaptor proteins (SLAP-1 and SLAP-2 were mainly studied in lymphocytes, where they act as negative regulators and provide fine control of receptor signaling, recently, several other functions of these proteins were discovered. In addition to the well-characterized immunoregulatory functions, SLAP proteins appear to have an essential role in the pathogenesis of type I hypersensitivity, osteoporosis, and numerous malignant diseases. Both adaptor proteins are expressed in a wide variety of tissues, where they have mostly inhibitory effects on multiple intracellular signaling pathways. In this review, we summarize the diverse effects of SLAP proteins.

  8. Portal hypertensiv gastropati

    DEFF Research Database (Denmark)

    Brinch, K; Møller, S; Henriksen, Jens Henrik Sahl

    1995-01-01

    Portal hypertensive gastropathy (PHG) as defined by congestive changes in the gastric mucosa owing to increased portal pressure, was first described about ten years ago. Whereas definition and grading of severity are still under debate, there is general agreement that PHG is a new clinical entity....... PHG is present in 50-80% of patients with liver cirrhosis. PHG is a major cause of upper gastrointestinal bleeding in patients with portal hypertension (25-90% depending on severity). Presence of portal hypertension is a prerequisite for the development of PHG, and reduction of portal pressure...

  9. PDZ-containing proteins: alternative splicing as a source of functional diversity.

    Science.gov (United States)

    Sierralta, Jimena; Mendoza, Carolina

    2004-12-01

    Scaffold proteins allow specific protein complexes to be assembled in particular regions of the cell at which they organize subcellular structures and signal transduction complexes. This characteristic is especially important for neurons, which are highly polarized cells. Among the domains contained by scaffold proteins, the PSD-95, Discs-large, ZO-1 (PDZ) domains are of particular relevance in signal transduction processes and maintenance of neuronal and epithelial polarity. These domains are specialized in the binding of the carboxyl termini of proteins allowing membrane proteins to be localized by the anchoring to the cytoskeleton mediated by PDZ-containing scaffold proteins. In vivo studies carried out in Drosophila have taught that the role of many scaffold proteins is not limited to a single process; thus, in many cases the same genes are expressed in different tissues and participate in apparently very diverse processes. In addition to the differential expression of interactors of scaffold proteins, the expression of variants of these molecular scaffolds as the result of the alternative processing of the genes that encode them is proving to be a very important source of variability and complexity on a main theme. Alternative splicing in the nervous system is well documented, where specific isoforms play roles in neurotransmission, ion channel function, neuronal cell recognition, and are developmentally regulated making it a major mechanism of functional diversity. Here we review the current state of knowledge about the diversity and the known function of PDZ-containing proteins in Drosophila with emphasis in the role played by alternatively processed forms in the diversity of functions attributed to this family of proteins.

  10. Identification of Abiotic Stress Protein Biomarkers by Proteomic Screening of Crop Cultivar Diversity

    OpenAIRE

    Barkla, Bronwyn J.

    2016-01-01

    Modern day agriculture practice is narrowing the genetic diversity in our food supply. This may compromise the ability to obtain high yield under extreme climactic conditions, threatening food security for a rapidly growing world population. To identify genetic diversity, tolerance mechanisms of cultivars, landraces and wild relatives of major crops can be identified and ultimately exploited for yield improvement. Quantitative proteomics allows for the identification of proteins that may cont...

  11. Hydrophobicity diversity in globular and nonglobular proteins measured with the Gini index.

    Science.gov (United States)

    Carugo, Oliviero

    2017-12-01

    Amino acids and their properties are variably distributed in proteins and different compositions determine all protein features, ranging from solubility to stability and functionality. Gini index, a tool to estimate distribution uniformity, is widely used in macroeconomics and has numerous statistical applications. Here, Gini index is used to analyze the distribution of hydrophobicity in proteins and to compare hydrophobicity distribution in globular and intrinsically disordered proteins. Based on the analysis of carefully selected high-quality data sets of proteins extracted from the Protein Data Bank (http://www.rcsb.org) and from the DisProt database (http://www.disprot.org/), it is observed that hydrophobicity is distributed in a more diverse way in intrinsically disordered proteins than in folded and soluble globular proteins. This correlates with the observation that the amino acid composition deviates from the uniformity (estimate with the Shannon and the Gini-Simpson indices) more in intrinsically disordered proteins than in globular and soluble proteins. Although statistical tools tike the Gini index have received little attention in molecular biology, these results show that they allow one to estimate sequence diversity and that they are useful to delineate trends that can hardly be described, otherwise, in simple and concise ways. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  12. The Portuguese Climate Portal

    Science.gov (United States)

    Gomes, Sandra; Deus, Ricardo; Nogueira, Miguel; Viterbo, Pedro; Miranda, Miguel; Antunes, Sílvia; Silva, Alvaro; Miranda, Pedro

    2016-04-01

    The Portuguese Local Warming Website (http://portaldoclima.pt) has been developed in order to support the society in Portugal in preparing for the adaptation to the ongoing and future effects of climate change. The climate portal provides systematic and easy access to authoritative scientific data ready to be used by a vast and diverse user community from different public and private sectors, key players and decision makers, but also to high school students, contributing to the increase in knowledge and awareness on climate change topics. A comprehensive set of regional climate variables and indicators are computed, explained and graphically presented. Variables and indicators were built in agreement with identified needs after consultation of the relevant social partners from different sectors, including agriculture, water resources, health, environment and energy and also in direct cooperation with the Portuguese National Strategy for Climate Change Adaptation (ENAAC) group. The visual interface allows the user to dynamically interact, explore, quickly analyze and compare, but also to download and import the data and graphics. The climate variables and indicators are computed from state-of-the-art regional climate model (RCM) simulations (e.g., CORDEX project), at high space-temporal detail, allowing to push the limits of the projections down to local administrative regions (NUTS3) and monthly or seasonal periods, promoting local adaptation strategies. The portal provides both historical data (observed and modelled for the 1971-2000 period) and future climate projections for different scenarios (modelled for the 2011-2100 period). A large effort was undertaken in order to quantify the impacts of the risk of extreme events, such as heavy rain and flooding, droughts, heat and cold waves, and fires. Furthermore the different climate scenarios and the ensemble of RCM models, with high temporal (daily) and spatial (~11km) detail, is taken advantage in order to

  13. NUCLEONICA: a nuclear science portal

    International Nuclear Information System (INIS)

    Magill, J.; Galy, J.; Dreher, R.; Hamilton, D.; Tufan, M.; Normand, C.; Schwenk-Ferrero, A.; Wiese, H.W.

    2008-01-01

    NUCLEONICA is a new nuclear science web portal from the European Commission's Joint Research Centre. The portal provides a customizable, integrated environment and collaboration platform for the nuclear sciences using the latest 'Web 2.0' dynamic technology. NUCLEONICA is aimed at professionals, academics and students working with radionuclides in fields as diverse as the life sciences (e.g., biology, medicine, agriculture), the earth sciences (geology, meteorology, environmental science) and the more traditional disciplines such as nuclear power, health physics and radiation protection, nuclear and radio-chemistry, and astrophysics. It is also used as a knowledge management tool to preserve nuclear knowledge built up over many decades by creating modern web-based versions of so-called legacy computer codes. (authors)

  14. Protein change in plant evolution: tracing one thread connecting molecular and phenotypic diversity

    Directory of Open Access Journals (Sweden)

    Madelaine eBartlett

    2013-10-01

    Full Text Available Proteins change over the course of evolutionary time. New protein-coding genes and gene families emerge and diversify, ultimately affecting an organism’s phenotype and interactions with its environment. Here we survey the range of structural protein change observed in plants and review the role these changes have had in the evolution of plant form and function. Verified examples tying evolutionary change in protein structure to phenotypic change remain scarce. We will review the existing examples, as well as draw from investigations into domestication, and quantitative trait locus (QTL cloning studies searching for the molecular underpinnings of natural variation. The evolutionary significance of many cloned QTL has not been assessed, but all the examples identified so far have begun to reveal the extent of protein structural diversity tolerated in natural systems. This molecular (and phenotypic diversity could come to represent part of natural selection’s source material in the adaptive evolution of novel traits. Protein structure and function can change in many distinct ways, but the changes we identified in studies of natural diversity and protein evolution were predicted to fall primarily into one of six categories: altered active and binding sites; hypomorphic and hypermorphic alleles; altered protein-protein interactions; altered domain content; altered protein stability; and altered activity as an activator or repressor. Variability was also observed in the evolutionary scale at which particular changes were observed. Some changes were detected at both micro- and macroevolutionary timescales, while others were observed primarily at deep or shallow phylogenetic levels. This variation might be used to determine the trajectory of future investigations in structural molecular evolution.

  15. The Seed Proteome Web Portal

    Directory of Open Access Journals (Sweden)

    Marc eGalland

    2012-06-01

    Full Text Available The Seed Proteome Web Portal (SPWP; http://www.seedproteome.com/ gives access to information both on quantitative seed proteomic data and on seed-related protocols. Firstly, the SPWP provides access to the 475 different Arabidopsis seed proteins annotated from 2 dimensional electrophoresis (2DE maps. Quantitative data are available for each protein according to their accumulation profile during the germination process. These proteins can be retrieved either in list format or directly on scanned 2DE maps. These proteomic data reveal that 40% of seed proteins maintain a stable abundance over germination, up to radicle protrusion. During sensu stricto germination (24 h upon imbibition about 50% of the proteins display quantitative variations, exhibiting an increased abundance (35% or a decreasing abundance (15%. Moreover, during radicle protrusion (24 h to 48 h upon imbibition, 41% proteins display quantitative variations with an increased (23% or a decreasing abundance (18%. In addition, an analysis of the seed proteome revealed the importance of protein post-translational modifications as demonstrated by the poor correlation (r2 = 0.29 between the theoretical (predicted from Arabidopsis genome and the observed protein isoelectric points. Secondly, the SPWP is a relevant technical resource for protocols specifically dedicated to Arabidopsis seed proteome studies. Concerning 2D electrophoresis, the user can find efficient procedures for sample preparation, electrophoresis coupled with gel analysis and protein identification by mass spectrometry, which we have routinely used during the last 12 years. Particular applications such as the detection of oxidized proteins or de novo synthetized proteins radiolabeled by [35S]-methionine are also given in great details. Future developments of this portal will include proteomic data from studies such as dormancy release and protein turnover through de novo protein synthesis analyses during germination.

  16. Noncirrhotic portal hypertension.

    Science.gov (United States)

    Da, Ben L; Koh, Christopher; Heller, Theo

    2018-05-01

    Noncirrhotic portal hypertension represents a heterogeneous group of liver disorders that is characterized by portal hypertension in the absence of cirrhosis. The purpose of this review is to serve as a guide on how to approach a patient with noncirrhotic portal hypertension with a focus on recent developments. Recent studies pertaining to noncirrhotic portal hypertension have investigated aetiological causes, mechanisms of disease, noninvasive diagnostic modalities, clinical characteristics in the paediatric population and novel treatment targets. Noncirrhotic portal hypertension is an underappreciated clinical entity that can be difficult to diagnosis without a healthy suspicion. Diagnosis then relies on a comprehensive understanding of the causes and clinical manifestations of this disease, as well as a careful interpretation of the liver biopsy. Noninvasive approaches to diagnosis may play a significant role moving forward in this disease. Treatment in NCPH remains largely targeted at the individual sequalae of portal hypertension.

  17. Hepatic angiography: Portal hypertension

    International Nuclear Information System (INIS)

    Oliver, T.W. Jr.; Sones, P.J. Jr.

    1985-01-01

    Portal hypertension is usually a manifestation of underlying hepatic parenchymal disease, although it may be secondary to portal or hepatic venous thrombosis and rarely to hyperdynamic portal states. Portal hypertension may present as encephalopathy, ascites, jaundice, hepatic failure, or catastrophic upper gastrointestinal hemorrhage. Radiologic investigation should include indirect or direct measurements of portal pressure, assessment of portal venous perfusion, visualization of collaterals, and demonstration of arterial and venous anatomy for potential shunt procedure. Following survival of initial variceal bleeding, the most effective procedure to prevent recurrent hemorrhage is a shunt to decompress the varices. The decision whether to intervene medically or surgically during the acute hemorrhagic episode as well as the type of shunt used to prevent future hemorrhage is the subject of continuing controversy

  18. Pediatric portal hypertension

    Science.gov (United States)

    Vogel, Clarissa Barbon

    2017-01-01

    Abstract: Pediatric portal hypertension management is a team approach between the patient, the patient's family, the primary caregiver, and specialty providers. Evidence-based practice guidelines have not been established in pediatrics. This article serves as a review for the primary care NP in the management of pediatric portal hypertension, discussing the etiology, pathophysiology, and clinical presentation of pediatric portal hypertension, diagnostic tests, and treatment and management options. PMID:28406835

  19. Usability of Discovery Portals

    OpenAIRE

    Bulens, J.D.; Vullings, L.A.E.; Houtkamp, J.M.; Vanmeulebrouk, B.

    2013-01-01

    As INSPIRE progresses to be implemented in the EU, many new discovery portals are built to facilitate finding spatial data. Currently the structure of the discovery portals is determined by the way spatial data experts like to work. However, we argue that the main target group for discovery portals are not spatial data experts but professionals with limited spatial knowledge, and a focus outside the spatial domain. An exploratory usability experiment was carried out in which three discovery p...

  20. High genetic diversity in the coat protein and 3' untranslated regions

    Indian Academy of Sciences (India)

    The 3′ terminal region consisting of the coat protein (CP) coding sequence and 3′ untranslated region (3′UTR) was cloned and sequenced from seven isolates. Sequence comparisons revealed considerable genetic diversity among the isolates in their CP and 3′UTR, making CdMV one of the highly variable members ...

  1. Genetic diversity of three surface protein genes in Plasmodium malariae from three Asian countries.

    Science.gov (United States)

    Srisutham, Suttipat; Saralamba, Naowarat; Sriprawat, Kanlaya; Mayxay, Mayfong; Smithuis, Frank; Nosten, Francois; Pukrittayakamee, Sasithon; Day, Nicholas P J; Dondorp, Arjen M; Imwong, Mallika

    2018-01-11

    Genetic diversity of the three important antigenic proteins, namely thrombospondin-related anonymous protein (TRAP), apical membrane antigen 1 (AMA1), and 6-cysteine protein (P48/45), all of which are found in various developmental stages of Plasmodium parasites is crucial for targeted vaccine development. While studies related to the genetic diversity of these proteins are available for Plasmodium falciparum and Plasmodium vivax, barely enough information exists regarding Plasmodium malariae. The present study aims to demonstrate the genetic variations existing among these three genes in P. malariae by analysing their diversity at nucleotide and protein levels. Three surface protein genes were isolated from 45 samples collected in Thailand (N = 33), Myanmar (N = 8), and Lao PDR (N = 4), using conventional polymerase chain reaction (PCR) assay. Then, the PCR products were sequenced and analysed using BioEdit, MEGA6, and DnaSP programs. The average pairwise nucleotide diversities (π) of P. malariae trap, ama1, and p48/45 were 0.00169, 0.00413, and 0.00029, respectively. The haplotype diversities (Hd) of P. malariae trap, ama1, and p48/45 were 0.919, 0.946, and 0.130, respectively. Most of the nucleotide substitutions were non-synonymous, which indicated that the genetic variations of these genes were maintained by positive diversifying selection, thus, suggesting their role as a potential target of protective immune response. Amino acid substitutions of P. malariae TRAP, AMA1, and P48/45 could be categorized to 17, 20, and 2 unique amino-acid variants, respectively. For further vaccine development, carboxyl terminal of P48/45 would be a good candidate according to conserved amino acid at low genetic diversity (π = 0.2-0.3). High mutational diversity was observed in P. malariae trap and ama1 as compared to p48/45 in P. malariae samples isolated from Thailand, Myanmar, and Lao PDR. Taken together, these results suggest that P48/45 might be a good vaccine

  2. Assessing Genetic Diversity Based on Gliadin Proteins in Aegilops cylindrica Populations from Northwest of Iran

    Directory of Open Access Journals (Sweden)

    Toraj KHABIRI

    2013-02-01

    Full Text Available Wild wheat progenitors served as a valuable gene pool in breeding perspectives. In this respect, gliadins could be an important tool in assessing genetic variability as protein markers. Thus, genetic diversity of gliadin protein patterns in seventeen populations of Aegilops cylindrica collected from northwest of Iran were investigated using acid polyacrylamide gel electrophoresis. Results showed that the highest number of bands in the electrophoregrams were related to the ω type of geliadins. Conversely, the lowest number of bands were pertained to the β type of gliadins. Genetic diversity between populations was greater than within population variation. Assessment of total variation for the three gliadin types indicated that the highest total variation was related to β type while, the lowest one was belonged to ω type. Cluster analysis using complete linkage method divided populations into two separated groups in which genetic diversity does not follow from geographical distribution.

  3. Dynamic protein S-palmitoylation mediates parasite life cycle progression and diverse mechanisms of virulence.

    Science.gov (United States)

    Brown, Robert W B; Sharma, Aabha I; Engman, David M

    2017-04-01

    Eukaryotic parasites possess complex life cycles and utilize an assortment of molecular mechanisms to overcome physical barriers, suppress and/or bypass the host immune response, including invading host cells where they can replicate in a protected intracellular niche. Protein S-palmitoylation is a dynamic post-translational modification in which the fatty acid palmitate is covalently linked to cysteine residues on proteins by the enzyme palmitoyl acyltransferase (PAT) and can be removed by lysosomal palmitoyl-protein thioesterase (PPT) or cytosolic acyl-protein thioesterase (APT). In addition to anchoring proteins to intracellular membranes, functions of dynamic palmitoylation include - targeting proteins to specific intracellular compartments via trafficking pathways, regulating the cycling of proteins between membranes, modulating protein function and regulating protein stability. Recent studies in the eukaryotic parasites - Plasmodium falciparum, Toxoplasma gondii, Trypanosoma brucei, Cryptococcus neoformans and Giardia lamblia - have identified large families of PATs and palmitoylated proteins. Many palmitoylated proteins are important for diverse aspects of pathogenesis, including differentiation into infective life cycle stages, biogenesis and tethering of secretory organelles, assembling the machinery powering motility and targeting virulence factors to the plasma membrane. This review aims to summarize our current knowledge of palmitoylation in eukaryotic parasites, highlighting five exemplary mechanisms of parasite virulence dependent on palmitoylation.

  4. Mini Heme-Proteins: Designability of Structure and Diversity of Functions.

    Science.gov (United States)

    Rai, Jagdish

    2017-08-30

    Natural heme proteins may have heme bound to poly-peptide chain as a cofactor via noncovalent forces or heme as a prosthetic group may be covalently bound to the proteins. Nature has used porphyrins in diverse functions like electron transfer, oxidation, reduction, ligand binding, photosynthesis, signaling, etc. by modulating its properties through diverse protein matrices. Synthetic chemists have tried to utilize these molecules in equally diverse industrial and medical applications due to their versatile electro-chemical and optical properties. The heme iron has catalytic activity which can be modulated and enhanced for specific applications by protein matrix around it. Heme proteins can be designed into novel enzymes for sterio specific catalysis ranging from oxidation to reduction. These designed heme-proteins can have applications in industrial catalysis and biosensing. A peptide folds around heme easily due to hydrophobic effect of the large aromatic ring of heme. The directional property of co-ordinate bonding between peptide and metal ion in heme further specifies the structure. Therefore heme proteins can be easily designed for targeted structure and catalytic activity. The central aromatic chemical entity in heme viz. porphyrin is a very ancient molecule. Its presence in the prebiotic soup and in all forms of life suggests that it has played a vital role in the origin and progressive evolution of living organisms. Porphyrin macrocycles are highly conjugated systems composed of four modified pyrrole subunits interconnected at their α -carbon atoms via methine (=CH-) bridges. Initial minimalist models of hemoproteins focused on effect of heme-ligand co-ordinate bonding on chemical reactivity, spectroscopy, electrochemistry and magnetic properties of heme. The great sensitivity of these spectroscopic features of heme to its surrounding makes them extremely useful in structural elucidation of designed heme-peptide complexes. Therefore heme proteins are

  5. Idiopathic Noncirrhotic Portal Hypertension: An Appraisal

    Science.gov (United States)

    Lee, Hwajeong; Rehman, Aseeb Ur; Fiel, M. Isabel

    2016-01-01

    Idiopathic noncirrhotic portal hypertension is a poorly defined clinical condition of unknown etiology. Patients present with signs and symptoms of portal hypertension without evidence of cirrhosis. The disease course appears to be indolent and benign with an overall better outcome than cirrhosis, as long as the complications of portal hypertension are properly managed. This condition has been recognized in different parts of the world in diverse ethnic groups with variable risk factors, resulting in numerous terminologies and lack of standardized diagnostic criteria. Therefore, although the diagnosis of idiopathic noncirrhotic portal hypertension requires clinical exclusion of other conditions that can cause portal hypertension and histopathologic confirmation, this entity is under-recognized clinically as well as pathologically. Recent studies have demonstrated that variable histopathologic entities with different terms likely represent a histologic spectrum of a single entity of which obliterative portal venopathy might be an underlying pathogenesis. This perception calls for standardization of the nomenclature and formulation of widely accepted diagnostic criteria, which will facilitate easier recognition of this disorder and will highlight awareness of this entity. PMID:26563701

  6. The Molecular Basis of Toxins’ Interactions with Intracellular Signaling via Discrete Portals

    Directory of Open Access Journals (Sweden)

    Adi Lahiani

    2017-03-01

    Full Text Available An understanding of the molecular mechanisms by which microbial, plant or animal-secreted toxins exert their action provides the most important element for assessment of human health risks and opens new insights into therapies addressing a plethora of pathologies, ranging from neurological disorders to cancer, using toxinomimetic agents. Recently, molecular and cellular biology dissecting tools have provided a wealth of information on the action of these diverse toxins, yet, an integrated framework to explain their selective toxicity is still lacking. In this review, specific examples of different toxins are emphasized to illustrate the fundamental mechanisms of toxicity at different biochemical, molecular and cellular- levels with particular consideration for the nervous system. The target of primary action has been highlighted and operationally classified into 13 sub-categories. Selected examples of toxins were assigned to each target category, denominated as portal, and the modulation of the different portal’s signaling was featured. The first portal encompasses the plasma membrane lipid domains, which give rise to pores when challenged for example with pardaxin, a fish toxin, or is subject to degradation when enzymes of lipid metabolism such as phospholipases A2 (PLA2 or phospholipase C (PLC act upon it. Several major portals consist of ion channels, pumps, transporters and ligand gated ionotropic receptors which many toxins act on, disturbing the intracellular ion homeostasis. Another group of portals consists of G-protein-coupled and tyrosine kinase receptors that, upon interaction with discrete toxins, alter second messengers towards pathological levels. Lastly, subcellular organelles such as mitochondria, nucleus, protein- and RNA-synthesis machineries, cytoskeletal networks and exocytic vesicles are also portals targeted and deregulated by other diverse group of toxins. A fundamental concept can be drawn from these seemingly different

  7. Post-translational processing targets functionally diverse proteins in Mycoplasma hyopneumoniae.

    Science.gov (United States)

    Tacchi, Jessica L; Raymond, Benjamin B A; Haynes, Paul A; Berry, Iain J; Widjaja, Michael; Bogema, Daniel R; Woolley, Lauren K; Jenkins, Cheryl; Minion, F Chris; Padula, Matthew P; Djordjevic, Steven P

    2016-02-01

    Mycoplasma hyopneumoniae is a genome-reduced, cell wall-less, bacterial pathogen with a predicted coding capacity of less than 700 proteins and is one of the smallest self-replicating pathogens. The cell surface of M. hyopneumoniae is extensively modified by processing events that target the P97 and P102 adhesin families. Here, we present analyses of the proteome of M. hyopneumoniae-type strain J using protein-centric approaches (one- and two-dimensional GeLC-MS/MS) that enabled us to focus on global processing events in this species. While these approaches only identified 52% of the predicted proteome (347 proteins), our analyses identified 35 surface-associated proteins with widely divergent functions that were targets of unusual endoproteolytic processing events, including cell adhesins, lipoproteins and proteins with canonical functions in the cytosol that moonlight on the cell surface. Affinity chromatography assays that separately used heparin, fibronectin, actin and host epithelial cell surface proteins as bait recovered cleavage products derived from these processed proteins, suggesting these fragments interact directly with the bait proteins and display previously unrecognized adhesive functions. We hypothesize that protein processing is underestimated as a post-translational modification in genome-reduced bacteria and prokaryotes more broadly, and represents an important mechanism for creating cell surface protein diversity. © 2016 The Authors.

  8. Portal cholangiopathy: case report

    Directory of Open Access Journals (Sweden)

    Maria Cecilia Almeida Maia

    2014-01-01

    Full Text Available The present report describes the case of a child that after blunt abdominal trauma presented with portal thrombosis followed by progressive splenomegaly and jaundice. Ultrasonography and percutaneous cholangiography revealed biliary dilatation secondary to choledochal stenosis caused by dilated peribiliary veins, characterizing a case of portal biliopathy. The present case report is aimed at presenting an uncommon cause of this condition.

  9. Genetic diversity of the merozoite surface protein-3 gene in Plasmodium falciparum populations in Thailand.

    Science.gov (United States)

    Pattaradilokrat, Sittiporn; Sawaswong, Vorthon; Simpalipan, Phumin; Kaewthamasorn, Morakot; Siripoon, Napaporn; Harnyuttanakorn, Pongchai

    2016-10-21

    An effective malaria vaccine is an urgently needed tool to fight against human malaria, the most deadly parasitic disease of humans. One promising candidate is the merozoite surface protein-3 (MSP-3) of Plasmodium falciparum. This antigenic protein, encoded by the merozoite surface protein (msp-3) gene, is polymorphic and classified according to size into the two allelic types of K1 and 3D7. A recent study revealed that both the K1 and 3D7 alleles co-circulated within P. falciparum populations in Thailand, but the extent of the sequence diversity and variation within each allelic type remains largely unknown. The msp-3 gene was sequenced from 59 P. falciparum samples collected from five endemic areas (Mae Hong Son, Kanchanaburi, Ranong, Trat and Ubon Ratchathani) in Thailand and analysed for nucleotide sequence diversity, haplotype diversity and deduced amino acid sequence diversity. The gene was also subject to population genetic analysis (F st ) and neutrality tests (Tajima's D, Fu and Li D* and Fu and Li' F* tests) to determine any signature of selection. The sequence analyses revealed eight unique DNA haplotypes and seven amino acid sequence variants, with a haplotype and nucleotide diversity of 0.828 and 0.049, respectively. Neutrality tests indicated that the polymorphism detected in the alanine heptad repeat region of MSP-3 was maintained by positive diversifying selection, suggesting its role as a potential target of protective immune responses and supporting its role as a vaccine candidate. Comparison of MSP-3 variants among parasite populations in Thailand, India and Nigeria also inferred a close genetic relationship between P. falciparum populations in Asia. This study revealed the extent of the msp-3 gene diversity in P. falciparum in Thailand, providing the fundamental basis for the better design of future blood stage malaria vaccines against P. falciparum.

  10. Roadside Tracker Portal-less Portal Monitor

    Energy Technology Data Exchange (ETDEWEB)

    Ziock, Klaus-Peter [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Cheriyadat, Anil M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Bradley, Eric Craig [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Cunningham, Mark F. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Fabris, Lorenzo [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Goddard, Jr, James Samuel [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Hornback, Donald Eric [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Karnowski, Thomas Paul [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Kerekes, Ryan A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Newby, Jason [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2013-07-01

    This report documents the full development cycle of the Roadside Tracker (RST) Portal-less Portal monitor (Fig. 1) funded by DHS DNDO. The project started with development of a proof-of-feasibility proto-type, proceeded through design and construction of a proof-of-concept (POC) prototype, a test-and-evaluation phase, participation in a Limited Use Exercise that included the Standoff Radiation Detections Systems developed under an Advanced Technology Demonstration and concluded with participation in a Characterization Study conducted by DNDO.

  11. The XCAT Science Portal

    Directory of Open Access Journals (Sweden)

    Sriram Krishnan

    2002-01-01

    Full Text Available This paper describes the design and prototype implementation of the XCAT Grid Science Portal. The portal lets grid application programmers script complex distributed computations and package these applications with simple interfaces for others to use. Each application is packaged as a notebook which consists of web pages and editable parameterized scripts. The portal is a workstation-based specialized personal web server, capable of executing the application scripts and launching remote grid applications for the user. The portal server can receive event streams published by the application and grid resource information published by Network Weather Service (NWS [35] or Autopilot [16] sensors. Notebooks can be published and stored in web based archives for others to retrieve and modify. The XCAT Grid Science Portal has been tested with various applications, including the distributed simulation of chemical processes in semiconductor manufacturing and collaboratory support for X-ray crystallographers.

  12. Proteomic investigation of aphid honeydew reveals an unexpected diversity of proteins.

    Directory of Open Access Journals (Sweden)

    Ahmed Sabri

    Full Text Available Aphids feed on the phloem sap of plants, and are the most common honeydew-producing insects. While aphid honeydew is primarily considered to comprise sugars and amino acids, its protein diversity has yet to be documented. Here, we report on the investigation of the honeydew proteome from the pea aphid Acyrthosiphon pisum. Using a two-Dimensional Differential in-Gel Electrophoresis (2D-Dige approach, more than 140 spots were isolated, demonstrating that aphid honeydew also represents a diverse source of proteins. About 66% of the isolated spots were identified through mass spectrometry analysis, revealing that the protein diversity of aphid honeydew originates from several organisms (i.e. the host aphid and its microbiota, including endosymbiotic bacteria and gut flora. Interestingly, our experiments also allowed to identify some proteins like chaperonin, GroEL and Dnak chaperones, elongation factor Tu (EF-Tu, and flagellin that might act as mediators in the plant-aphid interaction. In addition to providing the first aphid honeydew proteome analysis, we propose to reconsider the importance of this substance, mainly acknowledged to be a waste product, from the aphid ecology perspective.

  13. Diversity and evolution of ABC proteins in mycorrhiza-forming fungi.

    Science.gov (United States)

    Kovalchuk, Andriy; Kohler, Annegret; Martin, Francis; Asiegbu, Fred O

    2015-12-28

    Transporter proteins are predicted to have an important role in the mycorrhizal symbiosis, due to the fact that this type of an interaction between plants and fungi requires a continuous nutrient and signalling exchange. ABC transporters are one of the large groups of transporter proteins found both in plants and in fungi. The crucial role of plant ABC transporters in the formation of the mycorrhizal symbiosis has been demonstrated recently. Some of the fungal ABC transporter-encoding genes are also induced during the mycorrhiza formation. However, no experimental evidences of the direct involvement of fungal ABC transporters in this process are available so far. To facilitate the identification of fungal ABC proteins with a potential role in the establishment of the mycorrhizal symbiosis, we have performed an inventory of the ABC protein-encoding genes in the genomes of 25 species of mycorrhiza-forming fungi. We have identified, manually annotated and curated more than 1300 gene models of putative ABC protein-encoding genes. Out of those, more than 1000 models are predicted to encode functional proteins, whereas about 300 models represent gene fragments or putative pseudogenes. We have also performed the phylogenetic analysis of the identified sequences. The sets of ABC proteins in the mycorrhiza-forming species were compared to the related saprotrophic or plant-pathogenic fungal species. Our results demonstrate the high diversity of ABC genes in the genomes of mycorrhiza-forming fungi. Via comparison of transcriptomics data from different species, we have identified candidate groups of ABC transporters that might have a role in the process of the mycorrhiza formation. Results of our inventory will facilitate the identification of fungal transporters with a role in the mycorrhiza formation. We also provide the first data on ABC protein-coding genes for the phylum Glomeromycota and for orders Pezizales, Atheliales, Cantharellales and Sebacinales, contributing to

  14. Portal Vein Stenting for Portal Biliopathy with Jaundice

    Energy Technology Data Exchange (ETDEWEB)

    Hyun, Dongho, E-mail: mesentery@naver.com; Park, Kwang Bo, E-mail: kbjh.park@samsung.com [Sungkyunkwan University School of Medicine, Department of Radiology, Samsung Medical Center (Korea, Republic of); Lim, Seong Joo [Konyang University, Department of Radiology, College of Medicine, Konyang University Hospital (Korea, Republic of); Hwang, Jin Ho [Hallym University Sacred Heart Hospital, Department of Radiology (Korea, Republic of); Sinn, Dong Hyun [Sungkyunkwan University School of Medicine, Department of Medicine, Samsung Medical Center (Korea, Republic of)

    2016-04-15

    Portal biliopathy refers to obstruction of the bile duct by dilated peri- or para-ductal collateral channels following the main portal vein occlusion from various causes. Surgical shunt operation or endoscopic treatment has been reported. Herein, we report a case of portal biliopathy that was successfully treated by interventional portal vein recanalization.

  15. Plasmodium vivax merozoite surface protein-3 alpha: a high-resolution marker for genetic diversity studies.

    Science.gov (United States)

    Prajapati, Surendra Kumar; Joshi, Hema; Valecha, Neena

    2010-06-01

    Malaria, an ancient human infectious disease caused by five species of Plasmodium, among them Plasmodium vivax is the most widespread human malaria species and causes huge morbidity to its host. Identification of genetic marker to resolve higher genetic diversity for an ancient origin organism is a crucial task. We have analyzed genetic diversity of P. vivax field isolates using highly polymorphic antigen gene merozoite surface protein-3 alpha (msp-3 alpha) and assessed its suitability as high-resolution genetic marker for population genetic studies. 27 P. vivax field isolates collected during chloroquine therapeutic efficacy study at Chennai were analyzed for genetic diversity. PCR-RFLP was employed to assess the genetic variations using highly polymorphic antigen gene msp-3 alpha. We observed three distinct PCR alleles at msp-3 alpha, and among them allele A showed significantly high frequency (53%, chi2 = 8.22, p = 0.001). PCR-RFLP analysis revealed 14 and 17 distinct RFLP patterns for Hha1 and Alu1 enzymes respectively. Further, RFLP analysis revealed that allele A at msp-3 alpha is more diverse in the population compared with allele B and C. Combining Hha1 and Alu1 RFLP patterns revealed 21 distinct genotypes among 22 isolates reflects higher diversity resolution power of msp-3 alpha in the field isolates. P. vivax isolates from Chennai region revealed substantial amount of genetic diversity and comparison of allelic diversity with other antigen genes and microsatellites suggesting that msp-3 alpha could be a high-resolution marker for genetic diversity studies among P. vivax field isolates.

  16. Proteomic analysis reveals the diversity and complexity of membrane proteins in chickpea (Cicer arietinum L.

    Directory of Open Access Journals (Sweden)

    Jaiswal Dinesh Kumar

    2012-10-01

    Full Text Available Abstract Background Compartmentalization is a unique feature of eukaryotes that helps in maintaining cellular homeostasis not only in intra- and inter-organellar context, but also between the cells and the external environment. Plant cells are highly compartmentalized with a complex metabolic network governing various cellular events. The membranes are the most important constituents in such compartmentalization, and membrane-associated proteins play diverse roles in many cellular processes besides being part of integral component of many signaling cascades. Results To obtain valuable insight into the dynamic repertoire of membrane proteins, we have developed a proteome reference map of a grain legume, chickpea, using two-dimensional gel electrophoresis. MALDI-TOF/TOF and LC-ESI-MS/MS analysis led to the identification of 91 proteins involved in a variety of cellular functions viz., bioenergy, stress-responsive and signal transduction, metabolism, protein synthesis and degradation, among others. Significantly, 70% of the identified proteins are putative integral membrane proteins, possessing transmembrane domains. Conclusions The proteomic analysis revealed many resident integral membrane proteins as well as membrane-associated proteins including those not reported earlier. To our knowledge, this is the first report of membrane proteome from aerial tissues of a crop plant. The findings may provide a better understanding of the biochemical machinery of the plant membranes at the molecular level that might help in functional genomics studies of different developmental pathways and stress-responses.

  17. Portal vein thrombosis.

    Science.gov (United States)

    Chawla, Yogesh K; Bodh, Vijay

    2015-03-01

    Portal vein thrombosis is an important cause of portal hypertension. PVT occurs in association with cirrhosis or as a result of malignant invasion by hepatocellular carcinoma or even in the absence of associated liver disease. With the current research into its genesis, majority now have an underlying prothrombotic state detectable. Endothelial activation and stagnant portal blood flow also contribute to formation of the thrombus. Acute non-cirrhotic PVT, chronic PVT (EHPVO), and portal vein thrombosis in cirrhosis are the three main variants of portal vein thrombosis with varying etiological factors and variability in presentation and management. Procoagulant state should be actively investigated. Anticoagulation is the mainstay of therapy for acute non-cirrhotic PVT, with supporting evidence for its use in cirrhotic population as well. Chronic PVT (EHPVO) on the other hand requires the management of portal hypertension as such and with role for anticoagulation in the setting of underlying prothrombotic state, however data is awaited in those with no underlying prothrombotic states. TIPS and liver transplant may be feasible even in the setting of PVT however proper selection of candidates and type of surgery is warranted. Thrombolysis and thrombectomy have some role. TARE is a new modality for management of HCC with portal vein invasion.

  18. Probing conserved helical modules of portal complexes by mass spectrometry-based hydrogen/deuterium exchange.

    Science.gov (United States)

    Kang, Sebyung; Poliakov, Anton; Sexton, Jennifer; Renfrow, Matthew B; Prevelige, Peter E

    2008-09-05

    The Double-stranded DNA bacteriophage P22 has a ring-shaped dodecameric complex composed of the 84 kDa portal protein subunit that forms the central channel of the phage DNA packaging motor. The overall morphology of the P22 portal complex is similar to that of the portal complexes of Phi29, SPP1, T3, T7 phages and herpes simplex virus. Secondary structure prediction of P22 portal protein and its threading onto the crystal structure of the Phi29 portal complexes suggested that the P22 portal protein complex shares conserved helical modules that were found in the dodecameric interfaces of the Phi29 portal complex. To identify the amino acids involved in intersubunit contacts in the P22 portal ring complexes and validate the threading model, we performed comparative hydrogen/deuterium exchange analysis of monomeric and in vitro assembled portal proteins of P22 and the dodecameric Phi29 portal. Hydrogen/deuterium exchange experiments provided evidence of intersubunit interactions in the P22 portal complex similar to those in the Phi29 portal that map to the regions predicted to be conserved helical modules.

  19. Radiation portal evaluation parameters

    International Nuclear Information System (INIS)

    York, R.L.

    1998-01-01

    The detection of the unauthorized movement of radioactive materials is one of the most effective nonproliferation measures. Automatic special nuclear material (SNM) portal monitors are designed to detect this unauthorized movement and are an important part of the safeguard systems at US nuclear facilities. SNM portals differ from contamination monitors because they are designed to have high sensitivity for the low energy gamma-rays associated with highly enriched uranium (HEU) and plutonium. These instruments are now being installed at international borders to prevent the spread of radioactive contamination an SNM. In this paper the parameters important to evaluating radiation portal monitors are discussed. (author)

  20. A chess web portal

    OpenAIRE

    Volf, Žiga

    2011-01-01

    The aim of the thesis was to develop a web portal for chess players, which is intended to be a place for quality chess joining over the Internet and chess education. This need is caused by existing social networks and websites for playing chess, which offer you a very small amount of quality chess joining and education. As a result of the work the chess portal was created. We have presented the development of the chess portal in the thesis, which has all the features the chess players are i...

  1. Metabolic effects of portal vein sensing.

    Science.gov (United States)

    Mithieux, G

    2014-09-01

    The extrinsic gastrointestinal nerves are crucial in the sensing of nutrients and hormones and its translation in terms of control of food intake. Major macronutrients like glucose and protein are sensed by the extrinsic nerves located in the portal vein walls, which signal to the brain and account for the satiety phenomenon they promote. Glucose is sensed in the portal vein by neurons expressing the glucose receptor SGLT3, which activate the main regions of the brain involved in the control of food intake. Proteins indirectly act on food intake by inducing intestinal gluconeogenesis and its sensing by the portal glucose sensor. The mechanism involves a prior antagonism by peptides of the μ-opioid receptors present in the portal vein nervous system and a reflex arc with the brain inducing intestinal gluconeogenesis. In a comparable manner, short-chain fatty acids produced from soluble fibre act via intestinal gluconeogenesis to exert anti-obesity and anti-diabetic effects. In the case of propionate, the mechanism involves a prior activation of the free fatty acid receptor FFAR3 present in the portal nerves and a reflex arc initiating intestinal gluconeogenesis. © 2014 John Wiley & Sons Ltd.

  2. ASKME Enterprise Portal (internal) -

    Data.gov (United States)

    Department of Transportation — The ASKME Enterprise Portal Internal (AEPi) is envisioned to be an integrated, single-point-of-entry solution that contains modular components. The AEPi will provide...

  3. Liferay Portal Systems Development

    CERN Document Server

    Yuan, Jonas X

    2012-01-01

    This book focuses on teaching by example. Every chapter provides an overview, and then dives right into hands-on examples so you can see and play with the solution in your own environment. This book is for Java developers who don't need any prior experience with Liferay portal. Although Liferay portal makes heavy use of open source frameworks, no prior experience of using these is assumed.

  4. ELECTRONIC COMMERCE PORTAL

    OpenAIRE

    Georgeta Soava

    2011-01-01

    Today companies are faced with the need to exploit technology changing computer environments, in order to improve customer satisfaction and reduce costs. A successful approach to electronic portals is an effective demonstration of the new ways of relating to the client. The objectives that we have considered for the realization of e-commerce portal can be summarized as follows: structured communication, effective collaboration, complet and closed circuit of orders and deliveries, inventory op...

  5. Diverse Regulation of Temperature Sensation by Trimeric G-Protein Signaling in Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Tomoyo Ujisawa

    Full Text Available Temperature sensation by the nervous system is essential for life and proliferation of animals. The molecular-physiological mechanisms underlying temperature signaling have not been fully elucidated. We show here that diverse regulatory machinery underlies temperature sensation through trimeric G-protein signaling in the nematode Caenorhabditis elegans. Molecular-genetic studies demonstrated that cold tolerance is regulated by additive functions of three Gα proteins in a temperature-sensing neuron, ASJ, which is also known to be a light-sensing neuron. Optical recording of calcium concentration in ASJ upon temperature-changes demonstrated that three Gα proteins act in different aspects of temperature signaling. Calcium concentration changes in ASJ upon temperature change were unexpectedly decreased in a mutant defective in phosphodiesterase, which is well known as a negative regulator of calcium increase. Together, these data demonstrate commonalities and differences in the molecular components concerned with light and temperature signaling in a single sensory neuron.

  6. Diverse Regulation of Temperature Sensation by Trimeric G-Protein Signaling in Caenorhabditis elegans

    Science.gov (United States)

    Ujisawa, Tomoyo; Ohta, Akane; Uda-Yagi, Misato

    2016-01-01

    Temperature sensation by the nervous system is essential for life and proliferation of animals. The molecular-physiological mechanisms underlying temperature signaling have not been fully elucidated. We show here that diverse regulatory machinery underlies temperature sensation through trimeric G-protein signaling in the nematode Caenorhabditis elegans. Molecular-genetic studies demonstrated that cold tolerance is regulated by additive functions of three Gα proteins in a temperature-sensing neuron, ASJ, which is also known to be a light-sensing neuron. Optical recording of calcium concentration in ASJ upon temperature-changes demonstrated that three Gα proteins act in different aspects of temperature signaling. Calcium concentration changes in ASJ upon temperature change were unexpectedly decreased in a mutant defective in phosphodiesterase, which is well known as a negative regulator of calcium increase. Together, these data demonstrate commonalities and differences in the molecular components concerned with light and temperature signaling in a single sensory neuron. PMID:27788246

  7. Biology of portal hypertension.

    Science.gov (United States)

    McConnell, Matthew; Iwakiri, Yasuko

    2018-02-01

    Portal hypertension develops as a result of increased intrahepatic vascular resistance often caused by chronic liver disease that leads to structural distortion by fibrosis, microvascular thrombosis, dysfunction of liver sinusoidal endothelial cells (LSECs), and hepatic stellate cell (HSC) activation. While the basic mechanisms of LSEC and HSC dysregulation have been extensively studied, the role of microvascular thrombosis and platelet function in the pathogenesis of portal hypertension remains to be clearly characterized. As a secondary event, portal hypertension results in splanchnic and systemic arterial vasodilation, leading to the development of a hyperdynamic circulatory syndrome and subsequently to clinically devastating complications including gastroesophageal varices and variceal hemorrhage, hepatic encephalopathy from the formation of portosystemic shunts, ascites, and renal failure due to the hepatorenal syndrome. This review article discusses: (1) mechanisms of sinusoidal portal hypertension, focusing on HSC and LSEC biology, pathological angiogenesis, and the role of microvascular thrombosis and platelets, (2) the mesenteric vasculature in portal hypertension, and (3) future directions for vascular biology research in portal hypertension.

  8. Rapamycin-binding FKBP25 associates with diverse proteins that form large intracellular entities

    International Nuclear Information System (INIS)

    Galat, Andrzej; Thai, Robert

    2014-01-01

    Highlights: • The hFKBP25 interacts with diverse components of macromolecular entities. • We show that the endogenous human FKBP25 is bound to polyribosomes. • The endogenous hFKBP25 co-immunoprecipitated with nucleosomal proteins. • FKBP25 could induce conformational switch in macromolecular complexes. - Abstract: In this paper, we show some evidence that a member of the FK506-binding proteins, FKBP25 is associated to diverse components that are part of several different intracellular large-molecular mass entities. The FKBP25 is a high-affinity rapamycin-binding immunophilin, which has nuclear translocation signals present in its PPIase domain but it was detected both in the cytoplasm compartment and in the nuclear proteome. Analyses of antiFKBP25-immunoprecipitated proteins have revealed that the endogenous FKBP25 is associated to the core histones of the nucleosome, and with several proteins forming spliceosomal complexes and ribosomal subunits. Using polyclonal antiFKBP25 we have detected FKBP25 associated with polyribosomes. Added RNAs or 0.5 M NaCl release FKBP25 that was associated with the polyribosomes indicating that the immunophilin has an intrinsic capacity to form complexes with polyribonucleotides via its charged surface patches. Rapamycin or FK506 treatments of the polyribosomes isolated from porcine brain, HeLa and K568 cells caused a residual release of the endogenous FKBP25, which suggests that the immunophilin also binds to some proteins via its PPIase cavity. Our proteomics study indicates that the nuclear pool of the FKBP25 targets various nuclear proteins that are crucial for packaging of DNA, chromatin remodeling and pre-mRNA splicing whereas the cytosolic pool of this immunophilin is bound to some components of the ribosome

  9. Rapamycin-binding FKBP25 associates with diverse proteins that form large intracellular entities

    Energy Technology Data Exchange (ETDEWEB)

    Galat, Andrzej, E-mail: galat@dsvidf.cea.fr; Thai, Robert

    2014-08-08

    Highlights: • The hFKBP25 interacts with diverse components of macromolecular entities. • We show that the endogenous human FKBP25 is bound to polyribosomes. • The endogenous hFKBP25 co-immunoprecipitated with nucleosomal proteins. • FKBP25 could induce conformational switch in macromolecular complexes. - Abstract: In this paper, we show some evidence that a member of the FK506-binding proteins, FKBP25 is associated to diverse components that are part of several different intracellular large-molecular mass entities. The FKBP25 is a high-affinity rapamycin-binding immunophilin, which has nuclear translocation signals present in its PPIase domain but it was detected both in the cytoplasm compartment and in the nuclear proteome. Analyses of antiFKBP25-immunoprecipitated proteins have revealed that the endogenous FKBP25 is associated to the core histones of the nucleosome, and with several proteins forming spliceosomal complexes and ribosomal subunits. Using polyclonal antiFKBP25 we have detected FKBP25 associated with polyribosomes. Added RNAs or 0.5 M NaCl release FKBP25 that was associated with the polyribosomes indicating that the immunophilin has an intrinsic capacity to form complexes with polyribonucleotides via its charged surface patches. Rapamycin or FK506 treatments of the polyribosomes isolated from porcine brain, HeLa and K568 cells caused a residual release of the endogenous FKBP25, which suggests that the immunophilin also binds to some proteins via its PPIase cavity. Our proteomics study indicates that the nuclear pool of the FKBP25 targets various nuclear proteins that are crucial for packaging of DNA, chromatin remodeling and pre-mRNA splicing whereas the cytosolic pool of this immunophilin is bound to some components of the ribosome.

  10. Constraints on lateral gene transfer in promoting fimbrial usher protein diversity and function.

    Science.gov (United States)

    Stubenrauch, Christopher J; Dougan, Gordon; Lithgow, Trevor; Heinz, Eva

    2017-11-01

    Fimbriae are long, adhesive structures widespread throughout members of the family Enterobacteriaceae. They are multimeric extrusions, which are moved out of the bacterial cell through an integral outer membrane protein called usher. The complex folding mechanics of the usher protein were recently revealed to be catalysed by the membrane-embedded translocation and assembly module (TAM). Here, we examine the diversity of usher proteins across a wide range of extraintestinal (ExPEC) and enteropathogenic (EPEC) Escherichia coli , and further focus on a so far undescribed chaperone-usher system, with this usher referred to as UshC. The fimbrial system containing UshC is distributed across a discrete set of EPEC types, including model strains like E2348/67, as well as ExPEC ST131, currently the most prominent multi-drug-resistant uropathogenic E. coli strain worldwide. Deletion of the TAM from a naive strain of E. coli results in a drastic time delay in folding of UshC, which can be observed for a protein from EPEC as well as for two introduced proteins from related organisms, Yersinia and Enterobacter We suggest that this models why the TAM machinery is essential for efficient folding of proteins acquired via lateral gene transfer. © 2017 The Authors.

  11. On line portal imaging

    International Nuclear Information System (INIS)

    Munro, Peter

    1996-01-01

    Purpose/Objective: The purpose of this presentation is to examine the various imaging devices that have been developed for portal imaging; describe some of the image registration methods that have been developed to determine geometric errors quantitatively; discuss some of the ways that portal imaging has been incorporated into routine clinical practice; describe quality assurance procedures for these devices, and discuss the use of portal imaging devices for dosimetry applications. Discussion: Verification of patient positioning has always been an important aspect of external beam radiation therapy. Over the past decade many portal imaging devices have been developed by individual investigators and most accelerator manufacturers now offer 'on-line' portal imaging systems. The commercial devices can be classified into three categories: T.V. camera-based systems, liquid ionisation chamber systems, and amorphous silicon systems. Many factors influence the quality of images generated by these portal imaging systems. These include factors which are unavoidable (e.g., low subject contrast), factors which depend upon the individual imaging device forming the image (e.g., dose utilisation, spatial resolution) as well as factors which depend upon the characteristics of the linear accelerator irradiating the imaging system (x-ray source size, image magnification). The characteristics of individual imaging systems, such as spatial resolution, temporal response, and quantum utilisation will be discussed. One of the major advantages of on-line portal imaging is that many quantitative techniques have been developed to detect errors in patient positioning. The general approach is to register anatomic structures on a portal image with the same structures on a digitized simulator film. Once the anatomic structures have been registered, any discrepancies in the position of the patient can be identified. However, the task is not nearly as straight-forward as it sounds. One problem

  12. Diversity of Histologic Patterns and Expression of Cytoskeletal Proteins in Canine Skeletal Osteosarcoma.

    Science.gov (United States)

    Nagamine, E; Hirayama, K; Matsuda, K; Okamoto, M; Ohmachi, T; Kadosawa, T; Taniyama, H

    2015-09-01

    Osteosarcoma (OS), the most common bone tumor, includes OS of the head (OSH) and appendicular OS (OSA). In dogs, it is classified into 6 histologic subtypes: osteoblastic, chondroblastic, fibroblastic, telangiectatic, giant cell, and poorly differentiated. This study investigated the significance of the histologic classification relevant to clinical outcome and the histologic and immunohistochemical relationships between pleomorphism and expression of cytoskeletal proteins in 60 cases each of OSH and OSA. Most neoplasms exhibited histologic diversity, and 64% of OS contained multiple subtypes. In addition to the above 6 subtypes, myxoid, round cell, and epithelioid subtypes were observed. Although the epithelioid subtypes were observed in only OSH, no significant difference in the frequency of other subtypes was observed. Also, no significant relevance was observed between the clinical outcome and histologic subtypes. Cytokeratin (CK) was expressed in both epithelioid and sarcomatoid tumor cells in various subtypes, and all CK-positive tumor cells also expressed vimentin. Vimentin and α-smooth muscle actin (SMA) were expressed in all subtypes. A few SMA-positive spindle-shaped tumor cells exhibited desmin expression. Glial fibrillary acidic protein-positive tumor cells were observed in many subtypes, and some of these cells showed neurofilament expression. Although OSH exhibited significantly stronger immunoreactivity for SMA than OSA, no significant difference in other cytoskeletal proteins was observed. Some tumor cells had cytoskeletal protein expression compatible with the corresponding histologic subtypes, such as CK in the epithelioid subtype and SMA in the fibroblastic subtype. Thus, canine skeletal OS is composed of pleomorphic and heterogenous tumor cells as is reflected in the diversity of histologic patterns and expression of cytoskeletal proteins. © The Author(s) 2015.

  13. Extrahepatic portal hypertension in childhood

    International Nuclear Information System (INIS)

    Takehara, Hiroo; Komi, Nobuhiko; Goh, Masahiro; Yoshida, Sadahiro; Kameoka, Kazuhiro; Hino, Masao; Sui, Osamu

    1986-01-01

    Four pediatric patients with extrahepatic portal hypertension had undergone portography and computerized radionuclide angiography in order to examine shape of portal system and to evaluate hepatic blood flow before and aftersurgical treatment. In all patients, cavernous transformation of portal system was demonstrated by portography, and in one of them spontaneous splenorenal shunt occurred. In 3 of them, who underwent esophageal transsection combined with paraesophagogastric devascularization and splenectomy, so-called direct operation, increase of portal blood flow was revealed by computerized radionuclide angiography. It is suggested that direct operation increasing portal blood flow after surgery is effective in treating extrahepatic portal hypertension in childhood. (author)

  14. Proteomics for exploiting diversity of lupin seed storage proteins and their use as nutraceuticals for health and welfare.

    Science.gov (United States)

    Cabello-Hurtado, Francisco; Keller, Jean; Ley, José; Sanchez-Lucas, Rosa; Jorrín-Novo, Jesús V; Aïnouche, Abdelkader

    2016-06-30

    Lupins have a variety of both traditional and modern uses. In the last decade, reports assessing the benefits of lupin seed proteins have proliferated and, nowadays, the pharmaceutical industry is interested in lupin proteins for human health. Modern genomics and proteomics have hugely contributed to describing the diversity of lupin storage genes and, above all, proteins. Most of these studies have been centered on few edible lupin species. However, Lupinus genus comprises hundreds of species spread throughout the Old and New Worlds, and these resources have been scarcely explored and exploited. We present here a detailed review of the literature on the potential of lupin seed proteins as nutraceuticals, and the use of -omic tools to analyze seed storage polypeptides in main edible lupins and their diversity at the Lupinus inter- and intra-species level. In this sense, proteomics, more than any other, has been a key approach. Proteomics has shown that lupin seed protein diversity, where post-translational modifications yield a large number of peptide variants with a potential concern in bioactivity, goes far beyond gene diversity. The future extended use of second and third generation proteomics should definitely help to go deeper into coverage and characterization of lupin seed proteome. Some important topics concerning storage proteins from lupin seeds are presented and analyzed in an integrated way in this review. Proteomic approaches have been essential in characterizing lupin seed protein diversity, which goes far beyond gene diversity since the protein level adds to the latter differential proteolytic cleavage of conglutin pro-proteins and a diverse array of glycosylation forms and sites. Proteomics has also proved helpful for screening and studying Lupinus germplasm with the future aim of exploiting and improving food production, quality, and nutritional values. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. On line portal imaging

    International Nuclear Information System (INIS)

    Munro, Peter

    1997-01-01

    Purpose/Objective: The purpose of this presentation is to examine the various imaging devices that have been developed for portal imaging, describe some of the image registration methods that have been developed to determine geometric errors quantitatively, and discuss how portal imaging has been incorporated into clinical practice. Discussion: Verification of patient positioning has always been an important aspect of external beam radiation therapy. Over the past decade many portal imaging devices have been developed by individual investigators and most accelerator manufacturers now offer 'on-line' portal imaging systems. The commercial devices include T.V. camera-based systems, liquid ionisation chamber systems, and shortly, flat panel systems. The characteristics of these imaging systems will be discussed. In addition, other approaches such as the use of kilovoltage x-ray sources, video monitoring, and ultrasound have been proposed for improving patient positioning. Some of the advantages of these approaches will be discussed. One of the major advantages of on-line portal imaging is that many quantitative techniques have been developed to detect errors in patient positioning. The general approach is to register anatomic structures on a portal image with the same structures on a digitized simulator film. Once the anatomic structures have been registered, any discrepancies in the position of the patient can be identified. One problem is finding a common frame of reference for the simulator and portal images, since the location of the radiation field within the pixel matrix may differ for the two images. As a result, a common frame of reference has to be established before the anatomic structures in the images can be registered - generally by registering radiation field edges identified in the simulator and portal images. In addition, distortions in patient geometry or rotations out of the image plane can confound the image registration techniques. Despite the

  16. A diverse host thrombospondin-type-1 repeat protein repertoire promotes symbiont colonization during establishment of cnidarian-dinoflagellate symbiosis.

    Science.gov (United States)

    Neubauer, Emilie-Fleur; Poole, Angela Z; Neubauer, Philipp; Detournay, Olivier; Tan, Kenneth; Davy, Simon K; Weis, Virginia M

    2017-05-08

    The mutualistic endosymbiosis between cnidarians and dinoflagellates is mediated by complex inter-partner signaling events, where the host cnidarian innate immune system plays a crucial role in recognition and regulation of symbionts. To date, little is known about the diversity of thrombospondin-type-1 repeat (TSR) domain proteins in basal metazoans or their potential role in regulation of cnidarian-dinoflagellate mutualisms. We reveal a large and diverse repertoire of TSR proteins in seven anthozoan species, and show that in the model sea anemone Aiptasia pallida the TSR domain promotes colonization of the host by the symbiotic dinoflagellate Symbiodinium minutum . Blocking TSR domains led to decreased colonization success, while adding exogenous TSRs resulted in a 'super colonization'. Furthermore, gene expression of TSR proteins was highest at early time-points during symbiosis establishment. Our work characterizes the diversity of cnidarian TSR proteins and provides evidence that these proteins play an important role in the establishment of cnidarian-dinoflagellate symbiosis.

  17. Passive nuclear material detection in a personnel portal

    International Nuclear Information System (INIS)

    Fehlau, P.E.; Eaton, M.J.

    1979-01-01

    The concepts employed in the development of gamma-ray and neutron detection systems for a special nuclear materials booth portal monitor are described. The portal is designed for unattended use in detecting diversion by a technically sophisticated adversary and has possible application to International Atomic Energy Agency safeguards of a fast critical assembly facility. Preliminary evaluation results are given and plans for further parameter studies are noted

  18. Portal venous stent placement for treatment of portal hypertension caused by benign main portal vein stenosis.

    Science.gov (United States)

    Shan, Hong; Xiao, Xiang-Sheng; Huang, Ming-Sheng; Ouyang, Qiang; Jiang, Zai-Bo

    2005-06-07

    To evaluate the value of endovascular stent in the treatment of portal hypertension caused by benign main portal vein stenosis. Portal vein stents were implanted in six patients with benign main portal vein stenosis (inflammatory stenosis in three cases, postprocedure of liver transplantation in another three cases). Changes in portal vein pressure, portal vein patency, relative clinical symptoms, complications, and survival were evaluated. Six metallic stents were successfully placed across the portal vein stenotic or obstructive lesions in six patients. Mean portal venous pressure decreased significantly after stent implantation from (37.3+/-4.7) cm H(2)O to (18.0+/-1.9) cm H(2)O. The portal blood flow restored and the symptoms caused by portal hypertension were eliminated. There were no severe procedure-related complications. The patients were followed up for 1-48 mo. The portal vein remained patent during follow-up. All patients survived except for one patient who died of other complications of liver transplantation. Percutaneous portal vein stent placement for the treatment of portal hypertension caused by benign main portal vein stenosis is safe and effective.

  19. Pregnancy with Portal Hypertension

    Science.gov (United States)

    Aggarwal, Neelam; Negi, Neha; Aggarwal, Aakash; Bodh, Vijay; Dhiman, Radha K.

    2014-01-01

    Even though pregnancy is rare with cirrhosis and advanced liver disease, but it may co-exist in the setting of non-cirrhotic portal hypertension as liver function is preserved but whenever encountered together is a complex clinical dilemma. Pregnancy in a patient with portal hypertension presents a special challenge to the obstetrician as so-called physiological hemodynamic changes associated with pregnancy, needed for meeting demands of the growing fetus, worsen the portal hypertension thereby putting mother at risk of potentially life-threatening complications like variceal hemorrhage. Risks of variceal bleed and hepatic decompensation increase many fold during pregnancy. Optimal management revolves round managing the portal hypertension and its complications. Thus management of such cases requires multi-speciality approach involving obstetricians experienced in dealing with high risk cases, hepatologists, anesthetists and neonatologists. With advancement in medical field, pregnancy is not contra-indicated in these women, as was previously believed. This article focuses on the different aspects of pregnancy with portal hypertension with special emphasis on specific cause wise treatment options to decrease the variceal bleed and hepatic decompensation. Based on extensive review of literature, management from pre-conceptional period to postpartum is outlined in order to have optimal maternal and perinatal outcomes. PMID:25755552

  20. The NOAO NVO Portal

    Science.gov (United States)

    Miller, C. J.; Gasson, D.; Fuentes, E.

    2007-10-01

    The NOAO NVO Portal is a web application for one-stop discovery, analysis, and access to VO-compliant imaging data and services. The current release allows for GUI-based discovery of nearly a half million images from archives such as the NOAO Science Archive, the Hubble Space Telescope WFPC2 and ACS instruments, XMM-Newton, Chandra, and ESO's INT Wide-Field Survey, among others. The NOAO Portal allows users to view image metadata, footprint wire-frames, FITS image previews, and provides one-click access to science quality imaging data throughout the entire sky via the Firefox web browser (i.e., no applet or code to download). Users can stage images from multiple archives at the NOAO NVO Portal for quick and easy bulk downloads. The NOAO NVO Portal also provides simplified and direct access to VO analysis services, such as the WESIX catalog generation service. We highlight the features of the NOAO NVO Portal (http://nvo.noao.edu).

  1. Radioisotopic flow scanning for portal blood flow and portal hypertension

    International Nuclear Information System (INIS)

    Hesdorffer, C.S.; Bezwoda, W.R.; Danilewitz, M.D.; Esser, J.D.; Tobias, M.

    1987-01-01

    The use of a simple, noninvasive, isotope scanning technique for the determination of relative portal blood flow and detection of portal hypertension is described. Using this technique the presence of portal hypertension was demonstrated in seven of nine patients known to have elevated portal venous pressure. By contrast, esophageal varices were demonstrated in only five of these patients, illustrating the potential value of the method. Furthermore, this technique has been adapted to the study of portal blood flow in patients with myeloproliferative disorders with splenomegaly but without disturbances in hepatic architecture. Results demonstrate that the high relative splenic flow resulting from the presence of splenomegaly may in turn be associated with elevated relative portal blood flow and portal hypertension. The theoretic reasons for the development of flow-related portal hypertension and its relationship to splenic blood flow are discussed

  2. Morphological and biomechanical remodeling of the hepatic portal vein in a swine model of portal hypertension.

    Science.gov (United States)

    He, Xi-Ju; Huang, Tie-Zhu; Wang, Pei-Jun; Peng, Xing-Chun; Li, Wen-Chun; Wang, Jun; Tang, Jie; Feng, Na; Yu, Ming-Hua

    2012-02-01

    To obtain the morphological and biomechanical remodeling of portal veins in swine with portal hypertension (PHT), so as to provide some mechanical references and theoretical basis for clinical practice about PHT. Twenty white pigs were used in this study, 14 of them were subjected to both carbon tetrachloride- and pentobarbital-containing diet to induce experimental liver cirrhosis and PHT, and the remaining animals served as the normal controls. The morphological remodeling of portal veins was observed. Endothelial nitric oxide synthase expression profile in the vessel wall was assessed at both mRNA and protein level. The biomechanical changes of the hepatic portal veins were evaluated through assessing the following indicators: the incremental elastic modulus, pressure-strain elastic modulus, volume elastic modulus, and the incremental compliance. The swine PHT model was successfully established. The percentages for the microstructural components and the histological data significantly changed in the experimental group. Endothelial nitric oxide synthase expression was significantly downregulated in the portal veins of the experimental group. Three incremental elastic moduli (the incremental elastic modulus, pressure-strain elastic modulus, and volume elastic modulus) of the portal veins from PHT animals were significantly larger than those of the controls (P portal vein decreased. Our study suggests that the morphological and biomechanical properties of swine hepatic portal veins change significantly during the PHT process, which may play a critical role in the development of PHT and serve as potential therapeutic targets during clinical practice. Copyright © 2012 Annals of Vascular Surgery Inc. Published by Elsevier Inc. All rights reserved.

