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1

Illustrated Plant Identification Keys: An Interactive Tool to Learn Botany  

ERIC Educational Resources Information Center

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…

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

2011-01-01

2

ChiloKey, an interactive identification tool for the geophilomorph centipedes of Europe (Chilopoda, Geophilomorpha).  

PubMed

ChiloKey is a matrix-based, interactive key to all 179 species of Geophilomorpha (Chilopoda) recorded from Europe, including species of uncertain identity and those whose morphology is known partially only. The key is intended to assist in identification of subadult and adult specimens, by means of microscopy and simple dissection techniques whenever necessary. The key is freely available through the web at: http://www.biologia.unipd.it/chilokey/ and at http://www.interactive-keys.eu/chilokey/. PMID:25349493

Bonato, Lucio; Minelli, Alessandro; Lopresti, Massimo; Cerretti, Pierfilippo

2014-01-01

3

ChiloKey, an interactive identification tool for the geophilomorph centipedes of Europe (Chilopoda, Geophilomorpha)  

PubMed Central

Abstract ChiloKey is a matrix-based, interactive key to all 179 species of Geophilomorpha (Chilopoda) recorded from Europe, including species of uncertain identity and those whose morphology is known partially only. The key is intended to assist in identification of subadult and adult specimens, by means of microscopy and simple dissection techniques whenever necessary. The key is freely available through the web at: http://www.biologia.unipd.it/chilokey/ and at http://www.interactive-keys.eu/chilokey/. PMID:25349493

Bonato, Lucio; Minelli, Alessandro; Lopresti, Massimo; Cerretti, Pierfilippo

2014-01-01

4

Interactive Identification Using the Internet  

Microsoft Academic Search

Abstract Computer-based interactive keyshave several advantages over conventional keys: characters can be used, and their values changed, in any order; a correct identification can be made in spite of errors by the user or in the data; errors which were circumvented by the error-tolerance mechanismcan be located; the user can express uncertaintyby entering morethan one state value, or a range

M. J. Dallwitz; T. A. Paine; E. J. Zurcher

5

Ash Tree Identification Key Ash Tree Characteristics  

E-print Network

and furrows form diamond shapes in older bark (green & white ash) opposite arrangements ­ buds, leavesAsh Tree Identification Key Ash Tree Characteristics Bark Branches diamond patterned ­ ridges berries Walnut, Hickory, Mountain-Ash: alternate branching #12;Identifying Emerald Ash Borer what to do

Walter, M.Todd

6

Identification of Key Barriers in Workforce Development  

SciTech Connect

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.

None

2008-03-31

7

Species Identification Key of Korean Mammal Hair  

PubMed Central

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

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

2014-01-01

8

Non-interactive Public-Key Cryptography  

Microsoft Academic Search

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

Ueli M. Maurer; Yacov Yacobi

1991-01-01

9

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

PubMed Central

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

2013-01-01

10

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

PubMed Central

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

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

2014-01-01

11

Key Results of Interaction Models with Centering  

ERIC Educational Resources Information Center

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…

Afshartous, David; Preston, Richard A.

2011-01-01

12

MOSCHweb — a matrix-based interactive key to the genera of the Palaearctic Tachinidae (Insecta, Diptera)  

PubMed Central

Abstract We provide a general overview of features and technical specifications of an original interactive key web application for the identification of Palaearctic Tachinidae genera. The full list of terminal taxa included in the key, which is the most updated list of genera currently recorded for the Palaearctic Region, is given. We also briefly discuss the need for dealing with detailed and standardized taxa descriptions as a base to keep matrix-based interactive tools easily updated, by proposing a standardized protocol. PMID:22792031

Cerretti, Pierfilippo; Tschorsnig, Hans-Peter; Lopresti, Massimo; Giovanni, Filippo Di

2012-01-01

13

Decoding time for the identification of musical key.  

PubMed

This study examines the decoding times at which the brain processes structural information in music and compares them to timescales implicated in recent work on speech. Combining an experimental paradigm based on Ghitza and Greenberg (Phonetica, 66(1-2), 113-126, 2009) for speech with the approach of Farbood et al. (Journal of Experimental Psychology: Human Perception and Performance, 39(4), 911-918, 2013) for musical key-finding, listeners were asked to judge the key of short melodic sequences that were presented at a highly a compressed rate with varying durations of silence inserted in a periodic manner in the audio signal. The distorted audio signals comprised signal-silence alternations showing error rate curves that identify peak performance centered around an event rate of 5-7 Hz (143-200 ms interonset interval; 300-420 beats/min), where event rate is defined as the average rate of pitch change. The data support the hypothesis that the perceptual analysis of music entails the processes of parsing the signal into chunks of the appropriate temporal granularity and decoding the signal for recognition. The music-speech comparison points to similarities in how auditory processing builds on the specific temporal structure of the input, and how that structure interacts with the internal temporal dynamics of the neural mechanisms underpinning perception. PMID:25487869

Farbood, Morwaread M; Rowland, Jess; Marcus, Gary; Ghitza, Oded; Poeppel, David

2014-12-10

14

Identification keys to larval and adult female mosquitoes (Diptera: Culicidae) of New Zealand  

Microsoft Academic Search

Keys are presented for the identification of larval and adult female life stages of the 12 endemic and four exotic mosquito species known for New Zealand (the keys are to species not genera). The keys include the recent arrival, Ochlerotatus (Ochlerotatus) camptorhynchus (Thomson), and a monotypic genus endemic to New Zealand. A number of Aedine subgenera have been recently raised

Amy E. Snell

2005-01-01

15

Quantum key distribution using transverse spin wave-optical interactions  

NASA Astrophysics Data System (ADS)

We describe a frequency-coded scheme to implement the BB84 quantum key distribution protocol using spin wave (SW)-optical interactions. The interaction of SWs with optical coherent states allows TE<-->TM mode conversion with simultaneous change of frequency and polarization while introducing a phase difference between the two modes. To implement the BB84 protocol, key bits are encoded as relative phases between the TE and TM modes. The proposed scheme offers a higher key rate, due to a modulation frequency as high as 25 GHz, which also relaxes the specifications on the optical filter at the receiver. In addition, SW-optical interactions yield the added security of truly single-sideband modulation.

Kumar, Pradeep; Prabhakar, Anil

2011-03-01

16

Using Web-Based Key Character and Classification Instruction for Teaching Undergraduate Students Insect Identification  

NASA Astrophysics Data System (ADS)

The purpose of the study was to determine whether undergraduate students receiving web-based instruction based on traditional, key character, or classification instruction differed in their performance of insect identification tasks. All groups showed a significant improvement in insect identifications on pre- and post-two-dimensional picture specimen quizzes. The study also determined student performance on insect identification tasks was not as good as for family-level identification as compared to broader insect orders and arthropod classification identification tasks. Finally, students erred significantly more by misidentification than misspelling specimen names on prepared specimen quizzes. Results of this study support that short web-based insect identification exercises can improve insect identification performance. Also included is a discussion of how these results can be used in teaching and future research on biological identification.

Golick, Douglas A.; Heng-Moss, Tiffany M.; Steckelberg, Allen L.; Brooks, David. W.; Higley, Leon G.; Fowler, David

2013-08-01

17

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

E-print Network

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...

Law, James Michael

2012-06-07

18

Using Web-Based Key Character and Classification Instruction for Teaching Undergraduate Students Insect Identification  

ERIC Educational Resources Information Center

The purpose of the study was to determine whether undergraduate students receiving web-based instruction based on traditional, key character, or classification instruction differed in their performance of insect identification tasks. All groups showed a significant improvement in insect identifications on pre- and post-two-dimensional picture…

Golick, Douglas A.; Heng-Moss, Tiffany M.; Steckelberg, Allen L.; Brooks, David. W.; Higley, Leon G.; Fowler, David

2013-01-01

19

Weed Identification: Using Plant Structures as a Key  

E-print Network

Paul A. Baumann Professor and Extension W eed Specialist, The T exas A&M University System. B-6079 3-99 U si n g P lan t S t r u ct u r e s a s a Ke y W eed Identification: eed identification is necessary to the success of any... that develop below ground. Plant shoots can arise from undergroundnodes on these stems. o c r e a s o i l s u r f a c e r h i z o m e n o d e s 14 T ubers are thickened underground stems that develop at the end of rhizomes. Stolons are roots that grow...

Baumann, Paul A.

2002-04-15

20

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

ERIC Educational Resources Information Center

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…

Sorgo, Andrej

2006-01-01

21

A Key for the Identification of Eighteen Common Timbers.  

ERIC Educational Resources Information Center

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,…

Thomas, P. A.

1991-01-01

22

Identification of key amino acid residues in Neisseria polysaccharea amylosucrase.  

PubMed

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

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

2000-05-26

23

Statistical mechanics approach to lock-key supramolecular chemistry interactions.  

PubMed

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

Odriozola, Gerardo; Lozada-Cassou, Marcelo

2013-03-01

24

An identification key for the five most common species of Metastrongylus.  

PubMed

Species of the Metastrongylus genus, the lung nematodes of pigs that require an intermediate host (earthworm) to complete their cycle, pose a potential risk to both livestock and humans. This parasite which can result in lung pathology and mixed infections with other pathogens (e.g. viruses) can be fatal to pigs. Although this genus is distributed worldwide, there are no classification keys for identifying this common parasite species. In this work, we take advantage of parasitological surveys of wild boar (Sus scrofa) in northern and central Spain and southern Poland to develop a morphological identification key for the five most common Metastrongylus species (Metastrongylus apri, Metastrongylus pudendotectus, Metastrongylus salmi, Metastrongylus confusus and Metastrongylus asymetricus). In addition, we provide the first record of M. confusus in Spain, probably unidentified until now due to the lack of appropriate identification keys. We hope that this user-friendly identification key will enable parasitologists and veterinary practitioners to avoid further misclassifications of Metastrongylus species. PMID:25060317

Gassó, Diana; Rossi, Luca; Mentaberre, Gregorio; Casas, Encarna; Velarde, Roser; Nosal, Pawel; Serrano, Emmanuel; Segales, Joaquim; Fernandez-Llario, Pedro; Feliu, Carles

2014-09-01

25

New structural insights into the apelin receptor: identification of key residues for apelin binding.  

PubMed

Apelin is the endogenous ligand of the orphan 7-transmembrane domain GPCR APJ, now named the apelin receptor (ApelinR). Apelin plays a prominent role in body fluid and cardiovascular homeostasis. To better understand the structural organization of the ApelinR, we built 3 homology 3-dimensional (3D) models of the human ApelinR using the validated cholecystokinin receptor-1 3D model or the X-ray structures of the ?2-adrenergic and CXCR4 receptors as templates. Docking of the pyroglutamyl form of apelin 13 (pE13F) into these models revealed the conservation at the bottom of the binding site of a hydrophobic cavity in which the C-terminal Phe of pE13F was embedded. In contrast, at the top of the binding site, depending on the model, different interactions were visualized between acidic residues of the ApelinR and the basic residues of pE13F. Using site-directed mutagenesis, we showed that Asp 92, Glu 172, and Asp 282 of rat ApelinR are key residues in apelin binding by interacting with Lys 8, Arg 2, and Arg 4 of pE13F, respectively. These residues are only seen in the CXCR4-based ApelinR 3D model, further validating this model. These findings bring new insights into the structural organization of the ApelinR and the mode of apelin binding.-Gerbier, R., Leroux, V., Couvineau, P., Alvear-Perez, R., Maigret, B., Llorens-Cortes, C., Iturrioz, X. New structural insights into the apelin receptor: identification of key residues for apelin binding. PMID:25359495

Gerbier, Romain; Leroux, Vincent; Couvineau, Pierre; Alvear-Perez, Rodrigo; Maigret, Bernard; Llorens-Cortes, Catherine; Iturrioz, Xavier

2014-10-30

26

Magnon-Photon interactions for Quantum Key Distribution  

NASA Astrophysics Data System (ADS)

We propose an implementation of quantum key distribution (QKD) protocol using magnon-photon interactions in dielectric waveguides. Starting from the Hamiltonian of spin wave-optical interactions in a symmetric dielectric waveguide, we derive the single-photon transformations that allow us to define two non-orthogonal basis sets, which are isomorphic to polarization basis of single-photon. Implementation of the BB84 and B92 protocols is then straightforward. The principal advantage of our scheme is the higher quantum bit error rate (QBER) (37.5%) compared to polarization-coded scheme (25%) for simple intercept/resend attack. This considerably relaxes the specifications of optical components. Finally, we consider the effect of low conversion efficiency on QBER.

Kumar, P.; Prabhakar, A.

2011-07-01

27

Functional module identification in protein interaction networks by interaction patterns  

PubMed Central

Motivation: Identifying functional modules in protein–protein interaction (PPI) networks may shed light on cellular functional organization and thereafter underlying cellular mechanisms. Many existing module identification algorithms aim to detect densely connected groups of proteins as potential modules. However, based on this simple topological criterion of ‘higher than expected connectivity’, those algorithms may miss biologically meaningful modules of functional significance, in which proteins have similar interaction patterns to other proteins in networks but may not be densely connected to each other. A few blockmodel module identification algorithms have been proposed to address the problem but the lack of global optimum guarantee and the prohibitive computational complexity have been the bottleneck of their applications in real-world large-scale PPI networks. Results: In this article, we propose a novel optimization formulation LCP2 (low two-hop conductance sets) using the concept of Markov random walk on graphs, which enables simultaneous identification of both dense and sparse modules based on protein interaction patterns in given networks through searching for LCP2 by random walk. A spectral approximate algorithm SLCP2 is derived to identify non-overlapping functional modules. Based on a bottom-up greedy strategy, we further extend LCP2 to a new algorithm (greedy algorithm for LCP2) GLCP2 to identify overlapping functional modules. We compare SLCP2 and GLCP2 with a range of state-of-the-art algorithms on synthetic networks and real-world PPI networks. The performance evaluation based on several criteria with respect to protein complex prediction, high level Gene Ontology term prediction and especially sparse module detection, has demonstrated that our algorithms based on searching for LCP2 outperform all other compared algorithms. Availability and implementation: All data and code are available at http://www.cse.usf.edu/?xqian/fmi/slcp2hop/. Contact: yijie@mail.usf.edu or xqian@ece.tamu.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24085567

Wang, Yijie; Qian, Xiaoning

2014-01-01

28

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

USGS Publications Warehouse

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.

Robbins, E.I.

2000-01-01

29

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...

30

Image use in field guides and identification keys: review and recommendations  

PubMed Central

Background and aims Although illustrations have played an important role in identification keys and guides since the 18th century, their use has varied widely. Some keys lack all illustrations, while others are heavily illustrated. Even within illustrated guides, the way in which images are used varies considerably. Here, we review image use in paper and electronic guides, and establish a set of best practices for image use in illustrated keys and guides. Scope Our review covers image use in both paper and electronic guides, though we only briefly cover apps for mobile devices. With this one exception, we cover the full range of guides, from those that consist only of species descriptions with no keys, to lavishly illustrated technical keys. Emphasis is placed on how images are used, not on the operation of the guides and key, which has been reviewed by others. We only deal with operation when it impacts image use. Main points Few illustrated keys or guides use images in optimal ways. Most include too few images to show taxonomic variation or variation in characters and character states. The use of multiple images allows easier taxon identification and facilitates the understanding of characters. Most images are usually not standardized, making comparison between images difficult. Although some electronic guides allow images to be enlarged, many do not. Conclusions The best keys and guides use standardized images, displayed at sizes that are easy to see and arranged in a standardized manner so that similar images can be compared across species. Illustrated keys and glossaries should contain multiple images for each character state so that the user can judge variation in the state. Photographic backgrounds should not distract from the subject and, where possible, should be of a standard colour. When used, drawings should be prepared by professional botanical illustrators, and clearly labelled. Electronic keys and guides should allow images to be enlarged so that their details can be seen. PMID:22476475

Leggett, Roxanne; Kirchoff, Bruce K.

2011-01-01

31

Phage display library screening for identification of interacting protein partners.  

PubMed

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

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

2015-01-01

32

Identification of key genes affecting disease free survival time of pediatric acute lymphoblastic leukemia based on bioinformatic analysis.  

PubMed

The poor prognosis of pediatric acute lymphoblastic leukemia (ALL) indicates the existence of key candidate genes that affect pediatric ALL and its prognosis. The limma package in R was applied to screen differentially expressed genes (DEGs), and the Survival package and KMsurv package in R were used to screen disease free survival time related genes (prognosis genes). Then, based on latent pathway identification analysis (LPIA), latent pathways were identified, and pathway-pathway interaction network was constructed and visualized by Cytoscape. Based on the expression values of 8284 genes in 126 chips, 2796 DEGs and 353 prognosis genes were screened out. After overlapping DEGs and prognosis genes, 75 key genes were identified, which were most significantly enriched in 25 GO functions and chronic myeloid leukemia pathway. For the 75 key genes, 27 disease risk sub-pathways were identified, and HK3, HNMT, SULT2B1, KYNU, and PTGS2 were the significant key genes which were enriched in these sub-pathways. Furthermore, based on pathway-pathway interaction analysis, HK3 and PTGS2 were predicted as the most important genes. Through glycolysis and arachidonic acid metabolism, HK3 and PTGS2 might play important roles in pediatric ALL and its prognosis, and thus, might be potential targets for therapeutic intervention to suppress pediatric ALL. PMID:25172542

Gao, Hai-Yan; Luo, Xin-Guo; Chen, Xi; Wang, Jing-Hua

2015-01-01

33

Generalized Beimel-Chor Schemes for Broadcast Encryption and Interactive Key Distribution  

Microsoft Academic Search

In 1993, Beimel and Chor presented an unconditionally secure interactive protocolwhich allows a subset of users in a network to establish a common key. This schememade use of a key predistribution scheme due to Blom.In this paper, we describe some variations and generalizations of the Beimel-Chorscheme, including broadcast encryption schemes as well as interactive key distributionschemes. Our constructions use the

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

1998-01-01

34

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

PubMed

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

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

2014-01-01

35

PLANTMICROBEINSECT INTERACTIONS: Cytokinins as key regulators in plantmicrobeinsect  

E-print Network

. These phytohormones may have been the target of arthropods and pathogens over the course of the evolutionary arms race. Cytokinin-mediated effects strongly impact not only plant growth and defence but also the whole community, symbiosis Introduction Plants constitute key nutritional resources for many organ- isms on Earth

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

36

Recent analysis of key plasma wall interactions issues for ITER  

Microsoft Academic Search

Plasma wall interaction (PWI) is important for the material choice in ITER and for the plasma scenarios compatible with material constraints. In this paper, different aspects of the PWI are assessed in their importance for the initial wall materials choice: CFC for the strike point tiles, W in the divertor and baffle and Be on the first wall. Further material

Joachim Roth; E. Tsitrone; A. Loarte; Th. Loarer; G. Counsell; R. Neu; V. Philipps; S. Brezinsek; M. Lehnen; P. Coad; Ch. Grisolia; K. Schmid; K. Krieger; A. Kallenbach; B. Lipschultz; R. Doerner; R. Causey; V. Alimov; W. Shu; O. Ogorodnikova; A. Kirschner; G. Federici; A. Kukushkin

2009-01-01

37

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...

38

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

PubMed

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

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

2010-09-01

39

Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion  

PubMed Central

Gene regulatory interactions underlying the early stages of non-genotoxic carcinogenesis are poorly understood. Here, we have identified key candidate regulators of phenobarbital (PB)-mediated mouse liver tumorigenesis, a well-characterized model of non-genotoxic carcinogenesis, by applying a new computational modeling approach to a comprehensive collection of in vivo gene expression studies. We have combined our previously developed motif activity response analysis (MARA), which models gene expression patterns in terms of computationally predicted transcription factor binding sites with singular value decomposition (SVD) of the inferred motif activities, to disentangle the roles that different transcriptional regulators play in specific biological pathways of tumor promotion. Furthermore, transgenic mouse models enabled us to identify which of these regulatory activities was downstream of constitutive androstane receptor and ?-catenin signaling, both crucial components of PB-mediated liver tumorigenesis. We propose novel roles for E2F and ZFP161 in PB-mediated hepatocyte proliferation and suggest that PB-mediated suppression of ESR1 activity contributes to the development of a tumor-prone environment. Our study shows that combining MARA with SVD allows for automated identification of independent transcription regulatory programs within a complex in vivo tissue environment and provides novel mechanistic insights into PB-mediated hepatocarcinogenesis. PMID:24464994

Luisier, Raphaëlle; Unterberger, Elif B.; Goodman, Jay I.; Schwarz, Michael; Moggs, Jonathan; Terranova, Rémi; van Nimwegen, Erik

2014-01-01

40

Manoeuvring Ship Model Identification and Interacting Multiple Model Tracking Algorithm  

E-print Network

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

Mihaylova, Lyudmila

41

INTERACTIVE KEYS TO RUST FUNGI AND OTHER WEB-BASED RESOURCES  

Technology Transfer Automated Retrieval System (TEKTRAN)

A monographic treatment with an interactive key to species of Ravenelia worldwide is now available on the web at the USDA/ARS Systematic Botany and Mycology Laboratory (). This system includes descriptions, illustrations, nomenclators for teleomorph and anamorph names, hosts,...

42

THE USE OF SPME AND MULTIDIMENSIONAL GC-MS-OLFACTOMETRY SYSTEM FOR IDENTIFICATION OF KEY ODORANTS FROM SWINE MANURE  

Technology Transfer Automated Retrieval System (TEKTRAN)

Swine operations are sources of volatile organic compounds and odor with swine manure being the primary source of odor from swine operations. Identification of specific key odorants can improve the understanding of odor generation, odor fate, and odor control approaches. In this research, solid ph...

43

Interaction between Truth and Belief as the key to non-extensive  

E-print Network

Interaction between Truth and Belief as the key to non-extensive statistical physics Flemming. This rests on the primary assumption that truth and belief interact and on a natural variational principle observations and see if you can accept the considerations below (numbered 1 ­ 8). #12;1 Events have truth

Topsøe, Flemming

44

Identification of chikungunya virus interacting proteins in mammalian cells.  

PubMed

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

Paingankar, Mandar S; Arankalle, Vidya A

2014-06-01

45

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

PubMed Central

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

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

2012-01-01

46

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

PubMed Central

‘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

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

2015-01-01

47

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

PubMed

'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

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

2015-02-19

48

Characterization of the structural features and interactions of sclerostin: molecular insight into a key regulator of Wnt-mediated bone formation.  

PubMed

The secreted glycoprotein sclerostin has recently emerged as a key negative regulator of Wnt signaling in bone and has stimulated considerable interest as a potential target for therapeutics designed to treat conditions associated with low bone mass, such as osteoporosis. We have determined the structure of sclerostin, which resulted in the identification of a previously unknown binding site for heparin, suggestive of a functional role in localizing sclerostin to the surface of target cells. We have also mapped the interaction site for an antibody that blocks the inhibition of Wnt signaling by sclerostin. This shows minimal overlap with the heparin binding site and highlights a key role for this region of sclerostin in protein interactions associated with the inhibition of Wnt signaling. The conserved N- and C-terminal arms of sclerostin were found to be unstructured, highly flexible, and unaffected by heparin binding, which suggests a role in stabilizing interactions with target proteins. PMID:19208630

Veverka, Vaclav; Henry, Alistair J; Slocombe, Patrick M; Ventom, Andrew; Mulloy, Barbara; Muskett, Frederick W; Muzylak, Mariusz; Greenslade, Kevin; Moore, Adrian; Zhang, Li; Gong, Jianhua; Qian, Xueming; Paszty, Chris; Taylor, Richard J; Robinson, Martyn K; Carr, Mark D

2009-04-17

49

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

E-print Network

of the evolutionary arms race between plants and their biotic partners to hijack the plant metabolism, control its­microbe­insect interactions. 5. Cytokinin-mediated effects strongly impact not only plant growth and defence but also allocation, plant signalling, symbiosis Introduction Plants constitute key nutritional resources for many

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

50

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

PubMed

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

Kim, Hyunsung

2014-01-01

51

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

PubMed Central

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

Kim, Hyunsung

2014-01-01

52

Identification of non-pyramidal key blocks in jointed rock masses for tunnel excavation  

Microsoft Academic Search

Key block methods based on ubiquitous approaches have been widely used over the past 30 years to perform rapid analyses of rock mass stability. Although these methods have meant a great step forward, they only consider pyramidal key blocks.This paper provides a new geometrical method for identifying both pyramidal and non-pyramidal key blocks in discontinuous rock masses for tunnel excavation.

C. González-Palacio; A. Menéndez-Díaz; A. E. Álvarez-Vigil; C. González-Nicieza

2005-01-01

53

Identification of Protein Interactions Involved in Cellular Signaling  

PubMed Central

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

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

2013-01-01

54

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

PubMed

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

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

2014-09-01

55

Identification of key residues involved in adrenomedullin binding to the AM1 receptor  

PubMed Central

Background and Purpose Adrenomedullin (AM) is a peptide hormone whose receptors are members of the class B GPCR family. They comprise a heteromer between the GPCR, the calcitonin receptor-like receptor and one of the receptor activity-modifying proteins 1–3. AM plays a significant role in angiogenesis and its antagonist fragment AM22–52 can inhibit blood vessel and tumour growth. The mechanism by which AM interacts with its receptors is unknown. Experimental Approach We determined the AM22–52 binding epitope for the AM1 receptor extracellular domain using biophysical techniques, heteronuclear magnetic resonance spectroscopy and alanine scanning. Key Results Chemical shift perturbation experiments located the main binding epitope for AM22–52 at the AM1 receptor to the C-terminal 8 amino acids. Isothermal titration calorimetry of AM22–52 alanine-substituted peptides indicated that Y52, G51 and I47 are essential for AM1 receptor binding and that K46 and P49 and R44 have a smaller role to play. Characterization of these peptides at the full-length AM receptors was assessed in Cos7 cells by cAMP assay. This confirmed the essential role of Y52, G51 and I47 in binding to the AM1 receptor, with their substitution resulting in ?100-fold reduction in antagonist potency compared with AM22–52. R44A, K46A, S48A and P49A AM22–52 decreased antagonist potency by approximately 10-fold. Conclusions and Implications This study localizes the main binding epitope of AM22–52 to its C-terminal amino acids and distinguishes essential residues involved in this binding. This will inform the development of improved AM receptor antagonists. PMID:23351143

Watkins, HA; Au, M; Bobby, R; Archbold, JK; Abdul-Manan, N; Moore, JM; Middleditch, MJ; Williams, GM; Brimble, MA; Dingley, AJ; Hay, DL

2013-01-01

56

An interactive multi-entry key to the species of Megalostomis Chevrolat, with description of a new species from Paraguay (Chrysomelidae, Cryptocephalinae)  

PubMed Central

Abstract The main goal of this contribution is to release an interactive multi-entry key to all known species of the genus Megalostomis Chevrolat. This key constitutes a new tool created to aid the identification of the species of this diverse genus, which occasionally may be difficult to identify to the species-level, due to the lack of reference collections for most countries within its distribution range, and to the presence of intra-specific variation and secondary sexual characters. It is expected that this on-line key will facilitate future periodic updates, and will benefit all those persons interested in identifying these taxa. The present paper also includes the description of Megalostomis juanenrique sp. n., a new species from Paraguay. In addition, Megalostomis gigas Lacordaire, and Megalostomis robustipes Monrós are newly cited for the fauna of Paraguay. The online interactive Lucid key is available at http://keys.lucidcentral.org/keys/v3/megalostomis. Offline Lucid data files in LIF and SDD formats are also available at doi: 10.3897/zookeys.425.7631.app1 and doi: 10.3897/zookeys.425.7631.app2. PMID:25147449

Agrain, Federico A.

2014-01-01

57

GINIP, a G?i-interacting protein, functions as a key modulator of peripheral GABAB receptor-mediated analgesia.  

PubMed

One feature of neuropathic pain is a reduced GABAergic inhibitory function. Nociceptors have been suggested to play a key role in this process. However, the mechanisms behind nociceptor-mediated modulation of GABA signaling remain to be elucidated. Here we describe the identification of GINIP, a G?i-interacting protein expressed in two distinct subsets of nonpeptidergic nociceptors. GINIP null mice develop a selective and prolonged mechanical hypersensitivity in models of inflammation and neuropathy. GINIP null mice show impaired responsiveness to GABAB, but not to delta or mu opioid receptor agonist-mediated analgesia specifically in the spared nerve injury (SNI) model. Consistently, GINIP-deficient dorsal root ganglia neurons had lower baclofen-evoked inhibition of high-voltage-activated calcium channels and a defective presynaptic inhibition of lamina IIi interneurons. These results further support the role of unmyelinated C fibers in injury-induced modulation of spinal GABAergic inhibition and identify GINIP as a key modulator of peripherally evoked GABAB-receptors signaling. PMID:25242222

Gaillard, Stéphane; Lo Re, Laure; Mantilleri, Annabelle; Hepp, Régine; Urien, Louise; Malapert, Pascale; Alonso, Serge; Deage, Michael; Kambrun, Charline; Landry, Marc; Low, Sarah A; Alloui, Abdelkrim; Lambolez, Bertrand; Scherrer, Grégory; Le Feuvre, Yves; Bourinet, Emmanuel; Moqrich, Aziz

2014-10-01

58

SIM as a key of user identification: enabling seamless user identity management in communication networks  

Microsoft Academic Search

Easy and secure access is of key importance in acceptance of new mobile services. This paper extends the possible use of the SIM as authenticator in the online world. The paper proposes Near Field Communication (NFC) technology as a transfer technology between the mobile handset and other devices. A possible architecture is shown, future SIM requirements and secure key transfer

György Kálmán; Josef Noll

59

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

ERIC Educational Resources Information Center

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

Hager, Stephen B.; Cosentino, Bradley J.

2006-01-01

60

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.

61

Nanoparticle-protein interactions: from crucial plasma proteins to key enzymes  

NASA Astrophysics Data System (ADS)

Studying the effects of NPs on proteins may help understanding potential biological injuries such as changes in protein fibrillation, exposure of new antigenic epitopes, and loss of function such as enzymatic activity impairment. In this mini-review we present recent data which help understand the basis of NP-protein interactions and their subsequent potential effects on key mediators of biological functions such as enzymes.

Sanfins, Elodie; Dairou, Julien; Rodrigues-Lima, Fernando; Dupret, Jean-Marie

2011-07-01

62

Identification of novel CBP interacting proteins in embryonic orofacial tissue  

SciTech Connect

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.

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

63

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

ERIC Educational Resources Information Center

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)

Ragan, Lawrence C.

1991-01-01

64

Identification of key odorants related with high quality touriga nacional wine  

Microsoft Academic Search

High quality Touriga Nacional (TN) wines are characterised by a fruity-citric aroma described as sweet and of fresh citrus, evoking the bergamot fruit (Citrus bergamia). By sensory analysis the identification of the most important descriptors were found. Among 18 descriptors 3 were selected: ‘bergamot-like’ aroma, ‘orange-like’ and ‘violet’. A GCO of an extract of a typical TN wine allowed the

A. C. Silva Ferreira; E. Falqué; M. Castro; H. Oliveira e Silva; B. Machado; P. Guedes de Pinho

2006-01-01

65

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

NASA Astrophysics Data System (ADS)

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

Mizukami, Yuzo; Yamaguchi, Yuichi

66

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

PubMed Central

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

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

2011-01-01

67

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

PubMed

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

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

2011-01-01

68

Distinguishing Institutional Identification From Academic Goal Pursuit: Interactive Effects of Ethnic Identification and Race-Based Rejection Sensitivity  

Microsoft Academic Search

We examined the interactive effects of ethnic identification (EI) and race-based rejection sensitivity (RS–race) on institutional outcomes among African American college students. We distinguished between effects on institutional identification on the one hand and academic goal pursuit (e.g., staying in school, grade point average [GPA]) on the other. Supporting the utility of this distinction, we found that EI and RS–race

Rodolfo Mendoza-Denton; Janina Pietrzak; Geraldine Downey

2008-01-01

69

A Technique to Build a Secret Key in Integrated Circuits for Identification and Authentication Applications  

E-print Network

- tions such as intellectual property protection and soft- ware licensing as well as conventional ID cards and smart cards. However, storing secret information in digital form is known to be vulnerable to invasive- ricated using conventional manufacturing technology, we can create a key that cannot be cloned. (We note

Devadas, Srinivas

70

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

NASA Astrophysics Data System (ADS)

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.

