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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 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

3

Rock Identification Key  

NSDL National Science Digital Library

This identification key has been designed to assist teachers, students, or collectors in the identification of rocks. It consists of a series of "yes/no/then go to" questions that pertain to observations of structure, texture, color, hardness, and other properties of the specimen being examined.

Peck, Don

4

Key distribution system based on identification information  

Microsoft Academic Search

A key distribution system (KDS) based on identification information (ID-based KDS) is presented. The system is founded on the Diffie-Hellman public key distribution scheme and has an identity authentication function. It uses an individual user's identification information instead of the public file used in the Diffie-Hellman scheme. It does not require any services of a center to distribute work keys

EIJI OKAMOTO; KAZUE TANAKA

1989-01-01

5

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

6

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

E-print Network

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

Baumann, Paul A.

1999-08-30

7

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

8

Keys for Identification of Immature Insects  

Microsoft Academic Search

\\u000a The study of immature insects is important in forensic entomology, because the identification of the involved species is a\\u000a crucial step in calculating the post-mortem interval (PMI) and because it is the insect life stage most frequently collected\\u000a from corpses. The immature stage consists of the egg, nymph or larva with its average of three or four development instars,\\u000a and

Patricia J. Thyssen

9

Temporal dynamics and the identification of musical key.  

PubMed

A central process in music cognition involves the identification of key; however, little is known about how listeners accomplish this task in real time. This study derives from work that suggests overlap between the neural and cognitive resources underlying the analyses of both music and speech and is the first, to our knowledge, to explore the timescales at which the brain infers musical key. We investigated the temporal psychophysics of key-finding over a wide range of tempi using melodic sequences with strong structural cues, where statistical information about overall key profile was ambiguous. Listeners were able to provide robust judgments within specific limits, at rates as high as 400 beats per minute (bpm; ?7 Hz) and as low as 30 bpm (0.5 Hz), but not outside those bounds. These boundaries on reliable performance show that the process of key-finding is restricted to timescales that are closely aligned with beat induction and speech processing. PMID:23317116

Farbood, Morwaread Mary; Marcus, Gary; Poeppel, David

2013-08-01

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

Chretiennot-Dinet, Marie-Josephe; Desreumaux, Nicolas; Vignes-Lebbe, Regine

2014-01-01

11

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

PubMed

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

12

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

13

INTERACTIVITY IS THE KEY William Hibbard and David Santek  

E-print Network

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

Martin, Jonathan E.

14

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

15

The persistence of memory: Forensic identification and extraction of cryptographic keys  

Microsoft Academic Search

The increasing popularity of cryptography poses a great challenge in the field of digital forensics. Digital evidence protected by strong encryption may be impossible to decrypt without the correct key. We propose novel methods for cryptographic key identification and present a new proof of concept tool named Interrogate that searches through volatile memory and recovers cryptographic keys used by the

Carsten Maartmann-Moe; Steffen E. Thorkildsen; André Årnes

2009-01-01

16

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

17

Revised morphological identification key to the larval anopheline (Diptera: Culicidae) of Sri Lanka  

PubMed Central

Objective To revise morphological identification keys to the anophelines in Sri Lanka. Method Samples were collected from selected entomological sites in different districts in the country. Stage III and IV larvae were identified under a light microscope with an objective (×10) using standard larval keys developed for Sri Lankan anophelines. Key larval characters were recorded for each species based on original observations and previous usage in literature. Results This manuscript describes an illustrated key for the identification of 22 of 23 mosquitoes which are currently recognized as local anopheline species in Sri Lanka, as a guide to workers engaged in malaria surveillance and control in the country. Conclusions Revised morphological keys to the larval of these species may be helpful in easy and accurate identification at the field level. PMID:25183086

Gunathilaka, Nayana; Fernando, Thilan; Hapugoda, Menaka; Abeyewickreme, Wimaladharma; Wickremasinghe, Rajitha

2014-01-01

18

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

19

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

20

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

ERIC Educational Resources Information Center

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

Wood, Piers

2004-01-01

21

Modeling social interactions: Identification, empirical methods and policy implications  

E-print Network

Hosanagar & Catherine Tucker Published online: 26 July 2008 # Springer Science + Business Media, LLC 2008Modeling social interactions: Identification, empirical methods and policy implications Wesley R Abstract Social interactions occur when agents in a network affect other agents' choices directly

Dodds, Peter

22

Identification of Key Processes that Control Tumor Necrosis Factor Availability in a Tuberculosis Granuloma  

E-print Network

Identification of Key Processes that Control Tumor Necrosis Factor Availability in a Tuberculosis Medical School, Ann Arbor, Michigan, United States of America Abstract Tuberculosis (TB) granulomas in the lung as a result of immune response to Mycobacterium tuberculosis (Mtb) infection. Formation

Kirschner, Denise

23

Synopsis of Falsocis Pic (Coleoptera, Ciidae), new species, new records and an identification key  

PubMed Central

Abstract Three new species of Falsocis Pic are described: Falsocis aquilonius sp. n. from Panamá, Costa Rica and Colombia, Falsocis egregius sp. n. from a single locality in northern Brazil and Falsocis occultus sp. n. from two localities in southeastern and southern Brazil. New records, comparative notes and an identification key for male and female specimens of Falsocis species are also provided. PMID:22287884

Lopes-Andrade, Cristiano; Lawrence, John F.

2011-01-01

24

cDNA microarray and bioinformatic analysis for the identification of key genes in Alzheimer's disease.  

PubMed

In this study, gene expression profiles in peripheral blood monocytes from patients with Alzheimer's disease (AD) or mild cognitive impairment (MCI) were compared with those of healthy individuals to identify key differentially expressed genes (DEGs), in an effort to broaden our understanding of the pathogenesis of these diseases and identify potential therapeutic targets. The microarray data set GSE18309 was downloaded from Gene Expression Omnibus, including 3 AD, 3 MCI and 3 normal control (NC) samples. Raw data were processed and differential analysis was performed using the R multtest package. Two groups of comparisons (AD vs. NC and MCI vs. NC) were conducted and two groups of DEGs were acquired. The common DEGs were selected, for which functional enrichment analysis, as well as pathway enrichment analysis were performed to determine their roles in the development of the diseases in question. A total of 405 DEGs were identified in the AD vs. NC samples and 395 in the MCI vs. NC samples. A total of 60 common DEGs were obtained. Functional enrichment analysis revealed that the most common functions of the DEGs identified were response to nutrients, muscle contraction and cellular homeostasis. As shown by pathway enrichment analysis, the most common pathway associated with the DEGs identifed was the neuroactive ligand-receptor interaction pathway. A range of DEGs was identified in the present study, which may help to disclose the molecular mechanisms responsible for AD and may thus provide potential novel therapeutic strategies for Ad. PMID:24317476

Gu, Chao; Shen, Ting

2014-02-01

25

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

26

Underwater Human-Robot Interaction via Biological Motion Identification  

E-print Network

in the identification of their position, behavior and identity. In this paper we exploit motion signatures to facilitate possible image velocity), and exploit this in a control loop. We use the periodicity inherently presentUnderwater Human-Robot Interaction via Biological Motion Identification Junaed Sattar and Gregory

27

Conceptual response distance and intervening keys distinguish action goals in the Stroop color-identification task.  

PubMed

In previous studies, a physical response-distance effect was found in the two-choice Stroop color-identification task, with the Stroop effect being larger when the two response keys were physically close together than when they were far apart. In the present study, we found a conceptual response-distance effect, with the Stroop effect being larger when the response keys were conceptually close (labeled as "5" and "6") than when they were conceptually far (labeled as "1" and "9"). Moreover, a response-distance effect due to pure physical distance was not evident; rather, the effect was found only when additional keys were placed between the two far response keys. These results are in agreement with a view that response keys are coded as action goals, with farther conceptual distance and additional keys helping distinguish the action goals. The results are difficult to reconcile with accounts that place emphasis on the physical separation of the effectors or their inanimate extensions. PMID:24578092

Chen, Jing; Proctor, Robert W

2014-10-01

28

Principles of visual key construction-with a visual identification key to the Fagaceae of the southeastern United States  

PubMed Central

Background and aims Advances in digital imaging have made possible the creation of completely visual keys. By a visual key we mean a key based primarily on images, and that contains a minimal amount of text. Characters in visual keys are visually, not verbally defined. In this paper we create the first primarily visual key to a group of taxa, in this case the Fagaceae of the southeastern USA. We also modify our recently published set of best practices for image use in illustrated keys to make them applicable to visual keys. Methodology Photographs of the Fagaceae were obtained from internet and herbarium databases or were taken specifically for this project. The images were printed and then sorted into hierarchical groups. These hierarchical groups of images were used to create the ‘couplets’ in the key. A reciprocal process of key creation and testing was used to produce the final keys. Principal results Four keys were created, one for each of the parts—leaves, buds, fruits and bark. Species description pages consisting of multiple images were also created for each of the species in the key. Creation and testing of the key resulted in a modified list of best practices for image use visual keys. Conclusions The inclusion of images into paper and electronic keys has greatly increased their ease of use. However, virtually all of these keys are still based upon verbally defined, atomistic characters. The creation of primarily visual keys allows us to overcome the well-known limitations of linguistic-based characters and create keys that are much easier to use, especially for botanical novices. PMID:22476476

Kirchoff, Bruce K.; Leggett, Roxanne; Her, Va; Moua, Chue; Morrison, Jessica; Poole, Chamika

2011-01-01

29

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

PubMed

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

Yusseff-Vanegas, S

2014-09-01

30

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

PubMed Central

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

Newberry, Robert W.; Raines, Ronald T.

