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Sample records for pathways interaction effects

  1. Prediction of Effective Drug Combinations by Chemical Interaction, Protein Interaction and Target Enrichment of KEGG Pathways

    PubMed Central

    Chen, Lei; Zheng, Ming-Yue; Zhang, Jian; Feng, Kai-Yan; Cai, Yu-Dong

    2013-01-01

    Drug combinatorial therapy could be more effective in treating some complex diseases than single agents due to better efficacy and reduced side effects. Although some drug combinations are being used, their underlying molecular mechanisms are still poorly understood. Therefore, it is of great interest to deduce a novel drug combination by their molecular mechanisms in a robust and rigorous way. This paper attempts to predict effective drug combinations by a combined consideration of: (1) chemical interaction between drugs, (2) protein interactions between drugs' targets, and (3) target enrichment of KEGG pathways. A benchmark dataset was constructed, consisting of 121 confirmed effective combinations and 605 random combinations. Each drug combination was represented by 465 features derived from the aforementioned three properties. Some feature selection techniques, including Minimum Redundancy Maximum Relevance and Incremental Feature Selection, were adopted to extract the key features. Random forest model was built with its performance evaluated by 5-fold cross-validation. As a result, 55 key features providing the best prediction result were selected. These important features may help to gain insights into the mechanisms of drug combinations, and the proposed prediction model could become a useful tool for screening possible drug combinations. PMID:24083237

  2. Groundwater Surface Water Interaction Effects on Pesticide Persistence and Transformation Pathways

    NASA Astrophysics Data System (ADS)

    Smith, J. E.; Crowe, A. S.; Marenco, N.

    2004-05-01

    Historical DDT use at Point Pelee National Park (PPNP) has left a legacy of contamination found in the flora, fauna, soils, and groundwater. The transformation pathway and the rate of transformation of DDT to either DDE or DDD, and subsequent metabolites depends on many environmental factors including soil texture, soil moisture, temperature, organic carbon content, flooding, and microbial activity, (Guenzi and Beard 1968, 1976; Spencer et al. 1996; Aigner et al. 1998). Under aerobic conditions the transformation of DDT to DDE is the preferred pathway, whereas under anaerobic conditions, DDT to DDD is the preferred pathway. Also, the transformation of DDT to DDD under anaerobic conditions is faster than that for DDT to DDE under aerobic conditions. Given that one of the primary factors effecting the redox conditions of a soil is soil wetness, and that flooded soils tend to become anaerobic and reducing, it was hypothesized that there may be a relation between the dynamic nature of groundwater-surface water interactions at PPNP and the concentrations and proportions of DDT, DDE, and DDD. The soils are texturally sand and are mostly of the Brunisolic Soil Order (Inceptisols) with the Regosolic Soil Order (Entisols) on the sand dunes and the Organic Soil Order (Histosols) along the margins of the Marsh. The location of the groundwater-surface water interface coinciding with historic water levels within Lake Erie and the marsh has played a significant role.

  3. Effect of rod–cone interactions on mesopic visual performance mediated by chromatic and luminance pathways

    PubMed Central

    Zele, Andrew J.; Maynard, Michelle L.; Joyce, Daniel S.; Cao, Dingcai

    2014-01-01

    We studied the effect of rod–cone interactions on mesopic visual reaction time (RT). Rod and cone photoreceptor excitations were independently controlled using a four-primary photostimulator. It was observed that (1) lateral rod–cone interactions increase the cone-mediated RTs; (2) the rod–cone interactions are strongest when rod sensitivity is maximal in a dark surround, but weaker with increased rod activity in a light surround; and (3) the presence of a dark surround nonselectively increased the mean and variability of chromatic (+L−M, S-cone) and luminance (L + M + S) RTs independent of the level of rod activity. The results demonstrate that lateral rod–cone interactions must be considered when deriving mesopic luminous efficiency using RT. PMID:24695205

  4. Analysis of interaction of phenolic compounds with the cholecystokinin signaling pathway to explain effects on reducing food intake.

    PubMed

    Al Shukor, Nadin; Raes, Katleen; Van Camp, John; Smagghe, Guy

    2014-03-01

    Previous animal experiments demonstrated that phenolic compounds can reduce weight and food intake, but the exact mechanism(s) behind these effects remain unknown. For regulation of food intake, the cholecystokinin (CCK) hormone signaling pathway plays an important role as it induces satiety by binding on its specific receptor (CCK1R), hereby reducing food intake. In this study, we investigated the possible interactions of eight phenolic compounds of different classes (tannic acid, gallic acid, benzoic acid, hydroxybenzoic acid, protocatechuic acid, quercetin, kaempferol and resveratrol) with the CCK1R signaling pathway. As major results, the tested phenolic compounds could not activate the CCK1R in a specific cell-based bioassay. In contrast, we observed an anti-CCK1R activity. This antagonistic action might be explained by blocking of the functioning of the CCK1R receptor, although the exact mechanism of interaction remains unknown. For tannic acid, we also measured a sequestration activity of the CCK hormone in vitro. In conclusion, the reported activity of phenolic compounds against food intake and weight is not based on an activation of the CCK1R. Taking into account the complex regulation of food intake, further work is necessary to unravel other essential mechanisms involved to explain the reported effects of phenolic compounds against food intake.

  5. Pathway Analysis Incorporating Protein-Protein Interaction Networks Identified Candidate Pathways for the Seven Common Diseases

    PubMed Central

    Lin, Peng-Lin; Yu, Ya-Wen

    2016-01-01

    Pathway analysis has become popular as a secondary analysis strategy for genome-wide association studies (GWAS). Most of the current pathway analysis methods aggregate signals from the main effects of single nucleotide polymorphisms (SNPs) in genes within a pathway without considering the effects of gene-gene interactions. However, gene-gene interactions can also have critical effects on complex diseases. Protein-protein interaction (PPI) networks have been used to define gene pairs for the gene-gene interaction tests. Incorporating the PPI information to define gene pairs for interaction tests within pathways can increase the power for pathway-based association tests. We propose a pathway association test, which aggregates the interaction signals in PPI networks within a pathway, for GWAS with case-control samples. Gene size is properly considered in the test so that genes do not contribute more to the test statistic simply due to their size. Simulation studies were performed to verify that the method is a valid test and can have more power than other pathway association tests in the presence of gene-gene interactions within a pathway under different scenarios. We applied the test to the Wellcome Trust Case Control Consortium GWAS datasets for seven common diseases. The most significant pathway is the chaperones modulate interferon signaling pathway for Crohn’s disease (p-value = 0.0003). The pathway modulates interferon gamma, which induces the JAK/STAT pathway that is involved in Crohn’s disease. Several other pathways that have functional implications for the seven diseases were also identified. The proposed test based on gene-gene interaction signals in PPI networks can be used as a complementary tool to the current existing pathway analysis methods focusing on main effects of genes. An efficient software implementing the method is freely available at http://puppi.sourceforge.net. PMID:27622767

  6. Effective connectivity of ascending and descending frontalthalamic pathways during sustained attention: Complex brain network interactions in adolescence.

    PubMed

    Jagtap, Pranav; Diwadkar, Vaibhav A

    2016-07-01

    Frontal-thalamic interactions are crucial for bottom-up gating and top-down control, yet have not been well studied from brain network perspectives. We applied network modeling of fMRI signals [dynamic causal modeling (DCM)] to investigate frontal-thalamic interactions during an attention task with parametrically varying levels of demand. fMRI was collected while subjects participated in a sustained continuous performance task with low and high attention demands. 162 competing model architectures were employed in DCM to evaluate hypotheses on bilateral frontal-thalamic connections and their modulation by attention demand, selected at a second level using Bayesian model selection. The model architecture evinced significant contextual modulation by attention of ascending (thalamus → dPFC) and descending (dPFC → thalamus) pathways. However, modulation of these pathways was asymmetric: while positive modulation of the ascending pathway was comparable across attention demand, modulation of the descending pathway was significantly greater when attention demands were increased. Increased modulation of the (dPFC → thalamus) pathway in response to increased attention demand constitutes novel evidence of attention-related gain in the connectivity of the descending attention pathway. By comparison demand-independent modulation of the ascending (thalamus → dPFC) pathway suggests unbiased thalamic inputs to the cortex in the context of the paradigm. Hum Brain Mapp 37:2557-2570, 2016. © 2016 Wiley Periodicals, Inc.

  7. Minimal metabolic pathway structure is consistent with associated biomolecular interactions

    PubMed Central

    Bordbar, Aarash; Nagarajan, Harish; Lewis, Nathan E; Latif, Haythem; Ebrahim, Ali; Federowicz, Stephen; Schellenberger, Jan; Palsson, Bernhard O

    2014-01-01

    Pathways are a universal paradigm for functionally describing cellular processes. Even though advances in high-throughput data generation have transformed biology, the core of our biological understanding, and hence data interpretation, is still predicated on human-defined pathways. Here, we introduce an unbiased, pathway structure for genome-scale metabolic networks defined based on principles of parsimony that do not mimic canonical human-defined textbook pathways. Instead, these minimal pathways better describe multiple independent pathway-associated biomolecular interaction datasets suggesting a functional organization for metabolism based on parsimonious use of cellular components. We use the inherent predictive capability of these pathways to experimentally discover novel transcriptional regulatory interactions in Escherichia coli metabolism for three transcription factors, effectively doubling the known regulatory roles for Nac and MntR. This study suggests an underlying and fundamental principle in the evolutionary selection of pathway structures; namely, that pathways may be minimal, independent, and segregated. PMID:24987116

  8. Effects of Rivaroxaban on Platelet Activation and Platelet–Coagulation Pathway Interaction

    PubMed Central

    Heitmeier, Stefan; Laux, Volker

    2015-01-01

    Introduction: Activation of coagulation and platelets is closely linked, and arterial thrombosis involves coagulation activation as well as platelet activation and aggregation. In these studies, we investigated the possible synergistic effects of rivaroxaban in combination with antiplatelet agents on thrombin generation and platelet aggregation in vitro and on arterial thrombosis and hemostasis in rat models. Materials and Methods: Thrombin generation was measured by the Calibrated Automated Thrombogram method (0.5 pmol/L tissue factor) using human platelet-rich plasma (PRP) spiked with rivaroxaban (15, 30, or 60 ng/mL), ticagrelor (1.0 µg/mL), and acetylsalicylic acid (ASA; 100 µg/mL). Tissue factor-induced platelet aggregation was measured in PRP spiked with rivaroxaban (15 or 30 ng/mL), ticagrelor (1 or 3 µg/mL), or a combination of these. An arteriovenous (AV) shunt model in rats was used to determine the effects of rivaroxaban (0.01, 0.03, or 0.1 mg/kg), clopidogrel (1 mg/kg), ASA (3 mg/kg), and combinations on arterial thrombosis. Results: Rivaroxaban inhibited thrombin generation in a concentration-dependent manner and the effect was enhanced with ticagrelor and ticagrelor plus ASA. Rivaroxaban and ticagrelor also concentration-dependently inhibited tissue factor-induced platelet aggregation, and their combination increased the inhibition synergistically. In the AV shunt model, rivaroxaban dose-dependently reduced thrombus formation. Combining subefficacious or weakly efficacious doses of rivaroxaban with ASA or ASA plus clopidogrel increased the antithrombotic effect. Conclusion: These data indicate that the combination of rivaroxaban with single or dual antiplatelet agents works synergistically to reduce platelet activation, which may in turn lead to the delayed/reduced formation of coagulation complexes and vice versa, thereby enhancing antithrombotic potency. PMID:25848131

  9. Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype.

    PubMed

    Gagneur, Julien; Stegle, Oliver; Zhu, Chenchen; Jakob, Petra; Tekkedil, Manu M; Aiyar, Raeka S; Schuon, Ann-Kathrin; Pe'er, Dana; Steinmetz, Lars M

    2013-01-01

    Unraveling the molecular processes that lead from genotype to phenotype is crucial for the understanding and effective treatment of genetic diseases. Knowledge of the causative genetic defect most often does not enable treatment; therefore, causal intermediates between genotype and phenotype constitute valuable candidates for molecular intervention points that can be therapeutically targeted. Mapping genetic determinants of gene expression levels (also known as expression quantitative trait loci or eQTL studies) is frequently used for this purpose, yet distinguishing causation from correlation remains a significant challenge. Here, we address this challenge using extensive, multi-environment gene expression and fitness profiling of hundreds of genetically diverse yeast strains, in order to identify truly causal intermediate genes that condition fitness in a given environment. Using functional genomics assays, we show that the predictive power of eQTL studies for inferring causal intermediate genes is poor unless performed across multiple environments. Surprisingly, although the effects of genotype on fitness depended strongly on environment, causal intermediates could be most reliably predicted from genetic effects on expression present in all environments. Our results indicate a mechanism explaining this apparent paradox, whereby immediate molecular consequences of genetic variation are shared across environments, and environment-dependent phenotypic effects result from downstream integration of environmental signals. We developed a statistical model to predict causal intermediates that leverages this insight, yielding over 400 transcripts, for the majority of which we experimentally validated their role in conditioning fitness. Our findings have implications for the design and analysis of clinical omics studies aimed at discovering personalized targets for molecular intervention, suggesting that inferring causation in a single cellular context can benefit from

  10. Integrated pathway and epistasis analysis reveals interactive effect of genetic variants at TERF1 and AFAP1L2 loci on melanoma risk

    PubMed Central

    Vaysse, Amaury; Wei, Qingyi; Chen, Wei V.; Mohamdi, Hamida; Maubec, Eve; Lavielle, Nolwenn; Galan, Pilar; Lathrop, Mark; Avril, Marie-Françoise; Lee, Jeffrey E.

    2015-01-01

    Genome-wide association studies (GWASs) have characterized 13 loci associated with melanoma, which only account for a small part of melanoma risk. To identify new genes with too small an effect to be detected individually but which collectively influence melanoma risk and/or show interactive effects, we used a two-step analysis strategy including pathway analysis of genome-wide SNP data, in a first step, and epistasis analysis within significant pathways, in a second step. Pathway analysis, using the gene-set enrichment analysis (GSEA) approach and the gene ontology (GO) database, was applied to the outcomes of MELARISK (3,976 subjects) and MDACC (2,827 subjects) GWASs. Cross-gene SNP-SNP interaction analysis within melanoma-associated GOs was performed using the INTERSNP software. Five GO categories were significantly enriched in genes associated with melanoma (FDR≤5% in both studies): response to light stimulus, regulation of mitotic cell cycle, induction of programmed cell death, cytokine activity and oxidative phosphorylation. Epistasis analysis, within each of the five significant GOs, showed significant evidence for interaction for one SNP pair at TERF1 and AFAP1L2 loci (pmeta-int =2.0×10−7, which met both the pathway and overall multiple-testing corrected thresholds that are equal to 9.8×10−7 and 2.0×10−7, respectively) and suggestive evidence for another pair involving correlated SNPs at the same loci (pmeta-int =3.6×10−6 ). This interaction has important biological relevance given the key role of TERF1 in telomere biology and the reported physical interaction between TERF1 and AFAP1L2 proteins. This finding brings a novel piece of evidence for the emerging role of telomere dysfunction into melanoma development. PMID:25892537

  11. Interactive web service system for exploration of biological pathways.

    PubMed

    Yin, Zong-Xian; Li, Sin-Yan

    2014-09-01

    Existing bioinformatics databases such as KEGG (Kyoto Encyclopedia of Genes and Genomes) provide a wealth of information. However, they generally lack a user-friendly and interactive interface. The study proposes a web service system for exploring the contents of the KEGG database in an intuitive and interactive manner. In the proposed system, the requested pathways are uploaded from the KEGG database and are converted from a static format into an interactive format such that their contents can be more readily explored. The system supports two basic functions, namely an exhaustive search for all possible reaction paths between two specified genes in a biological pathway, and the identification of similar reaction sequences in different biological pathways. The feasibility of the proposed system is evaluated by means of an initial pilot study involving 10 students with varying degrees of experience of the KEGG website and its operations. The results indicate that the system provides a useful learning tool for investigating biological pathways. A system is proposed for converting the static pathway maps in KEGG into interactive maps such that they can be explored at will. The results of a preliminary trial confirm that the system is straightforward to use and provides a versatile and effective tool for examining and comparing biological pathways. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Exploring pathway interactions in insulin resistant mouse liver

    PubMed Central

    2011-01-01

    Background Complex phenotypes such as insulin resistance involve different biological pathways that may interact and influence each other. Interpretation of related experimental data would be facilitated by identifying relevant pathway interactions in the context of the dataset. Results We developed an analysis approach to study interactions between pathways by integrating gene and protein interaction networks, biological pathway information and high-throughput data. This approach was applied to a transcriptomics dataset to investigate pathway interactions in insulin resistant mouse liver in response to a glucose challenge. We identified regulated pathway interactions at different time points following the glucose challenge and also studied the underlying protein interactions to find possible mechanisms and key proteins involved in pathway cross-talk. A large number of pathway interactions were found for the comparison between the two diet groups at t = 0. The initial response to the glucose challenge (t = 0.6) was typed by an acute stress response and pathway interactions showed large overlap between the two diet groups, while the pathway interaction networks for the late response were more dissimilar. Conclusions Studying pathway interactions provides a new perspective on the data that complements established pathway analysis methods such as enrichment analysis. This study provided new insights in how interactions between pathways may be affected by insulin resistance. In addition, the analysis approach described here can be generally applied to different types of high-throughput data and will therefore be useful for analysis of other complex datasets as well. PMID:21843341

  13. PhID: an open-access integrated pharmacology interactions database for drugs, targets, diseases, genes, side-effects and pathways.

    PubMed

    Deng, Zhe; Tu, Weizhong; Deng, Zixin; Hu, Qian-Nan

    2017-09-14

    The current network pharmacology study encountered a bottleneck with a lot of public data scattered in different databases. There is the lack of open-access and consolidated platform that integrates this information for systemic research. To address this issue, we have developed PhID, an integrated pharmacology database which integrates >400,000 pharmacology elements (drug, target, disease, gene, side-effect, and pathway) and >200,000 element interactions in branches of public databases. The PhID has three major applications: (1) assists scientists searching through the overwhelming amount of pharmacology elements interaction data by names, public IDs, molecule structures, or molecular sub-structures; (2) helps visualizing pharmacology elements and their interactions with a web-based network graph; (3) provides prediction of drug-target interactions through two modules: PreDPI-ki and FIM, by which users can predict drug-target interactions of the PhID entities or some drug-target pairs they interest. To get a systems-level understanding of drug action and disease complexity, PhID as a network pharmacology tool was established from the perspective of data layer, visualization layer and prediction model layer to present information untapped by current databases. Database URL: http://phid.ditad.org/.

  14. Hsa-miR-590-5p Interaction with SMAD3 Transcript Supports Its Regulatory Effect on The TGFβ Signaling Pathway

    PubMed Central

    Jafarzadeh, Meisam; Soltani, Bahram M.

    2016-01-01

    Objective SMAD proteins are the core players of the transforming growth factor-beta (TGFβ) signaling pathway, a pathway which is involved in cell proliferation, differentiation and migration. On the other hand, hsa-miRNA-590-5p (miR-590-5p) is known to have a negative regulatory effect on TGFβ signaling pathway receptors. Since, RNAhybrid analy- sis suggested SMAD3 as a bona fide target gene for miR-590, we intended to investigate the effect of miR-590-5p on SMAD3 transcription. Materials and Methods In this experimental study, miR-590-5p was overexpressed in different cell lines and its increased expression was detected through quantitative reverse transcription-polymerase chain reaction (RT-qPCR). Western blot analysis was then used to investigate the effect of miR-590-5p overexpression on SMAD3 protein level. Next, the direct interaction of miR-590-5p with the 3´-UTR sequence of SMAD3 transcript was investigated using the dual luciferase assay. Finally, flow cytometery was used to inves- tigate the effect of miR-590-5p overexpression on cell cycle progression in HeLa and SW480 cell lines. Results miR-590-5p was overexpressed in the SW480 cell line and its overexpression resulted in significant reduction of the SMAD3 protein level. Consistently, direct interaction of miR-590-5p with 3´-UTR sequence of SMAD3 was detected. Finally, miR-590-5p over- expression did not show a significant effect on cell cycle progression of Hela and SW480 cell lines. Conclusion Consistent with previous reports about the negative regulatory effect of miR-590 on TGFβ receptors, our data suggest that miR-590-5p also attenuates the TGFβ signaling pathway through down-regulation of SMAD3. PMID:27054113

  15. Mechanism of action of Rhodiola, salidroside, tyrosol and triandrin in isolated neuroglial cells: an interactive pathway analysis of the downstream effects using RNA microarray data.

    PubMed

    Panossian, Alexander; Hamm, Rebecca; Wikman, Georg; Efferth, Thomas

    2014-09-25

    The aim of this study was to identify the targets (genes, interactive signaling pathways, and molecular networks) of Rhodiola rosea extract in isolated neuroglia cells and to predict the effects of Rhodiola extract on cellular functions and diseases. In addition, the potential mechanism of action of Rhodiola rosea extract was elucidated, and the "active principle" among the three isolated constituents (salidroside, triandrin, and tyrosol) was identified. Gene expression profiling was performed using the T98G human neuroglia cell line after treatment with the Rhodiola rosea SHR-5 extract and several of its individual constituents (salidroside, triandrin and tyrosol). An interactive pathway analysis of the downstream effects was performed using datasets containing significantly up- and down-regulated genes, and the effects on cellular functions and diseases were predicted. In total, the expression of 1062 genes was deregulated by the Rhodiola extract (631 analyzed, 336 - up-regulated, 295 - down-regulated), and 1052, 1062, and 1057 genes were deregulated by salidroside, triandrin, and tyrosol, respectively. The analysis of the downstream effects shows that the most significant effects of Rhodiola are associated with cardiovascular (72 deregulated genes), metabolic (63 genes), gastrointestinal (163 genes), neurological (95 genes), endocrine (60 genes), behavioral (50 genes), and psychological disorders (62 genes). The most significantly affected canonical pathways across the entire dataset, which contains the 1062 genes deregulated by Rhodiola, were the following: (a) communication between innate and adaptive immune cells, (b) eNOS signaling, (c) altered T and B cell signaling in rheumatoid arthritis, (d) axonal guidance signaling, (e) G-protein coupled receptor signaling, (f) glutamate receptor signaling, (g) ephrin receptor signaling, (h) cAMP-mediated, and (i) atherosclerosis signaling pathways. Genes associated with behavior and behavioral diseases were identified

  16. Effects of cannabidiol interactions with Wnt/β-catenin pathway and PPARγ on oxidative stress and neuroinflammation in Alzheimer's disease.

    PubMed

    Vallée, Alexandre; Lecarpentier, Yves; Guillevin, Rémy; Vallée, Jean-Noël

    2017-10-01

    Alzheimer's disease (AD) is a neurodegenerative disease, in which the primary etiology remains unknown. AD presents amyloid beta (Aβ) protein aggregation and neurofibrillary plaque deposits. AD shows oxidative stress and chronic inflammation. In AD, canonical Wingless-Int (Wnt)/β-catenin pathway is downregulated, whereas peroxisome proliferator-activated receptor γ (PPARγ) is increased. Downregulation of Wnt/β-catenin, through activation of glycogen synthase kinase-3β (GSK-3β) by Aβ, and inactivation of phosphatidylinositol 3-kinase/Akt signaling involve oxidative stress in AD. Cannabidiol (CBD) is a non-psychotomimetic phytocannabinoid from Cannabis sativa plant. In PC12 cells, Aβ-induced tau protein hyperphosphorylation is inhibited by CBD. This inhibition is associated with a downregulation of p-GSK-3β, an inhibitor of Wnt pathway. CBD may also increase Wnt/β-catenin by stimulation of PPARγ, inhibition of Aβ and ubiquitination of amyloid precursor protein. CBD attenuates oxidative stress and diminishes mitochondrial dysfunction and reactive oxygen species generation. CBD suppresses, through activation of PPARγ, pro-inflammatory signaling and may be a potential new candidate for AD therapy. © The Author 2017. Published by Oxford University Press on behalf of the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  17. Cardioprotection Effects of Sevoflurane by Regulating the Pathway of Neuroactive Ligand-Receptor Interaction in Patients Undergoing Coronary Artery Bypass Graft Surgery

    PubMed Central

    Wang, Jinquan; Cheng, Jian; Zhang, Chao

    2017-01-01

    This study was designed to identify attractor modules and further reveal the potential biological processes involving in sevoflurane-induced anesthesia in patients treated with coronary artery bypass graft (CABG) surgery. Microarray profile data (ID: E-GEOD-4386) on atrial samples obtained from patients receiving anesthetic gas sevoflurane prior to and following CABG procedure were downloaded from EMBL-EBI database for further analysis. Protein-protein interaction (PPI) networks of baseline and sevoflurane groups were inferred and reweighted according to Spearman correlation coefficient (SCC), followed by systematic modules inference using clique-merging approach. Subsequently, attract method was utilized to explore attractor modules. Finally, pathway enrichment analyses for genes in the attractor modules were implemented to illuminate the biological processes in sevoflurane group. Using clique-merging approach, 27 and 36 modules were obtained from the PPI networks of baseline and sevoflurane-treated samples, respectively. By comparing with the baseline condition, 5 module pairs with the same gene composition were identified. Subsequently, 1 out of 5 modules was identified as an attractor based on attract method. Additionally, pathway analysis indicated that genes in the attractor module were associated with neuroactive ligand-receptor interaction. Accordingly, sevoflurane might exert important functions in cardioprotection in patients following CABG, partially through regulating the pathway of neuroactive ligand-receptor interaction. PMID:28348638

  18. Pathway-based discovery of genetic interactions in breast cancer.

    PubMed

    Wang, Wen; Xu, Zack Z; Costanzo, Michael; Boone, Charles; Lange, Carol A; Myers, Chad L

    2017-09-01

    Breast cancer is the second largest cause of cancer death among U.S. women and the leading cause of cancer death among women worldwide. Genome-wide association studies (GWAS) have identified several genetic variants associated with susceptibility to breast cancer, but these still explain less than half of the estimated genetic contribution to the disease. Combinations of variants (i.e. genetic interactions) may play an important role in breast cancer susceptibility. However, due to a lack of statistical power, the current tests for genetic interactions from GWAS data mainly leverage prior knowledge to focus on small sets of genes or SNPs that are known to have an association with breast cancer. Thus, many genetic interactions, particularly among novel variants, remain understudied. Reverse-genetic interaction screens in model organisms have shown that genetic interactions frequently cluster into highly structured motifs, where members of the same pathway share similar patterns of genetic interactions. Based on this key observation, we recently developed a method called BridGE to search for such structured motifs in genetic networks derived from GWAS studies and identify pathway-level genetic interactions in human populations. We applied BridGE to six independent breast cancer cohorts and identified significant pathway-level interactions in five cohorts. Joint analysis across all five cohorts revealed a high confidence consensus set of genetic interactions with support in multiple cohorts. The discovered interactions implicated the glutathione conjugation, vitamin D receptor, purine metabolism, mitotic prometaphase, and steroid hormone biosynthesis pathways as major modifiers of breast cancer risk. Notably, while many of the pathways identified by BridGE show clear relevance to breast cancer, variants in these pathways had not been previously discovered by traditional single variant association tests, or single pathway enrichment analysis that does not consider SNP

  19. PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning.

    PubMed

    Melott, James M; Weinstein, John N; Broom, Bradley M

    2016-01-15

    PathwaysWeb is a resource-based, well-documented web system that provides publicly available information on genes, biological pathways, Gene Ontology (GO) terms, gene-gene interaction networks (importantly, with the directionality of interactions) and links to key-related PubMed documents. The PathwaysWeb API simplifies the construction of applications that need to retrieve and interrelate information across multiple, pathway-related data types from a variety of original data sources. PathwaysBrowser is a companion website that enables users to explore the same integrated pathway data. The PathwaysWeb system facilitates reproducible analyses by providing access to all versions of the integrated datasets. Although its GO subsystem includes data for mouse, PathwaysWeb currently focuses on human data. However, pathways for mouse and many other species can be inferred with a high success rate from human pathways. PathwaysWeb can be accessed via the Internet at http://bioinformatics.mdanderson.org/main/PathwaysWeb:Overview. jmmelott@mdanderson.org Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  20. Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models

    PubMed Central

    Salavert, Francisco; Hidago, Marta R.; Amadoz, Alicia; Çubuk, Cankut; Medina, Ignacio; Crespo, Daniel; Carbonell-Caballero, Jose; Dopazo, Joaquín

    2016-01-01

    The discovery of actionable targets is crucial for targeted therapies and is also a constituent part of the drug discovery process. The success of an intervention over a target depends critically on its contribution, within the complex network of gene interactions, to the cellular processes responsible for disease progression or therapeutic response. Here we present PathAct, a web server that predicts the effect that interventions over genes (inhibitions or activations that simulate knock-outs, drug treatments or over-expressions) can have over signal transmission within signaling pathways and, ultimately, over the cell functionalities triggered by them. PathAct implements an advanced graphical interface that provides a unique interactive working environment in which the suitability of potentially actionable genes, that could eventually become drug targets for personalized or individualized therapies, can be easily tested. The PathAct tool can be found at: http://pathact.babelomics.org. PMID:27137885

  1. Interaction of vitamin D with membrane-based signaling pathways

    PubMed Central

    Larriba, María Jesús; González-Sancho, José Manuel; Bonilla, Félix; Muñoz, Alberto

    2014-01-01

    Many studies in different biological systems have revealed that 1α,25-dihydroxyvitamin D3 (1α,25(OH)2D3) modulates signaling pathways triggered at the plasma membrane by agents such as Wnt, transforming growth factor (TGF)-β, epidermal growth factor (EGF), and others. In addition, 1α,25(OH)2D3 may affect gene expression by paracrine mechanisms that involve the regulation of cytokine or growth factor secretion by neighboring cells. Moreover, post-transcriptional and post-translational effects of 1α,25(OH)2D3 add to or overlap with its classical modulation of gene transcription rate. Together, these findings show that vitamin D receptor (VDR) cannot be considered only as a nuclear-acting, ligand-modulated transcription factor that binds to and controls the transcription of target genes. Instead, available data support the view that much of the complex biological activity of 1α,25(OH)2D3 resides in its capacity to interact with membrane-based signaling pathways and to modulate the expression and secretion of paracrine factors. Therefore, we propose that future research in the vitamin D field should focus on the interplay between 1α,25(OH)2D3 and agents that act at the plasma membrane, and on the analysis of intercellular communication. Global analyses such as RNA-Seq, transcriptomic arrays, and genome-wide ChIP are expected to dissect the interactions at the gene and molecular levels. PMID:24600406

  2. Pathways in Interactive Media Practices among Youths

    ERIC Educational Resources Information Center

    van den Beemt, Antoine; Akkerman, Sanne; Simons, P. Robert-Jan

    2010-01-01

    This qualitative study examines how 11 Dutch students aged 14-15 develop an interest in specific types of interactive media practices and how they perceive these practices in relation to others. The methods included semi-structured interviewing, autodriving visual elicitation and photo elicitation using moodboards. Our results show the importance…

  3. Pathways in Interactive Media Practices among Youths

    ERIC Educational Resources Information Center

    van den Beemt, Antoine; Akkerman, Sanne; Simons, P. Robert-Jan

    2010-01-01

    This qualitative study examines how 11 Dutch students aged 14-15 develop an interest in specific types of interactive media practices and how they perceive these practices in relation to others. The methods included semi-structured interviewing, autodriving visual elicitation and photo elicitation using moodboards. Our results show the importance…

  4. [A novel biological pathway expansion method based on the knowledge of protein-protein interactions].

    PubMed

    Zhao, Xiaolei; Zuo, Xiaoyu; Qin, Jiheng; Liang, Yan; Zhang, Naizun; Luan, Yizhao; Rao, Shaoqi

    2014-04-01

    Biological pathways have been widely used in gene function studies; however, the current knowledge for biological pathways is per se incomplete and has to be further expanded. Bioinformatics prediction provides us a cheap but effective way for pathway expansion. Here, we proposed a novel method for biological pathway prediction, by intergrating prior knowledge of protein?protein interactions and Gene Ontology (GO) database. First, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways to which the interacting neighbors of a targe gene (at the level of protein?protein interaction) belong were chosen as the candidate pathways. Then, the pathways to which the target gene belong were determined by testing whether the genes in the candidate pathways were enriched in the GO terms to which the target gene were annotated. The protein?protein interaction data obtained from the Human Protein Reference Database (HPRD) and Biological General Repository for Interaction Datasets (BioGRID) were respectively used to predict the pathway attribution(s) of the target gene. The results demanstrated that both the average accuracy (the ratio of the correctly predicted pathways to the totally pathways to which all the target genes were annotated) and the relative accuracy (of the genes with at least one annotated pathway being successful predicted, the percentage of the genes with all the annotated pathways being correctly predicted) for pathway predictions were increased with the number of the interacting neighbours. When the number of interacting neighbours reached 22, the average accuracy was 96.2% (HPRD) and 96.3% (BioGRID), respectively, and the relative accuracy was 93.3% (HPRD) and 84.1% (BioGRID), respectively. Further validation analysis of 89 genes whose pathway knowledge was updated in a new database release indicated that 50 genes were correctly predicted for at least one updated pathway, and 43 genes were accurately predicted for all the updated pathways, giving an

  5. Signaling Pathways Mediating Alcohol Effects

    PubMed Central

    Ron, Dorit

    2013-01-01

    Ethanol’s effects on intracellular signaling pathways contribute to acute effects of ethanol as well as to neuroadaptive responses to repeated ethanol exposure. In this chapter we review recent discoveries that demonstrate how ethanol alters signaling pathways involving several receptor tyrosine kinases and intracellular tyrosine and serine-threonine kinases, with consequences for regulation of cell surface receptor function, gene expression, protein translation, neuronal excitability and animal behavior. We also describe recent work that demonstrates a key role for ethanol in regulating the function of scaffolding proteins that organize signaling complexes into functional units. Finally, we review recent exciting studies demonstrating ethanol modulation of DNA and histone modification and the expression of microRNAs, indicating epigenetic mechanisms by which ethanol regulates neuronal gene expression and addictive behaviors. PMID:21877259

  6. The interactions of flavonoids within neuronal signalling pathways

    PubMed Central

    2007-01-01

    Emerging evidence suggests that dietary phytochemicals, in particular flavonoids, may exert beneficial effects in the central nervous system by protecting neurons against stress-induced injury, by suppressing neuroinflammation and by promoting neurocognitive performance, through changes in synaptic plasticity. It is likely that flavonoids exert such effects in neurons, through selective actions on different components within a number of protein kinase and lipid kinase signalling cascades, such as phosphatidylinositol-3 kinase (PI3K)/Akt, protein kinase C and mitogen-activated protein kinase. This review details the potential inhibitory or stimulatory actions of flavonoids within these pathways, and describes how such interactions are likely to affect cellular function through changes in the activation state of target molecules and/or by modulating gene expression. Although, precise sites of action are presently unknown, their abilities to: (1) bind to ATP binding sites on enzymes and receptors; (2) modulate the activity of kinases directly; (3) affect the function of important phosphatases; (4) preserve neuronal Ca2+ homeostasis; and (5) modulate signalling cascades lying downstream of kinases, are explored. Future research directions are outlined in relation to their precise site(s) of action within the signalling pathways and the sequence of events that allow them to regulate neuronal function in the central nervous system. PMID:18850181

  7. WW domain interactions regulate the Hippo tumor suppressor pathway

    PubMed Central

    Salah, Z; Aqeilan, R I

    2011-01-01

    The Hippo kinase pathway is emerging as a conserved signaling pathway that is essential for organ growth and tumorigenesis in Drosophila and mammalians. Although the signaling of the core kinases is relatively well understood, less is known about the upstream inputs, downstream outputs and regulation of the whole cascade. Enrichment of the Hippo pathway components with WW domains and their cognate proline-rich interacting motifs provides a versatile platform for further understanding the mechanisms that regulate organ growth and tumorigenesis. Here, we review recently discovered mechanisms of WW domain-mediated interactions that contribute to the regulation of the Hippo signaling pathway in tumorigenesis. We further discuss new insights and future directions on the emerging role of such regulation. PMID:21677687

  8. WW domain interactions regulate the Hippo tumor suppressor pathway.

    PubMed

    Salah, Z; Aqeilan, R I

    2011-06-16

    The Hippo kinase pathway is emerging as a conserved signaling pathway that is essential for organ growth and tumorigenesis in Drosophila and mammalians. Although the signaling of the core kinases is relatively well understood, less is known about the upstream inputs, downstream outputs and regulation of the whole cascade. Enrichment of the Hippo pathway components with WW domains and their cognate proline-rich interacting motifs provides a versatile platform for further understanding the mechanisms that regulate organ growth and tumorigenesis. Here, we review recently discovered mechanisms of WW domain-mediated interactions that contribute to the regulation of the Hippo signaling pathway in tumorigenesis. We further discuss new insights and future directions on the emerging role of such regulation.

  9. Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs

    PubMed Central

    Lin, Tien-Ho; Bar-Joseph, Ziv

    2011-01-01

    Abstract Proper subcellular localization is critical for proteins to perform their roles in cellular functions. Proteins are transported by different cellular sorting pathways, some of which take a protein through several intermediate locations until reaching its final destination. The pathway a protein is transported through is determined by carrier proteins that bind to specific sequence motifs. In this article, we present a new method that integrates protein interaction and sequence motif data to model how proteins are sorted through these sorting pathways. We use a hidden Markov model (HMM) to represent protein sorting pathways. The model is able to determine intermediate sorting states and to assign carrier proteins and motifs to the sorting pathways. In simulation studies, we show that the method can accurately recover an underlying sorting model. Using data for yeast, we show that our model leads to accurate prediction of subcellular localization. We also show that the pathways learned by our model recover many known sorting pathways and correctly assign proteins to the path they utilize. The learned model identified new pathways and their putative carriers and motifs and these may represent novel protein sorting mechanisms. Supplementary results and software implementation are available from http://murphylab.web.cmu.edu/software/2010_RECOMB_pathways/. PMID:21999284

  10. AN INTEGRATED NETWORK APPROACH TO IDENTIFYING BIOLOGICAL PATHWAYS AND ENVIRONMENTAL EXPOSURE INTERACTIONS IN COMPLEX DISEASES

    PubMed Central

    DARABOS, CHRISTIAN; QIU, JINGYA; MOORE, JASON H.

    2015-01-01

    Complex diseases are the result of intricate interactions between genetic, epigenetic and environmental factors. In previous studies, we used epidemiological and genetic data linking environmental exposure or genetic variants to phenotypic disease to construct Human Phenotype Networks and separately analyze the effects of both environment and genetic factors on disease interactions. To better capture the intricacies of the interactions between environmental exposure and the biological pathways in complex disorders, we integrate both aspects into a single “tripartite” network. Despite extensive research, the mechanisms by which chemical agents disrupt biological pathways are still poorly understood. In this study, we use our integrated network model to identify specific biological pathway candidates possibly disrupted by environmental agents. We conjecture that a higher number of co-occurrences between an environmental substance and biological pathway pair can be associated with a higher likelihood that the substance is involved in disrupting that pathway. We validate our model by demonstrating its ability to detect known arsenic and signal transduction pathway interactions and speculate on candidate cell-cell junction organization pathways disrupted by cadmium. The validation was supported by distinct publications of cell biology and genetic studies that associated environmental exposure to pathway disruption. The integrated network approach is a novel method for detecting the biological effects of environmental exposures. A better understanding of the molecular processes associated with specific environmental exposures will help in developing targeted molecular therapies for patients who have been exposed to the toxicity of environmental chemicals. PMID:26776169

  11. Protein Disulfide Isomerase-2 of Arabidopsis Mediates Protein Folding and Localizes to Both the Secretory Pathway and Nucleus, Where It Interacts with Maternal Effect Embryo Arrest Factor

    PubMed Central

    Cho, Eun Ju; Yuen, Christen Y.L.; Kang, Byung-Ho; Ondzighi, Christine A.; Staehelin, L. Andrew; Christopher, David A.

    2011-01-01

    Protein disulfide isomerase (PDI) is a thiodisulfide oxidoreductase that catalyzes the formation, reduction and rearrangement of disulfide bonds in proteins of eukaryotes. The classical PDI has a signal peptide, two CXXCcontaining thioredoxin catalytic sites (a,a′), two noncatalytic thioredoxin fold domains (b,b′), an acidic domain (c) and a C-terminal endoplasmic reticulum (ER) retention signal. Although PDI resides in the ER where it mediates the folding of nascent polypeptides of the secretory pathway, we recently showed that PDI5 of Arabidopsis thaliana chaperones and inhibits cysteine proteases during trafficking to vacuoles prior to programmed cell death of the endothelium in developing seeds. Here we describe Arabidopsis PDI2, which shares a primary structure similar to that of classical PDI. Recombinant PDI2 is imported into ER-derived microsomes and complements the E. coli protein- folding mutant, dsbA. PDI2 interacted with proteins in both the ER and nucleus, including ER-resident protein folding chaperone, BiP1, and nuclear embryo transcription factor, MEE8. The PDI2-MEE8 interaction was confirmed to occur in vitro and in vivo. Transient expression of PDI2- GFP fusions in mesophyll protoplasts resulted in labeling of the ER, nucleus and vacuole. PDI2 is expressed in multiple tissues, with relatively high expression in seeds and root tips. Immunoelectron microscopy with GFP- and PDI2-specific antisera on transgenic seeds (PDI2-GFP) and wild type roots demonstrated that PDI2 was found in the secretory pathway (ER, Golgi, vacuole, cell wall) and the nuclei. Our results indicate that PDI2 mediates protein folding in the ER and has new functional roles in the nucleus. PMID:21909944

  12. Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer

    PubMed Central

    Börnigen, Daniela; Tyekucheva, Svitlana; Wang, Xiaodong; Rider, Jennifer R.; Lee, Gwo-Shu; Mucci, Lorelei A.; Sweeney, Christopher; Huttenhower, Curtis

    2016-01-01

    Molecular research in cancer is one of the largest areas of bioinformatic investigation, but it remains a challenge to understand biomolecular mechanisms in cancer-related pathways from high-throughput genomic data. This includes the Nuclear-factor-kappa-B (NFκB) pathway, which is central to the inflammatory response and cell proliferation in prostate cancer development and progression. Despite close scrutiny and a deep understanding of many of its members’ biomolecular activities, the current list of pathway members and a systems-level understanding of their interactions remains incomplete. Here, we provide the first steps toward computational reconstruction of interaction mechanisms of the NFκB pathway in prostate cancer. We identified novel roles for ATF3, CXCL2, DUSP5, JUNB, NEDD9, SELE, TRIB1, and ZFP36 in this pathway, in addition to new mechanistic interactions between these genes and 10 known NFκB pathway members. A newly predicted interaction between NEDD9 and ZFP36 in particular was validated by co-immunoprecipitation, as was NEDD9's potential biological role in prostate cancer cell growth regulation. We combined 651 gene expression datasets with 1.4M gene product interactions to predict the inclusion of 40 additional genes in the pathway. Molecular mechanisms of interaction among pathway members were inferred using recent advances in Bayesian data integration to simultaneously provide information specific to biological contexts and individual biomolecular activities, resulting in a total of 112 interactions in the fully reconstructed NFκB pathway: 13 (11%) previously known, 29 (26%) supported by existing literature, and 70 (63%) novel. This method is generalizable to other tissue types, cancers, and organisms, and this new information about the NFκB pathway will allow us to further understand prostate cancer and to develop more effective prevention and treatment strategies. PMID:27078000

  13. Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer.

    PubMed

    Börnigen, Daniela; Tyekucheva, Svitlana; Wang, Xiaodong; Rider, Jennifer R; Lee, Gwo-Shu; Mucci, Lorelei A; Sweeney, Christopher; Huttenhower, Curtis

    2016-04-01

    Molecular research in cancer is one of the largest areas of bioinformatic investigation, but it remains a challenge to understand biomolecular mechanisms in cancer-related pathways from high-throughput genomic data. This includes the Nuclear-factor-kappa-B (NFκB) pathway, which is central to the inflammatory response and cell proliferation in prostate cancer development and progression. Despite close scrutiny and a deep understanding of many of its members' biomolecular activities, the current list of pathway members and a systems-level understanding of their interactions remains incomplete. Here, we provide the first steps toward computational reconstruction of interaction mechanisms of the NFκB pathway in prostate cancer. We identified novel roles for ATF3, CXCL2, DUSP5, JUNB, NEDD9, SELE, TRIB1, and ZFP36 in this pathway, in addition to new mechanistic interactions between these genes and 10 known NFκB pathway members. A newly predicted interaction between NEDD9 and ZFP36 in particular was validated by co-immunoprecipitation, as was NEDD9's potential biological role in prostate cancer cell growth regulation. We combined 651 gene expression datasets with 1.4M gene product interactions to predict the inclusion of 40 additional genes in the pathway. Molecular mechanisms of interaction among pathway members were inferred using recent advances in Bayesian data integration to simultaneously provide information specific to biological contexts and individual biomolecular activities, resulting in a total of 112 interactions in the fully reconstructed NFκB pathway: 13 (11%) previously known, 29 (26%) supported by existing literature, and 70 (63%) novel. This method is generalizable to other tissue types, cancers, and organisms, and this new information about the NFκB pathway will allow us to further understand prostate cancer and to develop more effective prevention and treatment strategies.

  14. Receptor kinase signaling pathways in plant-microbe interactions.

    PubMed

    Antolín-Llovera, Meritxell; Ried, Martina K; Binder, Andreas; Parniske, Martin

    2012-01-01

    Plant receptor-like kinases (RLKs) function in diverse signaling pathways, including the responses to microbial signals in symbiosis and defense. This versatility is achieved with a common overall structure: an extracytoplasmic domain (ectodomain) and an intracellular protein kinase domain involved in downstream signal transduction. Various surfaces of the leucine-rich repeat (LRR) ectodomain superstructure are utilized for interaction with the cognate ligand in both plant and animal receptors. RLKs with lysin-motif (LysM) ectodomains confer recognitional specificity toward N-acetylglucosamine-containing signaling molecules, such as chitin, peptidoglycan (PGN), and rhizobial nodulation factor (NF), that induce immune or symbiotic responses. Signaling downstream of RLKs does not follow a single pattern; instead, the detailed analysis of brassinosteroid (BR) signaling, innate immunity, and symbiosis revealed at least three largely nonoverlapping pathways. In this review, we focus on RLKs involved in plant-microbe interactions and contrast the signaling pathways leading to symbiosis and defense.

  15. Inferring molecular interactions pathways from eQTL data

    SciTech Connect

    Rashid, Imran; McDermott, Jason E.; Samudrala, Ram

    2009-04-20

    Analysis of expression quantitative trait loci (eQTL) helps elucidate the connection between genotype, gene expression levels, and phenotype. However, standard statistical genetics can only attribute changes in expression levels to loci on the genome, not specific genes. Each locus can contain many genes, making it very difficult to discover which gene is controlling the expression levels of other genes. Furthermore, it is even more difficult to find a pathway of molecular interactions responsible for controlling the expression levels. Here we describe a series of techniques for finding explanatory pathways by exploring graphs of molecular interactions. We show several simple methods can find complete pathways the explain the mechanism of differential expression in eQTL data.

  16. Integrated Interactive Chart as a Tool for Teaching Metabolic Pathways

    ERIC Educational Resources Information Center

    Kalogiannis, Stavros; Pagkalos, Ioannis; Koufoudakis, Panagiotis; Dashi, Ino; Pontikeri, Kyriaki; Christodoulou, Constantina

    2014-01-01

    An interactive chart of energy metabolism with didactic function, complementary to the already existing metabolic maps, located at the URL www.metpath.teithe.gr is being presented. The chart illustrates the major catabolic and biosynthetic pathways of glucose, fatty acids, and aminoacids, individually as well as in an integrated view. For every…

  17. Integrated Interactive Chart as a Tool for Teaching Metabolic Pathways

    ERIC Educational Resources Information Center

    Kalogiannis, Stavros; Pagkalos, Ioannis; Koufoudakis, Panagiotis; Dashi, Ino; Pontikeri, Kyriaki; Christodoulou, Constantina

    2014-01-01

    An interactive chart of energy metabolism with didactic function, complementary to the already existing metabolic maps, located at the URL www.metpath.teithe.gr is being presented. The chart illustrates the major catabolic and biosynthetic pathways of glucose, fatty acids, and aminoacids, individually as well as in an integrated view. For every…

  18. Cyclone-cyclone Interactions through the Ocean Pathway

    SciTech Connect

    Balaguru, Karthik; Taraphdar, Sourav; Leung, Lai-Yung R.; Foltz, Gregory R.; Knaff, John A.

    2014-10-16

    The intense SST (Sea Surface Temperature) cooling caused by hurricane-induced mixing is restored at timescales on the order of weeks(1) and thus may persist long enough to influence a later hurricane passing over it. Though many studies have evaluated the effects of SST cool-ing induced by a hurricane on its own intensification(2, 3), none has looked at its effect on later storms. Using an analysis of observations and numerical model simulations, we demonstrate that hurricanes may influence the intensity of later hurricanes that pass over their linger-ing wakes. On average, when hurricanes encounter cold wakes, they experience SSTs that are ~0.4oC lower than when they do not encounter wakes and consequently decay(intensify) at a rate that is nearly three times faster(slower). In the region of warm SSTs (* 26.5oC) where the most intense and damaging hurricanes tend to occur, the percentage of hurricanes that encounter lingering cold wakes increases with hurricane frequency and was found to be as high as 40%. Furthermore, we estimate that the cumulative power dissipated(4) by the most energetic hurricanes has been reduced by as much as ~7% in a season through this effect. As the debate on changes in Atlantic hurricane activity associated with global warming(5) continues, the negative feedback between hurricane frequency and intensity resulting from hurricane-hurricane interactions through the ocean pathway deserves attention.

  19. Interactions of Bacterial Proteins with Host Eukaryotic Ubiquitin Pathways

    PubMed Central

    Perrett, Charlotte Averil; Lin, David Yin-Wei; Zhou, Daoguo

    2011-01-01

    Ubiquitination is a post-translational modification in which one or more 76 amino acid polypeptide ubiquitin molecules are covalently linked to the lysine residues of target proteins. Ubiquitination is the main pathway for protein degradation that governs a variety of eukaryotic cellular processes, including the cell-cycle, vesicle trafficking, antigen presentation, and signal transduction. Not surprisingly, aberrations in the system have been implicated in the pathogenesis of many diseases including inflammatory and neurodegenerative disorders. Recent studies have revealed that viruses and bacterial pathogens exploit the host ubiquitination pathways to gain entry and to aid their survival/replication inside host cells. This review will summarize recent developments in understanding the biochemical and structural mechanisms utilized by bacterial pathogens to interact with the host ubiquitination pathways. PMID:21772834

  20. An Interactive, Integrated, Instructional Pathway to the LEAD Science Gateway

    NASA Astrophysics Data System (ADS)

    Yalda, S.; Clark, R.; Davis, L.; Wiziecki, E. N.

    2008-12-01

    of learning materials, as well as new tools and features, to enhance the appearance and use of the LEAD portal gateway and its underlying cyberinfrastructure in an educational setting. The development of educational materials has centered on promoting the accessibility and use of meteorological data and analysis tools through the LEAD portal by providing instructional materials, additional custom designed tools that build off of Unidata's Integrated Data Viewer (IDV) (e.g. IDV Basic and NCDestroyer), and an interactive component that takes the user through specific tasks utilizing multiple tools. In fact, select improvements to parameter lists and domain subsetting have inspired IDV developers to incorporate changes in IDV revisions that are now available to the entire community. This collection of materials, demonstrations, interactive guides, student exercises, and customized tools, which are now available to the educator and student through the LEAD portal gateway, can serve as an instructional pathway for a set of guided, phenomenon-based exercises (e.g. fronts, lake-effect snows, etc.). This paper will provide an overview of the LEAD education and outreach efforts with a focus on the design of Web-based educational materials and instructional approaches for user interaction with the LEAD portal gateway and the underlying cyberinfrastructure, and will encourage educators, especially those involved in undergraduate meteorology education, to begin incorporating these capabilities into their course materials.

  1. Differential genetic interactions of yeast stress response MAPK pathways

    PubMed Central

    Martin, Humberto; Shales, Michael; Fernandez-Piñar, Pablo; Wei, Ping; Molina, Maria; Fiedler, Dorothea; Shokat, Kevan M; Beltrao, Pedro; Lim, Wendell; Krogan, Nevan J

    2015-01-01

    Genetic interaction screens have been applied with great success in several organisms to study gene function and the genetic architecture of the cell. However, most studies have been performed under optimal growth conditions even though many functional interactions are known to occur under specific cellular conditions. In this study, we have performed a large-scale genetic interaction analysis in Saccharomyces cerevisiae involving approximately 49 × 1,200 double mutants in the presence of five different stress conditions, including osmotic, oxidative and cell wall-altering stresses. This resulted in the generation of a differential E-MAP (or dE-MAP) comprising over 250,000 measurements of conditional interactions. We found an extensive number of conditional genetic interactions that recapitulate known stress-specific functional associations. Furthermore, we have also uncovered previously unrecognized roles involving the phosphatase regulator Bud14, the histone methylation complex COMPASS and membrane trafficking complexes in modulating the cell wall integrity pathway. Finally, the osmotic stress differential genetic interactions showed enrichment for genes coding for proteins with conditional changes in phosphorylation but not for genes with conditional changes in gene expression. This suggests that conditional genetic interactions are a powerful tool to dissect the functional importance of the different response mechanisms of the cell. PMID:25888283

  2. Differential genetic interactions of yeast stress response MAPK pathways.

    PubMed

    Martin, Humberto; Shales, Michael; Fernandez-Piñar, Pablo; Wei, Ping; Molina, Maria; Fiedler, Dorothea; Shokat, Kevan M; Beltrao, Pedro; Lim, Wendell; Krogan, Nevan J

    2015-04-17

    Genetic interaction screens have been applied with great success in several organisms to study gene function and the genetic architecture of the cell. However, most studies have been performed under optimal growth conditions even though many functional interactions are known to occur under specific cellular conditions. In this study, we have performed a large-scale genetic interaction analysis in Saccharomyces cerevisiae involving approximately 49 × 1,200 double mutants in the presence of five different stress conditions, including osmotic, oxidative and cell wall-altering stresses. This resulted in the generation of a differential E-MAP (or dE-MAP) comprising over 250,000 measurements of conditional interactions. We found an extensive number of conditional genetic interactions that recapitulate known stress-specific functional associations. Furthermore, we have also uncovered previously unrecognized roles involving the phosphatase regulator Bud14, the histone methylation complex COMPASS and membrane trafficking complexes in modulating the cell wall integrity pathway. Finally, the osmotic stress differential genetic interactions showed enrichment for genes coding for proteins with conditional changes in phosphorylation but not for genes with conditional changes in gene expression. This suggests that conditional genetic interactions are a powerful tool to dissect the functional importance of the different response mechanisms of the cell.

  3. Interactions of TLR4 and PPARγ, Dependent on AMPK Signalling Pathway Contribute to Anti-Inflammatory Effects of Vaccariae Hypaphorine in Endothelial Cells.

    PubMed

    Sun, Haijian; Zhu, Xuexue; Lin, Wei; Zhou, Yuetao; Cai, Weiwei; Qiu, Liying

    2017-07-03

    Background /Aims: Accumulating evidence indicates that endothelial inflammation is one of the critical determinants in pathogenesis of atherosclerotic cardiovascular disease. Our previous studies had demonstrated that Vaccariae prevented high glucose or oxidative stress-triggered endothelial dysfunction in vitro. Very little is known about the potential effects of hypaphorine from Vaccariae seed on inflammatory response in endothelial cells. In the present study, we evaluated the anti-inflammatory effects of Vaccariae hypaphorine (VH) on lipopolysaccharide (LPS)-challenged endothelial EA.hy926 cells. The inflammatory cytokines including tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), monocyte chemoattractant protein 1 (MCP-1) and vascular cellular adhesion molecule-1 (VCAM-1) were measured by real-time PCR (RT-PCR). The expressions of adenosine monophosphate-activated protein kinase (AMPK), acetyl-CoA carboxylase (ACC), toll-like receptor 4 (TLR4), peroxisome proliferator-activated receptor γ (PPARγ) were detected by Western blotting or immunofluorescence. We showed that LPS stimulated the expressions of TNF-α, IL-1β, MCP-1, VCAM-1 and TLR4, but attenuated the phosphorylation of AMPK and ACC as well as PPARγ protein levels, which were reversed by VH pretreatment. Moreover, we observed that LPS-upregulated TLR4 protein expressions were inhibited by PPARγ agonist pioglitazone, and the downregulated PPARγ expressions in response to LPS were partially restored by knockdown of TLR4. The negative regulation loop between TLR4 and PPARγ response to LPS was modulated by AMPK agonist AICAR (5-Aminoimidazole-4-carboxamide riboside or acadesine) or A769662. Taken together, our results suggested that VH ameliorated LPS-induced inflammatory cytokines production in endothelial cells via inhibition of TLR4 and activation of PPARγ, dependent on AMPK signalling pathway. © 2017 The Author(s). Published by S. Karger AG, Basel.

  4. Signaling pathways and tissue interactions in neural plate border formation.

    PubMed

    Schille, Carolin; Schambony, Alexandra

    2017-01-01

    The neural crest is a transient cell population that gives rise to various cell types of multiple tissues and organs in the vertebrate embryo. Neural crest cells arise from the neural plate border, a region localized at the lateral borders of the prospective neural plate. Temporally and spatially coordinated interaction with the adjacent tissues, the non-neural ectoderm, the neural plate and the prospective dorsolateral mesoderm, is required for neural plate border specification. Signaling molecules, namely BMP, Wnt and FGF ligands and corresponding antagonists are derived from these tissues and interact to induce the expression of neural plate border specific genes. The present mini-review focuses on the current understanding of how the NPB territory is formed and accentuates the need for coordinated interaction of BMP and Wnt signaling pathways and precise tissue communication that are required for the definition of the prospective NC in the competent ectoderm.

  5. Automated identification of pathways from quantitative genetic interaction data

    PubMed Central

    Battle, Alexis; Jonikas, Martin C; Walter, Peter; Weissman, Jonathan S; Koller, Daphne

    2010-01-01

    High-throughput quantitative genetic interaction (GI) measurements provide detailed information regarding the structure of the underlying biological pathways by reporting on functional dependencies between genes. However, the analytical tools for fully exploiting such information lag behind the ability to collect these data. We present a novel Bayesian learning method that uses quantitative phenotypes of double knockout organisms to automatically reconstruct detailed pathway structures. We applied our method to a recent data set that measures GIs for endoplasmic reticulum (ER) genes, using the unfolded protein response as a quantitative phenotype. The results provided reconstructions of known functional pathways including N-linked glycosylation and ER-associated protein degradation. It also contained novel relationships, such as the placement of SGT2 in the tail-anchored biogenesis pathway, a finding that we experimentally validated. Our approach should be readily applicable to the next generation of quantitative GI data sets, as assays become available for additional phenotypes and eventually higher-level organisms. PMID:20531408

  6. Fgf and Sdf-1 pathways interact during zebrafish fin regeneration.

    PubMed

    Bouzaffour, Mohamed; Dufourcq, Pascale; Lecaudey, Virginie; Haas, Petra; Vriz, Sophie

    2009-06-08

    The chemokine stromal cell-derived factor-1 (SDF1) was originally identified as a pre-B cell stimulatory factor but has been recently implicated in several other key steps in differentiation and morphogenesis. In addition, SDF1 as well as FGF signalling pathways have recently been shown to be involved in the control of epimorphic regeneration. In this report, we address the question of a possible interaction between the two signalling pathways during adult fin regeneration in zebrafish. Using a combination of pharmaceutical and genetic tools, we show that during epimorphic regeneration, expression of sdf1, as well as of its cognate receptors, cxcr4a, cxcr4b and cxcr7 are controlled by FGF signalling. We further show that, Sdf1a negatively regulates the expression of fgf20a. Together, these results lead us to propose that: 1) the function of Fgf in blastema formation is, at least in part, relayed by the chemokine Sdf1a, and that 2) Sdf1 exerts negative feedback on the Fgf pathway, which contributes to a transient expression of Fgf20a downstream genes at the beginning of regeneration. However this feedback control can be bypassed since the Sdf1 null mutants regenerate their fin, though slower. Very few mutants for the regeneration process were isolated so far, illustrating the difficulty in identifying genes that are indispensable for regeneration. This observation supports the idea that the regeneration process involves a delicate balance between multiple pathways.

  7. Machine Learning of Protein Interactions in Fungal Secretory Pathways.

    PubMed

    Kludas, Jana; Arvas, Mikko; Castillo, Sandra; Pakula, Tiina; Oja, Merja; Brouard, Céline; Jäntti, Jussi; Penttilä, Merja; Rousu, Juho

    2016-01-01

    In this paper we apply machine learning methods for predicting protein interactions in fungal secretion pathways. We assume an inter-species transfer setting, where training data is obtained from a single species and the objective is to predict protein interactions in other, related species. In our methodology, we combine several state of the art machine learning approaches, namely, multiple kernel learning (MKL), pairwise kernels and kernelized structured output prediction in the supervised graph inference framework. For MKL, we apply recently proposed centered kernel alignment and p-norm path following approaches to integrate several feature sets describing the proteins, demonstrating improved performance. For graph inference, we apply input-output kernel regression (IOKR) in supervised and semi-supervised modes as well as output kernel trees (OK3). In our experiments simulating increasing genetic distance, Input-Output Kernel Regression proved to be the most robust prediction approach. We also show that the MKL approaches improve the predictions compared to uniform combination of the kernels. We evaluate the methods on the task of predicting protein-protein-interactions in the secretion pathways in fungi, S.cerevisiae, baker's yeast, being the source, T. reesei being the target of the inter-species transfer learning. We identify completely novel candidate secretion proteins conserved in filamentous fungi. These proteins could contribute to their unique secretion capabilities.

  8. Machine Learning of Protein Interactions in Fungal Secretory Pathways

    PubMed Central

    Kludas, Jana; Arvas, Mikko; Castillo, Sandra; Pakula, Tiina; Oja, Merja; Brouard, Céline; Jäntti, Jussi; Penttilä, Merja

    2016-01-01

    In this paper we apply machine learning methods for predicting protein interactions in fungal secretion pathways. We assume an inter-species transfer setting, where training data is obtained from a single species and the objective is to predict protein interactions in other, related species. In our methodology, we combine several state of the art machine learning approaches, namely, multiple kernel learning (MKL), pairwise kernels and kernelized structured output prediction in the supervised graph inference framework. For MKL, we apply recently proposed centered kernel alignment and p-norm path following approaches to integrate several feature sets describing the proteins, demonstrating improved performance. For graph inference, we apply input-output kernel regression (IOKR) in supervised and semi-supervised modes as well as output kernel trees (OK3). In our experiments simulating increasing genetic distance, Input-Output Kernel Regression proved to be the most robust prediction approach. We also show that the MKL approaches improve the predictions compared to uniform combination of the kernels. We evaluate the methods on the task of predicting protein-protein-interactions in the secretion pathways in fungi, S.cerevisiae, baker’s yeast, being the source, T. reesei being the target of the inter-species transfer learning. We identify completely novel candidate secretion proteins conserved in filamentous fungi. These proteins could contribute to their unique secretion capabilities. PMID:27441920

  9. Effects of PDT on the endocytic pathway

    NASA Astrophysics Data System (ADS)

    Kessel, David

    2010-02-01

    Two lines of evidence point to an early effect of photodamage on membrane trafficking. [1] Internalization of a fluorescent probe for hydrophobic membrane loci was impaired by prior photodamage. [2] Interference with the endocytic pathway by the PI-3 kinase antagonist wortmannin led to accumulation of cytoplasmic vacuoles suggesting a block in the recycling of plasma membrane components. Prior photodamage blocked this pathway so that no vacuoles were formed upon exposure of cells to wortmannin. In a murine hepatoma line, the endocytic pathway was preferentially sensitive to lysosomal photodamage. The role of photodamage to the endocytic pathway as a factor in PDT efficacy remains to be assessed.

  10. Probing the Pathways and Interactions Controlling Crystallization by Particle Attachment

    NASA Astrophysics Data System (ADS)

    De Yoreo, J. J.; Li, D.; Chun, J.; Schenter, G.; Mundy, C.; Rosso, K. M.

    2016-12-01

    Crystallization by particle attachment appears to be a widespread mechanism of mineralization. Yet many long-standing questions surrounding nucleation and assembly of precursor particles remain unanswered, due in part to a lack of tools to probe mineralization dynamics with adequate spatial and temporal resolution. Here we report results of liquid phase TEM studies of nucleation and particle assembly in a number of mineral systems. We interpret the results within a framework that considers the impact of both the complexity of free energy landscapes and kinetic factors associated with high supersaturation or slow dynamics. In the calcium carbonate system, the need for high supersturations to overcome the high barrier to nucleation of calcite leads to simultaneous occurrence of multiple pathways, including direct formation of all the common ploymorphs, as well as two-step pathways through which initial precursors, particularly ACC, undergo a direct transformation to a more stable phase. Introduction of highly charged polymers that bind calcium inhibits nucleation, but directs the pathway to a metastable amorphous phase that no longer transforms to more stable polymorphs. Experiments in the iron oxide and oxyhydroxide systems show that, when high supersaturations lead to nucleation of many nanoprticles, further growth occurs through a combination of particle aggregation events and Ostwald ripening. In some cases, aggregation occurs only through oriented attachment on lattice matched faces, leading to single crystals with complex topologies and internal twin boundaries, while in others aggregation results initially in poor co-alignment, but over time the particles undergo atomic rearrangements to achieve a single crystal structure. AFM-based measurements of forces between phyllosilicate surfaces reveal the importance of long-range dispersion interactions in driving alignment, as well as the impact of electrolyte concentration and temperature on the competition of those

  11. Protein interaction network of the mammalian Hippo pathway reveals mechanisms of kinase-phosphatase interactions.

    PubMed

    Couzens, Amber L; Knight, James D R; Kean, Michelle J; Teo, Guoci; Weiss, Alexander; Dunham, Wade H; Lin, Zhen-Yuan; Bagshaw, Richard D; Sicheri, Frank; Pawson, Tony; Wrana, Jeffrey L; Choi, Hyungwon; Gingras, Anne-Claude

    2013-11-19

    The Hippo pathway regulates organ size and tissue homeostasis in response to multiple stimuli, including cell density and mechanotransduction. Pharmacological inhibition of phosphatases can also stimulate Hippo signaling in cell culture. We defined the Hippo protein-protein interaction network with and without inhibition of serine and threonine phosphatases by okadaic acid. We identified 749 protein interactions, including 599 previously unrecognized interactions, and demonstrated that several interactions with serine and threonine phosphatases were phosphorylation-dependent. Mutation of the T-loop of MST2 (mammalian STE20-like protein kinase 2), which prevented autophosphorylation, disrupted its association with STRIPAK (striatin-interacting phosphatase and kinase complex). Deletion of the amino-terminal forkhead-associated domain of SLMAP (sarcolemmal membrane-associated protein), a component of the STRIPAK complex, prevented its association with MST1 and MST2. Phosphatase inhibition produced temporally distinct changes in proteins that interacted with MOB1A and MOB1B (Mps one binder kinase activator-like 1A and 1B) and promoted interactions with upstream Hippo pathway proteins, such as MST1 and MST2, and with the trimeric protein phosphatase 6 complex (PP6). Mutation of three basic amino acids that are part of a phospho-serine- and phospho-threonine-binding domain in human MOB1B prevented its interaction with MST1 and PP6 in cells treated with okadaic acid. Collectively, our results indicated that changes in phosphorylation orchestrate interactions between kinases and phosphatases in Hippo signaling, providing a putative mechanism for pathway regulation.

  12. Abscisic acid interacts antagonistically with salicylic acid signaling pathway in rice-Magnaporthe grisea interaction.

    PubMed

    Jiang, Chang-Jie; Shimono, Masaki; Sugano, Shoji; Kojima, Mikiko; Yazawa, Katsumi; Yoshida, Riichiro; Inoue, Haruhiko; Hayashi, Nagao; Sakakibara, Hitoshi; Takatsuji, Hiroshi

    2010-06-01

    Plant hormones play pivotal signaling roles in plant-pathogen interactions. Here, we report characterization of an antagonistic interaction of abscisic acid (ABA) with salicylic acid (SA) signaling pathways in the rice-Magnaporthe grisea interaction. Exogenous application of ABA drastically compromised the rice resistance to both compatible and incompatible M. grisea strains, indicating that ABA negatively regulates both basal and resistance gene-mediated blast resistance. ABA markedly suppressed the transcriptional upregulation of WRKY45 and OsNPR1, the two key components of the SA signaling pathway in rice, induced by SA or benzothiadiazole or by blast infection. Overexpression of OsNPR1 or WRKY45 largely negated the enhancement of blast susceptibility by ABA, suggesting that ABA acts upstream of WRKY45 and OsNPR1 in the rice SA pathway. ABA-responsive genes were induced during blast infection in a pattern reciprocal to those of WRKY45 and OsPR1b in the compatible rice-blast interaction but only marginally in the incompatible one. These results suggest that the balance of SA and ABA signaling is an important determinant for the outcome of the rice-M. grisea interaction. ABA was detected in hyphae and conidia of M. grisea as well as in culture media, implying that blast-fungus-derived ABA could play a role in triggering ABA signaling at host infection sites.

  13. Joint inhibition of TOR and JNK pathways interacts to extend the lifespan of Brachionus manjavacas (Rotifera)

    PubMed Central

    Snell, Terry W.; Johnston, Rachel K.; Rabeneck, Brett; Zipperer, Cody; Teat, Stephanie

    2014-01-01

    The TOR kinase pathway is central in modulating aging in a variety of animal models. The target of rapamycin (TOR) integrates a complex network of signals from growth conditions, nutrient availability, energy status, and physiological stresses and matches an organism’s growth rate to the resource environment. Important problems remaining are to identify the pathways that interact with TOR and characterize them as additive or synergistic. One of the most versatile stress sensors in metazoans is the Jun-N-terminal Kinase (JNK) signalling pathway. JNK is an evolutionarily conserved stress-activated protein kinase that is induced by a range of stressors, including UV irradiation, reactive oxygen species, DNA damage, heat, and bacterial antigens. JNK is thought to interact with the TOR pathway, but its effects on TOR are poorly understood. We used the rotifer Brachionus manjavacas as a model animal to probe the regulation of TOR and JNK pathways and explore their interaction. The effect of various chemical inhibitors was examined in life table and stressor challenge experiments. A survey of 12 inhibitors revealed two, rapamycin and JNK inhibitor, that significantly extended lifespan of B. manjavacas. At 1 μM concentration, exposure to rapamycin or JNK inhibitor extended mean rotifer lifespan by 35% and maximum lifespan by 37%. Exposure to both rapamycin and JNK inhibitor simultaneously extended mean rotifer lifespan 65% more than either alone. Exposure to a combination of rapamycin and JNK inhibitors conveyed greater protection to starvation, UV and osmotic stress than either inhibitor alone. RNAi knockdown of TOR and JNK gene expression was investigated for its ability to extend rotifer lifespan. RNAi knockdown of the TOR gene resulted in 29% extension of mean lifespan compared to control and knockdown of the JNK gene resulted in 51% mean lifespan extension. In addition to lifespan, we quantified mitochondria activity using the fluorescent marker Mitotracker and

  14. Joint inhibition of TOR and JNK pathways interacts to extend the lifespan of Brachionus manjavacas (Rotifera).

    PubMed

    Snell, Terry W; Johnston, Rachel K; Rabeneck, Brett; Zipperer, Cody; Teat, Stephanie

    2014-04-01

    The TOR kinase pathway is central in modulating aging in a variety of animal models. The target of rapamycin (TOR) integrates a complex network of signals from growth conditions, nutrient availability, energy status, and physiological stresses and matches an organism's growth rate to the resource environment. Important remaining problems are the identification of the pathways that interact with TOR and their characterization as additive or synergistic. One of the most versatile stress sensors in metazoans is the Jun-N-terminal kinase (JNK) signaling pathway. JNK is an evolutionarily conserved stress-activated protein kinase that is induced by a range of stressors, including UV irradiation, reactive oxygen species, DNA damage, heat, and bacterial antigens. JNK is thought to interact with the TOR pathway, but its effects on TOR are poorly understood. We used the rotifer Brachionus manjavacas as a model animal to probe the regulation of TOR and JNK pathways and explore their interaction. The effect of various chemical inhibitors was examined in life table and stressor challenge experiments. A survey of 12 inhibitors revealed two, rapamycin and JNK inhibitor, that significantly extended lifespan of B. manjavacas. At 1 μM concentration, exposure to rapamycin or JNK inhibitor extended mean rotifer lifespan by 35% and maximum lifespan by 37%. Exposure to both rapamycin and JNK inhibitor simultaneously extended mean rotifer lifespan by 65% more than either alone. Exposure to a combination of rapamycin and JNK inhibitors conveyed greater protection to starvation, UV and osmotic stress than either inhibitor alone. RNAi knockdown of TOR and JNK gene expression was investigated for its ability to extend rotifer lifespan. RNAi knockdown of the TOR gene resulted in 29% extension of the mean lifespan compared to control and knockdown of the JNK gene resulted in 51% mean lifespan extension. In addition to the lifespan, we quantified mitochondria activity using the fluorescent

  15. The Cbln family of proteins interact with multiple signaling pathways.

    PubMed

    Wei, Peng; Pattarini, Roberto; Rong, Yongqi; Guo, Hong; Bansal, Parmil K; Kusnoor, Sheila V; Deutch, Ariel Y; Parris, Jennifer; Morgan, James I

    2012-06-01

    Cerebellin precursor protein (Cbln1) is essential for synapse integrity in cerebellum through assembly into complexes that bridge pre-synaptic β-neurexins (Nrxn) to post-synaptic GluRδ2. However, GluRδ2 is largely cerebellum-specific, yet Cbln1 and its little studied family members, Cbln2 and Cbln4, are expressed throughout brain. Therefore, we investigated whether additional proteins mediate Cbln family actions. Whereas Cbln1 and Cbln2 bound to GluRδ2 and Nrxns1-3, Cbln4 bound weakly or not at all, suggesting it has distinct binding partners. In a candidate receptor-screening assay, Cbln4 (but not Cbln1 or Cbln2) bound selectively to the netrin receptor, (deleted in colorectal cancer (DCC) in a netrin-displaceable fashion. To determine whether Cbln4 had a netrin-like function, Cbln4-null mice were generated. Cbln4-null mice did not phenocopy netrin-null mice. Cbln1 and Cbln4 were likely co-localized in neurons thought to be responsible for synaptic changes in striatum of Cbln1-null mice. Furthermore, complexes containing Cbln1 and Cbln4 had greatly reduced affinity to DCC but increased affinity to Nrxns, suggesting a functional interaction. However, Cbln4-null mice lacked the striatal synaptic changes seen in Cbln null mice. Thus, Cbln family members interact with multiple receptors/signaling pathways in a subunit composition-dependent manner and have independent functions with Cbln4 potentially involved in the less well-characterized role of netrin/DCC in adult brain.

  16. Interactions and Attachment Pathways between Functionalized Gold Nanorods.

    PubMed

    Tan, Shu Fen; Anand, Utkarsh; Mirsaidov, Utkur

    2017-01-31

    Nanoparticle (NP) self-assembly has been recognized as an important technological process for forming ordered nanostructures. However, the detailed dynamics of the assembly processes remain poorly understood. Using in situ liquid cell transmission electron microscopy, we describe the assembly modes of gold (Au) nanorods (NRs) in solution mediated by hydrogen bonding between NR-bound cysteamine linker molecules. Our observations reveal that by tuning the linker concentration, two different NR assembly modes can be achieved. These assembly modes proceed via the (1) end-to-end and (2) side-to-side attachment of NRs at low and high linker concentrations in solution, respectively. In addition, our time-resolved observations reveal that the side-to-side NR assemblies can occur through two different pathways: (i) prealigned attachment, where two Au NRs prealign to be parallel prior to assembly, and (ii) postattachment alignment, where two Au NRs first undergo end-to-end attachment and pivot around the attachment point to form the side-to-side assembly. We attributed the observed assembly modes to the distribution of linkers on the NR surfaces and the electrostatic interactions between the NRs. The intermediate steps in the assembly reported here reveal how the shape and surface functionalities of NPs drive their self-assembly, which is important for the rational design of hierarchical nanostructures.

