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Sample records for heterogeneous ribonuclear proteins

  1. The heterogeneous ribonuclear protein C interacts with the hepatitis delta virus small antigen

    PubMed Central

    2011-01-01

    Background Hepatitis delta virus (HDV) is considered to be a satellite virus of the Hepatitis B virus. The genome consists of a 1679 nt ssRNA molecule in which a single ORF was identified. This ORF codes for a unique protein, the Delta antigen (HDAg). During transcription, two forms, small (S-HDAg; p24) and large (L-HDAg; p27) of this antigen are derived as a result of an editing mechanism catalyzed by cellular adenosine deaminase 1. Despite its simplicity, little is still known about the host factors that interact with the virus RNA and antigens being to modulate virus replication. Methods A yeast two-hybrid screening of a human liver cDNA library, using the hepatitis delta virus (HDV) small antigen (S-HDAg) as bait, was performed. Blot overlay and co-immunoprecipitation assays were used in an attempt to confirm the interaction of hnRNPC and S-HDAg. siRNA knockdown assays of hnRNPC were performed to assess the effect on HDV antigen expression. Results Thirty known proteins were identified as S-HDAg interactors in the yeast two-hybrid screening. One of the identified proteins, hnRNPC, was found to interact with S-HDAg in vitro and in vivo in human liver cells. The interaction of the two proteins is mediated by the C-terminal half of the S-HDAg which contains a RNA-binding domain (aa 98-195). HDV RNA, S-HDAg, and hnRNPC, were also found to co-localize in the nucleus of human liver cells. Knockdown of hnRNPC mRNA using siRNAs resulted in a marked decreased expression of HDV antigens. Conclusions S-HDAg was found to interact with human liver proteins previously assigned to different functional categories. Among those involved in nucleic acid metabolism, hnRNPC was found to interact in vitro and in vivo in human liver cells. Similar to other RNA viruses, it seems plausible that hnRNPC may also be involved in HDV replication. However, further investigation is mandatory to clarify this question. PMID:21774814

  2. Heterogeneous nuclear ribonuclear protein K interacts with Sindbis virus nonstructural proteins and viral subgenomic mRNA

    SciTech Connect

    Burnham, Andrew J.; Gong, Lei; Hardy, Richard W.

    2007-10-10

    Alphaviruses are a group of arthropod-borne human and animal pathogens that can cause epidemics of significant public health and economic consequence. Alphavirus RNA synthesis requires four virally encoded nonstructural proteins and probably a number of cellular proteins. Using comparative two-dimensional electrophoresis we were able to identify proteins enriched in cytoplasmic membrane fractions containing viral RNA synthetic complexes following infection with Sindbis virus. Our studies demonstrated the following: (i) the host protein hnRNP K is enriched in cytoplasmic membrane fractions following Sindbis virus infection, (ii) viral nonstructural proteins co-immunoprecipitate with hnRNP K, (iii) nsP2 and hnRNP K co-localize in the cytoplasm of Sindbis virus infected cells, (iv) Sindbis virus subgenomic mRNA, but not genomic RNA co-immunoprecipitates with hnRNP K, (v) viral RNA does not appear to be required for the interaction of hnRNP K with the nonstructural proteins. Potential functions of hnRNP K during virus replication are discussed.

  3. Heterogeneous ribonuclear protein E2 (hnRNP E2) is associated with TDP-43-immunoreactive neurites in Semantic Dementia but not with other TDP-43 pathological subtypes of Frontotemporal Lobar Degeneration.

    PubMed

    Davidson, Yvonne S; Robinson, Andrew C; Flood, Louis; Rollinson, Sara; Benson, Bridget C; Asi, Yasmine T; Richardson, Anna; Jones, Matthew; Snowden, Julie S; Pickering-Brown, Stuart; Lashley, Tammaryn; Mann, David M A

    2017-06-30

    Frontotemporal Lobar Degeneration (FTLD) encompasses certain related neurodegenerative disorders which alter personality and cognition. Heterogeneous ribonuclear proteins (hnRNPs) maintain RNA metabolism and changes in their function may underpin the pathogenesis of FTLD. Immunostaining for hnRNP E2 was performed on sections of frontal and temporal cortex with hippocampus from 80 patients with FTLD, stratified by pathology into FTLD-tau and FTLD-TDP type A, B and C subtypes, and by genetics into patients with C9orf72 expansions, MAPT or GRN mutations, or those with no known mutation, and on 10 healthy controls. Semi-quantitative analysis assessed hnRNP staining in frontal and temporal cortex, and in dentate gyrus (DG) of hippocampus, in the different pathology and genetic groups. We find that hnRNP E2 immunostaining detects the TDP-43 positive dystrophic neurites (DN) within frontal and temporal cortex, and the neuronal cytoplasmic inclusions (NCI) seen in DG granule cells, characteristic of patients with Semantic Dementia (SD) and type C TDP-43 pathology, but did not detect TDP-43 or tau inclusions in any of the other pathological or genetic variants of FTLD. Double immunofluorescence for hnRNP E2 and TDP-43 showed most TDP-43 immunopositive DN to contain hnRNP E2. Present findings indicate an association between TDP-43 and hnRNP E2 which might underlie the pathogenetic mechanism of this form of FTLD.

  4. Mechanistic Control of Carcinoembryonic Antigen-related Cell Adhesion Molecule-1 (CEACAM1) Splice Isoforms by the Heterogeneous Nuclear Ribonuclear Proteins hnRNP L, hnRNP A1, and hnRNP M*

    PubMed Central

    Dery, Kenneth J.; Gaur, Shikha; Gencheva, Marieta; Yen, Yun; Shively, John E.; Gaur, Rajesh K.

    2011-01-01

    Carcinoembryonic antigen-related cell adhesion molecule-1 (CEACAM1) is expressed in a variety of cell types and is implicated in carcinogenesis. Alternative splicing of CEACAM1 pre-mRNA generates two cytoplasmic domain splice variants characterized by the inclusion (L-isoform) or exclusion (S-isoform) of exon 7. Here we show that the alternative splicing of CEACAM1 pre-mRNA is regulated by novel cis elements residing in exon 7. We report the presence of three exon regulatory elements that lead to the inclusion or exclusion of exon 7 CEACAM1 mRNA in ZR75 breast cancer cells. Heterologous splicing reporter assays demonstrated that the maintenance of authentic alternative splicing mechanisms were independent of the CEACAM1 intron sequence context. We show that forced expression of these exon regulatory elements could alter CEACAM1 splicing in HEK-293 cells. Using RNA affinity chromatography, three members of the heterogeneous nuclear ribonucleoprotein family (hnRNP L, hnRNP A1, and hnRNP M) were identified. RNA immunoprecipitation of hnRNP L and hnRNP A1 revealed a binding motif located central and 3′ to exon 7, respectively. Depletion of hnRNP A1 or L by RNAi in HEK-293 cells promoted exon 7 inclusion, whereas overexpression led to exclusion of the variable exon. By contrast, overexpression of hnRNP M showed exon 7 inclusion and production of CEACAM1-L mRNA. Finally, stress-induced cytoplasmic accumulation of hnRNP A1 in MDA-MB-468 cells dynamically alters the CEACAM1-S:CEACAM1:L ratio in favor of the l-isoform. Thus, we have elucidated the molecular factors that control the mechanism of splice-site recognition in the alternative splicing regulation of CEACAM1. PMID:21398516

  5. A putative role of ribonuclear inclusions and MBNL1 in the impairment of gallbladder smooth muscle contractility with cholelithiasis in myotonic dystrophy type 1.

    PubMed

    Cardani, R; Mancinelli, E; Saino, G; Bonavina, L; Meola, G

    2008-08-01

    Myotonic dystrophy type 1 (DM1) is an autosomal dominant multisystemic disorder caused by expansion of unstable trinucleotide (CTG) repeats at 3' untranslated region of the DMPK gene on chromosome 19q13.3. Mutant transcripts are retained in muscle nuclei as ribonuclear inclusions and interact with RNA-binding proteins, such as muscleblind-like protein 1 (MBNL1), leading to a reduction in their activity. The reduced MBNL1 activity has been associated to skeletal and cardiac muscle dysfunction. However, other organs and systems may be involved. It has been reported that 25-50% of DM1 patients have abdominal symptoms due to cholelithiasis or gallstones. Since impaired gallbladder motility plays an important role in gallstones formation, we have analyzed by FISH combined with MBNL1-immunofluorescence, the gallbladder obtained from a woman affected by DM1 who required a cholecystectomy at the age of 30. Gallbladders obtained from two no-DM1 subjects have been used as controls. Ribonuclear inclusions and MBNL1 foci accumulate and colocalize in nuclei of DM1 gallbladder smooth muscle cells. On the contrary, no ribonuclear inclusions are detectable in cell nuclei of control gallbladders and MBNL1 is uniformly distributed in smooth muscle cell nuclei. These results suggest that nuclear accumulation of MBNL1 and ribonuclear inclusions may have a direct adverse effect on gallbladder smooth muscle contractility and thus contribute to gallstones formation in DM1 patients.

  6. Suppression of conformational heterogeneity at a protein-protein interface.

    PubMed

    Deis, Lindsay N; Wu, Qinglin; Wang, You; Qi, Yang; Daniels, Kyle G; Zhou, Pei; Oas, Terrence G

    2015-07-21

    Staphylococcal protein A (SpA) is an important virulence factor from Staphylococcus aureus responsible for the bacterium's evasion of the host immune system. SpA includes five small three-helix-bundle domains that can each bind with high affinity to many host proteins such as antibodies. The interaction between a SpA domain and the Fc fragment of IgG was partially elucidated previously in the crystal structure 1FC2. Although informative, the previous structure was not properly folded and left many substantial questions unanswered, such as a detailed description of the tertiary structure of SpA domains in complex with Fc and the structural changes that take place upon binding. Here we report the 2.3-Å structure of a fully folded SpA domain in complex with Fc. Our structure indicates that there are extensive structural rearrangements necessary for binding Fc, including a general reduction in SpA conformational heterogeneity, freezing out of polyrotameric interfacial residues, and displacement of a SpA side chain by an Fc side chain in a molecular-recognition pocket. Such a loss of conformational heterogeneity upon formation of the protein-protein interface may occur when SpA binds its multiple binding partners. Suppression of conformational heterogeneity may be an important structural paradigm in functionally plastic proteins.

  7. Heterogeneity in Retroviral Nucleocapsid Protein Function

    NASA Astrophysics Data System (ADS)

    Landes, Christy

    2009-03-01

    Time-resolved single-molecule fluorescence spectroscopy was used to study the human T-cell lymphotropic virus type 1 (HTLV-1) nucleocapsid protein (NC) chaperone activity as compared to that of the HIV-1 NC protein. HTLV-1 NC contains two zinc fingers with each having a CCHC binding motif similar to HIV-1 NC. HIV-1 NC is required for recognition and packaging of the viral RNA and is also a nucleic acid chaperone protein that facilitates nucleic acid restructuring during reverse transcription. Because of similarities in structures between the two retroviruses, we have used single-molecule fluorescence energy transfer to investigate the chaperoning activity of HTLV-1 NC protein. The results indicate that HTLV-1 NC protein induces structural changes by opening the transactivation response (TAR)-DNA hairpin to an even greater extent than HIV-1 NC. However, unlike HIV-1 NC, HTLV-1 NC does not chaperone the strand-transfer reaction involving TAR-DNA. These results suggest that despite its effective destabilization capability, HTLV-1 NC is not as effective at overall chaperone function as is its HIV-1 counterpart.

  8. Sequence heterogeneity accelerates protein search for targets on DNA

    SciTech Connect

    Shvets, Alexey A.; Kolomeisky, Anatoly B.

    2015-12-28

    The process of protein search for specific binding sites on DNA is fundamentally important since it marks the beginning of all major biological processes. We present a theoretical investigation that probes the role of DNA sequence symmetry, heterogeneity, and chemical composition in the protein search dynamics. Using a discrete-state stochastic approach with a first-passage events analysis, which takes into account the most relevant physical-chemical processes, a full analytical description of the search dynamics is obtained. It is found that, contrary to existing views, the protein search is generally faster on DNA with more heterogeneous sequences. In addition, the search dynamics might be affected by the chemical composition near the target site. The physical origins of these phenomena are discussed. Our results suggest that biological processes might be effectively regulated by modifying chemical composition, symmetry, and heterogeneity of a genome.

  9. Sequence heterogeneity accelerates protein search for targets on DNA

    NASA Astrophysics Data System (ADS)

    Shvets, Alexey A.; Kolomeisky, Anatoly B.

    2015-12-01

    The process of protein search for specific binding sites on DNA is fundamentally important since it marks the beginning of all major biological processes. We present a theoretical investigation that probes the role of DNA sequence symmetry, heterogeneity, and chemical composition in the protein search dynamics. Using a discrete-state stochastic approach with a first-passage events analysis, which takes into account the most relevant physical-chemical processes, a full analytical description of the search dynamics is obtained. It is found that, contrary to existing views, the protein search is generally faster on DNA with more heterogeneous sequences. In addition, the search dynamics might be affected by the chemical composition near the target site. The physical origins of these phenomena are discussed. Our results suggest that biological processes might be effectively regulated by modifying chemical composition, symmetry, and heterogeneity of a genome.

  10. Immunochemical studies on heterogeneity of IgD myeloma proteins.

    PubMed Central

    Ohtani, H; Sakaguchi, K; Saito, M

    1981-01-01

    An antigenic heterogeneity among IgD myeloma proteins was tested by immunoelectrophoresis and double immunodiffusion in agar with four kinds of anti-delta(Fc) antisera produced by immunization with isolated Fc fragments of IgD myeloma proteins. According to antigenicity of the Fc fragment, IgD myeloma proteins were divided into two different groups. Anti-delta(Fc)-T1 (S.T.) antiserum, absorbed with te Y.S. myeloma protein or serum, either gave a faint precipitin line or failed to react against the isolated IgD myeloma proteins or sera. With the papain-digested IgD myeloma proteins and sera, anti-delta(Fc)-T1 antiserum either gave heavy precipitin lines or failed to react. Of twelve papain-digested sera containing IgD myeloma proteins tested, nine (75%) showed positive precipitin lines using anti-delta(Fc)-T1 antiserum. No relationship was found between the two groups of myeloma proteins with respect to IgD levels. SDS polyacrylamide gel electrophoresis of the IgD myeloma proteins (S.T. and Y.S.) showed no difference in the molecular weights of the whole myeloma proteins, and their light and heavy chains. Polyacrylamide gel electrophoresis of the IgD myeloma proteins (S.T. and Y.S.), after treatment with papain, revealed almost the same patterns. Images Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 PMID:6168563

  11. Structural Heterogeneity and Conformational Relaxation in Heme Proteins

    NASA Astrophysics Data System (ADS)

    Chu, Kelvin

    The influence of cooling rate upon the structural heterogeneity of sperm whale myoglobin solutions at cryogenic temperatures was studied. Sample cooling rates were varied by almost four orders of magnitude. FTIR spectra of the CO stretch frequency region reveal that the population of the A states is highly sensitive to the glass transition temperature T_{rm g} of the solvent, which is in turn sensitive to the cooling rate. The structural heterogeneity within each substate was assessed by temperature-derivative spectroscopy (TDS); no significant changes of barrier distributions were found. We conclude that cooling rate plays a negligible role in the structural heterogeneity of protein solutions, and that conformational substates are an intrinsic part of protein systems. Flash photolysis experiments using both O _2 and CO adducts of sperm whale and horse myoglobin reveal an intermediate process that separates geminate and solvent rebinding. This process, named process II, is caused by thermally-induced relaxation (TIR) of the protein from the photoproduct (Mb*) to the deoxy (Mb) configuration. The conformational change Mb* --> Mb was originally modelled as a smooth shift of the rebinding barrier distribution towards higher enthalpies by extrapolation of the spectral position of band III and rebinding enthalpy. Data from light-induced relaxation (LIR) experiments suggest that the relaxation proceeds in discrete steps. A four-well sequential model is proposed in which a conformational change separates the inner two wells.

  12. Sequence Heterogeneity Accelerates Protein Search for Targets on DNA

    NASA Astrophysics Data System (ADS)

    Shvets, Alexey; Kolomeisky, Anatoly

    The process of protein search for specific binding sites on DNA is fundamentally important since it marks the beginning of all major biological processes. We present a theoretical investigation that probes the role of DNA sequence symmetry, heterogeneity and chemical composition in the protein search dynamics. Using a discrete-state stochastic approach with a first-passage events analysis, which takes into account the most relevant physical-chemical processes, a full analytical description of the search dynamics is obtained. It is found that, contrary to existing views, the protein search is generally faster on DNA with more heterogeneous sequences. In addition, the search dynamics might be affected by the chemical composition near the target site. The physical origins of these phenomena are discussed. Our results suggest that biological processes might be effectively regulated by modifying chemical composition, symmetry and heterogeneity of a genome. The work was supported by the Welch Foundation (Grant C-1559), by the NSF (Grant CHE-1360979), and by the Center for Theoretical Biological Physics sponsored by the NSF (Grant PHY-1427654).

  13. Phosphoric acid entrapment leads to apparent protein heterogeneity.

    PubMed

    Fountoulakis, M; Vilbois, F; Oesterhelt, G; Vetter, W

    1995-04-01

    Recombinant proteins produced in prokaryotes or eukaryotes show certain types of heterogeneity due to post-translational modifications. Some preparations of a soluble interferon gamma receptor, produced in Escherichia coli, appeared as a double band with slightly different mobilities in non-reducing sodium dodecylsulfate and native polyacrylamide gels. Ion spray mass spectrometry showed that the two forms had a mass difference of one to three multiples of 97 +/- 2 D. Gas chromatography-mass spectrometry analysis revealed the presence of phosphoric acid in the hydrolysate and in the intact protein. The more slowly migrating protein species had trapped molecules of phosphoric acid during the protein extraction. Most of the trapped phosphoric acid was loosely associated with the protein. One to three molecules were tightly, but non-covalently linked per receptor molecule. Phosphoric acid entrapment did not affect biological activity and most likely did not affect protein conformation. The species carrying phosphoric acid showed higher solubility. Trapping of phosphoric acid by proteins may be a general phenomenon and the results reported here thus useful in the characterization of other recombinant proteins.

  14. Heterogeneous Nucleation of Protein Crystals on Fluorinated Layered Silicate

    PubMed Central

    Ino, Keita; Udagawa, Itsumi; Iwabata, Kazuki; Takakusagi, Yoichi; Kubota, Munehiro; Kurosaka, Keiichi; Arai, Kazuhito; Seki, Yasutaka; Nogawa, Masaya; Tsunoda, Tatsuo; Mizukami, Fujio; Taguchi, Hayao; Sakaguchi, Kengo

    2011-01-01

    Here, we describe an improved system for protein crystallization based on heterogeneous nucleation using fluorinated layered silicate. In addition, we also investigated the mechanism of nucleation on the silicate surface. Crystallization of lysozyme using silicates with different chemical compositions indicated that fluorosilicates promoted nucleation whereas the silicates without fluorine did not. The use of synthesized saponites for lysozyme crystallization confirmed that the substitution of hydroxyl groups contained in the lamellae structure for fluorine atoms is responsible for the nucleation-inducing property of the nucleant. Crystallization of twelve proteins with a wide range of pI values revealed that the nucleation promoting effect of the saponites tended to increase with increased substitution rate. Furthermore, the saponite with the highest fluorine content promoted nucleation in all the test proteins regardless of their overall net charge. Adsorption experiments of proteins on the saponites confirmed that the density of adsorbed molecules increased according to the substitution rate, thereby explaining the heterogeneous nucleation on the silicate surface. PMID:21818343

  15. Heterogeneous interactome between Litopenaeus vannamei plasma proteins and Vibrio parahaemolyticus outer membrane proteins.

    PubMed

    Liu, Xiang; She, Xin-Tao; Zhu, Qing-Feng; Li, Hui; Peng, Xuan-Xian

    2013-01-01

    A great loss has been suffered by microbial infectious diseases under intensive shrimp farming in recent years. In this background, the understanding of shrimp innate immunity becomes an importantly scientific issue, but little is known about the heterogeneous protein-protein interaction between pathogenic cells and hosts, which is a key step for the invading microbes to infect internet organs through bloodstream. In the present study, bacterial outer membrane (OM) protein array and pull-down approaches are used to isolate both Vibrio parahaemolyticus OM proteins that bind to shrimp serum proteins and the shrimp serum proteins that interact with bacterial cells, respectively. Three interacting shrimp serum proteins, hemocyanin, β-1,3-glucan binding protein and LV_HP_RA36F08r and thirty interacting OM proteins were determined. They form 63 heterogeneous protein-protein interactions. Nine out of the 30 OM proteins were randomly demonstrated to be up-regulated or down-regulated when bacterial cells were cultured with shrimp sera, indicating the biological significance of the network. The interesting findings uncover the complexity of struggle between host immunity and bacterial infection. Compared with our previous report on heterogeneous interactome between fish grill and bacterial OM proteins, the present study further extends the investigation from lower vertebrates to invertebrates and develops a bacterial OM protein array to identify the OM proteins bound with shrimp serum proteins, which elevates the frequencies of the bound OM proteins. Our results highlight the way to determine and understand the heterogeneous interaction between hosts and microbes.

  16. Predicting protein function and other biomedical characteristics with heterogeneous ensembles

    PubMed Central

    Whalen, Sean; Pandey, Om Prakash

    2015-01-01

    Prediction problems in biomedical sciences, including protein function prediction (PFP), are generally quite difficult. This is due in part to incomplete knowledge of the cellular phenomenon of interest, the appropriateness and data quality of the variables and measurements used for prediction, as well as a lack of consensus regarding the ideal predictor for specific problems. In such scenarios, a powerful approach to improving prediction performance is to construct heterogeneous ensemble predictors that combine the output of diverse individual predictors that capture complementary aspects of the problems and/or datasets. In this paper, we demonstrate the potential of such heterogeneous ensembles, derived from stacking and ensemble selection methods, for addressing PFP and other similar biomedical prediction problems. Deeper analysis of these results shows that the superior predictive ability of these methods, especially stacking, can be attributed to their attention to the following aspects of the ensemble learning process: (i) better balance of diversity and performance, (ii) more effective calibration of outputs and (iii) more robust incorporation of additional base predictors. Finally, to make the effective application of heterogeneous ensembles to large complex datasets (big data) feasible, we present DataSink, a distributed ensemble learning framework, and demonstrate its sound scalability using the examined datasets. DataSink is publicly available from https://github.com/shwhalen/datasink. PMID:26342255

  17. Demonstration of heterogeneity among the antigenic proteins of Mobiluncus species.

    PubMed Central

    Schwebke, J R; Hillier, S L; Fohn, M J; Lukehart, S A

    1990-01-01

    The protein and antigenic profiles of the American Type Culture Collection type strains of Mobiluncus species and those of 114 clinical isolates were determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis and immunoblotting with homologous polyvalent antisera. The majority of isolates (82%) possessed characteristic protein profiles and could be identified to the species level by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis. The major protein bands were also antigenic, and some antigenic cross-reactivity was noted between the two Mobiluncus species. All of the isolates were examined for reactivity with a panel of 12 monoclonal antibodies previously prepared against the type strains. While 56 of 60 clinical isolates of Mobiluncus curtisii (93%) reacted with one or more of the monoclonal antibodies, only 23 of 54 clinical isolates which were identified as Mobiluncus mulieris by biochemical methods (48%) reacted with one or more of the monoclonal antibodies. One of the 4 M. curtisii isolates (25%) and 11 of the 31 M. mulieris isolates (35%) which did not react with the monoclonal antibodies also had atypical protein profiles. These results demonstrate a high degree of heterogeneity in the protein and antigenic profiles of Mobiluncus isolates and suggest that further taxonomic division may be appropriate. Images PMID:1691207

  18. Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made from RNA

    PubMed Central

    SILVERMAN, SCOTT K.

    2003-01-01

    Switches and sensors play important roles in our everyday lives. The chemical properties of RNA make it amenable for use as a switch or sensor, both artificially and in nature. This review focuses on recent advances in artificial RNA switches and sensors. Researchers have been applying classical biochemical principles such as allostery in elegant ways that are influencing the development of biosensors and other applications. Particular attention is given here to allosteric ribozymes (aptazymes) that are regulated by small organic molecules, by proteins, or by oligonucleotides. Also discussed are ribozymes whose activities are controlled by various nonallosteric strategies. PMID:12649489

  19. Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made from RNA.

    PubMed

    Silverman, Scott K

    2003-04-01

    Switches and sensors play important roles in our everyday lives. The chemical properties of RNA make it amenable for use as a switch or sensor, both artificially and in nature. This review focuses on recent advances in artificial RNA switches and sensors. Researchers have been applying classical biochemical principles such as allostery in elegant ways that are influencing the development of biosensors and other applications. Particular attention is given here to allosteric ribozymes (aptazymes) that are regulated by small organic molecules, by proteins, or by oligonucleotides. Also discussed are ribozymes whose activities are controlled by various nonallosteric strategies.

  20. CombFunc: predicting protein function using heterogeneous data sources.

    PubMed

    Wass, Mark N; Barton, Geraint; Sternberg, Michael J E

    2012-07-01

    Only a small fraction of known proteins have been functionally characterized, making protein function prediction essential to propose annotations for uncharacterized proteins. In recent years many function prediction methods have been developed using various sources of biological data from protein sequence and structure to gene expression data. Here we present the CombFunc web server, which makes Gene Ontology (GO)-based protein function predictions. CombFunc incorporates ConFunc, our existing function prediction method, with other approaches for function prediction that use protein sequence, gene expression and protein-protein interaction data. In benchmarking on a set of 1686 proteins CombFunc obtains precision and recall of 0.71 and 0.64 respectively for gene ontology molecular function terms. For biological process GO terms precision of 0.74 and recall of 0.41 is obtained. CombFunc is available at http://www.sbg.bio.ic.ac.uk/combfunc.

  1. Proteomic and genomic analysis reveals novel Campylobacter jejuni outer membrane proteins and potential heterogeneity.

    PubMed

    Watson, Eleanor; Sherry, Aileen; Inglis, Neil F; Lainson, Alex; Jyothi, Dushyanth; Yaga, Raja; Manson, Erin; Imrie, Lisa; Everest, Paul; Smith, David G E

    2014-09-01

    Gram-negative bacterial outer membrane proteins play important roles in the interaction of bacteria with their environment including nutrient acquisition, adhesion and invasion, and antibiotic resistance. In this study we identified 47 proteins within the Sarkosyl-insoluble fraction of Campylobacter jejuni 81-176, using LC-ESI-MS/MS. Comparative analysis of outer membrane protein sequences was visualised to reveal protein distribution within a panel of Campylobacter spp., identifying several C. jejuni-specific proteins. Smith-Waterman analyses of C. jejuni homologues revealed high sequence conservation amongst a number of hypothetical proteins, sequence heterogeneity of other proteins and several proteins which are absent in a proportion of strains.

  2. Theory of polyelectrolyte adsorption on heterogeneously charged surfaces applied to soluble protein-polyelectrolyte complexes

    NASA Astrophysics Data System (ADS)

    de Vries, R.; Weinbreck, F.; de Kruif, C. G.

    2003-03-01

    Existing theoretical approaches to polymer adsorption on heterogeneous surfaces are applied to the problems of polyelectrolyte and polyampholyte adsorption on randomly charged surfaces. Also, analytical estimates are developed for the critical pH at which weakly charged polyelectrolytes and globular proteins start forming soluble complexes. Below a critical salt concentration, soluble complexes form "on the wrong side" of the protein isoelectric point due to the heterogeneity of the protein surface charge distribution. The analytical estimates are consistent with experimental data on soluble complexes in mixtures of gum arabic and whey protein isolate.

  3. Charge heterogeneity study of a Fc-fusion protein, abatacept, using two-dimensional gel electrophoresis.

    PubMed

    Nebija, D; Noe, C R; Lachmann, B

    2015-08-01

    Medicinal products obtained by recombinant DNA technology are complex molecules and demonstrate a high degree of molecular heterogeneity. Charge heterogeneity and isoform pattern of this class of medicines, are parameters important for their quality, safety, and efficacy. In this study we report the application of two-dimensional gel electrophoresis (2-D electrophoresis) for the quality assessment, identification, charge heterogeneity and isoform pattern study of recombinant protein, CTLA4-Ig (abatacept), which has been selected as an example of the drug class, known as Fc-fusion proteins. In order to achieve an efficient separation of this complex analyte,2-D electrophoresis was optimized employing different experimental conditions regarding the selection of an immobilized pH gradient (IPG), sample pretreatment, presentation and detection procedure. Experimental datadocumented that 2-D electrophoresis is a suitable method for the assessment of identity, purity, structural integrity, isoform pattern and to monitor charge heterogeneity and post-translational glycosylation of the Fc-fusion protein, abatacept.

  4. Protein Dynamics and Conformational Heterogeneity Characterized with Two-Dimensional Infrared Spectroscopy

    NASA Astrophysics Data System (ADS)

    Thielges, Megan; Basom, Edward; Spearman, James

    2014-06-01

    Conformational heterogeneity and dynamics impact protein function, but their investigation is limited by the availability of methods for characterizing rapidly fluctuating protein states with both high spatial and temporal resolution. Multidimensional infrared spectroscopy is emerging as a powerful technique that directly probes the structural dynamics on fast timescales. To overcome the spectral congestion inherent to protein spectra that restricts application of infrared spectroscopy to protein systems, we incorporate into proteins vibrational probes with spectrally isolated frequencies and local-mode character that make possible rigorous analysis of protein environments and dynamics with infrared spectroscopy. In particular, both heme-bound carbon monoxide and nitriles selectively incorporated as unnatural amino acids are used as probes of cytochrome P450. 2D IR spectroscopy is used to investigate the impact of protein dynamics and conformational heterogeneity on the selectivity of its catalytic activity. Comparative studies of mutants of cytochrome P450 are used to unravel the contribution of specific residues to the protein's dynamics.

  5. Simulations of disordered proteins and systems with conformational heterogeneity.

    PubMed

    Levine, Zachary A; Shea, Joan-Emma

    2017-04-01

    Intrinsically disordered proteins (IDPs) and protein regions can facilitate a wide variety of complex physiological processes such as binding, signaling, and formation of membraneless organelles. They can however also play pathological roles by aggregating into cytotoxic oligomers and fibrils. Characterizing the structure and function of disordered proteins is an onerous task, primarily because these proteins adopt transient structures, which are difficult to capture in experiments. Simulations have emerged as a powerful tool for interpreting and augmenting experimental measurements of IDPs. In this review we focus on computer simulations of disordered protein structures, functions, assemblies, and emerging questions that, taken together, give an overview of the field as it exists today. Copyright © 2016. Published by Elsevier Ltd.

  6. Polar Fixation of Plasmids during Recombinant Protein Production in Bacillus megaterium Results in Population Heterogeneity.

    PubMed

    Münch, Karin M; Müller, Johannes; Wienecke, Sarah; Bergmann, Simone; Heyber, Steffi; Biedendieck, Rebekka; Münch, Richard; Jahn, Dieter

    2015-09-01

    During the past 2 decades, Bacillus megaterium has been systematically developed for the gram-per-liter scale production of recombinant proteins. The plasmid-based expression systems employed use a xylose-controlled promoter. Protein production analyses at the single-cell level using green fluorescent protein as a model product revealed cell culture heterogeneity characterized by a significant proportion of less productive bacteria. Due to the enormous size of B. megaterium, such bistable behavior seen in subpopulations was readily analyzed by time lapse microscopy and flow cytometry. Cell culture heterogeneity was not caused simply by plasmid loss: instead, an asymmetric distribution of plasmids during cell division was detected during the exponential-growth phase. Multicopy plasmids are generally randomly distributed between daughter cells. However, in vivo and in vitro experiments demonstrated that under conditions of strong protein production, plasmids are retained at one of the cell poles. Furthermore, it was found that cells with accumulated plasmids and high protein production ceased cell division. As a consequence, the overall protein production of the culture was achieved mainly by the subpopulation with a sufficient plasmid copy number. Based on our experimental data, we propose a model whereby the distribution of multicopy plasmids is controlled by polar fixation under protein production conditions. Thereby, cell lines with fluctuating plasmid abundance arise, which results in population heterogeneity. Our results provide initial insights into the mechanism of cellular heterogeneity during plasmid-based recombinant protein production in a Bacillus species.

  7. Terbium luminescence-lifetime heterogeneity and protein equilibrium conformational dynamics.

    PubMed Central

    Austin, R H; Stein, D L; Wang, J

    1987-01-01

    The fluorescence decay of the rare earth terbium when bound to the protein calmodulin changes from a simple exponential decay to a complex nonexponential decay as the temperature is lowered below 200 K. We have fit the observed decay curves by assuming that the terbium emission is a forced electric dipole transition and proteins have a distribution of continuous conformational states. Quantitative fits to the data indicate that the root-mean-square configurational deviation of the atoms surrounding the terbium ion is 0.2 A, in good agreement with other measurements. We further point out that because the protein seems to undergo a glass transition yet retains configurational order at room temperature, the proper name for the physical state of a protein at room temperature is the rubber-like state. PMID:3470740

  8. Intraclonal Protein Expression Heterogeneity in Recombinant CHO Cells

    PubMed Central

    Pilbrough, Warren; Munro, Trent P.; Gray, Peter

    2009-01-01

    Therapeutic glycoproteins have played a major role in the commercial success of biotechnology in the post-genomic era. But isolating recombinant mammalian cell lines for large-scale production remains costly and time-consuming, due to substantial variation and unpredictable stability of expression amongst transfected cells, requiring extensive clone screening to identify suitable high producers. Streamlining this process is of considerable interest to industry yet the underlying phenomena are still not well understood. Here we examine an antibody-expressing Chinese hamster ovary (CHO) clone at single-cell resolution using flow cytometry and vectors, which couple light and heavy chain transcription to fluorescent markers. Expression variation has traditionally been attributed to genetic heterogeneity arising from random genomic integration of vector DNA. It follows that single cell cloning should yield a homogeneous cell population. We show, in fact, that expression in a clone can be surprisingly heterogeneous (standard deviation 50 to 70% of the mean), approaching the level of variation in mixed transfectant pools, and each antibody chain varies in tandem. Phenotypic variation is fully developed within just 18 days of cloning, yet is not entirely explained by measurement noise, cell size, or the cell cycle. By monitoring the dynamic response of subpopulations and subclones, we show that cells also undergo slow stochastic fluctuations in expression (half-life 2 to 11 generations). Non-genetic diversity may therefore play a greater role in clonal variation than previously thought. This also has unexpected implications for expression stability. Stochastic gene expression noise and selection bias lead to perturbations from steady state at the time of cloning. The resulting transient response as clones reestablish their expression distribution is not ordinarily accounted for but can contribute to declines in median expression over timescales of up to 50 days. Noise

  9. Heterogeneous distribution of dye-labelled biomineralizaiton proteins in calcite crystals.

    PubMed

    Liu, Chuang; Xie, Liping; Zhang, Rongqing

    2015-12-17

    Biominerals are highly ordered crystals mediated by organic matters especially proteins in organisms. However, how specific proteins are distributed inside biominerals are not well understood. In the present study, we use fluorescein isothiocyanate (FITC) to label extracted proteins from the shells of bivalve Pinctada fucata. By confocal laser scanning microscopy (CLSM), we observe a heterogeneous distribution of dye-labelled proteins inside synthetic calcite at the microscale. Proteins from the prismatic calcite layers accumulate at the edge of crystals while proteins from the nacreous aragonite layers accumulate at the center of crystals. Raman and X-ray powder diffraction show that both the proteins cannot alter the crystal phase. Scanning electron microscope demonstrates both proteins are able to affect the crystal morphology. This study may provide a direct approach for the visualization of protein distributions in crystals by small-molecule dye-labelled proteins as the additives in the crystallization process and improve our understanding of intracrystalline proteins distribution in biogenic calcites.

  10. Heterogeneous distribution of dye-labelled biomineralizaiton proteins in calcite crystals

    NASA Astrophysics Data System (ADS)

    Liu, Chuang; Xie, Liping; Zhang, Rongqing

    2015-12-01

    Biominerals are highly ordered crystals mediated by organic matters especially proteins in organisms. However, how specific proteins are distributed inside biominerals are not well understood. In the present study, we use fluorescein isothiocyanate (FITC) to label extracted proteins from the shells of bivalve Pinctada fucata. By confocal laser scanning microscopy (CLSM), we observe a heterogeneous distribution of dye-labelled proteins inside synthetic calcite at the microscale. Proteins from the prismatic calcite layers accumulate at the edge of crystals while proteins from the nacreous aragonite layers accumulate at the center of crystals. Raman and X-ray powder diffraction show that both the proteins cannot alter the crystal phase. Scanning electron microscope demonstrates both proteins are able to affect the crystal morphology. This study may provide a direct approach for the visualization of protein distributions in crystals by small-molecule dye-labelled proteins as the additives in the crystallization process and improve our understanding of intracrystalline proteins distribution in biogenic calcites.

  11. Structural heterogeneity of 6 M GdmCl-denatured proteins: implications for the mechanism of protein folding.

    PubMed

    Chang, Jui-Yoa

    2009-10-13

    An in vitro experiment with protein folding is typically initiated with 6 M GdmCl-denatured proteins, which are generally considered fully unfolded. However, studies conducted by various laboratories have shown that many 6 M GdmCl-denatured proteins are structurally heterogeneous and still retain nativelike residual structures. The extent of conformational heterogeneity of the 6 M GdmCl-denatured protein has significant implications for the folding landscape as well as the interpretation of the observed early stage folding mechanism. Using the method of disulfide scrambling, we are able to gain rough insight into the diverse structural properties of 6 M GdmCl-denatured proteins. It demonstrates that most 6 M GdmCl-denatured proteins are approximately fully denatured, but partially unfolded. Most of them comprise diverse conformational isomers. We review here the cumulative evidence obtained from various laboratories and also provide experimental data obtained in our laboratory.

  12. Protein-nanoparticle interactions: the effects of surface compositional and structural heterogeneity are scale dependent

    NASA Astrophysics Data System (ADS)

    Huang, Rixiang; Carney, Randy P.; Stellacci, Francesco; Lau, Boris L. T.

    2013-07-01

    Nanoparticles (NPs) in the biological environment are exposed to a large variety and concentration of proteins. Proteins are known to adsorb in a `corona' like structure on the surface of NPs. In this study, we focus on the effects of surface compositional and structural heterogeneity on protein adsorption by examining the interaction of self-assembled monolayer coated gold NPs (AuNPs) with two types of proteins: ubiquitin and fibrinogen. This work was designed to systematically investigate the role of surface heterogeneity in nanoparticle-protein interaction. We have chosen the particles as well as the proteins to provide different types (in distribution and length-scale) of heterogeneity. The goal was to unveil the role of heterogeneity and of its length-scale in the particle-protein interaction. Dynamic light scattering and circular dichroism spectroscopy were used to reveal different interactions at pH above and below the isoelectric points of the proteins, which is related to the charge heterogeneity on the protein surface. At pH 7.4, there was only a monolayer of proteins adsorbed onto the NPs and the secondary structure of proteins remained intact. At pH 4.0, large aggregates of nanoparticle-protein complexes were formed and the secondary structures of the proteins were significantly disrupted. In terms of interaction thermodynamics, results from isothermal titration calorimetry showed that ubiquitin adsorbed differently onto (1) AuNPs with charged and nonpolar terminals organized into nano-scale structure (66-34 OT), (2) AuNPs with randomly distributed terminals (66-34 brOT), and (3) AuNPs with homogeneously charged terminals (MUS). This difference in adsorption behavior was not observed when AuNPs interacted with fibrinogen. The results suggested that the interaction between the proteins and AuNPs was influenced by the surface heterogeneity on the AuNPs, and this influence depends on the scale of surface heterogeneity and the size of the proteins

  13. Enhancing Accuracy in Molecular Weight Determination of Highly Heterogeneously Glycosylated Proteins by Native Tandem Mass Spectrometry.

    PubMed

    Wang, Guanbo; de Jong, Rob N; van den Bremer, Ewald T J; Parren, Paul W H I; Heck, Albert J R

    2017-05-02

    The determination of molecular weights (MWs) of heavily glycosylated proteins is seriously hampered by the physicochemical characteristics and heterogeneity of the attached carbohydrates. Glycosylation impacts protein migration during sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE) and size-exclusion chromatography (SEC) analysis. Standard electrospray ionization (ESI)-mass spectrometry does not provide a direct solution as this approach is hindered by extensive interference of ion signals caused by closely spaced charge states of broadly distributed glycoforms. Here, we introduce a native tandem MS-based approach, enabling charge-state resolution and charge assignment of protein ions including those that escape mass analysis under standard MS conditions. Using this method, we determined the MW of two model glycoproteins, the extra-cellular domains of the highly and heterogeneously glycosylated proteins CD38 and epidermal growth factor receptor (EGFR), as well as the overall MW and binding stoichiometries of these proteins in complex with a specific antibody.

  14. Heterogeneities in confined water and protein hydration water

    NASA Astrophysics Data System (ADS)

    Stanley, H. E.; Kumar, P.; Han, S.; Mazza, M. G.; Stokely, K.; Buldyrev, S. V.; Franzese, G.; Mallamace, F.; Xu, L.

    2009-12-01

    We report recent efforts to understand a broad range of experiments on confined water and protein hydration water, many initiated by a collaboration between workers at the University of Messina and MIT—the editors of this special issue. Preliminary calculations are not inconsistent with one tentative interpretation of these experiments as resulting from the system passing from the high-temperature high-pressure 'HDL' side of the Widom line (where the liquid might display non-Arrhenius behavior) to the low-temperature low-pressure 'LDL' side of the Widom line (where the liquid might display Arrhenius behavior). The Widom line—defined to be the line in the pressure-temperature plane where the correlation length has its maximum—arises if there is a critical point. Hence, interpreting the Messina-MIT experiments in terms of a Widom line is of potential relevance to testing, experimentally, the hypothesis that water displays a liquid-liquid critical point.

  15. Heterogeneous patterns on block copolymer thin film via solvent annealing: Effect on protein adsorption

    NASA Astrophysics Data System (ADS)

    Shen, Lei; Zhu, Jintao; Liang, Haojun

    2015-03-01

    Heterogeneous patterns consisting of nanometer-scaled hydrophobic/hydrophilic domains were generated by self-assembly of poly(styrene)-block-poly(2-hydroxyethyl methacrylate) (PS-b-PHEMA) block copolymer thin film. The effect of the heterogeneity of the polymer film surface on the nonspecific adsorption of the protein human plasma fibrinogen (FBN, 5.0 × 5.0 × 47.5 nm3) was investigated. The kinetics of the FBN adsorption varies from a single-component Langmuir model on homogeneous hydrophilic PHEMA to a two-stage spreading relaxation model on homogeneous hydrophobic PS surface. On a heterogeneous PS-b-PHEMA surface with majority PS part, the initial FBN adsorption rate remains the same as that on the homogeneous PS surface. However, hydrophilic PHEMA microdomains on the heterogeneous surface slow down the second spreading stage of the FBN adsorption process, leading to a surface excess of adsorbed FBN molecules less than the presumed one simply calculated as adsorption onto multiple domains. Importantly, when the PS-b-PHEMA surface is annealed to form minority domelike PS domains (diameter: ˜50-100 nm) surrounded by a majority PHEMA matrix, such surface morphology proves to be strongly protein-repulsive. These interesting findings can be attributed to the enhancement of the spread FBN molecule in a mobile state by the heterogeneity of polymer film surface before irreversible adsorption occurs.

  16. Intrafocal heterogeneity of ERG protein expression and gene fusion pattern in prostate cancer.

    PubMed

    Suh, Ja Hee; Park, Jeong Hwan; Lee, Cheol; Moon, Kyung Chul

    2017-10-01

    Prostate cancer is considered to be highly heterogeneous, with various morphologic features and biologic behaviors. The TMPRSS2-ERG gene fusion is the most frequently observed genetic aberration in prostate cancer. The aim of this study was to elucidate the intrafocal heterogeneity of ERG gene fusion status. ERG immunohistochemistry (IHC) was performed in samples from 168 prostate cancer patients who had undergone radical prostatectomy, and 40 cases showing ERG-positive IHC staining were selected for tissue microarray (TMA) construction. Two to six representative cores were selected from each tumor focus. In the cases with heterogeneous ERG IHC staining intensity, the areas showing different intensities were separately selected. Using the TMA blocks, IHC and fluorescence in situ hybridization (FISH) were conducted to evaluate the heterogeneity of ERG protein expression and ERG fusion gene patterns, respectively, in a single tumor focus. Heterogeneity of ERG IHC staining was defined as the simultaneous presence of negative and positive cores in the same tumor focus. Heterogeneity of ERG FISH was defined by the presence of cores with positive and negative FISH signals or cores with break-apart and interstitial deletion FISH signals in the same tumor focus. A total of 202 TMA cores were isolated from 40 ERG-positive cases. Of the 202 total cores, 19 were negative for ERG IHC staining, and 46 showed 1+, 52 showed 2+, and 85 showed 3+ ERG staining intensity. Eleven cores were negative for ERG FISH signal, 119 cores showed ERG break-apart FISH signals, and the remaining 72 cores revealed interstitial deletion. Intrafocal heterogeneity of ERG IHC staining was found in 20% (8/40) of cases, and intrafocal heterogeneity of ERG gene fusion pattern was found in 32.5% (13/40) of cases. In summary, this study showed significantly frequent intrafocal heterogeneity of ERG protein expression, gene fusion status and fusion pattern. This heterogeneity can be caused by the development

  17. Heterogeneous distribution of dye-labelled biomineralizaiton proteins in calcite crystals

    PubMed Central

    Liu, Chuang; Xie, Liping; Zhang, Rongqing

    2015-01-01

    Biominerals are highly ordered crystals mediated by organic matters especially proteins in organisms. However, how specific proteins are distributed inside biominerals are not well understood. In the present study, we use fluorescein isothiocyanate (FITC) to label extracted proteins from the shells of bivalve Pinctada fucata. By confocal laser scanning microscopy (CLSM), we observe a heterogeneous distribution of dye-labelled proteins inside synthetic calcite at the microscale. Proteins from the prismatic calcite layers accumulate at the edge of crystals while proteins from the nacreous aragonite layers accumulate at the center of crystals. Raman and X-ray powder diffraction show that both the proteins cannot alter the crystal phase. Scanning electron microscope demonstrates both proteins are able to affect the crystal morphology. This study may provide a direct approach for the visualization of protein distributions in crystals by small-molecule dye-labelled proteins as the additives in the crystallization process and improve our understanding of intracrystalline proteins distribution in biogenic calcites. PMID:26675363

  18. Exploring protein solution structure: Second moments of fluorescent spectra report heterogeneity of tryptophan rotamers.

    PubMed

    Gasymov, Oktay K; Abduragimov, Adil R; Glasgow, Ben J

    2015-01-01

    Trp fluorescent spectra appear as a log-normal function but are usually analyzed with λmax, full width at half maximum, and the first moment of incomplete spectra. Log-normal analyses have successfully separated fluorescence contributions from some multi-Trp proteins but deviations were observed in single Trp proteins. The possibility that disparate rotamer environments might account for these deviations was explored by moment spectral analysis of single Trp mutants spanning the sequence of tear lipocalin as a model. The analysis required full width Trp spectra. Composite spectra were constructed using log-normal analysis to derive the inaccessible blue edge, and the experimentally obtained spectra for the remainder. First moments of the composite spectra reflected the site-resolved secondary structure. Second moments were most sensitive for spectral deviations. A novel parameter, derived from the difference of the second moments of composite and simulated log-normal spectra correlated with known multiple heterogeneous rotamer conformations. Buried and restricted side chains showed the most heterogeneity. Analyses applied to other proteins further validated the method. The rotamer heterogeneity values could be rationalized by known conformational properties of Trp residues and the distribution of nearby charged groups according to the internal Stark effect. Spectral heterogeneity fits the rotamer model but does not preclude other contributing factors. Spectral moment analysis of full width Trp emission spectra is accessible to most laboratories. The calculations are informative of protein structure and can be adapted to study dynamic processes. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. Dynamics and heterogeneity of bovine hippocampal membranes: role of cholesterol and proteins.

    PubMed

    Mukherjee, Soumi; Kombrabail, Mamata; Krishnamoorthy, G; Chattopadhyay, Amitabha

    2007-09-01

    The structural and dynamic consequence of alterations in membrane lipid composition (specifically cholesterol) in neuronal membranes is poorly understood. Previous work from our laboratory has established bovine hippocampal membranes as a convenient natural source for studying neuronal receptors. In this paper, we have explored the role of cholesterol and proteins in the dynamics and heterogeneity of bovine hippocampal membranes using fluorescence lifetime distribution analysis of the environment-sensitive fluorescent probe Nile Red incorporated into such membranes by the maximum entropy method (MEM), and time-resolved fluorescence anisotropy measurements. The peak position and the width of the lifetime distribution of Nile Red show a progressive reduction with increasing cholesterol depletion from native hippocampal membranes indicating that the extent of heterogeneity decreases with decrease in membrane cholesterol content. This is accompanied by a concomitant decrease of the fluorescence anisotropy and rotational correlation time. Our results point out that the microenvironment experienced by Nile Red is relatively insensitive to the presence of proteins in hippocampal membranes. Interestingly, Nile Red lifetime distribution in liposomes of lipid extracts is similar to that of native membranes indicating that proteins do not contribute significantly to the high level of heterogeneity observed in native membranes. These results could be relevant in understanding the neuronal diseases characterized by defective membrane lipid metabolism.

  20. Heterogeneity of Zein mRNA and Protein in Maize 1

    PubMed Central

    Park, William D.; Lewis, Elizabeth D.; Rubenstein, Irwin

    1980-01-01

    Zein, the prolamine fraction of maize, is localized in the endosperm in membrane-bound structures called protein bodies, which have polyribosomes on their surfaces. These polysomes or the mRNA fraction isolated from them will direct the synthesis of zein-like proteins in vitro. The in vitro products consist primarily of two molecular weight classes but show considerable charge heterogeneity when analyzed by isoelectric focusing. Although the molecular weight classes are very similar for different inbred lines, the isoelectric focusing patterns differ. Results given here suggest that the extensive charge heterogeneity of zein proteins does not result from the presence of a large number of totally distinct mRNAs. Zein proteins synthesized in vitro fall into several families related by sequence homologies in their mRNAs. In Illinois High Protein (IHP) the major zein mRNAs can be classified into three families based on their binding to cloned complimentary DNA copies of IHP zein mRNA. Each of three other lines we have studied (W22, Oh43, and W64A) has zein mRNAs that are related to those of IHP. Among these four lines the molecular weights of the members of a given family are generally similar, but the number of members in a family and their isoelectric points differ. Images PMID:16661153

  1. Physical and Functional Interaction between Heterochromatin Protein 1α and the RNA-binding Protein Heterogeneous Nuclear Ribonucleoprotein U*

    PubMed Central

    Ameyar-Zazoua, Maya; Souidi, Mouloud; Fritsch, Lauriane; Robin, Philippe; Thomas, Audrey; Hamiche, Ali; Percipalle, Piergiorgio; Ait-Si-Ali, Slimane; Harel-Bellan, Annick

    2009-01-01

    By combining biochemical purification and mass spectrometry, we identified proteins associated with human heterochromatin protein 1α (HP1α) both in the nucleoplasm and in chromatin. Some of these are RNA-binding proteins, and among them is the protein heterogeneous nuclear ribonucleoprotein U (hnRNP U)/SAF-A, which is linked to chromatin organization and transcriptional regulation. Here, we demonstrate that hnRNP U is a bona fide HP1α-interacting molecule. More importantly, hnRNP U depletion reduces HP1α-dependent gene silencing and disturbs HP1α subcellular localization. Thus, our data demonstrate that hnRNP U is involved in HP1α function, shedding new light on the mode of action of HP1α and on the function of hnRNP U. PMID:19617346

  2. Molecular heterogeneity of arabinogalactan-protein from Coffea arabica instant coffee.

    PubMed

    Capek, P; Matulová, M; Navarini, L; Suggi-Liverani, F

    2013-08-01

    Arabinogalactan-protein complex (AGP), isolated from freeze-dried instant coffee powder of Coffea arabica beans, was subjected to ion-exchange chromatography. Stepwise elution with water and solutions of sodium chloride with increasing ionic strength afforded eight fractions (F1-F8). Chemical analyses have shown that compositions of individual conjugates varied in carbohydrate and protein contents, molecular mass and slightly in monosaccharide composition. Protein content was increasing by increasing ionic strength of the eluent and it was confirmed also by FT-IR spectra. NMR study has shown that carbohydrate moieties in individual ion exchange fractions differed in the degree of backbone and side chains branching. Performed study has confirmed a molecular heterogeneity of arabinogalactan-protein complex present in a commercial instant coffee.

  3. How Surface Heterogeneity Affects Protein Adsorption: Annealing of OTS Patterns and Albumin Adsorption Kinetics*

    PubMed Central

    Hodgkinson, Gerald N.; Hlady, Vladimir

    2009-01-01

    Fluorescence microscopy and intensity histogram analysis techniques were used to monitor spatially-resolved albumin adsorption kinetics to model heterogeneous surfaces on sub-μm scales. Several distinct protein subpopulations were resolved, each represented by a normal distribution of adsorption densities on the adsorbent surface. Histogram analyses provided dynamic information of mean adsorption density, spread in adsorption density, and surface area coverage for each distinct protein subpopulation. A simple adsorption model is proposed in which individual protein binding events are predicted by the summation of multiple protein's surface sub-site interactions with different binding energy sub-sites on adsorbent surfaces. This model is predictive of the albumin adsorption on the patterns produced by one step μ-contact printing (μCP) of octadecyltrichlorosilane (OTS) on glass but fails to describe adsorption once the same patterns are altered by a thermal annealing step. PMID:19746205

  4. Toward a quantitative description of microscopic pathway heterogeneity in protein folding.

    PubMed

    Gopi, Soundhararajan; Singh, Animesh; Suresh, Swaathiratna; Paul, Suvadip; Ranu, Sayan; Naganathan, Athi N

    2017-08-09

    How many structurally different microscopic routes are accessible to a protein molecule while folding? This has been a challenging question to address experimentally as single-molecule studies are constrained by the limited number of observed folding events while ensemble measurements, by definition, report only an average and not the distribution of the quantity under study. Atomistic simulations, on the other hand, are restricted by sampling and the inability to reproduce thermodynamic observables directly. We overcome these bottlenecks in the current work and provide a quantitative description of folding pathway heterogeneity by developing a comprehensive, scalable and yet experimentally consistent approach combining concepts from statistical mechanics, physical kinetics and graph theory. We quantify the folding pathway heterogeneity of five single-domain proteins under two thermodynamic conditions from an analysis of 100 000 folding events generated from a statistical mechanical model incorporating the detailed energetics from more than a million conformational states. The resulting microstate energetics predicts the results of protein engineering experiments, the thermodynamic stabilities of secondary-structure segments from NMR studies, and the end-to-end distance estimates from single-molecule force spectroscopy measurements. We find that a minimum of ∼3-200 microscopic routes, with a diverse ensemble of transition-path structures, are required to account for the total folding flux across the five proteins and the thermodynamic conditions. The partitioning of flux amongst the numerous pathways is shown to be subtly dependent on the experimental conditions that modulate protein stability, topological complexity and the structural resolution at which the folding events are observed. Our predictive methodology thus reveals the presence of rich ensembles of folding mechanisms that are generally invisible in experiments, reconciles the contradictory

  5. Heterogeneous nucleotide occupancy stimulates functionality of phage shock protein F, an AAA+ transcriptional activator.

    PubMed

    Joly, Nicolas; Schumacher, Jörg; Buck, Martin

    2006-11-17

    The catalytic AAA+ domain (PspF1-275) of an enhancer-binding protein is necessary and sufficient to contact sigma54-RNA polymerase holoenzyme (Esigma54), remodel it, and in so doing catalyze open promoter complex formation. Whether ATP binding and hydrolysis is coordinated between subunits of PspF and the precise nature of the nucleotide(s) bound to the oligomeric forms responsible for substrate remodeling are unknown. We demonstrate that ADP stimulates the intrinsic ATPase activity of PspF1-275 and propose that this heterogeneous nucleotide occupancy in a PspF1-275 hexamer is functionally important for specific activity. Binding of ADP and ATP triggers the formation of functional PspF1-275 hexamers as shown by a gain of specific activity. Furthermore, ATP concentrations congruent with stoichiometric ATP binding to PspF1-275 inhibit ATP hydrolysis and Esigma54-promoter open complex formation. Demonstration of a heterogeneous nucleotide-bound state of a functional PspF1-275.Esigma54 complex provides clear biochemical evidence for heterogeneous nucleotide occupancy in this AAA+ protein. Based on our data, we propose a stochastic nucleotide binding and a coordinated hydrolysis mechanism in PspF1-275 hexamers.

  6. Heterogeneous binding of the SH3 client protein to the DnaK molecular chaperone

    PubMed Central

    Lee, Jung Ho; Zhang, Dongyu; Hughes, Christopher; Okuno, Yusuke; Sekhar, Ashok; Cavagnero, Silvia

    2015-01-01

    The molecular chaperone heat shock protein 70 (Hsp70) plays a vital role in cellular processes, including protein folding and assembly, and helps prevent aggregation under physiological and stress-related conditions. Although the structural changes undergone by full-length client proteins upon interaction with DnaK (i.e., Escherichia coli Hsp70) are fundamental to understand chaperone-mediated protein folding, these changes are still largely unexplored. Here, we show that multiple conformations of the SRC homology 3 domain (SH3) client protein interact with the ADP-bound form of the DnaK chaperone. Chaperone-bound SH3 is largely unstructured yet distinct from the unfolded state in the absence of DnaK. The bound client protein shares a highly flexible N terminus and multiple slowly interconverting conformations in different parts of the sequence. In all, there is significant structural and dynamical heterogeneity in the DnaK-bound client protein, revealing that proteins may undergo some conformational sampling while chaperone-bound. This result is important because it shows that the surface of the Hsp70 chaperone provides an aggregation-free environment able to support part of the search for the native state. PMID:26195753

  7. Resolution of Disulfide Heterogeneity in Nogo Receptor 1 Fusion Proteins by Molecular Engineering

    SciTech Connect

    P Weinreb; D Wen; F Qian; C Wildes; E Garber; L Walus; M Jung; J Wang; J Relton; et al.

    2011-12-31

    NgRI (Nogo-66 receptor) is part of a signalling complex that inhibits axon regeneration in the central nervous system. Truncated soluble versions of NgRI have been used successfully to promote axon regeneration in animal models of spinal-cord injury, raising interest in this protein as a potential therapeutic target. The LRR (leucine-rich repeat) regions in NgRI are flanked by N- and C-terminal disulfide-containing 'cap' domains (LRRNT and LRRCT respectively). In the present work we show that, although functionally active, the NgRI(310)-Fc fusion protein contains mislinked and heterogeneous disulfide patterns in the LRRCT domain, and we report the generation of a series of variant molecules specifically designed to prevent this heterogeneity. Using these variants we explored the effects of modifying the NgRI truncation site or the spacing between the NgRI and Fc domains, or replacing cysteines within the NgRI or IgG hinge regions. One variant, which incorporates replacements of Cys{sup 266} and Cys{sup 309} with alanine residues, completely eliminated disulfide scrambling while maintaining functional in vitro and in vivo efficacy. This modified NgRI-Fc molecule represents a significantly improved candidate for further pharmaceutical development, and may serve as a useful model for the optimization of other IgG fusion proteins made from LRR proteins.

  8. The role of conformational heterogeneity in regulating the apoptotic activity of BAX protein.

    PubMed

    Kao, Te-Yu; Tsai, Chia-Jung; Lan, Yu-Jing; Chiang, Yun-Wei

    2017-04-05

    While activation of BAX is required for initiating mitochondria-mediated apoptosis, the underlying mechanisms remain unsettled. We studied conformations of BAX protein using pressure- and temperature-resolved ESR techniques and obtained the thermodynamic properties of the conformations. We show that inactive BAX is structurally heterogeneous and exists in equilibrium between two major populations of the conformations, UM and UM', of which the former is thermodynamically favored at room temperature. An increase in the population of UM', induced by either pressure or point mutations of BAX, renders BAX susceptible to oligomerization, which leads to cell death. This study uncovers the biological significance of BAX conformations and shows that the pro-apoptotic activity of BAX can be triggered by altering the equilibrium between the two states. It suggests that therapeutic intervention may focus on shifting the balance in the conformational heterogeneity.

  9. Proteins as templates for complex synthetic metalloclusters: towards biologically programmed heterogeneous catalysis.

    PubMed

    Fehl, Charlie; Davis, Benjamin G

    2016-05-01

    Despite nature's prevalent use of metals as prosthetics to adapt or enhance the behaviour of proteins, our ability to programme such architectural organization remains underdeveloped. Multi-metal clusters buried in proteins underpin the most remarkable chemical transformations in nature, but we are not yet in a position to fully mimic or exploit such systems. With the advent of copious, relevant structural information, judicious mechanistic studies and the use of accessible computational methods in protein design coupled with new synthetic methods for building biomacromolecules, we can envisage a 'new dawn' that will allow us to build de novo metalloenzymes that move beyond mono-metal centres. In particular, we highlight the need for systems that approach the multi-centred clusters that have evolved to couple electron shuttling with catalysis. Such hybrids may be viewed as exciting mid-points between homogeneous and heterogeneous catalysts which also exploit the primary benefits of biocatalysis.

  10. Proteins as templates for complex synthetic metalloclusters: towards biologically programmed heterogeneous catalysis

    PubMed Central

    Fehl, Charlie

    2016-01-01

    Despite nature’s prevalent use of metals as prosthetics to adapt or enhance the behaviour of proteins, our ability to programme such architectural organization remains underdeveloped. Multi-metal clusters buried in proteins underpin the most remarkable chemical transformations in nature, but we are not yet in a position to fully mimic or exploit such systems. With the advent of copious, relevant structural information, judicious mechanistic studies and the use of accessible computational methods in protein design coupled with new synthetic methods for building biomacromolecules, we can envisage a ‘new dawn’ that will allow us to build de novo metalloenzymes that move beyond mono-metal centres. In particular, we highlight the need for systems that approach the multi-centred clusters that have evolved to couple electron shuttling with catalysis. Such hybrids may be viewed as exciting mid-points between homogeneous and heterogeneous catalysts which also exploit the primary benefits of biocatalysis. PMID:27279776

  11. Impact of chemical heterogeneity on protein self-assembly in water.

    PubMed

    Chong, Song-Ho; Ham, Sihyun

    2012-05-15

    Hydrophobicity is thought to underlie self-assembly in biological systems. However, the protein surface comprises hydrophobic and hydrophilic patches, and understanding the impact of such a chemical heterogeneity on protein self-assembly in water is of fundamental interest. Here, we report structural and thermodynamic investigations on the dimer formation of full-length amyloid-β proteins in water associated with Alzheimer's disease. Spontaneous dimerization process--from the individual diffusive regime at large separations, through the approach stage in which two proteins come close to each other, to the structural adjustment stage toward compact dimer formation--was captured in full atomic detail via unguided, explicit-water molecular dynamics simulations. The integral-equation theory of liquids was then applied to simulated protein structures to analyze hydration thermodynamic properties and the water-mediated interaction between proteins. We demonstrate that hydrophilic residues play a key role in initiating the dimerization process. A long-range hydration force of enthalpic origin acting on the hydrophilic residues provides the major thermodynamic force that drives two proteins to approach from a large separation to a contact distance. After two proteins make atomic contacts, the nature of the water-mediated interaction switches from a long-range enthalpic attraction to a short-range entropic one. The latter acts both on the hydrophobic and hydrophilic residues. Along with the direct protein-protein interactions that lead to the formation of intermonomer hydrogen bonds and van der Waals contacts, the water-mediated attraction of entropic origin brings about structural adjustment of constituent monomer proteins toward the formation of a compact dimer structure.

  12. The heterogeneity of human antibody responses to vaccinia virus revealed through use of focused protein arrays

    PubMed Central

    Duke-Cohan, Jonathan S.; Wollenick, Kristin; Witten, Elizabeth A.; Seaman, Michael S.; Baden, Lindsey R.; Dolin, Raphael; Reinherz, Ellis L.

    2009-01-01

    The renewed interest in strategies to combat infectious agents with epidemic potential has led to a re-examination of vaccination protocols against smallpox. To help define which antigens elucidate a human antibody response, we have targeted proteins known or predicted to be presented on the surface of the intracellular mature virion (IMV) or the extracellular enveloped virion (EEV). The predicted ectodomains were expressed in a mammalian in vitro coupled transcription/translation reaction using tRNAlys precharged with lysine-ε-biotin followed by solid phase immobilization on 384 well neutravidin-coated plates. The generated array is highly specific and sensitive in a microELISA format. By comparison of binding of vaccinia-immune sera to the reticulocyte lysate-produced proteins and to secreted post-translationally-modified proteins, we demonstrate that for several proteins including the EEV proteins B5 and A33, proper recognition is dependent upon appropriate folding, with little dependence upon glycosylation per se. We further demonstrate that the humoral immune response to vaccinia among different individuals is not uniform in specificity or strength, as different IMV and EEV targets predominate within the group of immunogenic proteins. This heterogeneity likely results from the diversity of HLA Class II alleles and CD4 T helper cell epitopes stimulating B cell antibody production. Our findings have important implications both for design of new recombinant subunit vaccines as well as for methods of assaying the human antibody response utilizing recombinant proteins produced in vitro. PMID:19146908

  13. Quantitative Evaluation of Protein Heterogeneity within Herpes Simplex Virus 1 Particles.

    PubMed

    El Bilali, Nabil; Duron, Johanne; Gingras, Diane; Lippé, Roger

    2017-05-15

    Several virulence genes have been identified thus far in the herpes simplex virus 1 genome. It is also generally accepted that protein heterogeneity among virions further impacts viral fitness. However, linking this variability directly with infectivity has been challenging at the individual viral particle level. To address this issue, we resorted to flow cytometry (flow virometry), a powerful approach we recently employed to analyze individual viral particles, to identify which tegument proteins vary and directly address if such variability is biologically relevant. We found that the stoichiometry of the UL37, ICP0, and VP11/12 tegument proteins in virions is more stable than the VP16 and VP22 tegument proteins, which varied significantly among viral particles. Most interestingly, viruses sorted for their high VP16 or VP22 content yielded modest but reproducible increases in infectivity compared to their corresponding counterparts containing low VP16 or VP22 content. These findings were corroborated for VP16 in short interfering RNA experiments but proved intriguingly more complex for VP22. An analysis by quantitative Western blotting revealed substantial alterations of virion composition upon manipulation of individual tegument proteins and suggests that VP22 protein levels acted indirectly on viral fitness. These findings reaffirm the interdependence of the virion components and corroborate that viral fitness is influenced not only by the genome of viruses but also by the stoichiometry of proteins within each virion.IMPORTANCE The ability of viruses to spread in animals has been mapped to several viral genes, but other factors are clearly involved, including virion heterogeneity. To directly probe whether the latter influences viral fitness, we analyzed the protein content of individual herpes simplex virus 1 particles using an innovative flow cytometry approach. The data confirm that some viral proteins are incorporated in more controlled amounts, while others

  14. Multiscale conformational heterogeneity in staphylococcal protein a: possible determinant of functional plasticity.

    PubMed

    Deis, Lindsay N; Pemble, Charles W; Qi, Yang; Hagarman, Andrew; Richardson, David C; Richardson, Jane S; Oas, Terrence G

    2014-10-07

    The Staphylococcus aureus virulence factor staphylococcal protein A (SpA) is a major contributor to bacterial evasion of the host immune system, through high-affinity binding to host proteins such as antibodies. SpA includes five small three-helix-bundle domains (E-D-A-B-C) separated by conserved flexible linkers. Prior attempts to crystallize individual domains in the absence of a binding partner have apparently been unsuccessful. There have also been no previous structures of tandem domains. Here we report the high-resolution crystal structures of a single C domain, and of two B domains connected by the conserved linker. Both structures exhibit extensive multiscale conformational heterogeneity, which required novel modeling protocols. Comparison of domain structures shows that helix1 orientation is especially heterogeneous, coordinated with changes in side chain conformational networks and contacting protein interfaces. This represents the kind of structural plasticity that could enable SpA to bind multiple partners.

  15. Molecular heterogeneity of TIME-EA4, a timer protein in silkworm diapause eggs.

    PubMed

    Pitchayawasin-Thapphasaraphong, Suthasinee; Tani, Naoki; Isobe, Minoru; Kai, Hidenori; Kurahashi, Takuya; Kato, Junko; Trisunan, Saikwan

    2009-07-01

    TIME-EA4 is an ATPase that measures time intervals as a diapause-duration clock found in diapause eggs of the silkworm, Bombyx mori. In the current studies, we report the molecular heterogeneity of TIME-EA4 protein regarding not only amino acid L62V, but also the numbers and linkage patterns of the sugar chain attached to the Asn(22) residue. These sugar chain structures were determined in a pico-molar amount of the protein by combining the methods of chemical modification (Smith degradation) and nano-HPLC-electrospray ionization-quadrupole-time of fight-mass spectrometry (ESI-Q-TOF-MS) and -MS/MS. The Japanese and bi-voltine Thai silkworm strains were compared to show the heterogeneity represented by four kinds of molecular species. Judicious choice of the combination methods led us to find the first example of a linkage-position difference in the glycosidic bonds even in sugar moieties of the same molecular weight; thus, the Man(1-6)Man(1-4)GlcNAc(1-4)GlcNAc structure in the C108 pure strain and Man(1-3)Man(1-4)GlcNAc(1-4)GlcNAc structure in the Kinshu-Showa hybrid. A total of five kinds of molecular heterogeneity was determined, including the amino acids in TIME-EA4 protein. This paper describes the details for determining the sugar chain linkage in TIME-EA4 from the diapause eggs of various silkworm strains.

  16. Impact of chemical heterogeneity on protein self-assembly in water

    PubMed Central

    Chong, Song-Ho; Ham, Sihyun

    2012-01-01

    Hydrophobicity is thought to underlie self-assembly in biological systems. However, the protein surface comprises hydrophobic and hydrophilic patches, and understanding the impact of such a chemical heterogeneity on protein self-assembly in water is of fundamental interest. Here, we report structural and thermodynamic investigations on the dimer formation of full-length amyloid-β proteins in water associated with Alzheimer’s disease. Spontaneous dimerization process—from the individual diffusive regime at large separations, through the approach stage in which two proteins come close to each other, to the structural adjustment stage toward compact dimer formation—was captured in full atomic detail via unguided, explicit-water molecular dynamics simulations. The integral-equation theory of liquids was then applied to simulated protein structures to analyze hydration thermodynamic properties and the water-mediated interaction between proteins. We demonstrate that hydrophilic residues play a key role in initiating the dimerization process. A long-range hydration force of enthalpic origin acting on the hydrophilic residues provides the major thermodynamic force that drives two proteins to approach from a large separation to a contact distance. After two proteins make atomic contacts, the nature of the water-mediated interaction switches from a long-range enthalpic attraction to a short-range entropic one. The latter acts both on the hydrophobic and hydrophilic residues. Along with the direct protein–protein interactions that lead to the formation of intermonomer hydrogen bonds and van der Waals contacts, the water-mediated attraction of entropic origin brings about structural adjustment of constituent monomer proteins toward the formation of a compact dimer structure. PMID:22538814

  17. Heterogeneity of the Abnormal Prion Protein (PrPSc) of the Chandler Scrapie Strain

    PubMed Central

    Kasai, Kazuo; Iwamaru, Yoshifumi; Masujin, Kentaro; Imamura, Morikazu; Mohri, Shirou; Yokoyama, Takashi

    2013-01-01

    The pathological prion protein, PrPSc, displays various sizes of aggregates. In this study, we investigated the conformation, aggregation stability and proteinase K (PK)-sensitivity of small and large PrPSc aggregates of mouse-adapted prion strains. We showed that small PrPSc aggregates, previously thought to be PK-sensitive, are resistant to PK digestion. Furthermore, we showed that small PrPSc aggregates of the Chandler scrapie strain have greater resistance to PK digestion and aggregation-denaturation than large PrPSc aggregates of this strain. We conclude that this strain consists of heterogeneous PrPSc. PMID:25436883

  18. Matricellular protein SPARCL1 regulates tumor microenvironment–dependent endothelial cell heterogeneity in colorectal carcinoma

    PubMed Central

    Liebl, Andrea; Schellerer, Vera S.; Schütz, Manuela; Kölbel, Patrick; Schaal, Ute; Haep, Lisa; Regensburger, Daniela; Wittmann, Thomas; Klein-Hitpass, Ludger; Rau, Tilman T.; Dietel, Barbara; Méniel, Valérie S.; Clarke, Alan R.; Croner, Roland S.; Hohenberger, Werner

    2016-01-01

    Different tumor microenvironments (TMEs) induce stromal cell plasticity that affects tumorigenesis. The impact of TME-dependent heterogeneity of tumor endothelial cells (TECs) on tumorigenesis is unclear. Here, we isolated pure TECs from human colorectal carcinomas (CRCs) that exhibited TMEs with either improved (Th1-TME CRCs) or worse clinical prognosis (control-TME CRCs). Transcriptome analyses identified markedly different gene clusters that reflected the tumorigenic and angiogenic activities of the respective TMEs. The gene encoding the matricellular protein SPARCL1 was most strongly upregulated in Th1-TME TECs. It was also highly expressed in ECs in healthy colon tissues and Th1-TME CRCs but low in control-TME CRCs. In vitro, SPARCL1 expression was induced in confluent, quiescent ECs and functionally contributed to EC quiescence by inhibiting proliferation, migration, and sprouting, whereas siRNA-mediated knockdown increased sprouting. In human CRC tissues and mouse models, vessels with SPARCL1 expression were larger and more densely covered by mural cells. SPARCL1 secretion from quiescent ECs inhibited mural cell migration, which likely led to stabilized mural cell coverage of mature vessels. Together, these findings demonstrate TME-dependent intertumoral TEC heterogeneity in CRC. They further indicate that TEC heterogeneity is regulated by SPARCL1, which promotes the cell quiescence and vessel homeostasis contributing to the favorable prognoses associated with Th1-TME CRCs. PMID:27721236

  19. Heterogeneous expression of protein and mRNA in pyruvate dehydrogenase deficiency.

    PubMed Central

    Wexler, I D; Kerr, D S; Ho, L; Lusk, M M; Pepin, R A; Javed, A A; Mole, J E; Jesse, B W; Thekkumkara, T J; Pons, G

    1988-01-01

    Deficiency of pyruvate dehydrogenase [pyruvate:lipoamide 2-oxidoreductase (decarboxylating and acceptor-acetylating), EC 1.2.4.1], the first component of the pyruvate dehydrogenase complex, is associated with lactic acidosis and central nervous system dysfunction. Using both specific antibodies to pyruvate dehydrogenase and cDNAs coding for its two alpha and beta subunits, we characterized pyruvate dehydrogenase deficiency in 11 patients. Three different patterns were found on immunologic and RNA blot analyses. (i) Seven patients had immunologically detectable crossreactive material for the alpha and beta proteins of pyruvate dehydrogenase. (ii) Two patients had no detectable crossreactive protein for either the alpha or beta subunit but had normal amounts of mRNA for both alpha and beta subunits. (iii) The remaining two patients also had no detectable crossreactive protein but had diminished amounts of mRNA for the alpha subunit of pyruvate dehydrogenase only. These results indicate that loss of pyruvate dehydrogenase activity may be associated with either absent or catalytically inactive proteins, and in those cases in which this enzyme is absent, mRNA for one of the subunits may also be missing. When mRNA for one of the subunits is lacking, both protein subunits are absent, suggesting that a mutation affecting the expression of one of the subunit proteins causes the remaining uncomplexed subunit to be unstable. The results show that several different mutations account for the molecular heterogeneity of pyruvate dehydrogenase deficiency. Images PMID:3140238

  20. Cytoplasmic sequestration of FUS/TLS associated with ALS alters histone marks through loss of nuclear protein arginine methyltransferase 1.