2014-01-01

31

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

32

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...

33

Identification of paxilin domains interacting with ?-catenin  

PubMed Central

Barrier-protective agonists induce association of focal adhesions (FA) and adherens junctions (AJ) in endothelial cells. Here we identified specific domains of FA protein paxillin interacting with AJ protein and examined regulation of paxillin domain interactions with ?-catenin by Rac GTPase. Co-expression of paxillin LD-1,2; LD-3,4; LIM-1,2; and LIM-3,4 domains with ?-catenin showed exclusive interaction of LIM-1,2 and LIM-3,4 with ?-catenin, which was enhanced by agonist-induced Rac activation or expression of activated Rac mutant. These results demonstrate a novel function of paxillin LIM domains in targeting ?-catenin in a Rac-dependent manner, which may play a role in Rac-dependent control of FA-AJ interactions and monolayer integrity. PMID:22728435

Dubrovskyi, Oleksii; Tian, Xinyong; Poroyko, Valeriy; Yakubov, Bakhtiyor; Birukova, Anna A.; Birukov, Konstantin G.

2012-01-01

34

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, Raphaelle; Unterberger, Elif B.; Goodman, Jay I.; Schwarz, Michael; Moggs, Jonathan; Terranova, Remi; van Nimwegen, Erik

2014-01-01

35

Recent analysis of key plasma wall interactions issues for ITER  

NASA Astrophysics Data System (ADS)

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 options are addressed for comparison, such as W divertor/Be first wall and all-W or all-C. One main parameter in this evaluation is the particle flux to the main vessel wall. One detailed plasma scenario exists for a Q = 10 ITER discharge [G. Federici et al., J. Nucl. Mater. 290-293 (2001) 260] which was taken as the basis of further erosion and tritium retention evaluations. As the assessment of steady state wall fluxes from a scaling of present fusion devices indicates that global wall fluxes may be a factor of 4 ± 3 higher, this margin has been adopted as uncertainty of the scaling. With these wall and divertor fluxes, important PWI processes such as erosion and tritium accumulation have been evaluated: It was found that the steady state erosion is no problem for the lifetime of plasma-facing divertor components. Be wall erosion may pose a problem in case of a concentration of the wall fluxes to small wall areas. ELM erosion may drastically limit the PFC lifetime if ELMs are not mitigated to energies below 0.5 MJ. Dust generation is still a process which requires more attention. Conversion from gross or net erosion to dust and the assessment of dust on hot surfaces need to be investigated. For low- Z materials the build-up of the tritium inventory is dominated by co-deposition with eroded wall atoms. For W, where erosion and tritium co-deposition are small, the implantation, diffusion and bulk trapping constitute the dominant retention processes. First extrapolations with models based on laboratory data show small contributions to the inventory. For later ITER phases and the extrapolation to DEMO additional tritium trapping sites due to neutron-irradiation damage need to be taken into account. Finally, the expected values for erosion and tritium retention are compared to the ITER administrative limits for the lifetime, dust and tritium inventory.

Roth, Joachim; Tsitrone, E.; Loarte, A.; Loarer, Th.; Counsell, G.; Neu, R.; Philipps, V.; Brezinsek, S.; Lehnen, M.; Coad, P.; Grisolia, Ch.; Schmid, K.; Krieger, K.; Kallenbach, A.; Lipschultz, B.; Doerner, R.; Causey, R.; Alimov, V.; Shu, W.; Ogorodnikova, O.; Kirschner, A.; Federici, G.; Kukushkin, A.; EFDA PWI Task Force, ITER PWI Team, FusionEnergy, ITPA SOL/DIV

2009-06-01

36

Disease candidate gene identification and prioritization using protein interaction networks  

Microsoft Academic Search

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

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

2009-01-01

37

Identification of Wolbachiahost interacting factors through cytological analysis  

E-print Network

Review Identification of Wolbachia­host interacting factors through cytological analysis Uyen Tram. Cytological studies of the most common Wolbachia­induced phenotype, cytoplasmic incompatibility (CI), demonstrate that Wolbachia induce CI by altering host cell cycle timing. Cytological analyses also suggest

Sullivan, William T.

38

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

ERIC Educational Resources Information Center

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

Hoffner, Cynthia

1996-01-01

39

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

40

Mass spectrometry-based identification of proteins interacting with nucleic acids.  

PubMed

The identification of the regulatory proteins that control DNA transcription as well as RNA stability and translation represents a key step in the comprehension of gene expression regulation. Those proteins can be purified by DNA- or RNA-affinity chromatography, followed by identification by mass spectrometry. Although very simple in the concept, this represents a real technological challenge due to the low abundance of regulatory proteins compared to the highly abundant proteins binding to nucleic acids in a nonsequence-specific manner. Here we review the different strategies that have been set up to reach this purpose, discussing the key parameters that should be considered to increase the chances of success. Typically, two categories of biological questions can be distinguished: the identification of proteins that specifically interact with a precisely defined binding site, mostly addressed by quantitative mass spectrometry, and the identification in a non-comparative manner of the protein complexes recruited by a poorly characterized long regulatory region of nucleic acids. Finally, beside the numerous studies devoted to in vitro-assembled nucleic acid-protein complexes, the scarce data reported on proteomic analyses of in vivo-assembled complexes are described, with a special emphasis on the associated challenges. PMID:24060998

Tacheny, A; Dieu, M; Arnould, T; Renard, P

2013-12-01

41

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

ERIC Educational Resources Information Center

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

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

2009-01-01

42

Lichen Determination Keys  

NSDL National Science Digital Library

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

43

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

44

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

PubMed Central

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

2012-01-01

45

Key Factor and Interaction for Network Performance in Mobile Ad Hoc Networks  

Microsoft Academic Search

In this paper, we present a comprehensive statistical experiment and identify the key factors and interactions that impact network performance over mobile ad hoc networks. We use the design of experiments software named Design-Ease to establish the mathematical model for analyzing the set of simulation results from ns2. A variety of important parameters for network performance including routing protocol, node

Yiming Wang; Dritan Kaleshi; Michael H Barton; Jianhua He; Li Li; A. Munro; Zhong Fan

2007-01-01

46

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

47

A Teaching Exercise for the Identification of Bacteria Using An Interactive Computer Program.  

ERIC Educational Resources Information Center

Describes an interactive Fortran computer program which provides an exercise in the identification of bacteria. Provides a way of enhancing a student's approach to systematic bacteriology and numerical identification procedures. (Author/MA)

Bryant, Trevor N.; Smith, John E.

1979-01-01

48

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

NASA Astrophysics Data System (ADS)

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

Prakasam, P.; Madheswaran, M.

49

Key ingredients of the alkali atom - metal surface interaction: Chemical bonding versus spectral properties  

NASA Astrophysics Data System (ADS)

The interaction of alkali atoms with metal surfaces is reviewed. The peculiar electronic configuration of such atoms, with only one valence electron participating in the bond formation, suggested simple pictures to describe their interaction with a metal surface. But it was early evident that the adsorption properties depend on many aspects, related to the electronic structure of constituents, leading, for example, to different degrees of ionicity/covalency of the alkali atom-metal bond. Sophisticated theoretical modeling tried to shed light on this aspect. The spectral properties are the ultimate features in determining how the systems interact with each other. In this review the electronic and spectral properties are discussed focusing on different theoretical representations of the physical system and on their consequences. Surface projected energy gaps of the substrate as well as the substrate continuous spectrum are key aspects in determining the nature of the interaction and bonding with alkali adsorbates.

Trioni, M. I.; Achilli, S.; Chulkov, E. V.

2013-05-01

50

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

51

Crystal Structures of HIV-1 Reverse Transcriptase with Picomolar Inhibitors Reveal Key Interactions for Drug Design  

PubMed Central

X-ray crystal structures at 2.9 Å resolution are reported for complexes of catechol diethers 1 and 2 with HIV-1 reverse transcriptase. The results help elucidate the structural origins of the extreme antiviral activity of the compounds. The possibility of halogen bonding between the inhibitors and Pro95 is addressed. Structural analysis reveals key interactions with conserved residues P95 and W229 of importance for design of inhibitors with high potency and favorable resistance profiles. PMID:23163887

Frey, Kathleen M.; Bollini, Mariela; Mislak, Andrea C.; Cisneros, Jose A.; Gallardo-Macias, Ricardo; Jorgensen, William L.; Anderson, Karen S.