  17. Drug interaction prediction using ontology-driven hypothetical assertion framework for pathway generation followed by numerical simulation

    PubMed Central

    Arikuma, Takeshi; Yoshikawa, Sumi; Azuma, Ryuzo; Watanabe, Kentaro; Matsumura, Kazumi; Konagaya, Akihiko

    2008-01-01

    Background In accordance with the increasing amount of information concerning individual differences in drug response and molecular interaction, the role of in silico prediction of drug interaction on the pathway level is becoming more and more important. However, in view of the interferences for the identification of new drug interactions, most conventional information models of a biological pathway would have limitations. As a reflection of real world biological events triggered by a stimulus, it is important to facilitate the incorporation of known molecular events for inferring (unknown) possible pathways and hypothetic drug interactions. Here, we propose a new Ontology-Driven Hypothetic Assertion (OHA) framework including pathway generation, drug interaction detection, simulation model generation, numerical simulation, and hypothetic assertion. Potential drug interactions are detected from drug metabolic pathways dynamically generated by molecular events triggered after the administration of certain drugs. Numerical simulation enables to estimate the degree of side effects caused by the predicted drug interactions. New hypothetic assertions of the potential drug interactions and simulation are deduced from the Drug Interaction Ontology (DIO) written in Web Ontology Language (OWL). Results The concept of the Ontology-Driven Hypothetic Assertion (OHA) framework was demonstrated with known interactions between irinotecan (CPT-11) and ketoconazole. Four drug interactions that involved cytochrome p450 (CYP3A4) and albumin as potential drug interaction proteins were automatically detected from Drug Interaction Ontology (DIO). The effect of the two interactions involving CYP3A4 were quantitatively evaluated with numerical simulation. The co-administration of ketoconazole may increase AUC and Cmax of SN-38(active metabolite of irinotecan) to 108% and 105%, respectively. We also estimates the potential effects of genetic variations: the AUC and Cmax of SN-38 may

  18. Integrated Analysis Identifies Interaction Patterns between Small Molecules and Pathways

    PubMed Central

    Li, Yan; Li, Weiguo; Chen, Xin; Sun, Jiatong; Chen, Huan; Lv, Sali

    2014-01-01

    Previous studies have indicated that the downstream proteins in a key pathway can be potential drug targets and that the pathway can play an important role in the action of drugs. So pathways could be considered as targets of small molecules. A link map between small molecules and pathways was constructed using gene expression profile, pathways, and gene expression of cancer cell line intervened by small molecules and then we analysed the topological characteristics of the link map. Three link patterns were identified based on different drug discovery implications for breast, liver, and lung cancer. Furthermore, molecules that significantly targeted the same pathways tended to treat the same diseases. These results can provide a valuable reference for identifying drug candidates and targets in molecularly targeted therapy. PMID:25114931

  19. Interactions between Trypanosoma cruzi Secreted Proteins and Host Cell Signaling Pathways

    PubMed Central

    Watanabe Costa, Renata; da Silveira, Jose F.; Bahia, Diana

    2016-01-01

    Chagas disease is one of the prevalent neglected tropical diseases, affecting at least 6–7 million individuals in Latin America. It is caused by the protozoan parasite Trypanosoma cruzi, which is transmitted to vertebrate hosts by blood-sucking insects. After infection, the parasite invades and multiplies in the myocardium, leading to acute myocarditis that kills around 5% of untreated individuals. T. cruzi secretes proteins that manipulate multiple host cell signaling pathways to promote host cell invasion. The primary secreted lysosomal peptidase in T. cruzi is cruzipain, which has been shown to modulate the host immune response. Cruzipain hinders macrophage activation during the early stages of infection by interrupting the NF-kB P65 mediated signaling pathway. This allows the parasite to survive and replicate, and may contribute to the spread of infection in acute Chagas disease. Another secreted protein P21, which is expressed in all of the developmental stages of T. cruzi, has been shown to modulate host phagocytosis signaling pathways. The parasite also secretes soluble factors that exert effects on host extracellular matrix, such as proteolytic degradation of collagens. Finally, secreted phospholipase A from T. cruzi contributes to lipid modifications on host cells and concomitantly activates the PKC signaling pathway. Here, we present a brief review of the interaction between secreted proteins from T. cruzi and the host cells, emphasizing the manipulation of host signaling pathways during invasion. PMID:27065960

  20. Interaction pathways between soft lipid nanodiscs and plasma membranes: A molecular modeling study.

    PubMed

    Li, Shixin; Luo, Zhen; Xu, Yan; Ren, Hao; Deng, Li; Zhang, Xianren; Huang, Fang; Yue, Tongtao

    2017-10-01

    Lipid nanodisc, a model membrane platform originally synthesized for study of membrane proteins, has recently been used as the carrier to deliver amphiphilic drugs into target tumor cells. However, the central question of how cells interact with such emerging nanomaterials remains unclear and deserves our research for both improving the delivery efficiency and reducing the side effect. In this work, a binary lipid nanodisc is designed as the minimum model to investigate its interactions with plasma membranes by using the dissipative particle dynamics method. Three typical interaction pathways, including the membrane attachment with lipid domain exchange of nanodiscs, the partial membrane wrapping with nanodisc vesiculation, and the receptor-mediated endocytosis, are discovered. For the first pathway, the boundary normal lipids acting as ligands diffuse along the nanodisc rim to gather at the membrane interface, repelling the central bola lipids to reach a stable membrane attachment. If bola lipids are positioned at the periphery and act as ligands, they diffuse to form a large aggregate being wrapped by the membrane, leaving the normal lipids exposed on the membrane exterior by assembling into a vesicle. Finally, by setting both central normal lipids and boundary bola lipids as ligands, the receptor-mediated endocytosis occurs via both deformation and self-rotation of the nanodiscs. All above pathways for soft lipid nanodiscs are quite different from those for rigid nanoparticles, which may provide useful guidelines for design of soft lipid nanodiscs in widespread biomedical applications. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Interactions with community and institutions: Preventive pathways for child maltreatment

    PubMed Central

    Cao, Yiwen; Maguire-Jack, Kathryn

    2017-01-01

    Parents interact with their environment in important ways that may impact their ability to parent their children positively. The current study uses data from the age 3 wave of the Fragile Families and Child Wellbeing study to investigate whether neighborhood processes and community participation relate to internal control, and whether these three variables are associated with child maltreatment behaviors. Using structural equation modeling, the direct and indirect effects of the environment (neighborhood disorder, social control, and social cohesion) and community participation on child maltreatment are tested. The mediating variable tested is internal control. The results show that neighborhood processes and community participation are associated with child neglect, physical child abuse, and psychological aggression but that these associations are driven through their effect on internal control. PMID:27810636

  2. Differential expression of small RNA pathway genes associated with the Biomphalaria glabrata/Schistosoma mansoni interaction.

    PubMed

    Queiroz, Fábio Ribeiro; Silva, Luciana Maria; Jeremias, Wander de Jesus; Babá, Élio Hideo; Caldeira, Roberta Lima; Coelho, Paulo Marcos Zech; Gomes, Matheus de Souza

    2017-01-01

    The World Health Organization (WHO) estimates that approximately 240 million people in 78 countries require treatment for schistosomiasis, an endemic disease caused by trematodes of the genus Schistosoma. In Brazil, Schistosoma mansoni is the only species representative of the genus whose passage through an invertebrate host, snails of the genus Biomphalaria, is obligatory before infecting a mammalian host, including humans. The availability of the genome and transcriptome of B. glabrata makes studying the regulation of gene expression, particularly the regulation of miRNA and piRNA processing pathway genes, possible. This might assist in better understanding the biology of B. glabrata as well as its relationship to the parasite S. mansoni. Some aspects of this interaction are still poorly explored, including the participation of non-coding small RNAs, such as miRNAs and piRNAs, with lengths varying from 18 to 30 nucleotides in mature form, which are potent regulators of gene expression. Using bioinformatics tools and quantitative PCR, we characterized and validated the miRNA and piRNA processing pathway genes in B. glabrata. In silico analyses showed that genes involved in miRNA and piRNA pathways were highly conserved in protein domain distribution, catalytic site residue conservation and phylogenetic analysis. Our study showed differential expression of putative Argonaute, Drosha, Piwi, Exportin-5 and Tudor genes at different snail developmental stages and during infection with S. mansoni, suggesting that the machinery is required for miRNA and piRNA processing in B. glabrata at all stages. These data suggested that the silencing pathway mediated by miRNAs and piRNAs can interfere in snail biology throughout the life cycle of the snail, thereby influencing the B. glabrata/S. mansoni interaction. Further studies are needed to confirm the participation of the small RNA processing pathway proteins in the parasite/host relationship, mainly the effective

  3. Role of K+ channel opening and stimulation of cyclic GMP in the vasorelaxant effects of nicorandil in isolated piglet pulmonary and mesenteric arteries: relative efficacy and interactions between both pathways

    PubMed Central

    Pérez-Vizcaíno, Francisco; Cogolludo, Angel L; Villamor, Eduardo; Tamargo, Juan

    1998-01-01

    The effects of the K+ channel opener levcromakalim, the guanylate cyclase stimulant nitroprusside and the dual drug nicorandil (K+ channel opener and guanylate cyclase stimulant) were analysed in piglet isolated endothelium-denuded pulmonary (PA) and mesenteric (MA) arteries stimulated by noradrenaline (NA) or by the thromboxane A2 mimetic U46619.Nicorandil, levcromakalim and verapamil were less potent in PA than in MA, the efficacy of levcromakalim was also reduced in PA. The effects of nicorandil and levcromakalim were similar in arteries pre-contracted by NA and U46619, whereas verapamil was more potent in arteries pre-contracted by NA. Nitroprusside was equipotent in MA pre-contracted by either NA or U46619 and in PA pre-contracted by NA whereas in PA pre-contracted by U46619, nitroprusside showed lower potency and efficacy.The relaxant effects of levcromakalim and nitroprusside were inhibited by 10−5 M glibenclamide and 10−6 M ODQ, respectively. Nicorandil-induced relaxation was inhibited by ODQ in all experimental conditions, whereas glibenclamide had inhibitory effects in PA and MA pre-contracted by U46619, had no effect in PA pre-contracted by NA and in MA pre-contracted by NA it was only inhibitory in the presence of ODQ.No apparent interactions were found between nitroprusside and levcromakalim as indicated by the lack of effects of pretreatment with one of them (producing 20–35% relaxation) on the potency of the relaxant response to the other. However, in PA pre-contracted by U46619, where nitroprusside or levcromakalim induced only partial relaxation, the combination of both mechanisms (either by combining nitroprusside plus levcromakalim or by nicorandil) was able to induce full vasodilatation.In conclusion, K+ channel opening and guanylate cyclase stimulation are independent pathways that induce additive vasorelaxation in piglet PA and MA. The mechanism of action of nicorandil is dependent on the artery and on the nature of the agonist

  4. Interaction of a functionalized complex of the flavonoid hesperetin with the AhR pathway and CYP1A1 expression: involvement in its protective effects against benzo[a]pyrene-induced oxidative stress in human skin.

    PubMed

    Melchini, Antonietta; Catania, Stefania; Stancanelli, Rossana; Tommasini, Silvana; Costa, Chiara

    2011-10-01

    Skin cancer pathogenesis is partially associated to the oxidative stress conditions induced by environmentally carcinogens such as benzo[a]pyrene (BaP). The protective effects against BaP-induced oxidative stress of the flavonoid hesperetin as a complex with the 2-hydroxypropyl-β-cyclodextrin (HE/HP-β-CyD) have been evaluated using an ex vivo human skin model. Human healthy skin has been pre-treated with the functionalized complex HE/HP-β-CyD (0.5-50 μM) before BaP (5 μM) application simulating occupational and environmental exposure. Oxidative stress was evaluated in terms of 3-(4, 5-dimethylthiazol-2-yl)-2, 5-dipheyltetrazolium bromide reduction, protein peroxidation and reactive oxygen species (ROS) formation. Additionally, it has been investigated whether the potential protective effects of HE/HP-β-CyD may be correlated to the interaction with aryl hydrocarbon receptor (AhR) pathway. A significant protection by HE/HP-β-CyD against the BaP-induced increase in ROS and carbonyl compound production, as well as reduction in tissue viability, has been observed (p<0.001). Results obtained showed that HE/HP-β-CyD was also able to reduce BaP-induced AhR and CYP1A1 protein expression (p<0.001). Experimental evidences provided from this study suggest significant preventive properties of HE/HP-β-CyD in the toxicity caused by environmental carcinogens such as PAHs. © Springer Science+Business Media B.V. 2011

  5. BBS proteins interact genetically with the IFT pathway to influence SHH-related phenotypes.

    PubMed

    Zhang, Qihong; Seo, Seongjin; Bugge, Kevin; Stone, Edwin M; Sheffield, Val C

    2012-05-01

    There are numerous genes for which loss-of-function mutations do not produce apparent phenotypes even though statistically significant quantitative changes to biological pathways are observed. To evaluate the biological meaning of small effects is challenging. Bardet-Biedl syndrome (BBS) is a heterogeneous autosomal recessive disorder characterized by obesity, retinopathy, polydactyly, renal malformations, learning disabilities and hypogenitalism, as well as secondary phenotypes including diabetes and hypertension. BBS knockout mice recapitulate most human phenotypes including obesity, retinal degeneration and male infertility. However, BBS knockout mice do not develop polydacyly. Here we showed that the loss of BBS genes in mice result in accumulation of Smoothened and Patched 1 in cilia and have a decreased Shh response. Knockout of Bbs7 combined with a hypomorphic Ift88 allele (orpk as a model for Shh dysfuction) results in embryonic lethality with e12.5 embryos having exencephaly, pericardial edema, cleft palate and abnormal limb development, phenotypes not observed in Bbs7(-/-) mice. Our results indicate that BBS genes modulate Shh pathway activity and interact genetically with the intraflagellar transport (IFT) pathway to play a role in mammalian development. This study illustrates an effective approach to appreciate the biological significance of a small effect.

  6. Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception.

    PubMed

    Qian, Xiaoning; Yoon, Byung-Jun

    2011-02-15

    Human immunodeficiency virus type one (HIV-1) is the major pathogen that causes the acquired immune deficiency syndrome (AIDS). With the availability of large-scale protein-protein interaction (PPI) measurements, comparative network analysis can provide a promising way to study the host-virus interactions and their functional significance in the pathogenesis of AIDS. Until now, there have been a large number of HIV studies based on various animal models. In this paper, we present a novel framework for studying the host-HIV interactions through comparative network analysis across different species. Based on the proposed framework, we test our hypothesis that HIV-1 attacks essential biological pathways that are conserved across species. We selected the Homo sapiens and Mus musculus PPI networks with the largest coverage among the PPI networks that are available from public databases. By using a local network alignment algorithm based on hidden Markov models (HMMs), we first identified the pathways that are conserved in both networks. Next, we analyzed the HIV-1 susceptibility of these pathways, in comparison with random pathways in the human PPI network. Our analysis shows that the conserved pathways have a significantly higher probability of being intercepted by HIV-1. Furthermore, Gene Ontology (GO) enrichment analysis shows that most of the enriched GO terms are related to signal transduction, which has been conjectured to be one of the major mechanisms targeted by HIV-1 for the takeover of the host cell. This proof-of-concept study clearly shows that the comparative analysis of PPI networks across different species can provide important insights into the host-HIV interactions and the detailed mechanisms of HIV-1. We expect that comparative multiple network analysis of various species that have different levels of susceptibility to similar lentiviruses may provide a very effective framework for generating novel, and experimentally verifiable hypotheses on the

  7. BDNF-estrogen interactions in hippocampal mossy fiber pathway: implications for normal brain function and disease

    PubMed Central

    Harte-Hargrove, Lauren; MacLusky, Neil J.; Scharfman, Helen E.

    2013-01-01

    The neurotrophin BDNF and the steroid hormone estrogen exhibit potent effects on hippocampal neurons during development and in adulthood. BDNF and estrogen have also been implicated in the etiology of diverse types of neurological disorders or psychiatric illnesses, or have been discussed as potentially important in treatment. Although both are typically studied independently, it has been suggested that BDNF mediates several of the effects of estrogen in hippocampus, and that these interactions play a role in the normal brain as well as disease. Here we focus on the mossy fiber (MF) pathway of the hippocampus, a critical pathway in normal hippocampal function, and a prime example of a location where numerous studies support an interaction between BDNF and estrogen in the rodent brain. We first review the temporal and spatially-regulated expression of BDNF and estrogen in the MFs, as well as their receptors. Then we consider the results of studies that suggest that 17β-estradiol alters hippocampal function by its influence on BDNF expression in the MF pathway. We also address the hypothesis that estrogen influences hippocampus by mechanisms related not only to the mature form of BDNF, acting at trkB receptors, but also by regulating the precursor, proBDNF, acting at p75NTR. We suggest that the interactions between BDNF and 17β-estradiol in the MFs are potentially important in the normal function of the hippocampus, and have implications for sex differences in functions that depend on the MFs and in diseases where MF plasticity has been suggested to play an important role, Alzheimer’s disease, epilepsy and addiction. PMID:23276673

  8. Gene-Gene Interactions in the Folate Metabolic Pathway and the Risk of Conotruncal Heart Defects

    PubMed Central

    Lupo, Philip J.; Goldmuntz, Elizabeth; Mitchell, Laura E.

    2010-01-01

    Conotruncal and related heart defects (CTRD) are common, complex malformations. Although there are few established risk factors, there is evidence that genetic variation in the folate metabolic pathway influences CTRD risk. This study was undertaken to assess the association between inherited (i.e., case) and maternal gene-gene interactions in this pathway and the risk of CTRD. Case-parent triads (n = 727), ascertained from the Children's Hospital of Philadelphia, were genotyped for ten functional variants of nine folate metabolic genes. Analyses of inherited genotypes were consistent with the previously reported association between MTHFR A1298C and CTRD (adjusted P = .02), but provided no evidence that CTRD was associated with inherited gene-gene interactions. Analyses of the maternal genotypes provided evidence of a MTHFR C677T/CBS 844ins68 interaction and CTRD risk (unadjusted P = .02). This association is consistent with the effects of this genotype combination on folate-homocysteine biochemistry but remains to be confirmed in independent study populations. PMID:20111745

  9. The Arginine Decarboxylase Pathways of Host and Pathogen Interact to Impact Inflammatory Pathways in the Lung

    PubMed Central

    Dalluge, Joseph J.; Welchlin, Cole W.; Hughes, John; Han, Wei; Blackwell, Timothy S.; Laguna, Theresa A.; Williams, Bryan J.

    2014-01-01

    The arginine decarboxylase pathway, which converts arginine to agmatine, is present in both humans and most bacterial pathogens. In humans agmatine is a neurotransmitter with affinities towards α2-adrenoreceptors, serotonin receptors, and may inhibit nitric oxide synthase. In bacteria agmatine serves as a precursor to polyamine synthesis and was recently shown to enhance biofilm development in some strains of the respiratory pathogen Pseudomonas aeruginosa. We determined agmatine is at the center of a competing metabolism in the human lung during airways infections and is influenced by the metabolic phenotypes of the infecting pathogens. Ultra performance liquid chromatography with mass spectrometry detection was used to measure agmatine in human sputum samples from patients with cystic fibrosis, spent supernatant from clinical sputum isolates, and from bronchoalvelolar lavage fluid from mice infected with P. aeruginosa agmatine mutants. Agmatine in human sputum peaks during illness, decreased with treatment and is positively correlated with inflammatory cytokines. Analysis of the agmatine metabolic phenotype in clinical sputum isolates revealed most deplete agmatine when grown in its presence; however a minority appeared to generate large amounts of agmatine presumably driving sputum agmatine to high levels. Agmatine exposure to inflammatory cells and in mice demonstrated its role as a direct immune activator with effects on TNF-α production, likely through NF-κB activation. P. aeruginosa mutants for agmatine detection and metabolism were constructed and show the real-time evolution of host-derived agmatine in the airways during acute lung infection. These experiments also demonstrated pathogen agmatine production can upregulate the inflammatory response. As some clinical isolates have adapted to hypersecrete agmatine, these combined data would suggest agmatine is a novel target for immune modulation in the host-pathogen dynamic. PMID:25350753

  10. Novel alpha1-adrenergic receptor signaling pathways: secreted factors and interactions with the extracellular matrix.

    PubMed

    Shi, Ting; Duan, Zhong-Hui; Papay, Robert; Pluskota, Elzbieta; Gaivin, Robert J; de la Motte, Carol A; Plow, Edward F; Perez, Dianne M

    2006-07-01

    alpha1-Adrenergic receptor (alpha1-ARs) subtypes (alpha1A, alpha1B, and alpha1D) regulate multiple signal pathways, such as phospholipase C, protein kinase C (PKC), and mitogen-activated protein kinases. We employed oligonucleotide microarray technology to explore the effects of both short- (1 h) and long-term (18 h) activation of the alpha1A-AR to enable RNA changes to occur downstream of earlier well characterized signaling pathways, promoting novel couplings. Polymerase chain reaction (PCR) studies confirmed that PKC was a critical regulator of alpha1A-AR-mediated gene expression, and secreted interleukin (IL)-6 also contributed to gene expression alterations. We next focused on two novel signaling pathways that might be mediated through alpha1A-AR stimulation because of the clustering of gene expression changes for cell adhesion/motility (syndecan-4 and tenascin-C) and hyaluronan (HA) signaling. We confirmed that alpha1-ARs induced adhesion in three cell types to vitronectin, an interaction that was also integrin-, FGF7-, and PKC-dependent. alpha1-AR activation also inhibited cell migration, which was integrin- and PKC-independent but still required secretion of FGF7. alpha1-AR activation also increased the expression and deposition of HA, a glycosaminoglycan, which displayed two distinct structures: pericellular coats and long cable structures, as well as increasing expression of the HA receptor, CD44. Long cable structures of HA can bind leukocytes, which this suggests that alpha1-ARs may be involved in proinflammatory responses. Our results indicate alpha1-ARs induce the secretion of factors that interact with the extracellular matrix to regulate cell adhesion, motility and proinflammatory responses through novel signaling pathways.

  11. Protein/Protein Interactions in the Mammalian Heme Degradation Pathway

    PubMed Central

    Spencer, Andrea L. M.; Bagai, Ireena; Becker, Donald F.; Zuiderweg, Erik R. P.; Ragsdale, Stephen W.

    2014-01-01

    Heme oxygenase (HO) catalyzes the rate-limiting step in the O2-dependent degradation of heme to biliverdin, CO, and iron with electrons delivered from NADPH via cytochrome P450 reductase (CPR). Biliverdin reductase (BVR) then catalyzes conversion of biliverdin to bilirubin. We describe mutagenesis combined with kinetic, spectroscopic (fluorescence and NMR), surface plasmon resonance, cross-linking, gel filtration, and analytical ultracentrifugation studies aimed at evaluating interactions of HO-2 with CPR and BVR. Based on these results, we propose a model in which HO-2 and CPR form a dynamic ensemble of complex(es) that precede formation of the productive electron transfer complex. The 1H-15N TROSY NMR spectrum of HO-2 reveals specific residues, including Leu-201, near the heme face of HO-2 that are affected by the addition of CPR, implicating these residues at the HO/CPR interface. Alanine substitutions at HO-2 residues Leu-201 and Lys-169 cause a respective 3- and 22-fold increase in Km values for CPR, consistent with a role for these residues in CPR binding. Sedimentation velocity experiments confirm the transient nature of the HO-2·CPR complex (Kd = 15.1 μm). Our results also indicate that HO-2 and BVR form a very weak complex that is only captured by cross-linking. For example, under conditions where CPR affects the 1H-15N TROSY NMR spectrum of HO-2, BVR has no effect. Fluorescence quenching experiments also suggest that BVR binds HO-2 weakly, if at all, and that the previously reported high affinity of BVR for HO is artifactual, resulting from the effects of free heme (dissociated from HO) on BVR fluorescence. PMID:25196843

  12. PathPPI: an integrated dataset of human pathways and protein-protein interactions.

    PubMed

    Tang, HaiLin; Zhong, Fan; Liu, Wei; He, FuChu; Xie, HongWei

    2015-06-01

    Integration of pathway and protein-protein interaction (PPI) data can provide more information that could lead to new biological insights. PPIs are usually represented by a simple binary model, whereas pathways are represented by more complicated models. We developed a series of rules for transforming protein interactions from pathway to binary model, and the protein interactions from seven pathway databases, including PID, BioCarta, Reactome, NetPath, INOH, SPIKE and KEGG, were transformed based on these rules. These pathway-derived binary protein interactions were integrated with PPIs from other five PPI databases including HPRD, IntAct, BioGRID, MINT and DIP, to develop integrated dataset (named PathPPI). More detailed interaction type and modification information on protein interactions can be preserved in PathPPI than other existing datasets. Comparison analysis results indicate that most of the interaction overlaps values (O AB) among these pathway databases were less than 5%, and these databases must be used conjunctively. The PathPPI data was provided at http://proteomeview.hupo.org.cn/PathPPI/PathPPI.html.

  13. Interactions between PTEN and receptor tyrosine kinase pathways and their implications for glioma therapy

    PubMed Central

    Abounader, Roger

    2009-01-01

    Gliomas are the most common and deadly form of malignant primary brain tumors. Loss of the tumor-suppressor PTEN and activation of the receptor tyrosine kinases (RTKs) EGF receptor, c-Met, PDGF receptor and VEGF receptor are among the most common molecular dysfunctions associated with glioma malignancy. PTEN interacts with RTK-dependent signaling at multiple levels. These include the ability of PTEN to counteract PI3K activation by RTKs, as well as possible effects of PTEN on RTK activation of the MAPK pathway and RTK-dependent gene-expression regulation. Consequently, PTEN expression affects RTK-induced malignancy. Importantly, the PTEN status was recently found to be critical for the outcome of RTK-targeted clinical therapies that have been developed recently. Combining RTK-targeted therapies with therapies aimed at counteracting the effects of PTEN loss, such as mTOR inhibition, might also have therapeutic advantage. This article reviews the known molecular and functional interactions between PTEN and RTK pathways and their implications for glioma therapy. PMID:19192961

  14. Detecting differential patterns of interaction in molecular pathways

    PubMed Central

    Yajima, Masanao; Telesca, Donatello; Ji, Yuan; Müller, Peter

    2015-01-01

    We consider statistical inference for potentially heterogeneous patterns of association characterizing the expression of bio-molecular pathways across different biologic conditions. We discuss a modeling approach based on Gaussian-directed acyclic graphs and provide computational and methodological details needed for posterior inference. Our application finds motivation in reverse phase protein array data from a study on acute myeloid leukemia, where interest centers on contrasting refractory versus relapsed patients. We illustrate the proposed method through both synthetic and case study data. PMID:25519431

  15. Rod-cone interactions and the temporal impulse response of the cone pathway

    PubMed Central

    Zele, Andrew J.; Cao, Dingcai; Pokorny, Joel

    2008-01-01

    Dark-adapted rods suppress cone-mediated flicker detection. This study evaluates the effect that rod activity has on cone temporal processing by investigating whether rod mediated suppression changes the cone pathway impulse response function, regardless of the form of the temporal signal. Stimuli were generated with a 2-channel photostimulator that has four primaries for the central field and four primaries for the surround. Cone pathway temporal impulse response functions were derived from temporal contrast sensitivity data with periodic stimuli, and from two-pulse discrimination data in which pairs of briefly pulsed stimuli were presented successively at a series of stimulus onset asynchronies. Dark-adapted rods altered the amplitude and timing of cone pathway temporal impulse response functions, irrespective of whether they were derived from measurements with temporally periodic stimuli or in a brief presentation temporal resolution task with pulsed stimuli. Rod-cone interactions are a fundamental operation in visual temporal processing under mesopic light levels, acting to decrease the temporal bandwidth of the visual system. PMID:18486960

  16. Wolbachia-induced paternal defect in Drosophila is likely by interaction with the juvenile hormone pathway.

    PubMed

    Liu, Chen; Wang, Jia-Lin; Zheng, Ya; Xiong, En-Juan; Li, Jing-Jing; Yuan, Lin-Ling; Yu, Xiao-Qiang; Wang, Yu-Feng

    2014-06-01

    Wolbachia are endosymbionts that infect many insect species. They can manipulate the host's reproduction to increase their own maternal transmission. Cytoplasmic incompatibility (CI) is one such manipulation, which is expressed as embryonic lethality when Wolbachia-infected males mate with uninfected females. However, matings between males and females carrying the same Wolbachia strain result in viable progeny. The molecular mechanisms of CI are currently not clear. We have previously reported that the gene Juvenile hormone-inducible protein 26 (JhI-26) exhibited the highest upregulation in the 3rd instar larval testes of Drosophila melanogaster when infected by Wolbachia. This is reminiscent of an interaction between Wolbachia and juvenile hormone (JH) pathway in flies. Considering that Jhamt gene encodes JH acid methyltransferase, a key regulatory enzyme of JH biosynthesis, and that methoprene-tolerant (Met) has been regarded as the best JH receptor candidate, we first compared the expression of Jhamt and Met between Wolbachia-infected and uninfected fly testes to investigate whether Wolbachia infection influence the JH signaling pathway. We found that the expressions of Jhamt and Met were significantly increased in the presence of Wolbachia, suggesting an interaction of Wolbachia with the JH signaling pathway. Then, we found that overexpression of JhI-26 in Wolbachia-free transgenic male flies caused paternal-effect lethality that mimics the defects associated with CI. JhI-26 overexpressing males resulted in significantly decrease in hatch rate. Surprisingly, Wolbachia-infected females could rescue the egg hatch. In addition, we showed that overexpression of JhI-26 caused upregulation of the male accessory gland protein (Acp) gene CG10433, but not vice versa. This result suggests that JhI-26 may function at the upstream of CG10433. Likewise, overexpression of CG10433 also resulted in paternal-effect lethality. Both JhI-26 and CG10433 overexpressing males

  17. ALIX-CHMP4 Interactions in the Human ESCRT Pathway

    SciTech Connect

    McCullough, J.; Fisher, R.D.; Whitby, F.G.; Sundquist, W.I.; Hill, C.P.

    2009-05-26

    The ESCRT pathway facilitates membrane fission events during enveloped virus budding, multivesicular body formation, and cytokinesis. To promote HIV budding and cytokinesis, the ALIX protein must bind and recruit CHMP4 subunits of the ESCRT-III complex, which in turn participate in essential membrane remodeling functions. Here, we report that the Bro1 domain of ALIX binds specifically to C-terminal residues of the human CHMP4 proteins (CHMP4A-C). Crystal structures of the complexes reveal that the CHMP4 C-terminal peptides form amphipathic helices that bind across the conserved concave surface of ALIX{sub Bro1}. ALIX-dependent HIV-1 budding is blocked by mutations in exposed ALIX{sub Bro1} residues that help contribute to the binding sites for three essential hydrophobic residues that are displayed on one side of the CHMP4 recognition helix (M/L/IxxLxxW). The homologous CHMP1-3 classes of ESCRT-III proteins also have C-terminal amphipathic helices, but, in those cases, the three hydrophobic residues are arrayed with L/I/MxxxLxxL spacing. Thus, the distinct patterns of hydrophobic residues provide a 'code' that allows the different ESCRT-III subunits to bind different ESCRT pathway partners, with CHMP1-3 proteins binding MIT domain-containing proteins, such as VPS4 and Vta1/LIP5, and CHMP4 proteins binding Bro1 domain-containing proteins, such as ALIX.

  18. Interactions between genetic polymorphisms in the apoptotic pathway and environmental factors on esophageal adenocarcinoma risk.

    PubMed

    Wu, I-Chen; Zhao, Yang; Zhai, Rihong; Liu, Chen-yu; Chen, Feng; Ter-Minassian, Monica; Asomaning, Kofi; Su, Li; Heist, Rebecca S; Kulke, Matthew H; Liu, Geoffrey; Christiani, David C

    2011-04-01

    How genetic variations in apoptosis pathway interact with environmental factors to contribute to esophageal adenocarcinoma (EA) risk has not been comprehensively investigated. We conducted a case-only analysis in 335 Caucasian EA patients that were genotyped for 242 single nucleotide polymorphisms (SNPs) in 43 apoptotic genes. Gene-environment interactions were assessed using a two-step approach. First, random forest algorithm was used to screen for the potential interacting markers. Next, we used case-only logistic regression model to estimate the effects of gene-environment interactions on EA risk. Four SNPs (PERP rs648802; PIK3CA rs4855094, rs7644468 and TNFRSF1A rs4149579) had significant interaction with gastroesophageal reflux disease (GERD). The presence of variant alleles in TP53BP1 rs560191, CASP7 rs7907519 or BCL2 rs12454712 enhanced the risk of smoking by 2.08-2.58 times [interaction odds ratio (ORi)=2.08-2.58, adjusted P-value (Padj)=0.02-0.04]. Compared with patients carrying ≤1 risk genotype, the risk of GERD on EA was increased in persons with two (ORi=1.89, Padj=0.016) or ≥3 (ORi=4.30, Padj<0.0001) risk genotypes. Compared with cases with ≤1 risk genotype, smoking-associated EA risk increased by 3.15 times when ≥2 risk genotypes were present (ORi=3.15, Padj<0.0001). In conclusion, interactions among apoptotic SNPs and GERD or smoking play an important role in EA development.

  19. Interactions between genetic polymorphisms in the apoptotic pathway and environmental factors on esophageal adenocarcinoma risk

    PubMed Central

    Wu, I-Chen; Zhao, Yang; Zhai, Rihong; Liu, Chen-yu.; Chen, Feng; Ter-Minassian, Monica; Asomaning, Kofi; Su, Li; Heist, Rebecca S.; Kulke, Matthew H.; Liu, Geoffrey; Christiani, David C.

    2011-01-01

    How genetic variations in apoptosis pathway interact with environmental factors to contribute to esophageal adenocarcinoma (EA) risk has not been comprehensively investigated. We conducted a case-only analysis in 335 Caucasian EA patients that were genotyped for 242 single nucleotide polymorphisms (SNPs) in 43 apoptotic genes. Gene–environment interactions were assessed using a two-step approach. First, random forest algorithm was used to screen for the potential interacting markers. Next, we used case-only logistic regression model to estimate the effects of gene–environment interactions on EA risk. Four SNPs (PERP rs648802; PIK3CA rs4855094, rs7644468 and TNFRSF1A rs4149579) had significant interaction with gastroesophageal reflux disease (GERD). The presence of variant alleles in TP53BP1 rs560191, CASP7 rs7907519 or BCL2 rs12454712 enhanced the risk of smoking by 2.08–2.58 times [interaction odds ratio (ORi) = 2.08–2.58, adjusted P-value (Padj) = 0.02–0.04]. Compared with patients carrying ≤1 risk genotype, the risk of GERD on EA was increased in persons with two (ORi = 1.89, Padj = 0.016) or ≥3 (ORi = 4.30, Padj < 0.0001) risk genotypes. Compared with cases with ≤1 risk genotype, smoking-associated EA risk increased by 3.15 times when ≥2 risk genotypes were present (ORi = 3.15, Padj < 0.0001). In conclusion, interactions among apoptotic SNPs and GERD or smoking play an important role in EA development. PMID:21212151

  20. Meaningful relationships: the regulation of the Ras/Raf/MEK/ERK pathway by protein interactions.

    PubMed Central

    Kolch, W

    2000-01-01

    The Ras/Raf/MEK (mitogen-activated protein kinase/ERK kinase)/ERK (extracellular-signal-regulated kinase) pathway is at the heart of signalling networks that govern proliferation, differentiation and cell survival. Although the basic regulatory steps have been elucidated, many features of this pathway are only beginning to emerge. This review focuses on the role of protein-protein interactions in the regulation of this pathway, and how they contribute to co-ordinate activation steps, subcellular redistribution, substrate phosphorylation and cross-talk with other signalling pathways. PMID:11023813

  1. Transition model for ricin-aptamer interactions with multiple pathways and energy barriers

    NASA Astrophysics Data System (ADS)

    Wang, Bin; Xu, Bingqian

    2014-02-01

    We develop a transition model to interpret single-molecule ricin-aptamer interactions with multiple unbinding pathways and energy barriers measured by atomic force microscopy dynamic force spectroscopy. Molecular simulations establish the relationship between binding conformations and the corresponding unbinding pathways. Each unbinding pathway follows a Bell-Evans multiple-barrier model. Markov-type transition matrices are developed to analyze the redistribution of unbinding events among the pathways under different loading rates. Our study provides detailed information about complex behaviors in ricin-aptamer unbinding events.

  2. Interaction between muscarinic receptor subtype signal transduction pathways mediating bladder contraction

    PubMed Central

    BRAVERMAN, ALAN S.; TALLARIDA, RONALD J.; RUGGIERI, MICHAEL R.

    2012-01-01

    M3 muscarinic receptors mediate cholinergic-induced contraction in most smooth muscles. However, in the denervated rat bladder, M2 receptors participate in contraction because M3-selective antagonists [para-fluoro-hexahydro-sila-diphenidol (p-F-HHSiD) and 4-DAMP] have low affinities. However, the affinity of the M2-selective antagonist methoctramine in the denervated bladder is consistent with M3 receptor mediating contraction. It is possible that two pathways interact to mediate contraction: one mediated by the M2 receptor and one by the M3 receptor. To determine whether an interaction exists, the inhibitory potencies of combinations of methoctramine and p-F-HHSiD for reversing cholinergic contractions were measured. In normal bladders, all combinations gave additive effects. In denervated bladders, synergistic effects were seen with the 10:1 and 1:1 (methoctramine:p-F-HHSiD wt/wt) combinations. After application of the sarcoplasmic reticulum ATPase inhibitor thapsigargin to normal tissue, the 10:1 and 1:1 ratios became synergistic, mimicking denervated tissue. Thus in normal bladders both M2 and M3 receptors can induce contraction. In the denervated bladder, the M2 and the M3 receptors interact in a facilitatory manner to mediate contraction. PMID:12185001

  3. Predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins.

    PubMed

    Gao, Yu-Fei; Chen, Lei; Cai, Yu-Dong; Feng, Kai-Yan; Huang, Tao; Jiang, Yang

    2012-01-01

    Metabolic pathway analysis, one of the most important fields in biochemistry, is pivotal to understanding the maintenance and modulation of the functions of an organism. Good comprehension of metabolic pathways is critical to understanding the mechanisms of some fundamental biological processes. Given a small molecule or an enzyme, how may one identify the metabolic pathways in which it may participate? Answering such a question is a first important step in understanding a metabolic pathway system. By utilizing the information provided by chemical-chemical interactions, chemical-protein interactions, and protein-protein interactions, a novel method was proposed by which to allocate small molecules and enzymes to 11 major classes of metabolic pathways. A benchmark dataset consisting of 3,348 small molecules and 654 enzymes of yeast was constructed to test the method. It was observed that the first order prediction accuracy evaluated by the jackknife test was 79.56% in identifying the small molecules and enzymes in a benchmark dataset. Our method may become a useful vehicle in predicting the metabolic pathways of small molecules and enzymes, providing a basis for some further analysis of the pathway systems.

  4. SUMOylation of ATRIP potentiates DNA damage signaling by boosting multiple protein interactions in the ATR pathway.

    PubMed

    Wu, Ching-Shyi; Ouyang, Jian; Mori, Eiichiro; Nguyen, Hai Dang; Maréchal, Alexandre; Hallet, Alexander; Chen, David J; Zou, Lee

    2014-07-01

    The ATR (ATM [ataxia telangiectasia-mutated]- and Rad3-related) checkpoint is a crucial DNA damage signaling pathway. While the ATR pathway is known to transmit DNA damage signals through the ATR-Chk1 kinase cascade, whether post-translational modifications other than phosphorylation are important for this pathway remains largely unknown. Here, we show that protein SUMOylation plays a key role in the ATR pathway. ATRIP, the regulatory partner of ATR, is modified by SUMO2/3 at K234 and K289. An ATRIP mutant lacking the SUMOylation sites fails to localize to DNA damage and support ATR activation efficiently. Surprisingly, the ATRIP SUMOylation mutant is compromised in the interaction with a protein group, rather than a single protein, in the ATR pathway. Multiple ATRIP-interacting proteins, including ATR, RPA70, TopBP1, and the MRE11-RAD50-NBS1 complex, exhibit reduced binding to the ATRIP SUMOylation mutant in cells and display affinity for SUMO2 chains in vitro, suggesting that they bind not only ATRIP but also SUMO. Fusion of a SUMO2 chain to the ATRIP SUMOylation mutant enhances its interaction with the protein group and partially suppresses its localization and functional defects, revealing that ATRIP SUMOylation promotes ATR activation by providing a unique type of protein glue that boosts multiple protein interactions along the ATR pathway. © 2014 Wu et al.; Published by Cold Spring Harbor Laboratory Press.

  5. Interaction of PPARα With the Canonic Wnt Pathway in the Regulation of Renal Fibrosis.

    PubMed

    Cheng, Rui; Ding, Lexi; He, Xuemin; Takahashi, Yusuke; Ma, Jian-Xing

    2016-12-01

    Peroxisome proliferator-activated receptor-α (PPARα) displays renoprotective effects with an unclear mechanism. Aberrant activation of the canonical Wnt pathway plays a key role in renal fibrosis. Renal levels of PPARα were downregulated in both type 1 and type 2 diabetes models. The PPARα agonist fenofibrate and overexpression of PPARα both attenuated the expression of fibrotic factors, and suppressed high glucose-induced or Wnt3a-induced Wnt signaling in renal cells. Fenofibrate inhibited Wnt signaling in the kidney of diabetic rats. A more renal prominent activation of Wnt signaling was detected both in PPARα(-/-) mice with diabetes or obstructive nephropathy and in PPARα(-/-) tubular cells treated with Wnt3a. PPARα did not block the transcriptional activity of β-catenin induced by a constitutively active mutant of lipoprotein receptor-related protein 6 (LRP6) or β-catenin. LRP6 stability was decreased by overexpression of PPARα and increased in PPARα(-/-) tubular cells, suggesting that PPARα interacts with Wnt signaling at the Wnt coreceptor level. 4-Hydroxynonenal-induced reactive oxygen species production, which resulted in LRP6 stability, was suppressed by overexpression of PPARα and dramatically enhanced in PPARα(-/-) tubular cells. Diabetic PPARα(-/-) mice showed more prominent NADPH oxidase-4 overexpression compared with diabetic wild-type mice, suggesting that the inhibitory effect of PPARα on Wnt signaling may be ascribed to its antioxidant activity. These observations identified a novel interaction between PPARα and the Wnt pathway, which is responsible, at least partially, for the therapeutic effects of fenofibrate on diabetic nephropathy. © 2016 by the American Diabetes Association.

  6. Determining the elastic properties of aptamer-ricin single molecule multiple pathway interactions

    NASA Astrophysics Data System (ADS)

    Wang, Bin; Park, Bosoon; Kwon, Yongkuk; Xu, Bingqian

    2014-05-01

    We report on the elastic properties of ricin and anti-ricin aptamer interactions, which showed three stable binding conformations, each of which has its special elastic properties. These different unbinding pathways were investigated by the dynamic force spectroscopy. A series-spring model combining the worm-like-chain model and Hook's law was used to estimate the apparent spring constants of the aptamer and linker molecule polyethylene glycol. The aptamer in its three different unbinding pathways showed different apparent spring constants. The two reaction barriers in the unbinding pathways also influence the apparent spring constant of the aptamer. This special elastic behavior of aptamer was used to distinguish its three unbinding pathways under different loading rates. This method also offered a way to distinguish and discard the non-specific interactions in single molecule experiments.

  7. Peptides interfering with protein-protein interactions in the ethylene signaling pathway delay tomato fruit ripening

    PubMed Central

    Bisson, Melanie M. A.; Kessenbrock, Mareike; Müller, Lena; Hofmann, Alexander; Schmitz, Florian; Cristescu, Simona M.; Groth, Georg

    2016-01-01

    The plant hormone ethylene is involved in the regulation of several processes with high importance for agricultural applications, e.g. ripening, aging and senescence. Previous work in our group has identified a small peptide (NOP-1) derived from the nuclear localization signal of the Arabidopsis ethylene regulator ETHYLENE INSENSITIVE-2 (EIN2) C-terminal part as efficient inhibitor of ethylene responses. Here, we show that NOP-1 is also able to efficiently disrupt EIN2-ETR1 complex formation in tomato, indicating that the NOP-1 inhibition mode is conserved across plant species. Surface application of NOP-1 on green tomato fruits delays ripening similar to known inhibitors of ethylene perception (MCP) and ethylene biosynthesis (AVG). Fruits treated with NOP-1 showed similar ethylene production as untreated controls underlining that NOP-1 blocks ethylene signaling by targeting an essential interaction in this pathway, while having no effect on ethylene biosynthesis. PMID:27477591

  8. Peptides interfering with protein-protein interactions in the ethylene signaling pathway delay tomato fruit ripening

    NASA Astrophysics Data System (ADS)

    Bisson, Melanie M. A.; Kessenbrock, Mareike; Müller, Lena; Hofmann, Alexander; Schmitz, Florian; Cristescu, Simona M.; Groth, Georg

    2016-08-01

    The plant hormone ethylene is involved in the regulation of several processes with high importance for agricultural applications, e.g. ripening, aging and senescence. Previous work in our group has identified a small peptide (NOP-1) derived from the nuclear localization signal of the Arabidopsis ethylene regulator ETHYLENE INSENSITIVE-2 (EIN2) C-terminal part as efficient inhibitor of ethylene responses. Here, we show that NOP-1 is also able to efficiently disrupt EIN2-ETR1 complex formation in tomato, indicating that the NOP-1 inhibition mode is conserved across plant species. Surface application of NOP-1 on green tomato fruits delays ripening similar to known inhibitors of ethylene perception (MCP) and ethylene biosynthesis (AVG). Fruits treated with NOP-1 showed similar ethylene production as untreated controls underlining that NOP-1 blocks ethylene signaling by targeting an essential interaction in this pathway, while having no effect on ethylene biosynthesis.

  9. HPIminer: A text mining system for building and visualizing human protein interaction networks and pathways.

    PubMed

    Subramani, Suresh; Kalpana, Raja; Monickaraj, Pankaj Moses; Natarajan, Jeyakumar

    2015-04-01

    The knowledge on protein-protein interactions (PPI) and their related pathways are equally important to understand the biological functions of the living cell. Such information on human proteins is highly desirable to understand the mechanism of several diseases such as cancer, diabetes, and Alzheimer's disease. Because much of that information is buried in biomedical literature, an automated text mining system for visualizing human PPI and pathways is highly desirable. In this paper, we present HPIminer, a text mining system for visualizing human protein interactions and pathways from biomedical literature. HPIminer extracts human PPI information and PPI pairs from biomedical literature, and visualize their associated interactions, networks and pathways using two curated databases HPRD and KEGG. To our knowledge, HPIminer is the first system to build interaction networks from literature as well as curated databases. Further, the new interactions mined only from literature and not reported earlier in databases are highlighted as new. A comparative study with other similar tools shows that the resultant network is more informative and provides additional information on interacting proteins and their associated networks. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. A novel genetic score approach using instruments to investigate interactions between pathways and environment: application to air pollution.

    PubMed

    Bind, Marie-Abele; Coull, Brent; Suh, Helen; Wright, Robert; Baccarelli, Andrea; Vokonas, Pantel; Schwartz, Joel

    2014-01-01

    Air pollution has been associated with increased systemic inflammation markers. We developed a new pathway analysis approach to investigate whether gene variants within relevant pathways (oxidative stress, endothelial function, and metal processing) modified the association between particulate air pollution and fibrinogen, C-reactive protein (CRP), intercellular adhesion molecule-1 (ICAM-1), and vascular cell adhesion molecule-1 (VCAM-1). Our study population consisted of 822 elderly participants of the Normative Aging Study (1999-2011). To investigate the role of biological mechanisms and to reduce the number of comparisons in the analysis, we created pathway-specific scores using gene variants related to each pathway. To select the most appropriate gene variants, we used the least absolute shrinkage and selection operator (Lasso) to relate independent outcomes representative of each pathway (8-hydroxydeoxyguanosine for oxidative stress, augmentation index for endothelial function, and patella lead for metal processing) to gene variants. A high genetic score corresponds to a higher allelic risk profile. We fit mixed-effects models to examine modification by the genetic score of the weekly air pollution association with the outcome. Among participants with higher genetic scores within the oxidative stress pathway, we observed significant associations between particle number and fibrinogen, while we did not find any association among participants with lower scores (p(interaction) = 0.04). Compared to individuals with low genetic scores of metal processing gene variants, participants with higher scores had greater effects of particle number on fibrinogen (p(interaction) = 0.12), CRP (p(interaction) = 0.02), and ICAM-1 (pinteraction = 0.08). This two-stage penalization method is easy to implement and can be used for large-scale genetic applications.

  11. Plant responses to insect herbivory: interactions between photosynthesis, reactive oxygen species and hormonal signalling pathways.

    PubMed

    Kerchev, Pavel I; Fenton, Brian; Foyer, Christine H; Hancock, Robert D

    2012-02-01

    Under herbivore attack plants mount a defence response characterized by the accumulation of secondary metabolites and inhibitory proteins. Significant changes are observed in the transcriptional profiles of genes encoding enzymes of primary metabolism. Such changes have often been interpreted in terms of a requirement for an increased investment of resources to 'fuel' the synthesis of secondary metabolites. While enhanced secondary metabolism undoubtedly exerts an influence on primary metabolism, accumulating evidence suggests that rather than stimulating photosynthesis insect herbivory reduces photosynthetic carbon fixation and this response occurs by a re-programming of gene expression. Within this context, reactive oxygen species (ROS) and reductant/oxidant (redox) signalling play a central role. Accumulating evidence suggests that ROS signalling pathways are closely interwoven with hormone-signalling pathways in plant-insect interactions. Here we consider how insect infestation impacts on the stress signalling network through effects on ROS and cellular redox metabolism with particular emphasis on the roles of ROS in the plant responses to phloem-feeding insects.

  12. Infant Pathways to Externalizing Behavior: Evidence of Genotype x Environment Interaction

    PubMed Central

    Leve, Leslie D.; Kerr, David C. R.; Shaw, Daniel; Ge, Xiaojia; Neiderhiser, Jenae M.; Scaramella, Laura V.; Reid, John B.; Conger, Rand; Reiss, David

    2009-01-01

    To further the understanding of the effects of early experience on the pathways to externalizing behavior, 9-month-old infants were observed during a frustration task. The analytical sample was composed of 348 linked triads of participants (adoptive parents, adopted child, and birth parent[s]) from a prospective adoption study, thereby permitting an examination of the interplay between genetic characteristics and early environmental experiences. It was hypothesized that genetic risk for externalizing problems (indexed by birth parents’ externalizing behavior) and affect dysregulation in the home (indexed by adoptive parents’ anxious/depressive symptoms) would independently and interactively predict a known precursor to externalizing problems: heightened infant attention to frustrating events. The results from the SEM analyses supported the moderation hypotheses involving adoptive mother affect dysregulation but did not support those involving adoptive father affect dysregulation: infants at genetic risk showed heightened attention to frustrating events only when the adoptive mother had higher levels of anxious/depressive symptoms. The Genotype x Environment interaction pattern held when substance use during pregnancy was considered. Sex-specific patterns of effects and future directions are discussed. PMID:20331671

  13. Multi-shell effective interactions

    NASA Astrophysics Data System (ADS)

    Tsunoda, Naofumi; Takayanagi, Kazuo; Hjorth-Jensen, Morten; Otsuka, Takaharu

    2014-02-01

    Background: Effective interactions, either derived from microscopic theories or based on fitting selected properties of nuclei in specific mass regions, are widely used inputs to shell-model studies of nuclei. The commonly used unperturbed basis functions are given by the harmonic oscillator. Until recently, most shell-model calculations have been confined to a single oscillator shell like the sd shell or the pf shell. Recent interest in nuclei away from the stability line requires, however, larger shell-model spaces. Because the derivation of microscopic effective interactions has been limited to degenerate models spaces, there are both conceptual and practical limits to present shell-model calculations that utilize such interactions. Purpose: The aim of this work is to present a novel microscopic method to calculate effective nucleon-nucleon interactions for the nuclear shell model. Its main difference from existing theories is that it can be applied not only to degenerate model spaces but also to nondegenerate model spaces. This has important consequences, in particular for intershell matrix elements of effective interactions. Methods: The formalism is presented in the form of a many-body perturbation theory based on the recently developed extended Kuo-Krenciglowa method. Our method enables us to microscopically construct effective interactions not only in one oscillator shell but also for several oscillator shells. Results: We present numerical results using effective interactions within (i) a single oscillator shell (a so-called degenerate model space) like the sd shell or the pf shell and (ii) two major shells (nondegenerate model space) like the sdf7p3 shell or the pfg9 shell. We also present energy levels of several nuclei that have two valence nucleons on top of a given closed-shell core. Conclusions: Our results show that the present method works excellently in shell-model spaces that comprise several oscillator shells, as well as in a single oscillator

  14. Interactions between the jasmonic and salicylic acid pathway modulate the plant metabolome and affect herbivores of different feeding types.

    PubMed

    Schweiger, R; Heise, A-M; Persicke, M; Müller, C

    2014-07-01

    The phytohormones jasmonic acid (JA) and salicylic acid (SA) mediate induced plant defences and the corresponding pathways interact in a complex manner as has been shown on the transcript and proteine level. Downstream, metabolic changes are important for plant-herbivore interactions. This study investigated metabolic changes in leaf tissue and phloem exudates of Plantago lanceolata after single and combined JA and SA applications as well as consequences on chewing-biting (Heliothis virescens) and piercing-sucking (Myzus persicae) herbivores. Targeted metabolite profiling and untargeted metabolic fingerprinting uncovered different categories of plant metabolites, which were influenced in a specific manner, indicating points of divergence, convergence, positive crosstalk and pronounced mutual antagonism between the signaling pathways. Phytohormone-specific decreases of primary metabolite pool sizes in the phloem exudates may indicate shifts in sink-source relations, resource allocation, nutrient uptake or photosynthesis. Survival of both herbivore species was significantly reduced by JA and SA treatments. However, the combined application of JA and SA attenuated the negative effects at least against H. virescens suggesting that mutual antagonism between the JA and SA pathway may be responsible. Pathway interactions provide a great regulatory potential for the plant that allows triggering of appropriate defences when attacked by different antagonist species. © 2013 John Wiley & Sons Ltd.

  15. Thioredoxin-interacting protein regulates lipid metabolism via Akt/mTOR pathway in diabetic kidney disease.

    PubMed

    Du, Chunyang; Wu, Ming; Liu, Huan; Ren, Yunzhuo; Du, Yunxia; Wu, Haijiang; Wei, Jinying; Liu, Chuxin; Yao, Fang; Wang, Hui; Zhu, Yan; Duan, Huijun; Shi, Yonghong

    2016-10-01

    Abnormal lipid metabolism contributes to the renal lipid accumulation, which is associated with diabetic kidney disease, but its precise mechanism remains unclear. The growing evidence demonstrates that thioredoxin-interacting protein is involved in regulating cellular glucose and lipid metabolism. Here, we investigated the effects of thioredoxin-interacting protein on lipid accumulation in diabetic kidney disease. In contrast to the diabetic wild-type mice, the physical and biochemical parameters were improved in the diabetic thioredoxin-interacting protein knockout mice. The increased renal lipid accumulation, expression of acetyl-CoA carboxylase, fatty acid synthase and sterol regulatory element binding protein-1, and phosphorylated Akt and mTOR associated with diabetes in wild-type mice was attenuated in diabetic thioredoxin-interacting protein knockout mice. Furthermore, thioredoxin-interacting protein knockout significantly increased the expression of peroxisome proliferator-activated receptor-α, acyl-coenzyme A oxidase 1 and carnitine palmitoyltransferaser 1 in diabetic kidneys. In vitro experiments, using HK-2 cells, revealed that knockdown of thioredoxin-interacting protein inhibited high glucose-mediated lipid accumulation, expression of acetyl-CoA carboxylase, fatty acid synthase and sterol regulatory element binding protein-1, as well as activation of Akt and mTOR. Moreover, knockdown of thioredoxin-interacting protein reversed high glucose-induced reduction of peroxisome proliferator-activated receptor-α, acyl-coenzyme A oxidase 1 and carnitine palmitoyltransferaser 1 expression in HK-2 cells. Importantly, blockade of Akt/mTOR signaling pathway with LY294002, a specific PI3K inhibitor, replicated these effects of thioredoxin-interacting protein silencing. Taken together, these data suggest that thioredoxin-interacting protein deficiency alleviates diabetic renal lipid accumulation through regulation of Akt/mTOR pathway, thioredoxin-interacting

  16. Interaction between the TP63 and SHH pathways is an important determinant of epidermal homeostasis

    PubMed Central

    Chari, N S; Romano, R A; Koster, M I; Jaks, V; Roop, D; Flores, E R; Teglund, S; Sinha, S; Gruber, W; Aberger, F; Medeiros, L J; Toftgard, R; McDonnell, T J

    2013-01-01

    Deregulation of the hedgehog (HH) pathway results in overexpression of the GLI target BCL2 and is an initiating event in specific tumor types including basal cell carcinoma of the skin. Regulation of the HH pathway during keratinocyte differentiation is not well understood. We measured HH pathway activity in response to differentiation stimuli in keratinocytes. An upregulation of suppressor of fused (SUFU), a negative regulator of the HH pathway, lowered HH pathway activity and was accompanied by loss of BCL2 expression associated with keratinocyte differentiation. We used in vitro and in vivo models to demonstrate that ΔNp63α, a crucial regulator of epidermal development, activates SUFU transcription in keratinocytes. Increasing SUFU protein levels inhibited GLI-mediated gene activation in suprabasal keratinocytes and promoted differentiation. Loss of SUFU expression caused deregulation of keratinocyte differentiation and BCL2 overexpression. Using in vivo murine models, we also provide evidence of GLI-mediated regulation of the TP63 pathway. p63 expression appears essential to establish an optimally functioning HH pathway. These observations present a regulatory mechanism by which SUFU acts as an interacting node between the HH and TP63 pathways to mediate differentiation and maintain epidermal homeostasis. Disruption of this regulatory node can be an important contributor to multistep carcinogenesis. PMID:23686138

  17. Curcumin mediates anticancer effects by modulating multiple cell signaling pathways.

    PubMed

    Kunnumakkara, Ajaikumar B; Bordoloi, Devivasha; Harsha, Choudhary; Banik, Kishore; Gupta, Subash C; Aggarwal, Bharat B

    2017-08-01

    Curcumin, a component of a spice native to India, was first isolated in 1815 by Vogel and Pelletier from the rhizomes of Curcuma longa (turmeric) and, subsequently, the chemical structure of curcumin as diferuloylmethane was reported by Milobedzka et al. [(1910) 43., 2163-2170]. Since then, this polyphenol has been shown to exhibit antioxidant, anti-inflammatory, anticancer, antiviral, antibacterial, and antifungal activities. The current review primarily focuses on the anticancer potential of curcumin through the modulation of multiple cell signaling pathways. Curcumin modulates diverse transcription factors, inflammatory cytokines, enzymes, kinases, growth factors, receptors, and various other proteins with an affinity ranging from the pM to the mM range. Furthermore, curcumin effectively regulates tumor cell growth via modulation of numerous cell signaling pathways and potentiates the effect of chemotherapeutic agents and radiation against cancer. Curcumin can interact with most of the targets that are modulated by FDA-approved drugs for cancer therapy. The focus of this review is to discuss the molecular basis for the anticancer activities of curcumin based on preclinical and clinical findings. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  18. [Interactive effects between allelochemical substitutes].

    PubMed

    He, Huaqin; Shen, Lihua; Song, Biqing; Guo, Yuchun; Liang, Yiyuan; Liang, Kangjing; Lin, Wenxiong

    2005-05-01

    In order to understand the allelopathic mechanisms of rice on weed, the allelochemical substitutes salicylic acid, p-hydroxybenzonic acid, cinnamic acid, vanillic acid and ferulic acid were used in an orthogonally gyrating regression experiment to study their interactive effects on the growth of barnyardgrass. The results indicated that whether the interactive effects between two substitutes, e.g., between salicylic and cinnamic acid or between salicylic and p-hydrobanzonic acid, were synergistic or antagonistic depended on the concentrations of each substitutes in the mixture. In the mixture of salicylic acid and p-hydrobanzonic acid, the effect of salicylic acid was synergistic at < 0.14 mmol.L(-1) but antagonistic at > 0.14 mmol.L(-1), while p-hydrobanzonic acid showed an antagonistic effect at > 0.425 mmol.L(-1). Salicylic acid at all test concentrations exhibited antagonism to cinnamic acid, while cinnamic acid had a synergistic at < 0.14 mmol.L(-1), but an antagonistic effect at >0.14 mmol.L(-1) on alicylic acid. The interactive effects between cinnamic and ferulic acid were all synergistic at test concentrations.

  19. Uniform and Complementary Social Interaction: Distinct Pathways to Solidarity

    PubMed Central

    Koudenburg, Namkje; Postmes, Tom; Gordijn, Ernestine H.; van Mourik Broekman, Aafke

    2015-01-01

    We examine how different forms of co-action give rise to feelings of solidarity. We propose that (a) coordinated action elicits a sense of solidarity, and (b) the process through which such solidarity emerges differs for different forms of co-action. We suggest that whether solidarity within groups emerges from uniform action (e.g. synchronizing, as when people speak in unison) or from more complementary forms of action (e.g. alternating, when speaking in turns) has important consequences for the emergent position of individuals within the group. Uniform action relies on commonality, leaving little scope for individuality. In complementary action each individual makes a distinctive contribution to the group, thereby increasing a sense of personal value to the group, which should contribute to the emergence of solidarity. The predictions receive support from five studies, in which we study groups in laboratory and field settings. Results show that both complementary and uniform co-action increase a sense of solidarity compared to control conditions. However, in the complementary action condition, but not in the uniform action (or synchrony) condition, the effect on feelings of solidarity is mediated by a sense of personal value to the group. PMID:26047131

  20. Uniform and Complementary Social Interaction: Distinct Pathways to Solidarity.

    PubMed

    Koudenburg, Namkje; Postmes, Tom; Gordijn, Ernestine H; van Mourik Broekman, Aafke

    2015-01-01

    We examine how different forms of co-action give rise to feelings of solidarity. We propose that (a) coordinated action elicits a sense of solidarity, and (b) the process through which such solidarity emerges differs for different forms of co-action. We suggest that whether solidarity within groups emerges from uniform action (e.g. synchronizing, as when people speak in unison) or from more complementary forms of action (e.g. alternating, when speaking in turns) has important consequences for the emergent position of individuals within the group. Uniform action relies on commonality, leaving little scope for individuality. In complementary action each individual makes a distinctive contribution to the group, thereby increasing a sense of personal value to the group, which should contribute to the emergence of solidarity. The predictions receive support from five studies, in which we study groups in laboratory and field settings. Results show that both complementary and uniform co-action increase a sense of solidarity compared to control conditions. However, in the complementary action condition, but not in the uniform action (or synchrony) condition, the effect on feelings of solidarity is mediated by a sense of personal value to the group.

  1. Cooperative interaction of MUC1 with the HGF/c-Met pathway during hepatocarcinogenesis

    PubMed Central

    2012-01-01

    Background Hepatocyte growth factor (HGF) induced c-Met activation is known as the main stimulus for hepatocyte proliferation and is essential for liver development and regeneration. Activation of HGF/c-Met signaling has been correlated with aggressive phenotype and poor prognosis in hepatocellular carcinoma (HCC). MUC1 is a transmembrane mucin, whose over-expression is reported in most cancers. Many of the oncogenic effects of MUC1 are believed to occur through the interaction of MUC1 with signaling molecules. To clarify the role of MUC1 in HGF/c-Met signaling, we determined whether MUC1 and c-Met interact cooperatively and what their role(s) is in hepatocarcinogenesis. Results MUC1 and c-Met over-expression levels were determined in highly motile and invasive, mesenchymal-like HCC cell lines, and in serial sections of cirrhotic and HCC tissues, and these levels were compared to those in normal liver tissues. Co-expression of both c-Met and MUC1 was found to be associated with the differentiation status of HCC. We further demonstrated an interaction between c-Met and MUC1 in HCC cells. HGF-induced c-Met phosphorylation decreased this interaction, and down-regulated MUC1 expression. Inhibition of c-Met activation restored HGF-mediated MUC1 down-regulation, and decreased the migratory and invasive abilities of HCC cells via inhibition of β-catenin activation and c-Myc expression. In contrast, siRNA silencing of MUC1 increased HGF-induced c-Met activation and HGF-induced cell motility and invasion. Conclusions These findings indicate that the crosstalk between MUC1 and c-Met in HCC could provide an advantage for invasion to HCC cells through the β-catenin/c-Myc pathway. Thus, MUC1 and c-Met could serve as potential therapeutic targets in HCC. PMID:22962849

  2. Chemical combinations elucidate pathway interactions and regulation relevant to Hepatitis C replication

    PubMed Central

    Owens, Christopher M; Mawhinney, Christina; Grenier, Jill M; Altmeyer, Ralf; Lee, Margaret S; Borisy, Alexis A; Lehár, Joseph; Johansen, Lisa M

    2010-01-01

    The search for effective Hepatitis C antiviral therapies has recently focused on host sterol metabolism and protein prenylation pathways that indirectly affect viral replication. However, inhibition of the sterol pathway with statin drugs has not yielded consistent results in patients. Here, we present a combination chemical genetic study to explore how the sterol and protein prenylation pathways work together to affect hepatitis C viral replication in a replicon assay. In addition to finding novel targets affecting viral replication, our data suggest that the viral replication is strongly affected by sterol pathway regulation. There is a marked transition from antagonistic to synergistic antiviral effects as the combination targets shift downstream along the sterol pathway. We also show how pathway regulation frustrates potential hepatitis C therapies based on the sterol pathway, and reveal novel synergies that selectively inhibit hepatitis C replication over host toxicity. In particular, combinations targeting the downstream sterol pathway enzymes produced robust and selective synergistic inhibition of hepatitis C replication. Our findings show how combination chemical genetics can reveal critical pathway connections relevant to viral replication, and can identify potential treatments with an increased therapeutic window. PMID:20531405

  3. Interaction of the EGF Receptor and the Hippo Pathway in the Diabetic Kidney.

    PubMed

    Chen, Jianchun; Harris, Raymond C

    2016-06-01

    Activation of the EGF receptor (EGFR) or the Hippo signaling pathway can control cell proliferation, apoptosis, and differentiation, and the dysregulation of these pathways can contribute to tumorigenesis. Previous studies showed that activation of EGFR signaling in renal epithelial cells can exacerbate diabetic kidney injury. Moreover, EGFR has been implicated in regulating the Hippo signaling pathway in Drosophila; thus, we examined this potential interaction in mammalian diabetic kidney disease. Yes-associated protein (YAP) is a transcriptional regulator regulated by the Hippo signaling pathway. We found YAP protein expression and phosphorylation were upregulated in diabetic mouse renal proximal tubule epithelial cells, which were inhibited in diabetic proximal tubule EGFR-knockout mice (EGFR(ptKO)) or administration of an EGFR tyrosine kinase inhibitor erlotinib. Furthermore, activation of an EGFR-PI3K-Akt-CREB signaling pathway mediated YAP gene expression and YAP nuclear translocation and interaction with the TEA domain (TEAD) transcription factor complex, which led to upregulated expression of two TEAD-dependent genes, the connective tissue growth factor and amphiregulin genes. In a renal proximal tubule cell line, either pharmacologic or genetic inhibition of EGFR, Akt, or CREB blunted YAP expression in response to high-glucose treatment. Additionally, knocking down YAP expression by specific siRNA inhibited cell proliferation in response to high glucose or exogenous EGF. Therefore, these results link the Hippo pathway to EGFR-mediated renal epithelial injury in diabetes. Copyright © 2016 by the American Society of Nephrology.

  4. The gene-gene interaction of INSIG-SCAP-SREBP pathway on the risk of obesity in Chinese children.

    PubMed

    Liu, Fang-Hong; Song, Jie-Yun; Shang, Xiao-Rui; Meng, Xiang-Rui; Ma, Jun; Wang, Hai-Jun

    2014-01-01

    Childhood obesity has become a global public health problem in recent years. This study aimed to explore the association of genetic variants in INSIG-SCAP-SREBP pathway with obesity in Chinese children. A case-control study was conducted, including 705 obese cases and 1,325 nonobese controls. We genotyped 15 single nucleotide polymorphisms (SNPs) of five genes in INSIG-SCAP-SREBP pathway, including insulin induced gene 1 (INSIG1), insulin induced gene 2 (INSIG2), SREBP cleavage-activating protein gene (SCAP), sterol regulatory element binding protein gene 1 (SREBP1), and sterol regulatory element binding protein gene 2 (SREBP2). We used generalized multifactor dimensionality reduction (GMDR) and logistic regression to investigate gene-gene interactions. Single polymorphism analyses showed that SCAP rs12487736 and rs12490383 were nominally associated with obesity. We identified a 3-locus interaction on obesity in GMDR analyses (P = 0.001), involving 3 genetic variants of INSIG2, SCAP, and SREBP2. The individuals in high-risk group of the 3-locus combinations had a 79.9% increased risk of obesity compared with those in low-risk group (OR = 1.799, 95% CI: 1.475-2.193, P = 6.61 × 10(-9)). We identified interaction of three genes in INSIG-SCAP-SREBP pathway on risk of obesity, revealing that these genes affect obesity more likely through a complex interaction pattern than single gene effect.

  5. HIV's Nef interacts with β-catenin of the Wnt signaling pathway in HEK293 cells.

    PubMed

    Weiser, Keren; Barton, Meredith; Gershoony, Dafna; Dasgupta, Ramanuj; Cardozo, Timothy

    2013-01-01

    The Wnt signaling pathway is implicated in major physiologic cellular functions, such as proliferation, migration, cell fate specification, maintenance of pluripotency and induction of tumorigenicity. Proliferation and migration are important responses of T-cells, which are major cellular targets of HIV infection. Using an informatics screen, we identified a previously unsuspected interaction between HIV's Nef protein and β-catenin, a key component of the Wnt pathway. A segment in Nef contains identical amino acids at key positions and structurally mimics the β-catenin binding sites on endogenous β-catenin ligands. The interaction between Nef and β-catenin was confirmed in vitro and in a co-immunoprecipitation from HEK293 cells. Moreover, the introduction of Nef into HEK293 cells specifically inhibited a Wnt pathway reporter.

  6. The interaction of estrogen and CSE/H2S pathway in the development of atherosclerosis.

    PubMed

    Li, Hongzhu; Mani, Sarathi; Wu, Lingyun; Fu, Ming; Shuang, Tian; Xu, Changqing; Wang, Rui

    2017-03-01

    Both estrogen and hydrogen sulfide (H2S) have been shown to inhibit the development of atherosclerosis. We previously reported that cystathionine γ-lyase knockout (CSE-KO) male mice develop atherosclerosis earlier than male wild-type (WT) mice. The present study investigated the interaction of CSE/H2S pathway and estrogen on the development of atherosclerosis in female mice. Plasma estrogen levels were significantly lower in female CSE-KO mice than in female WT mice. NaHS treatment had no effect on plasma estrogen levels in both WT and CSE-KO female mice. After CSE-KO and WT female mice were fed with atherogenic diet for 12 wk, plasma lipid levels were significantly increased and triglyceride levels decreased compared with those of control diet-fed mice. Atherogenic diet induced more atherosclerotic lesion, oxidative stress, intracellular adhesion molecule-1 (ICAM-1), and NF-κB in CSE-KO mice than in WT mice. Estrogen treatment of atherogenic diet-fed WT mice attenuated hypercholesterolemia, oxidative stress, ICAM-1 expression, and NF-κB in WT mice but not in atherogenic diet-fed CSE-KO mice. Furthermore, H2S production in both the liver and vascular tissues was enhanced by estrogen in WT mice but not in CSE-KO mice. It is concluded that the antiatherosclerotic effect of estrogen is mediated by CSE-generated H2S. This study provides new insights into the interaction of H2S and estrogen signaling pathways on the regulation of cardiovascular functions.NEW & NOTEWORTHY Female cystathionine γ-lyase (CSE)-knockout mice have significantly lower plasma estrogen levels and more severe early atherosclerotic lesion than female wild-type mice. H2S production in liver and vascular tissues is enhanced by estrogen via its stimulatory effect on CSE activity. The antiatherosclerotic effect of estrogen is mediated by CSE-generated H2S. Copyright © 2017 the American Physiological Society.

  7. Unified theory of effective interaction

    SciTech Connect

    Takayanagi, Kazuo

    2016-09-15

    We present a unified description of effective interaction theories in both algebraic and graphic representations. In our previous work, we have presented the Rayleigh–Schrödinger and Bloch perturbation theories in a unified fashion by introducing the main frame expansion of the effective interaction. In this work, we start also from the main frame expansion, and present various nonperturbative theories in a coherent manner, which include generalizations of the Brandow, Brillouin–Wigner, and Bloch–Horowitz theories on the formal side, and the extended Krenciglowa–Kuo and the extended Lee–Suzuki methods on the practical side. We thus establish a coherent and comprehensive description of both perturbative and nonperturbative theories on the basis of the main frame expansion.

  8. Unified theory of effective interaction

    NASA Astrophysics Data System (ADS)

    Takayanagi, Kazuo

    2016-09-01

    We present a unified description of effective interaction theories in both algebraic and graphic representations. In our previous work, we have presented the Rayleigh-Schrödinger and Bloch perturbation theories in a unified fashion by introducing the main frame expansion of the effective interaction. In this work, we start also from the main frame expansion, and present various nonperturbative theories in a coherent manner, which include generalizations of the Brandow, Brillouin-Wigner, and Bloch-Horowitz theories on the formal side, and the extended Krenciglowa-Kuo and the extended Lee-Suzuki methods on the practical side. We thus establish a coherent and comprehensive description of both perturbative and nonperturbative theories on the basis of the main frame expansion.

  9. Effective interactions between fluid membranes

    NASA Astrophysics Data System (ADS)

    Lu, Bing-Sui; Podgornik, Rudolf

    2015-08-01

    A self-consistent theory is proposed for the general problem of interacting undulating fluid membranes subject to the constraint that they do not interpenetrate. We implement the steric constraint via an exact functional integral representation and, through the use of a saddle-point approximation, transform it into a novel effective steric potential. The steric potential is found to consist of two contributions: one generated by zero-mode fluctuations of the membranes and the other by thermal bending fluctuations. For membranes of cross-sectional area S , we find that the bending fluctuation part scales with the intermembrane separation d as d-2 for d ≪√{S } but crosses over to d-4 scaling for d ≫√{S } , whereas the zero-mode part of the steric potential always scales as d-2. For membranes interacting exclusively via the steric potential, we obtain closed-form expressions for the effective interaction potential and for the rms undulation amplitude σ , which becomes small at low temperatures T and/or large bending stiffnesses κ . Moreover, σ scales as d for d ≪√{S } but saturates at √{kBT S /κ } for d ≫√{S } . In addition, using variational Gaussian theory, we apply our self-consistent treatment to study intermembrane interactions subject to different types of potentials: (i) the Moreira-Netz potential for a pair of strongly charged membranes with an intervening solution of multivalent counterions, (ii) an attractive square well, (iii) the Morse potential, and (iv) a combination of hydration and van der Waals interactions.

  10. The PDZ Protein Canoe/AF-6 Links Ras-MAPK, Notch and Wingless/Wnt Signaling Pathways by Directly Interacting with Ras, Notch and Dishevelled

    PubMed Central

    Carmena, Ana; Speicher, Stephan; Baylies, Mary

    2006-01-01

    Over the past few years, it has become increasingly apparent that signal transduction pathways are not merely linear cascades; they are organized into complex signaling networks that require high levels of regulation to generate precise and unique cell responses. However, the underlying regulatory mechanisms by which signaling pathways cross-communicate remain poorly understood. Here we show that the Ras-binding protein Canoe (Cno)/AF-6, a PDZ protein normally associated with cellular junctions, is a key modulator of Wingless (Wg)/Wnt, Ras-Mitogen Activated Protein Kinase (MAPK) and Notch (N) signaling pathways cross-communication. Our data show a repressive effect of Cno/AF-6 on these three signaling pathways through physical interactions with Ras, N and the cytoplasmic protein Dishevelled (Dsh), a key Wg effector. We propose a model in which Cno, through those interactions, actively coordinates, at the membrane level, Ras-MAPK, N and Wg signaling pathways during progenitor specification. PMID:17183697

  11. Hodgkin disease risk: role of genetic polymorphisms and gene-gene interactions in inflammation pathway genes.

    PubMed

    Monroy, Claudia M; Cortes, Andrea C; Lopez, Mirtha S; D'Amelio, Anthony M; Etzel, Carol J; Younes, Anas; Strom, Sara S; El-Zein, Randa A

    2011-01-01

    Inflammation is a critical component of cancer development. The clinical and pathological features of Hodgkin disease (HD) reflect an abnormal immunity that results from cytokines secreted by Reed-Sternberg cells and the surrounding tumor. Numerous studies have reported the association between genetic polymorphisms in cytokine genes and the susceptibility to different hematologic cancers. However, the effects of such SNPs on modulating HD risk have not yet been investigated. We hypothesized that gene-gene interactions between candidate genes in the anti- and pro-inflammatory pathways carrying suspicious polymorphisms may contribute to susceptibility to HD. To test this hypothesis, we conducted a study on 200 HD cases and 220 controls to assess associations between HD risk and 38 functional SNPs in inflammatory genes. We evaluated potential gene-gene interactions using a multi-analytic strategy combining logistic regression, multi-factor dimensionality reduction, and classification and regression tree (CART) approaches. We observed that, in combination, allelic variants in the COX2, IL18, ILR4, and IL10 genes modify the risk for developing HD. Moreover, the cumulative genetic risk score (CGRS) revealed a significant trend where the risk for developing HD increases as the number of adverse alleles in the cytokine genes increase. These findings support the notion that epigenetic-interactions between these cytokines may influence pathogenesis of HD modulating the proliferation of regulatory T cells. In this way, the innate and adaptative immune responses may be altered and defy their usual functions in the host anti-tumor response. Our study is the first to report the association between polymorphisms in inflammation genes and HD susceptibility risk. © 2010 Wiley-Liss, Inc.

