Sample records for interactive identification key

  1. Illustrated Plant Identification Keys: An Interactive Tool to Learn Botany

    ERIC Educational Resources Information Center

    Silva, Helena; Pinho, Rosa; Lopes, Lisia; Nogueira, Antonio J. A.; Silveira, Paulo

    2011-01-01

    An Interactive Dichotomous Key (IDK) for 390 "taxa" of vascular plants from the Ria de Aveiro, available on a website, was developed to help teach botany to school and universitary students. This multimedia tool includes several links to Descriptive and Illustrated Glossaries. Questionnaires answered by high-school and undergraduate students about…

  2. Afrotropical Ophioninae (Hymenoptera, Ichneumonidae): an update of Gauld and Mitchell’s revision, including two new species and an interactive matrix identification key

    PubMed Central

    Rousse, Pascal; van Noort, Simon

    2014-01-01

    Abstract The revision of the Afrotropical Ophioninae is updated, based on the examination of about 800–900 individuals in the South African and European museum collections. A robust interactive matrix key was built to provide quick and reliable identifications. The key is available online at http://www.waspweb.org. Two new species are described: Dicamptus maxipol sp. n. and Enicospilus gauldetmitchellorum sp. n. Numerous new distribution and biological records are provided, and noticeable morphological intra-specific variations are detailed. Enicospilus batus Gauld & Mitchell, syn. n. is considered as a junior synonym of Enicospilus luebberti (Enderlein). PMID:25709521

  3. Identification of Key Barriers in Workforce Development

    SciTech Connect

    None

    2008-03-31

    This report documents the identification of key barriers in the development of an adequate national security workforce as part of the National Security Preparedness Project, being performed under a Department of Energy/National Nuclear Security Administration grant. Many barriers exist that prevent the development of an adequate number of propertly trained national security personnel. Some barriers can be eliminated in a short-term manner, whereas others will involve a long-term strategy that takes into account public policy.

  4. Species Identification Key of Korean Mammal Hair

    PubMed Central

    LEE, Eunok; CHOI, Tae-Young; WOO, Donggul; MIN, Mi-Sook; SUGITA, Shoei; LEE, Hang

    2014-01-01

    ABSTRACT The hair microstructures of Korean terrestrial mammals from 23 species (22 wild and one domestic) were analyzed using light and scanning electron microscopy (SEM) to construct a hair identification key. The hairs were examined using the medulla structures and cuticular scales of guard hairs from the dorsal regions of mature adult animals. All cuticular scale structures in the hair of Rodentia, Lagomorpha, Carnivora and Insectivora showed the petal pattern, and those of Artiodactyla and Chiroptera showed the wave pattern and coronal pattern, respectively. Rodentia, Lagomorpha and Carnivora showed multicellular, and Insectivora and Artiodactyla showed unicellular regular, mesh or columnar in the medulla structures, respectively. Chiroptera did not show the medulla structures in their hair. We found that it is possible to distinguish between species and order based on general appearance, medulla structures and cuticular scales. Thus, we constructed a hair identification key with morphological characteristics from each species. This study suggests that hair identification keys could be useful in fields, such as forensic science, food safety and foraging ecology. PMID:24451929

  5. Species identification key of Korean mammal hair.

    PubMed

    Lee, Eunok; Choi, Tae-Young; Woo, Donggul; Min, Mi-Sook; Sugita, Shoei; Lee, Hang

    2014-05-01

    The hair microstructures of Korean terrestrial mammals from 23 species (22 wild and one domestic) were analyzed using light and scanning electron microscopy (SEM) to construct a hair identification key. The hairs were examined using the medulla structures and cuticular scales of guard hairs from the dorsal regions of mature adult animals. All cuticular scale structures in the hair of Rodentia, Lagomorpha, Carnivora and Insectivora showed the petal pattern, and those of Artiodactyla and Chiroptera showed the wave pattern and coronal pattern, respectively. Rodentia, Lagomorpha and Carnivora showed multicellular, and Insectivora and Artiodactyla showed unicellular regular, mesh or columnar in the medulla structures, respectively. Chiroptera did not show the medulla structures in their hair. We found that it is possible to distinguish between species and order based on general appearance, medulla structures and cuticular scales. Thus, we constructed a hair identification key with morphological characteristics from each species. This study suggests that hair identification keys could be useful in fields, such as forensic science, food safety and foraging ecology. PMID:24451929

  6. 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

  7. Identification Schemes from Key Encapsulation Mechanisms

    NASA Astrophysics Data System (ADS)

    Anada, Hiroaki; Arita, Seiko

    We propose a generic conversion from a key encapsulation mechanism (KEM) to an identification (ID) scheme. The conversion derives the security for ID schemes against concurrent man-in-the-middle (cMiM) attacks from the security for KEMs against adaptive chosen ciphertext attacks on one-wayness (one-way-CCA2). Then, regarding the derivation as a design principle of ID schemes, we develop a series of concrete one-way-CCA2 secure KEMs. We start with El Gamal KEM and prove it secure against non-adaptive chosen ciphertext attacks on one-wayness (one-way-CCA1) in the standard model. Then, we apply a tag framework with the algebraic trick of Boneh and Boyen to make it one-way-CCA2 secure based on the Gap-CDH assumption. Next, we apply the CHK transformation or a target collision resistant hash function to exit the tag framework. And finally, as it is better to rely on the CDH assumption rather than the Gap-CDH assumption, we apply the Twin DH technique of Cash, Kiltz and Shoup. The application is not “black box” and we do it by making the Twin DH technique compatible with the algebraic trick. The ID schemes obtained from our KEMs show the highest performance in both computational amount and message length compared with previously known ID schemes secure against concurrent man-in-the-middle attacks.

  8. Identification and structural mechanism for a novel interaction between a ubiquitin ligase WWP1 and Nogo-A, a key inhibitor for central nervous system regeneration.

    PubMed

    Qin, Haina; Pu, Helen X; Li, Minfen; Ahmed, Sohail; Song, Jianxing

    2008-12-23

    Nogo-A has been extensively demonstrated to play key roles in inhibiting central nervous system regeneration, regulating endoplasmic reticulum formation, and maintaining the integrity of the neuromuscular junction. In this study, an E3 ubiquitin ligase WWP1 was first identified to be a novel interacting partner for Nogo-A both in vitro and in vivo. By using CD, ITC, and NMR, we have further conducted extensive studies on all four WWP1 WW domains and their interactions with a Nogo-A peptide carrying the only PPxY motif. The results lead to several striking findings. (1) Despite containing an unstructured region, the 186-residue WWP1 fragment containing all four WW domains is able to interact with the Nogo-A(650-666) peptide with a high affinity, with a dissociation constant (K(d)) of 1.68 microM. (2) Interestingly, four isolated WW domains show differential structural properties in the free states. WW1 and WW2 are only partially folded, while WW4 is well-folded. Nevertheless, they all become well-folded upon binding to Nogo-A(650-666), with K(d) values ranging from 1.03 to 3.85 microM. (3) The solution structure of the best-folded WW4 domain is determined, and the binding-perturbed residues were derived for both WW4 and Nogo-A(650-666) by NMR HSQC titrations. Moreover, on the basis of the NMR data, the complex model is constructed by HADDOCK 2.0. This study provides rationales as well as a template Nogo-A(650-666) for further design of molecules to intervene in the WWP1-Nogo-A interaction which may regulate the Nogo-A protein level by controlling its ubiquitination. PMID:19035836

  9. 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

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

    PubMed

    Jones, Timothy Mark

    2013-01-01

    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

  11. 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

  12. Session 2 summary and key issues identification

    NASA Technical Reports Server (NTRS)

    Robey, Judith

    1990-01-01

    Identification of specific areas for the technology development; payload/facility requirements; crew safety as the highest priority for the space station; identification of preliminary operational constraints (facilities/experiments requiring specialized equipment and/or procedures, and crew limitations and protective gear requirements); frame of reference of baseline of applicable waste handling experience; use of the workshop as a basis for assessing the current and applicable space station requirements; provision of an educational, and informational forum for government employees, contractors, experimental facility developers, and potential hardware suppliers involved with the Space Station program; and documentation of workshop results and follow-on study issues are examined.

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

    PubMed

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

    2014-01-01

    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

  14. 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

  15. 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…

  16. Molecular identification key for pest species of Scirtothrips (Thysanoptera: Thripidae).

    PubMed

    Rugman-Jones, Paul F; Hoddle, Mark S; Mound, Laurence A; Stouthamer, Richard

    2006-10-01

    Effective plant quarantine and biological control initiatives require rapid and accurate identification of exotic and potentially invasive taxa that may cause high economic losses or environmental 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 assigning specimens to the genus Scirtothrips is straightforward using traditional taxonomic methods, identification of species is much more difficult and requires expert knowledge of the genus. Furthermore, the validity of some Scirtothrips species is questionable. Therefore, an easy, accurate, and highly reliable technique is desirable for Scirtothrips identification. Here, we provide a simple molecular key based on the internal transcribed spacer regions 1 and 2 (ITS1 and ITS2) of nuclear ribosomal DNA. Individual specimens can be identified by amplification of their ITS1 and ITS2 regions with general primers and determining the size of the products by using standard agarose gel electrophoresis, followed in some instances by DNA digestion with the restriction enzymes SacII or PspOM I. The advantage of this identification system is that nonspecialists are able to quickly and cheaply identify individual specimens. Material analyzed for this work was collected in the United States (California), India, South Africa, Kenya, Mexico, Guatemala, Honduras, Nicaragua, Costa Rica, Panama, Australia, New Zealand and Raiatea (Society Islands French Polynesia). We have identified seven pest species with the molecular-based methods described here. It is hoped that this system can be extended to other members of the genus as their ITS1 and ITS2 sequences become available. We also provide molecular confirmation for two new Scirtothrips species, one species from Honduras and one species from New Zealand. PMID:17066817

  17. Key Results of Interaction Models with Centering

    ERIC Educational Resources Information Center

    Afshartous, David; Preston, Richard A.

    2011-01-01

    We consider the effect on estimation of simultaneous variable centering and interaction effects in linear regression. We technically define, review, and amplify many of the statistical issues for interaction models with centering in order to create a useful and compact reference for teachers, students, and applied researchers. In addition, we…

  18. 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

  19. Identification of Modules in Protein-Protein Interaction Networks

    NASA Astrophysics Data System (ADS)

    Erten, Sinan; Koyutürk, Mehmet

    In biological systems, most processes are carried out through orchestration of multiple interacting molecules. These interactions are often abstracted using network models. A key feature of cellular networks is their modularity, which contributes significantly to the robustness, as well as adaptability of biological systems. Therefore, modularization of cellular networks is likely to be useful in obtaining insights into the working principles of cellular systems, as well as building tractable models of cellular organization and dynamics. A common, high-throughput source of data on molecular interactions is in the form of physical interactions between proteins, which are organized into protein-protein interaction (PPI) networks. This chapter provides an overview on identification and analysis of functional modules in PPI networks, which has been an active area of research in the last decade.

  20. Strongly Resilient Non-Interactive Key Predistribution For Hierarchical Networks

    E-print Network

    Chen, Hao

    2010-01-01

    Key establishment is the basic necessary tool in the network security, by which pairs in the network can establish shared keys for protecting their pairwise communications. There have been some key agreement or predistribution schemes with the property that the key can be established without the interaction (\\cite{Blom84,BSHKY92,S97}). Recently the hierarchical cryptography and the key management for hierarchical networks have been active topics(see \\cite{BBG05,GHKRRW08,GS02,HNZI02,HL02,Matt04}. ). Key agreement schemes for hierarchical networks were presented in \\cite{Matt04,GHKRRW08} which is based on the Blom key predistribution scheme(Blom KPS, [1]) and pairing. In this paper we introduce generalized Blom-Blundo et al key predistribution schemes. These generalized Blom-Blundo et al key predistribution schemes have the same security functionality as the Blom-Blundo et al KPS. However different and random these KPSs can be used for various parts of the networks for enhancing the resilience. We also presentk...

  1. Some Ideas for Activities Involving the Construction of Computer-Based Identification Keys.

    ERIC Educational Resources Information Center

    Smith, Mark

    2002-01-01

    Discusses some ideas for applying information and communication technology (ICT) to constructing identification keys. Proposes the use of linked web pages as the most easily used and readily accessible for students aged 12-13. (DDR)

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

    E-print Network

    Law, James Michael

    1989-01-01

    AN IDENTIFICATION OF FINANCIAL AND PRODUCTION PERPORMANCE VARIABLES AS KEY INDICATORS OF DAIRY FIRIII FAILURE A Thesis by JAMES MICHAEL LAW Submitted to the Office of Graduate Studies of Texas A8dN University in partial fulfillment... of the requirements for the degree of MASTER OF SCIENCE May 1989 Major Subject: Agricultural Economics AN IDENTIFICATION OF FINANCIAL AND PRODUCTION PERFORMANCE VARIABLES AS KEY INDICATORS OF DAIRY FIRM FAILURE A Thesis by James Michael Law Approved...

  3. Dichotomous Identification Keys: A Ladder to Higher Order Knowledge about the Human Body

    ERIC Educational Resources Information Center

    Sorgo, Andrej

    2006-01-01

    We tried to enrich teaching human anatomy in high school biology lessons. Students construct dichotomous identification keys to the cells, tissues, organs, or body parts. By doing this, students have achieved higher-order cognitive levels of knowledge because construction of such keys is based on analysis, synthesis, and evaluation. Students found…

  4. A Dichotomous Key for the Identification of Common British Wild Flower Families

    ERIC Educational Resources Information Center

    Wood, Piers

    2004-01-01

    This article argues the need for, and provides, a dichotomous single access key for the identification of common British wild flower families. A minimum of technical vocabulary is used while at the same time retaining most of the recent botanical names of families. The key provides a user-friendly opportunity for school pupils to become familiar…

  5. Statistical mechanics approach to lock-key supramolecular chemistry interactions.

    PubMed

    Odriozola, Gerardo; Lozada-Cassou, Marcelo

    2013-03-01

    In the supramolecular chemistry field, intuitive concepts such as molecular complementarity and molecular recognition are used to explain the mechanism of lock-key associations. However, these concepts lack a precise definition, and consequently this mechanism is not well defined and understood. Here we address the physical basis of this mechanism, based on formal statistical mechanics, through Monte Carlo simulation and compare our results with recent experimental data for charged or uncharged lock-key colloids. We find that, given the size range of the molecules involved in these associations, the entropy contribution, driven by the solvent, rules the interaction, over that of the enthalpy. A universal behavior for the uncharged lock-key association is found. Based on our results, we propose a supramolecular chemistry definition. PMID:23521272

  6. 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,…

  7. Morphological keys for the identification of Italian phlebotomine sand flies (Diptera: Psychodidae: Phlebotominae).

    PubMed

    Dantas-Torres, Filipe; Tarallo, Viviana; Otranto, Domenico

    2014-10-17

    BackgroundPhlebotomine sand flies are small blood-feeding insects of great medical and veterinary significance. Their identification relies basically on the microscopic examination of key morphological characters. Therefore, identification keys are fundamental to any researcher dealing with these insects. The Italian fauna of phlebotomine sand flies consists of eight species (Phlebotomus perniciosus, Phlebotomus perfiliewi, Phlebotomus ariasi, Phlebotomus neglectus, Phlebotomus papatasi, Phlebotomus mascittii, Phlebotomus sergenti and Sergentomyia minuta), whose morphological delineation may be troublesome for non-taxonomists.MethodsA total of 8,757 pictures were taken from the 419 selected phlebotomine sand fly specimens collected on different occasions. Twenty-eight characters for the males and 23 for the females were examined, resulting in a database containing over 10,000 entries. Representative phlebotomine sand fly specimens for each species available were selected and relevant characters were drawn with the aid of a camera lucida.ResultsAfter detailed morphological study of representative specimens, comprehensive identification keys based on key characters (e.g., pharynx and spermathecae of females and male terminalia) were elaborated.ConclusionsThe identification keys provided herein allow the identification of genera and species of phlebotomine sand flies of Italy and they will facilitate future studies on these medically important insects. PMID:25323537

  8. Identification of a Key Structural Element for Protein Folding Within ?-Hairpin Turns

    Microsoft Academic Search

    Jaewon Kim; Stephen R. Brych; Jihun Lee; Timothy M. Logan; Michael Blaber

    2003-01-01

    Specific residues in a polypeptide may be key contributors to the stability and foldability of the unique native structure. Identification and prediction of such residues is, therefore, an important area of investigation in solving the protein folding problem. Atypical main-chain conformations can help identify strains within a folded protein, and by inference, positions where unique amino acids may have a

  9. 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...

  10. 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.

  11. Phage display library screening for identification of interacting protein partners.

    PubMed

    Addepalli, Balasubrahmanyam; Rao, Suryadevara; Hunt, Arthur G

    2015-01-01

    Phage display is a versatile high-throughput screening method employed to understand and improve the chemical biology, be it production of human monoclonal antibodies or identification of interacting protein partners. A majority of cell proteins operate in a concerted fashion either by stable or transient interactions. Such interactions can be mediated by recognition of small amino acid sequence motifs on the protein surface. Phage display can play a crucial role in identification of such motifs. This report describes the use of phage display for the identification of high affinity sequence motifs that could be responsible for interactions with a target (bait) protein. PMID:25487211

  12. Key to the identification of East and Central African freshwater snails of medical and veterinary importance*

    PubMed Central

    Mandahl-Barth, G.

    1962-01-01

    This identification key has been prepared to enable field workers in eastern and centra Africa to identify the species and subspecies of snails acting as intermediate hosts of various flukes causing bilharziasis and related diseases in man and his domestic stock. The area covered by the key is eastern Africa from the Sudan and Somalia in the north to Southern Rhodesia in the south. The key includes all species and subspecies of the three medically and veterinarily important genera, Lymnaea, Bulinus and Biomphalaria. All other freshwater pulmonates of the area can be identified as to genus only. Those features of the shells and soft parts of snails which are used in identification are discussed in some detail, and indications are given as to methods of collection, preservation and dissection of snails. PMID:14469160

  13. Strongly Resilient Non-Interactive Key Predistribution For Hierarchical Networks

    Microsoft Academic Search

    Hao Chen

    2010-01-01

    Key establishment is the basic necessary tool in the network security, by\\u000awhich pairs in the network can establish shared keys for protecting their\\u000apairwise communications. There have been some key agreement or predistribution\\u000aschemes with the property that the key can be established without the\\u000ainteraction (\\\\cite{Blom84,BSHKY92,S97}). Recently the hierarchical cryptography\\u000aand the key management for hierarchical networks have

  14. GRASP IDENTIFICATION OF HUMAN HANDS AND GRASP PLANNING OF DEXTEROUS HANDS Key words: Grasp planning, identification of human hand motion, Dexterous hand

    E-print Network

    * GRASP IDENTIFICATION OF HUMAN HANDS AND GRASP PLANNING OF DEXTEROUS HANDS Key words: Grasp planning, identification of human hand motion, Dexterous hand 0 NASA JPL [1]NASA Johnson [2]DLR C C2 xP OP yP 3 #12; 3 Fig.3 Palm systems of human hand and dexterous hand o RT o RT = 10

  15. Description of third instars of Cochliomyia minima (Diptera: Calliphoridae) from West Indies, and updated identification key.

    PubMed

    Yusseff-Vanegas, S

    2014-09-01

    The blow fly Cochliomyia minima Shannon is endemic to the Caribbean, and it has great potential for forensic applications because of its abundance and broad distribution in the region. However, its larval stages are unknown. Here, I update previously published identification keys by describing for the first time the morphology of C. minima larvae. The larvae of C. minima are found to be very similar to those of Cochliomyia macellaria F., but the former can be easily identified by the oral sclerite completely pigmented, visible as a spike between mouth hooks. The description of C. minima larvae in this study will be useful to forensic scientists in the Caribbean region. PMID:25276936

  16. Easier detection of invertebrate "identification-key characters" with light of different wavelengths

    PubMed Central

    2011-01-01

    The marine ?-taxonomist often encounters two problems. Firstly, the "environmental dirt" that is frequently present on the specimens and secondly the difficulty in distinguishing key-features due to the uniform colours which fixed animals often adopt. Here we show that illuminating animals with deep-blue or ultraviolet light instead of the normal white-light abrogates both difficulties; dirt disappears and important details become clearly visible. This light regime has also two other advantages. It allows easy detection of very small, normally invisible, animals (0.1 ?m range). And as these light wavelengths can induce fluorescence, new identification markers may be discovered by this approach. PMID:22040277

  17. 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

  18. THE IDENTIFICATION AND TESTING OF INTERACTION PATTERNS

    EPA Science Inventory

    This paper presents a method for identifying and assessing the significance of interaction patterns among various chemicals and chemical classes of importance to regulatory toxicologists. To this end, efforts were made to assemble and evaluate experimental data on toxicologically...

  19. 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

  20. 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

    , it is interesting to see that plant growth and defence can be regulated by similar phyto- hormones (Fig. 1). Various­microbe­insect interactions: connecting plant growth and defence David Giron*,1 , Enric Frago2 , Gaelle Glevarec3 , Corne M. J, Wageningen, NL-6700 EH the Netherlands1 Summary 1. Plant hormones play important roles in regulating plant

  1. 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

  2. Network modules help the identification of key transport routes, signaling pathways in cellular and other networks

    E-print Network

    Palotai, Robin

    2009-01-01

    Complex systems are successfully reduced to interacting elements via the network concept. Transport plays a key role in the survival of networks. For example the specialized signaling cascades of cellular networks filter noise and efficiently adapt the network structure to new stimuli. However, our general understanding of transport mechanisms and signaling pathways in complex systems is yet limited. Here we summarize the key network structures involved in transport, list the solutions available to overloaded systems for relaxing their load and outline a possible method for the computational determination of signaling pathways. We highlight that in addition to hubs, bridges and the network skeleton, the overlapping modular structure is also essential in network transport. Moreover, by locating network elements in the space of overlapping network modules and evaluating their distance in this "module space", it may be possible to approximate signaling pathways computationally, which, in turn could serve the ide...

  3. 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...

  4. Raman spectroscopic identification of scytonemin and its derivatives as key biomarkers in stressed environments.

    PubMed

    Varnali, Tereza; Edwards, Howell G M

    2014-12-13

    Raman spectroscopy has been identified as an important first-pass analytical technique for deployment on planetary surfaces as part of a suite of instrumentation in projected remote space exploration missions to detect extant or extinct extraterrestrial life signatures. Aside from the demonstrable advantages of a non-destructive sampling procedure and an ability to record simultaneously the molecular signatures of biological, geobiological and geological components in admixture in the geological record, the interrogation and subsequent interpretation of spectroscopic data from these experiments will be critically dependent upon the recognition of key biomolecular markers indicative of life existing or having once existed in extreme habitats. A comparison made with the characteristic Raman spectral wavenumbers obtained from standards is not acceptable because of shifts that can occur in the presence of other biomolecules and their host mineral matrices. In this paper, we identify the major sources of difficulty experienced in the interpretation of spectroscopic data centring on a key family of biomarker molecules, namely scytonemin and its derivatives; the parent scytonemin has been characterized spectroscopically in cyanobacterial colonies inhabiting some of the most extreme terrestrial environments and, with the support of theoretical calculations, spectra have been predicted for the characterization of several of its derivatives which could occur in novel extraterrestrial environments. This work will form the foundation for the identification of novel biomarkers and for their Raman spectroscopic discrimination, an essential step in the interpretation of potentially complex and hitherto unknown biological radiation protectants based on the scytoneman and scytonin molecular skeletons which may exist in niche geological scenarios in the surface and subsurface of planets and their satellites in our Solar System. PMID:25368346

  5. Lichen Determination Keys

    NSDL National Science Digital Library

    Published by the Botanic Garden and Botanical Museum (BGBM), Berlin-Dahlem, this Web site serves as on online guide to lichen identification. Users can choose from articulated identification keys for a large number of taxa, or follow links to keys organized by geographical region. There is also an interactive lichen identification database. The Web site has been recently updated to include a key for the genus Stereocaulon in Tropical America. Users should note that the keys listed are created by a number of different organizations, and thus vary in ease of use (some may not be available in English). The keys created by BGBM itself are simply presented and easy to follow, and should prove a useful resource for those pursuing lichen systematics.

  6. Comparative proteomic analysis of Lactobacillus plantarum for the identification of key proteins in bile tolerance

    PubMed Central

    2011-01-01

    Background Lactic acid bacteria are commonly marketed as probiotics based on their putative or proven health-promoting effects. These effects are known to be strain specific but the underlying molecular mechanisms remain poorly understood. Therefore, unravelling the determinants behind probiotic features is of particular interest since it would help select strains that stand the best chance of success in clinical trials. Bile tolerance is one of the most crucial properties as it determines the ability of bacteria to survive in the small intestine, and consequently their capacity to play their functional role as probiotics. In this context, the objective of this study was to investigate the natural protein diversity within the Lactobacillus plantarum species with relation to bile tolerance, using comparative proteomics. Results Bile tolerance properties of nine L. plantarum strains were studied in vitro. Three of them presenting different bile tolerance levels were selected for comparative proteomic analysis: L. plantarum 299 V (resistant), L. plantarum LC 804 (intermediate) and L. plantarum LC 56 (sensitive). Qualitative and quantitative differences in proteomes were analyzed using two-dimensional electrophoresis (2-DE), tryptic digestion, liquid chromatography-mass spectrometry analysis and database search for protein identification. Among the proteins correlated with differences in the 2-DE patterns of the bacterial strains, 15 have previously been reported to be involved in bile tolerance processes. The effect of a bile exposure on these patterns was investigated, which led to the identification of six proteins that may be key in the bile salt response and adaptation in L. plantarum: two glutathione reductases involved in protection against oxidative injury caused by bile salts, a cyclopropane-fatty-acyl-phospholipid synthase implicated in maintenance of cell envelope integrity, a bile salt hydrolase, an ABC transporter and a F0F1-ATP synthase which participate in the active removal of bile-related stress factors. Conclusions These results showed that comparative proteomic analysis can help understand the differential bacterial properties of lactobacilli. In the field of probiotic studies, characteristic proteomic profiles can be identified for individual properties that may serve as bacterial biomarkers for the preliminary selection of strains with the best probiotic potential. PMID:21447177

  7. 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

  8. Artemisinin rewires the protein interaction network in cancer cells: network analysis, pathway identification, and target prediction.

    PubMed

    Huang, Chao; Ba, Qian; Yue, Qingxi; Li, Junyang; Li, Jingquan; Chu, Ruiai; Wang, Hui

    2013-12-01

    Artemisinin and related compounds (artemisinins), as a frontline treatment for malaria, have been used to save millions of lives. Their potential application in cancer treatment is promising. Nevertheless, the precise mechanisms of action of artemisinins are still controversial. In particular, the system-level influence of artemisinins on protein interactions and regulatory networks remains unknown, limiting progress in development of this class of compounds as anticancer drugs. In the present study, we investigated the mechanism of action of artemisinins in cancer therapy through an analysis based on biological networks. According to experimental evidence from more than 400 literature studies, 558 key proteins were derived and the artemisinins-rewired protein interaction network was constructed. Topological properties were analyzed to show that the protein network was a scale-free biological system. And the modularity analysis and pathway identification were performed. Five key pathways including PI3K-Akt, T cell receptor, Toll-like receptor, TGF-beta and insulin signaling pathways were involved in artemisinins-mediated anticancer effects; their identification was confirmed by microarray data. Based on these results, predictions were made about the targets of artemisinins in various pathways. These results provide a deeper understanding of the molecular mechanisms of action of artemisinins and will contribute to the development and application of this class of compounds in cancer treatment. PMID:24085322

  9. 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

  10. A Linnaeus NG TM interactive key to the Lithocolletinae of North-West Europe aimed at accelerating the accumulation of reliable biodiversity data (Lepidoptera, Gracillariidae)

    PubMed Central

    Doorenweerd, Camiel; van Haren, Merel M.; Schermer, Maarten; Pieterse, Sander; van Nieukerken, Erik J.

    2014-01-01

    Abstract We present an interactive key that is available online through any web browser without the need to install any additional software, making it an easily accessible tool for the larger public. The key can be found at http://identify.naturalis.nl/lithocolletinae. The key includes all 86 North-West European Lithocolletinae, a subfamily of smaller moths (“micro-moths”) that is commonly not treated in field guides. The user can input data on several external morphological character systems in addition to distribution, host plant and even characteristics of the larval feeding traces to reach an identification. We expect that this will enable more people to contribute with reliable observation data on this group of moths and alleviate the workload of taxonomic specialists, allowing them to focus on other new keys or taxonomic work. PMID:25061390

  11. 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

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

    PubMed

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

    2015-02-19

    '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

  13. Freshness-preserving non-interactive hierarchical key agreement protocol over WHMS.

    PubMed

    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

  14. 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

  15. 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…

  16. 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

  17. Identification of novel CBP interacting proteins in embryonic orofacial tissue

    SciTech Connect

    Yin Xiaolong [Department of Molecular, Cellular and Craniofacial Biology, University of Louisville Birth Defects Center, ULSD Louisville, KY 40292 (United States); Warner, Dennis R. [Department of Molecular, Cellular and Craniofacial Biology, University of Louisville Birth Defects Center, ULSD Louisville, KY 40292 (United States); Roberts, Emily A. [Department of Molecular, Cellular and Craniofacial Biology, University of Louisville Birth Defects Center, ULSD Louisville, KY 40292 (United States); Pisano, M. Michele [Department of Molecular, Cellular and Craniofacial Biology, University of Louisville Birth Defects Center, ULSD Louisville, KY 40292 (United States); Greene, Robert M. [Department of Molecular, Cellular and Craniofacial Biology, University of Louisville Birth Defects Center, ULSD Louisville, KY 40292 (United States)]. E-mail: greene@louisville.edu

    2005-04-15

    cAMP response element-binding protein (CREB)-binding protein (CBP) plays an important role as a general co-integrator of multiple signaling pathways and interacts with a large number of transcription factors and co-factors, through its numerous protein-binding domains. To identify nuclear factors associated with CBP in developing orofacial tissue, a yeast two-hybrid screen of a cDNA library derived from orofacial tissue from gestational day 11 to 13 mouse embryos was conducted. Using the carboxy terminus (amino acid residues 1676-2441) of CBP as bait, several novel proteins that bind CBP were identified, including an Msx-interacting-zinc finger protein, CDC42 interaction protein 4/thyroid hormone receptor interactor 10, SH3-domain GRB2-like 1, CCR4-NOT transcription complex subunit 3, adaptor protein complex AP-1 {beta}1 subunit, eukaryotic translation initiation factor 2B subunit 1 ({alpha}), and cyclin G-associated kinase. Results of the yeast two-hybrid screen were confirmed by glutathione S-transferase pull-down assays. The identification of these proteins as novel CBP-binding partners allows exploration of new mechanisms by which CBP regulates and integrates diverse cell signaling pathways.

  18. Identification of key genes and crucial modules associated with coronary artery disease by bioinformatics analysis.

    PubMed

    Zhang, Xuemei; Cheng, Xiaoshu; Liu, Huifeng; Zheng, Chunhua; Rao, Kunrui; Fang, Yi; Zhou, Hairong; Xiong, Shenghe

    2014-09-01

    The aim of this study was to identify key genes associated with coronary artery disease (CAD) and to explore the related signaling pathways. Gene expression profiles of 110 CAD and 112 non-CAD, healthy patients [CAD index (CADi) >23 and =0, respectively] were downloaded from the Gene Expression Omnibus (GEO) database (accession: GSE12288). The differentially expressed genes (DEGs) in CAD were identified using t-tests, and protein-protein interaction (PPI) networks for these DEGs were constructed using the Search Tool for the Retrieval of InteractiNg Genes (STRING) database. The Database for Annotation, Visualization and Integrated Discovery (DAVID) tool was used to identify potentially enriched biological processes (BP) among the DEGs using Gene Ontology (GO) terms, and to identify the related pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. In addition, expression-activated subnetworks (crucial modules) of the constructed PPI networks were identified using the jActiveModule plug-in, and their topological properties were analyzed using NetworkAnalyzer, both available from Cytoscape. The patient specimens were classified as grade I, II and III based on CADi values. There were 151 DEGs in grade I, 362 in grade II and 425 in grade III. In the PPI network, the gene GRB2, encoding the growth factor receptor-bound protein 2, was the only common DEG among the three grades. In addition, 10 crucial modules were identified in the PPIs, 4 of which showed significant enrichment for GO BP terms. In the 12 nodes with the highest betweenness centrality, we found two genes, encoding GRB2 and the heat shock 70 kDa protein 8 (HSPA8). Moreover, the chemokine and focal adhesion signaling pathways were selected based on their relative abundance in CAD. The GRB2 and HSPA8 proteins, as well as the chemokine and focal adhension signaling pathways, might therefore be critical for the development of CAD. PMID:24969630

  19. The development of a healthy eating indicator shopping basket tool (HEISB) for use in food access studies-identification of key food items. — Measures of the Food Environment

    Cancer.gov

    Anderson A, Dewar J, Marshall D, Cummins S, Taylor M, Dawson J, Sparks L. The development of a healthy eating indicator shopping basket tool (HEISB) for use in food access studies-identification of key food items.

  20. 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)

  1. 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...

  2. 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

  3. 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...

  4. Elmidae (Coleoptera, Byrrhoidea) larvae in the state of São Paulo, Brazil: Identification key, new records and distribution

    PubMed Central

    Segura, Melissa Ottoboni; Valente-Neto, Francisco; Fonseca-Gessner, Alaíde Aparecida

    2011-01-01

    Abstract The family Elmidae Curtis, 1830 has cosmopolitan distribution and most species inhabit riffles on streams and rivers, hence the name “riffle beetle”. In recent years, this family has been featured in papers addressing the assessment and environmental monitoring of water quality. In Brazil, studies on the family remain scarce and the present investigation is a pioneering study in the state of São Paulo. This study aims to propose a taxonomic key for the identification of larvae of Elmidae genera known to occur in the State, as well as to report new records and the distribution of these genera. The material analyzed was collected from various locations in each of 15 drainage basins from 2005 to 2010. The identification key includes 12 genera (Austrolimnius Carter & Zeck, 1929, Heterelmis Sharp, 1882, Hexacylloepus Hinton, 1940, Hexanchorus Sharp, 1882, Huleechius Brown, 1981, Macrelmis Motschulsky, 1859, Microcylloepus Hinton, 1935, Neoelmis Musgrave, 1935, Phanocerus Sharp, 1882, Potamophilops Grouvelle, 1896, Stegoelmis Hinton, 1939 and Xenelmis Hinton, 1936) known in Brazil as well as three morphotypes designated herein as Genus A, Genus M and Genus X. The genus Hexanchorus is recorded for the first time in the state of São Paulo. PMID:22368452

  5. Poster Sessions Friday, 18 April 2008 183 Identification of key breast cancer phenotypes

    E-print Network

    Aickelin, Uwe

    Kingdom; 3 University of Milan, Institute of Medical Statistics and Biometry, Milan, Italy; 4 Nottingham. However, translation of this molecular genetic approach into routine clinical practice remains elusive to identify comparable classes. In this study, we extend this approach and further define the key criteria

  6. 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

  7. 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.

  8. Study on the identification of entrepreneurial environment key factors based on ISM

    Microsoft Academic Search

    Liu ZeShuang; Duan XiaoLiang

    2009-01-01

    Based on the study in the field of entrepreneurial environment factors abroad and at home, this article researched the interrelationship between entrepreneurial environment factors and key factors of entrepreneurial environment. Firstly, the article used interpretative structural model to construct the adjacency matrix about the factors, then shaped the hierarchy ISM of entrepreneurial environment factors by calculating the reachabilty matrix. Secondly,

  9. 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...

  10. Plant identification through images: Using feature extraction of key points on leaf contours1

    PubMed Central

    Gwo, Chih-Ying; Wei, Chia-Hung

    2013-01-01

    • Premise of the study: Because plant identification demands extensive knowledge and complex terminologies, even professional botanists require significant time in the field for mastery of the subject. As plant leaves are normally regarded as possessing useful characteristics for species identification, leaf recognition through images can be considered an important research issue for plant recognition. • Methods: This study proposes a feature extraction method for leaf contours, which describes the lines between the centroid and each contour point on an image. A length histogram is created to represent the distribution of distances in the leaf contour. Thereafter, a classifier is applied from a statistical model to calculate the matching score of the template and query leaf. • Results: The experimental results show that the top value achieves 92.7% and the first two values can achieve 97.3%. In the scale invariance test, those 45 correlation coefficients fall between the minimal value of 0.98611 and the maximal value of 0.99992. Like the scale invariance test, the rotation invariance test performed 45 comparison sets. The correlation coefficients range between 0.98071 and 0.99988. • Discussion: This study shows that the extracted features from leaf images are invariant to scale and rotation because those features are close to positive correlation in terms of coefficient correlation. Moreover, the experimental results indicated that the proposed method outperforms two other methods, Zernike moments and curvature scale space. PMID:25202493

  11. Interaction of deep and shallow convection is key to Madden-Julian Oscillation simulation

    NASA Astrophysics Data System (ADS)

    Zhang, Guang J.; Song, Xiaoliang

    2009-05-01

    This study investigates the role of the interaction between deep and shallow convection in MJO simulation using the NCAR CAM3. Two simulations were performed, one using a revised Zhang-McFarlane convection scheme for deep convection and the Hack scheme for shallow convection, and the other disallowing shallow convection below 700 mb in the tropical belt. The two simulations produce dramatically different MJO characteristics. While the control simulation produces realistic MJOs, the simulation without shallow convection has very weak MJO signals in the Indian Ocean and western Pacific. Composite analysis finds that shallow convection serves to precondition the lower troposphere by moistening it ahead of deep convection. It also produces enhanced low-level mass convergence below 850 mb ahead of deep convection. This work, together with previous studies, suggests that a correct simulation of the interaction between deep and shallow convection is key to MJO simulation in global climate models.

  12. Identification and Characterization of Key Human Performance Issues and Research in the Next Generation Air Transportation System (NextGen)

    NASA Technical Reports Server (NTRS)

    Lee, Paul U.; Sheridan, Tom; Poage, james L.; Martin, Lynne Hazel; Jobe, Kimberly K.

    2010-01-01

    This report identifies key human-performance-related issues associated with Next Generation Air Transportation System (NextGen) research in the NASA NextGen-Airspace Project. Four Research Focus Areas (RFAs) in the NextGen-Airspace Project - namely Separation Assurance (SA), Airspace Super Density Operations (ASDO), Traffic Flow Management (TFM), and Dynamic Airspace Configuration (DAC) - were examined closely. In the course of the research, it was determined that the identified human performance issues needed to be analyzed in the context of NextGen operations rather than through basic human factors research. The main gaps in human factors research in NextGen were found in the need for accurate identification of key human-systems related issues within the context of specific NextGen concepts and better design of the operational requirements for those concepts. By focusing on human-system related issues for individual concepts, key human performance issues for the four RFAs were identified and described in this report. In addition, mixed equipage airspace with components of two RFAs were characterized to illustrate potential human performance issues that arise from the integration of multiple concepts.

  13. Molecular genetic key for the identification of 17 Ixodes species of the United States (Acari:Ixodidae): a methods model.

    PubMed

    Poucher, K L; Hutcheson, H J; Keirans, J E; Durden, L A; Black, W C

    1999-08-01

    A taxonomic key, based on restriction enzyme analysis of the second internal-transcribed spacer (ITS-2) in the nuclear ribosomal DNA gene, was developed for identification of 17 Ixodes tick species in the United States. This key includes: Ixodes affinis Neumann, Ixodes angustus Neumann, Ixodes baergi Cooley and Kohls, Ixodes brunneus Koch, Ixodes cookei Packard, Ixodes dentatus Marx, Ixodes jellisoni Cooley and Kohls, Ixodes kingi Bishopp, Ixodes minor Neumann, Ixodes muris Bishopp and Smith, Ixodes pacificus Cooley and Kohls, Ixodes scapularis Say, Ixodes sculpularis Neumann, I. spinipalpis Hadwen and Nuttall, Ixodes texanus Banks, Ixodes uriae White, and Ixodes woodi Bishopp. A 900-bp fragment of the ITS-2 was amplified using the polymerase chain reaction. This fragment was then digested with the restriction enzymes MspI and CfoI, and the digested fragments were size fractionated on a 2.5% high-resolution agarose gel. A dichotomous key was developed based on digested fragment sizes relative to a standard set of size markers. Little intraspecific variation in restriction fragment banding patterns was detected. PMID:10461941

  14. Hubs Identification in Amino Acids Interaction Omar Gaci and Stefan Balev

    E-print Network

    Boyer, Edmond

    Hubs Identification in Amino Acids Interaction Networks Omar Gaci and Stefan Balev Universit´e du are the protein's amino acids and whose edges are the interactions between them. Using a graph theory approach, we and is not fully understood. The process is a result of interactions between the protein's amino acids which form

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

    SciTech Connect

    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 groundwater 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. The ten most important radionuclides in order of decreasing hazard are: /sup 99/Tc, /sup 129/I, /sup 237/Np, /sup 226/Ra, /sup 107/Pd, /sup 230/Th, /sup 210/Pb, /sup 126/Sn, /sup 79/Se, and /sup 242/Pu. Safety assessment studies and the design of engineered barriers should concentrate on containment of radionuclides in this list.

  16. [Sensitivity evaluation and key sensitive factors identification of soil erosion around Hangzhou Bay based on RUSLE].

    PubMed

    Li, Cheng; Li, Jun-Xiang; Zhu, Fei-Ge; Cao, Lu; Chen, Zhu; Wu, Tong; Wu, Ming; Sun, Hai-Jing

    2009-07-01

    By using GIS and RS techniques and RUSLE, the rainfall erosivity (R), soil erodibility (K), vegetation and management factor (C), and slope length and steepness factor (LS) around Hangzhou Bay of Zhejiang Province, China were calculated to make a comprehensive sensitivity evaluation of soil erosion in the study area. In the meantime, the contribution of each natural factor, i. e., rainfall, soil texture, slope, and elevation, was analyzed, and a new approach, overlapping and ordering method, was developed to identify the key affecting factors in the given sensitive areas. In the study area, soil erosion was mainly at non-sensitive and low sensitive levels. The percentages of the areas with different soil erosion sensitivity varied with the strength of the affecting factors. Soil erosion sensitivity increased with increasing rainfall and slope, and the percentage of the area with high soil erosion sensitivity was the largest at elevation 200-500 meters. The overlapping and ordering method was a practicable approach in identifying the key affecting factors in given sensitive areas, being helpful to understand the mechanisms causing soil erosion. PMID:19899454

  17. Redescription of Liza bandialensis (Teleostei: Mugilidae) with an identification key to mullet species of Eastern Central Atlantic.

    PubMed

    Trape, Sébastien; Harrison, Ian J; Diouf, Papa Samba; Durand, Jean-Dominique

    2012-02-01

    Liza bandialensis Diouf 1991 is redescribed because previous descriptions have not been in well-distributed publications and have lacked sufficient detail or reference to voucher specimens. The description provided here is based on specimens from the Sine Saloum estuary, Senegal (West Africa), from where the species was originally described. The distinctness of the species is confirmed both by meristic and molecular criteria. L. bandialensis presents a unique combination of characters with a low number of scales in the longitudinal series (32-33), 10.5-12 transverse scale rows, and distinctly yellowish dorsal, anal, and caudal fins. The currently known distribution of L. bandialensis includes coastal waters of Senegal, Gambia and Guinea Bissau. Finally, we provide a morphological identification key for the sixteen species of Mugilidae species occurring along the eastern central Atlantic coast of Africa. PMID:22325565

  18. Peptide Inhibitors of the Malaria Surface Protein, Apical Membrane Antigen 1: Identification of Key Binding Residues

    PubMed Central

    Lee, Erinna F.; Yao, Shenggen; Sabo, Jennifer K.; Fairlie, W. Douglas; Stevenson, Rachel A.; Harris, Karen S.; Anders, Robin F.; Foley, Michael; Norton, Raymond S.

    2011-01-01

    Apical membrane antigen 1 (AMA1) is essential for malaria parasite invasion of erythrocytes and is therefore an attractive target for drug development. Peptides that bind AMA1 have been identified from random peptide libraries expressed on the surface of phage. Of these, R1, which binds to a hydrophobic ligand binding site on AMA1, was a particularly potent inhibitor of parasite invasion of erythrocytes in vitro. The solution structure of R1 contains a turn-like conformation between residues 5–10. Here the importance of residues in this turn-like structure for binding to AMA1 was examined by site-directed mutagenesis and NMR spectroscopy. The peptide was expressed as a fusion protein following replacement of Met16 by Leu in order to accommodate cyanogen bromide cleavage. This modified peptide (R2) displayed the same affinity for AMA1 as R1, showing that the identity of the side chain at position 16 was not critical for binding. Substitution of Phe5, Pro7, Leu8, and Phe9 with alanine led to significant (7.5- to > 350-fold) decreases in affinity for AMA1. Comparison of backbone amide and C?H chemical shifts for these R2 analogues with corresponding values for R2 showed no significant changes, with the exception of R2(P7A), where slightly larger differences were observed, particularly for residues flanking position 7. The absence of significant changes in the secondary chemical shifts suggests that these mutations had little effect on the solution conformation of R2. The identification of a non-polar region of these peptides containing residues essential for AMA1 binding establishes a basis for the design of anti-malarial drugs based on R1 mimetics. PMID:21213258

  19. 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.

  20. 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.

  1. The cassava mealybug (Phenacoccus manihoti) in Asia: first records, potential distribution, and an identification key.