2012-01-01

52

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

53

The COP1 E3-ligase interacts with FIP200, a key regulator of mammalian autophagy  

PubMed Central

Background The ubiquitin ligase COP1, COnstitutively Photomorphogenic 1, functions in many biological responses in mammalian cells, but its downstream pathway remains unclear. Results Here, we identified FIP200, a key regulator of mammalian autophagy, as a novel COP1-interacting protein by yeast two-hybrid screening. The interaction was confirmed by a GST-pulldown assay. Split-GFP analysis revealed that interaction between COP1 and FIP200 predominantly occurred in the cytoplasm and was enhanced in cells treated with UV irradiation. Different forms of FIP200 protein were expressed in cultured mammalian cells, and ectopic expression of COP1 reduced one of such forms. Conclusions These data suggest that COP1 modulates FIP200-associated activities, which may contribute to a variety of cellular functions that COP1 is involved in. PMID:23289756

2013-01-01

54

Laplacian embedding and key points topology verification for large scale mobile visual identification$  

E-print Network

resolution camera, Bluetooth, Wi-fi, video/voice recorder, and so on. Such features have an immediate visual descriptor with minimum descriptor length. Preserving the visual identification performance while verification (TV) scheme to perform spatial consistency checking. In contrast to previous works on geometric

55

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

56

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

57

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.

58

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

Microsoft Academic Search

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

Krzysztof Szpila

59

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

E-print Network

Abstract Law enforcement agencies have exploited biometrics for decades as key tools in forensic to be investigated by forensic specialists, automation of forensic identification became inevitable. Postmortem (PM goals and objectives to its Automated Fingerprint Identification System (AFIS) but using dental

Abaza, Ayman

60

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

PubMed

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

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

2013-08-01

61

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

Microsoft Academic Search

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

Maarten Kappelle; Margret M. I. Van Vuuren; Pieter Baas

1999-01-01

62

New Records and an Annotated Key for the Identification of Graphis Adans. in South Korea  

PubMed Central

The following new species for the lichen genus Graphis in Korea are reported: G. chlorotica, G. nanodes and G. tenuirima. A brief description of these species, together with their distribution, ecology, and illustrations are provided. A key to all known species of this genus from Korea is also presented. PMID:23874128

Joshi, Santosh; Jayalal, Udeni; Oh, Soon-Ok; Park, Jung Shin

2013-01-01

63

Elmidae (Coleoptera, Byrrhoidea) larvae in the state of S?o 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, Alaide Aparecida

2011-01-01

64

A turn-key approach for large-scale identification of complex posttranslational modifications.  

PubMed

The conjugation of complex post-translational modifications (PTMs) such as glycosylation and Small Ubiquitin-like Modification (SUMOylation) to a substrate protein can substantially change the resulting peptide fragmentation pattern compared to its unmodified counterpart, making current database search methods inappropriate for the identification of tandem mass (MS/MS) spectra from such modified peptides. Traditionally it has been difficult to develop new algorithms to identify these atypical peptides because of the lack of a large set of annotated spectra from which to learn the altered fragmentation pattern. Using SUMOylation as an example, we propose a novel approach to generate large MS/MS training data from modified peptides and derive an algorithm that learns properties of PTM-specific fragmentation from such training data. Benchmark tests on data sets of varying complexity show that our method is 80-300% more sensitive than current state-of-the-art approaches. The core concepts of our method are readily applicable to developing algorithms for the identifications of peptides with other complex PTMs. PMID:24437954

Wang, Jian; Anania, Veronica G; Knott, Jeff; Rush, John; Lill, Jennie R; Bourne, Philip E; Bandeira, Nuno

2014-03-01

65

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

PubMed Central

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

Gwo, Chih-Ying; Wei, Chia-Hung

2013-01-01

66

Strategy for the identification of key odorants: application to shrimp aroma.  

PubMed

The GC-SNIF technique was used to obtain the olfactograms of shrimps, and their impact odorants were identified by MS hyphenated to the GC/olfactometric system and by comprehensive two-dimensional GC hyphenated to a time-of-flight MS. Confirming these identifications by their linear retention indices required application of a new strategy to compare retention indices between both instruments and with the in-house database. The aldehydes were confirmed by using their pentafluorophenylhydrazone derivatives, and 2-ethyl-3,5-dimethyl pyrazine had to be resolved from co-eluting compounds and then identified by multidimensional GC hyphenated to an MS and a sniff port. In both shrimp products, the most important odorants were trimethylamine, 2-acetyl-1-pyrroline, and 2-ethyl-3,5-dimethyl pyrazine, together with common carbonyl compounds. PMID:19651413

Rochat, S; Egger, J; Chaintreau, A

2009-09-01

67

Arginine 26 and aspartic acid 69 of the regulatory subunit are key residues of subunits interaction of acetohydroxyacid synthase isozyme III from E. coli.  

PubMed

Acetohydroxyacid synthase (AHAS), which catalyzes the first step in the biosynthesis of branched-chain amino acids, is composed of catalytic and regulatory subunits. The enzyme exhibits full activity only when the regulatory subunit (RSU) binds to the catalytic subunit (CSU). However, the crystal structure of the holoenzyme has not been reported yet, and the molecular interaction between the CSU and RSU is also unknown. Herein, we introduced a global-surface, site-directed labeling scanning method to determine the potential interaction region of the RSU. This approach relies on the insertion of a bulky fluorescent probe at the designated site on the surface of the RSU to cause a dramatic change in holoenzyme activity by perturbing subunit interaction. Then, the key amino acid residues in the potential interaction regions were identified by site-directed mutagenesis. Compared to the wild-type, the single-point mutants R26A and D69A showed 54 and 64?% activity, respectively, whereas the double mutant (R26A+D69A) gave 14?%, thus suggesting that residues Arg26 and Asp69 are the key residues of subunit interaction with cooperative action. Additionally, the results of GST pull-down assays and pH-dependence experiments suggested that polar interaction is the main force for subunits interaction. A plausible protein-protein interaction model of the holoenzyme of Escherichia coli AHAS III is proposed, based on the mutagenesis and protein docking studies. The protocol established here should be useful for the identification of the molecular interactions between proteins. PMID:23047433

Zhao, Yuefang; Wen, Xin; Niu, Congwei; Xi, Zhen

2012-11-01

68

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

E-print Network

Factors Affecting Dairy Viability Profitability Solvency Liquidity Milk Production Breeding Practices General Management Measurement Interactions Elasticity Measurement Trends tjualitative Choice Model The Logistic Transformation Logit... 26 27 40 41 42 45 Vl Page V. PREDICTION MODELS 47 Production Performance Factors Financial Performance Factors Production and Financial Variables Model Discussion 47 54 60 60 Vl. SUMMARY AND CONCLUSIONS 64 REFERENCES 67 VITA 70...

Law, James Michael

2012-06-07

69

Identification of some key parameters limiting the performance of high-efficiency silicon solar cells  

NASA Technical Reports Server (NTRS)

This paper presents, for the first time, a detailed sensitivity analysis of key cell parameters on silicon-cell efficiency by incorporating advanced solar cell physics in a sophisticated numerical simulation program. It delineates the true physical barriers to obtaining a high-efficiency silicon solar cell. Specific parameters presently limiting cell efficiency are identified to be the minority carrier lifetime and the recombination velocities at the front and back surfaces. Practical cell efficiencies in the vicinity of 22 percent are estimated to be attainable by using good quality silicon crystal and substantially reducing surface recombination velocities.

Mokashi, Anant R.; Daud, Taher; Kachare, Ram H.

1986-01-01

70

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

71

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

PubMed

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

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

2009-07-01

72

Identification of Key Residues Determining Isomerohydrolase Activity of Human RPE65.  

PubMed

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

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

2014-09-26

73

Identification of key regulators for the migration and invasion of rheumatoid synoviocytes through a systems approach  

PubMed Central

Rheumatoid synoviocytes, which consist of fibroblast-like synoviocytes (FLSs) and synovial macrophages (SMs), are crucial for the progression of rheumatoid arthritis (RA). Particularly, FLSs of RA patients (RA-FLSs) exhibit invasive characteristics reminiscent of cancer cells, destroying cartilage and bone. RA-FLSs and SMs originate differently from mesenchymal and myeloid cells, respectively, but share many pathologic functions. However, the molecular signatures and biological networks representing the distinct and shared features of the two cell types are unknown. We performed global transcriptome profiling of FLSs and SMs obtained from RA and osteoarthritis patients. By comparing the transcriptomes, we identified distinct molecular signatures and cellular processes defining invasiveness of RA-FLSs and proinflammatory properties of RA-SMs, respectively. Interestingly, under the interleukin-1? (IL-1?)–stimulated condition, the RA-FLSs newly acquired proinflammatory signature dominant in RA-SMs without losing invasive properties. We next reconstructed a network model that delineates the shared, RA-FLS–dominant (invasive), and RA-SM–dominant (inflammatory) processes. From the network model, we selected 13 genes, including periostin, osteoblast-specific factor (POSTN) and twist basic helix–loop–helix transcription factor 1 (TWIST1), as key regulator candidates responsible for FLS invasiveness. Of note, POSTN and TWIST1 expressions were elevated in independent RA-FLSs and further instigated by IL-1?. Functional assays demonstrated the requirement of POSTN and TWIST1 for migration and invasion of RA-FLSs stimulated with IL-1?. Together, our systems approach to rheumatoid synovitis provides a basis for identifying key regulators responsible for pathological features of RA-FLSs and -SMs, demonstrating how a certain type of cells acquires functional redundancy under chronic inflammatory conditions. PMID:24374632

You, Sungyong; Yoo, Seung-Ah; Choi, Susanna; Kim, Ji-Young; Park, Su-Jung; Ji, Jong Dae; Kim, Tae-Hwan; Kim, Ki-Jo; Cho, Chul-Soo; Hwang, Daehee; Kim, Wan-Uk

2014-01-01

74

Identification of key regulators for the migration and invasion of rheumatoid synoviocytes through a systems approach.  