    PubMed

    Tibshirani, Michael; Tradewell, Miranda L; Mattina, Katie R; Minotti, Sandra; Yang, Wencheng; Zhou, Hongru; Strong, Michael J; Hayward, Lawrence J; Durham, Heather D

    2015-02-01

    Mutations in the RNA-binding protein FUS/TLS (FUS) have been linked to the neurodegenerative disease amyotrophic lateral sclerosis (ALS). Although predominantly nuclear, this heterogenous nuclear ribonuclear protein (hnRNP) has multiple functions in RNA processing including intracellular trafficking. In ALS, mutant or wild-type (WT) FUS can form neuronal cytoplasmic inclusions. Asymmetric arginine methylation of FUS by the class 1 arginine methyltransferase, protein arginine methyltransferase 1 (PRMT1), regulates nucleocytoplasmic shuttling of FUS. In motor neurons of primary spinal cord cultures, redistribution of endogenous mouse and that of ectopically expressed WT or mutant human FUS to the cytoplasm led to nuclear depletion of PRMT1, abrogating methylation of its nuclear substrates. Specifically, hypomethylation of arginine 3 of histone 4 resulted in decreased acetylation of lysine 9/14 of histone 3 and transcriptional repression. Distribution of neuronal PRMT1 coincident with FUS also was detected in vivo in the spinal cord of FUS(R495X) transgenic mice. However, nuclear PRMT1 was not stable postmortem obviating meaningful evaluation of ALS autopsy cases. This study provides evidence for loss of PRMT1 function as a consequence of cytoplasmic accumulation of FUS in the pathogenesis of ALS, including changes in the histone code regulating gene transcription.

  1. Cytoplasmic sequestration of FUS/TLS associated with ALS alters histone marks through loss of nuclear protein arginine methyltransferase 1

    PubMed Central

    Tibshirani, Michael; Tradewell, Miranda L.; Mattina, Katie R.; Minotti, Sandra; Yang, Wencheng; Zhou, Hongru; Strong, Michael J.; Hayward, Lawrence J.; Durham, Heather D.

    2015-01-01

    Mutations in the RNA-binding protein FUS/TLS (FUS) have been linked to the neurodegenerative disease amyotrophic lateral sclerosis (ALS). Although predominantly nuclear, this heterogenous nuclear ribonuclear protein (hnRNP) has multiple functions in RNA processing including intracellular trafficking. In ALS, mutant or wild-type (WT) FUS can form neuronal cytoplasmic inclusions. Asymmetric arginine methylation of FUS by the class 1 arginine methyltransferase, protein arginine methyltransferase 1 (PRMT1), regulates nucleocytoplasmic shuttling of FUS. In motor neurons of primary spinal cord cultures, redistribution of endogenous mouse and that of ectopically expressed WT or mutant human FUS to the cytoplasm led to nuclear depletion of PRMT1, abrogating methylation of its nuclear substrates. Specifically, hypomethylation of arginine 3 of histone 4 resulted in decreased acetylation of lysine 9/14 of histone 3 and transcriptional repression. Distribution of neuronal PRMT1 coincident with FUS also was detected in vivo in the spinal cord of FUSR495X transgenic mice. However, nuclear PRMT1 was not stable postmortem obviating meaningful evaluation of ALS autopsy cases. This study provides evidence for loss of PRMT1 function as a consequence of cytoplasmic accumulation of FUS in the pathogenesis of ALS, including changes in the histone code regulating gene transcription. PMID:25274782

  2. MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers.

    PubMed

    Ohue, Masahito; Shimoda, Takehiro; Suzuki, Shuji; Matsuzaki, Yuri; Ishida, Takashi; Akiyama, Yutaka

    2014-11-15

    The application of protein-protein docking in large-scale interactome analysis is a major challenge in structural bioinformatics and requires huge computing resources. In this work, we present MEGADOCK 4.0, an FFT-based docking software that makes extensive use of recent heterogeneous supercomputers and shows powerful, scalable performance of >97% strong scaling. MEGADOCK 4.0 is written in C++ with OpenMPI and NVIDIA CUDA 5.0 (or later) and is freely available to all academic and non-profit users at: http://www.bi.cs.titech.ac.jp/megadock. akiyama@cs.titech.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

  3. Mutational definition of RNA-binding and protein-protein interaction domains of heterogeneous nuclear RNP C1.

    PubMed

    Wan, L; Kim, J K; Pollard, V W; Dreyfuss, G

    2001-03-09

    The heterogeneous nuclear ribonucleoprotein (hn- RNP) C proteins, among the most abundant pre-mRNA-binding proteins in the eukaryotic nucleus, have a single RNP motif RNA-binding domain. The RNA-binding domain (RBD) is comprised of approximately 80-100 amino acids, and its structure has been determined. However, relatively little is known about the role of specific amino acids of the RBD in the binding to RNA. We have devised a phage display-based screening method for the rapid identification of amino acids in hnRNP C1 that are essential for its binding to RNA. The identified mutants were further tested for binding to poly(U)-Sepharose, a substrate to which wild type hnRNP C1 binds with high affinity. We found both previously predicted, highly conserved residues as well as additional residues in the RBD to be essential for C1 RNA binding. We also identified three mutations in the leucine-rich C1-C1 interaction domain near the carboxyl terminus of the protein that both abolished C1 oligomerization and reduced RNA binding. These results demonstrate that although the RBD is the primary determinant of C1 RNA binding, residues in the C1-C1 interaction domain also influence the RNA binding activity of the protein. The experimental approach we described should be generally applicable for the screening and identification of amino acids that play a role in the binding of proteins to nucleic acid substrates.

  4. Ligand heterogeneity of the cysteine protease binding protein family in the parasitic protist Entamoeba histolytica.

    PubMed

    Marumo, Konomi; Nakada-Tsukui, Kumiko; Tomii, Kentaro; Nozaki, Tomoyoshi

    2014-08-01

    Lysosomal soluble proteins are targeted to endosomes and lysosomes by specific receptors resident in the endoplasmic reticulum and/or the Golgi apparatus. The enteric protozoan parasite Entamoeba histolytica has a novel class of lysosomal targeting receptors, named the cysteine protease binding protein family (CPBF). Among 11 CPBFs (CPBF1-11), ligands for three members, CPBF1, CPBF6 and CPBF8, were previously shown to be cysteine proteases, α- and γ- amylases, and β-hexosaminidase and lysozymes, respectively. To further understand the heterogeneity of the ligands of CPBFs, we attempted to isolate and identify the ligands for other members of CPBFs, namely CPBF2, 3, 4, 5, 7, 9, 10 and 11, by immunoprecipitation and mass spectrometric analysis. We found that CPBF2 and CPBF10 bound to α-amylases while CPBF7 bound to β-hexosaminidases. It is intriguing that cysteine protease are exclusively recognised by CPBF1, whereas three α-amylases and β-hexosaminidases are redundantly recognised by three and two CPBFs, respectively. It was shown by bioinformatics analysis and phylogenetic reconstruction that each CPBF contains six prepeptidase carboxyl-terminal domains, and the domain configuration is evolutionarily conserved among CPBFs. Taken together, CPBFs with unique and conserved domain organisation have a remarkable ligand heterogeneity toward cysteine protease and carbohydrate degradation enzymes. Further structural studies are needed to elucidate the structural basis of the ligand specificity.

  5. Heterogeneity of normal prion protein in two- dimensional immunoblot: presence of various glycosylated and truncated forms.

    PubMed

    Pan, Tao; Li, Ruliang; Wong, Boon-Seng; Liu, Tong; Gambetti, Pierluigi; Sy, Man-Sun

    2002-06-01

    The common use of one-dimensional (1-D) immunoblot with a single monoclonal antibody (Mab) engenders the notion that the normal or cellular prion protein (PrP(C) ) comprises few and simple forms. In this study we used two-dimensional (2-D) immunoblot with a panel Mabs to various regions of the prion protein to demonstrate the complexity of the PrP(C) present in human brain. We distinguished over 50 immunoblot spots, each representing a distinct PrP(C) species based on combinations of different molecular weights and isoelectric points (pIs). The PrP(C) heterogeneity is due to the presence of a full-length and two major truncated forms as well as to the diversity of the glycans linked to most of these forms. The two major truncated forms result from distinct cleavage sites located at the N-terminus. In addition, enzymatic removal of sialic acid and lectin binding studies indicate that the glycans linked to the full-length and truncated PrP(C) forms differ in their structure and ratios of the glycoforms. The truncation of PrP(C) and the heterogeneity of the linked glycans may play a role in regulating PrP(C) function. Furthermore, the presence of relatively large quantities of different PrP(C) species may provide additional mechanisms by which the diversity of prion strains could be generated.

  6. Improved Success of Sparse Matrix Protein Crystallization Screening with Heterogeneous Nucleating Agents

    PubMed Central

    Thakur, Anil S.; Robin, Gautier; Guncar, Gregor; Saunders, Neil F. W.; Newman, Janet; Martin, Jennifer L.; Kobe, Bostjan

    2007-01-01

    Background Crystallization is a major bottleneck in the process of macromolecular structure determination by X-ray crystallography. Successful crystallization requires the formation of nuclei and their subsequent growth to crystals of suitable size. Crystal growth generally occurs spontaneously in a supersaturated solution as a result of homogenous nucleation. However, in a typical sparse matrix screening experiment, precipitant and protein concentration are not sampled extensively, and supersaturation conditions suitable for nucleation are often missed. Methodology/Principal Findings We tested the effect of nine potential heterogenous nucleating agents on crystallization of ten test proteins in a sparse matrix screen. Several nucleating agents induced crystal formation under conditions where no crystallization occurred in the absence of the nucleating agent. Four nucleating agents: dried seaweed; horse hair; cellulose and hydroxyapatite, had a considerable overall positive effect on crystallization success. This effect was further enhanced when these nucleating agents were used in combination with each other. Conclusions/Significance Our results suggest that the addition of heterogeneous nucleating agents increases the chances of crystal formation when using sparse matrix screens. PMID:17971854

  7. Surface heterogeneity: a friend or foe of protein adsorption - insights from theoretical simulations.

    PubMed

    Penna, Matthew; Ley, Kamron; Maclaughlin, Shane; Yarovsky, Irene

    2016-10-06

    A lack in the detailed understanding of mechanisms through which proteins adsorb or are repelled at various solid/liquid interfaces limits the capacity to rationally design and produce more sophisticated surfaces with controlled protein adsorption in both biomedical and industrial settings. To date there are three main approaches to achieve anti biofouling efficacy, namely chemically adjusting the surface hydrophobicity and introducing various degrees of surface roughness, or a combination of both. More recently, surface nanostructuring has been shown to have an effect on protein adsorption. However, the current resolution of experimental techniques makes it difficult to investigate these three phase systems at the molecular level. In this molecular dynamics study we explore in all-atom detail the adsorption process of one of the most surface active proteins, EAS hydrophobin, known for its versatile ability to self-assemble on both hydrophobic and hydrophilic surfaces forming stable monolayers that facilitate further biofilm growth. We model the adsorption of this protein on organic ligand protected silica surfaces with varying degrees of chemical heterogeneity and roughness, including fully homogenous hydrophobic and hydrophilic surfaces for comparison. We present a detailed characterisation of the functionalised surface structure and dynamics for each of these systems, and the effect the ligands have on interfacial water, the adsorption process and conformational rearrangements of the protein. Results suggest that the ligand arrangement that produces the highest hydrophilic chain mobility and the lack of significant hydrophobic patches shows the most promising anti-fouling efficacy toward hydrophobin. However, the presence on the protein surface of a flexible loop with amphipathic character (the Cys3-Cys4 loop) is seen to facilitate EAS adsorption on all surfaces by enabling the protein to match the surface pattern.

  8. Protein Kinase C-{delta} mediates down-regulation of heterogeneous nuclear ribonucleoprotein K protein: involvement in apoptosis induction

    SciTech Connect

    Gao, Feng-Hou; Wu, Ying-Li; Zhao, Meng; Chen, Guo-Qiang

    2009-11-15

    We reported previously that NSC606985, a camptothecin analogue, induces apoptosis of acute myeloid leukemia (AML) cells through proteolytic activation of protein kinase C delta ({Delta}PKC-{delta}). By subcellular proteome analysis, heterogeneous nuclear ribonucleoprotein K (hnRNP K) was identified as being significantly down-regulated in NSC606985-treated leukemic NB4 cells. HnRNP K, a docking protein for DNA, RNA, and transcriptional or translational molecules, is implicated in a host of processes involving the regulation of gene expression. However, the molecular mechanisms of hnRNP K reduction and its roles during apoptosis are still not understood. In the present study, we found that, following the appearance of the {Delta}PKC-{delta}, hnRNP K protein was significantly down-regulated in NSC606985, doxorubicin, arsenic trioxide and ultraviolet-induced apoptosis. We further provided evidence that {Delta}PKC-{delta} mediated the down-regulation of hnRNP K protein during apoptosis: PKC-{delta} inhibitor could rescue the reduction of hnRNP K; hnRNP K failed to be decreased in PKC-{delta}-deficient apoptotic KG1a cells; conditional induction of {Delta}PKC-{delta} in U937T cells directly down-regulated hnRNP K protein. Moreover, the proteasome inhibitor also inhibited the down-regulation of hnRNP K protein by apoptosis inducer and the conditional expression of {Delta}PKC-{delta}. More intriguingly, the suppression of hnRNP K with siRNA transfection significantly induced apoptosis. To our knowledge, this is the first demonstration that proteolytically activated PKC-{delta} down-regulates hnRNP K protein in a proteasome-dependent manner, which plays an important role in apoptosis induction.

  9. Functional Heterogeneity of the UpaH Autotransporter Protein from Uropathogenic Escherichia coli

    PubMed Central

    Allsopp, Luke P.; Beloin, Christophe; Moriel, Danilo Gomes; Totsika, Makrina; Ghigo, Jean-Marc

    2012-01-01

    Uropathogenic Escherichia coli (UPEC) is responsible for the majority of urinary tract infections (UTI). To cause a UTI, UPEC must adhere to the epithelial cells of the urinary tract and overcome the shear flow forces of urine. This function is mediated primarily by fimbrial adhesins, which mediate specific attachment to host cell receptors. Another group of adhesins that contributes to UPEC-mediated UTI is autotransporter (AT) proteins. AT proteins possess a range of virulence properties, such as adherence, aggregation, invasion, and biofilm formation. One recently characterized AT protein of UPEC is UpaH, a large adhesin-involved-in-diffuse-adherence (AIDA-I)-type AT protein that contributes to biofilm formation and bladder colonization. In this study we characterized a series of naturally occurring variants of UpaH. We demonstrate that extensive sequence variation exists within the passenger-encoding domain of UpaH variants from different UPEC strains. This sequence variation is associated with functional heterogeneity with respect to the ability of UpaH to mediate biofilm formation. In contrast, all of the UpaH variants examined retained a conserved ability to mediate binding to extracellular matrix (ECM) proteins. Bioinformatic analysis of the UpaH passenger domain identified a conserved region (UpaHCR) and a hydrophobic region (UpaHHR). Deletion of these domains reduced biofilm formation but not the binding to ECM proteins. Despite variation in the upaH sequence, the transcription of upaH was repressed by a conserved mechanism involving the global regulator H-NS, and mutation of the hns gene relieved this repression. Overall, our findings shed new light on the regulation and functions of the UpaH AT protein. PMID:22904291

  10. Carbon-deuterium bonds as non-perturbative infrared probes of protein dynamics, electrostatics, heterogeneity, and folding.

    PubMed

    Zimmermann, Jörg; Romesberg, Floyd E

    2014-01-01

    Vibrational spectroscopy is uniquely able to characterize protein dynamics and microenvironmental heterogeneity because it possesses an inherently high temporal resolution and employs probes of ultimately high structural resolution-the bonds themselves. The use of carbon-deuterium (C-D) bonds as vibrational labels circumvents the spectral congestion that otherwise precludes the use of vibrational spectroscopy to proteins and makes the observation of single vibrations within a protein possible while being wholly non-perturbative. Thus, C-D probes can be used to site-specifically characterize conformational heterogeneity and thermodynamic stability. C-D probes are also uniquely useful in characterizing the electrostatic microenvironment experienced by a specific residue side chain or backbone due to its effect on the C-D absorption frequency. In this chapter we describe the experimental procedures required to use C-D bonds and FT IR spectroscopy to characterize protein dynamics, structural and electrostatic heterogeneity, ligand binding, and folding.

  11. Heterogeneous nuclear ribonucleoprotein B1 protein impairs DNA repair mediated through the inhibition of DNA-dependent protein kinase activity

    SciTech Connect

    Iwanaga, Kentaro; Sueoka, Naoko; Sato, Akemi; Hayashi, Shinichiro; Sueoka, Eisaburo . E-mail: sueokae@post.saga-med.ac.jp

    2005-08-05

    Heterogeneous nuclear ribonucleoprotein B1, an RNA binding protein, is overexpressed from the early stage of lung cancers; it is evident even in bronchial dysplasia, a premalignant lesion. We evaluated the proteins bound with hnRNP B1 and found that hnRNP B1 interacted with DNA-dependent protein kinase (DNA-PK) complex, and recombinant hnRNP B1 protein dose-dependently inhibited DNA-PK activity in vitro. To test the effect of hnRNP B1 on DNA repair, we performed comet assay after irradiation, using normal human bronchial epithelial (HBE) cells treated with siRNA for hnRNP A2/B1: reduction of hnRNP B1 treated with siRNA for hnRNP A2/B1 induced faster DNA repair in normal HBE cells. Considering these results, we assume that overexpression of hnRNP B1 occurring in the early stage of carcinogenesis inhibits DNA-PK activity, resulting in subsequent accumulation of erroneous rejoining of DNA double-strand breaks, causing tumor progression.

  12. Protein and gene expression characteristics of heterogeneous nuclear ribonucleoprotein H1 in esophageal squamous cell carcinoma

    PubMed Central

    Sun, Yu-Lin; Liu, Fei; Liu, Fang; Zhao, Xiao-Hang

    2016-01-01

    AIM To investigate the expression characteristics of heterogeneous nuclear ribonucleoprotein H1 (HNRNPH1) mRNA and protein in cell lines and tissues of esophageal squamous cell carcinoma (ESCC). METHODS Western blotting was used to assess the expression of HNRNPH1 protein in seven ESCC cell lines and 30 paired fresh tissue specimens. The subcellular localization of HNRNPH1 was determined by immunofluorescence in ESCC cells. The RNA sequencing data from 87 patients with ESCC were obtained from the cancer genome atlas (TCGA), and the expression and clinical characteristics analysis of different transcript variants of HNRNPH1 were evaluated in this dataset. In addition, immunohistochemistry was carried out to detect the expression of HNRNPH1 protein in 125 patients. RESULTS The expression of HNRNPH1 protein varied across different ESCC cell lines. It was exclusively restricted to the nucleus of the ESCC cells. There are two transcript variants of the HNRNPH1 gene. Variant 1 was constitutively expressed, and its expression did not change during tumorigenesis. In contrast, levels of variant 2 were low in non-tumorous tissues and were dramatically increased in ESCC (P = 0.0026). The high levels of variant 2 were associated with poorer differentiated tumors (P = 0.0287). Furthermore, in paired fresh tissue specimens, HNRNPH1 protein was overexpressed in 73.3% (22/30) of neoplastic tissues. HNRNPH1 was significantly upregulated in ESCC, with strong staining in 43.2% (54/125) of tumor tissues and 22.4% (28/125) of matched non-cancerous tissues (P = 0.0005). Positive HNRNPH1 expression was significantly associated with poor tumor differentiation degree (P = 0.0337). CONCLUSION The different alternative transcript variants of HNRNPH1 exhibited different expression changes during tumorigenesis. Its mRNA and protein were overexpressed in ESCC and associated with poorer differentiation of tumor cells. These findings highlight the potential of HNRNPH1 in the therapy and diagnosis

  13. Heterogeneous Expression of the Core Circadian Clock Proteins among Neuronal Cell Types in Mouse Retina

    PubMed Central

    Liu, Xiaoqin; Zhang, Zhijing; Ribelayga, Christophe P.

    2012-01-01

    Circadian rhythms in metabolism, physiology, and behavior originate from cell-autonomous circadian clocks located in many organs and structures throughout the body and that share a common molecular mechanism based on the clock genes and their protein products. In the mammalian neural retina, despite evidence supporting the presence of several circadian clocks regulating many facets of retinal physiology and function, the exact cellular location and genetic signature of the retinal clock cells remain largely unknown. Here we examined the expression of the core circadian clock proteins CLOCK, BMAL1, NPAS2, PERIOD 1(PER1), PERIOD 2 (PER2), and CRYPTOCHROME2 (CRY2) in identified neurons of the mouse retina during daily and circadian cycles. We found concurrent clock protein expression in most retinal neurons, including cone photoreceptors, dopaminergic amacrine cells, and melanopsin-expressing intrinsically photosensitive ganglion cells. Remarkably, diurnal and circadian rhythms of expression of all clock proteins were observed in the cones whereas only CRY2 expression was found to be rhythmic in the dopaminergic amacrine cells. Only a low level of expression of the clock proteins was detected in the rods at any time of the daily or circadian cycle. Our observations provide evidence that cones and not rods are cell-autonomous circadian clocks and reveal an important disparity in the expression of the core clock components among neuronal cell types. We propose that the overall temporal architecture of the mammalian retina does not result from the synchronous activity of pervasive identical clocks but rather reflects the cellular and regional heterogeneity in clock function within retinal tissue. PMID:23189207

  14. Molecular heterogeneity in deficiency of complement protein C2 type I.

    PubMed Central

    Wang, X; Circolo, A; Lokki, M L; Shackelford, P G; Wetsel, R A; Colten, H R

    1998-01-01

    Deficiency of the complement protein C2 (C2D), one of the most common genetic deficiencies of the complement system, is associated with rheumatological disorders and increased susceptibility to infection. Two types of C2D have been recognized, each in the context of specific major histocompatibility complex (MHC) haplotypes; type I, a deletion, frameshift and premature stop codon resulting in absence of detectable C2 protein synthesis, and type II, missense mutations resulting in a block in secretion of C2 proteins. Analysis of C2 expression in a child with C2 deficiency, a MHC haplotype different from those associated with type I or II C2D, and recurrent infections revealed additional molecular heterogeneity among C2 deficient patients. No detectable C2 protein was synthesized in the child's fibroblasts under conditions supporting C2 synthesis and secretion in normals and the child's C2 mRNA was reduced to 42% of normal. Nucleotide sequencing of RT-PCR fibroblast mRNA and genomic DNA revealed a type I C2 deficiency (28 base-pair deletion) on one allele and a previously unrecognized two base-pair deletion in exon 2 on the other. Expression of the closely linked factor B gene was markedly decreased (Bf mRNA 25% of normal), though Bf was up-regulated appropriately by interferon-gamma and the flanking sequence containing the Bf promoter was normal in this C2-deficient patient. Moreover, the concentration of Bf protein was normal in the patient's plasma. Images Figure 2 Figure 3 Figure 4 Figure 5 PMID:9616367

  15. Prediction of protein-protein interactions by label propagation with protein evolutionary and chemical information derived from heterogeneous network.

    PubMed

    Wen, Yu-Ting; Lei, Hai-Jun; You, Zhu-Hong; Lei, Bai-Ying; Chen, Xing; Li, Li-Ping

    2017-10-07

    Prediction of protein-protein interactions (PPIs) is of great significance. To achieve this, we propose a novel computational method for PPIs prediction based on a similarity network fusion (SNF) model for integrating the physical and chemical properties of proteins. Specifically, the physical and chemical properties of protein are the protein amino acid mutation rate and its hydrophobicity, respectively. The amino acid mutation rate is extracted using a BLOSUM62 matrix, which puts the protein sequence into block substitution matrix. The SNF model is exploited to fuse protein physical and chemical features of multiple data by iteratively updating each original network. Finally, the complementary features from the fused network are fed into a label propagation algorithm (LPA) for PPIs prediction. The experimental results show that the proposed method achieves promising performance and outperforms the traditional methods for the public dataset of H. pylori, Human, and Yeast. In addition, our proposed method achieves average accuracy of 76.65%, 81.98%, 84.56%, 84.01% and 84.38% on E. coli, C. elegans, H. sapien, H. pylori and M. musculus datasets, respectively. Comparison results demonstrate that the proposed method is very promising and provides a cost-effective alternative for predicting PPIs. The source code and all datasets are available at http://pan.baidu.com/s/1dF7rp7N. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Regional heterogeneity of cellular prion protein isoforms in the mouse brain.

    PubMed

    Beringue, Vincent; Mallinson, Gary; Kaisar, Maria; Tayebi, Mourad; Sattar, Zahid; Jackson, Graham; Anstee, David; Collinge, John; Hawke, Simon

    2003-09-01

    Prion diseases are a group of invariably fatal neurodegenerative disorders that include Creutzfeldt-Jakob disease in humans, scrapie in sheep and goats, and bovine spongiform encephalopathy in cattle. The infectious agent or prion is largely composed of an abnormal isoform (PrPSc) of a host encoded normal cellular protein (PrPc). The conversion of PrPc to PrPSc is a dynamic process and, for reasons that are not clear, the distribution of spongiform change and PrPSc deposition varies among prion strains. An obvious explanation for this would be that the transformation efficiency in any given brain region depends on favourable interactions between conformations of PrPc and the prion strain being propagated within it. However, identification of specific PrPc conformations has until now been hampered by a lack of suitable panels of antibodies that discriminate PrPc subspecies under native conditions. In this study, we show that monoclonal antibodies raised against recombinant human prion protein folded into alpha or beta conformations exhibit striking heterogeneity in their specificity for truncations and glycoforms of mouse brain PrPc. We then show that some of these PrPc isoforms are expressed differentially in certain mouse brain regions. This suggests that variation in the expression of PrPc conformations in different brain regions may dictate the pattern of PrPSc deposition and vacuolation, characteristic for different prion strains.

  17. Probing the Heterogeneity of Protein Kinase Activation in Cells by Super-resolution Microscopy

    PubMed Central

    2016-01-01

    Heterogeneity of mitogen-activated protein kinase (MAPK) activation in genetically identical cells, which occurs in response to epidermal growth factor receptor (EGFR) signaling, remains poorly understood. MAPK cascades integrate signals emanating from different EGFR spatial locations, including the plasma membrane and endocytic compartment. We previously hypothesized that in EGF-stimulated cells the MAPK phosphorylation (pMAPK) level and activity are largely determined by the spatial organization of the EGFR clusters within the cell. For experimental testing of this hypothesis, we used super-resolution microscopy to define EGFR clusters by receptor numbers (N) and average intracluster distances (d). From these data, we predicted the extent of pMAPK with 85% accuracy on a cell-to-cell basis with control data returning 54% accuracy (P < 0.001). For comparison, the prediction accuracy was only 61% (P = 0.382) when the diffraction-limited averaged fluorescence intensity/cluster was used. Large clusters (N ≥ 3) with d > 50 nm were most predictive for pMAPK level in cells. Electron microscopy revealed that these large clusters were primarily localized to the limiting membrane of multivesicular bodies (MVB). Many tighter packed dimers/multimers (d < 50 nm) were found on intraluminal vesicles within MVBs, where they were unlikely to activate MAPK because of the physical separation. Our results suggest that cell-to-cell differences in N and d contain crucial information to predict EGFR-activated cellular pMAPK levels and explain pMAPK heterogeneity in isogenic cells. PMID:27768850

  18. Resolving breast cancer heterogeneity by searching reliable protein cancer biomarkers in the breast fluid secretome

    PubMed Central

    2013-01-01

    Background One of the major goals in cancer research is to find and evaluate the early presence of biomarkers in human fluids and tissues. To resolve the complex cell heterogeneity of a tumor mass, it will be useful to characterize the intricate biomolecular composition of tumor microenvironment (the so called cancer secretome), validating secreted proteins as early biomarkers of cancer initiation and progression. This approach is not broadly applicable because of the paucity of well validated and FDA-approved biomarkers and because most of the candidate biomarkers are mainly organ-specific rather than tumor-specific. For these reasons, there is an urgent need to identify and validate a panel of biomarker combinations for early detection of human tumors. This is especially important for breast cancer, the cancer spread most worldwide among women. It is well known that patients with early diagnosed breast cancer live longer, require less extensive treatment and fare better than patients with more aggressive and/or advanced disease. Results In the frame of searching breast cancer biomarkers (especially using nipple aspirate fluid mirroring breast microenvironment), studies have highlighted an optimal combination of well-known biomarkers: uPA + PAI-1 + TF. When individually investigated they did not show perfect accuracy in predicting the presence of breast cancer, whereas the triple combination has been demonstrated to be highly predictive of pre-cancer and/or cancerous conditions, approaching 97-100% accuracy. Conclusion Despite the heterogeneous composition of breast cancer and the difficulties to find specific breast cancer biomolecules, the noninvasive analysis of the nipple aspirate fluid secretome may significantly improve the discovery of promising biomarkers, helping also the differentiation among benign and invasive breast diseases, opening new frontiers in early oncoproteomics. PMID:23849048

  19. High-throughput simultaneous analysis of RNA, protein, and lipid biomarkers in heterogeneous tissue samples.

    PubMed

    Reiser, Vladimír; Smith, Ryan C; Xue, Jiyan; Kurtz, Marc M; Liu, Rong; Legrand, Cheryl; He, Xuanmin; Yu, Xiang; Wong, Peggy; Hinchcliffe, John S; Tanen, Michael R; Lazar, Gloria; Zieba, Renata; Ichetovkin, Marina; Chen, Zhu; O'Neill, Edward A; Tanaka, Wesley K; Marton, Matthew J; Liao, Jason; Morris, Mark; Hailman, Eric; Tokiwa, George Y; Plump, Andrew S

    2011-11-01

    With expanding biomarker discovery efforts and increasing costs of drug development, it is critical to maximize the value of mass-limited clinical samples. The main limitation of available methods is the inability to isolate and analyze, from a single sample, molecules requiring incompatible extraction methods. Thus, we developed a novel semiautomated method for tissue processing and tissue milling and division (TMAD). We used a SilverHawk atherectomy catheter to collect atherosclerotic plaques from patients requiring peripheral atherectomy. Tissue preservation by flash freezing was compared with immersion in RNAlater®, and tissue grinding by traditional mortar and pestle was compared with TMAD. Comparators were protein, RNA, and lipid yield and quality. Reproducibility of analyte yield from aliquots of the same tissue sample processed by TMAD was also measured. The quantity and quality of biomarkers extracted from tissue prepared by TMAD was at least as good as that extracted from tissue stored and prepared by traditional means. TMAD enabled parallel analysis of gene expression (quantitative reverse-transcription PCR, microarray), protein composition (ELISA), and lipid content (biochemical assay) from as little as 20 mg of tissue. The mean correlation was r = 0.97 in molecular composition (RNA, protein, or lipid) between aliquots of individual samples generated by TMAD. We also demonstrated that it is feasible to use TMAD in a large-scale clinical study setting. The TMAD methodology described here enables semiautomated, high-throughput sampling of small amounts of heterogeneous tissue specimens by multiple analytical techniques with generally improved quality of recovered biomolecules.

  20. Activity-Based Protein Profiling Shows Heterogeneous Signaling Adaptations to BRAF Inhibition.

    PubMed

    Sharma, Ritin; Fedorenko, Inna; Spence, Paige T; Sondak, Vernon K; Smalley, Keiran S M; Koomen, John M

    2016-12-02

    Patients with BRAF V600E mutant melanoma are typically treated with targeted BRAF kinase inhibitors, such as vemurafenib and dabrafenib. Although these drugs are initially effective, they are not curative. Most of the focus to date has been upon genetic mechanisms of acquired resistance; therefore, we must better understand the global signaling adaptations that mediate escape from BRAF inhibition. In the current study, we have used activity-based protein profiling (ABPP) with ATP-analogue probes to enrich kinases and other enzyme classes that contribute to BRAF inhibitor (BRAFi) resistance in four paired isogenic BRAFi-naïve/resistant cell line models. Our analysis showed these cell line models, which also differ in their PTEN status, have considerable heterogeneity in their kinase ATP probe uptake in comparing both naïve cells and adaptations to chronic drug exposure. A number of kinases including FAK1, SLK, and TAOK2 had increased ATP probe uptake in BRAFi resistant cells, while KHS1 (M4K5) and BRAF had decreased ATP probe uptake in the BRAFi-resistant cells. Gene ontology (GO) enrichment analysis revealed BRAFi resistance is associated with a significant enhancement in ATP probe uptake in proteins implicated in cytoskeletal organization and adhesion, and decreases in ATP probe uptake in proteins associated with cell metabolic processes. The ABPP approach was able to identify key phenotypic mediators critical for each BRAFi resistant cell line. Together, these data show that common phenotypic adaptations to BRAF inhibition can be mediated through very different signaling networks, suggesting considerable redundancy within the signaling of BRAF mutant melanoma cells.

  1. The expression profile of RNA-binding proteins in primary and metastatic colorectal cancer: relationship of heterogeneous nuclear ribonucleoproteins with prognosis.

    PubMed

    Hope, Nicholas R; Murray, Graeme I

    2011-03-01

    The heterogeneous nuclear ribonucleoproteins are a group of RNA-binding proteins with a range of key cellular functions, which are dysregulated in tumorigenesis including regulation of translational and RNA processing. The aims of this study were to define the heterogeneous nuclear ribonucleoprotein expression profile in primary and metastatic colorectal cancer and to establish the clinicopathologic significance of this expression. A tissue microarray containing 515 primary colorectal cancers, 224 lymph node metastasis of colorectal cancer, and 50 normal colon samples was immunostained for 6 heterogeneous nuclear ribonucleoproteins. Heterogeneous nuclear ribonucleoprotein I, heterogeneous nuclear ribonucleoprotein K, and heterogeneous nuclear ribonucleoprotein L displayed the most frequent strong immunoreactivity in primary colorectal tumor samples. Heterogeneous nuclear ribonucleoprotein A1 (P < .001) and heterogeneous nuclear ribonucleoprotein U (P = .003) showed significant alterations in nuclear expression in tumors compared with normal colonic epithelium, whereas heterogeneous nuclear ribonucleoprotein A1 (P = .001), heterogeneous nuclear ribonucleoprotein I (P < .001), and heterogeneous nuclear ribonucleoprotein K (P < .001) all showed significant aberrant cytoplasmic immunoreactivity in tumor cells. There were also significant differences in cytoplasmic immunoreactivity between the primary tumor and the corresponding lymph node metastasis for heterogeneous nuclear ribonucleoprotein A1 (P = .001), heterogeneous nuclear ribonucleoprotein I (P < .001), and heterogeneous nuclear ribonucleoprotein K (P = .001). Nuclear heterogeneous nuclear ribonucleoprotein H (χ(2) = 72.1; P < .001), cytoplasmic heterogeneous nuclear ribonucleoprotein I (χ(2) = 28.1; P < .001), and cytoplasmic heterogeneous nuclear ribonucleoprotein K (χ(2) = 13.2; P = .04) all showed significant associations with tumor stage. There was a significant relationship between strong nuclear

  2. Heterogenic expression of genes encoding secreted proteins at the periphery of Aspergillus niger colonies.

    PubMed

    Vinck, Arman; de Bekker, Charissa; Ossin, Adam; Ohm, Robin A; de Vries, Ronald P; Wösten, Han A B

    2011-01-01

    Colonization of a substrate by fungi starts with the invasion of exploring hyphae. These hyphae secrete enzymes that degrade the organic material into small molecules that can be taken up by the fungus to serve as nutrients. We previously showed that only part of the exploring hyphae of Aspergillus niger highly express the glucoamylase gene glaA. This was an unexpected finding since all exploring hyphae are exposed to the same environmental conditions. Using GFP as a reporter, we here demonstrate that the acid amylase gene aamA, the α-glucuronidase gene aguA, and the feruloyl esterase gene faeA of A. niger are also subject to heterogenic expression within the exploring mycelium. Coexpression studies using GFP and dTomato as reporters showed that hyphae that highly express one of these genes also highly express the other genes encoding secreted proteins. Moreover, these hyphae also highly express the amylolytic regulatory gene amyR, and the glyceraldehyde-3-phosphate dehydrogenase gene gpdA. In situ hybridization demonstrated that the high expressers are characterized by a high 18S rRNA content. Taken together, it is concluded that two subpopulations of hyphae can be distinguished within the exploring mycelium of A. niger. The experimental data indicate that these subpopulations differ in their transcriptional and translational activity.

  3. Heterogeneity of elderly depression: increased risk of Alzheimer's disease and Aβ protein metabolism.

    PubMed

    Namekawa, Yuki; Baba, Hajime; Maeshima, Hitoshi; Nakano, Yoshiyuki; Satomura, Emi; Takebayashi, Naoko; Nomoto, Hiroshi; Suzuki, Toshihito; Arai, Heii

    2013-06-03

    Epidemiological studies have proposed that depression may increase the risk for Alzheimer's disease (AD), even in patients with early-onset depression. Although metabolism of amyloid β protein (Aβ) in elderly depression received attention in terms of their correlation, there is a serious heterogeneity in elderly depression in terms of age at onset of depression. Moreover, it is unknown whether early-onset major depressive disorder (MDD) has a long-term effect on the involvement of Aβ metabolism and later development of AD. Thus, we evaluated serum Aβ40 and Aβ42 levels, the Aβ40/Aβ42 ratio in 89 elderly (≥60 years of age) inpatients with MDD and 81 age-matched healthy controls, and compared them among patients with early-onset (<60 years) and late-onset (≥60years) MDD and controls. The results showed that the serum Aβ40/Aβ42 ratio was significantly higher in patients with both early- and late-onset MDD than in controls (early-onset, p=0.010; late-onset, p=0.043), and it is of great interest that the serum Aβ40/Aβ42 ratio was negatively correlated with the age at MDD onset (R=-0.201, p=0.032). These results suggest that an earlier onset of MDD may have a more serious abnormality in Aβ metabolism, possibly explaining a biological mechanism underlying the link between depression and AD.

  4. Machines vs. ensembles: effective MAPK signaling through heterogeneous sets of protein complexes.

    PubMed

    Suderman, Ryan; Deeds, Eric J

    2013-01-01

    Despite the importance of intracellular signaling networks, there is currently no consensus regarding the fundamental nature of the protein complexes such networks employ. One prominent view involves stable signaling machines with well-defined quaternary structures. The combinatorial complexity of signaling networks has led to an opposing perspective, namely that signaling proceeds via heterogeneous pleiomorphic ensembles of transient complexes. Since many hypotheses regarding network function rely on how we conceptualize signaling complexes, resolving this issue is a central problem in systems biology. Unfortunately, direct experimental characterization of these complexes has proven technologically difficult, while combinatorial complexity has prevented traditional modeling methods from approaching this question. Here we employ rule-based modeling, a technique that overcomes these limitations, to construct a model of the yeast pheromone signaling network. We found that this model exhibits significant ensemble character while generating reliable responses that match experimental observations. To contrast the ensemble behavior, we constructed a model that employs hierarchical assembly pathways to produce scaffold-based signaling machines. We found that this machine model could not replicate the experimentally observed combinatorial inhibition that arises when the scaffold is overexpressed. This finding provides evidence against the hierarchical assembly of machines in the pheromone signaling network and suggests that machines and ensembles may serve distinct purposes in vivo. In some cases, e.g. core enzymatic activities like protein synthesis and degradation, machines assembled via hierarchical energy landscapes may provide functional stability for the cell. In other cases, such as signaling, ensembles may represent a form of weak linkage, facilitating variation and plasticity in network evolution. The capacity of ensembles to signal effectively will ultimately

  5. Heterogeneity of high-mobility-group protein 2. Enrichment of a rapidly migrating form in testis.

    PubMed Central

    Bucci, L R; Brock, W A; Meistrich, M L

    1985-01-01

    A determination of the absolute amounts of high-mobility-group proteins 1 and 2 (HMG1 and HMG2) in rat tissues demonstrated that amounts of HMG2 were low in non-proliferating tissues, somewhat higher in proliferating and lymphoid tissues, but were extremely elevated in the testis. This increase was due to a germ-cell-specific form of HMG2 with increased mobility relative to somatic HMG2 on acid/urea/polyacrylamide-gel electrophoresis. To determine if the findings in the rat were a general feature of spermatogenesis, testis (germinal), spleen (lymphoid), and liver (non-proliferating) tissues from various vertebrate species were examined for their relative amounts of HMG1 and HMG2, and for HMG2 heterogeneity. Bull, chimpanzee, cynomologus monkey, dog, gopher, guinea pig, hamster, mouse, opossum, rabbit, rat, rhesus monkey, squirrel and toad (Xenopus) tissues were analysed. Nearly all species showed relatively high contents of HMG2 in testis tissue, whereas HMG1 contents were similar in all species and tissues. Ten of thirteen species showed a rapidly migrating HMG2 subtype in testis tissue, separable by acid/urea/polyacrylamide-gel electrophoresis. Xenopus, which lacks HMG2 in somatic tissues, showed an HMG2-like protein in testis tissue. Although the rapidly migrating HMG2 subtype in species other than rat was not testis-specific, it was always enriched in the testis. This study indicates that increased amounts of HMG2 and the enrichment of a rapidly migrating HMG2 subtype are general features of spermatogenic cells. Images Fig. 1. Fig. 2. Fig. 3. PMID:4038257

  6. Heterogeneity in spike protein genes of porcine epidemic diarrhea viruses isolated in Korea.

    PubMed

    Lee, Dong-Kyu; Park, Choi-Kyu; Kim, Seong-Hee; Lee, Changhee

    2010-05-01

    Porcine epidemic diarrhea virus (PEDV) has plagued the domestic swine industry in Korea causing significant economic impacts on pig production nationwide. In the present study, we determined the complete nucleotide sequences of the spike (S) glycoprotein genes of seven Korean PEDV isolates. The entire S genes of all isolates were found to be nine nucleotides longer in length than other PEDV reference strains. This size difference was due to the combined presence of notable 15 bp insertion and 6 bp deletion within the N-terminal region of the S1 domain of the Korean isolates. In addition, the largest number of amino acid variations was accumulated in the S1 N-terminal region, leading to the presence of hypervariability in the isolates. Sequence comparisons at the peptide level of the S proteins revealed that all seven Korean isolates shared diverse similarities ranging from a 93.6% to 99.6% identity with each other but exhibited a 92.2% to 93.7% identity with other reference strains. Collectively, the sequence analysis data indicate the diversity of the PEDV isolates currently prevalent in Korea that represents a heterogeneous group. Phylogenetic analyses showed two separate clusters, in which all Korean field isolates were grouped together in the second cluster (group 2). The results indicate that prevailing isolates in Korea are phylogenetically more closely related to each other rather than other reference strains. Interestingly, the tree topology based on the nucleotide sequences representing the S1 domain or the S1 N-terminal region most nearly resembled the full S gene-based phylogenetic tree. Therefore, our data implicates a potential usefulness of the partial S protein gene including the N-terminal region in unveiling genetic relatedness of PEDV isolates.

  7. Influences of heterogeneous native contact energy and many-body interactions on the prediction of protein folding mechanisms.

    PubMed

    Zhang, Zhuqing; Ouyang, Yanhua; Chen, Tao

    2016-11-16

    Since single-point mutant perturbation has been used to probe protein folding mechanisms in experiments, the ϕ-value has become a critical parameter to infer the transition state (TS) for two-state proteins. Experimentally, large scale analysis has shown a nearly single uniform ϕ-value with normally distributed error from 24 different proteins; moreover, in zero stability conditions, the intrinsic variable ϕ(0) is around 0.36. To explore how and to what extent theoretical models can capture experimental phenomena, we here use structure-based explicit chain coarse-grained models to investigate the influence of single-point mutant perturbation on protein folding for single domain two-state proteins. Our results indicate that uniform, additive contact energetic interactions cannot predict experimental Brønsted plots well. Those points deviate largely from the main data sets in Brønsted plots, are mostly hydrophobic, and are located in N- and C-terminal contacting regions. Heterogenous contact energy, which is dependent on sequence separation, can narrow the point dispersion in a Brønsted plot. Moreover, we demonstrate that combining many-body interactions with heterogeneous native contact energy can present mean ϕ-values consistent with experimental findings, with a comparable distributed error. This indicates that for more accurate elucidation of protein folding mechanisms by residue-level structure-based models, these elements should be considered.

  8. Intratubular germ cell neoplasia of the human testis: heterogeneous protein expression and relation to invasive potential.

    PubMed

    Mitchell, Rod T; E Camacho-Moll, Maria; Macdonald, Joni; Anderson, Richard A; Kelnar, Christopher J H; O'Donnell, Marie; Sharpe, Richard M; Smith, Lee B; Grigor, Ken M; Wallace, W Hamish B; Stoop, Hans; Wolffenbuttel, Katja P; Donat, Roland; Saunders, Philippa Tk; Looijenga, Leendert Hj

    2014-09-01

    Testicular germ cell cancer develops from premalignant intratubular germ cell neoplasia, unclassified cells that are believed to arise from failure of normal maturation of fetal germ cells from gonocytes (OCT4(+)/MAGEA4(-)) into pre-spermatogonia (OCT4(-)/MAGEA4(+)). Intratubular germ cell neoplasia cell subpopulations based on stage of germ cell differentiation have been described, however the importance of these subpopulations in terms of invasive potential has not been reported. We hypothesized that cells expressing an immature (OCT4(+)/MAGEA4(-)) germ cell profile would exhibit an increased proliferation rate compared with those with a mature profile (OCT4(+)/MAGEA4(+)). Therefore, we performed triple immunofluorescence and stereology to quantify the different intratubular germ cell neoplasia cell subpopulations, based on expression of germ cell (OCT4, PLAP, AP2γ, MAGEA4, VASA) and proliferation (Ki67) markers, in testis sections from patients with preinvasive disease, seminoma, and non-seminoma. We compared these subpopulations with normal human fetal testis and with seminoma cells. Heterogeneity of protein expression was demonstrated in intratubular germ cell neoplasia cells with respect to gonocyte and spermatogonial markers. It included an embryonic/fetal germ cell subpopulation lacking expression of the definitive intratubular germ cell neoplasia marker OCT4, that did not correspond to a physiological (fetal) germ cell subpopulation. OCT4(+)/MAGEA4(-) cells showed a significantly increased rate of proliferation compared with the OCT4(+)/MAGEA4(+) population (12.8 versus 3.4%, P<0.0001) irrespective of histological tumor type, reflected in the predominance of OCT4(+)/MAGEA4(-) cells in the invasive tumor component. Surprisingly, OCT4(+)/MAGEA4(-) cells in patients with preinvasive disease showed significantly higher proliferation compared to those with seminoma or non-seminoma (18.1 versus 10.2 versus 7.2%, P<0.05, respectively). In conclusion, this study

  9. Heterogeneous surface distribution of the fibrinogen-binding protein on Candida albicans.

    PubMed Central

    Martínez, J P; López-Ribot, J L; Chaffin, W L

    1994-01-01

    As detected by indirect immunofluorescence and confocal microscopy, fibrinogen binding was heterogeneously distributed on the surface of Candida albicans. A low level of binding was generally observed homogeneously distributed on some yeast and most hyphal extensions of germ tubes. However, on most hyphal extensions, there were randomly distributed areas of increased expression, as revealed by patches of greater fluorescence intensity. Images PMID:8300229

  10. Monoclonal antibodies specific for adenovirus early region 1A proteins: extensive heterogeneity in early region 1A products.

    PubMed Central

    Harlow, E; Franza, B R; Schley, C

    1985-01-01

    Hybridomas secreting monoclonal antibodies specific for the adenovirus early region 1A (E1A) proteins were prepared from BALB/c mice immunized with a bacterial trpE-E1A fusion protein. This protein is encoded by a hybrid gene that joins a portion of the Escherichia coli trpE gene and a cDNA copy of the E1A 13S mRNA (Spindler et al., J. Virol. 49:132-141, 1984). Eighty-three hybridomas that secrete antibodies which recognize the immunogen were isolated and single cell cloned. Twenty-nine of these antibodies are specific for the E1A portion of the fusion protein. Only 12 of the monoclonal antibodies can efficiently immunoprecipitate E1A polypeptides from detergent lysates of infected cells. E1A polypeptides were analyzed on one-dimensional, sodium dodecyl sulfate-polyacrylamide gels and two-dimensional, isoelectric focusing polyacrylamide gels. The E1A proteins that are specifically immunoprecipitated by the monoclonal antibodies are heterogeneous in size and charge and can be resolved into approximately 60 polypeptide species. This heterogeneity is due not only to synthesis from multiple E1A mRNAs, but also at least in part to post-translational modification. Several of the monoclonal antibodies divide the E1A polypeptides into immunological subclasses based on the ability of the antibodies to bind to the antigen. In particular, two of the monoclonal antibodies bind to the polypeptides synthesized from the 13S E1A mRNA, but not to other E1A proteins. Images PMID:3894685

  11. The Impact of Heterogeneity and Dark Acceptor States on FRET: Implications for Using Fluorescent Protein Donors and Acceptors

    PubMed Central

    Vogel, Steven S.; Nguyen, Tuan A.; van der Meer, B. Wieb; Blank, Paul S.

    2012-01-01

    Förster resonance energy transfer (FRET) microscopy is widely used to study protein interactions in living cells. Typically, spectral variants of the Green Fluorescent Protein (FPs) are incorporated into proteins expressed in cells, and FRET between donor and acceptor FPs is assayed. As appreciable FRET occurs only when donors and acceptors are within 10 nm of each other, the presence of FRET can be indicative of aggregation that may denote association of interacting species. By monitoring the excited-state (fluorescence) decay of the donor in the presence and absence of acceptors, dual-component decay analysis has been used to reveal the fraction of donors that are FRET positive (i.e., in aggregates)._However, control experiments using constructs containing both a donor and an acceptor FP on the same protein repeatedly indicate that a large fraction of these donors are FRET negative, thus rendering the interpretation of dual-component analysis for aggregates between separately donor-containing and acceptor-containing proteins problematic. Using Monte-Carlo simulations and analytical expressions, two possible sources for such anomalous behavior are explored: 1) conformational heterogeneity of the proteins, such that variations in the distance separating donor and acceptor FPs and/or their relative orientations persist on time-scales long in comparison with the excited-state lifetime, and 2) FP dark states. PMID:23152925

  12. Respiratory chain protein turnover rates in mice are highly heterogeneous but strikingly conserved across tissues, ages, and treatments

    PubMed Central

    Karunadharma, Pabalu P.; Basisty, Nathan; Chiao, Ying Ann; Dai, Dao-Fu; Drake, Rachel; Levy, Nick; Koh, William J.; Emond, Mary J.; Kruse, Shane; Marcinek, David; Maccoss, Michael J.; Rabinovitch, Peter S.

    2015-01-01

    The mitochondrial respiratory chain (RC) produces most of the cellular ATP and requires strict quality-control mechanisms. To examine RC subunit proteostasis in vivo, we measured RC protein half-lives (HLs) in mice by liquid chromatography-tandem mass spectrometry with metabolic [2H3]-leucine heavy isotope labeling under divergent conditions. We studied 7 tissues/fractions of young and old mice on control diet or one of 2 diet regimens (caloric restriction or rapamycin) that altered protein turnover (42 conditions in total). We observed a 6.5-fold difference in mean HL across tissues and an 11.5-fold difference across all conditions. Normalization to the mean HL of each condition showed that relative HLs were conserved across conditions (Spearman’s ρ = 0.57; P < 10–4), but were highly heterogeneous between subunits, with a 7.3-fold mean range overall, and a 2.2- to 4.6-fold range within each complex. To identify factors regulating this conserved distribution, we performed statistical analyses to study the correlation of HLs to the properties of the subunits. HLs significantly correlated with localization within the mitochondria, evolutionary origin, location of protein-encoding, and ubiquitination levels. These findings challenge the notion that all subunits in a complex turnover at comparable rates and suggest that there are common rules governing the differential proteolysis of RC protein subunits under divergent cellular conditions.—Karunadharma, P. P., Basisty, N., Chiao, Y. A., Dai, D.-F., Drake, R., Levy, N., Koh, W. J., Emond, M. J., Kruse, S., Marcinek, D., Maccoss, M. J., Rabinovitch, P. S. Respiratory chain protein turnover rates in mice are highly heterogeneous but strikingly conserved across tissues, ages, and treatments. PMID:25977255

  13. Surfactant protein-C chromatin-bound green fluorescence protein reporter mice reveal heterogeneity of surfactant protein C-expressing lung cells.

    PubMed

    Lee, Joo-Hyeon; Kim, Jonghwan; Gludish, David; Roach, Rebecca R; Saunders, Arven H; Barrios, Juliana; Woo, Andrew Jonghan; Chen, Huaiyong; Conner, David A; Fujiwara, Yuko; Stripp, Barry R; Kim, Carla F

    2013-03-01

    The regeneration of alveolar epithelial cells is a critical aspect of alveolar reorganization after lung injury. Although alveolar Type II (AT2) cells have been described as progenitor cells for alveolar epithelia, more remains to be understood about how their progenitor cell properties are regulated. A nuclear, chromatin-bound green fluorescence protein reporter (H2B-GFP) was driven from the murine surfactant protein-C (SPC) promoter to generate SPC H2B-GFP transgenic mice. The SPC H2B-GFP allele allowed the FACS-based enrichment and gene expression profiling of AT2 cells. Approximately 97% of AT2 cells were GFP-labeled on Postnatal Day 1, and the percentage of GFP-labeled AT2 cells decreased to approximately 63% at Postnatal Week 8. Isolated young adult SPC H2B-GFP(+) cells displayed proliferation, differentiation, and self-renewal capacity in the presence of lung fibroblasts in a Matrigel-based three-dimensional culture system. Heterogeneity within the GFP(+) population was revealed, because cells with distinct alveolar and bronchiolar gene expression arose in three-dimensional cultures. CD74, a surface marker highly enriched on GFP(+) cells, was identified as a positive selection marker, providing 3-fold enrichment for AT2 cells. In vivo, GFP expression was induced within other epithelial cell types during maturation of the distal lung. The utility of the SPC H2B-GFP murine model for the identification of AT2 cells was greatest in early postnatal lungs and more limited with age, when some discordance between SPC and GFP expression was observed. In adult mice, this allele may allow for the enrichment and future characterization of other SPC-expressing alveolar and bronchiolar cells, including putative stem/progenitor cell populations.

  14. Heterogeneity of polyelectrolyte diffusion in polyelectrolyte-protein coacervates: a 1H pulsed field gradient NMR study.

    PubMed

    Menjoge, Amrish R; Kayitmazer, A Basak; Dubin, Paul L; Jaeger, Werner; Vasenkov, Sergey

    2008-04-24

    Proton pulsed field gradient (PFG) NMR was used to study the diffusion of poly(diallyldimethylammonium chloride) (PDADMAC) in coacervates formed from this polycation and the protein bovine serum albumin (BSA). Application of high (up to 30 T/m) magnetic field gradients in PFG NMR measurements allowed probing the diffusion of PDADMAC on a length scale of displacements as small as 100 nm in coacervates formed at different pH's and ionic strengths, i.e., conditions of varying protein-polycation interaction energy. Studies were carried out for a broad range of diffusion times and corresponding values of the mean square displacements. Several ensembles of PDADMAC polycations with different diffusivities were observed in the measured range of diffusion times. The existence of these ensembles and the pattern of their changes with increasing diffusion time support the hypothesis about the microscopic heterogeneity of PDADMAC-BSA coacervates and also provide evidence for the dynamic disintegration and reformation of dense domains.

  15. Heterogenous turnover of sperm and seminal vesicle proteins in the mouse revealed by dynamic metabolic labeling.

    PubMed

    Claydon, Amy J; Ramm, Steven A; Pennington, Andrea; Hurst, Jane L; Stockley, Paula; Beynon, Robert

    2012-06-01

    Plasticity in ejaculate composition is predicted as an adaptive response to the evolutionary selective pressure of sperm competition. However, to respond rapidly to local competitive conditions requires dynamic modulation in the production of functionally relevant ejaculate proteins. Here we combine metabolic labeling of proteins with proteomics to explore the opportunity for such modulation within mammalian ejaculates. We assessed the rate at which proteins are synthesized and incorporated in the seminal vesicles of male house mice (Mus musculus domesticus), where major seminal fluid proteins with potential roles in sperm competition are produced. We compared rates of protein turnover in the seminal vesicle with those during spermatogenesis, the timing of which is well known in mice. The subjects were fed a diet containing deuterated valine ([(2)H(8)]valine) for up to 35 days, and the incorporation of dietary-labeled amino acid into seminal vesicle- or sperm-specific proteins was assessed by liquid chromatography-mass spectrometry of samples recovered from the seminal vesicle lumen and cauda epididymis, respectively. Analyses of epididymal contents were consistent with the known duration of spermatogenesis and sperm maturation in this species and in addition revealed evidence for a subset of epididymal proteins subject to rapid turnover. For seminal vesicle proteins, incorporation of the stable isotope was evident from day 2 of labeling, reaching a plateau of labeling by day 24. Hence, even in the absence of copulation, the seminal vesicle proteins and certain epididymal proteins demonstrate considerable turnover, a response that is consonant with the capacity to rapidly modulate protein production. These techniques can now be used to assess the extent of phenotypic plasticity in mammalian ejaculate production and allocation according to social and environmental cues of sperm competition.

  16. H-BLAST: a fast protein sequence alignment toolkit on heterogeneous computers with GPUs.

    PubMed

    Ye, Weicai; Chen, Ying; Zhang, Yongdong; Xu, Yuesheng

    2017-04-15

    The sequence alignment is a fundamental problem in bioinformatics. BLAST is a routinely used tool for this purpose with over 118 000 citations in the past two decades. As the size of bio-sequence databases grows exponentially, the computational speed of alignment softwares must be improved. We develop the heterogeneous BLAST (H-BLAST), a fast parallel search tool for a heterogeneous computer that couples CPUs and GPUs, to accelerate BLASTX and BLASTP-basic tools of NCBI-BLAST. H-BLAST employs a locally decoupled seed-extension algorithm for better performance on GPUs, and offers a performance tuning mechanism for better efficiency among various CPUs and GPUs combinations. H-BLAST produces identical alignment results as NCBI-BLAST and its computational speed is much faster than that of NCBI-BLAST. Speedups achieved by H-BLAST over sequential NCBI-BLASTP (resp. NCBI-BLASTX) range mostly from 4 to 10 (resp. 5 to 7.2). With 2 CPU threads and 2 GPUs, H-BLAST can be faster than 16-threaded NCBI-BLASTX. Furthermore, H-BLAST is 1.5-4 times faster than GPU-BLAST. https://github.com/Yeyke/H-BLAST.git. yux06@syr.edu. Supplementary data are available at Bioinformatics online.

  17. Characterization and molecular basis of heterogeneity of the African swine fever virus envelope protein p54.

    PubMed Central

    Rodriguez, F; Alcaraz, C; Eiras, A; Yáñez, R J; Rodriguez, J M; Alonso, C; Rodriguez, J F; Escribano, J M

    1994-01-01

    It has been reported that the propagation of African swine fever virus (ASFV) in cell culture generates viral subpopulations differing in protein p54 (C. Alcaraz, A. Brun, F. Ruiz-Gonzalvo, and J. M. Escribano, Virus Res. 23:173-182, 1992). A recombinant bacteriophage expressing a 328-bp fragment of the p54 gene was selected in a lambda phage expression library of ASFV genomic fragments by immunoscreening with antibodies against p54 protein. The sequence of this recombinant phage allowed the location of the p54 gene in the EcoRI E fragment of the ASFV genome. Nucleotide sequence obtained from this fragment revealed an open reading frame encoding a protein of 183 amino acids with a calculated molecular weight of 19,861. This protein contains a transmembrane domain and a Gly-Gly-X motif, a recognition sequence for protein processing of several ASFV structural proteins. In addition, two direct tandem repetitions were also found within this open reading frame. Further characterization of the transcription and gene product revealed that the p54 gene is translated from a late mRNA and the protein is incorporated to the external membrane of the virus particle. A comparison of the nucleotide sequence of the p54 gene carried by two virulent ASFV strains (E70 and E75) with that obtained from virus Ba71V showed 100% similarity. However, when p54 genes from viral clones generated by cell culture passage and coding for p54 proteins with different electrophoretic mobility were sequenced, they showed changes in the number of copies of a 12-nucleotide sequence repeat. These changes produce alterations in the number of copies of the amino acid sequence Pro-Ala-Ala-Ala present in p54, resulting in stepwise modifications in the molecular weight of the protein. These duplications and deletions of a tandem repeat sequence array within a protein coding region constitute a novel mechanism of genetic diversification in ASFV. Images PMID:7933107

  18. Characterization and molecular basis of heterogeneity of the African swine fever virus envelope protein p54.

    PubMed

    Rodriguez, F; Alcaraz, C; Eiras, A; Yáñez, R J; Rodriguez, J M; Alonso, C; Rodriguez, J F; Escribano, J M

    1994-11-01

    It has been reported that the propagation of African swine fever virus (ASFV) in cell culture generates viral subpopulations differing in protein p54 (C. Alcaraz, A. Brun, F. Ruiz-Gonzalvo, and J. M. Escribano, Virus Res. 23:173-182, 1992). A recombinant bacteriophage expressing a 328-bp fragment of the p54 gene was selected in a lambda phage expression library of ASFV genomic fragments by immunoscreening with antibodies against p54 protein. The sequence of this recombinant phage allowed the location of the p54 gene in the EcoRI E fragment of the ASFV genome. Nucleotide sequence obtained from this fragment revealed an open reading frame encoding a protein of 183 amino acids with a calculated molecular weight of 19,861. This protein contains a transmembrane domain and a Gly-Gly-X motif, a recognition sequence for protein processing of several ASFV structural proteins. In addition, two direct tandem repetitions were also found within this open reading frame. Further characterization of the transcription and gene product revealed that the p54 gene is translated from a late mRNA and the protein is incorporated to the external membrane of the virus particle. A comparison of the nucleotide sequence of the p54 gene carried by two virulent ASFV strains (E70 and E75) with that obtained from virus Ba71V showed 100% similarity. However, when p54 genes from viral clones generated by cell culture passage and coding for p54 proteins with different electrophoretic mobility were sequenced, they showed changes in the number of copies of a 12-nucleotide sequence repeat. These changes produce alterations in the number of copies of the amino acid sequence Pro-Ala-Ala-Ala present in p54, resulting in stepwise modifications in the molecular weight of the protein. These duplications and deletions of a tandem repeat sequence array within a protein coding region constitute a novel mechanism of genetic diversification in ASFV.

  19. A Novel Heterogeneous Nuclear Ribonucleoprotein-Like Protein Interacts with NS1 of the Minute Virus of Mice

    PubMed Central

    Harris, Colin E.; Boden, Richard A.; Astell, Caroline R.

    1999-01-01

    NS1, the major nonstructural parvovirus protein of the minute virus of mice, is a multifunctional protein responsible for several aspects of viral replication. NS1 transactivates the P38 promoter (used to express the structural proteins), as well as its own strong promoter, P4. To study the mechanism of activation and to map regions of NS1 responsible for transactivation, NS1 and various deletions of NS1 were cloned in frame with the GAL4DB and cotransfected into COS-7 and LA9 cells with a synthetic GAL4-responsive reporter plasmid. These studies showed NS1 can directly activate transcription through its 129 carboxyl-terminal amino acid residues. Any deletion from this region of the C terminus, even as few as 8 amino acids, completely abolishes transactivation. A yeast two-hybrid system used to identify protein-protein interactions demonstrated that NS1 is able to dimerize when expressed in yeast cells. However, only an almost complete NS11–638 bait was able to interact with the full-length NS1. A two-hybrid screen identified a HeLa cell cDNA clone (NS1-associated protein 1 [NSAP1]) that interacts with NS11–276 and NS11–638. An additional sequence was predicted from human EST (expressed sequence tag) data, and the cDNA was estimated to be at least 2,221 bp long, potentially encoding a 562-amino-acid protein product. A polyclonal antibody raised to a synthetic peptide within NSAP1 recognizes an ∼65-kDa cellular protein. This NSAP1 cDNA has not previously been characterized, but the predicted protein sequence is 80% identical to the recently identified heterogeneous nuclear ribonucleoprotein (hnRNP) R (W. Hassfeld et al., Nucleic Acids Res. 26:439–445, 1998). NSAP1 contains four ribonucleoprotein domains, as well as a highly repetitive C-terminal region. A closely related mouse cDNA (deduced from murine EST data) encodes a protein with only a single amino acid residue change from the human protein. NSAP1 is predicted to be a 65-kDa polynucleotide binding

  20. Experiment and theory for heterogeneous nucleation of protein crystals in a porous medium

    PubMed Central

    Chayen, Naomi E.; Saridakis, Emmanuel; Sear, Richard P.

    2006-01-01

    The determination of high-resolution structures of proteins requires crystals of suitable quality. Because of the new impetus given to structural biology by structural genomics/proteomics, the problem of crystallizing proteins is becoming increasingly acute. There is therefore an urgent requirement for the development of new efficient methods to aid crystal growth. Nucleation is the crucial step that determines the entire crystallization process. Hence, the holy grail is to design a “universal nucleant,” a substrate that induces the nucleation of crystals of any protein. We report a theory for nucleation on disordered porous media and its experimental testing and validation using a mesoporous bioactive gel-glass. This material induced the crystallization of the largest number of proteins ever crystallized using a single nucleant. The combination of the model and the experimental results opens up the scope for the rational design of nucleants, leading to alternative means of controlling crystallization. PMID:16407115

  1. Experiment and theory for heterogeneous nucleation of protein crystals in a porous medium.

    PubMed

    Chayen, Naomi E; Saridakis, Emmanuel; Sear, Richard P

    2006-01-17

    The determination of high-resolution structures of proteins requires crystals of suitable quality. Because of the new impetus given to structural biology by structural genomics/proteomics, the problem of crystallizing proteins is becoming increasingly acute. There is therefore an urgent requirement for the development of new efficient methods to aid crystal growth. Nucleation is the crucial step that determines the entire crystallization process. Hence, the holy grail is to design a "universal nucleant," a substrate that induces the nucleation of crystals of any protein. We report a theory for nucleation on disordered porous media and its experimental testing and validation using a mesoporous bioactive gel-glass. This material induced the crystallization of the largest number of proteins ever crystallized using a single nucleant. The combination of the model and the experimental results opens up the scope for the rational design of nucleants, leading to alternative means of controlling crystallization.

  2. Characterization of a heterogeneous chicken plasma protein, HEF, by analytical isotachophoresis in agarose gel.

    PubMed

    Nicolaisen, E M

    1985-02-22

    Chicken plasma contains proteins that associate with immunoglobulin. One of these proteins enhances the titre of haemagglutinating alloantibodies, and it was therefore named HEF, haemagglutination enhancing factor. A purified HEF preparation mixed with ampholytes splits into four bands in analytical agarose isotachophoresis. One of the HEF bands can be separated from two others with beta-alanine as discrete spacer. The separated HEF populations differ in molecular size and in their ability to enhance agglutination.

  3. Heterogeneous nuclear ribonucleoprotein A1 regulates rhythmic synthesis of mouse Nfil3 protein via IRES-mediated translation

    PubMed Central

    Kim, Hyo-Jin; Lee, Hwa-Rim; Seo, Ji-Young; Ryu, Hye Guk; Lee, Kyung-Ha; Kim, Do-Yeon; Kim, Kyong-Tai

    2017-01-01

    Nuclear factor, interleukin 3, regulated (Nfil3, also known as E4 Promoter-Binding Protein 4 (E4BP4)) protein is a transcription factor that binds to DNA and generally represses target gene expression. In the circadian clock system, Nfil3 binds to a D-box element residing in the promoter of clock genes and contributes to their robust oscillation. Here, we show that the 5′-untranslated region (5′-UTR) of Nfil3 mRNA contains an internal ribosome entry site (IRES) and that IRES-mediated translation occurs in a phase-dependent manner. We demonstrate that heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) binds to a specific region of Nfil3 mRNA and regulates IRES-mediated translation. Knockdown of hnRNP A1 almost completely abolishes protein oscillation without affecting mRNA oscillation. Moreover, we observe that intracellular calcium levels, which are closely related to bone formation, depend on Nfil3 levels in osteoblast cell lines. We suggest that the 5′-UTR mediated cap-independent translation of Nfil3 mRNA contributes to the rhythmic expression of Nfil3 by interacting with the RNA binding protein hnRNP A1. These data provide new evidence that the posttranscriptional regulation of clock gene expression is important during bone metabolism. PMID:28220845

  4. Respiratory chain protein turnover rates in mice are highly heterogeneous but strikingly conserved across tissues, ages, and treatments.

    PubMed

    Karunadharma, Pabalu P; Basisty, Nathan; Chiao, Ying Ann; Dai, Dao-Fu; Drake, Rachel; Levy, Nick; Koh, William J; Emond, Mary J; Kruse, Shane; Marcinek, David; Maccoss, Michael J; Rabinovitch, Peter S

    2015-08-01

    The mitochondrial respiratory chain (RC) produces most of the cellular ATP and requires strict quality-control mechanisms. To examine RC subunit proteostasis in vivo, we measured RC protein half-lives (HLs) in mice by liquid chromatography-tandem mass spectrometry with metabolic [(2)H3]-leucine heavy isotope labeling under divergent conditions. We studied 7 tissues/fractions of young and old mice on control diet or one of 2 diet regimens (caloric restriction or rapamycin) that altered protein turnover (42 conditions in total). We observed a 6.5-fold difference in mean HL across tissues and an 11.5-fold difference across all conditions. Normalization to the mean HL of each condition showed that relative HLs were conserved across conditions (Spearman's ρ = 0.57; P < 10(-4)), but were highly heterogeneous between subunits, with a 7.3-fold mean range overall, and a 2.2- to 4.6-fold range within each complex. To identify factors regulating this conserved distribution, we performed statistical analyses to study the correlation of HLs to the properties of the subunits. HLs significantly correlated with localization within the mitochondria, evolutionary origin, location of protein-encoding, and ubiquitination levels. These findings challenge the notion that all subunits in a complex turnover at comparable rates and suggest that there are common rules governing the differential proteolysis of RC protein subunits under divergent cellular conditions.

  5. Heterogeneous nuclear ribonucleoprotein A1 regulates rhythmic synthesis of mouse Nfil3 protein via IRES-mediated translation.

    PubMed

    Kim, Hyo-Jin; Lee, Hwa-Rim; Seo, Ji-Young; Ryu, Hye Guk; Lee, Kyung-Ha; Kim, Do-Yeon; Kim, Kyong-Tai

    2017-02-21

    Nuclear factor, interleukin 3, regulated (Nfil3, also known as E4 Promoter-Binding Protein 4 (E4BP4)) protein is a transcription factor that binds to DNA and generally represses target gene expression. In the circadian clock system, Nfil3 binds to a D-box element residing in the promoter of clock genes and contributes to their robust oscillation. Here, we show that the 5'-untranslated region (5'-UTR) of Nfil3 mRNA contains an internal ribosome entry site (IRES) and that IRES-mediated translation occurs in a phase-dependent manner. We demonstrate that heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) binds to a specific region of Nfil3 mRNA and regulates IRES-mediated translation. Knockdown of hnRNP A1 almost completely abolishes protein oscillation without affecting mRNA oscillation. Moreover, we observe that intracellular calcium levels, which are closely related to bone formation, depend on Nfil3 levels in osteoblast cell lines. We suggest that the 5'-UTR mediated cap-independent translation of Nfil3 mRNA contributes to the rhythmic expression of Nfil3 by interacting with the RNA binding protein hnRNP A1. These data provide new evidence that the posttranscriptional regulation of clock gene expression is important during bone metabolism.

  6. The A1 and A1B proteins of heterogeneous nuclear ribonucleoparticles modulate 5' splice site selection in vivo.

    PubMed Central

    Yang, X; Bani, M R; Lu, S J; Rowan, S; Ben-David, Y; Chabot, B

    1994-01-01

    Recent in vitro results suggest that the heterogeneous nuclear ribonucleoparticle (hnRNP) A1 protein modulates alternative splicing by favoring distal 5' splice site (5'SS) selection and exon skipping. We used a mouse erythroleukemia (MEL) cell line (CB3C7) deficient in the expression of hnRNP A1 to test whether variations in hnRNP A1 and AlB protein levels affected alternative splicing in vivo. In contrast to A1-expressing MEL cell lines, CB3C7 cells preferentially selected the proximal 13S and 12S 5'SS on the adenovirus E1A pre-mRNA. Transiently expressing the A1 or A1B cDNA in CB3C7 cells shifted 5'SS selection toward the more distal 9S donor site. A1 protein synthesis was required for this effect since the expression of a mutated A1 cDNA did not affect 5'SS selection. These results demonstrate that in vivo variations in hnRNP A1 protein levels can influence 5'SS selection. Images PMID:8041722

  7. Dynamics of backbone conformational heterogeneity in Bacillus subtilis ribonuclease P protein.

    PubMed

    Henkels, Christopher H; Chang, Yu-Chu; Chamberlin, Stacy I; Oas, Terrence G

    2007-12-25

    Interconversion of protein conformations is imperative to function, as evidenced by conformational changes associated with enzyme catalytic cycles, ligand binding and post-translational modifications. In this study, we used 15N NMR relaxation experiments to probe the fast (i.e., ps-ns) and slow (i.e., micros-ms) conformational dynamics of Bacillus subtilis ribonuclease P protein (P protein) in its folded state, bound to two sulfate anions. Using the Lipari-Szabo mapping method [Andrec, M., Montelione, G. T., and Levy, R. M. (2000) J. Biomol. NMR 18, 83-100] to interpret the data, we find evidence for P protein dynamics on the mus-ms time scale in the ensemble. The residues that exhibit these slow internal motions are found in regions that have been previously identified as part of the P protein-P RNA interface. These results suggest that structural flexibility within the P protein ensemble may be important for proper RNase P holoenzyme assembly and/or catalysis.