Zhang, Guang J.; Song, Xiaoliang

2009-05-01

71

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

NASA Technical Reports Server (NTRS)

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.

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

2010-01-01

72

Computational Identification of Key Biological Modules and Transcription Factors in Acute Lung Injury  

Microsoft Academic Search

Rationale: Mechanical ventilation augments the acute lung injury (ALI) caused by bacterial products. The molecular pathogenesis of this synergistic interaction remains incompletely understood. Objective: We sought to develop a computational framework to systematically identify gene regulatory networks activated in ALI. Methods: We have developed a mouse model in which the combina- tionofmechanicalventilationandintratrachealLPSproducessignif- icantly more injury to the lung than either

Sina A. Gharib; W. Conrad Liles; Gustavo Matute-Bello; Robb W. Glenny; Thomas R. Martin; William A. Altemeier

73

Identification of miR-145 as a key regulator of the pigmentary process.  

PubMed

The current treatments for hyperpigmentation are often associated with a lack of efficacy and adverse side effects. We hypothesized that microRNA (miRNA)-based treatments may offer an attractive alternative by specifically targeting key genes in melanogenesis. The aim of this study was to identify miRNAs interfering with the pigmentary process and to assess their functional role. miRNA profiling was performed on mouse melanocytes after three consecutive treatments involving forskolin and solar-simulated UV (ssUV) irradiation. Sixteen miRNAs were identified as differentially expressed in treated melan-a cells versus untreated cells. Remarkably, a 15-fold downregulation of miR-145 was detected. Overexpression or downregulation of miR-145 in melan-a cells revealed reduced or increased expression of Sox9, Mitf, Tyr, Trp1, Myo5a, Rab27a, and Fscn1, respectively. Moreover, a luciferase reporter assay demonstrated direct targeting of Myo5a by miR-145 in mouse and human melanocytes. Immunofluorescence tagging of melanosomes in miR-145-transfected human melanocytes displayed perinuclear accumulation of melanosomes with additional hypopigmentation of harvested cell pellets. In conclusion, this study has established an miRNA signature associated with forskolin and ssUV treatment. The significant down- or upregulation of major pigmentation genes, after modulating miR-145 expression, suggests a key role for miR-145 in regulating melanogenesis. PMID:22895360

Dynoodt, Peter; Mestdagh, Pieter; Van Peer, Gert; Vandesompele, Jo; Goossens, Karen; Peelman, Luc J; Geusens, Barbara; Speeckaert, Reinhart M; Lambert, Jo L W; Van Gele, Mireille J L

2013-01-01

74

Identification of Key Functional Residues in the Active Site of Human ?1,4-Galactosyltransferase 7  

PubMed Central

Glycosaminoglycans (GAGs) play a central role in many pathophysiological events, and exogenous xyloside substrates of ?1,4-galactosyltransferase 7 (?4GalT7), a major enzyme of GAG biosynthesis, have interesting biomedical applications. To predict functional peptide regions important for substrate binding and activity of human ?4GalT7, we conducted a phylogenetic analysis of the ?1,4-galactosyltransferase family and generated a molecular model using the x-ray structure of Drosophila ?4GalT7-UDP as template. Two evolutionary conserved motifs, 163DVD165 and 221FWGWGREDDE230, are central in the organization of the enzyme active site. This model was challenged by systematic engineering of point mutations, combined with in vitro and ex vivo functional assays. Investigation of the kinetic properties of purified recombinant wild-type ?4GalT7 and selected mutants identified Trp224 as a key residue governing both donor and acceptor substrate binding. Our results also suggested the involvement of the canonical carboxylate residue Asp228 acting as general base in the reaction catalyzed by human ?4GalT7. Importantly, ex vivo functional tests demonstrated that regulation of GAG synthesis is highly responsive to modification of these key active site amino acids. Interestingly, engineering mutants at position 224 allowed us to modify the affinity and to modulate the specificity of human ?4GalT7 toward UDP-sugars and xyloside acceptors. Furthermore, the W224H mutant was able to sustain decorin GAG chain substitution but not GAG synthesis from exogenously added xyloside. Altogether, this study provides novel insight into human ?4GalT7 active site functional domains, allowing manipulation of this enzyme critical for the regulation of GAG synthesis. A better understanding of the mechanism underlying GAG assembly paves the way toward GAG-based therapeutics. PMID:20843813

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

2010-01-01

75

Identification of candidate genes related to bovine marbling using protein-protein interaction networks.  

PubMed

Complex traits are determined by the combined effects of many loci and are affected by gene networks or biological pathways. Systems biology approaches have an important role in the identification of candidate genes related to complex diseases or traits at the system level. The present study systemically analyzed genes associated with bovine marbling score and identified their relationships. The candidate nodes were obtained using MedScan text-mining tools and linked by protein-protein interaction (PPI) from the Human Protein Reference Database (HPRD). To determine key node of marbling, the degree and betweenness centrality (BC) were used. The hub nodes and biological pathways of our network are consistent with the previous reports about marbling traits, and also suggest unknown candidate genes associated with intramuscular fat. Five nodes were identified as hub genes, which was consistent with the network analysis using quantitative reverse-transcription PCR (qRT-PCR). Key nodes of the PPI network have positive roles (PPAR?, C/EBP?, and RUNX1T1) and negative roles (RXRA, CAMK2A) in the development of intramuscular fat by several adipogenesis-related pathways. This study provides genetic information for identifying candidate genes for the marbling trait in bovine. PMID:21912507

Lim, Dajeong; Kim, Nam-Kuk; Park, Hye-Sun; Lee, Seung-Hwan; Cho, Yong-Min; Oh, Sung Jong; Kim, Tae-Hun; Kim, Heebal

2011-01-01

76

Hubs Identification in Amino Acids Interaction Omar Gaci and Stefan Balev  

E-print Network

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

Boyer, Edmond

77

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

NASA Technical Reports Server (NTRS)

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.

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

2000-01-01

78

Systematic identification of hypothetical bacteriophage proteins targeting key protein complexes of pseudomonas aeruginosa.  

PubMed

Addressing the functionality of predicted genes remains an enormous challenge in the postgenomic era. A prime example of genes lacking functional assignments are the poorly conserved, early expressed genes of lytic bacteriophages, whose products are involved in the subversion of the host metabolism. In this study, we focused on the composition of important macromolecular complexes of Pseudomonas aeruginosa involved in transcription, DNA replication, fatty acid biosynthesis, RNA regulation, energy metabolism, and cell division during infection with members of seven distinct clades of lytic phages. Using affinity purifications of these host protein complexes coupled to mass spectrometric analyses, 37 host complex-associated phage proteins could be identified. Importantly, eight of these show an inhibitory effect on bacterial growth upon episomal expression, suggesting that these phage proteins are potentially involved in hijacking the host complexes. Using complementary protein-protein interaction assays, we further mapped the inhibitory interaction of gp12 of phage 14-1 to the ? subunit of the RNA polymerase. Together, our data demonstrate the powerful use of interactomics to unravel the biological role of hypothetical phage proteins, which constitute an enormous untapped source of novel antibacterial proteins. (Data are available via ProteomeXchange with identifier PXD001199.). PMID:25185497

Van den Bossche, An; Ceyssens, Pieter-Jan; De Smet, Jeroen; Hendrix, Hanne; Bellon, Hannelore; Leimer, Nadja; Wagemans, Jeroen; Delattre, Anne-Sophie; Cenens, William; Aertsen, Abram; Landuyt, Bart; Minakhin, Leonid; Severinov, Konstantin; Noben, Jean-Paul; Lavigne, Rob

2014-10-01

79

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

PubMed

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

Parsa, Soroush; Kondo, Takumasa; Winotai, Amporn

2012-01-01

80

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

PubMed Central

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

Parsa, Soroush; Kondo, Takumasa; Winotai, Amporn

2012-01-01

81

Interaction between Truth and Belief as the key to entropy and other quantities of statistical physics  

E-print Network

The notion of entropy penetrates much of science. A key feature of the all-important notion of Boltzmann-Gibbs-Shannon entropy is its extensivity (additivity over independent subsystems). However, there is a need for other quantities. In statistical physics a parameterized family of non-extensive entropy measures, now mainly known under the name of Tsallis-entropies, have received much attention but also been met with criticism due mainly to a lack of convincing interpretations. Based on the hypothesis that interaction between Truth, held by ``Nature'', and Belief, as expressed by man, may take place, classical- as well as non-classical measures of entropy and other essential quantities are derived. The approach aims at providing a genuine interpretation, rather than relying either on analogies based on formal mathematical manipulations or else - more fruitfully, but not satisfactory - on axiomatic characterizations.

Flemming Topsoe

2008-07-27

82

Identification of key residues and regions important for porcupine-mediated Wnt acylation.  

PubMed

Wnts comprise a family of lipid-modified, secreted signaling proteins that control embryogenesis, as well as tissue homeostasis in adults. Post-translational attachment of palmitoleate (C16:1) to a conserved Ser in Wnt proteins is catalyzed by Porcupine (Porcn), a member of the membrane bound O-acyltransferase (MBOAT) family, and is required for Wnt secretion and signaling. Moreover, genetic alterations in the PORCN gene lead to focal dermal hypoplasia, an X-linked developmental disorder. Despite its physiological importance, the biochemical mechanism governing Wnt acylation by Porcn is poorly understood. Here, we use a cell-based fatty acylation assay that is a direct readout of Porcn acyltransferase activity to perform structure-function analysis of highly conserved residues in Porcn and Wnt3a. In total, 16-point mutations in Porcn and 13 mutations in Wnt3a were generated and analyzed. We identified key residues within Porcn required for enzymatic activity, stability, and Wnt3a binding and mapped these active site residues to predicted transmembrane domain 9. Analysis of focal dermal hypoplasia-associated mutations in Porcn revealed that loss of enzymatic activity arises from altered stability. A consensus sequence within Wnt3a was identified (CXCHGXSXXCXXKXC) that contains residues that mediate Porcn binding, fatty acid transfer, and Wnt signaling. We also showed that Ser or Thr, but not Cys, can serve as a fatty acylation site in Wnt, establishing Porcn as an O-acyltransferase. This analysis sheds light into the mechanism by which Porcn transfers fatty acids to Wnt proteins and provides insight into the mechanisms of fatty acid transfer by MBOAT family members. PMID:24798332

Rios-Esteves, Jessica; Haugen, Brittany; Resh, Marilyn D

2014-06-13

83

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

PubMed Central

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

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

2013-01-01

84

Plant cell wall biosynthesis: genetic, biochemical and functional genomics approaches to the identification of key genes.  

PubMed

Cell walls are dynamic structures that represent key determinants of overall plant form, plant growth and development, and the responses of plants to environmental and pathogen-induced stresses. Walls play centrally important roles in the quality and processing of plant-based foods for both human and animal consumption, and in the production of fibres during pulp and paper manufacture. In the future, wall material that constitutes the major proportion of cereal straws and other crop residues will find increasing application as a source of renewable fuel and composite manufacture. Although the chemical structures of most wall constituents have been defined in detail, the enzymes involved in their synthesis and remodelling remain largely undefined, particularly those involved in polysaccharide biosynthesis. There have been real recent advances in our understanding of cellulose biosynthesis in plants, but, with few exceptions, the identities and modes of action of polysaccharide synthases and other glycosyltransferases that mediate the biosynthesis of the major non-cellulosic wall polysaccharides are not known. Nevertheless, emerging functional genomics and molecular genetics technologies are now allowing us to re-examine the central questions related to wall biosynthesis. The availability of the rice, Populus trichocarpa and Arabidopsis genome sequences, a variety of mutant populations, high-density genetic maps for cereals and other industrially important plants, high-throughput genome and transcript analysis systems, extensive publicly available genomics resources and an increasing armoury of analysis systems for the definition of candidate gene function will together allow us to take a systems approach to the description of wall biosynthesis in plants. PMID:17177793

Farrokhi, Naser; Burton, Rachel A; Brownfield, Lynette; Hrmova, Maria; Wilson, Sarah M; Bacic, Antony; Fincher, Geoffrey B

2006-03-01

85

Identification of Key Contributory Factors Responsible for Vascular Dysfunction in Idiopathic Recurrent Spontaneous Miscarriage  

PubMed Central

Poor endometrial perfusion during implantation window is reported to be one of the possible causes of idiopathic recurrent spontaneous miscarriage (IRSM). We have tested the hypothesis that certain angiogenic and vasoactive factors are associated with vascular dysfunction during implantation window in IRSM and, therefore, could play a contributory role in making the endometrium unreceptive in these women. This is a prospective case-controlled study carried out on 66 women with IRSM and age and BMI matched 50 fertile women serving as controls. Endometrial expression of pro-inflammatory (IL-1?, TNF-?, IFN-?, TGF-?1), anti-inflammatory (IL-4, -10), angiogenesis-associated cytokines (IL-2, -6, -8), angiogenic and vasoactive factors including prostaglandin E2 (PGE2), vascular endothelial growth factor (VEGF), endothelial nitric oxide synthase (eNOS), nitric oxide (NO) and adrenomedullin (ADM) were measured during implantation window by ELISA. Subendometrial blood flow (SEBF) was assessed by color Doppler ultrasonography. Multivariate analysis was used to identify the significant factor(s) responsible for vascular dysfunction in IRSM women during window of implantation and further correlated with vascular dysfunction. Endometrial expression of pro-inflammatory cytokines and PGE2 were up-regulated and anti-inflammatory and angiogenesis-associated cytokines down-regulated in IRSM women as compared with controls. Further, the angiogenic and vasoactive factors including VEGF, eNOS, NO and ADM were found to be down-regulated and SEBF grossly affected in these women. Multivariate analysis identified IL-10, followed by VEGF and eNOS as the major factors contributing towards vascular dysfunction in IRSM women. Moreover, these factors strongly correlated with blood flow impairment. This study provides an understanding that IL-10, VEGF and eNOS are the principal key components having a contributory role in endometrial vascular dysfunction in women with IRSM. Down-regulation of these factors is also associated with impaired endometrial perfusion which possibly makes the endometrium unreceptive that may eventually cause early pregnancy loss. PMID:24260517

Dutta, Mainak; Subramani, Elavarasan; Khalpada, Jaydeep; RoyChoudhury, Sourav; Chakravarty, Baidyanath; Chaudhury, Koel

2013-01-01

86

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

E-print Network

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

Kanda, Takayuki

87

Integrative framework for identification of key cell identity genes uncovers determinants of ES cell identity and homeostasis  

PubMed Central

Identification of genes associated with specific biological phenotypes is a fundamental step toward understanding the molecular basis underlying development and pathogenesis. Although RNAi-based high-throughput screens are routinely used for this task, false discovery and sensitivity remain a challenge. Here we describe a computational framework for systematic integration of published gene expression data to identify genes defining a phenotype of interest. We applied our approach to rank-order all genes based on their likelihood of determining ES cell (ESC) identity. RNAi-mediated loss-of-function experiments on top-ranked genes unearthed many novel determinants of ESC identity, thus validating the derived gene ranks to serve as a rich and valuable resource for those working to uncover novel ESC regulators. Underscoring the value of our gene ranks, functional studies of our top-hit Nucleolin (Ncl), abundant in stem and cancer cells, revealed Ncl's essential role in the maintenance of ESC homeostasis by shielding against differentiation-inducing redox imbalance-induced oxidative stress. Notably, we report a conceptually novel mechanism involving a Nucleolin-dependent Nanog-p53 bistable switch regulating the homeostatic balance between self-renewal and differentiation in ESCs. Our findings connect the dots on a previously unknown regulatory circuitry involving genes associated with traits in both ESCs and cancer and might have profound implications for understanding cell fate decisions in cancer stem cells. The proposed computational framework, by helping to prioritize and preselect candidate genes for tests using complex and expensive genetic screens, provides a powerful yet inexpensive means for identification of key cell identity genes. PMID:24711389

Cinghu, Senthilkumar; Yellaboina, Sailu; Freudenberg, Johannes M.; Ghosh, Swati; Zheng, Xiaofeng; Oldfield, Andrew J.; Lackford, Brad L.; Zaykin, Dmitri V.; Hu, Guang; Jothi, Raja

2014-01-01

88

Integrative framework for identification of key cell identity genes uncovers determinants of ES cell identity and homeostasis.  

PubMed

Identification of genes associated with specific biological phenotypes is a fundamental step toward understanding the molecular basis underlying development and pathogenesis. Although RNAi-based high-throughput screens are routinely used for this task, false discovery and sensitivity remain a challenge. Here we describe a computational framework for systematic integration of published gene expression data to identify genes defining a phenotype of interest. We applied our approach to rank-order all genes based on their likelihood of determining ES cell (ESC) identity. RNAi-mediated loss-of-function experiments on top-ranked genes unearthed many novel determinants of ESC identity, thus validating the derived gene ranks to serve as a rich and valuable resource for those working to uncover novel ESC regulators. Underscoring the value of our gene ranks, functional studies of our top-hit Nucleolin (Ncl), abundant in stem and cancer cells, revealed Ncl's essential role in the maintenance of ESC homeostasis by shielding against differentiation-inducing redox imbalance-induced oxidative stress. Notably, we report a conceptually novel mechanism involving a Nucleolin-dependent Nanog-p53 bistable switch regulating the homeostatic balance between self-renewal and differentiation in ESCs. Our findings connect the dots on a previously unknown regulatory circuitry involving genes associated with traits in both ESCs and cancer and might have profound implications for understanding cell fate decisions in cancer stem cells. The proposed computational framework, by helping to prioritize and preselect candidate genes for tests using complex and expensive genetic screens, provides a powerful yet inexpensive means for identification of key cell identity genes. PMID:24711389

Cinghu, Senthilkumar; Yellaboina, Sailu; Freudenberg, Johannes M; Ghosh, Swati; Zheng, Xiaofeng; Oldfield, Andrew J; Lackford, Brad L; Zaykin, Dmitri V; Hu, Guang; Jothi, Raja

2014-04-22

89

Identification of key residues that confer Rhodobacter sphaeroides LPS activity at horse TLR4/MD-2.  

PubMed

The molecular determinants underpinning how hexaacylated lipid A and tetraacylated precursor lipid IVa activate Toll-like receptor 4 (TLR4) are well understood, but how activation is induced by other lipid A species is less clear. Species specificity studies have clarified how TLR4/MD-2 recognises different lipid A structures, for example tetraacylated lipid IVa requires direct electrostatic interactions for agonism. In this study, we examine how pentaacylated lipopolysaccharide from Rhodobacter sphaeroides (RSLPS) antagonises human TLR4/MD-2 and activates the horse receptor complex using a computational approach and cross-species mutagenesis. At a functional level, we show that RSLPS is a partial agonist at horse TLR4/MD-2 with greater efficacy than lipid IVa. These data suggest the importance of the additional acyl chain in RSLPS signalling. Based on docking analysis, we propose a model for positioning of the RSLPS lipid A moiety (RSLA) within the MD-2 cavity at the TLR4 dimer interface, which allows activity at the horse receptor complex. As for lipid IVa, RSLPS agonism requires species-specific contacts with MD-2 and TLR4, but the R2 chain of RSLA protrudes from the MD-2 pocket to contact the TLR4 dimer in the vicinity of proline 442. Our model explains why RSLPS is only partially dependent on horse TLR4 residue R385, unlike lipid IVa. Mutagenesis of proline 442 into a serine residue, as found in human TLR4, uncovers the importance of this site in RSLPS signalling; horse TLR4 R385G/P442S double mutation completely abolishes RSLPS activity without its counterpart, human TLR4 G384R/S441P, being able to restore it. Our data highlight the importance of subtle changes in ligand positioning, and suggest that TLR4 and MD-2 residues that may not participate directly in ligand binding can determine the signalling outcome of a given ligand. This indicates a cooperative binding mechanism within the receptor complex, which is becoming increasingly important in TLR signalling. PMID:24879320

Irvine, Katherine L; Gangloff, Monique; Walsh, Catherine M; Spring, David R; Gay, Nicholas J; Bryant, Clare E

2014-01-01

90

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

PubMed

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

El-Gayar, Amal K

2007-03-31

91

Identification of a Protein That Interacts With the Golli-Myelin Basic Protein  

E-print Network

-IF), a nuclear protein whose function is just beginning to be understood. It is a member of a broad family was the first member of this family shown to interact with nuclear LIM interac- tor (NLI). NLI coIdentification of a Protein That Interacts With the Golli-Myelin Basic Protein and With Nuclear LIM

Bongarzone, Ernesto R.

92

Mosaics of Visualization: An Approach to Embedded Interaction Through Identification Process  

Microsoft Academic Search

New forms of interaction are arising closer to the users and embedded in the intelligent environments. In this work we present a context- aware application through Radiofrequency Identification (RFID) offering services to the users in an implicit way. The only required interaction with the system is to wear a little device called tag (smart label). Some of these services such

José Bravo; Ramón Hervás; Gabriel Chavira; Salvador W. Nava

2006-01-01

93

Int. J. Modelling, Identification and Control, Vol. 20 , No.4,2013 319 Interactive Indoor Environment  

E-print Network

. Firstly, the Skeleton Tracking module builds a human skeleton model, extracts the skeleton joints skeleton Tracking; human-robot interaction Reference: to this paper should be made as follows: Cheng ZhaoInt. J. Modelling, Identification and Control, Vol. 20 , No.4,2013 319 Interactive Indoor

Hu, Huosheng

94

7?-Hydroxypregnenolone, a New Key Regulator of Locomotor Activity of Vertebrates: Identification, Mode of Action, and Functional Significance  

PubMed Central

Steroids synthesized de novo by the central and peripheral nervous systems are called neurosteroids. The formation of neurosteroids from cholesterol in the brain was originally demonstrated in mammals by Baulieu and colleagues. Our studies over the past two decades have also shown that, in birds and amphibians as in mammals, the brain expresses several kinds of steroidogenic enzymes and produces a variety of neurosteroids. Thus, de novo neurosteroidogenesis from cholesterol is a conserved property that occurs throughout vertebrates. However, the biosynthetic pathways of neurosteroids in the brain of vertebrates was considered to be still incompletely elucidated. Recently, 7?-hydroxypregnenolone was identified as a novel bioactive neurosteroid stimulating locomotor activity in the brain of newts and quail through activation of the dopaminergic system. Subsequently, diurnal and seasonal changes in synthesis of 7?-hydroxypregnenolone in the brain were demonstrated. Interestingly, melatonin derived from the pineal gland and eyes regulates 7?-hydroxypregnenolone synthesis in the brain, thus inducing diurnal locomotor changes. Prolactin, an adenohypophyseal hormone, regulates 7?-hydroxypregnenolone synthesis in the brain, and may also induce seasonal locomotor changes. This review highlights the identification, mode of action, and functional significance of 7?-hydroxypregnenolone, a new key regulator of locomotor activity of vertebrates, in terms of diurnal and seasonal changes in 7?-hydroxypregnenolone synthesis, and describes some of their regulatory mechanisms. PMID:22654788

Tsutsui, Kazuyoshi; Haraguchi, Shogo; Matsunaga, Masahiro; Inoue, Kazuhiko; Vaudry, Hubert

2010-01-01

95

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

PubMed Central

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

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

2014-01-01

96

Parameter identification for stochastic hybrid models of biological interaction networks  

E-print Network

with the structure of the model, identification is split in two subproblems: estimation of the genetic network regulating subtilin production from gene expression data, and estimation of population dynamics based on nutrient and population profiles. Techniques for parameter estimation from sparse and irregularly sampled

Ferrari-Trecate, Giancarlo

97

Key parameters in blood-surface interactions of 3D bioinspired ceramic materials.  

PubMed

Direct contact of materials with blood components may trigger numerous processes which ultimately lead to hemolysis, clot formation and recruitment of inflammatory cells. In this study, the blood-surface interactions for two inert bioinspired ceramic scaffolds obtained from natural resources; biomorphic carbon and silicon carbides (bioSiC) from different origins have been studied. The response of the blood in contact with carbon is well known, however little has been identified on the influence of their 3D porous structure. Moreover, to our knowledge, there is no reference in the literature about the hemocompatibility of biomorphic silicon carbide as a porous scaffold. The experimental results showed the surface energy to be crucial to evaluate the hemocompatibility of a material however the surface topography and material porosity are also parameters to be considered. Surface roughness modifies clot formation whereas for protein adsorption total sample porosity seems to be the key parameter to be considered for hydrophilic materials (biomorphic silicon carbides), while the size of the pores determines the hemolytic response. PMID:24907756

Díaz-Rodríguez, P; González, P; Serra, J; Landin, M

2014-08-01

98

Large-scale identification of yeast integral membrane protein interactions  

Microsoft Academic Search

We carried out a large-scale screen to identify interactions between integral membrane proteins of Saccharomyces cerevisiae by using a modified split-ubiquitin technique. Among 705 proteins annotated as integral membrane, we identified 1,985 putative interactions involving 536 proteins. To ascribe confidence levels to the interactions, we used a support vector machine algorithm to classify interactions based on the assay results and

John P. Miller; Russell S. Lo; Asa Ben-Hur; Cynthia Desmarais; Igor Stagljar; William Stafford Noble

2005-01-01

99

Complex dynamics of a nonlinear aerospace structure: Experimental identification and modal interactions  

NASA Astrophysics Data System (ADS)

Nonlinear system identification is a challenging task in view of the complexity and wide variety of nonlinear phenomena. The present paper addresses the identification of a real-life aerospace structure possessing a strongly nonlinear component with multiple mechanical stops. The complete identification procedure, from nonlinearity detection and characterization to parameter estimation, is carried out based upon experimental data. The combined use of various analysis techniques, such as the wavelet transform and the restoring force surface method, brings different perspectives to the dynamics. Specifically, the structure is shown to exhibit particularly interesting nonlinear behaviors, including jumps, modal interactions, force relaxation and chattering during impacts on the mechanical stops.

Noël, J. P.; Renson, L.; Kerschen, G.

2014-06-01

100

Modeling social interactions: Identification, empirical methods and policy implications  

Microsoft Academic Search

Social interactions occur when agents in a network affect other agents’ choices directly, as opposed to via the intermediation\\u000a of markets. The study of such interactions and the resultant outcomes has long been an area of interest across a wide variety\\u000a of social sciences. With the advent of electronic media that facilitate and record such interactions, this interest has grown

Wesley R. Hartmann; Puneet Manchanda; Harikesh Nair; Matthew Bothner; Peter Dodds; David Godes; Kartik Hosanagar; Catherine Tucker

2008-01-01

101

Multiple prey traits, multiple predators: keys to understanding complex species interactions.  

E-print Network

??Species interactions generate both natural selection and ecological community structure. Among the more interesting species interactions are those that create adaptive tradeoffs-where phenotypes conferring improved… (more)

Langerhans, Randall Brian

2012-01-01

102

Membrane topology and identification of key functional amino acid residues of murine acyl-CoA:diacylglycerol acyltransferase-2.  

PubMed

Triacylglycerols are the predominant molecules of energy storage in eukaryotes. However, excessive accumulation of triacylglycerols in adipose tissue leads to obesity and, in nonadipose tissues, is associated with tissue dysfunction. Hence, it is of great importance to have a better understanding of the molecular mechanisms of triacylglycerol synthesis. The final step in triacylglycerol synthesis is catalyzed by the acyl-CoA:diacylglycerol acyltransferase (DGAT) enzymes, DGAT1 and DGAT2. Although recent studies have shed light on metabolic functions of these enzymes, little is known about the molecular aspects of their structures or functions. Here we report the topology for murine DGAT2 and the identification of key amino acids that likely contribute to enzymatic function. Our data indicate that DGAT2 is an integral membrane protein with both the N and C termini oriented toward the cytosol. A long hydrophobic region spanning amino acids 66-115 likely comprises two transmembrane domains or, alternatively, a single domain that is embedded in the membrane bilayer. The bulk of the protein lies distal to the transmembrane domains. This region shares the highest degree of homology with other enzymes of the DGAT2 family and contains a sequence HPHG that is conserved in all family members. Mutagenesis of this sequence in DGAT2 demonstrated that it is required for full enzymatic function. Additionally, a neutral lipid-binding domain that is located in the putative first transmembrane domain was also required for full enzymatic function. Our findings provide the first insights into the topography and molecular aspects of DGAT2 and related enzymes. PMID:17035227

Stone, Scot J; Levin, Malin C; Farese, Robert V

2006-12-29

103

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

PubMed Central

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

Biondi, Maurizio; D’Alessandro, Paola

2012-01-01

104

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

PubMed Central

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

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

2014-01-01

105

Methods for comprehensive experimental identification of RNA-protein interactions  

PubMed Central

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

2014-01-01

106

Identification of differentially expressed genes at two key endosperm development stages using two maize inbreds with large and small grain and integration with detected QTL for grain weight  

Microsoft Academic Search

Maize endosperm accounts for more than 80% of the grain weight. Cell division and grain filling are the two key stages for\\u000a endosperm development. Previous studies showed that gene expression during differential stages in endosperm development is\\u000a greatly different. However, information on systematic identification and characterization of the differentially expressed\\u000a genes between the two stages are limited. In this study,

Y. Y. Liu; J. Z. Li; Y. L. Li; M. G. Wei; Q. X. Cui; Q. L. Wang

2010-01-01

107

Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data  

E-print Network

Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Abstract Mounting evidence shows that many protein complexes are conserved in evolution. Here we use combines protein interaction data, that are available for each of the two species, and orthology

Shamir, Ron

108

Transcriptional interaction-assisted identification of dynamic nucleosome positioning  

Microsoft Academic Search

BACKGROUND: Nucleosomes regulate DNA accessibility and therefore play a central role in transcription control. Computational methods have been developed to predict static nucleosome positions from DNA sequences, but nucleosomes are dynamic in vivo. RESULTS: Motivated by our observation that transcriptional interaction is discriminative information for nucleosome occupancy, we developed a novel computational approach to identify dynamic nucleosome positions at promoters

Zhiming Dai; Xianhua Dai; Qian Xiang; Jihua Feng; Yangyang Deng; Jiang Wang; Caisheng He

2009-01-01

109

Factor selection and structural identification in the interaction ANOVA model.  

PubMed

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

Post, Justin B; Bondell, Howard D

2013-03-01

110

Identification of Global Ferredoxin Interaction Networks in Chlamydomonas reinhardtii*  

PubMed Central

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

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

2013-01-01

111

Towards Practical Non-interactive Public Key Cryptosystems Using Non-maximal Imaginary Quadratic Orders (Extended Abstract)  

Microsoft Academic Search

We present a new non-interactive public key distribution system based on the class group of a non-maximal imaginary quadratic\\u000a order Cl(?p). The main advantage of our system over earlier proposals based on (?\\/n?). [19],[21] is that embedding id information into group elements in a cyclic subgroup of the class group is easy (straight-forward embedding\\u000a into prime ideals suffices) and secure,

Detlef Hühnlein; Damian Weber

112

Identification of protein disulfide isomerase 1 as a key isomerase for disulfide bond formation in apolipoprotein B100.  