PubMed

Rheumatoid synoviocytes, which consist of fibroblast-like synoviocytes (FLSs) and synovial macrophages (SMs), are crucial for the progression of rheumatoid arthritis (RA). Particularly, FLSs of RA patients (RA-FLSs) exhibit invasive characteristics reminiscent of cancer cells, destroying cartilage and bone. RA-FLSs and SMs originate differently from mesenchymal and myeloid cells, respectively, but share many pathologic functions. However, the molecular signatures and biological networks representing the distinct and shared features of the two cell types are unknown. We performed global transcriptome profiling of FLSs and SMs obtained from RA and osteoarthritis patients. By comparing the transcriptomes, we identified distinct molecular signatures and cellular processes defining invasiveness of RA-FLSs and proinflammatory properties of RA-SMs, respectively. Interestingly, under the interleukin-1? (IL-1?)-stimulated condition, the RA-FLSs newly acquired proinflammatory signature dominant in RA-SMs without losing invasive properties. We next reconstructed a network model that delineates the shared, RA-FLS-dominant (invasive), and RA-SM-dominant (inflammatory) processes. From the network model, we selected 13 genes, including periostin, osteoblast-specific factor (POSTN) and twist basic helix-loop-helix transcription factor 1 (TWIST1), as key regulator candidates responsible for FLS invasiveness. Of note, POSTN and TWIST1 expressions were elevated in independent RA-FLSs and further instigated by IL-1?. Functional assays demonstrated the requirement of POSTN and TWIST1 for migration and invasion of RA-FLSs stimulated with IL-1?. Together, our systems approach to rheumatoid synovitis provides a basis for identifying key regulators responsible for pathological features of RA-FLSs and -SMs, demonstrating how a certain type of cells acquires functional redundancy under chronic inflammatory conditions. PMID:24374632

You, Sungyong; Yoo, Seung-Ah; Choi, Susanna; Kim, Ji-Young; Park, Su-Jung; Ji, Jong Dae; Kim, Tae-Hwan; Kim, Ki-Jo; Cho, Chul-Soo; Hwang, Daehee; Kim, Wan-Uk

2014-01-01

75

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

76

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

77

Proteomic identification network analysis of haptoglobin as a key regulator associated with liver fibrosis.  

PubMed

Liver fibrosis (LF) is the final stage of liver dysfunction, characterized by diffuse fibrosis which is the main response to the liver injury. Haptoglobin (HP) protein, produced as an acute phase reactant during LF, preventing liver damage, may be potential molecular targets for early LF diagnostics and therapeutic applications. However, protein networks associated with the HP are largely unknown. To address this issue, we used a pathological mouse model of LF that was induced by treatment with carbon tetrachloride for 8 days. HP protein was separated and identified by two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry. HP protein was subjected to functional pathway analysis using STRING and Cytoscape software for better understanding of the protein-protein interaction (PPI) networks in biological context. Bioinformatics analyses revealed that HP expression associated with fibrosis was upregulated, and suggested that HP responsible for fibrosis may precede the onset and progression of LF. Using the web-based database, functional pathway analysis suggested the modulation of multiple vital physiological pathways, including antioxidation immunity, signal transduction, metabolic process, energy production, cell apoptosis, oxidation reduction, DNA repair process, cell communication, and regulation of cellular process. The generation of protein interaction networks clearly enhances the interpretation and understanding of the molecular mechanisms of HP. HP protein represents targets for further experimental investigation that will provide biological insight and potentially could be exploited for novel therapeutic approaches to combat LF. PMID:23274719

Zhang, Aihua; Sun, Hui; Sun, Wejun; Ye, Yuan; Wang, Xijun

2013-02-01

78

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

PubMed

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

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

1998-05-01

79

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

PubMed

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

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

2012-05-22

80

Interactive software for model predictive control with simultaneous identification  

E-print Network

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

Echeverria Del Rio, Pablo

2012-06-07

81

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

82

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

83

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

84

Interactive Vector Field Feature Identification Joel Daniels II, Erik W. Anderson, Student Member, IEEE,  

E-print Network

Interactive Vector Field Feature Identification Joel Daniels II, Erik W. Anderson, Student Member) of desired feature types. These control points guide a mapping of the vector field points to the interactive of these attributes forms a representation of the vector field samples in the attribute space. We project

Utah, University of

85

Person Identification and Interaction of Social Robots by Using Wireless Tags  

E-print Network

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

Kanda, Takayuki

86

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

PubMed

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

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

2014-01-01

87

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

88

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

PubMed

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

89

Automated identification of social interaction criteria in Drosophila melanogaster.  

PubMed

The study of social behaviour within groups has relied on fixed definitions of an 'interaction'. Criteria used in these definitions often involve a subjectively defined cut-off value for proximity, orientation and time (e.g. courtship, aggression and social interaction networks) and the same numerical values for these criteria are applied to all of the treatment groups within an experiment. One universal definition of an interaction could misidentify interactions within groups that differ in life histories, study treatments and/or genetic mutations. Here, we present an automated method for determining the values of interaction criteria using a pre-defined rule set rather than pre-defined values. We use this approach and show changing social behaviours in different manipulations of Drosophila melanogaster. We also show that chemosensory cues are an important modality of social spacing and interaction. This method will allow a more robust analysis of the properties of interacting groups, while helping us understand how specific groups regulate their social interaction space. PMID:25354920

Schneider, J; Levine, J D

2014-10-01

90

Large-scale identification and analysis of suppressive drug interactions.  

PubMed

One drug may suppress the effects of another. Although knowledge of drug suppression is vital to avoid efficacy-reducing drug interactions or discover countermeasures for chemical toxins, drug-drug suppression relationships have not been systematically mapped. Here, we analyze the growth response of Saccharomyces cerevisiae to anti-fungal compound ("drug") pairs. Among 440 ordered drug pairs, we identified 94 suppressive drug interactions. Using only pairs not selected on the basis of their suppression behavior, we provide an estimate of the prevalence of suppressive interactions between anti-fungal compounds as 17%. Analysis of the drug suppression network suggested that Bromopyruvate is a frequently suppressive drug and Staurosporine is a frequently suppressed drug. We investigated potential explanations for suppressive drug interactions, including chemogenomic analysis, coaggregation, and pH effects, allowing us to explain the interaction tendencies of Bromopyruvate. PMID:24704506

Cokol, Murat; Weinstein, Zohar B; Yilancioglu, Kaan; Tasan, Murat; Doak, Allison; Cansever, Dilay; Mutlu, Beste; Li, Siyang; Rodriguez-Esteban, Raul; Akhmedov, Murodzhon; Guvenek, Aysegul; Cokol, Melike; Cetiner, Selim; Giaever, Guri; Iossifov, Ivan; Nislow, Corey; Shoichet, Brian; Roth, Frederick P

2014-04-24

91

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

92

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

93

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

ERIC Educational Resources Information Center

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

Kohut, Connie K.; And Others

1993-01-01

94

Identification of Novel Interacting Partners of Sirtuin6  

PubMed Central

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

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

2012-01-01

95

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

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

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

2014-06-01

96

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

ERIC Educational Resources Information Center

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

Paulin, Kenneth C.; Bittner, John R.

97

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

E-print Network

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

Tomkins, Andrew

98

Separation individuation of parents of adolescents: A “multiple identification” perspective of the parent-child interaction  

Microsoft Academic Search

In this paper we present the process the parent undergoes in relationship to his adolescent child from the perspective of a “multiple identification” model of the parent-child interaction. From this perspective the parent is seen to identify both with parental roles as transmitted to him by his parents and with his child and the needs and conflicts he is phase-appropriately

Rachel B. Blass; H. Shmuel Erlich

1993-01-01

99

Identification of global ferredoxin interaction networks in Chlamydomonas reinhardtii.  