  3. Oral treponeme major surface protein: Sequence diversity and distributions within periodontal niches.

    Science.gov (United States)

    You, M; Chan, Y; Lacap-Bugler, D C; Huo, Y-B; Gao, W; Leung, W K; Watt, R M

    2017-12-01

    Treponema denticola and other species (phylotypes) of oral spirochetes are widely considered to play important etiological roles in periodontitis and other oral infections. The major surface protein (Msp) of T. denticola is directly implicated in several pathological mechanisms. Here, we have analyzed msp sequence diversity across 68 strains of oral phylogroup 1 and 2 treponemes; including reference strains of T. denticola, Treponema putidum, Treponema medium, 'Treponema vincentii', and 'Treponema sinensis'. All encoded Msp proteins contained highly conserved, taxon-specific signal peptides, and shared a predicted 'three-domain' structure. A clone-based strategy employing 'msp-specific' polymerase chain reaction primers was used to analyze msp gene sequence diversity present in subgingival plaque samples collected from a group of individuals with chronic periodontitis (n=10), vs periodontitis-free controls (n=10). We obtained 626 clinical msp gene sequences, which were assigned to 21 distinct 'clinical msp genotypes' (95% sequence identity cut-off). The most frequently detected clinical msp genotype corresponded to T. denticola ATCC 35405 T , but this was not correlated to disease status. UniFrac and libshuff analysis revealed that individuals with periodontitis and periodontitis-free controls harbored significantly different communities of treponeme clinical msp genotypes (Pdiversity than periodontitis-free controls (Mann-Whitney U-test, Pdiversity of Treponema clinical msp genotypes within their subgingival niches. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  4. Identification of Abiotic Stress Protein Biomarkers by Proteomic Screening of Crop Cultivar Diversity.

    Science.gov (United States)

    Barkla, Bronwyn J

    2016-09-08

    Modern day agriculture practice is narrowing the genetic diversity in our food supply. This may compromise the ability to obtain high yield under extreme climactic conditions, threatening food security for a rapidly growing world population. To identify genetic diversity, tolerance mechanisms of cultivars, landraces and wild relatives of major crops can be identified and ultimately exploited for yield improvement. Quantitative proteomics allows for the identification of proteins that may contribute to tolerance mechanisms by directly comparing protein abundance under stress conditions between genotypes differing in their stress responses. In this review, a summary is provided of the data accumulated from quantitative proteomic comparisons of crop genotypes/cultivars which present different stress tolerance responses when exposed to various abiotic stress conditions, including drought, salinity, high/low temperature, nutrient deficiency and UV-B irradiation. This field of research aims to identify molecular features that can be developed as biomarkers for crop improvement, however without accurate phenotyping, careful experimental design, statistical robustness and appropriate biomarker validation and verification it will be challenging to deliver what is promised.

  5. Identification of Abiotic Stress Protein Biomarkers by Proteomic Screening of Crop Cultivar Diversity

    Directory of Open Access Journals (Sweden)

    Bronwyn J. Barkla

    2016-09-01

    Full Text Available Modern day agriculture practice is narrowing the genetic diversity in our food supply. This may compromise the ability to obtain high yield under extreme climactic conditions, threatening food security for a rapidly growing world population. To identify genetic diversity, tolerance mechanisms of cultivars, landraces and wild relatives of major crops can be identified and ultimately exploited for yield improvement. Quantitative proteomics allows for the identification of proteins that may contribute to tolerance mechanisms by directly comparing protein abundance under stress conditions between genotypes differing in their stress responses. In this review, a summary is provided of the data accumulated from quantitative proteomic comparisons of crop genotypes/cultivars which present different stress tolerance responses when exposed to various abiotic stress conditions, including drought, salinity, high/low temperature, nutrient deficiency and UV-B irradiation. This field of research aims to identify molecular features that can be developed as biomarkers for crop improvement, however without accurate phenotyping, careful experimental design, statistical robustness and appropriate biomarker validation and verification it will be challenging to deliver what is promised.

  6. Genetic diversity and evolution of human metapneumovirus fusion protein over twenty years

    Directory of Open Access Journals (Sweden)

    Liem Alexis

    2009-09-01

    Full Text Available Abstract Background Human metapneumovirus (HMPV is an important cause of acute respiratory illness in children. We examined the diversity and molecular evolution of HMPV using 85 full-length F (fusion gene sequences collected over a 20-year period. Results The F gene sequences fell into two major groups, each with two subgroups, which exhibited a mean of 96% identity by predicted amino acid sequences. Amino acid identity within and between subgroups was higher than nucleotide identity, suggesting structural or functional constraints on F protein diversity. There was minimal progressive drift over time, and the genetic lineages were stable over the 20-year period. Several canonical amino acid differences discriminated between major subgroups, and polymorphic variations tended to cluster in discrete regions. The estimated rate of mutation was 7.12 × 10-4 substitutions/site/year and the estimated time to most recent common HMPV ancestor was 97 years (95% likelihood range 66-194 years. Analysis suggested that HMPV diverged from avian metapneumovirus type C (AMPV-C 269 years ago (95% likelihood range 106-382 years. Conclusion HMPV F protein remains conserved over decades. HMPV appears to have diverged from AMPV-C fairly recently.

  7. Genetic diversity and evolution of human metapneumovirus fusion protein over twenty years

    Science.gov (United States)

    Yang, Chin-Fen; Wang, Chiaoyin K; Tollefson, Sharon J; Piyaratna, Rohith; Lintao, Linda D; Chu, Marla; Liem, Alexis; Mark, Mary; Spaete, Richard R; Crowe, James E; Williams, John V

    2009-01-01

    Background Human metapneumovirus (HMPV) is an important cause of acute respiratory illness in children. We examined the diversity and molecular evolution of HMPV using 85 full-length F (fusion) gene sequences collected over a 20-year period. Results The F gene sequences fell into two major groups, each with two subgroups, which exhibited a mean of 96% identity by predicted amino acid sequences. Amino acid identity within and between subgroups was higher than nucleotide identity, suggesting structural or functional constraints on F protein diversity. There was minimal progressive drift over time, and the genetic lineages were stable over the 20-year period. Several canonical amino acid differences discriminated between major subgroups, and polymorphic variations tended to cluster in discrete regions. The estimated rate of mutation was 7.12 × 10-4 substitutions/site/year and the estimated time to most recent common HMPV ancestor was 97 years (95% likelihood range 66-194 years). Analysis suggested that HMPV diverged from avian metapneumovirus type C (AMPV-C) 269 years ago (95% likelihood range 106-382 years). Conclusion HMPV F protein remains conserved over decades. HMPV appears to have diverged from AMPV-C fairly recently. PMID:19740442

  8. Extraordinary Diversity of Immune Response Proteins among Sea Urchins: Nickel-Isolated Sp185/333 Proteins Show Broad Variations in Size and Charge

    Science.gov (United States)

    Sherman, Lauren S.; Schrankel, Catherine S.; Brown, Kristy J.; Smith, L. Courtney

    2015-01-01

    Effective protection against pathogens requires the host to produce a wide range of immune effector proteins. The Sp185/333 gene family, which is expressed by the California purple sea urchin Strongylocentrotus purpuratus in response to bacterial infection, encodes a highly diverse repertoire of anti-pathogen proteins. A subset of these proteins can be isolated by affinity to metal ions based on multiple histidines, resulting in one to four bands of unique molecular weight on standard Western blots, which vary depending on the individual sea urchin. Two dimensional gel electrophoresis (2DE) of nickel-isolated protein samples followed by Western blot was employed to detect nickel-isolated Sp185/333 (Ni-Sp185/333) proteins and to evaluate protein diversity in animals before and after immune challenge with marine bacteria. Ni-Sp185/333 proteins of the same molecular weight on standard Western blots appear as a broad complex of variants that differ in pI on 2DE Western blots. The Ni-Sp185/333 protein repertoire is variable among animals, and shows a variety of changes among individual sea urchins in response to immune challenges with both the same and different species of bacteria. The extraordinary diversity of the Ni-Sp185/333 proteins may provide significant anti-pathogen capabilities for sea urchins that survive solely on innate immunity. PMID:26406912

  9. Personalization Methods for Internet Portals

    OpenAIRE

    Barbara Dębska; Agnieszka Kubacka

    2012-01-01

    The article presents methods of acquiring and gathering data about users of internet portals, with particular emphasis on educational portals. Definitions, aims and tasks related to the process of personalization of e-learning portals are thoroughly discussed. So are knowledge acquisition techniques applied in personalization, especially artificial intelligence methods.

  10. Developing patient portals in a fragmented healthcare system.

    Science.gov (United States)

    Otte-Trojel, Terese; de Bont, Antoinette; Aspria, Marcello; Adams, Samantha; Rundall, Thomas G; van de Klundert, Joris; de Mul, Marleen

    2015-10-01

    Use of patient portals may contribute to improved patient health and experiences and better organizational performance. In the Netherlands, patient portals have gained considerable attention in recent years, as evidenced by various policy initiatives and practical efforts directed at developing portals. Due to the fragmented setup of the Dutch healthcare system patient portals that give patients access to information and services from across their providers are developed in inter-organizational collaboration. The objective of this paper is to identify and describe the types of collaborations, or networks, that have been established to develop patient portals in the Netherlands. Understanding the characteristics of these networks as well as the development of their respective portals enables us to assess the enabling and constraining effects of different network types on patient portal initiatives. We used qualitative methods including interview and documents analysis. In a first step, we interviewed eighteen experts and reviewed relevant national policy and strategy documents. Based on this orientation, we selected three networks we deemed to be representative of inter-organizational efforts to develop Dutch patient portals in 2012. In a second step, we interviewed twelve representatives of these patient portal networks and collected documents related to the portals. We applied content analytic techniques to analyze data from the three cases. The three studied networks differed in their number and diversity of actors, the degree to which these actors were mutually dependent, the degree to which network governance was decentralized, and the dynamics of the network structures. We observed that the portals developed in networks displaying the highest degree of these characteristics experienced most difficulties associated with developing patient portals - such as achieving interoperability, successful implementation, regulatory complaisance, and financial

  11. Altered blood-brain barrier permeability in rats with prehepatic portal hypertension turns to normal when portal pressure is lowered

    Science.gov (United States)

    Eizayaga, Francisco; Scorticati, Camila; Prestifilippo, Juan P; Romay, Salvador; Fernandez, Maria A; Castro, José L; Lemberg, Abraham; Perazzo, Juan C

    2006-01-01

    AIM: To study the blood-brain barrier integrity in prehepatic portal hypertensive rats induced by partial portal vein ligation, at 14 and 40 d after ligation when portal pressure is spontaneously normalized. METHODS: Adult male Wistar rats were divided into four groups: Group I: Sham14d , sham operated; Group II: PH14d , portal vein stenosis; (both groups were used 14 days after surgery); Group III: Sham40d, Sham operated and Group IV: PH40d Portal vein stenosis (Groups II and IV used 40 d after surgery). Plasma ammonia, plasma and cerebrospinal fluid protein and liver enzymes concentrations were determined. Trypan and Evans blue dyes, systemically injected, were investigated in hippocampus to study blood-brain barrier integrity. Portal pressure was periodically recorded. RESULTS: Forty days after stricture, portal pressure was normalized, plasma ammonia was moderately high, and both dyes were absent in central nervous system parenchyma. All other parameters were reestablished. When portal pressure was normalized and ammonia level was lowered, but not normal, the altered integrity of blood-brain barrier becomes reestablished. CONCLUSION: The impairment of blood-brain barrier and subsequent normalization could be a mechanism involved in hepatic encephalopathy reversibility. Hemodynamic changes and ammonia could trigger blood-brain barrier alterations and its reestablishment. PMID:16552803

  12. Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.

    Directory of Open Access Journals (Sweden)

    Holly J Atkinson

    Full Text Available The dramatic increase in heterogeneous types of biological data--in particular, the abundance of new protein sequences--requires fast and user-friendly methods for organizing this information in a way that enables functional inference. The most widely used strategy to link sequence or structure to function, homology-based function prediction, relies on the fundamental assumption that sequence or structural similarity implies functional similarity. New tools that extend this approach are still urgently needed to associate sequence data with biological information in ways that accommodate the real complexity of the problem, while being accessible to experimental as well as computational biologists. To address this, we have examined the application of sequence similarity networks for visualizing functional trends across protein superfamilies from the context of sequence similarity. Using three large groups of homologous proteins of varying types of structural and functional diversity--GPCRs and kinases from humans, and the crotonase superfamily of enzymes--we show that overlaying networks with orthogonal information is a powerful approach for observing functional themes and revealing outliers. In comparison to other primary methods, networks provide both a good representation of group-wise sequence similarity relationships and a strong visual and quantitative correlation with phylogenetic trees, while enabling analysis and visualization of much larger sets of sequences than trees or multiple sequence alignments can easily accommodate. We also define important limitations and caveats in the application of these networks. As a broadly accessible and effective tool for the exploration of protein superfamilies, sequence similarity networks show great potential for generating testable hypotheses about protein structure-function relationships.

  13. Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.

    Science.gov (United States)

    Atkinson, Holly J; Morris, John H; Ferrin, Thomas E; Babbitt, Patricia C

    2009-01-01

    The dramatic increase in heterogeneous types of biological data--in particular, the abundance of new protein sequences--requires fast and user-friendly methods for organizing this information in a way that enables functional inference. The most widely used strategy to link sequence or structure to function, homology-based function prediction, relies on the fundamental assumption that sequence or structural similarity implies functional similarity. New tools that extend this approach are still urgently needed to associate sequence data with biological information in ways that accommodate the real complexity of the problem, while being accessible to experimental as well as computational biologists. To address this, we have examined the application of sequence similarity networks for visualizing functional trends across protein superfamilies from the context of sequence similarity. Using three large groups of homologous proteins of varying types of structural and functional diversity--GPCRs and kinases from humans, and the crotonase superfamily of enzymes--we show that overlaying networks with orthogonal information is a powerful approach for observing functional themes and revealing outliers. In comparison to other primary methods, networks provide both a good representation of group-wise sequence similarity relationships and a strong visual and quantitative correlation with phylogenetic trees, while enabling analysis and visualization of much larger sets of sequences than trees or multiple sequence alignments can easily accommodate. We also define important limitations and caveats in the application of these networks. As a broadly accessible and effective tool for the exploration of protein superfamilies, sequence similarity networks show great potential for generating testable hypotheses about protein structure-function relationships.

  14. The Learning Portal

    Science.gov (United States)

    Staudt, Carolyn; Hanzlick-Burton, Camden; Williamson, Carol; McIntyre, Cynthia

    2015-01-01

    The Innovative Technology in Science Inquiry (ITSI) project is a learning portal with hundreds of free, customizable science, math, and engineering activities funded by the National Science Foundation at the Concord Consortium, a nonprofit research and development organization dedicated to transforming education through technology. The project…

  15. BRAZILIAN NEWS PORTALS CHARACTERISTICS

    Directory of Open Access Journals (Sweden)

    Heloiza G. Herckovitz

    2011-02-01

    Full Text Available A content analysis of four Brazilian news media portals found that economic news dominated the top headlines with little attention paid to education, the environment and welfare. Other trends included a focus on local events and national news sources, reliance on few sources, mostly official ones, and a low percentage of news that fitted the concept of newsworthiness (a combination of both social significance and deviance concepts. Other findings of a study of 432 top news stories published by UOL, Estadão, iG and Terra during a 15-day period between February and March 2008 indicate that the top portions of the portals’ front pages carry news that lacks story depth, editorial branding, and multimedia applications. The results suggest that online news portals are in their infancy although Brazil has the largest online population of Latin America. This study hopes to shed light on the gatekeeping process in Brazilian news portals. Brazilian media portals have yet to become a significant editorial force able to provide knowledge about social issues and public affairs in a socially responsible fashione.

  16. Reduced Fragment Diversity for Alpha and Alpha-Beta Protein Structure Prediction using Rosetta.

    Science.gov (United States)

    Abbass, Jad; Nebel, Jean-Christophe

    2017-01-01

    Protein structure prediction is considered a main challenge in computational biology. The biannual international competition, Critical Assessment of protein Structure Prediction (CASP), has shown in its eleventh experiment that free modelling target predictions are still beyond reliable accuracy, therefore, much effort should be made to improve ab initio methods. Arguably, Rosetta is considered as the most competitive method when it comes to targets with no homologues. Relying on fragments of length 9 and 3 from known structures, Rosetta creates putative structures by assembling candidate fragments. Generally, the structure with the lowest energy score, also known as first model, is chosen to be the "predicted one". A thorough study has been conducted on the role and diversity of 3-mers involved in Rosetta's model "refinement" phase. Usage of the standard number of 3-mers - i.e. 200 - has been shown to degrade alpha and alpha-beta protein conformations initially achieved by assembling 9-mers. Therefore, a new prediction pipeline is proposed for Rosetta where the "refinement" phase is customised according to a target's structural class prediction. Over 8% improvement in terms of first model structure accuracy is reported for alpha and alpha-beta classes when decreasing the number of 3- mers. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  17. Portal monitoring for detecting fissile materials and chemical explosives

    International Nuclear Information System (INIS)

    Albright, D.

    1992-01-01

    The portal monitoring of pedestrians, packages, equipment, and vehicles entering or leaving areas of high physical security has been common for many years. Many nuclear facilities rely on portal monitoring to prevent the theft or diversion of plutonium and highly enriched uranium. At commercial airports, portals are used to prevent firearms and explosives from being smuggled onto airplanes. An August 1989 Federal Aviation Administration (FAA) regulation requires US airlines to screen luggage on international flights for chemical explosives. This paper reports that portal monitoring is now being introduced into arms-control agreements. Because some of the portal-monitoring equipment that would be useful in verifying arms-control agreements is already widely used as part of the physical security systems at nuclear facilities and commercial airports, the authors review these uses of portal monitoring, as well as its role in verifying the INF treaty. Then the authors survey the major types of portal-monitoring equipment that would be most useful in detecting nuclear warheads or fissile material

  18. A comprehensive analysis of the Omp85/TpsB protein superfamily structural diversity, taxonomic occurrence, and evolution

    Science.gov (United States)

    Heinz, Eva; Lithgow, Trevor

    2014-01-01

    Members of the Omp85/TpsB protein superfamily are ubiquitously distributed in Gram-negative bacteria, and function in protein translocation (e.g., FhaC) or the assembly of outer membrane proteins (e.g., BamA). Several recent findings are suggestive of a further level of variation in the superfamily, including the identification of the novel membrane protein assembly factor TamA and protein translocase PlpD. To investigate the diversity and the causal evolutionary events, we undertook a comprehensive comparative sequence analysis of the Omp85/TpsB proteins. A total of 10 protein subfamilies were apparent, distinguished in their domain structure and sequence signatures. In addition to the proteins FhaC, BamA, and TamA, for which structural and functional information is available, are families of proteins with so far undescribed domain architectures linked to the Omp85 β-barrel domain. This study brings a classification structure to a dynamic protein superfamily of high interest given its essential function for Gram-negative bacteria as well as its diverse domain architecture, and we discuss several scenarios of putative functions of these so far undescribed proteins. PMID:25101071

  19. On line portal imaging

    International Nuclear Information System (INIS)

    Munro, Peter

    1995-01-01

    Purpose/Objective: The purpose of this presentation is to review the physics of imaging with high energy x-ray beams; examine the various imaging devices that have been developed for portal imaging; describe some of the image registration methods that have been developed to determine errors in patient positioning quantitatively; and discuss some of the ways that portal imaging has been incorporated into routine clinical practice. Verification of patient positioning has always been an important aspect of external beam radiation therapy. Checks of patient positioning have generally been done with film, however, film suffers from a number of drawbacks, such as poor image display and delays due to film development. Over the past decade many portal imaging devices have been developed by individual investigators and most accelerator manufacturers now offer 'on-line' portal imaging systems, which are intended to overcome the limitations of portal films. The commercial devices can be classified into three categories: T.V. camera-based systems, liquid ionisation chamber systems, and amorphous silicon systems. Many factors influence the quality of images generated by these portal imaging systems. These include factors which are unavoidable (e.g., low subject contrast), factors which depend upon the individual imaging device forming the image (e.g., dose utilisation, spatial resolution) as well as factors which depend upon the characteristics of the linear accelerator irradiating the imaging system (x-ray source size, image magnification). The fundamental factors which limit image quality and the characteristics of individual imaging systems, such as spatial resolution, temporal response, and quantum utilisation will be discussed. One of the major advantages of on-line portal imaging is that many quantitative techniques have been developed to detect errors in patient positioning. The general approach is to register anatomic structures on a portal image with the same

  20. Evolutionary Conservation and Emerging Functional Diversity of the Cytosolic Hsp70:J Protein Chaperone Network of Arabidopsis thaliana.

    Science.gov (United States)

    Verma, Amit K; Diwan, Danish; Raut, Sandeep; Dobriyal, Neha; Brown, Rebecca E; Gowda, Vinita; Hines, Justin K; Sahi, Chandan

    2017-06-07

    Heat shock proteins of 70 kDa (Hsp70s) partner with structurally diverse Hsp40s (J proteins), generating distinct chaperone networks in various cellular compartments that perform myriad housekeeping and stress-associated functions in all organisms. Plants, being sessile, need to constantly maintain their cellular proteostasis in response to external environmental cues. In these situations, the Hsp70:J protein machines may play an important role in fine-tuning cellular protein quality control. Although ubiquitous, the functional specificity and complexity of the plant Hsp70:J protein network has not been studied. Here, we analyzed the J protein network in the cytosol of Arabidopsis thaliana and, using yeast genetics, show that the functional specificities of most plant J proteins in fundamental chaperone functions are conserved across long evolutionary timescales. Detailed phylogenetic and functional analysis revealed that increased number, regulatory differences, and neofunctionalization in J proteins together contribute to the emerging functional diversity and complexity in the Hsp70:J protein network in higher plants. Based on the data presented, we propose that higher plants have orchestrated their "chaperome," especially their J protein complement, according to their specialized cellular and physiological stipulations. Copyright © 2017 Verma et al.

  1. TMEM16A regulates portal vein smooth muscle cell proliferation in portal hypertension.

    Science.gov (United States)

    Zeng, Xi; Huang, Ping; Chen, Mingkai; Liu, Shiqian; Wu, Nannan; Wang, Fang; Zhang, Jing

    2018-01-01

    The aim of the present study was to elucidate the effect of transmembrane protein 16A (TMEM16A) on portal vein smooth muscle cell (PVSMC) proliferation associated with portal vein remodeling in portal hypertension (PHT). Sprague-Dawley rats were subjected to bile duct ligation to establish a rat model of liver cirrhosis and PHT. Sham-operated animals served as controls. At 8 weeks after bile duct ligation, the extent of liver fibrosis and the portal vein wall thickness were assessed using hematoxylin-eosin staining. The protein expression levels of TMEM16A, extracellular signal-regulated kinase 1 and 2 (ERK1/2) and phosphorylated ERK1/2 (p-ERK1/2) in the portal vein were detected by immunohistochemistry and western blotting. In vitro , the lentivirus vectors were constructed and transfected into PVSMCs to upregulate the expression of TMEM16A. Isolated rat primary PVSMCs were treated with a small molecule inhibitor of TMEM16A, T16A-inhA01. Cell cycle was detected by flow cytometry. The activity of TMEM16A in the portal vein isolated from bile duct ligated rats was decreased, while the expression level of p-ERK1/2 was increased. However, in vitro , upregulation of TMEM16A promoted the proliferation PVSMCs, while inhibition of TMEM16A channels inhibited the proliferation of PVSMCs. The results indicated that TMEM16A contributes to PVSMCs proliferation in vitro , but in vivo , it may be a negative regulator of cell proliferation influenced by numerous factors.

  2. Anaplasma marginale major surface protein 1a: a marker of strain diversity with implications for control of bovine anaplasmosis.

    Science.gov (United States)

    Cabezas-Cruz, Alejandro; de la Fuente, José

    2015-04-01

    Classification of bacteria is challenging due to the lack of a theory-based framework. In addition, the adaptation of bacteria to ecological niches often results in selection of strains with diverse virulence, pathogenicity and transmission characteristics. Bacterial strain diversity presents challenges for taxonomic classification, which in turn impacts the ability to develop accurate diagnostics and effective vaccines. Over the past decade, the worldwide diversity of Anaplasma marginale, an economically important tick-borne pathogen of cattle, has become apparent. The extent of A. marginale strain diversity, formerly underappreciated, has contributed to the challenges of classification which, in turn, likely impacts the design and development of improved vaccines. Notably, the A. marginale surface protein 1a (MSP1a) is a model molecule for these studies because it serves as a marker for strain identity, is both an adhesin necessary for infection of cells and an immuno-reactive protein and is also an indicator of the evolution of strain diversity. Herein, we discuss a molecular taxonomic approach for classification of A. marginale strain diversity. Taxonomic analysis of this important molecule provides the opportunity to understand A. marginale strain diversity as it relates geographic and ecological factors and to the development of effective vaccines for control of bovine anaplasmosis worldwide. Copyright © 2015 Elsevier GmbH. All rights reserved.

  3. A Climate Information Portal for Copernicus: a central portal for European climate services?

    Science.gov (United States)

    Juckes, Martin; Swart, Rob; Thysse, Peter; Som de Cerff, Wim; Groot, Annemarie; Bennett, Victoria; Costa, Luis; Lückenkötter, Johannes; Callaghan, Sarah

    2015-04-01

    The FP7 project "Climate Information Portal for Copernicus" (CLIPC) is developing a demonstration portal for the Copernicus Climate Change Service (C3S). This project is one of a suite of FP7 research activities which are administratively independent of Copernicus, focussed on creating the technical and scientific building blocks needed for the service. It is to be expected that at EGU 2015 there will be many presentations describing portals delivering new and innovative ranges of services. It would be unwise to seek to replace all this creative activity with a single portal -- instead CLIPC is designing a portal to make distributed resources more accessible through flexible discovery systems. CLIPC needs to deliver more than a directory of resources: resources need to be presented in common protocols so that users can access multiple datasets. More information about the project objectives is available at www.clipc.eu. The gulf between the climate science communities and the end user communities is a central challenge being addressed in the project. It is important to understand that there is significant diversity and multiple communication barriers within these two sets of communities as well as between them. The CLIPC services must presentation will provide a review of progress towards this ambitious goal, through a discussion of user requirements activities, an overview of the proposed architecture, work on assessing and adjusting model biasses, and a discussion of the climate impact indicators which will be provided through the portal. When looking at the usability of data for the various users, CLIPC will implement a set of services functioning as a "knowledge base" supplying information to users about the data, including definitions of terminology used, quality of datasets, versioning, and user annotations.

  4. Angiography in portal hypertension

    Energy Technology Data Exchange (ETDEWEB)

    Zeitler, E

    1982-04-05

    We report on the cooperative possibilities the radiologist has as to diagnosis and therapy of portal hypertension. The catheter angiography allows to make a differentiation between pre- and intrahepatic bloc and the localization of bleeding esophagus varices. Only after all endoscopic measures with sclerotherapy and Laser coagulation have failed, catheter angiography will be carried out as a therapeutic measure. The future development, however, will give the opportunity to a series of therapeutic attempts on the field of interventional radiology.

  5. Angiography in portal hypertension

    International Nuclear Information System (INIS)

    Zeitler, E.

    1982-01-01

    We report on the cooperative possibilities the radiologist has as to diagnosis and therapy of portal hypertension. The catheter angiography allows to make a differentiation between pre- and intrahepatic bloc and the localization of bleeding esophagus varices. Only after all endoscopic measures with sclerotherapy and Laser coagulation have failed, catheter angiography will be carried out as a therapeutic measure. The future development, however, will give the opportunity to a series of therapeutic attempts on the field of interventional radiology. (orig.) [de

  6. Portal Annular Pancreas

    Science.gov (United States)

    Harnoss, Jonathan M.; Harnoss, Julian C.; Diener, Markus K.; Contin, Pietro; Ulrich, Alexis B.; Büchler, Markus W.; Schmitz-Winnenthal, Friedrich H.

    2014-01-01

    Abstract Portal annular pancreas (PAP) is an asymptomatic congenital pancreas anomaly, in which portal and/or mesenteric veins are encased by pancreas tissue. The aim of the study was to determine the role of PAP in pancreatic surgery as well as its management and potential complication, specifically, postoperative pancreatic fistula (POPF). On the basis of a case report, the MEDLINE and ISI Web of Science databases were systematically reviewed up to September 2012. All articles describing a case of PAP were considered. In summary, 21 studies with 59 cases were included. The overall prevalence of PAP was 2.4% and the patients' mean (SD) age was 55.9 (16.2) years. The POPF rate in patients with PAP (12 pancreaticoduodenectomies and 3 distal pancreatectomies) was 46.7% (in accordance with the definition of the International Study Group of Pancreatic Surgery). Portal annular pancreas is a quite unattended pancreatic variant with high prevalence and therefore still remains a clinical challenge to avoid postoperative complications. To decrease the risk for POPF, attentive preoperative diagnostics should also focus on PAP. In pancreaticoduodenectomy, a shift of the resection plane to the pancreas tail should be considered; in extensive pancreatectomy, coverage of the pancreatic remnant by the falciform ligament could be a treatment option. PMID:25207658

  7. Obliterative portal venopathy without portal hypertension: an underestimated condition.

    Science.gov (United States)

    Guido, Maria; Sarcognato, Samantha; Sonzogni, Aurelio; Lucà, Maria Grazia; Senzolo, Marco; Fagiuoli, Stefano; Ferrarese, Alberto; Pizzi, Marco; Giacomelli, Luciano; Colloredo, Guido

    2016-03-01

    Obliterative portal venopathy without portal hypertension has been described by a single study in a limited number of patients, thus very little is known about this clinical condition. This study aimed to investigate the prevalence of obliterative portal venopathy and its clinical-pathological correlations in patients with cryptogenic chronic liver test abnormalities without clinical signs of portal hypertension. We analysed 482 liver biopsies from adults with non-cirrhotic cryptogenic chronic liver disorders and without any clinical signs of portal hypertension, consecutively enrolled in a 5-year period. Twenty cases of idiopathic non-cirrhotic portal hypertension diagnosed in the same period, were included for comparison. Histological findings were matched with clinical and laboratory features. Obliterative portal venopathy was identified in 94 (19.5%) of 482 subjects and in all 20 cases of idiopathic non-cirrhotic portal hypertension: both groups shared the entire spectrum of histological changes described in the latter condition. The prevalence of incomplete fibrous septa and nodular regenerative hyperplasia was higher in the biopsies of idiopathic non-cirrhotic portal hypertension (P = 0.006 and P = 0.002), a possible hint of a more advanced stage of the disease. The two groups also shared several clinical laboratory features, including a similar liver function test profile, concomitant prothrombotic conditions and extrahepatic autoimmune disorders. Obliterative portal venopathy occurs in a substantial proportion of patients with unexplained chronic abnormal liver function tests without portal hypertension. The clinical-pathological profile of these subjects suggests that they may be in an early (non-symptomatic) stage of idiopathic non-cirrhotic portal hypertension. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  8. Portal hemodynamics in chronic portal-systemic encephalopathy

    International Nuclear Information System (INIS)

    Takashi, Motohide; Igarashi, Masahiko; Hino, Shinichi; Takayasu, Kenichi; Goto, Nobuaki; Musha, Hirotaka; Ohnishi, Kunihiko; Okuda, Kunio

    1985-01-01

    A portal hemodynamic study was made in 7 consecutive patients with chronic portal-systemic encephalopathy by percutaneous transhepatic catheterization of the portal vein and injecting contrast medium into the superior mesenteric vein or by superior mesenteric arterial portography in comparison with patients without encephalopathy studied by percutaneous catheterization of these veins. It is suggested that chronic portal-systemic encephalopathy is a result of a large collateral route shunting a large proportion of the superior mesenteric venous blood into systemic circulation, and that development of such collaterals precludes formation of large esophageal varices. (Auth.)

  9. Successful medical management of acute mesenteric ischemia due to superior mesenteric and portal vein thrombosis in a 27-year-old man with protein S deficiency: a case report.

    Science.gov (United States)

    Osti, N P; Sah, D N; Bhandari, R S

    2017-11-09

    Acute mesenteric ischemia poses a diagnostic challenge due to nonspecific clinical clues and lack of awareness owing to its rarity. Ischemia due to mesenteric venous thrombosis has a good prognosis compared to arterial cause and can be managed conservatively with early diagnosis. The portomesenteric venous system is an unusual site of thrombosis in patients with protein S deficiency, and its thrombosis is an uncommon cause of acute mesenteric ischemia. We present a case of a 27-year-old Mongolian man who presented with acute abdominal pain increasing in severity, and refractory to repeated attempts at treatment with a misdiagnosis of acute peptic ulcer disease. Contrast-enhanced computed tomography of his abdomen detected complete occlusion of the superior mesenteric vein, an extension of acute thrombus into the portal vein, and ischemic mid-jejunal loops. Early diagnosis and immediate anticoagulation with continuous intravenous infusion of unfractionated heparin prevented subsequent consequences. On further workup, our patient was diagnosed with isolated protein S deficiency. We started lifelong thromboprophylaxis with warfarin to prevent recurrence and our patient was asymptomatic on the latest follow-up 5 months after discharge. Despite accurate detection of acute mesenteric ischemia by contrast-enhanced computed tomography, high index of suspicion is indispensable for its early diagnosis. Early diagnosis and immediate anticoagulation will prevent subsequent complications and need for surgical intervention. Young patients without known risk factors presenting with venous thrombosis in atypical sites should be investigated for prothrombotic diseases.

  10. Platyhelminth Venom Allergen-Like (VAL) proteins: revealing structural diversity, class-specific features and biological associations across the phylum

    Science.gov (United States)

    CHALMERS, IAIN W.; HOFFMANN, KARL F.

    2012-01-01

    SUMMARY During platyhelminth infection, a cocktail of proteins is released by the parasite to aid invasion, initiate feeding, facilitate adaptation and mediate modulation of the host immune response. Included amongst these proteins is the Venom Allergen-Like (VAL) family, part of the larger sperm coating protein/Tpx-1/Ag5/PR-1/Sc7 (SCP/TAPS) superfamily. To explore the significance of this protein family during Platyhelminthes development and host interactions, we systematically summarize all published proteomic, genomic and immunological investigations of the VAL protein family to date. By conducting new genomic and transcriptomic interrogations to identify over 200 VAL proteins (228) from species in all 4 traditional taxonomic classes (Trematoda, Cestoda, Monogenea and Turbellaria), we further expand our knowledge related to platyhelminth VAL diversity across the phylum. Subsequent phylogenetic and tertiary structural analyses reveal several class-specific VAL features, which likely indicate a range of roles mediated by this protein family. Our comprehensive analysis of platyhelminth VALs represents a unifying synopsis for understanding diversity within this protein family and a firm context in which to initiate future functional characterization of these enigmatic members. PMID:22717097

  11. Knowledge Portals: Ontologies at Work

    OpenAIRE

    Staab, Steffen; Maedche, Alexander

    2001-01-01

    Knowledge portals provide views onto domain-specific information on the World Wide Web, thus helping their users find relevant, domain-specific information. The construction of intelligent access and the contribution of information to knowledge portals, however, remained an ad hoc task, requiring extensive manual editing and maintenance by the knowledge portal providers. To diminish these efforts, we use ontologies as a conceptual backbone for providing, accessing, and structuring information...

  12. Merozoite surface protein-1 genetic diversity in Plasmodium malariae and Plasmodium brasilianum from Brazil.

    Science.gov (United States)

    Guimarães, Lilian O; Wunderlich, Gerhard; Alves, João M P; Bueno, Marina G; Röhe, Fabio; Catão-Dias, José L; Neves, Amanda; Malafronte, Rosely S; Curado, Izilda; Domingues, Wilson; Kirchgatter, Karin

    2015-11-16

    The merozoite surface protein 1 (MSP1) gene encodes the major surface antigen of invasive forms of the Plasmodium erythrocytic stages and is considered a candidate vaccine antigen against malaria. Due to its polymorphisms, MSP1 is also useful for strain discrimination and consists of a good genetic marker. Sequence diversity in MSP1 has been analyzed in field isolates of three human parasites: P. falciparum, P. vivax, and P. ovale. However, the extent of variation in another human parasite, P. malariae, remains unknown. This parasite shows widespread, uneven distribution in tropical and subtropical regions throughout South America, Asia, and Africa. Interestingly, it is genetically indistinguishable from P. brasilianum, a parasite known to infect New World monkeys in Central and South America. Specific fragments (1 to 5) covering 60 % of the MSP1 gene (mainly the putatively polymorphic regions), were amplified by PCR in isolates of P. malariae and P. brasilianum from different geographic origin and hosts. Sequencing of the PCR-amplified products or cloned PCR fragments was performed and the sequences were used to construct a phylogenetic tree by the maximum likelihood method. Data were computed to give insights into the evolutionary and phylogenetic relationships of these parasites. Except for fragment 4, sequences from all other fragments consisted of unpublished sequences. The most polymorphic gene region was fragment 2, and in samples where this region lacks polymorphism, all other regions are also identical. The low variability of the P. malariae msp1 sequences of these isolates and the identification of the same haplotype in those collected many years apart at different locations is compatible with a low transmission rate. We also found greater diversity among P. brasilianum isolates compared with P. malariae ones. Lastly, the sequences were segregated according to their geographic origins and hosts, showing a strong genetic and geographic structure. Our data

  13. Duplex sonography in portal hypertension

    International Nuclear Information System (INIS)

    Kwon, Hyuk Po; Jang, J. C.; Park, B. H.

    1990-01-01

    We measure the diameter and blood velocity of the portal vein in 50 patients with cirrhosis of the liver and 40 healthy subjects, and calculated cross sectional area, mean blood flow velocity, blood flow volume and congestion index. In patients with cirrhosis of the liver, the cross sectional area of the portal vein was significantly increased: the mean blood flow volume was significantly reduced; the blood flow volume was significantly increased; the congestion index of the portal vein was significantly increased. Duples sonography may play an important role in the diagnosis of portal hypertension

  14. Diverse circular replication-associated protein encoding viruses circulating in invertebrates within a lake ecosystem.

    Science.gov (United States)

    Dayaram, Anisha; Galatowitsch, Mark L; Argüello-Astorga, Gerardo R; van Bysterveldt, Katherine; Kraberger, Simona; Stainton, Daisy; Harding, Jon S; Roumagnac, Philippe; Martin, Darren P; Lefeuvre, Pierre; Varsani, Arvind

    2016-04-01

    Over the last five years next-generation sequencing has become a cost effective and efficient method for identifying known and unknown microorganisms. Access to this technique has dramatically changed the field of virology, enabling a wide range of environmental viral metagenome studies to be undertaken of organisms and environmental samples from polar to tropical regions. These studies have led to the discovery of hundreds of highly divergent single stranded DNA (ssDNA) virus-like sequences encoding replication-associated proteins. Yet, few studies have explored how viruses might be shared in an ecosystem through feeding relationships. Here we identify 169 circular molecules (160 CRESS DNA molecules, nine circular molecules) recovered from a New Zealand freshwater lake, that we have tentatively classified into 51 putatively novel species and five previously described species (DflaCV-3, -5, -6, -8, -10). The CRESS DNA viruses identified in this study were recovered from molluscs (Echyridella menzeisii, Musculium novaezelandiae, Potamopyrgus antipodarum and Physella acuta) and insect larvae (Procordulia grayi, Xanthocnemis zealandica, and Chironomus zealandicus) collected from Lake Sarah, as well as from the lake water and benthic sediments. Extensive diversity was observed across most CRESS DNA molecules recovered. The putative capsid protein of one viral species was found to be most similar to those of members of the Tombusviridae family, thus expanding the number of known RNA-DNA hybrid viruses in nature. We noted a strong association between the CRESS DNA viruses and circular molecules identified in the water and browser organisms (C. zealandicus, P. antipodarum and P. acuta), and between water sediments and undefended prey species (C. zealandicus). However, we were unable to find any significant correlation of viral assemblages to the potential feeding relationships of the host aquatic invertebrates. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Rapid bursts of androgen-binding protein (Abp) gene duplication occurred independently in diverse mammals.

    Science.gov (United States)

    Laukaitis, Christina M; Heger, Andreas; Blakley, Tyler D; Munclinger, Pavel; Ponting, Chris P; Karn, Robert C

    2008-02-12

    The draft mouse (Mus musculus) genome sequence revealed an unexpected proliferation of gene duplicates encoding a family of secretoglobin proteins including the androgen-binding protein (ABP) alpha, beta and gamma subunits. Further investigation of 14 alpha-like (Abpa) and 13 beta- or gamma-like (Abpbg) undisrupted gene sequences revealed a rich diversity of developmental stage-, sex- and tissue-specific expression. Despite these studies, our understanding of the evolution of this gene family remains incomplete. Questions arise from imperfections in the initial mouse genome assembly and a dearth of information about the gene family structure in other rodents and mammals. Here, we interrogate the latest 'finished' mouse (Mus musculus) genome sequence assembly to show that the Abp gene repertoire is, in fact, twice as large as reported previously, with 30 Abpa and 34 Abpbg genes and pseudogenes. All of these have arisen since the last common ancestor with rat (Rattus norvegicus). We then demonstrate, by sequencing homologs from species within the Mus genus, that this burst of gene duplication occurred very recently, within the past seven million years. Finally, we survey Abp orthologs in genomes from across the mammalian clade and show that bursts of Abp gene duplications are not specific to the murid rodents; they also occurred recently in the lagomorph (rabbit, Oryctolagus cuniculus) and ruminant (cattle, Bos taurus) lineages, although not in other mammalian taxa. We conclude that Abp genes have undergone repeated bursts of gene duplication and adaptive sequence diversification driven by these genes' participation in chemosensation and/or sexual identification.

  16. Genetic diversity of plasmodium vivax merozoite surface protein-3alpha (Pvmsp-3alpha) gene in Jhapa District of Nepal

    DEFF Research Database (Denmark)

    Adhikari, Madhav; Ranjitkar, Samir; Schousboe, Mette Leth

    2012-01-01

    In Nepal, Plasmodium vivax accounts for approximately 80-90% of the malaria cases, but limited studies have been conducted on the genetic diversity of this parasite population. This study was carried out to determine the genetic diversity of P. vivax population sampled from subjects living...... in an endemic area of Jhapa District by analyzing the polymorphic merozoite surface protein-3alpha (Pvmsp-3alpha) gene by using PCR-restriction fragment length polymorphism. Three distinct genotypes were obtained from 96 samples; type A: 40 (71%), type B: 7 (13%), and type C: 9 (16%) which could be categorized...... into 13 allelic patterns: A1-A9, B1, B2, C1 and C2. These results indicated a high genetic diversity within the studied P. vivax population. As the transmission rate of malaria is low in Nepal, the diversity is most likely due to migration of people between the malaria endemic regions, either within...

  17. Genetic diversity in radish germplasm for morphological traits and seed storage proteins

    International Nuclear Information System (INIS)

    Jatoi, S.A.; Siddiqui, S.U.; Masood, M.S.; Javaid, A.; Iqbal, M.; Sayal, O.U.

    2011-01-01

    Genetic variation of forty-nine local and exotic radish genotypes including two checks was studied for morphological traits and seed storage protein electrophoresis using sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) markers. A high variation in germplasm for root shape, root length, root colour (internal and external), flesh texture and root type was observed. Among these genotypes, the genetic variation was apparent for most of the characters like plant biomass, root weight, leaf length, root length and root diameter that indicated the potential for crop improvement in these traits through simple selection. Exotic germplasm exhibited higher variation for plant biomass, root weight and root length which could be utilized through breeding programme. Cluster analysis on the basis of genetic diversity for seven quantitative traits resulted into four clusters. No clustering was found on the basis of origin. Low level of variance was observed for SDS-PAGE electrophoresis that suggested acquisition of more germplasm. On the basis of high yield and crispy root texture some genotypes (10076, 10362, 10429, 10658, 10662 and 10667) were identified for further testing under wide range of agro-ecological conditions. (author)

  18. CT portal venography manifestations of portal collateral circulation in patients with portal hypertension due to cirrhosis

    International Nuclear Information System (INIS)

    Ni Ming; Lv Weifu; Deng Kexue

    2009-01-01

    Objective: To analyze CT portal venography (CTPV) manifestations of portal collateral circulation in patients with cirrhosis by using a 16-detector row spiral CT scanner. Methods: CTPV was performed in 36 patients with portal hypertension due to cirrhosis, the diagnosis was proved by clinical data, hepatic function findings and imaging signs. By using post-processing reconstruction technique, 3D images of portal venous system and portal collateral circulation were obtained. Results: CTPV images displayed the portal venous system and its collateral circulation stereoscopically. Of 36 patients, left gastric varices were seen in 29(80.6%), lower esophageal varices in 18(50.0%), short gastric or posterior gastric varices in 15(41.7%), paraesophageal varices in 9(25.0%), gastro-renal or splenorenal shunts in 8(22.2%), spongelike transformation of portal vein in 7(19.4%), paraumbilical and abdominal wall varices in 6(16.7%), congenital cavernous in 6(16.7%) and paravertebral venous shunts in 4(11.1%). Conclusion: CTPV can well display the site, extent and severity of the portal collateral circulation in patients with portal hypertension due to cirrhosis,which is of great clinical importance for judging the patient's condition, for selecting therapeutic protocols and for estimating prognosis. (authors)

  19. Lunar and Vesta Web Portals

    Science.gov (United States)

    Law, E.; JPL Luna Mapping; Modeling Project Team

    2015-06-01

    The Lunar Mapping and Modeling Project offers Lunar Mapping and Modeling Portal (http://lmmp.nasa.gov) and Vesta Trek Portal (http://vestatrek.jpl.nasa.gov) providing interactive visualization and analysis tools to enable users to access mapped Lunar and Vesta data products.

  20. Portal dosimetry in wedged beams

    NARCIS (Netherlands)

    Spreeuw, Hanno; Rozendaal, Roel; Camargo, Priscilla; Mans, Anton; Wendling, Markus; Olaciregui-Ruiz, Igor; Sonke, Jan-Jakob; van Herk, Marcel; Mijnheer, Ben

    2015-01-01

    Portal dosimetry using electronic portal imaging devices (EPIDs) is often applied to verify high-energy photon beam treatments. Due to the change in photon energy spectrum, the resulting dose values are, however, not very accurate in the case of wedged beams if the pixel-to-dose conversion for the

  1. WLCG Operations portal demo tutorial

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    This is a navigation through http://wlcg-ops.web.cern.ch/ the Worldwide LHC Computing Grid (WLCG) Operations' portal. In this portal you will find documentation and information about WLCG Operation activities for: System Administrators at the WLCG sites LHC Experiments Operation coordination people, including Task Forces and Working Groups

  2. Health literacy and patient portals.

    Science.gov (United States)

    Gu, Yulong; Orr, Martin; Warren, Jim

    2015-06-01

    Health literacy has been described as the capacity to obtain, process, and understand basic health information and services needed to make appropriate health decisions. Improving health literacy may serve to promote concordance with therapy, engage patients in their own health care, and improve health outcomes. Patient portal technology aims at enabling patients and families to have easy access to key information in their own medical records and to communicate with their health care providers electronically. However, there is a gap in our understanding of how portals will improve patient outcome. The authors believe patient portal technology presents an opportunity to improve patient concordance with prescribed therapy, if adequate support is provided to equip patients (and family/carers) with the knowledge needed to utilise the health information available via the portals. Research is needed to understand what a health consumer will use patient portals for and how to support a user to realise the technology's potential.

  3. Portal monitoring technology control process

    International Nuclear Information System (INIS)

    York, R.L.

    1998-01-01

    Portal monitors are an important part of the material protection, control, and accounting (MPC and A) programs in Russia and the US. Although portal monitors are only a part of an integrated MPC and A system, they are an effective means of controlling the unauthorized movement of special nuclear material (SNM). Russian technical experts have gained experience in the use of SNM portal monitors from US experts ad this has allowed them to use the monitors more effectively. Several Russian institutes and companies are designing and manufacturing SNM portal monitors in Russia. Interactions between Russian and US experts have resulted in improvements to the instruments. SNM portal monitor technology has been effectively transferred from the US to Russia and should be a permanent part of the Russian MPC and A Program. Progress in the implementation of the monitors and improvements to how they are used are discussed

  4. Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource.

    Science.gov (United States)

    Sharpton, Thomas J; Jospin, Guillaume; Wu, Dongying; Langille, Morgan G I; Pollard, Katherine S; Eisen, Jonathan A

    2012-10-13

    New computational resources are needed to manage the increasing volume of biological data from genome sequencing projects. One fundamental challenge is the ability to maintain a complete and current catalog of protein diversity. We developed a new approach for the identification of protein families that focuses on the rapid discovery of homologous protein sequences. We implemented fully automated and high-throughput procedures to de novo cluster proteins into families based upon global alignment similarity. Our approach employs an iterative clustering strategy in which homologs of known families are sifted out of the search for new families. The resulting reduction in computational complexity enables us to rapidly identify novel protein families found in new genomes and to perform efficient, automated updates that keep pace with genome sequencing. We refer to protein families identified through this approach as "Sifting Families," or SFams. Our analysis of ~10.5 million protein sequences from 2,928 genomes identified 436,360 SFams, many of which are not represented in other protein family databases. We validated the quality of SFam clustering through statistical as well as network topology-based analyses. We describe the rapid identification of SFams and demonstrate how they can be used to annotate genomes and metagenomes. The SFam database catalogs protein-family quality metrics, multiple sequence alignments, hidden Markov models, and phylogenetic trees. Our source code and database are publicly available and will be subject to frequent updates (http://edhar.genomecenter.ucdavis.edu/sifting_families/).

  5. The use of protein patterns in genetic diversity analysis in some Brassica napus cultivars

    Directory of Open Access Journals (Sweden)

    Roya Razavizadeh

    2013-11-01

    Full Text Available In this study, protein variations of seeds and five-day old cotyledonal leaves of four selected Brassica napus cultivars including Elite, Ocapy, Tasilo and Zarfam were analyzed by SDS-PAGE to identify protein markers. The amount of total soluble protein of seed storage proteins did not show significant differences in all cultivars whereas it was different in cotyledonal leaves. Protein patterns of seeds and cotyledonal leaves showed significant differences using SDS-PAGE and consequence analysis of bands by ImageJ program. Relative expression of six protein bands in seeds and five-day old cotyledonal leaves were significantly different. Three protein markers were identified by protein patterns of seed and cotyledonal leaves. The results of relationship analysis based on presence and absence of the specific protein bands in protein pattern of seed storage proteins showed that Tasilo and Elite cultivars had the highest similarities.

  6. Variation in Orthologous Shell-Forming Proteins Contribute to Molluscan Shell Diversity.

    Science.gov (United States)

    Jackson, Daniel J; Reim, Laurin; Randow, Clemens; Cerveau, Nicolas; Degnan, Bernard M; Fleck, Claudia

    2017-11-01

    Despite the evolutionary success and ancient heritage of the molluscan shell, little is known about the molecular details of its formation, evolutionary origins, or the interactions between the material properties of the shell and its organic constituents. In contrast to this dearth of information, a growing collection of molluscan shell-forming proteomes and transcriptomes suggest they are comprised of both deeply conserved, and lineage specific elements. Analyses of these sequence data sets have suggested that mechanisms such as exon shuffling, gene co-option, and gene family expansion facilitated the rapid evolution of shell-forming proteomes and supported the diversification of this phylum specific structure. In order to further investigate and test these ideas we have examined the molecular features and spatial expression patterns of two shell-forming genes (Lustrin and ML1A2) and coupled these observations with materials properties measurements of shells from a group of closely related gastropods (abalone). We find that the prominent "GS" domain of Lustrin, a domain believed to confer elastomeric properties to the shell, varies significantly in length between the species we investigated. Furthermore, the spatial expression patterns of Lustrin and ML1A2 also vary significantly between species, suggesting that both protein architecture, and the regulation of spatial gene expression patterns, are important drivers of molluscan shell evolution. Variation in these molecular features might relate to certain materials properties of the shells of these species. These insights reveal an important and underappreciated source of variation within shell-forming proteomes that must contribute to the diversity of molluscan shell phenotypes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  7. Clusters of proteins in bio-membranes: insights into the roles of interaction potential shapes and of protein diversity

    OpenAIRE

    Meilhac, Nicolas; Destainville, Nicolas

    2011-01-01

    It has recently been proposed that proteins embedded in lipidic bio-membranes can spontaneously self-organize into stable small clusters, or membrane nano-domains, due to the competition between short-range attractive and longer-range repulsive forces between proteins, specific to these systems. In this paper, we carry on our investigation, by Monte Carlo simulations, of different aspects of cluster phases of proteins in bio-membranes. First, we compare different long-range potentials (includ...

  8. Visualization portal for genetic variation (VizGVar): a tool for interactive visualization of SNPs and somatic mutations in exons, genes and protein domains.

    Science.gov (United States)

    Solano-Román, Antonio; Alfaro-Arias, Verónica; Cruz-Castillo, Carlos; Orozco-Solano, Allan

    2018-03-15

    VizGVar was designed to meet the growing need of the research community for improved genomic and proteomic data viewers that benefit from better information visualization. We implemented a new information architecture and applied user centered design principles to provide a new improved way of visualizing genetic information and protein data related to human disease. VizGVar connects the entire database of Ensembl protein motifs, domains, genes and exons with annotated SNPs and somatic variations from PharmGKB and COSMIC. VizGVar precisely represents genetic variations and their respective location by colored curves to designate different types of variations. The structured hierarchy of biological data is reflected in aggregated patterns through different levels, integrating several layers of information at once. VizGVar provides a new interactive, web-based JavaScript visualization of somatic mutations and protein variation, enabling fast and easy discovery of clinically relevant variation patterns. VizGVar is accessible at http://vizport.io/vizgvar; http://vizport.io/vizgvar/doc/. asolano@broadinstitute.org or allan.orozcosolano@ucr.ac.cr.

  9. Protein Profiles Reveal Diverse Responsive Signaling Pathways in Kernels of Two Maize Inbred Lines with Contrasting Drought Sensitivity

    Directory of Open Access Journals (Sweden)

    Liming Yang

    2014-10-01

    Full Text Available Drought stress is a major factor that contributes to disease susceptibility and yield loss in agricultural crops. To identify drought responsive proteins and explore metabolic pathways involved in maize tolerance to drought stress, two maize lines (B73 and Lo964 with contrasting drought sensitivity were examined. The treatments of drought and well water were applied at 14 days after pollination (DAP, and protein profiles were investigated in developing kernels (35 DAP using iTRAQ (isobaric tags for relative and absolute quantitation. Proteomic analysis showed that 70 and 36 proteins were significantly altered in their expression under drought treatments in B73 and Lo964, respectively. The numbers and levels of differentially expressed proteins were generally higher in the sensitive genotype, B73, implying an increased sensitivity to drought given the function of the observed differentially expressed proteins, such as redox homeostasis, cell rescue/defense, hormone regulation and protein biosynthesis and degradation. Lo964 possessed a more stable status with fewer differentially expressed proteins. However, B73 seems to rapidly initiate signaling pathways in response to drought through adjusting diverse defense pathways. These changes in protein expression allow for the production of a drought stress-responsive network in maize kernels.

  10. New ICPP portal monitor

    International Nuclear Information System (INIS)

    Georgeson, M.A.; Nichols, C.E.

    1981-04-01

    A large area gas filled proportional-detector portal monitor mounted in a swinging door frame has been designed and developed at the Idaho Chemical Processing Plant (ICPP). This monitor extends the sensitivity and speed of personnel contamination detection to levels equal to or exceeding that obtained using hand-held portable survey techniques. The new monitor has state-of-the-art electronics which result in rapid response, and use statistical principles in the alarm logic to reduce or eliminate spurious alarms. In addition, the evaluation of this instrument indicates that it will detect small enough quantities of U-235 in shielded containers to meet current special nuclear materials (SNM) detection standards. Simultaneous detection of very low level contamination and small quantities of SNM results in a monitor particularly useful for nuclear installations

  11. Congestive index of portal vein

    International Nuclear Information System (INIS)

    Kim, Won Ho; Kim, H. K.; Lee, S. C.; Han, S. H.; Han, K. H.; Chung, J. B.; Choi, H. J.

    1989-01-01

    In patients with portal hypertension, the blood flow volume is maintained despite decreased blood flow velocity due to enlargement of the vascular cross sectional area. Thus, the 'congestion index' of the portal vein, which is the ratio between the cross sectional area (cm2) and the blood flow velocity (cm/sec) determined by a Doppler ultrasonography, may be a sensitive index by which to assess portal hypertension. We performed Doppler ultrasonography on 24 normal subjects, 14 patients with biopsy proved chronic active hepatitis and 55 patients with liver cirrhosis in order to assess the diagnostic value of the congestion index. The cross sectional area of the portal vein was significantly enlarged and the mean blood flow velocity was significantly reduced in patients with liver cirrhosis compared with controls. However, the blood flow volume was no difference. The congestion index of the portal vein was significantly increased in patients with liver cirrhosis (0.113+0.035) compared with patients with chronic active hepatitis(0.078+0.029) (p<0.001) and controls (0.053+0.016) (p<0.001). The sensitivity, specificity and predictability of the congestion index for detection of patients with the cirrhosis of the liver were 76.4%, 100% and 100% respectively, when the normal range was set at mean+2SD. The results suggest that the congestion index of the portal vein may pla a significant role in diagnosis of portal hypertensive patients

  12. Structural and regulatory diversity shape HLA-C protein expression levels

    DEFF Research Database (Denmark)

    Kaur, Gurman; Gras, Stephanie; Mobbs, Jesse I

    2017-01-01

    expression of HLA-C allomorphs at the cell surface by influencing the structure of the peptide-binding cleft and the diversity of peptides bound by the HLA-C molecules. Together with a phylogenetic analysis, these results highlight the diversity and long-term balancing selection of regulatory factors...

  13. A polyvalent hybrid protein elicits antibodies against the diverse allelic types of block 2 in Plasmodium falciparum merozoite surface protein 1.

    Science.gov (United States)

    Tetteh, Kevin K A; Conway, David J

    2011-10-13

    Merozoite surface protein 1 (MSP1) of Plasmodium falciparum has been implicated as an important target of acquired immunity, and candidate components for a vaccine include polymorphic epitopes in the N-terminal polymorphic block 2 region. We designed a polyvalent hybrid recombinant protein incorporating sequences of the three major allelic types of block 2 together with a composite repeat sequence of one of the types and N-terminal flanking T cell epitopes, and compared this with a series of recombinant proteins containing modular sub-components and similarly expressed in Escherichia coli. Immunogenicity of the full polyvalent hybrid protein was tested in both mice and rabbits, and comparative immunogenicity studies of the sub-component modules were performed in mice. The full hybrid protein induced high titre antibodies against each of the major block 2 allelic types expressed as separate recombinant proteins and against a wide range of allelic types naturally expressed by a panel of diverse P. falciparum isolates, while the sub-component modules had partial antigenic coverage as expected. This encourages further development and evaluation of the full MSP1 block 2 polyvalent hybrid protein as a candidate blood-stage component of a malaria vaccine. Copyright © 2011 Elsevier Ltd. All rights reserved.

  14. The NUCLEONICA Nuclear Science Portal

    International Nuclear Information System (INIS)

    Magill, Joseph; Dreher, Raymond

    2009-01-01

    NUCLEONICA (www.nucleonica.net) is a new nuclear science web portal which provides a customisable, integrated environment and collaboration platform using the latest internet 'Web 2.0' technology. NUCLEONICA is aimed at professionals, academics and students working in nuclear power, health physics and radiation protection, nuclear and radio-chemistry, and astrophysics. A unique feature of the portal is the wide range of user friendly web-based nuclear science applications. The portal is also ideal for education and training purposes and as a knowledge management platform to preserve nuclear knowledge built up over many decades.

  15. Information Portal Costs and Benefits

    Directory of Open Access Journals (Sweden)

    Lorena BATAGAN

    2006-01-01

    Full Text Available All transformations of our society are the product of the large use of Information and Communications Technologies (ICT and Internet. ICT are technologies which facilitate communication, processing, and transmission of information by electronic means. It is very important to use the new technologies to the correct value because this determinate an increase of global benefits. Portal provides a consistent way to select, evaluate, prioritize and plan the right information. In research we point the important costs and benefits for an informational portal. The portal for local administrative determinate for citizens the access to information of interest and on the other hand make easier for employer to manage the documents.

  16. The Higgs Portal and Cosmology

    Energy Technology Data Exchange (ETDEWEB)

    Assamagan, Ketevi [Brookhaven National Lab. (BNL), Upton, NY (United States); Chen, Chien-Yi [Perimeter Inst. for Theoretical Physics, Waterloo, ON (Canada); Univ. of Victoria, BC (Canada); Chou, John Paul [Rutgers Univ., Piscataway, NJ (United States); Curtin, David [Univ. of Maryland, College Park, MD (United States); Fedderke, Michael A. [Univ. of Chicago, IL (United States); Gershtein, Yuri [Rutgers Univ., Piscataway, NJ (United States); He, Xiao-Gang [Shanghai Jiao Tong Univ. (China); Klute, Markus [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Kozaczuk, Jonathon [TRIUMF, Vancouver, BC (Canada); Kotwal, Ashutosh [Duke Univ., Durham, NC (United States); Lowette, Steven [Vrije Univ., Brussels (Belgium); No, Jose Miguel [Univ. of Sussex, Brighton (United Kingdom); Plehn, Tilman [Heidelberg Univ. (Germany); Qian, Jianming [Univ. of Michigan, Ann Arbor, MI (United States); Ramsey-Musolf, Michael [Univ. of Massachusetts, Amherst, MA (United States); Safonov, Alexei [Texas A & M Univ., College Station, TX (United States); Shelton, Jessie [Univ. of Illinois, Urbana-Champaign, IL (United States); Spannowsky, Michael [Durham Univ. (United Kingdom); Su, Shufang [Univ. of Arizona, Tucson, AZ (United States); Walker, Devin G. E. [Univ. of Washington, Seattle, WA (United States); Willocq, Stephane [Univ. of Massachusetts, Amherst, MA (United States); Winslow, Peter [Univ. of Massachusetts, Amherst, MA (United States)

    2016-04-18

    Higgs portal interactions provide a simple mechanism for addressing two open problems in cosmology: dark matter and the baryon asymmetry. In the latter instance, Higgs portal interactions may contain the ingredients for a strong first-order electroweak phase transition as well as new CP-violating interactions as needed for electroweak baryogenesis. These interactions may also allow for a viable dark matter candidate. We survey the opportunities for probing the Higgs portal as it relates to these questions in cosmology at the LHC and possible future colliders.