PubMed

Apolipoprotein (apo) B is an obligatory component of very low density lipoprotein (VLDL), and its cotranslational and posttranslational modifications are important in VLDL synthesis, secretion, and hepatic lipid homeostasis. ApoB100 contains 25 cysteine residues and eight disulfide bonds. Although these disulfide bonds were suggested to be important in maintaining apoB100 function, neither the specific oxidoreductase involved nor the direct role of these disulfide bonds in apoB100-lipidation is known. Here we used RNA knockdown to evaluate both MTP-dependent and -independent roles of PDI1 in apoB100 synthesis and lipidation in McA-RH7777 cells. Pdi1 knockdown did not elicit any discernible detrimental effect under normal, unstressed conditions. However, it decreased apoB100 synthesis with attenuated MTP activity, delayed apoB100 oxidative folding, and reduced apoB100 lipidation, leading to defective VLDL secretion. The oxidative folding-impaired apoB100 was secreted mainly associated with LDL instead of VLDL particles from PDI1-deficient cells, a phenotype that was fully rescued by overexpression of wild-type but not a catalytically inactive PDI1 that fully restored MTP activity. Further, we demonstrate that PDI1 directly interacts with apoB100 via its redox-active CXXC motifs and assists in the oxidative folding of apoB100. Taken together, these findings reveal an unsuspected, yet key role for PDI1 in oxidative folding of apoB100 and VLDL assembly. PMID:25518935

Wang, Shiyu; Park, Shuin; Kodali, Vamsi K; Han, Jaeseok; Yip, Theresa; Chen, Zhouji; Davidson, Nicholas O; Kaufman, Randal J

2015-02-15

113

Membrane-protein interactions hold the key to understanding amyloid formation  

E-print Network

In this perspective we describe the critical role membranes play in modulating the structures of the Amyloid Precursor Proteins to produce the peptides involved in the Alzheimer's disease. Some of the key concepts related to protein aggregation including the potential role of the excited states of monomers in initiating protein aggregation are described.

Straub, John E

2014-01-01

114

Membrane-protein interactions hold the key to understanding amyloid formation  

E-print Network

In this perspective we describe the critical role membranes play in modulating the structures of the Amyloid Precursor Proteins to produce the peptides involved in the Alzheimer's disease. Some of the key concepts related to protein aggregation including the potential role of the excited states of monomers in initiating protein aggregation are described.

John E. Straub; D. Thirumalai

2014-07-07

115

Glycoconjugates Play a Key Role in Campylobacter jejuni Infection: Interactions between Host and Pathogen  

PubMed Central

Glycan based interactions between host and pathogen are critical in many bacterial and viral diseases. Glycan interactions range from initial receptor based adherence to protecting the infective agent from the host’s immune response through molecular mimicry. Campylobacter jejuni is an ideal model for studying the role of glycans in host–pathogen interactions, as well as the role of bacterial surface glycoconjugates in infection. Using glycan array analysis, C. jejuni has been shown to interact with a wide range of host glycoconjugates. Mannose and sialic acid residues appear to play a role in initial interactions between host and pathogen following environmental exposure, whereas fucose and galactose based interactions are likely to be required for prolonged colonization. Other studies have highlighted potential decoy receptor type interactions between host’s intestinal mucins and C. jejuni, demonstrating the importance of host glycoproteins as defense against C. jejuni infection as well as the role for glycoconjugates found in human breast milk in protection of breast feeding infants from infection with C. jejuni. C. jejuni can produce N- and O-linked glycoproteins, capsular polysaccharide (CPS) and/or lipooligosaccharide (LOS) which results in C. jejuni presenting its own diverse sugar coated displays on the cell surface. Bacterial glycans play an important and versatile role in infection and disease. Of these, the best understood is the molecular mimicry of human gangliosides presented by C. jejuni’s LOS and its link to the onset of autoimmune neuropathies such as the Guillain Barrè syndrome (GBS). However, the role of glycoconjugates presented by C. jejuni extends beyond expression of sialylated ganglioside structures involved in initiation of GBS. Expression of surface glycans by C. jejuni may also relate to the ability of this organism to interact with the glycoproteins for initial host–pathogen interactions and continued infectivity. PMID:22919601

Day, Christopher James; Semchenko, Evgeny Alexander; Korolik, Victoria

2012-01-01

116

Identification of Crew-Systems Interactions and Decision Related Trends  

NASA Technical Reports Server (NTRS)

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.

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

2013-01-01

117

Identification of membrane proteins mediating the interaction of human platelets  

PubMed Central

Membrane glycoproteins that mediate platelet-platelet interactions were investigated by identifying those associated with the cytoskeletal structures from aggregated platelets. The cytoskeletal structures from washed platelets, thrombin-activated platelets (platelets incubated with thrombin in the presence of mM EDTA to prevent aggregation) and thrombin- aggregated platelets (platelets activated in the presence of mM Ca(++) were prepared by first treating platelet suspensions with 1 percent Triton X-100 and 5 mM EGTA and then isolating the insoluble residue by centrifugation. The readily identifiable structures in electron micrographs of the residue from washed platelets had the shape and dimensions of actin filaments. Analysis of this residue from washed platelets had the shape and dimensions of actin filaments. Analysis of this residue by SDS gel electrophoresis showed that it consisted primarily of three proteins: actin (mol wt = 43,000), myosin (mol wt = 200,000) and a high molecular weight polypeptide (mol wt = 255,000) which had properties indentical to actin-binding protein (filamin). When platelets are activated with thrombin in the presence of EDTA to prevent aggregation, there was a marked increase in the amount of insoluble precipitate in the subsequent Triton extraction. Transmission electron microscopy showed that this residue not only contained the random array of actin filaments as seen above, but also organized structures from individual platelets which appeared as balls of electron-dense filamentous material approximately 1mum in diameter. SDS polyacrylamide gel analysis of the Triton residue of activated platelets showed that this preparation contained more actin, myosin and actin-binding protein than that from washed platelets plus polypeptides with mol wt of 56,000 and 90,000 and other minor polypeptides. Thus, thrombin activation appeared to increase polymerization of actin in association with other cytoskeletal proteins into structures that are observable after Triton extraction. The cytoskeletal structures from thrombin-aggregated platelets were similar to those from thrombin-activated platelets, except that the structural elements from individual platelets remained aggregated rather than randomly dispersed in the actin filaments. This suggested that the membrane components that mediate the direct interaction of platelets were in Triton residue from aggregated platelets. Only a small percentage of the membrane surface proteins and glycoproteins were found in the cytoskeletal structures from either washed platelets or thrombin-activated platelets. In contrast, the aggregated cytoskeletal structures from thrombin-aggregated platelets contained membrane glycoproteins IIb (26 percent of the total in pre-extracted platelets) and III (14 percent), suggesting that one or both of these glycoproteins participate in the direct interaction of platelets during aggregation. PMID:6893455

Phillips, D; Jennings, L; Edwards, H

1980-01-01

118

Identification of Early Interactions between Francisella and the Host  

PubMed Central

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

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

119

Identification of early interactions between Francisella and the host.  

PubMed

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

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; Frelinger, Jeffrey A

2014-06-01

120

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

PubMed Central

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

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

2014-01-01

121

Coordinate control of virulence gene expression in Francisella tularensis involves direct interaction between key regulators.  

PubMed

In Francisella tularensis, the putative DNA-binding protein PigR works in concert with the SspA protein family members MglA and SspA to control the expression of genes that are essential for the intramacrophage growth and survival of the organism. MglA and SspA form a complex that interacts with RNA polymerase (RNAP), and this interaction between the MglA-SspA complex and RNAP is thought to be critical to its regulatory function. How PigR works in concert with the MglA-SspA complex is not known; previously published findings differ over whether PigR interacts with the MglA-SspA complex, leading to disparate models for how PigR and the MglA-SspA complex exert their regulatory effects. Here, using a combination of genetic assays, we identify mutants of MglA and SspA that are specifically defective for interaction with PigR. Analysis of the MglA and SspA mutants in F. tularensis reveals that interaction between PigR and the MglA-SspA complex is essential in order for PigR to work coordinately with MglA and SspA to positively regulate the expression of virulence genes. Our findings uncover a surface of the MglA-SspA complex that is important for interaction with PigR and support the idea that PigR exerts its regulatory effects through an interaction with the RNAP-associated MglA-SspA complex. PMID:25070738

Rohlfing, Amy E; Dove, Simon L

2014-10-01

122

Identification of cell surface molecules that interact with pseudorabies virus.  

PubMed Central

The alphaherpesvirus pseudorabies virus (PrV) has been shown to attach to cells by interaction between the viral glycoprotein gC and cell membrane proteoglycans carrying heparan sulfate chains (HSPGs). A secondary binding step requires gD and presumably another, hitherto unidentified cellular receptor. By use of a virus overlay protein binding assay (VOPBA), cosedimentation analyses, and affinity chromatography, we identified three species of cell membrane constituents that bind PrV. By treatment with EDTA, peripheral HSPGs of very high apparent molecular mass (>200 kDa) could be extracted from Madin-Darby bovine kidney cells. Binding of PrV to these HSPGs in the VOPBA was sensitive to enzymatic digestion with heparinase or papain. Cosedimentation analyses indicated that binding between PrV and high-molecular-weight HSPG depended on the presence of gC in the virion. In addition, adsorption of radiolabeled PrV virions to cells could be inhibited by the addition of purified high-molecular-weight HSPG. By using urea extraction buffer, a second species of HSPG of approximately 140 kDa could be solubilized. Binding of PrV to this HSPG in the VOPBA was also dependent on the presence of heparan sulfate, since reactivity was abolished after suppression of glycosaminoglycan biosynthesis with NaClO3 and after heparinase treatment. In addition to HSPG, in cellular membrane extracts obtained by treatment with mild detergent, a 85-kDa membrane protein was demonstrated to bind PrV in the VOPBA and affinity chromatography. In summary, we identified three species of cell membrane constituents that bind PrV: a peripheral HSPG of high molecular weight, an integral HSPG of approximately 140 kDa, and an integral membrane protein of 85 kDa. It is tempting to speculate that interaction between PrV and the two species of HSPG mediates primary attachment of PrV and that the 85-kDa protein is involved in a subsequent attachment step. PMID:8642635

Karger, A; Mettenleiter, T C

1996-01-01

123

Automated identification of pathways from quantitative genetic interaction data  

PubMed Central

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

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

2010-01-01

124

The identification of surface interaction of apotransferrin with Candida albicans.  

PubMed

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

Han, Yongmoon

2014-10-01

125

Cycle-Time Key Factor Identification and Prediction in Semiconductor Manufacturing Using Machine Learning and Data Mining  

Microsoft Academic Search

Within the complex and competitive semiconductor manufacturing industry, lot cycle time (CT) remains one of the key performance indicators. Its reduction is of strategic importance as it contributes to cost decreasing, time-to-market shortening, faster fault detection, achieving throughput targets, and improving production-resource scheduling. To reduce CT, we suggest and investigate a data-driven approach that identifies key factors and predicts their

Yair Meidan; Boaz Lerner; Gad Rabinowitz; Michael Hassoun

2011-01-01

126

INSECTSYMBIONT INTERACTIONS Symbioses: A Key Driver of Insect Physiological Processes, Ecological  

E-print Network

Interactions, Evolutionary Diversification, and Impacts on Humans* K. D. KLEPZIG,1,4 A. S. ADAMS,2 J. HANDELSMAN,3 AND K. F. RAFFA2 Environ. Entomol. 38(1): 67Ð77 (2009) ABSTRACT Symbiosis is receiving increased, evolutionary, developmental, semiochemical, and pest management theory. Insects show a vast array of symbiotic

Handelsman, Jo

127

Improved Strategies for Rapid Identification of Chemically Cross-linked Peptides Using Protein Interaction Reporter Technology  

PubMed Central

Protein interaction reporter (PIR) technology can enable identification of in vivo protein interactions with the use of specialized chemical cross-linkers, liquid chromatography, and high-resolution mass spectrometry. PIR-cross-linkers contain labile bonds that are specifically fragmented under low energy collision or photodissociation conditions in the mass spectrometer source, thus releasing cross-linked peptides. Successful analysis of PIR-cross-linked proteins requires the use of expected mathematical relationships between cross-linked complexes released peptides after fragmentation of the labile PIR bonds. Presented here is a next-generation software tool, BLinks, for use in the analysis and identification of PIR-cross-linked proteins. BLinks is an advancement beyond our previous efforts by incorporation of chromatographic profiles that must match between cross-linked complexes and released peptides to enable estimation of p values to help filter true relationships from complex datasets. Additionally, BLinks was used to incorporate Mascot database searching results from subsequent MS/MS analysis of the released peptides to facilitate identification of cross-linked proteins. BLinks was used in the analysis of human serum albumin, and 46 inter-peptide relationships were found spanning thirty proximal residues with a 2.2% false discovery rate. BLinks was also used to track peptides involved in multiple, co-eluting relationships that make accurate identification of protein interactions difficult. An additional 10 inter-peptide relationships were identified despite poor correlation using the profiling tools provided with BLinks. Additionally, BLinks can be used to globally map all inter-peptide relationships from the data analysis and customize subsequent analysis to target specific peptides of interest, thus making it a useful tool for both discovery of protein interactions and mapping protein topology. PMID:20886857

Hoopmann, Michael R.; Weisbrod, Chad R.; Bruce, James E.

2010-01-01

128

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

PubMed

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

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

2014-04-01

129

Identification of response-modulated genetic interactions by sensitivity-based epistatic analysis  

PubMed Central

Background High-throughput genomics has enabled the global mapping of genetic interactions based on the phenotypic impact of combinatorial genetic perturbations. An important next step is to understand how these networks are dynamically remodelled in response to environmental stimuli. Here, we report on the development and testing of a method to identify such interactions. The method was developed from first principles by treating the impact on cellular growth of environmental perturbations equivalently to that of gene deletions. This allowed us to establish a novel neutrality function marking the absence of epistasis in terms of sensitivity phenotypes rather than fitness. We tested the method by identifying fitness- and sensitivity-based interactions involved in the response to drug-induced DNA-damage of budding yeast Saccharomyces cerevisiae using two mutant libraries - one containing transcription factor deletions, and the other containing deletions of DNA repair genes. Results Within the library of transcription factor deletion mutants, we observe significant differences in the sets of genetic interactions identified by the fitness- and sensitivity-based approaches. Notably, among the most likely interactions, only ~50% were identified by both methods. While interactions identified solely by the sensitivity-based approach are modulated in response to drug-induced DNA damage, those identified solely by the fitness-based method remained invariant to the treatment. Comparison of the identified interactions to transcriptional profiles and protein-DNA interaction data indicate that the sensitivity-based method improves the identification of interactions involved in the DNA damage response. Additionally, for the library containing DNA repair mutants, we observe that the sensitivity-based method improves the grouping of functionally related genes, as well as the identification of protein complexes, involved in DNA repair. Conclusion Our results show that the identification of response-modulated genetic interactions can be improved by incorporating the effect of a changing environment directly into the neutrality function marking the absence of epistasis. We expect that this extension of conventional epistatic analysis will facilitate the development of dynamic models of gene networks from quantitative measurements of genetic interactions. While the method was developed for growth phenotype, it should apply equally well for other phenotypes, including the expression of fluorescent reporters. PMID:20831804

2010-01-01

130

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

PubMed Central

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

Gao, Hui-Ming; Hong, Jau-shyong

2011-01-01

131

Nanodisc-based Co-immunoprecipitation for Mass Spectrometric Identification of Membrane-interacting Proteins*  

PubMed Central

Proteomic identification of protein interactions with membrane associated molecules in their native membrane environment pose a challenge because of technical problems of membrane handling. We investigate the possibility of employing membrane nanodiscs for harboring the membrane associated molecule to tackle the challenges. Nanodiscs are stable, homogenous pieces of membrane with a discoidal shape. They are stabilized by an encircling amphipatic protein with an engineered epitope tag. In the present study we employ the epitope tag of the nanodiscs for detection and co-immunoprecipitation of interaction partners of the glycolipid ganglioside GM1 harbored by nanodiscs. Highly specific binding activity for nanodisc-GM1 immobilized on sensorchips was observed by surface plasmon resonance in culture media from enterotoxigenic Escherischia coli. To isolate the interaction partner(s) from enterotoxigenic Escherischia coli, GM1-nanodiscs were employed for co-immunoprecipitation. The B subunit of heat labile enterotoxin was identified as a specific interaction partner by mass spectrometry, thus demonstrating that nanodisc technology is useful for highly specific detection and identification of interaction partners to specific lipids embedded in a membrane bilayer. PMID:21532009

Borch, Jonas; Roepstorff, Peter; Møller-Jensen, Jakob

2011-01-01

132

Interaction of environmental allergens with airway epithelium as a key component of asthma  

Microsoft Academic Search

Epithelial cells in the airway wall actively interact with environmental antigens\\/allergens, both in healthy individuals and\\u000a patients with asthma. In patients with (allergic) asthma, the epithelium is abnormal, showing damaged structures and continuous\\u000a activation similar to a repair phenotype cell. Epithelial cells bind allergens by a diversity of innate receptors, similar\\u000a and in part identical to the Toll-like receptor family,

Henk F. Kauffman

2003-01-01

133

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

E-print Network

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

Berkowitz, David

134

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

SciTech Connect

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.

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

135

A kinase interacting protein (AKIP1) is a key regulator of cardiac stress  

PubMed Central

cAMP-dependent protein kinase (PKA) regulates a myriad of functions in the heart, including cardiac contractility, myocardial metabolism, and gene expression. However, a molecular integrator of the PKA response in the heart is unknown. Here, we show that the PKA adaptor A-kinase interacting protein 1 (AKIP1) is up-regulated in cardiac myocytes in response to oxidant stress. Mice with cardiac gene transfer of AKIP1 have enhanced protection to ischemic stress. We hypothesized that this adaptation to stress was mitochondrial-dependent. AKIP1 interacted with the mitochondrial localized apoptosis inducing factor (AIF) under both normal and oxidant stress. When cardiac myocytes or whole hearts are exposed to oxidant and ischemic stress, levels of both AKIP1 and AIF were enhanced. AKIP1 is preferentially localized to interfibrillary mitochondria and up-regulated in this cardiac mitochondrial subpopulation on ischemic injury. Mitochondria isolated from AKIP1 gene-transferred hearts showed increased mitochondrial localization of AKIP1, decreased reactive oxygen species generation, enhanced calcium tolerance, decreased mitochondrial cytochrome C release, and enhance phosphorylation of mitochondrial PKA substrates on ischemic stress. These observations highlight AKIP1 as a critical molecular regulator and a therapeutic control point for stress adaptation in the heart. PMID:23319652

Sastri, Mira; Haushalter, Kristofer J.; Panneerselvam, Mathivadhani; Chang, Philip; Fridolfsson, Heidi; Finley, J. Cameron; Ng, Daniel; Schilling, Jan M.; Miyanohara, Atsushi; Day, Michele E.; Hakozaki, Hiro; Petrosyan, Susanna; Koller, Antonius; King, Charles C.; Darshi, Manjula; Blumenthal, Donald K.; Ali, Sameh Saad; Roth, David M.; Patel, Hemal H.; Taylor, Susan S.

2013-01-01

136

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

PubMed Central

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

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

2011-01-01

137

Input to interaction to instruction: three key shifts in the history of child language research.  

PubMed

In the early years of the Journal of Child Language, there was considerable disagreement about the role of language input or adult-child interaction in children's language acquisition. The view that quantity and quality of input to language-learning children is relevant to their language development has now become widely accepted as a principle guiding advice to parents and the design of early childhood education programs, even if it is not yet uncontested in the field of language development. The focus on variation in the language input to children acquires particular educational relevance when we consider variation in access to academic language - features of language particularly valued in school and related to success in reading and writing. Just as many children benefit from language environments that are intentionally designed to ensure adequate quantity and quality of input, even more probably need explicit instruction in the features of language that characterize its use for academic purposes. PMID:25023501

Snow, Catherine E

2014-07-01

138

Microbial Glycan Microarrays Define Key Features of Host-Microbial Interactions  

PubMed Central

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

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

139

Interaction with the surrounding water plays a key role in determining the aggregation propensity of proteins.  

PubMed

Understanding the molecular determinants of the relative propensities of proteins to aggregate in a cellular environment is a central issue for treating protein-aggregation diseases and developing peptide-based therapeutics. Despite the expectation that protein aggregation can largely be attributed to direct protein-protein interactions, a crucial role the surrounding water in determining the aggregation propensity of proteins both in?vitro and in?vivo was identified. The overall protein hydrophobicity, defined solely by the hydration free energy of a protein in its monomeric state sampling its equilibrium structures, was shown to be the predominant determinant of protein aggregation propensity in aqueous solution. Striking discrimination of positively and negatively charged residues by the surrounding water was also found. This effect depends on the protein net charge and plays a crucial role in regulating the solubility of the protein. These results pave the way for the design of aggregation-resistant proteins as biotherapeutics. PMID:24615814

Chong, Song-Ho; Ham, Sihyun

2014-04-01

140

Dynamic transcription factor activity profiles reveal key regulatory interactions during megakaryocytic and erythroid differentiation.  

PubMed

The directed differentiation toward erythroid (E) or megakaryocytic (MK) lineages by the MK-E progenitor (MEP) could enhance the ex vivo generation of red blood cells and platelets for therapeutic transfusions. The lineage choice at the MEP bifurcation is controlled in large part by activity within the intracellular signal transduction network, the output of which determines the activity of transcription factors (TFs) and ultimately gene expression. Although many TFs have been implicated, E or MK differentiation is a complex process requiring multiple days, and the dynamics of TF activities during commitment and terminal maturation are relatively unexplored. Herein, we applied a living cell array for the large-scale, dynamic quantification of TF activities during MEP bifurcation. A panel of hematopoietic TFs (GATA-1, GATA-2, SCL/TAL1, FLI-1, NF-E2, PU.1, c-Myb) was characterized during E and MK differentiation of bipotent K562 cells. Dynamic TF activity profiles associated with differentiation towards each lineage were identified, and validated with previous reports. From these activity profiles, we show that GATA-1 is an important hub during early hemin- and PMA-induced differentiation, and reveal several characteristic TF interactions for E and MK differentiation that confirm regulatory mechanisms documented in the literature. Additionally, we highlight several novel TF interactions at various stages of E and MK differentiation. Furthermore, we investigated the mechanism by which nicotinamide (NIC) promoted terminal MK maturation using an MK-committed cell line, CHRF-288-11 (CHRF). Concomitant with its enhancement of ploidy, NIC strongly enhanced the activity of three TFs with known involvement in terminal MK maturation: FLI-1, NF-E2, and p53. Dynamic profiling of TF activity represents a novel tool to complement traditional assays focused on mRNA and protein expression levels to understand progenitor cell differentiation. PMID:24853077

Duncan, Mark T; Shin, Seungjin; Wu, Jia J; Mays, Zachary; Weng, Stanley; Bagheri, Neda; Miller, William M; Shea, Lonnie D

2014-10-01

141

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

PubMed Central

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

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

2014-01-01

142

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

NASA Astrophysics Data System (ADS)

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.

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

2014-09-01

143

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

PubMed Central

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

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

2013-01-01

144

Symbioses: a key driver of insect physiological processes, ecological interactions, evolutionary diversification, and impacts on humans.  

PubMed

Symbiosis is receiving increased attention among all aspects of biology because of the unifying themes it helps construct across ecological, evolutionary, developmental, semiochemical, and pest management theory. Insects show a vast array of symbiotic relationships with a wide diversity of microorganisms. These relationships may confer a variety of benefits to the host (macrosymbiont), such as direct or indirect nutrition, ability to counter the defenses of plant or animal hosts, protection from natural enemies, improved development and reproduction, and communication. Benefits to the microsymbiont (including a broad range of fungi, bacteria, mites, nematodes, etc.) often include transport, protection from antagonists, and protection from environmental extremes. Symbiotic relationships may be mutualistic, commensal, competitive, or parasitic. In many cases, individual relationships may include both beneficial and detrimental effects to each partner during various phases of their life histories or as environmental conditions change. The outcomes of insect-microbial interactions are often strongly mediated by other symbionts and by features of the external and internal environment. These outcomes can also have important effects on human well being and environmental quality, by affecting agriculture, human health, natural resources, and the impacts of invasive species. We argue that, for many systems, our understanding of symbiotic relationships will advance most rapidly where context dependency and multipartite membership are integrated into existing conceptual frameworks. Furthermore, the contribution of entomological studies to overall symbiosis theory will be greatest where preoccupation with strict definitions and artificial boundaries is minimized, and integration of emerging molecular and quantitative techniques is maximized. We highlight symbiotic relations involving bark beetles to illustrate examples of the above trends. PMID:19791599

Klepzig, K D; Adams, A S; Handelsman, J; Raffa, K F

2009-02-01

145

Abscisic acid has a key role in modulating diverse plant-pathogen interactions.  

PubMed

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

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

2009-08-01

146

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

PubMed Central

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

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

2014-01-01

147

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

PubMed

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

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

2015-01-01

148

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

PubMed Central

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

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

2012-01-01

149

Identification of oxidative stress and Toll-like receptor 4 signaling as a key pathway of acute lung injury.  

PubMed

Multiple lung pathogens such as chemical agents, H5N1 avian flu, or SARS cause high lethality due to acute respiratory distress syndrome. Here we report that Toll-like receptor 4 (TLR4) mutant mice display natural resistance to acid-induced acute lung injury (ALI). We show that TLR4-TRIF-TRAF6 signaling is a key disease pathway that controls the severity of ALI. The oxidized phospholipid (OxPL) OxPAPC was identified to induce lung injury and cytokine production by lung macrophages via TLR4-TRIF. We observed OxPL production in the lungs of humans and animals infected with SARS, Anthrax, or H5N1. Pulmonary challenge with an inactivated H5N1 avian influenza virus rapidly induces ALI and OxPL formation in mice. Loss of TLR4 or TRIF expression protects mice from H5N1-induced ALI. Moreover, deletion of ncf1, which controls ROS production, improves the severity of H5N1-mediated ALI. Our data identify oxidative stress and innate immunity as key lung injury pathways that control the severity of ALI. PMID:18423196

Imai, Yumiko; Kuba, Keiji; Neely, G Greg; Yaghubian-Malhami, Rubina; Perkmann, Thomas; van Loo, Geert; Ermolaeva, Maria; Veldhuizen, Ruud; Leung, Y H Connie; Wang, Hongliang; Liu, Haolin; Sun, Yang; Pasparakis, Manolis; Kopf, Manfred; Mech, Christin; Bavari, Sina; Peiris, J S Malik; Slutsky, Arthur S; Akira, Shizuo; Hultqvist, Malin; Holmdahl, Rikard; Nicholls, John; Jiang, Chengyu; Binder, Christoph J; Penninger, Josef M

2008-04-18

150

Identification of key water quality characteristics affecting the filterability of biologically treated effluent in low-pressure membrane filtration.  

PubMed

There are many water quality characteristics which could influence the filterability of biologically treated effluent from Melbourne's Western Treatment Plant (WTP). Statistical correlation was used to identify the key water characteristics affecting the microfiltration (MF) and ultrafiltration (UF) filterability in terms of permeate volume of the treated effluent. The models developed showed that turbidity, dissolved organic carbon (DOC) and total suspended solids (TSS) were the key factors which influenced the MF and UF filterability. Turbidity was the dominant factor affecting the accuracy of the model for MF filterability while DOC was the major factor affecting the accuracy of the model for UF filterability. A prediction accuracy of 85% was obtained for MF and 86% for UF filterability of the WTP effluent. The characteristics of the organic components of the wastewater were demonstrated by EEM spectra to have seasonal variation which would have reduced the prediction accuracy. As turbidity, DOC and TSS can be determined on-line, the models would be useful for rapid prediction of the filterability of WTP effluent and this may assist the control of low-pressure membrane filtration processes. PMID:20962408

Nguyen, T; Fan, L; Roddick, F A; Harris, J L

2010-01-01

151

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

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.

Greeson, Phillip E.

1982-01-01

152

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

PubMed

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

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

2012-12-01

153

A review of soybean (Glycine max) seed, pod, and flower mycofloras in North America, with methods and a key for identification of selected fungi.  

PubMed

A review of the fungi associated with soybean seeds, pods, or flowers was conducted in North America. Species of Deuteromycetes are the most common fungi in each of the soybean flower organs followed by the Ascomycetes and Phycomycetes which comprise about one-fourth of the total mycoflora. Eighty genera and about 135 or more species occur in seeds, pods, or flowers. With regard to numbers of taxa from separate mycofloras, 63 genera and about 108 or more species occur in seeds, 65 genera and about 88 or more species occur in pods, and 36 genera and approximately 47 or more species occur in flowers. Most of the fungi which occur in flowers can be cultured from pods, and the majority of those fungi occur in seeds. Methods for and a key are provided for the identification of the 30 most important selected fungi. PMID:11392564

Roy, K W; Baird, R E; Abney, T S

2001-01-01

154

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

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

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

155

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

PubMed Central

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

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

2013-01-01

156

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

PubMed

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

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

2010-06-01

157

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

PubMed

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

Soruco, Marcela M L; Larschan, Erica

2014-12-01

158

A conifer ABI3-interacting protein plays important roles during key transitions of the plant life cycle.  

PubMed

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

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

2013-01-01

159

Identification of glucocorticoid-induced leucine zipper as a key regulator of tumor cell proliferation in epithelial ovarian cancer  

PubMed Central

Background Little is known about the molecules that contribute to tumor progression of epithelial ovarian cancer (EOC), currently a leading cause of mortality from gynecological malignancies. Glucocorticoid-Induced Leucine Zipper (GILZ), an intracellular protein widely expressed in immune tissues, has been reported in epithelial tissues and controls some of key signaling pathways involved in tumorigenesis. However, there has been no report on GILZ in EOC up to now. The objectives of the current study were to examine the expression of GILZ in EOC and its effect on tumor cell proliferation. Results GILZ expression was measured by immunohistochemical staining in tissue sections from 3 normal ovaries, 7 benign EOC and 50 invasive EOC. GILZ was not detected on the surface epithelium of normal ovaries and benign tumors. In contrast, it was expressed in the cytoplasm of tumor cells in 80% EOC specimens. GILZ immunostaining scores correlated positively to the proliferation marker Ki-67 (Spearman test in univariate analysis, P < 0.00001, r = 0.56). They were also higher in tumor cells containing large amounts of phosphorylated protein kinase B (p-AKT) (unpaired t test, P < 0.0001). To assess the effect of GILZ on proliferation and AKT activation, we used the BG-1 cell line derived from ovarian tumor cells as a cellular model. GILZ expression was either enhanced by stable transfection or decreased by the use of small interfering (si) RNA targeting GILZ. We found that GILZ increased cell proliferation, phospho-AKT cellular content and AKT kinase activity. Further, GILZ upregulated cyclin D1 and phosphorylated retinoblastoma (p-Rb), downregulated cyclin-dependent kinase inhibitor p21, and promoted the entry into S phase of cell cycle. Conclusion The present study is the first to identify GILZ as a molecule produced by ovarian cancer cells that promotes cell cycle progression and proliferation. Our findings clearly indicate that GILZ activates AKT, a crucial signaling molecule in tumorigenesis. GILZ thus appears as a potential key molecule in EOC. PMID:19814803

Redjimi, Nassima; Gaudin, Françoise; Touboul, Cyril; Emilie, Dominique; Pallardy, Marc; Biola-Vidamment, Armelle; Fernandez, Hervé; Prévot, Sophie; Balabanian, Karl; Machelon, Véronique

2009-01-01

160

Identification of key residues in transmembrane 4 responsible for the secondary, low-affinity conformation of the human ?1-adrenoceptor.  