PubMed

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

2013-12-01

100

Identification of histone 3 variant 2 interacting factors  

PubMed Central

The epigenome is defined as a type of information that can be transmitted independently of the DNA sequence, at the chromatin level, through post-translational modifications present on histone tails. Recent advances in the identification of histone 3 variants suggest a new model of information transmission through deposition of specific histone variants. To date, several non-centromeric histone 3 variants have been identified in mammals. Despite protein sequence similarity, specific deposition complexes have been characterized for both histone 3.1 (H3.1) and histone 3.3 (H3.3), whereas no deposition complex for histone 3.2 (H3.2) has been identified to date. Here, we identified human H3.2 partners by immunopurification of nuclear H3.2 complexes followed by mass spectrometry analysis. Further biochemical analyses highlighted two major complexes associated with H3.2, one containing chromatin associated factor-1 subunits and the other consisting of a subcomplex of mini chromosome maintenance helicases, together with Asf1. The purified complexes could associate with a DNA template in vitro. PMID:24393775

Latreille, Daniel; Bluy, Lisa; Benkirane, Monsef; Kiernan, Rosemary E.

2014-01-01

101

Connecting With The Biggest Loser: An Extended Model of Parasocial Interaction and Identification in Health-Related Reality TV Shows.  

PubMed

This study investigates audience responses to health-related reality TV shows in the setting of The Biggest Loser. It conceptualizes a model for audience members' parasocial interaction and identification with cast members and explores antecedents and outcomes of parasocial interaction and identification. Data analysis suggests the following direct relationships: (1) audience members' exposure to the show is positively associated with parasocial interaction, which in turn is positively associated with identification, (2) parasocial interaction is positively associated with exercise self-efficacy, whereas identification is negatively associated with exercise self-efficacy, and (3) exercise self-efficacy is positively associated with exercise behavior. Indirect effects of parasocial interaction and identification on exercise self-efficacy and exercise behavior are also significant. We discuss the theoretical and practical implications of these findings. PMID:24579692

Tian, Yan; Yoo, Jina H

2015-01-01

102

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

PubMed

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

103

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

PubMed Central

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

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

2013-01-01

104

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

105

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

106

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

PubMed

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

Wibowo, Tri Chandra S; Saad, Nordin

2010-07-01

107

Identification of a Potent Combination of Key Plasmodium falciparum Merozoite Antigens That Elicit Strain-Transcending Parasite-Neutralizing Antibodies  

PubMed Central

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

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

2013-01-01

108

Timing and abundance as key mechanisms affecting trophic interactions in variable environments  

Microsoft Academic Search

Climatic changes are disrupting otherwise tight trophic interactions between predator and prey. Most of the earlier studies have primarily focused on the temporal dimension of the relationship in the framework of the match-mismatch hypothesis. This hypothesis predicts that predator's recruitment will be high if the peak of the prey availability temporally matches the most energy-demanding period of the predators breeding

Joel M. Durant; Dag O. Hjermann; Tycho Anker-Nilssen; Gregory Beaugrand; Atle Mysterud; Nathalie Pettorelli; Nils Chr. Stenseth

2005-01-01

109

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

110

Identification of Minimally Interacting Modules in an Intrinsically Disordered Protein  

PubMed Central

The conformational characterization of intrinsically disordered proteins (IDPs) is complicated by their conformational heterogeneity and flexibility. If an IDP could somehow be divided into smaller fragments and reconstructed later, theoretical and spectroscopic studies could probe its conformational variability in detail. Here, we used replica molecular-dynamics simulations and network theory to explore whether such a divide-and-conquer strategy is feasible for ?-synuclein, a prototypical IDP. We characterized the conformational variability of ?-synuclein by conducting >100 unbiased all-atom molecular-dynamics simulations, for a total of >10 ?s of trajectories. In these simulations, ?-synuclein formed a heterogeneous ensemble of collapsed coil states in an aqueous environment. These states were stabilized by heterogeneous contacts between sequentially distant regions. We find that ?-synuclein contains residual secondary structures in the collapsed states, and the heterogeneity in the collapsed state makes it feasible to split ?-synuclein into sequentially contiguous minimally interacting fragments. This study reveals previously unknown characteristics of ?-synuclein and provides a new (to our knowledge) approach for studying other IDPs. PMID:22947936

Sethi, Anurag; Tian, Jianhui; Vu, Dung M.; Gnanakaran, S.

2012-01-01

111

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

112

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

PubMed Central

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

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

2010-01-01

113

Electric utility/advocacy group interaction: A case history report on the key outcomes of DSM/IRP interactive efforts and related advocacy group activities  

SciTech Connect

This article presents the findings derived from ten case studies of activities undertaken by energy efficiency advocacy groups (EEAGs) to influence the use of cost-effective Demand-Side Management (DSM) by electric utilities and to promote Integrated Resource Planning (IRP). Nine of these ten cases included some form of interactive effort involving utilities and, in almost all cases, other nonutility parties (NUPs) as well. All ten cases also included other EEAG activities. Key findings of the study include the following: interactive efforts had substantially greater effects on utility DSM usage and on relations among the involved parties than on regulatory policy; other EEAG activities had the great effect on regulatory policy and the least direct effect on utility DSM usage; and the discernible overall effects of interactive efforts were somewhat greater than those of the EEAGs' other activities, which often had less tangible and immediate effects.

Schweitzer, M. (Oak Ridge National Lab., TN (United States)); English, M.; Schexnayder, S. (Univ. of Tennessee, Knoxville, TN (United States). Energy, Environment and Resources Center); Altman, J.

1995-01-01

114

Understanding Schwann cell–neurone interactions: the key to Charcot–Marie–Tooth disease?*  

PubMed Central

Charcot–Marie–Tooth disease (CMT) comprises a heterogeneous group of disorders. The most frequent subtype is caused by increased PMP22 gene dosage or missense point mutations affecting the PMP22 gene (CMT type 1A; CMT1A). Animal models in rat and mouse with the corresponding PMP22 alterations are available and mimic many aspects of the human diseases. Detailed examinations of the animal mutants, together with complementary data from patients, point towards altered Schwann cell–neurone interactions as a major underlying mechanism of CMT1A and related hereditary neuropathies. This is evident from the finding that mutated proteins affecting either Schwann cells or neurones have a profound influence on their partner cells. Recently, a number of novel genes causing various forms of CMT have been identified which are expressed either mainly by Schwann cells and/or by the accompanying neurones. These genes can be viewed, in analogy to classic experiments routinely performed in lower vertebrates, as the result of a ‘functional screen’ revealing crucial players in the interactions between Schwann cells and neurones. Studying how Schwann cell and axon-encoded proteins are functionally interconnected will be an exciting task for the future. It will not only yield insights into the molecular and cellular basis of neuropathies but also provide crucial information about the interplay between Schwann cells and neurones in general. PMID:12090402

Maier, Marcel; Berger, Philipp; Suter, Ueli

2002-01-01

115

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

116

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

E-print Network

of the most coactivator proteins is an -LXXLL motif, where -L- is leucine and -X- is any amino acid (Heery D.M. et al. 1997). The -LXXLL- motif is responsible for the interaction of coactivator proteins with the AF-2 domain of NRs, therefore it is also... broadly classified into two types: (1) those involved in chromatin remodeling, and (2) those that directly bind to NRs, transcriptional machinery, and mRNA splicing factors serving as adaptor proteins. The identification of coactivator...

Zhang, Hongsheng

2008-01-01

117

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

PubMed

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

Hofmann, Thomas

2009-07-01

118

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

119

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

120

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

NASA Astrophysics Data System (ADS)

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

Roehner, Bertrand M.

2005-03-01

121

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. Biotechnol. Bioeng. 2014;111: 2082-2094. © 2014 Wiley Periodicals, Inc. 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

122

A Proposal of a Methodology for the Analysis of Robot-Environment Interaction through System Identification  

Microsoft Academic Search

Abstract—This paper,presents,a novel method,to analyse robot-environment interaction from mathematical,point of view in order,to understand,and,identify the,underlying,rules governing,this interaction. The method,finds its theoretical roots in robot training, system identification and dynamical systems theory. The method,is based,on identifying the whole,system,using two models,— i) the controller model,which,describes how,the actions of the robot are related to its own,perception,and,ii) the perception,model,which,describes,how,the perception,of the robot changes,as a

Ulrich Nehmzow; Steve Billings

123

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

PubMed

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

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

2013-07-01

124

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; Sanchez-Navarro, Jesus; Fagoaga, Carmen; Lopez, Carmelo; Navarro, Luis; Moreno, Pedro; Pena, Leandro

2013-01-01

125

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

126

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

127

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

PubMed Central

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

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

2014-01-01

128

The Odonata (Insecta) of Patagonia: a synopsis of their current status with illustrated keys for their identification.  