  17. Three-dimensional Structure of a Viral Genome-delivery Portal Vertex

    Energy Technology Data Exchange (ETDEWEB)

    A Olia; P Prevelige Jr.; J Johnson; G Cingolani

    2011-12-31

    DNA viruses such as bacteriophages and herpesviruses deliver their genome into and out of the capsid through large proteinaceous assemblies, known as portal proteins. Here, we report two snapshots of the dodecameric portal protein of bacteriophage P22. The 3.25-{angstrom}-resolution structure of the portal-protein core bound to 12 copies of gene product 4 (gp4) reveals a {approx}1.1-MDa assembly formed by 24 proteins. Unexpectedly, a lower-resolution structure of the full-length portal protein unveils the unique topology of the C-terminal domain, which forms a {approx}200-{angstrom}-long {alpha}-helical barrel. This domain inserts deeply into the virion and is highly conserved in the Podoviridae family. We propose that the barrel domain facilitates genome spooling onto the interior surface of the capsid during genome packaging and, in analogy to a rifle barrel, increases the accuracy of genome ejection into the host cell.

  18. IOOS Data Portals and Uniform On-line Browse Capabilities

    Science.gov (United States)

    Howard, M.; Currier, R. D.; Kobara, S.; Gayanilo, F.

    2015-12-01

    The Gulf of Mexico Coastal Ocean Observing System Regional Association (GCOOS-RA) is one of eleven Regional Associations organized under the NOAA-led U.S. Integrated Ocean Observing System (IOOS) Program Office. Each of the RAs operate standards-based regional data portals designed to aggregate near real-time and historical observed data and modeled outputs from distributed providers and to offer these and derived products in standardized ways to a diverse set of users. The RA's portals are based on the IOOS Data and Communications Plan which describes the functional elements needed for an interoperable system. One of these elements is called "Uniform On-line Browse" which is an informational service designed primarily to visualize the inventory of a portal. An on-line browse service supports the end user's need to discover what parameters are available, to learn the spatial and temporal extend of the holdings, and to examine the character of the data (e.g, variability, gappiness, etc). These pieces of information help the end user decide if the data are fit for his/her purpose and to construct valid data requests. Note that on-line browse is a distinctly different activity than data analysis because it seeks to yield knowledge about the inventory and not about what the data mean. "Uniform" on-line browse is a service that takes advantage of the standardization of the data portal's data access points. Most portals represent station locations on a map. This is a view of the data inventory but these plots are rarely generated by pulling data through the standards-based services offered to the end users but through methods only available to the portal programmers. This work will present results of Uniform On-line browse tools developed within GCOOS-RA and their applicability to other RA portals.

  19. Diversity Within the O-linked Protein Glycosylation Systems of Acinetobacter Species

    DEFF Research Database (Denmark)

    Scott, N. E.; Kinsella, R. L.; Edwards, A. V. G.

    2014-01-01

    nature of glycan biogenesis we investigated the composition, diversity, and properties of the Acinetobacter glycoproteome. Utilizing global and targeted mass spectrometry methods, we examined 15 strains and found extensive glycan diversity in the O-linked glycoproteome of Acinetobacter. Comparison......-linked glycosylation favors short (three to five residue) glycans with limited branching containing negatively charged sugars such as GlcNAc3NAcA4OAc or legionaminic/pseudaminic acid derivatives. These observations suggest that although highly diverse, the capsule/O-linked glycan biosynthetic pathways generate glycans...

  20. Short Linear Sequence Motif LxxPTPh Targets Diverse Proteins to Growing Microtubule Ends

    NARCIS (Netherlands)

    Kumar, Anil; Manatschal, Cristina; Rai, Ankit; Grigoriev, Ilya; Degen, Miriam Steiner; Jaussi, Rolf; Kretzschmar, Ines; Prota, Andrea E; Volkmer, Rudolf; Kammerer, Richard A.; Akhmanova, Anna; Steinmetz, Michel O.

    2017-01-01

    Microtubule plus-end tracking proteins (+TIPs) are involved in virtually all microtubule-based processes. End-binding (EB) proteins are considered master regulators of +TIP interaction networks, since they autonomously track growing microtubule ends and recruit a plethora of proteins to this

  1. Climate Outreach Using Regional Coastal Ocean Observing System Portals

    Science.gov (United States)

    Anderson, D. M.; Hernandez, D. L.; Wakely, A.; Bochenek, R. J.; Bickel, A.

    2015-12-01

    Coastal oceans are dynamic, changing environments affected by processes ranging from seconds to millennia. On the east and west coast of the U.S., regional observing systems have deployed and sustained a remarkable diverse array of observing tools and sensors. Data portals visualize and provide access to real-time sensor networks. Portals have emerged as an interactive tool for educators to help students explore and understand climate. Bringing data portals to outreach events, into classrooms, and onto tablets and smartphones enables educators to address topics and phenomena happening right now. For example at the 2015 Charleston Science Technology Engineering and Math (STEM) Festival, visitors navigated the SECOORA (Southeast Coastal Ocean Observing regional Association) data portal to view the real-time marine meteorological conditions off South Carolina. Map-based entry points provide an intuitive interface for most students, an array of time series and other visualizations depict many of the essential principles of climate science manifest in the coastal zone, and data down-load/ extract options provide access to the data and documentation for further inquiry by advanced users. Beyond the exposition of climate principles, the portal experience reveals remarkable technologies in action and shows how the observing system is enabled by the activity of many different partners.

  2. Genomics Portals: integrative web-platform for mining genomics data.

    Science.gov (United States)

    Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario

    2010-01-13

    A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

  3. Genomics Portals: integrative web-platform for mining genomics data

    Directory of Open Access Journals (Sweden)

    Ghosh Krishnendu

    2010-01-01

    Full Text Available Abstract Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc, and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

  4. LDL receptor-related protein 1 regulates the abundance of diverse cell-signaling proteins in the plasma membrane proteome.

    Science.gov (United States)

    Gaultier, Alban; Simon, Gabriel; Niessen, Sherry; Dix, Melissa; Takimoto, Shinako; Cravatt, Benjamin F; Gonias, Steven L

    2010-12-03

    LDL receptor-related protein 1 (LRP1) is an endocytic receptor, reported to regulate the abundance of other receptors in the plasma membrane, including uPAR and tissue factor. The goal of this study was to identify novel plasma membrane proteins, involved in cell-signaling, that are regulated by LRP1. Membrane protein ectodomains were prepared from RAW 264.7 cells in which LRP1 was silenced and control cells using protease K. Peptides were identified by LC-MS/MS. By analysis of spectral counts, 31 transmembrane and secreted proteins were regulated in abundance at least 2-fold when LRP1 was silenced. Validation studies confirmed that semaphorin4D (Sema4D), plexin domain-containing protein-1 (Plxdc1), and neuropilin-1 were more abundant in the membranes of LRP1 gene-silenced cells. Regulation of Plxdc1 by LRP1 was confirmed in CHO cells, as a second model system. Plxdc1 coimmunoprecipitated with LRP1 from extracts of RAW 264.7 cells and mouse liver. Although Sema4D did not coimmunoprecipitate with LRP1, the cell-surface level of Sema4D was increased by RAP, which binds to LRP1 and inhibits binding of other ligands. These studies identify Plxdc1, Sema4D, and neuropilin-1 as novel LRP1-regulated cell-signaling proteins. Overall, LRP1 emerges as a generalized regulator of the plasma membrane proteome.

  5. Chaperoning Proteins for Destruction: Diverse Roles of Hsp70 Chaperones and their Co-Chaperones in Targeting Misfolded Proteins to the Proteasome

    Directory of Open Access Journals (Sweden)

    Ayala Shiber

    2014-07-01

    Full Text Available Molecular chaperones were originally discovered as heat shock-induced proteins that facilitate proper folding of proteins with non-native conformations. While the function of chaperones in protein folding has been well documented over the last four decades, more recent studies have shown that chaperones are also necessary for the clearance of terminally misfolded proteins by the Ub-proteasome system. In this capacity, chaperones protect misfolded degradation substrates from spontaneous aggregation, facilitate their recognition by the Ub ligation machinery and finally shuttle the ubiquitylated substrates to the proteasome. The physiological importance of these functions is manifested by inefficient proteasomal degradation and the accumulation of protein aggregates during ageing or in certain neurodegenerative diseases, when chaperone levels decline. In this review, we focus on the diverse roles of stress-induced chaperones in targeting misfolded proteins to the proteasome and the consequences of their compromised activity. We further discuss the implications of these findings to the identification of new therapeutic targets for the treatment of amyloid diseases.

  6. Ozone (Environmental Health Student Portal)

    Science.gov (United States)

    Skip Navigation National Library of Medicine Environmental Health Student Portal Connecting Middle School Students to Environmental Health Information Menu Home Air Pollution Air Pollution Home Indoor Air Pollution Outdoor ...

  7. Pesticides (Environmental Health Student Portal)

    Science.gov (United States)

    Skip Navigation National Library of Medicine Environmental Health Student Portal Connecting Middle School Students to Environmental Health Information Menu Home Air Pollution Air Pollution Home Indoor Air Pollution Outdoor ...

  8. Radioisotopic evaluation of portal circulation

    International Nuclear Information System (INIS)

    Maliska, C.; Rosenthal, D.

    1986-01-01

    The use of a radio-tracer of portal circulation through the intestine, should prevent cruel punctures in the portal-vein or spleen as it is usually the case with traditional methods in the study of portal-system. The absorption of I-131 and Tc-99m, previously cheked in rabbits presented similar results in dogs. The time of circulation between terminal large-intestine and the liver (t-RF) was determined by external counting at hepatic level by recording radioactivity variation-time. In healthy animals the t-RF was from 20to 60 seconds, with average time of 42 seconds. In 2 animals with partial binding of portal-vein the t-RF went up to 110 and 120 seconds. (Author) [pt

  9. Automated Classification of Consumer Health Information Needs in Patient Portal Messages

    Science.gov (United States)

    Cronin, Robert M.; Fabbri, Daniel; Denny, Joshua C.; Jackson, Gretchen Purcell

    2015-01-01

    Patients have diverse health information needs, and secure messaging through patient portals is an emerging means by which such needs are expressed and met. As patient portal adoption increases, growing volumes of secure messages may burden healthcare providers. Automated classification could expedite portal message triage and answering. We created four automated classifiers based on word content and natural language processing techniques to identify health information needs in 1000 patient-generated portal messages. Logistic regression and random forest classifiers detected single information needs well, with area under the curves of 0.804–0.914. A logistic regression classifier accurately found the set of needs within a message, with a Jaccard index of 0.859 (95% Confidence Interval: (0.847, 0.871)). Automated classification of consumer health information needs expressed in patient portal messages is feasible and may allow direct linking to relevant resources or creation of institutional resources for commonly expressed needs. PMID:26958285

  10. Automated Classification of Consumer Health Information Needs in Patient Portal Messages.

    Science.gov (United States)

    Cronin, Robert M; Fabbri, Daniel; Denny, Joshua C; Jackson, Gretchen Purcell

    2015-01-01

    Patients have diverse health information needs, and secure messaging through patient portals is an emerging means by which such needs are expressed and met. As patient portal adoption increases, growing volumes of secure messages may burden healthcare providers. Automated classification could expedite portal message triage and answering. We created four automated classifiers based on word content and natural language processing techniques to identify health information needs in 1000 patient-generated portal messages. Logistic regression and random forest classifiers detected single information needs well, with area under the curves of 0.804-0.914. A logistic regression classifier accurately found the set of needs within a message, with a Jaccard index of 0.859 (95% Confidence Interval: (0.847, 0.871)). Automated classification of consumer health information needs expressed in patient portal messages is feasible and may allow direct linking to relevant resources or creation of institutional resources for commonly expressed needs.

  11. Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource

    Directory of Open Access Journals (Sweden)

    Sharpton Thomas J

    2012-10-01

    Full Text Available Abstract Background New computational resources are needed to manage the increasing volume of biological data from genome sequencing projects. One fundamental challenge is the ability to maintain a complete and current catalog of protein diversity. We developed a new approach for the identification of protein families that focuses on the rapid discovery of homologous protein sequences. Results We implemented fully automated and high-throughput procedures to de novo cluster proteins into families based upon global alignment similarity. Our approach employs an iterative clustering strategy in which homologs of known families are sifted out of the search for new families. The resulting reduction in computational complexity enables us to rapidly identify novel protein families found in new genomes and to perform efficient, automated updates that keep pace with genome sequencing. We refer to protein families identified through this approach as “Sifting Families,” or SFams. Our analysis of ~10.5 million protein sequences from 2,928 genomes identified 436,360 SFams, many of which are not represented in other protein family databases. We validated the quality of SFam clustering through statistical as well as network topology–based analyses. Conclusions We describe the rapid identification of SFams and demonstrate how they can be used to annotate genomes and metagenomes. The SFam database catalogs protein-family quality metrics, multiple sequence alignments, hidden Markov models, and phylogenetic trees. Our source code and database are publicly available and will be subject to frequent updates (http://edhar.genomecenter.ucdavis.edu/sifting_families/.

  12. Heart/liver ratios and portal vein pressure used in early cirrhosis diagnosis

    International Nuclear Information System (INIS)

    He Jingxiang; Li Wenfan; Liu Chun; Yang Peng; Chen Ming; Wang Hong

    2001-01-01

    Objective: To find a method which not only can comprehensively evaluate the rise of portal pressure, opening and establishment of portal collateral circulation, portal-systemic shunting, and liver and spleen functions in cirrhosis, but also aid the differential diagnosis of early and established cirrhosis. Methods: Heart/liver count (H/L) ratios were obtained at different times after per-rectal administration of 99m Tc-MIBI. Portal venous pressures at different times were calculated using a previously documented formula. The relationship between portal venous pressure and cirrhosis, including its pathological process, was then evaluated. Results: There was obvious discrepancy (t=2.810; p<0.05) in 90-150 minutes portal venous pressures between normal and late hepatitis groups; there was also obvious difference (t=2.348, p<0.05) in portal venous pressures between the cirrhosis group and other groups. The portal venous pressure of early cirrhosis group was also significantly different (t=2.167, p<0.05) from other groups and it was situated between those of normal, and hepatitis and cirrhosis groups. There was obvious diversity (t=2.287, p<0.05) in Child-Pugh classification levels in the late imaging phase. There was positive correlation between calculated portal venous pressure and H/L ratio (r=0.487, p<0.01). Conclusion: Using temporal portal venous recirculation imaging, an early H/L ratio of ≥0.65 and formula-calculated portal venous pressure of ≥1.9 kPa or a portal-systemic venous pressure difference of ≥1.5 kPa indicate cirrhosis; H/L ratio between 0.32 and 0.64 or portal venous pressure between 1.03 to 1.89 kPa suggest early cirrhosis. Our study showed that H/L ratios at specific times and computed portal vein pressure might be important in the diagnosis of hepatitis, impaired hepatic function caused by cirrhosis, portal-systemic shunting, and portal venous recirculation. It is a simple, sensitive, reliable, and non-invasive method, which can be helpful in

  13. Genetic diversity and structure analysis based on hordein protein polymorphism in barley landrace populations from jordan

    International Nuclear Information System (INIS)

    Baloch, A.W.; Ali, M.; Baloch, A.M.; Mangan, B.U.N.; Song, W

    2014-01-01

    Jordan is unanimously considered to be one of the centers of genetic diversity for barley, where wild and landraces of barley has been grown under different climatic conditions. The genetic diversity and genetic structure based on hordein polymorphism was assessed in 90 different accessions collected from four different sites of Jordan. A-PAGE was used to reveal hordein polymorphism among the genotypes. A total of 29 distinct bands were identified, out of them 9 bands were distinguished for D, 11 for C, and 9 for the B hordein regions. The observed genetic similarity was an exceptionally high between the populations than expected, which is probably due to high gene flow estimated between them. The genetic diversity parameters were not differ largely among the populations, indicating that local selection of a particular site did not play a key role in shaping genetic diversity. Analysis of molecular variance (AMOVA) revealed significant population structure when accessions were structured according to population site. There was 94% of hordein variation resided within the populations and only 8% present among the populations. Both Bayesian and Principale Coordinate Analysis (PCoA) concordantly demonstrated admixture genotypes of the landraces barley populations. Consequently, none of the population found to be clustered separately according to its population site. It is concluded that this approach can be useful to explore the germplasm for genetic diversity but perhaps is not suitable for determining phylogenic relations in barley. (author)

  14. Genetic diversity of plasmodium vivax merozoite surface protein-3alpha (Pvmsp-3alpha) gene in Jhapa District of Nepal.

    Science.gov (United States)

    Adhikari, Madhav; Ranjitkar, Samir; Schousboe, Mette Leth; Alifrangis, Michael; Imwong, Mallika; Bhatta, Dwij Raj; Banjara, Megha Raj

    2012-03-01

    In Nepal, Plasmodium vivax accounts for approximately 80-90% of the malaria cases, but limited studies have been conducted on the genetic diversity of this parasite population. This study was carried out to determine the genetic diversity of P. vivax population sampled from subjects living in an endemic area of Jhapa District by analyzing the polymorphic merozoite surface protein-3alpha (Pvmsp-3alpha) gene by using PCR-restriction fragment length polymorphism. Three distinct genotypes were obtained from 96 samples; type A: 40 (71%), type B: 7 (13%), and type C: 9 (16%) which could be categorized into 13 allelic patterns: A1-A9, B1, B2, C1 and C2. These results indicated a high genetic diversity within the studied P. vivax population. As the transmission rate of malaria is low in Nepal, the diversity is most likely due to migration of people between the malaria endemic regions, either within the country or between Nepal and India. Similar prevalence of the three genotypes of Pvmsp-3alpha between the two countries likely supports the latter explanation.

  15. PolarPortal.org Communicates Real-Time Developments in the Arctic

    Science.gov (United States)

    Langen, P. L.; Andersen, S. B.; Andersen, K. K.; Andersen, M. L.; Ahlstrom, A. P.; van As, D.; Barletta, V. R.; Box, J. E.; Citterio, M.; Colgan, W. T.; Dybkjær, G.; Forsberg, R.; Høyer, J. L.; Jensen, M. B.; Kliem, N.; Mottram, R.; Nielsen, K. P.; Olesen, M.; Quaglia, F. C.; Rasmussen, T. A.; Rodehacke, C. B.; Stendel, M.; Sandberg Sørensen, L.; Tonboe, R. T.

    2014-12-01

    PolarPortal.org was launched in June 2013 by a consortium of Danish institutions, including the Danish Meteorological Institute (DMI), the Geological Survey of Denmark and Greenland (GEUS) and the National Space Institute at the Technical University of Denmark (DTU-Space). Polar Portal is a single web portal presenting a wide range of near real-time information on both the Greenland ice sheet and Arctic sea-ice in a format geared for non-specialists. Polar Portal aims to meet widespread public interest in a diverse range of climate-cryosphere processes in the Arctic: What is the present Greenland ice sheet contribution to sea level rise? How quickly are outlet glaciers retreating or advancing right now? How extensive is Arctic sea-ice or how warm is the Arctic Ocean at this moment? Although public interest in such topics is widely acknowledged, an important primary task for the scientists behind Polar Portal was collaborating with media specialists to establish the knowledge range of the general public on these topics, in order for Polar Portal to appropriately present useful climate-cryosphere information. Consequently, Polar Portal is designed in a highly visual exploratory format, where individual data products are accompanied by plain written summaries, with hyperlinks to relevant journal papers for more scrutinizing users. Numerous satellite and in situ observations, together with model output, are channeled daily into the Greenland ice sheet and Arctic sea-ice divisions of Polar Portal.

  16. Heterogeneous genetic diversity pattern in Plasmodium vivax genes encoding merozoite surface proteins (MSP) -7E, -7F and -7L.

    Science.gov (United States)

    Garzón-Ospina, Diego; Forero-Rodríguez, Johanna; Patarroyo, Manuel A

    2014-12-13

    The msp-7 gene has become differentially expanded in the Plasmodium genus; Plasmodium vivax has the highest copy number of this gene, several of which encode antigenic proteins in merozoites. DNA sequences from thirty-six Colombian clinical isolates from P. vivax (pv) msp-7E, -7F and -7L genes were analysed for characterizing and studying the genetic diversity of these pvmsp-7 members which are expressed during the intra-erythrocyte stage; natural selection signals producing the variation pattern so observed were evaluated. The pvmsp-7E gene was highly polymorphic compared to pvmsp-7F and pvmsp-7L which were seen to have limited genetic diversity; pvmsp-7E polymorphism was seen to have been maintained by different types of positive selection. Even though these copies seemed to be species-specific duplications, a search in the Plasmodium cynomolgi genome (P. vivax sister taxon) showed that both species shared the whole msp-7 repertoire. This led to exploring the long-term effect of natural selection by comparing the orthologous sequences which led to finding signatures for lineage-specific positive selection. The results confirmed that the P. vivax msp-7 family has a heterogeneous genetic diversity pattern; some members are highly conserved whilst others are highly diverse. The results suggested that the 3'-end of these genes encode MSP-7 proteins' functional region whilst the central region of pvmsp-7E has evolved rapidly. The lineage-specific positive selection signals found suggested that mutations occurring in msp-7s genes during host switch may have succeeded in adapting the ancestral P. vivax parasite population to humans.

  17. A FREQUENCY-BASED LINGUISTIC APPROACH TO PROTEIN DECODING AND DESIGN: SIMPLE CONCEPTS, DIVERSE APPLICATIONS, AND THE SCS PACKAGE

    Directory of Open Access Journals (Sweden)

    Kenta Motomura

    2013-02-01

    Full Text Available Protein structure and function information is coded in amino acid sequences. However, the relationship between primary sequences and three-dimensional structures and functions remains enigmatic. Our approach to this fundamental biochemistry problem is based on the frequencies of short constituent sequences (SCSs or words. A protein amino acid sequence is considered analogous to an English sentence, where SCSs are equivalent to words. Availability scores, which are defined as real SCS frequencies in the non-redundant amino acid database relative to their probabilistically expected frequencies, demonstrate the biological usage bias of SCSs. As a result, this frequency-based linguistic approach is expected to have diverse applications, such as secondary structure specifications by structure-specific SCSs and immunological adjuvants with rare or non-existent SCSs. Linguistic similarities (e.g., wide ranges of scale-free distributions and dissimilarities (e.g., behaviors of low-rank samples between proteins and the natural English language have been revealed in the rank-frequency relationships of SCSs or words. We have developed a web server, the SCS Package, which contains five applications for analyzing protein sequences based on the linguistic concept. These tools have the potential to assist researchers in deciphering structurally and functionally important protein sites, species-specific sequences, and functional relationships between SCSs. The SCS Package also provides researchers with a tool to construct amino acid sequences de novo based on the idiomatic usage of SCSs.

  18. A frequency-based linguistic approach to protein decoding and design: Simple concepts, diverse applications, and the SCS Package

    Science.gov (United States)

    Motomura, Kenta; Nakamura, Morikazu; Otaki, Joji M.

    2013-01-01

    Protein structure and function information is coded in amino acid sequences. However, the relationship between primary sequences and three-dimensional structures and functions remains enigmatic. Our approach to this fundamental biochemistry problem is based on the frequencies of short constituent sequences (SCSs) or words. A protein amino acid sequence is considered analogous to an English sentence, where SCSs are equivalent to words. Availability scores, which are defined as real SCS frequencies in the non-redundant amino acid database relative to their probabilistically expected frequencies, demonstrate the biological usage bias of SCSs. As a result, this frequency-based linguistic approach is expected to have diverse applications, such as secondary structure specifications by structure-specific SCSs and immunological adjuvants with rare or non-existent SCSs. Linguistic similarities (e.g., wide ranges of scale-free distributions) and dissimilarities (e.g., behaviors of low-rank samples) between proteins and the natural English language have been revealed in the rank-frequency relationships of SCSs or words. We have developed a web server, the SCS Package, which contains five applications for analyzing protein sequences based on the linguistic concept. These tools have the potential to assist researchers in deciphering structurally and functionally important protein sites, species-specific sequences, and functional relationships between SCSs. The SCS Package also provides researchers with a tool to construct amino acid sequences de novo based on the idiomatic usage of SCSs. PMID:24688703

  19. DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats.

    Science.gov (United States)

    de Lange, Orlando; Wolf, Christina; Thiel, Philipp; Krüger, Jens; Kleusch, Christian; Kohlbacher, Oliver; Lahaye, Thomas

    2015-11-16

    Transcription Activator-Like Effectors (TALEs) of Xanthomonas bacteria are programmable DNA binding proteins with unprecedented target specificity. Comparative studies into TALE repeat structure and function are hindered by the limited sequence variation among TALE repeats. More sequence-diverse TALE-like proteins are known from Ralstonia solanacearum (RipTALs) and Burkholderia rhizoxinica (Bats), but RipTAL and Bat repeats are conserved with those of TALEs around the DNA-binding residue. We study two novel marine-organism TALE-like proteins (MOrTL1 and MOrTL2), the first to date of non-terrestrial origin. We have assessed their DNA-binding properties and modelled repeat structures. We found that repeats from these proteins mediate sequence specific DNA binding conforming to the TALE code, despite low sequence similarity to TALE repeats, and with novel residues around the BSR. However, MOrTL1 repeats show greater sequence discriminating power than MOrTL2 repeats. Sequence alignments show that there are only three residues conserved between repeats of all TALE-like proteins including the two new additions. This conserved motif could prove useful as an identifier for future TALE-likes. Additionally, comparing MOrTL repeats with those of other TALE-likes suggests a common evolutionary origin for the TALEs, RipTALs and Bats. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Cold and Heat Stress Diversely Alter Both Cauliflower Respiration and Distinct Mitochondrial Proteins Including OXPHOS Components and Matrix Enzymes

    Science.gov (United States)

    Rurek, Michał; Czołpińska, Magdalena; Pawłowski, Tomasz Andrzej; Krzesiński, Włodzimierz; Spiżewski, Tomasz

    2018-01-01

    Complex proteomic and physiological approaches for studying cold and heat stress responses in plant mitochondria are still limited. Variations in the mitochondrial proteome of cauliflower (Brassica oleracea var. botrytis) curds after cold and heat and after stress recovery were assayed by two-dimensional polyacrylamide gel electrophoresis (2D PAGE) in relation to mRNA abundance and respiratory parameters. Quantitative analysis of the mitochondrial proteome revealed numerous stress-affected protein spots. In cold, major downregulations in the level of photorespiratory enzymes, porine isoforms, oxidative phosphorylation (OXPHOS) and some low-abundant proteins were observed. In contrast, carbohydrate metabolism enzymes, heat-shock proteins, translation, protein import, and OXPHOS components were involved in heat response and recovery. Several transcriptomic and metabolic regulation mechanisms are also suggested. Cauliflower plants appeared less susceptible to heat; closed stomata in heat stress resulted in moderate photosynthetic, but only minor respiratory impairments, however, photosystem II performance was unaffected. Decreased photorespiration corresponded with proteomic alterations in cold. Our results show that cold and heat stress not only operate in diverse modes (exemplified by cold-specific accumulation of some heat shock proteins), but exert some associations at molecular and physiological levels. This implies a more complex model of action of investigated stresses on plant mitochondria. PMID:29547512

  1. Plasmodium falciparum Erythrocyte Membrane Protein 1 Diversity in Seven Genomes – Divide and Conquer

    DEFF Research Database (Denmark)

    Rask, Thomas Salhøj; Hansen, Daniel Aaen; Theander, Thor G.

    2010-01-01

    of a PfEMP1 based vaccine mimicking natural acquired immunity depends on a thorough understanding of the evolved PfEMP1 diversity, balancing antigenic variation against conserved receptor binding affinities. This study redefines and reclassifies the domains of PfEMP1 from seven genomes. Analysis...

  2. Portal pressure correlated to visceral circulation times

    Energy Technology Data Exchange (ETDEWEB)

    Friman, L [Serafimerlasarettet, Stockholm (Sweden)

    1979-01-01

    Visceral angiography was performed in 7 patients with normal portal pressure and in 10 with portal hypertension. Circulation times, size of vessels and portal pressure were determined. At celiac angiography, a direct correlation was found between time for maximum filling of portal vein and portal pressure, provided no vascular abnormalities existed. At superior mesenteric angiography such a correlation was not found; loss of flow by shunts in portal hypertension being one explanation. Portocaval shunts are common in the celiac system, but uncommon in the superior mesenteric system.

  3. Portal pressure correlated to visceral circulation times

    International Nuclear Information System (INIS)

    Friman, L.

    1979-01-01

    Visceral angiography was performed in 7 patients with normal portal pressure and in 10 with portal hypertension. Circulation times, size of vessels and portal pressure were determined. At celiac angiography, a direct correlation was found between time for maximum filling of portal vein and portal pressure, provided no vascular abnormalities existed. At superior mesenteric angiography such a correlation was not found; loss of flow by shunts in portal hypertension being one explanation. Portocaval shunts are common in the celiac system, but uncommon in the superior mesenteric system. (Auth.)

  4. Catalytic diversity and homotropic allostery of two Cytochrome P450 monooxygenase like proteins from Trichoderma brevicompactum.

    Science.gov (United States)

    Hussain, Razak; Kumari, Indu; Sharma, Shikha; Ahmed, Mushtaq; Khan, Tabreiz Ahmad; Akhter, Yusuf

    2017-12-01

    Trichothecenes are the secondary metabolites produced by Trichoderma spp. Some of these molecules have been reported for their ability to stimulate plant growth by suppressing plant diseases and hence enabling Trichoderma spp. to be efficiently used as biocontrol agents in modern agriculture. Many of the proteins involved in the trichothecenes biosynthetic pathway in Trichoderma spp. are encoded by the genes present in the tri cluster. Tri4 protein catalyzes three consecutive oxygenation reaction steps during biosynthesis of isotrichodiol in the trichothecenes biosynthetic pathway, while tri11 protein catalyzes the C4 hydroxylation of 12, 13-epoxytrichothec-9-ene to produce trichodermol. In the present study, we have homology modelled the three-dimensional structures of tri4 and tri11 proteins. Furthermore, molecular dynamics simulations were carried out to elucidate the mechanism of their action. Both tri4 and tri11 encode for cytochrome P450 monooxygenase like proteins. These data also revealed effector-induced allosteric changes on substrate binding at an alternative binding site and showed potential homotropic negative cooperativity. These analyses also showed that their catalytic mechanism relies on protein-ligand and protein-heme interactions controlled by hydrophobic and hydrogen-bonding interactions which orient the complex in optimal conformation within the active sites.

  5. The Diversity of Yellow-Related Proteins in Sand Flies (Diptera: Psychodidae.

    Directory of Open Access Journals (Sweden)

    Michal Sima

    Full Text Available Yellow-related proteins (YRPs present in sand fly saliva act as affinity binders of bioamines, and help the fly to complete a bloodmeal by scavenging the physiological signals of damaged cells. They are also the main antigens in sand fly saliva and their recombinant form is used as a marker of host exposure to sand flies. Moreover, several salivary proteins and plasmids coding these proteins induce strong immune response in hosts bitten by sand flies and are being used to design protecting vaccines against Leishmania parasites. In this study, thirty two 3D models of different yellow-related proteins from thirteen sand fly species of two genera were constructed based on the known protein structure from Lutzomyia longipalpis. We also studied evolutionary relationships among species based on protein sequences as well as sequence and structural variability of their ligand-binding site. All of these 33 sand fly YRPs shared a similar structure, including a unique tunnel that connects the ligand-binding site with the solvent by two independent paths. However, intraspecific modifications found among these proteins affects the charges of the entrances to the tunnel, the length of the tunnel and its hydrophobicity. We suggest that these structural and sequential differences influence the ligand-binding abilities of these proteins and provide sand flies with a greater number of YRP paralogs with more nuanced answers to bioamines. All these characteristics allow us to better evaluate these proteins with respect to their potential use as part of anti-Leishmania vaccines or as an antigen to measure host exposure to sand flies.

  6. Portal monitor incorporating smart probes

    International Nuclear Information System (INIS)

    Bartos, D.; Constantin, F.; Guta, T.

    2003-01-01

    Portal monitors are intended for detection of radioactive and special nuclear materials in vehicles, pedestrians, luggage, as well as for prevention of illegal traffic of radioactive sources. Monitors provide audio and visual alarms when radioactive and/or special nuclear materials are detected. They can be recommended to officers of customs, border guard and emergency services, civil defense, fire brigades, police and military departments or nuclear research or energetic facilities. The portal monitor developed by us consists in a portal frame, which sustains five intelligent probes having long plastic scintillator (0.5 liters each). The probes communicate, by serial transmission, with a Central Unit constructed on the basis of the 80552 microcontroller. This one manages the handshake, calculates the background, establishes the measuring time, starts and stops each measurement and makes all the other decisions. Sound signals and an infrared sensor monitor the passing through the portal and the measuring procedure. For each measurement the result is displayed on a LCD device contaminated/uncontaminated; for the contaminated case a loud and long sound signal is also issued. An RS 232 serial interface is provided in order to further developments or custom made devices. As a result, the portal monitor detects 1 μ Ci 137 Cs, spread all over a human body, in a 20 μR/h gamma background for a measuring time of 1.5 or 10 seconds giving a 99% confidence factor. (authors)

  7. The nonstructural proteins of Pneumoviruses are remarkably distinct in substrate diversity and specificity.

    Science.gov (United States)

    Ribaudo, Michael; Barik, Sailen

    2017-11-06

    Interferon (IFN) inhibits viruses by inducing several hundred cellular genes, aptly named 'interferon (IFN)-stimulated genes' (ISGs). The only two RNA viruses of the Pneumovirus genus of the Paramyxoviridae family, namely Respiratory Syncytial Virus (RSV) and Pneumonia Virus of Mice (PVM), each encode two nonstructural (NS) proteins that share no sequence similarity but yet suppress IFN. Since suppression of IFN underlies the ability of these viruses to replicate in the host cells, the mechanism of such suppression has become an important area of research. This Short Report is an important extension of our previous efforts in defining this mechanism. We show that, like their PVM counterparts, the RSV NS proteins also target multiple members of the ISG family. While significantly extending the substrate repertoire of the RSV NS proteins, these results, unexpectedly, also reveal that the target preferences of the NS proteins of the two viruses are entirely different. This is surprising since the two Pneumoviruses are phylogenetically close with similar genome organization and gene function, and the NS proteins of both also serve as suppressors of host IFN response. The finding that the NS proteins of the two highly similar viruses suppress entirely different members of the ISG family raises intriguing questions of pneumoviral NS evolution and mechanism of action.

  8. CT findings of portal vein aneurysm

    International Nuclear Information System (INIS)

    Yang, Dal Mo; Chang, Mi Son; Yoon, Myung Hwan; Kim, Hak Soo; Kim, Hyung Sik; Chung, Hyo Sun; Chung, Jin Woo

    1999-01-01

    To describe the CT findings of portal vein aneurysm in eight patients. All patients included in this study (two men and six women) underwent CT examinations between October 1996 and June1998. Of these eight, three were suffering from hepatic disease and portal hypertension. We determined the location, shape, size, and characteristics of the lesions, and the presence or absence of portal vein anomaly. Seven patients had intrahepatic portal vein aneurysm (at the umbilical portion of the left portal vein in five patients, between the transverse and umbilical portion of the left portal vein in one, and at the bifurcation of the anterior and posterior branch of the right portal vein in one), while extrahepatic portal vein aneurysm, at the confluence of the superior mesenteric and splenic vein was found in only one. Lesions were cyst-shaped in seven cases and saccular in one, and showed well-circumscribed, markedly enhanced mass, which communicated with the portal vein and/or gives off major branches. Portal vein anomaly, in which the right anterior segmental portal vein originated from the umbilical portion of the left portal vein, was seen in three patients. In all three, intrahepatic portal vein aneurysm was present at the umbilical portion of the left portal vein, and in one, the umbilical protion of the left portal vein was located to the right of the Cantlic line. CT examination can help reveal portal vein aneurysm by detecting a well-circumscribed, markedly enhanced mass which communicates with the portal vein and/or gives off major branches

  9. Portal hypertension as the initial manifestation of POEMS syndrome: a case report.

    Science.gov (United States)

    Wu, Lina; Li, Yue; Yao, Fang; Lu, Chongmei; Li, Jian; Zhou, Weixun; Qian, Jiaming

    2017-01-01

    Portal hypertension has a broad differential diagnosis. POEMS syndrome is an uncommon cause of it. POEMS syndrome is a rare disease involving multiple organs. In differential diagnosis of portal hypertension, POEMS syndrome should be considered especially when other symptoms such as numbness, organomegaly, endocrine alteration and skin changes also present, as it is highlighted by our case. We report a 46-year-old Chinese male, a teacher, presenting with portal hypertension. Electromyography revealed peripheral neuropathy. Immunofixation showed monoclonal immunoglobulin A lambda protein. The diagnosis of POEMS syndrome was established. After treatment of lenalidomide combined with dexamethasone over 2 years, the patient achieved a considerable improvement. This case highlights the manifestation of portal hypertension in POEMS syndrome. Lenalidomide with or without dexamethasone is effective for portal hypertension due to POEMS syndrome, though esophageal and gastric varices seems not reversible so easily.

  10. Identification of proteins in Streptococcus pneumoniae by reverse vaccinology and genetic diversity of these proteins in clinical isolates.

    Science.gov (United States)

    Argondizzo, Ana Paula Corrêa; da Mota, Fabio Faria; Pestana, Cristiane Pinheiro; Reis, Joice Neves; de Miranda, Antonio Basílio; Galler, Ricardo; Medeiros, Marco Alberto

    2015-02-01

    Streptococcus pneumoniae is a major cause of morbidity and mortality worldwide. Virulence-associated proteins common and conserved among all capsular types now represent the best strategy to combat pneumococcal infections. Our aim was to identify conserved targets in pneumococci that showed positive prediction for lipoprotein and extracellular subcellular location using bioinformatics programs and verify the distribution and the degree of conservation of these targets in pneumococci. These targets can be considered potential vaccine candidate to be evaluated in the future. A set of 13 targets were analyzed and confirmed the presence in all pneumococci tested. These 13 genes were highly conserved showing around >96 % of amino acid and nucleotide identity, but they were also present and show high identity in the closely related species Streptococcus mitis, Streptococcus oralis, and Streptococcus pseudopneumoniae. S. oralis clusters away from S. pneumoniae, while S. pseudopneumoniae and S. mitis cluster closer. The divergence between the selected targets was too small to be observed consistently in phylogenetic groups between the analyzed genomes of S. pneumoniae. The proteins analyzed fulfill two of the initial criteria of a vaccine candidate: targets are present in a variety of different pneumococci strains including different serotypes and are conserved among the samples evaluated.

  11. Environmental Distribution and Diversity of Insecticidal Proteins of Bacillus thuringiensis Berliner

    Directory of Open Access Journals (Sweden)

    Xavier, R.

    2007-01-01

    Full Text Available Bacillus thuringiensis Berliner based biopesticides have been successfully used world over for the control of agricultural pests and vectors of human diseases. Currently there are more than 200 B. thuringiensis strains with differing insecticidal activities are available as biocontrol agents and for developing transgenic plants. However, two major disadvantages are the development of insect resistance and high target specificity (narrow host range. Globally there is a continuous search for new B. thuringiensis strains with novel insecticidal activities. The present study aims to study the environmental distribution of B. thuringiensis and their toxic potential against insect pests. Soil and grain samples were collected from different environments and were processed by a modified acetate selection method. Initially B. thuringiensis isolates were screened on the basis of colony morphology and phase contrast microscopy for the presence of parasporal crystal inclusions. The population dynamics showed that B. thuringiensis is abundant in sericulture environment compared to other niches. Relative abundance of B. thuringiensis strains in sericulture environment shows the persistent association of B. thuringiensis with Bombyx mori (silk worm as insect pathogen. The protein profiles of the selected strains were studied by SDS-PAGE. The protein profiles of majority of B. thuringiensis isolates from grain storage facilities predominantly showing the 130 kDa and 68 kDa proteins, which is characteristics of lepidopteran active B. thuringiensis. However, one isolate BTRX-4 has 80-85 kDa protein, which is novel in that, this strain also exhibits antilepidopteran activity, which is normally presented by B. thuringiensis strains having 130 kDa and 68 kDa proteins. The protein profile of B. thuringiensis isolates from sericulture environment shows two different protein profiles. B. thuringiensis isolates BTRX-16 to BTRX-22 predominantly show 130 kDa protein

  12. The Higgs portal above threshold

    Energy Technology Data Exchange (ETDEWEB)

    Craig, Nathaniel [Department of Physics, University of California,Santa Barbara, CA 93106 (United States); Lou, Hou Keong [Department of Physics, Princeton University,Princeton, NJ 08540 (United States); McCullough, Matthew [Theory Division, CERN,1211 Geneva 23 (Switzerland); Thalapillil, Arun [Department of Physics and Astronomy, Rutgers University,Piscataway, NJ 08854 (United States)

    2016-02-18

    The discovery of the Higgs boson opens the door to new physics interacting via the Higgs Portal, including motivated scenarios relating to baryogenesis, dark matter, and electroweak naturalness. We systematically explore the collider signatures of singlet scalars produced via the Higgs Portal at the 14 TeV LHC and a prospective 100 TeV hadron collider. We focus on the challenging regime where the scalars are too heavy to be produced in the decays of an on-shell Higgs boson, and instead are produced primarily via an off-shell Higgs. Assuming these scalars escape the detector, promising channels include missing energy in association with vector boson fusion, monojets, and top pairs. We forecast the sensitivity of searches in these channels at √s=14 & 100 TeV and compare collider reach to the motivated parameter space of singlet-assisted electroweak baryogenesis, Higgs Portal dark matter, and neutral naturalness.

  13. The Higgs portal above threshold

    International Nuclear Information System (INIS)

    Craig, Nathaniel; Lou, Hou Keong; McCullough, Matthew; Thalapillil, Arun

    2016-01-01

    The discovery of the Higgs boson opens the door to new physics interacting via the Higgs Portal, including motivated scenarios relating to baryogenesis, dark matter, and electroweak naturalness. We systematically explore the collider signatures of singlet scalars produced via the Higgs Portal at the 14 TeV LHC and a prospective 100 TeV hadron collider. We focus on the challenging regime where the scalars are too heavy to be produced in the decays of an on-shell Higgs boson, and instead are produced primarily via an off-shell Higgs. Assuming these scalars escape the detector, promising channels include missing energy in association with vector boson fusion, monojets, and top pairs. We forecast the sensitivity of searches in these channels at √s=14 & 100 TeV and compare collider reach to the motivated parameter space of singlet-assisted electroweak baryogenesis, Higgs Portal dark matter, and neutral naturalness.

  14. The ADRICOSM STAR GeoPortal

    Science.gov (United States)

    Giorgetti, Alessandra; Cesarini, Claudia; Gambetta, Marco; Reseghetti, Franco; Vinci, Matteo

    2010-05-01

    From Stockholm (1972) to Rio de Janeiro (1992) and to Johannesburg (2002), environmental protection objectives are related to the principles of sustainable development. This includes the following important components: participation, information, communication, training (capacity building) and education. Better information ensure more participation from individuals, and allows citizens to take part in many different actions that can influence the policy process. Participation to political decisions need access to reliable and quality controlled information. The ADRICOSM Portal was developed in order to manage data diversity, provide access to any kind of product, provide metadata completeness and accuracy. The product, as defined in ADRICOSM, is anything that can be offered to a client and that might satisfy a want or need. This implied the implementation of services that was taking into consideration the diversity of the objects to be provided to users: observations, model outputs, maps, etc. The implementation of the portal was based on two metadata levels: 1. Directory level - consisting of broad descriptions of the contents of data sets; used to locate data sets of potential interest and 2. Data level - consisting of the actual data objects. The portal was developed as a simplified front end for the partners data management systems, giving emphasis on federated access points focused on thematic aspects. This was based on the idea that specialized customer-related access points can be better carried out by delegated teams of experts who know the needs of different customers, define the user software which is most suited to them. The data management systems provide facilities for two data tracks, one in real-time (or near-realtime) and one in delayed mode. Both tracks are based on the same data sources and transmission systems, but the data follow different routes and are processed differently depending on user requirements. The real-time data and model products

  15. Genetic diversity and natural selection of Plasmodium knowlesi merozoite surface protein 1 paralog gene in Malaysia.

    Science.gov (United States)

    Ahmed, Md Atique; Fauzi, Muh; Han, Eun-Taek

    2018-03-14

    Human infections due to the monkey malaria parasite Plasmodium knowlesi is on the rise in most Southeast Asian countries specifically Malaysia. The C-terminal 19 kDa domain of PvMSP1P is a potential vaccine candidate, however, no study has been conducted in the orthologous gene of P. knowlesi. This study investigates level of polymorphisms, haplotypes and natural selection of full-length pkmsp1p in clinical samples from Malaysia. A total of 36 full-length pkmsp1p sequences along with the reference H-strain and 40 C-terminal pkmsp1p sequences from clinical isolates of Malaysia were downloaded from published genomes. Genetic diversity, polymorphism, haplotype and natural selection were determined using DnaSP 5.10 and MEGA 5.0 software. Genealogical relationships were determined using haplotype network tree in NETWORK software v5.0. Population genetic differentiation index (F ST ) and population structure of parasite was determined using Arlequin v3.5 and STRUCTURE v2.3.4 software. Comparison of 36 full-length pkmsp1p sequences along with the H-strain identified 339 SNPs (175 non-synonymous and 164 synonymous substitutions). The nucleotide diversity across the full-length gene was low compared to its ortholog pvmsp1p. The nucleotide diversity was higher toward the N-terminal domains (pkmsp1p-83 and 30) compared to the C-terminal domains (pkmsp1p-38, 33 and 19). Phylogenetic analysis of full-length genes identified 2 distinct clusters of P. knowlesi from Malaysian Borneo. The 40 pkmsp1p-19 sequences showed low polymorphisms with 16 polymorphisms leading to 18 haplotypes. In total there were 10 synonymous and 6 non-synonymous substitutions and 12 cysteine residues were intact within the two EGF domains. Evidence of strong purifying selection was observed within the full-length sequences as well in all the domains. Shared haplotypes of 40 pkmsp1p-19 were identified within Malaysian Borneo haplotypes. This study is the first to report on the genetic diversity and natural

  16. Human HOX Proteins Use Diverse and Context-Dependent Motifs to Interact with TALE Class Cofactors.

    Science.gov (United States)

    Dard, Amélie; Reboulet, Jonathan; Jia, Yunlong; Bleicher, Françoise; Duffraisse, Marilyne; Vanaker, Jean-Marc; Forcet, Christelle; Merabet, Samir

    2018-03-13

    HOX proteins achieve numerous functions by interacting with the TALE class PBX and MEIS cofactors. In contrast to this established partnership in development and disease, how HOX proteins could interact with PBX and MEIS remains unclear. Here, we present a systematic analysis of HOX/PBX/MEIS interaction properties, scanning all paralog groups with human and mouse HOX proteins in vitro and in live cells. We demonstrate that a previously characterized HOX protein motif known to be critical for HOX-PBX interactions becomes dispensable in the presence of MEIS in all except the two most anterior paralog groups. We further identify paralog-specific TALE-binding sites that are used in a highly context-dependent manner. One of these binding sites is involved in the proliferative activity of HOXA7 in breast cancer cells. Together these findings reveal an extraordinary level of interaction flexibility between HOX proteins and their major class of developmental cofactors. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  17. Expression of measles virus nucleoprotein induces apoptosis and modulates diverse functional proteins in cultured mammalian cells.

    Directory of Open Access Journals (Sweden)

    Ashima Bhaskar

    Full Text Available BACKGROUND: Measles virus nucleoprotein (N encapsidates the viral RNA, protects it from endonucleases and forms a virus specific template for transcription and replication. It is the most abundant protein during viral infection. Its C-terminal domain is intrinsically disordered imparting it the flexibility to interact with several cellular and viral partners. PRINCIPAL FINDINGS: In this study, we demonstrate that expression of N within mammalian cells resulted in morphological transitions, nuclear condensation, DNA fragmentation and activation of Caspase 3 eventuating into apoptosis. The rapid generation of intracellular reactive oxygen species (ROS was involved in the mechanism of cell death. Addition of ascorbic acid (AA or inhibitor of caspase-3 in the extracellular medium partially reversed N induced apoptosis. We also studied the protein profile of cells expressing N protein. MS analysis revealed the differential expression of 25 proteins out of which 11 proteins were up regulated while 14 show signs of down regulation upon N expression. 2DE results were validated by real time and semi quantitative RT-PCR analysis. CONCLUSION: These results show the pro-apoptotic effects of N indicating its possible development as an apoptogenic tool. Our 2DE results present prima facie evidence that the MV nucleoprotein interacts with or causes differential expression of a wide range of cellular factors. At this stage it is not clear as to what the adaptive response of the host cell is and what reflects a strategic modulation exerted by the virus.

  18. Longitudinal and Cross-Sectional Genetic Diversity in the Korean Peninsula Based on the P vivax Merozoite Surface Protein Gene.

    Science.gov (United States)

    Kim, Jung-Yeon; Suh, Eun-Jung; Yu, Hyo-Soon; Jung, Hyun-Sik; Park, In-Ho; Choi, Yien-Kyeoug; Choi, Kyoung-Mi; Cho, Shin-Hyeong; Lee, Won-Ja

    2011-12-01

    Vivax malaria has reemerged and become endemic in Korea. Our study aimed to analyze by both longitudinal and cross-sectional genetic diversity of this malaria based on the P vivax Merozoite Surface Protein (PvMSP) gene parasites recently found in the Korean peninsula. PvMSP-1 gene sequence analysis from P vivax isolates (n = 835) during the 1996-2010 period were longitudinally analyzed and the isolates from the Korean peninsula through South Korea, the demilitarized zone and North Korea collected in 2008-2010 were enrolled in an overall analysis of MSP-1 gene diversity. New recombinant subtypes and severe multiple-cloneinfection rates were observed in recent vivax parasites. Regional variation was also observed in the study sites. This study revealed the great complexity of genetic variation and rapid dissemination of genes in P vivax. It also showed interesting patterns of diversity depending, on the region in the Korean Peninsula. Understanding the parasiteninsula. Under genetic variation may help to analyze trends and assess the extent of endemic malaria in Korea.

  19. Differential sequence diversity at merozoite surface protein-1 locus of Plasmodium knowlesi from humans and macaques in Thailand.

    Science.gov (United States)

    Putaporntip, Chaturong; Thongaree, Siriporn; Jongwutiwes, Somchai

    2013-08-01

    To determine the genetic diversity and potential transmission routes of Plasmodium knowlesi, we analyzed the complete nucleotide sequence of the gene encoding the merozoite surface protein-1 of this simian malaria (Pkmsp-1), an asexual blood-stage vaccine candidate, from naturally infected humans and macaques in Thailand. Analysis of Pkmsp-1 sequences from humans (n=12) and monkeys (n=12) reveals five conserved and four variable domains. Most nucleotide substitutions in conserved domains were dimorphic whereas three of four variable domains contained complex repeats with extensive sequence and size variation. Besides purifying selection in conserved domains, evidence of intragenic recombination scattering across Pkmsp-1 was detected. The number of haplotypes, haplotype diversity, nucleotide diversity and recombination sites of human-derived sequences exceeded that of monkey-derived sequences. Phylogenetic networks based on concatenated conserved sequences of Pkmsp-1 displayed a character pattern that could have arisen from sampling process or the presence of two independent routes of P. knowlesi transmission, i.e. from macaques to human and from human to humans in Thailand. Copyright © 2013 Elsevier B.V. All rights reserved.

  20. Genetic diversity in the merozoite surface protein 1 and 2 genes of Plasmodium falciparum from the Artibonite Valley of Haiti.

    Science.gov (United States)

    Londono-Renteria, Berlin; Eisele, Thomas P; Keating, Joseph; Bennett, Adam; Krogstad, Donald J

    2012-01-01

    Describing genetic diversity of the Plasmodium falciparum parasite provides important information about the local epidemiology of malaria. In this study, we examined the genetic diversity of P. falciparum isolates from the Artibonite Valley in Haiti using the allelic families of merozoite surface protein 1 and 2 genes (msp-1 and msp-2). The majority of study subjects infected with P. falciparum had a single parasite genotype (56% for msp-1 and 69% for msp-2: n=79); 9 distinct msp-1 genotypes were identified by size differences on agarose gels. K1 was the most polymorphic allelic family with 5 genotypes (amplicons from 100 to 300 base pairs [bp]); RO33 was the least polymorphic, with a single genotype (120-bp). Although both msp-2 alleles (3D7/IC1, FC27) had similar number of genotypes (n=4), 3D7/IC1 was more frequent (85% vs. 26%). All samples were screened for the presence of the K76T mutation on the P. falciparum chloroquine resistance transporter (pfcrt) gene with 10 of 79 samples positive. Of the 2 (out of 10) samples from individuals follow-up for 21 days, P. falciparum parasites were present through day 7 after treatment with chloroquine. No parasites were found on day 21. Our results suggest that the level of genetic diversity is low in this area of Haiti, which is consistent with an area of low transmission. Copyright © 2011 Elsevier B.V. All rights reserved.

  1. Assessment of genetic diversity among some accessions of sage (Salvia officinalis L. using electrophoresis of seed storage proteins

    Directory of Open Access Journals (Sweden)

    Seyed Abbas Mirjalili

    2016-06-01

    Full Text Available The genus Salvia (Lamiaceae comprises over 900 species in the world, with a relatively wide dispersion in the Iran’s flora. Until now, about 58 species of the genus have been reported and identified in Iran, in which 17 of them were endemic. In order to study, investigate and evaluate the intraspecific diversity, similarity and dissimilarity among Iranian Salvia officinalis accessions, an experiment was carried out using SDS-PAGE technique. In this study, the seeds from five accessions were collected from gene bank and were evaluated. The seed storage proteins were extracted by buffers and were measured. Phylogenetic relationships were analyzed according to presence and absence of bands on the gel. A dendrogram was prepared using calculation of the accession’s similarity index. Mean comparison were done by Tukey’s test. The seed protein contents showed significant differences (p≤0.01 among accessions. A total of 39 bands were indicated on the gel. The maximum diversity was detected in the accession No. 2 while, the lowest band’s number were recorded with the accessions No. 1 and 5. Based on dendrogram, the accessions were divided into two groups; one includes accession No. 1 and 4 other accessions were located in the second group further classified into two subgroup including accessions No. 2 and 3 in one clade and accessions No. 4 and 5 in the other ones.

  2. Building an Archival Collections Portal

    Directory of Open Access Journals (Sweden)

    Stuart Marquis

    2008-06-01

    Full Text Available Columbia University Libraries has developed the Archival Collections Portal, a unified search system helping users discover archival resources in a streamlined way. We combined the power of Lucene and Solr to search XML, parse JSON objects, create EAD-compliant documents, and deliver results in an easy-to-use interface. By reusing MARC records and employing new search engine features and techniques, we are able to bring important and hard-to-find collections to researchers and archivists. The canonical home page of the Portal is http://www.columbia.edu/library/archival/.

  3. 29 CFR 785.24 - Principles noted in Portal-to-Portal Bulletin.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 3 2010-07-01 2010-07-01 false Principles noted in Portal-to-Portal Bulletin. 785.24 Section 785.24 Labor Regulations Relating to Labor (Continued) WAGE AND HOUR DIVISION, DEPARTMENT OF LABOR... of Principles Preparatory and Concluding Activities § 785.24 Principles noted in Portal-to-Portal...

  4. Vif Proteins from Diverse Primate Lentiviral Lineages Use the Same Binding Site in APOBEC3G

    OpenAIRE

    Letko, Michael; Silvestri, Guido; Hahn, Beatrice H.; Bibollet-Ruche, Frederick; Gokcumen, Omer; Simon, Viviana; Ooms, Marcel

    2013-01-01

    APOBEC3G (A3G) is a cytidine deaminase that restricts human immunodeficiency virus type 1 (HIV-1) and other lentiviruses. Most of these viruses encode a Vif protein that directly binds A3G and leads to its proteasomal degradation. Both Vif proteins of HIV-1 and African green monkey simian immunodeficiency virus (SIVagm) bind residue 128 of A3G. However, this position does not control the A3G degradation by Vif variants derived from HIV-2 and SIVmac, which both originated from SIV of sooty man...

  5. From EGEE Operations Portal towards EGI Operations Portal

    Science.gov (United States)

    Cordier, Hélène; L'Orphelin, Cyril; Reynaud, Sylvain; Lequeux, Olivier; Loikkanen, Sinikka; Veyre, Pierre

    Grid operators in EGEE have been using a dedicated dashboard as their central operational tool, stable and scalable for the last 5 years despite continuous upgrade from specifications by users, monitoring tools or data providers. In EGEE-III, recent regionalisation of operations led the Operations Portal developers to conceive a standalone instance of this tool. We will see how the dashboard reorganization paved the way for the re-engineering of the portal itself. The outcome is an easily deployable package customized with relevant information sources and specific decentralized operational requirements. This package is composed of a generic and scalable data access mechanism, Lavoisier; a renowned php framework for configuration flexibility, Symfony and a MySQL database. VO life cycle and operational information, EGEE broadcast and Downtime notifications are next for the major reorganization until all other key features of the Operations Portal are migrated to the framework. Features specifications will be sketched at the same time to adapt to EGI requirements and to upgrade. Future work on feature regionalisation, on new advanced features or strategy planning will be tracked in EGI- Inspire through the Operations Tools Advisory Group, OTAG, where all users, customers and third parties of the Operations Portal are represented from January 2010.

  6. Oncogenomic portals for the visualization and analysis of genome-wide cancer data.

    Science.gov (United States)

    Klonowska, Katarzyna; Czubak, Karol; Wojciechowska, Marzena; Handschuh, Luiza; Zmienko, Agnieszka; Figlerowicz, Marek; Dams-Kozlowska, Hanna; Kozlowski, Piotr

    2016-01-05

    Somatically acquired genomic alterations that drive oncogenic cellular processes are of great scientific and clinical interest. Since the initiation of large-scale cancer genomic projects (e.g., the Cancer Genome Project, The Cancer Genome Atlas, and the International Cancer Genome Consortium cancer genome projects), a number of web-based portals have been created to facilitate access to multidimensional oncogenomic data and assist with the interpretation of the data. The portals provide the visualization of small-size mutations, copy number variations, methylation, and gene/protein expression data that can be correlated with the available clinical, epidemiological, and molecular features. Additionally, the portals enable to analyze the gathered data with the use of various user-friendly statistical tools. Herein, we present a highly illustrated review of seven portals, i.e., Tumorscape, UCSC Cancer Genomics Browser, ICGC Data Portal, COSMIC, cBioPortal, IntOGen, and BioProfiling.de. All of the selected portals are user-friendly and can be exploited by scientists from different cancer-associated fields, including those without bioinformatics background. It is expected that the use of the portals will contribute to a better understanding of cancer molecular etiology and will ultimately accelerate the translation of genomic knowledge into clinical practice.

  7. Quantitative vs. subjective portal verification using digital portal images.

    Science.gov (United States)

    Bissett, R; Leszczynski, K; Loose, S; Boyko, S; Dunscombe, P

    1996-01-15

    Off-line, computer-aided prescription (simulator) and treatment (portal) image registration using chamfer matching has been implemented on PC based viewing station. The purposes of this study were (a) to evaluate the performance of interactive anatomy and field edge extraction and subsequent registration, and (b) to compare observer's perceptions of field accuracy with measured discrepancies following anatomical registration. Prescription-treatment image pairs for 48 different patients were examined in this study. Digital prescription images were produced with the aid of a television camera and a digital frame grabber, while the treatment images were obtained directly from an on-line portal imaging system. To facilitate perception of low contrast anatomical detail, on-line portal images were enhanced with selective adaptive histogram equalization prior to extraction of anatomical edges. Following interactive extraction of anatomical and field border information by an experienced observer, the identified anatomy was registered using chamfer matching. The degree of conformity between the prescription and treatment fields was quantified using several parameters, which included relative prescription field coverage and overcoverage, as well as the translational and rotational displacements as measured by chamfer matching applied to the boundaries of the two fields. These quantitative measures were compared with subjective evaluations made by four radiation oncologists. All the images in this series that included a range of the most commonly seen treatment sites were registered and the conformity parameters were found. The mean treatment/prescription field coverage and overcoverage were approximately 95 and 7%, respectively before registration. The mean translational displacement in the transverse and cranio-caudal directions were 2.9 and 3.4 mm, respectively. The mean rotational displacement was approximately 2 degrees. For all four oncologists, the portals classified

  8. Pervasive adaptive protein evolution apparent in diversity patterns around amino acid substitutions in Drosophila simulans.

    Directory of Open Access Journals (Sweden)

    Shmuel Sattath

    2011-02-01

    Full Text Available In Drosophila, multiple lines of evidence converge in suggesting that beneficial substitutions to the genome may be common. All suffer from confounding factors, however, such that the interpretation of the evidence-in particular, conclusions about the rate and strength of beneficial substitutions-remains tentative. Here, we use genome-wide polymorphism data in D. simulans and sequenced genomes of its close relatives to construct a readily interpretable characterization of the effects of positive selection: the shape of average neutral diversity around amino acid substitutions. As expected under recurrent selective sweeps, we find a trough in diversity levels around amino acid but not around synonymous substitutions, a distinctive pattern that is not expected under alternative models. This characterization is richer than previous approaches, which relied on limited summaries of the data (e.g., the slope of a scatter plot, and relates to underlying selection parameters in a straightforward way, allowing us to make more reliable inferences about the prevalence and strength of adaptation. Specifically, we develop a coalescent-based model for the shape of the entire curve and use it to infer adaptive parameters by maximum likelihood. Our inference suggests that ∼13% of amino acid substitutions cause selective sweeps. Interestingly, it reveals two classes of beneficial fixations: a minority (approximately 3% that appears to have had large selective effects and accounts for most of the reduction in diversity, and the remaining 10%, which seem to have had very weak selective effects. These estimates therefore help to reconcile the apparent conflict among previously published estimates of the strength of selection. More generally, our findings provide unequivocal evidence for strongly beneficial substitutions in Drosophila and illustrate how the rapidly accumulating genome-wide data can be leveraged to address enduring questions about the genetic basis

  9. Pervasive adaptive protein evolution apparent in diversity patterns around amino acid substitutions in Drosophila simulans.

    Science.gov (United States)

    Sattath, Shmuel; Elyashiv, Eyal; Kolodny, Oren; Rinott, Yosef; Sella, Guy

    2011-02-10

    In Drosophila, multiple lines of evidence converge in suggesting that beneficial substitutions to the genome may be common. All suffer from confounding factors, however, such that the interpretation of the evidence-in particular, conclusions about the rate and strength of beneficial substitutions-remains tentative. Here, we use genome-wide polymorphism data in D. simulans and sequenced genomes of its close relatives to construct a readily interpretable characterization of the effects of positive selection: the shape of average neutral diversity around amino acid substitutions. As expected under recurrent selective sweeps, we find a trough in diversity levels around amino acid but not around synonymous substitutions, a distinctive pattern that is not expected under alternative models. This characterization is richer than previous approaches, which relied on limited summaries of the data (e.g., the slope of a scatter plot), and relates to underlying selection parameters in a straightforward way, allowing us to make more reliable inferences about the prevalence and strength of adaptation. Specifically, we develop a coalescent-based model for the shape of the entire curve and use it to infer adaptive parameters by maximum likelihood. Our inference suggests that ∼13% of amino acid substitutions cause selective sweeps. Interestingly, it reveals two classes of beneficial fixations: a minority (approximately 3%) that appears to have had large selective effects and accounts for most of the reduction in diversity, and the remaining 10%, which seem to have had very weak selective effects. These estimates therefore help to reconcile the apparent conflict among previously published estimates of the strength of selection. More generally, our findings provide unequivocal evidence for strongly beneficial substitutions in Drosophila and illustrate how the rapidly accumulating genome-wide data can be leveraged to address enduring questions about the genetic basis of adaptation.

  10. Pro-inflammatory Cytokine Response and Genetic Diversity in Merozoite Surface Protein 2 of Plasmodium falciparum Isolates from Nigeria.