  12. Pharmacokinetics of gyrase inhibitors, Part 2: Renal and hepatic elimination pathways and drug interactions.

    PubMed

    Sörgel, F; Kinzig, M

    1993-03-22

    This article focuses on the relationship of the physicochemical properties of gyrase inhibitors to their hepatic and renal elimination pathways. Luminal fluid concentrations of gyrase inhibitors are affected by an active process and can be inhibited by agents such as probenecid that inhibit tubular secretion of anions. Probenecid may inhibit base transport in the proximal tubule and appears to inhibit base transport as well. Available data suggest that all gyrase inhibitors can be secreted as anions by the proximal tubules. Cimetidine, which is cationic at physiologic pH, inhibits base transport in the proximal tubule and appears to inhibit base transport of gyrase inhibitors. Reabsorption also affects tubular concentrations. Models that describe the effects of urinary flow and pH are discussed. The N4'-methylated derivatives are the most lipophilic, and addition or removal of the methyl group can, but does not always, affect reabsorption. The data indicate that all gyrase inhibitors undergo tubular secretion as either acids or bases and that some also are significantly reabsorbed. Hepatic handling and resultant excretion of metabolites are also influenced by the presence or absence of N4'-methylation. A step in the hepatic handling of N4'-methylated gyrase inhibitors that leads to N4'-oxidation has not yet been found in rufloxacin. Rebiotransformation of N4'-oxides was described in liver perfusion experiments. The potential for interaction with theophylline is not identical for all gyrase inhibitors. Enoxacin is the strongest inhibitor of theophylline and caffeine metabolism, followed by tosufloxacin, ciprofloxacin, and pefloxacin. Fleroxacin, ofloxacin, rufloxacin, and sparfloxacin have no or negligible effects. A likely mechanism for this interaction is the inhibition of subsets of the cytochrome P-450 enzyme. Structure activity relationships were established for this interaction. Piperazine ring-cleaved compounds and naphthyridine nuclei were shown to be most

  13. Visualizing Interactions along the Escherichia coli Twin-Arginine Translocation Pathway Using Protein Fragment Complementation

    PubMed Central

    Kostecki, Jan S.; Li, Haiming; Turner, Raymond J.; DeLisa, Matthew P.

    2010-01-01

    The twin-arginine translocation (Tat) pathway is well known for its ability to export fully folded substrate proteins out of the cytoplasm of Gram-negative and Gram-positive bacteria. Studies of this mechanism in Escherichia coli have identified numerous transient protein-protein interactions that guide export-competent proteins through the Tat pathway. To visualize these interactions, we have adapted bimolecular fluorescence complementation (BiFC) to detect protein-protein interactions along the Tat pathway of living cells. Fragments of the yellow fluorescent protein (YFP) were fused to soluble and transmembrane factors that participate in the translocation process including Tat substrates, Tat-specific proofreading chaperones and the integral membrane proteins TatABC that form the translocase. Fluorescence analysis of these YFP chimeras revealed a wide range of interactions such as the one between the Tat substrate dimethyl sulfoxide reductase (DmsA) and its dedicated proofreading chaperone DmsD. In addition, BiFC analysis illuminated homo- and hetero-oligomeric complexes of the TatA, TatB and TatC integral membrane proteins that were consistent with the current model of translocase assembly. In the case of TatBC assemblies, we provide the first evidence that these complexes are co-localized at the cell poles. Finally, we used this BiFC approach to capture interactions between the putative Tat receptor complex formed by TatBC and the DmsA substrate or its dedicated chaperone DmsD. Our results demonstrate that BiFC is a powerful approach for studying cytoplasmic and inner membrane interactions underlying bacterial secretory pathways. PMID:20169075

  14. Effective Interactions for Light Nuclei

    NASA Astrophysics Data System (ADS)

    Caldwell, Bryan R.

    The G-matrix technique in which one is able to easily calculate ground and excited states of many-body systems is used to calculate the ground state energies and some excited levels of ^3H and ^4He. Energy independent effective interactions are obtained for these nuclei using the technique of Suzuki and Lee which requires the G-matrix and its derivatives with respect to starting energy. It is found that accurate energy derivatives of the G-matrix are necessary to obtain energy independence and thus analytic expressions are presented for these derivatives in both center-of-mass/relative and shell model coordinate systems. Several rules of thumb are given pertaining to the convergence criteria in both coordinate systems. Further, since the G-matrix includes only intra -channel two-body correlations outside the active space, we explore the effect on the binding energies when the active space is enlarged to include several major shells. By enlarging the active space, we hope to include the most important many-body correlations explicitly. It is found that when the active space includes more than 2 major shells, the effective interaction is well approximated by the G-matrix. Our results essentially agree with exact Faddeev calculations for ^3 H but underbind by about.5 MeV in ^4 He as compared to exact Yabukovsky and Green function Monte Carlo calculations. A possible reason for this underbinding, the inclusion of unlinked diagrams in the energy expansion, is studied. The energy independent G-matrix technique is then applied to the p-shell (^5He, ^6Li and ^7Li) where the active space includes all excitations up to 2 hbaromega. Zero, one, two and three -body effective interactions are extracted and it is found that a schematic two-parameter three-body potential can be used to approximate the effective three-body potential that results from the truncation of the active space.

  15. Fault Tolerance in Protein Interaction Networks: Stable Bipartite Subgraphs and Redundant Pathways

    PubMed Central

    Brady, Arthur; Maxwell, Kyle; Daniels, Noah; Cowen, Lenore J.

    2009-01-01

    As increasing amounts of high-throughput data for the yeast interactome become available, more system-wide properties are uncovered. One interesting question concerns the fault tolerance of protein interaction networks: whether there exist alternative pathways that can perform some required function if a gene essential to the main mechanism is defective, absent or suppressed. A signature pattern for redundant pathways is the BPM (between-pathway model) motif, introduced by Kelley and Ideker. Past methods proposed to search the yeast interactome for BPM motifs have had several important limitations. First, they have been driven heuristically by local greedy searches, which can lead to the inclusion of extra genes that may not belong in the motif; second, they have been validated solely by functional coherence of the putative pathways using GO enrichment, making it difficult to evaluate putative BPMs in the absence of already known biological annotation. We introduce stable bipartite subgraphs, and show they form a clean and efficient way of generating meaningful BPMs which naturally discard extra genes included by local greedy methods. We show by GO enrichment measures that our BPM set outperforms previous work, covering more known complexes and functional pathways. Perhaps most importantly, since our BPMs are initially generated by examining the genetic-interaction network only, the location of edges in the protein-protein physical interaction network can then be used to statistically validate each candidate BPM, even with sparse GO annotation (or none at all). We uncover some interesting biological examples of previously unknown putative redundant pathways in such areas as vesicle-mediated transport and DNA repair. PMID:19399174

  16. A comprehensive modular map of molecular interactions in RB/E2F pathway.

    PubMed

    Calzone, Laurence; Gelay, Amélie; Zinovyev, Andrei; Radvanyi, François; Barillot, Emmanuel

    2008-01-01

    We present, here, a detailed and curated map of molecular interactions taking place in the regulation of the cell cycle by the retinoblastoma protein (RB/RB1). Deregulations and/or mutations in this pathway are observed in most human cancers. The map was created using Systems Biology Graphical Notation language with the help of CellDesigner 3.5 software and converted into BioPAX 2.0 pathway description format. In the current state the map contains 78 proteins, 176 genes, 99 protein complexes, 208 distinct chemical species and 165 chemical reactions. Overall, the map recapitulates biological facts from approximately 350 publications annotated in the diagram. The network contains more details about RB/E2F interaction network than existing large-scale pathway databases. Structural analysis of the interaction network revealed a modular organization of the network, which was used to elaborate a more summarized, higher-level representation of RB/E2F network. The simplification of complex networks opens the road for creating realistic computational models of this regulatory pathway.

  17. Kinase Pathway Database: An Integrated Protein-Kinase and NLP-Based Protein-Interaction Resource

    PubMed Central

    Koike, Asako; Kobayashi, Yoshiyuki; Takagi, Toshihisa

    2003-01-01

    Protein kinases play a crucial role in the regulation of cellular functions. Various kinds of information about these molecules are important for understanding signaling pathways and organism characteristics. We have developed the Kinase Pathway Database, an integrated database involving major completely sequenced eukaryotes. It contains the classification of protein kinases and their functional conservation, ortholog tables among species, protein–protein, protein–gene, and protein–compound interaction data, domain information, and structural information. It also provides an automatic pathway graphic image interface. The protein, gene, and compound interactions are automatically extracted from abstracts for all genes and proteins by natural-language processing (NLP).The method of automatic extraction uses phrase patterns and the GENA protein, gene, and compound name dictionary, which was developed by our group. With this database, pathways are easily compared among species using data with more than 47,000 protein interactions and protein kinase ortholog tables. The database is available for querying and browsing at http://kinasedb.ontology.ims.u-tokyo.ac.jp/. PMID:12799355

  18. The segmentation clock in mice: interaction between the Wnt and Notch signalling pathways.

    PubMed

    Rodríguez-González, J G; Santillán, M; Fowler, A C; Mackey, Michael C

    2007-09-07

    In the last few years, the efforts to elucidate the mechanisms underlying the segmentation clock in various vertebrate species have multiplied. Early evidence suggested that oscillations are caused by one of the genes under the Notch signalling pathway (like those of the her or Hes families). Recently, Aulehla et al. [Wnt3a plays a major role in the segmentation clock controlling somitogenesis. Dev. Cell 4, 395-406] discovered that Axin2 (a gene under the Wnt3a signalling pathway) also oscillates in the presomitic mesoderm (PSM) of mice embryos and proposed some mechanisms through which the Notch and Wnt3a pathways may interact. They further suggested that a decreasing concentration of Wnt3a along the PSM may be the gradient the segmentation clock interacts with to form somites. These results were reviewed by Rida et al. [A notch feeling of somite segmentation and beyond. Dev. Biol. 265, 2-22], who introduced a complex clockwork comprising genes Hes1, Lfng (under the Notch pathway), and Axin2, as well as their multiple interactions. In the present work we develop a mathematical model based on the Rida et al. review and use it to tackle some of the questions raided by the Aulehla et al. paper: can the Axin2 feedback loop constitute a clock? Could a decreasing Wnt3a signaling constitute the wavefront, where phase is recorded and the spatial pattern laid down? What is the master oscillator?

  19. Visualization of ultradeformable liposomes penetration pathways and their skin interaction by confocal laser scanning microscopy.

    PubMed

    Subongkot, Thirapit; Wonglertnirant, Nanthida; Songprakhon, Pucharee; Rojanarata, Theerasak; Opanasopit, Praneet; Ngawhirunpat, Tanasait

    2013-01-30

    The objective of this study was to elucidate the skin penetration pathway of the generated ultradeformable liposomes (ULs) with terpenes for transdermal drug delivery of fluorescein sodium (NaFl). ULs with d-limonene were selected to investigate the penetration pathways and vesicle-skin interaction in terms of release and attachment processes via Confocal Laser Scanning Microscopy (CLSM). A co-localization technique was employed to visualize the skin penetration behavior of UL-labeled red fluorescence (Rh-PE) and fluorescence-entrapped drug (NaFl) through porcine skin. Our results suggested that ULs with entrapped drug might attach to any part of the skin before releasing the entrapped drug into the skin. Most ULs and entrapped drug penetrated through hair follicles more than through the nonfollicular region. In summary, the transfollicular pathway was the major penetration pathway of ULs with d-limonene for transdermal drug delivery of NaFl, whereas the intercellular and transcellular pathways were the minor penetration pathways.

  20. Differential interactions of sex pheromone and plant odour in the olfactory pathway of a male moth.

    PubMed

    Deisig, Nina; Kropf, Jan; Vitecek, Simon; Pevergne, Delphine; Rouyar, Angela; Sandoz, Jean-Christophe; Lucas, Philippe; Gadenne, Christophe; Anton, Sylvia; Barrozo, Romina

    2012-01-01

    Most animals rely on olfaction to find sexual partners, food or a habitat. The olfactory system faces the challenge of extracting meaningful information from a noisy odorous environment. In most moth species, males respond to sex pheromone emitted by females in an environment with abundant plant volatiles. Plant odours could either facilitate the localization of females (females calling on host plants), mask the female pheromone or they could be neutral without any effect on the pheromone. Here we studied how mixtures of a behaviourally-attractive floral odour, heptanal, and the sex pheromone are encoded at different levels of the olfactory pathway in males of the noctuid moth Agrotis ipsilon. In addition, we asked how interactions between the two odorants change as a function of the males' mating status. We investigated mixture detection in both the pheromone-specific and in the general odorant pathway. We used a) recordings from individual sensilla to study responses of olfactory receptor neurons, b) in vivo calcium imaging with a bath-applied dye to characterize the global input response in the primary olfactory centre, the antennal lobe and c) intracellular recordings of antennal lobe output neurons, projection neurons, in virgin and newly-mated males. Our results show that heptanal reduces pheromone sensitivity at the peripheral and central olfactory level independently of the mating status. Contrarily, heptanal-responding olfactory receptor neurons are not influenced by pheromone in a mixture, although some post-mating modulation occurs at the input of the sexually isomorphic ordinary glomeruli, where general odours are processed within the antennal lobe. The results are discussed in the context of mate localization.

  1. Differential Interactions of Sex Pheromone and Plant Odour in the Olfactory Pathway of a Male Moth

    PubMed Central

    Deisig, Nina; Kropf, Jan; Vitecek, Simon; Pevergne, Delphine; Rouyar, Angela; Sandoz, Jean-Christophe; Lucas, Philippe; Gadenne, Christophe

    2012-01-01

    Most animals rely on olfaction to find sexual partners, food or a habitat. The olfactory system faces the challenge of extracting meaningful information from a noisy odorous environment. In most moth species, males respond to sex pheromone emitted by females in an environment with abundant plant volatiles. Plant odours could either facilitate the localization of females (females calling on host plants), mask the female pheromone or they could be neutral without any effect on the pheromone. Here we studied how mixtures of a behaviourally-attractive floral odour, heptanal, and the sex pheromone are encoded at different levels of the olfactory pathway in males of the noctuid moth Agrotis ipsilon. In addition, we asked how interactions between the two odorants change as a function of the males' mating status. We investigated mixture detection in both the pheromone-specific and in the general odorant pathway. We used a) recordings from individual sensilla to study responses of olfactory receptor neurons, b) in vivo calcium imaging with a bath-applied dye to characterize the global input response in the primary olfactory centre, the antennal lobe and c) intracellular recordings of antennal lobe output neurons, projection neurons, in virgin and newly-mated males. Our results show that heptanal reduces pheromone sensitivity at the peripheral and central olfactory level independently of the mating status. Contrarily, heptanal-responding olfactory receptor neurons are not influenced by pheromone in a mixture, although some post-mating modulation occurs at the input of the sexually isomorphic ordinary glomeruli, where general odours are processed within the antennal lobe. The results are discussed in the context of mate localization. PMID:22427979

  2. Direct interaction of garcinol and related polyisoprenylated benzophenones of Garcinia cambogia fruits with the transcription factor STAT-1 as a likely mechanism of their inhibitory effect on cytokine signaling pathways.

    PubMed

    Masullo, Milena; Menegazzi, Marta; Di Micco, Simone; Beffy, Pascale; Bifulco, Giuseppe; Dal Bosco, Martina; Novelli, Michela; Pizza, Cosimo; Masiello, Pellegrino; Piacente, Sonia

    2014-03-28

    Garcinol (1), a polyisoprenylated benzophenone occurring in Garcinia species, has been reported to exert anti-inflammatory activity in LPS-stimulated macrophages, through inhibition of NF-κB and/or JAK/STAT-1 activation. In order to provide deeper insight into its effects on the cytokine signaling pathway and to clarify the underlying molecular mechanisms, 1 was isolated from the fruits of Garcinia cambogia along with two other polyisoprenylated benzophenones, guttiferones K (2) and guttiferone M (3), differing from each other in their isoprenyl moieties and their positions on the benzophenone core. The affinities of 1-3 for the STAT-1 protein have been evaluated by surface plasmon resonance and molecular docking studies and resulted in KD values in the micromolar range. Consistent with the observed high affinity toward the STAT-1 protein, garcinol and guttiferones K and M were able to modulate cytokine signaling in different cultured cell lines, mainly by inhibiting STAT-1 nuclear transfer and DNA binding, as assessed by an electrophorectic mobility shift assay.

  3. Ehrlichia chaffeensis Exploits Host SUMOylation Pathways To Mediate Effector-Host Interactions and Promote Intracellular Survival

    PubMed Central

    Dunphy, Paige Selvy; Luo, Tian

    2014-01-01

    Ehrlichia chaffeensis is an obligately intracellular Gram-negative bacterium that selectively infects mononuclear phagocytes. We recently reported that E. chaffeensis utilizes a type 1 secretion (T1S) system to export tandem repeat protein (TRP) effectors and demonstrated that these effectors interact with a functionally diverse array of host proteins. By way of these interactions, TRP effectors modulate host cell functions; however, the molecular basis of these interactions and their roles in ehrlichial pathobiology are not well defined. In this study, we describe the first bacterial protein posttranslational modification (PTM) by the small ubiquitin-like modifier (SUMO). The E. chaffeensis T1S effector TRP120 is conjugated to SUMO at a carboxy-terminal canonical consensus SUMO conjugation motif in vitro and in human cells. In human cells, TRP120 was selectively conjugated with SUMO2/3 isoforms. Disruption of TRP120 SUMOylation perturbed interactions with known host proteins, through predicted SUMO interaction motif-dependent and -independent mechanisms. E. chaffeensis infection did not result in dramatic changes in the global host SUMOylated protein profile, but a robust colocalization of predominately SUMO1 with ehrlichial inclusions was observed. Inhibiting the SUMO pathway with a small-molecule inhibitor had a significant impact on E. chaffeensis replication and recruitment of the TRP120-interacting protein polycomb group ring finger protein 5 (PCGF5) to the inclusion, indicating that the SUMO pathway is critical for intracellular survival. This study reveals the novel exploitation of the SUMO pathway by Ehrlichia, which facilitates effector-eukaryote interactions necessary to usurp the host and create a permissive intracellular niche. PMID:25047847

  4. The role of hydrogen-bonding interactions in acidic sugar reaction pathways.

    PubMed

    Qian, Xianghong; Johnson, David K; Himmel, Michael E; Nimlos, Mark R

    2010-09-03

    Previously, theoretical multiple sugar (beta-d-xylose and beta-d-glucose) reaction pathways were discovered that depended on the initial protonation site on the sugar molecules using Car-Parrinello-based molecular dynamics (CPMD) simulations [Qian, X. H.; Nimlos, M. R.; Davis, M.; Johnson, D. K.; Himmel, M. E. Carbohydr. Res.2005, 340, 2319-2327]. In addition, simulation results showed that water molecules could participate in the sugar reactions, thus altering the reaction pathways. In the present study, the temperature and water density effects on the sugar degradation pathways were investigated with CPMD. We found that changes in both temperature and water density could profoundly affect the mechanisms and pathways. We attributed these effects to both the strength of hydrogen bonding and proton affinity of water.

  5. The Cardiopulmonary Effects of Ambient Air Pollution and Mechanistic Pathways: A Comparative Hierarchical Pathway Analysis

    PubMed Central

    Thomas, Duncan C.; Zhang, Junfeng; Kipen, Howard M.; Rich, David Q.; Zhu, Tong; Huang, Wei; Hu, Min; Wang, Guangfa; Wang, Yuedan; Zhu, Ping; Lu, Shou-En; Ohman-Strickland, Pamela; Diehl, Scott R.; Eckel, Sandrah P.

    2014-01-01

    Previous studies have investigated the associations between exposure to ambient air pollution and biomarkers of physiological pathways, yet little has been done on the comparison across biomarkers of different pathways to establish the temporal pattern of biological response. In the current study, we aim to compare the relative temporal patterns in responses of candidate pathways to different pollutants. Four biomarkers of pulmonary inflammation and oxidative stress, five biomarkers of systemic inflammation and oxidative stress, ten parameters of autonomic function, and three biomarkers of hemostasis were repeatedly measured in 125 young adults, along with daily concentrations of ambient CO, PM2.5, NO2, SO2, EC, OC, and sulfate, before, during, and after the Beijing Olympics. We used a two-stage modeling approach, including Stage I models to estimate the association between each biomarker and pollutant over each of 7 lags, and Stage II mixed-effect models to describe temporal patterns in the associations when grouping the biomarkers into the four physiological pathways. Our results show that candidate pathway groupings of biomarkers explained a significant amount of variation in the associations for each pollutant, and the temporal patterns of the biomarker-pollutant-lag associations varied across candidate pathways (p<0.0001) and were not linear (from lag 0 to lag 3: p = 0.0629, from lag 3 to lag 6: p = 0.0005). These findings suggest that, among this healthy young adult population, the pulmonary inflammation and oxidative stress pathway is the first to respond to ambient air pollution exposure (within 24 hours) and the hemostasis pathway responds gradually over a 2–3 day period. The initial pulmonary response may contribute to the more gradual systemic changes that likely ultimately involve the cardiovascular system. PMID:25502951

  6. Vasoactive Intestinal Peptide modulates trophoblast-derived cell line function and interaction with phagocytic cells through autocrine pathways

    PubMed Central

    Vota, Daiana; Paparini, Daniel; Hauk, Vanesa; Toro, Ayelén; Merech, Fatima; Varone, Cecilia; Ramhorst, Rosanna; Pérez Leirós, Claudia

    2016-01-01

    Trophoblast cells migrate and invade the decidual stroma in a tightly regulated process to maintain immune homeostasis at the maternal-placental interface during the first weeks of pregnancy. Locally synthesized factors modulate trophoblast cell function and their interaction with maternal leukocytes to promote the silent clearance of apoptotic cells. The vasoactive intestinal peptide (VIP) is a pleiotropic polypeptide with trophic and anti-inflammatory effects in murine pregnancy models. We explored the effect of VIP on two human first trimester trophoblast cell lines, particularly on their migration, invasiveness and interaction with phagocytic cells, and the signalling and regulatory pathways involved. We found that VIP enhanced trophoblast cell migration and invasion through the activation of high affinity VPAC receptors and PKA-CRE signalling pathways. VIP knocked-down trophoblast cells showed reduced migration in basal and leukemic inhibitor factor (LIF)-elicited conditions. In parallel, VIP-silenced trophoblast cells failed to induce the phagocytosis of apoptotic bodies and the expression of immunosuppressant markers by human monocytes. Our results suggest that VIP-mediated autocrine pathways regulate trophoblast cell function and contribute to immune homeostasis maintenance at placentation and may provide new clues for therapeutic intervention in pregnancies complicated by defective deep placentation. PMID:27212399

  7. Differentially expressed genes and interacting pathways in bladder cancer revealed by bioinformatic analysis.

    PubMed

    Shen, Yinzhou; Wang, Xuelei; Jin, Yongchao; Lu, Jiasun; Qiu, Guangming; Wen, Xiaofei

    2014-10-01

    The goal of this study was to identify cancer-associated differentially expressed genes (DEGs), analyze their biological functions and investigate the mechanism(s) of cancer occurrence and development, which may provide a theoretical foundation for bladder cancer (BCa) therapy. We downloaded the mRNA expression profiling dataset GSE13507 from the Gene Expression Omnibus database; the dataset includes 165 BCa and 68 control samples. T‑tests were used to identify DEGs. To further study the biological functions of the identified DEGs, we performed a Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Next, we built a network of potentially interacting pathways to study the synergistic relationships among DEGs. A total of 12,105 genes were identified as DEGs, of which 5,239 were upregulated and 6,866 were downregulated in BCa. The DEGs encoding activator protein 1 (AP-1), nuclear factor of activated T-cells (NFAT) proteins, nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) and interleukin (IL)-10 were revealed to participate in the significantly enriched immune pathways that were downregulated in BCa. KEGG enrichment analysis revealed 7 significantly upregulated and 47 significantly downregulated pathways enriched among the DEGs. We found a crosstalk interaction among a total of 44 pathways in the network of BCa-affected pathways. In conclusion, our results show that BCa involves dysfunctions in multiple systems. Our study is expected to pave ways for immune and inflammatory research and provide molecular insights for cancer therapy.

  8. O/S-1/ interactions - The product channels. [collisional electron quenching and chemical reaction pathway frequencies

    NASA Technical Reports Server (NTRS)

    Slanger, T. G.; Black, G.

    1978-01-01

    The first measurements are reported of the reaction pathways for the interaction between oxygen atoms in the 4.19 eV S-1 state, and four molecules, N2O, CO2, H2O, and NO. Distinction is made between three possible paths - quenching to O(D-1), quenching to O(P-3), and chemical reaction. With N2O, the most reasonable interpretation of the data indicates that there no reaction, in sharp contrast with the interaction between O(D-1) and N2O, which proceeds entirely by reaction. Similarly, there is no reaction with CO2. With H2O, the reactive pathway is the dominant one, although electronic quenching is not negligible. With NO, O(D-1) is the preferred product.

  9. O/S-1/ interactions - The product channels. [collisional electron quenching and chemical reaction pathway frequencies

    NASA Technical Reports Server (NTRS)

    Slanger, T. G.; Black, G.

    1978-01-01

    The first measurements are reported of the reaction pathways for the interaction between oxygen atoms in the 4.19 eV S-1 state, and four molecules, N2O, CO2, H2O, and NO. Distinction is made between three possible paths - quenching to O(D-1), quenching to O(P-3), and chemical reaction. With N2O, the most reasonable interpretation of the data indicates that there no reaction, in sharp contrast with the interaction between O(D-1) and N2O, which proceeds entirely by reaction. Similarly, there is no reaction with CO2. With H2O, the reactive pathway is the dominant one, although electronic quenching is not negligible. With NO, O(D-1) is the preferred product.

  10. Neuroplasticity pathways and protein-interaction networks are modulated by vortioxetine in rodents.

    PubMed

    Waller, Jessica A; Nygaard, Sara Holm; Li, Yan; du Jardin, Kristian Gaarn; Tamm, Joseph A; Abdourahman, Aicha; Elfving, Betina; Pehrson, Alan L; Sánchez, Connie; Wernersson, Rasmus

    2017-08-04

    The identification of biomarkers that predict susceptibility to major depressive disorder and treatment response to antidepressants is a major challenge. Vortioxetine is a novel multimodal antidepressant that possesses pro-cognitive properties and differentiates from other conventional antidepressants on various cognitive and plasticity measures. The aim of the present study was to identify biological systems rather than single biomarkers that may underlie vortioxetine's treatment effects. We show that the biological systems regulated by vortioxetine are overlapping between mouse and rat in response to distinct treatment regimens and in different brain regions. Furthermore, analysis of complexes of physically-interacting proteins reveal that biomarkers involved in transcriptional regulation, neurodevelopment, neuroplasticity, and endocytosis are modulated by vortioxetine. A subsequent qPCR study examining the expression of targets in the protein-protein interactome space in response to chronic vortioxetine treatment over a range of doses provides further biological validation that vortioxetine engages neuroplasticity networks. Thus, the same biology is regulated in different species and sexes, different brain regions, and in response to distinct routes of administration and regimens. A recurring theme, based on the present study as well as previous findings, is that networks related to synaptic plasticity, synaptic transmission, signal transduction, and neurodevelopment are modulated in response to vortioxetine treatment. Regulation of these signaling pathways by vortioxetine may underlie vortioxetine's cognitive-enhancing properties.

  11. Interaction effects in comorbid psychopathology.

    PubMed

    Keeley, Jared W; Chmielewski, Michael S; Bagby, R Michael

    2015-07-01

    Comorbidity in psychopathology is the norm. Despite some initial evidence, few studies have examined if the presence of comorbid conditions changes the expression of the pathology, either through increased severity of the syndrome(s) or by expanding to symptoms beyond the syndrome(s) (i.e., symptom overextension). The following report provides an illustration of interactive effects and overextension in comorbid pathology. A large pool of patients from a university hospital were assessed using SCID-I/P interviews. Of these, 230 patients diagnosed with major depressive disorder, social phobia, or both were included in the study. Symptoms not belonging to either index condition (major depressive disorder or social phobia) reliably overextended in comorbid cases (odds ratios between 2.82 and 15.75). Current research methodologies (e.g., structured interviews) do not allow for the examination of overextended symptoms. The authors make a call for future psychopathological research to search systematically for interactive effects by adopting more inclusive or flexible assessments. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Interaction between glutamate dehydrogenase (GDH) and L-leucine catabolic enzymes: intersecting metabolic pathways.

    PubMed

    Hutson, Susan M; Islam, Mohammad Mainul; Zaganas, Ioannis

    2011-09-01

    Branched-chain amino acids (BCAAs) catabolism follows sequential reactions and their metabolites intersect with other metabolic pathways. The initial enzymes in BCAA metabolism, the mitochondrial branched-chain aminotransferase (BCATm), which deaminates the BCAAs to branched-chain α-keto acids (BCKAs); and the branched-chain α-keto acid dehydrogenase enzyme complex (BCKDC), which oxidatively decarboxylates the BCKAs, are organized in a supramolecular complex termed metabolon. Glutamate dehydrogenase (GDH1) is found in the metabolon in rat tissues. Bovine GDH1 binds to the pyridoxamine 5'-phosphate (PMP)-form of human BCATm (PMP-BCATm) but not to pyridoxal 5'-phosphate (PLP)-BCATm in vitro. This protein interaction facilitates reamination of the α-ketoglutarate (αKG) product of the GDH1 oxidative deamination reaction. Human GDH1 appears to act like bovine GDH1 but human GDH2 does not show the same enhancement of BCKDC enzyme activities. Another metabolic enzyme is also found in the metabolon is pyruvate carboxylase (PC). Kinetic results suggest that PC binds to the E1 decarboxylase of BCKDC but does not effect BCAA catabolism. The protein interaction of BCATm and GDH1 promotes regeneration of PLP-BCATm which then binds to BCKDC resulting in channeling of the BCKA products from BCATm first half reaction to E1 and promoting BCAA oxidation and net nitrogen transfer from BCAAs. The cycling of nitrogen through glutamate via the actions of BCATm and GDH1 releases free ammonia. Formation of ammonia may be important for astrocyte glutamine synthesis in the central nervous system. In peripheral tissue association of BCATm and GDH1 would promote BCAA oxidation at physiologically relevant BCAA concentrations.

  13. Special issue: redox active natural products and their interaction with cellular signalling pathways.

    PubMed

    Jacob, Claus

    2014-11-26

    During the last decade, research into natural products has experienced a certain renaissance. The urgent need for more and more effective antibiotics in medicine, the demand for ecologically friendly plant protectants in agriculture, "natural" cosmetics and the issue of a sustainable and healthy nutrition in an ageing society have fuelled research into Nature's treasure chest of "green gold". Here, redox active secondary metabolites from plants, fungi, bacteria and other (micro-)organisms often have been at the forefront of the most interesting developments. These agents provide powerful means to interfere with many, probably most cellular signaling pathways in humans, animals and lower organisms, and therefore can be used to protect, i.e., in form of antioxidants, and to frighten off or even kill, i.e., in form of repellants, antibiotics, fungicides and selective, often catalytic "sensor/effector" anticancer agents. Interestingly, whilst natural product research dates back many decades, in some cases even centuries, and compounds such as allicin and various flavonoids have been investigated thoroughly in the past, it has only recently become possible to investigate their precise interactions and mode(s) of action inside living cells. Here, fluorescent staining and labelling on the one side, and appropriate detection, either qualitatively under the microscope or quantitatively in flow cytometers and plate readers, on the other, enable researchers to obtain the various pieces of information necessary to construct a fairly complete puzzle of how such compounds act and interact in living cells. Complemented by the more traditional activity assays and Western Blots, and increasingly joined by techniques such as proteomics, chemogenetic screening and mRNA profiling, these cell based bioanalytical techniques form a powerful platform for "intracellular diagnostics". In the case of redox active compounds, especially of Reactive Sulfur Species (RSS), such techniques have

  14. Chlamydial histone-DNA interactions are disrupted by a metabolite in the methylerythritol phosphate pathway of isoprenoid biosynthesis.

    PubMed

    Grieshaber, Nicole A; Fischer, Elizabeth R; Mead, David J; Dooley, Cheryl A; Hackstadt, Ted

    2004-05-11

    The chlamydial developmental cycle is characterized by an intracellular replicative form, termed the reticulate body, and an extracellular form called the elementary body. Elementary bodies are characterized by a condensed chromatin, which is maintained by a histone H1-like protein, Hc1. Differentiation of elementary bodies to reticulate bodies is accompanied by dispersal of the chromatin as chlamydiae become transcriptionally active, although the mechanisms of Hc1 release from DNA have remained unknown. Dissociation of the nucleoid requires chlamydial transcription and translation with negligible loss of Hc1. A genetic screen was therefore designed to identify chlamydial genes rescuing Escherichia coli from the lethal effects of Hc1 overexpression. CT804, a gene homologous to ispE, which encodes an intermediate enzyme of the non-mevalonate methylerythritol phosphate (MEP) pathway of isoprenoid biosynthesis, was selected. E. coli coexpressing CT804 and Hc1 grew normally, although they expressed Hc1 to a level equivalent to that which condensed the chromatin of parent Hc1-expressing controls. Inhibition of the MEP pathway with fosmidomycin abolished IspE rescue of Hc1-expressing E. coli. Deproteinated extract from IspE-expressing bacteria caused dispersal of purified chlamydial nucleoids, suggesting that chlamydial histone-DNA interactions are disrupted by a small metabolite within the MEP pathway rather than by direct action of IspE. By partial reconstruction of the MEP pathway, we determined that 2-C-methylerythritol 2,4-cyclodiphosphate dissociated Hc1 from chlamydial chromatin. These results suggest that chlamydial histone-DNA interactions are disrupted upon germination by a small metabolite in the MEP pathway of isoprenoid biosynthesis.

  15. Pathway-Driven Approaches of Interaction between Oxidative Balance and Genetic Polymorphism on Metabolic Syndrome

    PubMed Central

    2017-01-01

    Despite evidences of association between basic redox biology and metabolic syndrome (MetS), few studies have evaluated indices that account for multiple oxidative effectors for MetS. Oxidative balance score (OBS) has indicated the role of oxidative stress in chronic disease pathophysiology. In this study, we evaluated OBS as an oxidative balance indicator for estimating risk of MetS with 6414 study participants. OBS is a multiple exogenous factor score for development of disease; therefore, we investigated interplay between oxidative balance and genetic variation for development of MetS focusing on biological pathways by using gene-set-enrichment analysis. As a result, participants in the highest quartile of OBS were less likely to be at risk for MetS than those in the lowest quartile. In addition, persons in the highest quartile of OBS had the lowest level of inflammatory markers including C-reactive protein and WBC. With GWAS-based pathway analysis, we found that VEGF signaling pathway, glutathione metabolism, and Rac-1 pathway were significantly enriched biological pathways involved with OBS on MetS. These findings suggested that mechanism of angiogenesis, oxidative stress, and inflammation can be involved in interaction between OBS and genetic variation on risk of MetS. PMID:28191276

  16. [Cell signaling pathways interaction in cellular proliferation: Potential target for therapeutic interventionism].

    PubMed

    Valdespino-Gómez, Víctor Manuel; Valdespino-Castillo, Patricia Margarita; Valdespino-Castillo, Víctor Edmundo

    2015-01-01

    Nowadays, cellular physiology is best understood by analysing their interacting molecular components. Proteins are the major components of the cells. Different proteins are organised in the form of functional clusters, pathways or networks. These molecules are ordered in clusters of receptor molecules of extracellular signals, transducers, sensors and biological response effectors. The identification of these intracellular signaling pathways in different cellular types has required a long journey of experimental work. More than 300 intracellular signaling pathways have been identified in human cells. They participate in cell homeostasis processes for structural and functional maintenance. Some of them participate simultaneously or in a nearly-consecutive progression to generate a cellular phenotypic change. In this review, an analysis is performed on the main intracellular signaling pathways that take part in the cellular proliferation process, and the potential use of some components of these pathways as target for therapeutic interventionism are also underlined. Copyright © 2015 Academia Mexicana de Cirugía A.C. Published by Masson Doyma México S.A. All rights reserved.

  17. A large scale Huntingtin protein interaction network implicates Rho GTPase signaling pathways in Huntington disease.

    PubMed

    Tourette, Cendrine; Li, Biao; Bell, Russell; O'Hare, Shannon; Kaltenbach, Linda S; Mooney, Sean D; Hughes, Robert E

    2014-03-07

    Huntington disease (HD) is an inherited neurodegenerative disease caused by a CAG expansion in the HTT gene. Using yeast two-hybrid methods, we identified a large set of proteins that interact with huntingtin (HTT)-interacting proteins. This network, composed of HTT-interacting proteins (HIPs) and proteins interacting with these primary nodes, contains 3235 interactions among 2141 highly interconnected proteins. Analysis of functional annotations of these proteins indicates that primary and secondary HIPs are enriched in pathways implicated in HD, including mammalian target of rapamycin, Rho GTPase signaling, and oxidative stress response. To validate roles for HIPs in mutant HTT toxicity, we show that the Rho GTPase signaling components, BAIAP2, EZR, PIK3R1, PAK2, and RAC1, are modifiers of mutant HTT toxicity. We also demonstrate that Htt co-localizes with BAIAP2 in filopodia and that mutant HTT interferes with filopodial dynamics. These data indicate that HTT is involved directly in membrane dynamics, cell attachment, and motility. Furthermore, they implicate dysregulation in these pathways as pathological mechanisms in HD.

  18. Association analysis of the perturbation of interactions in biological pathways and anticancer drug activity.

    PubMed

    Lee, Junehawk; Lee, Doheon

    2016-01-29

    Understanding how different genomic mutational landscapes in patients with cancer lead to different responses to anticancer drugs is an important challenge for realizing precision medicine for cancer. Many studies have analyzed the comprehensive anticancer drug-response profiles and genomic profiles of cancer cell lines to identify the relationship between the anticancer drug response and genomic alternations. However, few studies have focused on interpreting these profiles with a network perspective. In this work, we analyzed genomic alterations in cancer cell lines by considering which interactions in the signaling pathway were perturbed by mutations. With our interaction-centric approach, we identified novel interaction/drug response associations for two drugs (afatinib and ixabepilone) for which no gene-centric association could be found. When we compared the performance of classifiers for predicting the responses to 164 drugs, the classifiers trained with interaction-centric features outperformed the classifiers trained with gene-centric features, despite the smaller number of features (p-value = 2.0 × 10(-3)). By incorporating the interaction information from signaling pathways, we revealed associations between genomic alterations and drug responses that could be missed when using a gene-centric approach. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. IDENTIFYING MUTATION SPECIFIC CANCER PATHWAYS USING A STRUCTURALLY RESOLVED PROTEIN INTERACTION NETWORK

    PubMed Central

    ENGIN, H. BILLUR; HOFREE, MATAN; CARTER, HANNAH

    2014-01-01

    Here we present a method for extracting candidate cancer pathways from tumor ‘omics data while explicitly accounting for diverse consequences of mutations for protein interactions. Disease-causing mutations are frequently observed at either core or interface residues mediating protein interactions. Mutations at core residues frequently destabilize protein structure while mutations at interface residues can specifically affect the binding energies of protein-protein interactions. As a result, mutations in a protein may result in distinct interaction profiles and thus have different phenotypic consequences. We describe a protein structure-guided pipeline for extracting interacting protein sets specific to a particular mutation. Of 59 cancer genes with 3D co-complexed structures in the Protein Data Bank, 43 showed evidence of mutations with different functional consequences. Literature survey reciprocated functional predictions specific to distinct mutations on APC, ATRX, BRCA1, CBL and HRAS. Our analysis suggests that accounting for mutation-specific perturbations to cancer pathways will be essential for personalized cancer therapy. PMID:25592571

  20. Glutamate, Ornithine, Arginine, Proline, and Polyamine Metabolic Interactions: The Pathway Is Regulated at the Post-Transcriptional Level

    PubMed Central

    Majumdar, Rajtilak; Barchi, Boubker; Turlapati, Swathi A.; Gagne, Maegan; Minocha, Rakesh; Long, Stephanie; Minocha, Subhash C.

    2016-01-01

    The metabolism of glutamate into ornithine, arginine, proline, and polyamines is a major network of nitrogen-metabolizing pathways in plants, which also produces intermediates like nitric oxide, and γ-aminobutyric acid (GABA) that play critical roles in plant development and stress. While the accumulations of intermediates and the products of this network depend primarily on nitrogen assimilation, the overall regulation of the interacting sub-pathways is not well understood. We tested the hypothesis that diversion of ornithine into polyamine biosynthesis (by transgenic approach) not only plays a role in regulating its own biosynthesis from glutamate but also affects arginine and proline biosynthesis. Using two high putrescine producing lines of Arabidopsis thaliana (containing a transgenic mouse ornithine decarboxylase gene), we studied the: (1) effects of exogenous supply of carbon and nitrogen on polyamines and pools of soluble amino acids; and, (2) expression of genes encoding key enzymes in the interactive pathways of arginine, proline and GABA biosynthesis as well as the catabolism of polyamines. Our findings suggest that: (1) the overall conversion of glutamate to arginine and polyamines is enhanced by increased utilization of ornithine for polyamine biosynthesis by the transgene product; (2) proline and arginine biosynthesis are regulated independently of polyamines and GABA biosynthesis; (3) the expression of most genes (28 that were studied) that encode enzymes of the interacting sub-pathways of arginine and GABA biosynthesis does not change even though overall biosynthesis of Orn from glutamate is increased several fold; and (4) increased polyamine biosynthesis results in increased assimilation of both nitrogen and carbon by the cells. PMID:26909083

  1. The HVC microcircuit: the synaptic basis for interactions between song motor and vocal plasticity pathways.

    PubMed

    Mooney, Richard; Prather, Jonathan F

    2005-02-23

    Synaptic interactions between telencephalic neurons innervating descending motor or basal ganglia pathways are essential in the learning, planning, and execution of complex movements. Synaptic interactions within the songbird telencephalic nucleus HVC are implicated in motor and auditory activity associated with learned vocalizations. HVC contains projection neurons (PNs) (HVC(RA)) that innervate song premotor areas, other PNs (HVC(X)) that innervate a basal ganglia pathway necessary for vocal plasticity, and interneurons (HVC(INT)). During singing, HVC(RA) fire in temporally sparse bursts, possibly because of HVC(INT)-HVC(RA) interactions, and a corollary discharge can be detected in the basal ganglia pathway, likely because of synaptic transmission from HVC(RA) to HVC(X) cells. During song playback, local interactions, including inhibition onto HVC(X) cells, shape highly selective responses that distinguish HVC from its auditory afferents. To better understand the synaptic substrate for the motor and auditory properties of HVC, we made intracellular recordings from pairs of HVC neurons in adult male zebra finch brain slices and used spike-triggered averages to assess synaptic connectivity. A major synaptic interaction between the PNs was a disynaptic inhibition from HVC(RA) to HVC(X), which could link song motor signals in the two outputs of HVC and account for some of the song playback-evoked inhibition in HVC(X) cells. Furthermore, single interneurons made divergent connections onto PNs of both types, and either PN type could form reciprocal connections with interneurons. In these two regards, the synaptic architecture of HVC resembles that described in some pattern-generating networks, underscoring features likely to be important to singing and song learning.

  2. Feedback regulation on PTEN/AKT pathway by the ER stress kinase PERK mediated by interaction with the Vault complex.

    PubMed

    Zhang, Wei; Neo, Suat Peng; Gunaratne, Jayantha; Poulsen, Anders; Boping, Liu; Ong, Esther Hongqian; Sangthongpitag, Kanda; Pendharkar, Vishal; Hill, Jeffrey; Cohen, Stephen M

    2015-03-01

    The high proliferation rate of cancer cells, together with environmental factors such as hypoxia and nutrient deprivation can cause Endoplasmic Reticulum (ER) stress. The protein kinase PERK is an essential mediator in one of the three ER stress response pathways. Genetic and pharmacological inhibition of PERK has been reported to limit tumor growth in xenograft models. Here we provide evidence that inactive PERK interacts with the nuclear pore-associated Vault complex protein and that this compromises Vault-mediated nuclear transport of PTEN. Pharmacological inhibition of PERK under ER stress results is abnormal sequestration of the Vault complex, leading to increased cytoplasmic PTEN activity and lower AKT activation. As the PI3K/PTEN/AKT pathway is crucial for many aspects of cell growth and survival, this unexpected effect of PERK inhibitors on AKT activity may have implications for their potential use as therapeutic agents.

  3. Partial Activation of SA- and JA-Defensive Pathways in Strawberry upon Colletotrichum acutatum Interaction

    PubMed Central

    Amil-Ruiz, Francisco; Garrido-Gala, José; Gadea, José; Blanco-Portales, Rosario; Muñoz-Mérida, Antonio; Trelles, Oswaldo; de los Santos, Berta; Arroyo, Francisco T.; Aguado-Puig, Ana; Romero, Fernando; Mercado, José-Ángel; Pliego-Alfaro, Fernando; Muñoz-Blanco, Juan; Caballero, José L.

    2016-01-01

    Understanding the nature of pathogen host interaction may help improve strawberry (Fragaria × ananassa) cultivars. Plant resistance to pathogenic agents usually operates through a complex network of defense mechanisms mediated by a diverse array of signaling molecules. In strawberry, resistance to a variety of pathogens has been reported to be mostly polygenic and quantitatively inherited, making it difficult to associate molecular markers with disease resistance genes. Colletotrichum acutatum spp. is a major strawberry pathogen, and completely resistant cultivars have not been reported. Moreover, strawberry defense network components and mechanisms remain largely unknown and poorly understood. Assessment of the strawberry response to C. acutatum included a global transcript analysis, and acidic hormones SA and JA measurements were analyzed after challenge with the pathogen. Induction of transcripts corresponding to the SA and JA signaling pathways and key genes controlling major steps within these defense pathways was detected. Accordingly, SA and JA accumulated in strawberry after infection. Contrastingly, induction of several important SA, JA, and oxidative stress-responsive defense genes, including FaPR1-1, FaLOX2, FaJAR1, FaPDF1, and FaGST1, was not detected, which suggests that specific branches in these defense pathways (those leading to FaPR1-2, FaPR2-1, FaPR2-2, FaAOS, FaPR5, and FaPR10) were activated. Our results reveal that specific aspects in SA and JA dependent signaling pathways are activated in strawberry upon interaction with C. acutatum. Certain described defense-associated transcripts related to these two known signaling pathways do not increase in abundance following infection. This finding suggests new insight into a specific putative molecular strategy for defense against this pathogen. PMID:27471515

  4. Partial Activation of SA- and JA-Defensive Pathways in Strawberry upon Colletotrichum acutatum Interaction.

    PubMed

    Amil-Ruiz, Francisco; Garrido-Gala, José; Gadea, José; Blanco-Portales, Rosario; Muñoz-Mérida, Antonio; Trelles, Oswaldo; de Los Santos, Berta; Arroyo, Francisco T; Aguado-Puig, Ana; Romero, Fernando; Mercado, José-Ángel; Pliego-Alfaro, Fernando; Muñoz-Blanco, Juan; Caballero, José L

    2016-01-01

    Understanding the nature of pathogen host interaction may help improve strawberry (Fragaria × ananassa) cultivars. Plant resistance to pathogenic agents usually operates through a complex network of defense mechanisms mediated by a diverse array of signaling molecules. In strawberry, resistance to a variety of pathogens has been reported to be mostly polygenic and quantitatively inherited, making it difficult to associate molecular markers with disease resistance genes. Colletotrichum acutatum spp. is a major strawberry pathogen, and completely resistant cultivars have not been reported. Moreover, strawberry defense network components and mechanisms remain largely unknown and poorly understood. Assessment of the strawberry response to C. acutatum included a global transcript analysis, and acidic hormones SA and JA measurements were analyzed after challenge with the pathogen. Induction of transcripts corresponding to the SA and JA signaling pathways and key genes controlling major steps within these defense pathways was detected. Accordingly, SA and JA accumulated in strawberry after infection. Contrastingly, induction of several important SA, JA, and oxidative stress-responsive defense genes, including FaPR1-1, FaLOX2, FaJAR1, FaPDF1, and FaGST1, was not detected, which suggests that specific branches in these defense pathways (those leading to FaPR1-2, FaPR2-1, FaPR2-2, FaAOS, FaPR5, and FaPR10) were activated. Our results reveal that specific aspects in SA and JA dependent signaling pathways are activated in strawberry upon interaction with C. acutatum. Certain described defense-associated transcripts related to these two known signaling pathways do not increase in abundance following infection. This finding suggests new insight into a specific putative molecular strategy for defense against this pathogen.

  5. Final State Interactions Effects in Neutrino-Nucleus Interactions

    SciTech Connect

    Golan, Tomasz; Juszczak, Cezary; Sobczyk, Jan T.

    2012-07-01

    Final State Interactions effects are discussed in the context of Monte Carlo simulations of neutrino-nucleus interactions. A role of Formation Time is explained and several models describing this effect are compared. Various observables which are sensitive to FSI effects are reviewed including pion-nucleus interaction and hadron yields in backward hemisphere. NuWro Monte Carlo neutrino event generator is described and its ability to understand neutral current $\\pi^0$ production data in $\\sim 1$ GeV neutrino flux experiments is demonstrated.

  6. Interactions among the Imagination, Expertise Reversal, and Element Interactivity Effects

    ERIC Educational Resources Information Center

    Leahy, Wayne; Sweller, John

    2005-01-01

    Interactions among the imagination, expertise reversal, and element interactivity effects were investigated in 2 experiments. In Experiment 1, less knowledgeable primary school students learning to use a bus timetable produced better performance under study than imagination conditions, but an increase in their experience reversed the result,…

  7. Pharmacogenetic predictor of extrapyramidal symptoms induced by antipsychotics: multilocus interaction in the mTOR pathway.

    PubMed

    Mas, S; Gassó, P; Ritter, M A; Malagelada, C; Bernardo, M; Lafuente, A

    2015-01-01

    Antipsychotic (AP) treatment-emergent extrapyramidal symptoms (EPS) are acute adverse reactions of APs. The aim of the present study is to analyze gene-gene interactions in nine genes related to the mTOR pathway, in order to develop genetic predictors of the appearance of EPS. 243 subjects (78 presenting EPS: 165 not) from three cohorts participated in the present study: Cohort 1, patients treated with risperidone, (n=114); Cohort 2, patients treated with APs other than risperidone (n=102); Cohort 3, AP-naïve patients with first-episode psychosis treated with risperidone, paliperidone or amisulpride, n=27. We analyzed gene-gene interactions by multifactor dimensionality reduction assay (MDR). In Cohort 1, we identified a four-way interaction, including the rs1130214 (AKT1), rs456998 (FCHSD1), rs7211818 (Raptor) and rs1053639 (DDIT4), that correctly predicted 97 of the 114 patients (85% accuracy). We validated the predictive power of the four-way interaction in Cohort 2 and in Cohort 3 with 86% and 88% accuracy respectively. We develop and validate a powerful pharmacogenetic predictor of AP-induced EPS. For the first time, the mTOR pathway has been related to EPS susceptibility and AP response. However, validation in larger and independent populations will be necessary for optimal generalization.

  8. Evaluation of the cardiolipin biosynthetic pathway and its interactions in the diabetic heart

    PubMed Central

    Croston, Tara L.; Shepherd, Danielle L.; Thapa, Dharendra; Nichols, Cody E.; Lewis, Sara E.; Dabkowski, Erinne R.; Jagannathan, Rajaganapathi; Baseler, Walter A.; Hollander, John M.

    2013-01-01

    Aims We have previously reported alterations in cardiolipin content and inner mitochondrial membrane (IMM) proteomic make-up specifically in interfibrillar mitochondria (IFM) in the type 1 diabetic heart; however, the mechanism underlying this alteration is unknown. The goal of this study was to determine how the cardiolipin biosynthetic pathway and cardiolipin-IMM protein interactions are impacted by type 1 diabetes mellitus. Main methods Male FVB mice were made diabetic by multiple low-dose streptozotocin injections and sacrificed five weeks post-diabetic onset. Messenger RNA was measured and cardiac mitochondrial subpopulations were isolated. Further mitochondrial functional experimentation included evaluating the protein expression of the enzymes directly responsible for cardiolipin biosynthesis, as well as ATP synthase activity. Interactions between cardiolipin and ATP synthase subunits were also examined. Key findings Western blot analysis revealed a significant decrease in cardiolipin synthase (CRLS) protein content in diabetic IFM, with a concomitant decrease in its activity. ATP synthase activity was also significantly decreased. We identified two novel direct interactions between two subunits of the ATP synthase F0 complex (ATP5F1 and ATP5H), both of which were significantly decreased in diabetic IFM. Significance Overall, these results indicate that type 1 diabetes mellitus negatively impacts the cardiolipin biosynthetic pathway specifically at CRLS, contributing to decreased cardiolipin content and loss of interactions with key ATP synthase F0 complex constituents in the IFM. PMID:23872101

  9. A systems biology approach using metabolomic data reveals genes and pathways interacting to modulate divergent growth in cattle

    PubMed Central

    2013-01-01

    Background Systems biology enables the identification of gene networks that modulate complex traits. Comprehensive metabolomic analyses provide innovative phenotypes that are intermediate between the initiator of genetic variability, the genome, and raw phenotypes that are influenced by a large number of environmental effects. The present study combines two concepts, systems biology and metabolic analyses, in an approach without prior functional hypothesis in order to dissect genes and molecular pathways that modulate differential growth at the onset of puberty in male cattle. Furthermore, this integrative strategy was applied to specifically explore distinctive gene interactions of non-SMC condensin I complex, subunit G (NCAPG) and myostatin (GDF8), known modulators of pre- and postnatal growth that are only partially understood for their molecular pathways affecting differential body weight. Results Our study successfully established gene networks and interacting partners affecting growth at the onset of puberty in cattle. We demonstrated the biological relevance of the created networks by comparison to randomly created networks. Our data showed that GnRH (Gonadotropin-releasing hormone) signaling is associated with divergent growth at the onset of puberty and revealed two highly connected hubs, BTC and DGKH, within the network. Both genes are known to directly interact with the GnRH signaling pathway. Furthermore, a gene interaction network for NCAPG containing 14 densely connected genes revealed novel information concerning the functional role of NCAPG in divergent growth. Conclusions Merging both concepts, systems biology and metabolomic analyses, successfully yielded new insights into gene networks and interacting partners affecting growth at the onset of puberty in cattle. Genetic modulation in GnRH signaling was identified as key modifier of differential cattle growth at the onset of puberty. In addition, the benefit of our innovative concept without prior

  10. Excitability of the human trigeminal motoneuronal pool and interactions with other brainstem reflex pathways

    PubMed Central

    Cruccu, G; Truini, A; Priori, A

    2001-01-01

    We studied the properties of motoneurones and Ia-motoneuronal connections in the human trigeminal system, and their functional interactions with other brainstem reflex pathways mediated by non-muscular (Aβ) afferents. With surface EMG recordings we tested the recovery cycles of the heteronymous H-reflex in the temporalis muscle and the homonymous silent period in the masseter muscle both elicited by stimulation of the masseteric nerve at the infratemporal fossa in nine healthy subjects. In four subjects single motor-unit responses were recorded from the temporalis muscle. In six subjects we also tested the effect of the stimulus to the mental nerve on the temporalis H-reflex and, conversely, the effect of Ia input (stimulus to the masseteric nerve) on the R1 component of the blink reflex in the orbicularis oculi muscle. The recovery cycle of the H-reflex showed a suppression peaking at the 5-20 ms interval; conversely the time course of the masseteric silent period was facilitated at comparable intervals. The inhibition of the test H-reflex was inversely related to the level of background voluntary contraction. Single motor units were unable to fire consistently in response to the test stimulus at intervals shorter than 50 ms. Mental nerve stimulation strongly depressed the H-reflex. The time course of this inhibition coincided with the EMG inhibition elicited by mental nerve stimulation during voluntary contraction. The trigeminal Ia input facilitated the R1 component of the blink reflex when the supraorbital test stimulation preceded the masseteric conditioning stimulation by 2 ms. We conclude that the time course of the recovery cycle of the heteronymous H-reflex in the temporalis muscle reflects the after-hyperpolarization potential (AHP) of trigeminal motoneurones, and that the Ia trigeminal input is integrated with other brainstem reflexes. PMID:11230527

  11. Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks.

    PubMed

    Kirouac, Daniel C; Saez-Rodriguez, Julio; Swantek, Jennifer; Burke, John M; Lauffenburger, Douglas A; Sorger, Peter K

    2012-05-01

    Understanding the information-processing capabilities of signal transduction networks, how those networks are disrupted in disease, and rationally designing therapies to manipulate diseased states require systematic and accurate reconstruction of network topology. Data on networks central to human physiology, such as the inflammatory signalling networks analyzed here, are found in a multiplicity of on-line resources of pathway and interactome databases (Cancer CellMap, GeneGo, KEGG, NCI-Pathway Interactome Database (NCI-PID), PANTHER, Reactome, I2D, and STRING). We sought to determine whether these databases contain overlapping information and whether they can be used to construct high reliability prior knowledge networks for subsequent modeling of experimental data. We have assembled an ensemble network from multiple on-line sources representing a significant portion of all machine-readable and reconcilable human knowledge on proteins and protein interactions involved in inflammation. This ensemble network has many features expected of complex signalling networks assembled from high-throughput data: a power law distribution of both node degree and edge annotations, and topological features of a "bow tie" architecture in which diverse pathways converge on a highly conserved set of enzymatic cascades focused around PI3K/AKT, MAPK/ERK, JAK/STAT, NFκB, and apoptotic signaling. Individual pathways exhibit "fuzzy" modularity that is statistically significant but still involving a majority of "cross-talk" interactions. However, we find that the most widely used pathway databases are highly inconsistent with respect to the actual constituents and interactions in this network. Using a set of growth factor signalling networks as examples (epidermal growth factor, transforming growth factor-beta, tumor necrosis factor, and wingless), we find a multiplicity of network topologies in which receptors couple to downstream components through myriad alternate paths. Many of these

  12. Characterization of MRFAP1 turnover and interactions downstream of the NEDD8 pathway.

    PubMed

    Larance, Mark; Kirkwood, Kathryn J; Xirodimas, Dimitris P; Lundberg, Emma; Uhlen, Mathias; Lamond, Angus I

    2012-03-01

    The NEDD8-Cullin E3 ligase pathway plays an important role in protein homeostasis, in particular the degradation of cell cycle regulators and transcriptional control networks. To characterize NEDD8-cullin target proteins, we performed a quantitative proteomic analysis of cells treated with MLN4924, a small molecule inhibitor of the NEDD8 conjugation pathway. MRFAP1 and its interaction partner, MORF4L1, were among the most up-regulated proteins after NEDD8 inhibition in multiple human cell lines. We show that MRFAP1 has a fast turnover rate in the absence of MLN4924 and is degraded via the ubiquitin-proteasome system. The increased abundance of MRFAP1 after MLN4924 treatment results from a decreased rate of degradation. Characterization of the binding partners of both MRFAP1 and MORF4L1 revealed a complex protein-protein interaction network. MRFAP1 bound to a number of E3 ubiquitin ligases, including CUL4B, but not to components of the NuA4 complex, including MRGBP, which bound to MORF4L1. These data indicate that MRFAP1 may regulate the ability of MORF4L1 to interact with chromatin-modifying enzymes by binding to MORF4L1 in a mutually exclusive manner with MRGBP. Analysis of MRFAP1 expression in human tissues by immunostaining with a MRFAP1-specific antibody revealed that it was detectable in only a small number of tissues, in particular testis and brain. Strikingly, analysis of the seminiferous tubules of the testis showed the highest nuclear staining in the spermatogonia and much weaker staining in the spermatocytes and spermatids. MRGBP was inversely correlated with MRFAP1 expression in these cell types, consistent with an exchange of MORF4L1 interaction partners as cells progress through meiosis in the testis. These data highlight an important new arm of the NEDD8-cullin pathway.

  13. SNP-SNP interaction analysis of NF-κB signaling pathway on breast cancer survival

    PubMed Central

    Jamshidi, Maral; Fagerholm, Rainer; Khan, Sofia; Aittomäki, Kristiina; Czene, Kamila; Darabi, Hatef; Li, Jingmei; Andrulis, Irene L.; Chang-Claude, Jenny; Devilee, Peter; Fasching, Peter A.; Michailidou, Kyriaki; Bolla, Manjeet K.; Dennis, Joe; Wang, Qin; Guo, Qi; Rhenius, Valerie; Cornelissen, Sten; Rudolph, Anja; Knight, Julia A.; Loehberg, Christian R.; Burwinkel, Barbara; Marme, Frederik; Hopper, John L.; Southey, Melissa C.; Bojesen, Stig E.; Flyger, Henrik; Brenner, Hermann; Holleczek, Bernd; Margolin, Sara; Mannermaa, Arto; Kosma, Veli-Matti; Dyck, Laurien Van; Nevelsteen, Ines; Couch, Fergus J.; Olson, Janet E.; Giles, Graham G.; McLean, Catriona; Haiman, Christopher A.; Henderson, Brian E.; Winqvist, Robert; Pylkäs, Katri; Tollenaar, Rob A.E.M.; García-Closas, Montserrat; Figueroa, Jonine; Hooning, Maartje J.; Martens, John W.M.; Cox, Angela; Cross, Simon S.; Simard, Jacques; Dunning, Alison M.; Easton, Douglas F.; Pharoah, Paul D.P.; Hall, Per; Blomqvist, Carl; Schmidt, Marjanka K.; Nevanlinna, Heli

    2015-01-01

    In breast cancer, constitutive activation of NF-κB has been reported, however, the impact of genetic variation of the pathway on patient prognosis has been little studied. Furthermore, a combination of genetic variants, rather than single polymorphisms, may affect disease prognosis. Here, in an extensive dataset (n = 30,431) from the Breast Cancer Association Consortium, we investigated the association of 917 SNPs in 75 genes in the NF-κB pathway with breast cancer prognosis. We explored SNP-SNP interactions on survival using the likelihood-ratio test comparing multivariate Cox’ regression models of SNP pairs without and with an interaction term. We found two interacting pairs associating with prognosis: patients simultaneously homozygous for the rare alleles of rs5996080 and rs7973914 had worse survival (HRinteraction 6.98, 95% CI=3.3-14.4, P = 1.42E-07), and patients carrying at least one rare allele for rs17243893 and rs57890595 had better survival (HRinteraction 0.51, 95% CI=0.3-0.6, P = 2.19E-05). Based on in silico functional analyses and literature, we speculate that the rs5996080 and rs7973914 loci may affect the BAFFR and TNFR1/TNFR3 receptors and breast cancer survival, possibly by disturbing both the canonical and non-canonical NF-κB pathways or their dynamics, whereas, rs17243893-rs57890595 interaction on survival may be mediated through TRAF2-TRAIL-R4 interplay. These results warrant further validation and functional analyses. PMID:26317411

  14. Synergistic interaction between the fibroblast growth factor and bone morphogenetic protein signaling pathways in lens cells.

    PubMed

    Boswell, Bruce A; Musil, Linda S

    2015-07-01

    Fibroblast growth factors (FGFs) play a central role in two processes essential for lens transparency--fiber cell differentiation and gap junction-mediated intercellular communication (GJIC). Using serum-free primary cultures of chick lens epithelial cells (DCDMLs), we investigated how the FGF and bone morphogenetic protein (BMP) signaling pathways positively cooperate to regulate lens development and function. We found that culturing DCDMLs for 6 d with the BMP blocker noggin inhibits the canonical FGF-to-ERK pathway upstream of FRS2 activation and also prevents FGF from stimulating FRS2- and ERK-independent gene expression, indicating that BMP signaling is required at the level of FGF receptors. Other experiments revealed a second type of BMP/FGF interaction by which FGF promotes expression of BMP target genes as well as of BMP4. Together these studies reveal a novel mode of cooperation between the FGF and BMP pathways in which BMP keeps lens cells in an optimally FGF-responsive state and, reciprocally, FGF enhances BMP-mediated gene expression. This interaction provides a mechanistic explanation for why disruption of either FGF or BMP signaling in the lens leads to defects in lens development and function.

  15. Reciprocal regulatory interactions between the Notch and Ras signaling pathways in the Drosophila embryonic mesoderm.

    PubMed

    Carmena, Ana; Buff, Eugene; Halfon, Marc S; Gisselbrecht, Stephen; Jiménez, Fernando; Baylies, Mary K; Michelson, Alan M

    2002-04-15

    Convergent intercellular signals must be precisely integrated in order to elicit specific biological responses. During specification of muscle and cardiac progenitors from clusters of equivalent cells in the Drosophila embryonic mesoderm, the Ras/MAPK pathway--activated by both epidermal and fibroblast growth factor receptors--functions as an inductive cellular determination signal, while lateral inhibition mediated by Notch antagonizes this activity. A critical balance between these signals must be achieved to enable one cell of an equivalence group to segregate as a progenitor while its neighbors assume a nonprogenitor identity. We have investigated whether these opposing signals directly interact with each other, and we have examined how they are integrated by the responding cells to specify their unique fates. Our findings reveal that Ras and Notch do not function independently; rather, we have uncovered several modes of cross-talk between these pathways. Ras induces Notch, its ligand Delta, and the epidermal growth factor receptor antagonist, Argos. We show that Delta and Argos then synergize to nonautonomously block a positive autoregulatory feedback loop that amplifies a fate-inducing Ras signal. This feedback loop is characterized by Ras-mediated upregulation of proximal components of both the epidermal and fibroblast growth factor receptor pathways. In turn, Notch activation in nonprogenitors induces its own expression and simultaneously suppresses both Delta and Argos levels, thereby reinforcing a unidirectional inhibitory response. These reciprocal interactions combine to generate the signal thresholds that are essential for proper specification of progenitors and nonprogenitors from groups of initially equivalent cells.

  16. Paradigms and paradox in the ethylene signaling pathway and interaction network.

    PubMed

    Zhao, Qiong; Guo, Hong-Wei

    2011-07-01

    Phytohormone ethylene plays pivotal roles in plant response to developmental and environmental signals. During the past few years, the emerging evidence has led us to a new understanding of the signaling mechanisms and regulatory networks of the ethylene action. In this review, we focus on the major advances made in the past three years, particularly the findings leading to new paradigms and the observations under debate. With the recent demonstration of the regulation of the protein stability of numerous key signaling components including EIN3, EIL1, EIN2, ETR2, EBF1/EBF2, and ETP1/ETP2, we highlight proteasome-dependent protein degradation as an essential regulatory mechanism that is widely adopted in the ethylene signaling pathway. We also discuss the implication of the negative feedback mechanism in the ethylene signaling pathway in light of ethylene-induced ETR2 and EBF2 gene expression. Meanwhile, we summarize the controversy on the involvement of MKK9-MPK3/6 cascade in the ethylene signaling versus biosynthesis pathway, and discuss the possible role of this MAPK module in the ethylene action. Finally, we describe the complex interactions between ethylene and other signaling pathways including auxin, light, and plant innate immunity, and propose that EIN3/EIL1 act as a convergence point in the ethylene-initiated signaling network.

  17. [Cognition-Emotion Interactions and Psychopathic Personality: Distinct Pathways to Antisocial and Violent Behavior].

    PubMed

    Verona, Edelyn

    Researchers have long acknowledged heterogeneity among persons who exhibit antisocial and violent behaviours. The study of psychopathic personality or psychopathy can help elucidate this heterogeneity through examination of the different facets that constitute this disorder. In particular, the distinct correlates of the interpersonal-affective traits (Factor 1) and the impulsive-antisocial traits (Factor 2) of psychopathy suggest at least two possible pathways to antisocial behaviours. Building on basic studies in cognitive and affective neuroscience, we provide a focused, non-comprehensive review of work identifying the biopsychological mechanisms involved in these two pathways, with special attention to studies using event-related potential (ERP) methods. In specific, a series of studies are discussed which examined affective and cognitive processes that may distinguish offenders high on psychopathic traits from other offenders, with emphasis on alterations in emotion-cognition interactions related to each factor of psychopathy. The set of findings reviewed highlight a central conclusion: Factor 1 represents a pathway involving reduced emotional responding, exacerbated by attentional abnormalities, that make for a more deliberate and emotionally insensitive offender profile. In contrast, Factor 2 characterizes a pathway marked by emotional and behavioural dysregulation and cognitive control dysfunctions, particularly in emotional contexts. Implications for identifying etiological processes and the further understanding of antisocial and violent behaviours are discussed.

  18. Interaction of dietary polyphenols with molecular signaling pathways of antiestrogen resistance: possible role in breast cancer recurrence.

    PubMed

    Aiyer, Harini S; Bouker, Kerrie B; Cook, Katherine L; Facey, Caroline O B; Hu, Rong; Schwartz, Jessica L; Shajahan, Ayesha N; Hilakivi-Clarke, Leena; Clarke, Robert

    2012-04-01

    Abstract Breast cancer is the most common cancer diagnosed in women and its global incidence is rising rapidly. Adjuvant hormonal therapy, with antiestrogens (AE) such as tamoxifen and fulvestrant, is highly effective in the treatment of estrogen receptor-positive (ER+) breast cancers and is largely responsible for the increase in survival rates seen in the past four decades. However, nearly 50% of women with ER+ cancer display de novo or acquired resistance to AE therapies. Potential molecular mechanisms driving the resistance phenotype are beginning to be elucidated, allowing further development of more effective therapeutic and preventive strategies to reduce the overall mortality due to breast cancer. Over 70% of breast cancer survivors surveyed report increasing their comsumption of fruits, vegetables, and natural product supplements upon diagnosis. These are rich sources of dietary polyphenols (PPs) that can interact with cell-signaling pathways involved in the development of AE resistance. However, research on mechanisms by which these agents may affect AE resistance and whether PP intake can significantly change breast cancer recurrence is limited. We summarize the available data on the effects of PPs on breast cancer recurrence and the interactions of these compounds with some of the signaling pathways hypothesized to drive cell death and survival involved in the development of AE resistance in breast cancer.

  19. Consortium analysis of gene and gene-folate interactions in purine and pyrimidine metabolism pathways with ovarian carcinoma risk

    PubMed Central

    Kelemen, Linda E.; Terry, Kathryn L.; Goodman, Marc T.; Webb, Penelope M.; Bandera, Elisa V.; McGuire, Valerie; Rossing, Mary Anne; Wang, Qinggang; Dicks, Ed; Tyrer, Jonathan P.; Song, Honglin; Kupryjanczyk, Jolanta; Dansonka-Mieszkowska, Agnieszka; Plisiecka-Halasa, Joanna; Timorek, Agnieszka; Menon, Usha; Gentry-Maharaj, Aleksandra; Gayther, Simon A.; Ramus, Susan J.; Narod, Steven A.; Risch, Harvey A.; McLaughlin, John R.; Siddiqui, Nadeem; Glasspool, Rosalind; Paul, James; Carty, Karen; Gronwald, Jacek; Lubiński, Jan; Jakubowska, Anna; Cybulski, Cezary; Kiemeney, Lambertus A.; Massuger, Leon F. A. G.; van Altena, Anne M.; Aben, Katja K. H.; Olson, Sara H.; Orlow, Irene; Cramer, Daniel W.; Levine, Douglas A.; Bisogna, Maria; Giles, Graham G.; Southey, Melissa C.; Bruinsma, Fiona; Kjær, Susanne Krüger; Høgdall, Estrid; Jensen, Allan; Høgdall, Claus K.; Lundvall, Lene; Engelholm, Svend-Aage; Heitz, Florian; du Bois, Andreas; Harter, Philipp; Schwaab, Ira; Butzow, Ralf; Nevanlinna, Heli; Pelttari, Liisa M.; Leminen, Arto; Thompson, Pamela J.; Lurie, Galina; Wilkens, Lynne R.; Lambrechts, Diether; Van Nieuwenhuysen, Els; Lambrechts, Sandrina; Vergote, Ignace; Beesley, Jonathan; Fasching, Peter A.; Beckmann, Matthias W.; Hein, Alexander; Ekici, Arif B.; Doherty, Jennifer A.; Wu, Anna H.; Pearce, Celeste L.; Pike, Malcolm C.; Stram, Daniel; Chang-Claude, Jenny; Rudolph, Anja; Dörk, Thilo; Dürst, Matthias; Hillemanns, Peter; Runnebaum, Ingo B.; Bogdanova, Natalia; Antonenkova, Natalia; Odunsi, Kunle; Edwards, Robert P.; Kelley, Joseph L.; Modugno, Francesmary; Ness, Roberta B.; Karlan, Beth Y.; Walsh, Christine; Lester, Jenny; Orsulic, Sandra; Fridley, Brooke L.; Vierkant, Robert A.; Cunningham, Julie M.; Wu, Xifeng; Lu, Karen; Liang, Dong; Hildebrandt, Michelle A.T.; Weber, Rachel Palmieri; Iversen, Edwin S.; Tworoger, Shelley S.; Poole, Elizabeth M.; Salvesen, Helga B.; Krakstad, Camilla; Bjorge, Line; Tangen, Ingvild L.; Pejovic, Tanja; Bean, Yukie; Kellar, Melissa; Wentzensen, Nicolas; Brinton, Louise A.; Lissowska, Jolanta; Garcia-Closas, Montserrat; Campbell, Ian G.; Eccles, Diana; Whittemore, Alice S.; Sieh, Weiva; Rothstein, Joseph H.; Anton-Culver, Hoda; Ziogas, Argyrios; Phelan, Catherine M.; Moysich, Kirsten B.; Goode, Ellen L.; Schildkraut, Joellen M.; Berchuck, Andrew; Pharoah, Paul D.P.; Sellers, Thomas A.; Brooks-Wilson, Angela; Cook, Linda S.; Le, Nhu D.

    2014-01-01

    Scope We re-evaluated previously reported associations between variants in pathways of one-carbon (folate) transfer genes and ovarian carcinoma (OC) risk, and in related pathways of purine and pyrimidine metabolism, and assessed interactions with folate intake. Methods and Results Odds ratios (OR) for 446 genetic variants were estimated among 13,410 OC cases and 22,635 controls and among 2,281 cases and 3,444 controls with folate information. Following multiple testing correction, the most significant main effect associations were for DPYD variants rs11587873 (OR=0.92, P=6x10−5) and rs828054 (OR=1.06, P=1x10−4). Thirteen variants in the pyrimidine metabolism genes, DPYD, DPYS, PPAT and TYMS, also interacted significantly with folate in a multi-variant analysis (corrected P=9.9x10−6) but collectively explained only 0.2% of OC risk. Although no other associations were significant after multiple testing correction, variants in SHMT1 in one-carbon transfer, previously reported with OC, suggested lower risk at higher folate (Pinteraction=0.03-0.006). Conclusions Variation in pyrimidine metabolism genes, particularly DPYD, which was previously reported to be associated with OC, may influence risk; however, stratification by folate intake is unlikely to modify disease risk appreciably in these women. SHMT1 SNP-byfolate interactions are plausible but require further validation. Polymorphisms in selected genes in purine metabolism were not associated with OC. PMID:25066213

  20. Interactions between environmental factors and polymorphisms in angiogenesis pathway genes in esophageal adenocarcinoma risk: a case-only study.

    PubMed

    Zhai, Rihong; Zhao, Yang; Liu, Geoffrey; Ter-Minassian, Monica; Wu, I-Chen; Wang, Zhaoxi; Su, Li; Asomaning, Kofi; Chen, Feng; Kulke, Matthew H; Lin, Xihong; Heist, Rebecca S; Wain, John C; Christiani, David C

    2012-02-01

    Gastroesophageal reflux disease (GERD), higher body mass index (BMI), smoking, and genetic variants in angiogenic pathway genes have been individually associated with increased risk of esophageal adenocarcinoma. However, how angiogenic gene polymorphisms and environmental factors jointly affect esophageal adenocarcinoma development remains unclear. By using a case-only design (n = 335), the authors examined interactions between 141 functional/tagging angiogenic single nucleotide polymorphisms (SNPs) and environmental factors (GERD, BMI, smoking) in modulating esophageal adenocarcinoma risk. Gene-environment interactions were assessed by a 2-step approach. First, the authors applied random forest to screen for important SNPs that had either main or interaction effects. Second, they used case-only logistic regression to assess the effects of gene-environment interactions on esophageal adenocarcinoma risk, adjusting for covariates and false-discovery rate. Random forest analyses identified 3 sets of SNPs (17 SNPs-GERD, 26 SNPs-smoking, and 34 SNPs-BMI) that had the highest importance scores. In subsequent logistic regression analyses, interactions between 2 SNPs (rs2295778 of HIF1AN, rs13337626 of TSC2) and GERD, 2 SNPs (rs2295778 of HIF1AN, rs2296188 of VEGFR1) and smoking, and 7 SNPs (rs2114039 of PDGRFA, rs2296188 of VEGFR1, rs11941492 of VEGFR1, rs17708574 of PDGFRB, rs7324547 of VEGFR1, rs17619601 of VEGFR1, and rs17625898 of VEGFR1) and BMI were significantly associated with esophageal adenocarcinoma development (all false-discovery rates ≤0.10). Moreover, these interactions tended to have SNP dose-response effects for increased esophageal adenocarcinoma risk with increasing number of combined risk genotypes. These findings suggest that genetic variations in angiogenic genes may modify esophageal adenocarcinoma susceptibility through interactions with environmental factors in an SNP dose-response manner. Copyright © 2011 American Cancer Society.

