Sample records for interactive identification key

  1. Non-Interactive Key Exchange and Key Assignment Schemes

    E-print Network

    Paterson, Kenny

    -interactive key exchange (NIKE) scheme allows two users to compute a unique shared key without any interaction's public key pkB, along with some public parameters. We provide different security models for NIKE introduce arbitrary public keys in the system. We give constructions for secure NIKE, with respect to those

  2. Molecular identification key of the family Streptococcaceae.

    PubMed

    Kanyó, István; Nagy, Dénes

    2014-03-01

    The gene order conservation (GOC) between the species of family Streptococcaceae was analysed. The rate of GOC in the strains belonging to the same species is 70% or more. When we compared different species belonging to the same genus, the rate of GOC was 30-47% while it was below 20% when the species were from different genera. A molecular identification key was established for identifying those genera and species within the family Streptococcaceae which have an already known full genome sequence (24 Streptococcus and 2 Lactococcus species). Identical genome parts of the species belonging to the same genus were used for determination of genera. These are the sections surrounding the replication origin dnaA, the sequence from gene phaB to the gene accA, and the sequence of alr acpS secA. Sections around the genes pepX, leuS and rplM were used for identifying the species. The gene order analysis and data in molecular identification key showed that S. uberis and S. parauberis also belong to the same species, and our suggestion for their new names is S. uberis subsp. uberis and S uberis subsp. parauberis. Based on this data, a new definition of bacterial species is proposed: two isolates belong to the same species if the order of the genes in their genomes is almost identical. PMID:24631752

  3. Weed Identification: Using Plant Structures as a Key 

    E-print Network

    Baumann, Paul A.

    2002-04-15

    Weed identification is necessary to the success of any weed control program. Frequently, simple plant keys or "picture book identification guides are used to identify weeds. This handbook, which identifies and labels plant structures, can help one...

  4. Weed Identification: Using Plant Structures as a Key (Spanish) 

    E-print Network

    Baumann, Paul A.

    1999-08-30

    Weed identification is necessary to the success of any weed control program. Frequently, simple plant keys or "picture book identification guides are used to identify weeds. This handbook, which identifies and labels plant structures, is intended...

  5. Research on Identification Method of Key Customer Based on CRM

    Microsoft Academic Search

    Yanhui Wang

    2010-01-01

    The thesis first defined the conception of key customer, then set up key customer identification method based on customer value, customer loyalty degree and customer polymerization degree. The method adopted the analytic hierarchy process method to determine the weight of each index. The key customer is classified into three kinds, which include not only single key customers, but also the

  6. Customer satisfaction analysis: Identification of key drivers

    Microsoft Academic Search

    W. Michael Conklin; Ken Powaga; Stan Lipovetsky

    2004-01-01

    A problem of identifying key drivers in customer satisfaction analysis is considered in relation to Kano theory on the relationship between product quality and customer satisfaction using tools from Cooperative Game Theory and Risk Analysis. We use Shapley Value and Attributable Risk techniques to identify priorities of key drivers of customer satisfaction, or key dissatisfiers and key enhancers. We demonstrate

  7. A visual identification key utilizing both gestalt and analytic approaches to identification of Carices present in North America (Plantae, Cyperaceae)

    PubMed Central

    2013-01-01

    Abstract Images are a critical part of the identification process because they enable direct, immediate and relatively unmediated comparisons between a specimen being identified and one or more reference specimens. The Carices Interactive Visual Identification Key (CIVIK) is a novel tool for identification of North American Carex species, the largest vascular plant genus in North America, and two less numerous closely-related genera, Cymophyllus and Kobresia. CIVIK incorporates 1288 high-resolution tiled image sets that allow users to zoom in to view minute structures that are crucial at times for identification in these genera. Morphological data are derived from the earlier Carex Interactive Identification Key (CIIK) which in turn used data from the Flora of North America treatments. In this new iteration, images can be viewed in a grid or histogram format, allowing multiple representations of data. In both formats the images are fully zoomable. PMID:24723777

  8. Non-interactive Public-Key Cryptography

    Microsoft Academic Search

    Ueli M. Maurer; Yacov Yacobi

    1991-01-01

    An identity-based non-interactive public key distribution system is presented that is based on a novel trapdoor one-way function\\u000a allowing a trusted authority to compute the discrete logarithm of a given number modulo a publicly known composite number\\u000a m while this is infeasible for an adversary not knowing the factorization of m. Without interaction with a key distribution center or with

  9. Key Personnel: Identification and Assessment of Turnover Risk Craig Schreiber

    E-print Network

    Sadeh, Norman M.

    , Pennsylvania 15213 Tel: (412) 268-7527 Email: craigs@andrew.cmu.edu Keywords: Key Personnel, Turnover, HumanKey Personnel: Identification and Assessment of Turnover Risk Craig Schreiber Kathleen Carley. ______________________________________________________________ Contact: Craig Schreiber Institute for Software Research, International Center for the Computational

  10. XKey: A tool for the generation of identification keys

    Microsoft Academic Search

    M. Delgado Calvo-Flores; W. Fajardo Contreras; E. L. Gibaja Galindo; R. Perez-Perez

    This paper presents the development of XKey, a tool for generating taxonomical identification keys by means of decision tree construction. The tool is based on an XML standard for the representation of general taxonomical information, which makes it ideal for different fields of application. The article analyses the problem by examining the adaptation of machine learning techniques to the sphere

  11. An interactive key to the Chrysochromulina species (Haptophyta) described in the literature

    PubMed Central

    Chrétiennot-Dinet, Marie-Josèphe; Desreumaux, Nicolas; Vignes-Lebbe, Régine

    2014-01-01

    Abstract We present a general overview of features and technical specifications of an original interactive key web application for the identification of Chrysochromulina species. The list of species, originally described as belonging in the genus Chrysochromulina, is given and recent taxonomic changes in species and genera of the order Prymnesiales are provided. We briefly discuss the interest of such a key for the identification of phytoplanktonic species. PMID:24596492

  12. Identification key for coryneform bacteria derived by numerical taxonomic studies.

    PubMed

    Seiler, H

    1983-05-01

    Six main groups were formed from a complete linkage dendrogram on 557 bacteria tested for 53 physiological features. The organisms were obtained from culture collections and included representatives of the following genera: Arthrobacter, Brevibacterium, Caseobacter, Cellulomonas, Corynebacterium, Curtobacterium, Micrococcus, Microbacterium, Mycobacterium, Nocardia, Oerskovia and Rhodococcus. The six groups were individually subjected to a numerical taxonomic analysis based on linkage maps, which resulted in a total of 33 subclusters. An identification key to determine the affiliation of the bacteria to the six main clusters and five group-specific schemes is presented. Reference strains are proposed for the 33 subclusters. PMID:6413644

  13. Interaction: The Key to Successful Distance Learning.

    ERIC Educational Resources Information Center

    Byers, Al

    This paper discusses the impediments to distance education (DE) programs and the critical value of interaction and dialog in DE learning environments. The types of interaction to be considered when designing a DE program are listed, including interaction to increase learning, to increase participation, to develop communication, to receive…

  14. Hyperfine interactions, the key to multiquark physics

    SciTech Connect

    Likpink, H.J.

    1988-08-08

    Clues in the search for a fundamental description of hadron physics based on QCD may be obtained from a phenomenological constituent quark model in which the color-electric force binds quarks into saturated color-singlet hadrons, and finer details of the spectrum and multiquark physics are dominated by the color-magnetic hyperfine interaction. 47 refs.

  15. Identification of key recombinants in multiplex SMA families

    SciTech Connect

    Van Der Steege, G.; Cobben, J.M.; Osinga, J. [Univ. of Groningen (Netherlands)] [and others] [Univ. of Groningen (Netherlands); and others

    1994-07-01

    Recent reports have provided evidence that a major gene for autosomal recessive proximal spinal muscular atrophy (SMA) resides in a small genetic interval in bands q12-q13 of chromosome 5, a 4-cM region proximally flanked by D5S125 (EF(TG/AG)n) and distally by MAP1B/D5S112 or a 0.7-cM interval (range 0.1-2.1 cM) flanked by D5S435 proximally and MAP1B/D5S112 distally. The authors present the identification of key recombinants between SMA and the closest flanking DNA-markers in an analysis of Dutch and Italian SMA families. These crossovers may serve as reference points for new markers in this region and may thus be instrumental in a further refined mapping of the SMA gene. Two markers, D5S351 (I105) and D5S357 (Mfd151), could be mapped distally to SMA in the interval SMA-D5S112. 26 refs., 3 figs., 1 tab.

  16. INTERACTIVITY IS THE KEY William Hibbard and David Santek

    E-print Network

    Martin, Jonathan E.

    INTERACTIVITY IS THE KEY William Hibbard and David Santek Space Science and Engineering CenterORDS." Interactive, texture mapping, volume image, earth science. INTRODUCTION At the Space Science and Engineering such data sets, as part of the Space Science and Engineering Center's Man- computer Interactive Data Access

  17. PLANTMICROBEINSECT INTERACTIONS: Cytokinins as key regulators in plantmicrobeinsect

    E-print Network

    Giron, David - Institut de Recherche sur la Biologie de l'Insecte, Université François Rabelais

    PLANT­MICROBE­INSECT INTERACTIONS: Cytokinins as key regulators in plant. Cytokinins are plant hormones that play a key role in plant morphology, plant defence, leaf senescence/or morphology and successfully invade the plant. In the case of arthropods, cytokinin-induced phenotypes can

  18. Case Study 1: Determining Key Binding Interactions Between the Neurotransmitter

    E-print Network

    Stoltz, Brian M.

    Case Study 1: Determining Key Binding Interactions Between the Neurotransmitter and the Receptor ·Neurotransmitters generally carry a positive charge ·We have established that in several systems, that positive - the neurotransmitter - is ACh The nAChR also responds to nicotine, and the initial chemical event in nicotine addiction

  19. Identification of a Key Structural Element for Protein Folding Within b-Hairpin Turns

    E-print Network

    Blaber, Michael

    Identification of a Key Structural Element for Protein Folding Within b-Hairpin Turns Jaewon Kim position in defined b-hairpin turns within human acidic fibroblast growth factor, and demonstrate identified that Gly at the i þ 3 position within a subset of b-hairpin turns is a key contributor towards

  20. [Impact of interactivity on identification with characters in fiction].

    PubMed

    Soto-Sanfiel, María T; Aymerich-Franch, Laura; Ribes Guàrdia, Francesc Xavier

    2010-11-01

    The effect of interactivity on identification with characters in audiovisual fiction was observed. 310 participants were asked to watch a film in one of these two conditions: 1) interactive (they selected the plot), and 2) non-interactive (they consumed the fiction in a conventional way). After watching the movie, they completed a questionnaire with the EDI scale of identification and empathy with characters, created by Igartua and Paez. The capacity to intervene in the configuration of the plot (interactivity) affected identification with characters. The results provide data about the psychology of media and interactivity in communication and allow us to understand the processes of empathy and identification with characters. PMID:21044519

  1. A Key for the Identification of Eighteen Common Timbers.

    ERIC Educational Resources Information Center

    Thomas, P. A.

    1991-01-01

    Dichotomous key for 18 woods in common domestic and architectural use in Britain is provided. It is based upon structures visible with the naked eye and a hand-lens. Descriptions of the necessary anatomy and terminology are given. Timbers include yew, pine, spruce, oak, sweet chestnut, elm, ash, teak, cherry, walnut, mahogany, box, beech,…

  2. Identification of key amino acid residues in Neisseria polysaccharea amylosucrase.

    PubMed

    Sarçabal, P; Remaud-Simeon, M; Willemot, R; Potocki de Montalk, G; Svensson, B; Monsan, P

    2000-05-26

    Amylosucrase from Neisseria polysaccharea catalyzes the synthesis of an amylose-like polymer from sucrose. Sequence alignment revealed that it belongs to the glycoside hydrolase family 13. Site-directed mutagenesis enabled the identification of functionally important amino acid residues located at the active center. Asp-294 is proposed to act as the catalytic nucleophile and Glu-336 as general acid base catalyst in amylosucrase. The conserved Asp-401, His-195 and His-400 residues are critical for the enzymatic activity. These results provide strong support for the predicted close structural and functional relationship between the sucrose-glucosyltransferases and enzymes of the alpha-amylase family. PMID:10828446

  3. Evaluation of per-record identification risk by additive modeling of interaction for contingency table

    E-print Network

    Yamamoto, Hirosuke

    Evaluation of per-record identification risk by additive modeling of interaction for contingency- lation uniqueness of sample unique records in microdata sets. Moment estimation of the Lancaster) of the population uniques among the sample unique records with respect to a given set of key variables

  4. A Molecular Key for the Identification of Blow Flies in Southeastern Nebraska

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The identification of blow flies (Calliphoridae) (typically the first colonizers of cadavers) is difficult, especially in the earlier instars because of their small size, similarity and simplicity in external morphology. We consider how taxonomic keys based on molecular genetic data facilitate accur...

  5. Bacteria and Archaea in acidic environments and a key to morphological identification

    USGS Publications Warehouse

    Robbins, E.I.

    2000-01-01

    Natural and anthropogenic acidic environments are dominated by bacteria and Archaea. As many as 86 genera or species have been identified or isolated from pH <4.5 environments. This paper reviews the worldwide literature and provide tables of morphological characteristics, habitat information and a key for light microscope identification for the non-microbiologist.

  6. Identification of key players for the impact of perturbations in food webs

    E-print Network

    Identification of key players for the impact of perturbations in food webs By Helge Aufderheide1, complex system to a perturba- tion. Recent attempts to predict the behavior of food webs has revealed to efficiently arrive at this solution. Then, in our assessment of model food webs, we find that it is most

  7. Identification of key clinical phenotypes of breast cancer using a reduced panel

    E-print Network

    Aickelin, Uwe

    Identification of key clinical phenotypes of breast cancer using a reduced panel of protein D Macmillan6 , J M Garibaldi3,4 , G R Ball5 and I O Ellis1,2 1 Breast Cancer Pathology Research, Nottingham University Hospitals NHS Trust, Nottingham, UK Background: Breast cancer is a heterogeneous

  8. Bioactive nanofibers enable the identification of thrombospondin 2 as a key player in enamel regeneration.

    PubMed

    Huang, Zhan; Newcomb, Christina J; Lei, Yaping; Zhou, Yan; Bornstein, Paul; Amendt, Brad A; Stupp, Samuel I; Snead, Malcolm L

    2015-08-01

    Tissue regeneration and development involves highly synchronized signals both between cells and with the extracellular environment. Biomaterials can be tuned to mimic specific biological signals and control cell response(s). As a result, these materials can be used as tools to elucidate cell signaling pathways and candidate molecules involved with cellular processes. In this work, we explore enamel-forming cells, ameloblasts, which have a limited regenerative capacity. By exposing undifferentiated cells to a self-assembling matrix bearing RGDS epitopes, we elicited a regenerative signal at will that subsequently led to the identification of thrombospondin 2 (TSP2), an extracellular matrix protein that has not been previously recognized as a key player in enamel development and regeneration. Targeted disruption of the thrombospondin 2 gene (Thbs2) resulted in enamel formation with a disordered architecture that was highly susceptible to wear compared to their wild-type counterparts. To test the regenerative capacity, we injected the bioactive matrix into the enamel organ and discovered that the enamel organic epithelial cells in TSP-null mice failed to polarize on the surface of the artificial matrix, greatly reducing integrin ?1 and Notch1 expression levels, which represent signaling pathways known to be associated with TSP2. These results suggest TSP2 plays an important role in regulating cell-matrix interactions during enamel formation. Exploiting the signaling pathways activated by biomaterials can provide insight into native signaling mechanisms crucial for tooth development and cell-based strategies for enamel regeneration. PMID:26004236

  9. Interaction of key pathways in sorafenib-treated hepatocellular carcinoma based on a PCR-array

    PubMed Central

    Liu, Yan; Wang, Ping; Li, Shijie; Yin, Linan; Shen, Haiyang; Liu, Ruibao

    2015-01-01

    This study aimed to identify the key pathways and to explore the mechanism of sorafenib in inhibiting hepatocellular carcinoma (HCC). The gene expression profile of GSE33621, including 6 sorafenib treated group and 6 control samples, was downloaded from the GEO (Gene Expression Omnibus) database. The differentially expressed genes (DEGs) in HCC samples were screened using the ??Ct method with the homogenized internal GAPDH. Also, the functions and pathways of DEGs were analyzed using the DAVID. Moreover, the significant pathways of DEGs that involved in HCC were analyzed based on the Latent pathway identification analysis (LPIA). A total of 44 down-regulated DEGs were selected in HCC samples. Also, there were 84 biological pathways that these 44 DEGs involved in. Also, LPIA showed that Osteoclast differentiation and hsa04664-Fc epsilon RI signaling pathway was the most significant interaction pathways. Moreover, Apoptosis, Toll-like receptor signaling pathway, Chagas disease, and T cell receptor signaling pathway were the significant pathways that interacted with hsa04664. In addition, DEGs such as AKT1 (v-akt murine thymoma viral oncogene homolog 1), TNF (tumor necrosis factor), SYK (spleen tyrosine kinase), and PIK3R1 (phosphoinositide-3-kinase, regulatory subunit 1 (alpha)) were the common genes that involved in the significant pathways. Several pathway interaction pairs that caused by several downregulated genes such as SYK, PI3K, AKT1, and TNF, were identified play curial role in sorafenib treated HCC. Sorafenib played important inhibition roles in HCC by affecting a complicate pathway interaction network.

  10. The Interactive Routine as Key Construct in Theories of Interactive Behavior Wayne D. Gray (grayw@rpi.edu)

    E-print Network

    Gray, Wayne

    The Interactive Routine as Key Construct in Theories of Interactive Behavior Wayne D. Gray (grayw together in dependency networks of constraints to form interactive routines (Gray, Sims, Fu, & Schoelles, 2006). Interactive behavior proceeds by selecting one interactive routine after another or by selecting

  11. Dynamic, non-interactive key management for the bundle protocol

    Microsoft Academic Search

    William L. Van Besien

    2010-01-01

    Secure, low-overhead key establishment is crucial to maintaining the high level of trust and security that are required many types of Delay Tolerant Networks. Existing schemes for key negotiation and exchange that are currently in use on the Internet often cannot scale to meet the environmental and technical constraints of many Delay Tolerant Networks. The few works presenting solutions to

  12. Sea snakes in Australian waters (Serpentes: subfamilies Hydrophiinae and Laticaudinae)-a review with an updated identification key.

    PubMed

    Rasmussen, Arne Redsted; Sanders, Kate Laura; Guinea, Michael L; Amey, Andrew P

    2014-01-01

    Sea snakes (Elapidae, subfamilies Hydrophiinae and Laticaudinae) reach high species richness in the South China Sea and in the Australian region; however, most countries in the two regions still lack up-to-date checklists and identification tools for these snakes. We present an updated reviewed checklist and a new complete identification key to sea snakes in Australian waters. The identification key includes 29 species documented and 4 possibly occurring taxa and is based mostly on easy-to-use external characters. We find no evidence for breeding populations of Laticauda in Australian waters, but include the genus on the list of possibly occurring taxa.  PMID:25283923

  13. Interaction in Teleconferencing: The Key to Quality Instruction.

    ERIC Educational Resources Information Center

    Kruh, Janet J.; Murphy, Karen L.

    This paper examines classroom strategies for distance learning. It discusses the importance of participant interaction in all learning, and offers examples of interactive distance-learning situations. Focusing on interaction of learning, the paper is intended to assist public schools in assessing various distance-learning programs, including…

  14. Emotional Identification with Teacher Identities in Student Teachers' Narrative Interaction

    ERIC Educational Resources Information Center

    Karlsson, Marie

    2013-01-01

    The paper suggests that narrative interaction in student teacher peer groups is an important context for emotional identification with culturally available teacher identities. It addresses issues pointed out as problematic in research on teacher identity formation: focus on the individual and the underestimation of context. A positioning analysis…

  15. Children's Wishful Identification and Parasocial Interaction with Favorite Television Characters.

    ERIC Educational Resources Information Center

    Hoffner, Cynthia

    1996-01-01

    Interviewed about favorite TV characters, 91% of boys and 53% of girls ages 7-12 chose same-sex favorites. For male characters, wishful identification was predicted by intelligence and (for girls only) humor; parasocial interaction was predicted by intelligence, attractiveness, and (for boys only) strength. For female characters (chosen only by…

  16. Disease candidate gene identification and prioritization using protein interaction networks

    Microsoft Academic Search

    Jing Chen; Bruce J. Aronow; Anil G. Jegga

    2009-01-01

    BACKGROUND: Although most of the current disease candidate gene identification and prioritization methods depend on functional annotations, the coverage of the gene functional annotations is a limiting factor. In the current study, we describe a candidate gene prioritization method that is entirely based on protein-protein interaction network (PPIN) analyses. RESULTS: For the first time, extended versions of the PageRank and

  17. Manoeuvring Ship Model Identification and Interacting Multiple Model Tracking Algorithm

    E-print Network

    Mihaylova, Lyudmila

    Manoeuvring Ship Model Identification and Interacting Multiple Model Tracking Algorithm Design 1/95 with Bulgarian Science Fund. Abstract. Precise discrete models of the manoeuvring ship motion and xtended Kalman target motions [2, 5, 8] do not describe the nonlinear specificity of the manoeuvring ship. To solve

  18. PLANT-MICROBE-INSECT INTERACTIONS Cytokinins as key regulators in plantmicrobeinsect

    E-print Network

    Giron, David - Institut de Recherche sur la Biologie de l'Insecte, Université François Rabelais

    PLANT-MICROBE-INSECT INTERACTIONS Cytokinins as key regulators in plant­microbe­insect interactions the energetic requirements of the direct defence. 3. Cytokinins are plant hormones that play a key role in plant physiology and/or morphology and successfully invade the plant. In the case of arthropods, cytokinin

  19. Diptera of forensic importance in the Iberian Peninsula: larval identification key.

    PubMed

    Velásquez, Y; Magaña, C; Martínez-Sánchez, A; Rojo, S

    2010-09-01

    A revision of the species and families of sarcosaprophagous flies (Diptera: Calliphoridae, Sarcophagidae, Muscidae, Fanniidae, Drosophilidae, Phoridae, Piophilidae and Stratiomyidae) suitable for forensic purposes in the Iberian Peninsula is presented. Morphological characteristics that allow the accurate identification of third instars of the species present in the Iberian Peninsula are described and presented in the form of a diagnostic key. For larval Calliphoridae, characteristics such as the spines of the body segments were useful for the genus Calliphora whereas features of the anal segment and the cephalopharyngeal skeleton were useful for larvae of Lucilia. Identification of three Chrysominae species present in the Iberian Peninsula is included. For larval Sarcophagidae, characters such as the arrangement and shape of spiracular openings, structures of the anal segment and the cephalopharyngeal skeleton were used for the first time. A new record of Sarcophaga cultellata Pandellé, from a human corpse, is also included as well as recent incursions into the European cadaveric entomofauna such as Synthesiomyia nudiseta (van der Wulp) and Hermetia illucens (Linnaeus). This work provides useful new information that could be applied to forensic investigations in the Iberian Peninsula and in southern Europe. PMID:20557457

  20. Understanding Dengue Virus Capsid Protein Interaction with Key Biological Targets

    PubMed Central

    Faustino, André F.; Martins, Ivo C.; Carvalho, Filomena A.; Castanho, Miguel A. R. B.; Maurer-Stroh, Sebastian; Santos, Nuno C.

    2015-01-01

    Dengue virus (DENV) causes over 500,000 hospitalizations and 20,000 deaths worldwide every year. Dengue epidemics now reach temperate regions due to globalization of trade and travel and climate changes. Currently, there are no successful therapeutic or preventive approaches. We previously developed a peptide drug lead, pep14-23, that inhibits the biologically relevant interaction of DENV capsid (C) protein with lipid droplets (LDs). Surprisingly, pep14-23 also inhibits DENV C interaction with very low-density lipoproteins (VLDL). We thus investigated the similarity between the proposed DENV C molecular targets in LDs and VLDL, respectively, the proteins perilipin 3 (PLIN3) and apolipoprotein E (APOE). APOE N-terminal and PLIN3 C-terminal regions are remarkably similar, namely APOE ?-helix 4 (APOE?4) and PLIN3 ?-helix 5 (PLIN3?5) sequences, which are also highly superimposable structurally. Interestingly, APOE ?-helical N-terminal sequence and structure superimposes with DENV C ?-helices ?1 and ?2. Moreover, the DENV C hydrophobic cleft can accommodate the structurally analogous APOE?4 and PLIN3?5 helical regions. Mirroring DENV C-LDs interaction (previously shown experimentally to require PLIN3), we experimentally demonstrated that DENV C-VLDL interaction requires APOE. Thus, the results fit well with previous data and suggest future drug development strategies targeting the above mentioned ?-helical structures. PMID:26161501

  1. Understanding Dengue Virus Capsid Protein Interaction with Key Biological Targets.

    PubMed

    Faustino, André F; Martins, Ivo C; Carvalho, Filomena A; Castanho, Miguel A R B; Maurer-Stroh, Sebastian; Santos, Nuno C

    2015-01-01

    Dengue virus (DENV) causes over 500,000 hospitalizations and 20,000 deaths worldwide every year. Dengue epidemics now reach temperate regions due to globalization of trade and travel and climate changes. Currently, there are no successful therapeutic or preventive approaches. We previously developed a peptide drug lead, pep14-23, that inhibits the biologically relevant interaction of DENV capsid (C) protein with lipid droplets (LDs). Surprisingly, pep14-23 also inhibits DENV C interaction with very low-density lipoproteins (VLDL). We thus investigated the similarity between the proposed DENV C molecular targets in LDs and VLDL, respectively, the proteins perilipin 3 (PLIN3) and apolipoprotein E (APOE). APOE N-terminal and PLIN3 C-terminal regions are remarkably similar, namely APOE ?-helix 4 (APOE?4) and PLIN3 ?-helix 5 (PLIN3?5) sequences, which are also highly superimposable structurally. Interestingly, APOE ?-helical N-terminal sequence and structure superimposes with DENV C ?-helices ?1 and ?2. Moreover, the DENV C hydrophobic cleft can accommodate the structurally analogous APOE?4 and PLIN3?5 helical regions. Mirroring DENV C-LDs interaction (previously shown experimentally to require PLIN3), we experimentally demonstrated that DENV C-VLDL interaction requires APOE. Thus, the results fit well with previous data and suggest future drug development strategies targeting the above mentioned ?-helical structures. PMID:26161501

  2. A Key n ? ?* Interaction in N-Acyl Homoserine Lactones

    PubMed Central

    Newberry, Robert W.; Raines, Ronald T.

    2014-01-01

    Many Gram-negative bacteria employ N-acyl homoserine lactones (AHLs) as signal molecules for quorum sensing. The binding of AHLs to their target LuxR-type receptor proteins can effect changes in growth, virulence, and other phenotypes. LuxR-type receptors therefore present attractive pharmaceutical targets for control of bacterial pathogenesis. Here, we present X-ray crystallographic and computational evidence that the conformation of free AHLs is biased away from the conformation observed when bound to their cognate receptor due to the influence of an n??* interaction. In this n??* interaction, the p-type lone pair (n) of the N-acyl oxygen overlaps with the ?* orbital of the lactone carbonyl group. This overlap results in the release of approximately 0.64 kcal/mol of energy. We also show that this interaction can be attenuated by installing electron-withdrawing groups on the N-acyl chain. Modulating this previously unappreciated interaction could present a new avenue towards effective inhibitors of bacterial quorum sensing. PMID:24556113

  3. Key Role of Hydrodynamic Interactions in Colloidal Gelation

    Microsoft Academic Search

    Akira Furukawa; Hajime Tanaka

    2010-01-01

    Colloidal gelation is caused by the formation of a percolated network of colloidal particles suspended in a liquid. Thus far the major transport process leading to gelation has been believed to be the Brownian diffusion of particles. Contrary to this common belief, we reveal by numerical simulations that many-body hydrodynamic interactions between colloidal particles also play an essential role in

  4. Universally Composable Non-Interactive Key Exchange Eduarda S.V. Freire1

    E-print Network

    consider the notion of a non-interactive key exchange (NIKE). A NIKE scheme allows a party A to compute requires no interaction between A and B, a feature which distinguishes NIKE from regular (i.e., interactive is a formalization of NIKE protocols as ideal functionalities in the Universal Composability (UC) framework. As we

  5. On-line identification of interacting two-tank system

    Microsoft Academic Search

    Sea Cheon Oh; Yeong-Koo Yeo

    1996-01-01

    In order to demonstrate the effectiveness of the process identification algorithm, on-line parameter estimator is evaluated\\u000a experimentally by using two-tank system with interaction. On-line parameter estimator used in this paper is based on a recursive\\u000a parameter estimation algorithm. MIMO linear, bilinear and quadratic models based on ARMA model are used to identify two-tank\\u000a system. A quadratic model for two-tank system

  6. Identification of Modules in Protein-Protein Interaction Networks

    Microsoft Academic Search

    Sinan Erten; Mehmet Koyutürk

    2011-01-01

    \\u000a In biological systems, most processes are carried out through orchestration of multiple interacting molecules. These interactions\\u000a are often abstracted using network models. A key feature of cellular networks is their modularity, which contributes significantly\\u000a to the robustness, as well as adaptability of biological systems. Therefore, modularization of cellular networks is likely\\u000a to be useful in obtaining insights into the working

  7. Key role of hydrodynamic interactions in colloidal gelation.

    PubMed

    Furukawa, Akira; Tanaka, Hajime

    2010-06-18

    Colloidal gelation is caused by the formation of a percolated network of colloidal particles suspended in a liquid. Thus far the major transport process leading to gelation has been believed to be the brownian diffusion of particles. Contrary to this common belief, we reveal by numerical simulations that many-body hydrodynamic interactions between colloidal particles also play an essential role in gelation: They significantly promote gelation, or lower the colloid volume fraction threshold for percolation, as compared to their absence. We find that the incompressible nature of a liquid component and the resulting self-organization of hydrodynamic flow with a transverse (rotational) character are responsible for this enhancement of network-forming ability. PMID:20867312

  8. Key Role of Hydrodynamic Interactions in Colloidal Gelation

    NASA Astrophysics Data System (ADS)

    Furukawa, Akira; Tanaka, Hajime

    2010-06-01

    Colloidal gelation is caused by the formation of a percolated network of colloidal particles suspended in a liquid. Thus far the major transport process leading to gelation has been believed to be the Brownian diffusion of particles. Contrary to this common belief, we reveal by numerical simulations that many-body hydrodynamic interactions between colloidal particles also play an essential role in gelation: They significantly promote gelation, or lower the colloid volume fraction threshold for percolation, as compared to their absence. We find that the incompressible nature of a liquid component and the resulting self-organization of hydrodynamic flow with a transverse (rotational) character are responsible for this enhancement of network-forming ability.

  9. The Identification of Key Issues in the Development of Sustainable e-Learning and Virtual Campus Initiatives

    ERIC Educational Resources Information Center

    Stansfield, Mark; Connolly, Thomas; Cartelli, Antonio; Jimoyiannis, Athanassios; Magalhaes, Hugo; Maillet, Katherine

    2009-01-01

    This paper explores a number of key issues that have been identified as being important in the identification and evaluation of best practice within the context of e-learning and virtual campuses. The "Promoting Best Practice in Virtual Campuses" (PBP-VC) project is a two year European Commission Education Audiovisual and Culture Executive Agency…

  10. Data publication and dissemination of interactive keys under the open access model

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The concepts of publication, citation and dissemination of interactive keys and other online keys are discussed and illustrated by a sample paper published in the present issue (doi: 10.3897/zookeys.21.271). The present model is based on previous experience with several existing examples of publishi...

  11. Identification of chikungunya virus interacting proteins in mammalian cells.

    PubMed

    Paingankar, Mandar S; Arankalle, Vidya A

    2014-06-01

    Identification and characterization of virus host interactions is an essential step for the development of novel antiviral strategies. Very few studies have been targeted towards identification of chikungunya virus (CHIKV) interacting host proteins. In current study, virus overlay protein binding assay (VOPBA) and matrix-assisted laser desorption/ ionization time of flight analysis (MALDI TOF/TOF) were employed for the identification of CHIKV binding proteins in mammalian cells. HSP70 and actin were identified as virus binding proteins in HEK-293T and Vero-E6 cells, whereas STAT-2 was identified as an additional protein in Vero-E6 cells. Pre-incubation with anti-HSP70 antibody and miRNA silencing of HSP70 significantly reduced the CHIKV production in HEK-293T and Vero-E6 cells at early time points. These results suggest that CHIKV exploits the housekeeping molecules such as actin, HSP70 and STAT-2 to establish infection in the mammalian cells. PMID:24845503

  12. Constructing Compact Takagi-Sugeno Rule Systems: Identification of Complex Interactions in Epidemiological Data

    PubMed Central

    Zhou, Shang-Ming; Lyons, Ronan A.; Brophy, Sinead; Gravenor, Mike B.

    2012-01-01

    The Takagi-Sugeno (TS) fuzzy rule system is a widely used data mining technique, and is of particular use in the identification of non-linear interactions between variables. However the number of rules increases dramatically when applied to high dimensional data sets (the curse of dimensionality). Few robust methods are available to identify important rules while removing redundant ones, and this results in limited applicability in fields such as epidemiology or bioinformatics where the interaction of many variables must be considered. Here, we develop a new parsimonious TS rule system. We propose three statistics: R, L, and ?-values, to rank the importance of each TS rule, and a forward selection procedure to construct a final model. We use our method to predict how key components of childhood deprivation combine to influence educational achievement outcome. We show that a parsimonious TS model can be constructed, based on a small subset of rules, that provides an accurate description of the relationship between deprivation indices and educational outcomes. The selected rules shed light on the synergistic relationships between the variables, and reveal that the effect of targeting specific domains of deprivation is crucially dependent on the state of the other domains. Policy decisions need to incorporate these interactions, and deprivation indices should not be considered in isolation. The TS rule system provides a basis for such decision making, and has wide applicability for the identification of non-linear interactions in complex biomedical data. PMID:23272108

  13. The mosquitoes (Diptera: Culidae) of Seychelles: taxonomy, ecology, vectorial importance, and identification keys

    PubMed Central

    2012-01-01

    Background During recent periods, the islands of the Republic of Seychelles experienced many diseases such as dengue, chikungunya, Bancroft’s filaria and malaria. Mosquitoes transmit the agents that cause these diseases. Published information on mosquitoes in the Seychelles is notably dispersed in the literature. The maximum number of species obtained on a single field survey does not exceed 14 species. Methods We performed a comprehensive bibliographic review using mosquito and Seychelles as the key words, as well as conducted a mosquito field survey for larval and adult stages during the rainy season in December 2008. Sixteen sites were sampled on four granitic islands (Mahé, Praslin, La Digue and Aride) and six sites on coralline atolls in the extreme southwest of the country (Aldabra group). Results We found published references to 21 mosquito species identified at least on one occasion in the Seychelles. Our collections comprised 18 species of mosquitoes, all of them from the subfamily Culicinae; no Anophelinae was found. We also confirm that Aedes seychellensis is a junior synonym of Ae. (Aedimorphus) albocephalus. The first records for Culex antennatus and Cx. sunyaniensis are presented from the country, specifically from Aldabra and Praslin, respectively. Based on a comparison of the taxa occurring on the granitic versus coralline islands, only three species, Ae. albocephalus, Cx. scottii and Cx. simpsoni are shared. Aedes albopictus appeared to exclude largely Ae. aegypti on the granitic islands; however, Ae. aegypti was common on Aldabra, where Ae. albopictus has not been recorded. The notable aggressiveness of mosquitoes towards humans on coralline islands was mainly due to two species, the females of which are difficult to distinguish: Ae. fryeri and Ae. (Aedimorphus) sp. A. The number of mosquito species collected at least once in the Seychelles is now 22, among which five species (Ae. (Adm) sp. A, Cx. stellatus, Uranotaenia browni. Ur. nepenthes and Ur. pandani) and one subspecies (Ae. vigilax vansomerenae) are considered as endemic. Two illustrated identification keys, one for adult females and the other for larval stages, are presented. Conclusions The knowledge of the culicidian fauna in the Seychelles has been notably updated. The number of mosquito species is relatively large with regards to land surface and distances to continental Africa, although the anophelines are totally lacking. The complex natural history of mosquitoes in the Seychelles provides examples of both vicariance- and dispersal-mediated divergences. They present superb examples for theoretical and applied island biology. PMID:22999320

  14. Identification of Protein Interactions Involved in Cellular Signaling

    PubMed Central

    Westermarck, Jukka; Ivaska, Johanna; Corthals, Garry L.

    2013-01-01

    Protein-protein interactions drive biological processes. They are critical for all intra- and extracellular functions, and the technologies to analyze them are widely applied throughout the various fields of biological sciences. This study takes an in-depth view of some common principles of cellular regulation and provides a detailed account of approaches required to comprehensively map signaling protein-protein interactions in any particular cellular system or condition. We provide a critical review of the benefits and disadvantages of the yeast two-hybrid method and affinity purification coupled with mass spectrometric procedures for identification of signaling protein-protein interactions. In particular, we emphasize the quantitative and qualitative differences between tandem affinity and one-step purification (such as FLAG and Strep tag) methods. Although applicable to all types of interaction studies, a special section is devoted in this review to aspects that should be considered when attempting to identify signaling protein interactions that often are transient and weak by nature. Finally, we discuss shotgun and quantitative information that can be gleaned by MS-coupled methods for analysis of multiprotein complexes. PMID:23481661

  15. M-ary Shift Keying Modulation Scheme Identification Algorithm Using Wavelet Transform and Higher Order Statistical Moment

    NASA Astrophysics Data System (ADS)

    Prakasam, P.; Madheswaran, M.

    Centre for Advanced Research, Department of Electronics and Communication Engineering, In this study, a modulation identification algorithm for identifying M-ary Shift Keying is developed and described using wavelet Transform to examine histogram peak and 8th order statistical moment. The simulated results show that the exact modulation scheme can be identified for lower SNR. The performance was examined for Additive White Gaussian Noise (AWGN) channel based on the confusion matrix, throughput of the algorithm and the Receiver Operating Characteristics (ROC). When SNR is above 3 dB, the probability of detection is proved to be more than 0.984. The parameters of the developed algorithm has been compared with existing algorithms and found that the proposed algorithm can be considered to be the suitable identification method for M-ary Shift Keying with lower SNR (signal-to-noise ratio).

  16. Why and how might genetic and phylogenetic diversity be reflected in the identification of key biodiversity areas?

    PubMed Central

    Brooks, T. M.; Cuttelod, A.; Faith, D. P.; Garcia-Moreno, J.; Langhammer, P.; Pérez-Espona, S.

    2015-01-01

    Key biodiversity areas' are defined as sites contributing significantly to the global persistence of biodiversity. The identification of these sites builds from existing approaches based on measures of species and ecosystem diversity and process. Here, we therefore build from the work of Sgró et al. (2011 Evol. Appl. 4, 326–337. (doi:10.1111/j.1752-4571.2010.00157.x)) to extend a framework for how components of genetic diversity might be considered in the identification of key biodiversity areas. We make three recommendations to inform the ongoing process of consolidating a key biodiversity areas standard: (i) thresholds for the threatened species criterion currently consider a site's share of a threatened species' population; expand these to include the proportion of the species' genetic diversity unique to a site; (ii) expand criterion for ‘threatened species' to consider ‘threatened taxa’ and (iii) expand the centre of endemism criterion to identify as key biodiversity areas those sites holding a threshold proportion of the compositional or phylogenetic diversity of species (within a taxonomic group) whose restricted ranges collectively define a centre of endemism. We also recommend consideration of occurrence of EDGE species (i.e. threatened phylogenetic diversity) in key biodiversity areas to prioritize species-specific conservation actions among sites. PMID:25561678

  17. Identification of key genes associated with colorectal cancer based on the transcriptional network.

    PubMed

    Chen, Guoting; Li, Hengping; Niu, Xianping; Li, Guofeng; Han, Ning; Li, Xin; Li, Guang; Liu, Yangzhou; Sun, Guixin; Wang, Yong; Li, Zengchun; Li, Qinchuan

    2015-07-01

    Colorectal cancer (CRC) is among the most lethal human cancers, but the mechanism of the cancer is still unclear enough. We aimed to explore the key genes in CRC progression. The gene expression profile (GSE4183) of CRC was obtained from Gene Expression Omnibus database which included 8 normal samples, 15 adenoma samples, 15 CRC samples and 15 inflammatory bowel disease (IBD) samples. Thereinto, 8 normal, 15 adenoma, and 15 CRC samples were chosen for our research. The differentially expressed genes (DEGs) in normal vs. adenoma, normal vs. CRC, and adenoma vs. CRC, were identified using the Wilcoxon test method in R respectively. The interactive network of DEGs was constructed to select the significant modules using the Pearson's correlation. Meanwhile, transcriptional network of DEGs was also constructed using the g: Profiler. Totally, 2,741 DEGs in normal vs. adenoma, 1,484 DEGs in normal vs. CRC, and 396 DEGs in adenoma vs. CRC were identified. Moreover, function analysis of DEGs in each group showed FcR-mediated phagocytosis pathway in module 1, cardiac muscle contraction pathway in module 6, and Jak-STAT signaling pathway in module 19 were also enriched. Furthermore, MZF1 and AP2 were the transcription factor in module 6, with the target SP1, while SP1 was also a transcription in module 20. DEGs like NCF1, AKT, SP1, AP2, MZF1, and TPM might be used as specific biomarkers in CRC development. Therapy targeting on the functions of these key genes might provide novel perspective for CRC treatment. PMID:25613817

  18. Interactive Effects of Work Group and Organizational Identification on Job Satisfaction and Extra-Role Behavior

    ERIC Educational Resources Information Center

    van Dick, Rolf; van Knippenberg, Daan; Kerschreiter, Rudolf; Hertel, Guido; Wieseke, Jan

    2008-01-01

    Past research has focused on the differential relationships of organizational and work group identification with attitudes and behavior. However, no systematic effort has been undertaken yet to explore interactive effects "between" these foci of identification. We predicted that in cases of positive overlap of identifications (i.e. high work group…

  19. Non-Interactive Key Exchange Eduarda S.V. Freire1,

    E-print Network

    -Universit¨at Bochum Abstract Non-interactive key exchange (NIKE) is a fundamental but much-overlooked cryp- tographic primitive. It appears as a major contribution in the ground-breaking paper of Diffie and Hellman, but NIKE for this primitive and explore the relationships between them. We then give constructions for secure NIKE

  20. Sakai-Ohgishi-Kasahara Non-Interactive Identity-Based Key Exchange Scheme, Revisited

    E-print Network

    -interactive key exchange (IB-NIKE) is a powerful but a bit over- looked primitive in identity-based cryptography decades, IB-NIKE has re- mained largely unstudied. Currently, there are only few IB-NIKE schemes in the literature. Among them, Sakai-Ohgishi-Kasahara (SOK) scheme is the first efficient and secure IB- NIKE scheme

  1. Adaptive Multiparty Non-interactive Key Exchange Without Setup In The Standard Model

    E-print Network

    Abstract Non-interactive key exchange (NIKE) is a fundamental notion in Cryptography. This notion was introduced by Diffie and Hellman in 1976. They proposed the celebrated 2-party NIKE protocol and left open as a fascinating question, whether NIKE could be realized in the mul- tiparty setting. NIKE has since then been

  2. Guide and keys for the identification of Syllidae (Annelida, Phyllodocida) from the British Isles (reported and expected species)

    PubMed Central

    San Martín, Guillermo; Worsfold, Tim M.

    2015-01-01

    Abstract In November 2012, a workshop was carried out on the taxonomy and systematics of the family Syllidae (Annelida: Phyllodocida) at the Dove Marine Laboratory, Cullercoats, Tynemouth, UK for the National Marine Biological Analytical Quality Control (NMBAQC) Scheme. Illustrated keys for subfamilies, genera and species found in British and Irish waters were provided for participants from the major national agencies and consultancies involved in benthic sample processing. After the workshop, we prepared updates to these keys, to include some additional species provided by participants, and some species reported from nearby areas. In this paper, we provide the revised keys to enable rapid identification of Syllidae from the seas around Britain and Ireland. One new combination, Palposyllis propeweismanni, is proposed. PMID:25878521

  3. Guide and keys for the identification of Syllidae (Annelida, Phyllodocida) from the British Isles (reported and expected species).

    PubMed

    San Martín, Guillermo; Worsfold, Tim M

    2015-01-01

    In November 2012, a workshop was carried out on the taxonomy and systematics of the family Syllidae (Annelida: Phyllodocida) at the Dove Marine Laboratory, Cullercoats, Tynemouth, UK for the National Marine Biological Analytical Quality Control (NMBAQC) Scheme. Illustrated keys for subfamilies, genera and species found in British and Irish waters were provided for participants from the major national agencies and consultancies involved in benthic sample processing. After the workshop, we prepared updates to these keys, to include some additional species provided by participants, and some species reported from nearby areas. In this paper, we provide the revised keys to enable rapid identification of Syllidae from the seas around Britain and Ireland. One new combination, Palposyllispropeweismanni, is proposed. PMID:25878521

  4. Freshness-Preserving Non-Interactive Hierarchical Key Agreement Protocol over WHMS

    PubMed Central

    Kim, Hyunsung

    2014-01-01

    The digitization of patient health information (PHI) for wireless health monitoring systems (WHMSs) has brought many benefits and challenges for both patients and physicians. However, security, privacy and robustness have remained important challenges for WHMSs. Since the patient's PHI is sensitive and the communication channel, i.e., the Internet, is insecure, it is important to protect them against unauthorized entities, i.e., attackers. Otherwise, failure to do so will not only lead to the compromise of a patient's privacy, but will also put his/her life at risk. This paper proposes a freshness-preserving non-interactive hierarchical key agreement protocol (FNKAP) for WHMSs. The FNKAP is based on the concept of the non-interactive identity-based key agreement for communication efficiency. It achieves patient anonymity between a patient and physician, session key secrecy and resistance against various security attacks, especially including replay attacks. PMID:25513824

  5. An Identification Key to Rodent Prey in Owl Pellets from the Northwestern and Southeastern United States: Employing Incisor Size to Distinguish among Genera

    ERIC Educational Resources Information Center

    Hager, Stephen B.; Cosentino, Bradley J.

    2006-01-01

    We present an identification key to the common rodent prey found in owl pellets from the Northwestern (NW) and Southeastern (SE) United States that is based on differences in incisor size (arc diameter) among genera.

  6. Rapid identification of chemical genetic interactions in Saccharomyces cerevisiae.

    PubMed

    Dilworth, David; Nelson, Christopher J

    2015-01-01

    Determining the mode of action of bioactive chemicals is of interest to a broad range of academic, pharmaceutical, and industrial scientists. Saccharomyces cerevisiae, or budding yeast, is a model eukaryote for which a complete collection of ~6,000 gene deletion mutants and hypomorphic essential gene mutants are commercially available. These collections of mutants can be used to systematically detect chemical-gene interactions, i.e. genes necessary to tolerate a chemical. This information, in turn, reports on the likely mode of action of the compound. Here we describe a protocol for the rapid identification of chemical-genetic interactions in budding yeast. We demonstrate the method using the chemotherapeutic agent 5-fluorouracil (5-FU), which has a well-defined mechanism of action. Our results show that the nuclear TRAMP RNA exosome and DNA repair enzymes are needed for proliferation in the presence of 5-FU, which is consistent with previous microarray based bar-coding chemical genetic approaches and the knowledge that 5-FU adversely affects both RNA and DNA metabolism. The required validation protocols of these high-throughput screens are also described. PMID:25867090

  7. Hypermedia in the Plant Sciences: The Weed Key and Identification System/Videodisc.

    ERIC Educational Resources Information Center

    Ragan, Lawrence C.

    1991-01-01

    In cooperation with a university educational technology unit, an agronomy professor used hypercard and videodisk technology to develop a computer program for identification of 181 weed species based on user-selected characteristics. This solution was found during a search for a way to organize course content in a concise, manageable system. (MSE)

  8. MOLECULAR TAXONOMIC KEYS – ARE THEY THE SOLUTION FOR SPECIES IDENTIFICATION IN FORENSIC ENTOMOLOGY?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A functional diagnostic technique must have the ability to unambiguously identify and differentiate insect species. Insect species developing in cadavers are often used to estimate the time since death or postmortem interval (PMI). Accurate identification of the species involved is essential, but ex...

  9. Identification of key transcription factors in caerulein?induced pancreatitis through expression profiling data.

    PubMed

    Qi, Dachuan; Wu, Bo; Tong, Danian; Pan, Ye; Chen, Wei

    2015-08-01

    The current study aimed to isolate key transcription factors (TFs) in caerulein?induced pancreatitis, and to identify the difference between wild type and Mist1 knockout (KO) mice, in order to elucidate the contribution of Mist1 to pancreatitis. The gene profile of GSE3644 was downloaded from the Gene Expression Omnibus database then analyzed using the t?test. The isolated differentially expressed genes (DEGs) were mapped into a transcriptional regulatory network derived from the Integrated Transcription Factor Platform database and in the network, the interaction pairs involving at least one DEG were screened. Fisher's exact test was used to analyze the functional enrichment of the target genes. A total of 1,555 and 3,057 DEGs were identified in the wild type and Mist1KO mice treated with caerulein, respectively. DEGs screened in Mist1KO mice were predominantly enriched in apoptosis, mitogen?activated protein kinase signaling and other cancer?associated pathways. A total of 188 and 51 TFs associated with pathopoiesis were isolated in Mist1KO and wild type mice, respectively. Out of the top 10 TFs (ranked by P?value), 7 TFs, including S?phase kinase?associated protein 2 (Skp2); minichromosome maintenance complex component 3 (Mcm3); cell division cycle 6 (Cdc6); cyclin B1 (Ccnb1); mutS homolog 6 (Msh6); cyclin A2 (Ccna2); and cyclin B2 (Ccnb2), were expressed in the two types of mouse. These TFs were predominantly involved in phosphorylation, DNA replication, cell division and DNA mismatch repair. In addition, specific TFs, including minichromosome maintenance complex component 7 (Mcm7); lymphoid?specific helicase (Hells); and minichromosome maintenance complex component 6 (Mcm6), that function in the unwinding of DNA were identified to participate in Mist1KO pancreatitis. The DEGs, including Cdc6, Mcm6, Msh6 and Wdr1 are closely associated with the regulation of caerulein?induced pancreatitis. Furthermore, other identified TFs were also involved in this type of regulation. PMID:25975747

  10. Identification of Key Surface Wind Features Based on Nine Years (2000-2008) of Quick Scat Observations over the Mediterranean Basin

    NASA Astrophysics Data System (ADS)

    Chronis, T.; Papadopoulos, V.; Papadopoulos, A.

    2009-04-01

    Nine years (2000-2008) worth of Quick Scat hi-resolution (12.5x12.5 km) surface wind observations (magnitude and direction) are compiled in order to identify key features with respect to the seasonality of mean and extreme states of the Mediterranean and Black Seas. A key finding pertains to the effect of topography and its interaction to the dominant surface flow and its mean and extreme states. The Gulf of Lion and the Aegean Sea are the regions with consistently higher wind speeds and extreme event frequency occurrence for any given season. The anomalies of the seasonal means over the Central and Eastern Mediterranean can play the role of the predictor for the seasonal extreme event frequency. This contribution aims at the identification of key features of the two basins as well as their multi-disciplinary usage. Furthermore, the Hellenic Center for Marine Research Poseidon buoys are employed to validate Quick Scat surface wind observations over the eastern Mediterranean and the Greek Seas on a high-frequency (e.g. daily) and low frequency (e.g. monthly) basis .

  11. Key for the Identification of Third Instars of European Blowflies (Diptera: Calliphoridae) of Forensic Importance

    Microsoft Academic Search

    Krzysztof Szpila

    \\u000a In Europe larvae of blowflies are the main group of insects responsible for decomposition of exposed vertebrate remains, including\\u000a the human body. This determines their high forensic importance and frequent application for estimation of PMI. The importance\\u000a of proper identification of insects collected in forensic cases and experiments to the species level is underlined by all\\u000a manuals of forensic entomology

  12. Identification of Key Odorants in Withering-Flavored Green Tea by Aroma Extract Dilution Analysis

    NASA Astrophysics Data System (ADS)

    Mizukami, Yuzo; Yamaguchi, Yuichi

    This research aims to identify key odorants in withering-flavored green tea. Application of the aroma extract dilution analysis using the volatile fraction of green tea and withering-flavored green tea revealed 25 and 35 odor-active peaks with the flavor dilution factors of?4, respectively. 4-mercapto-4-methylpentan-2-one, (E)-2-nonenal, linalool, (E,Z)-2,6-nonadienal and 3-methylnonane-2,4-dione were key odorants in green tea with the flavor dilution factor of?16. As well as these 5 odorants, 1-octen-3-one, ?-damascenone, geraniol, ?-ionone, (Z)-methyljasmonate, indole and coumarine contributed to the withering flavor of green tea.

  13. The undecided have the key: Interaction-driven opinion dynamics in a three state model

    E-print Network

    Balenzuela, Pablo; Semeshenko, Viktoriya

    2015-01-01

    The effects of interpersonal interactions on individual's agreements result in a social aggregation process which is reflected in the formation of collective states, as for instance, groups of individuals with a similar opinion about a given issue. This field, which has been a longstanding concern of sociologists and psychologists, has been extended into an area of experimental social psychology, and even has attracted the attention of physicists and mathematicians. In this article, we present a novel model of opinion formation in which agents may either have a strict preference for a choice, or be undecided. The opinion shift emerges during interpersonal communications, as a consequence of a cumulative process of conviction for one of the two extremes opinions through repeated interactions. There are two main ingredients which play key roles in determining the steady state: the initial fraction of undecided agents and the conviction's sensitivity in each interaction. As a function of these two parameters, th...

  14. Identification of key residues for protein conformational transition using elastic network model

    NASA Astrophysics Data System (ADS)

    Su, Ji Guo; Jin Xu, Xian; Hua Li, Chun; Chen, Wei Zu; Wang, Cun Xin

    2011-11-01

    Proteins usually undergo conformational transitions between structurally disparate states to fulfill their functions. The large-scale allosteric conformational transitions are believed to involve some key residues that mediate the conformational movements between different regions of the protein. In the present work, a thermodynamic method based on the elastic network model is proposed to predict the key residues involved in protein conformational transitions. In our method, the key functional sites are identified as the residues whose perturbations largely influence the free energy difference between the protein states before and after transition. Two proteins, nucleotide binding domain of the heat shock protein 70 and human/rat DNA polymerase ?, are used as case studies to identify the critical residues responsible for their open-closed conformational transitions. The results show that the functionally important residues mainly locate at the following regions for these two proteins: (1) the bridging point at the interface between the subdomains that control the opening and closure of the binding cleft; (2) the hinge region between different subdomains, which mediates the cooperative motions between the corresponding subdomains; and (3) the substrate binding sites. The similarity in the positions of the key residues for these two proteins may indicate a common mechanism in their conformational transitions.

  15. Effects of climate change on biodiversity: a review and identification of key research issues

    Microsoft Academic Search

    MAARTEN KAPPELLE; MARGRET M. I. VAN VUUREN; PIETER BAAS

    1999-01-01

    Current knowledge of effects of climate change on biodiversity is briefly reviewed, and results are presented of a survey of biological research groups in the Netherlands, aimed at identifying key research issues in this field. In many areas of the world, biodiversity is being reduced by humankind through changes in land cover and use, pollution, invasions of exotic species and

  16. DETECTION AND IDENTIFICATION THRESHOLD VALUES FOR KEY FLAVOR COMPONENTS IN AN ORANGE JUICE MATRIX

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Due to the complex nature of orange juice, threshold values for key flavor components could differ significantly from those values reported in simpler systems, like water. In order to provide the citrus industry with reference values closer to the real situation in orange juice, different orange ju...

  17. Distinguishing institutional identification from academic goal pursuit: interactive effects of ethnic identification and race-based rejection sensitivity.

    PubMed

    Mendoza-Denton, Rodolfo; Pietrzak, Janina; Downey, Geraldine

    2008-08-01

    We examined the interactive effects of ethnic identification (EI) and race-based rejection sensitivity (RS-race) on institutional outcomes among African American college students. We distinguished between effects on institutional identification on the one hand and academic goal pursuit (e.g., staying in school, grade point average [GPA]) on the other. Supporting the utility of this distinction, we found that EI and RS-race interacted to predict these outcomes differently. Higher EI in combination with higher RS-race predicted reduced identification with the institution (Studies 1, 2, and 3a). This combination, however, did not lead to decreases in GPA over time. Moreover, EI was positively related to intentions to stay in school as well as to GPA increases among those lower in RS-race (Studies 1 and 3b). Implications for understanding identity negotiation vis-à-vis performance in institutional settings are discussed. PMID:18665706

  18. An identification of financial and production performance variables as key indicators of dairy firm failure 

    E-print Network

    Law, James Michael

    1989-01-01

    of the level of herd mastitis infection and thus a measure of the health expenses and milk production losses due to the disease. Age information may also give some indication of health costs which increase with the age of a cow. Finally. culling information.... Reasons for involuntary cullings are: reproductive problems, mastitis infection. feet and leg problems, other health problems, and death loss. Measurement Interactions Interactions between the measurements of the factors mentioned above may provide...

  19. Identification of key radionuclides in a nuclear waste repository in basalt

    NASA Astrophysics Data System (ADS)

    Barney, G. S.; Wood, B. J.

    1980-05-01

    Radionuclides were identified which appear to pose the greatest potential hazard to man during long term storage of nuclear waste in a repository mined in the Columbia Plateau basalt formation. The criteria used to select key radionuclides were as follows: quantity of radionuclide in stored waste; biological toxicity; leach rate of the wastes into groundwater; and transport rate via ground water flow. The waste forms were assumed to be either unreprocessed spent fuel or borosilicate glass containing reprocessed high level waste. The nuclear waste composition was assumed to be that from a light water reactor. Radionuclides were ranked according to quantity, toxicity, and release rate from the repository. These rankings were combined to obtain a single list of key radionuclides.

  20. Identification of glucose-6-phosphate transporter as a key regulator functioning at the autophagy initiation step.

    PubMed

    Ahn, Hye-Hyun; Oh, Yumin; Lee, Huikyong; Lee, WonJae; Chang, Jae-Woong; Pyo, Ha-Kyung; Nah, Do Hyung; Jung, Yong-Keun

    2015-07-22

    Autophagy is a catabolic process involving autophagosome formation via lysosome. However, the initiation step of autophagy is largely unknown. We found an interaction between ULK1 and ATG9 in mammalian cells and utilized the interaction to identify novel regulators of autophagy upstream of ULK1. We established a cell-based screening assay employing bimolecular fluorescence complementation. By performing gain-of-function screening, we identified G6PT as an autophagy activator. G6PT enhanced the interaction between N-terminal Venus-tagged ULK1 and C-terminal Venus-tagged ATG9, and increased autophagic flux independent of its transport activity. G6PT negatively regulated mTORC1 activity, demonstrating that G6PT functions upstream of mTORC1 in stimulating autophagy. PMID:25982172

  1. Key role of hydrazine to the interaction between oxaloacetic against phosphoenolpyruvic carboxykinase (PEPCK): ONIOM calculations.

    PubMed

    Prajongtat, Pongthep; Phromyothin, Darinee Sae-Tang; Hannongbua, Supa

    2013-08-01

    The interactions between oxaloacetic (OAA) and phosphoenolpyruvic carboxykinase (PEPCK) binding pocket in the presence and absence of hydrazine were carried out using quantum chemical calculations, based on the two-layered ONIOM (ONIOM2) approach. The complexes were partially optimized by ONIOM2 (B3LYP/6-31G(d):PM6) method while the interaction energies between OAA and individual residues surrounding the pocket were performed at the MP2/6-31G(d,p) level of theory. The calculated interaction energies (INT) indicated that Arg87, Gly237, Ser286, and Arg405 are key residues for binding to OAA with the INT values of -1.93, -2.06, -2.47, and -3.16 kcal mol(-1), respectively. The interactions are mainly due to the formation of hydrogen bonding interactions with OAA. Moreover, using ONIOM2 (B3LYP/6-31G(d):PM6) applied on the PEPCKHS complex, two proton transfers were observed; first, the proton was transferred from the carboxylic group of OAA to hydrazine while the second one was from Asp311 to Lys244. Such reactions cause the generation of binding strength of OAA to the pocket via electrostatic interaction. The orientations of Lys243, Lys244, His264, Asp311, Phe333, and Arg405 were greatly deviated after hydrazine incorporation. These indicate that hydrazine plays an important role in terms of not only changing the conformation of the binding pocket, but is also tightly bound to OAA resulting in its conformation change in the pocket. The understanding of such interaction can be useful for the design of hydrazine-based inhibitor for antichachexia agents. PMID:23624997

  2. Checklist and Simple Identification Key for Frogs and Toads from District IV of The MADA Scheme, Kedah, Malaysia

    PubMed Central

    Jaafar, Ibrahim; Chai, Teoh Chia; Sah, Shahrul Anuar Mohd; Akil, Mohd Abdul Muin Md.

    2009-01-01

    A survey was conducted to catalogue the diversity of anurans in District IV of the Muda Agriculture Development Authority Scheme (MADA) in Kedah Darul Aman, Malaysia, from July 1996 to January 1997. Eight species of anurans from three families were present in the study area. Of these, the Common Grass Frog (Fejevarya limnocharis) was the most abundant, followed by Mangrove Frog (Fejevarya cancrivora), Long-legged Frog (Hylarana macrodactyla), and Common Toad (Duttaphrynus melanostictus). Puddle Frog (Occidozyga lima), Taiwanese Giant Frog (Hoplobatrachus rugulosus), and Banded Bullfrog (Kaluola pulchra) were rare during the sampling period, and only one Paddy Frog (Hylarana erythraea) was captured. A simple identification key for the anurans of this area is included for use by scientists and laymen alike. PMID:24575178

  3. Interactive software for model predictive control with simultaneous identification

    E-print Network

    Echeverria Del Rio, Pablo

    2000-01-01

    This thesis is a unified practical framework in the theory of Model Predictive Control with Simultaneous Identification. The ability to change and visualize parameters on-line makes this toolbox attractive for control engineers, and for anyone...

  4. Interactive software for model predictive control with simultaneous identification 

    E-print Network

    Echeverria Del Rio, Pablo

    2000-01-01

    -loop experimentation. ~ Presence of constraints during identification. The issues of simultaneous control and identification seem to be obvious. The main question is how to perturb the system in such a way that it is possible to obtain the maximum information from... Predictive Control (MPC) provides the only methodology to handle constraints in a systematic way during the design and implementation of the controller. While MPC was originally designed for use in petrochemical plants, is widely applicable to a variety...

  5. Identification of key residues determining isomerohydrolase activity of human RPE65.

    PubMed

    Takahashi, Yusuke; Moiseyev, Gennadiy; Ma, Jian-xing

    2014-09-26

    RPE65 is the retinoid isomerohydrolase that converts all-trans-retinyl ester to 11-cis-retinol, a key reaction in the retinoid visual cycle. We have previously reported that cone-dominant chicken RPE65 (cRPE65) shares 90% sequence identity with human RPE65 (hRPE65) but exhibits substantially higher isomerohydrolase activity than that of bovine RPE65 or hRPE65. In this study, we sought to identify key residues responsible for the higher enzymatic activity of cRPE65. Based on the amino acid sequence comparison of mammalian and other lower vertebrates' RPE65, including cone-dominant chicken, 8 residues of hRPE65 were separately replaced by their counterparts of cRPE65 using site-directed mutagenesis. The enzymatic activities of cRPE65, hRPE65, and its mutants were measured by in vitro isomerohydrolase activity assay, and the retinoid products were analyzed by HPLC. Among the mutants analyzed, two single point mutants, N170K and K297G, and a double mutant, N170K/K297G, of hRPE65 exhibited significantly higher catalytic activity than WT hRPE65. Further, when an amino-terminal fragment (Met(1)-Arg(33)) of the N170K/K297G double mutant of hRPE65 was replaced with the corresponding cRPE65 fragment, the isomerohydrolase activity was further increased to a level similar to that of cRPE65. This finding contributes to the understanding of the structural basis for isomerohydrolase activity. This highly efficient human isomerohydrolase mutant can be used to improve the efficacy of RPE65 gene therapy for retinal degeneration caused by RPE65 mutations. PMID:25112876

  6. Visible Wavelength Spectroscopy of Ferric Minerals: A Key Tool for Identification of Ancient Martian Aqueous Environments

    NASA Technical Reports Server (NTRS)

    Murchie, Scott L.; Bell, J. F., III; Morris, Richard V.

    2000-01-01

    The mineralogic signatures of past aqueous alteration of a basaltic Martian crust may include iron oxides and oxyhydroxides, zeolites, carbonates, phyllosilicates, and silica. The identities, relative abundances, and crystallinities of the phases formed in a particular environment depend on physicochemical conditions. At one extreme, hot spring environments may be characterized by smectite-chlorite to talc-kaolinite silicate assemblages, plus crystalline ferric oxides dominated by hematite. However, most environments, including cold springs, pedogenic layers, and ponded surface water, are expected to deposit iron oxides and oxyhydroxides, carbonates, and smectite-dominated phyllosilicates. A substantial fraction of the ferric iron is expected to occur in nanophase form, with the exact mineralogy strongly influenced by Eh-pH conditions. Detection of these phases has been an objective of a large body of terrestrial telescopic, Mars orbital, and landed spectral investigations and in situ compositional measurements. However, clear identifications of many of these phases is lacking. Neither carbonate nor silica has been unequivocally detected by any method. Although phyllosilicates may occur near the limit of detection by remote sensing, in general they appear to occur in only poorly crystalline form. In contrast, compelling evidence for ferric iron minerals has been gathered by recent telescopic investigations, the Imager for Mars Pathfinder (IMP), and the Thermal Emission Spectrometer (TES) on the Mars Global Surveyor (MGS). These data yield two crucial findings: (1) In the global, high spatial resolution TES data set, highly crystalline ferric iron (as coarse-grained 'gray' hematite) has been recognized but with only very limited spatial occurrence and (2) Low-resolution telescopic reflectance spectroscopy, very limited orbital reflectance spectroscopy, and landed multispectral imaging provide strong indications that at least two broad classes of ferric iron minerals are commonplace in non-dust covered regions.

  7. Sensomics mapping and identification of the key bitter metabolites in Gouda cheese.

    PubMed

    Toelstede, Simone; Hofmann, Thomas

    2008-04-23

    Application of a sensomics approach on the water-soluble extract of a matured Gouda cheese including gel permeation chromatography, ultrafiltration, solid phase extraction, preparative RP-HPLC, and HILIC combined with analytical sensory tools enabled the comprehensive mapping of bitter-tasting metabolites. LC-MS-TOF and LC-MS/MS, independent synthesis, and sensory analysis revealed the identification of a total of 16 bitter peptides formed by proteolysis of caseins. Eleven previously unreported bitter peptides were aligned to beta-casein, among which 6 peptides were released from the sequence beta-CN(57-69) of the N terminus of beta-casein and 2 peptides originated from the C-terminal sequence beta-CN(198-206). The other peptides were liberated from miscellaneous regions of beta-casein, namely, beta-CN(22-28), beta-CN(74-86), beta-CN(74-77), and beta-CN(135-138), respectively. Six peptides were found to originate from alpha(s1)-casein and were shown to have the sequences alpha(s1)-CN(11-14), alpha(s1)-CN(56-60), alpha(s1)-CN(70/71-74), alpha(s1)-CN(110/111-114), and alpha(s1)-CN(135-136). Sensory evaluation of the purified, synthesized peptides revealed that 12 of these peptides showed pronounced bitter taste with recognition thresholds between 0.05 and 6.0 mmol/L. Among these peptides, the decapeptide YPFPGPIHNS exhibited a caffeine-like bitter taste quality at the lowest threshold concentration of 0.05 mmol/L. PMID:18355023

  8. Reduced and oxidised scytonemin: Theoretical protocol for Raman spectroscopic identification of potential key biomolecules for astrobiology

    NASA Astrophysics Data System (ADS)

    Varnali, Tereza; Edwards, Howell G. M.

    2014-01-01

    Scytonemin is an important UV-radiation protective biomolecule synthesised by extremophilic cyanobacteria in stressed terrestrial environments. Scytonemin and its reduced form have been both isolated experimentally and the Raman spectrum for scytonemin has been assigned and characterised experimentally both in extracts and in living extremophilic cyanobacterial colonies. Scytonemin is recognised as a key biomarker molecule for terrestrial organisms in stressed environments. We propose a new, theoretically plausible structure for oxidised scytonemin which has not been mentioned in the literature hitherto. DFT calculations for scytonemin, reduced scytonemin and the new structure modelled and proposed for oxidised scytonemin are reported along with their Raman spectroscopic data and ?max UV-absorption data obtained theoretically. Comparison of the vibrational spectroscopic assignments allows the three forms of scytonemin to be detected and identified and assist not only in the clarification of the major features in the experimentally observed Raman spectral data for the parent scytonemin but also support a protocol proposed for their analytical discrimination. The results of this study provide a basis for the search for molecules of this type in future astrobiological missions of exploration and the search for extinct and extant life terrestrially.