    PubMed

    Parsa, Soroush; Kondo, Takumasa; Winotai, Amporn

    2012-01-01

    Phenacoccus manihoti Matile-Ferrero (Hemiptera: Pseudococcidae), one of the most serious pests of cassava worldwide, has recently reached Asia, raising significant concern over its potential spread throughout the region. To support management decisions, this article reports recent distribution records, and estimates the climatic suitability for its regional spread using a CLIMEX distribution model. The article also presents a taxonomic key that separates P. manihoti from all other mealybug species associated with the genus Manihot. Model predictions suggest P. manihoti imposes an important, yet differential, threat to cassava production in Asia. Predicted risk is most acute in the southern end of Karnataka in India, the eastern end of the Ninh Thuan province in Vietnam, and in most of West Timor in Indonesia. The model also suggests P. manihoti is likely to be limited by cold stress across Vietnam's northern regions and in the entire Guangxi province in China, and by high rainfall across the wet tropics in Indonesia and the Philippines. Predictions should be particularly important to guide management decisions for high risk areas where P. manihoti is absent (e.g., India), or where it has established but populations remain small and localized (e.g., South Vietnam). Results from this article should help decision-makers assess site-specific risk of invasion, and develop proportional prevention and surveillance programs for early detection and rapid response. PMID:23077659

  2. The Cassava Mealybug (Phenacoccus manihoti) in Asia: First Records, Potential Distribution, and an Identification Key

    PubMed Central

    Parsa, Soroush; Kondo, Takumasa; Winotai, Amporn

    2012-01-01

    Phenacoccus manihoti Matile-Ferrero (Hemiptera: Pseudococcidae), one of the most serious pests of cassava worldwide, has recently reached Asia, raising significant concern over its potential spread throughout the region. To support management decisions, this article reports recent distribution records, and estimates the climatic suitability for its regional spread using a CLIMEX distribution model. The article also presents a taxonomic key that separates P. manihoti from all other mealybug species associated with the genus Manihot. Model predictions suggest P. manihoti imposes an important, yet differential, threat to cassava production in Asia. Predicted risk is most acute in the southern end of Karnataka in India, the eastern end of the Ninh Thuan province in Vietnam, and in most of West Timor in Indonesia. The model also suggests P. manihoti is likely to be limited by cold stress across Vietnam's northern regions and in the entire Guangxi province in China, and by high rainfall across the wet tropics in Indonesia and the Philippines. Predictions should be particularly important to guide management decisions for high risk areas where P. manihoti is absent (e.g., India), or where it has established but populations remain small and localized (e.g., South Vietnam). Results from this article should help decision-makers assess site-specific risk of invasion, and develop proportional prevention and surveillance programs for early detection and rapid response. PMID:23077659

  3. Identification of Key Drought Stress-Related Genes in the Hyacinth Bean

    PubMed Central

    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

  4. For realizing a robot working in human society, interaction with humans is the key issue. We have

    E-print Network

    Kanda, Takayuki

    Abstract For realizing a robot working in human society, interaction with humans is the key issue. We have developed a robot that interacts with humans based on visual recognition. This robot has two and a binocular stereo vision system. The binocular vision system indicates what the robot is looking

  5. Identification and characterization of a novel Nogo-interacting mitochondrial protein (NIMP)

    E-print Network

    Hu, Wen-Hui

    Identification and characterization of a novel Nogo-interacting mitochondrial protein (NIMP) Wen Abstract Nogo is a potent inhibitor of regeneration following spinal cord injury. To develop a better and identify proteins that interact with Nogo. We identified a novel mitochondrial protein designated Nogo

  6. 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

  7. Identification of direct targets of FUSCA3, a key regulator of Arabidopsis seed development.

    PubMed

    Wang, Fangfang; Perry, Sharyn E

    2013-03-01

    FUSCA3 (FUS3) is a B3 domain transcription factor that is a member of the LEAFY COTYLEDON (LEC) group of genes. The LEC genes encode proteins that also include LEC2, a B3 domain factor related to FUS3, and LEC1, a CCAAT box-binding factor. LEC1, LEC2, and FUS3 are essential for plant embryo development. All three loss-of-function mutants in Arabidopsis (Arabidopsis thaliana) prematurely exit embryogenesis and enter seedling developmental programs. When ectopically expressed, these genes promote embryo programs in seedlings. We report on chromatin immunoprecipitation-tiling array experiments to globally map binding sites for FUS3 that, along with other published work to assess transcriptomes in response to FUS3, allow us to determine direct from indirect targets. Many transcription factors associated with embryogenesis are direct targets of FUS3, as are genes involved in the seed maturation program. FUS3 regulates genes encoding microRNAs that, in turn, control transcripts encoding transcription factors involved in developmental phase changes. Examination of direct targets of FUS3 reveals that FUS3 acts primarily or exclusively as a transcriptional activator. Regulation of microRNA-encoding genes is one mechanism by which FUS3 may repress indirect target genes. FUS3 also directly up-regulates VP1/ABI3-LIKE1 (VAL1), encoding a B3 domain protein that functions as a repressor of transcription. VAL1, along with VAL2 and VAL3, is involved in the transition from embryo to seedling development. Many genes are responsive to FUS3 and to VAL1/VAL2 but with opposite regulatory consequences. The emerging picture is one of complex cross talk and interactions among embryo transcription factors and their target genes. PMID:23314941

  8. 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

  9. Identification of neutrino interactions using the DONUT spectrometer

    Microsoft Academic Search

    K. Kodama; C. Andreopoulos; N. Giokaris; N. Saoulidou; G. Tzanakos; B. Baller; D. Boehnlein; B. Lundberg; R. Rameika; J. S Song; C. S Yoon; S. H Chung; P. Berghaus; M. Kubantsev; N. W Reay; R. Sidwell; N. Stanton; S. Yoshida; S. Aoki; T. Hara; D. Ciampa; C. Erickson; K. Heller; R. Rusack; M. Graham; R. Schwienhorst; J. Sielaff; J. Trammell; J. Wilcox; K. Hoshino; H. Jiko; J. Kawada; T. Kawai; M. Komatsu; H. Matsuoka; M. Miyanishi; M. Nakamura; T. Nakano; K. Narita; K. Niwa; N. Nonaka; K. Okada; O. Sato; T. Toshito; T. Akdogan; A. Kulik; V. Paolone; C. Rosenfeld; T. Kafka; W. Oliver; J. Schneps; M. Skender

    2004-01-01

    The experimental apparatus used for the first direct observation of the tau neutrino (the DONUT experiment) is described. Its main features consisted of a target system composed of nuclear emulsion targets and scintillation fiber trackers, a magnetic charged-particle spectrometer and detectors for lepton identification. This paper will concentrate on the description of the electronic detectors and their performance in selecting

  10. Neuron-astrocyte interaction enhance GABAergic synaptic transmission in a manner dependent on key metabolic enzymes

    PubMed Central

    Kaczor, Przemys?aw; Rakus, Dariusz; Mozrzymas, Jerzy W.

    2015-01-01

    Gamma aminobutric acid (GABA) is the major inhibitory neurotransmitter in the adult brain and mechanisms of GABAergic inhibition have been intensely investigated in the past decades. Recent studies provided evidence for an important role of astrocytes in shaping GABAergic currents. One of the most obvious, but yet poorly understood, mechanisms of the cross-talk between GABAergic currents and astrocytes is metabolism including neurotransmitter homeostasis. In particular, how modulation of GABAergic currents by astrocytes depends on key enzymes involved in cellular metabolism remains largely unknown. To address this issue, we have considered two simple models of neuronal culture (NC): nominally astrocyte-free NC and neuronal-astrocytic co-cultures (ANCC). Miniature Inhibitory Postsynaptic Currents (mIPSCs) were recorded in control conditions and in the presence of different enzyme blockers. We report that enrichment of NC with astrocytes results in a marked increase in mIPSC frequency. This enhancement of GABAergic activity was accompanied by increased number of GAD65 and vGAT puncta, indicating that at least a part of the frequency enhancement was due to increased number of synaptic contacts. Inhibition of glutamine synthetase (Glns) (with MSO) strongly reduced mIPSC frequency in ANCC but had no effect in NC. Moreover, treatment of ANCC with inhibitor of glycogen phosphorylase (Gys) (BAYU6751) or with selective inhibitor of astrocytic Krebs cycle, fluoroacetate, resulted in a marked reduction of mIPSC frequency in ANCC having no effect in NC. We conclude that GABAergic synaptic transmission strongly depends on neuron-astrocyte interaction in a manner dependent on key metabolic enzymes as well as on the Krebs cycle.

  11. 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

  12. Quantum information technology with Sagnac interferometer: Interaction-free measurement, quantum key distribution and quantum secret sharing

    E-print Network

    Wellington Alves de Brito; Rubens Viana Ramos

    2007-06-08

    The interferometry of single-photon pulses has been used to implement quantum technology systems, like quantum key distribution, interaction-free measurement and some other quantum communication protocols. In most of these implementations, Mach-Zehnder, Michelson and Fabry-Perot interferometers are the most used. In this work we present optical setups for interaction-free measurement, quantum key distribution and quantum secret sharing using the Sagnac interferometer. The proposed setups are described as well the quantum protocols using them are explained.

  13. Identification and Biochemical Characterization of PGC-1beta-Interacting Proteins

    E-print Network

    Zhang, Hongsheng

    2008-01-01

    of these aforementioned processes represent key steps in the regulation of gene transcription. Therefore, the full functional activity of NRs depends upon their ability to interact with protein cofactors, termed coactivator and corepressor proteins. Metabolic syndrome...

  14. 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)

  15. Afrotropical flea beetle genera: a key to their identification, updated catalogue and biogeographical analysis (Coleoptera, Chrysomelidae, Galerucinae, Alticini)

    PubMed Central

    Biondi, Maurizio; D’Alessandro, Paola

    2012-01-01

    Abstract A revision of the Alticini genera from the Afrotropical region is reported. The paper includes the following for the flea beetle fauna occurring in Sub-Saharan Africa and Madagascar: a key to their identification; habitus photos of all the genera; microscope and scanning electron micrographs of many diagnostic morphological characters; and an updated annotated catalogue with biogeographical notes that include new distributional data. The following new synonymies are proposed: Aphthona Chevrolat, 1836 = Ethiopia Scherer, 1972 syn. n.; Sanckia Duvivier, 1891 = Eugonotes Jacoby, 1897 syn. n.; Eurylegna Weise, 1910a = Eurylegniella Scherer, 1972 syn. n.; Kimongona Bechyné, 1959a = Mesocrepis Scherer, 1963 syn. n.; Diphaulacosoma Jacoby, 1892a = Neoderina Bechyné, 1952 syn. n.; Sesquiphaera Bechyné, 1958a = Paropsiderma Bechyné, 1958a syn. n.; Podagrica Chevrolat, 1836 = Podagricina Csiki in Heikertinger and Csiki 1940 syn. n.; Amphimela Chapuis, 1875 = Sphaerophysa Baly, 1876a syn. n. The following new combinations are proposed: Blepharida insignis Brancsik, 1897 = Xanthophysca insignis (Brancsik, 1897) comb. n.; Blepharida multiguttata Duvivier, 1891 = Xanthophysca multiguttata (Duvivier, 1891) comb. n.; Hemipyxis balyana (Csiki in Heikertinger and Csiki 1940) = Pseudadorium balyanum (Csiki in Heikertinger and Csiki, 1940) comb. n.; Hemipyxis brevicornis (Jacoby, 1892a) = Pseudadorium brevicornis (Jacoby, 1892a) comb. n.; Hemipyxis cyanea (Weise, 1910b) = Pseudadorium cyaneum (Weise, 1910b) comb. n.; Hemipyxis gynandromorpha Bechyné, 1958c = Pseudadorium gynandromorphum (Bechyné, 1958c) comb. n.; Hemipyxis latiuscula Bechyné, 1958c = Pseudadorium latiusculum (Bechyné, 1958c) comb. n.; Hemipyxis soror (Weise, 1910b) = Pseudadorium soror (Weise, 1910b) comb. n. The genera Buphonella Jacoby, 1903aand Halticopsis Fairmaire, 1883a are transferred to the tribe Galerucini; the genus Biodontocnema Biondi, 2000 stat. prom. is considered to be valid and reinstated at generic level. Finally, a zoogeographical analysis of the flea beetle fauna in the Afrotropical region is provided. PMID:23378812

  16. Identification and Comparison of Aberrant Key Regulatory Networks in Breast, Colon, Liver, Lung, and Stomach Cancers through Methylome Database Analysis

    PubMed Central

    Kim, Byungtak; Kang, Seongeun; Jeong, Gookjoo; Park, Sung-Bin; Kim, Sun Jung

    2014-01-01

    Aberrant methylation of specific CpG sites at the promoter is widely responsible for genesis and development of various cancer types. Even though the microarray-based methylome analyzing techniques have contributed to the elucidation of the methylation change at the genome-wide level, the identification of key methylation markers or top regulatory networks appearing common in highly incident cancers through comparison analysis is still limited. In this study, we in silico performed the genome-wide methylation analysis on each 10 sets of normal and cancer pairs of five tissues: breast, colon, liver, lung, and stomach. The methylation array covers 27,578 CpG sites, corresponding to 14,495 genes, and significantly hypermethylated or hypomethylated genes in the cancer were collected (FDR adjusted p-value <0.05; methylation difference >0.3). Analysis of the dataset confirmed the methylation of previously known methylation markers and further identified novel methylation markers, such as GPX2, CLDN15, and KL. Cluster analysis using the methylome dataset resulted in a diagram with a bipartite mode distinguishing cancer cells from normal cells regardless of tissue types. The analysis further revealed that breast cancer was closest with lung cancer, whereas it was farthest from colon cancer. Pathway analysis identified that either the “cancer” related network or the “cancer” related bio-function appeared as the highest confidence in all the five cancers, whereas each cancer type represents its tissue-specific gene sets. Our results contribute toward understanding the essential abnormal epigenetic pathways involved in carcinogenesis. Further, the novel methylation markers could be applied to establish markers for cancer prognosis. PMID:24842468

  17. Global identification of yeast chromosome interactions using Genome conformation capture.

    PubMed

    Rodley, C D M; Bertels, F; Jones, B; O'Sullivan, J M

    2009-11-01

    The association of chromosomes with each other and other nuclear components plays a critical role in nuclear organization and Genome function. Here, using a novel and generally applicable methodology (Genome conformation capture [GCC]), we reveal the network of chromosome interactions for the yeast Saccharomyces cerevisiae. Inter- and intra-chromosomal interactions are non-random and the number of interactions per open reading frame depends upon the dispensability of the gene product. Chromosomal interfaces are organized and provide evidence of folding within chromosomes. Interestingly, the genomic connections also involve the 2 microm plasmid and the mitochondrial genome. Mitochondrial interaction partners include genes of alpha-proteobacterial origin and the ribosomal DNA. Organization of the 2 microm plasmid aligns two inverted repeats (IR1 and IR2) and displays the stability locus on a prominent loop thus making it available for plasmid clustering. Our results form the first global map of chromosomal interactions in a eukaryotic nucleus and demonstrate the highly connected nature of the yeast genome. These results have significant implications for understanding eukaryotic genome organization. PMID:19628047

  18. 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

  19. SIGN: reliable protein interaction identification by integrating the Similarity In GO and the similarity

    E-print Network

    Buffalo, State University of New York

    SIGN: reliable protein interaction identification by integrating the Similarity In GO, of high-throughput data. This unpleasantly high false positive rate could lead many devoted researches. The performance of many researches analyzing PPI was suffered by the in- trinsic weakness of high-throughput data

  20. Interactive Model Identification for Nonholonomic Cart Pushed by a Mobile Manipulator

    Microsoft Academic Search

    Yu Sunt; Ning Xit; Jindong Tant; Yuechao WangS

    2002-01-01

    A model identification method for unknown environments has been developed. By the interactions between a mobile manipulator and the unknown object, a nonholonomic cart, sensory information has been collected to estimate the model parameters of the cart, which are used to control the cart. Since the raw data are contaminated by noise they can not be modeled statistically, a wavelet

  1. Identification of potential therapeutic target genes, key miRNAs and mechanisms in acute myeloid leukemia based on bioinformatics analysis.

    PubMed

    Zhao, Yanhong; Zhang, Xuefang; Zhao, Yanqiu; Kong, Desheng; Qin, Fan; Sun, Jing; Dong, Ying

    2015-05-01

    The study was aimed to explore the underlying mechanisms and identify the potential target genes and key miRNAs for acute myeloid leukemia (AML) treatment by bioinformatics analysis. The microarray data of GSE9476 were downloaded from Gene Expression Omnibus database. A total of 64 samples, including 26 AML and 38 normal samples, were used to identify differentially expressed genes (DEGs) between AML and normal samples. The functional enrichment analysis was performed, and protein-protein interaction (PPI) network of the DEGs was constructed by Cytoscape software. Besides, the target miRNAs for DEGs were identified. Totally, 323 DEGs were identified, including 87 up-regulated and 236 down-regulated genes. Not only up-regulated genes but also down-regulated genes were related to hematopoietic-related functions. Besides, down-regulated genes were also enriched in primary immunodeficiency pathway. Tumor necrosis factor (TNF), interleukin 7 receptor (IL7R), lymphocyte-specific protein tyrosine kinase (LCK), CD79a molecule and immunoglobulin-associated alpha (CD79A) were identified in these functions. TNF and LCK were hub nodes in PPI networks. miR-124 and miR-181 were important miRNAs in this study. The hematopoietic-related functions and primary immunodeficiency pathway may be associated with AML development. Genes, such as TNF, IL7R, LCK and CD79A, may be potential therapeutic target genes for AML, and miR-124 and miR-181 may be key miRNAs in AML development. PMID:25832863

  2. A prototype framework for models of socio-hydrology: identification of key feedback loops and parameterisation approach

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    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 models of socio-hydrology applicable to agricultural catchments, made up of six key components that combine to form the coupled system dynamics: namely, catchment hydrology, population, economics, environment, socioeconomic sensitivity and collective response. The conceptual framework posits two novel constructs: (i) a composite socioeconomic driving variable, termed the Community Sensitivity state variable, which seeks to capture the perceived level of threat to a community's quality of life, and acts as a key link tying together one of the fundamental feedback loops of the coupled system, and (ii) a Behavioural Response variable as the observable feedback mechanism, which reflects land and water management decisions relevant to the hydrological context. The framework makes a further contribution through the introduction of three macro-scale parameters that enable it to normalise for differences in climate, socioeconomic and political gradients across study sites. In this way, the framework provides for both macro-scale contextual parameters, which allow for comparative studies to be undertaken, 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 socio-hydrological case studies, taken from the Australian experience, are presented and the parameterisation approach that would be taken in each case is discussed. Preliminary findings in the case studies lend support to the conceptual theories outlined in the framework. 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 improve social-ecological systems modelling through better representation of human feedbacks on hydrological processes.

  3. Computational Identification of Potential Molecular Interactions in Arabidopsis1[C][W

    PubMed Central

    Lin, Mingzhi; Hu, Bin; Chen, Lijuan; Sun, Peng; Fan, Yi; Wu, Ping; Chen, Xin

    2009-01-01

    Knowledge of the protein interaction network is useful to assist molecular mechanism studies. Several major repositories have been established to collect and organize reported protein interactions. Many interactions have been reported in several model organisms, yet a very limited number of plant interactions can thus far be found in these major databases. Computational identification of potential plant interactions, therefore, is desired to facilitate relevant research. In this work, we constructed a support vector machine model to predict potential Arabidopsis (Arabidopsis thaliana) protein interactions based on a variety of indirect evidence. In a 100-iteration bootstrap evaluation, the confidence of our predicted interactions was estimated to be 48.67%, and these interactions were expected to cover 29.02% of the entire interactome. The sensitivity of our model was validated with an independent evaluation data set consisting of newly reported interactions that did not overlap with the examples used in model training and testing. Results showed that our model successfully recognized 28.91% of the new interactions, similar to its expected sensitivity (29.02%). Applying this model to all possible Arabidopsis protein pairs resulted in 224,206 potential interactions, which is the largest and most accurate set of predicted Arabidopsis interactions at present. In order to facilitate the use of our results, we present the Predicted Arabidopsis Interactome Resource, with detailed annotations and more specific per interaction confidence measurements. This database and related documents are freely accessible at http://www.cls.zju.edu.cn/pair/. PMID:19592425

  4. Magnetic anisotropy, magnetostatic interactions and identification of magnetofossils

    NASA Astrophysics Data System (ADS)

    Li, Jinhua; Wu, Wenfang; Liu, Qingsong; Pan, Yongxin

    2012-12-01

    Single-domain magnetite particles produced by magnetotactic bacteria (MTB) and aligned in chains, called magnetosomes, are potentially important recorders of paleomagnetic, paleoenvironmental and paleolife signals. Rock magnetic properties related to the anisotropy of magnetosome chains have been widely used to identify fossilized magnetosomes (magnetofossils) preserved in geological materials. However, ambiguities exist when linking magnetic properties to the chain structure because of the complexity of chain integrity and magnetostatic interactions among magnetofossils that results from chain collapse during post-depositional diagenesis. In this paper, magnetic properties of three sets of samples containing extracted magnetosomes of the cultured Magnetospirillum magneticum strain AMB-1 were analyzed to determine how chain integrity and particle concentration influence magnetic properties. Intact MTB and well-dispersed magnetosome chains are characterized by strong magnetic anisotropy and weak magnetostatic interactions, but progressive chain breakup and particle clumping significantly increase the degree of magnetostatic interaction. This results in a change of the magnetic signature toward properties typical of interacting, single-domain particles, i.e., a decrease of the ratio of anhysteretic remanent magnetization to the saturation isothermal remanent magnetization, decreasing in the crossing point of the Wohlfarth-Cisowski test and in the delta ratio between losses of field and zero-field cooled remanent magnetization across the Verwey transition, as well as vertical broadening of the first-order reversal curve distribution. We propose a new diagram that summarizes the Verwey transition properties, with diagnostic limits for intact and collapsed chains of magnetosomes. This diagram can be used, in conjunction with other parameters, to identify unoxidized magnetofossils in sediments and rocks.

  5. Magnetic anisotropy, magnetostatic interactions and identification of magnetofossils

    NASA Astrophysics Data System (ADS)

    Li, Jinhua; Wu, Wenfang; Liu, Qingsong; Pan, Yongxin

    2012-12-01

    Single-domain magnetite particles produced by magnetotactic bacteria (MTB) and aligned in chains, called magnetosomes, are potentially important recorders of paleomagnetic, paleoenvironmental and paleolife signals. Rock magnetic properties related to the anisotropy of magnetosome chains have been widely used to identify fossilized magnetosomes (magnetofossils) preserved in geological materials. However, ambiguities exist when linking magnetic properties to the chain structure because of the complexity of chain integrity and magnetostatic interactions among magnetofossils that results from chain collapse during post-depositional diagenesis. In this paper, magnetic properties of three sets of samples containing extracted magnetosomes of the culturedMagnetospirillum magneticumstrain AMB-1 were analyzed to determine how chain integrity and particle concentration influence magnetic properties. Intact MTB and well-dispersed magnetosome chains are characterized by strong magnetic anisotropy and weak magnetostatic interactions, but progressive chain breakup and particle clumping significantly increase the degree of magnetostatic interaction. This results in a change of the magnetic signature toward properties typical of interacting, single-domain particles, i.e., a decrease of the ratio of anhysteretic remanent magnetization to the saturation isothermal remanent magnetization, decreasing in the crossing point of the Wohlfarth-Cisowski test and in the delta ratio between losses of field and zero-field cooled remanent magnetization across the Verwey transition, as well as vertical broadening of the first-order reversal curve distribution. We propose a new diagram that summarizes the Verwey transition properties, with diagnostic limits for intact and collapsed chains of magnetosomes. This diagram can be used, in conjunction with other parameters, to identify unoxidized magnetofossils in sediments and rocks.

  6. 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

  7. MIMO model of an interacting series process for Robust MPC via System Identification.

    PubMed

    Wibowo, Tri Chandra S; Saad, Nordin

    2010-07-01

    This paper discusses the empirical modeling using system identification technique with a focus on an interacting series process. The study is carried out experimentally using a gaseous pilot plant as the process, in which the dynamic of such a plant exhibits the typical dynamic of an interacting series process. Three practical approaches are investigated and their performances are evaluated. The models developed are also examined in real-time implementation of a linear model predictive control. The selected model is able to reproduce the main dynamic characteristics of the plant in open-loop and produces zero steady-state errors in closed-loop control system. Several issues concerning the identification process and the construction of a MIMO state space model for a series interacting process are deliberated. PMID:20304404

  8. 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.

  9. Identification of Early Interactions between Francisella and the Host

    PubMed Central

    Roberts, Lydia M.; Tuladhar, Shraddha; Steele, Shaun P.; Riebe, Kristina J.; Chen, Ching-ju; Cumming, R. Ian; Seay, Sarah; Frothingham, Richard; Sempowski, Gregory D.; Kawula, Thomas H.

    2014-01-01

    The adaptive immune response to Francisella tularensis is dependent on the route of inoculation. Intradermal inoculation with the F. tularensis live vaccine strain (LVS) results in a robust Th1 response in the lungs, whereas intranasal inoculation produces fewer Th1 cells and instead many Th17 cells. Interestingly, bacterial loads in the lungs are similar early after inoculation by these two routes. We hypothesize that the adaptive immune response is influenced by local events in the lungs, such as the type of cells that are first infected with Francisella. Using fluorescence-activated cell sorting, we identified alveolar macrophages as the first cell type infected in the lungs of mice intranasally inoculated with F. novicida U112, LVS, or F. tularensis Schu S4. Following bacterial dissemination from the skin to the lung, interstitial macrophages or neutrophils are infected. Overall, we identified the early interactions between Francisella and the host following two different routes of inoculation. PMID:24686053

  10. Large-scale identification of potential drug targets based on the topological features of human protein-protein interaction network.

    PubMed

    Li, Zhan-Chao; Zhong, Wen-Qian; Liu, Zhi-Qing; Huang, Meng-Hua; Xie, Yun; Dai, Zong; Zou, Xiao-Yong

    2015-04-29

    Identifying potential drug target proteins is a crucial step in the process of drug discovery and plays a key role in the study of the molecular mechanisms of disease. Based on the fact that the majority of proteins exert their functions through interacting with each other, we propose a method to recognize target proteins by using the human protein-protein interaction network and graph theory. In the network, vertexes and edges are weighted by using the confidence scores of interactions and descriptors of protein primary structure, respectively. The novel network topological features are defined and employed to characterize protein using existing databases. A widely used minimum redundancy maximum relevance and random forests algorithm are utilized to select the optimal feature subset and construct model for the identification of potential drug target proteins at the proteome scale. The accuracies of training set and test set are 89.55% and 85.23%. Using the constructed model, 2127 potential drug target proteins have been recognized and 156 drug target proteins have been validated in the database of drug target. In addition, some new drug target proteins can be considered as targets for treating diseases of mucopolysaccharidosis, non-arteritic anterior ischemic optic neuropathy, Bernard-Soulier syndrome and pseudo-von Willebrand, etc. It is anticipated that the proposed method may became a powerful high-throughput virtual screening tool of drug target. PMID:25847157

  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. Quantum key distribution

    Microsoft Academic Search

    N. L. Lutkenhaus

    2005-01-01

    The paper discussed on possible optimization set-ups for quantum key distribution (QKD). The large secret key resulting from QKD is a valuable resource in communication scenarios, e.g. for secret communication, authentication, identification and so forth.

  13. Identification of Proteins Interacting with GTP Cyclohydrolase I

    PubMed Central

    Du, Jianhai; Xu, Hao; Wei, Na; Wakim, Bassam; Halligan, Brian; Pritchard, Kirkwood A.; Shi, Yang

    2009-01-01

    GTP cyclohydrolase I (GCH-1) is the rate-limiting enzyme in the biosynthesis of tetrahydrobiopterin, an essential cofactor for nitric oxide synthase and aromatic amino acid hydroxylase. To explore the interactome of GCH-1, we established a HEK293 cell line stably expressing tetracycline-inducible FLAG-GCH-1. FLAG-GCH-1 and associated proteins were immunoprecipitated and analyzed by liquid chromatography/tandem mass spectrometry. Twenty-nine proteins, derived from different subcellular components such as cytosol, membranes, nucleus and mitochondria were identified to interact with GCH-1. Cell fractionation studies also showed that GCH-1 was present in the cytosol, membranes and nucleus. Gene ontology analysis revealed that GCH-1 interactome was involved in a variety of biological processes such as signal transduction, apoptosis, metabolism, transport and cell organization. To our knowledge, this study is the first to provide a comprehensive analysis of the GCH-1 interactome. Findings expand the number and diversity of proteins that are known to associate with GCH-1. PMID:19442649

  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. Identification of a potent combination of key Plasmodium falciparum merozoite antigens that elicit strain-transcending parasite-neutralizing antibodies.

    PubMed

    Pandey, Alok K; Reddy, K Sony; Sahar, Tajali; Gupta, Sonal; Singh, Hina; Reddy, E Jyotheeswara; Asad, Mohd; Siddiqui, Faiza A; Gupta, Pankaj; Singh, Bijender; More, Kunal R; Mohmmed, Asif; Chitnis, Chetan E; Chauhan, Virander S; Gaur, Deepak

    2013-02-01

    Blood-stage malaria vaccines that target single Plasmodium falciparum antigens involved in erythrocyte invasion have not induced optimal protection in field trials. Blood-stage malaria vaccine development has faced two major hurdles, antigenic polymorphisms and molecular redundancy, which have led to an inability to demonstrate potent, strain-transcending, invasion-inhibitory antibodies. Vaccines that target multiple invasion-related parasite proteins may inhibit erythrocyte invasion more efficiently. Our approach is to develop a receptor-blocking blood-stage vaccine against P. falciparum that targets the erythrocyte binding domains of multiple parasite adhesins, blocking their interaction with their receptors and thus inhibiting erythrocyte invasion. However, with numerous invasion ligands, the challenge is to identify combinations that elicit potent strain-transcending invasion inhibition. We evaluated the invasion-inhibitory activities of 20 different triple combinations of antibodies mixed in vitro against a diverse set of six key merozoite ligands, including the novel ligands P. falciparum apical asparagine-rich protein (PfAARP), EBA-175 (PfF2), P. falciparum reticulocyte binding-like homologous protein 1 (PfRH1), PfRH2, PfRH4, and Plasmodium thrombospondin apical merozoite protein (PTRAMP), which are localized in different apical organelles and are translocated to the merozoite surface at different time points during invasion. They bind erythrocytes with different specificities and are thus involved in distinct invasion pathways. The antibody combination of EBA-175 (PfF2), PfRH2, and PfAARP produced the most efficacious strain-transcending inhibition of erythrocyte invasion against diverse P. falciparum clones. This potent antigen combination was selected for coimmunization as a mixture that induced balanced antibody responses against each antigen and inhibited erythrocyte invasion efficiently. We have thus demonstrated a novel two-step screening approach to identify a potent antigen combination that elicits strong strain-transcending invasion inhibition, supporting its development as a receptor-blocking malaria vaccine. PMID:23184525

  16. 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

  17. Interactive voice response systems for medication identification requests: poison or cure?

    PubMed

    Benson, Blaine E

    2011-11-01

    Interactive voice response systems (IVR) have traditionally been used by banking and credit card industries to rapidly process information requests for their customers. Today IVR technology is being used in clinical medicine to randomize patients in clinical studies, to collect patient data, and to follow-up on recently discharged patients. Use of IVR systems by poison centers is relatively new. This commentary explores the advantages and disadvantages of applying IVR technology to the medication identification requests in poison centers. PMID:22077245

  18. IEEE TRANSACTIONS ON SEMICONDUCTOR MANUFACTURING, VOL. 24, NO. 2, MAY 2011 237 Cycle-Time Key Factor Identification and Prediction

    E-print Network

    Lerner, Boaz

    of other machine learning and statistical models, such as a decision tree, a neural network and competitive semiconductor manufacturing industry, lot cycle time (CT) remains one of the key performance-resource scheduling. To reduce CT, we suggest and investigate a data-driven approach that identifies key factors

  19. Topoisomerase II-Drug Interaction Domains: Identification of Substituents on Etoposide That Interact with the Enzyme

    E-print Network

    Berkowitz, David

    That Interact with the Enzyme Amy M. Wilstermann,,§ Ryan P. Bender, Murrell Godfrey,| Sungjo Choi, Clemens, and a pendent ring (E-ring) at the C1 position. Although drug-enzyme contacts, as opposed to drug on etoposide that interact with the enzyme have not been identified. Therefore, saturation transfer difference

  20. Identification of brain-specific angiogenesis inhibitor 2 as an interaction partner of glutaminase interacting protein

    SciTech Connect

    Zencir, Sevil [Department of Biochemistry, Faculty of Science, Ege University, Izmir 35100 (Turkey)] [Department of Biochemistry, Faculty of Science, Ege University, Izmir 35100 (Turkey); Ovee, Mohiuddin [Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849 (United States)] [Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849 (United States); Dobson, Melanie J. [Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada B3H 4R2 (Canada)] [Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada B3H 4R2 (Canada); Banerjee, Monimoy [Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849 (United States)] [Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849 (United States); Topcu, Zeki, E-mail: zeki.topcu@ege.edu.tr [Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Izmir 35100 (Turkey)] [Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Izmir 35100 (Turkey); Mohanty, Smita, E-mail: mohansm@auburn.edu [Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849 (United States)] [Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849 (United States)

    2011-08-12

    Highlights: {yields} Brain-specific angiogenesis inhibitor 2 (BAI2) is a new partner protein for GIP. {yields} BAI2 interaction with GIP was revealed by yeast two-hybrid assay. {yields} Binding of BAI2 to GIP was characterized by NMR, CD and fluorescence. {yields} BAI2 and GIP binding was mediated through the C-terminus of BAI2. -- Abstract: The vast majority of physiological processes in living cells are mediated by protein-protein interactions often specified by particular protein sequence motifs. PDZ domains, composed of 80-100 amino acid residues, are an important class of interaction motif. Among the PDZ-containing proteins, glutaminase interacting protein (GIP), also known as Tax Interacting Protein TIP-1, is unique in being composed almost exclusively of a single PDZ domain. GIP has important roles in cellular signaling, protein scaffolding and modulation of tumor growth and interacts with a number of physiological partner proteins, including Glutaminase L, {beta}-Catenin, FAS, HTLV-1 Tax, HPV16 E6, Rhotekin and Kir 2.3. To identify the network of proteins that interact with GIP, a human fetal brain cDNA library was screened using a yeast two-hybrid assay with GIP as bait. We identified brain-specific angiogenesis inhibitor 2 (BAI2), a member of the adhesion-G protein-coupled receptors (GPCRs), as a new partner of GIP. BAI2 is expressed primarily in neurons, further expanding GIP cellular functions. The interaction between GIP and the carboxy-terminus of BAI2 was characterized using fluorescence, circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy assays. These biophysical analyses support the interaction identified in the yeast two-hybrid assay. This is the first study reporting BAI2 as an interaction partner of GIP.

  1. 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

  2. Gene–environment interactions: key to unraveling the mystery of Parkinson’s disease

    PubMed Central

    Gao, Hui-Ming; Hong, Jau-shyong

    2011-01-01

    Parkinson’s disease (PD) is the second most common neurodegenerative disease. The gradual, irreversible loss of dopamine neurons in the substantia nigra isthe signature lesion of PD. Clinical symptoms of PD become apparent when 50–60% of nigral dopamine neurons are lost. PD progresses insidiously for 5–7 years (preclinical period) and then continues to worsen even under the symptomatic treatment. To determine what triggers the disease onset and what drives the chronic, self-propelling neurodegenerative process becomes critical and urgent, since lack of such knowledge impedes the discovery of effective treatments to retard PD progression. At present, available therapeutics only temporarily relieve PD symptoms. While the identification of causative gene defects in familial PD uncovers important genetic influences in this disease, the majority of PD cases are sporadic and idiopathic. The current consensus suggests that PD develops from multiple risk factors including aging, genetic predisposition, and environmental exposure. Here, we briefly review research on the genetic and environmental causes of PD. We also summarize very recent genome-wide association studies on risk gene polymorphisms in the emergence of PD. We highlight the new converging evidence on gene-environment interplay in the development of PD with an emphasis on newly developed multiple-hit PD models involving both genetic lesions and environmental triggers. PMID:21439347

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

    E-print Network

    Dolphin, Annette C.

    Kingdom, and 2School of Crystallography, Birkbeck College, London WC1E 7HX, United Kingdom The CaV 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

  4. Insight into the key interactions of bromodomain inhibitors based on molecular docking, interaction fingerprinting, molecular dynamics and binding free energy calculation.

    PubMed

    Ran, Ting; Zhang, Zhimin; Liu, Kejun; Lu, Yi; Li, Huifang; Xu, Jinxing; Xiong, Xiao; Zhang, Yanmin; Xu, Anyang; Lu, Shuai; Liu, Haichun; Lu, Tao; Chen, Yadong

    2015-04-21

    The bromodomain is a key protein-protein interaction module that specifically reads the acetylation marks of histones in epigenetic regulation. Currently, lots of inhibitors targeting the bromodomain have been reported as therapeutic agents. To better understand the interaction mechanism of bromodomain inhibitors, 20 diverse bromodomain inhibitors were studied using a combination of computational methods, including molecular docking, interaction fingerprinting, molecular dynamics simulation and binding free energy calculation. As a result, interactions important for the activity were critically analyzed, and the energy contribution in terms of individual residues was explored. These integrated results provided insights into two hot spots in the active site of the bromodomain, where the hydrophobic hot spot formed by Trp81, Val87, Leu92 and Ile146 played a central role in the interaction, and the hydrogen-bond hot spot mediated by Asn140 exhibited a moderate contribution to the binding affinity of the bromodomain inhibitors. This interaction mechanism study may facilitate the rational design of novel small-molecule bromodomain inhibitors. PMID:25758752

  5. 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

  6. 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

  7. Amino acid residues of Leishmania donovani cyclophilin key to interaction with its adenosine kinase: biological implications.

    PubMed

    Sen, Banibrata; Venugopal, V; Chakraborty, Anutosh; Datta, Rupak; Dolai, Subhankar; Banerjee, Rahul; Datta, Alok K

    2007-07-01

    Cyclophilins (CyPs), by interacting with a variety of proteins, often modulate their biological activities and thus have been implicated in several cellular functions. However, mechanisms that determine such interactions are poorly understood. We earlier reported that an endoplasmic reticulum (ER)-located cyclophilin (LdCyP) from the purine auxotrophic parasitic protozoan Leishmania donovani reactivated its adenosine kinase (AdK). The AdK-reactivating property of LdCyP was however abolished at high ionic strength but not by nonionic detergents. Modeling of LdCyP, based on its crystal structure solved at 1.97 A resolution, revealed several solvent-exposed hydrophobic and charged residues. Mutagenesis of several of such solvent-exposed residues was performed and their corresponding activities with regard to their (i) AdK reactivation property, (ii) ability to form complex with the enzyme, (iii) capacity to induce red shift in the intrinsic tryptophan fluorescence maxima of AdK, and (iv) efficiency to withdraw the ADP inhibition from the AdK-mediated reaction were compared to the wild-type protein. Results indicated that while the replacement of R147 with either A or D severely impaired all of the above characteristics displayed by the wild-type LdCyP, the effect of mutating K114 and K153 was although relatively less but nevertheless noticeable. Alteration of other exposed hydrophobic and charged residues apparently did not have any discernible effect. Under the condition of cellular stress, the ER-located LdCyP is released into the cytoplasm with concomitant increase both in the specific activity of the cytosol-resident AdK and the uptake of radiolabeled Ado into the cells. These experiments, besides demonstrating the importance of the positive charge, identified R147 as the most crucial residue in the LdCyP-AdK interaction and provide evidence for the stress-induced retrograde translocation of LdCyP from the ER to the cytoplasm. A possible implication of this interaction in the life cycle of the parasite is proposed. PMID:17552497

  8. Identification of DNA damage checkpoint-dependent protein interactions in Saccharomyces cerevisiae using quantitative mass spectrometry

    PubMed Central

    Bastos de Oliveira, Francisco M.; Smolka, Marcus B.

    2014-01-01

    Summary The DNA damage checkpoint (DDC) is an evolutionarily conserved signaling pathway that is crucial to maintain genomic integrity. In response to DNA damage, DDC kinases are rapidly activated and phosphorylate an elaborate network of substrates involved in multiple cellular processes. An important role of the DDC response is to assemble protein complexes. However, for most of the DDC substrates, how the DDC-dependent phosphorylation modulates their network of interactions remains to be established. Here, we present a protocol for the identification of DDC-dependent protein-protein interactions based on Stable Isotope Labeling of Amino acids in Cell culture (SILAC) followed by affinity-tagged protein purification and quantitative mass spectrometry analysis. Based on a model study using Saccharomyces cerevisiae, we provide a method that can be generally applied to study the role of kinases in mediating protein-protein interactions. PMID:24791994

  9. Environmental heterogeneity and interspecific interactions influence nest occupancy by key seed-dispersing ants.

    PubMed

    Warren, Robert J; Giladi, Itamar; Bradford, Mark A

    2012-06-01

    The complex interplay between species along environmental gradients ultimately shapes their distributions and additional community interactions. Ant-mediated seed dispersal fails in the wettest habitat of deciduous forest in eastern North America, and we examine whether this pattern corresponds with colony distributions for seed-dispersing ants and associated heterogeneity in abiotic and biotic variables. Specifically, we used spatial variation in soil moisture, temperature and diffuse light along natural habitat gradients and experimentally manipulated soil moisture gradients to examine ant habitat selection. We also examined niche segregation between effective (Aphaenogaster spp.) and ineffective (Lasius alienus Foerster) seed-dispersing ants across these environmental gradients. Whereas most research links ant foraging and nesting with temperature gradients, we find niche segregation between Aphaenogaster spp. and L. alienus by soil moisture along naturally occurring gradients and in experimentally irrigated upland habitat. The failure of Aphaenogaster spp. to occupy the wettest habitats, where L. alienus is present, is consistent with observed seed dispersal failure in these habitats. These results indicate that environmental heterogeneity drives niche segregation between effective (Aphaenogaster spp.) and ineffective (L. alienus) seed dispersers so each occupies distinct habitat. Most forest understory plants rely on ants for seed dispersal. Our research implies that climate-mediated interactions between effective and ineffective seed dispersing ant species may structure the microhabitat distributions for woodland herbs. PMID:22732603

  10. The tandem affinity purification method: an efficient system for protein complex purification and protein interaction identification.

    PubMed

    Xu, Xiaoli; Song, Yuan; Li, Yuhua; Chang, Jianfeng; Zhang, Hua; An, Lizhe

    2010-08-01

    Isolation and identification of protein partners in multi-protein complexes are important in gaining further insights into the cellular roles of proteins and determining the possible mechanisms by which proteins have an effect in the molecular environment. The tandem affinity purification (TAP) method was originally developed in yeast for the purification of protein complexes and identification of protein-protein interactions. With modifications to this method and many variations in the original tag made over the past few years, the TAP system could be applied in mammalian, plant, bacteria and other systems for protein complex analysis. In this review, we describe the application of the TAP method in various organisms, the modification in the tag, the disadvantages, the developments and the future prospects of the TAP method. PMID:20399864

  11. 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

  12. Strong-coupling superconductivity beyond BCS and the key pairing interaction in cuprate superconductors

    NASA Astrophysics Data System (ADS)

    Alexandrov, A. S.

    2011-03-01

    It has been now over 20 years since the discovery of the first high temperature superconductor by Georg Bednorz and Alex Müller in 1986 and yet, despite intensive effort, no universally accepted theory exists about the origin of high-temperature superconductivity. A controversial issue on whether the electron-phonon interaction (EPI) is crucial for high-temperature superconductivity or weak and inessential has been one of the most challenging problems of contemporary condensed matter physics. I briefly review our recent theoretical results, which in conjunction with a great number of experimental observations including isotope effects, angle-resolved photoemission (ARPES), pump-probe and tunnelling spectroscopies, normal state diamagnetism and magnetic quantum oscillations provide the definite answer to this fundamental question. The true origin of high-temperature superconductivity is found in a significant finite-range Fröhlich EPI of nonadiabatic polaronic carriers which is beyond the conventional BCS-Migdal-Eliashberg approximation.

  13. The diaphanous Gene of Drosophila Interacts Antagonistically with multiple wing hairs and Plays a Key Role in Wing Hair Morphogenesis

    PubMed Central

    Lu, Qiuheng; Adler, Paul N.

    2015-01-01

    The Drosophila wing is covered by an array of distally pointing hairs that has served as a key model system for studying planar cell polarity (PCP). The adult cuticular hairs are formed in the pupae from cell extensions that contain extensive actin filaments and microtubules. The importance of the actin cytoskeleton for hair growth and morphogenesis is clear from the wide range of phenotypes seen in mutations in well-known actin regulators. Formin proteins promote the formation of long actin filaments of the sort thought to be important for hair growth. We report here that the formin encoding diaphanous (dia) gene plays a key role in hair morphogenesis. Both loss of function mutations and the expression of a constitutively active Dia led to cells forming both morphologically abnormal hairs and multiple hairs. The conserved frizzled (fz)/starry night (stan) PCP pathway functions to restrict hair initiation and activation of the cytoskeleton to the distal most part of wing cells. It also ensures the formation of a single hair per cell. Our data suggest that the localized inhibition of Dia activity may be part of this mechanism. We found the expression of constitutively active Dia greatly expands the region for activation of the cytoskeleton and that dia functions antagonistically with multiple wing hairs (mwh), the most downstream member of the fz/stan pathway. Further we established that purified fragments of Dia and Mwh could be co-immunoprecipitated suggesting the genetic interaction could reflect a direct physical interaction. PMID:25730111

  14. The diaphanous Gene of Drosophila Interacts Antagonistically with multiple wing hairs and Plays a Key Role in Wing Hair Morphogenesis.

    PubMed

    Lu, Qiuheng; Adler, Paul N

    2015-01-01

    The Drosophila wing is covered by an array of distally pointing hairs that has served as a key model system for studying planar cell polarity (PCP). The adult cuticular hairs are formed in the pupae from cell extensions that contain extensive actin filaments and microtubules. The importance of the actin cytoskeleton for hair growth and morphogenesis is clear from the wide range of phenotypes seen in mutations in well-known actin regulators. Formin proteins promote the formation of long actin filaments of the sort thought to be important for hair growth. We report here that the formin encoding diaphanous (dia) gene plays a key role in hair morphogenesis. Both loss of function mutations and the expression of a constitutively active Dia led to cells forming both morphologically abnormal hairs and multiple hairs. The conserved frizzled (fz)/starry night (stan) PCP pathway functions to restrict hair initiation and activation of the cytoskeleton to the distal most part of wing cells. It also ensures the formation of a single hair per cell. Our data suggest that the localized inhibition of Dia activity may be part of this mechanism. We found the expression of constitutively active Dia greatly expands the region for activation of the cytoskeleton and that dia functions antagonistically with multiple wing hairs (mwh), the most downstream member of the fz/stan pathway. Further we established that purified fragments of Dia and Mwh could be co-immunoprecipitated suggesting the genetic interaction could reflect a direct physical interaction. PMID:25730111

  15. A bridge between liquids and socio-economic systems: the key role of interaction strengths

    NASA Astrophysics Data System (ADS)

    Roehner, Bertrand M.

    2005-03-01

    One distinctive and pervasive aspect of social systems is the fact that they involve several kinds of agents. Thus, in order to draw parallels with physical systems one is led to consider binary (or multi-component) compounds. Recent views about the mixing of liquids in solutions gained from neutron and X-ray scattering show these systems to have a number of similarities with socio-economic systems. It appears that such phenomena as rearrangement of bonds in a solution, gas condensation, and selective evaporation of molecules can be transposed in a natural way to some socio-economic phenomena. These connections provide with a novel perspective for looking at social systems which we illustrate through examples. For instance, we interpret suicide as an escape phenomenon and in order to test this interpretation we consider social systems characterized by very low levels of social interaction. For these systems suicide rates are found to be 10 to 100 times higher than in the general population. Another interesting parallel concerns the phase transition that occurs when locusts gather together to form swarms which may contain several billion insects. What hinders the thorough investigation of such cases from the standpoint of collective phenomena that we advocate is the lack or inadequacy of statistical data; up to now socio-economic data were collected for completely different purposes. Most essential, for further progress, are the statistics which would permit to estimate the strength of social ties and interactions. Once adequate data become available, rapid advancement may be expected. At the end of the paper, we will discuss whether or not the ergodic principle applies to social systems.