PubMed

The ?1-adrenoceptor exists in two agonist conformations/states: 1) a high-affinity state where responses to catecholamines and other agonists (e.g., cimaterol) are potently inhibited by ?1-adrenoceptor antagonists, and 2) a low-affinity secondary conformation where agonist responses, particularly CGP12177 [(-)-4-(3-tert-butylamino-2-hydroxypropoxy)-benzimidazol-2-one] are relatively resistant to inhibition by ?1-adrenoceptor antagonists. Although both states have been demonstrated in many species (including human), the precise nature of the secondary state is unknown and does not occur in the closely related ?2-adrenoceptor. Here, using site-directed mutagenesis and functional measurements of production of a cyclic AMP response element upstream of a secreted placental alkaline phosphatase reporter gene and accumulation of (3)H-cAMP, we examined the pharmacological consequences of swapping transmembrane (TM) regions of the human ?1- and ?2-adrenoceptors, followed by single point mutations, to determine the key residues involved in the ?1-adrenoceptor secondary conformation. We found that TM4 (particularly amino acids L195 and W199) had a major role in the generation of the secondary ?1-adrenoceptor conformation. Thus, unlike at the human ?1-wild-type adrenoceptor, at ?1-TM4 mutant receptors, cimaterol and CGP12177 responses were both potently inhibited by antagonists. CGP12177 acted as a simple partial agonist with similar KB and EC50 values in the ?1-TM4 but not ?1-wild-type receptors. Furthermore pindolol switched from a biphasic concentration response at human ?1-wild-type adrenoceptors to a monophasic concentration response in the ?1-TM4 mutant receptors. Mutation of these amino acids to those found in the ?2-adrenoceptor (L195Q and W199Y), or mutation of a single residue (W199D) in the human ?1-adrenoceptor thus abolished this secondary conformation and created a ?1-adrenoceptor with only one high-affinity agonist conformation. PMID:24608857

Baker, Jillian G; Proudman, Richard G W; Hill, Stephen J

2014-05-01

161

Identification of Key Residues in Transmembrane 4 Responsible for the Secondary, Low-Affinity Conformation of the Human ?1-Adrenoceptor  

PubMed Central

The ?1-adrenoceptor exists in two agonist conformations/states: 1) a high-affinity state where responses to catecholamines and other agonists (e.g., cimaterol) are potently inhibited by ?1-adrenoceptor antagonists, and 2) a low-affinity secondary conformation where agonist responses, particularly CGP12177 [(?)-4-(3-tert-butylamino-2-hydroxypropoxy)-benzimidazol-2-one] are relatively resistant to inhibition by ?1-adrenoceptor antagonists. Although both states have been demonstrated in many species (including human), the precise nature of the secondary state is unknown and does not occur in the closely related ?2-adrenoceptor. Here, using site-directed mutagenesis and functional measurements of production of a cyclic AMP response element upstream of a secreted placental alkaline phosphatase reporter gene and accumulation of 3H-cAMP, we examined the pharmacological consequences of swapping transmembrane (TM) regions of the human ?1- and ?2-adrenoceptors, followed by single point mutations, to determine the key residues involved in the ?1-adrenoceptor secondary conformation. We found that TM4 (particularly amino acids L195 and W199) had a major role in the generation of the secondary ?1-adrenoceptor conformation. Thus, unlike at the human ?1-wild-type adrenoceptor, at ?1-TM4 mutant receptors, cimaterol and CGP12177 responses were both potently inhibited by antagonists. CGP12177 acted as a simple partial agonist with similar KB and EC50 values in the ?1-TM4 but not ?1-wild-type receptors. Furthermore pindolol switched from a biphasic concentration response at human ?1-wild-type adrenoceptors to a monophasic concentration response in the ?1-TM4 mutant receptors. Mutation of these amino acids to those found in the ?2-adrenoceptor (L195Q and W199Y), or mutation of a single residue (W199D) in the human ?1-adrenoceptor thus abolished this secondary conformation and created a ?1-adrenoceptor with only one high-affinity agonist conformation. PMID:24608857

Proudman, Richard G. W.; Hill, Stephen J.

2014-01-01

162

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

NASA Astrophysics Data System (ADS)

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.

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

2012-12-01

163

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

PubMed

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

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

2014-05-01

164

Chemical and sensorial aroma characterization of freshly distilled Calvados. 2. Identification of volatile compounds and key odorants.  

PubMed

Eight samples of freshly distilled Calvados were extracted using pentane. Gas chromatography with either a mass spectrometer or flame ionization detector was used to determine the volatile compounds composition of the extracts. More than 120 molecules were identified in Calvados and then correlated with results obtained by olfactometric analysis in our earlier work [Guichard, H.; Lemesle, S.; Ledauphin, J.; Barillier, D.; Picoche, B. Chemical and Sensorial Aroma Characterization of Freshly Distilled Calvados. 1. Evaluation of Quality and Defects on the Basis of Key Odorants by Olfactometry and Sensory Analysis. J. Agric. Food Chem. 2002, 50, 424-432 (preceding paper in this issue)]. Of these, 16 of the 19 molecules that constitute the "aroma skeleton" were identified, including 5 esters, 2 ketones, 5 phenolic derivatives, 2 alcohols, and 2 carboxylic acids. Numerous compounds were also associated with odors found in part 1. These molecules can be considered as being responsible for the good quality of Calvados or, in contrast, for defects. Relative levels of some major olfactive compounds were also estimated and tentatively compared with olfactometric indices found in part 1. A good correlation was found in many cases. Two important markers of defects in Calvados were also identified. 3-Methylbut-2-en-1-ol leads to an "herbaceous" defect, and 1,1,3-triethoxypropane seems to give an "acrolein" defect in the product. "Floral" notes of the aroma of freshly distilled Calvados seem to be due to the presence of phenolic derivatives such as 2-phenylethanol and 2-phenylethyl acetate. Low-molecular-weight esters such as ethyl 2-methylpropanoate, ethyl 2-methylbutanoate, and 3-methylbutyl acetate give, in general, the "fruity" notes. However, the overall aroma of Calvados seems likely to be a subtle balance of various functionalized compounds. PMID:12517107

Ledauphin, Jérôme; Guichard, Hugues; Saint-Clair, Jean-François; Picoche, Bernard; Barillier, Daniel

2003-01-15

165

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

PubMed Central

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

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

2009-01-01

166

Identification of antisense RNA stem-loops that inhibit RNA-protein interactions using a bacterial reporter system.  

PubMed

RNA-protein interactions play important roles in gene regulation, functional RNA-protein complexes such as the ribosome, and in viral replication. Molecules that regulate specific RNA-protein interactions may be used to dissect biological processes, and to establish the validity of targeting an RNA-protein interaction. There are many examples of biological regulation by antisense RNA stem-loops that form loop-loop and loop-linear RNA-RNA interactions. Here, a bacterial reporter system for the identification of RNA stem-loops that inhibit the formation of RNA-protein complexes through RNA-RNA interactions is described. PMID:25352136

Harada, Kazuo

2015-01-01

167

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

PubMed

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

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

2015-02-01

168

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

PubMed Central

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

2013-01-01

169

Overcoming Asymmetric Goals in Teams: The Interactive Roles of Team Learning Orientation and Team Identification.  

PubMed

Although members of teams share a common, ultimate objective, they often have asymmetric or conflicting individual goals that shape the way they contribute to, and pursue, the shared goal of the team. Compounding this problem, they are frequently unaware of the nature of these goal asymmetries or even the fact that such differences exist. Drawing on, and integrating, social interdependence and representational gaps theories, we identify 2 emergent states that combine interactively to enable teams to overcome asymmetric goals: team identification and team learning orientation. Using data from long-term, real-life teams that engaged in a computer simulation designed to create both asymmetric goals and representational gaps about those goals, we found that teams were most effective when they had a high learning orientation coupled with high team identification and that this effect was mediated by teams' ability to form more accurate team goal mental models and engage in effective planning processes. Implications for theory and practice are discussed. (PsycINFO Database Record (c) 2014 APA, all rights reserved). PMID:25384202

Pearsall, Matthew J; Venkataramani, Vijaya

2014-11-10

170

Arabidopsis FHY3 defines a key phytochrome A signaling component directly interacting with its homologous partner FAR1  

PubMed Central

In Arabidopsis, phytochrome A (phyA) is the primary photoreceptor mediating various plant responses to far-red (FR) light. Here we show that phyA signaling involves a combinatorial action of downstream intermediates, which controls overlapping yet distinctive sets of FR responses. FHY3 is a prominent phyA signaling intermediate sharing structural similarity to FAR1, a previously identified phyA signaling component. The fhy3 and far1 mutants display similar yet distinctive defects in phyA signaling; however, overexpression of either FHY3 or FAR1 suppresses the mutant phenotype of both genes. Moreover, overexpression of partial fragments of FHY3 can cause a dominant-negative interference phenotype on phyA signaling that is stronger than those of the fhy3 or far1 null mutants. Further, we demonstrate that FHY3 and FAR1 are capable of homo- and hetero-interaction. Our data indicate that FHY3, together with FAR1, defines a key module in a signaling network underlying phyA-mediated FR light responses. PMID:11889039

Wang, Haiyang; Deng, Xing Wang

2002-01-01

171

Regulation of Host Cell Transcriptional Physiology by the Avian Pneumovirus Provides Key Insights into Host-Pathogen Interactions  

PubMed Central

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

Munir, Shirin; Kapur, Vivek

2003-01-01

172

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

Microsoft Academic Search

. 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

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

1996-01-01

173

Keys to Soil Taxonomy  

NSDL National Science Digital Library

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.

United States Department Of Agriculture, National C.

174

Keys to Soil Taxonomy  

NSDL National Science Digital Library

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

2006-12-25

175

Identification, quantitation, and characterization of biomolecules by capillary electrophoretic analysis of binding interactions.  

PubMed

The high resolving power of capillary electrophoresis combined with the specificity of binding interactions may be used with advantage to characterize the structure-function relationship of biomolecules, to quantitate specific analytes in complex sample matrices, and to determine the purity of pharmaceutical and other molecules. We here review recent and innovative methodologies and applications of high resolution affinity electrophoresis within the fields of binding constant determination, structure-activity studies, quantitative microassays, analysis of drug purity and protein conformation, and immobilized affinity ligands. Despite the virtues of these approaches with respect to applicability, resolving power, speed, and low sample consumption, problems remain with respect to analyte identification and low concentration limits of detection. The ongoing development of new detector technologies for capillary electrophoresis such as mass spectrometry, and possibly nuclear magnetic resonance and other spectroscopic methods, is therefore very promising for the continued increased use of affinity capillary electrophoresis. PMID:10596820

Heegaard, N H; Kennedy, R T

1999-10-01

176

??????-?????????????????? A Physical Identification Algorithm for High-Speed Railway Bridges with Consideration of Bridge-Soil Interaction  

Microsoft Academic Search

This paper intends to develop a physical identification algorithm for high-speed railway bridges under braking and acceleration conditions of a single moving vehicle, and to investigate the dynamic characteristics of the railway bridges. The bridge-soil interaction is considered, and the dynamic interaction of the bridge-foundation with the underlying soil is taken into account. A linear model is used for the

Ming-Chih Huang; Chern-Hwa Chen

177

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

PubMed

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 100 kD 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 9.3 viruses/ml to 83 viruses/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. PMID:12153016

Donaldson, K A; Griffin, D W; Paul, J H

2002-05-01

178

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

USGS Publications Warehouse

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.

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

2002-01-01

179

The flea genus Sigmactenus (Siphonaptera: Leptopsyllidae): three new taxa from Sulawesi, updated identification key, and distribution map for all known species and subspecies.  

PubMed

One new species and two new subspecies of fleas are described. These are S. sulawesiensis n. sp. from North and Central Sulawesi, S. alticola pilosus n. ssp. from Central Sulawesi, and S. alticola crassinavis n. ssp. from North Sulawesi. All three of these new taxa are ectoparasites of native, endemic murine rodents. Two of the new taxa, S. sulawesiensis and S. alticola crassinavis, coexist on the same mountain, Gunung Moajat, in North Sulawesi. The related S. alticola alticola, which becomes the nominate subspecies, parasitises the murine rodent Maxomys alticola in northern Borneo (Sabah) and it is hypothesized that Sigmactenus first colonized Sulawesi as an ectoparasite of ancestral Maxomys, or perhaps Rattus, as these murines dispersed from southeast Asia to Sulawesi; 15 endemic murine rodent species belonging to these two genera are known to currently inhabit Sulawesi. An identification key and distribution map are included for all known species and subspecies of Sigmactenus. In addition to the three new taxa and S. a. alticola, these include: S. celebensis from South Sulawesi, S. timorensis from Timor, S. toxopeusi from New Guinea, and S. werneri from the Philippines (Mindanao and Negros). PMID:11031750

Durden, L A; Beaucournu, J C

2000-09-01

180

Building Empathy Through Identification and Expression of Emotions: A Review of Interactive Tools for Children With Social Deficits  

Microsoft Academic Search

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 improve the social functioning of children. Children and

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

2011-01-01

181

Identification of key structural elements for neuronal calcium sensor-1 function in the regulation of the temperature-dependency of locomotion in C. elegans  

PubMed Central

Background Intracellular Ca2+ regulates many aspects of neuronal function through Ca2+ binding to EF hand-containing Ca2+ sensors that in turn bind target proteins to regulate their function. Amongst the sensors are the neuronal calcium sensor (NCS) family of proteins that are involved in multiple neuronal signalling pathways. Each NCS protein has specific and overlapping targets and physiological functions and specificity is likely to be determined by structural features within the proteins. Common to the NCS proteins is the exposure of a hydrophobic groove, allowing target binding in the Ca2+-loaded form. Structural analysis of NCS protein complexes with target peptides has indicated common and distinct aspects of target protein interaction. Two key differences between NCS proteins are the size of the hydrophobic groove that is exposed for interaction and the role of their non-conserved C-terminal tails. Results We characterised the role of NCS-1 in a temperature-dependent locomotion assay in C. elegans and identified a distinct phenotype in the ncs-1 null in which the worms do not show reduced locomotion at actually elevated temperature. Using rescue of this phenotype we showed that NCS-1 functions in AIY neurons. Structure/function analysis introducing single or double mutations within the hydrophobic groove based on information from characterised target complexes established that both N- and C-terminal pockets of the groove are functionally important and that deletion of the C-terminal tail of NCS-1 did not impair its ability to rescue. Conclusions The current work has allowed physiological assessment of suggestions from structural studies on the key structural features that underlie the interaction of NCS-1 with its target proteins. The results are consistent with the notion that full length of the hydrophobic groove is required for the regulatory interactions underlying NCS-1 function whereas the C-terminal tail of NCS-1 is not essential. This has allowed discrimination between two potential modes of interaction of NCS-1 with its targets. PMID:23981466

2013-01-01

182

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

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

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

2014-01-01

183

CR6-interacting factor 1 is a key regulator in A?-induced mitochondrial disruption and pathogenesis of Alzheimer's disease.  

PubMed

Mitochondrial dysfunction, often characterized by massive fission and other morphological abnormalities, is a well-known risk factor for Alzheimer's disease (AD). One causative mechanism underlying AD-associated mitochondrial dysfunction is thought to be amyloid-? (A?), yet the pathways between A? and mitochondrial dysfunction remain elusive. In this study, we report that CR6-interacting factor 1 (Crif1), a mitochondrial inner membrane protein, is a key player in A?-induced mitochondrial dysfunction. Specifically, we found that Crif1 levels were downregulated in the pathological regions of Tg6799 mice brains, wherein overexpressed A? undergoes self-aggregation. Downregulation of Crif1 was similarly observed in human AD brains as well as in SH-SY5Y cells treated with A?. In addition, knockdown of Crif1, using RNA interference, induced mitochondrial dysfunction with phenotypes similar to those observed in A?-treated cells. Conversely, Crif1 overexpression prevented A?-induced mitochondrial dysfunction and cell death. Finally, we show that A?-induced downregulation of Crif1 is mediated by enhanced reactive oxygen species (ROS) and ROS-dependent sumoylation of the transcription factor specificity protein 1 (Sp1). These results identify the ROS-Sp1-Crif1 pathway to be a new mechanism underlying A?-induced mitochondrial dysfunction and suggest that ROS-mediated downregulation of Crif1 is a crucial event in AD pathology. We propose that Crif1 may serve as a novel therapeutic target in the treatment of AD.Cell Death and Differentiation advance online publication, 7 November 2014; doi:10.1038/cdd.2014.184. PMID:25361083

Byun, J; Son, S M; Cha, M-Y; Shong, M; Hwang, Y J; Kim, Y; Ryu, H; Moon, M; Kim, K-S; Mook-Jung, I

2014-11-01

184

Identification of RNA-Protein Interaction Networks Involved in the Norovirus Life Cycle  

PubMed Central

Human noroviruses are one of the major causes of acute gastroenteritis in the developed world, yet our understanding of their molecular mechanisms of genome translation and replication lags behind that for many RNA viruses. Due to the nonculturable nature of human noroviruses, many related members of the Caliciviridae family of small RNA viruses are often used as model systems to dissect the finer details of the norovirus life cycle. Murine norovirus (MNV) has provided one such system with which to study the basic mechanisms of norovirus translation and replication in cell culture. In this report we describe the use of riboproteomics to identify host factors that interact with the extremities of the MNV genome. This network of RNA-protein interactions contains many well-characterized host factors, including PTB, La, and DDX3, which have been shown to play a role in the life cycle of other RNA viruses. By using RNA coimmunoprecipitation, we confirmed that a number of the factors identified using riboproteomics are associated with the viral RNA during virus replication in cell culture. We further demonstrated that RNA inhibition-mediated knockdown of the intracellular levels of a number of these factors inhibits or slows norovirus replication in cell culture, allowing identification of new intracellular targets for this important group of pathogens. PMID:22933270

Vashist, Surender; Urena, Luis; Chaudhry, Yasmin

2012-01-01

185

Heuristic Identification of Biological Architectures for Simulating Complex Hierarchical Genetic Interactions  

PubMed Central

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

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

2015-01-01

186

Identification of filamin A as a BRCA1-interacting protein required for efficient DNA repair  

PubMed Central

The product of the breast and ovarian cancer susceptibility gene BRCA1 has been implicated in several aspects of the DNA damage response but its biochemical function in these processes has remained elusive. In order to probe BRCA1 function we conducted a yeast two-hybrid screening to identify interacting partners to a conserved motif (Motif 6) in the central region of BRCA1. Here we report the identification of the actin-binding protein Filamin A (FLNA) as a BRCA1 partner and demonstrate that FLNA is required for efficient regulation of early stages of DNA repair processes. Cells lacking FLNA display a diminished BRCA1 IR-induced focus formation and a delayed kinetics of Rad51 focus formation. In addition, our data also demonstrate that FLNA is required to stabilize the interaction between components of the DNA-PK holoenzyme, DNA-PKcs and Ku86 in a BRCA1-independent fashion. Our data is consistent with a model in which absence of FLNA compromises homologous recombination and non-homologous end joining. Our findings have implications for the response to radiation-induced DNA damage. PMID:20305393

Velkova, Aneliya; Carvalho, Marcelo A.; Johnson, Joseph O.; Tavtigian, Sean V.; Monteiro, Alvaro N.A.

2011-01-01

187

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

PubMed

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

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

2015-01-01

188

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

ERIC Educational Resources Information Center

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…

Shayler, Hannah A.; Siver, Peter A.

2006-01-01

189

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)

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.

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

2014-01-01

190

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

PubMed

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

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

2014-01-01

191

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

PubMed Central

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

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

2013-01-01

192

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

PubMed Central

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

Kazanietz, Marcelo G.

2013-01-01

193

Visualisation and Identification of the Interaction between STIM1s in Resting Cells  

PubMed Central

Store-operated Ca2+ channels are a major Ca2+ entry pathway in nonexcitable cells, which drive various essential cellular functions. Recently, STIM1 and Orai proteins have been identified as the major molecular components of the Ca2+ release-activated Ca2+ (CRAC) channel. As the key subunit of the CRAC channel, STIM1 is the ER Ca2+ sensor and is essential for the recruitment and activation of Orai1. However, the mechanisms in transmission of information of STIM1 to Orai1 still need further investigation. Bimolecular fluorescence complementation (BiFC) is one of the most advanced and powerful tools for studying and visualising protein-protein interactions in living cells. We utilised BiFC and acceptor photobleaching fluorescence resonance energy transfer (FRET) experiments to visualise and determine the state of STIM1 in the living cells in resting state. Our results demonstrate that STIM1 exists in an oligomeric form in resting cells and that rather than the SAM motif, it is the C-terminus (residues 233–474) of STIM1 that is the key domain for the interaction between STIM1s. The STIM1 oligomers (BiFC-STIM1) and wild-type STIM1 colocalised and had a fibrillar distribution in resting conditions. Depletion of ER Ca2+ stores induced BiFC-STIM1 distribution to become punctate, an effect that could be prevented or reversed by 2-APB. After depletion of the Ca2+ stores, BiFC-STIM1 has the ability to form puncta that colocalise with wild-type STIM1 or Orai1 near the plasma membrane. Our data also indicate that the function of BiFC-STIM1 was not altered compared with that of wild-type STIM1. PMID:22438918

He, Jun; Yu, Tao; Pan, Jingying; Li, He

2012-01-01

194

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

PubMed Central

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

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

2014-01-01

195

Identification of protein-protein interaction and topologies in living cells by chemical cross-linking and mass spectrometry  

SciTech Connect

Current chemical cross-linking methods are commonly employed for mapping sites of interaction and three-dimensional structure in purified, known protein complexes. When applied in vivo in combination of co-immunoprecipitation methods, information on the sites of interaction between proteins are unattainable due to overwhelming sample complexity. We present results from a novel cross-linking strategy that allow simultaneous protein-protein interaction and surface topology measurement in vivo without any prior knowledge of the system. The strategy consists of: (i) cross-linking reaction: intact cell labeling with protein interaction reporters (PIRs); (ii) two-stage mass spectrometric analysis: stage 1 identification of PIR-labeled proteins and construction of a restricted database by 2D-LC/MS/MS; and stage 2 analysis of PIR-labeled peptides by multiplexed LC/FTICR-MS; (iii) data analysis: identification of cross-linked peptides and proteins of origin using accurate mass and other constraints. This strategy was applied to Shewanella oneidensis MR-1 bacterial cells and successfully identified a protein-protein interaction between SecA and a small outer membrane lipoprotein as well as their sites of interaction in vivo.

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

2008-10-20

196

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

NASA Astrophysics Data System (ADS)

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.

Al Azzawi, Dia

197

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

PubMed Central

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

2012-01-01

198

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

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

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

2013-01-01

199

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

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

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

2013-01-01

200

Computational modelling suggests dynamic interactions between Ca2+ IP3 and G protein-coupled modules are key to robust  

E-print Network

-coupled modules are key to robust Dictyostelium aggregation Najl V. Valeyev,*a Jung-Su Kim,b J. S. (Pat) Heslop oscillations26,28 which are one of the major characteristics of aggregation.26,29 Ca2+ has also been sh

Davies, Christopher

201

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

PubMed Central

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

Meng, Jun; Shi, Lin; Luan, Yushi

2014-01-01

202

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

SciTech Connect

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.

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

203

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

PubMed

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

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

2014-11-01

204

Identification of NADPH oxidase as a key mediator in the post-ischemia-induced sequestration and degradation of the GluA2 AMPA receptor subunit.  

PubMed

A hallmark of ischemic/reperfusion injury is a change in subunit composition of synaptic AMPARs. This change in AMPAR subunit composition leads to an increase in surface expression of GluA2-lacking Ca(2+) /Zn(2+) permeable AMPARs. These GluA2-lacking AMPARs play a key role in promoting delayed neuronal death following ischemic injury. At present, the mechanism(s) responsible for the ischemia/reperfusion-induced subunit composition switch and degradation of the GluA2 subunit remain unclear. In this study, we investigated the role of NADPH oxidase, and its importance in mediating endocytosis and subsequent degradation of the GluA2 AMPAR subunit in adult rat hippocampal slices subjected to oxygen-glucose deprivation/reperfusion (OGD/R) injury. In hippocampal slices pretreated with the NADPH oxidase inhibitor apocynin attenuated OGD/R-mediated sequestration of GluA2 and GluA1 as well as prevent the degradation of GluA2. We provide compelling evidence that NADPH oxidase mediated sequestration of GluA1- and GluA2- involved activation of p38 MAPK. Furthermore, we demonstrate that inhibition of NADPH oxidase blunts the OGD/R-induced association of GluA2 with protein interacting with C kinase-1 (PICK1). In summary, this study identifies a novel mechanism that may underlie the ischemia/reperfusion-induced AMPAR subunit composition switch and a potential therapeutic target. This article is protected by copyright. All rights reserved. PMID:25475532

Beske, Phillip H; Byrnes, Nicole M; Astruc-Diaz, Fanny; Jackson, Darrell A

2014-12-01

205

Predicting the paths of peripherals: The interaction of identification and future possibilities  

E-print Network

Two studies investigated how both degree of identification and the individual's position within the group influence aspects of group loyalty. The authors considered ingroup position in terms of both the individual's current ...

Jetten, J.; Branscombe, Nyla R.; Spears, R.; McKimmie, B. M.

2003-01-01

206

Oxyanion steering and CH-? interactions as key elements in an N-heterocyclic carbene-catalyzed [4 + 2] cycloaddition.  

PubMed

The N-heterocyclic carbene catalyzed [4 + 2] cycloaddition has been shown to give ?,?-unsaturated ?-lactones in excellent enantio- and diastereoselectivity. However, preliminary computational studies of the geometry of the intermediate enolate rendered ambiguous both the origins of selectivity and the reaction pathway. Here, we show that a concerted, but highly asynchronous, Diels-Alder reaction occurs rather than the stepwise Michael-type or Claisen-type pathways. In addition, two crucial interactions are identified that enable high selectivity: an oxyanion-steering mechanism and a CH-? interaction. The calculations accurately predict the enantioselectivity of a number of N-heterocyclic carbene catalysts in the hetero-Diels-Alder reaction. PMID:22765294

Allen, Scott E; Mahatthananchai, Jessada; Bode, Jeffrey W; Kozlowski, Marisa C

2012-07-25

207

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

ERIC Educational Resources Information Center

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…

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

2005-01-01

208

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

PubMed

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

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

2014-03-01

209

Dichotomous Keys for Arthropods  

NSDL National Science Digital Library

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

210

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

PubMed Central

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

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

2009-01-01

211

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)

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).

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

2013-04-01

212

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

PubMed

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

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

2014-10-21

213

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

PubMed

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

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

2015-01-01

214

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

PubMed

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

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

2012-12-01

215

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

Microsoft Academic Search

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

Ernesto Estrada; Edificio CACTUS

2005-01-01

216

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

PubMed Central

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

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

2011-01-01

217

Identification of genome-wide SNP-SNP and SNP-clinical Boolean interactions in age-related macular degeneration.  

PubMed

We propose here a methodology to uncover modularities in the network of SNP-SNP interactions most associated with disease. We start by computing all possible Boolean binary SNP interactions across the whole genome. By constructing a weighted graph of the most relevant interactions and via a combinatorial optimization approach, we find the most highly interconnected SNPs. We show that the method can be easily extended to find SNP/environment interactions. Using a modestly sized GWAS dataset of age-related macular degeneration (AMD), we identify a group of only 19 SNPs, which include those in previously reported regions associated to AMD. We also uncover a larger set of loci pointing to a matrix of key processes and functions that are affected. The proposed integrative methodology extends and overlaps traditional statistical analysis in a natural way. Combinatorial optimization techniques allow us to find the kernel of the most central interactions, complementing current methods of GWAS analysis and also enhancing the search for gene-environment interaction. PMID:25403535

Riveros, Carlos; Vimieiro, Renato; Holliday, Elizabeth G; Oldmeadow, Christopher; Wang, Jie Jin; Mitchell, Paul; Attia, John; Scott, Rodney J; Moscato, Pablo A

2015-01-01

218

A new species of Parapinnanema (Nematoda, Chromadoridae) from Dr Theodor Mortensen's Pacific Expedition 1914-16 with an identification key to the genus.  

PubMed

A new species from the family Chromadoridae is described from samples collected during Dr Mortensen's Pacific Expedition 1914-16 to Honolulu, Hawaii. Parapinnanema hawaiiensis sp. nov. is characterized by a low c' ratio and especially by a peculiar complex morphology of the median part of the gubernaculum. An updated and modified key to all the valid species of Parapinnanema is proposed. PMID:25543649

Semprucci, Federica; Sørensen, Martin V

2014-01-01

219

Detection and identification of huwentoxin-IV interacting proteins by biotin-avidin chemistry combined with mass spectrometry  

PubMed Central

Background Numerous spider toxins are of interest as tools for neurophysiological research or as lead molecules for the development of pharmaceuticals and insecticides. Direct detection and identification of the interacting proteins of a spider toxin are helpful for its action-mechanism analysis and practical application. The present study employed a combinative strategy for the analysis of interacting proteins of huwentoxin-IV (HWTX-IV), a peptidic neurotoxin from the venom of the spider Selenocosmia huwena. Results HWTX-IV was first lightly labeled with biotin under the optimized mild experimental conditions and the toxin labeled with a single biotin group (monobiotinylated HWTX-IV) was demonstrated by electrophysiological experiments to retain its original bioactivity and was used in combination with far-western blotting to detect its interacting proteins. Comparative experiments indicated that some membrane proteins from rat neuromuscular junction preparations bind to monobiotinylated HWTX-IV after being transferred onto a PVDF membrane from the SDS-gel. With capillary high performance liquid chromatography-tandem mass spectrometry, several membrane proteins with which HWTX-IV potentially interacted were identified from the preparations and then bioinformatically analyzed. Conclusions This work has provided not only a new insight into the action mechanism of HWTX-IV but also a reference technology for the relevant researches. PMID:24803923

2014-01-01

220

Comparative Identification of Differential Interactions from Trajectories of Dynamic Biological Networks.  