  9. Molecular Identification of Atlantic Bluefin Tuna (Thunnus thynnus, Scombridae) Larvae and Development of a DNA Character-Based Identification Key for Mediterranean Scombrids

    PubMed Central

    Puncher, Gregory Neils; Arrizabalaga, Haritz; Alemany, Francisco; Cariani, Alessia; Oray, Isik K.; Karakulak, F. Saadet; Basilone, Gualtiero; Cuttitta, Angela; Mazzola, Salvatore; Tinti, Fausto

    2015-01-01

    The Atlantic bluefin tuna, Thunnus thynnus, is a commercially important species that has been severely over-exploited in the recent past. Although the eastern Atlantic and Mediterranean stock is now showing signs of recovery, its current status remains very uncertain and as a consequence their recovery is dependent upon severe management informed by rigorous scientific research. Monitoring of early life history stages can inform decision makers about the health of the species based upon recruitment and survival rates. Misidentification of fish larvae and eggs can lead to inaccurate estimates of stock biomass and productivity which can trigger demands for increased quotas and unsound management conclusions. Herein we used a molecular approach employing mitochondrial and nuclear genes (CO1 and ITS1, respectively) to identify larvae (n = 188) collected from three spawning areas in the Mediterranean Sea by different institutions working with a regional fisheries management organization. Several techniques were used to analyze the genetic sequences (sequence alignments using search algorithms, neighbour joining trees, and a genetic character-based identification key) and an extensive comparison of the results is presented. During this process various inaccuracies in related publications and online databases were uncovered. Our results reveal important differences in the accuracy of the taxonomic identifications carried out by different ichthyoplanktologists following morphology-based methods. While less than half of larvae provided were bluefin tuna, other dominant taxa were bullet tuna (Auxis rochei), albacore (Thunnus alalunga) and little tunny (Euthynnus alletteratus). We advocate an expansion of expertise for a new generation of morphology-based taxonomists, increased dialogue between morphology-based and molecular taxonomists and increased scrutiny of public sequence databases. PMID:26147931

  10. Person Identification and Interaction of Social Robots by Using Wireless Tags

    E-print Network

    Kanda, Takayuki

    Person Identification and Interaction of Social Robots by Using Wireless Tags Takayuki Kanda1 , Takayuki Hirano1 , Daniel Eaton1 , and Hiroshi Ishiguro1&2 1 ATR Intelligent Robotics and Communication-mail: kanda@atr.co.jp Abstract - This paper reports a trial of immersing interactive humanoid robots

  11. Identification of the key residues determining the product specificity of isomerohydrolase

    PubMed Central

    Takahashi, Yusuke; Moiseyev, Gennadiy; Nikolaeva, Olga; Ma, Jian-xing

    2012-01-01

    The efficient recycling of the chromophore of visual pigments, 11-cis retinal, through the retinoid visual cycle is an essential process for maintaining normal vision. RPE65 is the isomerohydrolase in retinal pigment epithelium and generates predominantly 11-cis retinol (11cROL) and a minor amount of 13-cis retinol (13cROL), from all-trans retinyl ester (atRE). We recently identified and characterized novel homologs of RPE65, RPE65c and 13-cis isomerohydrolase (13cIMH), which are expressed in the zebrafish inner retina and brain, respectively. Although these two homologs share 97% amino acid sequence identity, they exhibit distinct product specificities. Under the same assay conditions, RPE65c generated predominantly 11cROL, similar to RPE65, while 13cIMH generated exclusively 13cROL from atRE substrate. To study the impacts of the key residues determining isomerization product specificity of RPE65, we replaced candidate residues by site-directed mutagenesis in RPE65c and 13cIMH. Point mutations at residues Tyr58, Phe103 and Leu133 in RPE65c resulted in significantly altered isomerization product specificities. Particularly, our results showed that residue 58 is a primary determinant of isomerization specificity, since the Y58N mutation in RPE65c and its reciprocal N58Y mutation in 13cIMH completely reversed the respective enzyme isomerization product specificities. These findings will contribute to the elucidation of molecular mechanisms underlying the isomerization reaction catalyzed by RPE65. PMID:22512451

  12. Identification of key drought stress-related genes in the hyacinth bean.

    PubMed

    Yao, Lu-Ming; Wang, Biao; Cheng, Lin-Jing; Wu, Tian-Long

    2013-01-01

    Hyacinth bean (Lablab purpureus [Linn.] Sweet) possesses excellent characteristics for field production, but the response of this plant to drought stress has not been described at the molecular level. Suppression subtraction hybridization (SSH) is an effective way to exploit key factors for plant responses to drought stress that are involved in transcriptional and metabolic activities. In this study, forward and reverse SSH libraries were generated from root tissues of the drought-tolerant hyacinth bean genotype MEIDOU 2012 under water-stress conditions. A total of 1,287 unigenes (94 contigs and 1,193 singletons) were derived from sequence alignment and cluster assembly of 1400 ESTs, and 80.6% of those hit against NCBI non-redundant (nr) database with E value <1E-06. BLASTX analysis revealed that the majority top matches were proteins form Glycine max (L.) Merrill. (61.5%). According to a gene ontology (GO) functional classification, 816 functionally annotated unigenes were assigned to the biological process category (74.1%), and 83.9% of them classified into molecular function and 69.2% involved in cellular component. A total of 168 sequences were further annotated with 207 Enzyme Commission (EC) codes and mapped to 83 different KEGG pathways. Seventeen functionally relevant genes were found to be overrepresented under drought stress using enrichment analysis. Differential expression of unigenes were confirmed by quantitative real-time PCR assays, and their transcript profiles generally divided into three patterns, depending on the expression peaked levels after 6, 8 or 10 days dehydration, which indicated that these genes are functionally associated in the drought-stress response. PMID:23472143

  13. Biochemical identification and biological origin of key odor components in livestock waste.

    PubMed

    Mackie, R I; Stroot, P G; Varel, V H

    1998-05-01

    Animal production results in conversion of feeds into valuable products such as meat, milk, eggs, and wool as well as into unavoidable and less desirable waste products. Intensification of animal numbers and increasing urbanization has resulted in considerable attention to odorous gases produced from animal wastes. It is clear that animal manure was, and still is, a valuable resource. However, it may be a major obstacle to future development of the animal industry if its impact on the environment is not properly controlled. Poor odor prevention and control from animal wastes is related to a lack of knowledge of the fundamental nature of odor and its production by farm animals. Odor, like noise, is a nuisance or disturbance and there is no universally accepted definition of an objectionable odor. Thus, regulation and control of odors in the environment is difficult because of the technical difficulties of defining odor limits and their measurement and evaluation. A variety of direct (sensory) and indirect (analytical instruments) methods for measuring odor intensity and determination of individual or key odor components are discussed. The biological origins of the four principal classes of odor compounds, namely branched- and straight-chain VFA, ammonia and volatile amines, indoles and phenols, and the volatile sulfur-containing compounds, are reviewed. Because more than 50% of N from animals is excreted as urea, one strategy to conserve N in waste is to inhibit the urease enzyme that converts urea to ammonia. Laboratory studies to evaluate di- and triamide compounds to control urea hydrolysis in slurries of cattle and swine wastes are presented. Finally, a brief overview of various intervention strategies is provided. Multiple combinations of nutritional management, housing systems, treatment options as well as storage and disposal of animal wastes will be required to reduce environmental pollution and provide for long-term sustainable growth. PMID:9621939

  14. Compulsory citizenship behavior and organizational citizenship behavior: the role of organizational identification and perceived interactional justice.

    PubMed

    Zhao, Hongdan; Peng, Zhenglong; Chen, Hsiu-Kuei

    2014-01-01

    This article examines the psychological mechanism underlying the relationship between compulsory citizenship behavior (CCB) and organizational citizenship behavior (OCB) by developing a moderated mediation model. The model focuses on the mediating role of organizational identification and the moderating role of interactional justice in influencing the mediation. Using a time-lagged research design, the authors collected two waves of data from 388 supervisor-subordinate dyads in 67 teams to test the moderated mediation model. Results revealed that CCB negatively influenced OCB via impairing organizational identification. Moreover, interactional justice moderated the strength of the indirect effect of CCB on OCB (through organizational identification), such that the mediated relationship was stronger under low interactional justice than under high interactional justice. PMID:24684078

  15. Studies on some trematode parasites of stray dogs in Egypt with a key to the identification of intestinal trematodes of dogs.

    PubMed

    El-Gayar, Amal K

    2007-03-31

    Fourteen of 30 stray dogs examined from Ismailia City, Egypt were infected with one or more species of intestinal trematodes, including Mesostephanus appendiculatus, Mesostephanus milvi, Mesostephanus fajardensis, Echinochasmus liliputanus, Heterophyes dispar, and Pygidiopsis genata. The morphology of each species was compared with earlier descriptions and a key to the identification of canine intestinal trematodes in this geographic region was developed. PMID:17208378

  16. Calcaridorylaimus castaneae sp. n. (Nematoda, Dorylaimidae) from Bulgaria with an identification key to the species of the genus

    PubMed Central

    Nedelchev, Sevdan; Elshishka, Milka; Lazarova, Stela; Radoslavov, Georgi; Hristov, Peter; Peneva, Vlada

    2014-01-01

    Abstract An unknown species belonging to the genusCalcaridorylaimus Andrássy, 1986 was collected from the litter of broadleaf forests dominated by Castanea sativa Mill. and mixed with Quercus daleshampii Ten. and Fagus sylvatica L. on Belasitsa Mountain, south-western Bulgaria. Calcaridorylaimus castaneae sp. n. is characterised by its long body (1.4–2.1 mm), lip region practically not offset, vulva transverse, short odontostyle (14.5–16 ?m) and tail (75.5–110.5 ?m, c=14.7–23.6; c’=2.9–4.4) in females and 38–46 ?m long spicules with small spur before their distant end in males. It is most similar to C. andrassyi Ahmad & Shaheen, 2004, but differs in having transverse vs pore-like vulva and shorter spicules (38–46 ?m vs 52–57 ?m). An identification key to the species of the genus Calcaridorylaimus is proposed. Phylogenetic analyses were performed on 18S and D2-D3 expansion domains of 28S rRNA genes by Neighbor-Joining, Maximum Likelihood and Bayesian Inference methods. The phylograms inferred from 18S sequences showed closest relationships of the new species with some species belonging to the genus Mesodorylaimus. However, insufficient molecular data for members of both genera do not allow the phylogenetic relationships of Calcaridorylaimus and the new species described herein to be elucidated. PMID:24899849

  17. MAX--An Interactive Computer Program for Teaching Identification of Clay Minerals by X-ray Diffraction.

    ERIC Educational Resources Information Center

    Kohut, Connie K.; And Others

    1993-01-01

    Discusses MAX, an interactive computer program for teaching identification of clay minerals based on standard x-ray diffraction characteristics. The program provides tutorial-type exercises for identification of 16 clay standards, self-evaluation exercises, diffractograms of 28 soil clay minerals, and identification of nonclay minerals. (MDH)

  18. Methods for comprehensive experimental identification of RNA-protein interactions

    PubMed Central

    2014-01-01

    The importance of RNA-protein interactions in controlling mRNA regulation and non-coding RNA function is increasingly appreciated. A variety of methods exist to comprehensively define RNA-protein interactions. We describe these methods and the considerations required for designing and interpreting these experiments. PMID:24467948

  19. Identification of a key catalytic intermediate demonstrates that nitrogenase is activated by the reversible exchange of N? for H?.

    PubMed

    Lukoyanov, Dmitriy; Yang, Zhi-Yong; Khadka, Nimesh; Dean, Dennis R; Seefeldt, Lance C; Hoffman, Brian M

    2015-03-18

    Freeze-quenching nitrogenase during turnover with N2 traps an S = ½ intermediate that was shown by ENDOR and EPR spectroscopy to contain N2 or a reduction product bound to the active-site molybdenum-iron cofactor (FeMo-co). To identify this intermediate (termed here EG), we turned to a quench-cryoannealing relaxation protocol. The trapped state is allowed to relax to the resting E0 state in frozen medium at a temperature below the melting temperature; relaxation is monitored by periodically cooling the sample to cryogenic temperature for EPR analysis. During -50 °C cryoannealing of EG prepared under turnover conditions in which the concentrations of N2 and H2 ([H2], [N2]) are systematically and independently varied, the rate of decay of EG is accelerated by increasing [H2] and slowed by increasing [N2] in the frozen reaction mixture; correspondingly, the accumulation of EG is greater with low [H2] and/or high [N2]. The influence of these diatomics identifies EG as the key catalytic intermediate formed by reductive elimination of H2 with concomitant N2 binding, a state in which FeMo-co binds the components of diazene (an N-N moiety, perhaps N2 and two [e(-)/H(+)] or diazene itself). This identification combines with an earlier study to demonstrate that nitrogenase is activated for N2 binding and reduction through the thermodynamically and kinetically reversible reductive-elimination/oxidative-addition exchange of N2 and H2, with an implied limiting stoichiometry of eight electrons/protons for the reduction of N2 to two NH3. PMID:25741750

  20. Mass personalization: social and interactive applications using sound-track identification

    E-print Network

    Tomkins, Andrew

    Mass personalization: social and interactive applications using sound-track identification Michael Media, LLC 2006 Abstract This paper describes mass personalization, a framework for combining mass media with a highly personalized Web-based experience. We introduce four applications for mass personalization

  1. Identification of Novel Interacting Partners of Sirtuin6

    PubMed Central

    Polyakova, Oxana; Borman, Satty; Grimley, Rachel; Vamathevan, Jessica; Hayes, Brian; Solari, Roberto

    2012-01-01

    SIRT6 is a member of the Sirtuin family of histone deacetylases that has been implicated in inflammatory, aging and metabolic pathways. Some of its actions have been suggested to be via physical interaction with NF?B and HIF1? and transcriptional regulation through its histone deacetylase activity. Our previous studies have investigated the histone deacetylase activity of SIRT6 and explored its ability to regulate the transcriptional responses to an inflammatory stimulus such as TNF?. In order to develop a greater understanding of SIRT6 function we have sought to identify SIRT6 interacting proteins by both yeast-2-hybrid and co-immunoprecipitation studies. We report a number of interacting partners which strengthen previous findings that SIRT6 functions in base excision repair (BER), and novel interactors which suggest a role in nucleosome and chromatin remodeling, the cell cycle and NF?B biology. PMID:23240041

  2. Identification of proteins interacting with Arabidopsis ACD11.

    PubMed

    Petersen, Nikolaj H T; Joensen, Jan; McKinney, Lea V; Brodersen, Peter; Petersen, Morten; Hofius, Daniel; Mundy, John

    2009-04-01

    The Arabidopsis ACD11 gene encodes a sphingosine transfer protein and was identified by the accelerated cell death phenotype of the loss of function acd11 mutant, which exhibits heightened expression of genes involved in the disease resistance hypersensitive response (HR). We used ACD11 as bait in a yeast two-hybrid screen of an Arabidopsis cDNA library to identify ACD11 interacting proteins. One interactor identified is a protein of unknown function with an RNA recognition motif (RRM) designated BPA1 (binding partner of ACD11). Co-immunoprecipitation experiments confirmed the ACD11-BPA1 interactions in vivo and in vitro. Two other ACD11 interactors (PRA7 and PRA8) are homologous to each other and to mammalian PRA1, and both were subsequently shown to interact with BPA1 in yeast. A fourth interactor (VAP27-1) is homologous to mammalian VAP-A, and was found to interact more strongly with a homolog of ACD11 than ACD11 itself. All interactors were shown to be associated with membrane fractions, suggesting that ACD11 function could be related to the regulation of membrane compartments. PMID:18845362

  3. Factor selection and structural identification in the interaction ANOVA model.

    PubMed

    Post, Justin B; Bondell, Howard D

    2013-03-01

    When faced with categorical predictors and a continuous response, the objective of an analysis often consists of two tasks: finding which factors are important and determining which levels of the factors differ significantly from one another. Often times, these tasks are done separately using Analysis of Variance (ANOVA) followed by a post hoc hypothesis testing procedure such as Tukey's Honestly Significant Difference test. When interactions between factors are included in the model the collapsing of levels of a factor becomes a more difficult problem. When testing for differences between two levels of a factor, claiming no difference would refer not only to equality of main effects, but also to equality of each interaction involving those levels. This structure between the main effects and interactions in a model is similar to the idea of heredity used in regression models. This article introduces a new method for accomplishing both of the common analysis tasks simultaneously in an interaction model while also adhering to the heredity-type constraint on the model. An appropriate penalization is constructed that encourages levels of factors to collapse and entire factors to be set to zero. It is shown that the procedure has the oracle property implying that asymptotically it performs as well as if the exact structure were known beforehand. We also discuss the application to estimating interactions in the unreplicated case. Simulation studies show the procedure outperforms post hoc hypothesis testing procedures as well as similar methods that do not include a structural constraint. The method is also illustrated using a real data example. PMID:23323643

  4. Lipid shape is a key factor for membrane interactions of amphipathic helical peptides.

    PubMed

    Strandberg, Erik; Tiltak, Deniz; Ehni, Sebastian; Wadhwani, Parvesh; Ulrich, Anne S

    2012-07-01

    The membrane alignment of the amphiphilic alpha-helical model peptide MSI-103 (sequence [KIAGKIA]3-NH2) was examined by solid state 2H-NMR in different lipid systems by systematically varying the acyl chain length and degree of saturation, the lipid head group type, and the peptide-to-lipid molar ratio. In liquid crystalline phosphatidylcholine (PC) lipids with saturated chains, the amphiphilic helix changes its orientation from a surface-bound "S-state" to a tilted "T-state" with increasing peptide concentration. In PC lipids with unsaturated chains, on the other hand, the S-state is found throughout all concentrations. Using phosphatidylethanolamine lipids with a small head group or by addition of lyso-lipids with only one acyl chain, the spontaneous curvature of the bilayer was purposefully changed. In the first case with a negative curvature only the S-state was found, whereas in systems with a positive curvature the peptide preferred the obliquely immersed T-state at high concentration. The orientation of MSI-103 thus correlates very well with the shape of the lipid molecules constituting the membrane. Lipid charge, on the other hand, was found to affect only the initial electrostatic attraction to the membrane surface but not the alignment preferences. In bilayers that are "sealed" with 20% cholesterol, MSI-103 cannot bind in a well-oriented manner and forms immobilized aggregates instead. We conclude that the curvature properties of a membrane are a key factor in the interactions of amphiphilic helical peptides in general, whose re-alignment and immersion preferences may thus be inferred in a straightforward manner from the lipid-shape concept. PMID:22409944

  5. DNA nucleoside interaction and identification with carbon nanotubes.

    PubMed

    Meng, Sheng; Maragakis, Paul; Papaloukas, Costas; Kaxiras, Efthimios

    2007-01-01

    We investigate the interaction of individual DNA nucleosides with a carbon nanotube (CNT) in vacuum and in the presence of external gate voltage. We propose a scheme to discriminate between nucleosides on CNTs based on measurement of electronic features through a local probe such as scanning tunneling spectroscopy. We demonstrate through quantum mechanical calculations that these measurements can achieve 100% efficiency in identifying DNA bases. Our results support the practicality of ultrafast DNA sequencing using electrical measurements. PMID:17212438

  6. Identification of global ferredoxin interaction networks in Chlamydomonas reinhardtii.

    PubMed

    Peden, Erin A; Boehm, Marko; Mulder, David W; Davis, Reanna; Old, William M; King, Paul W; Ghirardi, Maria L; Dubini, Alexandra

    2013-12-01

    Ferredoxins (FDXs) can distribute electrons originating from photosynthetic water oxidation, fermentation, and other reductant-generating pathways to specific redox enzymes in different organisms. The six FDXs identified in Chlamydomonas reinhardtii are not fully characterized in terms of their biological function. In this report, we present data from the following: (a) yeast two-hybrid screens, identifying interaction partners for each Chlamydomonas FDX; (b) pairwise yeast two-hybrid assays measuring FDX interactions with proteins from selected biochemical pathways; (c) affinity pulldown assays that, in some cases, confirm and even expand the interaction network for FDX1 and FDX2; and (d) in vitro NADP(+) reduction and H2 photo-production assays mediated by each FDX that verify their role in these two pathways. Our results demonstrate new potential roles for FDX1 in redox metabolism and carbohydrate and fatty acid biosynthesis, for FDX2 in anaerobic metabolism, and possibly in state transition. Our data also suggest that FDX3 is involved in nitrogen assimilation, FDX4 in glycolysis and response to reactive oxygen species, and FDX5 in hydrogenase maturation. Finally, we provide experimental evidence that FDX1 serves as the primary electron donor to two important biological pathways, NADPH and H2 photo-production, whereas FDX2 is capable of driving these reactions at less than half the rate observed for FDX1. PMID:24100040

  7. Identification of Global Ferredoxin Interaction Networks in Chlamydomonas reinhardtii*

    PubMed Central

    Peden, Erin A.; Boehm, Marko; Mulder, David W.; Davis, ReAnna; Old, William M.; King, Paul W.; Ghirardi, Maria L.; Dubini, Alexandra

    2013-01-01

    Ferredoxins (FDXs) can distribute electrons originating from photosynthetic water oxidation, fermentation, and other reductant-generating pathways to specific redox enzymes in different organisms. The six FDXs identified in Chlamydomonas reinhardtii are not fully characterized in terms of their biological function. In this report, we present data from the following: (a) yeast two-hybrid screens, identifying interaction partners for each Chlamydomonas FDX; (b) pairwise yeast two-hybrid assays measuring FDX interactions with proteins from selected biochemical pathways; (c) affinity pulldown assays that, in some cases, confirm and even expand the interaction network for FDX1 and FDX2; and (d) in vitro NADP+ reduction and H2 photo-production assays mediated by each FDX that verify their role in these two pathways. Our results demonstrate new potential roles for FDX1 in redox metabolism and carbohydrate and fatty acid biosynthesis, for FDX2 in anaerobic metabolism, and possibly in state transition. Our data also suggest that FDX3 is involved in nitrogen assimilation, FDX4 in glycolysis and response to reactive oxygen species, and FDX5 in hydrogenase maturation. Finally, we provide experimental evidence that FDX1 serves as the primary electron donor to two important biological pathways, NADPH and H2 photo-production, whereas FDX2 is capable of driving these reactions at less than half the rate observed for FDX1. PMID:24100040

  8. Identification of interspecies interactions affecting Porphyromonas gingivalis virulence phenotypes

    PubMed Central

    Tenorio, Elizabeth L.; Klein, Brian A.; Cheung, Wai S.; Hu, Linden T.

    2011-01-01

    Background Periodontitis is recognized as a complex polymicrobial disease, however, the impact of the bacterial interactions among the 700–1,000 different species of the oral microbiota remains poorly understood. We conducted an in vitro screen for oral bacteria that mitigate selected virulence phenotypes of the important periodontal pathogen, Porphyromonas gingivalis. Method We isolated and identified oral anaerobic bacteria from subgingival plaque of dental patients. When cocultured with P. gingivalis W83, specific isolates reduced the cytopathogenic effects of P. gingivalis on oral epithelial cells. Result In an initial screen of 103 subgingival isolates, we identified 19 distinct strains from nine species of bacteria (including Actinomyces naeslundii, Streptococcus oralis, Streptococcus mitis, and Veilonella dispar) that protect oral epithelial cells from P. gingivalis-induced cytotoxicity. We found that some of these strains inhibited P. gingivalis growth in plate assays through the production of organic acids, whereas some decreased the gingipain activity of P. gingivalis in coculture or mixing experiments. Conclusion In summary, we identified 19 strains isolated from human subgingival plaque that interacted with P. gingivalis, resulting in mitigation of its cytotoxicity to oral epithelial cells, inhibition of growth, and/or reduction of gingipain activity. Understanding the mechanisms of interaction between bacteria in the oral microbial community may lead to the development of new probiotic agents and new strategies for interrupting the development of periodontal disease. PMID:22022641

  9. Simple Protein Complex Purification and Identification Method Suitable for High- throughput Mapping of Protein Interaction Networks

    SciTech Connect

    Markillie, Lye Meng; Lin, Chiann Tso; Adkins, Joshua N.; Auberry, Deanna L.; Hill, Eric A.; Hooker, Brian S.; Moore, Priscilla A.; Moore, Ronald J.; Shi, Liang; Wiley, H. S.; Kery, Vladimir

    2005-04-11

    Most of the current methods for purification and identification of protein complexes use endogenous expression of affinity tagged bait, tandem affinity tag purification of protein complexes followed by specific elution of complexes from beads, gel separation, in-gel digestion and mass spectrometric analysis of protein interactors. We propose a single affinity tag in vitro pulldown assay with denaturing elution, trypsin digestion in organic solvent and LC ESI MS/MS protein identification using SEQUEST analysis. Our method is simple, easy to scale up and automate thus suitable for high throughput mapping of protein interaction networks and functional proteomics.

  10. Identification of Crew-Systems Interactions and Decision Related Trends

    NASA Technical Reports Server (NTRS)

    Jones, Sharon Monica; Evans, Joni K.; Reveley, Mary S.; Withrow, Colleen A.; Ancel, Ersin; Barr, Lawrence

    2013-01-01

    NASA Vehicle System Safety Technology (VSST) project management uses systems analysis to identify key issues and maintain a portfolio of research leading to potential solutions to its three identified technical challenges. Statistical data and published safety priority lists from academic, industry and other government agencies were reviewed and analyzed by NASA Aviation Safety Program (AvSP) systems analysis personnel to identify issues and future research needs related to one of VSST's technical challenges, Crew Decision Making (CDM). The data examined in the study were obtained from the National Transportation Safety Board (NTSB) Aviation Accident and Incident Data System, Federal Aviation Administration (FAA) Accident/Incident Data System and the NASA Aviation Safety Reporting System (ASRS). In addition, this report contains the results of a review of safety priority lists, information databases and other documented references pertaining to aviation crew systems issues and future research needs. The specific sources examined were: Commercial Aviation Safety Team (CAST) Safety Enhancements Reserved for Future Implementation (SERFIs), Flight Deck Automation Issues (FDAI) and NTSB Most Wanted List and Open Recommendations. Various automation issues taxonomies and priority lists pertaining to human factors, automation and flight design were combined to create a list of automation issues related to CDM.

  11. Establishment of a Protein Frequency Library and Its Application in the Reliable Identification of Specific Protein Interaction Partners*

    PubMed Central

    Boulon, Séverine; Ahmad, Yasmeen; Trinkle-Mulcahy, Laura; Verheggen, Céline; Cobley, Andy; Gregor, Peter; Bertrand, Edouard; Whitehorn, Mark; Lamond, Angus I.

    2010-01-01

    The reliable identification of protein interaction partners and how such interactions change in response to physiological or pathological perturbations is a key goal in most areas of cell biology. Stable isotope labeling with amino acids in cell culture (SILAC)-based mass spectrometry has been shown to provide a powerful strategy for characterizing protein complexes and identifying specific interactions. Here, we show how SILAC can be combined with computational methods drawn from the business intelligence field for multidimensional data analysis to improve the discrimination between specific and nonspecific protein associations and to analyze dynamic protein complexes. A strategy is shown for developing a protein frequency library (PFL) that improves on previous use of static “bead proteomes.” The PFL annotates the frequency of detection in co-immunoprecipitation and pulldown experiments for all proteins in the human proteome. It can provide a flexible and objective filter for discriminating between contaminants and specifically bound proteins and can be used to normalize data values and facilitate comparisons between data obtained in separate experiments. The PFL is a dynamic tool that can be filtered for specific experimental parameters to generate a customized library. It will be continuously updated as data from each new experiment are added to the library, thereby progressively enhancing its utility. The application of the PFL to pulldown experiments is especially helpful in identifying either lower abundance or less tightly bound specific components of protein complexes that are otherwise lost among the large, nonspecific background. PMID:20023298

  12. Establishment of a protein frequency library and its application in the reliable identification of specific protein interaction partners.

    PubMed

    Boulon, Séverine; Ahmad, Yasmeen; Trinkle-Mulcahy, Laura; Verheggen, Céline; Cobley, Andy; Gregor, Peter; Bertrand, Edouard; Whitehorn, Mark; Lamond, Angus I

    2010-05-01

    The reliable identification of protein interaction partners and how such interactions change in response to physiological or pathological perturbations is a key goal in most areas of cell biology. Stable isotope labeling with amino acids in cell culture (SILAC)-based mass spectrometry has been shown to provide a powerful strategy for characterizing protein complexes and identifying specific interactions. Here, we show how SILAC can be combined with computational methods drawn from the business intelligence field for multidimensional data analysis to improve the discrimination between specific and nonspecific protein associations and to analyze dynamic protein complexes. A strategy is shown for developing a protein frequency library (PFL) that improves on previous use of static "bead proteomes." The PFL annotates the frequency of detection in co-immunoprecipitation and pulldown experiments for all proteins in the human proteome. It can provide a flexible and objective filter for discriminating between contaminants and specifically bound proteins and can be used to normalize data values and facilitate comparisons between data obtained in separate experiments. The PFL is a dynamic tool that can be filtered for specific experimental parameters to generate a customized library. It will be continuously updated as data from each new experiment are added to the library, thereby progressively enhancing its utility. The application of the PFL to pulldown experiments is especially helpful in identifying either lower abundance or less tightly bound specific components of protein complexes that are otherwise lost among the large, nonspecific background. PMID:20023298

  13. MicroRNA-301a Mediated Regulation of Kv4.2 in Diabetes: Identification of Key Modulators

    PubMed Central

    Panguluri, Siva K.; Tur, Jared; Chapalamadugu, Kalyan C.; Katnik, Chris; Cuevas, Javier; Tipparaju, Srinivas M.

    2013-01-01

    Diabetes is a metabolic disorder that ultimately results in major pathophysiological complications in the cardiovascular system. Diabetics are predisposed to higher incidences of sudden cardiac deaths (SCD). Several studies have associated diabetes as a major underlying risk for heart diseases and its complications. The diabetic heart undergoes remodeling to cope up with the underlying changes, however ultimately fails. In the present study we investigated the changes associated with a key ion channel and transcriptional factors in a diabetic heart model. In the mouse db/db model, we identified key transcriptional regulators and mediators that play important roles in the regulation of ion channel expression. Voltage-gated potassium channel (Kv4.2) is modulated in diabetes and is down regulated. We hypothesized that Kv4.2 expression is altered by potassium channel interacting protein-2 (KChIP2) which is regulated upstream by NFkB and miR-301a. We utilized qRT-PCR analysis and identified the genes that are affected in diabetes in a regional specific manner in the heart. At protein level we identified and validated differential expression of Kv4.2 and KChIP2 along with NFkB in both ventricles of diabetic hearts. In addition, we identified up-regulation of miR-301a in diabetic ventricles. We utilized loss and gain of function approaches to identify and validate the role of miR-301a in regulating Kv4.2. Based on in vivo and in vitro studies we conclude that miR-301a may be a central regulator for the expression of Kv4.2 in diabetes. This miR-301 mediated regulation of Kv4.2 is independent of NFkB and Irx5 and modulates Kv4.2 by direct binding on Kv4.2 3?untranslated region (3?-UTR). Therefore targeting miR-301a may offer new potential for developing therapeutic approaches. PMID:23573265

  14. The identification of surface interaction of apotransferrin with Candida albicans.

    PubMed

    Han, Yongmoon

    2014-10-01

    Our recent data indicate that apotransferrin, an iron-chelating protein, has anti-candidal activity by binding to the Candida albicans surface rather than just simple iron-chelation. Following that study, in this present study, we investigated the nature of the candidal surface substance that is responsible for the anticandidal activity by using (59)Fe(3+)-apotransferrin and biological assay methods. Data resulting from the binding studies showed that the yeast cells had one class of binding sites as analyzed by the Scatchard equation, and the binding was specific as determined by competitive binding assay with unlabeled and labeled transferrin. All these observations indicate that there is a substance(s) that mediates the binding. Thus, a mannoprotein-like substance was extracted from C. albicans surface using hot water-treatment. Radioisotope binding study revealed that the substance blocked the transferrin binding. At 25 ?g of IHS (inhibitory substance) addition, there was 65 % inhibition of the transferrin binding to C. albicans (5 × 10(7) cells/ml) (P < 0.05). The blockage of the transferrin binding disrupted the anticandidal activity of transferrin, resulting in a full recovery from growth inhibition. These results explain our previous observation that there is partial growth inhibition when C. albicans interacts directly with iron-saturated transferrin (100 %). Thus, it was concluded that a candidate for transferrin receptor is involved in the anticandidal activity of transferrin when in direct contact with C. albicans. PMID:24263410

  15. BMRF-MI: integrative identification of protein interaction network by modeling the gene dependency

    PubMed Central

    2015-01-01

    Background Identification of protein interaction network is a very important step for understanding the molecular mechanisms in cancer. Several methods have been developed to integrate protein-protein interaction (PPI) data with gene expression data for network identification. However, they often fail to model the dependency between genes in the network, which makes many important genes, especially the upstream genes, unidentified. It is necessary to develop a method to improve the network identification performance by incorporating the dependency between genes. Results We proposed an approach for identifying protein interaction network by incorporating mutual information (MI) into a Markov random field (MRF) based framework to model the dependency between genes. MI is widely used in information theory to measure the uncertainty between random variables. Different from traditional Pearson correlation test, MI is capable of capturing both linear and non-linear relationship between random variables. Among all the existing MI estimators, we choose to use k-nearest neighbor MI (kNN-MI) estimator which is proved to have minimum bias. The estimated MI is integrated with an MRF framework to model the gene dependency in the context of network. The maximum a posterior (MAP) estimation is applied on the MRF-based model to estimate the network score. In order to reduce the computational complexity of finding the optimal network, a probabilistic searching algorithm is implemented. We further increase the robustness and reproducibility of the results by applying a non-parametric bootstrapping method to measure the confidence level of the identified genes. To evaluate the performance of the proposed method, we test the method on simulation data under different conditions. The experimental results show an improved accuracy in terms of subnetwork identification compared to existing methods. Furthermore, we applied our method onto real breast cancer patient data; the identified protein interaction network shows a close association with the recurrence of breast cancer, which is supported by functional annotation. We also show that the identified subnetworks can be used to predict the recurrence status of cancer patients by survival analysis. Conclusions We have developed an integrated approach for protein interaction network identification, which combines Markov random field framework and mutual information to model the gene dependency in PPI network. Improvements in subnetwork identification have been demonstrated with simulation datasets compared to existing methods. We then apply our method onto breast cancer patient data to identify recurrence related subnetworks. The experiment results show that the identified genes are enriched in the pathway and functional categories relevant to progression and recurrence of breast cancer. Finally, the survival analysis based on identified subnetworks achieves a good result of classifying the recurrence status of cancer patients. PMID:26099273

  16. Protein interaction network analysis—Approach for potential drug target identification in Mycobacterium tuberculosis

    Microsoft Academic Search

    Sandeep K. Kushwaha; Madhvi Shakya

    2010-01-01

    In host–parasite diseases like tuberculosis, non-homologous proteins (enzymes) as drug target are first preference. Most potent drug target can be identified among large number of non-homologous protein through protein interaction network analysis. In this study, the entire promising dimension has been explored for identification of potential drug target. A comparative metabolic pathway analysis of the host Homo sapiens and the

  17. Team-oriented leadership: the interactive effects of leader group prototypicality, accountability, and team identification.

    PubMed

    Giessner, Steffen R; van Knippenberg, Daan; van Ginkel, Wendy; Sleebos, Ed

    2013-07-01

    We examined the interactive effects of leader group prototypicality, accountability, and team identification on team-oriented behavior of leaders, thus extending the social identity perspective on leadership to the study of leader behavior. An experimental study (N = 152) supported our hypothesis that leader accountability relates more strongly to team-oriented behavior for group nonprototypical leaders than for group prototypical leaders. A multisource field study with leaders (N = 64) and their followers (N = 209) indicated that this interactive effect is more pronounced for leaders who identify more strongly with their team. We discuss how these findings further develop the social identity analysis of leadership. PMID:23565892

  18. Student Value Structures: Key to Interpersonal Interaction in the College Community.

    ERIC Educational Resources Information Center

    Paulin, Kenneth C.; Bittner, John R.

    This study attempts to discover whether personal value structures are present at the personality level of student interaction (1) when there are no specific issues confronting the student, or (2) when issues are present and interaction results in linkage of the student value structure with a particular issue. Based on the results of a differential…

  19. Identification of the key bitter compounds in our daily diet is a prerequisite for the understanding of the hTAS2R gene polymorphisms affecting food choice.

    PubMed

    Hofmann, Thomas

    2009-07-01

    In order to decode genetic variations affecting food choice and to determine whether to accept or to reject certain food products, it is a necessary prerequisite to deorphanize the hTAS2R/ligand pairs using the key bitter compounds in foods as stimuli rather than doing this either by using artificial molcules, to which the normal consumer had never been exposed, or by using food-born molecules which do not at all contribute to the overall bitterness. Therefore, the chemical structure of the most active bitter molecules in foods needs to be unequivocally determined in order to be sure that hTAS2R polymorphisms are related to the key molecules which really contribute to the overall bitterness perception of food products. As most studies focused primarily on quantitatively predominating compounds, rather than selecting the target compounds to be identified with regard to taste-activity, it seems that yet unknown components play a key role in evoking the bitter taste of food products. Driven by the need to discover the key players inducing the food taste, the research area "sensomics" made tremendous efforts in recent years to map the sensometabolome and to identify the most intense taste-active metabolites in fresh and processed foods. The present article summarizes recent studies on the identification of orphan key bitter stimuli in fresh, fermented, and thermally processed foods using carrots, cheese, and roasted coffee as examples. PMID:19686121

  20. Identification of major rock-water interactions on either side of a hydrologic barrier in the Wanapum Formation, Washington

    E-print Network

    Dean, Warren Theodore

    1993-01-01

    IDENTIFICATION OF MAJOR ROCK-WATER INTERACTIONS ON EITHER SIDE OF A HYDROLOGIC BARRIER IN THE WANAPUM FORMATION, WASHINGTON A Thesis WARREN THEODORE DEAN Submitted to the Offic of Graduate Studies of Texas A&M University in partial fulfillmen... of the requirements for the degree of MASTER OF SCIENCE August 1993 Major Subject: Geology IDENTIFICATION OF MAJOR ROCK-WATER INTERACTIONS ON EITHER SIDE OF A HYDROLOGIC BARRIER IN THE WANAPUM FORMATION, WASHINGTON A Thesis WARREN THEODORE DEAN Submitted...

  1. Quantification of cytosolic interactions identifies Ede1 oligomers as key organizers of endocytosis

    PubMed Central

    Boeke, Dominik; Trautmann, Susanne; Meurer, Matthias; Wachsmuth, Malte; Godlee, Camilla; Knop, Michael; Kaksonen, Marko

    2014-01-01

    Clathrin-mediated endocytosis is a highly conserved intracellular trafficking pathway that depends on dynamic protein–protein interactions between up to 60 different proteins. However, little is known about the spatio-temporal regulation of these interactions. Using fluorescence (cross)-correlation spectroscopy in yeast, we tested 41 previously reported interactions in vivo and found 16 to exist in the cytoplasm. These detected cytoplasmic interactions included the self-interaction of Ede1, homolog of mammalian Eps15. Ede1 is the crucial scaffold for the organization of the early stages of endocytosis. We show that oligomerization of Ede1 through its central coiled coil domain is necessary for its localization to the endocytic site and we link the oligomerization of Ede1 to its function in locally concentrating endocytic adaptors and organizing the endocytic machinery. Our study sheds light on the importance of the regulation of protein–protein interactions in the cytoplasm for the assembly of the endocytic machinery in vivo. PMID:25366307

  2. Identification of Essential Proteins Based on a New Combination of Local Interaction Density and Protein Complexes

    PubMed Central

    Luo, Jiawei; Qi, Yi

    2015-01-01

    Background Computational approaches aided by computer science have been used to predict essential proteins and are faster than expensive, time-consuming, laborious experimental approaches. However, the performance of such approaches is still poor, making practical applications of computational approaches difficult in some fields. Hence, the development of more suitable and efficient computing methods is necessary for identification of essential proteins. Method In this paper, we propose a new method for predicting essential proteins in a protein interaction network, local interaction density combined with protein complexes (LIDC), based on statistical analyses of essential proteins and protein complexes. First, we introduce a new local topological centrality, local interaction density (LID), of the yeast PPI network; second, we discuss a new integration strategy for multiple bioinformatics. The LIDC method was then developed through a combination of LID and protein complex information based on our new integration strategy. The purpose of LIDC is discovery of important features of essential proteins with their neighbors in real protein complexes, thereby improving the efficiency of identification. Results Experimental results based on three different PPI(protein-protein interaction) networks of Saccharomyces cerevisiae and Escherichia coli showed that LIDC outperformed classical topological centrality measures and some recent combinational methods. Moreover, when predicting MIPS datasets, the better improvement of performance obtained by LIDC is over all nine reference methods (i.e., DC, BC, NC, LID, PeC, CoEWC, WDC, ION, and UC). Conclusions LIDC is more effective for the prediction of essential proteins than other recently developed methods. PMID:26125187

  3. Identification of Essential Proteins Based on Ranking Edge-Weights in Protein-Protein Interaction Networks

    PubMed Central

    Wang, Yan; Sun, Huiyan; Du, Wei; Blanzieri, Enrico; Viero, Gabriella; Xu, Ying; Liang, Yanchun

    2014-01-01

    Essential proteins are those that are indispensable to cellular survival and development. Existing methods for essential protein identification generally rely on knock-out experiments and/or the relative density of their interactions (edges) with other proteins in a Protein-Protein Interaction (PPI) network. Here, we present a computational method, called EW, to first rank protein-protein interactions in terms of their Edge Weights, and then identify sub-PPI-networks consisting of only the highly-ranked edges and predict their proteins as essential proteins. We have applied this method to publicly-available PPI data on Saccharomyces cerevisiae (Yeast) and Escherichia coli (E. coli) for essential protein identification, and demonstrated that EW achieves better performance than the state-of-the-art methods in terms of the precision-recall and Jackknife measures. The highly-ranked protein-protein interactions by our prediction tend to be biologically significant in both the Yeast and E. coli PPI networks. Further analyses on systematically perturbed Yeast and E. coli PPI networks through randomly deleting edges demonstrate that the proposed method is robust and the top-ranked edges tend to be more associated with known essential proteins than the lowly-ranked edges. PMID:25268881

  4. Information flow between interacting human brains: Identification, validation, and relationship to social expertise.

    PubMed

    Bilek, Edda; Ruf, Matthias; Schäfer, Axel; Akdeniz, Ceren; Calhoun, Vince D; Schmahl, Christian; Demanuele, Charmaine; Tost, Heike; Kirsch, Peter; Meyer-Lindenberg, Andreas

    2015-04-21

    Social interactions are fundamental for human behavior, but the quantification of their neural underpinnings remains challenging. Here, we used hyperscanning functional MRI (fMRI) to study information flow between brains of human dyads during real-time social interaction in a joint attention paradigm. In a hardware setup enabling immersive audiovisual interaction of subjects in linked fMRI scanners, we characterize cross-brain connectivity components that are unique to interacting individuals, identifying information flow between the sender's and receiver's temporoparietal junction. We replicate these findings in an independent sample and validate our methods by demonstrating that cross-brain connectivity relates to a key real-world measure of social behavior. Together, our findings support a central role of human-specific cortical areas in the brain dynamics of dyadic interactions and provide an approach for the noninvasive examination of the neural basis of healthy and disturbed human social behavior with minimal a priori assumptions. PMID:25848050

  5. Site identification in high-throughput RNA–protein interaction data

    PubMed Central

    Uren, Philip J.; Bahrami-Samani, Emad; Burns, Suzanne C.; Qiao, Mei; Karginov, Fedor V.; Hodges, Emily; Hannon, Gregory J.; Sanford, Jeremy R.; Penalva, Luiz O. F.; Smith, Andrew D.

    2012-01-01

    Motivation: Post-transcriptional and co-transcriptional regulation is a crucial link between genotype and phenotype. The central players are the RNA-binding proteins, and experimental technologies [such as cross-linking with immunoprecipitation- (CLIP-) and RIP-seq] for probing their activities have advanced rapidly over the course of the past decade. Statistically robust, flexible computational methods for binding site identification from high-throughput immunoprecipitation assays are largely lacking however. Results: We introduce a method for site identification which provides four key advantages over previous methods: (i) it can be applied on all variations of CLIP and RIP-seq technologies, (ii) it accurately models the underlying read-count distributions, (iii) it allows external covariates, such as transcript abundance (which we demonstrate is highly correlated with read count) to inform the site identification process and (iv) it allows for direct comparison of site usage across cell types or conditions. Availability and implementation: We have implemented our method in a software tool called Piranha. Source code and binaries, licensed under the GNU General Public License (version 3) are freely available for download from http://smithlab.usc.edu. Contact: andrewds@usc.edu Supplementary information: Supplementary data available at Bioinformatics online. PMID:23024010

  6. Phosphotransferase protein EIIANtr interacts with SpoT, a key enzyme of the stringent response, in Ralstonia eutropha H16.

    PubMed

    Karstens, Katja; Zschiedrich, Christopher P; Bowien, Botho; Stülke, Jörg; Görke, Boris

    2014-04-01

    EIIA(Ntr) is a member of a truncated phosphotransferase (PTS) system that serves regulatory functions and exists in many Proteobacteria in addition to the sugar transport PTS. In Escherichia coli, EIIA(Ntr) regulates K(+) homeostasis through interaction with the K(+) transporter TrkA and sensor kinase KdpD. In the ?-Proteobacterium Ralstonia eutropha H16, EIIA(Ntr) influences formation of the industrially important bioplastic poly(3-hydroxybutyrate) (PHB). PHB accumulation is controlled by the stringent response and induced under conditions of nitrogen deprivation. Knockout of EIIA(Ntr) increases the PHB content. In contrast, absence of enzyme I or HPr, which deliver phosphoryl groups to EIIA(Ntr), has the opposite effect. To clarify the role of EIIA(Ntr) in PHB formation, we screened for interacting proteins that co-purify with Strep-tagged EIIA(Ntr) from R. eutropha cells. This approach identified the bifunctional ppGpp synthase/hydrolase SpoT1, a key enzyme of the stringent response. Two-hybrid and far-Western analyses confirmed the interaction and indicated that only non-phosphorylated EIIA(Ntr) interacts with SpoT1. Interestingly, this interaction does not occur between the corresponding proteins of E. coli. Vice versa, interaction of EIIA(Ntr) with KdpD appears to be absent in R. eutropha, although R. eutropha EIIA(Ntr) can perfectly substitute its homologue in E. coli in regulation of KdpD activity. Thus, interaction with KdpD might be an evolutionary 'ancient' task of EIIA(Ntr) that was subsequently replaced by interaction with SpoT1 in R. eutropha. In conclusion, EIIA(Ntr) might integrate information about nutritional status, as reflected by its phosphorylation state, into the stringent response, thereby controlling cellular PHB content in R. eutropha. PMID:24515609

  7. Revision of the new world genus Crassomicrodus Ashmead (Hymenoptera, Braconidae, Agathidinae), with an identification key to species

    PubMed Central

    Figueroa, José Isaac; Sharkey, Michael Joseph; Nápoles, Jesus Romero; García, José Antonio Sánchez; Martínez, Ana Mabel; López-Martínez, Victor; Pineda, Samuel

    2011-01-01

    Abstract A key to species and descriptions are presented for 14 species of the New World genus Crassomicrodus Ashmead. Seven new species, Crassomicrodus azteca, Crassomicrodus clypealis, Crassomicrodus costaricensis, Crassomicrodus jalisciensis, Crassomicrodus mariae, Crassomicrodus oaxaquensis,and Crassomicrodus olgae are described. Crassomicrodus fenestratus (Viereck) is synonymized with Crassomicrodus nigriceps (Cresson). Crassomicrodus melanopleurus (Ashmead) is recognized as a valid species. PMID:22144862

  8. A gallery of the key characters to ease identification of Dermanyssus gallinae (Acari: Gamasida: Dermanyssidae) and allow differentiation from Ornithonyssus sylviarum (Acari: Gamasida: Macronyssidae)

    PubMed Central

    2012-01-01

    Background Dermanyssus gallinae (poultry red mite) is a major threat for the poultry industry and is of significant interest for public health. Identification of D. gallinae can be difficult for scientists not familiar with mite morphology and terminology especially when trying to use identification keys. Moreover, this species may easily be confused with another dermanyssoid mite, Ornithonyssus sylviarum (northern fowl mite), which often shares the same hosts and environment. Methods Specimens of D. gallinae were collected at poultry farms in the Puglia and performed for light and scanning electron microscopy observations, identification and micrographs. Moreover specimens of O. sylviarum were collected separately macerated and mounted on slides for light microscopy observations, identification and pictures. Results The micrographs used in this study, based on LM and SEM observations, highlight the following important identifying characters of D. gallinae: the prominent shoulders of the dorsal shield and the jagged edges of the shield reticulations, the position of setae j1, s1 and the epigynal pores, and the presence on tibia IV pl of one seta. Additional micrographs highlighting the shape of the dorsal (abruptly narrowed posteriorly) and epigynal (narrowly rounded posteriorly) shields and the chelicera (elongate, with distinct digits) of O. sylviarum enable its differentiation from D.gallinae. Conclusion The photographic support provided here (both LM and SEM pictures) can be considered a practical tool for scientists who are not well acquainted with the morphology of D.gallinae, and who are involved with classical and molecular systematics, veterinary and human health aspects of poultry red mites. PMID:22647594

  9. Cellular/Molecular Interaction via a Key Tryptophan in the III Linker of

    E-print Network

    Dolphin, Annette C.

    and Molecular Neuroscience, Department of Pharmacology, University College London, London WC1E 6BT, United to an alanine within the -interacting domain (AID) in the I­II linker of CaV2.2. We showed that the mutation W391 virtually abolishes the binding of CaV 1b and CaV 2a to the CaV2.2 I­II linker

  10. Identification of cytoplasmic proteins interacting with unliganded estrogen receptor ? and ? in human breast cancer cells.

    PubMed

    Stellato, Claudia; Nassa, Giovanni; Tarallo, Roberta; Giurato, Giorgio; Ravo, Maria; Rizzo, Francesca; Marchese, Giovanna; Alexandrova, Elena; Cordella, Angela; Baumann, Marc; Nyman, Tuula A; Weisz, Alessandro; Ambrosino, Concetta

    2015-06-01

    Estrogen receptor subtypes (ER? and ER?) are transcription factors sharing a similar structure but exerting opposite roles in breast cancer cells. Besides the well-characterized genomic actions of nuclear ERs upon ligand binding, specific actions of ligand-free ERs in the cytoplasm also affect cellular functions. The identification of cytoplasmic interaction partners of unliganded ER? and ER? may help characterize the molecular basis of the extra-nuclear mechanism of action of these receptors, revealing novel mechanisms to explain their role in breast cancer response or resistance to endocrine therapy. To this aim, cytoplasmic extracts from human breast cancer MCF-7 cells stably expressing tandem affinity purification-tagged ER? and ER? and maintained in estrogen-free medium were subject to affinity-purification and MS analysis, leading to the identification of 84 and 142 proteins associated with unliganded ER? and ER?, respectively. Functional analyses of ER subtype-specific interactomes revealed significant differences in the molecular pathways targeted by each receptor in the cytoplasm. This work, reporting the first identification of the unliganded ER? and ER? cytoplasmic interactomes in breast cancer cells, provides novel experimental evidence on the nongenomic effects of ERs in the absence of hormonal stimulus. All MS data have been deposited in the ProteomeXchange with identifier PXD001202 (http://proteomecentral.proteomexchange.org/dataset/PXD001202). PMID:25604459

  11. Identification of Cys255 in HIF-1? as a novel site for development of covalent inhibitors of HIF-1?/ARNT PasB domain protein–protein interaction

    PubMed Central

    Cardoso, Rosa; Love, Robert; Nilsson, Carol L; Bergqvist, Simon; Nowlin, Dawn; Yan, Jiangli; Liu, Kevin K-C; Zhu, Jing; Chen, Ping; Deng, Ya-Li; Dyson, H Jane; Greig, Michael J; Brooun, Alexei

    2012-01-01

    The heterodimer HIF-1? (hypoxia inducible factor)/HIF-? (also known as ARNT-aryl hydrocarbon nuclear translocator) is a key mediator of cellular response to hypoxia. The interaction between these monomer units can be modified by the action of small molecules in the binding interface between their C-terminal heterodimerization (PasB) domains. Taking advantage of the presence of several cysteine residues located in the allosteric cavity of HIF-1? PasB domain, we applied a cysteine-based reactomics “hotspot identification” strategy to locate regions of HIF-1? PasB domain critical for its interaction with ARNT. COMPOUND 5 was identified using a mass spectrometry-based primary screening strategy and was shown to react specifically with Cys255 of the HIF-1? PasB domain. Biophysical characterization of the interaction between PasB domains of HIF-1? and ARNT revealed that covalent binding of COMPOUND 5 to Cys255 reduced binding affinity between HIF-1? and ARNT PasB domains approximately 10-fold. Detailed NMR structural analysis of HIF-1?-PasB-COMPOUND 5 conjugate showed significant local conformation changes in the HIF-1? associated with key residues involved in the HIF-1?/ARNT PasB domain interaction as revealed by the crystal structure of the HIF-1?/ARNT PasB heterodimer. Our screening strategy could be applied to other targets to identify pockets surrounding reactive cysteines suitable for development of small molecule modulators of protein function. PMID:23033253

  12. Conductive biomolecules and their THz vibrational interactions: key aspects of bioelectronics

    NASA Astrophysics Data System (ADS)

    Ramadurai, Dinakar; Yamanaka, Takayuki; Li, Yang; Sankar, Viswanath; Dutta, Mitra; Stroscio, Michael A.; Rajh, Tijana; Saponjic, Zoran; Xu, Song

    2006-05-01

    This paper focuses on understanding the THz-phonon mediated transport of polarons in biomolecules, with particular attention on polaron transport in DNA. In order to exploit biology-based approaches to realizing new electronic systems, it is necessary to understand the electrical transport properties and THz-phonon interactions of biomolecules that portend applications both as electrically conductive wires and as structures that facilitate the chemically-directed assembly of massively integrated ensembles of nanoscale semiconducting elements into terascale integrated networks. Special attention is given to charge transport in biomolecules using indirect-bandgap colloidal nanocrystals linked with biomolecules.

  13. Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

    PubMed Central

    Zong, Shan; Deng, Shuyun; Chen, Kenian; Wu, Jia Qian

    2015-01-01

    Hematopoietic stem cells (HSCs) are used clinically for transplantation treatment to rebuild a patient's hematopoietic system in many diseases such as leukemia and lymphoma. Elucidating the mechanisms controlling HSCs self-renewal and differentiation is important for application of HSCs for research and clinical uses. However, it is not possible to obtain large quantity of HSCs due to their inability to proliferate in vitro. To overcome this hurdle, we used a mouse bone marrow derived cell line, the EML (Erythroid, Myeloid, and Lymphocytic) cell line, as a model system for this study. RNA-sequencing (RNA-Seq) has been increasingly used to replace microarray for gene expression studies. We report here a detailed method of using RNA-Seq technology to investigate the potential key factors in regulation of EML cell self-renewal and differentiation. The protocol provided in this paper is divided into three parts. The first part explains how to culture EML cells and separate Lin-CD34+ and Lin-CD34? cells. The second part of the protocol offers detailed procedures for total RNA preparation and the subsequent library construction for high-throughput sequencing. The last part describes the method for RNA-Seq data analysis and explains how to use the data to identify differentially expressed transcription factors between Lin-CD34+ and Lin-CD34? cells. The most significantly differentially expressed transcription factors were identified to be the potential key regulators controlling EML cell self-renewal and differentiation. In the discussion section of this paper, we highlight the key steps for successful performance of this experiment. In summary, this paper offers a method of using RNA-Seq technology to identify potential regulators of self-renewal and differentiation in EML cells. The key factors identified are subjected to downstream functional analysis in vitro and in vivo. PMID:25407807

  14. Identification of the key odorants in barley malt (caramalt) using GC/MS techniques and odour dilution analyses.

    PubMed

    Fickert, B; Schieberle, P

    1998-12-01

    Application of the aroma extract dilution analysis (AEDA) on a distillate prepared from ground caramalt kernels followed by identification experiments revealed 3-methylbutanal (malty), 1-octen-3-one (mushroom-like), methional (cooked potato), (E,E)-2,4-decadienal (fatty, waxy), vanillin (vanilla-like), 2- and 3-methylbutanoic acid (sweaty) and 4-hydroxy-2,5-dimethyl-3-(2H)-furanone (caramel-like) as the most odor-active compounds. Using static headspace/olfactometry, the very volatile odorants dimethyl sulfide (cooked vegetable-like) and 2-methylpropanal (malty) were identified as additional odorants contributing to the overall rye-bread crust-like odour of the caramalt. PMID:9881363

  15. Microbial Glycan Microarrays Define Key Features of Host-Microbial Interactions

    PubMed Central

    Stowell, Sean R.; Arthur, Connie M.; McBride, Ryan; Berger, Oren; Razi, Nahid; Heimburg-Molinaro, Jamie; Rodrigues, Lilian C.; Gourdine, Jean-Philippe; Noll, Alexander J.; von Gunten, Stephan; Smith, David F.; Knirel, Yuriy A.; Paulson, James C.; Cummings, Richard D.

    2014-01-01

    Genomic approaches continue to provide unprecedented insight into the microbiome, yet host immune interactions with diverse microbiota can be difficult to study. We therefore generated a microbial microarray containing defined antigens isolated from a broad range of microbial flora to examine adaptive and innate immunity. Serological studies with this microarray show that immunoglobulins from multiple mammalian species exhibit unique patterns of reactivity, while exposure of animals to distinct microbes induces specific serological recognition. While adaptive immunity exhibited plasticity toward microbial antigens, immunological tolerance limits reactivity toward self. We discovered that several innate immune galectins exhibit specific recognition of microbes that express self-like antigens, leading to direct killing of a broad range of gram negative and positive microbes. Thus, host protection against microbes appears to represent a balance between adaptive and innate immunity to defend against evolving antigenic determinants while protecting against molecular mimicry. PMID:24814672

  16. SimSphere model sensitivity analysis towards establishing its use for deriving key parameters characterising land surface interactions

    NASA Astrophysics Data System (ADS)

    Petropoulos, G. P.; Griffiths, H. M.; Carlson, T. N.; Ioannou-Katidis, P.; Holt, T.

    2014-09-01

    Being able to accurately estimate parameters characterising land surface interactions is currently a key scientific priority due to their central role in the Earth's global energy and water cycle. To this end, some approaches have been based on utilising the synergies between land surface models and Earth observation (EO) data to retrieve relevant parameters. One such model is SimSphere, the use of which is currently expanding, either as a stand-alone application or synergistically with EO data. The present study aimed at exploring the effect of changing the atmospheric sounding profile on the sensitivity of key variables predicted by this model assuming different probability distribution functions (PDFs) for its inputs/outputs. To satisfy this objective and to ensure consistency and comparability to analogous studies conducted previously on the model, a sophisticated, cutting-edge sensitivity analysis (SA) method adopting Bayesian theory was implemented on SimSphere. Our results did not show dramatic changes in the nature or ranking of influential model inputs in comparison to previous studies. Model outputs examined using SA were sensitive to a small number of the inputs; a significant amount of first-order interactions between the inputs was also found, suggesting strong model coherence. Results showed that the assumption of different PDFs for the model inputs/outputs did not have an important bearing on mapping the most responsive model inputs and interactions, but only the absolute SA measures. This study extends our understanding of SimSphere's structure and further establishes its coherence and correspondence to that of a natural system's behaviour. Consequently, the present work represents a significant step forward in the global efforts on SimSphere verification, especially those focusing on the development of global operational products from the model synergy with EO data.

  17. Frugivores and seed dispersal: mechanisms and consequences for biodiversity of a key ecological interaction.

    PubMed

    Jordano, Pedro; Forget, Pierre-Michel; Lambert, Joanna E; Böhning-Gaese, Katrin; Traveset, Anna; Wright, S Joseph

    2011-06-23

    The 5th Symposium on Frugivores and Seed Dispersal, held in Montpellier (France), 13-18 June 2010, brought together more than 220 researchers exemplifying a wide diversity of approaches to the study of frugivory and dispersal of seeds. Following Ted Fleming and Alejandro Estrada's initiative in 1985, this event was a celebration of the 25th anniversary of the first meeting in Veracruz, Mexico. Frugivory and seed dispersal are active research areas that have diversified in multiple directions since 1985 to include evolution (e.g. phylogenetic diversity and dispersal adaptations), physiology (e.g. sensory cues and digestion), landscape ecology (movement patterns), molecular ecology (e.g. gene flow, genetic diversity and structure), community ecology (e.g. mutualistic interaction networks) and conservation biology (effects of hunting, fragmentation, invasion and extinction), among others. This meeting provided an opportunity to assess conceptual and methodological progress, to present ever more sophisticated insights into frugivory in animals and dispersal patterns in plants, and to report the advances made in examining the mechanisms and consequences of seed dispersal for plants and frugivores. PMID:21084336

  18. Small-world network approach to identify key residues in protein-protein interaction.

    PubMed

    del Sol, Antonio; O'Meara, Paul

    2005-02-15

    We show that protein complexes can be represented as small-world networks, exhibiting a relatively small number of highly central amino-acid residues occurring frequently at protein-protein interfaces. We further base our analysis on a set of different biological examples of protein-protein interactions with experimentally validated hot spots, and show that 83% of these predicted highly central residues, which are conserved in sequence alignments and nonexposed to the solvent in the protein complex, correspond to or are in direct contact with an experimentally annotated hot spot. The remaining 17% show a general tendency to be close to an annotated hot spot. On the other hand, although there is no available experimental information on their contribution to the binding free energy, detailed analysis of their properties shows that they are good candidates for being hot spots. Thus, highly central residues have a clear tendency to be located in regions that include hot spots. We also show that some of the central residues in the protein complex interfaces are central in the monomeric structures before dimerization and that possible information relating to hot spots of binding free energy could be obtained from the unbound structures. PMID:15617065

  19. New records of acanthocephalans from birds in the Philippines with a description of a new Porrorchis species and identification keys for the genus.

    PubMed

    Lisitsyna, Olga I; Tkach, Vasyl V; Bush, Sarah E

    2012-12-01

    Three acanthocephalan species, Sphaerirostris turdi from the island thrush (Turdus poliocephalus), and Porrorchis centropusi and Porrorchis kinsellai n. sp., both from Philippine scops owls (Otus megalotis), are reported from Aurora Province, Luzon Island, Philippines. Porrorchis kinsellai n. sp. can be readily differentiated from previously known members of the genus by an almost perfectly spherical proboscis and presence of a characteristic finger-like process at the female posterior end, among other features. Porrorchis centropusi and Porrorchis hylae are regarded as synonyms by some authors, but based on several morphological features, they are considered separate species here. A key to the identification of all known species of Porrorchis (other than insufficiently described Porrorchis brevicanthus) is provided. PMID:22663559

  20. Identification of Proteins from Prunus persica That Interact with Peach Latent Mosaic Viroid?

    PubMed Central

    Dubé, Audrey; Bisaillon, Martin; Perreault, Jean-Pierre

    2009-01-01

    Peach latent mosaic viroid (PLMVd) is a small, single-stranded, circular RNA pathogen that infects Prunus persica trees. As with all other known viroids, the PLMVd genome does not encode any proteins. Consequently, it must interact with host cellular factors in order to ensure its life cycle. With the objective of identifying cellular proteins that interact with PLMVd, Northwestern hybridizations were performed using partially purified peach leaf extracts. Mass spectrometric analysis of the detected RNA-protein complexes led to the identification of six putative RNA-binding proteins. One of these was found to be elongation factor 1-alpha (eEF1A), and because of its known involvement in the replication and translation of various RNA viruses, further characterizations were performed. Initially, the existence of this interaction received support from an experiment that immunoprecipitated the eEF1A from a crude extract of infected peach leaves, coupled with reverse transcription-PCR detection of the PLMVd. Subsequently, eEF1A interaction with PLMVd strands of both polarities was confirmed in vitro by electrophoresis mobility shift assays, fluorescence spectroscopy, and the prediction of an altered PLMVd RNase mapping profile in the presence of the protein. The potential contribution of eEF1A to the molecular biology of PLMVd, including for viroid replication, is discussed. PMID:19759139

  1. Revalidation and redescription of Triatoma brasiliensis macromelasoma Galvão, 1956 and an identification key for the Triatoma brasiliensis complex (Hemiptera: Reduviidae: Triatominae)

    PubMed Central

    Costa, Jane; Correia, Nathália Cordeiro; Neiva, Vanessa Lima; Gonçalves, Teresa Cristina Monte; Felix, Márcio

    2013-01-01

    Triatoma brasiliensis macromelasoma is revalidated based on the results of previous multidisciplinary studies on the Triatoma brasiliensis complex, consisting of crossing experiments and morphological, biological, ecological and molecular analyses. These taxonomic tools showed the closest relationship between T. b. macromelasoma and Triatoma brasiliensis brasiliensis. T. b. macromelasoma is redescribed based on specimens collected in the type locality and specimens from a F1 colony. The complex now comprises T. b. brasiliensis, T. b. macromelasoma, Triatoma melanica, Triatoma juazeirensis and Triatoma sherlocki. An identification key for all members of the complex is presented. This detailed comparative study of the morphological features of T. b. macromelasoma and the remaining members of the complex corroborates results from multidisciplinary analyses, suggesting that the subspecific status is applicable. This subspecies can be distinguished by the following combination of features: a pronotum with 1+1 narrow brownish-yellow stripes on the submedian carinae, not attaining its apex, hemelytra with membrane cells darkened on the central portion and legs with an incomplete brownish-yellow ring on the apical half of the femora. Because the T. brasiliensis complex is of distinct epidemiological importance throughout its geographic distribution, a precise identification of its five members is important for monitoring and controlling actions against Chagas disease transmission. PMID:24037202

  2. Citrus tristeza virus p23: a unique protein mediating key virus-host interactions.

    PubMed

    Flores, Ricardo; Ruiz-Ruiz, Susana; Soler, Nuria; Sánchez-Navarro, Jesús; Fagoaga, Carmen; López, Carmelo; Navarro, Luis; Moreno, Pedro; Peña, Leandro

    2013-01-01

    The large RNA genome of Citrus tristeza virus (CTV; ca. 20 kb) contains 12 open reading frames, with the 3'-terminal one corresponding to a protein of 209 amino acids (p23) that is expressed from an abundant subgenomic RNA. p23, an RNA-binding protein with a putative zinc-finger domain and some basic motifs, is unique to CTV because no homologs have been found in other closteroviruses, including the type species of the genus Beet yellows virus (despite both viruses having many homologous genes). Consequently, p23 might have evolved for the specific interaction of CTV with its citrus hosts. From a functional perspective p23 has been involved in many roles: (i) regulation of the asymmetrical accumulation of CTV RNA strands, (ii) induction of the seedling yellows syndrome in sour orange and grapefruit, (iii) intracellular suppression of RNA silencing, (iv) elicitation of CTV-like symptoms when expressed ectopically as a transgene in several Citrus spp., and (v) enhancement of systemic infection (and virus accumulation) in sour orange and CTV release from the phloem in p23-expressing transgenic sweet and sour orange. Moreover, transformation of Mexican lime with intron-hairpin constructs designed for the co-inactivation of p23 and the two other CTV silencing suppressors results in complete resistance against the homologous virus. From a cellular point of view, recent data indicate that p23 accumulates preferentially in the nucleolus, being the first closterovirus protein with such a subcellular localization, as well as in plasmodesmata. These major accumulation sites most likely determine some of the functional roles of p23. PMID:23653624

  3. Citrus tristeza virus p23: a unique protein mediating key virus–host interactions

    PubMed Central

    Flores, Ricardo; Ruiz-Ruiz, Susana; Soler, Nuria; Sánchez-Navarro, Jesús; Fagoaga, Carmen; López, Carmelo; Navarro, Luis; Moreno, Pedro; Peña, Leandro

    2013-01-01

    The large RNA genome of Citrus tristeza virus (CTV; ca. 20 kb) contains 12 open reading frames, with the 3?-terminal one corresponding to a protein of 209 amino acids (p23) that is expressed from an abundant subgenomic RNA. p23, an RNA-binding protein with a putative zinc-finger domain and some basic motifs, is unique to CTV because no homologs have been found in other closteroviruses, including the type species of the genus Beet yellows virus (despite both viruses having many homologous genes). Consequently, p23 might have evolved for the specific interaction of CTV with its citrus hosts. From a functional perspective p23 has been involved in many roles: (i) regulation of the asymmetrical accumulation of CTV RNA strands, (ii) induction of the seedling yellows syndrome in sour orange and grapefruit, (iii) intracellular suppression of RNA silencing, (iv) elicitation of CTV-like symptoms when expressed ectopically as a transgene in several Citrus spp., and (v) enhancement of systemic infection (and virus accumulation) in sour orange and CTV release from the phloem in p23-expressing transgenic sweet and sour orange. Moreover, transformation of Mexican lime with intron-hairpin constructs designed for the co-inactivation of p23 and the two other CTV silencing suppressors results in complete resistance against the homologous virus. From a cellular point of view, recent data indicate that p23 accumulates preferentially in the nucleolus, being the first closterovirus protein with such a subcellular localization, as well as in plasmodesmata. These major accumulation sites most likely determine some of the functional roles of p23. PMID:23653624

  4. Research on Key Factors and Their Interaction Effects of Electromagnetic Force of High-Speed Solenoid Valve

    PubMed Central

    Fan, Liyun; Xu, De; Ma, Xiuzhen; Song, Enzhe

    2014-01-01

    Analysis consisting of numerical simulations along with lab experiments of interaction effects between key parameters on the electromagnetic force based on response surface methodology (RSM) has been also proposed to optimize the design of high-speed solenoid valve (HSV) and improve its performance. Numerical simulation model of HSV has been developed in Ansoft Maxwell environment and its accuracy has been validated through lab experiments. Effect of change of core structure, coil structure, armature structure, working air gap, and drive current on the electromagnetic force of HSV has been analyzed through simulation model and influence rules of various parameters on the electromagnetic force have been established. The response surface model of the electromagnetic force has been utilized to analyze the interaction effect between major parameters. It has been concluded that six interaction factors including working air gap with armature radius, drive current with armature thickness, coil turns with side pole radius, armature thickness with its radius, armature thickness with side pole radius, and armature radius with side pole radius have significant influence on the electromagnetic force. Optimal match values between coil turns and side pole radius; armature thickness and side pole radius; and armature radius and side pole radius have also been determined. PMID:25243217

  5. Identification of the Key Astringent Compounds in Spinach ( Spinacia oleracea ) by Means of the Taste Dilution Analysis

    Microsoft Academic Search

    Annika Brock; Thomas Hofmann

    2008-01-01

    Application of sequential solvent extraction and reverse phase high-performance liquid chromatography separation in combination\\u000a with the taste dilution analysis, followed by liquid chromatography–mass spectroscopy and 1D\\/2D nuclear magnetic resonance\\u000a experiments revealed 11 flavon-3-ol-O-glycosides as the key astringent and mouth-drying compounds in blanched leaves of spinach (Spinacia oleracea). Among these, in particular, 3?,5-dihydroxy-3-methoxy-6:7-methylendioxy-flavon-4?-O-?-d-glucuronide (3), 5-hydroxy-3,3?-dimethoxy-6:7-methylendioxy-flavon-4?-O-?-d-glucuronide (11), and patuletin-3-O-?-d-glucopyranosyl(1?6)-?-d-glucopyranoside (5) were found

  6. Key Structures and Interactions for Binding of Mycobacterium tuberculosis Protein Kinase B Inhibitors from Molecular Dynamics Simulation.