  16. 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

  17. 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.

  18. Chemical profiles and identification of key compound caffeine in marine-derived traditional Chinese medicine Ostreae concha.

    PubMed

    Yang, Xue; Zhou, Shi-Lu; Ma, Ai-Cui; Xu, Hai-Tao; Guan, Hua-Shi; Liu, Hong-Bing

    2012-05-01

    To compare the chemical differences between the medicinal and cultured oyster shells, their chemical profiles were investigated. Using the ultra performance liquid chromatography-electron spraying ionization-mass spectrometry (UPLC-ESI-MS), combined with principal component analysis (PCA) and orthogonal projection to latent structures discriminant analysis (OPLS-DA), the discrimination of the chemical characteristics among the medicinal and cultured oyster shells was established. Moreover, the chemometric analysis revealed some potential key compounds. After a large-scale extraction and isolation, one target key compound was unambiguously identified as caffeine based on extensive spectroscopic data analysis (1D and 2D NMR, MS, and UV) and comparison with literature data. PMID:22822365

  19. 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

  20. 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

  1. 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

  2. Identification of novel 14-3-3? interacting proteins by quantitative immunoprecipitation combined with knockdown (QUICK).

    PubMed

    Ge, Feng; Li, Wen-Liang; Bi, Li-Jun; Tao, Sheng-Ce; Zhang, Zhi-Ping; Zhang, Xian-En

    2010-11-01

    The family of 14-3-3 proteins has emerged as critical regulators of diverse cellular responses under both physiological and pathological conditions. To gain insight into the molecular action of 14-3-3? in multiple myeloma (MM), we performed a systematic proteomic analysis of 14-3-3?-associated proteins. This analysis, recently developed by Matthias Mann, termed quantitative immunoprecipitation combined with knockdown (QUICK), integrates RNAi, SILAC, immunoprecipitation, and quantitative MS technologies. Quantitative mass spectrometry analysis allowed us to distinguish 14-3-3?-interacting proteins from background proteins, resulting in the identification of 292 proteins in total with 95 novel interactions. Three 14-3-3?-interacting proteins-BAX, HSP70, and BAG3-were further confirmed by reciprocal coimmunoprecipitations and colocalization analysis. Our results therefore not only uncover a large number of novel 14-3-3?-associated proteins that possess a variety of cellular functions, but also provide new research directions for the study of the functions of 14-3-3?. This study also demonstrated that QUICK is a useful approach to detect specific protein-protein interactions with very high confidence and may have a wide range of applications in the investigation of protein complex interaction networks. PMID:20879785

  3. Identification of key amino acid differences contributing to neonicotinoid sensitivity between two nAChR ? subunits from Pardosa pseudoannulata.

    PubMed

    Meng, Xiangkun; Zhang, Yixi; Guo, Beina; Sun, Huahua; Liu, Chuanjun; Liu, Zewen

    2015-01-01

    Chemical insecticides are still primary methods to control rice planthoppers in China, which not only cause environmental pollution, insecticide residue and insecticide resistance, but also have negative effects on natural enemies, such as Pardosa pseudoannulata (the pond wolf spider), an important predatory enemy of rice planthoppers. Neonicotinoids insecticides, such as imidacloprid and thiacloprid, are insect-selective nAChRs agonists that are used extensively in the areas of crop protection and animal health, but have hypotoxicity to P. pseudoannulata. In the present study, two nAChR ? subunits, Pp?1 or Pp?8, were found to be successfully expressed with r?2 in Xenopus oocytes, but with much different sensitivity to imidacloprid and thiacloprid on two recombinant receptors Pp?1/r?2 and Pp?8/r?2. Key amino acid differences were found in and between the important loops for ligand binding. In order to well understand the relationship between the amino acid differences and neonicotinoid sensitivities, different segments in Pp?8 or Pp?1 with key amino acid differences were introduced into the corresponding regions of Pp?1 or Pp?8 to construct chimeras and then co-expressed with r?2 subunit in Xenopus oocytes. The results from chimeras of both Pp?8 and Pp?1 showed that segments ?5, ?6, and ?7 contributed to neonicotinoid sensitivities directly between two receptors. Although the segment ?4 including all loop B region had no direct influences on neonicotinoid sensitivities, it could more remarkably influence neonicotinoid sensitivities when co-introductions with ?5, ?6 or ?7. So, key amino acid differences in these four segments were important to neonicotinoid sensitivities, but the difference in ?4 was likely ignored because of its indirect effects. PMID:25459289

  4. Parasitoids of Monochamus galloprovincialis (Coleoptera, Cerambycidae), vector of the pine wood nematode, with identification key for the Palaearctic region

    PubMed Central

    Petersen-Silva, Ricardo; Pujade-Villar, Juli; Naves, Pedro; Edmundo Sousa; Belokobylskij,  Sergey

    2012-01-01

    Abstract The parasitoid complex associated with Monochamus galloprovincialis (Olivier), vector of the pine wood nematode, is discussed. Four species of the family Braconidae and one Ichneumonidae were found associated with Monochamus galloprovincialis in Portugal, namely Atanycolus denigrator (Linnaeus), Atanycolus ivanowi (Kokujev), Cyanopterus flavator (Fabricius), Doryctes striatellus (Nees) (Braconidae), and Xorides depressus (Holmgren) (Ichneumonidae). Atanycolus ivanowi, Atanycolus denigrator, Doryctes striatellus and Xorides depressus are new species for Portugal fauna, and Monochamus galloprovincialis is recorded as a new host of Xorides depressus. A key for determination of the ichneumonoid parasitoids of the pine sawyer is provided for the Palaearctic fauna. PMID:23378807

  5. Uncertainties in Biologically-Based Modeling of Formaldehyde-Induced Respiratory Cancer Risk: Identification of Key Issues

    PubMed Central

    Subramaniam, Ravi P.; Chen, Chao; Crump, Kenny S.; DeVoney, Danielle; Fox, John F.; Portier, Christopher J.; Schlosser, Paul M.; Thompson, Chad M.; White, Paul

    2009-01-01

    In a series of articles and a health-risk assessment report, scientists at the CIIT Hamner Institutes developed a model (CIIT model) for estimating respiratory cancer risk due to inhaled formaldehyde within a conceptual framework incorporating extensive mechanistic information and advanced computational methods at the toxicokinetic and toxicodynamic levels. Several regulatory bodies have utilized predictions from this model; on the other hand, upon detailed evaluation the California EPA has decided against doing so. In this article, we study the CIIT model to identify key biological and statistical uncertainties that need careful evaluation if such two-stage clonal expansion models are to be used for extrapolation of cancer risk from animal bioassays to human exposure. Broadly, these issues pertain to the use and interpretation of experimental labeling index and tumor data, the evaluation and biological interpretation of estimated parameters, and uncertainties in model specification, in particular that of initiated cells. We also identify key uncertainties in the scale-up of the CIIT model to humans, focusing on assumptions underlying model parameters for cell replication rates and formaldehyde-induced mutation. We discuss uncertainties in identifying parameter values in the model used to estimate and extrapolate DNA protein cross-link levels. The authors of the CIIT modeling endeavor characterized their human risk estimates as “conservative in the face of modeling uncertainties.” The uncertainties discussed in this article indicate that such a claim is premature. PMID:18564991

  6. 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

  7. An annotated key to the identification of commonly occurring and dominant genera of algae observed in the phytoplankton of the United States

    USGS Publications Warehouse

    Greeson, Phillip E.

    1982-01-01

    In early 1979, a retrieval was made for all phytoplankton data contained in the computerized data file of the U. S. Geological Survey. The retrieval revealed the analytical results of 17,959 samples collected and processed between October 1973 and October 1978. Of the approximately 500 genera of freshwater algae reported in the United States, the U.S. Geological Survey observed 321 genera in the phytoplankton. Fifty-two genera were considered to be commonly occurring and 42 genera were considered to be community dominants. The report lists, describes, and provides a detailed taxonomic key to the identification of 58 genera of algae considered either commonly occurring or dominant. Also included is a summary of environmental conditions under which each algal genus was observed, as well as a glossary and an extensive list of selected references.

  8. 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

  9. A new player in X identification: the CLAMP protein is a key factor in Drosophila dosage compensation.

    PubMed

    Soruco, Marcela M L; Larschan, Erica

    2014-12-01

    Dosage compensation adjusts the expression levels of genes on one or both targeted sex chromosomes in heterogametic species. This process results in the normalized transcriptional output of important and essential gene families encoded on multiple chromosomes. The mechanisms of dosage compensation have been studied in many model organisms, including Drosophila melanogaster (fly), Caenorhabditis elegans (worm), and Mus musculus (mouse). Although the mechanisms of dosage compensations differ among these species, all of these processes rely on the initial discrimination of the X chromosome from autosomes. Recently, a new paradigm for how the X chromosome is targeted for regulation was identified in Drosophila. This mechanism involves a newly identified zinc finger protein, CLAMP. Here, we review important factors involved in dosage compensation across species with special focus on the fly. Understanding how the newly identified CLAMP protein is involved in X targeting in the fly could provide key insights into how the X chromosome is initially identified across species. PMID:25102930

  10. Identification of a key residue for oligomerisation and pore-formation of Clostridium perfringens NetB.

    PubMed

    Fernandes da Costa, Sérgio P; Savva, Christos G; Bokori-Brown, Monika; Naylor, Claire E; Moss, David S; Basak, Ajit K; Titball, Richard W

    2014-03-01

    Necrotic enteritis toxin B (NetB) is a ?-pore-forming toxin produced by Clostridium perfringens and has been identified as a key virulence factor in the pathogenesis of avian necrotic enteritis, a disease causing significant economic damage to the poultry industry worldwide. In this study, site-directed mutagenesis was used to identify amino acids that play a role in NetB oligomerisation and pore-formation. NetB K41H showed significantly reduced toxicity towards LMH cells and human red blood cells relative to wild type toxin. NetB K41H was unable to oligomerise and form pores in liposomes. These findings suggest that NetB K41H could be developed as a genetic toxoid vaccine to protect against necrotic enteritis. PMID:24625763

  11. [Seed germination and key to seedling identification for six native tree species of wetlands from Southeast Mexico].

    PubMed

    Zamora-Cornelio, Luis Felipe; Ochoa-Gaona, Susana; Vargas Simón, Georgina; Castellanos Albores, Jorge; Jong, Bernardus H J de

    2010-06-01

    Wetland tree species are of importance for economic and restoration purposes. We describe the germination process and seedling morphology of six arboreal native species typical of Southeastern Mexico: Annona glabra, Ceiba pentandra, Pachira aquatica, Haematoxylum campechianum, Coccoloba barbadensis and Crataeva tapia. A total of 300 seeds per species were planted in a mixture of sand, cocoa plant husk and black soil (1:1:1), and maintained in a tree nursery with 30% artificial shade, from February to November of 2007. We carried out the morphological characterization, and elaborated a key to seedlings based on: 1) germination type 2) seedling axis and 3) leaf elements. P. aquatica has cryptocotylar hypogeal germination, the others have phanerocotylar epigeal germination. Germination rates were high (>86%), except for C. barbadensis (69%). PMID:20527471

  12. Identification of key areas for Aedes aegypti control through geoprocessing in Nova Iguaçu, Rio de Janeiro State, Brazil.

    PubMed

    Lagrotta, Marcos Thadeu Fernandes; Silva, Wellington da Costa; Souza-Santos, Reinaldo

    2008-01-01

    This study discusses the use of geoprocessing to identify key areas for Aedes aegypti control, based on the infestation index obtained in the Aedes aegypti Infestation Index Rapid Survey (LIRAa). The study was conducted in November 2004 in Nova Iguaçu, Rio de Janeiro State, Brazil. The results were analyzed on two scales, neighborhoods and blocks, with the building infestation index assigned to the neighborhood polygons and the Breteau index to the blocks. Kernel estimation was used in the spatial pattern analysis. The Breteau index spatial distribution showed five areas with high and medium density of positive Ae. aegypti breeding sites, highlighting small block clusters with high larval density, strategic for vector control. Based on the results, we recommend this method for dengue vector surveillance. PMID:18209835

  13. Identification of a Key Residue for Oligomerisation and Pore-Formation of Clostridium perfringens NetB

    PubMed Central

    Fernandes da Costa, Sérgio P.; Savva, Christos G.; Bokori-Brown, Monika; Naylor, Claire E.; Moss, David S.; Basak, Ajit K.; Titball, Richard W.

    2014-01-01

    Necrotic enteritis toxin B (NetB) is a ?-pore-forming toxin produced by Clostridium perfringens and has been identified as a key virulence factor in the pathogenesis of avian necrotic enteritis, a disease causing significant economic damage to the poultry industry worldwide. In this study, site-directed mutagenesis was used to identify amino acids that play a role in NetB oligomerisation and pore-formation. NetB K41H showed significantly reduced toxicity towards LMH cells and human red blood cells relative to wild type toxin. NetB K41H was unable to oligomerise and form pores in liposomes. These findings suggest that NetB K41H could be developed as a genetic toxoid vaccine to protect against necrotic enteritis. PMID:24625763

  14. Identification of the interaction between vimentin and nucleocapsid protein of transmissible gastroenteritis virus.

    PubMed

    Zhang, Xin; Shi, HongYan; Chen, JianFei; Shi, Da; Dong, Hui; Feng, Li

    2015-03-16

    Nucleocapsid (N) protein of transmissible gastroenteritis virus (TGEV) packages viral RNA genome to form a ribonucleoprotein complex. In addition to its function as a structural protein, N protein is involved in cell apoptosis or cell-cycle regulation. N protein possibly interacts with host factors to modulate cellular functions. To identify cellular proteins that interacted with N protein of TGEV, methods of GST pull-down and Co-IP were utilized to precipitate cellular proteins of swine testicular (ST). Bound cellular proteins were resolved by SDS-PAGE. Analysis of interacting proteins by mass spectrometry allowed identification of 15 cellular protein bands representative of 12 cellular proteins including vimentin that bound to N protein. Furthermore, the function of vimentin cytoskeleton in ST cells during TGEV infection was examined. Vimentin cytoskeleton was required for virus replication. The present study thus provides protein-related information about interaction of TGEV N protein with host cell that should be useful for understanding host cell response to coronavirus pathogenesis infection and the underlying mechanism of coronavirus replication. PMID:25533531

  15. Molecular identification of microsomal acyl-CoA:glycerol-3-phosphate acyltransferase, a key enzyme in de novo triacylglycerol synthesis

    PubMed Central

    Cao, Jingsong; Li, Jian-Liang; Li, Dongmei; Tobin, James F.; Gimeno, Ruth E.

    2006-01-01

    Acyl-CoA:glycerol-3-phosphate acyltransferase (GPAT) catalyzes the first step during de novo synthesis of triacylglycerol. It has been well recognized that mammals possess multiple enzymatically distinct proteins with GPAT activity. Although the mitochondrial-associated GPAT has been cloned and extensively characterized, the molecular identity of the endoplasmic reticulum (ER)-associated GPAT, which accounts for the majority of total GPAT activity in most tissues, has remained elusive. Here we report the identification of genes encoding human and mouse ER-associated GPAT (termed GPAT3). GPAT3 is a member of the acyltransferase family predominantly expressed in tissues characterized by active lipid metabolism, such as adipose tissue, small intestine, kidney, and heart. Ectopic expression of GPAT3 leads to a significant increase in N-ethylmaleimide-sensitive GPAT activity, whereas acyltransferase activity toward a variety of other lysophospholipids, as well as neutral lipid substrates, is not altered. Overexpression of GPAT3 in mammalian cells results in increased triacylglycerol, but not phospholipid, formation. GPAT3 is localized to the ER when overexpressed in COS-7 cells. GPAT3 mRNA is dramatically up-regulated during adipocyte differentiation, is reciprocally regulated in adipose tissue and liver of ob/ob mice, and is up-regulated in mice treated with a peroxisome proliferator-activated receptor ? (PPAR?) agonist. A substantial loss of GPAT activity in 3T3-L1 adipocytes was achieved by reducing GPAT3 mRNA levels through GPAT3-specific siRNA knockdown. These findings identify GPAT3 as a previously uncharacterized triacylglycerol biosynthetic enzyme. Similar to other lipogenic enzymes, GPAT3 may be useful as a target for the treatment of obesity. PMID:17170135

  16. 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

  17. A Hierarchical Non-interactive Key-Sharing Scheme with Low Memory Size and High Resistance against Collusion Attacks

    Microsoft Academic Search

    Goichiro Hanaoka; Tsuyoshi Nishioka; Yuliang Zheng; Hideki Imai

    2002-01-01

    Efficient ID-based key sharing schemes are desired worldwide for secure communications on Internet and other networks. The Key Predistribution Systems (KPSs) are a large class of such key sharing schemes. The remarkable property of KPSs is that in order to share the key, a participant should only input its partner's identifier to its secret KPS algorithm. Although it has many

  18. Proteomic characterization of Aspergillus fumigatus treated with an antifungal coumarin for identification of novel target molecules of key pathways.

    PubMed

    Singh, Seema; Gupta, Shilpi; Singh, Bharat; Sharma, Sunil K; Gupta, Vijay K; Sharma, Gainda L

    2012-06-01

    A synthetic coumarin, N,N,N-triethyl-11-(4-methyl-2-oxo-2H-chromen-7-yloxy)-11-oxoundecan-1-aminium bromide (SCD-1), having potent activity against pathogenic Aspergilli (MIC90 15.62 ?g/mL), was investigated to identify its molecular targets in the pathogen. The proteome of Aspergillus fumigatus was developed after treatment with sublethal doses of compound and analyzed. The results demonstrated 143 differentially expressed proteins on treatment with SCD-1. The expression of four proteins, namely cell division control protein, ubiquitin-like activating enzyme, vacuolar ATP synthase catalytic subunit A, and UTP-glucose-1-phosphate uridylyltransferase of A. fumigatus, was completely inhibited, whereas there were 13 newly expressed and 96 overexpressed proteins, mainly belonging to stress pathway. The treatment of A. fumigatus with SCD-1 also led to attenuation of proteins involved in cell replication and other important biosynthetic processes, including riboflavin biosynthesis, which has been pathogen-specific. In addition to key enzymatic players and antioxidants, nine hypothetical proteins were also identified, seven of which have been novel, being described for the first time. As no cellular functions have yet been described for these hypothetical proteins, their alteration in response to SCD-1 provides significant information about their putative roles in pathogen defense. PMID:22533410

  19. 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

  20. Identification of key amino acids for the evolution of promoter target specificity of anthocyanin and proanthocyanidin regulating MYB factors.

    PubMed

    Heppel, Simon C; Jaffé, Felix W; Takos, Adam M; Schellmann, Swen; Rausch, Thomas; Walker, Amanda R; Bogs, Jochen

    2013-07-01

    A complex of R2R3-MYB and bHLH transcription factors, stabilized by WD40 repeat proteins, regulates gene transcription for plant cell pigmentation and epidermal cell morphology. It is the MYB component of this complex which specifies promoter target activation. The Arabidopsis MYB TT2 regulates proanthocyanidin (PA) biosynthesis by activating the expression of ANR (anthocyanidin reductase), the gene product of which catalyzes the first committed step of this pathway. Conversely the closely related MYB PAP4 (AtMYB114) regulates the anthocyanin pathway and specifically activates UFGT (UDP-glucose:flavonoid-3-O-glucosyltransferase), encoding the first enzyme of the anthocyanin pathway. Both at the level of structural and regulatory genes, evolution of PA biosynthesis proceeded anthocyanin biosynthesis and we have identified key residues in these MYB transcription factors for the evolution of target promoter specificity. Using chimeric and point mutated variants of TT2 and PAP4 we found that exchange of a single amino acid, Gly/Arg(39) in the R2 domain combined with an exchange of a four amino acid motif in the R3 domain, could swap the pathway selection of TT2 and PAP4, thereby converting in planta specificity of the PA towards the anthocyanin pathway and vice versa. The general importance of these amino acids for target specificity was also shown for the grapevine transcription factors VvMYBPA2 and VvMYBA2 which regulate PAs and anthocyanins, respectively. These results provide an insight into the evolution of the different flavonoid regulators from a common ancestral gene. PMID:23689818

  1. 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

  2. Functional identification of APIP as human mtnB, a key enzyme in the methionine salvage pathway.

    PubMed

    Mary, Camille; Duek, Paula; Salleron, Lisa; Tienz, Petra; Bumann, Dirk; Bairoch, Amos; Lane, Lydie

    2012-01-01

    The methionine salvage pathway is widely distributed among some eubacteria, yeast, plants and animals and recycles the sulfur-containing metabolite 5-methylthioadenosine (MTA) to methionine. In eukaryotic cells, the methionine salvage pathway takes place in the cytosol and usually involves six enzymatic activities: MTA phosphorylase (MTAP, EC 2.4.2.28), 5'-methylthioribose-1-phosphate isomerase (mtnA, EC 5.3.1.23), 5'-methylthioribulose-1-phosphate dehydratase (mtnB, EC: 4.2.1.109), 2,3-dioxomethiopentane-1-phosphate enolase/phosphatase (mtnC, EC 3.1.3.77), aci-reductone dioxygenase (mtnD, EC 1.13.11.54) and 4-methylthio-2-oxo-butanoate (MTOB) transaminase (EC 2.6.1.-). The aim of this study was to complete the available information on the methionine salvage pathway in human by identifying the enzyme responsible for the dehydratase step. Using a bioinformatics approach, we propose that a protein called APIP could perform this role. The involvement of this protein in the methionine salvage pathway was investigated directly in HeLa cells by transient and stable short hairpin RNA interference. We show that APIP depletion specifically impaired the capacity of cells to grow in media where methionine is replaced by MTA. Using a Shigella mutant auxotroph for methionine, we confirm that the knockdown of APIP specifically affects the recycling of methionine. We also show that mutation of three potential phosphorylation sites does not affect APIP activity whereas mutation of the potential zinc binding site completely abrogates it. Finally, we show that the N-terminal region of APIP that is missing in the short isoform is required for activity. Together, these results confirm the involvement of APIP in the methionine salvage pathway, which plays a key role in many biological functions like cancer, apoptosis, microbial proliferation and inflammation. PMID:23285211

  3. Design of optimal food-based complementary feeding recommendations and identification of key "problem nutrients" using goal programming.

    PubMed

    Ferguson, Elaine L; Darmon, Nicole; Fahmida, Umi; Fitriyanti, Suci; Harper, Timothy B; Premachandra, Inguruwatte M

    2006-09-01

    The WHO is urging countries to promote improved complementary feeding practices to ensure optimal health, growth, and development of young children. To help achieve this, a rigorous 4-phase approach for designing optimal population- specific food-based complementary feeding recommendations (CFRs) was developed and is illustrated here. In phase I, an optimized diet is selected, using goal programming (Model #1), which aims to provide a desired nutrient content with respect to habitual diet patterns and cost. Based on its food patterns, a set of draft CFRs is designed. In phase II, their success for ensuring a nutritionally adequate diet is assessed via linear programming (Model type #2) by sequentially minimizing and maximizing the level of each nutrient (i.e., worst and best-case scenarios) while respecting the CFRs. For nutrients that are <70% of desired levels, the best food sources are identified via linear programming in phase III (Model #3). Different combinations of these foods are incorporated into the original draft of the CFRs to produce alternative CFRs, which are then compared on the basis of their cost, flexibility, and "worst-case scenario" nutrient levels (Model type #2) to select, in phase IV, a final set of CFRs. A hypothetical example is used to illustrate this approach. Outcomes include a set of optimal, population-specific CFRs and practical information regarding key "problem nutrients" in the local diet. Such information is valuable for nutrition promotion, as well as nutrition program planning and advocacy, to help achieve global initiatives for improving the complementary feeding practices of young children living in disadvantaged environments. PMID:16920861

  4. 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.

  5. Network understanding of herb medicine via rapid identification of ingredient-target interactions.

    PubMed

    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. PMID:24429698

  6. 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.

  7. Identification of tissue interaction of terahertz radiation toward functional tissue imaging

    NASA Astrophysics Data System (ADS)

    Yokus, Hamdullah; Baughman, William; Balci, Soner; Bolus, Michael; Wilbert, David; Kung, Patrick; Kim, Seongsin M.

    2013-02-01

    In recent years, many applications have been recognized for biomedical imaging techniques utilizing terahertz frequency radiation. This is largely due to the capability of unique tissue identification resulting from the nature of the interaction between THz radiation and the molecular structure of the cells. By THz identification methods, tissue changes in tooth enamel, cartilage, and malignant cancer cells have already been demonstrated. Terahertz Time-Domain Spectroscopy (THz-TDS) remains one of the most versatile methods for spectroscopic image acquisition for its ability to simultaneously determine amplitude and phase over a broad spectral range. In this study we investigate the use of THz imaging techniques to uniquely identify damage types in tissue samples for both forensic and treatment applications. Using THz-TDS imaging in both transmission and reflection schemes, we examine tissue samples which have been damaged using a variety of acids. Each method of damage causes structural deterioration to the tissue by a different mechanism, thus leaving the remaining tissue uniquely changed based on the damage type. We correlate the change in frequency spectra, phase shift for each damage type to the mechanisms and severity of injury.

  8. 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.

  9. 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

  10. Identification of additive, dominant, and epistatic variation conferred by key genes in cellulose biosynthesis pathway in Populus tomentosa†

    PubMed Central

    Du, Qingzhang; Tian, Jiaxing; Yang, Xiaohui; Pan, Wei; Xu, Baohua; Li, Bailian; Ingvarsson, Pär K.; Zhang, Deqiang

    2015-01-01

    Economically important traits in many species generally show polygenic, quantitative inheritance. The components of genetic variation (additive, dominant and epistatic effects) of these traits conferred by multiple genes in shared biological pathways remain to be defined. Here, we investigated 11 full-length genes in cellulose biosynthesis, on 10 growth and wood-property traits, within a population of 460 unrelated Populus tomentosa individuals, via multi-gene association. To validate positive associations, we conducted single-marker analysis in a linkage population of 1,200 individuals. We identified 118, 121, and 43 associations (P< 0.01) corresponding to additive, dominant, and epistatic effects, respectively, with low to moderate proportions of phenotypic variance (R2). Epistatic interaction models uncovered a combination of three non-synonymous sites from three unique genes, representing a significant epistasis for diameter at breast height and stem volume. Single-marker analysis validated 61 associations (false discovery rate, Q ? 0.10), representing 38 SNPs from nine genes, and its average effect (R2 = 3.8%) nearly 2-fold higher than that identified with multi-gene association, suggesting that multi-gene association can capture smaller individual variants. Moreover, a structural gene–gene network based on tissue-specific transcript abundances provides a better understanding of the multi-gene pathway affecting tree growth and lignocellulose biosynthesis. Our study highlights the importance of pathway-based multiple gene associations to uncover the nature of genetic variance for quantitative traits and may drive novel progress in molecular breeding. PMID:25428896

  11. Identification of additive, dominant, and epistatic variation conferred by key genes in cellulose biosynthesis pathway in Populus tomentosa†.

    PubMed

    Du, Qingzhang; Tian, Jiaxing; Yang, Xiaohui; Pan, Wei; Xu, Baohua; Li, Bailian; Ingvarsson, Pär K; Zhang, Deqiang

    2015-02-01

    Economically important traits in many species generally show polygenic, quantitative inheritance. The components of genetic variation (additive, dominant and epistatic effects) of these traits conferred by multiple genes in shared biological pathways remain to be defined. Here, we investigated 11 full-length genes in cellulose biosynthesis, on 10 growth and wood-property traits, within a population of 460 unrelated Populus tomentosa individuals, via multi-gene association. To validate positive associations, we conducted single-marker analysis in a linkage population of 1,200 individuals. We identified 118, 121, and 43 associations (P< 0.01) corresponding to additive, dominant, and epistatic effects, respectively, with low to moderate proportions of phenotypic variance (R(2)). Epistatic interaction models uncovered a combination of three non-synonymous sites from three unique genes, representing a significant epistasis for diameter at breast height and stem volume. Single-marker analysis validated 61 associations (false discovery rate, Q ? 0.10), representing 38 SNPs from nine genes, and its average effect (R(2) = 3.8%) nearly 2-fold higher than that identified with multi-gene association, suggesting that multi-gene association can capture smaller individual variants. Moreover, a structural gene-gene network based on tissue-specific transcript abundances provides a better understanding of the multi-gene pathway affecting tree growth and lignocellulose biosynthesis. Our study highlights the importance of pathway-based multiple gene associations to uncover the nature of genetic variance for quantitative traits and may drive novel progress in molecular breeding. PMID:25428896

  12. 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

  13. 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

  14. Key Role of Local Regulation in Chemosensing Revealed by a New Molecular Interaction-Based Modeling Method

    PubMed Central

    Meier-Schellersheim, Martin; Xu, Xuehua; Angermann, Bastian; Kunkel, Eric J; Jin, Tian; Germain, Ronald N

    2006-01-01

    The signaling network underlying eukaryotic chemosensing is a complex combination of receptor-mediated transmembrane signals, lipid modifications, protein translocations, and differential activation/deactivation of membrane-bound and cytosolic components. As such, it provides particularly interesting challenges for a combined computational and experimental analysis. We developed a novel detailed molecular signaling model that, when used to simulate the response to the attractant cyclic adenosine monophosphate (cAMP), made nontrivial predictions about Dictyostelium chemosensing. These predictions, including the unexpected existence of spatially asymmetrical, multiphasic, cyclic adenosine monophosphate–induced PTEN translocation and phosphatidylinositol-(3,4,5)P3 generation, were experimentally verified by quantitative single-cell microscopy leading us to propose significant modifications to the current standard model for chemoattractant-induced biochemical polarization in this organism. Key to this successful modeling effort was the use of “Simmune,” a new software package that supports the facile development and testing of detailed computational representations of cellular behavior. An intuitive interface allows user definition of complex signaling networks based on the definition of specific molecular binding site interactions and the subcellular localization of molecules. It automatically translates such inputs into spatially resolved simulations and dynamic graphical representations of the resulting signaling network that can be explored in a manner that closely parallels wet lab experimental procedures. These features of Simmune were critical to the model development and analysis presented here and are likely to be useful in the computational investigation of many aspects of cell biology. PMID:16854213

  15. Trade-offs Between Communication and Storage in Unconditionally Secure Schemes for Broadcast Encryption and Interactive Key Distribution

    Microsoft Academic Search

    Carlo Blundo; Luiz A. Frota Mattos; Douglas R. Stinson

    1996-01-01

    . In 1993, Beimel and Chor presented an unconditionally secureinteractive protocol which allows a subset of users in a network toestablish a common key. This scheme made use of a key predistributionscheme due to Blom.In this paper, we describe some variations and generalizations of theBeimel-Chor scheme, including broadcast encryption schemes as well asinteractive key distribution schemes. Our constructions use the

  16. Building Empathy through Identification and Expression of Emotions: A Review of Interactive Tools for Children with Social Deficits

    ERIC Educational Resources Information Center

    Maynard, Angelina S.; Monk, Jessica D.; Booker, Kimberly Wilson

    2011-01-01

    This article is a review of available interactive aids designed to enhance the identification and expression of feelings in children. These skills are part of the overall development of empathy. The development of empathy, in turn, is crucial for social competence, social relatedness, and prosocial behavior. Improving these skills is likely to…

  17. fMRI connectivity, meaning and empiricism Comments on: Roebroeck at al. The identification of interacting networks

    E-print Network

    Paris-Sud XI, Université de

    Commentary 1 fMRI connectivity, meaning and empiricism Comments on: Roebroeck at al. The identification of interacting networks in the brain using fMRI: model selection, causality and deconvolution networks using fMRI. Their nice methodological review has been triggered by our recent work (David et al

  18. Identification of photoluminescence through electron-phonon interaction by isotopically modified single-walled carbon-13 nanotubes

    E-print Network

    Maruyama, Shigeo

    Identification of photoluminescence through electron-phonon interaction by isotopically modified, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan Photoluminescence (PL) of single-walled carbon nanotubes (SWNTs). However, there are many unassigned peaks in the 2-D photoluminescence map

  19. Discovery of novel interacting partners of PSMD9, a proteasomal chaperone: Role of an Atypical and versatile PDZ-domain motif interaction and identification of putative functional modules

    PubMed Central

    Sangith, Nikhil; Srinivasaraghavan, Kannan; Sahu, Indrajit; Desai, Ankita; Medipally, Spandana; Somavarappu, Arun Kumar; Verma, Chandra; Venkatraman, Prasanna

    2014-01-01

    PSMD9 (Proteasome Macropain non-ATPase subunit 9), a proteasomal assembly chaperone, harbors an uncharacterized PDZ-like domain. Here we report the identification of five novel interacting partners of PSMD9 and provide the first glimpse at the structure of the PDZ-domain, including the molecular details of the interaction. We based our strategy on two propositions: (a) proteins with conserved C-termini may share common functions and (b) PDZ domains interact with C-terminal residues of proteins. Screening of C-terminal peptides followed by interactions using full-length recombinant proteins, we discovered hnRNPA1 (an RNA binding protein), S14 (a ribosomal protein), CSH1 (a growth hormone), E12 (a transcription factor) and IL6 receptor as novel PSMD9-interacting partners. Through multiple techniques and structural insights, we clearly demonstrate for the first time that human PDZ domain interacts with the predicted Short Linear Sequence Motif (SLIM) at the C-termini of the client proteins. These interactions are also recapitulated in mammalian cells. Together, these results are suggestive of the role of PSMD9 in transcriptional regulation, mRNA processing and editing, hormone and receptor activity and protein translation. Our proof-of-principle experiments endorse a novel and quick method for the identification of putative interacting partners of similar PDZ-domain proteins from the proteome and for discovering novel functions. PMID:25009770

  20. How Ethnic Identification Attitudes and Acculturative Stress Interact to Predict Suicide & Eating Disorder Symptomatology in Individuals of African Descent

    Microsoft Academic Search

    Daniel Leighton Hollar

    2006-01-01

    The purpose of this study is to examine the relationship between culture and psychopathology to determine if proposed psychological risk factors (i.e., ethnic identification and acculturative stress) are predictive of several key mental health variables related to suicide and eating disorder behaviors (i.e., depression, anxiety, suicidality, body dissatisfaction and drive for thinness) in minority versus non-minority undergraduate students. The main

  1. Heuristic Identification of Biological Architectures for Simulating Complex Hierarchical Genetic Interactions

    PubMed Central

    Moore, Jason H; Amos, Ryan; Kiralis, Jeff; Andrews, Peter C

    2015-01-01

    Simulation plays an essential role in the development of new computational and statistical methods for the genetic analysis of complex traits. Most simulations start with a statistical model using methods such as linear or logistic regression that specify the relationship between genotype and phenotype. This is appealing due to its simplicity and because these statistical methods are commonly used in genetic analysis. It is our working hypothesis that simulations need to move beyond simple statistical models to more realistically represent the biological complexity of genetic architecture. The goal of the present study was to develop a prototype genotype–phenotype simulation method and software that are capable of simulating complex genetic effects within the context of a hierarchical biology-based framework. Specifically, our goal is to simulate multilocus epistasis or gene–gene interaction where the genetic variants are organized within the framework of one or more genes, their regulatory regions and other regulatory loci. We introduce here the Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions (HIBACHI) method and prototype software for simulating data in this manner. This approach combines a biological hierarchy, a flexible mathematical framework, a liability threshold model for defining disease endpoints, and a heuristic search strategy for identifying high-order epistatic models of disease susceptibility. We provide several simulation examples using genetic models exhibiting independent main effects and three-way epistatic effects. PMID:25395175

  2. Heuristic identification of biological architectures for simulating complex hierarchical genetic interactions.

    PubMed

    Moore, Jason H; Amos, Ryan; Kiralis, Jeff; Andrews, Peter C

    2015-01-01

    Simulation plays an essential role in the development of new computational and statistical methods for the genetic analysis of complex traits. Most simulations start with a statistical model using methods such as linear or logistic regression that specify the relationship between genotype and phenotype. This is appealing due to its simplicity and because these statistical methods are commonly used in genetic analysis. It is our working hypothesis that simulations need to move beyond simple statistical models to more realistically represent the biological complexity of genetic architecture. The goal of the present study was to develop a prototype genotype-phenotype simulation method and software that are capable of simulating complex genetic effects within the context of a hierarchical biology-based framework. Specifically, our goal is to simulate multilocus epistasis or gene-gene interaction where the genetic variants are organized within the framework of one or more genes, their regulatory regions and other regulatory loci. We introduce here the Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions (HIBACHI) method and prototype software for simulating data in this manner. This approach combines a biological hierarchy, a flexible mathematical framework, a liability threshold model for defining disease endpoints, and a heuristic search strategy for identifying high-order epistatic models of disease susceptibility. We provide several simulation examples using genetic models exhibiting independent main effects and three-way epistatic effects. PMID:25395175

  3. Identification of unique SUN-interacting nuclear envelope proteins with diverse functions in plants.

    PubMed

    Zhou, Xiao; Graumann, Katja; Wirthmueller, Lennart; Jones, Jonathan D G; Meier, Iris

    2014-06-01

    Although a plethora of nuclear envelope (NE) transmembrane proteins (NETs) have been identified in opisthokonts, plant NETs are largely unknown. The only known NET homologues in plants are Sad1/UNC-84 (SUN) proteins, which bind Klarsicht/ANC-1/Syne-1 homology (KASH) proteins. Therefore, de novo identification of plant NETs is necessary. Based on similarities between opisthokont KASH proteins and the only known plant KASH proteins, WPP domain-interacting proteins, we used a computational method to identify the KASH subset of plant NETs. Ten potential plant KASH protein families were identified, and five candidates from four of these families were verified for their NE localization, depending on SUN domain interaction. Of those, Arabidopsis thaliana SINE1 is involved in actin-dependent nuclear positioning in guard cells, whereas its paralogue SINE2 contributes to innate immunity against an oomycete pathogen. This study dramatically expands our knowledge of plant KASH proteins and suggests that plants and opisthokonts have recruited different KASH proteins to perform NE regulatory functions. PMID:24891605

  4. 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.

  5. 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.

  6. New findings and a new species of the genus Ammothea (Pycnogonida, Ammotheidae), with an updated identification key to all Antarctic and sub-Antarctic species

    NASA Astrophysics Data System (ADS)

    Cano-Sánchez, E.; López-González, P. J.

    2014-03-01

    Specimens of the pycnogonid genus Ammothea collected during the Polarstern cruise XXIII/8 (23 November 2006-30 January 2007) were studied. Nine species were recognized in this collection: Ammothea bentartica, A. bicorniculata, A. carolinensis, A. clausi, A. longispina, A. minor, A. spinosa, A. striata and A. tibialis. Three of them ( A. bentartica, A. bicorniculata and A. tibialis) are reported for the second time, enlarging their known geographical and bathymetric range. In the present contribution, the observed morphological variability of all collected Ammothea species is described and discussed. For the identification and description of the material, different museum specimens were consulted. Among them, we have consulted part of the Discovery collection housed at the Natural History Museum in London. That material was initially identified by Isabella Gordon, a reputed author in the field of pycnogonid taxonomy. A new species, based on a museum specimen previously highly confused in the literature, is proposed in the present contribution as Ammothea isabellae n. sp. The new taxon is compared with its closest congeners, especially with A. longispina and A. stylirostris. Finally, we propose an updated dichotomous key to species covering all currently known Antarctic and sub-Antarctic Ammothea species.

  7. In vitro characterization of LmbK and LmbO: identification of GDP-D-erythro-?-D-gluco-octose as a key intermediate in lincomycin A biosynthesis.

    PubMed

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

    2014-01-22

    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

  8. Quantum identification system

    Microsoft Academic Search

    Miloslav Dusek; Ondrej Haderka; Martin Hendrych; Robert Myska

    1999-01-01

    A secure quantum identification system combining a classical identification procedure and quantum key distribution is proposed. Each identification sequence is always used just once and sequences are ``refueled'' from a shared provably secret key transferred through the quantum channel. Two identification protocols are devised. The first protocol can be applied when legitimate users have an unjammable public channel at their

  9. Using on-line surveys to measure three key constructs of the quality of human–computer interaction in web sites: psychometric properties and implications

    Microsoft Academic Search

    Paul van Schaik; Jonathan Ling

    2003-01-01

    On-line surveys are now an important tool for data collection on the World Wide Web (the Web). Determining the psychometric properties of key constructs such as disorientation, ease of use and flow is of paramount importance in establishing the quality of users’ interactions with web sites. The current study used techniques of experimental research and on-line surveys to investigate the

  10. "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…

  11. Identification of RNA-protein interaction networks using PAR-CLIP.

    PubMed

    Ascano, Manuel; Hafner, Markus; Cekan, Pavol; Gerstberger, Stefanie; Tuschl, Thomas

    2012-01-01

    All mRNA molecules are subject to some degree of post-transcriptional gene regulation (PTGR) involving sequence-dependent modulation of splicing, cleavage and polyadenylation, editing, transport, stability, and translation. The recent introduction of deep-sequencing technologies enabled the development of new methods for broadly mapping interaction sites between RNA-binding proteins (RBPs) and their RNA target sites. In this article, we review crosslinking and immunoprecipitation (CLIP) methods adapted for large-scale identification of target RNA-binding sites and the respective RNA recognition elements. CLIP methods have the potential to detect hundreds of thousands of binding sites in single experiments although the separation of signal from noise can be challenging. As a consequence, each CLIP method has developed different strategies to distinguish true targets from background. We focus on photoactivatable ribonucleoside-enhanced CLIP, which relies on the intracellular incorporation of photoactivatable ribonucleoside analogs into nascent transcripts, and yields characteristic sequence changes upon crosslinking that facilitate the separation of signal from noise. The precise knowledge of the position and distribution of binding sites across mature and primary mRNA transcripts allows critical insights into cellular localization and regulatory function of the examined RBP. When coupled with other systems-wide approaches measuring transcript and protein abundance, the generation of high-resolution RBP-binding site maps across the transcriptome will broaden our understanding of PTGR and thereby lead to new strategies for therapeutic treatment of genetic diseases perturbing these processes. PMID:22213601

  12. Homodimeric Intrinsic Membrane Proteins. Identification and Modulation of Interactions between Mitochondrial Transporter (Carrier) Subunits

    PubMed Central

    Wohlrab, Hartmut

    2010-01-01

    Transporter (carrier) proteins of the inner mitochondrial membrane link metabolic pathways within the matrix and the cytosol with transport/exchange of metabolites and inorganic ions. Their strict control of these fluxes is required for oxidative phosphorylation. Understanding the ternary complex transport mechanism with which most of these transporters function requires an accounting of the number and interactions of their subunits. The phosphate transporter (PTP, Mir1p) subunit readily forms homodimers with intersubunit affinities changeable by mutations. Cys28, likely at the subunit interface, is a site for mutations yielding transport inhibition or a channel-like transport mode. Such mutations yield a small increase or decrease in affinity between the subunits. The PTP inhibitor N-ethylmaleimide decreases subunit affinity by a small amount. PTP mutations that yield the highest (40%) and the lowest (2%) liposome incorporation efficiencies (LIE) are clustered near Cys28. Such mutant subunits show the lowest and highest subunit affinities respectively. The oxaloacetate transporter (Oac1p) subunit has an almost 2-fold lower affinity than the PTP subunit. The Oac1p, dicarboxylate (Dic1p) and PTP transporter subunits form heterodimers with even lower affinities. These results form a firm basis for detailed studies to establish the effect of subunit affinities on transport mode and activity and for the identification of the mechanism that prevents formation of heterodimers that surely will negatively impact oxidative phosphorylation and ATP levels with serious consequences for the cell. PMID:20171189

  13. Genome-wide identification of non-coding RNAs interacted with microRNAs in soybean

    PubMed Central

    Ye, Chu-Yu; Xu, Hao; Shen, Enhui; Liu, Yang; Wang, Yu; Shen, Yifei; Qiu, Jie; Zhu, Qian-Hao; Fan, Longjiang

    2014-01-01

    A wide range of RNA species interacting with microRNAs (miRNAs) form a complex gene regulation network and play vital roles in diverse biological processes. In this study, we performed a genome-wide identification of endogenous target mimics (eTMs) for miRNAs and phased-siRNA-producing loci (PHAS) in soybean with a focus on those involved in lipid metabolism. The results showed that a large number of eTMs and PHAS genes could be found in soybean. Additionally, we found that lipid metabolism related genes were potentially regulated by 28 miRNAs, and nine of them were potentially further regulated by a number of eTMs with expression evidence. Thirty-three miRNAs were found to trigger production of phasiRNAs from 49 PHAS genes, which were able to target lipid metabolism related genes. Degradome data supported miRNA- and/or phasiRNA-mediated cleavage of genes involved in lipid metabolism. Most eTMs for miRNAs involved in lipid metabolism and phasiRNAs targeting lipid metabolism related genes showed a tissue-specific expression pattern. Our bioinformatical evidences suggested that lipid metabolism in soybean is potentially regulated by a complex non-coding network, including miRNAs, eTMs, and phasiRNAs, and the results extended our knowledge on functions of non-coding RNAs. PMID:25566308

  14. A New RFID-USB Key

    Microsoft Academic Search

    Yuli Fu; Wei Liu

    2007-01-01

    In light of radio frequency Identification (RFID) and universal serial bus (USB) Key techniques, an RFID-USB key is designed. With both advantages of RFID and USB key, this RFID-USB key can be used to establish some safe environments of authentication, identification and other applications feasibly. The idea of this design is detailed and an implementation solution of the design is

  15. 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.

  16. Identification of protein-interacting nucleotides in a RNA sequence using composition profile of tri-nucleotides.

    PubMed

    Panwar, Bharat; Raghava, Gajendra P S

    2015-04-01

    The RNA-protein interactions play a diverse role in the cells, thus identification of RNA-protein interface is essential for the biologist to understand their function. In the past, several methods have been developed for predicting RNA interacting residues in proteins, but limited efforts have been made for the identification of protein-interacting nucleotides in RNAs. In order to discriminate protein-interacting and non-interacting nucleotides, we used various classifiers (NaiveBayes, NaiveBayesMultinomial, BayesNet, ComplementNaiveBayes, MultilayerPerceptron, J48, SMO, RandomForest, SMO and SVM(light)) for prediction model development using various features and achieved highest 83.92% sensitivity, 84.82 specificity, 84.62% accuracy and 0.62 Matthew's correlation coefficient by SVM(light) based models. We observed that certain tri-nucleotides like ACA, ACC, AGA, CAC, CCA, GAG, UGA, and UUU preferred in protein-interaction. All the models have been developed using a non-redundant dataset and are evaluated using five-fold cross validation technique. A web-server called RNApin has been developed for the scientific community (http://crdd.osdd.net/raghava/rnapin/). PMID:25640448

  17. A guide to the Simulium damnosum complex (Diptera: Simuliidae) in Nigeria, with a cytotaxonomic key for the identification of the sibling species

    PubMed Central

    Post, R J; Onyenwe, E; Somiari, S A E; Mafuyai, H B; Crainey, J L; Ubachukwu, P O

    2011-01-01

    Although approximately 40% of all the people blinded by Onchocerca volvulus are Nigerians, almost nothing was known about the various cytospecies of the blackfly vectors present in Nigeria until 1981. The activation of the Nigerian National Onchocerciasis Control Programme in 1986 (and that programme’s initiation of mass distributions of ivermectin in 1991) provided a significant stimulus to understand the biology of the Nigerian vectors but the exploration of any possible differences between the cytospecies has been hampered by a lack of accessible taxonomic information. This review attempts to satisfy that need. There are nine different cytoforms reliably recorded from Nigeria (Simulium damnosum s.s. Nile form, S. damnosum s.s. Volta form, S. sirbanum Sirba form, S. sirbanum Sudanense form, S. soubrense Beffa form, S. squamosum A, S. squamosum B, S. squamosum C and S. yahense typical form), and three more are known from surrounding countries and might be reasonably expected to occur in Nigeria. All of these cytospecies are presumed to be vectors, although there have been almost no identifications of the vectors of O. volvulus in Nigeria. The biogeographical distribution of the cytoforms is broadly similar to that known in other parts of West Africa (although many of the cytoforms remain insufficiently studied). The physico–chemical hydrology of the Nigerian breeding sites of the cytospecies does not, however, correspond to that seen elsewhere in West Africa, and it is not clear whether this might be related to differences in the cytoforms. An illustrated cytotaxonomic key is presented to facilitate and encourage future studies. PMID:21871165

  18. An annotated list of the species of Gangesia Woodland, 1924 (Cestoda: Proteocephalidea), parasites of catfishes in Asia, with new synonyms and a key to their identification.