  1. Can nutrient pathways and biotic interactions control eutrophication in riverine ecosystems? Evidence from a model driven mesocosm experiment.

    PubMed

    Jäger, Christoph G; Hagemann, Jeske; Borchardt, Dietrich

    2017-05-15

    Ecological theory predicts that the relative importance of benthic to planktonic primary production usually changes along the rivers' continuum from a predomination of benthic algae in lower stream orders to a predomination of planktonic algae at higher orders. Underlying mechanisms driving the interaction between algae in these habitats, its controlling factors and consequences for riverine ecosystems are, however, only partly understood. We present a mechanistic analysis of the governing ecological processes using a simplified, numerical model and examine how abiotic factors and biotic interactions influence benthic and planktonic algae by changing resource competition. We compare the outcome of the model with the results of a factorial mesocosm experiment mimicking the parameter spaces of the model. The results show a remarkable similarity with regard to the temporal development of benthic and pelagic algal biomass and shifting dominance patterns. In particular we analyse the effects of the pathways of nutrient supply (upwelling from the hyporheic zone, direct supply to the surface water, or via both pathways) and grazing in a gradient of river depths. Our results show that detachment of benthic algae, sinking of planktonic algae and the pathway of nutrient supply are key processes determining the respective algal biomass distributions particularly in shallow and intermediate deep systems. Increasing nutrient supply increases algal biomasses, but does not change the general pattern of the interactions. Decreasing light supply decreases the dominance of planktonic algae, but increases dissolved nutrients. At intermediate to high grazing rates algal biomass can be controlled by grazers, but however, at high grazing rates, dissolved nutrients accumulate in the surface water. Our results indicate that nutrient pathways, resource competition and internal control by grazing need to be considered explicitly for the understanding and explanation of eutrophication

  2. Genetic association and epistatic interaction of the interleukin-10 signaling pathway in pediatric inflammatory bowel disease

    PubMed Central

    Lin, Zhenwu; Wang, Zhong; Hegarty, John P; Lin, Tony R; Wang, Yunhua; Deiling, Sue; Wu, Rongling; Thomas, Neal J; Floros, Joanna

    2017-01-01

    AIM To study the genetic association and epistatic interaction of the interleukin (IL)-10 and IL-10/STAT3 pathways in pediatric inflammatory bowel disease (IBD). METHODS A total of 159 pediatric inflammatory IBD patients (Crohn’s disease, n = 136; ulcerative colitis, n = 23) and 129 matched controls were studied for genetic association of selected single nucleotide polymorphisms (SNPs) of the IL-10 gene and the genes IL10RA, IL10RB, STAT3, and HO1, from the IL-10/STAT3 signaling pathway. As interactions between SNPs from different loci may significantly affect the associated risk for disease, additive (a) and dominant (d) modeling of SNP interactions was also performed to examine high-order epistasis between combinations of the individual SNPs. RESULTS The results showed that IL-10 rs304496 was associated with pediatric IBD (P = 0.022), but no association was found for two other IL-10 SNPs, rs1800872 and rs2034498, or for SNPs in genes IL10RA, IL10RB, STAT3, and HO1. However, analysis of epistatic interaction among these genes showed significant interactions: (1) between two IL-10 SNPs rs1800872 and rs3024496 (additive-additive P = 0.00015, Bonferroni P value (Bp) = 0.003); (2) between IL-10RB rs2834167 and HO1 rs2071746 (dominant-additive, P = 0.0018, Bp = 0.039); and (3) among IL-10 rs1800872, IL10RB rs2834167, and HO1 rs2071746 (additive-dominant-additive, P = 0.00015, Bp = 0.005), as well as weak interactions among IL-10 rs1800872, IL-10 rs3024496, and IL-10RA (additive-additive-additive, P = 0.003; Bp = 0.099), and among IL10RA, IL10RB, and HO1 genes (additive-dominant-additive, P = 0.008, Bp = 0.287). CONCLUSION These results indicate that both the IL-10 gene itself, and through epistatic interaction with genes within the IL-10/STAT3 signaling pathway, contribute to the risk of pediatric IBD. PMID:28785144

  3. Signaling pathways regulating neuron-glia interaction and their implications in Alzheimer’s disease

    PubMed Central

    Lian, Hong; Zheng, Hui

    2015-01-01

    Astrocytes are the most abundant cells in the central nervous system. They play critical roles in neuronal homeostasis through their physical properties and neuron-glia signaling pathways. Astrocytes become reactive in response to neuronal injury and this process, referred to as reactive astrogliosis, is a common feature accompanying neurodegenerative conditions, particularly Alzheimer’s disease. Reactive astrogliosis represents a continuum of pathobiological processes and is associated with morphological, functional and gene expression changes of varying degrees. There has been a substantial growth of knowledge regarding the signaling pathways regulating glial biology and pathophysiology in recent years. Here we attempt to provide an unbiased review of some of the well-known players, namely calcium, proteoglycan, TGFβ, NFκB, and complement, in mediating neuron-glia interaction under physiological conditions as well as in Alzheimer’s disease. PMID:26546579

  4. Neuro-immune interactions via the cholinergic anti-inflammatory pathway

    PubMed Central

    Gallowitsch-Puerta, Margot; Pavlov, Valentin A.

    2010-01-01

    The overproduction of TNF and other cytokines can cause the pathophysiology of numerous diseases. Controlling cytokine synthesis and release is critical for preventing unrestrained inflammation and maintaining health. Recent studies identified an efferent vagus nerve-based mechanism termed “the cholinergic anti-inflammatory pathway” that controls cytokine production and inflammation. Here we review current advances related to the role of this pathway in neuro-immune interactions that prevent excessive inflammation. Experimental evidence indicates that vagus nerve cholinergic anti-inflammatory signaling requires alpha7 nicotinic acetylcholine receptors expressed on non-neuronal cytokine producing cells. Alpha7 nicotinic acetylcholine receptor agonists inhibit cytokine release and protect animals in a variety of experimental lethal inflammatory models. Knowledge related to the cholinergic anti-inflammatory pathway can be exploited in therapeutic approaches directed towards counteracting abnormal chronic and hyper-activated inflammatory responses. PMID:17289087

  5. Modeling of the dorsal gradient across species reveals interaction between embryo morphology and Toll signaling pathway during evolution.

    PubMed

    Ambrosi, Priscilla; Chahda, Juan Sebastian; Koslen, Hannah R; Chiel, Hillel J; Mizutani, Claudia Mieko

    2014-08-01

    Morphogenetic gradients are essential to allocate cell fates in embryos of varying sizes within and across closely related species. We previously showed that the maternal NF-κB/Dorsal (Dl) gradient has acquired different shapes in Drosophila species, which result in unequally scaled germ layers along the dorso-ventral axis and the repositioning of the neuroectodermal borders. Here we combined experimentation and mathematical modeling to investigate which factors might have contributed to the fast evolutionary changes of this gradient. To this end, we modified a previously developed model that employs differential equations of the main biochemical interactions of the Toll (Tl) signaling pathway, which regulates Dl nuclear transport. The original model simulations fit well the D. melanogaster wild type, but not mutant conditions. To broaden the applicability of this model and probe evolutionary changes in gradient distributions, we adjusted a set of 19 independent parameters to reproduce three quantified experimental conditions (i.e. Dl levels lowered, nuclear size and density increased or decreased). We next searched for the most relevant parameters that reproduce the species-specific Dl gradients. We show that adjusting parameters relative to morphological traits (i.e. embryo diameter, nuclear size and density) alone is not sufficient to reproduce the species Dl gradients. Since components of the Tl pathway simulated by the model are fast-evolving, we next asked which parameters related to Tl would most effectively reproduce these gradients and identified a particular subset. A sensitivity analysis reveals the existence of nonlinear interactions between the two fast-evolving traits tested above, namely the embryonic morphological changes and Tl pathway components. Our modeling further suggests that distinct Dl gradient shapes observed in closely related melanogaster sub-group lineages may be caused by similar sequence modifications in Tl pathway components, which

  6. Structural and Functional Characterization of a Caenorhabditis elegans Genetic Interaction Network within Pathways

    PubMed Central

    Boucher, Benjamin; Lee, Anna Y.; Hallett, Michael; Jenna, Sarah

    2016-01-01

    A genetic interaction (GI) is defined when the mutation of one gene modifies the phenotypic expression associated with the mutation of a second gene. Genome-wide efforts to map GIs in yeast revealed structural and functional properties of a GI network. This provided insights into the mechanisms underlying the robustness of yeast to genetic and environmental insults, and also into the link existing between genotype and phenotype. While a significant conservation of GIs and GI network structure has been reported between distant yeast species, such a conservation is not clear between unicellular and multicellular organisms. Structural and functional characterization of a GI network in these latter organisms is consequently of high interest. In this study, we present an in-depth characterization of ~1.5K GIs in the nematode Caenorhabditis elegans. We identify and characterize six distinct classes of GIs by examining a wide-range of structural and functional properties of genes and network, including co-expression, phenotypical manifestations, relationship with protein-protein interaction dense subnetworks (PDS) and pathways, molecular and biological functions, gene essentiality and pleiotropy. Our study shows that GI classes link genes within pathways and display distinctive properties, specifically towards PDS. It suggests a model in which pathways are composed of PDS-centric and PDS-independent GIs coordinating molecular machines through two specific classes of GIs involving pleiotropic and non-pleiotropic connectors. Our study provides the first in-depth characterization of a GI network within pathways of a multicellular organism. It also suggests a model to understand better how GIs control system robustness and evolution. PMID:26871911

  7. Photoperiodic and thermosensory pathways interact through CONSTANS to promote flowering at high temperature under short days.

    PubMed

    Fernández, Virginia; Takahashi, Yasuyuki; Le Gourrierec, José; Coupland, George

    2016-06-01

    Plants detect changes in day length to induce seasonal patterns of flowering. The photoperiodic pathway accelerates the flowering of Arabidopsis thaliana under long days (LDs) whereas it is inactive under short days (SDs), resulting in delayed flowering. This delay is overcome by exposure of plants to high temperature (27°C) under SDs (27°C-SD). Previously, the high-temperature flowering response was proposed to involve either the impaired activity of MADS-box transcription factor (TF) floral repressors or PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) TF-mediated activation of FLOWERING LOCUS T (FT), which encodes the output signal of the photoperiodic pathway. We integrate these observations by studying several PIFs, the MADS-box SHORT VEGETATIVE PHASE (SVP) and the photoperiodic pathway under 27°C-SD. We find that the mRNAs of FT and its paralogue TWIN SISTER OF FT (TSF) are increased at dusk under 27°C-SD compared with 21°C-SD, and that this requires PIF4 and PIF5 as well as CONSTANS (CO), a TF that promotes flowering under LDs. The CO and PIF4 proteins are present at dusk under 27°C-SD, and they physically interact. Although Col-0 plants flower at similar times under 27°C-SD and 21°C-LD the expression level of FT is approximately 10-fold higher under 21°C-LD, suggesting that responsiveness to FT is also increased under 27°C-SD, perhaps as a result of the reduced activity of SVP in the meristem. Accordingly, only svp-41 ft-10 tsf-1 plants flowered at the same time under 21°C-SD and 27°C-SD. Thus, we propose that under non-inductive SDs, elevated temperatures increase the activity and sensitize the response to the photoperiod pathway.

  8. 5-HT4 Receptors Constitutively Promote the Non-Amyloidogenic Pathway of APP Cleavage and Interact with ADAM10

    PubMed Central

    2012-01-01

    In addition to the amyloidogenic pathway, amyloid precursor protein (APP) can be cleaved by α-secretases, producing soluble and neuroprotective APP alpha (sAPPα) (nonamyloidogenic pathway) and thus preventing the generation of pathogenic amyloid-β. However, the mechanisms regulating APP cleavage by α-secretases remain poorly understood. Here, we showed that expression of serotonin type 4 receptors (5-HT4Rs) constitutively (without agonist stimulation) induced APP cleavage by the α-secretase ADAM10 and the release of neuroprotective sAPPα in HEK-293 cells and cortical neurons. This effect was independent of cAMP production. Interestingly, we demonstrated that 5-HT4 receptors physically interacted with the mature form of ADAM10. Stimulation of 5-HT4 receptors by an agonist further increased sAPPα secretion, and this effect was mediated by cAMP/Epac signaling. These findings describe a new mechanism whereby a GPCR constitutively stimulates the cleavage of APP by α-secretase and promotes the nonamyloidogenic pathway of APP processing. PMID:23336052

  9. 5-HT4 receptors constitutively promote the non-amyloidogenic pathway of APP cleavage and interact with ADAM10.

    PubMed

    Cochet, Maud; Donneger, Romain; Cassier, Elisabeth; Gaven, Florence; Lichtenthaler, Stefan F; Marin, Philippe; Bockaert, Joël; Dumuis, Aline; Claeysen, Sylvie

    2013-01-16

    In addition to the amyloidogenic pathway, amyloid precursor protein (APP) can be cleaved by α-secretases, producing soluble and neuroprotective APP alpha (sAPPα) (nonamyloidogenic pathway) and thus preventing the generation of pathogenic amyloid-β. However, the mechanisms regulating APP cleavage by α-secretases remain poorly understood. Here, we showed that expression of serotonin type 4 receptors (5-HT(4)Rs) constitutively (without agonist stimulation) induced APP cleavage by the α-secretase ADAM10 and the release of neuroprotective sAPPα in HEK-293 cells and cortical neurons. This effect was independent of cAMP production. Interestingly, we demonstrated that 5-HT(4) receptors physically interacted with the mature form of ADAM10. Stimulation of 5-HT(4) receptors by an agonist further increased sAPPα secretion, and this effect was mediated by cAMP/Epac signaling. These findings describe a new mechanism whereby a GPCR constitutively stimulates the cleavage of APP by α-secretase and promotes the nonamyloidogenic pathway of APP processing.

  10. Forest disturbance interactions and successional pathways in the Southern Rocky Mountains

    USGS Publications Warehouse

    Lu Liang,; Hawbaker, Todd J.; Zhu, Zhiliang; Xuecao Li,; Peng Gong,

    2016-01-01

    The pine forests in the southern portion of the Rocky Mountains are a heterogeneous mosaic of disturbance and recovery. The most extensive and intensive stress and mortality are received from human activity, fire, and mountain pine beetles (MPB;Dendroctonus ponderosae). Understanding disturbance interactions and disturbance-succession pathways are crucial for adapting management strategies to mitigate their impacts and anticipate future ecosystem change. Driven by this goal, we assessed the forest disturbance and recovery history in the Southern Rocky Mountains Ecoregion using a 13-year time series of Landsat image stacks. An automated classification workflow that integrates temporal segmentation techniques and a random forest classifier was used to examine disturbance patterns. To enhance efficiency in selecting representative samples at the ecoregion scale, a new sampling strategy that takes advantage of the scene-overlap among adjacent Landsat images was designed. The segment-based assessment revealed that the overall accuracy for all 14 scenes varied from 73.6% to 92.5%, with a mean of 83.1%. A design-based inference indicated the average producer’s and user’s accuracies for MPB mortality were 85.4% and 82.5% respectively. We found that burn severity was largely unrelated to the severity of pre-fire beetle outbreaks in this region, where the severity of post-fire beetle outbreaks generally decreased in relation to burn severity. Approximately half the clear-cut and burned areas were in various stages of recovery, but the regeneration rate was much slower for MPB-disturbed sites. Pre-fire beetle outbreaks and subsequent fire produced positive compound effects on seedling reestablishment in this ecoregion. Taken together, these results emphasize that although multiple disturbances do play a role in the resilience mechanism of the serotinous lodgepole pine, the overall recovery could be slow due to the vast area of beetle mortality.

  11. Genetic loci in the photoperiod pathway interactively modulate reproductive development of winter wheat.

    PubMed

    Wang, Shuwen; Carver, Brett; Yan, Liuling

    2009-05-01

    Responses to photoperiod and low temperature are the two primary adaptive mechanisms which enable wheat plants to synchronize developmental processes with changes in seasonal climate. In this study, the developmental process was characterized at two stages: stem length during the onset of stem elongation and heading date. These two developmental events were monitored and mapped in recombinant inbred lines (RILs) of a population generated from a cross between two complementary and locally adapted hard winter wheat cultivars. 'Intrada' undergoes stem elongation earlier but reaches heading later, whereas 'Cimarron' undergoes stem elongation later but reaches heading earlier. Variation in the developmental process in this population was associated with three major QTLs centered on Xbarc200 on chromosome 2B, PPD-D1 on chromosome 2D, and Xcfd14 on chromosome 7D. The Intrada Xbarc200 and Xcfd14 alleles and the Cimarron PPD-D1 allele accelerated both stem elongation and heading stages, or the Cimarron Xbarc200 and Xcfd14 alleles and the Intrada PPD-D1 allele delayed both stem elongation and heading stages. Integrative effects of the three QTLs accounted for 43% (initial stem length) and 68% (heading date) of the overall phenotypic variation in this population. PPD-D1 is a reasonable candidate gene for the QTL on chromosome 2D, PPD-B1 could be associated with the QTL on chromosome 2B, but VRN-D3 (=FT-D1) was not linked with the QTL on chromosome 7D, suggesting that this is a novel locus involved in winter wheat development. Because the PPD-D1 QTL was observed to interact with other two QTLs, all of these QTLs could play a role in the same pathway as involved in photoperiod response of winter wheat.

  12. Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression

    NASA Astrophysics Data System (ADS)

    Kelley, David R.; Kingsford, Carl

    Genetic interactions (such as synthetic lethal interactions) have become quantifiable on a large-scale using the epistatic miniarray profile (E-MAP) method. An E-MAP allows the construction of a large, weighted network of both aggravating and alleviating genetic interactions between genes. By clustering genes into modules and establishing relationships between those modules, we can discover compensatory pathways. We introduce a general framework for applying greedy clustering heuristics to probabilistic graphs. We use this framework to apply a graph clustering method called graph summarization to an E-MAP that targets yeast chromosome biology. This results in a new method for clustering E-MAP data that we call Expected Graph Compression (EGC). We validate modules and compensatory pathways using enriched Gene Ontology annotations and a novel method based on correlated gene expression. EGC finds a number of modules that are not found by any previous methods to cluster E-MAP data. EGC also uncovers core submodules contained within several previously found modules, suggesting that EGC can reveal the finer structure of E-MAP networks.

  13. Direct molecular interactions between Beclin 1 and the canonical NFκB activation pathway.

    PubMed

    Niso-Santano, Mireia; Criollo, Alfredo; Malik, Shoaib Ahmad; Michaud, Michael; Morselli, Eugenia; Mariño, Guillermo; Lachkar, Sylvie; Galluzzi, Lorenzo; Maiuri, Maria Chaira; Kroemer, Guido

    2012-02-01

    General (macro)autophagy and the activation of NFκB constitute prominent responses to a large array of intracellular and extracellular stress conditions. The depletion of any of the three subunits of the inhibitor of NFκB (IκB) kinase (IKKα, IKKβ, IKKγ/NEMO), each of which is essential for the canonical NFκB activation pathway, limits autophagy induction by physiological or pharmacological triggers, while constitutive active IKK subunits suffice to stimulate autophagy. The activation of IKK usually relies on TGFβ-activated kinase 1 (TAK1), which is also necessary for the optimal induction of autophagy in multiple settings. TAK1 interacts with two structurally similar co-activators, TAK1-binding proteins 2 and 3 (TAB2 and TAB3). Importantly, in resting conditions both TAB2 and TAB3 bind the essential autophagic factor Beclin 1, but not TAK1. In response to pro-autophagic stimuli, TAB2 and TAB3 dissociate from Beclin 1 and engage in stimulatory interactions with TAK1. The inhibitory interaction between TABs and Beclin 1 is mediated by their coiled-coil domains (CCDs). Accordingly, the overexpression of either TAB2 or TAB3 CCD stimulates Beclin 1- and TAK1-dependent autophagy. These results point to the existence of a direct molecular crosstalk between the canonical NFκB activation pathway and the autophagic core machinery that guarantees the coordinated induction of these processes in response to stress.

  14. Constructing a molecular interaction network for thyroid cancer via large-scale text mining of gene and pathway events.

    PubMed

    Wu, Chengkun; Schwartz, Jean-Marc; Brabant, Georg; Peng, Shao-Liang; Nenadic, Goran

    2015-01-01

    Biomedical studies need assistance from automated tools and easily accessible data to address the problem of the rapidly accumulating literature. Text-mining tools and curated databases have been developed to address such needs and they can be applied to improve the understanding of molecular pathogenesis of complex diseases like thyroid cancer. We have developed a system, PWTEES, which extracts pathway interactions from the literature utilizing an existing event extraction tool (TEES) and pathway named entity recognition (PathNER). We then applied the system on a thyroid cancer corpus and systematically extracted molecular interactions involving either genes or pathways. With the extracted information, we constructed a molecular interaction network taking genes and pathways as nodes. Using curated pathway information and network topological analyses, we highlight key genes and pathways involved in thyroid carcinogenesis. Mining events involving genes and pathways from the literature and integrating curated pathway knowledge can help improve the understanding of molecular interactions of complex diseases. The system developed for this study can be applied in studies other than thyroid cancer. The source code is freely available online at https://github.com/chengkun-wu/PWTEES.

  15. Solar wind-magnetosphere interaction: energy transfer pathways and their predictability

    NASA Astrophysics Data System (ADS)

    Vassiliadis, D.

    2001-09-01

    The coupling of the solar wind to planets has been studied for several decades now. Much of the recent progress in understanding the complexity of the interaction is due to the variability of the magnetospheres in the solar system. The interaction with the terrestrial system is evidently the best known, although by far not the simplest one. The geospace and the surrounding solar wind constitute an input-output system where the various parts of the energy budget are measured simultaneously by a fleet of spacecraft. We integrate these measurements by combining plasma physics and simulation models with system analysis methods. The large-scale energy transfer is dominated by magnetic reconnection and its effects which supply electromagnetic and kinetic energy at the rate of ~10^15 W to the magnetosphere with part of it eventually dissipating at the ionospheric boundary. The storage-release of magnetic energy and its transformation to kinetic energy takes place continually through convection and more explosively during magnetospheric substorms. Long known from its effects, ranging from auroral displays to the more recent disruptions of electric power grid operation, this interaction involves many spatial and temporal pathways: The overall disturbance levels are represented by regional and global magnetic indices. Index time series were the first to be reproduced accurately by nonlinear dynamical systems driven by solar wind parameter data. The models have subsequently been used in prediction of the indices based on real-time interplanetary field and plasma parameters from the ACE and WIND spacecraft (http://lep694.gsfc.nasa.gov/RTSM/). The model time scales represent the physical responses, namely the directly driven convection and the less predictable substorm. Currently the approach has been extended to modeling the spatial distribution as well as temporal variations. Data from ground magnetometer arrays have replaced the scalar indices to provide magnetic field maps

  16. Interaction of biologically active amines with mitochondria and their role in the mitochondrial-mediated pathway of apoptosis.

    PubMed

    Toninello, A; Salvi, M; Mondovì, B

    2004-09-01

    The natural polyamines spermine, spermidine and putrescine, polycationic molecules at physiological pH, interact with mitochondrial membranes at two specific binding sites exhibiting low affinity and high binding capacity. This binding represents the first step in the electrophoretic mechanism of polyamine transport into mitochondria. Spermine accumulated into the mitochondrial matrix is able to flow out by an electroneutral mechanism. This process promotes bi-directional transport of polyamines in and out of mitochondria, driven by electrical potential and pH gradient, respectively. Polyamines and biogenic amines are oxidized by cytosolic and mitochondrial amine oxidases with the production of hydrogen peroxide and aldehydes, both of which are involved in the induction and/or amplification of the mitochondrial permeability transition (MPT). This phenomenon, which provokes a bioenergetic collapse and redox catastrophe, is strongly inhibited by polyamines in isolated mitochondria. Monoamines also exhibit an inhibitory effect at higher concentrations, but at low concentrations behave as inducer agents. MPT is characterized by the opening of a channel, the transition pore, which permits non-specific bi-directional traffic of solutes across the inner membrane, leading to swelling of the organelle and release of cytochrome c and apoptosis-inducing factors. These proteins in turn activate the caspase-cascade, which triggers the apoptotic pathway. Depending on their cytosolic concentration, metabolic conditions and cell type, polyamines act as promoting, modulating or protective agents in mitochondrial-mediated apoptosis. While their protective effect could reflect inhibition of MPT and retention of cytochrome c, the promoting effect can be explained by the generation of reactive oxygen species that induce the opposite effect on MPT and cytochrome c release. Polyamines and other active amines can also participate in the regulation of apoptotic pathways by interacting with

  17. Insect-plant interactions: new pathways to a better comprehension of ecological communities in Neotropical savannas.

    PubMed

    Del-Claro, Kleber; Torezan-Silingardi, Helena M

    2009-01-01

    The causal mechanisms shaping and structuring ecological communities are among the most important themes in ecology. The study of insect-plant interactions in trophic nets is pointed out as basic to improve our knowledge on this issue. The cerrado tropical savanna, although extremely diverse, distributed in more than 20% of the Brazilian territory and filled up with rich examples of multitrophic interactions, is underexplored in terms of biodiversity interaction. Here, this ecosystem is suggested as valuable to the study of insect-plant interactions whose understanding can throw a new light at the ecological communities' theory. Three distinct systems: extrafloral nectary plants or trophobiont herbivores and the associated ant fauna; floral herbivores-predators-pollinators; and plants-forest engineers and associated fauna, will serve as examples to illustrate promising new pathways in cerrado. The aim of this brief text is to instigate young researchers, mainly entomologists, to initiate more elaborated field work, including experimental manipulations in multitrophic systems, to explore in an interactive way the structure that maintain preserved viable communities in the Neotropical savanna.

  18. Sharing, liking, commenting, and distressed? The pathway between Facebook interaction and psychological distress.

    PubMed

    Chen, Wenhong; Lee, Kye-Hyoung

    2013-10-01

    Studies on the mental health implications of social media have generated mixed results. Drawing on a survey of college students (N=513), this research uses structural equation modeling to assess the relationship between Facebook interaction and psychological distress and two underlying mechanisms: communication overload and self-esteem. It is the first study, to our knowledge, that examines how communication overload mediates the mental health implications of social media. Frequent Facebook interaction is associated with greater distress directly and indirectly via a two-step pathway that increases communication overload and reduces self-esteem. The research sheds light on new directions for understanding psychological well-being in an increasingly mediated social world as users share, like, and comment more and more.

  19. Interaction of SecB with intermediates along the folding pathway of maltose-binding protein.

    PubMed Central

    Diamond, D. L.; Strobel, S.; Chun, S. Y.; Randall, L. L.

    1995-01-01

    SecB, a molecular chaperone involved in protein export in Escherichia coli, displays the remarkable ability to selectively bind many different polypeptide ligands whose only common feature is that of being nonnative. The selectivity is explained in part by a kinetic partitioning between the folding of a polypeptide and its association with SecB. SecB has no affinity for native, stably folded polypeptides but interacts tightly with polypeptides that are nonnative. In order to better understand the nature of the binding, we have examined the interaction of SecB with intermediates along the folding pathway of maltose-binding protein. Taking advantage of forms of maltose-binding protein that are altered in their folding properties, we show that the first intermediate in folding, represented by the collapsed state, binds to SecB, and that the polypeptide remains active as a ligand until it crosses the final energy barrier to attain the native state. PMID:7549876

  20. Combinatorial drug screening identifies compensatory pathway interactions and adaptive resistance mechanisms

    PubMed Central

    Axelrod, Mark; Gordon, Vicki L.; Conaway, Mark; Tarcsafalvi, Adel; Neitzke, Daniel J.; Gioeli, Daniel; Weber, Michael J.

    2013-01-01

    Constitutively activated signaling molecules are often the primary drivers of malignancy, and are favored targets for therapeutic intervention. However, the effectiveness of targeted inhibition of cell signaling can be blunted by compensatory signaling which generates adaptive resistance mechanisms and reduces therapeutic responses. Therefore, it is important to identify and target these compensatory pathways with combinations of targeted agents to achieve durable clinical benefit. In this report, we demonstrate the use of high-throughput combinatorial drug screening as a discovery tool to identify compensatory pathways that generate resistance to the cytotoxic effects of targeted therapy. We screened 420 drug combinations in 14 different cell lines representing three cancer lineages, and assessed the ability of each combination to cause synergistic cytotoxicity. Drug substitution studies were used to validate the functionally important drug targets. Of the 84 combinations that caused robust synergy in multiple cell lines, none were synergistic in more than half of the lines tested, and we observed no pattern of lineage specificity in the observed synergies. This reflects the plasticity of cell signaling networks, even among cell lines of the same tissue of origin. Mechanistic analysis of one novel synergistic combination identified in the screen, the multi-kinase inhibitor Ro31-8220 and lapatinib, demonstrated compensatory crosstalk between the p70S6 kinase and EGF receptor pathways. In addition, we identified BAD as a node of convergence between these two pathways that may be playing a role in the enhanced apoptosis observed upon combination treatment. PMID:23599172

  1. Detecting Pathway-Based Gene-Gene and Gene-Environment Interactions in Pancreatic Cancer

    PubMed Central

    Duell, Eric J.; Bracci, Paige M.; Moore, Jason H.; Burk, Robert D.; Kelsey, Karl T.; Holly, Elizabeth A.

    2015-01-01

    Data mining and data reduction methods to detect interactions in epidemiologic data are being developed and tested. In these analyses, multifactor dimensionality reduction, focused interaction testing framework, and traditional logistic regression models were used to identify potential interactions with up to three factors. These techniques were used in a population-based case-control study of pancreatic cancer from the San Francisco Bay Area (308 cases, 964 controls). From 7 biochemical pathways, along with tobacco smoking, 26 polymorphisms in 20 genes were included in these analyses. Combinations of genetic markers and cigarette smoking were identified as potential risk factors for pancreatic cancer, including genes in base excision repair (OGG1), nucleotide excision repair (XPD, XPA, XPC), and double-strand break repair (XRCC3). XPD.751, XPD.312, and cigarette smoking were the best single-factor predictors of pancreatic cancer risk, whereas XRCC3.241*smoking and OGG1.326*XPC.PAT were the best two-factor predictors. There was some evidence for a three-factor combination of OGG1.326*XPD.751*smoking, but the covariate-adjusted relative-risk estimates lacked precision. Multifactor dimensionality reduction and focused interaction testing framework showed little concordance, whereas logistic regression allowed for covariate adjustment and model confirmation. Our data suggest that multiple common alleles from DNA repair pathways in combination with cigarette smoking may increase the risk for pancreatic cancer, and that multiple approaches to data screening and analysis are necessary to identify potentially new risk factor combinations. PMID:18559563

  2. Interaction of PACAP with Sonic hedgehog reveals complex regulation of the hedgehog pathway by PKA.

    PubMed

    Niewiadomski, Pawel; Zhujiang, Annie; Youssef, Mary; Waschek, James A

    2013-11-01

    Sonic hedgehog (Shh) signaling is essential for proliferation of cerebellar granule cell progenitors (cGCPs) and its aberrant activation causes a cerebellar cancer medulloblastoma. Pituitary adenylate cyclase activating polypeptide (PACAP) inhibits Shh-driven proliferation of cGCPs and acts as tumor suppressor in murine medulloblastoma. We show that PACAP blocks canonical Shh signaling by a mechanism that involves activation of protein kinase A (PKA) and inhibition of the translocation of the Shh-dependent transcription factor Gli2 into the primary cilium. PKA is shown to play an essential role in inhibiting gene transcription in the absence of Shh, but global PKA activity levels are found to be a poor predictor of the degree of Shh pathway activation. We propose that the core Shh pathway regulates a small compartmentalized pool of PKA in the vicinity of primary cilia. GPCRs that affect global PKA activity levels, such as the PACAP receptor, cooperate with the canonical Shh signal to regulate Gli protein phosphorylation by PKA. This interaction serves to fine-tune the transcriptional and physiological function of the Shh pathway.

  3. The cannabinoid CB1 receptor and mTORC1 signalling pathways interact to modulate glucose homeostasis in mice

    PubMed Central

    Bermudez-Silva, Francisco J.; Romero-Zerbo, Silvana Y.; Haissaguerre, Magalie; Ruz-Maldonado, Inmaculada; Lhamyani, Said; El Bekay, Rajaa; Tabarin, Antoine; Marsicano, Giovanni; Cota, Daniela

    2016-01-01

    ABSTRACT The endocannabinoid system (ECS) is an intercellular signalling mechanism that is present in the islets of Langerhans and plays a role in the modulation of insulin secretion and expansion of the β-cell mass. The downstream signalling pathways mediating these effects are poorly understood. Mammalian target of rapamycin complex 1 (mTORC1) signalling is a key intracellular pathway involved in energy homeostasis and is known to importantly affect the physiology of pancreatic islets. We investigated the possible relationship between cannabinoid type 1 (CB1) receptor signalling and the mTORC1 pathway in the endocrine pancreas of mice by using pharmacological analysis as well as mice genetically lacking the CB1 receptor or the downstream target of mTORC1, the kinase p70S6K1. In vitro static secretion experiments on islets, western blotting, and in vivo glucose and insulin tolerance tests were performed. The CB1 receptor antagonist rimonabant decreased glucose-stimulated insulin secretion (GSIS) at 0.1 µM while increasing phosphorylation of p70S6K1 and ribosomal protein S6 (rpS6) within the islets. Specific pharmacological blockade of mTORC1 by 3 nM rapamycin, as well as genetic deletion of p70S6K1, impaired the CB1-antagonist-mediated decrease in GSIS. In vivo experiments showed that 3 mg/kg body weight rimonabant decreased insulin levels and induced glucose intolerance in lean mice without altering peripheral insulin sensitivity; this effect was prevented by peripheral administration of low doses of rapamycin (0.1 mg/kg body weight), which increased insulin sensitivity. These findings suggest a functional interaction between the ECS and the mTORC1 pathway within the endocrine pancreas and at the whole-organism level, which could have implications for the development of new therapeutic approaches for pancreatic β-cell diseases. PMID:26563389

  4. Effect of curcumin on aged Drosophila melanogaster: a pathway prediction analysis.

    PubMed

    Zhang, Zhi-guo; Niu, Xu-yan; Lu, Ai-ping; Xiao, Gary Guishan

    2015-02-01

    To re-analyze the data published in order to explore plausible biological pathways that can be used to explain the anti-aging effect of curcumin. Microarray data generated from other study aiming to investigate effect of curcumin on extending lifespan of Drosophila melanogaster were further used for pathway prediction analysis. The differentially expressed genes were identified by using GeneSpring GX with a criterion of 3.0-fold change. Two Cytoscape plugins including BisoGenet and molecular complex detection (MCODE) were used to establish the protein-protein interaction (PPI) network based upon differential genes in order to detect highly connected regions. The function annotation clustering tool of Database for Annotation, Visualization and Integrated Discovery (DAVID) was used for pathway analysis. A total of 87 genes expressed differentially in D. melanogaster melanogaster treated with curcumin were identified, among which 50 were up-regulated significantly and 37 were remarkably down-regulated in D. melanogaster melanogaster treated with curcumin. Based upon these differential genes, PPI network was constructed with 1,082 nodes and 2,412 edges. Five highly connected regions in PPI networks were detected by MCODE algorithm, suggesting anti-aging effect of curcumin may be underlined through five different pathways including Notch signaling pathway, basal transcription factors, cell cycle regulation, ribosome, Wnt signaling pathway, and p53 pathway. Genes and their associated pathways in D. melanogaster melanogaster treated with anti-aging agent curcumin were identified using PPI network and MCODE algorithm, suggesting that curcumin may be developed as an alternative therapeutic medicine for treating aging-associated diseases.

  5. Pathways from parental AIDS to child psychological, educational and sexual risk: developing an empirically-based interactive theoretical model.

    PubMed

    Cluver, Lucie; Orkin, Mark; Boyes, Mark E; Sherr, Lorraine; Makasi, Daphne; Nikelo, Joy

    2013-06-01

    Increasing evidence demonstrates negative psychological, health, and developmental outcomes for children associated with parental HIV/AIDS illness and death. However, little is known about how parental AIDS leads to negative child outcomes. This study used a structural equation modelling approach to develop an empirically-based theoretical model of interactive relationships between parental or primary caregiver AIDS-illness, AIDS-orphanhood and predicted intervening factors associated with children's psychological distress, educational access and sexual health. Cross-sectional data were collected in 2009-2011, from 6002 children aged 10-17 years in three provinces of South Africa using stratified random sampling. Comparison groups included children orphaned by AIDS, orphaned by other causes and non-orphans, and children whose parents or primary caregivers were unwell with AIDS, unwell with other causes or healthy. Participants reported on psychological symptoms, educational access, and sexual health risks, as well as hypothesized sociodemographic and intervening factors. In order to build an interactive theoretical model of multiple child outcomes, multivariate regression and structural equation models were developed for each individual outcome, and then combined into an overall model. Neither AIDS-orphanhood nor parental AIDS-illness were directly associated with psychological distress, educational access, or sexual health. Instead, significant indirect effects of AIDS-orphanhood and parental AIDS-illness were obtained on all measured outcomes. Child psychological, educational and sexual health risks share a common set of intervening variables including parental disability, poverty, community violence, stigma, and child abuse that together comprise chain effects. In all models, parental AIDS-illness had stronger effects and more risk pathways than AIDS-orphanhood, especially via poverty and parental disability. AIDS-orphanhood and parental AIDS-illness impact

  6. Protective effect of resveratrol against nigrostriatal pathway injury in striatum via JNK pathway.

    PubMed

    Li, Dan; Liu, Nan; Zhao, Liang; Tong, Lei; Kawano, Hitoshi; Yan, Hong-Jing; Li, Hong-Peng

    2017-01-01

    Nigrostriatal pathway injury is one of the traumatic brain injury models that usually lead to neurological dysfunction or neuron necrosis. Resveratrol-induced benefits have recently been demonstrated in several models of neuronal degeneration diseases. However, the protective properties of resveratrol against neurodegeneration have not been explored definitely. Thus, we employ the nigrostriatal pathway injury model to mimic the insults on the brain. Resveratrol decreased the p-ERK expression and increased the p-JNK expression compared to the DMSO group, but not alter the p38 MAPK proteins around the lesion site by Western blot. Prior to the injury, mice were infused with resveratrol intracerebroventricularly with or without JNK-IN-8, a specific c-JNK pathway inhibitor for JNK1, JNK2 and JNK4. The study assessed modified improved neurological function score (mNSS) and beam/walking test, the level of inflammatory cytokines IL-1β, IL-6 and TNF-α, and striatal expression of Bax and Bcl-2 proteins associated with neuronal apoptosis. The results revealed that resveratrol exerted a neuroprotective effect as shown by the improved mNSS and beam latency, anti-inflammatory effects as indicated by the decreased level of IL-1β, TNF-α and IL-6. Furthermore, resveratrol up-regulated the protein expression of p-JNK and Bcl-2, down-regulated the expression of Bax and the number of Fluoro-Jade C (FJC) positive neurons. However, these advantages of resveratrol were abolished by JNK-IN-8 treatment. Overall, we demonstrated that resveratrol treatment attenuates the nigrostriatal pathway injury-induced neuronal apoptosis and inflammation via activation of c-JNK signaling. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Notch1 Regulates Hippocampal Plasticity Through Interaction with the Reelin Pathway, Glutamatergic Transmission and CREB Signaling.

    PubMed

    Brai, Emanuele; Marathe, Swananda; Astori, Simone; Fredj, Naila Ben; Perry, Elisabeth; Lamy, Christophe; Scotti, Alessandra; Alberi, Lavinia

    2015-01-01

    Notch signaling plays a crucial role in adult brain function such as synaptic plasticity, memory and olfaction. Several reports suggest an involvement of this pathway in neurodegenerative dementia. Yet, to date, the mechanism underlying Notch activity in mature neurons remains unresolved. In this work, we investigate how Notch regulates synaptic potentiation and contributes to the establishment of memory in mice. We observe that Notch1 is a postsynaptic receptor with functional interactions with the Reelin receptor, apolipoprotein E receptor 2 (ApoER2) and the ionotropic receptor, N-methyl-D-aspartate receptor (NMDAR). Targeted loss of Notch1 in the hippocampal CA fields affects Reelin signaling by influencing Dab1 expression and impairs the synaptic potentiation achieved through Reelin stimulation. Further analysis indicates that loss of Notch1 affects the expression and composition of the NMDAR but not AMPAR. Glutamatergic signaling is further compromised through downregulation of CamKII and its secondary and tertiary messengers resulting in reduced cAMP response element-binding (CREB) signaling. Our results identify Notch1 as an important regulator of mechanisms involved in synaptic plasticity and memory formation. These findings emphasize the possible involvement of this signaling receptor in dementia. In this paper, we propose a mechanism for Notch1-dependent plasticity that likely underlies the function of Notch1 in memory formation: Notch1 interacts with another important developmental pathway, the Reelin cascade.Notch1 regulates both NMDAR expression and composition.Notch1 influences a cascade of cellular events culminating in CREB activation.

  8. Interactions between Melanin Enzymes and Their Atypical Recruitment to the Secretory Pathway by Palmitoylation

    PubMed Central

    Upadhyay, Srijana; Xu, Xinping

    2016-01-01

    ABSTRACT Melanins are biopolymers that confer coloration and protection to the host organism against biotic or abiotic insults. The level of protection offered by melanin depends on its biosynthesis and its subcellular localization. Previously, we discovered that Aspergillus fumigatus compartmentalizes melanization in endosomes by recruiting all melanin enzymes to the secretory pathway. Surprisingly, although two laccases involved in the late steps of melanization are conventional secretory proteins, the four enzymes involved in the early steps of melanization lack a signal peptide or a transmembrane domain and are thus considered “atypical” secretory proteins. In this work, we found interactions among melanin enzymes and all melanin enzymes formed protein complexes. Surprisingly, the formation of protein complexes by melanin enzymes was not critical for their trafficking to the endosomal system. By palmitoylation profiling and biochemical analyses, we discovered that all four early melanin enzymes were strongly palmitoylated during conidiation. However, only the polyketide synthase (PKS) Alb1 was strongly palmitoylated during both vegetative hyphal growth and conidiation when constitutively expressed alone. This posttranslational lipid modification correlates the endosomal localization of all early melanin enzymes. Intriguingly, bioinformatic analyses predict that palmitoylation is a common mechanism for potential membrane association of polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) in A. fumigatus. Our findings indicate that protein-protein interactions facilitate melanization by metabolic channeling, while posttranslational lipid modifications help recruit the atypical enzymes to the secretory pathway, which is critical for compartmentalization of secondary metabolism. PMID:27879337

  9. Non-equilibrium colloidal assembly pathways via synergistic dipolar, depletion, and hydrodynamic interactions

    NASA Astrophysics Data System (ADS)

    Coughlan, Anna; Bevan, Michael

    The ability to assemble nano- and micro- colloidal particles into ordered materials and controllable devices provides the basis for emerging technologies. However, current capabilities for manipulating colloidal assembly are limited by the degree of order, time to generate/reconfigure structures, and scalability to large areas. These limitations are due to problems with designing, controlling, and optimizing the thermodynamics and kinetics of colloidal assembly. Our approach is to provide viable non-equilibrium pathways for rapid assembly of defect free colloidal crystals using combinations of magnetic field and depletion mediated assembly. Results include video microscopy experiments and Stokesian Dynamic computer simulations of superparamagnetic colloidal particles experiencing depletion attraction in time varying magnetic fields. Findings show multi-body hydrodynamic interactions and magnetic dipole relaxation mechanisms are essential to capture assembly and annealing of attractive colloidal crystals. With the ability to measure, model and tune colloidal interactions and dynamics, we demonstrate the use of time varying fields to manipulate non-equilibrium pathways for the assembly, disassembly, and repair of colloidal microstructures.

  10. Interactions Between the Canonical WNT/Beta-Catenin Pathway and PPAR Gamma on Neuroinflammation, Demyelination, and Remyelination in Multiple Sclerosis.

    PubMed

    Vallée, Alexandre; Vallée, Jean-Noël; Guillevin, Rémy; Lecarpentier, Yves

    2017-09-13

    Multiple sclerosis (MS) is marked by neuroinflammation and demyelination with loss of oligodendrocytes in the central nervous system. The immune response is regulated by WNT/beta-catenin pathway in MS. Activated NF-kappaB, a major effector of neuroinflammation, and upregulated canonical WNT/beta-catenin pathway positively regulate each other. Demyelinating events present an upregulation of WNT/beta-catenin pathway, whereas proper myelinating phases show a downregulation of WNT/beta-catenin pathway essential for the promotion of oligodendrocytes precursors cells proliferation and differentiation. The activation of WNT/beta-catenin pathway results in differentiation failure and impairment in remyelination. However, PI3K/Akt pathway and TCF7L2, two downstream targets of WNT/beta-catenin pathway, are upregulated and promote proper remyelination. The interactions of these signaling pathways remain unclear. PPAR gamma activation can inhibit NF-kappaB, and can also downregulate the WNT/beta-catenin pathway. PPAR gamma and canonical WNT/beta-catenin pathway act in an opposite manner. PPAR gamma agonists appear as a promising treatment for the inhibition of demyelination and the promotion of proper remyelination through the control of both NF-kappaB activity and canonical WNT/beta-catenin pathway.

  11. Interaction of Prenatal Exposure to Cigarettes and MAOA Genotype in Pathways to Youth Antisocial Behavior

    PubMed Central

    Wakschlag, Lauren S.; Kistner, Emily O.; Pine, Daniel S.; Biesecker, Gretchen; Pickett, Kate E.; Skol, Andrew; Dukic, Vanja; Blair, R. James; Leventhal, Bennett L.; Cox, Nancy; Burns, James; Kasza, Kristen E.; Wright, Rosalind J.; Cook, Edwin H.

    2009-01-01

    Genetic susceptibility to antisocial behavior may increase fetal sensitivity to prenatal exposure to cigarette smoke. Testing putative Gene × Exposure mechanisms requires precise measurement of exposure and outcomes. We tested whether a functional polymorphism in the gene encoding the enzyme monoamine oxidase A (MAOA) interacts with exposure to predict pathways to adolescent antisocial behavior. We assessed both clinical and information-processing outcomes. 176 adolescents and their mothers participated in a follow-up of a pregnancy cohort with well-characterized exposure. A sex-specific pattern of gene × exposure interaction was detected. Exposed boys with the low activity MAOA 5’ untranslated region variable number of tandem repeats (uVNTR) genotype were at increased risk for Conduct Disorder (CD) symptoms. In contrast, exposed girls with the high activity MAOA uVNTR genotype were at increased risk for both CD symptoms and hostile attribution bias on a face-processing task. There was no evidence of a gene-environment correlation (rGE). Findings suggest that the MAOA uVNTR genotype, prenatal exposure to cigarettes, and sex interact to predict antisocial behavior and related information-processing patterns. Future research to replicate and extend these findings may focus on elucidating how gene × exposure interactions may shape behavior via associated changes in brain function. PMID:19255579

  12. Quantifying causal pathways of interactions in the complex tropical climate system

    NASA Astrophysics Data System (ADS)

    Runge, Jakob; Donges, Jonathan; Hlinka, Jaroslav; Jajcay, Nicola; Marwan, Norbert; Palus, Milan; Kurths, Jürgen

    2015-04-01

    The focus of this work is to better understand the complex interplay between different subprocesses in the climate system, especially how tropical processes such as El Nino-Southern Oscillation (ENSO), the Indian Ocean Dipole, Tropical Atlantic Variability, and the tropical monsoons affect global climate. Here a novel data-driven method is proposed based on: (1) a dimension reduction of the global surface pressure field yielding components that represent various known subprocesses such as ENSO or the North Atlantic Oscillation, (2) a causal reconstruction algorithm to detect which subprocesses are only indirectly interacting or are only spuriously correlated due to common drivers, and (3) measures to identify causal pathways in the reconstructed interaction network. Two main results will be presented: (1) an hypothesis of a mechanism by which ENSO influences the Indian Monsoon within the surface pressure field. (2) In an explorative analysis it is shown that the method correctly identifies the major regions of upwelling convergence in the tropical oceans and also regions of strong downwelling. The approach provides a novel causal interaction perspective on complex spatio-temporal systems. Reference: Runge, J., Petoukhov, V., & Kurths, J. (2014). Quantifying the strength and delay of climatic interactions: the ambiguities of cross correlation and a novel measure based on graphical models. Journal of Climate, 27(2), 720-739. doi:10.1175/JCLI-D-13-00159.1

  13. Interaction of prenatal exposure to cigarettes and MAOA genotype in pathways to youth antisocial behavior.

    PubMed

    Wakschlag, L S; Kistner, E O; Pine, D S; Biesecker, G; Pickett, K E; Skol, A D; Dukic, V; Blair, R J R; Leventhal, B L; Cox, N J; Burns, J L; Kasza, K E; Wright, R J; Cook, E H

    2010-09-01

    Genetic susceptibility to antisocial behavior may increase fetal sensitivity to prenatal exposure to cigarette smoke. Testing putative gene x exposure mechanisms requires precise measurement of exposure and outcomes. We tested whether a functional polymorphism in the gene encoding the enzyme monoamine oxidase A (MAOA) interacts with exposure to predict pathways to adolescent antisocial behavior. We assessed both clinical and information-processing outcomes. One hundred seventy-six adolescents and their mothers participated in a follow-up of a pregnancy cohort with well-characterized exposure. A sex-specific pattern of gene x exposure interaction was detected. Exposed boys with the low-activity MAOA 5' uVNTR (untranslated region variable number of tandem repeats) genotype were at increased risk for conduct disorder (CD) symptoms. In contrast, exposed girls with the high-activity MAOA uVNTR genotype were at increased risk for both CD symptoms and hostile attribution bias on a face-processing task. There was no evidence of a gene-environment correlation (rGE). Findings suggest that the MAOA uVNTR genotype, prenatal exposure to cigarettes and sex interact to predict antisocial behavior and related information-processing patterns. Future research to replicate and extend these findings should focus on elucidating how gene x exposure interactions may shape behavior through associated changes in brain function.

  14. Cdc42p-Interacting Protein Bem4p Regulates the Filamentous-Growth Mitogen-Activated Protein Kinase Pathway

    PubMed Central

    Pitoniak, Andrew; Chavel, Colin A.; Chow, Jacky; Smith, Jeremy; Camara, Diawoye; Karunanithi, Sheelarani; Li, Boyang; Wolfe, Kennith H.

    2014-01-01

    The ubiquitous Rho (Ras homology) GTPase Cdc42p can function in different settings to regulate cell polarity and cellular signaling. How Cdc42p and other proteins are directed to function in a particular context remains unclear. We show that the Cdc42p-interacting protein Bem4p regulates the mitogen-activated protein kinase (MAPK) pathway that controls filamentous growth in Saccharomyces cerevisiae. Bem4p controlled the filamentous-growth pathway but not other MAPK pathways (mating or high-osmolarity glycerol response [HOG]) that also require Cdc42p and other shared components. Bem4p associated with the plasma membrane (PM) protein, Sho1p, to regulate MAPK activity and cell polarization under nutrient-limiting conditions that favor filamentous growth. Bem4p also interacted with the major activator of Cdc42p, the guanine nucleotide exchange factor (GEF) Cdc24p, which we show also regulates the filamentous-growth pathway. Bem4p interacted with the pleckstrin homology (PH) domain of Cdc24p, which functions in an autoinhibitory capacity, and was required, along with other pathway regulators, to maintain Cdc24p at polarized sites during filamentous growth. Bem4p also interacted with the MAPK kinase kinase (MAPKKK) Ste11p. Thus, Bem4p is a new regulator of the filamentous-growth MAPK pathway and binds to general proteins, like Cdc42p and Ste11p, to promote a pathway-specific response. PMID:25384973

  15. Learning to Teach: Comparing the Effectiveness of Three Pathways

    ERIC Educational Resources Information Center

    Chiero, Robin; Tracz, Susan M.; Marshall, James; Torgerson, Colleen; Beare, Paul

    2012-01-01

    This study examined the differential effectiveness of three pathways to an elementary teaching credential across a large public university system. The study compared traditional campus-based, intern, and online credential programs across a 22-campus system using ratings of program preparation by 12,590 graduates after their first year of teaching…

  16. Interactions between Melanin Enzymes and Their Atypical Recruitment to the Secretory Pathway by Palmitoylation.

    PubMed

    Upadhyay, Srijana; Xu, Xinping; Lin, Xiaorong

    2016-11-22

    Melanins are biopolymers that confer coloration and protection to the host organism against biotic or abiotic insults. The level of protection offered by melanin depends on its biosynthesis and its subcellular localization. Previously, we discovered that Aspergillus fumigatus compartmentalizes melanization in endosomes by recruiting all melanin enzymes to the secretory pathway. Surprisingly, although two laccases involved in the late steps of melanization are conventional secretory proteins, the four enzymes involved in the early steps of melanization lack a signal peptide or a transmembrane domain and are thus considered "atypical" secretory proteins. In this work, we found interactions among melanin enzymes and all melanin enzymes formed protein complexes. Surprisingly, the formation of protein complexes by melanin enzymes was not critical for their trafficking to the endosomal system. By palmitoylation profiling and biochemical analyses, we discovered that all four early melanin enzymes were strongly palmitoylated during conidiation. However, only the polyketide synthase (PKS) Alb1 was strongly palmitoylated during both vegetative hyphal growth and conidiation when constitutively expressed alone. This posttranslational lipid modification correlates the endosomal localization of all early melanin enzymes. Intriguingly, bioinformatic analyses predict that palmitoylation is a common mechanism for potential membrane association of polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) in A. fumigatus Our findings indicate that protein-protein interactions facilitate melanization by metabolic channeling, while posttranslational lipid modifications help recruit the atypical enzymes to the secretory pathway, which is critical for compartmentalization of secondary metabolism. Subcellular compartmentalization is increasingly recognized as an important aspect of fungal secondary metabolism. It facilitates sequential enzymatic reactions, provides

  17. Modeling of Non-Steroidal Anti-Inflammatory Drug Effect within Signaling Pathways and miRNA-Regulation Pathways

    PubMed Central

    Li, Jian; Mansmann, Ulrich R.

    2013-01-01

    To date, it is widely recognized that Non-Steroidal Anti-Inflammatory Drugs (NSAIDs) can exert considerable anti-tumor effects regarding many types of cancers. The prolonged use of NSAIDs is highly associated with diverse side effects. Therefore, tailoring down the NSAID application onto individual patients has become a necessary and relevant step towards personalized medicine. This study conducts the systemsbiological approach to construct a molecular model (NSAID model) containing a cyclooxygenase (COX)-pathway and its related signaling pathways. Four cancer hallmarks are integrated into the model to reflect different developmental aspects of tumorigenesis. In addition, a Flux-Comparative-Analysis (FCA) based on Petri net is developed to transfer the dynamic properties (including drug responsiveness) of individual cellular system into the model. The gene expression profiles of different tumor-types with available drug-response information are applied to validate the predictive ability of the NSAID model. Moreover, two therapeutic developmental strategies, synthetic lethality and microRNA (miRNA) biomarker discovery, are investigated based on the COX-pathway. In conclusion, the result of this study demonstrates that the NSAID model involving gene expression, gene regulation, signal transduction, protein interaction and other cellular processes, is able to predict the individual cellular responses for different therapeutic interventions (such as NS-398 and COX-2 specific siRNA inhibition). This strongly indicates that this type of model is able to reflect the physiological, developmental and pathological processes of an individual. The approach of miRNA biomarker discovery is demonstrated for identifying miRNAs with oncogenic and tumor suppressive functions for individual cell lines of breast-, colon- and lung-tumor. The achieved results are in line with different independent studies that investigated miRNA biomarker related to diagnostics of cancer treatments

  18. Building A Learning Pathway: An Interactive How-to Guide to Course Design

    DTIC Science & Technology

    2013-08-01

    Poster Chapter 10: Students’ Pathway to Success: The Course Syllabus Chapter 11 : Anticipating the Challenges Ahead References Cited Appendices...2000; Jones et al., 2009; Tagg, 2003) have learned a great deal in the last 20 years or so about what it really means to be an effective college-level...historically dominated higher education. According to the Chronicle of Higher Education (2010), the 6- year graduation rate at four- year public institutions

  19. Deciphering the biological effects of acupuncture treatment modulating multiple metabolism pathways.

    PubMed

    Zhang, Aihua; Yan, Guangli; Sun, Hui; Cheng, Weiping; Meng, Xiangcai; Liu, Li; Xie, Ning; Wang, Xijun

    2016-02-16

    Acupuncture is an alternative therapy that is widely used to treat various diseases. However, detailed biological interpretation of the acupuncture stimulations is limited. We here used metabolomics and proteomics technology, thereby identifying the serum small molecular metabolites into the effect and mechanism pathways of standardized acupuncture treatments at 'Zusanli' acupoint which was the most often used acupoint in previous reports. Comprehensive overview of serum metabolic profiles during acupuncture stimulation was investigated. Thirty-four differential metabolites were identified in serum metabolome and associated with ten metabolism pathways. Importantly, we have found that high impact glycerophospholipid metabolism, fatty acid metabolism, ether lipid metabolism were acutely perturbed by acupuncture stimulation. As such, these alterations may be useful to clarify the biological mechanism of acupuncture stimulation. A series of differentially expressed proteins were identified and such effects of acupuncture stimulation were found to play a role in transport, enzymatic activity, signaling pathway or receptor interaction. Pathway analysis further revealed that most of these proteins were found to play a pivotal role in the regulation of multiple metabolism pathways. It demonstrated that the metabolomics coupled with proteomics as a powerful approach for potential applications in understanding the biological effects of acupuncture stimulation.

  20. Uncertainty quantification of effective nuclear interactions

    SciTech Connect

    Pérez, R. Navarro; Amaro, J. E.; Arriola, E. Ruiz

    2016-03-02

    We give a brief review on the development of phenomenological NN interactions and the corresponding quanti cation of statistical uncertainties. We look into the uncertainty of effective interactions broadly used in mean eld calculations through the Skyrme parameters and effective eld theory counter-terms by estimating both statistical and systematic uncertainties stemming from the NN interaction. We also comment on the role played by different tting strategies on the light of recent developments.

  1. The Clickable Guard Cell, Version II: Interactive Model of Guard Cell Signal Transduction Mechanisms and Pathways.

    PubMed

    Kwak, June M; Mäser, Pascal; Schroeder, Julian I

    2008-01-01

    Guard cells are located in the leaf epidermis and pairs of guard cells surround and form stomatal pores, which regulate CO(2) influx from the atmosphere into leaves for photosynthetic carbon fixation. Stomatal guard cells also regulate water loss of plants via transpiration to the atmosphere. Signal transduction mechanisms in guard cells integrate a multitude of different stimuli to modulate stomatal apertures. Stomata open in response to light. Stomata close in response to drought stress, elevated CO(2), ozone and low humidity. In response to drought, plants synthesize the hormone abscisic acid (ABA) that triggers closing of stomatal pores. Guard cells have become a highly developed model system for dissecting signal transduction mechanisms in plants and for elucidating how individual signaling mechanisms can interact within a network in a single cell. Many new findings have been made in the last few years. This chapter is an update of an electronic interactive chapter in the previous edition of The Arabidopsis Book (Mäser et al. 2003). Here we focus on mechanisms for which genes and mutations have been characterized, including signaling components for which there is substantial signaling, biochemical and genetic evidence. Ion channels have been shown to represent targets of early signal transduction mechanisms and provide functional signaling and quantitative analysis points to determine where and how mutations affect branches within the guard cell signaling network. Although a substantial number of genes and proteins that function in guard cell signaling have been identified in recent years, there are many more left to be identified and the protein-protein interactions within this network will be an important subject of future research. A fully interactive clickable electronic version of this publication can be accessed at the following web site: http://www-biology.ucsd.edu/labs/schroeder/clickablegc2/. The interactive clickable version includes the following

  2. Gene Interactions Provide Evidence for Signaling Pathways Involved in Cleft Lip/Palate in Humans.

    PubMed

    Velázquez-Aragón, J A; Alcántara-Ortigoza, M A; Estandia-Ortega, B; Reyna-Fabián, M E; Méndez-Adame, C D; González-Del Angel, A

    2016-10-01

    Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common craniofacial birth defect that has a complex etiology. Genome-wide association studies have recently identified new loci associated with NSCL/P, but these loci have not been analyzed in a Mexican Mestizo population. A complex etiology implies the presence of genetic interactions, but there is little available information regarding this in NSCL/P, and no signaling pathway has been clearly implicated in humans. Here, we analyzed the associations of 24 single nucleotide polymorphisms (SNPs) with NSCL/P in a Mexican Mestizo population (133 cases, 263 controls). The multifactorial dimensionality reduction method was used to examine gene-gene and gene-folic acid consumption interactions for the 24 SNPs analyzed in this study and for 2 additional SNPs that had previously been genotyped in the same study population. Six SNPs located in paired box 7, ventral anterior homeobox 1, sprouty RTK signaling antagonist 2, bone morphogenetic protein 4, and tropomyosin 1 genes were associated with higher risks of NSCL/P (P = 0.0001 to 0.04); 2 SNPs, 1 each in netrin 1 and V-maf avian musculoaponeurotic fibrosarcoma oncogene homolog B, were associated with a lower risk of NSCL/P (P = 0.013 to 0.03); and 2 SNPs, 1 each in ATP binding cassette subfamily A member 4 (ABCA4) and noggin, showed associations with NSCL/P that approached the threshold of significance (P = 0.056 to 0.07). In addition, 6 gene-gene interactions (P = 0.0001 to 0.001) and an ABCA4-folic acid consumption interaction (P < 0.0001) were identified. On the basis of these results, combined with those of previous association studies in the literature and biological characterizations of murine models, we propose an interaction network in which interferon regulatory factor 6 plays a central role in the etiology of NSCL/P.

  3. The Hippo Pathway and YAP/TAZ-TEAD Protein-Protein Interaction as Targets for Regenerative Medicine and Cancer Treatment.

    PubMed

    Santucci, Matteo; Vignudelli, Tatiana; Ferrari, Stefania; Mor, Marco; Scalvini, Laura; Bolognesi, Maria Laura; Uliassi, Elisa; Costi, Maria Paola

    2015-06-25

    The Hippo pathway is an important organ size control signaling network and the major regulatory mechanism of cell-contact inhibition. Yes associated protein (YAP) and transcriptional co-activator with PDZ-binding motif (TAZ) are its targets and terminal effectors: inhibition of the pathway promotes YAP/TAZ translocation to the nucleus, where they interact with transcriptional enhancer associate domain (TEAD) transcription factors and coactivate the expression of target genes, promoting cell proliferation. Defects in the pathway can result in overgrowth phenotypes due to deregulation of stem-cell proliferation and apoptosis; members of the pathway are directly involved in cancer development. The pharmacological regulation of the pathway might be useful in cancer prevention, treatment, and regenerative medicine applications; currently, a few compounds can selectively modulate the pathway. In this review, we present an overview of the Hippo pathway, the sequence and structural analysis of YAP/TAZ, the known pharmacological modulators of the pathway, especially those targeting YAP/TAZ-TEAD interaction.

  4. Improved Protein Arrays for Quantitative Systems Analysis of the Dynamics of Signaling Pathway Interactions

    SciTech Connect

    YANG, CHIN-RANG

    2013-12-11

    Astronauts and workers in nuclear plants who repeatedly exposed to low doses of ionizing radiation (IR, <10 cGy) are likely to incur specific changes in signal transduction and gene expression in various tissues of their body. Remarkable advances in high throughput genomics and proteomics technologies enable researchers to broaden their focus from examining single gene/protein kinetics to better understanding global gene/protein expression profiling and biological pathway analyses, namely Systems Biology. An ultimate goal of systems biology is to develop dynamic mathematical models of interacting biological systems capable of simulating living systems in a computer. This Glue Grant is to complement Dr. Boothman’s existing DOE grant (No. DE-FG02-06ER64186) entitled “The IGF1/IGF-1R-MAPK-Secretory Clusterin (sCLU) Pathway: Mediator of a Low Dose IR-Inducible Bystander Effect” to develop sensitive and quantitative proteomic technology that suitable for low dose radiobiology researches. An improved version of quantitative protein array platform utilizing linear Quantum dot signaling for systematically measuring protein levels and phosphorylation states for systems biology modeling is presented. The signals are amplified by a confocal laser Quantum dot scanner resulting in ~1000-fold more sensitivity than traditional Western blots and show the good linearity that is impossible for the signals of HRP-amplification. Therefore this improved protein array technology is suitable to detect weak responses of low dose radiation. Software is developed to facilitate the quantitative readout of signaling network activities. Kinetics of EGFRvIII mutant signaling was analyzed to quantify cross-talks between EGFR and other signaling pathways.

  5. gigantea Suppresses immutans Variegation by Interactions with Cytokinin and Gibberellin Signaling Pathways1[W][OPEN

    PubMed Central

    Putarjunan, Aarthi; Rodermel, Steve

    2014-01-01

    The immutans (im) variegation mutant of Arabidopsis (Arabidopsis thaliana) is an ideal model to gain insight into factors that control chloroplast biogenesis. im defines the gene for PTOX, a plastoquinol terminal oxidase that participates in the control of thylakoid redox. Here, we report that the im defect can be suppressed during the late stages of plant development by gigantea (gi2), which defines the gene for GI, a central component of the circadian clock that plays a poorly understood role in diverse plant developmental processes. imgi2 mutants are late flowering and display other well-known phenotypes associated with gi2, such as starch accumulation and resistance to oxidative stress. We show that the restoration of chloroplast biogenesis in imgi2 is caused by a development-specific derepression of cytokinin signaling that involves cross talk with signaling pathways mediated by gibberellin (GA) and SPINDLY (SPY), a GA response inhibitor. Suppression of the plastid defect in imgi2 is likely caused by a relaxation of excitation pressures in developing plastids by factors contributed by gi2, including enhanced rates of photosynthesis and increased resistance to oxidative stress. Interestingly, the suppression phenotype of imgi can be mimicked by crossing im with the starch accumulation mutant, starch excess1 (sex1), perhaps because sex1 utilizes pathways similar to gi. We conclude that our studies provide a direct genetic linkage between GI and chloroplast biogenesis, and we construct a model of interactions between signaling pathways mediated by gi, GA, SPY, cytokinins, and sex1 that are required for chloroplast biogenesis. PMID:25349324

  6. Gene-environment interactions in male reproductive health: special reference to the aryl hydrocarbon receptor signaling pathway.

    PubMed

    Brokken, Leon J S; Giwercman, Yvonne Lundberg

    2014-01-01

    Over the last few decades, there have been numerous reports of adverse effects on the reproductive health of wildlife and laboratory animals caused by exposure to endocrine disrupting chemicals (EDCs). The increasing trends in human male reproductive disorders and the mounting evidence for causative environmental factors have therefore sparked growing interest in the health threat posed to humans by EDCs, which are substances in our food, environment and consumer items that interfere with hormone action, biosynthesis or metabolism, resulting in disrupted tissue homeostasis or reproductive function. The mechanisms of EDCs involve a wide array of actions and pathways. Examples include the estrogenic, androgenic, thyroid and retinoid pathways, in which the EDCs may act directly as agonists or antagonists, or indirectly via other nuclear receptors. Dioxins and dioxin-like EDCs exert their biological and toxicological actions through activation of the aryl hydrocarbon-receptor, which besides inducing transcription of detoxifying enzymes also regulates transcriptional activity of other nuclear receptors. There is increasing evidence that genetic predispositions may modify the susceptibility to adverse effects of toxic chemicals. In this review, potential consequences of hereditary predisposition and EDCs are discussed, with a special focus on the currently available publications on interactions between dioxin and androgen signaling.

  7. Gene-environment interactions in male reproductive health: Special reference to the aryl hydrocarbon receptor signaling pathway

    PubMed Central

    Brokken, Leon J S; Giwercman, Yvonne Lundberg

    2014-01-01

    Over the last few decades, there have been numerous reports of adverse effects on the reproductive health of wildlife and laboratory animals caused by exposure to endocrine disrupting chemicals (EDCs). The increasing trends in human male reproductive disorders and the mounting evidence for causative environmental factors have therefore sparked growing interest in the health threat posed to humans by EDCs, which are substances in our food, environment and consumer items that interfere with hormone action, biosynthesis or metabolism, resulting in disrupted tissue homeostasis or reproductive function. The mechanisms of EDCs involve a wide array of actions and pathways. Examples include the estrogenic, androgenic, thyroid and retinoid pathways, in which the EDCs may act directly as agonists or antagonists, or indirectly via other nuclear receptors. Dioxins and dioxin-like EDCs exert their biological and toxicological actions through activation of the aryl hydrocarbon-receptor, which besides inducing transcription of detoxifying enzymes also regulates transcriptional activity of other nuclear receptors. There is increasing evidence that genetic predispositions may modify the susceptibility to adverse effects of toxic chemicals. In this review, potential consequences of hereditary predisposition and EDCs are discussed, with a special focus on the currently available publications on interactions between dioxin and androgen signaling. PMID:24369137

  8. Effective interactions of DNA-stars

    NASA Astrophysics Data System (ADS)

    Abaurrea Velasco, Clara; Likos, Christos N.; Kahl, Gerhard

    2015-09-01

    We put forward a model that allows the calculation of the effective potential of two interacting DNA-stars, i.e., three-armed, Y-shaped, charged macromolecules, built up by three intertwined single-stranded DNAs. These particles are assumed to float on a flat interface separating two media with different dielectric properties. As the only input, our model requires the charge density along the branches and the interaction between two infinitesimally short segments, along two interacting rods. With this effective interaction at hand, a detailed investigations of the self-assembly scenarios of these molecules either via computer simulations or via theoretical frameworks comes within reach.

  9. PRL-3 activates NF-κB signaling pathway by interacting with RAP1.

    PubMed

    Lian, Shenyi; Meng, Lin; Liu, Caiyun; Xing, Xiaofang; Song, Qian; Dong, Bin; Han, Yong; Yang, Yongyong; Peng, Lirong; Qu, Like; Shou, Chengchao

    2013-01-04

    Phosphatase of regenerating liver (PRL-3) promotes cancer metastasis through enhanced cell motility and invasiveness, however its role in tumorigenesis remains unclear. Herein, we reported that PRL-3 interacts with telomere-related protein RAP1. PRL-3 promotes the cytosolic localization of RAP1, which is counteracted by silencing of PRL-3. Immunohistochemical staining of colon cancer tissue array (n=170) revealed that high level of PRL-3 associates with cytosolic localization of RAP1 (p=0.01). Microarray analysis showed that PRL-3 regulates expression of diverse genes and enhances phosphorylation of p65 subunit of NF-κB in a RAP1-dependent manner. Furthermore, PRL-3 transcriptionally activates RAP1 expression, which is counteracted by ablating p65. Therefore, our results demonstrate PRL-3 as a novel regulator of NF-κB signaling pathway through RAP1.

  10. Cellular and molecular pathways of extremely-low-frequency electromagnetic field interactions with living systems

    SciTech Connect

    Tenforde, T.S.

    1992-06-01

    There is growing evidence that environmental electric and magnetic fields in the extremely-low-frequency (ELF) band below 300 Hz can influence biological functions by mechanisms that are only poorly understood at the present time. The primary objectives of this paper are to review the physical properties of ELF fields, their interactions with living systems at the tissue, cellular, and subcellular levels, and the key role of cell membranes ;in the transduction of signals from imposed ELF fields. Topics of discussion include signal-to-noise ratios for single cells and cell aggregates, resonance phenomena involving a combination of static and ELF magnetic fields, and the possible influence of ELF fields on molecular signaling pathways that involve membrane receptors and cytoplasmic second messengers.

  11. Cellular and molecular pathways of extremely-low-frequency electromagnetic field interactions with living systems

    SciTech Connect

    Tenforde, T.S.

    1992-06-01

    There is growing evidence that environmental electric and magnetic fields in the extremely-low-frequency (ELF) band below 300 Hz can influence biological functions by mechanisms that are only poorly understood at the present time. The primary objectives of this paper are to review the physical properties of ELF fields, their interactions with living systems at the tissue, cellular, and subcellular levels, and the key role of cell membranes ;in the transduction of signals from imposed ELF fields. Topics of discussion include signal-to-noise ratios for single cells and cell aggregates, resonance phenomena involving a combination of static and ELF magnetic fields, and the possible influence of ELF fields on molecular signaling pathways that involve membrane receptors and cytoplasmic second messengers.

  12. Interaction of Chlamydia trachomatis serovar L2 with the host autophagic pathway.

    PubMed

    Al-Younes, Hesham M; Brinkmann, Volker; Meyer, Thomas F

    2004-08-01

    Chlamydiae are obligate intracellular pathogens that replicate within a membrane-bound compartment (the inclusion) and are associated with important human diseases, such as trachoma, pneumonia, and atherosclerosis. We have examined the interaction of the host autophagic pathway with Chlamydia trachomatis serovar L2 by using the specific autophagosomal stain monodansylcadaverine, antibodies to autophagosome-associated markers, and traditionally used autophagic inhibitors, particularly 3-methyladenine and amino acids. Chlamydial inclusions did not sequester monodansylcadaverine, suggesting absence of fusion with autophagosomes. Interestingly, exposure of cultures infected for 19 h to 3-methyladenine or single amino acids until the end of infection (44 h) caused various degrees of abnormalities in the inclusion maturation and in the progeny infectivity. Incubation of host cells with chemicals throughout the entire period of infection modulated the growth of Chlamydia even more dramatically. Remarkably, autophagosomal markers MAP-LC3 and calreticulin were redistributed to the inclusion of Chlamydia, a process that appears to be sensitive to 3-methyladenine and some amino acids. The present data indicate the lack of autophagosomal fusion with the inclusion because it was devoid of monodansylcadaverine and no distinct rim of autophagosomal protein-specific staining around the inclusion could be observed. However, high sensitivity of Chlamydia to conditions that could inhibit host autophagic pathway and the close association of MAP-LC3 and calreticulin with the inclusion membrane still suggest a potential role of host autophagy in the pathogenesis of Chlamydia.

  13. Applied neuroanatomy elective to reinforce and promote engagement with neurosensory pathways using interactive and artistic activities.

    PubMed

    Dao, Vinh; Yeh, Pon-Hsiu; Vogel, Kristine S; Moore, Charleen M

    2015-01-01

    One in six Americans is currently affected by neurologic disease. As the United States population ages, the number of neurologic complaints is expected to increase. Thus, there is a pressing need for more neurologists as well as more neurology training in other specialties. Often interest in neurology begins during medical school, so improving education in medical neural courses is a critical step toward producing more neurologists and better neurology training in other specialists. To this end, a novel applied neuroanatomy elective was designed at the University of Texas Health Science Center at San Antonio (UTHSCSA) to complement the traditional first-year medical neuroscience course and promote engagement and deep learning of the material with a focus on neurosensory pathways. The elective covered four neurosensory modalities (proprioception/balance, vision, auditory, and taste/olfaction) over four sessions, each with a short classroom component and a much longer activity component. At each session, students reviewed the neurosensory pathways through structured presentations and then applied them to preplanned interactive activities, many of which allowed students to utilize their artistic talents. Students were required to complete subjective pre-course and post-course surveys and reflections. The survey results and positive student comments suggest that the elective was a valuable tool when used in parallel with the traditional medical neuroscience course in promoting engagement and reinforcement of the neurosensory material.

  14. A Candidate-Pathway Approach to Identify Gene-Environment Interactions: Analyses of Colon Cancer Risk and Survival

    PubMed Central

    Sharafeldin, Noha; Slattery, Martha L.; Liu, Qi; Franco-Villalobos, Conrado; Caan, Bette J.; Potter, John D.