PubMed

It is often challenging to reconstruct accurately a complete dynamic biological network due to the scarcity of data collected in cost-effective experiments. This paper addresses the possibility of comparatively identifying qualitative interaction shifts between two dynamical networks from comparative time course data. An innovative approach is developed to achieve differential interaction detection by statistically comparing the trajectories, instead of numerically comparing the reconstructed interactions. The core of this approach is a statistical heterogeneity test that compares two multiple linear regression equations for the derivatives in nonlinear ordinary differential equations, statistically instead of numerically. In detecting any shift of an interaction, the uncertainty in estimated regression coefficients is taken into account by this test, while it is ignored by the reconstruction-based numerical comparison. The heterogeneity test is accomplished by assessing the gain in goodness-of-fit from using a single common interaction to using a pair of differential interactions. Compared with previous numerical comparison methods, the proposed statistical comparison always achieves higher statistical power. As sample size decreases or noise increases in a certain range, the improvement becomes substantial. The advantage is illustrated by a simulation study on the statistical power as functions of the noise level, the sample size, and the interaction complexity. This method is also capable of detecting interaction shifts in the oscillated and excitable domains of a dynamical system model describing cdc2-cyclin interactions during cell division cycle. Generally, the described approach is applicable to comparing dynamical systems of additive nonlinear ordinary differential equations. PMID:25285064

Ouyang, Zhengyu; Song, Mingzhou Joe

2009-01-01

221

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

PubMed Central

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

2014-01-01

222

Identification of Binding Partners for the Cytoplasmic Loop of Connexin43: A Novel Interaction with ?-Tubulin  

PubMed Central

Connexin43 (Cx43), a component of gap junctions, has a relatively large carboxy-terminal region with multiple proteomic interactions. Proteomic interactions with its cytoplasmic loop, however, are poorly defined. The goal of this study is to examine proteomic interactions involving the cytoplasmic loop (CL) of Cx43. The authors utilized various techniques, including glutathione-S-transferase (GST) pull-down, immunoblot analysis, two-dimensional (2D) gel electrophoresis, and mass spectrometry, to elucidate binding partners for Cx43-CL. The authors identified novel interactions with Cx43-CL involving ?- and ?-tubulin, myelin basic protein, and Pur?. Because tubulin interacts with the C-terminus of Cx43 (Cx43-CT), the authors further investigated the nature of the interaction between ?-tubulin and Cx43-CL. ?-Tubulin binds with the full length of Cx43-CL with approximately one-fifth the affinity of the interaction between Cx43-CT and ?-tubulin. This study demonstrates novel proteomic interactions involving Cx43-CL that may lead to a more complete understanding of trafficking and gating of gap junction channels. PMID:19274588

Kang, Eunice Y.; Ponzio, Marc; Gupta, Pritha P.; Liu, Fangyu; Butensky, Adam; Gutstein, David E.

2009-01-01

223

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

Microsoft Academic Search

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

Jian Cui; Jinghua Liu; Yuhua Li; Tieliu Shi; Vladimir Uversky

2011-01-01

224

Evaluation of perrecord identification risk by additive modeling of interaction for contingency table  

E-print Network

terms for cell probabilities of contingency tables to evaluate the conditional probability of popu of cell probabili­ ties of the contingency table corresponding to a microdata set, where all the key probabilities of contingency tables. In this paper we consider fitting the Lancaster­type additive model

Yamamoto, Hirosuke

225

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

E-print Network

terms for cell probabilities of contingency tables to evaluate the conditional probability of popu of cell probabili- ties of the contingency table corresponding to a microdata set, where all the key probabilities of contingency tables. In this paper we consider fitting the Lancaster-type additive model

Yamamoto, Hirosuke

226

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

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

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

227

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

PubMed Central

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

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

2004-01-01

228

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.

229

Key Facts  

Cancer.gov

Key Facts Scientists know that: I-131 breaks down rapidly in the atmosphere and environment Exposure was highest in the first few days after each nuclear test explosion Most exposure occurred through drinking fresh milk People received little exposure

230

Stability of the transthyretin molecule as a key factor in the interaction with a-beta peptide--relevance in Alzheimer's disease.  

PubMed

Transthyretin (TTR) protects against A-Beta toxicity by binding the peptide thus inhibiting its aggregation. Previous work showed different TTR mutations interact differently with A-Beta, with increasing affinities correlating with decreasing amyloidogenecity of the TTR mutant; this did not impact on the levels of inhibition of A-Beta aggregation, as assessed by transmission electron microscopy. Our work aimed at probing differences in binding to A-Beta by WT, T119M and L55P TTR using quantitative assays, and at identifying factors affecting this interaction. We addressed the impact of such factors in TTR ability to degrade A-Beta. Using a dot blot approach with the anti-oligomeric antibody A11, we showed that A-Beta formed oligomers transiently, indicating aggregation and fibril formation, whereas in the presence of WT and T119M TTR the oligomers persisted longer, indicative that these variants avoided further aggregation into fibrils. In contrast, L55PTTR was not able to inhibit oligomerization or to prevent evolution to aggregates and fibrils. Furthermore, apoptosis assessment showed WT and T119M TTR were able to protect against A-Beta toxicity. Because the amyloidogenic potential of TTR is inversely correlated with its stability, the use of drugs able to stabilize TTR tetrameric fold could result in increased TTR/A-Beta binding. Here we showed that iododiflunisal, 3-dinitrophenol, resveratrol, [2-(3,5-dichlorophenyl)amino] (DCPA) and [4-(3,5-difluorophenyl)] (DFPB) were able to increase TTR binding to A-Beta; however only DCPA and DFPB improved TTR proteolytic activity. Thyroxine, a TTR ligand, did not influence TTR/A-Beta interaction and A-Beta degradation by TTR, whereas RBP, another TTR ligand, not only obstructed the interaction but also inhibited TTR proteolytic activity. Our results showed differences between WT and T119M TTR, and L55PTTR mutant regarding their interaction with A-Beta and prompt the stability of TTR as a key factor in this interaction, which may be relevant in AD pathogenesis and for the design of therapeutic TTR-based therapies. PMID:23028965

Ribeiro, Carlos A; Saraiva, Maria João; Cardoso, Isabel

2012-01-01

231

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

PubMed Central

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

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

2014-01-01

232

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

PubMed

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

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

2014-09-01

233

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

NASA Astrophysics Data System (ADS)

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.

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

2014-09-01

234

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

NASA Astrophysics Data System (ADS)

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.

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

2014-09-01

235

Identification, structural and pharmacological characterization of ?-CnVA, a conopeptide that selectively interacts with somatostatin sst3 receptor.  

PubMed

Conopeptides are a diverse array of small linear and reticulated peptides that interact with high potency and selectivity with a large diversity of receptors and ion channels. They are used by cone snails for prey capture or defense. Recent advances in venom gland transcriptomic and venom peptidomic/proteomic technologies combined with bioactivity screening approaches lead to the identification of new toxins with original pharmacological profiles. Here, from transcriptomic/proteomic analyses of the Conus consors cone snail, we identified a new conopeptide called ?-CnVA, which displays the typical cysteine framework V of the T1-conotoxin superfamily. This peptide was chemically synthesized and its three-dimensional structure was solved by NMR analysis and compared to that of TxVA belonging to the same family, revealing very few common structural features apart a common orientation of the intercysteine loop. Because of the lack of a clear biological function associated with the T-conotoxin family, ?-CnVA was screened against more than fifty different ion channels and receptors, highlighting its capacity to interact selectively with the somatostatine sst3 receptor. Pharmacological and functional studies show that ?-CnVA displays a micromolar (Ki of 1.5?M) antagonist property for the sst3 receptor, being currently the only known toxin to interact with this GPCR subfamily. PMID:23567999

Petrel, C; Hocking, H G; Reynaud, M; Upert, G; Favreau, Ph; Biass, D; Paolini-Bertrand, M; Peigneur, S; Tytgat, J; Gilles, N; Hartley, O; Boelens, R; Stocklin, R; Servent, D

2013-06-01

236

Target Identification by Chromatographic Co-elution: Monitoring of Drug-Protein Interactions without Immobilization or Chemical Derivatization*  

PubMed Central

Bioactive molecules typically mediate their biological effects through direct physical association with one or more cellular proteins. The detection of drug-target interactions is therefore essential for the characterization of compound mechanism of action and off-target effects, but generic label-free approaches for detecting binding events in biological mixtures have remained elusive. Here, we report a method termed target identification by chromatographic co-elution (TICC) for routinely monitoring the interaction of drugs with cellular proteins under nearly physiological conditions in vitro based on simple liquid chromatographic separations of cell-free lysates. Correlative proteomic analysis of drug-bound protein fractions by shotgun sequencing is then performed to identify candidate target(s). The method is highly reproducible, does not require immobilization or derivatization of drug or protein, and is applicable to diverse natural products and synthetic compounds. The capability of TICC to detect known drug-protein target physical interactions (Kd range: micromolar to nanomolar) is demonstrated both qualitatively and quantitatively. We subsequently used TICC to uncover the sterol biosynthetic enzyme Erg6p as a novel putative anti-fungal target. Furthermore, TICC identified Asc1 and Dak1, a core 40 S ribosomal protein that represses gene expression, and dihydroxyacetone kinase involved in stress adaptation, respectively, as novel yeast targets of a dopamine receptor agonist. PMID:22357554

Chan, Janet N. Y.; Vuckovic, Dajana; Sleno, Lekha; Olsen, Jonathan B.; Pogoutse, Oxana; Havugimana, Pierre; Hewel, Johannes A.; Bajaj, Navgeet; Wang, Yale; Musteata, Marcel F.; Nislow, Corey; Emili, Andrew

2012-01-01

237

Identification of Surface Residues Involved in Protein-Protein Interaction A Support Vector  

E-print Network

-protein interactions are becoming increasingly important (reviewed in Teichmann et al., 2001; Valencia and Pazos, 2002 (Gallet et al., 2000), multiple sequence alignment (Casarai et al., 1995; Lichtarge et al., 1996; Pazos et

Honavar, Vasant

238

Identification of MANF as a protein interacting with RTN1-C.  

PubMed

Reticulons (RTNs) constitute a family of endoplasmic reticulum (ER)-associated proteins with a reticular distribution. Recently, evidence has shown that they exert a cancer-speci?c proapoptotic function via interaction or modulation of speci?c proteins. Such evidence is particularly associated with the RTN1-C family members. In order to explore proteins that interact with RTN1-C, the yeast two-hybrid system and regular molecular biological techniques were used to screen the human fetal brain cDNA library. As a result, seven RTN1-C interacting proteins including Homo sapiens mesencephalic astrocyte-derived neurotrophic factor (MANF) were obtained. The interactions between RTN1-C and its interacting proteins were confirmed by ?-galactosidase assay and growth test in selective media. Moreover, the MANF/RTN1-C interaction was verified in vitro by glutathione S-transferase pull-down assay and in vivo by immunoprecipitation assay. By immuno?uorescence assay, it was found that MANF co-localized with RTN1-C in the ER. Knockdown of RTN1-C reduced the localization of MANF in the ER. These results provide clues to further explore the function of RTN1-C and MANF in neurodegenerative diseases and cancer. PMID:25543119

Chen, Lijian; Wan, Lijuan; Du, Jian; Shen, Yuxian

2015-02-01

239

Identification of Mycoplasma suis MSG1 interaction proteins on porcine erythrocytes.  

PubMed

Adhesion protein MSG1 mediating adherence to porcine erythrocytes in Mycoplasma suis (M. suis) invasion has been identified previously. In order to determine the host membrane proteins that interact with MSG1, recombinant His-tagged MSG1 (rMSG1) was used to screen for interacting proteins in the protein extracts of porcine erythrocyte membrane. Potential rMSG1-interacting proteins were initially identified as band 3 and ?-actin with molecular weight of 46 and 45 kDa, respectively. Immune fluorescence results showed that rMSG1 can specifically bind with the ?-actin of HeLa, BHK-21, and HEK-293A cells, respectively. RNA interference assays further demonstrated that the interaction between ?-actin and rMSG1 on HeLa cells was specific and dose dependent. Confocal microscopy showed that both rMSG1 and M. suis can partially co-localize with ?-actin on the surface of porcine erythrocytes. Pull-down assays showed that rMSG1 can directly interact with ?-actin. Our study is the first to report the interaction of MSG1 with ?-actin, which will be of help to understand the pathogenesis of M. suis and develop a cultivation system. PMID:25344885

Zhang, Yaning; Zou, Yao; Ma, Peipei; Muhammad, Hassan Mushtaq; Li, Yufeng; Jiang, Ping

2015-03-01

240

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

PubMed Central

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

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

241

Identification of Cellular Proteins Interacting with Equine Infectious Anemia Virus S2 Protein  

PubMed Central

The macrophage-tropic lentivirus, equine infectious anemia virus (EIAV), encodes the small auxiliary protein S2 from a short open reading frame that overlaps the amino terminus of env. EIAV S2 is dispensable for virus replication in cultured cells but is required for disease production. S2 is approximately 7kDa and has no overall amino acid sequence homology to other cellular or viral proteins. Therefore it is likely that S2 plays a role as an adaptor protein. To further investigate S2 function we performed a yeast-2-hybrid screen to identify cellular proteins that interact with EIAV S2. The screen identified two human cellular proteins, amplified in osteosarcoma (OS-9) and proteasome 26S ATPase subunit 3 (PSMC3) that interact with S2. The equine homologues of these proteins were cloned and their interactions with S2 confirmed using co-immunoprecipitation assays. We identified two OS9 isoforms that interact with S2 and a third splice variant that does not, indicating a region of OS9 apparently required for the S2 interaction. The roles of these cellular proteins during EIAV infection have not been determined. PMID:20417672

Covaleda, Lina; Gno, Bich-Ty; Fuller, Fredrick J.; Payne, Susan L.

2010-01-01

242

Identification of cellular proteins interacting with equine infectious anemia virus S2 protein.  

PubMed

The macrophage-tropic lentivirus, equine infectious anemia virus (EIAV), encodes the small auxiliary protein S2 from a short open reading frame that overlaps the amino terminus of env EIAV S2 is dispensable for virus replication in cultured cells but is required for disease production. S2 is approximately 7 kDa and has no overall amino acid sequence homology to other cellular or viral proteins. Therefore it is likely that S2 plays a role as an adaptor protein. To further investigate S2 function we performed a yeast-2-hybrid screen to identify cellular proteins that interact with EIAV S2. The screen identified two human cellular proteins, amplified in osteosarcoma (OS-9) and proteasome 26S ATPase subunit 3 (PSMC3) that interact with S2. The equine homologues of these proteins were cloned and their interactions with S2 confirmed using co-immunoprecipitation assays. We identified two OS-9 isoforms that interact with S2 and a third splice variant that does not, indicating a region of OS-9 apparently required for the S2 interaction. The roles of these cellular proteins during EIAV infection have not been determined. PMID:20417672

Covaleda, Lina; Gno, Bich-Ty; Fuller, Fredrick J; Payne, Susan L

2010-08-01

243

Ganglioside inhibition of neurite outgrowth requires Nogo receptor function: identification of interaction sites and development of novel antagonists.  

PubMed

Gangliosides are key players in neuronal inhibition, with antibody-mediated clustering of gangliosides blocking neurite outgrowth in cultures and axonal regeneration post injury. In this study we show that the ganglioside GT1b can form a complex with the Nogo-66 receptor NgR1. The interaction is shown by analytical ultracentrifugation sedimentation and is mediated by the sialic acid moiety on GT1b, with mutations in FRG motifs on NgR1 attenuating the interaction. One FRG motif was developed into a cyclic peptide (N-AcCLQKFRGSSC-NH(2)) antagonist of GT1b, reversing the GT1b antibody inhibition of cerebellar granule cell neurite outgrowth. Interestingly, the peptide also antagonizes neurite outgrowth inhibition mediated by soluble forms of the myelin-associated glycoprotein (MAG). Structure function analysis of the peptide point to the conserved FRG triplet being the minimal functional motif, and mutations within this motif inhibit NgR1 binding to both GT1b and MAG. Finally, using gene ablation, we show that the cerebellar neuron response to GT1b antibodies and soluble MAG is indeed dependent on NgR1 function. The results suggest that gangliosides inhibit neurite outgrowth by interacting with FRG motifs in the NgR1 and that this interaction can also facilitate the binding of MAG to the NgR1. Furthermore, the results point to a rational strategy for developing novel ganglioside antagonists. PMID:18411262

Williams, Gareth; Wood, Andrew; Williams, Emma-Jane; Gao, Ying; Mercado, Mary L; Katz, Alan; Joseph-McCarthy, Diane; Bates, Brian; Ling, Huai-Ping; Aulabaugh, Ann; Zaccardi, Joe; Xie, Yuhong; Pangalos, Menelas N; Walsh, Frank S; Doherty, Patrick

2008-06-13

244

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

SciTech Connect

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.

Richard L. Blanton

2004-02-19

245

NIMIN-1, NIMIN-2 and NIMIN-3, members of a novel family of proteins from Arabidopsis that interact with NPR1\\/NIM1, a key regulator of systemic acquired resistance in plants  

Microsoft Academic Search

NPR1\\/NIM1 is a key regulator of systemic acquired resistance (SAR) in Arabidopsis. Using the yeast two-hybrid system, we have identified three novel genes, NIMIN-1, NIMIN-2 and NIMIN-3 (NIMIN for NIM1-interacting) that encode structurally related proteins interacting physically with NPR1\\/NIM1. NIMIN-1 and NIMIN-2 both bind strongly to NPR1\\/NIM1 via a common binding motif interacting with the C-terminal moiety of NPR1\\/NIM1, whereas

Ralf R. Weigel; Christoph Bäuscher; Artur J. P. Pfitzner; Ursula M. Pfitzner

2001-01-01

246

Identification and characterization of molecular interactions between mortalin/mtHsp70 and HSP60  

PubMed Central

Mortalin/mtHsp70 (mitochondrial Hsp70) and HSP60 (heat-shock protein 60) are heat-shock proteins that reside in multiple subcellular compartments, with mitochondria being the predominant one. In the present study, we demonstrate that the two proteins interact both in vivo and in vitro, and that the N-terminal region of mortalin is involved in these interactions. Suppression of HSP60 expression by shRNA (short hairpin RNA) plasmids caused the growth arrest of cancer cells similar to that obtained by suppression of mortalin expression by ribozymes. An overexpression of mortalin, but not of HSP60, extended the in vitro lifespan of normal fibroblasts (TIG-1). Taken together, this study for the first time delineates: (i) molecular interactions of HSP60 with mortalin; (ii) their co- and exclusive localizations in vivo; (iii) their involvement in tumorigenesis; and (iv) their functional distinction in pathways involved in senescence. PMID:15957980

2005-01-01

247

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

SciTech Connect

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.

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

248

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

SciTech Connect

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.

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

2008-04-01

249

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

PubMed Central

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

2013-01-01

250

Florida Keys  

NASA Technical Reports Server (NTRS)

The Florida Keys are a chain of islands, islets and reefs extending from Virginia Key to the Dry Tortugas for about 309 kilometers (192 miles). The keys are chiefly limestone and coral formations. The larger islands of the group are Key West (with its airport), Key Largo, Sugarloaf Key, and Boca Chica Key. A causeway extends from the mainland to Key West.

This image was acquired on October 28, 2001, by the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) on NASA's Terra satellite. With its 14 spectral bands from the visible to the thermal infrared wavelength region, and its high spatial resolution of 15 to 90 meters (about 50 to 300 feet), ASTER images Earth to map and monitor the changing surface of our planet.

ASTER is one of five Earth-observing instruments launched December 18, 1999, on NASA's Terra satellite. The instrument was built by Japan's Ministry of Economy, Trade and Industry. A joint U.S./Japan science team is responsible for validation and calibration of the instrument and the data products.

The broad spectral coverage and high spectral resolution of ASTER will provide scientists in numerous disciplines with critical information for surface mapping, and monitoring of dynamic conditions and temporal change. Example applications are: monitoring glacial advances and retreats; monitoring potentially active volcanoes; identifying crop stress; determining cloud morphology and physical properties; wetlands evaluation; thermal pollution monitoring; coral reef degradation; surface temperature mapping of soils and geology; and measuring surface heat balance.

Dr. Anne Kahle at NASA's Jet Propulsion Laboratory, Pasadena, Calif., is the U.S. Science team leader; Bjorn Eng of JPL is the project manager. The Terra mission is part of NASA's Earth Science Enterprise, a long- term research effort to understand and protect our home planet. Through the study of Earth, NASA will help to provide sound science to policy and economic decision-makers so as to better life here, while developing the technologies needed to explore the universe and search for life beyond our home planet.

Size: 51.6 by 29.7 kilometers ( 32.0 by 18.4 miles) Location: 24.7 degrees North latitude, 81.5 degrees West longitude Orientation: North at top Image Data: ASTER bands 1, 2, and 3 Original Data Resolution: 15 meters (49.2 feet) Date Acquired: October 28, 2001

2002-01-01

251

Identification of Genes in Xanthomonas campestris pv. vesicatoria Induced during Its Interaction with Tomato?  

PubMed Central

Xanthomonas campestris pv. vesicatoria is the causal agent of bacterial spot disease of tomato and pepper. The disease process is interactive and very intricate and involves a plethora of genes in the pathogen and in the host. In the pathogen, different genes are activated in response to the changing environment to enable it to survive, adapt, evade host defenses, propagate, and damage the host. To understand the disease process, it is imperative to broaden our understanding of the gene machinery that participates in it, and the most reliable way is to identify these genes in vivo. Here, we have adapted a recombinase-based in vivo expression technology (RIVET) to study the genes activated in X. campestris pv. vesicatoria during its interaction with one of its hosts, tomato. This is the first study that demonstrates the feasibility of this approach for identifying in vivo induced genes in a plant pathogen. RIVET revealed 61 unique X. campestris pv. vesicatoria genes or operons that delineate a picture of the different processes involved in the pathogen-host interaction. To further explore the role of some of these genes, we generated knockout mutants for 13 genes and characterized their ability to grow in planta and to cause disease symptoms. This analysis revealed several genes that may be important for the interaction of the pathogen with its host, including a citH homologue gene, encoding a citrate transporter, which was shown to be required for wild-type levels of virulence. PMID:17573477

Tamir-Ariel, Dafna; Navon, Naama; Burdman, Saul

2007-01-01

252

Proteomic-Based Identification of CD4-Interacting Proteins in Human Primary Macrophages  

PubMed Central

Background Human macrophages (M?) express low levels of CD4 glycoprotein, which is constitutively recycled, and 40–50% of its localization is intracellular at steady-state. Although CD4-interacting proteins in lymphoid cells are well characterised, little is known about the CD4 protein interaction-network in human M?, which notably lack LCK, a Src family protein tyrosine kinase believed to stabilise CD4 at the surface of T cells. As CD4 is the main cellular receptor used by HIV-1, knowledge of its molecular interactions is important for the understanding of viral infection strategies. Methodology/Principal Findings We performed large-scale anti-CD4 immunoprecipitations in human primary M? followed by high-resolution mass spectrometry analysis to elucidate the protein interaction-network involved in induced CD4 internalization and degradation. Proteomic analysis of CD4 co-immunoisolates in resting M? showed CD4 association with a range of proteins found in the cellular cortex, membrane rafts and components of clathrin-adaptor proteins, whereas in induced internalization and degradation CD4 is associated with components of specific signal transduction, transport and the proteasome. Conclusions/Significance This is the first time that the anti-CD4 co-immunoprecipitation sub-proteome has been analysed in human primary M?. Our data have identified important M? cell surface CD4-interacting proteins, as well as regulatory proteins involved in internalization and degradation. The data give valuable insights into the molecular pathways involved in the regulation of CD4 expression in M? and provide candidates/targets for further biochemical studies. PMID:21533244

Raposo, Rui André Saraiva; Thomas, Benjamin; Ridlova, Gabriela; James, William

2011-01-01

253

Molecular identification key based on PCR/RFLP for three polychaete sibling species of the genus Marenzelleria, and the species' current distribution in the Baltic Sea  

NASA Astrophysics Data System (ADS)

Studies of Marenzelleria species were often hampered by identification uncertainties when using morphological characters only. A newly developed PCR/RFLP protocol allows a more efficient discrimination of the three species Marenzelleria viridis, Marenzelleria neglecta and Marenzelleria arctia currently known for the Baltic Sea. The protocol is based on PCR amplification of two mitochondrial DNA gene segments (16S, COI) followed by digestion with restriction enzymes. As it is faster and cheaper than PCR/sequencing protocols used so far, the protocol is recommended for large-scale analyses. The markers allow an undoubted determination of species irrespective of life stage or condition of the worms in the samples. The protocol was validated on about 950 specimens sampled at more than 30 sites of the Baltic and the North Sea, and on specimens from populations of the North American east coast. Besides this test we used mitochondrial DNA sequences (16S, COI, Cytb) and starch gel electrophoresis to further investigate the distribution of the three Marenzelleria species in the Baltic Sea. The results show that M. viridis (formerly genetic type I or M. cf. wireni) occurred in the Öresund area, in the south western as well as in the eastern Baltic Sea, where it is found sympatric with M. neglecta. Allozyme electrophoresis indicated an introduction by range expansion from the North Sea. The second species, M. arctia, was only found in the northern Baltic Sea, where it sometimes occurred sympatric with M. neglecta or M. viridis. For Baltic M. arctia, the most probable way of introduction is by ship ballast water from the European Arctic. There is an urgent need for a new genetic analysis of all Marenzelleria populations of the Baltic Sea to unravel the current distribution of the three species.

Blank, M.; Laine, A. O.; Jürss, K.; Bastrop, R.

2008-06-01

254

Key Literature.  

ERIC Educational Resources Information Center

Provides an annotated bibliography of the literature considered by the contributing authors to this journal issue to be of key importance to the subjects covered in their articles. These subjects include: transfer, vocational education, remedial education, English as a second language (ESL), assessment, student services, faculty and professional…

New Directions for Community Colleges, 2002

2002-01-01

255

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

PubMed Central

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

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

2014-01-01

256

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

NASA Astrophysics Data System (ADS)

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.

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

2011-03-01

257

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

PubMed Central

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

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

2011-01-01

258

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

PubMed

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

Prévost, M; Vertongen, P; Waelbroeck, M

2012-10-01

259

Identification and Comparative Analysis of Hepatitis C Virus-Host Cell Protein Interactions  

PubMed Central

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

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

2014-01-01

260

Identification of G-protein coupled receptors and ligands interactions on a chemo-genomic scale  

Microsoft Academic Search

G-protein coupled receptors (GPCR) represent a class of important therapeutic targets. Seeking novel ligands as potential drugs targeting GPCRs and identifying natural ligands for orphan GPCRs have been long-standing efforts of academic and pharmaceutical industrial research. To accelerate this effort, there is a critical need for methods capable of predicting GPCR-ligand interactions on a large scale. Such methods also may

Wang Ting; Duan Yong

2009-01-01

261

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

PubMed

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. PMID:24985433

Ji, Xiaoxi; Wu, Yu; Sheng, Wenbo; Lin, Wei

2014-06-01

262

Proteomic allergen-peptide/protein interaction assay for the identification of human skin sensitizers.  

PubMed

Modification of proteins by skin sensitizers is a pivotal step in T cell mediated allergic contact dermatitis (ACD). In this process small reactive chemicals interact covalently or non-covalently with cellular or extracellular skin self-proteins or self-peptides to become recognized by the human immune system. Aiming to develop a novel non-animal in vitro test system for predicting sensitization potential of small reactive chemicals in human skin the allergen-peptide/protein interaction assay (APIA) has been developed. By applying modern proteomic technologies together with a target peptide containing all amino acids, the assay permits the profiling of all amino acid specific allergen-peptide interactions. Moreover, potentially crucial allergen-specific Cys-modifications are qualitatively monitored by mass spectrometry and confirmed by a dual peptide approach. Assay conditions chosen mimic the distinct human epidermal reactivity compartments of the skin surface (pH 5.5), stratum basale (pH 6.8), and typical physiological conditions (pH 7.4). An extreme as well as a moderate human contact sensitizer produced Cys-specific mass shifts, whereas a skin irritant did not. Our data indicate that MALDI-MS based and skin-related in vitro technology platforms - like the APIA - are promising tools in developing alternative non-animal allergen assays. This will assist in chemical classification and next generation risk assessment strategies, including REACH and experimental immunotoxicology. PMID:22926046

Dietz, Lisa; Kinzebach, Sven; Ohnesorge, Stefanie; Franke, Bastian; Goette, Irina; Koenig-Gressel, Dieter; Thierse, Hermann-Josef

2013-04-01

263

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

PubMed Central

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

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

2013-01-01

264

Genetic Identification of a Network of Factors that Functionally Interact with the Nucleosome Remodeling ATPase ISWI  

PubMed Central

Nucleosome remodeling and covalent modifications of histones play fundamental roles in chromatin structure and function. However, much remains to be learned about how the action of ATP-dependent chromatin remodeling factors and histone-modifying enzymes is coordinated to modulate chromatin organization and transcription. The evolutionarily conserved ATP-dependent chromatin-remodeling factor ISWI plays essential roles in chromosome organization, DNA replication, and transcription regulation. To gain insight into regulation and mechanism of action of ISWI, we conducted an unbiased genetic screen to identify factors with which it interacts in vivo. We found that ISWI interacts with a network of factors that escaped detection in previous biochemical analyses, including the Sin3A gene. The Sin3A protein and the histone deacetylase Rpd3 are part of a conserved histone deacetylase complex involved in transcriptional repression. ISWI and the Sin3A/Rpd3 complex co-localize at specific chromosome domains. Loss of ISWI activity causes a reduction in the binding of the Sin3A/Rpd3 complex to chromatin. Biochemical analysis showed that the ISWI physically interacts with the histone deacetylase activity of the Sin3A/Rpd3 complex. Consistent with these findings, the acetylation of histone H4 is altered when ISWI activity is perturbed in vivo. These findings suggest that ISWI associates with the Sin3A/Rpd3 complex to support its function in vivo. PMID:18535655

Burgio, Giosalba; La Rocca, Gaspare; Sala, Anna; Arancio, Walter; Di Gesù, Dario; Collesano, Marianna; Sperling, Adam S.; Armstrong, Jennifer A.; van Heeringen, Simon J.; Logie, Colin; Tamkun, John W.; Corona, Davide F. V.

2008-01-01

265

Identification of interactions in fractional-order systems with high dimensions  

SciTech Connect

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.

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

266

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

PubMed

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

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

2014-01-01

267

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

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

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

2013-05-01

268

Cucujus tulliae sp. n. – an endemic Mediterranean saproxylic beetle from genus Cucujus Fabricius, 1775 (Coleoptera, Cucujidae), and keys for identification of adults and larvae native to Europe  

PubMed Central

Abstract Cucujus tulliae sp. n. is described as a new member of genus Cucujus Fabricius, 1775 (Coleoptera, Cucujidae), which enumerates at present eleven species distributed in Eurasia and northern America. This saproxylic beetle is the first Cucujus species known only from Mediterranean and it is probably endemic to Calabria (Italy). The species was found especially in old–growth mountain forests of high conservation value (i.e. national parks) dominated by Calabrian pine (Pinus laricio calabrica). We hypothesize that Cucujus tulliae sp. n. probably evolved from isolated populations of Cucujus haematodes Erichson, 1845. The species is thus relictual and of high conservation value, corresponding at least to endangered (EN) category with respect to recent IUCN criterion. Cucujus tulliae sp. n. is here compared with two species native to Europe – Cucujus haematodes and Cucujus cinnaberinus (Scopoli, 1763) and with the Caucasian Cucujus haematodes caucasicus Motschulsky, 1845, which is confirmed as a valid subspecies. The male genitalia of this Caucasian form have been examined and illustrated for the first time. A comprehensive key to adults and larvae of European species is provided. PMID:22933850

Bonacci, Teresa; Mazzei, Antonio; Horák, Jakub; Brandmayr, Pietro

2012-01-01

269

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

SciTech Connect

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.