    PubMed

    Ash, Anirban; de Chambrier, Alain; Shimazu, Takeshi; Ermolenko, Alexey; Scholz, Tomáš

    2015-05-01

    An annotated list of tapeworms of the genus Gangesia Woodland, 1924 (Cestoda: Proteocephalidea), parasites of siluriform fishes in Asia, is provided. Based on the morphological examination of museum specimens and newly collected material from China, Japan and Russia, as well as the results of a previous revision of the Indomalayan species, only eight of more than 50 nominal taxa are considered to be valid. These are: from India and neighbouring countries, Gangesia bengalensis (Southwell, 1913) (type-species), G. agraensis Verma, 1928, both from Wallago attu (Bloch & Schneider) (Siluridae), G. macrones Woodland, 1924 from Sperata seenghala (Sykes) (Bagridae) and G. vachai (Gupta & Parmar, 1988) from different catfishes (type-host Eutropiichthys vacha (Hamilton); Schilbeidae), and, from the Palaearctic, G. margolisi Shimazu, 1994, a parasite of Silurus biwaensis (Tomoda) (Siluridae) in Japan, G. oligonchis Roitman & Freze, 1964 from Tachysurus fulvidraco (Richardson) (Bagridae) in Russia, and G. parasiluri Yamaguti, 1934 and G. polyonchis Roitman & Freze, 1964, both from Silurus asotus L. (Siluridae) in Japan and Russia, respectively. The poorly known G. oligonchis is redescribed. Seven new synonyms are proposed: G. chauhani Mathur & Srivastav, 2000, G. wallaguae Pradhan, Kulkarni, Kale & Wakle, 2010 and G. shivajiraoi Dhole, Waghmare & Chavan, 2012 are synonymised with G. agraensis; G. striatusii Bhure & Nanaware, 2012 and Silurotaenia govindii Sawarkar, 2013 with G. macrones; G. spasskajae Demshin, 1987 with G. polyonchis; and Silurotaenia spinula Chen, 1984 with Postgangesia orientalis Akhmerov, 1969. Gangesia pseudobagrae Chen, 1962 is considered to be a species inquirenda, whereas G. chauhani Mathur, 1992 and G. dineshei Jaysingpure, 2002 are recognised as unavailable names. An amended generic diagnosis of Gangesia and a key to the identification of its recognised species are also provided. PMID:25862030

  19. Revision of the genus Tanycypris (Ostracoda, Cypricercinae) with the description of Tanycypris alfonsi n. sp., and an identification key to the genus.

    PubMed

    Nagler, Christina; Geist, Juergen; Matzke-Karasz, Renate

    2014-01-01

    Specimens of a new species of the non-marine ostracod genus, Tanycypris Triebel, 1959 were found in samples from water plant containers, displayed in a greenhouse of the botanical garden in Munich, Germany. Beside the ubiquitous species Cypridopsis vidua O.F. Müller, 1776, the samples contained four alien species of the subfamily Cypricercinae, namely Chlamydotheca arcuata Sars, 1901, Strandesia bicuspis Claus, 1892, Tanycypris centa Chang et al., 2012, and Tanycypris alfonsi n. sp.. The genus Tanycypris has mainly been reported (native) from Asia, and (invasive) from Italian rice fields.        The Cypricercinae unite all species possessing a Triebel loop, a character of the caudal rami attachment. The subfamily is split into the tribes Cypricercini McKenzie, 1971, Bradleystrandesiini Savatenalinton & Martens, 2009 and Nealecypridini Savatenalinton & Martens, 2009, the latter of which comprises the genera Tanycypris Triebel, 1959, Astenocypris G.W. Müller, 1912, Diaphanocypris Würdig & Pinto, 1990 and Nealecypris Savatenalinton & Martens, 2009.        During the process of describing the new species, a number of taxonomic uncertainties were detected within the genus Tanycypris, leading to a revision of the nine species currently ascribed to it: Tanycypris camaguinensis (Tressler, 1937), Tanycypris centa Chang et al., 2012 Tanycypris clavigera (G.W. Müller, 1898) (now: Nealecypris clavigera nov. comb.), Tanycypris madagascarensis (G.W. Müller, 1898), Tanycypris marina (Hartmann, 1965) (now: Dolerocypris marina nov. comb.), Tanycypris pedroensis (Tressler, 1950) (now: Diaphanocypris pedroensis nov. comb.), Tanycypris pellucida (Klie, 1932), Tanycypris siamensis Savatenalinton & Martens, 2009a, and Tanycypris telavivensis (Krampner, 1928) (now: Herpetocypris telavivensis). An identification key has been developed to the species of the genus Tanycypris. PMID:24989755

  20. Identification of a key catalytic intermediate demonstrates that nitrogenase is activated by the reversible exchange of n2 for h2.

    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 = (1)/2 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

  1. Aircraft Abnormal Conditions Detection, Identification, and Evaluation Using Innate and Adaptive Immune Systems Interaction

    NASA Astrophysics Data System (ADS)

    Al Azzawi, Dia

    Abnormal flight conditions play a major role in aircraft accidents frequently causing loss of control. To ensure aircraft operation safety in all situations, intelligent system monitoring and adaptation must rely on accurately detecting the presence of abnormal conditions as soon as they take place, identifying their root cause(s), estimating their nature and severity, and predicting their impact on the flight envelope. Due to the complexity and multidimensionality of the aircraft system under abnormal conditions, these requirements are extremely difficult to satisfy using existing analytical and/or statistical approaches. Moreover, current methodologies have addressed only isolated classes of abnormal conditions and a reduced number of aircraft dynamic parameters within a limited region of the flight envelope. This research effort aims at developing an integrated and comprehensive framework for the aircraft abnormal conditions detection, identification, and evaluation based on the artificial immune systems paradigm, which has the capability to address the complexity and multidimensionality issues related to aircraft systems. Within the proposed framework, a novel algorithm was developed for the abnormal conditions detection problem and extended to the abnormal conditions identification and evaluation. The algorithm and its extensions were inspired from the functionality of the biological dendritic cells (an important part of the innate immune system) and their interaction with the different components of the adaptive immune system. Immunity-based methodologies for re-assessing the flight envelope at post-failure and predicting the impact of the abnormal conditions on the performance and handling qualities are also proposed and investigated in this study. The generality of the approach makes it applicable to any system. Data for artificial immune system development were collected from flight tests of a supersonic research aircraft within a motion-based flight simulator. The abnormal conditions considered in this work include locked actuators (stabilator, aileron, rudder, and throttle), structural damage of the wing, horizontal tail, and vertical tail, malfunctioning sensors, and reduced engine effectiveness. The results of applying the proposed approach to this wide range of abnormal conditions show its high capability in detecting the abnormal conditions with zero false alarms and very high detection rates, correctly identifying the failed subsystem and evaluating the type and severity of the failure. The results also reveal that the post-failure flight envelope can be reasonably predicted within this framework.

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

    Microsoft Academic Search

    Sansanee Noisakran; Suchada Sengsai; Visith Thongboonkerd; Rattiyaporn Kanlaya; Supachok Sinchaikul; Shui-Tein Chen; Chunya Puttikhunt; Watchara Kasinrerk; Thawornchai Limjindaporn; Wiyada Wongwiwat; Prida Malasit; Pa-thai Yenchitsomanus

    2008-01-01

    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

  3. Interaction of subject and experimenter sex with the body percept in verbal concept identification

    Microsoft Academic Search

    Edward S. Rosenbluh

    1972-01-01

    Classified 64 male and 64 female undergraduates as having a high or low body percept based on Holtzman Inkblot Technique scores. Ss were then given a task involving verbal concept identification of body parts. Variables measured included verbal concept identification, talk time, number of responses, intelligence, and abstract ability. The Es were 1 male and 1 female, each of whom

  4. 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

  5. Law enforcement agencies have exploited biometrics for decades as key tools in forensic identification. With the evolution in information technology and the huge volume of

    E-print Network

    Abaza, Ayman

    identification. With the evolution in information technology and the huge volume of cases that need as withstand severe conditions usually encountered in mass disasters. Dental features are the best candidates in its strategic plan the creation of an Automated Dental Identification System (ADIS), with similar

  6. 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

  7. Proteomic identification of dysferlin-interacting protein complexes in human vascular endothelium

    SciTech Connect

    Leung, Cleo; Utokaparch, Soraya; Sharma, Arpeeta; Yu, Carol; Abraham, Thomas; Borchers, Christoph [UBC James Hogg Research Centre, Institute for Heart and Lung Health, Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia (Canada) [UBC James Hogg Research Centre, Institute for Heart and Lung Health, Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia (Canada); University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia (Canada); Bernatchez, Pascal, E-mail: pbernatc@mail.ubc.ca [UBC James Hogg Research Centre, Institute for Heart and Lung Health, Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia (Canada) [UBC James Hogg Research Centre, Institute for Heart and Lung Health, Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia (Canada); University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia (Canada)

    2011-11-18

    Highlights: Black-Right-Pointing-Pointer Bi-directional (inward and outward) movement of GFP-dysferlin in COS-7 cells. Black-Right-Pointing-Pointer Dysferlin interacts with key signaling proteins for transcytosis in EC. Black-Right-Pointing-Pointer Dysferlin mediates trafficking of vesicles carrying protein cargos in EC. -- Abstract: Dysferlin is a membrane-anchored protein known to facilitate membrane repair in skeletal muscles following mechanical injury. Mutations of dysferlin gene impair sarcolemma integrity, a hallmark of certain forms of muscular dystrophy in patients. Dysferlin contains seven calcium-dependent C2 binding domains, which are required to promote fusion of intracellular membrane vesicles. Emerging evidence reveal the unexpected expression of dysferlin in non-muscle, non-mechanically active tissues, such as endothelial cells, which cast doubts over the belief that ferlin proteins act exclusively as membrane repair proteins. We and others have shown that deficient trafficking of membrane bound proteins in dysferlin-deficient cells, suggesting that dysferlin might mediate trafficking of client proteins. Herein, we describe the intracellular trafficking and movement of GFP-dysferlin positive vesicles in unfixed reconstituted cells using live microscopy. By performing GST pull-down assays followed by mass spectrometry, we identified dysferlin binding protein complexes in human vascular endothelial cells. Together, our data further support the claims that dysferlin not only mediates membrane repair but also trafficking of client proteins, ultimately, help bridging dysferlinopathies to aberrant membrane signaling.

  8. Integrative Identification of Arabidopsis Mitochondrial Proteome and Its Function Exploitation through Protein Interaction Network

    PubMed Central

    Cui, Jian; Liu, Jinghua; Li, Yuhua; Shi, Tieliu

    2011-01-01

    Mitochondria are major players on the production of energy, and host several key reactions involved in basic metabolism and biosynthesis of essential molecules. Currently, the majority of nucleus-encoded mitochondrial proteins are unknown even for model plant Arabidopsis. We reported a computational framework for predicting Arabidopsis mitochondrial proteins based on a probabilistic model, called Naive Bayesian Network, which integrates disparate genomic data generated from eight bioinformatics tools, multiple orthologous mappings, protein domain properties and co-expression patterns using 1,027 microarray profiles. Through this approach, we predicted 2,311 candidate mitochondrial proteins with 84.67% accuracy and 2.53% FPR performances. Together with those experimental confirmed proteins, 2,585 mitochondria proteins (named CoreMitoP) were identified, we explored those proteins with unknown functions based on protein-protein interaction network (PIN) and annotated novel functions for 26.65% CoreMitoP proteins. Moreover, we found newly predicted mitochondrial proteins embedded in particular subnetworks of the PIN, mainly functioning in response to diverse environmental stresses, like salt, draught, cold, and wound etc. Candidate mitochondrial proteins involved in those physiological acitivites provide useful targets for further investigation. Assigned functions also provide comprehensive information for Arabidopsis mitochondrial proteome. PMID:21297957

  9. 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

  10. Identification of white campion (Silene latifolia) guaiacol O-methyltransferase involved in the biosynthesis of veratrole, a key volatile for pollinator attraction

    PubMed Central

    2012-01-01

    Background Silene latifolia and its pollinator, the noctuid moth Hadena bicruris, represent an open nursery pollination system wherein floral volatiles, especially veratrole (1, 2-dimethoxybenzene), lilac aldehydes, and phenylacetaldehyde are of key importance for floral signaling. Despite the important role of floral scent in ensuring reproductive success in S. latifolia, the molecular basis of scent biosynthesis in this species has not yet been investigated. Results We isolated two full-length cDNAs from S. latifolia that show similarity to rose orcinol O-methyltransferase. Biochemical analysis showed that both S. latifolia guaiacol O-methyltransferase1 (SlGOMT1) &S. latifolia guaiacol O-methyltransferase2 (SlGOMT2) encode proteins that catalyze the methylation of guaiacol to form veratrole. A large Km value difference between SlGOMT1 (~10 ?M) and SlGOMT2 (~501 ?M) resulted that SlGOMT1 is 31-fold more catalytically efficient than SlGOMT2. qRT-PCR expression analysis showed that the SlGOMT genes are specifically expressed in flowers and male S. latifolia flowers had 3- to 4-folds higher level of GOMT gene transcripts than female flower tissues. Two related cDNAs, S. dioica O-methyltransferase1 (SdOMT1) and S. dioica O-methyltransferase2 (SdOMT2), were also obtained from the sister species Silene dioica, but the proteins they encode did not methylate guaiacol, consistent with the lack of veratrole emission in the flowers of this species. Our evolutionary analysis uncovered that SlGOMT1 and SlGOMT2 genes evolved under positive selection, whereas SdOMT1 and SdOMT2 genes show no evidence for selection. Conclusions Altogether, we report the identification and functional characterization of the gene, SlGOMT1 that efficiently catalyzes veratrole formation, whereas another copy of this gene with only one amino acid difference, SlGOMT2 was found to be less efficient for veratrole synthesis in S. latifolia. PMID:22937972

  11. Exploiting Partial Problem Spaces Learned from Users' Interactions to Provide Key Tutoring Services in Procedural and Ill-Defined Domains

    Microsoft Academic Search

    Philippe Fournier-viger; Roger Nkambou; Engelbert Mephu Nguifo

    2009-01-01

    In previous works, we showed how sequential pattern mining can be used to extract a partial problem space from logged user interactions for a procedural and ill-defined domain where classic domain knowledge acquisition approaches don\\

  12. Identification of soil–structure interaction effect in base-isolated bridges from earthquake records

    Microsoft Academic Search

    M. T. A. Chaudhary; M. Abé; Y. Fujino

    2001-01-01

    Identification of system parameters with the help of records made on base-isolated bridge during earthquakes provides an excellent opportunity to study the performance of the various components of such bridge systems. Using a two-stage system identification methodology for non-classically damped systems, modal and structural parameters of four base-isolated bridges are reliably identified using acceleration data recorded during 18 earthquakes. Physical

  13. Improving the performance of protein kinase identification via high dimensional protein-protein interactions and substrate structure data.

    PubMed

    Xu, Xiaoyi; Li, Ao; Zou, Liang; Shen, Yi; Fan, Wenwen; Wang, Minghui

    2014-03-01

    As a crucial post-translational modification, protein phosphorylation regulates almost all basic cellular processes. Recently, thousands of phosphorylation sites have been discovered by large-scale phospho-proteomics studies, but only about 20% of them have information regarding catalytic kinases, which brings a great challenge for correct identification of the protein kinases responsible for experimentally verified phosphorylation sites. In most existing identification tools, only a local sequence was selected to construct predictive models, and information regarding protein-protein interaction (PPI) was adopted for further filtering. However, the limited information utilized by these tools is not sufficient to identify protein kinases responsible for phosphorylated proteins. In this work, a novel computational approach that fully incorporates PPI and substrate structure information is proposed to improve the performance of human protein kinase identification. To handle the issue of high-dimensional PPI and structure data, a two-step feature selection algorithm that incorporates a support vector machine (SVM), is designed to detect information useful in discriminating the corresponding kinase of phosphorylation sites. Benchmark datasets for kinase identification are constructed using human protein phosphorylation data extracted from the latest Phospho.ELM database. With the selected PPI and structure features, the performance of kinase identification is significantly enhanced as compared with that obtained by using only sequence information. To further verify our method, we compared it with the state-of-the-art tools NetworKIN and IGPS at two stringency levels with medium (>90.0%) and high (>99.0%) specificity. The results show that our method outperforms existing tools in identifying protein kinases. Further evaluation demonstrates that our method also has superior performance on different hierarchical levels including kinase, subfamily, family and group. PMID:24448631

  14. Freud, ESP, and Interpersonal Relationships: Projective Identification and the Mobius Interaction.

    ERIC Educational Resources Information Center

    Ginter, Earl J.; Bonney, Warren

    1993-01-01

    Provides historical overview of changes in psychodynamic theory that have provided foundation for reassessing significance of client-mental health counselor interactions. Introduces Mobius interaction, interaction qualitatively different from Freud's concepts of transference and countertransference. Argues that Mobius interaction results from…

  15. 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

  16. 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

  17. Validation of a tRNA-Glu-cytochrome b key for the molecular identification of 12 hake species (Merluccius spp.) and Atlantic Cod (Gadus morhua) using PCR-RFLPs, FINS, and BLAST.

    PubMed

    Pérez, Montse; Presa, Pablo

    2008-11-26

    The goal of this study was to develop a diagnostic key for hake meat to solve the limitations of previous identification methodologies, mainly related to the high degradation of the DNA recovered from processed foods. We describe the development of two molecular tools based on polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphisms of the cytochrome b gene, respectively, to identify DNA from 12 hake species in commercial products. The first assay is an exclusion test consisting of the PCR amplification of a 122 bp fragment using nested primers interspecifically conserved in Merluccius spp. and in Gadus morhua. This 122 bp amplicon, being the shortest one so far designed for hake DNA, is a useful traceability tool for highly degraded samples because its sequence contains enough interspecific diagnostic variation to identify 10 hake species and cod and has been successfully amplified from most commercial products so far tested. The second identification key follows a positive outcome of the exclusion test and consists of the PCR amplification of a 464-465 bp fragment and its digestion with three restriction enzymes whose targets map at interspecifically nonconserved sites of the cytochrome b. The key presented here has passed through a rigorous methodological calibration including its testing for genus specificity, its validation on a large number of authenticated sample types from each species range, and its implementation with a maximum likelihood method for the assignment of unknown samples. Together, these two procedures constitute the most complete molecular key so far developed for Merluccius spp., which is optimal for routine identification of hakes in large commercial samples at a reasonable cost-time ratio. PMID:18950183

  18. The pros and cons of interactive whiteboards in relation to the key stage 3 strategy and framework

    Microsoft Academic Search

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

    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 technology. The teachers focused primarily on developing their use

  19. 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…

  20. 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…

  1. Enacting Teaching and Learning in the Interaction Process: "Keys" for Developing Skills in Piano Lessons through Four-Hand Improvisations

    ERIC Educational Resources Information Center

    Laroche, Julien; Kaddouch, Ilan

    2014-01-01

    Embodied mind theories underline the role of the body in the act of knowing. According to the enactive approach, we learn to perceive and to know through our bodily interactions with the world (Varela, Thompson & Rosch, 1991). However, such an approach remains incomplete as long as sociality is not taken into account (Froese & Di Paolo,…

  2. Design and Implementation of the Web-Based Real-Time Remote Expert Identification System: Used for Biological Quarantine

    Microsoft Academic Search

    Jinfeng Ma; Zhenzhou Ji; Maosen Cui; Youcai Zhang; Xiaobin Wu; Yingnan Li; Chao Zheng

    2010-01-01

    The development of computer technology provides a possible to carry out remote identification for biological quarantine specimens effectively, while at the present stage, most of the identification methods are lack of real-time interaction which makes the identification cost a lot of time. In this paper, we study the key technologies of web-based real-time remote expert identification, mainly in three parts:

  3. A Network Inference Method for Large-Scale Unsupervised Identification of Novel Drug-Drug Interactions

    PubMed Central

    Guimerà, Roger; Sales-Pardo, Marta

    2013-01-01

    Characterizing interactions between drugs is important to avoid potentially harmful combinations, to reduce off-target effects of treatments and to fight antibiotic resistant pathogens, among others. Here we present a network inference algorithm to predict uncharacterized drug-drug interactions. Our algorithm takes, as its only input, sets of previously reported interactions, and does not require any pharmacological or biochemical information about the drugs, their targets or their mechanisms of action. Because the models we use are abstract, our approach can deal with adverse interactions, synergistic/antagonistic/suppressing interactions, or any other type of drug interaction. We show that our method is able to accurately predict interactions, both in exhaustive pairwise interaction data between small sets of drugs, and in large-scale databases. We also demonstrate that our algorithm can be used efficiently to discover interactions of new drugs as part of the drug discovery process. PMID:24339767

  4. Identification of Protein-Protein Interactions and Topologies in Living Cells with Chemical Cross-linking and Mass Spectrometry*S?

    PubMed Central

    Zhang, Haizhen; Tang, Xiaoting; Munske, Gerhard R.; Tolic, Nikola; Anderson, Gordon A.; Bruce, James E.

    2009-01-01

    We present results from a novel strategy that enables concurrent identification of protein-protein interactions and topologies in living cells without specific antibodies or genetic manipulations for immuno-/affinity purifications. The strategy consists of (i) a chemical cross-linking reaction: intact cell labeling with a novel class of chemical cross-linkers, protein interaction reporters (PIRs); (ii) two-stage mass spectrometric analysis: stage 1 identification of PIR-labeled proteins and construction of a restricted database by two-dimensional LC/MSMS and stage 2 analysis of PIR-labeled peptides by multiplexed LC/FTICR-MS; and (iii) data analysis: identification of cross-linked peptides and proteins of origin using accurate mass and other constraints. The primary advantage of the PIR approach and distinction from current technology is that protein interactions together with topologies are detected in native biological systems by stabilizing protein complexes with new covalent bonds while the proteins are present in the original cellular environment. Thus, weak or transient interactions or interactions that require properly folded, localized, or membrane-bound proteins can be labeled and identified through the PIR approach. This strategy was applied to Shewanella oneidensis bacterial cells, and initial studies resulted in identification of a set of protein-protein interactions and their contact/binding regions. Furthermore most identified interactions involved membrane proteins, suggesting that the PIR approach is particularly suited for studies of membrane protein-protein interactions, an area under-represented with current widely used approaches. PMID:18936057

  5. Examination of the folding pathway of the antigenomic hepatitis delta virus ribozyme reveals key interactions of the L3 loop.

    PubMed

    Reymond, Cédric; Ouellet, Jonathan; Bisaillon, Martin; Perreault, Jean-Pierre

    2007-01-01

    With the goal of gaining insight into the tertiary structure of the hepatitis delta virus ribozyme, cross-linking experiments using 4-thiouridine residues introduced in either the 5'-end portion of the substrate, or at seven strategic positions within the ribozyme, were performed. Mapping of the newly formed covalent bonds in cross-linked species obtained under various conditions, as well as using several mutated ribozymes, permitted monitoring of the formation of the ribozyme-substrate complex as the ribozyme proceeded along the folding pathway. In order to aid visualization of the tertiary structure transformation, an in silico animation of the "on" folding pathway was developed. In combination with those of the cleavage assays of structured substrates, these data shed light on the key contribution of the L3 loop in the formation of an active tertiary complex. PMID:17105991

  6. Identification of Metarhizium anisopliae transcripts expressed during the fungus- insect interaction

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The identification of genes contributing to the establishment and disease progression of entomopathogenic fungi within their insect hosts has been conducted to date largely using in vitro systems mimicking specific phases of the infection. We are exploring the use of in vivo techniques to identify f...

  7. Virtual Identification of Essential Proteins Within the Protein Interaction Network of Yeast

    Microsoft Academic Search

    Ernesto Estrada; Edificio CACTUS

    2005-01-01

    Topological analysis of large scale protein-protein interaction networks (PINs) is important for understanding the organisational and functional principles of individual proteins. The number of interactions that a protein has in a PIN has been observed to be correlated with its indispensability. Essential proteins generally have more interactions than the non-essential ones. We show here that the lethality associated with removal

  8. Identification of a key recombinant narrows the CADASIL gene region to 8 cM and argues against allelism of CADASIL and familial hemiplegic migraine

    SciTech Connect

    Dichgans, M.; Mayer, M.; Straube, A. [Univ. of Munich (Germany)] [and others] [Univ. of Munich (Germany); and others

    1996-02-15

    This article reports on new information regarding the genetic mapping of the human CADASIL gene region. Previously, the gene had been mapped to human chromosome 19q12. Using the identification of a chromosomal crossover, the region has been refined to an 8-cM interval. 11 refs., 2 figs., 1 tab.

  9. Interactions between phytoplankton organisms and key carbonate system properties in the southern Adriatic Sea: seasonal variability within an annual cycle

    NASA Astrophysics Data System (ADS)

    Luchetta, Anna; Boldrin, Alfredo; Langone, Leonardo; Socal, Giorgio; Bernardi Aubry, Fabrizio; Cantoni, Carolina

    2013-04-01

    Although the impact of CO2 uptake on ocean chemistry has been recognizing for the last decades, ocean acidification has emerged as a key issue of global concern in less than a decade. Studies of the impacts on marine organisms, ecosystems and biogeochemical processes are only at the beginning and the results are still contrasting. In open sea, the pool of particulate organic carbon is mainly determined by phytoplankton production (controlled by light and nutrient availabilities). However pH and key carbonate system properties (AT, DIC, calcium carbonate saturation states), influencing phytoplankton population and communities can play a fundamental role in determining the autothrophic production and its cycle. In the perspective of lighting possible impacts of climatic changes on natural phytoplankton communities of the Southern Adriatic open sea region, this contribute describes the relationships between pH/carbonate system and the phytoplankton during almost one year (Sept 2007-June 2008), with particular regard to calcareous phytoplankton. A few seasonal campaigns were conducted within the frame of the Italian VECTOR project, on a repeated section from Bari to Dubrovnik. The dynamics of phytoplankton community have been analyzed considering the export of particulate organic matter from the photic layer (collected in sediment traps at 150 m). The phytoplankton cycle from September 07 to late June 08 was determined analysing samples collected from CTD bottles. It appears to be characterized by short time blooms of different groups: in autumn the main component (62%) was represented by siliceous plankton (diatoms), in late winter calcareous plankton (coccolithophores) reached 31% of total biomass, whereas flagellates appeared the dominant group (84%) during summer. Downward fluxes of organic carbon (at 150 m), strictly depending on the upper layer autotrophic activity, were well correlated with carbonate fluxes. A succession of different dominant productive groups was observed through the year (confirming the very dynamic seasonal pattern of species composition). Blooms were relatively short time events (less than 15 days): diatoms showed peaks in late winter-spring, while coccolithophores showed an evident bloom in February. Biogeochemical conditions (nutrients, dissolved oxygen, AT, DIC, pH) fitted well to the described phytoplankton biomass abundances and species composition; in particular the decrease of both AT and DIC between February and June suggest the occurrence of calcification process, in good agreement with calcareous plankton bloom observed as a peak in the sediment traps. The relevance of calcareous community in Southern Adriatic Sea is evidenced by the BSi /CaCO3 ratio in sediment trap samples. Regarding the export of particles, the southern Adriatic can be considered a carbonate system with short-time, silica-dominated events (mainly occurring in the period March-April).

  10. Key role of receptor density in colloid/cell specific interaction: a quantitative biomimetic study on giant vesicles

    NASA Astrophysics Data System (ADS)

    Lamblet, M.; Delord, B.; Johannes, L.; van Effenterre, D.; Bassereau, P.

    2008-05-01

    This paper presents an experimental study of the adsorption of colloids on model membranes mediated by specific ligand-receptor interactions. The colloids consist of lipid multilamellar liposomes (spherulites) functionalized with the B-subunit of Shiga Toxin (STxB), while the membranes are lipid Giant Unilamellar Vesicles (GUV) containing STxB lipid receptor, Globotriaosylceramide (Gb3). Through confocal microscopy and flow cytometry, we show the specificity of the adsorption. Moreover, we show that flow cytometry can be used to efficiently quantify the kinetics of colloid adsorption on GUVs with very good statistics. By varying the bulk colloid concentration and receptor density in the membrane, we point out the existence of an optimum Gb3 density for adsorption. We propose that this optimum corresponds to a transition between reversible colloid adsorption at low Gb3 density and irreversible adsorption, and likely spherulite fusion, at high density. We compare our results both to STxB-colloids adhering on living cells and to free STxB proteins interacting with GUVs containing Gb3. This biomimetic system could be used for a quantitative evaluation of the early stage of virus infection or drug delivery.

  11. Chemical modification of Nafion membranes by protic ionic liquids: the key role of ionomer-cation interactions.

    PubMed

    Lu, Fei; Gao, Xinpei; Xie, Shuting; Sun, Nan; Zheng, Liqiang

    2014-10-21

    Chemically modified Nafion composite membranes were successfully fabricated using five kinds of protic ionic liquids (PILs) with different cations, 1-butylammonium methanesulfonate (BA-MS), tributylammonium methanesulfonate (TBA-MS), 2,4,6-trimethylphenylammonium methanesulfonate (TMA-MS), butane-1,4-diammonium methanesulfonate (BDA-MS), and N-(2-aminoethyl)ethane-1,2-diammonium methanesulfonate (DETA-MS). The PIL incorporated Nafion composite membranes were characterized by impedance spectroscopy, small-angle X-ray scattering (SAXS), dynamic-mechanical analysis (DMA) and thermogravimetric analysis (TGA). In general, the Nafion/PIL composite membranes exhibit a significant increase in the ionic conductivities than Nafion under anhydrous conditions. The interactions between the Nafion ionomer and different geometric cations of PILs were also discussed by the comparison of nanostructures, dynamic-mechanical properties and thermal stabilities of the Nafion/PIL composite membranes. PMID:25148206

  12. Palmitoylation as a key factor to modulate SP-C-lipid interactions in lung surfactant membrane multilayers.

    PubMed

    Roldan, Nuria; Goormaghtigh, Erik; Pérez-Gil, Jesús; Garcia-Alvarez, Begoña

    2015-01-01

    Surfactant protein C (SP-C) has been regarded as the most specific protein linked to development of mammalian lungs, and great efforts have been done to understand its structure-function relationships. Previous evidence has outlined the importance of SP-C palmitoylation to sustain the proper dynamics of lung surfactant, but the mechanism by which this posttranslational modification aids SP-C to stabilize the interfacial surfactant film along the compression-expansion breathing cycles, is still unrevealed. In this work we have compared the structure, orientation and lipid-protein interactions of a native palmitoylated SP-C with those of a non-palmitoylated recombinant SP-C (rSP-C) form in air-exposed multilayer membrane environments, by means of ATR-FTIR spectroscopy. Palmitoylation does not affect the secondary structure of the protein, which exhibits a full ?-helical conformation in partly dehydrated phospholipid multilayer films. However, differences between the Amide I band of the IR spectrum of palmitoylated and non-palmitoylated proteins suggest subtle differences affecting the environment of their helical component. These differences are accompanied by differential effects on the IR bands from phospholipid phosphates, indicating that palmitoylation modulates lipid-protein interactions at the headgroup region of phospholipid layers. On the other hand, the relative dichroic absorption of polarized IR has allowed calculating that the palmitoylated protein adopts a more tilted transmembrane orientation than the non-palmitoylated SP-C, likely contributing to more compact, dehydrated and possibly stable multilayer lipid-protein films. As a whole, the behavior of multilayer films containing palmitoylated SP-C may reflect favorable structural properties for surfactant reservoirs at the air-liquid respiratory interface. PMID:25306965

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. The identification of Pcl1-interacting proteins that genetically interact with Cla4 may indicate a link between G1 progression and mitotic exit.

    PubMed Central

    Keniry, Megan E; Kemp, Hilary A; Rivers, David M; Sprague, George F

    2004-01-01

    In budding yeast, Cla4 and Ste20, two p21-activated kinases, contribute to numerous morphogenetic processes. Loss of Ste20 or Cla4 individually confers distinct phenotypes, implying that they regulate different processes. However, loss of both proteins is lethal, suggesting some functional overlap. To explore the role(s) of Cla4, we and others have sought mutations that are lethal in a cla4 Delta strain. These mutations define >60 genes. Recently, both Ste20 and Cla4 have been implicated in mitotic exit. Here, we identify a genetic interaction between PHO85, which encodes a cyclin-dependent kinase, and CLA4. We further show that the Pho85-coupled G(1) cyclins Pcl1 and Pcl2 contribute to this Pho85 role. We performed a two-hybrid screen with Pcl1. Three Pcl1-interacting proteins were identified: Ncp1, Hms1, and a novel ATPase dubbed Epa1. Each of these proteins interacts with Pcl1 in GST pull-down experiments and is specifically phosphorylated by Pcl1.Pho85 complexes. NCP1, HMS1, and EPA1 also genetically interact with CLA4. Like Cla4, the proteins Hms1, Ncp1, and Pho85 appear to affect mitotic exit, a conclusion that follows from the mislocalization of Cdc14, a key mitotic regulator, in strains lacking these proteins. We propose a model in which the G(1) Pcl1.Pho85 complex regulates mitotic exit machinery. PMID:15082539

  1. S.AfrJ.Bot., 1992, 58(4): 277 -285 277 Synoptic key and computer database for identification of species of

    E-print Network

    29 October 199/.. revised 19 May 1992 Ceratocystis sensu lato, incorporating Ceratocystis, Ophiostoma of Ceratocystis. Ophiostoma and Ceratocystiopsis. The key can thus be used manually or with the aid of a computer. Ceratocystis sensu lato, bestaande uit Ceratocystis. Ophiostoma en Ceratocystiopsis, sluit meer as 'n honderd

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

    PubMed Central

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

    2014-01-01

    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

  3. 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

  4. Reliable Identification of Cross-Linked Products in Protein Interaction Studies by 13C-Labeled p-Benzoylphenylalanine

    NASA Astrophysics Data System (ADS)

    Pettelkau, Jens; Ihling, Christian H.; Frohberg, Petra; van Werven, Lars; Jahn, Olaf; Sinz, Andrea

    2014-09-01

    We describe the use of the 13C-labeled artificial amino acid p-benzoyl-L-phenylalanine (Bpa) to improve the reliability of cross-linked product identification. Our strategy is exemplified for two protein-peptide complexes. These studies indicate that in many cases the identification of a cross-link without additional stable isotope labeling would result in an ambiguous assignment of cross-linked products. The use of a 13C-labeled photoreactive amino acid is considered to be preferred over the use of deuterated cross-linkers as retention time shifts in reversed phase chromatography can be ruled out. The observation of characteristic fragment ions additionally increases the reliability of cross-linked product assignment. Bpa possesses a broad reactivity towards different amino acids and the derived distance information allows mapping of spatially close amino acids and thus provides more solid structural information of proteins and protein complexes compared to the longer deuterated amine-reactive cross-linkers, which are commonly used for protein 3D-structure analysis and protein-protein interaction studies.

  5. User Identification for Healthcare Service Robots: Multidisciplinary Design for Implementation of Interactive Services

    Microsoft Academic Search

    I. Han Kuo; Chandimal Jayawardena; Priyesh Tiwari; Elizabeth Broadbent; Bruce A. MacDonald

    2010-01-01

    \\u000a Human robot interaction (HRI) is core to the design of service robots. The interaction during a service application determines\\u000a how a user perceives the robot, which affects the user’s experience and how well the user accepts the robot and its services.\\u000a During the last decade, robotics service applications in close proximity to human users have been a popular research area.

  6. Identification of a Deubiquitinating Enzyme as a Novel AGS3Interacting Protein

    Microsoft Academic Search

    Zhuojin Xu; Bin Xia; Qiang Gong; Jeffrey Bailey; Benjamin Groves; Monte Radeke; Stephen A. Wood; Karen K. Szumlinski; Dzwokai Ma; Karl-Wilhelm Koch

    2010-01-01

    Activator of G protein Signaling 3 (AGS3) is a receptor-independent G protein activator that has been implicated in multiple biological events such as brain development, neuroplasticity and addiction, cardiac function, Golgi structure\\/function, macroautophagy and metabolism. However, how AGS3 is regulated is little known. We demonstrate here that AGS3 interacts with a ubiquitin specific protease USP9x, and this interaction is at

  7. Identification of a Novel Protein Interaction Motif in the Regulatory Subunit of Casein Kinase 2

    PubMed Central

    Cao, Jennifer Yinuo; Shire, Kathy; Landry, Cameron; Gish, Gerald D.; Pawson, Tony

    2014-01-01

    Casein kinase 2 (CK2) regulates multiple cellular processes and can promote oncogenesis. Interactions with the CK2? regulatory subunit of the enzyme target its catalytic subunit (CK2? or CK2??) to specific substrates; however, little is known about the mechanisms by which these interactions occur. We previously showed that by binding CK2?, the Epstein-Barr virus (EBV) EBNA1 protein recruits CK2 to promyelocytic leukemia (PML) nuclear bodies, where increased CK2-mediated phosphorylation of PML proteins triggers their degradation. Here we have identified a KSSR motif near the dimerization interface of CK2? as forming part of a protein interaction pocket that mediates interaction with EBNA1. We show that the EBNA1-CK2? interaction is primed by phosphorylation of EBNA1 on S393 (within a polyserine region). This phosphoserine is critical for EBNA1-induced PML degradation but does not affect EBNA1 functions in EBV replication or segregation. Using comparative proteomics of wild-type (WT) and KSSR mutant CK2?, we identified an uncharacterized cellular protein, C18orf25/ARKL1, that also binds CK2? through the KSSR motif and show that this involves a polyserine sequence resembling the CK2? binding sequence in EBNA1. Therefore, we have identified a new mechanism of CK2 interaction used by viral and cellular proteins. PMID:24216761

  8. Identification of a novel protein interaction motif in the regulatory subunit of casein kinase 2.

    PubMed

    Cao, Jennifer Yinuo; Shire, Kathy; Landry, Cameron; Gish, Gerald D; Pawson, Tony; Frappier, Lori

    2014-01-01

    Casein kinase 2 (CK2) regulates multiple cellular processes and can promote oncogenesis. Interactions with the CK2? regulatory subunit of the enzyme target its catalytic subunit (CK2? or CK2?') to specific substrates; however, little is known about the mechanisms by which these interactions occur. We previously showed that by binding CK2?, the Epstein-Barr virus (EBV) EBNA1 protein recruits CK2 to promyelocytic leukemia (PML) nuclear bodies, where increased CK2-mediated phosphorylation of PML proteins triggers their degradation. Here we have identified a KSSR motif near the dimerization interface of CK2? as forming part of a protein interaction pocket that mediates interaction with EBNA1. We show that the EBNA1-CK2? interaction is primed by phosphorylation of EBNA1 on S393 (within a polyserine region). This phosphoserine is critical for EBNA1-induced PML degradation but does not affect EBNA1 functions in EBV replication or segregation. Using comparative proteomics of wild-type (WT) and KSSR mutant CK2?, we identified an uncharacterized cellular protein, C18orf25/ARKL1, that also binds CK2? through the KSSR motif and show that this involves a polyserine sequence resembling the CK2? binding sequence in EBNA1. Therefore, we have identified a new mechanism of CK2 interaction used by viral and cellular proteins. PMID:24216761

  9. Molecular mechanisms and modulation of key pathways underlying the synergistic interaction of sorafenib with erlotinib in non-small-cell-lung cancer (NSCLC) cells.

    PubMed

    Giovannetti, E; Labots, M; Dekker, H; Galvani, E; Lind, J S W; Sciarrillo, R; Honeywell, R; Smit, E F; Verheul, H M; Peters, G J

    2013-01-01

    Combination of drugs with different targets is a logical approach to overcome multilevel cross-stimulation among key pathways in NSCLC progression such as EGFR, K-Ras and VEGFR. The sorafenib-erlotinib combination showed clinical activity and acceptable safety. Therefore, we evaluated mechanisms underlying sorafenib-erlotinib interaction in seven NSCLC cell lines selected for their heterogeneous pattern of EGFR and Raf-kinase-inhibitor protein (RKIP) expression, and EGFR/K-Ras mutations. Pharmacologic interaction was studied using MTT/SRB assays and the combination index (CI) method, while effects on EGFR, Erk1/2 and Akt phosphorylation, cell cycle and apoptosis were studied with western-blot, ELISA, and flow cytometry. Intracellular drug concentrations were measured with LC-MS/MS, whereas kinase activity profiles were generated on tyrosine kinase peptide substrate arrays. Synergism was detected in all cell lines, with CIs < 0.6 in K-Ras mutated A549, SW1573 and H460, as well as in H1975 (EGFR-T790M) cells. Sorafenib slowed cell cycle progression and induced apoptosis, which was significantly increased in the combination. Moreover, sorafenib reduced Akt/ERK phosphorylation in erlotinib-resistant cells, associated with significant RKIP up-regulation. No direct drug interaction was detected by LC-MS/MS measurement, while lysates from A549 and H1975 cells exposed to erlotinib+sorafenib showed a significant inhibition in the phosphorylation of 16 overlapping peptides, including sites from RAF, VEGFR2, PDGFR, CDK2 and SRC, suggesting new markers to identify NSCLC patients who are likely to respond to this treatment. In conclusion, several mechanisms, including apoptosis-induction, modulation of expression/phosphorylation of RKIP and crucial kinases contribute to erlotinib-sorafenib synergistic interaction and should be evaluated in future trials for the rational development of this combination in NSCLC. PMID:22973961

  10. 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

  11. Bird Identification

    NSDL National Science Digital Library

    This clever bird identification key was created by Eric Haines, a birding enthusiast and professional in the field of computer graphics. The online key focuses on birds found in eastern sections of the United States and Canada and is based on _Quick-Key Guide to Birds_ by John T. Emlen, and David Archbald. Site users can pinpoint numerous bird species by selecting specific characteristics under such categories as Action (e.g. Swimming, Hopping or Climbing); Size (e.g. Larger Than Robin, Smaller Than Robin); Habitat (e.g. Wood, Marsh, Field); Markings (e.g. Eye Ring, Crown Patch); and more. Bird profiles list basic distinguishing characteristics, and link to images of the bird in Google Images. This website also links to a Bird Quiz Program that can be self-tailored to suit the preferences of different quiz-takers and to identification keys for trees and wildflowers.

  12. 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

  13. 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.

  14. 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

  15. Identification of Cellular Proteins Interacting with the Retroviral Restriction Factor SAMHD1

    PubMed Central

    St. Gelais, Corine; de Silva, Suresh; Hach, Jocelyn C.; White, Tommy E.; Diaz-Griffero, Felipe; Yount, Jacob S.

    2014-01-01

    ABSTRACT Human and mouse SAMHD1 proteins block human immunodeficiency virus type 1 (HIV-1) infection in noncycling human monocytic cells by reducing the intracellular deoxynucleoside triphosphate (dNTP) concentrations. Phosphorylation of human SAMHD1 at threonine 592 (T592) by cyclin-dependent kinase 1 (CDK1) and cyclin A2 impairs its HIV-1 restriction activity, but not the dNTP hydrolase activity, suggesting that dNTP depletion is not the sole mechanism of SAMHD1-mediated HIV-1 restriction. Using coimmunoprecipitation and mass spectrometry, we identified and validated two additional host proteins interacting with human SAMHD1, namely, cyclin-dependent kinase 2 (CDK2) and S-phase kinase-associated protein 2 (SKP2). We observed that mouse SAMHD1 specifically interacted with cyclin A2, cyclin B1, CDK1, and CDK2. Given the role of these SAMHD1-interacting proteins in cell cycle progression, we investigated the regulation of these host proteins by monocyte differentiation and activation of CD4+ T cells and examined their effect on the phosphorylation of human SAMHD1 at T592. Our results indicate that primary monocyte differentiation and CD4+ T-cell activation regulate the expression of these SAMHD1-interacting proteins. Furthermore, our results suggest that, in addition to CDK1 and cyclin A2, CDK2 phosphorylates T592 of human SAMHD1 and thereby regulates its HIV-1 restriction function. IMPORTANCE SAMHD1 is the first dNTP triphosphohydrolase found in mammalian cells. Human and mouse SAMHD1 proteins block HIV-1 infection in noncycling cells. Previous studies suggested that phosphorylation of human SAMHD1 at threonine 592 by CDK1 and cyclin A2 negatively regulates its HIV-1 restriction activity. However, it is unclear whether human SAMHD1 interacts with other host proteins in the cyclin A2 and CDK1 complex and whether mouse SAMHD1 shares similar cellular interacting partners. Here, we identify five cell cycle-related host proteins that interact with human and mouse SAMHD1, including three previously unknown cellular proteins (CDK2, cyclin B1, and SKP2). Our results demonstrate that several SAMHD1-interacting cellular proteins regulate phosphorylation of SAMHD1 and play an important role in HIV-1 restriction function. Our findings help define the role of these cellular interacting partners of SAMHD1 that regulate its HIV-1 restriction function. PMID:24623419

  16. Structure of the RNA Polymerase Assembly Factor Crl and Identification of Its Interaction Surface with Sigma S

    PubMed Central

    Banta, Amy B.; Cuff, Marianne E.; Lin, Hueylie; Myers, Angela R.; Ross, Wilma; Joachimiak, Andrzej

    2014-01-01

    Bacteria utilize multiple sigma factors that associate with core RNA polymerase (RNAP) to control transcription in response to changes in environmental conditions. In Escherichia coli and Salmonella enterica, Crl positively regulates the ?S regulon by binding to ?S to promote its association with core RNAP. We recently characterized the determinants in ?S responsible for specific binding to Crl. However, little is known about the determinants in Crl required for this interaction. Here, we present the X-ray crystal structure of a Crl homolog from Proteus mirabilis in conjunction with in vivo and in vitro approaches that probe the Crl-?S interaction in E. coli. We show that the P. mirabilis, Vibrio harveyi, and E. coli Crl homologs function similarly in E. coli, indicating that Crl structure and function are likely conserved throughout gammaproteobacteria. We utilize phylogenetic conservation and bacterial two-hybrid analyses to predict residues in Crl important for the interaction with ?S. The results of p-benzoylphenylalanine (BPA)-mediated UV cross-linking studies further support the model in which an evolutionarily conserved central cleft is the surface on Crl that binds to ?S. Within this conserved binding surface, we identify a key residue in Crl that is critical for activation of E?S-dependent transcription in vivo and in vitro. Our study provides a physical basis for understanding the ?S-Crl interaction. PMID:25002538

  17. The Dictyostelium discoideum cellulose synthase: Structure/function analysis and identification of interacting proteins

    SciTech Connect

    Richard L. Blanton

    2004-02-19

    OAK-B135 The major accomplishments of this project were: (1) the initial characterization of dcsA, the gene for the putative catalytic subunit of cellulose synthase in the cellular slime mold Dictyostelium discoideum; (2) the detection of a developmentally regulated event (unidentified, but perhaps a protein modification or association with a protein partner) that is required for cellulose synthase activity (i.e., the dcsA product is necessary, but not sufficient for cellulose synthesis); (3) the continued exploration of the developmental context of cellulose synthesis and DcsA; (4) the isolation of a GFP-DcsA-expressing strain (work in progress); and (5) the identification of Dictyostelium homologues for plant genes whose products play roles in cellulose biosynthesis. Although our progress was slow and many of our results negative, we did develop a number of promising avenues of investigation that can serve as the foundation for future projects.