  8. Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics

    PubMed Central

    Cho, Samuel S.; Levy, Yaakov; Wolynes, Peter G.

    2009-01-01

    Energy landscape theory requires that the protein-folding mechanism is generally globally directed or funneled toward the native state. The collective nature of transition state ensembles further suggests that sufficient averaging of the native interactions can occur so that the knowledge of the native topology may suffice for predicting the mechanism. Nevertheless, while simple homogeneously weighted native topology-based models predict the folding mechanisms for many proteins, for other proteins knowledge of the native topology, by itself, seems not to suffice in determining the folding mechanism. Simulations of proteins with differing topologies reveal that the failure of homogeneously weighted topology-based models can, however, be completely understood within the framework of a funneled energy landscape and can be quantified by comparing the fluctuation of entropy cost for forming contacts to the expected fluctuations in contact energy. To be precise, we find the transition state ensembles of proteins with all-α topologies, which are more uniform in the specific entropy cost of contact formation, have transition state ensembles that are more readily perturbed by differences in energetic weights than are the transition state ensembles of proteins with significant amounts of β-structure, where the specific entropy costs of contact formation are more widely distributed. This behavior is consistent with a random-field Ising model analogy that follows from the free energy functional approach to folding. PMID:19075236

  9. A Map of Dielectric Heterogeneity in a Membrane Protein: the Hetero-Oligomeric Cytochrome b6f Complex

    PubMed Central

    2015-01-01

    The cytochrome b6f complex, a member of the cytochrome bc family that mediates energy transduction in photosynthetic and respiratory membranes, is a hetero-oligomeric complex that utilizes two pairs of b-hemes in a symmetric dimer to accomplish trans-membrane electron transfer, quinone oxidation–reduction, and generation of a proton electrochemical potential. Analysis of electron storage in this pathway, utilizing simultaneous measurement of heme reduction, and of circular dichroism (CD) spectra, to assay heme–heme interactions, implies a heterogeneous distribution of the dielectric constants that mediate electrostatic interactions between the four hemes in the complex. Crystallographic information was used to determine the identity of the interacting hemes. The Soret band CD signal is dominated by excitonic interaction between the intramonomer b-hemes, bn and bp, on the electrochemically negative and positive sides of the complex. Kinetic data imply that the most probable pathway for transfer of the two electrons needed for quinone oxidation–reduction utilizes this intramonomer heme pair, contradicting the expectation based on heme redox potentials and thermodynamics, that the two higher potential hemes bn on different monomers would be preferentially reduced. Energetically preferred intramonomer electron storage of electrons on the intramonomer b-hemes is found to require heterogeneity of interheme dielectric constants. Relative to the medium separating the two higher potential hemes bn, a relatively large dielectric constant must exist between the intramonomer b-hemes, allowing a smaller electrostatic repulsion between the reduced hemes. Heterogeneity of dielectric constants is an additional structure–function parameter of membrane protein complexes. PMID:24867491

  10. Subpopulations of cholinergic, GABAergic and glutamatergic neurons in the pedunculopontine nucleus contain calcium-binding proteins and are heterogeneously distributed.

    PubMed

    Martinez-Gonzalez, Cristina; Wang, Hui-Ling; Micklem, Benjamin R; Bolam, J Paul; Mena-Segovia, Juan

    2012-03-01

    Neurons in the pedunculopontine nucleus (PPN) are highly heterogeneous in their discharge properties, their neurochemical markers, their pattern of connectivity and the behavioural processes in which they participate. Three main transmitter phenotypes have been described, cholinergic, GABAergic and glutamatergic, and yet electrophysiological evidence suggests heterogeneity within these subtypes. To gain further insight into the molecular composition of these three populations in the rat, we investigated the pattern of expression of calcium binding proteins (CBPs) across distinct regions of the PPN and in relation to the presence of other neurochemical markers. Calbindin- and calretinin-positive neurons are as abundant as cholinergic neurons, and their expression follows a rostro-caudal gradient, whereas parvalbumin is expressed by a low number of neurons. We observed a high degree of expression of CBPs by GABAergic and glutamatergic neurons, with a large majority of calbindin- and calretinin-positive neurons expressing GAD or VGluT2 mRNA. Notably, CBP-positive neurons expressing GAD mRNA were more concentrated in the rostral PPN, whereas the caudal PPN was characterized by a higher density of CBP-positive neurons expressing VGluT2 mRNA. In contrast to these two large populations, in cholinergic neurons expression of calretinin is observed only in low numbers and expression of calbindin is virtually non-existent. These findings thus identify novel subtypes of cholinergic, GABAergic and glutamatergic neurons based on their expression of CBPs, and further contribute to the notion of the PPN as a highly heterogeneous structure, an attribute that is likely to underlie its functional complexity.

  11. Promiscuous stimulation of ParF protein polymerization by heterogeneous centromere binding factors.

    PubMed

    Machón, Cristina; Fothergill, Timothy J G; Barillà, Daniela; Hayes, Finbarr

    2007-11-16

    The segrosome is the nucleoprotein complex that mediates accurate segregation of bacterial plasmids. The segrosome of plasmid TP228 comprises ParF and ParG proteins that assemble on the parH centromere. ParF, which exemplifies one clade of the ubiquitous ParA superfamily of segregation proteins, polymerizes extensively in response to ATP binding. Polymerization is modulated by the ParG centromere binding factor (CBF). The segrosomes of plasmids pTAR, pVT745 and pB171 include ParA homologues of the ParF subgroup, as well as diverse homodimeric CBFs with no primary sequence similarity to ParG, or each other. Centromere binding by these analogues is largely specific. Here, we establish that the ParF homologues of pTAR and pB171 filament modestly with ATP, and that nucleotide hydrolysis is not required for this polymerization, which is more prodigious when the cognate CBF is also present. By contrast, the ParF homologue of plasmid pVT745 did not respond appreciably to ATP alone, but polymerized extensively in the presence of both its cognate CBF and ATP. The co-factors also stimulated nucleotide-independent polymerization of cognate ParF proteins. Moreover, apart from the CBF of pTAR, the disparate ParG analogues promoted polymerization of non-cognate ParF proteins suggesting that filamentation of the ParF proteins is enhanced by a common mechanism. Like ParG, the co-factors may be modular, possessing a centromere-specific interaction domain linked to a flexible region containing determinants that promiscuously stimulate ParF polymerization. The CBFs appear to function as bacterial analogues of formins, microtubule-associated proteins or related ancillary factors that regulate eucaryotic cytoskeletal dynamics.

  12. Quaternary Structure Heterogeneity of Oligomeric Proteins: A SAXS and SANS Study of the Dissociation Products of Octopus vulgaris Hemocyanin

    PubMed Central

    Spinozzi, Francesco; Mariani, Paolo; Mičetić, Ivan; Ferrero, Claudio; Pontoni, Diego; Beltramini, Mariano

    2012-01-01

    Octopus vulgaris hemocyanin shows a particular self-assembling pattern, characterized by a hierarchical organization of monomers. The highest molecular weight aggregate is a decamer, the stability of which in solution depends on several parameters. Different pH values, buffer compositions, H2O/D2O ratios and Hofmeister’s salts result in modifications of the aggregation state of Octopus vulgaris hemocyanin. The new QUAFIT method, recently applied to derive the structure of the decameric and the monomeric assembly from small-angle scattering data, is used here to model the polydisperse system that results from changing the solution conditions. A dataset of small-angle X-rays and neutron scattering curves is analysed by QUAFIT to derive structure, composition and concentration of different assemblies present in solution. According to the hierarchy of the association/dissociation processes and the possible number of different aggregation products in solution, each sample has been considered as a heterogeneous mixture composed of the entire decamer, the dissociated “loose” monomer and all the intermediate dissociation products. Scattering curves corresponding to given experimental conditions are well fitted by using a linear combination of single particle form factors. QUAFIT has proved to be a method of general validity to describe solutions of proteins that, even after purification processes, result to be intrinsically heterogeneous. PMID:23166737

  13. The unconventional secretion of stress-inducible protein 1 by a heterogeneous population of extracellular vesicles.

    PubMed

    Hajj, Glaucia N M; Arantes, Camila P; Dias, Marcos Vinicios Salles; Roffé, Martín; Costa-Silva, Bruno; Lopes, Marilene H; Porto-Carreiro, Isabel; Rabachini, Tatiana; Lima, Flávia R; Beraldo, Flávio H; Prado, Marco A M; Prado, Marco M A; Linden, Rafael; Martins, Vilma R

    2013-09-01

    The co-chaperone stress-inducible protein 1 (STI1) is released by astrocytes, and has important neurotrophic properties upon binding to prion protein (PrP(C)). However, STI1 lacks a signal peptide and pharmacological approaches pointed that it does not follow a classical secretion mechanism. Ultracentrifugation, size exclusion chromatography, electron microscopy, vesicle labeling, and particle tracking analysis were used to identify three major types of extracellular vesicles (EVs) released from astrocytes with sizes ranging from 20-50, 100-200, and 300-400 nm. These EVs carry STI1 and present many exosomal markers, even though only a subpopulation had the typical exosomal morphology. The only protein, from those evaluated here, present exclusively in vesicles that have exosomal morphology was PrP(C). STI1 partially co-localized with Rab5 and Rab7 in endosomal compartments, and a dominant-negative for vacuolar protein sorting 4A (VPS4A), required for formation of multivesicular bodies (MVBs), impaired EV and STI1 release. Flow cytometry and PK digestion demonstrated that STI1 localized to the outer leaflet of EVs, and its association with EVs greatly increased STI1 activity upon PrP(C)-dependent neuronal signaling. These results indicate that astrocytes secrete a diverse population of EVs derived from MVBs that contain STI1 and suggest that the interaction between EVs and neuronal surface components enhances STI1-PrP(C) signaling.

  14. MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers

    PubMed Central

    Ohue, Masahito; Shimoda, Takehiro; Suzuki, Shuji; Matsuzaki, Yuri; Ishida, Takashi; Akiyama, Yutaka

    2014-01-01

    Summary: The application of protein–protein docking in large-scale interactome analysis is a major challenge in structural bioinformatics and requires huge computing resources. In this work, we present MEGADOCK 4.0, an FFT-based docking software that makes extensive use of recent heterogeneous supercomputers and shows powerful, scalable performance of >97% strong scaling. Availability and Implementation: MEGADOCK 4.0 is written in C++ with OpenMPI and NVIDIA CUDA 5.0 (or later) and is freely available to all academic and non-profit users at: http://www.bi.cs.titech.ac.jp/megadock. Contact: akiyama@cs.titech.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online PMID:25100686

  15. A simple two-state protein unfolds mechanically via multiple heterogeneous pathways at single-molecule resolution

    NASA Astrophysics Data System (ADS)

    Schönfelder, Jörg; Perez-Jimenez, Raul; Muñoz, Victor

    2016-06-01

    A major drive in protein folding has been to develop experimental technologies to resolve the myriads of microscopic pathways and complex mechanisms that purportedly underlie simple two-state folding behaviour. This is key for cross-validating predictions from theory and modern computer simulations. Detecting such complexity experimentally has remained elusive even using methods with improved time, structural or single-molecule resolution. Here, we investigate the mechanical unfolding of cold shock protein B (Csp), a showcase two-state folder, using single-molecule force-spectroscopy. Under controlled-moderate pulling forces, the unfolding of Csp emerges as highly heterogeneous with trajectories ranging from single sweeps to different combinations of multiple long-lived mechanical intermediates that also vary in order of appearance. Steered molecular dynamics simulations closely reproduce the experimental observations, thus matching unfolding patterns with structural events. Our results provide a direct glimpse at the nanoscale complexity underlying two-state folding, and postulate these combined methods as unique tools for dissecting the mechanical unfolding mechanisms of such proteins.

  16. A simple two-state protein unfolds mechanically via multiple heterogeneous pathways at single-molecule resolution

    PubMed Central

    Schönfelder, Jörg; Perez-Jimenez, Raul; Muñoz, Victor

    2016-01-01

    A major drive in protein folding has been to develop experimental technologies to resolve the myriads of microscopic pathways and complex mechanisms that purportedly underlie simple two-state folding behaviour. This is key for cross-validating predictions from theory and modern computer simulations. Detecting such complexity experimentally has remained elusive even using methods with improved time, structural or single-molecule resolution. Here, we investigate the mechanical unfolding of cold shock protein B (Csp), a showcase two-state folder, using single-molecule force-spectroscopy. Under controlled-moderate pulling forces, the unfolding of Csp emerges as highly heterogeneous with trajectories ranging from single sweeps to different combinations of multiple long-lived mechanical intermediates that also vary in order of appearance. Steered molecular dynamics simulations closely reproduce the experimental observations, thus matching unfolding patterns with structural events. Our results provide a direct glimpse at the nanoscale complexity underlying two-state folding, and postulate these combined methods as unique tools for dissecting the mechanical unfolding mechanisms of such proteins. PMID:27248054

  17. Protein Stable Isotope Fingerprinting (P-SIF): A New Tool to Understand Natural Isotopic Heterogeneity of Mixed Microbial Ecosystems

    NASA Astrophysics Data System (ADS)

    Pearson, A.; Mohr, W.; Tang, T.; Sattin, S.; Bovee, R.

    2014-12-01

    Protein stable isotope fingerprinting (P-SIF) is a method to measure the carbon isotope ratios of whole proteins separated from complex mixtures, including cultures and environmental samples. The goal of P-SIF is to expose the links between identity and function in microbial ecosystems by (i) determining the ratios of 13C/12C (values of δ13C) for different taxonomic divisions, and (ii) using those values as clues to the metabolic pathways employed by the respective organisms, while (iii) not perturbing the system, i.e., not adding exogenous substrates or isotope labels. To accomplish this, we employ two-dimensional HPLC to resolve a sample containing ca. 5-10 mg of mixed proteins into 960-1440 fractions. Each fraction then is split in two aliquots: The first is digested with trypsin for peptide sequencing, while the second is measured in triplicate using an isotope-ratio mass spectrometer interfaced with a spooling wire microcombustion device. Data from pure cultures show that bacteria have a narrow distribution of protein δ13C values within individual taxa (±0.7-1.2‰, 1σ). This is moderately larger than the mean precision of the triplicate isotope measurements (±0.5‰, 1σ) and may reflect heterogeneous distribution of 13C among the amino acids. When cells from different species are mixed together prior to protein extraction and separation, the results can predict accurately (to within ±1σ) the δ13C values of the original taxa. The number of data points required for this endmember prediction is ≥20/taxon, yielding a theoretical resolution of ca. 10 taxonomic units/sample. Initial tests on environmental samples suggest the approach will be useful to determine the overall trophic breadth of mixed microbial ecosystems.

  18. Mapping protein conformational heterogeneity under pressure with site-directed spin labeling and double electron–electron resonance

    PubMed Central

    Lerch, Michael T.; Yang, Zhongyu; Brooks, Evan K.; Hubbell, Wayne L.

    2014-01-01

    The dominance of a single native state for most proteins under ambient conditions belies the functional importance of higher-energy conformational states (excited states), which often are too sparsely populated to allow spectroscopic investigation. Application of high hydrostatic pressure increases the population of excited states for study, but structural characterization is not trivial because of the multiplicity of states in the ensemble and rapid (microsecond to millisecond) exchange between them. Site-directed spin labeling in combination with double electron–electron resonance (DEER) provides long-range (20–80 Å) distance distributions with angstrom-level resolution and thus is ideally suited to resolve conformational heterogeneity in an excited state populated under high pressure. DEER currently is performed at cryogenic temperatures. Therefore, a method was developed for rapidly freezing spin-labeled proteins under pressure to kinetically trap the high-pressure conformational ensemble for subsequent DEER data collection at atmospheric pressure. The methodology was evaluated using seven doubly-labeled mutants of myoglobin designed to monitor selected interhelical distances. For holomyoglobin, the distance distributions are narrow and relatively insensitive to pressure. In apomyoglobin, on the other hand, the distributions reveal a striking conformational heterogeneity involving specific helices in the pressure range of 0–3 kbar, where a molten globule state is formed. The data directly reveal the amplitude of helical fluctuations, information unique to the DEER method that complements previous rate determinations. Comparison of the distance distributions for pressure- and pH-populated molten globules shows them to be remarkably similar despite a lower helical content in the latter. PMID:24707053

  19. Primary structures of the heterogeneous nuclear ribonucleoprotein A2, B1, and C2 proteins: a diversity of RNA binding proteins is generated by small peptide inserts.

    PubMed Central

    Burd, C G; Swanson, M S; Görlach, M; Dreyfuss, G

    1989-01-01

    We have isolated cDNAs for the major heterogeneous nuclear ribonucleoprotein (hnRNP) A2, B1, and C2 proteins and determined their nucleotide and deduced amino acid sequences. The A2 and B1 cDNAs are identical except for a 36-nucleotide in-frame insert in B1. Similarly, the sequence of the C2 protein cDNA is related to that of C1 in that C2 contains an extra 39 in-frame nucleotides. Therefore, the B1 amino acid sequence is identical to A2 except for the insertion of 12 amino acids near its amino terminus, and C1 and C2 are also identical to each other except for an extra 13 amino acids near the middle of C2. All three proteins are members of a large family of RNA binding proteins that contain the consensus sequence-type RNA binding domain (CS-RBD). The A2 and B1 proteins have a modular structure similar to that of the hnRNP protein A1: they contain two CS-RBDs and a glycine-rich auxiliary domain at the carboxyl terminus. The CS-RBDs of A2 and B1 have approximately 80% amino acid identity with those of A1, whereas the glycine-rich auxiliary domain is considerably more divergent with less than 30% of the amino acids being identical. These findings indicate that the addition of small peptides, probably by alternative pre-mRNA splicing, generates some of the diversity apparent among hnRNP proteins. Images PMID:2557628

  20. Heterogeneity of the cold-insoluble globulin of human plasma (CIg), a circulating cell surface protein.

    PubMed

    Chen, A B; Amrani, D L; Mosesson, M W

    1977-08-23

    The cold-insoluble globulin of human plasma (CIg), a circulating cell surface protein, exists in multiple molecular forms. Most molecules are found as two chain (MR approximately 220 000 per chain) disulfide-bridged dimeric units but several minor components of smaller size have also been identified; based upon their migration rates in dodecyl sulfate gel electrophoretic experiments, the smaller molecules characterized in this study range in molecular size from 235 000 to 146 000. The component of molecular weight 235 000 apparently represents a two chain disulfide-bridged derivative of larger parent molecules (one chain of 220 000 plus a smaller remnant), whereas smaller CIg components appear to be single chain proteins. These observations plus electrophoretic analyses of samples of plasmic digests of CIg indicate that the interchain disulfide bridging in the two chain molecule is located in a segment within approx. 175 residues of the NH2- or COOH-terminus.

  1. Energy transfer at heterogeneous protein-protein interfaces to investigate the molecular behaviour in the crowding environment

    NASA Astrophysics Data System (ADS)

    Ota, Chikashi

    2017-03-01

    Investigation of the behaviour of proteins in crowded environments is crucial for understanding the role of proteins in biological environments. In this study, the behaviour of bovine serum albumin (BSA) in crowded (highly concentrated) environments was investigated using time-resolved fluorescence spectroscopy as a model system. By using energy transfer as a molecular ruler, the crowding effect was clearly observed in the time resolved spectra. In addition, by using both time resolved anisotropy measurement and Raman spectroscopy, more detail insights from conformational and dynamic points of view were described. Consequently, it was revealed that in the highly concentrated solution, most of the BSA molecules are in the fast-reversible oligomeric state and the association at the "hard" and "soft" interfaces between protein surfaces occurred in a highly crowded environment with the aid of a charge-charge and short-range attractive interface. From both the conformational and dynamic aspects, the detail spectroscopic understanding of the behaviour of BSA in the crowding environment was obtained.

  2. Heterogeneity of Arabinogalactan-Proteins on the Plasma Membrane of Rose Cells.

    PubMed Central

    Serpe, M. D.; Nothnagel, E. A.

    1996-01-01

    Arabinogalactan-proteins (AGPs) have been purified from the plasma membrane of suspension-cultured Paul's Scarlet rose (Rosa sp.) cells. The two most abundant and homogeneous plasma membrane AGP fractions were named plasma membrane AGP1 (PM-AGP1) and plasma membrane AGP2 (PM-AGP2) and had apparent molecular masses of 140 and 217 kD, respectively. Both PM-AGP1 and PM-AGP2 had [beta]-(1-3)-, [beta]-(1,6)-, and [beta]-(1,3,6)-galactopyranosyl residues, predominantly terminal [alpha]-arabinofuranosyl residues, and (1,4)- and terminal glucuronopyranosyl residues. The protein moieties of PM-AGP1 and PM-AGP2 were both rich in hydroxyproline, alanine, and serine, but differed in the abundance of hydroxyproline, which was 1.6 times higher in PM-AGP2 than in PM-AGP1. Another difference was the overall protein content, which was 3.7% (w/w) in PM-AGP1 and 15% in PM-AGP2. As judged by their behavior on reverse-phase chromatography, PM-AGP1 and PM-AGP2 were not more hydrophobic than AGPs from the cell wall or culture medium. In contrast, a minor plasma membrane AGP fraction eluted later on reverse-phase chromatography and was more negatively charged at pH 5 than either PM-AGP1 or PM-AGP2. The more negatively charged fraction contained molecules with a glycosyl composition characteristic of AGPs and included at least two different macromolecules. The results of this investigation indicate that Rosa plasma membrane contains at least four distinct AGPs or AGP-like molecules. These molecules differed from each other in size, charge, hydrophobicity, amino-acyl composition, and/or protein content. PMID:12226444

  3. Protein Interaction Network Underpins Concordant Prognosis Among Heterogeneous Breast Cancer Signatures

    PubMed Central

    Chen, James; Sam, Lee; Huang, Yong; Lee, Younghee; Li, Jianrong; Liu, Yang; Xing, H. Rosie; Lussier, Yves A.

    2010-01-01

    Characterizing the biomolecular systems’ properties underpinning prognosis signatures derived from gene expression profiles remains a key clinical and biological challenge. In breast cancer, while different “poor-prognosis” sets of genes have predicted patient survival outcome equally well in independent cohorts, these prognostic signatures have surprisingly little genetic overlap. We examine ten such published expression-based signatures that are predictors or distinct breast cancer phenotypes, uncover their mechanistic interconnectivity through a protein-protein interaction network, and introduce a novel cross-“gene expression signature” analysis method using (i) domain knowledge to constrain multiple comparisons in a mechanistically relevant single-gene network interactions, and (ii) scale-free permutation resampling to statistically control for hubness (SPAN - Single Protein Analysis of Network with constant node degree per protein). At adjusted p-values < 5%, 54 genes thus identified have a significantly greater connectivity than those through meticulous permutation resampling of the context-constrained network. More importantly, eight of ten genetically non-overlapping signatures are connected through well-established mechanisms of breast cancer oncogenesis and progression. Gene Ontology enrichment studies demonstrate common markers of cell cycle regulation. Kaplan-Meier analysis of three independent historical gene expression sets confirms this network-signature’s inherent ability to identify “poor outcome” in ER(+) patients without the requirement of machine learning. We provide a novel demonstration that genetically distinct prognosis signatures, developed from independent clinical datasets, occupy overlapping prognostic space of breast cancer via shared mechanisms that are mediated by genetically different yet mechanistically comparable interactions among proteins of differentially expressed genes in the signatures. This is the first study

  4. Structure of a heterogeneous, glycosylated, lipid-bound, in vivo-grown protein crystal at atomic resolution from the viviparous cockroach Diploptera punctata

    PubMed Central

    Banerjee, Sanchari; Coussens, Nathan P.; Gallat, François-Xavier; Sathyanarayanan, Nitish; Srikanth, Jandhyam; Yagi, Koichiro J.; Gray, James S. S.; Tobe, Stephen S.; Stay, Barbara; Chavas, Leonard M. G.; Ramaswamy, Subramanian

    2016-01-01

    Macromolecular crystals for X-ray diffraction studies are typically grown in vitro from pure and homogeneous samples; however, there are examples of protein crystals that have been identified in vivo. Recent developments in micro-crystallography techniques and the advent of X-ray free-electron lasers have allowed the determination of several protein structures from crystals grown in cellulo. Here, an atomic resolution (1.2 Å) crystal structure is reported of heterogeneous milk proteins grown inside a living organism in their functional niche. These in vivo-grown crystals were isolated from the midgut of an embryo within the only known viviparous cockroach, Diploptera punctata. The milk proteins crystallized in space group P1, and a structure was determined by anomalous dispersion from the native S atoms. The data revealed glycosylated proteins that adopt a lipocalin fold, bind lipids and organize to form a tightly packed crystalline lattice. A single crystal is estimated to contain more than three times the energy of an equivalent mass of dairy milk. This unique storage form of nourishment for developing embryos allows access to a constant supply of complete nutrients. Notably, the crystalline cockroach-milk proteins are highly heterogeneous with respect to amino-acid sequence, glycosylation and bound fatty-acid composition. These data present a unique example of protein heterogeneity within a single in vivo-grown crystal of a natural protein in its native environment at atomic resolution. PMID:27437115

  5. Structure of a heterogeneous, glycosylated, lipid-bound, in vivo-grown protein crystal at atomic resolution from the viviparous cockroach Diploptera punctata.

    PubMed

    Banerjee, Sanchari; Coussens, Nathan P; Gallat, François-Xavier; Sathyanarayanan, Nitish; Srikanth, Jandhyam; Yagi, Koichiro J; Gray, James S S; Tobe, Stephen S; Stay, Barbara; Chavas, Leonard M G; Ramaswamy, Subramanian

    2016-07-01

    Macromolecular crystals for X-ray diffraction studies are typically grown in vitro from pure and homogeneous samples; however, there are examples of protein crystals that have been identified in vivo. Recent developments in micro-crystallography techniques and the advent of X-ray free-electron lasers have allowed the determination of several protein structures from crystals grown in cellulo. Here, an atomic resolution (1.2 Å) crystal structure is reported of heterogeneous milk proteins grown inside a living organism in their functional niche. These in vivo-grown crystals were isolated from the midgut of an embryo within the only known viviparous cockroach, Diploptera punctata. The milk proteins crystallized in space group P1, and a structure was determined by anomalous dispersion from the native S atoms. The data revealed glycosylated proteins that adopt a lipocalin fold, bind lipids and organize to form a tightly packed crystalline lattice. A single crystal is estimated to contain more than three times the energy of an equivalent mass of dairy milk. This unique storage form of nourishment for developing embryos allows access to a constant supply of complete nutrients. Notably, the crystalline cockroach-milk proteins are highly heterogeneous with respect to amino-acid sequence, glycosylation and bound fatty-acid composition. These data present a unique example of protein heterogeneity within a single in vivo-grown crystal of a natural protein in its native environment at atomic resolution.

  6. Regional and phenotype heterogeneity of cellular prion proteins in the human brain.

    PubMed

    Kuczius, Thorsten; Koch, Richard; Keyvani, Kathy; Karch, Helge; Grassi, Jacques; Groschup, Martin H

    2007-05-01

    Transmissible spongiform encephalopathies (TSEs) are neurological disorders that include genetic, infectious and sporadic forms of human Creutzfeldt-Jakob disease (CJD). The pathogenic agent is the prion protein that is composed of an abnormal isoform (PrP(Sc)) of a host-encoded protein (PrP(C)). Analysis of the relative amounts of PrP(Sc) glycoforms has been used to discriminate between various agents involved in TSE. The distribution and efficiency of conversion to PrP(Sc) can be influenced by differences in the expression of PrP(C). However, little attention has been given so far to the banding patterns of PrP(C). Using four different antibodies recognizing amino- and carboxyl-terminal PrP sequences we analysed the glycoforms of PrP(C) in seven regions of the human brain using brains obtained from six subjects. For determination of the staining intensities, signals were quantified by densitometry and reproducible patterns were accomplished by many repeated immunoblot analyses. When amino-terminal binding antibodies were used for detection, PrP(C) in the frontal neocortex, nucleus lentiformis, thalamus, hippocampus and cerebellum displayed a glycotype with high staining of the diglycosylated isoforms. This was different from patterns in the pons and medulla oblongata, which showed a high intensity of the nonglycosylated isoform, and PrP(C) proteins, approximately 27 kDa in size, exhibited high staining using the carboxyl-terminal binding antibodies. This intense staining followed from an overlay of full-length and truncated PrP(C) isoforms. Furthermore, we found marked differences in the expression of PrP(C). Variations in the processing of PrP(C) may lead to interregional differences in the glycoform composition of PrP(Sc) in human brains.

  7. Quantitative model for the heterogeneity of atomic position fluctuations in proteins: A simulation study

    SciTech Connect

    Kneller, Gerald R.; Hinsen, Konrad

    2009-07-28

    We propose a simple analytical model for the elastic incoherent structure factor of proteins measured by neutron scattering, which allows extracting the distribution of atomic position fluctuations from a fit of the model to the experimental data. The method is validated by applying it to elastic incoherent structure factors of lysozyme which have been obtained by molecular dynamics simulation and by normal mode analysis, respectively, and for which distributions of the atomic position fluctuations can be generated numerically for direct comparison with the predictions of the model. The comparison shows a remarkable agreement, in particular, concerning the lower limit for the position fluctuations, which is pronounced in the numerical data.

  8. An eriophyid mite-transmitted plant virus contains eight genomic RNA segments with unusual heterogeneity in the nucleocapsid protein.

    PubMed

    Tatineni, Satyanarayana; McMechan, Anthony J; Wosula, Everlyne N; Wegulo, Stephen N; Graybosch, Robert A; French, Roy; Hein, Gary L

    2014-10-01

    Eriophyid mite-transmitted, multipartite, negative-sense RNA plant viruses with membrane-bound spherical virions are classified in the genus Emaravirus. We report here that the eriophyid mite-transmitted Wheat mosaic virus (WMoV), an Emaravirus, contains eight genomic RNA segments, the most in a known negative-sense RNA plant virus. Remarkably, two RNA 3 consensus sequences, encoding the nucleocapsid protein, were found with 12.5% sequence divergence, while no heterogeneity was observed in the consensus sequences of additional genomic RNA segments. The RNA-dependent RNA polymerase, glycoprotein precursor, nucleocapsid, and P4 proteins of WMoV exhibited limited sequence homology with the orthologous proteins of other emaraviruses, while proteins encoded by additional genomic RNA segments displayed no significant homology with proteins reported in GenBank, suggesting that the genus Emaravirus evolved further with a divergent octapartite genome. Phylogenetic analyses revealed that WMoV formed an evolutionary link between members of the Emaravirus genus and the family Bunyaviridae. Furthermore, genomic-length virus- and virus-complementary (vc)-sense strands of all WMoV genomic RNAs accumulated asymmetrically in infected wheat, with 10- to 20-fold more virus-sense genomic RNAs than vc-sense RNAs. These data further confirm the octapartite negative-sense polarity of the WMoV genome. In WMoV-infected wheat, subgenomic-length mRNAs of vc sense were detected for genomic RNAs 3, 4, 7, and 8 but not for other RNA species, suggesting that the open reading frames present in the complementary sense of genomic RNAs are expressed through subgenomic- or near-genomic-length vc-sense mRNAs. Importance: Wheat mosaic virus (WMoV), an Emaravirus, is the causal agent of High Plains disease of wheat and maize. In this study, we demonstrated that the genome of WMoV comprises eight negative-sense RNA segments with an unusual sequence polymorphism in an RNA encoding the nucleocapsid protein

  9. Molecular heterogeneity in major urinary proteins of Mus musculus subspecies: potential candidates involved in speciation

    PubMed Central

    Hurst, Jane L.; Beynon, Robert J.; Armstrong, Stuart D.; Davidson, Amanda J.; Roberts, Sarah A.; Gómez-Baena, Guadalupe; Smadja, Carole M.; Ganem, Guila

    2017-01-01

    When hybridisation carries a cost, natural selection is predicted to favour evolution of traits that allow assortative mating (reinforcement). Incipient speciation between the two European house mouse subspecies, Mus musculus domesticus and M.m.musculus, sharing a hybrid zone, provides an opportunity to understand evolution of assortative mating at a molecular level. Mouse urine odours allow subspecific mate discrimination, with assortative preferences evident in the hybrid zone but not in allopatry. Here we assess the potential of MUPs (major urinary proteins) as candidates for signal divergence by comparing MUP expression in urine samples from the Danish hybrid zone border (contact) and from allopatric populations. Mass spectrometric characterisation identified novel MUPs in both subspecies involving mostly new combinations of amino acid changes previously observed in M.m.domesticus. The subspecies expressed distinct MUP signatures, with most MUPs expressed by only one subspecies. Expression of at least eight MUPs showed significant subspecies divergence both in allopatry and contact zone. Another seven MUPs showed divergence in expression between the subspecies only in the contact zone, consistent with divergence by reinforcement. These proteins are candidates for the semiochemical barrier to hybridisation, providing an opportunity to characterise the nature and evolution of a putative species recognition signal. PMID:28337988

  10. Heterogeneous nuclear expression of the promyelocytic leukemia (PML) protein in normal and neoplastic human tissues.

    PubMed Central

    Gambacorta, M.; Flenghi, L.; Fagioli, M.; Pileri, S.; Leoncini, L.; Bigerna, B.; Pacini, R.; Tanci, L. N.; Pasqualucci, L.; Ascani, S.; Mencarelli, A.; Liso, A.; Pelicci, P. G.; Falini, B.

    1996-01-01

    The RING-finger promyelocytic leukemia (PML) protein is the product of the PML gene that fuses with the retinoic acid receptor-alpha gene in the t(15; 17) translocation of acute promyelocytic leukemia. Wild-type PML localizes in the nucleus with a typical speckled pattern that is a consequence of the concentration of the protein within discrete subnuclear domains known as nuclear bodies. Delocalization of PML from nuclear bodies has been documented in acute promyelocytic leukemia cells and suggested to contribute to leukemogenesis. In an attempt to get new insights into the function of the wild-type PML protein and to investigate whether it displays an altered expression pattern in neoplasms other than acute promyelocytic leukemia, we stained a large number of normal and neoplastic human tissues with a new murine monoclonal antibody (PG-M3) directed against the amino-terminal region of PML. As the PG-M3 epitope is partially resistant to fixatives, only cells that overexpress PML are detected by the antibody in microwave-heated paraffin sections. Among normal tissues, PML was characteristically up-regulated in activated epithelioid histiocytes and fibroblasts in a variety of pathological conditions, columnar epithelium in small active thyroid follicles, well differentiated foamy cells in the center of sebaceous glands, and hypersecretory endometria (Arias-Stella). Interferons, the PML of which is a primary target gene, and estrogens are likely to represent some of the cytokines and/or hormones that may be involved in the up-regulation of PML under these circumstances. In keeping with this concept, we found that PML is frequently overexpressed in Hodgkin and Reed-Sternberg cells of Hodgkin's disease, a tumor of cytokine-producing cells. Among solid tumors, overexpression of PML was frequently found in carcinomas of larynx and thyroid (papillary), epithelial thymomas, and Kaposi's sarcoma, whereas carcinomas of the lung, thyroid (follicular), breast, and colon were

  11. Intratumoral heterogeneity analysis reveals hidden associations between protein expression losses and patient survival in clear cell renal cell carcinoma

    PubMed Central

    Devarajan, Karthik; Parsons, Theodore; Wang, Qiong; O'Neill, Raymond; Solomides, Charalambos; Peiper, Stephen C.; Testa, Joseph R.; Uzzo, Robert; Yang, Haifeng

    2017-01-01

    Intratumoral heterogeneity (ITH) is a prominent feature of kidney cancer. It is not known whether it has utility in finding associations between protein expression and clinical parameters. We used ITH that is detected by immunohistochemistry (IHC) to aid the association analysis between the loss of SWI/SNF components and clinical parameters.160 ccRCC tumors (40 per tumor stage) were used to generate tissue microarray (TMA). Four foci from different regions of each tumor were selected. IHC was performed against PBRM1, ARID1A, SETD2, SMARCA4, and SMARCA2. Statistical analyses were performed to correlate biomarker losses with patho-clinical parameters. Categorical variables were compared between groups using Fisher's exact tests. Univariate and multivariable analyses were used to correlate biomarker changes and patient survivals. Multivariable analyses were performed by constructing decision trees using the classification and regression trees (CART) methodology. IHC detected widespread ITH in ccRCC tumors. The statistical analysis of the “Truncal loss” (root loss) found additional correlations between biomarker losses and tumor stages than the traditional “Loss in tumor (total)”. Losses of SMARCA4 or SMARCA2 significantly improved prognosis for overall survival (OS). Losses of PBRM1, ARID1A or SETD2 had the opposite effect. Thus “Truncal Loss” analysis revealed hidden links between protein losses and patient survival in ccRCC. PMID:28445125

  12. Genomic and transcriptional analysis of protein heterogeneity of the honeybee venom allergen Api m 6.

    PubMed

    Peiren, N; de Graaf, D C; Evans, J D; Jacobs, F J

    2006-10-01

    Several components of honeybee venom are known to cause allergenic responses in humans and other vertebrates. One such component, the minor allergen Api m 6, has been known to show amino acid variation but the genetic mechanism for this variation is unknown. Here we show that Api m 6 is derived from a single locus, and that substantial protein-level variation has a simple genome-level cause, without the need to invoke multiple loci or alternatively spliced exons. Api m 6 sits near a misassembled section of the honeybee genome sequence, and we propose that a substantial number of indels at and near Api m 6 might be the root cause of this misassembly. We suggest that genes such as Api m 6 with coding-region or untranslated region indels might have had a strong effect on the assembly of this draft of the honeybee genome.

  13. Evidence for conformational heterogeneity of fission protein Fis1 from Saccharomyces cerevisiae.

    PubMed

    Picton, Lora K; Casares, Salvador; Monahan, Ann C; Majumdar, Ananya; Hill, R Blake

    2009-07-21

    Fission 1 (Fis1) is an evolutionarily conserved, type II integral membrane protein implicated in maintaining the proper morphology of mitochondria and peroxisomes. A concave surface on the cytosolic domain of Fis1 from Saccharomyces cerevisiae is implicated in binding other fission proteins, yet structural studies reveal that this surface is sterically occluded by its N-terminal arm. Here we address the question of whether the N-terminal arm of yeast Fis1 exists in a dynamic equilibrium that would allow access to this functionally important surface. NMR measurements sensitive to dynamics occurring on a wide range of time scales (picoseconds to minutes) were used to assess whether the Fis1 arm is dynamic. Hydrogen-deuterium exchange experiments revealed that the Fis1 arm, alpha-helix 6, and proximal loops were not protected from solvent exchange, consistent with motions on the second to minute time scale. An engineered cysteine, I85C, located on the concave surface that lies underneath the Fis1 arm, was readily modified by a fluorescent probe, revealing more solvent accessibility of this position than would be predicted from the structure. Chemical denaturation, NMR chemical shift perturbation, and residual dipolar coupling experiments support the idea that the dynamic equilibrium can be shifted on the basis of changing pH and temperature, with the changes primarily localizing to the Fis1 arm and proximal regions. The data as a whole are consistent with the Fis1 arm adopting a primarily "closed" conformational state able to undergo dynamic excursions that reveal the concave surface and therefore may be important for binding other fission factors and for Fis1 function.

  14. Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems

    NASA Astrophysics Data System (ADS)

    Johnson, Margaret E.; Hummer, Gerhard

    2014-07-01

    We present a new algorithm for simulating reaction-diffusion equations at single-particle resolution. Our algorithm is designed to be both accurate and simple to implement, and to be applicable to large and heterogeneous systems, including those arising in systems biology applications. We combine the use of the exact Green's function for a pair of reacting particles with the approximate free-diffusion propagator for position updates to particles. Trajectory reweighting in our free-propagator reweighting (FPR) method recovers the exact association rates for a pair of interacting particles at all times. FPR simulations of many-body systems accurately reproduce the theoretically known dynamic behavior for a variety of different reaction types. FPR does not suffer from the loss of efficiency common to other path-reweighting schemes, first, because corrections apply only in the immediate vicinity of reacting particles and, second, because by construction the average weight factor equals one upon leaving this reaction zone. FPR applications include the modeling of pathways and networks of protein-driven processes where reaction rates can vary widely and thousands of proteins may participate in the formation of large assemblies. With a limited amount of bookkeeping necessary to ensure proper association rates for each reactant pair, FPR can account for changes to reaction rates or diffusion constants as a result of reaction events. Importantly, FPR can also be extended to physical descriptions of protein interactions with long-range forces, as we demonstrate here for Coulombic interactions.

  15. Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems

    PubMed Central

    Hummer, Gerhard

    2015-01-01

    We present a new algorithm for simulating reaction-diffusion equations at single-particle resolution. Our algorithm is designed to be both accurate and simple to implement, and to be applicable to large and heterogeneous systems, including those arising in systems biology applications. We combine the use of the exact Green's function for a pair of reacting particles with the approximate free-diffusion propagator for position updates to particles. Trajectory reweighting in our free-propagator reweighting (FPR) method recovers the exact association rates for a pair of interacting particles at all times. FPR simulations of many-body systems accurately reproduce the theoretically known dynamic behavior for a variety of different reaction types. FPR does not suffer from the loss of efficiency common to other path-reweighting schemes, first, because corrections apply only in the immediate vicinity of reacting particles and, second, because by construction the average weight factor equals one upon leaving this reaction zone. FPR applications include the modeling of pathways and networks of protein-driven processes where reaction rates can vary widely and thousands of proteins may participate in the formation of large assemblies. With a limited amount of bookkeeping necessary to ensure proper association rates for each reactant pair, FPR can account for changes to reaction rates or diffusion constants as a result of reaction events. Importantly, FPR can also be extended to physical descriptions of protein interactions with long-range forces, as we demonstrate here for Coulombic interactions. PMID:26005592

  16. Heterogeneous nuclear ribonucleoprotein F/H proteins modulate the alternative splicing of the apoptotic mediator Bcl-x.

    PubMed

    Garneau, Daniel; Revil, Timothée; Fisette, Jean-François; Chabot, Benoit

    2005-06-17

    Bcl-x is a member of the Bcl-2 family of proteins that are key regulators of apoptosis. The Bcl-x pre-mRNA is alternatively spliced to yield Bcl-x(S) and Bcl-x(L), two isoforms that have been associated, respectively, with the promotion and the prevention of apoptosis. We have investigated some of the elements and factors involved in the production of these two splice variants. Deletion mutagenesis using a human Bcl-x minigene identifies two regions in exon 2 that modulate Bcl-x 5'-splice site selection in human HeLa cells. One region (B3) is located upstream of the Bcl-x(L) 5'-splice site and enforces Bcl-x(L) production in cells and splicing extracts. The other region (B2) is located immediately downstream of the 5'-splice site of Bcl-x(S) and favors Bcl-x(S) production in vivo and in vitro. A 30-nucleotide G-rich element (B2G) is responsible for the activity of the B2 element. We show that recombinant heterogeneous nuclear ribonucleoprotein (hnRNP) F and H proteins bind to B2G, and mutating the G stretches abolishes binding. Moreover, the addition of hnRNP F to a HeLa extract improved the production of the Bcl-x(S) variant in a manner that was dependent on the integrity of the G stretches in B2G. Consistent with the in vitro results, small interfering RNA-mediated RNA interference targeting hnRNP F and H decreased the Bcl-x(S)/Bcl-x(L) ratio of plasmid-derived and endogenously produced Bcl-x transcripts. Our results document a positive role for the hnRNP F/H proteins in the production of the proapoptotic regulator Bcl-x(S.).

  17. Restriction of immunoglobulin heterogeneity, autoimmunity and serum protein levels in aged people.

    PubMed Central

    Riesen, W; Keller, H; Skvaril, F; Morell, A; Barandun, S

    1976-01-01

    Ninety-one sera of persons above 80 years of age were screened for autoantibody activity against lipoproteins (anti-LDL 7, anti-HDL 6 positive), for rheumatoid factor activity (Latex 14, Waaler-Rose 7 positive) and for antinuclear factors (11 positive). Among the sera with autoantibody activity 29 percent showed deviations of the normal kappa/lambda ratio of immunoglobulins, as opposed to 22 percent of the sera without detected autoantibody activity. In 3 percent of the sera an M component was detected. Determination of the alpha1-acid glycoprotein, alpha1-antitrypsin, haptoglobin, haemopexin, complement component C3c and C4, IgG, IgA and IgM levels showed significant increases in alpha-, and beta-globulins as well as in IgG and IgA in sera of the aged persons as compared to a normal population between 20 and 60 years old. No significant difference was noted between the gamma-globulin concentration in sera of aged persons with or without autoantibody activity. The evaluation of the relationship between serum protein levels and alterations of the kappa/lambda ratio indicated that the alpha- and the beta-globulins were significantly raised in sera with altered kappa/lambda ratios, whereas, with the exception of M component containing sera the gamma-globulin levels seemed not significantly affected by changes in this ratio. PMID:62632

  18. Heterogeneous nuclear ribonucleoprotein E1 regulates protein disulphide isomerase translation in oxidized low-density lipoprotein-activated endothelial cells.

    PubMed

    Meng, N; Peng, N; Huang, S; Wang, S Q; Zhao, J; Su, L; Zhang, Y; Zhang, S; Zhao, B; Miao, J

    2015-03-01

    Endothelium-derived protein disulphide isomerase (PDI) is required for thrombus formation in vivo. But, how to control PDI overproduction in oxidized low-density lipoprotein (oxLDL)-activated vascular endothelial cells (VECs) is not well understood. In this study, we try to answer this question using our newly identified activator of mTOC1 3-benzyl-5-((2-nitrophenoxy) methyl)-dihydrofuran-2 (3H)-one (3BDO) that has been shown to protect VECs. First, we performed a proteomics analysis on the oxLDL-activated vascular VECs in the presence or absence of 3BDO. Next, we constructed the heterogeneous nuclear ribonucleoprotein E1 (hnRNP E1) mutants at Ser43 and used the RNA-ChIP technique to investigate the relationship between hnRNP E1 and PDI production. Furthermore, we examined the effect of 3BDO on oxLDL-altered phosphorylation of Akt1 and Akt2. Finally, we studied the effect of 3BDO on oxLDL-altered PDI protein level in apolipoprotein E(-/-) mice with advanced atherosclerosis. In VECs, oxLDL-increased PDI protein level, induced hnRNP E1 phosphorylation at Ser43, suppressed the binding of hnRNP E1 to PDI 5'UTR and induced the phosphorylation of Akt2 but not Akt1. All of these processes were blocked by 3BDO. Importantly, Ser43 mutant of hnRNP E1 inhibited the increase of PDI protein level and the decrease of the binding of hnRNP E1 and PDI 5'UTR induced by oxLDL. Furthermore, 3BDO suppressed oxLDL-induced PDI protein increase in the serum and plaque endothelium of apolipoprotein E(-/-) mice. hnRNP E1 is a new regulator of PDI translation in oxLDL-activated VECs, and 3BDO is a powerful agent for controlling PDI overproduction. © 2014 Scandinavian Physiological Society. Published by John Wiley & Sons Ltd.

  19. Conformational heterogeneity of the protein-free human spliceosomal U2-U6 snRNA complex

    PubMed Central

    Zhao, Caijie; Bachu, Ravichandra; Popović, Milena; Devany, Matthew; Brenowitz, Michael; Schlatterer, Jörg C.; Greenbaum, Nancy L.

    2013-01-01

    The complex formed between the U2 and U6 small nuclear (sn)RNA molecules of the eukaryotic spliceosome plays a critical role in the catalysis of precursor mRNA splicing. Here, we have used enzymatic structure probing, 19F NMR, and analytical ultracentrifugation techniques to characterize the fold of a protein-free biophysically tractable paired construct representing the human U2-U6 snRNA complex. Results from enzymatic probing and 19F NMR for the complex in the absence of Mg2+ are consistent with formation of a four-helix junction structure as a predominant conformation. However, 19F NMR data also identify a lesser fraction (up to 14% at 25°C) of a three-helix conformation. Based upon this distribution, the calculated ΔG for inter-conversion to the four-helix structure from the three-helix structure is approximately −4.6 kJ/mol. In the presence of 5 mM Mg2+, the fraction of the three-helix conformation increased to ∼17% and the Stokes radius, measured by analytical ultracentrifugation, decreased by 2%, suggesting a slight shift to an alternative conformation. NMR measurements demonstrated that addition of an intron fragment to the U2-U6 snRNA complex results in displacement of U6 snRNA from the region of Helix III immediately 5′ of the ACAGAGA sequence of U6 snRNA, which may facilitate binding of the segment of the intron adjacent to the 5′ splice site to the ACAGAGA sequence. Taken together, these observations indicate conformational heterogeneity in the protein-free human U2-U6 snRNA complex consistent with a model in which the RNA has sufficient conformational flexibility to facilitate inter-conversion between steps of splicing in situ. PMID:23426875

  20. Conformational heterogeneity of the protein-free human spliceosomal U2-U6 snRNA complex.

    PubMed

    Zhao, Caijie; Bachu, Ravichandra; Popovic, Milena; Devany, Matthew; Brenowitz, Michael; Schlatterer, Jörg C; Greenbaum, Nancy L

    2013-04-01

    The complex formed between the U2 and U6 small nuclear (sn)RNA molecules of the eukaryotic spliceosome plays a critical role in the catalysis of precursor mRNA splicing. Here, we have used enzymatic structure probing, (19)F NMR, and analytical ultracentrifugation techniques to characterize the fold of a protein-free biophysically tractable paired construct representing the human U2-U6 snRNA complex. Results from enzymatic probing and (19)F NMR for the complex in the absence of Mg(2+) are consistent with formation of a four-helix junction structure as a predominant conformation. However, (19)F NMR data also identify a lesser fraction (up to 14% at 25°C) of a three-helix conformation. Based upon this distribution, the calculated ΔG for inter-conversion to the four-helix structure from the three-helix structure is approximately -4.6 kJ/mol. In the presence of 5 mM Mg(2+), the fraction of the three-helix conformation increased to ∼17% and the Stokes radius, measured by analytical ultracentrifugation, decreased by 2%, suggesting a slight shift to an alternative conformation. NMR measurements demonstrated that addition of an intron fragment to the U2-U6 snRNA complex results in displacement of U6 snRNA from the region of Helix III immediately 5' of the ACAGAGA sequence of U6 snRNA, which may facilitate binding of the segment of the intron adjacent to the 5' splice site to the ACAGAGA sequence. Taken together, these observations indicate conformational heterogeneity in the protein-free human U2-U6 snRNA complex consistent with a model in which the RNA has sufficient conformational flexibility to facilitate inter-conversion between steps of splicing in situ.

  1. Molecular characterization of two small heat shock protein genes in rice: their expression patterns, localizations, networks, and heterogeneous overexpressions.

    PubMed

    Ham, Deok-Jae; Moon, Jun-Chul; Hwang, Sun-Goo; Jang, Cheol Seong

    2013-09-28

    Heat stress is an example of a severe abiotic stress that plants can suffer in the field, causing a significant detrimental effect on their growth and productivity. Understanding the mechanism of plant response to heat stress is important for improving the productivity of crop plants under global warming. We used a microarray dataset that is deposited in the public database to evaluate plant responses to heat stress, and we selected the top 10 genes that are highly expressed under heat stress in rice. Two genes, OsSHSP1 (Os03g16030) and OsSHSP2 (Os01g04380), were selected for further study. These genes were highly induced in response to salt and drought but not in response to cold. In addition, OsSHSP1 and OsSHSP2 gene transcripts were induced under abscisic acid and salicylic acid but not under jasmonic acid and ethylene. Subcellular localization of proteins of 35S::OsSHSP1 were associated with the cytosol, whereas those of and 35S::OsSHSP2 were associated with the cytosol and nucleus. Heterogeneous overexpression of both genes exhibited higher germination rates than those of wild-type plants under the salt treatment, but not under heat or drought stress, supporting a hypothesis regarding functional specialization of members of small heat-shock protein family over evolutionary time. The network of both genes harboring nine sHSPs as well as at least 13 other chaperone genes might support the idea of a role for sHSPs in the chaperone network. Our findings might provide clues to shed light on the molecular functions of OsSHSP1 and OsSHSP2 in response to abiotic stresses, especially heat stress.

  2. Multidimensional endotyping in patients with severe asthma reveals inflammatory heterogeneity in matrix metalloproteinases and chitinase 3-like protein 1.

    PubMed

    Hinks, Timothy S C; Brown, Tom; Lau, Laurie C K; Rupani, Hitasha; Barber, Clair; Elliott, Scott; Ward, Jon A; Ono, Junya; Ohta, Shoichiro; Izuhara, Kenji; Djukanović, Ratko; Kurukulaaratchy, Ramesh J; Chauhan, Anoop; Howarth, Peter H

    2016-07-01

    Disease heterogeneity in patients with severe asthma and its relationship to inflammatory mechanisms remain poorly understood. We aimed to identify and replicate clinicopathologic endotypes based on analysis of blood and sputum parameters in asthmatic patients. One hundred ninety-four asthmatic patients and 21 control subjects recruited from 2 separate centers underwent detailed clinical assessment, sputum induction, and phlebotomy. One hundred three clinical, physiologic, and inflammatory parameters were analyzed by using topological data analysis and Bayesian network analysis. Severe asthma was associated with anxiety and depression, obesity, sinonasal symptoms, decreased quality of life, and inflammatory changes, including increased sputum chitinase 3-like protein 1 (YKL-40) and matrix metalloproteinase (MMP) 1, 3, 8, and 12 levels. Topological data analysis identified 6 clinicopathobiologic clusters replicated in both geographic cohorts: young, mild paucigranulocytic; older, sinonasal disease; obese, high MMP levels; steroid resistant TH2 mediated, eosinophilic; mixed granulocytic with severe obstruction; and neutrophilic, low periostin levels, severe obstruction. Sputum IL-5 levels were increased in patients with severe particularly eosinophilic forms, whereas IL-13 was suppressed and IL-17 levels did not differ between clusters. Bayesian network analysis separated clinical features from intricately connected inflammatory pathways. YKL-40 levels strongly correlated with neutrophilic asthma and levels of myeloperoxidase, IL-8, IL-6, and IL-6 soluble receptor. MMP1, MMP3, MMP8, and MMP12 levels were associated with severe asthma and were correlated positively with sputum IL-5 levels but negatively with IL-13 levels. In 2 distinct cohorts we have identified and replicated 6 clinicopathobiologic clusters based on blood and induced sputum measures. Our data underline a disconnect between clinical features and underlying inflammation, suggest IL-5 production is

  3. SUMO meets meiosis: an encounter at the synaptonemal complex: SUMO chains and sumoylated proteins suggest that heterogeneous and complex interactions lie at the centre of the synaptonemal complex.

    PubMed

    Watts, Felicity Z; Hoffmann, Eva

    2011-07-01

    Recent discoveries have identified the small ubiquitin-like modifier (SUMO) as the potential 'missing link' that could explain how the synaptonemal complex (SC) is formed during meiosis. The SC is important for a variety of chromosome interactions during meiosis and appears ladder-like. It is formed when 'axes' of the two homologous chromosomes become connected by the deposition of transverse filaments, forming the steps of the ladder. Although several components of axial and transverse elements have been identified, how the two are connected to form the SC has remained an enigma. Recent discoveries suggest that SUMO modification underlies protein-protein interactions within the SC of budding yeast. The versatility of SUMO in regulating protein-protein interactions adds an exciting new dimension to our understanding of the SC and suggests that SCs are not homogenous structures throughout the nucleus. We propose that this heterogeneity may allow differential regulation of chromosome structure and function.

  4. Surfactant Protein–C Chromatin-Bound Green Fluorescence Protein Reporter Mice Reveal Heterogeneity of Surfactant Protein C–Expressing Lung Cells

    PubMed Central

    Lee, Joo-Hyeon; Kim, Jonghwan; Gludish, David; Roach, Rebecca R.; Saunders, Arven H.; Barrios, Juliana; Woo, Andrew Jonghan; Chen, Huaiyong; Conner, David A.; Fujiwara, Yuko; Stripp, Barry R.

    2013-01-01

    The regeneration of alveolar epithelial cells is a critical aspect of alveolar reorganization after lung injury. Although alveolar Type II (AT2) cells have been described as progenitor cells for alveolar epithelia, more remains to be understood about how their progenitor cell properties are regulated. A nuclear, chromatin-bound green fluorescence protein reporter (H2B-GFP) was driven from the murine surfactant protein–C (SPC) promoter to generate SPC H2B-GFP transgenic mice. The SPC H2B-GFP allele allowed the FACS-based enrichment and gene expression profiling of AT2 cells. Approximately 97% of AT2 cells were GFP-labeled on Postnatal Day 1, and the percentage of GFP-labeled AT2 cells decreased to approximately 63% at Postnatal Week 8. Isolated young adult SPC H2B-GFP+ cells displayed proliferation, differentiation, and self-renewal capacity in the presence of lung fibroblasts in a Matrigel-based three-dimensional culture system. Heterogeneity within the GFP+ population was revealed, because cells with distinct alveolar and bronchiolar gene expression arose in three-dimensional cultures. CD74, a surface marker highly enriched on GFP+ cells, was identified as a positive selection marker, providing 3-fold enrichment for AT2 cells. In vivo, GFP expression was induced within other epithelial cell types during maturation of the distal lung. The utility of the SPC H2B-GFP murine model for the identification of AT2 cells was greatest in early postnatal lungs and more limited with age, when some discordance between SPC and GFP expression was observed. In adult mice, this allele may allow for the enrichment and future characterization of other SPC-expressing alveolar and bronchiolar cells, including putative stem/progenitor cell populations. PMID:23204392

  5. Functional heterogeneity of the fucoxanthins and fucoxanthin-chlorophyll proteins in diatom cells revealed by their electrochromic response and fluorescence and linear dichroism spectra

    NASA Astrophysics Data System (ADS)

    Szabó, Milán; Premvardhan, Lavanya; Lepetit, Bernard; Goss, Reimund; Wilhelm, Christian; Garab, Győző

    2010-07-01

    In this work, by analyzing the electrochromic transient spectra, the 77 K fluorescence emission and excitation, as well as the linear dichroism (LD) and circular dichroism (CD) spectra of low-light (LL) and high-light (HL) grown Phaeodactylum tricornutum cells, we show that the fucoxanthins (Fx) and fucoxanthin-chlorophyll proteins (FCP) exhibit marked functional heterogeneity. Electrochromic transients reveal that LL and HL cells differ substantially in their relative contents of two Fx forms, which absorb at 501 and 550 nm; they exhibit distinct LD signals but are CD silent. Fluorescence emission and excitation spectra at 77 K reveal that although both forms efficiently transfer excitation energy to Chl a, the red form feeds somewhat more energy to photosystem II than to photosystem I. Similar data obtained in Cyclotella meneghiniana cells suggest that the heterogeneity of the FCP pool, with different Fx forms, plays a role in the regulation of energy utilization in FCP-containing organisms.

  6. Lipid lateral heterogeneity in phosphatidylcholine/phosphatidylserine/diacylglycerol vesicles and its influence on protein kinase C activation.

    PubMed Central

    Dibble, A R; Hinderliter, A K; Sando, J J; Biltonen, R L

    1996-01-01

    To test the hypothesis that the activation of protein kinase C (PKC) is influenced by lateral heterogeneities of the components of the lipid bilayer, the thermotropic phase behavior of dimyristoylphosphatidylcholine (DMPC)/dimyristoylphosphatidylserine (DMPS)/dioleoylglycerol (DO) vesicles was compared with the activation of PKC by this system. Differential scanning calorimetry (DSC) and Fourier transform infrared (FTIR) spectroscopy were used to monitor the main transition (i.e., the gel-to-fluid phase transition) as a function of mole fraction DO (chi(DO)) in DMPC/DO, DMPS/DO, and [DMPC/DMPS (1:1, mol/mol)]/DO multilamellar vesicles (MLVs). In each case, when chi(DO) < or approximately 0.3, DO significantly broadened the main transition and shifted it to lower temperatures; but when chi(DO) > approximately 0.3, the main transition became highly cooperative, i.e., narrow, again. The coexistence of overlapping narrow and broad transitions was clearly evident in DSC thermograms from chi(DO) approximately 0.1 to chi(DO) approximately 0.3, with the more cooperative transition growing at the expense of the broader one as chi(DO) increased. FTIR spectroscopy, using analogs of DMPC and DMPS with perdeuterated acyl chains, showed that the melting profiles of all three lipid components in [DMPC/DMPS (1:1, mol/mol)]/DO MLVs virtually overlay when chi(DO) = 0.33, suggesting that a new type of phase, with a phospholipid/DO mole ratio near 2:1, is formed in this system. Collectively, the results are consistent with the coexistence of DO-poor and DO-rich domains throughout the compositions chi(DO) approximately 0.1 to chi(DO) approximately 0.3, even at temperatures above the main transition. Comparison of the phase behavior of the binary mixtures with that of the ternary mixtures suggests that DMPS/DO interactions may be more favorable than DMPC/DO interactions in the ternary system, especially in the gel state. PKC activity was measured using [DMPC/DMPS (1:1, mol/mol)]/DO MLVs

  7. Copper and Zinc Interactions with Cellular Prion Proteins Change Solubility of Full-Length Glycosylated Isoforms and Induce the Occurrence of Heterogeneous Phenotypes.

    PubMed

    Brim, Svetlana; Groschup, Martin H; Kuczius, Thorsten

    2016-01-01

    Prion diseases are characterized biochemically by protein aggregation of infectious prion isoforms (PrPSc), which result from the conformational conversion of physiological prion proteins (PrPC). PrPC are variable post-translationally modified glycoproteins, which exist as full length and as aminoterminally truncated glycosylated proteins and which exhibit differential detergent solubility. This implicates the presence of heterogeneous phenotypes, which overlap as protein complexes at the same molecular masses. Although the biological function of PrPC is still enigmatic, evidence reveals that PrPC exhibits metal-binding properties, which result in structural changes and decreased solubility. In this study, we analyzed the yield of PrPC metal binding affiliated with low solubility and changes in protein banding patterns. By implementing a high-speed centrifugation step, the interaction of zinc ions with PrPC was shown to generate large quantities of proteins with low solubility, consisting mainly of full-length glycosylated PrPC; whereas unglycosylated PrPC remained in the supernatants as well as truncated glycosylated proteins which lack of octarepeat sequence necessary for metal binding. This effect was considerably lower when PrPC interacted with copper ions; the presence of other metals tested exhibited no effect under these conditions. The binding of zinc and copper to PrPC demonstrated differentially soluble protein yields within distinct PrPC subtypes. PrPC-Zn2+-interaction may provide a means to differentiate glycosylated and unglycosylated subtypes and offers detailed analysis of metal-bound and metal-free protein conversion assays.

  8. Copper and Zinc Interactions with Cellular Prion Proteins Change Solubility of Full-Length Glycosylated Isoforms and Induce the Occurrence of Heterogeneous Phenotypes

    PubMed Central

    Brim, Svetlana; Groschup, Martin H.; Kuczius, Thorsten

    2016-01-01

    Prion diseases are characterized biochemically by protein aggregation of infectious prion isoforms (PrPSc), which result from the conformational conversion of physiological prion proteins (PrPC). PrPC are variable post-translationally modified glycoproteins, which exist as full length and as aminoterminally truncated glycosylated proteins and which exhibit differential detergent solubility. This implicates the presence of heterogeneous phenotypes, which overlap as protein complexes at the same molecular masses. Although the biological function of PrPC is still enigmatic, evidence reveals that PrPC exhibits metal-binding properties, which result in structural changes and decreased solubility. In this study, we analyzed the yield of PrPC metal binding affiliated with low solubility and changes in protein banding patterns. By implementing a high-speed centrifugation step, the interaction of zinc ions with PrPC was shown to generate large quantities of proteins with low solubility, consisting mainly of full-length glycosylated PrPC; whereas unglycosylated PrPC remained in the supernatants as well as truncated glycosylated proteins which lack of octarepeat sequence necessary for metal binding. This effect was considerably lower when PrPC interacted with copper ions; the presence of other metals tested exhibited no effect under these conditions. The binding of zinc and copper to PrPC demonstrated differentially soluble protein yields within distinct PrPC subtypes. PrPC–Zn2+-interaction may provide a means to differentiate glycosylated and unglycosylated subtypes and offers detailed analysis of metal-bound and metal-free protein conversion assays. PMID:27093554

  9. Purification and partial sequencing of the nuclear autoantigen RA33 shows that it is indistinguishable from the A2 protein of the heterogeneous nuclear ribonucleoprotein complex.

    PubMed Central

    Steiner, G; Hartmuth, K; Skriner, K; Maurer-Fogy, I; Sinski, A; Thalmann, E; Hassfeld, W; Barta, A; Smolen, J S

    1992-01-01

    RA33 is a nuclear autoantigen with an apparent molecular mass of 33 kD. Autoantibodies against RA33 are found in about 30% of sera from RA patients, but only occasionally in sera from patients with other connective tissue diseases. To characterize RA33, the antigen was purified from HeLa cell nuclear extracts to more than 90% homogeneity by affinity chromatography on heparin-Sepharose and by chromatofocusing. Sequence analysis of five tryptic peptides revealed that their sequences matched corresponding sequences of the A2 protein of the heterogeneous nuclear ribonucleoprotein (hnRNP) complex. Furthermore, RA33 was shown to be present in the 40S hnRNP complex and to behave indistinguishably from A2 in binding to single stranded DNA. In summary, these data strongly indicate that RA33 and A2 are the same protein, and thus identify on a molecular level a new autoantigen. Images PMID:1522214

  10. The human telomerase RNA component, hTR, activates the DNA-dependent protein kinase to phosphorylate heterogeneous nuclear ribonucleoprotein A1.

    PubMed

    Ting, Nicholas S Y; Pohorelic, Brant; Yu, Yaping; Lees-Miller, Susan P; Beattie, Tara L

    2009-10-01

    Telomere integrity in human cells is maintained by the dynamic interplay between telomerase, telomere associated proteins, and DNA repair proteins. These interactions are vital to suppress DNA damage responses and unfavorable changes in chromosome dynamics. The DNA-dependent protein kinase (DNA-PK) is critical for this process. Cells deficient for functional DNA-PKcs show increased rates of telomere loss, accompanied by chromosomal fusions and translocations. Treatment of cells with specific DNA-PK kinase inhibitors leads to similar phenotypes. These observations indicate that the kinase activity of DNA-PK is required for its function at telomeres possibly through phosphorylation of essential proteins needed for telomere length maintenance. Here we show that the heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a direct substrate for DNA-PK in vitro. Phosphorylation of hnRNP A1 is stimulated not only by the presence of DNA but also by the telomerase RNA component, hTR. Furthermore, we show that hnRNP A1 is phosphorylated in vivo in a DNA-PK-dependent manner and that this phosphorylation is greatly reduced in cell lines which lack hTR. These data are the first to report that hTR stimulates the kinase activity of DNA-PK toward a known telomere-associated protein, and may provide further insights into the function of DNA-PK at telomeres.

  11. Immunohistochemical localization of adenosine deaminase complexing protein in intestinal mucosa and in colorectal adenocarcinoma as a marker for tumour cell heterogeneity.

    PubMed

    Ten Kate, J; Wijnen, J T; Boldewijn, J; Khan, P M; Bosman, F T

    1985-01-01

    Adenosine deaminase complexing protein (ADCP), a dimeric glycoprotein, has been reported to be decreased or deficient in transformed or cancer-derived cell lines, indicating its potential significance as an indicator of malignant transformation. A similar deficiency was reported in total homogenates of tumours of colon, kidney, lung and liver. In previous biochemical studies we failed to confirm the consistent reduction in ADCP concentration in cancer tissues. A possible explanation for our findings was thought to be intercellular heterogeneity in ADCP expression in individual tumour cells. To study ADCP expression in individual cells, we developed an immunohistochemical method which was applied to tissue sections. Paraformaldehyde--lysine--periodate (PLP) solution was found to be a suitable fixative. Fixed tissue samples were paraffin-embedded, sectioned and stained for ADCP, using an indirect peroxidase-labelled antibody procedure. The protein was localized in normal colonic mucosa, mainly in the brush border region of the luminal epithelium and in cytoplasmic granules. Intense ADCP immunoreactivity was found also in the basal part of some cells. In cancer cells, three staining patterns were observed: membranous, diffuse cytoplasmic and granular cytoplasmic. The adenocarcinomas exhibited significant intratumour and intertumour heterogeneity in their staining types. Further studies on ADCP expression in colorectal cancer in relation to clinical and histopathological characteristics are warranted in order to fully evaluate the potential significance of ADCP as a cancer associated antigen.

  12. Bio-mimetic nanostructure self-assembled from Au@Ag heterogeneous nanorods and phage fusion proteins for targeted tumor optical detection and photothermal therapy.

    PubMed

    Wang, Fei; Liu, Pei; Sun, Lin; Li, Cuncheng; Petrenko, Valery A; Liu, Aihua

    2014-10-28

    Nanomaterials with near-infrared (NIR) absorption have been widely studied in cancer detection and photothermal therapy (PTT), while it remains a great challenge in targeting tumor efficiently with minimal side effects. Herein we report a novel multifunctional phage-mimetic nanostructure, which was prepared by layer-by-layer self-assembly of Au@Ag heterogenous nanorods (NRs) with rhodamine 6G, and specific pVIII fusion proteins. Au@Ag NRs, first being applied for PTT, exhibited excellent stability, cost-effectivity, biocompatibility and tunable NIR absorption. The fusion proteins were isolated from phage DDAGNRQP specifically selected from f8/8 landscape phage library against colorectal cancer cells in a high-throughput way. Considering the definite charge distribution and low molecular weight, phage fusion proteins were assembled on the negatively charged NR core by electrostatic interactions, exposing the N-terminus fused with DDAGNRQP peptide on the surface. The fluorescent images showed that assembled phage fusion proteins can direct the nanostructure into cancer cells. The nanostructure was more efficient than gold nanorods and silver nanotriangle-based photothermal agents and was capable of specifically ablating SW620 cells after 10 min illumination with an 808 nm laser in the light intensity of 4 W/cm(2). The prepared nanostructure would become an ideal reagent for simutaneously targeted optical imaging and PTT of tumor.

  13. Bio-mimetic Nanostructure Self-assembled from Au@Ag Heterogeneous Nanorods and Phage Fusion Proteins for Targeted Tumor Optical Detection and Photothermal Therapy

    NASA Astrophysics Data System (ADS)

    Wang, Fei; Liu, Pei; Sun, Lin; Li, Cuncheng; Petrenko, Valery A.; Liu, Aihua

    2014-10-01

    Nanomaterials with near-infrared (NIR) absorption have been widely studied in cancer detection and photothermal therapy (PTT), while it remains a great challenge in targeting tumor efficiently with minimal side effects. Herein we report a novel multifunctional phage-mimetic nanostructure, which was prepared by layer-by-layer self-assembly of Au@Ag heterogenous nanorods (NRs) with rhodamine 6G, and specific pVIII fusion proteins. Au@Ag NRs, first being applied for PTT, exhibited excellent stability, cost-effectivity, biocompatibility and tunable NIR absorption. The fusion proteins were isolated from phage DDAGNRQP specifically selected from f8/8 landscape phage library against colorectal cancer cells in a high-throughput way. Considering the definite charge distribution and low molecular weight, phage fusion proteins were assembled on the negatively charged NR core by electrostatic interactions, exposing the N-terminus fused with DDAGNRQP peptide on the surface. The fluorescent images showed that assembled phage fusion proteins can direct the nanostructure into cancer cells. The nanostructure was more efficient than gold nanorods and silver nanotriangle-based photothermal agents and was capable of specifically ablating SW620 cells after 10 min illumination with an 808 nm laser in the light intensity of 4 W/cm2. The prepared nanostructure would become an ideal reagent for simutaneously targeted optical imaging and PTT of tumor.

  14. Identification of the methylation preference region in heterogeneous nuclear ribonucleoprotein K by protein arginine methyltransferase 1 and its implication in regulating nuclear/cytoplasmic distribution

    SciTech Connect

    Chang, Yuan-I; Hsu, Sheng-Chieh; Chau, Gar-Yang; Huang, Chi-Ying F.; Sung, Jung-Sung; Hua, Wei-Kai; Lin, Wey-Jinq

    2011-01-21

    Research highlights: {yields} Verifying by direct methylation assay the substrate sites of PRMT1 in the hnRNP K protein. {yields} Identifying the preferred PMRT1 methylation regions in hnRNP K by kinetic analysis. {yields} Linking methylation in regulating nuclear localization of hnRNP K. -- Abstract: Protein arginine methylation plays crucial roles in numerous cellular processes. Heterogeneous nuclear ribonucleoprotein K (hnRNP K) is a multi-functional protein participating in a variety of cellular functions including transcription and RNA processing. HnRNP K is methylated at multiple sites in the glycine- and arginine-rich (RGG) motif. Using various RGG domain deletion mutants of hnRNP K as substrates, here we show by direct methylation assay that protein arginine methyltransferase 1 (PRMT1) methylated preferentially in a.a. 280-307 of the RGG motif. Kinetic analysis revealed that deletion of a.a. 280-307, but not a.a. 308-327, significantly inhibited rate of methylation. Importantly, nuclear localization of hnRNP K was significantly impaired in mutant hnRNP K lacking the PRMT1 methylation region or upon pharmacological inhibition of methylation. Together our results identify preferred PRMT1 methylation sequences of hnRNP K by direct methylation assay and implicate a role of arginine methylation in regulating intracellular distribution of hnRNP K.