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

270

Identification of a New Endogenous Metabolite and the Characterization of Its Protein Interactions through an Immobilization Approach  

PubMed Central

The emerging field of global mass-based metabolomics provides a platform for discovering unknown metabolites and their specific biochemical pathways. We report the identification of a new endogenous metabolite, N4-(N-acetylaminopropyl)spermidine and the use of a novel proteomics based method for the investigation of its protein interaction using metabolite immobilization on agarose beads. The metabolite was isolated from the organism Pyrococcus furiosus, and structurally characterized through an iterative process of synthesizing candidate molecules and comparative analysis using accurate mass LC-MS/MS. An approach developed for the selective preparation of N1-acetylthermospermine, one of the possible structures of the unknown metabolite, provides a convenient route to new polyamine derivatives through methylation on the N8 and N4 of the thermospermine scaffold. The biochemical role of the novel metabolite as well as that of two other polyamines: spermidine and agmatine is investigated through metabolite immobilization and incubation with native proteins. The identification of eleven proteins that uniquely bind with N4-(N-acetylaminopropyl)spermidine, provides information on the role of this novel metabolite in the native organism. Identified proteins included hypothetical ones such as PF0607 and PF1199, and those involved in translation, DNA synthesis and the urea cycle like translation initiation factor IF-2, 50S ribosomal protein L14e, DNA-directed RNA polymerase, and ornithine carbamoyltransferase. The immobilization approach demonstrated here has the potential for application to other newly discovered endogenous metabolites found through untargeted metabolomics, as a preliminary screen for generating a list of proteins that could be further investigated for specific activity. PMID:19055353

Kalisiak, Jaros?aw; Trauger, Sunia A.; Kalisiak, Ewa; Morita, Hirotoshi; Fokin, Valery V.; Adams, Mike W. W.; Sharpless, K. Barry; Siuzdak, Gary

2009-01-01

271

Key distributionKey distribution Key distribution, symmetric encryption  

E-print Network

COMP 522 Key distributionKey distribution COMP 522 Key distribution, symmetric encryption From in a secure way and must keep the key secure" · Important issue: how to distribute secret keys? COMP 522 Key distribution, manual delivery For two parties A and B: · A key could be created by A and delivered physically

Fisher, Michael

272

Identification of Significant Association and Gene-Gene Interaction of GABA Receptor Subunit Genes in Autism  

PubMed Central

Autism is a common neurodevelopmental disorder with a significant genetic component. Existing research suggests that multiple genes contribute to autism and that epigenetic effects or gene-gene interactions are likely contributors to autism risk. However, these effects have not yet been identified. Gamma-aminobutyric acid (GABA), the primary inhibitory neurotransmitter in the adult brain, has been implicated in autism etiology. Fourteen known autosomal GABA receptor subunit genes were studied to look for the genes associated with autism and their possible interactions. Single-nucleotide polymorphisms (SNPs) were screened in the following genes: GABRG1, GABRA2, GABRA4, and GABRB1 on chromosome 4p12; GABRB2, GABRA6, GABRA1, GABRG2, and GABRP on 5q34-q35.1; GABRR1 and GABRR2 on 6q15; and GABRA5, GABRB3, and GABRG3 on 15q12. Intronic and/or silent mutation SNPs within each gene were analyzed in 470 white families with autism. Initially, SNPs were used in a family-based study for allelic association analysis—with the pedigree disequilibrium test and the family-based association test—and for genotypic and haplotypic association analysis—with the genotype-pedigree disequilibrium test (geno-PDT), the association in the presence of linkage (APL) test, and the haplotype family-based association test. Next, with the use of five refined independent marker sets, extended multifactor-dimensionality reduction (EMDR) analysis was employed to identify the models with locus joint effects, and interaction was further verified by conditional logistic regression. Significant allelic association was found for markers RS1912960 (in GABRA4; P = .01) and HCV9866022 (in GABRR2; P = .04). The geno-PDT found significant genotypic association for HCV8262334 (in GABRA2), RS1912960 and RS2280073 (in GABRA4), and RS2617503 and RS12187676 (in GABRB2). Consistent with the allelic and genotypic association results, EMDR confirmed the main effect at RS1912960 (in GABRA4). EMDR also identified a significant two-locus gene-gene effect model involving RS1912960 in GABRA4 and RS2351299 in GABRB1. Further support for this two-locus model came from both the multilocus geno-PDT and the APL test, which indicated a common genotype and haplotype combination positively associated with disease. Finally, these results were also consistent with the results from the conditional logistic regression, which confirmed the interaction between GABRA4 and GABRB1 (odds ratio = 2.9 for interaction term; P = .002). Through the convergence of all analyses, we conclude that GABRA4 is involved in the etiology of autism and potentially increases autism risk through interaction with GABRB1. These results support the hypothesis that GABA receptor subunit genes are involved in autism, most likely via complex gene-gene interactions. PMID:16080114

Ma, D. Q.; Whitehead, P. L.; Menold, M. M.; Martin, E. R.; Ashley-Koch, A. E.; Mei, H.; Ritchie, M. D.; DeLong, G. R.; Abramson, R. K.; Wright, H. H.; Cuccaro, M. L.; Hussman, J. P.; Gilbert, J. R.; Pericak-Vance, M. A.

2005-01-01

273

Witnessing the Key Early Phase of Quasar Evolution: An Obscured Active Galactic Nucleus Pair in the Interacting Galaxy IRAS 20210+1121  

NASA Astrophysics Data System (ADS)

We report the discovery of an active galactic nucleus (AGN) pair in the interacting galaxy system IRAS 20210+1121 at z = 0.056. An XMM-Newton observation reveals the presence of an obscured (N H ~ 5 × 1023 cm-2), Seyfert-like (L 2-10 keV = 4.7 × 1042 erg s-1) nucleus in the northern galaxy, which lacks unambiguous optical AGN signatures. Our spectral analysis also provides strong evidence that the IR-luminous southern galaxy hosts a Type 2 quasar embedded in a bright starburst emission. In particular, the X-ray primary continuum from the nucleus appears totally depressed in the XMM-Newton band as expected in the case of a Compton-thick absorber, and only the emission produced by Compton scattering ("reflection") of the continuum from circumnuclear matter is seen. As such, IRAS 20210+1121 seems to provide an excellent opportunity to witness a key, early phase in the quasar evolution predicted by the theoretical models of quasar activation by galaxy collisions.

Piconcelli, Enrico; Vignali, Cristian; Bianchi, Stefano; Mathur, Smita; Fiore, Fabrizio; Guainazzi, Matteo; Lanzuisi, Giorgio; Maiolino, Roberto; Nicastro, Fabrizio

2010-10-01

274

WITNESSING THE KEY EARLY PHASE OF QUASAR EVOLUTION: AN OBSCURED ACTIVE GALACTIC NUCLEUS PAIR IN THE INTERACTING GALAXY IRAS 20210+1121  

SciTech Connect

We report the discovery of an active galactic nucleus (AGN) pair in the interacting galaxy system IRAS 20210+1121 at z = 0.056. An XMM-Newton observation reveals the presence of an obscured (N {sub H} {approx} 5 x 10{sup 23} cm{sup -2}), Seyfert-like (L {sub 2-10keV} = 4.7 x 10{sup 42} erg s{sup -1}) nucleus in the northern galaxy, which lacks unambiguous optical AGN signatures. Our spectral analysis also provides strong evidence that the IR-luminous southern galaxy hosts a Type 2 quasar embedded in a bright starburst emission. In particular, the X-ray primary continuum from the nucleus appears totally depressed in the XMM-Newton band as expected in the case of a Compton-thick absorber, and only the emission produced by Compton scattering ('reflection') of the continuum from circumnuclear matter is seen. As such, IRAS 20210+1121 seems to provide an excellent opportunity to witness a key, early phase in the quasar evolution predicted by the theoretical models of quasar activation by galaxy collisions.

Piconcelli, Enrico; Fiore, Fabrizio; Maiolino, Roberto; Nicastro, Fabrizio [Osservatorio Astronomico di Roma (INAF), Via Frascati 33, I-00040 Monte Porzio Catone (Roma) (Italy); Vignali, Cristian [Dipartimento di Astronomia, Universita di Bologna, Via Ranzani 1, I-40127 Bologna (Italy); Bianchi, Stefano [Dipartimento di Fisica, Universita degli Studi Roma Tre, via della Vasca Navale 84, I-00146 Roma (Italy); Mathur, Smita [Ohio State University, 140 West 18th Avenue, Columbus, OH 43210 (United States); Guainazzi, Matteo [European Space Astronomy Centre of the European Space Agency, P.O. Box 78, Villanueva de la Canada, E-28691 Madrid (Spain); Lanzuisi, Giorgio, E-mail: enrico.piconcelli@oa-roma.inaf.i [IASF - INAF, via del Fosso del Cavaliere 100, I-00133 Roma (Italy)

2010-10-20

275

Modelling the effect of heterogeneity of shedding on the within herd Coxiella burnetii spread and identification of key parameters by sensitivity analysis.  

PubMed

Coxiella burnetii is the bacterium responsible for Q fever, a worldwide zoonosis. Ruminants, especially cattle, are recognized as the most important source of human infections. Although a great heterogeneity between shedder cows has been described, no previous studies have determined which features such as shedding route and duration or the quantity of bacteria shed have the strongest impact on the environmental contamination and thus on the zoonotic risk. Our objective was to identify key parameters whose variation highly influences C. burnetii spread within a dairy cattle herd, especially those related to the heterogeneity of shedding. To compare the impact of epidemiological parameters on different dynamical aspects of C. burnetii infection, we performed a sensitivity analysis on an original stochastic model describing the bacterium spread and representing the individual variability of the shedding duration, routes and intensity as well as herd demography. This sensitivity analysis consisted of a principal component analysis followed by an ANOVA. Our findings show that the most influential parameters are the probability distribution governing the levels of shedding, especially in vaginal mucus and faeces, the characteristics of the bacterium in the environment (i.e. its survival and the fraction of bacteria shed reaching the environment), and some physiological parameters related to the intermittency of shedding (transition probability from a non-shedding infected state to a shedding state) or to the transition from one type of shedder to another one (transition probability from a seronegative shedding state to a seropositive shedding state). Our study is crucial for the understanding of the dynamics of C. burnetii infection and optimization of control measures. Indeed, as control measures should impact the parameters influencing the bacterium spread most, our model can now be used to assess the effectiveness of different control strategies of Q fever within dairy cattle herds. PMID:21723294

Courcoul, Aurélie; Monod, Hervé; Nielen, Mirjam; Klinkenberg, Don; Hogerwerf, Lenny; Beaudeau, François; Vergu, Elisabeta

2011-09-01

276

Sighting characteristics and photo-identification of Cuvier's beaked whales (Ziphius cavirostris) near San Clemente Island, California: a key area for beaked whales and the military?  

PubMed

The relationship between beaked whales and certain anthropogenic sounds remains poorly understood and of great interest. Although Cuvier's beaked whales (Ziphius cavirostris) are widely distributed, little is known of their behavior and population structure throughout much of their range. We conducted a series of five combined visual-acoustic marine mammal surveys from 2006 to 2008 in the southern San Nicolas Basin, a site of frequent naval activity off the southern California coast, west of San Clemente Island. The study area was defined by a 1,800 km(2) array of 88 bottom-mounted hydrophones at depths up to 1,850 m. The array was used to vector visual observers toward vocalizing marine mammal species. Thirty-seven groups of Cuvier's beaked whales were encountered during the study period. The overall encounter rate was one group for every 21.0 h of survey effort, and was as high as one group per 10.2 h of effort during the October 2007 survey. Whales were encountered in the deepest portion of the study area, at a mean bottom depth of 1,580 m (SD 138). The average group size was 3.8 individuals (SD 2.4), which was higher than has been reported from other studies of this species. Twenty-four groups were observed over multiple surfacings (median = 4 surfacings, range 2-15). The mean encounter duration of extended sightings was 104 min (SD 98, range 12-466 min) and the mean distance moved over the course of sightings was 1.66 km (SD 1.56, range 0.08-6.65 km). Temporal surfacing patterns during extended encounters were similar to dive behavior described from Cuvier's beaked whales carrying time-depth recording tags. Seventy-eight photographic identifications were made of 58 unique individuals, for an overall resighting rate of 0.26. Whales were sighted on up to 4 days, with duration from first to last sighting spanning 2-79 days. For those whales sighted on subsequent days, the mean distance between subsequent sightings was 8.6 km (SD 7.9). Individuals resighted over 2-3 days were usually in association with previous group members. Approximately one-third of groups contained more than one adult male, and many of the repeated associations involved adult males. These observations suggest the basin west of San Clemente Island may be an important region for Cuvier's beaked whales, and also one which affords an unusual opportunity to collect detailed data on this species. Given its status as an active military range, it can also provide the ability to monitor the behavior of individuals in the presence of naval sonar, a critical step in the management of this and other beaked whale populations worldwide. PMID:24391238

Falcone, Erin A; Schorr, Gregory S; Douglas, Annie B; Calambokidis, John; Henderson, Elizabeth; McKenna, Megan F; Hildebrand, John; Moretti, David

2009-01-01

277

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

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

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

2014-01-01

278

Identification of Nucleolin as New ErbB Receptors- Interacting Protein  

PubMed Central

Background The ErbB receptor tyrosine kinases are major contributors to malignant transformation. These receptors are frequently overexpressed in a variety of human carcinomas. The role of the ErbB receptors and their ligands in carcinomas and the mechanism by which their overexpression leads to cancer development is still unclear. Ligand binding to specific ErbB receptor is followed by receptor dimerization, phosphorylation and recruitment of SH2 containing cytoplasmic proteins, which initiate the cascade of signaling events. Nevertheless, increasing data suggest that there are non-phosphorylated receptor–substrate interactions that may affect ErbB-mediated responses. Methodology/Principal Findings In the present study, using GST-ErbB4 fusion protein pull down assay and mass spectroscopic analysis, we have found the ErbB receptors interact with nucleolin via their cytoplasmic tail. Nucleolin is a ubiquitous, nonhistone, nucleolar, multifunctional phosphoprotein that is also overexpressed in cancer cells. Our results demonstrate that overexpression of ErbB1 and nucleolin may lead to receptor dimerization, phosphorylation and to anchorage independent growth. Conclusions/Significance The oncogenic potential of ErbB depends on receptor levels and activation. Our results suggest that nucleolin may affect ErbB dimerization and activation leading to enhanced cell growth. PMID:18523588

Di Segni, Ayelet; Farin, Keren; Pinkas-Kramarski, Ronit

2008-01-01

279

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

PubMed Central

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

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

2014-01-01

280

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

SciTech Connect

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.

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

2012-05-04

281

A systematic identification of multiple toxin-target interactions based on chemical, genomic and toxicological data.  

PubMed

Although the assessment of toxicity of various agents, -omics (genomic, proteomic, metabolomic, etc.) data has been accumulated largely, the acquirement of toxicity information of variety of molecules through experimental methods still remains a difficult task. Presently, a systems toxicology approach that integrates massive diverse chemical, genomic and toxicological information was developed for prediction of the toxin targets and their related networks. The procedures are: (1) by use of two powerful statistical methods, i.e., support vector machine (SVM) and random forest (RF), a systemic model for prediction of multiple toxin-target interactions using the extracted chemical and genomic features has been developed with its reliability and robustness estimated. And the qualitative classification of targets according to the phenotypic diseases has been taken into account to further uncover the biological meaning of the targets, as well as to validate the robustness of the in silico models. (2) Based on the predicted toxin-target interactions, a genome-scale toxin-target-disease network exampled by cardiovascular disease is generated. (3) A topological analysis of the network is carried out to identify those targets that are most susceptible in human to topical agents including the most critical toxins, as well as to uncover both the toxin-specific mechanisms and pathways. The methodologies presented herein for systems toxicology will make drug development, toxin environmental risk assessment more efficient, acceptable and cost-effective. PMID:23313661

Zhou, Wei; Huang, Chao; Li, Yan; Duan, Jinyou; Wang, Yonghua; Yang, Ling

2013-02-01

282

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

SciTech Connect

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.

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

283

Identification of SRC as a key PKA-stimulated tyrosine kinase involved in the capacitation-associated hyperactivation of murine spermatozoa.  

PubMed

Fertilization of the mammalian oocyte depends on the ability of spermatozoa to undergo a process known as capacitation as they ascend the female reproductive tract. A fundamental feature of this process is a marked increase in tyrosine phosphorylation by an unusual protein kinase A (PKA)-mediated pathway. To date, the identity of the intermediate PKA-activated tyrosine kinase driving capacitation is still unresolved. In this study, we have identified SRC as a candidate intermediate kinase centrally involved in the control of sperm capacitation. Consistent with this conclusion, the SRC kinase inhibitor SU6656 was shown to suppress both tyrosine phosphorylation and hyperactivation in murine spermatozoa. Moreover, SRC co-immunoprecipitated with PKA and this interaction was found to lead to an activating phosphorylation of SRC at position Y416. We have also used difference-in-2D-gel-electrophoresis (DIGE) in combination with mass spectrometry to identify a number of SRC substrates that become phosphorylated during capacitation including enolase, HSP90 and tubulin. Our data further suggest that the activation of SRC during capacitation is negatively controlled by C-terminal SRC kinase. The latter was localized to the acrosome and flagellum of murine spermatozoa by immunocytochemistry, whereas capacitation was associated with an inactivating serine phosphosphorylation of this inhibitory kinase. PMID:16835269

Baker, Mark A; Hetherington, Louise; Aitken, R John

2006-08-01

284

Identification of selected therapeutic agents as inhibitors of carboxylesterase 1: potential sources of metabolic drug interactions.  

PubMed

A series of studies were designed and carried out in order to explore the potential for the major human hepatic hydrolase, carboxylesterase 1 (hCES1), to serve as a target of metabolic inhibition by a variety of medications. The risk of adverse drug-drug interaction(s) is present when metabolic inhibitors are combined with known or suspected substrates of a given enzyme. In the present report the abundantly expressed hepatic enzyme, hCES1, was examined as a potential target of metabolic inhibition by a number of routinely prescribed medications. hCES1 has been seldom assessed in this regard despite its role in the metabolism and detoxification of many compounds. The psychostimulant methylphenidate (MPH) was chosen as an hCES1 selective substrate. In vitro studies were performed using previously developed cell lines which overexpress hCES1 with both p-nitrophenyl acetate and d-MPH serving as known substrates. Aripiprazole, perphenazine, thioridazine, and fluoxetine were determined to be the potent hCES1 inhibitors. A complementary animal study followed in vitro screening studies to further evaluate the inhibitory effect of aripiprazole on CES1 activity in FVB mice. The results suggest that the concurrent administration of racemic (i.e. dl-) MPH with aripiprazole significantly increased the plasma concentrations of both total MPH as well as the less active l-isomer. The ratio of d-MPH and l-MPH plasma concentrations was significantly decreased in the mice treated with aripiprazole compared to the control animals, indicating an overall decrease of CES1 catalytic activity in aripiprazole treated animals. Additionally, a quantitative structure-activity relationship based analysis identified a number of structural similarities of CES1 inhibitors. In conclusion, drug-drug interactions with MPH are likely mediated via CES1 inhibition as a result of concomitant drug therapies. CES1 inhibition represents an overlooked and little studied source of variability in MPH disposition, tolerability, and response. PMID:20097249

Zhu, Hao-Jie; Appel, David I; Peterson, Yuri K; Wang, Zichao; Markowitz, John S

2010-04-11

285

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

NASA Astrophysics Data System (ADS)

In order to facilitate the development of a hybrid acoustic and electromagnetic (EM) system for buried object detection, a number of analytical solutions and a novel numerical technique are developed to analyze the complex interaction between acoustic and EM scattering. The essence of the interaction lies in the fact that identifiable acoustic properties of an object, such as acoustic resonances, can be observed in the scattered EM Doppler spectrum. Using a perturbation approach, analytical solutions are derived for the EM scattering from infinitely long circular cylinders, both metallic and dielectric, under acoustic vibration in a homogeneous background medium. Results indicate that both the shape variation and dielectric constant contribute to the scattered EM Doppler spectrum. To model the effect of a cylinder beneath an acoustically excited half-space, a new analytical solution is presented for EM scattering from a cylinder beneath a slightly rough surface. The solution is achieved by using plane-wave expansion of the fields and an iterative technique to account for the multiple interactions between the cylinder and rough surface. Following a similar procedure, a novel solution for elastic-wave scattering from a solid cylinder embedded in a solid half-space is developed and used to calculate the surface displacement. Simulations indicate that only a finite range of spatial surface frequencies, corresponding to surface roughness on the order of the EM wavelength; affect the EM scattering from buried objects and suggest that object detection can be improved if the acoustic excitation induces surface roughness outside this range. To extend the study to non-canonical scenarios, a novel numerical approach is introduced in which time-varying impedance boundary conditions (IBCs) are used in conjunction with the method of moments (MoM) to model the EM scattering from vibrating metallic objects of arbitrary shape. It is shown that the standard IBC provides a first order solution for TM polarization, but a second order IBC is needed for TE polarization. The crucial factor in the calculation of the potentially small Doppler components is that the time-varying nature of the cylinder boundary, contained within the surface impedance expressions, can be isolated from the unperturbed terms in the scattered field.

Lawrence, Daniel Edward

2002-09-01

286

Identification and analysis of unsatisfactory psychosocial work situations: a participatory approach employing video-computer interaction.  

PubMed

A method for psychosocial evaluation of potentially stressful or unsatisfactory situations in manual work was developed. It focuses on subjective responses regarding specific situations and is based on interactive worker assessment when viewing video recordings of oneself. The worker is first video-recorded during work. The video is then displayed on the computer terminal, and the filmed worker clicks on virtual controls on the screen whenever an unsatisfactory psychosocial situation appears; a window of questions regarding psychological demands, mental strain and job control is then opened. A library with pictorial information and comments on the selected situations is formed in the computer. The evaluation system, called PSIDAR, was applied in two case studies, one of manual materials handling in an automotive workshop and one of a group of workers producing and testing instrument panels. The findings indicate that PSIDAR can provide data that are useful in a participatory ergonomic process of change. PMID:11209828

Hanse, J J; Forsman, M

2001-02-01

287

Protein interaction hotspot identification using sequence-based frequency-derived features.  

PubMed

Finding good descriptors, capable of discriminating hotspot residues from others, is still a challenge in many attempts to understand protein interaction. In this paper, descriptors issued from the analysis of amino acid sequences using digital signal processing (DSP) techniques are shown to be as good as those derived from protein tertiary structure and/or information on the complex. The simulation results show that our descriptors can be used separately to predict hotspots, via a random forest classifier, with an accuracy of 79% and a precision of 75%. They can also be used jointly with features derived from tertiary structures to boost the performance up to an accuracy of 82% and a precision of 80%. PMID:21742567

Nguyen, Quang-Thang; Fablet, Ronan; Pastor, Dominique

2013-11-01

288

Identification of a phospholipase C beta2 region that interacts with Gbeta-gamma.  

PubMed Central

To delineate the phospholipase C (PLC; EC 3.1.4.3) beta2 sequences involved in interactions with the beta-gamma subunits of G proteins, we prepared a number of mammalian expression plasmids encoding a series of PLC beta2 segments that span the region from the beginning of the X box to the end of the Y box. We found the sequence extending from residue Glu-435 to residue Val-641 inhibited Gbeta-gamma-mediated activation of PLC beta2 in transfected COS-7 cells. This PLC beta2 sequence also inhibited ligand-induced activation of PLC in COS-7 cells cotransfected with cDNAs encoding the complement component C5a receptor and PLC beta2 but not in cells transfected with the alpha1B-adrenergic receptor, suggesting that the PLC beta2 residues (Glu-435 to Val-641) inhibit the Gbeta-gamma-mediated but not the Galpha-mediated effect. The inhibitory effect on Gbeta-gamma-mediated activation of PLC beta2 may be the result of the interaction between Gbeta-gamma and the PLC beta2 fragment. This idea was confirmed by the observation that a fusion protein comprising these residues (Glu-435 to Val-641) of PLC beta2 and glutathione S-transferase (GST) bound to Gbeta-gamma in an in vitro binding assay. The Gbeta-gamma-binding region was further narrowed down to 62 amino acids (residues Leu-580 to Val-641) by testing fusion proteins comprising various PLC beta2 sequences and GST in the in vitro binding assay. Images Fig. 3 Fig. 4 Fig. 5 PMID:8610151

Kuang, Y; Wu, Y; Smrcka, A; Jiang, H; Wu, D

1996-01-01

289

Identification of Genetic Loci That Interact With cut During Drosophila Wing-Margin Development  

PubMed Central

The Drosophila selector gene cut is a hierarchal regulator of external sensory organ identity and is required to pattern the sensory and nonsensory cells of the wing margin. Cut performs the latter function, in part, by maintaining expression of the secreted morphogen encoded by wingless (wg). We find that Cut is required for wing-margin sensory organ specification in addition to and independently of Wg maintenance. In addition, we performed a genetic modifier screen to identify other genes that interact with cut in the regulation of wing-margin patterning. In total, 45 genetic loci (35 gain-of-function and 10 loss-of-function loci) were identified by virtue of their ability to suppress the wing-margin defects resulting from gypsy retrotransposon-mediated insulation of the cut wing-margin enhancer. Further genetic characterization identified several subgroups of candidate cut interacting loci. One group consists of putative regulators of gypsy insulator activity. A second group is potentially required for the regulation of Cut expression and/or activity and includes longitudinals lacking, a gene that encodes a family of BTB-domain zinc-finger transcription factors. A third group, which includes a component of the Brahma chromatin remodeling complex encoded by moira, affects the level of Cut expression in two opposing ways by suppressing the gypsy-mediated ctK phenotype and enhancing the non-gypsy ct53d phenotype. This suggests that the Brahma complex modulates both enhancer-controlled transcription and gypsy-mediated gene insulation of the cut locus. PMID:15956666

Krupp, Joshua J.; Yaich, Lauren E.; Wessells, Robert J.; Bodmer, Rolf

2005-01-01

290

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

PubMed Central

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

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

2013-01-01

291

A subunit interaction site in human luteinizing hormone: identification by photoaffinity cross-linking.  

PubMed

The sites of noncovalent association between the alpha- (common) and beta- (hormone-specific) subunits in the glycoprotein hormones [LH, human CG (hCG), FSH, and TSH] remain to be completely defined. This information is essential to efforts to map the three-dimensional structure of the hormones and to help explain the stability of the hormone heterodimer in the circulation. Among numerous approaches that have been employed to identify these sites of subunit interaction, chemical or photoaffinity cross-linking has the advantage of identifying the complementary sites of contact on the respective subunits. We have used the stable photoaffinity ligand, L-benzoylphenylalanine (Bpa), to evaluate subunit interaction by the hLH beta sequence (1-15). A peptide from this region of hCG beta has been shown previously to inhibit subunit association. The 3H-labeled Bpa was incorporated into the peptide at position 8 (Trp) during solid-phase synthesis. After incubation with alpha under long-wavelength (366 nm) ultraviolet light, a Bpa- (1-15)-labeled-alpha-fraction was isolated. Control experiments showed the binding to be covalent and specific to (1-15). Two other Bpa-labeled beta-fragments, the receptor-binding loop (38-57) and the (30-43) peptide containing the highly conserved CAGY sequence, did not cross-link. The site of contact in alpha was localized by peptide mapping and sequence analysis to the N-terminal fragment (18-33), most likely at Met-29 or Gly-30. Both the alpha- and beta-sites are adjacent to or overlapping receptor-binding regions. Subunit contact sites and receptor-binding segments may thus be oriented in close proximity to provide a multicomponent receptor-binding domain imparting full activity to the native hormone. PMID:7679977

Keutmann, H T; Rubin, D A

1993-03-01

292

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

PubMed Central

Background Studies in mothers of Down syndrome individuals (MDS) point to a role for polymorphisms in folate metabolic genes in increasing chromosome damage and maternal risk for a Down syndrome (DS) pregnancy, suggesting complex gene-gene interactions. This study aimed to analyze a dataset of genetic and cytogenetic data in an Italian group of MDS and mothers of healthy children (control mothers) to assess the predictive capacity of artificial neural networks assembled in TWIST system in distinguish consistently these two different conditions and to identify the variables expressing the maximal amount of relevant information to the condition of being mother of a DS child. The dataset consisted of the following variables: the frequency of chromosome damage in peripheral lymphocytes (BNMN frequency) and the genotype for 7 common polymorphisms in folate metabolic genes (MTHFR 677C>T and 1298A>C, MTRR 66A>G, MTR 2756A>G, RFC1 80G>A and TYMS 28bp repeats and 1494 6bp deletion). Data were analysed using TWIST system in combination with supervised artificial neural networks, and a semantic connectivity map. Results TWIST system selected 6 variables (BNMN frequency, MTHFR 677TT, RFC1 80AA, TYMS 1494 6bp +/+, TYMS 28bp 3R/3R and MTR 2756AA genotypes) that were subsequently used to discriminate between MDS and control mothers with 90% accuracy. The semantic connectivity map provided important information on the complex biological connections between the studied variables and the two conditions (being MDS or control mother). Conclusions Overall, the study suggests a link between polymorphisms in folate metabolic genes and DS risk in Italian women. PMID:20868477

2010-01-01

293

Interactions of nitrifying bacteria and heterotrophs: identification of a Micavibrio-like putative predator of Nitrospira spp.  

PubMed

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 (13)C-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 (13)C-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

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

2013-03-01

294

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

PubMed

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. Copyright © 2015 John Wiley & Sons, Ltd. PMID:25601690

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

2015-01-01

295

Identification of genes involved in interactions between Biomphalaria glabrata and Schistosoma mansoni by suppression subtractive hybridization.  

PubMed

Biomphalaria glabrata is an intermediate snail host for Schistosoma mansoni, a medically important schistosome. In order to identify transcripts involved in snail-schistosome interactions, subtractive cDNA libraries were prepared, using suppression subtractive hybridization (SSH) between a parasite-exposed schistosome-resistant and a susceptible strain of B. glabrata, and also between schistosome-exposed and unexposed snails from the resistant snail line. Separate libraries were made from both haemocytes and the haemopoietic organ. Subtraction was performed in both directions enriching for cDNAs differentially expressed between parasite-exposed resistant and susceptible samples and up or down-regulated in the resistant line after challenge. The resulting eight libraries were screened and eight genes, differentially expressed between the haemocytes of resistant and susceptible snail strains, were identified and confirmed with reverse transcriptase PCR, including two transcripts expected to be involved in the stress response mechanism for regulating the damaging oxidative burst pathways involved in cytotoxic killing of the parasite: the iron-storage and immunoregulatory molecule, ferritin, and HtrA2, a serine protease involved in the cellular stress response. Transcripts with elevated levels in the resistant strain, had the same expression patterns in the subtracted libraries and unsubtracted controls; higher levels in exposed resistant snails compared to susceptible ones and down-regulated in exposed compared with unexposed resistant snails. Differential expression of two of the transcripts with no known function from the susceptible strain, was independently confirmed in a repeat exposure experiment. PMID:17081633

Lockyer, Anne E; Spinks, Jennifer; Noble, Leslie R; Rollinson, David; Jones, Catherine S

2007-01-01

296

Identification of FUSE-binding proteins as interacting partners of TIA proteins  

SciTech Connect

TIA-1 and TIAR are closely related RNA-binding proteins involved in several mechanisms of RNA metabolism, including alternative hnRNA splicing and mRNA translation regulation. In particular, TIA-1 represses tumor necrosis factor (TNF) mRNA translation by binding to the AU-rich element (ARE) present in the mRNA 3' untranslated region. Here, we demonstrate that TIA proteins interact with FUSE-binding proteins (FBPs) and that fbp genes are co-expressed with tia genes during Xenopus embryogenesis. FBPs participate in various steps of RNA processing and degradation. In Cos cells, FBPs co-localize with TIA proteins in the nucleus and migrate into TIA-enriched cytoplasmic granules upon oxidative stress. Overexpression of FBP2-KH3 RNA-binding domain fused to EGFP induces the specific sequestration of TIA proteins in cytoplasmic foci, thereby precluding their nuclear accumulation. In cytosolic RAW 264.7 macrophage extracts, FBPs are found associated in EMSA to the TIA-1/TNF-ARE complex. Together, our results indicate that TIA and FBP proteins may thus be relevant biological involved in common events of RNA metabolism occurring both in the nucleus and the cytoplasm.