  18. Identification and verification of proteins interacting with the kappa opioid receptor (KOPR).

    PubMed

    Chen, Chongguang; Huang, Peng; Liu-Chen, Lee-Yuan

    2015-01-01

    Proteins that interact with the human kappa opioid receptor (hKOPR) may contribute to regulation and signaling of the receptor. In this paper, we focus on the protein 14-3-3zeta that regulates anterograde transport of the hKOPR from the endoplasmic reticulum (ER) to the Golgi apparatus. 14-3-3zeta interacts with the C-terminal domain of the receptor and promotes cell surface expression of the hKOPR by inhibiting coatomer protein I (COPI) and RVR motif-mediated ER retension of the hKOPR. Here we describe three experimental procedures we used to evaluate the interaction between hKOPR and 14-3-3zeta: co-immunoprecipitation, pull-down assay and immunofluorescence microscopy. PMID:25293321

  19. Identification of Residues That Underpin Interactions within the Eukaryotic Initiation Factor (eIF2) 2B Complex

    PubMed Central

    Wang, Xuemin; Wortham, Noel C.; Liu, Rui; Proud, Christopher G.

    2012-01-01

    Eukaryotic initiation factor 2B (eIF2B) plays a key role in protein synthesis and in its control. It comprises five different subunits, ?-?, of which eIF2B? contains the catalytic domain. Formation of the complete complex is crucial for full activity and proper control of eIF2B. Mutations in the genes for eIF2B cause an often severe neurological disorder, “vanishing white matter.” eIF2B? and eIF2B? contain homologous and conserved domains with sequence similarity to nucleotidyl transferases (NTs) and acyl transferases and can form a binary complex. The latter contain a hexad repeat that mainly comprises isoleucyl residues (hence termed the “I-patch” region). These data reveal that certain residues in the NT domains of eIF2B?/?, which are highly conserved throughout eukaryotes, play key roles in the interactions between subunits in the eIF2B complex. Our data show that the I-patch regions are important in the interactions between the catalytic eIF2B?? complex and the other subunits. We also studied the functional effects of vanishing white matter mutations in the NT and I-patch domains. Lastly, our data show that eIF2B? promotes the expression of eIF2B?, providing a mechanism for achieving correct stoichiometry of these eIF2B subunits in the cell. PMID:22238342

  20. 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.

  1. A Conifer ABI3-Interacting Protein Plays Important Roles during Key Transitions of the Plant Life Cycle1[C][W][OA

    PubMed Central

    Zeng, Ying; Zhao, Tiehan; Kermode, Allison R.

    2013-01-01

    ABI3 (for ABSCISIC ACID INSENSITIVE3), a transcription factor of the abscisic acid signal transduction pathway, plays a major role during seed development, dormancy inception, and dormancy maintenance. This protein appears to also function in meristematic and vegetative plant tissues and under certain stress conditions. We have isolated the ABI3 gene ortholog (CnABI3) from yellow cedar (Callitropsis nootkatensis) and found that it was functionally similar to other ABI3 genes of angiosperms. Here, we report that using a yeast (Saccharomyces cerevisiae) two-hybrid approach, we have identified another protein of yellow cedar (CnAIP2; for CnABI3 INTERACTING PROTEIN2) that physically interacts with CnABI3. Functional analyses revealed that CnAIP2 plays important roles during key transitions in the plant life cycle: (1) CnAIP2 impaired seed development and reduced seed dormancy; (2) CnAIP2 promoted root development, particularly the initiation of lateral roots, and the CnAIP2 gene promoter was exquisitely auxin sensitive; and (3) CnAIP2 promoted the transition from vegetative growth to reproductive initiation (i.e. flowering). The nature of the effects of CnAIP2 on these processes and other evidence place CnAIP2 in the category of a “global” regulator, whose actions are antagonistic to those of ABI3. PMID:23144188

  2. 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

  3. 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...

  4. Identification of Parent-Child Interaction Characteristics of High and Low Achieving Elementary Students.

    ERIC Educational Resources Information Center

    Portes, Pedro R.; And Others

    The present study was designed to identify parent-child interaction patterns that might differentiate bright from below average elementary students in order to test the hypothesis that environmental processes related to regulation of executive processes influence both children's learning and developmental level. Thirty-two mother-child dyads (16…

  5. Identification of Karyopherin ?1 and ?7 Interacting Proteins in Porcine Tissue

    PubMed Central

    Park, Ki-Eun; Inerowicz, H. Dorota; Wang, Xin; Li, Yanfang; Koser, Stephanie; Cabot, Ryan A.

    2012-01-01

    Specialized trafficking systems in eukaryotic cells serve a critical role in partitioning intracellular proteins between the nucleus and cytoplasm. Cytoplasmic proteins (including chromatin remodeling enzymes and transcription factors) must gain access to the nucleus to exert their functions to properly program fundamental cellular events ranging from cell cycle progression to gene transcription. Knowing that nuclear import mediated by members of the karyopherin ? family of transport receptors plays a critical role in regulating development and differentiation, we wanted to determine the identity of proteins that are trafficked by this karyopherin ? pathway. To this end, we performed a GST pull-down assay using porcine orthologs of karyopherin ?1 (KPNA1) and karyopherin ?7 (KPNA7) and prey protein derived from porcine fibroblast cells and used a liquid chromatography and tandem mass spectrometry (LC-MS/MS) approach to determine the identity of KPNA1 and KPNA7 interacting proteins. Our screen revealed that the proteins that interact with KPNA1 and KPNA7 are generally nuclear proteins that possess nuclear localization signals. We further validated two candidate proteins from this screen and showed that they are able to be imported into the nucleus in vivo and also interact with members of the karyopherin ? family of proteins in vitro. Our results also reveal the utility of using a GST pull-down approach coupled with LC-MS/MS to screen for protein interaction partners in a non-traditional model system. PMID:22720010

  6. Identification of interacting transcription factors regulating tissue gene expression in human

    Microsoft Academic Search

    Zihua Hu; Steven M Gallo

    2010-01-01

    BACKGROUND: Tissue gene expression is generally regulated by multiple transcription factors (TFs). A major first step toward understanding how tissues achieve their specificity is to identify, at the genome scale, interacting TFs regulating gene expression in different tissues. Despite previous discoveries, the mechanisms that control tissue gene expression are not fully understood. RESULTS: We have integrated a function conservation approach,

  7. MEG source reconstruction based on identification of directed source interactions on whole-brain anatomical networks.

    PubMed

    Fukushima, Makoto; Yamashita, Okito; Knösche, Thomas R; Sato, Masa-aki

    2015-01-15

    We present an MEG source reconstruction method that simultaneously reconstructs source amplitudes and identifies source interactions across the whole brain. In the proposed method, a full multivariate autoregressive (MAR) model formulates directed interactions (i.e., effective connectivity) between sources. The MAR coefficients (the entries of the MAR matrix) are constrained by the prior knowledge of whole-brain anatomical networks inferred from diffusion MRI. Moreover, to increase the accuracy and robustness of our method, we apply an fMRI prior on the spatial activity patterns and a sparse prior on the MAR coefficients. The observation process of MEG data, the source dynamics, and a series of the priors are combined into a Bayesian framework using a state-space representation. The parameters, such as the source amplitudes and the MAR coefficients, are jointly estimated from a variational Bayesian learning algorithm. By formulating the source dynamics in the context of MEG source reconstruction, and unifying the estimations of source amplitudes and interactions, we can identify the effective connectivity without requiring the selection of regions of interest. Our method is quantitatively and qualitatively evaluated on simulated and experimental data, respectively. Compared with non-dynamic methods, in which the interactions are estimated after source reconstruction with no dynamic constraints, the proposed dynamic method improves most of the performance measures in simulations, and provides better physiological interpretation and inter-subject consistency in real data applications. PMID:25290887

  8. Identification and characterization of multiple novel Rab–myosin Va interactions

    PubMed Central

    Lindsay, Andrew J.; Jollivet, Florence; Horgan, Conor P.; Khan, Amir R.; Raposo, Graça; McCaffrey, Mary W.; Goud, Bruno

    2013-01-01

    Myosin Va is a widely expressed actin-based motor protein that binds members of the Rab GTPase family (3A, 8A, 10, 11A, 27A) and is implicated in many intracellular trafficking processes. To our knowledge, myosin Va has not been tested in a systematic screen for interactions with the entire Rab GTPase family. To that end, we report a yeast two-hybrid screen of all human Rabs for myosin Va-binding ability and reveal 10 novel interactions (3B, 3C, 3D, 6A, 6A?, 6B, 11B, 14, 25, 39B), which include interactions with three new Rab subfamilies (Rab6, Rab14, Rab39B). Of interest, myosin Va interacts with only a subset of the Rabs associated with the endocytic recycling and post-Golgi secretory systems. We demonstrate that myosin Va has three distinct Rab-binding domains on disparate regions of the motor (central stalk, an alternatively spliced exon, and the globular tail). Although the total pool of myosin Va is shared by several Rabs, Rab10 and Rab11 appear to be the major determinants of its recruitment to intracellular membranes. We also present evidence that myosin Va is necessary for maintaining a peripheral distribution of Rab11- and Rab14-positive endosomes. PMID:24006491

  9. Effects of Incorrect Interaction Identification on Image Resolution in HPGe Compton Cameras

    Microsoft Academic Search

    J. Gillam; T. Beveridge; S. Midgley; H. C. Boston; A. J. Boston; R. J. Cooper; A. Grint; A. R. Mather; P. J. Nolan; D. P. Scraggs; I. Svalbe; G. Turk; C. J. Hall; I. Lazarus; A. Berry; R. A. Lewis

    2006-01-01

    The performance of Compton imaging systems is limited by the angular uncertainty arising from the detector geometry and spatial resolution [Ordonez et al., 1997 amd 1999], When closely spaced multiple interactions are incorrectly recorded as a single event [Solomon and Ott, 1988], termed \\

  10. New deep-sea free-living marine nematodes from the Sea of Japan: the genera Siphonolaimus and Halichoanolaimus (Nematoda: Chromadorea) with keys to species identifications.

    PubMed

    Julia, Zograf; Yulia, Trebukhova; Olga, Pavlyuk

    2015-01-01

    In deep-sea sediments from the Sea of Japan, two new species, Halichoanolaimus brandtae sp. n. and Siphonolaimus japonicus sp. n., were found and described. Siphonolaimus japonicus sp. n. is characterized by having short anterior sensillae, body length of 3670-4500 ?m, buccal cavity with axial spear, and length of the spicules. Halichoanolaimus brandtae sp.n is characterized by the number of amphideal rings, long spicules, five precloacal supplements and by having a long cylindrical part of the tail. Keys to species level are provided.  PMID:25661596

  11. Identification of proteins that interact with alpha A-crystallin using a human proteome microarray

    PubMed Central

    Fan, Qi; Huang, Lv-Zhen; Zhu, Xiang-Jia; Zhang, Ke-Ke; Ye, Hong-Fei; Luo, Yi; Sun, Xing-Huai; Zhou, Peng

    2014-01-01

    Purpose To identify proteins interacting with alpha A-crystallin (CRYAA) and to investigate the potential role that these protein interactions play in the function of CRYAA using a human proteome (HuProt) microarray. Methods The active full-length CRYAA protein corresponding to amino acids 1–173 of CRYAA was recombined. A HuProt microarray composed of 17,225 human full-length proteins with N-terminal glutathione S-transferase (GST) tags was used to identify protein–protein interactions. The probes were considered detectable when the signal to noise ratio (SNR) was over 1.2. The identified proteins were subjected to subsequent bioinformatics analysis using the DAVID database. Results The HuProt microarray results showed that the signals of 343 proteins were higher in the recombinant CRYAA group than in the control group. The SNR of 127 proteins was ? 1.2. The SNR of the following eight proteins was > 3.0: hematopoietic cell-specific Lyn substrate 1 (HCLS1), Kelch domain-containing 6 (KLHDC6), sarcoglycan delta (SGCD), KIAA1706 protein (KIAA1706), RNA guanylyltransferase and 5?-phosphatase (RNGTT), chromosome 10 open reading frame 57 (C10orf57), chromosome 9 open reading frame 52 (C9orf52), and plasminogen activator, urokinase receptor (PLAUR). The bioinformatics analysis revealed 127 proteins associated with phosphoproteins, alternative splicing, acetylation, DNA binding, the nuclear lumen, ribonucleotide binding, the cell cycle, WD40 repeats, protein transport, transcription factor activity, GTP binding, and cellular response to stress. Functional annotation clustering showed that they belong to cell cycle, organelle or nuclear lumen, protein transport, and DNA binding and repair clusters. CRYAA interacted with these proteins to maintain their solubility and decrease the accumulation of denatured target proteins. The protein–protein interactions may help CRYAA carry out multifaceted functions. Conclusions One-hundred and twenty-seven of 17,225 human full-length proteins were identified that interact with CRYAA. The advent of microarray analysis enables a better understanding of the functions of CRYAA as a molecular chaperone. PMID:24453475

  12. 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

  13. Label-Free Proteomic Identification of Endogenous, Insulin-Stimulated Interaction Partners of Insulin Receptor Substrate-1

    PubMed Central

    Geetha, Thangiah; Langlais, Paul; Luo, Moulun; Mapes, Rebekka; Lefort, Natalie; Chen, Shu-Chuan; Mandarino, Lawrence J.; Yi, Zhengping

    2011-01-01

    Protein–protein interactions are key to most cellular processes. Tandem mass spectrometry (MS/MS)-based proteomics combined with co-immunoprecipitation (CO-IP) has emerged as a powerful approach for studying protein complexes. However, a majority of systematic proteomics studies on protein–protein interactions involve the use of protein overexpression and/or epitope-tagged bait proteins, which might affect binding stoichiometry and lead to higher false positives. Here, we report an application of a straightforward, label-free CO-IP-MS/MS method, without the use of protein overexpression or protein tags, to the investigation of changes in the abundance of endogenous proteins associated with a bait protein, which is in this case insulin receptor substrate-1 (IRS-1), under basal and insulin stimulated conditions. IRS-1 plays a central role in the insulin signaling cascade. Defects in the protein–protein interactions involving IRS-1 may lead to the development of insulin resistance and type 2 diabetes. HPLC-ESI-MS/MS analyses identified eleven novel endogenous insulin-stimulated IRS-1 interaction partners in L6 myotubes reproducibly, including proteins play an important role in protein dephosphorylation [protein phosphatase 1 regulatory subunit 12A, (PPP1R12A)], muscle contraction and actin cytoskeleton rearrangement, endoplasmic reticulum stress, and protein folding, as well as protein synthesis. This novel application of label-free CO-IP-MS/MS quantification to assess endogenous interaction partners of a specific protein will prove useful for understanding how various cell stimuli regulate insulin signal transduction. PMID:21472564

  14. Label-Free Proteomic Identification of Endogenous, Insulin-Stimulated Interaction Partners of Insulin Receptor Substrate-1

    NASA Astrophysics Data System (ADS)

    Geetha, Thangiah; Langlais, Paul; Luo, Moulun; Mapes, Rebekka; Lefort, Natalie; Chen, Shu-Chuan; Mandarino, Lawrence J.; Yi, Zhengping

    2011-03-01

    Protein-protein interactions are key to most cellular processes. Tandem mass spectrometry (MS/MS)-based proteomics combined with co-immunoprecipitation (CO-IP) has emerged as a powerful approach for studying protein complexes. However, a majority of systematic proteomics studies on protein-protein interactions involve the use of protein overexpression and/or epitope-tagged bait proteins, which might affect binding stoichiometry and lead to higher false positives. Here, we report an application of a straightforward, label-free CO-IP-MS/MS method, without the use of protein overexpression or protein tags, to the investigation of changes in the abundance of endogenous proteins associated with a bait protein, which is in this case insulin receptor substrate-1 (IRS-1), under basal and insulin stimulated conditions. IRS-1 plays a central role in the insulin signaling cascade. Defects in the protein-protein interactions involving IRS-1 may lead to the development of insulin resistance and type 2 diabetes. HPLC-ESI-MS/MS analyses identified eleven novel endogenous insulin-stimulated IRS-1 interaction partners in L6 myotubes reproducibly, including proteins play an important role in protein dephosphorylation [protein phosphatase 1 regulatory subunit 12A, (PPP1R12A)], muscle contraction and actin cytoskeleton rearrangement, endoplasmic reticulum stress, and protein folding, as well as protein synthesis. This novel application of label-free CO-IP-MS/MS quantification to assess endogenous interaction partners of a specific protein will prove useful for understanding how various cell stimuli regulate insulin signal transduction.

  15. Identification and Plant Interaction of a Phyllobacterium sp., a Predominant Rhizobacterium of Young Sugar Beet Plants

    PubMed Central

    Lambert, Bart; Joos, Henk; Dierickx, Sabine; Vantomme, Robert; Swings, Jean; Kersters, Karel; Van Montagu, Marc

    1990-01-01

    The second most abundant bacterium on the root surface of young sugar beet plants was identified as a Phyllobacterium sp. (Rhizobiaceae) based on a comparison of the results of 39 conventional identification tests, 167 API tests, 30 antibiotic susceptibility tests, and sodium dodecyl sulfate-polyacrylamide gel electrophoretic fingerprints of total cellular proteins with type strains of Phyllobacterium myrsinacearum and Phyllobacterium rubiacearum. It was found on 198 of 1,100 investigated plants between the 2nd and 10th leaf stage on three different fields in Belgium and one field in Spain. Densities ranged from 2 × 104 to 2 × 108 CFU/g of root. Five isolates exerted a broad-spectrum in vitro antifungal activity. DNA-DNA hybridizations showed that Phyllobacterium sp. does not contain DNA sequences that are homologous with the attachment genes chvA, chvB, the transferred-DNA (T-DNA) hormone genes iaaH and ipt from Agrobacterium tumefaciens, iaaM from A. tumefaciens and Pseudomonas savastanoi, or the nitrogenase genes nifHDK from Klebsiella pneumoniae. Phyllobacterium sp. produces indolylacetic acid in in vitro cultures and induces auxinlike effects when cocultivated with callus tissue of tobacco. When Phyllobacterium sp. was transformed with a Ti plasmid derivative, it gained the capacity to induce tumors on Kalanchoe daigremontiana. The potential role of Phyllobacterium sp. in this newly recognized niche is discussed. Images PMID:16348158

  16. Identification of mammalian mitochondrial proteins that interact with IAPs via N-terminal IAP binding motifs

    Microsoft Academic Search

    A M Verhagen; T K Kratina; C J Hawkins; J Silke; P G Ekert; D L Vaux

    2007-01-01

    Direct IAP binding protein with low pI\\/second mitochondrial activator of caspases, HtrA2\\/Omi and GstPT\\/eRF3 are mammalian proteins that bind via N-terminal inhibitor of apoptosis protein (IAP) binding motifs (IBMs) to the baculoviral IAP repeat (BIR) domains of IAPs. These interactions can prevent IAPs from inhibiting caspases, or displace active caspases, thereby promoting cell death. We have identified several additional potential

  17. A procedure for systematic identification of bacteriophage–host interactions of P. aeruginosa phages

    Microsoft Academic Search

    Bart Roucourt; Elke Lecoutere; Andrew Chibeu; Kirsten Hertveldt; Guido Volckaert; Rob Lavigne

    2009-01-01

    Immediately after bacteriophage infection, phage early proteins establish optimal conditions for phage infection, often through a direct interaction with host-cell proteins. We implemented a yeast two-hybrid approach for Pseudomonas aeruginosa phages as a first step in the analysis of these – often uncharacterized – proteins. A 24-fold redundant prey library of P. aeruginosa PAO1 (7.32×106 independent clones), was screened against

  18. Identification and comparative analysis of hepatitis C virus-host cell protein interactions.

    PubMed

    Dolan, Patrick T; Zhang, Chaoying; Khadka, Sudip; Arumugaswami, Vaithilingaraja; Vangeloff, Abbey D; Heaton, Nicholas S; Sahasrabudhe, Sudhir; Randall, Glenn; Sun, Ren; LaCount, Douglas J

    2013-12-01

    Hepatitis C virus (HCV) alters the global behavior of the host cell to create an environment conducive to its own replication, but much remains unknown about how HCV proteins elicit these changes. Thus, a better understanding of the interface between the virus and host cell is required. Here we report the results of a large-scale yeast two-hybrid screen to identify protein-protein interactions between HCV genotype 2a (strain JFH1) and cellular factors. Our study identified 112 unique interactions between 7 HCV and 94 human proteins, over 40% of which have been linked to HCV infection by other studies. These interactions develop a more complete picture of HCV infection, providing insight into HCV manipulation of pathways, such as lipid and cholesterol metabolism, that were previously linked to HCV infection and implicating novel targets within microtubule-organizing centers, the complement system and cell cycle regulatory machinery. In an effort to understand the relationship between HCV and related viruses, we compared the HCV 2a interactome to those of other HCV genotypes and to the related dengue virus. Greater overlap was observed between HCV and dengue virus targets than between HCV genotypes, demonstrating the value of parallel screening approaches when comparing virus-host cell interactomes. Using siRNAs to inhibit expression of cellular proteins, we found that five of the ten shared targets tested (CUL7, PCM1, RILPL2, RNASET2, and TCF7L2) were required for replication of both HCV and dengue virus. These shared interactions provide insight into common features of the viral life cycles of the family Flaviviridae. PMID:24136289

  19. Identification of NIPSNAP1 as a nocistatin-interacting protein involving pain transmission.

    PubMed

    Okuda-Ashitaka, Emiko; Minami, Toshiaki; Tsubouchi, Shingo; Kiyonari, Hiroshi; Iwamatsu, Akihiro; Noda, Tetsuo; Handa, Hiroshi; Ito, Seiji

    2012-03-23

    4-Nitrophenylphosphatase domain and non-neuronal SNAP25-like protein homolog 1 (NIPSNAP1) is a molecule of physiologically unknown function, although it is predominantly expressed in the brain, spinal cord, liver, and kidney. We identified NIPSNAP1 as a protein that interacts with the neuropeptide nocistatin (NST) from synaptosomal membranes of mouse spinal cord using high-performance affinity latex beads. NST, which is produced from the same precursor protein as an opioid-like neuropeptide nociceptin/orphanin FQ (N/OFQ), has opposite effects on pain transmission evoked by N/OFQ. The calculated full-length pre-protein of NIPSNAP1 was 33 kDa, whereas the N-terminal truncated form of NIPSNAP1 (29 kDa) was ubiquitously expressed in the neuronal tissues, especially in synaptic membrane and mitochondria of brain. The 29-kDa NIPSNAP1 was distributed on the cell surface, and NST interacted with the 29-kDa but not the 33-kDa NIPSNAP1. Although intrathecal injection of N/OFQ induced tactile allodynia in both wild-type and NIPSNAP1-deficient mice, the inhibition of N/OFQ-evoked tactile allodynia by NST seen in wild-type mice was completely lacking in the deficient mice. These results suggest that NIPSNAP1 is an interacting molecule of NST and plays a crucial role in pain transmission. PMID:22311985

  20. The identification of novel PMADS3 interacting proteins indicates a role in post-transcriptional control.

    PubMed

    Li, Xin; Ning, Guogui; Han, Xueping; Liu, Caixian; Bao, Manzhu

    2015-06-10

    PMADS3, a known MADS-box transcriptional factor and a C-class gene for floral development, plays dual roles in controlling the identity of inner floral organs and the termination of flower meristems in petunia. In this study, it was confirmed by bimolecular fluorescence complementation (BiFC) assays that the PMADS3 protein can interact individually with E-class proteins FBP2, FBP5, FBP9 and PMADS12. A yeast two-hybrid cDNA library was screened using the entire PMADS3 as bait, and this identified further potential interaction candidates. Two novel genes, PheIF3f and PhAGO10, were isolated, and suggested to regulate mRNA and translational processes according to the analysis of protein functional domains and subcellular localization predictions. Notably, the PhAGO10 protein belongs to the Argonaute family, members of which are major players in small-RNA-guided gene silencing processes via mRNA cleavage or translational inhibition. The results of yeast two-hybrid and BiFC assays indicated that PheIF3f and PhAGO10 could interact with PMADS3. Our findings indicate that the C-class gene PMADS3 potentially participates in post-transcriptional control, as well as transcriptional regulation. PMID:25827715

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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

  6. A report of rifampin-resistant leprosy from northern and eastern India: identification and in silico analysis of molecular interactions.

    PubMed

    Vedithi, Sundeep Chaitanya; Lavania, Mallika; Kumar, Manoj; Kaur, Punit; Turankar, Ravindra P; Singh, Itu; Nigam, Astha; Sengupta, Utpal

    2015-04-01

    Presence of point mutations within the drug resistance determining regions of Mycobacterium leprae (M. leprae) genome confers molecular basis of drug resistance to dapsone, rifampin and ofloxacin in leprosy. This study is focused on the identification of mutations within the rpoB gene region of M. leprae that are specific for rifampin interaction, and further in silico analysis was carried out to determine the variations in the interactions. DNA and RNA were isolated from slit skin scrapings of 60 relapsed leprosy patients. PCR targeting rpoB gene region and amplicon sequencing was performed to determine point mutations. mRNA expression levels of rpoB and high-resolution melt analysis of mutants were performed using Rotor Gene Q Realtime PCR. Molecular docking was performed using LigandFit Software. Ten cases having point mutations within the rpoB gene region were identified and were clinically confirmed to be resistant to rifampin. A new mutation at codon position Gln442His has been identified. There is a 9.44-fold upregulation in the mRNA expression of rpoB gene in mutant/resistant samples when compared with the wild/sensitive samples. In silico docking analysis of rifampin with wild-type and Gln442His mutant RpoB proteins revealed a variation in the hydrogen-bonding pattern leading to a difference in the total interaction energy and conformational change at position Asp441. These preliminary downstream functional observations revealed that the presence of point mutations within the rifampin resistance determining regions of rpoB gene plays a vital role in conferring genetic and molecular basis of resistance to rifampin in leprosy. PMID:25201810

  7. Identification of key regulators in glycogen utilization in E. coli based on the simulations from a hybrid functional Petri net model

    PubMed Central

    2013-01-01

    Background Glycogen and glucose are two sugar sources available during the lag phase of E. coli, but the mechanism that regulates their utilization is still unclear. Methods Attempting to unveil the relationship between glucose and glycogen, we propose an integrated hybrid functional Petri net (HFPN) model including glycolysis, PTS, glycogen metabolic pathway, and their internal regulatory systems. Results and conclusions By comparing known biological results to this model, basic necessary regulatory mechanism for utilizing glucose and glycogen were identified as a feedback circuit in which HPr and EIIAGlc play key roles. Based on this regulatory HFPN model, we discuss the process of glycogen utilization in E. coli in the context of a systematic understanding of carbohydrate metabolism. PMID:24565082

  8. Identification of Adenovirus Serotype 5 Hexon Regions That Interact with Scavenger Receptors

    SciTech Connect

    Khare, Reeti; Reddy, Vijay S.; Nemerow, Glen R.; Barry, Michael A. (Scripps); (Mayo)

    2012-05-04

    Most of an intravenous dose of species C adenovirus serotype 5 (Ad5) is destroyed by liver Kupffer cells. In contrast, another species C virus, Ad6, evades these cells to mediate more efficient liver gene delivery. Given that this difference in Kupffer cell interaction is mediated by the hypervariable (HVR) loops of the virus hexon protein, we genetically modified each of the seven HVRs of Ad5 with a cysteine residue to enable conditional blocking of these sites with polyethylene glycol (PEG). We show that these modifications do not affect in vitro virus transduction. In contrast, after intravenous injection, targeted PEGylation at HVRs 1, 2, 5, and 7 increased viral liver transduction up to 20-fold. Elimination or saturation of liver Kupffer cells did not significantly affect this increase in the liver transduction. In vitro, PEGylation blocked uptake of viruses via the Kupffer cell scavenger receptor SRA-II. These data suggest that HVRs 1, 2, 5, and 7 of Ad5 may be involved in Kupffer cell recognition and subsequent destruction. These data also demonstrate that this conditional genetic-chemical mutation strategy is a useful tool for investigating the interactions of viruses with host tissues.

  9. Identification of a Deubiquitinating Enzyme as a Novel AGS3-Interacting Protein

    PubMed Central

    Xu, Zhuojin; Xia, Bin; Gong, Qiang; Bailey, Jeffrey; Groves, Benjamin; Radeke, Monte; Wood, Stephen A.; Szumlinski, Karen K.; Ma, Dzwokai

    2010-01-01

    Activator of G protein Signaling 3 (AGS3) is a receptor-independent G protein activator that has been implicated in multiple biological events such as brain development, neuroplasticity and addiction, cardiac function, Golgi structure/function, macroautophagy and metabolism. However, how AGS3 is regulated is little known. We demonstrate here that AGS3 interacts with a ubiquitin specific protease USP9x, and this interaction is at least partially mediated through the C-terminal G protein regulatory domain of AGS3. Knockdown of USP9x causes a moderate reduction in the level of AGS3. In contrast, overexpression of either USP9x or its deubiquitinating domain UCH increases the amount of AGS3, whereas expression of the mutant UCH domain that lacks deubiquitinating activity does not have the same effect. As previously observed in AGS3 knockdown cells, the localization of several marker proteins of the late Golgi compartments is disturbed in cells depleted of USP9x. Taken together, our study suggests that USP9x can modulate the level of a subpopulation of AGS3, and this modulation plays a role in regulating the structure of the late Golgi compartments. Finally, we have found that levels of AGS3 and USP9x are co-regulated in the prefrontal cortex of rats withdrawn from repeated cocaine treatment. In conjunction with the above data, this observation indicates a potential role of USP9X in the regulation of the AGS3 level during cocaine-induced neuroplasticity. PMID:20305814

  10. Identification of a deubiquitinating enzyme as a novel AGS3-interacting protein.

    PubMed

    Xu, Zhuojin; Xia, Bin; Gong, Qiang; Bailey, Jeffrey; Groves, Benjamin; Radeke, Monte; Wood, Stephen A; Szumlinski, Karen K; Ma, Dzwokai

    2010-01-01

    Activator of G protein Signaling 3 (AGS3) is a receptor-independent G protein activator that has been implicated in multiple biological events such as brain development, neuroplasticity and addiction, cardiac function, Golgi structure/function, macroautophagy and metabolism. However, how AGS3 is regulated is little known. We demonstrate here that AGS3 interacts with a ubiquitin specific protease USP9x, and this interaction is at least partially mediated through the C-terminal G protein regulatory domain of AGS3. Knockdown of USP9x causes a moderate reduction in the level of AGS3. In contrast, overexpression of either USP9x or its deubiquitinating domain UCH increases the amount of AGS3, whereas expression of the mutant UCH domain that lacks deubiquitinating activity does not have the same effect. As previously observed in AGS3 knockdown cells, the localization of several marker proteins of the late Golgi compartments is disturbed in cells depleted of USP9x. Taken together, our study suggests that USP9x can modulate the level of a subpopulation of AGS3, and this modulation plays a role in regulating the structure of the late Golgi compartments. Finally, we have found that levels of AGS3 and USP9x are co-regulated in the prefrontal cortex of rats withdrawn from repeated cocaine treatment. In conjunction with the above data, this observation indicates a potential role of USP9X in the regulation of the AGS3 level during cocaine-induced neuroplasticity. PMID:20305814

  11. 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

  12. Identification of Beta-2 as a Key Cell Adhesion Molecule in PCa Cell Neurotropic Behavior: A Novel Ex Vivo and Biophysical Approach

    PubMed Central

    Jansson, Keith H.; Castillo, Deborah G.; Morris, Joseph W.; Boggs, Mary E.; Czymmek, Kirk J.; Adams, Elizabeth L.; Schramm, Lawrence P.; Sikes, Robert A.

    2014-01-01

    Prostate cancer (PCa) is believed to metastasize through the blood/lymphatics systems; however, PCa may utilize the extensive innervation of the prostate for glandular egress. The interaction of PCa and its nerve fibers is observed in 80% of PCa and is termed perineural invasion (PNI). PCa cells have been observed traveling through the endoneurium of nerves, although the underlying mechanisms have not been elucidated. Voltage sensitive sodium channels (VSSC) are multimeric transmembrane protein complexes comprised of a pore-forming ? subunit and one or two auxiliary beta (?) subunits with inherent cell adhesion molecule (CAM) functions. The beta-2 isoform (gene SCN2B) interacts with several neural CAMs, while interacting putatively with other prominent neural CAMs. Furthermore, beta-2 exhibits elevated mRNA and protein levels in highly metastatic and castrate-resistant PCa. When overexpressed in weakly aggressive LNCaP cells (2BECFP), beta-2 alters LNCaP cell morphology and enhances LNCaP cell metastasis associated behavior in vitro. We hypothesize that PCa cells use beta-2 as a CAM during PNI and subsequent PCa metastasis. The objective of this study was to determine the effect of beta-2 expression on PCa cell neurotropic metastasis associated behavior. We overexpressed beta-2 as a fusion protein with enhanced cyan fluorescence protein (ECFP) in weakly aggressive LNCaP cells and observed neurotropic effects utilizing our novel ex vivo organotypic spinal cord co-culture model, and performed functional assays with neural matrices and atomic force microscopy. With increased beta-2 expression, PCa cells display a trend of enhanced association with nerve axons. On laminin, a neural CAM, overexpression of beta-2 enhances PCa cell migration, invasion, and growth. 2BECFP cells exhibit marked binding affinity to laminin relative to LNECFP controls, and recombinant beta-2 ectodomain elicits more binding events to laminin than BSA control. Functional overexpression of VSSC beta subunits in PCa may mediate PCa metastatic behavior through association with neural matrices. PMID:24892658

  13. Proximity User Identification Using Correlogram Shervin Shahidi1

    E-print Network

    Paris-Sud XI, Université de

    have been studied in many fields such as Human Computer Interaction (HCI) and Computer Security. As an instance, User Identification has tight resemblance with intrusion detection, which is the key to solve two data to a previously made distribution over a known user data to indicate an intrusion. The problem

  14. Identification of a key functional region in harpins from Xanthomonas that suppresses protein aggregation and mediates harpin expression in E. coli.

    PubMed

    Wang, Xiaoyu; Li, Ming; Zhang, Jiahuan; Zhang, Yan; Zhang, Guiying; Wang, Jinsheng

    2007-09-01

    In the current study, we identified a key functional region in harpins from Xanthomonas that suppressed protein aggregation and mediated its expression in E. coli. Our data suggested that the presence of two common features in harpins [Wei et al. (1992) Science 257:85-88], namely, high glycine content and lack of cysteine residues, were not sufficient for Xanthomonas to elicit hypersensitive response (HR) activity or heat stability. Additionally, bioinformatic analyses revealed that the secondary structure of a conserved N-terminal region consisting of 12 highly hydrophilic amino acids (QGISEKQLDQLL) was alpha-helical. Following site-directed mutagenesis deletion of this region, the three mutated harpin proteins, in cultures induced at 37 degrees C, failed to elicit a HR in tobacco leaves. However, at 24 degrees C, two mutated harpins retained the ability to elicit HR, albeit with lower expression levels than that noted with the wild-type. SDS-PAGE and Western blot data suggested the HpaG mutant protein was found almost entirely in the inclusion body. These data demonstrated that these conserved amino acid residues played a critical role in protein aggregation and inclusion body formation in harpins from Xanthomonas. PMID:17180733

  15. 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

  16. 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

    2014-07-01

    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

  17. Scale Insects, edition 2, a tool for the identification of potential pest scales at U.S.A. ports-of-entry (Hemiptera, Sternorrhyncha, Coccoidea)

    PubMed Central

    Miller, Douglass R.; Rung, Alessandra; Parikh, Grishma

    2014-01-01

    Abstract We provide a general overview of features and technical specifications of an online, interactive tool for the identification of scale insects of concern to the U.S.A. ports-of-entry. Full lists of terminal taxa included in the keys (of which there are four), a list of features used in them, and a discussion of the structure of the tool are provided. We also briefly discuss the advantages of interactive keys for the identification of potential scale insect pests. The interactive key is freely accessible on http://idtools.org/id/scales/index.php PMID:25152668

  18. Key Nutrients.

    ERIC Educational Resources Information Center

    Federal Extension Service (USDA), Washington, DC.

    Lessons written to help trainer agents prepare aides for work with families in the Food and Nutrition Program are presented in this booklet. The key nutrients discussed in the 10 lessons are protein, carbohydrates, fat, calcium, iron, iodine, and Vitamins A, B, C, and D. the format of each lesson is as follows: Purpose, Presentation, Application…

  19. 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

  20. Comparative in vivo toxicity of topical JP-8 jet fuel and its individual hydrocarbon components: identification of tridecane and tetradecane as key constituents responsible for dermal irritation.

    PubMed

    Muhammad, F; Monteiro-Riviere, N A; Riviere, J E

    2005-01-01

    Despite widespread exposure to military jet fuels, there remains a knowledge gap concerning the actual toxic entities responsible for irritation observed after topical fuel exposure. The present studies with individual hydrocarbon (HC) constituents of JP-8 jet fuel shed light on this issue. To mimic occupational scenarios, JP-8, 8 aliphatic HC (nonane, decane, undecane, dodecane, tridecane, tetradecane, pentadecane, hexadecane) and 6 aromatic HC (ethyl benzene, o-xylene, trimethyl benzene, cyclohexyl benzene, naphthalene, dimethyl naphthalene) soaked cotton fabrics were topically exposed to pigs for 1 day and with repeated daily exposures for 4 days. Erythema, epidermal thickness, and epidermal cell layers were quantitated. No erythema was noted in 1-day in vivo HC exposures but significant erythema was observed in 4-day tridecane, tetradecane, pentadecane, and JP-8 exposed sites. The aromatic HCs did not produce any macroscopic lesions in 1 or 4 days of in vivo exposures. Morphological observations revealed slight intercellular and intracellular epidermal edema in 4-day exposures with the aliphatic HCs. Epidermal thickness and number of cell layers significantly increased (p < 0.05) in tridecane, tetradecane, pentadecane, and JP-8-treated sites. No significant differences were observed in the aromatic HC-exposed sites. Subcorneal microabscesses containing inflammatory cells were observed with most of the long-chain aliphatic HCs and JP-8 in 4-day exposures. Ultrastructural studies depicted that jet fuel HC-induced cleft formation within intercellular lipid lamellar bilayers of the stratum corneum. The degree of damage to the skin was proportional to the length of in vivo HC exposures. These data coupled with absorption and toxicity studies of jet fuel HC revealed that specific HCs (tridecane and tetradecane) might be the key constituents responsible for jet fuel-induced skin irritation. PMID:15902969

  1. Identification of the Key Differential Transcriptional Responses of Human Whole Blood Following TLR2 or TLR4 Ligation In-Vitro

    PubMed Central

    Blankley, Simon; Graham, Christine M.; Howes, Ashleigh; Bloom, Chloe I.; Berry, Matthew P. R.; Chaussabel, Damien; Pascual, Virginia; Banchereau, Jacques; Lipman, Marc; O’Garra, Anne

    2014-01-01

    The use of human whole blood for transcriptomic analysis has potential advantages over the use of isolated immune cells for studying the transcriptional response to pathogens and their products. Whole blood stimulation can be carried out in a laboratory without the expertise or equipment to isolate immune cells from blood, with the added advantage of being able to undertake experiments using very small volumes of blood. Toll like receptors (TLRs) are a family of pattern recognition receptors which recognise highly conserved microbial products. Using the TLR2 ligand (Pam3CSK4) and the TLR4 ligand (LPS), human whole blood was stimulated for 0, 1, 3, 6, 12 or 24 hours at which times mRNA was isolated and a comparative microarray was undertaken. A common NF?B transcriptional programme was identified following both TLR2 and TLR4 ligation which peaked at between 3 to 6 hours including upregulation of many of the NF?B family members. In contrast an interferon transcriptional response was observed following TLR4 but not TLR2 ligation as early as 1 hour post stimulation and peaking at 6 hours. These results recapitulate the findings observed in previously published studies using isolated murine and human myeloid cells indicating that in vitro stimulated human whole blood can be used to interrogate the early transcriptional kinetic response of innate cells to TLR ligands. Our study demonstrates that a transcriptomic analysis of mRNA isolated from human whole blood can delineate both the temporal response and the key transcriptional differences following TLR2 and TLR4 ligation. PMID:24842522

  2. Identification of molecular crystals capable of undergoing an acyl-transfer reaction based on intermolecular interactions in the crystal lattice.

    PubMed

    Tamboli, Majid I; Krishnaswamy, Shobhana; Gonnade, Rajesh G; Shashidhar, Mysore S

    2013-09-16

    Investigation of the intermolecular acyl-transfer reactivity in molecular crystals of myo-inositol orthoester derivatives and its correlation with crystal structures enabled us to identify the essential parameters to support efficient acyl-transfer reactions in crystals: 1)?the favorable geometry of the nucleophile (-OH) and the electrophile (C-O) and 2)?the molecular assembly, reinforced by C-H???? interactions, which supports a domino-type reaction in crystals. These parameters were used to identify another reactive crystal through a data-mining study of the Cambridge Structural Database. A 2:1 co-crystal of 2,3-naphthalene diol and its di-p-methylbenzoate was selected as a potentially reactive crystal and its reactivity was tested by heating the co-crystals in the presence of solid sodium carbonate. A facile intermolecular p-toluoyl group transfer was observed as predicted. The successful identification of reactive crystals opens up a new method for the detection of molecular crystals capable of exhibiting acyl-transfer reactivity. PMID:23934729

  3. Identification and separation of saxitoxins using hydrophilic interaction liquid chromatography coupled to traveling wave ion mobility-mass spectrometry.

    PubMed

    Poyer, Salomé; Loutelier-Bourhis, Corinne; Coadou, Gaël; Mondeguer, Florence; Enche, Julien; Bossée, Anne; Hess, Philipp; Afonso, Carlos

    2015-01-01

    The aim of this work was to develop a reliable and efficient analytical method to characterise and differentiate saxitoxin analogues (STX), including sulphated (gonyautoxins, GTX) and non-sulphated analogues. For this purpose, hydrophilic interaction liquid chromatography (HILIC) was used to separate sulphated analogues. We also resorted to ion mobility spectrometry to differentiate the STX analogues because this technique adds a new dimension of separation based on ion gas phase conformation. Positive and negative ionisation modes were used for gonyautoxins while positive ionisation mode was used for non-sulphated analogues. Subsequently, the coupling of these three complementary techniques, HILIC-IM-MS, permitted the separation and identification of STX analogues; isomer differentiation was achieved in HILIC dimension while non-sulphated analogues were separated in the IM-MS dimension. Additional structural characteristics concerning the conformation of STXs could be obtained using IM-MS measurements. Thus, the collision cross sections (CCS) of STXs are reported for the first time in the positive ionisation mode. These experimental CCSs correlated well with the calculated CCS values using the trajectory method. PMID:25601690

  4. Interactions of tensin with actin and identification of its three distinct actin-binding domains

    PubMed Central

    1994-01-01

    Tensin, a 200-kD phosphoprotein of focal contacts, contains sequence homologies to Src (SH2 domain), and several actin-binding proteins. These features suggest that tensin may link the cell membrane to the cytoskeleton and respond directly to tyrosine kinase signalling pathways. Here we identify three distinct actin-binding domains within tensin. Recombinant tensin purified after overexpression by a baculovirus system binds to actin filaments with Kd = 0.1 microM, cross- links actin filaments at a molar ratio of 1:10 (tensin/actin), and retards actin assembly by barbed end capping with Kd = 20 nM. Tensin fragments were constructed and expressed as fusion proteins to map domains having these activities. Three regions from tensin interact with actin: two regions composed of amino acids 1 to 263 and 263 to 463, cosediment with F-actin but do not alter the kinetics of actin assembly; a region composed of amino acids 888-989, with sequence homology to insertin, retards actin polymerization. A claw-shaped tensin dimer would have six potential actin-binding sites and could embrace the ends of two actin filaments at focal contacts. PMID:8195290

  5. Identification of the interaction region between hemagglutinin components of the botulinum toxin complex.

    PubMed

    Suzuki, Tomonori; Miyashita, Shin-Ichiro; Hayashi, Shintaro; Miyata, Keita; Inui, Ken; Kondo, Yosuke; Miyazaki, Satoru; Ohyama, Tohru; Niwa, Koichi; Watanabe, Toshihiro; Sagane, Yoshimasa

    2014-04-01

    The large toxin complex (L-TC) produced by Clostridium botulinum is formed from the M-TC (BoNT/NTNHA complex) by conjugation of M-TC with HA-33/HA-17 trimer consists of two HA-33 proteins and a single HA-17 protein. This association is mediated by HA-70, which interacts with HA-17. The current study aims to identify the regions of the HA-70 molecule that adhere to the HA-33/HA-17 complex. Products from limited proteolysis of HA-70 were resolved by SDS-PAGE and transferred onto PVDF membranes, where they were probed with HA-33/HA-17 in a far-western blot. Among the HA-70 fragments, HA-33/HA-17 bound to those containing at least the C-terminal half of the HA-70 molecule, but not those carrying the N-terminal half. Additional docking simulation analysis indicated that the HA-70 region Gln420-Tyr575 is responsible for binding to HA-17, which is consistent with the far-western blot data. The findings here reveal additional details concerning the three-dimensional structure of the functional HA sub-complex in the botulinum toxin complex. PMID:24472509

  6. Identification and clarification of the role of key active site residues in bacterial glutathione S-transferase zeta/maleylpyruvate isomerase

    SciTech Connect

    Fang, Ti [Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071 (China)] [Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071 (China); Li, De-Feng [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)] [National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Zhou, Ning-Yi, E-mail: n.zhou@pentium.whiov.ac.cn [Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071 (China)] [Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071 (China)

    2011-07-08

    Highlights: {yields} Application of site-directed mutagenesis to probe the active site residues of glutathione-dependent maleylpyruvate isomerase. {yields} Two conserved residues, Arg8 and Arg176, in zeta class glutathione S-transferases are critical for maleylpyruvate orientation and enolization. {yields} Arg109, found exclusively in NagL, participates in k{sub cat} regulation. {yields} The T11A mutant exhibited a significantly decreased K{sub m} value for glutathione with little impact on maleylpyruvate kinetics. {yields} The Thr11 residue appears to have significance in the evolution of glutathione S-transferase classes. -- Abstract: The maleylpyruvate isomerase NagL from Ralstonia sp. strain U2, which has been structurally characterized previously, catalyzes the isomerization of maleylpyruvate to fumarylpyruvate. It belongs to the class zeta glutathione S-transferases (GSTZs), part of the cytosolic GST family (cGSTs). In this study, site-directed mutagenesis was conducted to probe the functions of 13 putative active site residues. Steady-state kinetic information for mutants in the reduced glutathione (GSH) binding site, suggested that (a) Gln64 and Asp102 interact directly with the glutamyl moiety of glutathione, (b) Gln49 and Gln64 are involved in a potential electron-sharing network that influences the ionization of the GSH thiol. The information also suggests that (c) His38, Asn108 and Arg109 interact with the GSH glycine moiety, (d) His104 has a role in the ionization of the GSH sulfur and the stabilization of the maleyl terminal carboxyl group in the reaction intermediate and (e) Arg110 influences the electron distribution in the active site and therefore the ionization of the GSH thiolate. Kinetic data for mutants altered in the substrate-binding site imply that (a) Arg8 and Arg176 are critical for maleylpyruvate orientation and enolization, and (b) Arg109 (exclusive to NagL) participates in k{sub cat} regulation. Surprisingly, the T11A mutant had a decreased GSH K{sub m} value, whereas little impact on maleylpyruvate kinetics was observed, suggesting that this residue plays an important role in GSH binding. An evolutionary trend in this residue appears to have developed not only in prokaryotic and eukaryotic GSTZs, but also among the wider class of cGSTs.