    PubMed

    Punkvang, Auradee; Kamsri, Pharit; Saparpakorn, Patchreenart; Hannongbua, Supa; Wolschann, Peter; Irle, Stephan; Pungpo, Pornpan

    2015-07-01

    Substituted aminopyrimidine inhibitors have recently been introduced as antituberculosis agents. These inhibitors show impressive activity against protein kinase B, a Ser/Thr protein kinase that is essential for cell growth of M. tuberculosis. However, up to now, X-ray structures of the protein kinase B enzyme complexes with the substituted aminopyrimidine inhibitors are currently unavailable. Consequently, structural details of their binding modes are questionable, prohibiting the structural-based design of more potent protein kinase B inhibitors in the future. Here, molecular dynamics simulations, in conjunction with molecular mechanics/Poisson-Boltzmann surface area binding free-energy analysis, were employed to gain insight into the complex structures of the protein kinase B inhibitors and their binding energetics. The complex structures obtained by the molecular dynamics simulations show binding free energies in good agreement with experiment. The detailed analysis of molecular dynamics results shows that Glu93, Val95, and Leu17 are key residues responsible to the binding of the protein kinase B inhibitors. The aminopyrazole group and the pyrimidine core are the crucial moieties of substituted aminopyrimidine inhibitors for interaction with the key residues. Our results provide a structural concept that can be used as a guide for the future design of protein kinase B inhibitors with highly increased antagonistic activity. PMID:25354564

  7. Overcoming asymmetric goals in teams: The interactive roles of team learning orientation and team identification.

    PubMed

    Pearsall, Matthew J; Venkataramani, Vijaya

    2015-05-01

    Although members of teams share a common, ultimate objective, they often have asymmetric or conflicting individual goals that shape the way they contribute to, and pursue, the shared goal of the team. Compounding this problem, they are frequently unaware of the nature of these goal asymmetries or even the fact that such differences exist. Drawing on, and integrating, social interdependence and representational gaps theories, we identify 2 emergent states that combine interactively to enable teams to overcome asymmetric goals: team identification and team learning orientation. Using data from long-term, real-life teams that engaged in a computer simulation designed to create both asymmetric goals and representational gaps about those goals, we found that teams were most effective when they had a high learning orientation coupled with high team identification and that this effect was mediated by teams' ability to form more accurate team goal mental models and engage in effective planning processes. Implications for theory and practice are discussed. (PsycINFO Database Record PMID:25384202

  8. Identification of a key residue in Kv7.1 potassium channel essential for sensing external potassium ions.

    PubMed

    Wang, Wenying; Flores, Maria Cristina Perez; Sihn, Choong-Ryoul; Kim, Hyo Jeong; Zhang, Yinuo; Doyle, Karen J; Chiamvimonvat, Nipavan; Zhang, Xiao-Dong; Yamoah, Ebenezer N

    2015-03-01

    Kv7.1 voltage-gated K(+) (Kv) channels are present in the apical membranes of marginal cells of the stria vascularis of the inner ear, where they mediate K(+) efflux into the scala media (cochlear duct) of the cochlea. As such, they are exposed to the K(+)-rich (? 150 mM of external K(+) (K(+) e)) environment of the endolymph. Previous studies have shown that Kv7.1 currents are substantially suppressed by high K(+) e (independent of the effects of altering the electrochemical gradient). However, the molecular basis for this inhibition, which is believed to involve stabilization of an inactivated state, remains unclear. Using sequence alignment of S5-pore linkers of several Kv channels, we identified a key residue, E290, found in only a few Kv channels including Kv7.1. We used substituted cysteine accessibility methods and patch-clamp analysis to provide evidence that the ability of Kv7.1 to sense K(+) e depends on E290, and that the charge at this position is essential for Kv7.1's K(+) e sensitivity. We propose that Kv7.1 may use this feedback mechanism to maintain the magnitude of the endocochlear potential, which boosts the driving force to generate the receptor potential of hair cells. The implications of our findings transcend the auditory system; mutations at this position also result in long QT syndrome in the heart. PMID:25712016

  9. Network Understanding of Herb Medicine via Rapid Identification of Ingredient-Target Interactions

    NASA Astrophysics Data System (ADS)

    Zhang, Hai-Ping; Pan, Jian-Bo; Zhang, Chi; Ji, Nan; Wang, Hao; Ji, Zhi-Liang

    2014-01-01

    Today, herb medicines have become the major source for discovery of novel agents in countermining diseases. However, many of them are largely under-explored in pharmacology due to the limitation of current experimental approaches. Therefore, we proposed a computational framework in this study for network understanding of herb pharmacology via rapid identification of putative ingredient-target interactions in human structural proteome level. A marketing anti-cancer herb medicine in China, Yadanzi (Brucea javanica), was chosen for mechanistic study. Total 7,119 ingredient-target interactions were identified for thirteen Yadanzi active ingredients. Among them, about 29.5% were estimated to have better binding affinity than their corresponding marketing drug-target interactions. Further Bioinformatics analyses suggest that simultaneous manipulation of multiple proteins in the MAPK signaling pathway and the phosphorylation process of anti-apoptosis may largely answer for Yadanzi against non-small cell lung cancers. In summary, our strategy provides an efficient however economic solution for systematic understanding of herbs' power.

  10. Identification of cyclin D3 as a new interaction partner of lamin A/C

    SciTech Connect

    Mariappan, Indumathi [Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007 (India); Gurung, Ritika [Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007 (India); Thanumalayan, Subramonian [Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007 (India); Parnaik, Veena K. [Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007 (India)]. E-mail: veenap@ccmb.res.in

    2007-04-20

    Lamin A/C is a major component of the nuclear lamina. An intact nuclear lamina has been proposed to be necessary for muscle differentiation. Cyclin D3 is known to be upregulated in differentiated muscle cells and to form insoluble complexes with cell-cycle regulatory factors in these cells. We have examined the possibility of direct binding interactions between lamin A/C and cyclin D3 by in vitro binding assays and co-immunoprecipitation studies with muscle cells. Our results indicate that cyclin D3 binds specifically to amino acid residues 383-474 of lamin A/C and associates with lamin A/C in muscle cells. The identification of cyclin D3 as a novel binding partner of lamin A/C has important implications for a role for lamin A/C in muscle differentiation.

  11. CH3-? interaction of explosives with cavity of a TPE macrocycle: the key cause for highly selective detection of TNT.

    PubMed

    Feng, Hai-Tao; Wang, Jin-Hua; Zheng, Yan-Song

    2014-11-26

    The identification of explosives is critical for analyzing the background of terrorism activities and the origin of pollution aroused by the explosives, but it is a challenge to discriminate the explosives with a very similar structure. Herein we report a series of TPE-based macrocycles with an AIE effect for the 0.2-4 ppb level detection of TNT among a number of nitro-aromatic compounds through fluorescence quenching in natural water sources, whereas the contact mode approach using portable paper sensors exhibited a high sensitivity for the detection of TNT at 1.0 × 10(-13) M level. The reliability of the quantitative analysis has been confirmed by HPLC. Our findings demonstrate that the TPE-based macrocycles have great potential as excellent sensors for TNT. Moreover, it was found for the first time that the macrocycles could selectively recognize nitroaromatics explosives bearing methyl group through a CH3-? interactions, and even exhibit a sole selectivity for TNT among the very difficultly differentiating nitroaromatics including trinitrophenol and trinitrobenzene. PMID:25319016

  12. Evidence-based identification of key beliefs explaining adult male circumcision motivation in Zimbabwe: targets for behavior change messaging.

    PubMed

    Montaño, Daniel E; Kasprzyk, Danuta; Hamilton, Deven T; Tshimanga, Mufuta; Gorn, Gerald

    2014-05-01

    Male circumcision (MC) reduces HIV acquisition among men, leading WHO/UNAIDS to recommend a goal to circumcise 80 % of men in high HIV prevalence countries. Significant investment to increase MC capacity in priority countries was made, yet only 5 % of the goal has been achieved in Zimbabwe. The integrated behavioral model (IBM) was used as a framework to investigate the factors affecting MC motivation among men in Zimbabwe. A survey instrument was designed based on elicitation study results, and administered to a representative household-based sample of 1,201 men aged 18-30 from two urban and two rural areas in Zimbabwe. Multiple regression analysis found all five IBM constructs significantly explained MC Intention. Nearly all beliefs underlying the IBM constructs were significantly correlated with MC Intention. Stepwise regression analysis of beliefs underlying each construct respectively found that 13 behavioral beliefs, 5 normative beliefs, 4 descriptive norm beliefs, 6 efficacy beliefs, and 10 control beliefs were significant in explaining MC Intention. A final stepwise regression of the five sets of significant IBM construct beliefs identified 14 key beliefs that best explain Intention. Similar analyses were carried out with subgroups of men by urban-rural and age. Different sets of behavioral, normative, efficacy, and control beliefs were significant for each sub-group, suggesting communication messages need to be targeted to be most effective for sub-groups. Implications for the design of effective MC demand creation messages are discussed. This study demonstrates the application of theory-driven research to identify evidence-based targets for intervention messages to increase men's motivation to get circumcised and thereby improve demand for male circumcision. PMID:24443147

  13. Identification of key functional groups of microbes in the oxygen minimum zone (OMZ) of the NE equatorial Pacific

    NASA Astrophysics Data System (ADS)

    Kim, M.; Cho, H.; Kim, K.; Ju, S.; Hyun, J.

    2012-12-01

    In order to explicate high secondary production of heterotrophic prokaryotes (hereafter bacteria; 2.35mgCm-3d-1 in subsurface chlorophyll maximum (SCM; 44m in depth), 1.73mgCm-3d-1 in OMZ core (700m in depth)) and to gauge dominated microbial groups in the oxygen minimum layer, we performed phylogenetic analysis based on bacterial and archaeal 16S rRNA gene in the NE equatorial Pacific. A total of 290 bacterial clones and 261 archaeal clones were sequenced and used to compare microbial diversity between SCM layer and OMZ in July, 2010. Major groups of bacteria in the SCM layer (171.68?mol O2) were Cyanobacteria (28.1%), ?-proteobacteria (25.0%) and Bacterioidetes (6.3%). OMZ core (12.05?mol O2) was dominated by ?-proteobacteria (40.2%), ?-proteobacteria (19.6%), and ?-proteobacteria (12.4%) in order. The deeper layer of the OMZ (800m in depth, 19.20?mol O2) had the largest number of ?-proteobacteria (24.7%), followed by ?-proteobacteria (20.6%), and ?-proteobacteria (18.6%). In case of archaea, euryarchaeal Marine Group-? (MG-?) were dominated in the SCM layer (95.2%). On the other hand, in the OMZ core and the deeper layer of the OMZ, Crenarchaea (MG- ?) were most abundant (69.4% of 700m, 71.8% of 800m) and MG-? was the second (21.2% of 700m, 21.1% of 800m). In summary, bacterial clone libraries were dominated by ?-proteobacteria and ?-proteobacteria and archaeal clone libraries were dominated by MG- ? in the OMZ. It is generally known that Microbes involved in anaerobic processes are among those groups. Comparative phylogenic analysis of microbial communities have the potential to provide more detail information on diversity and identify key functional groups of bacteria in the OMZ.

  14. STRUCTURES OF A KEY INTERACTION PROTEIN FROM THE TRYPANOSOMA BRUCEI EDITOSOME IN COMPLEX WITH SINGLE DOMAIN ANTIBODIES

    PubMed Central

    Wu, Meiting; Park, Young-jun; Pardon, Els; Turley, Stewart; Hayhurst, Andrew; Deng, Junpeng; Steyaert, Jan; Hol, Wim G. J.

    2010-01-01

    Several major global diseases are caused by single-cell parasites called trypanosomatids. These organisms exhibit many unusual features including a unique and essential U-insertion-deletion RNA editing process in their single mitochondrion. Many key RNA editing steps occur in ~ 20S editosomes, which have a core of 12 proteins. Among these, the “interaction protein” KREPA6 performs a central role in maintaining the integrity of the editosome core and also binds to ssRNA. The use of llama single domain antibodies (VHH domains) accelerated crystal growth of KREPA6 from Trypanosoma brucei dramatically. All three structures obtained are heterotetramers with a KREPA6 dimer in the center, and one VHH domain bound to each KREPA6 subunit. Two of the resultant heterotetramers use complementarity determining region 2 (CDR2) and framework residues to form a parallel pair of beta strands with KREPA6 – a mode of interaction not seen before in VHH domain-antigen complexes. The third type of VHH domain binds in a totally different manner to KREPA6. Intriguingly, while KREPA6 forms tetramers in solution adding either one of the three VHH domains results in the formation of a heterotetramer in solution, in perfect agreement with the crystal structures. Biochemical solution studies indicate that the C-terminal tail of KREPA6 is involved in the dimerization of KREPA6 dimers to form tetramers. The implications of these crystallographic and solution studies for possible modes of interaction of KREPA6 with its many binding partners in the editosome are discussed. PMID:20969962

  15. Identification of key factors influencing primary productivity in two river-type reservoirs by using principal component regression analysis.

    PubMed

    Lee, Yeonjung; Ha, Sun-Yong; Park, Hae-Kyung; Han, Myung-Soo; Shin, Kyung-Hoon

    2015-04-01

    To understand the factors controlling algal production in two lakes located on the Han River in South Korea, Lake Cheongpyeong and Lake Paldang, a principal component regression model study was conducted using environmental monitoring and primary productivity data. Although the two lakes were geographically close and located along the same river system, the main factors controlling primary productivity in each lake were different: hydraulic retention time and light conditions predominantly influenced algal productivity in Lake Cheongpyeong, while hydraulic retention time, chlorophyll a-specific productivity, and zooplankton grazing rate were most important in Lake Paldang. This investigation confirmed the utility of principal component regression analysis using environmental monitoring data for predicting complex biological processes such as primary productivity; in addition, the study also increased the understanding of explicit interactions between environmental variables. The findings obtained in this research will be useful for the adaptive management of water reservoirs. The results will also aid in the development of management strategies for water resources, thereby improving total environmental conservation. PMID:25813033

  16. in silico identification of protein-protein interactions in Silkworm, Bombyx mori

    PubMed Central

    Sumathy, Ramasamy; Rao, Ashwath Southekal Krishna; Chandrakanth, Nalavadi; Gopalakrishnan, Velliyur Kanniappan

    2014-01-01

    The Domesticated silkworm, Bombyx mori, an economically important insect has been used as a lepidopteran molecular model next only to Drosophila. Compared to the genomic information in silkworm, the protein-protein interaction data are limited. Therefore experimentally identified PPI maps from five model organisms such as E.coli, C.elegans, D.melanogaster, H. sapiens, S. cerevisiae were used to infer the PPI network of silkworm using the well-recognized Interlog based method. Among the 14623 silkworm proteins, 7736 protein-protein interaction pairs were predicted which include 2700 unique proteins of the silkworms. Using the iPfam interaction domains and the gene expression data, these predictions were validated. In that 625 PPI pairs of predicted network were associated with the iPfam domain-domain interactions and the random network has average of 9. In the gene expression method, the average PCC value of the predicted network and random network was 0.29 and 0.23100±0.00042 respectively. It reveals that the predicted PPI networks of silkworm are highly significant and reliable. This is the first PPI network for the silkworm which will provide a framework for deciphering the cellular processes governing key metabolic pathways in the silkworm, Bombyx mori and available at SilkPPI (http://210.212.197.30/SilkPPI/). PMID:24616555

  17. in silico identification of protein-protein interactions in Silkworm, Bombyx mori.

    PubMed

    Sumathy, Ramasamy; Rao, Ashwath Southekal Krishna; Chandrakanth, Nalavadi; Gopalakrishnan, Velliyur Kanniappan

    2014-01-01

    The Domesticated silkworm, Bombyx mori, an economically important insect has been used as a lepidopteran molecular model next only to Drosophila. Compared to the genomic information in silkworm, the protein-protein interaction data are limited. Therefore experimentally identified PPI maps from five model organisms such as E.coli, C.elegans, D.melanogaster, H. sapiens, S. cerevisiae were used to infer the PPI network of silkworm using the well-recognized Interlog based method. Among the 14623 silkworm proteins, 7736 protein-protein interaction pairs were predicted which include 2700 unique proteins of the silkworms. Using the iPfam interaction domains and the gene expression data, these predictions were validated. In that 625 PPI pairs of predicted network were associated with the iPfam domain-domain interactions and the random network has average of 9. In the gene expression method, the average PCC value of the predicted network and random network was 0.29 and 0.23100±0.00042 respectively. It reveals that the predicted PPI networks of silkworm are highly significant and reliable. This is the first PPI network for the silkworm which will provide a framework for deciphering the cellular processes governing key metabolic pathways in the silkworm, Bombyx mori and available at SilkPPI (http://210.212.197.30/SilkPPI/). PMID:24616555

  18. Transcription profile of soybean-root-knot nematode interaction reveals a key role of phythormones in the resistance reaction

    PubMed Central

    2013-01-01

    Background Root-knot nematodes (RKN– Meloidogyne genus) present extensive challenges to soybean crop. The soybean line (PI 595099) is known to be resistant against specific strains and races of nematode species, thus its differential gene expression analysis can lead to a comprehensive gene expression profiling in the incompatible soybean-RKN interaction. Even though many disease resistance genes have been studied, little has been reported about phytohormone crosstalk on modulation of ROS signaling during soybean-RKN interaction. Results Using 454 technology to explore the common aspects of resistance reaction during both parasitism and resistance phases it was verified that hormone, carbohydrate metabolism and stress related genes were consistently expressed at high levels in infected roots as compared to mock control. Most noteworthy genes include those encoding glycosyltransferases, peroxidases, auxin-responsive proteins and gibberellin-regulated genes. Our data analysis suggests the key role of glycosyltransferases, auxins and components of gibberellin signal transduction, biosynthesis and deactivation pathways in the resistance reaction and their participation in jasmonate signaling and redox homeostasis in mediating aspects of plant growth and responses to biotic stress. Conclusions Based on this study we suggest a reasonable model regarding to the complex mechanisms of crosstalk between plant hormones, mainly gibberellins and auxins, which can be crucial to modulate the levels of ROS in the resistance reaction to nematode invasion. The model also includes recent findings concerning to the participation of DELLA-like proteins and ROS signaling controlling plant immune or stress responses. Furthermore, this study provides a dataset of potential candidate genes involved in both nematode parasitism and resistance, which can be tested further for their role in this biological process using functional genomics approaches. PMID:23663436

  19. Detection, quantitation and identification of enteroviruses from surface waters and sponge tissue from the Florida Keys using real-time RT-PCR

    USGS Publications Warehouse

    Donaldson, K.A.; Griffin, Dale W.; Paul, J.H.

    2002-01-01

    A method was developed for the quantitative detection of pathogenic human enteroviruses from surface waters in the Florida Keys using Taqman (R) one-step Reverse transcription (RT)-PCR with the Model 7700 ABI Prism (R) Sequence Detection System. Viruses were directly extracted from unconcentrated grab samples of seawater, from seawater concentrated by vortex flow filtration using a 100kD filter and from sponge tissue. Total RNA was extracted from the samples, purified and concentrated using spin-column chromatography. A 192-196 base pair portion of the 5??? untranscribed region was amplified from these extracts. Enterovirus concentrations were estimated using real-time RT-PCR technology. Nine of 15 sample sites or 60% were positive for the presence of pathogenic human enteroviruses. Considering only near-shore sites, 69% were positive with viral concentrations ranging from 9.3viruses/ml to 83viruses/g of sponge tissue (uncorrected for extraction efficiency). Certain amplicons were selected for cloning and sequencing for identification. Three strains of waterborne enteroviruses were identified as Coxsackievirus A9, Coxsackievirus A16, and Poliovirus Sabin type 1. Time and cost efficiency of this one-step real-time RT-PCR methodology makes this an ideal technique to detect, quantitate and identify pathogenic enteroviruses in recreational waters. Copyright ?? 2002 Elsevier Science Ltd.

  20. In vitro Characterization of LmbK and LmbO: Identification of GDP-D-erythro-?-D-gluco-Octose as a Key Intermediate in Lincomycin A Biosynthesis

    PubMed Central

    Lin, Chia-I; Sasaki, Eita; Zhong, Aoshu; Liu, Hung-wen

    2014-01-01

    Lincomycin A is a clinically useful antibiotic isolated from Streptomyces lincolnensis. It contains an unusual methylmercapto-substituted octose, methylthiolincosamide (MTL). While it has been demonstrated that the C8 backbone of MTL moiety is derived from D-fructose 6-phosphate and D-ribose 5-phosphate via a transaldol reaction catalyzed by LmbR, the subsequent enzymatic transformations leading to the MTL moiety remain elusive. Here, we report the identification of GDP-D-erythro-?-D-gluco-octose (GDP-D-?-D-octose) as a key intermediate in the MTL biosynthetic pathway. Our data show that the octose 1,8-bisphosphate intermediate is first converted to octose 1-phosphate by a phosphatase, LmbK. The subsequent conversion of the octose 1-phosphate to GDP-D-?-D-octose is catalyzed by the octose 1-phosphate guanylyltransferase, LmbO. These results provide significant insight into the lincomycin biosynthetic pathway, because the activated octose likely serves as the acceptor for the installation of the C1 sulfur appendage of MTL. PMID:24380627

  1. Regulation of host cell transcriptional physiology by the avian pneumovirus provides key insights into host-pathogen interactions.

    PubMed

    Munir, Shirin; Kapur, Vivek

    2003-04-01

    Infection with a viral pathogen triggers several pathways in the host cell that are crucial to eliminating infection, as well as those that are used by the virus to enhance its replication and virulence. We have here used suppression subtractive hybridization and cDNA microarray analyses to characterize the host transcriptional response in an avian pneumovirus model of infection. The results of our investigations reveal a dynamic host response that includes the regulation of genes with roles in a vast array of cellular functions as well as those that have not been described previously. The results show a considerable upregulation in transcripts representing the interferon-activated family of genes, predicted to play a role in virus replication arrest. The analysis also identified transcripts for proinflammatory leukocyte chemoattractants, adhesion molecules, and complement that were upregulated and may account for the inflammatory pathology that is the hallmark of viral respiratory infection. Interestingly, alterations in the transcription of several genes in the ubiquitin and endosomal protein trafficking pathways were observed, suggesting a role for these pathways in virus maturation and budding. Taken together, the results of our investigations provide key insights into individual genes and pathways that constitute the host cell's response to avian pneumovirus infection, and they have enabled the development of resources and a model of host-pathogen interaction for an important avian respiratory tract pathogen. PMID:12663796

  2. Keys to Soil Taxonomy

    NSDL National Science Digital Library

    United States Department of Agriculture, National Cooperative Soil Survey

    This United States Department of Agriculture (USDA) publication (11th edition, 2010) contains taxonomic keys necessary for the classification of soils in a form easily used in the field. The book describes soils in general, how to differentiate between them, and how the identification process works. The taxonomic key includes all known soil types, including mollisols, oxisols, alfisols, and others.

  3. Keys to Soil Taxonomy

    NSDL National Science Digital Library

    This United States Department of Agriculture (USDA) publication (9th edition, 2003) contains taxonomic keys necessary for the classification of soils in a form easily used in the field. The book describes soils in general, how to differentiate between them, and how the identification process works. The taxonomic key includes all known soil types, including mollisols, oxisols, alfisols, and others.

  4. "Key to Freshwater Algae": A Web-Based Tool to Enhance Understanding of Microscopic Biodiversity

    ERIC Educational Resources Information Center

    Shayler, Hannah A.; Siver, Peter A.

    2006-01-01

    The Freshwater Ecology Laboratory at Connecticut College has developed an interactive, Web-based identification key to freshwater algal genera using the Lucid Professional and Lucid 3 software developed by the Centre for Biological Information Technology at the University of Queensland, Brisbane, Australia. The "Key to Freshwater Algae" was funded…

  5. A prototype framework for models of socio-hydrology: identification of key feedback loops with application to two Australian case-studies

    NASA Astrophysics Data System (ADS)

    Elshafei, Y.; Sivapalan, M.; Tonts, M.; Hipsey, M. R.

    2014-01-01

    It is increasingly acknowledged that, in order to sustainably manage global freshwater resources, it is critical that we better understand the nature of human-hydrology interactions at the broader catchment system-scale. Yet to date, a generic conceptual framework for building models of catchment systems that include adequate representation of socioeconomic systems - and the dynamic feedbacks between human and natural systems - has remained elusive. In an attempt to work towards such a model, this paper outlines a generic framework for a model of socio-hydrology that posits a novel construct, a composite Community Sensitivity state variable, as a key link to elucidate the drivers of behavioural response in a hydrological context. The framework provides for both macro-scale contextual parameters, which allow it to be applied across climate, socioeconomic and political gradients, and catchment-specific conditions, by way of tailored "closure relationships", in order to ensure that site-specific and application-specific contexts of socio-hydrologic problems can be accommodated. To demonstrate how such a framework would be applied, two different socio-hydrological case studies, taken from the Australian experience, are presented and discussed. It is envisioned that the application of this framework across study sites and gradients will aid in developing our understanding of the fundamental interactions and feedbacks in such complex human-hydrology systems, and allow hydrologists to participate in the growing field of social-ecological systems modelling.

  6. Phlebotomine sand flies from Madagascar (Diptera: Psychodidae). VII. An identification key for Phlebotomus with the description of Phlebotomus (Anaphlebotomus) vaomalalae n. sp.

    PubMed Central

    Randrianambinintsoa, Fano José; Léger, Nicole; Robert, Vincent; Depaquit, Jérôme

    2013-01-01

    An identification key of the Phlebotomus in Madagascar is proposed as well as the description of the male and female Phlebotomus (Anaphlebotomus) vaomalalae n. sp. from Mikea Forest in the south-west of Madagascar. The assignation of this new species to the genus Phlebotomus is based on the presence of mesanepisternal setae. Its inclusion in the subgenus Anaphlebotomus is based on the males on the presence of four spines on the style, the lack of a coxite basal process and the existence of a bifurcated paramere. The female has cibarial and pharyngeal armature and spermathecal architecture similar to Phlebotomus fertei and Phlebotomus berentiensis, two other Malagasy species which belong to Anaphlebotomus. Male and female are held to belong to the same species because of their morphological characters, the homology (100%) of their partial cytochrome b mtDNA sequences and their capture in the same trap. P. vaomalalae n. sp. is a small species compared to the other Phlebotomus species of Madagascar. The cibarium of the male and the female of P. vaomalalae n. sp. is armed with teeth, like those of other Malagasy Phlebotomus. However, it differs in the arrangement and shape of the respective teeth and denticles. The male of P. vaomalalae n. sp. looks like that of P. fontenillei due to its tuft of coxal setae (lacking in P. berentiensis and P. fertei) but differs from this species by the location of this tuft. As P. fertei and P. berentiensis, there is no spermathecal common duct in P. vaomalalae n. sp. PMID:23419267

  7. Regulation of Transcriptional Networks by PKC Isozymes: Identification of c-Rel as a Key Transcription Factor for PKC-Regulated Genes

    PubMed Central

    Kazanietz, Marcelo G.

    2013-01-01

    Background Activation of protein kinase C (PKC), a family of serine-threonine kinases widely implicated in cancer progression, has major impact on gene expression. In a recent genome-wide analysis of prostate cancer cells we identified distinctive gene expression profiles controlled by individual PKC isozymes and highlighted a prominent role for PKC? in transcriptional activation. Principal Findings Here we carried out a thorough bioinformatics analysis to dissect transcriptional networks controlled by PKC?, PKC?, and PKC?, the main diacylglycerol/phorbol ester PKCs expressed in prostate cancer cells. Despite the remarkable differences in the patterns of transcriptional responsive elements (REs) regulated by each PKC, we found that c-Rel represents the most frequent RE in promoters regulated by all three PKCs. In addition, promoters of PKC?-regulated genes were particularly enriched with REs for CREB, NF-E2, RREB, SRF, Oct-1, Evi-1, and NF-?B. Most notably, by using transcription factor-specific RNAi we were able to identify subsets of PKC?-regulated genes modulated by c-Rel and CREB. Furthermore, PKC?-regulated genes condensed under the c-Rel transcriptional regulation display significant functional interconnections with biological processes such as angiogenesis, inflammatory response, and cell motility. Conclusion/Significance Our study identified candidate transcription factors in the promoters of PKC regulated genes, in particular c-Rel was found as a key transcription factor in the control of PKC?-regulated genes. The deconvolution of PKC-regulated transcriptional networks and their nodes may greatly help in the identification of PKC effectors and have significant therapeutics implications. PMID:23826267

  8. A food-derived synergist of NGF signaling: identification of protein tyrosine phosphatase 1B as a key regulator of NGF receptor-initiated signal transduction.

    PubMed

    Shibata, Takahiro; Nakahara, Hiroko; Kita, Narumi; Matsubara, Yui; Han, Chunguang; Morimitsu, Yasujiro; Iwamoto, Noriko; Kumagai, Yoshito; Nishida, Motohiro; Kurose, Hitoshi; Aoki, Naohito; Ojika, Makoto; Uchida, Koji

    2008-12-01

    Neurotrophins, such as the nerve growth factor (NGF), play an essential role in the growth, development, survival and functional maintenance of neurons in the central and peripheral systems. They also prevent neuronal cell death under various stressful conditions, such as ischemia and neurodegenerative disorders. NGF induces cell differentiation and neurite outgrowth by binding with and activating the NGF receptor tyrosine kinase followed by activation of a variety of signaling cascades. We have investigated the NGF-dependent neuritogenesis enhancer potential of a food-derived small molecule contained in Brassica vegetables and identified the protein tyrosine phosphatase (PTP) 1B as a key regulator of the NGF receptor-initiated signal transduction. Based on an extensive screening of Brassica vegetable extracts for the neuritogenic-promoting activity in the rat pheochromocytoma cell line PC12, we found the Japanese horseradish, wasabi (Wasabia japonica, syn. Eutrema wasabi), as the richest source and identified 6-methylsulfinylhexyl isothiocyanate (6-HITC), an analogue of sulforaphane isolated from broccoli, as one of the major neuritogenic enhancers in the wasabi. 6-HITC strongly enhanced the neurite outgrowth and neurofilament expression elicited by a low-concentration of NGF that alone was insufficient to induce neuronal differentiation. 6-HITC also facilitated the sustained-phosphorylation of the extracellular signal-regulated kinase and the autophosphorylation of the NGF receptor TrkA. It was found that PTP1B act as a phosphatase capable of dephosphorylating Tyr-490 of TrkA and was inactivated by 6-HITC in a redox-dependent manner. The identification of PTP1B as a regulator of NGF signaling may provide new clues about the chemoprotective potential of food components, such as isothiocyanates. PMID:18796006

  9. Plant microRNA-Target Interaction Identification Model Based on the Integration of Prediction Tools and Support Vector Machine

    PubMed Central

    Meng, Jun; Shi, Lin; Luan, Yushi

    2014-01-01

    Background Confident identification of microRNA-target interactions is significant for studying the function of microRNA (miRNA). Although some computational miRNA target prediction methods have been proposed for plants, results of various methods tend to be inconsistent and usually lead to more false positive. To address these issues, we developed an integrated model for identifying plant miRNA–target interactions. Results Three online miRNA target prediction toolkits and machine learning algorithms were integrated to identify and analyze Arabidopsis thaliana miRNA-target interactions. Principle component analysis (PCA) feature extraction and self-training technology were introduced to improve the performance. Results showed that the proposed model outperformed the previously existing methods. The results were validated by using degradome sequencing supported Arabidopsis thaliana miRNA-target interactions. The proposed model constructed on Arabidopsis thaliana was run over Oryza sativa and Vitis vinifera to demonstrate that our model is effective for other plant species. Conclusions The integrated model of online predictors and local PCA-SVM classifier gained credible and high quality miRNA-target interactions. The supervised learning algorithm of PCA-SVM classifier was employed in plant miRNA target identification for the first time. Its performance can be substantially improved if more experimentally proved training samples are provided. PMID:25051153

  10. Identification and Characterization of Noncovalent Interactions That Drive Binding and Specificity in DD-Peptidases and ?-Lactamases

    PubMed Central

    2015-01-01

    Bacterial resistance to standard (i.e., ?-lactam-based) antibiotics has become a global pandemic. Simultaneously, research into the underlying causes of resistance has slowed substantially, although its importance is universally recognized. Key to unraveling critical details is characterization of the noncovalent interactions that govern binding and specificity (DD-peptidases, antibiotic targets, versus ?-lactamases, the evolutionarily derived enzymes that play a major role in resistance) and ultimately resistance as a whole. Herein, we describe a detailed investigation that elicits new chemical insights into these underlying intermolecular interactions. Benzylpenicillin and a novel ?-lactam peptidomimetic complexed to the Stremptomyces R61 peptidase are examined using an arsenal of computational techniques: MD simulations, QM/MM calculations, charge perturbation analysis, QM/MM orbital analysis, bioinformatics, flexible receptor/flexible ligand docking, and computational ADME predictions. Several key molecular level interactions are identified that not only shed light onto fundamental resistance mechanisms, but also offer explanations for observed specificity. Specifically, an extended ?–? network is elucidated that suggests antibacterial resistance has evolved, in part, due to stabilizing aromatic interactions. Additionally, interactions between the protein and peptidomimetic substrate are identified and characterized. Of particular interest is a water-mediated salt bridge between Asp217 and the positively charged N-terminus of the peptidomimetic, revealing an interaction that may significantly contribute to ?-lactam specificity. Finally, interaction information is used to suggest modifications to current ?-lactam compounds that should both improve binding and specificity in DD-peptidases and their physiochemical properties. PMID:24803854

  11. The Identification of Novel Protein-Protein Interactions in Liver that Affect Glucagon Receptor Activity

    PubMed Central

    Froese, Sean; Dai, Feihan F.; Robitaille, Mélanie; Bhattacharjee, Alpana; Huang, Xinyi; Jia, Weiping; Angers, Stéphane; Wheeler, Michael B.; Wei, Li

    2015-01-01

    Glucagon regulates glucose homeostasis by controlling glycogenolysis and gluconeogenesis in the liver. Exaggerated and dysregulated glucagon secretion can exacerbate hyperglycemia contributing to type 2 diabetes (T2D). Thus, it is important to understand how glucagon receptor (GCGR) activity and signaling is controlled in hepatocytes. To better understand this, we sought to identify proteins that interact with the GCGR to affect ligand-dependent receptor activation. A Flag-tagged human GCGR was recombinantly expressed in Chinese hamster ovary (CHO) cells, and GCGR complexes were isolated by affinity purification (AP). Complexes were then analyzed by mass spectrometry (MS), and protein-GCGR interactions were validated by co-immunoprecipitation (Co-IP) and Western blot. This was followed by studies in primary hepatocytes to assess the effects of each interactor on glucagon-dependent glucose production and intracellular cAMP accumulation, and then in immortalized CHO and liver cell lines to further examine cell signaling. Thirty-three unique interactors were identified from the AP-MS screening of GCGR expressing CHO cells in both glucagon liganded and unliganded states. These studies revealed a particularly robust interaction between GCGR and 5 proteins, further validated by Co-IP, Western blot and qPCR. Overexpression of selected interactors in mouse hepatocytes indicated that two interactors, LDLR and TMED2, significantly enhanced glucagon-stimulated glucose production, while YWHAB inhibited glucose production. This was mirrored with glucagon-stimulated cAMP production, with LDLR and TMED2 enhancing and YWHAB inhibiting cAMP accumulation. To further link these interactors to glucose production, key gluconeogenic genes were assessed. Both LDLR and TMED2 stimulated while YWHAB inhibited PEPCK and G6Pase gene expression. In the present study, we have probed the GCGR interactome and found three novel GCGR interactors that control glucagon-stimulated glucose production by modulating cAMP accumulation and genes that control gluconeogenesis. These interactors may be useful targets to control glucose homeostasis in T2D. PMID:26075596

  12. Relationship among the physiologic channel interactions, spectral-ripple discrimination, and vowel identification in cochlear implant users.

    PubMed

    Won, Jong Ho; Humphrey, Elizabeth L; Yeager, Kelly R; Martinez, Alexis A; Robinson, Camryn H; Mills, Kristen E; Johnstone, Patti M; Moon, Il Joon; Woo, Jihwan

    2014-11-01

    The hypothesis of this study was that broader patterns of physiological channel interactions in the local region of the cochlea are associated with poorer spectral resolution in the same region. Electrically evoked compound action potentials (ECAPs) were measured for three to six probe electrodes per subject to examine the channel interactions in different regions across the electrode array. To evaluate spectral resolution at a confined location within the cochlea, spectral-ripple discrimination (SRD) was measured using narrowband ripple stimuli with the bandwidth spanning five electrodes: Two electrodes apical and basal to the ECAP probe electrode. The relationship between the physiological channel interactions, spectral resolution in the local cochlear region, and vowel identification was evaluated. Results showed that (1) there was within- and across-subject variability in the widths of ECAP channel interaction functions and in narrowband SRD performance, (2) significant correlations were found between the widths of the ECAP functions and narrowband SRD thresholds, and between mean bandwidths of ECAP functions averaged across multiple probe electrodes and broadband SRD performance across subjects, and (3) the global spectral resolution reflecting the entire electrode array, not the local region, predicts vowel identification. PMID:25373971

  13. Insights into the key interactions between human protein phosphatase 5 and cantharidin using molecular dynamics and site-directed mutagenesis bioassays

    PubMed Central

    Liu, Ji-Yuan; Chen, Xi-En; Zhang, Ya-Lin

    2015-01-01

    Serine/threonine protein phosphatase 5 (PP5) is a promising novel target for anticancer therapies. This work aims to uncover the key interactions at the atomic level between PP5 and three inhibitors (cantharidin, norcantharidin and endothall). We found that, unlike previous report, Arg 100 contributes less to PP5-inhibitor binding, and the residues His 69, Asn 128, His 129, Arg 225, His 252 and Arg 250 are of importance to PP5-inhibitor binding. The hydrophobic interactions established between the residues Val 254, Phe 271 and Tyr 276, especially Glu 253, are very important to enhance the inhibitive interaction. We suggested that, to increase the inhibitory activity, the interactions of inhibitor with three negatively charged unfavorable interaction residues, Asp 99, Glu 130 and Asp 213, should be avoided. However, the interactions of inhibitor with favorable interaction residue Arg 250 could enhance the inhibitory activity. The Manganese ion 2 (MN2) unfavorably contribute to the total interaction free energies. The coordination between MN2 and chemical group of inhibitor should be eliminated. This work provides insight into how cantharidin and its analogs bind to PP5c at the atomic level and will facilitate modification of cantharidin-like chemicals to rationally develop more specific and less cytotoxic anti-cancer drugs. PMID:26190207

  14. Revolving SEM images visualising 3D taxonomic characters: application to six species of the millipede genus Ommatoiulus Latzel, 1884, with description of seven new species and an interactive key to the Tunisian members of the genus (Diplopoda, Julida, Julidae)

    PubMed Central

    Akkari, Nesrine; Cheung, David Koon-Bong; Enghoff, Henrik; Stoev, Pavel

    2013-01-01

    Abstract A novel illustration technique based on scanning electron microscopy is used for the first time to enhance taxonomic descriptions. The male genitalia (gonopods) of six species of millipedes are used for construction of interactive imaging models. Each model is a compilation of a number of SEM images taken consecutively while rotating the SEM stage 360°, which allows the structure in question to be seen from all angles of view in one plane. Seven new species of the genus Ommatoiulus collected in Tunisia are described: Ommatoiulus chambiensis, Ommatoiulus crassinigripes, Ommatoiulus kefi, Ommatoiulus khroumiriensis, Ommatoiulus xerophilus, Ommatoiulus xenos, and Ommatoiulus zaghouani spp. n. Size differences between syntopic adult males of Ommatoiulus chambiensis and Ommatoiulus xerophilus spp. n. from Châambi Mountain are illustrated using scatter diagrams. A similar diagram is used to illustrate size differences in Ommatoiulus crassinigripes, Ommatoiulus khroumiriensis spp. n. and Ommatoiulus punicus (Brölemann, 1894). In addition to morphological differences, the latter three species display allopatric distribution and different habitat preferences. A dichotomous interactive key with a high visual impact and an intuitive user interface is presented to serve identification of the 12 Ommatoiulus species so far known from Tunisia. Updates on the North African Ommatoiulus fauna in general are presented. PMID:24146546

  15. Identification of key binding site residues of MCT1 for AR-C155858 reveals the molecular basis of its isoform selectivity.

    PubMed

    Nancolas, Bethany; Sessions, Richard B; Halestrap, Andrew P

    2015-02-15

    The proton-linked monocarboxylate transporters (MCTs) are required for lactic acid transport into and out of all mammalian cells. Thus, they play an essential role in tumour cells that are usually highly glycolytic and are promising targets for anti-cancer drugs. AR-C155858 is a potent MCT1 inhibitor (Ki ~2 nM) that also inhibits MCT2 when associated with basigin but not MCT4. Previous work [Ovens, M.J. et al. (2010) Biochem. J. 425, 523-530] revealed that AR-C155858 binding to MCT1 occurs from the intracellular side and involves transmembrane helices (TMs) 7-10. In the present paper, we generate a molecular model of MCT4 based on our previous models of MCT1 and identify residues in the intracellular substrate-binding cavity that differ significantly between MCT4 and MCT1/MCT2 and so might account for differences in inhibitor binding. We tested their involvement using site-directed mutagenesis (SDM) of MCT1 to change residues individually or in combination with their MCT4 equivalent and determined inhibitor sensitivity following expression in Xenopus oocytes. Phe360 and Ser364 were identified as important for AR-C155858 binding with the F360Y/S364G mutant exhibiting >100-fold reduction in inhibitor sensitivity. To refine the binding site further, we used molecular dynamics (MD) simulations and additional SDM. This approach implicated six more residues whose involvement was confirmed by both transport studies and [3H]-AR-C155858 binding to oocyte membranes. Taken together, our data imply that Asn147, Arg306 and Ser364 are important for directing AR-C155858 to its final binding site which involves interaction of the inhibitor with Lys38, Asp302 and Phe360 (residues that also play key roles in the translocation cycle) and also Leu274 and Ser278. PMID:25437897

  16. Identification of key binding site residues of MCT1 for AR-C155858 reveals the molecular basis of its isoform selectivity

    PubMed Central

    Nancolas, Bethany; Sessions, Richard B.; Halestrap, Andrew P.

    2014-01-01

    The proton-linked monocarboxylate transporters (MCTs) are required for lactic acid transport into and out of all mammalian cells. Thus, they play an essential role in tumour cells that are usually highly glycolytic and are promising targets for anti-cancer drugs. AR-C155858 is a potent MCT1 inhibitor (Ki ~2 nM) that also inhibits MCT2 when associated with basigin but not MCT4. Previous work [Ovens, M.J. et al. (2010) Biochem. J. 425, 523–530] revealed that AR-C155858 binding to MCT1 occurs from the intracellular side and involves transmembrane helices (TMs) 7–10. In the present paper, we generate a molecular model of MCT4 based on our previous models of MCT1 and identify residues in the intracellular substrate-binding cavity that differ significantly between MCT4 and MCT1/MCT2 and so might account for differences in inhibitor binding. We tested their involvement using site-directed mutagenesis (SDM) of MCT1 to change residues individually or in combination with their MCT4 equivalent and determined inhibitor sensitivity following expression in Xenopus oocytes. Phe360 and Ser364 were identified as important for AR-C155858 binding with the F360Y/S364G mutant exhibiting >100-fold reduction in inhibitor sensitivity. To refine the binding site further, we used molecular dynamics (MD) simulations and additional SDM. This approach implicated six more residues whose involvement was confirmed by both transport studies and [3H]-AR-C155858 binding to oocyte membranes. Taken together, our data imply that Asn147, Arg306 and Ser364 are important for directing AR-C155858 to its final binding site which involves interaction of the inhibitor with Lys38, Asp302 and Phe360 (residues that also play key roles in the translocation cycle) and also Leu274 and Ser278. PMID:25437897

  17. Identification of GPCR-Interacting Cytosolic Proteins Using HDL Particles and Mass Spectrometry-Based Proteomic Approach

    PubMed Central

    Chung, Ka Young; Day, Peter W.; Vélez-Ruiz, Gisselle; Sunahara, Roger K.; Kobilka, Brian K.

    2013-01-01

    G protein-coupled receptors (GPCRs) have critical roles in various physiological and pathophysiological processes, and more than 40% of marketed drugs target GPCRs. Although the canonical downstream target of an agonist-activated GPCR is a G protein heterotrimer; there is a growing body of evidence suggesting that other signaling molecules interact, directly or indirectly, with GPCRs. However, due to the low abundance in the intact cell system and poor solubility of GPCRs, identification of these GPCR-interacting molecules remains challenging. Here, we establish a strategy to overcome these difficulties by using high-density lipoprotein (HDL) particles. We used the ?2-adrenergic receptor (?2AR), a GPCR involved in regulating cardiovascular physiology, as a model system. We reconstituted purified ?2AR in HDL particles, to mimic the plasma membrane environment, and used the reconstituted receptor as bait to pull-down binding partners from rat heart cytosol. A total of 293 proteins were identified in the full agonist-activated ?2AR pull-down, 242 proteins in the inverse agonist-activated ?2AR pull-down, and 210 proteins were commonly identified in both pull-downs. A small subset of the ?2AR-interacting proteins isolated was confirmed by Western blot; three known ?2AR-interacting proteins (Gs?, NHERF-2, and Grb2) and 3 newly identified known ?2AR-interacting proteins (AMPK?, acetyl-CoA carboxylase, and UBC-13). Profiling of the identified proteins showed a clear bias toward intracellular signal transduction pathways, which is consistent with the role of ?2AR as a cell signaling molecule. This study suggests that HDL particle-reconstituted GPCRs can provide an effective platform method for the identification of GPCR binding partners coupled with a mass spectrometry-based proteomic analysis. PMID:23372797

  18. Piecewise Linear Dynamic Modeling and Identification of Gene-Protein Interaction Networks

    Microsoft Academic Search

    Ronald L. Westra

    In this lecture we will focus on piece-wise linear state space models for gene-protein interaction networks. Moreover, this lecture is concerned with the identifiability and controllability of natural in- formation processing networks under chaos and noise. Fundamental questions considered include: what are the basic mechanisms involved in the interactions, how does macroscopic complexity arise from microscopic interactions, what is the

  19. Key Factors for the Development of a Culturally Appropriate Interactive Multimedia Informative Program for Aboriginal Health Workers

    ERIC Educational Resources Information Center

    El Sayed, Faeka; Soar, Jeffrey; Wang, Zoe

    2012-01-01

    This research aims to create and evaluate a model for a culturally appropriate, interactive, multimedia and informative health program for Aboriginal and Torres Strait Islander health workers that aims to improve the capacity to independently control their learning within an attractive learning environment. The research also aims to provide…

  20. The Pros and Cons of Interactive Whiteboards in Relation to the Key Stage 3 Strategy and Framework

    ERIC Educational Resources Information Center

    Gray, Carol; Hagger-Vaughan, Lesley; Pilkington, Rachel; Tomkins, Sally-Ann

    2005-01-01

    The article describes data emerging from a study of a group of language teachers integrating use of the interactive whiteboard (IWB) into their classroom practice. Data collection tools were developed which allowed participants freedom of action and expression whilst providing a framework for reflection designed to focus on pedagogy rather than…

  1. Plant Identification

    NSDL National Science Digital Library

    This unit on plant identification helps students prepare for their fieldwork by developing their observational skills and introducing them to resources that will help them with plant identification. It's designed to be completed in five or more sessions and has comprehensive curriculum materials information for teachers, including overviews of binomial nomenclature and dichotomous keys. Additionally, a guide to finding local specialists is available online. There are optional activites and information on supplemental resources available on line.

  2. Association between the Interaction of Key Genes Involved in Effector T-Cell Pathways and Susceptibility to Developallergic Rhinitis: A Population-Based Case-Control Association Study

    PubMed Central

    Zhang, Yuan; Li, Jingyun; Wang, Chengshuo; Zhang, Luo

    2015-01-01

    Background Evidence suggests that interaction between key genes mediating signaling and transcriptional networks involving effector T-cell responses may influence an individual’s susceptibility to develop allergic rhinitis(AR). Objective The aim of this study was todetermine whether specific interactions between key genes involved in effector T-cell pathways are associated with an individual’s susceptibility to develop AR in Han Chinese subjects. Method A cohort of 489 patients with AR and 421 healthy controls was enrolled from the Han Chinese population in Beijing, China. AR was established by questionnaire and clinical examination, and peripheral blood was drawn from all subjects for DNA extraction. A total of 96 single nucleotide polymorphisms (SNPs) in 26 reprehensive candidate genes involved in T helper 1 (Th1), Th2, Th17, Th9 and T regulatory cell pathways were selected from the International Haplotype Mappingdatabase for Han Chinese in Beijing (CHB) population, and IlluminaGoldenGate assay was conducted for SNP genotyping. The PLINK software package was used to perform statistical analyses. Results Simple SNP-phenotype association analysis using logistic regression showed SNP rs8193036 in IL17A gene, rs2569254 in IL-12 and rs1898413 in ROR? weresignificantlyassociatedwith AR.Simple SNP-phenotype association analysis with genetic models demonstrated thatrs2569254 in IL-12, rs1031508 in STAT4, and rs3741809 in IL-26 were likely to be recessive, rs8193036 in IL17A allelic, rs897200in STAT4 genotypic, and rs1898413 in ROR? dominant. Epistasis analyses exhibited that 83 SNPs in 23 genes were significantly interactive; of which 59 interactions/SNP pairs demonstrated OR values higher than 2 or lower than 0.5, and 12 interactions/SNP pairs OR values higher than 4 or lower than 0.25. STAT3, ROR? and IL-26, involved in Th17 pathway,were the mostfrequentlyinteractive genes. Conclusion This study suggests that interactions between several SNPs in key genes involved in effector T-cell pathways are likely to influence an individual’s susceptibility to develop AR. PMID:26196693

  3. Comparative and Functional Genomics of Legionella Identified Eukaryotic Like Proteins as Key Players in Host–Pathogen Interactions

    PubMed Central

    Gomez-Valero, Laura; Rusniok, Christophe; Cazalet, Christel; Buchrieser, Carmen

    2011-01-01

    Although best known for its ability to cause severe pneumonia in people whose immune defenses are weakened, Legionella pneumophila and Legionella longbeachae are two species of a large genus of bacteria that are ubiquitous in nature, where they parasitize protozoa. Adaptation to the host environment and exploitation of host cell functions are critical for the success of these intracellular pathogens. The establishment and publication of the complete genome sequences of L. pneumophila and L. longbeachae isolates paved the way for major breakthroughs in understanding the biology of these organisms. In this review we present the knowledge gained from the analyses and comparison of the complete genome sequences of different L. pneumophila and L. longbeachae strains. Emphasis is given on putative virulence and Legionella life cycle related functions, such as the identification of an extended array of eukaryotic like proteins, many of which have been shown to modulate host cell functions to the pathogen’s advantage. Surprisingly, many of the eukaryotic domain proteins identified in L. pneumophila as well as many substrates of the Dot/Icm type IV secretion system essential for intracellular replication are different between these two species, although they cause the same disease. Finally, evolutionary aspects regarding the eukaryotic like proteins in Legionella are discussed. PMID:22059087

  4. The identification of complex interactions in epidemiology and toxicology: a simulation study of boosted regression trees

    PubMed Central

    2014-01-01

    Background There is a need to evaluate complex interaction effects on human health, such as those induced by mixtures of environmental contaminants. The usual approach is to formulate an additive statistical model and check for departures using product terms between the variables of interest. In this paper, we present an approach to search for interaction effects among several variables using boosted regression trees. Methods We simulate a continuous outcome from real data on 27 environmental contaminants, some of which are correlated, and test the method’s ability to uncover the simulated interactions. The simulated outcome contains one four-way interaction, one non-linear effect and one interaction between a continuous variable and a binary variable. Four scenarios reflecting different strengths of association are simulated. We illustrate the method using real data. Results The method succeeded in identifying the true interactions in all scenarios except where the association was weakest. Some spurious interactions were also found, however. The method was also capable to identify interactions in the real data set. Conclusions We conclude that boosted regression trees can be used to uncover complex interaction effects in epidemiological studies. PMID:24993424

  5. Identification of Potential Plk1 Targets in a Cell-Cycle Specific Proteome through Structural Dynamics of Kinase and Polo Box-Mediated Interactions

    PubMed Central

    Bibi, Nousheen; Parveen, Zahida; Rashid, Sajid

    2013-01-01

    Polo like kinase 1 (Plk1) is a key player in orchestrating the wide variety of cell-cycle events ranging from centrosome maturation, mitotic entry, checkpoint recovery, transcriptional control, spindle assembly, mitotic progression, cytokinesis and DNA damage checkpoints recovery. Due to its versatile nature, Plk1 is considered an imperative regulator to tightly control the diverse aspects of the cell cycle network. Interactions among Plk1 polo box domain (PBD) and its putative binding proteins are crucial for the activation of Plk1 kinase domain (KD). To date, only a few substrate candidates have been characterized through the inclusion of both polo box and kinase domain-mediated interactions. Thus it became compelling to explore precise and specific Plk1 substrates through reassessment and extension of the structure-function paradigm. To narrow this apparently wide gap in knowledge, here we employed a thorough sequence search of Plk1 phosphorylation signature containing proteins and explored their structure-based features like conceptual PBD-binding capabilities and subsequent recruitment of KD directed phosphorylation to dissect novel targets of Plk1. Collectively, we identified 4,521 phosphodependent proteins sharing similarity to the consensus phosphorylation and PBD recognition motifs. Subsequent application of filters including similarity index, Gene Ontology enrichment and protein localization resulted in stringent pre-filtering of irrelevant candidates and isolated unique targets with well-defined roles in cell-cycle machinery and carcinogenesis. These candidates were further refined structurally using molecular docking and dynamic simulation assays. Overall, our screening approach enables the identification of several undefined cell-cycle associated functions of Plk1 by uncovering novel phosphorylation targets. PMID:23967120

  6. Dichotomous Keys for Arthropods

    NSDL National Science Digital Library

    This reference tool allows students to identify an arthropod's order by making a series of guided decisions, such as six legs or more, well-developed or missing wing, and chewing or sucking mouthparts. The key, which includes only adult arthropods, is available as an interactive key on the AMNH's Web site that can be downloaded to your computer.

  7. A Cell-Based Method for Screening RNA-Protein Interactions: Identification of Constitutive Transport Element-Interacting Proteins

    PubMed Central

    Nakamura, Robert L.; Landt, Stephen G.; Mai, Emily; Nejim, Jemiel; Chen, Lily; Frankel, Alan D.

    2012-01-01

    We have developed a mammalian cell-based screening platform to identify proteins that assemble into RNA-protein complexes. Based on Tat-mediated activation of the HIV LTR, proteins that interact with an RNA target elicit expression of a GFP reporter and are captured by fluorescence activated cell sorting. This “Tat-hybrid” screening platform was used to identify proteins that interact with the Mason Pfizer monkey virus (MPMV) constitutive transport element (CTE), a structured RNA hairpin that mediates the transport of unspliced viral mRNAs from the nucleus to the cytoplasm. Several hnRNP-like proteins, including hnRNP A1, were identified and shown to interact with the CTE with selectivity in the reporter system comparable to Tap, a known CTE-binding protein. In vitro gel shift and pull-down assays showed that hnRNP A1 is able to form a complex with the CTE and Tap and that the RGG domain of hnRNP A1 mediates binding to Tap. These results suggest that hnRNP-like proteins may be part of larger export-competent RNA-protein complexes and that the RGG domains of these proteins play an important role in directing these binding events. The results also demonstrate the utility of the screening platform for identifying and characterizing new components of RNA-protein complexes. PMID:23133567

  8. Acoustic and electromagnetic wave interaction in the detection and identification of buried objects

    Microsoft Academic Search

    Daniel Edward Lawrence

    2002-01-01

    In order to facilitate the development of a hybrid acoustic and electromagnetic (EM) system for buried object detection, a number of analytical solutions and a novel numerical technique are developed to analyze the complex interaction between acoustic and EM scattering. The essence of the interaction lies in the fact that identifiable acoustic properties of an object, such as acoustic resonances,

  9. Identification of subunits of acetylcholine receptor that interact with a cholesterol photoaffinity probe

    SciTech Connect

    Middlemas, D.S.; Raftery, M.A.

    1987-03-10

    All four subunits of the acetylcholine receptor in membrane vesicles isolated from Torpedo californica have been labeled with (/sup 3/H)cholesteryl diazoacetate. As this probe incorporates into lipid bilayers analogously to cholesterol, this result indicates that acetylcholine receptor interacts with cholesterol. This investigation also demonstrates that this probe is a useful reagent for studying the interaction of cholesterol with membrane proteins.

  10. Identification of a Novel Protein-Protein Interaction Motif Mediating Interaction of GPCR-Associated Sorting Proteins with G Protein-Coupled Receptors

    PubMed Central

    Bornert, Olivier; Møller, Thor C.; Boeuf, Julien; Candusso, Marie-Pierre; Wagner, Renaud; Martinez, Karen L.; Simonin, Frederic

    2013-01-01

    GPCR desensitization and down-regulation are considered key molecular events underlying the development of tolerance in vivo. Among the many regulatory proteins that are involved in these complex processes, GASP-1 have been shown to participate to the sorting of several receptors toward the degradation pathway. This protein belongs to the recently identified GPCR-associated sorting proteins (GASPs) family that comprises ten members for which structural and functional details are poorly documented. We present here a detailed structure–function relationship analysis of the molecular interaction between GASPs and a panel of GPCRs. In a first step, GST-pull down experiments revealed that all the tested GASPs display significant interactions with a wide range of GPCRs. Importantly, the different GASP members exhibiting the strongest interaction properties were also characterized by the presence of a small, highly conserved and repeated “GASP motif” of 15 amino acids. We further showed using GST-pull down, surface plasmon resonance and co-immunoprecipitation experiments that the central domain of GASP-1, which contains 22 GASP motifs, is essential for the interaction with GPCRs. We then used site directed mutagenesis and competition experiments with synthetic peptides to demonstrate that the GASP motif, and particularly its highly conserved core sequence SWFW, is critically involved in the interaction with GPCRs. Overall, our data show that several members of the GASP family interact with GPCRs and highlight the presence within GASPs of a novel protein-protein interaction motif that might represent a new target to investigate the involvement of GASPs in the modulation of the activity of GPCRs. PMID:23441177

  11. Inverse Material Identification in Coupled Acoustic-Structure Interaction using a Modified Error in Constitutive Equation Functional.

    PubMed

    Warner, James E; Diaz, Manuel I; Aquino, Wilkins; Bonnet, Marc

    2014-09-01

    This work focuses on the identification of heterogeneous linear elastic moduli in the context of frequency-domain, coupled acoustic-structure interaction (ASI), using either solid displacement or fluid pressure measurement data. The approach postulates the inverse problem as an optimization problem where the solution is obtained by minimizing a modified error in constitutive equation (MECE) functional. The latter measures the discrepancy in the constitutive equations that connect kinematically admissible strains and dynamically admissible stresses, while incorporating the measurement data as additional quadratic error terms. We demonstrate two strategies for selecting the MECE weighting coefficient to produce regularized solutions to the ill-posed identification problem: 1) the discrepancy principle of Morozov, and 2) an error-balance approach that selects the weight parameter as the minimizer of another functional involving the ECE and the data misfit. Numerical results demonstrate that the proposed methodology can successfully recover elastic parameters in 2D and 3D ASI systems from response measurements taken in either the solid or fluid subdomains. Furthermore, both regularization strategies are shown to produce accurate reconstructions when the measurement data is polluted with noise. The discrepancy principle is shown to produce nearly optimal solutions, while the error-balance approach, although not optimal, remains effective and does not need a priori information on the noise level. PMID:25339790

  12. Inverse material identification in coupled acoustic-structure interaction using a modified error in constitutive equation functional

    NASA Astrophysics Data System (ADS)

    Warner, James E.; Diaz, Manuel I.; Aquino, Wilkins; Bonnet, Marc

    2014-09-01

    This work focuses on the identification of heterogeneous linear elastic moduli in the context of frequency-domain, coupled acoustic-structure interaction (ASI), using either solid displacement or fluid pressure measurement data. The approach postulates the inverse problem as an optimization problem where the solution is obtained by minimizing a modified error in constitutive equation (MECE) functional. The latter measures the discrepancy in the constitutive equations that connect kinematically admissible strains and dynamically admissible stresses, while incorporating the measurement data as additional quadratic error terms. We demonstrate two strategies for selecting the MECE weighting coefficient to produce regularized solutions to the ill-posed identification problem: 1) the discrepancy principle of Morozov, and 2) an error-balance approach that selects the weight parameter as the minimizer of another functional involving the ECE and the data misfit. Numerical results demonstrate that the proposed methodology can successfully recover elastic parameters in 2D and 3D ASI systems from response measurements taken in either the solid or fluid subdomains. Furthermore, both regularization strategies are shown to produce accurate reconstructions when the measurement data is polluted with noise. The discrepancy principle is shown to produce nearly optimal solutions, while the error-balance approach, although not optimal, remains effective and does not need a priori information on the noise level.

  13. Fatty Acid-binding Proteins Interact with Comparative Gene Identification-58 Linking Lipolysis with Lipid Ligand Shuttling.

    PubMed

    Hofer, Peter; Boeszoermenyi, Andras; Jaeger, Doris; Feiler, Ursula; Arthanari, Haribabu; Mayer, Nicole; Zehender, Fabian; Rechberger, Gerald; Oberer, Monika; Zimmermann, Robert; Lass, Achim; Haemmerle, Guenter; Breinbauer, Rolf; Zechner, Rudolf; Preiss-Landl, Karina

    2015-07-24

    The coordinated breakdown of intracellular triglyceride (TG) stores requires the exquisitely regulated interaction of lipolytic enzymes with regulatory, accessory, and scaffolding proteins. Together they form a dynamic multiprotein network designated as the "lipolysome." Adipose triglyceride lipase (Atgl) catalyzes the initiating step of TG hydrolysis and requires comparative gene identification-58 (Cgi-58) as a potent activator of enzyme activity. Here, we identify adipocyte-type fatty acid-binding protein (A-Fabp) and other members of the fatty acid-binding protein (Fabp) family as interaction partners of Cgi-58. Co-immunoprecipitation, microscale thermophoresis, and solid phase assays proved direct protein/protein interaction between A-Fabp and Cgi-58. Using nuclear magnetic resonance titration experiments and site-directed mutagenesis, we located a potential contact region on A-Fabp. In functional terms, A-Fabp stimulates Atgl-catalyzed TG hydrolysis in a Cgi-58-dependent manner. Additionally, transcriptional transactivation assays with a luciferase reporter system revealed that Fabps enhance the ability of Atgl/Cgi-58-mediated lipolysis to induce the activity of peroxisome proliferator-activated receptors. Our studies identify Fabps as crucial structural and functional components of the lipolysome. PMID:25953897

  14. Identification of phases in the interaction layer between U-Mo-Zr/Al and U-Mo-Zr/Al-Si

    SciTech Connect

    Varela, C.L. Komar; Arico, S.F.; Mirandou, M.; Balart, S.N. [Departamento Materiales, GIDAT, GAEN, CNEA, Avda. Gral Paz 1499, B1650KNA, San Martin (Argentina); Gribaudo, L.M. [Departamento Materiales, GIDAT, GAEN, CNEA, Avda. Gral Paz 1499, B1650KNA, San Martin (Argentina); CONICET, Avda. Rivadavia 1917, C1033AAJ, Buenos Aires (Argentina)

    2008-07-15

    Out-of-pile diffusion experiments were performed between U-7wt.% Mo-1wt.% Zr and Al or Al A356 (7,1wt.% Si) at 550 deg. C. In this work morphological characterization and phase identification on both interaction layer are presented. They were carried out by the use of different techniques: optical and scanning electron microscopy, X-Ray diffraction and WDS microanalysis. In the interaction layer U-7wt.% Mo-1wt.% Zr/Al, the phases UAl{sub 3}, UAl{sub 4}, Al{sub 20}Mo{sub 2}U and Al{sub 43}Mo{sub 4}U{sub 6} were identified. In the interaction layer U-7wt.% Mo-1wt.% Zr/Al A356, the phases U(Al, Si) with 25at.% Si and Si{sub 5}U{sub 3} were identified. This last phase, with a higher Si concentration, was identified with XRD Synchrotron radiation performed at the National Synchrotron Light Laboratory (LNLS), Campinas, Brasil. (author)

  15. Establishing and evaluating the key functions of an interactive systems framework using an assets-getting to outcomes intervention.

    PubMed

    Chinman, Matthew; Acosta, Joie; Ebener, Patricia; Q Burkhart; Clifford, Michael; Corsello, Maryann; Duffey, Tim; Hunter, Sarah; Jones, Margaret; Lahti, Michel; Malone, Patrick S; Paddock, Susan; Phillips, Andrea; Savell, Susan; Scales, Peter C; Tellett-Royce, Nancy

    2012-12-01

    Community practitioners can face difficulty in achieving outcomes demonstrated by prevention science. Building a community practitioner's prevention capacity-the knowledge and skills needed to conduct critical prevention practices-could improve the quality of prevention and its outcomes. The purpose of this article is to: (1) describe how an intervention called Assets-Getting To Outcomes (AGTO) was used to establish the key functions of the ISF and present early lessons learned from that intervention's first 6 months and (2) examine whether there is an empirical relationship between practitioner capacity at the individual level and the performance of prevention at the program level-a relationship predicted by the ISF but untested. The article describes an operationalization of the ISF in the context of a five-year randomized controlled efficacy trial that combines two complementary models designed to build capacity: Getting To Outcomes (GTO) and Developmental Assets. The trial compares programs and individual practitioners from six community-based coalitions using AGTO with programs and practitioners from six similar coalitions that are not. In this article, we primarily focus on what the ISF calls innovation specific capacity and discuss how the combined AGTO innovation structures and uses feedback about its capacity-building activities, which can serve as a model for implementing the ISF. Focus group discussions used to gather lessons learned from the first 6 months of the AGTO intervention suggest that while the ISF may have been conceptualized as three distinct systems, in practice they are less distinct. Findings from the baseline wave of data collection of individual capacity and program performance suggest that practitioner capacity predicts, in part, performance of prevention programs. Empirically linking practitioner capacity and performance of prevention provides empirical support for both the ISF and AGTO. PMID:22446975

  16. Establishing and Evaluating the Key Functions of an Interactive Systems Framework Using an Assets-Getting to Outcomes Intervention

    PubMed Central

    Chinman, Matthew; Acosta, Joie; Ebener, Patricia; Burkhart, Q; Clifford, Michael; Corsello, Maryann; Duffey, Tim; Hunter, Sarah; Jones, Margaret; Lahti, Michel; Malone, Patrick S.; Paddock, Susan; Phillips, Andrea; Savell, Susan; Scales, Peter C.; Tellett-Royce, Nancy

    2012-01-01

    Community practitioners can face difficulty in achieving outcomes demonstrated by prevention science. Building a community practitioner’s prevention capacity—the knowledge and skills needed to conduct critical prevention practices—could improve the quality of prevention and its outcomes. The purpose of this article is to: (1) describe how an intervention called Assets-Getting To Outcomes (AGTO) was used to establish the key functions of the ISF and present early lessons learned from that intervention’s first 6 months and (2) examine whether there is an empirical relationship between practitioner capacity at the individual level and the performance of prevention at the program level—a relationship predicted by the ISF but untested. The article describes an operationalization of the ISF in the context of a five-year randomized controlled efficacy trial that combines two complementary models designed to build capacity: Getting To Outcomes (GTO) and Developmental Assets. The trial compares programs and individual practitioners from six community-based coalitions using AGTO with programs and practitionersfrom six similar coalitions that are not. In this article, we primarily focus on what the ISF calls innovation specific capacity and discuss how the combined AGTO innovation structures and uses feedback about its capacity-building activities, which can serve as a model for implementing the ISF. Focus group discussions used to gather lessons learned from the first 6 months of the AGTO intervention suggest that while the ISF may have been conceptualized as three distinct systems, in practice they are less distinct. Findings from the baseline wave of data collection of individual capacity and program performance suggest that practitioner capacity predicts, in part, performance of prevention programs. Empirically linking practitioner capacity and performance of prevention provides empirical support for both the ISF and AGTO. PMID:22446975

  17. Identification and measurement of intermolecular interaction in polyester/polystyrene blends by FTIR-photoacoustic spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fourier transform infrared photoacoustic spectrometry was used to reveal and identify n-p type intermolecular interaction formed in plastic comprising binary blends of polystyrene and a biodegradable polymer, either polylactic acid, polycaprolactone or poly(tetramethyleneadipate-co-terephthalate)....