    2015-01-01

    Background: Genetic association studies have traditionally focused on associations between individual single nucleotide polymorphisms (SNPs) and disease. Standard analysis ignores interactions between multiple SNPs and environmental exposures explaining a small portion of disease heritability: the often-cited issue of “missing heritability.” Methods: We present a novel three-step analytic framework for modeling gene-environment interactions (GEIs) between an angiogenesis candidate-gene pathway and three lifestyle exposures (dietary protein, smoking, and alcohol consumption) on colon cancer risk and survival. Logic regression was used to summarize the gene-pathway effects, and GEIs were modeled using logistic regression and Cox proportional hazards models. We analyzed data from 1541 colon cancer case patients and 1934 control subjects in the Diet, Activity and Lifestyle as a Risk Factor for Colon Cancer Study. Results: We identified five statistically significant GEIs for colon cancer risk. For risk interaction, odds ratios (ORINT) and 95% confidence intervals (CIs) were FLT1(rs678714) and BMP4(rs17563) and smoking (ORINT = 1.64, 95% CI = 1.11 to 2.41 and ORINT = 1.60, 95% CI = 1.10 to 2.32, respectively); FLT1(rs2387632 OR rs9513070) and protein intake (ORINT = 1.69, 95% CI = 1.03 to 2.77); KDR(rs6838752) and TLR2(rs3804099) and alcohol (ORINT = 1.53, 95% CI = 1.10 to 2.13 and ORINT = 1.59, 95% CI = 1.05 to 2.38, respectively). Three GEIs between TNF, BMP1, and BMPR2 genes and the three exposures were statistically significant at the 5% level in relation to colon cancer survival but not after multiple-testing adjustment. Conclusions: Adopting a comprehensive biologically informed candidate-pathway approach identified GEI effects on colon cancer. Findings may have important implications for public health and personalized medicine targeting prevention and therapeutic strategies. Findings from this study need to be validated in other studies. PMID:26072521

  15. Notch1 Regulates Hippocampal Plasticity Through Interaction with the Reelin Pathway, Glutamatergic Transmission and CREB Signaling

    PubMed Central

    Brai, Emanuele; Marathe, Swananda; Astori, Simone; Fredj, Naila Ben; Perry, Elisabeth; Lamy, Christophe; Scotti, Alessandra; Alberi, Lavinia

    2015-01-01

    Notch signaling plays a crucial role in adult brain function such as synaptic plasticity, memory and olfaction. Several reports suggest an involvement of this pathway in neurodegenerative dementia. Yet, to date, the mechanism underlying Notch activity in mature neurons remains unresolved. In this work, we investigate how Notch regulates synaptic potentiation and contributes to the establishment of memory in mice. We observe that Notch1 is a postsynaptic receptor with functional interactions with the Reelin receptor, apolipoprotein E receptor 2 (ApoER2) and the ionotropic receptor, N-methyl-D-aspartate receptor (NMDAR). Targeted loss of Notch1 in the hippocampal CA fields affects Reelin signaling by influencing Dab1 expression and impairs the synaptic potentiation achieved through Reelin stimulation. Further analysis indicates that loss of Notch1 affects the expression and composition of the NMDAR but not AMPAR. Glutamatergic signaling is further compromised through downregulation of CamKII and its secondary and tertiary messengers resulting in reduced cAMP response element-binding (CREB) signaling. Our results identify Notch1 as an important regulator of mechanisms involved in synaptic plasticity and memory formation. These findings emphasize the possible involvement of this signaling receptor in dementia. Highlights In this paper, we propose a mechanism for Notch1-dependent plasticity that likely underlies the function of Notch1 in memory formation: Notch1 interacts with another important developmental pathway, the Reelin cascade. Notch1 regulates both NMDAR expression and composition. Notch1 influences a cascade of cellular events culminating in CREB activation. PMID:26635527

  16. Inherited mitochondrial DNA variants can affect complement, inflammation and apoptosis pathways: insights into mitochondrial–nuclear interactions

    PubMed Central

    Cristina Kenney, M.; Chwa, Marilyn; Atilano, Shari R.; Falatoonzadeh, Payam; Ramirez, Claudio; Malik, Deepika; Tarek, Mohamed; Cáceres-del-Carpio, Javier; Nesburn, Anthony B.; Boyer, David S.; Kuppermann, Baruch D.; Vawter, Marquis; Michal Jazwinski, S.; Miceli, Michael; Wallace, Douglas C.; Udar, Nitin

    2014-01-01

    Age-related macular degeneration (AMD) is the leading cause of vision loss in developed countries. While linked to genetic polymorphisms in the complement pathway, there are many individuals with high risk alleles that do not develop AMD, suggesting that other ‘modifiers’ may be involved. Mitochondrial (mt) haplogroups, defined by accumulations of specific mtDNA single nucleotide polymorphisms (SNPs) which represent population origins, may be one such modifier. J haplogroup has been associated with high risk for AMD while the H haplogroup is protective. It has been difficult to assign biological consequences for haplogroups so we created human ARPE-19 cybrids (cytoplasmic hybrids), which have identical nuclei but mitochondria of either J or H haplogroups, to investigate their effects upon bioenergetics and molecular pathways. J cybrids have altered bioenergetic profiles compared with H cybrids. Q-PCR analyses show significantly lower expression levels for seven respiratory complex genes encoded by mtDNA. J and H cybrids have significantly altered expression of eight nuclear genes of the alternative complement, inflammation and apoptosis pathways. Sequencing of the entire mtDNA was carried out for all the cybrids to identify haplogroup and non-haplogroup defining SNPs. mtDNA can mediate cellular bioenergetics and expression levels of nuclear genes related to complement, inflammation and apoptosis. Sequencing data suggest that observed effects are not due to rare mtDNA variants but rather the combination of SNPs representing the J versus H haplogroups. These findings represent a paradigm shift in our concepts of mt–nuclear interactions. PMID:24584571

  17. Inflammation and MiR-21 pathways functionally interact to downregulate PDCD4 in colorectal cancer.

    PubMed

    Peacock, Oliver; Lee, Andrew C; Cameron, Fraser; Tarbox, Rebecca; Vafadar-Isfahani, Natasha; Tufarelli, Cristina; Lund, Jonathan N

    2014-01-01

    Inflammation plays a direct role in colorectal cancer (CRC) progression; however the molecular mechanisms responsible for this effect are unclear. The inflammation induced cyclooxygenase 2 (COX-2) enzyme required for the production of Prostaglandin E2 (PGE2), can promote colorectal cancer by decreasing expression of the tumour suppressor gene Programmed Cell Death 4 (PDCD4). As PDCD4 is also a direct target of the oncogene microRNA-21 (miR-21) we investigated the relationship between the COX-2 and miR-21 pathways in colorectal cancer progression. Gene expression profile in tumour and paired normal mucosa from 45 CRC patients demonstrated that up-regulation of COX-2 and miR-21 in tumour tissue correlates with worse Dukes' stage. In vitro studies in colonic adenocarcinoma cells revealed that treatment with the selective COX-2 inhibitor NS398 significantly decreased miR-21 levels (p = 0.0067) and increased PDCD4 protein levels (p<0.001), whilst treatment with PGE2 up-regulated miR-21 expression (p = 0.019) and down-regulated PDCD4 protein (p<0.05). These findings indicate that miR-21 is a component of the COX-2 inflammation pathway and that this pathway promotes worsening of disease stage in colorectal cancer by inducing accumulation of PGE2 and increasing expression of miR-21 with consequent downregulation of the tumour suppressor gene PDCD4.

  18. Inhibition of TRAF6-Ubc13 interaction in NFkB inflammatory pathway by analyzing the hotspot amino acid residues and protein-protein interactions using molecular docking simulations.

    PubMed

    Biswas, Ria; Bagchi, Angshuman

    2017-10-01

    Protein-protein interactions (PPIs) are important in most of the biochemical processes. Hotspot amino acid residues in proteins are the most important contributors for proper protein-protein interactions. Hotspot amino acid residues have been looked down upon as important therapeutic targets in inhibiting PPIs. Interaction between TRAF6 and Ubc13 is a crucial point in the NFkB inflammatory pathway. Dysfunction of the NFkB pathway is associated with numerous human diseases including cancer and neurodenegeration disorders. Ubc13 also interacts specifically to TRAF6 and not with other proteins of the TRAF family and this makes the TRAF6-Ubc13 complex an important target for specific inhibition. Hence, interfering with the TRAF6-Ubc13 association may prove effective in suppressing the NFkB disease pathway. In the present study, we searched the TRAF6-Ubc13 interaction interface to analyze their binding hotspot amino acid residues using various computational techniques. Heterocyclic compounds are known for their medicinal properties. We screened for heterocyclic analogues to the known TRAF6 inhibitor PDTC, to predict a better inhibitor using in silico protein-ligand and protein-protein interaction studies. Our in silico prediction results suggest that tetrahydro-2-thiophenecarbothioamide (Chemspider ID 36027528) binds one of the major hot-spot residues of TRAF6-Ubc13 interface and can be a better alternative in suppressing TRA6-Ubc13 complex formation in chronic inflammation than PDTC. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Protein-Protein Interactions in the Yeast Pheromone Response Pathway: Ste5p Interacts with All Members of the Map Kinase Cascade

    PubMed Central

    Printen, J. A.; Sprague-Jr., G. F.

    1994-01-01

    We have used the two-hybrid system of Fields and Song to identify protein-protein interactions that occur in the pheromone response pathway of the yeast Saccharomyces cerevisiae. Pathway components Ste4p, Ste5p, Ste7p, Ste11p, Ste12p, Ste20p, Fus3p and Kss1p were tested in all pairwise combinations. All of the interactions we detected involved at least one member of the MAP kinase cascade that is a central element of the response pathway. Ste5p, a protein of unknown biochemical function, interacted with protein kinases that operate at each step of the MAP kinase cascade, specifically with Ste11p (an MEKK), Ste7p (an MEK), and Fus3p (a MAP kinase). This finding suggests that one role of Ste5p is to serve as a scaffold to facilitate interactions among members of the kinase cascade. In this role as facilitator, Ste5p may make both signal propagation and signal attenuation more efficient. Ste5p may also help minimize cross-talk with other MAP kinase cascades and thus ensure the integrity of the pheromone response pathway. We also found that both Ste11p and Ste7p interact with Fus3p and Kss1p. Finally, we detected an interaction between one of the MAP kinases, Kss1p, and a presumptive target, the transcription factor Ste12p. We failed to detect interactions of Ste4p or Ste20p with any other component of the response pathway. PMID:7851759

  20. Insights into the TOR-S6K signaling pathway in maize (Zea mays L.). pathway activation by effector-receptor interaction.

    PubMed

    Garrocho-Villegas, Verónica; Aguilar C, Raúl; Sánchez de Jiménez, Estela

    2013-12-23

    The primordial TOR pathway, known to control growth and cell proliferation, has still not been fully described for plants. Nevertheless, in maize, an insulin-like growth factor (ZmIGF) peptide has been reported to stimulate this pathway. This research provides further insight into the TOR pathway in maize, using a biochemical approach in cultures of fast-growing (FG) and slow-growing (SG) calli, as a model system. Our results revealed that addition of either ZmIGF or insulin to SG calli stimulated DNA synthesis and increased the growth rate through cell proliferation and increased the rate of ribosomal protein (RP) synthesis by the selective mobilization of RP mRNAs into polysomes. Furthermore, analysis of the phosphorylation status of the main TOR and S6K kinases from the TOR pathway revealed stimulation by ZmIGF or insulin, whereas rapamycin inhibited its activation. Remarkably, a putative maize insulin-like receptor was recognized by a human insulin receptor antibody, as demonstrated by immunoprecipitation from membrane protein extracts of maize callus. Furthermore, competition experiments between ZmIGF and insulin for the receptor site on maize protoplasts suggested structural recognition of the putative receptor by either effector. These data were confirmed by confocal immunolocalization within the cell membrane of callus cells. Taken together, these data indicate that cell growth and cell proliferation in maize depend on the activation of the TOR-S6K pathway through the interaction of an insulin-like growth factor and its receptor. This evidence suggests that higher plants as well as metazoans have conserved this biochemical pathway to regulate their growth, supporting the conclusion that it is a highly evolved conserved pathway.

  1. The Hippo pathway target, YAP, promotes metastasis through its TEAD-interaction domain.

    PubMed

    Lamar, John M; Stern, Patrick; Liu, Hui; Schindler, Jeffrey W; Jiang, Zhi-Gang; Hynes, Richard O

    2012-09-11

    The transcriptional coactivator Yes-associated protein (YAP) is a major regulator of organ size and proliferation in vertebrates. As such, YAP can act as an oncogene in several tissue types if its activity is increased aberrantly. Although no activating mutations in the yap1 gene have been identified in human cancer, yap1 is located on the 11q22 amplicon, which is amplified in several human tumors. In addition, mutations or epigenetic silencing of members of the Hippo pathway, which represses YAP function, have been identified in human cancers. Here we demonstrate that, in addition to increasing tumor growth, increased YAP activity is potently prometastatic in breast cancer and melanoma cells. Using a Luminex-based approach to multiplex in vivo assays, we determined that the domain of YAP that interacts with the TEAD/TEF family of transcription factors but not the WW domains or PDZ-binding motif, is essential for YAP-mediated tumor growth and metastasis. We further demonstrate that, through its TEAD-interaction domain, YAP enhances multiple processes known to be important for tumor progression and metastasis, including cellular proliferation, transformation, migration, and invasion. Finally, we found that the metastatic potential of breast cancer and melanoma cells is strongly correlated with increased TEAD transcriptional activity. Together, our results suggest that increased YAP/TEAD activity plays a causal role in cancer progression and metastasis.

  2. Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.

    PubMed

    Gorenshteyn, Dmitriy; Zaslavsky, Elena; Fribourg, Miguel; Park, Christopher Y; Wong, Aaron K; Tadych, Alicja; Hartmann, Boris M; Albrecht, Randy A; García-Sastre, Adolfo; Kleinstein, Steven H; Troyanskaya, Olga G; Sealfon, Stuart C

    2015-09-15

    Many functionally important interactions between genes and proteins involved in immunological diseases and processes are unknown. The exponential growth in public high-throughput data offers an opportunity to expand this knowledge. To unlock human-immunology-relevant insight contained in the global biomedical research effort, including all public high-throughput datasets, we performed immunological-pathway-focused Bayesian integration of a comprehensive, heterogeneous compendium comprising 38,088 genome-scale experiments. The distillation of this knowledge into immunological networks of functional relationships between molecular entities (ImmuNet), and tools to mine this resource, are accessible to the public at http://immunet.princeton.edu. The predictive capacity of ImmuNet, established by rigorous statistical validation, is easily accessed by experimentalists to generate data-driven hypotheses. We demonstrate the power of this approach through the identification of unique host-virus interaction responses, and we show how ImmuNet complements genetic studies by predicting disease-associated genes. ImmuNet should be widely beneficial for investigating the mechanisms of the human immune system and immunological diseases. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Interaction studies between periplasmic cytochromes provide insights into extracellular electron transfer pathways of Geobacter sulfurreducens.

    PubMed

    Fernandes, Ana P; Nunes, Tiago C; Paquete, Catarina M; Salgueiro, Carlos A

    2017-02-20

    Geobacter bacteria usually prevail among other microorganisms in soils and sediments where Fe(III) reduction has a central role. This reduction is achieved by extracellular electron transfer (EET), where the electrons are exported from the interior of the cell to the surrounding environment. Periplasmic cytochromes play an important role in establishing an interface between inner and outer membrane electron transfer components. In addition, periplasmic cytochromes, in particular nanowire cytochromes that contain at least 12 haem groups, have been proposed to play a role in electron storage in conditions of an environmental lack of electron acceptors. Up to date, no redox partners have been identified in Geobacter sulfurreducens, and concomitantly, the EET and electron storage mechanisms remain unclear. In this work, NMR chemical shift perturbation measurements were used to probe for an interaction between the most abundant periplasmic cytochrome PpcA and the dodecahaem cytochrome GSU1996, one of the proposed nanowire cytochromes in G. sulfurreducens The perturbations on the haem methyl signals of GSU1996 and PpcA showed that the proteins form a transient redox complex in an interface that involves haem groups from two different domains located at the C-terminal of GSU1996. Overall, the present study provides for the first time a clear evidence for an interaction between periplasmic cytochromes that might be relevant for the EET and electron storage pathways in G. sulfurreducens. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

  4. Targeting Plant Ethylene Responses by Controlling Essential Protein-Protein Interactions in the Ethylene Pathway.

    PubMed

    Bisson, Melanie M A; Groth, Georg

    2015-08-01

    The gaseous plant hormone ethylene regulates many processes of high agronomic relevance throughout the life span of plants. A central element in ethylene signaling is the endoplasmic reticulum (ER)-localized membrane protein ethylene insensitive2 (EIN2). Recent studies indicate that in response to ethylene, the extra-membranous C-terminal end of EIN2 is proteolytically processed and translocated from the ER to the nucleus. Here, we report that the conserved nuclear localization signal (NLS) mediating nuclear import of the EIN2 C-terminus provides an important domain for complex formation with ethylene receptor ethylene response1 (ETR1). EIN2 lacking the NLS domain shows strongly reduced affinity for the receptor. Interaction of EIN2 and ETR1 is also blocked by a synthetic peptide of the NLS motif. The corresponding peptide substantially reduces ethylene responses in planta. Our results uncover a novel mechanism and type of inhibitor interfering with ethylene signal transduction and ethylene responses in plants. Disruption of essential protein-protein interactions in the ethylene signaling pathway as shown in our study for the EIN2-ETR1 complex has the potential to guide the development of innovative ethylene antagonists for modern agriculture and horticulture.

  5. Broccoli Consumption Interacts with GSTM1 to Perturb Oncogenic Signalling Pathways in the Prostate

    PubMed Central

    Traka, Maria; Gasper, Amy V.; Melchini, Antonietta; Bacon, James R.; Needs, Paul W.; Frost, Victoria; Chantry, Andrew; Jones, Alexandra M. E.; Ortori, Catharine A.; Barrett, David A.; Ball, Richard Y.; Mills, Robert D.; Mithen, Richard F.

    2008-01-01

    Background Epidemiological studies suggest that people who consume more than one portion of cruciferous vegetables per week are at lower risk of both the incidence of prostate cancer and of developing aggressive prostate cancer but there is little understanding of the underlying mechanisms. In this study, we quantify and interpret changes in global gene expression patterns in the human prostate gland before, during and after a 12 month broccoli-rich diet. Methods and Findings Volunteers were randomly assigned to either a broccoli-rich or a pea-rich diet. After six months there were no differences in gene expression between glutathione S-transferase mu 1 (GSTM1) positive and null individuals on the pea-rich diet but significant differences between GSTM1 genotypes on the broccoli-rich diet, associated with transforming growth factor beta 1 (TGFβ1) and epidermal growth factor (EGF) signalling pathways. Comparison of biopsies obtained pre and post intervention revealed more changes in gene expression occurred in individuals on a broccoli-rich diet than in those on a pea-rich diet. While there were changes in androgen signalling, regardless of diet, men on the broccoli diet had additional changes to mRNA processing, and TGFβ1, EGF and insulin signalling. We also provide evidence that sulforaphane (the isothiocyanate derived from 4-methylsuphinylbutyl glucosinolate that accumulates in broccoli) chemically interacts with TGFβ1, EGF and insulin peptides to form thioureas, and enhances TGFβ1/Smad-mediated transcription. Conclusions These findings suggest that consuming broccoli interacts with GSTM1 genotype to result in complex changes to signalling pathways associated with inflammation and carcinogenesis in the prostate. We propose that these changes may be mediated through the chemical interaction of isothiocyanates with signalling peptides in the plasma. This study provides, for the first time, experimental evidence obtained in humans to support observational studies

  6. Learning Communities: Pathways for Educational Success and Social Transformation through Interactive Groups in Mathematics

    ERIC Educational Resources Information Center

    García-Carrión, Rocío; Díez-Palomar, Javier

    2015-01-01

    Schools as learning communities have been recommended by the European Commission as an effective model to support school quality and development. Aiming at studying how these schools are achieving such positive results, this article focuses on the analysis of a particular classroom intervention called "interactive groups". A five-year…

  7. Learning Communities: Pathways for Educational Success and Social Transformation through Interactive Groups in Mathematics

    ERIC Educational Resources Information Center

    García-Carrión, Rocío; Díez-Palomar, Javier

    2015-01-01

    Schools as learning communities have been recommended by the European Commission as an effective model to support school quality and development. Aiming at studying how these schools are achieving such positive results, this article focuses on the analysis of a particular classroom intervention called "interactive groups". A five-year…

  8. Partitioning the effects of an ecosystem engineer: kangaroo rats control community structure via multiple pathways.

    PubMed

    Prugh, Laura R; Brashares, Justin S

    2012-05-01

    1. Ecosystem engineers impact communities by altering habitat conditions, but they can also have strong effects through consumptive, competitive and other non-engineering pathways. 2. Engineering effects can lead to fundamentally different community dynamics than non-engineering effects, but the relative strengths of these interactions are seldom quantified. 3. We combined structural equation modelling and exclosure experiments to partition the effects of a keystone engineer, the giant kangaroo rat (Dipodomys ingens), on plants, invertebrates and vertebrates in a semi-arid California grassland. 4. We separated the effects of burrow creation from kangaroo rat density and found that kangaroo rats increased the diversity and abundance of other species via both engineering and non-engineering pathways. 5. Engineering was the primary factor structuring plant and small mammal communities, whereas non-engineering effects structured invertebrate communities and increased lizard abundance. 6. These results highlight the importance of the non-engineering effects of ecosystem engineers and shed new light on the multiple pathways by which strong-interactors shape communities. © 2011 The Authors. Journal of Animal Ecology © 2011 British Ecological Society.

  9. Cortical and subcortical interactions during action reprogramming and their related white matter pathways

    PubMed Central

    Neubert, Franz-Xaver; Mars, Rogier B.; Buch, Ethan R.; Olivier, Etienne; Rushworth, Matthew F. S.

    2010-01-01

    The right inferior frontal gyrus (rIFG) and the presupplementary motor area (pre-SMA) have been identified with cognitive control—the top-down influence on other brain areas when nonroutine behavior is required. It has been argued that they “inhibit” habitual motor responses when environmental changes mean a different response should be made. However, whether such “inhibition” can be equated with inhibitory physiological interactions has been unclear, as has the areas’ relationship with each other and the anatomical routes by which they influence movement execution. Paired-pulse transcranial magnetic stimulation (ppTMS) was applied over rIFG and primary motor cortex (M1) or over pre-SMA and M1 to measure their interactions, at a subsecond scale, during either inhibition and reprogramming of actions or during routine action selection. Distinct patterns of functional interaction between pre-SMA and M1 and between rIFG and M1 were found that were specific to action reprogramming trials; at a physiological level, direct influences of pre-SMA and rIFG on M1 were predominantly facilitatory and inhibitory, respectively. In a subsequent experiment, it was shown that the rIFG's inhibitory influence was dependent on pre-SMA. A third experiment showed that pre-SMA and rIFG influenced M1 at two time scales. By regressing white matter fractional anisotropy from diffusion-weighted magnetic resonance images against TMS-measured functional connectivity, it was shown that short-latency (6 ms) and longer latency (12 ms) influences were mediated by cortico-cortical and subcortical pathways, respectively, with the latter passing close to the subthalamic nucleus. PMID:20622155

  10. Pathway-Dependent Effectiveness of Network Algorithms for Gene Prioritization

    PubMed Central

    Shim, Jung Eun; Hwang, Sohyun; Lee, Insuk

    2015-01-01

    A network-based approach has proven useful for the identification of novel genes associated with complex phenotypes, including human diseases. Because network-based gene prioritization algorithms are based on propagating information of known phenotype-associated genes through networks, the pathway structure of each phenotype might significantly affect the effectiveness of algorithms. We systematically compared two popular network algorithms with distinct mechanisms – direct neighborhood which propagates information to only direct network neighbors, and network diffusion which diffuses information throughout the entire network – in prioritization of genes for worm and human phenotypes. Previous studies reported that network diffusion generally outperforms direct neighborhood for human diseases. Although prioritization power is generally measured for all ranked genes, only the top candidates are significant for subsequent functional analysis. We found that high prioritizing power of a network algorithm for all genes cannot guarantee successful prioritization of top ranked candidates for a given phenotype. Indeed, the majority of the phenotypes that were more efficiently prioritized by network diffusion showed higher prioritizing power for top candidates by direct neighborhood. We also found that connectivity among pathway genes for each phenotype largely determines which network algorithm is more effective, suggesting that the network algorithm used for each phenotype should be chosen with consideration of pathway gene connectivity. PMID:26091506

  11. Meissner effect and a stringlike interaction

    NASA Astrophysics Data System (ADS)

    Chatterjee, Chandrasekhar; Choudhury, Ishita Dutta; Lahiri, Amitabha

    2017-05-01

    We find that a recently proposed interaction involving the vorticity current of electrons, which radiatively induces a photon mass in 3+1 dimensions in the low-energy effective theory, corresponds to confining strings (linear potential) between electrons.

  12. Plasma interactions and surface/material effects

    NASA Technical Reports Server (NTRS)

    Mandel, M.; Chutjian, A.; Hall, W.; Leung, P.; Robinson, P.; Stevens, N. J.

    1986-01-01

    A discussion on plasma interactions and surface/material effects is summarized. The key issues in this area were: (1) the lack of data on the material properties of common spacecraft surface materials; (2) lack of understanding of the contamination and decontamination processes; and (3) insufficient analytical tools to model synergistic phenomena related to plasma interactions. Without an adequate database of material properties, accurate system performance predictions cannot be made. The interdisciplinary nature of the surface-plasma interactions area makes it difficult to plan and maintain a coherent theoretical and experimental program. The shuttle glow phenomenon is an excellent example of an unanticipated, complex interaction involving synergism between surface and plasma effects. Building an adequate technology base for understanding and predicting surface-plasma interactions will require the coordinated efforts of engineers, chemists, and physicists. An interdisciplinary R and D program should be organized to deal with similar problems that the space systems of the 21st century may encounter.

  13. Construction of a protein-protein interaction network of Wilms' tumor and pathway prediction of molecular complexes.

    PubMed

    Teng, W J; Zhou, C; Liu, L J; Cao, X J; Zhuang, J; Liu, G X; Sun, C G

    2016-05-23

    Wilms' tumor (WT), or nephroblastoma, is the most common malignant renal cancer that affects the pediatric population. Great progress has been achieved in the treatment of WT, but it cannot be cured at present. Nonetheless, a protein-protein interaction network of WT should provide some new ideas and methods. The purpose of this study was to analyze the protein-protein interaction network of WT. We screened the confirmed disease-related genes using the Online Mendelian Inheritance in Man database, created a protein-protein interaction network based on biological function in the Cytoscape software, and detected molecular complexes and relevant pathways that may be included in the network. The results showed that the protein-protein interaction network of WT contains 654 nodes, 1544 edges, and 5 molecular complexes. Among them, complex 1 is predicted to be related to the Jak-STAT signaling pathway, regulation of hematopoiesis by cytokines, cytokine-cytokine receptor interaction, cytokine and inflammatory responses, and hematopoietic cell lineage pathways. Molecular complex 4 shows a correlation of WT with colorectal cancer and the ErbB signaling pathway. The proposed method can provide the bioinformatic foundation for further elucidation of the mechanisms of WT development.

  14. A Model of an Integrated Immune System Pathway in Homo sapiens and Its Interaction with Superantigen Producing Expression Regulatory Pathway in Staphylococcus aureus: Comparing Behavior of Pathogen Perturbed and Unperturbed Pathway

    PubMed Central

    Tomar, Namrata; De, Rajat K.

    2013-01-01

    Response of an immune system to a pathogen attack depends on the balance between the host immune defense and the virulence of the pathogen. Investigation of molecular interactions between the proteins of a host and a pathogen helps in identifying the pathogenic proteins. It is necessary to understand the dynamics of a normally behaved host system to evaluate the capacity of its immune system upon pathogen attack. In this study, we have compared the behavior of an unperturbed and pathogen perturbed host system. Moreover, we have developed a formalism under Flux Balance Analysis (FBA) for the optimization of conflicting objective functions. We have constructed an integrated pathway system, which includes Staphylococcal Superantigen (SAg) expression regulatory pathway and TCR signaling pathway of Homo sapiens. We have implemented the method on this pathway system and observed the behavior of host signaling molecules upon pathogen attack. The entire study has been divided into six different cases, based on the perturbed/unperturbed conditions. In other words, we have investigated unperturbed and pathogen perturbed human TCR signaling pathway, with different combinations of optimization of concentrations of regulatory and signaling molecules. One of these cases has aimed at finding out whether minimization of the toxin production in a pathogen leads to the change in the concentration levels of the proteins coded by TCR signaling pathway genes in the infected host. Based on the computed results, we have hypothesized that the balance between TCR signaling inhibitory and stimulatory molecules can keep TCR signaling system into resting/stimulating state, depending upon the perturbation. The proposed integrated host-pathogen interaction pathway model has accurately reflected the experimental evidences, which we have used for validation purpose. The significance of this kind of investigation lies in revealing the susceptible interaction points that can take back the

  15. Mutual interactions between flavonoids and enzymatic and transporter elements responsible for flavonoid disposition via phase II metabolic pathways

    PubMed Central

    Jiang, Wen; Hu, Ming

    2014-01-01

    Flavonoids, existing mainly as glycosides in nature, have multiple “claimed” beneficial effects in humans. Flavonoids are extensively metabolized in enterocytes and hepatocytes by phase II enzymes such as UGTs and SULTs to form glucuronides and sulfates, respectively. These glucuronides and sulfates are subsequently excreted via ABC transporters (e.g., MRP2 or BCRP). Therefore, it is the interplay between phase II enzymes and efflux transporters that affects the disposition of flavonoids and leads to the low bioavailability of flavonoid aglycones. Flavonoids can also serve as chemical regulators that affect the activity or expression levels of phase II enzymes including UGTs, SULTs and GSTs, and transporters including P-gp, MRP2, BCRP, OATP and OAT. In general, flavonoids may exert the inhibitory or inductive effects on the phase II enzymes and transporters via multiple mechanisms that may involve different nuclear receptors. Since flavonoids may affect the metabolic pathways shared by many important clinical drugs, drug-flavonoid interaction is becoming an increasingly important concern. This review article focused on the disposition of flavonoids and effects of flavonoids on relevant enzymes (e.g. UGTs and SULTs) and transporters (e.g. MRP2 and BCRP) involved in the interplay between phase II enzymes and efflux transporters. The effects of flavonoids on other metabolic enzymes (e.g. GSTs) or transporters (e.g. P-gp, OATP and OAT) are also addressed but that is not the emphasis of this review. PMID:25400909

  16. Mutual interactions between flavonoids and enzymatic and transporter elements responsible for flavonoid disposition via phase II metabolic pathways.

    PubMed

    Jiang, Wen; Hu, Ming

    2012-09-21

    Flavonoids, existing mainly as glycosides in nature, have multiple "claimed" beneficial effects in humans. Flavonoids are extensively metabolized in enterocytes and hepatocytes by phase II enzymes such as UGTs and SULTs to form glucuronides and sulfates, respectively. These glucuronides and sulfates are subsequently excreted via ABC transporters (e.g., MRP2 or BCRP). Therefore, it is the interplay between phase II enzymes and efflux transporters that affects the disposition of flavonoids and leads to the low bioavailability of flavonoid aglycones. Flavonoids can also serve as chemical regulators that affect the activity or expression levels of phase II enzymes including UGTs, SULTs and GSTs, and transporters including P-gp, MRP2, BCRP, OATP and OAT. In general, flavonoids may exert the inhibitory or inductive effects on the phase II enzymes and transporters via multiple mechanisms that may involve different nuclear receptors. Since flavonoids may affect the metabolic pathways shared by many important clinical drugs, drug-flavonoid interaction is becoming an increasingly important concern. This review article focused on the disposition of flavonoids and effects of flavonoids on relevant enzymes (e.g. UGTs and SULTs) and transporters (e.g. MRP2 and BCRP) involved in the interplay between phase II enzymes and efflux transporters. The effects of flavonoids on other metabolic enzymes (e.g. GSTs) or transporters (e.g. P-gp, OATP and OAT) are also addressed but that is not the emphasis of this review.

  17. Effective pairing interactions with isospin density dependence

    SciTech Connect

    Margueron, J.; Sagawa, H.; Hagino, K.

    2008-05-15

    We perform Hartree-Fock-Bogoliubov (HFB) calculations for semi-magic calcium, nickel, tin, and lead isotopes and N=20,28,50, and 82 isotones using density-dependent pairing interactions recently derived from a microscopic nucleon-nucleon interaction. These interactions have an isovector component so that the pairing gaps in symmetric and neutron matter are reproduced. Our calculations well account for the experimental data for the neutron number dependence of binding energy, two-neutron separation energy, and odd-even mass staggering of these isotopes. This result suggests that by introducing the isovector term in the pairing interaction, one can construct a global effective pairing interaction that is applicable to nuclei in a wide range of the nuclear chart. It is also shown with the local density approximation that the pairing field deduced from the pairing gaps in infinite matter reproduces qualitatively well the pairing field for finite nuclei obtained with the HFB method.

  18. HIV’s Nef Interacts with β-Catenin of the Wnt Signaling Pathway in HEK293 Cells

    PubMed Central

    Weiser, Keren; Barton, Meredith; Gershoony, Dafna; DasGupta, Ramanuj; Cardozo, Timothy

    2013-01-01

    The Wnt signaling pathway is implicated in major physiologic cellular functions, such as proliferation, migration, cell fate specification, maintenance of pluripotency and induction of tumorigenicity. Proliferation and migration are important responses of T-cells, which are major cellular targets of HIV infection. Using an informatics screen, we identified a previously unsuspected interaction between HIV’s Nef protein and β-catenin, a key component of the Wnt pathway. A segment in Nef contains identical amino acids at key positions and structurally mimics the β-catenin binding sites on endogenous β-catenin ligands. The interaction between Nef and β-catenin was confirmed in vitro and in a co-immunoprecipitation from HEK293 cells. Moreover, the introduction of Nef into HEK293 cells specifically inhibited a Wnt pathway reporter. PMID:24130899

  19. Emory University: High-Throughput Protein-Protein Interaction Analysis for Hippo Pathway Profiling | Office of Cancer Genomics

    Cancer.gov

    The CTD2 Center at Emory University used high-throughput protein-protein interaction (PPI) mapping for Hippo signaling pathway profiling to rapidly unveil promising PPIs as potential therapeutic targets and advance functional understanding of signaling circuitry in cells. Read the abstract.

  20. From a Subtractive to Multiplicative Approach: A Concept-Driven Interactive Pathway on the Selective Absorption of Light

    ERIC Educational Resources Information Center

    Viennot, Laurence; de Hosson, Cécile

    2015-01-01

    This research documents the aims and the impact of a teaching experiment on how the absorption of light depends on the thickness of the absorbing medium. This teaching experiment is more specifically characterized as bringing to bear a "concept-driven interactive pathway". It is designed to make students analyse the absorption of light…

  1. From a Subtractive to Multiplicative Approach: A Concept-Driven Interactive Pathway on the Selective Absorption of Light

    ERIC Educational Resources Information Center

    Viennot, Laurence; de Hosson, Cécile

    2015-01-01

    This research documents the aims and the impact of a teaching experiment on how the absorption of light depends on the thickness of the absorbing medium. This teaching experiment is more specifically characterized as bringing to bear a "concept-driven interactive pathway". It is designed to make students analyse the absorption of light…

  2. Nectin-4 Co-stimulates the Prolactin Receptor by Interacting with SOCS1 and Inhibiting Its Activity on the JAK2-STAT5a Signaling Pathway.

    PubMed

    Maruoka, Masahiro; Kedashiro, Shin; Ueda, Yuki; Mizutani, Kiyohito; Takai, Yoshimi

    2017-03-03

    Cell surface cytokine receptors are regulated by their cis-interacting stimulatory and inhibitory co-receptors. We previously showed that the immunoglobulin-like cell adhesion molecule nectin-4 cis-interacts with the prolactin receptor through the extracellular region and stimulates prolactin-induced prolactin receptor activation and signaling, resulting in alveolar development in the mouse mammary gland. However, it remains unknown how this interaction stimulates these effects. We show here that the cis-interaction of the extracellular region of nectin-4 with the prolactin receptor was not sufficient for eliciting these effects and that nectin-4's cytoplasmic region was also required for eliciting these effects. The cytoplasmic region of nectin-4 directly interacted with suppressor of cytokine signaling (SOCS) 1, but not SOCS3, JAK2, or STAT5a, and inhibited SOCS1's interaction with JAK2, eventually resulting in the increased phosphorylation of STAT5a. The juxtamembrane region of nectin-4 interacts with the Src homology 2 domain of SOCS1. Both the interactions of nectin-4 with the extracellular region of the prolactin receptor and the interactions of SOCS1 with nectin-4's cytoplasmic region were required for the stimulatory effect of nectin-4 on the prolactin-induced prolactin receptor activation. The third immunoglobulin-like domain of nectin-4 and the second fibronectin type-III domain of the prolactin receptor were involved in this cis-interaction, and both the extracellular and transmembrane regions of nectin-4 and the prolactin receptor were required for this direct interaction. These results indicate that nectin-4 serves as a stimulatory co-receptor for the prolactin receptor by regulating the feedback inhibition of SOCS1 in the JAK2-STAT5a signaling pathway.

  3. Atrophin controls developmental signaling pathways via interactions with Trithorax-like

    PubMed Central

    Yeung, Kelvin; Boija, Ann; Karlsson, Edvin; Holmqvist, Per-Henrik; Tsatskis, Yonit; Nisoli, Ilaria; Yap, Damian; Lorzadeh, Alireza; Moksa, Michelle; Hirst, Martin; Aparicio, Samuel; Fanto, Manolis; Stenberg, Per; Mannervik, Mattias; McNeill, Helen

    2017-01-01

    Mutations in human Atrophin1, a transcriptional corepressor, cause dentatorubral-pallidoluysian atrophy, a neurodegenerative disease. Drosophila Atrophin (Atro) mutants display many phenotypes, including neurodegeneration, segmentation, patterning and planar polarity defects. Despite Atro’s critical role in development and disease, relatively little is known about Atro’s binding partners and downstream targets. We present the first genomic analysis of Atro using ChIP-seq against endogenous Atro. ChIP-seq identified 1300 potential direct targets of Atro including engrailed, and components of the Dpp and Notch signaling pathways. We show that Atro regulates Dpp and Notch signaling in larval imaginal discs, at least partially via regulation of thickveins and fringe. In addition, bioinformatics analyses, sequential ChIP and coimmunoprecipitation experiments reveal that Atro interacts with the Drosophila GAGA Factor, Trithorax-like (Trl), and they bind to the same loci simultaneously. Phenotypic analyses of Trl and Atro clones suggest that Atro is required to modulate the transcription activation by Trl in larval imaginal discs. Taken together, these data indicate that Atro is a major Trl cofactor that functions to moderate developmental gene transcription. DOI: http://dx.doi.org/10.7554/eLife.23084.001 PMID:28327288

  4. Two Pathways for Water Interaction with Oxygen Adatoms on TiO2(110) Surfaces

    SciTech Connect

    Lyubinetsky, Igor; Du, Yingge; Deskins, N. Aaron; Zhang, Zhenrong; Dohnalek, Zdenek; Dupuis, Michel

    2010-08-04

    Atomic-level investigation of the interaction of H2O with a partially re-oxidized TiO2(110) has been performed at 300 K by combining scanning tunneling microscopy and density functional theory. In particular, we demonstrate that oxygen adatoms (Oa), produced during O2 exposure of reduced TiO2(110) surfaces, alter water dissociation/ recombination chemistry through two different pathways. When H2O diffuses to Oa on the same Ti row, it becomes trapped near the Oa, exchanges a proton easily to dissociate and form a pair of terminal hydroxyls (OHt) along the row, which can then readily recombine and re-dissociate many times or overcome the barrier to move away. When H2O passes along the Oa on an adjacent row, an across-row proton transfer facilitated by the bridging O atom results in spontaneous dissociation of H2O on a Ti trough leading to the formation of a stable across-row OHt pair, which after awhile can recombine and H2O diffuses away. The across-row process has not been reported previously, and it starts from a ‘‘pseudo-dissociated’’ state of water. We also show how the H2O dissociation and OHt pair statistical reformation induce an apparent along- or across-row shift of Oa as a result of the oxygen scrambling process between H2O and Oa.

  5. FOXP2 drives neuronal differentiation by interacting with retinoic acid signaling pathways

    PubMed Central

    Devanna, Paolo; Middelbeek, Jeroen; Vernes, Sonja C.

    2014-01-01

    FOXP2 was the first gene shown to cause a Mendelian form of speech and language disorder. Although developmentally expressed in many organs, loss of a single copy of FOXP2 leads to a phenotype that is largely restricted to orofacial impairment during articulation and linguistic processing deficits. Why perturbed FOXP2 function affects specific aspects of the developing brain remains elusive. We investigated the role of FOXP2 in neuronal differentiation and found that FOXP2 drives molecular changes consistent with neuronal differentiation in a human model system. We identified a network of FOXP2 regulated genes related to retinoic acid signaling and neuronal differentiation. FOXP2 also produced phenotypic changes associated with neuronal differentiation including increased neurite outgrowth and reduced migration. Crucially, cells expressing FOXP2 displayed increased sensitivity to retinoic acid exposure. This suggests a mechanism by which FOXP2 may be able to increase the cellular differentiation response to environmental retinoic acid cues for specific subsets of neurons in the brain. These data demonstrate that FOXP2 promotes neuronal differentiation by interacting with the retinoic acid signaling pathway and regulates key processes required for normal circuit formation such as neuronal migration and neurite outgrowth. In this way, FOXP2, which is found only in specific subpopulations of neurons in the brain, may drive precise neuronal differentiation patterns and/or control localization and connectivity of these FOXP2 positive cells. PMID:25309332

  6. Atrophin controls developmental signaling pathways via interactions with Trithorax-like.

    PubMed

    Yeung, Kelvin; Boija, Ann; Karlsson, Edvin; Holmqvist, Per-Henrik; Tsatskis, Yonit; Nisoli, Ilaria; Yap, Damian; Lorzadeh, Alireza; Moksa, Michelle; Hirst, Martin; Aparicio, Samuel; Fanto, Manolis; Stenberg, Per; Mannervik, Mattias; McNeill, Helen

    2017-03-22

    Mutations in human Atrophin1, a transcriptional corepressor, cause dentatorubral-pallidoluysian atrophy, a neurodegenerative disease. Drosophila Atrophin (Atro) mutants display many phenotypes, including neurodegeneration, segmentation, patterning and planar polarity defects. Despite Atro's critical role in development and disease, relatively little is known about Atro's binding partners and downstream targets. We present the first genomic analysis of Atro using ChIP-seq against endogenous Atro. ChIP-seq identified 1300 potential direct targets of Atro including engrailed, and components of the Dpp and Notch signaling pathways. We show that Atro regulates Dpp and Notch signaling in larval imaginal discs, at least partially via regulation of thickveins and fringe. In addition, bioinformatics analyses, sequential ChIP and coimmunoprecipitation experiments reveal that Atro interacts with the Drosophila GAGA Factor, Trithorax-like (Trl), and they bind to the same loci simultaneously. Phenotypic analyses of Trl and Atro clones suggest that Atro is required to modulate the transcription activation by Trl in larval imaginal discs. Taken together, these data indicate that Atro is a major Trl cofactor that functions to moderate developmental gene transcription.

  7. Molecular interaction between K-Ras and H-REV107 in the Ras signaling pathway.

    PubMed

    Han, Chang Woo; Jeong, Mi Suk; Jang, Se Bok

    2017-09-16

    Ras proteins are small GTPases that serve as master moderators of a large number of signaling pathways involved in various cellular processes. Activating mutations in Ras are found in about one-third of cancers. H-REV107, a K-Ras binding protein, plays an important role in determining K-Ras function. H-REV107 is a member of the HREV107 family of class II tumor suppressor genes and a growth inhibitory Ras target gene that suppresses cellular growth, differentiation, and apoptosis. Expression of H-REV107 was strongly reduced in about 50% of human carcinoma cell lines. However, the specific molecular mechanism by which H-REV107 inhibits Ras is still unknown. In the present study, we suggest that H-REV107 forms a strong complex with activating oncogenic mutation Q61H K-Ras from various biochemical binding assays and modeled structures. In addition, the interaction sites between K-Ras and H-REV107 were predicted based on homology modeling. Here, we found that some structure-based mutants of the K-Ras disrupted the complex formation with H-REV107. Finally, a novel molecular mechanism describing K-Ras and H-REV107 binding is suggested and insights into new K-Ras effector target drugs are provided. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. How does the Royal Family of Tudor rule the PIWI-interacting RNA pathway?

    PubMed Central

    Siomi, Mikiko C.; Mannen, Taro; Siomi, Haruhiko

    2010-01-01

    PIWI (P-element-induced wimpy testis) proteins are a subset of the Argonaute proteins and are expressed predominantly in the germlines of a variety of organisms, including Drosophila and mammals. PIWI proteins associate specifically with PIWI-interacting RNAs (piRNAs), small RNAs that are also expressed predominantly in germlines, and silence transposable DNA elements and other genes showing complementarities to the sequences of associated piRNAs. This mechanism helps to maintain the integrity of the genome and the development of gametes. PIWI proteins have been shown recently to contain symmetrical dimethyl arginines (sDMAs), and this modification is mediated by the methyltransferase PRMT5 (also known as Dart5 or Capsuleen). It was then demonstrated that multiple members of the Tudor (Tud) family of proteins, which are necessary for gametogenesis in both flies and mice, associate with PIWI proteins specifically through sDMAs in various but particular combinations. Although Tud domains in Tud family members are known to be sDMA-binding modules, involvement of the Tudor family at the molecular level in the piRNA pathway has only recently come into focus. PMID:20360382

  9. Nutrition, movement and sleep behaviours: their interactions in pathways to obesity and cardiometabolic diseases.

    PubMed

    Dulloo, A G; Miles-Chan, J L; Montani, J-P

    2017-02-01

    Among the multitude of dietary and lifestyle behaviours that have been proposed to contribute to the obesity epidemic, those that have generated considerable research scrutiny in the past decade are centred upon sleep behaviours, sedentary behaviours (sitting or lying while awake) and diminished low-level physical activities of everyday life, with each category of behaviours apparently presenting an independent risk for obesity and/or cardiometabolic diseases. These behaviours are highly complex, operate in synergy with each other, disrupt the link between regulation of the circadian clock and metabolic physiology and impact on various components of daily energy expenditure and feeding behaviours to promote obesity and hinder the outcome of obesity therapy. As such, this behavioural triad (nutrition, movement and sleep) presents plenty of scope for intervention and optimization in the context of body weight regulation and lifestyle-related disease prevention. It is against this background that recent advances relevant to the theme of 'Nutrition, Movement & Sleep Behaviors: their interactions in pathways to obesity and cardiometabolic diseases' are addressed in this overview and the nine review articles in this supplement reporting the proceedings of the 8th Fribourg Obesity Research Conference. © 2017 World Obesity Federation.

  10. Novel miRNA-mRNA interactions conserved in essential cancer pathways

    PubMed Central

    Andrés-León, Eduardo; Cases, Ildefonso; Alonso, Sergio; Rojas, Ana M.

    2017-01-01

    Cancer is a complex disease in which unrestrained cell proliferation results in tumour development. Extensive research into the molecular mechanisms underlying tumorigenesis has led to the characterization of oncogenes and tumour suppressors that are key elements in cancer growth and progression, as well as that of other important elements like microRNAs. These genes and miRNAs appear to be constitutively deregulated in cancer. To identify signatures of miRNA-mRNA interactions potentially conserved in essential cancer pathways, we have conducted an integrative analysis of transcriptomic data, also taking into account methylation and copy number alterations. We analysed 18,605 raw transcriptome samples from The Cancer Genome Atlas covering 15 of the most common types of human tumours. From this global transcriptome study, we recovered known cancer-associated miRNA-targets and importantly, we identified new potential targets from miRNA families, also analysing the phenotypic outcomes of these genes/mRNAs in terms of survival. Further analyses could lead to novel approaches in cancer therapy. PMID:28387377

  11. Wnt/β-Catenin and Sonic Hedgehog Pathways Interact in the Regulation of the Development of the Dorsal Mesenchymal Protrusion

    PubMed Central

    Briggs, Laura E.; Burns, Tara A.; Lockhart, Marie M.; Phelps, Aimee L.; Van den Hoff, Maurice J.B.; Wessels, Andy

    2016-01-01

    Background The dorsal mesenchymal protrusion (DMP) is a second heart field (SHF) derived tissue involved in cardiac septation. Molecular mechanisms controlling SHF/DMP development include the Bone Morphogenetic Protein and Wnt/β-catenin signaling pathways. Reduced expression of components in these pathways leads to inhibition of proliferation of the SHF/DMP precursor population and failure of the DMP to develop. While the Sonic Hedgehog (Shh) pathway has also been demonstrated to be critically important for SHF/DMP development and atrioventricular septation, its role in the regulation of SHF proliferation is contentious. Results Tissue-specific deletion of the Shh receptor Smoothened from the SHF resulted in compromised DMP formation and atrioventricular septal defects (AVSDs). Immunohistochemical analysis at critical stages of DMP development showed significant proliferation defect as well as reduction in levels of the Wnt/β-catenin pathway-intermediates β-catenin, Lef1, and Axin2. To determine whether the defects seen in the conditional Smoothened knock-out mouse could be attributed to reduced Wnt/β-catenin signaling, LiCl, a pharmacological activator of this Wnt/β-catenin pathway, was administered. This resulted in restoration of proliferation and partial rescue of the AVSD phenotype. Conclusions The data presented suggest that the Wnt/β-catenin pathway interact with the Shh pathway in the regulation of SHF/DMP-precursor proliferation and, hence, the development of the DMP. PMID:26297872

  12. Technology Improvement Pathways to Cost-Effective Vehicle Electrification

    SciTech Connect

    Brooker, A.; Thornton, M.; Rugh, J. P.

    2010-04-01

    Electrifying transportation can reduce or eliminate dependence on foreign fuels, emission of green house gases, and emission of pollutants. One challenge is finding a pathway for vehicles that gains wide market acceptance to achieve a meaningful benefit. This paper evaluates several approaches aimed at making plug-in electric vehicles (EV) and plug-in hybrid electric vehicles (PHEVs) cost-effective including opportunity charging, replacing the battery over the vehicle life, improving battery life, reducing battery cost, and providing electric power directly to the vehicle during a portion of its travel. Many combinations of PHEV electric range and battery power are included. For each case, the model accounts for battery cycle life and the national distribution of driving distances to size the battery optimally. Using the current estimates of battery life and cost, only the dynamically plugged-in pathway was cost-effective to the consumer. Significant improvements in battery life and battery cost also made PHEVs more cost-effective than today's hybrid electric vehicles (HEVs) and conventional internal combustion engine vehicles (CVs).

  13. Potential Interactions Between Genetic Polymorphisms of the Transforming Growth Factor-β Pathway and Environmental Factors in Abdominal Aortic Aneurysms.

    PubMed

    Zuo, S; Xiong, J; Wei, Y; Chen, D; Chen, F; Liu, K; Wu, T; Hu, Y; Guo, W

    2015-07-01

    Evidence has accumulated that multiple polymorphisms in the transforming growth factor (TGF)-β pathway and renin-angiotensin system play important roles in determining susceptibility to abdominal aortic aneurysm (AAA). Few studies have considered interactions between these gene polymorphisms and environmental factors. The aim of this study was to evaluate the contribution of single nucleotide polymorphisms (SNPs) and complex gene-environment interactions in AAA. Six SNPs located in TGFB, TGFBR1, TGFBR2 and AGTR1 were selected. Genotyping of blood samples and collection of lifestyle factors were performed in 155 unrelated participants with AAAs and 310 non-AAA controls. Unconditional logistic regression was performed to assess the effects of SNPs on the risk of AAA. Generalized multifactor dimensionality reduction (GMDR) was used to evaluate gene-gene and gene-environment interactions. Participants carrying TGFB1 rs1800469 TT (odds ratio [OR] 1.83, 95% confidence interval [CI] 1.18-2.85) or AGTR1 rs12695895 TT (OR 4.21, 95% CI 1.41-12.53) genotypes had a higher risk of AAA than those with the common CC genotype. The gene-gene interaction of AGTR1 rs5182, TGFBR1 rs1626340, and TGFB1 rs1800469 was found to be the best model according to the results of the GMDR analysis (cross validation consistency [CVC]) 10/10; p = .010). Smoking, dyslipidemia, and rs1800469 together contributed to the risk of AAA, which demonstrated a potential and complex gene-environment interaction among the three variants that might affect AAA risk (CVC 6/10; p = .001). In this study of the Chinese population, homozygosity of TGFB1 rs1800469-T and AGTR1 rs12695895-T might be associated with increased risk of AAA. The complex gene-gene and gene-environment interactions might contribute to the risk of AAA. As a small study, the preliminary results need extensive validation and replication in larger populations. Copyright © 2015 European Society for Vascular Surgery. Published by Elsevier Ltd

  14. A membrane-embedded pathway delivers general anesthetics to two interacting binding sites in the Gloeobacter violaceus ion channel.

    PubMed

    Arcario, Mark J; Mayne, Christopher G; Tajkhorshid, Emad

    2017-06-09

    General anesthetics exert their effects on the central nervous system by acting on ion channels, most notably pentameric ligand-gated ion channels. Although numerous studies have focused on pentameric ligand-gated ion channels, the details of anesthetic binding and channel modulation are still debated. A better understanding of the anesthetic mechanism of action is necessary for the development of safer and more efficacious drugs. Herein, we present a computational study identifying two anesthetic binding sites in the transmembrane domain of the Gloeobacter violaceus ligand-gated ion channel (GLIC) channel, characterize the putative binding pathway, and observe structural changes associated with channel function. Molecular simulations of desflurane reveal a binding pathway to GLIC via a membrane-embedded tunnel using an intrasubunit protein lumen as the conduit, an observation that explains the Meyer-Overton hypothesis, or why the lipophilicity of an anesthetic and its potency are generally proportional. Moreover, employing high concentrations of ligand led to the identification of a second transmembrane site (TM2) that inhibits dissociation of anesthetic from the TM1 site and is consistent with the high concentrations of anesthetics required to achieve clinical effects. Finally, asymmetric binding patterns of anesthetic to the channel were found to promote an iris-like conformational change that constricts and dehydrates the ion pore, creating a 13.5 kcal/mol barrier to ion translocation. Together with previous studies, the simulations presented herein demonstrate a novel anesthetic binding site in GLIC that is accessed through a membrane-embedded tunnel and interacts with a previously known site, resulting in conformational changes that produce a non-conductive state of the channel. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. Effects of an invasive plant transcend ecosystem boundaries through a dragonfly-mediated trophic pathway.

    PubMed

    Burkle, Laura A; Mihaljevic, Joseph R; Smith, Kevin G

    2012-12-01

    Trophic interactions can strongly influence the structure and function of terrestrial and aquatic communities through top-down and bottom-up processes. Species with life stages in both terrestrial and aquatic systems may be particularly likely to link the effects of trophic interactions across ecosystem boundaries. Using experimental wetlands planted with purple loosestrife (Lythrum salicaria), we tested the degree to which the bottom-up effects of floral density of this invasive plant could trigger a chain of interactions, changing the behavior of terrestrial flying insect prey and predators and ultimately cascading through top-down interactions to alter lower trophic levels in the aquatic community. The results of our experiment support the linkage of terrestrial and aquatic food webs through this hypothesized pathway, with high loosestrife floral density treatments attracting high levels of visiting insect pollinators and predatory adult dragonflies. High floral densities were also associated with increased adult dragonfly oviposition and subsequently high larval dragonfly abundance in the aquatic community. Finally, high-flower treatments were coupled with changes in zooplankton species richness and shifts in the composition of zooplankton communities. Through changes in animal behavior and trophic interactions in terrestrial and aquatic systems, this work illustrates the broad and potentially cryptic effects of invasive species, and provides additional compelling motivation for ecologists to conduct investigations that cross traditional ecosystem boundaries.

  16. Electrostatic Interactions in the Binding Pathway of a Transient Protein Complex Studied by NMR and Isothermal Titration Calorimetry*

    PubMed Central

    Meneses, Erick; Mittermaier, Anthony

    2014-01-01

    Much of our knowledge of protein binding pathways is derived from extremely stable complexes that interact very tightly, with lifetimes of hours to days. Much less is known about weaker interactions and transient complexes because these are challenging to characterize experimentally. Nevertheless, these types of interactions are ubiquitous in living systems. The combination of NMR relaxation dispersion Carr–Purcell–Meiboom–Gill (CPMG) experiments and isothermal titration calorimetry allows the quantification of rapid binding kinetics for complexes with submillisecond lifetimes that are difficult to study using conventional techniques. We have used this approach to investigate the binding pathway of the Src homology 3 (SH3) domain from the Fyn tyrosine kinase, which forms complexes with peptide targets whose lifetimes are on the order of about a millisecond. Long range electrostatic interactions have been shown to play a critical role in the binding pathways of tightly binding complexes. The role of electrostatics in the binding pathways of transient complexes is less well understood. Similarly to previously studied tight complexes, we find that SH3 domain association rates are enhanced by long range electrostatics, whereas short range interactions are formed late in the docking process. However, the extent of electrostatic association rate enhancement is several orders of magnitudes less, whereas the electrostatic-free basal association rate is significantly greater. Thus, the SH3 domain is far less reliant on electrostatic enhancement to achieve rapid association kinetics than are previously studied systems. This suggests that there may be overall differences in the role played by electrostatics in the binding pathways of extremely stable versus transient complexes. PMID:25122758

  17. Electrostatic interactions in the binding pathway of a transient protein complex studied by NMR and isothermal titration calorimetry.

    PubMed

    Meneses, Erick; Mittermaier, Anthony

    2014-10-03

    Much of our knowledge of protein binding pathways is derived from extremely stable complexes that interact very tightly, with lifetimes of hours to days. Much less is known about weaker interactions and transient complexes because these are challenging to characterize experimentally. Nevertheless, these types of interactions are ubiquitous in living systems. The combination of NMR relaxation dispersion Carr-Purcell-Meiboom-Gill (CPMG) experiments and isothermal titration calorimetry allows the quantification of rapid binding kinetics for complexes with submillisecond lifetimes that are difficult to study using conventional techniques. We have used this approach to investigate the binding pathway of the Src homology 3 (SH3) domain from the Fyn tyrosine kinase, which forms complexes with peptide targets whose lifetimes are on the order of about a millisecond. Long range electrostatic interactions have been shown to play a critical role in the binding pathways of tightly binding complexes. The role of electrostatics in the binding pathways of transient complexes is less well understood. Similarly to previously studied tight complexes, we find that SH3 domain association rates are enhanced by long range electrostatics, whereas short range interactions are formed late in the docking process. However, the extent of electrostatic association rate enhancement is several orders of magnitudes less, whereas the electrostatic-free basal association rate is significantly greater. Thus, the SH3 domain is far less reliant on electrostatic enhancement to achieve rapid association kinetics than are previously studied systems. This suggests that there may be overall differences in the role played by electrostatics in the binding pathways of extremely stable versus transient complexes.

  18. Estimating Interaction Effects With Incomplete Predictor Variables

    PubMed Central

    Enders, Craig K.; Baraldi, Amanda N.; Cham, Heining

    2014-01-01

    The existing missing data literature does not provide a clear prescription for estimating interaction effects with missing data, particularly when the interaction involves a pair of continuous variables. In this article, we describe maximum likelihood and multiple imputation procedures for this common analysis problem. We outline 3 latent variable model specifications for interaction analyses with missing data. These models apply procedures from the latent variable interaction literature to analyses with a single indicator per construct (e.g., a regression analysis with scale scores). We also discuss multiple imputation for interaction effects, emphasizing an approach that applies standard imputation procedures to the product of 2 raw score predictors. We thoroughly describe the process of probing interaction effects with maximum likelihood and multiple imputation. For both missing data handling techniques, we outline centering and transformation strategies that researchers can implement in popular software packages, and we use a series of real data analyses to illustrate these methods. Finally, we use computer simulations to evaluate the performance of the proposed techniques. PMID:24707955

  19. Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and tissue-specific protein interactions

    PubMed Central

    Qian, David C.; Byun, Jinyoung; Han, Younghun; Greene, Casey S.; Field, John K.; Hung, Rayjean J.; Brhane, Yonathan; Mclaughlin, John R.; Fehringer, Gordon; Landi, Maria Teresa; Rosenberger, Albert; Bickeböller, Heike; Malhotra, Jyoti; Risch, Angela; Heinrich, Joachim; Hunter, David J.; Henderson, Brian E.; Haiman, Christopher A.; Schumacher, Fredrick R.; Eeles, Rosalind A.; Easton, Douglas F.; Seminara, Daniela; Amos, Christopher I.

    2015-01-01

    Results from genome-wide association studies (GWAS) have indicated that strong single-gene effects are the exception, not the rule, for most diseases. We assessed the joint effects of germline genetic variations through a pathway-based approach that considers the tissue-specific contexts of GWAS findings. From GWAS meta-analyses of lung cancer (12 160 cases/16 838 controls), breast cancer (15 748 cases/18 084 controls) and prostate cancer (14 160 cases/12 724 controls) in individuals of European ancestry, we determined the tissue-specific interaction networks of proteins expressed from genes that are likely to be affected by disease-associated variants. Reactome pathways exhibiting enrichment of proteins from each network were compared across the cancers. Our results show that pathways associated with all three cancers tend to be broad cellular processes required for growth and survival. Significant examples include the nerve growth factor (P = 7.86 × 10−33), epidermal growth factor (P = 1.18 × 10−31) and fibroblast growth factor (P = 2.47 × 10−31) signaling pathways. However, within these shared pathways, the genes that influence risk largely differ by cancer. Pathways found to be unique for a single cancer focus on more specific cellular functions, such as interleukin signaling in lung cancer (P = 1.69 × 10−15), apoptosis initiation by Bad in breast cancer (P = 3.14 × 10−9) and cellular responses to hypoxia in prostate cancer (P = 2.14 × 10−9). We present the largest comparative cross-cancer pathway analysis of GWAS to date. Our approach can also be applied to the study of inherited mechanisms underlying risk across multiple diseases in general. PMID:26483192

  20. Frontal-Brainstem Pathways Mediating Placebo Effects on Social Rejection.

    PubMed

    Koban, Leonie; Kross, Ethan; Woo, Choong-Wan; Ruzic, Luka; Wager, Tor D

    2017-03-29

    Placebo treatments can strongly affect clinical outcomes, but research on how they shape other life experiences and emotional well-being is in its infancy. We used fMRI in humans to examine placebo effects on a particularly impactful life experience, social pain elicited by a recent romantic rejection. We compared these effects with placebo effects on physical (heat) pain, which are thought to depend on pathways connecting prefrontal cortex and periaqueductal gray (PAG). Placebo treatment, compared with control, reduced both social and physical pain, and increased activity in the dorsolateral prefrontal cortex (dlPFC) in both modalities. Placebo further altered the relationship between affect and both dlPFC and PAG activity during social pain, and effects on behavior were mediated by a pathway connecting dlPFC to the PAG, building on recent work implicating opioidergic PAG activity in the regulation of social pain. These findings suggest that placebo treatments reduce emotional distress by altering affective representations in frontal-brainstem systems.SIGNIFICANCE STATEMENT Placebo effects are improvements due to expectations and the socio-medical context in which treatment takes place. Whereas they have been extensively studied in the context of somatic conditions such as pain, much less is known of how treatment expectations shape the emotional experience of other important stressors and life events. Here, we use brain imaging to show that placebo treatment reduces the painful feelings associated with a recent romantic rejection by recruiting a prefrontal-brainstem network and by shifting the relationship between brain activity and affect. Our findings suggest that this brain network may be important for nonspecific treatment effects across a wide range of therapeutic approaches and mental health conditions. Copyright © 2017 the authors 0270-6474/17/373621-11$15.00/0.

  1. Cadmium and cellular signaling cascades: interactions between cell death and survival pathways.

    PubMed

    Thévenod, Frank; Lee, Wing-Kee

    2013-10-01

    Cellular stress elicited by the toxic metal Cd(2+) does not coerce the cell into committing to die from the onset. Rather, detoxification and adaptive processes are triggered concurrently, allowing survival until normal function is restored. With high Cd(2+), death pathways predominate. However, if sublethal stress levels affect cells for prolonged periods, as in chronic low Cd(2+) exposure, adaptive and survival mechanisms may deregulate, such that tumorigenesis ensues. Hence, death and malignancy are the two ends of a continuum of cellular responses to Cd(2+), determined by magnitude and duration of Cd(2+) stress. Signaling cascades are the key factors affecting cellular reactions to Cd(2+). This review critically surveys recent literature to outline major features of death and survival signaling pathways as well as their activation, interactions and cross talk in cells exposed to Cd(2+). Under physiological conditions, receptor activation generates 2nd messengers, which are short-lived and act specifically on effectors through their spatial and temporal dynamics to transiently alter effector activity. Cd(2+) recruits physiological 2nd messenger systems, in particular Ca(2+) and reactive oxygen species (ROS), which control key Ca(2+)- and redox-sensitive molecular switches dictating cell function and fate. Severe ROS/Ca(2+) signals activate cell death effectors (ceramides, ASK1-JNK/p38, calpains, caspases) and/or cause irreversible damage to vital organelles, such as mitochondria and endoplasmic reticulum (ER), whereas low localized ROS/Ca(2+) levels act as 2nd messengers promoting cellular adaptation and survival through signal transduction (ERK1/2, PI3K/Akt-PKB) and transcriptional regulators (Ref1-Nrf2, NF-κB, Wnt, AP-1, bestrophin-3). Other cellular proteins and processes targeted by ROS/Ca(2+) (metallothioneins, Bcl-2 proteins, ubiquitin-proteasome system, ER stress-associated unfolded protein response, autophagy, cell cycle) can evoke death or survival

  2. Neuroprotective effects of hydrogen sulfide and the underlying signaling pathways.

    PubMed

    Chen, Wen-Lin; Niu, Ying-Ying; Jiang, Wei-Zheng; Tang, Hui-Lan; Zhang, Chong; Xia, Qi-Ming; Tang, Xiao-Qing

    2015-01-01

    Hydrogen sulfide (H2S) is an endogenously produced gas that represents a novel third gaseous signaling molecule, neurotransmitter and cytoprotectant. Cystathionine β-synthase (CBS), cystathionine γ-lyase (CSE), 3-mercaptopyruvate sulfur transferase with cysteine aminotransferase (3-MST/CAT) and 3-mercaptopyruvate sulfur transferase with d-amino acid oxidase (3-MST/DAO) pathways are involved in the generation of endogenous H2S despite the ubiquitous or restricted distribution of those enzymes. CBS, 3-MST/CAT and 3-MST/DAO can be found in the brain, while CSE is widely located in other organs. There also exist up-taking or recycling and scavenging mechanisms in H2S metabolism to maintain its persistence for physiological function. In recent years, investigating the role that H2S plays in the central nervous system and cardiovascular system has always been a hotspot. To date, effects of H2S are at least partially verified in multiple animal models or neuron cell lines of Alzheimer's disease, Parkinson's disease, cerebral ischemia, major depression disorders and febrile seizure, although subsequent studies are still badly needed. This article presents an overview of current knowledge of H2S focusing on its neuroprotective effects and corresponding signaling pathways, together with connections to potential therapeutic strategies in the clinic.

  3. Impact of organic-mineral matter interactions on thermal reaction pathways for coal model compounds

    SciTech Connect

    Buchanan, A.C. III; Britt, P.F.; Struss, J.A.

    1995-07-01

    Coal is a complex, heterogeneous solid that includes interdispersed mineral matter. However, knowledge of organic-mineral matter interactions is embryonic, and the impact of these interactions on coal pyrolysis and liquefaction is incomplete. Clay minerals, for example, are known to be effective catalysts for organic reactions. Furthermore, clays such as montmorillonite have been proposed to be key catalysts in the thermal alteration of lignin into vitrinite during the coalification process. Recent studies by Hatcher and coworkers on the evolution of coalified woods using microscopy and NMR have led them to propose selective, acid-catalyzed, solid state reaction chemistry to account for retained structural integrity in the wood. However, the chemical feasibility of such reactions in relevant solids is difficult to demonstrate. The authors have begun a model compound study to gain a better molecular level understanding of the effects in the solid state of organic-mineral matter interactions relevant to both coal formation and processing. To satisfy the need for model compounds that remain nonvolatile solids at temperatures ranging to 450 C, model compounds are employed that are chemically bound to the surface of a fumed silica (Si-O-C{sub aryl}linkage). The organic structures currently under investigation are phenethyl phenyl ether (C{sub 6}H{sub 5}CH{sub 2}CH{sub 2}OC{sub 6}H{sub 5}) derivatives, which serve as models for {beta}-alkyl aryl ether units that are present in lignin and lignitic coals. The solid-state chemistry of these materials at 200--450 C in the presence of interdispersed acid catalysts such as small particle size silica-aluminas and montmorillonite clay will be reported. Initial focus will be on defining the potential impact of these interactions on coal pyrolysis and liquefaction.

  4. Planning for effective interaction with FDA.

    PubMed

    Spurgin, Elizabeth A

    2004-12-01

    Manufacturers of diabetes devices can facilitate the formal regulatory approval process through early interaction with the U.S. Food and Drug Administration (FDA). Effective planning can help manage commonly perceived risks of interaction with the Agency, introduce new technologies to regulatory reviewers, and inform the manufacturer's product development strategy. This article reviews key aspects of the FDA evaluation process and suggests strategies that may facilitate effective communication with the Agency. Integrating early communication with FDA into broader product commercialization planning can streamline regulatory review and lead to early product launch into reimbursed markets.

  5. Synergistic Neuroprotective Effects of Two Herbal Ingredients via CREB-Dependent Pathway

    PubMed Central

    Liu, Xu; Wang, Dongxiao; Zhao, Runqing; Dong, Xianzhe; Hu, Yuan; Liu, Ping

    2016-01-01

    As two natural oligosaccharide esters, 3,6’-Disinapoyl sucrose (DISS) and tenuifolisideA (TFSA) are originating from the root of Polygala tenuifolia Willd, a traditional Chinese medicine used in treatment of mental disorders. Previous reports have shown that both of them possess in vitro neuroprotective effects by stimulating different upstream pathways related with cyclic AMP-responsive element-binding protein (CREB). In the present study, we investigated the additive neuroprotective effects of DISS and TFSA on Glu-induced damage of SY5Y cells and purposed the possible underlying mechanism. The interaction between DISS and TFSA showed a clear-cut synergistic effect as evidenced by combination index (CI). Additional evidence from biochemical (NOS activity) assays confirmed their additive inhibition on the Glu-induced NOS hyperactivation. Moreover, we showed that co-treatment of DISS and TFSA resulted in an additively up-regulated phosphorylation of CREB as well as increased expressions of CRTC1 and BDNF. Neuroprotective effects of DISS and TFSA on Glu-induced decrease in cell viability were blocked by MAPK/ERK1/2 inhibitor (U0126) and PI3-K inhibitor (LY290042). Nevertheless, the CRTC1 or BDNF expression induced by these two compounds was significantly reduced in the presence of either ERK or PI3-K inhibitor, indicating that the two oligosaccharide esters shared some common pathways in the regulation of CREB-BDNF pathway. Taken together, we, for the first time, showed that DISS and TFSA exerted the additive neuroprotective effects on CREB-BDNF signaling pathway through complementary mechanisms. PMID:27729863

  6. Synergistic Neuroprotective Effects of Two Herbal Ingredients via CREB-Dependent Pathway.

    PubMed

    Liu, Xu; Wang, Dongxiao; Zhao, Runqing; Dong, Xianzhe; Hu, Yuan; Liu, Ping

    2016-01-01

    As two natural oligosaccharide esters, 3,6'-Disinapoyl sucrose (DISS) and tenuifolisideA (TFSA) are originating from the root of Polygala tenuifolia Willd, a traditional Chinese medicine used in treatment of mental disorders. Previous reports have shown that both of them possess in vitro neuroprotective effects by stimulating different upstream pathways related with cyclic AMP-responsive element-binding protein (CREB). In the present study, we investigated the additive neuroprotective effects of DISS and TFSA on Glu-induced damage of SY5Y cells and purposed the possible underlying mechanism. The interaction between DISS and TFSA showed a clear-cut synergistic effect as evidenced by combination index (CI). Additional evidence from biochemical (NOS activity) assays confirmed their additive inhibition on the Glu-induced NOS hyperactivation. Moreover, we showed that co-treatment of DISS and TFSA resulted in an additively up-regulated phosphorylation of CREB as well as increased expressions of CRTC1 and BDNF. Neuroprotective effects of DISS and TFSA on Glu-induced decrease in cell viability were blocked by MAPK/ERK1/2 inhibitor (U0126) and PI3-K inhibitor (LY290042). Nevertheless, the CRTC1 or BDNF expression induced by these two compounds was significantly reduced in the presence of either ERK or PI3-K inhibitor, indicating that the two oligosaccharide esters shared some common pathways in the regulation of CREB-BDNF pathway. Taken together, we, for the first time, showed that DISS and TFSA exerted the additive neuroprotective effects on CREB-BDNF signaling pathway through complementary mechanisms.

  7. Interacting parallel pathways associate sounds with visual identity in auditory cortices.

    PubMed

    Ahveninen, Jyrki; Huang, Samantha; Ahlfors, Seppo P; Hämäläinen, Matti; Rossi, Stephanie; Sams, Mikko; Jääskeläinen, Iiro P

    2016-01-01

    Spatial and non-spatial information of sound events is presumably processed in parallel auditory cortex (AC) "what" and "where" streams, which are modulated by inputs from the respective visual-cortex subsystems. How these parallel processes are integrated to perceptual objects that remain stable across time and the source agent's movements is unknown. We recorded magneto- and electroencephalography (MEG/EEG) data while subjects viewed animated video clips featuring two audiovisual objects, a black cat and a gray cat. Adaptor-probe events were either linked to the same object (the black cat meowed twice in a row in the same location) or included a visually conveyed identity change (the black and then the gray cat meowed with identical voices in the same location). In addition to effects in visual (including fusiform, middle temporal or MT areas) and frontoparietal association areas, the visually conveyed object-identity change was associated with a release from adaptation of early (50-150ms) activity in posterior ACs, spreading to left anterior ACs at 250-450ms in our combined MEG/EEG source estimates. Repetition of events belonging to the same object resulted in increased theta-band (4-8Hz) synchronization within the "what" and "where" pathways (e.g., between anterior AC and fusiform areas). In contrast, the visually conveyed identity changes resulted in distributed synchronization at higher frequencies (alpha and beta bands, 8-32Hz) across different auditory, visual, and association areas. The results suggest that sound events become initially linked to perceptual objects in posterior AC, followed by modulations of representations in anterior AC. Hierarchical what and where pathways seem to operate in parallel after repeating audiovisual associations, whereas the resetting of such associations engages a distributed network across auditory, visual, and multisensory areas.

  8. A systems biology approach to detect key pathways and interaction networks in gastric cancer on the basis of microarray analysis.

    PubMed

    Guo, Leilei; Song, Chunhua; Wang, Peng; Dai, Liping; Zhang, Jianying; Wang, Kaijuan

    2015-11-01

    The aim of the present study was to explore key molecular pathways contributing to gastric cancer (GC) and to construct an interaction network between significant pathways and potential biomarkers. Publicly available gene expression profiles of GSE29272 for GC, and data for the corresponding normal tissue, were downloaded from Gene Expression Omnibus. Pre‑processing and differential analysis were performed with R statistical software packages, and a number of differentially expressed genes (DEGs) were obtained. A functional enrichment analysis was performed for all the DEGs with a BiNGO plug‑in in Cytoscape. Their correlation was analyzed in order to construct a network. The modularity analysis and pathway identification operations were used to identify graph clusters and associated pathways. The underlying molecular mechanisms involving these DEGs were also assessed by data mining. A total of 249 DEGs, which were markedly upregulated and downregulated, were identified. The extracellular region contained the most significantly over‑represented functional terms, with respect to upregulated and downregulated genes, and the closest topological matches were identified for taste transduction and regulation of autophagy. In addition, extracellular matrix‑receptor interactions were identified as the most relevant pathway associated with the progression of GC. The genes for fibronectin 1, secreted phosphoprotein 1, collagen type 4 variant α‑1/2 and thrombospondin 1, which are involved in the pathways, may be considered as potential therapeutic targets for GC. A series of associations between candidate genes and key pathways were also identified for GC, and their correlation may provide novel insights into the pathogenesis of GC.

  9. FYVE1/FREE1 Interacts with the PYL4 ABA Receptor and Mediates its Delivery to the Vacuolar Degradation Pathway.

    PubMed

    Belda-Palazon, Borja; Rodriguez, Lesia; Fernandez, Maria A; Castillo, Mari-Cruz; Anderson, Erin A; Gao, Caiji; González-Guzmán, Miguel; Peirats-Llobet, Marta; Zhao, Qiong; De Winne, Nancy; Gevaert, Kris; De Jaeger, Geert; Jiang, Liwen; Leon, Jose; Mullen, Robert T; Rodriguez, Pedro L

    2016-08-05

    Recently, we described the ubiquitylation of PYL4 and PYR1 by the RING E3 ubiquitin ligase RSL1 at the plasma membrane of Arabidopsis thaliana. This suggested that ubiquitylated ABA receptors might be targeted to the vacuolar degradation pathway because such ubiquitylation is usually an internalization signal for the endocytic route. Here, we show that FYVE1 (previously termed FREE1), a recently described component of the endosomal sorting complex required for transport (ESCRT) machinery, interacted with RSL1-receptor complexes and recruited PYL4 to endosomal compartments. Although the ESCRT pathway has been assumed to be reserved for integral membrane proteins, we show the involvement of this pathway in the degradation of ABA receptors, which can be associated with membranes but are not integral membrane proteins. Knock-down fyve1 alleles are hypersensitive to ABA, illustrating the biological relevance of the ESCRT pathway for the modulation of ABA signaling. In addition, fyve1 mutants are impaired in the targeting of ABA receptors for vacuolar degradation, leading to increased accumulation of PYL4 and an enhanced response to ABA. Pharmacological and genetic approaches revealed a dynamic turnover of ABA receptors from the plasma membrane to the endosomal/vacuolar degradation pathway, which was mediated by FYVE1 and was dependent on RSL1. This process involves clathrin-mediated endocytosis and trafficking of PYL4 through the ESCRT pathway, which helps to regulate the turnover of ABA receptors and attenuate ABA signaling. © 2016 American Society of Plant Biologists. All rights reserved.