  15. Bio-mimetic Nanostructure Self-assembled from Au@Ag Heterogeneous Nanorods and Phage Fusion Proteins for Targeted Tumor Optical Detection and Photothermal Therapy

    PubMed Central

    Wang, Fei; Liu, Pei; Sun, Lin; Li, Cuncheng; Petrenko, Valery A.; Liu, Aihua

    2014-01-01

    Nanomaterials with near-infrared (NIR) absorption have been widely studied in cancer detection and photothermal therapy (PTT), while it remains a great challenge in targeting tumor efficiently with minimal side effects. Herein we report a novel multifunctional phage-mimetic nanostructure, which was prepared by layer-by-layer self-assembly of Au@Ag heterogenous nanorods (NRs) with rhodamine 6G, and specific pVIII fusion proteins. Au@Ag NRs, first being applied for PTT, exhibited excellent stability, cost-effectivity, biocompatibility and tunable NIR absorption. The fusion proteins were isolated from phage DDAGNRQP specifically selected from f8/8 landscape phage library against colorectal cancer cells in a high-throughput way. Considering the definite charge distribution and low molecular weight, phage fusion proteins were assembled on the negatively charged NR core by electrostatic interactions, exposing the N-terminus fused with DDAGNRQP peptide on the surface. The fluorescent images showed that assembled phage fusion proteins can direct the nanostructure into cancer cells. The nanostructure was more efficient than gold nanorods and silver nanotriangle-based photothermal agents and was capable of specifically ablating SW620 cells after 10 min illumination with an 808 nm laser in the light intensity of 4 W/cm2. The prepared nanostructure would become an ideal reagent for simutaneously targeted optical imaging and PTT of tumor. PMID:25348392

  16. Heterogeneous Catalysis.

    ERIC Educational Resources Information Center

    Miranda, R.

    1989-01-01

    Described is a heterogeneous catalysis course which has elements of materials processing embedded in the classical format of catalytic mechanisms and surface chemistry. A course outline and list of examples of recent review papers written by students are provided. (MVL)

  17. Heterogeneous Catalysis.

    ERIC Educational Resources Information Center

    Miranda, R.

    1989-01-01

    Described is a heterogeneous catalysis course which has elements of materials processing embedded in the classical format of catalytic mechanisms and surface chemistry. A course outline and list of examples of recent review papers written by students are provided. (MVL)

  18. Heterogeneous catalysis.

    PubMed

    Schlögl, Robert

    2015-03-09

    A heterogeneous catalyst is a functional material that continually creates active sites with its reactants under reaction conditions. These sites change the rates of chemical reactions of the reactants localized on them without changing the thermodynamic equilibrium between the materials.

  19. A single molecule approach for measuring the transport properties and energetics of membrane proteins in heterogeneous planar bio-mimetic assemblies

    NASA Astrophysics Data System (ADS)

    Poudel, Kumud Raj

    The significance of transmembrane protein research is well documented. Numerous studies have clearly established the biological, biophysical and pharmaceutical importance that these membrane components serve. Communications through receptors regulate countless body functions and they also provide structural support to the cell. However, a lack of high-resolution structure data has limited our understanding of these proteins that make it necessary to study them in in-vitro platforms or 'bio-mimetic' assemblies. Albeit that an assortment of platforms have been suggested for in-vitro studies, the issues, however, remain the same. The lack of mobility of the proteins in artificial environments, the question of functionality that arises with mobility and the search in general for the best assembly, is still a work in progress. In this work, we have taken some of the most accepted platforms in the field and characterized them through the lens of single molecule spectroscopy. We have addressed the question of mobility by reducing it down to a single molecule and comparing it with the bulk. By utilizing the Serotonin Receptor 5HT3A we have shown that techniques such as passivation of the substrates in the assemblies by Bovine Serum Albumin has a significant effect at the molecular level. The larger size of the intracellular domain for the 5HT3A served as a great probe to understand and evaluate the interaction of a surface passivator with the integrated membrane protein. We have also taken this a step further by developing a novel, single cushion 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) assembly and added another degree of complexity- through a phase transition. We have utilized phase transition to get an insight into the local protein environment, activation energies, heterogeneity and diffusion characteristics by using Annexin V as our probe. The work presented here studies two completely different biological platforms using two entirely different transmembrane

  20. Phosphorylation of serine residues in histidine-tag sequences attached to recombinant protein kinases: a cause of heterogeneity in mass and complications in function.

    PubMed

    Du, Ping; Loulakis, Pat; Luo, Chun; Mistry, Anil; Simons, Samuel P; LeMotte, Peter K; Rajamohan, Francis; Rafidi, Kristina; Coleman, Kevin G; Geoghegan, Kieran F; Xie, Zhi

    2005-12-01

    High-level recombinant expression of protein kinases in eukaryotic cells or Escherichia coli commonly gives products that are phosphorylated by autocatalysis or by the action of endogenous kinases. Here, we report that phosphorylation occurred on serine residues adjacent to hexahistidine affinity tags (His-tags) derived from several commercial expression vectors and fused to overexpressed kinases. The result was observed with a variety of recombinant kinases expressed in either insect cells or E. coli. Multiple phosphorylations of His-tagged full-length Aurora A, a protein serine/threonine kinase, were detected by mass spectrometry when it was expressed in insect cells in the presence of okadaic acid, a protein phosphatase inhibitor. Peptide mapping by liquid chromatography-mass spectrometry detected phosphorylations on all three serine residues in an N-terminal tag, alpha-N-acetyl-MHHHHHHSSGLPRGS. The same sequence was also phosphorylated, but only at a low level, when a His-tagged protein tyrosine kinase, Pyk2 was expressed in insect cells and activated in vitro. When catalytic domains of Aurora A and several other protein serine/threonine kinases were expressed in E. coli, serines in the affinity tag sequence GSSHHHHHHSSGLVPRGS were also variably phosphorylated. His-Aurora A with hyperphosphorylation of the serine residues in the tag aggregated and resisted thrombin-catalyzed removal of the tag. Treatment with alkaline phosphatase partly restored sensitivity to thrombin. The same His-tag sequence was also detected bearing alpha-N-d-gluconoylation in addition to multiple phosphorylations. The results show that histidine-tag sequences can receive complicated posttranslational modification, and that the hyperphosphorylation and resulting heterogeneity of the recombinant fusion proteins can interfere with downstream applications.

  1. Surface-labelling studies on skeletal-muscle cells in vitro. Heterogeneity of iodinated cell-surface proteins.

    PubMed Central

    Cates, G A; Holland, P C

    1980-01-01

    1. Two distinct classes of protein were detected at the surface of chick-embryo skeletal-muscle cells after iodination of the cells in monolayer culture. 2. The two classes of iodinated proteins differed in their ability to co-purify with a vesicular plasma-membrane fraction prepared from surface-labelled cells. 3. One class consisted of predominantly high-molecular-weight glycoproteins that co-purified with the plasma-membrane fraction, but showed no significant qualitative or quantitative alterations in labelling with 125I and lactoperoxidase during myogenesis. 4. A second class of predominantly lower-molecular-weight proteins showed reproducible quantitative alterations in 125I-labelling during myogenesis but failed to co-purify with the plasma-membrane fraction. 5. This second class of proteins may represent matrix proteins involved in intercellular adhesion or adhesion of cells to the substratum. They are unlikely to be directly required for the process of plasma-membrane fusion during myogenesis, since they do not copurify with a vesicular plasma-membrane fraction known to be capable of Ca2+-dependent fusion in vitro. PMID:7370009

  2. Chemical heterogeneity as a result of hydroxylamine cleavage of a fusion protein of human insulin-like growth factor I.

    PubMed Central

    Canova-Davis, E; Eng, M; Mukku, V; Reifsnyder, D H; Olson, C V; Ling, V T

    1992-01-01

    Recombinant DNA techniques were used to biosynthesize human insulin-like growth factor I (hIGF-I) as a fusion protein wherein the fusion polypeptide is an IgG-binding moiety derived from staphylococcal protein A. This fusion protein is produced in Escherichia coli and secreted into the fermentation broth. In order to release mature recombinant-derived hIGF-I (rhIGF-I), the fusion protein is treated with hydroxylamine, which cleaves a susceptible Asn-Gly bond that has been engineered into the fusion protein gene. Reversed-phase h.p.l.c. was used to estimate the purity of the rhIGF-I preparations, especially for the quantification of the methionine sulphoxide-containing variant. It was determined that hydroxylamine cleavage of the fusion protein produced, as a side reaction, hydroxamates of the asparagine and glutamine residues in rhIGF-I. Although isoelectric focusing was effective in detecting, and reversed-phase h.p.l.c. for producing enriched fractions of the hydroxamate variants, ion-exchange chromatography was a more definitive procedure, as it allowed quantification and facile removal of these variants. The identity of the variants as hydroxamates was established by Staphylococcus aureus V8 proteinase digestion, followed by m.s., as the modification was transparent to amino acid and N-terminal sequence analyses. The biological activity of rhIGF-I was established by its ability to incorporate [3H]thymidine into the DNA of BALB/c373 cells and by a radioreceptor assay utilizing human placental membranes. Both assays demonstrate that the native, recombinant and methionine sulphoxide and hydroxamate IGF-I variants are essentially equipotent. Images Fig. 2. PMID:1637301

  3. The C-protein tetramer binds 230 to 240 nucleotides of pre-mRNA and nucleates the assembly of 40S heterogeneous nuclear ribonucleoprotein particles.

    PubMed Central

    Huang, M; Rech, J E; Northington, S J; Flicker, P F; Mayeda, A; Krainer, A R; LeStourgeon, W M

    1994-01-01

    A series of in vitro protein-RNA binding studies using purified native (C1)3C2 and (A2)3B1 tetramers, total soluble heterogeneous nuclear ribonucleoprotein (hnRNP), and pre-mRNA molecules differing in length and sequence have revealed that a single C-protein tetramer has an RNA site size of 230 to 240 nucleotides (nt). Two tetramers bind twice this RNA length, and three tetramers fold monoparticle lengths of RNA (700 nt) into a unique 19S triangular complex. In the absence of this unique structure, the basic A- and B-group proteins bind RNA to form several different artifactual structures which are not present in preparations of native hnRNP and which do not function in hnRNP assembly. Three (A2)3B1 tetramers bind the 19S complex to form a 35S assembly intermediate. Following UV irradiation to immobilize the C proteins on the packaged RNA, the 19S triangular complex is recovered as a remnant structure from both native and reconstituted hnRNP particles. C protein-RNA complexes composed of three, six, or nine tetramers (one, two, or three triangular complexes) nucleate the stoichiometric assembly of monomer, dimer, and trimer hnRNP particles. The binding of C-protein tetramers to RNAs longer than 230 nt is through a self-cooperative combinatorial mode. RNA packaged in the 19S complex and in 40S hnRNP particles is efficiently spliced in vitro. These findings demonstrate that formation of the triangular C protein-RNA complex is an obligate first event in the in vitro and probably the in vivo assembly the 40S hnRNP core particle, and they provide insight into the mechanism through which the core proteins package 700-nt increments of RNA. These findings also demonstrate that unless excluded by other factors, the C proteins are likely to be located along the length of nascent transcripts. Images PMID:8264621

  4. Heterogeneous reaction kinetics and mechanism of the nitration of aerosolized protein by O3 and NO2

    NASA Astrophysics Data System (ADS)

    Shiraiwa, Manabu; Sosedova, Yulia; Rouvière, Aurélie; Ammann, Markus; Pöschl, Ulrich

    2010-05-01

    The effects of air pollution on allergic diseases are not yet well-understood. Proteins contained in biogenic aerosol particles (pollen, spores, bacteria, etc.), which accounts for up to 5% of urban air particulate matter, are efficiently nitrated in polluted environments before inhalation and deposition in the human respiratory tract [1], which is likely to trigger immune reactions for allergies. Proteins undergo a nitration reaction that leads to the formation of 3-nitrotyrosine residues. The kinetics and reaction mechanism of protein nitration are still largely unknown. The kinetics of nitration of protein particles by O3 and NO2 was measured using the short-lived radioactive tracer 13N. The routine for the online production of 13N-labeled nitrogen dioxide and the main experimental setup were reported previously [2]. Bovine serum albumin (BSA) was used as a model protein compound. Deliquesced NaCl particles were also used as a reference. Particles generated by an ultrasonic nebulizer were mixed with O3 (0 - 150 ppb) and NO2 (5 - 100 ppb) in a flow tube reactor under humid conditions (30 - 75 % RH), which lead to gel-like swelling of the protein [3, 4]. The reaction time was varied in the range of 4 -10 min by changing the position of the inlet of the reactor. The surface concentration of particles was monitored by a scanning mobility particle sizer (SMPS). After passing through the flow tube reactor, the gas and aerosol flow entered a narrow parallel-plate diffusion denuder coated to selectively absorb gas phase NO2, followed by a particle filter collecting the particles. The γ detectors were attached to each denuders and the filter to count the amount of gamma quanta, which are emitted in the decay of 13N. From the count-rate, the concentration of the corresponding species was derived, which was used for the calculation of uptake coefficients of NO2 (γNO2). In absence of O3 in the flow tube reactor, NO2 uptake by both BSA and deliquesced NaCl were below the

  5. A transferable heterogeneous two-hybrid system in Escherichia coli based on polyhydroxyalkanoates synthesis regulatory protein PhaR

    PubMed Central

    2011-01-01

    Background Polyhydroxyalkanoate (PHA) synthesis regulatory protein PhaR contains a DNA binding domain (DBD) and a PHA granule binding domain (GBD), it anchors to the promoter region of PHA granule-associated protein (PhaP) to repress phaP expression. However, PhaR will bind to PHB granules and be released from phaP promoter region when PHA granules are formed in vivo, initiating expression of phaP gene. Based on this regulatory mechanism, a bacterial two-hybrid system was developed: PhaR was separated into two parts: DBD was used to fuse with the bait, GBD with the prey, and phaP was replaced by a reporter gene lacZ. However, GBD protein expressed in vivo formed inclusion bodies. Thus, PhaP with strong binding ability to PHB granules was employed to replace GBD. Results Three model interaction partners bFos, bJun and bATF2 were used to study the feasibility of this bacterial two-hybrid system compared with the controls lacking one or more essential elements of this system. Results showed that bFos, bJun and bATF2 bound tightly in pairs to allow strong expression of β-galactosidase in different expression levels. In contrast, very weak β-galactosidase activity was detected in all control groups. Conclusion β-Galactosidase activity level precisely correlated with the interaction force of tested protein pairs, and very weak β-galactosidase expression was detected throughout the control groups, which demonstrated the feasibility of this system for studying protein interactions. PMID:21477323

  6. Heterogenous ribonucleoprotein A18 (hnRNP A18) promotes tumor growth by increasing protein translation of selected transcripts in cancer cells.

    PubMed

    Chang, Elizabeth T; Parekh, Palak R; Yang, Qingyuan; Nguyen, Duc M; Carrier, France

    2016-03-01

    The heterogenous ribonucleoprotein A18 (hnRNP A18) promotes tumor growth by coordinating the translation of selected transcripts associated with proliferation and survival. hnRNP A18 binds to and stabilizes the transcripts of pro-survival genes harboring its RNA signature motif in their 3'UTRs. hnRNP A18 binds to ATR, RPA, TRX, HIF-1α and several protein translation factor mRNAs on polysomes and increases de novo protein translation under cellular stress. Most importantly, down regulation of hnRNP A18 decreases proliferation, invasion and migration in addition to significantly reducing tumor growth in two mouse xenograft models, melanoma and breast cancer. Moreover, tissue microarrays performed on human melanoma, prostate, breast and colon cancer indicate that hnRNP A18 is over expressed in 40 to 60% of these malignant tissue as compared to normal adjacent tissue. Immunohistochemistry data indicate that hnRNP A18 is over expressed in the stroma and hypoxic areas of human tumors. These data thus indicate that hnRNP A18 can promote tumor growth in in vivo models by coordinating the translation of pro-survival transcripts to support the demands of proliferating cells and increase survival under cellular stress. hnRNP A18 therefore represents a new target to selectively inhibit protein translation in tumor cells.

  7. Heterogenous ribonucleoprotein A18 (hnRNP A18) promotes tumor growth by increasing protein translation of selected transcripts in cancer cells

    PubMed Central

    Chang, Elizabeth T.; Parekh, Palak R.; Yang, Qingyuan; Nguyen, Duc M.; Carrier, France

    2016-01-01

    The heterogenous ribonucleoprotein A18 (hnRNP A18) promotes tumor growth by coordinating the translation of selected transcripts associated with proliferation and survival. hnRNP A18 binds to and stabilizes the transcripts of pro-survival genes harboring its RNA signature motif in their 3′UTRs. hnRNP A18 binds to ATR, RPA, TRX, HIF-1α and several protein translation factor mRNAs on polysomes and increases de novo protein translation under cellular stress. Most importantly, down regulation of hnRNP A18 decreases proliferation, invasion and migration in addition to significantly reducing tumor growth in two mouse xenograft models, melanoma and breast cancer. Moreover, tissue microarrays performed on human melanoma, prostate, breast and colon cancer indicate that hnRNP A18 is over expressed in 40 to 60% of these malignant tissue as compared to normal adjacent tissue. Immunohistochemistry data indicate that hnRNP A18 is over expressed in the stroma and hypoxic areas of human tumors. These data thus indicate that hnRNP A18 can promote tumor growth in in vivo models by coordinating the translation of pro-survival transcripts to support the demands of proliferating cells and increase survival under cellular stress. hnRNP A18 therefore represents a new target to selectively inhibit protein translation in tumor cells. PMID:26824423

  8. Conformational Heterogeneity Determined by Folding and Oligomer Assembly Routes of the Interferon Response Inhibitor NS1 Protein, Unique to Human Respiratory Syncytial Virus.

    PubMed

    Pretel, Esteban; Sánchez, Ignacio E; Fassolari, Marisol; Chemes, Lucía B; de Prat-Gay, Gonzalo

    2015-08-25

    The nonstructural NS1 protein is an essential virulence factor of the human respiratory syncytial virus, with a predominant role in the inhibition of the host antiviral innate immune response. This inhibition is mediated by multiple protein-protein interactions and involves the formation of large oligomeric complexes. There is neither a structure nor sequence or functional homologues of this protein, which points to a distinctive mechanism for blocking the interferon response among viruses. The NS1 native monomer follows a simple unfolding kinetics via a nativelike transition state ensemble, with a half-life of 45 min, in agreement with a highly stable core structure at equilibrium. Refolding is a complex process that involves several slowly interconverting species compatible with proline isomerization. However, an ultrafast folding event with a half-life of 0.2 ms is indicative of a highly folding compatible species within the unfolded state ensemble. On the other hand, the oligomeric assembly route from the native monomer, which does not involve unfolding, shows a monodisperse and irreversible end-point species triggered by a mild temperature change, with half-lives of 160 and 26 min at 37 and 47 °C, respectively, and at a low protein concentration (10 μM). A large secondary structure change into β-sheet structure and the formation of a dimeric nucleus precede polymerization by the sequential addition of monomers at the surprisingly low rate of one monomer every 34 s. The polymerization phase is followed by the binding to thioflavin-T indicative of amyloid-like, albeit soluble, repetitive β-sheet quaternary structure. The overall process is reversible only up until ~8 min, a time window in which most of the secondary structure change takes place. NS1's multiple binding activities must be accommodated in a few binding interfaces at most, something to be considered remarkable given its small size (15 kDa). Thus, conformational heterogeneity, and in particular

  9. Patient-derived glioblastoma cells show significant heterogeneity in treatment responses to the inhibitor-of-apoptosis-protein antagonist birinapant

    PubMed Central

    Zakaria, Z; Tivnan, A; Flanagan, L; Murray, D W; Salvucci, M; Stringer, B W; Day, B W; Boyd, A W; Kögel, D; Rehm, M; O'Brien, D F; Byrne, A T; Prehn, J H M

    2016-01-01

    Background: Resistance to temozolomide (TMZ) greatly limits chemotherapeutic effectiveness in glioblastoma (GBM). Here we analysed the ability of the Inhibitor-of-apoptosis-protein (IAP) antagonist birinapant to enhance treatment responses to TMZ in both commercially available and patient-derived GBM cells. Methods: Responses to TMZ and birinapant were analysed in a panel of commercial and patient-derived GBM cell lines using colorimetric viability assays, flow cytometry, morphological analysis and protein expression profiling of pro- and antiapoptotic proteins. Responses in vivo were analysed in an orthotopic xenograft GBM model. Results: Single-agent treatment experiments categorised GBM cells into TMZ-sensitive cells, birinapant-sensitive cells, and cells that were insensitive to either treatment. Combination treatment allowed sensitisation to therapy in only a subset of resistant GBM cells. Cell death analysis identified three principal response patterns: Type A cells that readily activated caspase-8 and cell death in response to TMZ while addition of birinapant further sensitised the cells to TMZ-induced cell death; Type B cells that readily activated caspase-8 and cell death in response to birinapant but did not show further sensitisation with TMZ; and Type C cells that showed no significant cell death or moderately enhanced cell death in the combined treatment paradigm. Furthermore, in vivo, a Type C patient-derived cell line that was TMZ-insensitive in vitro and showed a strong sensitivity to TMZ and TMZ plus birinapant treatments. Conclusions: Our results demonstrate remarkable differences in responses of patient-derived GBM cells to birinapant single and combination treatments, and suggest that therapeutic responses in vivo may be greatly affected by the tumour microenvironment. PMID:26657652

  10. Rate heterogeneity in six protein-coding genes from the holoparasite Balanophora (Balanophoraceae) and other taxa of Santalales.

    PubMed

    Su, Huei-Jiun; Hu, Jer-Ming

    2012-11-01

    The holoparasitic flowering plant Balanophora displays extreme floral reduction and was previously found to have enormous rate acceleration in the nuclear 18S rDNA region. So far, it remains unclear whether non-ribosomal, protein-coding genes of Balanophora also evolve in an accelerated fashion and whether the genes with high substitution rates retain their functionality. To tackle these issues, six different genes were sequenced from two Balanophora species and their rate variation and expression patterns were examined. Sequences including nuclear PI, euAP3, TM6, LFY and RPB2 and mitochondrial matR were determined from two Balanophora spp. and compared with selected hemiparasitic species of Santalales and autotrophic core eudicots. Gene expression was detected for the six protein-coding genes and the expression patterns of the three B-class genes (PI, AP3 and TM6) were further examined across different organs of B. laxiflora using RT-PCR. Balanophora mitochondrial matR is highly accelerated in both nonsynonymous (d(N)) and synonymous (d(S)) substitution rates, whereas the rate variation of nuclear genes LFY, PI, euAP3, TM6 and RPB2 are less dramatic. Significant d(S) increases were detected in Balanophora PI, TM6, RPB2 and d(N) accelerations in euAP3. All of the protein-coding genes are expressed in inflorescences, indicative of their functionality. PI is restrictively expressed in tepals, synandria and floral bracts, whereas AP3 and TM6 are widely expressed in both male and female inflorescences. Despite the observation that rates of sequence evolution are generally higher in Balanophora than in hemiparasitic species of Santalales and autotrophic core eudicots, the five nuclear protein-coding genes are functional and are evolving at a much slower rate than 18S rDNA. The mechanism or mechanisms responsible for rapid sequence evolution and concomitant rate acceleration for 18S rDNA and matR are currently not well understood and require further study in Balanophora

  11. Rate heterogeneity in six protein-coding genes from the holoparasite Balanophora (Balanophoraceae) and other taxa of Santalales

    PubMed Central

    Su, Huei-Jiun; Hu, Jer-Ming

    2012-01-01

    Background and Aims The holoparasitic flowering plant Balanophora displays extreme floral reduction and was previously found to have enormous rate acceleration in the nuclear 18S rDNA region. So far, it remains unclear whether non-ribosomal, protein-coding genes of Balanophora also evolve in an accelerated fashion and whether the genes with high substitution rates retain their functionality. To tackle these issues, six different genes were sequenced from two Balanophora species and their rate variation and expression patterns were examined. Methods Sequences including nuclear PI, euAP3, TM6, LFY and RPB2 and mitochondrial matR were determined from two Balanophora spp. and compared with selected hemiparasitic species of Santalales and autotrophic core eudicots. Gene expression was detected for the six protein-coding genes and the expression patterns of the three B-class genes (PI, AP3 and TM6) were further examined across different organs of B. laxiflora using RT-PCR. Key Results Balanophora mitochondrial matR is highly accelerated in both nonsynonymous (dN) and synonymous (dS) substitution rates, whereas the rate variation of nuclear genes LFY, PI, euAP3, TM6 and RPB2 are less dramatic. Significant dS increases were detected in Balanophora PI, TM6, RPB2 and dN accelerations in euAP3. All of the protein-coding genes are expressed in inflorescences, indicative of their functionality. PI is restrictively expressed in tepals, synandria and floral bracts, whereas AP3 and TM6 are widely expressed in both male and female inflorescences. Conclusions Despite the observation that rates of sequence evolution are generally higher in Balanophora than in hemiparasitic species of Santalales and autotrophic core eudicots, the five nuclear protein-coding genes are functional and are evolving at a much slower rate than 18S rDNA. The mechanism or mechanisms responsible for rapid sequence evolution and concomitant rate acceleration for 18S rDNA and matR are currently not well

  12. Heterogeneous side chain conformation highlights a network of interactions implicated in hysteresis of the knotted protein, minimal tied trefoil

    NASA Astrophysics Data System (ADS)

    Burban, David J.; Haglund, Ellinor; Capraro, Dominique T.; Jennings, Patricia A.

    2015-09-01

    Hysteresis is a signature for a bistability in the native landscape of a protein with significant transition state barriers for the interconversion of stable species. Large global stability, as in GFP, contributes to the observation of this rare hysteretic phenomenon in folding. The signature for such behavior is non-coincidence in the unfolding and refolding transitions, despite waiting significantly longer than the time necessary for complete denaturation. Our work indicates that hysteresis in the knotted protein, the minimal tied trefoil from Thermotoga maritma (MTTTm), is mediated by a network of side chain interactions within a tightly packed core. These initially identified interactions include proline 62 from a tight β-like turn, phenylalanine 65 at the beginning of the knotting loop, and histidine 114 that initiates the threading element. It is this tightly packed region and the knotting element that we propose is disrupted with prolonged incubation in the denatured state, and is involved in the observed hysteresis. Interestingly, the disruption is not linked to backbone interactions, but rather to the packing of side chains in this critical region.

  13. NonO, a non-POU-domain-containing, octamer-binding protein, is the mammalian homolog of Drosophila nonAdiss.

    PubMed

    Yang, Y S; Hanke, J H; Carayannopoulos, L; Craft, C M; Capra, J D; Tucker, P W

    1993-09-01

    We have cloned the ubiquitous form of an octamer-binding, 60-kDa protein (NonO) that appears to be the mammalian equivalent of the Drosophila visual and courtship song behavior protein, no-on-transient A/dissonance (nonAdiss). A region unprecedently rich in aromatic amino acids containing two ribonuclear protein binding motifs is highly conserved between the two proteins. A ubiquitous form of NonO is present in all adult tissues, whereas lymphocytes and retina express unique forms of NonO mRNA. The ubiquitous form contains a potential helix-turn-helix motif followed by a highly charged region but differs from prototypic octamer-binding factors by lacking the POU DNA-binding domain. In addition to its conventional octamer duplex-binding, NonO binds single-stranded DNA and RNA at a site independent of the duplex site.

  14. Epigenetics targeted protein-vorinostat nanomedicine inducing apoptosis in heterogeneous population of primary acute myeloid leukemia cells including refractory and relapsed cases.

    PubMed

    Chandran, Parwathy; Kavalakatt, Anu; Malarvizhi, Giridharan Loghanathan; Vasanthakumari, Divya Rani Vikraman Nair; Retnakumari, Archana Payickattu; Sidharthan, Neeraj; Pavithran, Keechilat; Nair, Shantikumar; Koyakutty, Manzoor

    2014-05-01

    Aberrant epigenetics play a key role in the onset and progression of acute myeloid leukemia (AML). Herein we report in silico modelling based development of a novel, protein-vorinostat nanomedicine exhibiting selective and superior anti-leukemic activity against heterogeneous population of AML patient samples (n=9), including refractory and relapsed cases, and three representative cell lines expressing CD34(+)/CD38(-) stem cell phenotype (KG-1a), promyelocytic phenotype (HL-60) and FLT3-ITD mutation (MV4-11). Nano-vorinostat having ~100nm size exhibited enhanced cellular uptake rendering significantly lower IC50 in AML cell lines and patient samples, and induced enhanced HDAC inhibition, oxidative injury, cell cycle arrest and apoptosis compared to free vorinostat. Most importantly, nanomedicine showed exceptional single-agent activity against the clonogenic proliferative capability of bone marrow derived leukemic progenitors, while remaining non-toxic to healthy bone marrow cells. Collectively, this epigenetics targeted nanomedicine appears to be a promising therapeutic strategy against various French-American-British (FAB) classes of AML. Through the use of a protein-vorinostat agent, exceptional single-agent activity was demonstrated against the clonogenic proliferative capability of bone marrow derived leukemic progenitors, while remaining non-toxic to healthy bone marrow cells. The studied epigenetics targeted nanomedicine approach is a promising therapeutic strategy against various French-American-British classes of acute myeloid leukemia. © 2014 Elsevier Inc. All rights reserved.

  15. Re-emergence of circulatory foot-and-mouth disease virus serotypes Asia1 in Bangladesh and VP1 protein heterogeneity with vaccine strain IND 63/72.

    PubMed

    Ullah, H; Siddique, M A; Al Amin, Md; Das, B C; Sultana, M; Hossain, M A

    2015-02-01

    Foot-and-mouth disease virus (FMDV) serotypes O, A and Asia1 are responsible for significant number of disease outbreaks in Bangladesh; however serotype Asia1 has not been reported in circulation since 1996. The present investigation reports the detection of serotype FMDV Asia1 from local farms in 2012 and 2013 outbreaks. The farms were located in Jessore and Gazipur districts, and one of these farms was under vaccine control programme. Phylogenetic analysis of the complete VP1 gene revealed that FMDV Asia1 is under genetic lineage C having close similarity to the Asia1 sequences of Indian origin. The circulatory genotype Asia1 showed VP1 protein sequence heterogeneity of eight amino acid substitutions within the G-H loop with the vaccine strain [IND 63/72 (AY304994)] used in vaccination programme. ELISA assay revealed that, of seven, only one local field serum sample (cattle vaccinated 38 days earlier) was positive at a titre level of >2.4 (log10) but failed to protect the cattle from infection occurred by the virus. This investigation focused that the eight amino acid substitution in VP1 protein at G-H loop of the locally circulated FMDV serotype Asia1 strain may be a reason for current vaccination failure.

  16. Endogenous myelin basic protein-serum factors (MBP-SFs) in Lewis rats. Evidence for their heterogeneity and reactivity with anti-MBP antibodies of different affinities.

    PubMed

    Day, E D; Varitek, V A; Paterson, P Y

    1981-01-01

    MBP-SF, previously described as an endogenous myelin basic protein-serum factor in Lewis rats with a suggested function as a neuroautotolerogen, appears not to be a single factor but a heterogeneous collection of serum factors (MBP-SFs), most probably small fragments of MBP, each cross-reactive with a different region of the multideterminant parent molecule. The heterogeneity of the MBP-SFs in any serum sample is defined and limited by the spectrum of binding affinities of the antibody populations represented in a given reagent anti-MBP antiserum. Some samples of normal Lewis rat serum have been found to contain high affinity MBP-SFs which coexist with low affinity anti-MBP antibodies whereas other sera have shown the reversed pattern, viz. low affinity MBP-SFs and high affinity antibodies. Additional sera have been found to contain MBP-SFs of several different affinities. In time-course studies of rats sensitized to neuroantigen-adjuvant a variety of MBP-SFs and anti-MBP antibodies of different affinities may be observed in sequentially collected sera from a given animal. In no animal has any serum sample been found to contain the full spectrum of MBP-SFs. Although some MBP-SFs have been found to increase temporarily during the 2nd week after neuroantigen/CFA sensitization, all MBP-SFs tend to disappear in the 2nd week and to be replaced by anti-MBP antibodies of differing affinities 3-4 weeks following sensitization.

  17. Lateral dynamics of charged lipids and peripheral proteins in spatially heterogeneous membranes: comparison of continuous and Monte Carlo approaches.

    PubMed

    Kiselev, Vladimir Yu; Leda, Marcin; Lobanov, Alexey I; Marenduzzo, Davide; Goryachev, Andrew B

    2011-10-21

    Biological membranes are complex environments whose physico-chemical properties are of utmost importance for the understanding of many crucial biological processes. Much attention has been given in the literature to the description of membranes along the z-axis perpendicular to the membrane. Here, we instead consider the lateral dynamics of lipids and peripheral proteins due to their electrostatic interaction. Previously, we constructed a Monte Carlo automaton capable of simulating mutual diffusive dynamics of charged lipids and associated positively charged peptides. Here, we derive and numerically analyze a system of Poisson-Boltzmann-Nernst-Planck (PBNP) equations that provide a mean-field approximation compatible with our Monte Carlo model. The thorough comparison between the mean-field PBNP equations and Monte Carlo simulations demonstrates that both the approaches are in a good qualitative agreement in all tested scenarios. We find that the two methods quantitatively deviate when the local charge density is high, presumably because the Poisson-Boltzmann formalism is applicable in the so-called weak coupling limit, whose validity is restricted to low charge densities. Nevertheless, we conclude that the mean-field PBNP approach provides a good approximation for the considerably more detailed Monte Carlo model at only a fraction of the associated computational cost and allows simulation of the membrane lateral dynamics on the space and time scales relevant for the realistic biological problems. © 2011 American Institute of Physics

  18. Targeting eNOS and beyond: Emerging heterogeneity of the role of endothelial Rho proteins in stroke protection

    PubMed Central

    Sawada, Naoki; Liao, James K.

    2010-01-01

    Summary Currently available modalities for the treatment of acute ischemic stroke are aimed to preserve or augment cerebral blood flow (CBF). Experimental evidence suggests that statins, which show 25–30% reduction of stroke incidence in clinical trials, confer stroke protection by upregulation of eNOS and increasing CBF. The upregulation of eNOS by statins is mediated by inhibition of small GTP-binding protein RhoA. Our recent study uncovered a unique role for a Rho-family member Rac1 in stroke protection. Rac1 in endothelium does not affect CBF. Instead, inhibition of endothelial Rac1 leads to broad upregulation of genes relevant to neurovascular protection. Intriguingly, inhibition of endothelial Rac1 enhances neuronal cell survival through endothelium-derived neurotrophic factors including artemin. This review discusses the emerging therapeutic opportunities to target the neurovascular signaling beyond the blood-brain barrier, with special emphasis on the novel role of endothelial Rac1 in stroke protection. PMID:19673606

  19. Heterogeneity of myofibrillar proteins in lobster fast and slow muscles: variants of troponin, paramyosin, and myosin light chains comprise four distinct protein assemblages

    SciTech Connect

    Mykles, D.L.

    1985-01-01

    Fast and slow muscles from the claws and abdomen of the American lobster Homarus americanus were examined for adenosine triphosphatase (ATPase) activity and for differences in myofibrillar proteins. Both myosin and actomyosin ATPase were correlated with fiber composition and contractile speed. Four distinct patterns of myofibrilla proteins observed in sodium dodecyl sulfate-polyacrylamide gels were distinguished by different assemblages of regulatory and contractile protein variants. A total of three species of troponin-T, five species of troponin-I, and three species of troponin-C were observed. Lobster myosins contained two groups of light chains (LC), termed alpha and beta. There were three ..cap alpha..-LC variants and two ..beta..-LC variants. There were no apparent differences in myosin heavy chain, actin, and tropomyosin. Only paramyosin showed a pattern completely consistent with muscle fiber type: slow fibers contained a species (105 kD) slightly smaller than the principle variant (110 kD) in fast fibers. It is proposed that the type of paramyosin present could provide a biochemical marker to identify the fiber composition of muscles that have not been fully characterized. The diversity of troponin and myosin LC variants suggests that subtle differences in physiological performance exist within the broader categories of fast- and slow-twitch muscles. 31 references, 6 figures, 2 tables.

  20. Molecular Basis for Structural Heterogeneity of an Intrinsically Disordered Protein Bound to a Partner by Combined ESI-IM-MS and Modeling

    NASA Astrophysics Data System (ADS)

    D'Urzo, Annalisa; Konijnenberg, Albert; Rossetti, Giulia; Habchi, Johnny; Li, Jinyu; Carloni, Paolo; Sobott, Frank; Longhi, Sonia; Grandori, Rita

    2015-03-01

    Intrinsically disordered proteins (IDPs) form biologically active complexes that can retain a high degree of conformational disorder, escaping structural characterization by conventional approaches. An example is offered by the complex between the intrinsically disordered NTAIL domain and the phosphoprotein X domain (PXD) from measles virus (MeV). Here, distinct conformers of the complex are detected by electrospray ionization-mass spectrometry (ESI-MS) and ion mobility (IM) techniques yielding estimates for the solvent-accessible surface area (SASA) in solution and the average collision cross-section (CCS) in the gas phase. Computational modeling of the complex in solution, based on experimental constraints, provides atomic-resolution structural models featuring different levels of compactness. The resulting models indicate high structural heterogeneity. The intermolecular interactions are predominantly hydrophobic, not only in the ordered core of the complex, but also in the dynamic, disordered regions. Electrostatic interactions become involved in the more compact states. This system represents an illustrative example of a hydrophobic complex that could be directly detected in the gas phase by native mass spectrometry. This work represents the first attempt to modeling the entire NTAIL domain bound to PXD at atomic resolution.

  1. Differential protein structural disturbances and suppression of assembly partners produced by nonsense GABRG2 epilepsy mutations: implications for disease phenotypic heterogeneity.

    PubMed

    Wang, Juexin; Shen, Dingding; Xia, Geqing; Shen, Wangzhen; Macdonald, Robert L; Xu, Dong; Kang, Jing-Qiong

    2016-10-20

    Mutations in GABAA receptor subunit genes are frequently associated with epilepsy, and nonsense mutations in GABRG2 are associated with several epilepsy syndromes including childhood absence epilepsy, generalized tonic clonic seizures and the epileptic encephalopathy, Dravet syndrome. The molecular basis for the phenotypic heterogeneity of mutations is unclear. Here we focused on three nonsense mutations in GABRG2 (GABRG2(R136*), GABRG2(Q390*) and GABRG2(W429*)) associated with epilepsies of different severities. Structural modeling and structure-based analysis indicated that the surface of the wild-type γ2 subunit was naturally hydrophobic, which is suitable to be buried in the cell membrane. Different mutant γ2 subunits had different stabilities and different interactions with their wild-type subunit binding partners because they adopted different conformations and had different surface hydrophobicities and different tendency to dimerize. We utilized flow cytometry and biochemical approaches in combination with lifted whole cell patch-clamp recordings. We demonstrated that the truncated subunits had no to minimal surface expression and unchanged or reduced surface expression of wild-type partnering subunits. The amplitudes of GABA-evoked currents from the mutant α1β2γ2(R136*), α1β2γ2(Q390*) and α1β2γ2(W429*) receptors were reduced compared to the currents from α1β2γ2 receptors but with differentially reduced levels. This thus suggests differential protein structure disturbances are correlated with disease severity.

  2. Differential protein structural disturbances and suppression of assembly partners produced by nonsense GABRG2 epilepsy mutations: implications for disease phenotypic heterogeneity

    PubMed Central

    Wang, Juexin; Shen, Dingding; Xia, Geqing; Shen, Wangzhen; Macdonald, Robert L.; Xu, Dong; Kang, Jing-Qiong

    2016-01-01

    Mutations in GABAA receptor subunit genes are frequently associated with epilepsy, and nonsense mutations in GABRG2 are associated with several epilepsy syndromes including childhood absence epilepsy, generalized tonic clonic seizures and the epileptic encephalopathy, Dravet syndrome. The molecular basis for the phenotypic heterogeneity of mutations is unclear. Here we focused on three nonsense mutations in GABRG2 (GABRG2(R136*), GABRG2(Q390*) and GABRG2(W429*)) associated with epilepsies of different severities. Structural modeling and structure-based analysis indicated that the surface of the wild-type γ2 subunit was naturally hydrophobic, which is suitable to be buried in the cell membrane. Different mutant γ2 subunits had different stabilities and different interactions with their wild-type subunit binding partners because they adopted different conformations and had different surface hydrophobicities and different tendency to dimerize. We utilized flow cytometry and biochemical approaches in combination with lifted whole cell patch-clamp recordings. We demonstrated that the truncated subunits had no to minimal surface expression and unchanged or reduced surface expression of wild-type partnering subunits. The amplitudes of GABA-evoked currents from the mutant α1β2γ2(R136*), α1β2γ2(Q390*) and α1β2γ2(W429*) receptors were reduced compared to the currents from α1β2γ2 receptors but with differentially reduced levels. This thus suggests differential protein structure disturbances are correlated with disease severity. PMID:27762395

  3. [Heterogeneity and polymorphism of functionally specialized blood proteins in migratory fish: case study of the North Caspian population of the Russian sturgeon during sea and river periods of life. 1. Albumins].

    PubMed

    Luk'ianenko, V I; Khabarov, M V; Luk'ianenko, V V

    2002-01-01

    A comparative study of the levels of heterogeneity and polymorphism of albumins, the most important functionally specialized blood proteins, has been carried out. The albumin system of Russian sturgeon undergoes distinct changes while the fish change habitat during the spawning migration from sea to river. They are expressed as an increased level of heterogeneity, an increased content of serum albumins in fish during the river period of life as compared to the sea period, and an increased share of a slow component of albuminograms. These changes suggest a significant role of the blood albumin system in adaptation of the Caspian sturgeon migratory species to fresh water life conditions.

  4. The heterogeneity of spermatogonia is revealed by their topology and expression of marker proteins including the germ cell-specific proteins Nanos2 and Nanos3.

    PubMed

    Suzuki, Hitomi; Sada, Aiko; Yoshida, Shosei; Saga, Yumiko

    2009-12-15

    Spermatogonial stem cells (SSCs) reside in undifferentiated type-A spermatogonia and contribute to continuous spermatogenesis by maintaining the balance between self-renewal and differentiation, thereby meeting the biological demand in the testis. Spermatogonia have to date been characterized principally through their morphology, but we herein report the detailed characterization of undifferentiated spermatogonia in mouse testes based on their gene expression profiles in combination with topological features. The detection of the germ cell-specific proteins Nanos2 and Nanos3 as markers of spermatogonia has enabled the clear dissection of complex populations of these cells as Nanos2 was recently shown to be involved in the maintenance of stem cells. Nanos2 is found to be almost exclusively expressed in A(s) to A(pr) cells, whereas Nanos3 is detectable in most undifferentiated spermatogonia (A(s) to A(al)) and differentiating A(1) spermatogonia. In our present study, we find that A(s) and A(pr) can be basically classified into three categories: (1) GFRalpha1(+)Nanos2(+)Nanos3(-)Ngn3(-), (2) GFRalpha1(+)Nanos2(+)Nanos3(+)Ngn3(-), and (3) GFRalpha1(-)Nanos2(+/-)Nanos3(+)Ngn3(+). We propose that the first of these groups is most likely to include the stem cell population and that Nanos3 may function in transit amplifying cells.

  5. Heterogeneity of Raft-Type Membrane Microdomains Associated with VP4, the Rotavirus Spike Protein, in Caco-2 and MA 104 Cells▿

    PubMed Central

    Delmas, Olivier; Breton, Michelyne; Sapin, Catherine; Le Bivic, André; Colard, Odile; Trugnan, Germain

    2007-01-01

    Previous studies have shown that rotavirus virions, a major cause of infantile diarrhea, assemble within small intestinal enterocytes and are released at the apical pole without significant cell lysis. In contrast, for the poorly differentiated kidney epithelial MA 104 cells, which have been used extensively to study rotavirus assembly, it has been shown that rotavirus is released by cell lysis. The subsequent discovery that rotavirus particles associate with raft-type membrane microdomains (RTM) in Caco-2 cells provided a simple explanation for rotavirus polarized targeting. However, the results presented here, together with those recently published by another group, demonstrate that rotavirus also associates with RTM in MA 104 cells, thus indicating that a simple interaction of rotavirus with rafts is not sufficient to explain its apical targeting in intestinal cells. In the present study, we explore the possibility that RTM may have distinct physicochemical properties that may account for the differences observed in the rotavirus cell cycle between MA 104 and Caco-2 cells. We show here that VP4 association with rafts is sensitive to cholesterol extraction by methyl-β-cyclodextrin treatment in MA 104 cells and insensitive in Caco-2 cells. Using the VP4 spike protein as bait, VP4-enriched raft subsets were immunopurified. They contained 10 to 15% of the lipids present in total raft membranes. We found that the nature and proportion of phospholipids and glycosphingolipids were different between the two cell lines. We propose that this raft heterogeneity may support the cell type dependency of virus assembly and release. PMID:17135322

  6. Human milk fat globules: polar lipid composition and in situ structural investigations revealing the heterogeneous distribution of proteins and the lateral segregation of sphingomyelin in the biological membrane.

    PubMed

    Lopez, Christelle; Ménard, Olivia

    2011-03-01

    Although human milk fat globules (MFG) are of primary importance since they are the exclusive lipid delivery carriers in the gastrointestinal tract of breast-fed infants, they remain the poorly understood aspect of milk. The objectives of this study were to investigate these unique colloidal assemblies and their interfacial properties, i.e. composition and structure of their biological membrane. In mature breast milk, MFG have a mean diameter of 4-5 microm, a surface area of about 2m(2)/g fat and an apparent zeta potential ζ=-6.7 ± 0.5 mV at 37°C. Human MFG contain 3-4mg polar lipids/g fat as quantified by HPLC/ELSD. The main polar lipids are sphingomyelin (SM; 36-45%, w/w), phosphatidylcholine (19-23%, w/w) and phosphatidylethanolamine (10-15%, w/w). In situ structural investigations of human MFG have been performed using light and confocal microscopy with adapted fluorescent probes, i.e. Nile Red, the extrinsic phospholipid Rh-DOPE, Fast Green and the lectin WGA-488. This study revealed a spatial heterogeneity in the human milk fat globule membrane (MFGM), with the lateral segregation of SM in liquid-ordered phase domains of various shapes and sizes surrounded by a liquid-disordered phase composed of the glycerophospholipids in which the proteins are dispersed. The glycocalyx formed by glycoproteins and cytoplasmic remnents have also been characterised around human MFG. A new model for the structure of the human MFGM is proposed and discussed. The unique composition and lateral organisation of the human MFGM components could be of metabolic significance and have health impact for the infants that need to be further explored.

  7. Tracer-based estimates of protein flux in cases of incomplete product renewal: evidence and implications of heterogeneity in collagen turnover

    PubMed Central

    Zhou, Haihong; Wang, Sheng-Ping; Herath, Kithsiri; Kasumov, Takhar; Sadygov, Rovshan G.; Kelley, David E.

    2015-01-01

    The synthesis of various molecules can be estimated by measuring the incorporation of a labeled precursor into a product of interest. Unfortunately, a central problem in many studies has been an inability to estimate the intracellular dilution of the precursor and therein correctly calculate the synthesis of the product; it is generally assumed that measuring the true product labeling is straightforward. We initiated a study to examine liver collagen synthesis and identified an apparent problem with assumptions regarding measurements of the product labeling. Since it is well known that collagen production is relatively slow, we relied on the use of [2H]H2O labeling (analogous to a primed infusion) and sampled animals over the course of 16 days. Although the water labeling (the precursor) remained stable and we observed the incorporation of labeled amino acids into collagen, the asymptotic protein labeling was considerably lower than what would be expected based on the precursor labeling. Although this observation is not necessarily surprising (i.e., one might expect that a substantial fraction of the collagen pool would appear “inert” or turn over at a very slow rate), its implications are of interest in certain areas. Herein, we discuss a novel situation in which tracers are used to quantify rates of flux under conditions where a product may not undergo complete replacement. We demonstrate how heterogeneity in the product pool can lead one to the wrong conclusions regarding estimates of flux, and we outline an approach that may help to minimize errors surrounding data interpretation. PMID:26015435

  8. Regulation of Etioplast Pigment-Protein Complexes, Inner Membrane Architecture, and Protochlorophyllide a Chemical Heterogeneity by Light-Dependent NADPH:Protochlorophyllide Oxidoreductases A and B1

    PubMed Central

    Franck, Fabrice; Sperling, Ulrich; Frick, Geneviève; Pochert, Babette; van Cleve, Barbara; Apel, Klaus; Armstrong, Gregory A.

    2000-01-01

    The etioplast of dark-grown angiosperms is characterized by the prolamellar body (PLB) inner membrane, the absence of chlorophyll, and the accumulation of divinyl and monovinyl derivatives of protochlorophyll(ide) a [Pchl(ide) a]. Either of two structurally related, but differentially expressed light-dependent NADPH:Pchlide oxidoreductases (PORs), PORA and PORB, can assemble the PLB and form dark-stable ternary complexes containing enzymatically photoactive Pchlide-F655. Here we have examined in detail whether these polypeptides play redundant roles in etioplast differentiation by manipulating the total POR content and the PORA-to-PORB ratio of etiolated Arabidopsis seedlings using antisense and overexpression approaches. POR content correlates closely with PLB formation, the amounts, spectroscopic properties, and photoreduction kinetics of photoactive Pchlide, the ratio of photoactive Pchlide-F655 to non-photoactive Pchl(ide)-F632, and the ratio of divinyl- to monovinyl-Pchl(ide). This last result defines POR as the first endogenous protein factor demonstrated to influence the chemical heterogeneity of Pchl(ide) in angiosperms. It is intriguing that excitation energy transfer between different spectroscopic forms of Pchl(ide) in etiolated cotyledons remains largely independent of POR content. We therefore propose that the PLB contains a minimal structural unit with defined pigment stoichiometries, within which a small amount of non-photoactive Pchl(ide) transfers excitation energy to a large excess of photoactive Pchlide-F655. In addition, our data suggests that POR may bind not only stoichiometric amounts of photoactive Pchlide, but also substoichiometric amounts of non-photoactive Pchl(ide). We conclude that the typical characteristics of etioplasts are closely related to total POR content, but not obviously to the specific presence of PORA or PORB. PMID:11115885

  9. Interacting protein partners of Arabidopsis RNA-binding protein AtRBP45b.

    PubMed

    Muthuramalingam, M; Wang, Y; Li, Y; Mahalingam, R

    2017-05-01

    RNA binding proteins, important players in post-transcriptional gene regulation, usually exist in ribonuclear complexes. However, even in model systems like Arabidopsis characterisation of RBP associated proteins is limited. In this study, we investigated the interacting proteins of the Arabidopsis AtRBP45b, which is involved in stress signalling. In vivo localisation of AtRBP45b was conducted using 35S-GFP. FLAG-tagged AtRBP45b under control of the 35S promoter in the Atrbp45b-1 mutant background was used to pull down AtRBP45b interacting proteins. Yeast two-hybrid analysis, fluorescence energy resonance transfer assays were used to confirm the veracity of the AtRBP45b interacting proteins. In planta GFP-tagging indicated AtRBP45b is localised to the nucleus and the cytosol. AtRBP45b protein has a N-terminal proline-rich region and a C-terminal glutamine-rich domain that are usually involved in protein-protein interactions. Co-immunoprecipitation followed by mass spectrometry-based protein sequencing led to identification of 30 proteins that interacted with AtRBP45b. Using information from interactome databases (BIOGRID, INTACT and STRING), pull-down assays and localisation data, 12 putative interacting proteins were selected for yeast two-hybrid analysis. Cap-binding protein (CBP20, At5g44200) and polyA-binding protein (PAB8, At1g49760) were shown to interact with AtRBP45b. Based on its interacting partners we speculate that AtRBP45b may play an important role in RNA metabolism, especially in aspects related to mRNA stability and translation initiation during stress conditions in plants.

  10. iWRAP: An interface threading approach with application to prediction of cancer related protein-protein interactions

    PubMed Central

    Hosur, R.; Xu, J.; Bienkowska, J.; Berger, B.

    2010-01-01

    Current homology modeling methods for predicting protein-protein interactions (PPIs) have difficulty in the “twilight zone” (<40%) of sequence identities. Threading methods extend coverage further into the twilight zone by aligning primary sequences for a pair of proteins to a best-fit template complex to predict an entire three-dimensional structure. We introduce a threading approach, iWRAP, which focuses on only the protein interface. Our approach combines a novel linear programming formulation for interface alignment with a boosting classifier for interaction prediction. We demonstrate its efficacy on SCOPPI, a classification of PPIs in the Protein Databank, and on the entire yeast genome. iWRAP provides significantly improved prediction of PPIs and their interfaces in stringent cross-validation on SCOPPI. Furthermore, by combining our predictions with a full-complex threader, we achieve coverage of 13% for the yeast PPIs, which is close to a 50% increase over previous methods at a higher sensitivity. As an application, we effectively combine iWRAP with genomic data to identify novel cancer related genes involved in chromatin remodeling, nucleosome organization and ribonuclear complex assembly. iWRAP is available at http://iwrap.csail.mit.edu. PMID:21130772

  11. A Heterogeneous Nuclear Ribonucleoprotein A/B-Related Protein Binds to Single-Stranded DNA near the 5′ End or within the Genome of Feline Parvovirus and Can Modify Virus Replication

    PubMed Central

    Wang, Dai; Parrish, Colin R.

    1999-01-01

    Phage display of cDNA clones prepared from feline cells was used to identify host cell proteins that bound to DNA-containing feline panleukopenia virus (FPV) capsids but not to empty capsids. One gene found in several clones encoded a heterogeneous nuclear ribonucleoprotein (hnRNP)-related protein (DBP40) that was very similar in sequence to the A/B-type hnRNP proteins. DBP40 bound specifically to oligonucleotides representing a sequence near the 5′ end of the genome which is exposed on the outside of the full capsid but did not bind most other terminal sequences. Adding purified DBP40 to an in vitro fill-in reaction using viral DNA as a template inhibited the production of the second strand after nucleotide (nt) 289 but prior to nt 469. DBP40 bound to various regions of the viral genome, including a region between nt 295 and 330 of the viral genome which has been associated with transcriptional attenuation of the parvovirus minute virus of mice, which is mediated by a stem-loop structure of the DNA and cellular proteins. Overexpression of the protein in feline cells from a plasmid vector made them largely resistant to FPV infection. Mutagenesis of the protein binding site within the 5′ end viral genome did not affect replication of the virus. PMID:10438866

  12. Purification, cloning, and expression of a murine phosphoprotein that binds the kappa B motif in vitro identifies it as the homolog of the human heterogeneous nuclear ribonucleoprotein K protein. Description of a novel DNA-dependent phosphorylation process.

    PubMed

    Ostrowski, J; Van Seuningen, I; Seger, R; Rauch, C T; Sleath, P R; McMullen, B A; Bomsztyk, K

    1994-07-01

    The kappa B enhancer element regulates expression of many genes involved in immune responses and other processes. kappa B motif binds a number of proteins, some but not all, are related to the NF-kappa B family of transcription factors. We have previously identified a 65-kDa phosphoprotein that is specifically recognized by the kappa B motif (Ostrowski, J., Sims, J. E., Sibley, C. H., Valentine, M. A., Dower, S. K., Meier, K. E., and Bomsztyk, K. (1991) J. Biol. Chem. 266, 12722-12733). This protein is closely associated with a serine/threonine kinase that is responsive to treatment of cells with interleukin-1 and other agents. We report here purification, cloning, and expression of this kappa B motif-binding phosphoprotein. The primary structure deduced from the isolated murine cDNA, identifies the protein as the homolog of the human heterogeneous nuclear ribonucleoprotein K protein. Antipeptide antibodies and expression of the cloned cDNA in Escherichia coli, demonstrated that the K protein is the authentic phosphoprotein that binds the kappa B motif in vitro. We also demonstrate that the in vitro phosphorylation of the natural and the recombinant K proteins by the associated kinase is stimulated by the kappa B motif.

  13. Heterogeneity of vertebrate brain tubulins.

    PubMed Central

    Field, D J; Collins, R A; Lee, J C

    1984-01-01

    We have examined the extent of brain tubulin heterogeneity in six vertebrate species commonly used in tubulin research (rat, calf, pig, chicken, human, and lamb) using isoelectric focusing, two-dimensional electrophoresis, and peptide mapping procedures that provide higher resolution than previously available. The extent of heterogeneity is extremely similar in all of these organisms, as judged by number, range of isoelectric points, and distribution of the isotubulins. A minimum of 6 alpha and 12 beta tubulins was resolved from all sources. Even the pattern of spots on two-dimensional peptide maps is remarkably similar. These similarities suggest that the populations of tubulin in all of these brains should have similar overall physical properties. It is particularly interesting that chicken, which has only four or five beta-tubulin genes, contains approximately 12 beta tubulins. Thus, post-translational modification must generate at least some of the tubulin heterogeneity. Mammalian species, which contain 15-20 tubulin DNA sequences, do not show any more tubulin protein heterogeneity than does chicken. This suggests that expression of only a small number of the mammalian genes may be required to generate the observed tubulin heterogeneity. Images PMID:6588378

  14. A physical mechanism of cancer heterogeneity

    NASA Astrophysics Data System (ADS)

    Chen, Cong; Wang, Jin

    2016-02-01

    We studied a core cancer gene regulatory network motif to uncover possible source of cancer heterogeneity from epigenetic sources. When the time scale of the protein regulation to the gene is faster compared to the protein synthesis and degradation (adiabatic regime), normal state, cancer state and an intermediate premalignant state emerge. Due to the epigenetics such as DNA methylation and histone remodification, the time scale of the protein regulation to the gene can be slower or comparable to the protein synthesis and degradation (non-adiabatic regime). In this case, many more states emerge as possible phenotype alternations. This gives the origin of the heterogeneity. The cancer heterogeneity is reflected from the emergence of more phenotypic states, larger protein concentration fluctuations, wider kinetic distributions and multiplicity of kinetic paths from normal to cancer state, higher energy cost per gene switching, and weaker stability.

  15. A physical mechanism of cancer heterogeneity

    PubMed Central

    Chen, Cong; Wang, Jin

    2016-01-01

    We studied a core cancer gene regulatory network motif to uncover possible source of cancer heterogeneity from epigenetic sources. When the time scale of the protein regulation to the gene is faster compared to the protein synthesis and degradation (adiabatic regime), normal state, cancer state and an intermediate premalignant state emerge. Due to the epigenetics such as DNA methylation and histone remodification, the time scale of the protein regulation to the gene can be slower or comparable to the protein synthesis and degradation (non-adiabatic regime). In this case, many more states emerge as possible phenotype alternations. This gives the origin of the heterogeneity. The cancer heterogeneity is reflected from the emergence of more phenotypic states, larger protein concentration fluctuations, wider kinetic distributions and multiplicity of kinetic paths from normal to cancer state, higher energy cost per gene switching, and weaker stability. PMID:26854017

  16. Analyzing protein micro-heterogeneity in chicken ovalbumin by high-resolution native mass spectrometry exposes qualitatively and semi-quantitatively 59 proteoforms.

    PubMed

    Yang, Yang; Barendregt, Arjan; Kamerling, Johannis P; Heck, Albert J R

    2013-12-17

    Taking chicken Ovalbumin as a prototypical example of a eukaryotic protein we use high-resolution native electrospray ionization mass spectrometry on a modified Exactive Orbitrap mass analyzer to qualitatively and semiquantitatively dissect 59 proteoforms in the natural protein. This variety is largely induced by the presence of multiple phosphorylation sites and a glycosylation site that we find to be occupied by at least 45 different glycan structures. Mass analysis of the intact protein in its native state is straightforward and fast, requires very little sample preparation, and provides a direct view on the stoichiometry of all different coappearing modifications that are distinguishable in mass. As such, this proof-of-principal analysis shows that native electrospray ionization mass spectrometry in combination with an Orbitrap mass analyzer offers a means to characterize proteins in a manner highly complementary to standard bottom-up shot-gun proteome analysis.

  17. Treponema pallidum subsp. pallidum TP0136 Protein Is Heterogeneous among Isolates and Binds Cellular and Plasma Fibronectin via its NH2-Terminal End

    PubMed Central

    Ke, Wujian; Molini, Barbara J.; Lukehart, Sheila A.; Giacani, Lorenzo

    2015-01-01

    Adherence-mediated colonization plays an important role in pathogenesis of microbial infections, particularly those caused by extracellular pathogens responsible for systemic diseases, such as Treponema pallidum subsp. pallidum (T. pallidum), the agent of syphilis. Among T. pallidum adhesins, TP0136 is known to bind fibronectin (Fn), an important constituent of the host extracellular matrix. To deepen our understanding of the TP0136-Fn interaction dynamics, we used two naturally-occurring sequence variants of the TP0136 protein to investigate which region of the protein is responsible for Fn binding, and whether TP0136 would adhere to human cellular Fn in addition to plasma Fn and super Fn as previously reported. Fn binding assays were performed with recombinant proteins representing the two full-length TP0136 variants and their discrete regions. As a complementary approach, we tested inhibition of T. pallidum binding to Fn by recombinant full-length TP0136 proteins and fragments, as well as by anti-TP0136 immune sera. Our results show that TP0136 adheres more efficiently to cellular Fn than to plasma Fn, that the TP0136 NH2-terminal conserved region of the protein is primarily responsible for binding to plasma Fn but that binding sites for cellular Fn are also present in the protein’s central and COOH-terminal regions. Additionally, message quantification studies show that tp0136 is highly transcribed during experimental infection, and that its message level increases in parallel to the host immune pressure on the pathogen, which suggests a possible role for this protein in T. pallidum persistence. In a time where syphilis incidence is high, our data will help in the quest to identify suitable targets for development of a much needed vaccine against this important disease. PMID:25793702

  18. Quantitative and qualitative heterogeneity of partially hydrolysed serum proteins of cancer patients and normal individuals, analysed by polyacrylamide disc gel cationic electrophoresis. I. Breast cancer.

    PubMed

    Delinassios, J G

    1978-01-01

    Serum samples from patients with primary breast carcinoma, breast carcinoma with metastases, chronic mastitis and fibroadenoma, and healthy individuals, were treated with hydrochloric acid and urea and analysed by polyacrylamide disc gel cationic electrophoresis. The discrete and highly reproducible patterns received showed variations from individual to individual. The frequencies of the presence and of the color intensity of every protein band were compared and profound differences were found for several bands between the four groups of patients and the healthy controls studied. The results suggest that a correlation exists between the electrophoretic profiles of partially hydrolysed serum cationic proteins and occurrence of disease, possibly useful for the early diagnosis of preneoplastic states.

  19. Lipid rafts: heterogeneity on the high seas.

    PubMed Central

    Pike, Linda J

    2004-01-01

    Lipid rafts are membrane microdomains that are enriched in cholesterol and glycosphingolipids. They have been implicated in processes as diverse as signal transduction, endocytosis and cholesterol trafficking. Recent evidence suggests that this diversity of function is accompanied by a diversity in the composition of lipid rafts. The rafts in cells appear to be heterogeneous both in terms of their protein and their lipid content, and can be localized to different regions of the cell. This review summarizes the data supporting the concept of heterogeneity among lipid rafts and outlines the evidence for cross-talk between raft components. Based on differences in the ways in which proteins interact with rafts, the Induced-Fit Model of Raft Heterogeneity is proposed to explain the establishment and maintenance of heterogeneity within raft populations. PMID:14662007

  20. Heterogeneity in ess transcriptional organization and variable contribution of the Ess/Type VII protein secretion system to virulence across closely related Staphylocccus aureus strains.

    PubMed

    Kneuper, Holger; Cao, Zhen Ping; Twomey, Kate B; Zoltner, Martin; Jäger, Franziska; Cargill, James S; Chalmers, James; van der Kooi-Pol, Magdalena M; van Dijl, Jan Maarten; Ryan, Robert P; Hunter, William N; Palmer, Tracy

    2014-09-01

    The Type VII protein secretion system, found in Gram-positive bacteria, secretes small proteins, containing a conserved W-x-G amino acid sequence motif, to the growth medium. Staphylococcus aureus has a conserved Type VII secretion system, termed Ess, which is dispensable for laboratory growth but required for virulence. In this study we show that there are unexpected differences in the organization of the ess gene cluster between closely related strains of S. aureus. We further show that in laboratory growth medium different strains of S. aureus secrete the EsxA and EsxC substrate proteins at different growth points, and that the Ess system in strain Newman is inactive under these conditions. Systematic deletion analysis in S. aureus RN6390 is consistent with the EsaA, EsaB, EssA, EssB, EssC and EsxA proteins comprising core components of the secretion machinery in this strain. Finally we demonstrate that the Ess secretion machinery of two S. aureus strains, RN6390 and COL, is important for nasal colonization and virulence in the murine lung pneumonia model. Surprisingly, however, the secretion system plays no role in the virulence of strain SA113 under the same conditions.

  1. Heterogeneity in ess transcriptional organization and variable contribution of the Ess/Type VII protein secretion system to virulence across closely related Staphylocccus aureus strains

    PubMed Central

    Kneuper, Holger; Cao, Zhen Ping; Twomey, Kate B; Zoltner, Martin; Jäger, Franziska; Cargill, James S; Chalmers, James; van der Kooi-Pol, Magdalena M; van Dijl, Jan Maarten; Ryan, Robert P; Hunter, William N; Palmer, Tracy

    2014-01-01

    The Type VII protein secretion system, found in Gram-positive bacteria, secretes small proteins, containing a conserved W-x-G amino acid sequence motif, to the growth medium. Staphylococcus aureus has a conserved Type VII secretion system, termed Ess, which is dispensable for laboratory growth but required for virulence. In this study we show that there are unexpected differences in the organization of the ess gene cluster between closely related strains of S. aureus. We further show that in laboratory growth medium different strains of S. aureus secrete the EsxA and EsxC substrate proteins at different growth points, and that the Ess system in strain Newman is inactive under these conditions. Systematic deletion analysis in S. aureus RN6390 is consistent with the EsaA, EsaB, EssA, EssB, EssC and EsxA proteins comprising core components of the secretion machinery in this strain. Finally we demonstrate that the Ess secretion machinery of two S. aureus strains, RN6390 and COL, is important for nasal colonization and virulence in the murine lung pneumonia model. Surprisingly, however, the secretion system plays no role in the virulence of strain SA113 under the same conditions. PMID:25040609

  2. Inferring biological dynamics in heterogeneous cellular environments

    NASA Astrophysics Data System (ADS)

    Pressé, Steve

    In complex environments, it often appears that biomolecules such as proteins do not diffuse normally. That is, their mean square displacement does not scale linearly with time. This anomalous diffusion happens for multiple reasons: proteins can bind to structures and other proteins; fluorophores used to label proteins may flicker or blink making it appear that the labeled protein is diffusing anomalously; and proteins can diffuse in differently crowded environments. Here we describe methods for learning about such processes from imaging data collected inside the heterogeneous environment of the living cell. Refs.: ''Inferring Diffusional Dynamics from FCS in Heterogeneous Nuclear Environments'' Konstantinos Tsekouras, Amanda Siegel, Richard N. Day, Steve Pressé*, Biophys. J. , 109, 7 (2015). ''A data-driven alternative to the fractional Fokker-Planck equation'' Steve Pressé*, J. Stat. Phys.: Th. and Expmt. , P07009 (2015).

  3. Phenotypically heterogeneous populations in spatially heterogeneous environments

    NASA Astrophysics Data System (ADS)

    Patra, Pintu; Klumpp, Stefan

    2014-03-01

    The spatial expansion of a population in a nonuniform environment may benefit from phenotypic heterogeneity with interconverting subpopulations using different survival strategies. We analyze the crossing of an antibiotic-containing environment by a bacterial population consisting of rapidly growing normal cells and slow-growing, but antibiotic-tolerant persister cells. The dynamics of crossing is characterized by mean first arrival times and is found to be surprisingly complex. It displays three distinct regimes with different scaling behavior that can be understood based on an analytical approximation. Our results suggest that a phenotypically heterogeneous population has a fitness advantage in nonuniform environments and can spread more rapidly than a homogeneous population.

  4. Sequence heterogeneity in the gene encoding the rhoptry-associated protein-1 (RAP-1) of Babesia caballi isolates from South Africa.

    PubMed

    Bhoora, Raksha; Quan, Melvyn; Zweygarth, Erich; Guthrie, Alan J; Prinsloo, Sandra A; Collins, Nicola E

    2010-05-11

    A competitive-inhibition enzyme-linked immunosorbent assay (cELISA) developed for the detection of antibody specific for Babesia caballi was used to test sera collected from 1237 South African horses. None of these samples tested positive using the cELISA, although 63 samples tested positive for B. caballi antibody using the indirect fluorescent antibody test (IFAT). We therefore characterized the rap-1 gene that codes for the antigen (rhoptry-associated protein, RAP-1) used in the cELISA, from South African B. caballi isolates. Three sets of primers were designed to amplify the complete gene and flanking regions (approximately 1800 bp), but only one set of primers yielded PCR products, and we were only able to amplify a region at the 5' end of the gene (615 bp) from ten South African B. caballiin vitro-cultured isolates. Sequence data from seven of these were obtained. The sequences showed between 79% and 81% identity to B. caballirap-1 gene sequences that have been reported in the literature (accession numbers: AF092736 and AB017700). The GenomeWalker Universal kit (Clonetech) was used to amplify the regions flanking the 615bp B. caballirap-1 fragment from two South African isolates. Amplified products were cloned into the pGEM-T Easy vector and sequenced. The complete rap-1 gene sequence, comprising a single open reading frame of 1479 bp that encodes a protein consisting of 493 amino acids, was obtained from the two South African isolates. This sequence data was used to redesign the amplification primers and rap-1 homologues were obtained from a further eight isolates. BLASTP analysis indicated an amino acid identity of between 57.9% and 65.1% to the two RAP-1 protein sequences, AF092736 and AB017700, with most differences occurring at the carboxy-terminus. The amino acid sequence differences probably explain why it was not possible to detect B. caballi antibody in IFAT positive sera from South Africa using the cELISA. Redesigning the current cELISA using a

  5. The Heterogeneity of Mutational Tolerance in a Protein is Dependent on the Strength of Selective Pressure Correlating with Sectors of Co-evolving Residues

    NASA Astrophysics Data System (ADS)

    Stiffler, Michael; Ranganathan, Rama

    2011-03-01

    Proteins are capable of tolerating mutations at many positions while still maintaining fold and function. Previous studies have failed to consider how tolerance to random mutagenesis might depend on the strength of selective pressure. To examine this, we measured the fitness of every single point mutation of TEM-1 beta-lactamase across a range of ampicillin concentrations utilizing a novel application of deep-sequencing. We found that the relative mutational robustness between positions varied considerably with respect to ampicillin concentration: at a low ampicillin concentration only a few positions are intolerant of mutations, while at a higher ampicillin concentration many additional positions are as equally intolerant of mutations. Using an analytic method termed statistical coupling analysis (SCA) to measure the co-variation between all positions in a sequence alignment of beta-lactamases revealed sectors of co-evolving positions associated with groups of residues having increased sensitivity to mutagenesis at either low or high ampicillin concentrations. Our findings suggest that nature has ``designed'' proteins to be robust to random mutagenesis by loading the constraints for fitness on discrete networks of co-evolving positions depending on the strength of selective pressure.

  6. Control of Messenger RNA Fate by RNA-Binding Proteins: An Emphasis on Mammalian Spermatogenesis

    PubMed Central

    IDLER, R. KEEGAN; YAN, WEI

    2017-01-01

    Posttranscriptional status of messenger RNAs (mRNA) can be affected by many factors, most of which are RNA-binding proteins (RBP) that either bind mRNA in a nonspecific manner or through specific motifs, usually located in the 39 untranslated regions. RBPs can also be recruited by small noncoding RNAs (sncRNA), which have been shown to be involved in posttranscriptional regulations and transposon repression (eg, microRNAs or P-element–induced wimpy testis–interacting RNA) as components of the sncRNA effector complex. Non–sncRNA-binding RBPs have much more diverse effects on their target mRNAs. Some can cause degradation of their target transcripts and/or repression of translation, whereas others can stabilize and/or activate translation. The splicing and exportation of transcripts from the nucleus to the cytoplasm are often mediated by sequence-specific RBPs. The mechanisms by which RBPs regulate mRNA transcripts involve manipulating the 39 poly(A) tail, targeting the transcript to polysomes or to other ribonuclear protein particles, recruiting regulatory proteins, or competing with other RBPs. Here, we briefly review the known mechanisms of posttranscriptional regulation mediated by RBPs, with an emphasis on how these mechanisms might control spermatogenesis in general. PMID:21757510

  7. Tumour Cell Heterogeneity

    PubMed Central

    Gay, Laura; Baker, Ann-Marie; Graham, Trevor A.

    2016-01-01

    The population of cells that make up a cancer are manifestly heterogeneous at the genetic, epigenetic, and phenotypic levels. In this mini-review, we summarise the extent of intra-tumour heterogeneity (ITH) across human malignancies, review the mechanisms that are responsible for generating and maintaining ITH, and discuss the ramifications and opportunities that ITH presents for cancer prognostication and treatment. PMID:26973786

  8. The proximal region of the 3'-untranslated region of cyclooxygenase-2 is recognized by a multimeric protein complex containing HuR, TIA-1, TIAR, and the heterogeneous nuclear ribonucleoprotein U.

    PubMed

    Cok, Steven J; Acton, Stephen J; Morrison, Aubrey R

    2003-09-19

    Cyclooxygenase-2 (COX-2) is an early response gene induced in renal mesangial cells by interleukin-1beta (IL-1beta). The 3'-untranslated region (3'-UTR) of COX-2 mRNA plays an important role in IL-1beta induction by regulating message stability and translational efficiency. The first 60 nucleotides of the 3'-UTR of COX-2 are highly conserved and contain multiple copies of the regulatory sequence AUUUA. Introduction of the 60-nucleotide sequence into the 3'-UTR of a heterologous reporter gene resulted in a 70% decrease in reporter gene expression. Electrophoretic mobility shift assays (EMSAs) demonstrated that mesangial cell nuclear fractions contain a multimeric protein complex that bound this region of COX-2 mRNA in a sequence-specific manner. We identified four members of the protein-RNA complex as HuR, TIA-1, TIAR, and the heterogeneous nuclear ribonucleoprotein U (hnRNP U). Treatment of mesangial cells with IL-1beta caused an increase in cytosolic HuR, which was accompanied by an increase in COX-2 mRNA that co-immunoprecipitated with cytosolic HuR. Therefore, we propose that HuR binds to the proximal region of the 3'-UTR of COX-2 following stimulation by IL-1beta and increases the expression of COX-2 mRNA by facilitating its transport out of the nucleus.