  18. The identification of recurrent tertiary motifs by interactions of protein secondary structure units

    E-print Network

    Hodges, Hamilton Courtney

    2013-02-22

    secondary structure units: alpha helices, beta strands, beta hairpins, and loops. We also identified three physical interactions between the secondary structure units: (1) hydrogen bonds were found by a continuous energy potential; (2) salt bridges were...

  19. Towards Improving our Understanding on the Retrievals of Key Parameters Characterising Land Surface Interactions from Space: Introduction & First Results from the PREMIER-EO Project

    NASA Astrophysics Data System (ADS)

    Ireland, Gareth; North, Matthew R.; Petropoulos, George P.; Srivastava, Prashant K.; Hodges, Crona

    2015-04-01

    Acquiring accurate information on the spatio-temporal variability of soil moisture content (SM) and evapotranspiration (ET) is of key importance to extend our understanding of the Earth system's physical processes, and is also required in a wide range of multi-disciplinary research studies and applications. The utility and applicability of Earth Observation (EO) technology provides an economically feasible solution to derive continuous spatio-temporal estimates of key parameters characterising land surface interactions, including ET as well as SM. Such information is of key value to practitioners, decision makers and scientists alike. The PREMIER-EO project recently funded by High Performance Computing Wales (HPCW) is a research initiative directed towards the development of a better understanding of EO technology's present ability to derive operational estimations of surface fluxes and SM. Moreover, the project aims at addressing knowledge gaps related to the operational estimation of such parameters, and thus contribute towards current ongoing global efforts towards enhancing the accuracy of those products. In this presentation we introduce the PREMIER-EO project, providing a detailed overview of the research aims and objectives for the 1 year duration of the project's implementation. Subsequently, we make available the initial results of the work carried out herein, in particular, related to an all-inclusive and robust evaluation of the accuracy of existing operational products of ET and SM from different ecosystems globally. The research outcomes of this project, once completed, will provide an important contribution towards addressing the knowledge gaps related to the operational estimation of ET and SM. This project results will also support efforts ongoing globally towards the operational development of related products using technologically advanced EO instruments which were launched recently or planned be launched in the next 1-2 years. Key Words: PREMIER-EO, HPC Wales, Soil Moisture, Evapotranspiration, , Earth Observation

  20. Identification of New Protein Interactions between Dengue Fever Virus and Its Hosts, Human and Mosquito

    PubMed Central

    Mairiang, Dumrong; Zhang, Huamei; Sodja, Ann; Murali, Thilakam; Suriyaphol, Prapat; Malasit, Prida; Limjindaporn, Thawornchai; Finley, Russell L.

    2013-01-01

    The four divergent serotypes of dengue virus are the causative agents of dengue fever, dengue hemorrhagic fever and dengue shock syndrome. About two-fifths of the world's population live in areas where dengue is prevalent, and thousands of deaths are caused by the viruses every year. Dengue virus is transmitted from one person to another primarily by the yellow fever mosquito, Aedes aegypti. Recent studies have begun to define how the dengue viral proteins interact with host proteins to mediate viral replication and pathogenesis. A combined analysis of these studies, however, suggests that many virus-host protein interactions remain to be identified, especially for the mosquito host. In this study, we used high-throughput yeast two-hybrid screening to identify mosquito and human proteins that physically interact with dengue proteins. We tested each identified host protein against the proteins from all four serotypes of dengue to identify interactions that are conserved across serotypes. We further confirmed many of the interactions using co-affinity purification assays. As in other large-scale screens, we identified some previously detected interactions and many new ones, moving us closer to a complete host – dengue protein interactome. To help summarize and prioritize the data for further study, we combined our interactions with other published data and identified a subset of the host-dengue interactions that are now supported by multiple forms of evidence. These data should be useful for understanding the interplay between dengue and its hosts and may provide candidates for drug targets and vector control strategies. PMID:23326450

  1. Visualisation and Identification of the Interaction between STIM1s in Resting Cells

    Microsoft Academic Search

    Jun He; Tao Yu; Jingying Pan; He Li

    2012-01-01

    Store-operated Ca2+ channels are a major Ca2+ entry pathway in nonexcitable cells, which drive various essential cellular functions. Recently, STIM1 and Orai proteins have been identified as the major molecular components of the Ca2+ release-activated Ca2+ (CRAC) channel. As the key subunit of the CRAC channel, STIM1 is the ER Ca2+ sensor and is essential for the recruitment and activation

  2. Interactions with M Cells and Macrophages as Key Steps in the Pathogenesis of Enterohemorragic Escherichia coli Infections

    PubMed Central

    Etienne-Mesmin, Lucie; Chassaing, Benoit; Sauvanet, Pierre; Denizot, Jérémy; Blanquet-Diot, Stéphanie; Darfeuille-Michaud, Arlette; Pradel, Nathalie; Livrelli, Valérie

    2011-01-01

    Enterohemorrhagic Escherichia coli (EHEC) are food-borne pathogens that can cause serious infections ranging from diarrhea to hemorrhagic colitis (HC) and hemolytic-uremic syndrome (HUS). Translocation of Shiga-toxins (Stx) from the gut lumen to underlying tissues is a decisive step in the development of the infection, but the mechanisms involved remain unclear. Many bacterial pathogens target the follicle-associated epithelium, which overlies Peyer's patches (PPs), cross the intestinal barrier through M cells and are captured by mucosal macrophages. Here, translocation across M cells, as well as survival and proliferation of EHEC strains within THP-1 macrophages were investigated using EHEC O157:H7 reference strains, isogenic mutants, and 15 EHEC strains isolated from HC/HUS patients. We showed for the first time that E. coli O157:H7 strains are able to interact in vivo with murine PPs, to translocate ex vivo through murine ileal mucosa with PPs and across an in vitro human M cell model. EHEC strains are also able to survive and to produce Stx in macrophages, which induce cell apoptosis and Stx release. In conclusion, our results suggest that the uptake of EHEC by M cells and underlying macrophages in the PP may be a critical step in Stx translocation and release in vivo. A new model for EHEC infection in humans is proposed that could help in a fuller understanding of EHEC-associated diseases. PMID:21858177

  3. ATP control of dynamic P1 ParA–DNA interactions: a key role for the nucleoid in plasmid partition

    PubMed Central

    Vecchiarelli, Anthony G; Han, Yong-Woon; Tan, Xin; Mizuuchi, Michiyo; Ghirlando, Rodolfo; Biertümpfel, Christian; Funnell, Barbara E; Mizuuchi, Kiyoshi

    2010-01-01

    P1 ParA is a member of the Walker-type family of partition ATPases involved in the segregation of plasmids and bacterial chromosomes. ATPases of this class interact with DNA non-specifically in vitro and colocalize with the bacterial nucleoid to generate a variety of reported patterns in vivo. Here, we directly visualize ParA binding to DNA using total internal reflection fluorescence microscopy. This activity depends on, and is highly specific for ATP. DNA-binding activity is not coupled to ATP hydrolysis. Rather, ParA undergoes a slow multi-step conformational transition upon ATP binding, which licenses ParA to bind non-specific DNA. The kinetics provide a time-delay switch to allow slow cycling between the DNA binding and non-binding forms of ParA. We propose that this time delay, combined with stimulation of ParA's ATPase activity by ParB bound to the plasmid DNA, generates an uneven distribution of the nucleoid-associated ParA, and provides the motive force for plasmid segregation prior to cell division. PMID:20659294

  4. Identification of new genetic susceptibility loci for breast cancer through consideration of gene-environment interactions.

    PubMed

    Schoeps, Anja; Rudolph, Anja; Seibold, Petra; Dunning, Alison M; Milne, Roger L; Bojesen, Stig E; Swerdlow, Anthony; Andrulis, Irene; Brenner, Hermann; Behrens, Sabine; Orr, Nicholas; Jones, Michael; Ashworth, Alan; Li, Jingmei; Cramp, Helen; Connley, Dan; Czene, Kamila; Darabi, Hatef; Chanock, Stephen J; Lissowska, Jolanta; Figueroa, Jonine D; Knight, Julia; Glendon, Gord; Mulligan, Anna M; Dumont, Martine; Severi, Gianluca; Baglietto, Laura; Olson, Janet; Vachon, Celine; Purrington, Kristen; Moisse, Matthieu; Neven, Patrick; Wildiers, Hans; Spurdle, Amanda; Kosma, Veli-Matti; Kataja, Vesa; Hartikainen, Jaana M; Hamann, Ute; Ko, Yon-Dschun; Dieffenbach, Aida K; Arndt, Volker; Stegmaier, Christa; Malats, Núria; Arias Perez, José I; Benítez, Javier; Flyger, Henrik; Nordestgaard, Børge G; Truong, Thérèse; Cordina-Duverger, Emilie; Menegaux, Florence; dos Santos Silva, Isabel; Fletcher, Olivia; Johnson, Nichola; Häberle, Lothar; Beckmann, Matthias W; Ekici, Arif B; Braaf, Linde; Atsma, Femke; van den Broek, Alexandra J; Makalic, Enes; Schmidt, Daniel F; Southey, Melissa C; Cox, Angela; Simard, Jacques; Giles, Graham G; Lambrechts, Diether; Mannermaa, Arto; Brauch, Hiltrud; Guénel, Pascal; Peto, Julian; Fasching, Peter A; Hopper, John; Flesch-Janys, Dieter; Couch, Fergus; Chenevix-Trench, Georgia; Pharoah, Paul D P; Garcia-Closas, Montserrat; Schmidt, Marjanka K; Hall, Per; Easton, Douglas F; Chang-Claude, Jenny

    2014-01-01

    Genes that alter disease risk only in combination with certain environmental exposures may not be detected in genetic association analysis. By using methods accounting for gene-environment (G × E) interaction, we aimed to identify novel genetic loci associated with breast cancer risk. Up to 34,475 cases and 34,786 controls of European ancestry from up to 23 studies in the Breast Cancer Association Consortium were included. Overall, 71,527 single nucleotide polymorphisms (SNPs), enriched for association with breast cancer, were tested for interaction with 10 environmental risk factors using three recently proposed hybrid methods and a joint test of association and interaction. Analyses were adjusted for age, study, population stratification, and confounding factors as applicable. Three SNPs in two independent loci showed statistically significant association: SNPs rs10483028 and rs2242714 in perfect linkage disequilibrium on chromosome 21 and rs12197388 in ARID1B on chromosome 6. While rs12197388 was identified using the joint test with parity and with age at menarche (P-values = 3 × 10(-07)), the variants on chromosome 21 q22.12, which showed interaction with adult body mass index (BMI) in 8,891 postmenopausal women, were identified by all methods applied. SNP rs10483028 was associated with breast cancer in women with a BMI below 25 kg/m(2) (OR = 1.26, 95% CI 1.15-1.38) but not in women with a BMI of 30 kg/m(2) or higher (OR = 0.89, 95% CI 0.72-1.11, P for interaction = 3.2 × 10(-05)). Our findings confirm comparable power of the recent methods for detecting G × E interaction and the utility of using G × E interaction analyses to identify new susceptibility loci. PMID:24248812

  5. Identification of New Genetic Susceptibility Loci for Breast Cancer Through Consideration of Gene-Environment Interactions

    PubMed Central

    Schoeps, Anja; Rudolph, Anja; Seibold, Petra; Dunning, Alison M.; Milne, Roger L.; Bojesen, Stig E.; Swerdlow, Anthony; Andrulis, Irene; Brenner, Hermann; Behrens, Sabine; Orr, Nicholas; Jones, Michael; Ashworth, Alan; Li, Jingmei; Cramp, Helen; Connley, Dan; Czene, Kamila; Darabi, Hatef; Chanock, Stephen J.; Lissowska, Jolanta; Figueroa, Jonine D.; Knight, Julia; Glendon, Gord; Mulligan, Anna M.; Dumont, Martine; Severi, Gianluca; Baglietto, Laura; Olson, Janet; Vachon, Celine; Purrington, Kristen; Moisse, Matthieu; Neven, Patrick; Wildiers, Hans; Spurdle, Amanda; Kosma, Veli-Matti; Kataja, Vesa; Hartikainen, Jaana M.; Hamann, Ute; Ko, Yon-Dschun; Dieffenbach, Aida K.; Arndt, Volker; Stegmaier, Christa; Malats, Núria; Arias Perez, JoséI.; Benítez, Javier; Flyger, Henrik; Nordestgaard, Børge G.; Truong, Théresè; Cordina-Duverger, Emilie; Menegaux, Florence; Silva, Isabel dos Santos; Fletcher, Olivia; Johnson, Nichola; Häberle, Lothar; Beckmann, Matthias W.; Ekici, Arif B.; Braaf, Linde; Atsma, Femke; van den Broek, Alexandra J.; Makalic, Enes; Schmidt, Daniel F.; Southey, Melissa C.; Cox, Angela; Simard, Jacques; Giles, Graham G.; Lambrechts, Diether; Mannermaa, Arto; Brauch, Hiltrud; Guénel, Pascal; Peto, Julian; Fasching, Peter A.; Hopper, John; Flesch-Janys, Dieter; Couch, Fergus; Chenevix-Trench, Georgia; Pharoah, Paul D. P.; Garcia-Closas, Montserrat; Schmidt, Marjanka K.; Hall, Per; Easton, Douglas F.; Chang-Claude, Jenny

    2014-01-01

    Genes that alter disease risk only in combination with certain environmental exposures may not be detected in genetic association analysis. By using methods accounting for gene-environment (G × E) interaction, we aimed to identify novel genetic loci associated with breast cancer risk. Up to 34,475 cases and 34,786 controls of European ancestry from up to 23 studies in the Breast Cancer Association Consortium were included. Overall, 71,527 single nucleotide polymorphisms (SNPs), enriched for association with breast cancer, were tested for interaction with 10 environmental risk factors using three recently proposed hybrid methods and a joint test of association and interaction. Analyses were adjusted for age, study, population stratification, and confounding factors as applicable. Three SNPs in two independent loci showed statistically significant association: SNPs rs10483028 and rs2242714 in perfect linkage disequilibrium on chromosome 21 and rs12197388 in ARID1B on chromosome 6. While rs12197388 was identified using the joint test with parity and with age at menarche (P-values = 3 × 10?07), the variants on chromosome 21 q22.12, which showed interaction with adult body mass index (BMI) in 8,891 postmenopausal women, were identified by all methods applied. SNP rs10483028 was associated with breast cancer in women with a BMI below 25 kg/m2 (OR = 1.26, 95% CI 1.15–1.38) but not in women with a BMI of 30 kg/m2 or higher (OR = 0.89, 95% CI 0.72–1.11, P for interaction = 3.2 × 10?05). Our findings confirm comparable power of the recent methods for detecting G × E interaction and the utility of using G × E interaction analyses to identify new susceptibility loci. PMID:24248812

  6. Identification of the PP2A-interacting region of heat shock transcription factor 2.

    PubMed

    Xing, Hongyan; Hong, Yiling; Sarge, Kevin D

    2007-01-01

    Previous work in our laboratory demonstrated the existence of an association between heat shock transcription factor 2 (HSF2) and the serine/threonine phosphatase 2A, which is mediated by interaction between HSF2 and the A subunit (also called PR65) of this protein phosphatase. In light of the importance of HSF2-PP2A association for HSF2 cellular function, in this study, we have sought to dissect the sequences within HSF2 that are important for interaction with the A subunit of PP2A. The results of these experiments indicate that the HSF2 region comprising amino acids 343-363 is important for A subunit interaction. This region includes part of the C-terminal leucine zipper motif of HSF2 called heptad repeat C (HR-C). The results of transfection/immunoprecipitation experiments also show that deletion of the 6 amino acids from 343 to 348 from HSF2 (HSF2 (delta343-348)), is sufficient to prevent HSF2 from interacting with PP2A. These data provide insight into a new functional domain of HSF2, the PP2A A subunit-interacting region. PMID:17688198

  7. Abscisic Acid Has a Key Role in Modulating Diverse Plant-Pathogen Interactions1[C][W][OA

    PubMed Central

    Fan, Jun; Hill, Lionel; Crooks, Casey; Doerner, Peter; Lamb, Chris

    2009-01-01

    We isolated an activation-tagged Arabidopsis (Arabidopsis thaliana) line, constitutive disease susceptibility2-1D (cds2-1D), that showed enhanced bacterial growth when challenged with various Pseudomonas syringae strains. Systemic acquired resistance and systemic PATHOGENESIS-RELATED GENE1 induction were also compromised in cds2-1D. The T-DNA insertion adjacent to NINE-CIS-EPOXYCAROTENOID DIOXYGENASE5 (NCED5), one of six genes encoding the abscisic acid (ABA) biosynthetic enzyme NCED, caused a massive increase in transcript level and enhanced ABA levels >2-fold. Overexpression of NCED genes recreated the enhanced disease susceptibility phenotype. NCED2, NCED3, and NCED5 were induced, and ABA accumulated strongly following compatible P. syringae infection. The ABA biosynthetic mutant aba3-1 showed reduced susceptibility to virulent P. syringae, and ABA, whether through exogenous application or endogenous accumulation in response to mild water stress, resulted in increased bacterial growth following challenge with virulent P. syringae, indicating that ABA suppresses resistance to P. syringae. Likewise ABA accumulation also compromised resistance to the biotrophic oomycete Hyaloperonospora arabidopsis, whereas resistance to the fungus Alternaria brassicicola was enhanced in cds2-1D plants and compromised in aba3-1 plants, indicating that ABA promotes resistance to this necrotroph. Comparison of the accumulation of salicylic acid and jasmonic acid in the wild type, cds2-1D, and aba3-1 plants challenged with P. syringae showed that ABA promotes jasmonic acid accumulation and exhibits a complex antagonistic relationship with salicylic acid. Our findings provide genetic evidence that the abiotic stress signal ABA also has profound roles in modulating diverse plant-pathogen interactions mediated at least in part by cross talk with the jasmonic acid and salicylic acid biotic stress signal pathways. PMID:19571312

  8. The Impact of Nonlinear Smoking Effects on the Identification of Gene-by-Smoking Interactions in COPD Genetics Studies

    PubMed Central

    Castaldi, P.J.; Demeo, D.L; Hersh, C.P.; Lomas, D.A.; Soerheim, I.C.; Gulsvik, A.; Bakke, P.; Rennard, Stephen; Pare, Peter; Vestbo, Jørgen; Silverman, E.K.

    2012-01-01

    Background The identification of gene-by-environment interactions is important to understand the genetic basis of chronic obstructive pulmonary disease (COPD). Many COPD genetic association analyses assume a linear relationship between pack-years of smoking exposure and FEV1; however, this assumption has not been evaluated empirically in cohorts with a wide spectrum of COPD severity. Methods We examined the relationship between FEV1 and pack-years of smoking exposure in 4 large cohorts assembled for the purpose of identifying genetic associations with COPD. Using data from the Alpha-1 Antitrypsin Genetic Modifiers Study, we compared the accuracy and power of two different approaches to model smoking by performing a simulation study of a genetic variant with a range of gene-by-smoking interaction effects. Results We identified nonlinear relationships between smoking and FEV1 in 4 large cohorts. We demonstrated that in most situations where the relationship between pack-years and FEV1 is nonlinear, a piecewise-linear approach to model smoking and gene-by-smoking interactions is preferable to the commonly used total pack-years approach. We applied the piecewise linear approach to a genetic association analysis of the PI*Z allele in the Norway case-control cohort and identified a potential PI*Z-by-smoking interaction (p=0.03 for FEV1 analysis, p= 0.01 for COPD susceptibility analysis). Conclusion In study samples with subjects having a wide range of COPD severity, a nonlinear relationship between pack-years of smoking and FEV1 is likely. In this setting, approaches that account for this nonlinearity can be more powerful and less-biased than the commonly-used approach of using total pack-years to model the smoking effect. PMID:21163806

  9. Identification of the key odorants in Tahitian cured vanilla beans (Vanilla tahitensis) by GC-MS and an aroma extract dilution analysis.

    PubMed

    Takahashi, Makoto; Inai, Yoko; Miyazawa, Norio; Kurobayashi, Yoshiko; Fujita, Akira

    2013-01-01

    The key odorants of Tahitian vanilla beans (Vanilla tahitensis) were characterized by a sensory evaluation, aroma extract dilution analysis (AEDA), quantification, and aroma reconstitution. Vanillin and anisaldehyde were identified in the same highest flavor dilution (FD) factor as the most characteristic odor-active compounds in Tahitian vanilla beans, followed by anisyl alcohol and anisyl acetate. Vanillin and anisyl alcohol were by far the most abundant odorants present with the highest concentration in the beans, followed by acetic acid, anisaldehyde, and anisyl acetate. A sensory evaluation of Tahitian vanilla beans and its reconstitute aroma concentrate characterized both samples as similar. These results indicated vanillin, anisaldehyde, anisyl alcohol, and anisyl acetate to be the key odorants in Tahitian vanilla beans. 3-Methylnonane-2,4-dione were identified for the first time in vanilla beans. ?-Damascenone and phenylacetic acid were identified for the first time in Tahitian vanilla beans. PMID:23470766

  10. In Vivo Identification of the Outer Membrane Protein OmcA-MtrC Interaction Network in Shewanella oneidensis MR-1 Cells Using Novel Hydrophobic Chemical Cross-Linkers

    SciTech Connect

    Zhang, Haizhen; Tang, Xiaoting; Munske, Gerhard R.; Zakharova, Natalia L.; Yang, Li; Zheng, Chunxiang; Wolff, Meagan A.; Tolic, Nikola; Anderson, Gordon A.; Shi, Liang; Marshall, Matthew J.; Fredrickson, Jim K.; Bruce, James E.

    2008-04-01

    Outer membrane (OM) cytochromes OmcA (SO1779) and MtrC (SO1778) are the integral components of electron transfer used by Shewanella oneidensis for anaerobic respiration of metal (hydr)oxides. Here the OmcA-MtrC interaction was identified in vivo using a novel hydrophobic chemical cross-linker (MRN) combined with immunoprecipitation techniques. In addition, identification of other OM proteins from the cross-linked complexes allows first visualization of the OmcA-MtrC interaction network. Further experiments on omcA and mtrC mutant cells showed OmcA plays a central role in the network interaction. For comparison, two commercial cross-linkers were also used in parallel and both resulted in fewer OM protein identifications, indicating the superior properties of MRN for identification of membrane protein interactions. Finally, comparison experiments of in vivo cross-linking and cell lysate cross-linking resulted in significantly different protein interaction data, demonstrating the importance of in vivo cross-linking for study of protein-protein interactions in cells.

  11. In Vivo Identification of the Outer Membrane Protein OmcA–MtrC Interaction Network in Shewanella oneidensis MR-1 Cells Using Novel Hydrophobic Chemical Cross-Linkers

    PubMed Central

    Zhang, Haizhen; Tang, Xiaoting; Munske, Gerhard R.; Zakharova, Natalia; Yang, Li; Zheng, Chunxiang; Wolff, Megan A.; Tolic, Nikola; Anderson, Gordon A.; Shi, Liang; Marshall, Matthew J.; Fredrickson, James K.; Bruce, James E.

    2008-01-01

    Outer membrane (OM) cytochromes OmcA (SO1779) and MtrC (SO1778) are the integral components of electron transfer used by Shewanella oneidensis for anaerobic respiration of metal (hydr)oxides. Here the OmcA–MtrC interaction was identified in vivo using a novel hydrophobic chemical cross-linker (MRN) combined with immunoprecipitation techniques. In addition, identification of other OM proteins from the cross-linked complexes allows first visualization of the OmcA–MtrC interaction network. Further experiments on omcA and mtrC mutant cells showed OmcA plays a central role in the network interaction. For comparison, two commercial cross-linkers were also used in parallel, and both resulted in fewer OM protein identifications, indicating the superior properties of MRN for identification of membrane protein interactions. Finally, comparison experiments of in vivo cross-linking and cell lysate cross-linking resulted in significantly different protein interaction data, demonstrating the importance of in vivo cross-linking for study of protein–protein interactions in cells. PMID:18303833

  12. Identification of new interacting partners of the shuttling protein ubinuclein (Ubn-1)

    SciTech Connect

    Lupo, Julien [Unit of Virus Host Cell Interactions (UVHCI), UMI 3265 UJF-EMBL-CNRS, 6 rue Jules Horowitz, BP 181, F-38042 Grenoble Cedex 9 (France) [Unit of Virus Host Cell Interactions (UVHCI), UMI 3265 UJF-EMBL-CNRS, 6 rue Jules Horowitz, BP 181, F-38042 Grenoble Cedex 9 (France); CHU de Grenoble, BP217, 38043 Grenoble Cedex 9 (France); Conti, Audrey [Unit of Virus Host Cell Interactions (UVHCI), UMI 3265 UJF-EMBL-CNRS, 6 rue Jules Horowitz, BP 181, F-38042 Grenoble Cedex 9 (France)] [Unit of Virus Host Cell Interactions (UVHCI), UMI 3265 UJF-EMBL-CNRS, 6 rue Jules Horowitz, BP 181, F-38042 Grenoble Cedex 9 (France); Sueur, Charlotte [Unit of Virus Host Cell Interactions (UVHCI), UMI 3265 UJF-EMBL-CNRS, 6 rue Jules Horowitz, BP 181, F-38042 Grenoble Cedex 9 (France) [Unit of Virus Host Cell Interactions (UVHCI), UMI 3265 UJF-EMBL-CNRS, 6 rue Jules Horowitz, BP 181, F-38042 Grenoble Cedex 9 (France); CHU de Grenoble, BP217, 38043 Grenoble Cedex 9 (France); Coly, Pierre-Alain [Unit of Virus Host Cell Interactions (UVHCI), UMI 3265 UJF-EMBL-CNRS, 6 rue Jules Horowitz, BP 181, F-38042 Grenoble Cedex 9 (France)] [Unit of Virus Host Cell Interactions (UVHCI), UMI 3265 UJF-EMBL-CNRS, 6 rue Jules Horowitz, BP 181, F-38042 Grenoble Cedex 9 (France); Coute, Yohann [CEA, IRTSV, Laboratoire Biologie a Grande Echelle, F-38054 Grenoble (France) [CEA, IRTSV, Laboratoire Biologie a Grande Echelle, F-38054 Grenoble (France); INSERM, U1038, F-38054 Grenoble (France); Universite Joseph Fourier, Grenoble 1, F-38000 Grenoble Cedex 09 (France); Hunziker, Walter [Institute of Molecular and Cell Biology, Epithelial Cell Biology Laboratory, Singapore 1386473 (Singapore)] [Institute of Molecular and Cell Biology, Epithelial Cell Biology Laboratory, Singapore 1386473 (Singapore); Burmeister, Wim P. [Unit of Virus Host Cell Interactions (UVHCI), UMI 3265 UJF-EMBL-CNRS, 6 rue Jules Horowitz, BP 181, F-38042 Grenoble Cedex 9 (France)] [Unit of Virus Host Cell Interactions (UVHCI), UMI 3265 UJF-EMBL-CNRS, 6 rue Jules Horowitz, BP 181, F-38042 Grenoble Cedex 9 (France); Germi, Raphaelle [Unit of Virus Host Cell Interactions (UVHCI), UMI 3265 UJF-EMBL-CNRS, 6 rue Jules Horowitz, BP 181, F-38042 Grenoble Cedex 9 (France) [Unit of Virus Host Cell Interactions (UVHCI), UMI 3265 UJF-EMBL-CNRS, 6 rue Jules Horowitz, BP 181, F-38042 Grenoble Cedex 9 (France); CHU de Grenoble, BP217, 38043 Grenoble Cedex 9 (France); Manet, Evelyne; Gruffat, Henri [INSERM U758, Unite de Virologie humaine, Lyon, 46 allee d'Italie F-69007 France (France) [INSERM U758, Unite de Virologie humaine, Lyon, 46 allee d'Italie F-69007 France (France); Ecole Normale Superieure de Lyon, F-69007 France (France); Universite Lyon1, F-69007, Lyon (France); and others

    2012-03-10

    We have previously characterized ubinuclein (Ubn-1) as a NACos (Nuclear and Adherent junction Complex components) protein which interacts with viral or cellular transcription factors and the tight junction (TJ) protein ZO-1. The purpose of the present study was to get more insights on the binding partners of Ubn-1, notably those present in the epithelial junctions. Using an in vivo assay of fluorescent protein-complementation assay (PCA), we demonstrated that the N-terminal domains of the Ubn-1 and ZO-1 proteins triggered a functional interaction inside the cell. Indeed, expression of both complementary fragments of venus fused to the N-terminal parts of Ubn-1 and ZO-1 was able to reconstitute a fluorescent venus protein. Furthermore, nuclear expression of the chimeric Ubn-1 triggered nuclear localization of the chimeric ZO-1. We could localize this interaction to the PDZ2 domain of ZO-1 using an in vitro pull-down assay. More precisely, a 184-amino acid region (from amino acids 39 to 223) at the N-terminal region of Ubn-1 was responsible for the interaction with the PDZ2 domain of ZO-1. Co-imunoprecipitation and confocal microscopy experiments also revealed the tight junction protein cingulin as a new interacting partner of Ubn-1. A proteomic approach based on mass spectrometry analysis (MS) was then undertaken to identify further binding partners of GST-Ubn-1 fusion protein in different subcellular fractions of human epithelial HT29 cells. LYRIC (Lysine-rich CEACAM1-associated protein) and RACK-1 (receptor for activated C-kinase) proteins were validated as bona fide interacting partners of Ubn-1. Altogether, these results suggest that Ubn-1 is a scaffold protein influencing protein subcellular localization and is involved in several processes such as cell-cell contact signalling or modulation of gene activity.

  13. Identification and Characterization of a Novel Host-Toxin Interaction in the Wheat - Stagonospora Nodorum Pathosystem

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Stagonospora nodorum, casual agent of Stagonospora nodorum blotch (SNB) of wheat, produces a number of host-selective toxins (HSTs) known to be important in disease. To date, four HSTs and corresponding host sensitivity genes have been reported, and all four host-toxin interactions are significant f...

  14. Identification of interaction partners of the dynamin-like protein DynA from Bacillus subtilis.

    PubMed

    Bürmann, Frank; Sawant, Prachi; Bramkamp, Marc

    2012-07-01

    Membrane dynamics are involved in crucial processes in eukaryotic and prokaryotic cells. Membrane fusion and fission events are often catalyzed by proteins that belong to the dynamin family of large GTPases. It has recently been shown that members of the dynamin superfamily are also present in many bacterial species. Although structural information about full length bacterial dynamin-like proteins is available, their molecular role remains unclear. We have shown previously that DynA, a dynamin-like protein found in the firmicute Bacillus subtilis is able to fuse membranes in vitro. In contrast to other members of the dynamin family this membrane remodeling activity was not dependent on guanosine nucleotides, but required magnesium. DynA assemblies localize in foci that are often enriched at sites of septation and hence a potential role during bacterial cytokinesis was discussed. In order to identify potential interaction partners we constructed a bacterial-two hybrid (B2H) library and screened for DynA interacting proteins. Three potential interaction partner have been identified, YneK, RNaseY (YmdA), and YwpG. Localization of these proteins phenocopies that of DynA, supporting the potential interaction in vivo. PMID:23060960

  15. Biomarker Identification for Prostate Cancer and Lymph Node Metastasis from Microarray Data and Protein Interaction Network Using Gene Prioritization Method

    PubMed Central

    Arias, Carlos Roberto; Yeh, Hsiang-Yuan; Soo, Von-Wun

    2012-01-01

    Finding a genetic disease-related gene is not a trivial task. Therefore, computational methods are needed to present clues to the biomedical community to explore genes that are more likely to be related to a specific disease as biomarker. We present biomarker identification problem using gene prioritization method called gene prioritization from microarray data based on shortest paths, extended with structural and biological properties and edge flux using voting scheme (GP-MIDAS-VXEF). The method is based on finding relevant interactions on protein interaction networks, then scoring the genes using shortest paths and topological analysis, integrating the results using a voting scheme and a biological boosting. We applied two experiments, one is prostate primary and normal samples and the other is prostate primary tumor with and without lymph nodes metastasis. We used 137 truly prostate cancer genes as benchmark. In the first experiment, GP-MIDAS-VXEF outperforms all the other state-of-the-art methods in the benchmark by retrieving the truest related genes from the candidate set in the top 50 scores found. We applied the same technique to infer the significant biomarkers in prostate cancer with lymph nodes metastasis which is not established well. PMID:22654636

  16. Optical key system

    DOEpatents

    Hagans, Karla G. (Livermore, CA); Clough, Robert E. (Danville, CA)

    2000-01-01

    An optical key system comprises a battery-operated optical key and an isolated lock that derives both its operating power and unlock signals from the correct optical key. A light emitting diode or laser diode is included within the optical key and is connected to transmit a bit-serial password. The key user physically enters either the code-to-transmit directly, or an index to a pseudorandom number code, in the key. Such person identification numbers can be retained permanently, or ephemeral. When a send button is pressed, the key transmits a beam of light modulated with the password information. The modulated beam of light is received by a corresponding optical lock with a photovoltaic cell that produces enough power from the beam of light to operate a password-screen digital logic. In one application, an acceptable password allows a two watt power laser diode to pump ignition and timing information over a fiberoptic cable into a sealed engine compartment. The receipt of a good password allows the fuel pump, spark, and starter systems to each operate. Therefore, bypassing the lock mechanism as is now routine with automobile thieves is pointless because the engine is so thoroughly disabled.

  17. Rice phytochrome-interacting factor-like protein OsPIL1 functions as a key regulator of internode elongation and induces a morphological response to drought stress

    PubMed Central

    Todaka, Daisuke; Nakashima, Kazuo; Maruyama, Kyonoshin; Kidokoro, Satoshi; Osakabe, Yuriko; Ito, Yusuke; Matsukura, Satoko; Fujita, Yasunari; Yoshiwara, Kyouko; Ohme-Takagi, Masaru; Kojima, Mikiko; Sakakibara, Hitoshi; Shinozaki, Kazuo; Yamaguchi-Shinozaki, Kazuko

    2012-01-01

    The mechanisms for plant growth restriction during stress conditions remains unclear. Here, we demonstrate that a phytochrome-interacting factor-like protein, OsPIL1/OsPIL13, acts as a key regulator of reduced internode elongation in rice under drought conditions. The level of OsPIL1 mRNA in rice seedlings grown under nonstressed conditions with light/dark cycles oscillated in a circadian manner with peaks in the middle of the light period. Under drought stress conditions, OsPIL1 expression was inhibited during the light period. We found that OsPIL1 was highly expressed in the node portions of the stem using promoter-glucuronidase analysis. Overexpression of OsPIL1 in transgenic rice plants promoted internode elongation. In contrast, transgenic rice plants with a chimeric repressor resulted in short internode sections. Alteration of internode cell size was observed in OsPIL1 transgenic plants, indicating that differences in cell size cause the change in internode length. Oligoarray analysis revealed OsPIL1 downstream genes, which were enriched for cell wall-related genes responsible for cell elongation. These data suggest that OsPIL1 functions as a key regulatory factor of reduced plant height via cell wall-related genes in response to drought stress. This regulatory system may be important for morphological stress adaptation in rice under drought conditions. PMID:22984180

  18. Identification of OmpR-Family Response Regulators Interacting with Thioredoxin in the Cyanobacterium Synechocystis sp. PCC 6803

    PubMed Central

    Kadowaki, Taro; Nishiyama, Yoshitaka; Hisabori, Toru; Hihara, Yukako

    2015-01-01

    The redox state of the photosynthetic electron transport chain is known to act as a signal to regulate the transcription of key genes involved in the acclimation responses to environmental changes. We hypothesized that the protein thioredoxin (Trx) acts as a mediator connecting the redox state of the photosynthetic electron transport chain and transcriptional regulation, and established a screening system to identify transcription factors (TFs) that interact with Trx. His-tagged TFs and S-tagged mutated form of Trx, TrxMC35S, whose active site cysteine 35 was substituted with serine to trap the target interacting protein, were co-expressed in E. coli cells and Trx-TF complexes were detected by immuno-blotting analysis. We examined the interaction between Trx and ten OmpR family TFs encoded in the chromosome of the cyanobacterium Synechocystis sp. PCC 6803 (S.6803). Although there is a highly conserved cysteine residue in the receiver domain of all OmpR family TFs, only three, RpaA (Slr0115), RpaB (Slr0946) and ManR (Slr1837), were identified as putative Trx targets. The recombinant forms of wild-type TrxM, RpaA, RpaB and ManR proteins from S.6803 were purified following over-expression in E. coli and their interaction was further assessed by monitoring changes in the number of cysteine residues with free thiol groups. An increase in the number of free thiols was observed after incubation of the oxidized TFs with Trx, indicating the reduction of cysteine residues as a consequence of interaction with Trx. Our results suggest, for the first time, the possible regulation of OmpR family TFs through the supply of reducing equivalents from Trx, as well as through the phospho-transfer from its cognate sensor histidine kinase. PMID:25774906

  19. Identification of OmpR-family response regulators interacting with thioredoxin in the Cyanobacterium Synechocystis sp. PCC 6803.

    PubMed

    Kadowaki, Taro; Nishiyama, Yoshitaka; Hisabori, Toru; Hihara, Yukako

    2015-01-01

    The redox state of the photosynthetic electron transport chain is known to act as a signal to regulate the transcription of key genes involved in the acclimation responses to environmental changes. We hypothesized that the protein thioredoxin (Trx) acts as a mediator connecting the redox state of the photosynthetic electron transport chain and transcriptional regulation, and established a screening system to identify transcription factors (TFs) that interact with Trx. His-tagged TFs and S-tagged mutated form of Trx, TrxMC35S, whose active site cysteine 35 was substituted with serine to trap the target interacting protein, were co-expressed in E. coli cells and Trx-TF complexes were detected by immuno-blotting analysis. We examined the interaction between Trx and ten OmpR family TFs encoded in the chromosome of the cyanobacterium Synechocystis sp. PCC 6803 (S.6803). Although there is a highly conserved cysteine residue in the receiver domain of all OmpR family TFs, only three, RpaA (Slr0115), RpaB (Slr0946) and ManR (Slr1837), were identified as putative Trx targets. The recombinant forms of wild-type TrxM, RpaA, RpaB and ManR proteins from S.6803 were purified following over-expression in E. coli and their interaction was further assessed by monitoring changes in the number of cysteine residues with free thiol groups. An increase in the number of free thiols was observed after incubation of the oxidized TFs with Trx, indicating the reduction of cysteine residues as a consequence of interaction with Trx. Our results suggest, for the first time, the possible regulation of OmpR family TFs through the supply of reducing equivalents from Trx, as well as through the phospho-transfer from its cognate sensor histidine kinase. PMID:25774906

  20. Answer Keys

    NSDL National Science Digital Library

    2010-01-01

    Answer keys provide acceptable answers to the questions posed in a case. Since these questions are intended to be answered by students and are often graded, keys are password-protected and access limited to registered instructors affiliated with an educational institution.

  1. Probing the Sialic Acid Binding Site of the Hemagglutinin-Neuraminidase of Newcastle Disease Virus: Identification of Key Amino Acids Involved in Cell Binding, Catalysis, and Fusion

    Microsoft Academic Search

    Helen Connaris; Toru Takimoto; Rupert Russell; Susan Crennell; Ibrahim Moustafa; Allen Portner; Garry Taylor

    2002-01-01

    We recently reported the first crystal structure of a paramyxovirus hemagglutinin-neuraminidase (HN) from Newcastle disease virus. This multifunctional protein is responsible for binding to cellular sialyl-glycoconju- gate receptors, promotion of fusion through interaction with the second viral surface fusion (F) glycoprotein, and processing progeny virions by removal of sialic acid from newly synthesized viral coat proteins. Our structural studies suggest

  2. Polymorphisms in folate-metabolizing genes, chromosome damage, and risk of Down syndrome in Italian women: identification of key factors using artificial neural networks

    Microsoft Academic Search

    Fabio Coppedè; Enzo Grossi; Francesca Migheli; Lucia Migliore

    2010-01-01

    BACKGROUND: Studies in mothers of Down syndrome individuals (MDS) point to a role for polymorphisms in folate metabolic genes in increasing chromosome damage and maternal risk for a Down syndrome (DS) pregnancy, suggesting complex gene-gene interactions. This study aimed to analyze a dataset of genetic and cytogenetic data in an Italian group of MDS and mothers of healthy children (control

  3. Parameter identification for planetary soil based on a decoupled analytical wheel-soil interaction terramechanics model

    Microsoft Academic Search

    Liang Ding; Kazuya Yoshida; Keiji Nagatani; Haibo Gao; Zongquan Deng

    2009-01-01

    Identifying planetary soil parameters is not only an important scientific goal, but also necessary for exploration rover to optimize its control strategy and realize high-fidelity simulation. An improved wheel-soil interaction mechanics model is introduced, and it is then simplified by linearizing the normal stress and shearing stress to derive closed-form analytical equations. Eight unknown soil parameters are divided into three

  4. Identification of Genes Interacting with rnt-1 Through Large-Scale RNAi Screening in Caenorhabditis elegans

    PubMed Central

    Lee, Kiho; Shim, Jiwon; Lee, Jihyun; Lee, Junho

    2013-01-01

    Although many critical roles of the RUNX family proteins have already been identified, little attention has been given to how these proteins interact with other factors. Elucidating RUNX protein interactions will help extend our understanding of their roles in normal development and tumorigenesis. In this study, we performed large-scale RNAi screening to identify genes that genetically interact with rnt-1, the sole homolog of RUNX protein in the nematode Caenorhabditis elegans. To this end, we took advantage of the fact that C. elegans can survive a severe loss of RNT-1 function with only mild phenotypes, and we looked for genes that caused a synthetic phenotype in the rnt-1 mutant background. We identified seven genes, three of which (cdk-8, cic-1, and sur-2) are involved in transcription, two of which (pgp-2 and cct-5) are involved in stress response, and two of which (D2045.7 and W09D10.4) are involved in signaling cascades, according to their functional gene ontology terms. We further confirmed that the CDK8-containing mediator complex genetically interacts with RNT-1 by showing that knockdown of each component of the CDK8 mediator complex caused a synthetic phenotype, that is, the exploded intestine through the vulva (Eiv) phenotype, in the rnt-1 mutant background. We also identified a putative target gene, acs-4, which is regulated by the RNT-1 and CDK8 mediator complex. Our results strengthen the notion that the CDK8 mediator complex may also act together with RUNX proteins in mammals. PMID:23979934

  5. Identification of interactions in fractional-order systems with high dimensions

    SciTech Connect

    Ji, Xiaoxi; Wu, Yu; Sheng, Wenbo [School of Mathematical Sciences and Centre for Computational Systems Biology, Fudan University, Shanghai 200433 (China)] [School of Mathematical Sciences and Centre for Computational Systems Biology, Fudan University, Shanghai 200433 (China); Lin, Wei, E-mail: wlin@fudan.edu.cn [School of Mathematical Sciences and Centre for Computational Systems Biology, Fudan University, Shanghai 200433 (China) [School of Mathematical Sciences and Centre for Computational Systems Biology, Fudan University, Shanghai 200433 (China); Shanghai Key Laboratory of Data Science, LMNS, and Shanghai Center for Mathematical Sciences, Shanghai 200433 (China)

    2014-06-15

    This article proposes an approach to identify fractional-order systems with sparse interaction structures and high dimensions when observation data are supposed to be experimentally available. This approach includes two steps: first, it is to estimate the value of the fractional order by taking into account the solution properties of fractional-order systems; second, it is to identify the interaction coefficients among the system variables by employing the compressed sensing technique. An error analysis is provided analytically for this approach and a further improved approach is also proposed. Moreover, the applicability of the proposed approach is fully illustrated by two examples: one is to estimate the mutual interactions in a complex dynamical network described by fractional-order systems, and the other is to identify a high fractional-order and homogeneous sequential differential equation, which is frequently used to describe viscoelastic phenomena. All the results demonstrate the feasibility of figuring out the system mechanisms behind the data experimentally observed in physical or biological systems with viscoelastic evolution characters.

  6. Identification and Validation of Novel Small Molecule Disruptors of HuR-mRNA Interaction.

    PubMed

    Wu, Xiaoqing; Lan, Lan; Wilson, David Michael; Marquez, Rebecca T; Tsao, Wei-Chung; Gao, Philip; Roy, Anuradha; Turner, Benjamin Andrew; McDonald, Peter; Tunge, Jon A; Rogers, Steven A; Dixon, Dan A; Aubé, Jeffrey; Xu, Liang

    2015-06-19

    HuR, an RNA binding protein, binds to adenine- and uridine-rich elements (ARE) in the 3'-untranslated region (UTR) of target mRNAs, regulating their stability and translation. HuR is highly abundant in many types of cancer, and it promotes tumorigenesis by interacting with cancer-associated mRNAs, which encode proteins that are implicated in different tumor processes including cell proliferation, cell survival, angiogenesis, invasion, and metastasis. Drugs that disrupt the stabilizing effect of HuR upon mRNA targets could have dramatic effects on inhibiting cancer growth and persistence. In order to identify small molecules that directly disrupt the HuR-ARE interaction, we established a fluorescence polarization (FP) assay optimized for high throughput screening (HTS) using HuR protein and an ARE oligo from Musashi RNA-binding protein 1 (Msi1) mRNA, a HuR target. Following the performance of an HTS of ?6000 compounds, we discovered a cluster of potential disruptors, which were then validated by AlphaLISA (Amplified Luminescent Proximity Homogeneous Assay), surface plasmon resonance (SPR), ribonucleoprotein immunoprecipitation (RNP IP) assay, and luciferase reporter functional studies. These compounds disrupted HuR-ARE interactions at the nanomolar level and blocked HuR function by competitive binding to HuR. These results support future studies toward chemical probes for a HuR function study and possibly a novel therapy for HuR-overexpressing cancers. PMID:25750985

  7. Comparative genome analysis and identification of competitive and cooperative interactions in a polymicrobial disease.

    PubMed

    Endo, Akiko; Watanabe, Takayasu; Ogata, Nachiko; Nozawa, Takashi; Aikawa, Chihiro; Arakawa, Shinichi; Maruyama, Fumito; Izumi, Yuichi; Nakagawa, Ichiro

    2015-03-01

    Polymicrobial diseases are caused by combinations of multiple bacteria, which can lead to not only mild but also life-threatening illnesses. Periodontitis represents a polymicrobial disease; Porphyromonas gingivalis, Treponema denticola and Tannerella forsythia, called 'the red complex', have been recognized as the causative agents of periodontitis. Although molecular interactions among the three species could be responsible for progression of periodontitis, the relevant genetic mechanisms are unknown. In this study, we uncovered novel interactions in comparative genome analysis among the red complex species. Clustered regularly interspaced short palindromic repeats (CRISPRs) of T. forsythia might attack the restriction modification system of P. gingivalis, and possibly work as a defense system against DNA invasion from P. gingivalis. On the other hand, gene deficiencies were mutually compensated in metabolic pathways when the genes of all the three species were taken into account, suggesting that there are cooperative relationships among the three species. This notion was supported by the observation that each of the three species had its own virulence factors, which might facilitate persistence and manifestations of virulence of the three species. Here, we propose new mechanisms of bacterial symbiosis in periodontitis; these mechanisms consist of competitive and cooperative interactions. Our results might shed light on the pathogenesis of periodontitis and of other polymicrobial diseases. PMID:25171331

  8. The toxofilin–actin–PP2C complex of Toxoplasma: identification of interacting domains

    PubMed Central

    Jan, Gaelle; Delorme, Violaine; David, Violaine; Revenu, Celine; Rebollo, Angelita; Cayla, Xavier; Tardieux, Isabelle

    2006-01-01

    Toxofilin is a 27 kDa protein isolated from the human protozoan parasite Toxoplasma gondii, which causes toxoplasmosis. Toxofilin binds to G-actin, and in vitro studies have shown that it controls elongation of actin filaments by sequestering actin monomers. Toxofilin affinity for G-actin is controlled by the phosphorylation status of its Ser53, which depends on the activities of a casein kinase II and a type 2C serine/threonine phosphatase (PP2C). To get insights into the functional properties of toxofilin, we undertook a structure–function analysis of the protein using a combination of biochemical techniques. We identified a domain that was sufficient to sequester G-actin and that contains three peptide sequences selectively binding to G-actin. Two of these sequences are similar to sequences present in several G- and F-actin-binding proteins, while the third appears to be specific to toxofilin. Additionally, we identified two toxofilin domains that interact with PP2C, one of which contains the Ser53 substrate. In addition to characterizing the interacting domains of toxofilin with its partners, the present study also provides information on an in vivo-based approach to selectively and competitively disrupt the protein–protein interactions that are important to parasite motility. PMID:17014426

  9. Jointly They Edit: Examining the Impact of Community Identification on Political Interaction in Wikipedia

    PubMed Central

    Neff, Jessica J.; Laniado, David; Kappler, Karolin E.; Volkovich, Yana; Aragón, Pablo; Kaltenbrunner, Andreas

    2013-01-01

    Background In their 2005 study, Adamic and Glance coined the memorable phrase ‘divided they blog’, referring to a trend of cyberbalkanization in the political blogosphere, with liberal and conservative blogs tending to link to other blogs with a similar political slant, and not to one another. As political discussion and activity increasingly moves online, the power of framing political discourses is shifting from mass media to social media. Methodology/Principal Findings Continued examination of political interactions online is critical, and we extend this line of research by examining the activities of political users within the Wikipedia community. First, we examined how users in Wikipedia choose to display their political affiliation. Next, we analyzed the patterns of cross-party interaction and community participation among those users proclaiming a political affiliation. In contrast to previous analyses of other social media, we did not find strong trends indicating a preference to interact with members of the same political party within the Wikipedia community. Conclusions/Significance Our results indicate that users who proclaim their political affiliation within the community tend to proclaim their identity as a ‘Wikipedian’ even more loudly. It seems that the shared identity of ‘being Wikipedian’ may be strong enough to triumph over other potentially divisive facets of personal identity, such as political affiliation. PMID:23573269

  10. Identification of human hnRNP C1/C2 as a dengue virus NS1-interacting protein

    SciTech Connect

    Noisakran, Sansanee [Medical Biotechnology Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani 12120 (Thailand); Medical Molecular Biology Unit, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Adulyadejvikrom Building (12th Floor), Mahidol University, Bangkok 10700 (Thailand); Sengsai, Suchada [Medical Molecular Biology Unit, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Adulyadejvikrom Building (12th Floor), Mahidol University, Bangkok 10700 (Thailand); Thongboonkerd, Visith; Kanlaya, Rattiyaporn [Medical Molecular Biology Unit, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Adulyadejvikrom Building (12th Floor), Mahidol University, Bangkok 10700 (Thailand); Medical Proteomics Unit, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700 (Thailand); Sinchaikul, Supachok [Institute of Biological Chemistry and Genomic Research Center, Academia Sinica, Taipei, Taiwan (China); Chen, Shui-Tein [Institute of Biological Chemistry and Genomic Research Center, Academia Sinica, Taipei, Taiwan (China); Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan (China); Puttikhunt, Chunya [Medical Biotechnology Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani 12120 (Thailand); Medical Molecular Biology Unit, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Adulyadejvikrom Building (12th Floor), Mahidol University, Bangkok 10700 (Thailand)] (and others)

    2008-07-18

    Dengue virus nonstructural protein 1 (NS1) is a key glycoprotein involved in the production of infectious virus and the pathogenesis of dengue diseases. Very little is known how NS1 interacts with host cellular proteins and functions in dengue virus-infected cells. This study aimed at identifying NS1-interacting host cellular proteins in dengue virus-infected cells by employing co-immunoprecipitation, two-dimensional gel electrophoresis, and mass spectrometry. Using lysates of dengue virus-infected human embryonic kidney cells (HEK 293T), immunoprecipitation with an anti-NS1 monoclonal antibody revealed eight isoforms of dengue virus NS1 and a 40-kDa protein, which was subsequently identified by quadrupole time-of-flight tandem mass spectrometry (Q-TOF MS/MS) as human heterogeneous nuclear ribonucleoprotein (hnRNP) C1/C2. Further investigation by co-immunoprecipitation and co-localization confirmed the association of hnRNP C1/C2 and dengue virus NS1 proteins in dengue virus-infected cells. Their interaction may have implications in virus replication and/or cellular responses favorable to survival of the virus in host cells.

  11. Identification of AREG and PLK1 pathway modulation as a potential key of the response of intracranial 9L tumor to microbeam radiation therapy.

    PubMed

    Bouchet, Audrey; Sakakini, Nathalie; Atifi, Michèle El; Le Clec'h, Céline; Bräuer-Krisch, Elke; Rogalev, Léonid; Laissue, Jean Albert; Rihet, Pascal; Le Duc, Géraldine; Pelletier, Laurent

    2015-06-01

    Synchrotron microbeam radiation therapy (MRT) relies on the spatial fractionation of a synchrotron beam into parallel micron-wide beams allowing deposition of hectogray doses. MRT controls the intracranial tumor growth in rodent models while sparing normal brain tissues. Our aim was to identify the early biological processes underlying the differential effect of MRT on tumor and normal brain tissues. The expression of 28,000 transcripts was tested by microarray 6 hr after unidirectional MRT (400 Gy, 50 µm-wide microbeams, 200 µm spacing). The specific response of tumor tissues to MRT consisted in the significant transcriptomic modulation of 431 probesets (316 genes). Among them, 30 were not detected in normal brain tissues, neither before nor after MRT. Areg, Trib3 and Nppb were down-regulated, whereas all others were up-regulated. Twenty-two had similar expression profiles during the 2 weeks observed after MRT, including Ccnb1, Cdc20, Pttg1 and Plk1 related to the mitotic role of the Polo-like kinase (Plk) pathway. The up-regulation of Areg expression may indicate the emergence of survival processes in tumor cells triggered by the irradiation; while the modulation of the "mitotic role of Plk1" pathway, which relates to cytokinetic features of the tumor observed histologically after MRT, may partially explain the control of tumor growth by MRT. The identification of these tumor-specific responses permit to consider new strategies that might potentiate the antitumoral effect of MRT. PMID:25382544

  12. First species of Leptochelia Dana, 1849 (Crustacea: Tanaidacea) from the Eastern Pacific, with an annotated checklist and identification keys for the genus.

    PubMed

    Jarquín-González, Jani; García-Madrigal, María Del Socorro; Carrera-Parra, Luis Fernando

    2015-01-01

    Forty three species of leptocheliids are known worldwide. In the American region only eight species have been described from the Western Atlantic, while for the Eastern Pacific none have been described, suggesting that the diversity of this family has been severely underestimated in this region. Here we describe the first species of Leptochelia from the Eastern Pacific, Leptochelia mexicana n. sp., which is characterized by the males having a spiniform seta on the second segment of uropodal endopod, a novel feature for the genus. In addition, the first annotated checklist and a taxonomic key with illustrations for Leptochelia species are included. The list includes the type locality, type depository, distribution, habitat and, in some cases, remarks. PMID:25781398

  13. Identification of key functional residues in the active site of human {beta}1,4-galactosyltransferase 7: a major enzyme in the glycosaminoglycan synthesis pathway.

    PubMed

    Talhaoui, Ibtissam; Bui, Catherine; Oriol, Rafael; Mulliert, Guillermo; Gulberti, Sandrine; Netter, Patrick; Coughtrie, Michael W H; Ouzzine, Mohamed; Fournel-Gigleux, Sylvie

    2010-11-26

    Glycosaminoglycans (GAGs) play a central role in many pathophysiological events, and exogenous xyloside substrates of ?1,4-galactosyltransferase 7 (?4GalT7), a major enzyme of GAG biosynthesis, have interesting biomedical applications. To predict functional peptide regions important for substrate binding and activity of human ?4GalT7, we conducted a phylogenetic analysis of the ?1,4-galactosyltransferase family and generated a molecular model using the x-ray structure of Drosophila ?4GalT7-UDP as template. Two evolutionary conserved motifs, (163)DVD(165) and (221)FWGWGREDDE(230), are central in the organization of the enzyme active site. This model was challenged by systematic engineering of point mutations, combined with in vitro and ex vivo functional assays. Investigation of the kinetic properties of purified recombinant wild-type ?4GalT7 and selected mutants identified Trp(224) as a key residue governing both donor and acceptor substrate binding. Our results also suggested the involvement of the canonical carboxylate residue Asp(228) acting as general base in the reaction catalyzed by human ?4GalT7. Importantly, ex vivo functional tests demonstrated that regulation of GAG synthesis is highly responsive to modification of these key active site amino acids. Interestingly, engineering mutants at position 224 allowed us to modify the affinity and to modulate the specificity of human ?4GalT7 toward UDP-sugars and xyloside acceptors. Furthermore, the W224H mutant was able to sustain decorin GAG chain substitution but not GAG synthesis from exogenously added xyloside. Altogether, this study provides novel insight into human ?4GalT7 active site functional domains, allowing manipulation of this enzyme critical for the regulation of GAG synthesis. A better understanding of the mechanism underlying GAG assembly paves the way toward GAG-based therapeutics. PMID:20843813

  14. Identification of Odorant-Receptor Interactions by Global Mapping of the Human Odorome

    PubMed Central

    Audouze, Karine; Tromelin, Anne; Le Bon, Anne Marie; Belloir, Christine; Petersen, Rasmus Koefoed; Kristiansen, Karsten; Brunak, Søren; Taboureau, Olivier

    2014-01-01

    The human olfactory system recognizes a broad spectrum of odorants using approximately 400 different olfactory receptors (hORs). Although significant improvements of heterologous expression systems used to study interactions between ORs and odorant molecules have been made, screening the olfactory repertoire of hORs remains a tremendous challenge. We therefore developed a chemical systems level approach based on protein-protein association network to investigate novel hOR-odorant relationships. Using this new approach, we proposed and validated new bioactivities for odorant molecules and OR2W1, OR51E1 and OR5P3. As it remains largely unknown how human perception of odorants influence or prevent diseases, we also developed an odorant-protein matrix to explore global relationships between chemicals, biological targets and disease susceptibilities. We successfully experimentally demonstrated interactions between odorants and the cannabinoid receptor 1 (CB1) and the peroxisome proliferator-activated receptor gamma (PPAR?). Overall, these results illustrate the potential of integrative systems chemical biology to explore the impact of odorant molecules on human health, i.e. human odorome. PMID:24695519

  15. Systematic identification of transcriptional regulatory modules from protein–protein interaction networks

    PubMed Central

    Diez, Diego; Hutchins, Andrew Paul; Miranda-Saavedra, Diego

    2014-01-01

    Transcription factors (TFs) combine with co-factors to form transcriptional regulatory modules (TRMs) that regulate gene expression programs with spatiotemporal specificity. Here we present a novel and generic method (rTRM) for the reconstruction of TRMs that integrates genomic information from TF binding, cell type-specific gene expression and protein–protein interactions. rTRM was applied to reconstruct the TRMs specific for embryonic stem cells (ESC) and hematopoietic stem cells (HSC), neural progenitor cells, trophoblast stem cells and distinct types of terminally differentiated CD4+ T cells. The ESC and HSC TRM predictions were highly precise, yielding 77 and 96 proteins, of which ?75% have been independently shown to be involved in the regulation of these cell types. Furthermore, rTRM successfully identified a large number of bridging proteins with known roles in ESCs and HSCs, which could not have been identified using genomic approaches alone, as they lack the ability to bind specific DNA sequences. This highlights the advantage of rTRM over other methods that ignore PPI information, as proteins need to interact with other proteins to form complexes and perform specific functions. The prediction and experimental validation of the co-factors that endow master regulatory TFs with the capacity to select specific genomic sites, modulate the local epigenetic profile and integrate multiple signals will provide important mechanistic insights not only into how such TFs operate, but also into abnormal transcriptional states leading to disease. PMID:24137002

  16. Identification of mammalin cytosolic proteins that can interact specifically with FACC

    SciTech Connect

    Youssoufian, H.; Lu, C. [Brigham and Women`s Hospital and Harvard Medical School, Boston, MA (United States); Verlander, P. [Rockefeller Univ., NY (United States)] [and others

    1994-09-01

    Fanconi`s anemia is an autosomal recessive disorder characterized by congenital anomalies and chromosomal instability. Although the gene defective in complementation group C (FACC) has been isolated, the biochemical function of the FACC-encoded polypeptide is poorly understood. We have shown previously that this protein resides predominantly in the cytoplasm of mammalian cells, and is thus unlikely to play a direct role in DNA repair. The intracellular interactions of FACC could help to elucidate its function. In order to search for cellular proteins that potentially interact with FACC, we have screened a number of nuclear and cytosolic extracts with a chimeric FACC-immunoglobulin affinity reagent bound to protein A-agarose beads. We identified at least three such proteins from cytosolic, but not nuclear, extracts of multiple human and other mammalian cell lines. These proteins failed to bind to other chimeric immunoglobulin molecules. We conclude that mammalian cells contain a family of proteins that have readily detectable FACC-binding activity. The identity of these proteins could shed light on the function of FACC.

  17. Quantification of Ligand-Regulated Nuclear Receptor Corepressor and Coactivator Binding, Key Interactions Determining Ligand Potency and Efficacy for Thyroid Hormone Receptor

    PubMed Central

    Jeyakumar, M.; Webb, Paul; Baxter, John D.; Scanlan, Thomas S.; Katzenellenbogen, John A.

    2008-01-01

    The potency and efficacy of ligands for nuclear receptors (NR) result both from the affinity of the ligand for the receptor and the affinity that various coregulatory proteins have for ligand-receptor complexes; the latter interaction, however, is rarely quantified. To understand the molecular basis for ligand potency and efficacy, we developed dual time-resolved fluorescence resonance energy transfer (tr-FRET) assays and quantified both ligand and coactivator/corepressor binding to the thyroid hormone receptor (TR). Promoter-bound TR exerts dual transcriptional regulatory functions, recruiting corepressor proteins and repressing transcription in absence of thyroid hormones (THs), and shedding corepressors in favor of coactivators upon binding agonists, activating transcription. Our tr-FRET assays involve a TRE sequence labeled with terbium (fluorescence donor), TR?•RXR? heterodimer and fluorescein-labeled NR interaction domains of coactivator SRC3 or corepressor NCoR (fluorescence acceptors). Through coregulator titrations, we could determine the affinity of SRC3 or NCoR for TRE-bound TR•RXR heterodimers, unliganded or saturated with different THs. Alternatively, through ligand titrations, we could determine the relative potencies of different THs. TR agonist potencies were GC-1~T3~TRIAC~T4>>rT3, for both coactivator recruitment and corepressor dissociation; the affinity of SRC3 binding to TR-ligand complexes followed a similar trend. This highlights that the low activity of rT3 derives both from its low affinity for TR and the low affinity of SRC for the TR-rT3 complex. The TR antagonist NH-3 failed to induce SRC3 recruitment but did effect NCoR dissociation. These assays provide quantitative information on the affinity of two key interactions that are determinants of NR ligand potency and efficacy. PMID:18558711

  18. Identification of Weakly Interacting Massive Particles Through a Combined Measurement of Axial and Scalar Couplings

    NASA Astrophysics Data System (ADS)

    Bertone, G.; Cerdeño, D. G.; Collar, J. I.; Odom, B.

    2007-10-01

    We study the prospects for detecting weakly interacting massive particles (WIMPs) in a number of phenomenological scenarios, with a detector composed of a target simultaneously sensitive to both spin-dependent and spin-independent couplings, as is the case of COUPP (Chicagoland Observatory for Underground Particle Physics). First, we show that sensitivity to both couplings optimizes chances of initial WIMP detection. Second, we demonstrate that, in case of detection, a comparison of the signal on two complementary targets, such as in COUPP CF3I and C4F10 bubble chambers, allows a significantly more precise determination of the dark matter axial and scalar couplings. This strategy would provide crucial information on the nature of the WIMPs and possibly allow discrimination between neutralino and Kaluza-Klein dark matter.

  19. Identification of weakly interacting massive particles through a combined measurement of axial and scalar couplings.

    PubMed

    Bertone, G; Cerdeño, D G; Collar, J I; Odom, B

    2007-10-12

    We study the prospects for detecting weakly interacting massive particles (WIMPs) in a number of phenomenological scenarios, with a detector composed of a target simultaneously sensitive to both spin-dependent and spin-independent couplings, as is the case of COUPP (Chicagoland Observatory for Underground Particle Physics). First, we show that sensitivity to both couplings optimizes chances of initial WIMP detection. Second, we demonstrate that, in case of detection, a comparison of the signal on two complementary targets, such as in COUPP CF3I and C4F10 bubble chambers, allows a significantly more precise determination of the dark matter axial and scalar couplings. This strategy would provide crucial information on the nature of the WIMPs and possibly allow discrimination between neutralino and Kaluza-Klein dark matter. PMID:17995155

  20. [Identification of rat and human hemoglobin acetilation sites after its interaction with acetylsalicylic acid].

    PubMed

    Shre?ner, E V; Murashko, E A; Dubrovski?, Ia D; Krasnov, N V; Podol'skaia, E P; Babakov, V N

    2012-01-01

    The possibility of interaction of 0.1 mg/mL acetylsalicylic acid with purified human and rat globin in vitro during 24 h at 37 degrees C was investigated. The rat globin can be modified with acetylsalicylic acid on aminoacid residues K-17, K-57, K-91, K-140 in alpha subunit as well as on K-18, K-77 in beta subunit. The human globin can be modified with acetylsalicylic acid on aminoacid residues K-17, K-41, K-57 and K-91 in alpha subunit as well as on K-18, K-96 and K- 133 in beta subunit. We identified of acetetylated lysines K-17 and K-57 in alpha subunit of human hemoglobin after incubation whole blood with 0.1 mg/mL acetylsalicylic acid during 3 h. PMID:22792718

  1. Identification of the Mind Bomb1 Interaction Domain in Zebrafish DeltaD

    PubMed Central

    Palardy, Gregory; Chitnis, Ajay B.

    2015-01-01

    Ubiquitylation promotes endocytosis of the Notch ligands like Delta and Serrate and is essential for them to effectively activate Notch in a neighboring cell. The RING E3 ligase Mind bomb1 (Mib1) ubiquitylates DeltaD to facilitate Notch signaling in zebrafish. We have identified a domain in the intracellular part of the zebrafish Notch ligand DeltaD that is essential for effective interactions with Mib1. We show that elimination of the Mind bomb1 Interaction Domain (MID) or mutation of specific conserved motifs in this domain prevents effective Mib1-mediated ubiquitylation and internalization of DeltaD. Lateral inhibition mediated by Notch signaling regulates early neurogenesis in zebrafish. In this context, Notch activation suppresses neurogenesis, while loss of Notch-mediated lateral inhibition results in a neurogenic phenotype, where too many cells are allowed to become neurons. While Mib1-mediated endocytosis of DeltaD is essential for effective activation of Notch in a neighboring cell (in trans) it is not required for DeltaD to inhibit function of Notch receptors in the same cell (in cis). As a result, forms of DeltaD that have the MID can activate Notch in trans and suppress early neurogenesis when mRNA encoding it is ectopically expressed in zebrafish embryos. On the other hand, when the MID is eliminated/mutated in DeltaD, its ability to activate Notch in trans fails but ability to inhibit in cis is retained. As a result, ectopic expression of DeltaD lacking an effective MID results in a failure of Notch-mediated lateral inhibition and a neurogenic phenotype. PMID:26020642

  2. Identification of the Ubiquitin-like Domain of Midnolin as a New Glucokinase Interaction Partner*

    PubMed Central

    Hofmeister-Brix, Anke; Kollmann, Katrin; Langer, Sara; Schultz, Julia; Lenzen, Sigurd; Baltrusch, Simone

    2013-01-01

    Glucokinase acts as a glucose sensor in pancreatic beta cells. Its posttranslational regulation is important but not yet fully understood. Therefore, a pancreatic islet yeast two-hybrid library was produced and searched for glucokinase-binding proteins. A protein sequence containing a full-length ubiquitin-like domain was identified to interact with glucokinase. Mammalian two-hybrid and fluorescence resonance energy transfer analyses confirmed the interaction between glucokinase and the ubiquitin-like domain in insulin-secreting MIN6 cells and revealed the highest binding affinity at low glucose. Overexpression of parkin, an ubiquitin E3 ligase exhibiting an ubiquitin-like domain with high homology to the identified, diminished insulin secretion in MIN6 cells but had only some effect on glucokinase activity. Overexpression of the elucidated ubiquitin-like domain or midnolin, containing exactly this ubiquitin-like domain, significantly reduced both intrinsic glucokinase activity and glucose-induced insulin secretion. Midnolin has been to date classified as a nucleolar protein regulating mouse development. However, we could not confirm localization of midnolin in nucleoli. Fluorescence microscopy analyses revealed localization of midnolin in nucleus and cytoplasm and co-localization with glucokinase in pancreatic beta cells. In addition we could show that midnolin gene expression in pancreatic islets is up-regulated at low glucose and that the midnolin protein is highly expressed in pancreatic beta cells and also in liver, muscle, and brain of the adult mouse and cell lines of human and rat origin. Thus, the results of our study suggest that midnolin plays a role in cellular signaling of adult tissues and regulates glucokinase enzyme activity in pancreatic beta cells. PMID:24187134

  3. A reappraisal of the Pleurotus eryngii complex - new species and taxonomic combinations based on the application of a polyphasic approach, and an identification key to Pleurotus taxa associated with Apiaceae plants.