PubMed

Patagonia is a vast landmass with a distinctive environmental and biotic heterogeneity. Its Odonata biodiversity is the best known of South America, and it is composed of 36 species, of which more than 50% are endemic. We summarize the main taxonomic, distributional and biological information including illustrated keys for adults and known larvae, and distributional maps. PMID:24872061

Muzón, Javier; Pessacq, Pablo; Lozano, Federico

2014-01-01

129

Site identification in high-throughput RNA–protein interaction data  

PubMed Central

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

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

2012-01-01

130

Chemical Profiles and Identification of Key Compound Caffeine in Marine-Derived Traditional Chinese Medicine Ostreae concha  

PubMed Central

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

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

2012-01-01

131

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

PubMed

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

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

2014-01-01

132

CH3-? Interaction of Explosives with Cavity of a TPE Macrocycle: The Key Cause for Highly Selective Detection of TNT.  

PubMed

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

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

2014-11-26

133

Bcl-2 is a novel interacting partner for the 2-oxoglutarate carrier and a key regulator of mitochondrial glutathione  

PubMed Central

Despite making up only a minor fraction of the total cellular glutathione, recent studies indicate that the mitochondrial glutathione pool is essential for cell survival. Selective depletion of mitochondrial glutathione is sufficient to sensitize cells to mitochondrial oxidative stress (MOS)1 and intrinsic apoptosis. Glutathione is synthesized exclusively in the cytoplasm and must be actively transported into mitochondria. Therefore, regulation of mitochondrial glutathione transport is a key factor in maintaining the antioxidant status of mitochondria. Bcl-2 is resident in the outer mitochondrial membrane where it acts as a central regulator of the intrinsic apoptotic cascade. In addition, Bcl-2 displays an antioxidant-like function that has been linked experimentally to the regulation of cellular glutathione content. We have previously demonstrated a novel interaction between recombinant Bcl-2 and reduced glutathione (GSH) which was antagonized by either Bcl-2 homology-3 domain (BH3) mimetics or a BH3-only protein, recombinant Bim. These previous findings prompted us to investigate if this novel Bcl-2/GSH interaction might play a role in regulating mitochondrial glutathione transport. Incubation of primary cultures of cerebellar granule neurons (CGNs) with the BH3 mimetic, HA14-1, induced MOS and caused specific depletion of the mitochondrial glutathione pool. Bcl-2 was co-immunoprecipitated with GSH following chemical cross-linking in CGNs and this Bcl-2/GSH interaction was antagonized by pre-incubation with HA14-1. Moreover, both HA14-1 and recombinant Bim inhibited GSH transport into isolated rat brain mitochondria. To further investigate a possible link between Bcl-2 function and mitochondrial glutathione transport, we next examined if Bcl-2 associated with the 2-oxoglutarate carrier (OGC), an inner mitochondrial membrane protein known to transport glutathione in liver and kidney. Following co-transfection of CHO cells, Bcl-2 was co-immunoprecipitated with OGC and this novel interaction was significantly enhanced by glutathione monoethylester (GSH-MEE). Similarly, recombinant Bcl-2 interacted with recombinant OGC in the presence of GSH. Bcl-2 and OGC co-transfection in CHO cells significantly increased the mitochondrial glutathione pool. Finally, the ability of Bcl-2 to protect CHO cells from apoptosis induced by hydrogen peroxide was significantly attenuated by the OGC inhibitor phenylsuccinate. These data suggest that GSH binding by Bcl-2 enhances its affinity for the OGC. Bcl-2 and OGC appear to act in a coordinated manner to increase the mitochondrial glutathione pool and enhance resistance of cells to oxidative stress. We conclude that regulation of mitochondrial glutathione transport is a principal mechanism by which Bcl-2 suppresses MOS. PMID:22115789

Wilkins, Heather M.; Marquardt, Kristin; Lash, Lawrence H.; Linseman, Daniel A.

2011-01-01

134

Bcl-2 is a novel interacting partner for the 2-oxoglutarate carrier and a key regulator of mitochondrial glutathione.  

PubMed

Despite making up only a minor fraction of the total cellular glutathione, recent studies indicate that the mitochondrial glutathione pool is essential for cell survival. Selective depletion of mitochondrial glutathione is sufficient to sensitize cells to mitochondrial oxidative stress (MOS) and intrinsic apoptosis. Glutathione is synthesized exclusively in the cytoplasm and must be actively transported into mitochondria. Therefore, regulation of mitochondrial glutathione transport is a key factor in maintaining the antioxidant status of mitochondria. Bcl-2 resides in the outer mitochondrial membrane where it acts as a central regulator of the intrinsic apoptotic cascade. In addition, Bcl-2 displays an antioxidant-like function that has been linked experimentally to the regulation of cellular glutathione content. We have previously demonstrated a novel interaction between recombinant Bcl-2 and reduced glutathione (GSH), which was antagonized by either Bcl-2 homology-3 domain (BH3) mimetics or a BH3-only protein, recombinant Bim. These previous findings prompted us to investigate if this novel Bcl-2/GSH interaction might play a role in regulating mitochondrial glutathione transport. Incubation of primary cultures of cerebellar granule neurons (CGNs) with the BH3 mimetic HA14-1 induced MOS and caused specific depletion of the mitochondrial glutathione pool. Bcl-2 was coimmunoprecipitated with GSH after chemical cross-linking in CGNs and this Bcl-2/GSH interaction was antagonized by preincubation with HA14-1. Moreover, both HA14-1 and recombinant Bim inhibited GSH transport into isolated rat brain mitochondria. To further investigate a possible link between Bcl-2 function and mitochondrial glutathione transport, we next examined if Bcl-2 associated with the 2-oxoglutarate carrier (OGC), an inner mitochondrial membrane protein known to transport glutathione in liver and kidney. After cotransfection of CHO cells, Bcl-2 was coimmunoprecipitated with OGC and this novel interaction was significantly enhanced by glutathione monoethyl ester. Similarly, recombinant Bcl-2 interacted with recombinant OGC in the presence of GSH. Bcl-2 and OGC cotransfection in CHO cells significantly increased the mitochondrial glutathione pool. Finally, the ability of Bcl-2 to protect CHO cells from apoptosis induced by hydrogen peroxide was significantly attenuated by the OGC inhibitor phenylsuccinate. These data suggest that GSH binding by Bcl-2 enhances its affinity for the OGC. Bcl-2 and OGC appear to act in a coordinated manner to increase the mitochondrial glutathione pool and enhance resistance of cells to oxidative stress. We conclude that regulation of mitochondrial glutathione transport is a principal mechanism by which Bcl-2 suppresses MOS. PMID:22115789

Wilkins, Heather M; Marquardt, Kristin; Lash, Lawrence H; Linseman, Daniel A

2012-01-15

135

Promyelocytic leukemia zinc-finger induction signs mesenchymal stem cell commitment: identification of a key marker for stemness maintenance?  

PubMed Central

Introduction Mesenchymal stem cells (MSCs) are an attractive cell source for cartilage and bone tissue engineering given their ability to differentiate into chondrocytes and osteoblasts. However, the common origin of these two specialized cell types raised the question about the identification of regulatory pathways determining the differentiation fate of MSCs into chondrocyte or osteoblast. Methods Chondrogenesis, osteoblastogenesis, and adipogenesis of human and mouse MSC were induced by using specific inductive culture conditions. Expression of promyelocytic leukemia zinc-finger (PLZF) or differentiation markers in MSCs was determined by RT-qPCR. PLZF-expressing MSC were implanted in a mouse osteochondral defect model and the neotissue was analyzed by routine histology and microcomputed tomography. Results We found out that PLZF is not expressed in MSCs and its expression at early stages of MSC differentiation is the mark of their commitment toward the three main lineages. PLZF acts as an upstream regulator of both Sox9 and Runx2, and its overexpression in MSC enhances chondrogenesis and osteogenesis while it inhibits adipogenesis. In vivo, implantation of PLZF-expressing MSC in mice with full-thickness osteochondral defects resulted in the formation of a reparative tissue resembling cartilage and bone. Conclusions Our findings demonstrate that absence of PLZF is required for stemness maintenance and its expression is an early event at the onset of MSC commitment during the differentiation processes of the three main lineages. PMID:24564963

2014-01-01

136

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

Microsoft Academic Search

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

Annika Brock; Thomas Hofmann

2008-01-01

137

[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

138

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

139

Identification of novel protein-protein interactions using a versatile mammalian tandem affinity purification expression system.  