    Science.gov (United States)

    Ajibaye, Olusola; Osuntoki, Akinniyi A; Ebuehi, Albert Ot; Iwalokun, Bamidele A; Balogun, Emmanuel O; Egbuna, Kathleen N

    2017-01-01

    Polymorphisms in Plasmodium falciparum merozoite surface protein-2 ( msp -2) and associated parasite genetic diversity which varies between malaria-endemic regions remain a limitation in malaria vaccine development. Pro-inflammatory cytokines are important in immunity against malaria, understanding the influence of genetic diversity on cytokine response is important for effective vaccine design. P. falciparum isolates obtained from 300 Nigerians with uncomplicated falciparum malaria at Ijede General Hospital, Ijede (IJE), General Hospital Ajeromi, Ajeromi (AJE) and Saint Kizito Mission Hospital, Lekki, were genotyped by nested polymerase chain reaction of msp -2 block 3 while ELISA was used to determine the pro-inflammatory cytokine response to describe the genetic diversity of P. falciparum . Eighteen alleles were observed for msp -2 loci. Of the 195 isolates, 61 (31.0%) had only FC27-type alleles, 38 (19.7%) had only 3D7-type alleles, and 49.3% had multiple parasite lines with both alleles. Band sizes were 275-625 bp for FC27 and 150-425 bp for 3D7. Four alleles were observed from LEK, 2 (375-425 bp) and 2 (275-325 bp) of FC27-and 3D7-types, respectively; 12 alleles from AJE, 9 (275-625 bp) and 3 (325-425 bp) of FC27-types and 3D7-types, respectively; while IJE had a total of 12 alleles, 9 (275-625 bp) and 3 (325-425 bp) of FC27-types and 3D7-types, respectively. Mean multiplicity of infection (MOI) was 1.54. Heterozygosity ( H E ) ranged from 0.77 to 0.87 and was highest for IJE (0.87). Cytokine response was higher among 0.05) but with neither parasite density nor infection type. P. falciparum genetic diversity is extensive in Nigeria, protection via pro-inflammatory cytokines have little or no interplay with infection multiplicity.

  11. Diversity of membrane transport proteins for vitamins in bacteria and archaea

    NARCIS (Netherlands)

    Jähme, Michael; Slotboom, Dirk Jan

    BACKGROUND: All organisms use cofactors to extend the catalytic capacities of proteins. Many bacteria and archaea can synthesize cofactors from primary metabolites, but there are also prokaryotes that do not have the complete biosynthetic pathways for all essential cofactors. These organisms are

  12. Diversity and dispersal of a ubiquitous protein family: acyl-CoA dehydrogenases.

    Science.gov (United States)

    Shen, Yao-Qing; Lang, B Franz; Burger, Gertraud

    2009-09-01

    Acyl-CoA dehydrogenases (ACADs), which are key enzymes in fatty acid and amino acid catabolism, form a large, pan-taxonomic protein family with at least 13 distinct subfamilies. Yet most reported ACAD members have no subfamily assigned, and little is known about the taxonomic distribution and evolution of the subfamilies. In completely sequenced genomes from approximately 210 species (eukaryotes, bacteria and archaea), we detect ACAD subfamilies by rigorous ortholog identification combining sequence similarity search with phylogeny. We then construct taxonomic subfamily-distribution profiles and build phylogenetic trees with orthologous proteins. Subfamily profiles provide unparalleled insight into the organisms' energy sources based on genome sequence alone and further predict enzyme substrate specificity, thus generating explicit working hypotheses for targeted biochemical experimentation. Eukaryotic ACAD subfamilies are traditionally considered as mitochondrial proteins, but we found evidence that in fungi one subfamily is located in peroxisomes and participates in a distinct beta-oxidation pathway. Finally, we discern horizontal transfer, duplication, loss and secondary acquisition of ACAD genes during evolution of this family. Through these unorthodox expansion strategies, the ACAD family is proficient in utilizing a large range of fatty acids and amino acids-strategies that could have shaped the evolutionary history of many other ancient protein families.

  13. Identification of diverse archaeal proteins with class III signal peptides cleaved by distinct archaeal prepilin peptidases

    NARCIS (Netherlands)

    Szabó, Zalán; Oliveira Stahl, Adriana; Albers, Sonja-V.; Kissinger, Jessica C.; Driessen, Arnold J.M.; Pohlschröder, Mechthild; Pohlschroder, M.

    2007-01-01

    Most secreted archaeal proteins are targeted to the membrane via a tripartite signal composed of a charged N terminus and a hydrophobic domain, followed by a signal peptidase-processing site. Signal peptides of archaeal flagellins, similar to class III signal peptides of bacterial type IV pilins,

  14. Release of the herpes simplex virus 1 protease by self cleavage is required for proper conformation of the portal vertex

    International Nuclear Information System (INIS)

    Yang, Kui; Wills, Elizabeth G.; Baines, Joel D.

    2012-01-01

    We identify an NLS within herpes simplex virus scaffold proteins that is required for optimal nuclear import of these proteins into infected or uninfected nuclei, and is sufficient to mediate nuclear import of GFP. A virus lacking this NLS replicated to titers reduced by 1000-fold, but was able to make capsids containing both scaffold and portal proteins suggesting that other functions can complement the NLS in infected cells. We also show that Vp22a, the major scaffold protein, is sufficient to mediate the incorporation of portal protein into capsids, whereas proper portal immunoreactivity in the capsid requires the larger scaffold protein pU L 26. Finally, capsid angularization in infected cells did not require the HSV-1 protease unless full length pU L 26 was expressed. These data suggest that the HSV-1 portal undergoes conformational changes during capsid maturation, and reveal that full length pU L 26 is required for this conformational change.

  15. Magnetic Resonance Imaging of a Liver Hydatid Cyst Invading the Portal Vein and Causing Portal Cavernomatosis.

    Science.gov (United States)

    Herek, Duygu; Sungurtekin, Ugur

    2015-01-01

    Hepatic hydatid cysts rarely invade portal veins causing portal cavernomatosis as a secondary complication. We report the case of a patient with direct invasion of the right portal vein by hydatid cysts causing portal cavernomatosis diagnosed via magnetic resonance imaging (MRI). The presented case highlights the useful application of MRI with T2-weighted images and gadolinium-enhanced T1-weighted images in the diagnosis of hepatic hydatid lesions presenting with a rare complication of portal cavernomatosis.

  16. Genetic diversity of merozoite surface protein-2 in Plasmodium falciparum isolates from Aceh province, Indonesia

    Science.gov (United States)

    Jamil, K. F.; Supargiyono, S.; Syafruddin, D.; Pratama, N.; Silvy, S.

    2018-03-01

    Estimated 3.3 million Indonesian population were infected with malaria. However, extensive genetic polymorphism of the field isolates MSP-2 of P. falciparum represents a major obstacle for the development of malaria treatment. The aim of this study to investigate the genetic diversity of MSP-2 genotype in field isolates of P. falciparum collected in Aceh Province. A total of 90 patients enrolled in this study who were selected from positive malaria from eleven district Hospitals in Aceh from 2013-2015. Data was collected by anamnesis, complete physical examination and laboratory tests for MSP-2. All protocol to diagnose malaria assigned following the WHO 2010 guideline. All samples were stored in Eijkman Biology Molecular Institute, Jakarta.Among 90 samples were 57.7% male and 42.3% female with the most cases ages between 21-30 years old. Allele typing analysis displayed the polymorphic nature of P. falciparum. The MSP-2 have two alleles, 62.2% (56/90) for FC27 type and 58.9% (53/90) for 3D7 type and 21.2% (19/90) for mixed FC27 and 3D7 infection were identified. Diverse allele types from Aceh Province was identified in MSP-2 P. falciparum patients; there is the almost similar number of patients infected with both allele. A moderate level of the mixed allele was also observed.

  17. Radiologic investigation of portal hypertension

    International Nuclear Information System (INIS)

    Becker, C.; Wegmueller, H.

    1993-01-01

    Radiologic evaluation of patients with portal hypertension in the pre- and postoperative period can be done with several non-invasive or invasive imaging modalities which offer complementary information. Doppler-ultrasonography (-US) is the method of choice for initial non-invasive screening as well as for follow-up tests after shunt surgery. The diagnostic information provided by Doppler-US regarding morphology and blood flow in the upper abdominal organs and vessels is sufficient in many instances. Dynamic computed tomography (CT), magnetic resonance tomography (MRT) and recently, magnetic resonance angiography (MRA) are additional non-invasive imaging techniques that may add valuable information if necessary. Conventional angiography is usually performed immediately prior to surgery to demonstrate the vascular morphology. The standard angiographic technique to demonstrate both the arterial and portal venous system is arterioportography (late-phase portography) by means of selective catheterization of the celiac, the splenic, the superior mesenteric or inferior mesenteric arteries. The dose of iodinated contrast material may be reduced by 50% if digital subtraction angiography is used instead of the conventional technique. Inferior venacavography and hepatic venography are indicated in patients with suspected postsinusoidal portal hypertension, e.g. the Budd-Chiari syndrome; hepatic wedge manometry offers valuable information regarding pressure gradients between the portal and systemic venous system prior to shunt surgery. The angiographic access through the inferior vena cava is also used for direct catheterization of surgical porto-caval or spleno-renal shunts for both angiography, manometry and, if necessary, balloon angioplasty. (authors)

  18. Fibroblast Activation Protein-Alpha, a Serine Protease that Facilitates Metastasis by Modification of Diverse Microenvironments

    Science.gov (United States)

    2011-10-01

    diabetes and hematopoietic stem cell engraftment [21]. Sitagliptin is a DPPIV inhibitor already approved for type 2 diabetes because it has...activation protein (FAP) in hepatitis C virus infection. Adv Exp Med Biol 524:235–243 12. Levy MT, McCaughan GW, Abbott CA, Park JE, Cunningham AM...kb ( Abbott et al., 1994). Three different splice variants of FAP have been observed in mouse embryonic tissues, with all three predicted to encode

  19. Sonographic detection of portal venous gas

    International Nuclear Information System (INIS)

    Lee, Wang Yul; Lee, S. K.; Cho, O. K.

    1989-01-01

    Portal venous gas suggests underlying bowel disease such as strangulating intestinal obstruction and its demonstration carries with it an important implications with respect to patient management. Radiography has been the gold standard for the detection of portal venous gas. We have experienced two cases of portal venous gas diagnosed by ultrasound. Sonographic findings were floating echoes in the main portal vein and highly echogenic linear or patchy echoes within the hepatic parenchyma. Simple abdominal films of those cases failed to demonstrate gas in the portal venous system

  20. Chitinase family GH18: evolutionary insights from the genomic history of a diverse protein family

    Directory of Open Access Journals (Sweden)

    Aronson Nathan N

    2007-06-01

    Full Text Available Abstract Background Chitinases (EC.3.2.1.14 hydrolyze the β-1,4-linkages in chitin, an abundant N-acetyl-β-D-glucosamine polysaccharide that is a structural component of protective biological matrices such as insect exoskeletons and fungal cell walls. The glycoside hydrolase 18 (GH18 family of chitinases is an ancient gene family widely expressed in archea, prokaryotes and eukaryotes. Mammals are not known to synthesize chitin or metabolize it as a nutrient, yet the human genome encodes eight GH18 family members. Some GH18 proteins lack an essential catalytic glutamic acid and are likely to act as lectins rather than as enzymes. This study used comparative genomic analysis to address the evolutionary history of the GH18 multiprotein family, from early eukaryotes to mammals, in an effort to understand the forces that shaped the human genome content of chitinase related proteins. Results Gene duplication and loss according to a birth-and-death model of evolution is a feature of the evolutionary history of the GH18 family. The current human family likely originated from ancient genes present at the time of the bilaterian expansion (approx. 550 mya. The family expanded in the chitinous protostomes C. elegans and D. melanogaster, declined in early deuterostomes as chitin synthesis disappeared, and expanded again in late deuterostomes with a significant increase in gene number after the avian/mammalian split. Conclusion This comprehensive genomic study of animal GH18 proteins reveals three major phylogenetic groups in the family: chitobiases, chitinases/chitolectins, and stabilin-1 interacting chitolectins. Only the chitinase/chitolectin group is associated with expansion in late deuterostomes. Finding that the human GH18 gene family is closely linked to the human major histocompatibility complex paralogon on chromosome 1, together with the recent association of GH18 chitinase activity with Th2 cell inflammation, suggests that its late expansion

  1. Intelligent interaction based on holographic personalized portal

    Directory of Open Access Journals (Sweden)

    Yadong Huang

    2017-06-01

    Full Text Available Purpose – The purpose of this paper is to study the architecture of holographic personalized portal, user modeling, commodity modeling and intelligent interaction. Design/methodology/approach – In this paper, the authors propose crowd-science industrial ecological system based on holographic personalized portal and its interaction. The holographic personality portal is based on holographic enterprises, commodities and consumers, and the personalized portal consists of accurate ontology, reliable supply, intelligent demand and smart cyberspace. Findings – The personalized portal can realize the information acquisition, characteristic analysis and holographic presentation. Then, the intelligent interaction, e.g. demand decomposition, personalized search, personalized presentation and demand prediction, will be implemented within the personalized portal. Originality/value – The authors believe that their work on intelligent interaction based on holographic personalized portal, which has been first proposed in this paper, is innovation focusing on the interaction between intelligence and convenience.

  2. Thrombospondin-1 expression may be implicated in liver atrophic mechanism due to obstructed portal venous flow.

    Science.gov (United States)

    Hayashi, Hiromitsu; Kuroki, Hideyuki; Higashi, Takaaki; Takeyama, Hideaki; Yokoyama, Naomi; Okabe, Hirohisa; Nitta, Hidetoshi; Beppu, Toru; Takamori, Hiroshi; Baba, Hideo

    2017-07-01

    Liver is an amazing organ that can undergo regenerative and atrophic changes inversely, depending on blood flow conditions. Although the regenerative mechanism has been extensively studied, the atrophic mechanism remains to be elucidated. To assess the molecular mechanism of liver atrophy due to reduced portal blood flow, we analyzed the gene expressions between atrophic and hypertrophic livers induced by portal vein embolization in three human liver tissues using microarray analyses. Thrombospondin (TSP)-1 is an extracellular protein and a negative regulator of liver regeneration through its activation of the transforming growth factor-β/Smad signaling pathway. TSP-1 was extracted as the most upregulated gene in atrophic liver compared to hypertrophic liver due to portal flow obstruction in human. Liver atrophic and hypertrophic changes were confirmed by HE and proliferating cell nuclear antigen staining and terminal deoxynucleotidyl transferase-mediated digoxigenin-dUTP nick-end labeling. In an in vivo model with portal ligation, TSP-1 and phosphorylated Smad2 expression were continuously induced at 6 h and thereafter in the portal ligated liver, whereas the induction was transient at 6 h in the portal non-ligated liver. Indeed, while cell proliferation represented by proliferating cell nuclear antigen expression at 48 h was induced in the portal ligated liver, the sinusoidal dilatation and hepatocyte cell death with terminal deoxynucleotidyl transferase-mediated digoxigenin-dUTP nick-end labeling was detectable at 48 h in the portal ligated liver. Obstructed portal flow induces persistent TSP-1 expression and transforming growth factor-β/Smad signal activation in atrophic liver. Thrombospondin-1 may be implicated in the liver atrophic change due to obstructed portal flow as a pro-atrophic factor. © 2016 The Japan Society of Hepatology.

  3. Structure-Function Analysis of the DNA Translocating Portal of the Bacteriophage T4 Packaging Machine

    Science.gov (United States)

    Padilla-Sanchez, Victor; Gao, Song; Kim, Hyung Rae; Kihara, Daisuke; Sun, Lei; Rossmann, Michael G.; Rao, Venigalla B.

    2013-01-01

    Tailed bacteriophages and herpesviruses consist of a structurally well conserved dodecameric portal at a special five-fold vertex of the capsid. The portal plays critical roles in head assembly, genome packaging, neck/tail attachment, and genome ejection. Although the structures of portals from phages φ29, SPP1 and P22 have been determined, their mechanistic roles have not been well understood. Structural analysis of phage T4 portal (gp20) has been hampered because of its unusual interaction with the E. coli inner membrane. Here, we predict atomic models for the T4 portal monomer and dodecamer, and fit the dodecamer into the cryoEM density of the phage portal vertex. The core structure, like that from other phages, is cone-shaped with the wider end containing the “wing” and “crown” domains inside the phage head. A long “stem” encloses a central channel, and a narrow “stalk” protrudes outside the capsid. A biochemical approach was developed to analyze portal function by incorporating plasmid-expressed portal protein into phage heads and determining the effect of mutations on head assembly, DNA translocation, and virion production. We found that the protruding loops of the stalk domain are involved in assembling the DNA packaging motor. A loop that connects the stalk to the channel might be required for communication between the motor and portal. The “tunnel” loops that project into the channel are essential for sealing the packaged head. These studies established that the portal is required throughout the DNA packaging process, with different domains participating at different stages of genome packaging. PMID:24126213

  4. Structure-function analysis of the DNA translocating portal of the bacteriophage T4 packaging machine.

    Science.gov (United States)

    Padilla-Sanchez, Victor; Gao, Song; Kim, Hyung Rae; Kihara, Daisuke; Sun, Lei; Rossmann, Michael G; Rao, Venigalla B

    2014-03-06

    Tailed bacteriophages and herpesviruses consist of a structurally well conserved dodecameric portal at a special 5-fold vertex of the capsid. The portal plays critical roles in head assembly, genome packaging, neck/tail attachment, and genome ejection. Although the structures of portals from phages φ29, SPP1, and P22 have been determined, their mechanistic roles have not been well understood. Structural analysis of phage T4 portal (gp20) has been hampered because of its unusual interaction with the Escherichia coli inner membrane. Here, we predict atomic models for the T4 portal monomer and dodecamer, and we fit the dodecamer into the cryo-electron microscopy density of the phage portal vertex. The core structure, like that from other phages, is cone shaped with the wider end containing the "wing" and "crown" domains inside the phage head. A long "stem" encloses a central channel, and a narrow "stalk" protrudes outside the capsid. A biochemical approach was developed to analyze portal function by incorporating plasmid-expressed portal protein into phage heads and determining the effect of mutations on head assembly, DNA translocation, and virion production. We found that the protruding loops of the stalk domain are involved in assembling the DNA packaging motor. A loop that connects the stalk to the channel might be required for communication between the motor and the portal. The "tunnel" loops that project into the channel are essential for sealing the packaged head. These studies established that the portal is required throughout the DNA packaging process, with different domains participating at different stages of genome packaging. © 2013.

  5. Diverse supramolecular structures formed by self‐assembling proteins of the B acillus subtilis spore coat

    Science.gov (United States)

    Jiang, Shuo; Wan, Qiang; Krajcikova, Daniela; Tang, Jilin; Tzokov, Svetomir B.; Barak, Imrich

    2015-01-01

    Summary Bacterial spores (endospores), such as those of the pathogens C lostridium difficile and B acillus anthracis, are uniquely stable cell forms, highly resistant to harsh environmental insults. B acillus subtilis is the best studied spore‐former and we have used it to address the question of how the spore coat is assembled from multiple components to form a robust, protective superstructure. B . subtilis coat proteins (CotY, CotE, CotV and CotW) expressed in E scherichia coli can arrange intracellularly into highly stable macro‐structures through processes of self‐assembly. Using electron microscopy, we demonstrate the capacity of these proteins to generate ordered one‐dimensional fibres, two‐dimensional sheets and three‐dimensional stacks. In one case (CotY), the high degree of order favours strong, cooperative intracellular disulfide cross‐linking. Assemblies of this kind could form exquisitely adapted building blocks for higher‐order assembly across all spore‐formers. These physically robust arrayed units could also have novel applications in nano‐biotechnology processes. PMID:25872412

  6. How Diverse are the Protein-Bound Conformations of Small-Molecule Drugs and Cofactors?

    Science.gov (United States)

    Friedrich, Nils-Ole; Simsir, Méliné; Kirchmair, Johannes

    2018-03-01

    Knowledge of the bioactive conformations of small molecules or the ability to predict them with theoretical methods is of key importance to the design of bioactive compounds such as drugs, agrochemicals and cosmetics. Using an elaborate cheminformatics pipeline, which also evaluates the support of individual atom coordinates by the measured electron density, we compiled a complete set (“Sperrylite Dataset”) of high-quality structures of protein-bound ligand conformations from the PDB. The Sperrylite Dataset consists of a total of 10,936 high-quality structures of 4548 unique ligands. Based on this dataset, we assessed the variability of the bioactive conformations of 91 small molecules—each represented by a minimum of ten structures—and found it to be largely independent of the number of rotatable bonds. Sixty-nine molecules had at least two distinct conformations (defined by an RMSD greater than 1 Å). For a representative subset of 17 approved drugs and cofactors we observed a clear trend for the formation of few clusters of highly similar conformers. Even for proteins that share a very low sequence identity, ligands were regularly found to adopt similar conformations. For cofactors, a clear trend for extended conformations was measured, although in few cases also coiled conformers were observed. The Sperrylite Dataset is available for download from http://www.zbh.uni-hamburg.de/sperrylite_dataset.

  7. Survey of large protein complexes D. vulgaris reveals great structural diversity

    Energy Technology Data Exchange (ETDEWEB)

    Han, B.-G.; Dong, M.; Liu, H.; Camp, L.; Geller, J.; Singer, M.; Hazen, T. C.; Choi, M.; Witkowska, H. E.; Ball, D. A.; Typke, D.; Downing, K. H.; Shatsky, M.; Brenner, S. E.; Chandonia, J.-M.; Biggin, M. D.; Glaeser, R. M.

    2009-08-15

    An unbiased survey has been made of the stable, most abundant multi-protein complexes in Desulfovibrio vulgaris Hildenborough (DvH) that are larger than Mr {approx} 400 k. The quaternary structures for 8 of the 16 complexes purified during this work were determined by single-particle reconstruction of negatively stained specimens, a success rate {approx}10 times greater than that of previous 'proteomic' screens. In addition, the subunit compositions and stoichiometries of the remaining complexes were determined by biochemical methods. Our data show that the structures of only two of these large complexes, out of the 13 in this set that have recognizable functions, can be modeled with confidence based on the structures of known homologs. These results indicate that there is significantly greater variability in the way that homologous prokaryotic macromolecular complexes are assembled than has generally been appreciated. As a consequence, we suggest that relying solely on previously determined quaternary structures for homologous proteins may not be sufficient to properly understand their role in another cell of interest.

  8. Mammalian keratin associated proteins (KRTAPs) subgenomes: disentangling hair diversity and adaptation to terrestrial and aquatic environments.

    Science.gov (United States)

    Khan, Imran; Maldonado, Emanuel; Vasconcelos, Vítor; O'Brien, Stephen J; Johnson, Warren E; Antunes, Agostinho

    2014-09-10

    Adaptation of mammals to terrestrial life was facilitated by the unique vertebrate trait of body hair, which occurs in a range of morphological patterns. Keratin associated proteins (KRTAPs), the major structural hair shaft proteins, are largely responsible for hair variation. We exhaustively characterized the KRTAP gene family in 22 mammalian genomes, confirming the existence of 30 KRTAP subfamilies evolving at different rates with varying degrees of diversification and homogenization. Within the two major classes of KRTAPs, the high cysteine (HS) subfamily experienced strong concerted evolution, high rates of gene conversion/recombination and high GC content. In contrast, high glycine-tyrosine (HGT) KRTAPs showed evidence of positive selection and low rates of gene conversion/recombination. Species with more hair and of higher complexity tended to have more KRATP genes (gene expansion). The sloth, with long and coarse hair, had the most KRTAP genes (175 with 141 being intact). By contrast, the "hairless" dolphin had 35 KRTAPs and the highest pseudogenization rate (74% relative to the 19% mammalian average). Unique hair-related phenotypes, such as scales (armadillo) and spines (hedgehog), were correlated with changes in KRTAPs. Gene expression variation probably also influences hair diversification patterns, for example human have an identical KRTAP repertoire as apes, but much less hair. We hypothesize that differences in KRTAP gene repertoire and gene expression, together with distinct rates of gene conversion/recombination, pseudogenization and positive selection, are likely responsible for micro and macro-phenotypic hair diversification among mammals in response to adaptations to ecological pressures.

  9. Genetic diversity of pneumococcal surface protein A in invasive pneumococcal isolates from Korean children, 1991-2016.

    Science.gov (United States)

    Yun, Ki Wook; Choi, Eun Hwa; Lee, Hoan Jong

    2017-01-01

    Pneumococcal surface protein A (PspA) is an important virulence factor of pneumococci and has been investigated as a primary component of a capsular serotype-independent pneumococcal vaccine. Thus, we sought to determine the genetic diversity of PspA to explore its potential as a vaccine candidate. Among the 190 invasive pneumococcal isolates collected from Korean children between 1991 and 2016, two (1.1%) isolates were found to have no pspA by multiple polymerase chain reactions. The full length pspA genes from 185 pneumococcal isolates were sequenced. The length of pspA varied, ranging from 1,719 to 2,301 base pairs with 55.7-100% nucleotide identity. Based on the sequences of the clade-defining regions, 68.7% and 49.7% were in PspA family 2 and clade 3/family 2, respectively. PspA clade types were correlated with genotypes using multilocus sequence typing and divided into several subclades based on diversity analysis of the N-terminal α-helical regions, which showed nucleotide sequence identities of 45.7-100% and amino acid sequence identities of 23.1-100%. Putative antigenicity plots were also diverse among individual clades and subclades. The differences in antigenicity patterns were concentrated within the N-terminal 120 amino acids. In conclusion, the N-terminal α-helical domain, which is known to be the major immunogenic portion of PspA, is genetically variable and should be further evaluated for antigenic differences and cross-reactivity between various PspA types from pneumococcal isolates.

  10. Genetic Diversity, Natural Selection and Haplotype Grouping of Plasmodium knowlesi Gamma Protein Region II (PkγRII): Comparison with the Duffy Binding Protein (PkDBPαRII).

    Science.gov (United States)

    Fong, Mun Yik; Rashdi, Sarah A A; Yusof, Ruhani; Lau, Yee Ling

    2016-01-01

    Plasmodium knowlesi is a simian malaria parasite that has been reported to cause malaria in humans in Southeast Asia. This parasite invades the erythrocytes of humans and of its natural host, the macaque Macaca fascicularis, via interaction between the Duffy binding protein region II (PkDBPαRII) and the Duffy antigen receptor on the host erythrocytes. In contrast, the P. knowlesi gamma protein region II (PkγRII) is not involved in the invasion of P. knowlesi into humans. PkγRII, however, mediates the invasion of P. knowlesi into the erythrocytes of M. mulata, a non-natural host of P. knowlesi via a hitherto unknown receptor. The haplotypes of PkDBPαRII in P. knowlesi isolates from Peninsular Malaysia and North Borneo have been shown to be genetically distinct and geographically clustered. Also, the PkDBPαRII was observed to be undergoing purifying (negative) selection. The present study aimed to determine whether similar phenomena occur in PkγRII. Blood samples from 78 knowlesi malaria patients were used. Forty-eight of the samples were from Peninsular Malaysia, and 30 were from Malaysia Borneo. The genomic DNA of the samples was extracted and used as template for the PCR amplification of the PkγRII. The PCR product was cloned and sequenced. The sequences obtained were analysed for genetic diversity and natural selection using MEGA6 and DnaSP (version 5.10.00) programmes. Genetic differentiation between the PkγRII of Peninsular Malaysia and North Borneo isolates was estimated using the Wright's FST fixation index in DnaSP (version 5.10.00). Haplotype analysis was carried out using the Median-Joining approach in NETWORK (version 4.6.1.3). A total of 78 PkγRII sequences was obtained. Comparative analysis showed that the PkγRII have similar range of haplotype (Hd) and nucleotide diversity (π) with that of PkDBPαRII. Other similarities between PkγRII and PkDBPαRII include undergoing purifying (negative) selection, geographical clustering of haplotypes

  11. Extensive diversity in the allelic frequency of Plasmodium falciparum merozoite surface proteins and glutamate-rich protein in rural and urban settings of southwestern Nigeria.

    Science.gov (United States)

    Funwei, Roland I; Thomas, Bolaji N; Falade, Catherine O; Ojurongbe, Olusola

    2018-01-02

    Nigeria carries a high burden of malaria which makes continuous surveillance for current information on genetic diversity imperative. In this study, the merozoite surface proteins (msp-1, msp-2) and glutamate-rich protein (glurp) of Plasmodium falciparum collected from two communities representing rural and urban settings in Ibadan, southwestern Nigeria were analysed. A total of 511 febrile children, aged 3-59 months, whose parents/guardians provided informed consent, were recruited into the study. Capillary blood was obtained for malaria rapid diagnostic test, thick blood smears for parasite count and blood spots on filter paper for molecular analysis. Three-hundred and nine samples were successfully genotyped for msp-1, msp-2 and glurp genes. The allelic distribution of the three genes was not significantly different in the rural and urban communities. R033 and 3D7 were the most prevalent alleles in both rural and urban communities for msp-1 and msp-2, respectively. Eleven of glurp RII region genotypes, coded I-XII, with sizes ranging from 500 to 1100 base pairs were detected in the rural setting. Genotype XI (1000-1050 bp) had the highest prevalence of 41.5 and 38.5% in rural and urban settings, respectively. Overall, 82.1 and 70.0% of samples had multiclonal infection with msp-1 gene resulting in a mean multiplicity of infection (MOI) of 2.8 and 2.6 for rural and urban samples, respectively. Msp-1 and msp-2 genes displayed higher levels of diversity and higher MOI rates than the glurp gene. Significant genetic diversity was observed between rural and urban parasite populations in Ibadan, southwestern Nigeria. The results of this study show that malaria transmission intensity in these regions is still high. No significant difference was observed between rural and urban settings, except for a completely different msp-1 allele, compared to previous reports, thereby confirming the changing face of malaria transmission in these communities. This study provides

  12. Genetic Diversity, Natural Selection and Haplotype Grouping of Plasmodium knowlesi Gamma Protein Region II (PkγRII: Comparison with the Duffy Binding Protein (PkDBPαRII.

    Directory of Open Access Journals (Sweden)

    Mun Yik Fong

    Full Text Available Plasmodium knowlesi is a simian malaria parasite that has been reported to cause malaria in humans in Southeast Asia. This parasite invades the erythrocytes of humans and of its natural host, the macaque Macaca fascicularis, via interaction between the Duffy binding protein region II (PkDBPαRII and the Duffy antigen receptor on the host erythrocytes. In contrast, the P. knowlesi gamma protein region II (PkγRII is not involved in the invasion of P. knowlesi into humans. PkγRII, however, mediates the invasion of P. knowlesi into the erythrocytes of M. mulata, a non-natural host of P. knowlesi via a hitherto unknown receptor. The haplotypes of PkDBPαRII in P. knowlesi isolates from Peninsular Malaysia and North Borneo have been shown to be genetically distinct and geographically clustered. Also, the PkDBPαRII was observed to be undergoing purifying (negative selection. The present study aimed to determine whether similar phenomena occur in PkγRII.Blood samples from 78 knowlesi malaria patients were used. Forty-eight of the samples were from Peninsular Malaysia, and 30 were from Malaysia Borneo. The genomic DNA of the samples was extracted and used as template for the PCR amplification of the PkγRII. The PCR product was cloned and sequenced. The sequences obtained were analysed for genetic diversity and natural selection using MEGA6 and DnaSP (version 5.10.00 programmes. Genetic differentiation between the PkγRII of Peninsular Malaysia and North Borneo isolates was estimated using the Wright's FST fixation index in DnaSP (version 5.10.00. Haplotype analysis was carried out using the Median-Joining approach in NETWORK (version 4.6.1.3.A total of 78 PkγRII sequences was obtained. Comparative analysis showed that the PkγRII have similar range of haplotype (Hd and nucleotide diversity (π with that of PkDBPαRII. Other similarities between PkγRII and PkDBPαRII include undergoing purifying (negative selection, geographical clustering of

  13. Allelic Diversity and Geographical Distribution of the Gene Encoding Plasmodium falciparum Merozoite Surface Protein-3 in Thailand.

    Science.gov (United States)

    Sawaswong, Vorthon; Simpalipan, Phumin; Siripoon, Napaporn; Harnyuttanakorn, Pongchai; Pattaradilokrat, Sittiporn

    2015-04-01

    Merozoite surface proteins (MSPs) of malaria parasites play critical roles during the erythrocyte invasion and so are potential candidates for malaria vaccine development. However, because MSPs are often under strong immune selection, they can exhibit extensive genetic diversity. The gene encoding the merozoite surface protein-3 (MSP-3) of Plasmodium falciparum displays 2 allelic types, K1 and 3D7. In Thailand, the allelic frequency of the P. falciparum msp-3 gene was evaluated in a single P. falciparum population in Tak at the Thailand and Myanmar border. However, no study has yet looked at the extent of genetic diversity of the msp-3 gene in P. falciparum populations in other localities. Here, we genotyped the msp-3 alleles of 63 P. falciparum samples collected from 5 geographical populations along the borders of Thailand with 3 neighboring countries (Myanmar, Laos, and Cambodia). Our study indicated that the K1 and 3D7 alleles coexisted, but at different proportions in different Thai P. falciparum populations. K1 was more prevalent in populations at the Thailand-Myanmar and Thailand-Cambodia borders, whilst 3D7 was more prevalent at the Thailand-Laos border. Global analysis of the msp-3 allele frequencies revealed that proportions of K1 and 3D7 alleles of msp-3 also varied in different continents, suggesting the divergence of malaria parasite populations. In conclusion, the variation in the msp-3 allelic patterns of P. falciparum in Thailand provides fundamental knowledge for inferring the P. falciparum population structure and for the best design of msp-3 based malaria vaccines.

  14. Genetic diversity in the block 2 region of the merozoite surface protein-1 of Plasmodium falciparum in central India

    Directory of Open Access Journals (Sweden)

    Bharti Praveen K

    2012-03-01

    Full Text Available Abstract Background Malaria continues to be a significant health problem in India. Several of the intended Plasmodium falciparum vaccine candidate antigens are highly polymorphic. The genetic diversity of P. falciparum merozoite surface protein-1 (MSP-1 has been extensively studied from various parts of the world. However, limited data are available from India. The aim of the present study was a molecular characterization of block 2 region of MSP-1 gene from the tribal-dominated, forested region of Madhya Pradesh. Methods DNA sequencing analysis was carried out in 71 field isolates collected between July 2005 to November 2005 and in 98 field isolates collected from July 2009 to December 2009. Alleles identified by DNA sequencing were aligned with the strain 3D7 and polymorphism analysis was done by using Edit Sequence tool (DNASTAR. Results The malaria positivity was 26% in 2005, which rose to 29% in 2009 and P. falciparum prevalence was also increased from 72% in 2005 to 81% in 2009. The overall allelic prevalence was higher in K1 (51% followed by MAD20 (28% and RO33 (21% in 2005 while in 2009, RO33 was highest (40% followed by K1 (36% and MAD20 (24%. Conclusions The present study reports extensive genetic variations and dynamic evolution of block 2 region of MSP-1 in central India. Characterization of antigenic diversity in vaccine candidate antigens are valuable for future vaccine trials as well as understanding the population dynamics of P. falciparum parasites in this area.

  15. RNAi pathways in Mucor: A tale of proteins, small RNAs and functional diversity.

    Science.gov (United States)

    Torres-Martínez, Santiago; Ruiz-Vázquez, Rosa M

    2016-05-01

    The existence of an RNA-mediated silencing mechanism in the opportunistic fungal pathogen Mucor circinelloides was first described in the early 2000. Since then, Mucor has reached an outstanding position within the fungal kingdom as a model system to achieve a deeper understanding of regulation of endogenous functions by the RNA interference (RNAi) machinery. M. circinelloides combines diverse components of its RNAi machinery to carry out functions not only limited to the defense against invasive nucleic acids, but also to regulate expression of its own genes by producing different classes of endogenous small RNA molecules (esRNAs). The recent discovery of a novel RNase that participates in a new RNA degradation pathway adds more elements to the gene silencing-mediated regulation. This review focuses on esRNAs in M. circinelloides, the different pathways involved in their biogenesis, and their roles in regulating specific physiological and developmental processes in response to environmental signals, highlighting the complexity of silencing-mediated regulation in fungi. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. Novel Bacterial Proteins and Lipids Reveal the Diversity of Triterpenoid Biomarker Synthesis

    Science.gov (United States)

    Wei, J. H.; Banta, A. B.; Gill, C. C. C.; Giner, J. L.; Welander, P. V.

    2017-12-01

    Lipids preserved in sediments and rocks function as organic biomarkers providing evidence for the types of organisms that lived in ancient environments. We use a combined approach utilizing comparative genomics, molecular biology, and lipid analysis to discover novel cyclic triteprenoid lipids and their biosynthetic pathways in bacteria. Here, we present two cases of bacterial synthesis of pentacylic triterpenols previously thought to be indicative of eukaryotes, which address current incongruities in the fossil record. Cyclic triterpenoid lipids, such as hopanoids and sterols, are generally associated with bacteria and eukaryotes, respectively. The pentacyclic triterpenoid tetrahymanol, first discovered in the ciliate Tetrahymena pyriformis, and its diagenetic product gammacerane, have been previously interpreted as markers for eukaryotes and linked to water column stratification. Yet the occurrence of tetrahymanol in bacteria implies our knowledge of extant tetrahymanol producers is not complete. Through comparative genomics we identified a new gene required for tetrahymanol synthesis in the bacterium Methylomicrobium alcaliphilum. This gene encodes a novel enzyme, Tetrahymanol synthase (THS), that synthesizes tetrahymanol from the hopanoid diploptene demonstrating a pathway for tetrahymanol production in bacteria distinct from that in eukaryotes. We bionformatically identified THS homologs in 104 bacterial genomes and 472 metagenomes, implying a great diversity of tetrahymanol producers. Lipids of the arborane class, such as iso-arborinol, are commonly found in modern angiosperms. Arobranes are synthesized by the enzyme oxidosqualene cyclase (OSC), which in plants can form both tetra and pentacyclic molecules. While bacteria are known to produce tetracyclic sterol compounds, bacterial synthesis of pentacyclic arborane class triterpenols of this class were previously undiscovered. We have identified a bacterium, Eudoraea adriatica, whose OSC synthesizes

  17. Regional Ocean Data Portal: Transforming Information to Knowledge

    Science.gov (United States)

    Howard, M. K.; Gayanilo, F. C.; Jochens, A. E.

    2009-12-01

    The mission of the Gulf of Mexico Coastal Ocean Observing System’s (GCOOS) regional data portal is to aggregate data and model output from distributed providers and to offer these, and derived products, through a single access point in standardized ways to a diverse set of users. The portal evolved under the NOAA-led U.S. Integrated Ocean Observing System (IOOS) program where automated largely-unattended machine-to-machine interoperability has always been a guiding tenet for system design. Initially, the portal focused on aggregating relatively homogeneous oceanographic and marine meteorological data from the principal Gulf of Mexico data providers. Obtaining community agreements from the data providers on data formats, vocabularies, and levels of service was relatively easy because the technical barriers to participation were low and we were able to provide financial support to them to make small additions or changes to their local data systems. Over time, the portal requirements became more complex as new parameters, new providers and heterogeneous data streams were added and the spatial domain increased to include beaches and adjacent wetlands. This began to strain our resources and take us outside our science domains of expertise. During the same period, the Gulf of Mexico Alliance (GOMA), a new environmental quality initiative involving the five Gulf states and Mexico with similar goals and directives as those of our sponsor, gained momentum and demanded both our attention and participation. GOMA is working, mostly among themselves, to discover or establish community standards for various types of data sets - e.g. water quality and nutrients. In addition to aggregation, the portal is also tasked with producing products from the collected information streams. Arriving at a prioritized list of desired products has been a major part of the business conducted by the GCOOS Regional Association (RA). Numerous stakeholder (e.g. emergency responders, oil and gas

  18. The secondary metabolite bioinformatics portal

    DEFF Research Database (Denmark)

    Weber, Tilmann; Kim, Hyun Uk

    2016-01-01

    . In this context, this review gives a summary of tools and databases that currently are available to mine, identify and characterize natural product biosynthesis pathways and their producers based on ‘omics data. A web portal called Secondary Metabolite Bioinformatics Portal (SMBP at http...... analytical and chemical methods gave access to this group of compounds, nowadays genomics-based methods offer complementary approaches to find, identify and characterize such molecules. This paradigm shift also resulted in a high demand for computational tools to assist researchers in their daily work......Natural products are among the most important sources of lead molecules for drug discovery. With the development of affordable whole-genome sequencing technologies and other ‘omics tools, the field of natural products research is currently undergoing a shift in paradigms. While, for decades, mainly...

  19. The OpenForest Portal as an Open Learning Ecosystem: Co-Developing in the Study of a Multidisciplinary Phenomenon in a Cultural Context

    Science.gov (United States)

    Liljeström, Anu; Enkenberg, Jorma; Vanninen, Petteri; Vartiainen, Henriikka; Pöllänen, Sinikka

    2014-01-01

    This paper discusses the OpenForest portal and its related multidisciplinary learning project. The OpenForest portal is an open learning environment and ecosystem, in which students can participate in co-developing and co-creating practices. The aim of the OpenForest ecosystem is to create an extensive interactive network of diverse learning…

  20. Quantitative vs. subjective portal verification using digital portal images

    International Nuclear Information System (INIS)

    Bissett, Randy; Leszczynski, Konrad; Loose, Stephen; Boyko, Susan; Dunscombe, Peter

    1996-01-01

    Purpose: Off-line, computer-aided prescription (simulator) and treatment (portal) image registration using chamfer matching has been implemented on PC based viewing station. The purposes of this study were (a) to evaluate the performance of interactive anatomy and field edge extraction and subsequent registration, and (b) to compare observer's perceptions of field accuracy with measured discrepancies following anatomical registration. Methods and Materials: Prescription-treatment image pairs for 48 different patients were examined in this study. Digital prescription images were produced with the aid of a television camera and a digital frame grabber, while the treatment images were obtained directly from an on-line portal imaging system. To facilitate perception of low contrast anatomical detail, on-line portal images were enhanced with selective adaptive histogram equalization prior to extraction of anatomical edges. Following interactive extraction of anatomical and field border information by an experienced observer, the identified anatomy was registered using chamber matching. The degree of conformity between the prescription and treatment fields was quantified using several parameters, which included relative prescription field coverage and overcoverage, as well as the translational and rotational displacements as measured by chamfer matching applied to the boundaries of the two fields. These quantitative measures were compared with subjective evaluations made by four radiation oncologists. Results: All the images in this series that included a range of the most commonly seen treatment sites were registered and the conformity parameters were found. The mean treatment/prescription field coverage and overcoverage were approximately 95 and 7%, respectively before registration. The mean translational displacement in the transverse and cranio-caudal directions were 2.9 and 3.4 mm, respectively. The mean rotational displacement was approximately 2 deg. . For all

  1. Genetic diversity and molecular evolution of Ornithogalum mosaic virus based on the coat protein gene sequence

    Directory of Open Access Journals (Sweden)

    Fangluan Gao

    2018-03-01

    Full Text Available Ornithogalum mosaic virus (OrMV has a wide host range and affects the production of a variety of ornamentals. In this study, the coat protein (CP gene of OrMVwas used to investigate the molecular mechanisms underlying the evolution of this virus. The 36 OrMV isolates fell into two groups which have significant subpopulation differentiation with an FST value of 0.470. One isolate was identified as a recombinant and the other 35 recombination-free isolates could be divided into two major clades under different evolutionary constraints with dN/dS values of 0.055 and 0.028, respectively, indicating a role of purifying selection in the differentiation of OrMV. In addition, the results from analysis of molecular variance (AMOVA indicated that the effect of host species on the genetic divergence of OrMV is greater than that of geography. Furthermore, OrMV isolates from the genera Ornithogalum, Lachenalia and Diuri tended to group together, indicating that OrMV diversification was maintained, in part, by host-driven adaptation.

  2. Differential 3’ processing of specific transcripts expands regulatory and protein diversity across neuronal cell types

    Science.gov (United States)

    Jereb, Saša; Hwang, Hun-Way; Van Otterloo, Eric; Govek, Eve-Ellen; Fak, John J; Yuan, Yuan; Hatten, Mary E

    2018-01-01

    Alternative polyadenylation (APA) regulates mRNA translation, stability, and protein localization. However, it is unclear to what extent APA regulates these processes uniquely in specific cell types. Using a new technique, cTag-PAPERCLIP, we discovered significant differences in APA between the principal types of mouse cerebellar neurons, the Purkinje and granule cells, as well as between proliferating and differentiated granule cells. Transcripts that differed in APA in these comparisons were enriched in key neuronal functions and many differed in coding sequence in addition to 3’UTR length. We characterize Memo1, a transcript that shifted from expressing a short 3’UTR isoform to a longer one during granule cell differentiation. We show that Memo1 regulates granule cell precursor proliferation and that its long 3’UTR isoform is targeted by miR-124, contributing to its downregulation during development. Our findings provide insight into roles for APA in specific cell types and establish a platform for further functional studies. PMID:29578408

  3. EVALUATION OF ENEMAS CONTAINING SUCRALFATE IN TISSUE CONTENT OF MUC-2 PROTEIN IN EXPERIMENTAL MODEL OF DIVERSION COLITIS.

    Science.gov (United States)

    Fernandez, Oscar Orlando Araya; Pereira, José Aires; Campos, Fábio Guilherme; Araya, Carolina Mardegan; Marinho, Gabriele Escocia; Novo, Rafaela de Souza; Oliveira, Thais Silva de; Franceschi, Yara Tinoco; Martinez, Carlos Augusto Real

    2017-01-01

    The effects of topical application of sucralfate (SCF) on the tissue content of MUC-2 protein have not yet been evaluated in experimental models of diversion colitis. To measure the tissue content of MUC-2 protein in the colonic mucosa diverted from fecal stream submitted to the SCF intervention. Thirty-six rats underwent derivation of intestinal transit through proximal colostomy and distal mucous fistula. The animals were divided into three groups which were submitted application of enemas with saline, SCF 1 g/kg/day and SCF 2 g/kg/day. Each group was divided into two subgroups, according to euthanasia was done after two or four weeks. The colitis diagnosis was established by histopathological study and the inflammatory intensity was evaluated by previously validated scale. The MUC-2 protein was identified by immunohistochemistry and the tissue content was measured computerized morphometry). The application of enemas with SCF in the concentration of 2 g/kg/day reduced inflammatory score of the segments that were diverted from fecal stream. The content of MUC-2 in diverted colon of the animals submitted to the intervention with SCF, independently of intervention period and the used concentration, was significantly greater than animals submitted to the application of enemas containing saline (p< 0.01). The content of MUC-2 after the intervention with SCF in the concentration of 2 g/kg/day was significantly higher when compared to the animals submitted to the application containing SCF at concentration of 1.0 g/kg/day (p<0.01). The tissue content of MUC-2 reached the highest values after intervention with SCF in the concentration of 2 g/kg/day for four weeks (p<0.01). Conclusion: The preventive application of enemas containing SCF reduces the inflammatory score and avoids the reduction of tissue content of MUC-2, suggesting that the substance is a valid therapeutic strategy to preserve the mucus layer that covers the intestinal epithelium.

  4. Uzbekistan Radiation Portal Monitoring System

    International Nuclear Information System (INIS)

    Richardson, J; Knapp, R; Loshak, A; Yuldashev, B; Petrenko, V

    2005-01-01

    The work proposed in this presentation builds on the foundation set by the DTRA funded demonstration project begun in 2000 and completed in December of 2003. This previous work consisted of two phases whose overall objective was to install portal radiation monitors at four select ports-of-entry in Uzbekistan (Tashkent International Airport, Gisht-Kuprik (Kazakhstan border), Alat (Turkmenistan border), and Termez (Afghanistan border)) in order to demonstrate their effectiveness in preventing the illicit trafficking of nuclear materials. The objectives also included developing and demonstrating capabilities in the design, installation, operation, training, and maintenance of a radiation portal monitoring system. The system and demonstration project has proved successful in many ways. An effective working relationship among the Uzbekistan Customs Services, Uzbekistan Border Guards, and Uzbekistan Institute of Nuclear Physics has been developed. There has been unprecedented openness with the sharing of portal monitor data with Lawrence Livermore National Laboratory. The system has proved to be effective, with detection of illicit trafficking, and, at Alat, an arrest of three persons illegally transporting radioactive materials into Turkmenistan. The demonstration project has made Uzbekistan a model nonproliferation state in Central Asia and, with an expanded program, places them in a position to seal a likely transit route for illicit nuclear materials. These results will be described. In addition, this work is currently being expanded to include additional ports-of-entry in Uzbekistan. The process for deciding on which additional ports-of-entry to equip will also be described

  5. Treatment of portal hypertension caused by benign main portal vein stenosis with endovascular stent

    International Nuclear Information System (INIS)

    Huang Mingsheng; Shan Hong; Jiang Zaibo; Guan Shouhai; Zhu Kangshun; Li Zhengran; Zhou Yubin; He Bingjun

    2004-01-01

    Objective: To evaluate the value of endovascular stent in the treatment of portal hypertension caused by benign main portal vein stenosis. Methods: Portal vein stents were implanted in 6 patients with benign main portal vein stenosis (inflammatory stenosis in 3 cases, postprocedure of liver transplantation in another 3 cases). The change of portal vein pressure, the patency of portal vein, relative clinical symptoms, complications, and survival were evaluated. Results: Six metallic stents were successfully placed across the portal vein stenotic or obstructive lesions in all 6 patients. Mean portal venous pressure decreased significantly after stent implantation from (37.3 ± 4.7) cm H 2 O (1 cm H 2 O=0.098 kPa) to (18.0 ± 1.9) cm H 2 O (P<0.001). The portal blood flow was restored, and the symptoms caused by portal hypertension were eliminated. There was no severe procedure-related complication. Follow-up time was from 5 to 36 months. The portal vein remained patent during the follow-up. All patients survived except one patient who died of other complications of liver transplantation. Conclusion: Percutaneous portal vein stent placement for the treatment of the benign main portal vein stenosis is safe and effective. (authors)

  6. The effect of partial portal decompression on portal blood flow and effective hepatic blood flow in man: a prospective study.

    Science.gov (United States)

    Rosemurgy, A S; McAllister, E W; Godellas, C V; Goode, S E; Albrink, M H; Fabri, P J

    1995-12-01

    With the advent of transjugular intrahepatic porta-systemic stent shunt and the wider application of the surgically placed small diameter prosthetic H-graft portacaval shunt (HGPCS), partial portal decompression in the treatment of portal hypertension has received increased attention. The clinical results supporting the use of partial portal decompression are its low incidence of variceal rehemorrhage due to decreased portal pressures and its low rate of hepatic failure, possibly due to maintenance of blood flow to the liver. Surprisingly, nothing is known about changes in portal hemodynamics and effective hepatic blood flow following partial portal decompression. To prospectively evaluate changes in portal hemodynamics and effective hepatic blood flow brought about by partial portal decompression, the following were determined in seven patients undergoing HGPCS: intraoperative pre- and postshunt portal vein pressures and portal vein-inferior vena cava pressure gradients, intraoperative pre- and postshunt portal vein flow, and pre- and postoperative effective hepatic blood flow. With HGPCS, portal vein pressures and portal vein-inferior vena cava pressure gradients decreased significantly, although portal pressures remained above normal. In contrast to the significant decreases in portal pressures, portal vein blood flow and effective hepatic blood flow do not decrease significantly. Changes in portal vein pressures and portal vein-inferior vena cava pressure gradients are great when compared to changes in portal vein flow and effective hepatic blood flow. Reduction of portal hypertension with concomitant maintenance of hepatic blood flow may explain why hepatic dysfunction is avoided following partial portal decompression.

  7. Diversity and impact of rare variants in genes encoding the platelet G protein-coupled receptors.

    Science.gov (United States)

    Jones, Matthew L; Norman, Jane E; Morgan, Neil V; Mundell, Stuart J; Lordkipanidzé, Marie; Lowe, Gillian C; Daly, Martina E; Simpson, Michael A; Drake, Sian; Watson, Steve P; Mumford, Andrew D

    2015-04-01

    Platelet responses to activating agonists are influenced by common population variants within or near G protein-coupled receptor (GPCR) genes that affect receptor activity. However, the impact of rare GPCR gene variants is unknown. We describe the rare single nucleotide variants (SNVs) in the coding and splice regions of 18 GPCR genes in 7,595 exomes from the 1,000-genomes and Exome Sequencing Project databases and in 31 cases with inherited platelet function disorders (IPFDs). In the population databases, the GPCR gene target regions contained 740 SNVs (318 synonymous, 410 missense, 7 stop gain and 6 splice region) of which 70 % had global minor allele frequency (MAF) < 0.05 %. Functional annotation using six computational algorithms, experimental evidence and structural data identified 156/740 (21 %) SNVs as potentially damaging to GPCR function, most commonly in regions encoding the transmembrane and C-terminal intracellular receptor domains. In 31 index cases with IPFDs (Gi-pathway defect n=15; secretion defect n=11; thromboxane pathway defect n=3 and complex defect n=2) there were 256 SNVs in the target regions of 15 stimulatory platelet GPCRs (34 unique; 12 with MAF< 1 % and 22 with MAF≥ 1 %). These included rare variants predicting R122H, P258T and V207A substitutions in the P2Y12 receptor that were annotated as potentially damaging, but only partially explained the platelet function defects in each case. Our data highlight that potentially damaging variants in platelet GPCR genes have low individual frequencies, but are collectively abundant in the population. Potentially damaging variants are also present in pedigrees with IPFDs and may contribute to complex laboratory phenotypes.

  8. The questions of working out radiology patterns of portal hypertension

    International Nuclear Information System (INIS)

    Vyikman, Ya.E.

    2008-01-01

    A foundation for radiological patterns of each type of portal hypertension (PH) at various stages of its development. Portal blood pressure, diameter of splenic and portal veins, volume blood flow velocity in the portal and splenic veins, incidence of hypersplenism, enlargement of the caudate lobe of the liver and gallbladder fossa are the most informative in differentiation of various forms of portal hypertension

  9. Cavernous transformation of the portal vein

    International Nuclear Information System (INIS)

    Lehotska, V.; Dostalova, K.; Durkovsky, A.; Samal, V.

    1995-01-01

    In this contribution, the authors give an account of a rare case of a cavernous transformation of the portal vein that may have originated secondarily in a proliferative hematogenous disease with a polyglobulia and thrombosis in the periferal blood count as well as development of portal hypertension of a prehepatal type. The state of hyper-coagulation in a myeloproliferative disease may have lead to a chronic thrombosis of the portal vein with a subsequent malformation of the portal vein in terms of a cavernous transformation of the portal vein. The case is an interesting one because of the discrepancy between the gravity of the thrombotic complication and slightness of the symptoms in the clinical picture. The authors point out the importance of ultrasonography and computed tomography examination following the intravenous application of a water solution of a contrast medium in a morphologic diagnosing of a rare complication of a chronic thrombotic clot of the portal vein - the cavernous transformation. (authors)

  10. [Predictive value of ultrasonography in portal hypertension].

    Science.gov (United States)

    Moreno, E; Torres, P; Trejo, C; Barra Ostoni, V; Ortega, C; Römer, H

    1991-01-01

    Portal hypertension is a common pathology in childhood and one of its most common causes is cavernomatosis of the portal vein. This obstruction causes hemodynamic changes which lead to splenomegaly and collateral circulation. Esophageal varices are one of the most important sequelae, which endanger the patient's life because of a bleeding tendency. Ecosonography helps to detect the thickening of the lesser omentum vis a vis the aortic diameter, caused by the collateral circulation. We studied 15 children presenting with portal hypertension resulting from portal vein cavernomatosis; we performed an upper GI endoscopy and abdominal ecosonography. The endoscopy revealed grade II esophageal varices in 20% of cases, the remaining 80% had grade III and grade IV. Ecosonography revealed an increased lesser omentum/aorta ratio in children with portal hypertension, compared to controls (p portal hypertension.

  11. Intrahepatic upregulation of MRTF-A signaling contributes to increased hepatic vascular resistance in cirrhotic rats with portal hypertension.

    Science.gov (United States)

    Zheng, Lei; Qin, Jun; Sun, Longci; Gui, Liang; Zhang, Chihao; Huang, Yijun; Deng, Wensheng; Huang, An; Sun, Dong; Luo, Meng

    2017-06-01

    Portal hypertension in cirrhosis is mediated, in part, by increased intrahepatic resistance, reflecting massive structural changes associated with fibrosis and intrahepatic vasoconstriction. Activation of the Rho/MRTF/SRF signaling pathway is essential for the cellular regulatory network of fibrogenesis. The aim of this study was to investigate MRTF-A-mediated regulation of intrahepatic fibrogenesis in cirrhotic rats. Portal hypertension was induced in rats via an injection of CCl 4 oil. Hemodynamic measurements were obtained using a polyethylene PE-50 catheter and pressure transducers. Expression of hepatic fibrogenesis was measured using histological staining. Expression of protein was measured using western blotting. Upregulation of MRTF-A protein expression in the livers of rats with CCl 4 -induced cirrhosis was relevant to intrahepatic resistance and hepatic fibrogenesis in portal hypertensive rats with increased modeling time. Inhibition of MRTF-A by CCG-1423 decelerated hepatic fibrosis, decreased intrahepatic resistance and portal pressure, and alleviated portal hypertension. Increased intrahepatic resistance in rats with CCl 4 -induced portal hypertension is associated with an upregulation of MRTF-A signaling. Inhibition of this pathway in the liver can decrease hepatic fibrosis and intrahepatic resistance, as well as reduce portal pressure in cirrhotic rats with CCl 4 -induced portal hypertension. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  12. Determining the optimal portal blood volume in a shunt before surgery in extrahepatic portal hypertension

    Directory of Open Access Journals (Sweden)

    Yurchuk Vladimir A

    2016-04-01

    Full Text Available The aim of the study: To determine the necessary shunt diameter and assess the optimal portal blood volume in a shunt in children with extrahepatic portal hypertension before the portosystemic shunt surgery. Changes in the liver hemodynamics were studied in 81 children aged from 4 to 7 years with extrahepatic portal hypertension. We established that it is necessary to calculate the shunt diameter and the blood volume in a shunt in patients with extrahepatic portal hypertension before the portosystemic shunt surgery. It allows us to preserve the hepatic portal blood flow and effectively decrease the pressure in the portal system. Portosystemic shunt surgery in patients with extrahepatic portal hypertension performed in accordance with the individualized shunt volume significantly decreases portal pressure, preserves stable hepatic hemodynamics and prevents gastro-esophageal hemorrhage.

  13. Noncirrhotic portal fibrosis after Wilms' tumor therapy

    International Nuclear Information System (INIS)

    Barnard, J.A.; Marshall, G.S.; Neblett, W.W.; Gray, G.; Ghishan, F.K.

    1986-01-01

    A 9-yr-old girl developed massive hemorrhage from esophageal varices 2 yr after combined modality therapy for Wilms' tumor. Evaluation showed a patent extrahepatic portal venous system and an elevated splenic pulp pressure. In contrast to previous reports of hepatopathy after irradiation injury, histologic sections of the liver did not demonstrate occlusion of the central veins, but rather a diffuse obliteration of intrahepatic portal venous radicles. This pattern of noncirrhotic portal fibrosis has not been described following antitumor therapy

  14. A View on Electronic Learning Portals

    OpenAIRE

    Zavaraqi, Rasoul

    2009-01-01

    Portals are less than a decade old. They have come to cover are areas of electronic services, including electronic learning. With their efficient communication and information capabilities, these portals are capable of realizing novel learning concepts such as structuralism, active and cooperative learning. The present paper endeavors to discuss the latest understanding, theories and concepts regarding E-learning portals and to review the issues and steps that should be considered in designin...

  15. Preduodenal portal vein: its surgical significance.

    Science.gov (United States)

    Makey, D A; Bowen, J C

    1978-11-01

    Preduodenal portal vein is a rare anatomical variant which may be one of many anomalies in the neonate with duodenal "atresia." Preduodenal portal vein also may be an occasional finding in an adult undergoing biliary, gastric, or pancreatic surgery. Awareness and recognition of the anomaly are essential for the avoidance of injury during such operations. We report here a symptomless patient whose preduodenal portal vein was discovered at cholecystectomy.

  16. Strain-specific diversity of mucus-binding proteins in the adhesion and aggregation properties of Lactobacillus reuteri.

    Science.gov (United States)

    Mackenzie, Donald A; Jeffers, Faye; Parker, Mary L; Vibert-Vallet, Amandine; Bongaerts, Roy J; Roos, Stefan; Walter, Jens; Juge, Nathalie

    2010-11-01

    Mucus-binding proteins (MUBs) have been revealed as one of the effector molecules involved in mechanisms of the adherence of lactobacilli to the host; mub, or mub-like, genes are found in all of the six genomes of Lactobacillus reuteri that are available. We recently reported the crystal structure of a Mub repeat from L. reuteri ATCC 53608 (also designated strain 1063), revealing an unexpected recognition of immunoglobulins. In the current study, we explored the diversity of the ATCC 53608 mub gene, and MUB expression levels in a large collection of L. reuteri strains isolated from a range of vertebrate hosts. This analysis revealed that the MUB was only detectable on the cell surface of two highly related isolates when using antibodies that were raised against the protein. There was considerable variation in quantitative mucus adhesion in vitro among L. reuteri strains, and mucus binding showed excellent correlation with the presence of cell-surface ATCC 53608 MUB. ATCC 53608 MUB presence was further highly associated with the autoaggregation of L. reuteri strains in washed cell suspensions, suggesting a novel role of this surface protein in cell aggregation. We also characterized MUB expression in representative L. reuteri strains. This analysis revealed that one derivative of strain 1063 was a spontaneous mutant that expressed a C-terminally truncated version of MUB. This frameshift mutation was caused by the insertion of a duplicated 13 nt sequence at position 4867 nt in the mub gene, producing a truncated MUB also lacking the C-terminal LPxTG region, and thus unable to anchor to the cell wall. This mutant, designated 1063N (mub-4867(i)), displayed low mucus-binding and aggregation capacities, further providing evidence for the contribution of cell-wall-anchored MUB to such phenotypes. In conclusion, this study provided novel information on the functional attributes of MUB in L. reuteri, and further demonstrated that MUB and MUB-like proteins

  17. Web-based Service Portal in Healthcare

    Science.gov (United States)

    Silhavy, Petr; Silhavy, Radek; Prokopova, Zdenka

    Information delivery is one the most important task in healthcare. The growing sector of electronic healthcare has an important impact on the information delivery. There are two basic approaches towards information delivering. The first is web portal and second is touch-screen terminal. The aim of this paper is to investigate the web-based service portal. The most important advantage of web-based portal in the field of healthcare is an independent access for patients. This paper deals with the conditions and frameworks for healthcare portals

  18. Mitochondrial Biogenesis in Diverse Cauliflower Cultivars under Mild and Severe Drought. Impaired Coordination of Selected Transcript and Proteomic Responses, and Regulation of Various Multifunctional Proteins

    Directory of Open Access Journals (Sweden)

    Michał Rurek

    2018-04-01

    Full Text Available Mitochondrial responses under drought within Brassica genus are poorly understood. The main goal of this study was to investigate mitochondrial biogenesis of three cauliflower (Brassica oleracea var. botrytis cultivars with varying drought tolerance. Diverse quantitative changes (decreases in abundance mostly in the mitochondrial proteome were assessed by two-dimensional gel electrophoresis (2D PAGE coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS. Respiratory (e.g., complex II, IV (CII, CIV and ATP synthase subunits, transporter (including diverse porin isoforms and matrix multifunctional proteins (e.g., components of RNA editing machinery were diversely affected in their abundance under two drought levels. Western immunoassays showed additional cultivar-specific responses of selected mitochondrial proteins. Dehydrin-related tryptic peptides (found in several 2D spots immunopositive with dehydrin-specific antisera highlighted the relevance of mitochondrial dehydrin-like proteins for the drought response. The abundance of selected mRNAs participating in drought response was also determined. We conclude that mitochondrial biogenesis was strongly, but diversely affected in various cauliflower cultivars, and associated with drought tolerance at the proteomic and functional levels. However, discussed alternative oxidase (AOX regulation at the RNA and protein level were largely uncoordinated due to the altered availability of transcripts for translation, mRNA/ribosome interactions, and/or miRNA impact on transcript abundance and translation.