  9. Heterogeneity of mast cells and expression of Annexin A1 protein in a second degree burn model with silver sulfadiazine treatment

    PubMed Central

    Souza, Helena Ribeiro; de Azevedo, Lucas Ribeiro; Possebon, Lucas; Costa, Sara de Souza; Iyomasa-Pilon, Melina Mizusaki; Oliani, Sonia Maria; Girol, Ana Paula

    2017-01-01

    Mast cells (MCs) participate in all stages of skin healing and one of their mediators is the Annexin A1 protein (AnxA1), linked to inflammation, proliferation, migration and apoptosis processes, but not studied in thermal burns yet. Therefore, our objectives were to evaluate the behavior of MCs and AnxA1 in a second degree burn model, treated or not with silver sulfadiazine 1% (SDP 1%) and associated to macrophages quantification and cytokines dosages. MCs counts showed few cells in the early stages of repair but increased MCs in the final phases in the untreated group. The normal skin presented numerous tryptase-positive MCs that were reduced after burning in all analyzed periods. Differently, few chymase-positive MCs were observed in the early stages of healing, however, increased chymase-positive MCs were found at the final phase in the untreated group. MCs also showed high immunoreactivity for AnxA1 on day 3 in both groups. In the tissue there was a strong protein expression in the early stages of healing, but in the final phases only in the SDP treated animals. TNF-α, IL-1β, IL-6, IL-10 and MCP-1 levels and macrophages quantification were increased in inflammation and reepithelialization phases. Reduced IL-1β, IL-6 and IL-10 levels and numerous macrophages occurred in the treated animals during tissue repair. Our results indicate modulation in the profile of MCs and AnxA1expression during healing by the treatment with SDP 1%, pointing them as targets for therapeutic interventions on skin burns. PMID:28278234

  10. Epitope mapping with synthetic peptides of 52-kD SSA/Ro protein reveals heterogeneous antibody profiles in human autoimmune sera.

    PubMed Central

    Ricchiuti, V; Briand, J P; Meyer, O; Isenberg, D A; Pruijn, G; Muller, S

    1994-01-01

    The reactivity of autoantibodies present in the sera of 489 patients with Sjögren's syndrome (SS), systemic lupus erythematosus (SLE) and other autoimmune diseases was investigated by ELISA using recombinant 52-kD SSA/Ro protein (rRo52) and 39 overlapping synthetic peptides representing the entire sequence of Ro52. We report that IgG antibodies reacting with rRo52 were present in the sera of a large number of patients with SS (67% of patients with primary SS and 46% of patients with SS associated with SLE), whereas they were less frequent (10-25%) in SLE, rheumatoid arthritis (RA), juvenile chronic arthritis (JCA) and mixed connective tissue disease (MCTD), and absent in scleroderma. Among the 39 peptides tested, five were recognized by sera from 30-65% of patients with SS, namely peptides representing residues 2-11, 107-122, 107-126, 277-292 and 365-382. Patients with JCA had raised levels of IgG antibodies reacting with peptides 2-11 and 365-382, and 51% of patients with MCTD had raised levels of IgG antibodies reacting with peptide 365-382. None of the five peptides was recognized by more than 20% of sera from patients with SLE and RA. Interestingly, and of importance in the field of diagnostic tests based on peptides, the reactivity of antibodies to the Ro52 synthetic peptides varied greatly according to the origin of sera. Inhibition experiments using either patients' sera or antibodies induced in rabbits against Ro52 peptides showed that the four domains 2-11, 107-122, 277-292 and 365-382 are accessible on the surface of the Ro52 protein. These regions may thus be involved in the induction of specific antibodies in autoimmune patients. Images Fig. 5 PMID:7511075

  11. A heterogeneous tag-attachment to the homodimeric type 1 photosynthetic reaction center core protein in the green sulfur bacterium Chlorobaculum tepidum.

    PubMed

    Azai, Chihiro; Kim, Kwang; Kondo, Toru; Harada, Jiro; Itoh, Shigeru; Oh-oka, Hirozo

    2011-07-01

    The 6xHis-tag-pscA gene, which was genetically engineered to express N-terminally histidine (His)-tagged PscA, was inserted into a coding region of the recA gene in the green sulfur bacterium Chlorobaculum tepidum (C. tepidum). Although the inactivation of the recA gene strongly suppressed a homologous recombination in C. tepidum genomic DNA, the mutant grew well under normal photosynthetic conditions. The His-tagged reaction center (RC) complex could be obtained simply by Ni(2+)-affinity chromatography after detergent solubilization of chlorosome-containing membranes. The complex consisted of three subunits, PscA, PscB, and PscC, in addition to the Fenna-Matthews-Olson protein, but there was no PscD. Low-temperature EPR spectroscopic studies in combination with transient absorption measurements indicated that the complex contained all intrinsic electron transfer cofactors as detected in the wild-type strain. Furthermore, the LC/MS/MS analysis revealed that the core protein consisted of a mixture of a His-/His-tagged PscA homodimer and a non-/His-tagged PscA heterodimer. The development of the pscA gene duplication method presented here, thus, enables not only a quick and large-scale preparation of the RC complex from C. tepidum but also site-directed mutagenesis experiments on the artificially incorporated 6xHis-tag-pscA gene itself, since the expression of the authentic PscA/PscA homodimeric RC complex could complement any defect in mutated His-tagged PscA. This method would provide an invaluable tool for structural and functional analyses of the homodimeric type 1 RC complex.

  12. Heterogeneous Atmospheric Chemistry

    NASA Astrophysics Data System (ADS)

    Schryer, David R.

    In the past few years it has become increasingly clear that heterogeneous, or multiphase, processes play an important role in the atmosphere. Unfortunately the literature on the subject, although now fairly extensive, is still rather dispersed. Furthermore, much of the expertise regarding heterogeneous processes lies in fields not directly related to atmospheric science. Therefore, it seemed desirable to bring together for an exchange of ideas, information, and methodologies the various atmospheric scientists who are actively studying heterogeneous processes as well as other researchers studying similar processes in the context of other fields.

  13. Cellular heterogeneity during embryonic stem cell differentiation to epiblast stem cells is revealed by the ShcD/RaLP adaptor protein.

    PubMed

    Turco, Margherita Y; Furia, Laura; Dietze, Anja; Fernandez Diaz, Luis; Ronzoni, Simona; Sciullo, Anna; Simeone, Antonio; Constam, Daniel; Faretta, Mario; Lanfrancone, Luisa

    2012-11-01

    The Shc family of adaptor proteins are crucial mediators of a plethora of receptors such as the tyrosine kinase receptors, cytokine receptors, and integrins that drive signaling pathways governing proliferation, differentiation, and migration. Here, we report the role of the newly identified family member, ShcD/RaLP, whose expression in vitro and in vivo suggests a function in embryonic stem cell (ESC) to epiblast stem cells (EpiSCs) transition. The transition from the naïve (ESC) to the primed (EpiSC) pluripotent state is the initial important step for ESCs to commit to differentiation and the mechanisms underlying this process are still largely unknown. Using a novel approach to simultaneously assess pluripotency, apoptosis, and proliferation by multiparameter flow cytometry, we show that ESC to EpiSC transition is a process involving a tight coordination between the modulation of the Oct4 expression, cell cycle progression, and cell death. We also describe, by high-content immunofluorescence analysis and time-lapse microscopy, the emergence of cells expressing caudal-related homeobox 2 (Cdx2) transcription factor during ESC to EpiSC transition. The use of the ShcD knockout ESCs allowed the unmasking of this process as they presented deregulated Oct4 modulation and an enrichment in Oct4-negative Cdx2-positive cells with increased MAPK/extracellular-regulated kinases 1/2 activation, within the differentiating population. Collectively, our data reveal ShcD as an important modulator in the switch of key pathway(s) involved in determining EpiSC identity. Copyright © 2012 AlphaMed Press.

  14. Heterogeneous atmospheric chemistry

    NASA Technical Reports Server (NTRS)

    Schryer, D. R.

    1982-01-01

    The present conference on heterogeneous atmospheric chemistry considers such topics concerning clusters, particles and microparticles as common problems in nucleation and growth, chemical kinetics, and catalysis, chemical reactions with aerosols, electron beam studies of natural and anthropogenic microparticles, and structural studies employing molecular beam techniques, as well as such gas-solid interaction topics as photoassisted reactions, catalyzed photolysis, and heterogeneous catalysis. Also discussed are sulfur dioxide absorption, oxidation, and oxidation inhibition in falling drops, sulfur dioxide/water equilibria, the evidence for heterogeneous catalysis in the atmosphere, the importance of heterogeneous processes to tropospheric chemistry, soot-catalyzed atmospheric reactions, and the concentrations and mechanisms of formation of sulfate in the atmospheric boundary layer.

  15. Stability of Heterogeneous Ecosystem

    NASA Astrophysics Data System (ADS)

    Liu, Yang-Yu; Yan, Gang; Barabasi, Alber-Laszlo

    2014-03-01

    Stability of ecosystem measures the tendency of a community to return to equilibrium after environmental perturbation, which is severely constrained by the underlying network structure. Despite significant advances in uncovering the relationship between stability and network structure, little attention has been paid to the impact of the degree heterogeneity that exists in real ecosystems. Here we show that for networks with mixed interactions of competition and mutualism the degree heterogeneity always destabilizes the ecosystem. Surprisingly, for predator-prey interactions (e.g., food webs) high heterogeneity is destabilizing yet moderate heterogeneity is stabilizing. These findings deepen our understanding of the stability of real ecosystems and may also have implications in studying the stability of more general complex dynamical systems.

  16. Heterogeneous atmospheric chemistry

    NASA Technical Reports Server (NTRS)

    Schryer, D. R.

    1982-01-01

    The present conference on heterogeneous atmospheric chemistry considers such topics concerning clusters, particles and microparticles as common problems in nucleation and growth, chemical kinetics, and catalysis, chemical reactions with aerosols, electron beam studies of natural and anthropogenic microparticles, and structural studies employing molecular beam techniques, as well as such gas-solid interaction topics as photoassisted reactions, catalyzed photolysis, and heterogeneous catalysis. Also discussed are sulfur dioxide absorption, oxidation, and oxidation inhibition in falling drops, sulfur dioxide/water equilibria, the evidence for heterogeneous catalysis in the atmosphere, the importance of heterogeneous processes to tropospheric chemistry, soot-catalyzed atmospheric reactions, and the concentrations and mechanisms of formation of sulfate in the atmospheric boundary layer.

  17. Towards heterogeneous distributed debugging

    SciTech Connect

    Damodaran-Kamal, S.K.

    1995-04-01

    Several years of research and development in parallel debugger design have given up several techniques, though implemented in a wide range of tools for an equally wide range of systems. This paper is an evaluation of these myriad techniques as applied to the design of a heterogeneous distributed debugger. The evaluation is based on what features users perceive as useful, as well as the ease of implementation of the features using the available technology. A preliminary architecture for such a heterogeneous tool is proposed. Our effort in this paper is significantly different from the other efforts at creating portable and heterogeneous distributed debuggers in that we concentrate on support for all the important issues in parallel debugging, instead of simply concentrating on portability and heterogeneity.

  18. Heterogeneous basic catalysis

    SciTech Connect

    Hattori, Hideshi

    1995-05-01

    Heterogeneous acid catalysis attracted much attention primarily because heterogeneous acidic catalysts act as catalysts in petroleum refinery and are known as a main catalyst in the cracking process which is the largest process among the industrial chemical processes. In contrast to these extensive studies of heterogeneous acidic catalysts, fewer efforts have been given to the study of heterogeneous basic catalysts. The types of heterogeneous basic catalysts are listed in Table 1. Except for non-oxide catalysts, the basic sites are believed to be surface O atoms. The studies of heterogeneous catalysis have been continuous and progressed steadily. They have never been reviewed in the chemical Reviews before. It is more useful and informative to describe the studies of heterogeneous basic catalysis performed for a long period. In the present article, therefore, the cited papers are not restricted to those published recently, but include those published for the last 25 years. The paper first describes the generation of basic sites before describing methods used in the characterization of basic surfaces. These are indicator methods, temperature programmed desorption (TPD) of CO{sub 2}, UV absorption and luminescence spectroscopies, TPD of H{sub 2}, XPS, IR of CO{sub 2}, IR of pyrrole, and oxygen exchange between CO{sub 2} and the surface. The paper then discusses studies on the catalysis by heterogeneous basic catalysts. Some of these reactions are dehydration, dehydrogenation, hydrogenation, amination, alkylation, ring transformation, and reactions of organosilanes. Catalysts discussed are single component metal oxides, zeolites, non-oxide types, and superbasic catalysts. 141 refs.

  19. Characterization of Paper Heterogeneity

    NASA Astrophysics Data System (ADS)

    Considine, John M.

    Paper and paperboard are the most widely-used green materials in the world because they are renewable, recyclable, reusable, and compostable. Continued and expanded use of these materials and their potential use in new products requires a comprehensive understanding of the variability of their mechanical properties. This work develops new methods to characterize the mechanical properties of heterogeneous materials through a combination of techniques in experimental mechanics, materials science and numerical analysis. Current methods to analyze heterogeneous materials focus on crystalline materials or polymer-crystalline composites, where material boundaries are usually distinct. This work creates a methodology to analyze small, continuously-varying stiffness gradients in 100% polymer systems and is especially relevant to paper materials where factors influencing heterogeneity include local mass, fiber orientation, individual pulp fiber properties, local density, and drying restraint. A unique approach was used to understand the effect of heterogeneity on paper tensile strength. Additional variation was intentionally introduced, in the form of different size holes, and their effect on strength was measured. By modifying two strength criteria, an estimate of strength in the absence of heterogeneity was determined. In order to characterize stiffness heterogeneity, a novel load fixture was developed to excite full-field normal and shear strains for anisotropic stiffness determination. Surface strains were measured with digital image correlation and were analyzed with the VFM (Virtual Fields Method). This approach led to VFM-identified stiffnesses that were similar to values determined by conventional tests. The load fixture and VFM analyses were used to measure local stiffness and local stiffness variation on heterogeneous anisotropic materials. The approach was validated on simulated heterogeneous materials and was applied experimentally to three different paperboards

  20. Heterogeneity in hand veins responses to acetylcholine is not associated with polymorphisms in the G-protein beta3-subunit (C825T) and endothelial nitric oxide synthase (G894T) genes but with serum low density lipoprotein cholesterol.

    PubMed

    Grossmann, M; Dobrev, D; Siffert, W; Kirch, W

    2001-06-01

    Vascular responses to acetylcholine (ACh) are notoriously variable, the reason for this phenomenon is unknown. We tested the hypothesis that the variability in venous response to acetylcholine may be associated with two recently identified genetic polymorphisms for proteins involved in the signal transduction pathway, i.e. the G-protein beta3-subunit (GNB3) and endothelial nitric oxide synthase (eNOS). The dorsal hand vein technique was used in 37 healthy subjects. Hand veins were preconstricted with the alpha1-adrenoceptor agonist phenylephrine and the venodilator response to local ACh infusion was measured with and without comedication of acetylsalicylic acid or co-infusion of N(G)-monomethyl-L-arginine (L-NMMA). In addition, all subjects received routine laboratory tests and 26 of them were genotyped for the C825T polymorphism of the GNB3 gene and for the G894T polymorphism of the eNOS gene. A striking variability in venous response to ACh was found with dilation observed in the low ACh concentration range and reduced dilation or even constriction at high concentrations. ACh-induced venodilation was mediated by muscarinic receptors and abolished in the presence of both acetylsalicylic acid and L-NMMA suggesting dependence on endothelium. We did not find any association of the variability in ACh response with GNB3 or eNOS allele status. On the other hand, a significant positive correlation between ACh responsiveness and low density lipoprotein-cholesterol status was detected. Two recently discovered gene polymorphisms are not responsible for the profound heterogeneity in venodilator response to ACh. Surprisingly, this variability appears to relate to the lipid status of the subjects. The exact nature of this new finding requires further study.

  1. Proteins.

    ERIC Educational Resources Information Center

    Doolittle, Russell F.

    1985-01-01

    Examines proteins which give rise to structure and, by virtue of selective binding to other molecules, make genes. Binding sites, amino acids, protein evolution, and molecular paleontology are discussed. Work with encoding segments of deoxyribonucleic acid (exons) and noncoding stretches (introns) provides new information for hypotheses. (DH)

  2. Proteins.

    ERIC Educational Resources Information Center

    Doolittle, Russell F.

    1985-01-01

    Examines proteins which give rise to structure and, by virtue of selective binding to other molecules, make genes. Binding sites, amino acids, protein evolution, and molecular paleontology are discussed. Work with encoding segments of deoxyribonucleic acid (exons) and noncoding stretches (introns) provides new information for hypotheses. (DH)

  3. Protein

    USDA-ARS?s Scientific Manuscript database

    Proteins are the major structural and functional components of all cells in the body. They are macromolecules that comprise 1 or more chains of amino acids that vary in their sequence and length and are folded into specific 3-dimensional structures. The sizes and conformations of proteins, therefor...

  4. Heterogeneity in breast cancer.

    PubMed

    Polyak, Kornelia

    2011-10-01

    Breast cancer is a heterogeneous disease. There is a high degree of diversity between and within tumors as well as among cancer-bearing individuals, and all of these factors together determine the risk of disease progression and therapeutic resistance. Advances in technologies such as whole-genome sequencing and functional viability screens now allow us to analyze tumors at unprecedented depths. However, translating this increasing knowledge into clinical practice remains a challenge in part due to tumor evolution driven by the diversity of cancer cell populations and their microenvironment. The articles in this Review series discuss recent advances in our understanding of breast tumor heterogeneity, therapies tailored based on this knowledge, and future ways of assessing and treating heterogeneous tumors.

  5. Monocyte and macrophage heterogeneity.

    PubMed

    Gordon, Siamon; Taylor, Philip R

    2005-12-01

    Heterogeneity of the macrophage lineage has long been recognized and, in part, is a result of the specialization of tissue macrophages in particular microenvironments. Circulating monocytes give rise to mature macrophages and are also heterogeneous themselves, although the physiological relevance of this is not completely understood. However, as we discuss here, recent studies have shown that monocyte heterogeneity is conserved in humans and mice, allowing dissection of its functional relevance: the different monocyte subsets seem to reflect developmental stages with distinct physiological roles, such as recruitment to inflammatory lesions or entry to normal tissues. These advances in our understanding have implications for the development of therapeutic strategies that are targeted to modify particular subpopulations of monocytes.

  6. Spatial heterogeneity in medulloblastoma.

    PubMed

    Morrissy, A Sorana; Cavalli, Florence M G; Remke, Marc; Ramaswamy, Vijay; Shih, David J H; Holgado, Borja L; Farooq, Hamza; Donovan, Laura K; Garzia, Livia; Agnihotri, Sameer; Kiehna, Erin N; Mercier, Eloi; Mayoh, Chelsea; Papillon-Cavanagh, Simon; Nikbakht, Hamid; Gayden, Tenzin; Torchia, Jonathon; Picard, Daniel; Merino, Diana M; Vladoiu, Maria; Luu, Betty; Wu, Xiaochong; Daniels, Craig; Horswell, Stuart; Thompson, Yuan Yao; Hovestadt, Volker; Northcott, Paul A; Jones, David T W; Peacock, John; Wang, Xin; Mack, Stephen C; Reimand, Jüri; Albrecht, Steffen; Fontebasso, Adam M; Thiessen, Nina; Li, Yisu; Schein, Jacqueline E; Lee, Darlene; Carlsen, Rebecca; Mayo, Michael; Tse, Kane; Tam, Angela; Dhalla, Noreen; Ally, Adrian; Chuah, Eric; Cheng, Young; Plettner, Patrick; Li, Haiyan I; Corbett, Richard D; Wong, Tina; Long, William; Loukides, James; Buczkowicz, Pawel; Hawkins, Cynthia E; Tabori, Uri; Rood, Brian R; Myseros, John S; Packer, Roger J; Korshunov, Andrey; Lichter, Peter; Kool, Marcel; Pfister, Stefan M; Schüller, Ulrich; Dirks, Peter; Huang, Annie; Bouffet, Eric; Rutka, James T; Bader, Gary D; Swanton, Charles; Ma, Yusanne; Moore, Richard A; Mungall, Andrew J; Majewski, Jacek; Jones, Steven J M; Das, Sunit; Malkin, David; Jabado, Nada; Marra, Marco A; Taylor, Michael D

    2017-04-10

    Spatial heterogeneity of transcriptional and genetic markers between physically isolated biopsies of a single tumor poses major barriers to the identification of biomarkers and the development of targeted therapies that will be effective against the entire tumor. We analyzed the spatial heterogeneity of multiregional biopsies from 35 patients, using a combination of transcriptomic and genomic profiles. Medulloblastomas (MBs), but not high-grade gliomas (HGGs), demonstrated spatially homogeneous transcriptomes, which allowed for accurate subgrouping of tumors from a single biopsy. Conversely, somatic mutations that affect genes suitable for targeted therapeutics demonstrated high levels of spatial heterogeneity in MB, malignant glioma, and renal cell carcinoma (RCC). Actionable targets found in a single MB biopsy were seldom clonal across the entire tumor, which brings the efficacy of monotherapies against a single target into question. Clinical trials of targeted therapies for MB should first ensure the spatially ubiquitous nature of the target mutation.

  7. Protein

    MedlinePlus

    ... Search for: Harvard T.H. Chan School of Public Health Email People Departments Calendar Careers Give my.harvard ... Nutrition Source Harvard T.H. Chan School of Public Health > The Nutrition Source > What Should I Eat? > Protein ...

  8. Cancer heterogeneity and imaging.

    PubMed

    O'Connor, James P B

    2016-10-04

    There is interest in identifying and quantifying tumor heterogeneity at the genomic, tissue pathology and clinical imaging scales, as this may help better understand tumor biology and may yield useful biomarkers for guiding therapy-based decision making. This review focuses on the role and value of using x-ray, CT, MRI and PET based imaging methods that identify, measure and map tumor heterogeneity. In particular we highlight the potential value of these techniques and the key challenges required to validate and qualify these biomarkers for clinical use.

  9. Why does heterogeneity matter?

    Treesearch

    K.B. Pierce

    2007-01-01

    This is a review of the book "Ecosystem function in heterogeneous landscapes" published in 2005. The authors are G. Lovett, C. Jones, M.G. Turner, and K.C. Weathers. It was published by Springer, New York. The book is a synthesis of the 10th Gary conference held at the Institute of Ecosystem Studies in Millbrook, New York, in 2003.

  10. Heterogeneous waste processing

    DOEpatents

    Vanderberg, Laura A.; Sauer, Nancy N.; Brainard, James R.; Foreman, Trudi M.; Hanners, John L.

    2000-01-01

    A combination of treatment methods are provided for treatment of heterogeneous waste including: (1) treatment for any organic compounds present; (2) removal of metals from the waste; and, (3) bulk volume reduction, with at least two of the three treatment methods employed and all three treatment methods emplyed where suitable.

  11. Heterogeneous Uncertainty Management

    DTIC Science & Technology

    2008-03-08

    probabilistic ( HTP ) agents, the concept of probabilistic version of XML and RDF, and probabilistic methods to reason about collections of moving objects. S...heterogeneous temporal probabilistic ( HTP ) agents, the concept of probabilistic version of XML and RDF, and probabilistic methods to reason about...temporal probabilistic ( HTP ) agent. HTP agents can build temporal probabilistic reasoning capabilities on top of multiple databases and software

  12. Phosphorylation of the C proteins in heterogeneous ribonucleoprotein (hnRNP) particles in HeLa cells: Characterization of in vivo phosphorylation, comparison with in vitro phosphorylation using casein kinase II, and preliminary studies on the effects of phosphorylation on particle structure

    SciTech Connect

    Kleiman, N.J.

    1989-01-01

    Newly formed pre-messenger RNA associates with protein to form heterogeneous ribonucleoprotein (hnRNP) particles. In HeLa cells, hnRNP particles contain six core proteins. Two proteins, termed C{sub 1} and C{sub 2}, are phosphorylated in vitro by casein kinase 11 (CKII). C{sub 1} protein became {sup 32}P-labeled after HeLa cells were incubated with ({sup 32}P)-orthophosphate in vivo (ibid). Because phosphorylation is a ubiquitous regulatory mechanism, C protein phosphorylation was studied in greater detail. C protein phosphorylation in hnRNP particles was investigated in HeLa cells incubated with ({sup 32}P)-orthophosphate in vivo. Immunoblotting in pH 3.5-10 isoelectric focusing (IEF) gels indicated that C proteins focus only at pH 5.0. In pH 4.5-5.5 IEF gels, individually purified C, and 2 proteins resolve into the same four closely spaced, {sup 32}P-labeled bands. A fifth, unlabeled, more basic species was detached when hnRNP particles were purified without NaF. All {sup 32}P-labeled species contained identical amounts of {sup 32}P per unit protein suggesting that charge heterogeneity is not due to differential phosphorylation. Attempts to detect bound carbohydrate were unsuccessful. {sup 32}P-labeled phosphate was readily removed by potato acid phosphatase. E. coli alkaline phosphatase and snake venom phosphodiesterase were ineffective. {sup 32}P-label was found exclusively in phosphoserine. One-dimensional peptide mapping with chymotrypsin and S. aureus protease detected two phosphorylated peptides. C protein phosphorylation was also investigated in vitro. Incubation of hnRNP particles with rabbit liver CKII and {sup 32}P-ATP followed by IEF in pH 4.5-5.5 gels indicated that all four C protein species were {sup 32}P-labeled. {sup 32}P-label was found exclusively in phosphoserine.

  13. Scales of mantle heterogeneity

    NASA Astrophysics Data System (ADS)

    Moore, J. C.; Akber-Knutson, S.; Konter, J.; Kellogg, J.; Hart, S.; Kellogg, L. H.; Romanowicz, B.

    2004-12-01

    A long-standing question in mantle dynamics concerns the scale of heterogeneity in the mantle. Mantle convection tends to both destroy (through stirring) and create (through melt extraction and subduction) heterogeneity in bulk and trace element composition. Over time, these competing processes create variations in geochemical composition along mid-oceanic ridges and among oceanic islands, spanning a range of scales from extremely long wavelength (for example, the DUPAL anomaly) to very small scale (for example, variations amongst melt inclusions). While geochemical data and seismic observations can be used to constrain the length scales of mantle heterogeneity, dynamical mixing calculations can illustrate the processes and timescales involved in stirring and mixing. At the Summer 2004 CIDER workshop on Relating Geochemical and Seismological Heterogeneity in the Earth's Mantle, an interdisciplinary group evaluated scales of heterogeneity in the Earth's mantle using a combined analysis of geochemical data, seismological data and results of numerical models of mixing. We mined the PetDB database for isotopic data from glass and whole rock analyses for the Mid-Atlantic Ridge (MAR) and the East Pacific Rise (EPR), projecting them along the ridge length. We examined Sr isotope variability along the East Pacific rise by looking at the difference in Sr ratio between adjacent samples as a function of distance between the samples. The East Pacific Rise exhibits an overall bowl shape of normal MORB characteristics, with higher values in the higher latitudes (there is, however, an unfortunate gap in sampling, roughly 2000 km long). These background characteristics are punctuated with spikes in values at various locations, some, but not all of which are associated with off-axis volcanism. A Lomb-Scargle periodogram for unevenly spaced data was utilized to construct a power spectrum of the scale lengths of heterogeneity along both ridges. Using the same isotopic systems (Sr, Nd

  14. Heterogeneous Antibody Responses in Tuberculosis

    PubMed Central

    Lyashchenko, Konstantin; Colangeli, Roberto; Houde, Michel; Al Jahdali, Hamdan; Menzies, Dick; Gennaro, Maria Laura

    1998-01-01

    Antibody responses during tuberculosis were analyzed by an enzyme-linked immunosorbent assay with a panel of 10 protein antigens of Mycobacterium tuberculosis. It was shown that serum immunoglobulin G antibodies were produced against a variety of M. tuberculosis antigens and that the vast majority of sera from tuberculosis patients contained antibodies against one or more M. tuberculosis antigens. The number and the species of serologically reactive antigens varied greatly from individual to individual. In a given serum, the level of specific antibodies also varied with the antigen irrespective of the total number of antigens recognized by that particular serum. These findings indicate that person-to-person heterogeneity of antigen recognition, rather than recognition of particular antigens, is a key attribute of the antibody response in tuberculosis. PMID:9673283

  15. Heterogeneity in Desiccated Solutions: Implications for Biostabilization

    PubMed Central

    Ragoonanan, Vishard; Aksan, Alptekin

    2008-01-01

    Biopreservation processes such as freezing and drying inherently introduce heterogeneity. We focused on exploring the mechanisms responsible for heterogeneity in isothermal, diffusively dried biopreservation solutions that contain a model protein. The biopreservation solutions used contained trehalose (a sugar known for its stabilization effect) and salts (LiCl, NaCl, MgCl2, and CaCl2). Performing Fourier transform infrared spectroscopy analysis on the desiccated droplets, spatial distributions of the components within the dried droplet, as well as their specific interactions, were investigated. It was established that the formation of multiple thermodynamic states was induced by the spatial variations in the cosolute concentration gradients, directly affecting the final structure of the preserved protein. The spatial distribution gradients were formed by two competing flows that formed within the drying droplet: a dominant peripheral flow, induced by contact line pinning, and the Marangoni flow, induced by surface tension gradients. It was found that the changes in cosolute concentrations and drying conditions affected the spatial heterogeneity and stability of the product. It was also found that trehalose and salts had a synergistic stabilizing effect on the protein structure, which originated from destructuring of the vicinal water, which in turn mediated the interactions of trehalose with the protein. This interaction was observed by the change in the glycosidic CO, and the CH stretch vibrations of the trehalose molecule. PMID:18055531

  16. The membrane: transertion as an organizing principle in membrane heterogeneity

    PubMed Central

    Matsumoto, Kouji; Hara, Hiroshi; Fishov, Itzhak; Mileykovskaya, Eugenia; Norris, Vic

    2015-01-01

    The bacterial membrane exhibits a significantly heterogeneous distribution of lipids and proteins. This heterogeneity results mainly from lipid–lipid, protein–protein, and lipid–protein associations which are orchestrated by the coupled transcription, translation and insertion of nascent proteins into and through membrane (transertion). Transertion is central not only to the individual assembly and disassembly of large physically linked groups of macromolecules (alias hyperstructures) but also to the interactions between these hyperstructures. We review here these interactions in the context of the processes in Bacillus subtilis and Escherichia coli of nutrient sensing, membrane synthesis, cytoskeletal dynamics, DNA replication, chromosome segregation, and cell division. PMID:26124753

  17. Heterogeneity of monoclonal antibodies.

    PubMed

    Liu, Hongcheng; Gaza-Bulseco, Georgeen; Faldu, Dinesh; Chumsae, Chris; Sun, Joanne

    2008-07-01

    Heterogeneity of monoclonal antibodies is common due to the various modifications introduced over the lifespan of the molecules from the point of synthesis to the point of complete clearance from the subjects. The vast number of modifications presents great challenge to the thorough characterization of the molecules. This article reviews the current knowledge of enzymatic and nonenzymatic modifications of monoclonal antibodies including the common ones such as incomplete disulfide bond formation, glycosylation, N-terminal pyroglutamine cyclization, C-terminal lysine processing, deamidation, isomerization, and oxidation, and less common ones such as modification of the N-terminal amino acids by maleuric acid and amidation of the C-terminal amino acid. In addition, noncovalent associations with other molecules, conformational diversity and aggregation of monoclonal antibodies are also discussed. Through a complete understanding of the heterogeneity of monoclonal antibodies, strategies can be employed to better identify the potential modifications and thoroughly characterize the molecules.

  18. Heterogeneities in granular dynamics

    PubMed Central

    Mehta, A.; Barker, G. C.; Luck, J. M.

    2008-01-01

    The absence of Brownian motion in granular media is a source of much complexity, including the prevalence of heterogeneity, whether static or dynamic, within a given system. Such strong heterogeneities can exist as a function of depth in a box of grains; this is the system we study here. First, we present results from three-dimensional, cooperative and stochastic Monte Carlo shaking simulations of spheres on heterogeneous density fluctuations. Next, we juxtapose these with results obtained from a theoretical model of a column of grains under gravity; frustration via competing local fields is included in our model, whereas the effect of gravity is to slow down the dynamics of successively deeper layers. The combined conclusions suggest that the dynamics of a real granular column can be divided into different phases—ballistic, logarithmic, activated, and glassy—as a function of depth. The nature of the ground states and their retrieval (under zero-temperature dynamics) is analyzed; the glassy phase shows clear evidence of its intrinsic (“crystalline”) states, which lie below a band of approximately degenerate ground states. In the other three phases, by contrast, the system jams into a state chosen randomly from this upper band of metastable states. PMID:18541918

  19. Tumour Heterogeneity: The Key Advantages of Single-Cell Analysis.

    PubMed

    Tellez-Gabriel, Marta; Ory, Benjamin; Lamoureux, Francois; Heymann, Marie-Francoise; Heymann, Dominique

    2016-12-20

    Tumour heterogeneity refers to the fact that different tumour cells can show distinct morphological and phenotypic profiles, including cellular morphology, gene expression, metabolism, motility, proliferation and metastatic potential. This phenomenon occurs both between tumours (inter-tumour heterogeneity) and within tumours (intra-tumour heterogeneity), and it is caused by genetic and non-genetic factors. The heterogeneity of cancer cells introduces significant challenges in using molecular prognostic markers as well as for classifying patients that might benefit from specific therapies. Thus, research efforts for characterizing heterogeneity would be useful for a better understanding of the causes and progression of disease. It has been suggested that the study of heterogeneity within Circulating Tumour Cells (CTCs) could also reflect the full spectrum of mutations of the disease more accurately than a single biopsy of a primary or metastatic tumour. In previous years, many high throughput methodologies have raised for the study of heterogeneity at different levels (i.e., RNA, DNA, protein and epigenetic events). The aim of the current review is to stress clinical implications of tumour heterogeneity, as well as current available methodologies for their study, paying specific attention to those able to assess heterogeneity at the single cell level.

  20. Tumour Heterogeneity: The Key Advantages of Single-Cell Analysis

    PubMed Central

    Tellez-Gabriel, Marta; Ory, Benjamin; Lamoureux, Francois; Heymann, Marie-Francoise; Heymann, Dominique

    2016-01-01

    Tumour heterogeneity refers to the fact that different tumour cells can show distinct morphological and phenotypic profiles, including cellular morphology, gene expression, metabolism, motility, proliferation and metastatic potential. This phenomenon occurs both between tumours (inter-tumour heterogeneity) and within tumours (intra-tumour heterogeneity), and it is caused by genetic and non-genetic factors. The heterogeneity of cancer cells introduces significant challenges in using molecular prognostic markers as well as for classifying patients that might benefit from specific therapies. Thus, research efforts for characterizing heterogeneity would be useful for a better understanding of the causes and progression of disease. It has been suggested that the study of heterogeneity within Circulating Tumour Cells (CTCs) could also reflect the full spectrum of mutations of the disease more accurately than a single biopsy of a primary or metastatic tumour. In previous years, many high throughput methodologies have raised for the study of heterogeneity at different levels (i.e., RNA, DNA, protein and epigenetic events). The aim of the current review is to stress clinical implications of tumour heterogeneity, as well as current available methodologies for their study, paying specific attention to those able to assess heterogeneity at the single cell level. PMID:27999407

  1. Unravelling mononuclear phagocyte heterogeneity

    PubMed Central

    Geissmann, Frédéric; Gordon, Siamon; Hume, David A.; Mowat, Allan M.; Randolph, Gwendalyn J.

    2011-01-01

    When Ralph Steinman and Zanvil Cohn first described dendritic cells (DCs) in 1973 it took many years to convince the immunology community that these cells were truly distinct from macrophages. Almost four decades later, the DC is regarded as the key initiator of adaptive immune responses; however, distinguishing DCs from macrophages still leads to confusion and debate in the field. Here, Nature Reviews Immunology asks five experts to discuss the issue of heterogeneity in the mononuclear phagocyte system and to give their opinion on the importance of defining these cells for future research. PMID:20467425

  2. Intratumor Heterogeneity in Breast Cancer.

    PubMed

    Beca, Francisco; Polyak, Kornelia

    2016-01-01

    Intratumor heterogeneity is the main obstacle to effective cancer treatment and personalized medicine. Both genetic and epigenetic sources of intratumor heterogeneity are well recognized and several technologies have been developed for their characterization. With the technological advances in recent years, investigators are now elucidating intratumor heterogeneity at the single cell level and in situ. However, translating the accumulated knowledge about intratumor heterogeneity to clinical practice has been slow. We are certain that better understanding of the composition and evolution of tumors during disease progression and treatment will improve cancer diagnosis and the design of therapies. Here we review some of the most important considerations related to intratumor heterogeneity. We discuss both genetic and epigenetic sources of intratumor heterogeneity and review experimental approaches that are commonly used to quantify it. We also discuss the impact of intratumor heterogeneity on cancer diagnosis and treatment and share our perspectives on the future of this field.

  3. Heterogeneity in tuberculosis.

    PubMed

    Cadena, Anthony M; Fortune, Sarah M; Flynn, JoAnne L

    2017-07-24

    Infection with Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), results in a range of clinical presentations in humans. Most infections manifest as a clinically asymptomatic, contained state that is termed latent TB infection (LTBI); a smaller subset of infected individuals present with symptomatic, active TB. Within these two seemingly binary states, there is a spectrum of host outcomes that have varying symptoms, microbiologies, immune responses and pathologies. Recently, it has become apparent that there is diversity of infection even within a single individual. A good understanding of the heterogeneity that is intrinsic to TB - at both the population level and the individual level - is crucial to inform the development of intervention strategies that account for and target the unique, complex and independent nature of the local host-pathogen interactions that occur in this infection. In this Review, we draw on model systems and human data to discuss multiple facets of TB biology and their relationship to the overall heterogeneity observed in the human disease.

  4. Heterogeneity of reactive astrocytes

    PubMed Central

    Anderson, Mark A.; Ao, Yan; Sofroniew, Michael V.

    2014-01-01

    Astrocytes respond to injury and disease in the central nervous system (CNS) with a process referred to as reactive astrogliosis. Recent progress demonstrates that reactive astrogliosis is not a simple all-or-none phenomenon, but is a finely gradated continuum of changes that range from reversible alterations in gene expression and cell hypertrophy, to scar formation with permanent tissue rearrangement. There is now compelling evidence that reactive astrocytes exhibit a substantial potential for heterogeneity at multiple levels, including gene expression, cell morphology, topography (distance from lesions), CNS regions, local (among neighboring cells), cell signaling and cell function. Structural and functional changes are regulated in reactive astrocytes by many different potential signaling events that occur in a context dependent manner. It is noteworthy that different stimuli of astrocyte reactivity can lead to similar degrees of GFAP upregulation while causing substantially different changes in transcriptome profiles and cell function. Thus, it is not possible to equate simple and uniform measures such as cell hypertrophy and upregulation of GFAP expression with a single, uniform concept of astrocyte reactivity. Instead, it is necessary to recognize the considerable potential for heterogeneity and determine the functional implications of astrocyte reactivity in a context specific manner as regulated by specific signaling events. PMID:24361547

  5. Heterogeneous photonic integrated circuits

    NASA Astrophysics Data System (ADS)

    Fang, Alexander W.; Fish, Gregory; Hall, Eric

    2012-01-01

    Photonic Integrated Circuits (PICs) have been dichotomized into circuits with high passive content (silica and silicon PLCs) and high active content (InP tunable lasers and transceivers) due to the trade-off in material characteristics used within these two classes. This has led to restrictions in the adoption of PICs to systems in which only one of the two classes of circuits are required to be made on a singular chip. Much work has been done to create convergence in these two classes by either engineering the materials to achieve the functionality of both device types on a single platform, or in epitaxial growth techniques to transfer one material to the next, but have yet to demonstrate performance equal to that of components fabricated in their native substrates. Advances in waferbonding techniques have led to a new class of heterogeneously integrated photonic circuits that allow for the concurrent use of active and passive materials within a photonic circuit, realizing components on a transferred substrate that have equivalent performance as their native substrate. In this talk, we review and compare advances made in heterogeneous integration along with demonstrations of components and circuits enabled by this technology.

  6. Membrane adhesion and the formation of heterogeneities: biology, biophysics, and biotechnology

    PubMed Central

    Gordon, V. D.; O’Halloran, T.J.; Shindell, O.

    2015-01-01

    Membrane adhesion is essential to many vital biological processes. Sites of membrane adhesion are often associated with heterogeneities in the lipid and protein composition of the membrane. These heterogeneities are thought to play functional roles by facilitating interactions between proteins. However, the causal links between membrane adhesion and membrane heterogeneities are not known. Here we survey the state of the field and indicate what we think are understudied areas ripe for development. PMID:25866854

  7. Disordered hyperuniform heterogeneous materials.

    PubMed

    Torquato, Salvatore

    2016-10-19

    Disordered hyperuniform many-body systems are distinguishable states of matter that lie between a crystal and liquid: they are like perfect crystals in the way they suppress large-scale density fluctuations and yet are like liquids or glasses in that they are statistically isotropic with no Bragg peaks. These systems play a vital role in a number of fundamental and applied problems: glass formation, jamming, rigidity, photonic and electronic band structure, localization of waves and excitations, self-organization, fluid dynamics, quantum systems, and pure mathematics. Much of what we know theoretically about disordered hyperuniform states of matter involves many-particle systems. In this paper, we derive new rigorous criteria that disordered hyperuniform two-phase heterogeneous materials must obey and explore their consequences. Two-phase heterogeneous media are ubiquitous; examples include composites and porous media, biological media, foams, polymer blends, granular media, cellular solids, and colloids. We begin by obtaining some results that apply to hyperuniform two-phase media in which one phase is a sphere packing in d-dimensional Euclidean space [Formula: see text]. Among other results, we rigorously establish the requirements for packings of spheres of different sizes to be 'multihyperuniform'. We then consider hyperuniformity for general two-phase media in [Formula: see text]. Here we apply realizability conditions for an autocovariance function and its associated spectral density of a two-phase medium, and then incorporate hyperuniformity as a constraint in order to derive new conditions. We show that some functional forms can immediately be eliminated from consideration and identify other forms that are allowable. Specific examples and counterexamples are described. Contact is made with well-known microstructural models (e.g. overlapping spheres and checkerboards) as well as irregular phase-separation and Turing-type patterns. We also ascertain a family

  8. Disordered hyperuniform heterogeneous materials

    NASA Astrophysics Data System (ADS)

    Torquato, Salvatore

    2016-10-01

    Disordered hyperuniform many-body systems are distinguishable states of matter that lie between a crystal and liquid: they are like perfect crystals in the way they suppress large-scale density fluctuations and yet are like liquids or glasses in that they are statistically isotropic with no Bragg peaks. These systems play a vital role in a number of fundamental and applied problems: glass formation, jamming, rigidity, photonic and electronic band structure, localization of waves and excitations, self-organization, fluid dynamics, quantum systems, and pure mathematics. Much of what we know theoretically about disordered hyperuniform states of matter involves many-particle systems. In this paper, we derive new rigorous criteria that disordered hyperuniform two-phase heterogeneous materials must obey and explore their consequences. Two-phase heterogeneous media are ubiquitous; examples include composites and porous media, biological media, foams, polymer blends, granular media, cellular solids, and colloids. We begin by obtaining some results that apply to hyperuniform two-phase media in which one phase is a sphere packing in d-dimensional Euclidean space {{{R}}d} . Among other results, we rigorously establish the requirements for packings of spheres of different sizes to be ‘multihyperuniform’. We then consider hyperuniformity for general two-phase media in {{{R}}d} . Here we apply realizability conditions for an autocovariance function and its associated spectral density of a two-phase medium, and then incorporate hyperuniformity as a constraint in order to derive new conditions. We show that some functional forms can immediately be eliminated from consideration and identify other forms that are allowable. Specific examples and counterexamples are described. Contact is made with well-known microstructural models (e.g. overlapping spheres and checkerboards) as well as irregular phase-separation and Turing-type patterns. We also ascertain a family of

  9. Astrocyte heterogeneity in the brain: from development to disease

    PubMed Central

    Schitine, Clarissa; Nogaroli, Luciana; Costa, Marcos R.; Hedin-Pereira, Cecilia

    2015-01-01

    In the last decades, astrocytes have risen from passive supporters of neuronal activity to central players in brain function and cognition. Likewise, the heterogeneity of astrocytes starts to become recognized in contrast to the homogeneous population previously predicted. In this review, we focused on astrocyte heterogeneity in terms of their morphological, protein expression and functional aspects, and debate in a historical perspective the diversity encountered in glial progenitors and how they may reflect mature astrocyte heterogeneity. We discussed data that show that different progenitors may have unsuspected roles in developmental processes. We have approached the functions of astrocyte subpopulations on the onset of psychiatric and neurological diseases. PMID:25852472

  10. Population heterogeneity and causal inference.

    PubMed

    Xie, Yu

    2013-04-16

    Population heterogeneity is ubiquitous in social science. The very objective of social science research is not to discover abstract and universal laws but to understand population heterogeneity. Due to population heterogeneity, causal inference with observational data in social science is impossible without strong assumptions. Researchers have long been concerned with two potential sources of bias. The first is bias in unobserved pretreatment factors affecting the outcome even in the absence of treatment. The second is bias due to heterogeneity in treatment effects. In this article, I show how "composition bias" due to population heterogeneity evolves over time when treatment propensity is systematically associated with heterogeneous treatment effects. A form of selection bias, composition bias, arises dynamically at the aggregate level even when the classic assumption of ignorability holds true at the microlevel.

  11. Population heterogeneity and causal inference

    PubMed Central

    Xie, Yu

    2013-01-01

    Population heterogeneity is ubiquitous in social science. The very objective of social science research is not to discover abstract and universal laws but to understand population heterogeneity. Due to population heterogeneity, causal inference with observational data in social science is impossible without strong assumptions. Researchers have long been concerned with two potential sources of bias. The first is bias in unobserved pretreatment factors affecting the outcome even in the absence of treatment. The second is bias due to heterogeneity in treatment effects. In this article, I show how “composition bias” due to population heterogeneity evolves over time when treatment propensity is systematically associated with heterogeneous treatment effects. A form of selection bias, composition bias, arises dynamically at the aggregate level even when the classic assumption of ignorability holds true at the microlevel. PMID:23530202

  12. Heterogeneity in Waardenburg syndrome.

    PubMed Central

    Hageman, M J; Delleman, J W

    1977-01-01

    Heterogeneity of Waardenburg syndrome is demonstrated in a review of 1,285 patients from the literature and 34 previously unreported patients in five families in the Netherlands. The syndrome seems to consist of two genetically distinct entities that can be differentiated clinically: type I, Waardenburg syndrome with dystopia canthorum; and type II, Waardenburg syndrome without dystopia canthorum. Both types have an autosomal dominant mode of inheritance. The incidence of bilateral deafness in the two types of the syndrome was found in one-fourth with type I and about half of the patients with type II. This difference has important consequences for genetic counseling. Images Fig. 7 Fig. 8 Fig. 9 PMID:331943

  13. Ventilation heterogeneity in obesity.

    PubMed

    Pellegrino, Riccardo; Gobbi, Alessandro; Antonelli, Andrea; Torchio, Roberto; Gulotta, Carlo; Pellegrino, Giulia Michela; Dellacà, Raffaele; Hyatt, Robert E; Brusasco, Vito

    2014-05-01

    Obesity is associated with important decrements in lung volumes. Despite this, ventilation remains normally or near normally distributed at least for moderate decrements in functional residual capacity (FRC). We tested the hypothesis that this is because maximum flow increases presumably as a result of an increased lung elastic recoil. Forced expiratory flows corrected for thoracic gas compression volume, lung volumes, and forced oscillation technique at 5-11-19 Hz were measured in 133 healthy subjects with a body mass index (BMI) ranging from 18 to 50 kg/m(2). Short-term temporal variability of ventilation heterogeneity was estimated from the interquartile range of the frequency distribution of the difference in inspiratory resistance between 5 and 19 Hz (R5-19_IQR). FRC % predicted negatively correlated with BMI (r = -0.72, P < 0.001) and with an increase in slope of either maximal (r = -0.34, P < 0.01) or partial flow-volume curves (r = -0.30, P < 0.01). Together with a slight decrease in residual volume, this suggests an increased lung elastic recoil. Regression analysis of R5-19_IQR against FRC % predicted and expiratory reserve volume (ERV) yielded significantly higher correlation coefficients by nonlinear than linear fitting models (r(2) = 0.40 vs. 0.30 for FRC % predicted and r(2) = 0.28 vs. 0.19 for ERV). In conclusion, temporal variability of ventilation heterogeneities increases in obesity only when FRC falls approximately below 65% of predicted or ERV below 0.6 liters. Above these thresholds distribution is quite well preserved presumably as a result of an increase in lung recoil.

  14. Phenotypic Heterogeneity of Monogenic Frontotemporal Dementia

    PubMed Central

    Benussi, Alberto; Padovani, Alessandro; Borroni, Barbara

    2015-01-01

    Frontotemporal dementia (FTD) is a genetically and pathologically heterogeneous disorder characterized by personality changes, language impairment, and deficits of executive functions associated with frontal and temporal lobe degeneration. Different phenotypes have been defined on the basis of presenting clinical symptoms, i.e., the behavioral variant of FTD, the agrammatic variant of primary progressive aphasia, and the semantic variant of PPA. Some patients have an associated movement disorder, either parkinsonism, as in progressive supranuclear palsy and corticobasal syndrome, or motor neuron disease (FTD–MND). A family history of dementia is found in 40% of cases of FTD and about 10% have a clear autosomal-dominant inheritance. Genetic studies have identified several genes associated with monogenic FTD: microtubule-associated protein tau, progranulin, TAR DNA-binding protein 43, valosin-containing protein, charged multivesicular body protein 2B, fused in sarcoma, and the hexanucleotide repeat expansion in intron 1 of the chromosome 9 open reading frame 72. Patients often present with an extensive phenotypic variability, even among different members of the same kindred carrying an identical disease mutation. The objective of the present work is to review and evaluate available literature data in order to highlight recent advances in clinical, biological, and neuroimaging features of monogenic frontotemporal lobar degeneration and try to identify different mechanisms underlying the extreme phenotypic heterogeneity that characterizes this disease. PMID:26388768

  15. Aggregation of Heterogeneously Charged Colloids.

    PubMed

    Dempster, Joshua M; Olvera de la Cruz, Monica

    2016-06-28

    Patchy colloids are attractive as programmable building blocks for metamaterials. Inverse patchy colloids, in which a charged surface is decorated with patches of the opposite charge, are additionally noteworthy as models for heterogeneously charged biological materials such as proteins. We study the phases and aggregation behavior of a single charged patch in an oppositely charged colloid with a single-site model. This single-patch inverse patchy colloid model shows a large number of phases when varying patch size. For large patch sizes we find ferroelectric crystals, while small patch sizes produce cross-linked gels. Intermediate values produce monodisperse clusters and unusual worm structures that preserve finite ratios of area to volume. The polarization observed at large patch sizes is robust under extreme disorder in patch size and shape. We examine phase-temperature dependence and coexistence curves and find that large patch sizes produce polarized liquids, in contrast to mean-field predictions. Finally, we introduce small numbers of unpatched charged colloids. These can either suppress or encourage aggregation depending on their concentration and the size of the patches on the patched colloids. These effects can be exploited to control aggregation and to measure effective patch size.

  16. Interconnecting heterogeneous database management systems

    NASA Technical Reports Server (NTRS)

    Gligor, V. D.; Luckenbaugh, G. L.

    1984-01-01

    It is pointed out that there is still a great need for the development of improved communication between remote, heterogeneous database management systems (DBMS). Problems regarding the effective communication between distributed DBMSs are primarily related to significant differences between local data managers, local data models and representations, and local transaction managers. A system of interconnected DBMSs which exhibit such differences is called a network of distributed, heterogeneous DBMSs. In order to achieve effective interconnection of remote, heterogeneous DBMSs, the users must have uniform, integrated access to the different DBMs. The present investigation is mainly concerned with an analysis of the existing approaches to interconnecting heterogeneous DBMSs, taking into account four experimental DBMS projects.

  17. p53 mutation heterogeneity in cancer

    SciTech Connect

    Soussi, T. . E-mail: thierry.soussi@free.fr; Lozano, G.

    2005-06-10

    The p53 gene is inactivated in about 50% of human cancers and the p53 protein is an essential component of the cell response induced by genotoxic stresses such as those generated by radiotherapy or chemotherapy. It is therefore highly likely that these alterations are an important component in tumor resistance to therapy. The particular characteristics of these alterations, 80% of which are missense mutations leading to functionally heterogeneous proteins, make p53 a unique gene in the class of tumor suppressor genes. A considerable number of mutant p53 proteins probably have an oncogenic activity per se and therefore actively participate in cell transformation. The fact that the apoptotic and antiproliferative functions of p53 can be dissociated in certain mutants also suggests another level of complexity in the relationships between p53 inactivation and neoplasia.

  18. Etiologic heterogeneity in alcoholism.

    PubMed

    Gilligan, S B; Reich, T; Cloninger, C R

    1987-01-01

    Etiologic heterogeneity in alcohol abuse was evaluated in 195 extended pedigrees, comprising 288 nuclear families of 140 male and 55 female Caucasian American hospitalized alcoholics. Previous adoption studies in Sweden demonstrated differential heritability of two patterns of alcohol abuse in men: type-2 alcoholism exhibited early onset of abuse associated with criminal behavior, while type-1 abuse began at a later age, uncomplicated by antisocial traits. Alcohol abuse in female Swedish adoptees was relatively homogeneous and similar to the late-onset, type-1 abuse. The notion of etiologic heterogeneity, as suggested by the Stockholm Adoption Studies, was examined in the American pedigrees by contrasting the models of familial transmission of susceptibility to alcoholism obtained via segregation analyses of families of male versus female probands. Families of male probands demonstrated significant familial resemblance, accounted for by a multifactorial-polygenic background in addition to a major (gene) effect. In contrast, familial resemblance in the pedigrees of female probands was attributed solely to a multifactorial-polygenic effect. We considered whether some families of male alcoholics were similar to families of female probands, who expressed type-1 abuse predominantly. Pedigrees of male probands were separated in two groups: (1) "female-like" families had a better likelihood for the model obtained for families of female probands than the one for families of all male probands, (2) "male-like" families had a better likelihood for the model of familial transmission describing families of all male probands. A statistically significant difference in the pattern of familial transmission was observed between the "male-like" and "female-like" groups. Discriminant function analysis of alcohol-related symptoms showed that the familial subtypes differed in clinical features as well. Alcohol abuse by male relatives in "male-like" families was characterized by the

  19. Interference Management in Heterogeneous Networks

    DTIC Science & Technology

    2013-06-01

    INTERFERENCE MANAGEMENT IN HETEROGENEOUS NETWORKS UNIVERSITY OF MARYLAND JUNE 2013 FINAL TECHNICAL REPORT APPROVED...3. DATES COVERED (From - To) AUG 2011 – FEB 2013 4. TITLE AND SUBTITLE INTERFERENCE MANAGEMENT IN HETEROGENEOUS NETWORKS 5a. CONTRACT NUMBER...However, such deployments require efficient frequency allocation schemes for managing interference from the pico- and macro base stations that are

  20. Data manipulation in heterogeneous databases

    SciTech Connect

    Chatterjee, A.; Segev, A.

    1991-10-01

    Many important information systems applications require access to data stored in multiple heterogeneous databases. This paper examines a problem in inter-database data manipulation within a heterogeneous environment, where conventional techniques are no longer useful. To solve the problem, a broader definition for join operator is proposed. Also, a method to probabilistically estimate the accuracy of the join is discussed.

  1. Reference Point Heterogeneity

    PubMed Central

    Terzi, Ayse; Koedijk, Kees; Noussair, Charles N.; Pownall, Rachel

    2016-01-01

    It is well-established that, when confronted with a decision to be taken under risk, individuals use reference payoff levels as important inputs. The purpose of this paper is to study which reference points characterize decisions in a setting in which there are several plausible reference levels of payoff. We report an experiment, in which we investigate which of four potential reference points: (1) a population average payoff level, (2) the announced expected payoff of peers in a similar decision situation, (3) a historical average level of earnings that others have received in the same task, and (4) an announced anticipated individual payoff level, best describes decisions in a decontextualized risky decision making task. We find heterogeneity among individuals in the reference points they employ. The population average payoff level is the modal reference point, followed by experimenter's stated expectation of a participant's individual earnings, followed in turn by the average earnings of other participants in previous sessions of the same experiment. A sizeable share of individuals show multiple reference points simultaneously. The reference point that best fits the choices of the individual is not affected by a shock to her income. PMID:27672374

  2. Angiotensin II receptor heterogeneity

    SciTech Connect

    Herblin, W.F.; Chiu, A.T.; McCall, D.E.; Ardecky, R.J.; Carini, D.J.; Duncia, J.V.; Pease, L.J.; Wong, P.C.; Wexler, R.R.; Johnson, A.L. )

    1991-04-01

    The possibility of receptor heterogeneity in the angiotensin II (AII) system has been suggested previously, based on differences in Kd values or sensitivity to thiol reagents. One of the authors earliest indications was the frequent observation of incomplete inhibition of the binding of AII to adrenal cortical membranes. Autoradiographic studies demonstrated that all of the labeling of the rat adrenal was blocked by unlabeled AII or saralasin, but not by DuP 753. The predominant receptor in the rat adrenal cortex (80%) is sensitive to dithiothreitol (DTT) and DuP 753, and is designated AII-1. The residual sites in the adrenal cortex and almost all of the sites in the rat adrenal medulla are insensitive to both DTT and DuP 753, but were blocked by EXP655. These sites have been confirmed by ligand binding studies and are designated AII-2. The rabbit adrenal cortex is unique in yielding a nonuniform distribution of AII-2 sites around the outer layer of glomerulosa cells. In the rabbit kidney, the sites on the glomeruli are AII-1, but the sites on the kidney capsule are AII-2. Angiotensin III appears to have a higher affinity for AII-2 sites since it inhibits the binding to the rabbit kidney capsule but not the glomeruli. Elucidation of the distribution and function of these diverse sites should permit the development of more selective and specific therapeutic strategies.

  3. Heterogeneous recording media

    NASA Astrophysics Data System (ADS)

    Sukhanov, Vitaly I.

    1991-02-01

    The paper summarizes the results of investigations performed to obtain deep 3-D holograms with 102 i0 mkm physical thickness allowing the postexposure amplification and the a posteriori changing of the grating parameters. This aim has been achieved by developing heterogeneous systems on the basis of porous glass with light-sensitive compositions introduced into it. 1. INTRODUCTION. LIGHT-SENSITIVE MEDIA FOR 3-D HOLOGRAMS RECORDING. The 3-D holograms have many useful properties: very high diffraction efficiency angular and spectral selectivity but low level of noise. It shoud be noted that in this case deep 3-D holograms are dealt with whose physical thickness is as high as 102 -i mkm. Such hologram recording is usually done using homogeneous light-sensitive media for example dyed acid-halide and electrooptical crystals photochrome glass photostructurized polimer compositions and so on. The nature of photophisical and photochemical processes responsible for the light sensitivity of these materials exclude the possibility of post-exposure treatment. This does not allow to enhance the recorded holograms and considerably hampers their fixing or makes it practically impossible. The object of our work is to create the media which are quite suitable for two-stage processes of the deep hologram formation with post-exposure processing. Such material must satisfy the following requirements: a)they must have high permeability for the developing substances in order to make the development duration suitable for practical applications b)they must be shrinkproof to prevent deformation of the

  4. Reference Point Heterogeneity.

    PubMed

    Terzi, Ayse; Koedijk, Kees; Noussair, Charles N; Pownall, Rachel

    2016-01-01

    It is well-established that, when confronted with a decision to be taken under risk, individuals use reference payoff levels as important inputs. The purpose of this paper is to study which reference points characterize decisions in a setting in which there are several plausible reference levels of payoff. We report an experiment, in which we investigate which of four potential reference points: (1) a population average payoff level, (2) the announced expected payoff of peers in a similar decision situation, (3) a historical average level of earnings that others have received in the same task, and (4) an announced anticipated individual payoff level, best describes decisions in a decontextualized risky decision making task. We find heterogeneity among individuals in the reference points they employ. The population average payoff level is the modal reference point, followed by experimenter's stated expectation of a participant's individual earnings, followed in turn by the average earnings of other participants in previous sessions of the same experiment. A sizeable share of individuals show multiple reference points simultaneously. The reference point that best fits the choices of the individual is not affected by a shock to her income.

  5. Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

    PubMed Central

    Math, M.; Tarpey, Patrick; Varela, Ignacio; Phillimore, Benjamin; Begum, Sharmin; McDonald, Neil Q.; Butler, Adam; Jones, David; Raine, Keiran; Latimer, Calli; Santos, Claudio R.; Nohadani, Mahrokh; Eklund, Aron C.; Spencer-Dene, Bradley; Clark, Graham; Pickering, Lisa; Stamp, Gordon; Gore, Martin; Szallasi, Zoltan; Downward, Julian; Futreal, P. Andrew

    2016-01-01

    Background Intratumor heterogeneity may foster tumor evolution and adaptation and hinder personalized-medicine strategies that depend on results from single tumor-biopsy samples. Methods To examine intratumor heterogeneity, we performed exome sequencing, chromosome aberration analysis, and ploidy profiling on multiple spatially separated samples obtained from primary renal carcinomas and associated metastatic sites. We characterized the consequences of intratumor heterogeneity using immunohistochemical analysis, mutation functional analysis, and profiling of messenger RNA expression. Results Phylogenetic reconstruction revealed branched evolutionary tumor growth, with 63 to 69% of all somatic mutations not detectable across every tumor region. Intratumor heterogeneity was observed for a mutation within an autoinhibitory domain of the mammalian target of rapamycin (mTOR) kinase, correlating with S6 and 4EBP phosphorylation in vivo and constitutive activation of mTOR kinase activity in vitro. Mutational intratumor heterogeneity was seen for multiple tumor-suppressor genes converging on loss of function; SETD2, PTEN, and KDM5C underwent multiple distinct and spatially separated inactivating mutations within a single tumor, suggesting convergent phenotypic evolution. Gene-expression signatures of good and poor prognosis were detected in different regions of the same tumor. Allelic composition and ploidy profiling analysis revealed extensive intratumor heterogeneity, with 26 of 30 tumor samples from four tumors harboring divergent allelic-imbalance profiles and with ploidy heterogeneity in two of four tumors. Conclusions Intratumor heterogeneity can lead to underestimation of the tumor genomics landscape portrayed from single tumor-biopsy samples and may present major challenges to personalized-medicine and biomarker development. Intratumor heterogeneity, associated with heterogeneous protein function, may foster tumor adaptation and therapeutic failure through

  6. Processing heterogeneous biomass

    PubMed Central

    Buyel, Johannes F.; Fischer, Rainer

    2013-01-01

    Plants have been developed as an alternative platform for the production of biopharmaceutical proteins, culminating recently with the FDA approval of the first plant-derived recombinant pharmaceutical enzyme for human use (ELELYSOÔ by Protalix Biotherapeutics). Among the many different plant-based technologies that have been proposed, transient expression mediated by Agrobacterium tumefaciens has proven to be particularly suitable for the rapid production of vaccines in response to emerging pandemics. However, one potential drawback of transient expression in whole plants is the large variation in recombinant protein expression levels among different leaves, which introduces a level of uncertainty in process design that can increase the regulatory burden and production costs. Transient expression is also used to test expression constructs prior to the longer and more expensive process of generating transgenic plants, and here the variation can produce misleading results leading to erroneous conclusions about the relative activity of different promoters and other regulatory elements. Such variation can be caused by loosely controlled environmental and process factors such incubation temperature, plant characteristics and the method and timing of harvesting. Here we discuss differences between transgenic plants and transient expression in intact plants, and their specific pitfalls for model building. We also highlight which aspects researchers should consider when using a DoE approach to investigate protein expression in plants, both for fundamental research and process development. PMID:22895059

  7. Emerging Understanding of Multiscale Tumor Heterogeneity

    PubMed Central

    Gerdes, Michael J.; Sood, Anup; Sevinsky, Christopher; Pris, Andrew D.; Zavodszky, Maria I.; Ginty, Fiona

    2014-01-01

    Cancer is a multifaceted disease characterized by heterogeneous genetic alterations and cellular metabolism, at the organ, tissue, and cellular level. Key features of cancer heterogeneity are summarized by 10 acquired capabilities, which govern malignant transformation and progression of invasive tumors. The relative contribution of these hallmark features to the disease process varies between cancers. At the DNA and cellular level, germ-line and somatic gene mutations are found across all cancer types, causing abnormal protein production, cell behavior, and growth. The tumor microenvironment and its individual components (immune cells, fibroblasts, collagen, and blood vessels) can also facilitate or restrict tumor growth and metastasis. Oncology research is currently in the midst of a tremendous surge of comprehension of these disease mechanisms. This will lead not only to novel drug targets but also to new challenges in drug discovery. Integrated, multi-omic, multiplexed technologies are essential tools in the quest to understand all of the various cellular changes involved in tumorigenesis. This review examines features of cancer heterogeneity and discusses how multiplexed technologies can facilitate a more comprehensive understanding of these features. PMID:25566504

  8. Node assignment in heterogeneous computing

    NASA Technical Reports Server (NTRS)

    Som, Sukhamoy

    1993-01-01

    A number of node assignment schemes, both static and dynamic, are explored for the Algorithm to Architecture Mapping Model (ATAMM). The architecture under consideration consists of heterogeneous processors and implements dataflow models of real-time applications. Terminology is developed for heterogeneous computing. New definitions are added to the ATAMM for token and assignment classifications. It is proved that a periodic execution is possible for dataflow graphs. Assignment algorithms are developed and proved. A design procedure is described for satisfying an objective function in an heterogeneous architecture. Several examples are provided for illustration.

  9. Homogeneous, Heterogeneous, and Enzymatic Catalysis.

    ERIC Educational Resources Information Center

    Oyama, S. Ted; Somorjai, Gabor A.

    1988-01-01

    Discusses three areas of catalysis: homegeneous, heterogeneous, and enzymatic. Explains fundamentals and economic impact of catalysis. Lists and discusses common industrial catalysts. Provides a list of 107 references. (MVL)

  10. Homogeneous, Heterogeneous, and Enzymatic Catalysis.

    ERIC Educational Resources Information Center

    Oyama, S. Ted; Somorjai, Gabor A.

    1988-01-01

    Discusses three areas of catalysis: homegeneous, heterogeneous, and enzymatic. Explains fundamentals and economic impact of catalysis. Lists and discusses common industrial catalysts. Provides a list of 107 references. (MVL)

  11. Heterogeneity in motor driven transport

    NASA Astrophysics Data System (ADS)

    Tabei, Ali

    2015-03-01

    I will discuss quantitative analysis of particle tracking data for motor driven vesicles inside an insulin secreting cell. We use this method to study the dynamical and structural heterogeneity inside the cell. I will discuss our effort to explain the origin of observed heterogeneity in intracellular transport. Finally, I will explain how analyzing directional correlations in transport trajectories reveals self-similarity in the diffusion media.

  12. Integrating Heterogeneous Datasets for Cancer Module Identification.

    PubMed

    Azad, A K M

    2017-01-01

    The availability of multiple heterogeneous high-throughput datasets provides an enabling resource for cancer systems biology. Types of data include: Gene expression (GE), copy number aberration (CNA), miRNA expression, methylation, and protein-protein Interactions (PPI). One important problem that can potentially be solved using such data is to determine which of the possible pair-wise interactions among genes contributes to a range of cancer-related events, from tumorigenesis to metastasis. It has been shown by various studies that applying integrated knowledge from multi-omics datasets elucidates such complex phenomena with higher statistical significance than using a single type of dataset individually. However, computational methods for processing multiple data types simultaneously are needed. This chapter reviews some of the computational methods that use integrated approaches to find cancer-related modules.

  13. Heterogeneity in schistosomiasis transmission dynamics.

    PubMed

    Mari, Lorenzo; Ciddio, Manuela; Casagrandi, Renato; Perez-Saez, Javier; Bertuzzo, Enrico; Rinaldo, Andrea; Sokolow, Susanne H; De Leo, Giulio A; Gatto, Marino

    2017-11-07

    Simple models of disease propagation often disregard the effects of transmission heterogeneity on the ecological and epidemiological dynamics associated with host-parasite interactions. However, for some diseases like schistosomiasis, a widespread parasitic infection caused by Schistosoma worms, accounting for heterogeneity is crucial to both characterize long-term dynamics and evaluate opportunities for disease control. Elaborating on the classic Macdonald model for macroparasite transmission, we analyze families of models including explicit descriptions of heterogeneity related to differential transmission risk within a community, water contact patterns, the distribution of the snail host population, human mobility, and the seasonal fluctuations of the environment. Through simple numerical examples, we show that heterogeneous multigroup communities may be more prone to schistosomiasis than homogeneous ones, that the availability of multiple water sources can hinder parasite transmission, and that both spatial and temporal heterogeneities may have nontrivial implications for disease endemicity. Finally, we discuss the implications of heterogeneity for disease control. Although focused on schistosomiasis, results from this study may apply as well to other parasitic infections with complex transmission cycles, such as cysticercosis, dracunculiasis and fasciolosis. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  14. PUNCH: Population Characterization of Heterogeneity

    PubMed Central

    Tunc, Birkan; Ghanbari, Yasser; Smith, Alex R.; Pandey, Juhi; Browne, Aaron; Schultz, Robert T.; Verma, Ragini

    2014-01-01

    Neuropsychiatric disorders are notoriously heterogeneous in their presentation, which precludes straightforward and objective description of the differences between affected and typical populations that therefore makes finding reliable biomarkers a challenge. This difficulty underlines the need for reliable methods to capture sample characteristics of heterogeneity using a single continuous measure, incorporating the multitude of scores used to describe different aspects of functioning. This study addresses this challenge by proposing a general method of identifying and quantifying the heterogeneity of any clinical population using a severity measure called the PUNCH (Population Characterization of Heterogeneity). PUNCH is a decision level fusion technique to incorporate decisions of various phenotypic scores, while providing interpretable weights for scores. We provide an application of our framework to a simulated dataset and to a large sample of youth with Autism Spectrum Disorder (ASD). Next we stratify PUNCH scores in our ASD sample and show how severity moderates findings of group differences in diffusion weighted brain imaging data; more severely affected subgroups of ASD show expanded differences compared to age and gender matched healthy controls. Results demonstrate the ability of our measure in quantifying the underlying heterogeneity of the clinical samples, and suggest its utility in providing researchers with reliable severity assessments incorporating population heterogeneity. PMID:24799135

  15. Compositional heterogeneity and phylogenomic inference of metazoan relationships.

    PubMed

    Nesnidal, Maximilian P; Helmkampf, Martin; Bruchhaus, Iris; Hausdorf, Bernhard

    2010-09-01

    Compositional heterogeneity of sequences between taxa may cause systematic error in phylogenetic inference. The potential influence of such bias might be mitigated by strategies to reduce compositional heterogeneity in the data set or by phylogeny reconstruction methods that account for compositional heterogeneity. We adopted several of these strategies to analyze a large ribosomal protein data set representing all major metazoan taxa. Posterior predictive tests revealed that there is compositional bias in this data set. Only a few taxa with strongly deviating amino acid composition had to be excluded to reduce this bias. Thus, this is a good solution, if these taxa are not central to the phylogenetic question at hand. Deleting individual proteins from the data matrix may be an appropriate method, if compositional heterogeneity among taxa is concentrated in a few proteins. However, half of the ribosomal proteins had to be excluded to reduce the compositional heterogeneity to a degree that the CAT model was no longer significantly violated. Recoding of amino acids into groups is another alternative but causes a loss of information and may result in badly resolved trees as demonstrated by the present data set. Bayesian inference with the CAT-BP model directly accounts for compositional heterogeneity between lineages by introducing breakpoints along the branches of the phylogeny at which the amino acid composition is allowed to change but is computationally expensive. Finally, a neighbor joining tree based on equal input distances that consider pattern and rate heterogeneity showed several unusual groupings, which are most likely artifacts, probably caused by the loss of information resulting from the transformation of the sequence data into distances. As long as no more efficient phylogenetic inference methods are available that can directly account for compositional heterogeneity in large data sets, using methods for reducing compositional heterogeneity in the data

  16. Dealing with spatial heterogeneity

    NASA Astrophysics Data System (ADS)

    Marsily, Gh.; Delay, F.; Gonçalvès, J.; Renard, Ph.; Teles, V.; Violette, S.

    2005-03-01

    Heterogeneity can be dealt with by defining homogeneous equivalent properties, known as averaging, or by trying to describe the spatial variability of the rock properties from geologic observations and local measurements. The techniques available for these descriptions are mostly continuous Geostatistical models, or discontinuous facies models such as the Boolean, Indicator or Gaussian-Threshold models and the Markov chain model. These facies models are better suited to treating issues of rock strata connectivity, e.g. buried high permeability channels or low permeability barriers, which greatly affect flow and, above all, transport in aquifers. Genetic models provide new ways to incorporate more geology into the facies description, an approach that has been well developed in the oil industry, but not enough in hydrogeology. The conclusion is that future work should be focused on improving the facies models, comparing them, and designing new in situ testing procedures (including geophysics) that would help identify the facies geometry and properties. A world-wide catalog of aquifer facies geometry and properties, which could combine site genesis and description with methods used to assess the system, would be of great value for practical applications. On peut aborder le problème de l'hétérogénéité en s'efforçant de définir une perméabilité équivalente homogène, par prise de moyenne, ou au contraire en décrivant la variation dans l'espace des propriétés des roches à partir des observations géologiques et des mesures locales. Les techniques disponibles pour une telle description sont soit continues, comme l'approche Géostatistique, soit discontinues, comme les modèles de faciès, Booléens, ou bien par Indicatrices ou Gaussiennes Seuillées, ou enfin Markoviens. Ces modèles de faciès sont mieux capables de prendre en compte la connectivité des strates géologiques, telles que les chenaux enfouis à forte perméabilité, ou au contraire les faci

  17. Directly measuring single-molecule heterogeneity using force spectroscopy

    PubMed Central

    Hinczewski, Michael; Thirumalai, D.