  10. Dissecting Rotavirus Particle-Raft Interaction with Small Interfering RNAs: Insights into Rotavirus Transit through the Secretory Pathway

    PubMed Central

    Cuadras, Mariela A.; Bordier, Bruno B.; Zambrano, Jose L.; Ludert, Juan E.; Greenberg, Harry B.

    2006-01-01

    Studies of rotavirus morphogenesis, transport, and release have shown that although these viruses are released from the apical surface of polarized intestinal cells before cellular lysis, they do not follow the classic exocytic pathway. Furthermore, increasing evidence suggests that lipid rafts actively participate in the exit of rotavirus from the infected cell. In this study, we silenced the expression of VP4, VP7, and NSP4 by using small interfering RNAs (siRNAs) and evaluated the effect of shutting down the expression of these proteins on rotavirus-raft interactions. Silencing of VP4 and NSP4 reduced the association of rotavirus particles with rafts; in contrast, inhibition of VP7 synthesis slightly affected the migration of virions into rafts. We found that inhibition of rotavirus migration into lipid rafts, by either siRNAs or tunicamycin, also specifically blocked the targeting of VP4 to rafts, suggesting that the association of VP4 with rafts is mostly mediated by the formation of viral particles in the endoplasmic reticulum (ER). We showed that two populations of VP4 exist, one small population that is independently targeted to rafts and a second large pool of VP4 whose association with rafts is mediated by particle formation in the ER. We also present evidence to support the hypothesis that assembly of VP4 into mature virions takes place in the late stages of transit through the ER. Finally, we analyzed the progression of rotavirus proteins in the exocytic pathway and found that VP4 and virion-assembled VP7 colocalized with ERGIC-53, suggesting that rotavirus particles transit through the intermediate compartment between the ER and the Golgi complex. PMID:16571810

  11. Set-Based Joint Test of Interaction Between SNPs in the VEGF Pathway and Exogenous Estrogen Finds Association With Age-Related Macular Degeneration

    PubMed Central

    Courtenay, Monique D.; Cade, William H.; Schwartz, Stephen G.; Kovach, Jaclyn L.; Agarwal, Anita; Wang, Gaofeng; Haines, Jonathan L.; Pericak-Vance, Margaret A.; Scott, William K.

    2014-01-01

    Purpose. Age-related macular degeneration (AMD) is the leading cause of irreversible visual loss in developed countries. Its etiology includes genetic and environmental factors. Although VEGFA variants are associated with AMD, the joint action of variants within the VEGF pathway and their interaction with nongenetic factors have not been investigated. Methods. Affymetrix 6.0 chipsets were used to genotype 668,238 single nucleotide polymorphisms (SNPs) in 1207 AMD cases and 686 controls. Environmental exposures were collected by questionnaire. A set-based test was conducted using the χ2 statistic at each SNP derived from Kraft's two degree of freedom (2df) joint test. Pathway- and gene-based test statistics were calculated as the mean of all independent SNP statistics. Phenotype labels were permuted 10,000 times to generate an empirical P value. Results. While a main effect of the VEGF pathway was not identified, the pathway was associated with neovascular AMD in women when accounting for birth control pill (BCP) use (P = 0.017). Analysis of VEGF's subpathways showed that SNPs in the proliferation subpathway were associated with neovascular AMD (P = 0.029) when accounting for BCP use. Nominally significant genes within this subpathway were also observed. Stratification by BCP use revealed novel significant genetic effects in women who had taken BCPs. Conclusions. These results illustrate that some AMD genetic risk factors may be revealed only when complex relationships among risk factors are considered. This shows the utility of exploring pathways of previously associated genes to find novel effects. It also demonstrates the importance of incorporating environmental exposures in tests of genetic association at the SNP, gene, or pathway level. PMID:25015356

  12. Deduction and Analysis of the Interacting Stress Response Pathways of Metal/Radionuclide-reducing Bacteria

    SciTech Connect

    Zhou, Jizhong; He, Zhili

    2010-02-28

    Project Title: Deduction and Analysis of the Interacting Stress Response Pathways of Metal/Radionuclide-reducing Bacteria DOE Grant Number: DE-FG02-06ER64205 Principal Investigator: Jizhong (Joe) Zhou (University of Oklahoma) Key members: Zhili He, Aifen Zhou, Christopher Hemme, Joy Van Nostrand, Ye Deng, and Qichao Tu Collaborators: Terry Hazen, Judy Wall, Adam Arkin, Matthew Fields, Aindrila Mukhopadhyay, and David Stahl Summary Three major objectives have been conducted in the Zhou group at the University of Oklahoma (OU): (i) understanding of gene function, regulation, network and evolution of Desulfovibrio vugaris Hildenborough in response to environmental stresses, (ii) development of metagenomics technologies for microbial community analysis, and (iii) functional characterization of microbial communities with metagenomic approaches. In the past a few years, we characterized four CRP/FNR regulators, sequenced ancestor and evolved D. vulgaris strains, and functionally analyzed those mutated genes identified in salt-adapted strains. Also, a new version of GeoChip 4.0 has been developed, which also includes stress response genes (StressChip), and a random matrix theory-based conceptual framework for identifying functional molecular ecological networks has been developed with the high throughput functional gene array hybridization data as well as pyrosequencing data from 16S rRNA genes. In addition, GeoChip and sequencing technologies as well as network analysis approaches have been used to analyze microbial communities from different habitats. Those studies provide a comprehensive understanding of gene function, regulation, network, and evolution in D. vulgaris, and microbial community diversity, composition and structure as well as their linkages with environmental factors and ecosystem functioning, which has resulted in more than 60 publications.

  13. Interaction between transcellular and paracellular water transport pathways through Aquaporin 5 and the tight junction complex

    PubMed Central

    Kawedia, Jitesh D.; Nieman, Michelle L.; Boivin, Gregory P.; Melvin, James E.; Kikuchi, Ken-Ichiro; Hand, Arthur R.; Lorenz, John N.; Menon, Anil G.

    2007-01-01

    To investigate potential physiological interactions between the transcellular and paracellular pathways of water transport, we asked whether targeted deletion of Aquaporin 5 (AQP5), the major transcellular water transporter in salivary acinar cells, affected paracellular transport of 4-kDa FITC-labeled dextran (FITC-D), which is transported through the paracellular but not the transcellular route. After i.v. injection of FITC-D into either AQP5 wild-type or AQP5−/− mice and saliva collection for fixed time intervals, we show that the relative amount of FITC-D transported in the saliva of AQP5−/− mice is half that in matched AQP5+/+ mice, indicating a 2-fold decrease in permeability of the paracellular barrier in mice lacking AQP5. We also found a significant difference in the proportion of transcellular vs. paracellular transport between male and female mice. Freeze-fracture electron microscopy revealed an increase in the number of tight junction strands of both AQP5+/+ and AQP5−/− male mice after pilocarpine stimulation but no change in strand number in female mice. Average acinar cell volume was increased by ≈1.4-fold in glands from AQP5−/− mice, suggesting an alteration in the volume-sensing machinery of the cell. Western blots revealed that expression of Claudin-7, Claudin-3, and Occludin, critical proteins that regulate the permeability of the tight junction barrier, were significantly decreased in AQP5−/− compared with AQP5+/+ salivary glands. These findings reveal the existence of a gender-influenced molecular mechanism involving AQP5 that allows transcellular and paracellular routes of water transport to act in conjunction. PMID:17360692

  14. Effective interactions between biopolymers in aqueous media

    NASA Astrophysics Data System (ADS)

    Mashl, Robert Jay

    1998-12-01

    We examine the effective interactions in aqueous media between rod-like and planar macroions. Experiments investigating the self-assembly of DNA and lipids in solution and the adsorption of DNA onto oppositely charged surfaces have fostered renewed interest in testing our notions of fundamental electrostatic interactions. Understanding these interactions is crucial to emerging technologies such as gene therapy. Both analytic and particle simulation methodologies are used to explore a range of length scales ranging from large distances down to lengths at which the interaction energy between two point charges is comparable to thermal energies. The mean-field Debye-Huckel and Poisson-Boltzmann theories provide approximate descriptions of electrostatic interactions, while Brownian dynamics simulations are used to study the effects of discretizing the macroion charges and the role of discrete salt particles in the aqueous medium. We show that short-ranged attractions, due to ion-ion correlations, occur between two like-charged rods (modeling DNA molecules) or a rod and like-charged surface (cell membrane). From the modeling point of view, the size of the rod, or, equivalently, the magnitude of the ion-rod binding energy, is an important control parameter for determining whether the interaction is attractive or repulsive. Simulations of surfaces with discrete, mobile charges, modeling lipids found in multi-component cell membranes, enhance these short-ranged attractions through polarization effects. Debye-Huckel theory predicts the correct order of magnitude of the force between rods and an oppositely charged surface, suggesting that further work using continuum theories may prove useful in predicting interactions between oppositely charged macroions.

  15. Construction of gene/protein interaction networks for primary myelofibrosis and KEGG pathway-enrichment analysis of molecular compounds.

    PubMed

    Sun, C G; Cao, X J; Zhou, C; Liu, L J; Feng, F B; Liu, R J; Zhuang, J; Li, Y J

    2015-12-08

    The objective of this study was the development of a gene/protein interaction network for primary myelofibrosis based on gene expression, and the enrichment analysis of KEGG pathways underlying the molecular complexes in this network. To achieve this, genes involved in primary myelofibrosis were selected from the OMIM database. A gene/protein interaction network for primary myelofibrosis was obtained through Cytoscape with the literature mining performed using the Agilent Literature Search plugin. The molecular complexes in the network were detected by ClusterViz plugin and KEGG pathway enrichment of molecular complexes was performed using DAVID online. We found 75 genes associated with primary myelofibrosis in the OMIM database. The gene/protein interaction network of primary myelofibrosis contained 608 nodes, 2086 edges, and 4 molecular complexes with a correlation integral value greater than 4. Molecular complexes involved in KEGG pathways are related to cytokine regulation, immune function regulation, ECM-receptor interaction, focal adhesion, actin cytoskeleton regulation, cell adhesion molecules, and other biological behavior of tumors, which can provide a reliable direction for the treatment of primary myelofibrosis and the bioinformatic foundation for further understanding the molecular mechanisms of this disease.

  16. LRP4 association to bone properties and fracture and interaction with genes in the Wnt- and BMP signaling pathways.

    PubMed

    Kumar, Jitender; Swanberg, Maria; McGuigan, Fiona; Callreus, Mattias; Gerdhem, Paul; Akesson, Kristina

    2011-09-01

    Osteoporosis is a common complex disorder in postmenopausal women leading to changes in the micro-architecture of bone and increased risk of fracture. Members of the low-density lipoprotein receptor-related protein (LRP) gene family regulates the development and physiology of bone through the Wnt/β-catenin (Wnt) pathway that in turn cross-talks with the bone morphogenetic protein (BMP) pathway. In two cohorts of Swedish women: OPRA (n=1002; age 75 years) and PEAK-25 (n=1005; age 25 years), eleven single nucleotide polymorphisms (SNPs) from Wnt pathway genes (LRP4; LRP5; G protein-coupled receptor 177, GPR177) were analyzed for association with Bone Mineral Density (BMD), rate of bone loss, hip geometry, quantitative ultrasound and fracture. Additionally, interaction of LRP4 with LRP5, GPR177 and BMP2 were analyzed. LRP4 (rs6485702) was associated with higher total body (TB) and lumbar spine (LS) BMD in the PEAK-25 cohort (p=0.006 and 0.005 respectively), and interaction was observed with LRP5 (p=0.007) and BMP2 (p=0.004) for TB BMD. LRP4 also showed significant interaction with LRP5 for femoral neck (FN) and LS BMD in this cohort. In the OPRA cohort, LRP4 polymorphisms were associated with significantly lower fracture incidence overall (p=0.008-0.001) and fewer hip fractures (rs3816614, p=0.006). Significant interaction in the OPRA cohort was observed for LRP4 with BMP2 and GPR177 for FN BMD as well as for rate of bone loss at TB and FN (p=0.007-0.0001). In conclusion, LRP4 and interaction between LRP4 and genes in the Wnt and BMP signaling pathways modulate bone phenotypes including peak bone mass and fracture, the clinical endpoint of osteoporosis.

  17. Effectiveness of Teacher-Child Interaction Therapy

    ERIC Educational Resources Information Center

    Hight, Stevie Gail

    2013-01-01

    Teacher-Child Interaction Therapy (TCIT) is an emerging evidence-based form of therapy used to treat preschool children experiencing different types of externalizing behavior problems (Lyon et al., 2009). The current study attempted to add to the literature concerning TCIT by implementing and examining the effectiveness of TCIT on five students…

  18. Allosteric pathway identification through network analysis: from molecular dynamics simulations to interactive 2D and 3D graphs.

    PubMed

    Allain, Ariane; Chauvot de Beauchêne, Isaure; Langenfeld, Florent; Guarracino, Yann; Laine, Elodie; Tchertanov, Luba

    2014-01-01

    Allostery is a universal phenomenon that couples the information induced by a local perturbation (effector) in a protein to spatially distant regulated sites. Such an event can be described in terms of a large scale transmission of information (communication) through a dynamic coupling between structurally rigid (minimally frustrated) and plastic (locally frustrated) clusters of residues. To elaborate a rational description of allosteric coupling, we propose an original approach - MOdular NETwork Analysis (MONETA) - based on the analysis of inter-residue dynamical correlations to localize the propagation of both structural and dynamical effects of a perturbation throughout a protein structure. MONETA uses inter-residue cross-correlations and commute times computed from molecular dynamics simulations and a topological description of a protein to build a modular network representation composed of clusters of residues (dynamic segments) linked together by chains of residues (communication pathways). MONETA provides a brand new direct and simple visualization of protein allosteric communication. A GEPHI module implemented in the MONETA package allows the generation of 2D graphs of the communication network. An interactive PyMOL plugin permits drawing of the communication pathways between chosen protein fragments or residues on a 3D representation. MONETA is a powerful tool for on-the-fly display of communication networks in proteins. We applied MONETA for the analysis of communication pathways (i) between the main regulatory fragments of receptors tyrosine kinases (RTKs), KIT and CSF-1R, in the native and mutated states and (ii) in proteins STAT5 (STAT5a and STAT5b) in the phosphorylated and the unphosphorylated forms. The description of the physical support for allosteric coupling by MONETA allowed a comparison of the mechanisms of (a) constitutive activation induced by equivalent mutations in two RTKs and (b) allosteric regulation in the activated and non

  19. A melanin-independent interaction between Mc1r and Met signalling pathways is required for HGF-dependent melanoma

    PubMed Central

    Wolnicka-Glubisz, Agnieszka; Strickland, Faith M.; Wielgus, Albert; Anver, Miriam; Merlino, Glenn; De Fabo, Edward C.; Noonan, Frances P.

    2014-01-01

    Melanocortin 1 receptor (MC1R) signaling stimulates black eumelanin production through a cAMP dependent pathway. MC1R polymorphisms can impair this process, resulting in a predominance of red phaeomelanin. The red hair, fair skin and UV sensitive phenotype is a well-described melanoma risk factor. MC1R polymorphisms also confer melanoma risk independent of pigment. We investigated the effect of Mc1r deficiency in a mouse model of UV-induced melanoma. C57BL/6-Mc1r+/+-HGF transgenic mice have a characteristic hyperpigmented black phenotype with extra-follicular dermal melanocytes located at the dermal/epidermal junction. UVB induces melanoma, independent of melanin pigmentation, but UVA-induced and spontaneous melanomas are dependent on black eumelanin. We crossed these mice with yellow C57BL/6-Mc1re/e animals which have a non-functional Mc1r and produce predominantly yellow phaeomelanin. Yellow C57BL/6-Mc1re/e-HGF mice produced no melanoma in response to UVR or spontaneously even though the HGF transgene and its receptor Met were expressed. Total melanin was less than in C57BL/6-Mc1r+/+-HGF mice, hyperpigmentation was not observed and there were few extra-follicular melanocytes. Thus, functional Mc1r was required for expression of the transgenic HGF phenotype. Heterozygous C57BL/6-Mc1re/+-HGF mice were black and hyperpigmented and, although extra-follicular melanocytes and skin melanin content were similar to C57BL/6-Mc1r+/+-HGF animals, they developed UV-induced and spontaneous melanomas with significantly less efficiency by all criteria. Thus, heterozygosity for Mc1r was sufficient to restore the transgenic HGF phenotype but insufficient to fully restore melanoma. We conclude that a previously unsuspected melanin-independent interaction between Mc1r and Met signaling pathways is required for HGF-dependent melanoma and postulate that this pathway is involved in human melanoma. PMID:24975581

  20. A melanin-independent interaction between Mc1r and Met signaling pathways is required for HGF-dependent melanoma.

    PubMed

    Wolnicka-Glubisz, Agnieszka; Strickland, Faith M; Wielgus, Albert; Anver, Miriam; Merlino, Glenn; De Fabo, Edward C; Noonan, Frances P

    2015-02-15

    Melanocortin 1 receptor (MC1R) signaling stimulates black eumelanin production through a cAMP-dependent pathway. MC1R polymorphisms can impair this process, resulting in a predominance of red phaeomelanin. The red hair, fair skin and UV sensitive phenotype is a well-described melanoma risk factor. MC1R polymorphisms also confer melanoma risk independent of pigment. We investigated the effect of Mc1r deficiency in a mouse model of UV-induced melanoma. C57BL/6-Mc1r+/+-HGF transgenic mice have a characteristic hyperpigmented black phenotype with extra-follicular dermal melanocytes located at the dermal/epidermal junction. UVB induces melanoma, independent of melanin pigmentation, but UVA-induced and spontaneous melanomas are dependent on black eumelanin. We crossed these mice with yellow C57BL/6-Mc1re/e animals which have a non-functional Mc1r and produce predominantly yellow phaeomelanin. Yellow C57BL/6-Mc1re/e-HGF mice produced no melanoma in response to UVR or spontaneously even though the HGF transgene and its receptor Met were expressed. Total melanin was less than in C57BL/6-Mc1r+/+-HGF mice, hyperpigmentation was not observed and there were few extra-follicular melanocytes. Thus, functional Mc1r was required for expression of the transgenic HGF phenotype. Heterozygous C57BL/6-Mc1re/+-HGF mice were black and hyperpigmented and, although extra-follicular melanocytes and skin melanin content were similar to C57BL/6-Mc1r+/+-HGF animals, they developed UV-induced and spontaneous melanomas with significantly less efficiency by all criteria. Thus, heterozygosity for Mc1r was sufficient to restore the transgenic HGF phenotype but insufficient to fully restore melanoma. We conclude that a previously unsuspected melanin-independent interaction between Mc1r and Met signaling pathways is required for HGF-dependent melanoma and postulate that this pathway is involved in human melanoma.

  1. Interactions with community members and institutions: Preventive pathways for child maltreatment.

    PubMed

    Cao, Yiwen; Maguire-Jack, Kathryn

    2016-12-01

    Parents interact with their environment in important ways that may impact their ability to parent their children positively. The current study uses data from the age 3 wave of the Fragile Families and Child Wellbeing study to investigate whether neighborhood processes and community participation relate to internal control, and whether these three variables are associated with child maltreatment behaviors. Using structural equation modeling, the direct and indirect effects of the environment (neighborhood disorder, social control, and social cohesion) and community participation on child maltreatment are tested. The mediating variable tested is internal control. The results show that neighborhood processes and community participation are associated with child neglect, physical child abuse, and psychological aggression but that these associations are driven through their effect on internal control.

  2. Different forms of effective connectivity in primate frontotemporal pathways

    PubMed Central

    Petkov, Christopher I.; Kikuchi, Yukiko; Milne, Alice E.; Mishkin, Mortimer; Rauschecker, Josef P.; Logothetis, Nikos K.

    2015-01-01

    It is generally held that non-primary sensory regions of the brain have a strong impact on frontal cortex. However, the effective connectivity of pathways to frontal cortex is poorly understood. Here we microstimulate sites in the superior temporal and ventral frontal cortex of monkeys and use functional magnetic resonance imaging to evaluate the functional activity resulting from the stimulation of interconnected regions. Surprisingly, we find that, although certain earlier stages of auditory cortical processing can strongly activate frontal cortex, downstream auditory regions, such as voice-sensitive cortex, appear to functionally engage primarily an ipsilateral temporal lobe network. Stimulating other sites within this activated temporal lobe network shows strong activation of frontal cortex. The results indicate that the relative stage of sensory processing does not predict the level of functional access to the frontal lobes. Rather, certain brain regions engage local networks, only parts of which have a strong functional impact on frontal cortex. PMID:25613079

  3. Different forms of effective connectivity in primate frontotemporal pathways.

    PubMed

    Petkov, Christopher I; Kikuchi, Yukiko; Milne, Alice E; Mishkin, Mortimer; Rauschecker, Josef P; Logothetis, Nikos K

    2015-01-23

    It is generally held that non-primary sensory regions of the brain have a strong impact on frontal cortex. However, the effective connectivity of pathways to frontal cortex is poorly understood. Here we microstimulate sites in the superior temporal and ventral frontal cortex of monkeys and use functional magnetic resonance imaging to evaluate the functional activity resulting from the stimulation of interconnected regions. Surprisingly, we find that, although certain earlier stages of auditory cortical processing can strongly activate frontal cortex, downstream auditory regions, such as voice-sensitive cortex, appear to functionally engage primarily an ipsilateral temporal lobe network. Stimulating other sites within this activated temporal lobe network shows strong activation of frontal cortex. The results indicate that the relative stage of sensory processing does not predict the level of functional access to the frontal lobes. Rather, certain brain regions engage local networks, only parts of which have a strong functional impact on frontal cortex.

  4. Nuclear reaction inputs based on effective interactions

    NASA Astrophysics Data System (ADS)

    Hilaire, S.; Goriely, S.; Péru, S.; Dubray, N.; Dupuis, M.; Bauge, E.

    2016-11-01

    Extensive nuclear structure studies have been performed for decades using effective interactions as sole input. They have shown a remarkable ability to describe rather accurately many types of nuclear properties. In the early 2000s, a major effort has been engaged to produce nuclear reaction input data out of the Gogny interaction, in order to challenge its quality also with respect to nuclear reaction observables. The status of this project, well advanced today thanks to the use of modern computers as well as modern nuclear reaction codes, is reviewed and future developments are discussed.

  5. Interactions between auditory 'what' and 'where' pathways revealed by enhanced near-threshold discrimination of frequency and position.

    PubMed

    Tardif, Eric; Spierer, Lucas; Clarke, Stephanie; Murray, Micah M

    2008-03-07

    Partially segregated neuronal pathways ("what" and "where" pathways, respectively) are thought to mediate sound recognition and localization. Less studied are interactions between these pathways. In two experiments, we investigated whether near-threshold pitch discrimination sensitivity (d') is altered by supra-threshold task-irrelevant position differences and likewise whether near-threshold position discrimination sensitivity is altered by supra-threshold task-irrelevant pitch differences. Each experiment followed a 2 x 2 within-subjects design regarding changes/no change in the task-relevant and task-irrelevant stimulus dimensions. In Experiment 1, subjects discriminated between 750 Hz and 752 Hz pure tones, and d' for this near-threshold pitch change significantly increased by a factor of 1.09 when accompanied by a task-irrelevant position change of 65 micros interaural time difference (ITD). No response bias was induced by the task-irrelevant position change. In Experiment 2, subjects discriminated between 385 micros and 431 micros ITDs, and d' for this near-threshold position change significantly increased by a factor of 0.73 when accompanied by task-irrelevant pitch changes (6 Hz). In contrast to Experiment 1, task-irrelevant pitch changes induced a response criterion bias toward responding that the two stimuli differed. The collective results are indicative of facilitative interactions between "what" and "where" pathways. By demonstrating how these pathways may cooperate under impoverished listening conditions, our results bear implications for possible neuro-rehabilitation strategies. We discuss our results in terms of the dual-pathway model of auditory processing.

  6. Osmolyte Effects on the Unfolding Pathway of β-Lactoglobulin

    NASA Astrophysics Data System (ADS)

    Meng, Wei; Pan, Hai; Qin, Meng; Cao, Yi; Wang, Wei

    2013-10-01

    There are large amounts of osmolytes inside cells, which impact many physiological processes by complicated mechanisms. The osmolyte effects on the stability and folding of proteins have been studied in detail using simple two-state folding proteins. However, many important functional proteins fold in complex pathways involving various intermediates. Little is known about the osmolyte effects on the folding and unfolding of these proteins. It is noted that β-lactoglobulin (BLG) is an example of such proteins, whose unfolding involves an obvious intermediate state. Using equilibrium chemical denaturation and stopped-flow kinetics, we investigate the unfolding of BLG in the presence of different osmolytes, e.g., glycerol, ethylene glycol (EG) and poly(ethylene glycol)400 (PEG400). It is found that all these osmolytes can stabilize the unfolding intermediate by modulating the relative unfolding kinetics of the native and the intermediate states. The stabilization effects are similar for EG and PEG400 but distinct for glycerol. Since the unfolding intermediates of many proteins are directly related to protein misfolding diseases, evaluation of the osmolyte effects for the unfolding of these proteins in vitro should be beneficial for the understanding of the occurrence of the related diseases in vivo.

  7. Evaluating protein-protein interaction (PPI) networks for diseases pathway, target discovery, and drug-design using 'in silico pharmacology'.

    PubMed

    Chakraborty, Chiranjib; Doss C, George Priya; Chen, Luonan; Zhu, Hailong

    2014-01-01

    In silico pharmacology is a promising field in the current state-of drug discovery. This area exploits "protein-protein Interaction (PPI) network analysis for drug discovery using the drug "target class". To document the current status, we have discussed in this article how this an integrated system of PPI networks contribute to understand the disease pathways, present state-of-the-art drug target discovery and drug discovery process. This review article enhances our knowledge on conventional drug discovery and current drug discovery using in silico techniques, best "target class", universal architecture of PPI networks, the present scenario of disease pathways and protein-protein interaction networks as well as the method to comprehend the PPI networks. Taken all together, ultimately a snapshot has been discussed to be familiar with how PPI network architecture can used to validate a drug target. At the conclusion, we have illustrated the future directions of PPI in target discovery and drug-design.

  8. Alcohol interacts with genetic alteration of the Hippo tumor suppressor pathway to modulate tissue growth in Drosophila.

    PubMed

    Ilanges, Anoj; Jahanshahi, Maryam; Balobin, Denis M; Pfleger, Cathie M

    2013-01-01

    Alcohol-mediated cancers represent more than 3.5% of cancer-related deaths, yet how alcohol promotes cancer is a major open question. Using Drosophila, we identified novel interactions between dietary ethanol and loss of tumor suppressor components of the Hippo Pathway. The Hippo Pathway suppresses tumors in flies and mammals by inactivating transcriptional co-activator Yorkie, and the spectrum of cancers associated with impaired Hippo signaling overlaps strikingly with those associated with alcohol. Therefore, our findings may implicate loss of Hippo Pathway tumor suppression in alcohol-mediated cancers. Ethanol enhanced overgrowth from loss of the expanded, hippo, or warts tumor suppressors but, surprisingly, not from over-expressing the yorkie oncogene. We propose that in parallel to Yorkie-dependent overgrowth, impairing Hippo signaling in the presence of alcohol may promote overgrowth via additional alcohol-relevant targets. We also identified interactions between alcohol and Hippo Pathway over-activation. We propose that exceeding certain thresholds of alcohol exposure activates Hippo signaling to maintain proper growth control and prevent alcohol-mediated mis-patterning and tissue overgrowth.

  9. Alcohol Interacts with Genetic Alteration of the Hippo Tumor Suppressor Pathway to Modulate Tissue Growth in Drosophila

    PubMed Central

    Ilanges, Anoj; Jahanshahi, Maryam; Balobin, Denis M.; Pfleger, Cathie M.

    2013-01-01

    Alcohol-mediated cancers represent more than 3.5% of cancer-related deaths, yet how alcohol promotes cancer is a major open question. Using Drosophila, we identified novel interactions between dietary ethanol and loss of tumor suppressor components of the Hippo Pathway. The Hippo Pathway suppresses tumors in flies and mammals by inactivating transcriptional co-activator Yorkie, and the spectrum of cancers associated with impaired Hippo signaling overlaps strikingly with those associated with alcohol. Therefore, our findings may implicate loss of Hippo Pathway tumor suppression in alcohol-mediated cancers. Ethanol enhanced overgrowth from loss of the expanded, hippo, or warts tumor suppressors but, surprisingly, not from over-expressing the yorkie oncogene. We propose that in parallel to Yorkie-dependent overgrowth, impairing Hippo signaling in the presence of alcohol may promote overgrowth via additional alcohol-relevant targets. We also identified interactions between alcohol and Hippo Pathway over-activation. We propose that exceeding certain thresholds of alcohol exposure activates Hippo signaling to maintain proper growth control and prevent alcohol-mediated mis-patterning and tissue overgrowth. PMID:24205337

  10. Conservation and expression of PIWI-interacting RNA pathway genes in male and female adult gonad of amniotes.

    PubMed

    Lim, Shu Ly; Tsend-Ayush, Enkhjargal; Kortschak, R Daniel; Jacob, Reuben; Ricciardelli, Carmela; Oehler, Martin K; Grützner, Frank

    2013-12-01

    The PIWI-interacting RNA (piRNA) pathway is essential for germline development and transposable element repression. Key elements of this pathway are members of the piRNA-binding PIWI/Argonaute protein family and associated factors (e.g., VASA, MAELSTROM, and TUDOR domain proteins). PIWI-interacting RNAs have been identified in mouse testis and oocytes, but information about the expression of the different piRNA pathway genes, in particular in the mammalian ovary, remains incomplete. We investigated the evolution and expression of piRNA pathway genes in gonads of amniote species (chicken, platypus, and mouse). Database searches confirm a high level of conservation and revealed lineage-specific gain and loss of Piwi genes in vertebrates. Expression analysis in mammals shows that orthologs of Piwi-like (Piwil) genes, Mael (Maelstrom), Mvh (mouse vasa homolog), and Tdrd1 (Tudor domain-containing protein 1) are expressed in platypus adult testis. In contrast to mouse, Piwil4 is expressed in platypus and human adult testis. We found evidence for Mael and Piwil2 expression in mouse Sertoli cells. Importantly, we show mRNA expression of Piwil2, Piwil4, and Mael in oocytes and supporting cells of human, mouse, and platypus ovary. We found no Piwil1 expression in mouse and chicken ovary. The conservation of gene expression in somatic parts of the gonad and germ cells of species that diverged over 800 million yr ago indicates an important role in adult male and female gonad.

  11. Quercetin, a Natural Flavonoid Interacts with DNA, Arrests Cell Cycle and Causes Tumor Regression by Activating Mitochondrial Pathway of Apoptosis

    PubMed Central

    Srivastava, Shikha; Somasagara, Ranganatha R.; Hegde, Mahesh; Nishana, Mayilaadumveettil; Tadi, Satish Kumar; Srivastava, Mrinal; Choudhary, Bibha; Raghavan, Sathees C.

    2016-01-01

    Naturally occurring compounds are considered as attractive candidates for cancer treatment and prevention. Quercetin and ellagic acid are naturally occurring flavonoids abundantly seen in several fruits and vegetables. In the present study, we evaluate and compare antitumor efficacies of quercetin and ellagic acid in animal models and cancer cell lines in a comprehensive manner. We found that quercetin induced cytotoxicity in leukemic cells in a dose-dependent manner, while ellagic acid showed only limited toxicity. Besides leukemic cells, quercetin also induced cytotoxicity in breast cancer cells, however, its effect on normal cells was limited or none. Further, quercetin caused S phase arrest during cell cycle progression in tested cancer cells. Quercetin induced tumor regression in mice at a concentration 3-fold lower than ellagic acid. Importantly, administration of quercetin lead to ~5 fold increase in the life span in tumor bearing mice compared to that of untreated controls. Further, we found that quercetin interacts with DNA directly, and could be one of the mechanisms for inducing apoptosis in both, cancer cell lines and tumor tissues by activating the intrinsic pathway. Thus, our data suggests that quercetin can be further explored for its potential to be used in cancer therapeutics and combination therapy. PMID:27068577

  12. Gene-gene interactions in the folate metabolic pathway influence the risk for acute lymphoblastic leukemia in children.

    PubMed

    Petra, Bohanec Grabar; Janez, Jazbec; Vita, Dolzan

    2007-04-01

    Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer. Genetic polymorphisms in the folate metabolic pathway may contribute to the susceptibility to childhood ALL because they affect the DNA synthesis, methylation and repair. We analysed common genetic polymorphisms of 5,10-methylenetetrahydrofolate reductase (MTHFR), thymidylate synthase (TS), methionine synthase (MS) and methionine synthase reductase (MTRR) in 68 children with ALL and 258 healthy controls to investigate their influence on the risk for ALL. No significant differences in frequencies of separate polymorphisms were observed between both groups. Combined MTHFR 677CT/TT and MS 2756AG/GG genotypes showed a nonsignificant tendency to reduce the risk for ALL 2.24-fold (CI: 0.191 - 1.037, P: 0.061). The risk was significantly reduced in carriers of combined MTHFR 677CT/TT, MS 2756AG/GG and MTRR 66AG/GG genotypes (OR: 0.312; CI: 0.107 - 0.907; P: 0.032). Our results suggest that gene - gene interactions that may decrease the methylation capacity might have a protective effect on the risk for childhood ALL.

  13. Effective colloidal interactions in rotating magnetic fields

    NASA Astrophysics Data System (ADS)

    Coughlan, Anna C. H.; Bevan, Michael A.

    2017-08-01

    Non-equilibrium, steady-state effective pair potentials of micron-sized superparamagnetic particles in rotating magnetic fields are obtained vs. field frequency and amplitude. Trajectories of center-to-center distance between particle pairs from Brownian dynamic simulations, which were previously matched to experimental measurements, are analyzed to obtain local drift and diffusion coefficients. These coefficients are used to obtain effective interaction potentials from solving a one-dimensional Fokker-Planck equation. Biased sampling of the effective energy landscape was implemented by intermittent switching between the field of interest and a repulsive field. Our findings show how the shape and attractive well-depth of pair interactions can be tuned by changing field frequency and amplitude.

  14. The effects on clinical coding of the critical pathway recording methodology.

    PubMed

    Cameron, Moira; Robinson, Kerin

    2004-01-01

    A two-stage study aimed to identify the effects of the critical pathway recording methodology on clinical coding practice and to determine coders' participation in pathway development. Critical pathways were found to be in widespread use, with low coder participation in pathway development and poor education on pathway data extraction. Coders favoured the traditional medical record format; private sector coders predominated amongst those who preferred to code from records containing pathways because of poor private sector clinical documentation. The documentation factors that most affected the clinical coding process were consistent with those identified previously and were primarily doctor-related.

  15. A Large Scale Huntingtin Protein Interaction Network Implicates Rho GTPase Signaling Pathways in Huntington Disease*♦

    PubMed Central

    Tourette, Cendrine; Li, Biao; Bell, Russell; O'Hare, Shannon; Kaltenbach, Linda S.; Mooney, Sean D.; Hughes, Robert E.

    2014-01-01

    Huntington disease (HD) is an inherited neurodegenerative disease caused by a CAG expansion in the HTT gene. Using yeast two-hybrid methods, we identified a large set of proteins that interact with huntingtin (HTT)-interacting proteins. This network, composed of HTT-interacting proteins (HIPs) and proteins interacting with these primary nodes, contains 3235 interactions among 2141 highly interconnected proteins. Analysis of functional annotations of these proteins indicates that primary and secondary HIPs are enriched in pathways implicated in HD, including mammalian target of rapamycin, Rho GTPase signaling, and oxidative stress response. To validate roles for HIPs in mutant HTT toxicity, we show that the Rho GTPase signaling components, BAIAP2, EZR, PIK3R1, PAK2, and RAC1, are modifiers of mutant HTT toxicity. We also demonstrate that Htt co-localizes with BAIAP2 in filopodia and that mutant HTT interferes with filopodial dynamics. These data indicate that HTT is involved directly in membrane dynamics, cell attachment, and motility. Furthermore, they implicate dysregulation in these pathways as pathological mechanisms in HD. PMID:24407293

  16. Exploring communication pathways to better health: Clinician communication of expectations for acupuncture effectiveness

    PubMed Central

    Street, Richard L.; Cox, Vanessa; Kallen, Michael A.; Suarez-Almazor, Maria E.

    2012-01-01

    Objective This study tested a pathway whereby acupuncturists’ communication of optimism for treatment effectiveness would enhance patients’ satisfaction during treatment, which in turn would contribute to better pain and function outcomes for patients with osteoarthritis of the knee. Methods Secondary analysis from a 2 arm (real vs. sham acupuncture, high vs. neutral expectations) RCT. 311 patients with knee osteoarthritis received acupuncture over 10–12 sessions. Coders rated the degree to which acupuncturists communicated optimism for the treatment’s effectiveness. Satisfaction with acupuncture was assessed 4 weeks into treatment. Pain and function were assessed 6 weeks following treatment. Results Patients experiencing better outcomes were more satisfied with acupuncture during treatment, were younger, and had better baseline pain and function scores. Satisfaction during treatment was greater when patients interacted with more optimistic clinicians and had higher pretreatment expectations for acupuncture efficacy. Conclusion Acupuncturists’ communication of optimism about treatment effectiveness contributed to pain and function outcomes indirectly through its effect on satisfaction during treatment. Future research should model pathways through which clinician-patient communication affects mediating variables that in turn lead to improved health outcomes. Practical Implications While clinicians should not mislead patients, communicating hope and optimism for treatment effectiveness has therapeutic value for patients. PMID:22857778

  17. New paradigm in ethylene signaling: EIN2, the central regulator of the signaling pathway, interacts directly with the upstream receptors.

    PubMed

    Bisson, Melanie M A; Groth, Georg

    2011-01-01

    The membrane protein ETHYLENE INSENSITIVE2 (EIN2), which is supposed to act between the soluble serine/threonine kinase CTR1 and the EIN3/EIL family of transcription factors, is a central and most critical element of the ethylene signaling pathway in Arabidopsis. In a recent study, we have identified that EIN2 interacts tightly with all members of the Arabidopsis ethylene receptor family - proteins that mark the starting point of the signaling pathway. Our studies show consistently that the kinase domain of the receptors is essential for the formation of the EIN2-receptor complex. Furthermore, mutational analysis demonstrates that phosphorylation is a key mechanism in controlling the interaction of EIN2 and the ethylene receptors. Interaction studies in the presence of the ethylene agonist cyanide revealed a causal link between hormone binding and complex formation. In the presence of the plant hormone agonist the auto-kinase activity of the receptors is inhibited and the non-phosphorylated kinase domain of the receptors binds tightly to the carboxyl-terminal domain of EIN2. In the absence of cyanide inhibition of the auto-kinase activity is relieved and complex formation with the phosphorylated kinase domain of the receptors is reduced. Our data suggest a novel model on the integration of EIN2 in the ethylene signaling pathway.

  18. Effective Interactions from No Core Shell Model

    SciTech Connect

    Dikmen, E.; Lisetskiy, A. F.; Barrett, B. R.; Navratil, P.; Vary, J. P.

    2008-11-11

    We construct the many-body effective Hamiltonian for pf-shell by carrying out 2({Dirac_h}/2{pi}){omega}. NCSM calculations at the 2-body cluster level. We demonstrate how the effective Hamiltonian derived from realistic nucleon-nucleon (NN) potentials for the 2({Dirac_h}/2{pi}){omega} NCSM space should be modified to properly account for the many-body correlations produced by truncating to the major pf-shell. We obtain two-body effective interactions for the pf-shell by using direct projection and use them to reproduce the results of large scale NCSM for other light Ca isotopes.

  19. The Efimov effect with finite range interactions

    NASA Astrophysics Data System (ADS)

    Platter, Lucas

    2017-01-01

    Systems of strongly interacting atoms are receiving a lot of attention because of their interesting features in the few- and many-body sector. Strong interactions are frequently obtained in experiment by using a Feshbach resonance to tune the scattering to large values. A striking feature of three-body systems with a large scattering is the emergence of a discrete scaling symmetry that is also known as the Efimov effect. The Efimov effect has been observed through the measurement of loss rates in experiments with ultracold atoms. It is, however, also relevant to nuclear physics where the three-nucleon bound state and some halo nuclei are considered to be examples of Efimov states. Such systems can be modeled conveniently with the zero-range limit, however, in many of such experiments the finite range of the interaction leads to significant corrections that need to be taken into account. I will discuss how a finite effective range can be included in calculations for three-body systems that display the Efimov effect and how this leads to novel universal relations. Applications to experiments with homonuclear and heteronuclear ultracold atomic gases are discussed. National Science Foundation PHY-1516077, PHY-1555030.

  20. Arachidonic acid potentiates currents through Ca2+-permeable AMPA receptors by interacting with a CaMKII pathway.

    PubMed

    Nishizaki, T; Matsuoka, T; Nomura, T; Enikolopov, G; Sumikawa, K

    1999-04-06

    The present study investigated the effect of arachidonic acid on the alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors, presumably heteromeric receptors formed of GluR1, GluR2, and GluR3, expressed in Xenopus oocytes. Arachidonic acid (10 microM) potentiated currents through receptors expressing GluR1 and 3 (GluR1,3) to 170% of basal level during initial 20 min following application, being still evident at 60-min washing-out of the drug, while it never or little enhanced currents through receptors expressing GluR1 and 2 (GluR1,2) or GluR1, 2, and 3 (GluR1,2,3) (110% 30 min after treatment). The effect of arachidonic acid on GluR1,3 currents was not observed in Ca2+-free extracellular solution, and the potentiation was blocked by either KN-93, a selective Ca2+/calmodulin-dependent protein kinase II (CaMKII) inhibitor, or NP217, an active CaMKII inhibitor peptide, when co-expressed with the receptors. In contrast, the protein synthesis inhibitor, cycloheximide, the selective inhibitor of cAMP-dependent protein kinase (PKA), H-89, the selective inhibitors of protein kinase C (PKC), PKCI and GF109203X, the mitogen-activated protein (MAP) kinase kinase inhibitor, PD98059, or the inactive CaMKII inhibitors, KN-92 and NP218, had no effect on the currents. In the assay of intracellular calcium mobilizations, Ca2+ influx in response to receptor activation was greatest with receptors formed in oocytes expressing GluR1,3. The results of the present study indicate that arachidonic acid induces a long-lasting potentiation of GluR1,3 currents, possibly as a result of the interaction with a CaMKII pathway. Copyright 1999 Elsevier Science B.V.

  1. A proteomic analysis of LRRK2 binding partners reveals interactions with multiple signaling components of the WNT/PCP pathway.

    PubMed

    Salašová, Alena; Yokota, Chika; Potěšil, David; Zdráhal, Zbyněk; Bryja, Vítězslav; Arenas, Ernest

    2017-07-11

    Autosomal-dominant mutations in the Park8 gene encoding Leucine-rich repeat kinase 2 (LRRK2) have been identified to cause up to 40% of the genetic forms of Parkinson's disease. However, the function and molecular pathways regulated by LRRK2 are largely unknown. It has been shown that LRRK2 serves as a scaffold during activation of WNT/β-catenin signaling via its interaction with the β-catenin destruction complex, DVL1-3 and LRP6. In this study, we examine whether LRRK2 also interacts with signaling components of the WNT/Planar Cell Polarity (WNT/PCP) pathway, which controls the maturation of substantia nigra dopaminergic neurons, the main cell type lost in Parkinson's disease patients. Co-immunoprecipitation and tandem mass spectrometry was performed in a mouse substantia nigra cell line (SN4741) and human HEK293T cell line in order to identify novel LRRK2 binding partners. Inhibition of the WNT/β-catenin reporter, TOPFlash, was used as a read-out of WNT/PCP pathway activation. The capacity of LRRK2 to regulate WNT/PCP signaling in vivo was tested in Xenopus laevis' early development. Our proteomic analysis identified that LRRK2 interacts with proteins involved in WNT/PCP signaling such as the PDZ domain-containing protein GIPC1 and Integrin-linked kinase (ILK) in dopaminergic cells in vitro and in the mouse ventral midbrain in vivo. Moreover, co-immunoprecipitation analysis revealed that LRRK2 binds to two core components of the WNT/PCP signaling pathway, PRICKLE1 and CELSR1, as well as to FLOTILLIN-2 and CULLIN-3, which regulate WNT secretion and inhibit WNT/β-catenin signaling, respectively. We also found that PRICKLE1 and LRRK2 localize in signalosomes and act as dual regulators of WNT/PCP and β-catenin signaling. Accordingly, analysis of the function of LRRK2 in vivo, in X. laevis revelaed that LRKK2 not only inhibits WNT/β-catenin pathway, but induces a classical WNT/PCP phenotype in vivo. Our study shows for the first time that LRRK2 activates the WNT

  2. Negative Regulation of Grb10 Interacting GYF Protein 2 on Insulin-Like Growth Factor-1 Receptor Signaling Pathway Caused Diabetic Mice Cognitive Impairment

    PubMed Central

    Xie, Jing; Wei, Qianping; Deng, Huacong; Li, Gang; Ma, Lingli; Zeng, Hui

    2014-01-01

    Heterozygous Gigyf2+/− mice exhibits histopathological evidence of neurodegeneration such as motor dysfunction. Several lines of evidence have demonstrated the important role of insulin-like growth factor-1 receptor (IGF1R) signaling pathway in the neuropathogenic process of cognitive impairment, while decreased Grb10-Interacting GYF Protein 2 (GIGYF2) expression can alter IGF1R trafficking and its downstream signaling pathways. Growth factor receptor-bound protein 10 (Grb10), a suppressor of IGF1R pathway, has been shown to play a critical role in regulating diabetes-associated cognitive impairment. It remains unknown whether endogenous GIGYF2 expression contributes to the development of diabetes-associated cognitive impairment. Using streptozotocin (STZ)-induced diabetic mice model, we first demonstrated that a significantly increased level of GIGYF2 expression was correlated with a significant decrease in the expression of phosphorylated IGF1R as well as the phosphorylation of AKT and ERK1/2, two signaling pathways downstream of IGF1R, in the hippocampus of diabetic mice. On the contrary, in situ knockdown of GIGYF2 expression in hippocampus resulted in increased expression of phosphorylated IGF1R expression and correspondingly reversed the down-regulation of ERK1/2 phsophorylation but had no obvious effect on Grb10 expression. Functionally, knockdown of GIGYF2 expression markedly ameliorated diabetes-associated cognitive dysfunction as well as the ultrastructural pathology and abnormal neurobehavioral changes. These results suggest that increased expression of GIGYF2 might contribute to the development of diabetes-associated cognitive disorder via negatively regulating IGF1R signaling pathway. Therefore, down-regulation of GIGYF2 expression may provide a potential novel approach to treat diabetes-associated cognitive impairment caused by aberrant IGF1R signaling pathway. PMID:25268761

  3. Moesin is a glioma progression marker that induces proliferation and Wnt/β-catenin pathway activation via interaction with CD44.

    PubMed

    Zhu, Xiaoping; Morales, Fabiana C; Agarwal, Nitin Kumar; Dogruluk, Turgut; Gagea, Mihai; Georgescu, Maria-Magdalena

    2013-02-01

    Moesin is an ERM family protein that connects the actin cytoskeleton to transmembrane receptors. With the identification of the ERM family protein NF2 as a tumor suppressor in glioblastoma, we investigated roles for other ERM proteins in this malignancy. Here, we report that overexpression of moesin occurs generally in high-grade glioblastoma in a pattern correlated with the stem cell marker CD44. Unlike NF2, moesin acts as an oncogene by increasing cell proliferation and stem cell neurosphere formation, with its ectopic overexpression sufficient to shorten survival in an orthotopic mouse model of glioblastoma. Moesin was the major ERM member activated by phosphorylation in glioblastoma cells, where it interacted and colocalized with CD44 in membrane protrusions. Increasing the levels of moesin competitively displaced NF2 from CD44, increasing CD44 expression in a positive feedback loop driven by the Wnt/β-catenin signaling pathway. Therapeutic targeting of the moesin-CD44 interaction with the small-molecule inhibitor 7-cyanoquinocarcinol (DX-52-1) or with a CD44-mimetic peptide specifically reduced the proliferation of glioblastoma cells overexpressing moesin, where the Wnt/β-catenin pathway was activated. Our findings establish moesin and CD44 as progression markers and drugable targets in glioblastoma, relating their oncogenic effects to activation of the Wnt/β-catenin pathway.

  4. p53 amplifies Toll-like receptor 5 response in human primary and cancer cells through interaction with multiple signal transduction pathways

    PubMed Central

    Shatz, Maria; Shats, Igor; Menendez, Daniel; Resnick, Michael A.

    2015-01-01

    The p53 tumor suppressor regulates transcription of genes associated with diverse cellular functions including apoptosis, growth arrest, DNA repair and differentiation. Recently, we established that p53 can modulate expression of Toll-like receptor (TLR) innate immunity genes but the degree of cross-talk between p53 and TLR pathways remained unclear. Here, using gene expression profiling we characterize the global effect of p53 on the TLR5-mediated transcription in MCF7 cells. We found that combined activation of p53 and TLR5 pathways synergistically increases expression of over 200 genes, mostly associated with immunity and inflammation. The synergy was observed in several human cancer cells and primary lymphocytes. The p53-dependent amplification of transcriptional response to TLR5 activation required expression of NFκB subunit p65 and was mediated by several molecular mechanisms including increased phosphorylation of p38 MAP kinase, PI3K and STAT3 signaling. Additionally, p53 induction increased cytokine expression in response to TNFα, another activator of NFκB and MAP kinase pathways, suggesting a broad interaction between p53 and these signaling pathways. The expression of many synergistically induced genes is elevated in breast cancer patients responsive to chemotherapy. We suggest that p53's capacity to enhance immune response could be exploited to increase antitumor immunity and to improve cancer treatment. PMID:26220208

  5. The effect of insulin on expression of genes and biochemical pathways in human skeletal muscle.

    PubMed

    Wu, Xuxia; Wang, Jelai; Cui, Xiangqin; Maianu, Lidia; Rhees, Brian; Rosinski, James; So, W Venus; Willi, Steven M; Osier, Michael V; Hill, Helliner S; Page, Grier P; Allison, David B; Martin, Mitchell; Garvey, W Timothy

    2007-02-01

    To study the insulin effects on gene expression in skeletal muscle, muscle biopsies were obtained from 20 insulin sensitive individuals before and after euglycemic hyperinsulinemic clamps. Using microarray analysis, we identified 779 insulin-responsive genes. Particularly noteworthy were effects on 70 transcription factors, and an extensive influence on genes involved in both protein synthesis and degradation. The genetic program in skeletal muscle also included effects on signal transduction, vesicular traffic and cytoskeletal function, and fuel metabolic pathways. Unexpected observations were the pervasive effects of insulin on genes involved in interacting pathways for polyamine and S-adenoslymethionine metabolism and genes involved in muscle development. We further confirmed that four insulin-responsive genes, RRAD, IGFBP5, INSIG1, and NGFI-B (NR4A1), were significantly up-regulated by insulin in cultured L6 skeletal muscle cells. Interestingly, insulin caused an accumulation of NGFI-B (NR4A1) protein in the nucleus where it functions as a transcription factor, without translocation to the cytoplasm to promote apoptosis. The role of NGFI-B (NR4A1) as a new potential mediator of insulin action highlights the need for greater understanding of nuclear transcription factors in insulin action.

  6. Pathway Design Effects on Synthetic Vision Head-Up Displays

    NASA Technical Reports Server (NTRS)

    Kramer, Lynda J.; Prinzel, Lawrence J., III; Arthur, Jarvis J., III; Bailey, Randall E.

    2004-01-01

    NASA s Synthetic Vision Systems (SVS) project is developing technologies with practical applications that will eliminate low visibility conditions as a causal factor to civil aircraft accidents while replicating the operational benefits of clear day flight operations, regardless of the actual outside visibility condition. A major thrust of the SVS project involves the development/demonstration of affordable, certifiable display configurations that provide intuitive out-the-window terrain and obstacle information with advanced pathway guidance for transport aircraft. This experiment evaluated the influence of different tunnel and guidance concepts upon pilot situation awareness (SA), mental workload, and flight path tracking performance for Synthetic Vision display concepts using a Head-Up Display (HUD). Two tunnel formats (dynamic, minimal) were evaluated against a baseline condition (no tunnel) during simulated IMC approaches to Reno-Tahoe International airport. Two guidance cues (tadpole, follow-me aircraft) were also evaluated to assess their influence on the tunnel formats. Results indicated that the presence of a tunnel on an SVS HUD had no effect on flight path performance but that it did have significant effects on pilot SA and mental workload. The dynamic tunnel concept with the follow-me aircraft guidance symbol produced the lowest workload and provided the highest SA among the tunnel concepts evaluated.

  7. Intergenerational continuity in parenting behavior: mediating pathways and child effects.

    PubMed

    Neppl, Tricia K; Conger, Rand D; Scaramella, Laura V; Ontai, Lenna L

    2009-09-01

    This prospective, longitudinal investigation examined mechanisms proposed to explain continuities in parenting behavior across 2 generations (G1, G2). Data came from 187 G2 adults, their mothers (G1), and their children (G3). Prospective information regarding G2 was collected both during adolescence and early adulthood. G1 data were collected during G2's adolescence, and G3 data were generated during the preschool years. Assessments included both observational and self-report measures. The results indicated a direct relationship between G1 and G2 harsh parenting, and between G1 and G2 positive parenting. As predicted, specific mediators accounted for intergenerational continuity in particular types of parenting behavior. G2 externalizing behavior mediated the relationship between G1 and G2 harsh parenting, whereas G2 academic attainment mediated the relationship between G1 and G2 positive parenting. In addition, the hypothesized mediating pathways remained statistically significant after taking into account possible G2 effects on G1 parenting and G3 effects on G2 parenting.

  8. Intergenerational Continuity in Parenting Behavior: Mediating Pathways and Child Effects

    PubMed Central

    Neppl, Tricia K.; Conger, Rand D.; Scaramella, Laura V.; Ontai, Lenna L.

    2009-01-01

    This prospective, longitudinal investigation examined mechanisms proposed to explain continuities in parenting behavior across two generations (G1, G2). Data came from 187 G2 adults, their mothers (G1), and their children (G3). Prospective information regarding G2 was collected both during adolescence and early adulthood. G1 data were collected during G2’s adolescence and G3 data were generated during the preschool years. Assessments included both observational and self-report measures. The results indicated a direct relationship between G1 and G2 harsh parenting and between G1 and G2 positive parenting. As predicted, specific mediators accounted for intergenerational continuity in particular types of parenting behavior. G2 externalizing behavior mediated the relationship between G1 and G2 harsh parenting, while G2 academic attainment mediated the relationship between G1 and G2 positive parenting. In addition, the hypothesized mediating pathways remained statistically significant after taking into account possible G2 effects on G1 parenting and G3 effects on G2 parenting. PMID:19702389

  9. Nature of the effective interaction between dendrimers

    SciTech Connect

    Mandal, Taraknath Dasgupta, Chandan Maiti, Prabal K.

    2014-10-14

    We have performed fully atomistic classical molecular dynamics simulations to calculate the effective interaction between two polyamidoamine dendrimers. Using the umbrella sampling technique, we have obtained the potential of mean force (PMF) between the dendrimers and investigated the effects of protonation level and dendrimer size on the PMF. Our results show that the interaction between the dendrimers can be tuned from purely repulsive to partly attractive by changing the protonation level. The PMF profiles are well-fitted by the sum of an exponential and a Gaussian function with the weight of the exponential function dominating over that of the Gaussian function. This observation is in disagreement with the results obtained in previous analytic [C. Likos, M. Schmidt, H. Löwen, M. Ballauff, D. Pötschke, and P. Lindner, Macromolecules 34, 2914 (2001)] and coarse-grained simulation [I. Götze, H. Harreis, and C. Likos, J. Chem. Phys. 120, 7761 (2004)] studies which predicted the effective interaction to be Gaussian.

  10. Tumor-Derived Suppressor of Fused Mutations Reveal Hedgehog Pathway Interactions.

    PubMed

    Urman, Nicole M; Mirza, Amar; Atwood, Scott X; Whitson, Ramon J; Sarin, Kavita Y; Tang, Jean Y; Oro, Anthony E

    2016-01-01

    The Hedgehog pathway is a potent regulator of cellular growth and plays a central role in the development of many cancers including basal cell carcinoma (BCC). The majority of BCCs arise from mutations in the Patched receptor resulting in constitutive activation of the Hedgehog pathway. Secondary driver mutations promote BCC oncogenesis and occur frequently due to the high mutational burden resulting from sun exposure of the skin. Here, we uncover novel secondary mutations in Suppressor of Fused (SUFU), the major negative regulator of the Hedgehog pathway. SUFU normally binds to a Hedgehog transcriptional activator, GLI1, in order to prevent it from initiating transcription of Hedgehog target genes. We sequenced tumor-normal pairs from patients with early sporadic BCCs. This resulted in the discovery of nine mutations in SUFU, which were functionally investigated to determine whether they help drive BCC formation. Our results show that four of the SUFU mutations inappropriately activate the Hedgehog pathway, suggesting they may act as driver mutations for BCC development. Indeed, all four of the loss of function SUFU variants were found to disrupt its binding to GLI, leading to constitutive pathway activation. Our results from functional characterization of these mutations shed light on SUFU's role in Hedgehog signaling, tumor progression, and highlight a way in which BCCs can arise.

  11. Tumor-Derived Suppressor of Fused Mutations Reveal Hedgehog Pathway Interactions

    PubMed Central

    Urman, Nicole M.; Mirza, Amar; Atwood, Scott X.; Whitson, Ramon J.; Sarin, Kavita Y.; Tang, Jean Y.; Oro, Anthony E.

    2016-01-01

    The Hedgehog pathway is a potent regulator of cellular growth and plays a central role in the development of many cancers including basal cell carcinoma (BCC). The majority of BCCs arise from mutations in the Patched receptor resulting in constitutive activation of the Hedgehog pathway. Secondary driver mutations promote BCC oncogenesis and occur frequently due to the high mutational burden resulting from sun exposure of the skin. Here, we uncover novel secondary mutations in Suppressor of Fused (SUFU), the major negative regulator of the Hedgehog pathway. SUFU normally binds to a Hedgehog transcriptional activator, GLI1, in order to prevent it from initiating transcription of Hedgehog target genes. We sequenced tumor-normal pairs from patients with early sporadic BCCs. This resulted in the discovery of nine mutations in SUFU, which were functionally investigated to determine whether they help drive BCC formation. Our results show that four of the SUFU mutations inappropriately activate the Hedgehog pathway, suggesting they may act as driver mutations for BCC development. Indeed, all four of the loss of function SUFU variants were found to disrupt its binding to GLI, leading to constitutive pathway activation. Our results from functional characterization of these mutations shed light on SUFU’s role in Hedgehog signaling, tumor progression, and highlight a way in which BCCs can arise. PMID:28030567

  12. Inhibitory effects of marine-derived DNA-binding anti-tumour tetrahydroisoquinolines on the Fanconi anaemia pathway

    PubMed Central

    Martínez, Sandra; Pérez, Laura; Galmarini, Carlos M; Aracil, Miguel; Tercero, Juan C; Gago, Federico; Albella, Beatriz; Bueren, Juan A

    2013-01-01

    BACKGROUND AND PURPOSE We have previously shown that cells with a defective Fanconi anaemia (FA) pathway are hypersensitive to trabectedin, a DNA-binding anti-cancer tetrahydroisoquinoline (DBAT) whose adducts functionally mimic a DNA inter-strand cross link (ICL). Here we expand these observations to new DBATs and investigate whether our findings in primary untransformed cells can be reproduced in human cancer cells. EXPERIMENTAL APPROACH Initially, the sensitivity of transformed and untransformed cells, deficient or not in one component of the FA pathway, to mitomycin C (MMC) and three DBATs, trabectedin, Zalypsis and PM01183, was assessed. Then, the functional interaction of these drugs with the FA pathway was comparatively investigated. KEY RESULTS While untransformed FA-deficient haematopoietic cells were hypersensitive to both MMC and DBATs, the response of FA-deficient squamous cell carcinoma (SCC) cells to DBATs was similar to that of their respective FA-competent counterparts, even though these FA-deficient SCC cells were hypersensitive to MMC. Furthermore, while MMC always activated the FA pathway, the DBATs inhibited the FA pathway in the cancer cell lines tested and this enhanced their response to MMC. CONCLUSIONS AND IMPLICATIONS Our data show that although DBATs functionally interact with DNA as do agents that generate classical ICL, these drugs should be considered as FA pathway inhibitors rather than activators. Moreover, this effect was most significant in a variety of cancer cells. These inhibitory effects of DBATs on the FA pathway could be exploited clinically with the aim of ‘fanconizing’ cancer cells in order to make them more sensitive to other anti-tumour drugs. PMID:23937566

  13. AtVPS41-mediated endocytic pathway is essential for pollen tube–stigma interaction in Arabidopsis

    PubMed Central

    Hao, Lihong; Liu, Jingjing; Zhong, Sheng; Gu, Hongya; Qu, Li-Jia

    2016-01-01

    In flowering plants, extensive male–female interactions are required for successful fertilization in which various signaling cascades are involved. Prevacuolar compartments (PVC) and vacuoles are two types of subcellular compartments that terminate signal transduction by sequestrating signaling molecules in yeast and mammalian cells; however, the manner in which they might be involved in male–female interactions in plants is unknown. In this study, we identified Arabidopsis thaliana vacuolar protein sorting 41 (AtVPS41), encoded by a single-copy gene with sequence similarity to yeast Vps41p, as a new factor controlling pollen tube–stigma interaction. Loss of AtVPS41 function disrupted penetration of pollen tubes into the transmitting tissue and thus led to failed male transmission. In the pollen tubes, AtVPS41 protein is associated with PVCs and the tonoplast. We demonstrate that AtVPS41 is required for the late stage of the endocytic pathway (i.e., endomembrane trafficking from PVCs to vacuoles) because internalization of cell-surface molecules was normal in the vps41-deficient pollen tubes, whereas PVC-to-vacuole trafficking was impaired. We further show that the CHCR domain is required for subcellular localization and biological functioning of AtVPS41. These results indicate that the AtVPS41-mediated late stage of the endocytic pathway is essential for pollen tube–stigma interaction in Arabidopsis. PMID:27185920

  14. Studies of protein-protein interactions in Fanconi anemia pathway to unravel the DNA interstrand crosslink repair mechanism.

    PubMed

    Siddiqui, Mohd Quadir; Rajpurohit, Yogendra S; Thapa, Pankaj S; Maurya, Ganesh Kumar; Banerjee, Kuheli; Khan, Mudassar Ali; Panda, Pragnya; Hasan, Syed K; Gadewal, Nikhil; Misra, Hari S; Varma, Ashok K

    2017-11-01

    Fanconi anemia (FA), a cancer predisposition syndrome exhibits hallmark feature of radial chromosome formation, and hypersensitivity to DNA crosslinking agents. A set of FA pathway proteins mainly FANCI, FANCD2 and BRCA2 are expressed to repair the covalent crosslink between the dsDNA. However, FA, BRCA pathways play an important role in DNA ICL repair as well as in homologous recombination repair, but the presumptive role of FA-BRCA proteins has not clearly explored particularly in context to function associated protein-protein interactions (PPIs). Here, in-vivo, in-vitro and in-silico studies have been performed for functionally relevant domains of FANCI, FANCD2 and BRCA2. To our conclusion, FANCI ARM repeat interacts with FANCD2 CUE domain and BRCA2 C-terminal region. Interestingly, FANCD2 CUE domain also interacts strongly with BRCA2 C-terminal region. Interactions between BRCA2 CTR and functionally relevant mutations Ser222Ala (cell cycle checkpoint mutant) and Leu231Arg (DNA ICL repair mutant) present in FANCD2 CUE domain have been analysed. To our finding, these mutations abrogate the binding between FANCD2 CUE domain and BRCA2 CTR. Furthermore, (1) different domain of FANCI, FANCD2 and BRCA2 are playing important role in PPIs, (2) mutations cause the impairment in the PPIs which in turn may disrupt the DNA ICL repair mechanism. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. An ERP study of the interaction between verbal information and conditioning pathways to fear.

    PubMed

    Ugland, Carina C O; Dyson, Benjamin J; Field, Andy P

    2013-01-01

    Two experiments are described that explore the effects of verbal information and direct conditioning in the acquisition and extinction of fear responses. Participants were given verbal threat information about novel animals before conditioning trials in which the animals were presented alongside an aversive outcome (Experiment 1), or positive information about the animals before extinction trials (Experiment 2). Fear was measured using self-reported fear beliefs, expectancy of the unconditioned stimulus (US) and event-related brain potential (ERP). The results showed a direct effect of verbal information on acquisition (Experiment 1) and extinction (Experiment 2). There was a P2 peak latency shift at acquisition (Experiment 1) and P1 mean amplitude response at extinction (Experiment 2) based on the interaction between verbal information and US-contingency. However, the P2 response showed little evidence for an enhanced conditioned response (CR) when verbal threat information and direct conditioning combined: earlier P2 responses were found for all animals that had been associated with either threat information or the aversive US. Additionally, increase in P1 mean amplitude response (Experiment 2) seemed to stem from the conflict between verbal information and contingency information, rather than the predicted decrease in response where positive information and extinction training were combined. Future studies are suggested that might explore whether attention/arousal modulate the P1 response as a result of such expectation violations.

  16. Apoptosis-linked gene-2 (ALG-2)/Sec31 interactions regulate endoplasmic reticulum (ER)-to-Golgi transport: a potential effector pathway for luminal calcium.

    PubMed

    Helm, Jared R; Bentley, Marvin; Thorsen, Kevin D; Wang, Ting; Foltz, Lauren; Oorschot, Viola; Klumperman, Judith; Hay, Jesse C

    2014-08-22

    Luminal calcium released from secretory organelles has been suggested to play a regulatory role in vesicle transport at several steps in the secretory pathway; however, its functional roles and effector pathways have not been elucidated. Here we demonstrate for the first time that specific luminal calcium depletion leads to a significant decrease in endoplasmic reticulum (ER)-to-Golgi transport rates in intact cells. Ultrastructural analysis revealed that luminal calcium depletion is accompanied by increased accumulation of intermediate compartment proteins in COPII buds and clusters of unfused COPII vesicles at ER exit sites. Furthermore, we present several lines of evidence suggesting that luminal calcium affected transport at least in part through calcium-dependent interactions between apoptosis-linked gene-2 (ALG-2) and the Sec31A proline-rich region: 1) targeted disruption of ALG-2/Sec31A interactions caused severe defects in ER-to-Golgi transport in intact cells; 2) effects of luminal calcium and ALG-2/Sec31A interactions on transport mutually required each other; and 3) Sec31A function in transport required luminal calcium. Morphological phenotypes of disrupted ALG-2/Sec31A interactions were characterized. We found that ALG-2/Sec31A interactions were not required for the localization of Sec31A to ER exit sites per se but appeared to acutely regulate the stability and trafficking of the cargo receptor p24 and the distribution of the vesicle tether protein p115. These results represent the first outline of a mechanism that connects luminal calcium to specific protein interactions regulating vesicle trafficking machinery. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. A role for Drosophila Cyclin J in oogenesis revealed by genetic interactions with the piRNA pathway.

    PubMed

    Atikukke, Govindaraja; Albosta, Paul; Zhang, Huamei; Finley, Russell L

    2014-08-01

    Cyclin J (CycJ) is a poorly characterized member of the Cyclin superfamily of cyclin-dependent kinase regulators, many of which regulate the cell cycle or transcription. Although CycJ is conserved in metazoans its cellular function has not been identified and no mutant defects have been described. In Drosophila, CycJ transcript is present primarily in ovaries and very early embryos, suggesting a role in one or both of these tissues. The CycJ gene (CycJ) lies immediately downstream of armitage (armi), a gene involved in the Piwi-associated RNA (piRNA) pathways that are required for silencing transposons in the germline and adjacent somatic cells. Mutations in armi result in oogenesis defects but a role for CycJ in oogenesis has not been defined. Here we assessed oogenesis in CycJ mutants in the presence or absence of mutations in armi or other piRNA pathway genes. CycJ null ovaries appeared normal, indicating that CycJ is not essential for oogenesis under normal conditions. In contrast, armi null ovaries produced only two egg chambers per ovariole and the eggs had severe axis specification defects, as observed previously for armi and other piRNA pathway mutants. Surprisingly, the CycJ armi double mutant failed to produce any mature eggs. The double null ovaries generally had only one egg chamber per ovariole and the egg chambers frequently contained an overabundance of differentiated germline cells. Production of these compound egg chambers could be suppressed with CycJ transgenes but not with mutations in the checkpoint gene mnk, which suppress oogenesis defects in armi mutants. The CycJ null showed similar genetic interactions with the germline and somatic piRNA pathway gene piwi, and to a lesser extent with aubergine (aub), a member of the germline-specific piRNA pathway. The strong genetic interactions between CycJ and piRNA pathway genes reveal a role for CycJ in early oogenesis. Our results suggest that CycJ is required to regulate egg chamber production or

  18. A role for Drosophila Cyclin J in oogenesis revealed by genetic interactions with the piRNA pathway

    PubMed Central

    Atikukke, Govindaraja; Albosta, Paul; Zhang, Huamei; Finley, Russell L.

    2014-01-01

    Cyclin J (CycJ) is a poorly characterized member of the Cyclin superfamily of cyclin-dependent kinase regulators, many of which regulate the cell cycle or transcription. Although CycJ is conserved in metazoans its cellular function has not been identified and no mutant defects have been described. In Drosophila, CycJ transcript is present primarily in ovaries and very early embryos, suggesting a role in one or both of these tissues. The CycJ gene (CycJ) lies immediately downstream of armitage (armi), a gene involved in the Piwi-associated RNA (piRNA) pathways that are required for silencing transposons in the germline and adjacent somatic cells. Mutations in armi result in oogenesis defects but a role for CycJ in oogenesis has not been defined. Here we assessed oogenesis in CycJ mutants in the presence or absence of mutations in armi or other piRNA pathway genes. CycJ null ovaries appeared normal, indicating that CycJ is not essential for oogenesis under normal conditions. In contrast, armi null ovaries produced only two egg chambers per ovariole and the eggs had severe axis specification defects, as observed previously for armi and other piRNA pathway mutants. Surprisingly, the CycJ armi double mutant failed to produce any mature eggs. The double null ovaries generally had only one egg chamber per ovariole and the egg chambers frequently contained an overabundance of differentiated germline cells. Production of these compound egg chambers could be suppressed with CycJ transgenes but not with mutations in the checkpoint gene mnk, which suppress oogenesis defects in armi mutants. The CycJ null showed similar genetic interactions with the germline and somatic piRNA pathway gene piwi, and to a lesser extent with aubergine (aub), a member of the germline-specific piRNA pathway. The strong genetic interactions between CycJ and piRNA pathway genes reveal a role for CycJ in early oogenesis. Our results suggest that CycJ is required to regulate egg chamber production or

  19. Stress Effects on Multiple Memory System Interactions

    PubMed Central

    Ness, Deborah; Calabrese, Pasquale

    2016-01-01

    Extensive behavioural, pharmacological, and neurological research reports stress effects on mammalian memory processes. While stress effects on memory quantity have been known for decades, the influence of stress on multiple memory systems and their distinct contributions to the learning process have only recently been described. In this paper, after summarizing the fundamental biological aspects of stress/emotional arousal and recapitulating functionally and anatomically distinct memory systems, we review recent animal and human studies exploring the effects of stress on multiple memory systems. Apart from discussing the interaction between distinct memory systems in stressful situations, we will also outline the fundamental role of the amygdala in mediating such stress effects. Additionally, based on the methods applied in the herein discussed studies, we will discuss how memory translates into behaviour. PMID:27034845

  20. Contamination Effects Due to Space Environmental Interactions

    NASA Technical Reports Server (NTRS)

    Chen, Philip T.; Paquin, Krista C. (Technical Monitor)

    2001-01-01

    Molecular and particulate contaminants are commonly generated from the orbital spacecraft operations that are under the influence of the space environment. Once generated, these contaminants may attach to the surfaces of the spacecraft or may remain in the vicinity of the spacecraft. In the event these contaminants come to rest on the surfaces of the spacecraft or situated in the line-of-sight of the observation path, they will create various degrees of contamination effect which may cause undesirable effects for normal spacecraft operations, There will be circumstances in which the spacecraft may be subjected to special space environment due to operational conditions. Interactions between contaminants and special space environment may alter or greatly increase the contamination effect due to the synergistic effect. This paper will address the various types of contamination generation on orbit, the general effects of the contamination on spacecraft systems, and the typical impacts on the spacecraft operations due to the contamination effect. In addition, this paper will explain the contamination effect induced by the space environment and will discuss the intensified contamination effect resulting from the synergistic effect with the special space environment.

  1. Effectiveness and pathways of electrochemical degradation of pretilachlor herbicides.

    PubMed

    Wei, Jinzhi; Feng, Yujie; Sun, Xiaojun; Liu, Junfeng; Zhu, Limin

    2011-05-15

    Pretilachlor used as one kind of acetanilide herbicides is potentially dangerous and biorefractory. In this work, electrochemical degradation of lab-synthetic pretilachlor wastewater was carried out with Sb doped Ti/SnO(2) electrode as anode and stainless steel as cathode. The effect of current density on pretilachlor degradation was investigated, and the degradation pathway of pretilachlor was inferred by analyzing its main degradation intermediates. The results showed that the removal of pretilachlor and TOC in treatment time of 60 min were 98.8% and 43.1% under the conditions of current density of 20 mA cm(-2), initial concentration of pretilachlor of 60 mg L(-1), Na(2)SO(4) dosage of 0.1 mol L(-1), pH of 7.2, respectively, while the energy consumption was 15.8 kWhm(-3). The main reactions for electrochemical degradation of pretilachlor included hydroxylation, oxidation, dechlorination, C-O bond and C-N bond cleavage, resulting in the formation of nine main intermediates. Copyright © 2011 Elsevier B.V. All rights reserved.

  2. Bone Biomarkers on the Pathway to Effective Spaceflight Countermeasures

    NASA Technical Reports Server (NTRS)

    Spatz, Jordan

    2009-01-01

    Osteocyte cells are the most abundant yet least understood bone cell type in the human body. However, recent discovers in osteocyte cell biology have shed light on their importance as key mechanosensing cells regulating the bone remodeling process. Thus, we propose the first ever in vitro gene expression evaluation of osteocytes exposed to simulated microgravity to determine mechanistic pathways of their gravity sensing ability. Improved understanding of the fundamental mechanisms at the osteocyte cellular level may lead to improved treatment options to mitigate the effects of bone loss encountered by astronauts on long duration space missions and provide tailored treatment options for maintaining bone strength of immobilized/partially paralyzed patients here on Earth. Aim 1: Characterize the gene expression patterns and protein levels following exposure of murine osteocytelike cell line (MLO-Y4) to simulated microgravity using the NASA Rotating Wall Vessel (RWV) Bioreactor. Osteocytes are theorized to be the mechanosensors and transducers of mechanical load for bones, yet the biological mechanism of this action remains elusive. We propose to investigate the genetic regulation of the mechanism of the MLO-Y4 cell in the NASA Bioreactor as it is the accepted ground-based analog for simulating vector averaged microgravity.

  3. Integrating both interaction pathways between warming and pesticide exposure on upper thermal tolerance in high- and low-latitude populations of an aquatic insect.

    PubMed

    Op de Beeck, Lin; Verheyen, Julie; Stoks, Robby

    2017-05-01

    Global warming and chemical pollution are key anthropogenic stressors with the potential to interact. While warming can change the impact of pollutants and pollutants can change the sensitivity to warming, both interaction pathways have never been integrated in a single experiment. Therefore, we tested the effects of warming and multiple pesticide pulses (allowing accumulation) of chlorpyrifos on upper thermal tolerance (CTmax) and associated physiological traits related to aerobic/anaerobic energy production in the damselfly Ischnura elegans. To also assess the role of latitude-specific thermal adaptation in shaping the impact of warming and pesticide exposure on thermal tolerance, we exposed larvae from replicated high- and low-latitude populations to the pesticide in a common garden rearing experiment at 20 and 24 °C, the mean summer water temperatures at high and low latitudes. As expected, exposure to chlorpyrifos resulted in a lower CTmax. Yet, this pesticide effect on CTmax was lower at 24 °C compared to 20 °C because of a lower accumulation of chlorpyrifos in the medium at 24 °C. The effects on CTmax could partly be explained by reduction of the aerobic scope. Given that these effects did not differ between latitudes, gradual thermal evolution is not expected to counteract the negative effect of the pesticide on thermal tolerance. By for the first time integrating both interaction pathways we were not only able to provide support for both of them, but more importantly demonstrate that they can directly affect each other. Indeed, the warming-induced reduction in pesticide impact generated a lower pesticide-induced climate change sensitivity (in terms of decreased upper thermal tolerance). Our results indicate that, assuming no increase in pesticide input, global warming might reduce the negative effect of multiple pulse exposures to pesticides on sensitivity to elevated temperatures.