  19. Mitochondrial Biogenesis in Diverse Cauliflower Cultivars under Mild and Severe Drought. Impaired Coordination of Selected Transcript and Proteomic Responses, and Regulation of Various Multifunctional Proteins

    Science.gov (United States)

    Rurek, Michał; Czołpińska, Magdalena; Staszak, Aleksandra Maria; Nowak, Witold; Krzesiński, Włodzimierz; Spiżewski, Tomasz

    2018-01-01

    Mitochondrial responses under drought within Brassica genus are poorly understood. The main goal of this study was to investigate mitochondrial biogenesis of three cauliflower (Brassica oleracea var. botrytis) cultivars with varying drought tolerance. Diverse quantitative changes (decreases in abundance mostly) in the mitochondrial proteome were assessed by two-dimensional gel electrophoresis (2D PAGE) coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Respiratory (e.g., complex II, IV (CII, CIV) and ATP synthase subunits), transporter (including diverse porin isoforms) and matrix multifunctional proteins (e.g., components of RNA editing machinery) were diversely affected in their abundance under two drought levels. Western immunoassays showed additional cultivar-specific responses of selected mitochondrial proteins. Dehydrin-related tryptic peptides (found in several 2D spots) immunopositive with dehydrin-specific antisera highlighted the relevance of mitochondrial dehydrin-like proteins for the drought response. The abundance of selected mRNAs participating in drought response was also determined. We conclude that mitochondrial biogenesis was strongly, but diversely affected in various cauliflower cultivars, and associated with drought tolerance at the proteomic and functional levels. However, discussed alternative oxidase (AOX) regulation at the RNA and protein level were largely uncoordinated due to the altered availability of transcripts for translation, mRNA/ribosome interactions, and/or miRNA impact on transcript abundance and translation. PMID:29642585

  20. Circulating CXCL10 in cirrhotic portal hypertension might reflect systemic inflammation and predict ACLF and mortality

    DEFF Research Database (Denmark)

    Lehmann, Jennifer M; Claus, Karina; Jansen, Christian

    2018-01-01

    BACKGROUND & AIMS: CXCR% ligands play an important role in hepatic injury, inflammation and fibrosis. While CXCL9 and CXCL11 are associated with survival in patients receiving transjugular intrahepatic portosystemic shunt (TIPS), the role of CXCL10 in severe portal hypertension remains unknown...... inflammation and it is correlated with acute decompensation, ACLF and complications in patients with severe portal hypertension receiving TIPS. CXCL10 predicts survival in these patients and a decrease in CXCL10 after TIPS may be considered a good prognostic factor........ METHODS: A total of 89 cirrhotic patients were analysed. CXCL10 protein levels were measured in portal and hepatic blood at TIPS insertion and 2 weeks later in 24 patients. CXCL10 and IL8 levels were assessed in portal, hepatic, cubital vein and right atrium blood in a further 25 patients at TIPS...

  1. Portal control of viral prohead expansion and DNA packaging

    International Nuclear Information System (INIS)

    Ray, Krishanu; Oram, Mark; Ma, Jinxia; Black, Lindsay W.

    2009-01-01

    Bacteriophage T4 terminase packages DNA in vitro into empty small or large proheads (esps or elps). In vivo maturation of esps yields the more stable and voluminous elps required to contain the 170 kb T4 genome. Functional proheads can be assembled containing portal-GFP fusion proteins. In the absence of terminase activity these accumulated in esps in vivo, whereas wild-type portals were found in elps. By nuclease protection assay dsDNAs of lengths 0.1, 0.2, 0.5, 5, 11, 20, 40 or 170 kb were efficiently packaged into wild-type elps in vitro, but less so into esps and gp20-GFP elps; particularly with DNAs shorter than 11 kb. However, 0.1 kb substrates were equally efficiently packaged into all types of proheads as judged by fluorescence correlation spectroscopy. These data suggest the portal controls the expansion of the major capsid protein lattice during prohead maturation, and that this expansion is necessary for DNA protection but not for packaging.

  2. House spider genome uncovers evolutionary shifts in the diversity and expression of black widow venom proteins associated with extreme toxicity.

    Science.gov (United States)

    Gendreau, Kerry L; Haney, Robert A; Schwager, Evelyn E; Wierschin, Torsten; Stanke, Mario; Richards, Stephen; Garb, Jessica E

    2017-02-16

    Black widow spiders are infamous for their neurotoxic venom, which can cause extreme and long-lasting pain. This unusual venom is dominated by latrotoxins and latrodectins, two protein families virtually unknown outside of the black widow genus Latrodectus, that are difficult to study given the paucity of spider genomes. Using tissue-, sex- and stage-specific expression data, we analyzed the recently sequenced genome of the house spider (Parasteatoda tepidariorum), a close relative of black widows, to investigate latrotoxin and latrodectin diversity, expression and evolution. We discovered at least 47 latrotoxin genes in the house spider genome, many of which are tandem-arrayed. Latrotoxins vary extensively in predicted structural domains and expression, implying their significant functional diversification. Phylogenetic analyses show latrotoxins have substantially duplicated after the Latrodectus/Parasteatoda split and that they are also related to proteins found in endosymbiotic bacteria. Latrodectin genes are less numerous than latrotoxins, but analyses show their recruitment for venom function from neuropeptide hormone genes following duplication, inversion and domain truncation. While latrodectins and other peptides are highly expressed in house spider and black widow venom glands, latrotoxins account for a far smaller percentage of house spider venom gland expression. The house spider genome sequence provides novel insights into the evolution of venom toxins once considered unique to black widows. Our results greatly expand the size of the latrotoxin gene family, reinforce its narrow phylogenetic distribution, and provide additional evidence for the lateral transfer of latrotoxins between spiders and bacterial endosymbionts. Moreover, we strengthen the evidence for the evolution of latrodectin venom genes from the ecdysozoan Ion Transport Peptide (ITP)/Crustacean Hyperglycemic Hormone (CHH) neuropeptide superfamily. The lower expression of latrotoxins in

  3. A user-oriented model for global enterprise portal design

    NARCIS (Netherlands)

    Feng, X.; Ehrenhard, Michel Léon; Hicks, Jeff; Maathuis, Stephanus Johannes; Maathuis, S.J.; Hou, Y.

    2010-01-01

    Enterprise portals collect and synthesise information from various systems to deliver personalised and highly relevant information to users. Enterprise portals' design and applications are widely discussed in the literature; however, the implications of portal design in a global networked

  4. Patient portals - An online tool for your health

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/patientinstructions/000880.htm Patient portals - an online tool for your health To ... is private and secure. What is in a Patient Portal? With a patient portal, you can: Make ...

  5. The LCOGT Observation Portal, Data Pipeline and Science Archive

    Science.gov (United States)

    Lister, Tim; LCOGT Science Archive Team

    2014-01-01

    Las Cumbres Observatory Global Telescope (LCOGT) is building and deploying a world-wide network of optical telescopes dedicated to time-domain astronomy. During 2012-2013, we successfully deployed and commissioned nine new 1m telescopes at McDonald Observatory (Texas), CTIO (Chile), SAAO (South Africa) and Siding Spring Observatory (Australia). New, improved cameras and additional telescopes will be deployed during 2014. To enable the diverse LCOGT user community of scientific and educational users to request observations on the LCOGT Network and to see their progress and get access to their data, we have developed an Observation Portal system. This Observation Portal integrates proposal submission and observation requests with seamless access to the data products from the data pipelines in near-realtime and long-term products from the Science Archive. We describe the LCOGT Observation Portal and the data pipeline, currently in operation, which makes use of the ORAC-DR automated recipe-based data reduction pipeline and illustrate some of the new data products. We also present the LCOGT Science Archive, which is being developed in partnership with the Infrared Processing and Analysis Center (IPAC) and show some of the new features the Science Archive provides.

  6. Diverse replication-associated protein encoding circular DNA viruses in guano samples of Central-Eastern European bats.

    Science.gov (United States)

    Kemenesi, Gábor; Kurucz, Kornélia; Zana, Brigitta; Földes, Fanni; Urbán, Péter; Vlaschenko, Anton; Kravchenko, Kseniia; Budinski, Ivana; Szodoray-Parádi, Farkas; Bücs, Szilárd; Jére, Csaba; Csősz, István; Szodoray-Parádi, Abigél; Estók, Péter; Görföl, Tamás; Boldogh, Sándor; Jakab, Ferenc

    2018-03-01

    Circular replication-associated protein encoding single-stranded DNA (CRESS DNA) viruses are increasingly recognized worldwide in a variety of samples. Representative members include well-described veterinary pathogens with worldwide distribution, such as porcine circoviruses or beak and feather disease virus. In addition, numerous novel viruses belonging to the family Circoviridae with unverified pathogenic roles have been discovered in different human samples. Viruses of the family Genomoviridae have also been described as being highly abundant in different faecal and environmental samples, with case reports showing them to be suspected pathogens in human infections. In order to investigate the genetic diversity of these viruses in European bat populations, we tested guano samples from Georgia, Hungary, Romania, Serbia and Ukraine. This resulted in the detection of six novel members of the family Circoviridae and two novel members of the family Genomoviridae. Interestingly, a gemini-like virus, namely niminivirus, which was originally found in raw sewage samples in Nigeria, was also detected in our samples. We analyzed the nucleotide composition of members of the family Circoviridae to determine the possible host origins of these viruses. This study provides the first dataset on CRESS DNA viruses of European bats, and members of several novel viral species were discovered.

  7. Application of the major capsid protein as a marker of the phylogenetic diversity of Emiliania huxleyi viruses.

    Science.gov (United States)

    Rowe, Janet M; Fabre, Marie-Françoise; Gobena, Daniel; Wilson, William H; Wilhelm, Steven W

    2011-05-01

    Studies of the Phycodnaviridae have traditionally relied on the DNA polymerase (pol) gene as a biomarker. However, recent investigations have suggested that the major capsid protein (MCP) gene may be a reliable phylogenetic biomarker. We used MCP gene amplicons gathered across the North Atlantic to assess the diversity of Emiliania huxleyi-infecting Phycodnaviridae. Nucleotide sequences were examined across >6000 km of open ocean, with comparisons between concentrates of the virus-size fraction of seawater and of lysates generated by exposing host strains to these same virus concentrates. Analyses revealed that many sequences were only sampled once, while several were over-represented. Analyses also revealed nucleotide sequences distinct from previous coastal isolates. Examination of lysed cultures revealed a new richness in phylogeny, as MCP sequences previously unrepresented within the existing collection of E. huxleyi viruses (EhV) were associated with viruses lysing cultures. Sequences were compared with previously described EhV MCP sequences from the North Sea and a Norwegian Fjord, as well as from the Gulf of Maine. Principal component analysis indicates that location-specific distinctions exist despite the presence of sequences common across these environments. Overall, this investigation provides new sequence data and an assessment on the use of the MCP gene. © 2011 Federation of European Microbiological Societies Published by Blackwell Publishing Ltd. All rights reserved.

  8. Portal Web 2.0

    OpenAIRE

    Barba Hidalgo, José Manuel

    2008-01-01

    El tema que es tracta en aquest projecte gira al voltant del concepte Web 2.0. Després d’una introducció on es comenten les principals característiques que defineixen el conjunt d’aplicacions agrupades al voltant d’aquesta filosofia, s’analitzen diferents entorns de desenvolupament d’aplicacions Web, amb l’objectiu de crear un portal que segueixi els principis Web 2.0. El resultat de l’estudi presenta a Ruby on Rails com un ferm candidat, això fa que es procedeixi a estudiar aq...

  9. Portal web para comunicaciones seguras

    OpenAIRE

    Jurado Villalobos, Rodrigo

    2015-01-01

    Proyecto teórico-práctico de investigación, enfocado a obtener un mayor conocimiento del funcionamiento de los protocolos y funciones de seguridad criptógrafica así como explorar las limitaciones y buscar nuevas vías de implementar la seguridad de las comunicaciones a través del desarrollo de una aplicación que dé uso en un entorno “real” de estos protocolos de seguridad. Dicha aplicación consistirá en un portal web de mensajería entre usuarios que empleará sistemas criptográficos tanto en el...

  10. Doppler US evaluation of the hypertensive portal system

    International Nuclear Information System (INIS)

    Needleman, L.; Kurtz, A.B.; Bezzi, M.; Rifkin, M.D.; Pasto, M.E.; Pennell, R.G.; Baltarowich, O.H.; Goldberg, B.B.

    1986-01-01

    In patients with known portal hypertension, pulsed Doppler US was used for qualitative and directional evaluation of flow in the portal venous system and collateral vessels. Most patients had normal hepatopetal flow. Doppler US revealed the following abnormal blood flow patterns: hepatofugal portal flow, bidirectional portal flow, intrahepatic portal shunting, flow in portasystemic collaterals, and hepatic vein obstruction. Doppler US can provide important clinical information in the evaluation of portal hypertension

  11. Portal in the power sector - it is vision or reality?

    International Nuclear Information System (INIS)

    Hornak, L.

    2004-01-01

    The goal of the presentation is to introduce the portal solutions, to describe the types, characteristic features and abilities of the portal and to define required attributes of the portal in the power segment. The author will try to answer the questions whether such portal exists at the present time, what is needed in order to implement the portal and how to do the portal maintenance and management

  12. Noninvasive measurement of nutrient portal blood shunting: an experimental study with [14C]ursodeoxycholic acid

    International Nuclear Information System (INIS)

    Nordlinger, B.; Parquet, M.; Infante, R.; Moreels, R.; Blondiau, P.; Boschat, M.; Groussard, M.; Huguet, C.

    1982-01-01

    All of the methods proposed for measuring portal blood flow are either invasive, estimate total rather than nutrient flow, and none has proved reliable in cirrhotic patients. A method has been derived from pharmacokinetic principles used for the calculation of bioavailability of drugs according to the route of administration (i.v. or p.o.) and tested experimentally in 20 pigs. A tracer dose of [ 14 C]ursodeoxycholic acid, a biliary acid with a high-liver first-pass effect, is administered in the duodenum, and serial peripheral blood samples are taken. Later, the same dose of the same drug is administered i.v. The shunt fraction of portal blood F is obtained by the ratio of the areas under the plasma level vs. time curves (AUC) after p.o. and i.v. administrations: (see formula in text). The pigs were divided into three experimental groups. (i) Group I: undisturbed portal flow; (ii) Group II: total diversion of portal blood with an end-to-side portacaval shunt, and (iii) Group III: partial diversion of portal blood through a side-to-side portacaval shunt. Portal flow was measured during surgery with an electromagnetic flowmeter above and below the shunt and the degree of shunting calculated. Results show that the shunt fraction measured with ursodeoxycholic acid is well-correlated with hemodynamic data. No overlap between Groups I and III is observed. It is concluded that the shunt fraction of nutrient portal blood can be measured with this noninvasive method. Minute amounts of ursodeoxycholic acid were used in order to be completely metabolized by the liver, even in spite of hepatocellular dysfunction. Therefore, this method should be valid in cirrhotic patients and be useful to decide the type of portasystemic shunt to propose for the decompression of gastroesophageal varices

  13. Distinct DNA exit and packaging portals in the virus Acanthamoeba polyphaga mimivirus.

    Science.gov (United States)

    Zauberman, Nathan; Mutsafi, Yael; Halevy, Daniel Ben; Shimoni, Eyal; Klein, Eugenia; Xiao, Chuan; Sun, Siyang; Minsky, Abraham

    2008-05-13

    Icosahedral double-stranded DNA viruses use a single portal for genome delivery and packaging. The extensive structural similarity revealed by such portals in diverse viruses, as well as their invariable positioning at a unique icosahedral vertex, led to the consensus that a particular, highly conserved vertex-portal architecture is essential for viral DNA translocations. Here we present an exception to this paradigm by demonstrating that genome delivery and packaging in the virus Acanthamoeba polyphaga mimivirus occur through two distinct portals. By using high-resolution techniques, including electron tomography and cryo-scanning electron microscopy, we show that Mimivirus genome delivery entails a large-scale conformational change of the capsid, whereby five icosahedral faces open up. This opening, which occurs at a unique vertex of the capsid that we coined the "stargate", allows for the formation of a massive membrane conduit through which the viral DNA is released. A transient aperture centered at an icosahedral face distal to the DNA delivery site acts as a non-vertex DNA packaging portal. In conjunction with comparative genomic studies, our observations imply a viral packaging pathway akin to bacterial DNA segregation, which might be shared by diverse internal membrane-containing viruses.

  14. Distinct DNA exit and packaging portals in the virus Acanthamoeba polyphaga mimivirus.

    Directory of Open Access Journals (Sweden)

    Nathan Zauberman

    2008-05-01

    Full Text Available Icosahedral double-stranded DNA viruses use a single portal for genome delivery and packaging. The extensive structural similarity revealed by such portals in diverse viruses, as well as their invariable positioning at a unique icosahedral vertex, led to the consensus that a particular, highly conserved vertex-portal architecture is essential for viral DNA translocations. Here we present an exception to this paradigm by demonstrating that genome delivery and packaging in the virus Acanthamoeba polyphaga mimivirus occur through two distinct portals. By using high-resolution techniques, including electron tomography and cryo-scanning electron microscopy, we show that Mimivirus genome delivery entails a large-scale conformational change of the capsid, whereby five icosahedral faces open up. This opening, which occurs at a unique vertex of the capsid that we coined the "stargate", allows for the formation of a massive membrane conduit through which the viral DNA is released. A transient aperture centered at an icosahedral face distal to the DNA delivery site acts as a non-vertex DNA packaging portal. In conjunction with comparative genomic studies, our observations imply a viral packaging pathway akin to bacterial DNA segregation, which might be shared by diverse internal membrane-containing viruses.

  15. Virtual research environments from portals to science gateways

    CERN Document Server

    Allan, Robert N

    2009-01-01

    Virtual Research Environments examines making Information and Communication Technologies (ICT) usable by researchers working to solve "grand challenge” problems in many disciplines from social science to particle physics. It is driven by research the authors have carried out to evaluate researchers' requirements in using information services via web portals and in adapting collaborative learning tools to meet their more diverse needs, particularly in a multidisciplinary study.This is the motivation for what the authors have helped develop into the UK Virtual Research Environments (VRE)

  16. The diverse functions of the hepatitis B core/capsid protein (HBc) in the viral life cycle: Implications for the development of HBc-targeting antivirals.

    Science.gov (United States)

    Diab, Ahmed; Foca, Adrien; Zoulim, Fabien; Durantel, David; Andrisani, Ourania

    2018-01-01

    Virally encoded proteins have evolved to perform multiple functions, and the core protein (HBc) of the hepatitis B virus (HBV) is a perfect example. While HBc is the structural component of the viral nucleocapsid, additional novel functions for the nucleus-localized HBc have recently been described. These results extend for HBc, beyond its structural role, a regulatory function in the viral life cycle and potentially a role in pathogenesis. In this article, we review the diverse roles of HBc in HBV replication and pathogenesis, emphasizing how the unique structure of this protein is key to its various functions. We focus in particular on recent advances in understanding the significance of HBc phosphorylations, its interaction with host proteins and the role of HBc in regulating the transcription of host genes. We also briefly allude to the emerging niche for new direct-acting antivirals targeting HBc, known as Core (protein) Allosteric Modulators (CAMs). Copyright © 2017 Elsevier B.V. All rights reserved.

  17. The Gulf of Mexico Coastal Ocean Observing System: A Gulf Science Portal

    Science.gov (United States)

    Howard, M.; Gayanilo, F.; Kobara, S.; Jochens, A. E.

    2013-12-01

    The Gulf of Mexico Coastal Ocean Observing System's (GCOOS) regional science portal (gcoos.org) was designed to aggregate data and model output from distributed providers and to offer these, and derived products, through a single access point in standardized ways to a diverse set of users. The portal evolved under the NOAA-led U.S. Integrated Ocean Observing System (IOOS) program where automated largely-unattended machine-to-machine interoperability has always been a guiding tenet for system design. The web portal has a business unit where membership lists, new items, and reference materials are kept, a data portal where near real-time and historical data are held and served, and a products portal where data are fused into products tailored for specific or general stakeholder groups. The staff includes a system architect who built and maintains the data portal, a GIS expert who built and maintains the current product portal, the executive director who marshals resources to keep news items fresh and data manger who manages most of this. The business portal is built using WordPress which was selected because it appeared to be the easiest content management system for non-web programmers to add content to, maintain and enhance. The data portal is custom built and uses database, PHP, and web services based on Open Geospatial Consortium standards-based Sensor Observation Service (SOS) with Observations and Measurements (O&M) encodings. We employ a standards-based vocabulary, which we helped develop, which is registered at the Marine Metadata Interoperability Ontology Registry and Repository (http://mmisw.org). The registry is currently maintained by one of the authors. Products appearing in the products portal are primarily constructed using ESRI software by a Ph.D. level Geographer. Some products were built with other software, generally by graduate students over the years. We have been sensitive to the private sector when deciding which products to produce. While

  18. Factors Affecting Faculty Web Portal Usability

    Science.gov (United States)

    Bringula, Rex P.; Basa, Roselle S.

    2011-01-01

    The study investigated the factors that might significantly affect web portal usability. Results of the study were intended to serve as inputs for faculty web portal development of the University of the East-Manila. Descriptive statistics utilized questionnaire data from 82 faculty members. The data showed that most of the respondents were…

  19. Portal circulation aneurysms: two case reviews

    International Nuclear Information System (INIS)

    Perret, W. L.; Silva, A de.; Elzarka, A.; Schelleman, A.

    2007-01-01

    Venous aneurysms of the superior mesenteric vein and portal vein are an uncommon occurrence and often an incidental finding. They can also be associated with hepatocellular disease and portal hypertension. We present CT and ultrasound findings of these entities. The management of venous aneurysms is generally conservative with serial imaging

  20. Optimization of portal placement for endoscopic calcaneoplasty

    NARCIS (Netherlands)

    van Sterkenburg, Maayke N.; Groot, Minke; Sierevelt, Inger N.; Spennacchio, Pietro A.; Kerkhoffs, Gino M. M. J.; van Dijk, C. Niek

    2011-01-01

    The purpose of our study was to determine an anatomic landmark to help locate portals in endoscopic calcaneoplasty. The device for optimal portal placement (DOPP) was developed to measure the distance from the distal fibula tip to the calcaneus (DFC) in 28 volunteers to determine the location of the

  1. Percutaneous transhepatic portal vein stenting in a patient with benign non-transplant postoperative portal vein stenosis: A case report

    OpenAIRE

    Madhusudhan, KS; Agrawal, Nikhil; Srivastava, Deep N; Pal, Sujoy; Gupta, Arun K

    2013-01-01

    Extrahepatic portal vein stenosis is caused by a variety of benign and malignant diseases and results in development of symptoms due to portal hypertension. Benign post-surgical adhesions causing portal vein stenosis in non-transplant population is an uncommon etiology of portal hypertension. Endovascular treatment of such patients with angioplasty and stenting is uncommonly reported in literature. We report a case of portal hypertension caused by benign postoperative portal vein fibrosis, su...

  2. Isocurvature constraints on portal couplings

    Energy Technology Data Exchange (ETDEWEB)

    Kainulainen, Kimmo; Nurmi, Sami; Vaskonen, Ville [Department of Physics, University of Jyväskylä, P.O.Box 35 (YFL), FI-40014 University of Jyväskylä (Finland); Tenkanen, Tommi; Tuominen, Kimmo, E-mail: kimmo.kainulainen@jyu.fi, E-mail: sami.t.nurmi@jyu.fi, E-mail: tommi.tenkanen@helsinki.fi, E-mail: kimmo.i.tuominen@helsinki.fi, E-mail: ville.vaskonen@jyu.fi [Department of Physics, University of Helsinki P.O. Box 64, FI-00014, Helsinki (Finland)

    2016-06-01

    We consider portal models which are ultraweakly coupled with the Standard Model, and confront them with observational constraints on dark matter abundance and isocurvature perturbations. We assume the hidden sector to contain a real singlet scalar s and a sterile neutrino ψ coupled to s via a pseudoscalar Yukawa term. During inflation, a primordial condensate consisting of the singlet scalar s is generated, and its contribution to the isocurvature perturbations is imprinted onto the dark matter abundance. We compute the total dark matter abundance including the contributions from condensate decay and nonthermal production from the Standard Model sector. We then use the Planck limit on isocurvature perturbations to derive a novel constraint connecting dark matter mass and the singlet self coupling with the scale of inflation: m {sub DM}/GeV ∼< 0.2λ{sub s}{sup 3/8} ( H {sub *}/10{sup 11} GeV){sup −3/2}. This constraint is relevant in most portal models ultraweakly coupled with the Standard Model and containing light singlet scalar fields.

  3. Ultrasonography for Noninvasive Assessment of Portal Hypertension.

    Science.gov (United States)

    Maruyama, Hitoshi; Yokosuka, Osamu

    2017-07-15

    Portal hypertension is a major pathophysiology in patients with cirrhosis. Portal pressure is the gold standard to evaluate the severity of portal hypertension, and radiological intervention is the only procedure for pressure measurement. Ultrasound (US) is a simple and noninvasive imaging modality available worldwide. B-mode imaging allows broad applications for patients to detect and characterize chronic liver diseases and focal hepatic lesions. The Doppler technique offers real-time observation of blood flow with qualitative and quantitative assessments, and the application of microbubble-based contrast agents has improved the detectability of peripheral blood flow. In addition, elastography for the liver and spleen covers a wider field beyond the original purpose of fibrosis assessment. These developments enhance the practical use of US in the evaluation of portal hemodynamic abnormalities. This article reviews the recent progress of US in the assessment of portal hypertension.

  4. Idiopathic noncirrhotic portal hypertension: current perspectives.

    Science.gov (United States)

    Riggio, Oliviero; Gioia, Stefania; Pentassuglio, Ilaria; Nicoletti, Valeria; Valente, Michele; d'Amati, Giulia

    2016-01-01

    The term idiopathic noncirrhotic portal hypertension (INCPH) has been recently proposed to replace terms, such as hepatoportal sclerosis, idiopathic portal hypertension, incomplete septal cirrhosis, and nodular regenerative hyperplasia, used to describe patients with a hepatic presinusoidal cause of portal hypertension of unknown etiology, characterized by features of portal hypertension (esophageal varices, nonmalignant ascites, porto-venous collaterals), splenomegaly, patent portal, and hepatic veins and no clinical and histological signs of cirrhosis. Physicians should learn to look for this condition in a number of clinical settings, including cryptogenic cirrhosis, a disease known to be associated with INCPH, drug administration, and even chronic alterations in liver function tests. Once INCPH is clinically suspected, liver histology becomes mandatory for the correct diagnosis. However, pathologists should be familiar with the histological features of INCPH, especially in cases in which histology is not only requested to exclude liver cirrhosis.

  5. Enterprise Information Management with Plone Portals

    Directory of Open Access Journals (Sweden)

    Marcello Peixoto Bax

    2009-05-01

    Full Text Available The article shows that it is possible to implement a corporate portal using open source software, in an integrated manner with the proprietary MS Windows environment. As it is the real scenario in the vast majority of businesses and organizations today, a portal that meets these specific requirements is highly representative, mainly because MS Windows integration in the client environment (not in the server is not trivial for an open source portal. The paper shows that, by deploying a portal in this context the company considerably moves forward regarding information management. To show this, the article focuses on the key positive aspects arising from the deployment of a intranet / extranet portal in that context, i.e., MS Windows integration; editing with MS Office or other similar applications; shared editing control (with check-in and check-out; universal web access; and the use of metadata and workflow.

  6. Comparative Proteomics of Rubber Latex Revealed Multiple Protein Species of REF/SRPP Family Respond Diversely to Ethylene Stimulation among Different Rubber Tree Clones

    Directory of Open Access Journals (Sweden)

    Zheng Tong

    2017-05-01

    Full Text Available Rubber elongation factor (REF and small rubber particle protein (SRPP are two key factors for natural rubber biosynthesis. To further understand the roles of these proteins in rubber formation, six different genes for latex abundant REF or SRPP proteins, including REF138,175,258 and SRPP117,204,243, were characterized from Hevea brasiliensis Reyan (RY 7-33-97. Sequence analysis showed that REFs have a variable and long N-terminal, whereas SRPPs have a variable and long C-terminal beyond the REF domain, and REF258 has a β subunit of ATPase in its N-terminal. Through two-dimensional electrophoresis (2-DE, each REF/SRPP protein was separated into multiple protein spots on 2-DE gels, indicating they have multiple protein species. The abundance of REF/SRPP proteins was compared between ethylene and control treatments or among rubber tree clones with different levels of latex productivity by analyzing 2-DE gels. The total abundance of each REF/SRPP protein decreased or changed a little upon ethylene stimulation, whereas the abundance of multiple protein species of the same REF/SRPP changed diversely. Among the three rubber tree clones, the abundance of the protein species also differed significantly. Especially, two protein species of REF175 or REF258 were ethylene-responsive only in the high latex productivity clone RY 8-79 instead of in RY 7-33-97 and PR 107. Some individual protein species were positively related to ethylene stimulation and latex productivity. These results suggested that the specific protein species could be more important than others for rubber production and post-translational modifications might play important roles in rubber biosynthesis.

  7. The expression of PEDF and VEGF in the gastric wall of prehepatic portal hypertensive rats.

    Science.gov (United States)

    Pan, Wei-Dong; Liu, Yanzhang; Lin, Nan; Xu, Ruiyun

    2011-01-01

    Upper gastrointestinal bleeding of portal hypertension cases may result from gastric mucosal lesions due to portal hypertensive gastropathy. The pathological changes in the vessels of the gastric wall are very important in the pathogenesis of portal hypertensive gastropathy. However, the mechanisms of these pathological changes are not completely understood. In this study, we examined the expression levels of PEDF and VEGF in the gastric wall in rats with prehepatic portal hypertension. Eighteen healthy Wistar rats were randomly divided into groups A and B. Group A was used to establish the prehepatic portal hypertensive model and group B to evaluate a sham surgery. The VEGF and PEDF expression in the rat gastric wall were detected by immunohistochemical staining and western blotting. VEGF and PEDF were mainly expressed in the basal layer of the mucosal glands. The expression levels of VEGF and PEDF in group A were higher than that in group B at 7, 10 and 14 days after surgery. The expression levels of VEFG and PEDF in group B did not show significant changes. The results from the present study showed a significantly elevated expression of both VEGF and PEDF in the gastric walls during the development of portal hypertension. The expression of these proteins was mainly located in the basal layer of the gastric mucosa.

  8. Diverse mitotic functions of the cytoskeletal cross-linking protein Shortstop suggest a role in Dynein/Dynactin activity.

    Science.gov (United States)

    Dewey, Evan B; Johnston, Christopher A

    2017-09-15

    Proper assembly and orientation of the bipolar mitotic spindle is critical to the fidelity of cell division. Mitotic precision fundamentally contributes to cell fate specification, tissue development and homeostasis, and chromosome distribution within daughter cells. Defects in these events are thought to contribute to several human diseases. The underlying mechanisms that function in spindle morphogenesis and positioning remain incompletely defined, however. Here we describe diverse roles for the actin-microtubule cross-linker Shortstop (Shot) in mitotic spindle function in Drosophila Shot localizes to mitotic spindle poles, and its knockdown results in an unfocused spindle pole morphology and a disruption of proper spindle orientation. Loss of Shot also leads to chromosome congression defects, cell cycle progression delay, and defective chromosome segregation during anaphase. These mitotic errors trigger apoptosis in Drosophila epithelial tissue, and blocking this apoptotic response results in a marked induction of the epithelial-mesenchymal transition marker MMP-1. The actin-binding domain of Shot directly interacts with Actin-related protein-1 (Arp-1), a key component of the Dynein/Dynactin complex. Knockdown of Arp-1 phenocopies Shot loss universally, whereas chemical disruption of F-actin does so selectively. Our work highlights novel roles for Shot in mitosis and suggests a mechanism involving Dynein/Dynactin activation. © 2017 Dewey and Johnston. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  9. Neuropeptide Y restores non-receptor-mediated vasoconstrictive action in superior mesenteric arteries in portal hypertension.

    Science.gov (United States)

    Hartl, Johannes; Dietrich, Peter; Moleda, Lukas; Müller-Schilling, Martina; Wiest, Reiner

    2015-12-01

    Vascular hyporeactivity to vasoconstrictors contributes to splanchnic arterial vasodilatation and hemodynamic dysregulation in portal hypertension. Neuropeptide Y (NPY), a sympathetic cotransmitter, has been shown to improve adrenergic vascular contractility in portal hypertensive rats and markedly attenuate hyperdynamic circulation. To further characterize the NPY-effects in portal hypertension, we investigated its role for non-receptor-mediated vasoconstriction in the superior mesenteric artery (SMA) of portal vein ligated (PVL) and sham-operated rats. Ex vivo SMA perfusion of PVL and sham rats was used to analyse the effects of NPY on pressure response to non-receptor-mediated vasoconstriction. Dose-response curves to KCl (30-300 mM) were used to bypass G protein-coupled receptor mechanisms. Potential involvement of the cyclooxygenase-pathway was tested by non-selective cyclooxygenase-inhibition using indomethacin. KCl-induced vascular contractility but not vascular sensitivity was significantly attenuated in PVL rats as compared with sham rats. Administration of NPY resulted in an augmentation of KCl-evoked vascular sensitivity being not different between study groups. However, KCl-induced vascular contractility was markedly more enhanced in PVL rats, thus, vascular response was no more significantly different between PVL and sham rats after addition of NPY. Administration of indomethacin abolished the NPY-induced enhancement of vasoconstriction. Receptor-independent vascular contractility is impaired in mesenteric arteries in portal hypertension. NPY improves non-receptor mediated mesenteric vasoconstriction more effective in portal hypertension than in healthy conditions correcting splanchnic vascular hyporesponsiveness. This beneficial vasoactive action of NPY adds to its well known more pronounced effects on adrenergic vasoconstriction in portal hypertension making it a promising therapeutic agent in portal hypertension. © 2015 John Wiley & Sons A

  10. Effects of Nuclear Factor-E2-related factor 2/Heme Oxygenase 1 on splanchnic hemodynamics in experimental cirrhosis with portal hypertension.

    Science.gov (United States)

    Qin, Jun; He, Yue; Duan, Ming; Luo, Meng

    2017-05-01

    We explored the effects of Nuclear Factor-E2-related factor 2 (Nrf2) and Heme Oxygenase 1 (HO-1) on splanchnic hemodynamics in portal hypertensive rats. Experimental cirrhosis with portal hypertension was induced by intraperitoneal injection of carbon tetrachloride. The expression of proteins was examined by immunoblotting. Hemodynamic studies were performed by radioactive microspheres. The vascular perfusion system was used to measure the contractile response of mesentery arterioles in rats. Nrf2 expression in the nucleus and HO-1 expression in cytoplasm was significantly enhanced in portal hypertensive rats. Portal pressure, as well as regional blood flow, increased significantly in portal hypertension and can be blocked by tin protoporphyrin IX. The expression of endogenous nitric oxide synthase and vascular endothelial growth factors increased significantly compared to normal rats, while HO-1 inhibition decreased the expression of these proteins significantly. The contractile response of mesenteric arteries decreased in portal hypertension, but can be partially recovered through tin protoporphyrin IX treatment. The expression of Nrf2/HO-1 increased in mesenteric arteries of portal hypertensive rats, which was related to oxidative stress. HO-1was involved in increased portal pressure and anomaly splanchnic hemodynamics in portal hypertensive rats. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. PSUP: A Planetary SUrface Portal

    Science.gov (United States)

    Poulet, F.; Quantin-Nataf, C.; Ballans, H.; Dassas, K.; Audouard, J.; Carter, J.; Gondet, B.; Lozac'h, L.; Malapert, J.-C.; Marmo, C.; Riu, L.; Séjourné, A.

    2018-01-01

    The large size and complexity of planetary data acquired by spacecraft during the last two decades create a demand within the planetary community for access to the archives of raw and high level data and for the tools necessary to analyze these data. Among the different targets of the Solar System, Mars is unique as the combined datasets from the Viking, Mars Global Surveyor, Mars Odyssey, Mars Express and Mars Reconnaissance Orbiter missions provide a tremendous wealth of information that can be used to study the surface of Mars. The number and the size of the datasets require an information system to process, manage and distribute data. The Observatories of Paris Sud (OSUPS) and Lyon (OSUL) have developed a portal, called PSUP (Planetary SUrface Portal), for providing users with efficient and easy access to data products dedicated to the Martian surface. The objectives of the portal are: 1) to allow processing and downloading of data via a specific application called MarsSI (Martian surface data processing Information System); 2) to provide the visualization and merging of high level (image, spectral, and topographic) products and catalogs via a web-based user interface (MarsVisu), and 3) to distribute some of these specific high level data with an emphasis on products issued by the science teams of OSUPS and OSUL. As the MarsSI service is extensively described in a companion paper (Quantin-Nataf et al., companion paper, submitted to this special issue), the present paper focus on the general architecture and the functionalities of the web-based user interface MarsVisu. This service provides access to many data products for Mars: albedo, mineral and thermal inertia global maps from spectrometers; mosaics from imagers; image footprints and rasters from the MarsSI tool; high level specific products (defined as catalogs or vectors). MarsVisu can be used to quickly assess the visualized processed data and maps as well as identify areas that have not been mapped yet

  12. The feasible study of vasodilators in portal vein targeting infusion for treating portal hypertension

    International Nuclear Information System (INIS)

    Wu Hanping; Liang Huiming; Zheng Chuansheng; Feng Gansheng

    2002-01-01

    Objective: To find out the ideal portal vein tar getting injection routes for portal hypertension treatment. Methods: 28 cirrhotic rat models with portal hypertension induced by CCl 4 were divided into 4 groups: inferior caval vein injection group, portal vein injection group, hepatic artery injection group, spleen injection group. The changes in portal vein pressure (PVP), inferior caval vein pressure (ICVP), mean artery pressure (MAP) and heart rate (HR) were monitored before and after prazosin injection. Results: After intra-portal, intra-hepatic arterial or spleen injection of prazosin, larger decrease in PVP and lesser effects on MAP than intravenous injection had been induced. The effect on HR showed no difference among these four groups. Conclusions: Hepatic artery and spleen prazosin administration have the same advantages on treatment of portal hypertension as those of intra-portal infusion, that is the greater decrease on portal vein pressure, the lesser effects on systemic hemodynamics. Vasodilation drugs for hepatic artery infusion through percutaneous port catheter system by hepatic artery implantation would be an ideal method for portal hypertension treatment

  13. Peering down the barrel of a bacteriophage portal: the genome packaging and release valve in p22.

    Science.gov (United States)

    Tang, Jinghua; Lander, Gabriel C; Olia, Adam S; Olia, Adam; Li, Rui; Casjens, Sherwood; Prevelige, Peter; Cingolani, Gino; Baker, Timothy S; Johnson, John E

    2011-04-13

    The encapsidated genome in all double-strand DNA bacteriophages is packaged to liquid crystalline density through a unique vertex in the procapsid assembly intermediate, which has a portal protein dodecamer in place of five coat protein subunits. The portal orchestrates DNA packaging and exit, through a series of varying interactions with the scaffolding, terminase, and closure proteins. Here, we report an asymmetric cryoEM reconstruction of the entire P22 virion at 7.8 Å resolution. X-ray crystal structure models of the full-length portal and of the portal lacking 123 residues at the C terminus in complex with gene product 4 (Δ123portal-gp4) obtained by Olia et al. (2011) were fitted into this reconstruction. The interpreted density map revealed that the 150 Å, coiled-coil, barrel portion of the portal entraps the last DNA to be packaged and suggests a mechanism for head-full DNA signaling and transient stabilization of the genome during addition of closure proteins. Copyright © 2011 Elsevier Ltd. All rights reserved.

  14. An endoplasmic reticulum-localized Coffea arabica BURP domain-containing protein affects the response of transgenic Arabidopsis plants to diverse abiotic stresses.

    Science.gov (United States)

    Dinh, Sy Nguyen; Kang, Hunseung

    2017-11-01

    The Coffea arabica BURP domain-containing gene plays an important role in the response of transgenic Arabidopsis plants to abiotic stresses via regulating the level of diverse proteins. Although the functions of plant-specific BURP domain-containing proteins (BDP) have been determined for a few plants, their roles in the growth, development, and stress responses of most plant species, including coffee plant (Coffea arabica), are largely unknown. In this study, the function of a C. arabica BDP, designated CaBDP1, was investigated in transgenic Arabidopsis plants. The expression of CaBDP1 was highly modulated in coffee plants subjected to drought, cold, salt, or ABA. Confocal analysis of CaBDP1-GFP fusion proteins revealed that CaBDP1 is localized in the endoplasmic reticulum. The ectopic expression of CaBDP1 in Arabidopsis resulted in delayed germination of the transgenic plants under abiotic stress and in the presence of ABA. Cotyledon greening and seedling growth of the transgenic plants were inhibited in the presence of ABA due to the upregulation of ABA signaling-related genes like ABI3, ABI4, and ABI5. Proteome analysis revealed that the levels of several proteins are modulated in CaBDP1-expressing transgenic plants. The results of this study underscore the importance of BURP domain proteins in plant responses to diverse abiotic stresses.

  15. CERN & Society launches donation portal

    CERN Multimedia

    Cian O'Luanaigh

    2014-01-01

    The CERN & Society programme brings together projects in the areas of education and outreach, innovation and knowledge exchange, and culture and arts, that spread the CERN spirit of scientific curiosity for the inspiration and benefit of society. Today, CERN & Society is launching its "giving" website – a portal to allow donors to contribute to various projects and forge new relationships with CERN.   "The CERN & Society initiative in its embryonic form began almost three years ago, with the feeling that the laboratory could play a bigger role for the benefit of society," says Matteo Castoldi, Head of the CERN Development Office, who, with his team, is seeking supporters and ambassadors for the CERN & Society initiative. "The concept is not completely new – in some sense it is embedded in CERN’s DNA, as the laboratory helps society by creating knowledge and new technologies – but we would like to d...

  16. Portal hydatid with secondary cavernomatosis.

    Science.gov (United States)

    Rodríguez Sanz, Mª Belén; Roldán Cuena, Mª Del Mar; Blanco Álvarez, Carlos Alberto; Sánchez Jiménez, Raúl

    2017-03-01

    The hydatid cyst is a parasitic infection included within the category of zoonoses, in which there exists a direct or indirect relation with animals, particularly with dogs. We report a clinical case of a patient who has undergone surgery of hydatid cyst in the right hepatic lobe. Seven years later the patient presents hydatid cyst in portal vein with secondary cavernomatosis, which is a rare complication. There are few cases described in the literature. The symtomatology presented by hydatid cyst is variable and the diagnosis is made by ultrasonography, TC and/or RNM. The treatment of choice is the surgical removal of the cyst, prior to surgery Albendazol must be administered for 1-2 weeks and be maintained for 4 more weeks after surgery.

  17. BSD Portals for LINUX 2.0

    Science.gov (United States)

    McNab, A. David; woo, Alex (Technical Monitor)

    1999-01-01

    Portals, an experimental feature of 4.4BSD, extend the file system name space by exporting certain open () requests to a user-space daemon. A portal daemon is mounted into the file name space as if it were a standard file system. When the kernel resolves a pathname and encounters a portal mount point, the remainder of the path is passed to the portal daemon. Depending on the portal "pathname" and the daemon's configuration, some type of open (2) is performed. The resulting file descriptor is passed back to the kernel which eventually returns it to the user, to whom it appears that a "normal" open has occurred. A proxy portalfs file system is responsible for kernel interaction with the daemon. The overall effect is that the portal daemon performs an open (2) on behalf of the kernel, possibly hiding substantial complexity from the calling process. One particularly useful application is implementing a connection service that allows simple scripts to open network sockets. This paper describes the implementation of portals for LINUX 2.0.

  18. Genetic Diversity of Plasmodium falciparum Merozoite Surface Protein-1 Block 2 in Sites of Contrasting Altitudes and Malaria Endemicities in the Mount Cameroon Region

    OpenAIRE

    Wanji, Samuel; Kengne-Ouafo, Arnaud J.; Joan Eyong, Ebanga E.; Kimbi, Helen K.; Tendongfor, Nicholas; Ndamukong-Nyanga, Judith L.; Nana-Djeunga, Hugues C.; Bourguinat, Catherine; Sofeu-Feugaing, David D.; Charvet, Claude L.

    2012-01-01

    The present study analyzed the relationship between the genetic diversity of Plasmodium falciparum and parasitologic/entomologic indices in the Mount Cameroon region by using merozoite surface protein 1 as a genetic marker. Blood samples were collected from asymptomatic children from three altitude zones (high, intermediate, and low). Parasitologic and entomologic indices were determined by microscopy and landing catch mosquito collection/circumsporozoite protein–enzyme-linked immunosorbent a...

  19. Patient portals and broadband internet inequality.

    Science.gov (United States)

    Perzynski, Adam T; Roach, Mary Joan; Shick, Sarah; Callahan, Bill; Gunzler, Douglas; Cebul, Randall; Kaelber, David C; Huml, Anne; Thornton, John Daryl; Einstadter, Douglas

    2017-09-01

    Patient portals have shown potential for increasing health care quality and efficiency. Internet access and other factors influencing patient portal use could worsen health disparities. Observational study of adults with 1 or more visits to the outpatient clinics of an urban public health care system from 2012 to 2015. We used mixed effects logistic regression to evaluate the association between broadband internet access and (1) patient portal initiation (whether a patient logged in at least 1 time) and (2) messaging, controlling for demographic and neighborhood characteristics. There were 243 248 adults with 1 or more visits during 2012-2015 and 70 835 (29.1%) initiated portal use. Portal initiation was 34.1% for whites, 23.4% for blacks, and 23.8% for Hispanics, and was lower for Medicaid (26.5%), Medicare (23.4%), and uninsured patients (17.4%) than commercially insured patients (39.3%). In multivariate analysis, both initiation of portal use (odds ratio [OR] = 1.24 per quintile, 95% confidence interval [CI], 1.23-1.24, P  internet access. The majority of adults with outpatient visits to a large urban health care system did not use the patient portal, and initiation of use was lower for racial and ethnic minorities, persons of lower socioeconomic status, and those without neighborhood broadband internet access. These results suggest the emergence of a digital divide in patient portal use. Given the scale of investment in patient portals and other internet-dependent health information technologies, efforts are urgently needed to address this growing inequality. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  20. Benign hepatic portal venous gas following caustic ingestion

    International Nuclear Information System (INIS)

    Lewin, Maite; Tubiana, Jean-Michel; Pocard, Marc; Caplin, Scott; Parc, Rolland; Blain, Antoine

    2002-01-01

    Hepatic portal vein gas has been documented in numerous conditions and is traditionally regarded as a poor prognostic sign. There are, however, several reports of portal vein gas with a benign course. We report the first case of transient hepatic portal vein gas secondary to the ingestion of a caustic substance. The literature of hepatic portal vein gas in benign disease is reviewed. (orig.)

  1. Radionuclide splenoportography in patients with portal hypertension

    International Nuclear Information System (INIS)

    Kuriya, Kouji; Nagamachi, Shigeki; Hoshi, Hiroaki; Ohnishi, Takashi; Jinnouchi, Masashi; Futami, Sigemi; Yoshida, Akira; Watanabe, Katsuji

    1991-01-01

    Splenoportography using 99m Tc-pertechnetate was performed in 18 patients with portal hypertension. 99m Tc pertechnetate (370 MBq) was directly injected into the spleen. Co-lateral circulation of portal vein was observed in 13 of 18 patients (72%). L/H ratio was also calculated by the time activity curve of dynamic images. L/H ratio was significantly lower (p<0.05) in patients with colateral vessels and severe esophageal varix. Radionuclide splenography was an useful method for evaluating hemodynamics of portal vein. (author)

  2. Predictive model of portal venous system thrombosis in cirrhotic portal hypertensive patients after splenectomy

    OpenAIRE

    He, Shasha; He, Fangping

    2015-01-01

    Objective: This study is to investigate the risk factors of portal venous system thrombosis (PVT) in patients with cirrhotic portal hypertension after splenectomy and to establish a Logistic regression prediction model. Methods: A total of 119 patients with cirrhotic portal hypertension were enrolled. Their clinical data was retrospectively analyzed. They were divided into PVT group (n = 18) and non-PVT group (n = 101). One-way analysis and multivariate Logistic regression analysis were perfo...

  3. Macronodular hepatic tuberculosis associated with portal vein thrombosis and portal hypertension

    International Nuclear Information System (INIS)

    Venkatesh, S.K.; Tan, L.K.A.; Siew, E.P.Y.; Putti, T.C.

    2005-01-01

    Tuberculosis (TB) of the liver is usually associated with miliary spread. Macronodular TB of the liver is rare. A case of macronodular TB of the liver in a 31-year-old woman causing portal vein thrombosis and portal hypertension is presented. Ultrasound and CT appearances are described. There was coexistent ileo-caecal TB with extensive mesenteric and retroperitoneal lymphadenopathy. Macronodular TB should be considered in the differential diagnosis when a patient presents with multiple calcified masses in the liver with portal vein thrombosis and portal hypertension. Copyright (2005) Blackwell Science Pty Ltd

  4. Analysis of Dynamic Characteristics of Portal Frame with Variable Section

    OpenAIRE

    Hao Jianing

    2016-01-01

    Combined with a portal frame design, by the use of finite element software ANSYS, the finite element model of single specimens of portal rigid frame and the overall portal rigid frame building are established. portal rigid frame’s beam and column is variable cross section. Through the modal analysis, comparative analysis of the frequency and vibration type of the radiolabeling specimens and finite element model of the whole, for the further development of variable cross-section portal rigid f...

  5. Federal High End Computing (HEC) Information Portal

    Data.gov (United States)

    Networking and Information Technology Research and Development, Executive Office of the President — This portal provides information about opportunities to engage in U.S. Federal government high performance computing activities, including supercomputer use,...

  6. Autonomic dysfunction in cirrhosis and portal hypertension

    DEFF Research Database (Denmark)

    Dümcke, Christine Winkler; Møller, Søren

    2008-01-01

    Liver cirrhosis and portal hypertension are frequently associated with signs of circulatory dysfunction and peripheral polyneuropathy, which includes defects of the autonomic nervous system. Autonomic dysfunction, which is seen in both alcoholic and non-alcoholic liver cirrhosis and increases...

  7. Scintiphotosplenoportography in patients with portal hypertension

    International Nuclear Information System (INIS)

    Aijaz, A.

    1990-01-01

    Scintiphotosplenoportograpy (SSP) was performed in five normals and 25 patients with portal hypertension using Tc-99m tin colloid. 12 patients were cirrhotic and 13 had idiopathic portal hypertension (IPH). Analogue and fast frame dynamic studies were performed and subsequently processed. Intra hepatic shunt index in cirrhotics was significantly different from the IPH group. Extra hepatic shunt index, however, was not significantly different in the two groups but was related more to the severity of the disease process. Spleno hepatic and spleno cardiac transit times were significantly lower cirrhotics as compared to the IPH group. We conclude that SSP is a technically simple, rapid and a much less invasive method of visualizing the portal circulatory system and assessing the portal haemo dynamics. it also provides clinically important measure of shunted blood nd allows for the quantification of circulatory time from spleen to liver and heart. (author)

  8. [Emphysematous gastritis with concomitant portal venous air].

    Science.gov (United States)

    Jeong, Min Yeong; Kim, Jin Il; Kim, Jae Young; Kim, Hyun Ho; Jo, Ik Hyun; Seo, Jae Hyun; Kim, Il Kyu; Cheung, Dae Young

    2015-02-01

    Emphysematous gastritis is a rare form of gastritis caused by infection of the stomach wall by gas forming bacteria. It is a very rare condition that carries a high mortality rate. Portal venous gas shadow represents elevation of intestinal luminal pressure which manifests as emphysematous gastritis or gastric emphysema. Literature reviews show that the mortality rate is especially high when portal venous gas shadow is present on CT scan. Until recently, the treatment of emphysematous gastritis has been immediate surgical intervention. However, there is a recent trend of avoiding surgery because of the frequent occurrence of post-operative complications such as anastomosis leakage. In addition, aggressive surgical treatment has failed to show significant improvement in prognosis. Recently, the authors experienced a case of emphysematous gastritis accompanied by portal venous gas which was treated successfully by conservative treatment without immediate surgical intervention. Herein, we present a case of emphysematous gastritis with concomitant portal venous air along with literature review.

  9. [Association of biliary calculosis and portal cavernomatosis].

    Science.gov (United States)

    Crespi, C; De Giorgio, A M

    1992-08-01

    This paper reports the case of a woman, who underwent surgery because of cholelithiasis, with intraoperative finding of prehepatic portal hypertension from portal vein thrombosis ("portal cavernoma") with healthy liver, later confirmed by angiographic studies. This rare pathologic association carries a higher risk of major operative complications; therefore the Authors agree with the general belief that, for these cases, biliary tract surgery should be as simple and safe as possible. In the case of preoperative diagnosis of biliary disease associated with portal cavernoma, should a surgical approach on the biliary tract be required, we agree on the advisability of performing a shunting procedure before any kind of biliary surgery. In case of variceal bleeding endoscopic sclerotherapy will be the first choice; surgical procedures (shunting) should be seen as a second choice in case of rebleeding after sclerotherapy.

  10. The International Human Epigenome Consortium Data Portal.

    Science.gov (United States)

    Bujold, David; Morais, David Anderson de Lima; Gauthier, Carol; Côté, Catherine; Caron, Maxime; Kwan, Tony; Chen, Kuang Chung; Laperle, Jonathan; Markovits, Alexei Nordell; Pastinen, Tomi; Caron, Bryan; Veilleux, Alain; Jacques, Pierre-Étienne; Bourque, Guillaume

    2016-11-23

    The International Human Epigenome Consortium (IHEC) coordinates the production of reference epigenome maps through the characterization of the regulome, methylome, and transcriptome from a wide range of tissues and cell types. To define conventions ensuring the compatibility of datasets and establish an infrastructure enabling data integration, analysis, and sharing, we developed the IHEC Data Portal (http://epigenomesportal.ca/ihec). The portal provides access to >7,000 reference epigenomic datasets, generated from >600 tissues, which have been contributed by seven international consortia: ENCODE, NIH Roadmap, CEEHRC, Blueprint, DEEP, AMED-CREST, and KNIH. The portal enhances the utility of these reference maps by facilitating the discovery, visualization, analysis, download, and sharing of epigenomics data. The IHEC Data Portal is the official source to navigate through IHEC datasets and represents a strategy for unifying the distributed data produced by international research consortia. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

  11. R2 Water Quality Portal Monitoring Stations

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Water Quality Data Portal (WQP) provides an easy way to access data stored in various large water quality databases. The WQP provides various input parameters on...

  12. Low level of sequence diversity at merozoite surface protein-1 locus of Plasmodium ovale curtisi and P. ovale wallikeri from Thai isolates.

    Science.gov (United States)

    Putaporntip, Chaturong; Hughes, Austin L; Jongwutiwes, Somchai

    2013-01-01

    The merozoite surface protein-1 (MSP-1) is a candidate target for the development of blood stage vaccines against malaria. Polymorphism in MSP-1 can be useful as a genetic marker for strain differentiation in malarial parasites. Although sequence diversity in the MSP-1 locus has been extensively analyzed in field isolates of Plasmodium falciparum and P. vivax, the extent of variation in its homologues in P. ovale curtisi and P. ovale wallikeri, remains unknown. Analysis of the mitochondrial cytochrome b sequences of 10 P. ovale isolates from symptomatic malaria patients from diverse endemic areas of Thailand revealed co-existence of P. ovale curtisi (n = 5) and P. ovale wallikeri (n = 5). Direct sequencing of the PCR-amplified products encompassing the entire coding region of MSP-1 of P. ovale curtisi (PocMSP-1) and P. ovale wallikeri (PowMSP-1) has identified 3 imperfect repeated segments in the former and one in the latter. Most amino acid differences between these proteins were located in the interspecies variable domains of malarial MSP-1. Synonymous nucleotide diversity (πS) exceeded nonsynonymous nucleotide diversity (πN) for both PocMSP-1 and PowMSP-1, albeit at a non-significant level. However, when MSP-1 of both these species was considered together, πS was significantly greater than πN (pdiversity at this locus prior to speciation. Phylogenetic analysis based on conserved domains has placed PocMSP-1 and PowMSP-1 in a distinct bifurcating branch that probably diverged from each other around 4.5 million years ago. The MSP-1 sequences support that P. ovale curtisi and P. ovale wallikeri are distinct species. Both species are sympatric in Thailand. The low level of sequence diversity in PocMSP-1 and PowMSP-1 among Thai isolates could stem from persistent low prevalence of these species, limiting the chance of outcrossing at this locus.

  13. Evaluation of portal hypertension by MR portography

    International Nuclear Information System (INIS)

    Nagaoka, Shirou; Hagiwara, Masaru; Imanisi, Yosimasa

    1997-01-01

    Seventy-eight examinations of MR portography were totally performed in 24 controls and 33 patients with esophageal varices. Portal vein, SMV, hepatic vein, and IVC were entirely depicted in 21, 24, 22, and 24, respectively, of the 24 controls. As to intrahepatic upward branches of portal vein in the right lobe of the liver, the 4th branch was at least depicted in all of the 24. Although the portal vein trunk and SMV were entirely depicted in all of the 8 patients without treatment and liver dysfunction of Child A, there was no depiction of them in 1 of the 8 patients with liver dysfunction of Child B, and 1 of 5 patients with liver dysfunction of Child C. The 4th upward branch of portal vein in the right lobe of the liver was depicted in none of the 33 patients. Besides, none of the intrahepatic portal branches were depicted in 1 of 8 patients without treatment and liver dysfunction of Child B, and 1 of the 5 patients without treatment and liver dysfunction of Child C. There was a significant difference of depicted terminal upward branch of portal vein between the controls and patients without any treatment. In the patients without any significant difference of depicted terminal upward branch of portal vein was also present between Child's classification A and Child's classification B and C. Gastric coronary vein varices were detected by MR portography is 18 of 19 patients without treatment on the esophageal varices, and paraesophageal/esophageal varices were also depicted by MR portography in 13 of the 19. The collaterals were depicted by MR portography in all of the 6 patients with recurrent collaterals after Hassab's operation or splenectomy. MR portography was able to depict flow in trunk branches and collaterals of the portal vein system in a physiological state. (K.H.)

  14. Getting started with Citrix CloudPortal

    CERN Document Server

    U, Puthiyavan

    2013-01-01

    The book will follow a step-by-step, tutorial-based approach and show readers how to take advantage of Citrix CloudPortal's capabilities.This book is ideal for administrators and engineers new to the Citrix Cloud Solution CPSM, CPBM, and who are looking to get a good grounding in Citrix's new product. It's assumed that you will have some experience in the basics of cloud computing already. No prior knowledge of CloudPortal is expected.

  15. Evaluation of portal hypertension by MR portography

    Energy Technology Data Exchange (ETDEWEB)

    Nagaoka, Shirou; Hagiwara, Masaru; Imanisi, Yosimasa [St. Marianna Univ., Kawasaki, Kanagawa (Japan). School of Medicine

    1997-02-01

    Seventy-eight examinations of MR portography were totally performed in 24 controls and 33 patients with esophageal varices. Portal vein, SMV, hepatic vein, and IVC were entirely depicted in 21, 24, 22, and 24, respectively, of the 24 controls. As to intrahepatic upward branches of portal vein in the right lobe of the liver, the 4th branch was at least depicted in all of the 24. Although the portal vein trunk and SMV were entirely depicted in all of the 8 patients without treatment and liver dysfunction of Child A, there was no depiction of them in 1 of the 8 patients with liver dysfunction of Child B, and 1 of 5 patients with liver dysfunction of Child C. The 4th upward branch of portal vein in the right lobe of the liver was depicted in none of the 33 patients. Besides, none of the intrahepatic portal branches were depicted in 1 of 8 patients without treatment and liver dysfunction of Child B, and 1 of the 5 patients without treatment and liver dysfunction of Child C. There was a significant difference of depicted terminal upward branch of portal vein between the controls and patients without any treatment. In the patients without any significant difference of depicted terminal upward branch of portal vein was also present between Child`s classification A and Child`s classification B and C. Gastric coronary vein varices were detected by MR portography is 18 of 19 patients without treatment on the esophageal varices, and paraesophageal/esophageal varices were also depicted by MR portography in 13 of the 19. The collaterals were depicted by MR portography in all of the 6 patients with recurrent collaterals after Hassab`s operation or splenectomy. MR portography was able to depict flow in trunk branches and collaterals of the portal vein system in a physiological state. (K.H.)

  16. Portal de empleo JobFinder.com

    OpenAIRE

    Cozar Campoy, Javier

    2012-01-01

    Con este proyecto se pretende crear un portal web para la búsqueda de empleo. Las empresas inscritas en el sistema pueden publicar diferentes ofertas de trabajo y del mismo modo los usuarios registrados pueden inscribirse en éstas. Amb aquest projecte es pretén crear un portal web per a la cerca de feina. Les empreses inscrites en el sistema poden publicar diferents ofertes de feina i de la mateixa manera els usuaris registrats poden inscriure's en aquestes.

  17. Management of Portal Hypertension After Liver Transplantation.

    Science.gov (United States)

    Korda, D; Deák, P Á; Kiss, G; Gerlei, Z; Kóbori, L; Görög, D; Fehérvári, I; Piros, L; Máthé, Z; Doros, A

    2017-09-01

    Post-transplantation portal hypertension has severe complications, such as esophageal varix bleeding, therapy refractory ascites, extreme splenomegaly, and graft dysfunction. The aim of our study was to analyze the effectiveness of the therapeutic strategies and how to visualize the procedure. A retrospective study involving liver transplantation patients from the Semmelweis University Department of Transplantation and Surgery was performed between 2005 and 2015. The prevalence, etiology, and leading complications of the condition were determined. The applied interventions' effects on the patients' ascites volume, splenic volume, and the occurrence of variceal bleeding were determined. Mean portal blood flow velocity and congestion index values were calculated using Doppler ultrasonography. The prevalence of post-transplantation portal hypertension requiring intervention was 2.8%. The most common etiology of the disease was portal anastomotic stenosis. The most common complications were esophageal varix bleeding and therapy refractory ascites. The patients' ascites volume decreased significantly (2923.3 ± 1893.2 mL vs. 423.3 ± 634.3 mL; P portal hypertension. After the interventions, these parameters shifted towards the physiologic ranges. The interventions performed in our clinic were effective in most cases. The patients' ascites volume, splenic volume, and the prevalence of variceal bleeding decreased after the treatment. Doppler ultrasonography has proved to be a valuable imaging modality in the diagnosis and the follow-up of post-transplantation portal hypertension. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Search Engine For Ebook Portal

    Directory of Open Access Journals (Sweden)

    Prashant Kanade

    2017-05-01

    Full Text Available The purpose of this paper is to establish the textual analytics involved in developing a search engine for an ebook portal. We have extracted our dataset from Project Gutenberg using a robot harvester. Textual Analytics is used for efficient search retrieval. The entire dataset is represented using Vector Space Model where each document is a vector in the vector space. Further for computational purposes we represent our dataset in the form of a Term Frequency- Inverse Document Frequency tf-idf matrix. The first step involves obtaining the most coherent sequence of words of the search query entered. The entered query is processed using Front End algorithms this includes-Spell Checker Text Segmentation and Language Modeling. Back End processing includes Similarity Modeling Clustering Indexing and Retrieval. The relationship between documents and words is established using cosine similarity measured between the documents and words in Vector Space. Clustering performed is used to suggest books that are similar to the search query entered by the user. Lastly the Lucene Based Elasticsearch engine is used for indexing on the documents. This allows faster retrieval of data. Elasticsearch returns a dictionary and creates a tf-idf matrix. The processed query is compared with the dictionary obtained and tf-idf matrix is used to calculate the score for each match to give most relevant result.

  19. Expression, stabilization and purification of membrane proteins via diverse protein synthesis systems and detergents involving cell-free associated with self-assembly peptide surfactants.