    2016-01-01

    One of the most intriguing results of single-molecule experiments on proteins and nucleic acids is the discovery of functional heterogeneity: the observation that complex cellular machines exhibit multiple, biologically active conformations. The structural differences between these conformations may be subtle, but each distinct state can be remarkably long-lived, with interconversions between states occurring only at macroscopic timescales, fractions of a second or longer. Although we now have proof of functional heterogeneity in a handful of systems—enzymes, motors, adhesion complexes—identifying and measuring it remains a formidable challenge. Here, we show that evidence of this phenomenon is more widespread than previously known, encoded in data collected from some of the most well-established single-molecule techniques: atomic force microscopy or optical tweezer pulling experiments. We present a theoretical procedure for analyzing distributions of rupture/unfolding forces recorded at different pulling speeds. This results in a single parameter, quantifying the degree of heterogeneity, and also leads to bounds on the equilibration and conformational interconversion timescales. Surveying 10 published datasets, we find heterogeneity in 5 of them, all with interconversion rates slower than 10 s−1. Moreover, we identify two systems where additional data at realizable pulling velocities is likely to find a theoretically predicted, but so far unobserved crossover regime between heterogeneous and nonheterogeneous behavior. The significance of this regime is that it will allow far more precise estimates of the slow conformational switching times, one of the least understood aspects of functional heterogeneity. PMID:27317744

  18. River Meandering in Heterogeneous Floodplains

    NASA Astrophysics Data System (ADS)

    Guneralp, I.; Rhoads, B. L.

    2011-12-01

    Freely-meandering natural rivers typically evolve into complex planforms characterized by compound loops or multilobes or into irregular patterns. It is widely acknowledged that spatial heterogeneity in floodplain erodibility should affect the planform evolution of meandering rivers; however, past studies have not systematically explored the importance of this effect. In this study, we systematically analyze how the scale, magnitude, and stochasticity of floodplain erosional variability influence meander evolution and the emergence of bend complexity and planform irregularity. We employ a physically-based model of meander morphodynamics and stochastically-generated heterogeneous landscapes with a range of spatial scales that represent spatial heterogeneity (i.e., patchiness) in floodplain erosional resistance. The heterogeneous mosaics of differential resistance with different scales of patchiness are meant to represent spatial arrangements of factors influencing migration and varying with scale, such as sedimentological complexity, patches of floodplain vegetation, and human activities. We also evaluate the effects of stochasticity in bank erodibility on the spatial characteristics of planform evolution. The results show that both the spatial scale of heterogeneity and the magnitude of variability in erodibility have a strong influence on meander evolution. The planform morphologies generated by simulations with spatially-heterogeneous landscapes are remarkably similar, both visually and in their spectral signatures, to those of natural meandering rivers. Landscapes with patch sizes larger than the initial meander size promote the evolution of highly elongated, upstream-skewed meanders with high variability in amplitudes. As patch size becomes smaller than the initial meander size, bend complexity and planform irregularities increase, resulting in downstream-skewed bends and compound loops or multilobes. Fine-grained heterogeneity results in meanders similar to

  19. Using Inorganic Crystals To Grow Protein Crystals

    NASA Technical Reports Server (NTRS)

    Shlichta, Paul J.; Mcpherson, Alexander A.

    1989-01-01

    Solid materials serve as nucleating agents. Protein crystals induced by heterogeneous nucleation and in some cases by epitaxy to grow at lower supersaturations than needed for spontaneous nucleation. Heterogeneous nucleation makes possible to grow large, defect-free single crystals of protein more readily. Such protein crystals benefits research in biochemistry and pharmacology.

  20. Using Inorganic Crystals To Grow Protein Crystals

    NASA Technical Reports Server (NTRS)

    Shlichta, Paul J.; Mcpherson, Alexander A.

    1989-01-01

    Solid materials serve as nucleating agents. Protein crystals induced by heterogeneous nucleation and in some cases by epitaxy to grow at lower supersaturations than needed for spontaneous nucleation. Heterogeneous nucleation makes possible to grow large, defect-free single crystals of protein more readily. Such protein crystals benefits research in biochemistry and pharmacology.

  1. Reaction Selectivity in Heterogeneous Catalysis

    SciTech Connect

    Somorjai, Gabor A.; Kliewer, Christopher J.

    2009-02-02

    The understanding of selectivity in heterogeneous catalysis is of paramount importance to our society today. In this review we outline the current state of the art in research on selectivity in heterogeneous catalysis. Current in-situ surface science techniques have revealed several important features of catalytic selectivity. Sum frequency generation vibrational spectroscopy has shown us the importance of understanding the reaction intermediates and mechanism of a heterogeneous reaction, and can readily yield information as to the effect of temperature, pressure, catalyst geometry, surface promoters, and catalyst composition on the reaction mechanism. DFT calculations are quickly approaching the ability to assist in the interpretation of observed surface spectra, thereby making surface spectroscopy an even more powerful tool. HP-STM has revealed three vitally important parameters in heterogeneous selectivity: adsorbate mobility, catalyst mobility, and selective site-blocking. The development of size controlled nanoparticles from 0.8 to 10 nm, of controlled shape, and of controlled bimetallic composition has revealed several important variables for catalytic selectivity. Lastly, DFT calculations may be paving the way to guiding the composition choice for multi-metallic heterogeneous catalysis for the intelligent design of catalysts incorporating the many factors of selectivity we have learned.

  2. Organizational heterogeneity of vertebrate genomes.

    PubMed

    Frenkel, Svetlana; Kirzhner, Valery; Korol, Abraham

    2012-01-01

    Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as "texts" using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS) analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers) in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter--GDM) allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.

  3. Phenotypic heterogeneity promotes adaptive evolution

    PubMed Central

    Nevozhay, Dmitry; Kalapis, Dorottya; Lázár, Viktória; Csörgő, Bálint; Nyerges, Ákos; Szamecz, Béla; Fekete, Gergely; Papp, Balázs; Araújo, Hugo; Oliveira, José L.; Moura, Gabriela; Santos, Manuel A. S.; Székely Jr, Tamás; Balázsi, Gábor

    2017-01-01

    Genetically identical cells frequently display substantial heterogeneity in gene expression, cellular morphology and physiology. It has been suggested that by rapidly generating a subpopulation with novel phenotypic traits, phenotypic heterogeneity (or plasticity) accelerates the rate of adaptive evolution in populations facing extreme environmental challenges. This issue is important as cell-to-cell phenotypic heterogeneity may initiate key steps in microbial evolution of drug resistance and cancer progression. Here, we study how stochastic transitions between cellular states influence evolutionary adaptation to a stressful environment in yeast Saccharomyces cerevisiae. We developed inducible synthetic gene circuits that generate varying degrees of expression stochasticity of an antifungal resistance gene. We initiated laboratory evolutionary experiments with genotypes carrying different versions of the genetic circuit by exposing the corresponding populations to gradually increasing antifungal stress. Phenotypic heterogeneity altered the evolutionary dynamics by transforming the adaptive landscape that relates genotype to fitness. Specifically, it enhanced the adaptive value of beneficial mutations through synergism between cell-to-cell variability and genetic variation. Our work demonstrates that phenotypic heterogeneity is an evolving trait when populations face a chronic selection pressure. It shapes evolutionary trajectories at the genomic level and facilitates evolutionary rescue from a deteriorating environmental stress. PMID:28486496

  4. Cancer heterogeneity determined by functional proteomics.

    PubMed

    Szász, A Marcell; Győrffy, Balázs; Marko-Varga, György

    2016-08-26

    Current manuscript gives a synopsis of tumor heterogeneity related to patient samples analyzed by proteomics, protein expression analysis and imaging mass spectrometry. First, we discuss the pathophysiologocal background of cancer biology as a multifactorial and challenging diseases. Disease pathology forms the basis for protein target selection. Therefore, histopathological diagnostics and grading of tumors is highlighted. Pathology is the cornerstone of state-of-the-art diagnostics of tumors today both by establishing dignity and - when needed - describing molecular properties of the cancers. Drug development by the pharmaceutical industry utilizes proteomics studies to pinpoint the most relevant targets. Molecular studies profiling affinity-interactions of the protein(s) with targeted small drug molecules to reach efficacy and optimal patient safety are today requested by the FDA and other agencies for new drug development. An understading of basic mechanisms, controlling drug action and drug binding is central, as a new era of personalized medicine becomes an important milestone solution for the healthcare sector as well as the Pharma and Biotech industry. Development of further diagnostic, prognostic and predictive tests will aid current and future treatment of cancer patients. In the paper we present current status of Proteomics that we believe requires attention in order to collectively advance forward in the fight against cancer, addressing the burning opportunities and challenges.

  5. Tubulin heterogeneity in the trypanosome Crithidia fasciculata.

    PubMed Central

    Russell, D G; Miller, D; Gull, K

    1984-01-01

    The interphase cell of Crithidia fasciculata has three discrete tubulin populations: the subpellicular microtubules, the axonemal microtubules, and the nonpolymerized cytoplasmic pool protein. These three tubulin populations were independently and selectively purified, yielding, in each case, microtubule protein capable of self-assembly. All three preparations polymerized to form ribbons and sheets rather than the more usual microtubular structures. Analyses of the tubulin by two-dimensional polyacrylamide gel electrophoresis, isoelectric focusing, and peptide mapping indicated that the beta-tubulin complex remained constant regardless of source but that some heterogeneity was present in the alpha subunit. Cytoplasmic pool alpha tubulins (alpha 1/alpha 2) were the only alpha isotypes in the cytoplasm and also formed most of the alpha tubulin species in the pellicular fraction. Flagellar alpha tubulin (alpha 3) was the sole alpha isotype in the flagella; it appeared in small amounts in the pellicular fraction but was completely absent from the cytoplasm. In vitro translation products from polyadenylated RNA from C. fasciculata were also examined by two-dimensional polyacrylamide gel electrophoresis and possessed a protein corresponding to alpha 1/alpha 2 tubulin but lacked any alpha 3 tubulin. The alpha 3 polypeptide arose from a post-translational modification of a precursor polypeptide not identifiable by two-dimensional polyacrylamide gel electrophoresis as alpha 3. Peptide mapping data indicated that cytoplasmic alpha tubulin is the most likely precursor. These results demonstrate alpha-tubulin heterogeneity in this organism and also how close the relationship between flagellar and cytoskeletal tubulins can be among lower eucaryotes. Images PMID:6717441

  6. Static heterogeneities in liquid water

    NASA Astrophysics Data System (ADS)

    Stanley, H. Eugene; Buldyrev, Sergey V.; Giovambattista, Nicolas

    2004-10-01

    The thermodynamic behavior of water seems to be closely related to static heterogeneities. These static heterogeneities are related to the local structure of water molecules, and when properly characterized, may offer an economical explanation of thermodynamic data. The key feature of liquid water is not so much that the existence of hydrogen bonds, first pointed out by Linus Pauling, but rather the local geometry of the liquid molecules is not spherical or oblong but tetrahedral. In the consideration of static heterogeneities, this local geometry is critical. Recent experiments suggested more than one phase of amorphous solid water, while simulations suggest that one of these phases is metastable with respect to another, so that in fact there are only two stable phases.

  7. Resource heterogeneity can facilitate cooperation

    PubMed Central

    Kun, Ádám; Dieckmann, Ulf

    2013-01-01

    Although social structure is known to promote cooperation, by locally exposing selfish agents to their own deeds, studies to date assumed that all agents have access to the same level of resources. This is clearly unrealistic. Here we find that cooperation can be maintained when some agents have access to more resources than others. Cooperation can then emerge even in populations in which the temptation to defect is so strong that players would act fully selfishly if their resources were distributed uniformly. Resource heterogeneity can thus be crucial for the emergence and maintenance of cooperation. We also show that resource heterogeneity can hinder cooperation once the temptation to defect is significantly lowered. In all cases, the level of cooperation can be maximized by managing resource heterogeneity. PMID:24088665

  8. Quantifying tumour heterogeneity with CT

    PubMed Central

    Miles, Kenneth A.

    2013-01-01

    Abstract Heterogeneity is a key feature of malignancy associated with adverse tumour biology. Quantifying heterogeneity could provide a useful non-invasive imaging biomarker. Heterogeneity on computed tomography (CT) can be quantified using texture analysis which extracts spatial information from CT images (unenhanced, contrast-enhanced and derived images such as CT perfusion) that may not be perceptible to the naked eye. The main components of texture analysis can be categorized into image transformation and quantification. Image transformation filters the conventional image into its basic components (spatial, frequency, etc.) to produce derived subimages. Texture quantification techniques include structural-, model- (fractal dimensions), statistical- and frequency-based methods. The underlying tumour biology that CT texture analysis may reflect includes (but is not limited to) tumour hypoxia and angiogenesis. Emerging studies show that CT texture analysis has the potential to be a useful adjunct in clinical oncologic imaging, providing important information about tumour characterization, prognosis and treatment prediction and response. PMID:23545171

  9. Simulator for heterogeneous dataflow architectures

    NASA Technical Reports Server (NTRS)

    Malekpour, Mahyar R.

    1993-01-01

    A new simulator is developed to simulate the execution of an algorithm graph in accordance with the Algorithm to Architecture Mapping Model (ATAMM) rules. ATAMM is a Petri Net model which describes the periodic execution of large-grained, data-independent dataflow graphs and which provides predictable steady state time-optimized performance. This simulator extends the ATAMM simulation capability from a heterogenous set of resources, or functional units, to a more general heterogenous architecture. Simulation test cases show that the simulator accurately executes the ATAMM rules for both a heterogenous architecture and a homogenous architecture, which is the special case for only one processor type. The simulator forms one tool in an ATAMM Integrated Environment which contains other tools for graph entry, graph modification for performance optimization, and playback of simulations for analysis.

  10. Resource heterogeneity can facilitate cooperation.

    PubMed

    Kun, Ádám; Dieckmann, Ulf

    2013-01-01

    Although social structure is known to promote cooperation, by locally exposing selfish agents to their own deeds, studies to date assumed that all agents have access to the same level of resources. This is clearly unrealistic. Here we find that cooperation can be maintained when some agents have access to more resources than others. Cooperation can then emerge even in populations in which the temptation to defect is so strong that players would act fully selfishly if their resources were distributed uniformly. Resource heterogeneity can thus be crucial for the emergence and maintenance of cooperation. We also show that resource heterogeneity can hinder cooperation once the temptation to defect is significantly lowered. In all cases, the level of cooperation can be maximized by managing resource heterogeneity.

  11. Simulator for heterogeneous dataflow architectures

    NASA Astrophysics Data System (ADS)

    Malekpour, Mahyar R.

    1993-09-01

    A new simulator is developed to simulate the execution of an algorithm graph in accordance with the Algorithm to Architecture Mapping Model (ATAMM) rules. ATAMM is a Petri Net model which describes the periodic execution of large-grained, data-independent dataflow graphs and which provides predictable steady state time-optimized performance. This simulator extends the ATAMM simulation capability from a heterogenous set of resources, or functional units, to a more general heterogenous architecture. Simulation test cases show that the simulator accurately executes the ATAMM rules for both a heterogenous architecture and a homogenous architecture, which is the special case for only one processor type. The simulator forms one tool in an ATAMM Integrated Environment which contains other tools for graph entry, graph modification for performance optimization, and playback of simulations for analysis.

  12. Dynamic fracture of heterogeneous materials

    SciTech Connect

    Stout, M.G.; Liu, C.; Addessio, F.L.; Williams, T.O.; Bennett, J.G.; Haberman, K.S.; Asay, B.W.

    1998-12-31

    This is the final report of a one-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The objective of this project was to investigate the fundamental aspects of the process of dynamic fracture propagation in heterogeneous materials. The work focused on three important, but poorly understood, aspects of dynamic fracture for materials with a heterogeneous microstructure. These were: the appropriateness of using a single-parameter asymptotic analysis to describe dynamic crack-tip deformation fields, the temperature rises at the tip and on the flanks of a running crack, and the constitutive modeling of damage initiation and accumulation.

  13. Macrophages heterogeneity in atherosclerosis - implications for therapy.

    PubMed

    Wilson, Heather M

    2010-08-01

    Atherosclerosis is a chronic inflammatory disease occurring within the artery wall and is an underlying cause of cardiovascular complications, including myocardial infarction, stroke and peripheral vascular disease. Its pathogenesis involves many immune cell types with a well accepted role for monocyte/macrophages. Cholesterol-loaded macrophages are a characteristic feature of plaques and are major players in all stages of plaque development. As well as modulating lipid metabolism, macrophages secrete inflammatory cytokines, chemokines and reactive oxygen and nitrogen species that drive pathogenesis. They also produce proteases and tissue factor that contribute to plaque rupture and thrombosis. Macrophages are however heterogeneous cells and when appropriately activated, they phagocytose cytotoxic lipoproteins, clear apoptotic bodies, secrete anti-inflammatory cytokines and synthesize matrix repair proteins that stabilize vulnerable plaques. Pharmacological modulation of macrophage activity therefore represents a potential therapeutic strategy for atherosclerosis. The aim of this review is to provide an overview of the current understanding of the different macrophage subsets and their monocyte precursors, and, the implications of these subsets for atherosclerosis. This will present a foundation for highlighting novel opportunities to exploit the heterogeneity of macrophages as important diagnostic and therapeutic targets for atherosclerosis and its associated diseases. © 2010 The Author Journal compilation © 2010 Foundation for Cellular and Molecular Medicine/Blackwell Publishing Ltd.

  14. Polypyrimidine tract-binding protein is critical for the turnover and subcellular distribution of CD40 ligand mRNA in CD4+ T cells.

    PubMed

    Matus-Nicodemos, Rodrigo; Vavassori, Stefano; Castro-Faix, Moraima; Valentin-Acevedo, Anibal; Singh, Karnail; Marcelli, Valentina; Covey, Lori R

    2011-02-15

    CD40L (CD154) is regulated at the posttranscriptional level by an activation-induced process that results in a highly stable transcript at extended times of T cell activation. Transcript stability is mediated by polypyrimidine tract-binding protein (PTB)-containing complexes (complex I and II) that bind to three adjacent CU-rich sequences within the 3' untranslated region. To assess the role of PTB in the expression and distribution of CD40L mRNA, PTB was targeted using short hairpin RNA in both primary T cells and a T cell line that recapitulates the stability phase of regulated CD40L mRNA decay. PTB knockdown resulted in a marked decrease in the mRNA stability that resulted in lowered CD40L surface expression. PTB was also critical for appropriate distribution of CD40L mRNA between the nucleus and cytoplasm and in the cytoplasm between the cytosol and the translating polysomes. The activation-induced formation of PTB-specific ribonucleoprotein complexes was observed only with cytoplasmic and not nuclear PTB indicating functional differences in the protein defined by cellular localization. Finally, we observed that cytoplasmic and nuclear PTB isoforms were differentially modified relative to each other and that the changes in cytoplasmic PTB were consistent with activation-induced phosphorylation. Together this work suggests that differentially modified PTB regulates CD40L expression at multiple steps by 1) retaining CD40L mRNA in the nucleus, 2) directly regulating mRNA stability at late times of activation, and 3) forming a ribonuclear complex that preferentially associates with translating ribosomes thus leading to an enhanced level of CD40L protein.

  15. Upstream reciprocity in heterogeneous networks.

    PubMed

    Iwagami, Akio; Masuda, Naoki

    2010-08-07

    Many mechanisms for the emergence and maintenance of altruistic behavior in social dilemma situations have been proposed. Indirect reciprocity is one such mechanism, where other-regarding actions of a player are eventually rewarded by other players with whom the original player has not interacted. The upstream reciprocity (also called generalized indirect reciprocity) is a type of indirect reciprocity and represents the concept that those helped by somebody will help other unspecified players. In spite of the evidence for the enhancement of helping behavior by upstream reciprocity in rats and humans, theoretical support for this mechanism is not strong. In the present study, we numerically investigate upstream reciprocity in heterogeneous contact networks, in which the players generally have different number of neighbors. We show that heterogeneous networks considerably enhance cooperation in a game of upstream reciprocity. In heterogeneous networks, the most generous strategy, by which a player helps a neighbor on being helped and in addition initiates helping behavior, first occupies hubs in a network and then disseminates to other players. The scenario to achieve enhanced altruism resembles that seen in the case of the Prisoner's Dilemma game in heterogeneous networks. Copyright 2010 Elsevier Ltd. All rights reserved.

  16. Floodplain heterogeneity and meander migration

    USDA-ARS?s Scientific Manuscript database

    The impact of horizontal heterogeneity of floodplain soils on rates and patterns of meander migration is analyzed with a Ikeda et al. (1981)-type model for hydrodynamics and bed morphodynamics, coupled with a physically-based bank erosion model according to the approach developed by Motta et al. (20...

  17. Modeling large heterogeneous RF structures

    SciTech Connect

    Li, Zenghai; Ko, Kwok; Srinivas, V.; Higo, Toshiyasu

    1996-11-01

    Large heterogeneous structures are difficult to model on a numerical grid because of the limitations on computing resources, so that alternate approaches such as equivalent circuits and mode-matching have been developed to treat this problem. This paper will describe the three methods and will analyze a structure representative of the SLAC and JLC detuned structures to compare the efficacy of each approach.

  18. Genetic heterogeneity in human disease.

    PubMed

    McClellan, Jon; King, Mary-Claire

    2010-04-16

    Strong evidence suggests that rare mutations of severe effect are responsible for a substantial portion of complex human disease. Evolutionary forces generate vast genetic heterogeneity in human illness by introducing many new variants in each generation. Current sequencing technologies offer the possibility of finding rare disease-causing mutations and the genes that harbor them. Copyright 2010 Elsevier Inc. All rights reserved.

  19. Teaching about Heterogeneous Response Models

    ERIC Educational Resources Information Center

    Murray, Michael P.

    2014-01-01

    Individuals vary in their responses to incentives and opportunities. For example, additional education will affect one person differently than another. In recent years, econometricians have given increased attention to such heterogeneous responses and to the consequences of such responses for interpreting regression estimates, especially…

  20. Heterogeneous porous media in hydrology

    NASA Astrophysics Data System (ADS)

    Ababou, Rachid

    In natural geologic formations, flow and transport-related processes are perturbed by multidimensional and anisotropic material heterogeneities of diverse sizes, shapes, and origins (bedding, layering, inclusions, fractures, grains, for example). Heterogeneity tends to disperse and mix transported quantities and may initiate new transfer mechanisms not seen in ideally homogeneous porous media. Effective properties such as conductivity and dispersivity may not be simple averages of locally measured quantities.The special session, “Effective Constitutive Laws for Heterogeneous Porous Media,” convened at AGU's 1992 Fall Meeting in San Francisco, addressed these issue. Over forty-five contributions, both oral and poster, covering a broad range of physical phenomena were presented. The common theme was the macroscale characterization and modeling of flow and flow-related processes in geologic media that are heterogeneous at various scales (from grain size or fracture aperture, up to regional scales). The processes analyzed in the session included coupled hydro-mechanical processes; Darcy-type flow in the saturated, unsaturated, or two-phase regimes; tracer transport, dilution, and dispersion. These processes were studied for either continuous (porous) or discontinuous (fractured) media.

  1. Molecular ingredients of heterogeneous catalysis

    SciTech Connect

    Somorjai, G.A.

    1982-06-01

    The purpose of this paper is to present a review and status report to those in theoretical chemistry of the rapidly developing surface science of heterogeneous catalysis. The art of catalysis is developing into science. This profound change provides one with opportunities not only to understand the molecular ingredients of important catalytic systems but also to develop new and improved catalyst. The participation of theorists to find answers to important questions is sorely needed for the sound development of the field. It is the authors hope that some of the outstanding problems of heterogeneous catalysis that are identified in this paper will be investigated. For this purpose the paper is divided into several sections. The brief Introduction to the methodology and recent results of the surface science of heterogeneous catalysis is followed by a review of the concepts of heterogeneous catalysis. Then, the experimental results that identified the three molecular ingredients of catalysis, structure, carbonaceous deposit and the oxidation state of surface atoms are described. Each section is closed with a summary and a list of problems that require theoretical and experimental scrutiny. Finally attempts to build new catalyst systems and the theoretical and experimental problems that appeared in the course of this research are described.

  2. Heterogeneous catalytic alcoholysis of benzonitrile

    SciTech Connect

    Kagarlitskii, A.D.; Dmumakaev, K.Kh.; Bekova, N.S.

    1986-04-01

    The authors investigate the possibility of the direct heterogeneous catalytic synthesis of ethylbenzoate from benzonitrile. The catalysts tested were oxides of aluminium, titanium, and vanadium. The main conversion product detected chromatographically was ethylbenzoate; benzaldehyde, benzamide, and benzanilide were also identified. Aluminium oxide was found to be the most effective catalyst.

  3. Social Capital and Community Heterogeneity

    ERIC Educational Resources Information Center

    Coffe, Hilde

    2009-01-01

    Recent findings indicate that more pronounced community heterogeneity is associated with lower levels of social capital. These studies, however, concentrate on specific aspects in which people differ (such as income inequality or ethnic diversity). In the present paper, we introduce the number of parties in the local party system as a more…

  4. Surface science of heterogeneous reactions.

    PubMed

    White, J M

    1982-10-29

    Some of the present and future directions for surface science as a growing and naturally interdisciplinary subject are reviewed. Particular attention is given to surface reaction chemistry as it is related to heterogenous catalysis, a subject area where there are abundant opportunities for detailed measurements of structure and dynamics at the molecular level.

  5. Social Capital and Community Heterogeneity

    ERIC Educational Resources Information Center

    Coffe, Hilde

    2009-01-01

    Recent findings indicate that more pronounced community heterogeneity is associated with lower levels of social capital. These studies, however, concentrate on specific aspects in which people differ (such as income inequality or ethnic diversity). In the present paper, we introduce the number of parties in the local party system as a more…

  6. Flammability of Heterogeneously Combusting Metals

    NASA Technical Reports Server (NTRS)

    Jones, Peter D.

    1998-01-01

    Most engineering materials, including some metals, most notably aluminum, burn in homogeneous combustion. 'Homogeneous' refers to both the fuel and the oxidizer being in the same phase, which is usually gaseous. The fuel and oxidizer are well mixed in the combustion reaction zone, and heat is released according to some relation like q(sub c) = delta H(sub c)c[((rho/rho(sub 0))]exp a)(exp -E(sub c)/RT), Eq. (1) where the pressure exponent a is usually close to unity. As long as there is enough heat released, combustion is sustained. It is useful to conceive of a threshold pressure beyond which there is sufficient heat to keep the temperature high enough to sustain combustion, and beneath which the heat is so low that temperature drains away and the combustion is extinguished. Some materials burn in heterogeneous combustion, in which the fuel and oxidizer are in different phases. These include iron and nickel based alloys, which burn in the liquid phase with gaseous oxygen. Heterogeneous combustion takes place on the surface of the material (fuel). Products of combustion may appear as a solid slag (oxide) which progressively covers the fuel. Propagation of the combustion melts and exposes fresh fuel. Heterogeneous combustion heat release also follows the general form of Eq.(1), except that the pressure exponent a tends to be much less than 1. Therefore, the increase in heat release with increasing pressure is not as dramatic as it is in homogeneous combustion. Although the concept of a threshold pressure still holds in heterogeneous combustion, the threshold is more difficult to identify experimentally, and pressure itself becomes less important relative to the heat transfer paths extant in any specific application. However, the constants C, a, and E(sub c) may still be identified by suitable data reduction from heterogeneous combustion experiments, and may be applied in a heat transfer model to judge the flammability of a material in any particular actual

  7. Surface heterogeneity of small asteroids

    NASA Astrophysics Data System (ADS)

    Sasaki, Sho

    A rubble pile model of asteroid origin would predict averaged rather homogeneous surface of an asteroid. Previous spacecraft observations (mostly S-type asteroids) did not show large color/albedo variation on the surface. Vesta would be exceptional since HST observation suggested that its surface should be heterogeneous due to the impact excavation of the interior. As for a young asteroid (832) Karin (age being 5Ma), Sasaki et al. (2004) detected variation of infrared spectra which could be explained by the difference of the space weathering degree. They discussed the possibility of the survival of the old surface. However, the variation was not confirmed by later observation (Chapman et al., 2007; Vernazza et al., 2007). Recent observation of a small (550m) asteroid Itokawa by Hayabusa spacecraft revealed that Itokawa is heterogeneous in color and albedo although the overall rocky structure is considered as a rubble pile (Saito et al., 2006). The color difference can be explained by the difference of weathering degree (Ishiguro et al., 2008). The heterogeneity could be explained by mass movement caused by rapid rotation from YORP effect (Scheeres et al., 2007) or seismic shaking (Sasaki, 2006). Probably small silicate asteroids without significant regolith could have heterogeneous in color and albedo. On large asteroids (˜ a few 10km), regolith reaccumulation should have covered the underlying heterogeneity. References: Chapman, C. R. et al (2007) Icarus, 191, 323-329 Ishiguro, M. et al. (2008) MAPS, in press. Saito, J. et al. (2006) Science, 312, 1341-1344 Sasaki, S. (2006) in Spacecraft Reconnaissance of Asteroid and Comet Interiors Sasaki, T. et al (2004) Astrophys. J. 615, L161-L164 Scheeres, D. J. (2007) Icarus 188, 425-429 Vernazza, P. et al. (2007) Icarus 191, 330-336.

  8. Resolution of structural heterogeneity in dynamic crystallography.

    PubMed

    Ren, Zhong; Chan, Peter W Y; Moffat, Keith; Pai, Emil F; Royer, William E; Šrajer, Vukica; Yang, Xiaojing

    2013-06-01

    Dynamic behavior of proteins is critical to their function. X-ray crystallography, a powerful yet mostly static technique, faces inherent challenges in acquiring dynamic information despite decades of effort. Dynamic `structural changes' are often indirectly inferred from `structural differences' by comparing related static structures. In contrast, the direct observation of dynamic structural changes requires the initiation of a biochemical reaction or process in a crystal. Both the direct and the indirect approaches share a common challenge in analysis: how to interpret the structural heterogeneity intrinsic to all dynamic processes. This paper presents a real-space approach to this challenge, in which a suite of analytical methods and tools to identify and refine the mixed structural species present in multiple crystallographic data sets have been developed. These methods have been applied to representative scenarios in dynamic crystallography, and reveal structural information that is otherwise difficult to interpret or inaccessible using conventional methods.

  9. Clinical and genetic heterogeneity of erythrokeratoderma variabilis.

    PubMed

    Common, John E A; O'Toole, Edel A; Leigh, Irene M; Thomas, Anna; Griffiths, William A D; Venning, Vanessa; Grabczynska, Sophie; Peris, Zdravko; Kansky, Aleksej; Kelsell, David P

    2005-11-01

    The skin disease erythrokeratoderma variabilis (EKV) has been shown to be associated with mutations in GJB3 and GJB4 encoding connexin (Cx)31 and Cx30.3, respectively. Gap junctions composed of Cx proteins are intracellular channels providing a mechanism of synchronized cellular response facilitating metabolic and electronic functions of the cell. In the skin, Cx31 and Cx30.3 are expressed in the stratum granulosum of the epidermis with a suggested role in late keratinocyte differentiation. Molecular investigations of GJB3 and GJB4 were performed in five pedigrees and three sporadic cases of EKV. Mutational analyzes revealed disease-associated Cx31 or Cx30.3 mutations in only three probands of which two were novel mutations and one was a recurrent mutation. These genetic studies further demonstrate the heterogeneous nature of the erythrokeratodermas as not all individuals that were clinically diagnosed with EKV harbor Cx31 or Cx30.3 mutations.

  10. Resolution of structural heterogeneity in dynamic crystallography

    PubMed Central

    Ren, Zhong; Chan, Peter W. Y.; Moffat, Keith; Pai, Emil F.; Royer, William E.; Šrajer, Vukica; Yang, Xiaojing

    2013-01-01

    Dynamic behavior of proteins is critical to their function. X-­ray crystallography, a powerful yet mostly static technique, faces inherent challenges in acquiring dynamic information despite decades of effort. Dynamic ‘structural changes’ are often indirectly inferred from ‘structural differences’ by comparing related static structures. In contrast, the direct observation of dynamic structural changes requires the initiation of a biochemical reaction or process in a crystal. Both the direct and the indirect approaches share a common challenge in analysis: how to interpret the structural heterogeneity intrinsic to all dynamic processes. This paper presents a real-space approach to this challenge, in which a suite of analytical methods and tools to identify and refine the mixed structural species present in multiple crystallographic data sets have been developed. These methods have been applied to representative scenarios in dynamic crystallography, and reveal structural information that is otherwise difficult to interpret or inaccessible using conventional methods. PMID:23695239

  11. Heterogeneous ribonucleoprotein C displays a repressor activity mediated by T-cell intracellular antigen-1-related/like protein to modulate Fas exon 6 splicing through a mechanism involving Hu antigen R.

    PubMed

    Izquierdo, José M

    2010-12-01

    T-cell intracellular antigen (TIA)-proteins are known regulators of alternative pre-mRNA splicing. In this study, pull-down experiments and mass spectrometry indicate that TIAR/TIAL1 and hnRNP C1/C2 are associated in HeLa nuclear extracts. Co-immunoprecipitation and GST-pull-down assays confirmed this interaction. Interestingly, binding requires the glutamine-rich (Q-rich) C-terminal domain of TIAR and the leucine-rich plus acidic residues-rich C-terminal domains of hnRNP C1/C2. This interaction also occurs in an RNA-dependent manner. Recombinant GFP-TIAR and RFP-hnRNP C1 proteins display partial nuclear co-localization when overexpressed in HeLa cells, and this requires the Q-rich domain of TIAR. hnRNP C1 overexpression in the presence of rate-limiting amounts of TIAR in HeLa and HEK293 cells affects alternative splicing of Fas and FGFR2 minigenes, promoting Fas exon 6 and FGFR2 exon K-SAM skipping, respectively. The repressor activity of hnRNP C1 on Fas exon 6 splicing is mediated by Hu antigen R (HuR). Experiments involving tethering approaches showed that the repressor capacity of hnRNP C1 is associated with an exonic splicing silencer in Fas exon 6. This effect was reversed by splice-site strengthening and is linked to its basic leucine zipper-like motif. These results suggest that hnRNP C1/C2 acts as a bridge between HuR and TIAR to modulate alternative Fas splicing.

  12. Biodiesel production using heterogeneous catalysts.

    PubMed

    Semwal, Surbhi; Arora, Ajay K; Badoni, Rajendra P; Tuli, Deepak K

    2011-02-01

    The production and use of biodiesel has seen a quantum jump in the recent past due to benefits associated with its ability to mitigate greenhouse gas (GHG). There are large number of commercial plants producing biodiesel by transesterification of vegetable oils and fats based on base catalyzed (caustic) homogeneous transesterification of oils. However, homogeneous process needs steps of glycerol separation, washings, very stringent and extremely low limits of Na, K, glycerides and moisture limits in biodiesel. Heterogeneous catalyzed production of biodiesel has emerged as a preferred route as it is environmentally benign needs no water washing and product separation is much easier. The present report is review of the progress made in development of heterogeneous catalysts suitable for biodiesel production. This review shall help in selection of suitable catalysts and the optimum conditions for biodiesel production.

  13. A chicken mRNA similar to heterogeneous nuclear ribonucleoprotein H1.

    PubMed

    Mozdziak, Paul E; Giamario, Carol; Dibner, Julia J; McCoy, Darell W

    2004-01-01

    Heterogeneous nuclear ribonucleoproteins are predominantly nuclear RNA-binding proteins that function in a variety of cellular activities. The objective of these experiments was to clone a cDNA for a chicken protein similar to other previously reported heterogeneous ribonucleoproteins for other species. The 5' and 3' ends of the chicken mRNA were cloned using Rapid Amplification of cDNA Ends (RACE). Subsequently, the expression of the mRNA sequence was confirmed via Northern analysis. The deduced amino acid sequence was approximately 86% identical to corresponding regions of human, mouse, or zebrafish proteins similar to heterogeneous nuclear ribonucleoprotein H1. The expression data confirmed the size of the predicted mRNA sequence. The newly identified sequence may be employed in future studies aimed at understanding the role of heterogeneous nuclear ribonucleoproteins in avian species.

  14. Temperature chaos and quenched heterogeneities

    NASA Astrophysics Data System (ADS)

    Barucca, Paolo; Parisi, Giorgio; Rizzo, Tommaso

    2014-03-01

    We present a treatable generalization of the Sherrington-Kirkpatrick (SK) model which introduces correlations in the elements of the coupling matrix through multiplicative disorder on the single variables and investigate the consequences on the phase diagram. We define a generalized qEA parameter and test the structural stability of the SK results in this correlated case evaluating the de Almeida-Thouless line of the model. As a main result we demonstrate the increase of temperature chaos effects due to heterogeneities.

  15. Measuring heterogeneous remanence in paleomagnetism

    NASA Astrophysics Data System (ADS)

    Borradaile, Graham J.; Geneviciene, Ieva

    2007-06-01

    Remanence directions of from the same block-sample may be inconsistent or unrepresentative due to orientation and location heterogeneity of their remanence-bearing minerals (RBM). Magnetization-heterogeneity is usually undetectable at the specimen-level but we replicated its effects by measuring 8 small specimens with stable magnetizations (8 or 5.2 cm3). These were assembled into a single large multi-specimen inside 125 cm3 containers that were measured in a Molspin ``BigSpin'' magnetometer. Large-specimen remanence directions deflect towards the direction of any strongly magnetized sub-specimen. Differences between the large-specimen remanence and that for the group of individually measured sub-specimens worsened when one sub-specimen was mis-oriented. These discrepancies were cancelled or reduced using larger numbers of specimen orientations in the magnetometer. Conventional schemes with 4 or 6 different measurement-orientations may fail to suppress heterogeneity-effects whereas our 12-orientation protocol may succeed. For most specimens, acceptable remanence-homogeneity is present where similar remanence-directions are recorded from 4, 6, and 12 different spin-orientations.

  16. On comparing heterogeneity across biomarkers.

    PubMed

    Steininger, Robert J; Rajaram, Satwik; Girard, Luc; Minna, John D; Wu, Lani F; Altschuler, Steven J

    2015-06-01

    Microscopy reveals complex patterns of cellular heterogeneity that can be biologically informative. However, a limitation of microscopy is that only a small number of biomarkers can typically be monitored simultaneously. Thus, a natural question is whether additional biomarkers provide a deeper characterization of the distribution of cellular states in a population. How much information about a cell's phenotypic state in one biomarker is gained by knowing its state in another biomarker? Here, we describe a framework for comparing phenotypic states across biomarkers. Our approach overcomes the current limitation of microscopy by not requiring costaining biomarkers on the same cells; instead, we require staining of biomarkers (possibly separately) on a common collection of phenotypically diverse cell lines. We evaluate our approach on two image datasets: 33 oncogenically diverse lung cancer cell lines stained with 7 biomarkers, and 49 less diverse subclones of one lung cancer cell line stained with 12 biomarkers. We first validate our method by comparing it to the "gold standard" of costaining. We then apply our approach to all pairs of biomarkers and use it to identify biomarkers that yield similar patterns of heterogeneity. The results presented in this work suggest that many biomarkers provide redundant information about heterogeneity. Thus, our approach provides a practical guide for selecting independently informative biomarkers and, more generally, will yield insights into both the connectivity of biological networks and the complexity of the state space of biological systems.

  17. Soft Dielectrics: Heterogeneity and Instabilities

    NASA Astrophysics Data System (ADS)

    Rudykh, Stephan; Debotton, Gal; Bhattacharya, Kaushik

    2012-02-01

    Dielectric Elastomers are capable of large deformations in response to electrical stimuli. Heterogeneous soft dielectrics with proper microstructures demonstrate much stronger electromechanical coupling than their homogeneous constituents. In turn, the heterogeneity is an origin for instability developments leading to drastic change in the composite microstructure. In this talk, the electromechanical instabilities are considered. Stability of anisotropic soft dielectrics is analyzed. Ways to achieve giant deformations and manipulating extreme material properties are discussed. 1. S. Rudykh and G. deBotton, ``Instabilities of Hyperelastic Fiber Composites: Micromechanical Versus Numerical Analyses.'' Journal of Elasticity, 2011. http://dx.doi.org/2010.1007/s10659-011-9313-x 2. S. Rudykh, K. Bhattacharya and G. deBotton, ``Snap-through actuation of thick-wall electroactive balloons.'' International Journal of Non-Linear Mechanics, 2011. http://dx.doi.org/10.1016/j.ijnonlinmec.2011.05.006 3. S. Rudykh and G. deBotton, ``Stability of Anisotropic Electroactive Polymers with Application to Layered Media.'' Zeitschrift f"ur angewandte Mathematik und Physik, 2011. http://dx.doi.org/10.1007/s00033-011-0136-1 4. S. Rudykh, A. Lewinstein, G. Uner and G. deBotton, ``Giant Enhancement of the Electromechanical Coupling in Soft Heterogeneous Dielectrics.'' 2011 http://arxiv.org/abs/1105.4217v1

  18. Analyzing and modeling heterogeneous behavior

    NASA Astrophysics Data System (ADS)

    Lin, Zhiting; Wu, Xiaoqing; He, Dongyue; Zhu, Qiang; Ni, Jixiang

    2016-05-01

    Recently, it was pointed out that the non-Poisson statistics with heavy tail existed in many scenarios of human behaviors. But most of these studies claimed that power-law characterized diverse aspects of human mobility patterns. In this paper, we suggest that human behavior may not be driven by identical mechanisms and can be modeled as a Semi-Markov Modulated Process. To verify our suggestion and model, we analyzed a total of 1,619,934 records of library visitations (including undergraduate and graduate students). It is found that the distribution of visitation intervals is well fitted with three sections of lines instead of the traditional power law distribution in log-log scale. The results confirm that some human behaviors cannot be simply expressed as power law or any other simple functions. At the same time, we divided the data into groups and extracted period bursty events. Through careful analysis in different groups, we drew a conclusion that aggregate behavior might be composed of heterogeneous behaviors, and even the behaviors of the same type tended to be different in different period. The aggregate behavior is supposed to be formed by "heterogeneous groups". We performed a series of experiments. Simulation results showed that we just needed to set up two states Semi-Markov Modulated Process to construct proper representation of heterogeneous behavior.

  19. NASA GSFC Perspective on Heterogeneous Processing

    NASA Technical Reports Server (NTRS)

    Powell, Wesley A.

    2016-01-01

    This presentation provides an overview of NASA GSFC, our onboard processing applications, the applicability heterogeneous processing to these applications, and necessary developments to enable heterogeneous processing to be infused into our missions.

  20. [Study of the genetic heterogeneity of gangliosidoses in humans].

    PubMed

    Akhunov, V S; Aronovich, E L; Krasnopol'skaia, K D; Mirenburg, T V

    1989-10-01

    A study of genetic heterogeneity of GM1 and GM2 gangliosidoses was performed using a wide set of cultured fibroblast lines of patients with leukodystrophies. In addition to commonly used methods for enzyme diagnosis and for isozyme fractionating, following assays were developed for locus and allele differentiation: loading tests with 3H-GM1 and 3H-GM2, analytical chromatofocusing and activity determination of activator protein for GM2.

  1. Interference, heterogeneity and disease gene mapping

    SciTech Connect

    Keats, B.

    1996-12-31

    The Human Genome Project has had a major impact on genetic research over the past five years. The number of mapped genes is now over 3,000 compared with approximately 1,600 in 1989 and only about 260 ten years before that. The realization that extensive variation could be detected in anonymous DNA segments greatly enhanced the potential for mapping by linkage analysis. Previously, linkage studies had depended on polymorphisms that could be detected in red blood cell antigens, proteins (revealed by electrophoresis and isoelectric focusing), and cytogenetic heteromorphisms. The identification of thousands of polymorphic DNA markers throughout the human genome has led to the construction of high density genetic linkage maps. These maps provide the data necessary to test hypotheses concerning differences in recombination rates and levels of interference. They are also important for disease gene mapping because the existence of these genes must be inferred from the phenotype. Showing linkage of a disease gene to a DNA marker is the first step towards isolating the disease gene, determining its protein product, and developing effective therapies. However, interpretation of results is not always straightforward. Factors such as etiological heterogeneity and undetected irregular segregation can lead to confusing linkage results and incorrect conclusions about the locations of disease genes. This paper will discuss these phenomena and present examples that illustrate the problems, as well as approaches to dealing with them. 23 refs., 3 figs., 3 tabs.

  2. Cellular heterogeneity and molecular evolution in cancer.

    PubMed

    Almendro, Vanessa; Marusyk, Andriy; Polyak, Kornelia

    2013-01-24

    Intratumor heterogeneity represents a major obstacle to effective cancer treatment and personalized medicine. However, investigators are now elucidating intratumor heterogeneity at the single-cell level due to improvements in technologies. Better understanding of the composition of tumors, and monitoring changes in cell populations during disease progression and treatment, will improve cancer diagnosis and therapeutic design. Measurements of intratumor heterogeneity may also be used as biomarkers to predict the risk of progression and therapeutic resistance. We summarize important considerations related to intratumor heterogeneity during tumor evolution. We also discuss experimental approaches that are commonly used to infer intratumor heterogeneity and describe how these methodologies can be translated into clinical practice.

  3. Modeling heterogeneous responsiveness of intrinsic apoptosis pathway

    PubMed Central

    2013-01-01

    molecular numbers. Furthermore, the extrinsic noise represented by random variations of two key apoptotic proteins, namely Cytochrome C and inhibitor of apoptosis proteins (IAP), is modeled separately or in combination with intrinsic noise. The resultant stochasticity in the timing of intrinsic apoptosis response shows that the fluctuating protein variations can induce cell-to-cell stochastic variability at a quantitative level agreeing with experiments. Finally, simulations illustrate that the mean abundance of fluctuating IAP protein is positively correlated with the degree of cellular stochasticity of the intrinsic apoptosis pathway. Conclusions Our theoretical and computational study shows that the pronounced non-genetic heterogeneity in intrinsic apoptosis responses among individual cells plausibly arises from extrinsic rather than intrinsic origin of fluctuations. In addition, it predicts that the IAP protein could serve as a potential therapeutic target for suppression of the cell-to-cell variation in the intrinsic apoptosis responsiveness. PMID:23875784

  4. Hypomorphic mutation in hnRNP U results in post-implantation lethality.

    PubMed

    Roshon, Michael J; Ruley, H Earl

    2005-04-01

    The present study characterized an embryonic lethal mutation induced by insertion of the U3Neo gene trap retrovirus into an intron of the gene encoding heterogeneous ribonuclear protein U (Hnrnpu), which maps to the distal arm of mouse chromosome 1. Murine hnRNP U was found to be identical to the human protein at all but one of 341 amino acid residues. Embryos homozygous for the provirus showed obvious abnormalities after 6.5 days of development (E6.5) and were resorbed by E10.5. Expression of the inserted neomycin-resistance gene involved alternative splicing to a cryptic 3' splice site located in the neomycin resistance gene resulting in a hypomorphic mutation. Homozygous mutant cell lines isolated from preimplantation blastocysts expressed hnRNP U transcripts at levels 2 to 5 times lower than wild-type cells, suggesting that nearly wild-type levels of hnRNP U are required for embryonic development.

  5. Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway

    PubMed Central

    Iwamoto, Kazunari; Shindo, Yuki; Takahashi, Koichi

    2016-01-01

    Cellular heterogeneity, which plays an essential role in biological phenomena, such as drug resistance and migration, is considered to arise from intrinsic (i.e., reaction kinetics) and extrinsic (i.e., protein variability) noise in the cell. However, the mechanistic effects of these types of noise to determine the heterogeneity of signal responses have not been elucidated. Here, we report that the output of epidermal growth factor (EGF) signaling activity is modulated by cellular noise, particularly by extrinsic noise of particular signaling components in the pathway. We developed a mathematical model of the EGF signaling pathway incorporating regulation between extracellular signal-regulated kinase (ERK) and nuclear pore complex (NPC), which is necessary for switch-like activation of the nuclear ERK response. As the threshold of switch-like behavior is more sensitive to perturbations than the graded response, the effect of biological noise is potentially critical for cell fate decision. Our simulation analysis indicated that extrinsic noise, but not intrinsic noise, contributes to cell-to-cell heterogeneity of nuclear ERK. In addition, we accurately estimated variations in abundance of the signal proteins between individual cells by direct comparison of experimental data with simulation results using Apparent Measurement Error (AME). AME was constant regardless of whether the protein levels varied in a correlated manner, while covariation among proteins influenced cell-to-cell heterogeneity of nuclear ERK, suppressing the variation. Simulations using the estimated protein abundances showed that each protein species has different effects on cell-to-cell variation in the nuclear ERK response. In particular, variability of EGF receptor, Ras, Raf, and MEK strongly influenced cellular heterogeneity, while others did not. Overall, our results indicated that cellular heterogeneity in response to EGF is strongly driven by extrinsic noise, and that such heterogeneity

  6. Cognitive heterogeneity in Williams syndrome.

    PubMed

    Porter, Melanie A; Coltheart, Max

    2005-01-01

    This study used the Woodcock-Johnson Tests of Cognitive Ability-Revised to investigate a wide range of cognitive abilities in people with Williams syndrome (WS). It involved a comparatively large sample of 31 people with WS, but took a case-series approach. The study addressed the widespread claims of a characteristic "WS cognitive profile" by looking for heterogeneity rather than homogeneity. People with WS showed a variety of preserved (significantly above mental age [MA]), expected (at MA), and significantly impaired (significantly below MA) levels of functioning. Such results provide clear evidence for heterogeneity in cognitive functions within WS. We found the most homogeneity on a test of phonological processing and a test of phonological short-term memory, with half of the WS sample performing at MA levels on these tests. Interestingly, no WS individual showed a weakness on a test of nonverbal reasoning, and only one WS individual showed a weakness on a test of verbal comprehension. In addition, we found that strengths on analysis-synthesis and verbal analogies occurred only for WS individuals with an MA less than 5.5 years (our sample median MA); people with an MA greater than 5.5 years performed at MA level on these 2 tests. Results also provided preliminary evidence for distinct subgroups of WS people based on their cognitive strengths and weaknesses on a broad range of cognitive functions. On the basis of the findings, caution should be made in declaring a single cognitive profile that is characteristic of all individuals with WS. Just as there is heterogeneity in genetic and physical anomalies within WS, not all WS individuals share the same cognitive strengths and weaknesses. Also, not all WS individuals show the profile of a strength in verbal abilities and a weakness in spatial functions.

  7. Heterogeneous photocatalysts in organic synthesis

    NASA Astrophysics Data System (ADS)

    Cherevatskaya, M.; König, B.

    2014-03-01

    The review deals with the application of inorganic semiconductors in organic synthesis. Although the majority of reported reactions still aim at the photocatalytic decomposition of organic compounds, the number of examples in synthetic applications is growing. The principal mechanisms of heterogeneous semiconductor photocatalysis are considered and examples illustrating the use of inorganic semiconductors in organic synthesis are given. The discussion is arranged according to the required excitation wavelength (UV or visible light) and to the new bond that is formed (carbon-carbon or carbon-heteroatom bond). The bibliography includes 47 references.

  8. Interregional equilibrium with heterogeneous labor.

    PubMed

    Michel, P; Perrot, A; Thisse J-f

    1996-02-01

    "The impact of labor migration on interregional equilibrium is studied when workers are heterogeneous in productivity and regional mobility. The skilled respond to market disequilibrium by moving into the most attractive region. The unskilled are immobile in the short-run and move with the skilled in the long-run. Both regions have a neoclassical production function affected by an externality depending on the number of skilled. Workers move according to the utility differential when regional amenities vary with population or according to the wage differential. The equilibrium pattern depends on the unskilled's mobility and on migration incentives. Typically, regional imbalance characterizes the equilibrium which is often suboptimal."

  9. A Heterogeneous Medium Analytical Benchmark

    SciTech Connect

    Ganapol, B.D.

    1999-09-27

    A benchmark, called benchmark BLUE, has been developed for one-group neutral particle (neutron or photon) transport in a one-dimensional sub-critical heterogeneous plane parallel medium with surface illumination. General anisotropic scattering is accommodated through the Green's Function Method (GFM). Numerical Fourier transform inversion is used to generate the required Green's functions which are kernels to coupled integral equations that give the exiting angular fluxes. The interior scalar flux is then obtained through quadrature. A compound iterative procedure for quadrature order and slab surface source convergence provides highly accurate benchmark qualities (4- to 5- places of accuracy) results.

  10. Stress relaxation in heterogeneous polymers

    NASA Astrophysics Data System (ADS)

    Witten, T. A.

    1992-05-01

    When heterogeneous polymers such as diblock copolymers form a microdomain phase, an imposed strain gives rise to stress from two sources, and several mechanisms of stress relaxation. The release of stress by disentanglement is strongly influenced by the effective confinement of the junction points to the domain boundaries and by the stretching of the chains. Using accepted notions of entangled chain kinetics, it is argued that the relaxation time for sliding stress is exponential in the chainlength to the 7/9 power. A method for calculating the frequency-dependent dynamic modulus is sketched. Despite the slow relaxation implied by these mechanisms, it appears possible to create domains of high energy.

  11. Shock Initiation of Heterogeneous Explosives

    SciTech Connect

    Reaugh, J E

    2004-05-10

    The fundamental picture that shock initiation in heterogeneous explosives is caused by the linking of hot spots formed at inhomogeneities was put forward by several researchers in the 1950's and 1960's, and more recently. Our work uses the computer hardware and software developed in the Advanced Simulation and Computing (ASC) program of the U.S. Department of Energy to explicitly include heterogeneities at the scale of the explosive grains and to calculate the consequences of realistic although approximate models of explosive behavior. Our simulations are performed with ALE-3D, a three-dimensional, elastic-plastic-hydrodynamic Arbitrary Lagrange-Euler finite-difference program, which includes chemical kinetics and heat transfer, and which is under development at this laboratory. We developed the parameter values for a reactive-flow model to describe the non-ideal detonation behavior of an HMX-based explosive from the results of grain-scale simulations. In doing so, we reduced the number of free parameters that are inferred from comparison with experiment to a single one - the characteristic defect dimension. We also performed simulations of the run to detonation in small volumes of explosive. These simulations illustrate the development of the reaction zone and the acceleration of the shock front as the flame fronts start from hot spots, grow, and interact behind the shock front. In this way, our grain-scale simulations can also connect to continuum experiments directly.

  12. Simulating Heterogeneous Tumor Cell Populations

    PubMed Central

    Bar-Sagi, Dafna; Mishra, Bud

    2016-01-01

    Certain tumor phenomena, like metabolic heterogeneity and local stable regions of chronic hypoxia, signify a tumor’s resistance to therapy. Although recent research has shed light on the intracellular mechanisms of cancer metabolic reprogramming, little is known about how tumors become metabolically heterogeneous or chronically hypoxic, namely the initial conditions and spatiotemporal dynamics that drive these cell population conditions. To study these aspects, we developed a minimal, spatially-resolved simulation framework for modeling tissue-scale mixed populations of cells based on diffusible particles the cells consume and release, the concentrations of which determine their behavior in arbitrarily complex ways, and on stochastic reproduction. We simulate cell populations that self-sort to facilitate metabolic symbiosis, that grow according to tumor-stroma signaling patterns, and that give rise to stable local regions of chronic hypoxia near blood vessels. We raise two novel questions in the context of these results: (1) How will two metabolically symbiotic cell subpopulations self-sort in the presence of glucose, oxygen, and lactate gradients? We observe a robust pattern of alternating striations. (2) What is the proper time scale to observe stable local regions of chronic hypoxia? We observe the stability is a function of the balance of three factors related to O2—diffusion rate, local vessel release rate, and viable and hypoxic tumor cell consumption rate. We anticipate our simulation framework will help researchers design better experiments and generate novel hypotheses to better understand dynamic, emergent whole-tumor behavior. PMID:28030620

  13. Heterogeneous Integration of Compound Semiconductors

    NASA Astrophysics Data System (ADS)

    Moutanabbir, Oussama; Gösele, Ulrich

    2010-08-01

    The ability to tailor compound semiconductors and to integrate them onto foreign substrates can lead to superior or novel functionalities with a potential impact on various areas in electronics, optoelectronics, spintronics, biosensing, and photovoltaics. This review provides a brief description of different approaches to achieve this heterogeneous integration, with an emphasis on the ion-cut process, also known commercially as the Smart-Cut™ process. This process combines semiconductor wafer bonding and undercutting using defect engineering by light ion implantation. Bulk-quality heterostructures frequently unattainable by direct epitaxial growth can be produced, provided that a list of technical criteria is fulfilled, thus offering an additional degree of freedom in the design and fabrication of heterogeneous and flexible devices. Ion cutting is a generic process that can be employed to split and transfer fine monocrystalline layers from various crystals. Materials and engineering issues as well as our current understanding of the underlying physics involved in its application to cleaving thin layers from freestanding GaN, InP, and GaAs wafers are presented.

  14. Socially Aware Heterogeneous Wireless Networks

    PubMed Central

    Kosmides, Pavlos; Adamopoulou, Evgenia; Demestichas, Konstantinos; Theologou, Michael; Anagnostou, Miltiades; Rouskas, Angelos

    2015-01-01

    The development of smart cities has been the epicentre of many researchers’ efforts during the past decade. One of the key requirements for smart city networks is mobility and this is the reason stable, reliable and high-quality wireless communications are needed in order to connect people and devices. Most research efforts so far, have used different kinds of wireless and sensor networks, making interoperability rather difficult to accomplish in smart cities. One common solution proposed in the recent literature is the use of software defined networks (SDNs), in order to enhance interoperability among the various heterogeneous wireless networks. In addition, SDNs can take advantage of the data retrieved from available sensors and use them as part of the intelligent decision making process contacted during the resource allocation procedure. In this paper, we propose an architecture combining heterogeneous wireless networks with social networks using SDNs. Specifically, we exploit the information retrieved from location based social networks regarding users’ locations and we attempt to predict areas that will be crowded by using specially-designed machine learning techniques. By recognizing possible crowded areas, we can provide mobile operators with recommendations about areas requiring datacell activation or deactivation. PMID:26110402

  15. Groundwater pumping by heterogeneous users

    NASA Astrophysics Data System (ADS)

    Saak, Alexander E.; Peterson, Jeffrey M.

    2012-08-01

    Farm size is a significant determinant of both groundwater-irrigated farm acreage and groundwater-irrigation-application rates per unit land area. This paper analyzes the patterns of groundwater exploitation when resource users in the area overlying a common aquifer are heterogeneous. In the presence of user heterogeneity, the common resource problem consists of inefficient dynamic and spatial allocation of groundwater because it impacts income distribution not only across periods but also across farmers. Under competitive allocation, smaller farmers pump groundwater faster if farmers have a constant marginal periodic utility of income. However, it is possible that larger farmers pump faster if the Arrow-Pratt coefficient of relative risk-aversion is sufficiently decreasing in income. A greater farm-size inequality may either moderate or amplify income inequality among farmers. Its effect on welfare depends on the curvature properties of the agricultural output function and the farmer utility of income. Also, it is shown that a flat-rate quota policy that limits the quantity of groundwater extraction per unit land area may have unintended consequences for the income distribution among farmers.

  16. Heterogeneous Transmutation Sodium Fast Reactor

    SciTech Connect

    S. E. Bays

    2007-09-01

    The threshold-fission (fertile) nature of Am-241 is used to destroy this minor actinide by capitalizing upon neutron capture instead of fission within a sodium fast reactor. This neutron-capture and its subsequent decay chain leads to the breeding of even neutron number plutonium isotopes. A slightly moderated target design is proposed for breeding plutonium in an axial blanket located above the active “fast reactor” driver fuel region. A parametric study on the core height and fuel pin diameter-to-pitch ratio is used to explore the reactor and fuel cycle aspects of this design. This study resulted in both non-flattened and flattened core geometries. Both of these designs demonstrated a high capacity for removing americium from the fuel cycle. A reactivity coefficient analysis revealed that this heterogeneous design will have comparable safety aspects to a homogeneous reactor of comparable size. A mass balance analysis revealed that the heterogeneous design may reduce the number of fast reactors needed to close the current once-through light water reactor fuel cycle.

  17. Dispersivity in heterogeneous permeable media

    SciTech Connect

    Chesnut, D.A.

    1994-01-01

    When one fluid displaces another through a one-dimensional porous medium, the composition changes from pure displacing fluid at the inlet to pure displaced fluid some distance downstream. The distance over which an arbitrary percentage of this change occurs is defined as the mixing zone length, which increases with increasing average distance traveled by the displacement front. For continuous injection, the mixing zone size can be determined from a breakthrough curve as the time required for the effluent displacing fluid concentration to change from, say, 10% to 90%. In classical dispersion theory, the mixing zone grows in proportion to the square root of the mean distance traveled, or, equivalently, to the square root of the mean breakthrough time. In a multi-dimensional heterogeneous medium, especially at field scales, the size of the mixing zone grows almost linearly with mean distance or travel time. If an observed breakthrough curve is forced to fit the, clinical theory, the resulting effective dispersivity, instead of being constant, also increases almost linearly with the spatial or temporal scale of the problem. This occurs because the heterogeneity in flow properties creates a corresponding velocity distribution along the different flow pathways from the inlet to the outlet of the system. Mixing occurs mostly at the outlet, or wherever the fluid is sampled, rather than within the medium. In this paper, we consider the effects. of this behavior on radionuclide or other contaminant migration.

  18. Thermal properties of heterogeneous grains

    NASA Technical Reports Server (NTRS)

    Lien, David J.

    1988-01-01

    Cometary dust is not spherical nor homogeneous, yet these are the assumptions used to model its thermal, optical, and dynamical properties. To better understand the effects of heterogeneity on the thermal and optical properties of dust grains, the effective dielectric constant for an admixture of magnetite and a silicate were calculated using two different effective medium theories: the Maxwell-Garnett theory and the Bruggeman theory. In concept, the MG theory describes the effective dielectric constant of a matrix material into which is embedded a large number of very small inclusions of a second material. The Bruggeman theory describes the dielectric constant of a well mixed aggregate of two or more types of materials. Both theories assume that the individual particles are much smaller than the wavelength of the incident radiation. The refractivity for a heterogeneous grain using the MG theory is very similar to the refractivity of the matrix material, even for large volume fractions of the inclusion. The equilibrium grain temperature for spherical particles sized from .001 to 100 microns in radius at 1 astronomical unit from the sun was calculated. Further explanation is given.

  19. Proteomics analysis of heterogeneous flagella in brown algae (stramenopiles).

    PubMed

    Fu, Gang; Nagasato, Chikako; Oka, Seiko; Cock, J Mark; Motomura, Taizo

    2014-09-01

    Flagella are conserved organelles among eukaryotes and they are composed of many proteins, which are necessary for flagellar assembly, maintenance and function. Stramenopiles, which include brown algae, diatoms and oomycetes, possess two laterally inserted flagella. The anterior flagellum (AF) extends forward and bears tripartite mastigonemes, whilst the smooth posterior flagellum (PF) often has a paraflagellar body structure. These heterogeneous flagella have served as crucial structures in algal studies especially from a viewpoint of phylogeny. However, the protein compositions of the flagella are still largely unknown. Here we report a LC-MS/MS based proteomics analysis of brown algal flagella. In total, 495 flagellar proteins were identified. Functional annotation of the proteome data revealed that brown algal flagellar proteins were associated with cell motility, signal transduction and various metabolic activities. We separately isolated AF and PF and analyzed their protein compositions. This analysis led to the identification of several AF- and PF-specific proteins. Among the PF-specific proteins, we found a candidate novel blue light receptor protein involved in phototaxis, and named it HELMCHROME because of the steering function of PF. Immunological analysis revealed that this protein was localized along the whole length of the PF and concentrated in the paraflagellar body.

  20. Marked heterogeneity of HER2/NEU gene amplification in endometrial serous carcinoma.

    PubMed

    Buza, Natalia; Hui, Pei

    2013-12-01

    Significant heterogeneity of HER2 protein expression has been recently observed in HER2 positive endometrial serous carcinomas. Tumor cells with HER2 overexpression and/or gene amplification in a heterogeneous tumor may represent a biologically more aggressive subclone that is clinically relevant to prognosis and potential targeted therapy. To correlate with HER2 protein heterogeneity, we investigated the heterogeneity of HER2/NEU gene amplification in endometrial serous carcinoma. A total of 17 endometrial serous carcinomas with heterogeneous HER2 protein expression were selected for the study, including nine cases with a 3+ and eight cases with a 2+ immunohistochemical score. Initial reflex HER2 FISH was available for seven of the eight 2+ cases, five of which showed HER2/NEU gene amplification. All 17 cases underwent repeat FISH targeting larger tumor tissue areas. Ten cases (72%) displayed striking heterogeneity of HER2/NEU gene copy number in the form of cluster amplification. Diffuse HER2 amplification was observed in four cases, no amplification was seen in three tumors. In cases with cluster amplification, HER2 protein overexpression by immunohistochemistry closely correlated at the cellular level with HER2/NEU gene amplification. In conclusion, the significant percentage of cases with heterogeneous HER2/NEU gene amplification indicates that the existing HER2 testing guidelines designed for breast cancer may not be applicable to endometrial serous carcinoma. Clinical testing on multiple different tumor samples or large tumor tissue sections is recommended for both immunohistochemistry and FISH assessment of HER2 status. Direct comparison with the HER2 immunostaining pattern may be helpful in detecting HER2 amplified areas in a heterogeneous tumor.

  1. Age-dependent heterogeneity of familiar hypertrophic cardiomyopathy phenotype: a role of cardiovascular magnetic resonance.

    PubMed

    Glaveckaitė, Sigita; Rudys, Alfredas; Mikštienė, Violeta; Valevičienė, Nomeda; Palionis, Darius; Laucevičius, Aleksandras

    2013-01-01

    In this case report, we present familiar hypertrophic cardiomyopathy with age-dependent heterogeneity of the disease phenotype among the members of one family who carry the same mutation of the myosin-binding protein C gene. Phenotypic heterogeneity is common in patients with familial forms of hypertrophic cardiomyopathy, both in clinical expression and outcome. Compared with other noninvasive cardiac imaging modalities, cardiovascular magnetic resonance provides an opportunity to more accurately characterize the varying phenotypic presentations of hypertrophic cardiomyopathy.

  2. Unlocking Proteomic Heterogeneity in Complex Diseases through Visual Analytics

    PubMed Central

    Bhavnani, Suresh K.; Dang, Bryant; Bellala, Gowtham; Divekar, Rohit; Visweswaran, Shyam; Brasier, Allan; Kurosky, Alex

    2015-01-01

    Despite years of preclinical development, biological interventions designed to treat complex diseases like asthma often fail in phase III clinical trials. These failures suggest that current methods to analyze biomedical data might be missing critical aspects of biological complexity such as the assumption that cases and controls come from homogeneous distributions. Here we discuss why and how methods from the rapidly evolving field of visual analytics can help translational teams (consisting of biologists, clinicians, and bioinformaticians) to address the challenge of modeling and inferring heterogeneity in the proteomic and phenotypic profiles of patients with complex diseases. Because a primary goal of visual analytics is to amplify the cognitive capacities of humans for detecting patterns in complex data, we begin with an overview of the cognitive foundations for the field of visual analytics. Next, we organize the primary ways in which a specific form of visual analytics called networks have been used to model and infer biological mechanisms, which help to identify the properties of networks that are particularly useful for the discovery and analysis of proteomic heterogeneity in complex diseases. We describe one such approach called subject-protein networks, and demonstrate its application on two proteomic datasets. This demonstration provides insights to help translational teams overcome theoretical, practical, and pedagogical hurdles for the widespread use of subject-protein networks for analyzing molecular heterogeneities, with the translational goal of designing biomarker-based clinical trials, and accelerating the development of personalized approaches to medicine. PMID:25684269

  3. Heterogeneity of monoclonal antibodies revealed by charge-sensitive methods.

    PubMed

    Vlasak, J; Ionescu, R

    2008-12-01

    The expanding field of monoclonal antibody-based pharmaceuticals has triggered increased interest in analytical characterization of these large proteins and in understanding of their heterogeneity and degradation pathways. As a result, a large number of enzymatic modifications as well as chemical and physical degradations have been reported in monoclonal antibodies in recent years. Most heterogeneity is related to changes in the surface charge of the antibody, either directly, as a change in the number of charged residues, or indirectly as a chemical or physical alteration that changes surface-charge distribution. This review presents an overview of the sources of charge-related heterogeneity in monoclonal antibodies and the methods used for their detection. A detailed section is dedicated to deamidation of asparagine and isomerization of aspartic acid residues, two ubiquitous degradation pathways detected in antibodies and other proteins as well. Finally, kinetic modeling of the accumulation of antibody variants is presented as a tool to determine the expected fraction of molecules that have undergone one or more degradation reactions.

  4. Heterogeneity of Aspergillus niger Microcolonies in Liquid Shaken Cultures▿ †

    PubMed Central

    de Bekker, Charissa; van Veluw, G. Jerre; Vinck, Arman; Wiebenga, L. Ad; Wösten, Han A. B.

    2011-01-01

    The fungus Aspergillus niger forms (sub)millimeter microcolonies within a liquid shaken culture. Here, we show that such microcolonies are heterogeneous with respect to size and gene expression. Microcolonies of strains expressing green fluorescent protein (GFP) from the promoter of the glucoamlyase gene glaA or the ferulic acid esterase gene faeA were sorted on the basis of diameter and fluorescence using the Complex Object Parametric Analyzer and Sorter (COPAS) technology. Statistical analysis revealed that the liquid shaken culture consisted of two populations of microcolonies that differ by 90 μm in diameter. The population of small microcolonies of strains expressing GFP from the glaA or faeA promoter comprised 39% and 25% of the culture, respectively. Two populations of microcolonies could also be distinguished when the expression of GFP in these strains was analyzed. The population expressing a low level of GFP consisted of 68% and 44% of the culture, respectively. We also show that mRNA accumulation is heterogeneous within microcolonies of A. niger. Central and peripheral parts of the mycelium were isolated with laser microdissection and pressure catapulting (LMPC), and RNA from these samples was used for quantitative PCR analysis. This analysis showed that the RNA content per hypha was about 45 times higher at the periphery than in the center of the microcolony. Our data imply that the protein production of A. niger can be improved in industrial fermentations by reducing the heterogeneity within the culture. PMID:21169437

  5. Data Integration for Heterogenous Datasets

    PubMed Central

    2014-01-01

    Abstract More and more, the needs of data analysts are requiring the use of data outside the control of their own organizations. The increasing amount of data available on the Web, the new technologies for linking data across datasets, and the increasing need to integrate structured and unstructured data are all driving this trend. In this article, we provide a technical overview of the emerging “broad data” area, in which the variety of heterogeneous data being used, rather than the scale of the data being analyzed, is the limiting factor in data analysis efforts. The article explores some of the emerging themes in data discovery, data integration, linked data, and the combination of structured and unstructured data. PMID:25553272

  6. Heterogeneous fuel for hybrid rocket

    NASA Technical Reports Server (NTRS)

    Stickler, David B. (Inventor)

    1996-01-01

    Heterogeneous fuel compositions suitable for use in hybrid rocket engines and solid-fuel ramjet engines, The compositions include mixtures of a continuous phase, which forms a solid matrix, and a dispersed phase permanently distributed therein. The dispersed phase or the matrix vaporizes (or melts) and disperses into the gas flow much more rapidly than the other, creating depressions, voids and bumps within and on the surface of the remaining bulk material that continuously roughen its surface, This effect substantially enhances heat transfer from the combusting gas flow to the fuel surface, producing a correspondingly high burning rate, The dispersed phase may include solid particles, entrained liquid droplets, or gas-phase voids having dimensions roughly similar to the displacement scale height of the gas-flow boundary layer generated during combustion.

  7. HETEROGENEOUS REBURNING BY MIXED FUELS

    SciTech Connect

    Wei-Yin Chen; Benson B. Gathitu

    2005-01-14

    Recent studies of heterogeneous reburning, i.e., reburning involving a coal-derived char, have elucidated its variables, kinetics and mechanisms that are valuable to the development of a highly efficient reburning process. Young lignite chars contain catalysts that not only reduce NO, but they also reduce HCN that is an important intermediate that recycles to NO in the burnout zone. Gaseous CO scavenges the surface oxides that are formed during NO reduction, regenerating the active sites on the char surface. Based on this mechanistic information, cost-effective mixed fuels containing these multiple features has been designed and tested in a simulated reburning apparatus. Remarkably high reduction of NO and HCN has been observed and it is anticipated that mixed fuel will remove 85% of NO in a three-stage reburning process.

  8. Genetic heterogeneity of hepatocellular carcinoma

    SciTech Connect

    Unsal, H.; Isselbacher, K.J. ); Yakicier, C.; Marcais, C.; Ozturk, M. ); Kew, M. ); Volkmann, M. ); Zentgraf, H. )

    1994-01-18

    The authors studied 80 hepatocellular carcinomas from three continents for p53 gene (TP53) mutations and hepatitis B virus (HBV) sequences. p53 mutations were frequent in tumors from Mozambique but not in tumors from South Africa, China, and Germany. Independent of geographic origin, most tumors were positive for HBV sequences. X gene coding sequences of HBV were detected in 78% of tumors, whereas viral sequences in the surface antigen- and core antigen-encoding regions were present in less than 35% of tumors. These observations indicate that hepatocellular carcinomas are genetically heterogeneous. Mozambican-types of hepatocellular carcinomas are characterized by a high incidence of p53 mutations related to aflatoxins. In other tumors, the rarity of p53 mutations combined with the frequent presence of viral X gene coding sequences suggests a possible interference of HBV with the wild-type p53 function.

  9. Surface science and heterogeneous catalysis

    SciTech Connect

    Somorjai, G.A.

    1980-05-01

    The catalytic reactions studied include hydrocarbon conversion over platinum, the transition metal-catalyzed hydrogenation of carbon monoxide, and the photocatalyzed dissociation of water over oxide surfaces. The method of combined surface science and catalytic studies is similar to those used in synthetic organic chemistry. The single-crystal models for the working catalyst are compared with real catalysts by comparing the rates of cyclopropane ring opening on platinum and the hydrogenation of carbon monoxide on rhodium single crystal surface with those on practical commercial catalyst systems. Excellent agreement was obtained for these reactions. This document reviews what was learned about heterogeneous catalysis from these surface science approaches over the past 15 years and present models of the active catalyst surface.

  10. Heterogeneous Reburning By Mixed Fuels

    SciTech Connect

    Anderson Hall

    2009-03-31

    Recent studies of heterogeneous reburning, i.e., reburning involving a coal-derived char, have elucidated its variables, kinetics and mechanisms that are valuable to the development of a highly efficient reburning process. Young lignite chars contain catalysts that not only reduce NO, but they also reduce HCN that is an important intermediate that recycles to NO in the burnout zone. Gaseous CO scavenges the surface oxides that are formed during NO reduction, regenerating the active sites on the char surface. Based on this mechanistic information, cost-effective mixed fuels containing these multiple features has been designed and tested in a simulated reburning apparatus. Remarkably high reduction of NO and HCN has been observed and it is anticipated that mixed fuel will remove 85% of NO in a three-stage reburning process.