  4. Novel pathway analysis of genomic polymorphism-cancer risk interaction in the Breast Cancer Prevention Trial

    PubMed Central

    Dunn, Barbara K; Greene, Mark H; Kelley, Jenny M; Costantino, Joseph P; Clifford, Robert J; Hu, Ying; Tang, Gong; Kazerouni, Neely; Rosenberg, Philip S; Meerzaman, Daoud M; Buetow, Kenneth H

    2010-01-01

    Purpose: Tamoxifen was approved for breast cancer risk reduction in high-risk women based on the National Surgical Adjuvant Breast and Bowel Project's Breast Cancer Prevention Trial (P-1:BCPT), which showed 50% fewer breast cancers with tamoxifen versus placebo, supporting tamoxifen's efficacy in preventing breast cancer. Poor metabolizing CYP2D6 variants are currently the subject of intensive scrutiny regarding their impact on clinical outcomes in the adjuvant setting. Our study extends to variants in a wider spectrum of tamoxifen-metabolizing genes and applies to the prevention setting. Methods: Our case-only study, nested within P-1:BCPT, explored associations of polymorphisms in estrogen/tamoxifen-metabolizing genes with responsiveness to preventive tamoxifen. Thirty-nine candidate polymorphisms in 17 candidate genes were genotyped in 249 P-1:BCPT cases. Results: CVP2D6_C1111T, individually and within a CYP2D6 haplotype, showed borderline significant association with treatment arm. Path analysis of the entire tamoxifen pathway gene network showed that the tamoxifen pathway model was consistent with the pattern of observed genotype variability within the placebo-arm dataset. However, correlation of variations in genes in the tamoxifen arm differed significantly from the predictions of the tamoxifen pathway model. Strong correlations between allelic variation in the tamoxifen pathway at CYP1A1-CYP3A4, CYP3A4-CYP2C9, and CYP2C9-SULT1A2, in addition to CYP2D6 and its adjacent genes, were seen in the placebo-arm but not the tamoxifen-arm. In conclusion, beyond reinforcing a role for CYP2D6 in tamoxifen response, our pathway analysis strongly suggests that specific combinations of allelic variants in other genes make major contributions to the tamoxifen-resistance phenotype. PMID:21152245

  5. A microphysical pathway analysis to investigate aerosol effects on convective clouds

    NASA Astrophysics Data System (ADS)

    Heikenfeld, Max; White, Bethan; Labbouz, Laurent; Stier, Philip

    2017-04-01

    The impact of aerosols on ice- and mixed-phase processes in convective clouds remains highly uncertain, which has strong implications for estimates of the role of aerosol-cloud interactions in the climate system. The wide range of interacting microphysical processes are still poorly understood and generally not resolved in global climate models. To understand and visualise these processes and to conduct a detailed pathway analysis, we have added diagnostic output of all individual process rates for number and mass mixing ratios to two commonly-used cloud microphysics schemes (Thompson and Morrison) in WRF. This allows us to investigate the response of individual processes to changes in aerosol conditions and the propagation of perturbations throughout the development of convective clouds. Aerosol effects on cloud microphysics could strongly depend on the representation of these interactions in the model. We use different model complexities with regard to aerosol-cloud interactions ranging from simulations with different levels of fixed cloud droplet number concentration (CDNC) as a proxy for aerosol, to prognostic CDNC with fixed modal aerosol distributions. Furthermore, we have implemented the HAM aerosol model in WRF-chem to also perform simulations with a fully interactive aerosol scheme. We employ a hierarchy of simulation types to understand the evolution of cloud microphysical perturbations in atmospheric convection. Idealised supercell simulations are chosen to present and test the analysis methods for a strongly confined and well-studied case. We then extend the analysis to large case study simulations of tropical convection over the Amazon rainforest. For both cases we apply our analyses to individually tracked convective cells. Our results show the impact of model uncertainties on the understanding of aerosol-convection interactions and have implications for improving process representation in models.

  6. Identification of Links Between Cellular Pathways by Genetic Interaction Mapping (GIM).

    PubMed

    Malabat, Christophe; Saveanu, Cosmin

    2016-01-01

    The yeast systematic deletion collection offered the basis for a number of different strategies that establish functional links between genes by analyzing the phenotype of cells that combine two different deletions or mutations. A distinguishing feature of the collection is the presence of molecular barcodes at each deleted locus, which can be used to quantify the presence and abundance of cells bearing a given allele in a complex mix. As a result, a large number of mutants can be tested in batch cultures, replacing tedious manipulation of thousands of individual strains with a barcode microarray readout. Barcode-based genetic screens like Genetic Interaction Mapping (GIM) thus require little investment in terms of specific equipment, are fast to perform, and allow precise measurements of double mutant growth rates for both aggravating (synthetic sick) and alleviating (epistatic) effects. We describe here protocols for preparing the pools of haploid double mutant S. cerevisiae cells, testing their composition with barcode microarrays, and analyzing the results to extract useful functional information.

  7. Dual specificity phosphotase 18, interacting with SAPK, dephosphorylates SAPK and inhibits SAPK/JNK signal pathway in vivo.

    PubMed

    Wu, Qihan; Huang, Shengdong; Sun, Yaqiong; Gu, Shaohua; Lu, Fanglin; Dai, Jianfeng; Yin, Gang; Sun, Liyun; Zheng, Dan; Dou, Chao; Feng, Congjing; Ji, Chaoneng; Xie, Yi; Mao, Yumin

    2006-09-01

    The SAPK/JNKs play important roles in numerous cellular processes, and for this reason they have become putative drug targets. Most dual-specificity protein phosphatases (DSPs) play important roles in the regulation of mitogenic signal transduction and cell cycle control in response to extracellular stimuli. Dual-specificity phosphatase 18 (DUSP18), a newly recognized SAPK/JNK phosphatase, is widely expressed. This expression is modulated in response to extracellular stimuli. By phosphorylation assay, pull down and coimmunoprecipitation experiments, it is shown here that DUSP18 interacts with SAPK/JNK and dephosphorylates it both in vitro and in vivo. DUSP18 does not dephosphorylate p38 or p44ERK1. Furthermore, DUSP18 inhibits SAPK/JNK pathway in vivo. Based on these findings, DUSP18 appears to serve an important role by regulation of SAPK/JNK pathway.

  8. Role of the neural pathway from hindbrain to hypothalamus in interaction of GLP1 and leptin in rats.

    PubMed

    Akieda-Asai, Sayaka; Poleni, Paul-Emile; Hasegawa, Kazuya; Date, Yukari

    2014-02-01

    Glucagon-like peptide-1 (GLP1) and leptin are anorectic hormones. Previously, we have shown that i.p. coadministration of subthreshold GLP1 with leptin dramatically reduced food intake in rats. In this study, by using midbrain-transected rats, we investigated the role of the neural pathway from the hindbrain to the hypothalamus in the interaction of GLP1 and leptin in reducing food intake. Food intake reduction induced by coinjection of GLP1 and leptin was blocked in midbrain-transected rats. These findings indicate that the ascending neural pathway from the hindbrain plays an important role in transmitting the anorectic signals provided by coinjection of GLP1 and leptin.

  9. Targeting the interaction of Aurora kinases and SIRT1 mediated by Wnt signaling pathway in colorectal cancer: A critical review.

    PubMed

    Subramaniyan, Boopathi; Jagadeesan, Kaviya; Ramakrishnan, Sabitha; Mathan, Ganeshan

    2016-08-01

    The Aurora kinases belong to the family of serine/threonine kinase, a central regulator of mitosis and their expression increased during G2/M phase. It is classified into Aurora A, B and C, each has distinct roles in cellular processes, which includes regulation of spindle assembly, function of centrosomes, cytoskeleton and cytokinesis. During cancer growth, their rapid increase makes most attractive marker for cancer treatment at present. However Aurora A kinase is known to be a marker for cancer therapy, the most important serine/threonine kinase of Aurora B kinase involvement in cancer is still inadequate. Subsequently, the recent findings revealed that the class III histone deacetylase of SIRT1 is a key regulator to activate Aurora kinases from S phase damaged DNA through Wnt signaling pathway. Even if both Aurora A kinase and SIRT1 serve as a marker for cancer therapy, the present review reveals it is interaction in Wnt signaling pathway that solely for colorectal cancer.

  10. Interactions of polybrominated diphenyl ethers with the aryl hydrocarbon receptor pathway.

    PubMed

    Peters, A K; Nijmeijer, S; Gradin, K; Backlund, M; Bergman, A; Poellinger, L; Denison, M S; Van den Berg, M

    2006-07-01

    Polybrominated diphenyl ethers (PBDEs) are brominated flame retardants that have been in use as additives in various consumer products. Structural similarities of PBDEs with other polyhalogenated aromatic hydrocarbons that show affinity for the aryl hydrocarbon receptor (AhR), such as some polychlorinated biphenyls, raised concerns about their possible dioxin-like properties. We studied the ability of environmentally relevant PBDEs (BDE-47, -99, -100, -153, -154, and -183) and the "planar" congener BDE-77 to bind and/or activate the AhR in stably transfected rodent hepatoma cell lines with an AhR-responsive enhanced green fluorescent protein (AhR-EGFP) reporter gene (H1G1.1c3 mouse and H4G1.1c2 rat hepatoma). 7-Ethoxyresorufin-O-deethylation (EROD) was used as a marker for CYP1A1 activity. Dose- and bromination-specific inhibition of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-induced responses was measured by their ability to inhibit the induction of AhR-EGFP expression and EROD activity. Individual exposure to these PBDEs did not result in any increase in induction of AhR-EGFP or CYP1A1 activity. The lower brominated PBDEs showed the strongest inhibitory effect on TCDD-induced activities in both cell lines. While the highest brominated PBDE tested, BDE-183, inhibited EROD activity, it did not affect the induction of AhR-EGFP expression. Similar findings were observed after exposing stably transfected human hepatoma (xenobiotic response element [XRE]-HepG2) cells to these PBDEs, resulting in a small but statically significant agonistic effect on XRE-driven luciferase activity. Co-exposure with TCDD resulted again in antagonistic effects, confirming that the inhibitory effect of these PBDEs on TCDD-induced responses was not only due to direct interaction at receptor level but also at DNA-binding level. This antagonism was confirmed for BDE-99 in HepG2 cells transiently transfected with a Gal4-AhR construct and the corresponding Gal4-Luc reporter gene. In addition, a

  11. Polymorphisms in maternal folate pathway genes interact with arsenic in drinking water to influence risk of myelomeningocele

    PubMed Central

    Mazumdar, Maitreyi; Valeri, Linda; Rodrigues, Ema G.; Hasan, Md Omar Sharif Ibne; Hamid, Rezina; Paul, Ligi; Selhub, Jacob; Silva, Fareesa; Mostofa, MdGolam; Quamruzzaman, Quazi; Rahman, Mahmuder; Christiani, David C.

    2015-01-01

    Background Arsenic induces neural tube defects in many animal models. Additionally, studies have shown that mice with specific genetic defects in folate metabolism and transport are more susceptible to arsenic-induced neural tube defects. We sought to determine whether 14 single-nucleotide polymorphisms in genes involved in folate metabolism modified the effect of exposure to drinking water contaminated with inorganic arsenic and posterior neural tube defect (myelomeningocele) risk. Methods Fifty-four mothers of children with myelomeningocele and 55 controls were enrolled through clinical sites in rural Bangladesh in a case-control study of the association between environmental arsenic exposure and risk of myelomeningocele. We assessed participants for level of myelomeningocele, administered questionnaires, conducted biological and environmental sample collection, and performed genotyping. Inductively coupled plasma mass spectrometry (ICP-MS) was used to measure inorganic arsenic concentration in drinking water. Candidate single-nucleotide polymorphisms were identified through review of the literature. Results Drinking water inorganic arsenic concentration was associated with increased risk of myelomeningocele for participants with 4 of the 14 studied single-nucleotide polymorphisms in genes involved in folate metabolism: the AA/AG genotype of rs2236225 (MTHFD1), the GG genotype of rs1051266 (SLC19A1), the TT genotype of rs7560488 (DNMT3A), and the GG genotype of rs3740393 (AS3MT) with adjusted OR of 1.13, 1.31, 1.20, and 1.25 for rs2236225, rs1051266, rs7560488, and rs3740393, respectively. Conclusions Our results support the hypothesis that environmental arsenic exposure increases the risk of myelomeningocele via interaction with folate metabolic pathways. PMID:26250961

  12. Polymorphisms in maternal folate pathway genes interact with arsenic in drinking water to influence risk of myelomeningocele.

    PubMed

    Mazumdar, Maitreyi; Valeri, Linda; Rodrigues, Ema G; Ibne Hasan, Md Omar Sharif; Hamid, Rezina; Paul, Ligi; Selhub, Jacob; Silva, Fareesa; Mostofa, Md Golam; Quamruzzaman, Quazi; Rahman, Mahmuder; Christiani, David C

    2015-09-01

    Arsenic induces neural tube defects in many animal models. Additionally, studies have shown that mice with specific genetic defects in folate metabolism and transport are more susceptible to arsenic-induced neural tube defects. We sought to determine whether 14 single-nucleotide polymorphisms in genes involved in folate metabolism modified the effect of exposure to drinking water contaminated with inorganic arsenic and posterior neural tube defect (myelomeningocele) risk. Fifty-four mothers of children with myelomeningocele and 55 controls were enrolled through clinical sites in rural Bangladesh in a case-control study of the association between environmental arsenic exposure and risk of myelomeningocele. We assessed participants for level of myelomeningocele, administered questionnaires, conducted biological and environmental sample collection, and performed genotyping. Inductively coupled plasma mass spectrometry was used to measure inorganic arsenic concentration in drinking water. Candidate single-nucleotide polymorphisms were identified through review of the literature. Drinking water inorganic arsenic concentration was associated with increased risk of myelomeningocele for participants with 4 of the 14 studied single-nucleotide polymorphisms in genes involved in folate metabolism: the AA/AG genotype of rs2236225 (MTHFD1), the GG genotype of rs1051266 (SLC19A1), the TT genotype of rs7560488 (DNMT3A), and the GG genotype of rs3740393 (AS3MT) with adjusted odds ratio of 1.13, 1.31, 1.20, and 1.25 for rs2236225, rs1051266, rs7560488, and rs3740393, respectively. Our results support the hypothesis that environmental arsenic exposure increases the risk of myelomeningocele by means of interaction with folate metabolic pathways. © 2015 Wiley Periodicals, Inc.

  13. Ecosystem services capacity across heterogeneous forest types: understanding the interactions and suggesting pathways for sustaining multiple ecosystem services.

    PubMed

    Alamgir, Mohammed; Turton, Stephen M; Macgregor, Colin J; Pert, Petina L

    2016-10-01

    As ecosystem services supply from tropical forests is declining due to deforestation and forest degradation, much effort is essential to sustain ecosystem services supply from tropical forested landscapes, because tropical forests provide the largest flow of multiple ecosystem services among the terrestrial ecosystems. In order to sustain multiple ecosystem services, understanding ecosystem services capacity across heterogeneous forest types and identifying certain ecosystem services that could be managed to leverage positive effects across the wider bundle of ecosystem services are required. We sampled three forest types, tropical rainforests, sclerophyll forests, and rehabilitated plantation forests, over an area of 32,000m(2) from Wet Tropics bioregion, Australia, aiming to compare supply and evaluate interactions and patterns of eight ecosystem services (global climate regulation, air quality regulation, erosion regulation, nutrient regulation, cyclone protection, habitat provision, energy provision, and timber provision). On average, multiple ecosystem services were highest in the rainforests, lowest in sclerophyll forests, and intermediate in rehabilitated plantation forests. However, a wide variation was apparent among the plots across the three forest types. Global climate regulation service had a synergistic impact on the supply of multiple ecosystem services, while nutrient regulation service was found to have a trade-off impact. Considering multiple ecosystem services, most of the rehabilitated plantation forest plots shared the same ordination space with rainforest plots in the ordination analysis, indicating that rehabilitated plantation forests may supply certain ecosystem services nearly equivalent to rainforests. Two synergy groups and one trade-off group were identified. Apart from conserving rainforests and sclerophyll forests, our findings suggest two additional integrated pathways to sustain the supply of multiple ecosystem services from a

  14. A novel pathway for amyloids self-assembly in aggregates at nanomolar concentration mediated by the interaction with surfaces

    PubMed Central

    Banerjee, Siddhartha; Hashemi, Mohtadin; Lv, Zhengjian; Maity, Sibaprasad; Rochet, Jean-Christophe; Lyubchenko, Yuri L.

    2017-01-01

    A limitation of the amyloid hypothesis in explaining the development of neurodegenerative diseases is that the level of amyloidogenic polypeptide in vivo is below the critical concentration required to form the aggregates observed in post-mortem brains. We discovered a novel, on-surface aggregation pathway of amyloidogenic polypeptide that eliminates this long-standing controversy. We applied atomic force microscope (AFM) to demonstrate directly that on-surface aggregation takes place at a concentration at which no aggregation in solution is observed. The experiments were performed with the full-size Aβ protein (Aβ42), a decapeptide Aβ(14-23) and α-synuclein; all three systems demonstrate a dramatic preference of the on-surface aggregation pathway compared to the aggregation in the bulk solution. Time-lapse AFM imaging, in solution, show that over time, oligomers increase in size and number and release in solution, suggesting that assembled aggregates can serve as nuclei for aggregation in bulk solution. Computational modeling performed with the all-atom MD simulations for Aβ(14-23) peptide shows that surface interactions induce conformational transitions of the monomer, which facilitate interactions with another monomer that undergoes conformational changes stabilizing the dimer assembly. Our findings suggest that interactions of amyloidogenic polypeptides with cellular surfaces play a major role in determining disease onset. PMID:28358113

  15. Interplay Between Hydrophobic Effect and Dipole Interactions in Peptide Aggregation

    NASA Astrophysics Data System (ADS)

    Ganesan, Sai; Matysiak, Silvina

    In the past decade, the development of various coarse-grained models for proteins have provided key insights into the driving forces in folding and aggregation.We recently developed a low resolution Water Explicit Polarizable PROtein coarse-grained Model by adding oppositely charged dummy particles inside protein backbone beads.With this model,we were able to achieve significant α/ β secondary structure content,without any added bias.We now extend the model to study peptide aggregation at hydrophobic-hydrophilic interface using elastin-like octapeptides (GV)4 as a model system.A condensation-ordering mechanism of aggregation is observed in water.Our results suggest that backbone interpeptide dipolar interactions,not hydrophobicity,plays a more significant role in fibril-like peptide aggregation.We observe a cooperative effect in hydrogen bonding or dipolar interactions, with increase in aggregate size in water and interface.Based on this cooperative effect, we provide a potential explanation for the observed nucleus size in peptide aggregation pathways.Without dipolar particles,peptide aggregation is not observed at the hydrophilic-hydrophobic interface.Thus,the presence of dipoles,not hydrophobicity plays a key role in aggregation observed at hydrophobic interfaces.

  16. The effect of giant flank collapses on magma pathways and location of volcanic vents

    NASA Astrophysics Data System (ADS)

    Maccaferri, Francesco; Richter, Nicole; Walter, Thomas

    2017-04-01

    Flank collapses have been identified at tall volcanoes and ocean islands worldwide. They are recurrent processes, significantly contributing to the morphological and structural evolution of volcanic edifices, and they often occur in interaction with magmatic activity. Moreover, it has been observed that the intrusion pathways and eruption's sites often differ before and after flank collapses. While it is understood that dyke intrusions might destabilise a volcano flank, and a moving flank might create the space needed for further intrusions, the effect of collapses on the magma pathways has been rarely addressed. Here we use a boundary element model for dyke propagation to study the effect of the stress redistribution due to a flank collapse on the location of eruptive vents. We use our model to simulate the path of magmatic intrusion after the collapse of the eastern flank of Fogo Volcano, Cabe Verde. We find that the competition between loading stress due to the volcanic edifice and unloading due to the collapse of a flank favours magmatic activity to cluster within the collapse scar, displaced with respect to the pre-collapse volcanic centre. Our results are compared with geomorphological observations at Fogo Island and are discussed in the general context of the long-term evolution intraplate volcanic ocean islands worldwide.

  17. eQTL epistasis: detecting epistatic effects and inferring hierarchical relationships of genes in biological pathways.

    PubMed

    Kang, Mingon; Zhang, Chunling; Chun, Hyung-Wook; Ding, Chris; Liu, Chunyu; Gao, Jean

    2015-03-01

    Epistasis is the interactions among multiple genetic variants. It has emerged to explain the 'missing heritability' that a marginal genetic effect does not account for by genome-wide association studies, and also to understand the hierarchical relationships between genes in the genetic pathways. The Fisher's geometric model is common in detecting the epistatic effects. However, despite the substantial successes of many studies with the model, it often fails to discover the functional dependence between genes in an epistasis study, which is an important role in inferring hierarchical relationships of genes in the biological pathway. We justify the imperfectness of Fisher's model in the simulation study and its application to the biological data. Then, we propose a novel generic epistasis model that provides a flexible solution for various biological putative epistatic models in practice. The proposed method enables one to efficiently characterize the functional dependence between genes. Moreover, we suggest a statistical strategy for determining a recessive or dominant link among epistatic expression quantitative trait locus to enable the ability to infer the hierarchical relationships. The proposed method is assessed by simulation experiments of various settings and is applied to human brain data regarding schizophrenia. The MATLAB source codes are publicly available at: http://biomecis.uta.edu/epistasis. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  18. Cell cycle regulators interact with pathways that modulate microtubule stability in Saccharomyces cerevisiae.

    PubMed

    Shohat-Tal, Aya; Eshel, Dan

    2011-12-01

    The integrity of mitosis is dependent upon strict regulation of microtubule stability and dynamics. Although much information has been accumulated on regulators of the microtubule cytoskeleton, our knowledge of the specific pathways involved is still limited. Here we designed genetic screens to identify regulators of microtubule stability that are dispensable in the wild type yet become essential under microtubule-disrupting conditions. We found that the transcriptional cofactor Swi6p and activator Swi4p, as well as the G(2)/M-specific cyclin Clb2p, are required in a microtubule-destabilizing environment. Swi6p and Swi4p can combine as a transcriptional complex, called the SBF complex (SBF for Swi4/6 cell cycle box [SCB]-binding factor) that is functionally homologous to the metazoan DP1/2-E2F complex and that controls the G(1)/S transition through the genes it regulates. We show that Swi6p's contribution to microtubule stability can be either dependent or independent of the SBF complex. The SBF-dependent pathway requires downregulation of SBF complex levels and may thereby reroute the transcriptional program in favor of greater microtubule stability. This pathway can be triggered by overexpression of Fcp1p, a phosphatase in the general transcription machinery, or by expression of an allele of SWI6 that is associated with reduced transcription from SBF-controlled promoters. The SBF-independent pathway is activated by a constitutively nuclear allele of Swi6p. Our results introduce novel roles in microtubule stability for genes whose participation in the process may be masked under normal conditions yet nonetheless acquire a dominant role when microtubule stability is compromised.

  19. Phytohormone signaling pathway analysis method for comparing hormone responses in plant-pest interactions.

    PubMed

    Studham, Matthew E; MacIntosh, Gustavo C

    2012-07-31

    Phytohormones mediate plant defense responses to pests and pathogens. In particular, the hormones jasmonic acid, ethylene, salicylic acid, and abscisic acid have been shown to dictate and fine-tune defense responses, and identification of the phytohormone components of a particular defense response is commonly used to characterize it. Identification of phytohormone regulation is particularly important in transcriptome analyses. Currently there is no computational tool to determine the relative activity of these hormones that can be applied to transcriptome analyses in soybean. We developed a pathway analysis method that provides a broad measure of the activation or suppression of individual phytohormone pathways based on changes in transcript expression of pathway-related genes. The magnitude and significance of these changes are used to determine a pathway score for a phytohormone for a given comparison in a microarray experiment. Scores for individual hormones can then be compared to determine the dominant phytohormone in a given defense response. To validate this method, it was applied to publicly available data from previous microarray experiments that studied the response of soybean plants to Asian soybean rust and soybean cyst nematode. The results of the analyses for these experiments agreed with our current understanding of the role of phytohormones in these defense responses. This method is useful in providing a broad measure of the relative induction and suppression of soybean phytohormones during a defense response. This method could be used as part of microarray studies that include individual transcript analysis, gene set analysis, and other methods for a comprehensive defense response characterization.

  20. The role of Lsa23 to mediate the interaction of Leptospira interrogans with the terminal complement components pathway.

    PubMed

    Siqueira, Gabriela H; de Souza, Gisele O; Heinemann, Marcos B; Vasconcellos, Silvio A; Nascimento, Ana L T O

    2017-09-28

    Leptospirosis is a severe worldwide zoonotic disease caused by pathogenic Leptospira spp. It has been demonstrated that pathogenic leptospires are resistant to the bactericidal activity of normal human serum while saprophytic strains are susceptible. Pathogenic strains have the ability to bind soluble complement regulators and these activities are thought to contribute to bacterial immune evasion. One strategy used by some pathogens to evade the complement cascade, which is not well explored, is to block the terminal pathway. We have, thus, examined whether leptospires are able to interact with components of the terminal complement pathway. ELISA screening using anti-leptospires serum has shown that the pathogenic, virulent strain L. interrogans L1-130 can bind to immobilized human C8 (1 μg). However, virulent and saprophyte L. biflexa strains showed the ability to interact with C8 and C9, when these components were employed at physiological concentration (50 μg/mL), but the virulent strain seemed more competent. Lsa23, a putative leptospiral adhesin only present in pathogenic strains, interacts with C8 and C9 in a dose-dependent mode, suggesting that this protein could mediate the binding of virulent Leptospira with these components. To our knowledge, this is the first work reporting the binding of Leptospira to C8 and C9 terminal complement components, suggesting that the inhibition of this pathway is part of the strategy used by leptospires to evade the innate immunity. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Oncogenic activation of the PI3K/Akt pathway promotes cellular glucose uptake by downregulating the expression of thioredoxin-interacting protein.

    PubMed

    Hong, Shin Yee; Yu, Fa-Xing; Luo, Yan; Hagen, Thilo

    2016-05-01

    Oncogenic activation of the PI3K/Akt pathway is known to play an important role to promote glucose metabolism in cancer cells. However, the molecular mechanism through which the PI3K/Akt signalling pathway promotes glucose utilisation in cancer cells is still not well understood. It has recently been shown that the oncogenic activation of the PI3K/Akt/mTOR signalling in lung adenocarcinoma is important in promoting the localisation of glucose transporter 1 (GLUT1) at the plasma membrane. We thus hypothesised that the effect of constitutive activation of the PI3K/AKT signalling on glucose metabolism is mediated by thioredoxin interacting protein (TXNIP), a known regulator of the GLUT1 plasma membrane localisation. Consistent with previous studies, inhibition of the PI3K/Akt pathway decreased cellular glucose uptake. Furthermore, inhibition of PI3K/Akt signalling in non-small cell lung cancer (NSCLC) cell lines using clinically used tyrosine kinase inhibitors (TKIs) resulted in a decrease in GLUT1 membrane localisation. We also observed that inhibition of the PI3K/Akt pathway in various cell lines, including NSCLC cells, resulted in an increase in TXNIP expression. Importantly, knockdown of TXNIP using siRNA in the NSCLC cells promoted GLUT1 to be localised at the plasma membrane and reversed the effect of PI3K/Akt inhibitors. Together, our results suggest that the oncogenic activation of PI3K/Akt signalling promotes cellular glucose uptake, at least in part, through the regulation of TXNIP expression. This mechanism may contribute to the Warburg effect in cancer cells.

  2. Ecosystem engineering strengthens bottom-up and weakens top-down effects via trait-mediated indirect interactions

    PubMed Central

    Li, Xiaofei; Pearson, Dean; Wang, Deli; Sanders, Dirk; Zhu, Yu; Wang, Ling

    2017-01-01

    Trophic interactions and ecosystem engineering are ubiquitous and powerful forces structuring ecosystems, yet how these processes interact to shape natural systems is poorly understood. Moreover, trophic effects can be driven by both density- and trait-mediated interactions. Microcosm studies demonstrate that trait-mediated interactions may be as strong as density-mediated interactions, but the relative importance of these pathways at natural spatial and temporal scales is underexplored. Here, we integrate large-scale field experiments and microcosms to examine the effects of ecosystem engineering on trophic interactions while also exploring how ecological scale influences density- and trait-mediated interaction pathways. We demonstrate that (i) ecosystem engineering can shift the balance between top-down and bottom-up interactions, (ii) such effects can be driven by cryptic trait-mediated interactions, and (iii) the relative importance of density- versus trait-mediated interaction pathways can be scale dependent. Our findings reveal the complex interplay between ecosystem engineering, trophic interactions, and ecological scale in structuring natural systems. PMID:28931733

  3. MANORAA (Mapping Analogous Nuclei Onto Residue And Affinity) for identifying protein–ligand fragment interaction, pathways and SNPs

    PubMed Central

    Tanramluk, Duangrudee; Narupiyakul, Lalita; Akavipat, Ruj; Gong, Sungsam; Charoensawan, Varodom

    2016-01-01

    Protein–ligand interaction analysis is an important step of drug design and protein engineering in order to predict the binding affinity and selectivity between ligands to the target proteins. To date, there are more than 100 000 structures available in the Protein Data Bank (PDB), of which ∼30% are protein–ligand (MW below 1000 Da) complexes. We have developed the integrative web server MANORAA (Mapping Analogous Nuclei Onto Residue And Affinity) with the aim of providing a user-friendly web interface to assist structural study and design of protein–ligand interactions. In brief, the server allows the users to input the chemical fragments and present all the unique molecular interactions to the target proteins with available three-dimensional structures in the PDB. The users can also link the ligands of interest to assess possible off-target proteins, human variants and pathway information using our all-in-one integrated tools. Taken together, we envisage that the server will facilitate and improve the study of protein–ligand interactions by allowing observation and comparison of ligand interactions with multiple proteins at the same time. (http://manoraa.org). PMID:27131358

  4. Assessing Spurious Interaction Effects in Structural Equation Modeling

    ERIC Educational Resources Information Center

    Harring, Jeffrey R.; Weiss, Brandi A.; Li, Ming

    2015-01-01

    Several studies have stressed the importance of simultaneously estimating interaction and quadratic effects in multiple regression analyses, even if theory only suggests an interaction effect should be present. Specifically, past studies suggested that failing to simultaneously include quadratic effects when testing for interaction effects could…

  5. Assessing Spurious Interaction Effects in Structural Equation Modeling

    ERIC Educational Resources Information Center

    Harring, Jeffrey R.; Weiss, Brandi A.; Li, Ming

    2015-01-01

    Several studies have stressed the importance of simultaneously estimating interaction and quadratic effects in multiple regression analyses, even if theory only suggests an interaction effect should be present. Specifically, past studies suggested that failing to simultaneously include quadratic effects when testing for interaction effects could…

  6. The Halo Effect: An Unintended Benefit of Care Pathways.

    PubMed

    Barber, Collin; Fraser, James F; Mendez, Guillermo G; Bradley, Barrie; Loftus, Terry J; Jacofsky, David J

    2017-03-01

    The objective of this study was to determine if implementation of a simplified care pathway for total knee arthroplasty (TKA) would affect outcomes of total hip arthroplasty (THA) patients in the same health care system. Data were collected from a total of 5,095 consecutive THA patients in the year before and 2 years after implementation of the care pathway for TKA patients. Postimplementation increases were observed in both early activity (p < 0.0001) and continuous urinary catheter avoidance (p < 0.0001) among THA patients. These improvements in protocol adherence were associated with decreased complications (p < 0.0001), fewer 30-day readmissions (p < 0.0019), and decreased hospital length of stay (p < 0.0001). Based on these results, the implementation of a simplified care pathway for TKA patients can also improve outcomes for THA patients in the same health care system.

  7. Effective connectivity of neural pathways underlying disgust by multivariate Granger causality analysis

    NASA Astrophysics Data System (ADS)

    Yan, Hao; Wang, Yonghui; Tian, Jie; Liu, Yijun

    2011-03-01

    The disgust system arises phylogenetically in response to dangers to the internal milieu from pathogens and their toxic products. Functional imaging studies have demonstrated that a much wider range of neural structures was involved in triggering disgust reactions. However, less is known regarding how and what neural pathways these neural structures interact. To address this issue, we adopted an effective connectivity based analysis, namely the multivariate Granger causality approach, to explore the causal interactions within these brain networks. Results presented that disgust can induce a wide range of brain activities, such as the insula, the anterior cingulate cortex, the parahippocampus lobe, the dorsal lateral prefrontal cortex, the superior occipital gyrus, and the supplementary motor cortex. These brain areas constitute as a whole, with much denser connectivity following disgust stimuli, in comparison with that of the neutral condition. Moreover, the anterior insula, showing multiple casual interactions with limbic and subcortical areas, was implicated as a central hub in organizing multiple information processing in the disgust system.

  8. Relating drug–protein interaction network with drug side effects

    PubMed Central

    Mizutani, Sayaka; Pauwels, Edouard; Stoven, Véronique; Goto, Susumu; Yamanishi, Yoshihiro

    2012-01-01

    Motivation: Identifying the emergence and underlying mechanisms of drug side effects is a challenging task in the drug development process. This underscores the importance of system–wide approaches for linking different scales of drug actions; namely drug-protein interactions (molecular scale) and side effects (phenotypic scale) toward side effect prediction for uncharacterized drugs. Results: We performed a large-scale analysis to extract correlated sets of targeted proteins and side effects, based on the co-occurrence of drugs in protein-binding profiles and side effect profiles, using sparse canonical correlation analysis. The analysis of 658 drugs with the two profiles for 1368 proteins and 1339 side effects led to the extraction of 80 correlated sets. Enrichment analyses using KEGG and Gene Ontology showed that most of the correlated sets were significantly enriched with proteins that are involved in the same biological pathways, even if their molecular functions are different. This allowed for a biologically relevant interpretation regarding the relationship between drug–targeted proteins and side effects. The extracted side effects can be regarded as possible phenotypic outcomes by drugs targeting the proteins that appear in the same correlated set. The proposed method is expected to be useful for predicting potential side effects of new drug candidate compounds based on their protein-binding profiles. Supplementary information: Datasets and all results are available at http://web.kuicr.kyoto-u.ac.jp/supp/smizutan/target-effect/. Availability: Software is available at the above supplementary website. Contact: yamanishi@bioreg.kyushu-u.ac.jp, or goto@kuicr.kyoto-u.ac.jp PMID:22962476

  9. Interaction between Treg Apoptosis Pathways, Treg Function and HLA Risk Evolves during Type 1 Diabetes Pathogenesis

    PubMed Central

    Glisic, Sanja; Jailwala, Parthav

    2012-01-01

    We have previously reported increased apoptosis of regulatory T cells (Tregs) in recent-onset Type 1 Diabetes subjects (RO T1D) in the honeymoon phase and in multiple autoantibody-positive (Ab+) subjects, some of which are developing T1D. We have also reported that increased Treg apoptosis was associated with High HLA risk and that it subsided with cessation of honeymoon period. In this report, we present results generated using genetics, genomics, functional cell-based assays and flow cytometry to assess cellular changes at the T-cell level during T1D pathogenesis. We measured ex vivo Treg apoptosis and Treg function, surface markers expression, expression of HLA class II genes, the influence of HLA risk on Treg apoptosis and function, and evaluated contribution of genes reported to be involved in the apoptosis process. This integrated comprehensive approach uncovered important information that can serve as a basis for future studies aimed to modulate Treg cell responsiveness to apoptotic signals in autoimmunity. For example, T1D will progress in those subjects where increased Treg apoptosis is accompanied with decreased Treg function. Furthermore, Tregs from High HLA risk healthy controls had increased Treg apoptosis levels and overexpressed FADD but not Fas/FasL. Tregs from RO T1D subjects in the honeymoon phase were primarily dying through withdrawal of growth hormones with contribution of oxidative stress, mitochondrial apoptotic pathways, and employment of TNF-receptor family members. Ab+ subjects, however, expressed high inflammation level, which probably contributed to Treg apoptosis, although other apoptotic pathways were also activated: withdrawal of growth hormones, oxidative stress, mitochondrial apoptosis and Fas/FasL apoptotic pathways. The value of these results lie in potentially different preventive treatment subjects would receive depending on disease progression stage when treated. PMID:22563437

  10. GAIP Interacting Protein C-Terminus Regulates Autophagy and Exosome Biogenesis of Pancreatic Cancer through Metabolic Pathways

    PubMed Central

    Bhattacharya, Santanu; Pal, Krishnendu; Sharma, Anil K.; Dutta, Shamit K.; Lau, Julie S.; Yan, Irene K.; Wang, Enfeng; Elkhanany, Ahmed; Alkharfy, Khalid M.; Sanyal, Arunik; Patel, Tushar C.; Chari, Suresh T.; Spaller, Mark R.; Mukhopadhyay, Debabrata

    2014-01-01

    GAIP interacting protein C terminus (GIPC) is known to play an important role in a variety of physiological and disease states. In the present study, we have identified a novel role for GIPC as a master regulator of autophagy and the exocytotic pathways in cancer. We show that depletion of GIPC-induced autophagy in pancreatic cancer cells, as evident from the upregulation of the autophagy marker LC3II. We further report that GIPC regulates cellular trafficking pathways by modulating the secretion, biogenesis, and molecular composition of exosomes. We also identified the involvement of GIPC on metabolic stress pathways regulating autophagy and microvesicular shedding, and observed that GIPC status determines the loading of cellular cargo in the exosome. Furthermore, we have shown the overexpression of the drug resistance gene ABCG2 in exosomes from GIPC-depleted pancreatic cancer cells. We also demonstrated that depletion of GIPC from cancer cells sensitized them to gemcitabine treatment, an avenue that can be explored as a potential therapeutic strategy to overcome drug resistance in cancer. PMID:25469510

  11. GAIP interacting protein C-terminus regulates autophagy and exosome biogenesis of pancreatic cancer through metabolic pathways.

    PubMed

    Bhattacharya, Santanu; Pal, Krishnendu; Sharma, Anil K; Dutta, Shamit K; Lau, Julie S; Yan, Irene K; Wang, Enfeng; Elkhanany, Ahmed; Alkharfy, Khalid M; Sanyal, Arunik; Patel, Tushar C; Chari, Suresh T; Spaller, Mark R; Mukhopadhyay, Debabrata

    2014-01-01

    GAIP interacting protein C terminus (GIPC) is known to play an important role in a variety of physiological and disease states. In the present study, we have identified a novel role for GIPC as a master regulator of autophagy and the exocytotic pathways in cancer. We show that depletion of GIPC-induced autophagy in pancreatic cancer cells, as evident from the upregulation of the autophagy marker LC3II. We further report that GIPC regulates cellular trafficking pathways by modulating the secretion, biogenesis, and molecular composition of exosomes. We also identified the involvement of GIPC on metabolic stress pathways regulating autophagy and microvesicular shedding, and observed that GIPC status determines the loading of cellular cargo in the exosome. Furthermore, we have shown the overexpression of the drug resistance gene ABCG2 in exosomes from GIPC-depleted pancreatic cancer cells. We also demonstrated that depletion of GIPC from cancer cells sensitized them to gemcitabine treatment, an avenue that can be explored as a potential therapeutic strategy to overcome drug resistance in cancer.

  12. RNA-Seq and Network Analysis Revealed Interacting Pathways in TGF-β-Treated Lung Cancer Cell Lines

    PubMed Central

    Li, Yan; Rouhi, Omid; Chen, Hankui; Ramirez, Rolando; Borgia, Jeffrey A; Deng, Youping

    2014-01-01

    Whole transcriptome shotgun sequencing (RNA-Seq) is a useful tool for analyzing the transcriptome of a biological sample. With appropriate statistical and bioinformatic processing, this platform is capable of identifying significant differences in gene expression within the transcriptome and permits pathway and network analyses to determine how these genes interact biologically. In this study, we examined gene expression in two lung adenocarcinoma cell lines (H358 and A459) that were treated with transforming growth factor-β (TGF-β) as a model for induction of the epithelial-to-mesenchymal transition (EMT), commonly associated with disease progression. We performed this study in order to illustrate a workflow for identifying interesting genes and processes that are regulated early in EMT and to determine their gene pathway/network relationships and regulation. With this, we identified 137 upregulated and 32 downregulated genes common to both cell lines after TGF-β treatment that represent components of multiple canonical pathways and biological networks associated with the induction of EMT. These findings were also verified against reposited Affymetrix U133a expression profiles from multiple trials examining metastatic progression in patient cohorts (n = 731 total) to further establish the clinical relevance and translational significance of the model system. Together, these findings help validate the relevance of the TGF-β model for the study of EMT and provide new insights into early events in EMT. PMID:25991908

  13. Approaches to Testing Interaction Effects Using Structural Equation Modeling Methodology.

    ERIC Educational Resources Information Center

    Li, Fuzhong; Harmer, Peter; Duncan, Terry E.; Duncan, Susan C.; Acock, Alan; Boles, Shawn

    1998-01-01

    Reviews a single indicator approach and multiple indicator approaches that simplify testing interaction effects using structural equation modeling. An illustrative application examines the interactive effect of perceptions of competence and perceptions of autonomy on exercise-intrinsic motivation. (SLD)

  14. [Adverse effects and interactions of phytotherapeutic drugs].

    PubMed

    Iten, F; Reichling, J; Saller, R

    2002-06-01

    The significantly increased sales figures many phytopharmaceuticals have achieved during the last years prove the confidence that a great part of the population has in herbal remedies. This is primarily due to the wide-spread opinion that herbal remedies are free from side-effects. The long tradition and presumed 'natural' origin are no guarantee for safety in the treatment with herbal remedies. Even if a large proportion of the undesirable events is traceable to falsifications, impurities and lacking quality controls, herbal drugs with controlled quality should not be generally classified as harmless. In the meantime it has been possible to prove the presence of active substances with toxic and cancerogenic properties in various phytopharmaceuticals. Interactions with other drugs have been documented in a number of notes, where phytopharmaceuticals could influence the blood plasma level of various drugs, presumably by activating or inhibiting the cytochrom-P450-system. At present, especially data about adverse effects during long-term administration of herbal remedies are under-represented. Particularly because of their presumed harmlessness they often are prescribed in the case of chronic diseases and then taken over a longer period of time. The frequency of undesirable effects of phytopharmaceuticals is remarkably low, even if the present lack of data about side-effects is considered.

  15. Protocol-based care: 2. Developing pathways with effective teams.

    PubMed

    Docherty, Brendan; McCombe, Jane; Simpson, Sue

    2003-10-01

    An integrated care pathway aims to ensure quality of care. A successful model hinges on the strength of the multidisciplinary ICP team and its members' ability to work together. Part two of this 12-part series focuses on how one topic--acute coronary syndrome--was chosen at one trust, and highlights the experiences of setting up a multidisciplinary cardiac care ICP team.

  16. A nuclear-receptor-dependent phosphatidylcholine pathway with antidiabetic effects

    USDA-ARS?s Scientific Manuscript database

    Nuclear hormone receptors regulate diverse metabolic pathways and the orphan nuclear receptor LRH-1 (also known as NR5A2) regulates bile acid biosynthesis. Structural studies have identified phospholipids as potential LRH-1 ligands, but their functional relevance is unclear. Here we show that an unu...

  17. Interactions between the genes of vasodilatation pathways influence blood pressure and nitric oxide level in hypertension.

    PubMed

    Kumar, Rahul; Kohli, Samantha; Mishra, Aastha; Garg, Ritu; Alam, Perwez; Stobdan, Tsering; Nejatizadeh, Azim; Gupta, Mohit; Tyagi, Sanjay; Pasha, M A Qadar

    2015-02-01

    This study investigates the contribution of genetic interactions between the β-2 adrenergic receptor (ADRB2) and nitric oxide synthase (NOS3) genes to the complex etiology of hypertension. Using single nucleotide polymorphism (SNP) markers, we studied potential interactions between ADRB2 and NOS3 variants and their correlation with clinical, biochemical, and expression levels in 546 individuals with hypertension and 884 age-, sex-, and ethnicity-matched unrelated control subjects. Generalized multifactor dimensionality reduction (GMDR) analysis identified the models for genotype interaction. The best models to represent association of genotypes with augmented hypertension susceptibility were the 4- and 5-locus interacting GMDR models of ADRB2 and NOS3 compared with within-gene 6-locus ADRB2 and 2-locus NOS3 (odds ratio (OR) = 4.8, P = 0.04; OR = 5.6, P = 0.02, respectively). Stratification of 4- and 5-locus GMDR models on the basis of risk alleles (in increasing order) increased the ORs from 1.26 to 14.17 and from 0.81 to 14.18, respectively, and correlated linearly with increased systolic blood pressure, diastolic blood pressure, and mean arterial pressure and decreased nitric oxide level (P ≤ 0.0004). We performed various analyses, such as single-locus, genetic interactions, sliding-window, and comparative analysis. Each analysis consistently revealed the 46A allele of ADRB2 46G/A SNP and 4a allele of NOS3 4b/4a SNP to be associated with risk of hypertension. These risk-conferring markers were associated with decreased ADRB2 and NOS3 expression and decreased nitric oxide level in the patients (P ≤ 0.04). Evidence of interaction between the genetic loci of ADRB2 and NOS3 points to varied clinical, biochemical, and expression levels and a role in hypertension susceptibility. © American Journal of Hypertension, Ltd 2014. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  18. Negative Functional Interaction Between Cell Integrity MAPK Pathway and Rho1 GTPase in Fission Yeast

    PubMed Central

    Viana, Raul A.; Pinar, Mario; Soto, Teresa; Coll, Pedro M.; Cansado, Jose; Pérez, Pilar

    2013-01-01

    Rho1 GTPase is the main activator of cell wall glucan biosynthesis and regulates actin cytoskeleton in fungi, including Schizosaccharomyces pombe. We have obtained a fission yeast thermosensitive mutant strain carrying the rho1-596 allele, which displays reduced Rho1 GTPase activity. This strain has severe cell wall defects and a thermosensitive growth, which is partially suppressed by osmotic stabilization. In a global screening for rho1-596 multicopy suppresors the pmp1+ gene was identified. Pmp1 is a dual specificity phosphatase that negatively regulates the Pmk1 mitogen-activated protein kinase (MAPK) cell integrity pathway. Accordingly, elimination of Pmk1 MAPK partially rescued rho1-596 thermosensitivity, corroborating the unexpected antagonistic functional relationship of these genes. We found that rho1-596 cells displayed increased basal activation of the cell integrity MAPK pathway and therefore were hypersensitive to MgCl2 and FK506. Moreover, the absence of calcineurin was lethal for rho1-596. We found a higher level of calcineurin activity in rho1-596 than in wild-type cells, and overexpression of constitutively active calcineurin partially rescued rho1-596 thermosensitivity. All together our results suggest that loss of Rho1 function causes an increase in the cell integrity MAPK activity, which is detrimental to the cells and turns calcineurin activity essential. PMID:23934882

  19. Non-Smc element 5 (Nse5) of the Smc5/6 complex interacts with SUMO pathway components.

    PubMed

    Bustard, Denise E; Ball, Lindsay G; Cobb, Jennifer A

    2016-06-15

    The Smc5/6 complex in Saccharomyces cerevisiae contains six essential non-Smc elements, Nse1-6. With the exception of Nse2 (also known as Mms21), which is an E3 small ubiquitin-like modifier (SUMO) ligase, very little is understood about the role of these components or their contribution to Smc5/6 functionality. Our characterization of Nse5 establishes a previously unidentified relationship between the Smc5/6 complex and factors of the SUMO pathway. Nse5 physically associates with the E2 conjugating enzyme, Ubc9, where contacts are stabilized by non-covalent interactions with SUMO. SUMO also mediates the interactions between Nse5 and the two PIAS family E3 SUMO ligases, Siz1 and Siz2. Cells carrying the nse5-ts1 allele or lacking either SIZ1 or SIZ2 exhibit a reduction in Smc5 sumoylation upon MMS treatment and demonstrate functional redundancy for SUMO mediated events in the presence of DNA damage. Overall, given the extensive connection between Nse5 and components of the SUMO pathway, we speculate that one function of the Smc5/6 complex might be as a scaffold center to enable sumoylation events in budding yeast.

  20. Non-Smc element 5 (Nse5) of the Smc5/6 complex interacts with SUMO pathway components

    PubMed Central

    Bustard, Denise E.; Ball, Lindsay G.

    2016-01-01

    ABSTRACT The Smc5/6 complex in Saccharomyces cerevisiae contains six essential non-Smc elements, Nse1-6. With the exception of Nse2 (also known as Mms21), which is an E3 small ubiquitin-like modifier (SUMO) ligase, very little is understood about the role of these components or their contribution to Smc5/6 functionality. Our characterization of Nse5 establishes a previously unidentified relationship between the Smc5/6 complex and factors of the SUMO pathway. Nse5 physically associates with the E2 conjugating enzyme, Ubc9, where contacts are stabilized by non-covalent interactions with SUMO. SUMO also mediates the interactions between Nse5 and the two PIAS family E3 SUMO ligases, Siz1 and Siz2. Cells carrying the nse5-ts1 allele or lacking either SIZ1 or SIZ2 exhibit a reduction in Smc5 sumoylation upon MMS treatment and demonstrate functional redundancy for SUMO mediated events in the presence of DNA damage. Overall, given the extensive connection between Nse5 and components of the SUMO pathway, we speculate that one function of the Smc5/6 complex might be as a scaffold center to enable sumoylation events in budding yeast. PMID:27215325

  1. Thioredoxin interacting protein (TXNIP) regulates tubular autophagy and mitophagy in diabetic nephropathy through the mTOR signaling pathway

    PubMed Central

    Huang, Chunling; Zhang, Yuan; Kelly, Darren J.; Tan, Christina Y. R.; Gill, Anthony; Cheng, Delfine; Braet, Filip; Park, Jin-Sung; Sue, Carolyn M.; Pollock, Carol A.; Chen, Xin-Ming

    2016-01-01

    Hyperglycemia upregulates thioredoxin interacting protein (TXNIP) expression, which in turn induces ROS production, inflammatory and fibrotic responses in the diabetic kidney. Dysregulation of autophagy contributes to the development of diabetic nephropathy. However, the interaction of TXNIP with autophagy/mitophagy in diabetic nephropathy is unknown. In this study, streptozotocin-induced diabetic rats were given TXNIP DNAzyme or scrambled DNAzyme for 12 weeks respectively. Fibrotic markers, mitochondrial function and mitochondrial reactive oxygen species (mtROS) were assessed in kidneys. Tubular autophagy and mitophagy were determined in kidneys from both human and rats with diabetic nephropathy. TXNIP and autophagic signaling molecules were examined. TXNIP DNAzyme dramatically attenuated extracellular matrix deposition in the diabetic kidneys compared to the control DNAzyme. Accumulation of autophagosomes and reduced autophagic clearance were shown in tubular cells of human diabetic compared to non-diabetic kidneys, which was reversed by TXNIP DNAzyme. High glucose induced mitochondrial dysfunction and mtROS production, and inhibited mitophagy in proximal tubular cells, which was reversed by TXNIP siRNA. TXNIP inhibition suppressed diabetes-induced BNIP3 expression and activation of the mTOR signaling pathway. Collectively, hyperglycemia-induced TXNIP contributes to the dysregulation of tubular autophagy and mitophagy in diabetic nephropathy through activation of the mTOR signaling pathway. PMID:27381856

  2. Therapeutic effect of CNP on renal osteodystrophy by antagonizing the FGF-23/MAPK pathway.

    PubMed

    Hu, Peng; Huang, Bao Yu; Xia, Xun; Xuan, Qiang; Hu, Bo; Qin, Yuan Han

    2016-01-01

    Renal osteodystrophy (ROD) is highly prevalent in chronic kidney disease (CKD). Because most patients with ROD are asymptomatic in the early stage and bone biopsy remains not a routine procedure in many clinical settings; therefore, several biochemical parameters may help to identify the existence of ROD. C-type natriuretic peptide (CNP) is considered as a positive regulator of bone formation. Both urinary excretion and renal expression of CNP are markedly up-regulated in the early stages of CKD, whereas they are still progressively declined accompanied by CKD progression, which invites speculation that the progressive decline of CNP may contribute, in part, to the pathogenesis of ROD. In addition, fibroblast growth factor (FGF)-23 is a bone-derived endocrine regulator of phosphate homeostasis. The elevation of serum FGF-23 has been recognized as a common feature in CKD to maintain normophosphatemia at the expense of declining 1,25-dihydroxyvitamin D values. Since the effects of CNP and FGF-23 on bone formation appear to oppose each other, it is reasonable to propose a direct interaction of their signaling pathways during the progression of ROD. CNP and FGF-23 act through a close or reciprocal pathway and are in agreement with recent studies demonstrating a down-regulatory role of the mitogen-activated protein kinase activity by CNP. The specific node may act at the level of RAF-1 through the activation of cyclic guanosine monophosphate-dependent protein kinases II.

  3. Effects of photorespiration, the cytochrome pathway, and the alternative pathway on the triple isotopic composition of atmospheric O2

    NASA Astrophysics Data System (ADS)

    Angert, Alon; Rachmilevitch, Shimon; Barkan, Eugeni; Luz, Boaz

    2003-03-01

    The triple isotopic composition of atmospheric O2 is a new tracer used to estimate changes in global productivity. To estimate such changes, knowledge of the relationship between the discrimination against 17O and the discrimination against 18O is needed. This relationship is presented as θ = ln(17α)/ln(18α). Here, the value of theta was evaluated for the most important processes that affect the isotopic composition of oxygen. Similar values were found for dark respiration through the cytochrome pathway (0.516 ± 0.001) and the alternative pathway (0.514 ± 0.001), and slightly higher value was found for diffusion in air (0.521 ± 0.001). The combined effect of diffusion and respiration on the atmosphere was shown to be close to that of dark respiration. The value we found for photorespiration (0.506 ± 0.005) is considerably lower than that of dark respiration. Our results clearly show that the triple isotopic composition of the atmosphere is affected by the relative rates of photorespiration and dark respiration. Also, we show that closing the current global isotopic balance will enable the estimation of the current global rate of photorespiration. Using the Last Glacial Maximum as a case study, we show that variations in global rate of photorespiration affected the triple isotopic composition in the past. Strong fractionations measured in illuminated plants indicated that the alternative pathway is activated in the same conditions that favor high rate of photorespiration. This activation suggests that the global rate of the alternative pathway is higher than believed thus far, and may help to close the gap between the calculated and measured Dole Effect.

  4. Interactions between leukotriene C4 and interleukin 13 signaling pathways in a mouse model of airway disease.

    PubMed

    Chavez, Jaime; Young, Hays W J; Corry, David B; Lieberman, Michael W

    2006-04-01

    During an asthmatic episode, leukotriene C4 (LTC4) and interleukin 13 (IL-13) are released into the airways and are thought to be central mediators of the asthmatic response. However, little is known about how these molecules interact or affect each other's signaling pathway. To determine if the LTC4 and IL-13 signaling pathways interact with each other's pathways. We examined airway responsiveness, cysteinyl LTs (Cys-LTs), and Cys-LT and IL-13 receptor transcript levels in wild-type mice and in mice that were deficient in gamma-glutamyl leukotrienase (an enzyme that converts LTC4 to LTD4), STAT6 (signal transducer and activator of transcription 6 [a critical molecule in IL-13 signaling]), and IL-4Ralpha (a subunit of the IL-13 receptor). Wild-type (C57BL/129SvEv) and gamma-glutamyl leukotrienase-deficient mice showed increased airway responsiveness after intranasal instillation of IL-13; similar results were observed after intranasal instillation of IL-13 or LTC4 in a second wild-type strain (BALB/c). Interleukin 13 treatment reduced levels of Cys-LTs in bronchoalveolar lavage fluid. This change was unaccompanied by changes in other arachidonic acid metabolites or in RNA transcript levels of enzymes associated with Cys-LT synthesis. Interleukin 13 treatment also increased transcript levels of the Cys-LT 1 and Cys-LT 2 receptors, while LTC4 increased transcript levels of the alpha1 chain of the IL-13 receptor. Furthermore, IL-4Ralpha-deficient mice had increased airway responsiveness to LTC4 but not to IL-13, whereas STAT6-deficient mice failed to respond to either agonist. These findings indicate that LTC4 and IL-13 are dependent on or signal through STAT6 to increase airway responsiveness and that both agonists regulate expression of each other's receptors.

  5. [Effect of Astragalus and Salvia's effective components and their compatibility on JAK/STAT pathway].

    PubMed

    Li, Jun; Cao, Yi-Xuan; Wang, Dong; Zhou, Ping; Yang, Xiao-Min

    2011-09-01

    To study the effect of Astragalus and Salvia's effective components and their compatibility on JAK/STAT pathway of rats' renal fibrosis. 66 SD rats were randomly divided into 7 groups: normal group,model group,fosinopril group, salvianolic acids group, astragalus saponins group, granules compatibility of Astragalus and Salvia group, components combination of Astragalus and Salvia group. The variation of beta2-microglobulin(beta2-MG), the changes of renal pathology and JAK/STAT pathway were observed. The changes in renal pathology of treatment groups had different degrees of improvement; Astragalus and Salvia could reduce the urinary beta2-MG of unilateral ureteral obstruction (UUO) rat (P < 0.05), which was equal with fosinopril group. The rest of the treatment groups decreased especially fosinopril group while the difference was not significant when compared with the model group. Astragalus and its effective components could reduce the expression of renal tissue JAK, STAT1, STAT3 protein, among which fosinopril group and granules compatibility of Astragalus decreased significantly. Astragalus saponins group was not obvious, and the rest of the treatment group had significantly minor effect. Astragalus and Salvia's effective components and their compatibility may protect renal tubular function in unilateral ureteral obstruction, which may interfere with UUO rat kidney with JAK/STAT signaling pathway.

  6. CDK5RAP2 interaction with components of the Hippo signaling pathway may play a role in primary microcephaly.

    PubMed

    Sukumaran, Salil K; Stumpf, Maria; Salamon, Sarah; Ahmad, Ilyas; Bhattacharya, Kurchi; Fischer, Sarah; Müller, Rolf; Altmüller, Janine; Budde, Birgit; Thiele, Holger; Tariq, Muhammad; Malik, Naveed Altaf; Nürnberg, Peter; Baig, Shahid Mahmood; Hussain, Muhammad Sajid; Noegel, Angelika A

    2017-04-01

    Autosomal recessive primary microcephaly (MCPH) is characterized by a substantial reduction in brain size but with normal architecture. It is often linked to mutations in genes coding for centrosomal proteins; however, their role in brain size regulation is not completely understood. By combining homozygosity mapping and whole-exome sequencing in an MCPH family from Pakistan, we identified a novel mutation (XM_011518861.1; c.4114C > T) in CDK5RAP2, the gene associated with primary microcephaly-3 (MCPH3), leading to a premature stop codon (p.Arg1372*). CDK5RAP2 is a component of the pericentriolar material important for the microtubule-organizing function of the centrosome. Patient-derived primary fibroblasts had strongly decreased CDK5RAP2 amounts, showed centrosomal and nuclear abnormalities and exhibited changes in cell size and migration. We further identified an interaction of CDK5RAP2 with the Hippo pathway components MST1 kinase and the transcriptional regulator TAZ. This finding potentially provides a mechanism through which the Hippo pathway with its roles in the regulation of centrosome number is linked to the centrosome. In the patient fibroblasts, we observed higher levels of TAZ and YAP. However, common target genes of the Hippo pathway were downregulated as compared to the control with the exception of BIRC5 (Survivin), which was significantly upregulated. We propose that the centrosomal deficiencies and the altered cellular properties in the patient fibroblasts can also result from the observed changes in the Hippo pathway components which could thus be relevant for MCPH and play a role in brain size regulation and development.

  7. Structural insight into dimeric interaction of the SARAH domains from Mst1 and RASSF family proteins in the apoptosis pathway

    PubMed Central

    Hwang, Eunha; Ryu, Kyoung-Seok; Pääkkönen, Kimmo; Güntert, Peter; Cheong, Hae-Kap; Lim, Dae-Sik; Lee, Jie-Oh; Jeon, Young Ho; Cheong, Chaejoon

    2007-01-01

    In eukaryotic cells, apoptosis and cell cycle arrest by the Ras → RASSF → MST pathway are controlled by the interaction of SARAH (for Salvador/Rassf/Hippo) domains in the C-terminal part of tumor suppressor proteins. The Mst1 SARAH domain interacts with its homologous domain of Rassf1 and Rassf5 (also known as Nore1) by forming a heterodimer that mediates the apoptosis process. Here, we describe the homodimeric structure of the human Mst1 SARAH domain and its heterotypic interaction with the Rassf5 and Salvador (Sav) SARAH domain. The Mst1 SARAH structure forms a homodimer containing two helices per monomer. An antiparallel arrangement of the long α-helices (h2/h2′) provides an elongated binding interface between the two monomers, and the short 310 helices (h1/h1′) are folded toward that of the other monomer. Chemical shift perturbation experiments identified an elongated, tight-binding interface with the Rassf5 SARAH domain and a 1:1 heterodimer formation. The linker region between the kinase and the SARAH domain is shown to be disordered in the free protein. These results imply a novel mode of interaction with RASSF family proteins and provide insight into the mechanism of apoptosis control by the SARAH domain. PMID:17517604

  8. Interaction between Tbx1 and Hoxd10 and connection with TGFβ-BMP signal pathway during kidney development.

    PubMed

    Fu, Yu; Li, Fei; Zhao, Diana Yue; Zhang, Jing-Shu; Lv, Yuan; Li-Ling, Jesse

    2014-02-15

    Renal malformations are commonly found among patients carrying a 22q11 deletion which renders loss of Tbx1 gene, an important transcriptional factor implicated in a number of developmental processes. Smad1 is known to interact with Tbx1, but the exact mechanism remains unknown. In this study, we have measured the expression of Tbx1 in both murine and human tissues using RT-PCR, and analyzed its protein product and protein-protein interactions with Western blotting and immunoprecipitation assays. Precipitated proteins were verified with mass spectrometry. As discovered, Tbx1 binds with Hoxd10. Tbx1 and Hoxd10 genes also have similar expression profiles during murine kidney development. Based on homology between mouse and human, we hypothesized that such interaction also exists in human. Through a RNA interference experiment using a human embryonic kidney HEK293 cell line, we demonstrated that TBX1 can alter TGF-β/BMP, an important signaling pathway, through interacting with HOXD10. Above findings may shed light on the mechanism of TBX1 mutations leading to renal malformations found in patients carrying a 22q11 deletion.

  9. The Stability of Ribosome Biogenesis Factor WBSCR22 Is Regulated by Interaction with TRMT112 via Ubiquitin-Proteasome Pathway

    PubMed Central

    Õunap, Kadri; Leetsi, Lilian; Matsoo, Maarja; Kurg, Reet

    2015-01-01

    The human WBSCR22 protein is a 18S rRNA methyltransferase involved in pre-rRNA processing and ribosome 40S subunit biogenesis. Recent studies have shown that the protein function in ribosome synthesis is independent of its enzymatic activity. In this work, we have studied the WBSCR22 protein interaction partners by SILAC-coupled co-immunoprecipitation assay and identified TRMT112 as the interaction partner of WBSCR22. Knock-down of TRMT112 expression decreased the WBSCR22 protein level in mammalian cells, suggesting that the stability of WBSCR22 is regulated through the interaction with TRMT112. The localization of the TRMT112 protein is determined by WBSCR22, and the WBSCR22-TRMT112 complex is localized in the cell nucleus. We provide evidence that the interaction between WBSCR22/Bud23 and TRMT112/Trm112 is conserved between mammals and yeast, suggesting that the function of TRMT112 as a co-activator of methyltransferases is evolutionarily conserved. Finally, we show that the transiently expressed WBSCR22 protein is ubiquitinated and degraded through the proteasome pathway, revealing the tight control of the WBSCR22 protein level in the cells. PMID:26214185

  10. Interaction between phosphoinositide turnover system and cyclic AMP pathway for the secretion of pancreastatin and somatostatin from QGP-1N cells.

    PubMed

    Tateishi, K; Funakoshi, A; Kitayama, N; Matsuoka, Y

    1992-06-30

    It is found that secretion of pancreastatin and somatostatin from QGP-1N cells is regulated through muscarinic receptor-mediated activation of phosphatidylinositide hydrolysis system. In this report, whether the cAMP pathway interacts with the phosphoinositide turnover system for the secretion of pancreastatin and somatostatin from QGP-1N cells through muscarinic receptors was studied. Stimulation of QGP-1N cells with carbachol increased intracellular cAMP levels. The carbachol-induced increase in cAMP levels was inhibited by atropine. Calcium ionophore (A23187) and phorbol 12-myristate 13-acetate increased cAMP synthesis. Dibutyryl cAMP, forskolin and theophylline stimulated secretion of pancreastatin and somatostatin. When either dibutyryl cAMP, forskolin or theophylline was added in culture medium with A23187, phorbol ester or carbachol, a synergistic effect was found on pancreastatin and somatostatin secretion. These results suggest that interaction between the phosphoinositide turnover system and the cAMP pathway occurs in QGP-1N cells through muscarinic receptor stimulation for the secretion of pancreastatin and somatostatin.

  11. Hadronization of QCD and effective interactions

    SciTech Connect

    Frank, M.R.

    1994-07-01

    An introductory treatment of hadronization through functional integral calculus and bifocal Bose fields is given. Emphasis is placed on the utility of this approach for providing a connection between QCD and effective hadronic field theories. The hadronic interactions obtained by this method are nonlocal due to the QCD substructure, yet, in the presence of an electromagnetic field, maintain the electromagnetic gauge invariance manifest at the quark level. A local chiral model which is structurally consistent with chiral perturbation theory is obtained through a derivative expansion of the nonlocalities with determined, finite coefficients. Tree-level calculations of the pion form factor and {pi} {minus} {pi} scattering, which illustrate the dual constituent-quark-chiral-model nature of this approach, are presented.

  12. Quasiconfigurations and the theory of effective interactions

    NASA Astrophysics Data System (ADS)

    Poves, A.; Zuker, A.

    1981-05-01

    Perturbation theory is reformulated. Schrödinger's equation is recast as a non linear integral equation which yields by Neumann expansion a linked cluster series for the degenerate, quasi degenerate or non degenerate problem. An effective interaction theory emerges that can be formulated in a biorthogonal basis leading to a non Hermitian secular problem. Hermiticity can be recovered in a clear and rigorous way. As the mathematical form of the theory is dictated by the request of physical clarity the latter is obtained naturally. When written in diagrammatic many body language, the integral equation produces a set of linked coupled equations for the degenerate case. The classic summations (Brueckner, Bethe-Faddeev and RPA) emerge naturally. Possible extensions of nuclear matter theory are suggested.

  13. Identification of a genetic interaction between the tumor suppressor EAF2 and the retinoblastoma protein (Rb) signaling pathway in C. elegans and prostate cancer cells

    SciTech Connect

    Cai, Liquan; Wang, Dan; Fisher, Alfred L.; Wang, Zhou

    2014-05-02

    Highlights: • RNAi screen identified genetic enhancers for the C. elegans homolog of EAF2. • EAF2 and RBBP4 proteins physically bind to each other and alter transcription. • Overexpression of EAF2 and RBBP4 induces the cell death in prostate cancer cells. - Abstract: The tumor suppressor EAF2 is regulated by androgen signaling and associated with prostate cancer. While EAF2 and its partner ELL have been shown to be members of protein complexes involved in RNA polymerase II transcriptional elongation, the biologic roles for EAF2 especially with regards to the development of cancer remains poorly understood. We have previously identified the eaf-1 gene in Caenorhabditiselegans as the ortholog of EAF2, and shown that eaf-1 interacts with the ELL ortholog ell-1 to control development and fertility in worms. To identify genetic pathways that interact with eaf-1, we screened RNAi libraries consisting of transcription factors, phosphatases, and chromatin-modifying factors to identify genes which enhance the effects of eaf-1(tm3976) on fertility. From this screen, we identified lin-53, hmg-1.2, pha-4, ruvb-2 and set-6 as hits. LIN-53 is the C. elegans ortholog of human retinoblastoma binding protein 4/7 (RBBP 4/7), which binds to the retinoblastoma protein and inhibits the Ras signaling pathway. We find that lin-53 showed a synthetic interaction with eaf-1(tm3976) where knockdown of lin-53 in an eaf-1(tm3976) mutant resulted in sterile worms. This phenotype may be due to cell death as the treated worms contain degenerated embryos with increased expression of the ced-1:GFP cell death marker. Further we find that the interaction between eaf-1 and lin-53/RBBP4/7 also exists in vertebrates, which is reflected by the formation of a protein complex between EAF2 and RBBP4/7. Finally, overexpression of either human EAF2 or RBBP4 in LNCaP cells induced the cell death while knockdown of EAF2 in LNCaP enhanced cell proliferation, indicating an important role of EAF2 in

  14. Identification of a genetic interaction between the tumor suppressor EAF2 and the retinoblastoma protein (Rb) signaling pathway in C. elegans and prostate cancer cells.

    PubMed

    Cai, Liquan; Wang, Dan; Fisher, Alfred L; Wang, Zhou

    2014-05-02

    The tumor suppressor EAF2 is regulated by androgen signaling and associated with prostate cancer. While EAF2 and its partner ELL have been shown to be members of protein complexes involved in RNA polymerase II transcriptional elongation, the biologic roles for EAF2 especially with regards to the development of cancer remains poorly understood. We have previously identified the eaf-1 gene in Caenorhabditiselegans as the ortholog of EAF2, and shown that eaf-1 interacts with the ELL ortholog ell-1 to control development and fertility in worms. To identify genetic pathways that interact with eaf-1, we screened RNAi libraries consisting of transcription factors, phosphatases, and chromatin-modifying factors to identify genes which enhance the effects of eaf-1(tm3976) on fertility. From this screen, we identified lin-53, hmg-1.2, pha-4, ruvb-2 and set-6 as hits. LIN-53 is the C. elegans ortholog of human retinoblastoma binding protein 4/7 (RBBP 4/7), which binds to the retinoblastoma protein and inhibits the Ras signaling pathway. We find that lin-53 showed a synthetic interaction with eaf-1(tm3976) where knockdown of lin-53 in an eaf-1(tm3976) mutant resulted in sterile worms. This phenotype may be due to cell death as the treated worms contain degenerated embryos with increased expression of the ced-1:GFP cell death marker. Further we find that the interaction between eaf-1 and lin-53/RBBP4/7 also exists in vertebrates, which is reflected by the formation of a protein complex between EAF2 and RBBP4/7. Finally, overexpression of either human EAF2 or RBBP4 in LNCaP cells induced the cell death while knockdown of EAF2 in LNCaP enhanced cell proliferation, indicating an important role of EAF2 in controlling the growth and survival of prostate cancer cells. Together these findings identify a novel physical and functional interaction between EAF2 and the Rb pathway. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. Interaction Effects in Double Layer Systems

    NASA Astrophysics Data System (ADS)

    Zheng, Lian

    A number of properties of two dimensional electron systems are investigated in this thesis. In the absence of a magnetic field, interaction effects for a double layer system are studied by employing the self-consistent STLS approximation. Results from using the RPA and the STLS are contrasted. An attempt to use standard finite-temperature perturbation theory to study the strongly-correlated system of electrons in a partially filled Landau level is discussed. The perturbative calculation for the grand potential of up to the third order is obtained. We also evaluate the sum of particle-particle ladder diagrams and show that, at zero temperature, it leads to a ground state energy with a cusp at v = 1/2. We study effects of disorder and the correlation of disorder potentials on the tunneling features of a double layer system and suggest that the electron lifetimes can be determined from the tunneling experiment. We derive an expression for the interlayer frictional drag in a double layer system, which can incorporate the effects of disorder and magnetic field. The disorder enhancement to the interlayer scattering is studied. We discuss the possibility of using the drag experiment to probe the properties of a single layer FQHE system.

  16. Interaction between susceptibility loci in cGAS-STING pathway, MHC gene and HPV infection on the risk of cervical precancerous lesions in Chinese population.

    PubMed

    Xiao, Di; Huang, Weihuang; Ou, Meiling; Guo, Congcong; Ye, Xingguang; Liu, Yang; Wang, Man; Zhang, Baohuan; Zhang, Na; Huang, Shiqi; Zang, Jiankun; Zhou, Zixing; Wen, Zihao; Zeng, Chengli; Wu, Chenfei; Huang, Chuican; Wei, Xiangcai; Yang, Guang; Jing, Chunxia

    2016-12-20

    Human papillomavirus (HPV) infection is a definite risk factor for cervical cancer. Nevertheless, only some infected individuals actually develop cervical cancer. The cGAS-STING pathway in innate immunity plays an important role in protecting against HPV infection. Chen et al. described that the rs2516448 SNP in the MHC locus may affect susceptibility to cervical cancer, a finding that we attempted to replicate in a Chinese population. To investigate the effects of cGAS, STING and MHC polymorphisms on susceptibility to cervical precancerous lesions, 9 SNPs were analyzed in 164 cervical precancerous lesion cases and 428 controls. Gene-gene and gene-environment interactions were also evaluated. We found a significantly decreased risk of cervical precancerous lesions for the GG genotype of rs311678 in the cGAS gene (ORadjusted = 0.40, 95% CI: 0.16-0.98). Moreover, MDR analysis identified a significant three-locus interaction model, involving HPV infection, age at menarche and rs311678 in cGAS. Additionally, a significant antagonistic interaction between HPV infection and rs311678 was found on an additive scale. In conclusion, our results indicate that the rs311678 polymorphism in the cGAS gene confers genetic susceptibility to cervical precancerous lesions. Moreover, the three-way gene-environment interactions further demonstrate that the rs311678 polymorphism in cGAS can significantly decrease the risk of HPV infection and the elder at menarche.

  17. The effect of chronic seaweed subsidies on herbivory: plant-mediated fertilization pathway overshadows lizard-mediated predator pathways.

    PubMed

    Piovia-Scott, Jonah; Spiller, David A; Takimoto, Gaku; Yang, Louie H; Wright, Amber N; Schoener, Thomas W

    2013-08-01

    Flows of energy and materials link ecosystems worldwide and have important consequences for the structure of ecological communities. While these resource subsidies typically enter recipient food webs through multiple channels, most previous studies focussed on a single pathway of resource input. We used path analysis to evaluate multiple pathways connecting chronic marine resource inputs (in the form of seaweed deposits) and herbivory in a shoreline terrestrial ecosystem. We found statistical support for a fertilization effect (seaweed increased foliar nitrogen content, leading to greater herbivory) and a lizard numerical response effect (seaweed increased lizard densities, leading to reduced herbivory), but not for a lizard diet-shift effect (seaweed increased the proportion of marine-derived prey in lizard diets, but lizard diet was not strongly associated with herbivory). Greater seaweed abundance was associated with greater herbivory, and the fertilization effect was larger than the combined lizard effects. Thus, the bottom-up, plant-mediated effect of fertilization on herbivory overshadowed the top-down effects of lizard predators. These results, from unmanipulated shoreline plots with persistent differences in chronic seaweed deposition, differ from those of a previous experimental study of the short-term effects of a pulse of seaweed deposition: while the increase in herbivory in response to chronic seaweed deposition was due to the fertilization effect, the short-term increase in herbivory in response to a pulse of seaweed deposition was due to the lizard diet-shift effect. This contrast highlights the importance of the temporal pattern of resource inputs in determining the mechanism of community response to resource subsidies.