  7. 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

  8. Unnatural selection: talent identification and development in sport.

    PubMed

    Abbott, Angela; Button, Chris; Pepping, Gert-Jan; Collins, Dave

    2005-01-01

    The early identification of talented individuals has become increasingly important across many performance domains. Current talent identification (TI) schemes in sport typically select on the basis of discrete, unidimensional measures at unstable periods in the athlete's development. In this article, the concept of talent is revised as a complex, dynamical system in which future behaviors emerge from an interaction of key performance determinants such as psychological behaviors, motor abilities, and physical characteristics. Key nonlinear dynamics concepts are related to TI approaches such as sensitivity to initial conditions, transitions, and exponential behavioral distributions. It is concluded that many TI models place an overemphasis on early identification rather than the development of potentially talented performers. A generic model of talent identification and development is proposed that addresses these issues and provides direction for future research. PMID:15629068

  9. 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

  10. Identification and Modulation of the Key Amino Acid Residue Responsible for the pH Sensitivity of Neoculin, a Taste-Modifying Protein

    PubMed Central

    Nakajima, Ken-ichiro; Yokoyama, Kanako; Koizumi, Taichi; Koizumi, Ayako; Asakura, Tomiko; Terada, Tohru; Masuda, Katsuyoshi; Ito, Keisuke; Shimizu-Ibuka, Akiko; Misaka, Takumi; Abe, Keiko

    2011-01-01

    Neoculin occurring in the tropical fruit of Curculigo latifolia is currently the only protein that possesses both a sweet taste and a taste-modifying activity of converting sourness into sweetness. Structurally, this protein is a heterodimer consisting of a neoculin acidic subunit (NAS) and a neoculin basic subunit (NBS). Recently, we found that a neoculin variant in which all five histidine residues are replaced with alanine elicits intense sweetness at both neutral and acidic pH but has no taste-modifying activity. To identify the critical histidine residue(s) responsible for this activity, we produced a series of His-to-Ala neoculin variants and evaluated their sweetness levels using cell-based calcium imaging and a human sensory test. Our results suggest that NBS His11 functions as a primary pH sensor for neoculin to elicit taste modification. Neoculin variants with substitutions other than His-to-Ala were further analyzed to clarify the role of the NBS position 11 in the taste-modifying activity. We found that the aromatic character of the amino acid side chain is necessary to elicit the pH-dependent sweetness. Interestingly, since the His-to-Tyr variant is a novel taste-modifying protein with alternative pH sensitivity, the position 11 in NBS can be critical to modulate the pH-dependent activity of neoculin. These findings are important for understanding the pH-sensitive functional changes in proteinaceous ligands in general and the interaction of taste receptor–taste substance in particular. PMID:21559382

  11. Identification of genes differentially expressed during interaction of Mexican lime tree infected with "Candidatus Phytoplasma aurantifolia"

    PubMed Central

    2011-01-01

    Background "Candidatus Phytoplasma aurantifolia", is the causative agent of witches' broom disease in Mexican lime trees (Citrus aurantifolia L.), and is responsible for major losses of Mexican lime trees in Southern Iran and Oman. The pathogen is strictly biotrophic, and thus is completely dependent on living host cells for its survival. The molecular basis of compatibility and disease development in this system is poorly understood. Therefore, we have applied a cDNA- amplified fragment length polymorphism (AFLP) approach to analyze gene expression in Mexican lime trees infected by "Ca. Phytoplasma aurantifolia". Results We carried out cDNA-AFLP analysis on grafted infected Mexican lime trees of the susceptible cultivar at the representative symptoms stage. Selective amplifications with 43 primer combinations allowed the visualisation of 55 transcript-derived fragments that were expressed differentially between infected and non-infected leaves. We sequenced 51 fragments, 36 of which were identified as lime tree transcripts after homology searching. Of the 36 genes, 70.5% were down-regulated during infection and could be classified into various functional groups. We showed that Mexican lime tree genes that were homologous to known resistance genes tended to be repressed in response to infection. These included the genes for modifier of snc1 and autophagy protein 5. Furthermore, down-regulation of genes involved in metabolism, transcription, transport and cytoskeleton was observed, which included the genes for formin, importin ? 3, transducin, L-asparaginase, glycerophosphoryl diester phosphodiesterase, and RNA polymerase ?. In contrast, genes that encoded a proline-rich protein, ubiquitin-protein ligase, phosphatidyl glycerol specific phospholipase C-like, and serine/threonine-protein kinase were up-regulated during the infection. Conclusion The present study identifies a number of candidate genes that might be involved in the interaction of Mexican lime trees with "Candidatus Phytoplasma aurantifolia". These results should help to elucidate the molecular basis of the infection process and to identify genes that could be targeted to increase plant resistance and inhibit the growth and reproduction of the pathogen. PMID:21194490

  12. Identification of a Novel Cellular TPR-Containing Protein, SGT, That Interacts with the Nonstructural Protein NS1 of Parvovirus H-1

    Microsoft Academic Search

    CELINA CZIEPLUCH; ELISABETH KORDES; REMY POIREY; ANNABEL GREWENIG; JEAN ROMMELAERE; JEAN-CLAUDE JAUNIAUX

    1998-01-01

    The nonstructural protein NS1 of autonomous parvoviruses is essential for viral DNA amplification and gene expression and is also the major cytopathic effector of these viruses. NS1 acts as nickase, helicase, and ATPase and upregulates P38-driven transcription of the capsid genes. We report here the identification of a novel cellular protein that interacts with NS1 from parvovirus H-1 and which

  13. Magnetic hyperthermia properties of nanoparticles inside lysosomes using kinetic Monte Carlo simulations: Influence of key parameters and dipolar interactions, and evidence for strong spatial variation of heating power

    NASA Astrophysics Data System (ADS)

    Tan, R. P.; Carrey, J.; Respaud, M.

    2014-12-01

    Understanding the influence of dipolar interactions in magnetic hyperthermia experiments is of crucial importance for fine optimization of nanoparticle (NP) heating power. In this study we use a kinetic Monte Carlo algorithm to calculate hysteresis loops that correctly account for both time and temperature. This algorithm is shown to correctly reproduce the high-frequency hysteresis loop of both superparamagnetic and ferromagnetic NPs without any ad hoc or artificial parameters. The algorithm is easily parallelizable with a good speed-up behavior, which considerably decreases the calculation time on several processors and enables the study of assemblies of several thousands of NPs. The specific absorption rate (SAR) of magnetic NPs dispersed inside spherical lysosomes is studied as a function of several key parameters: volume concentration, applied magnetic field, lysosome size, NP diameter, and anisotropy. The influence of these parameters is illustrated and comprehensively explained. In summary, magnetic interactions increase the coercive field, saturation field, and hysteresis area of major loops. However, for small amplitude magnetic fields such as those used in magnetic hyperthermia, the heating power as a function of concentration can increase, decrease, or display a bell shape, depending on the relationship between the applied magnetic field and the coercive/saturation fields of the NPs. The hysteresis area is found to be well correlated with the parallel or antiparallel nature of the dipolar field acting on each particle. The heating power of a given NP is strongly influenced by a local concentration involving approximately 20 neighbors. Because this local concentration strongly decreases upon approaching the surface, the heating power increases or decreases in the vicinity of the lysosome membrane. The amplitude of variation reaches more than one order of magnitude in certain conditions. This transition occurs on a thickness corresponding to approximately 1.3 times the mean distance between two neighbors. The amplitude and sign of this variation is explained. Finally, implications of these various findings are discussed in the framework of magnetic hyperthermia optimization. It is concluded that feedback on two specific points from biology experiments is required for further advancement of the optimization of magnetic NPs for magnetic hyperthermia. The present simulations will be an advantageous tool to optimize magnetic NPs heating power and interpret experimental results.

  14. Demonstration of the in vivo interaction of key cell death regulators by structure-based design of second-site suppressors

    Microsoft Academic Search

    Jay Parrish; Helen Metters; Lin Chen; Ding Xue

    2000-01-01

    Demonstrating in vivo interaction of two important biomolecules and the relevance of the interaction to a biological process have been difficult issues in biomedical research. Here, we report the use of a homology modeling approach to establish the significance of protein interactions in governing the activation of programmed cell death in Caenorhabditis elegans. A protein interaction cascade has been postulated

  15. 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

  16. 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

  17. 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: 1/8" "D" shaped "S" shaped tunnels small, 3/4" metallic green beetles 1/8 D shaped exit holes

  18. 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.

  19. Identification of NS1 domains of avian H5N1 influenza virus which influence the interaction with the NOLC1 protein.

    PubMed

    Zhu, Chun-Yu; Zheng, Fang-Liang; She, Xiao-Shuang; Zhao, Dan; Gu, Ying; Duan, Yan-Ting; Chang, Alan K; Liu, Hong-Sheng

    2015-04-01

    Non-structural protein 1 (NS1) is an important virulence factor encoded by influenza A virus. NS1 can interact with a variety of host cell proteins to interfere with the host innate immune response and to promote effective viral replication. Our previous work has shown that only the effector domain of NS1 (amino acid residues 74-230/237) is sufficient to interact with nucleolar and coiled-body phosphoprotein 1 (NOLC1). To investigate the exact region of NS1 that interacts with NOLC1, we used only the effector domain of NS1 and constructed various mutants having different deletions, and then tested their ability to interact with NOLC1 via pull-down assay. Only the mutant containing amino acid residues 104-200 showed positive interaction with NOLC1. To further determine the key amino acids of the NS1 effector domain which are crucial for interaction with NOLC1, several mutants containing a single amino acid substitution were made and their interaction with NOLC1 was tested. Only the mutant D120A or R195A showed reduced binding with NOLC1, suggesting that D120 and R195 were crucial to the binding of NS1 to NOLC1. This study lays the foundation for further research aiming at furthering our understanding of the interaction between NS1 and host cells. PMID:25645906

  20. Construction and use of Plasmodium falciparum phage display libraries to identify host parasite interactions

    Microsoft Academic Search

    Sonja B Lauterbach; Roberto Lanzillotti; Theresa L Coetzer

    2003-01-01

    BACKGROUND: The development of Plasmodium falciparum within human erythrocytes induces a wide array of changes in the ultrastructure, function and antigenic properties of the host cell. Numerous proteins encoded by the parasite have been shown to interact with the erythrocyte membrane. The identification of new interactions between human erythrocyte and P. falciparum proteins has formed a key area of malaria

  1. 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

  2. Rapid testing and identification of actuator using dSPACE real-time emulator

    Microsoft Academic Search

    Daocheng Xie; Zhongwei Wang; Qinghua Zeng

    2011-01-01

    To solve the problem of model identification of actuator in control system design of aerocraft, testing system based on dSPACE emulator is established, sending testing signal and receiving feedback voltage are realized using dSPACE interactive cards, communication between signal generating equipment and feedback voltage acquisition equipment is synchronized. This paper introduces the hardware architecture and key technologies of the simulation

  3. Mineral Identification

    NSDL National Science Digital Library

    rmesser

    2010-11-16

    Imagine you are hiking with your family and this shiney looking crystal catches your eye. You bring it home and no one in your family is able to tell you what it is. How do you find out? First you need to practice. Identifying minerals. Click on the following link. Identify all five minerals. On your peice of paper tell me their Name Color Luster Cleavage/Fracture Hardness Glenco simple mineral identification Now try and identify 7 real minerals using a virtual key. Answer the following questions What properties do you use to identify the mineral? Which ...

  4. Identification of a structural motif that confers specific interaction with the WD40 repeat domain of Arabidopsis COP1.

    PubMed

    Holm, M; Hardtke, C S; Gaudet, R; Deng, X W

    2001-01-15

    Arabidopsis COP1 is a photomorphogenesis repressor capable of directly interacting with the photomorphogenesis-promoting factor HY5. This interaction between HY5 and COP1 results in targeted deg radation of HY5 by the 26S proteasome. Here we characterized the WD40 repeat domain-mediated interactions of COP1 with HY5 and two new proteins. Mutational analysis of those interactive partners revealed a conserved motif responsible for the interaction with the WD40 domain. This novel motif, with the core sequence V-P-E/D-?-G (? = hydrophobic residue) in conjunction with an upstream stretch of 4-5 negatively charged residues, interacts with a defined surface area of the ss-propeller assembly of the COP1 WD40 repeat domain through both hydrophobic and ionic interactions. Several residues in the COP1 WD40 domain that are critical for the interaction with this motif have been revealed. The fact that point mutations either in the COP1 WD40 domain or in the HY5 motif that abolish the interaction between COP1 and HY5 in yeast result in a dramatic reduction of HY5 degradation in transgenic plants validates the biological significance of this defined interaction. PMID:11226162

  5. 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

  6. 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)

  7. Identification of a novel nuclear localization signal and speckle-targeting sequence of tuftelin-interacting protein 11, a splicing factor involved in spliceosome disassembly

    SciTech Connect

    Tannukit, Sissada [Center for Craniofacial Molecular Biology, University of Southern California, 2250 Alcazar Street, CSA Rm103, Los Angeles, CA 90033-1004 (United States)] [Center for Craniofacial Molecular Biology, University of Southern California, 2250 Alcazar Street, CSA Rm103, Los Angeles, CA 90033-1004 (United States); Crabb, Tara L.; Hertel, Klemens J. [Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA 92697-4025 (United States)] [Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, CA 92697-4025 (United States); Wen, Xin [Center for Craniofacial Molecular Biology, University of Southern California, 2250 Alcazar Street, CSA Rm103, Los Angeles, CA 90033-1004 (United States)] [Center for Craniofacial Molecular Biology, University of Southern California, 2250 Alcazar Street, CSA Rm103, Los Angeles, CA 90033-1004 (United States); Jans, David A. [Department of Biochemistry and Molecular Biology, Nuclear Signalling Laboratory, Monash University, Clayton, Victoria 3800 (Australia)] [Department of Biochemistry and Molecular Biology, Nuclear Signalling Laboratory, Monash University, Clayton, Victoria 3800 (Australia); Paine, Michael L., E-mail: paine@usc.edu [Center for Craniofacial Molecular Biology, University of Southern California, 2250 Alcazar Street, CSA Rm103, Los Angeles, CA 90033-1004 (United States)

    2009-12-18

    Tuftelin-interacting protein 11 (TFIP11) is a protein component of the spliceosome complex that promotes the release of the lariat-intron during late-stage splicing through a direct recruitment and interaction with DHX15/PRP43. Expression of TFIP11 is essential for cell and organismal survival. TFIP11 contains a G-patch domain, a signature motif of RNA-processing proteins that is responsible for TFIP11-DHX15 interactions. No other functional domains within TFIP11 have been described. TFIP11 is localized to distinct speckled regions within the cell nucleus, although excluded from the nucleolus. In this study sequential C-terminal deletions and mutational analyses have identified two novel protein elements in mouse TFIP11. The first domain covers amino acids 701-706 (VKDKFN) and is an atypical nuclear localization signal (NLS). The second domain is contained within amino acids 711-735 and defines TFIP11's distinct speckled nuclear localization. The identification of a novel TFIP11 nuclear speckle-targeting sequence (TFIP11-STS) suggests that this domain directly interacts with additional spliceosomal components. These data help define the mechanism of nuclear/nuclear speckle localization of the splicing factor TFIP11, with implications for it's function.

  8. Interaction

    NSDL National Science Digital Library

    Wolfgang Christian

    Set values for the initial position, velocity, and mass of the two particles, and click on the button "Initialize Animation" to play the animation using your specified values. Note, if m or v are too large, the particles may actually pass through one another which will seem a little strange. Note: the interaction between the particles is a "non-contact" interaction, much like the electrostatic force on two charges. Mathematically, it is actually a Hooke's law interaction.

  9. 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

  10. Alcohol-induced sedation and synergistic interactions between alcohol and morphine: A key mechanistic role for Toll-like receptors and MyD88-dependent signaling.

    PubMed

    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

    2015-03-01

    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-signaling participant), NF-?B, Interleukin-1? (IL-1?; as a downstream proinflammatory effector molecule) and the ? opioid receptor (MOR; as a classical site for morphine action) in acute alcohol-induced sedation (4.5g/kg) and alcohol (2.5g/kg) interaction with morphine (5mg/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

  11. Identification of a host 14-3-3 Protein that Interacts with Xanthomonas effector AvrRxv

    Technology Transfer Automated Retrieval System (TEKTRAN)

    AvrRxv is a member of a family of pathogen effectors from both plant and mammalian pathogens. Using a yeast two hybrid screen, we identified a 14-3-3 protein from tomato that interacts with AvrRxv called AvrRxv Interactor 1 (ARI1). The interaction was confirmed in vitro with affinity chromatograph...

  12. Dynamic Conformations of Nucleophosmin (NPM1) at a Key Monomer-Monomer Interface Affect Oligomer Stability and Interactions with Granzyme B

    PubMed Central

    Duan-Porter, Wei D.; Woods, Virgil L.; Maurer, Kimberly D.; Li, Sheng; Rosen, Antony

    2014-01-01

    Nucleophosmin (NPM1) is an abundant, nucleolar tumor antigen with important roles in cell proliferation and putative contributions to oncogenesis. Wild-type NPM1 forms pentameric oligomers through interactions at the amino-terminal core domain. A truncated form of NPM1 found in some hepatocellular carcinoma tissue formed an unusually stable oligomer and showed increased susceptibility to cleavage by granzyme B. Initiation of translation at the seventh methionine generated a protein (M7-NPM) that shared all these properties. We used deuterium exchange mass spectrometry (DXMS) to perform a detailed structural analysis of wild-type NPM1 and M7-NPM, and found dynamic conformational shifts or local “unfolding” at a specific monomer-monomer interface which included the ?-hairpin “latch.” We tested the importance of interactions at the ?-hairpin “latch” by replacing a conserved tyrosine in the middle of the ?-hairpin loop with glutamic acid, generating Y67E-NPM. Y67E-NPM did not form stable oligomers and further, prevented wild-type NPM1 oligomerization in a dominant-negative fashion, supporting the critical role of the ?-hairpin “latch” in monomer-monomer interactions. Also, we show preferential cleavage by granzyme B at one of two available aspartates (either D161 or D122) in M7-NPM and Y67E-NPM, whereas wild-type NPM1 was cleaved at both sites. Thus, we observed a correlation between the propensity to form oligomers and granzyme B cleavage site selection in nucleophosmin proteins, suggesting that a small change at an important monomer-monomer interface can affect conformational shifts and impact protein-protein interactions. PMID:25490769

  13. 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.

  14. Identification of Protein-Protein Interaction Inhibitors Targeting Vaccinia Virus Processivity Factor for Development of Antiviral Agents ? †

    PubMed Central

    Schormann, Norbert; Sommers, Charnell Inglis; Prichard, Mark N.; Keith, Kathy A.; Noah, James W.; Nuth, Manunya; Ricciardi, Robert P.; Chattopadhyay, Debasish

    2011-01-01

    Poxvirus uracil DNA glycosylase D4 in association with A20 and the catalytic subunit of DNA polymerase forms the processive polymerase complex. The binding of D4 and A20 is essential for processive polymerase activity. Using an AlphaScreen assay, we identified compounds that inhibit protein-protein interactions between D4 and A20. Effective interaction inhibitors exhibited both antiviral activity and binding to D4. These results suggest that novel antiviral agents that target the protein-protein interactions between D4 and A20 can be developed for the treatment of infections with poxviruses, including smallpox. PMID:21844323

  15. 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

  16. Identification of protein regions involved in the interaction of human respiratory syncytial virus phosphoprotein and nucleoprotein: significance for nucleocapsid assembly and formation of cytoplasmic inclusions.

    PubMed Central

    García-Barreno, B; Delgado, T; Melero, J A

    1996-01-01

    We have reported previously that the nucleoprotein (N), the phosphoprotein (P), and the 22-kDa protein of human respiratory syncytial virus (HRSV) are components of the cytoplasmic inclusion bodies observed in HEp-2-infected cells. In addition, coexpression of N and P was sufficient to induce the formation of N-P complexes detectable by either coimmunoprecipitation with anti-P antibodies or generation of cytoplasmic inclusions. We now report the identification of protein regions required for these interactions. Deletion mutant analysis of the P protein gene indicated that its C-terminal end was essential for interacting with N. This conclusion was strengthened by the finding that an anti-P monoclonal antibody (021/12P), reacting with a 21-residue P protein C-terminal peptide, apparently displaced N from N-P complexes. The same effect was observed with high concentrations of the C-terminal peptide. However, sequence requirements for the P protein C-terminal end were not absolute, and mutants with the substitution Ser-237-->Ala or Ser-237-->Thr were as efficient as the wild type in interacting with N. In addition, P and N proteins from strains of different HRSV antigenic groups, with sequence differences in the P protein C-terminal end, were able to coimmunoprecipitate and formed cytoplasmic inclusions. Deletion mutant analysis of the N gene indicated that large segments of this polypeptide were required for interacting with P. The relevance of these interactions for HRSV is discussed in comparison with those of analogous proteins from related viruses. PMID:8551618

  17. 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

  18. 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

  19. Identification of a host 14-3-3 protein that interacts with Xanthomonas effector AvrRxv

    Microsoft Academic Search

    Maureen C. Whalen; Todd Richter; Kseniya Zakhareyvich; Masayasu Yoshikawa; Dana Al-Azzeh; Adeshola Adefioye; Greg Spicer; Laura L. Mendoza; Christine Q. Morales; Vicki Klassen; Gina Perez-Baron; Carole S. Toebe; Ageliki Tzovolous; Emily Gerstman; Erika Evans; Cheryl Thompson; Mary Lopez; Pamela C. Ronald

    2008-01-01

    AvrRxv is a member of a family of pathogen effectors present in pathogens of both plant and mammalian species. Xanthomonas campestris pv. vesicatoria strains carrying AvrRxv induce a hypersensitive response (HR) in the tomato cultivar Hawaii 7998. Using a yeast two-hybrid screen, we identified a 14-3-3 protein from tomato that interacts with AvrRxv called AvrRxv interactor 1 (ARI1). The interaction

  20. Identification of electrostatic and van der Waals interaction forces between a micrometer-size sphere and a flat substrate

    Microsoft Academic Search

    B. Gady; D. Schleef; R. Reifenberger; D. Rimai; L. P. Demejo

    1996-01-01

    The interaction force gradient between a micron-size polystyrene sphere and an atomically flat highly oriented pyrolytic graphite substrate has been analyzed as a function of surface-to-surface separation distance z0 using an oscillating cantilever technique. The interaction force gradient was found to have two contributions. For z0>=30 nm, an electrostatic force due to charges trapped on the polystyrene sphere dominates. For

  1. Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study

    PubMed Central

    2012-01-01

    Background There is a need for automated methods to learn general features of the interactions of a ligand class with its diverse set of protein receptors. An appropriate machine learning approach is Inductive Logic Programming (ILP), which automatically generates comprehensible rules in addition to prediction. The development of ILP systems which can learn rules of the complexity required for studies on protein structure remains a challenge. In this work we use a new ILP system, ProGolem, and demonstrate its performance on learning features of hexose-protein interactions. Results The rules induced by ProGolem detect interactions mediated by aromatics and by planar-polar residues, in addition to less common features such as the aromatic sandwich. The rules also reveal a previously unreported dependency for residues cys and leu. They also specify interactions involving aromatic and hydrogen bonding residues. This paper shows that Inductive Logic Programming implemented in ProGolem can derive rules giving structural features of protein/ligand interactions. Several of these rules are consistent with descriptions in the literature. Conclusions In addition to confirming literature results, ProGolem’s model has a 10-fold cross-validated predictive accuracy that is superior, at the 95% confidence level, to another ILP system previously used to study protein/hexose interactions and is comparable with state-of-the-art statistical learners. PMID:22783946

  2. Identification of human sperm proteins that interact with human zona pellucida3 (ZP3) using yeast two-hybrid system

    PubMed Central

    Naz, Rajesh K.; Dhandapani, Latha

    2010-01-01

    Sperm proteins that interact with zona pellucida 3 (ZP3) have not been clearly identified in humans. In the present study, the yeast two-hybrid (Y2H) system was used to identify human sperm proteins that interact with human ZP3. Human ZP3 cDNA was cloned into pAS2-1 yeast vector and used as bait to find reactive proteins in the human testis cDNA library. Six specific clones were obtained that were further confirmed for interaction using the mammalian two-hybrid system. These six clones showed homologies with several proteins in the GenBank database. Of these, the strongest ZP3 interacting protein, that shows 97% homology with ubiquitin associated protein-2 like (UBAP2L), was tested in the hemizona assay. UBAP2L antibodies significantly (p < 0.001) inhibited human sperm-zona binding in this assay. We conclude that the Y2H system is a useful strategy for identifying novel genes encoding proteins that interact with ZP proteins. To our knowledge, this is the first study using the Y2H system to identify sperm proteins that interact with human oocyte ZP3. Novel proteins identified using this system may find applications in elucidating the fertilization cascade, development of a new generation of non-steroidal contraceptives, and specific diagnosis and treatment of human infertility. PMID:19945174

  3. NMR identification of endogenous metabolites interacting with fatted and non-fatted human serum albumin in blood plasma: Fatty acids influence the HSA-metabolite interaction

    NASA Astrophysics Data System (ADS)

    Jupin, Marc; Michiels, Paul J.; Girard, Frederic C.; Spraul, Manfred; Wijmenga, Sybren S.

    2013-03-01

    Metabolites and their concentrations are direct reporters on body biochemistry. Thanks to technical developments metabolic profiling of body fluids, such as blood plasma, by for instance NMR has in the past decade become increasingly accurate enabling successful clinical diagnostics. Human Serum Albumin (HSA) is the main plasma protein (˜60% of all plasma protein) and responsible for the transport of endogenous (e.g. fatty acids) and exogenous metabolites, which it achieves thanks to its multiple binding sites and its flexibility. HSA has been extensively studied with regard to its binding of drugs (exogenous metabolites), but only to a lesser extent with regard to its binding of endogenous (non-fatty acid) metabolites. To obtain correct NMR measured metabolic profiles of blood plasma and/or potentially extract information on HSA and fatty acids content, it is necessary to characterize these endogenous metabolite/plasma protein interactions. Here, we investigate these metabolite-HSA interactions in blood plasma and blood plasma mimics. The latter contain the roughly twenty metabolites routinely detected by NMR (also most abundant) in normal relative concentrations with fatted or non-fatted HSA added or not. First, we find that chemical shift changes are small and seen only for a few of the metabolites. In contrast, a significant number of the metabolites display reduced resonance integrals and reduced free concentrations in the presence of HSA or fatted HSA. For slow-exchange (or strong) interactions, NMR resonance integrals report the free metabolite concentration, while for fast exchange (weak binding) the chemical shift reports on the binding. Hence, these metabolites bind strongly to HSA and/or fatted HSA, but to a limited degree because for most metabolites their concentration is smaller than the HSA concentration. Most interestingly, fatty acids decrease the metabolite-HSA binding quite significantly for most of the interacting metabolites. We further find that competition between the metabolites for binding is absent for most of these metabolites. These mappings in plasma mimics may thus open new opportunities for improved metabolic profiling of blood plasma. For instance, correct metabolite concentrations can be determined for the non-interacting metabolites and/or concentration corrections made for interacting metabolites. Secondly, the interacting metabolites could be used to act as reporters on HSA and fatty acid concentration in plasma, and thus potentially act as biomarker in diagnostic studies of trauma or cardiovascular diseases. Finally, we find in the blood plasma mimics that after ultrafiltration, commonly used to remove the protein from plasma, the measured concentration equals the total metabolite concentration, except for the strongest binding metabolite citrate.

  4. 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.

  5. Interaction of Chandipura Virus N and P Proteins: Identification of Two Mutually Exclusive Domains of N Involved in Interaction with P

    PubMed Central

    Sarkar, Sandipto; Mukherjee, Jishnu; Ganguly, Tridib; Chattopadhyay, Dhrubajyoti

    2012-01-01

    The nucleocapsid protein (N) and the phosphoprotein (P) of nonsegmented negative-strand (NNS) RNA viruses interact with each other to accomplish two crucial events necessary for the viral replication cycle. First, the P protein binds to the aggregation prone nascent N molecules maintaining them in a soluble monomeric (N0) form (N0-P complex). It is this form that is competent for specific encapsidation of the viral genome. Second, the P protein binds to oligomeric N in the nucleoprotein complex (N-RNA-P complex), and thereby facilitates the recruitment of the viral polymerase (L) onto its template. All previous attempts to study these complexes relied on co-expression of the two proteins in diverse systems. In this study, we have characterised these different modes of N-P interaction in detail and for the first time have been able to reconstitute these complexes individually in vitro in the chandipura virus (CHPV), a human pathogenic NNS RNA virus. Using a battery of truncated mutants of the N protein, we have been able to identify two mutually exclusive domains of N involved in differential interaction with the P protein. An unique N-terminal binding site, comprising of amino acids (aa) 1–180 form the N0-P interacting region, whereas, C-terminal residues spanning aa 320–390 is instrumental in N-RNA-P interactions. Significantly, the ex-vivo data also supports these observations. Based on these results, we suggest that the P protein acts as N-specific chaperone and thereby partially masking the N-N self-association region, which leads to the specific recognition of viral genome RNA by N0. PMID:22485180

  6. Identification of important residues of insulin-like peptide 5 and its receptor RXFP4 for ligand-receptor interactions.

    PubMed

    Wang, Xin-Yi; Guo, Yu-Qi; Shao, Xiao-Xia; Liu, Ya-Li; Xu, Zeng-Guang; Guo, Zhan-Yun

    2014-09-15

    Insulin-like peptide 5 (INSL5) is an insulin/relaxin superfamily peptide involved in the regulation of glucose homeostasis by activating its receptor RXFP4, which can also be activated by relaxin-3 in vitro. To determine the interaction mechanism of INSL5 with its receptor RXFP4, we studied their electrostatic interactions using a charge-exchange mutagenesis approach. First, we identified three negatively charged extracellular residues (Glu100, Asp104 and Glu182) in human RXFP4 that were important for receptor activation by wild-type INSL5. Second, we demonstrated that two positively charged B-chain Arg residues (B13Arg and B23Arg) in human INSL5 were involved in receptor binding and activation. Third, we proposed probable electrostatic interactions between INSL5 and RXFP4: the B-chain central B13Arg of INSL5 interacts with both Asp104 and Glu182 of RXFP4, meanwhile the B-chain C-terminal B23Arg of INSL5 interacts with both Glu100 and Asp104 of RXFP4. The present electrostatic interactions between INSL5 and RXFP4 were similar to our previously identified interactions between relaxin-3 and RXFP4, but had subtle differences that might be caused by the different B-chain C-terminal conformations of relaxin-3 and INSL5 because a dipeptide exchange at the B-chain C-terminus significantly decreased the activity of INSL5 and relaxin-3 to receptor RXFP4. PMID:25043977

  7. 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

  8. 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

  9. RUNX1 is a key target in t(4;11) leukemias that contributes to gene activation through an AF4-MLL complex interaction.

    PubMed

    Wilkinson, Adam C; Ballabio, Erica; Geng, Huimin; North, Phillip; Tapia, Marta; Kerry, Jon; Biswas, Debabrata; Roeder, Robert G; Allis, C David; Melnick, Ari; de Bruijn, Marella F T R; Milne, Thomas A

    2013-01-31

    The Mixed Lineage Leukemia (MLL) protein is an important epigenetic regulator required for the maintenance of gene activation during development. MLL chromosomal translocations produce novel fusion proteins that cause aggressive leukemias in humans. Individual MLL fusion proteins have distinct leukemic phenotypes even when expressed in the same cell type, but how this distinction is delineated on a molecular level is poorly understood. Here, we highlight a unique molecular mechanism whereby the RUNX1 gene is directly activated by MLL-AF4 and the RUNX1 protein interacts with the product of the reciprocal AF4-MLL translocation. These results support a mechanism of transformation whereby two oncogenic fusion proteins cooperate by activating a target gene and then modulating the function of its downstream product. PMID:23352661

  10. Identification of two Amino Acids in the C-terminal Domain of Mouse CRY2 Essential for PER2 Interaction

    PubMed Central

    2010-01-01

    Background Cryptochromes (CRYs) are a class of flavoprotein blue-light signaling receptors found in plants and animals, and they control plant development and the entrainment of circadian rhythms. They also act as integral parts of the central circadian oscillator in humans and other animals. In mammals, the CLOCK-BMAL1 heterodimer activates transcription of the Per and Cry genes as well as clock-regulated genes. The PER2 proteins interact with CRY and CKI?, and the resulting ternary complexes translocate into the nucleus, where they negatively regulate the transcription of Per and Cry core clock genes and other clock-regulated output genes. Recent studies have indicated that the extended C-termini of the mammalian CRYs, as compared to photolyase proteins, interact with PER proteins. Results We identified a region on mCRY2 (between residues 493 and 512) responsible for direct physical interaction with mPER2 by mammalian two-hybrid and co-immunoprecipitation assays. Moreover, using oligonucleotide-based degenerate PCR, we discovered that mutation of Arg-501 and Lys-503 of mCRY2 within this C-terminal region totally abolishes interaction with PER2. Conclusions Our results identify mCRY2 amino acid residues that interact with the mPER2 binding region and suggest the potential for rational drug design to inhibit CRYs for specific therapeutic approaches. PMID:20840750

  11. Identification of a Suppressive Mechanism for Hedgehog Signaling through a Novel Interaction of Gli with 14-3-3*

    PubMed Central

    Asaoka, Yoshinari; Kanai, Fumihiko; Ichimura, Tohru; Tateishi, Keisuke; Tanaka, Yasuo; Ohta, Miki; Seto, Motoko; Tada, Motohisa; Ijichi, Hideaki; Ikenoue, Tsuneo; Kawabe, Takao; Isobe, Toshiaki; Yaffe, Michael B.; Omata, Masao

    2010-01-01

    Gli transcription factors are central effectors of Hedgehog signaling in development and tumorigenesis. Using a tandem affinity purification (TAP) strategy and mass spectrometry, we have found that Gli1 interacts with 14-3-3?, and that Gli2 and Gli3 also bind to 14-3-3? through homologous sites. This interaction depends on their phosphorylation, and cAMP-dependent protein kinase (PKA), a known negative regulator of Hedgehog signaling serves as a responsible kinase. A Gli2 mutant engineered to eliminate this interaction exhibited increased transcriptional activity (2 ? 3×). Transcriptional repression by 14-3-3 binding was also observed with Gli3, when its N-terminal repressor domain was deleted. The phosphorylation sites responsible for the binding to 14-3-3 are distinct from those required for proteolysis, the known mechanism for PKA-induced repression of Hh signaling. Our data propose a novel mechanism in which PKA down-regulates Hedgehog signaling by promoting the interaction between Gli and 14-3-3 as well as proteolysis. Given the certain neuronal or malignant disorders in human caused by the abnormality of 17p13 encompassing 14-3-3? overlap with increased Hh signaling, the Gli-14-3-3 interaction may have pathological significance for those human diseases. PMID:19996099

  12. 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.

  13. Sortase A mediated site-specific immobilization for identification of protein interactions in affinity purification-mass spectrometry experiments.

    PubMed

    Kuropka, Benno; Royla, Nadine; Freund, Christian; Krause, Eberhard

    2015-04-01

    Proteomics approaches using MS in combination with affinity purification have emerged as powerful tools to study protein-protein interactions. Here we make use of the specificity of sortase A transpeptidation reaction to prepare affinity matrices in which a protein bait is covalently linked to the matrix via a short C-terminal linker region. As a result of this site-directed immobilization, the bait remains functionally accessible to protein interactions. To apply this approach, we performed SILAC-based pull-down experiments and demonstrate the suitability of the approach. PMID:25504886

  14. VISUAL KEYS TO ARCHITECTURAL DESIGN

    Microsoft Academic Search

    H. NEUCKERMANS; A. HEYLIGHEN; KU Leuven CADLAB; Kasteel van Arenberg Kasteelpark; P. MORISSE

    This paper presents a new mechanism to access and interact with DYNAMO, a collective case base for architectural design developed as a Web-based tool. The system is fully operational since a few years in the context of architectural design education as well as for seminars on architectural theory. We have now developed a set of visual keys structured at the

  15. Filamin B plays a key role in vascular endothelial growth factor-induced endothelial cell motility through its interaction with Rac-1 and Vav-2.

    PubMed

    Del Valle-Pérez, Beatriz; Martínez, Vanesa Gabriela; Lacasa-Salavert, Cristina; Figueras, Agnès; Shapiro, Sandor S; Takafuta, Toshiro; Casanovas, Oriol; Capellà, Gabriel; Ventura, Francesc; Viñals, Francesc

    2010-04-01

    Actin-binding proteins filamin A (FLNA) and B (FLNB) are expressed in endothelial cells and play an essential role during vascular development. In order to investigate their role in adult endothelial cell function, we initially confirmed their expression pattern in different adult mouse tissues and cultured cell lines and found that FLNB expression is concentrated mainly in endothelial cells, whereas FLNA is more ubiquitously expressed. Functionally, small interfering RNA knockdown of endogenous FLNB in human umbilical vein endothelial cells inhibited vascular endothelial growth factor (VEGF)-induced in vitro angiogenesis by decreasing endothelial cell migration capacity, whereas FLNA ablation did not alter these parameters. Moreover, FLNB-depleted cells increased their substrate adhesion with more focal adhesions. The molecular mechanism underlying this effect implicates modulation of small GTP-binding protein Rac-1 localization and activity, with altered activation of its downstream effectors p21 protein Cdc42/Rac-activated kinase (PAK)-4/5/6 and its activating guanine nucleotide exchange factor Vav-2. Moreover, our results suggest the existence of a signaling complex, including FLNB, Rac-1, and Vav-2, under basal conditions that would further interact with VEGFR2 and integrin alphavbeta5 after VEGF stimulation. In conclusion, our results reveal a crucial role for FLNB in endothelial cell migration and in the angiogenic process in adult endothelial cells. PMID:20110358

  16. 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

  17. Identification of nucleolin as a lipid-raft-dependent ?1-integrin-interacting protein in A375 cell migration.

    PubMed

    Bi, Jiajia; Wang, Ruifei; Zhang, Yue; Han, Xiaoqing; Ampah, Khamal Kwesi; Liu, Wenguang; Zeng, Xianlu

    2013-12-01

    Lipid rafts are related to cell surface receptor function. Integrin is a major surface receptor protein in cell adhesion and migration on the extracellular matrix (ECM). Here, we showed that lipid rafts played a critical role in human melanoma A375 cell spreading and migration on fibronectin; an important component of the ECM that interacts with ?1 integrin. We found that the disruption of lipid rafts did not markedly inhibit the expression and activation of ?1 integrin. By coimmunoprecipitation and mass spectrometry, we investigated the influence of lipid rafts on the ?1 integrin complex and identified nucleolin as a potential lipid-raft-dependent ?1-integrin-interacting protein. Upon confirmation of the interaction between ?1 integrin and nucleolin, further studies revealed that nucleolin colocalized with ?1 integrin in lipid rafts and raft disruption interrupted their association. In addition, knockdown of nucleolin markedly attenuated A375 cell spreading and migration on fibronectin. Taken together, we demonstrated that nucleolin is a critical lipid-raft-dependent ?1-integrin-interacting protein in A375 cell spreading and migration on fibronectin. PMID:24292944

  18. Identification of amelotin- and ODAM-interacting enamel matrix proteins using the yeast two-hybrid system.

    PubMed

    Holcroft, James; Ganss, Bernhard

    2011-12-01

    The formation of dental enamel is a prototype of functional tissue development through biomineralization. Amelotin (AMTN) is a recently discovered secreted enamel protein predominantly expressed during the maturation stage of enamel formation. It accumulates in a basal lamina-like structure at the interface between ameloblasts and enamel mineral and it co-localizes with another recently described enamel protein, odontogenic ameloblast-associated protein (ODAM). The purpose of this study was to determine whether AMTN and ODAM bind to each other and/or to other well-established enamel matrix proteins. The coding sequences of all enamel proteins were cloned into appropriate vectors of the GAL4-based Matchmaker Gold Yeast Two-Hybrid System. The growth of yeast cells on selective media and color induction were used as indicators for reporter gene expression through protein-protein interactions in combinations of prey and bait constructs. We found that AMTN interacts with itself and with ODAM, but not with amelogenin (AMEL), ameloblastin (AMBN), or enamelin (ENAM). Using ODAM as bait, the interaction with AMTN was confirmed. Furthermore, ODAM was found to bind to itself and to AMBN, as well as weakly to AMEL but not to ENAM. We propose a model where the distinct expression of AMTN and ODAM and their interaction are involved in defining the enamel microstructure at the enamel surface. PMID:22243260

  19. Identification of Nucleolin as a Lipid-Raft-Dependent ?1-Integrin-Interacting Protein in A375 Cell Migration

    PubMed Central

    Bi, Jiajia; Wang, Ruifei; Zhang, Yue; Han, Xiaoqing; Ampah, Khamal Kwesi; Liu, Wenguang; Zeng, Xianlu

    2013-01-01

    Lipid rafts are related to cell surface receptor function. Integrin is a major surface receptor protein in cell adhesion and migration on the extracellular matrix (ECM). Here, we showed that lipid rafts played a critical role in human melanoma A375 cell spreading and migration on fibronectin; an important component of the ECM that interacts with ?1 integrin. We found that the disruption of lipid rafts did not markedly inhibit the expression and activation of ?1 integrin. By coimmunoprecipitation and mass spectrometry, we investigated the influence of lipid rafts on the ?1 integrin complex and identified nucleolin as a potential lipid-raft-dependent ?1-integrin-interacting protein. Upon confirmation of the interaction between ?1 integrin and nucleolin, further studies revealed that nucleolin colocalized with ?1 integrin in lipid rafts and raft disruption interrupted their association. In addition, knockdown of nucleolin markedly attenuated A375 cell spreading and migration on fibronectin. Taken together, we demonstrated that nucleolin is a critical lipid-raft-dependent ?1-integrin-interacting protein in A375 cell spreading and migration on fibronectin. PMID:24292944

  20. Identification of a new lactone contributing to overripe orange aroma in Bordeaux dessert wines via perceptual interaction phenomena.

    PubMed

    Stamatopoulos, Panagiotis; Frérot, Eric; Tempère, Sophie; Pons, Alexandre; Darriet, Philippe

    2014-03-26

    Recent studies have demonstrated the existence of a typical sensory concept for Bordeaux dessert wines, including the world famous wines of Sauternes. Volatile compounds from several chemical families (thiols, aldehydes, and lactones) were identified and correlated with aromatic typicality in these wines. However, these studies were unable to indicate "key" aromas of overripe fruits, especially overripe orange. The alternative strategy developed in this research combined both analytical and sensory studies of fractions of dessert wine extracts obtained by semipreparative high-performance liquid chromatography (HPLC). Multidimensional gas chromatography coupled to olfactometry and mass spectrometry (MDGC-O/MS) was applied to some of the HPLC fractions recalling "overripe fruit", and a new lactone, 2-nonen-4-olide, was identified. Reconstitution and omission tests using the HPLC fractions highlighted the importance of specific compounds, particularly 2-nonen-4-olide, in the expression of overripe orange notes. Although this lactone presents minty and fruity odors, its key contribution to the typical aroma of orange in Bordeaux dessert wines was revealed through perceptual blending. PMID:24559261

  1. 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

  2. A Quantum Cipher with Near Optimal Key-Recycling

    E-print Network

    Salvail, Louis

    A Quantum Cipher with Near Optimal Key-Recycling Ivan Damg°ard, Thomas Brochmann Pedersen an arbitrary number of message bits, independently of the length of the initial key. Moreover, the key-recycling of interaction and more communication. Key-words: quantum cryptography, key-recycling, unconditional security

  3. Identification of significant pathways in gastric cancer based on protein-protein interaction networks and cluster analysis

    PubMed Central

    Hu, Kongwang; Chen, Feihu

    2012-01-01

    Gastric cancer is one of the most common and lethal cancers worldwide. However, despite its clinical importance, the regulatory mechanisms involved in the aggressiveness of this cancer are still poorly understood. A better understanding of the biology, genetics and molecular mechanisms of gastric cancer would be useful in developing novel targeted approaches for treating this disease. In this study we used protein-protein interaction networks and cluster analysis to comprehensively investigate the cellular pathways involved in gastric cancer. A primary immunodeficiency pathway, focal adhesion, ECM-receptor interactions and the metabolism of xenobiotics by cytochrome P450 were identified as four important pathways associated with the progression of gastric cancer. The genes in these pathways, e.g., ZAP70, IGLL1, CD79A, COL6A3, COL3A1, COL1A1, CYP2C18 and CYP2C9, may be considered as potential therapeutic targets for gastric cancer. PMID:23055812

  4. Purification of Polyglutamine Aggregates and Identification of Elongation Factor1 and Heat Shock Protein 84 as Aggregate Interacting Proteins

    Microsoft Academic Search

    Kenichi Mitsui; Hiroshi Nakayama; Takumi Akagi; Munenori Nekooki; Kenji Ohtawa; Koji Takio; Tsutomu Hashikawa; Nobuyuki Nukina

    2002-01-01

    Aggregates of green fluorescent protein (GFP)-fused truncated N-terminal huntingtin containing abnormally long polyglutamine tracts (150 repeats of glutamine residue) were purified from an ecdysone-inducible mutant neuro2A cell line (HD150Q-28) by using a fluorescence-activated cell sorter. To analyze the aggregate-interacting proteins, we subjected the purified ag- gregates to SDS-PAGE; prominent protein bands in the gel were digested with Achromobactor lysyl endopeptidase,

  5. 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

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

    PubMed

    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

  7. Identification of Amino Acids that Account for Long-Range Interactions in Two Triosephosphate Isomerases from Pathogenic Trypanosomes

    SciTech Connect

    García-Torres, Itzhel; Cabrera, Nallely; Torres-Larios, Alfredo; Rodríguez-Bolaños, Mónica; Díaz-Mazariegos, Selma; Gómez-Puyou, Armando; Perez-Montfort, Ruy (UNAM-Mexico)

    2012-04-02

    For a better comprehension of the structure-function relationship in proteins it is necessary to identify the amino acids that are relevant for measurable protein functions. Because of the numerous contacts that amino acids establish within proteins and the cooperative nature of their interactions, it is difficult to achieve this goal. Thus, the study of protein-ligand interactions is usually focused on local environmental structural differences. Here, using a pair of triosephosphate isomerase enzymes with extremely high homology from two different organisms, we demonstrate that the control of a seventy-fold difference in reactivity of the interface cysteine is located in several amino acids from two structurally unrelated regions that do not contact the cysteine sensitive to the sulfhydryl reagent methylmethane sulfonate, nor the residues in its immediate vicinity. The change in reactivity is due to an increase in the apparent pKa of the interface cysteine produced by the mutated residues. Our work, which involved grafting systematically portions of one protein into the other protein, revealed unsuspected and multisite long-range interactions that modulate the properties of the interface cysteines and has general implications for future studies on protein structure-function relationships.