    Science.gov (United States)

    Zheng, Xuan; Dong, Shuangshuang; Zheng, Jie; Li, Duanhua; Li, Feng; Luo, Zhongli

    2014-01-01

    G-protein coupled receptors (GPCRs) are involved in regulating most of physiological actions and metabolism in the bodies, which have become most frequently addressed therapeutic targets for various disorders and diseases. Purified GPCR-based drug discoveries have become routine that approaches to structural study, novel biophysical and biochemical function analyses. However, several bottlenecks that GPCR-directed drugs need to conquer the problems including overexpression, solubilization, and purification as well as stabilization. The breakthroughs are to obtain efficient protein yield and stabilize their functional conformation which are both urgently requiring of effective protein synthesis system methods and optimal surfactants. Cell-free protein synthesis system is superior to the high yields and post-translation modifications, and early signs of self-assembly peptide detergents also emerged to superiority in purification of membrane proteins. We herein focus several predominant protein synthesis systems and surfactants involving the novel peptide detergents, and uncover the advantages of cell-free protein synthesis system with self-assembling peptide detergents in purification of functional GPCRs. This review is useful to further study in membrane proteins as well as the new drug exploration. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. High Diversity of Myocyanophage in Various Aquatic Environments Revealed by High-Throughput Sequencing of Major Capsid Protein Gene With a New Set of Primers

    Directory of Open Access Journals (Sweden)

    Weiguo Hou

    2018-05-01

    Full Text Available Myocyanophages, a group of viruses infecting cyanobacteria, are abundant and play important roles in elemental cycling. Here we investigated the particle-associated viral communities retained on 0.2 μm filters and in sediment samples (representing ancient cyanophage communities from four ocean and three lake locations, using high-throughput sequencing and a newly designed primer pair targeting a gene fragment (∼145-bp in length encoding the cyanophage gp23 major capsid protein (MCP. Diverse viral communities were detected in all samples. The fragments of 142-, 145-, and 148-bp in length were most abundant in the amplicons, and most sequences (>92% belonged to cyanophages. Additionally, different sequencing depths resulted in different diversity estimates of the viral community. Operational taxonomic units obtained from deep sequencing of the MCP gene covered the majority of those obtained from shallow sequencing, suggesting that deep sequencing exhibited a more complete picture of cyanophage community than shallow sequencing. Our results also revealed a wide geographic distribution of marine myocyanophages, i.e., higher dissimilarities of the myocyanophage communities corresponded with the larger distances between the sampling sites. Collectively, this study suggests that the newly designed primer pair can be effectively used to study the community and diversity of myocyanophage from different environments, and the high-throughput sequencing represents a good method to understand viral diversity.

  1. MR and angiography: Evaluation of the hemodynamics of portal hypertension

    International Nuclear Information System (INIS)

    Torres, W.E.; Gaylord, G.M.; Whitmire, L.; Chuang, V.P.; Bernardino, M.E.

    1986-01-01

    Forty-two MR imaging examinations and angiographic procedures in 38 patients with portal hypertension were compared for how well the images depicted portal perfusion and direction of flow, portal vein thrombosis, and the presence and type of shunt. Thirty-three MR imaging studies indicated grade I or II portal flow. In 29 cases portal flow was grade I or II by angiography; in the remaining cases the flow was grade IV. In a total of eight cases portal flow was grade IV by angiography, but none appeared to be grade IV on MR imaging. Both MR imaging and angiography detected portal vein thrombosis (41 of 42 cases). MR imaging and angiography agreed as to whether a shunt was present or absent, and patent or occluded (41 of 42 cases). Currently, MR imaging is an unsatisfactory modality by which to grade portal flow. MR imaging does depict portal vein thrombosis well, and can be used to determine patency of surgical shunts

  2. Applications of portals in the energetic sector; Aplicaciones de portales en el sector energetico

    Energy Technology Data Exchange (ETDEWEB)

    Santos Dominguez, Martin; Arroyo Figueroa, Gustavo [Instituto de Investigaciones Electricas, Temixco, Morelos (Mexico)

    2000-07-01

    An operative portal joins the applications, contents and services of the company in a single page of Intranet such way that promises to change deeply the information technology in the next years. The corporative portals will change what people visualize in the screen of their computer at the beginning of every working day. Unlike seeing the network (Web) only with pages of language of hypertext bearing (HTML), the corporative portal acts as a gate between Internet and the private networks. This article presents a general vision of the benefits of the corporative portals, the existing technologies and the potential markets. [Spanish] Un portal operativo une las aplicaciones, contenidos y servicios de la empresa en una sola pagina de Intranet, de tal forma que promete cambiar, profundamente la tecnologia de la informacion en los proximos anos. Los portales corporativos cambiaran lo que la gente visualiza en la pantalla de su computadora al comienzo de cada dia de trabajo. A diferencia de ver la red (Web) solo con paginas de lenguaje de marcacion de hipertexto (HTML), el portal corporativo actua como compuerta entre Internet y las redes privadas. Este articulo presenta una vision general de los beneficios de los portales corporativos, las tecnologias y los mercados potenciales existentes.

  3. Genetic diversity of Plasmodium falciparum merozoite surface protein-1 (block 2), glutamate-rich protein and sexual stage antigen Pfs25 from Chandigarh, North India.

    Science.gov (United States)

    Kaur, Hargobinder; Sehgal, Rakesh; Goyal, Kapil; Makkar, Nikita; Yadav, Richa; Bharti, Praveen K; Singh, Neeru; Sarmah, Nilanju P; Mohapatra, Pradyumna K; Mahanta, Jagadish; Bansal, Devendra; Sultan, Ali A; Kanwar, Jagat R

    2017-12-01

    To elucidate the genetic diversity of Plasmodium falciparum in residual transmission foci of northern India. Clinically suspected patients with malaria were screened for malaria infection by microscopy. 48 P. falciparum-infected patients were enrolled from tertiary care hospital in Chandigarh, India. Blood samples were collected from enrolled patients, genomic DNA extraction and nested PCR was performed for further species confirmation. Sanger sequencing was carried out using block 2 region of msp1, R2 region of glurp and pfs25-specific primers. Extensive diversity was found in msp1 alleles with predominantly RO33 alleles. Overall allelic prevalence was 55.8% for RO33, 39.5% for MAD20 and 4.7% for K1. Six variants were observed in MAD20, whereas no variant was found in RO33 and K1 alleles. A phylogenetic analysis of RO33 alleles indicated more similarity to South African isolates, whereas MAD20 alleles showed similarity with South-East Asian isolates. In glurp, extensive variation was observed with eleven different alleles based on the AAU repeats. However, pfs25 showed less diversity and was the most stable among the targeted genes. Our findings document the genetic diversity among circulating strains of P. falciparum in an area of India with low malaria transmission and could have implications for control strategies to reach the national goal of malaria elimination. © 2017 John Wiley & Sons Ltd.

  4. Characterization of a spectrally diverse set of fluorescent proteins as FRET acceptors for mTurquoise2

    NARCIS (Netherlands)

    Mastop, M.; Bindels, D.S.; Shaner, N.C.; Postma, M.; Gadella, T.W.J.; Goedhart, J.

    2017-01-01

    The performance of Förster Resonance Energy Transfer (FRET) biosensors depends on brightness and photostability, which are dependent on the characteristics of the fluorescent proteins that are employed. Yellow fluorescent protein (YFP) is often used as an acceptor but YFP is prone to photobleaching

  5. Deciphering common recognition principles of nucleoside mono/di and tri-phosphates binding in diverse proteins via structural matching of their binding sites.

    Science.gov (United States)

    Bhagavat, Raghu; Srinivasan, Narayanaswamy; Chandra, Nagasuma

    2017-09-01

    Nucleoside triphosphate (NTP) ligands are of high biological importance and are essential for all life forms. A pre-requisite for them to participate in diverse biochemical processes is their recognition by diverse proteins. It is thus of great interest to understand the basis for such recognition in different proteins. Towards this, we have used a structural bioinformatics approach and analyze structures of 4677 NTP complexes available in Protein Data Bank (PDB). Binding sites were extracted and compared exhaustively using PocketMatch, a sensitive in-house site comparison algorithm, which resulted in grouping the entire dataset into 27 site-types. Each of these site-types represent a structural motif comprised of two or more residue conservations, derived using another in-house tool for superposing binding sites, PocketAlign. The 27 site-types could be grouped further into 9 super-types by considering partial similarities in the sites, which indicated that the individual site-types comprise different combinations of one or more site features. A scan across PDB using the 27 structural motifs determined the motifs to be specific to NTP binding sites, and a computational alanine mutagenesis indicated that residues identified to be highly conserved in the motifs are also most contributing to binding. Alternate orientations of the ligand in several site-types were observed and rationalized, indicating the possibility of some residues serving as anchors for NTP recognition. The presence of multiple site-types and the grouping of multiple folds into each site-type is strongly suggestive of convergent evolution. Knowledge of determinants obtained from this study will be useful for detecting function in unknown proteins. Proteins 2017; 85:1699-1712. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  6. An Approach for harmonizing European Water Portals

    Science.gov (United States)

    Pesquer, Lluís; Stasch, Christoph; Masó, Joan; Jirka, Simon; Domingo, Xavier; Guitart, Francesc; Turner, Thomas; Hinderk Jürrens, Eike

    2017-04-01

    A number of European funded research projects is developing novel solutions for water monitoring, modeling and management. To generate innovations in the water sector, third parties from industry and the public sector need to take up the solutions and bring them into the market. A variety of portals exists to support this move into the market. Examples on the European level are the EIP Water Online Marketplace(1), the WaterInnEU Marketplace(2), the WISE RTD Water knowledge portal(3), the WIDEST- ICT for Water Observatory(4) or the SWITCH-ON Virtual Product Market and Virtual Water-Science Laboratory(5). Further innovation portals and initiatives exist on the national or regional level, for example, the Denmark knows water platform6 or the Dutch water alliance(7). However, the different portals often cover the same projects, the same products and the same services. Since they are technically separated and have their own data models and databases, people need to duplicate information and maintain it at several endpoints. This requires additional efforts and hinders the interoperable exchange between these portals and tools using the underlying data. In this work, we provide an overview on the existing portals and present an approach for harmonizing and integrating common information that is provided across different portals. The approach aims to integrate the common in formation in a common database utilizing existing vocabularies, where possible. An Application Programming Interface allows access the information in a machine-readable way and utilizing the information in other applications beyond description and discovery purposes. (1) http://www.eip-water.eu/my-market-place (2) https://marketplace.waterinneu.org (3) http://www.wise-rtd.info/ (4) http://iwo.widest.eu (5) http://www.switch-on-vwsl.eu/ (6) http://www.rethinkwater.dk/ (7) http://wateralliance.nl/

  7. Next Gen One Portal Usability Evaluation

    Science.gov (United States)

    Cross, E. V., III; Perera, J. S.; Hanson, A. M.; English, K.; Vu, L.; Amonette, W.

    2018-01-01

    Each exercise device on the International Space Station (ISS) has a unique, customized software system interface with unique layouts / hierarchy, and operational principles that require significant crew training. Furthermore, the software programs are not adaptable and provide no real-time feedback or motivation to enhance the exercise experience and/or prevent injuries. Additionally, the graphical user interfaces (GUI) of these systems present information through multiple layers resulting in difficulty navigating to the desired screens and functions. These limitations of current exercise device GUI's lead to increased crew time spent on initiating, loading, performing exercises, logging data and exiting the system. To address these limitations a Next Generation One Portal (NextGen One Portal) Crew Countermeasure System (CMS) was developed, which utilizes the latest industry guidelines in GUI designs to provide an intuitive ease of use approach (i.e., 80% of the functionality gained within 5-10 minutes of initial use without/limited formal training required). This is accomplished by providing a consistent interface using common software to reduce crew training, increase efficiency & user satisfaction while also reducing development & maintenance costs. Results from the usability evaluations showed the NextGen One Portal UI having greater efficiency, learnability, memorability, usability and overall user experience than the current Advanced Resistive Exercise Device (ARED) UI used by astronauts on ISS. Specifically, the design of the One-Portal UI as an app interface similar to those found on the Apple and Google's App Store, assisted many of the participants in grasping the concepts of the interface with minimum training. Although the NextGen One-Portal UI was shown to be an overall better interface, observations by the test facilitators noted specific exercise tasks appeared to have a significant impact on the NextGen One-Portal UI efficiency. Future updates to

  8. Elevated mitochondrial gene expression during rat liver regeneration after portal vein ligation.

    Science.gov (United States)

    Shimizu, Y; Suzuki, H; Nimura, Y; Onoue, S; Nagino, M; Tanaka, M; Ozawa, T

    1995-10-01

    We explored the molecular basis of mitochondrial energy production during rat liver regeneration after portal vein ligation. Ligation of the left branch of the portal vein induces an increase in the weight of the nonligated lobe, counterbalancing the reduced weight of the ligated lobe. Using this model, we investigated changes in mitochondrial DNA-binding proteins, mitochondrial DNA, and mitochondrial messenger RNA (mRNA) in rat hepatocytes of the nonligated lobes. The amount of mitochondrial DNA-binding protein increased maximally (200% to 300% of the preoperative level) at 12 hours after the operation, before an increase (390%) in mitochondrial DNA content at 24 hours, and parallel to an increase (240%) in mitochondrial mRNA levels at 12 hours. These results suggest that the energy supply for liver regeneration is achieved through enhancement of mitochondrial DNA replication as well as transcription, in which the mitochondrial DNA-binding proteins probably play regulatory roles. We also found that in the nonligated lobes, mRNA levels of hepatocyte growth factor increased to a detectable level only 12 hours after the operation. These molecular biochemical data help explain why preoperative portal vein embolization, which is a modification of portal vein branch ligation, is an effective method to prevent posthepatectomy liver failure.

  9. Leptin receptor blockade reduces intrahepatic vascular resistance and portal pressure in an experimental model of rat liver cirrhosis.

    Science.gov (United States)

    Delgado, María Gabriela; Gracia-Sancho, Jordi; Marrone, Giusi; Rodríguez-Vilarrupla, Aina; Deulofeu, Ramon; Abraldes, Juan G; Bosch, Jaume; García-Pagán, Juan Carlos

    2013-10-01

    Increased hepatic vascular resistance mainly due to elevated vascular tone and to fibrosis is the primary factor in the development of portal hypertension in cirrhosis. Leptin, a hormone associated with reduction in nitric oxide bioavailability, vascular dysfunction, and liver fibrosis, is increased in patients with cirrhosis. We aimed at evaluating whether leptin influences the increased hepatic resistance in portal hypertension. CCl4-cirrhotic rats received the leptin receptor-blocker ObR antibody, or its vehicle, every other day for 1 wk. Hepatic and systemic hemodynamics were measured in both groups. Hepatic nitric oxide production and bioavailability, together with oxidative stress, nitrotyrosinated proteins, and liver fibrosis, were evaluated. In cirrhotic rats, leptin-receptor blockade significantly reduced portal pressure without modifying portal blood flow, suggesting a reduction in the intrahepatic resistance. Portal pressure reduction was associated with increased nitric oxide bioavailability and with decreased O2(-) levels and nitrotyrosinated proteins. No changes in systemic hemodynamics and liver fibrosis were observed. In conclusion, the present study shows that blockade of the leptin signaling pathway in cirrhosis significantly reduces portal pressure. This effect is probably due to a nitric oxide-mediated reduction in the hepatic vascular tone.

  10. The Sydney West Knowledge Portal: Evaluating the Growth of a Knowledge Portal to Support Translational Research.

    Science.gov (United States)

    Janssen, Anna; Robinson, Tracy Elizabeth; Provan, Pamela; Shaw, Tim

    2016-06-29

    The Sydney West Translational Cancer Research Centre is an organization funded to build capacity for translational research in cancer. Translational research is essential for ensuring the integration of best available evidence into practice and for improving patient outcomes. However, there is a low level of awareness regarding what it is and how to conduct it optimally. One solution to addressing this gap is the design and deployment of web-based knowledge portals to disseminate new knowledge and engage with and connect dispersed networks of researchers. A knowledge portal is an web-based platform for increasing knowledge dissemination and management in a specialized area. To measure the design and growth of an web-based knowledge portal for increasing individual awareness of translational research and to build organizational capacity for the delivery of translational research projects in cancer. An adaptive methodology was used to capture the design and growth of an web-based knowledge portal in cancer. This involved stakeholder consultations to inform initial design of the portal. Once the portal was live, site analytics were reviewed to evaluate member usage of the portal and to measure growth in membership. Knowledge portal membership grew consistently for the first 18 months after deployment, before leveling out. Analysis of site metrics revealed members were most likely to visit portal pages with community-generated content, particularly pages with a focus on translational research. This was closely followed by pages that disseminated educational material about translational research. Preliminary data from this study suggest that knowledge portals may be beneficial tools for translating new evidence and fostering an environment of communication and collaboration.

  11. The MISTRALS programme data portal

    Science.gov (United States)

    Fleury, Laurence; Brissebrat, Guillaume; Belmahfoud, Nizar; Boichard, Jean-Luc; Brosolo, Laetitia; Cloché, Sophie; Descloitres, Jacques; Ferré, Hélène; Focsa, Loredana; Labatut, Laurent; Mastrorillo, Laurence; Mière, Arnaud; Petit de la Villéon, Loïc; Ramage, Karim; Schmechtig, Catherine

    2014-05-01

    different file formats and data processing tools. The MISTRALS data portal - http://mistrals.sedoo.fr/ - has been designed and developed as a unified tool to share scientific data in spite of many sources of heterogeneity, and to foster collaboration between research communities. The metadata (data description) are standardized and comply with international standards (ISO 19115-19139; INSPIRE European Directive; Global Change Master Directory Thesaurus). A search tool allows to browse the catalogue by keyword or by multicriteria selection (location, period, physical property...) and to access data. Data sets managed by different data centres (ICARE, IPSL, SEDOO, CORIOLIS) are available through interoperability protocols (OPeNDAP, xml requests...) or archive synchronisation. At present the MISTRALS data portal allows to access more than 400 datasets and counts more than 500 registered users. The number of available datasets is increasing daily, due to the provision of campaign datasets (2012, 2013) by several projects. Every in situ data set is available in the native format, but the favorite data sets have been homogenized (property names, units, quality flags...) and inserted in a relational database, in order to enable more accurate data selection, and download of different datasets in a shared format. Every scientist is invited to make use of the different MISTRALS tools and data. Do not hesitate to browse the catalogue and fill the online registration form. Feel free to contact mistrals-contact@sedoo.fr for any question.

  12. The MISTRALS programme data portal

    Science.gov (United States)

    Brissebrat, Guillaume; Belmahfoud, Nizar; Cloché, Sophie; Darras, Sabine; Descloitres, Jacques; Drocourt, Yoann; Ferré, Hélène; Henriot, Nicolas; Ramage, Karim

    2017-04-01

    different file formats and data processing tools. The MISTRALS data portal - http://mistrals.sedoo.fr/ - has been designed and developed as a unified tool for sharing scientific data in spite of many sources of heterogeneity, and for fostering collaboration between research communities. The metadata (data description) are standardized and comply with international standards (ISO 19115-19139; INSPIRE European Directive; Global Change Master Directory Thesaurus). A search tool allows to browse the catalog by keyword or multicriteria selection (area, period, physical property...) and to access data. Every in situ dataset is available in the native format, but the most commonly used datasets have been homogenized (property names, units, quality flags...) and inserted in a relational database, in order to enable accurate data selection, and download in standard formats. At present the MISTRALS data portal enables to access about 650 datasets. It counts more than 675 registered users and about 100 data requests every month. The number of available datasets is increasing daily, due to the provision of campaign datasets by several projects. Every scientist is invited to browse the catalog, complete the online registration and use MISTRALS data. Feel free to contact mistrals-contact@sedoo.fr for any question.

  13. A theoretical approach to calibrate radiation portal monitor (RPM) systems

    International Nuclear Information System (INIS)

    Nafee, Sherif S.; Abbas, Mahmoud I.

    2008-01-01

    Radiation portal monitor (RPM) systems are widely used at international border crossings, where they are applied to the task of detecting nuclear devices, special nuclear material, and radiation dispersal device materials that could appear at borders. The requirements and constraints on RPM systems deployed at high-volume border crossings are significantly different from those at weapons facilities or steel recycling plants, the former being required to rapidly detect localized sources of radiation with a very high detection probability and low false-alarm rate, while screening all of the traffic without impeding the flow of commerce [Chambers, W.H., Atwater, H.F., Fehlau, P.E., Hastings, R.D., Henry, C.N., Kunz, W.E., Sampson, T.E., Whittlesey, T.H., Worth, G.M., 1974. Portal Monitor for Diversion Safeguards. LA-5681, Los Alamos Scientific Laboratory, Los Alamos, NM]. In the present work, compact analytical formulae are derived and used to calibrate two RPM systems with isotropic radiating sources: (i) polyvinyltoluene (PVT) or plastic and (ii) thallium-doped crystalline sodium iodide, NaI(Tl), gamma-ray detector materials. The calculated efficiencies are compared to measured values reported in the literatures, showing very good agreement

  14. Effects of raloxifene on portal hypertension and hepatic encephalopathy in cirrhotic rats.

    Science.gov (United States)

    Chang, Ching-Chih; Lee, Wen-Shin; Chuang, Chiao-Lin; Hsin, I-Fang; Hsu, Shao-Jung; Chang, Ting; Huang, Hui-Chun; Lee, Fa-Yauh; Lee, Shou-Dong

    2017-05-05

    Raloxifene, a selective estrogen receptor modulator, has been used extensively for osteoporosis. In addition to the effect of osteoporosis treatment, emerging evidences show that raloxifene affects the vascular function in different tissues. Cirrhosis is characterized with portal hypertension and complicated with hepatic encephalopathy. Portal hypertension affects portal-systemic shunt which leads to hepatic encephalopathy that the vascular modulation might influence severity of hepatic encephalopathy. Herein, we evaluated the impact of raloxifene on bile duct ligation (BDL)-induced cirrhotic rats. The female Sprague-Dawley rats received BDL plus ovariectomy or sham-operation. Four weeks later, rats were divided into 2 subgroups respectively to receive of raloxifene (10mg/kg/day) or saline (vehicle) for 14 days. On the 43th day, motor activities and hemodynamic parameters were measured. Hepatic and vascular mRNA and protein expressions were determined. The histopathological change of liver was examined. We found that the liver biochemistry, ammonia level and motor activity were similar between cirrhotic rats with or without raloxifene administration. The hemodynamic parameters were not significantly different except that raloxifene reduced portal venous inflow. Raloxifene exacerbated hepatic fibrosis and up-regulated hepatic endothelin-1 and cyclooxygenase 2 protein expressions. In addition, raloxifene modulated the mRNA expressions of endothelial nitric oxide synthase, cyclooxygenase and endothelin-1 in the superior mesenteric artery and collateral vessel. In conclusion, raloxifene aggravates hepatic fibrosis and decreases portal venous inflow in cirrhotic rats without adversely affecting portal hypertension and hepatic encephalopathy. The modulation of hepatic and vascular endothelin-1, endothelial nitric oxide synthase and cyclooxygenase expressions may play a role in the mechanism. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Calcification in the portal venous system demonstrated by computed tomography

    Energy Technology Data Exchange (ETDEWEB)

    Hadar, H; Sommer, R

    1983-08-01

    The CT appearance of calcification in the portal venous system in a patient with chronic alcoholic cirrhosis is presented. Reported cases of radiologically detectable calcification in the portal system are rare, and most of them have been associated with longstanding portal hypertension. We presume that with CT this diagnosis will be made more frequently. In the presence of calcification in the portal venous system, portal vein thrombosis is highly probable. This information is of obvious importance to the surgeon contemplating a portal decompressive shunt procedure.

  16. Unexpected disappearance of portal cavernoma on long-term anticoagulation.

    Science.gov (United States)

    Silva-Junior, Gilberto; Turon, Fanny; Hernandez-Gea, Virginia; Darnell, Anna; García-Criado, Ángeles; García-Pagán, Juan Carlos

    2014-08-01

    Idiopathic non-cirrhotic portal hypertension is a rare disease of unknown etiology. Patients with idiopathic non-cirrhotic portal hypertension have an increased risk of developing portal vein thrombosis and this is especially prevalent when HIV is also present. We describe a unique case of a patient with idiopathic non-cirrhotic portal hypertension associated to HIV, who developed acute portal vein thrombosis that despite anticoagulation transformed in portal cavernoma and disappeared completely after five years of follow-up on continuous anticoagulation. Copyright © 2014 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

  17. Regional blood flows by the microsphere method: reproducibility in portal hypertensive rats and influence of a portal vein catheter

    International Nuclear Information System (INIS)

    Hadengue, A.; Lee, S.S.; Koshy, A.; Girod, C.; Lebrec, D.

    1988-01-01

    To determine the reproducibility of splanchnic blood flow measurements by the microsphere method in rats with portal hypertension and the effects of laparotomy with portal vein cannulation, eight groups of 10 rats were studied. Microspheres were labelled with 113 Sn or 141 Ce. Laparotomy with portal cannulation had no significant effect in sham-operated rats. In awake portal hypertensive rats, cardiac output and splanchnic blood flow were lower in portal vein cannulated rats compared with those of non-cannulated animals. In anesthetized portal hypertensive rats blood flows were unaffected by portal cannulation, but arterial pressure and heart rate were elevated. Anesthesia also decreased portal pressure in portal hypertensive rats. We conclude that the microsphere method remains reproducible in portal hypertensive rat models. Laparotomy with portal cannulation can alter systemic and splanchnic hemodynamics in portal hypertensive rats; these effects can also be changed during pentobarbital anesthesia. Regional blood flow measurements in portal hypertensive rats should be performed in animals without portal cannulation and preferably in the awake state

  18. A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family.

    Directory of Open Access Journals (Sweden)

    Gregory D Friedland

    2009-05-01

    Full Text Available Conformational ensembles are increasingly recognized as a useful representation to describe fundamental relationships between protein structure, dynamics and function. Here we present an ensemble of ubiquitin in solution that is created by sampling conformational space without experimental information using "Backrub" motions inspired by alternative conformations observed in sub-Angstrom resolution crystal structures. Backrub-generated structures are then selected to produce an ensemble that optimizes agreement with nuclear magnetic resonance (NMR Residual Dipolar Couplings (RDCs. Using this ensemble, we probe two proposed relationships between properties of protein ensembles: (i a link between native-state dynamics and the conformational heterogeneity observed in crystal structures, and (ii a relation between dynamics of an individual protein and the conformational variability explored by its natural family. We show that the Backrub motional mechanism can simultaneously explore protein native-state dynamics measured by RDCs, encompass the conformational variability present in ubiquitin complex structures and facilitate sampling of conformational and sequence variability matching those occurring in the ubiquitin protein family. Our results thus support an overall relation between protein dynamics and conformational changes enabling sequence changes in evolution. More practically, the presented method can be applied to improve protein design predictions by accounting for intrinsic native-state dynamics.

  19. The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

    Energy Technology Data Exchange (ETDEWEB)

    Nordberg, Henrik [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Cantor, Michael [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Dusheyko, Serge [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Hua, Susan [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Poliakov, Alexander [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Shabalov, Igor [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Smirnova, Tatyana [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Grigoriev, Igor V. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Dubchak, Inna [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

    2013-11-12

    The U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a national user facility, serves the diverse scientific community by providing integrated high-throughput sequencing and computational analysis to enable system-based scientific approaches in support of DOE missions related to clean energy generation and environmental characterization. The JGI Genome Portal (http://genome.jgi.doe.gov) provides unified access to all JGI genomic databases and analytical tools. The JGI maintains extensive data management systems and specialized analytical capabilities to manage and interpret complex genomic data. A user can search, download and explore multiple data sets available for all DOE JGI sequencing projects including their status, assemblies and annotations of sequenced genomes. In this paper, we describe major updates of the Genome Portal in the past 2 years with a specific emphasis on efficient handling of the rapidly growing amount of diverse genomic data accumulated in JGI.

  20. Genetic diversity of Plasmodium Vivax revealed by the merozoite surface protein-1 icb5-6 fragment.

    Science.gov (United States)

    Ruan, Wei; Zhang, Ling-Ling; Feng, Yan; Zhang, Xuan; Chen, Hua-Liang; Lu, Qiao-Yi; Yao, Li-Nong; Hu, Wei

    2017-06-05

    Plasmodium vivax remains a potential cause of morbidity and mortality for people living in its endemic areas. Understanding the genetic diversity of P. vivax from different regions is valuable for studying population dynamics and tracing the origins of parasites. The PvMSP-1 gene is highly polymorphic and has been used as a marker in many P. vivax population studies. The aim of this study was to investigate the genetic diversity of the PvMSP-1 gene icb5-6 fragment and to provide more genetic polymorphism data for further studies on P. vivax population structure and tracking of the origin of clinical cases. Nested PCR and sequencing of the PvMSP-1 icb5-6 marker were performed to obtain the nucleotide sequences of 95 P. vivax isolates collected from Zhejiang province, China. To investigate the genetic diversity of PvMSP-1, the 95 nucleotide sequences of the PvMSP-1 icb5-6 fragment were genotyped and analyzed using DnaSP v5, MEGA software. The 95 P. vivax isolates collected from Zhejiang province were either indigenous cases or imported cases from different regions around the world. A total of 95 sequences ranging from 390 to 460 bp were obtained. The 95 sequences were genotyped into four allele-types (Sal I, Belem, R-III and R-IV) and 17 unique haplotypes. R-III and Sal I were the predominant allele-types. The haplotype diversity (Hd) and nucleotide diversity (Pi) were estimated to be 0.729 and 0.062, indicating that the PvMSP-1 icb5-6 fragment had the highest level of polymorphism due to frequent recombination processes and single nucleotide polymorphism. The values of dN/dS and Tajima's D both suggested neutral selection for the PvMSP-1icb5-6 fragment. In addition, a rare recombinant style of R-IV type was identified. This study presented high genetic diversity in the PvMSP-1 marker among P. vivax strains from around the world. The genetic data is valuable for expanding the polymorphism information on P. vivax, which could be helpful for further study on

  1. In-depth mapping of the mouse brain N-glycoproteome reveals widespread N-glycosylation of diverse brain proteins.

    Science.gov (United States)

    Fang, Pan; Wang, Xin-Jian; Xue, Yu; Liu, Ming-Qi; Zeng, Wen-Feng; Zhang, Yang; Zhang, Lei; Gao, Xing; Yan, Guo-Quan; Yao, Jun; Shen, Hua-Li; Yang, Peng-Yuan

    2016-06-21

    N-glycosylation is one of the most prominent and abundant posttranslational modifications of proteins. It is estimated that over 50% of mammalian proteins undergo glycosylation. However, the analysis of N-glycoproteins has been limited by the available analytical technology. In this study, we comprehensively mapped the N-glycosylation sites in the mouse brain proteome by combining complementary methods, which included seven protease treatments, four enrichment techniques and two fractionation strategies. Altogether, 13492 N-glycopeptides containing 8386 N-glycosylation sites on 3982 proteins were identified. After evaluating the performance of the above methods, we proposed a simple and efficient workflow for large-scale N-glycosylation site mapping. The optimized workflow yielded 80% of the initially identified N-glycosylation sites with considerably less effort. Analysis of the identified N-glycoproteins revealed that many of the mouse brain proteins are N-glycosylated, including those proteins in critical pathways for nervous system development and neurological disease. Additionally, several important biomarkers of various diseases were found to be N-glycosylated. These data confirm that N-glycosylation is important in both physiological and pathological processes in the brain, and provide useful details about numerous N-glycosylation sites in brain proteins.

  2. Evidence for functional diversity between the voltage-gated proton channel Hv1 and its closest related protein HVRP1.

    Directory of Open Access Journals (Sweden)

    Iris H Kim

    Full Text Available The Hv1 channel and voltage-sensitive phosphatases share with voltage-gated sodium, potassium, and calcium channels the ability to detect changes in membrane potential through voltage-sensing domains (VSDs. However, they lack the pore domain typical of these other channels. NaV, KV, and CaV proteins can be found in neurons and muscles, where they play important roles in electrical excitability. In contrast, VSD-containing proteins lacking a pore domain are found in non-excitable cells and are not involved in neuronal signaling. Here, we report the identification of HVRP1, a protein related to the Hv1 channel (from which the name Hv1 Related Protein 1 is derived, which we find to be expressed primarily in the central nervous system, and particularly in the cerebellum. Within the cerebellar tissue, HVRP1 is specifically expressed in granule neurons, as determined by in situ hybridization and immunohistochemistry. Analysis of subcellular distribution via electron microscopy and immunogold labeling reveals that the protein localizes on the post-synaptic side of contacts between glutamatergic mossy fibers and the granule cells. We also find that, despite the similarities in amino acid sequence and structural organization between Hv1 and HVRP1, the two proteins have distinct functional properties. The high conservation of HVRP1 in vertebrates and its cellular and subcellular localizations suggest an important function in the nervous system.

  3. Percutaneous transhepatic portal vein stenting in a patient with benign non-transplant postoperative portal vein stenosis: A case report

    Directory of Open Access Journals (Sweden)

    KS Madhusudhan

    2013-01-01

    Full Text Available Extrahepatic portal vein stenosis is caused by a variety of benign and malignant diseases and results in development of symptoms due to portal hypertension. Benign post-surgical adhesions causing portal vein stenosis in non-transplant population is an uncommon etiology of portal hypertension. Endovascular treatment of such patients with angioplasty and stenting is uncommonly reported in literature. We report a case of portal hypertension caused by benign postoperative portal vein fibrosis, successfully treated by self-expandable metallic stent.

  4. The FXR agonist PX20606 ameliorates portal hypertension by targeting vascular remodelling and sinusoidal dysfunction.

    Science.gov (United States)

    Schwabl, Philipp; Hambruch, Eva; Seeland, Berit A; Hayden, Hubert; Wagner, Michael; Garnys, Lukas; Strobel, Bastian; Schubert, Tim-Lukas; Riedl, Florian; Mitteregger, Dieter; Burnet, Michael; Starlinger, Patrick; Oberhuber, Georg; Deuschle, Ulrich; Rohr-Udilova, Nataliya; Podesser, Bruno K; Peck-Radosavljevic, Markus; Reiberger, Thomas; Kremoser, Claus; Trauner, Michael

    2017-04-01

    Steroidal farnesoid X receptor (FXR) agonists demonstrated potent anti-fibrotic activities and lowered portal hypertension in experimental models. The impact of the novel non-steroidal and selective FXR agonist PX20606 on portal hypertension and fibrosis was explored in this study. In experimental models of non-cirrhotic (partial portal vein ligation, PPVL, 7days) and cirrhotic (carbon tetrachloride, CCl 4 , 14weeks) portal hypertension, PX20606 (PX,10mg/kg) or the steroidal FXR agonist obeticholic acid (OCA,10mg/kg) were gavaged. We then measured portal pressure, intrahepatic vascular resistance, liver fibrosis and bacterial translocation. PX decreased portal pressure in non-cirrhotic PPVL (12.6±1.7 vs. 10.4±1.1mmHg; p=0.020) and cirrhotic CCl 4 (15.2±0.5 vs. 11.8±0.4mmHg; p=0.001) rats. In PPVL animals, we observed less bacterial translocation (-36%; p=0.041), a decrease in lipopolysaccharide binding protein (-30%; p=0.024) and splanchnic tumour necrosis factor α levels (-39%; p=0.044) after PX treatment. In CCl 4 rats, PX decreased fibrotic Sirius Red area (-43%; p=0.005), hepatic hydroxyproline (-66%; pportal pressure (-14%; p=0.041) by restoring endothelial function, 14week PX therapy additionally inhibited sinusoidal remodelling and decreased portal pressure to a greater extent (-22%; p=0.001). In human liver sinusoidal endothelial cells, PX increased eNOS and DDAH expression. The non-steroidal FXR agonist PX20606 ameliorates portal hypertension by reducing liver fibrosis, vascular remodelling and sinusoidal dysfunction. The novel drug PX20606 activates the bile acid receptor FXR and shows beneficial effects in experimental liver cirrhosis: In the liver, it reduces scarring and inflammation, and also widens blood vessels. Thus, PX20606 leads to an improved blood flow through the liver and decreases hypertension of the portal vein. Additionally, PX20606 improves the altered intestinal barrier and decreases bacterial migration from the gut. Copyright

  5. Best Practices for Building Web Data Portals

    Science.gov (United States)

    Anderson, R. A.; Drew, L.

    2013-12-01

    With a data archive of more than 1.5 petabytes and a key role as the NASA Distributed Active Archive Center (DAAC) for synthetic aperture radar (SAR) data, the Alaska Satellite Facility (ASF) has an imperative to develop effective Web data portals. As part of continuous enhancement and expansion of its website, ASF recently created two data portals for distribution of SAR data: one for the archiving and distribution of NASA's MEaSUREs Wetlands project and one for newly digitally processed data from NASA's 1978 Seasat satellite. These case studies informed ASF's development of the following set of best practices for developing Web data portals. 1) Maintain well-organized, quality data. This is fundamental. If data are poorly organized or contain errors, credibility is lost and the data will not be used. 2) Match data to likely data uses. 3) Identify audiences in as much detail as possible. ASF DAAC's Seasat and Wetlands portals target three groups of users: a) scientists already familiar with ASF DAAC's SAR archive and our data download tool, Vertex; b) scientists not familiar with SAR or ASF, but who can use the data for their research of oceans, sea ice, volcanoes, land deformation and other Earth sciences; c) audiences wishing to learn more about SAR and its use in Earth sciences. 4) Identify the heaviest data uses and the terms scientists search for online when trying to find data for those uses. 5) Create search engine optimized (SEO) Web content that corresponds to those searches. Because search engines do not yet search raw data, so Web data portals must include content that ties the data to its likely uses. 6) Create Web designs that best serves data users (user centered design), not for how the organization views itself or its data. Usability testing was conducted for the ASF DAAC Wetlands portal to improve the user experience. 7) Use SEO tips and techniques. The ASF DAAC Seasat portal used numerous SEO techniques, including social media, blogging

  6. Radionuclide assessment of portal hypertension syndrome

    International Nuclear Information System (INIS)

    Aliev, M.A.; Khusain, Sh.K.; Alpeisova, Sh.T.

    2005-01-01

    This paper presents review of radionuclide studies for portal hypertension patients. Presented results showed that portal hypertension signs were revealed for the first group patients. The signs become apparent by splenomegaly and increase of colloid accumulation in it. Accumulation of the chemical in spleen was evidence of ingestion rate increase of reticuloendothelial system owing to its hyperplasia as well as liver phagocytic activity decrease due to pathological paren-chematous process and inter liver blockade. The most typical scintigraphic signs of portal hypertension were determined according chemical accumulation decreased in spleen and marrow sequentially. It is determined radionuclide method contributes to assessment of structural and functional aberrations character in liver and spleen for cirrhosis patients. (author)

  7. ERNIE performance with TSA portals Initial Results

    Energy Technology Data Exchange (ETDEWEB)

    Labov, S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2018-01-05

    This project extends the “Enhanced Radiological Nuclear Inspection and Evaluation” (ERNIE) system developed with CBP and DNDO to improve performance of PVT-based Radiation Portal Monitors (RPMs). ERNIE was designed to be used with any RPM system. The first implementation was with the SAIC (Leidos) RPM-8 systems. In this project, we are demonstrating how effective the ERNIE approach can be when applied to the VM250 TSA portals used in NSDD programs. Part of the challenge in adapting ERNIE to handle VM250 portals is the lack of gamma spectral information. We report here on the first results showing how the ERNIE analysis can improve analysis of measurements with the VM250 RPMs.

  8. Perivesical varices and portal hypertension: imaging study

    International Nuclear Information System (INIS)

    Mallorquin Jimenez, F.; Medina Benitez, A.; Lopez Machado, E.; Pardo Moreno, M.D.; Garrido Moreno, C.; Pastor Rull, J.

    1995-01-01

    Nine patients with portal hypertension syndrome and Perivesical varices are studied retrospectively by means of imaging techniques including ultrasound, duplex Doppler, color Doppler, CT and angiography. All the patients presented portal thrombosis and thickening of the bladder wall. These collaterals either represent a shunting of hepato pedal flow or correspond to blood stasis associated with said syndrome. Ultrasound, whether involving duplex Doppler or color Doppler techniques, is highly useful to detect the presence of Perivesical varices which appear as tubular or rounded hypo echogenic areas in the bladder wall. Given the association of this entity with bladder wall thickening, it should be taken into account in any clinical situation involving said change, especially in patients with portal hypertension; moreover knowledge of its presence is of great importance when the possibility of creating shunts by means of interventional or surgical vascular procedures or other types of abdominal procedures are being considered because of the risk of bleeding. (Author)

  9. Configuring Mobile Commerce Portals for Business Success

    DEFF Research Database (Denmark)

    Dholakia, Nikhilesh; Rask, Morten

    2004-01-01

    -portals must attract and retain customers. Success in mobile portal markets will depend on dynamic strategies that blend elements of personalization, permission, and specification of content. This chapter reviews the key differences between traditional e-commerce and the emergent m-commerce. It reviews...... the core concepts of personalization, permission, and content specification as they apply to e-commerce and m-commerce. The chapter presents a framework for developing effective business strategies for developing and managing mobile portals. http://www.morten-rask.dk/2003c.htm......M-commerce entails transactions conducted via mobile telecommunications networks using communication, information, and payment devices such as mobile phones or palmtop units. Geographic positioning and location capabilities are also being added to such networks and devices. Rather than using...

  10. Portal monitor evaluation and test procedure

    International Nuclear Information System (INIS)

    Johnson, L.O.; Gupta, V.P.; Stevenson, R.L.; Rich, B.L.

    1983-10-01

    The purpose was to develop techniques and procedures to allow users to measure performance and sensitivity of portal monitors. Additionally, a methodology was developed to assist users in optimizing monitor performance. The two monitors tested utilized thin-window gas-flow proportional counters sensitive to beta and gamma radiation. Various tests were performed: a) background count rate and the statistical variability, b) detector efficiency at different distances, c) moving source sensitivity for various size sources and speeds, and d) false alarm rates at different background levels. A model was developed for the moving source measurements to compare the experimental data with measured results, and to test whether it is possible to adequately model the behavior of a portal monitor's response to a moving source. The model results were compared with the actual test results. A procedure for testing portal monitors is also given. 1 reference, 9 figures, 8 tables

  11. Building a Smart Portal for Astronomy

    Science.gov (United States)

    Derriere, S.; Boch, T.

    2011-07-01

    The development of a portal for accessing astronomical resources is not an easy task. The ever-increasing complexity of the data products can result in very complex user interfaces, requiring a lot of effort and learning from the user in order to perform searches. This is often a design choice, where the user must explicitly set many constraints, while the portal search logic remains simple. We investigated a different approach, where the query interface is kept as simple as possible (ideally, a simple text field, like for Google search), and the search logic is made much more complex to interpret the query in a relevant manner. We will present the implications of this approach in terms of interpretation and categorization of the query parameters (related to astronomical vocabularies), translation (mapping) of these concepts into the portal components metadata, identification of query schemes and use cases matching the input parameters, and delivery of query results to the user.

  12. pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families.

    Science.gov (United States)

    Suplatov, Dmitry; Kirilin, Eugeny; Arbatsky, Mikhail; Takhaveev, Vakil; Svedas, Vytas

    2014-07-01

    The new web-server pocketZebra implements the power of bioinformatics and geometry-based structural approaches to identify and rank subfamily-specific binding sites in proteins by functional significance, and select particular positions in the structure that determine selective accommodation of ligands. A new scoring function has been developed to annotate binding sites by the presence of the subfamily-specific positions in diverse protein families. pocketZebra web-server has multiple input modes to meet the needs of users with different experience in bioinformatics. The server provides on-site visualization of the results as well as off-line version of the output in annotated text format and as PyMol sessions ready for structural analysis. pocketZebra can be used to study structure-function relationship and regulation in large protein superfamilies, classify functionally important binding sites and annotate proteins with unknown function. The server can be used to engineer ligand-binding sites and allosteric regulation of enzymes, or implemented in a drug discovery process to search for potential molecular targets and novel selective inhibitors/effectors. The server, documentation and examples are freely available at http://biokinet.belozersky.msu.ru/pocketzebra and there are no login requirements. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Application of the smart portal in transportation

    International Nuclear Information System (INIS)

    Kercel, S.W.; Baylor, V.M.; Dress, W.B.; Hickerson, T.W.; Jatko, W.B.; Labaj, L.E.; Muhs, J.D.; Pack, R.M.

    1996-01-01

    Under a program sponsored by the Department of Energy, the Oak Ridge complex is developed a ''Portal-of-the-Future'', or ''smart portal''. This is a security portal for vehicular traffic which is intended to quickly detect explosives, hidden passengers, etc. It uses several technologies, including microwaves, weigh-in-motion, digital image processing, and electroacoustic wavelet-based heartbeat detection. A novel component of particular interest is the Enclosed Space Detection System (ESDS), which detects the presence of persons hiding in a vehicle. The system operates by detecting the presence of a human ballistocardiographic signature. Each time the heart beats, it generates a small but measurable shock wave that propagates through the body. The wave, whose graph is called a ballistocardiogram, is the mechanical analog of the electrocardiogram, which is routinely used for medical diagnosis. The wave is, in turn, coupled to any surface or object with which the body is in contact. If the body is located in an enclosed space, this will result in a measurable deflection of the surface of the enclosure. Independent testing has shown ESDS to be highly reliable. The technologies used in the smart portal operate in real time and allow vehicles to be checked through the portal in much less time than would be required for human inspection. Although not originally developed for commercial transportation, the smart portal has the potential to solve several transportation problems. It could relieve congestion at international highway border crossings by reducing the time required to inspect each vehicle while increasing the level of security. It can reduce highway congestion at the entrance of secure facilities such as prisons. Also, it could provide security at intermodal transfer points, such as airport parking lots and car ferry terminals

  14. Application of the smart portal in transportation

    Energy Technology Data Exchange (ETDEWEB)

    Kercel, S.W.; Baylor, V.M.; Dress, W.B.; Hickerson, T.W.; Jatko, W.B.; Labaj, L.E.; Muhs, J.D.; Pack, R.M.

    1996-12-31

    Under a program sponsored by the Department of Energy, the Oak Ridge complex is developed a ``Portal-of-the-Future``, or ``smart portal``. This is a security portal for vehicular traffic which is intended to quickly detect explosives, hidden passengers, etc. It uses several technologies, including microwaves, weigh-in-motion, digital image processing, and electroacoustic wavelet-based heartbeat detection. A novel component of particular interest is the Enclosed Space Detection System (ESDS), which detects the presence of persons hiding in a vehicle. The system operates by detecting the presence of a human ballistocardiographic signature. Each time the heart beats, it generates a small but measurable shock wave that propagates through the body. The wave, whose graph is called a ballistocardiogram, is the mechanical analog of the electrocardiogram, which is routinely used for medical diagnosis. The wave is, in turn, coupled to any surface or object with which the body is in contact. If the body is located in an enclosed space, this will result in a measurable deflection of the surface of the enclosure. Independent testing has shown ESDS to be highly reliable. The technologies used in the smart portal operate in real time and allow vehicles to be checked through the portal in much less time than would be required for human inspection. Although not originally developed for commercial transportation, the smart portal has the potential to solve several transportation problems. It could relieve congestion at international highway border crossings by reducing the time required to inspect each vehicle while increasing the level of security. It can reduce highway congestion at the entrance of secure facilities such as prisons. Also, it could provide security at intermodal transfer points, such as airport parking lots and car ferry terminals.

  15. Interactive monitoring portal for fusion simulations

    International Nuclear Information System (INIS)

    Abla, G.; Schissel, D.P.; Kim, E.N.; Flanagan, S.M.; Lee, X.

    2012-01-01

    Highlights: ► We designed a web-based monitoring system that tracks the status of fusion simulations. ► Our system is scalable to monitor the simulations running on distributed supercomputers and clusters located at multiple geographical locations. ► The monitoring portal provides a web-based interface for post-run analysis, such as visualizing the results, logging the user comments, and rating the simulation quality. ► Our system utilizes the open source software, such as Python, Django, MySQL, Apache, and MDSplus. - Abstract: The Center for Simulation of RF Wave Interactions with Magnetohydrodynamics (SWIM) Project is a proto-Fusion Simulation Program (FSP) whose goal is to study high-performance fusion plasmas and perform comprehensive simulations that are essential to the development of fusion. SWIM team members are geographically distributed and utilize distributed supercomputers for computational simulations. Due to the highly distributed computational work environment, the SWIM team has the difficulty of monitoring code runs and discovering historical runs. To alleviate this difficulty a web-based monitoring portal has been developed and deployed. The monitoring portal tracks the progress of simulations and automatically collects metadata in real-time. This capability helps scientists to effectively utilize precious computer resources. Furthermore, the portal provides a web-based interface for post-run analysis, such as visualizing the results, logging the user comments, and rating the simulation quality. The user interface provides rapid discovery capability via multi-field searching and sorting. The development of the monitoring portal used open source software, such as Python, Django, MySQL, and Apache. It uses MDSplus for data management, Memcached for data caches, and OpenID for single sign-on security. This paper describes the software architecture, related technologies and deployment experiences of the monitoring portal.

  16. Application of the smart portal in transportation

    Science.gov (United States)

    Kercel, Stephen W.; Baylor, Vivian M.; Dress, William B.; Hickerson, Tim W.; Jatko, William B.; Labaj, Leo E.; Muhs, Jeffrey D.; Pack, Richard M.

    1997-02-01

    Under a program sponsored by the Department of Energy, the Oak Ridge complex is developing a `Portal-of-the-Future', or `smart portal.' This is a security portal for vehicular traffic which is intended to quickly detect explosives, hidden passengers, etc. It uses several technologies, including microwaves, weigh-in-motion, digital image processing, and electroacoustic wavelet-based heartbeat detection. A novel component of particular interest is the Enclosed Space Detection System (ESDS), which detects the presence of persons hiding in a vehicle. The system operates by detecting the presence of a human ballistocardiographic signature. Each time the heart beats, it generates a small but measurable shock wave that propagates through the body. The wave, whose graph is called a ballistocardiogram, is the mechanical analog of the electrocardiograms, which is routinely used for medical diagnosis. The wave is, in turn, coupled to any surface or object with which the body is in contact. If the body is located in an enclosed space, this will result in a measurable deflection of the surface of the enclosure. Independent testing has shown ESDS to be highly reliable. The technologies used in the smart portal operate in real time and allow vehicles to be checked through the portal in much less time than would be required for human inspection. Although not originally developed for commercial transportation, the smart portal has the potential to solve several transportation problems. It could relieve congestion at international highway border crossings by reducing the time required to inspect each vehicle while increasing the level of security. It can reduce highway congestion at the entrance of secure facilities such as prisons. Also, it could provide security at intermodal transfer points, such as airport parking lots and car ferry terminals.

  17. Portal placement in elbow arthroscopy by novice surgeons: cadaver study.

    Science.gov (United States)

    Claessen, Femke M A P; Kachooei, Amir R; Kolovich, Gregory P; Buijze, Geert A; Oh, Luke S; van den Bekerom, Michel P J; Doornberg, Job N

    2017-07-01

    In this anatomical cadaver study, the distance between major nerves and ligaments at risk for injury and portal sites created by trainees was measured. Trainees, inexperienced in elbow arthroscopy, have received a didactic lecture and cadaver instruction prior to portal placement. The incidence of iatrogenic injury from novice portal placement was also determined. Anterolateral, direct lateral, and anteromedial arthroscopic portals were created in ten cadavers by ten inexperienced trainees in elbow arthroscopy. After creating each portal, the trajectory of the portal was marked with a guide pin. Subsequently, the cadavers were dissected and the distances between the guide pin in the anterolateral, direct lateral, and anteromedial portals and important ligaments and nerves were measured. The difference between the distance of the direct lateral portal and the posterior antebrachial cutaneous nerve (PABCN) (22 mm, p cadaver instruction session alone. Level of evidence V.

  18. Genetic diversity of Plasmodium falciparum isolates from naturally infected children in north-central Nigeria using the merozoite surface protein-2 as molecular marker.

    Science.gov (United States)

    Oyedeji, Segun Isaac; Awobode, Henrietta Oluwatoyin; Anumudu, Chiaka; Kun, Jürgen

    2013-08-01

    To characterize the genetic diversity of Plasmodium falciparum (P. falciparum) field isolates in children from Lafia, North-central Nigeria, using the highly polymorphic P. falciparum merozoite surface protein 2 (MSP-2) gene as molecular marker. Three hundred and twenty children were enrolled into the study between 2005 and 2006. These included 140 children who presented with uncomplicated malaria at the Dalhatu Araf Specialist Hospital, Lafia and another 180 children from the study area with asymptomatic infection. DNA was extracted from blood spot on filter paper and MSP-2 genes were genotyped using allele-specific nested PCR in order to analyze the genetic diversity of parasite isolates. A total of 31 and 34 distinct MSP-2 alleles were identified in the asymptomatic and uncomplicated malaria groups respectively. No difference was found between the multiplicity of infection in the asymptomatic group and that of the uncomplicated malaria group (P>0.05). However, isolates of the FC27 allele type were dominant in the asymptomatic group whereas isolates of the 3D7 allele type were dominant in the uncomplicated malaria group. This study showed a high genetic diversity of P. falciparum isolates in North-central Nigeria and is comparable to reports from similar areas with high malaria transmission intensity. Copyright © 2013 Hainan Medical College. Published by Elsevier B.V. All rights reserved.

  19. In-Depth Characterization of the Phaseolin Protein Diversity of Common Bean (Phaseolus vulgaris L. Based on Two-Dimensional Electrophoresis and Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    María López-Pedrouso

    2012-01-01

    Full Text Available Phaseolin is the major seed storage protein of common bean. It comprises a complex set of glycoproteins heterogeneous in their polypeptide composition that is encoded by a gene family. Analyses of phaseolin banding patterns by one-dimensional electrophoresis (SDS-PAGE have been central to the current understanding of the diversity of wild and cultivated common beans. In this work, we have carried out a detailed description and interpretation of phaseolin diversity in cultivated common beans of different geographic origins (Mesoamerican and Andean gene pools based on the current two-dimensional electrophoresis (2-DE technology and mass spectrometry (MS. High-quality 2-DE gel images revealed very complex phaseolin patterns across the studied cultivars. Specifically, patterns of phaseolin within cultivars were organized in a horizontal string of multiple isospot pairs varying in isoelectric point and molecular mass. The degree of similarity among phaseolin patterns was estimated from the percentage of spots shared between pairs of cultivars. Analyses of proteomic distances between phaseolin types by non-metrical multidimensional scaling revealed that 2-DE phaseolin profiles are more similar among cultivars belonging to the same gene pool. However, higher differentiation was found among cultivars of the Andean gene pool. Analysis of genetic variations of the PCR-based SCAR marker of phaseolin seed protein was in general agreement with 2-DE phaseolin patterns, but provided supplementary information regarding diversity among cultivars. Furthermore, the molecular basis responsible for the complexity of 2-DE phaseolin patterns was investigated. Thus, identification of phaseolin spots from 2-DE gels by MALDI-TOF and MALDI-TOF/TOF MS showed that each single isospot pair contained only one type (α or β of phaseolin polypeptide, but pairs with higher and lower molecular mass corresponded to α- and β-type polypeptides, respectively. In addition, partial

  20. Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis.

    Science.gov (United States)

    Yutin, Natalya; Bäckström, Disa; Ettema, Thijs J G; Krupovic, Mart; Koonin, Eugene V

    2018-04-10

    Analysis of metagenomic sequences has become the principal approach for the study of the diversity of viruses. Many recent, extensive metagenomic studies on several classes of viruses have dramatically expanded the visible part of the virosphere, showing that previously undetected viruses, or those that have been considered rare, actually are important components of the global virome. We investigated the provenance of viruses related to tail-less bacteriophages of the family Tectiviridae by searching genomic and metagenomics sequence databases for distant homologs of the tectivirus-like Double Jelly-Roll major capsid proteins (DJR MCP). These searches resulted in the identification of numerous genomes of virus-like elements that are similar in size to tectiviruses (10-15 kilobases) and have diverse gene compositions. By comparison of the gene repertoires, the DJR MCP-encoding genomes were classified into 6 distinct groups that can be predicted to differ in reproduction strategies and host ranges. Only the DJR MCP gene that is present by design is shared by all these genomes, and most also encode a predicted DNA-packaging ATPase; the rest of the genes are present only in subgroups of this unexpectedly diverse collection of DJR MCP-encoding genomes. Only a minority encode a DNA polymerase which is a hallmark of the family Tectiviridae and the putative family "Autolykiviridae". Notably, one of the identified putative DJR MCP viruses encodes a homolog of Cas1 endonuclease, the integrase involved in CRISPR-Cas adaptation and integration of transposon-like elements called casposons. This is the first detected occurrence of Cas1 in a virus. Many of the identified elements are individual contigs flanked by inverted or direct repeats and appear to represent complete, extrachromosomal viral genomes, whereas others are flanked by bacterial genes and thus can be considered as proviruses. These contigs come from metagenomes of widely different environments, some dominated by

  1. R2 Water Quality Portal Monitoring Stations

    Science.gov (United States)

    The Water Quality Data Portal (WQP) provides an easy way to access data stored in various large water quality databases. The WQP provides various input parameters on the form including location, site, sampling, and date parameters to filter and customize the returned results. The The Water Quality Portal (WQP) is a cooperative service sponsored by the United States Geological Survey (USGS), the Environmental Protection Agency (EPA) and the National Water Quality Monitoring Council (NWQMC) that integrates publicly available water quality data from the USGS National Water Information System (NWIS) the EPA STOrage and RETrieval (STORET) Data Warehouse, and the USDA ARS Sustaining The Earth??s Watersheds - Agricultural Research Database System (STEWARDS).

  2. Duplication of the Portal Vein: A Case Report

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sang Won; Shin, Hyeong Cheol; Jou, Sung Shick; Han, Jong Kyu; Kim, Il Young [Soonchunhyang University Cheonan Hospital, Cheonan (Korea, Republic of)

    2009-12-15

    The duplication of the portal vein is an uncommon congenital anomaly. To date, only four cases have been reported in the medical literature. This anomaly can cause portal hypertension in pediatric patients. In addition, duplication of the portal vein has various patterns of connection with a splenic vein or mesenteric veins, and it can lie anterior or posterior to the duodenum. We report the MDCT findings of an adult patient with duplication of the portal vein that was found incidentally

  3. [The effect of portal blood stasis on lung and renal injury induced by hepatic ischemia reperfusion in a rabbit model].

    Science.gov (United States)

    Wang, Ye; Yang, Jia-mei; Hou, Yuan-kai; Li, Dian-qi; Hu, Ming-hua; Liu, Peng

    2008-04-15

    To investigate the effect and mechanism of portal blood stasis on lung and renal injury induced by hepatic ischemia reperfusion. A rabbit hepatic ischemia reperfusion injury model was established by hepatic portal occlusion and in situ hypothermic irrigation for 30 min. Twenty-four New Zealand white rabbits were employed and randomly divided into 3 groups equally by different dosage of portal blood stasis removal: group A5 (5 ml blood removal), group A10 (10 ml blood removal),and group B (no blood removal). Eight rabbits were served as controls with no hepatic portal occlusion and hypothermic irrigation. After reperfusion 4 h serum endotoxin content, tumor necrosis factor-alpha (TNF-alpha), urea nitrogen (BUN), and creatinine (Cr) were examined respectively, meantime lung and kidney tissues were sampled to determine the content of malondialdehyde (MDA), superoxide dismutase (SOD), the pathology, and wet to dry weight ratio, broncho-alveolar lavage fluid protein content in lung tissues. Removing portal blood stasis ameliorated lung and renal injury as shown by decreasing the level of serum endotoxin, TNF-alpha, BUN, Cr, wet to dry weight ratio, broncho-alveolar lavage fluid protein content, MDA, SOD. TNF-alpha, Cr, broncho-alveolar lavage fluid protein content in lung tissues and MDA in kidney tissue in group A5 were significantly reduced compared with those in group B (P portal blood stasis before the resume of splanchnic circulation may ameliorate the lung and renal injury induced by hepatic ischemia reperfusion. The possible mechanism may be that portal blood stasis removal reduces endotoxin absorption, and further decreases production of serum TNF-alpha.

  4. Assessment of the quality of educational portals

    Directory of Open Access Journals (Sweden)

    R. G. Bolbakov

    2017-01-01

    Full Text Available The article describes the results of theoretical and experimental studies on the evaluation of the quality of educational information placed on information and educational portals. The methodology allows you to compare not only portals, but also the results of training on exam scores and test scores. The methodological basis of the assessment is the cognitive approach and the negentropic approach. The article gives a comparison of entropy and negentropy. On the basis of comparison, the authors propose a negentropic approach to assessing the quality of educational resources obtained as a result of information retrieval. The search results are evaluated by cognitive and perpetual scores. Estimates are introduced into the entropy formula and converted to the formula of negentropy. The negentropic approach serves as the basis for calculating the statistical amount of information obtained as a result of information retrieval. The cognitive approach serves as a basis for assessing the qualitative characteristics of educational information, such as: visibility, perceptibility, interpretability. Open information portalsare the source of educational resources. The article shows that modern information portals are often clogged with unreliable or unnecessary information, which makes it difficult to find relevant educational information. In contrast to the widespread methods for one relevanceassess of the information retrieval, this article differentiates the notion of the relevance of the information retrieval. The article introduces three qualitatively different notions of relevance: formal, semantic and perpetual – relevance. The article introduces new additional characteristics of the quality of information search, the coefficient of cognition and the coefficient of perpetuation. These coefficients are introduced into the formula for estimating entropy and obtain the cognitive-entropy formula. As a result, a new method for assessing the content of

  5. Portal Hypertension Secondary to Spontaneous Arterio-Portal Venous Fistulas: Transcatheter Arterial Embolization with n-Butyl Cyanoacrylate and Microcoils

    International Nuclear Information System (INIS)

    Yamagami, Takuji; Nakamura, Toshiyuki; Nishimura, Tsunehiko

    2000-01-01

    We report a 73-year-old man with recurrent variceal bleeding due to portal hypertension caused by multiple intrahepatic arterio-portal venous fistulas, which were successfully occluded by embolization with n-butyl cyanoacrylate and micro-coils

  6. MASCP Gator: An overview of the Arabidopsis proteomic aggregation portal

    Directory of Open Access Journals (Sweden)

    Gregory W Mann

    2013-10-01

    Full Text Available A key challenge in the area of bioinformatics in the coming decades is the ability to manage the wealth of information that is being generated from the variety of high throughput methodologies currently being undertaken in laboratories across the world. While these approaches have made available large volumes of data to the research community, less attention has been given to the problem of how to intuitively present the data to enable greater biological insights. Recently, an attempt was made to tackle this problem in the area of Arabidopsis proteomics. The model plant has been the target of countless proteomics surveys producing an exhaustive array of data and online repositories. The MASCP Gator is an aggregation portal for proteomic data currently being produced by the community and unites a large collection of specialized resources to a single portal (http://gator.masc-proteomics.org/. Here we describe the latest additions, upgrades and features to this resource further expanding its role into protein modifications and genome sequence variations.

  7. Base of tongue varices associated with portal hypertension

    OpenAIRE

    Jassar, P; Jaramillo, M; Nunez, D

    2000-01-01

    A symptomatic case of tongue base varices in a patient with portal hypertension secondary to liver cirrhosis is presented. There are no previously documented cases in the world literature. Oesophageal varices may not be the only source of expectorated blood in a patient with portal hypertension.


Keywords: portal hypertension; lingual; tongue; varicose vein

  8. User Needs of Digital Service Web Portals: A Case Study

    Science.gov (United States)

    Heo, Misook; Song, Jung-Sook; Seol, Moon-Won

    2013-01-01

    The authors examined the needs of digital information service web portal users. More specifically, the needs of Korean cultural portal users were examined as a case study. The conceptual framework of a web-based portal is that it is a complex, web-based service application with characteristics of information systems and service agents. In…

  9. Velocity Estimation of the Main Portal Vein with Transverse Oscillation

    DEFF Research Database (Denmark)

    Brandt, Andreas Hjelm; Hansen, Kristoffer Lindskov; Nielsen, Michael Bachmann

    2015-01-01

    This study evaluates if Transverse Oscillation (TO) can provide reliable and accurate peak velocity estimates of blood flow the main portal vein. TO was evaluated against the recommended and most widely used technique for portal flow estimation, Spectral Doppler Ultrasound (SDU). The main portal...