  18. Effectiveness of Artistic Interaction through Video Conferencing

    ERIC Educational Resources Information Center

    Eristi, Suzan Duygu

    2011-01-01

    This study investigated Turkish and Canadian primary school students' ways of expressing their perception of interactive art education through video conferencing and that of cultural interaction through pictorial representations. The qualitative research data were collected in the form of pictures and interviews on interactive art education along…

  19. An Epidemiologic Study of Genetic Variation in Hormonal Pathways in Relation to the Effect of Hormone Replacement Therapy on Breast Cancer Risk

    DTIC Science & Technology

    2008-04-01

    breast cancer risk to be modestly associated with one SNPs in each GSTP1 (rs1695: OR = 1.4 [95% CI: 1.02-1.9] for carriers of A allele); CYP1B1 ...In a multi-gene model including two genes with single gene effects within the estrogen pathway ( CYP1B1 *2 and GSTP1), breast cancer risk was 1.6 (95...pathways. 15. SUBJECT TERMS Genetic polymorphisms , epidemiology, exogenous risk factors, gene-environment interactions, hormonal pathway, estrogen

  20. The Pathway Active Learning Environment: An interactive web-based tool for physics education

    NASA Astrophysics Data System (ADS)

    Nakamura, Christopher Matthew

    The work described here represents an effort to design, construct, and test an interactive online multimedia learning environment that can provide physics instruction to students in their homes. The system was designed with one-on-one human tutoring in mind as the mode of instruction. The system uses an original combination of a video-based tutor that incorporates natural language processing video-centered lessons and additional illustrative multimedia. Our Synthetic Interview (SI) tutor provides pre-recorded video answers from expert physics instructors in response to students' typed natural language questions. Our lessons cover Newton's laws and provide a context for the tutoring interaction to occur, connect physics ideas to real-world behavior of mechanical systems, and allow for quantitative testing of physics. Additional multimedia can be used to supplement the SI tutors' explanations and illustrate the physics of interest. The system is targeted at students of algebra-based and concept-based physics at the college and high school level. The system logs queries to the SI tutor, responses to lesson questions and several other interactions with the system, tagging those interactions with a username and timestamp. We have provided several groups of students with access to our system under several different conditions ranging from the controlled conditions of our interview facility to the naturalistic conditions of use at home. In total nearly two-hundred students have accessed the system. To gain insight into the ways students might use the system and understand the utility of its various components we analyzed qualitative interview data collected with 22 algebra-based physics students who worked with our system in our interview facility. We also performed a descriptive analysis of data from the system's log of user interactions. Finally we explored the use of machine learning to explore the possibility of using automated assessment to augment the interactive

  1. The effect of ball milling grinding pathways on the bulk and reactivity properties of calcium phosphate cements.

    PubMed

    Lopez-Heredia, M A; Bohner, M; Zhou, W; Winnubst, A J A; Wolke, J G C; Jansen, J A

    2011-07-01

    Calcium phosphate cements (CPCs) are significant alternatives to autologous bone grafting. CPCs can be composed of biphasic or multiphase calcium phosphate (CaP) compounds. A common way to process CPCs is by ball milling. Ball milling can be used for grinding or mechanosynthesis. The aim of this study was to determine the effect of well-defined ball milling grinding parameters, applied via different milling pathways, on the properties of CPCs. Starting CaP compounds used included α-tricalcium phosphate, dicalcium phosphate anhydrous and precipitated hydroxyapatite. Scanning electron microscopy showed changes in the powder morphology, which were related to the behavior of the starting CaP materials. Specific surface area (SSA) and particle size (PS) measurements exposed the effect of ball milling on the CaP compounds and CPC powders. X-ray diffraction revealed no effect of ball milling pathways or milling time on the composition of CPCs or the starting materials, but affected their crystallographic properties. No contamination of the milling media or transformation into an amorphous calcium phosphate compound was found. The milling pathways affected setting and cohesion. Fourier transform infrared spectroscopy (FTIR) revealed differences on the CPC v₄-PO₄³⁻ bands according to the interaction, created between the CaP compounds by the milling pathways. FTIR confirmed that the milling pathways changed the crystallographic properties. This study demonstrates that the pathways used for milling grinding modify the PS, SSA, and crystallographic properties of the powders, without affecting their composition. These modifications affected the bulk and reactivity properties of the CPCs by creating different setting and cohesion behaviors.

  2. Local and distal effects of arbuscular mycorrhizal colonization on direct pathway Pi uptake and root growth in Medicago truncatula.

    PubMed

    Watts-Williams, Stephanie J; Jakobsen, Iver; Cavagnaro, Timothy R; Grønlund, Mette

    2015-07-01

    Two pathways exist for plant Pi uptake from soil: via root epidermal cells (direct pathway) or via associations with arbuscular mycorrhizal (AM) fungi, and the two pathways interact in a complex manner. This study investigated distal and local effects of AM colonization on direct root Pi uptake and root growth, at different soil P levels. Medicago truncatula was grown at three soil P levels in split-pots with or without AM fungal inoculation and where one root half grew into soil labelled with (33)P. Plant genotypes included the A17 wild type and the mtpt4 mutant. The mtpt4 mutant, colonized by AM fungi, but with no functional mycorrhizal pathway for Pi uptake, was included to better understand effects of AM colonization per se. Colonization by AM fungi decreased expression of direct Pi transporter genes locally, but not distally in the wild type. In mtpt4 mutant plants, direct Pi transporter genes and the Pi starvation-induced gene Mt4 were more highly expressed than in wild-type roots. In wild-type plants, less Pi was taken up via the direct pathway by non-colonized roots when the other root half was colonized by AM fungi, compared with non-mycorrhizal plants. Colonization by AM fungi strongly influenced root growth locally and distally, and direct root Pi uptake activity locally, but had only a weak influence on distal direct pathway activity. The responses to AM colonization in the mtpt4 mutant suggested that in the wild type, the increased P concentration of colonized roots was a major factor driving the effects of AM colonization on direct root Pi uptake.

  3. Lovastatin Induces Multiple Stress Pathways Including LKB1/AMPK Activation That Regulate Its Cytotoxic Effects in Squamous Cell Carcinoma Cells

    PubMed Central

    Ma, Laurie; Niknejad, Nima; Gorn-Hondermann, Ivan; Dayekh, Khalil; Dimitroulakos, Jim

    2012-01-01

    Background Cellular stress responses trigger signaling cascades that inhibit proliferation and protein translation to help alleviate the stress or if the stress cannot be overcome induce apoptosis. In recent studies, we demonstrated the ability of lovastatin, an inhibitor of mevalonate synthesis, to induce the Integrated Stress Response as well as inhibiting epidermal growth factor receptor (EGFR) activation. Methodology/Principal Findings In this study, we evaluated the effects of lovastatin on the activity of the LKB1/AMPK pathway that is activated upon cellular energy shortage and can interact with the above pathways. In the squamous cell carcinoma (SCC) cell lines SCC9 and SCC25, lovastatin treatment (1–25 µM, 24 hrs) induced LKB1 and AMPK activation similar to metformin (1–10 mM, 24 hrs), a known inducer of this pathway. Lovastatin treatment impaired mitochondrial function and also decreased cellular ADP/ATP ratios, common triggers of LKB1/AMPK activation. The cytotoxic effects of lovastatin were attenuated in LKB1 null MEFs indicating a role for this pathway in regulating lovastatin-induced cytotoxicity. Of clinical relevance, lovastatin induces synergistic cytotoxicity in combination with the EGFR inhibitor gefitinib. In LKB1 deficient (A549, HeLa) and expressing (SCC9, SCC25) cell lines, metformin enhanced gefitinib cytotoxicity only in LKB1 expressing cell lines while both groups showed synergistic cytotoxic effects with lovastatin treatments. Furthermore, the combination of lovastatin with gefitinib induced a potent apoptotic response without significant induction of autophagy that is often induced during metabolic stress inhibiting cell death. Conclusion/Significance Thus, targeting multiple metabolic stress pathways including the LKB1/AMPK pathway enhances lovastatin’s ability to synergize with gefitinib in SCC cells. PMID:23029387

  4. Local and distal effects of arbuscular mycorrhizal colonization on direct pathway Pi uptake and root growth in Medicago truncatula

    PubMed Central

    Watts-Williams, Stephanie J.; Jakobsen, Iver; Cavagnaro, Timothy R.; Grønlund, Mette

    2015-01-01

    Two pathways exist for plant Pi uptake from soil: via root epidermal cells (direct pathway) or via associations with arbuscular mycorrhizal (AM) fungi, and the two pathways interact in a complex manner. This study investigated distal and local effects of AM colonization on direct root Pi uptake and root growth, at different soil P levels. Medicago truncatula was grown at three soil P levels in split-pots with or without AM fungal inoculation and where one root half grew into soil labelled with 33P. Plant genotypes included the A17 wild type and the mtpt4 mutant. The mtpt4 mutant, colonized by AM fungi, but with no functional mycorrhizal pathway for Pi uptake, was included to better understand effects of AM colonization per se. Colonization by AM fungi decreased expression of direct Pi transporter genes locally, but not distally in the wild type. In mtpt4 mutant plants, direct Pi transporter genes and the Pi starvation-induced gene Mt4 were more highly expressed than in wild-type roots. In wild-type plants, less Pi was taken up via the direct pathway by non-colonized roots when the other root half was colonized by AM fungi, compared with non-mycorrhizal plants. Colonization by AM fungi strongly influenced root growth locally and distally, and direct root Pi uptake activity locally, but had only a weak influence on distal direct pathway activity. The responses to AM colonization in the mtpt4 mutant suggested that in the wild type, the increased P concentration of colonized roots was a major factor driving the effects of AM colonization on direct root Pi uptake. PMID:25944927

  5. Pathways of Understanding: the Interactions of Humanity and Global Environmental Change

    NASA Technical Reports Server (NTRS)

    Jacobson, Harold K.; Katzenberger, John; Lousma, Jack; Mooney, Harold A.; Moss, Richard H.; Kuhn, William; Luterbacher, Urs; Wiegandt, Ellen

    1992-01-01

    How humans, interacting within social systems, affect and are affected by global change is explored. Recognizing the impact human activities have on the environment and responding to the need to document the interactions among human activities, the Consortium for International Earth Science Information Network (CIESIN) commissioned a group of 12 scientists to develop a framework illustrating the key human systems that contribute to global change. This framework, called the Social Process Diagram, will help natural and social scientists, educators, resource managers and policy makers envision and analyze how human systems interact among themselves and with the natural system. The Social Process Diagram consists of the following blocks that constitute the Diagram's structural framework: (1) fund of knowledge and experience; (2) preferences and expectations; (3) factors of production and technology; (4) population and social structure; (5) economic systems; (6) political systems and institutions; and (7) global scale environmental processes. To demonstrate potential ways the Diagram can be used, this document includes 3 hypothetical scenarios of global change issues: global warming and sea level rise; the environmental impact of human population migration; and energy and the environment. These scenarios demonstrate the Diagram's usefulness for visualizing specific processes that might be studied to evaluate a particular global change issues. The scenario also shows that interesting and unanticipated questions may emerge as links are explored between categories on the Diagram.

  6. Functional interactions between the macaque dorsal and ventral visual pathways during three-dimensional object vision.

    PubMed

    Janssen, Peter; Verhoef, Bram-Ernst; Premereur, Elsie

    2017-02-03

    The division of labor between the dorsal and the ventral visual stream in the primate brain has inspired numerous studies on the visual system in humans and in nonhuman primates. However, how and under which circumstances the two visual streams interact is still poorly understood. Here we review evidence from anatomy, modelling, electrophysiology, electrical microstimulation (EM), reversible inactivation and functional imaging in the macaque monkey aimed at clarifying at which levels in the hierarchy of visual areas the two streams interact, and what type of information might be exchanged between the two streams during three-dimensional (3D) object viewing. Neurons in both streams encode 3D structure from binocular disparity, synchronized activity between parietal and inferotemporal areas is present during 3D structure categorization, and clusters of 3D structure-selective neurons in parietal cortex are anatomically connected to ventral stream areas. In addition, caudal intraparietal cortex exerts a causal influence on 3D-structure related activations in more anterior parietal cortex and in inferotemporal cortex. Thus, both anatomical and functional evidence indicates that the dorsal and the ventral visual stream interact during 3D object viewing.

  7. Pathways of understanding: The interactions of humanity and global environmental change

    SciTech Connect

    Jacobson, H.K.; Katzenberger, J.; Lousma, J.; Mooney, H.A.; Moss, R.H.; Kuhn, W.; Luterbacher, U.; Wiegandt, E.

    1992-01-01

    How humans, interacting within social systems, affect and are affected by global change is explored. Recognizing the impact human activities have on the environment and responding to the need to document the interactions among human activities, the Consortium for International Earth Science Information Network (CIESIN) commissioned a group of 12 scientists to develop a framework illustrating the key human systems that contribute to global change. This framework, called the Social Process Diagram, will help natural and social scientists, educators, resource managers and policy makers envision and analyze how human systems interact among themselves and with the natural system. The Social Process Diagram consists of the following blocks that constitute the Diagram's structural framework: (1) fund of knowledge and experience; (2) preferences and expectations; (3) factors of production and technology; (4) population and social structure; (5) economic systems; (6) political systems and institutions; and (7) global scale environmental processes. To demonstrate potential ways the Diagram can be used, this document includes 3 hypothetical scenarios of global change issues: global warming and sea level rise; the environmental impact of human population migration; and energy and the environment. These scenarios demonstrate the Diagram's usefulness for visualizing specific processes that might be studied to evaluate a particular global change issues. The scenario also shows that interesting and unanticipated questions may emerge as links are explored between categories on the Diagram.

  8. Effects of bursty protein production on the noisy oscillatory properties of downstream pathways

    NASA Astrophysics Data System (ADS)

    Toner, D. L. K.; Grima, R.

    2013-08-01

    Experiments show that proteins are translated in sharp bursts; similar bursty phenomena have been observed for protein import into compartments. Here we investigate the effect of burstiness in protein expression and import on the stochastic properties of downstream pathways. We consider two identical pathways with equal mean input rates, except in one pathway proteins are input one at a time and in the other proteins are input in bursts. Deterministically the dynamics of these two pathways are indistinguishable. However the stochastic behavior falls in three categories: (i) both pathways display or do not display noise-induced oscillations; (ii) the non-bursty input pathway displays noise-induced oscillations whereas the bursty one does not; (iii) the reverse of (ii). We derive necessary conditions for these three cases to classify systems involving autocatalysis, trimerization and genetic feedback loops. Our results suggest that single cell rhythms can be controlled by regulation of burstiness in protein production.

  9. Interactive effects of pests increase seed yield.

    PubMed

    Gagic, Vesna; Riggi, Laura Ga; Ekbom, Barbara; Malsher, Gerard; Rusch, Adrien; Bommarco, Riccardo

    2016-04-01

    Loss in seed yield and therefore decrease in plant fitness due to simultaneous attacks by multiple herbivores is not necessarily additive, as demonstrated in evolutionary studies on wild plants. However, it is not clear how this transfers to crop plants that grow in very different conditions compared to wild plants. Nevertheless, loss in crop seed yield caused by any single pest is most often studied in isolation although crop plants are attacked by many pests that can cause substantial yield losses. This is especially important for crops able to compensate and even overcompensate for the damage. We investigated the interactive impacts on crop yield of four insect pests attacking different plant parts at different times during the cropping season. In 15 oilseed rape fields in Sweden, we estimated the damage caused by seed and stem weevils, pollen beetles, and pod midges. Pest pressure varied drastically among fields with very low correlation among pests, allowing us to explore interactive impacts on yield from attacks by multiple species. The plant damage caused by each pest species individually had, as expected, either no, or a negative impact on seed yield and the strongest negative effect was caused by pollen beetles. However, seed yield increased when plant damage caused by both seed and stem weevils was high, presumably due to the joint plant compensatory reaction to insect attack leading to overcompensation. Hence, attacks by several pests can change the impact on yield of individual pest species. Economic thresholds based on single species, on which pest management decisions currently rely, may therefore result in economically suboptimal choices being made and unnecessary excessive use of insecticides.

  10. An Age-Dependent Interaction with Leptin Unmasks Ghrelin's Bone-Protective Effects

    PubMed Central

    van der Velde, Martijn; van der Eerden, Bram C.J.; Sun, Yuxiang; Almering, Julia M.M.; van der Lely, Aart-Jan; Delhanty, Patric J.D.; Smith, Roy G.

    2012-01-01

    The mutual interplay between energy homeostasis and bone metabolism is an important emerging concept. Ghrelin and leptin antagonize each other in regulating energy balance, but the role of this interaction in bone metabolism is unknown. Using ghrelin receptor and leptin-deficient mice, we show that ghrelin has dual effects on osteoclastogenesis, inhibiting osteoclast progenitors directly and stimulating osteoclastogenesis via a more potent systemic/central pathway. Using mice with combined ghrelin receptor and leptin deficiency, we find that this systemic osteoclastogenic activity is suppressed by leptin, thus balancing the two counterregulatory ghrelin pathways and leading to an unchanged bone structure. With aging, this osteoclastogenic ghrelin pathway is lost, unmasking the direct protective effect of ghrelin on bone structure. In conclusion, we identify a novel regulatory network linking orexigenic and anorectic metabolic factors with bone metabolism that is age dependent. PMID:22700774

  11. Interaction of the Human Papillomavirus E6 Oncoprotein with Sorting Nexin 27 Modulates Endocytic Cargo Transport Pathways

    PubMed Central

    Ganti, Ketaki; Massimi, Paola; Manzo-Merino, Joaquin; Tomaić, Vjekoslav; Pim, David; Playford, Martin P.; Lizano, Marcela; Roberts, Sally; Kranjec, Christian; Doorbar, John; Banks, Lawrence

    2016-01-01

    A subset of high-risk Human Papillomaviruses (HPVs) are the causative agents of a large number of human cancers, of which cervical is the most common. Two viral oncoproteins, E6 and E7, contribute directly towards the development and maintenance of malignancy. A characteristic feature of the E6 oncoproteins from cancer-causing HPV types is the presence of a PDZ binding motif (PBM) at its C-terminus, which confers interaction with cellular proteins harbouring PDZ domains. Here we show that this motif allows E6 interaction with Sorting Nexin 27 (SNX27), an essential component of endosomal recycling pathways. This interaction is highly conserved across E6 proteins from multiple high-risk HPV types and is mediated by a classical PBM-PDZ interaction but unlike many E6 targets, SNX27 is not targeted for degradation by E6. Rather, in HPV-18 positive cell lines the association of SNX27 with components of the retromer complex and the endocytic transport machinery is altered in an E6 PBM-dependent manner. Analysis of a SNX27 cargo, the glucose transporter GLUT1, reveals an E6-dependent maintenance of GLUT1 expression and alteration in its association with components of the endocytic transport machinery. Furthermore, knockdown of E6 in HPV-18 positive cervical cancer cells phenocopies the loss of SNX27, both in terms of GLUT1 expression levels and its vesicular localization, with a concomitant marked reduction in glucose uptake, whilst loss of SNX27 results in slower cell proliferation in low nutrient conditions. These results demonstrate that E6 interaction with SNX27 can alter the recycling of cargo molecules, one consequence of which is modulation of nutrient availability in HPV transformed tumour cells. PMID:27649450

  12. NMR studies on the interactions between yeast Vta1 and Did2 during the multivesicular bodies sorting pathway

    PubMed Central

    Shen, Jie; Yang, Zhongzheng; Wang, Jiaolong; Zhao, Bin; Lan, Wenxian; Wang, Chunxi; Zhang, Xu; Wild, Cody J.; Liu, Maili; Xu, Zhaohui; Cao, Chunyang

    2016-01-01

    As an AAA-ATPase, Vps4 is important for function of multivesicular bodies (MVB) sorting pathway, which involves in cellular phenomena ranging from receptor down-regulation to viral budding to cytokinesis. The activity of Vps4 is stimulated by the interactions between Vta1 N-terminus (named as Vta1NTD) and Did2 fragment (176–204 aa) (termed as Did2176–204) or Vps60 (128–186 aa) (termed as Vps60128–186). The structural basis of how Vta1NTD binds to Did2176–204 is still unclear. To address this, in this report, the structure of Did2176–204 in complex with Vta1NTD was determined by NMR techniques, demonstrating that Did2176–204 interacts with Vta1NTD through its helix α6′ extending over the 2nd and the 3rd α-helices of Vta1NTD microtubule interacting and transport 1 (MIT1) domain. The residues within Did2176–204 helix α6′ in the interface make up of an amino acid sequence as E192′xxL195′xxR198′L199′xxL202′R203′, identical to type 1 MIT-interacting motif (MIM1) (D/E)xxLxxRLxxL(K/R) of CHMP1A180–196 observed in Vps4-CHMP1A complex structure, indicating that Did2 binds to Vta1NTD through canonical MIM1 interactions. Moreover, the Did2 binding does not result in Vta1NTD significant conformational changes, revealing that Did2, similar to Vps60, enhances Vta1 stimulation of Vps4 ATPase activity in an indirect manner. PMID:27924850

  13. Interaction of sonic hedgehog (SHH) pathway with cancer stem cell genes in gastric cancer.

    PubMed

    Samadani, Ali Akbar; Akhavan-Niaki, Haleh

    2015-03-01

    Gastric cancer may appear by frequent genetic or epigenetic changes in oncogenes, tumor suppressor or DNA mismatch repair genes. Molecular studies show the possibility of involvement of certain cancer pathways in gastric cancer. In this respect, DNA methylation is one of the most important epigenetic alterations in gastric cancer and identifying the signaling mechanism and also methylation of some genes that are involved in gastric cancer can help to improve treatment strategies. Relatively, there are many reported methylation alteration of genes in stem cells in all kinds of tumors with some of these genes having a key role in tumor development. Correspondingly, KLF5, CDX1/2, WNT1 and FEM1A are considerable genes in gastric cancer, although many researches and studies have illustrated that sonic hedgehog and expression of its signaling cascade proteins are related in gastric cancer. Relatively, modification in these genes causes many eclectic cancers such as rhabdomyosarcoma and diverse kinds of digestive system tumor development. Conspicuously, these master genes have a noticeable role in stem cell's growth regulation as well as other kinds of cancer such as breast cancer and leukemia. Hence, we concluded that research and studies on methylation and expression of these genes and also the investigation of molecular signaling in gastric cancer can acquire impressive conclusions in order to control and treat this common place and serious problem.

  14. Conformational selection in a protein-protein interaction revealed by dynamic pathway analysis

    SciTech Connect

    Chakrabarti, Kalyan S.; Agafonov, Roman V.; Pontiggia, Francesco; Otten, Renee; Higgins, Matthew K.; Schertler, Gebhard F. X.; Oprian, Daniel D.; Kern, Dorothee

    2015-12-24

    Molecular recognition plays a central role in biology, and protein dynamics has been acknowledged to be important in this process. However, it is highly debated whether conformational changes happen before ligand binding to produce a binding-competent state (conformational selection) or are caused in response to ligand binding (induced fit). Proposals for both mechanisms in protein/protein recognition have been primarily based on structural arguments. However, the distinction between them is a question of the probabilities of going via these two opposing pathways. Here we present a direct demonstration of exclusive conformational selection in protein/protein recognition by measuring the flux for rhodopsin kinase binding to its regulator recoverin, an important molecular recognition in the vision system. Using NMR spectroscopy, stopped-flow kinetics and isothermal titration calorimetry we show that recoverin populates a minor conformation in solution that exposes a hydrophobic binding pocket responsible for binding rhodopsin kinase. Lastly, protein dynamics in free recoverin limits the overall rate of binding.

  15. Conformational selection in a protein-protein interaction revealed by dynamic pathway analysis

    DOE PAGES

    Chakrabarti, Kalyan S.; Agafonov, Roman V.; Pontiggia, Francesco; ...

    2015-12-24

    Molecular recognition plays a central role in biology, and protein dynamics has been acknowledged to be important in this process. However, it is highly debated whether conformational changes happen before ligand binding to produce a binding-competent state (conformational selection) or are caused in response to ligand binding (induced fit). Proposals for both mechanisms in protein/protein recognition have been primarily based on structural arguments. However, the distinction between them is a question of the probabilities of going via these two opposing pathways. Here we present a direct demonstration of exclusive conformational selection in protein/protein recognition by measuring the flux for rhodopsinmore » kinase binding to its regulator recoverin, an important molecular recognition in the vision system. Using NMR spectroscopy, stopped-flow kinetics and isothermal titration calorimetry we show that recoverin populates a minor conformation in solution that exposes a hydrophobic binding pocket responsible for binding rhodopsin kinase. Lastly, protein dynamics in free recoverin limits the overall rate of binding.« less

  16. Respiratory responses to cold water immersion: neural pathways, interactions, and clinical consequences awake and asleep.

    PubMed

    Datta, Avijit; Tipton, Michael

    2006-06-01

    The ventilatory responses to immersion and changes in temperature are reviewed. A fall in skin temperature elicits a powerful cardiorespiratory response, termed "cold shock," comprising an initial gasp, hypertension, and hyperventilation despite a profound hypocapnia. The physiology and neural pathways of this are examined with data from original studies. The respiratory responses to skin cooling override both conscious and other autonomic respiratory controls and may act as a precursor to drowning. There is emerging evidence that the combination of the reestablishment of respiratory rhythm following apnea, hypoxemia, and coincident sympathetic nervous and cyclic vagal stimulation appears to be an arrhythmogenic trigger. The potential clinical implications of this during wakefulness and sleep are discussed in relation to sudden death during immersion, underwater birth, and sleep apnea. A drop in deep body temperature leads to a slowing of respiration, which is more profound than the reduced metabolic demand seen with hypothermia, leading to hypercapnia and hypoxia. The control of respiration is abnormal during hypothermia, and correction of the hypoxia by inhalation of oxygen may lead to a further depression of ventilation and even respiratory arrest. The immediate care of patients with hypothermia needs to take these factors into account to maximize the chances of a favorable outcome for the rescued casualty.

  17. Prioritizing disease-linked variants, genes, and pathways with an interactive whole genome analysis pipeline

    PubMed Central

    Lee, In-Hee; Lee, Kyungjoon; Hsing, Michael; Choe, Yongjoon; Park, Jin-Ho; Kim, Shu Hee; Bohn, Justin M.; Neu, Matthew B.; Hwang, Kyu-Baek; Green, Robert C.; Kohane, Isaac S.; Kong, Sek Won

    2014-01-01

    Whole genome sequencing (WGS) studies are uncovering disease-associated variants in both rare and non-rare diseases. Utilizing the next-generation sequencing for WGS requires a series of computational methods for alignment, variant detection, and annotation, and the accuracy and reproducibility of annotation results are essential for clinical implementation. However, annotating WGS with up to date genomic information is still challenging for biomedical researchers. Here we present one of the fastest and highly scalable annotation, filtering, and analysis pipeline –gNOME – to prioritize phenotype-associated variants while minimizing false positive findings. Intuitive graphical user interface of gNOME facilitates the selection of phenotype associated variants, and the result summaries are provided at variant-, gene-, and genome-levels. Moreover, the enrichment results of specific variants, genes, and gene sets between two groups or compared to population scale WGS datasets that is already integrated in the pipeline can help the interpretation. We found a small number of discordant results between annotation software tools in part due to different reporting strategies for the variants with complex impacts. Using two published whole exome datasets of uveal melanoma and bladder cancer, we demonstrated gNOME's accuracy of variant annotation and the enrichment of loss of function variants in known cancer pathways. gNOME web-server and source codes are freely available to the academic community. PMID:24478219

  18. Reciprocal interaction of Wnt and RXR-α pathways in hepatocyte development and hepatocellular carcinoma.

    PubMed

    Li, Jinyu; Chanrion, Maia; Sawey, Eric; Wang, Tim; Chow, Edward; Tward, Aaron; Su, Yi; Xue, Wen; Lucito, Robert; Zender, Lars; Lowe, Scott W; Bishop, J Michael; Powers, Scott

    2015-01-01

    Genomic analysis of human hepatocellular carcinoma (HCC) is potentially confounded by the differentiation state of the hepatic cell-of-origin. Here we integrated genomic analysis of mouse HCC (with defined cell-of-origin) along with normal development. We found a major shift in expression of Wnt and RXR-α pathway genes (up and down, respectively) coincident with the transition from hepatoblasts to hepatocytes. A combined Wnt and RXR-α gene signature categorized HCCs into two subtypes (high Wnt, low RXR-α and low Wnt, high RXR-α), which matched cell-of-origin in mouse models and the differentiation state of human HCC. Suppression of RXR-α levels in hepatocytes increased Wnt signaling and enhanced tumorigenicity, whereas ligand activation of RXR-α achieved the opposite. These results corroborate that there are two main HCC subtypes that correspond to the degree of hepatocyte differentation and that RXR-α, in part via Wnt signaling, plays a key functional role in the hepatocyte-like subtype and potentially could serve as a selective therapeutic target.

  19. TROL-FNR interaction reveals alternative pathways of electron partitioning in photosynthesis.

    PubMed

    Vojta, Lea; Carić, Dejana; Cesar, Vera; Antunović Dunić, Jasenka; Lepeduš, Hrvoje; Kveder, Marina; Fulgosi, Hrvoje

    2015-06-04

    In photosynthesis, final electron transfer from ferredoxin to NADP(+) is accomplished by the flavo enzyme ferredoxin:NADP(+) oxidoreductase (FNR). FNR is recruited to thylakoid membranes via integral membrane thylakoid rhodanase-like protein TROL. We address the fate of electrons downstream of photosystem I when TROL is absent. We have employed electron paramagnetic resonance (EPR) spectroscopy to study free radical formation and electron partitioning in TROL-depleted chloroplasts. DMPO was used to detect superoxide anion (O2(.-)) formation, while the generation of other free radicals was monitored by Tiron. Chloroplasts from trol plants pre-acclimated to different light conditions consistently exhibited diminished O2(.-) accumulation. Generation of other radical forms was elevated in trol chloroplasts in all tested conditions, except for the plants pre-acclimated to high-light. Remarkably, dark- and growth light-acclimated trol chloroplasts were resilient to O2(.-) generation induced by methyl-viologen. We propose that the dynamic binding and release of FNR from TROL can control the flow of photosynthetic electrons prior to activation of the pseudo-cyclic electron transfer pathway.

  20. TROL-FNR interaction reveals alternative pathways of electron partitioning in photosynthesis

    PubMed Central

    Vojta, Lea; Carić, Dejana; Cesar, Vera; Antunović Dunić, Jasenka; Lepeduš, Hrvoje; Kveder, Marina; Fulgosi, Hrvoje

    2015-01-01

    In photosynthesis, final electron transfer from ferredoxin to NADP+ is accomplished by the flavo enzyme ferredoxin:NADP+ oxidoreductase (FNR). FNR is recruited to thylakoid membranes via integral membrane thylakoid rhodanase-like protein TROL. We address the fate of electrons downstream of photosystem I when TROL is absent. We have employed electron paramagnetic resonance (EPR) spectroscopy to study free radical formation and electron partitioning in TROL-depleted chloroplasts. DMPO was used to detect superoxide anion (O2.−) formation, while the generation of other free radicals was monitored by Tiron. Chloroplasts from trol plants pre-acclimated to different light conditions consistently exhibited diminished O2.− accumulation. Generation of other radical forms was elevated in trol chloroplasts in all tested conditions, except for the plants pre-acclimated to high-light. Remarkably, dark- and growth light-acclimated trol chloroplasts were resilient to O2.− generation induced by methyl-viologen. We propose that the dynamic binding and release of FNR from TROL can control the flow of photosynthetic electrons prior to activation of the pseudo-cyclic electron transfer pathway. PMID:26041075

  1. The Tat pathway in Streptomyces lividans: interaction of Tat subunits and their role in translocation.

    PubMed

    De Keersmaeker, Sophie; Vrancken, Kristof; Van Mellaert, Lieve; Anné, Jozef; Geukens, Nick

    2007-04-01

    The twin-arginine translocation (Tat) pathway transports folded proteins across bacterial cytoplasmic membranes. The Tat system of Streptomyces lividans consists of TatA, TatB and TatC, unlike most Gram-positive bacteria, which only have TatA and TatC subunits. Interestingly, in S. lividans TatA and TatB are localized in both the cytoplasm and the membrane. In the cytoplasm soluble TatA and TatB were found as monomers or as part of a hetero-oligomeric complex. Further analysis showed that specific information for recognition of the precursor by the soluble Tat components is mainly present in the twin-arginine signal peptide. Study of the role of the Tat subunits in complex assembly and stability in the membrane and cytoplasm showed that TatB stabilizes TatC whereas a key role in driving Tat complex assembly is suggested for TatC. Finally, by analysis of the oligomeric properties of TatA in the membrane of S. lividans and study of the affinity of membrane-embedded TatA for Tat/Sec precursors, a role for TatA as a translocator is postulated.

  2. Conformational selection in a protein-protein interaction revealed by dynamic pathway analysis

    DOE PAGES

    Chakrabarti, Kalyan S.; Agafonov, Roman V.; Pontiggia, Francesco; ...

    2015-12-24

    Molecular recognition plays a central role in biology, and protein dynamics has been acknowledged to be important in this process. However, it is highly debated whether conformational changes happen before ligand binding to produce a binding-competent state (conformational selection) or are caused in response to ligand binding (induced fit). Proposals for both mechanisms in protein/protein recognition have been primarily based on structural arguments. However, the distinction between them is a question of the probabilities of going via these two opposing pathways. Here we present a direct demonstration of exclusive conformational selection in protein/protein recognition by measuring the flux for rhodopsinmore » kinase binding to its regulator recoverin, an important molecular recognition in the vision system. Using NMR spectroscopy, stopped-flow kinetics and isothermal titration calorimetry we show that recoverin populates a minor conformation in solution that exposes a hydrophobic binding pocket responsible for binding rhodopsin kinase. Lastly, protein dynamics in free recoverin limits the overall rate of binding.« less

  3. Molecular interaction of the first 3 enzymes of the de novo pyrimidine biosynthetic pathway of Trypanosoma cruzi.

    PubMed

    Nara, Takeshi; Hashimoto, Muneaki; Hirawake, Hiroko; Liao, Chien-Wei; Fukai, Yoshihisa; Suzuki, Shigeo; Tsubouchi, Akiko; Morales, Jorge; Takamiya, Shinzaburo; Fujimura, Tsutomu; Taka, Hikari; Mineki, Reiko; Fan, Chia-Kwung; Inaoka, Daniel Ken; Inoue, Masayuki; Tanaka, Akiko; Harada, Shigeharu; Kita, Kiyoshi; Aoki, Takashi

    2012-02-03

    The first 3 reaction steps of the de novo pyrimidine biosynthetic pathway are catalyzed by carbamoyl-phosphate synthetase II (CPSII), aspartate transcarbamoylase (ATC), and dihydroorotase (DHO), respectively. In eukaryotes, these enzymes are structurally classified into 2 types: (1) a CPSII-DHO-ATC fusion enzyme (CAD) found in animals, fungi, and amoebozoa, and (2) stand-alone enzymes found in plants and the protist groups. In the present study, we demonstrate direct intermolecular interactions between CPSII, ATC, and DHO of the parasitic protist Trypanosoma cruzi, which is the causative agent of Chagas disease. The 3 enzymes were expressed in a bacterial expression system and their interactions were examined. Immunoprecipitation using an antibody specific for each enzyme coupled with Western blotting-based detection using antibodies for the counterpart enzymes showed co-precipitation of all 3 enzymes. From an evolutionary viewpoint, the formation of a functional tri-enzyme complex may have preceded-and led to-gene fusion to produce the CAD protein. This is the first report to demonstrate the structural basis of these 3 enzymes as a model of CAD. Moreover, in conjunction with the essentiality of de novo pyrimidine biosynthesis in the parasite, our findings provide a rationale for new strategies for developing drugs for Chagas disease, which target the intermolecular interactions of these 3 enzymes. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. Traf2 interacts with Smad4 and regulates BMP signaling pathway in MC3T3-E1 osteoblasts

    SciTech Connect

    Shimada, Koichi; Ikeda, Kyoko; Ito, Koichi

    2009-12-18

    Bone morphogenetic proteins (BMPs) play important roles in osteoblast differentiation and maturation. In mammals, the BMP-induced receptor-regulated Smads form complexes with Smad4. These complexes translocate and accumulate in the nucleus, where they regulate the transcription of various target genes. However, the function of Smad4 remains unclear. We performed a yeast two-hybrid screen using Smad4 as bait and a cDNA library derived from bone marrow, to indentify the proteins interacting with Smad4. cDNA clones for Tumor necrosis factor (TNF) receptor-associated factor 2 (Traf2) were identified, and the interaction between the endogenous proteins was confirmed in the mouse osteoblast cell line MC3T3-E1. To investigate the function of Traf2, we silenced it with siRNA. The level of BMP-2 protein in the medium, the expression levels of the Bmp2 gene and BMP-induced transcription factor genes, including Runx2, Dlx5, Msx2, and Sp7, and the phosphorylated-Smad1 protein level were increased in cells transfected with Traf2 siRNA. The nuclear accumulation of Smad1 increased with TNF-{alpha} stimulation for 30 min at Traf2 silencing. These results suggest that the TNF-{alpha}-stimulated nuclear accumulation of Smad1 may be dependent on Traf2. Thus, the interaction between Traf2 and Smad4 may play a role in the cross-talk between TNF-{alpha} and BMP signaling pathways.

  5. Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE).

    PubMed

    Paull, Evan O; Carlin, Daniel E; Niepel, Mario; Sorger, Peter K; Haussler, David; Stuart, Joshua M

    2013-11-01

    Identifying the cellular wiring that connects genomic perturbations to transcriptional changes in cancer is essential to gain a mechanistic understanding of disease initiation, progression and ultimately to predict drug response. We have developed a method called Tied Diffusion Through Interacting Events (TieDIE) that uses a network diffusion approach to connect genomic perturbations to gene expression changes characteristic of cancer subtypes. The method computes a subnetwork of protein-protein interactions, predicted transcription factor-to-target connections and curated interactions from literature that connects genomic and transcriptomic perturbations. Application of TieDIE to The Cancer Genome Atlas and a breast cancer cell line dataset identified key signaling pathways, with examples impinging on MYC activity. Interlinking genes are predicted to correspond to essential components of cancer signaling and may provide a mechanistic explanation of tumor character and suggest subtype-specific drug targets. Software is available from the Stuart lab's wiki: https://sysbiowiki.soe.ucsc.edu/tiedie. jstuart@ucsc.edu. Supplementary data are available at Bioinformatics online.

  6. Pentamidine blocks the interaction between mutant S100A5 and RAGE V domain and inhibits the RAGE signaling pathway.

    PubMed

    Cho, Ching Chang; Chou, Ruey Hwang; Yu, Chin

    2016-08-19

    The human S100 protein family contains small, dimeric and acidic proteins that contain two EF-hand motifs and bind calcium. When S100A5 binds calcium, its conformation changes and promotes interaction with the target protein. The extracellular domain of RAGE (Receptor of Advanced Glycation End products) contain three domains: C1, C2 and V. The RAGE V domain is the target protein of S100A5 that promotes cell survival, growth and differentiation by activating several signaling pathways. Pentamidine is an apoptotic and antiparasitic drug that is used to treat or prevent pneumonia. Here, we found that pentamidine interacts with S100A5 using HSQC titration. We elucidated the interactions of S100A5 with RAGE V domain and pentamidine using fluorescence and NMR spectroscopy. We generated two binary models-the S100A5-RAGE V domain and S100A5-Pentamidine complex-and then observed that the pentamidine and RAGE V domain share a similar binding region in mS100A5. We also used the WST-1 assay to investigate the bioactivity of S100A5, RAGE V domain and pentamidine. These results indicated that pentamidine blocks the binding between S100A5 and RAGE V domain. This finding is useful for the development of new anti-proliferation drugs. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Converting cell lines representing hematological malignancies from glucocorticoid-resistant to glucocorticoid-sensitive: signaling pathway interactions.

    PubMed

    Garza, Anna S; Miller, Aaron L; Johnson, Betty H; Thompson, E Brad

    2009-05-01

    Mitogen-activated protein kinases (MAPKs), protein kinase A (PKA) and mTOR pathways modulate the apoptotic effects of glucocorticoids (GCs) in human lymphoblastic leukemia CEM cells. We now show that manipulation of these pathways converts several cell lines, representing other lymphoid malignancies, from GC-resistant to GC-sensitive. Basal levels of phosphorylated JNK and ERK were elevated in the GC-resistant cells. Treatments that directly or indirectly reduced phosphorylated JNK and ERK resulted in Dex sensitivity in five resistant lymphoid cell lines. Sensitivity to GC-driven apoptosis correlated with GC-dependent increases in phosphorylated and total glucocorticoid receptor, and in increased levels of the pro-apoptotic protein Bim.

  8. Interactions between PPAR Gamma and the Canonical Wnt/Beta-Catenin Pathway in Type 2 Diabetes and Colon Cancer

    PubMed Central

    Claes, Victor

    2017-01-01

    In both colon cancer and type 2 diabetes, metabolic changes induced by upregulation of the Wnt/beta-catenin signaling and downregulation of peroxisome proliferator-activated receptor gamma (PPAR gamma) may help account for the frequent association of these two diseases. In both diseases, PPAR gamma is downregulated while the canonical Wnt/beta-catenin pathway is upregulated. In colon cancer, upregulation of the canonical Wnt system induces activation of pyruvate dehydrogenase kinase and deactivation of the pyruvate dehydrogenase complex. As a result, a large part of cytosolic pyruvate is converted into lactate through activation of lactate dehydrogenase. Lactate is extruded out of the cell by means of activation of monocarboxylate lactate transporter-1. This phenomenon is called Warburg effect. PPAR gamma agonists induce beta-catenin inhibition, while inhibition of the canonical Wnt/beta-catenin pathway activates PPAR gamma. PMID:28298922

  9. Optimal Scaling of Interaction Effects in Generalized Linear Models

    ERIC Educational Resources Information Center

    van Rosmalen, Joost; Koning, Alex J.; Groenen, Patrick J. F.

    2009-01-01

    Multiplicative interaction models, such as Goodman's (1981) RC(M) association models, can be a useful tool for analyzing the content of interaction effects. However, most models for interaction effects are suitable only for data sets with two or three predictor variables. Here, we discuss an optimal scaling model for analyzing the content of…

  10. Optimal Scaling of Interaction Effects in Generalized Linear Models

    ERIC Educational Resources Information Center

    van Rosmalen, Joost; Koning, Alex J.; Groenen, Patrick J. F.

    2009-01-01

    Multiplicative interaction models, such as Goodman's (1981) RC(M) association models, can be a useful tool for analyzing the content of interaction effects. However, most models for interaction effects are suitable only for data sets with two or three predictor variables. Here, we discuss an optimal scaling model for analyzing the content of…

  11. Pathway deviation-based biomarker and multi-effect target identification in asbestos-related squamous cell carcinoma of the lung

    PubMed Central

    Du, Jiang; Zhang, Lin

    2017-01-01

    Asbestos-related lung carcinoma is one of the most devastating occupational cancers, and effective techniques for early diagnosis are still lacking. In the present study, a systematic approach was applied to detect a potential biomarker for asbestos-related lung cancer (ARLC); in particular asbestos-related squamous cell carcinoma (ARLC-SCC). Microarray data (GSE23822) were retrieved from the Gene Expression Omnibus database, including 26 ARLC-SCCs and 30 non-asbestos-related squamous cell lung carcinomas (NARLC-SCCs). Differentially expressed genes (DEGs) were identified by the limma package, and then a protein-protein interaction (PPI) network was constructed according to the BioGRID and HPRD databases. A novel scoring approach integrating an expression deviation score and network degree of the gene was then proposed to weight the DEGs. Subsequently, the important genes were uploaded to DAVID for pathway enrichment analysis. Pathway correlation analysis was carried out using Spearman's rank correlation coefficient of the pathscore. In total, 1,333 DEGs, 391 upregulated and 942 downregulated, were obtained between the ARLC-SCCs and NARLC-SCCs. A total of 524 important genes for ARLC-SCC were significantly enriched in 22 KEGG pathways. Correlation analysis of these pathways showed that the pathway of SNARE interactions in vesicular transport was significantly correlated with 12 other pathways. Additionally, obvious correlations were found between multiple pathways by sharing cross-talk genes (EGFR, PRKX, PDGFB, PIK3R3, SLK, IGF1, CDC42 and PRKCA). On the whole, our data demonstrate that 8 cross-talk genes were found to bridge multiple ARLC-SCC-specific pathways, which may be used as candidate biomarkers and potential multi-effect targets. As these genes are involved in multiple pathways, it is possible that drugs targeting these genes may thus be able to influence multiple pathways simultaneously. PMID:28204826

  12. Designing Interactions for Learning: Physicality, Interactivity, and Interface Effects in Digital Environments

    ERIC Educational Resources Information Center

    Hoffman, Daniel L.

    2013-01-01

    The purpose of the study is to better understand the role of physicality, interactivity, and interface effects in learning with digital content. Drawing on work in cognitive science, human-computer interaction, and multimedia learning, the study argues that interfaces that promote physical interaction can provide "conceptual leverage"…

  13. Designing Interactions for Learning: Physicality, Interactivity, and Interface Effects in Digital Environments

    ERIC Educational Resources Information Center

    Hoffman, Daniel L.

    2013-01-01

    The purpose of the study is to better understand the role of physicality, interactivity, and interface effects in learning with digital content. Drawing on work in cognitive science, human-computer interaction, and multimedia learning, the study argues that interfaces that promote physical interaction can provide "conceptual leverage"…

  14. Phenolic compounds: The inhibition effect on polyol pathway enzymes.

    PubMed

    Aslan, Hatice Esra; Beydemir, Şükrü

    2017-03-25

    The polyol pathway called as sorbitol way is a small part of glycose metabolism. The pathway is regarded as an important element in the pathogenesis of various diabetic complications in individuals with diabetes mellitus. The pathway plays a crucial role in hyperglycemia. The polyol pathway contains two enzymes as aldose reductase (AR) and sorbitol dehydrogenase (SDH). In the present study, AR and SDH were purified from sheep liver by using simple chromatographic methods. AR was purified with a yield of 2.11% and approximately 162 fold and SDH was purified with a yield of 0.53% and approximately 9.07 purification fold. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) was performed to check the purity and determine the subunit molecular weights of the enzymes. Subunit molecular weights of AR and SDH were 38.82 kDa and 37.74 kDa, respectively. Optimal pH, optimal ionic strength, optimal temperature, activation energy, activation enthalpy, Q10 value and stable pH were determined as 5.5, 10 mM, 50 °C, 2.16 kcal, 1.52 kcal, 1.33 and 8.0 for AR enzyme, respectively. The kinetic parameters Km and Vmax for AR were determined as 0.45 mM and 0.55 EU/mL, respectively. These parameters were studied for only AR in the present study, because it was previously studied for SDH. IC50 values of 3,4-dihydroxybenzoic acid, 3,5-dihydroxybenzoic acid, 3-hydroxybenzoic acid, 4-hydroxybenzoic acid, salicylic acid, p-coumaric acid, ellagic acid, gallic acid, ferrulic acid and caffeic acid on AR and SDH activities were found as 120, 92.0, 49.0, 39.0, 40.0, 690, 7.00, 103, 84.0, 3.00 μM for AR enzyme and 5060, 8350, 6730, 7070, 5780, 24.0, 13.0, 26.0, 17.0, 21.0 μM for SDH enzyme, respectively. According to these results, caffeic acid was the strongest inhibitor for AR activity compared to the other phenolic acids and ellagic acid was also the strongest inhibitor for SDH activity.

  15. Phototropism: a "simple" physiological response modulated by multiple interacting photosensory-response pathways.

    PubMed

    Liscum, E; Stowe-Evans, E L

    2000-09-01

    Phototropism is the process by which plants reorient growth of various organs, most notably stems, in response to lateral differences in light quantity and/or quality. The ubiquitous nature of the phototropic response in the plant kingdom implies that it provides some adaptive evolutionary advantage. Upon visual inspection it is tempting to surmise that phototropic curvatures result from a relatively simple growth response to a directional stimulus. However, detailed photophysiological, and more recently genetic and molecular, studies have demonstrated that phototropism is in fact regulated by complex interactions among several photosensory systems. At least two receptors, phototropin and a presently unidentified receptor, appear to mediate the primary photoreception of directional blue light cues in dark-grown plants. PhyB may also function as a primary receptor to detect lateral increases in far-red light in neighbor-avoidance responses of light-grown plants. Phytochromes (phyA and phyB at a minimum) also appear to function as secondary receptors to regulate adaptation processes that ultimately modulate the magnitude of curvature induced by primary photoperception. As a result of the interactions of these multiple photosensory systems plants are able to maximize the adaptive advantage of the phototropic response in ever changing light environments.

  16. AEG-1/MTDH/LYRIC: Signaling Pathways, Downstream Genes, Interacting Proteins, and Regulation of Tumor Angiogenesis

    PubMed Central

    Emdad, Luni; Das, Swadesh K.; Dasgupta, Santanu; Hu, Bin; Sarkar, Devanand; Fisher, Paul B.

    2014-01-01

    Astrocyte elevated gene-1 (AEG-1), also known as metadherin (MTDH) and lysine-rich CEACAM1 coisolated (LYRIC), was initially cloned in 2002. AEG-1/MTDH/LYRIC has emerged as an important oncogene that is overexpressed in multiple types of human cancer. Expanded research on AEG-1/MTDH/LYRIC has established a functional role of this molecule in several crucial aspects of tumor progression, including transformation, proliferation, cell survival, evasion of apoptosis, migration and invasion, metastasis, angiogenesis, and chemoresistance. The multifunctional role of AEG-1/MTDH/LYRIC in tumor development and progression is associated with a number of signaling cascades, and recent studies identified several important interacting partners of AEG-1/MTDH/LYRIC in regulating cancer promotion and other biological functions. This review evaluates the current literature on AEG-1/MTDH/LYRIC function relative to signaling changes, interacting partners, and angiogenesis and highlights new perspectives of this molecule, indicating its potential as a significant target for the clinical treatment of various cancers and other diseases. PMID:23889988

  17. A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways

    PubMed Central

    Taipale, Mikko; Tucker, George; Peng, Jian; Krykbaeva, Irina; Lin, Zhen-Yuan; Larsen, Brett; Choi, Hyungwon; Berger, Bonnie; Gingras, Anne-Claude; Lindquist, Susan

    2014-01-01

    Chaperones are abundant cellular proteins that promote the folding and function of their substrate proteins (clients). In vivo, chaperones also associate with a large and diverse set of co-factors (co-chaperones) that regulate their specificity and function. However, how these co-chaperones regulate protein folding and whether they have chaperone-independent biological functions is largely unknown. We have combined mass spectrometry and quantitative high-throughput LUMIER assays to systematically characterize the chaperone/co-chaperone/client interaction network in human cells. We uncover hundreds of novel chaperone clients, delineate their participation in specific co-chaperone complexes, and establish a surprisingly distinct network of protein/protein interactions for co-chaperones. As a salient example of the power of such analysis, we establish that NUDC family co-chaperones specifically associate with structurally related but evolutionarily distinct β-propeller folds. We provide a framework for deciphering the proteostasis network, its regulation in development and disease, and expand the use of chaperones as sensors for drug/target engagement. PMID:25036637

  18. Effects of the Insulin-like Growth Factor Pathway on the Regulation of Mammary Gland Development

    PubMed Central

    Ha, Woo Tae; Jeong, Ha Yeon; Lee, Seung Yoon; Song, Hyuk

    2016-01-01

    The insulin-like growth factor (IGF) pathway is a key signal transduction pathway involved in cell proliferation, migration, and apoptosis. In dairy cows, IGF family proteins and binding receptors, including their intracellular binding partners, regulate mammary gland development. IGFs and IGF receptor interactions in mammary glands influence the early stages of mammogenesis, i.e., mammary ductal genesis until puberty. The IGF pathway includes three major components, IGFs (such as IGF-I, IGF-II, and insulin), their specific receptors, and their high-affinity binding partners (IGF binding proteins [IGFBPs]; i.e., IGFBP1–6), including specific proteases for each IGFBP. Additionally, IGFs and IGFBP interactions are critical for the bioactivities of various intracellular mechanisms, including cell proliferation, migration, and apoptosis. Notably, the interactions between IGFs and IGFBPs in the IGF pathway have been difficult to characterize during specific stages of bovine mammary gland development. In this review, we aim to describe the role of the interaction between IGFs and IGFBPs in overall mammary gland development in dairy cows. PMID:27795999

  19. Defining Adverse Outcome Pathways for Effects of the Fungicide Propiconazole of Fish Reproduction

    EPA Science Inventory

    Adverse outcome pathways (AOPs) are used to describe the linkage of chemical interactions in terms of molecular initiating events to whole organism responses suitable for risk assessment. This study was conducted to develop AOPs for the model fungicide propiconazole relative to r...

  20. Defining Adverse Outcome Pathways for Effects of the Fungicide Propiconazole of Fish Reproduction

    EPA Science Inventory

    Adverse outcome pathways (AOPs) are used to describe the linkage of chemical interactions in terms of molecular initiating events to whole organism responses suitable for risk assessment. This study was conducted to develop AOPs for the model fungicide propiconazole relative to r...

  1. A short revisit to Kuo-Brown effective interactions

    NASA Astrophysics Data System (ADS)

    Wang, XiaoBao; Dong, GuoXiang

    2015-10-01

    This paper is a short revisit to Kuo-Brown effective interaction derived from the Hamada-Johnston nucleon-nucleon potential, done by Gerry Brown and Tom Kuo. This effective interaction, derived in year 1966, is the first attempt to describe nuclear structure properties from the free nucleon-nucleon potential. Nowadays much progress has been achieved for the effective interactions in shell model. We would compare the effective interactions obtained in the 1966 paper with up-to-date shell-model interactions in sd-shell and pf-shell model space. Recent knowledge of effective interactions on nuclear structure, can also be traced in the Kuo- Brown effective interaction, i.e., the universal roles of central and tensor forces, which reminds us that such discovery should be noticed much earlier.

  2. Oxazoloisoindolinones with in vitro antitumor activity selectively activate a p53-pathway through potential inhibition of the p53-MDM2 interaction.

    PubMed

    Soares, Joana; Pereira, Nuno A L; Monteiro, Ângelo; Leão, Mariana; Bessa, Cláudia; Dos Santos, Daniel J V A; Raimundo, Liliana; Queiroz, Glória; Bisio, Alessandra; Inga, Alberto; Pereira, Clara; Santos, Maria M M; Saraiva, Lucília

    2015-01-23

    One of the most appealing targets for anticancer treatment is the p53 tumor suppressor protein. In half of human cancers, this protein is inactivated due to endogenous negative regulators such as MDM2. Actually, restoring the p53 activity, particularly through the inhibition of its interaction with MDM2, is considered a valuable therapeutic strategy against cancers with a wild-type p53 status. In this work, we report the synthesis of nine enantiopure phenylalaninol-derived oxazolopyrrolidone lactams and the evaluation of their biological effects as p53-MDM2 interaction inhibitors. Using a yeast-based screening assay, two oxazoloisoindolinones, compounds 1b and 3a, were identified as potential p53-MDM2 interaction inhibitors. The molecular mechanism of oxazoloisoindolinone 3a was further validated in human colon adenocarcinoma HCT116 cells with wild-type p53 (HCT116 p53(+/+)) and in its isogenic derivative without p53 (HCT116 p53(-/-)). Indeed, using these cells, we demonstrated that oxazoloisoindolinone 3a exhibited a p53-dependent in vitro antitumor activity through induction of G0/G1-phase cell cycle arrest and apoptosis. The selective activation of a p53-apoptotic pathway by oxazoloisoindolinone 3a was further supported by the occurrence of PARP cleavage only in p53-expressing HCT116 cells. Moreover, oxazoloisoindolinone 3a led to p53 protein stabilization and to the up-regulation of p53 transcriptional activity with increased expression levels of several p53 target genes, as p21(WAF1/CIP1), MDM2, BAX and PUMA, in p53(+/+) but not in p53(-/-) HCT116 cells. Additionally, the ability of oxazoloisoindolinone 3a to block the p53-MDM2 interaction in HCT116 p53(+/+) cells was confirmed by co-immunoprecipitation. Finally, the molecular docking analysis of the interactions between the synthesized compounds and MDM2 revealed that oxazoloisoindolinone 3a binds to MDM2. Altogether, this work adds, for the first time, the oxazoloisoindolinone scaffold to the list of

  3. Integrative analysis reveals novel pathways mediating the interaction between adipose tissue and pancreatic islets in obesity in rats.

    PubMed

    Malpique, Rita; Figueiredo, Hugo; Esteban, Yaiza; Rebuffat, Sandra A; Hanzu, Felicia A; Vinaixa, Maria; Yanes, Oscar; Correig, Xavier; Barceló-Batllori, Sílvia; Gasa, Rosa; Kalko, Susana G; Gomis, Ramon

    2014-06-01

    Comprehensive characterisation of the interrelation between the peripancreatic adipose tissue and the pancreatic islets promises novel insights into the mechanisms that regulate beta cell adaptation to obesity. Here, we sought to determine the main pathways and key molecules mediating the crosstalk between these two tissues during adaptation to obesity by the way of an integrated inter-tissue, multi-platform analysis. Wistar rats were fed a standard or cafeteria diet for 30 days. Transcriptomic variations by diet in islets and peripancreatic adipose tissue were examined through microarray analysis. The secretome from peripancreatic adipose tissue was subjected to a non-targeted metabolomic and proteomic analysis. Gene expression variations in islets were integrated with changes in peripancreatic adipose tissue gene expression and protein and metabolite secretion using an integrated inter-tissue pathway and network analysis. The highest level of data integration, linking genes differentially expressed in both tissues with secretome variations, allowed the identification of significantly enriched canonical pathways, such as the activation of liver/retinoid X receptors, triacylglycerol degradation, and regulation of inflammatory and immune responses, and underscored interaction network hubs, such as cholesterol and the fatty acid binding protein 4, which were unpredicted through single-tissue analysis and have not been previously implicated in the peripancreatic adipose tissue crosstalk with beta cells. The integrated analysis reported here allowed the identification of novel mechanisms and key molecules involved in peripancreatic adipose tissue interrelation with beta cells during the development of obesity; this might help the development of novel strategies to prevent type 2 diabetes.

  4. Interactions between BDNF Val66Met polymorphism and early life stress predict brain and arousal pathways to syndromal depression and anxiety.

    PubMed

    Gatt, J M; Nemeroff, C B; Dobson-Stone, C; Paul, R H; Bryant, R A; Schofield, P R; Gordon, E; Kemp, A H; Williams, L M

    2009-07-01

    Individual risk markers for depression and anxiety disorders have been identified but the explicit pathways that link genes and environment to these markers remain unknown. Here we examined the explicit interactions between the brain-derived neurotrophic factor (BDNF) Val66Met gene and early life stress (ELS) exposure in brain (amygdala-hippocampal-prefrontal gray matter volume), body (heart rate), temperament and cognition in 374 healthy European volunteers assessed for depression and anxiety symptoms. Brain imaging data were based on a subset of 89 participants. Multiple regression analysis revealed main effects of ELS for body arousal (resting heart rate, P=0.005) and symptoms (depression and anxiety, P<0.001) in the absence of main effects for BDNF. In addition, significant BDNF-ELS interactions indicated that BDNF Met carriers exposed to greater ELS have smaller hippocampal and amygdala volumes (P=0.013), heart rate elevations (P=0.0002) and a decline in working memory (P=0.022). Structural equation path modeling was used to determine if this interaction predicts anxiety and depression by mediating effects on the brain, body and cognitive measures. The combination of Met carrier status and exposure to ELS predicted reduced gray matter in hippocampus (P<0.001), and associated lateral prefrontal cortex (P<0.001) and, in turn, higher depression (P=0.005). Higher depression was associated with poorer working memory (P=0.005), and slowed response speed. The BDNF Met-ELS interaction also predicted elevated neuroticism and higher depression and anxiety by elevations in body arousal (P<0.001). In contrast, the combination of BDNF V/V genotype and ELS predicted increases in gray matter of the amygdala (P=0.003) and associated medial prefrontal cortex (P<0.001), which in turn predicted startle-elicited heart rate variability (P=0.026) and higher anxiety (P=0.026). Higher anxiety was linked to verbal memory, and to impulsivity. These effects were specific to the BDNF

  5. Interacting appetite-regulating pathways in the hypothalamic regulation of body weight.

    PubMed

    Kalra, S P; Dube, M G; Pu, S; Xu, B; Horvath, T L; Kalra, P S

    1999-02-01

    Various aspects of the complex spatio-temporal patterning of hypothalamic signaling that leads to the development of synchronized nocturnal feeding in the rat are critically examined. Undoubtedly, as depicted in Fig. 7, a distinct ARN in the hypothalamus is involved in the control of nocturnal appetite. At least four basic elements operate within this ARN. These are: 1) A discrete appetite-driving or orexigenic network of NPY, NE, GABA, GAL, EOP, and orexin transduces and releases appetite-stimulating signals. 2) Similarly, anorexigenic signal-producing pathways (e.g., CRH, GLP-1, alpha MSH, and CART) orchestrate neural events for dissipation of appetite and to terminate feeding, possibly by interrupting NPY efflux and action at a postsynaptic level within the hypothalamus. It is possible that some of these may represent the physiologically relevant "off" switches under the influence of GABA alone, or AgrP alone, or in combination with NPY released from the NPY-, GABA-, and AgrP-coproducing neurons. 3) Recent evidence shows that neural elements in the VMN-DMN complex tonically restrain the orexigenic signals during the intermeal interval; the restraint is greatly aided by leptin's action via diminution of orexigenic (NPY) and augmentation of anorexigenic (GLP-1, alpha MSH, and CART) signals. Since interruption of neurotransmission in the VMN resulted in hyperphagia and development of leptin resistance, it seems likely that the VMN is an effector site for the restraint exercised by leptin. The daily rhythms in leptin synthesis and release are temporally dissociable because the onset of daily rise in leptin gene expression in adipocytes precedes that in leptin secretion. Nevertheless, these rhythms are in phase with daily ingestive behavior because the peak in circulating leptin levels occurs during the middle of the feeding period. These observations, coupled with the fact that circulating levels of leptin are directly related to adiposity, pose a new challenge for

  6. Interactions of fluoroquinolone antibacterial agents with aqueous chlorine: reaction kinetics, mechanisms, and transformation pathways.

    PubMed

    Dodd, Michael C; Shah, Amisha D; von Gunten, Urs; Huang, Ching-Hua

    2005-09-15

    Kinetics, products, and mechanistic aspects of reactions between free available chlorine (HOCl/OCl-), ciprofloxacin (CF), and enrofloxacin (EF) were extensively investigated to elucidate the behavior of fluoroquinolone antibacterial agents during water chlorination processes. Although the molecular structures of these two substrates differ only with respect to degree of N(4) amine alkylation, CF and EF exhibit markedly different HOCl reaction kinetics and transformation pathways. HOCI reacts very rapidly at CF's secondary N(4) amine, forming a chloramine intermediate that spontaneously decays in aqueous solution by concerted piperazine fragmentation. In contrast, HOCl reacts relatively slowly at EF's tertiary N(4) amine, apparently forming a highly reactive chlorammonium intermediate (R3N-(4)Cl+) that can catalytically halogenate EF or other substrates present in solution. Flumequine, a fluoroquinolone that lacks the characteristic piperazine ring, exhibits no apparent reactivity toward HOCI but appears to undergo facile halodecarboxylation in the presence of R3N(4)-Cl+ species derived from EF. Measured reaction kinetics were validated in real water matrixes by modeling CF and EF losses in the presence of free chlorine residuals. Combined chlorine (CC) kinetics were determined under selected conditions to evaluate the potential significance of reactions with chloramines. CF's rapid kinetics in direct reactions with HOCl, and relatively high reactivity toward CC, indicate that secondary amine-containing fluoroquinolones should be readily transformed during chlorination of real waters, whether applied chlorine doses are present as free or combined residuals. However, EF's slower HOCl reaction kinetics, recalcitrance toward CC, and participation in the catalytic halogenation cycle described herein suggest that tertiary amine-containing fluoroquinolones will be comparatively stable during most full-scale water chlorination processes.

  7. Cytosolic clearance of replication-deficient mutants reveals Francisella tularensis interactions with the autophagic pathway.

    PubMed

    Chong, Audrey; Wehrly, Tara D; Child, Robert; Hansen, Bryan; Hwang, Seungmin; Virgin, Herbert W; Celli, Jean

    2012-09-01

    Cytosolic bacterial pathogens must evade intracellular innate immune recognition and clearance systems such as autophagy to ensure their survival and proliferation. The intracellular cycle of the bacterium Francisella tularensis is characterized by rapid phagosomal escape followed by extensive proliferation in the macrophage cytoplasm. Cytosolic replication, but not phagosomal escape, requires the locus FTT0369c, which encodes the dipA gene (deficient in intracellular replication A). Here, we show that a replication-deficient, ∆dipA mutant of the prototypical SchuS4 strain is eventually captured from the cytosol of murine and human macrophages into double-membrane vacuoles displaying the late endosomal marker, LAMP1, and the autophagy-associated protein, LC3, coinciding with a reduction in viable intracellular bacteria. Capture of SchuS4ΔdipA was not dipA-specific as other replication-deficient bacteria, such as chloramphenicol-treated SchuS4 and a purine auxotroph mutant SchuS4ΔpurMCD, were similarly targeted to autophagic vacuoles. Vacuoles containing replication-deficient bacteria were labeled with ubiquitin and the autophagy receptors SQSTM1/p62 and NBR1, and their formation was decreased in macrophages from either ATG5-, LC3B- or SQSTM1-deficient mice, indicating recognition by the ubiquitin-SQSTM1-LC3 pathway. While a fraction of both the wild-type and the replication-impaired strains were ubiquitinated and recruited SQSTM1, only the replication-defective strains progressed to autophagic capture, suggesting that wild-type Francisella interferes with the autophagic cascade. Survival of replication-deficient strains was not restored in autophagy-deficient macrophages, as these bacteria died in the cytosol prior to autophagic capture. Collectively, our results demonstrate that replication-impaired strains of Francisella are cleared by autophagy, while replication-competent bacteria seem to interfere with autophagic recognition, therefore ensuring survival

  8. Neuron-astrocyte interactions, pyruvate carboxylation and the pentose phosphate pathway in the neonatal rat brain.

    PubMed

    Morken, Tora Sund; Brekke, Eva; Håberg, Asta; Widerøe, Marius; Brubakk, Ann-Mari; Sonnewald, Ursula

    2014-01-01

    Glucose and acetate metabolism and the synthesis of amino acid neurotransmitters, anaplerosis, glutamate-glutamine cycling and the pentose phosphate pathway (PPP) have been extensively investigated in the adult, but not the neonatal rat brain. To do this, 7 day postnatal (P7) rats were injected with [1-(13)C]glucose and [1,2-(13)C]acetate and sacrificed 5, 10, 15, 30 and 45 min later. Adult rats were injected and sacrificed after 15 min. To analyse pyruvate carboxylation and PPP activity during development, P7 rats received [1,2-(13)C]glucose and were sacrificed 30 min later. Brain extracts were analysed using (1)H- and (13)C-NMR spectroscopy. Numerous differences in metabolism were found between the neonatal and adult brain. The neonatal brain contained lower levels of glutamate, aspartate and N-acetylaspartate but similar levels of GABA and glutamine per mg tissue. Metabolism of [1-(13)C]glucose at the acetyl CoA stage was reduced much more than that of [1,2-(13)C]acetate. The transfer of glutamate from neurons to astrocytes was much lower while transfer of glutamine from astrocytes to glutamatergic neurons was relatively higher. However, transport of glutamine from astrocytes to GABAergic neurons was lower. Using [1,2-(13)C]glucose it could be shown that despite much lower pyruvate carboxylation, relatively more pyruvate from glycolysis was directed towards anaplerosis than pyruvate dehydrogenation in astrocytes. Moreover, the ratio of PPP/glucose-metabolism was higher. These findings indicate that only the part of the glutamate-glutamine cycle that transfers glutamine from astrocytes to neurons is operating in the neonatal brain and that compared to adults, relatively more glucose is prioritised to PPP and pyruvate carboxylation. Our results may have implications for the capacity to protect the neonatal brain against excitotoxicity and oxidative stress.

  9. Direct and indirect effects of predation and predation risk in old-field interaction webs.

    PubMed

    Schmitz, O J

    1998-04-01

    Indirect effects emerge when a change in the abundance of one species indirectly affects another by changing the abundances of intermediate species-called density-mediated indirect effects-or they arise when one species modifies how two other species interact-called trait-mediated indirect effects. I report on field experiments that evaluated how grass and herb biomass in old-field interaction webs was influenced indirectly by a spider carnivore through its interactions with a generalist and a grass-specialist grasshopper species. I manipulated interaction pathways between the spider and the plants using different combinations of the grasshopper species. I changed the modality of predator-prey interactions to isolate density-mediated from trait-mediated effects using natural spiders (predation spiders) or spiders that were prevented from subduing prey by mouthpart manipulation (risk spiders). I found that indirect effects were stronger in speciose, reticulate food webs than in linear food chains owing to a trait-mediated effect, a diet shift by herbivores in response to predation risk. Spiders alone did not have significant effects on grasshopper densities in the field experiments, removing any possibility of density-mediated indirect effects. The study illustrates that ecologists should not underestimate the importance of behavioral ecology in determining community-level interactions.

  10. Genetic Allee effects and their interaction with ecological Allee effects.

    PubMed

    Wittmann, Meike J; Stuis, Hanna; Metzler, Dirk

    2016-10-12

    It is now widely accepted that genetic processes such as inbreeding depression and loss of genetic variation can increase the extinction risk of small populations. However, it is generally unclear whether extinction risk from genetic causes gradually increases with decreasing population size or whether there is a sharp transition around a specific threshold population size. In the ecological literature, such threshold phenomena are called 'strong Allee effects' and they can arise for example from mate limitation in small populations. In this study, we aim to (i) develop a meaningful notion of a 'strong genetic Allee effect', (ii) explore whether and under what conditions such an effect can arise from inbreeding depression due to recessive deleterious mutations, and (iii) quantify the interaction of potential genetic Allee effects with the well-known mate-finding Allee effect. We define a strong genetic Allee effect as a genetic process that causes a population's survival probability to be a sigmoid function of its initial size. The inflection point of this function defines the critical population size. To characterize survival-probability curves, we develop and analyse simple stochastic models for the ecology and genetics of small populations. Our results indicate that inbreeding depression can indeed cause a strong genetic Allee effect, but only if individuals carry sufficiently many deleterious mutations (lethal equivalents). Populations suffering from a genetic Allee effect often first grow, then decline as inbreeding depression sets in and then potentially recover as deleterious mutations are purged. Critical population sizes of ecological and genetic Allee effects appear to be often additive, but even superadditive interactions are possible. Many published estimates for the number of lethal equivalents in birds and mammals fall in the parameter range where strong genetic Allee effects are expected. Unfortunately, extinction risk due to genetic Allee effects

  11. FMR1 and AKT/mTOR signalling pathways: potential functional interactions controlling folliculogenesis in human granulosa cells.

    PubMed

    Rehnitz, Julia; Alcoba, Diego D; Brum, Ilma S; Hinderhofer, Katrin; Youness, Berthe; Strowitzki, Thomas; Vogt, Peter H

    2017-08-04

    Granulosa cells (GCs) play a major role in folliculogenesis and are crucial for oocyte maturation and growth. In these cells, the mTOR/AKT signalling pathway regulates early folliculogenesis by maintaining the dormancy of primordial follicles, while FSH induces their further differentiation and maturation. Because changes in number of CGG triplets in FMR1 exon 1 (below or beyond normal values of 26-34 triplets) affect ovarian reserve and pre-mutations containing >54 CGG triplets represent a known risk factor for premature ovarian insufficiency/failure, we investigated in the human GC model (COV434) how FMR1/FMRP and mTOR/AKT are expressed and potentially interact during GC proliferation. As FMR protein (FMRP) is expressed mainly in human ovarian GCs, we used these after inducing their proliferation using recombinant FSH (rFSH) and the repression of the mTOR/AKT signalling pathway. We showed that AKT and mTOR expression levels significantly increase after stimulation with rFSH, while S6K and FMR1 expression decrease. After inhibiting mTOR and AKT, FMR1 and S6K expression significantly increased. Only AKT inhibition led to decreased FMRP levels, as expected due to the known FMR1/FMRP negative feedback loop. But rFSH and the mTOR inhibition increased them, indicating a decoupling of this FMR1/FMRP negative feedback loop in our model system. Copyright © 2017 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

  12. Receptor-Drug Interaction: Europium Employment for Studying the Biochemical Pathway of G-Protein-Coupled Receptor Activation

    PubMed Central

    Antonio, Colabufo Nicola; Grazia, Perrone Maria; Marialessandra, Contino; Francesco, Berardi; Roberto, Perrone

    2007-01-01

    In medicinal chemistry field, the biochemical pathways, involved in 7-transmembrane domains G-protein coupled receptors (GPCRs) activation, are commonly studied to establish the activity of ligands towards GPCRs. The most studied steps are the measurement of activated GTP-α subunit and stimulated intracellular cAMP. At the present, many researchers defined agonist or antagonist activity of potential GPCRs drugs employing [35S]GTPγS or [3H]cAMP as probes. Recently, the corresponding lanthanide labels Eu-GTP and Eu-cAMP as alternative to radiochemicals have been developed because they are highly sensitive, easy to automate, easily synthesized, they display a much longer shelf-life and they can be used in multilabel experiments. In the present review, the receptor-drug interaction by europium employment for studying the biochemical pathway of GPCR activation has been focused. Moreover, comparative studies between lanthanide label probes and the corresponding radiolabeled compounds have been carried out. PMID:18350113

  13. The PUB domain: a putative protein-protein interaction domain implicated in the ubiquitin-proteasome pathway.

    PubMed

    Suzuki, T; Park, H; Till, E A; Lennarz, W J

    2001-10-12

    Cytoplasmic peptide:N-glycanase (PNGase) is a de-N-glycosylating enzyme which may be involved in the proteasome-dependent pathway for degradation of misfolded glycoproteins formed in the endoplasmic reticulum (ER) that are exported into the cytoplasm. A cytoplasmic PNGase found in Saccharomyces cerevisiae, Png1p, is widely distributed in higher eukaryotes as well as in yeast (Suzuki, T., et al. J. Cell Biol. 149, 1039-1051, 2000). The recently uncovered complete genome sequence of Arabidopsis thaliana prompted us to search for the protein homologue of Png1p in this organism. Interestingly, when the mouse Png1p homologue sequence was used as a query, not only a Png1p homologue containing a transglutaminase-like domain that is believed to contain a catalytic triad for PNGase activity, but also four proteins which had a domain of 46 amino acids in length that exhibited significant similarity to the N-terminus of mouse Png1p were identified. Moreover, three of these homologous proteins were also found to possess a UBA or UBX domain, which are found in various proteins involved in the ubiquitin-related pathway. We name this newly found homologous region the PUB (Peptide:N-glycanase/UBA or UBX-containing proteins) domain and propose that this domain may mediate protein-protein interactions.

  14. Pathway to a Phenocopy: Heat Stress Effects in Early Embryogenesis

    PubMed Central

    Crews, Sarah M.; McCleery, W. Tyler; Hutson, M. Shane

    2015-01-01

    Background Heat shocks applied at the onset of gastrulation in early Drosophila embryos frequently lead to phenocopies of U-shaped mutants – having characteristic failures in the late morphogenetic processes of germband retraction and dorsal closure. The pathway from non-specific heat stress to phenocopied abnormalities is unknown. Results Drosophila embryos subjected to 30-min, 38-°C heat shocks at gastrulation appear to recover and restart morphogenesis. Post-heat-shock development appears normal, albeit slower, until a large fraction of embryos develop amnioserosa holes (diameters > 100 μm). These holes are positively correlated with terminal U-shaped phenocopies. They initiate between amnioserosa cells and open over tens of minutes by evading normal wound healing responses. They are not caused by tissue-wide increases in mechanical stress or decreases in cell-cell adhesion, but instead appear to initiate from isolated apoptosis of amnioserosa cells. Conclusions The pathway from heat shock to U-shaped phenocopies involves the opening of one or more large holes in the amnioserosa that compromise its structural integrity and lead to failures in morphogenetic processes that rely on amnioserosa-generated tensile forces. The proposed mechanism by which heat shock leads to hole initiation and expansion is heterochonicity – i.e., disruption of morphogenetic coordination between embryonic and extra-embryonic cell types. PMID:26498920

  15. Pathway to a phenocopy: Heat stress effects in early embryogenesis.

    PubMed

    Crews, Sarah M; McCleery, W Tyler; Hutson, M Shane

    2016-03-01

    Heat shocks applied at the onset of gastrulation in early Drosophila embryos frequently lead to phenocopies of U-shaped mutants-having characteristic failures in the late morphogenetic processes of germband retraction and dorsal closure. The pathway from nonspecific heat stress to phenocopied abnormalities is unknown. Drosophila embryos subjected to 30-min, 38 °C heat shocks at gastrulation appear to recover and restart morphogenesis. Post-heat-shock development appears normal, albeit slower, until a large fraction of embryos develop amnioserosa holes (diameters > 100 µm). These holes are positively correlated with terminal U-shaped phenocopies. They initiate between amnioserosa cells and open over tens of minutes by evading normal wound healing responses. They are not caused by tissue-wide increases in mechanical stress or decreases in cell-cell adhesion, but instead appear to initiate from isolated apoptosis of amnioserosa cells. The pathway from heat shock to U-shaped phenocopies involves the opening of one or more large holes in the amnioserosa that compromise its structural integrity and lead to failures in morphogenetic processes that rely on amnioserosa-generated tensile forces. The proposed mechanism by which heat shock leads to hole initiation and expansion is heterochonicity, i.e., disruption of morphogenetic coordination between embryonic and extra-embryonic cell types. © 2015 Wiley Periodicals, Inc.

  16. Neuron-glia interactions through the Heartless FGF receptor signaling pathway med