    PubMed

    Zervakis, Georgios I; Ntougias, Spyridon; Gargano, Maria Letizia; Besi, Maria I; Polemis, Elias; Typas, Milton A; Venturella, Giuseppe

    2014-01-01

    The Pleurotus eryngii species-complex comprises choice edible mushrooms growing on roots and lower stem residues of Apiaceae (umbellifers) plants. Material deriving from extensive sampling was studied by mating compatibility, morphological and ecological criteria, and through analysis of ITS1-5.8S-ITS2 and IGS1 rRNA sequences. Results revealed that P. eryngii sensu stricto forms a diverse and widely distributed aggregate composed of varieties elaeoselini, eryngii, ferulae, thapsiae, and tingitanus. Pleurotuseryngii subsp. tuoliensis comb. nov. is a phylogenetically sister group to the former growing only on various Ferula species in Asia. The existence of Pleurotusnebrodensis outside of Sicily (i.e., in Greece) is reported for the first time on the basis of molecular data, while P. nebrodensis subsp. fossulatus comb. nov. is a related Asiatic taxon associated with the same plant (Prangos ferulacea). Last, Pleurotusferulaginis sp. nov. grows on Ferulago campestris in northeast Italy, Slovenia and Hungary; it occupies a distinct phylogenetic position accompanied with significant differences in spore size and mating incompatibility versus other Pleurotus populations. Coevolution with umbellifers and host/substrate specificity seem to play key roles in speciation processes within this fungal group. An identification key to the nine Pleurotus taxa growing in association with Apiaceae plants is provided. PMID:25209640

  4. Quantitative versus qualitative approaches: a comparison of two research methods applied to identification of key health issues for working horses in Lesotho.

    PubMed

    Upjohn, M M; Attwood, G A; Lerotholi, T; Pfeiffer, D U; Verheyen, K L P

    2013-03-01

    The relative merits and potential complementarity of participatory methods and classical epidemiological techniques in veterinary-related research is a current topic of discussion. Few reported studies have applied both methodologies within the same research framework to enable direct comparison. The aim of this study was to compare issues identified by a classical epidemiological study of horses and their owners with those identified by owner communities using participatory approaches. In 2009, a cross-sectional survey was undertaken as part of an impact assessment study of farrier and saddler training programmes, and a small-scale nutrition trial, implemented in Lesotho by a UK-based equine charity. In total, 245 horses and their 237 owners participated in the survey which comprised a face-to-face structured questionnaire covering knowledge and practices relating to equine husbandry and primary healthcare, clinical examination and sampling of horses, and examination of tack used on those horses. In early 2010, 56 owners in three survey regions, some of whom participated in the survey, attended a participatory workshop. Each workshop group created a local resource map whilst discussing and identifying key issues associated with horse ownership and what might have an adverse impact on horse health and work. Following map completion, each group began by prioritising the identified issues, and then ranked them using a pairwise/ranking matrix to reflect how important issues were in relation to each other. Overall priority issues were: mouth problems, hunger and nutrition, diseases (including infectious diseases, parasites and colic), husbandry (including wound management), and feet and limb problems. Major health issues identified by cross-sectional study included sharp enamel points on teeth, endo- and ectoparasite infestation, suboptimal nutrition, tack-associated wounds, overgrown and poorly balanced feet and poor owner husbandry knowledge and practices. Whilst common issues were identified through the two research approaches, key differences also emerged. The classical, more quantitative approach provided objective measurement of problem frequency, which was compared with owners' perceptions of importance. The qualitative participatory approach provided greater opportunity for researchers to gain detailed understanding of local issues and appreciate how owners defined and prioritised problems affecting them and their animals. Both approaches provided valuable and complementary information that can be used to inform interventions aimed at providing sustainable improvements in the health and wellbeing of working animals and their owners. It is recommended that both quantitative and qualitative approaches are employed as part of detailed needs assessment work prior to defining and prioritising the charity's future interventions. PMID:23419786

  5. Identification of key residues for the binding of glucagon to the N-terminal domain of its receptor: an alanine scan and modeling study.

    PubMed

    Prévost, M; Vertongen, P; Waelbroeck, M

    2012-10-01

    Glucagon plays an essential role in the glycemia maintenance during fasting, but also aggravates hyperglycemia in diabetic patients. A series of analogues of glucagon were synthesized replacing each amino acid of the C-terminal region (residues 15-29) with alanine. The residues affecting the binding to the glucagon receptor are found to be located on one face of the glucagon helix. Several 3-dimensional models of the N-terminal domain of the glucagon receptor in complex with its ligand peptide were built and used to analyze the peptide-receptor interface in terms of the nature of the peptide residues and the interactions they form with the receptor. The models suggest that glucagon keeps its native helical structure upon binding, and that a large part of the interface formed with the receptor is hydrophobic. We find that in the C-terminal region, F22, V23, M27, and D15 are the most important residues for peptide binding. They bury a large portion of their solvent accessible surface area and make numerous interactions with the receptor mainly of the hydrophobic type. PMID:22893257

  6. Interactions of Nitrifying Bacteria and Heterotrophs: Identification of a Micavibrio-Like Putative Predator of Nitrospira spp.

    PubMed Central

    Dolinšek, Jan; Lagkouvardos, Ilias; Wanek, Wolfgang; Wagner, Michael

    2013-01-01

    Chemolithoautotrophic nitrifying bacteria release soluble organic compounds, which can be substrates for heterotrophic microorganisms. The identities of these heterotrophs and the specificities of their interactions with nitrifiers are largely unknown. In this study, we incubated nitrifying activated sludge with 13C-labeled bicarbonate and used stable isotope probing of 16S rRNA to monitor the flow of carbon from uncultured nitrifiers to heterotrophs. To facilitate the identification of heterotrophs, the abundant 16S rRNA molecules from nitrifiers were depleted by catalytic oligonucleotides containing locked nucleic acids (LNAzymes), which specifically cut the 16S rRNA of defined target organisms. Among the 13C-labeled heterotrophs were organisms remotely related to Micavibrio, a microbial predator of Gram-negative bacteria. Fluorescence in situ hybridization revealed a close spatial association of these organisms with microcolonies of nitrite-oxidizing sublineage I Nitrospira in sludge flocs. The high specificity of this interaction was confirmed by confocal microscopy and a novel image analysis method to quantify the localization patterns of biofilm microorganisms in three-dimensional (3-D) space. Other isotope-labeled bacteria, which were affiliated with Thermomonas, colocalized less frequently with nitrifiers and thus were commensals or saprophytes rather than specific symbionts or predators. These results suggest that Nitrospira spp. are subject to bacterial predation, which may influence the abundance and diversity of these nitrite oxidizers and the stability of nitrification in engineered and natural ecosystems. In silico screening of published next-generation sequencing data sets revealed a broad environmental distribution of the uncultured Micavibrio-like lineage. PMID:23335755

  7. Morphological and molecular differentiation of two new species of Pseudoacanthocephalus Petrochenko, 1958 (Acanthocephala: Echinorhynchidae) from amphibians and reptiles in the Philippines, with identification key for the genus.

    PubMed

    Tkach, Vasyl V; Lisitsyna, Olga I; Crossley, Janna L; Binh, Tran Thi; Bush, Sarah E

    2013-05-01

    The genus Pseudoacanthocephalus Petrochenko, 1958 currently includes 14 species of acanthocephalans parasitic in amphibians and reptiles worldwide. This work describes two new species of Pseudoacanthocephalus from amphibians and reptiles collected in several localities on Luzon Island, Philippines. Pseudoacanthocephalus nickoli n. sp. was found in two species of frogs, Rana luzonensis Boulenger and Rana similis (Günther), and Pseudoacanthocephalus smalesi n. sp. was found in a scincid lizard, Sphenomorphus abdictus Brown & Alcala. Differential diagnoses of the two new species of Pseudoacanthocephalus from their congeners are provided. Comparative analysis of nuclear ribosomal rRNA sequences encompassing the 3' end of 18S nuclear rDNA gene, internal transcribed spacer region (ITS1+5.8S+ITS2), and 5' end of the 28S gene strongly corroborated the morphological evidence and demonstrated significant differences between the two new species as well as between these species and closely related species from continental China and Vietnam. No intraspecific sequence variability was detected among different individuals representing each of the examined species. This is the first report of Pseudoacanthocephalus in the Philippines. A key to known species of Pseudoacanthocephalus is provided. PMID:23595488

  8. Proteomic responses to lead-induced oxidative stress in Talinum triangulare Jacq. (Willd.) roots: identification of key biomarkers related to glutathione metabolisms.

    PubMed

    Kumar, Abhay; Majeti, Narasimha Vara Prasad

    2014-01-01

    In this study, Talinum triangulare Jacq. (Willd.) treated with different lead (Pb) concentrations for 7 days has been investigated to understand the mechanisms of ascorbate-glutathione metabolisms in response to Pb-induced oxidative stress. Proteomic study was performed for control and 1.25 mM Pb-treated plants to examine the root protein dynamics in the presence of Pb. Results of our analysis showed that Pb treatment caused a decrease in non-protein thiols, reduced glutathione (GSH), total ascorbate, total glutathione, GSH/oxidized glutathione (GSSG) ratio, and activities of glutathione reductase and ?-glutamylcysteine synthetase. Conversely, cysteine and GSSG contents and glutathione-S-transferase activity was increased after Pb treatment. Fourier transform infrared spectroscopy confirmed our metabolic and proteomic studies and showed that amino, phenolic, and carboxylic acids as well as alcoholic, amide, and ester-containing biomolecules had key roles in detoxification of Pb/Pb-induced toxic metabolites. Proteomic analysis revealed an increase in relative abundance of 20 major proteins and 3 new proteins (appeared only in 1.25 mM Pb). Abundant proteins during 1.25 mM Pb stress conditions have given a very clear indication about their involvement in root architecture, energy metabolism, reactive oxygen species (ROS) detoxification, cell signaling, primary and secondary metabolisms, and molecular transport systems. Relative accumulation patterns of both common and newly identified proteins are highly correlated with our other morphological, physiological, and biochemical parameters. PMID:24705950

  9. Talent identification in youth soccer.

    PubMed

    Unnithan, Viswanath; White, Jordan; Georgiou, Andreas; Iga, John; Drust, Barry

    2012-01-01

    The purpose of this review article was firstly to evaluate the traditional approach to talent identification in youth soccer and secondly present pilot data on a more holistic method for talent identification. Research evidence exists to suggest that talent identification mechanisms that are predicated upon the physical (anthropometric) attributes of the early maturing individual only serve to identify current performance levels. Greater body mass and stature have both been related to faster ball shooting speed and vertical jump capacity respectively in elite youth soccer players. This approach, however, may prematurely exclude those late maturing individuals. Multiple physiological measures have also been used in an effort to determine key predictors of performance; with agility and sprint times, being identified as variables that could discriminate between elite and sub-elite groups of adolescent soccer players. Successful soccer performance is the product of multiple systems interacting with one another. Consequently, a more holistic approach to talent identification should be considered. Recent work, with elite youth soccer players, has considered whether multiple small-sided games could act as a talent identification tool in this population. The results demonstrated that there was a moderate agreement between the more technically gifted soccer player and success during multiple small-sided games. PMID:23046427

  10. Strontium isotopic identification of water-rock interaction and ground water mixing.

    PubMed

    Frost, Carol D; Toner, Rachel N

    2004-01-01

    87Sr/86Sr ratios of ground waters in the Bighorn and Laramie basins' carbonate and carbonate-cemented aquifer systems, Wyoming, United States, reflect the distinctive strontium isotope signatures of the minerals in their respective aquifers. Well water samples from the Madison Aquifer (Bighorn Basin) have strontium isotopic ratios that match their carbonate host rocks. Casper Aquifer ground waters (Laramie Basin) have strontium isotopic ratios that differ from the bulk host rock; however, stepwise leaching of Casper Sandstone indicates that most of the strontium in Casper Aquifer ground waters is acquired from preferential dissolution of carbonate cement. Strontium isotope data from both Bighorn and Laramie basins, along with dye tracing experiments in the Bighorn Basin and tritium data from the Laramie Basin, suggest that waters in carbonate or carbonate-cemented aquifers acquire their strontium isotope composition very quickly--on the order of decades. Strontium isotopes were also used successfully to verify previously identified mixed Redbeds-Casper ground waters in the Laramie Basin. The strontium isotopic compositions of ground waters near Precambrian outcrops also suggest previously unrecognized mixing between Casper and Precambrian aquifers. These results demonstrate the utility of strontium isotopic ratio data in identifying ground water sources and aquifer interactions. PMID:15161158

  11. Identification of a nuclear-specific cyclophilin which interacts with the proteinase inhibitor eglin c.

    PubMed Central

    Wang, B B; Hayenga, K J; Payan, D G; Fisher, J M

    1996-01-01

    We have identified a novel human cyclophilin (hCyP-60) which interacts with the proteinase inhibitor eglin c using the yeast two-hybrid system. A cDNA isolated from a Raji B lymphocyte library reveals a domain showing sequence similarity to known cyclophilins flanked by unique N- and C-terminal residues. In addition, hCyP-60 contains a tyrosine residue (Tyr 389) instead of a tryptophan residue found in most eukaryotic cyclophilins at a position important for cyclosporin binding. Northern and Western analysis reveal widespread expression with considerable tissue-specific variation. Specifically, the highest levels of mRNA are detected in the thymus, pancreas, testis, and K-562 cell line, while the most protein is detected in the kidney. Immunohistochemistry indicates a nuclear-specific localization both in transfected cells and tissue sections. hCyP-60's specific subcellular localization and conserved amino acid sequence suggest that it may play a specific role in the nucleus. PMID:8660300

  12. Rain-vapor interaction and vapor source identification using stable isotopes from semiarid western India

    NASA Astrophysics Data System (ADS)

    Deshpande, R. D.; Maurya, A. S.; Kumar, Bhishm; Sarkar, A.; Gupta, S. K.

    2010-12-01

    Results of a 4 year (2005-2008) study of stable isotopic composition of daily rain and ground-level vapor (GLV) at a semiarid station in western India are reported. The GLV samples were collected by complete cryogenic trapping. The sampling was mostly limited to the rainy season (June, July, August, and September) and about a month before and after. The maximum number of samples was collected during the year 2007. The GLV has a steady baseline ?18O and ?D composition without distinguishable seasonal differences. The d-excess of GLV indicates that its isotopic composition has a significant contribution from kinetic evaporation of nonlocal water sources. During a rain event, GLV rapidly interacts with raindrops and tends to move toward isotopic equilibrium. On cessation of rain, the ?18O and ?D of GLV quickly return to the typical baseline values. Therefore, use of isotopic composition of monthly rainfall for estimating average monthly isotopic composition of GLV can lead to erroneous results. Within a rainy season, certain large rain events have depleted ?18O and ?D values compared to other equally large rain events with significantly enriched ?18O and ?D. These isotopic differences are apparently not related to amount of rainfall. Variable magnitude of evaporation from falling raindrops and/or cloud liquid water fraction cannot explain the observed differences. Instead, it is shown that varying source regions (Arabian Sea or Bay of Bengal) and cloud top temperature may be responsible for observed differences.

  13. Identification of a Soybean Protein That Interacts with GAGA Element Dinucleotide Repeat DNA1

    PubMed Central

    Sangwan, Indu; O'Brian, Mark R.

    2002-01-01

    Dinucleotide repeat DNA with the pattern (GA)n/(TC)n, so-called GAGA elements, control gene expression in animals, and are recognized by a specific regulatory protein. Here, a yeast one-hybrid screen was used to isolate soybean (Glycine max) cDNA encoding a GAGA-binding protein (GBP) that binds to (GA)n/(CT)n DNA. Soybean GBP was dissimilar from the GAGA factor of Drosophila melanogaster. Recombinant GBP protein did not bind to dinucleotide repeat sequences other than (GA)n/(CT)n. GBP bound to the promoter of the heme and chlorophyll synthesis gene Gsa1, which contains a GAGA element. Removal of that GAGA element abrogated binding of GBP to the promoter. Furthermore, insertion of the GAGA element to a nonspecific DNA conferred GBP-binding activity on that DNA. Thus, the GAGA element of the Gsa1 promoter is both necessary and sufficient for GBP binding. Gbp mRNA was expressed in leaves and was induced in symbiotic root nodules elicited by the bacterium Bradyrhizobium japonicum. In addition, Gbp transcripts were much higher in leaves of dark-treated etiolated plantlets than in those exposed to light for 24 h. Homologs of GBP were found in other dicots and in the monocot rice (Oryza sativa), as well. We suggest that interaction between GAGA elements and GBP-like proteins is a regulatory feature in plants. PMID:12177492

  14. Investigation of antioxidant interactions between Radix Astragali and Cimicifuga foetida and identification of synergistic antioxidant compounds.

    PubMed

    Wang, Fei; Zhao, Shancang; Li, Feng; Zhang, Bo; Qu, Yi; Sun, Tianlei; Luo, Ting; Li, Dapeng

    2014-01-01

    The medicinal plants of Huang-qi (Radix Astragali) and Sheng-ma (Cimicifuga foetida) demonstrate significantly better antioxidant effects when used in combination than when used alone. However, the bioactive components and interactional mechanism underlying this synergistic action are still not well understood. In the present study, 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay was employed to investigate the antioxidant capacity of single herbs and their combination with the purpose of screening synergistic antioxidant compounds from them. Chromatographic isolation was performed on silica gel, Sephadex LH-20 columns and HPLC, and consequently to yield formononetin, calycosin, ferulic acid and isoferulic acid, which were identified by their retention time, UV ?max, MS and MS/MS data. The combination of isoferulic acid and calycosin at a dose ratio of 1?1 resulted in significant synergy in scavenging DPPH radicals and ferric reducing antioxidant power (FRAP) assay. Furthermore, the protective effects of these four potential synergistic compounds were examined using H2O2-induced HepG2 Cells bioassay. Results revealed that the similar synergy was observed in the combination of isoferulic acid and calycosin. These findings might provide some theoretical basis for the purported synergistic efficiency of Huang-qi and Sheng-ma as functional foods, dietary supplements and medicinal drugs. PMID:24498048

  15. Phylogeny of genes for secretion NTPases: identification of the widespread tadA subfamily and development of a diagnostic key for gene classification.

    PubMed

    Planet, P J; Kachlany, S C; DeSalle, R; Figurski, D H

    2001-02-27

    Macromolecular transport systems in bacteria currently are classified by function and sequence comparisons into five basic types. In this classification system, type II and type IV secretion systems both possess members of a superfamily of genes for putative NTP hydrolase (NTPase) proteins that are strikingly similar in structure, function, and sequence. These include VirB11, TrbB, TraG, GspE, PilB, PilT, and ComG1. The predicted protein product of tadA, a recently discovered gene required for tenacious adherence of Actinobacillus actinomycetemcomitans, also has significant sequence similarity to members of this superfamily and to several unclassified and uncharacterized gene products of both Archaea and Bacteria. To understand the relationship of tadA and tadA-like genes to those encoding the putative NTPases of type II/IV secretion, we used a phylogenetic approach to obtain a genealogy of 148 NTPase genes and reconstruct a scenario of gene superfamily evolution. In this phylogeny, clear distinctions can be made between type II and type IV families and their constituent subfamilies. In addition, the subgroup containing tadA constitutes a novel and extremely widespread subfamily of the family encompassing all putative NTPases of type IV secretion systems. We report diagnostic amino acid residue positions for each major monophyletic family and subfamily in the phylogenetic tree, and we propose an easy method for precisely classifying and naming putative NTPase genes based on phylogeny. This molecular key-based method can be applied to other gene superfamilies and represents a valuable tool for genome analysis. PMID:11226268

  16. A key gene of the RNA interference pathway in the black tiger shrimp, Penaeus monodon: identification and functional characterisation of Dicer-1.

    PubMed

    Su, Jianguo; Oanh, Dang T H; Lyons, Russell E; Leeton, Lisa; van Hulten, Marielle C W; Tan, Siok-Hwee; Song, Linsheng; Rajendran, K V; Walker, Peter J

    2008-02-01

    RNA interference (RNAi) is an evolutionarily conserved mechanism by which double-stranded RNA (dsRNA) initiates post-transcriptional silencing of homologous genes. Here we report the amplification and characterisation of a full length cDNA from black tiger shrimp (Penaeus monodon) that encodes the bidentate RNAase III Dicer, a key component of the RNAi pathway. The full length of the shrimp Dicer (Pm Dcr1) cDNA is 7629bp in length, including a 5' untranslated region (UTR) of 130bp, a 3' UTR of 77bp, and an open reading frame of 7422bp encoding a polypeptide of 2473 amino acids with an estimated molecular mass of 277.895kDa and a predicted isoelectric point of 4.86. Analysis of the deduced amino acid sequence indicated that the mature peptide contains all the seven recognised functional domains and is most similar to the mosquito (Aedes aegypti) Dicer-1 sequence with a similarity of 34.6%. Quantitative RT-PCR analysis showed that Pm Dcr1 mRNA is most highly expressed in haemolymph and lymphoid organ tissues (P<0.05). However, there was no correlation between Pm Dcr1 mRNA levels in lymphoid organ and the viral genetic loads in shrimp naturally infected with gill-associated virus (GAV) and Mourilyan virus (P>0.05). Treatment with synthetic dsRNA corresponding to Pm Dcr1 sequence resulted in knock-down of Pm Dcr1 mRNA expression in both uninfected shrimp and shrimp infected experimentally with GAV. Knock-down of Pm Dcr1 expression resulted in more rapid mortalities and higher viral loads. These data demonstrated that Dicer is involved in antiviral defence in shrimp. PMID:18166489

  17. Identification of Novel Interaction between ADAM17 (a Disintegrin and Metalloprotease 17) and Thioredoxin-1*

    PubMed Central

    Aragão, Annelize Z. B.; Nogueira, Maria Luiza C.; Granato, Daniela C.; Simabuco, Fernando M.; Honorato, Rodrigo V.; Hoffman, Zaira; Yokoo, Sami; Laurindo, Francisco R. M.; Squina, Fabio M.; Zeri, Ana Carolina M.; Oliveira, Paulo S. L.; Sherman, Nicholas E.; Paes Leme, Adriana F.

    2012-01-01

    ADAM17, which is also known as TNF?-converting enzyme, is the major sheddase for the EGF receptor ligands and is considered to be one of the main proteases responsible for the ectodomain shedding of surface proteins. How a membrane-anchored proteinase with an extracellular catalytic domain can be activated by inside-out regulation is not completely understood. We characterized thioredoxin-1 (Trx-1) as a partner of the ADAM17 cytoplasmic domain that could be involved in the regulation of ADAM17 activity. We induced the overexpression of the ADAM17 cytoplasmic domain in HEK293 cells, and ligands able to bind this domain were identified by MS after protein immunoprecipitation. Trx-1 was also validated as a ligand of the ADAM17 cytoplasmic domain and full-length ADAM17 recombinant proteins by immunoblotting, immunolocalization, and solid phase binding assay. In addition, using nuclear magnetic resonance, it was shown in vitro that the titration of the ADAM17 cytoplasmic domain promotes changes in the conformation of Trx-1. The MS analysis of the cross-linked complexes showed cross-linking between the two proteins by lysine residues. To further evaluate the functional role of Trx-1, we used a heparin-binding EGF shedding cell model and observed that the overexpression of Trx-1 in HEK293 cells could decrease the activity of ADAM17, activated by either phorbol 12-myristate 13-acetate or EGF. This study identifies Trx-1 as a novel interaction partner of the ADAM17 cytoplasmic domain and suggests that Trx-1 is a potential candidate that could be involved in ADAM17 activity regulation. PMID:23105116

  18. Identification of stromal cell products that interact with pre-B cells

    PubMed Central

    1996-01-01

    Our understanding of lympho-hematopoietic microenvironments is incomplete, and a new cloning strategy was developed to identify molecules that bind to B lineage lymphocyte precursors. A cell sorting procedure was used for initial enrichment of cDNAs from stromal cell mRNA that contained signal sequences and were therefore likely to encode transmembrane or secreted proteins. A second step involved expression of the library as soluble Ig fusion proteins. Finally, pools representing these proteins were screened for the ability to recognize pre-B cells. This approach resulted in the cloning of biglycan, syndecan 4, collagen type I, clusterin, matrix glycoprotein sc1, osteonectin, and one unknown molecule (designated SIM). The full-length cDNA of SIM revealed that it is a type I transmembrane protein, and its intracellular domain has weak homology with myosin heavy chain and related proteins. Staining of established cell lines and freshly isolated hematopoietic cells with the Ig fusion proteins revealed distinct patterns of reactivity and differential dependence on divalent cations. Biglycan-, sc1-, and SIM-Ig fusion proteins selectively increased interleukin 7-dependent proliferation of pre-B cells. Overexpression of the entire SIM protein affected the morphology of 293T cells, while expression of just the extracellular portion was without effect. Thus, a series of stromal cell surface molecules has been identified that interact with blood cell precursors. Three of them promoted the survival and/or proliferation of pre-B cells in culture, and all merit further study in relation to lympho-hematopoiesis. PMID:8707854

  19. Identification of specificity and promiscuity of PDZ domain interactions through their dynamic behavior.

    PubMed

    Gerek, Z Nevin; Keskin, Ozlem; Ozkan, S Banu

    2009-12-01

    PDZ domains (PDZs), the most common interaction domain proteins, play critical roles in many cellular processes. PDZs perform their job by binding specific protein partners. However, they are very promiscuous, binding to more than one protein, yet selective at the same time. We examined the binding related dynamics of various PDZs to have insight about their specificity and promiscuity. We used full atomic normal mode analysis and a modified coarse-grained elastic network model to compute the binding related dynamics. In the latter model, we introduced specificity for each single parameter constant and included the solvation effect implicitly. The modified model, referred to as specific-Gaussian Network Model (s-GNM), highlights some interesting differences in the conformational changes of PDZs upon binding to Class I or Class II type peptides. By clustering the residue fluctuation profiles of PDZs, we have shown: (i) binding selectivities can be discriminated from their dynamics, and (ii) the dynamics of different structural regions play critical roles for Class I and Class II specificity. s-GNM is further tested on a dual-specific PDZ which showed only Class I specificity when a point mutation exists on the betaA-betaB loop. We observe that the binding dynamics change consistently in the mutated and wild type structures. In addition, we found that the binding induced fluctuation profiles can be used to discriminate the binding selectivity of homolog structures. These results indicate that s-GNM can be a powerful method to study the changes in binding selectivities for mutant or homolog PDZs. PMID:19585657

  20. Interaction of CO with OH on Au(111): HCOO, CO3, and HOCO as Key Intermediates in the Water-Gas Shift Reaction

    SciTech Connect

    Senanayake, S.; Stacchiola, D; Liu, P; Mullins, C; Hrbek, J; Rodriguez, J

    2009-01-01

    We have investigated the role of formate (HCOO), carbonate (CO{sub 3}), and carboxyl (HOCO) species as possible intermediates in the OH{sub ads} + CO{sub gas} {yields} CO{sub 2,gas} + 0.5H{sub 2,gas} reaction on Au(111) using synchrotron-based core level photoemission, near-edge X-ray absorption fine structure (NEXAFS), and infrared absorption spectroscopy (IR). Adsorbed HCOO, CO{sub 3}, and OH species were prepared by adsorbing formic acid, carbon dioxide, and water on a Au(111) surface precovered with 0.2 ML of atomic oxygen, respectively. HCOOH interacts weakly with Au(111), but on O/Au(111) it dissociates its acidic H to yield adsorbed formate. The results of NEXAFS, IR, and density-functional calculations indicate that the formate adopts a bidentate configuration on Au(111). Since the HCOO groups are stable on Au(111) up to temperatures near 350 K, it is not likely that formate is a key intermediate for the OH{sub ads} + CO{sub gas} {yields} CO{sub 2,gas} + 0.5H{sub 2,gas} reaction at low temperatures. In fact, the formation of this species could lead eventually to surface poisoning. When compared to a formate species, a carbonate species formed by the reaction of CO{sub 2} with O/Au(111) has low stability, decomposing at temperatures between 100 and 125 K, and should not poison the gold surface. Neither HCOO nor CO{sub 3} was detected during the reaction of CO with OH on Au(111) at 90-120 K. The results of photoemission and IR spectroscopy point to HO {leftrightarrow} CO interactions, consistent with the formation of an unstable HOCO intermediate which has a very short lifetime on the gold surface. The possible mechanism for the low-temperature water-gas shift on gold catalysts is discussed in light of these results.

  1. Histone demethylase jumonji AT-rich interactive domain 1B (JARID1B) controls mammary gland development by regulating key developmental and lineage specification genes.

    PubMed

    Zou, Mike Ran; Cao, Jian; Liu, Zongzhi; Huh, Sung Jin; Polyak, Kornelia; Yan, Qin

    2014-06-20

    The JmjC domain-containing H3K4 histone demethylase jumonji AT-rich interactive domain 1B (JARID1B) (also known as KDM5B and PLU1) is overexpressed in breast cancer and is a potential target for breast cancer treatment. To investigate the in vivo function of JARID1B, we developed Jarid1b(-/-) mice and characterized their phenotypes in detail. Unlike previously reported Jarid1b(-/-) strains, the majority of these Jarid1b(-/-) mice were viable beyond embryonic and neonatal stages. This allowed us to further examine phenotypes associated with the loss of JARID1B in pubertal development and pregnancy. These Jarid1b(-/-) mice exhibited decreased body weight, premature mortality, decreased female fertility, and delayed mammary gland development. Related to these phenotypes, JARID1B loss decreased serum estrogen level and reduced mammary epithelial cell proliferation in early puberty. In mammary epithelial cells, JARID1B loss diminished the expression of key regulators for mammary morphogenesis and luminal lineage specification, including FOXA1 and estrogen receptor ?. Mechanistically, JARID1B was required for GATA3 recruitment to the Foxa1 promoter to activate Foxa1 expression. These results indicate that JARID1B positively regulates mammary ductal development through both extrinsic and cell-autonomous mechanisms. PMID:24802759

  2. Identification of key factors governing chemistry in groundwater near the water course recharged by reclaimed water at Miyun County, Northern China.

    PubMed

    Yu, Yilei; Song, Xianfang; Zhang, Yinghua; Zheng, Fandong; Liang, Ji; Han, Dongmei; Ma, Ying; Bu, Hongmei

    2013-09-01

    Reclaimed water was successfully used to recover the dry Chaobai River in Northern China, but groundwater may be polluted. To ensure groundwater protection, it is therefore critical to identify the governing factors of groundwater chemistry. Samples of reclaimed water, river and groundwater were collected monthly at Chaobai River from January to September in 2010. Fifteen water parameters were analyzed. Two kinds of reclaimed water were different in type (Na-Ca-Mg-Cl-HCO3 or Na-Ca-Cl-HCO3) and concentration of nitrogen. The ionic concentration and type in river were similar to reclaimed water. Some shallow wells near the river bed had the same type (Na-Ca-Mg-Cl-HCO3) and high concentration as reclaimed water, but others were consistent with the deep wells (Ca-Mg-HCO3). Using cluster analysis, the 9 months were divided into two periods (dry and wet seasons), and all samples were grouped into several spatial clusters, indicating different controlling mechanisms. Principal component analysis and conventional ionic plots showed that calcium, magnesium and bicarbonate were controlled by water-rock interaction in all deep and some shallow wells. This included the dissolution of calcite and carbonate weathering. Sodium, potassium, chloride and sulfate in river and some shallow wells recharged by river were governed by evaporation crystallization and mixing of reclaimed water. But groundwater chemistry was not controlled by precipitation. During the infiltration of reclaimed water, cation exchange took place between (sodium, potassium) and (calcium, magnesium). Nitrification and denitrification both happened in most shallow groundwater, but only denitrification in deep groundwater. PMID:24520717

  3. The ENA Ribbon and the ISN Flow as Key Tools for the ISM-Heliosphere Interaction - Open Questions, the Need for Future Observations with IBEX and IMAP

    NASA Astrophysics Data System (ADS)

    Moebius, E.; Bzowski, M.; Frisch, P. C.; Funsten, H. O.; Fuselier, S.; Kucharek, H.; McComas, D. J.; Schwadron, N.; Wimmer-Schweingruber, R. F.; Wurz, P.; Zank, G. P.

    2014-12-01

    The unexpected ribbon in the IBEX energetic neutral atom (ENA) maps is still far from understood. According to most models, the interstellar magnetic field (BISM) controls its location and shape, with the direction in agreement with the termination shock (TS) asymmetry found by the Voyagers, the deflection of the interstellar neutral (ISN) flow, and the high energy cosmic ray anisotropy. With direct ISN flow velocity vector VISM and temperature observations, along with secondary neutrals, most likely from the outer heliosheath, IBEX also probes the conditions and interaction outside the heliospheric boundary. Precise knowledge of the ISN flow direction is key, because small differences have substantial leverage on the VISM-BISM plane, which controls the large-scale heliosphere structure. For quantitative tools, the ribbon formation must be understood and the ISN flow parameters must be further refined. IBEX maps show that the latitudinal ribbon structure carries the imprint of fast and slow solar wind (SW). These results support models that involve charge exchange with the SW, currently in two renditions: secondary ENAs from neutral SW reaching into the outer heliosheath and reflection of SW at the TS. In the TS model, the ribbon distance maps the TS, and reactions to changing SW at 1 AU follow within 1 - 2 years. In the secondary ENA model, ribbon ENAs provide an energy-dependent spatio-temporal probe of the outer heliosheath over several years after SW changes at 1 AU. Therefore, observations over a full solar cycle with IBEX, probing the ribbon depth with SW modulation, are key to its understanding. Likewise, expanding the successful variation of the IBEX pointing strategy over times with varying ionization rates will refine the ISN flow vector. The capabilities of the Interstellar Mapping and Acceleration Probe (IMAP), which has highest priority in the recent NRC Heliophysics Decadal Survey, are needed to probe the spatio-temporal fine-structure of the ribbon, extend observations to higher energy with better resolution, and provide precision observations of the ISN flow and secondary neutrals from different vantage points. To that end, IMAP will provide a combination of increased collecting power, angular, and energy resolution, the capability to scan the ISN flow, and a dedicated pickup ion instrument.

  4. Identification of SHRUBBY, a SHORT-ROOT and SCARECROW interacting protein that controls root growth and radial patterning.

    PubMed

    Koizumi, Koji; Gallagher, Kimberly L

    2013-03-01

    The timing and extent of cell division is particularly important for the growth and development of multicellular organisms. Roots of the model organism Arabidopsis thaliana have been widely studied as a paradigm for organ development in plants. In the Arabidopsis root, the plant-specific GRAS family transcription factors SHORT-ROOT (SHR) and SCARECROW (SCR) are key regulators of root growth and of the asymmetric cell divisions that separate the ground tissue into two separate layers: the endodermis and cortex. To elucidate the role of SHR in root development, we identified 17 SHR-interacting proteins. Among those isolated was At5g24740, which we named SHRUBBY (SHBY). SHBY is a vacuolar sorting protein with similarity to the gene responsible for Cohen syndrome in humans. Hypomorphic alleles of shby caused poor root growth, decreased meristematic activity and defects in radial patterning that are characterized by an increase in the number of cell divisions in the ground tissue that lead to extra cells in the cortex and endodermis, as well as additional cell layers. Analysis of genetic and molecular markers indicates that SHBY acts in a pathway that partially overlaps with SHR, SCR, PLETHORA1 and PLETHORA2 (PLT1 and PLT2). The shby-1 root phenotype was partially phenocopied by treatment of wild-type roots with the proteosome inhibitor MG132 or the gibberellic acid (GA) synthesis inhibitor paclobutrazol (PAC). Our results indicate that SHBY controls root growth downstream of GA in part through the regulation of SHR and SCR. PMID:23444357

  5. Revision of the African pollen beetle genera Tarchonanthogethes and Xenostrongylogethes, with insect-host plant relationships, identification key, and cladistic analysis of the Anthystrix genus-complex (Coleoptera: Nitidulidae: Meligethinae).

    PubMed

    Audisio, Paolo; Cline, Andrew R; Trizzino, Marco; Mancini, Emiliano; Antonini, Gloria; Sabatelli, Simone; Cerretti, Pierfilippo

    2015-01-01

    The Afrotropical endemic pollen beetle genera Tarchonanthogethes Audisio & Cline and Xenostrongylogethes Audisio & Cline, of the Anthystrix genus-complex, are revised. Eleven new species of Tarchonanthogethes (T. autumnalis, sp. nov., T. bisignatus, sp. nov., T. fasciatus, sp. nov., T. gratiellae, sp. nov., T. hermani, sp. nov., T. hystrix, sp. nov., T. lilliputianus, sp. nov., T. maasai, sp. nov., T. manconiae, sp. nov., T. pectinipes, sp. nov., T. thalycriformis, sp. nov.) and one new Xenostrongylogethes (X. cychramoides, sp. nov.) are described, illustrated and compared with related taxa. Tarchonanthogethes hirtus Kirejtshuk & Easton, 1988 is synonymized with T. martini (syn. nov.). Meligethes assutus Easton, 1960 from Kenya is transferred from Afrogethes Audisio & Cline to Tarchonanthogethes (comb. nov.). Meligethes singularis Grouvelle, 1919 from southern Africa is transferred from Tarchonanthogethes to Meligethinus Grouvelle, 1906 (comb. nov.). Larval host-plants for Tarchonanthogethes and Xenostrongylogethes include dioecious bushes and trees of Tarchonantheae Asteraceae (genera Brachylaena R.Br. and Tarchonanthus L.). All species currently attributed to the genera Anthystrix Kirejtshuk, Sebastiangethes Audisio, Kirk-Spriggs & Cline, Tarchonanthogethes and Xenostrongylogethes (Anthystrix genus-complex) are included in a morphology-based cladistic analysis to provide a rigorous hypothesis of phylogenetic relationships. An identification key to all 25 known species in the Anthystrix genus-complex, including all available data on insect host plant relationships, is presented. PMID:25781242

  6. Ash Tree Identification Key Ash Tree Characteristics

    E-print Network

    Walter, M.Todd

    berries Walnut, Hickory, Mountain-Ash: alternate branching #12;Identifying Emerald Ash Borer what to do if you think you have the ash-killing Emerald Ash Borer (EAB) in your ash tree Verify the signs of EAB: 1 activity Educate Yourself: Emerald Ash Borer information and links can be found at http://nyis.info Report

  7. Experimental identification of the lateral human-structure interaction mechanism and assessment of the inverted-pendulum biomechanical model

    NASA Astrophysics Data System (ADS)

    Carroll, S. P.; Owen, J. S.; Hussein, M. F. M.

    2014-10-01

    Within the context of crowd-induced lateral bridge vibration, human-structure interaction (HSI) is a widely studied phenomenon. Central to this study is the self-excited component of the ground reaction force (GRF). This force harmonic, induced by a walking pedestrian, resonates with lateral deck motion, irrespective of the pedestrian's pacing frequency. Its presence can lead to positive feedback between pedestrian GRFs and structural motion. Characterisation of the self-excited force as equivalent structural mass and damping has greatly improved the understanding of HSI and its role in developing lateral dynamic instability. However, despite this evolving understanding, a key question has remained unanswered; what are the features of a pedestrian's balance response to base motion that gives rise to the self-excited force? The majority of the literature has focussed on the effects of HSI with the underlying mechanism receiving comparatively little attention. This paper presents data from experimental testing in which 10 subjects walked individually on a laterally oscillating treadmill. Lateral deck motion as well as the GRFs imposed by the subject was recorded. Three-dimensional motion capture equipment was used to track the position of visual markers mounted on the subject. Thus whole body response to base motion was captured in addition to the GRFs generated. The data presented herein supports the authors' previous findings that the self-excited force is a frequency sideband harmonic resulting from amplitude modulation of the lateral GRF. The gait behaviour responsible for this amplitude modulation is a periodic modulation of stride width in response to a sinusoidally varying inertia force induced by deck motion. In a separate analysis the validity of the passive inverted pendulum model, stabilised by active control of support placement was confirmed. This was established through comparison of simulated and observed frontal plane CoM motion. Despite the relative simplicity of this biomechanical model, remarkable agreement was observed.

  8. SÁDI - Statistical Analysis for Data Type Identification

    Microsoft Academic Search

    Sarah J. Moody; Robert F. Erbacher

    2008-01-01

    A key task in digital forensic analysis is the location of relevant information within the computer system. Identification of the relevancy of data is often dependent upon the identification of the type of data being examined. Typical file type identification is based upon file extension or magic keys. These typical techniques fail in many typical forensic analysis scenarios such as

  9. An annotated list of species of the Proteocephalus Weinland, 1858 aggregate sensu de Chambrier et al. (2004) (Cestoda: Proteocephalidea), parasites of fishes in the Palaearctic Region, their phylogenetic relationships and a key to their identification.

    PubMed

    Scholz, Tomás; Hanzelová, Vladimíra; Skeríková, Andrea; Shimazu, Takeshi; Rolbiecki, Leszek

    2007-06-01

    A list and key to the identification of valid species of tapeworms of the Proteocephalus Weinland, 1858 aggregate sensu de Chambrier et al. (2004), i.e. species of the genus occurring in fresh- and brackish-water fishes in the Palaearctic Region, are provided, with data on their hosts and geographical distribution. Instead of 32 taxa listed by Schmidt (1986) and subsequent authors, only the following 14 species are considered to be valid: P. ambiguus (Dujardin, 1845) (type-species); P. cernuae (Gmelin, 1790); P. filicollis (Rudolphi, 1802); P. fluviatilis Bangham, 1925; P. gobiorum Dogiel & Bychowsky, 1939; P. longicollis (Zeder, 1800); P. macrocephalus (Creplin, 1825); P. midoriensis Shimazu, 1990; P. percae (Müller, 1780); P. plecoglossi Yamaguti, 1934; P. sagittus (Grimm, 1872); P. tetrastomus (Rudolphi, 1810); P. thymalli (Annenkova-Chlopina, 1923); and P. torulosus (Batsch, 1786). An analysis of sequences of the nuclear genes (ITS2 and V4 region of 18S rDNA) revealed the following phylogenetic relationships for these taxa: P. torulosus ((P. midoriensis, P. sagittus) (P. fluviatilis (P. filicollis, P. gobiorum, P. macrocephalus)) (P. cernuae, P. plecoglossi, P. tetrastomus ((P. longicollis, P. percae) (P. ambiguus, P. thymalli)))). P. pronini Rusinek, 2001 from grayling Thymallus arcticus nigrescens is synonymised with P. thymalli. P. esocis La Rue, 1911 is apparently invalid but its conspecificity with either P. percae or P. longicollis could not be confirmed due to the absence of the scolex in the holotype and the unavailability of other material for morphological and molecular studies. P. osculatus (Goeze, 1782) has recently been transferred to Glanitaenia de Chambrier, Mariaux, Vaucher & Zehnder, 2004. The validity of the genus is supported by the position of G. osculata within the Proteocephalidea, based on molecular data, as well as its morphology and nature of the definitive host (the European wels Silurus glanis). P. hemispherous Rahemo & Al-Niaeemi, 2001, described from S. glanis in Iraq, is transferred to Postgangesia Akhmerov, 1960 as Postgangesia hemispherous (Rahemo & Al-Niaeemi, 2001) n. comb. PMID:17473908

  10. Detecting Protein-Protein Interactions with a Green Fluorescent Protein Fragment Reassembly Trap: Scope and

    E-print Network

    Mochrie, Simon

    Detecting Protein-Protein Interactions with a Green Fluorescent Protein Fragment Reassembly Trap-mail: lynne.regan@yale.edu Abstract: Identification of protein binding partners is one of the key challenges of proteomics. We recently introduced a screen for detecting protein-protein interactions based on reassembly

  11. Mass Spectrometric Protein Identification Using the Global Proteome Machine

    E-print Network

    Chait, Brian T.

    189 Chapter 11 Mass Spectrometric Protein Identification Using the Global Proteome Machine David Fenyö, Jan Eriksson, and Ronald Beavis Abstract Protein identification by mass spectrometry is widely, rho-diagrams, and spectrum databases. Key words: Proteomics, Mass spectrometry, Protein identification

  12. Ferenczi's concept of identification with the aggressor: understanding dissociative structure with interacting victim and abuser self-states.

    PubMed

    Howell, Elizabeth F

    2014-03-01

    No one has described more passionately than Ferenczi the traumatic induction of dissociative trance with its resulting fragmentation of the personality. Ferenczi introduced the concept and term, identification with the aggressor in his seminal "Confusion of Tongues" paper, in which he described how the abused child becomes transfixed and robbed of his senses. Having been traumatically overwhelmed, the child becomes hypnotically transfixed by the aggressor's wishes and behavior, automatically identifying by mimicry rather than by a purposeful identification with the aggressor's role. To expand upon Ferenczi's observations, identification with the aggressor can be understood as a two-stage process. The first stage is automatic and initiated by trauma, but the second stage is defensive and purposeful. While identification with the aggressor begins as an automatic organismic process, with repeated activation and use, gradually it becomes a defensive process. Broadly, as a dissociative defense, it has two enacted relational parts, the part of the victim and the part of the aggressor. This paper describes the intrapersonal aspects (how aggressor and victim self-states interrelate in the internal world), as well as the interpersonal aspects (how these become enacted in the external). This formulation has relevance to understanding the broad spectrum of the dissociative structure of mind, borderline personality disorder, and dissociative identity disorder. PMID:24603172

  13. The Role of Interactive Learning to Close the “Innovation Gap” in SME-Based Local Economies: A Furniture Cluster in the Basque Country and its Key Policy Implications

    Microsoft Academic Search

    M. D. Parrilli; M. J. Aranguren; M. Larrea

    2010-01-01

    This paper identifies an “innovation gap” in the (in)efficient relation between innovation structures and production systems in SME-based economies and, by elucidating an implicit aspect of key theoretical contributions from Lundvall and Cooke, among others, sets the basis for a policy focus that may help reducing those margins of inefficiency. In this work, we identify three interdependent drivers of innovation:

  14. Identification of PTM5 protein interaction partners, a MADS-box gene involved in aspen tree vegetative development

    Microsoft Academic Search

    Leland J. Cseke; Namritha Ravinder; Ajay K. Pandey; Gopi K. Podila

    2007-01-01

    In a past article, our lab described the identification and characterization of a novel vegetative MADS-box gene from quaking aspen trees, Populus tremuloides MADS-box 5 (PTM5). PTM5 was shown to be a member of the SOC1\\/TM3 class of MADS-box genes with a seasonal expression pattern specific to developing vascular tissues including the vascular cambium, the precursor to all woody branches,

  15. Identification and characterization of the linear region of ATG3 that interacts with ATG7 in higher eukaryotes.

    PubMed

    Ohashi, Kazuto; Otomo, Takanori

    2015-07-31

    Transfer of GABARAP thioester from the E1 ATG7 to the E2 ATG3 requires the interaction between the N-terminal domain of ATG7 and the flexible region (FR) of ATG3. This interaction has been visualized in the yeast Atg7-Atg3 complex crystal structure, but remains to be defined in higher eukaryotes. Here, our NMR data precisely define the region of the FR of human ATG3 that interacts with ATG7 (RIA7) and demonstrate RIA7 partially overlaps with the E3-interacting region, explaining how the E1-E2 and E2-E3 interactions are mutually exclusive. Mutational analyses identify critical residues of the RIA7 for the E1 interaction and GABARAP transfer, advancing our understanding of a molecular mechanism of the autophagic conjugation cascade in higher eukaryotes. PMID:26043688

  16. PURIFICATION OF THE ROTAVIRUS NSP4 ENTEROTOXIN AND DISCERNMENT OF KEY HOST-CELL INTERACTIONS THAT CONTRIBUTE TO NSP4 SECRETION FROM THE CELL 

    E-print Network

    Aguirre, Rene 1989-

    2011-05-04

    identified enterotoxin associated with RV infections. Our main focus was to understand how this protein interacted with infected host-cell molecules, thus inducing disease symptoms. We utilized a yeast expression system that had been transformed with a...

  17. In Vivo Protein Interaction Network Identified with a Novel Real-Time Cross-Linked Peptide Identification Strategy

    PubMed Central

    Weisbrod, Chad R.; Chavez, Juan D.; Eng, Jimmy K.; Yang, Li; Zheng, Chunxiang; Bruce, James E.

    2013-01-01

    Protein interaction topologies are critical determinants of biological function. Large-scale or proteome-wide measurements of protein interaction topologies in cells currently pose an unmet challenge that could dramatically improve understanding of complex biological systems. A primary impediment includes direct protein topology and interaction measurements from living systems since interactions that lack biological significance may be introduced during cell lysis. Furthermore, many biologically relevant protein interactions will likely not survive the lysis/sample preparation and may only be measured with in vivo methods. As a step toward meeting this challenge, a new mass spectrometry method called Real-time Analysis for Cross-linked peptide Technology (ReACT) has been developed that enables assignment of cross-linked peptides “on-the-fly”. Using ReACT, 708 unique cross-linked (<5% FDR) peptide pairs were identified from cross-linked E. coli cells. These data allow assembly of the first protein interaction network that also contains topological features of every interaction, as it existed in cells during cross-linker application. Of the identified interprotein cross-linked peptide pairs, 40% are derived from known interactions and provide new topological data that can help visualize how these interactions exist in cells. Other identified cross-linked peptide pairs are from proteins known to be involved within the same complex, but yield newly discovered direct physical interactors. ReACT enables the first view of these interactions inside cells, and the results acquired with this method suggest cross-linking can play a major role in future efforts to map the interactome in cells. PMID:23413883

  18. Novel Insights into CB1 Cannabinoid Receptor Signaling: A Key Interaction Identified between the Extracellular-3 Loop and Transmembrane Helix 2S?

    PubMed Central

    Marcu, Jahan; Shore, Derek M.; Kapur, Ankur; Trznadel, Megan; Makriyannis, Alexandros; Reggio, Patricia H.

    2013-01-01

    Activation of the cannabinoid CB1 receptor (CB1) is modulated by aspartate residue D2.63176 in transmembrane helix (TMH) 2. Interestingly, D2.63 does not affect the affinity for ligand binding at the CB1 receptor. Studies in class A G protein-coupled receptors have suggested an ionic interaction between residues of TMH2 and 7. In this report, modeling studies identified residue K373 in the extracellular-3 (EC-3) loop in charged interactions with D2.63. We investigated this possibility by performing reciprocal mutations and biochemical studies. D2.63176A, K373A, D2.63176A-K373A, and the reciprocal mutant with the interacting residues juxtaposed D2.63176K-K373D were characterized using radioligand binding and guanosine 5?-3-O-(thio)triphosphate functional assays. None of the mutations resulted in a significant change in the binding affinity of N-(piperidiny-1-yl)-5-(4-chlorophenyl)-1-(2,4-dichloro-phenyl)-4-methyl-1H-pyrazole-3-carboxamide hydrochloride (SR141716A) or (?)-3cis -[2-hydroxyl-4-(1,1-dimethyl-heptyl)phenyl]-trans-4-[3-hydroxyl-propyl] cyclohexan-1-ol (CP55,940). Modeling studies indicated that binding-site interactions and energies of interaction for CP55,940 were similar between wild-type and mutant receptors. However, the signaling of CP55,940, and (R)-(+)-[2,3-dihydro-5-methyl-3-[(4-morpholinyl)methyl]-pyrrolo[1,2,3-de]-1,4-benzoxazin-6-yl](1-naphthalenyl)-methanone mesylate (WIN55,212-2) was impaired at the D2.63176A-K373A and the single-alanine mutants. In contrast, the reciprocal D2.63176K-K373D mutant regained function for both CP55,940 and WIN55,212-2. Computational results indicate that the D2.63176-K373 ionic interaction strongly influences the conformation(s) of the EC-3 loop, providing a structure-based rationale for the importance of the EC-3 loop to signal transduction in CB1. The putative ionic interaction results in the EC-3 loop pulling over the top (extracellular side) of the receptor; this EC-3 loop conformation may serve protective and mechanistic roles. These results suggest that the ionic interaction between D2.63176 and K373 is important for CB1 signal transduction. PMID:23426954

  19. Key-Insulated Public Key Cryptosystems

    Microsoft Academic Search

    Yevgeniy Dodis; Jonathan Katz; Shouhuai Xu; Moti Yung

    2002-01-01

    Cryptographic computations (decryption, signature generation, etc.) are often performed on a relatively insecure device (e.g., a mobile device or an Internet-connected host) which cannot be trusted to maintain secrecy of the pri- vate key. We propose and investigate the notion of key-insulated security whose goal is to minimize the damage caused by secret-key exposures. In our model, the secret key(s)

  20. Interaction of Mycobacterium leprae with Human Airway Epithelial Cells: Adherence, Entry, Survival, and Identification of Potential Adhesins by Surface Proteome Analysis

    PubMed Central

    Silva, Carlos A. M.; Danelishvili, Lia; McNamara, Michael; Berredo-Pinho, Márcia; Bildfell, Robert; Biet, Franck; Rodrigues, Luciana S.; Oliveira, Albanita V.

    2013-01-01

    This study examined the in vitro interaction between Mycobacterium leprae, the causative agent of leprosy, and human alveolar and nasal epithelial cells, demonstrating that M. leprae can enter both cell types and that both are capable of sustaining bacterial survival. Moreover, delivery of M. leprae to the nasal septum of mice resulted in macrophage and epithelial cell infection in the lung tissue, sustaining the idea that the airways constitute an important M. leprae entry route into the human body. Since critical aspects in understanding the mechanisms of infection are the identification and characterization of the adhesins involved in pathogen-host cell interaction, the nude mouse-derived M. leprae cell surface-exposed proteome was studied to uncover potentially relevant adhesin candidates. A total of 279 cell surface-exposed proteins were identified based on selective biotinylation, streptavidin-affinity purification, and shotgun mass spectrometry; 11 of those proteins have been previously described as potential adhesins. In vitro assays with the recombinant forms of the histone-like protein (Hlp) and the heparin-binding hemagglutinin (HBHA), considered to be major mycobacterial adhesins, confirmed their capacity to promote bacterial attachment to epithelial cells. Taking our data together, they suggest that the airway epithelium may act as a reservoir and/or portal of entry for M. leprae in humans. Moreover, our report sheds light on the potentially critical adhesins involved in M. leprae-epithelial cell interaction that may be useful in designing more effective tools for leprosy control. PMID:23670556

  1. Identification of the interaction domains of white spot syndrome virus envelope proteins VP28 and VP24.

    PubMed

    Li, Zaipeng; Chen, Weiyu; Xu, Limei; Li, Fang; Yang, Feng

    2015-03-16

    VP28 and VP24 are two major envelope proteins of white spot syndrome virus (WSSV). The direct interaction between VP28 and VP24 has been described in previous studies. In this study, we confirmed this interaction and mapped the interaction domains of VP28 and VP24 by constructing a series of deletion mutants. By co-immunoprecipitation, two VP28-binding domains of VP24 were located at amino acid residues 46-61 and 148-160, while VP24-binding domain of VP28 was located at amino acid residues 31-45. These binding domains were further corroborated by peptide blocking assay, in which synthetic peptides spanning the binding domains were able to inhibit VP28-VP24 interaction, whereas same-size control peptides from non-binging regions did not. PMID:25637460

  2. Optimizing Requirements Decisions with KEYS

    NASA Technical Reports Server (NTRS)

    Jalali, Omid; Menzies, Tim; Feather, Martin

    2008-01-01

    Recent work with NASA's Jet Propulsion Laboratory has allowed for external access to five of JPL's real-world requirements models, anonymized to conceal proprietary information, but retaining their computational nature. Experimentation with these models, reported herein, demonstrates a dramatic speedup in the computations performed on them. These models have a well defined goal: select mitigations that retire risks which, in turn, increases the number of attainable requirements. Such a non-linear optimization is a well-studied problem. However identification of not only (a) the optimal solution(s) but also (b) the key factors leading to them is less well studied. Our technique, called KEYS, shows a rapid way of simultaneously identifying the solutions and their key factors. KEYS improves on prior work by several orders of magnitude. Prior experiments with simulated annealing or treatment learning took tens of minutes to hours to terminate. KEYS runs much faster than that; e.g for one model, KEYS ran 13,000 times faster than treatment learning (40 minutes versus 0.18 seconds). Processing these JPL models is a non-linear optimization problem: the fewest mitigations must be selected while achieving the most requirements. Non-linear optimization is a well studied problem. With this paper, we challenge other members of the PROMISE community to improve on our results with other techniques.

  3. The Development of High-Quality Interaction and Thinking Alongside the Extension of Child-Initiated Learning into Key Stage One: A Whole School Initiative

    ERIC Educational Resources Information Center

    Hood, Philip

    2013-01-01

    A UK East Midlands urban infant (four to seven years) school is working to design, implement and evaluate a new pedagogy across all three year groups in the school. The focus is on the implementation of a negotiated progressive skills matrix, centred on continuous and enhanced provision and on creating high-quality interactions between adults and…

  4. Alcohol-induced sedation and synergistic interactions between alcohol and morphine: A key mechanistic role for Toll-Like Receptors and MyD88-dependent signalling

    PubMed Central

    Corrigan, Frances; Wu, Yue; Tuke, Jonathan; Coller, Janet K.; Rice, Kenner C.; Diener, Kerrilyn R.; Hayball, John D.; Watkins, Linda R.; Somogyi, Andrew A.; Hutchinson, Mark R.

    2015-01-01

    Increasing evidence demonstrates induction of proinflammatory Toll-like receptor (TLR) 2 and TLR4 signaling by morphine and, TLR4 signaling by alcohol; thus indicating a common site of drug action and a potential novel innate immune-dependent hypothesis for opioid and alcohol drug interactions. Hence, the current study aimed to assess the role of TLR2, TLR4, MyD88 (as a critical TLR-signalling participant), NF-?B, Interleukin-1? (IL-1?; as a downstream proinflammatory effector molecule) and the µ opioid receptor (MOR; as a classical site for morphine action) in acute alcohol-induced sedation (4.5 g/kg) and alcohol (2.5 g/kg) interaction with morphine (5 mg/kg) by assessing the loss of righting reflex (LORR) as a measure of sedation. Wild-type male Balb/c mice and matched genetically-deficient TLR2, TLR4, and MyD88 strains were utilized, together with pharmacological manipulation of MOR, NF-?B, TLR4 and Interleukin-1?. Alcohol induced significant LORR in wild-type mice; this was halved by MyD88 and TLR4 deficiency, and surprisingly nearly completely eliminated by TLR2 deficiency. In contrast, the interaction between morphine and alcohol was found to be MOR-, NF-?B-, TLR2- and MyD88-dependent, but did not involve TLR4 or Interleukin-1?. Morphine-alcohol interactions caused acute elevations in microglial cell counts and NF-?B-p65 positive cells in the motor cortex in concordance with wild-type and TLR2 deficient mouse behavioral data, implicating neuroimmunopharmacological signaling as a pivotal mechanism in this clinically problematic drug-drug interaction. PMID:25542736

  5. A comprehensive study of the spontaneous formation of nanoassemblies in water by a "lock-and-key" interaction between two associative polymers.

    PubMed

    Othman, Mohammad; Bouchemal, Kawthar; Couvreur, Patrick; Desmaële, Didier; Morvan, Estelle; Pouget, Thierry; Gref, Ruxandra

    2011-02-15

    Nanoassemblies (NAs) with sizes ranging from 60 to 160nm were spontaneously formed in water after mixing a host polymer (polymerized cyclodextrin (p?-CD)) and a guest polymer (dextran grafted with lauroyl side chains (MD)). The combination of microscopy, dynamic light scattering (DLS), nuclear magnetic resonance ((1)H NMR), isothermal titration calorimetry (ITC) and molecular modelling was used to investigate the parameters which govern the association between MD and p?-CD. Remarkably, when p?-CD was progressively added to a solution of MD, NAs with a well-defined diameter were spontaneously formed and their diameter was constant whatever the composition of the system. According to NMR data, almost all the alkyl chains of MD were included into CDs' cavities of the polymer when the molar ratio lauroyl chain (C(12))/CD was ?1. The hydrophobic interaction between C(12) and the hydrophobic cavities of CDs appears as the main driving force for NAs' formation, with a minor contribution arising from van der Waals' interactions. The inclusion of C(12) into ?-CD cavities is almost a completely enthalpy-driven process, whereas the MD-C(12)/p?-CD interaction was found to be an entropy-driven process. Major conclusions which can be drawn from these studies are that the interactions between the two polymers are restricted neither by the MD substitution yield, nor by the micellization of MD. The simultaneous effects of several CD linked together in p?-CD and of many alkyl chains grafted on dextran were necessary to generate these stable NAs. PMID:21131000

  6. In situ identification of the Martian surface material and its interaction with the Martian atmosphere using DTA/GC

    NASA Technical Reports Server (NTRS)

    Mancinelli, R. L.; White, M. R.

    1992-01-01

    Little is known about the mineralogy of the martian surface material. Several techniques have been suggested as candidates for the in situ identification of the martian surface material. The most promising of these techniques include differential thermal analysis (DTA) coupled with gas chromatography (GC) and differential scanning calorimetry (DSC) coupled with either mass spectrometry (MS) or GC. Our studies showed that differential thermal analysis coupled with gas chromatography (DTA/GC) is a more appropriate analytical technique than DSC/MS or DSC/GC to identify the mineralogy of the martian surface material in situ. DTA/GC can be regarded as an advancement from pyrolytic GC analyses that were successfully flown on previous missions, but have supplied only limited mineralogical information.

  7. Unlocking the Keys to Vortex/Flame Interactions in Turbulent Gas-Jet Diffusion Flames--Dynamic Behavior Explored on the Space Shuttle

    NASA Technical Reports Server (NTRS)

    Stocker, Dennis P.

    1999-01-01

    Most combustion processes in industrial applications (e.g., furnaces and engines) and in nature (e.g., forest fires) are turbulent. A better understanding of turbulent combustion could lead to improved combustor design, with enhanced efficiency and reduced emissions. Despite its importance, turbulent combustion is poorly understood because of its complexity. The rapidly changing and random behavior of such flames currently prevents detailed analysis, whether experimentally or computationally. However, it is possible to learn about the fundamental behavior of turbulent flames by exploring the controlled interaction of steady laminar flames and artificially induced flow vortices. These interactions are an inherent part of turbulent flames, and understanding them is essential to the characterization of turbulent combustion. Well-controlled and defined experiments of vortex interaction with laminar flames are not possible in normal gravity because of the interference of buoyancy- (i.e., gravity) induced vortices. Therefore, a joint microgravity study was established by researchers from the Science and Technology Development Corp. and the NASA Lewis Research Center. The experimental study culminated in the conduct of the Turbulent Gas-Jet Diffusion Flames (TGDF) Experiment on the STS-87 space shuttle mission in November 1997. The fully automated hardware, shown in photo, was designed and built at Lewis. During the mission, the experiment was housed in a Get Away Special (GAS) canister in the cargo bay.

  8. What is the Key to Classification?

    NSDL National Science Digital Library

    Lesson plan defines dichotomous key and its role in classification. Students learn how to make a key and identify important organisms from a biofilm community in Chesapeake Bay. An interactive, online key with photos and species profiles challenges students to identify 8 invertebrates and an interactive quiz helps them test their understanding. Designed for use with the MD Sea Grant "Biofilms & Biodiversity" activity. Outlines learning objectives, skills and processes, biology concepts covered, and related activities.

  9. Carboxyl Group Footprinting Mass Spectrometry and Molecular Dynamics Identify Key Interactions in the HER2-HER3 Receptor Tyrosine Kinase Interface* ?

    PubMed Central

    Collier, Timothy S.; Diraviyam, Karthikeyan; Monsey, John; Shen, Wei; Sept, David; Bose, Ron

    2013-01-01

    The HER2 receptor tyrosine kinase is a driver oncogene in many human cancers, including breast and gastric cancer. Under physiologic levels of expression, HER2 heterodimerizes with other members of the EGF receptor/HER/ErbB family, and the HER2-HER3 dimer forms one of the most potent oncogenic receptor pairs. Previous structural biology studies have individually crystallized the kinase domains of HER2 and HER3, but the HER2-HER3 kinase domain heterodimer structure has yet to be solved. Using a reconstituted membrane system to form HER2-HER3 kinase domain heterodimers and carboxyl group footprinting mass spectrometry, we observed that HER2 and HER3 kinase domains preferentially form asymmetric heterodimers with HER3 and HER2 monomers occupying the donor and acceptor kinase positions, respectively. Conformational changes in the HER2 activation loop, as measured by changes in carboxyl group labeling, required both dimerization and nucleotide binding but did not require activation loop phosphorylation at Tyr-877. Molecular dynamics simulations on HER2-HER3 kinase dimers identify specific inter- and intramolecular interactions and were in good agreement with MS measurements. Specifically, several intermolecular ionic interactions between HER2 Lys-716-HER3 Glu-909, HER2 Glu-717-HER3 Lys-907, and HER2 Asp-871-HER3 Arg-948 were identified by molecular dynamics. We also evaluated the effect of the cancer-associated mutations HER2 D769H/D769Y, HER3 E909G, and HER3 R948K (also numbered HER3 E928G and R967K) on kinase activity in the context of this new structural model. This study provides valuable insights into the EGF receptor/HER/ErbB kinase structure and interactions, which can guide the design of future therapies. PMID:23843458

  10. Systems Integration of Biodefense Omics Data for Analysis of Pathogen-Host Interactions and Identification of Potential Targets

    Microsoft Academic Search

    Peter B. McGarvey; Hongzhan Huang; Raja Mazumder; Jian Zhang; Yongxing Chen; Chengdong Zhang; Stephen Cammer; Rebecca Will; Margie Odle; Bruno Sobral; Margaret Moore; Cathy H. Wu; Jörg Hoheisel

    2009-01-01

    The NIAID (National Institute for Allergy and Infectious Diseases) Biodefense Proteomics program aims to identify targets for potential vaccines, therapeutics, and diagnostics for agents of concern in bioterrorism, including bacterial, parasitic, and viral pathogens. The program includes seven Proteomics Research Centers, generating diverse types of pathogen-host data, including mass spectrometry, microarray transcriptional profiles, protein interactions, protein structures and biological reagents.

  11. An Interdisciplinary Approach to Studying Gene–Environment Interactions: From Twin Studies to Gene Identification and Back

    Microsoft Academic Search

    Danielle M. Dick

    2011-01-01

    There has been a surge of interest in studying gene–environment interaction; however, research in this area faces a number of challenges. Interdisciplinary collaborations are critical at this juncture. This article reviews studies that illustrate how findings across different literatures can be synthesized to characterize how genetic and environmental influences impact developmental pathways. Developmental scientists are poised to make important contributions

  12. Single-step protease cleavage elution for identification of protein-protein interactions from GST pull-down and mass spectrometry.