  11. (90377) Sedna: Heterogeneous Surface Composition

    NASA Astrophysics Data System (ADS)

    Dalle Ore, Cristina M.; Barucci, M.; Alvarez-Candal, A.; de Bergh, C.; Merlin, F.; Dumas, C.; Cruikshank, D. P.

    2010-10-01

    The peculiar TNO (90377) Sedna is one of the most remote solar system objects accessible to investigations (current heliocentric distance 88AU). This dwarf planet is one of the reddest objects following the taxonomic group RR. To better constrain its surface composition and to investigate the possible heterogeneity of the surface of Sedna, several observations have been carried out at ESO-VLT with the powerful spectrometer SINFONI, which observes the H and K bands simultaneously. Even if Sedna, given its faintness, was at the limit of observations, the new analyzed spectra (obtained in 2005, 2007, and 2008) show a different behavior, particularly in the K band. Spectral modeling using the Shkuratov radiative transfer method has been performed using the various sets of data, including visible and Spitzer data, for a large wavelength range 0.4-4.5 microns, and the albedo value (0.21) estimated by Stansberry et al. (2008). We find that the surface of Sedna is not completely homogeneous. The visible and near-IR spectra can be modeled with organic materials (triton and titan tholin), serpentine, and H2O ice in fairly significant amounts, and CH4, N2 and C2H6 in varying trace amounts. One of the spectra, showing a different signature in the K-band, observed as part of the October 2005 group of data, is best modeled with CH3OH in place of CH4, with reduced amounts of serpentine and with the addition of olivine. The compositional surface heterogeneity can give clues to the origin and past history of this peculiar distant object.

  12. Constructing module maps for integrated analysis of heterogeneous biological networks

    PubMed Central

    Amar, David; Shamir, Ron

    2014-01-01

    Improved methods for integrated analysis of heterogeneous large-scale omic data are direly needed. Here, we take a network-based approach to this challenge. Given two networks, representing different types of gene interactions, we construct a map of linked modules, where modules are genes strongly connected in the first network and links represent strong inter-module connections in the second. We develop novel algorithms that considerably outperform prior art on simulated and real data from three distinct domains. First, by analyzing protein–protein interactions and negative genetic interactions in yeast, we discover epistatic relations among protein complexes. Second, we analyze protein–protein interactions and DNA damage-specific positive genetic interactions in yeast and reveal functional rewiring among protein complexes, suggesting novel mechanisms of DNA damage response. Finally, using transcriptomes of non–small-cell lung cancer patients, we analyze networks of global co-expression and disease-dependent differential co-expression and identify a sharp drop in correlation between two modules of immune activation processes, with possible microRNA control. Our study demonstrates that module maps are a powerful tool for deeper analysis of heterogeneous high-throughput omic data. PMID:24497192

  13. Nonlinear Poisson Equation for Heterogeneous Media

    PubMed Central

    Hu, Langhua; Wei, Guo-Wei

    2012-01-01

    The Poisson equation is a widely accepted model for electrostatic analysis. However, the Poisson equation is derived based on electric polarizations in a linear, isotropic, and homogeneous dielectric medium. This article introduces a nonlinear Poisson equation to take into consideration of hyperpolarization effects due to intensive charges and possible nonlinear, anisotropic, and heterogeneous media. Variational principle is utilized to derive the nonlinear Poisson model from an electrostatic energy functional. To apply the proposed nonlinear Poisson equation for the solvation analysis, we also construct a nonpolar solvation energy functional based on the nonlinear Poisson equation by using the geometric measure theory. At a fixed temperature, the proposed nonlinear Poisson theory is extensively validated by the electrostatic analysis of the Kirkwood model and a set of 20 proteins, and the solvation analysis of a set of 17 small molecules whose experimental measurements are also available for a comparison. Moreover, the nonlinear Poisson equation is further applied to the solvation analysis of 21 compounds at different temperatures. Numerical results are compared to theoretical prediction, experimental measurements, and those obtained from other theoretical methods in the literature. A good agreement between our results and experimental data as well as theoretical results suggests that the proposed nonlinear Poisson model is a potentially useful model for electrostatic analysis involving hyperpolarization effects. PMID:22947937

  14. Nonlinear Poisson equation for heterogeneous media.

    PubMed

    Hu, Langhua; Wei, Guo-Wei

    2012-08-22

    The Poisson equation is a widely accepted model for electrostatic analysis. However, the Poisson equation is derived based on electric polarizations in a linear, isotropic, and homogeneous dielectric medium. This article introduces a nonlinear Poisson equation to take into consideration of hyperpolarization effects due to intensive charges and possible nonlinear, anisotropic, and heterogeneous media. Variational principle is utilized to derive the nonlinear Poisson model from an electrostatic energy functional. To apply the proposed nonlinear Poisson equation for the solvation analysis, we also construct a nonpolar solvation energy functional based on the nonlinear Poisson equation by using the geometric measure theory. At a fixed temperature, the proposed nonlinear Poisson theory is extensively validated by the electrostatic analysis of the Kirkwood model and a set of 20 proteins, and the solvation analysis of a set of 17 small molecules whose experimental measurements are also available for a comparison. Moreover, the nonlinear Poisson equation is further applied to the solvation analysis of 21 compounds at different temperatures. Numerical results are compared to theoretical prediction, experimental measurements, and those obtained from other theoretical methods in the literature. A good agreement between our results and experimental data as well as theoretical results suggests that the proposed nonlinear Poisson model is a potentially useful model for electrostatic analysis involving hyperpolarization effects.

  15. Heterogeneity in pepper isolates of cucumber mosaic virus

    USGS Publications Warehouse

    Rodriguez-Alvarado, G.; Kurath, G.; Dodds, J.A.

    1995-01-01

    Twenty-four cucumber mosaic cucumovirus (CMV) field isolates from pepper crops in Cali-fornia were characterized and compared by nucleic acid hybridization subgrouping, virion electrophoresis, and biological effects in several hosts. Isolates, belonging to subgroup I or subgroup II, were found that induced severe symptoms in mechanically inoculated bell pep-pers. Only two isolates, both from subgroup II, were mild. A group of 19 isolates collected from a single field were all in subgroup II and appeared identical by virion electrophoresis, but they exhibited varying degrees of symptom severity in peppers. As a more detailed indicator of heterogeneity, these 19 isolates were examined by RNase protection assays to delect sequence variation in the coat protein gene region of their genomes. The patterns of bands observed were complex and a high degree of genomic heterogeneity was detected between isolates, with no apparent correlation to symptomatology in bell pepper.

  16. Facilitated diffusion on mobile DNA: configurational traps and sequence heterogeneity.

    PubMed

    Brackley, C A; Cates, M E; Marenduzzo, D

    2012-10-19

    We present Brownian dynamics simulations of the facilitated diffusion of a protein, modeled as a sphere with a binding site on its surface, along DNA, modeled as a semiflexible polymer. We consider both the effect of DNA organization in three dimensions and of sequence heterogeneity. We find that in a network of DNA loops, which are thought to be present in bacterial DNA, the search process is very sensitive to the spatial location of the target within such loops. Therefore, specific genes might be repressed or promoted by changing the local topology of the genome. On the other hand, sequence heterogeneity creates traps which normally slow down facilitated diffusion. When suitably positioned, though, these traps can, surprisingly, render the search process much more efficient.

  17. Passive ventricular remodeling in cardiac disease: focus on heterogeneity

    PubMed Central

    Kessler, Elise L.; Boulaksil, Mohamed; van Rijen, Harold V. M.; Vos, Marc A.; van Veen, Toon A. B.

    2014-01-01

    Passive ventricular remodeling is defined by the process of molecular ventricular adaptation to different forms of cardiac pathophysiology. It includes changes in tissue architecture, such as hypertrophy, fiber disarray, alterations in cell size and fibrosis. Besides that, it also includes molecular remodeling of gap junctions, especially those composed by Connexin43 proteins (Cx43) in the ventricles that affect cell-to-cell propagation of the electrical impulse, and changes in the sodium channels that modify excitability. All those alterations appear mainly in a heterogeneous manner, creating irregular and inhomogeneous electrical and mechanical coupling throughout the heart. This can predispose to reentry arrhythmias and adds to a further deterioration into heart failure. In this review, passive ventricular remodeling is described in Hypertrophic Cardiomyopathy (HCM), Dilated Cardiomyopathy (DCM), Ischemic Cardiomyopathy (ICM), and Arrhythmogenic Cardiomyopathy (ACM), with a main focus on the heterogeneity of those alterations mentioned above. PMID:25566084

  18. Inferring Diffusion Dynamics from FCS in Heterogeneous Nuclear Environments

    PubMed Central

    Tsekouras, Konstantinos; Siegel, Amanda P.; Day, Richard N.; Pressé, Steve

    2015-01-01

    Fluorescence correlation spectroscopy (FCS) is a noninvasive technique that probes the diffusion dynamics of proteins down to single-molecule sensitivity in living cells. Critical mechanistic insight is often drawn from FCS experiments by fitting the resulting time-intensity correlation function, G(t), to known diffusion models. When simple models fail, the complex diffusion dynamics of proteins within heterogeneous cellular environments can be fit to anomalous diffusion models with adjustable anomalous exponents. Here, we take a different approach. We use the maximum entropy method to show—first using synthetic data—that a model for proteins diffusing while stochastically binding/unbinding to various affinity sites in living cells gives rise to a G(t) that could otherwise be equally well fit using anomalous diffusion models. We explain the mechanistic insight derived from our method. In particular, using real FCS data, we describe how the effects of cell crowding and binding to affinity sites manifest themselves in the behavior of G(t). Our focus is on the diffusive behavior of an engineered protein in 1) the heterochromatin region of the cell’s nucleus as well as 2) in the cell’s cytoplasm and 3) in solution. The protein consists of the basic region-leucine zipper (BZip) domain of the CCAAT/enhancer-binding protein (C/EBP) fused to fluorescent proteins. PMID:26153697

  19. Understanding the Executive Functioning Heterogeneity in Schizophrenia

    ERIC Educational Resources Information Center

    Raffard, Stephane; Bayard, Sophie

    2012-01-01

    Schizophrenia is characterized by heterogeneous brain abnormalities involving cerebral regions implied in the executive functioning. The dysexecutive syndrome is one of the most prominent and functionally cognitive features of schizophrenia. Nevertheless, it is not clear to what extend executive deficits are heterogeneous in schizophrenia…

  20. The composition of heterogeneous control laws

    NASA Technical Reports Server (NTRS)

    Kuipers, Benjamin; Astrom, Karl

    1991-01-01

    The fuzzy control literature and industrial practice provide certain nonlinear methods for combining heterogeneous control laws, but these methods have been very difficult to analyze theoretically. An alternate formulation and extension of this approach is presented that has several practical and theoretical benefits. An example of heterogeneous control is given and two alternate analysis methods are presented.

  1. Functional Heterogeneity and Senior Management Team Effectiveness

    ERIC Educational Resources Information Center

    Benoliel, Pascale; Somech, Anit

    2016-01-01

    Purpose: There has been an increasing trend toward the creation of senior management teams (SMTs) which are characterized by a high degree of functional heterogeneity. Although such teams may create better linkages to information, along with the benefits of functional heterogeneity comes the potential for conflicts that stem from the value…

  2. Understanding the Executive Functioning Heterogeneity in Schizophrenia

    ERIC Educational Resources Information Center

    Raffard, Stephane; Bayard, Sophie

    2012-01-01

    Schizophrenia is characterized by heterogeneous brain abnormalities involving cerebral regions implied in the executive functioning. The dysexecutive syndrome is one of the most prominent and functionally cognitive features of schizophrenia. Nevertheless, it is not clear to what extend executive deficits are heterogeneous in schizophrenia…

  3. Heterogeneous Factor Analysis Models: A Bayesian Approach.

    ERIC Educational Resources Information Center

    Ansari, Asim; Jedidi, Kamel; Dube, Laurette

    2002-01-01

    Developed Markov Chain Monte Carlo procedures to perform Bayesian inference, model checking, and model comparison in heterogeneous factor analysis. Tested the approach with synthetic data and data from a consumption emotion study involving 54 consumers. Results show that traditional psychometric methods cannot fully capture the heterogeneity in…

  4. Chemical and seismological constraints on mantle heterogeneity.

    PubMed

    Helffrich, George

    2002-11-15

    Recent seismological studies that use scattered waves to detect heterogeneities in the mantle reveal the presence of a small, distributed elastic heterogeneity in the lower mantle which does not appear to be thermal in nature. The characteristic size of these heterogeneities appears to be ca. 8 km, suggesting that they represent subducted recycled oceanic crust. With this stimulus, old ideas that the mantle is heterogeneous in structure, rather than stratified, are reinterpreted and a simple, end-member model for the heterogeneity structure is proposed. The volumetrically largest components in the model are recycled oceanic crust, which contains the heat-producing elements, and mantle depleted of these and other incompatible trace elements. About 10% of the mantle's mass is made up of recycled oceanic crust, which is associated with the observed small-scale seismic heterogeneity. The way this heterogeneity is distributed is in convectively stretched and thinned bodies ranging downwards in size from 8 km. With the present techniques to detect small bodies through scattering, only ca. 55% of the mantle's small-scale heterogeneities are detectable seismically.

  5. Functional Heterogeneity and Senior Management Team Effectiveness

    ERIC Educational Resources Information Center

    Benoliel, Pascale; Somech, Anit

    2016-01-01

    Purpose: There has been an increasing trend toward the creation of senior management teams (SMTs) which are characterized by a high degree of functional heterogeneity. Although such teams may create better linkages to information, along with the benefits of functional heterogeneity comes the potential for conflicts that stem from the value…

  6. Distributional Scaling in Heterogeneous Aquifers

    NASA Astrophysics Data System (ADS)

    Polsinelli, J. F.

    2015-12-01

    An investigation is undertaken into the fractal scaling properties of the piezometric head in a heterogeneous unconfined aquifer. The governing equations for the unconfined flow are derived from conservation of mass and the Darcy law. The Dupuit approximation will be used to model the dynamics. The spatially varying nature of the tendency to conduct flow (e.g. the hydraulic conductivity) is represented as a stochastic process. Experimental studies in the literature have indicated that the conductivity belongs to a class of non-stationary stochastic fields, called H-ss fields. The uncertainty in the soil parameters is imparted onto the flow variables; in groundwater investigations the potentiometric head will be a random function. The structure of the head field will be analyzed with an emphasis on the scaling properties. The scaling scheme for the modeling equations and the simulation procedure for the saturated hydraulic conductivity process will be explained, then the method will be validated through numerical experimentation using the USGS Modflow-2005 software. The results of the numerical simulations demonstrate that the head will exhibit multi-fractal scaling if the hydraulic conductivity exhibits multi-fractal scaling and the differential equations for the groundwater equation satisfy a particular set of scale invariance conditions.

  7. Spectral heterogeneity of honeybee ommatidia

    NASA Astrophysics Data System (ADS)

    Wakakuwa, Motohiro; Kurasawa, Masumi; Giurfa, Martin; Arikawa, Kentaro

    2005-10-01

    The honeybee compound eye is equipped with ultraviolet, blue, and green receptors, which form the physiological basis of a trichromatic color vision system. We studied the distribution of the spectral receptors by localizing the three mRNAs encoding the opsins of the ultraviolet-, blue- and green-absorbing visual pigments. The expression patterns of the three opsin mRNAs demonstrated that three distinct types ommatidia exist, refuting the common assumption that the ommatidia composing the bee compound eye contain identical sets of spectral receptors. We found that type I ommatidia contain one ultraviolet and one blue receptor, type II ommatidia contain two ultraviolet receptors, and type III ommatidia have two blue receptors. All the three ommatidial types contain six green receptors. The ommatidia appear to be distributed rather randomly over the retina. The ratio of type I, II, and III ommatidia was about 44:46:10. Type III ommatidia appeared to be slightly more frequent (18%) in the anterior part of the ventral region of the eye. Retinal heterogeneity and ommatidial randomness, first clearly demonstrated in butterflies, seems to be a common design principle of the eyes of insects.

  8. Clinical significance of monocyte heterogeneity.

    PubMed

    Stansfield, Brian K; Ingram, David A

    2015-01-01

    Monocytes are primitive hematopoietic cells that primarily arise from the bone marrow, circulate in the peripheral blood and give rise to differentiated macrophages. Over the past two decades, considerable attention to monocyte diversity and macrophage polarization has provided contextual clues into the role of myelomonocytic derivatives in human disease. Until recently, human monocytes were subdivided based on expression of the surface marker CD16. "Classical" monocytes express surface markers denoted as CD14(++)CD16(-) and account for greater than 70% of total monocyte count, while "non-classical" monocytes express the CD16 antigen with low CD14 expression (CD14(+)CD16(++)). However, recognition of an intermediate population identified as CD14(++)CD16(+) supports the new paradigm that monocytes are a true heterogeneous population and careful identification of specific subpopulations is necessary for understanding monocyte function in human disease. Comparative studies of monocytes in mice have yielded more dichotomous results based on expression of the Ly6C antigen. In this review, we will discuss the use of monocyte subpopulations as biomarkers of human disease and summarize correlative studies in mice that may yield significant insight into the contribution of each subset to disease pathogenesis.

  9. Adaptation Driven by Spatial Heterogeneities

    NASA Astrophysics Data System (ADS)

    Hermsen, Rutger

    2011-03-01

    Biological evolution and ecology are intimately linked, because the reproductive success or ``fitness'' of an organism depends crucially on its ecosystem. Yet, most models of evolution (or population genetics) consider homogeneous, fixed-size populations subjected to a constant selection pressure. To move one step beyond such ``mean field'' descriptions, we discuss stochastic models of evolution driven by spatial heterogeneity. We imagine a population whose range is limited by a spatially varying environmental parameter, such as a temperature or the concentration of an antibiotic drug. Individuals in the population replicate, die and migrate stochastically. Also, by mutation, they can adapt to the environmental stress and expand their range. This way, adaptation and niche expansion go hand in hand. This mode of evolution is qualitatively different from the usual notion of a population climbing a fitness gradient. We analytically calculate the rate of adaptation by solving a first passage time problem. Interestingly, the joint effects of reproduction, death, mutation and migration result in two distinct parameter regimes depending on the relative time scales of mutation and migration. We argue that the proposed scenario may be relevant for the rapid evolution of antibiotic resistance. This work was supported by the Center for Theoretical Biological Physics sponsored by the National Science Foundation (NSF) (Grant PHY-0822283).

  10. Operating a heterogeneous telescope network

    NASA Astrophysics Data System (ADS)

    Allan, Alasdair; Bischoff, Karsten; Burgdorf, Martin; Cavanagh, Brad; Christian, Damien; Clay, Neil; Dickens, Rob; Economou, Frossie; Fadavi, Mehri; Frazer, Stephen; Granzer, Thomas; Grosvenor, Sandy; Hessman, Frederic V.; Jenness, Tim; Koratkar, Anuradha; Lehner, Matthew; Mottram, Chris; Naylor, Tim; Saunders, Eric S.; Solomos, Nikolaos; Steele, Iain A.; Tuparev, Georg; Vestrand, W. Thomas; White, Robert R.; Yost, Sarah

    2006-06-01

    In the last few years the ubiquitous availability of high bandwidth networks has changed the way both robotic and non-robotic telescopes operate, with single isolated telescopes being integrated into expanding "smart" telescope networks that can span continents and respond to transient events in seconds. The Heterogeneous Telescope Networks (HTN)* Consortium represents a number of major research groups in the field of robotic telescopes, and together we are proposing a standards based approach to providing interoperability between the existing proprietary telescope networks. We further propose standards for interoperability, and integration with, the emerging Virtual Observatory. We present the results of the first interoperability meeting held last year and discuss the protocol and transport standards agreed at the meeting, which deals with the complex issue of how to optimally schedule observations on geographically distributed resources. We discuss a free market approach to this scheduling problem, which must initially be based on ad-hoc agreements between the participants in the network, but which may eventually expand into a electronic market for the exchange of telescope time.

  11. Denaturation patterns in heterogeneous DNA.

    PubMed

    Zoli, Marco

    2010-05-01

    The thermodynamical properties of heterogeneous DNA sequences are computed by path-integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time-dependent paths whose amplitudes are consistent with the model potential for the hydrogen bonds between complementary strands. The portion of configuration space contributing to the partition function is determined, at any temperature, by selecting the ensemble of paths which fulfill the second law of thermodynamics. For a short DNA fragment, the denaturation is signaled by a succession of peaks in the specific-heat plots while the entropy grows continuously versus T. Thus, the opening of the double strand with bubble formation appears as a smooth crossover due to base pair fluctuation effects which are accounted for by the path-integral method. The multistep transition is driven by the adenine-thymine- (AT) rich regions of the DNA fragment. The base pairs path ensemble shows an enhanced degree of cooperativity at about the same temperatures for which the specific-heat peaks occur. These findings establish a link between microscopic and macroscopic signatures of the transition. The fractions of mean base pair stretchings are computed by varying the AT base pairs content and taking some threshold values for the occurrence of the molecule denaturation.

  12. Shock initiation in heterogeneous explosives

    SciTech Connect

    Nunziato, J.W.; Kipp, M.E.; Setchell, R.E.; Walsh, E.K.

    1982-09-01

    It is generally accepted that the shock initiation of heterogeneous explosives begins with the formation of hot spots in the vicinity of microstructural defects such as voids, grain boundaries, and phase boundaries where there can be significant localized deformation as a result of material viscosity, plastic work, and intergranular friction. In this report, we describe this phenomenon in the context of a recently developed theory of chemically reacting, multiphase mixtures. In particular, we consider a granular explosive with an energetic binder (e.g. PBX-9404) and represent it as a three-phase, saturated mixture consisting of the granular reactant, the binder phase, and the product gases. Under dynamic loading, viscous dissipation results in high temperatures in the binder phase which subsequently thermally explodes to form product gases. Decomposition of the granular reactant is achieved by laminar grain burning. This model has been incorporated into a 1-D Lagrangian finite-difference code (WONDY) and the evolution of compressive shock and acceleration (ramp) waves have been calculated for PBX-9404. The calculated wave growth at the front, as well as the reaction-induced pressure wave behind the front, are shown to be in good agreement with experimental observations.

  13. Anomalous transport in heterogeneous media

    NASA Astrophysics Data System (ADS)

    Horbach, Jürgen; Siboni, Nima H.; Schnyder, Simon K.

    2017-08-01

    The diffusion dynamics of particles in heterogeneous media is studied using particle-based simulation techniques. A special focus is placed on systems where the transport of particles at long times exhibits anomalies such as subdiffusive or superdiffusive behavior. First, a two-dimensional model system is considered containing gas particles (tracers) that diffuse through a random arrangement of pinned, disk-shaped particles. This system is similar to a classical Lorentz gas. However, different from the original Lorentz model, soft instead of hard interactions are considered and we also discuss the case where the tracer particles interact with each other. We show that the modification from hard to soft interactions strongly affects anomalous-diffusive transport at high obstacle densities. Second, non-linear active micro-rheology in a glass-forming binary Yukawa mixture is investigated, pulling single particles through a deeply supercooled state by applying a constant force. Here, we observe superdiffusion in force direction and analyze its origin. Finally, we consider the Brownian dynamics of a particle which is pulled through a two-dimensional random force field. We discuss the similarities of this model with the Lorentz gas as well as active micro-rheology in glass-forming systems.

  14. Genetic heterogeneity in juvenile NCL

    SciTech Connect

    Hart, Y.M.; Andermann, E.; Mitchison, H.M.

    1994-09-01

    The neuronal ceroid lipofuscinoses (NCL) are a group of related lysosomal storage diseases classified according to the age of onset, clinical syndrome, and pathology. The clinical syndromes include myoclonus, visual failure, progressive dementia, ataxia and generalized tonic clonic seizures in varying combinations depending on the age of onset and pathology. The mode of inheritance is autosomal recessive in most cases, except for several families with the adult form (Kufs` disease) which have autosomal dominant inheritance. Linkage for the infantile (Halatia-Santavuori) form (CLN1), characterized ultrastructurally by lysosomal granular osmiophilic deposits (GROD), has been demonstrated with markers on chromosome lp, while the gene for the typical juvenile (Spielmeyer-Vogt) form (CLN3), characterized by fingerprint-profile inclusions, has been linked to chromosome 16p. The gene locations of the late infantile (Jansky-Bielschowsky) and adult (Kufs` disease) forms are unknown, although it has recently been shown that the late infantile form does not link to chromosome 16p. We describe three siblings, including a pair of monozygotic twins, with juvenile onset NCL with GROD in whom linkage to the CLN3 region of chromsome 16p has been excluded. This would suggest that there is genetic heterogeneity not only among the different clinical syndromes, but also among identical clinical syndromes with different ultrastructural characteristics. Preliminary studies of linkage to chromosome 1p employing the microsatellite marker HY-TM1 have been uninformative. Further studies with other chromosome 1 markers are underway.

  15. Heterogeneity assessment of functional T cell avidity

    PubMed Central

    Ioannidou, Kalliopi; Baumgaertner, Petra; Gannon, Philippe O.; Speiser, Michel F.; Allard, Mathilde; Hebeisen, Michael; Rufer, Nathalie; Speiser, Daniel E.

    2017-01-01

    The potency of cellular immune responses strongly depends on T cell avidity to antigen. Yet, functional avidity measurements are rarely performed in patients, mainly due to the technical challenges of characterizing heterogeneous T cells. The mean functional T cell avidity can be determined by the IFN-γ Elispot assay, with titrated amounts of peptide. Using this assay, we developed a method revealing the heterogeneity of functional avidity, represented by the steepness/hillslope of the peptide titration curve, documented by proof of principle experiments and mathematical modeling. Our data show that not only natural polyclonal CD8 T cell populations from cancer patients, but also monoclonal T cells differ strongly in their heterogeneity of functional avidity. Interestingly, clones and polyclonal cells displayed comparable ranges of heterogeneity. We conclude that besides the mean functional avidity, it is feasible and useful to determine its heterogeneity (hillslope) for characterizing T cell responses in basic research and patient investigation. PMID:28287160

  16. MALDI Imaging-Guided Microproteomic Analyses of Heterogeneous Breast Tumors - A Pilot Study.

    PubMed

    Alberts, Deborah; Pottier, Charles; Smargiasso, Nicolas; Baiwir, Dominique; Mazzucchelli, Gabriel; Delvenne, Philippe; Kriegsmann, Mark; Kazdal, Daniel; Warth, Arne; De Pauw, Edwin; Longuespée, Rémi

    2017-08-11

    Matrix-assisted laser desorption/ionization (MALDI) imaging is an ideal tool to study intratumor heterogeneity (ITH) and its implication in prognostic stratification of patients. However there are some drawbacks concerning protein identification. On the other hand, laser microdissection (LMD)-based microproteomics allows retrieving thousands of protein identifications from small tissue pieces. As a proof of concept, we combined these two complementary approaches to analyze heterogeneous regions in breast tumors. Invasive ductal breast cancer FFPE tissue sections from five patients were analyzed by MALDI imaging and the dataset were processed by segmentation. Heterogeneous regions within tumors were processed by LMD-based microproteomics, in duplicates. Liquid chromatography-tandem mass spectrometry data were classified by hierarchical clustering. Heterogeneous tissue regions were discriminated on the basis of their actual molecular heterogeneity. The dataset was correlated with MALDI imaging to identify m/z values discriminating heterogeneous regions. The molecular characterization of cell clones in tumors related to bad patient outcome could have great impact for pathology. We presented a combined application of LMD-based microproteomics and MALDI imaging for ITH studies. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  17. Interoperability of heterogeneous distributed systems

    NASA Astrophysics Data System (ADS)

    Zaschke, C.; Essendorfer, B.; Kerth, C.

    2016-05-01

    To achieve knowledge superiority in today's operations interoperability is the key. Budget restrictions as well as the complexity and multiplicity of threats combined with the fact that not single nations but whole areas are subject to attacks force nations to collaborate and share information as appropriate. Multiple data and information sources produce different kinds of data, real time and non-real time, in different formats that are disseminated to the respective command and control level for further distribution. The data is most of the time highly sensitive and restricted in terms of sharing. The question is how to make this data available to the right people at the right time with the right granularity. The Coalition Shared Data concept aims to provide a solution to these questions. It has been developed within several multinational projects and evolved over time. A continuous improvement process was established and resulted in the adaptation of the architecture as well as the technical solution and the processes it supports. Coming from the idea of making use of existing standards and basing the concept on sharing of data through standardized interfaces and formats and enabling metadata based query the concept merged with a more sophisticated service based approach. The paper addresses concepts for information sharing to facilitate interoperability between heterogeneous distributed systems. It introduces the methods that were used and the challenges that had to be overcome. Furthermore, the paper gives a perspective how the concept could be used in the future and what measures have to be taken to successfully bring it into operations.

  18. Isotopic heterogeneity in volcanic rocks

    NASA Astrophysics Data System (ADS)

    Wolff, J. A.; Ramos, F. C.; Tollstrup, D. L.

    2003-04-01

    The growing microsample database on volcanic rocks is showing that isotopic disequilibrium between and among phenocryst phases, their melt inclusions, and groundmass is the rule rather than the exception. This applies even in cases of little or no petrographic evidence for disequilibrium. Erupted magmas must therefore be regarded, to some extent, as mechanical mixtures of isotopically distinct components assembled from different sources. The preservation of isotopic disequilibrium requires that the assembly takes place before diffusion can eradicate evidence of disequilibrium. For a wide range of magmas (mafic, intermediate and felsic, silica under- and oversaturated) from different volcano types (flood basalts, monogenetic cones, stratocones, silicic calderas) this timescale ranges from thousands of years down to one year or less, with no consistent pattern of mixing-to-eruption time vs. volcano or magma type. Among many issues arising from these findings, we note that estimation of magmatic temperatures from application of equilibrium thermodynamics to phenocryst assemblages in volcanic rocks should be approached with extreme caution. The isotope ratio variations observed among the components of a single volcanic rock sample, in most cases, indicate interaction between magma and the local wall-rock. This is consistent with the view that the vast majority of magmas undergo modification during transport through and residence within the crust. Three physical origins of heterogeneity have been proposed: melting of wallrock, magmatic recharge, and mixing of components within a magma chamber initially segregated into melt-rich and crystal-rich portions. Time constraints on preservation of disequilibrium imply either a causal link with eruption, or that these processes occur through the lifetime of a chamber.

  19. Mechanical heterogeneities and lithospheric extension

    NASA Astrophysics Data System (ADS)

    Duretz, Thibault; Petri, Benoit; Mohn, Geoffroy; Schenker, Filippo L.; Schmalholz, Stefan

    2016-04-01

    Detailed geological and geophysical studies of passive margins have highlighted the multi-stage and depth-dependent aspect of lithospheric thinning. Lithospheric thinning involves a variety of structures (normal faults, low angle detachments, extensional shear zones, extraction faults) and leads to a complex architecture of passive margins (with e.g. necking zone, mantle exhumation, continental allochthons). The processes controlling the generation and evolution of these structures as well as the impact of pre-rift inheritance are so far incompletely understood. In this study, we investigate the impact of pre-rift inheritance on the development of rifted margins using two-dimensional thermo-mechanical models of lithospheric thinning. To first order, we represent the pre-rift mechanical heterogeneities with lithological layering. The rheologies are kept simple (visco-plastic) and do not involve any strain softening mechanism. Our models show that mechanical layering causes multi-stage and depth-dependent extension. In the initial rifting phase, lithospheric extension is decoupled: as the crust undergoes thinning by brittle (frictional-plastic) faults, the lithospheric mantle accommodates extension by symmetric ductile necking. In a second rifting phase, deformation in the crust and lithospheric mantle is coupled and marks the beginning of an asymmetric extension stage. Low angle extensional shear zones develop across the lithosphere and exhume subcontinental mantle. Furthemore, crustal allochthons and adjacent basins develop coevally. We describe as well the thermal evolution predicted by the numerical models and discuss the first-order implications of our results in the context of the Alpine geological history.

  20. Molecular modeling of heterogeneous catalysis

    NASA Astrophysics Data System (ADS)

    Gislason, Jason Joseph

    A novel method for modeling heterogeneous catalysis was developed to further facilitate the understanding of catalytic reactor mechanisms. The method employs molecular dynamics simulations, statistical mechanical, and Unity Bond Index - Quadratic Exponential Potential (UBI-QEP) calculations to calculate the rate constants for reactions on metal surfaces. The primary difficulty of molecular dynamics simulations on metal surfaces has been the lack of reliable reactive potential energy surfaces. We have overcome this through the development of the Normalized Bond Index - Reactive Potential Function (NBI-RPF), which can accurately describe the reaction of adsorbates on metal surfaces. The first calculations of rate constants for a reaction on a metal surface using molecular dynamics simulations are presented. This method is applied to the determination of the mechanism for selective hydrogenation of acetylene in an ethylene rich flow. It was determined that the selectivity for acetylene hydrogenation is attributable to the higher reactivity of acetylene versus ethylene with respect to hydrogenation by molecular hydrogen. It was shown that hydrogen transfer from the carbonaceous layer to acetylene or ethylene is insignificant in the hydrogenation process. Molecular dynamics simulations and molecular mechanics calculations were used to determine the diffusion rate constants for dimethylnaphthalene isomers is mordenite. 2,6-dimethylnaphthalene and 2,7-dimethylnaphthalene were found to have similar diffusion rate constants. Grand canonical Monte Carlo calculations were performed on the competitive adsorption of 2,6-dimethylnaphthalene and 2,7-dimethylnaphthalene in type X zeolites exchanged individually with barium, calcium, potassium, and rubidium ions, calcium exchanged MCM-22, and hydrogen form mordenite (MOR), X zeolite, Y zeolite, hypBEB, ZSM- 12, and MCM-22. These calculations showed that barium exchanged X zeolite was the most selective toward 2

  1. Frictional Heterogeneities Along Carbonate Faults

    NASA Astrophysics Data System (ADS)

    Collettini, C.; Carpenter, B. M.; Scuderi, M.; Tesei, T.

    2014-12-01

    The understanding of fault-slip behaviour in carbonates has an important societal impact as a) a significant number of earthquakes nucleate within or propagate through these rocks, and b) half of the known petroleum reserves occur within carbonate reservoirs, which likely contain faults that experience fluid pressure fluctuations. Field studies on carbonate-bearing faults that are exhumed analogues of currently active structures of the seismogenic crust, show that fault rock types are systematically controlled by the lithology of the faulted protolith: localization associated with cataclasis, thermal decomposition and plastic deformation commonly affect fault rocks in massive limestone, whereas distributed deformation, pressure-solution and frictional sliding along phyllosilicates are observed in marly rocks. In addition, hydraulic fractures, indicating cyclic fluid pressure build-ups during the fault activity, are widespread. Standard double direct friction experiments on fault rocks from massive limestones show high friction, velocity neutral/weakening behaviour and significant re-strengthening during hold periods, on the contrary, phyllosilicate-rich shear zones are characterized by low friction, significant velocity strengthening behavior and no healing. We are currently running friction experiments on large rock samples (20x20 cm) in order to reproduce and characterize the interaction of fault rock frictional heterogeneities observed in the field. In addition we have been performing experiments at near lithostatic fluid pressure in the double direct shear configuration within a pressure vessel to test the Rate and State friction stability under these conditions. Our combination of structural observations and mechanical data have been revealing the processes and structures that are at the base of the broad spectrum of fault slip behaviors recently documented by high-resolution geodetic and seismological data.

  2. Heterochronic phosphorelay gene expression as a source of heterogeneity in Bacillus subtilis spore formation.

    PubMed

    de Jong, Imke G; Veening, Jan-Willem; Kuipers, Oscar P

    2010-04-01

    In response to limiting nutrient sources and cell density signals, Bacillus subtilis can differentiate and form highly resistant endospores. Initiation of spore development is governed by the master regulator Spo0A, which is activated by phosphorylation via a multicomponent phosphorelay. Interestingly, only part of a clonal population will enter this developmental pathway, a phenomenon known as sporulation bistability or sporulation heterogeneity. How sporulation heterogeneity is established is largely unknown. To investigate the origins of sporulation heterogeneity, we constructed promoter-green fluorescent protein (GFP) fusions to the main phosphorelay genes and perturbed their expression levels. Using time-lapse fluorescence microscopy and flow cytometry, we showed that expression of the phosphorelay genes is distributed in a unimodal manner. However, single-cell trajectories revealed that phosphorelay gene expression is highly dynamic or "heterochronic" between individual cells and that stochasticity of phosphorelay gene transcription might be an important regulatory mechanism for sporulation heterogeneity. Furthermore, we showed that artificial induction or depletion of the phosphorelay phosphate flow results in loss of sporulation heterogeneity. Our data suggest that sporulation heterogeneity originates from highly dynamic and variable gene activity of the phosphorelay components, resulting in large cell-to-cell variability with regard to phosphate input into the system. These transcriptional and posttranslational differences in phosphorelay activity appear to be sufficient to generate a heterogeneous sporulation signal without the need of the positive-feedback loop established by the sigma factor SigH.

  3. Tumor Heterogeneity: Mechanisms and Bases for a Reliable Application of Molecular Marker Design

    PubMed Central

    Diaz-Cano, Salvador J.

    2012-01-01

    Tumor heterogeneity is a confusing finding in the assessment of neoplasms, potentially resulting in inaccurate diagnostic, prognostic and predictive tests. This tumor heterogeneity is not always a random and unpredictable phenomenon, whose knowledge helps designing better tests. The biologic reasons for this intratumoral heterogeneity would then be important to understand both the natural history of neoplasms and the selection of test samples for reliable analysis. The main factors contributing to intratumoral heterogeneity inducing gene abnormalities or modifying its expression include: the gradient ischemic level within neoplasms, the action of tumor microenvironment (bidirectional interaction between tumor cells and stroma), mechanisms of intercellular transference of genetic information (exosomes), and differential mechanisms of sequence-independent modifications of genetic material and proteins. The intratumoral heterogeneity is at the origin of tumor progression and it is also the byproduct of the selection process during progression. Any analysis of heterogeneity mechanisms must be integrated within the process of segregation of genetic changes in tumor cells during the clonal expansion and progression of neoplasms. The evaluation of these mechanisms must also consider the redundancy and pleiotropism of molecular pathways, for which appropriate surrogate markers would support the presence or not of heterogeneous genetics and the main mechanisms responsible. This knowledge would constitute a solid scientific background for future therapeutic planning. PMID:22408433

  4. Genetic heterogeneity and HOMOG analysis in British malignant hyperthermia families.

    PubMed Central

    Robinson, R; Curran, J L; Hall, W J; Halsall, P J; Hopkins, P M; Markham, A F; Stewart, A D; West, S P; Ellis, F R

    1998-01-01

    Malignant hyperthermia (MH) is an autosomal dominant genetic condition that presents in susceptible people undergoing general anaesthesia. The clinical disorder is a major cause of anaesthetic morbidity and mortality. The UK Malignant Hyperthermia Group has performed genetic linkage analysis on 20 large, well defined malignant hyperthermia families, using hypervariable markers on chromosome 19q13.1, including the candidate MH gene RYR1, the gene coding for the skeletal muscle ryanodine receptor protein. The results were analysed using LINKAGE to perform two point and multipoint lod scores, then HOMOG to calculate levels of heterogeneity. The results clearly showed genetic heterogeneity between MH families; nine of the families gave results entirely consistent with linkage to the region around RYR1 while the same region was clearly excluded in three families. In the remaining eight MHS families there were single recombinant events between RYR1 and MH susceptibility. HOMOG analysis was of little added benefit in determining the likelihood of linkage to RYR1 in these families. This confirmation of the presence of heterogeneity in the UK MH population, along with the possibility of the presence of two MH genes in some pedigrees, indicates that it would be premature and potentially dangerous to offer diagnosis of MH by DNA based methods at this time. PMID:9541102

  5. Transcriptional and phenotypical heterogeneity of Trypanosoma cruzi cell populations

    PubMed Central

    Seco-Hidalgo, Víctor; De Pablos, Luis Miguel; Osuna, Antonio

    2015-01-01

    Trypanosoma cruzi has a complex life cycle comprising pools of cell populations which circulate among humans, vectors, sylvatic reservoirs and domestic animals. Recent experimental evidence has demonstrated the importance of clonal variations for parasite population dynamics, survival and evolution. By limiting dilution assays, we have isolated seven isogenic clonal cell lines derived from the Pan4 strain of T. cruzi. Applying different molecular techniques, we have been able to provide a comprehensive characterization of the expression heterogeneity in the mucin-associated surface protein (MASP) gene family, where all the clonal isogenic populations were transcriptionally different. Hierarchical cluster analysis and sequence comparison among different MASP cDNA libraries showed that, despite the great variability in MASP expression, some members of the transcriptome (including MASP pseudogenes) are conserved, not only in the life-cycle stages but also among different strains of T. cruzi. Finally, other important aspects for the parasite, such as growth, spontaneous metacyclogenesis or excretion of different catabolites, were also compared among the clones, demonstrating that T. cruzi populations of cells are also phenotypically heterogeneous. Although the evolutionary strategy that sustains the MASP expression polymorphism remains unknown, we suggest that MASP clonal variability and phenotypic heterogeneities found in this study might provide an advantage, allowing a rapid response to environmental pressure or changes during the life cycle of T. cruzi. PMID:26674416

  6. A model of electrophysiological heterogeneity in periglomerular cells

    PubMed Central

    Sethupathy, Praveen; Rubin, Daniel B.; Li, Guoshi; Cleland, Thomas A.

    2013-01-01

    Olfactory bulb (OB) periglomerular (PG) cells are heterogeneous with respect to several features, including morphology, connectivity, patterns of protein expression, and electrophysiological properties. However, these features rarely correlate with one another, suggesting that the differentiating properties of PG cells may arise from multiple independent adaptive variables rather than representing discrete cell classes. We use computational modeling to assess this hypothesis with respect to electrophysiological properties. Specifically, we show that the heterogeneous electrophysiological properties demonstrated in PG cell recordings can be explained solely by differences in the relative expression levels of ion channel species in the cell, without recourse to modifying channel kinetic properties themselves. This PG cell model can therefore be used as the basis for diverse cellular and network-level analyses of OB computations. Moreover, this simple basis for heterogeneity contributes to an emerging hypothesis that glomerular-layer interneurons may be better described as a single population expressing distributions of partially independent, potentially plastic properties, rather than as a set of discrete cell classes. PMID:23637658

  7. Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics

    PubMed Central

    Breckels, Lisa M.; Holden, Sean B.; Wojnar, David; Mulvey, Claire M.; Christoforou, Andy; Groen, Arnoud; Trotter, Matthew W. B.; Kohlbacher, Oliver; Lilley, Kathryn S.; Gatto, Laurent

    2016-01-01

    Sub-cellular localisation of proteins is an essential post-translational regulatory mechanism that can be assayed using high-throughput mass spectrometry (MS). These MS-based spatial proteomics experiments enable us to pinpoint the sub-cellular distribution of thousands of proteins in a specific system under controlled conditions. Recent advances in high-throughput MS methods have yielded a plethora of experimental spatial proteomics data for the cell biology community. Yet, there are many third-party data sources, such as immunofluorescence microscopy or protein annotations and sequences, which represent a rich and vast source of complementary information. We present a unique transfer learning classification framework that utilises a nearest-neighbour or support vector machine system, to integrate heterogeneous data sources to considerably improve on the quantity and quality of sub-cellular protein assignment. We demonstrate the utility of our algorithms through evaluation of five experimental datasets, from four different species in conjunction with four different auxiliary data sources to classify proteins to tens of sub-cellular compartments with high generalisation accuracy. We further apply the method to an experiment on pluripotent mouse embryonic stem cells to classify a set of previously unknown proteins, and validate our findings against a recent high resolution map of the mouse stem cell proteome. The methodology is distributed as part of the open-source Bioconductor pRoloc suite for spatial proteomics data analysis. PMID:27175778

  8. Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics.

    PubMed

    Breckels, Lisa M; Holden, Sean B; Wojnar, David; Mulvey, Claire M; Christoforou, Andy; Groen, Arnoud; Trotter, Matthew W B; Kohlbacher, Oliver; Lilley, Kathryn S; Gatto, Laurent

    2016-05-01

    Sub-cellular localisation of proteins is an essential post-translational regulatory mechanism that can be assayed using high-throughput mass spectrometry (MS). These MS-based spatial proteomics experiments enable us to pinpoint the sub-cellular distribution of thousands of proteins in a specific system under controlled conditions. Recent advances in high-throughput MS methods have yielded a plethora of experimental spatial proteomics data for the cell biology community. Yet, there are many third-party data sources, such as immunofluorescence microscopy or protein annotations and sequences, which represent a rich and vast source of complementary information. We present a unique transfer learning classification framework that utilises a nearest-neighbour or support vector machine system, to integrate heterogeneous data sources to considerably improve on the quantity and quality of sub-cellular protein assignment. We demonstrate the utility of our algorithms through evaluation of five experimental datasets, from four different species in conjunction with four different auxiliary data sources to classify proteins to tens of sub-cellular compartments with high generalisation accuracy. We further apply the method to an experiment on pluripotent mouse embryonic stem cells to classify a set of previously unknown proteins, and validate our findings against a recent high resolution map of the mouse stem cell proteome. The methodology is distributed as part of the open-source Bioconductor pRoloc suite for spatial proteomics data analysis.

  9. Evaluating heterogeneity in cumulative meta-analyses

    PubMed Central

    Villanueva, Elmer V; Zavarsek, Silva

    2004-01-01

    Background Recently developed measures such as I2 and H allow the evaluation of the impact of heterogeneity in conventional meta-analyses. There has been no examination of the development of heterogeneity in the context of a cumulative meta-analysis. Methods Cumulative meta-analyses of five smoking cessation interventions (clonidine, nicotine replacement therapy using gum and patch, physician advice and acupuncture) were used to calculate I2 and H. These values were plotted by year of publication, control event rate and sample size to trace the development of heterogeneity over these covariates. Results The cumulative evaluation of heterogeneity varied according to the measure of heterogeneity used and the basis of cumulation. Plots produced from the calculations revealed areas of heterogeneity useful in the consideration of potential sources for further study. Conclusion The examination of heterogeneity in conjunction with summary effect estimates in a cumulative meta-analysis offered valuable insight into the evolution of variation. Such information is not available in the context of conventional meta-analysis and has the potential to lead to the development of a richer picture of the effectiveness of interventions. PMID:15251035

  10. Evaluating heterogeneity in cumulative meta-analyses.

    PubMed

    Villanueva, Elmer V; Zavarsek, Silva

    2004-07-13

    Recently developed measures such as I2 and H allow the evaluation of the impact of heterogeneity in conventional meta-analyses. There has been no examination of the development of heterogeneity in the context of a cumulative meta-analysis. Cumulative meta-analyses of five smoking cessation interventions (clonidine, nicotine replacement therapy using gum and patch, physician advice and acupuncture) were used to calculate I2 and H. These values were plotted by year of publication, control event rate and sample size to trace the development of heterogeneity over these covariates. The cumulative evaluation of heterogeneity varied according to the measure of heterogeneity used and the basis of cumulation. Plots produced from the calculations revealed areas of heterogeneity useful in the consideration of potential sources for further study. The examination of heterogeneity in conjunction with summary effect estimates in a cumulative meta-analysis offered valuable insight into the evolution of variation. Such information is not available in the context of conventional meta-analysis and has the potential to lead to the development of a richer picture of the effectiveness of interventions.

  11. Molecular genetic heterogeneity in undifferentiated endometrial carcinomas.

    PubMed

    Rosa-Rosa, Juan M; Leskelä, Susanna; Cristóbal-Lana, Eva; Santón, Almudena; López-García, Ma Ángeles; Muñoz, Gloria; Pérez-Mies, Belen; Biscuola, Michele; Prat, Jaime; Esther, Oliva E; Soslow, Robert A; Matias-Guiu, Xavier; Palacios, Jose

    2016-11-01

    Undifferentiated and dedifferentiated endometrial carcinomas are rare and highly aggressive subtypes of uterine cancer, not well characterized at a molecular level. To investigate whether dedifferentiated carcinomas carry molecular genetic alterations similar to those of pure undifferentiated carcinomas, and to gain insight into the pathogenesis of these tumors, we selected a cohort of 18 undifferentiated endometrial carcinomas, 8 of them with a well-differentiated endometrioid carcinoma component (dedifferentiated endometrioid carcinomas), and studied them by immunohistochemistry and massive parallel and Sanger sequencing. Whole-exome sequencing of the endometrioid and undifferentiated components, as well as normal myometrium, was also carried out in one case. According to The Cancer Genome Atlas classification, we distributed 95% of the undifferentiated carcinomas in this series as follows: (a) hypermutated tumors with loss of any mismatch repair protein expression and microsatellite instability (eight cases, 45%); (b) ultramutated carcinomas carrying mutations in the exonuclease domain of POLE (two cases, 11%); (c) high copy number alterations (copy-number high) tumors group exhibiting only TP53 mutations and high number of alterations detected by FISH (two cases, 11%); and (d) low copy number alterations (copy-number low) tumors with molecular alterations typical of endometrioid endometrial carcinomas (five cases, 28%). Two of the latter cases, however, also had TP53 mutations and higher number of alterations detected by FISH and could have progressed to a copy-number high phenotype. Most dedifferentiated carcinomas belonged to the hypermutated group, whereas pure undifferentiated carcinomas shared molecular genetic alterations with copy-number low or copy-number high tumors. These results indicate that undifferentiated and dedifferentiated endometrial carcinomas are molecularly heterogeneous tumors, which may have prognostic value.

  12. Heterogeneous Chemistry Involving Methanol in Tropospheric Clouds

    NASA Technical Reports Server (NTRS)

    Tabazadeh, A.; Yokelson, R. J.; Singh, H. B.; Hobbs, P. V.; Crawford, J. H.; Iraci, L. T.

    2004-01-01

    In this report we analyze airborne measurements to suggest that methanol in biomass burning smoke is lost heterogeneously in clouds. When a smoke plume intersected a cumulus cloud during the SAFARI 2000 field project, the observed methanol gas phase concentration rapidly declined. Current understanding of gas and aqueous phase chemistry cannot explain the loss of methanol documented by these measurements. Two plausible heterogeneous reactions are proposed to explain the observed simultaneous loss and production of methanol and formaldehyde, respectively. If the rapid heterogeneous processing of methanol, seen in a cloud impacted by smoke, occurs in more pristine clouds, it could affect the oxidizing capacity of the troposphere on a global scale.

  13. Modeling the detonation structure of heterogeneous explosives

    NASA Astrophysics Data System (ADS)

    Dionne, J. P.; Lee, J. H. S.

    1998-07-01

    A simplified ZND calculation for the one-dimensional detonation (infinite diameter) of heterogeneous explosives is proposed. The effects of thermal relaxation within the two-phase products is incorporated into a source term in the chemical rate law. The explosive is then approximated as a homogeneous mixture of two phases. The source term is based on the rate of heat transfer from the liquid explosive to the inert heterogeneities. The effect of the properties of the heterogeneities (size, heat capacity, density) on this additional term is discussed.

  14. A heterogeneous graph-based recommendation simulator

    SciTech Connect

    Yeonchan, Ahn; Sungchan, Park; Lee, Matt Sangkeun; Sang-goo, Lee

    2013-01-01

    Heterogeneous graph-based recommendation frameworks have flexibility in that they can incorporate various recommendation algorithms and various kinds of information to produce better results. In this demonstration, we present a heterogeneous graph-based recommendation simulator which enables participants to experience the flexibility of a heterogeneous graph-based recommendation method. With our system, participants can simulate various recommendation semantics by expressing the semantics via meaningful paths like User Movie User Movie. The simulator then returns the recommendation results on the fly based on the user-customized semantics using a fast Monte Carlo algorithm.

  15. Heterogeneous Chemistry Involving Methanol in Tropospheric Clouds

    NASA Technical Reports Server (NTRS)

    Tabazadeh, A.; Yokelson, R. J.; Singh, H. B.; Hobbs, P. V.; Crawford, J. H.; Iraci, L. T.

    2004-01-01

    In this report we analyze airborne measurements to suggest that methanol in biomass burning smoke is lost heterogeneously in clouds. When a smoke plume intersected a cumulus cloud during the SAFARI 2000 field project, the observed methanol gas phase concentration rapidly declined. Current understanding of gas and aqueous phase chemistry cannot explain the loss of methanol documented by these measurements. Two plausible heterogeneous reactions are proposed to explain the observed simultaneous loss and production of methanol and formaldehyde, respectively. If the rapid heterogeneous processing of methanol, seen in a cloud impacted by smoke, occurs in more pristine clouds, it could affect the oxidizing capacity of the troposphere on a global scale.

  16. Computational Mechanics for Heterogeneous Materials

    SciTech Connect

    Lechman, Jeremy B.; Baczewski, Andrew David; Stephen Bond; Erikson, William W.; Lehoucq, Richard B.; Mondy, Lisa Ann; Noble, David R.; Pierce, Flint; Roberts, Christine; van Swol, Frank B.; Yarrington, Cole

    2013-11-01

    The subject of this work is the development of models for the numerical simulation of matter, momentum, and energy balance in heterogeneous materials. These are materials that consist of multiple phases or species or that are structured on some (perhaps many) scale(s). By computational mechanics we mean to refer generally to the standard type of modeling that is done at the level of macroscopic balance laws (mass, momentum, energy). We will refer to the flow or flux of these quantities in a generalized sense as transport. At issue here are the forms of the governing equations in these complex materials which are potentially strongly inhomogeneous below some correlation length scale and are yet homogeneous on larger length scales. The question then becomes one of how to model this behavior and what are the proper multi-scale equations to capture the transport mechanisms across scales. To address this we look to the area of generalized stochastic process that underlie the transport processes in homogeneous materials. The archetypal example being the relationship between a random walk or Brownian motion stochastic processes and the associated Fokker-Planck or diffusion equation. Here we are interested in how this classical setting changes when inhomogeneities or correlations in structure are introduced into the problem. Aspects of non-classical behavior need to be addressed, such as non-Fickian behavior of the mean-squared-displacement (MSD) and non-Gaussian behavior of the underlying probability distribution of jumps. We present an experimental technique and apparatus built to investigate some of these issues. We also discuss diffusive processes in inhomogeneous systems, and the role of the chemical potential in diffusion of hard spheres is considered. Also, the relevance to liquid metal solutions is considered. Finally we present an example of how inhomogeneities in material microstructure introduce fluctuations at the meso-scale for a thermal conduction problem

  17. Increasing selection response by Bayesian modeling of heterogeneous environmental variances

    USDA-ARS?s Scientific Manuscript database

    Heterogeneity of environmental variance among genotypes reduces selection response because genotypes with higher variance are more likely to be selected than low-variance genotypes. Modeling heterogeneous variances to obtain weighted means corrected for heterogeneous variances is difficult in likel...

  18. Heterogeneity of amplification of HER2, EGFR, CCND1 and MYC in gastric cancer.

    PubMed

    Stahl, Phillip; Seeschaaf, Carsten; Lebok, Patrick; Kutup, Asad; Bockhorn, Maximillian; Izbicki, Jakob R; Bokemeyer, Carsten; Simon, Ronald; Sauter, Guido; Marx, Andreas H

    2015-02-05

    Intra-tumor heterogeneity is a potential cause for failure of targeted therapy in gastric cancer, but the extent of heterogeneity of established (HER2) or potential (EGFR, CCND1) target genes and prognostic gene alterations (MYC) had not been systematically studied. To study heterogeneity of these genes in a large patient cohort, a heterogeneity tissue microarray was constructed containing 0.6 mm tissue cores from 9 different areas of the primary gastric cancers of 113 patients and matched lymph node metastases from 61 of these patients. Dual color fluorescence in-situ hybridization was performed to assess amplification of HER2, EGFR, CCND1 and MYC using established thresholds (ratio ≥ 2.0). Her2 immunohistochemistry (IHC) was performed in addition. Amplification was found in 17.4% of 109 interpretable cases for HER2, 6.4% for EGFR, 17.4% for CCND1, and 24.8% for MYC. HER2 amplification was strongly linked to protein overexpression by IHC in a spot-by-spot analysis (p < 0.0001). Intra-tumor heterogeneity was found in the primary tumors of 9 of 19 (47.3%) cancers with HER2, 8 of 17 (47.0%) cancers with CCND1, 5 of 7 (71.4%) cancers with EGFR, and 23 of 27 (85.2%) cancers with MYC amplification. Amplification heterogeneity was particularly frequent in case of low-level amplification (<10 gene copies). While the amplification status was often different between metastases, unequivocal intra-tumor heterogeneity was not found in individual metastases. The data of our study demonstrate that heterogeneity is common for biomarkers in gastric cancer. Given that both TMA tissue cores and clinical tumor biopsies analyze only a small fraction of the tumor bulk, it can be concluded that such heterogeneity may potentially limit treatment decisions based on the analysis of a single clinical cancer biopsy.

  19. Exploring heterogeneous market hypothesis using realized volatility

    NASA Astrophysics Data System (ADS)

    Chin, Wen Cheong; Isa, Zaidi; Mohd Nor, Abu Hassan Shaari

    2013-04-01

    This study investigates the heterogeneous market hypothesis using high frequency data. The cascaded heterogeneous trading activities with different time durations are modelled by the heterogeneous autoregressive framework. The empirical study indicated the presence of long memory behaviour and predictability elements in the financial time series which supported heterogeneous market hypothesis. Besides the common sum-of-square intraday realized volatility, we also advocated two power variation realized volatilities in forecast evaluation and risk measurement in order to overcome the possible abrupt jumps during the credit crisis. Finally, the empirical results are used in determining the market risk using the value-at-risk approach. The findings of this study have implications for informationally market efficiency analysis, portfolio strategies and risk managements.

  20. Heterogeneity and Risk Sharing in Village Economies*

    PubMed Central

    Chiappori, Pierre-André; Samphantharak, Krislert; Schulhofer-Wohl, Sam; Townsend, Robert M.

    2013-01-01

    We show how to use panel data on household consumption to directly estimate households’ risk preferences. Specifically, we measure heterogeneity in risk aversion among households in Thai villages using a full risk-sharing model, which we then test allowing for this heterogeneity. There is substantial, statistically significant heterogeneity in estimated risk preferences. Full insurance cannot be rejected. As the risk sharing, as-if-complete-markets theory might predict, estimated risk preferences are unrelated to wealth or other characteristics. The heterogeneity matters for policy: Although the average household would benefit from eliminating village-level risk, less-risk-averse households who are paid to absorb that risk would be worse off by several percent of household consumption. PMID:24932226

  1. Heterogeneous photocatalytic oxidation of atmospheric trace contaminants

    NASA Technical Reports Server (NTRS)

    Ollis, David F.

    1993-01-01

    Work performed during the period 1 May - 31 Oct. 1992 on heterogeneous photocatalytic oxidation of atmospheric trace contaminants is presented. Topics discussed include photoreactor monolith fundamental studies and monolith reactor operation: batch recirculation system.

  2. Heterogeneous Clustering: Operational and User Impacts

    NASA Technical Reports Server (NTRS)

    Salm, Saita Wood

    1999-01-01

    Heterogeneous clustering can improve overall utilization of multiple hosts and can provide better turnaround to users by balancing workloads across hosts. Building a cluster requires both operational changes and revisions in user scripts.

  3. Heterogeneity and Risk Sharing in Village Economies.

    PubMed

    Chiappori, Pierre-André; Samphantharak, Krislert; Schulhofer-Wohl, Sam; Townsend, Robert M

    2014-03-01

    We show how to use panel data on household consumption to directly estimate households' risk preferences. Specifically, we measure heterogeneity in risk aversion among households in Thai villages using a full risk-sharing model, which we then test allowing for this heterogeneity. There is substantial, statistically significant heterogeneity in estimated risk preferences. Full insurance cannot be rejected. As the risk sharing, as-if-complete-markets theory might predict, estimated risk preferences are unrelated to wealth or other characteristics. The heterogeneity matters for policy: Although the average household would benefit from eliminating village-level risk, less-risk-averse households who are paid to absorb that risk would be worse off by several percent of household consumption.

  4. Heterogeneous treatment in the variational nodal method

    SciTech Connect

    Fanning, T.H.; Palmiotti, G.

    1995-06-01

    The variational nodal transport method is reduced to its diffusion form and generalized for the treatment of heterogeneous nodes while maintaining nodal balances. Adapting variational methods to heterogeneous nodes requires the ability to integrate over a node with discontinuous cross sections. In this work, integrals are evaluated using composite gaussian quadrature rules, which permit accurate integration while minimizing computing time. Allowing structure within a nodal solution scheme avoids some of the necessity of cross section homogenization, and more accurately defines the intra-nodal flux shape. Ideally, any desired heterogeneity can be constructed within the node; but in reality, the finite set of basis functions limits the practical resolution to which fine detail can be defined within the node. Preliminary comparison tests show that the heterogeneous variational nodal method provides satisfactory results even if some improvements are needed for very difficult, configurations.

  5. NMR analysis of compositional heterogeneity in polysaccharides

    USDA-ARS?s Scientific Manuscript database

    Many copolysaccharides are compositionally heterogeneous, and the composition determined by the usual analytical or spectroscopic methods provides only an average value. For some polysaccharides, the NMR data contain copolymer sequence information, such as diad, triad, and tetrad sequence intensiti...

  6. Eradication of infectious diseases in heterogeneous populations

    SciTech Connect

    Travis, C.C.; Lenhart, S.M.

    1987-04-01

    A model is presented of infectious disease in heterogeneous populations, which allows for variable intra- to intergroup contact ratios. The authors give necessary and sufficient conditions for disease eradication by means of vaccination. Smallpox is used as an illustrative example.

  7. Electrostatic attraction between cationic-anionic assemblies with surface compositional heterogeneities

    NASA Astrophysics Data System (ADS)

    Velichko, Y. S.; Olvera de la Cruz, M.

    2006-06-01

    Electrostatics play a key role in biomolecular assembly. Oppositely charged biomolecules, for instance, can be coassembled into functional units, such as DNA and histone proteins into nucleosomes and actin-binding protein complexes into cytoskeleton components, at appropriate ionic conditions. These cationic-anionic coassemblies often have surface charge heterogeneities that result from the delicate balance between electrostatics and packing constraints. Despite their importance, the precise role of surface charge heterogeneities in the organization of cationic-anionic coassemblies is not well understood. We show here that coassemblies with charge heterogeneities strongly interact through polarization of the domains. We find that this leads to symmetry breaking, which is important for functional capabilities, and structural changes, which is crucial in the organization of coassemblies. We determine the range and strength of the attraction as a function of the competition between the steric and hydrophobic constraints and electrostatic interactions.

  8. A 1998 Workshop on Heterogeneous Computing

    DTIC Science & Technology

    2007-11-02

    support for heterogeneous computing," in The Computer Science and Engineering Handbook , A. B. Tucker, Jr., ed., CRC Press, Boca Raton, FL, 1997, pp...for heterogeneous computing," in The Computer Science and Engineering Handbook , edited by Allen B. Tucker, Jr., CRC Press, Boca Raton, FL, 1997, pp... Handbook . CRC Press, Boca Ra- ton, FL, 1997. [35] V. S. Sunderam. PVM: A framework for paral- lel distributed computing. Concurrency: Practice and

  9. Intelligent Classification in Huge Heterogeneous Data Sets

    DTIC Science & Technology

    2015-06-01

    signals and through data dimension reduction, and to develop and tailor algorithms for the extraction of intelligence from several huge heterogeneous...dimension reduction and feature extraction . These techniques are employed when no training set is available, and therefore also no target output...algorithms for application to huge, heterogeneous data sets enabling the extraction of intelligence from information. The approach uses two-scale supervised

  10. Heterogeneity of a human T-lymphoblastoid cell line

    SciTech Connect

    Snow, K.; Judd, W.

    1987-08-01

    A human T-lymphoblastoid cell line (Jurkat) was cloned, and four resulting sublines were characterized in a variety of ways with the objective of gaining information on heterogeneity in cell lines. Within a few weeks of cloning, distinct cellular morphologies and growth patterns became apparent in the four sublines. Growth rate measurements made over 3 months did not show any significant differences between the sublines. Surface protein profiles obtained by radioimmunoprecipitation using antisera in conjunction with extracts from (/sup 35/S)Met and /sup 125/I-labeled cells revealed differences between the sublines. Analysis of total cell DNA showed that one of the sublines possessed only half the chromosome complement of the other sublines and the parental line. Karyotyping confirmed this result and, in addition, demonstrated that chromosome numbers fluctuated around a mean value for each subline. Karyotypic variability became apparent within 2 months of cloning and tended to increase with time in culture. G-banding analysis showed that the analyzed cell populations contained distinctive cytogenetic aberrations. Properties of the cloned sublines were monitored over a 9-month period. One of the sublines that had shown heterogeneous morphology even after 6 weeks maintained the heterogeneity throughout this time. Another subline underwent a marked change in morphology (round to irregular) and growth habit (single cells to large clumps) with increasing time in culture. Interestingly, several alterations to surface proteins accompanied these growth changes. A third subline had relatively stable morphology and chromosome number throughout the 9-month period. The modal chromosome number was hypotetraploid for three sublines and the parent line, but was diploid for another subline.

  11. Unlocking proteomic heterogeneity in complex diseases through visual analytics.

    PubMed

    Bhavnani, Suresh K; Dang, Bryant; Bellala, Gowtham; Divekar, Rohit; Visweswaran, Shyam; Brasier, Allan R; Kurosky, Alex

    2015-04-01

    Despite years of preclinical development, biological interventions designed to treat complex diseases such as asthma often fail in phase III clinical trials. These failures suggest that current methods to analyze biomedical data might be missing critical aspects of biological complexity such as the assumption that cases and controls come from homogeneous distributions. Here we discuss why and how methods from the rapidly evolving field of visual analytics can help translational teams (consisting of biologists, clinicians, and bioinformaticians) to address the challenge of modeling and inferring heterogeneity in the proteomic and phenotypic profiles of patients with complex diseases. Because a primary goal of visual analytics is to amplify the cognitive capacities of humans for detecting patterns in complex data, we begin with an overview of the cognitive foundations for the field of visual analytics. Next, we organize the primary ways in which a specific form of visual analytics called networks has been used to model and infer biological mechanisms, which help to identify the properties of networks that are particularly useful for the discovery and analysis of proteomic heterogeneity in complex diseases. We describe one such approach called subject-protein networks, and demonstrate its application on two proteomic datasets. This demonstration provides insights to help translational teams overcome theoretical, practical, and pedagogical hurdles for the widespread use of subject-protein networks for analyzing molecular heterogeneities, with the translational goal of designing biomarker-based clinical trials, and accelerating the development of personalized approaches to medicine. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Materials properties: heterogeneity and appropriate sampling modes.

    PubMed

    Esbensen, Kim H

    2015-01-01

    The target audience for this Special Section comprises parties related to the food and feed sectors, e.g., field samplers, academic and industrial scientists, laboratory personnel, companies, organizations, regulatory bodies, and agencies who are responsible for sampling, as well as project leaders, project managers, quality managers, supervisors, and directors. All these entities face heterogeneous materials, and the characteristics of heterogeneous materials needs to be competently understood by all of them. Before delivering analytical results for decision-making, one form or other of primary sampling is always necessary, which must counteract the effects of the sampling target heterogeneity. Up to five types of sampling error may arise as a specific sampling process interacts with a heterogeneous material; two sampling errors arise because of the heterogeneity of the sampling target, and three additional sampling errors are produced by the sampling process itself-if not properly understood, reduced, and/or eliminated, which is the role of Theory of Sampling. This paper discusses the phenomenon and concepts involved in understanding, describing, and managing the adverse effects of heterogeneity in sampling.

  13. Genomic and epigenomic heterogeneity of hepatocellular carcinoma.

    PubMed

    Lin, De-Chen; Mayakonda, Anand; Dinh, Huy Q; Huang, Pinbo; Lin, Lehang; Liu, Xiaoping; Ding, Ling-Wen; Wang, Jie; Berman, Benjamin; Song, Erwei; Yin, Dong; Koeffler, H Phillip

    2017-02-20

    Understanding the intratumoral heterogeneity of hepatocellular carcinoma (HCC) is instructive for developing personalized therapy and identifying molecular biomarkers. Here we applied whole-exome sequencing to 69 samples from 11 patients to resolve the genetic architecture of subclonal diversification. Spatial genomic diversity was found in all 11 HCC cases, with 29% of driver mutations being heterogeneous, including TERT, ARID1A, NOTCH2, and STAG2. Similar with other cancer types, TP53 mutations were always shared between all tumor regions i.e. located on the "trunk" of the evolutionary tree. In addition, we found that variants within several drug targets such as KIT, SYK and PIK3CA were mutated in a fully clonal manner, indicating their therapeutic potentials for HCC. Temporal dissection of mutational signatures suggested that mutagenic processes associated with exposure to aristolochic acid and aflatoxin might play a more important role in early, as opposed to late, stages of HCC development. Moreover, we observed extensive intratumoral epigenetic heterogeneity in HCC based on multiple independent analytical methods and showed that intratumoral methylation heterogeneity might play important roles in the biology of HCC cells. Our results also demonstrated prominent heterogeneity of intratumoral methylation even in a stable HCC genome. Together, these findings highlight widespread intratumoral heterogeneity at both the genomic and epigenomic levels in HCC and provide an important molecular foundation for better understanding the pathogenesis of this malignancy.

  14. Genetic heterogeneity in Malattia Leventinese.

    PubMed

    Toto, L; Parodi, M B; Baralle, F; Casari, G; Ravalico, G; Romano, M

    2002-11-01

    Malattia Leventinese (ML) is a dominant macular dystrophy characterized by drusen at the posterior pole. ML has been associated with a single mutation (R345W) in the EGF-containing fibulin-like extracellular matrix protein 1 (EFEMP-1) gene, but also the EFEMP-2 gene, known to share genetic homology with EFEMP-1, is considered a candidate gene for this genetic disorder. We have characterized clinically and genetically seven members of a three-generation family affected by ML. Results showed that five family members were clinically affected but the DNA sequencing failed to reveal the typical R345W mutation. Furthermore, the linkage analysis to EFEMP-1 (using polymorphic markers D2S337 and D2S2368) and to EFEMP-2 (using D11S987 and D11S1314 markers) gave negative results. Therefore, our results suggest EFEMP-1 or EFEMP-2 genes cannot be excluded as being responsible for ML but other genes have to be considered in the pathogenesis of the disease.

  15. Colloid straining within saturated heterogeneous porous media.

    PubMed

    Porubcan, Alexis A; Xu, Shangping

    2011-02-01

    The transport of 0.46 μm, 2.94 μm, 5.1 μm and 6.06 μm latex particles in heterogeneous porous media prepared from the mixing of 0.78 mm, 0.46 mm and 0.23 mm quartz sands was investigated through column transport experiments. It was observed that the 0.46 μm particles traveled conservatively within the heterogeneous porous media, suggesting that under the experimental conditions employed in this research the strong repulsive interactions between the negatively charged latex particles and the clean quartz sands led to minimal colloid immobilization due to physicochemical filtration. The immobilization of the 2.94 μm, 5.1 μm and 6.06 μm latex particles was thus attributed to colloid straining. Experimental results showed that the straining of colloidal particles within heterogeneous sand mixtures increased when the fraction of finer sands increased. The mathematical model that was developed and tested based on results obtained using uniform sands (Xu et al., 2006) was found to be able to describe colloid straining within heterogeneous porous media. Examination of the relationship between the best-fit values of the clean-bed straining rate coefficients (k(0)) and the ratio of colloid diameter (d(p)) and sand grain size (d(g)) indicated that when number-average sizes were used to represent the size of the heterogeneous porous media, there existed a consistent relationship for both uniform sands and heterogeneous sand mixtures. Similarly, the use of the number-averaged sizes for the heterogeneous porous media produced a uniform relationship between the colloid straining capacity term (λ) and the ratio of d(p)/d(g) for all the sand treatments.

  16. Determination of Tumor Heterogeneity in Colorectal Cancers Using Heterogeneity Tissue Microarrays.

    PubMed

    Stahl, Phillip R; Schnellert, Jessica; Koop, Christina; Simon, Ronald; Marx, Andreas; Izbicki, Jakob R; Sauter, Guido; Quaas, Alexander

    2015-09-01

    Cancer is often heterogeneous both on a morphological and on a genetic level. Though resected tumors are often large, molecular tumor analysis is usually restricted to one tissue block. In this project we introduce a new tool for a high-throughput heterogeneity analysis of colorectal cancer. A heterogeneity tissue microarray (TMA) was manufactured from tissues of 340 patients with colorectal cancer. For this purpose 8 different tissue spots were taken from as many different cancer blocks per patient as possible (at least 4 different blocks). Additional tissue samples from 1 to 4 corresponding lymph node metastases were added from 134 patients. The system was then validated by analysing one parameter each known for minimal (p53) or substantial (HER2) heterogeneity in colorectal cancer. P53 alterations as detected by immunohistochemistry were seen in 174 (51.3 %) of 339 analyzable primary tumors of which 23 (13.2 % of positive cases) showed a heterogeneous distribution pattern. HER2 overexpression was seen in 18 (5.4 %) of 336 evaluable tumors. HER2 amplification occurred in 6 (33.3 %) of the 18 cases with HER2 overexpression. Genomic heterogeneity was more prevalent for HER2 alterations than for p53 alterations. For immunohistochemical expression analysis, 16 of 18 positive cases were heterogeneous (88.9 %) and for amplification 3 of 6 cases (50 %) were heterogeneous. Large section validation revealed, however a considerable fraction of heterogeneous cases were due to technical artifacts. In summary, our data suggest, that heterogeneity TMAs are a powerful tool to rapidly screen for molecular heterogeneity in colorectal cancer.