PubMed

Identification of protein-protein interactions is essential for elucidating the biochemical mechanism of signal transduction. Purification and identification of individual proteins in mammalian cells have been difficult, however, due to the sheer complexity of protein mixtures obtained from cellular extracts. Recently, a tandem affinity purification (TAP) method has been developed as a tool that allows rapid purification of native protein complexes expressed at their natural level in engineered yeast cells. To adapt this method to mammalian cells, we have created a TAP tag retroviral expression vector to allow stable expression of the TAP-tagged protein at close to physiological levels. To demonstrate the utility of this vector, we have fused a TAP tag, consisting of a protein A tag, a cleavage site for the tobacco etch virus (TEV) protease, and the FLAG epitope, to the N terminus of human SMAD3 and SMAD4. We have stably expressed these proteins in mammalian cells at desirable levels by retroviral gene transfer and purified native SMAD3 protein complexes from cell lysates. The combination of two different affinity tags greatly reduced the number of nonspecific proteins in the mixture. We have identified HSP70 as a specific interacting protein of SMAD3. We demonstrated that SMAD3, but not SMAD1, binds HSP70 in vivo, validating the TAP purification approach. This method is applicable to virtually any protein and provides an efficient way to purify unknown proteins to homogeneity from the complex mixtures found in mammalian cell lysates in preparation for identification by mass spectrometry. PMID:12963786

Knuesel, Matthew; Wan, Yong; Xiao, Zhan; Holinger, Eric; Lowe, Nick; Wang, Wei; Liu, Xuedong

2003-11-01

140

Identification of Human Disease Genes from Interactome Network Using Graphlet Interaction  

PubMed Central

Identifying genes related to human diseases, such as cancer and cardiovascular disease, etc., is an important task in biomedical research because of its applications in disease diagnosis and treatment. Interactome networks, especially protein-protein interaction networks, had been used to disease genes identification based on the hypothesis that strong candidate genes tend to closely relate to each other in some kinds of measure on the network. We proposed a new measure to analyze the relationship between network nodes which was called graphlet interaction. The graphlet interaction contained 28 different isomers. The results showed that the numbers of the graphlet interaction isomers between disease genes in interactome networks were significantly larger than random picked genes, while graphlet signatures were not. Then, we designed a new type of score, based on the network properties, to identify disease genes using graphlet interaction. The genes with higher scores were more likely to be disease genes, and all candidate genes were ranked according to their scores. Then the approach was evaluated by leave-one-out cross-validation. The precision of the current approach achieved 90% at about 10% recall, which was apparently higher than the previous three predominant algorithms, random walk, Endeavour and neighborhood based method. Finally, the approach was applied to predict new disease genes related to 4 common diseases, most of which were identified by other independent experimental researches. In conclusion, we demonstrate that the graphlet interaction is an effective tool to analyze the network properties of disease genes, and the scores calculated by graphlet interaction is more precise in identifying disease genes. PMID:24465923

Yang, Lun; Wei, Dong-Qing; Qi, Ying-Xin; Jiang, Zong-Lai

2014-01-01

141

Revalidation and redescription of Triatoma brasiliensis macromelasoma Galv?o, 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, Nathalia Cordeiro; Neiva, Vanessa Lima; Goncalves, Teresa Cristina Monte; Felix, Marcio

2013-01-01

142

The identification of tyrosine as a common key residue in unrelated H-2Kd restricted antigenic peptides.  

PubMed

We have compared the activity of several Kd- or Ld-restricted antigenic peptides as competitors in a functional competition assay using cytolytic T lymphocyte (CTL) clones. All of four unrelated Kd-restricted peptides tested could compete with each other but not with the Ld-restricted peptide P91A-. 12-24 (P91A). Moreover, the P91A peptide failed to compete with the four Kd-restricted peptides. In contrast, another Ld-restricted peptide [mouse cytomegalovirus (MCMV) pp89 167-176] could clearly compete with both Kd- and Ld-restricted peptides. The comparison of a series of modified MCMV pp89 peptides suggested that distinct structural features allow the interaction of the peptide with the two different MHC class I molecules. We showed previously that the competitor activity of two different Kd-restricted antigenic peptides was reduced substantially upon Ala substitution of the single Tyr residues present in these peptides. We now show a similar effect for two additional Kd-restricted peptides. Our results thus suggest that Tyr may function as an 'anchor' residue for many antigenic peptides that bind to the Kd molecule. Molecular modeling of the presumed antigen-binding site of the Kd molecule revealed the presence of two deep cavities that may be involved in binding peptide amino acid side chains. A model illustrating one possible interaction of a Tyr-containing peptide with the Kd molecule is presented. PMID:1721832

Maryanski, J L; Romero, P; Van Pel, A; Boon, T; Salemme, F R; Cerottini, J C; Corradin, G

1991-10-01

143

Identification of Key Hinge Residues Important for Nucleotide-Dependent Allostery in E. coli Hsp70/DnaK  

PubMed Central

DnaK is a molecular chaperone that has important roles in protein folding. The hydrolysis of ATP is essential to this activity, and the effects of nucleotides on the structure and function of DnaK have been extensively studied. However, the key residues that govern the conformational motions that define the apo, ATP-bound, and ADP-bound states are not entirely clear. Here, we used molecular dynamics simulations, mutagenesis, and enzymatic assays to explore the molecular basis of this process. Simulations of DnaK's nucleotide-binding domain (NBD) in the apo, ATP-bound, and ADP/Pi-bound states suggested that each state has a distinct conformation, consistent with available biochemical and structural information. The simulations further suggested that large shearing motions between subdomains I-A and II-A dominated the conversion between these conformations. We found that several evolutionally conserved residues, especially G228 and G229, appeared to function as a hinge for these motions, because they predominantly populated two distinct states depending on whether ATP or ADP/Pi was bound. Consistent with the importance of these “hinge” residues, alanine point mutations caused DnaK to have reduced chaperone activities in vitro and in vivo. Together, these results clarify how sub-domain motions communicate allostery in DnaK. PMID:24277995

Ung, Peter Man-Un; Thompson, Andrea D.; Chang, Lyra; Gestwicki, Jason E.; Carlson, Heather A.

2013-01-01

144

Identification of key performance indicators for on-farm animal welfare incidents: possible tools for early warning and prevention  

PubMed Central

Background The objective of this study was to describe aspects of case study herds investigated by the Department of Agriculture, Fisheries and Food (DAFF) in which animal welfare incidents occurred and to identify key performance indicators (KPIs) that can be monitored to enhance the Early Warning System (EWS). Despite an EWS being in place for a number of years, animal welfare incidents continue to occur. Questionnaires regarding welfare incidents were sent to Superintending Veterinary Inspectors (SVIs), resulting in 18 herds being chosen as case study herds, 12 of which had a clearly defined welfare incident date. For each study herd, data on six potential KPIs were extracted from DAFF databases. The KPIs for those herds with a clearly defined welfare incident date were studied for a consecutive four year window, with the fourth year being the 'incident year', when the welfare incident was disclosed. For study herds without a clearly defined welfare incident date, the KPIs were determined on a yearly basis between 2001 and 2009. Results We found that the late registration of calves, the use of on-farm burial as a method of carcase disposal, an increasing number of moves to knackeries over time and records of animals moved to 'herd unknown' were notable on the case farms. Conclusion Four KPIs were prominent on the case study farms and warrant further investigation in control herds to determine their potential to provide a framework for refining current systems of early warning and prevention. PMID:21982340

2011-01-01

145

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

146

Identification and Functional Analysis of Delta-9 Desaturase, a Key Enzyme in PUFA Synthesis, Isolated from the Oleaginous Diatom Fistulifera  

PubMed Central

Oleaginous microalgae are one of the promising resource of nonedible biodiesel fuel (BDF) feed stock alternatives. Now a challenge task is the decrease of the long-chain polyunsaturated fatty acids (PUFAs) content affecting on the BDF oxidative stability by using gene manipulation techniques. However, only the limited knowledge has been available concerning the fatty acid and PUFA synthesis pathways in microalgae. Especially, the function of ?9 desaturase, which is a key enzyme in PUFA synthesis pathway, has not been determined in diatom. In this study, 4 ?9 desaturase genes (fD9desA, fD9desB, fD9desC and fD9desD) from the oleaginous diatom Fistulifera were newly isolated and functionally characterized. The putative ?9 acyl-CoA desaturases in the endoplasmic reticulum (ER) showed 3 histidine clusters that are well-conserved motifs in the typical ?9 desaturase. Furthermore, the function of these ?9 desaturases was confirmed in the Saccharomyces cerevisiae ole1 gene deletion mutant (?ole1). All the putative ?9 acyl-CoA desaturases showed ?9 desaturation activity for C16?0 fatty acids; fD9desA and fD9desB also showed desaturation activity for C18?0 fatty acids. This study represents the first functional analysis of ?9 desaturases from oleaginous microalgae and from diatoms as the first enzyme to introduce a double bond in saturated fatty acids during PUFA synthesis. The findings will provide beneficial insights into applying metabolic engineering processes to suppressing PUFA synthesis in this oleaginous microalgal strain. PMID:24039966

Muto, Masaki; Kubota, Chihiro; Tanaka, Masayoshi; Satoh, Akira; Matsumoto, Mitsufumi; Yoshino, Tomoko; Tanaka, Tsuyoshi

2013-01-01

147

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

PubMed

Today, herb medicines have become the major source for discovery of novel agents in countermining diseases. However, many of them are largely under-explored in pharmacology due to the limitation of current experimental approaches. Therefore, we proposed a computational framework in this study for network understanding of herb pharmacology via rapid identification of putative ingredient-target interactions in human structural proteome level. A marketing anti-cancer herb medicine in China, Yadanzi (Brucea javanica), was chosen for mechanistic study. Total 7,119 ingredient-target interactions were identified for thirteen Yadanzi active ingredients. Among them, about 29.5% were estimated to have better binding affinity than their corresponding marketing drug-target interactions. Further Bioinformatics analyses suggest that simultaneous manipulation of multiple proteins in the MAPK signaling pathway and the phosphorylation process of anti-apoptosis may largely answer for Yadanzi against non-small cell lung cancers. In summary, our strategy provides an efficient however economic solution for systematic understanding of herbs' power. PMID:24429698