    PubMed

    Luo, Lin; King, Nathan P; Yeo, Jeremy C; Jones, Alun; Stow, Jennifer L

    2014-01-01

    The study of protein-protein interactions is a major theme in biological disciplines. Pull-down or affinity-precipitation assays using GST fusion proteins have become one of the most common and valuable approaches to identify novel binding partners for proteins of interest (bait). Non-specific binding of prey proteins to the beads or to GST itself, however, inevitably complicates and impedes subsequent analysis of pull-down results. A variety of measures, each with inherent advantages and limitations, can minimise the extent of the background. This technical brief details and tests a modification of established GST pull-down protocols. By specifically eluting only the bait (minus the GST tag) and the associated non-specific binding proteins with a simple, single-step protease cleavage, a cleaner platform for downstream protein identification with MS is established. We present a proof of concept for this method, as evidenced by a GST pull-down/MS case study of the small guanosine triphosphatase (GTPase) Rab31 in which: (i) sensitivity was enhanced, (ii) a reduced level of background was observed, (iii) distinguishability of non-specific contaminant proteins from genuine binders was improved and (iv) a putative new protein-protein interaction was discovered. Our protease cleavage step is readily applicable to all further affinity tag pull-downs. PMID:24259493

  13. Pharmacophore mapping based inhibitor selection and molecular interaction studies for identification of potential drugs on calcium activated potassium channel blockers, tamulotoxin

    PubMed Central

    Kumar, R. Barani; Suresh, M. Xavier

    2013-01-01

    Background: Tamulotoxin (TmTx) from Buthus tamulus was found to be a highly venomous toxin which accelerates the neurotransmitter release that directly affects the cardiovascular tissues and the respiratory system leading to death. TmTx from red Indian scorpion is a crucial inhibitor for Ca2+ activated K+ channel in humans. Objective: The study is aimed at the identification of potential inhibitors of TmTx through pharmacophore based inhibitor screening and understanding the molecular level interactions. Materials and Method: The potential inhibitors for TmTx were identified using pharmacophore model based descriptor information present in existing drugs with the analysis of pharmacokinetic properties. The compounds with good ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) descriptors were subjected to molecular interaction studies. The stability of bound toxin-inhibitor complex was studied using molecular dynamics simulation over a period of one nanosecond. Results: From a dataset of 3406 compounds, few compounds were selected as potential inhibitors based on the generated best pharmacophore models, pharmacokinetic analysis, molecular docking and molecular dynamics studies. Conclusion: In conclusion, two compounds containing better inhibition properties against TmTx are suggested to be better lead molecules for drug development in future and this study will help us to explore more inhibitors from natural origin against tamulotoxin. PMID:23772102

  14. PHONETIC SPEAKER IDENTIFICATION Qin Jin, Tanja Schultz, Alex Waibel

    E-print Network

    Schultz, Tanja

    PHONETIC SPEAKER IDENTIFICATION Qin Jin, Tanja Schultz, Alex Waibel Interactive Systems Laboratory of text­independent speaker identification using novel approaches based on speakers' phonetic features instead of traditional acoustic features. Different phonetic speaker identification approaches

  15. PHONETIC SPEAKER IDENTIFICATION Qin Jin, Tanja Schultz, Alex Waibel

    E-print Network

    Schultz, Tanja

    PHONETIC SPEAKER IDENTIFICATION Qin Jin, Tanja Schultz, Alex Waibel Interactive Systems Laboratory of text-independent speaker identification using novel approaches based on speakers' phonetic features instead of traditional acoustic features. Different phonetic speaker identification approaches

  16. Myosin Binding Protein C Positioned to Play a Key Role in Regulation of Muscle Contraction: Structure and Interactions of Domain C1

    PubMed Central

    Ababou, Abdessamad; Rostkova, Elena; Mistry, Shreena; Masurier, Clare Le; Gautel, Mathias; Pfuhl, Mark

    2008-01-01

    Myosin binding protein C (MyBP-C) is a thick filament protein involved in the regulation of muscle contraction. Mutations in the gene for MyBP-C are the second most frequent cause of hypertrophic cardiomyopathy. MyBP-C binds to myosin with two binding sites, one at its C-terminus and another at its N-terminus. The N-terminal binding site, consisting of immunoglobulin domains C1 and C2 connected by a flexible linker, interacts with the S2 segment of myosin in a phosphorylation-regulated manner. It is assumed that the function of MyBP-C is to act as a tether that fixes the S1 heads in a resting position and that phosphorylation releases the S1 heads into an active state. Here, we report the structure and binding properties of domain C1. Using a combination of site-directed mutagenesis and NMR interaction experiments, we identified the binding site of domain C1 in the immediate vicinity of the S1–S2 hinge, very close to the light chains. In addition, we identified a zinc binding site on domain C1 in close proximity to the S2 binding site. Its zinc binding affinity (Kd of approximately 10–20 ?M) might not be sufficient for a physiological effect. However, the familial hypertrophic cardiomyopathy-related mutation of one of the zinc ligands, glutamine 210 to histidine, will significantly increase the binding affinity, suggesting that this mutation may affect S2 binding. The close proximity of the C1 binding site to the hinge, the light chains and the S1 heads also provides an explanation for recent observations that (a) shorter fragments of MyBP-C unable to act as a tether still have an effect on the actomyosin ATPase and (b) as to why the myosin head positions in phosphorylated wild-type mice and MyBP-C knockout mice are so different: Domain C1 bound to the S1–S2 hinge is able to manipulate S1 head positions, thus influencing force generation without tether. The potentially extensive extra interactions of C1 are expected to keep it in place, while phosphorylation dislodges the C1–C2 linker and domain C2. As a result, the myosin heads would always be attached to a tether that has phosphorylation-dependent length regulation. PMID:18926831

  17. Myosin binding protein C positioned to play a key role in regulation of muscle contraction: structure and interactions of domain C1.

    PubMed

    Ababou, Abdessamad; Rostkova, Elena; Mistry, Shreena; Le Masurier, Clare; Gautel, Mathias; Pfuhl, Mark

    2008-12-19

    Myosin binding protein C (MyBP-C) is a thick filament protein involved in the regulation of muscle contraction. Mutations in the gene for MyBP-C are the second most frequent cause of hypertrophic cardiomyopathy. MyBP-C binds to myosin with two binding sites, one at its C-terminus and another at its N-terminus. The N-terminal binding site, consisting of immunoglobulin domains C1 and C2 connected by a flexible linker, interacts with the S2 segment of myosin in a phosphorylation-regulated manner. It is assumed that the function of MyBP-C is to act as a tether that fixes the S1 heads in a resting position and that phosphorylation releases the S1 heads into an active state. Here, we report the structure and binding properties of domain C1. Using a combination of site-directed mutagenesis and NMR interaction experiments, we identified the binding site of domain C1 in the immediate vicinity of the S1-S2 hinge, very close to the light chains. In addition, we identified a zinc binding site on domain C1 in close proximity to the S2 binding site. Its zinc binding affinity (K(d) of approximately 10-20 microM) might not be sufficient for a physiological effect. However, the familial hypertrophic cardiomyopathy-related mutation of one of the zinc ligands, glutamine 210 to histidine, will significantly increase the binding affinity, suggesting that this mutation may affect S2 binding. The close proximity of the C1 binding site to the hinge, the light chains and the S1 heads also provides an explanation for recent observations that (a) shorter fragments of MyBP-C unable to act as a tether still have an effect on the actomyosin ATPase and (b) as to why the myosin head positions in phosphorylated wild-type mice and MyBP-C knockout mice are so different: Domain C1 bound to the S1-S2 hinge is able to manipulate S1 head positions, thus influencing force generation without tether. The potentially extensive extra interactions of C1 are expected to keep it in place, while phosphorylation dislodges the C1-C2 linker and domain C2. As a result, the myosin heads would always be attached to a tether that has phosphorylation-dependent length regulation. PMID:18926831

  18. Identification of structural motifs in the E2 glycoprotein of Chikungunya involved in virus-host interaction.

    PubMed

    Asnet Mary, J; Paramasivan, R; Tyagi, B K; Surender, M; Shenbagarathai, R

    2013-10-01

    Chikungunya fever is one of the reemerging vector-borne diseases. It has become a major global health problem especially in the developing countries. There are no vaccines or specific antiviral drugs available to date. This study reports small molecule inhibitors of envelope glycoprotein 2 (E2 glycoprotein) which are predicted based on Chikungunya virus-host interactions. E2 glycoprotein of Chikungunya virus interacts at 216 residue of the host receptor protein which plays a vital role in initiating infection. Understanding the structural aspects of E2 glycoprotein is crucial to develop specific inhibitors to prevent the virus binding from host receptors. In silico method was adopted to predict the sequence motifs of envelope protein, as the method like yeast two hybrid system is laborious, time consuming, and costly. The E2 glycoprotein structure of the Indian isolate was modeled using two templates (2XFC and 3JOC) and then validated. The class III PDZ domain binding motif was found to be identified at 213-216 amino acids. The corresponding peptide structures which recognize the PDZ domain binding motif were identified by the literature search and were used for generating five point pharmacophore model (ADDDR) containing acceptor, donor and aromatic ring features. Databases such as Asinex, TosLab and Maybridge were searched for the matches for the predicted pharmacophore model. Two compounds were identified as lead molecules as their glide score is?>?5?kcal/mol. Since the pharmacophore model is developed based on Chikungunya virus-host interaction, it can be used for designing promising antiviral lead compounds for the treatment of Chikungunya fever.An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:21. PMID:23025271

  19. Identification of proteins interacting with protein kinase C?? in hyperthermia?induced apoptosis and thermotolerance of Tca8113 cells.

    PubMed

    Liu, Jianqi; Huang, Wenchuan; Lin, Yunhong; Bian, Li; He, Yongwen

    2015-09-01

    The purpose of the present study was to investigate the differential proteins that interact with protein kinase C?? (PKC??) in hyperthermia?induced apoptosis as well as thermotolerance in Tca8113 cells, and furthermore, to investigate the mechanisms of these processes in tumor cells. Activation of PKC?? was previously indicated to be involved in the heat sensitivity and thermal resistance of tongue squamous carcinoma cells. Tca8113 cell apoptosis was induced by incubation at 43?C for 80 min and the thermotolerant Tca8113 cells (TT?Tca8113) were generated through a gradient temperature?elevating method. The apoptotic rate of the cells was determined by flow cytometry, while cleavage and activation of PKC?? were analyzed by western blot analysis. The proteins that interacted with PKC?? in the Tca8113 and TT?Tca8113 cells were identified by co?immunoprecipitation coupled with mass spectrometry. Co?immunoprecipitation analysis followed by electrospray ionization mass spectrometric analysis were utilized to identify the pro? and anti?apoptotic proteins that interacted with PKC??. Significant cell apoptosis was observed in Tca8113 cells following hyperthermia, and the apoptotic rate was significantly higher than that in the control group (P<0.05). Marked PKC?? cleavage fragmentation was also identified. By contrast, the apoptotic rate of the TT?Tca8113 cells was not significantly increased following hyperthermia and no PKC?? cleavage fragmentation was observed. Among the proteins interacting with PKC??, 39 were found to be involved in the promotion of apoptosis and 16 in the inhibition of apoptosis of Tca8113 cells; these proteins were known to be involved in the regulation of cell proliferation, apoptosis, transcription and intracellular protein transport. The results of the present study provided evidence that PKC?? is a crucial factor in the heat sensitivity and thermal resistance of tongue squamous carcinoma cells and elucidated the underlying molecular basis, which may aid in the improvement of hyperthermic cancer treatments. PMID:26017369

  20. Identification of main effects, epistatic effects and their environmental interactions of QTLs for yield traits in rice

    Microsoft Academic Search

    Xinhua Zhao; Yang Qin; Jae-Keun Sohn

    2010-01-01

    Quantitative trait loci (QTLs) controlling yield and yield components were identified by using a doubled haploid (DH) population\\u000a of 120 lines from a sub-specific cross between ‘Samgang’ (Indica) and ‘Nagdong’ (Japonica). Main effects, epistatic effects, their environment interactions of QTLs were analyzed via mixed linear model approach across\\u000a different environments. A total of 17 putative QTLs were identified on 8

  1. Identification of a Small Molecule That Modifies MglA/SspA Interaction and Impairs Intramacrophage Survival of Francisella tularensis

    PubMed Central

    Wrench, Algevis P.; Gardner, Christopher L.; Gonzalez, Claudio F.; Lorca, Graciela L.

    2013-01-01

    The transcription factors MglA and SspA of Francisella tularensis form a heterodimer complex and interact with the RNA polymerase to regulate the expression of the Francisella pathogenicity island (FPI) genes. These genes are essential for this pathogen’s virulence and survival within host cells. In this study, we used a small molecule screening to identify quinacrine as a thermal stabilizing compound for F. tularensis SCHU S4 MglA and SspA. A bacterial two-hybrid system was used to analyze the in vivo effect of quinacrine on the heterodimer complex. The results show that quinacrine affects the interaction between MglA and SspA, indicated by decreased ?-galactosidase activity. Further in vitro analyses, using size exclusion chromatography, indicated that quinacrine does not disrupt the heterodimer formation, however, changes in the alpha helix content were confirmed by circular dichroism. Structure-guided site-directed mutagenesis experiments indicated that quinacrine makes contact with amino acid residues Y63 in MglA, and K97 in SspA, both located in the “cleft” of the interacting surfaces. In F. tularensis subsp. novicida, quinacrine decreased the transcription of the FPI genes, iglA, iglD, pdpD and pdpA. As a consequence, the intramacrophage survival capabilities of the bacteria were affected. These results support use of the MglA/SspA interacting surface, and quinacrine’s chemical scaffold, for the design of high affinity molecules that will function as therapeutics for the treatment of Tularemia. PMID:23372736

  2. Identification of Ran-binding protein M as a stanniocalcin 2 interacting protein and implications for androgen receptor activity

    PubMed Central

    Shin, Jihye; Sohn, Young Chang

    2014-01-01

    Stanniocalcin (STC), a glycoprotein hormone originally discovered in fish, has been implicated in calcium and phosphate homeostasis. While fishes and mammals possess two STC homologs (STC1 and STC2), the physiological roles of STC2 are largely unknown compared with those of STC1. In this study, we identified Ran-binding protein M (RanBPM) as a novel binding partner of STC2 using yeast two-hybrid screening. The interaction between STC2 and RanBPM was confirmed in mammalian cells by immunoprecipitation. STC2 enhanced the RanBPM-mediated transactivation of liganded androgen receptor (AR), but not thyroid receptor ?, glucocorticoid receptor, or estrogen receptor ?. We also found that AR interacted with RanBPM in both the absence and presence of testosterone (T). Furthermore, we discovered that STC2 recruits RanBPM/AR complex in T-dependent manner. Taken together, our findings suggest that STC2 is a novel RanBPM-interacting protein that promotes AR transactivation. [BMB Reports 2014; 47(11): 643-648] PMID:25154718

  3. Identification of novel GAPDH-derived antimicrobial peptides secreted by Saccharomyces cerevisiae and involved in wine microbial interactions.

    PubMed

    Branco, Patrícia; Francisco, Diana; Chambon, Christophe; Hébraud, Michel; Arneborg, Nils; Almeida, Maria Gabriela; Caldeira, Jorge; Albergaria, Helena

    2014-01-01

    Saccharomyces cerevisiae plays a primordial role in alcoholic fermentation and has a vast worldwide application in the production of fuel-ethanol, food and beverages. The dominance of S. cerevisiae over other microbial species during alcoholic fermentations has been traditionally ascribed to its higher ethanol tolerance. However, recent studies suggested that other phenomena, such as microbial interactions mediated by killer-like toxins, might play an important role. Here we show that S. cerevisiae secretes antimicrobial peptides (AMPs) during alcoholic fermentation that are active against a wide variety of wine-related yeasts (e.g. Dekkera bruxellensis) and bacteria (e.g. Oenococcus oeni). Mass spectrometry analyses revealed that these AMPs correspond to fragments of the S. cerevisiae glyceraldehyde 3-phosphate dehydrogenase (GAPDH) protein. The involvement of GAPDH-derived peptides in wine microbial interactions was further sustained by results obtained in mixed cultures performed with S. cerevisiae single mutants deleted in each of the GAPDH codifying genes (TDH1-3) and also with a S. cerevisiae mutant deleted in the YCA1 gene, which codifies the apoptosis-involved enzyme metacaspase. These findings are discussed in the context of wine microbial interactions, biopreservation potential and the role of GAPDH in the defence system of S. cerevisiae. PMID:24292082

  4. Transcript profiles of maize embryo sacs and preliminary identification of genes involved in the embryo sac–pollen tube interaction

    PubMed Central

    Wang, Shuai Shuai; Wang, Fang; Tan, Su Jian; Wang, Ming Xiu; Sui, Na; Zhang, Xian Sheng

    2014-01-01

    The embryo sac, the female gametophyte of flowering plants, plays important roles in the pollination and fertilization process. Maize (Zea mays L.) is a model monocot, but little is known about the interactions between its embryo sac and the pollen tube. In this study, we compared the transcript profiles of mature embryo sacs, mature embryo sacs 14–16 h after pollination, and mature nucelli. Comparing the transcript profiles of the embryo sacs before and after the entry of the pollen tube, we identified 3467 differentially expressed transcripts (3382 differentially expressed genes; DEGs). The DEGs were grouped into 22 functional categories. Among the DEGs, 221 genes were induced upon the entry of the pollen tube, and many of them encoded proteins involved in RNA binding, processing, and transcription, signaling, miscellaneous enzyme family processes, and lipid metabolism processes. Genes in the DEG dataset were grouped into 17 classes in a gene ontology enrichment analysis. The DEGs included many genes encoding proteins involved in protein amino acid phosphorylation and protein ubiquitination, implying that these processes might play important roles in the embryo sac–pollen tube interaction. Additionally, our analyses indicate that the expression of 112 genes encoding cysteine-rich proteins (CRPs) is induced during pollination and fertilization. The CRPs likely regulate pollen tube guidance and embryo sac development. These results provide important information on the genes involved in the embryo sac–pollen tube interaction in maize. PMID:25566277

  5. Identification of TyeA residues required to interact with YopN and to regulate Yop secretion.

    PubMed

    Joseph, Sabrina S; Plano, Gregory V

    2007-01-01

    The secretion of Yops via the Yersinia type III secretion system (T3SS) is controlled, in part, by a cytoplasmic YopN/TyeA complex. This complex is required to prevent Yop secretion in the presence of extracellular calcium and prior to contact between the bacterium and a eukaryotic cell. In this study we utilized site-directed mutagenesis to analyze the role of specific TyeA regions and residues in the regulation of Yop secretion. We identified two spatially distinct, surface-exposed regions of the TyeA molecule that were required to regulate Yop secretion. One region, identified by residues M51, F55 and P56, was required for TyeA to interact with YopN. A second region, identified by residues R19, W20 and D25 was not involved in the interaction of TyeA with YopN, but may be required for the YopN/TyeA complex to interact with the T3S apparatus in a manner that blocks Yop secretion. PMID:17966420

  6. Identification of Ran-binding protein M as a stanniocalcin 2 interacting protein and implications for androgen receptor activity.

    PubMed

    Shin, Jihye; Sohn, Young Chang

    2014-11-01

    Stanniocalcin (STC), a glycoprotein hormone originally discovered in fish, has been implicated in calcium and phosphate homeostasis. While fishes and mammals possess two STC homologs (STC1 and STC2), the physiological roles of STC2 are largely unknown compared with those of STC1. In this study, we identified Ran-binding protein M (RanBPM) as a novel binding partner of STC2 using yeast two-hybrid screening. The interaction between STC2 and RanBPM was confirmed in mammalian cells by immunoprecipitation. STC2 enhanced the RanBPM-mediated transactivation of liganded androgen receptor (AR), but not thyroid receptor ?, glucocorticoid receptor, or estrogen receptor ?. We also found that AR interacted with RanBPM in both the absence and presence of testosterone (T). Furthermore, we discovered that STC2 recruits RanBPM/AR complex in T-dependent manner. Taken together, our findings suggest that STC2 is a novel RanBPM-interacting protein that promotes AR transactivation. PMID:25154718

  7. Transcriptional control by two interacting regulatory proteins: identification of the PtxS binding site at PtxR.

    PubMed

    Daddaoua, Abdelali; Krell, Tino; Ramos, Juan-Luis

    2013-12-01

    The PtxS and PtxR regulators control the expression of the glucose dehydrogenase genes from the Pgad promoter in Pseudomonas aeruginosa. These regulators bind to their cognate operators, that are separated by ?50 nt, within the promoter region and interact with each other creating a DNA-loop that prevents RNA polymerase promoter access. Binding of the 2-ketogluconate effector to PtxS caused PtxS/PtxR complex dissociation and led to the dissolution of the repression loop facilitating the entry of the RNA polymerase and enabling the transcription of the gad gene. We have identified a hydrophobic surface patch on the PtxR putative surface that was hypothesized to correspond to the binding site for PtxS. Two surface-exposed residues in this patch, V173 and W269, were replaced by alanine. Isothermal titration calorimetry assays showed that PtxS does not interact with the mutant variants of PtxR. Electrophoretic mobility shift assay and DNAase I footprinting assays proved that both regulators bind to their target operators and that failure to interact with each other prevented the formation of the DNA-loop. In vitro transcription showed that PtxS per se is sufficient to inhibit transcription from the Pgad promoter, but that affinity of PtxS for its effector is modulated by PtxR. PMID:24019239

  8. Identification and characterization of MUS81 point mutations that abolish interaction with the SLX4 scaffold protein.

    PubMed

    Nair, Nidhi; Castor, Dennis; Macartney, Thomas; Rouse, John

    2014-12-01

    MUS81-EME1 is a conserved structure-selective endonuclease with a preference for branched DNA substrates in vitro that correspond to intermediates of DNA repair. Cells lacking MUS81 or EME1 show defects in the repair of DNA interstrand crosslinks (ICL) resulting in hypersensitivity to agents such as mitomycin C. In metazoans, a proportion of cellular MUS81-EME1 binds the SLX4 scaffold protein, which is itself instrumental for ICL repair. It was previously reported that mutations in SLX4 that abolished interaction with MUS81 affected ICL repair in human cells but not in murine cells. In this study we looked the other way around by pinpointing amino acid residues in MUS81 that when mutated abolish the interaction with SLX4. These mutations fully rescued the mitomycin C hypersensitivity of MUS81 knockout murine cells, but they were unable to rescue the sensitivity of two different human cell lines defective in MUS81. These data support an SLX4-dependent role for MUS81 in the repair, but not the induction of ICL-induced double-strand breaks. This study sheds light on the extent to which MUS81 function in ICL repair requires interaction with SLX4. PMID:25224045

  9. Identification of small molecules that inhibit the interaction of TEM8 with anthrax protective antigen using a FRET assay

    PubMed Central

    Cryan, Lorna M.; Habeshian, Kaiane A.; Caldwell, Thomas P.; Morris, Meredith T.; Ackroyd, P. Christine; Christensen, Kenneth A.; Rogers, Michael S.

    2013-01-01

    Tumor marker endothelial 8 (TEM8) is a receptor for the Protective Antigen (PA) component of anthrax toxin. TEM8 is upregulated on endothelial cells lining the blood vessels within tumors, compared to normal blood vessels. A number of studies have demonstrated a pivotal role for TEM8 in developmental and tumor angiogenesis. We have also shown that targeting the anthrax receptors with a mutated form of PA inhibits angiogenesis and tumor formation in vivo. Here we describe the development and testing of a high-throughput fluorescence resonance energy transfer assay to identify molecules that strongly inhibit the interaction of PA and TEM8. The assay we describe is sensitive and robust, with a Z-prime value of 0.8. A preliminary screen of 2310 known bioactive library compounds identified ebselen and thimerosal as inhibitors of the TEM8-PA interaction. These molecules each contain a cysteine-reactive transition metal, and complimentary studies indicate that their inhibition of interaction is due to modification of a cysteine residue in the TEM8 extracellular domain. This is the first demonstration of a high-throughput screening assay that identifies inhibitors of TEM8, with potential application for anti-anthrax and anti-angiogenic diseases. PMID:23479355

  10. Identification and characterization of GIV, a novel Galpha i/s-interacting protein found on COPI, endoplasmic reticulum-Golgi transport vesicles.

    PubMed

    Le-Niculescu, Helen; Niesman, Ingrid; Fischer, Thierry; DeVries, Luc; Farquhar, Marilyn G

    2005-06-10

    In this report, we characterize GIV (Galpha-interacting vesicle-associated protein), a novel protein that binds members of the Galpha(i) and Galpha subfamilies of heterotrimeric G proteins. The Galpha(s) interaction site was mapped to an 83-amino acid region of GIV that is enriched in highly charged amino acids. BLAST searches revealed two additional mammalian family members, Daple and an uncharacterized protein, FLJ00354. These family members share the highest homology at the Galpha binding domain, are homologous at the N terminus and central coiled coil domain but diverge at the C terminus. Using affinity-purified IgG made against two different regions of the protein, we localized GIV to COPI, endoplasmic reticulum (ER)-Golgi transport vesicles concentrated in the Golgi region in GH3 pituitary cells and COS7 cells. Identification as COPI vesicles was based on colocalization with beta-COP, a marker for these vesicles. GIV also codistributes in the Golgi region with endogenous calnuc and the KDEL receptor, which are cis Golgi markers and with Galpha(i3)-yellow fluorescent protein expressed in COS7 cells. By immunoelectron microscopy, GIV colocalizes with beta-COP and Galpha(i3) on vesicles found in close proximity to ER exit sites and to cis Golgi cisternae. In cell fractions prepared from rat liver, GIV is concentrated in a carrier vesicle fraction (CV2) enriched in ER-Golgi transport vesicles. beta-COP and several Galpha subunits (Galpha(i1-3), Galpha(s)) are also most enriched in CV2. Our results demonstrate the existence of a novel Galpha-interacting protein associated with COPI transport vesicles that may play a role in Galpha-mediated effects on vesicle trafficking within the Golgi and/or between the ER and the Golgi. PMID:15749703

  11. Views on Identification.

    ERIC Educational Resources Information Center

    CAG Communicator, 1990

    1990-01-01

    The articles in this issue consider key issues in the selection of populations for gifted education program services. Titles and authors of articles include: "The Identification Blues and How to Cure Them" (Ernesto Bernal); "Recognizing Giftedness in Your Child" (Linda Kreger Silverman); "Instructional Grouping, GATE and Honors Classes" (Bill…

  12. Plant Identification, Abridged

    NSDL National Science Digital Library

    This unit helps students prepare for their fieldwork by developing their observational skills and introducing them to resources that will help them with plant identification. It's designed to be completed in five or more sessions and has information for teachers, including overviews of binomial nomenclature and dichotomous keys. Additionally, a guide to finding local specialists is available online.

  13. Interactive effects of climate change with nutrients, mercury, and freshwater acidification on key taxa in the North Atlantic Landscape Conservation Cooperative region.

    PubMed

    Pinkney, Alfred E; Driscoll, Charles T; Evers, David C; Hooper, Michael J; Horan, Jeffrey; Jones, Jess W; Lazarus, Rebecca S; Marshall, Harold G; Milliken, Andrew; Rattner, Barnett A; Schmerfeld, John; Sparling, Donald W

    2015-07-01

    The North Atlantic Landscape Conservation Cooperative LCC (NA LCC) is a public-private partnership that provides information to support conservation decisions that may be affected by global climate change (GCC) and other threats. The NA LCC region extends from southeast Virginia to the Canadian Maritime Provinces. Within this region, the US National Climate Assessment documented increases in air temperature, total precipitation, frequency of heavy precipitation events, and rising sea level, and predicted more drastic changes. Here, we synthesize literature on the effects of GCC interacting with selected contaminant, nutrient, and environmental processes to adversely affect natural resources within this region. Using a case study approach, we focused on 3 stressors with sufficient NA LCC region-specific information for an informed discussion. We describe GCC interactions with a contaminant (Hg) and 2 complex environmental phenomena-freshwater acidification and eutrophication. We also prepared taxa case studies on GCC- and GCC-contaminant/nutrient/process effects on amphibians and freshwater mussels. Several avian species of high conservation concern have blood Hg concentrations that have been associated with reduced nesting success. Freshwater acidification has adversely affected terrestrial and aquatic ecosystems in the Adirondacks and other areas of the region that are slowly recovering due to decreased emissions of N and sulfur oxides. Eutrophication in many estuaries within the region is projected to increase from greater storm runoff and less denitrification in riparian wetlands. Estuarine hypoxia may be exacerbated by increased stratification. Elevated water temperature favors algal species that produce harmful algal blooms (HABs). In several of the region's estuaries, HABs have been associated with bird die-offs. In the NA LCC region, amphibian populations appear to be declining. Some species may be adversely affected by GCC through higher temperatures and more frequent droughts. GCC may affect freshwater mussel populations via altered stream temperatures and increased sediment loading during heavy storms. Freshwater mussels are sensitive to un-ionized ammonia that more toxic at higher temperatures. We recommend studying the interactive effects of GCC on generation and bioavailability of methylmercury and how GCC-driven shifts in bird species distributions will affect avian exposure to methylmercury. Research is needed on how decreases in acid deposition concurrent with GCC will alter the structure and function of sensitive watersheds and surface waters. Studies are needed to determine how GCC will affect HABs and avian disease, and how more severe and extensive hypoxia will affect fish and shellfish populations. Regarding amphibians, we suggest research on 1) thermal tolerance and moisture requirements of species of concern, 2) effects of multiple stressors (temperature, desiccation, contaminants, nutrients), and 3) approaches to mitigate impacts of increased temperature and seasonal drought. We recommend studies to assess which mussel species and populations are vulnerable and which are resilient to rising stream temperatures, hydrological shifts, and ionic pollutants, all of which are influenced by GCC. Integr Environ Assess Manag 2015;11:355-369. © 2015 SETAC. PMID:25556986

  14. Identification of the bud emergence gene BEM4 and its interactions with rho-type GTPases in Saccharomyces cerevisiae.

    PubMed Central

    Mack, D; Nishimura, K; Dennehey, B K; Arbogast, T; Parkinson, J; Toh-e, A; Pringle, J R; Bender, A; Matsui, Y

    1996-01-01

    The Rho-type GTPase Cdc42p is required for cell polarization and bud emergence in Saccharomyces cerevisiae. To identify genes whose functions are linked to CDC42, we screened for (i) multicopy suppressors of a Ts- cdc42 mutant, (ii) mutants that require multiple copies of CDC42 for survival, and (iii) mutations that display synthetic lethality with a partial-loss-of-function allele of CDC24, which encodes a guanine nucleotide exchange factor for Cdc42p. In all three screens, we identified a new gene, BEM4. Cells from which BEM4 was deleted were inviable at 37 degrees C. These cells became unbudded, large, and round, consistent with a model in which Bem4p acts together with Cdc42p in polarity establishment and bud emergence. In some strains, the ability of CDC42 to serve as a multicopy suppressor of the Ts- growth defect of deltabem4 cells required co-overexpression of Rho1p, which is an essential Rho-type GTPase necessary for cell wall integrity. This finding suggests that Bem4p also affects Rho1p function. Bem4p displayed two-hybrid interactions with Cdc42p, Rho1p, and two of the three other known yeast Rho-type GTPases, suggesting that Bem4p can interact with multiple Rho-type GTPases. Models for the role of Bem4p include that it serves as a chaperone or modulates the interaction of these GTPases with one or more of their targets or regulators. PMID:8754839

  15. Identification of paired immunoglobulin-like type 2 receptor ? as hepatitis B virus DNA polymerase transactivated protein 1 interacting proteins.

    PubMed

    Lun, Yong-Zhi; Chi, Qing; Wang, Xue-Lei; Wang, Fang; Sui, Wen

    2014-02-01

    Hepatitis B Virus (HBV) DNA polymerase transactivated protein 1 (HBVDNAPTP1) is a novel protein transfected by HBV DNA polymerase, which has been screened by a suppression subtractive hybridization technique. In the present study, a yeast two-hybrid system was used to screen the proteins interacting with HBVDNAPTP1 in leukocytes in order to investigate the biological function of HBVDNAPTP1. The HBVDNAPTP1 coding sequence was cloned into a pGEM-T vector. Subsequent to sequencing, the HBVDNAPTP1 was subcloned into the bait plasmid pGBKT7 and transformed into yeast AH109. Western blotting confirmed the presence of HBVDNAPTP1 expression in the AH109 yeast strains. The transformed yeast AH109 cells were mated with Y187 yeast cells containing the leucocyte cDNA library pACT2 plasmids in 2X yeast extract peptone D-glucose adenine (YPDA) medium. For selection and screening, diploid yeast was plated on synthetic dropout medium (SD/-Trp-Leu-His-Ade) containing X-?-gal. Following sequencing and the verification of the open reading frames of positive colonies, four different proteins were obtained. To further confirm the interaction between HBVDNAPTP1 and the screened proteins, paired immunoglobulin-like type 2 receptor ? (PILRA), one of the positive colonies, was cloned. The glutathione S-transferase pull-down in vitro assay and a co-immunoprecipitation in vivo assay were used to examine the interaction between HBVDNAPTP1 and PILRA, respectively. HBVDNAPTP1 may be involved in the negative regulation of the PILRA?mediated Janus-activated kinase/signal tranducer and activator of transcription signaling pathway, and exert a positive effect on the initiation of monocyte apoptosis. These results contribute our knowledge of the biological functions of HBVDNAPTP1 and provide novel data to aid in the further analysis of the regulatory mechanism of this protein. PMID:24253495

  16. Considering interactive effects in the identification of influential regions with extremely rare variants via fixed bin approach

    PubMed Central

    2014-01-01

    In this study, we analyze the Genetic Analysis Workshop 18 (GAW18) data to identify regions of single-nucleotide polymorphisms (SNPs), which significantly influence hypertension status among individuals. We have studied the marginal impact of these regions on disease status in the past, but we extend the method to deal with environmental factors present in data collected over several exam periods. We consider the respective interactions between such traits as smoking status and age with the genetic information and hope to augment those genetic regions deemed influential marginally with those that contribute via an interactive effect. In particular, we focus only on rare variants and apply a procedure to combine signal among rare variants in a number of "fixed bins" along the chromosome. We extend the procedure in Agne et al [1] to incorporate environmental factors by dichotomizing subjects via traits such as smoking status and age, running the marginal procedure among each respective category (i.e., smokers or nonsmokers), and then combining their scores into a score for interaction. To avoid overlap of subjects, we examine each exam period individually. Out of a possible 629 fixed-bin regions in chromosome 3, we observe that 11 show up in multiple exam periods for gene-smoking score. Fifteen regions exhibit significance for multiple exam periods for gene-age score, with 4 regions deemed significant for all 3 exam periods. The procedure pinpoints SNPs in 8 "answer" genes, with 5 of these showing up as significant in multiple testing schemes (Gene-Smoking, Gene-Age for Exams 1, 2, and 3). PMID:25519400

  17. Laser Shock Processing of Metallic Materials: Coupling of Laser-Plasma Interaction and Material Behaviour Models for the Assessment of Key Process Issues

    SciTech Connect

    Ocana, J. L.; Morales, M.; Molpeceres, C.; Porro, J. A. [Centro Laser UPM. Universidad Politecnica de Madrid, Campus Sur UPM. Edificio La Arboleda. Ctra. de Valencia, km. 7.3. 28031 Madrid (Spain)

    2010-10-08

    Profiting by the increasing availability of laser sources delivering intensities above 109 W/cm{sup 2} with pulse energies in the range of several Joules and pulse widths in the range of nanoseconds, laser shock processing (LSP) is consolidating as an effective technology for the improvement of surface mechanical and corrosion resistance properties of metals. The main advantage of the laser shock processing technique consists on its capability of inducing a relatively deep compression residual stresses field into metallic alloy pieces allowing an improved mechanical behaviour, explicitly, the life improvement of the treated specimens against wear, crack growth and stress corrosion cracking. Although significant work from the experimental side has been contributed to explore the optimum conditions of application of the treatments and to assess their ultimate capability to provide enhanced mechanical behaviour to work-pieces of typical materials, only limited attempts have been developed in the way of full comprehension and predictive assessment of the characteristic physical processes and material transformations with a specific consideration of real material properties. In the present paper, a review on the physical issues dominating the development of LSP processes from a high intensity laser-matter interaction point of view is presented along with the theoretical and computational methods developed by the authors for their predictive assessment and practical results at laboratory scale on the application of the technique to different materials.

  18. Site-directed mutations and kinetic studies show key residues involved in alkylammonium interactions and reveal two sites for phosphorylcholine in Pseudomonas aeruginosa phosphorylcholine phosphatase.

    PubMed

    Beassoni, Paola R; Otero, Lisandro H; Boetsch, Cristhian; Domenech, Carlos E; González-Nilo, Fernado D; Lisa, Angela T

    2011-07-01

    Pseudomonas aeruginosa phosphorylcholine phosphatase (PchP) catalyzes the hydrolysis of phosphorylcholine (Pcho) to produce choline and inorganic phosphate. PchP belongs to the haloacid dehalogenase superfamily (HAD) and possesses the three characteristic motifs of this family: motif I ((31)D and (33)D), motif II ((166)S), and motif III ((242)K, (261)G, (262)D and (267)D), which fold to form the catalytic site that binds the metal ion and the phosphate moiety of Pcho. Based on comparisons to the PHOSPHO1 and PHOSPHO2 human enzymes and the choline-binding proteins of Gram-(+) bacteria, we selected residues (42)E and (43)E and the aromatic triplet (82)YYY(84) for site-directed mutagenesis to study the interactions with Pcho and p-nitrophenylphosphate as substrates of PchP. Because mutations in (42)E, (43)E and the three tyrosine residues affect both the substrate affinity and the inhibitory effect produced by high Pcho concentrations, we postulate that two sites, one catalytic and one inhibitory, are present in PchP and that they are adjacent and share residues. PMID:21515416

  19. PASSENGER SERVICE INTEGRATION KEY TO METRO SUCCESS

    Microsoft Academic Search

    Wendy Adam; Parsons Brinckerhoff

    SUMMARY Drawing upon data from an intensive cross-sectional case study of 18 of the world's major modern metro rail systems, it was clear that planning for urban transit service integration from the start was the key success factor for metro services in all parts of the world. Using case studies and examples, the paper illustrates how early and strategic identification

  20. Escherichia Coli--Key to Modern Genetics.

    ERIC Educational Resources Information Center

    Bregegere, Francois

    1982-01-01

    Mid-nineteenth century work by Mendel on plant hybrids and by Pasteur on fermentation gave birth by way of bacterial genetics to modern-day molecular biology. The bacterium Escherichia Coli has occupied a key position in genetic studies leading from early gene identification with DNA to current genetic engineering using recombinant DNA technology.…

  1. Identification and Function of Leucine-Rich Repeat Flightless-I-Interacting Protein 2 (LRRFIP2) in Litopenaeus vannamei

    PubMed Central

    Zhang, Shuang; Yan, Hui; Li, Chao-Zheng; Chen, Yi-Hong; Yuan, Feng-hua; Chen, Yong-gui; Weng, Shao-Ping; He, Jian-Guo

    2013-01-01

    Leucine-rich repeat flightless-I-interacting protein 2 (LRRFIP2) is a myeloid differentiation factor 88-interacting protein with a positive regulatory function in toll-like receptor signaling. In this study, seven LRRFIP2 protein variants (LvLRRFIP2A-G) were identified in Litopenaeus vannamei. All the seven LvLRRFIP2 protein variants encode proteins with a DUF2051 domain. LvLRRFIP2s were upregulated in hemocytes after challenged with lipopolysaccharide, poly I:C, CpG-ODN2006, Vibrio parahaemolyticus, Staphylococcus aureus, and white spot syndrome virus (WSSV). Dual-luciferase reporter assays in Drosophila Schneider 2 cells revealed that LvLRRFIP2 activates the promoters of Drosophila and shrimp AMP genes. The knockdown of LvLRRFIP2 by RNA interference resulted in higher cumulative mortality of L. vannamei upon V. parahaemolyticus but not S. aureus and WSSV infections. The expression of L. vannamei AMP genes were reduced by dsLvLRRFIP2 interference. These results indicate that LvLRRFIP2 has an important function in antibacterials via the regulation of AMP gene expression. PMID:23468989

  2. Identification through Combinatorial Random and Rational Mutagenesis of a Substrate-interacting Exosite in the ? Domain of Streptokinase*

    PubMed Central

    Yadav, Suman; Aneja, Rachna; Kumar, Prakash; Datt, Manish; Sinha, Sonali; Sahni, Girish

    2011-01-01

    To identify new structure-function correlations in the ? domain of streptokinase, mutants were generated by error-prone random mutagenesis of the ? domain and its adjoining region in the ? domain followed by functional screening specifically for substrate plasminogen activation. Single-site mutants derived from various multipoint mutation clusters identified the importance of discrete residues in the ? domain that are important for substrate processing. Among the various residues, aspartate at position 328 was identified as critical for substrate human plasminogen activation through extensive mutagenesis of its side chain, namely D328R, D328H, D328N, and D328A. Other mutants found to be important in substrate plasminogen activation were, namely, R319H, N339S, K334A, K334E, and L335Q. When examined for their 1:1 interaction with human plasmin, these mutants were found to retain the native-like high affinity for plasmin and also to generate amidolytic activity with partner plasminogen in a manner similar to wild type streptokinase. Moreover, cofactor activities of the mutants precomplexed with plasmin against microplasminogen as the substrate as well as in silico modeling studies suggested that the region 315–340 of the ? domain interacts with the serine protease domain of the macromolecular substrate. Overall, our results identify the presence of a substrate specific exosite in the ? domain of streptokinase. PMID:21169351

  3. Single-cell analysis of thymocyte differentiation: identification of transcription factor interactions and a major stochastic component in ??-lineage commitment.

    PubMed

    Boudil, Amine; Skhiri, Lamia; Candéias, Serge; Pasqualetto, Valérie; Legrand, Agnès; Bedora-Faure, Marie; Gautreau-Rolland, Laetitia; Rocha, Benedita; Ezine, Sophie

    2013-01-01

    T cell commitment and ??/?? lineage specification in the thymus involves interactions between many different genes. Characterization of these interactions thus requires a multiparameter analysis of individual thymocytes. We developed two efficient single-cell methods: (i) the quantitative evaluation of the co-expression levels of nine different genes, with a plating efficiency of 99-100% and a detection limit of 2 mRNA molecules/cell; and (ii) single-cell differentiation cultures, in the presence of OP9 cells transfected with the thymus Notch1 ligand DeltaL4. We show that during T cell commitment, Gata3 has a fundamental, dose-dependent role in maintaining Notch1 expression, with thymocytes becoming T-cell-committed when they co-express Notch1, Gata3 and Bc11b. Of the transcription factor expression patterns studied here, only that of Bcl11b was suggestive of a role in Pu1 down-regulation. Individual thymocytes became ??/?? lineage-committed at very different stages (from the TN2a stage onwards). However, 20% of TN3 cells are not ??/??-lineage committed and TN4 cells comprise two main subpopulations with different degrees of maturity. The existence of a correlation between differentiation potential and expression of the pre-TCR showed that 83% of ??-committed cells do not express the pre-TCR and revealed a major stochastic component in ??-lineage specification. PMID:24098325

  4. Genome-wide identification, phylogenetic analysis, expression profiling, and protein-protein interaction properties of TOPLESS gene family members in tomato.

    PubMed

    Hao, Yanwei; Wang, Xinyu; Li, Xian; Bassa, Carole; Mila, Isabelle; Audran, Corinne; Maza, Elie; Li, Zhengguo; Bouzayen, Mondher; van der Rest, Benoit; Zouine, Mohamed

    2014-03-01

    Members of the TOPLESS gene family emerged recently as key players in gene repression in several mechanisms, especially in auxin perception. The TOPLESS genes constitute, in 'higher-plant' genomes, a small multigenic family comprising four to 11 members. In this study, this family was investigated in tomato, a model plant for Solanaceae species and fleshy fruits. Six open reading frames predicted to encode topless-like proteins (SlTPLs) containing the canonical domains (LisH, CTLH, and two WD40 repeats) were identified in the tomato genome. Nuclear localization was confirmed for all members of the SlTPL family with the exception SlTPL6, which localized at the cytoplasm and was excluded from the nucleus. SlTPL genes displayed distinctive expression patterns in different tomato organs, with SlTPL1 showing the highest levels of transcript accumulation in all tissues tested except in ripening fruit where SlTPL3 and SlTPL4 were the most prominently expressed. To gain insight into the specificity of the different TOPLESS paralogues, a protein-protein interaction map between TOPLESS and auxin/indole-3-acetic acid (Aux/IAA) proteins was built using a yeast two-hybrid approach. The PPI map enabled the distinction of two patterns: TOPLESS isoforms interacting with the majority of Aux/IAA, and isoforms with limited capacity for interaction with these protein partners. Interestingly, evolutionary analyses of the TOPLESS gene family revealed that the highly expressed isoforms (SlTPL1, SlTPL3, and SlTPL4) corresponded to the three TPL-related genes undergoing the strongest purifying selection, while the selection was much weaker for SlTPL6, which was expressed at a low level and encoded a protein lacking the capacity to interact with Aux/IAAs. PMID:24399174

  5. Genome-wide identification, phylogenetic analysis, expression profiling, and protein–protein interaction properties of TOPLESS gene family members in tomato

    PubMed Central

    Hao, Yanwei; Wang, Xinyu; van der Rest, Benoit; Zouine, Mohamed

    2014-01-01

    Members of the TOPLESS gene family emerged recently as key players in gene repression in several mechanisms, especially in auxin perception. The TOPLESS genes constitute, in ‘higher-plant’ genomes, a small multigenic family comprising four to 11 members. In this study, this family was investigated in tomato, a model plant for Solanaceae species and fleshy fruits. Six open reading frames predicted to encode topless-like proteins (SlTPLs) containing the canonical domains (LisH, CTLH, and two WD40 repeats) were identified in the tomato genome. Nuclear localization was confirmed for all members of the SlTPL family with the exception SlTPL6, which localized at the cytoplasm and was excluded from the nucleus. SlTPL genes displayed distinctive expression patterns in different tomato organs, with SlTPL1 showing the highest levels of transcript accumulation in all tissues tested except in ripening fruit where SlTPL3 and SlTPL4 were the most prominently expressed. To gain insight into the specificity of the different TOPLESS paralogues, a protein–protein interaction map between TOPLESS and auxin/indole-3-acetic acid (Aux/IAA) proteins was built using a yeast two-hybrid approach. The PPI map enabled the distinction of two patterns: TOPLESS isoforms interacting with the majority of Aux/IAA, and isoforms with limited capacity for interaction with these protein partners. Interestingly, evolutionary analyses of the TOPLESS gene family revealed that the highly expressed isoforms (SlTPL1, SlTPL3, and SlTPL4) corresponded to the three TPL-related genes undergoing the strongest purifying selection, while the selection was much weaker for SlTPL6, which was expressed at a low level and encoded a protein lacking the capacity to interact with Aux/IAAs. PMID:24399174

  6. Assessing Effects and interactions among key variables affecting the growth of mixotrophic microalgae: pH, inoculum volume, and growth medium composition.

    PubMed

    Ale, M T; Pinelo, M; Meyer, A S

    2014-01-01

    A 2(3) + 3 full factorial experimental design was used to evaluate growth rate and biomass productivity of four selected, high-biomass-yielding microalgae species,namely, Chlorella vulgaris (CV), Scenedesmus acutus (SA), Chlamydomonas reinhardtii (CR), and Chlamydomonas debaryana (CD), in mixtures of growth medium (MWC) and wastewater at different proportions (from 20 to 50% of MWC) and at different pH (from 7 to 9). Multilinear regression analysis of the biomass productivity data showed that for SA and CD the biomass productivity was independent of the proportion of medium (MWC), while the growth of CV and CR slowed down in mixtures with high proportions of wastewater. However, the biomass productivity of SA was dependent on pH, while the growth of the other microalgae was independent of pH (7-9). When evaluating the influence of pH and proportion of medium, CD appeared most robust among the algae species, despite its lower biomass productivity. All the four species reduced 80-90% of the nitrate [Formula: see text] and 60-70% of the ammonia [Formula: see text] initially present in the wastewater:medium mixture, although the extent of the reduction was dependent on the initial [Formula: see text] ratio. Both SA and CV reduced ?20-25% of the chemical oxygen demand (COD) contained in the wastewater. This study shows the remarkable influence of certain variables that are often ignored in the search for optimal conditions of microalgal growth and also reveals the importance of considering interactions among growth variables in potential applications at large scale, particularly in the field of bioremediation. PMID:24274013

  7. Identification of Age-Related Macular Degeneration Related Genes by Applying Shortest Path Algorithm in Protein-Protein Interaction Network

    PubMed Central

    Zhang, Jian; Jiang, Min; Yuan, Fei; Feng, Kai-Yan; Cai, Yu-Dong; Xu, Xun; Chen, Lei

    2013-01-01

    This study attempted to find novel age-related macular degeneration (AMD) related genes based on 36 known AMD genes. The well-known shortest path algorithm, Dijkstra's algorithm, was applied to find the shortest path connecting each pair of known AMD related genes in protein-protein interaction (PPI) network. The genes occurring in any shortest path were considered as candidate AMD related genes. As a result, 125 novel AMD genes were predicted. The further analysis based on betweenness and permutation test indicates that there are 10 genes involved in the formation or development of AMD and may be the actual AMD related genes with high probability. We hope that this contribution would promote the study of age-related macular degeneration and discovery of novel effective treatments. PMID:24455700

  8. A reversible Renilla luciferase protein complementation assay for rapid identification of protein–protein interactions reveals the existence of an interaction network involved in xyloglucan biosynthesis in the plant Golgi apparatus

    PubMed Central

    Lund, Christian H.; Bromley, Jennifer R.; Stenbæk, Anne; Rasmussen, Randi E.; Scheller, Henrik V.; Sakuragi, Yumiko

    2015-01-01

    A growing body of evidence suggests that protein–protein interactions (PPIs) occur amongst glycosyltransferases (GTs) required for plant glycan biosynthesis (e.g. cell wall polysaccharides and N-glycans) in the Golgi apparatus, and may control the functions of these enzymes. However, identification of PPIs in the endomembrane system in a relatively fast and simple fashion is technically challenging, hampering the progress in understanding the functional coordination of the enzymes in Golgi glycan biosynthesis. To solve the challenges, we adapted and streamlined a reversible Renilla luciferase protein complementation assay (Rluc-PCA), originally reported for use in human cells, for transient expression in Nicotiana benthamiana. We tested Rluc-PCA and successfully identified luminescence complementation amongst Golgi-localizing GTs known to form a heterodimer (GAUT1 and GAUT7) and those which homooligomerize (ARAD1). In contrast, no interaction was shown between negative controls (e.g. GAUT7, ARAD1, IRX9). Rluc-PCA was used to investigate PPIs amongst Golgi-localizing GTs involved in biosynthesis of hemicelluloses. Although no PPI was identified among six GTs involved in xylan biosynthesis, Rluc-PCA confirmed three previously proposed interactions and identified seven novel PPIs amongst GTs involved in xyloglucan biosynthesis. Notably, three of the novel PPIs were confirmed by a yeast-based split-ubiquitin assay. Finally, Gateway-enabled expression vectors were generated, allowing rapid construction of fusion proteins to the Rluc reporters and epitope tags. Our results show that Rluc-PCA coupled with transient expression in N. benthamiana is a fast and versatile method suitable for analysis of PPIs between Golgi resident proteins in an easy and mid-throughput fashion in planta. PMID:25326916

  9. A reversible Renilla luciferase protein complementation assay for rapid identification of protein-protein interactions reveals the existence of an interaction network involved in xyloglucan biosynthesis in the plant Golgi apparatus.

    PubMed

    Lund, Christian H; Bromley, Jennifer R; Stenbæk, Anne; Rasmussen, Randi E; Scheller, Henrik V; Sakuragi, Yumiko

    2015-01-01

    A growing body of evidence suggests that protein-protein interactions (PPIs) occur amongst glycosyltransferases (GTs) required for plant glycan biosynthesis (e.g. cell wall polysaccharides and N-glycans) in the Golgi apparatus, and may control the functions of these enzymes. However, identification of PPIs in the endomembrane system in a relatively fast and simple fashion is technically challenging, hampering the progress in understanding the functional coordination of the enzymes in Golgi glycan biosynthesis. To solve the challenges, we adapted and streamlined a reversible Renilla luciferase protein complementation assay (Rluc-PCA), originally reported for use in human cells, for transient expression in Nicotiana benthamiana. We tested Rluc-PCA and successfully identified luminescence complementation amongst Golgi-localizing GTs known to form a heterodimer (GAUT1 and GAUT7) and those which homooligomerize (ARAD1). In contrast, no interaction was shown between negative controls (e.g. GAUT7, ARAD1, IRX9). Rluc-PCA was used to investigate PPIs amongst Golgi-localizing GTs involved in biosynthesis of hemicelluloses. Although no PPI was identified among six GTs involved in xylan biosynthesis, Rluc-PCA confirmed three previously proposed interactions and identified seven novel PPIs amongst GTs involved in xyloglucan biosynthesis. Notably, three of the novel PPIs were confirmed by a yeast-based split-ubiquitin assay. Finally, Gateway-enabled expression vectors were generated, allowing rapid construction of fusion proteins to the Rluc reporters and epitope tags. Our results show that Rluc-PCA coupled with transient expression in N. benthamiana is a fast and versatile method suitable for analysis of PPIs between Golgi resident proteins in an easy and mid-throughput fashion in planta. PMID:25326916

  10. Interaction Interaction

    E-print Network

    Hehner, Eric C.R.

    Interaction 1/54 #12;Interaction shared variables 2/54 #12;Interaction shared variables can be read and written by any process (most interaction) 3/54 #12;Interaction shared variables can be read and written by any process (most interaction) difficult to implement 4/54 #12;Interaction shared variables can

  11. A VSS identification scheme for time-varying parameters

    Microsoft Academic Search

    Jian-Xin Xu; Ya-Jun Pan; Tong-Heng Lee

    2003-01-01

    Based on variable structure system theory and sliding mode, we develop an identification scheme suitable for time-varying parameters. The new identification scheme, working in closed-loop, addresses several key issues in system identification simultaneously: unstable process, highly nonlinear and uncertain dynamics, fast time varying parameters and rational nonlinear in the parametric space. Other important issues associated with identification, such as the

  12. Fragment-based identification of an inducible binding site on cell surface receptor CD44 for the design of protein-carbohydrate interaction inhibitors.

    PubMed

    Liu, Li-Kai; Finzel, Barry C

    2014-03-27

    Selective inhibitors of hyaluronan (HA) binding to the cell surface receptor CD44 will have value as probes of CD44-mediated signaling and have potential as therapeutic agents in chronic inflammation, cardiovascular disease, and cancer. Using biophysical binding assays, fragment screening, and crystallographic characterization of complexes with the CD44 HA binding domain, we have discovered an inducible pocket adjacent to the HA binding groove into which small molecules may bind. Iterations of fragment combination and structure-driven design have allowed identification of a series of 1,2,3,4-tetrahydroisoquinolines as the first nonglycosidic inhibitors of the CD44-HA interaction. The affinity of these molecules for the CD44 HA binding domain parallels their ability to interfere with CD44 binding to polymeric HA in vitro. X-ray crystallographic complexes of lead compounds are described and compared to a new complex with a short HA tetrasaccharide, to establish the tetrahydroisoquinoline pharmacophore as an attractive starting point for lead optimization. PMID:24606063

  13. Semi-Automated Identification of N-Glycopeptides by Hydrophilic Interaction Chromatography, nano-Reverse-Phase LC-MS/MS, and Glycan Database Search

    PubMed Central

    Pompach, Petr; Chandler, Kevin B.; Lan, Renny; Edwards, Nathan; Goldman, Radoslav

    2012-01-01

    Glycoproteins fulfill many indispensable biological functions and changes in protein glycosylation have been observed in various diseases. Improved analytical methods are needed to allow a complete characterization of this complex and common posttranslational modification. In this study, we present a workflow for the analysis of the microheterogeneity of N-glycoproteins which couples hydrophilic interaction and nano-reverse-phase C18 chromatography to tandem QTOF mass spectrometric analysis. A glycan database search program, GlycoPeptideSearch, was developed to match N-glycopeptide MS/MS spectra with the glycopeptides comprised of a glycan drawn from the GlycomeDB glycan structure database and a peptide from a user-specified set of potentially glycosylated peptides. Application of the workflow to human haptoglobin and hemopexin, two microheterogeneous N-glycoproteins, identified a total of 57 distinct site-specific glycoforms in the case of haptoglobin and 14 site-specific glycoforms of hemopexin. Using glycan oxonium ions, peptide-characteristic glycopeptide fragment ions, and by collapsing topologically redundant glycans, the search software was able to make unique N-glycopeptide assignments for 51% of assigned spectra, with the remaining assignments primarily representing isobaric topological rearrangements. The optimized workflow, coupled with GlycoPeptideSearch, is expected to make high-throughput semi-automated glycopeptide identification feasible for a wide range of users. PMID:22239659

  14. Identification, expression and interaction analyses of calcium-dependent protein kinase (CPK) genes in canola (Brassica napus L.)

    PubMed Central

    2014-01-01

    Background Canola (Brassica napus L.) is one of the most important oil-producing crops in China and worldwide. The yield and quality of canola is frequently threatened by environmental stresses including drought, cold and high salinity. Calcium is a well-known ubiquitous intracellular secondary messenger in plants. Calcium-dependent protein kinases (CPKs) are Ser/Thr protein kinases found only in plants and some protozoans. CPKs are Ca2+ sensors that have both Ca2+ sensing function and kinase activity within a single protein and play crucial roles in plant development and responses to various environmental stresses. Results In this study, we mined the available expressed sequence tags (ESTs) of B. napus and identified a total of 25 CPK genes, among which cDNA sequences of 23 genes were successfully cloned from a double haploid cultivar of canola. Phylogenetic analysis demonstrated that they could be clustered into four subgroups. The subcellular localization of five selected BnaCPKs was determined using green fluorescence protein (GFP) as the reporter. Furthermore, the expression levels of 21 BnaCPK genes in response to salt, drought, cold, heat, abscisic acid (ABA), low potassium (LK) and oxidative stress were studied by quantitative RT-PCR and were found to respond to multiple stimuli, suggesting that canola CPKs may be convergence points of different signaling pathways. We also identified and cloned five and eight Clade A basic leucine zipper (bZIP) and protein phosphatase type 2C (PP2C) genes from canola and, using yeast two-hybrid and bimolecular fluorescence complementation (BiFC), determined the interaction between individual BnaCPKs and BnabZIPs or BnaPP2Cs (Clade A). We identified novel, interesting interaction partners for some of the BnaCPK proteins. Conclusion We present the sequences and characterization of CPK gene family members in canola for the first time. This work provides a foundation for further crop improvement and improved understanding of signal transduction in plants. PMID:24646378

  15. Amino acid-dependent growth of Campylobacter jejuni : key roles for aspartase (AspA) under microaerobic and oxygen-limited conditions and identification of AspB (Cj0762), essential for growth on glutamate

    Microsoft Academic Search

    Edward Guccione; Maria del Rocio Leon-Kempis; Bruce M. Pearson; Edward Hitchin; Francis Mulholland; Pauline M. van Diemen; Mark P. Stevens; David J. Kelly

    2008-01-01

    Summary Amino acids are key carbon and energy sources for the asaccharolytic food-borne human pathogen Campylobacter jejuni. During microaerobic growth in amino acid rich complex media, aspartate, glutamate, proline and serine are the only amino acids signifi- cantly utilized by strain NCTC 11168. The catabolism of aspartate and glutamate was investigated. An aspartase (aspA) mutant (unable to utilize any amino

  16. Identification of distinct domains for signaling and receptor interaction of the sensory rhodopsin I transducer, HtrI.

    PubMed Central

    Yao, V J; Spudich, E N; Spudich, J L

    1994-01-01

    The phototaxis-deficient mutant of Halobacterium salinarium, Pho81, lacks both sensory rhodopsin I (SR-I) and its putative transducer protein HtrI, according to immunoblotting and spectroscopic criteria. From restriction analysis and selected DNA sequencing, we have determined that the SR-I- HtrI- phenotype results from an insertion of a 520-bp transposable element, ISH2, into the coding region of the SR-I apoprotein gene sopI and deletion of 11 kbp upstream of ISH2 including the first 164 bp of sopI and the entire htrI gene. SR-I and HtrI expression as well as full phototaxis sensitivity are restored by transformation with a halobacterial plasmid carrying the htrI-sopI gene pair and their upstream promoter region. An internal deletion of a portion of htrI encoding the putative methylation and signaling domains of HtrI (253 residues) prevents the restoration of phototaxis, providing further evidence for the role of HtrI as a transducer for SR-I. Analysis of flash-induced photochemical reactions of SR-I over a range of pH shows that the partially deleted HtrI maintains SR-I interactions sites responsible for modulation of the SR-I photocycle. Images PMID:7961454

  17. Cross-target view to feature selection: identification of molecular interaction features in ligand-target space.

    PubMed

    Niijima, Satoshi; Yabuuchi, Hiroaki; Okuno, Yasushi

    2011-01-24

    There is growing interest in computational chemogenomics, which aims to identify all possible ligands of all target families using in silico prediction models. In particular, kernel methods provide a means of integrating compounds and proteins in a principled manner and enable the exploration of ligand-target binding on a genomic scale. To better understand the link between ligands and targets, it is of fundamental interest to identify molecular interaction features that contribute to prediction of ligand-target binding. To this end, we describe a feature selection approach based on kernel dimensionality reduction (KDR) that works in a ligand-target space defined by kernels. We further propose an efficient algorithm to overcome a computational bottleneck and thereby provide a useful general approach to feature selection for chemogenomics. Our experiment on cytochrome P450 (CYP) enzymes has shown that the algorithm is capable of identifying predictive features, as well as prioritizing features that are indicative of ligand preference for a given target family. We further illustrate its applicability on the mutation data of HIV protease by identifying influential mutated positions within protease variants. These results suggest that our approach has the potential to uncover the molecular basis for ligand selectivity and off-target effects. PMID:21142044

  18. Identification and characterisation of the RalA-ERp57 interaction: evidence for GDI activity of ERp57.

    PubMed

    Brymora, Adam; Duggin, Iain G; Berven, Leise A; van Dam, Ellen M; Roufogalis, Basil D; Robinson, Phillip J

    2012-01-01

    RalA is a membrane-associated small GTPase that regulates vesicle trafficking. Here we identify a specific interaction between RalA and ERp57, an oxidoreductase and signalling protein. ERp57 bound specifically to the GDP-bound form of RalA, but not the GTP-bound form, and inhibited the dissociation of GDP from RalA in vitro. These activities were inhibited by reducing agents, but no disulphide bonds were detected between RalA and ERp57. Mutation of all four of ERp57's active site cysteine residues blocked sensitivity to reducing agents, suggesting that redox-dependent conformational changes in ERp57 affect binding to RalA. Mutations in the switch II region of the GTPase domain of RalA specifically reduced or abolished binding to ERp57, but did not block GTP-specific binding to known RalA effectors, the exocyst and RalBP1. Oxidative treatment of A431 cells with H(2)O(2) inhibited cellular RalA activity, and the effect was exacerbated by expression of recombinant ERp57. The oxidative treatment significantly increased the amount of RalA localised to the cytosol. These findings suggest that ERp57 regulates RalA signalling by acting as a redox-sensitive guanine-nucleotide dissociation inhibitor (RalGDI). PMID:23226417

  19. Identification and preliminary characterization of saliva-interacting surface antigens of Streptococcus mutans by immunoblotting, ligand blotting, and immunoprecipitation.

    PubMed Central

    Ogier, J A; Klein, J P; Sommer, P; Frank, R M

    1984-01-01

    The ability of surface protein antigens of Streptococcus mutans to interact with salivary components was examined by Western blot and immunoprecipitation methods. Immunoblotting of S. mutans OMZ175 wall-associated antigens revealed 10 major antigens, designated according to their estimated molecular weights. Four of them, with molecular weights of 135,000, 125,000, 120,000, and 115,000 in their denaturated form, bound salivary components. This property was further investigated by immunoprecipitation experiments: the reactivity with saliva was confirmed for antigens with molecular weights of 135,000, 125,000, and 120,000 in their native form, and their locations on the bacterial cell surface were established. These three antigens were characterized as glycoproteins; they directly bound concanavalin A, and pronase abolished their antigenicity, which was partly retained after treatment with NaIO4. Because of their distribution in several other stains of S. mutans, it will be of interest to study their possible implication in the mechanism of attachment of streptococcal strains to saliva-coated tooth surfaces. Images PMID:6735462

  20. Identification and Characterisation of the RalA-ERp57 Interaction: Evidence for GDI Activity of ERp57

    PubMed Central

    Berven, Leise A.; van Dam, Ellen M.; Roufogalis, Basil D.; Robinson, Phillip J.

    2012-01-01

    RalA is a membrane-associated small GTPase that regulates vesicle trafficking. Here we identify a specific interaction between RalA and ERp57, an oxidoreductase and signalling protein. ERp57 bound specifically to the GDP-bound form of RalA, but not the GTP-bound form, and inhibited the dissociation of GDP from RalA in vitro. These activities were inhibited by reducing agents, but no disulphide bonds were detected between RalA and ERp57. Mutation of all four of ERp57’s active site cysteine residues blocked sensitivity to reducing agents, suggesting that redox-dependent conformational changes in ERp57 affect binding to RalA. Mutations in the switch II region of the GTPase domain of RalA specifically reduced or abolished binding to ERp57, but did not block GTP-specific binding to known RalA effectors, the exocyst and RalBP1. Oxidative treatment of A431 cells with H2O2 inhibited cellular RalA activity, and the effect was exacerbated by expression of recombinant ERp57. The oxidative treatment significantly increased the amount of RalA localised to the cytosol. These findings suggest that ERp57 regulates RalA signalling by acting as a redox-sensitive guanine-nucleotide dissociation inhibitor (RalGDI). PMID:23226417

  1. Molecular identification and interaction assay of the gene (OsUbc13) encoding a ubiquitin-conjugating enzyme in rice*

    PubMed Central

    Wang, Ya; Xu, Meng-yun; Liu, Jian-ping; Wang, Mu-gui; Yin, Hai-qing; Tu, Ju-min

    2014-01-01

    The ubiquitin (Ub)-conjugating enzyme, Ubc13, has been known to be involved in error-free DNA damage tolerance (or post-replication repair) via catalyzing Lys63-linked polyubiquitin chains formation together with a Ubc variant. However, its functions remain largely unknown in plant species, especially in monocotyledons. In this study, we cloned a Ub-conjugating enzyme, OsUbc13, that shares the conserved domain of Ubc with AtUBC13B in Oryza sativa L., which encodes a protein of 153 amino acids; the deduced sequence shares high similarities with other homologs. Real-time quantitative polymerase chain reaction (PCR) indicated that OsUbc13 transcripts could be detected in all tissues examined, and the expression level was higher in palea, pistil, stamen, and leaf, and lower in root, stem, and lemma; the expression of OsUbc13 was induced by low temperature, methylmethane sulfate (MMS), and H2O2, but repressed by mannitol, abscisic acid (ABA), and NaCl. OsUbc13 was probably localized in the plasma and nuclear membranes. About 20 proteins, which are responsible for the positive yeast two-hybrid interaction of OsUbc13, were identified. These include the confirmed OsVDAC (correlated with apoptosis), OsMADS1 (important for development of floral organs), OsB22EL8 (related to reactive oxygen species (ROS) scavenging and DNA protection), and OsCROC-1 (required for formation of Lys63 polyubiquitylation and error-free DNA damage tolerance). The molecular characterization provides a foundation for the functional study of OsUbc13. PMID:25001222

  2. Identification of an in Vitro Interaction between an Insect Immune Suppressor Protein (CrV2) and G? Proteins*

    PubMed Central

    Cooper, Tamara H.; Bailey-Hill, Kelly; Leifert, Wayne R.; McMurchie, Edward J.; Asgari, Sassan; Glatz, Richard V.

    2011-01-01

    The protein CrV2 is encoded by a polydnavirus integrated into the genome of the endoparasitoid Cotesia rubecula (Hymenoptera:Braconidae:Microgastrinae) and is expressed in host larvae with other gene products of the polydnavirus to allow successful development of the parasitoid. CrV2 expression has previously been associated with immune suppression, although the molecular basis for this was not known. Here, we have used time-resolved Förster resonance energy transfer (TR-FRET) to demonstrate high affinity binding of CrV2 to G? subunits (but not the G?? dimer) of heterotrimeric G-proteins. Signals up to 5-fold above background were generated, and an apparent dissociation constant of 6.2 nm was calculated. Protease treatment abolished the TR-FRET signal, and the presence of unlabeled CrV2 or G? proteins also reduced the TR-FRET signal. The activation state of the G? subunit was altered with aluminum fluoride, and this decreased the affinity of the interaction with CrV2. It was also demonstrated that CrV2 preferentially bound to Drosophila G?o compared with rat G?i1. In addition, three CrV2 homologs were detected in sequences derived from polydnaviruses from Cotesia plutellae and Cotesia congregata (including the immune-related early expressed transcript, EP2). These data suggest a potential mode-of-action of immune suppressors not previously reported, which in addition to furthering our understanding of insect immunity may have practical benefits such as facilitating development of novel controls for pest insect species. PMID:21233205

  3. Identification of guanine nucleotide exchange factors (GEFs) for the Rap1 GTPase. Regulation of MR-GEF by M-Ras-GTP interaction.

    PubMed

    Rebhun, J F; Castro, A F; Quilliam, L A

    2000-11-10

    Although the Ras subfamily of GTPases consists of approximately 20 members, only a limited number of guanine nucleotide exchange factors (GEFs) that couple extracellular stimuli to Ras protein activation have been identified. Furthermore, no novel downstream effectors have been identified for the M-Ras/R-Ras3 GTPase. Here we report the identification and characterization of three Ras family GEFs that are most abundantly expressed in brain. Two of these GEFs, MR-GEF (M-Ras-regulated GEF, KIAA0277) and PDZ-GEF (KIAA0313) bound specifically to nucleotide-free Rap1 and Rap1/Rap2, respectively. Both proteins functioned as Rap1 GEFs in vivo. A third GEF, GRP3 (KIAA0846), activated both Ras and Rap1 and shared significant sequence homology with the calcium- and diacylglycerol-activated GEFs, GRP1 and GRP2. Similarly to previously identified Rap GEFs, C3G and Smg GDS, each of the newly identified exchange factors promoted the activation of Elk-1 in the LNCaP prostate tumor cell line where B-Raf can couple Rap1 to the extracellular receptor-activated kinase cascade. MR-GEF and PDZ-GEF both contain a region immediately N-terminal to their catalytic domains that share sequence homology with Ras-associating or RalGDS/AF6 homology (RA) domains. By searching for in vitro interaction with Ras-GTP proteins, PDZ-GEF specifically bound to Rap1A- and Rap2B-GTP, whereas MR-GEF bound to M-Ras-GTP. C-terminally truncated MR-GEF, lacking the GEF catalytic domain, retained its ability to bind M-Ras-GTP, suggesting that the RA domain is important for this interaction. Co-immunoprecipitation studies confirmed the interaction of M-Ras-GTP with MR-GEF in vivo. In addition, a constitutively active M-Ras(71L) mutant inhibited the ability of MR-GEF to promote Rap1A activation in a dose-dependent manner. These data suggest that M-Ras may inhibit Rap1 in order to elicit its biological effects. PMID:10934204

  4. 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-activated STAT5 proteins. Our theoretical prediction based on results obtained with MONETA was validated for KIT by in vitro experiments. MONETA is a versatile analytical and visualization tool entirely devoted to the understanding of the functioning/malfunctioning of allosteric regulation in proteins - a crucial basis to guide the discovery of next-generation allosteric drugs. PMID:25340971

  5. Modular Connector Keying Concept

    NASA Technical Reports Server (NTRS)

    Ishman, Scott; Dukes, Scott; Warnica, Gary; Conrad, Guy; Senigla, Steven

    2013-01-01

    For panel-mount-type connectors, keying is usually "built-in" to the connector body, necessitating different part numbers for each key arrangement. This is costly for jobs that require small quantities. This invention was driven to provide a cost savings and to reduce documentation of individual parts. The keys are removable and configurable in up to 16 combinations. Since the key parts are separate from the connector body, a common design can be used for the plug, receptacle, and key parts. The keying can then be set at the next higher assembly.