  10. Release of the herpes simplex virus 1 protease by self cleavage is required for proper conformation of the portal vertex

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Kui; Wills, Elizabeth G. [Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853 (United States); Baines, Joel D., E-mail: jdb11@cornell.edu [Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853 (United States)

    2012-07-20

    We identify an NLS within herpes simplex virus scaffold proteins that is required for optimal nuclear import of these proteins into infected or uninfected nuclei, and is sufficient to mediate nuclear import of GFP. A virus lacking this NLS replicated to titers reduced by 1000-fold, but was able to make capsids containing both scaffold and portal proteins suggesting that other functions can complement the NLS in infected cells. We also show that Vp22a, the major scaffold protein, is sufficient to mediate the incorporation of portal protein into capsids, whereas proper portal immunoreactivity in the capsid requires the larger scaffold protein pU{sub L}26. Finally, capsid angularization in infected cells did not require the HSV-1 protease unless full length pU{sub L}26 was expressed. These data suggest that the HSV-1 portal undergoes conformational changes during capsid maturation, and reveal that full length pU{sub L}26 is required for this conformational change.

  11. Uses of phage display in agriculture: a review of food-related protein-protein interactions discovered by biopanning over diverse baits.

    Science.gov (United States)

    Kushwaha, Rekha; Payne, Christina M; Downie, A Bruce

    2013-01-01

    This review highlights discoveries made using phage display that impact the use of agricultural products. The contribution phage display made to our fundamental understanding of how various protective molecules serve to safeguard plants and seeds from herbivores and microbes is discussed. The utility of phage display for directed evolution of enzymes with enhanced capacities to degrade the complex polymers of the cell wall into molecules useful for biofuel production is surveyed. Food allergies are often directed against components of seeds; this review emphasizes how phage display has been employed to determine the seed component(s) contributing most to the allergenic reaction and how it has played a central role in novel approaches to mitigate patient response. Finally, an overview of the use of phage display in identifying the mature seed proteome protection and repair mechanisms is provided. The identification of specific classes of proteins preferentially bound by such protection and repair proteins leads to hypotheses concerning the importance of safeguarding the translational apparatus from damage during seed quiescence and environmental perturbations during germination. These examples, it is hoped, will spur the use of phage display in future plant science examining protein-ligand interactions.

  12. Uses of Phage Display in Agriculture: A Review of Food-Related Protein-Protein Interactions Discovered by Biopanning over Diverse Baits

    Directory of Open Access Journals (Sweden)

    Rekha Kushwaha

    2013-01-01

    Full Text Available This review highlights discoveries made using phage display that impact the use of agricultural products. The contribution phage display made to our fundamental understanding of how various protective molecules serve to safeguard plants and seeds from herbivores and microbes is discussed. The utility of phage display for directed evolution of enzymes with enhanced capacities to degrade the complex polymers of the cell wall into molecules useful for biofuel production is surveyed. Food allergies are often directed against components of seeds; this review emphasizes how phage display has been employed to determine the seed component(s contributing most to the allergenic reaction and how it has played a central role in novel approaches to mitigate patient response. Finally, an overview of the use of phage display in identifying the mature seed proteome protection and repair mechanisms is provided. The identification of specific classes of proteins preferentially bound by such protection and repair proteins leads to hypotheses concerning the importance of safeguarding the translational apparatus from damage during seed quiescence and environmental perturbations during germination. These examples, it is hoped, will spur the use of phage display in future plant science examining protein-ligand interactions.

  13. Transplantation of endothelial progenitor cells ameliorates vascular dysfunction and portal hypertension in carbon tetrachloride-induced rat liver cirrhotic model.

    Science.gov (United States)

    Sakamoto, Masaharu; Nakamura, Toru; Torimura, Takuji; Iwamoto, Hideki; Masuda, Hiroshi; Koga, Hironori; Abe, Mitsuhiko; Hashimoto, Osamu; Ueno, Takato; Sata, Michio

    2013-01-01

    In cirrhosis, sinusoidal endothelial cell injury results in increased endothelin-1 (ET-1) and decreased nitric oxide synthase (NOS) activity, leading to portal hypertension. However, the effects of transplanted endothelial progenitor cells (EPCs) on the cirrhotic liver have not yet been clarified. We investigated whether EPC transplantation reduces portal hypertension. Cirrhotic rats were created by the administration of carbon tetrachloride (CCl(4) ) twice weekly for 10 weeks. From week 7, rat bone marrow-derived EPCs were injected via the tail vein in this model once a week for 4 weeks. Endothelial NOS (eNOS), vascular endothelial growth factor (VEGF) and caveolin expressions were examined by Western blots. Hepatic tissue ET-1 was measured by a radioimmunoassay (RIA). Portal venous pressure, mean aortic pressure, and hepatic blood flow were measured. Endothelial progenitor cell transplantation reduced liver fibrosis, α-smooth muscle actin-positive cells, caveolin expression, ET-1 concentration and portal venous pressure. EPC transplantation increased hepatic blood flow, protein levels of eNOS and VEGF. Immunohistochemical analyses of eNOS and isolectin B4 demonstrated that the livers of EPC-transplanted animals had markedly increased vascular density, suggesting reconstitution of sinusoidal blood vessels with endothelium. Transplantation of EPCs ameliorates vascular dysfunction and portal hypertension, suggesting this treatment may provide a new approach in the therapy of portal hypertension with liver cirrhosis. © 2012 Journal of Gastroenterology and Hepatology Foundation and Wiley Publishing Asia Pty Ltd.

  14. Development and implementation of an empirical frequency map for use in MD simulations of isotope-edited proteins, and, Development, implementation, and evaluation of an online student portal as a textbook replacement in an advanced general chemistry course

    Science.gov (United States)

    Shorb, Justin Matthew

    The first portion of this thesis describes an extension of work done in the Skinner group to develop an empirical frequency map for N-methylacetamide (NMA) in water. NMA is a peptide bond capped on either side by a methyl group and is therefore a common prototypical molecule used when studying complicated polypeptides and proteins. This amide bond is present along the backbone of every protein as it connects individual component amino acids. This amide bond also has a strong observable frequency in the IR due to the Amide-I mode (predominantly carbon-oxygen stretching motion). This project describes the simplification of the prior model for mapping the frequency of the Amide-I mode from the electric field due to the environment and develops a parallel implementation of this algorithm for use in larger biological systems, such as the trans-membrane portion of the tetrameric polypeptide bundle protein CD3zeta. The second portion of this thesis describes the development, implementation and evaluation of an online textbook within the context of a cohesive theoretical framework. The project begins by describing what is meant when discussing a digital textbook, including a survey of various types of digital media being used to deliver textbook-like content. This leads into the development of a theoretical framework based on constructivist pedagogical theory, hypertext learning theory, and chemistry visualization and representation frameworks. The implementation and design of ChemPaths, the general chemistry online text developed within the Chemistry Education Digital Library (ChemEd DL) is then described. The effectiveness of ChemPaths being used as a textbook replacement in an advanced general chemistry course is evaluated within the developed theoretical framework both qualitatively and quantitatively.

  15. Anaplasma ovis genetic diversity detected by major surface protein 1a and its prevalence in small ruminants.

    Science.gov (United States)

    Aktas, Munir; Özübek, Sezayi

    2018-04-01

    Anaplasma ovis is a widely distributed tick-borne rickettsial pathogen of sheep, goats, and wild ruminants. The aims of this study were to assess the prevalence, associations of Anaplasma ovis in sheep and goats, as well as its genetic diversity based on analysis of the msp1α gene. A total of 416 DNA samples from sheep (n = 236) and goats (n = 180) from four provinces in southeastern Turkey were analyzed by PCR. The overall A. ovis prevalence was 18% (CI 14.4-22.1). The infection rates of A. ovis varied from 15.9% to 21.8% in sampled provinces, and they were not significantly different. There was no difference between Anaplasma ovis infection in sheep (20.3%, CI 15.4-26.0) and goats (15.0%, CI 10.1-21.1) or in infection rate of animals 1 year (16.4%, CI 12.4-21.2). A significant association between A. ovis infection and the presence of Rhipicephalus bursa and Rhipicephalus turanicus was observed (P diversity of A. ovis were found in small ruminants in Turkey. Copyright © 2018 Elsevier B.V. All rights reserved.

  16. Novel Rat Model of Repetitive Portal Venous Embolization Mimicking Human Non-Cirrhotic Idiopathic Portal Hypertension

    DEFF Research Database (Denmark)

    Klein, Sabine; Hinüber, Christian; Hittatiya, Kanishka

    2016-01-01

    BACKGROUND: Non-cirrhotic idiopathic portal hypertension (NCIPH) is characterized by splenomegaly, anemia and portal hypertension, while liver function is preserved. However, no animal models have been established yet. This study assessed a rat model of NCIPH and characterized the hemodynamics......, and compared it to human NCIPH. METHODS: Portal pressure (PP) was measured invasively and coloured microspheres were injected in the ileocecal vein in rats. This procedure was performed weekly for 3 weeks (weekly embolization). Rats without and with single embolization served as controls. After four weeks (one...... in the weekly embolization group. Fibrotic markers αSMA and Desmin were upregulated in weekly embolized rats. DISCUSSION: This study establishes a model using repetitive embolization via portal veins, comparable with human NCIPH and may serve to test new therapies....

  17. GENIUS: a web portal for the grid

    International Nuclear Information System (INIS)

    Andronico, A.; Barbera, R.; Falzone, A.; Lo Re, G.; Pulvirenti, A.; Rodolico, A.

    2003-01-01

    The architecture and the current implementation of the grid portal GENIUS (Grid Enabled web environment for site Independent User job Submission), jointly developed by INFN and NICE within the context of the INFN Grid and DataGrid Project, is presented and discussed

  18. Diagnosis of portal hypertension with radioactive isotopes

    Energy Technology Data Exchange (ETDEWEB)

    Lewitus, Z

    1974-01-01

    Administration of /sup 131/I in a microclysma and simultaneous recording of the radioactivity in the liver and precordium allows the diagnosis of portal hypertension in at least 90 percent of the cases. This test has been used now for more than 5 years in patients with liver diseases. The simplicity of the test makes it a valuable bedside procedure.

  19. Extrahepatic complications to cirrhosis and portal hypertension

    DEFF Research Database (Denmark)

    Møller, Søren; Henriksen, Jens H; Bendtsen, Flemming

    2014-01-01

    In addition to complications relating to the liver, patients with cirrhosis and portal hypertension develop extrahepatic functional disturbances of multiple organ systems. This can be considered a multiple organ failure that involves the heart, lungs, kidneys, the immune systems, and other organ...

  20. Liver surgery in cirrhosis and portal hypertension.

    Science.gov (United States)

    Hackl, Christina; Schlitt, Hans J; Renner, Philipp; Lang, Sven A

    2016-03-07

    The prevalence of hepatic cirrhosis in Europe and the United States, currently 250 patients per 100000 inhabitants, is steadily increasing. Thus, we observe a significant increase in patients with cirrhosis and portal hypertension needing liver resections for primary or metastatic lesions. However, extended liver resections in patients with underlying hepatic cirrhosis and portal hypertension still represent a medical challenge in regard to perioperative morbidity, surgical management and postoperative outcome. The Barcelona Clinic Liver Cancer classification recommends to restrict curative liver resections for hepatocellular carcinoma in cirrhotic patients to early tumor stages in patients with Child A cirrhosis not showing portal hypertension. However, during the last two decades, relevant improvements in preoperative diagnostic, perioperative hepatologic and intensive care management as well as in surgical techniques during hepatic resections have rendered even extended liver resections in higher-degree cirrhotic patients with portal hypertension possible. However, there are few standard indications for hepatic resections in cirrhotic patients and risk stratifications have to be performed in an interdisciplinary setting for each individual patient. We here review the indications, the preoperative risk-stratifications, the morbidity and the mortality of extended resections for primary and metastatic lesions in cirrhotic livers. Furthermore, we provide a review of literature on perioperative management in cirrhotic patients needing extrahepatic abdominal surgery and an overview of surgical options in the treatment of hepatic cirrhosis.

  1. [Evaluation and treatment of portal hypertension].

    Science.gov (United States)

    Brůha, Radan; Petrtýl, Jaromír

    Liver cirrhosis is a serious disease shortening the life expectancy. Unavoidable consequence of cirrhosis is portal hypertension, which usually limits the prognosis by its complications. Portal hypertension is a prognostic factor for cirrhosis decompensation, variceal bleeding and even the mortality in cirrhotic patients. In the evaluation of portal hypertension hepatic venous pressure gradient (HVPG) measurement is used.Measurement of HVPG is used in clinical praxis in these situations: diagnosis of portal hypertension, evaluation of prognosis of patients with cirrhosis, monitoring the treatment efficacy in the prevention of variceal bleeding, management of acute variceal bleeding. Decrease of HVPG below 12 mmHg or at least for more than 20% of initial value in the treatment by beta-blockers is associated with the lower risk of bleeding from varices or other complications. HVPG above 20 mm Hg is associated with the high risk of early rebleeding from varices and can discriminate those patients profiting from early TIPS.HVPG measurement is an invasive, but simple, reproducible and safe catheterization technique with minimal complication rate. The most frequent complication could be incorrect assessment of obtained values. HVPG measurement should be a routine technique in centers specialized to liver diseases.

  2. Measuring Problem Solving Skills in "Portal 2"

    Science.gov (United States)

    Shute, Valerie J.; Wang, Lubin

    2013-01-01

    This paper examines possible improvement to problem solving skills as a function of playing the video game "Portal 2." Stealth assessment is used in the game to evaluate students' problem solving abilities--specifically basic and flexible rule application. The stealth assessment measures will be validated against commonly accepted…

  3. Portal hypertension due to choledochal cyst

    International Nuclear Information System (INIS)

    Athar, M.; Haider, M.H.R.; Khan, M.A.; Khaliq, T.; Ahmad, N.

    2002-01-01

    A case of portal hypertension secondary to choledochal cyst is reported. A young female presented with haematemesis, malena and splenomegaly in addition to the classic triad of jaundice, pain and abdominal mass. Oesophagogastroscopy revealed second degree varices. Excision of cyst and hepaticojejunostomy was performed. At six months follow up patient was completely asymptomatic with no endoscopic evidence of varices. (author)

  4. An Empirical Investigation of Campus Portal Usage

    Science.gov (United States)

    Saghapour, Mohsen; Iranmanesh, Mohammad; Zailani, Suhaiza; Goh, Gerald Guan Gan

    2018-01-01

    This study has determined the determinants of the perceived ease of use and perceived usefulness and their influence on campus portal usage. A quantitative approach was employed, using a five-point Likert scale questionnaire, adapted from previous studies. Data were gathered through a survey conducted with 341 staff working in the University of…

  5. Physics Experiments at the UNEDLabs Portal

    Directory of Open Access Journals (Sweden)

    Juan pedro Sánchez

    2012-01-01

    Full Text Available UNEDLabs is a web portal based on a free, modern, open source, and well-known learning management system: Moodle. This portal joins two theme networks of virtual and remote laboratories (one for Control Engineering and another one for Physics, named AutomatL@bs and FisL@bs, respectively together. AutomatL@bs has been operative for five years now. Following AutomatL@bs’ scheme, FisL@bs was created as a network of remote and virtual laboratories for physics university education via the Internet to offer students the possibility of performing hands-on experiences in different fields of physics in two ways: simulation and real remote operation. Now, both FisL@bs and AutomatL@bs join together (while maintaining their independency into an unique new web portal called UNEDLabs. This work focuses on this new web environment and gives a detailed account of a novel way in Physics to let distance learning students gain practical experience autonomously. This paper explains how the new portal works and the software tools used for creating it. In addition, it also describes the physics experiments which are already operative.

  6. ICPP digital wide area portal monitor

    International Nuclear Information System (INIS)

    Nichols, C.E.

    1978-01-01

    A portal montior is described which is used to check personnel for contamination. The monitor is extremely sensitive. In addition to personnel contamination control, it serves as an extremely effective SNM detector capable of detecting U-235 in half the quantities specified in Federal Standards

  7. A neutron portal monitor for vehicles

    International Nuclear Information System (INIS)

    Coop, K.L.; Fehlau, P.E.; Atwater, H.F.

    1987-01-01

    We have designed and built a portal vehicle monitoring systems for detecting neutron-emitting special nuclear material (SNM) such as plutonium. Monte Carlo calculations were used to optimize the design of the 15-cm-deep x 122-cm-high x 244-cm-long detector chambers, which utilize 3 He proportional counters inside a hollow polyethylene box. Results for a variety of parametric studies, including polyethylene thickness and detector number, are described. Our experimental measurements are in good agreement with the computer calculations. The monitor's decision logic uses the Sequential Probability Ratio Test (SPRT) on Poisson distributed counting data, which is superior to other statistical tests in many applications. We performed computer simulations of the SPRT logic to determine expected false-positive decision rates. A controller unit of our design that uses this SPRT was built commercially. The cost of the complete monitoring system is similar to that of vehicle portal monitors that detect gamma rays. This new neutron monitor can serve as an addition to standard gamma-ray vehicle portals or as a stand-alone portal monitor in particular safeguards monitoring situations. The monitor is being tested at Los Alamos and is scheduled for in-plant evaluation of another DOE facility in 1987. 7 refs

  8. Left-sided portal hypertension revisited

    Directory of Open Access Journals (Sweden)

    Antonio Manenti

    2016-12-01

    Conclusions: In every case of left-sided portal hypertension, upper digestive endoscopy and close follow-up are recommended. Besides, computed tomography can demonstrate particular conditions directly favoring gastroesophageal varices, and aid in selection of the appropriate therapeutic decisions. [Arch Clin Exp Surg 2016; 5(4.000: 211-215

  9. Portal hypertension in schistosomiasis: pathophysiology and treatment

    Directory of Open Access Journals (Sweden)

    Luiz Caetano da Silva

    1992-01-01

    Full Text Available In heavily infected young patients, there is a "non-congestive" phase of the disease with splenomegaly which can improve after chemoterapy. A strong correlation between hepatosplenic form and worm burden in young patients has been repeatedly shown. The pattern of vascular intrhepatic lesions seems to depend on two mechanisms: (a egg embolization, with a partial blocking of the portal vasculature; (b the appearance of small portal collaterals along the intrahepatic portal sistem. The role played by hepatitis B virus (HBV and C virus infections in the pathogenesis of liver lesions is variably considered. Selective arteriography shows a reduced diameter of hepatic artery with thin and arched branches outlining vascular gaps. A rich arterial network , as described in autopsy cases, is usually not seen in vivo, except after splenectomy or shunt surgery. An augmented hepatic arterial flow was demonstrated in infected animals. These facts suggest that the poor intrahepatic arterial vascularization demonstrated by selective arteriography in humans is due to a "functional deviation"of arterial blood to the splenic territory. The best results obtained in treatment of portal hypertension were: esophagogastric desvascularization and splenectomy (EGDS, although risk of rebleeding persists; classical (proximal splenorenal shunt (SRS should be abandoned; distal splenorenal shunt may complicate with hepatic encephalopaty, although later and in a lower percentage than in SRS. Propranolol is currently under investigation. In our Department, schistosomotic patients with esophageal varices bleeding are treated by EGDS and, if rebleeding occurs, by sclerosis of the varices.

  10. Portal Environment in Today’s Business

    OpenAIRE

    Aldubaikhi, Ammar

    2015-01-01

    Companies can get benefits from new business models as they can have better and efficient collaboration system and this can be derived from the discussed application in this paper. Companies that easily personalize the SAP enterprise portal are more productive and this reflects their interests in business

  11. Wall shear stress in portal vein of cirrhotic patients with portal hypertension.

    Science.gov (United States)

    Wei, Wei; Pu, Yan-Song; Wang, Xin-Kai; Jiang, An; Zhou, Rui; Li, Yu; Zhang, Qiu-Juan; Wei, Ya-Juan; Chen, Bin; Li, Zong-Fang

    2017-05-14

    To investigate wall shear stress (WSS) magnitude and distribution in cirrhotic patients with portal hypertension using computational fluid dynamics. Idealized portal vein (PV) system models were reconstructed with different angles of the PV-splenic vein (SV) and superior mesenteric vein (SMV)-SV. Patient-specific models were created according to enhanced computed tomography images. WSS was simulated by using a finite-element analyzer, regarding the blood as a Newtonian fluid and the vessel as a rigid wall. Analysis was carried out to compare the WSS in the portal hypertension group with that in healthy controls. For the idealized models, WSS in the portal hypertension group (0-10 dyn/cm 2 ) was significantly lower than that in the healthy controls (10-20 dyn/cm 2 ), and low WSS area (0-1 dyn/cm 2 ) only occurred in the left wall of the PV in the portal hypertension group. Different angles of PV-SV and SMV-SV had different effects on the magnitude and distribution of WSS, and low WSS area often occurred in smaller PV-SV angle and larger SMV-SV angle. In the patient-specific models, WSS in the cirrhotic patients with portal hypertension (10.13 ± 1.34 dyn/cm 2 ) was also significantly lower than that in the healthy controls ( P portal hypertension, the low WSS area extended to wider levels and the magnitude of WSS reached lower levels, thereby being more prone to disturbed flow occurrence. Cirrhotic patients with portal hypertension show dramatic hemodynamic changes with lower WSS and greater potential for disturbed flow, representing a possible causative factor of PV thrombosis.

  12. Genetic diversity of the movement and coat protein genes of South American isolates of Prunus necrotic ringspot virus.

    Science.gov (United States)

    Fiore, Nicola; Fajardo, Thor V M; Prodan, Simona; Herranz, María Carmen; Aparicio, Frederic; Montealegre, Jaime; Elena, Santiago F; Pallás, Vicente; Sánchez-Navarro, Jesús

    2008-01-01

    Prunus necrotic ringspot virus (PNRSV) is distributed worldwide, but no molecular data have been previously reported from South American isolates. The nucleotide sequences corresponding to the movement (MP) and coat (CP) proteins of 23 isolates of PNRSV from Chile, Brazil, and Uruguay, and from different Prunus species, have been obtained. Phylogenetic analysis performed with full-length MP and CP sequences from all the PNRSV isolates confirmed the clustering of the isolates into the previously reported PV32-I, PV96-II and PE5-III phylogroups. No association was found between specific sequences and host, geographic origin or symptomatology. Comparative analysis showed that both MP and CP have phylogroup-specific amino acids and all of the motifs previously characterized for both proteins. The study of the distribution of synonymous and nonsynonymous changes along both open reading frames revealed that most amino acid sites are under the effect of negative purifying selection.

  13. Chemogenomic analysis of G-protein coupled receptors and their ligands deciphers locks and keys governing diverse aspects of signalling.

    Directory of Open Access Journals (Sweden)

    Jörg D Wichard

    Full Text Available Understanding the molecular mechanism of signalling in the important super-family of G-protein-coupled receptors (GPCRs is causally related to questions of how and where these receptors can be activated or inhibited. In this context, it is of great interest to unravel the common molecular features of GPCRs as well as those related to an active or inactive state or to subtype specific G-protein coupling. In our underlying chemogenomics study, we analyse for the first time the statistical link between the properties of G-protein-coupled receptors and GPCR ligands. The technique of mutual information (MI is able to reveal statistical inter-dependence between variations in amino acid residues on the one hand and variations in ligand molecular descriptors on the other. Although this MI analysis uses novel information that differs from the results of known site-directed mutagenesis studies or published GPCR crystal structures, the method is capable of identifying the well-known common ligand binding region of GPCRs between the upper part of the seven transmembrane helices and the second extracellular loop. The analysis shows amino acid positions that are sensitive to either stimulating (agonistic or inhibitory (antagonistic ligand effects or both. It appears that amino acid positions for antagonistic and agonistic effects are both concentrated around the extracellular region, but selective agonistic effects are cumulated between transmembrane helices (TMHs 2, 3, and ECL2, while selective residues for antagonistic effects are located at the top of helices 5 and 6. Above all, the MI analysis provides detailed indications about amino acids located in the transmembrane region of these receptors that determine G-protein signalling pathway preferences.

  14. Antigenic characterization of an abnormal isoform of prion protein using a new diverse panel of monoclonal antibodies

    International Nuclear Information System (INIS)

    Kim, Chan-Lan; Umetani, Atsushi; Matsui, Toshio; Ishiguro, Naotaka; Shinagawa, Morikazu; Horiuchi, Motohiro

    2004-01-01

    We established a panel of monoclonal antibodies (mAbs) against prion protein (PrP) by immunizing PrP gene-ablated mice with the pathogenic isoform of prion protein (PrP Sc ) or recombinant prion protein (rPrP). The mAbs could be divided into at least 10 groups by fine epitope analyses using mutant rPrPs and pepspot analysis. Seven linear epitopes, lying within residues 56-90, 119-127, 137-143, 143-149, 147-151, 163-169, and 219-229, were defined by seven groups of mAbs, although the remaining three groups of mAbs recognized discontinuous epitopes. We attempted to examine whether any of these epitopes are located on the accessible surface of PrP Sc . However, no mAbs reacted with protease-treated PrP Sc purified from scrapie-affected mice, even when PrP Sc was dispersed into a detergent-lipid protein complex, to reduce the size of PrP Sc aggregates. In contrast, denaturation of PrP Sc by guanidine hydrochloride efficiently exposed all of the epitopes. This suggests that any epitope recognized by this panel of mAbs is buried within the PrP Sc aggregates. Alternatively, if the corresponding region(s) are on the surface of PrP Sc , the region(s) may be folded into conformations to which the mAbs cannot bind. The reactivity of a panel of mAb also showed that the state of PrP Sc aggregation influenced the denaturation process, and the sensitivity to denaturation appeared to vary between epitopes. Our results demonstrate that this new panel of well-characterized mAbs will be valuable for studying the biochemistry and biophysics of PrP molecules as well as for the immuno-diagnosis of prion diseases

  15. Cloned Erwinia chrysanthemi out genes enable Escherichia coli to selectively secrete a diverse family of heterologous proteins to its milieu.

    OpenAIRE

    He, S Y; Lindeberg, M; Chatterjee, A K; Collmer, A

    1991-01-01

    The out genes of the enterobacterial plant pathogen Erwinia chrysanthemi are responsible for the efficient extracellular secretion of multiple plant cell wall-degrading enzymes, including four isozymes of pectate lyase, exo-poly-alpha-D-galacturonosidase, pectin methylesterase, and cellulase. Out- mutants of Er. chrysanthemi are unable to export any of these proteins beyond the periplasm and are severely reduced in virulence. We have cloned out genes from Er. chrysanthemi in the stable, low-c...

  16. Genetic diversity of penicillin-binding protein 2B and 2X genes from Streptococcus pneumoniae in South Africa.

    OpenAIRE

    Smith, A M; Klugman, K P; Coffey, T J; Spratt, B G

    1993-01-01

    Streptococcus pneumoniae (the pneumococcus) is believed to have developed resistance to penicillin by the production of altered forms of penicillin-binding proteins (PBPs) that have decreased affinity for penicillin. Sixty-eight clinical isolates of serogroup 6 and 19 pneumococci (MICs, < 0.015 to 8 micrograms/ml) were randomly selected from hospitals across South Africa which are at substantial geographic distance from each other. The polymerase chain reaction was used to isolate the penicil...

  17. Genetic diversity of Plasmodium falciparum merozoite surface protein-1 block 2 in sites of contrasting altitudes and malaria endemicities in the Mount Cameroon region.

    Science.gov (United States)

    Wanji, Samuel; Kengne-Ouafo, Arnaud J; Eyong, Ebanga E Joan; Kimbi, Helen K; Tendongfor, Nicholas; Ndamukong-Nyanga, Judith L; Nana-Djeunga, Hugues C; Bourguinat, Catherine; Sofeu-Feugaing, David D; Charvet, Claude L

    2012-05-01

    The present study analyzed the relationship between the genetic diversity of Plasmodium falciparum and parasitologic/entomologic indices in the Mount Cameroon region by using merozoite surface protein 1 as a genetic marker. Blood samples were collected from asymptomatic children from three altitude zones (high, intermediate, and low). Parasitologic and entomologic indices were determined by microscopy and landing catch mosquito collection/circumsporozoite protein-enzyme-linked immunosorbent assay, respectively. A total of 142 randomly selected P. falciparum-positive blood samples were genotyped by using a nested polymerase chain reaction-based technique. K-1 polymerase chain reaction products were also sequenced. As opposed to high altitude, the highest malaria prevalence (70.65%) and entomologic inoculation rate (2.43 infective/bites/night) were recorded at a low altitude site. Seven (18.91%), 22 (36.66%), and 19 (42.22%) samples from high, intermediate, and low altitudes, respectively, contained multiclonal infections. A new K-1 polymorphism was identified. This study shows a positive non-linear association between low/intermediate altitude (high malaria transmission) and an increase in P. falciparum merozoite surface protein 1 block 2 polymorphisms.

  18. Palliative treatment of TIPS to portal vein tumor thrombosis complicated with portal vein hypertension

    International Nuclear Information System (INIS)

    Jiang Zaibo; Shan Hong; Guan Shouhai; Zhu Kangshun; Huang Mingsheng; Li Zhengran; Guo Tiansheng; Liu Lang

    2002-01-01

    Objective: To evaluate the palliative therapeutic effects of transjugular intrahepatic portosystemic shunt (TIPS) in portal vein tumor thrombosis (PVTT) complicated with portal vein hypertension, and to discuss the technical skills. Methods: There were 14 cases of end-stage hepatocellular carcinoma complicated with PVTT and portal vein hypertension, the average age was 53.6 yr. There were 8 cases with complete occlusion of main portal vein, 6 eases with incomplete thrombosis, and 5 cases combined with portal vein cavernous transformation. One case had simple hemorrhage, 3 eases had intractable ascites, and 10 cases had hemorrhage accompanied by intractable ascites. Results: The procedure of TIPS was successful in 10 cases, the successful rate was about 71%. The mean portal vein pressure was reduced from 37.2 mm Hg to 18.2 mm Hg, with an average reduction of 19.0 mm Hg. After the procedure of TIPS, the ascites decreased, hemorrhage stopped and the clinical symptoms disappeared. The average survival period was 132.3 days. The procedure were failing in 4 cases. Conclusion: TIPS was an effective palliative therapeutic methods to control the hemorrhage and ascites aroused by hepatic carcinoma complicated with PVTT

  19. The application of TIPSS in portal vein cancerous thrombosis complicated with portal hypertension

    International Nuclear Information System (INIS)

    Jiang Zaibo; Shan Hong; Guan Shouhai; Zhu Kangshun; Huang Mingsheng; Li Zhengran; Zhu Wenke; Liu Lang; Guo Tiansheng

    2002-01-01

    Objective: To discuss the technical skills and the contraindication of trans-jugular intrahepatic portosystemic shunt stent (TIPSS) in portal vein cancerous thrombosis (PVCT) complicated with portal hypertension. Methods: There were 16 cases of PVCT with portal hypertension, and average age of 53.6 yr. There were 9 cases with complete occlusion of portal vein trunk and 7 cases with incomplete thrombosis. There were 5 cases with cavernous transformation of the portal vein (CTPV). 1 case of simple upper gastro-intestinal tract (GIT) massive bleeding, 4 with refractory ascites and 11 with upper GIT massive bleeding and refractory ascites. Results: The procedure of TIPS was successful in 11 cases, the successful rate reached about 68.8%. The mean portal vein pressure was reduced from 4.9 kPa to 2.4 kPa with average 2. 5 kPa reduction. Ascites decreased, bleeding stopped and the clinical symptoms disappeared. The average survival period was 136 days. The procedure failed in 5 cases. Conclusions: TIPSS is an effective method to control the bleeding and ascites caused by PVCT. The PV cavernous transformation was the contraindication of TIPSS

  20. Anatomy of the Portal Vein Bifurcation: Implication for Transjugular Intrahepatic Portal Systemic Shunts

    International Nuclear Information System (INIS)

    Kwok, Philip Chong-hei; Ng, Wai Fu; Lam, Christine Suk-yee; Tsui, Polly Po; Faruqi, Asma

    2003-01-01

    Purpose: The relationship of the portalvein bifurcation to the liver capsule in Asians, which is an important landmark for transjugular intrahepatic portosystemic shunt, has not previously been described. Methods: The anatomy of the portal vein bifurcation was studied in 70 adult Chinese cadavers; it was characterized as intrahepatic or extrahepatic. The length of the exposed portion of the right and left portal veins was measured when the bifurcation was extrahepatic. Results: The portal vein bifurcation was intrahepatic in 37 cadavers (53%) and extrahepatic in 33 cadavers (47%). The mean length of the right and left extrahepatic portal veins was 0.96 cm and 0.85 cm respectively.Both were less than or equal to 2 cm in 94% of the cadavers with extrahepatic bifurcation. There was no correlation between the presence of cirrhosis and the location of the portal vein bifurcation(p 1.0). There was no statistically significant difference in liver mass in cadavers with either extrahepatic or intrahepatic bifurcation (p =0.40). Conclusions: These findings suggest that fortransjugular intrahepatic portosystemic shunt placement, a portal vein puncture 2 cm from the bifurcation will be safe in most cases

  1. Radioisotopic splenoportography in patients with portal hypertension

    International Nuclear Information System (INIS)

    Samejima, Natsuki; Ikeda, Koichiro; Yokoyama, Yasuhiro; Hirata, Satoru

    1989-01-01

    Radio-isotopic splenoportography was performed by injecting 99m TcO 4 - into the spleens of 46 patients with portal hypertension and 14 patients with various disorders not having portal hypertension. No collateral circulation was demonstrated in the 14 patients without portal hypertension whereas some RI-images of portosystemic collaterals were found in 40 (87.0 per cent) of the 46 patients with portal hypertension. Collaterals were divided into an ascending group and a descending group, the appearance rate of ascending collaterals being 80.4 per cent and that of descending collaterals, 41.3 per cent. There were 3 image patterns in the ascending group, namely, an AZ-pattern in which the azygos vein was demonstrated; a SC-pattern in which the RI-bolus ascended along the esophagus to the neck and the subclavian vein; and an EG-pattern which showed stagnation of the RI-bolus in the esophagogastric region. There were 4 patterns in the descending group, namely; a pattern of gastro-renal caval shunt (GR-pattern); reverse flow patterns into the umbilical or paraumbilical veins (UV-pattern); into the superior mesenteric vein (SMV-pattern); and into the inferior mesenteric vein (IMV-pattern). The appearance of the EG-pattern was seen most frequently (74.4 per cent). The usefulness of this method for surveying the collateral circulation in portal hypertension, estimating the risk of esophageal variceal bleeding and evaluating its treatments, was suggested by the results of this study. (author)

  2. CT of portal vein tumor thrombosis. Usefulness of dynamic CT

    Energy Technology Data Exchange (ETDEWEB)

    Takemoto, Kazumasa; Inoue, Yuichi; Tanaka, Masahiro; Nemoto, Yutaka; Nakamura, Kenji [Osaka City Univ. (Japan). Faculty of Medicine

    1983-08-01

    We evaluated CT findings of portal vein tumor thrombosis in 16 hepatomas by plain, contrast and dynamic CT. Plain and contrast CT findings were an enlargement of the portal vein (81%), intraluminal low density area (63%). Dynamic CT enhanced the diagnostic capability of the tumor thrombus as a relatively low density area because of the marked enhancement of the portal vein. In addition, dynamic CT newly demonstrated hyperdense peripheral ring (35%) and arterio portal shunt (35%). It is advisable to select the scan level to include the portal vein when dynamic CT is performed in the patient of hepatocellular carcinoma.

  3. Portal hypertension as portrayed by marked hepatosplenomegaly: case report

    International Nuclear Information System (INIS)

    Greene, R.A.

    1987-01-01

    The liver is vulnerable to as host of disease processes, including portal hypertension. This is a severe hepatic condition in which the liver is subject to numerous imbalances: increased hepatic blood flow, increased portal vein pressure due to extrahepatic portal vein obstruction, and/or increases in hepatic blood flow resistance. Although many diseases states may be responsible for the development of portal hypertension, it is most commonly associated with moderately severe or advanced cirrhosis. Advanced, untreated portal hypertension may cause additional complications such as hepatosplenomegaly, gastrointestinal bleeding, and ascites

  4. Splenomegaly, hyperkinetic splenic flow and portal hypertension in colitis

    Energy Technology Data Exchange (ETDEWEB)

    Friman, L [Serafimerlasarettet, Stockholm (Sweden)

    1980-01-01

    Four patients with a long history of colitis, splenomegaly, hypersplenism and portal hypertension were examined with angiography, both with contrast medium and isotopes, liver-spleen scintigraphy and recording of portal pressure. At angiography hyperkinetic splenic and portal blood flow was demonstrated. The increased flow causes increased portal pressure, which probably gives rise to changes in the liver often considered as slight cirrhosis at microscopy. The scintigraphic findings differed from Laennec cirrhosis. The liver uptake was homogeneous and no activity in the skeleton was recorded. Splenectomy cures both the hypersplenism and portal hypertension.

  5. Pathophysiology of Portal Hypertension and Its Clinical Links

    Science.gov (United States)

    Seo, Yeon Seok; Shah, Vijay H

    2011-01-01

    Portal hypertension is a major cause of morbidity and mortality in patients with liver cirrhosis. Intrahepatic vascular resistance due to architectural distortion and intrahepatic vasoconstriction, increased portal blood flow due to splanchnic vasodilatation, and development of collateral circulation have been considered as major factors for the development of portal hypertension. Recently, sinusoidal remodeling and angiogenesis have been focused as potential etiologic factors and various researchers have tried to improve portal hypertension by modulating these new targets. This article reviews potential new treatments in the context of portal hypertension pathophysiology concepts. PMID:25755320

  6. Splenomegaly, hyperkinetic splenic flow and portal hypertension in colitis

    International Nuclear Information System (INIS)

    Friman, L.

    1980-01-01

    Four patients with a long history of colitis, splenomegaly, hypersplenism and portal hypertension were examined with angiography, both with contrast medium and isotopes, liver-spleen scintigraphy and recording of portal pressure. At angiography hyperkinetic splenic and portal blood flow was demonstrated. The increased flow causes increased portal pressure, which probably gives rise to changes in the liver often considered as slight cirrhosis at microscopy. The scintigraphic findings differed from Laennec cirrhosis. The liver uptake was homogeneous and no activity in the skeleton was recorded. Splenectomy cures both the hypersplenism and portal hypertension. (Auth.)

  7. Analysis of Dynamic Characteristics of Portal Frame with Variable Section

    Directory of Open Access Journals (Sweden)

    Hao Jianing

    2016-01-01

    Full Text Available Combined with a portal frame design, by the use of finite element software ANSYS, the finite element model of single specimens of portal rigid frame and the overall portal rigid frame building are established. portal rigid frame’s beam and column is variable cross section. Through the modal analysis, comparative analysis of the frequency and vibration type of the radiolabeling specimens and finite element model of the whole, for the further development of variable cross-section portal rigid frame of earthquake and wind vibration analysis lay the foundation.

  8. Spatial variation in genetic diversity and natural selection on the thrombospondin-related adhesive protein locus of Plasmodium vivax (PvTRAP.

    Directory of Open Access Journals (Sweden)

    Rattiporn Kosuwin

    Full Text Available Thrombospondin-related adhesive protein (TRAP of malaria parasites is essential for sporozoite motility and invasions into mosquito's salivary gland and vertebrate's hepatocyte; thereby, it is a promising target for pre-erythrocytic vaccine. TRAP of Plasmodium vivax (PvTRAP exhibits sequence heterogeneity among isolates, an issue relevant to vaccine development. To gain insights into variation in the complete PvTRAP sequences of parasites in Thailand, 114 vivax malaria patients were recruited in 2006-2007 from 4 major endemic provinces bordering Myanmar (Tak in the northwest, n = 30 and Prachuap Khirikhan in the southwest, n = 25, Cambodia (Chanthaburi in the east, n = 29 and Malaysia (Yala and Narathiwat in the south, n = 30. In total, 26 amino acid substitutions were detected and 9 of which were novel, resulting in 44 distinct haplotypes. Haplotype and nucleotide diversities were lowest in southern P. vivax population while higher levels of diversities were observed in other populations. Evidences of positive selection on PvTRAP were demonstrated in domains II and IV and purifying selection in domains I, II and VI. Genetic differentiation was significant between each population except that between populations bordering Myanmar where transmigration was common. Regression analysis of pairwise linearized Fst and geographic distance suggests that P. vivax populations in Thailand have been isolated by distance. Sequence diversity of PvTRAP seems to be temporally stable over one decade in Tak province based on comparison of isolates collected in 1996 (n = 36 and 2006-2007. Besides natural selection, evidences of intragenic recombination have been supported in this study that could maintain and further generate diversity in this locus. It remains to be investigated whether amino acid substitutions in PvTRAP could influence host immune responses although several predicted variant T cell epitopes drastically altered the epitope

  9. Portal Vein Dopplerflowmetry in healthy sheep according to age

    Directory of Open Access Journals (Sweden)

    Alexandra F. Belotta

    Full Text Available ABSTRACT: Pulsed Doppler ultrasound was used to evaluate portal blood flow, portal velocity and portal congestion index in 24 healthy sheep divided into groups (lambs, yearlings and ewes, according to age. Measurements were performed at the 11th right intercostal space using ideal insonation angle and uniform insonation method. Mean values obtained in each group were compared with one-way ANOVA, followed by Tukey post-hoc test. Portal velocity and portal blood flow were statistically similar between the groups (P>0.05. Mean portal velocity were 17.75; 17.13 and 16.75; while mean portal blood flow were 26.65; 31.04 and 24.32 for lambs, yearlings and ewes, respectively. Portal congestion index was statistically distinct between the groups and values for lambs, yearlings and ewes were 0.009; 0.058 and 0.09, respectively (P<0.01. Statistical differences were observed in portal vein diameter, portal vein area and portal congestion index between the groups, presumably due to influence of weight and not to age.

  10. Cloned Erwinia chrysanthemi out genes enable Escherichia coli to selectively secrete a diverse family of heterologous proteins to its milieu.

    Science.gov (United States)

    He, S Y; Lindeberg, M; Chatterjee, A K; Collmer, A

    1991-02-01

    The out genes of the enterobacterial plant pathogen Erwinia chrysanthemi are responsible for the efficient extracellular secretion of multiple plant cell wall-degrading enzymes, including four isozymes of pectate lyase, exo-poly-alpha-D-galacturonosidase, pectin methylesterase, and cellulase. Out- mutants of Er. chrysanthemi are unable to export any of these proteins beyond the periplasm and are severely reduced in virulence. We have cloned out genes from Er. chrysanthemi in the stable, low-copy-number cosmid pCPP19 by complementing several transposon-induced mutations. The cloned out genes were clustered in a 12-kilobase chromosomal DNA region, complemented all existing out mutations in Er. chrysanthemi EC16, and enabled Escherichia coli strains to efficiently secrete the extracellular pectic enzymes produced from cloned Er. chrysanthemi genes, while retaining the periplasmic marker protein beta-lactamase. DNA sequencing of a 2.4-kilobase EcoRI fragment within the out cluster revealed four genes arranged colinearly and sharing substantial similarity with the Klebsiella pneumoniae genes pulH, pulI, pulJ, and pulK, which are necessary for pullulanase secretion. However, K. pneumoniae cells harboring the cloned Er. chrysanthemi pelE gene were unable to secrete the Erwinia pectate lyase. Furthermore, the Er. chrysanthemi Out system was unable to secrete an extracellular pectate lyase encoded by a gene from a closely related plant pathogen. Erwinia carotovora ssp. carotovora. The results suggest that these enterobacteria secrete polysaccharidases by a conserved mechanism whose protein-recognition capacities have diverged.

  11. Strategi Branding Portal Online Www.tripriau.com Dalam Membangun Brand Awareness Sebagai Portal Online Pariwisata Provinsi Riau

    OpenAIRE

    Rahmadhani, Yuri; Lubis, Evawani Elysa

    2017-01-01

    Online portal www.tripriau.com online portal is one of the online portal in Riau Province that has its own uniqueness. These portals contain local content and the potential of tourism in the province of Riau. Since its establishment, www.tripriau.com do branding strategy in order to build brand awareness or trust the reader to be known as a tourism-themed online portal. As the selection of brand name Trip Riau, Riau Guide My tagline, as well as the implementation of travel instagram photo con...

  12. Colangiopatía portal: complicación poco frecuente de la hipertensión portal

    OpenAIRE

    Veloso, Victoria; Servente, Liliana; Hernández, Nelia

    2017-01-01

    Resumen: Se describe el caso clínico de una mujer de 62 años en la que se diagnostica una estenosis del colédoco en el contexto de hipertensión portal prehepática (cavernomatosis portal). Abstract: We report the case of a 62 years old woman with a choledochal stricture and chronic obstruction of the portal vein (portal cavernomatosis). Resumo: Relatamos o caso de uma mulher de 62 anos com diagnóstico de estenose do colédoco no contexto da hipertensão portal pré-hepática (cavernomat...

  13. Diversity of extracellular proteins during the transition from the ‘proto-apicomplexan’ alveolates to the apicomplexan obligate parasites

    KAUST Repository

    Templeton, Thomas J.

    2015-11-20

    The recent completion of high-coverage draft genome sequences for several alveolate protozoans – namely, the chromerids, Chromera velia and Vitrella brassicaformis ; the perkinsid Perkinsus marinus ; the apicomplexan, Gregarina niphandrodes , as well as high coverage transcriptome sequence information for several colpodellids, allows for new genome-scale comparisons across a rich landscape of apicomplexans and other alveolates. Genome annotations can now be used to help interpret fine ultrastructure and cell biology, and guide new studies to describe a variety of alveolate life strategies, such as symbiosis or free living, predation, and obligate intracellular parasitism, as well to provide foundations to dissect the evolutionary transitions between these niches. This review focuses on the attempt to identify extracellular proteins which might mediate the physical interface of cell–cell interactions within the above life strategies, aided by annotation of the repertoires of predicted surface and secreted proteins encoded within alveolate genomes. In particular, we discuss what descriptions of the predicted extracellular proteomes reveal regarding a hypothetical last common ancestor of a pre-apicomplexan alveolate – guided by ultrastructure, life strategies and phylogenetic relationships – in an attempt to understand the evolution of obligate parasitism in apicomplexans.

  14. Diversity of extracellular proteins during the transition from the ‘proto-apicomplexan’ alveolates to the apicomplexan obligate parasites

    KAUST Repository

    Templeton, Thomas J.; Pain, Arnab

    2015-01-01

    The recent completion of high-coverage draft genome sequences for several alveolate protozoans – namely, the chromerids, Chromera velia and Vitrella brassicaformis ; the perkinsid Perkinsus marinus ; the apicomplexan, Gregarina niphandrodes , as well as high coverage transcriptome sequence information for several colpodellids, allows for new genome-scale comparisons across a rich landscape of apicomplexans and other alveolates. Genome annotations can now be used to help interpret fine ultrastructure and cell biology, and guide new studies to describe a variety of alveolate life strategies, such as symbiosis or free living, predation, and obligate intracellular parasitism, as well to provide foundations to dissect the evolutionary transitions between these niches. This review focuses on the attempt to identify extracellular proteins which might mediate the physical interface of cell–cell interactions within the above life strategies, aided by annotation of the repertoires of predicted surface and secreted proteins encoded within alveolate genomes. In particular, we discuss what descriptions of the predicted extracellular proteomes reveal regarding a hypothetical last common ancestor of a pre-apicomplexan alveolate – guided by ultrastructure, life strategies and phylogenetic relationships – in an attempt to understand the evolution of obligate parasitism in apicomplexans.

  15. PROTEOMIC PROFILE REVEALS THE DIVERSITY AND COMPLEXITY OF LEAF PROTEINS IN SPINACH (BETA VULGARIS VAR. ALL GREEN

    Directory of Open Access Journals (Sweden)

    Sudip Ghosh

    2016-06-01

    Full Text Available Leaf is a source organ that serves dual function in photosynthesis and transpiration. As a primary interface between plant and ecosystem, it performs a range of biological processes from carbon assimilation and metabolite partitioning to plant productivity. Basic features of the leaf functionality are conserved in angiosperms exhibiting common and unique characteristics. Spinach has been the model crop for studying leaf function, primarily photosynthesis. It is a reservoir of several hundreds of primary and secondary biomolecules. To better understand the molecular basis for photochemical reaction and metabolic partitioning, we developed leaf proteome of Indian spinach (Beta vulgaris var. all green. LC-ESI-MS/MS analysis identified 639 proteins exhibiting discrete molecular features and functions, including photosynthesis, transpiration, gaseous exchange, transport, redox status, cell defense, and floral induction besides the presence of proteins with unknown function. This represents the first comprehensive foliage proteome of green leafy vegetable. Together, this work provides important insights into the molecular networks underlying spinach leaf biological processes.

  16. Review of Theoretical Prediction Models for Organic Extract Metabolites, Effect of Drying Temperature on Smooth Muscle Relaxing Activity Induced by Organic Extracts Specially Cecropia Obtusifolia Portal and Web Server Predictors of Drug-Protein Interaction.

    Science.gov (United States)

    Aguirre-Crespo, Francisco; García-Mera, Xerardo; Guillén-Poot, Mónica Anahi; May-Díaz, Héctor Fernado; Tun-Suárez, Adrián; Aguirre-Crespo, A; Hernández-Rodríguez, J; Vergara-Galicia, Jorge; Rodríguez-López, V; Prado-Prado, Francisco J

    2015-02-19

    Cecropia obtusifolia bertol is medicinal specie used in the treatment of diabetes mellitus and hypertension and it has scientific studies that support the traditional use. However, it is required to understand the influence of drying temperature on the yield and pharmacological activity. Drying rate, extraction efficiency, changes in the UV-Vis spectrum and estimating chlorophylls were stimulated with the increasing temperature. Finally, relaxant activity of vascular smooth muscle is increased by 70ºC and reducing ability by the method of CARF increases with temperature. Analytical studies are required to identify changes in the metabolic content and those that ensure the safety and efficacy for human consumption. In this sense, bioinformatic studies may be helpful. Studies such as QSAR can help us to study these metabolites derived from natural products. MIND-BETS model and NL MIND-BETS model to predict DPIs was introduced using MARCH-INSIDE (MI) software to calculate structural parameters for drugs and enzymes respectively. We firstly revised the state-of-art on the design with review of previous works with hypertension activity based on theoretical studies. A study, evaluating the effect of drying temperature of leaves of C. obtusifolia on the relaxing of vascular smooth muscle, antioxidant activity and the presence of chlorophylls, with a focus on Cecropia metabolites. Last, we carried out QSAR studies using MIND-BEST and NL MIND-BEST web servers in order to understand the essential metabolites structural requirement for binding with receptors for FDA proteins.

  17. Genetic Diversity of Plasmodium falciparum Field Isolates in Central Sudan Inferred by PCR Genotyping of Merozoite Surface Protein 1 and 2.

    Science.gov (United States)

    Hamid, Muzamil M Abdel; Mohammed, Sara B; El Hassan, Ibrahim M

    2013-02-01

    Characterization of Plasmodium falciparum diversity is commonly achieved by amplification of the polymorphic regions of the merozoite surface proteins 1 (MSP1) and 2 (MSP2) genes. The present study aimed to determine the allelic variants distribution of MSP1 and MSP2 and multiplicity of infection in P. falciparum field isolates from Kosti, central Sudan, an area characterized by seasonal malaria transmission. Total 121 samples (N = 121) were collected during a cross-sectional survey between March and April 2003. DNA was extracted and MSP1 and MSP2 polymorphic loci were genotyped. The total number of alleles identified in MSP1 block 2 was 11, while 16 alleles were observed in MSP2 block 3. In MSP1, RO33 was found to be the predominant allelic type, carried alone or in combination with MAD20 and K1 types, whereas FC27 family was the most prevalent in MSP2. Sixty two percent of isolates had multiple genotypes and the overall mean multiplicity of infection was 1.93 (CI 95% 1.66-2.20). Age correlated with parasite density (P = 0.017). In addition, a positive correlation was observed between parasite densities and the number of alleles (P = 0.022). Genetic diversity in P. falciparum field isolates in central Sudan was high and consisted of multiple clones.

  18. Kupffer cells are activated in cirrhotic portal hypertension and not normalised by TIPS.

    Science.gov (United States)

    Holland-Fischer, Peter; Grønbæk, Henning; Sandahl, Thomas Damgaard; Moestrup, Søren K; Riggio, Oliviero; Ridola, Lorenzo; Aagaard, Niels Kristian; Møller, Holger Jon; Vilstrup, Hendrik

    2011-10-01

    Hepatic macrophages (Kupffer cells) undergo inflammatory activation during the development of portal hypertension in experimental cirrhosis; this activation may play a pathogenic role or be an epiphenomenon. Our objective was to study serum soluble CD163 (sCD163), a sensitive marker of macrophage activation, before and after reduction of portal venous pressure gradient by insertion of a transjugular intrahepatic portosystemic shunt (TIPS) in patients with cirrhosis. sCD163 was measured in 11 controls and 36 patients before and 1, 4 and 26 weeks after TIPS. We used lipopolysaccharide binding protein (LBP) levels as a marker of endotoxinaemia. Liver function and clinical status of the patients were assessed by galactose elimination capacity and Model for End Stage Liver Disease score. The sCD163 concentration was more than threefold higher in the patients than in the controls (median 5.22 mg/l vs 1.45 mg/l, pportal venous pressure gradient (r(2)=0.24, pportal vein (pportal hypertension. The activation was not alleviated by the mechanical reduction of portal hypertension and the decreasing signs of endotoxinaemia. The findings suggest that Kupffer cell activation is a constitutive event that may play a pathogenic role for portal hypertension.

  19. DES Science Portal: Computing Photometric Redshifts

    Energy Technology Data Exchange (ETDEWEB)

    Gschwend, Julia [LIneA, Rio de Janeiro

    2016-01-01

    An important challenge facing photometric surveys for cosmological purposes, such as the Dark Energy Survey (DES), is the need to produce reliable photometric redshifts (photo-z). The choice of adequate algorithms and configurations and the maintenance of an up-to-date spectroscopic database to build training sets, for example, are challenging tasks when dealing with large amounts of data that are regularly updated and constantly growing. In this paper, we present the first of a series of tools developed by DES, provided as part of the DES Science Portal, an integrated web-based data portal developed to facilitate the scientific analysis of the data, while ensuring the reproducibility of the analysis. We present the DES Science Portal photometric redshift tools, starting from the creation of a spectroscopic sample to training the neural network photo-z codes, to the final estimation of photo-zs for a large photometric catalog. We illustrate this operation by calculating well calibrated photo-zs for a galaxy sample extracted from the DES first year (Y1A1) data. The series of processes mentioned above is run entirely within the Portal environment, which automatically produces validation metrics, and maintains the provenance between the different steps. This system allows us to fine tune the many steps involved in the process of calculating photo-zs, making sure that we do not lose the information on the configurations and inputs of the previous processes. By matching the DES Y1A1 photometry to a spectroscopic sample, we define different training sets that we use to feed the photo-z algorithms already installed at the Portal. Finally, we validate the results under several conditions, including the case of a sample limited to i<22.5 with the color properties close to the full DES Y1A1 photometric data. This way we compare the performance of multiple methods and training configurations. The infrastructure presented here is an effcient way to test several methods of

  20. Improving diabetes management with a patient portal: a qualitative study of diabetes self-management portal.

    Science.gov (United States)

    Urowitz, Sara; Wiljer, David; Dupak, Kourtney; Kuehner, Zachary; Leonard, Kevin; Lovrics, Emily; Picton, Peter; Seto, Emily; Cafazzo, Joe

    2012-11-30

    Effective management and care of diabetes is crucial to reducing associated risks such as heart disease and kidney failure. With increasing access and use of the Internet, online chronic disease management is being explored as a means of providing patients with support and the necessary tools to monitor and manage their disease. The objective of our study was to evaluate the experience of patients and providers using an online diabetes management portal for patients. Participants were recruited from a large sample population of 887 for a follow-up questionnaire to be completed after 6 months of using the patient portal. Participants were presented with the option to participate in an additional interview and, if the participant agreed, a time and date was scheduled for the interview. A 5-item, open-ended questionnaire was used to capture providers' opinions of the patient portal. Providers included general practitioners (GPs), nurses, nurse practitioners (NPs), dieticians, diabetes educators (DECs), and other clinical staff. A total of 854 patients were consented for the questionnaire. Seventeen (8 male, 9 female) patients agreed to participate in a telephone interview. Sixty-four health care providers completed the five open-ended questions; however, an average of 48.2 responses were recorded per question. Four major themes were identified and will be discussed in this paper. These themes have been classified as: facilitators of disease management, barriers to portal use, patient-provider communication and relationship, and recommendations for portal improvements. This qualitative study shows that online chronic disease management portals increase patient access to information and engagement in their health care, but improvements in the portal itself may improve usability and reduce attrition. Furthermore, this study identifies a grey area that exists in the roles that GPs and AHPs should play in the facilitation of online disease management.

  1. Genetic diversity in the C-terminus of merozoite surface protein 1 among Plasmodium knowlesi isolates from Selangor and Sabah Borneo, Malaysia.

    Science.gov (United States)

    Yap, Nan Jiun; Goh, Xiang Ting; Koehler, Anson V; William, Timothy; Yeo, Tsin Wen; Vythilingam, Indra; Gasser, Robin B; Lim, Yvonne A L

    2017-10-01

    Plasmodium knowlesi, a malaria parasite of macaques, has emerged as an important parasite of humans. Despite the significance of P. knowlesi malaria in parts of Southeast Asia, very little is known about the genetic variation in this parasite. Our aim here was to explore sequence variation in a molecule called the 42kDa merozoite surface protein-1 (MSP-1), which is found on the surface of blood stages of Plasmodium spp. and plays a key role in erythrocyte invasion. Several studies of P. falciparum have reported that the C-terminus (a 42kDa fragment) of merozoite surface protein-1 (MSP-1 42 ; consisting of MSP-1 19 and MSP-1 33 ) is a potential candidate for a malaria vaccine. However, to date, no study has yet investigated the sequence diversity of the gene encoding P. knowlesi MSP-1 42 (comprising Pk-msp-1 19 and Pk-msp-1 33 ) among isolates in Malaysia. The present study explored this aspect. Twelve P. knowlesi isolates were collected from patients from hospitals in Selangor and Sabah Borneo, Malaysia, between 2012 and 2014. The Pk-msp-1 42 gene was amplified by PCR and directly sequenced. Haplotype diversity (Hd) and nucleotide diversity (л) were studied among the isolates. There was relatively high genetic variation among P. knowlesi isolates; overall Hd and л were 1±0.034 and 0.01132±0.00124, respectively. A total of nine different haplotypes related to amino acid alterations at 13 positions, and the Pk-MSP-1 19 sequence was found to be more conserved than Pk-msp-1 33 . We have found evidence for negative selection in Pk-msp- 42 as well as the 33kDa and 19kDa fragments by comparing the rate of non-synonymous versus synonymous substitutions. Future investigations should study large numbers of samples from disparate geographical locations to critically assess whether this molecule might be a potential vaccine target for P. knowlesi. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. canEvolve: a web portal for integrative oncogenomics.

    Directory of Open Access Journals (Sweden)

    Mehmet Kemal Samur

    Full Text Available BACKGROUND & OBJECTIVE: Genome-wide profiles of tumors obtained using functional genomics platforms are being deposited to the public repositories at an astronomical scale, as a result of focused efforts by individual laboratories and large projects such as the Cancer Genome Atlas (TCGA and the International Cancer Genome Consortium. Consequently, there is an urgent need for reliable tools that integrate and interpret these data in light of current knowledge and disseminate results to biomedical researchers in a user-friendly manner. We have built the canEvolve web portal to meet this need. RESULTS: canEvolve query functionalities are designed to fulfill most frequent analysis needs of cancer researchers with a view to generate novel hypotheses. canEvolve stores gene, microRNA (miRNA and protein expression profiles, copy number alterations for multiple cancer types, and protein-protein interaction information. canEvolve allows querying of results of primary analysis, integrative analysis and network analysis of oncogenomics data. The querying for primary analysis includes differential gene and miRNA expression as well as changes in gene copy number measured with SNP microarrays. canEvolve provides results of integrative analysis of gene expression profiles with copy number alterations and with miRNA profiles as well as generalized integrative analysis using gene set enrichment analysis. The network analysis capability includes storage and visualization of gene co-expression, inferred gene regulatory networks and protein-protein interaction information. Finally, canEvolve provides correlations between gene expression and clinical outcomes in terms of univariate survival analysis. CONCLUSION: At present canEvolve provides different types of information extracted from 90 cancer genomics studies comprising of more than 10,000 patients. The presence of multiple data types, novel integrative analysis for identifying regulators of oncogenesis, network

  3. The evolution and diversity of a low complexity vaccine candidate, merozoite surface protein 9 (MSP-9), in Plasmodium vivax and closely related species.

    Science.gov (United States)

    Chenet, Stella M; Pacheco, M Andreína; Bacon, David J; Collins, William E; Barnwell, John W; Escalante, Ananias A

    2013-12-01

    The merozoite surface protein-9 (MSP-9) has been considered a target for an anti-malarial vaccine since it is one of many proteins involved in the erythrocyte invasion, a critical step in the parasite life cycle. Orthologs encoding this antigen have been found in all known species of Plasmodium parasitic to primates. In order to characterize and investigate the extent and maintenance of MSP-9 genetic diversity, we analyzed DNA sequences of the following malaria parasite species: Plasmodium falciparum, Plasmodium reichenowi, Plasmodium chabaudi, Plasmodium yoelii, Plasmodium berghei, Plasmodium coatneyi, Plasmodium gonderi, Plasmodium knowlesi, Plasmodium inui, Plasmodium simiovale, Plasmodium fieldi, Plasmodium cynomolgi and Plasmodium vivax and evaluated the signature of natural selection in all MSP-9 orthologs. Our findings suggest that the gene encoding MSP-9 is under purifying selection in P. vivax and closely related species. We further explored how selection affected different regions of MSP-9 by comparing the polymorphisms in P. vivax and P. falciparum, and found contrasting patterns between these two species that suggest differences in functional constraints. This observation implies that the MSP-9 orthologs in human parasites may interact differently with the host immune response. Thus, studies carried out in one species cannot be directly translated into the other. Copyright © 2013 Elsevier B.V. All rights reserved.

  4. Portal hypertensive polyps, a new entity?

    Directory of Open Access Journals (Sweden)

    Verónica Martín-Domínguez

    Full Text Available Presentamos el caso clínico de una mujer de 62 años de edad, con antecedentes de cirrosis hepática secundaria a hepatitis autoinmune, hipertensión portal y coagulopatía, quien presenta en gastroscopia, unas lesiones polipoideas, semipediculadas, polilobuladas en la región prepilórica, que se extirpan y cuya anatomía patológica se describe como pólipos hiperplásicos con edema, congestión vascular e hiperplasia del músculo liso, sin displasia ni cambios adenomatosos, correspondientes a "pólipos de la hipertensión portal" (PHP.