  8. 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

  9. 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

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

    PubMed Central

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

    2014-01-01

    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

  11. 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

  12. 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

  13. Identification of the retinol-binding protein (RBP) interaction site and functional state of RBPs for the membrane receptor.

    PubMed

    Redondo, Clara; Vouropoulou, Maria; Evans, Jonathan; Findlay, John B C

    2008-04-01

    This laboratory has advanced a model whereby retinol is transported around the body bound to retinol-binding protein (RBP), is transferred across the membrane of cells by a specific receptor/transporter, and is picked up from the membrane by an intracellular homolog, cellular retinol-binding protein (CRBP). This process involves a number of protein-protein interactions, and we hypothesized that conformational changes were an integral part of the retinol transfer mechanism. Previously we identified the potential interaction site on RBP for its membrane receptor. Here we confirm by the analysis of chimera containing a grafted CD loop from RBP that this is indeed the receptor interaction site and go on to demonstrate that the conformational changes that occur to this region on the apo to holo transition in RBP also take place in a chimera binding a quite different ligand, thus establishing the concept. We have also gone on to support the hypothesis that CRBP may also bind to a receptor in the membrane. Previous evidence has indicated that one such receptor might be lecithin:retinol acyltransferase, an enzyme that catalyzes retinol esterification. Here we provide the first evidence that the plasma membrane receptor for RBP could be the same as that for CRBP. This observation offers support for the intracellular phase of the uptake process for retinol, providing an efficient and highly unique mechanism in eukaryotic biology. PMID:17991731

  14. 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.…

  15. Team building: key to executive success.

    PubMed

    Jacobsen-Webb, M L

    1985-02-01

    The key to executive success is management of the information overload provided by today's high technology era. Team building, through identification of behavioral styles, helps to enhance self-esteem, utilize inherent skills of individuals, and maximize decision making. The style of the team leader who shares leadership promotes communication patterns that lead to participatory management and harmony within institutions. PMID:3844447

  16. Identification of two p23 co-chaperone isoforms in Leishmania braziliensis exhibiting similar structures and Hsp90 interaction properties despite divergent stabilities.

    PubMed

    Batista, Fernanda A H; Almeida, Glessler S; Seraphim, Thiago V; Silva, Kelly P; Murta, Silvane M F; Barbosa, Leandro R S; Borges, Júlio C

    2015-01-01

    The small acidic protein called p23 acts as a co-chaperone for heat-shock protein of 90 kDa (Hsp90) during its ATPase cycle. p23 proteins inhibit Hsp90 ATPase activity and show intrinsic chaperone activity. A search for p23 in protozoa, especially trypanosomatids, led us to identify two putative proteins in the Leishmania braziliensis genome that share approximately 30% identity with each other and with the human p23. To understand the presence of two p23 isoforms in trypanosomatids, we obtained the recombinant p23 proteins of L. braziliensis (named Lbp23A and Lbp23B) and performed structural and functional studies. The recombinant proteins share similar solution structures; however, temperature- and chemical-induced unfolding experiments showed that Lbp23A is more stable than Lbp23B, suggesting that they may have different functions. Lbp23B prevented the temperature-induced aggregation of malic dehydrogenase more efficiently than did Lbp23A, whereas the two proteins had equivalent efficiencies with respect to preventing the temperature-induced aggregation of luciferase. Both proteins interacted with L. braziliensis Hsp90 (LbHsp90) and inhibited its ATPase activity, although their efficiencies differed. In vivo identification studies suggested that both proteins are present in L. braziliensis cells grown under different conditions, although Lbp23B may undergo post-translation modifications. Interaction studies indicated that both Lbp23 proteins interact with LbHsp90. Taken together, our data suggest that the two protozoa p23 isoforms act similarly when regulating Hsp90 function. However, they also have some differences, indicating that the L. braziliensis Hsp90 machine has features providing an opportunity for novel forms of selective inhibition of protozoan Hsp90. PMID:25369258

  17. Identification of human protein complexes from local sub-graphs of protein-protein interaction network based on random forest with topological structure features.

    PubMed

    Li, Zhan-Chao; Lai, Yan-Hua; Chen, Li-Li; Zhou, Xuan; Dai, Zong; Zou, Xiao-Yong

    2012-03-01

    In the post-genomic era, one of the most important and challenging tasks is to identify protein complexes and further elucidate its molecular mechanisms in specific biological processes. Previous computational approaches usually identify protein complexes from protein interaction network based on dense sub-graphs and incomplete priori information. Additionally, the computational approaches have little concern about the biological properties of proteins and there is no a common evaluation metric to evaluate the performance. So, it is necessary to construct novel method for identifying protein complexes and elucidating the function of protein complexes. In this study, a novel approach is proposed to identify protein complexes using random forest and topological structure. Each protein complex is represented by a graph of interactions, where descriptor of the protein primary structure is used to characterize biological properties of protein and vertex is weighted by the descriptor. The topological structure features are developed and used to characterize protein complexes. Random forest algorithm is utilized to build prediction model and identify protein complexes from local sub-graphs instead of dense sub-graphs. As a demonstration, the proposed approach is applied to protein interaction data in human, and the satisfied results are obtained with accuracy of 80.24%, sensitivity of 81.94%, specificity of 80.07%, and Matthew's correlation coefficient of 0.4087 in 10-fold cross-validation test. Some new protein complexes are identified, and analysis based on Gene Ontology shows that the complexes are likely to be true complexes and play important roles in the pathogenesis of some diseases. PCI-RFTS, a corresponding executable program for protein complexes identification, can be acquired freely on request from the authors. PMID:22305895

  18. Evaluating the effects of machine pre-annotation and an interactive annotation interface on manual de-identification of clinical text.

    PubMed

    South, Brett R; Mowery, Danielle; Suo, Ying; Leng, Jianwei; Ferrández, Óscar; Meystre, Stephane M; Chapman, Wendy W

    2014-08-01

    The Health Insurance Portability and Accountability Act (HIPAA) Safe Harbor method requires removal of 18 types of protected health information (PHI) from clinical documents to be considered "de-identified" prior to use for research purposes. Human review of PHI elements from a large corpus of clinical documents can be tedious and error-prone. Indeed, multiple annotators may be required to consistently redact information that represents each PHI class. Automated de-identification has the potential to improve annotation quality and reduce annotation time. For instance, using machine-assisted annotation by combining de-identification system outputs used as pre-annotations and an interactive annotation interface to provide annotators with PHI annotations for "curation" rather than manual annotation from "scratch" on raw clinical documents. In order to assess whether machine-assisted annotation improves the reliability and accuracy of the reference standard quality and reduces annotation effort, we conducted an annotation experiment. In this annotation study, we assessed the generalizability of the VA Consortium for Healthcare Informatics Research (CHIR) annotation schema and guidelines applied to a corpus of publicly available clinical documents called MTSamples. Specifically, our goals were to (1) characterize a heterogeneous corpus of clinical documents manually annotated for risk-ranked PHI and other annotation types (clinical eponyms and person relations), (2) evaluate how well annotators apply the CHIR schema to the heterogeneous corpus, (3) compare whether machine-assisted annotation (experiment) improves annotation quality and reduces annotation time compared to manual annotation (control), and (4) assess the change in quality of reference standard coverage with each added annotator's annotations. PMID:24859155

  19. Identification of a Skp1-Like Protein Interacting with SFB, the Pollen S Determinant of the Gametophytic Self-Incompatibility in Prunus1[W

    PubMed Central

    Matsumoto, Daiki; Yamane, Hisayo; Abe, Kazuyuki; Tao, Ryutaro

    2012-01-01

    Many species in Rosaceae, Solanaceae, and Plantaginaceae exhibit S-RNase-based self-incompatibility (SI). In this system, the pistil and pollen specificities are determined by S-RNase and the S locus F-box protein, respectively. The pollen S determinant F-box protein in Prunus (Rosaceae) is referred to by two different terms, SFB (for S-haplotype-specific F-box protein) and SLF (for S locus F box), whereas it is called SLF in Solanaceae and Plantaginaceae. Prunus SFB is thought to be a molecule indispensable for its cognate S-RNase to exert cytotoxicity and to arrest pollen tube growth in incompatible reactions. Although recent studies have demonstrated the molecular function of SCFSLF in the SI reaction of Solanaceae and Plantaginaceae, how SFB participates in the Prunus SI mechanism remains to be elucidated. Here we report the identification of sweet cherry (Prunus avium) SFB (PavSFB)-interacting Skp1-like1 (PavSSK1) using a yeast (Saccharomyces cerevisiae) two-hybrid screening against the pollen cDNA library. Phylogenetic analysis showed that PavSSK1 belongs to the same clade as Antirrhinum hispanicum SLF-interacting Skp1-like1 and Petunia hybrida SLF-interacting Skp1-like1 (PhSSK1). In yeast, PavSSK1 interacted not only with PavSFBs from different S haplotypes and Cullin1-likes (PavCul1s), but also with S-locus F-box-likes. A pull-down assay confirmed the interactions between PavSSK1 and PavSFB and between PavSSK1 and PavCul1s. These results collectively indicate that PavSSK1 could be a functional component of the SCF complex and that PavSFB may function as a component of the SCF complex. We discuss the molecular function of PavSFB in self-/nonself-recognition in the gametophytic SI of Prunus. PMID:22548785

  20. Interaction Domain of Glycoproteins gB and gH of Marek's Disease Virus and Identification of an Antiviral Peptide with Dual Functions

    PubMed Central

    Chi, Xiao-Jing; Lu, Yi-Xin; Zhao, Peng; Li, Chuan-Gen; Wang, Xiao-Jia; Wang, Ming

    2013-01-01

    Our previous study reported that both glycoproteins gB and gH of the herpesvirus Marek's disease virus (MDV) contain eleven potential heptad repeat domains. These domains overlap with ?-helix-enriched hydrophobic regions, including the gH-derived HR1 (gHH1) and HR3 (gHH3) and gB-derived HR1 (gBH1) regions, which demonstrate effective antiviral activity, with 50% inhibitory concentrations (IC50) of less than 12 µM. Plaque formation and chicken embryo infection assays confirmed these results. In this study, biochemical and biophysical analyses detected potential interactions between these peptides. gHH1, gHH3, and gBH1 were found to interact with each other in pairs. The complex formed by gHH3 and gBH1 showed the most stable interaction at a molar ratio of 1:3, the binding between gHH1 and gBH1 was relatively weak, and no interaction was observed between the three HR peptides. These results indicate that gHH3 and gBH1 are likely the key contributors to the interaction between gB and gH. Furthermore, each HR peptide from herpesvirus glycoproteins did not effectively inhibit virus infection compared with peptides from a class I enveloped virus. In this report, the HR mimic peptide modified with a double glutamic acid (EE) or a double lysine (KK) at the non-interactive sites (i.e., solvent-accessible sites) did not noticeably affect the antiviral activity compared with the wild-type HR peptide, whereas tandem peptides from gH-derived gHH1 and gB-derived gBH1 (i.e., gBH1-Linker-gHH1) produced efficient antiviral effects, unlike the individual peptides. The proposed interpretation of inhibition of entry has been addressed. Our results support the hypothesis that the interaction domain between glycoproteins gH and gB is a critical target in the design of inhibitors of herpesvirus infection. PMID:23405092

  1. 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

  2. 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

  3. Identification of protostellar clusters in the inner part of the milky way : Interaction between the ISM and star forming regions.

    NASA Astrophysics Data System (ADS)

    Beuret, M.; Billot, N.; Cambrésy, L.; Elia, D.; Molinari, S.; Pezzuto, S.; Pestalozzi, M.; Schisano, E.

    2014-12-01

    Interactions between the interstellar medium (ISM) and young stellar objects (YSO) need to be investigated to better understand star formation. We used the Minimum Spanning Tree (MST) method to identify protostellar clusters in the inner part of galactic plane. Using heliocentric distance estimates, we obtained about 230 clusters over a 140 × 2 square degree region. Most of these clusters are correlated with Infrared Dark Cloud (IRDC) or H II regions. We conclude that clustering is more important for protostars than for prestellar clumps and that a strong correlation can be established between the distribution of H II regions, known star formation complexes and the YSOs identified in the Hi-GAL data.

  4. 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

  5. Identification of SH3 Domain Proteins Interacting with the Cytoplasmic Tail of the A Disintegrin and Metalloprotease 10 (ADAM10)

    PubMed Central

    Ebsen, Henriette; Lettau, Marcus; Kabelitz, Dieter; Janssen, Ottmar

    2014-01-01

    The a disintegrin and metalloproteases (ADAMs) play a pivotal role in the control of development, adhesion, migration, inflammation and cancer. Although numerous substrates of ADAM10 have been identified, the regulation of its surface expression and proteolytic activity is still poorly defined. One current hypothesis is that both processes are in part modulated by protein-protein interactions mediated by the intracellular portion of the protease. For related proteases, especially proline-rich regions serving as docking sites for Src homology domain 3 (SH3) domain-containing proteins proved to be important for mediating regulatory interactions. In order to identify ADAM10-binding SH3 domain proteins, we screened the All SH3 Domain Phager library comprising 305 human SH3 domains using a GST fusion protein with the intracellular region of human ADAM10 as a bait for selection. Of a total of 291 analyzed phage clones, we found 38 SH3 domains that were precipitated with the ADAM10-derived fusion protein but not with GST. We verified the binding to the cytosolic portion of ADAM10 for several candidates by co-immunoprecipitation and/or pull down analyses. Intriguingly, several of the identified proteins have been implicated in regulating surface appearance and/or proteolytic activity of related ADAMs. Thus, it seems likely that they also play a role in ADAM10 biology. PMID:25036101

  6. Single-Cell Analysis of Thymocyte Differentiation: Identification of Transcription Factor Interactions and a Major Stochastic Component in ??-Lineage Commitment

    PubMed Central

    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

  7. Large scale identification of genes involved in plant-fungal interactions using Illumina's sequencing-by-synthesis technology.

    PubMed

    Venu, R C; Zhang, Yuan; Weaver, Brian; Carswell, Peter; Mitchell, Thomas K; Meyers, Blake C; Boehm, Michael J; Wang, Guo-Liang

    2011-01-01

    Deep transcriptome profiling of pathogen-infected tissues enhances the understanding of molecular mechanisms underlying host-pathogen interactions. Illumina's next generation sequencing technology sequencing-by-synthesis (SBS) is a powerful tool to rapidly sequence genomes and transcriptomes at an affordable rate. We modified the procedure for SBS library construction to significantly increase the efficiency of library construction. Using our improved method, two Sclerotinia homoeocarpa libraries were constructed from mycelia grown in potato dextrose broth (PDB) or potato dextrose agar (PDA) for 96 h, respectively, and two creeping bentgrass libraries were constructed from leaves 96 h after inoculation with S. homoeocarpa or water sprayed, respectively. About 4-7 million mRNA signatures were sequenced from each library. Sequence analysis using BLAST was performed against sequenced fungal genomes and rice genomic sequence to identify the expressed genes in both S. homoeocarpa mycelia and creeping bentgrass. Bioinformatic analysis identified many expressed genes in the pathogen and host. A public database to access the sequence data was developed at http://www.dstidb.org . Our results demonstrate how SBS technology can unravel transcriptome complexity during the creeping bentgrass-S. homoeocarpa interaction. PMID:21590420

  8. 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

  9. 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

  10. Key amino acid residues involved in multi-point binding interactions between brazzein, a sweet protein, and the T1R2-T1R3 human sweet receptor

    PubMed Central

    Assadi-Porter, Fariba M.; Maillet, Emeline L.; Radek, James T.; Quijada, Jeniffer; Markley, John L.; Max, Marianna

    2010-01-01

    The sweet protein brazzein activates the human sweet receptor, a heterodimeric G-protein coupled receptor (GPCR) composed of subunits T1R2 and T1R3. In order to elucidate the key amino acid(s) responsible for this interaction, we mutated residues in brazzein and each of the two subunits of the receptor. The effects of brazzein mutations were assayed by a human taste panel and by an in vitro assay involving receptor subunits expressed recombinantly in human embryonic kidney cells; the effects of the receptor mutations were assayed by the in vitro assay. We mutated surface residues of brazzein at three putative interaction sites: Site 1 (Loop43), Site 2 (N- and C-terminus and adjacent Glu36, Loop33), and Site 3 (Loop9–19). Basic residues in Site 1 and acidic residues in Site 2 were essential for positive responses from each assay. Mutation of Y39A (Site 1) greatly reduced positive responses. A bulky side chain at position 54 (Site 2), rather than a side chain with hydrogen bonding potential, was required for positive responses as was the presence of the native disulfide bond in Loop 9–19 (Site 3). Results from mutagenesis and chimeras of the receptor indicated that brazzein interacts with both T1R2 and T1R3 and that the Venus fly trap module of T1R2 is important for brazzein agonism. With one exception, all mutations of receptor residues at putative interaction sites predicted by wedge models failed to yield the expected decrease in the brazzein response. The exception, hT1R2:R217A-hT1R3, which contained a substitution in lobe 2 at the interface between the two subunits, exhibited a small selective decrease in brazzein activity. However, because the mutation was found to increase the positive cooperativity of binding by multiple ligands proposed to bind both T1R subunits (brazzein, monellin, and sucralose) but not those that bind to a single subunit (neotame and cyclamate), we suggest that this site in involved in subunit-subunit interaction rather than direct brazzein binding. Results from this study support a multipoint interaction between brazzein and the sweet receptor by some mechanism other than the proposed wedge models. PMID:20302879

  11. Identification of extracellular signal-regulated kinase 3 as a new interaction partner of cyclin D3

    SciTech Connect

    Sun Maoyun [State Key Laboratory of Genetic Engineering and Gene Research Center, Shanghai Medical College of Fudan University, Shanghai 200032 (China); Wei Yuanyan [State Key Laboratory of Genetic Engineering and Gene Research Center, Shanghai Medical College of Fudan University, Shanghai 200032 (China); Yao Luyang [State Key Laboratory of Genetic Engineering and Gene Research Center, Shanghai Medical College of Fudan University, Shanghai 200032 (China); Xie Jianhui [State Key Laboratory of Genetic Engineering and Gene Research Center, Shanghai Medical College of Fudan University, Shanghai 200032 (China); Chen Xiaoning [State Key Laboratory of Genetic Engineering and Gene Research Center, Shanghai Medical College of Fudan University, Shanghai 200032 (China); Wang Hanzhou [State Key Laboratory of Genetic Engineering and Gene Research Center, Shanghai Medical College of Fudan University, Shanghai 200032 (China); Jiang Jianhai [State Key Laboratory of Genetic Engineering and Gene Research Center, Shanghai Medical College of Fudan University, Shanghai 200032 (China); Gu Jianxin [State Key Laboratory of Genetic Engineering and Gene Research Center, Shanghai Medical College of Fudan University, Shanghai 200032 (China)]. E-mail: jxgu@shmu.edu.cn

    2006-02-03

    Cyclin D3, like cyclin D1 and D2 isoforms, is a crucial component of the core cell cycle machinery in mammalian cells. It also exhibits its unique properties in many other physiological processes. In the present study, using yeast two-hybrid screening, we identified ERK3, an atypical mitogen-activated protein kinase (MAPK), as a cyclin D3 binding partner. GST pull-down assays showed that cyclin D3 interacts directly and specifically with ERK3 in vitro. The binding of cyclin D3 and ERK3 was further confirmed in vivo by co-immunoprecipitation assay and confocal microscopic analysis. Moreover, carboxy-terminal extension of ERK3 was responsible for its association with intact cyclin D3. These findings further expand distinct roles of cyclin D3 and suggest the potential activity of ERK3 in cell proliferation.

  12. Identification of Colorectal Cancer Related Genes with mRMR and Shortest Path in Protein-Protein Interaction Network

    PubMed Central

    Liu, Lei; Cai, Yu-Dong; Chou, Kuo-Chen

    2012-01-01

    One of the most important and challenging problems in biomedicine and genomics is how to identify the disease genes. In this study, we developed a computational method to identify colorectal cancer-related genes based on (i) the gene expression profiles, and (ii) the shortest path analysis of functional protein association networks. The former has been used to select differentially expressed genes as disease genes for quite a long time, while the latter has been widely used to study the mechanism of diseases. With the existing protein-protein interaction data from STRING (Search Tool for the Retrieval of Interacting Genes), a weighted functional protein association network was constructed. By means of the mRMR (Maximum Relevance Minimum Redundancy) approach, six genes were identified that can distinguish the colorectal tumors and normal adjacent colonic tissues from their gene expression profiles. Meanwhile, according to the shortest path approach, we further found an additional 35 genes, of which some have been reported to be relevant to colorectal cancer and some are very likely to be relevant to it. Interestingly, the genes we identified from both the gene expression profiles and the functional protein association network have more cancer genes than the genes identified from the gene expression profiles alone. Besides, these genes also had greater functional similarity with the reported colorectal cancer genes than the genes identified from the gene expression profiles alone. All these indicate that our method as presented in this paper is quite promising. The method may become a useful tool, or at least plays a complementary role to the existing method, for identifying colorectal cancer genes. It has not escaped our notice that the method can be applied to identify the genes of other diseases as well. PMID:22496748

  13. Identification of QTLs with additive, epistatic and QTL × development interaction effects for seed dormancy in rice.

    PubMed

    Wang, Ling; Cheng, Jinping; Lai, Yanyan; Du, Wenli; Huang, Xi; Wang, Zhoufei; Zhang, Hongsheng

    2014-02-01

    Seed dormancy (SD) is an important agronomic trait affecting crop yield and quality. In this study, one rice population of recombinant inbred lines (RILs) was used to determine the genetic characteristics of SD at the early (4 weeks after heading), middle (5 weeks after heading) and late (6 weeks after heading) development stages. The level of SD decreased with the process of seed development, and the SD was significantly affected by the heading date (HD) and temperature at the early and middle development stages. A total of eight additive quantitative trait loci (QTLs) for SD were identified at three development stages, and more QTLs were expressed at the early and late development stages. Among them, four, one and three additive QTLs were identified at the early, middle and late development stages, respectively. Epistatic QTLs and QTL-by-development interactions were detected by the joint analysis of multi-development phenotypic values, and one additive and two epistatic QTLs were identified. The phenotypic variation of SD explained by each additive, epistatic QTL and QTL × development interaction ranged from 8.0 to 13.5 %, 0.7 to 3.9 % and 1.3 to 2.8 %, respectively. One major QTL qSD7.1 for SD was tightly linked to the major QTL qHD7.4 for HD, which might be applied to reveal the relationship of SD and HD. By comparing chromosomal positions of these additive QTLs with those previously identified, five additive QTLs qSD1.1, qSD2.1, qSD2.2, qSD4.1 and qSD4.2 might represent novel genes. The best three cross combinations for the development of RIL populations were predicted to improve SD. The selected RILs and the identified QTLs might be applicable to improve the rice pre-harvest sprouting tolerance by the marker-assisted selection approach. PMID:24189714

  14. 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.

  15. 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

  16. The subset keys and identity tickets (SKIT) key distribution scheme

    Microsoft Academic Search

    Mahalingam Ramkumar

    2010-01-01

    Probabilistic key predistribution schemes (P-KPSs) which place modest demands on hardware are good candidates for securing interactions between resource limited computers. Collusion susceptible P-KPSs are trade-offs between security and complexity. Some facets of complexity include computation, bandwidth, and storage overhead. Metrics for security include resistance to passive eavesdropping attacks, and active message injection attacks. The contributions of this paper are

  17. 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.

  18. 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.

  19. Identification and Characterization of the Direct Interaction between Methotrexate (MTX) and High-Mobility Group Box 1 (HMGB1) Protein

    PubMed Central

    Kusayanagi, Tomoe; Kuramochi, Kouji; Imai, Takahiko; Hirayama, Tomoko; Ito, Ichiaki; Yoshida, Michiteru; Sakaguchi, Kengo; Sugawara, Fumio

    2013-01-01

    Background Methotrexate (MTX) is an agent used in chemotherapy of tumors and autoimmune disease including rheumatoid arthritis (RA). In addition, MTX has some anti-inflammatory activity. Although dihydrofolate reductase (DHFR) is a well-known target for the anti-tumor effect of MTX, the mode of action for the anti-inflammatory activity of MTX is not fully understood. Methodology/Result Here, we performed a screening of MTX-binding proteins using T7 phage display with a synthetic biotinylated MTX derivative. We then characterized the interactions using surface plasmon resonance (SPR) analysis and electrophoretic mobility shift assay (EMSA). Using a T7 phage display screen, we identified T7 phages that displayed part of high-mobility group box 1 (HMGB1) protein (K86-V175). Binding affinities as well as likely binding sites were characterized using genetically engineered truncated versions of HMGB1 protein (Al G1-K87, Bj: F88-K181), indicating that MTX binds to HMGB1 via two independent sites with a dissociation constants (KD) of 0.50±0.03 µM for Al and 0.24±0.01 µM for Bj. Although MTX did not inhibit the binding of HMGB1 to DNA via these domains, HMGB1/RAGE association was impeded in the presence of MTX. These data suggested that binding of MTX to part of the RAGE-binding region (K149-V175) in HMGB1 might be significant for the anti-inflammatory effect of MTX. Indeed, in murine macrophage-like cells (RAW 264.7), TNF-? release and mitogenic activity elicited by specific RAGE stimulation with a truncated monomeric HMGB1 were inhibited in the presence of MTX. Conclusions/Significance These data demonstrate that HMGB1 is a direct binding protein of MTX. Moreover, binding of MTX to RAGE-binding region in HMGB1 inhibited the HMGB1/RAGE interaction at the molecular and cellular levels. These data might explain the molecular basis underlying the mechanism of action for the anti-inflammatory effect of MTX. PMID:23658798

  20. Identification of a cyclase-associated protein (CAP) homologue in Dictyostelium discoideum and characterization of its interaction with actin.

    PubMed Central

    Gottwald, U; Brokamp, R; Karakesisoglou, I; Schleicher, M; Noegel, A A

    1996-01-01

    In search for novel actin binding proteins in Dictyostelium discoideum we have isolated a cDNA clone coding for a protein of approximately 50 kDa that is highly homologous to the class of adenylyl cyclase-associated proteins (CAP). In Saccharomyces cerevisiae the amino-terminal part of CAP is involved in the regulation of the adenylyl cyclase whereas the loss of the carboxyl-terminal domain results in morphological and nutritional defects. To study the interaction of Dictyostelium CAP with actin, the complete protein and its amino-terminal and carboxyl-terminal domains were expressed in Escherichia coli and used in actin binding assays. CAP sequestered actin in a Ca2+ independent way. This activity was localized to the carboxyl-terminal domain. CAP and its carboxyl-terminal domain led to a fluorescence enhancement of pyrene-labeled G-actin up to 50% indicating a direct interaction, whereas the amino-terminal domain did not enhance. In polymerization as well as in viscometric assays the ability of the carboxyl-terminal domain to sequester actin and to prevent F-actin formation was approximately two times higher than that of intact CAP. The sequestering activity of full length CAP could be inhibited by phosphatidylinositol 4,5-bisphosphate (PIP2), whereas the activity of the carboxyl-terminal domain alone was not influenced, suggesting that the amino-terminal half of the protein is required for the PIP2 modulation of the CAP function. In profilin-minus cells the CAP concentration is increased by approximately 73%, indicating that CAP may compensate some profilin functions in vivo. In migrating D. discoideum cells CAP was enriched at anterior and posterior plasma membrane regions. Only a weak staining of the cytoplasm was observed. In chemotactically stimulated cells the protein was very prominent in leading fronts. The data suggest an involvement of D. discoideum CAP in microfilament reorganization near the plasma membrane in a PIP2-regulated manner. Images PMID:8688557

  1. 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

  2. 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

  3. 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

  4. Identification of mRNA transcript and screening of amino acids in response to interaction of salinity and nitrate in aquatic fern Azolla caroliniana.

    PubMed

    Tammam, A A; Mostafa, E M

    2012-06-01

    The mechanisms by which Azolla caroliniana respond to salt stress in absence and presence of nitrate is investigated. Screening of amino acid and differential display is used to compare overall differences in gene expression between salinity-stressed and unstressed Azolla caroliniana by quantitative reverse transcriptase polymerase chain reaction (RT-PC R). Results showed that under saline conditions, aspartic acid, glutamic acid, alanine and leucine were the amino acids found to be abundant in Azolla caroliniana, accounting for 11.26%, 8.66%, 9.43%, and 12.36%, respectively. Following salinity stress, a decrease in free glutamate concomitant with a parallel decrease in free proline was indeed evident. Interaction between nitrate and salinity stress increased proline content significantly. By screening a cDNA library, we have identified protein products by homology with known proteins. The RNA transcripts encoding protein influencing secondary metabolites and vacuolar Na+/H+ antiporter that facilitate the transport system. The databasematched under interaction of nitrate and 50 mM NaCl were associated with wall biosynthesis, disease resistance, metabolite transport and protein regulator, other gene for metabolism of steroids and secondary transport. Results obtained from this research could represent a key step in understanding the molecular mechanism of salt tolerance of Azolla caroliniana in the presence and absence of nitrate. PMID:22695523

  5. Identification of Secreted Proteins that Mediate Cell-Cell Interactions in an In Vitro Model of the Lung Cancer Microenvironment

    PubMed Central

    Zhong, Li; Roybal, Jonathon; Chaerkady, Raghothama; Zhang, Wan; Choi, Kuicheon; Alvarez, Cristina A.; Tran, Hai; Yan, Shaoyu; Strieter, Robert M.; Pandey, Akhilesh; Kurie, Jonathan M.

    2008-01-01

    Non-small cell lung cancer (NSCLC) cells with somatic mutations in K-ras recruit to the tumor a variety of cell types (hereafter collectively termed “stromal cells”) that can promote or inhibit tumorigenesis by mechanisms that have not been fully elucidated. Here we postulated that stromal cells in the tumor microenvironment alter the tumor cell secretome, including those proteins required for tumor growth and dissemination, and we developed an in vitro model to test this hypothesis. Co-culturing a murine K-ras-mutant lung adenocarcinoma cell line (LKR-13) with a murine lung stromal cell (macrophage, endothelial cell, or fibroblast) enhanced stromal cell migration, induced endothelial tube formation, increased LKR-13 cell proliferation, and regulated the secretion of proteins involved in angiogenesis, inflammation, cell proliferation, and epithelial-to-mesenchymal transition. Among these proteins, CXCL1 has been reported to promote NSCLC development, whereas interleukin-18 (IL18) has an undefined role. Genetic and pharmacologic strategies to inhibit CXCL1 and IL18 revealed that stromal cell migration, LKR-13 cell proliferation, and LKR-13 cell tumorigenicity required one or both of these proteins. We conclude that stromal cells enhanced LKR-13 cell tumorigenicity partly through their effects on the secretome of LKR-13 cells. Strategies to inhibit tumor/stromal cell interactions may be useful as therapeutic approaches in NSCLC patients. PMID:18757440

  6. Identification of novel isomeric pectic oligosaccharides using hydrophilic interaction chromatography coupled to traveling-wave ion mobility mass spectrometry.

    PubMed

    Leijdekkers, Antonius G M; Huang, Jie-Hong; Bakx, Edwin J; Gruppen, Harry; Schols, Henk A

    2015-03-01

    Separation and characterization of complex mixtures of pectic oligosaccharides still remains challenging and often requires the use of multiple analytical techniques, especially when isomeric structures are present. In this work, it is demonstrated that the coupling of hydrophilic interaction chromatography (HILIC) to traveling-wave ion mobility mass spectrometry (TWIMMS) enabled the simultaneous separation and characterization of complex mixtures of various isomeric pectic oligosaccharides. Labeling of oligosaccharides with 3-aminoquinoline (3-AQ) improved MS-ionization efficiency of the oligosaccharides and reduced the complexity of the product ion mass spectra, without losing resolution of the HILIC separation. In addition, labeling enabled quantification of oligosaccharides on molar basis using in-line fluorescence detection. Isomeric structures were distinguished using TWIMMS. The 3-AQ-HILIC-TWIMMS method was used to characterize a series of isomeric sugar beet rhamnogalacturonan I derived oligosaccharides carrying a glucuronic acid substituent. Thereby, some novel structural features were identified for the first time: glucuronic acid was attached to O-3 or to O-2 of galacturonic acid residues and a single galacturonic acid residue within an oligomer could contain both an acetyl group and a glucuronic acid substituent. PMID:25647688

  7. Flavivirus enzyme-substrate interactions studied with chimeric proteinases: identification of an intragenic locus important for substrate recognition.

    PubMed Central

    Preugschat, F; Lenches, E M; Strauss, J H

    1991-01-01

    The proteins of flaviviruses are translated as a single long polyprotein which is co- and posttranslationally processed by both cellular and viral proteinases. We have studied the processing of flavivirus polyproteins in vitro by a viral proteinase located within protein NS3 that cleaves at least three sites within the nonstructural region of the polyprotein, acting primarily autocatalytically. Recombinant polyproteins in which part of the polyprotein is derived from yellow fever virus and part from dengue virus were used. We found that polyproteins containing the yellow fever virus cleavage sites were processed efficiently by the yellow fever virus enzyme, by the dengue virus enzyme, and by various chimeric enzymes. In contrast, dengue virus cleavage sites were cleaved inefficiently by the dengue virus enzyme and not at all by the yellow fever virus enzyme. Studies with chimeric proteinases and with site-directed mutants provided evidence for a direct interaction between the cleavage sites and the proposed substrate-binding pocket of the enzyme. We also found that the efficiency and order of processing could be altered by site-directed mutagenesis of the proposed substrate-binding pocket. Images PMID:1651406

  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. Identification of the basic amino acid residues on the PsbP protein involved in the electrostatic interaction with photosystem II.

    PubMed

    Nishimura, Taishi; Uno, Chihiro; Ido, Kunio; Nagao, Ryo; Noguchi, Takumi; Sato, Fumihiko; Ifuku, Kentaro

    2014-09-01

    The PsbP protein is an extrinsic subunit of photosystem II (PSII) that is essential for photoautotrophic growth in higher plants. Several crystal structures of PsbP have been reported, but the binding topology of PsbP in PSII has not yet been clarified. In this study, we report that the basic pocket of PsbP, which consists of conserved Arg48, Lys143, and Lys160, is important for the electrostatic interaction with the PSII complex. Our release-reconstitution experiment showed that the binding affinities of PsbP-R48A, -K143A, and -K160A mutated proteins to PSII were lower than that of PsbP-WT, and triple mutations of these residues greatly diminished the binding affinity to PSII. Even when maximum possible binding had occurred, the R48A, K143A, and K160A proteins showed a reduced ability to restore the rate of oxygen evolution at low chloride concentrations. Fourier transform infrared resonance (FTIR) difference spectroscopy results were consistent with the above finding, and suggested that these mutated proteins were not able to induce the normal conformational change around the Mn cluster during S1 to S2 transition. Finally, chemical cross-linking experiments suggested that the interaction between the N-terminus of PsbP with PsbE was inhibited by these mutations. These data suggest that the basic pocket of PsbP is important for proper association and interaction with PSII. This article is part of a special issue entitled: photosynthesis research for sustainability: keys to produce clean energy. PMID:24388917

  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. 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

  12. 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

  13. Work Keys USA.

    ERIC Educational Resources Information Center

    Work Keys USA, 1998

    1998-01-01

    "Work Keys" is a comprehensive program for assessing and teaching workplace skills. This serial "special issue" features 18 first-hand reports on Work Keys projects in action in states across North America. They show how the Work Keys is helping businesses and educators solve the challenge of building a world-class work force. The reports are as…

  14. 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

  15. A fast method for the quantitation of key metabolites of the methionine pathway in liver tissue by high-resolution mass spectrometry and hydrophilic interaction ultra-performance liquid chromatography.

    PubMed

    van Liempd, S; Cabrera, D; Mato, J M; Falcon-Perez, J M

    2013-06-01

    We developed an assay for the extraction and simultaneous quantitation of five key metabolites of the methionine metabolic pathway in liver tissue. The metabolites included were 5'-methylthioadenosine, methionine, homocysteine, S-adenosyl-L-homocysteine, and S-adenosyl-L-methionine. The metabolites were extracted using a bead-based homogenization method, and quantitation was carried out using hydrophilic interaction chromatography and time-of-flight mass spectrometry. The extraction procedure was optimized by testing the effect of various solvent combinations. The chromatographic method was optimized for peak shape, signal intensity, and carry-over. With a total chromatographic run time of 5 min, this assay is suitable for the analysis of large sample sets. Time-of-flight mass spectrometry provided high mass accuracy which, combined with isotope pattern matching and use of chemical standards, guarantees high specificity. Moreover, by operating the mass spectrometer in enhanced duty cycle mode the signal strength for the analytes increased three- to tenfold in comparison with the generic full-scan mode. For quantitation, a matrix-spiked calibration method was used. The lowest analyte levels detected and quantified using our method were within the range of concentrations found in the liver. The inter-day coefficients of variance for the analytes were between 5 and 15% in pooled tissue samples. Interestingly, the CVs between individual liver tissue aliquots were about twice as high. Additional experiments suggested that this higher variability was caused by uneven distribution of the analytes within the liver. In conclusion, an optimized and robust assay is now available for the extraction and quantification of key metabolites in the methionine metabolic pathway. PMID:23535742

  16. 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.

  17. 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…

  18. Intelligent card access keys

    SciTech Connect

    Tennefoss, M.R.

    1987-07-01

    A newly developed access control technology allows information about users to be stored on key-like EEPROM devices. The keys store encrypted information about the user and his or her authorized access activity. Specially developed key readers scan, decrypt, and process the key data, and make the decision whether entry should be granted or denied. The key readers can function as complete, stand-alone facility management systems, incorporating access control, security monitoring, and remote control. In this configuration, the key readers provide anti-passback protection and other special features without requiring any data lines between readers. The key readers also feature sophisticated algorithmic processing for performing complex operations such as two-man control or cross zoned security annunciation. Key readers can also be interconnected with an MCM-1000 Multiples Monitoring System to form a distributed processing local area network. In such a configuration, changes in key reader status can be uploaded to the MCM-1000, and programming changes and operator commands can be downloaded to the key readers.

  19. 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.

  20. 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)

  1. Introduction Key Predistribution

    E-print Network

    Ramkumar, Mahalingam

    Key Predistribution Infrastructure (KPI) 1 Introduction Trusted Devices Renewal KDS Requirements 2 Key Devices Renewal KDS Requirements Emerging Models of Trust Paradigm shift in the model of trust in emerging) Trusted Devices Renewal KDS Requirements Trusted Devices Devices "play by the rules" Compliance

  2. 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...

  3. Democratic Key Escrow Scheme

    Microsoft Academic Search

    Chor Wah Man; Reihaneh Safavi-naini

    1997-01-01

    Recently, key escrow schemes have been the topic of much debate and confusion. On the one hand, cryptography allows privacy of electronic communication for the honest citizens. On the other hand, it can be used by criminals to thwart law enforcement efforts. It seems that only by escrowing everyone's private key can we tackle this dilemma. In recent years, numerous

  4. Identification of a putative cognate sensor kinase for the two-component response regulator HrpG, a key regulator controlling the expression of the hrp genes in Xanthomonas campestris pv. campestris.

    PubMed

    Li, Rui-Fang; Lu, Guang-Tao; Li, Lei; Su, Hui-Zhao; Feng, Guo-fang; Chen, Ya; He, Yong-Qiang; Jiang, Bo-Le; Tang, Dong-Jie; Tang, Ji-Liang

    2014-07-01

    The bacterial phytopathogen Xanthomonas campestris pv. campestris (Xcc) relies on the hrp (hypersensitive response and pathogenicity) genes to cause disease and induce hypersensitive response (HR). The hrp genes of bacterial phytopathogens are divided into two groups. Xcc hrp genes belong to group II. It has long been known that the group II hrp genes are activated by an AraC-type transcriptional regulator whose expression is controlled by a two-component system (TCS) response regulator (named HrpG in Xcc). However, no cognate sensor kinase has yet been identified. Here, we present evidence showing that the Xcc open-reading frame XC_3670 encodes a TCS sensor kinase (named HpaS). Mutation of hpaS almost completely abolished the HR induction and virulence. Bacterial two-hybrid and protein pull-down assays revealed that HpaS physically interacted with HrpG. Phos-tag™ SDS-PAGE analysis showed that mutation in hpaS reduced markedly the phosphorylation of HrpG?in vivo. These data suggest that HpaS and HrpG are most likely to form a TCS. We also showed that XC_3669 (named hpaR2), which is adjacent to hpaS and encodes a putative TCS response regulator, is required for full virulence but not HR induction. HpaR2 also physically interacted with HpaS, suggesting that HpaS may also form another TCS with HpaR2. PMID:23906314

  5. Sequential Key Derivation Patterns for Broadcast Encryption and Key Predistribution Schemes

    Microsoft Academic Search

    Nuttapong Attrapadung; Kazukuni Kobara; Hideki Imai

    2003-01-01

    We study two closely related primitives: Broadcast Encryp- tion and Key Predistribution Schemes (KPS). Broadcast Encryption allows a broadcaster to broadcast an encrypted message so that only a designated group of users can decrypt it. KPS allows a designated group of users to establish a common key non-interactively. We discover a generic method to construct e-cient broadcast encryption schemes and

  6. Statistics Netherlands: Key Figures

    NSDL National Science Digital Library

    1998-01-01

    This site, provided by the Central Bureau of Statistics in the Netherlands, offers current data on key social and economic indicators. These include population, labor, industry, prices, energy, health and welfare, and the environment.

  7. The Role of Gender in Opportunity Identification

    Microsoft Academic Search

    Dawn R. DeTienne; Gaylen N. Chandler

    2007-01-01

    Opportunity identification is rapidly becoming a key focal point of research in the entrepreneurship domain. This study is the first to explore gender differences in opportunity identification. Utilizing two distinct samples (95 senior undergraduate students, 189 entrepreneurs in two high-technology industries), we found that women and men utilize their unique stocks of human capital to identify opportunities and that they

  8. Stereotype Threat in Classroom Settings: The Interactive Effect of Domain Identification, Task Difficulty and Stereotype Threat on Female Students' Maths Performance

    ERIC Educational Resources Information Center

    Keller, Johannes

    2007-01-01

    Background: Stereotype threat research revealed that negative stereotypes can disrupt the performance of persons targeted by such stereotypes. This paper contributes to stereotype threat research by providing evidence that domain identification and the difficulty level of test items moderate stereotype threat effects on female students' maths…

  9. 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.

  10. In Vivo Localization of Iris yellow spot Tospovirus (Bunyaviridae)-Encoded Proteins and Identification of Interacting Regions of Nucleocapsid and Movement Proteins

    PubMed Central

    Tripathi, Diwaker; Raikhy, Gaurav; Goodin, Michael M.; Dietzgen, Ralf G.; Pappu, Hanu R.

    2015-01-01

    Background Localization and interaction studies of viral proteins provide important information about their replication in their host plants. Tospoviruses (Family Bunyaviridae) are economically important viruses affecting numerous field and horticultural crops. Iris yellow spot virus (IYSV), one of the tospoviruses, has recently emerged as an important viral pathogen of Allium spp. in many parts of the world. We studied the in vivo localization and interaction patterns of the IYSV proteins in uninfected and infected Nicotiana benthamiana and identified the interacting partners. Principal Findings Bimolecular fluorescence complementation (BiFC) analysis demonstrated homotypic and heterotypic interactions between IYSV nucleocapsid (N) and movement (NSm) proteins. These interactions were further confirmed by pull-down assays. Additionally, interacting regions of IYSV N and NSm were identified by the yeast-2-hybrid system and ?-galactosidase assay. The N protein self-association was found to be mediated through the N- and C-terminal regions making head to tail interaction. Self-interaction of IYSV NSm was shown to occur through multiple interacting regions. In yeast-2-hybrid assay, the N- and C-terminal regions of IYSV N protein interacted with an N-terminal region of IYSV NSm protein. Conclusion/Significance Our studies provide new insights into localization and interactions of IYSV N and NSm proteins. Molecular basis of these interactions was studied and is discussed in the context of tospovirus assembly, replication, and infection processes. PMID:25781476

  11. LACIE analyst interpretation keys

    NASA Technical Reports Server (NTRS)

    Baron, J. G.; Payne, R. W.; Palmer, W. F. (principal investigators)

    1979-01-01

    Two interpretation aids, 'The Image Analysis Guide for Wheat/Small Grains Inventories' and 'The United States and Canadian Great Plains Regional Keys', were developed during LACIE phase 2 and implemented during phase 3 in order to provide analysts with a better understanding of the expected ranges in color variation of signatures for individual biostages and of the temporal sequences of LANDSAT signatures. The keys were tested using operational LACIE data, and the results demonstrate that their use provides improved labeling accuracy in all analyst experience groupings, in all geographic areas within the U.S. Great Plains, and during all periods of crop development.