Rothe, Francoise [Laboratoire de Chimie Biologique, Institut de Biologie et de Medecine Moleculaires, Universite Libre de Bruxelles, 6041 Gosselies (Belgium); Gueydan, Cyril [Laboratoire de Chimie Biologique, Institut de Biologie et de Medecine Moleculaires, Universite Libre de Bruxelles, 6041 Gosselies (Belgium); Bellefroid, Eric [Laboratoire d' Embryologie Moleculaire, Institut de Biologie et de Medecine Moleculaires, Universite Libre de Bruxelles, 6041 Gosselies (Belgium); Huez, Georges [Laboratoire de Chimie Biologique, Institut de Biologie et de Medecine Moleculaires, Universite Libre de Bruxelles, 6041 Gosselies (Belgium); Kruys, Veronique [Laboratoire de Chimie Biologique, Institut de Biologie et de Medecine Moleculaires, Universite Libre de Bruxelles, 6041 Gosselies (Belgium)]. E-mail: vkruys@ulb.ac.be

2006-04-28

297

Investigation of Antioxidant Interactions between Radix Astragali and Cimicifuga foetida and Identification of Synergistic Antioxidant Compounds  

PubMed Central

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

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

2014-01-01

298

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)

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.

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

2014-12-01

299

Talent identification in youth soccer.  

PubMed

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

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

2012-01-01

300

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

PubMed Central

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

1996-01-01

301

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

PubMed Central

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

2011-01-01

302

Simplified technique for identification of the aerobic spore-forming bacteria by phenotype.  

PubMed

The use of modern research approaches of genetics, biochemistry and molecular biology has led to progress in bacterial taxonomy. Systematic study of the aerobic spore-forming bacteria has resulted in the realignment of the genus Bacillus into several new genera. In the meantime, the identification process has become more difficult for the non-specialist in Bacillus taxonomy. This paper presents a key for the simplified phenotypic identification of the mesophilic, aerobic, spore-forming bacteria belonging to the genera Bacillus, Paenibacillus, Brevibacillus, Aneurinibacillus, Geobacillus and Virgibacillus. A total of 81 species were included and 115 morphological and physiological tests were analysed for their discriminative efficiency. This key is practical for rough but quick identification of aerobic spore-forming bacteria isolated from nature. Such preliminary identification will be helpful for the selection of reference strains and methods for more precise identification using the newest techniques. The reliability of the proposed identification key was tested on 100 cultures from the Ukrainian Collection of Microorganisms. The developed identification key is represented in interactive mode on a website (http://www/imv.kiev.ua/key/). PMID:11491334

Reva, O N; Sorokulova, I B; Smirnov, V V

2001-07-01

303

Automated spectral line identification  

NASA Astrophysics Data System (ADS)

Software has been developed to automate the intricate and tedious process of stellar line identification. A set of unknown stellar wavelengths and intensities is compared with a master multiplet list composed of the Revised Multiplet Table plus extensions. Potential identifications are evaluated on the basis of several criteria including Cowley's wavelength coincidence statistics, wavelength displacement, and the orderly filling of the associated multiplet. All data for each unknown stellar line are displayed and the user interactively decides on the best identification(s). To aid in this process another identification of a similar star can be simultaneously displayed. Comparisons with line identifications by Bidelman and by Adelman show virtually complete agreement.

Gulliver, Austin F.; Stadel, Joachim G.

1990-05-01

304

Interaction of a nuclear location signal with isolated nuclear envelopes and identification of signal-binding proteins by photoaffinity labeling.  

PubMed

The nuclear envelope (NE) separates the two major compartments of eukaryotic cells, the nucleus and the cytoplasm. Recent studies suggest that the uptake of nuclear proteins into the nucleus is initiated by binding of nuclear location signals (NLSs) contained within these proteins to receptors in the NE, followed by translocation through the nuclear pore complex. To examine the binding step without interference from intranuclear events, we have used a system consisting of (i) purified rat liver NEs fixed onto glass slides and (ii) the prototype simian virus 40 large T antigen (SV40 T) NLS conjugated to nonnuclear carrier proteins, and we have visualized the receptor-ligand interaction by indirect immunofluorescence. In this system, incubation of isolated NEs with the wild-type SV40 T NLS conjugate with carrier proteins resulted in binding that was signal sequence-dependent, could be competitively blocked with excess conjugated and unconjugated wild-type peptide, did not require ATP, and was not affected by the transport-inhibiting lectin wheat germ agglutinin. In contrast, only minimal binding was observed with a mutant SV40 T NLS conjugate. These results are consistent with those obtained in other, more complex in vitro systems and suggest that binding of the SV40 T NLS is receptor-mediated. Binding is largely abolished by extraction of the NE with the nonionic detergent Triton X-100, suggesting that the receptor is soluble in detergent. We find in the Triton X-100 supernatant four major NLS-binding proteins with apparent molecular masses of 76, 67, 59, and 58 kDa by photoaffinity labeling with a highly specific crosslinker, azido-NLS. The reduced complexity of the system described here should be useful for the functional study of other potential NLSs for the identification and isolation of their binding sites and for the screening of antibodies raised against these binding sites. PMID:2556708

Benditt, J O; Meyer, C; Fasold, H; Barnard, F C; Riedel, N

1989-12-01

305

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

PubMed

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

Koizumi, Koji; Gallagher, Kimberly L

2013-03-01

306

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

PubMed

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

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

2007-06-01

307

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

NASA Astrophysics Data System (ADS)

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.

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

2014-10-01

308

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

E-print Network

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

Mochrie, Simon

309

Key-Insulated Public Key Cryptosystems  

Microsoft Academic Search

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)

Yevgeniy Dodis; Jonathan Katz; Shouhuai Xu; Moti Yung

2002-01-01

310

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

PubMed

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

Howell, Elizabeth F

2014-03-01

311

Identification of Ca2+-dependent binding partners for the neuronal calcium sensor protein neurocalcin delta: interaction with actin, clathrin and tubulin.  

PubMed Central

The neuronal calcium sensors are a family of EF-hand-containing Ca(2+)-binding proteins expressed predominantly in retinal photoreceptors and neurons. One of the family members is neurocalcin delta, the function of which is unknown. As an approach to elucidating the protein interactions made by neurocalcin delta, we have identified brain cytosolic proteins that bind to neurocalcin delta in a Ca(2+)-dependent manner. We used immobilized recombinant myristoylated neurocalcin delta combined with protein identification using MS. We demonstrate a specific interaction with clathrin heavy chain, alpha- and beta-tubulin, and actin. These interactions were dependent upon myristoylation of neurocalcin delta indicating that the N-terminal myristoyl group may be important for protein-protein interactions in addition to membrane association. Direct binding of neurocalcin delta to clathrin, tubulin and actin was confirmed using an overlay assay. These interactions were also demonstrated for endogenous neurocalcin delta by co-immunoprecipitation from rat brain cytosol. When expressed in HeLa cells, neurocalcin delta was cytosolic at resting Ca(2+) levels but translocated to membranes, including a perinuclear compartment (trans-Golgi network) where it co-localized with clathrin, following Ca(2+) elevation. These data suggest the possibility that neurocalcin delta functions in the control of clathrin-coated vesicle traffic. PMID:11964161

Ivings, Lenka; Pennington, Stephen R; Jenkins, Roz; Weiss, Jamie L; Burgoyne, Robert D

2002-01-01

312

Identification of proteins that interact with a protein of interest: Applications of the yeast two-hybrid system  

Microsoft Academic Search

The yeast two-hybrid system is a molecular genetic test for protein interaction. Here we describe a step by step procedure to screen for proteins that interact with a protein of interest using the two-hybrid system. This process includes, construction and testing of the bait plasmid, screening a plasmid library for interacting fusion proteins, elimination of false positives and deletion analysis

R. Daniel Gietz; Barbara Triggs-Raine; Anne Robbins; Kevin C. Graham; Robin A. Woods

1997-01-01

313

Interaction of GapA with HPr and Its Homologue, Crh: Novel Levels of Regulation of a Key Step of Glycolysis in Bacillus subtilis?? †  

PubMed Central

In Bacillus subtilis cells, we identified a new partner of HPr, an enzyme of the glycolysis pathway, the glyceraldehyde-3-phosphate dehydrogenase GapA. We showed that, in vitro, phosphorylated and unphosphorylated forms of HPr and its homologue, Crh, could interact with GapA, but only their seryl-phosphorylated forms were able to inhibit its activity. PMID:17142398

Pompeo, Frédérique; Luciano, Jennifer; Galinier, Anne

2007-01-01

314

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

ERIC Educational Resources Information Center

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

Hood, Philip

2013-01-01

315

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

PubMed

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

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

2001-01-15

316

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

PubMed Central

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 ?-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

Holm, Magnus; Hardtke, Christian S.; Gaudet, Rachelle; Deng, Xing-Wang

2001-01-01

317

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

PubMed Central

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

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

2014-01-01

318

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)

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.

Stocker, Dennis P.

1999-01-01

319

Interaction  

NSDL National Science Digital Library

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.

Christian, Wolfgang; Belloni, Mario

2008-02-19

320

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...

321

Interactions among Dendrolimus punctatus cypovirus proteins and identification of the genomic segment encoding its A-spike.  

PubMed

Revealing the interactions among cypovirus proteins would facilitate our understanding of the replication and assembly of this virus. In the present study, interactions among proteins encoded by the 10 segments of Dendrolimus punctatus cypovirus (DpCPV) were identified using yeast two-hybrid (Y2H) and far-Western blotting assays. In total, 24 pairs of interactions were detected. Twelve pairs of one-direction interactions, four pairs of binary interactions and four pairs of self-associations were identified in the Y2H assays. Another four pairs of interactions were identified by far-Western blotting. The interactions between the methyltransferase domain of the turret protein (VP3) and VP4 as well as between polyhedrin and VP4 were further confirmed by far-Western blotting and pull-down assays, respectively. In addition, immunogold labelling showed that the A-spike of DpCPV is formed by VP4. In conclusion, we obtained a protein-protein interaction network of DpCPV and showed that its A-spike is formed by VP4 encoded by genomic segment 6. PMID:24700101

Cheng, Chuangang; Shao, Yunpeng; Su, Lan; Zhou, Yin; Sun, Xiulian

2014-07-01

322

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.

323

Identification of the potential regions of Epap-1 that interacts with V3 loop of HIV-1 gp120.  

PubMed

Early pregnancy associated protein-1 (Epap-1), a 90kDa glycoprotein present in first trimester placental tissue, inhibits HIV-1 entry through interaction with HIV-1 gp120 at V3 and C5 regions. In the present study, we have identified the specific 32 mer region of Epap-1 that can interact with V3 loop. This was achieved by docking between Epap-1 molecular model and gp120 and studying the interaction of peptides with gp120 in vitro. Out of four peptides analyzed, two peptides (P-2 and P-3) showed significant interaction with V3 domain (N=8; N=7) of gp120. In the studies conducted using soluble gp120 and virus, peptide P-2 has shown conserved interaction at V3 loop regions recognized by 257D and F425 antibodies and higher anti-viral activity. Also, P-2 inhibited cell fusion mediated dye transfer between gp120 expressing HL2/3 and CD4 expressing Sup T1 cells suggesting its inhibition of viral entry, which is further confirmed by its action on HIV infection mediated by Tat activated beta gal expression in TZM-bl cells. Further optimization of P-2 peptide showed that the anti-viral activity and gp120 interaction residues lie in the N-terminal region of the peptide. These results together suggest that P-2 inhibits viral entry through specific interaction at V3 loop region. PMID:23360764

Bhaskar, C; Reddy, Palakolanu S; Chandra, K Sarath; Sabde, Sudeep; Mitra, Debashis; Kondapi, Anand K

2013-04-01

324

Identification of a Cellular Protein That Specifically Interacts with the Essential Cysteine Region of the HIV1 Tat Transactivator  

Microsoft Academic Search

The Tat protein of the human immunodeficiency virus (HIV) is a powerful activator of HIV gene expression. Genetic and biochemical evidence suggests that one or more cellular cofactors may be important for Tat activity. We have used two-hybrid interactive cloning in yeast to identify a partial cDNA clone (clone 10) from a human B-lymphoblastoid library that specifically interacts with the

J. KAMINE; B. ELANGOVAN; T. SUBRAMANIAN; D. COLEMAN; G. CHINNADURAI

1996-01-01

325

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

SciTech Connect

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

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

2010-10-08

326

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

NASA Astrophysics Data System (ADS)

Profiting by the increasing availability of laser sources delivering intensities above 109 W/cm2 with pulse energies in the range of several Joules and pulse widths in the range of nanoseconds, laser shock processing (LSP) is consolidating as an effective technology for the improvement of surface mechanical and corrosion resistance properties of metals. The main advantage of the laser shock processing technique consists on its capability of inducing a relatively deep compression residual stresses field into metallic alloy pieces allowing an improved mechanical behaviour, explicitly, the life improvement of the treated specimens against wear, crack growth and stress corrosion cracking. Although significant work from the experimental side has been contributed to explore the optimum conditions of application of the treatments and to assess their ultimate capability to provide enhanced mechanical behaviour to work-pieces of typical materials, only limited attempts have been developed in the way of full comprehension and predictive assessment of the characteristic physical processes and material transformations with a specific consideration of real material properties. In the present paper, a review on the physical issues dominating the development of LSP processes from a high intensity laser-matter interaction point of view is presented along with the theoretical and computational methods developed by the authors for their predictive assessment and practical results at laboratory scale on the application of the technique to different materials.

Ocaña, J. L.; Morales, M.; Molpeceres, C.; Porro, J. A.

2010-10-01

327

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

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

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

328

Identification of Shigella flexneri IcsA Residues Affecting Interaction with N-WASP, and Evidence for IcsA-IcsA Co-Operative Interaction  

PubMed Central

The Shigella flexneri IcsA (VirG) protein is a polarly distributed outer membrane protein that is a fundamental virulence factor which interacts with neural Wiskott-Aldrich syndrome protein (N-WASP). The activated N-WASP then activates the Arp2/3 complex which initiates de novo actin nucleation and polymerisation to form F-actin comet tails and allows bacterial cell-to-cell spreading. In a previous study, IcsA was found to have three N-WASP interacting regions (IRs): IR I (aa 185–312), IR II (aa 330–382) and IR III (aa 508–730). The aim of this study was to more clearly define N-WASP interacting regions II and III by site-directed mutagenesis of specific amino acids. Mutant IcsA proteins were expressed in both smooth lipopolysaccharide (S-LPS) and rough LPS (R-LPS) S. flexneri strains and characterised for IcsA production level, N-WASP recruitment and F-actin comet tail formation. We have successfully identified new amino acids involved in N-WASP recruitment within different N-WASP interacting regions, and report for the first time using co-expression of mutant IcsA proteins, that N-WASP activation involves interactions with different regions on different IcsA molecules as shown by Arp3 recruitment. In addition, our findings suggest that autochaperone (AC) mutant protein production was not rescued by another AC region provided in trans, differing to that reported for two other autotransporters, PrtS and BrkA autotransporters. PMID:23405119

Teh, Min Yan; Morona, Renato

2013-01-01

329

A new hypothesis about hematopoietic Pbx-interaction protein (HPIP): can it be a key factor in neurodegeneration in the post-menopausal period?  

PubMed

Neuronal degeneration in the post-menopausal term leads to cognitive symptoms such as anxiety, difficulty in concentrating, overreacting to minor upsets, quickly becoming irritated and forgetfulness in approximately 70-80% of all women around the world. These symptoms, which result from microtubule damage in the axon extensions of hippocampal neurons in during menopause, greatly reduce individuals' life quality. Thus, an investigation of the estrogen receptor-signaling pathway-microtubule dynamic triangle and the possible links between them is important when it comes to explaining the possible mechanism of neurodegeneration. Hematopoietic Pbx-interaction protein (HPIP), a microtubule-binding protein, is a novel scaffolding protein. The detection of this protein on neurons represents the most important step in our hypothesis. The importance of the hypothesis is that it might provide important clues about the possible role of HPIP and its mechanism through in vivo and in vitro studies of estrogen receptors-microtubules and the HPIP triangle in terms of neuronal degeneration in the post-menopausal period. A preliminary study was performed to test the main part of our hypothesis using real-time PCR. According to the results, the mRNA expression of HPIP was found in hippocampal neurons. After the detection of this novel protein in neurons, it was observed that there were differences in the experimental groups when compared with the control group relating to the mRNA expression of this protein. An important scientific question remains concerning the mechanisms of neurodegeneration appearing in the post-menopausal period and the receptors, proteins, and signaling pathways that play a role in this degeneration. In consideration of the data from in vivo and in vitro studies used to test our hypothesis, we will try to address the relevant questions. As this issue is resolved, new studies and treatment procedures that can help to prevent the possible difficulties in the menopausal period will be illuminated. PMID:23845560

Karamese, Murat; Aksak, Selina; Gundogdu, Ozge Beyza; Unal, Bunyami

2013-09-01

330

Escherichia Coli--Key to Modern Genetics.  

ERIC Educational Resources Information Center

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.…

Bregegere, Francois

1982-01-01

331

Co-immunoprecipitation-based identification of putative BAX INHIBITOR-1-interacting proteins involved in cell death regulation and plant-powdery mildew interactions.  

PubMed

The endoplasmic reticulum (ER)-resident BAX INHIBITOR-1 (BI-1) protein is one of a few cell death suppressors known to be conserved in animals and plants. The function of BI-1 proteins in response to various biotic and abiotic stress factors is well established. However, little is known about the underlying mechanisms. We conducted co-immunoprecipitation (co-IP) experiments to identify Arabidopsis thaliana?BI-1-interacting proteins to obtain a potentially better understanding of how BI-1 functions during plant-pathogen interactions and as a suppressor of cell death. Liquid chromatography and tandem mass spectrometry (LC-MS/MS) identified 95 proteins co-immunoprecipitated with green fluorescing protein (GFP)-tagged BI-1. Five selected candidate proteins, a RIBOPHORIN II (RPN2) family protein, VACUOLAR ATP SYNTHASE SUBUNIT A (VHA-A), cytochrome P450 83A1 (CYP83A1), H(+) -ATPASE 1 (AHA1) and PROHIBITIN 2 (PHB2), were further investigated with regard to their role in BI-1-associated processes. To this end, we analysed a set of Arabidopsis mutants in the interaction with the adapted powdery mildew fungus Erysiphe cruciferarum and on cell death-inducing treatments. Two independent rpn2 knock-down mutants tended to better support powdery mildew, and a phb2 mutant showed altered responses to cell death-inducing Alternaria alternata f.sp. lycopersici (AAL) toxin treatment. Two independent cyp83a1 mutants showed a strong powdery mildew resistance phenotype and enhanced sensitivity to AAL toxin. Moreover, co-localization studies and fluorescence resonance energy transfer (FRET) experiments suggested a direct interaction of BI-1 with CYP83A1 at the ER. PMID:23782494

Weis, Corina; Pfeilmeier, Sebastian; Glawischnig, Erich; Isono, Erika; Pachl, Fiona; Hahne, Hannes; Kuster, Bernhard; Eichmann, Ruth; Hückelhoven, Ralph

2013-10-01

332

A Protein that Interacts with Members of the Nuclear Hormone Receptor Family: Identification and cDNA Cloning  

Microsoft Academic Search

In search of proteins which interact with activated steroid hormone receptors, we screened a human liver lambdagt11 expression library with the glucocorticoid receptor. We identified and cloned a cDNA sequence of 1322 bp that encodes a protein of 274 aa. This protein consists predominantly of hydrophilic amino acids and contains a putative bipartite nuclear localization signal. The in vitro translated

Matthias Zeiner; Ulrich Gehring

1995-01-01

333

Identification of a Novel Sequence in PDZ-RhoGEF That Mediates Interaction with the Actin Cytoskeleton  

PubMed Central

Small GTPases of the Rho family are crucial regulators of actin cytoskeleton rearrangements. Rho is activated by members of the Rho guanine-nucleotide exchange factor (GEF) family; however, mechanisms that regulate RhoGEFs are not well understood. This report demonstrates that PDZ-RhoGEF, a member of a subfamily of RhoGEFs that contain regulator of G protein signaling domains, is partially localized at or near the plasma membranes in 293T, COS-7, and Neuro2a cells, and this localization is coincident with cortical actin. Disruption of the cortical actin cytoskeleton in cells by using latrunculin B prevents the peri-plasma membrane localization of PDZ-RhoGEF. Coimmunoprecipitation and F-actin cosedimentation assays demonstrate that PDZ-RhoGEF binds to actin. Extensive deletion mutagenesis revealed the presence of a novel 25-amino acid sequence in PDZ-RhoGEF, located at amino acids 561–585, that is necessary and sufficient for localization to the actin cytoskeleton and interaction with actin. Last, PDZ-RhoGEF mutants that fail to interact with the actin cytoskeleton display enhanced Rho-dependent signaling compared with wild-type PDZ-RhoGEF. These results identify interaction with the actin cytoskeleton as a novel function for PDZ-RhoGEF, thus implicating actin interaction in organizing PDZ-RhoGEF signaling. PMID:14742719

Banerjee, Jayashree; Wedegaertner, Philip B.

2004-01-01

334

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

Microsoft Academic Search

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

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

2009-01-01

335

Putative identification of functional interactions between DNA intercalating agents and topoisomerase II using the V79 in vitro micronucleus assay.  

PubMed

Clastogenicity is frequently observed following treatment of mammalian cells with new chemical entities. This clastogenicity, unless proven otherwise, is assumed to result from the imperfect repair of DNA lesions produced from covalent chemical/DNA interaction. However, clastogenicity can also arise via other mechanisms such as non-covalent chemical intercalation into DNA resulting in poisoning of cellular DNA topoisomerase II (topo II) and stabilization of DNA double strand breaks. We have recently reported modifications to the V79 in vitro micronucleus assay which allow an indirect evaluation of both the intercalative and topoisomerase-interactive activities of chemical agents. In the present studies we have used these modified assays to further assess the validity of this approach in an evaluation of a number of intercalating and non-intercalating polycyclic compounds. It is shown that intercalating agents may be catalytic topo II inhibitors (e.g. chloroquine (CHL), tacrine (TAC), 9-aminoacridine (9AA), ethidium bromide (EB)) or topo II poisons (e.g. proflavine (PROF), auramine O (AUR) and curcumin (CURC)). Still other intercalators are shown to lack detectable topo II-interactions, (e.g. imipramine (IMP), quinacrine (QUIN), 2-aminoanthracene (AA), iminostilbene (IMN) and promethazine (PHE)). It is concluded that (1) the clastogenicity of three agents, PROF (a typical DNA intercalating agent), and AUR and CURC (both structurally atypical intercalating agents, with unknown clastogenic mechanisms), may be due to topo II poisoning; (2) other intercalating agents may either act as catalytic topo II inhibitors or exhibit no functional topo II interaction; (3) The use of these cell-based approaches may provide a logical first step in determining if unexpected clastogenicity associated with test article exposure is due to a topo II interaction. PMID:12052500

Snyder, Ronald D; Arnone, Marc R

2002-06-19

336

Identification of Novel Ryanodine Receptor 1 (RyR1) Protein Interaction with Calcium Homeostasis Endoplasmic Reticulum Protein (CHERP)*?  

PubMed Central

The ryanodine receptor type 1 (RyR1) is a homotetrameric Ca2+ release channel located in the sarcoplasmic reticulum of skeletal muscle where it plays a role in the initiation of skeletal muscle contraction. A soluble, 6×-histidine affinity-tagged cytosolic fragment of RyR1 (amino acids 1–4243) was expressed in HEK-293 cells, and metal affinity chromatography under native conditions was used to purify the peptide together with interacting proteins. When analyzed by gel-free liquid chromatography mass spectrometry (LC-MS), 703 proteins were identified under all conditions. This group of proteins was filtered to identify putative RyR interacting proteins by removing those proteins found in only 1 RyR purification and proteins for which average spectral counts were enriched by less than 4-fold over control values. This resulted in 49 potential RyR1 interacting proteins, and 4 were selected for additional interaction studies: calcium homeostasis endoplasmic reticulum protein (CHERP), endoplasmic reticulum-Golgi intermediate compartment 53-kDa protein (LMAN1), T-complex protein, and phosphorylase kinase. Western blotting showed that only CHERP co-purified with affinity-tagged RyR1 and was eluted with imidazole. Immunofluorescence showed that endogenous CHERP co-localizes with endogenous RyR1 in the sarcoplasmic reticulum of rat soleus muscle. A combination of overexpression of RyR1 in HEK-293 cells with siRNA-mediated suppression of CHERP showed that CHERP affects Ca2+ release from the ER via RyR1. Thus, we propose that CHERP is an RyR1 interacting protein that may be involved in the regulation of excitation-contraction coupling. PMID:21454501

Ryan, Timothy; Sharma, Parveen; Ignatchenko, Alex; MacLennan, David H.; Kislinger, Thomas; Gramolini, Anthony O.

2011-01-01

337

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

PubMed

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

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

2014-03-26

338

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

PubMed Central

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

Kumar, R. Barani; Suresh, M. Xavier

2013-01-01

339

A Key to Common Caterpillar Pests of Vegetables  

E-print Network

This publication is an aid to identifying caterpillar pests. There are detailed drawings, color photos, and an illustrated identification key. Depicted are fall armyworm, cabbage looper, saltmarsh caterpillar, tomato pinworm, parsley worm and many...

Sparks Jr., Alton N.; Liu, Tong-Xian

2001-08-10

340

Transcription factor profiling leading to the identification of putative transcription factors involved in the Medicago truncatula – Uromyces striatus interaction  

Microsoft Academic Search

Understanding the host response to Uromyces sp., the causal agent of rust in many crop species, is crucial in elucidating the specific biology of rust resistance. In\\u000a an attempt to unravel the Medicago truncatula–U. striatus interaction, we performed a global analysis of transcription factor (TF) expression in resistant and susceptible accessions\\u000a of the model plant M. truncatula during infection with

J. Gil; D. Rubiales; F. Krajinski; A. Schlereth; T. Millán

2010-01-01

341

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

PubMed Central

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

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

2013-01-01

342

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

PubMed

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

Shin, Jihye; Sohn, Young Chang

2014-11-01

343

Identification of Novel NPRAP/?-Catenin-Interacting Proteins and the Direct Association of NPRAP with Dynamin 2  

PubMed Central

Neural plakophilin-related armadillo protein (NPRAP or ?-catenin) is a neuronal-specific protein that is best known for its interaction with presenilin 1 (PS1). Interestingly, the hemizygous loss of NPRAP is associated with severe mental retardation in cri du chat syndrome (CDCS), and mutations in PS1 cause an aggressive, early-onset form of Alzheimer's disease. Until recently, studies on the function of NPRAP have focused on its ability to modulate dendritic protrusion elaboration through its binding to cell adhesion and scaffolding molecules. However, mounting evidence indicates that NPRAP participates in intracellular signaling and exists in the nucleus, where it modulates gene expression. This apparent bifunctional nature suggests an elaborate neuronal role, but how NPRAP came to participate in such distinct subcellular events remains a mystery. To gain insight into this pathway, we immunoprecipitated NPRAP from human SH SY5Y cells and identified several novel interacting proteins by mass spectrometry. These included neurofilament alpha-internexin, interferon regulatory protein 2 binding factors, and dynamins 1 and 2. We further validated dynamin 2/NPRAP colocalization and direct interaction in vivo, confirming their bona fide partnership. Interestingly, dynamin 2 has established roles in endocytosis and actin assembly, and both of these processes have the potential to interface with the cell adhesion and intracellular signaling processes that involve NPRAP. Our data provide new avenues for approaching NPRAP biology and suggest a broader role for this protein than previously thought. PMID:22022388

Koutras, Carolina; Lévesque, Georges

2011-01-01

344

Identification of novel NPRAP/?-catenin-interacting proteins and the direct association of NPRAP with dynamin 2.  

PubMed

Neural plakophilin-related armadillo protein (NPRAP or ?-catenin) is a neuronal-specific protein that is best known for its interaction with presenilin 1 (PS1). Interestingly, the hemizygous loss of NPRAP is associated with severe mental retardation in cri du chat syndrome (CDCS), and mutations in PS1 cause an aggressive, early-onset form of Alzheimer's disease. Until recently, studies on the function of NPRAP have focused on its ability to modulate dendritic protrusion elaboration through its binding to cell adhesion and scaffolding molecules. However, mounting evidence indicates that NPRAP participates in intracellular signaling and exists in the nucleus, where it modulates gene expression. This apparent bifunctional nature suggests an elaborate neuronal role, but how NPRAP came to participate in such distinct subcellular events remains a mystery. To gain insight into this pathway, we immunoprecipitated NPRAP from human SH SY5Y cells and identified several novel interacting proteins by mass spectrometry. These included neurofilament alpha-internexin, interferon regulatory protein 2 binding factors, and dynamins 1 and 2. We further validated dynamin 2/NPRAP colocalization and direct interaction in vivo, confirming their bona fide partnership. Interestingly, dynamin 2 has established roles in endocytosis and actin assembly, and both of these processes have the potential to interface with the cell adhesion and intracellular signaling processes that involve NPRAP. Our data provide new avenues for approaching NPRAP biology and suggest a broader role for this protein than previously thought. PMID:22022388

Koutras, Carolina; Lévesque, Georges

2011-01-01

345

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

PubMed Central

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

Shin, Jihye; Sohn, Young Chang

2014-01-01

346

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

SciTech Connect

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.

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

347

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

PubMed Central

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

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

2013-01-01

348

Identification of interacting proteins of retinoid-related orphan nuclear receptor gamma in HepG2 cells.  

PubMed

The retinoid-related orphan nuclear receptor gamma (ROR ?) plays critical roles in regulation of development, immunity and metabolism. As transcription factor usually forms a protein complex to function, thus capturing and dissecting of the ROR ? protein complex will be helpful for exploring the mechanisms underlying those functions. After construction of the recombinant tandem affinity purification (TAP) plasmid, pMSCVpuro ROR ?-CTAP(SG), the nuclear localization of ROR ?-CTAP(SG) fusion protein was verified. Following isolation of ROR ? protein complex by TAP strategy, seven candidate interacting proteins were identified. Finally, the heat shock protein 90 (HSP90) and receptor-interacting protein 140 (RIP140) were confirmed to interplay with ROR ? by co-immunoprecipitation. Interference of HSP90 or/and RIP140 genes resulted in dramatically decreased expression of CYP2C8 gene, the ROR ? target gene. Data from this study demonstrate that HSP90 and RIP140 proteins interact with ROR ? protein in a complex format and function as co-activators in the ROR ?-mediated regulatory processes of HepG2 cells. PMID:22732217

Huang, Ze-Min; Wu, Jun; Jia, Zheng-Cai; Tian, Yi; Tang, Jun; Tang, Yan; Wang, Ying; Wu, Yu-Zhang; Ni, Bing

2012-06-01

349

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

PubMed Central

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

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

2014-01-01

350

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

PubMed Central

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

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

2014-01-01

351

PHONETIC SPEAKER IDENTIFICATION Qin Jin, Tanja Schultz, Alex Waibel  

E-print Network

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

Schultz, Tanja

352

PHONETIC SPEAKER IDENTIFICATION Qin Jin, Tanja Schultz, Alex Waibel  

E-print Network

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

Schultz, Tanja

353

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

PubMed

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

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

2014-08-01

354

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

PubMed

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

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

355

Group key management  

SciTech Connect

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.

Dunigan, T.; Cao, C.

1997-08-01

356

Modular Connector Keying Concept  

NASA Technical Reports Server (NTRS)

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.