  6. Group key management

    SciTech Connect

    Dunigan, T.; Cao, C.

    1997-08-01

    This report describes an architecture and implementation for doing group key management over a data communications network. The architecture describes a protocol for establishing a shared encryption key among an authenticated and authorized collection of network entities. Group access requires one or more authorization certificates. The implementation includes a simple public key and certificate infrastructure. Multicast is used for some of the key management messages. An application programming interface multiplexes key management and user application messages. An implementation using the new IP security protocols is postulated. The architecture is compared with other group key management proposals, and the performance and the limitations of the implementation are described.

  7. An Interactive Guide to Massachusetts Snakes

    NSDL National Science Digital Library

    Haver, Nancy.

    This wonderful site is more than a State guide to snakes. Provided by University of Massachusetts Extension, the Website includes a well-written introduction to snake biology, a history of snakes (mythology and reality), information on the conservation of snakes, and even a discussion of snake phobias. The heart of the site is the interactive dichotomous key for snake identification, however, where the user may select between two options to proceed towards a positive identification. The snake key is beautifully illustrated, with color paintings and drawings of fourteen species -- ranging from Black Racer to Worm Snake. Beginning students to seasoned researchers will find this well-conceived, informative resource both useful and pleasing.

  8. Crystal structures of resorcin[4]arene and pyrogallol[4]arene complexes with DL-pipecolinic acid. Model compounds for the recognition of the pipecolinyl ring, a key fragment of FK506, through C-H⋯? interaction

    NASA Astrophysics Data System (ADS)

    Fujisawa, Ikuhide; Kitamura, Yuji; Kato, Ryo; Murayama, Kazutaka; Aoki, Katsuyuki

    2014-01-01

    Resorcin[4]arene (resorcinol cyclic tetramer, abbreviated as RCT) or pyrogallol[4]arene (pyrogallol cyclic tetramer, PCT) form host-guest 1:1 complexes with DL-pipecolinic acid (DL-pipeH), RCT·DL-pipeH·EtOH·8H2O (1), PCT DL-pipeH·EtOH·4H2O (2), and PCT·DL-pipeH·3H2O (3), whose crystal structures have been determined. In each complex, the pipeH ligand is incorporated into the bowl-shaped cavity of the RCT or PCT host molecules through C-H⋯? interactions between alkyl protons of the piperidine ring of pipeH and ?-rings of RCT or PCT, forming an [(RCT/PCT)·pipeH] structural fragment. In 1 and 3, two [(RCT/PCT) pipeH] fragments self-associate across an inversion center to form a guest-mediated, obliquely declined dimeric structure [(RCT/PCT)·L-pipeH·D-pipeH (RCT/PCT)]. In 2, each PCT-capped pipeH ligand bridges to two adjacent PCT molecules to form guest-mediated, optically-discrete helical polymers [PCT·L-pipeH]n or [PCT·D-pipeH]n. An 1H NMR experiment shows that the complexation through C-H⋯? interaction between the piperidine ring of pipeH and ?-rings of RCT or PCT occurs also in solution, with the binding constants of 9.7 ± 0.6 M-1 for RCT and 26.5 ± 1.5 M-1 for PCT. These complexes provide a synthetic model for the recognition of the pipecolinyl-ring moiety, a key constituent of immunosuppressant drugs such as FK506, FK520 or rapamycin, by their binding proteins through C-H⋯? interaction.

  9. Bunch identification module

    SciTech Connect

    Fox, J.D.

    1981-01-01

    This module provides bunch identification and timing signals for the PEP Interaction areas. Timing information is referenced to the PEP master oscillator, and adjusted in phase as a function of region. Identification signals are generated in a manner that allows observers in all interaction regions to agree on an unambiguous bunch identity. The module provides bunch identification signals via NIM level logic, upon CAMAC command, and through LED indicators. A front panel ''region select'' switch allows the same module to be used in all regions. The module has two modes of operation: a bunch identification mode and a calibration mode. In the identification mode, signals indicate which of the three bunches of electrons and positrons are interacting, and timing information about beam crossing is provided. The calibration mode is provided to assist experimenters making time of flight measurements. In the calibration mode, three distinct gating signals are referenced to a selected bunch, allowing three timing systems to be calibrated against a common standard. Physically, the bunch identifier is constructed as a single width CAMAC module. 2 figs., 1 tab.

  10. Public Key Cryptography.

    ERIC Educational Resources Information Center

    Tapson, Frank

    1996-01-01

    Describes public key cryptography, also known as RSA, which is a system using two keys, one used to put a message into cipher and another used to decipher the message. Presents examples using small prime numbers. (MKR)

  11. Certificateless Public Key Cryptography

    Microsoft Academic Search

    Sattam S. Al-riyami; Kenneth G. Paterson

    2003-01-01

    This paper introduces and makes concrete the concept of certiflcateless public key cryptography (CL-PKC), a model for the use of public key cryp- tography which avoids the inherent escrow of identity-based cryptography and yet which does not require certiflcates to guarantee the authenticity of public keys. The lack of certiflcates and the presence of an adversary who has access to

  12. Key Process Benchmarking for Continuous Improvement in Higher Education.

    ERIC Educational Resources Information Center

    Stewart, Robert Grisham

    The objectives of this study were identification and verification of key processes that could be used by higher education quality administrators to implement continuous improvement programs and benchmarking processes. East Tennessee State University's Continuous Improvement Key Process Relationship Matrix was used as the basis of a 44-item…

  13. The degradation (by distinct pathways) of human D-amino acid oxidase and its interacting partner pLG72--two key proteins in D-serine catabolism in the brain.

    PubMed

    Cappelletti, Pamela; Campomenosi, Paola; Pollegioni, Loredano; Sacchi, Silvia

    2014-02-01

    Human D-amino acid oxidase (EC 1.4.3.3; hDAAO) is a peroxisomal flavoenzyme significantly enriched in the mammalian brain. hDAAO has been proposed to play (with serine racemase; EC 5.1.1.18) an essential role in the catabolism of D-serine, an 'atypical' key signalling molecule that acts as allosteric activator of the N-methyl-D-aspartate-type glutamate receptor (NMDAr). hDAAO and its interacting partner pLG72 have been related to schizophrenia, a highly disabling psychiatric disorder in which a dysfunction of NMDA-mediated neurotransmission is widely assumed to occur. We previously demonstrated that the D-serine cellular concentration depends on hDAAO and pLG72 expression levels and that newly-synthesized hDAAO interacts with its modulator in the cytosol, being progressively destabilized and inactivated. To obtain insight into the mechanisms regulating cellular D-serine levels, we investigated the degradation pathways of hDAAO and pLG72 in U87 glioblastoma cells stably expressing enhanced yellow fluorescent protein-hDAAO (peroxisomal), hDAAO-enhanced yellow fluorescent protein (cytosolic) or pLG72-enhanced cyan fluorescent protein (mitochondrial) proteins. hDAAO is a long-lived protein: the peroxisomal fraction of this flavoprotein is degraded via the lysosomal/endosomal pathway (and blocking this pathway increases the cellular hDAAO activity and decreases D-serine levels), whereas the cytosolic portion is ubiquitinated and targeted to the proteasome. By contrast, pLG72 shows a rapid turnover (t(1/2) ? 25-40 min) and is degraded via the proteasome system, albeit not ubiquitinated. Overexpression of pLG72 increases the turnover of hDAAO, in turn playing a protective role against excessive D-serine depletion. PMID:24237903

  14. The "Key" Method of Identifying Igneous and Metamorphic Rocks in Introductory Laboratory.

    ERIC Educational Resources Information Center

    Eves, Robert Leo; Davis, Larry Eugene

    1987-01-01

    Proposes that identification keys provide an orderly strategy for the identification of igneous and metamorphic rocks in an introductory geology course. Explains the format employed in the system and includes the actual key guides for both igneous and metamorphic rocks. (ML)

  15. Identifying key sources of uncertainty in the modelling of greenhouse gas emissions from wastewater treatment.

    PubMed

    Sweetapple, Christine; Fu, Guangtao; Butler, David

    2013-09-01

    This study investigates sources of uncertainty in the modelling of greenhouse gas emissions from wastewater treatment, through the use of local and global sensitivity analysis tools, and contributes to an in-depth understanding of wastewater treatment modelling by revealing critical parameters and parameter interactions. One-factor-at-a-time sensitivity analysis is used to screen model parameters and identify those with significant individual effects on three performance indicators: total greenhouse gas emissions, effluent quality and operational cost. Sobol's method enables identification of parameters with significant higher order effects and of particular parameter pairs to which model outputs are sensitive. Use of a variance-based global sensitivity analysis tool to investigate parameter interactions enables identification of important parameters not revealed in one-factor-at-a-time sensitivity analysis. These interaction effects have not been considered in previous studies and thus provide a better understanding wastewater treatment plant model characterisation. It was found that uncertainty in modelled nitrous oxide emissions is the primary contributor to uncertainty in total greenhouse gas emissions, due largely to the interaction effects of three nitrogen conversion modelling parameters. The higher order effects of these parameters are also shown to be a key source of uncertainty in effluent quality. PMID:23770480

  16. eFloras.org: ActKey

    NSDL National Science Digital Library

    Provided by the Harvard University Herbarium, ActKey allows visitors to locate and use a key for identifying an unknown specimen. As is noted on the site, "ActKey was developed to enable ready-access to on-line interactive keys. The program is web-based. Common Internet browsers may be used to access the interface." Thus, by visiting the site, users can choose from over five pages of keys, ranging from Aceraceae to Urticaceae. Once at a key, the user is queried for information such as: habit, stems, leaves, stipules, petiole, leaf blade, and more. In the end, you will hopefully have pinned down your specimen to a specific species. Definitely a great site for the recreational botanist, students, and researchers.

  17. Identification of Keratinocyte Growth Factor as a Target of microRNA-155 in Lung Fibroblasts: Implication in Epithelial-Mesenchymal Interactions

    PubMed Central

    Chevalier, Benoit; Puisségur, Marie-Pierre; Lebrigand, Kevin; Robbe-Sermesant, Karine; Bertero, Thomas; Lino Cardenas, Christian L.; Courcot, Elisabeth; Rios, Géraldine; Fourre, Sandra; Lo-Guidice, Jean-Marc; Marcet, Brice; Cardinaud, Bruno; Barbry, Pascal; Mari, Bernard

    2009-01-01

    Background Epithelial-mesenchymal interactions are critical in regulating many aspects of vertebrate embryo development, and for the maintenance of homeostatic equilibrium in adult tissues. The interactions between epithelium and mesenchyme are believed to be mediated by paracrine signals such as cytokines and extracellular matrix components secreted from fibroblasts that affect adjacent epithelia. In this study, we sought to identify the repertoire of microRNAs (miRNAs) in normal lung human fibroblasts and their potential regulation by the cytokines TNF-?, IL-1? and TGF-?. Methodology/Principal Findings MiR-155 was significantly induced by inflammatory cytokines TNF-? and IL-1? while it was down-regulated by TGF-?. Ectopic expression of miR-155 in human fibroblasts induced modulation of a large set of genes related to “cell to cell signalling”, “cell morphology” and “cellular movement”. This was consistent with an induction of caspase-3 activity and with an increase in cell migration in fibroblasts tranfected with miR-155. Using different miRNA bioinformatic target prediction tools, we found a specific enrichment for miR-155 predicted targets among the population of down-regulated transcripts. Among fibroblast-selective targets, one interesting hit was keratinocyte growth factor (KGF, FGF-7), a member of the fibroblast growth factor (FGF) family, which owns two potential binding sites for miR-155 in its 3?-UTR. Luciferase assays experimentally validated that miR-155 can efficiently target KGF 3?-UTR. Site-directed mutagenesis revealed that only one out of the 2 potential sites was truly functional. Functional in vitro assays experimentally validated that miR-155 can efficiently target KGF 3?-UTR. Furthermore, in vivo experiments using a mouse model of lung fibrosis showed that miR-155 expression level was correlated with the degree of lung fibrosis. Conclusions/Significance Our results strongly suggest a physiological function of miR-155 in lung fibroblasts. Altogether, this study implicates this miRNA in the regulation by mesenchymal cells of surrounding lung epithelium, making it a potential key player during tissue injury. PMID:19701459

  18. Construction of a High-Quality Yeast Two-Hybrid Library and Its Application in Identification of Interacting Proteins with Brn1 in Curvularia lunata

    PubMed Central

    Gao, Jin-Xin; Jing, Jing; Yu, Chuan-Jin; Chen, Jie

    2015-01-01

    Curvularia lunata is an important maize foliar fungal pathogen that distributes widely in maize growing area in China, and several key pathogenic factors have been isolated. An yeast two-hybrid (Y2H) library is a very useful platform to further unravel novel pathogenic factors in C. lunata. To construct a high-quality full length-expression cDNA library from the C. lunata for application to pathogenesis-related protein-protein interaction screening, total RNA was extracted. The SMART (Switching Mechanism At 5? end of the RNA Transcript) technique was used for cDNA synthesis. Double-stranded cDNA was ligated into the pGADT7-Rec vector with Herring Testes Carrier DNA using homologous recombination method. The ligation mixture was transformed into competent yeast AH109 cells to construct the primary cDNA library. Eventually, a high qualitative library was successfully established according to an evaluation on quality. The transformation efficiency was about 6.39 ×105 transformants/3 ?g pGADT7-Rec. The titer of the primary cDNA library was 2.5×108 cfu/mL. The numbers for the cDNA library was 2.46×105. Randomly picked clones show that the recombination rate was 88.24%. Gel electrophoresis results indicated that the fragments ranged from 0.4 kb to 3.0 kb. Melanin synthesis protein Brn1 (1,3,8-hydroxynaphthalene reductase) was used as a “bait” to test the sufficiency of the Y2H library. As a result, a cDNA clone encoding VelB protein that was known to be involved in the regulation of diverse cellular processes, including control of secondary metabolism containing melanin and toxin production in many filamentous fungi was identified. Further study on the exact role of the VelB gene is underway.

  19. Construction of a High-Quality Yeast Two-Hybrid Library and Its Application in Identification of Interacting Proteins with Brn1 in Curvularia lunata.

    PubMed

    Gao, Jin-Xin; Jing, Jing; Yu, Chuan-Jin; Chen, Jie

    2015-06-01

    Curvularia lunata is an important maize foliar fungal pathogen that distributes widely in maize growing area in China, and several key pathogenic factors have been isolated. An yeast two-hybrid (Y2H) library is a very useful platform to further unravel novel pathogenic factors in C. lunata. To construct a high-quality full length-expression cDNA library from the C. lunata for application to pathogenesis-related protein-protein interaction screening, total RNA was extracted. The SMART (Switching Mechanism At 5' end of the RNA Transcript) technique was used for cDNA synthesis. Double-stranded cDNA was ligated into the pGADT7-Rec vector with Herring Testes Carrier DNA using homologous recombination method. The ligation mixture was transformed into competent yeast AH109 cells to construct the primary cDNA library. Eventually, a high qualitative library was successfully established according to an evaluation on quality. The transformation efficiency was about 6.39 ×10(5) transformants/3 ?g pGADT7-Rec. The titer of the primary cDNA library was 2.5×10(8) cfu/mL. The numbers for the cDNA library was 2.46×10(5). Randomly picked clones show that the recombination rate was 88.24%. Gel electrophoresis results indicated that the fragments ranged from 0.4 kb to 3.0 kb. Melanin synthesis protein Brn1 (1,3,8-hydroxynaphthalene reductase) was used as a "bait" to test the sufficiency of the Y2H library. As a result, a cDNA clone encoding VelB protein that was known to be involved in the regulation of diverse cellular processes, including control of secondary metabolism containing melanin and toxin production in many filamentous fungi was identified. Further study on the exact role of the VelB gene is underway. PMID:26060429

  20. Atsena Otie Key Island

    USGS Multimedia Gallery

    Atsena Otie Key is one of thirteen islands on Florida's Gulf Coast that make up Cedar Keys National Wildlife Refuge. Nearby waters support a multi-million dollar clam-farming industry. USGS documented pre-oil coastal conditions near the Refuge with baseline petrochemical measurements and aerial phot...

  1. Generalized minimum shift keying

    NASA Astrophysics Data System (ADS)

    Korn, I.

    1980-03-01

    A generalized minimum shift keying (GMSK) signal is defined, and its equivalence to a modified offset quadrature shift keying signal is shown. A simple formula for the spectrum of a GMSK signal is presented and the spectrum and out-of-band power are computed for two examples.

  2. Systems pharmacology of the nerve growth factor pathway: use of a systems biology model for the identification of key drug targets using sensitivity analysis and the integration of physiology and pharmacology.

    PubMed

    Benson, Neil; Matsuura, Tomomi; Smirnov, Sergey; Demin, Oleg; Jones, Hannah M; Dua, Pinky; van der Graaf, Piet H

    2013-04-01

    The nerve growth factor (NGF) pathway is of great interest as a potential source of drug targets, for example in the management of certain types of pain. However, selecting targets from this pathway either by intuition or by non-contextual measures is likely to be challenging. An alternative approach is to construct a mathematical model of the system and via sensitivity analysis rank order the targets in the known pathway, with respect to an endpoint such as the diphosphorylated extracellular signal-regulated kinase concentration in the nucleus. Using the published literature, a model was created and, via sensitivity analysis, it was concluded that, after NGF itself, tropomyosin receptor kinase A (TrkA) was one of the most sensitive druggable targets. This initial model was subsequently used to develop a further model incorporating physiological and pharmacological parameters. This allowed the exploration of the characteristics required for a successful hypothetical TrkA inhibitor. Using these systems models, we were able to identify candidates for the optimal drug targets in the known pathway. These conclusions were consistent with clinical and human genetic data. We also found that incorporating appropriate physiological context was essential to drawing accurate conclusions about important parameters such as the drug dose required to give pathway inhibition. Furthermore, the importance of the concentration of key reactants such as TrkA kinase means that appropriate contextual data are required before clear conclusions can be drawn. Such models could be of great utility in selecting optimal targets and in the clinical evaluation of novel drugs. PMID:24427523

  3. Term identification in the biomedical literature

    Microsoft Academic Search

    Michael Krauthammer; Goran Nenadic

    2004-01-01

    Sophisticated information technologies are needed for effective data acquisition and integration from a growing body of the biomedical literature. Successful term identification is key to getting access to the stored literature information, as it is the terms (and their relationships) that convey knowledge across scientific articles. Due to the complexities of a dynamically changing biomedical terminology, term identification has been

  4. PublicPublic--Key EncryptionKey Encryption Public-key, or asymmetric encryption

    E-print Network

    Fisher, Michael

    COMP 522 PublicPublic--Key EncryptionKey Encryption COMP 522 Public-key, or asymmetric encryption Public-key encryption techniques. It is particular and most important kind of Asymmetric encryption (or asymmetric key encryption): · One key is used for encryption (usually publicly known, public key); · Another

  5. Key Regression: Enabling Efficient Key Distribution for Secure Distributed Storage

    Microsoft Academic Search

    Kevin Fu; Seny Kamara; Yoshi Kohno

    2006-01-01

    The Plutus file system introduced the notion of key rotation as a means to derive a sequence of temporally- related keys from the most recent key. In this paper we show that, despite natural intuition to the contrary, key rotation schemes cannot generically be used to key other cryptographic objects; in fact, keying an encryp- tion scheme with the output

  6. Identification and determination of trapping parameters as key site parameters for CO2 storage for the active CO2 storage site in Ketzin (Germany) - Comparison of different experimental approaches and analysis of field data

    NASA Astrophysics Data System (ADS)

    Zemke, Kornelia; Liebscher, Axel

    2015-04-01

    Petrophysical properties like porosity and permeability are key parameters for a safe long-term storage of CO2 but also for the injection operation itself. The accurate quantification of residual trapping is difficult, but very important for both storage containment security and storage capacity; it is also an important parameter for dynamic simulation. The German CO2 pilot storage in Ketzin is a Triassic saline aquifer with initial conditions of the target sandstone horizon of 33.5 ° C/6.1 MPa at 630 m. One injection and two observation wells were drilled in 2007 and nearly 200 m of core material was recovered for site characterization. From June 2008 to September 2013, slightly more than 67 kt food-grade CO2 has been injected and continuously monitored. A fourth observation well has been drilled after 61 kt injected CO2 in summer 2012 at only 25 m distance to the injection well and new core material was recovered that allow study CO2 induced changes in petrophysical properties. The observed only minor differences between pre-injection and post-injection petrophysical parameters of the heterogeneous formation have no severe consequences on reservoir and cap rock integrity or on the injection behavior. Residual brine saturation for the Ketzin reservoir core material was estimated by different methods. Brine-CO2 flooding experiments for two reservoir samples resulted in 36% and 55% residual brine saturation (Kiessling, 2011). Centrifuge capillary pressure measurements (pc = 0.22 MPa) yielded the smallest residual brine saturation values with ~20% for the lower part of the reservoir sandstone and ~28% for the upper part (Fleury, 2010). The method by Cerepi (2002), which calculates the residual mercury saturation after pressure release on the imbibition path as trapped porosity and the retracted mercury volume as free porosity, yielded unrealistic low free porosity values of only a few percent, because over 80% of the penetrated mercury remained in the samples after pressure release to atmospheric pressure. The results from the centrifuge capillary pressure measurements were then used for calibrating the cutoff time of NMR T2 relaxation (average value 8 ms) to differentiate between the mobile and immobile water fraction (standard for clean sandstone 33 ms). Following Norden (2010) a cutoff time of 10 ms was applied to estimate the residual saturation as Bound Fluid Volume for the Ketzin core materials and to estimate NMR permeability after Timur-Coates. This adapted cutoff value is also consistent with results from RST logging after injection. The maximum measured CO2 saturation corresponds to the effective porosity for the upper most CO2 filled sandstone horizon. The directly measured values and the estimated residual brine saturations from NMR measurements with the adapted cutoff time of 10 ms are within the expected range compared to the literature data with a mean residual brine saturation of 53%. A. Cerepi et al., 2002, Journal of Petroleum Science and Engineering 35. M. Fleury et al., 2011, SCA2010-06. D. Kiessling et al., 2010, International Journal of Greenhouse Gas Control 4. B. Norden et al. 2010, SPE Reservoir Evaluation & Engineering 13. .

  7. Central locus for nonspeech context effects on phonetic identification (L)

    E-print Network

    Holt, Lori L.

    Central locus for nonspeech context effects on phonetic identification (L) Andrew J. Lottoa sounds can influence phonetic identification of a target syllable even when the context sounds to conclude that phonetic context effects are mostly due to nonperipheral auditory interactions

  8. SCIENCE MATTERS KEY CHAIN

    NSDL National Science Digital Library

    1900-01-01

    Brushed nickel key chain commemorating the launch of the new Science Matters initiative. Limited edition. All proceeds from the sale of this item go to fund the John Glenn Center for Science Education.

  9. Public-Key Steganography

    Microsoft Academic Search

    Luis Von Ahn; Nicholas J. Hopper

    2004-01-01

    Informally, a public-key steganography protocol allows two parties, who have never met or exchanged a secret, to send hidden mes- sages over a public channel so that an adversary cannot even detect that these hidden messages are being sent. Unlike previous settings in which provable security has been applied to steganography, public-key steganography is information-theoretically impossible. In this work we

  10. Timestamps in key distribution protocols

    Microsoft Academic Search

    Dorothy E. Denning; Giovanni Maria Sacco

    1981-01-01

    The distribution of keys in a computer network using single key or public key encryption is discussed. We consider the possibility that communication keys may be compromised, and show that key distribution protocols with timestamps prevent replays of compromised keys. The timestamps have the additional benefit of replacing a two-step handshake.

  11. Integrative network-based approach identifies key genetic elements in breast invasive carcinoma

    PubMed Central

    2015-01-01

    Background Breast cancer is a genetically heterogeneous type of cancer that belongs to the most prevalent types with a high mortality rate. Treatment and prognosis of breast cancer would profit largely from a correct classification and identification of genetic key drivers and major determinants driving the tumorigenesis process. In the light of the availability of tumor genomic and epigenomic data from different sources and experiments, new integrative approaches are needed to boost the probability of identifying such genetic key drivers. We present here an integrative network-based approach that is able to associate regulatory network interactions with the development of breast carcinoma by integrating information from gene expression, DNA methylation, miRNA expression, and somatic mutation datasets. Results Our results showed strong association between regulatory elements from different data sources in terms of the mutual regulatory influence and genomic proximity. By analyzing different types of regulatory interactions, TF-gene, miRNA-mRNA, and proximity analysis of somatic variants, we identified 106 genes, 68 miRNAs, and 9 mutations that are candidate drivers of oncogenic processes in breast cancer. Moreover, we unraveled regulatory interactions among these key drivers and the other elements in the breast cancer network. Intriguingly, about one third of the identified driver genes are targeted by known anti-cancer drugs and the majority of the identified key miRNAs are implicated in cancerogenesis of multiple organs. Also, the identified driver mutations likely cause damaging effects on protein functions. The constructed gene network and the identified key drivers were compared to well-established network-based methods. Conclusion The integrated molecular analysis enabled by the presented network-based approach substantially expands our knowledge base of prospective genomic drivers of genes, miRNAs, and mutations. For a good part of the identified key drivers there exists solid evidence for involvement in the development of breast carcinomas. Our approach also unraveled the complex regulatory interactions comprising the identified key drivers. These genomic drivers could be further investigated in the wet lab as potential candidates for new drug targets. This integrative approach can be applied in a similar fashion to other cancer types, complex diseases, or for studying cellular differentiation processes. PMID:26040466

  12. Key Biodiversity Areas as Site Conservation Targets

    NSDL National Science Digital Library

    GÃ?VEN EKEN, LEON BENNUN, THOMAS M. BROOKS, WILL DARWALL, LINCOLN D. C. FISHPOOL, MATT FOSTER, DAVID KNOX, PENNY LANGHAMMER, PAUL MATIKU, ELIZABETH RADFORD, PAUL SALAMAN, WES SECHREST, MICHAEL L. SMITH, SACHA SPECTOR, and ANDREW TORDOFF (; )

    2004-12-01

    This peer-reviewed resource from Bioscience journal discusses the concept of key biodiversity areas (KBAs) for use in site conservation. Site conservation is among the most effective means to reduce global biodiversity loss. Therefore, it is critical to identify those sites where unique biodiversity must be conserved immediately. To this end, the concept of key biodiversity areas (KBAs) has been developed, seeking to identify and, ultimately, ensure that networks of globally important sites are safeguarded. This methodology builds up from the identification of species conservation targets (through the IUCN Red List) and nests within larger-scale conservation approaches. Sites are selected using standardized, globally applicable, threshold-based criteria, driven by the distribution and population of species that require site-level conservation. The criteria address the two key issues for setting site conservation priorities: vulnerability and irreplaceability. We also propose quantitative thresholds for the identification of KBAs meeting each criterion, based on a review of existing approaches and ecological theory to date. However, these thresholds require extensive testing, especially in aquatic systems.

  13. Mediated semiquantum key distribution

    NASA Astrophysics Data System (ADS)

    Krawec, Walter O.

    2015-03-01

    In this work, we design a quantum key distribution protocol, allowing two limited semiquantum or "classical" users to establish a shared secret key with the help of a fully quantum server. A semiquantum user can prepare and measure qubits only in the computational basis and so must rely on this quantum server to produce qubits in alternative bases and also to perform alternative measurements. However, we assume that the server is untrusted and we prove the unconditional security of our protocol even in the worst case: when this quantum server is an all-powerful adversary. We also compute a lower bound of the key rate of our protocol, in the asymptotic scenario, as a function of the observed error rate in the channel, allowing us to compute the maximally tolerated error of our protocol. Our results show that a semiquantum protocol may hold similar security to a fully quantum one.

  14. Input from Key Stakeholders in the National Security Technology Incubator

    SciTech Connect

    None

    2008-01-31

    This report documents the input from key stakeholders of the National Security Technology Incubator (NSTI) in developing a new technology incubator and related programs for southern New Mexico. The technology incubator is being developed as part of the National Security Preparedness Project (NSPP), funded by a Department of Energy (DOE)/National Nuclear Security Administration (NNSA) grant. This report includes identification of key stakeholders as well as a description and analysis of their input for the development of an incubator.

  15. Copyright Some Key Questions

    E-print Network

    Ollivier-Gooch, Carl

    #12;#12;Copyright Matters! Some Key Questions and Answers for Teachers 2nd Edition, 2005 From the Authors The authors of Copyright Matters! are pleased to offer teachers this revised edition. It replaces the first edition published in 2000. Many changes have occurred in the area of copyright since that original

  16. Kidnapped in Key West

    NSDL National Science Digital Library

    Kerri Caudill

    2012-07-09

    This lesson is focused on the text Kidnapped in Key West. It integrates Florida history into this historical fiction piece that is rich with complex characters, events and mystery that will captivate every reader. The opportunities for in-depth inquiry both through conversation and writing are limitless. Through writing the students will develop and enhance their writing and language skills.

  17. Cryptographic Key Management System

    SciTech Connect

    No, author

    2014-02-21

    This report summarizes the outcome of U.S. Department of Energy (DOE) contract DE-OE0000543, requesting the design of a Cryptographic Key Management System (CKMS) for the secure management of cryptographic keys for the energy sector infrastructure. Prime contractor Sypris Electronics, in collaboration with Oak Ridge National Laboratories (ORNL), Electric Power Research Institute (EPRI), Valicore Technologies, and Purdue University's Center for Education and Research in Information Assurance and Security (CERIAS) and Smart Meter Integration Laboratory (SMIL), has designed, developed and evaluated the CKMS solution. We provide an overview of the project in Section 3, review the core contributions of all contractors in Section 4, and discuss bene#12;ts to the DOE in Section 5. In Section 6 we describe the technical construction of the CKMS solution, and review its key contributions in Section 6.9. Section 7 describes the evaluation and demonstration of the CKMS solution in different environments. We summarize the key project objectives in Section 8, list publications resulting from the project in Section 9, and conclude with a discussion on commercialization in Section 10 and future work in Section 11.

  18. Selecting Cryptographic Key Sizes

    Microsoft Academic Search

    Arjen K. Lenstra; Eric R. Verheul

    2001-01-01

    In this article we offer guidelines for the determination of key sizes forsymmetric cryptosystems, RSA, and discrete logarithm based cryptosystems bothover finite fields and over groups of elliptic curves over prime fields. Ourrecommendations are based on a set of explicitly formulated hypotheses, combinedwith existing data points about the cryptosystems.

  19. Fluency: A Key Link between Word Identification and Comprehension

    ERIC Educational Resources Information Center

    Bashir, Anthony S.; Hook, Pamela E.

    2009-01-01

    Purpose: The purpose of this article is to respond to A. G. Kamhi's (2007) challenge to consider two points of view on reading--the broad and the narrow. Each point of view includes a component of the reading process; namely, comprehension and word recognition. Taken separately, each point of view is insufficient for our understanding of the…

  20. Weed Identification: Using Plant Structures as a Key

    E-print Network

    Baumann, Paul A.

    2002-04-15

    cultural Extension Service, The Texas A&M University System. Educational programs of the Texas AgriLife Extension Service are open to all people without regard to race, color, sex, disability, religion, age, or national origin. Produced by Agri... , generally does not have a ligule or an auricle. l e a f b l a d e l i g u l e a u r i c l e l e a f c o l l a r s h e a t h n o d e Plant Parts 4 The cross-sections of grasses may be eitherround or oval (flattened), compared to a sedge, which exhibits...

  1. Molecular Identification Key for Pest Species of Scirtothrips (Thysanoptera: Thripidae)

    Microsoft Academic Search

    Paul F. Rugman-Jones; Mark S. Hoddle; Laurence A. Mound; Richard Stouthamer

    2006-01-01

    Effective plant quarantine and biological control initiatives require rapid and accurate identiÞcation of exotic and potentially invasive taxa that may cause high economic losses or envi- ronmental damage. The genus Scirtothrips Shull includes several species that are serious agricultural pests, and, because of their minute size and cryptic behavior, prone to undetected transport through international trade of plant material. Although

  2. Entropy driven key-lock assembly.

    PubMed

    Odriozola, G; Jiménez-Angeles, F; Lozada-Cassou, M

    2008-09-21

    The effective interaction between a sphere with an open cavity (lock) and a spherical macroparticle (key), both immersed in a hard sphere fluid, is studied by means of Monte Carlo simulations. As a result, a two-dimensional map of the key-lock effective interaction potential is constructed, which leads to the proposal of a self-assembling mechanism: There exists trajectories through which the key-lock pair could assemble avoiding trespassing potential barriers. Hence, solely the entropic contribution can induce their self-assembling even in the absence of attractive forces. This study points out the solvent contribution within the underlying mechanisms of substrate-protein assemblydisassembly processes, which are important steps of the enzyme catalysis and protein mediated transport. PMID:19044943

  3. Redundant coding of simulated tactile key clicks with audio signals

    Microsoft Academic Search

    Hsiang-Yu Chen; Jaeyoung Park; Hong Z. Tan; Steve Dai

    2010-01-01

    The present study examined the efficacy of using audio cues for redundant coding of tactile key clicks simulated with a piezoelectric actuator. The tactile stimuli consisted of six raised cosine pulses at two levels of frequency and three levels of amplitude. An absolute identification experiment was conducted to measure the information transfers associated with the tactile-audio signal set. Results from

  4. A diagnostic key for identifying organisms recovered from rotten eggs

    Microsoft Academic Search

    Patricia A. Board; R. G. Board

    1968-01-01

    A collection of 119 cultures of bacteria was assembled from eggs which had rotted on the premises of producers. All but 13 of the isolates were Gram?negative. These were characterised in detail and the data used (i) to devise a determinative key that permits rot?producing bacteria to be identified at generic level, and (it) to establish systems whereby identification at

  5. Virtual screening against p50 NF-kappaB transcription factor for the identification of inhibitors of the NF-kappaB-DNA interaction and expression of NF-kappaB upregulated genes.

    PubMed

    Piccagli, Laura; Fabbri, Enrica; Borgatti, Monica; Bianchi, Nicoletta; Bezzerri, Valentino; Mancini, Irene; Nicolis, Elena; Dechecchi, Cristina M; Lampronti, Ilaria; Cabrini, Giulio; Gambari, Roberto

    2009-12-01

    Virtual screening against NF-kappaB p50 using docking simulations was applied by starting from a three-dimensional (3D) database containing more than 4.6 million commercially available structures. This database was filtered by specifying a subset of commercially available compounds sharing a (2E,Z)-3-(2-hydroxyphenyl)-2-propenoate substructure and relevant druglike properties. Docking to p50 NF-kappaB was performed with a test set of six known inhibitors of NF-kappaB-DNA interactions. In agreement with docking results, the highest-scored compound displayed a high level of inhibitory activity in electrophoretic mobility shift assay (EMSA) experiments (inhibition of NF-kappaB-DNA interactions) and on biological functions dependent on NF-kappaB activity (inhibition of IL-8 gene expression in cystic fibrosis IB3-1 cells). We found that this in silico screening approach is suitable for the identification of low-molecular-weight compounds that inhibit NF-kappaB-DNA interactions and NF-kappaB-dependent functions. Information deduced from the discovery of the new lead compound and its binding mode could result in further lead optimization resulting in more potent NF-kappaB inhibitors. PMID:19806632

  6. Limitations and extensions of the lock-and-key principle: differences between gas state, solution and solid state structures.

    PubMed

    Schneider, Hans-Jörg

    2015-01-01

    The lock-and-key concept is discussed with respect to necessary extensions. Formation of supramolecular complexes depends not only, and often not even primarily on an optimal geometric fit between host and guest. Induced fit and allosteric interactions have long been known as important modifications. Different binding mechanisms, the medium used and pH effects can exert a major influence on the affinity. Stereoelectronic effects due to lone pair orientation can lead to variation of binding constants by orders of magnitude. Hydrophobic interactions due to high-energy water inside cavities modify the mechanical lock-and-key picture. That optimal affinities are observed if the cavity is only partially filled by the ligand can be in conflict with the lock-and-key principle. In crystals other forces than those between host and guest often dominate, leading to differences between solid state and solution structures. This is exemplified in particular with calixarene complexes, which by X-ray analysis more often than other hosts show guest molecules outside their cavity. In view of this the particular problems with the identification of weak interactions in crystals is discussed. PMID:25815592

  7. Distribution of Key Variables

    Cancer.gov

    Skip to Main Content Home   |   Data   |   Statistics   |   Tools   |   Collaborations   |   Work with Us   |   Publications   |   About   |   Links Distribution of Key Variables Women Exam year 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 381,827 499,159 622,446 638,678 650,759 657,167 699,081 667,762 669,994 566,657 498,019 500,055 498,798 502,488 Unique

  8. Quantum Key Distribution

    NASA Astrophysics Data System (ADS)

    Hughes, Richard

    2004-05-01

    Quantum key distribution (QKD) uses single-photon communications to generate the shared, secret random number sequences that are used to encrypt and decrypt secret communications. The unconditional security of QKD is based on the interplay between fundamental principles of quantum physics and information theory. An adversary can neither successfully tap the transmissions, nor evade detection (eavesdropping raises the key error rate above a threshold value). QKD could be particularly attractive for free-space optical communications, both ground-based and for satellites. I will describe a QKD experiment performed over multi-kilometer line-of-sight paths, which serves as a model for a satellite-to-ground key distribution system. The system uses single-photon polarization states, without active polarization switching, and for the first time implements the complete BB84 QKD protocol including, reconciliation, privacy amplification and the all-important authentication stage. It is capable of continuous operation throughout the day and night, achieving the self-sustaining production of error-free, shared, secret bits. I will also report on the results of satellite-to-ground QKD modeling.

  9. Identification and monitoring of Ulmus americana transcripts during in vitro interactions with the Dutch elm disease pathogen Ophiostoma novo-ulmi

    Microsoft Academic Search

    Mirella Aoun; Volker Jacobi; Brian Boyle; Louis Bernier

    2010-01-01

    Molecular mechanisms underlying the interaction leading to Dutch elm disease were studied in vitro using Ulmus americana L. callus culture inoculated with budding cells of the fungal pathogen Ophiostoma novo-ulmi (Brasier). An interaction cDNA library employing suppression subtractive hybridization was constructed from infected elm callus tissue 72 h post-inoculation. Five hundred and thirty-five expressed sequence tags, mostly from the host, were

  10. Identification of distinct nisin leader peptide regions that determine interactions with the modification enzymes NisB and NisC.

    PubMed

    Khusainov, Rustem; Moll, Gert N; Kuipers, Oscar P

    2013-01-01

    Nisin is the most prominent and applied bacteriocin that serves as a model for class I lantibiotics. The nisin leader peptide importantly determines interactions between precursor nisin and its modification enzymes NisB and NisC that mature nisin posttranslationally. NisB dehydrates serines and threonines, while NisC catalyzes the subsequent coupling of the formed dehydroamino acids to form lanthionines. Currently, little is known about how the nisin leader interacts with NisB and even less is known about its interactions with NisC. To investigate the nisin leader peptide requirements for functional interaction with the modification enzymes NisB and NisC, we systematically replaced six regions, of 2-4 amino acids each, with all-alanine regions. By performing NisB and NisC co-purification studies with these mutant leader peptides, we demonstrate that the nisin leader regions STKD(-22-19), FNLD(-18-15) and PR(-2-1) importantly contribute to the interactions of precursor nisin with both NisB and NisC, whereas the nisin leader region LVSV(-14-11) additionally contributes to the interaction of precursor nisin with NisC. PMID:23772400

  11. Identification of distinct nisin leader peptide regions that determine interactions with the modification enzymes NisB and NisC?

    PubMed Central

    Khusainov, Rustem; Moll, Gert N.; Kuipers, Oscar P.

    2013-01-01

    Nisin is the most prominent and applied bacteriocin that serves as a model for class I lantibiotics. The nisin leader peptide importantly determines interactions between precursor nisin and its modification enzymes NisB and NisC that mature nisin posttranslationally. NisB dehydrates serines and threonines, while NisC catalyzes the subsequent coupling of the formed dehydroamino acids to form lanthionines. Currently, little is known about how the nisin leader interacts with NisB and even less is known about its interactions with NisC. To investigate the nisin leader peptide requirements for functional interaction with the modification enzymes NisB and NisC, we systematically replaced six regions, of 2–4 amino acids each, with all-alanine regions. By performing NisB and NisC co-purification studies with these mutant leader peptides, we demonstrate that the nisin leader regions STKD(-22-19), FNLD(-18-15) and PR(-2-1) importantly contribute to the interactions of precursor nisin with both NisB and NisC, whereas the nisin leader region LVSV(-14-11) additionally contributes to the interaction of precursor nisin with NisC. PMID:23772400

  12. Key Infection, Secrecy Transfer, and Key Evolution for Sensor Networks

    Microsoft Academic Search

    Zhihong Liu; Jianfeng Ma; Qingqi Pei; Liaojun Pang; YoungHo Park

    2010-01-01

    Sensor networks are composed of a large number of low power sensor devices. For secure communication among sensors, secret keys are required to be established between them. Considering the strict resource constraints of sensors, key infection has been proposed by Anderson, Chan, and Perrig. However, because the communication keys are broadcasted in plaintext in key infection, some of them may

  13. Anonymous-key quantum cryptography and unconditionally secure quantum bit commitment

    E-print Network

    Horace P. Yuen

    2000-09-27

    A new cryptographic tool, anonymous quantum key technique, is introduced that leads to unconditionally secure key distribution and encryption schemes that can be readily implemented experimentally in a realistic environment. If quantum memory is available, the technique would have many features of public-key cryptography; an identification protocol that does not require a shared secret key is provided as an illustration. The possibility is also indicated for obtaining unconditionally secure quantum bit commitment protocols with this technique.

  14. Mineral Identification

    NSDL National Science Digital Library

    Michael Passow

    In this activity, students use written and online materials to answer a set of questions on the general properties and identification of minerals. They will learn about physical properties such as color, hardness, and cleavage; special properties such as fluorescence and effervescence; and complete a chart listing properties for a selection of minerals. Links to the necessary information are provided.

  15. Identification of two proteins that interact with the Erp virulence factor from Mycobacterium tuberculosis by using the bacterial two-hybrid system

    PubMed Central

    Klepp, Laura I; Soria, Marcelo; Blanco, Federico C; Bianco, María V; Santangelo, María P; Cataldi, Angel A; Bigi, Fabiana

    2009-01-01

    Background The exported repetitive protein (erp) gene encodes a secreted 36-kDa protein with a central domain containing several proline-glycine-leucine-threonine-serine (PGLTS) repeats. It has been demonstrated that erp is a virulence-associated factor since the disruption of this gene impairs the growth of Mycobacterium bovis and Mycobacterium tuberculosis in mice. Results In order to elucidate the function of Erp we searched for Erp-binding proteins from M. tuberculosis by using a bacterial two-hybrid system. Our results indicate that Erp interacts specifically with two putative membrane proteins, Rv1417 and Rv2617c. Further analysis revealed that the latter two interact with each other, indicating that Rv1417, Rv2617c and Erp are connected through multiple interactions. While Rv1417 is disseminated in several Actinomycetales genera, orthologues of Rv2617c are exclusively present in members of the M. tuberculosis complex (MTC). The central and amino-terminal regions of Erp were determined to be involved in the interaction with Rv1417 and Rv2627c. Erp forms from Mycobacterium smegmatis and Mycobacterium leprae were not able to interact with Rv2617c in two-hybrid assays. Immunolocalization experiments showed that Rv1417 and Rv2617c are found on the cell membrane and Erp on the bacterial cell wall. Finally, comparative genomics and expression studies revealed a possible role of Rv1417 in riboflavin metabolism. Conclusion We identified interactive partners of Erp, an M. tuberculosis protein involved in virulence, which will be the focus of future investigation to decipher the function of the Erp family protein. PMID:19159459

  16. Key recycling in authentication

    E-print Network

    Christopher Portmann

    2014-09-29

    In their seminal work on authentication, Wegman and Carter propose that to authenticate multiple messages, it is sufficient to reuse the same hash function as long as each tag is encrypted with a one-time pad. They argue that because the one-time pad is perfectly hiding, the hash function used remains completely unknown to the adversary. Since their proof is not composable, we revisit it using a composable security framework. It turns out that the above argument is insufficient: if the adversary learns whether a corrupted message was accepted or rejected, information about the hash function is leaked, and after a bounded finite amount of rounds it is completely known. We show however that this leak is very small: Wegman and Carter's protocol is still $\\epsilon$-secure, if $\\epsilon$-almost strongly universal$_2$ hash functions are used. This implies that the secret key corresponding to the choice of hash function can be reused in the next round of authentication without any additional error than this $\\epsilon$. We also show that if the players have a mild form of synchronization, namely that the receiver knows when a message should be received, the key can be recycled for any arbitrary task, not only new rounds of authentication.

  17. Identification of bZIP interaction partners of viral proteins HBZ, MEQ, BZLF1, and K-bZIP using coiled-coil arrays

    E-print Network

    Reinke, Aaron Wade

    Basic-region leucine-zipper transcription factors (bZIPs) contain a segment rich in basic amino acids that can bind DNA, followed by a leucine zipper that can interact with other leucine zippers to form coiled-coil homo- ...

  18. Identification of Stearoyl-CoA Desaturase (SCD) Gene Interactions in Korean Native Cattle Based on the Multifactor-dimensionality Reduction Method

    PubMed Central

    Oh, Dong-yep; Jin, Me-hyun; Lee, Yoon-seok; Ha, Jae-jung; Kim, Byung-ki; Yeo, Jung-sou; Lee, Jea-young

    2013-01-01

    Fat quality is determined by the composition of fatty acids. Genetic relationships between this composition and single nucleotide polymorphisms (SNPs) in the stearoyl-CoA desaturase1 (SCD1) gene were examined using 513 Korean native cattle. Single and epistatic effects of 7 SNP genetic variations were investigated, and the multifactor dimensionality reduction (MDR) method was used to investigate gene interactions in terms of oleic acid (C18:1), mono-unsaturated fatty acids (MUFAs) and marbling score (MS). The g.6850+77 A>G and g.14047 C>T SNP interactions were identified as the statistically optimal combination (C18:1, MUFAs and MS permutation p-values were 0.000, 0.000 and 0.001 respectively) of two-way gene interactions. The interaction effects of g.6850+77 A>G, g.10213 T>C and g.14047 C>T reflected the highest training-balanced accuracy (63.76%, 64.70% and 61.85% respectively) and was better than the individual effects for C18:1, MUFAs and MS. In addition, the superior genotype groups were AATTCC, AGTTCC, GGTCCC, AGTCCT, GGCCCT and AGCCTT. These results suggest that the selected SNP combination of the SCD1 gene and superior genotype groups can provide useful inferences for the improvement of the fatty acid composition in Korean native cattle. PMID:25049903

  19. Identification of a cytoplasmic interaction partner of the large regulatory proteins Rep78/Rep68 of adeno-associated virus type 2 (AAV-2)

    SciTech Connect

    Weger, Stefan [Institut fuer Virologie, Charite Campus Benjamin Franklin, Freie Universitaet Berlin, Hindenburgdamm 27, 12203 Berlin (Germany)]. E-mail: stefan.weger@charite.de; Hammer, Eva [Institut fuer Virologie, Charite Campus Benjamin Franklin, Freie Universitaet Berlin, Hindenburgdamm 27, 12203 Berlin (Germany); Goetz, Anne [Institut fuer Virologie, Charite Campus Benjamin Franklin, Freie Universitaet Berlin, Hindenburgdamm 27, 12203 Berlin (Germany); Heilbronn, Regine [Institut fuer Virologie, Charite Campus Benjamin Franklin, Freie Universitaet Berlin, Hindenburgdamm 27, 12203 Berlin (Germany)

    2007-05-25

    Through yeast two-hybrid analysis and coimmunoprecipitation studies, we have identified a novel cellular AAV-2 Rep78/Rep68 interaction partner located predominantly in the cytoplasm. In public databases, it has been assigned as KCTD5, because of a region of high similarity to the cytoplasmic tetramerization domain of voltage-gated potassium channels. Whereas Rep/KCTD5 interaction relied on the region surrounding the Rep nuclear localization signal, nuclear accumulation of Rep was not required. Wildtype Rep78/Rep68 proteins induced the translocation of large portions of KCTD5 into the nucleus pointing to functional interactions both in the cytoplasm and the nucleus. In line with an anticipated functional interference in the cytoplasm, KCTD5 overexpression completely abrogated Rep68-mediated posttranscriptional activation of a HIV-LTR driven luciferase reporter gene. Our study expands the panel of already identified nuclear Rep interaction partners to a cytoplasmic protein, which raises the awareness that important steps in the AAV life cycle may be regulated in this compartment.

  20. > REPLACE THIS LINE WITH YOUR PAPER IDENTIFICATION NUMBER (DOUBLE-CLICK HERE TO EDIT) < 1 Abstract--The interaction of light and object surfaces generates

    E-print Network

    Schettini, Raimondo

    the characteristic of smoothness of surface reflectance functions, a lot of work has been done in the analysis that completely characterizes the physical property of surfaces responsible for color is the reflectance spectrum-- The interaction of light and object surfaces generates color signals in the visible band that are responsible

  1. Interaction between poly(3-hydroxybutyrate) granule-associated proteins as revealed by two-hybrid analysis and identification of a new phasin in Ralstonia eutropha H16.

    PubMed

    Pfeiffer, Daniel; Jendrossek, Dieter

    2011-10-01

    A large number of polypeptides are attached to poly(3-hydroxybutyrate) (PHB) granules of Ralstonia eutropha, such as PHB synthase (PhaC1), several PHB depolymerases (PhaZs) and phasins (PhaPs), the regulator protein PhaR(Reu), and possibly others. In this study we used the bacterial adenylate cyclase-based two-hybrid assay to investigate interactions between known PHB granule-associated proteins (PGAPs) and to screen for new PGAPs. The utility of the system was tested by the in vivo verification of previously postulated interactions of the PHB synthase subunits of R. eutropha (PhaC1 homo-oligomerization) and of Bacillus megaterium (PhaC(Bmeg)-PhaR(Bmeg) hetero-oligomerization). Nine proteins (PhaA, PhaB1, PhaC1, PhaP1-PhaP4, PhaZ1 and PhaR), with established functions in PHB metabolism of R. eutropha, were tested for interaction in all combinations. While no significant interaction was detected between the PHB synthase PhaC1 and any of the other eight tested Pha proteins, strong interactions were found between all phasin proteins, in particular between PhaP2 and PhaP4. When PhaP2 was used as bait in a two-hybrid screening experiment with a genomic library of R. eutropha, the B1934 gene product was identified in 24 out of 53 isolated clones. B1934 encodes a hypothetical protein (15.7 kDa) with similarity to phasins of PHB-accumulating bacteria. A fusion protein of eYfp and the B1934 gene product colocalized with PHB granules, confirming that B1934 represents a new phasin (PhaP5). PhaP5 was not essential for PHB granule formation, but overexpression of PhaP5 increased the number of cells with PHB granules at the cell poles. PMID:21737497

  2. Key to Freshwater Algae: A Web-based Tool to Enhance Understanding of Microscopic Biodiversity

    NASA Astrophysics Data System (ADS)

    Shayler, Hannah A.; Siver, Peter A.

    2006-10-01

    The Freshwater Ecology Laboratory at Connecticut College has developed an interactive, Web-based identification key to freshwater algal genera using the Lucid Professional and Lucid 3 software developed by the Centre for Biological Information Technology at the University of Queensland, Brisbane, Australia. The Key to Freshwater Algae was funded by the National Science Foundation (Award #CCLI-0229531) to encourage awareness of microscopic diversity through a creative, investigative approach to learning. Users may answer questions in any order to quickly and efficiently narrow down the list of taxa to only those that match the characteristics they have chosen. All characters and terms are clearly explained for ease of use by those unfamiliar with the algae. This non-hierarchical, user-friendly key is linked to Web pages containing a wealth of resources, including images, movies, and information about the morphology, ecology, and reproduction of each organism. These materials are especially well suited for classroom use in conjunction with cultures purchased from the Carolina Biological Supply Company, a popular distributor of biological materials. Cultures from the Carolina Biological Supply Company representing nearly 75 freshwater genera from a variety of algal groups were observed and photographed using high resolution digital imaging to fully document cellular structure and highlight distinguishing features. High quality video footage of each taxon incorporating titles, diagrams, and structural terminology was outputted as QuickTime movies, on DVD, and on VHS cassettes. The Key to Freshwater Algae and supplemental materials are available online at http://silicasecchidisk.conncoll.edu to provide an innovative alternative to traditional dichotomous keys that is particularly appropriate for introducing students in undergraduate life science courses to the algal groups and genera.

  3. Key Separation and Key Reuse Practice: Key Reuse in EMV Theory: Joint Security of Combined Signature and Encryption Theory & Practice: Joint Secur Key Reuse in Public Key Cryptography

    E-print Network

    Paterson, Kenny

    Key Separation and Key Reuse Practice: Key Reuse in EMV Theory: Joint Security of Combined Signature and Encryption Theory & Practice: Joint Secur Key Reuse in Public Key Cryptography: Theory in EMV Theory: Joint Security of Combined Signature and Encryption Theory & Practice: Joint Secur Outline

  4. Identification and functional assay of the interaction motifs in the partner protein OsNAR2.1 of the two-component system for high-affinity nitrate transport

    PubMed Central

    Liu, Xiaoqin; Huang, Daimin; Tao, Jinyuan; Miller, Anthony J; Fan, Xiaorong; Xu, Guohua

    2014-01-01

    A partner protein, NAR2, is essential for high-affinity nitrate transport of the NRT2 protein in plants. However, the NAR2 motifs that interact with NRT2s for their plasma membrane (PM) localization and nitrate transporter activity have not been functionally characterized. In this study, OsNAR2.1 mutations with different carbon (C)-terminal deletions and nine different point mutations in the conserved regions of NAR2 homologs in plants were generated to explore the essential motifs involved in the interaction with OsNRT2.3a. Screening using the membrane yeast two-hybrid system and Xenopus oocytes for nitrogen-15 (15N) uptake demonstrated that either R100G or D109N point mutations impaired the OsNAR2.1 interaction with OsNRT2.3a. Western blotting and visualization using green fluorescent protein fused to either the N- or C-terminus of OsNAR2.1 indicated that OsNAR2.1 is expressed in both the PM and cytoplasm. The split-yellow fluorescent protein (YFP)/BiFC analyses indicated that OsNRT2.3a was targeted to the PM in the presence of OsNAR2.1, while either R100G or D109N mutation resulted in the loss of OsNRT2.3a-YFP signal in the PM. Based on these results, arginine 100 and aspartic acid 109 of the OsNAR2.1 protein are key amino acids in the interaction with OsNRT2.3a, and their interaction occurs in the PM but not cytoplasm. PMID:25103875

  5. Mineral Identification

    NSDL National Science Digital Library

    John Pratte

    This lesson discusses the question 'What is a mineral?' in the context of the guessing game 'Animal, Vegetable, or Mineral?'. It introduces a definition of the term, discusses the criteria used in the definition, and presents the common physical properties used in mineral identification. The lesson includes an activity in which students observe and record the physical properties of ten specimens and attempt to identify them using an online reference for practice.

  6. Identification of Regions Interacting with Ovo(d) Mutations: Potential New Genes Involved in Germline Sex Determination or Differentiation in Drosophila Melanogaster

    PubMed Central

    Pauli, D.; Oliver, B.; Mahowald, A. P.

    1995-01-01

    Only a few Drosophila melanogaster germline sex determination genes are known, and there have been no systematic screens to identify new genes involved in this important biological process. The ovarian phenotypes produced by females mutant for dominant alleles of the ovo gene are modified in flies with altered doses of other loci involved in germline sex determination in Drosophila (Sex-lethal(+), sans fille(+) and ovarian tumor(+)). This observation constitutes the basis for a screen to identify additional genes required for proper establishment of germline sexual identity. We tested 300 deletions, which together cover ~58% of the euchromatic portion of the genome, for genetic interactions with ovo(D). Hemizygosity for more than a dozen small regions show interactions that either partially suppress or enhance the ovarian phenotypes of females mutant for one or more of the three dominant ovo mutations. These regions probably contain genes whose products act in developmental hierarchies that include ovo(+) protein. PMID:7713427

  7. Identification of cellular proteins that interact with Newcastle Disease Virus and human Respiratory Syncytial Virus by a two-dimensional virus overlay protein binding assay (VOPBA).

    PubMed

    Holguera, Javier; Villar, Enrique; Muñoz-Barroso, Isabel

    2014-10-13

    Although it is well documented that the initial attachment receptors for Newcastle Disease Virus (NDV) and Respiratory Syncytial Virus (RSV) are sialic acid-containing molecules and glycosaminoglycans respectively, the exact nature of the receptors for both viruses remains to be deciphered. Moreover, additional molecules at the host cell surface might be involved in the entry mechanism. With the aim of identifying the cellular proteins that interact with NDV and RSV at the cell surface, we performed a virus overlay protein binding assay (VOPBA). Cell membrane lysates were separated by two dimensional (2D) gel electrophoresis and electrotransferred to PVDF membranes, after which they were probed with high viral concentrations. NDV interacted with a Protein Disulfide Isomerase from chicken fibroblasts. In the case of RSV, we detected 15 reactive spots, which were identified as six different proteins, of which nucleolin was outstanding. We discuss the possible role of PDI and nucleolin in NDV and RSV entry, respectively. PMID:25109545

  8. Interaction of valerian extracts of different polarity with adenosine receptors: Identification of isovaltrate as an inverse agonist at A 1 receptors

    Microsoft Academic Search

    Svenja K. Lacher; Ralf Mayer; Kathrin Sichardt; Karen Nieber; Christa E. Müller

    2007-01-01

    A series of extracts of valerian roots (Valeriana officinalis L.) was prepared with solvents of different polarity. Polar as well as nonpolar extracts were found to interact with adenosine A1 receptors. While polar extracts activated A1 receptors (partial agonistic activity), nonpolar extracts showed antagonistic or inverse agonistic activity at A1 receptors, as demonstrated by GTP?S binding assays at human recombinant

  9. Proteomic analysis of the interaction of Bifidobacterium longum NCC2705 with the intestine cells Caco-2 and identification of plasminogen receptors.

    PubMed

    Wei, Xiao; Yan, Xiabei; Chen, Xuannan; Yang, Zhan; Li, Huan; Zou, Dayang; He, Xiang; Wang, Simiao; Cui, Qian; Liu, Wei; Zhurina, Daria; Wang, Xuesong; Zhao, Xiangna; Huang, Liuyu; Zeng, Ming; Ye, Qinong; Riedel, Christian U; Yuan, Jing

    2014-08-28

    To identify proteins with a potential role in the interaction of Bifidobacterium longum with intestinal epithelial cells, we profiled the protein response of B. longum NCC2705 following interaction with Caco-2 cells. Thirty-one protein spots, belonging to a total of 23 proteins, which exhibited a change in abundance of at least 3-fold were identified in B. longum NCC2705 following co-culture with Caco-2 cells, and were subsequently identified. Changes in expression were confirmed at the transcriptional level for a selection of these proteins. Enolase (Eno) and elongation factor Tu (EF-Tu) were amongst the proteins that showed the most prominent increase in abundance. Interaction of these proteins with plasminogen (Plg) was analyzed by Plg overlay assays, glutathione S-transferase (GST)-pull down, and western blot analysis. The results suggested that EF-Tu and Eno serve as surface receptors for B. longum NCC2705 binding to human plasminogen. Purified GST-EF-Tu and GST-Eno inhibited adhesion of B. longum NCC2705 to Caco-2 cells. Collectively, our data suggest that Eno and EF-Tu moonlight as adhesions, and are possibly involved in the protective role played by B. longum NCC2705 in defense against enteric pathogens. Biological significance The interaction of bifidobacteria with the human host plasminogen/plasmin system confirms the existence of a new component in the molecular cross-talk between bacteria and the host. Our study analyzed proteins EF-Tu and Eno with Plg binding activity, and they can inhibit adhesion of B. longum NCC2705 to Caco-2 cells, suggesting their role in the bacterial adherent to the enterocyte surface. PMID:24840471

  10. Identification of a Region Critically Involved in the Interaction of Phlorizin with the Rabbit Sodium-D-Glucose Cotransporter SGLT1

    Microsoft Academic Search

    R. Novakova; D. Homerova; R. K. H. Kinne; E. Kinne-Saffran; J. T. Lin

    2001-01-01

    .   In order to define potential interaction sites of SGLT1 with the transport inhibitor phlorizin, mutagenesis studies were\\u000a performed in a hydrophobic region of loop 13 (aa 604–610), located extracellularly, close to the C-terminus. COS 7 cells were\\u000a transiently transfected with the mutants and the kinetic parameters of ?-methyl-d-glucopyranoside (AMG) uptake into the cells were investigated. Replacement of the respective

  11. Reconstructing RSA Private Keys from Random Key Bits

    E-print Network

    Plotkin, Joshua B.

    Reconstructing RSA Private Keys from Random Key Bits Nadia Heninger and Hovav Shacham Princeton. If read in a 1, that bit must be 1. If read in 0, original bit could have been 0 or 1. The decay order to reconstruct from about 25% of bits. [HSHCPCFAF 08] Reconstruct an AES key schedule from 30% of bits. [Tsow 09

  12. 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

    2014-05-01

    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. PMID:24727455

  13. Key issues in HCI curriculum design

    Microsoft Academic Search

    J. Preece; Laurie Keller

    1990-01-01

    This paper reports on key issues that needed to be resolved in developing a large postgraduate distance education course in human-computer interaction intended for practicing software developers and technical managers.The multi-disciplinary nature of HCI is identified as being highly controversial when deciding what to teach and how. Questions about the balance of theory verses practice and providing tools verses knowledge

  14. The PYL4 A194T mutant uncovers a key role of PYR1-LIKE4/PROTEIN PHOSPHATASE 2CA interaction for abscisic acid signaling and plant drought resistance.

    PubMed

    Pizzio, Gaston A; Rodriguez, Lesia; Antoni, Regina; Gonzalez-Guzman, Miguel; Yunta, Cristina; Merilo, Ebe; Kollist, Hannes; Albert, Armando; Rodriguez, Pedro L

    2013-09-01

    Because abscisic acid (ABA) is recognized as the critical hormonal regulator of plant stress physiology, elucidating its signaling pathway has raised promise for application in agriculture, for instance through genetic engineering of ABA receptors. PYRABACTIN RESISTANCE1/PYR1-LIKE (PYL)/REGULATORY COMPONENTS OF ABA RECEPTORS ABA receptors interact with high affinity and inhibit clade A phosphatases type-2C (PP2Cs) in an ABA-dependent manner. We generated an allele library composed of 10,000 mutant clones of Arabidopsis (Arabidopsis thaliana) PYL4 and selected mutations that promoted ABA-independent interaction with PP2CA/ABA-HYPERSENSITIVE3. In vitro protein-protein interaction assays and size exclusion chromatography confirmed that PYL4(A194T) was able to form stable complexes with PP2CA in the absence of ABA, in contrast to PYL4. This interaction did not lead to significant inhibition of PP2CA in the absence of ABA; however, it improved ABA-dependent inhibition of PP2CA. As a result, 35S:PYL4(A194T) plants showed enhanced sensitivity to ABA-mediated inhibition of germination and seedling establishment compared with 35S:PYL4 plants. Additionally, at basal endogenous ABA levels, whole-rosette gas exchange measurements revealed reduced stomatal conductance and enhanced water use efficiency compared with nontransformed or 35S:PYL4 plants and partial up-regulation of two ABA-responsive genes. Finally, 35S:PYL4(A194T) plants showed enhanced drought and dehydration resistance compared with nontransformed or 35S:PYL4 plants. Thus, we describe a novel approach to enhance plant drought resistance through allele library generation and engineering of a PYL4 mutation that enhances interaction with PP2CA. PMID:23864556

  15. Smooth Phase Interpolated Keying

    NASA Technical Reports Server (NTRS)

    Borah, Deva K.

    2007-01-01

    Smooth phase interpolated keying (SPIK) is an improved method of computing smooth phase-modulation waveforms for radio communication systems that convey digital information. SPIK is applicable to a variety of phase-shift-keying (PSK) modulation schemes, including quaternary PSK (QPSK), octonary PSK (8PSK), and 16PSK. In comparison with a related prior method, SPIK offers advantages of better performance and less complexity of implementation. In a PSK scheme, the underlying information waveform that one seeks to convey consists of discrete rectangular steps, but the spectral width of such a waveform is excessive for practical radio communication. Therefore, the problem is to smooth the step phase waveform in such a manner as to maintain power and bandwidth efficiency without incurring an unacceptably large error rate and without introducing undesired variations in the amplitude of the affected radio signal. Although the ideal constellation of PSK phasor points does not cause amplitude variations, filtering of the modulation waveform (in which, typically, a rectangular pulse is converted to a square-root raised cosine pulse) causes amplitude fluctuations. If a power-efficient nonlinear amplifier is used in the radio communication system, the fluctuating-amplitude signal can undergo significant spectral regrowth, thus compromising the bandwidth efficiency of the system. In the related prior method, one seeks to solve the problem in a procedure that comprises two major steps: phase-value generation and phase interpolation. SPIK follows the two-step approach of the related prior method, but the details of the steps are different. In the phase-value-generation step, the phase values of symbols in the PSK constellation are determined by a phase function that is said to be maximally smooth and that is chosen to minimize the spectral spread of the modulated signal. In this step, the constellation is divided into two groups by assigning, to information symbols, phase values that result in equal numbers of clockwise and counter-clockwise phase rotations for equally likely symbols. The purpose served by assigning phase values in this way is to prevent unnecessary generation of spectral lines and prevent net shifts of the carrier signal. In the phase-interpolation step, the smooth phase values are interpolated over a number, n, of consecutive symbols (including the present symbol) by means of an unconventional spline curve fit.

  16. Email-Based Identification and Authentication: An Alternative to PKI?

    Microsoft Academic Search

    Simson L. Garfinkel

    2003-01-01

    E-mail-based identification and authentication is an emerging alternative to public-key infrastructure. It overcomes many problems inherent with traditional authentication techniques, such as social security numbers, and. provides functional security when used within a limited context.

  17. DCCPS: BRP: PCRB: Key Initiatives

    Cancer.gov

    Twitter Multimedia Home About Key Initiatives Funding Resources Tools Cancer Control & Population Sciences Home Behavioral Research Program Home Process of Care Research Branch Process of Care Research Branch (PCRB) Key Initiatives Priority Areas for

  18. DCCPS: BRP: PCRB: Key Initiatives

    Cancer.gov

    Skip Navigation Twitter Multimedia Home About Key Initiatives Funding Resources Tools Cancer Control & Population Sciences Home Behavioral Research Program Home Process of Care Research Branch Process of Care Research Branch (PCRB) Key Initiatives The

  19. MycoKey

    NSDL National Science Digital Library

    Laessoe, Thomas.

    This interesting site, by two Research Associates of the Department of Systematic Botany, University of Aarhus (Denmark), aims to provide a simple means for navigating through the various taxa of fungi. Currently covering 279 genera and 1,090 illustrated species, MycoKey includes "the genera of basidiomycota with stem and cap (Agarics, Boletes etc.), polypores and club fungi from Northern Europe (i.e. Europe north of the Alps)." A second version detailing "most genera of sexual fungi forming fruitbodies" is slated for release in summer 2001. To navigate the site, select the "easy" (pictorial characters only) or "full" (pictorial characters accompanied by descriptive botanical terms) version; then select the appropriate character and proceed to the next question. At any point, users may choose to browse images of all genera that apply to that description -- this includes close-up color images for each genus/species that fits the characters they have selected. Note that use of this resource is currently free of charge but requires a cookie (check your browser preferences).

  20. Identification of distinctive interdomain interactions among ZP-N, ZP-C and other domains of zona pellucida glycoproteins underlying association of chicken egg-coat matrix

    PubMed Central

    Okumura, Hiroki; Sato, Takahiro; Sakuma, Rio; Fukushima, Hideaki; Matsuda, Tsukasa; Ujita, Minoru

    2015-01-01

    The vertebrate egg coat, including mammalian zona pellucida, is an oocyte-specific extracellular matrix comprising two to six zona pellucida (ZP) glycoproteins. The egg coat plays important roles in fertilization, especially in species-specific interactions with sperm to induce the sperm acrosome reaction and to form the block to polyspermy. It is suggested that the physiological functions of the egg coat are mediated and/or regulated coordinately by peptide and carbohydrate moieties of the ZP glycoproteins that are spatially arranged in the egg coat, whereas a comprehensive understanding of the architecture of vertebrate egg-coat matrix remains elusive. Here, we deduced the orientations and/or distributions of chicken ZP glycoproteins, ZP1, ZP3 and ZPD, in the egg-coat matrix by confocal immunofluorescent microscopy, and in the ZP1–ZP3 complexes generated in vitro by co-immunoprecipitation assays. We further confirmed interdomain interactions of the ZP glycoproteins by far-Western blot analyses of the egg-coat proteins and pull-down assays of ZP1 in the serum, using recombinant domains of ZP glycoproteins as probes. Our results suggest that the ZP1 and ZP3 bind through their ZP-C domains to form the ZP1–ZP3 complexes and fibrils, which are assembled into bundles through interactions between the repeat domains of ZP1 to form the ZP1–ZP3 matrix, and that the ZPD molecules self-associate and bind to the ZP1–ZP3 matrix through its ZP-N and ZP-C domains to form the egg-coat matrix. Based on these results, we propose a tentative model for the architecture of the chicken egg-coat matrix that might be applicable to other vertebrate ones.