  12. Related-Key Statistical Cryptanalysis

    Microsoft Academic Search

    Darakhshan J. Mir; Poorvi L. Vora

    This paper studies the information-theoretic limits of block cipher statistical key-recovery attacks, which typically use several known plaintext\\/ciphertext (P\\/C) pairs to determine a single key. In particular, it studies related-key statistical key recovery, where the adversary uses n related keys, generated from k independent ones. Unlike classical related-key attacks such as dierential related-key cryptanalysis, this attack does not exploit a

  13. Identification of Microorganisms Encountered in the Upper Respiratory Tract

    NSDL National Science Digital Library

    Iris L. Sun (Purdue University; )

    1996-01-01

    This resource is a detailed laboratory manual for instructing students in a laboratory exercise focusing on the identification of the micro-organisms commonly found in the upper respiratory tract. Detailed information on different micro-organisms including identification keys and laboratory tests. This would be a suitable introduction to bacterial identification for any course requiring such taxonomic skills.

  14. 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.

  15. Mangrove Key Islets

    USGS Multimedia Gallery

    Beyond the mangrove key islets that make up the Ten Thousand Islands, lies the Gulf of Mexico. The Ten Thousand Islands are comprised of hundreds of mangrove islands that extend northward from the northwest corner of Everglades National Park. These uninhabited islands stretch for 60-miles al...

  16. Key Reference Agilent Technologies

    E-print Network

    Anlage, Steven

    Key Reference Agilent Technologies E8257D/67D PSG Signal Generators This guide applies: http://www.agilent.com/find/psg Manufacturing Part Number: E8251- 90354 Printed in USA July 2007 © Copyright 2004- 2007 Agilent Technologies, Inc. #12;ii Notice The material in this document is provided "as

  17. Key Reference Agilent Technologies

    E-print Network

    Anlage, Steven

    Key Reference Agilent Technologies PSG Signal Generators This guide applies to the following signal: www.agilent.com/find/psg Manufacturing Part Number: E8251-90254 Printed in USA December 2003 © Copyright 2002, 2003 Agilent Technologies, Inc. #12;ii Notice The material contained in this document

  18. 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.

  19. 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

  20. Some reflections on identification.

    PubMed

    Szpilka, J

    1999-12-01

    The author presents a view of identification based on a rereading of two of Freud's key texts and an approach derived from an academic interpretation of Hegel dating from the 1930s. These aspects are considered at length. The importance of the human and anthropogenic element is stressed. The human subject is presented as coming into being through language; being called upon to be what he is not and not to be what he is, the subject appears as wishful in nature, desiring the wish of the other at the same time as he desires the object of the other's wish. The author argues that identification as a problem arises only in a human being who speaks or has received an injunction to speak; this raises the question of who or what he is and of being as such. Analytic treatment may in his view therefore proceed in one of two directions, one based on the interplay of projection and introjection with identification as an end, and the other on resistance and repression where the Oedipus complex is seen as the nuclear issue. Identification is seen in terms of overcoming the negative identity of not being all other subjects, and identity is found to be a conscious response that might even have a political element. PMID:10669967

  1. The protein-protein interaction map of Helicobacter pylori.

    PubMed

    Rain, J C; Selig, L; De Reuse, H; Battaglia, V; Reverdy, C; Simon, S; Lenzen, G; Petel, F; Wojcik, J; Schächter, V; Chemama, Y; Labigne, A; Legrain, P

    2001-01-11

    With the availability of complete DNA sequences for many prokaryotic and eukaryotic genomes, and soon for the human genome itself, it is important to develop reliable proteome-wide approaches for a better understanding of protein function. As elementary constituents of cellular protein complexes and pathways, protein-protein interactions are key determinants of protein function. Here we have built a large-scale protein-protein interaction map of the human gastric pathogen Helicobacter pylori. We have used a high-throughput strategy of the yeast two-hybrid assay to screen 261 H. pylori proteins against a highly complex library of genome-encoded polypeptides. Over 1,200 interactions were identified between H. pylori proteins, connecting 46.6% of the proteome. The determination of a reliability score for every single protein-protein interaction and the identification of the actual interacting domains permitted the assignment of unannotated proteins to biological pathways. PMID:11196647

  2. 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.

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

    E-print Network

    Baumann, Paul A.

    1999-08-30

    para el ?xito de cualquier programa de manejo de malezas. Frecuentemente, claves simples para identificar plantas o gu?as para identificar malezas basadas en fotograf?as o dibujos se usan para identificar malezas. Sin embargo, algunas claves taxon...?micas para plantas pueden ser complejas y requerir un conocimiento avanzado de las estructuras de las plantas y la terminolog?a taxon?mica. Aunque sea m?s dif?cil usarla, una gu?a o clave detallada permite la precisa identificaci?n de malezas. La intenci...

  4. 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…

  5. Weed Identification: Using Plant Structures as a Key

    E-print Network

    Baumann, Paul A.

    2002-04-15

    entire, serrated, pinnately lobed and palmately lobed leaf margins are shown. Pinnately lobed leaves can be distinguished frompalmately lobed leaves by examining the veinson the leaves. In a pinnately lobed leaf, the veinswill arise from several points...

  6. Statistical Identification of Key Phrases for Text Classification

    E-print Network

    Coenen, Frans

    Sanderson, and Yanbo J. Wang Department of Computer Science, The University of Liverpool, Ashton Building, Ashton Street, Liverpool L69 3BX, United Kingdom {frans,phl,azaroth,jwang}@csc.liv.ac.uk Abstract such as natural language parsing P. Perner (Ed.): MLDM 2007, LNAI 4571, pp. 838­853, 2007. c Springer

  7. A SINE-based dichotomous key for primate identification

    Microsoft Academic Search

    Scott W. Herke; Jinchuan Xing; David A. Ray; Jacquelyn W. Zimmerman; Richard Cordaux; Mark A. Batzer

    2007-01-01

    For DNA samples or ‘divorced’ tissues, identifying the organism from which they were taken generally requires some type of analytical method. The ideal approach would be robust even in the hands of a novice, requiring minimal equipment, time, and effort. Genotyping SINEs (Short INterspersed Elements) is such an approach as it requires only PCR-related equipment, and the analysis consists solely

  8. Modeling Key Compromise Impersonation Attacks on Group Key Exchange Protocols

    Microsoft Academic Search

    M. Choudary Gorantla; Colin Boyd; Juan Manuel González Nieto

    2009-01-01

    A key exchange protocol allows a set of parties to agree upon a secret session key over a public network. Two-party key exchange (2PKE) protocols have been rigorously analyzed under various models considering different adversarial actions. However, the analysis of group key exchange (GKE) protocols has not been as extensive as that of 2PKE protocols. Particularly, the security attribute of

  9. Ar evised determination key of freshwater crayfish in Europe von

    Microsoft Academic Search

    Leopold FÜREDER; Yoichi MACHINO

    Since more than 100 years several crayfish-determination keys have been published in Europe. Although crayfish species identification does not seem to be so difficult to do (at least to us), in several occasions we encountered museums, crayfish amateurs and \\

  10. Identification of a Heteromeric Interaction That Influences the Rectification, Gating, and pH Sensitivity of Kir4.1/Kir5.1

    E-print Network

    Tucker, Stephen J.

    ) channels are not only important for the regulation of the resting membrane potential and cellular membrane potential and allow K to recycle via the Na /K -ATPase pow- ering most of the transepithelial control of this process is one of the key mechanisms of K homeostasis. Kir channels in the apical membrane

  11. Shoe Dichotomous Key

    NSDL National Science Digital Library

    Twin Cities Public Television, Inc.

    2006-01-01

    In this activity (on page 2 of the PDF), learners will develop their own version of a tool used by biologists, a dichotomous key, by collecting all their left shoes. Learners brainstorm different characteristics and decide how to divide the pile into two groups with a common characteristic. A chart should be made as they continue to divide each group in two until each shoe has its own group. Learners use the chart to identify each person's shoe. Relates to the linked video, DragonflyTV GPS: Cactus.

  12. Identification of a Minimal Hydrophobic Domain in the Herpes Simplex Virus Type 1 Scaffolding Protein Which Is Required for Interaction with the Major Capsid Protein

    Microsoft Academic Search

    ZHI HONG; MICHELE BEAUDET-MILLER; JAMES DURKIN; RUMIN ZHANG; ANDANN D. KWONG

    1996-01-01

    lysatescontainingVP5.TheinteractionbetweenGST\\/CTandVP5wasdeterminedbycoprecipitationofthetwo proteins with glutathione Sepharose beads. Our results revealed that the GST\\/CT fusion protein specifically interactswithVP5,suggestingthattheC-terminaldomainaloneissufficientforinteractionwithVP5.Deletion analysis of the GST\\/CT binding domain mapped the interaction to a minimal 12-amino-acid motif. Substitu- tionmutationsfurtherrevealedthatthereplacementofhydrophobicresidueswithchargedresiduesinthecore regionofthemotifabolishedtheinteraction,suggestingthattheinteractionisahydrophobicone.Achaotropic detergent, 0.1% Nonidet P-40, also abolished the interaction, further supporting the hydrophobic nature of the interaction.Computeranalysispredictedthattheminimalbindingmotifcouldformastrong a-helixstructure. Most interestingly, the a-helix model maximizes the hydropathicity of the

  13. Identification of Three Interactions to Determine the Conformation Change and to Maintain the Function of Kir2.1 Channel Protein

    NASA Astrophysics Data System (ADS)

    Li, Jun-Wei; Xiao, Shao-Ying; Xie, Xiao-Xiao; Yu, Hui; Zhang, Hai-Lin; Zhan, Yong; An, Hai-Long

    2015-02-01

    We find that a conserved mutation residue Glu to residue Asp (E303D), which both have the same polar and charged properties, makes Kir2.1 protein lose its function. To understand the mechanism, we identify three interactions which control the conformation change and maintain the function of the Kir2.1 protein by combining homology modeling and molecular dynamics with targeted molecular dynamics. We find that the E303D mutation weakens these interactions and results in the loss of the related function. Our data indicate that not only the amino residues but also the interactions determine the function of proteins.

  14. Photo interpretation key to Michigan land cover/use

    NASA Technical Reports Server (NTRS)

    Enslin, W. R.; Hudson, W. D.; Lusch, D. P.

    1983-01-01

    A set of photo interpretation keys is presented to provide a structured approach to the identification of land cover/use categories as specified in the Michigan Resource Inventory Act. The designated categories are urban and; built up lands; agricultural lands; forest land; nonforested land; water bodies; wetlands; and barren land. The keys were developed for use with medium scale (1:20,000 to 1:24,000) color infrared aerial photography. Although each key is generalized in that it relies only upon the most distinguishing photo characteristics in separating the various land cover/use categories, additional interpretation characteristics, distinguishing features and background material are given.

  15. Key Management in Historical Context

    E-print Network

    ;Rolling Keys Why change keys? --- cryptoperiod (intrinsic to cryptosystem) --- management issuesKey Management in Historical Context Whitfield Diffie Internet Corporation for Assigned Names to become the security or insecurity of the message. #12;Key management systems both reflect and shape

  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. MOR Is Not Enough: Identification of Novel mu-Opioid Receptor Interacting Proteins Using Traditional and Modified Membrane Yeast Two-Hybrid Screens

    PubMed Central

    Jin, Jay; Wong, Victoria; Kittanakom, Saranya; Ferraro, Thomas N.; Stagljar, Igor; Levenson, Robert

    2013-01-01

    The mu-opioid receptor (MOR) is the G-protein coupled receptor primarily responsible for mediating the analgesic and rewarding properties of opioid agonist drugs such as morphine, fentanyl, and heroin. We have utilized a combination of traditional and modified membrane yeast two-hybrid screening methods to identify a cohort of novel MOR interacting proteins (MORIPs). The interaction between the MOR and a subset of MORIPs was validated in pulldown, co-immunoprecipitation, and co-localization studies using HEK293 cells stably expressing the MOR as well as rodent brain. Additionally, a subset of MORIPs was found capable of interaction with the delta and kappa opioid receptors, suggesting that they may represent general opioid receptor interacting proteins (ORIPS). Expression of several MORIPs was altered in specific mouse brain regions after chronic treatment with morphine, suggesting that these proteins may play a role in response to opioid agonist drugs. Based on the known function of these newly identified MORIPs, the interactions forming the MOR signalplex are hypothesized to be important for MOR signaling and intracellular trafficking. Understanding the molecular complexity of MOR/MORIP interactions provides a conceptual framework for defining the cellular mechanisms of MOR signaling in brain and may be critical for determining the physiological basis of opioid tolerance and addiction. PMID:23840749

  18. Identification of the Novel Interacting Partners of the Mammalian Target of Rapamycin Complex 1 in Human CCRF-CEM and HEK293 Cells

    PubMed Central

    Rahman, Hazir; Qasim, Muhammad; Oellerich, Michael; Asif, Abdul R.

    2014-01-01

    The present study was undertaken to identify proteins that interact with the mammalian target of rapamycin complex 1 (mTORC1) to enable it to carry out its crucial cell signaling functions. Endogenous and myc-tag mTORC1 was purified, in-gel tryptic digested and then identified by nano-LC ESI Q-TOF MS/MS analysis. A total of nine novel interacting proteins were identified in both endogenous and myc-tag mTORC1 purifications. These new mTORC1 interacting partners include heterogeneous nuclear ribonucleoproteins A2/B1, enhancer of mRNA decapping protein 4, 60S acidic ribosomal protein, P0, nucleolin, dynamin 2, glyceraldehyde 3 phosphate dehydrogenase, 2-oxoglutarate dehydrogenase, glycosyl transferase 25 family member 1 and prohibitin 2. Furthermore hnRNP A2/B1 and dynamin 2 interaction with mTORC1 was confirmed on immunoblotting. The present study has for the first time identified novel interacting partners of mTORC1 in human T lymphoblasts (CCRF-CEM) and human embryonic kidney (HEK293) cells. These new interacting proteins may offer new targets for therapeutic interventions in human diseases caused by perturbed mTORC1 signaling. PMID:24646917

  19. MOR is not enough: identification of novel mu-opioid receptor interacting proteins using traditional and modified membrane yeast two-hybrid screens.

    PubMed

    Petko, Jessica; Justice-Bitner, Stephanie; Jin, Jay; Wong, Victoria; Kittanakom, Saranya; Ferraro, Thomas N; Stagljar, Igor; Levenson, Robert

    2013-01-01

    The mu-opioid receptor (MOR) is the G-protein coupled receptor primarily responsible for mediating the analgesic and rewarding properties of opioid agonist drugs such as morphine, fentanyl, and heroin. We have utilized a combination of traditional and modified membrane yeast two-hybrid screening methods to identify a cohort of novel MOR interacting proteins (MORIPs). The interaction between the MOR and a subset of MORIPs was validated in pulldown, co-immunoprecipitation, and co-localization studies using HEK293 cells stably expressing the MOR as well as rodent brain. Additionally, a subset of MORIPs was found capable of interaction with the delta and kappa opioid receptors, suggesting that they may represent general opioid receptor interacting proteins (ORIPS). Expression of several MORIPs was altered in specific mouse brain regions after chronic treatment with morphine, suggesting that these proteins may play a role in response to opioid agonist drugs. Based on the known function of these newly identified MORIPs, the interactions forming the MOR signalplex are hypothesized to be important for MOR signaling and intracellular trafficking. Understanding the molecular complexity of MOR/MORIP interactions provides a conceptual framework for defining the cellular mechanisms of MOR signaling in brain and may be critical for determining the physiological basis of opioid tolerance and addiction. PMID:23840749

  20. Publicly verifiable partial key escrow

    Microsoft Academic Search

    Wenbo Mao; Bristol BS

    1997-01-01

    . A partial key escrow cryptosystem based on publicly verifiableencryption is proposed. Partial key escrow adds a great deal ofdifficulty to mass privacy intrusion interested by malicious authorities(e.g., a human rights abusive government). Public verifiability improvesefficiency and guarantees correctness in the establishment of partiallyescrowed key.1 IntroductionThis paper proposes a publicly verifiable partial key escrow cryptosystem.In partial key escrow, a portion

  1. Identification of residues critical for Ras(17N) growth-inhibitory phenotype and for Ras interaction with guanine nucleotide exchange factors.

    PubMed Central

    Quilliam, L A; Kato, K; Rabun, K M; Hisaka, M M; Huff, S Y; Campbell-Burk, S; Der, C J

    1994-01-01

    The Ras(17N) dominant negative antagonizes endogenous Ras function by forming stable, inactive complexes with Ras guanine nucleotide exchange factors (GEFs; e.g., SOS1). We have used the growth-inhibitory phenotype of Ras(17N) to characterize two aspects of Ras interaction with GEFs. First, we used a nonprenylated version of Ras(17N), designated Ras(17N/186S), which no longer associates with the plasma membrane and lacks the growth-inhibitory phenotype, to address the importance of Ras subcellular location and posttranslational modification for its interaction with GEFs. We observed that addition of an N-terminal myristylation signal to Ras(17N/186S) restored the growth-inhibitory activity of nonprenylated Ras(17N). Thus, membrane association, rather than prenylation, is critical for Ras interaction with Ras GEFs. Second, we used a biological selection approach to identify Ras residues which are critical for Ras(17N) growth inhibition and hence for interaction with Ras GEFs. We identified mutations at residues 75, 76, and 78 that abolished the growth-inhibitory activity of Ras(17N). Since GEF interaction is dispensable for oncogenic but not normal Ras function, our demonstration that single-amino-acid substitutions at these three positions impaired the transforming activity of normal but not oncogenic Ras provides further support for the role of these residues in Ras-GEF interactions. Finally, Ras(WT) proteins with mutations at these residues were no longer activated by mammalian SOS1. Altogether, these results suggest that the Ras intracellular location and Ras residues 75 to 78 are critical for Ras-GEF interaction. Images PMID:8289792

  2. Identification and characterization of protein interactions in the mammalian mRNA processing body using a novel two-hybrid assay

    SciTech Connect

    Bloch, Donald B., E-mail: bloch@helix.mgh.harvard.edu; Nobre, Rita A.; Bernstein, Gillian A.; Yang, Wei-Hong

    2011-09-10

    Components of the mRNA processing body (P-body) regulate critical steps in mRNA storage, transport, translation and degradation. At the core of the P-body is the decapping complex, which removes the 5' cap from de-adenylated mRNAs and mediates an irreversible step in mRNA degradation. The assembly of P-bodies in Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster has been previously described. Less is known about the assembly of mammalian P-bodies. To investigate the interactions that occur between components of mammalian P-bodies, we developed a fluorescence-based, two-hybrid assay system. The assay depends on the ability of one P-body component, fused to an exogenous nuclear localization sequence (NLS), to recruit other P-body components to the nucleus. The assay was used to investigate interactions between P-body components Ge-1, DCP2, DCP1, EDC3, RAP55, and RCK. The results of this study show that the modified two-hybrid assay can be used to identify protein interactions that occur in a macromolecular complex. The assay can also be used to efficiently detect protein interaction domains. The results provide important insights into mammalian P-body assembly and demonstrate similarities, and critical differences, between P-body assembly in mammalian cells compared with that of other species. -- Research highlights: {yields} A two-hybrid assay was developed to study interactions in macromolecular complexes. {yields} The assay was applied to interactions between components of mRNA P-bodies. {yields} The assay effectively and efficiently identified protein interaction domains. {yields} P-body assembly in mammalian cells differs from that in other species.

  3. How do pigs behave before starting an aggressive interaction? Identification of typical body positions in the early stage of aggression using video labelling techniques.

    PubMed

    Ismayilova, Gunel; Oczak, Maciej; Costa, Annamaria; Sonoda, Lilia Thays; Viazzi, Stefano; Fels, Michaela; Vranken, Erik; Hartung, Jörg; Bahr, Claudia; Berckmans, Daniel; Guarino, Marcella

    2013-01-01

    The aim of this study was to identify, quantify, and describe pre-signs of aggression in pigs and the early stages of aggressive interactions. The experiment was carried out at a commercial farm on a group of 11 male pigs weighing on average 23 kg and kept in a pen of4 m x 2.5 m. In total 8 hours were videorecorded during the first 3 days after mixing. As a result, 177 aggressive interactions were identified and labelled to find pre-sign body positions before aggressive interactions, attack positions and aggressive acts performed from these positions. A total of 12 positions were classified as pre-signs (P1-P12) and 7 of them were identified immediately at the start of aggressive interactions (P6-P12). Most common pre-sign positions were P3-pigs approaching and facing each other (24%) and P2-initiator pigs approaching from the lateral side (18%). In 80% of the cases the duration of pre-signs was 1-2 sec 72% of all aggressive interactions were short (1 to 10 sec). The most frequent attack positions were P12-inverse parallel (39.5%), P7-nose to nose, 90 degrees (19.77%) and P9-nose to head (13.5%). The most frequent aggressive acts from attack positions were head knocking (34.4%), pressing (34.4%) and biting of different body parts (29.4%). Head knocking was mostly observed in relation to P7 and P2 positions and biting was common in the P7 position. In conclusion, pigs adopt specific pre-signs and body positions before the escalation of aggressive interactions. This could be used as potential sign to identify a beginning aggression. PMID:23540193

  4. Fibronectin interactions with osteoblasts: identification of a non-integrin-mediated binding mechanism using a real-time fluorescence binding assay.

    PubMed

    Sim, Bushra; Cladera, Josep; O'Shea, Paul

    2004-02-01

    Fibronectin (Fn) is an extracellular matrix protein that interacts with specific integrins on the cell surface, initiating signal transduction processes that lead to a reorganization of the cytoskeleton and the assembly of focal adhesions. Cell surface proteoglycans or glycosaminoglycans (GAGs) such as heparan sulfate are also known to participate in the interaction of Fn with the cell surface by binding to two different heparin-binding domains. The influence of Fn and GAGs on the spreading and differentiation of human osteoblasts was also previously described. In the current work, a method developed in our laboratory is established to evaluate the interaction between Fn and human osteoblasts and the influence of GAGs on such interactions. This technique makes use of fluoresceinphosphatidylethanolamine (FPE) such that when inserted into the lipidic bilayer, it acts as a fluorescent indicator of membrane interactions. The results indicate that the binding profile of Fn with the osteoblast cell surface is best represented by a hyperbolic single binding site model with a membrane affinity of 120 nM. Removal of cell surface heparan sulfate by treatment with heparitinase indicates that the cell surface moiety is directly involved in the binding process. Studies directed to assess the influence of heparin on the interaction of Fn with osteoblasts reveal that although it does not hamper Fn binding to the cell surface, it blocks the initial attachment to Fn-coated surfaces, indicating that binding to the integrin receptor alone is not enough to promote cell attachment but that the participation of the cell-surface GAGs is also a necessary condition. PMID:14704977

  5. Projective identification: a concept overburdened.

    PubMed

    Kulish, N M

    The term projective identification has been broadened from its original meaning as set forth by Melanie Klein to include the interpersonal sphere. A review of the psychoanalytic literature on projective identification shows varying uses, definitional problems, and conceptual confusion and raises serious questions regarding the possibility of integrating intrapersonal and interpersonal models of the mind. Clinical material is presented to show that phenomena commonly described as projective identification are variable, complex patterns of behavior that are not well understood. The author concludes that the major definitional and conceptual difficulties with the term justify that its usage be limited. At the same time, the powerful clinical phenomena--the transference-countertransference interactions--described as projective identification cannot be ignored. PMID:4086187

  6. KeyNote: Trust Management for Public-Key Infrastructures

    Microsoft Academic Search

    Matt Blaze; Joan Feigenbaum; Angelos D. Keromytis

    This paper discusses the rationale for designing a simple trust-management system for public-key infrastructures, called KeyNote. The motivating principles are expressibility, simplicity, and extensibility. We believe that none of the existing public-key\\u000a infrastructure proposals provide as good a combination of these three factors.

  7. Leaf Identification

    NSDL National Science Digital Library

    2008-09-12

    This straightforward tutorial on leaf identification comes from the Department of Horticulture at Penn State University. Simple diagrams, helpful photos, and clear explanations make short work of learning the basics of leaf identification. The website even includes a section on why anyone should bother learning this skill (i.e. it's not just for dedicated horticulturists and botanists). The tutorial covers leaf structure, blade shape, margins, venation, and so on. The self-testing component appears to be unavailable at this time, but this site as a whole is definitely worth a look.

  8. Bone Identification

    NSDL National Science Digital Library

    Twin Cities Public Television, Inc.

    2006-01-01

    This activity (page 3 of the PDF) is a full inquiry investigation into fossil hunting and identification. Groups of learners will sift through a commercially prepared owl pellet, looking for bone pieces that they will attempt to match to an identification chart and subsequently arrange into a rough skeleton. Learners use this exercise to consider how animal skeletons help researchers determine what kinds of animals live together in an ecosystem as well compare the bones they find to the bones in their own body. Relates to linked video, DragonflyTV GPS: Dinosaurs.

  9. Binary pulsars studies with multiwavelength sky surveys - I. Companion star identification

    NASA Astrophysics Data System (ADS)

    Mignani, R. P.; Corongiu, A.; Pallanca, C.; Oates, S. R.; Yershov, V. N.; Breeveld, A. A.; Page, M. J.; Ferraro, F. R.; Possenti, A.; Jackson, A. C.

    2014-09-01

    The identification of the stellar companions to binary pulsars is key to studying the evolution of the binary system and how this is influenced by the interactions between the two stars. For only a fraction of the known binary pulsars, the stellar companions have been identified. Here, we used 11 source catalogues available from multiwavelength (ultraviolet, optical, infrared) imaging sky surveys to search for the stellar companions of a sample of 144 field binary pulsars (i.e. not in globular clusters) selected from the Australia Telescope National Facility data base (version 1.48) and from the public list of ?-ray pulsars detected by Fermi. We found positional associations in at least one source catalogue for 22 pulsars, of which 10 are detected in ?-rays by Fermi, including 15 millisecond pulsars. For six pulsars in our compilation, we confirm their identifications. For another seven pulsars that had yet not been identified, we examine potential identifications. In particular, we identified a likely companion star candidate to PSR J2317+1439, whereas for both PSR B1953+29 and PSR J1935+1726 the companion star identification is more uncertain. Follow-up observations of these three pulsars are needed to settle the proposed identifications. For the remaining nine pulsars that had been already identified, we provide additional spectral information in at least one of the surveys' spectral bands, which we will use to better constrain the stars' spectral energy distributions.

  10. RAPID PHASE IDENTIFICATION OF MIXED CRYSTALLINE SOLIDS

    EPA Science Inventory

    The identification of crystal phases and crystal chemistry can be critical to understanding the mechanisms of waste material interaction with native soils. nderstanding these mechanisms can suggest correct methods for remediation and treatment. rogram is outlined and examples are...

  11. 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.

  12. 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- ...

  13. Identification of conserved amino acids in the herpes simplex virus type 1 UL8 protein required for DNA synthesis and UL52 primase interaction in the virus replisome.

    PubMed

    Muylaert, Isabella; Zhao, Zhiyuan; Andersson, Torbjörn; Elias, Per

    2012-09-28

    We have used oriS-dependent transient replication assays to search for species-specific interactions within the herpes simplex virus replisome. Hybrid replisomes derived from herpes simplex virus type 1 (HSV-1) and equine herpesvirus type 1 (EHV-1) failed to support DNA replication in cells. Moreover, the replisomes showed a preference for their cognate origin of replication. The results demonstrate that the herpesvirus replisome behaves as a molecular machine relying on functionally important interactions. We then searched for functional interactions in the replisome context by subjecting HSV-1 UL8 protein to extensive mutagenesis. 52 mutants were made by replacing single or clustered charged amino acids with alanines. Four mutants showed severe replication defects. Mutant A23 exhibited a lethal phenotype, and mutants A49, A52 and A53 had temperature-sensitive phenotypes. Mutants A49 and A53 did not interact with UL52 primase as determined by co-immunoprecipitation experiments. Using GFP-tagged UL8, we demonstrate that all mutants were unable to support formation of ICP8-containing nuclear replication foci. Extended mutagenesis suggested that a highly conserved motif corresponding to mutant A49 serves an important role for establishing a physical contact between UL8 and UL52. The replication-defective mutations affected conserved amino acids, and similar phenotypes were observed when the corresponding mutations were introduced into EHV-1 UL8. PMID:22851167

  14. 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

  15. Identification of Conserved Amino Acids in the Herpes Simplex Virus Type 1 UL8 Protein Required for DNA Synthesis and UL52 Primase Interaction in the Virus Replisome*

    PubMed Central

    Muylaert, Isabella; Zhao, Zhiyuan; Andersson, Torbjörn; Elias, Per

    2012-01-01

    We have used oriS-dependent transient replication assays to search for species-specific interactions within the herpes simplex virus replisome. Hybrid replisomes derived from herpes simplex virus type 1 (HSV-1) and equine herpesvirus type 1 (EHV-1) failed to support DNA replication in cells. Moreover, the replisomes showed a preference for their cognate origin of replication. The results demonstrate that the herpesvirus replisome behaves as a molecular machine relying on functionally important interactions. We then searched for functional interactions in the replisome context by subjecting HSV-1 UL8 protein to extensive mutagenesis. 52 mutants were made by replacing single or clustered charged amino acids with alanines. Four mutants showed severe replication defects. Mutant A23 exhibited a lethal phenotype, and mutants A49, A52 and A53 had temperature-sensitive phenotypes. Mutants A49 and A53 did not interact with UL52 primase as determined by co-immunoprecipitation experiments. Using GFP-tagged UL8, we demonstrate that all mutants were unable to support formation of ICP8-containing nuclear replication foci. Extended mutagenesis suggested that a highly conserved motif corresponding to mutant A49 serves an important role for establishing a physical contact between UL8 and UL52. The replication-defective mutations affected conserved amino acids, and similar phenotypes were observed when the corresponding mutations were introduced into EHV-1 UL8. PMID:22851167

  16. > REPLACE THIS LINE WITH YOUR PAPER IDENTIFICATION NUMBER (DOUBLE-CLICK HERE TO EDIT) < 2 Abstract--Interactive robots participating in our daily lives

    E-print Network

    Kanda, Takayuki

    communicate with humans. In this paper, we propose a mechanism for two social communication abilities by name using RFID tags; 2) it adapts its interactive behaviors for each child based on a pseudo is to develop a communication robot that operates in an everyday environment, such as a school or a museum

  17. Identification of the residues in the Myb domain of maize C1 that specify the interaction with the bHLH cofactor R

    PubMed Central

    Grotewold, Erich; Sainz, Manuel B.; Tagliani, Laura; Hernandez, J. Marcela; Bowen, Ben; Chandler, Vicki L.

    2000-01-01

    The maize Myb transcription factor C1 depends on the basic helix–loop–helix (bHLH) proteins R or B for regulatory function, but the closely related Myb protein P does not. We have used the similarity between the Myb domains of C1 and P to identify residues that specify the interaction between the Myb domain of C1 and the N-terminal region of R. Substitution of four predicted solvent-exposed residues in the first helix of the second Myb repeat of P with corresponding residues from C1 is sufficient to confer on P the ability to physically interact with R. However, two additional Myb domain amino acid changes are needed to make the P regulatory activity partially dependent on R in maize cells. Interestingly, when P is altered so that it interacts with R, it can activate the Bz1 promoter, normally regulated by C1 + R but not by P. Together, these findings demonstrate that the change of a few amino acids within highly similar Myb domains can mediate differential interactions with a transcriptional coregulator that plays a central role in the regulatory specificity of C1, and that Myb domains play important roles in combinatorial transcriptional regulation. PMID:11095727

  18. Epiphytic microorganisms on strawberry plants ( Fragaria ananassa cv. Elsanta): identification of bacterial isolates and analysis of their interaction with leaf surfaces

    Microsoft Academic Search

    Ursula Krimm; Daniel Abanda-Nkpwatt; Wilfried Schwab; Lukas Schreiber

    2005-01-01

    Epiphytic bacteria were isolated from strawberry plants cultivated in the field or in the greenhouse in order to investigate their interaction with leaf-surface transport properties. Colonization of lower leaf sides was higher on field-grown plants, whereas upper leaf sides were more densely colonized on plants cultivated in the greenhouse. Fungal isolates significantly contributed to total microbial biomass on leaf surfaces

  19. Interaction-Dependent PCR: Identification of Ligand-Target Pairs from Libraries of Ligands and Libraries of Targets in a Single Solution-Phase

    E-print Network

    Liu, David R.

    of interest must successively be assayed against libraries of potential ligands and (ii) the general reliance on immobilized targets or ligands.1 The first constraint limits assay throughput significantly when researchers, interaction-dependent PCR (IDPCR). IDPCR is based on the melting temperature (Tm) difference between duplex

  20. Nanofluids Research: Key Issues

    NASA Astrophysics Data System (ADS)

    Wang, Liqiu; Fan, Jing

    2010-08-01

    Nanofluids are a new class of fluids engineered by dispersing nanometer-size structures (particles, fibers, tubes, droplets) in base fluids. The very essence of nanofluids research and development is to enhance fluid macroscopic and megascale properties such as thermal conductivity through manipulating microscopic physics (structures, properties and activities). Therefore, the success of nanofluid technology depends very much on how well we can address issues like effective means of microscale manipulation, interplays among physics at different scales and optimization of microscale physics for the optimal megascale properties. In this work, we take heat-conduction nanofluids as examples to review methodologies available to effectively tackle these key but difficult problems and identify the future research needs as well. The reviewed techniques include nanofluids synthesis through liquid-phase chemical reactions in continuous-flow microfluidic microreactors, scaling-up by the volume averaging and constructal design with the constructal theory. The identified areas of future research contain microfluidic nanofluids, thermal waves and constructal nanofluids.

  1. Heroin Key Points

    E-print Network

    unknown authors

    The number of heroin border detections in 2006–07 is the highest on record. The weight of heroin detections at the border increased by 65 percent compared with 2005–06. However, it remains the third lowest weight in the last decade. ‘Scatter ’ importations through the postal and air cargo streams continue to account for the largest number of heroin detections. South-East Asia remains the primary embarkation point of heroin into Australia. India has become a key embarkation point. In 2006–07, the weight of national heroin seizures increased by 192 percent. 48 ILLICIT DRUG DATA REPORT 2006–07Main Forms Heroin (diacetylmorphine) is derived from the opium poppy, Papaver somniferum. It is a highly addictive opiate which acts as a depressant on the central nervous system and has strong pain killing characteristics (AIC, 2007). Opium, morphine and codeine are all natural derivatives of the opium poppy. Heroin is harvested from hardened opium gum, which is collected from scored opium seed pods. The gum is then processed with other chemicals, such as ammonium chloride, acetic anhydride and hydrochloric acid, to produce heroin (Interpol, 2007).

  2. 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).

  3. Key recycling in authentication

    E-print Network

    Portmann, Christopher

    2012-01-01

    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 universally composable framework. It turns out that the above argument is insufficient: information about the hash function is in fact leaked in every round to the adversary, and after a bounded finite amount of rounds it is completely known. We show however that this leak is very small, and Wegman and Carter's protocol is still \\epsilon-secure, if \\epsilon-almost strongly universal hash functions are used. This implies that the secret key corresponding to the choice of hash function can be recycled for any task without any additional error than this \\epsilon. For example, if all the messages from many rounds of quant...

  4. Interactive Investigator

    NSDL National Science Digital Library

    Interactive Investigator, available through Virtual Museum Canada, is a website "for anyone with an interest in the different scientific methods used to solve crimes." Users will find a database of forensic science, containing short but informative essays on forensic entomology, toxicology, alcohol analysis, and various other forensic science topics. A simple timeline reviews key dates in the development of forensics, starting with the creation of the Paris Institute for Forensic Science in 1868. But the main feature (and the most fun) is an interactive game, in which players collect and analyze crime scene clues to solve a murder case. Interactive Investigator is also available in French.

  5. Robert Keys Jr Oral History

    E-print Network

    Keys, Robert Jr; Nelson, Ben

    2009-12-07

    Oral history interview with Robert Keys, Jr., conducted by Ben Nelson on December 7, 2009. In this interview, Robert Keys, Jr., a member of the Topeka Bible Church congregation, describes his experiences growing up attending ...

  6. DCCPS: BRP: HBRB: Key Initiatives

    Cancer.gov

    Skip Navigation Twitter Multimedia Home About Key Initiatives Funding Resources Tools Cancer Control & Population Sciences Home Behavioral Research Program Home Health Behaviors Research Branch Health Behaviors Research Branch (HBRB) Key Initiatives Transdisciplinary

  7. DCCPS: BRP: HCIRB: Key Initiatives

    Cancer.gov

    Skip Navigation Twitter Multimedia Home About Key Initiatives Funding Resources Tools Cancer Control & Population Sciences Home Behavioral Research Program Home Health Communication and Informatics Research Branch Key Initiatives Centers of Excellence

  8. DCCPS: BRP: TCRB: Key Initiatives

    Cancer.gov

    Skip Navigation Twitter Multimedia Home About Key Initiatives Funding Resources Tools Cancer Control & Population Sciences Home Behavioral Research Program Home Tobacco Control Research Branch Key Initiatives Active research topic areas and projects Cessation Collaborative

  9. Identification of an Atg8-Atg3 protein-protein interaction inhibitor from the medicines for Malaria Venture Malaria Box active in blood and liver stage Plasmodium falciparum parasites.

    PubMed

    Hain, Adelaide U P; Bartee, David; Sanders, Natalie G; Miller, Alexia S; Sullivan, David J; Levitskaya, Jelena; Meyers, Caren Freel; Bosch, Jürgen

    2014-06-12

    Atg8 is a ubiquitin-like autophagy protein in eukaryotes that is covalently attached (lipidated) to the elongating autophagosomal membrane. Autophagy is increasingly appreciated as a target in diverse diseases from cancer to eukaryotic parasitic infections. Some of the autophagy machinery is conserved in the malaria parasite, Plasmodium. Although Atg8's function in the parasite is not well understood, it is essential for Plasmodium growth and survival and partially localizes to the apicoplast, an indispensable organelle in apicomplexans. Here, we describe the identification of inhibitors from the Malaria Medicine Venture Malaria Box against the interaction of PfAtg8 with its E2-conjugating enzyme, PfAtg3, by surface plasmon resonance. Inhibition of this protein-protein interaction prevents PfAtg8 lipidation with phosphatidylethanolamine. These small molecule inhibitors share a common scaffold and have activity against both blood and liver stages of infection by Plasmodium falciparum. We have derivatized this scaffold into a functional platform for further optimization. PMID:24786226

  10. 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.

  11. Lander Detection and Identification of Hydrothermal Deposits

    NASA Astrophysics Data System (ADS)

    Urquhart, M. L.; Gulick, V.

    2001-01-01

    The role of hydrothermal activity on Mars in altering crustal materials and sequestering volatiles is a critical component in understanding the interactions between the atmosphere, surface, and hydrosphere of Mars. In turn, these interactions are key elements in understanding the martian climate history, surface geology, and potential for past life on Mars. Identification of hydrothermal deposits at the surface of Mars, especially within a region in which the geologic context is clear (e.g. a volcanic region such as a Apollinarius Patera), would provide valuable information about the geologic history of the planet, and would be indicative of a potential site for the search for evidence of life on Mars. Specific hydrothermal mineral assemblages will be dependent on the environmental conditions under which the country rock was altered. Mini-TES, however, has the capacity to identify a wide range of alteration products, and Mossbauer Spectrometer will be able to identify both altered and unaltered iron-bearing bearing minerals, and will yield information on the environment in which iron oxidation has occurred. The instruments on the 2003 rover will have the capability to identify hydrothermal deposits present at the surface of the landing site, potentially yielding information about the nature of the environment in which hydrothermal alteration occurred.

  12. 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

  13. 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

  14. Facing social identity change: interactive effects of current and projected collective identification on expectations regarding future self-esteem and psychological well-being.

    PubMed

    Packer, Dominic J; Chasteen, Alison L; Kang, Sonia K

    2011-09-01

    We hypothesized that prospective changes in social identity that involve transitioning out of a currently valued group would be associated with negative expectations regarding future states, but that this effect would be mitigated among individuals who expect to belong to a future in-group of similar importance. Consistent with predictions, strongly identified young adults in two studies projected significantly lower self-esteem/psychological well-being in old age than weakly identified young adults. Critically, however, this effect was fully attenuated if they expected to identify with their future aged in-group when they were old. Study 2 showed that the capacity for projected identification to buffer projected well-being among strongly identified young adults was contingent on their membership in the future in-group being highly salient. Analyses of participants' written descriptions of old age (Study 1) and a valence manipulation (Study 2) indicated that these effects were not attributable to the anticipated valence of future selves/states, but rather to the value placed on current and future group memberships. PMID:21884542

  15. Identification and Mutagenesis of a Highly Conserved Domain in Troponin T Responsible for Troponin I Binding: Potential Role for Coiled Coil Interaction

    Microsoft Academic Search

    Raymund Stefancsik; Prakash K. Jha; Satyapriya Sarkar

    1998-01-01

    Troponin T (TnT), a thin filament myofibrillar protein, is essential for the Ca2+ regulation of striated muscle contraction in vertebrates, both in vivo and in vitro. To understand the role of TnT in this process, its interaction with two other troponin components, troponin I (TnI) and troponin C (TnC) was examined by using the yeast two hybrid system, which is

  16. Identification of Novel Inhibitors of Human Immunodeficiency Virus Type 1 Replication by In Silico Screening Targeting Cyclin T1/Tat Interaction

    PubMed Central

    Hamasaki, Takayuki; Okamoto, Mika

    2013-01-01

    Human immunodeficiency virus type 1 (HIV-1) transcription is essential for viral replication and the only step for viral genome amplification. Cyclin T1 (CycT1) interacts with HIV-1 Tat and transactivation-responsive (TAR) RNA, leading to the activation of viral transcription through the hyperphosphorylation of RNA polymerase II (RNAPII). Thus, the CycT1/Tat/TAR RNA interaction represents a novel target for inhibition of HIV-1 replication. In this study, we conducted in silico screening of compounds targeting the CycT1/Tat/TAR RNA complex and found that two structurally related compounds (C1 and C2) had high docking scores for a model of the complex. These compounds proved inhibitory to HIV-1 replication in tumor necrosis factor alpha-stimulated chronically infected cells. In addition, C3, a derivative of C1 and C2, was found to be a more potent inhibitor of HIV-1 replication in chronically infected cells. C3 also inhibited HIV-1 replication in acutely infected cells. The compound could suppress Tat-mediated HIV-1 long terminal repeat-driven gene expression and phosphorylation of RNAPII through inhibition of Tat binding to CycT1. Furthermore, the docking pose of C3 was defined by analyses for its in silico docking energy and in vitro antiviral activity, which indicates that C3 interacts with Tat-binding amino acids of CycT1. Thus, a series of compounds described herein are novel inhibitors of HIV-1 transcription through inhibition of CycT1/Tat interaction. PMID:23274668

  17. Identification of a protein, G0S2, that lacks Bcl-2 homology domains and interacts with and antagonizes Bcl-2

    PubMed Central

    Welch, Christian; Santra, Manas K.; El-Assaad, Wissal; Zhu, Xiaochun; Huber, Wade E.; Keys, Richard A.; Teodoro, Jose G.; Green, Michael R.

    2010-01-01

    The Bcl-2 family of proteins consists of both anti-apoptotic and pro-apoptotic factors, which share sequence homology within conserved regions known as Bcl-2 homology (BH) domains. Interactions between Bcl-2 family members, as well as with other proteins, regulate apoptosis through control of mitochondrial membrane permeability and release of cytochrome c. Here we identify a novel regulator of apoptosis that lacks BH domains but acts by binding Bcl-2 and modulating its anti-apoptotic activity. To identify regulators of apoptosis, we performed expression profiling in human primary fibroblasts treated with tumor necrosis factor alpha (TNF?), a potent inflammatory cytokine that can regulate apoptosis and functions, at least in part, by inducing expression of specific genes through NF-?B. We found that the gene undergoing maximal transcriptional induction following TNF? treatment was G0/G1 switch gene 2 (G0S2), whose activation also required NF-?B. We show that G0S2 encodes a mitochondrial protein that specifically interacts with Bcl-2 and promotes apoptosis by preventing the formation of protective Bcl-2/Bax heterodimers. We further demonstrate that ectopic expression of G0S2 induces apoptosis in diverse human cancer cell lines in which endogenous G0S2 is normally epigenetically silenced. Our results reveal a novel pro-apoptotic factor that is induced by TNF? through NF-?B, and which interacts with and antagonizes Bcl-2. PMID:19706769

  18. Identification of potential drug-drug interactions between antiretroviral drugs from prescriptions in the private health-care sector in South Africa.

    PubMed

    Katende-Kyenda, N L; Lubbe, M S; Serfontein, J H P; Truter, I

    2012-03-01

    The aim of this study was to identify potential drug-drug interactions (DDIs) between antiretroviral drugs (ARVs) and to determine whether prescribed daily doses (PDDs) from prescriptions can be used in the evaluation of these interactions. A quantitative, retrospective drug utilization study was performed on 49,995 and 81,096 ARV prescriptions from a South African pharmacy benefit management company, which were prescribed to 7664 and 10,162 HIV patients for 2005 and 2006, respectively. Potential DDIs identified across different age groups were 778 for 2005 and 1155 for 2006; the majority occurred in patients aged 19 to ?45 years. The potential DDIs identified between ARVs were all interacting at clinical significance level 2 according to guidelines indicated by Tatro. These results demonstrate that potential DDIs were identified between ARVs mostly in three ARV combinations: Kaletra(®) (lopinavir/ritonavir) and efavirenz, lopinavir/ritonavir and nevirapine and combinations of indinavir and ritonavir. There is a need for more education on the prescribing protocols for ARVs in the treatment of HIV-infected patients in the private health-care sector in South Africa. PMID:22581868

  19. Bugguide Identification, Images, & Information For Insects, Spiders & Their Kin For the United States & Canada

    NSDL National Science Digital Library

    0000-00-00

    BugGuide is devoted to identification and natural history of insects through imagery. The images are uploaded and examined by amateur volunteers, and the site is hosted by Iowa State University. All of the insect orders and several non-insect arthropods are included in the database. There also is an interactive Lucid key available. Attempts are made to follow current taxonomic efforts. The site is easy to navigable through and has some very nice photos. (Not all photos were reviewed for taxonomic accuracy.)

  20. On Compression of Cryptographic Keys

    E-print Network

    Chan, Aldar C-F

    2007-01-01

    Any secured system can be modeled as a capability-based access control system in which each user is given a set of secret keys of the resources he is granted access to. In some large systems with resource-constrained devices, such as sensor networks and RFID systems, the design is sensitive to memory or key storage cost. With a goal to minimize the maximum users' key storage, key compression based on key linking, that is, deriving one key from another without compromising security, is studied. A lower bound on key storage needed for a general access structure with key derivation is derived. This bound demonstrates the theoretic limit of any systems which do not trade off security and can be treated as a negative result to provide ground for designs with security tradeoff. A concrete, provably secure key linking scheme based on pseudorandom functions is given. Using the key linking framework, a number of key pre-distribution schemes in the literature are analyzed.