  17. Phylogenetic Quantification of Intra-tumour Heterogeneity

    PubMed Central

    Schwarz, Roland F.; Trinh, Anne; Sipos, Botond; Brenton, James D.; Goldman, Nick; Markowetz, Florian

    2014-01-01

    Intra-tumour genetic heterogeneity is the result of ongoing evolutionary change within each cancer. The expansion of genetically distinct sub-clonal populations may explain the emergence of drug resistance, and if so, would have prognostic and predictive utility. However, methods for objectively quantifying tumour heterogeneity have been missing and are particularly difficult to establish in cancers where predominant copy number variation prevents accurate phylogenetic reconstruction owing to horizontal dependencies caused by long and cascading genomic rearrangements. To address these challenges, we present MEDICC, a method for phylogenetic reconstruction and heterogeneity quantification based on a Minimum Event Distance for Intra-tumour Copy-number Comparisons. Using a transducer-based pairwise comparison function, we determine optimal phasing of major and minor alleles, as well as evolutionary distances between samples, and are able to reconstruct ancestral genomes. Rigorous simulations and an extensive clinical study show the power of our method, which outperforms state-of-the-art competitors in reconstruction accuracy, and additionally allows unbiased numerical quantification of tumour heterogeneity. Accurate quantification and evolutionary inference are essential to understand the functional consequences of tumour heterogeneity. The MEDICC algorithms are independent of the experimental techniques used and are applicable to both next-generation sequencing and array CGH data. PMID:24743184

  18. Heterogeneity of liver cancer and personalized therapy.

    PubMed

    Li, Liang; Wang, Hongyang

    2016-09-01

    Liver cancer is an extraordinarily heterogeneous malignant disease among the tumors that have so far been identified. Hepatocellular carcinoma (HCC) arises most frequently in the setting of chronic liver inflammation and fibrosis, and takes a variety of course in individual patients to process to tumor. The risk factors such as HBV and/or HCV infections, aflatoxin infection, abuse alcohol intake, metabolic syndrome, obesity and diabetes are closely related to the environmental and genetic susceptibilities to HCC. The consequent resulting genomic instability, molecular and signal transduction network disorders and microenvironmental discrepancies are characterized by the extraordinary heterogeneity of liver cancer. The histology-based definition of the morphological heterogeneity of liver cancer has been modified and refined to treat patients with targeted therapies, but this still cannot solve all the problems. Lack of consistent outcome for anticancer agents and conventional therapies in liver cancer treatment calls for assessing the benefits of new molecularly targeted drugs and combined therapy, under the heterogeneity condition of tumor. The present review article will provide the complex mechanism and phenotype of liver cancer heterogeneity, and help us to execute precision medicine in a really personalized manner.

  19. Emergence of Persistent Infection due to Heterogeneity

    NASA Astrophysics Data System (ADS)

    Agrawal, Vidit; Moitra, Promit; Sinha, Sudeshna

    2017-02-01

    We explore the emergence of persistent infection in a closed region where the disease progression of the individuals is given by the SIRS model, with an individual becoming infected on contact with another infected individual. We investigate the persistence of contagion qualitatively and quantitatively, under increasing heterogeneity in the partitioning of the population into different disease compartments, as well as increasing heterogeneity in the phases of the disease among individuals within a compartment. We observe that when the initial population is uniform, consisting of individuals at the same stage of disease progression, infection arising from a contagious seed does not persist. However when the initial population consists of randomly distributed refractory and susceptible individuals, a single source of infection can lead to sustained infection in the population, as heterogeneity facilitates the de-synchronization of the phases in the disease cycle of the individuals. We also show how the average size of the window of persistence of infection depends on the degree of heterogeneity in the initial composition of the population. In particular, we show that the infection eventually dies out when the entire initial population is susceptible, while even a few susceptibles among an heterogeneous refractory population gives rise to a large persistent infected set.

  20. Emergence of Persistent Infection due to Heterogeneity.

    PubMed

    Agrawal, Vidit; Moitra, Promit; Sinha, Sudeshna

    2017-02-01

    We explore the emergence of persistent infection in a closed region where the disease progression of the individuals is given by the SIRS model, with an individual becoming infected on contact with another infected individual. We investigate the persistence of contagion qualitatively and quantitatively, under increasing heterogeneity in the partitioning of the population into different disease compartments, as well as increasing heterogeneity in the phases of the disease among individuals within a compartment. We observe that when the initial population is uniform, consisting of individuals at the same stage of disease progression, infection arising from a contagious seed does not persist. However when the initial population consists of randomly distributed refractory and susceptible individuals, a single source of infection can lead to sustained infection in the population, as heterogeneity facilitates the de-synchronization of the phases in the disease cycle of the individuals. We also show how the average size of the window of persistence of infection depends on the degree of heterogeneity in the initial composition of the population. In particular, we show that the infection eventually dies out when the entire initial population is susceptible, while even a few susceptibles among an heterogeneous refractory population gives rise to a large persistent infected set.

  1. Heterogeneous physicochemistry of the winter polar stratosphere

    NASA Technical Reports Server (NTRS)

    Turco, R. P.; Toon, O. B.

    1988-01-01

    Present chemical theories of the Antarctic ozone hole assume that heterogeneous reactions involving polar stratospheric clouds (PSCs) are the precursor of springtime ozone depletions. However, none of the theories quantify the rates of proposed heterogeneous processed, and none utilize the extensive data base on PSC's. Thus, all of the theories must be considered incomplete until the heterogeneous mechanisms are properly defined. A unified treatment developed of the cloud related processes, both physical and chemical, and the importance of these processes using observation data is calibrated. The rates are compared competitive heterogeneous processes to place reasonable limits on critical mechanisms such as the denitrification and dechlorination of the polar winter stratosphere. Among the subjects addressed here are the physical/chemical properties of PSC's including their relevant microphysical, optical and compositional characteristics, mass transfer rates of gaseous constituents to cloud particles, adsorption, accommodation and sticking coefficients on cloud particles, time constants for condensation, absorption and other microphysical processes, effects of solubility and vapor pressure on cloud composition, the statistics of cloud processing of chemically active condensible species, rate limiting steps in heterogeneous chemical reactions, and the nonlinear dependence of ozone loss on physical and chemical parameters.

  2. Emergence of Persistent Infection due to Heterogeneity

    PubMed Central

    Agrawal, Vidit; Moitra, Promit; Sinha, Sudeshna

    2017-01-01

    We explore the emergence of persistent infection in a closed region where the disease progression of the individuals is given by the SIRS model, with an individual becoming infected on contact with another infected individual. We investigate the persistence of contagion qualitatively and quantitatively, under increasing heterogeneity in the partitioning of the population into different disease compartments, as well as increasing heterogeneity in the phases of the disease among individuals within a compartment. We observe that when the initial population is uniform, consisting of individuals at the same stage of disease progression, infection arising from a contagious seed does not persist. However when the initial population consists of randomly distributed refractory and susceptible individuals, a single source of infection can lead to sustained infection in the population, as heterogeneity facilitates the de-synchronization of the phases in the disease cycle of the individuals. We also show how the average size of the window of persistence of infection depends on the degree of heterogeneity in the initial composition of the population. In particular, we show that the infection eventually dies out when the entire initial population is susceptible, while even a few susceptibles among an heterogeneous refractory population gives rise to a large persistent infected set. PMID:28145522

  3. Estimating flow heterogeneity in natural fracture systems

    NASA Astrophysics Data System (ADS)

    Leckenby, Robert J.; Sanderson, David J.; Lonergan, Lidia

    2005-10-01

    Examples of small to medium scale fault systems have been mapped in Jurassic sedimentary rocks in north Somerset, England. These examples include contractional and dilational strike-slip oversteps as well as normal faults. These maps form the basis of calculations performed to investigate heterogeneity in natural fracture systems with the aim of predicting fluid flow localisation in different fault styles. As there is no way to measure fracture aperture directly, we use vein thickness to represent an integrated flow path or 'palaeo-aperture' from which we derive a representation of the flow distribution. Three different methods are used to estimate flow heterogeneity based on: (1) fracture density (the ratio of fracture length to area), (2) fracture aperture (fracture porosity) and (3) hydraulic conductance (fracture permeability normalised to the pressure gradient and fluid properties). Our results show that fracture density and hydraulic conductance are poorly correlated and that fracture density does not fully represent the natural heterogeneity of fracture systems. Fracture aperture and hydraulic conductance indicate stronger degrees of flow localisation. Different types of structures also seem to display characteristic and predictable patterns of heterogeneity. Normal fault systems show the highest magnitude of localisation along the faults rather than in the relay ramps, while contractional and dilational strike-slip systems show very strong localisation in the faults and oversteps, respectively. In all cases the amount of damage in the oversteps can modify such patterns of heterogeneity.

  4. Computational model of heterogeneous heating in melanin

    NASA Astrophysics Data System (ADS)

    Kellicker, Jason; DiMarzio, Charles A.; Kowalski, Gregory J.

    2015-03-01

    Melanin particles often present as an aggregate of smaller melanin pigment granules and have a heterogeneous surface morphology. When irradiated with light within the absorption spectrum of melanin, these heterogeneities produce measurable concentrations of the electric field that result in temperature gradients from thermal effects that are not seen with spherical or ellipsoidal modeling of melanin. Modeling melanin without taking into consideration the heterogeneous surface morphology yields results that underestimate the strongest signals or over{estimate their spatial extent. We present a new technique to image phase changes induced by heating using a computational model of melanin that exhibits these surface heterogeneities. From this analysis, we demonstrate the heterogeneous energy absorption and resulting heating that occurs at the surface of the melanin granule that is consistent with three{photon absorption. Using the three{photon dluorescence as a beacon, we propose a method for detecting the extents of the melanin granule using photothermal microscopy to measure the phase changes resulting from the heating of the melanin.

  5. Understanding cancer stem cell heterogeneity and plasticity

    PubMed Central

    Tang, Dean G

    2012-01-01

    Heterogeneity is an omnipresent feature of mammalian cells in vitro and in vivo. It has been recently realized that even mouse and human embryonic stem cells under the best culture conditions are heterogeneous containing pluripotent as well as partially committed cells. Somatic stem cells in adult organs are also heterogeneous, containing many subpopulations of self-renewing cells with distinct regenerative capacity. The differentiated progeny of adult stem cells also retain significant developmental plasticity that can be induced by a wide variety of experimental approaches. Like normal stem cells, recent data suggest that cancer stem cells (CSCs) similarly display significant phenotypic and functional heterogeneity, and that the CSC progeny can manifest diverse plasticity. Here, I discuss CSC heterogeneity and plasticity in the context of tumor development and progression, and by comparing with normal stem cell development. Appreciation of cancer cell plasticity entails a revision to the earlier concept that only the tumorigenic subset in the tumor needs to be targeted. By understanding the interrelationship between CSCs and their differentiated progeny, we can hope to develop better therapeutic regimens that can prevent the emergence of tumor cell variants that are able to found a new tumor and distant metastases. PMID:22357481

  6. Implications of Heterogeneity in Multiple Myeloma

    PubMed Central

    de Mel, Sanjay; Lim, Su Hong; Tung, Moon Ley; Chng, Wee-Joo

    2014-01-01

    Multiple myeloma is the second most common hematologic malignancy in the world. Despite improvement in outcome, the disease is still incurable for most patients. However, not all myeloma are the same. With the same treatment, some patients can have very long survival whereas others can have very short survival. This suggests that there is underlying heterogeneity in myeloma. Studies over the years have revealed multiple layers of heterogeneity. First, clinical parameters such as age and tumor burden could significantly affect outcome. At the genetic level, there are also significant heterogeneity ranging for chromosome numbers, genetic translocations, and genetic mutations. At the clonal level, there appears to be significant clonal heterogeneity with multiple clones coexisting in the same patient. At the cell differentiation level, there appears to be a hierarchy of clonally related cells that have different clonogenic potential and sensitivity to therapies. These levels of complexities present challenges in terms of treatment and prognostication as well as monitoring of treatment. However, if we can clearly delineate and dissect this heterogeneity, we may also be presented with unique opportunities for precision and personalized treatment of myeloma. Some proof of concepts of such approaches has been demonstrated. PMID:25101266

  7. Predicting cancer involvement of genes from heterogeneous data

    PubMed Central

    Aragues, Ramon; Sander, Chris; Oliva, Baldo

    2008-01-01

    Background Systematic approaches for identifying proteins involved in different types of cancer are needed. Experimental techniques such as microarrays are being used to characterize cancer, but validating their results can be a laborious task. Computational approaches are used to prioritize between genes putatively involved in cancer, usually based on further analyzing experimental data. Results We implemented a systematic method using the PIANA software that predicts cancer involvement of genes by integrating heterogeneous datasets. Specifically, we produced lists of genes likely to be involved in cancer by relying on: (i) protein-protein interactions; (ii) differential expression data; and (iii) structural and functional properties of cancer genes. The integrative approach that combines multiple sources of data obtained positive predictive values ranging from 23% (on a list of 811 genes) to 73% (on a list of 22 genes), outperforming the use of any of the data sources alone. We analyze a list of 20 cancer gene predictions, finding that most of them have been recently linked to cancer in literature. Conclusion Our approach to identifying and prioritizing candidate cancer genes can be used to produce lists of genes likely to be involved in cancer. Our results suggest that differential expression studies yielding high numbers of candidate cancer genes can be filtered using protein interaction networks. PMID:18371197

  8. Information flow in heterogeneously interacting systems.

    PubMed

    Yamaguti, Yutaka; Tsuda, Ichiro; Takahashi, Yoichiro

    2014-02-01

    Motivated by studies on the dynamics of heterogeneously interacting systems in neocortical neural networks, we studied heterogeneously-coupled chaotic systems. We used information-theoretic measures to investigate directions of information flow in heterogeneously coupled Rössler systems, which we selected as a typical chaotic system. In bi-directionally coupled systems, spontaneous and irregular switchings of the phase difference between two chaotic oscillators were observed. The direction of information transmission spontaneously switched in an intermittent manner, depending on the phase difference between the two systems. When two further oscillatory inputs are added to the coupled systems, this system dynamically selects one of the two inputs by synchronizing, selection depending on the internal phase differences between the two systems. These results indicate that the effective direction of information transmission dynamically changes, induced by a switching of phase differences between the two systems.

  9. Metabolic heterogeneity in human lung tumors

    PubMed Central

    Hensley, Christopher T.; Faubert, Brandon; Yuan, Qing; Lev-Cohain, Naama; Jin, Eunsook; Kim, Jiyeon; Jiang, Lei; Ko, Bookyung; Skelton, Rachael; Loudat, Laurin; Wodzak, Michelle; Klimko, Claire; McMillan, Elizabeth; Butt, Yasmeen; Ni, Min; Oliver, Dwight; Torrealba, Jose; Malloy, Craig R.; Kernstine, Kemp; Lenkinski, Robert E.; DeBerardinis, Ralph J.

    2015-01-01

    SUMMARY Non-small cell lung cancer (NSCLC) is heterogeneous in the genetic and environmental parameters that influence cell metabolism in culture. Here, we assessed the impact of these factors on human NSCLC metabolism in vivo using intra-operative 13C-glucose infusions in nine NSCLC patients to compare metabolism between tumors and benign lung. While enhanced glycolysis and glucose oxidation were common among these tumors, we observed evidence for oxidation of multiple nutrients in each of them, including lactate as a potential carbon source. Moreover, metabolically heterogeneous regions were identified within and between tumors, and surprisingly, our data suggested potential contributions of non-glucose nutrients in well-perfused tumor areas. Our findings not only demonstrate the heterogeneity in tumor metabolism in vivo but also highlight the strong influence of the microenvironment on this feature. PMID:26853473

  10. Microfabricated components for heterogeneously catalysed reactions

    NASA Astrophysics Data System (ADS)

    Wießmeier, Georg; Hönicke, Dieter

    1996-06-01

    Microsystems offer considerable industrial potential for unit operations, e.g. heat transfer, mass transport, and mixing of gases and liquids. The development of techniques for performing chemical reactions in microsystems has high priority. Only a few examples are known of using microreactors for performing homogeneous chemical reactions and heterogeneously catalysed liquid-phase enzyme reactions. However, heterogeneously catalysed gas-phase reactions in microreactors have not been reported at all. This is due to the lack of surfaces having enough catalytically active sites. The present article describes a method for treating the surfaces of channels in a microreactor in order to achieve adequate numbers of catalytically active and selective sites - which is the main prerequisite for the performance of heterogeneously catalysed reactions. The experimental procedure and the measurements of characteristic parameters are described. An envisaged scheme for a chemical microsystem similar to a chemical microplant is presented, and its scaling up via replication is addressed.

  11. Multiple roles of graphene in heterogeneous catalysis.

    PubMed

    Fan, Xiaobin; Zhang, Guoliang; Zhang, Fengbao

    2015-05-21

    Scientific interest in graphene as a catalyst and as a catalyst support in heterogeneous catalytic reactions has grown dramatically over the past several years. The present critical review summarizes the multiple roles of graphene in heterogeneous catalysis and highlights the influence of defects, heteroatom-containing functionalities, and graphene's two-dimensional structure on catalytic performance. We first discuss the role and advantages of graphene as a catalyst support, with emphasis on its interactions with the catalytic phases and the influence of mass transfer processes. We then clarify the origin of the intrinsic catalytic activity of graphene in heterogeneous catalytic reactions. Finally we suggest challenges and potential practical applications for graphene in industrial processes.

  12. Microswimmers in Complex Environments with Heterogeneous Microstructure

    NASA Astrophysics Data System (ADS)

    Hyon, Yunkyong; Fu, Henry

    2011-11-01

    We will discuss the swimming of microorganisms in complex and heterogeneous environments. Microswimmers in biological complex fluids, for instance, bacteria and sperm, are often greatly influenced by heterogeneous medium microstructure with length scales comparable to themselves. We characterize the interaction between the microswimmer and the medium microstructure using the model Golestanian three-sphere swimmer, treating the hydrodynamic interaction with the microstructure through the Oseen tensor. In this investigation, the microstructure of the heterogeneous environment is modeled by fixed spheres representing obstacles, or chains consisting of spheres connected with elastic springs. We find that the swimming speed of the swimmer depends on the force and deformation exerted on micro-structure. Furthermore, we find that while short freely suspended chains and short chains anchored at their ends interact with swimmer quite differently, long enough chains interact similarly, that is, a long mobile chain acts like a anchored chain. We discuss the implications for swimmer interactions with polymer solutions and compliant networks.

  13. Heterogeneous Distributed Computing for Computational Aerosciences

    NASA Technical Reports Server (NTRS)

    Sunderam, Vaidy S.

    1998-01-01

    The research supported under this award focuses on heterogeneous distributed computing for high-performance applications, with particular emphasis on computational aerosciences. The overall goal of this project was to and investigate issues in, and develop solutions to, efficient execution of computational aeroscience codes in heterogeneous concurrent computing environments. In particular, we worked in the context of the PVM[1] system and, subsequent to detailed conversion efforts and performance benchmarking, devising novel techniques to increase the efficacy of heterogeneous networked environments for computational aerosciences. Our work has been based upon the NAS Parallel Benchmark suite, but has also recently expanded in scope to include the NAS I/O benchmarks as specified in the NHT-1 document. In this report we summarize our research accomplishments under the auspices of the grant.

  14. Self-attracting walk on heterogeneous networks

    NASA Astrophysics Data System (ADS)

    Kim, Kanghun; Kyoung, Jaegu; Lee, D.-S.

    2016-05-01

    Understanding human mobility in cyberspace becomes increasingly important in this information era. While human mobility, memory-dependent and subdiffusive, is well understood in Euclidean space, it remains elusive in random heterogeneous networks like the World Wide Web. Here we study the diffusion characteristics of self-attracting walks, in which a walker is more likely to move to the locations visited previously than to unvisited ones, on scale-free networks. Under strong attraction, the number of distinct visited nodes grows linearly in time with larger coefficients in more heterogeneous networks. More interestingly, crossovers to sublinear growths occur in strongly heterogeneous networks. To understand these phenomena, we investigate the characteristic volumes and topology of the cluster of visited nodes and find that the reinforced attraction to hubs results in expediting exploration first but delaying later, as characterized by the scaling exponents that we derive. Our findings and analysis method can be useful for understanding various diffusion processes mediated by human.

  15. Self-attracting walk on heterogeneous networks.

    PubMed

    Kim, Kanghun; Kyoung, Jaegu; Lee, D-S

    2016-05-01

    Understanding human mobility in cyberspace becomes increasingly important in this information era. While human mobility, memory-dependent and subdiffusive, is well understood in Euclidean space, it remains elusive in random heterogeneous networks like the World Wide Web. Here we study the diffusion characteristics of self-attracting walks, in which a walker is more likely to move to the locations visited previously than to unvisited ones, on scale-free networks. Under strong attraction, the number of distinct visited nodes grows linearly in time with larger coefficients in more heterogeneous networks. More interestingly, crossovers to sublinear growths occur in strongly heterogeneous networks. To understand these phenomena, we investigate the characteristic volumes and topology of the cluster of visited nodes and find that the reinforced attraction to hubs results in expediting exploration first but delaying later, as characterized by the scaling exponents that we derive. Our findings and analysis method can be useful for understanding various diffusion processes mediated by human.

  16. Heterogeneous Chemistry Related to Stratospheric Aircraft

    NASA Technical Reports Server (NTRS)

    Tolbert, Margaret A.

    1995-01-01

    Emissions from stratospheric aircraft that may directly or indirectly affect ozone include NO(y), H2O, soot and sulfuric acid. To fully assess the impact of such emissions, it is necessary to have a full understanding of both the homogeneous and heterogeneous transformations that may occur in the stratosphere. Heterogeneous reactions on stratospheric particles play a key role in partitioning ozone-destroying species between their active and reservoir forms. In particular, heterogeneous reactions tend to activate odd chlorine while deactivating odd nitrogen. Accurate modeling of the net atmospheric effects of stratospheric aircraft requires a thorough understanding of the competing effects of this activation/deactivation. In addition, a full understanding of the potential aircraft impacts requires that the abundance, composition and formation mechanisms of the particles themselves be established. Over the last three years with support from the High Speed Research Program, we have performed laboratory experiments to determine the chemical composition, formation mechanism, and reactivity of stratospheric aerosols.

  17. Heterogeneity and thermal modeling of ground water.

    PubMed

    Ferguson, Grant

    2007-01-01

    Heat transport in aquifers is becoming an increasingly important topic due to recent growth in the use of ground water in thermal applications. However, the effect of heterogeneity on heat transport in aquifers has yet to be examined in the same detail as it has been for solute transport, and it is unclear what effect this may have on our ability to create accurate models. This study examines this issue through stochastic modeling using the geostatistics for two aquifers with low and high degrees of heterogeneity. The results indicate that there is considerable uncertainty in the distribution of heat associated with injection of warm water into an aquifer. Heterogeneity in the permeability field was also found to slightly reduce the ability to recover this introduced heat at a later time. These simulations also reveal that hydrodynamic macrodispersion is an important consideration in some heat flow problems.

  18. Deconstructing transcriptional heterogeneity in pluripotent stem cells.

    PubMed

    Kumar, Roshan M; Cahan, Patrick; Shalek, Alex K; Satija, Rahul; DaleyKeyser, A Jay; Li, Hu; Zhang, Jin; Pardee, Keith; Gennert, David; Trombetta, John J; Ferrante, Thomas C; Regev, Aviv; Daley, George Q; Collins, James J

    2014-12-04

    Pluripotent stem cells (PSCs) are capable of dynamic interconversion between distinct substates; however, the regulatory circuits specifying these states and enabling transitions between them are not well understood. Here we set out to characterize transcriptional heterogeneity in mouse PSCs by single-cell expression profiling under different chemical and genetic perturbations. Signalling factors and developmental regulators show highly variable expression, with expression states for some variable genes heritable through multiple cell divisions. Expression variability and population heterogeneity can be influenced by perturbation of signalling pathways and chromatin regulators. Notably, either removal of mature microRNAs or pharmacological blockage of signalling pathways drives PSCs into a low-noise ground state characterized by a reconfigured pluripotency network, enhanced self-renewal and a distinct chromatin state, an effect mediated by opposing microRNA families acting on the Myc/Lin28/let-7 axis. These data provide insight into the nature of transcriptional heterogeneity in PSCs.

  19. Deconstructing transcriptional heterogeneity in pluripotent stem cells

    PubMed Central

    Shalek, Alex K.; Satija, Rahul; DaleyKeyser, AJay; Li, Hu; Zhang, Jin; Pardee, Keith; Gennert, David; Trombetta, John J.; Ferrante, Thomas C.; Regev, Aviv; Daley, George Q.; Collins, James J.

    2014-01-01

    SUMMARY Pluripotent stem cells (PSCs) are capable of dynamic interconversion between distinct substates, but the regulatory circuits specifying these states and enabling transitions between them are not well understood. We set out to characterize transcriptional heterogeneity in PSCs by single-cell expression profiling under different chemical and genetic perturbations. Signaling factors and developmental regulators show highly variable expression, with expression states for some variable genes heritable through multiple cell divisions. Expression variability and population heterogeneity can be influenced by perturbation of signaling pathways and chromatin regulators. Strikingly, either removal of mature miRNAs or pharmacologic blockage of signaling pathways drives PSCs into a low-noise ground state characterized by a reconfigured pluripotency network, enhanced self-renewal, and a distinct chromatin state, an effect mediated by opposing miRNA families acting on the c-myc / Lin28 / let-7 axis. These data illuminate the nature of transcriptional heterogeneity in PSCs. PMID:25471879

  20. Characterizing hydrogeologic heterogeneity using lithologic data

    SciTech Connect

    Flach, G.; Hamm, LL.L.; Harris, M.K.; Thayer, P.A.; Haselow, J.S.; Smits, A.D.

    1997-06-13

    Large-scale (>1 m) variability in hydraulic conductivity is usually the main influence on field-scale groundwater flow patterns and dispersive transport. Incorporating realistic hydraulic conductivity heterogeneity into flow and transport models is paramount to accurate simulations, particularly for contaminant migration. Sediment lithologic descriptions and geophysical logs typically offer finer spatial resolution, and therefore more potential information about site-scale heterogeneity, than other site characterization data. In this study, a technique for generating a heterogeneous, three- dimensional hydraulic conductivity field from sediment lithologic descriptions is presented. The approach involves creating a three-dimensional, fine-scale representation of mud (silt and clay) percentage using a stratified interpolation algorithm. Mud percentage is then translated into horizontal and vertical conductivity using direct correlations derived from measured data and inverse groundwater flow modeling. Lastly, the fine-scale conductivity fields are averaged to create a coarser grid for use in groundwater flow and transport modeling.

  1. Genetic heterogeneity among kindreds with Alport syndrome.

    PubMed Central

    Hasstedt, S J; Atkin, C L; San Juan, A C

    1986-01-01

    Twenty-three kindreds were ascertained through patients at renal clinics at University of Utah Associated Hospitals. Urinalysis indicated glomerulonephritis in 231 of 997 examined kindred members; medical records documented kidney disease consistent with glomerulonephritis in 88 unexamined kindred members. Renal biopsies of 35 persons in a subset of 14 kindreds showed ultrastructural changes and absence of immune phenomena consistent with the diagnosis of Alport syndrome. End-stage renal disease (ESRD) had occurred in 72 (49%) of 148 known affected males and in 13 (8%) of 171 known affected females. No father-son affected pairs occurred in any of the kindreds; 84% of daughters of affected fathers were affected, and 49% of sons and 48% of daughters of affected mothers were affected. One of three phenotypes (juvenile Alport syndrome with deafness, adult Alport syndrome with deafness, or adult Alport syndrome without deafness or other defects) occurred in each of the 23 kindreds. We applied likelihood analysis to test for genetic heterogeneity underlying the phenotypic heterogeneity. In the first application (the admixture test), we tested for the occurrence of two forms of the disease without specifying which kindred had which form; we found insufficient evidence of admixture. In the second application (the predivided-sample test), we tested for genetic heterogeneity expressed as phenotypic heterogeneity. Kindreds were successively divided into two subgroups, with admission to the first subgroup dependent upon: (1) having greater than or equal to 2 males with ESRD, (2) occurrence of deafness in most nephrologically affected male family members, and (3) intrakindred mean age of ESRD in males later than age 31. Weak evidence of heterogeneity was found for category (1); stronger evidence of heterogeneity was found for category (3). Penetrance of microscopic hematuria in female heterozygotes was estimated as 82% overall, 85% for adult Alport syndrome, and 28% for

  2. Temperature dependent heterogeneous rotational correlation in lipids

    NASA Astrophysics Data System (ADS)

    Dadashvand, Neda; Othon, Christina M.

    2016-12-01

    Lipid structures exhibit complex and highly dynamic lateral structure; and changes in lipid density and fluidity are believed to play an essential role in membrane targeting and function. The dynamic structure of liquids on the molecular scale can exhibit complex transient density fluctuations. Here the lateral heterogeneity of lipid dynamics is explored in free standing lipid monolayers. As the temperature is lowered the probes exhibit increasingly broad and heterogeneous rotational correlation. This increase in heterogeneity appears to exhibit a critical onset, similar to those observed for glass forming fluids. We explore heterogeneous relaxation in in a single constituent lipid monolayer of 1, 2-dimyristoyl-sn-glycero-3-phosphocholine by measuring the rotational diffusion of a fluorescent probe (1-palmitoyl-2-[1]-sn-glycero-3-phosphocholine), which is embedded in the lipid monolayer at low labeling density. Dynamic distributions are measured using wide-field time-resolved fluorescence anisotropy. The observed relaxation exhibits a narrow, liquid-like distribution at high temperatures (τ ˜ 2.4 ns), consistent with previous experimental measures (Dadashvand et al 2014 Struct. Dyn. 1 054701, Loura and Ramalho 2007 Biochim. Biophys. Acta 1768 467-478). However, as the temperature is quenched, the distribution broadens, and we observe the appearance of a long relaxation population (τ ˜ 16.5 ns). This supports the heterogeneity observed for lipids at high packing densities, and demonstrates that the nanoscale diffusion and reorganization in lipid structures can be significantly complex, even in the simplest amorphous architectures. Dynamical heterogeneity of this form can have a significant impact on the organization, permeability and energetics of lipid membrane structures.

  3. Temperature dependent heterogeneous rotational correlation in lipids.

    PubMed

    Dadashvand, Neda; Othon, Christina M

    2016-11-15

    Lipid structures exhibit complex and highly dynamic lateral structure; and changes in lipid density and fluidity are believed to play an essential role in membrane targeting and function. The dynamic structure of liquids on the molecular scale can exhibit complex transient density fluctuations. Here the lateral heterogeneity of lipid dynamics is explored in free standing lipid monolayers. As the temperature is lowered the probes exhibit increasingly broad and heterogeneous rotational correlation. This increase in heterogeneity appears to exhibit a critical onset, similar to those observed for glass forming fluids. We explore heterogeneous relaxation in in a single constituent lipid monolayer of 1, 2-dimyristoyl-sn-glycero-3-phosphocholine  by measuring the rotational diffusion of a fluorescent probe (1-palmitoyl-2-[1]-sn-glycero-3-phosphocholine), which is embedded in the lipid monolayer at low labeling density. Dynamic distributions are measured using wide-field time-resolved fluorescence anisotropy. The observed relaxation exhibits a narrow, liquid-like distribution at high temperatures (τ ∼ 2.4 ns), consistent with previous experimental measures (Dadashvand et al 2014 Struct. Dyn. 1 054701, Loura and Ramalho 2007 Biochim. Biophys. Acta 1768 467-478). However, as the temperature is quenched, the distribution broadens, and we observe the appearance of a long relaxation population (τ ∼ 16.5 ns). This supports the heterogeneity observed for lipids at high packing densities, and demonstrates that the nanoscale diffusion and reorganization in lipid structures can be significantly complex, even in the simplest amorphous architectures. Dynamical heterogeneity of this form can have a significant impact on the organization, permeability and energetics of lipid membrane structures.

  4. Psoriatic arthritis: embracing pathogenetic and clinical heterogeneity?

    PubMed

    McInnes, Iain B

    2016-01-01

    Psoriatic arthritis (PsA) is a clinically heterogeneous condition of skin, joint, enthesis and bone that provides considerable unmet therapeutic need. Recent treatment advances have offered new opportunities to improve quality of life and long term well being for afflicted patients. It is timely therefore, to consider the underlying heterogeneity inherent in the disease from a pathologic aspect so as to best optimise the choice and order of therapeutic application over time. Herein I will discuss the various contributions made by immune pathways to discrete tissue compartments that in turn might allow a more targeted approach to the management of PsA in which different tissues express variable severity of involvement.

  5. Stabilizing metal nanoparticles for heterogeneous catalysis.

    PubMed

    Cao, Anmin; Lu, Rongwen; Veser, Götz

    2010-11-07

    Metal nanoparticles hold great promise for heterogeneous catalysis due to their high dispersion, large concentration of highly undercoordinated surface sites, and the presence of quantum confinement effects, which can drastically alter their reactivity. However, the poor thermal stability of nano-sized particles limits their use to low temperature conditions and constitutes one of the key hurdles towards industrial application. The present perspective paper briefly reviews the mechanisms underlying nanoparticle sintering, and then gives an overview of emerging approaches towards stabilizing metal nanoparticles for heterogeneous catalysis. We conclude by highlighting the current needs for further developments in the field.

  6. Method for Accessing Distributed Heterogeneous Databases

    NASA Technical Reports Server (NTRS)

    Jacobs, B. E.

    1984-01-01

    A scenario of relational, hierarchial, and network data bases is presented and a distributed access view integrated data base system (DAVID) is described for uniformly accessing data bases which are heterogeneous and physically distributed. The DAVID system is based on data base logic so that the relational approach is generalized to the heterogeneous approach. The global data manager is explained as are global data manipulation languages which can operate on all the data bases and can query the data dictionary and the data directory.

  7. Heterogeneity and Scaling in Geologic Media

    SciTech Connect

    Gregory N. Boitnott; Gilles Y. Bussod; Paul N. Hagin; Stephen R. Brown

    2005-04-18

    The accurate characterization and remediation of contaminated subsurface environments requires the detailed knowledge of subsurface structures and flow paths. Enormous resources are invested in scoping and characterizing sites using core sampling, 3-D geophysical surveys, well tests, etc.... Unfortunately, much of the information acquired is lost to compromises and simplifications made in constructing numerical grids for the simulators used to predict flow and transport from the contaminated area to the accessible environment. In rocks and soils, the bulk geophysical and transport properties of the matrix and of fracture systems are determined by the juxtaposition of geometric features at many length scales. In the interest of computational efficiency, recognized heterogeneities are simplified, averaged out, or entirely ignored in spite of recent studies that recognize that: (1) Structural and lithologic heterogeneities exist on all scales in rocks. (2) Small heterogeneities influence, and can control the physical and chemical properties of rocks. In this work we propose a physically based approach for the description and treatment of heterogeneities, that highlights the use of laboratory equipment designed to measure the effect on physical properties of fine scale heterogeneities observed in rocks and soils. We then discuss the development of an integration methodology that uses these measurements to develop and upscale flow and transport models. Predictive simulations are 'calibrated' to the measured heterogeneity data, and subsequently upscaled in a way that is consistent with the transport physics and the efficient use of environmental geophysics. This methodology provides a more accurate interpretation and representation of the subsurface for both environmental engineering and remediation. We show through examples, (i) the important influence of even subtle heterogeneity in the interpreting of geophysical data, and (ii) how physically based upscaling can lead

  8. Strip and microstrip line periodic heterogeneities

    NASA Astrophysics Data System (ADS)

    Lerer, A. M.; Lerer, B. M.; Ryazanov, V. D.; Sledkov, V. A.

    1985-04-01

    A quasistatic method is described for analyzing periodic heterogeneities in single and coupled strip lines and microstrip lines. An ALGOL program on a BESM-6 computer calculated the running inductance and capacitance, wave impedances and delay coefficients for single and coupled strip lines and microstrip lines with periodic heterogeneities of arbitrary form. The analyzed quantities are investigated as a function of distance (from side shield to the strip), number of terms in the series and number of approximated functions. The method demonstrates good convergence and requires little machine time and results were verified experimentally.

  9. Atmospheric pressure microwave assisted heterogeneous catalytic reactions.

    PubMed

    Chemat-Djenni, Zoubida; Hamada, Boudjema; Chemat, Farid

    2007-07-11

    The purpose of the study was to investigate microwave selective heating phenomena and their impact on heterogeneous chemical reactions. We also present a tool which will help microwave chemists to answer to such questions as "My reaction yields 90% after 7 days at reflux; is it possible to obtain the same yield after a few minutes under microwaves?" and to have an approximation of their reactions when conducted under microwaves with different heterogeneous procedures. This model predicting reaction kinetics and yields under microwave heating is based on the Arrhenius equation, in agreement with experimental data and procedures.

  10. Method for Accessing Distributed Heterogeneous Databases

    NASA Technical Reports Server (NTRS)

    Jacobs, B. E.

    1984-01-01

    A scenario of relational, hierarchial, and network data bases is presented and a distributed access view integrated data base system (DAVID) is described for uniformly accessing data bases which are heterogeneous and physically distributed. The DAVID system is based on data base logic so that the relational approach is generalized to the heterogeneous approach. The global data manager is explained as are global data manipulation languages which can operate on all the data bases and can query the data dictionary and the data directory.

  11. Micro- and nanorobots swimming in heterogeneous liquids.

    PubMed

    Nelson, Bradley J; Peyer, Kathrin E

    2014-09-23

    Essentially all experimental investigations of swimming micro- and nanorobots have focused on swimming in homogeneous Newtonian liquids. In this issue of ACS Nano, Schamel et al. investigate the actuation of "nanopropellers" in a viscoelastic biological gel that illustrates the importance of the size of the nanostructure relative to the gel mesh size. In this Perspective, we shed further light on the swimming performance of larger microrobots swimming in heterogeneous liquids. One of the interesting results of our work is that earlier findings on the swimming performance of motile bacteria in heterogeneous liquids agree, in principle, with our results. We also discuss future research directions that should be pursued in this fascinating interdisciplinary field.

  12. Overcoming semantic heterogeneity in spatial data infrastructures

    NASA Astrophysics Data System (ADS)

    Lutz, M.; Sprado, J.; Klien, E.; Schubert, C.; Christ, I.

    2009-04-01

    In current spatial data infrastructures (SDIs), it is still often difficult to effectively exchange or re-use geographic data sets. A main reason for this is semantic heterogeneity, which occurs at different levels: at the metadata, the schema and the data content level. It is the goal of the work presented in this paper to overcome the problems caused by semantic heterogeneity on all three levels. We present a method based on ontologies and logical reasoning, which enhances the discovery, retrieval, interpretation and integration of geographic data in SDIs. Its benefits and practical use are illustrated with examples from the domains of geology and hydrology.

  13. Retinal regionalization and heterogeneity of butterfly eyes

    NASA Astrophysics Data System (ADS)

    Stavenga, D.; Kinoshita, M.; Yang, E.-C.; Arikawa, K.

    2001-11-01

    The regional characteristics of the eyes of butterflies from different families have been surveyed using epi-illumination microscopy, utilizing the eyeshine visible due to the tapetum situated proximally to the rhabdom. All butterflies studied have a high spatial acuity in the frontal region. The facet diameter varies slightly across the eye, and the interommatidial angle and the eye parameter p are especially large dorsally. Whereas the ommatidial lattice is generally highly regular, the eyeshine colours distinctly depend on the species. Sometimes the eyeshine is locally uniform, but often it is heterogeneous. It is hypothesized that the regional characteristics as well as the local heterogeneity are adaptations that optimize spectral discrimination.

  14. Retinal regionalization and heterogeneity of butterfly eyes.

    PubMed

    Stavenga, D G; Kinoshita, M; Yang, E C; Arikawa, K

    2001-11-01

    The regional characteristics of the eyes of butterflies from different families have been surveyed using epi-illumination microscopy, utilizing the eyeshine visible due to the tapetum situated proximally to the rhabdom. All butterflies studied have a high spatial acuity in the frontal region. The facet diameter varies slightly across the eye, and the interommatidial angle and the eye parameter p are especially large dorsally. Whereas the ommatidial lattice is generally highly regular, the eyeshine colours distinctly depend on the species. Sometimes the eyeshine is locally uniform, but often it is heterogeneous. It is hypothesized that the regional characteristics as well as the local heterogeneity are adaptations that optimize spectral discrimination.

  15. Aspergillus fumigatus Photobiology Illuminates the Marked Heterogeneity between Isolates

    PubMed Central

    Fuller, Kevin K.; Cramer, Robert A.; Zegans, Michael E.

    2016-01-01

    ABSTRACT The given strain of Aspergillus fumigatus under study varies across laboratories, ranging from a few widely used “standards,” e.g., Af293 or CEA10, to locally acquired isolates that may be unique to one investigator. Since experiments concerning physiology or gene function are seldom replicated by others, i.e., in a different A. fumigatus background, the extent to which behavioral heterogeneity exists within the species is poorly understood. As a proxy for assessing such intraspecies variability, we analyzed the light response of 15 A. fumigatus isolates and observed striking quantitative and qualitative heterogeneity among them. The majority of the isolates fell into one of two seemingly mutually exclusive groups: (i) “photopigmenters” that robustly accumulate hyphal melanin in the light and (ii) “photoconidiators” that induce sporulation in the light. These two distinct responses were both governed by the same upstream blue light receptor, LreA, indicating that a specific protein’s contribution can vary in a strain-dependent manner. Indeed, while LreA played no apparent role in regulating cell wall homeostasis in strain Af293, it was essential in that regard in strain CEA10. The manifest heterogeneity in the photoresponses led us to compare the virulence levels of selected isolates in a murine model; remarkably, the virulence did vary greatly, although not in a manner that correlated with their overt light response. Taken together, these data highlight the extent to which isolates of A. fumigatus can vary, with respect to both broad physiological characteristics (e.g., virulence and photoresponse) and specific protein functionality (e.g., LreA-dependent phenotypes). PMID:27651362

  16. Higher expression of the heterogeneous nuclear ribonucleoprotein k in melanoma.

    PubMed

    Wen, Fushi; Shen, Alex; Shanas, Reneé; Bhattacharyya, Achyut; Lian, Fangru; Hostetter, Galen; Shi, Jiaqi

    2010-10-01

    The heterogeneous nuclear ribonucleoprotein (hnRNP) K is an essential RNA and DNA binding protein involved in gene expression and signal transduction. The role of hnRNP K in cancer is relatively understudied. However, several cellular functions strongly indicate that hnRNP K is involved in tumorigenesis. Oncogenes c-Src, c-myc, and eIF4E are regulated by hnRNP K. We have shown an increased cytoplasmic hnRNP K in pancreatic cancer. In the present study, we investigated the altered expression of hnRNP K protein and its correlation with p-ERK in melanoma using human melanoma cell lines and tissue microarray. The protein levels of hnRNP K and p-ERK in 8 human melanoma cell lines and a melanoma progression tissue microarray containing 80 melanoma, 23 dysplastic nevi, and 14 benign nevi specimens were analyzed using Western blot and immunohistochemistry analysis. hnRNP K was knocked down by siRNA, and its effect on melanoma cells was assessed. We showed a higher hnRNP K protein level in both melanoma cell lines and melanoma tissue specimens, which correlated with a higher c-myc expression. An increase in the cytoplasmic hnRNP K and eIF4E protein levels in melanoma cells is also seen. p-ERK level was also higher in dysplastic nevi and melanoma tissues, but did not correlate with hnRNP K protein level. We then demonstrated that knocking down of hnRNP K by siRNA inhibited melanoma cell growth and colony formation, as well as c-myc expression. hnRNP K expression correlated with melanoma and may play a role in melanoma tumorigenesis.

  17. Homogeneity and heterogeneity in amylase production by Bacillus subtilis under different growth conditions.

    PubMed

    Ploss, Tina N; Reilman, Ewoud; Monteferrante, Carmine G; Denham, Emma L; Piersma, Sjouke; Lingner, Anja; Vehmaanperä, Jari; Lorenz, Patrick; van Dijl, Jan Maarten

    2016-03-29

    Bacillus subtilis is an important cell factory for the biotechnological industry due to its ability to secrete commercially relevant proteins in large amounts directly into the growth medium. However, hyper-secretion of proteins, such as α-amylases, leads to induction of the secretion stress-responsive CssR-CssS regulatory system, resulting in up-regulation of the HtrA and HtrB proteases. These proteases degrade misfolded proteins secreted via the Sec pathway, resulting in a loss of product. The aim of this study was to investigate the secretion stress response in B. subtilis 168 cells overproducing the industrially relevant α-amylase AmyM from Geobacillus stearothermophilus, which was expressed from the strong promoter P(amyQ)-M. Here we show that activity of the htrB promoter as induced by overproduction of AmyM was "noisy", which is indicative for heterogeneous activation of the secretion stress pathway. Plasmids were constructed to allow real-time analysis of P(amyQ)-M promoter activity and AmyM production by, respectively, transcriptional and out-of-frame translationally coupled fusions with gfpmut3. Our results show the emergence of distinct sub-populations of high- and low-level AmyM-producing cells, reflecting heterogeneity in the activity of P(amyQ)-M. This most likely explains the heterogeneous secretion stress response. Importantly, more homogenous cell populations with regard to P(amyQ)-M activity were observed for the B. subtilis mutant strain 168degUhy32, and the wild-type strain 168 under optimized growth conditions. Expression heterogeneity of secretory proteins in B. subtilis can be suppressed by degU mutation and optimized growth conditions. Further, the out-of-frame translational fusion of a gene for a secreted target protein and gfp represents a versatile tool for real-time monitoring of protein production and opens novel avenues for Bacillus production strain improvement.

  18. Molecular and clinical heterogeneity in palmoplantar keratoderma (PPK)

    SciTech Connect

    Hennis, H.C.; Sperling, K.; Reis, A.

    1994-09-01

    Palmoplantar keratoderma (PPK) is a frequent hereditary disorder of keratinization in man. Various clinically, histopathologically, and genetically distinct phenotypes can be diagnosed. Recently, we have identified mutations in the keratin 9 gene on chromosome 17q21 in a number of patients with the epidermolytic form of palmoplantar keratoderma (EPPK). We have now investigated three large families with clinically different types of PPK for linkage to either the type II keratin gene cluster on chromosome 12q or the type I keratin gene cluster on chromosome 17q using microsatellites and polymorphisms in several keratin genes. One family each with diffuse PPK associated with carcinoma of the esophagus (type Clarke-Howel-Evans-McConnell), PPK associated with sensorineural hearing loss, and keratolytic winter erythema (Oudtshoorn skin disease) was analyzed. We were able to exclude both type I and type II keratin genes as candidate genes for all these genodermatoses. In addition, linkage to a number of further candidate regions could also be excluded in these three families; the gene for transglutaminase 1 on chromosome 14q11, chromosome 1q21 containing a cluster of genes encoding intermediate filament-associated and cell envelope-associated proteins, and chromosome 18q12 with several genes for desmosomal glycoproteins. These findings reveal that mutations in genes other than keratin genes can be involved in the etiology of hyperkeratosis of palms and soles. Thus, the clinical heterogeneity in PPK is mirrored by heterogeneity at the molecular level.

  19. Compositional Heterogeneity in Ternary Models for the Cell Membrane

    NASA Astrophysics Data System (ADS)

    Smith, Robin; Heberle, Frederick; Wu, Jing; Feigenson, Gerald

    2010-03-01

    Ternary models for the cell membrane comprised of cholesterol (Chol) plus high and low melting temperature lipids exhibit rich phase behavior as a function of temperature and composition. Of particular interest is a region of coexisting disordered and ordered fluid phases that is thought to indicate how lipids organize to promote protein function in the cell membrane. We have used fluorescence resonance energy transfer to investigate the ternary mixtures DOPC(1,2-dioleoyl-sn-glycero-3-phosphocholine)/bSM (porcine brainsphingomyelin)/Chol and POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine)/bSM/Chol at high compositional resolution. We confirmed liquid coexistence for DOPC/bSM/Chol at 15 and 25C that melts by 35C, but in contrast to previous studies we detected no fluid-phase compositional heterogeneity for POPC/bSM/Chol from 5-35C. If domains exist, they must be smaller than the approximately 5 nm sensitivity provided by the fluorescent lipid analogs employed. We propose electron spin resonance and x-ray scattering for measuring whether liquid-phase compositional heterogeneity occurs for POPC/bSM/Chol. Understanding POPC/bSM/Chol phase behavior will provide a framework for investigating peptide/lipid interactions in a biologically relevant lipid mixture.

  20. Heterogeneity of lipoprotein particles in hepatic Golgi fractions

    PubMed Central

    1982-01-01

    Newly synthesized phospholipids, labeled with either [14C]choline, [3H]myo-inositol, or [33P]phosphate, partioned preferentially (greater than 80% of total incorporated radioactivity) in a Golgi membrane subfraction, although the cognate content subfraction contained a relatively large amount of secretory lipoproteins. The labeling pattern was the same for all phospholipids tested in the two subfractions. An active exchange process of polar lipids between Golgi membranes and Golgi secretory lipoproteins is postulated as a plausible explanation for these findings. Less than half of all Golgi lipoprotein particles have the density of serum VLDLs and a similar, but not identical, biochemical composition. The remaining lipoprotein particles are characterized by a continuous spectrum of sizes, and (to the extent tested) by a lipid and protein composition different from that of serum VLDLs and HDLs. Results obtained in control experiments rule out the possibility that the heterogeneous population of Golgi lipoprotein particles is an artefact caused by our preparation procedures. It is assumed that these heterogeneous particles are immature precursors of both VLDLs and HDLs. PMID:7085757

  1. Macrophages heterogeneity in atherosclerosis – implications for therapy

    PubMed Central

    Wilson, Heather M

    2010-01-01

    Abstract Atherosclerosis is a chronic inflammatory disease occurring within the artery wall and is an underlying cause of cardiovascular complications, including myocardial infarction, stroke and peripheral vascular disease. Its pathogenesis involves many immune cell types with a well accepted role for monocyte/macrophages. Cholesterol-loaded macrophages are a characteristic feature of plaques and are major players in all stages of plaque development. As well as modulating lipid metabolism, macrophages secrete inflammatory cytokines, chemokines and reactive oxygen and nitrogen species that drive pathogenesis. They also produce proteases and tissue factor that contribute to plaque rupture and thrombosis. Macrophages are however heterogeneous cells and when appropriately activated, they phagocytose cytotoxic lipoproteins, clear apoptotic bodies, secrete anti-inflammatory cytokines and synthesize matrix repair proteins that stabilize vulnerable plaques. Pharmacological modulation of macrophage activity therefore represents a potential therapeutic strategy for atherosclerosis. The aim of this review is to provide an overview of the current understanding of the different macrophage subsets and their monocyte precursors, and, the implications of these subsets for atherosclerosis. This will present a foundation for highlighting novel opportunities to exploit the heterogeneity of macrophages as important diagnostic and therapeutic targets for atherosclerosis and its associated diseases. PMID:20629993

  2. Heterogeneity of group A streptococcal pyrogenic exotoxin type B.

    PubMed Central

    Barsumian, E L; Cunningham, C M; Schlievert, P M; Watson, D W

    1978-01-01

    Streptococcal pyrogenic exotoxin type B purified from culture filtrates of either the NY-5 or T-19 strain of group A streptococcus was found to be heterogeneous in charge. Three protein fractions with isoelectric points of 8.0, 8.4, and 9.0 were isolated by differential solubility in ethanol and acetate-buffered saline followed by isoelectric focusing and shown to be antigenically identical to streptococcal pyrogenic exotoxin type B. The molecular weights of all three fractions were approximately 17,500, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, with aggregates forming in the presence of hyaluronic acid. Only the pI 8.4 fraction showed the characteristic activities of streptococcal pyrogenic exotoxin in rabbits: pyrogenicity and ability to enhance susceptibility to lethal endotoxin shock. The pI 8.0 and pI 9.0 fractions were not pyrogenic, but could be used to immunize against pyrogenicity. These two fractions failed either to enhance lethal endotoxin shock or to immunize against enhancement activity. When the isolated fractions were electrofocused again they appeared heterogeneous, suggesting an instability of the B toxin molecular forms. Images PMID:352946

  3. Increasing silk fibre strength through heterogeneity of bundled fibrils.

    PubMed

    Cranford, Steven W

    2013-05-06

    Can naturally arising disorder in biological materials be beneficial? Materials scientists are continuously attempting to replicate the exemplary performance of materials such as spider silk, with detailed techniques and assembly procedures. At the same time, a spider does not precisely machine silk-imaging indicates that its fibrils are heterogeneous and irregular in cross section. While past investigations either focused on the building material (e.g. the molecular scale protein sequence and behaviour) or on the ultimate structural component (e.g. silk threads and spider webs), the bundled structure of fibrils that compose spider threads has been frequently overlooked. Herein, I exploit a molecular dynamics-based coarse-grain model to construct a fully three-dimensional fibril bundle, with a length on the order of micrometres. I probe the mechanical behaviour of bundled silk fibrils with variable density of heterogenic protrusions or globules, ranging from ideally homogeneous to a saturated distribution. Subject to stretching, the model indicates that cooperativity is enhanced by contact through low-force deformation and shear 'locking' between globules, increasing shear stress transfer by up to 200 per cent. In effect, introduction of a random and disordered structure can serve to improve mechanical performance. Moreover, addition of globules allows a tuning of free volume, and thus the wettability of silk (with implications for supercontraction). These findings support the ability of silk to maintain near-molecular-level strength at the scale of silk threads, and the mechanism could be easily adopted as a strategy for synthetic fibres.

  4. Diffusion and Surface Reaction in Heterogeneous Catalysis

    ERIC Educational Resources Information Center

    Baiker, A.; Richarz, W.

    1978-01-01

    Ethylene hydrogenation on a platinum catalyst, electrolytically applied to a tube wall, is a good system for the study of the interactions between diffusion and surface reaction in heterogeneous catalysis. Theoretical background, apparatus, procedure, and student performance of this experiment are discussed. (BB)

  5. Children of Teen Parents: Heterogeneity of Outcomes.

    ERIC Educational Resources Information Center

    Moore, Kristin A.; And Others

    This report is based on evidence that despite the negative outcomes so often associated with early childbearing, not all teenage parents experience difficult lives. Given the heterogeneity of outcomes among teenage parents and their children, the issue addressed in the research is to identify the factors that explain variations in academic…

  6. Detecting Heterogeneity in Logistic Regression Models

    ERIC Educational Resources Information Center

    Balazs, Katalin; Hidegkuti, Istvan; De Boeck, Paul

    2006-01-01

    In the context of item response theory, it is not uncommon that person-by-item data are correlated beyond the correlation that is captured by the model--in other words, there is extra binomial variation. Heterogeneity of the parameters can explain this variation. There is a need for proper statistical methods to indicate possible extra…

  7. Reactor heterogeneity with saccharopolyspora erythraea airlift fermentations

    PubMed

    Pollard; Ison; Shamlou; Lilly

    1998-06-05

    Bioreactor heterogeneity has been studied in a multiconfigurable pilot-scale airlift reactor (0.25 m3) which created different degrees of heterogeneity. The impact of the two sparger configurations, i.e. in the draft tube or the annulus, in conjunction with a marine propeller fitted at the base of the downcomer, on the physiology of Saccharopolyspora erythraea was studied. Cellular growth, morphology, and productivity were compared between airlift and stirred tank reactors. Dissolved oxygen tension heterogeneity caused by differences in dissolved oxygen tension around the vessel did not affect growth, but the reduction of heterogeneity improved the specific erythromycin production rate and final specific production. Erythromycin production was shown to be proportional to the energy dissipation rate. The enhancement of bubble coalescence with increasing apparent viscosity led to the reduction of the sectional gas holdups and the improvement of liquid mixing. The extent of the changes with increasing apparent viscosity was dependent on the broth morphology, reactor configurations, and operating conditions. Copyright 1998 John Wiley & Sons, Inc.

  8. Heterogeneous photocatalytic oxidation of atmospheric trace contaminants

    NASA Technical Reports Server (NTRS)

    Ollis, David F.

    1993-01-01

    The progress report on heterogeneous photocatalytic oxidation of atmospheric trace contaminants covering the period from 1 May - 31 Oct. 1992 is presented. The two topics discussed are photoreactor monolith fundamental studies and monolith reactor operation: batch recirculation system. Concentration profiles are shown.

  9. Towards inverse modeling of intratumor heterogeneity

    NASA Astrophysics Data System (ADS)

    Brutovsky, Branislav; Horvath, Denis

    2015-08-01

    Development of resistance limits efficiency of present anticancer therapies and preventing it remains a big challenge in cancer research. It is accepted, at the intuitive level, that resistance emerges as a consequence of the heterogeneity of cancer cells at the molecular, genetic and cellular levels. Produced by many sources, tumor heterogeneity is extremely complex time dependent statistical characteristics which may be quantified by measures defined in many different ways, most of them coming from statistical mechanics. In this paper, we apply the Markovian framework to relate population heterogeneity to the statistics of the environment. As, from an evolutionary viewpoint, therapy corresponds to a purposeful modi- fication of the cells' fitness landscape, we assume that understanding general relationship between the spatiotemporal statistics of a tumor microenvironment and intratumor heterogeneity will allow to conceive the therapy as an inverse problem and to solve it by optimization techniques. To account for the inherent stochasticity of biological processes at cellular scale, the generalized distancebased concept was applied to express distances between probabilistically described cell states and environmental conditions, respectively.

  10. Heterogeneous nucleation of ice on carbon surfaces.

    PubMed

    Lupi, Laura; Hudait, Arpa; Molinero, Valeria

    2014-02-26

    Atmospheric aerosols can promote the heterogeneous nucleation of ice, impacting the radiative properties of clouds and Earth's climate. The experimental investigation of heterogeneous freezing of water droplets by carbonaceous particles reveals widespread ice freezing temperatures. It is not known which structural and chemical characteristics of soot account for the variability in ice nucleation efficiency. Here we use molecular dynamics simulations to investigate the nucleation of ice from liquid water in contact with graphitic surfaces. We find that atomically flat carbon surfaces promote heterogeneous nucleation of ice, while molecularly rough surfaces with the same hydrophobicity do not. Graphitic surfaces and other surfaces that promote ice nucleation induce layering in the interfacial water, suggesting that the order imposed by the surface on liquid water may play an important role in the heterogeneous nucleation mechanism. We investigate a large set of graphitic surfaces of various dimensions and radii of curvature and find that variations in nanostructures alone could account for the spread in the freezing temperatures of ice on soot in experiments. We conclude that a characterization of the nanostructure of soot is needed to predict its ice nucleation efficiency.

  11. Heterogeneous catalysis: More than skimming the surface

    NASA Astrophysics Data System (ADS)

    (Feng) Tao, Franklin; Tang, Yu

    2016-10-01

    The high temperatures and pressures used in heterogeneous catalysis make it difficult to observe catalysts using conventional techniques. Now, adsorbed product molecules on the surface of a single-crystal model catalyst have been observed during catalysis using a custom-built scanning tunnelling microscope that can work in situ.

  12. Physical Heterogeneity and Aquatic Community Function in ...

    EPA Pesticide Factsheets

    The geomorphological character of a river network provides the template upon which evolution acts to create unique biological communities. Deciphering commonly observed patterns and processes within riverine landscapes resulting from the interplay between physical and biological components is a central tenet for the interdisciplinary field of river science. Relationships between the physical heterogeneity and food web character of functional process zones (FPZs) – large tracts of river with a similar geomorphic character - in the Kanawha River (West Virginia, USA) are examined in this study. Food web character was measured as food chain length (FCL), which reflects ecological community structure and ecosystem function. Our results show the same basal resources were present throughout the Kanawha River but their assimilation into the aquatic food web by primary consumers differed between FPZs. Differences in the trophic position of secondary consumers – fish - were also recorded between FPZs. Overall, both the morphological heterogeneity and heterogeneity of the river bed sediment of FPZs were significantly correlated with FCL. Specifically, FCL increases with greater FPZ physical heterogeneity, supporting tenet 8 of the river ecosystem synthesis. In previous research efforts, we delineated the functional process zones (FPZs) of the Kanawha River. In this study, we examined the relationship between the hydrogeomorphically-derived zones with food webs.

  13. Stabilized Laccases as Heterogeneous Bioelectrocatalysts (Postprint)

    DTIC Science & Technology

    2012-10-01

    significant application in the textile industry , as well as commercial success in bio-bleaching and waste -stream remediation. Another widely used large...demonstrate why laccases continue to be biotechnologically relevant enzymes. The methodologies for immobilization of laccases are described including the use... industry , pharmaceutical synthesis and environmental applications, specifically where stabilization through heterogenization of the enzyme is critical to

  14. Synthesis of RNA oligomers on heterogeneous templates

    NASA Technical Reports Server (NTRS)

    Ertem, G.; Ferris, J. P.

    1996-01-01

    The concept of an RNA world in the chemical origin of life is appealing, as nucleic acids are capable of both information storage and acting as templates that catalyse the synthesis of complementary molecules. Template-directed synthesis has been demonstrated for homogeneous oligonucleotides that, like natural nucleic acids, have 3',5' linkages between the nucleotide monomers. But it seems likely that prebiotic routes to RNA-like molecules would have produced heterogeneous molecules with various kinds of phosphodiester linkages and both linear and cyclic nucleotide chains. Here we show that such heterogeneity need be no obstacle to the templating of complementary molecules. Specifically, we show that heterogeneous oligocytidylates, formed by the montmorillonite clay-catalysed condensation of actuated monomers, can serve as templates for the synthesis of oligoguanylates. Furthermore, we show that oligocytidylates that are exclusively 2',5'-linked can also direct synthesis of oligoguanylates. Such heterogeneous templating reactions could have increased the diversity of the pool of protonucleic acids from which life ultimately emerged.

  15. Heterogeneity: The key to failure forecasting

    PubMed Central

    Vasseur, Jérémie; Wadsworth, Fabian B.; Lavallée, Yan; Bell, Andrew F.; Main, Ian G.; Dingwell, Donald B.

    2015-01-01

    Elastic waves are generated when brittle materials are subjected to increasing strain. Their number and energy increase non-linearly, ending in a system-sized catastrophic failure event. Accelerating rates of geophysical signals (e.g., seismicity and deformation) preceding large-scale dynamic failure can serve as proxies for damage accumulation in the Failure Forecast Method (FFM). Here we test the hypothesis that the style and mechanisms of deformation, and the accuracy of the FFM, are both tightly controlled by the degree of microstructural heterogeneity of the material under stress. We generate a suite of synthetic samples with variable heterogeneity, controlled by the gas volume fraction. We experimentally demonstrate that the accuracy of failure prediction increases drastically with the degree of material heterogeneity. These results have significant implications in a broad range of material-based disciplines for which failure forecasting is of central importance. In particular, the FFM has been used with only variable success to forecast failure scenarios both in the field (volcanic eruptions and landslides) and in the laboratory (rock and magma failure). Our results show that this variability may be explained, and the reliability and accuracy of forecast quantified significantly improved, by accounting for material heterogeneity as a first-order control on forecasting power. PMID:26307196

  16. Heterogeneous multidimensional scaling for complex networks

    NASA Astrophysics Data System (ADS)

    Xuan, Qi; Ma, Xiaodi; Fu, Chenbo; Dong, Hui; Zhang, Guijun; Yu, Li

    2015-07-01

    Many real-world networks are essentially heterogeneous, where the nodes have different abilities to gain connections. Such networks are difficult to be embedded into low-dimensional Euclidean space if we ignore the heterogeneity and treat all the nodes equally. In this paper, based on a newly defined heterogeneous distance and a generalized network distance under the constraints of network and triangle inequalities, respectively, we propose a new heterogeneous multidimensional scaling method (HMDS) to embed different networks into proper Euclidean spaces. We find that HMDS behaves much better than the traditional multidimensional scaling method (MDS) in embedding different artificial and real-world networks into Euclidean spaces. Besides, we also propose a method to estimate the appropriate dimensions of Euclidean spaces for different networks, and find that the estimated dimensions are quite close to the real dimensions for those geometrical networks under study. These methods thus can help to better understand the evolution of real-world networks, and have practical importance in network visualization, community detection, link prediction and localization of wireless sensors.

  17. Scale Reliability Evaluation with Heterogeneous Populations

    ERIC Educational Resources Information Center

    Raykov, Tenko; Marcoulides, George A.

    2015-01-01

    A latent variable modeling approach for scale reliability evaluation in heterogeneous populations is discussed. The method can be used for point and interval estimation of reliability of multicomponent measuring instruments in populations representing mixtures of an unknown number of latent classes or subpopulations. The procedure is helpful also…

  18. Colloid Straining within Saturated Heterogeneous Porous Media

    NASA Astrophysics Data System (ADS)

    Porubcan, A.; Walczak, J.; Xu, S.

    2008-12-01

    A thorough understanding of colloid movement in the subsurface system is critical to the assessment of groundwater pollution by pathogenic bacteria and colloid-bound contaminants. It is increasingly recognized that straining, a process that occurs when the pore space is too small to allow for a particle's passage, represents an important process in colloid immobilization within groundwater systems. Previously published studies have focused on the kinetics of colloid straining within sand packs composed of uniform mineral grains. Natural aquifers, however, are usually characterized by physically heterogeneous sediments. In this study, we conducted column transport experiments with carboxylated latex particles and quartz sand to investigate the impact of sediment texture (i.e., the size distribution of mineral grains) on colloid straining kinetics. The quartz sands used in the experiment were thoroughly cleaned and the strong repulsive interactions between colloid particles and quartz sands resulted in minimal physicochemical deposition so the straining kinetics can be quantified unambiguously. Sand packs of different textures were prepared by mixing sands of various sizes (mesh sizes of 20-25, 35-40 and 60-70). Our results suggested that the ratio of colloid size and the median sand grain size was insufficient to predict colloid straining within heterogeneous sediments. Soil texture, which was related to the size distribution of the sand grains, must be considered. A relationship between colloid straining kinetics and the heterogeneity of porous media that can be useful for the prediction of colloid transport within heterogeneous sediments was presented.

  19. Accelerating Mathematics Achievement Using Heterogeneous Grouping

    ERIC Educational Resources Information Center

    Burris, Carol Corbett; Heubert, Jay P.; Levin, Henry M.

    2006-01-01

    This longitudinal study examined the effects of providing an accelerated mathematics curriculum in heterogeneously grouped middle school classes in a diverse suburban school district. A quasi-experimental cohort design was used to evaluate subsequent completion of advanced high school math courses as well as academic achievement. Results showed…

  20. Scale Reliability Evaluation with Heterogeneous Populations

    ERIC Educational Resources Information Center

    Raykov, Tenko; Marcoulides, George A.

    2015-01-01

    A latent variable modeling approach for scale reliability evaluation in heterogeneous populations is discussed. The method can be used for point and interval estimation of reliability of multicomponent measuring instruments in populations representing mixtures of an unknown number of latent classes or subpopulations. The procedure is helpful also…

  1. [Single-cell sequencing and tumour heterogeneity].

    PubMed

    Jordan, Bertrand

    2014-12-01

    The heterogeneity of tumours is now beginning to be documented precisely by single-cell new-generation sequencing. Recently published results on breast tumours show that each of the cells analysed displays a unique pattern of point mutations. This extensive genetic diversity is present before any treatment, and is likely to cause resistance to initially successful targeted therapies.

  2. Diffusion and Surface Reaction in Heterogeneous Catalysis

    ERIC Educational Resources Information Center

    Baiker, A.; Richarz, W.

    1978-01-01

    Ethylene hydrogenation on a platinum catalyst, electrolytically applied to a tube wall, is a good system for the study of the interactions between diffusion and surface reaction in heterogeneous catalysis. Theoretical background, apparatus, procedure, and student performance of this experiment are discussed. (BB)

  3. Fragmentation of metal particles during heterogeneous explosion

    NASA Astrophysics Data System (ADS)

    Ripley, R. C.; Donahue, L.; Zhang, F.

    2015-03-01

    Heterogeneous explosives contain a mixture of standard explosive material and reactive metal particles. The inclusion of metal particles alters the energy density and energy release timescales involved in the blast event. Available experimental evidence indicates that metal particles may be damaged or fragmented during heterogeneous blast, altering the distribution of particle sizes from their initial state. This paper discusses adaptation and application of fragmentation theory and physical models for particle damage during condensed matter detonation, aerodynamic breakup of molten particles, and particle impact fragmentation with nearby structures. The shock compression and impact fragmentation models are based on the energy methods for dynamic fragmentation by Grady and Kipp, while aerodynamic breakup is treated according to Weber number stability criteria for droplets. These particle fragmentation models are validated against fundamental test cases from the literature. The models are then applied to heterogeneous blast scenarios including free field and wall reflection in a semi-confined urban street. Comparison with experimental records of pressure shows good agreement despite challenges inherent in the complexity of heterogeneous blast measurement and multiphase simulation.

  4. A Note on the Heterogeneous Choice Model

    ERIC Educational Resources Information Center

    Rohwer, Goetz

    2015-01-01

    The heterogeneous choice model (HCM) has been proposed as an extension of the standard logit and probit models, which allows taking into account different error variances of explanatory variables. In this note, I show that in an important special case, this model is just another way to specify an interaction effect.

  5. Programming Models for Heterogeneous Multicore Systems

    DTIC Science & Technology

    2011-08-08

    Badia, F.D. Igual, J. Labarta, R. Mayo and E.S. Quintana- Orti . “An extension of the StarSs Programming Model for Platforms with Multiple GPUs...R. Mayo, J.M. Perez, J. Planas, E.S. Quintana- Orti . “A Proposal to Extend the OpenMP Tasking Model for Heterogeneous Architectures ” LNCS Vol. 5568

  6. Passive cutaneous anaphylaxis inhibition: evidence for heterogeneity in IgE mast cell interaction.

    PubMed Central

    Lehrer, S B; McCants, M L; Farris, P N; Bazin, H

    1981-01-01

    Recent evidence suggests that IgE molecules are heterogeneous with respect to ability to compete with IgE myeloma for sensitization of histamine release from chopped human lung and ability to passively sensitize human basophils for antigen-induced histamine release. These observations prompted further investigation of the possibility that there exists a functional heterogeneity in the IgE molecules with respect to mast-cell binding properties. Using eight different purified rat IgE myeloma proteins, we found that they differ in their ability to inhibit the passive cutaneous anaphylaxis (PCA) reaction of mouse reaginic antisera. This suggests that IgE molecules differ in their ability to bind to mast cell receptors. Since maximal inhibition of different mouse reaginic antisera and mouse IgE hybridomas is achieved with different IgE myelomas, there may exist a functional heterogeneity in mast-cell binding receptors as well. PMID:7319556

  7. Characterization of oil and gas reservoir heterogeneity

    SciTech Connect

    Tyler, N.; Barton, M.D.; Bebout, D.G.; Fisher, R.S.; Grigsby, J.D.; Guevara, E.; Holtz, M.; Kerans, C.; Nance, H.S.; Levey, R.A.

    1992-10-01

    Research described In this report addresses the internal architecture of two specific reservoir types: restricted-platform carbonates and fluvial-deltaic sandstones. Together, these two reservoir types contain more than two-thirds of the unrecovered mobile oil remaining ill Texas. The approach followed in this study was to develop a strong understanding of the styles of heterogeneity of these reservoir types based on a detailed outcrop description and a translation of these findings into optimized recovery strategies in select subsurface analogs. Research targeted Grayburg Formation restricted-platform carbonate outcrops along the Algerita Escarpment and In Stone Canyon In southeastern New Mexico and Ferron deltaic sandstones in central Utah as analogs for the North Foster (Grayburg) and Lake Creek (Wilcox) units, respectively. In both settings, sequence-stratigraphic style profoundly influenced between-well architectural fabric and permeability structure. It is concluded that reservoirs of different depositional origins can therefore be categorized Into a heterogeneity matrix'' based on varying intensity of vertical and lateral heterogeneity. The utility of the matrix is that it allows prediction of the nature and location of remaining mobile oil. Highly stratified reservoirs such as the Grayburg, for example, will contain a large proportion of vertically bypassed oil; thus, an appropriate recovery strategy will be waterflood optimization and profile modification. Laterally heterogeneous reservoirs such as deltaic distributary systems would benefit from targeted infill drilling (possibly with horizontal wells) and improved areal sweep efficiency. Potential for advanced recovery of remaining mobile oil through heterogeneity-based advanced secondary recovery strategies In Texas is projected to be an Incremental 16 Bbbl. In the Lower 48 States this target may be as much as 45 Bbbl at low to moderate oil prices over the near- to mid-term.

  8. Forecasting the failure of heterogeneous magmas

    NASA Astrophysics Data System (ADS)

    Vasseur, J.; Wadsworth, F. B.; Lavallée, Y.; Bell, A. F.; Main, I. G.; Dingwell, D. B.

    2015-12-01

    Eruption prediction is a long-sought-after goal of volcanology. Yet applying existing techniques retrospectively (hindcasting), we fail to predict events more often than we success. As much of the seismicity associated with intermediate to silicic volcanic eruptions comes from the brittle response of the ascending magma itself, we clearly require a good understanding of the parameters that control the ability to forecast magma failure itself. Here, we present suites of controlled experiments at magmatic temperatures using a range of synthetic magmas to investigate the control of microstructures on the efficacy of forecast models for material failure. We find that the failure of magmas with very little microstructural heterogeneity - such as melts - is very challenging to predict; whereas, the failure of very heterogeneous magmas is always well-predicted. To shed further light on this issue, we provide a scaling law based on the relationship between the microstructural heterogeneity in a magma and the error in the prediction of its failure time. We propose this method be used to elucidate the variable success rate of predicting volcanic predictions. We discuss this scaling in the context of the birth, life and death of structural heterogeneity during magma ascent with specific emphasis on obsidian-forming eruptions such as Chaitèn, 2008. During such eruptions, the repetitive creation and destruction of fractures filled with granular magma, which are thought to be the in situ remnants of seismogenic fracturing itself, are expressions of the life-cycle of heterogeneity in an otherwise coherent, melt-rich magma. We conclude that the next generation of failure forecast tools available to monitoring teams should incorporate some acknowledgment of the magma microstructure and not be solely based on the geophysical signals prior to eruption.

  9. Intra-tumour heterogeneity - going beyond genetics.

    PubMed

    Caiado, Francisco; Silva-Santos, Bruno; Norell, Håkan

    2016-06-01

    Cancer patients die primarily due to disease recurrence after transient treatment responses. The emergence of therapy-resistant escape variants is fuelled by intra-tumour heterogeneity, underpinned by interference and Darwinian evolution among continuously developing sub-clones in the mutating tumour. Novel cancer cell variants build upon the pre-existing genetic landscape and tumour heterogeneity is often ascribed largely to genetic variability. While mutations are required for cancer development and studies of genetic evolution of tumours have improved our understanding of cancer biology, genetics only represents one dimension of the fitness of each cancer cell. Beyond the mutations, several non-genetic factors also add significant variability, resulting in a complex and highly dynamic tumour cell population that can drive disease under almost any condition. This viewpoint article summarizes the genetic basis of intra-tumour heterogeneity, before dissecting four major interdependent non-genetic factors we think critically contribute to the overall variability of tumour cells in all types of cancer: epigenetic regulation, cellular differentiation hierarchies, gene expression stochasticity and tumour microenvironment. We finally present the relevant technological approaches to address the combined contribution of both genetic and non-genetic factors to intra-tumour heterogeneity, focusing on genomic profiling, cellular lineage tracing and single-cell RNA sequencing technologies. This strategy will ultimately allow dissection of the full range and depth of intra-tumour heterogeneity. We thus believe that understanding how cancer genetics synergize with the emerging non-genetic factors will be key for development of therapies able to