  1. Identification of the AntiListerial Constituents in Partially Purified Column Chromatography Fractions of Garcinia kola Seeds and Their Interactions with Standard Antibiotics

    PubMed Central

    Penduka, D.; Buwa, L.; Mayekiso, B.; Basson, A. K.; Okoh, A. I.

    2014-01-01

    Partially purified fractions of the n-hexane extract of Garcinia kola seeds were obtained through column chromatography and their constituents were identified through the use of gas chromatography coupled to mass spectrometry (GC-MS). Three fractions were obtained by elution with benzene as the mobile phase and silica gel 60 as the stationery phase and these were named Benz1, Benz2, and Benz3 in the order of their elution. The antiListerial activities of these fractions were assessed through MIC determination and only Benz2 and Benz3 were found to be active with MIC's ranging from 0.625 to 2.5?mg/mL. The results of the GC-MS analysis showed Benz2 to have 9 compounds whilst Benz3 had 7 compounds, with the major compounds in both fractions being 9,19-Cyclolanost-24-en-3-ol, (3.?.) and 9,19-Cyclolanostan-3-ol,24-methylene-, (3.?.). The Benz2 fraction was found to have mainly indifferent interactions with ampicillin and penicillin G whilst mainly additive interactions were observed with ciprofloxacin. The Benz3 fraction's interactions were found to be 50% synergistic with penicillin G and 25% synergistic with ciprofloxacin and ampicillin. A commercially available 9,19-Cyclolanost-24-en-3-ol, (3.?.) was found not to exhibit any antiListerial activities at maximum test concentrations of 5?mg/mL, suggesting that the compound could be acting in synergy with the other compounds in the eluted fractions of Garcinia kola seeds. PMID:24527056

  2. Identification of in vivo HSP90-interacting proteins reveals modularity of HSP90 complexes is dependent on the environment in psychrophilic bacteria

    PubMed Central

    García-Descalzo, Laura; Alcazar, Alberto; Baquero, Fernando

    2010-01-01

    Heat shock protein 90 (HSP90) is a conserved molecular chaperone that functions as part of complexes in which different client proteins target it to diverse sets of substrates. In this paper, HSP90 complexes were investigated in ?-proteobacteria from mild (Shewanella oneidensis) and cold environments (Shewanella frigidimarina and Psychrobacter frigidicola), to determine changes in HSP90 interactions with client proteins in response to the adaptation to cold environments. HSP90 participation in cold adaptation was determined using the specific inhibitor 17-allylamino-geldanamycin. Then, HSP90 was immunoprecipitated from bacterial cultures, and the proteins in HSP90 complexes were analyzed by two-dimensional gel electrophoresis and identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. According to HSP90-associated protein analysis, only 15 common proteins were found in both species from the same genus, S. oneidensis and S. frigidimarina, whereas a significant higher number of common proteins were found in both psychrophilic species S. frigidimarina and P. frigidicola 21 (p?interacting proteins, the chaperone proteins DnaK and GroEL, were common to the three species. Interestingly, some proteins related to energy metabolism (isocitrate lyase, succinyl-CoA synthetase, alcohol dehydrogenase, NAD(+) synthase, and malate dehydrogenase) and some translation factors only interacted with HSP90 in psychrophilic bacteria. We can conclude that HSP90 and HSP90-associated proteins might take part in the mechanism of adaptation to cold environments, and interestingly, organisms living in similar environments conserve similar potential HSP90 interactors in opposition to phylogenetically closely related organisms of the same genus but from different environments. PMID:20890740

  3. Data Encryption by Two Keys

    Microsoft Academic Search

    Fan Jing; Zhu Xian

    2009-01-01

    This Paper presents a new data encryption conception and algorithm. In this paper, one general data encryption key is used, and one more method encryption key is used too. By two keys method (TKE), the new algorithm obtain many useful properties, it operates quickly and easy perform by hardware, it has high encryption intensity and just like the DES when

  4. Security of 2^t-Root Identification and Signatures

    Microsoft Academic Search

    Claus-peter Schnorr; Fachbereich Mathematik

    1996-01-01

    Ong-Schnorr identification and signatures are variants of the Fiat-Shamir scheme with short and fast communication and signatures.\\u000a This scheme uses secret keys that are 2t-roots modulo N of the public keys, whereas Fiat-Shamir uses square roots modulo N. Security for particular cases has recently been proved by Micali [M94] and Shoup [Sh96].\\u000a \\u000a We prove that identification and signatures are secure

  5. Studies of the Interaction between Isoimperatorin and Human Serum Albumin by Multispectroscopic Method: Identification of Possible Binding Site of the Compound Using Esterase Activity of the Protein

    PubMed Central

    Ranjbar, Samira; Shokoohinia, Yalda; Ghobadi, Sirous; Gholamzadeh, Saeed; Moradi, Nastaran; Ashrafi-Kooshk, Mohammad Reza; Aghaei, Abbas

    2013-01-01

    Isoimperatorin is one of the main components of Prangos ferulacea as a linear furanocoumarin and used as anti-inflammatory, analgesic, antispasmodic, and anticancer drug. Human serum albumin (HSA) is a principal extracellular protein with a high concentration in blood plasma and carrier for many drugs to different molecular targets. Since the carrying of drug by HSA may affect on its structure and action, we decided to investigate the interaction between HSA and isoimperatorin using fluorescence and UV spectroscopy. Fluorescence data indicated that isoimperatorin quenches the intrinsic fluorescence of the HSA via a static mechanism and hydrophobic interaction play the major role in the drug binding. The binding average distance between isoimperatorin and Trp 214 of HSA was estimated on the basis of the theory of Förster energy transfer. Decrease of protein surface hydrophobicity (PSH) was also documented upon isoimperatorin binding. Furthermore, the synchronous fluorescence spectra show that the microenvironment of the tryptophan residues does not have obvious changes. Site marker compettive and fluorescence experiments revealed that the binding of isoimperatorin to HSA occurred at or near site I. Finally, the binding details between isoimperatorin and HSA were further confirmed by molecular docking and esterase activity inhibition studies which revealed that drug was bound at subdomain IIA. PMID:24319355

  6. In vitro and in vivo identification of metabolites of magnoflorine by LC LTQ-Orbitrap MS and its potential pharmacokinetic interaction in Coptidis Rhizoma decoction in rat.

    PubMed

    Xue, Baojuan; Zhao, Yuanyuan; Miao, Qing; Miao, Peipei; Yang, Xiaoyan; Sun, Guixia; Su, Jin; Ye, Jing; Wei, Baohong; Zhang, Yuanyuan; Zhang, Yujie

    2015-08-01

    Magnoflorine, an important aporphine alkaloid in Coptidis Rhizoma, is increasingly attracting research attention because of its pharmacological activities. The in vivo and in vitro metabolism of magnoflorine was investigated by LC LTQ-Orbitrap MS. In vivo samples including rat urine, feces, plasma and bile were collected separately after both oral (50?mg?kg(-1) ) and intravenous administration (10?mg?kg(-1) ) of magnoflorine, along with in vitro samples prepared by incubating magnoflorine with rat intestinal flora and liver microsome. As a result, 12 metabolites were found in biological samples. Phase I metabolites were identified in all biological samples, while phase II metabolites were mainly detected in urine, plasma and bile. In a pharmacokinetic study, rats were not only dosed with magnoflorine via oral (15, 30 and 60?mg?kg(-1) ) and intravenous administration (10?mg?kg(-1) ) but also dosed with Coptidis Rhizoma decoction (equivalent to 30?mg?kg(-1) of magnoflorine) by intragastric administration to investigate the interaction of magnoflorine with the rest of compounds in Coptidis Rhizoma. Studies showed that magnoflorine possessed lower bioavailability and faster absorption and elimination. However, pharmacokinetic parameters altered significantly (p?interactions between magnoflorine and the rest of ingredients in Coptidis Rhizoma. Copyright © 2015 John Wiley & Sons, Ltd. PMID:25611590

  7. Identification of Influenza A/H7N9 Virus Infection-Related Human Genes Based on Shortest Paths in a Virus-Human Protein Interaction Network

    PubMed Central

    Huang, Tao; Cai, Yu-Dong

    2014-01-01

    The recently emerging Influenza A/H7N9 virus is reported to be able to infect humans and cause mortality. However, viral and host factors associated with the infection are poorly understood. It is suggested by the “guilt by association” rule that interacting proteins share the same or similar functions and hence may be involved in the same pathway. In this study, we developed a computational method to identify Influenza A/H7N9 virus infection-related human genes based on this rule from the shortest paths in a virus-human protein interaction network. Finally, we screened out the most significant 20 human genes, which could be the potential infection related genes, providing guidelines for further experimental validation. Analysis of the 20 genes showed that they were enriched in protein binding, saccharide or polysaccharide metabolism related pathways and oxidative phosphorylation pathways. We also compared the results with those from human rhinovirus (HRV) and respiratory syncytial virus (RSV) by the same method. It was indicated that saccharide or polysaccharide metabolism related pathways might be especially associated with the H7N9 infection. These results could shed some light on the understanding of the virus infection mechanism, providing basis for future experimental biology studies and for the development of effective strategies for H7N9 clinical therapies. PMID:24955349

  8. Genetic identification of forensically important flesh flies (Diptera: Sarcophagidae)

    Microsoft Academic Search

    Richard Zehner; Jens Amendt; Svenja Schütt; Jan Sauer; Roman Krettek; Dalibor Povolný

    2004-01-01

    Unequivocal identification of fly specimens is an essential requirement in forensic entomology. However, not all species can be determined at every developmental stage, which is illustrated by the flesh flies (Diptera: Sarcophagidae), important members of the necrophagous insect fauna. Up to now no suitable key for the identification of the immature stages of this family of flies exists. DNA analysis

  9. Feature Selection Using Stochastic Search: An Application to System Identification

    Microsoft Academic Search

    Sandro Saitta; Prakash Kripakaran; Benny Raphael; Ian F. C. Smith

    2010-01-01

    System identification using multiple-model strategies may involve thousands of models with several parameters. However, only a few models are close to the correct model. A key task involves finding which parameters are important for explaining candidate models. The application of feature selection to system identification is studied in this paper. A new feature selection algorithm is proposed. It is based

  10. The Role of Nostalgia in Determining Consumers' Sport Team Identification

    Microsoft Academic Search

    Michael Volkov; Jane Summers

    With the many benefits related to high levels of sport team identification, sport marketers, team management and communities at large desire fans to be highly identified with sport teams. Moreover, research has identified that key to developing high levels of team identification within fans are social- psychological mechanisms such as nostalgia (Fink et al., 2002; Funk & James, 2006; Gladden

  11. The Fund Identification Challenge

    NSDL National Science Digital Library

    Susan Moncada

    Knowing the fund structure for state and local governments is a key concept students must master early in their study of governmental accounting. In addition, students must be able to identify which fund would be used to account for various activities in which a government engages. This PowerPoint game is a drill and practice/review activity fashioned after the popular TV game show, Hollywood Squares. The celebrities in the Fund Identification Challenge are past Presidents of the United States. The Presidents have responded to a question, and the game participants either agree or disagree with the response to earn the square. The 27 real-world examples found in the game were derived by examining the Comprehensive Annual Financial Reports (CAFR) of various cities.

  12. Whale Identification

    NASA Technical Reports Server (NTRS)

    1991-01-01

    R:BASE for DOS, a computer program developed under NASA contract, has been adapted by the National Marine Mammal Laboratory and the College of the Atlantic to provide and advanced computerized photo matching technique for identification of humpback whales. The program compares photos with stored digitized descriptions, enabling researchers to track and determine distribution and migration patterns. R:BASE is a spinoff of RIM (Relational Information Manager), which was used to store data for analyzing heat shielding tiles on the Space Shuttle Orbiter. It is now the world's second largest selling line of microcomputer database management software.

  13. Identification of two novel HSP90 proteins in Babesia orientalis: molecular characterization, and computational analyses of their structure, function, antigenicity and inhibitor interaction

    PubMed Central

    2014-01-01

    Background HSP90 protects the cells from heat stress and facilitates protein maturation and stability. The full genome sequences of piroplasms contain two putative HSP90 proteins, which are yet uncharacterized. To this end, the two putative HSP90 proteins of Babesia orientalis were identified and characterized by molecular and in silico methods. Methods The two putative proteins in B. orientalis genome showing homology with putative HSP90 of other piroplasms were cloned and sequenced. A computational analysis was carried out to predict the antigenic determinants, structure and function of these proteins. The interactions of two HSP90 isoforms with respective inhibitors were also examined through docking analysis. Results The length of BoHSP90-A gene (amplified from gDNA) was 2706 bp with one intron from position 997 to 1299 bp. This gene amplified from cDNA corresponded to full length CDS with an open reading frame (ORF) of 2403 bp encoding a 800 amino acid (AA) polypeptide with a predicted size of 91.02 kDa. The HSP90-B gene was intronless with an ORF of 2349 bp, and predicted polypeptide comprised of 797 AA with a size of 90.59 kDa. The AA sequences of these two proteins of B. orientalis were the most identical to those of B. bovis. The BoHSP90-A and BoHSP90-B were recognized as 90 kDa in the parasite lysate by the rabbit antisera raised against the recombinant BoHSP90 proteins. The anti-B. orientalis buffalo serum reacted with the rBoHSP90s expressed in E. coli, indicating that these proteins might be secreted by the parasite before entry into host cells. The overall structure and functional analyses showed several domains involved in ATPase activity, client protein binding and HSP90 dimerization. Likewise, several HSP90 inhibitors showed binding to ATP binding pockets of BoHSP90-A and BoHSP90-B, as observed through protein structure-ligand interaction analysis. Conclusions The two putative HSP90 proteins in B. orientalis were recognized as 90 kDa. The rBoHSP90-A and rBoHSP90-B were reacted with the B. orientalis infected buffalo serum. The computational structure and functional analyses revealed that these two proteins may have chaperonic activity. The protein structure-ligand interaction analyses indicated that these two proteins had many drug target sites. PMID:24970594

  14. Methyl scanning: total synthesis of demethylasterriquinone B1 and derivatives for identification of sites of interaction with and isolation of its receptor(s).

    PubMed

    Pirrung, Michael C; Liu, Yufa; Deng, Liu; Halstead, Diana K; Li, Zhitao; May, John F; Wedel, Michael; Austin, Darrell A; Webster, Nicholas J G

    2005-04-01

    The principle of methyl scanning is proposed for determination of the sites of interaction between biologically active small molecules and their macromolecular target(s). It involves the systematic preparation of a family of methylated derivatives of a compound and their biological testing. As a functional assay, the method can identify the regions of a molecule that are important (and unimportant) for biological activity against even unknown targets, and thus provides an excellent complement to structural biology. Methyl scanning was applied to demethylasterriquinone B1, a small-molecule mimetic of insulin. A new, optimal total synthesis of this natural product was developed that enables the family of methyl scan derivatives to be concisely prepared for evaluation in a cellular assay. The results of this experiment were used to design a biotin-demethylasterriquinone conjugate for use as an affinity reagent. This compound was prepared in tens of milligram quantities in a four-step synthesis. PMID:15796526

  15. Goodpasture antigen-binding protein (GPBP) directs myofibril formation: identification of intracellular downstream effector 130-kDa GPBP-interacting protein (GIP130).

    PubMed

    Revert-Ros, Francisco; López-Pascual, Ernesto; Granero-Moltó, Froilán; Macías, Jesús; Breyer, Richard; Zent, Roy; Hudson, Billy G; Saadeddin, Anas; Revert, Fernando; Blasco, Raül; Navarro, Carmen; Burks, Deborah; Saus, Juan

    2011-10-01

    Goodpasture antigen-binding protein-1 (GPBP-1) is an exportable non-conventional Ser/Thr kinase that regulates glomerular basement membrane collagen organization. Here we provide evidence that GPBP-1 accumulates in the cytoplasm of differentiating mouse myoblasts prior to myosin synthesis. Myoblasts deficient in GPBP-1 display defective myofibril formation, whereas myofibrils assemble with enhanced efficiency in those overexpressing GPBP-1. We also show that GPBP-1 targets the previously unidentified GIP130 (GPBP-interacting protein of 130 kDa), which binds to myosin and promotes its myofibrillar assembly. This report reveals that GPBP-1 directs myofibril formation, an observation that expands its reported role in supramolecular organization of structural proteins to the intracellular compartment. PMID:21832087

  16. Rapid screening and identification of active ingredients in licorice extract interacting with V3 loop region of HIV-1 gp120 using ACE and CE-MS.

    PubMed

    Li, Zhongjie; Zhao, Yiran; Lin, Weiwei; Ye, Min; Ling, Xiaomei

    2015-07-10

    The binding of envelope protein gp120 to glycosphingolipids is very important during the human immunodeficiency virus entering into the host cell. This step occurs in the V3 loop region in particularly. The conserved core sequence of V3 loop in gp120 was named R15K. Anti-HIV drug targeting to R15K would avoid the drug-resistance caused by HIV-1 genetic diversity. Here, for the first time, affinity capillary electrophoresis (ACE) and capillary electrophoresis-mass spectrometry (CE-MS) were used for establishing a simple, rapid and effective method of screening the licorice extract for biological activity (anti-HIV), which avoided the complicated isolation and purification process. R15K, 3'-sialyllactose (the positive control), and d-galactose (the negative control) were used for the development and validation of ACE method. After the interaction between licorice extract and R15K was confirmed by ACE, the relative active ingredients were isolated by SPE and their structures were determined by CE-ESI-MS online. In this research, two mixtures from licorice extract were found to be active. Furthermore, glycyrrhizin and licorice saponin G2 were verified as the main ingredients that significantly interacted with R15K via CE-MS and LC-MS. The results of quantitative assays showed that the active mixture contained glycyrrhizin of 74.23% and licorice saponin G2 of 9.52%. Calculated by Scatchard analysis method, glycyrrhizin/R15K complex had the highest binding constant (1.69±0.08)×10(7)L/mol among 27 compounds isolated from licorice extract. The anti-HIV activity of glycyrrhizin was further confirmed by bioactive experiment of cellular level. This strategy might provide a high throughput screening and identifying platform for seeking HIV-1 inhibitors in natural products. PMID:25854854

  17. Regulation of the neural-specific gene VGF in PC12 cells. Identification of transcription factors interacting with NGF-responsive elements.

    PubMed

    Luc, P V; Wagner, J A

    1997-06-01

    Nerve growth factor (NGF) is an important regulator of differentiation and survival in both the peripheral and central nervous systems. We have begun to analyze the mechanism by which NGF induces the expression of a neural specific gene, VGF, in PC12 cells. Using DNase I footprinting and transient transfection analysis, we identified two VGF promoter regions, V1 and V2, that are required for basal promoter expression as well as gene induction by NGF, epidermal growth factor (EGF), and cAMP. The V1 element is essential for VGF promoter function, but it is not sufficient to confer NGF responsiveness to a heterologous promoter. In contrast, the V2 element can independently stimulate the expression of a linked herpes simplex virus (HSV) thymidine kinase promoter in response to NGF. We showed that the V2 region also contains a sequence that acts as a promoter-specific negative regulator of basal VGF gene expression. As determined by gel mobility shift and Southwestern analysis, the V1 sequence is recognized by a novel PC12 nuclear protein of about 110-kDa molecular mass. Using oligonucleotide competition and antibody supershift assays, we demonstrated that the cAMP-response element (CRE) motif within the V2 element interacted specifically with proteins related to cAMP-response element binding (CREB), JunB, and JunD transcription factors. The JunB-related binding activities were transiently induced by NGF, suggesting that part of the mechanism utilized by NGF to activate VGF transcription includes increased synthesis of a V2 binding protein. Taken together, our analysis suggests that the VGF promoter is regulated by a complex mechanism, and its activation requires combinatorial action of several transcription factors interacting with multiple promoter elements. PMID:9297634

  18. Identification of RanBP 9/10 as Interacting Partners for Protein Kinase C (PKC) ?/? and the D1 Dopamine Receptor: Regulation of PKC-Mediated Receptor Phosphorylation

    PubMed Central

    Rex, Elizabeth B.; Rankin, Michele L.; Yang, Yu; Lu, Quansheng; Gerfen, Charles R.; Jose, Pedro A.

    2010-01-01

    We reported previously that ethanol treatment regulates D1 receptor phosphorylation and signaling in a protein kinase C (PKC) ?- and PKC?-dependent fashion by a mechanism that may involve PKC isozyme-specific interacting proteins. Using a PKC isozyme-specific coimmunoprecipitation approach coupled to mass spectrometry, we report the identification of RanBP9 and RanBP10 as novel interacting proteins for both PKC? and PKC?. Both RanBP9 and RanBP10 were found to specifically coimmunoprecipitate with both PKC? and PKC?; however, this association did not seem to mediate the ethanol regulation of the PKCs. It is noteworthy that the D1 receptor was also found to specifically coimmunoprecipitate with RanBP9/10 from human embryonic kidney (HEK) 293T cells and with endogenous RanBP9 from rat kidney. RanBP9 and RanBP10 were also found to colocalize at the cellular level with the D1 receptor in both kidney and brain tissue. Although overexpression of RanBP9 or RanBP10 in HEK293T cells did not seem to alter the kinase activities of either PKC? or PKC?, both RanBP proteins regulated D1 receptor phosphorylation, signaling, and, in the case of RanBP9, expression. Specifically, overexpression of either RanBP9 or RanBP10 enhanced basal D1 receptor phosphorylation, which was associated with attenuation of D1 receptor-stimulated cAMP accumulation. Moreover, treatment of cells with select PKC inhibitors blocked the RanBP9/10-dependent increase in basal receptor phosphorylation, suggesting that phosphorylation of the receptor by PKC is regulated by RanBP9/10. These data support the idea that RanBP9 and RanBP10 may function as signaling integrators and dictate the efficient regulation of D1 receptor signaling by PKC? and PKC?. PMID:20395553

  19. Identification and targeting of an interaction between a tyrosine motif within hepatitis C virus core protein and AP2M1 essential for viral assembly.

    PubMed

    Neveu, Gregory; Barouch-Bentov, Rina; Ziv-Av, Amotz; Gerber, Doron; Jacob, Yves; Einav, Shirit

    2012-01-01

    Novel therapies are urgently needed against hepatitis C virus infection (HCV), a major global health problem. The current model of infectious virus production suggests that HCV virions are assembled on or near the surface of lipid droplets, acquire their envelope at the ER, and egress through the secretory pathway. The mechanisms of HCV assembly and particularly the role of viral-host protein-protein interactions in mediating this process are, however, poorly understood. We identified a conserved heretofore unrecognized YXX? motif (? is a bulky hydrophobic residue) within the core protein. This motif is homologous to sorting signals within host cargo proteins known to mediate binding of AP2M1, the ? subunit of clathrin adaptor protein complex 2 (AP-2), and intracellular trafficking. Using microfluidics affinity analysis, protein-fragment complementation assays, and co-immunoprecipitations in infected cells, we show that this motif mediates core binding to AP2M1. YXX? mutations, silencing AP2M1 expression or overexpressing a dominant negative AP2M1 mutant had no effect on HCV RNA replication, however, they dramatically inhibited intra- and extracellular infectivity, consistent with a defect in viral assembly. Quantitative confocal immunofluorescence analysis revealed that core's YXX? motif mediates recruitment of AP2M1 to lipid droplets and that the observed defect in HCV assembly following disruption of core-AP2M1 binding correlates with accumulation of core on lipid droplets, reduced core colocalization with E2 and reduced core localization to trans-Golgi network (TGN), the presumed site of viral particles maturation. Furthermore, AAK1 and GAK, serine/threonine kinases known to stimulate binding of AP2M1 to host cargo proteins, regulate core-AP2M1 binding and are essential for HCV assembly. Last, approved anti-cancer drugs that inhibit AAK1 or GAK not only disrupt core-AP2M1 binding, but also significantly inhibit HCV assembly and infectious virus production. These results validate viral-host interactions essential for HCV assembly and yield compounds for pharmaceutical development. PMID:22916011

  20. The hepatitis C virus core protein inhibits adipose triglyceride lipase (ATGL)-mediated lipid mobilization and enhances the ATGL interaction with comparative gene identification 58 (CGI-58) and lipid droplets.

    PubMed

    Camus, Gregory; Schweiger, Martina; Herker, Eva; Harris, Charles; Kondratowicz, Andrew S; Tsou, Chia-Lin; Farese, Robert V; Herath, Kithsiri; Previs, Stephen F; Roddy, Thomas P; Pinto, Shirly; Zechner, Rudolf; Ott, Melanie

    2014-12-26

    Liver steatosis is a common health problem associated with hepatitis C virus (HCV) and an important risk factor for the development of liver fibrosis and cancer. Steatosis is caused by triglycerides (TG) accumulating in lipid droplets (LDs), cellular organelles composed of neutral lipids surrounded by a monolayer of phospholipids. The HCV nucleocapsid core localizes to the surface of LDs and induces steatosis in cultured cells and mouse livers by decreasing intracellular TG degradation (lipolysis). Here we report that core at the surface of LDs interferes with the activity of adipose triglyceride lipase (ATGL), the key lipolytic enzyme in the first step of TG breakdown. Expressing core in livers or mouse embryonic fibroblasts of ATGL(-/-) mice no longer decreases TG degradation as observed in LDs from wild-type mice, supporting the model that core reduces lipolysis by engaging ATGL. Core must localize at LDs to inhibit lipolysis, as ex vivo TG hydrolysis is impaired in purified LDs coated with core but not when free core is added to LDs. Coimmunoprecipitation experiments revealed that core does not directly interact with the ATGL complex but, unexpectedly, increased the interaction between ATGL and its activator CGI-58 as well as the recruitment of both proteins to LDs. These data link the anti-lipolytic activity of the HCV core protein with altered ATGL binding to CGI-58 and the enhanced association of both proteins with LDs. PMID:25381252

  1. A KEY AND COMPENDIUM TO THE SPECIES OF THE GENUS MERLINIUS SIDDIQI, 1970, WITH DESCRIPTION OF ONE NEW SPECIES PARASITIZING DATE PALM

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An identification key to 32 valid species of stunt nematodes (Merlinius spp.) is given. A compendium of the most important diagnostic characters for use in identification of species is included as a practical alternative and supplement to the key. The diagnosis of Merlinius is emended, and a list of...

  2. “We Do Science Here”: Underrepresented Students’ Interactions with Faculty in Different College Contexts

    PubMed Central

    Hurtado, Sylvia; Eagan, M. Kevin; Tran, Minh C.; Newman, Christopher B.; Chang, Mitchell J.; Velasco, Paolo

    2011-01-01

    Faculty members play a key role in the identification and training of the next generation of scientific talent. In the face of the need to advance and diversify the scientific workforce, we examine whether and how specific institutional contexts shape student interactions with faculty. We conducted a mixed methods study to understand institutional contextual differences in the experiences of aspiring scientists. Data from a qualitative five-campus case study and a quantitative longitudinal study of students from over 117 higher education institutions were analyzed to determine how aspiring scientists interact with faculty and gain access to resources that will help them achieve their educational goals. Findings indicate that important structural differences exist between institutions in shaping students’ interactions with faculty. For example, students at more selective institutions typically have less frequent, less personal interactions with faculty whereas Black students at HBCUs report having more support and frequent interactions with faculty. PMID:23503924

  3. Interaction of valerian extracts of different polarity with adenosine receptors: identification of isovaltrate as an inverse agonist at A1 receptors.

    PubMed

    Lacher, Svenja K; Mayer, Ralf; Sichardt, Kathrin; Nieber, Karen; Müller, Christa E

    2007-01-15

    A series of extracts of valerian roots (Valeriana officinalis L.) was prepared with solvents of different polarity. Polar as well as nonpolar extracts were found to interact with adenosine A(1) receptors. While polar extracts activated A(1) receptors (partial agonistic activity), nonpolar extracts showed antagonistic or inverse agonistic activity at A(1) receptors, as demonstrated by GTPgammaS binding assays at human recombinant A(1) receptors stably expressed in Chinese hamster ovary (CHO) cells. Guided by radioligand binding assays, fractionation of a lipophilic petroleum ether:diethyl ether (1:1) extract led to the isolation of isovaltrate, which was characterized as a potent, highly efficacious inverse agonist at adenosine A(1) receptors (K(i) rat A(1): 2.05 microM). In experiments at rat brain slices measuring post-synaptic potentials (PSPs) in cortical neurons, isovaltrate at least partly reversed the reduction in the PSPs induced by the adenosine A(1) receptor agonist N(6)-cyclopentyladenosine (CPA). Isovaltrate may serve as a new lead structure for the development of inverse agonists at adenosine A(1) receptors. The common use of hydrophilic, but not lipophilic valerian extracts as mild sleep-inducing agents is consistent with the opposite actions of hydrophilic and lipophilic extracts on adenosine receptors. PMID:17097622

  4. Identification of proteins that interact with mammalian peptide:N-glycanase and implicate this hydrolase in the proteasome-dependent pathway for protein degradation

    PubMed Central

    Park, Hangil; Suzuki, Tadashi; Lennarz, William J.

    2001-01-01

    Peptide:N-glycanase (PNGase) cleaves oligosaccharide chains from glycopeptides and glycoproteins. Recently the deduced amino acid sequence of a cytoplasmic PNGase has been identified in various eukaryotes ranging from yeast to mammals, suggesting that deglycosylation may play a central role in some catabolic process. Several lines of evidence indicate that the cytoplasmic enzyme is involved in the quality control system for newly synthesized glycoproteins. Two-hybrid library screening by using mouse PNGase as the target yielded several PNGase-interacting proteins that previously had been implicated in proteasome-dependent protein degradation: mHR23B, ubiquitin, a regulatory subunit of the 19S proteasome, as well as a protein containing an ubiquitin regulatory motif (UBX) and an ubiquitin-associated motif (UBA). These findings by using the two-hybrid system were further confirmed either by in vitro binding assays or size fractionation assays. These results suggest that PNGase may be required for efficient proteasome-mediated degradation of misfolded glycoproteins in mammalian cells. PMID:11562482

  5. Identification of mZnf8, a Mouse Krüppel-Like Transcriptional Repressor, as a Novel Nuclear Interaction Partner of Smad1

    PubMed Central

    Jiao, Kai; Zhou, Yingna; Hogan, Brigid L. M.

    2002-01-01

    To identify novel genes that play critical roles in mediating bone morphogenetic protein (BMP) signal pathways, we performed a yeast two-hybrid screen using Smad1 as bait. A novel mouse Krüppel-type zinc finger protein, mZnf8, was isolated. Interactions between mZnf8 and Smad proteins were further analyzed with various in vitro and in vivo approaches, including mammalian two-hybrid, in vitro glutathione S-transferase pulldown, and copurification assays. Results from functional analysis indicate that mZnf8 is a nuclear transcriptional repressor. Overexpression of mZnf8 represses activity of BMP and transforming growth factor beta (TGF-?) reporters. Silencing the expression of endogenous mZnf8 with an RNA interference approach caused a significant increase in the expression of one BMP reporter. These results suggest that mZnf8 negatively regulates the TGF-?/BMP signaling pathway in vivo. Transcription of mZnf8 is ubiquitous in mouse embryos, but high levels are specifically observed in adult mouse testes, with the same cell- and stage-specific transcription pattern as Smad1. Our data support the hypothesis that mZnf8 plays critical roles in mediating BMP signaling during spermatogenesis. PMID:12370310

  6. Dynamics of Rickettsia-tick interactions: identification and characterization of differentially expressed mRNAs in uninfected and infected Dermacentor variabilis.

    PubMed

    Mulenga, A; Macaluso, K R; Simser, J A; Azad, A F

    2003-04-01

    To begin to explore the molecular dynamics of rickettsial tick interaction, subtractive hybridization was used to screen mRNAs in Rickettsia montanensis-infected and uninfected Dermacentor variabilis. We isolated 30 cDNA fragments, 22 of which were up-regulated and eight were down-regulated in response to rickettsial infection. Based on a putative identity of 11 cDNA fragments with similarity to known protein families, the tick genetic factors have been assigned into three groups including, the tick immune response factors (alpha-2 macroglobulin and IgE-dependent histamine release factor), the receptor/adhesion molecules (the signal transducer and activator of transcription-1/3 protein inhibitor, the clathrin adaptor protein and tetraspanin) and the stress response proteins (aldose reductase, glutathione-S transferase, ferritin, nucleosome assembly protein and cyclin A protein). Density analyses of semiquantitative RT-PCR amplified products demonstrated differential expression for 18 of the 23 tested genetic factors, apparently representing a 78% agreement with results obtained by subtractive hybridization. Additionally, mRNA transcripts of 17 of the 23 tested genetic factors were amplified from tick haemocytes/circulatory cells demonstrating that their expression is not restricted to the ovaries and suggesting a potential involvement in the immune response. PMID:12653940

  7. Adversarial Model for Radio Frequency Identification

    Microsoft Academic Search

    G. Avoine

    2006-01-01

    Abstract Radio Frequency Identification (RFID) systems aim to identify objects in open en - vironments with neither physical nor visual contact They consist of transponders inserted into objects, of readers, and usually of a database which contains information about the objects The key point is that authorised readers must be able to identify tags without an adversary being able to

  8. Key Role of CRF in the Skin Stress Response System

    PubMed Central

    Zmijewski, Michal A.; Zbytek, Blazej; Tobin, Desmond J.; Theoharides, Theoharis C.; Rivier, Jean

    2013-01-01

    The discovery of corticotropin-releasing factor (CRF) or CRH defining the upper regulatory arm of the hypothalamic-pituitary-adrenal (HPA) axis, along with the identification of the corresponding receptors (CRFRs 1 and 2), represents a milestone in our understanding of central mechanisms regulating body and local homeostasis. We focused on the CRF-led signaling systems in the skin and offer a model for regulation of peripheral homeostasis based on the interaction of CRF and the structurally related urocortins with corresponding receptors and the resulting direct or indirect phenotypic effects that include regulation of epidermal barrier function, skin immune, pigmentary, adnexal, and dermal functions necessary to maintain local and systemic homeostasis. The regulatory modes of action include the classical CRF-led cutaneous equivalent of the central HPA axis, the expression and function of CRF and related peptides, and the stimulation of pro-opiomelanocortin peptides or cytokines. The key regulatory role is assigned to the CRFR-1? receptor, with other isoforms having modulatory effects. CRF can be released from sensory nerves and immune cells in response to emotional and environmental stressors. The expression sequence of peptides includes urocortin/CRF?pro-opiomelanocortin?ACTH, MSH, and ?-endorphin. Expression of these peptides and of CRFR-1? is environmentally regulated, and their dysfunction can lead to skin and systemic diseases. Environmentally stressed skin can activate both the central and local HPA axis through either sensory nerves or humoral factors to turn on homeostatic responses counteracting cutaneous and systemic environmental damage. CRF and CRFR-1 may constitute novel targets through the use of specific agonists or antagonists, especially for therapy of skin diseases that worsen with stress, such as atopic dermatitis and psoriasis. PMID:23939821

  9. Key role of CRF in the skin stress response system.

    PubMed

    Slominski, Andrzej T; Zmijewski, Michal A; Zbytek, Blazej; Tobin, Desmond J; Theoharides, Theoharis C; Rivier, Jean

    2013-12-01

    The discovery of corticotropin-releasing factor (CRF) or CRH defining the upper regulatory arm of the hypothalamic-pituitary-adrenal (HPA) axis, along with the identification of the corresponding receptors (CRFRs 1 and 2), represents a milestone in our understanding of central mechanisms regulating body and local homeostasis. We focused on the CRF-led signaling systems in the skin and offer a model for regulation of peripheral homeostasis based on the interaction of CRF and the structurally related urocortins with corresponding receptors and the resulting direct or indirect phenotypic effects that include regulation of epidermal barrier function, skin immune, pigmentary, adnexal, and dermal functions necessary to maintain local and systemic homeostasis. The regulatory modes of action include the classical CRF-led cutaneous equivalent of the central HPA axis, the expression and function of CRF and related peptides, and the stimulation of pro-opiomelanocortin peptides or cytokines. The key regulatory role is assigned to the CRFR-1? receptor, with other isoforms having modulatory effects. CRF can be released from sensory nerves and immune cells in response to emotional and environmental stressors. The expression sequence of peptides includes urocortin/CRF?pro-opiomelanocortin?ACTH, MSH, and ?-endorphin. Expression of these peptides and of CRFR-1? is environmentally regulated, and their dysfunction can lead to skin and systemic diseases. Environmentally stressed skin can activate both the central and local HPA axis through either sensory nerves or humoral factors to turn on homeostatic responses counteracting cutaneous and systemic environmental damage. CRF and CRFR-1 may constitute novel targets through the use of specific agonists or antagonists, especially for therapy of skin diseases that worsen with stress, such as atopic dermatitis and psoriasis. PMID:23939821

  10. Peptide identification

    DOEpatents

    Jarman, Kristin H [Richland, WA; Cannon, William R [Richland, WA; Jarman, Kenneth D [Richland, WA; Heredia-Langner, Alejandro [Richland, WA

    2011-07-12

    Peptides are identified from a list of candidates using collision-induced dissociation tandem mass spectrometry data. A probabilistic model for the occurrence of spectral peaks corresponding to frequently observed partial peptide fragment ions is applied. As part of the identification procedure, a probability score is produced that indicates the likelihood of any given candidate being the correct match. The statistical significance of the score is known without necessarily having reference to the actual identity of the peptide. In one form of the invention, a genetic algorithm is applied to candidate peptides using an objective function that takes into account the number of shifted peaks appearing in the candidate spectrum relative to the test spectrum.

  11. Getting a feel for parameters: using interactive parallel plots as a tool for parameter identification in the new rainfall-runoff model WALRUS

    NASA Astrophysics Data System (ADS)

    Brauer, Claudia; Torfs, Paul; Teuling, Ryan; Uijlenhoet, Remko

    2015-04-01

    Recently, we developed the Wageningen Lowland Runoff Simulator (WALRUS) to fill the gap between complex, spatially distributed models often used in lowland catchments and simple, parametric models which have mostly been developed for mountainous catchments (Brauer et al., 2014ab). This parametric rainfall-runoff model can be used all over the world in both freely draining lowland catchments and polders with controlled water levels. The open source model code is implemented in R and can be downloaded from www.github.com/ClaudiaBrauer/WALRUS. The structure and code of WALRUS are simple, which facilitates detailed investigation of the effect of parameters on all model variables. WALRUS contains only four parameters requiring calibration; they are intended to have a strong, qualitative relation with catchment characteristics. Parameter estimation remains a challenge, however. The model structure contains three main feedbacks: (1) between groundwater and surface water; (2) between saturated and unsaturated zone; (3) between catchment wetness and (quick/slow) flowroute division. These feedbacks represent essential rainfall-runoff processes in lowland catchments, but increase the risk of parameter dependence and equifinality. Therefore, model performance should not only be judged based on a comparison between modelled and observed discharges, but also based on the plausibility of the internal modelled variables. Here, we present a method to analyse the effect of parameter values on internal model states and fluxes in a qualitative and intuitive way using interactive parallel plotting. We applied WALRUS to ten Dutch catchments with different sizes, slopes and soil types and both freely draining and polder areas. The model was run with a large number of parameter sets, which were created using Latin Hypercube Sampling. The model output was characterised in terms of several signatures, both measures of goodness of fit and statistics of internal model variables (such as the percentage of rain water travelling through the quickflow reservoir). End users can then eliminate parameter combinations with unrealistic outcomes based on expert knowledge using interactive parallel plots. In these plots, for instance, ranges can be selected for each signature and only model runs which yield signature values in these ranges are highlighted. The resulting selection of realistic parameter sets can be used for ensemble simulations. C.C. Brauer, A.J. Teuling, P.J.J.F. Torfs, R. Uijlenhoet (2014a): The Wageningen Lowland Runoff Simulator (WALRUS): a lumped rainfall-runoff model for catchments with shallow groundwater, Geoscientific Model Development, 7, 2313-2332, www.geosci-model-dev.net/7/2313/2014/gmd-7-2313-2014.pdf C.C. Brauer, P.J.J.F. Torfs, A.J. Teuling, R. Uijlenhoet (2014b): The Wageningen Lowland Runoff Simulator (WALRUS): application to the Hupsel Brook catchment and Cabauw polder, Hydrology and Earth System Sciences, 18, 4007-4028, www.hydrol-earth-syst-sci.net/18/4007/2014/hess-18-4007-2014.pdf

  12. Florida Keys NMS: Coral Reefs

    NSDL National Science Digital Library

    Florida Keys National Marine Sanctuary's page with information on coral reefs and links to information on research, restoration and monitoring. Wealth of information on the protection of Florida's coral reefs and the Florida Keys as a whole. Includes an in-class activity for grades K-5, as well as information on a Keys field experience and teacher workshops. Information on safe diving and snorkeling. Education materials available for purchase, including the Seagrass Toolbox.

  13. Key Management for UMTS MBMS

    Microsoft Academic Search

    Shin-ming Cheng; Wei-ru Lai; Kwang-cheng Chen

    2008-01-01

    3GPP 33.246 proposes key management mechanism (KMM) to distribute security keys for universal mobile telecommunications system (UMTS) multimedia broadcast and multicast service (MBMS). KMM introduces extra communication overhead to UMTS. The previous study, key-tree scheme (KTS), resolves this issue for the IP multicast network. However, this scheme may not be so efficient while applied in UMTS MBMS due to lots

  14. Workplace Keys. Piloting the Key Competencies in Workplace Training.

    ERIC Educational Resources Information Center

    Hager, Paul; McIntyre, John; Moy, Janelle; Comyn, Paul; Stone, Jacqui; Schwenke, Cristina; Gonczi, Andrew

    A project investigated the integration of key competencies into workplace training in Australia. Part 1 of the project researched the work of personnel engaged in on-the-job training (OJT) curriculum development in five industries to find out how key competencies were being incorporated into OJT curricula and to suggest models to guide this…

  15. Dynamic Feature Identification: The Satellite Palette

    NSDL National Science Digital Library

    COMET

    2006-01-10

    This series addresses the use of satellite imagery and focuses attention on the identification of dynamic features using high-resolution satellite imagery with NWP verification. The series will eventually include more than 20 feature presentations on topics such as comma clouds, jet streaks, deformation zones, surface features, convection, and blocking. Each feature presentation includes interactive identification exercises, analysis and diagnosis, conceptual models, and forecast implications.

  16. Cloud Identification

    NSDL National Science Digital Library

    2012-08-03

    In this online, interactive module, students learn about the ten common cloud types and how they are formed and how to identify different cloud types on satellite images. The module is part of an online course for grades 7-12 in satellite meteorology, which includes 10 interactive modules. The site also includes lesson plans developed by teachers and links to related resources. Each module is designed to serve as a stand-alone lesson, however, a sequential approach is recommended. Designed to challenge students through the end of 12th grade, middle school teachers and students may choose to skim or skip a few sections.

  17. Sectorized Location Dependent Key Management

    Microsoft Academic Search

    Mohammad Reza Faghani; S. M. Amin Motahari

    2009-01-01

    Wireless sensor networks (WSNs) have been deployed largely due to recent advances in wireless communication technologies. These sensors may be deployed in adverse or even hostile environments so they should consider security issues in their communications. In this paper we proposed sectorized location dependent key management (SLDK) based on Anjum's LDK algorithm in which generation of link securing keys, depends

  18. Secret Public Key Protocols Revisited

    NASA Astrophysics Data System (ADS)

    Lim, Hoon Wei; Paterson, Kenneth G.

    Password-based protocols are important and popular means of providing human-to-machine authentication. The concept of secret public keys was proposed more than a decade ago as a means of securing password-based authentication protocols against off-line password guessing attacks, but was later found vulnerable to various attacks. In this paper, we revisit the concept and introduce the notion of identity-based secret public keys. Our new identity-based approach allows secret public keys to be constructed in a very natural way using arbitrary random strings, eliminating the structure found in, for example, RSA or ElGamal keys. We examine identity-based secret public key protocols and give informal security analyses, indicating that they are secure against off-line password guessing and other attacks.

  19. Automated twin identification technique for use with electron backscatter diffraction.

    SciTech Connect

    Henrie, B. L. (Benjamin Lyman); Mason, T. A. (Thomas A.); Bingert, J. F. (John F.)

    2004-01-01

    Historically, twinning information has been obtained by optical microscopy, TEM, and neutron diffraction. Recent research has shown that automated electron backscatter diffraction (EBSD) can be used to extract reliable twinning statistics. An automated twin identification technique for use with EBSD has facilitated a greater understanding of deformation twinning in materials. The key features of this automated framework are the use of the crystallographic definition of twin relationships, the inclination of the common K, plane at a twin boundary, and the correct identification of the parent orientation in a parent/twin pair. The complex nature of the parent/twin interactions required the use of a voting scheme to correctly identify parent orientations. In those few cases were the voting scheme was unable to determine parent orientation (< 2 pct) the algorithm allows for manual selection. Twin area fractions are categorized by operative twin systems along with secondary and tertiary twinning. These statistics are reported for {alpha}-zirconium and 316L stainless steel. These improved twin statistics can help quantify deformation processes as well as provide validation of plasticity models for materials that exhibit deformation twinning.

  20. Bacterial Identification Virtual Lab

    NSDL National Science Digital Library

    Created by the Howard Hughes Medical Institute (HHMI), the Virtual Bacterial Identification Lab provides interested parties with a great way to learn about the science and techniques used to identify different types of bacteria based on their DNA sequences. Visitors can enter the lab and get started by preparing samples from a patient, copying the desired pieces of the DNA, and then sequencing and analyzing the DNA. The entire experience is quite interactive: visitors can record their observations in the Notebook area and also learn about the various samples, which were obtained from stool, lymph nodes, urine, and blood. Finally, there's the Reference area, which contains a glossary of terms, a list of tools in the lab, and an encyclopedia of selected bacteria and other pathogens.

  1. PINS chemical identification software

    DOEpatents

    Caffrey, Augustine J.; Krebs, Kennth M.

    2004-09-14

    An apparatus and method for identifying a chemical compound. A neutron source delivers neutrons into the chemical compound. The nuclei of chemical elements constituting the chemical compound emit gamma rays upon interaction with the neutrons. The gamma rays are characteristic of the chemical elements constituting the chemical compound. A spectrum of the gamma rays is generated having a detection count and an energy scale. The energy scale is calibrated by comparing peaks in the spectrum to energies of pre-selected chemical elements in the spectrum. A least-squares fit completes the calibration. The chemical elements constituting the chemical compound can be readily determined, which then allows for identification of the chemical compound.

  2. Secret-Key Agreement without Public-Key Cryptography

    Microsoft Academic Search

    Frank Thomson Leighton; Silvio Micali

    1993-01-01

    In this paper, we describe novel approaches to secret-key agreement. Our schemes are not based on public-key cryptography\\u000a nor number theory. They are extremely efficient implemented in software or make use of very simple unexpensive hardware. Our\\u000a technology is particularly well-suited for use in cryptographic scenarios like those of the Clipper Chip, the recent encryption\\u000a proposal put forward by the

  3. The LOFAR Transients Key Project

    E-print Network

    Rob Fender; Robert Braun; Ben Stappers; Ralph Wijers; Michael Wise; Thijs Coenen; Heino Falcke; Jean-Mathias Griessmeier; Michiel van Haarlem; Peter Jonker; Casey Law; Sera Markoff; Joseph Masters; James Miller-Jones; Rachel Osten; Bart Scheers; Hanno Spreeuw; John Swinbank; Corina Vogt; Rudy Wijnands; Philippe Zarka

    2006-11-09

    LOFAR, the Low Frequency Array, is a new radio telescope under construction in the Netherlands, designed to operate between 30 and 240 MHz. The Transients Key Project is one of the four Key Science Projects which comprise the core LOFAR science case. The remit of the Transients Key Project is to study variable and transient radio sources detected by LOFAR, on timescales from milliseconds to years. This will be achieved via both regular snapshot monitoring of historical and newly-discovered radio variables and, most radically, the development of a `Radio Sky Monitor' which will survey a large fraction of the northern sky on a daily basis.

  4. Free-Space Quantum Key Distribution using Polarization Entangled Photons

    NASA Astrophysics Data System (ADS)

    Kurtsiefer, Christian

    2007-06-01

    We report on a complete experimental implementation of a quantum key distribution protocol through a free space link using polarization-entangled photon pairs from a compact parametric down-conversion source [1]. Based on a BB84-equivalent protocol, we generated without interruption over 10 hours a secret key free-space optical link distance of 1.5 km with a rate up to 950 bits per second after error correction and privacy amplification. Our system is based on two time stamp units and relies on no specific hardware channel for coincidence identification besides an IP link. For that, initial clock synchronization with an accuracy of better than 2 ns is achieved, based on a conventional NTP protocol and a tiered cross correlation of time tags on both sides. Time tags are used to servo a local clock, allowing a streamed measurement on correctly identified photon pairs. Contrary to the majority of quantum key distribution systems, this approach does not require a trusted large-bandwidth random number generator, but integrates that into the physical key generation process. We discuss our current progress of implementing a key distribution via an atmospherical link during daylight conditions, and possible attack scenarios on a physical timing information side channel to a entanglement-based key distribution system. [1] I. Marcikic, A. Lamas-Linares, C. Kurtsiefer, Appl. Phys. Lett. 89, 101122 (2006).

  5. A secure and efficient conference key distribution system

    Microsoft Academic Search

    Mike Burmester; Yvo Desmedt

    We present practical conference key distribution systems based on public keys, which authenticate the users and which are\\u000a ‘proven’ secure provided the Diffie-Hellman problem is intractable. A certain number of interactions is needed but the overall\\u000a cost is low. There is a complexity tradeoff. Depending on the network used, we either have a constant (in the number of conference\\u000a participants)

  6. The Role of Ethnic and National Identifications in Perceived Discrimination for Asian Americans: Toward a Better Understanding of the Buffering Effect of Group Identifications on Psychological Distress

    PubMed Central

    Huynh, Que-Lam; Devos, Thierry; Goldberg, Robyn

    2013-01-01

    A robust relationship between perceived racial discrimination and psychological distress has been established. Yet, mixed evidence exists regarding the extent to which ethnic identification moderates this relationship, and scarce attention has been paid to the moderating role of national identification. We propose that the role of group identifications in the perceived discrimination–psychological distress relationship is best understood by simultaneously and interactively considering ethnic and national identifications. A sample of 259 Asian American students completed measures of perceived discrimination, group identifications (specific ethnic identification stated by respondents and national or “mainstream American” identification), and psychological distress (anxiety and depression symptoms). Regression analyses revealed a significant three-way interaction of perceived discrimination, ethnic identification, and national identification on psychological distress. Simple-slope analyses indicated that dual identification (strong ethnic and national identifications) was linked to a weaker relationship between perceived discrimination and psychological distress compared with other group identification configurations. These findings underscore the need to consider the interconnections between ethnic and national identifications to better understand the circumstances under which group identifications are likely to buffer individuals against the adverse effects of racial discrimination. PMID:25258674

  7. Global Climate Change Key Indicators

    NSDL National Science Digital Library

    This website charts measurement of key indicators of global climate change. Simple explanations and "What Does This Mean?" sections accompany each area of sea level, carbon dioxide concentration, global surface temperature, Arctic sea ice and land ice.

  8. Security of Quantum Key Distribution

    E-print Network

    Renato Renner

    2006-01-11

    We propose various new techniques in quantum information theory, including a de Finetti style representation theorem for finite symmetric quantum states. As an application, we give a proof for the security of quantum key distribution which applies to arbitrary protocols.

  9. 37 Keys to Laboratory Design.

    ERIC Educational Resources Information Center

    Ruys, Theodorus

    1969-01-01

    Flexibility, adaptability, and expandability are requirements for good laboratory design. This report contains suggestions for improving laboratory planning, construction, and utilization in certain key areas. Special attention is given to incorporating safety equipment and special nonreactive materials. (RA)

  10. DCCPS: BRP: TCRB: Key Initiatives

    Cancer.gov

    Twitter Multimedia Home About Key Initiatives Funding Resources Tools Cancer Control & Population Sciences Home Behavioral Research Program Home Tobacco Control Research Branch Research Topics: Special Populations and Tobacco Tobacco and Health of Women

  11. Key Management in Sensor Networks

    Microsoft Academic Search

    Dahai Xu; Jeffrey Dwoskin; Jianwei Huang; Tian Lan; Ruby Lee; Mung Chiang

    \\u000a Secure communications in wireless ad hoc networks require setting up end-to-end secret keys for communicating node pairs.\\u000a It is widely believed that although being more complex, a probabilistic key predistribution scheme is much more resilient\\u000a against node capture than a deterministic one in lightweight wireless ad hoc networks. Supported by the surprisingly large\\u000a successful attack probabilities (SAPs) computed in this

  12. System Identification of Civil Engineering Structures through Wireless Structural Monitoring and Subspace System Identification Methods

    E-print Network

    Lynch, Jerome P.

    System Identification of Civil Engineering Structures through Wireless Structural Monitoring of the requirements for the degree of Doctor of Philosophy (Civil Engineering) in The University of Michigan 2011 engineers; amazingly, there were many keys which unlocked many civil engineering problems. All achievements

  13. Identification of Terrestrial Reflectance From Remote Sensing

    NASA Technical Reports Server (NTRS)

    Alter-Gartenberg, Rachel; Nolf, Scott R.; Stacy, Kathryn (Technical Monitor)

    2000-01-01

    Correcting for atmospheric effects is an essential part of surface-reflectance recovery from radiance measurements. Model-based atmospheric correction techniques enable an accurate identification and classification of terrestrial reflectances from multi-spectral imagery. Successful and efficient removal of atmospheric effects from remote-sensing data is a key factor in the success of Earth observation missions. This report assesses the performance, robustness and sensitivity of two atmospheric-correction and reflectance-recovery techniques as part of an end-to-end simulation of hyper-spectral acquisition, identification and classification.

  14. Knowledge-guided inference of domain–domain interactions from incomplete protein–protein interaction networks

    E-print Network

    Liu, Mei; Chen, Xue-wen; Jothi, Raja

    2009-08-10

    identification of binding sites; (iii) acquisition of insights into the causes of deleterious mutations at interaction sites; and (iv) most importantly, development of drugs to inhibit pathological protein interactions. In addition, knowledge derived from known...

  15. What are the Benefits of Interacting with Nature?

    PubMed Central

    Keniger, Lucy E.; Gaston, Kevin J.; Irvine, Katherine N.; Fuller, Richard A.

    2013-01-01

    There is mounting empirical evidence that interacting with nature delivers measurable benefits to people. Reviews of this topic have generally focused on a specific type of benefit, been limited to a single discipline, or covered the benefits delivered from a particular type of interaction. Here we construct novel typologies of the settings, interactions and potential benefits of people-nature experiences, and use these to organise an assessment of the benefits of interacting with nature. We discover that evidence for the benefits of interacting with nature is geographically biased towards high latitudes and Western societies, potentially contributing to a focus on certain types of settings and benefits. Social scientists have been the most active researchers in this field. Contributions from ecologists are few in number, perhaps hindering the identification of key ecological features of the natural environment that deliver human benefits. Although many types of benefits have been studied, benefits to physical health, cognitive performance and psychological well-being have received much more attention than the social or spiritual benefits of interacting with nature, despite the potential for important consequences arising from the latter. The evidence for most benefits is correlational, and although there are several experimental studies, little as yet is known about the mechanisms that are important for delivering these benefits. For example, we do not know which characteristics of natural settings (e.g., biodiversity, level of disturbance, proximity, accessibility) are most important for triggering a beneficial interaction, and how these characteristics vary in importance among cultures, geographic regions and socio-economic groups. These are key directions for future research if we are to design landscapes that promote high quality interactions between people and nature in a rapidly urbanising world. PMID:23466828

  16. Identification of Immature Insects

    NSDL National Science Digital Library

    0000-00-00

    A Virginia Tech. page devoted to identification of household insect pest immatures. Eight illustrated categories allow the user to match their pest to a likely species. This is just one of several pages devoted to insect identification.

  17. Obtaining material identification with cosmic ray radiography

    SciTech Connect

    Morris, C. L.; Borozdin, Konstantin; Bacon, Jeffrey; Chen, Elliott; Lukic, Zarija; Milner, Edward; Miyadera, Haruo; Perry, John [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Schwellenbach, Dave; Aberle, Derek; Dreesen, Wendi; Green, J. Andrew; McDuff, George G. [National Security Technologies, Los Alamos, NM 87544 (United States); Nagamine, Kanetada [KEK, Tsukuba, Ibaraki, 305-0801 (Japan); RIKEN, Wako, Saitama, 351-0198 (Japan) and UC-Riverside, CA 92521 (United States); Sossong, Michael [Decision Sciences, 12345 First American Way, Suite 130, Poway, CA 92064 (United States); Spore, Candace; Toleman, Nathan [Department of Chemical and Nuclear Engineering, University of New Mexico, Albuquerque, NM 87131-0001 (United States)

    2012-12-15

    The passage of muons through matter is dominated by the Coulomb interaction with electrons and nuclei in the matter. The muon interaction with the electrons leads to continuous energy loss and stopping of the muons. The muon interaction with nuclei leads to angular diffusion. Using both stopped muons and angle diffusion interactions allows us to determine density and identify materials. Here we demonstrate material identification using data taken at Los Alamos with a particle tracker built from a set of sealed drift tubes with commercial electronics and software, the Mini Muon Tracker (MMT).

  18. Keys and Pseudo-Keys Detection for Web Datasets Cleansing and Interlinking

    E-print Network

    Paris-Sud XI, Université de

    Keys and Pseudo-Keys Detection for Web Datasets Cleansing and Interlinking Manuel Atencia1,2 , J-Keys Detection for Web Datasets Cleansing 145 term pseudo-key. We also put forward to associate discovered keys

  19. Work Keys: Integrating Work Keys in the Business Environment.

    ERIC Educational Resources Information Center

    Hater, John J.

    Work Keys (occupational tests developed by American College Testing) could support an employer's human resource function in a number of ways: (1) communicating to educators the skill requirements for an employer's particular jobs on a national basis; (2) providing students with a realistic preview of skills needed for jobs and an assessment of…

  20. Simultaneous identification of moving masses and structural damage

    Microsoft Academic Search

    Qingxia Zhang; ?ukasz Jankowski; Zhongdong Duan

    2010-01-01

    A method for simultaneous identification of moving masses and damages of the supporting structure from measured responses\\u000a is presented. The interaction forces between the masses and the structure are used as excitation. Masses and damage extents\\u000a are used as the optimization variables; compared to the approaches based on identification of the interaction forces, it allows\\u000a ill-conditioning to be avoided and

  1. One-way information reconciliation schemes of quantum key distribution

    E-print Network

    Li Yang; Zhao Li

    2012-05-14

    Information reconciliation(IR) is a basic step of quantum key distribution (QKD). Classical message interaction is necessary in a practical IR scheme, and the communication complexity has become a bottleneck of QKD's development. Here we propose a concatenated method of IR scheme which requires only one time one-way communication to achieve any given error rate level. A QKD scheme with the concatenated IR can work without the special interaction of error rate estimation.

  2. Obtaining material identification with cosmic ray radiography

    E-print Network

    Morris, Christopher; Bacon, Jeffrey; Chen, Elliott; Luki?, Zarija; Milner, Edward; Miyadera, Haruo; Perry, John; Schwellenbach, Dave; Aberle, Derek; Dreesen, Wendi; Green, J Andrew; McDuff, George G; Nagamine, Kanetada; Sossong, Michael; Spore, Candace; Toleman, Nathan

    2012-01-01

    The passage of muons through matter is mostly affected by their Coulomb interactions with electrons and nuclei. The muon interactions with electrons lead to continuous energy loss and stopping of muons, while their scattering off nuclei lead to angular 'diffusion'. By measuring both the number of stopped muons and angular changes in muon trajectories we can estimate density and identify materials. Here we demonstrate the material identification using data taken at Los Alamos with the Mini Muon Tracker.

  3. Obtaining material identification with cosmic ray radiography

    E-print Network

    Christopher Morris; Konstantin Borozdin; Jeffrey Bacon; Elliott Chen; Zarija Luki?; Edward Milner; Haruo Miyadera; John Perry; Dave Schwellenbach; Derek Aberle; Wendi Dreesen; J. Andrew Green; George G. McDuff; Kanetada Nagamine; Michael Sossong; Candace Spore; Nathan Toleman

    2012-10-23

    The passage of muons through matter is mostly affected by their Coulomb interactions with electrons and nuclei. The muon interactions with electrons lead to continuous energy loss and stopping of muons, while their scattering off nuclei lead to angular 'diffusion'. By measuring both the number of stopped muons and angular changes in muon trajectories we can estimate density and identify materials. Here we demonstrate the material identification using data taken at Los Alamos with the Mini Muon Tracker.

  4. Florida Everglades and Keys, USA

    NASA Technical Reports Server (NTRS)

    1991-01-01

    Though much of southern Florida is covered by clouds, the Florida Everglades and Keys (25.0N, 82.0W) remain relatively clear in this nearly vertical view. The view covers the Gulf of Mexico port city of Ft. Myers, and Lake Okeechobee, at the top of the scene, in the north, The Everglades, in the center and the entire Florida Key Chain at the bottom. Even with the many popcorn clouds, ground detail and the city of Miami is easily discerned.

  5. Network security via private-key certificates

    Microsoft Academic Search

    Don Davis; Ralph R. Swick

    1990-01-01

    We present some practical security protocols that use private-key encryption in the public-key style. Our system combines a new notion of private-key certificates, a simple key-translation protocol, and key-distribution. These certificates can be administered and used much as public-key certificates are, so that users can communicate securely while sharing neither an encryption key nor a network connection.

  6. Key questions regarding work engagement

    Microsoft Academic Search

    Arnold B. Bakker; Simon L. Albrecht; Michael P. Leiter

    2011-01-01

    This article discusses the concept of work engagement and summarizes research on its most important antecedents. The authors formulate 10 key questions and shape a research agenda for engagement. In addition to the conceptual development and measurement of enduring work engagement, the authors discuss the importance of state work engagement. Further, they argue that the social context is crucial and

  7. Results: The Key to Renewal.

    ERIC Educational Resources Information Center

    Schmoker, Mike; Wilson, Richard B.

    1995-01-01

    The key to renewal is emphasis on results and the conditions favoring them. Short-term results are pivotal to improvement efforts, particularly for automobile plants and schools striving to apply Deming's TQM principles. Success depends on regular collaboration focused on well-defined, measurable student performance goals and frequent monitoring…

  8. Reggio Emilia: Four Key Ideas.

    ERIC Educational Resources Information Center

    Albrecht, Kay

    1996-01-01

    Applies key components of the Reggio Emilia approach to Hearts Home, a Houston school: (1) parent-teacher-child interdependence, including home visits, communication, training sessions, and field trips; (2) children's competence; (3) utilizing functional and beautiful learning environments; and (4) teachers as partners in co-construction of…

  9. Quantum key distribution over 300

    NASA Astrophysics Data System (ADS)

    Ozhegov, R.; Elezov, M.; Kurochkin, Y.; Kurochkin, V.; Divochiy, A.; Kovalyuk, V.; Vachtomin, Y.; Smirnov, K.; Goltsman, G.

    2014-12-01

    We discuss the possibility of polarization state reconstruction and measurement over 302 km by Superconducting Single- Photon Detectors (SSPDs). Because of the excellent characteristics and the possibility to be effectively coupled to singlemode optical fiber many applications of the SSPD have already been reported. The most impressive one is the quantum key distribution (QKD) over 250 km distance. This demonstration shows further possibilities for the improvement of the characteristics of quantum-cryptographic systems such as increasing the bit rate and the quantum channel length, and decreasing the quantum bit error rate (QBER). This improvement is possible because SSPDs have the best characteristics in comparison with other single-photon detectors. We have demonstrated the possibility of polarization state reconstruction and measurement over 302.5 km with superconducting single-photon detectors. The advantage of an autocompensating optical scheme, also known as "plugandplay" for quantum key distribution, is high stability in the presence of distortions along the line. To increase the distance of quantum key distribution with this optical scheme we implement the superconducting single photon detectors (SSPD). At the 5 MHz pulse repetition frequency and the average photon number equal to 0.4 we measured a 33 bit/s quantum key generation for a 101.7 km single mode ber quantum channel. The extremely low SSPD dark count rate allowed us to keep QBER at 1.6% level.

  10. Two Party RSA Key Generation

    Microsoft Academic Search

    Niv Gilboa

    1999-01-01

    . We present a protocol for two parties to generate an RSAkey in a distributed manner. At the end of the protocol the public key: amodulus N = PQ, and an encryption exponent e are known to both parties.Individually, neither party obtains information about the decryptionkey d and the prime factors of N : P and Q. However, d is

  11. Fair Encryption of RSA Keys

    Microsoft Academic Search

    Guillaume Poupard; Jacques Stern

    2000-01-01

    Cryptography is more and more concerned with elaborate protocols involving many participants. In some cases, it is crucial to be sure that players behave fairly especially when they use public key en- cryption. Accordingly, mechanisms are needed to check the correctness of encrypted data, without compromising secrecy. We consider an op- timistic scenario in which users have pairs of public

  12. Key Issues in Hadronic Physics

    SciTech Connect

    Simon Capstick; et. Al.

    2000-12-01

    A group of fifty physicists met in Duck, NC, Nov. 6-9 to discuss the current status and future goals of hadronic physics. The main purpose of the meeting was to define the field by identifying its key issues, challenges, and opportunities. The conclusions, incorporating considerable input from the community at large, are presented in this white paper.

  13. Ten Keys to the Portal

    ERIC Educational Resources Information Center

    Schaffhauser, Dian

    2011-01-01

    Successful web portals help users stay informed, in touch, and up to speed. They are also a telling window into the efficiency of one's institution. To develop a cutting-edge portal takes planning, communication, and research. In this article, the author presents and discusses 10 keys to portal success: (1) make critical info visible; (2) make the…

  14. Key Request Form OSC Room 641

    E-print Network

    Arizona, University of

    Key Request Form OSC Room 641 **Valid CatCard and OSC Key Card are needed to process key requests free to call the OSC Accounting Office at 621-4600 or 621-4151. BUILDING;Meinel/McKale/Gould-Simpson Building Key Policies The OSC Accounting Office handles all requests for keys

  15. INTRODUCTION Hedgehog (Hh) signaling plays a key role in inductive

    E-print Network

    Chuang, Pao-Tien

    INTRODUCTION Hedgehog (Hh) signaling plays a key role in inductive interactions in many tissues. For example, sonic hedgehog (Shh) expression in the notochord and floor plate patterns the ventral neural tube is transduced through hedgehog binding to patched 1 (Ptch), a multipass transmembrane protein (reviewed

  16. Integration of Biological Data Resources Using Image Object Keying

    Microsoft Academic Search

    Nawaz Khan; Shahedur Rahman; A. G. Stockman

    2003-01-01

    This paper presents a novel approach to integrate biological data from multiple resources into a single page using image object keying. In this interactive approach, a gel electrophoresis protein spot is selected by the user which initiates the retrieval of corresponding 3D structure of the protein. It provides a set of operators to access and to collect elements content of

  17. An Efficient Key Management Solution for Personal Network Federations

    Microsoft Academic Search

    Shahab Mirzadeh; Haitham Cruickshank; Rahim Tafazolli

    2008-01-01

    Personal network federation (PN-F) aims to provide secure interactions between a subset of devices of different personal networks (PN) for achieving a common goal or providing some services in collaborative environments. Security and privacy is one of the major concerns in the development and acceptance of PN-F like collaborative networks and as any other security architecture, the key management is

  18. The growing “magic” of automatic identification

    Microsoft Academic Search

    J. Swartz

    1999-01-01

    Automatic identification represents a set of technologies that seems to work like magic. It's knowing instantly what's in a crate from 30 feet away; talking or looking into a machine that will automatically unlock a door; laser zapping a simple stamp-sized paper-and-ink symbol that describes an entire truck's contents; or instantly identifying a fingerprint-an unalterable and unique personal key to

  19. Cycle Structure of the DES for Keys Having Palindromic (or Antipalindromic) Sequences of Round Keys

    Microsoft Academic Search

    Judy H. Moore; Gustavus J. Simmons

    1987-01-01

    Certain DES keys have been called weak or semiweak based upon the number of distinct round keys which they produce. For the weak keys, all 16 round keys are identical and encryption is the same as decryption. For the semiweak keys, there are only two distinct round keys but no specific weakness of the DES with these keys has been

  20. Efficient biometric authenticated key agreements based on extended chaotic maps for telecare medicine information systems.

    PubMed

    Lou, Der-Chyuan; Lee, Tian-Fu; Lin, Tsung-Hung

    2015-05-01

    Authenticated key agreements for telecare medicine information systems provide patients, doctors, nurses and health visitors with accessing medical information systems and getting remote services efficiently and conveniently through an open network. In order to have higher security, many authenticated key agreement schemes appended biometric keys to realize identification except for using passwords and smartcards. Due to too many transmissions and computational costs, these authenticated key agreement schemes are inefficient in communication and computation. This investigation develops two secure and efficient authenticated key agreement schemes for telecare medicine information systems by using biometric key and extended chaotic maps. One scheme is synchronization-based, while the other nonce-based. Compared to related approaches, the proposed schemes not only retain the same security properties with previous schemes, but also provide users with privacy protection and have fewer transmissions and lower computational cost. PMID:25795325