Ishman, Scott; Dukes, Scott; Warnica, Gary; Conrad, Guy; Senigla, Steven

2013-01-01

357

Modeling Identification Strategies Using the MCC Methodology  

Microsoft Academic Search

this paper, we describe twodifferent tools for identification. The first, MAKEY, allows to build identification graphs(otherwise called decision trees, clinical algorithms or identification keys) which can then beused to identify subjects. The second, XPER, allows without this preliminary phase ofconstruction to identify directly a given subject. These two tools have in common the use asinput of particular knowledge bases containing

Karine CAUSSE; Jacques LEBBE

1995-01-01

358

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

PubMed

The sweet protein brazzein [recombinant protein with sequence identical with the native protein lacking the N-terminal pyroglutamate (the numbering system used has Asp2 as the N-terminal residue)] activates the human sweet receptor, a heterodimeric G-protein-coupled receptor composed of subunits Taste type 1 Receptor 2 (T1R2) and Taste type 1 Receptor 3 (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 in vitro assay. We mutated surface residues of brazzein at three putative interaction sites: site 1 (Loop43), site 2 (N- and C-termini 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 Loop9-19 (site 3). Results from mutagenesis and chimeras of the receptor indicated that brazzein interacts with both T1R2 and T1R3 and that the Venus flytrap 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 brazzein response. The exception, hT1R2 (human T1R2 subunit of the sweet receptor):R217A/hT1R3 (human T1R3 subunit of the sweet receptor), 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 is involved in subunit-subunit interaction rather than in direct brazzein binding. Results from this study support a multi-point interaction between brazzein and the sweet receptor by some mechanism other than the proposed wedge models. PMID:20302879

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

2010-05-14

359

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

PubMed Central

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

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

2012-01-01

360

Identification of Proteins that Interact with TANK Binding Kinase 1 and Testing for Mutations Associated with Glaucoma  

PubMed Central

Purpose Copy number variations (duplications) of TANK binding kinase 1 (TBK1) have been associated with normal tension glaucoma (NTG), a common cause of blindness worldwide. Mutations in other genes involved in autophagy (TLR4 and OPTN) have been associated with NTG. Here we report searching for additional proteins involved in autophagy that may also have roles in NTG. Materials and methods HEK-293T cells were transfected to produce synthetic TBK1 protein with FLAG and S tags. Proteins that associate with TBK1 were isolated from HEK-293T lysates using tandem affinity purification (TAP) and polyacrylamide gel electrophoresis (PAGE). Isolated proteins were identified with mass spectrometry. A cohort of 148 NTG patients and 77 controls from Iowa were tested for glaucoma-causing mutations in genes that encode identified proteins that interact with TBK1 using high resolution melt (HRM) analysis and DNA sequencing. Results TAP studies show that three proteins expressed in HEK-293T cells (NAP1, TANK and TBKBP1) interact with TBK1. Testing cohorts of NTG and normal controls for disease-causing mutations in TANK, identified a total of nine unique variants including three non-synonymous changes, one synonymous changes and five intronic changes. When analyzed alone or as a group, the non-synonymous TBK1 coding sequence changes were not associated with either NTG or primary open angle glaucoma. Conclusion TAP showed that NAP1, TANK and TBKBP1 interact with TBK1 and are good candidates for contributing to NTG. A mutation screen of TANK detected three non-synonymous variants. Although, it remains possible that one or more of these TANK mutations may have a role in NTG, the data in this report do not provide statistical support for an association between TANK variants and NTG. PMID:23286385

Seo, Seongjin; Solivan-Timpe, Frances; Roos, Ben R.; Robin, Alan L.; Stone, Edwin M.; Kwon, Young H.; Alward, Wallace L.M.; Fingert, John H.

2013-01-01

361

Identification of electrostatic interaction sites between the regulatory and catalytic subunits of cyclic AMP-dependent protein kinase.  

PubMed

Two classes of molecules inhibit the catalytic subunit (C) of the cyclic AMP-dependent protein kinase (cAPK), the heat-stable protein kinase inhibitors (PKIs) and the regulatory (R) subunits. Basic sites on C, previously identified as important for R/C interaction in yeast TPK1 and corresponding to Lys213, Lys217, and Lys189 in murine C alpha, were replaced with either Ala or Thr and characterized for their kinetic properties and ability to interact with RI and PKI. rC(K213A) and rC(K217A) were both defective in forming holoenzyme with RI but were inhibited readily with PKI. This contrasts with rC(R133A), which is defective in binding PKI but not RI (Wen & Taylor, 1994). Thus, the C-subunit employs two distinct electrostatic surfaces to achieve high-affinity binding with these two types of inhibitory molecules even though all inhibitors share a common consensus site that occupies the active site cleft. Unlike TPK1, mutation of Lys189 had no effect. The mutant C subunits that were defective in binding RI, rC(K213A) and rC(K217A), were then paired with three RI mutants, rRI(D140A), rRI(E143A), and rRI(D258A), shown previously to be defective in recognition of C. Although the mutations at Asp140 and Asp258 in RI were additive with respect to the C mutations. rC(K213A) and rRI(E143A) were compensatory, thus identifying a specific electrostatic interaction site between RI and C. The results are discussed in terms of the RI and C crystal structures and the sequence homology between the yeast and mammalian enzymes. PMID:9300482

Gibson, R M; Ji-Buechler, Y; Taylor, S S

1997-09-01

362

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

PubMed Central

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

2014-01-01

363

Identification of Conserved Amino Acid Residues of the Salmonella ?S Chaperone Crl Involved in Crl-?S Interactions ?  

PubMed Central

Proteins that bind ? factors typically attenuate the function of the ? factor by restricting its access to the RNA polymerase (RNAP) core enzyme. An exception to this general rule is the Crl protein that binds the stationary-phase sigma factor ?S (RpoS) and enhances its affinity for the RNAP core enzyme, thereby increasing expression of ?S-dependent genes. Analyses of sequenced bacterial genomes revealed that crl is less widespread and less conserved at the sequence level than rpoS. Seventeen residues are conserved in all members of the Crl family. Site-directed mutagenesis of the crl gene from Salmonella enterica serovar Typhimurium and complementation of a ?crl mutant of Salmonella indicated that substitution of the conserved residues Y22, F53, W56, and W82 decreased Crl activity. This conclusion was further confirmed by promoter binding and abortive transcription assays. We also used a bacterial two-hybrid system (BACTH) to show that the four substitutions in Crl abolish Crl-?S interaction and that residues 1 to 71 in ?S are dispensable for Crl binding. In Escherichia coli, it has been reported that Crl also interacts with the ferric uptake regulator Fur and that Fur represses crl transcription. However, the Salmonella Crl and Fur proteins did not interact in the BACTH system. In addition, a fur mutation did not have any significant effect on the expression level of Crl in Salmonella. These results suggest that the relationship between Crl and Fur is different in Salmonella and E. coli. PMID:20008066

Monteil, Véronique; Kolb, Annie; D'Alayer, Jacques; Beguin, Pierre; Norel, Françoise

2010-01-01

364

Orchids of Wisconsin: An Interactive Flora  

NSDL National Science Digital Library

Orchid enthusiasts may appreciate this Web site developed by Jeff Hapeman, graduate student at the University of Wisconsin-Madison. Information including "photos, typical taxonomic descriptive information, a description of similar species to aid in identification, habitat information, blooming dates, a section on pollination biology (if information is available), herbarium records, and a range map" are included for each species of orchid (native and naturalized) found in Wisconsin. Species can be viewed through an alphabetical listing of genera or by navigating through the interactive key. However, even though it is an interesting Web site for browsing orchid information, those without botanical background may be frustrated by the technical terms used throughout the key.

365

Views on Identification.  

ERIC Educational Resources Information Center

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

CAG Communicator, 1990

1990-01-01

366

The Key to Security.  

ERIC Educational Resources Information Center

Provides tips on using low-tech, traditional key and lock systems for effectively securing university and college facilities. Discusses providing keys with utility patents as well as the need to design doors that offer greater deterrence to vandalism. (GR)

Kennedy, Mike

2001-01-01

367

Public Key Cryptography.  

ERIC Educational Resources Information Center

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)

Tapson, Frank

1996-01-01

368

Keys for XML  

Microsoft Academic Search

We discuss the deflnition of keys for XML documents, paying particular attention to the concept of a relative key, which is commonly used in hierarchically structured documents and scientiflc databases.

Peter Buneman; Susan B. Davidson; Wenfei Fan; Carmem S. Hara; Wang-Chiew Tan

2001-01-01

369

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

PubMed Central

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

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

2014-01-01

370

Interaction of Bordetella pertussis filamentous hemagglutinin with human TLR2: identification of the TLR2-binding domain.  

PubMed

Filamentous hemagglutinin (FHA) is a major adhesion and virulence factor of Bordetella pertussis and also a main component of acellular pertussis vaccines. Interaction of FHA with different receptors on human epithelial and immune cells facilitates entrance and colonization of bacteria as well as immunomodulation of the host immune response. Three overlapping segments of the FHA gene were cloned in a prokaryotic expression vector and the recombinant proteins were purified. These recombinant fragments along with the native FHA protein were employed to assess their potential Toll-like receptor (TLR) stimulatory effects and to localize the TLR binding region. TLR stimulation was monitored by applying HEK293-Blue cell lines cotransfected with TLR2, 4, or 5 and a NF-?B reporter gene. Culture supernatants were checked for secretion of the reporter gene product and IL-8 as indicators of TLR stimulation. Native FHA was found to strongly stimulate TLR2, but not TLR4 or TLR5 transfected cells. Among recombinant FHA fragments only the fragment spanning amino acid residues 1544-1917 was able to exhibit the TLR2 stimulating property of FHA. Interaction of FHA with TLR2 suggests its involvement in induction of the innate immune system against Bordetella pertussis. The TLR2-binding domain of FHA may contribute to immunoprotection against pertussis infection. PMID:25353353

Asgarian-Omran, Hossein; Amirzargar, Ali Akbar; Zeerleder, Sacha; Mahdavi, Marzieh; van Mierlo, Gerard; Solati, Shabnam; Jeddi-Tehrani, Mahmood; Rabbani, Hodjatallah; Aarden, Leucien; Shokri, Fazel

2015-02-01

371

Identification of a novel contactin-associated transmembrane receptor with multiple domains implicated in protein-protein interactions.  

PubMed Central

Receptor protein tyrosine phosphatase beta (RPTPbeta) expressed on the surface of glial cells binds to the glycosylphosphatidylinositol (GPI)-anchored recognition molecule contactin on neuronal cells leading to neurite outgrowth. We describe the cloning of a novel contactin-associated transmembrane receptor (p190/Caspr) containing a mosaic of domains implicated in protein-protein interactions. The extracellular domain of Caspr contains a neurophilin/coagulation factor homology domain, a region related to fibrinogen beta/gamma, epidermal growth factor-like repeats, neurexin motifs as well as unique PGY repeats found in a molluscan adhesive protein. The cytoplasmic domain of Caspr contains a proline-rich sequence capable of binding to a subclass of SH3 domains of signaling molecules. Caspr and contactin exist as a complex in rat brain and are bound to each other by means of lateral (cis) interactions in the plasma membrane. We propose that Caspr may function as a signaling component of contactin, enabling recruitment and activation of intracellular signaling pathways in neurons. The binding of RPTPbeta to the contactin-Caspr complex could provide a mechanism for cell-cell communication between glial cells and neurons during development. PMID:9118959

Peles, E; Nativ, M; Lustig, M; Grumet, M; Schilling, J; Martinez, R; Plowman, G D; Schlessinger, J

1997-01-01

372

Identification of P2X(4) receptor transmembrane residues contributing to channel gating and interaction with ivermectin.  

PubMed

Ivermectin (IVM), a large macrocyclic lactone, specifically enhances P2X(4) receptor-channel function by interacting with residues of transmembrane (TM) helices in the open conformation state. In this paper, we used cysteine-scanning mutagenesis of rat P2X(4)-TMs to identify and map residues of potential importance for channel gating and interaction with IVM. The receptor function was unchanged by mutations in 29 different residues, and among them, the IVM effects were altered in Gln(36), Leu(40), Val(43), Val(47), Trp(50), Asn(338), Gly(342), Leu(346), Ala(349), and Ile(356) mutants. The substitution-sensitive Arg(33) and Cys(353) mutants could also be considered as IVM-sensitive hits. The pattern of these 12 residues was consistent with helical topology of both TMs, with every third or fourth amino acid affected by substitution. These predominantly hydrophobic-nonpolar residues are also present in the IVM-sensitive Schistosoma mansoni P2X subunit. They lie on the same side of their helices and could face lipids in the open conformation state and provide the binding pocket for IVM. In contrast, the IVM-independent hits Met(31), Tyr(42), Gly(45), Val(49), Gly(340), Leu(343), Ala(344), Gly(347), Thr(350), Asp(354), and Val(357) map on the opposite side of their helices, probably facing the pore of receptor or protein and playing important roles in gating. PMID:18427835

Jelínkova, Irena; Vávra, Vojtech; Jindrichova, Marie; Obsil, Tomas; Zemkova, Hana W; Zemkova, Hana; Stojilkovic, Stanko S

2008-08-01

373

Genome-wide identification, phylogenetic analysis, expression profiling, and protein–protein interaction properties of TOPLESS gene family members in tomato  

PubMed Central

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

Hao, Yanwei; Wang, Xinyu; van der Rest, Benoit; Zouine, Mohamed

2014-01-01

374

Certificateless Public Key Cryptography  

Microsoft Academic Search

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

Sattam S. Al-riyami; Kenneth G. Paterson

2003-01-01

375

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)

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.

Fujisawa, Ikuhide; Kitamura, Yuji; Kato, Ryo; Murayama, Kazutaka; Aoki, Katsuyuki

2014-01-01

376

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

SciTech Connect

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.

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

377

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

PubMed

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

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

2014-02-01

378

The N-terminal extension of ?B1-crystallin: identification of a critical region which modulates protein interactions with ?A3-crystallin  

PubMed Central

The human lens proteins ?-crystallins are subdivided into acidic (?A1-?A4) and basic (?B1-?B3) subunit groups. These structural proteins exist at extremely high concentrations and associate into oligomers under physiological conditions. Crystallin acidic-basic pairs tend to form strong heteromolecular associations. The long N-terminal extensions of ?-crystallins may influence both homo- and heteromolecular interactions. However, identification of the critical regions of the extensions mediating protein associations have not been previously addressed. This was studied by comparing the self association and heteromolecular associations of wild-type recombinant ?A3 and ?B1 crystallins and their N-terminal truncated counterparts (?A3?N30 and ?B1?N56) using several biophysical techniques including analytical ultracentrifugation and fluorescence spectroscopy. Removal of the N-terminal extension of ?A3 had no effect on dimerization or heteromolecular tetramer formation with ?B1. In contrast, the self association of ?B1?N56 increased resulting in homotetramer formation and heteromolecular association with ?A3 was blocked. Limited proteolysis of ?B1 produced ?B1?N47, which similar to intact protein formed dimers but in contrast showed enhanced heteromolecular tetramer formation with ?A3. The tryptic digestion was of physiological significance, corresponding to protease processing sites observed in-vivo. Molecular modeling of the N-terminal ?B1 extension indicates structural features which position a mobile loop in the vicinity of these processing sites. The loop is derived from residues 48-56 which appear critical for mediating protein interactions with ?A3-crystallin. PMID:19746987

Dolinska, Monika B.; Sergeev, Yuri V.; Chan, May P.; Palmer, Ira; Wingfield, Paul T.

2009-01-01

379

Semi-Automated Identification of N-Glycopeptides by Hydrophilic Interaction Chromatography, nano-Reverse-Phase LC-MS/MS, and Glycan Database Search  

PubMed Central

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

Pompach, Petr; Chandler, Kevin B.; Lan, Renny; Edwards, Nathan; Goldman, Radoslav

2012-01-01

380

Identification, affinity characterisation and biological interactions of lectin-like peptide-carbohydrate complexes derived from human TNF-alpha using high-resolution mass spectrometry.  

PubMed

A cyclic disulfide heptadecapeptide (TIP17ox; 2) derived from the lectin-like 17-amino acid domain of human tumor necrosis factor-alpha [TNF-alpha (100-116)] was synthesised and demonstrated to bind specifically to N,N-diacetylchitobiose, a disaccharide present in many glycan structures of glycoproteins. Although the TIP domain forms a loop structure in the native TNF-alpha protein, we show in this study by high-resolution ESI-FTICR mass spectrometry that a homologous linear heptadecapeptide (TIP17rd; 1) binds with comparable affinity to chitobiose, suggesting that cyclisation is not essential for carbohydrate binding. ESI-FTICR-MS was used as an efficient tool for the direct molecular characterisation of TIP peptide-carbohydrate complexes. The specific binding of the TNF-TIP domain to chitobiose and other carbohydrate motifs in glycoproteins may explain the high proteolytic stability of these peptides in biological fluids. A considerably higher proteolytic stability in human plasma was found by mass spectrometric analysis for the cyclic TIP peptide 2, compared to the linear peptide 1. Furthermore, affinity-proteomics studies using immobilised cyclic TIP peptide 2 provided the identification of specific interacting glycoproteins in plasma. PMID:17918767

Marquardt, Andreas; Bernevic, Bogdan; Przybylski, Michael

2007-12-01

381

The 3.2 Å resolution structure of a Receptor:CheA:CheW signaling complex defines overlapping binding sites and key residue interactions within bacterial chemosensory arrays  

PubMed Central

Bacterial chemosensory arrays are composed of extended networks of chemoreceptors (also known as methyl-accepting chemotaxis proteins, MCPs), the histidine kinase CheA, and the adaptor protein CheW. Models of these arrays have been developed from cryoelectron microscopy, crystal structures of binary and ternary complexes, NMR spectroscopy, mutational data and biochemical studies. A new 3.2 Å resolution crystal structure of a T. maritima MCP protein interaction region in complex with the CheA kinase-regulatory module (P4–P5) and adaptor protein CheW provides sufficient detail to define residue contacts at the interfaces formed among the three proteins. As in a previous 4.5 Å resolution structure, CheA-P5 and CheW interact through conserved hydrophobic surfaces at the ends of their ?-barrels to from pseudo six-fold symmetric rings in which the two proteins alternate around the circumference. The interface between P5 subdomain 1 and CheW subdomain 2 was anticipated from previous studies, whereas the related interface between CheW subdomain 1 and P5 subdomain 2 has only been observed in these ring assemblies. The receptor forms an unexpected structure in that the helical hairpin tip of each subunit has “unzipped” into a continuous ?-helix; four such helices associate into a bundle and the tetramers bridge adjacent P5-CheW rings in the lattice through interactions with both P5 and CheW. P5 and CheW each bind a receptor helix with a groove of conserved hydrophobic residues between subdomains 1 and 2. P5 binds the receptor helix N-terminal to the tip region (lower site), whereas CheW binds the same helix with inverted polarity near the bundle end (upper site). Sequence comparisons among different evolutionary classes of chemotaxis proteins show that the binding partners undergo correlated changes at key residue positions that involve the lower site. Such evolutionary analyses argue that both CheW and P5 bind to the receptor tip at overlapping positions. Computational genomics further reveal that two distinct CheW proteins in Thermotogae utilize the analogous recognition motifs to couple different receptor classes to the same CheA kinase. Important residues for function previously identified by mutagenesis, chemical modification and biophysical approaches also map to these same interfaces. Thus, although the native CheW-receptor interaction is not observed in the present crystal structure, the bioinformatics and previous data predict key features of this interface. The companion study of the P5-receptor interface in native arrays (Piasta et al. (2013) Biochemistry; Companion paper) shows that, despite the non-native receptor fold in the present crystal structure, the local helix-in-groove contacts of the crystallographic P5-receptor interaction are present in native arrays and are essential for receptor regulation of kinase activity. PMID:23668907

Li, Xiaoxiao; Fleetwood, Aaron D.; Bayas, Camille; Bilwes, Alexandrine M.; Ortega, Davi R.; Falke, Joseph J.; Zhulin, Igor B.; Crane, Brian R.

2013-01-01

382

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

PubMed Central

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

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

2013-01-01

383

Identification, expression and interaction analyses of calcium-dependent protein kinase (CPK) genes in canola (Brassica napus L.)  

PubMed Central

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

2014-01-01

384

Identification and Characterisation of the RalA-ERp57 Interaction: Evidence for GDI Activity of ERp57  

PubMed Central

RalA is a membrane-associated small GTPase that regulates vesicle trafficking. Here we identify a specific interaction between RalA and ERp57, an oxidoreductase and signalling protein. ERp57 bound specifically to the GDP-bound form of RalA, but not the GTP-bound form, and inhibited the dissociation of GDP from RalA in vitro. These activities were inhibited by reducing agents, but no disulphide bonds were detected between RalA and ERp57. Mutation of all four of ERp57’s active site cysteine residues blocked sensitivity to reducing agents, suggesting that redox-dependent conformational changes in ERp57 affect binding to RalA. Mutations in the switch II region of the GTPase domain of RalA specifically reduced or abolished binding to ERp57, but did not block GTP-specific binding to known RalA effectors, the exocyst and RalBP1. Oxidative treatment of A431 cells with H2O2 inhibited cellular RalA activity, and the effect was exacerbated by expression of recombinant ERp57. The oxidative treatment significantly increased the amount of RalA localised to the cytosol. These findings suggest that ERp57 regulates RalA signalling by acting as a redox-sensitive guanine-nucleotide dissociation inhibitor (RalGDI). PMID:23226417

Berven, Leise A.; van Dam, Ellen M.; Roufogalis, Basil D.; Robinson, Phillip J.

2012-01-01

385

Identification and Characterization of Putative Tumor Suppressor NGB, a GTP-Binding Protein That Interacts with the Neurofibromatosis 2 Protein?  

PubMed Central

Mutations of the neurofibromatosis 2 (NF2) tumor suppressor gene have frequently been detected not only in schwannomas and other central nervous system tumors of NF2 patients but also in their sporadic counterparts and malignant tumors unrelated to the NF2 syndrome such as malignant mesothelioma, indicating a broader role for the NF2 gene in human tumorigenesis. However, the mechanisms by which the NF2 product, merlin or schwannomin, is regulated and controls cell proliferation remain elusive. Here, we identify a novel GTP-binding protein, dubbed NGB (referring to NF2-associated GTP binding protein), which binds to merlin. NGB is highly conserved between Saccharomyces cerevisiae, Caenorhabditis elegans, and human cells, and its GTP-binding region is very similar to those found in R-ras and Rap2. However, ectopic expression of NGB inhibits cell growth, cell aggregation, and tumorigenicity in tumorigenic schwanomma cells. Down-regulation and infrequent mutation of NGB were detected in human glioma cell lines and primary tumors. The interaction of NGB with merlin impairs the turnover of merlin, yet merlin does not affect the GTPase nor GTP-binding activity of NGB. Finally, the tumor suppressor functions of NGB require merlin and are linked to its ability to suppress cyclin D1 expression. Collectively, these findings indicate that NGB is a tumor suppressor that regulates and requires merlin to suppress cell proliferation. PMID:17210637

Lee, Hansoo; Kim, Donghwa; Dan, Han C.; Wu, Eric L.; Gritsko, Tatiana M.; Cao, Chuanhai; Nicosia, Santo V.; Golemis, Erica A.; Liu, Wanguo; Coppola, Domenico; Brem, Steven S.; Testa, Joseph R.; Cheng, Jin Q.

2007-01-01

386

Identification of Real-world Objects in Multiple Databases  

Microsoft Academic Search

Object identification is an important issue for integration of data from different sources. The identification task is complicated, if no global and consistent identifier is shared by the sources. Then, object identification can only be performed through the identifying information, the objects data provides itself. Unfortunately real-world data is dirty, hence identification mechanisms like natural keys fail mostly — we

Mattis Neiling

2005-01-01

387

Posttranscriptional control of renin synthesis: identification of proteins interacting with renin mRNA 3'-untranslated region.  

PubMed

Stabilization and correct localization of mRNA are important features of renin synthesis. To elucidate the molecular basis of cAMP-mediated posttranscriptional control via mRNA stabilization, we analyzed the interaction of human preprorenin (hREN) mRNA 3'-untranslated region (3'-UTR) with proteins of renin synthesizing Calu-6 cells and investigated their functional impact on messenger integrity. To identify hREN mRNA binding proteins, electrophoretic mobility shift assays, UV cross-linking and RNA-affinity chromatography with subsequent matrix-assisted laser desorption/ionization time-of-flight mass spectrometry were performed. The following six proteins were unambiguously identified as hREN mRNA 3'-UTR binding proteins: hnRNP E1 (synonyms alpha-CP or PCBP), hnRNP K, dynamin, nucleolin, YB-1, and MINT-homologous protein. All proteins contain various RNA binding motifs, and most have been described in the context of mRNA binding and mRNA stabilization. Four proteins for which antibodies were available were verified by immunological techniques (dynamin, nucleolin, hnRNP E1, and YB-1). Forskolin, an activator of cAMP synthesis, considerably stimulates renin synthesis via inhibition of REN mRNA decay. Functionally, this cAMP-based mRNA stabilization is accompanied by a 3- to 6-fold upregulation of REN mRNA binding proteins. RNase degradation assays confirm that 3'-UTR binding proteins are able to protect and stabilize REN mRNA in vitro. PMID:12600897

Skalweit, Angela; Doller, Anke; Huth, Antje; Kähne, Thilo; Persson, Pontus B; Thiele, Bernd-Joachim

2003-03-01

388

Molecular identification and interaction assay of the gene (OsUbc13) encoding a ubiquitin-conjugating enzyme in rice*  

PubMed Central

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

Wang, Ya; Xu, Meng-yun; Liu, Jian-ping; Wang, Mu-gui; Yin, Hai-qing; Tu, Ju-min

2014-01-01

389

Male Phyllotreta striolata (F.) produce an aggregation pheromone: identification of male-specific compounds and interaction with host plant volatiles.  

PubMed

The chrysomelid beetle Phyllotreta striolata is an important pest of Brassicaceae in Southeast Asia and North America. Here, we identified the aggregation pheromone of a population of P. striolata from Taiwan, and host plant volatiles that interact with the pheromone. Volatiles emitted by feeding male P. striolata attracted males and females in the field. Headspace volatile analyses revealed that six sesquiterpenes were emitted specifically by feeding males. Only one of these, however, elicited an electrophysiological response from antennae of both sexes. A number of host plant volatiles, e.g., 1-hexanol, (Z)-3-hexen-1-ol, and the glucosinolate hydrolysis products allyl isothiocyanate (AITC), 3-butenyl isothiocyanate, and 4-pentenyl isothiocyanate also elicited clear responses from the antenna. The active male-specific compound was identified as (+)-(6R,7S)-himachala-9,11-diene by chiral stationary phase gas-chromatography with coupled mass spectrometry, and by comparison with reference samples from Abies nordmanniana, which is known to produce the corresponding enantiomer. The pheromone compound was synthesized starting from (-)-?-himachalene isolated from Cedrus atlantica. Under field conditions, the activity of the synthetic pheromone required concomitant presence of the host plant volatile allyl isothiocyanate. However, both synthetic (+)-(6R,7S)-himachala-9,11-diene alone and in combination with AITC were attractive in a two-choice laboratory assay devoid of other natural olfactory stimuli. We hypothesize that P. striolata adults respond to the pheromone only if specific host volatiles are present. In the same laboratory set up, more beetles were attracted by feeding males than by the synthetic stimuli. Thus, further research will be necessary to reveal the components of a more complex blend of host or male-produced semiochemicals that might enhance trap attractiveness in the field. PMID:21181241

Beran, Franziska; Mewis, Inga; Srinivasan, Ramasamy; Svoboda, Ji?í; Vial, Christian; Mosimann, Hervé; Boland, Wilhelm; Büttner, Carmen; Ulrichs, Christian; Hansson, Bill S; Reinecke, Andreas

2011-01-01

390

Identification of guanine nucleotide exchange factors (GEFs) for the Rap1 GTPase. Regulation of MR-GEF by M-Ras-GTP interaction.  

PubMed

Although the Ras subfamily of GTPases consists of approximately 20 members, only a limited number of guanine nucleotide exchange factors (GEFs) that couple extracellular stimuli to Ras protein activation have been identified. Furthermore, no novel downstream effectors have been identified for the M-Ras/R-Ras3 GTPase. Here we report the identification and characterization of three Ras family GEFs that are most abundantly expressed in brain. Two of these GEFs, MR-GEF (M-Ras-regulated GEF, KIAA0277) and PDZ-GEF (KIAA0313) bound specifically to nucleotide-free Rap1 and Rap1/Rap2, respectively. Both proteins functioned as Rap1 GEFs in vivo. A third GEF, GRP3 (KIAA0846), activated both Ras and Rap1 and shared significant sequence homology with the calcium- and diacylglycerol-activated GEFs, GRP1 and GRP2. Similarly to previously identified Rap GEFs, C3G and Smg GDS, each of the newly identified exchange factors promoted the activation of Elk-1 in the LNCaP prostate tumor cell line where B-Raf can couple Rap1 to the extracellular receptor-activated kinase cascade. MR-GEF and PDZ-GEF both contain a region immediately N-terminal to their catalytic domains that share sequence homology with Ras-associating or RalGDS/AF6 homology (RA) domains. By searching for in vitro interaction with Ras-GTP proteins, PDZ-GEF specifically bound to Rap1A- and Rap2B-GTP, whereas MR-GEF bound to M-Ras-GTP. C-terminally truncated MR-GEF, lacking the GEF catalytic domain, retained its ability to bind M-Ras-GTP, suggesting that the RA domain is important for this interaction. Co-immunoprecipitation studies confirmed the interaction of M-Ras-GTP with MR-GEF in vivo. In addition, a constitutively active M-Ras(71L) mutant inhibited the ability of MR-GEF to promote Rap1A activation in a dose-dependent manner. These data suggest that M-Ras may inhibit Rap1 in order to elicit its biological effects. PMID:10934204

Rebhun, J F; Castro, A F; Quilliam, L A

2000-11-10

391

An Interactive Guide to Massachusetts Snakes  

NSDL National Science Digital Library

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.

Haver, Nancy.

392

Mapping the Interactions of Dengue Virus NS1 Protein with Human Liver Proteins Using a Yeast Two-Hybrid System: Identification of C1q as an Interacting Partner  

PubMed Central

Dengue constitutes a global health concern. The clinical manifestation of this disease varies from mild febrile illness to severe hemorrhage and/or fatal hypovolemic shock. Flavivirus nonstructural protein 1 (NS1) is a secreted glycoprotein that is displayed on the surface of infected cells but is absent in viral particles. NS1 accumulates at high levels in the plasma of dengue virus (DENV)-infected patients, and previous reports highlight its involvement in immune evasion, dengue severity, liver dysfunction and pathogenesis. In the present study, we performed a yeast two-hybrid screen to search for DENV2 NS1-interacting partners using a human liver cDNA library. We identified fifty genes, including human complement component 1 (C1q), which was confirmed by coimmunoprecipitation, ELISA and immunofluorescence assays, revealing for the first time the direct binding of this protein to NS1. Furthermore, the majority of the identified genes encode proteins that are secreted into the plasma of patients, and most of these proteins are classified as acute-phase proteins (APPs), such as plasminogen, haptoglobin, hemopexin, ?-2-HS-glycoprotein, retinol binding protein 4, transferrin, and C4. The results presented here confirm the direct interaction of DENV NS1 with a key protein of the complement system and suggest a role for this complement protein in the pathogenesis of DENV infection. PMID:23516407

Allonso, Diego; Nogueira, Mauricio L.; Mohana-Borges, Ronaldo

2013-01-01

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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...

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