  5. Novel treatment options for portal hypertension

    Science.gov (United States)

    Laleman, Wim

    2017-01-01

    Abstract Portal hypertension is most frequently associated with cirrhosis and is a major driver for associated complications, such as variceal bleeding, ascites or hepatic encephalopathy. As such, clinically significant portal hypertension forms the prelude to decompensation and impacts significantly on the prognosis of patients with liver cirrhosis. At present, non-selective β-blockers, vasopressin analogues and somatostatin analogues are the mainstay of treatment but these strategies are far from satisfactory and only target splanchnic hyperemia. In contrast, safe and reliable strategies to reduce the increased intrahepatic resistance in cirrhotic patients still represent a pending issue. In recent years, several preclinical and clinical trials have focused on this latter component and other therapeutic avenues. In this review, we highlight novel data in this context and address potentially interesting therapeutic options for the future. PMID:28533907

  6. Portal Vein Embolization: What Do We Know?

    Energy Technology Data Exchange (ETDEWEB)

    Denys, Alban, E-mail: Alban.Denys@chuv.ch [Centre Hospitalo Universitaire Vaudois, Department of Radiology and Interventional Radiology Unit (Switzerland); Prior, John [Centre Hospitalo Universitaire Vaudois, Department of Nuclear Medicine (Switzerland); Bize, Pierre; Duran, Rafael [Centre Hospitalo Universitaire Vaudois, Department of Radiology and Interventional Radiology Unit (Switzerland); Baere, Thierry De [Institut Gustave Roussy, Department of Interventional Radiology (France); Halkic, Nermin; Demartines, Nicolas [Centre Hospitalo Universitaire Vaudois, Department of Visceral Surgery (Switzerland)

    2012-10-15

    Portal vein embolization (PVE) has been developed to increase the size of the future remnant liver (FRL) left in place after major hepatectomy, thus reducing the risk of postoperative liver insufficiency. PVE consist in embolizing preoperatively portal branches of the segments that will be resected. Indication is based on preoperative measurements of the FRL by computed tomography and its ratio with either the theoretical liver volume or by direct measurement of the functional liver volume. After PVE, the volume and function of the FRL increases in 3 to 6 weeks, permitting extensive resections in patients otherwise contraindicated for liver resection. The PVE technique is variable from one center to another; however n-butyl-cyano-acrylate provides an interesting compromise between hypertrophy rate and procedure risk.

  7. Spin-0± portal induced Dark Matter

    Science.gov (United States)

    Dutta, Sukanta; Goyal, Ashok; Saini, Lalit Kumar

    2018-02-01

    Standard model (SM) spin-zero singlets are constrained through their di-Bosonic decay channels via an effective coupling induced by a vector-like quark (VLQ) loop at the LHC for √{s}=13 TeV. These spin-zero resonances are then considered as portals for scalar, vector or fermionic dark matter particle interactions with SM gauge bosons. We find that the model is validated with respect to the observations from LHC data and from cosmology, indirect and direct detection experiments for an appreciable range of scalar, vector and fermionic DM masses greater than 300 GeV and VLQ masses ≥ 400 GeV, corresponding to the three choice of portal masses 270 GeV, 500 GeV and 750 GeV respectively.

  8. Development of integrated containment and surveillance system for fast critical facility FCA. Portal and penetration monitors

    International Nuclear Information System (INIS)

    Mukaiyama, Takehiko; Ogawa, Hironobu; Yokota, Yasuhiro.

    1998-01-01

    Manpower and radiation exposure problems, accompanied by frequent Non Destructive Assay (NDA) based inspections at the Fast Critical Facility FCA of Japan Atomic Energy Research Institute (JAERI), are a burden for both the inspectorates and the facility operator. In the hope of alleviating these burdens, the development of containment and surveillance measures for the FCA was initiated in 1979. The integrated containment and surveillance system consists of a portal monitor and a penetration monitor. The reactor building provides an ideal containment measure because of its explosion-proof, airtight structure and limited number of penetrations. The function of the portal monitor is to detect undeclared removal of nuclear material from the reactor building through the doorway. The penetration monitor is designed for surveillance of diversion routes through containment boundaries, and of safeguards related activities for bypassing the portal monitor. The combination of monitoring by the penetration monitor of containment boundaries and all their penetrations except for the doorway, and monitoring by the portal monitor, provides complete coverage of realistic diversion routes. The development of the system was completed in 1988 and the field trial test was conducted for the period of twelve running months. The final report on the field trial was concluded on January 1990. The major conclusion of the report was that the system is effective, reliable and efficient. Following this successful conclusion, the International Atomic Energy Agency (IAEA) accepted the system for meeting its safeguards goals at the FCA on condition that an independent IAEA authentication equipment is provided. The development of the authentication equipment is accomplished as an separate Japan Support Programme for Agency Safeguards (JASPAS) task. (author)

  9. An analysis of splenoportographic findings in portal hypertension

    Energy Technology Data Exchange (ETDEWEB)

    Jung, Eun Mi; Moon, Sook Ran; Kim, Han Suk [National Medical Center, Seoul (Korea, Republic of); Park, Soo Soung [College of Medicine, Chung Ang University, Seoul (Korea, Republic of)

    1983-12-15

    Splenoportography has been proved as a useful method for the evaluation of circulatory disturbances in portal hypertension. Authors analyzed the various aspects of these disturbance on splenoportography in 22 cases that was performed under the clinical suspicion of portal hypertension during recent 6 years, from May, 1976 to July 1982 at the Department of Radiology, National Medical Center. The results were as follows: 1. Liver cirrhosis was the most frequent cause of intrahepatic obstruction type in portal hypertension (86%). 2. The portal pressure was more than 400 mmH{sub 2}0 in 67% of the cases (range; 300-540 mmH{sub 2}0). 3. In the majority of the cases, the higher the portal pressure was, the more dilated splenic and portal veins were. The diameter of portal vein was more than 15 mm in 79%, more than 21 mm in 47% of the cases (range; 10-26 mm). The diameter of splenic vein was more than 15 mm in 48% of the cases (range; 7-23 mm). Especially the diameter of splenic vein was larger than that of portal vein in 20% of the cases. 4. There was no definite correlation between the development of collateral circulation and the diameter of splenic and portal veins. 5. The filling of collateral circulation was definite sign of portal hypertension, though not regular. In portal hypertension, the collateral circulation was formed via coronary vein (91%), short gastric vein (64%), inferior mesenteric vein (36%). 6. Splenic-hilum time was delayed in 64% of the cases. Intrahepatic portal vein emptying time was more than 6 seconds in all the cases. 7. Most of the cases (91%) could be diagnosed as portal hypertension with vasculogram and hepatogram.

  10. An analysis of splenoportographic findings in portal hypertension

    International Nuclear Information System (INIS)

    Jung, Eun Mi; Moon, Sook Ran; Kim, Han Suk; Park, Soo Soung

    1983-01-01

    Splenoportography has been proved as a useful method for the evaluation of circulatory disturbances in portal hypertension. Authors analyzed the various aspects of these disturbance on splenoportography in 22 cases that was performed under the clinical suspicion of portal hypertension during recent 6 years, from May, 1976 to July 1982 at the Department of Radiology, National Medical Center. The results were as follows: 1. Liver cirrhosis was the most frequent cause of intrahepatic obstruction type in portal hypertension (86%). 2. The portal pressure was more than 400 mmH 2 0 in 67% of the cases (range; 300-540 mmH 2 0). 3. In the majority of the cases, the higher the portal pressure was, the more dilated splenic and portal veins were. The diameter of portal vein was more than 15 mm in 79%, more than 21 mm in 47% of the cases (range; 10-26 mm). The diameter of splenic vein was more than 15 mm in 48% of the cases (range; 7-23 mm). Especially the diameter of splenic vein was larger than that of portal vein in 20% of the cases. 4. There was no definite correlation between the development of collateral circulation and the diameter of splenic and portal veins. 5. The filling of collateral circulation was definite sign of portal hypertension, though not regular. In portal hypertension, the collateral circulation was formed via coronary vein (91%), short gastric vein (64%), inferior mesenteric vein (36%). 6. Splenic-hilum time was delayed in 64% of the cases. Intrahepatic portal vein emptying time was more than 6 seconds in all the cases. 7. Most of the cases (91%) could be diagnosed as portal hypertension with vasculogram and hepatogram

  11. Computed tomographic evaluation of the portal vein in the hepatomas

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Kee Hyung; Lee, Seung Chul; Bae, Man Gil; Seo, Heung Suk; Kim, Soon Yong; Lee, Min Ho; Kee, Choon Suhk; Park, Kyung Nam [Hanyang University College of Medicine, Seoul (Korea, Republic of)

    1986-10-15

    Computed tomography and pornographic findings of 63 patients with hepatoma, undergone hepatic angiography and superior mesenteric pornography for evaluation of tumor and thrombosis of portal vein and determination of indication of transcatheter arterial embolization for palliative treatment of hepatoma from April, 85 to June, 86 in Hanyang university hospital, were reviewed. The results were as follows: 1. In 36 cases, portal vein thrombosis was detected during photography. Nineteen of 37 cases which revealed localized hepatoma in the right lobe of the liver showed portal vein thrombosis; 9 of 11 cases of the left lobe; 8 of 14 cases which were involved in entire liver revealed thrombosis. One case localized in the caudate lobe showed no evidence of invasion to portal vein. 2. Twenty-four of 34 cases with diffuse infiltrative hepatoma revealed portal vein thrombosis and the incidence of portal vein thrombosis in this type were higher than in the cases of the nodular type. 3. The portal vein thrombosis appeared as filling defects of low density in the lumen of the portal veins in CT and they did not reveal contrast enhancement. 4. CT revealed well the evidence of obstructions in the cases of portal vein thrombosis and the findings were well-corresponded to the findings of the superior mesenteric photography. 5. Five of the cases of the portal vein thrombosis were missed in the CT and the causes were considered as due to partial volume effect of enhanced portal vein with partial occlusion or arterioportal shunts. 6. Six of 13 cases with occlusion of main portal vein showed cavernous transformation and they were noted as multiple small enhanced vascularities around the porta hepatis in the CT. According to the results, we conclude that CT is a useful modality to detect the changes of the portal veins in the patients of the hepatoma.

  12. Computed tomographic evaluation of the portal vein in the hepatomas

    International Nuclear Information System (INIS)

    Lee, Kee Hyung; Lee, Seung Chul; Bae, Man Gil; Seo, Heung Suk; Kim, Soon Yong; Lee, Min Ho; Kee, Choon Suhk; Park, Kyung Nam

    1986-01-01

    Computed tomography and pornographic findings of 63 patients with hepatoma, undergone hepatic angiography and superior mesenteric pornography for evaluation of tumor and thrombosis of portal vein and determination of indication of transcatheter arterial embolization for palliative treatment of hepatoma from April, 85 to June, 86 in Hanyang university hospital, were reviewed. The results were as follows: 1. In 36 cases, portal vein thrombosis was detected during photography. Nineteen of 37 cases which revealed localized hepatoma in the right lobe of the liver showed portal vein thrombosis; 9 of 11 cases of the left lobe; 8 of 14 cases which were involved in entire liver revealed thrombosis. One case localized in the caudate lobe showed no evidence of invasion to portal vein. 2. Twenty-four of 34 cases with diffuse infiltrative hepatoma revealed portal vein thrombosis and the incidence of portal vein thrombosis in this type were higher than in the cases of the nodular type. 3. The portal vein thrombosis appeared as filling defects of low density in the lumen of the portal veins in CT and they did not reveal contrast enhancement. 4. CT revealed well the evidence of obstructions in the cases of portal vein thrombosis and the findings were well-corresponded to the findings of the superior mesenteric photography. 5. Five of the cases of the portal vein thrombosis were missed in the CT and the causes were considered as due to partial volume effect of enhanced portal vein with partial occlusion or arterioportal shunts. 6. Six of 13 cases with occlusion of main portal vein showed cavernous transformation and they were noted as multiple small enhanced vascularities around the porta hepatis in the CT. According to the results, we conclude that CT is a useful modality to detect the changes of the portal veins in the patients of the hepatoma.

  13. Inpatient Portals for Hospitalized Patients and Caregivers: A Systematic Review.

    Science.gov (United States)

    Kelly, Michelle M; Coller, Ryan J; Hoonakker, Peter Lt

    2018-06-01

    Patient portals, web-based personal health records linked to electronic health records (EHRs), provide patients access to their healthcare information and facilitate communication with providers. Growing evidence supports portal use in ambulatory settings; however, only recently have portals been used with hospitalized patients. Our objective was to review the literature evaluating the design, use, and impact of inpatient portals, which are patient portals designed to give hospitalized patients and caregivers inpatient EHR clinical information for the purpose of engaging them in hospital care. Literature was reviewed from 2006 to 2017 in PubMed, Web of Science, CINALPlus, Cochrane, and Scopus to identify English language studies evaluating patient portals, engagement, and inpatient care. Data were analyzed considering the following 3 themes: inpatient portal design, use and usability, and impact. Of 731 studies, 17 were included, 9 of which were published after 2015. Most studies were qualitative with small samples focusing on inpatient portal design; 1 nonrandomized trial was identified. Studies described hospitalized patients' and caregivers' information needs and design recommendations. Most patient and caregiver participants in included studies were interested in using an inpatient portal, used it when offered, and found it easy to use and/or useful. Evidence supporting the role of inpatient portals in improving patient and caregiver engagement, knowledge, communication, and care quality and safety is limited. Included studies indicated providers had concerns about using inpatient portals; however, the extent to which these concerns have been realized remains unclear. Inpatient portal research is emerging. Further investigation is needed to optimally design inpatient portals to maximize potential benefits for hospitalized patients and caregivers while minimizing unintended consequences for healthcare teams. © 2017 Society of Hospital Medicine.

  14. Diavideos: a diabetes health video portal.

    Science.gov (United States)

    Sánchez-Bocanegra, C L; Rivero-Rodriguez, A; Fernández-Luque, L; Sevillano, J L

    2013-01-01

    Diavideos is a web platform that collects trustworthy diabetes health videos from YouTube and offers them in a easy way. YouTube is a big repository of health videos, but good content is sometimes mixed with misleading and harmful videos such as promoting anorexia [1]. Diavideos is a web portal that provides easy access to a repository of trustworthy diabetes videos. This poster describes Diavideos and explains the crawling method used to retrieve these videos from trusted channels.

  15. Liferay 6.x portal enterprise intranets cookbook

    CERN Document Server

    Filipowicz, Piotr

    2015-01-01

    If you are a Java developer or administrator with a technical background and want to install and configure Liferay Portal as an enterprise intranet, this is the book for you. In short, reusable recipes help you realize business goals as working features in Liferay. This book will also give you useful hints on how to easily improve the default functionality of the system and its performance.

  16. State of the SOOS GCMD Portal

    Science.gov (United States)

    Ritz, Scott

    2018-01-01

    A brief status update on NASA’s latest Global Change Master Directory (GCMD) keyword update, description of the differences between DIF-9 and DIF-10 formats in advance of the deprecation of DIF-9 support in Earth Observing System Data and Information System (EOSDIS) with specifics on the DIF-10.3 schema, transition schedule, and some usage metrics for the GCMD Southern Ocean Observing System (SOOS) Portal.

  17. Comparative methods of concrete portal frame design

    OpenAIRE

    A, Letengsang

    2014-01-01

    The objective of this thesis was to design a concrete portal frame with two column spacings of 12 meters and 6 meters and its structural elements in a building located in Hämeenlinna city, Finland. A comprehension study on the concrete design chapter of Eurocode 2 was done before proceeding on the calculation process, the materials’ properties. The corresponding ca-pacity diagrams from concrete product manufacturers in Finland can be assistance tools during the calculation process. ...

  18. Portal verification for breast cancer radiotherapy

    International Nuclear Information System (INIS)

    Petkovska, Sonja; Pejkovikj, Sasho; Apostolovski, Nebojsha

    2013-01-01

    At the University Clinic in Skopje, breast cancer irradiation is being planned and performed by using a mono-iso centrical method, which means that a unique isocenter (I C) for all irradiation fields is used. The goal of this paper is to present the patient’s position in all coordinates before the first treatment session, relative to the position determined during the CT simulation. Deviation of up to 5 mm is allowed. The analysis was made by using a portal verification. Sixty female patients at random selection are reviewed. The matching results show that for each patient deviation exists at least on one axis. The largest deviations are in the longitudinal direction (head-feet) up to 4 mm, mean 1.8 mm. In 60 out of 85 analysed fields, the deviation is towards the head. In lateral direction, median deviation is 1.1 mm and in 65% of the analysed portals those deviations are in medial direction – contralateral breast which can increases the dose in the lung and in the contralateral breast. This deviation for supraclavicular field can increase the dose in the spinal cord. Although these doses are well below the limit, this fact should be taken into account in setting the treatment fields. The final conclusion from the research is that despite of the fact we are dealing with small deviations, in conditions when accuracy in positioning is done with portal, the portal verification needs to be done in the coming weeks of the treatment, not only before the first treatment. This provides information for an intra fractional set-up deviation. (Author)

  19. Allelic diversity of the Plasmodium falciparum erythrocyte membrane protein 1 entails variant-specific red cell surface epitopes.

    Directory of Open Access Journals (Sweden)

    Inès Vigan-Womas

    Full Text Available The clonally variant Plasmodium falciparum PfEMP1 adhesin is a virulence factor and a prime target of humoral immunity. It is encoded by a repertoire of functionally differentiated var genes, which display architectural diversity and allelic polymorphism. Their serological relationship is key to understanding the evolutionary constraints on this gene family and rational vaccine design. Here, we investigated the Palo Alto/VarO and IT4/R29 and 3D7/PF13_003 parasites lines. VarO and R29 form rosettes with uninfected erythrocytes, a phenotype associated with severe malaria. They express an allelic Cys2/group A NTS-DBL1α(1 PfEMP1 domain implicated in rosetting, whose 3D7 ortholog is encoded by PF13_0003. Using these three recombinant NTS-DBL1α(1 domains, we elicited antibodies in mice that were used to develop monovariant cultures by panning selection. The 3D7/PF13_0003 parasites formed rosettes, revealing a correlation between sequence identity and virulence phenotype. The antibodies cross-reacted with the allelic domains in ELISA but only minimally with the Cys4/group B/C PFL1955w NTS-DBL1α. By contrast, they were variant-specific in surface seroreactivity of the monovariant-infected red cells by FACS analysis and in rosette-disruption assays. Thus, while ELISA can differentiate serogroups, surface reactivity assays define the more restrictive serotypes. Irrespective of cumulated exposure to infection, antibodies acquired by humans living in a malaria-endemic area also displayed a variant-specific surface reactivity. Although seroprevalence exceeded 90% for each rosetting line, the kinetics of acquisition of surface-reactive antibodies differed in the younger age groups. These data indicate that humans acquire an antibody repertoire to non-overlapping serotypes within a serogroup, consistent with an antibody-driven diversification pressure at the population level. In addition, the data provide important information for vaccine design, as

  20. Sequence diversity of the C-terminal region of Plasmodium falciparum merozoite surface protein 1 in southern Iran.

    Science.gov (United States)

    Zamani, Zahra; Razavi, Mohammad Reza; Sadeghi, Sedigheh; Naddaf, Saeed; Pourfallah, Fatemeh; Mirkhani, Fatemeh; Arjmand, Mohammad; Feizhaddad, Hossein; Rad, Mina Ebrahimi; Ebrahimi Rad, Mina; Tameemi, Marzieh; Assmar, Mehdi

    2009-01-01

    The C-terminal region of the merozoite surface protein 1 (MSP-1) of Plasmodium falciparum is a strong vaccine candidate as it is associated with immunity to the parasite. This corresponds approximately to the conserved 17th block of the gene and is composed of two EGF- like domains. These domains exhibit only four single amino acid substitutions which show several potential variants in this region of the gene. As the variations might be important for a regional vaccine design, a study was carried out to determine the variations present in P. falciparum isolates from southern Iran. Besides the usual E-T-S-R-L and the Q-K-N-G-F types, we found Q-T-S-R-L, E-K-N-G-F, E-T-S-G-L, Z-T-S-G-L and Z-T-S-R-L types, where Z was E or Q signifying the presence of mixed clones in single isolates.

  1. Fibrinogen-Related Proteins in Tissue Repair: How a Unique Domain with a Common Structure Controls Diverse Aspects of Wound Healing.

    Science.gov (United States)

    Zuliani-Alvarez, Lorena; Midwood, Kim S

    2015-05-01

    Significance: Fibrinogen-related proteins (FRePs) comprise an intriguing collection of extracellular molecules, each containing a conserved fibrinogen-like globe (FBG). This group includes the eponymous fibrinogen as well as the tenascin, angiopoietin, and ficolin families. Many of these proteins are upregulated during tissue repair and exhibit diverse roles during wound healing. Recent Advances: An increasing body of evidence highlights the specific expression of a number of FRePs following tissue injury and infection. Upon induction, each FReP uses its FBG domain to mediate quite distinct effects that contribute to different stages of tissue repair, such as driving coagulation, pathogen detection, inflammation, angiogenesis, and tissue remodeling. Critical Issues: Despite a high degree of homology among FRePs, each contains unique sequences that enable their diversification of function. Comparative analysis of the structure and function of FRePs and precise mapping of regions that interact with a variety of ligands has started to reveal the underlying molecular mechanisms by which these proteins play very different roles using their common domain. Future Directions: Fibrinogen has long been used in the clinic as a synthetic matrix serving as a scaffold or a delivery system to aid tissue repair. Novel therapeutic strategies are now emerging that harness the use of other FRePs to improve wound healing outcomes. As we learn more about the underlying mechanisms by which each FReP contributes to the repair response, specific blockade, or indeed potentiation, of their function offers real potential to enable regulation of distinct processes during pathological wound healing.

  2. Cellular organization and spectral diversity of GFP-like proteins in live coral cells studied by single and multiphoton imaging and microspectroscopy

    Science.gov (United States)

    Salih, Anya; Cox, Guy C.; Larkum, Anthony W.

    2003-07-01

    Tissues of many marine invertebrates of class Anthozoa contain intensely fluorescent or brightly coloured pigments. These pigments belong to a family of photoactive proteins closely related to Green Fluorescent Protein (GFP), and their emissions range from blue to red wavelengths. The great diversity of these pigments has only recently been realised. To investigate the role of these proteins in corals, we have performed an in vivo fluorescent pigment (FP) spectral and cellular distribution analyses in live coral cells using single and multi-photon laser scanning imaging and microspectroscopy. These analyses revealed that even single colour corals contain spectroscopically heterogeneous pigment mixtures, with 2-5 major colour types in the same area of tissue. They were typically arranged in step-wise light emission energy gradients (e.g. blue, green, yellow, red). The successive overlapping emission-excitation spectral profiles of differently coloured FPs suggested that they were suited for sequential energy coupling. Traces of red FPs (emission = 570-660 nm) were present, even in non-red corals. We confirmed that radiative energy transfer could occur between separate granules of blue and green FPs and that energy transfer was inversely proportional to the square of the distance between them. Multi-photon micro-spectrofluorometric analysis gave significantly improved spectral resolution by restricting FP excitation to a single point in the focal plane of the sample. Pigment heterogeneity at small scales within granules suggested that fluorescence resonance energy transfer (FRET) might be occurring, and we confirmed that this was the case. Thus, energy transfer can take place both radiatively and by FRET, probably functioning in photoprotection by dissipation of excessive solar radiation.

  3. Exploratory portals of research data in education

    Directory of Open Access Journals (Sweden)

    Di Blas Nicoletta

    2015-12-01

    Full Text Available This paper presents a powerful tool to enhance research in education: ‘exploratory portals’, supporting effective storage, sharing and exploration of large sets of research data. The workflow is the following: data are gathered by a research group; they are then classified according to a taxonomy (the one that best fits the group’s research interest; once uploaded in the portal, they can be ‘explored’ via a combination of faceted search (enriched by Boolean operators and data mining techniques. The system can thus answer in a few seconds to sophisticated user’s queries that otherwise would require hours; it can save a session’s results and materials for sharing with other scholars or for further investigation. The paper presents a case study of exploratory portal, dealing with data on (technology-based education. The portal has effectively been used by five different research groups, to run complex investigations of data about technology integration into schools.

  4. Idiopathic non-cirrhotic portal hypertension

    Directory of Open Access Journals (Sweden)

    CHEN Jie

    2013-07-01

    Full Text Available The pathogenesis of idiopathic non-cirrhotic portal hypertension (INCPH remains unknown and the disease is diagnosed by the absence of recognized clinical indicators of cirrhosis and of any other known etiologies of portal hypertension. To promote understanding of this disease, a comprehensive overview of potential etiologies, clinical manifestations, histopathological features, methods of diagnosis and potential differential diagnoses, and outcome of clinical management is presented in this review. In particular, we discuss the findings from INCPH studies and their implications in regards to each of the above-mentioned categories. For example, associations with various comorbidities have suggested a possible immune system component to INCPH development and/or progression. In addition, the common clinical characteristics of patients upon presentation can not only help to recognize disease suspects but may also provide insights into the pathogenesis and prognosis. Finally, prognosis following the various intervention strategies appears to depend mainly on severity of the portal hypertension, as well as its various accompanying complications.

  5. The DIRAC Web Portal 2.0

    Science.gov (United States)

    Mathe, Z.; Casajus Ramo, A.; Lazovsky, N.; Stagni, F.

    2015-12-01

    For many years the DIRAC interware (Distributed Infrastructure with Remote Agent Control) has had a web interface, allowing the users to monitor DIRAC activities and also interact with the system. Since then many new web technologies have emerged, therefore a redesign and a new implementation of the DIRAC Web portal were necessary, taking into account the lessons learnt using the old portal. These new technologies allowed to build a more compact, robust and responsive web interface that enables users to have better control over the whole system while keeping a simple interface. The web framework provides a large set of “applications”, each of which can be used for interacting with various parts of the system. Communities can also create their own set of personalised web applications, and can easily extend already existing ones with a minimal effort. Each user can configure and personalise the view for each application and save it using the DIRAC User Profile service as RESTful state provider, instead of using cookies. The owner of a view can share it with other users or within a user community. Compatibility between different browsers is assured, as well as with mobile versions. In this paper, we present the new DIRAC Web framework as well as the LHCb extension of the DIRAC Web portal.

  6. Grid Portal for Image and Video Processing

    International Nuclear Information System (INIS)

    Dinitrovski, I.; Kakasevski, G.; Buckovska, A.; Loskovska, S.

    2007-01-01

    Users are typically best served by G rid Portals . G rid Portals a re web servers that allow the user to configure or run a class of applications. The server is then given the task of authentication of the user with the Grid and invocation of the required grid services to launch the user's application. PHP is a widely-used general-purpose scripting language that is especially suited for Web development and can be embedded into HTML. PHP is powerful and modern server-side scripting language producing HTML or XML output which easily can be accessed by everyone via web interface (with the browser of your choice) and can execute shell scripts on the server side. The aim of our work is development of Grid portal for image and video processing. The shell scripts contains gLite and globus commands for obtaining proxy certificate, job submission, data management etc. Using this technique we can easily create web interface to the Grid infrastructure. The image and video processing algorithms are implemented in C++ language using various image processing libraries. (Author)

  7. Interventional Radiologic Treatment for Idiopathic Portal Hypertension

    International Nuclear Information System (INIS)

    Hirota, Shozo; Ichikawa, Satoshi; Matsumoto, Shinichi; Motohara, Tomofumi; Fukuda, Tetsuya; Yoshikawa, Takeshi

    1999-01-01

    Purpose: To evaluate the usefulness of interventional radiological treatment for idiopathic portal hypertension. Methods: Between 1995 and 1998, we performed an interventional radiological treatment in five patients with idiopathic portal hypertension, four of whom had refused surgery and one of whom had undergone surgery. Three patients with gastroesophageal varices (GEV) were treated by partial splenic embolization (PSE), one patient with esophageal varices (EV) and massive ascites by transjugular intrahepatic portosytemic shunt (TIPS) and PSE, and one patient with GEV by percutaneous transhepatic obliteration (PTO). Midterm results were analyzed in terms of the effect on esophageal and/or gastric varices. Results: In one woman with severe GEV who underwent three sessions of PSE, there was endoscopic confirmation that the GEV had disappeared. In one man his EV shrunk markedly after two sessions of PSE. In two patients slight reduction of the EV was obtained with one application of PSE combined with endoscopic variceal ligation therapy. PTO for GV in one patient resulted in good control of the varices. All patients have survived for 16-42 months since the first interventional treatment, and varices are well controlled. Conclusion: Interventional radiological treatment is effective for patients with idiopathic portal hypertension, whether or not they have undergone surgery

  8. Transjugular intrahepatic portosystemic shunt in patients with active variceal bleeding due to portal hypertension and portal vein thrombosis

    International Nuclear Information System (INIS)

    Shin, Hyun Woong; Ryeom, Hun Kyu; Lee, Sang Kwon; Lee, Jong Min; Kim, Young Sun; Suh, Kyung Jin; Kim, Tae Hun; Kim, Yong Joo

    1997-01-01

    To evaluate the feasibility and efficacy of transjugular intrahepatic portosystemic shunt (TIPS) in patients with active variceal bleeding due to liver cirrhosis and pre-existing portal vein thrombosis. Of a total of 123 patients who underwent TIPS, 14 patients with intractable variceal bleeding due to portal hypertension and portal vein thrombosis were included in this study. Noncavernomatous portal vein occlusion was seen in eight patients, and complete portal vein occlusion with cavernomatous trans-formation in six. For all patients, the methods used for TIPS placement were the same as those used in patients with patents portal veins. In seven of eight patients with noncavernomatous occlusion, right hepatic vein-right portal vein shunting was performed; in one with knoncavernomatous occlusion, a shunt was created between the right hepatic and left portal vein. In five of six patients with cavernomatous occlusion, the right hepatic and main portal vein were connected via a collateral vein. The procedures were technically successful in all except one patient. Immediate hemostatis was achieved after all technically successful procedures, and no significant complications were encountered. Minor complications were noted in six patients (three biliary tree punctures, one transperitoneal puncture, one splenic vein perforation, one hepatic subcapsular hematoma). TIPS is a technically feasible and hemodynamically effective procedure, even in patients with active variceal bleeding due to cirrhosis and complete portal vein occlusion

  9. Índice de congestão portal e a ocorrência de trombose portal pós-dape Portal congestion and thrombosis after EDS

    Directory of Open Access Journals (Sweden)

    Fabio Gonçalves Ferreira

    2005-08-01

    Full Text Available OBJETIVO: Comparar os dados obtidos pela ultra-sonografia com doppler no pré-operatório de esquistossomóticos submetidos à desconexão ázigo-portal com esplenectomia (DAPE, calculando o índice de congestão portal, e sua correlação com a trombose portal no pós-operatório. MÉTODOS: Foram estudados 65 pacientes submetidos à DAPE por hipertensão portal esquistossomótica com antecedente de hemorragia digestiva, divididos em dois grupos: Grupo A (28 pacientes que não desenvolveram trombose portal pós-operatória e Grupo B (37 pacientes com trombose portal no pós-operatório. Analisaram-se através de ultra-sonografia com doppler no pré-operatório os seguintes parâmetros da veia porta: diâmetro, área, velocidade média de fluxo do sangue, fluxo de sangue, e estabeleceu-se o índice de congestão portal. RESULTADOS: O diâmetro, área e o fluxo da veia porta foram maiores no grupo B (média de 1,52 cm; 1,77 cm² e 2533,12 ml/min em relação ao grupo A (média de 1,33 cm; 1,44 cm² e 1609,03 ml/min com p = 0,03; 0,03 e 0,04 respectivamente. O índice de congestão portal não foi estatisticamente significativo na comparação dos dois grupos (p = 0,07. CONCLUSÃO: O índice de congestão portal obtido no pré-operatório através da ultra-sonografia com doppler não se mostrou preditivo de trombose portal no pós-operatório dos doentes estudados.BACKGROUND: The study compared the preoperative portal vein congestion index estimated by Doppler ultrasound and the postoperative portal vein thrombosis of patients submitted to esophagogastric devascularization and splenectomy (EDS. METHODS: 65 patients with portal hypertension due to schistosomiasis and previous gastrointestinal bleeding submitted to EDS were divided into two groups: GROUP A (28 patients without postoperative portal vein thrombosis and GROUP B (37 patients with postoperative portal vein thrombosis. The following parameters of preoperative Doppler ultrasound of the

  10. Transjugular Intrahepatic Portosystemic Shunt for Portal Hypertension in Hepatocellular Carcinoma with Portal Vein Tumor Thrombus.

    Science.gov (United States)

    Qiu, Bin; Li, Kai; Dong, Xiaoqun; Liu, Fu-Quan

    2017-09-01

    In patients with hepatocellular carcinoma (HCC), limited therapeutic options are available for portal hypertension resulted from portal vein tumor thrombus (PVTT). We aimed to determine safety and efficacy of TIPS for treatment of symptomatic portal hypertension in HCC with PVTT. We evaluated clinical characteristics of 95 patients with HCC and PVTT out of 992 patients who underwent TIPS. The primary endpoints included success rate, procedural mortality, serious complications, decrease in portosystemic pressure gradient, and symptom relief. The secondary endpoints included recurrence of portal hypertension, overall survival, adverse events related to treatments for HCC, and quality of life measured by Karnofsky Performance Status Scale (KPS). Success rate of TIPS was 95.8% (91/95), with procedural mortality of 1.1%. Serious complications related to TIPS procedure occurred in 2.1% (2/95) of patients. The symptoms of portal hypertension were well relieved. Variceal bleeding was successfully controlled and terminated in 100% of patients, with a recurrence rate of 39.2% in 12 months. Refractory ascites/hydrothorax was controlled partially or completely in 92.9% of patients during 1 month after TIPS, with a recurrence rate of 17.9% in 12 months. Survival rate at 6, 12, 24, and 36 months was 75.8, 52.7, 26.4, and 3.3%, respectively. No unexpected adverse event related to treatments for HCC was observed. The KPS score was 49 ± 4.5 and 63 ± 4.7 before and 1 month after TIPS, respectively (p portal hypertension in HCC with PVTT.

  11. Disastrous Portal Vein Embolization Turned into a Successful Intervention

    Energy Technology Data Exchange (ETDEWEB)

    Dobrocky, Tomas, E-mail: tomas.dobrocky@insel.ch [University of Bern, Department of Interventional, Pediatric and Diagnostic Radiology, Inselspital, University Hospital (Switzerland); Kettenbach, Joachim, E-mail: joachim.kettenbach@stpoelten.lknoe.at [Universitätsklinikum St. Pölten-Lilienfeld, Institute of Medical Radiology, Diagnostic, Intervention (Austria); Lopez-Benitez, Ruben, E-mail: Ruben.lopez@insel.ch; Kara, Levent, E-mail: levent.kara@insel.ch [University of Bern, Department of Interventional, Pediatric and Diagnostic Radiology, Inselspital, University Hospital (Switzerland)

    2015-10-15

    Portal vein embolization (PVE) may be performed before hemihepatectomy to increase the volume of future liver remnant (FLR) and to reduce the risk of postoperative liver insufficiency. We report the case of a 71-year-old patient with hilar cholangiocarcinoma undergoing PVE with access from the right portal vein using a mixture of n-butyl-2-cyanoacrylate and ethiodized oil. During the procedure, nontarget embolization of the left portal vein occurred. An aspiration maneuver of the polymerized plug failed; however, the embolus obstructing portal venous flow in the FLR was successfully relocated into the right portal vein while carefully bypassing the plug with a balloon catheter, inflating the balloon, and pulling the plug into the main right portal vein.

  12. Patient activation and use of an electronic patient portal.

    Science.gov (United States)

    Ancker, Jessica S; Osorio, Snezana N; Cheriff, Adam; Cole, Curtis L; Silver, Michael; Kaushal, Rainu

    2015-01-01

    Electronic patient portals give patients access to personal medical data, potentially creating opportunities to improve knowledge, self-efficacy, and engagement in healthcare. The combination of knowledge, self-efficacy, and engagement has been termed activation. Our objective was to assess the relationship between patient activation and outpatient use of a patient portal. Survey. A telephone survey was conducted with 180 patients who had been given access to a portal, 113 of whom used it and 67 of whom did not. The validated patient activation measure (PAM) was administered along with questions about demographics and behaviors. Portal users were no different from nonusers in patient activation. Portal users did have higher education level and more frequent Internet use, and were more likely to have precisely 2 prescription medications than to have more or fewer. Patients who chose to use an electronic patient portal were not more highly activated than nonusers, although they were more educated and more likely to be Internet users.

  13. A New Data Acquisition Portal for the Sacramento River Settlement Contractors

    Science.gov (United States)

    Narlesky, P. E., C. A.; Williams, P. E., A. M.

    2017-12-01

    In 1964, the United States Bureau of Reclamation (Reclamation) executed settlement contracts with the Sacramento River Settlement Contractors (SRSC), entities which hold water rights along the Sacramento River with area of origin protection or that are senior to Reclamation's water rights for Shasta Reservoir. Shasta is the cornerstone of the federal Central Valley Project (CVP), one of the nation's largest multi-purpose water conservation programs. In order to optimize CVP operations for multiple beneficial uses including water supply, fisheries, water quality, and waterfowl habitat, the SRSC voluntarily agreed to adaptively manage diversions throughout the year in close coordination with Reclamation. MBK Engineers assists the SRSC throughout this process by collecting, organizing, compiling, and distributing diversion data to Reclamation and others involved in operational decisions related to Shasta Reservoir and the CVP. To improve and expand participation in diversions reporting, we have developed the SRSC Web Portal, which launches a data-entry dashboard for members of the SRSC to facilitate recording and transmittal of both predicted and observed monthly and daily flow diversion data. This cloud-hosted system leverages a combination of Javascript interactive visualization libraries with a database-backed Python web framework to present streamlined data-entry forms and valuable SRSC program summary illustrations. SRSC program totals, which can now be aggregated through queries to the web-app's database backend, are used by Reclamation, SRSC, fish agencies, and others to inform operational decisions. By submitting diversion schedules and tracking actual diversions through the portal, contractors will also be directly contributing to the development of a richer and more consistently-formatted historical record for demand hydrology in the Sacramento River Watershed; this may be useful in future water supply studies. Adoption of this technology will foster an

  14. Portal Still Alive and Portal 2: Lessons from Critical Narrative Gaming Pedagogy

    OpenAIRE

    Yamasaki, Lisa Josefina

    2016-01-01

    Due to the increasing popularity of video games in mass media culture, I will be investigating one particular video game series, Portal: Still Alive and Portal 2, and the manner by which players learn from them. After observing that most instructors use these games in physics and math classes, I want to expand more on the way that video games enact a new story-telling feature through experiential means, which also serves a pedagogical function. I assert that players learn from games through...

  15. Large vehicle portal monitor for perimeter safeguards applications

    International Nuclear Information System (INIS)

    Caldwell, J.T.; Atwater, H.F.; Bernard, W.; Bieri, J.M.; Shunk, E.R.

    1979-01-01

    We have developed a class of vehicle portal monitors based on shielded 4π geometry neutron counting. we have derived and experimentally verified an analytical expression relating the detection sensitivity of the neutron tunnel vehicle portal monitor to four design parameters of the system. For a given number of neutron detectors, this design achieves one or more orders of magnitude improvement in nuclear materials detection sensitivity over previous vehicle portal monitors

  16. Multidetector CT portal venography in evaluation of portosystemic collateral vessels

    International Nuclear Information System (INIS)

    Agarwal, A.; Jain, M.

    2008-01-01

    This essay shows the usefulness of multidetector CT angiography for evaluation of the splenoportal venous system, which is essential in the management of patients with portal hypertension and its complications, such as portal vein thrombosis. By providing scanning with reconstruction of thin axial source images and reformatting into thicker multiplanar reformats, multidetector CT can help to determine the extent and location of portosystemic collateral vessels in patients with portal hypertension and is probably the optimal imaging technique in this setting.

  17. Arachidonic acid metabolites and endothelial dysfunction of portal hypertension.

    Science.gov (United States)

    Sacerdoti, David; Pesce, Paola; Di Pascoli, Marco; Brocco, Silvia; Cecchetto, Lara; Bolognesi, Massimo

    2015-07-01

    Increased resistance to portal flow and increased portal inflow due to mesenteric vasodilatation represent the main factors causing portal hypertension in cirrhosis. Endothelial cell dysfunction, defined as an imbalance between the synthesis, release, and effect of endothelial mediators of vascular tone, inflammation, thrombosis, and angiogenesis, plays a major role in the increase of resistance in portal circulation, in the decrease in the mesenteric one, in the development of collateral circulation. Reduced response to vasodilators in liver sinusoids and increased response in the mesenteric arterioles, and, viceversa, increased response to vasoconstrictors in the portal-sinusoidal circulation and decreased response in the mesenteric arterioles are also relevant to the pathophysiology of portal hypertension. Arachidonic acid (AA) metabolites through the three pathways, cyclooxygenase (COX), lipoxygenase, and cytochrome P450 monooxygenase and epoxygenase, are involved in endothelial dysfunction of portal hypertension. Increased thromboxane-A2 production by liver sinusoidal endothelial cells (LSECs) via increased COX-1 activity/expression, increased leukotriens, increased epoxyeicosatrienoic acids (EETs) (dilators of the peripheral arterial circulation, but vasoconstrictors of the portal-sinusoidal circulation), represent a major component in the increased portal resistance, in the decreased portal response to vasodilators and in the hyper-response to vasoconstrictors. Increased prostacyclin (PGI2) via COX-1 and COX-2 overexpression, and increased EETs/heme-oxygenase-1/K channels/gap junctions (endothelial derived hyperpolarizing factor system) play a major role in mesenteric vasodilatation, hyporeactivity to vasoconstrictors, and hyper-response to vasodilators. EETs, mediators of liver regeneration after hepatectomy and of angiogenesis, may play a role in the development of regenerative nodules and collateral circulation, through stimulation of vascular endothelial

  18. TUX-INTERO: A Portal for secure interoperation of Grids

    OpenAIRE

    Shashi Bhanwar; Seema Bawa

    2010-01-01

    In this paper, we propose TUX-INTERO - a portlet-based Grid portal for integrating existing grid technologies under a common interface and providing reliable services to the users. We have developed a prototype of TUX-INTERO - a grid portal using portlet technology. The paper presents design and development of TUXINTERO. The requirements for the portal, its design and technology choices lead to the utilization of Globus Toolkit as middleware for connecting global resources, SUN N1 GE6 and Con...

  19. Aneurysmal malformation of the extrahepatic portal vein: a case report

    International Nuclear Information System (INIS)

    Lee, Jeong Min; Kang, Sung Soo; Kim, Chong Soo; Han, Hyeun Young

    1999-01-01

    Aneurysmal malformation of the portal vein is a rare entity. To our knowledge, only scattered reports of portal vein aneurysms appear in the literature in English, and there is no previously published report in Korean. We describe a case exhibiting aneurysmal malformation of the extrahepatic portal vein at the hepatic hilum ; the findings demonstrated by ultrasound, CT and angiography are discussed, a review of previously described cases is included

  20. Bacillus subtilis genome diversity.

    Science.gov (United States)

    Earl, Ashlee M; Losick, Richard; Kolter, Roberto

    2007-02-01

    Microarray-based comparative genomic hybridization (M-CGH) is a powerful method for rapidly identifying regions of genome diversity among closely related organisms. We used M-CGH to examine the genome diversity of 17 strains belonging to the nonpathogenic species Bacillus subtilis. Our M-CGH results indicate that there is considerable genetic heterogeneity among members of this species; nearly one-third of Bsu168-specific genes exhibited variability, as measured by the microarray hybridization intensities. The variable loci include those encoding proteins involved in antibiotic production, cell wall synthesis, sporulation, and germination. The diversity in these genes may reflect this organism's ability to survive in diverse natural settings.

  1. Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations.

    Science.gov (United States)

    Wang, Bo; Li, Liwei; Hurley, Thomas D; Meroueh, Samy O

    2013-10-28

    End-point free energy calculations using MM-GBSA and MM-PBSA provide a detailed understanding of molecular recognition in protein-ligand interactions. The binding free energy can be used to rank-order protein-ligand structures in virtual screening for compound or target identification. Here, we carry out free energy calculations for a diverse set of 11 proteins bound to 14 small molecules using extensive explicit-solvent MD simulations. The structure of these complexes was previously solved by crystallography and their binding studied with isothermal titration calorimetry (ITC) data enabling direct comparison to the MM-GBSA and MM-PBSA calculations. Four MM-GBSA and three MM-PBSA calculations reproduced the ITC free energy within 1 kcal·mol(-1) highlighting the challenges in reproducing the absolute free energy from end-point free energy calculations. MM-GBSA exhibited better rank-ordering with a Spearman ρ of 0.68 compared to 0.40 for MM-PBSA with dielectric constant (ε = 1). An increase in ε resulted in significantly better rank-ordering for MM-PBSA (ρ = 0.91 for ε = 10), but larger ε significantly reduced the contributions of electrostatics, suggesting that the improvement is due to the nonpolar and entropy components, rather than a better representation of the electrostatics. The SVRKB scoring function applied to MD snapshots resulted in excellent rank-ordering (ρ = 0.81). Calculations of the configurational entropy using normal-mode analysis led to free energies that correlated significantly better to the ITC free energy than the MD-based quasi-harmonic approach, but the computed entropies showed no correlation with the ITC entropy. When the adaptation energy is taken into consideration by running separate simulations for complex, apo, and ligand (MM-PBSAADAPT), there is less agreement with the ITC data for the individual free energies, but remarkably good rank-ordering is observed (ρ = 0.89). Interestingly, filtering MD snapshots by prescoring

  2. Treatment of surgical brain injury by immune tolerance induced by intrathymic and hepatic portal vein injection of brain antigens.

    Science.gov (United States)

    Yang, Weijian; Liu, Yong; Liu, Baolong; Tan, Huajun; Lu, Hao; Wang, Hong; Yan, Hua

    2016-08-24

    Surgical brain injury (SBI) defines complications induced by intracranial surgery, such as cerebral edema and other secondary injuries. In our study, intrathymic and hepatic portal vein injection of allogeneic myelin basic protein (MBP) or autogeneic brain cell suspensions were administered to a standard SBI model. Serum pro-inflammatory IL-2, anti-inflammatory IL-4 concentrations and the CD4(+)T/CD8(+)T ratio were measured at 1, 3, 7, 14 and 21 d after surgery to verify the establishment of immune tolerance. Furthermore, we confirmed neuroprotective effects by evaluating neurological scores at 1, 3, 7, 14 and 21 d after SBI. Anti-Fas ligand (FasL) immunohistochemistry and TUNEL assays of brain sections were tested at 21 d after surgery. Intrathymic injections of MBP or autogeneic brain cell suspensions functioned by both suppressing secondary inflammatory reactions and improving prognoses, whereas hepatic portal vein injections of autogeneic brain cell suspensions exerted a better effect than MBP. Intrathymic and hepatic portal vein injections of MBP had equal effects on reducing secondary inflammation and improving prognoses. Otherwise, hepatic portal vein injections of autogeneic brain cell suspensions had better outcomes than intrathymic injections of autogeneic brain cell suspensions. Moreover, the benefit of injecting antigens into the thymus was outweighed by hepatic portal vein injections.

  3. Genetic diversity and natural selection in the rhoptry-associated protein 1 (RAP-1) of recent Plasmodium knowlesi clinical isolates from Malaysia.

    Science.gov (United States)

    Rawa, Mira Syahfriena Amir; Fong, Mun-Yik; Lau, Yee-Ling

    2016-02-05

    The Plasmodium rhoptry-associated protein 1 (RAP-1) plays a role in the formation of the parasitophorous vacuole following the parasite's invasion of red blood cells. Although there is some evidence that the protein is recognized by the host's immune system, study of Plasmodium falciparum RAP-1 (PfRAP-1) suggests that it is not under immune pressure. A previous study on five old (1953-1962) P. knowlesi strains suggested that RAP-1 has limited genetic polymorphism and might be under negative selection. In the present study, 30 recent P. knowlesi isolates were studied to obtain a better insight into the polymorphism and natural selection of PkRAP-1. Blood samples from 30 knowlesi malaria patients were used. These samples were collected between 2010 and 2014. The PkRAP-1 gene, which contains two exons, was amplified by PCR, cloned into Escherichia coli and sequenced. Genetic diversity and phylogenetic analyses were performed using MEGA6 and DnaSP ver. 5.10.00 programs. Thirty PkRAP-1 sequences were obtained. The nucleotide diversity (π) of exons 1, 2 and the total coding region (0.00915, 0.01353 and 0.01298, respectively) were higher than those of the old strains. Further analysis revealed a lower rate of non-synonymous (dN) than synonymous (dS) mutations, suggesting negative (purifying) selection of PkRAP-1. Tajima's D test and Fu and Li's D test values were not significant. At the amino acid level, 22 haplotypes were established with haplotype H7 having the highest frequency (7/34, 20.5 %). In the phylogenetic analysis, two distinct haplotype groups were observed. The first group contained the majority of the haplotypes, whereas the second had fewer haplotypes. The present study found higher genetic polymorphism in the PkRAP-1 gene than the polymorphism level reported in a previous study. This observation may stem from the difference in sample size between the present (n = 30) and the previous (n = 5) study. Synonymous and non-synonymous mutation analysis indicated

  4. Congenital absence of the portal vein presenting as pulmonary hypertension

    International Nuclear Information System (INIS)

    Jun, Sur Young; Lee, Whal; Cheon, Jung Eun; Kim, Woo Sun; Kim, In One; Yeon, Kyung Mo

    2007-01-01

    Congenital absence of the portal vein (CAPV) is a rare malformation in which intestinal and splenic venous flow bypasses the liver and drains directly into the systemic circulation via a congenital portosystemic shunt. We describe two cases of CAPV presenting as pulmonary hypertension that were initially suspected as primary pulmonary hypertension. However, subsequent ultrasonography and CT detected the absence of a portal vein and the presence of a portosystemic shunt. Pulmonary hypertension is a recognized complication of liver disease and portal hypertension. However, these two cases illustrate that CAPV may result in pulmonary hypertension without liver disease or portal hypertension

  5. Indications for portal pressure measurement in chronic liver disease

    DEFF Research Database (Denmark)

    Hobolth, Lise; Bendtsen, Flemming; Møller, Søren

    2012-01-01

    Portal hypertension leads to development of serious complications such as esophageal varices, ascites, renal and cardiovascular dysfunction. The importance of the degree of portal hypertension has been substantiated within recent years. Measurement of the portal pressure is simple and safe...... and the hepatic venous pressure gradient (HVPG) independently predicts survival and development of complications such as ascites, HCC and bleeding from esophageal varices. Moreover, measurements of HVPG can be used to guide pharmacotherapy for primary and secondary prophylaxis for variceal bleeding. Assessment...... of HVPG should therefore be considered as a part of the general characterization of patients with portal hypertension in departments assessing and treating this condition....

  6. Congenital absence of the portal vein presenting as pulmonary hypertension

    Energy Technology Data Exchange (ETDEWEB)

    Jun, Sur Young; Lee, Whal; Cheon, Jung Eun; Kim, Woo Sun; Kim, In One; Yeon, Kyung Mo [Seoul National University Hospital, Seoul (Korea, Republic of)

    2007-11-15

    Congenital absence of the portal vein (CAPV) is a rare malformation in which intestinal and splenic venous flow bypasses the liver and drains directly into the systemic circulation via a congenital portosystemic shunt. We describe two cases of CAPV presenting as pulmonary hypertension that were initially suspected as primary pulmonary hypertension. However, subsequent ultrasonography and CT detected the absence of a portal vein and the presence of a portosystemic shunt. Pulmonary hypertension is a recognized complication of liver disease and portal hypertension. However, these two cases illustrate that CAPV may result in pulmonary hypertension without liver disease or portal hypertension.

  7. 1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions.

    Science.gov (United States)

    Joshi, Hiren J; Christiansen, Katy M; Fitz, Joffrey; Cao, Jun; Lipzen, Anna; Martin, Joel; Smith-Moritz, A Michelle; Pennacchio, Len A; Schackwitz, Wendy S; Weigel, Detlef; Heazlewood, Joshua L

    2012-05-15

    The sequencing of over a thousand natural strains of the model plant Arabidopsis thaliana is producing unparalleled information at the genetic level for plant researchers. To enable the rapid exploitation of these data for functional proteomics studies, we have created a resource for the visualization of protein information and proteomic datasets for sequenced natural strains of A. thaliana. The 1001 Proteomes portal can be used to visualize amino acid substitutions or non-synonymous single-nucleotide polymorphisms in individual proteins of A. thaliana based on the reference genome Col-0. We have used the available processed sequence information to analyze the conservation of known residues subject to protein phosphorylation among these natural strains. The substitution of amino acids in A. thaliana natural strains is heavily constrained and is likely a result of the conservation of functional attributes within proteins. At a practical level, we demonstrate that this information can be used to clarify ambiguously defined phosphorylation sites from phosphoproteomic studies. Protein sets of available natural variants are available for download to enable proteomic studies on these accessions. Together this information can be used to uncover the possible roles of specific amino acids in determining the structure and function of proteins in the model plant A. thaliana. An online portal to enable the community to exploit these data can be accessed at http://1001proteomes.masc-proteomics.org/

  8. In-cell intrabody selection from a diverse human library identifies C12orf4 protein as a new player in rodent mast cell degranulation.

    Directory of Open Access Journals (Sweden)

    Elsa Mazuc

    Full Text Available The high specificity of antibodies for their antigen allows a fine discrimination of target conformations and post-translational modifications, making antibodies the first choice tool to interrogate the proteome. We describe here an approach based on a large-scale intracellular expression and selection of antibody fragments in eukaryotic cells, so-called intrabodies, and the subsequent identification of their natural target within living cell. Starting from a phenotypic trait, this integrated system allows the identification of new therapeutic targets together with their companion inhibitory intrabody. We applied this system in a model of allergy and inflammation. We first cloned a large and highly diverse intrabody library both in a plasmid and a retroviral eukaryotic expression vector. After transfection in the RBL-2H3 rat basophilic leukemia cell line, we performed seven rounds of selection to isolate cells displaying a defect in FcεRI-induced degranulation. We used high throughput sequencing to identify intrabody sequences enriched during the course of selection. Only one intrabody was common to both plasmid and retroviral selections, and was used to capture and identify its target from cell extracts. Mass spectrometry analysis identified protein RGD1311164 (C12orf4, with no previously described function. Our data demonstrate that RGD1311164 is a cytoplasmic protein implicated in the early signaling events following FcεRI-induced cell activation. This work illustrates the strength of the intrabody-based in-cell selection, which allowed the identification of a new player in mast cell activation together with its specific inhibitor intrabody.

  9. Expression Profiling of Mitogen-Activated Protein Kinase Genes Reveals Their Evolutionary and Functional Diversity in Different Rubber Tree (Hevea brasiliensis Cultivars

    Directory of Open Access Journals (Sweden)

    Xiang Jin

    2017-10-01

    Full Text Available Rubber tree (Hevea brasiliensis is the only commercially cultivated plant for producing natural rubber, one of the most essential industrial raw materials. Knowledge of the evolutionary and functional characteristics of kinases in H. brasiliensis is limited because of the long growth period and lack of well annotated genome information. Here, we reported mitogen-activated protein kinases in H. brasiliensis (HbMPKs by manually checking and correcting the rubber tree genome. Of the 20 identified HbMPKs, four members were validated by proteomic data. Protein motif and phylogenetic analyses classified these members into four known groups comprising Thr-Glu-Tyr (TEY and Thr-Asp-Tyr (TDY domains, respectively. Evolutionary and syntenic analyses suggested four duplication events: HbMPK3/HbMPK6, HbMPK8/HbMPK9/HbMPK15, HbMPK10/HbMPK12 and HbMPK11/HbMPK16/HbMPK19. Expression profiling of the identified HbMPKs in roots, stems, leaves and latex obtained from three cultivars with different latex yield ability revealed tissue- and variety-expression specificity of HbMPK paralogues. Gene expression patterns under osmotic, oxidative, salt and cold stresses, combined with cis-element distribution analyses, indicated different regulation patterns of HbMPK paralogues. Further, Ka/Ks and Tajima analyses suggested an accelerated evolutionary rate in paralogues HbMPK10/12. These results revealed HbMPKs have diverse functions in natural rubber biosynthesis, and highlighted the potential possibility of using MPKs to improve stress tolerance in future rubber tree breeding.

  10. Congenital Portal Vein Aneurysm Associated with Peliosis Hepatis and Intestinal Lymphangiectasia

    Directory of Open Access Journals (Sweden)

    Zeynel Mungan

    2009-01-01

    Full Text Available Portal vein aneurisym (PVA, peliosis hepatis (PH and intestinal lymphangiectasia (IL all are very uncommon entities. Herein, we presented a unique patient with these three rare entities who was admitted to our hospital because of portal hypertensive ascites rich in protein and lymphocyte. PVA was extrahepatic and associated with coronary vein aneurysm. Peliosis hepatis was of microscopic form. Lymphangiectasia was present in peritoneum and small intestine. Diagnoses of these rare entities were made by imaging techniques and histopathological findings. Patient also had hydronephrosis caused by ureteropelvic junction narrowing. Best of our knowledge, there is no such a case reported previously with the association of PVA, PH and IL. Therefore, we propose PVAPHIL syndrome to define this novel association.

  11. The influence of culture on enterprise portal design in a global environment

    NARCIS (Netherlands)

    Feng, Xiuzhen; Ehrenhard, Michel Léon; Hicks, Jeff; Hou, Yibin; Khosrow-Pour, M.

    2007-01-01

    Enterprise portals collect and synthesize information from various systems to deliver personalized and highly relevant information to suppliers, customers and employees. While enterprise portal design and portal applications have been widely discussed in the literature, the implications that arise

  12. Portal vein stenting for delayed jejunal varix bleeding associated with portal venous occlusion after hepatoiliary and pancreatic surgery

    Energy Technology Data Exchange (ETDEWEB)

    Hyun, Dong Ho; Park, Kwang Bo; Cho, Sung Ki; Park, Hong Suk; Shin, Sung Wook; Choo, Sung Wook; Do, Young Soo; Choo, In Wook; Choi, Dong Wook [Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of)

    2017-09-15

    The study aimed to describe portal stenting for postoperative portal occlusion with delayed (≥ 3 months) variceal bleeding in the afferent jejunal loop. Eleven consecutive patients (age range, 2–79 years; eight men and three women) who underwent portal stenting between April 2009 and December 2015 were included in the study. Preoperative medical history and the postoperative clinical course were reviewed. Characteristics of portal occlusion and details of procedures were also investigated. Technical success, treatment efficacy (defined as disappearance of jejunal varix on follow-up CT), and clinical success were analyzed. Primary stent patency rate was plotted using the Kaplan-Meier method. All patients underwent hepatobiliary-pancreatic cancer surgery except two children with liver transplantation for biliary atresia. Portal occlusion was caused by benign postoperative change (n = 6) and local tumor recurrence (n = 5). Variceal bleeding occurred at 27 months (4 to 72 months) and portal stenting was performed at 37 months (4 to 121 months), on average, postoperatively. Technical success, treatment efficacy, and clinical success rates were 90.9, 100, and 81.8%, respectively. The primary patency rate of portal stent was 88.9% during the mean follow-up period of 9 months. Neither procedure-related complication nor mortality occurred. Interventional portal stenting is an effective treatment for delayed jejunal variceal bleeding due to portal occlusion after hepatobiliary-pancreatic surgery.

  13. Portal vein stenting for delayed jejunal varix bleeding associated with portal venous occlusion after hepatoiliary and pancreatic surgery

    International Nuclear Information System (INIS)

    Hyun, Dong Ho; Park, Kwang Bo; Cho, Sung Ki; Park, Hong Suk; Shin, Sung Wook; Choo, Sung Wook; Do, Young Soo; Choo, In Wook; Choi, Dong Wook

    2017-01-01

    The study aimed to describe portal stenting for postoperative portal occlusion with delayed (≥ 3 months) variceal bleeding in the afferent jejunal loop. Eleven consecutive patients (age range, 2–79 years; eight men and three women) who underwent portal stenting between April 2009 and December 2015 were included in the study. Preoperative medical history and the postoperative clinical course were reviewed. Characteristics of portal occlusion and details of procedures were also investigated. Technical success, treatment efficacy (defined as disappearance of jejunal varix on follow-up CT), and clinical success were analyzed. Primary stent patency rate was plotted using the Kaplan-Meier method. All patients underwent hepatobiliary-pancreatic cancer surgery except two children with liver transplantation for biliary atresia. Portal occlusion was caused by benign postoperative change (n = 6) and local tumor recurrence (n = 5). Variceal bleeding occurred at 27 months (4 to 72 months) and portal stenting was performed at 37 months (4 to 121 months), on average, postoperatively. Technical success, treatment efficacy, and clinical success rates were 90.9, 100, and 81.8%, respectively. The primary patency rate of portal stent was 88.9% during the mean follow-up period of 9 months. Neither procedure-related complication nor mortality occurred. Interventional portal stenting is an effective treatment for delayed jejunal variceal bleeding due to portal occlusion after hepatobiliary-pancreatic surgery

  14. A novel canine model of portal vein stenosis plus thioacetamide administration-induced cirrhotic portal hypertension with hypersplenism.

    Science.gov (United States)

    Lin, Dexin; Wu, Xianbin; Ji, Xiaoke; Zhang, Qiyu; Lin, YuanWei; Chen, WeiJian; Jin, Wangxun; Deng, Liming; Chen, Yunzhi; Chen, Bicheng; Li, Jianmin

    2012-01-01

    Current large animal models that could closely resemble the typical features of cirrhotic portal hypertension in human have not been well established. Thus, we aimed to develop and describe a reliable and reproducible canine cirrhosis model of portal hypertension. A total of 30 mongrel dogs were randomly divided into four groups: 1 (control; n = 5), 2 (portal vein stenosis [PVS]; n = 5], 3 (thioacetamide [TAA]; n = 5), and 4 (PVS plus TAA; n = 15). After 4-months modeling period, liver and spleen CT perfusion, abdominal CT scans, portal hemodynamics, gastroscopy, hepatic function, blood routine, the bone marrow, liver, and spleen histology were studied. The animals in group 2 (PVS) developed extrahepatic portosystemic collateral circulation, particularly esophageal varices, without hepatic cirrhosis and portal hypertension. Animals from group 3 (TAA) presented mild cirrhosis and portal hypertension without significant symptoms of esophageal varices and hypersplenism. In contrast, animals from group 4 (PVS + TAA) showed well-developed micronodular and macronodular cirrhosis, associated with significant portal hypertension and hypersplenism. The combination of PVS and TAA represents a novel, reliable, and reproducible canine cirrhosis model of portal hypertension, which is associated with the typical characteristics of portal hypertension, including hypersplenism.

  15. Novel Rat Model of Repetitive Portal Venous Embolization Mimicking Human Non-Cirrhotic Idiopathic Portal Hypertension.

    Science.gov (United States)

    Klein, Sabine; Hinüber, Christian; Hittatiya, Kanishka; Schierwagen, Robert; Uschner, Frank Erhard; Strassburg, Christian P; Fischer, Hans-Peter; Spengler, Ulrich; Trebicka, Jonel

    2016-01-01

    Non-cirrhotic idiopathic portal hypertension (NCIPH) is characterized by splenomegaly, anemia and portal hypertension, while liver function is preserved. However, no animal models have been established yet. This study assessed a rat model of NCIPH and characterized the hemodynamics, and compared it to human NCIPH. Portal pressure (PP) was measured invasively and coloured microspheres were injected in the ileocecal vein in rats. This procedure was performed weekly for 3 weeks (weekly embolization). Rats without and with single embolization served as controls. After four weeks (one week after last embolization), hemodynamics were investigated, hepatic fibrosis and accumulation of myofibroblasts were analysed. General characteristics, laboratory analyses and liver histology were collected in patients with NCIPH. Weekly embolization induced a hyperdynamic circulation, with increased PP. The mesenteric flow and hepatic hydroxyproline content was significantly higher in weekly embolized compared to single embolized rats (mesenteric flow +54.1%, hydroxyproline +41.7%). Mesenteric blood flow and shunt volumes increased, whereas splanchnic vascular resistance was decreased in the weekly embolization group. Fibrotic markers αSMA and Desmin were upregulated in weekly embolized rats. This study establishes a model using repetitive embolization via portal veins, comparable with human NCIPH and may serve to test new therapies.

  16. Fundamental factors influencing portal image quality

    International Nuclear Information System (INIS)

    Jaffray, D.A.

    1995-01-01

    It has been recognized that improved methods of verifying radiation field placement in external beam radiotherapy are required in order to make frequent checks of field placement feasible. As a result, a large number of electronic portal imaging systems have been developed as possible replacements for film. These developments have produced digital systems with faster acquisition and improved display contrast, however, the quality of the images acquired with such systems is still disappointing. This presentation examines many of the fundamental factors which limit the quality of radiographs obtained with a megavoltage radiotherapy beam. The size and shape of the radiation sources (focal and extra-focal) in radiotherapy machines and their influence on the spatial resolution of portal images are examined. Monte Carlo simulations of x-ray interactions within the patient determined that a significant fraction of the x-ray scatter generated in the patient is due to bremsstrahlung and posi