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

2014-01-01

148

Identification of gene-environment interactions in cancer studies using penalization  

PubMed Central

High-throughput cancer studies have been extensively conducted, searching for genetic markers associated with outcomes beyond clinical and environmental risk factors. Gene–environment interactions can have important implications beyond main effects. The commonly-adopted single-marker analysis cannot accommodate the joint effects of a large number of markers. The existing joint-effects methods also have limitations. Specifically, they may suffer from high computational cost, do not respect the “main effect, interaction” hierarchical structure, or use ineffective techniques. We develop a penalization method for the identification of important G × E interactions and main effects. It has an intuitive formulation, respects the hierarchical structure, accommodates the joint effects of multiple markers, and is computationally affordable. In numerical study, we analyze prognosis data under the AFT (accelerated failure time) model. Simulation shows satisfactory performance of the proposed method. Analysis of an NHL (non-Hodgkin lymphoma) study with SNP measurements shows that the proposed method identifies markers with important implications and satisfactory prediction performance. PMID:23994599

Liu, Jin; Huang, Jian; Zhang, Yawei; Lan, Qing; Rothman, Nathaniel; Zheng, Tongzhang; Ma, Shuangge

2013-01-01

149

Screening and identification of DnaJ interaction proteins in Streptococcus pneumoniae.  

PubMed

Streptococcus pneumoniae DnaJ is recognized as a virulence factor whose role in pneumococcal virulence remains unclear. Here, we attempted to reveal the contribution of DnaJ in pneumococcal virulence from the identification of its interacting proteins using co-immunoprecipitation method. dnaJ was cloned into plasmid pAE03 generating pAE03-dnaJ-gfp which was used to transform S. pneumoniae D39 strain. Then anti-GFP coated beads were used to capture GFP-coupled proteins from the bacterial lysate. The resulting protein mixtures were subjected to SDS-PAGE and those differential bands were determined by matrix-assisted laser desorption/ionization time of flight mass spectrometry. We finally obtained nine proteins such as DnaK, Gap, Eno, SpxB using this method. Furthermore, to confirm the interaction between DnaJ and these candidates, bacterial two-hybrid system was employed to reveal, for example, the interaction between DnaJ and DnaK, Eno, SpxB. Further protein expression experiments suggested that DnaJ prevented denaturation of Eno and SpxB at high temperature. These results help to understand the role of DnaJ in the pathogenesis of S. pneumoniae. PMID:23907491

Cai, YingYing; Yan, WenJuan; Xu, WenChun; Yin, YiBing; He, YuJuan; Wang, Hong; Zhang, XueMei

2013-12-01

150

Identification and prediction of dynamic systems using an interactively recurrent self-evolving fuzzy neural network.  

PubMed

This paper presents a novel recurrent fuzzy neural network, called an interactively recurrent self-evolving fuzzy neural network (IRSFNN), for prediction and identification of dynamic systems. The recurrent structure in an IRSFNN is formed as an external loops and internal feedback by feeding the rule firing strength of each rule to others rules and itself. The consequent part in the IRSFNN is composed of a Takagi-Sugeno-Kang (TSK) or functional-link-based type. The proposed IRSFNN employs a functional link neural network (FLNN) to the consequent part of fuzzy rules for promoting the mapping ability. Unlike a TSK-type fuzzy neural network, the FLNN in the consequent part is a nonlinear function of input variables. An IRSFNNs learning starts with an empty rule base and all of the rules are generated and learned online through a simultaneous structure and parameter learning. An on-line clustering algorithm is effective in generating fuzzy rules. The consequent update parameters are derived by a variable-dimensional Kalman filter algorithm. The premise and recurrent parameters are learned through a gradient descent algorithm. We test the IRSFNN for the prediction and identification of dynamic plants and compare it to other well-known recurrent FNNs. The proposed model obtains enhanced performance results. PMID:24808284

Lin, Yang-Yin; Chang, Jyh-Yeong; Lin, Chin-Teng

2013-02-01

151

The Mitochondrial Phosphate Carrier Interacts with Cyclophilin D and May Play a Key Role in the Permeability Transition*S?  

PubMed Central

The mitochondrial permeability transition pore (MPTP) plays a key role in cell death, yet its molecular identity remains uncertain. Although knock-out studies have confirmed critical roles for both cyclophilin-D (CyP-D) and the adenine nucleotide translocase (ANT), given a strong enough stimulus MPTP opening can occur in the absence of either. Here we provide evidence that the mitochondrial phosphate carrier (PiC) may also be a critical component of the MPTP. Phenylarsine oxide (PAO) was found to activate MPTP opening in the presence of carboxyatractyloside (CAT) that prevents ANT binding to immobilized PAO. Only four proteins from solubilized CAT-treated beef heart inner mitochondrial membranes bound to immobilized PAO, one of which was the PiC. GST-CyP-D pull-down and co-immunoprecipitation studies revealed CsA-sensitive binding of PiC to CyP-D; this increased following diamide treatment. Co-immunoprecipitation of the ANT with the PiC was also observed but was insensitive to CsA treatment. N-ethylmaleimide and ubiquinone analogues (UQ0 and Ro 68-3400) inhibited phosphate transport into rat liver mitochondria with the same concentration dependence as their inhibition of MPTP opening. UQ0 and Ro 68-3400 also induced the “m” conformation of the ANT, as does NEM, and reduced the binding of both the PiC and ANT to the PAO column. We propose a model for the MPTP in which a calcium-triggered conformational change of the PiC, facilitated by CyP-D, induces pore opening. An interaction of the PiC with the ANT may enable agents that bind to either transporter to modulate pore opening. PMID:18667415

Leung, Anna W. C.; Varanyuwatana, Pinadda; Halestrap, Andrew P.

2008-01-01

152

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

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

153

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

154

??????-?????????????????? 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

155

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

156

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

157

1 | P a g e Summary of Fish-Barge Interaction Research and Fixed Dual Frequency Identification Sonar  

E-print Network

experiments to assess the potential impacts of barge tows traversing the electric dispersal barrier system of barge tows traversing the electric dispersal barrier system in the Chicago Sanitary and Ship Canal (CSSC1 | P a g e Summary of Fish-Barge Interaction Research and Fixed Dual Frequency Identification

US Army Corps of Engineers

158

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

ERIC Educational Resources Information Center

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…

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

2011-01-01

159

Application of chemometrically processed thermogravimetric data for identification of baclofen-excipient interactions.  

PubMed

Studies are constantly being conducted on the elaboration of efficient methods to confirm the compatibility of active pharmaceutical ingredients (APIs) and excipients, since medicinal products, apart from their APIs, also contain numerous excipients that not only have important functions in pharmaceutical preparations but can also initiate or participate in interactions with drug substances, which eventually lead to a decline in drug quality. With this in mind, research was undertaken to evaluate two of the most often applied pattern recognition methods, hierarchical cluster analysis (HCA) and principal component analysis (PCA), as supporting techniques in the identification of potential physicochemical interactions that may occur during the preformulation of solid dosage forms. The investigation performed with the use of baclofen and selected excipients has shown that with thermogravimetric analysis, HCA and PCA fulfill their role as supporting techniques in the interpretation of the data obtained. Based on these methods, it is possible to detect incompatibilities between baclofen and excipients, and the data obtained concur strongly with the results of differential scanning calorimetry and IR spectrometry analyses. PMID:22816258

Wesolowski, Marek; Rojek, Barbara; Piotrowska, Joanna

2012-01-01

160

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

161

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

162

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

PubMed

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

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

2014-01-22

163

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

NASA Astrophysics Data System (ADS)

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

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

2014-03-01

164

Description of the third instar of Hygrobia nigra (Clark, 1862) Coleoptera: Paelobiidae), with a key for the identification of mature larvae of Hygrobia Latreille, 1804 and phylogenetic analysis.  

PubMed

The mature larva of the squeak beetle Hygrobia nigra (Clark, 1862) (Paelobiidae) is studied for the first time based on detailed descriptions and illustrations of selected structures, with special emphasis on morphometry and chaetotaxy. A key for the identification of mature larvae of four of the six species of Hygrobia Latreille, 1804 known worldwide is presented. The phylogenetic relationships of the species are analyzed based on a cladistic analysis of a combined data set including larval and adult characters. Hygrobia nigra shares with the other known species of the genus several larval apomorphies including the presence of paramedian lip-like lobes on the epipharynx, a well-developed gula, gills on thoracic and first three abdominal sterna, and the maxillary stipites inserted into submental pouches, and is unique in the presence of a larger number of secondary setae on the metacoxa. The presence of a compact group of minute sensilla in the place where the galea is commonly located suggests that members of Hygrobia lost the galea, a condition independently evolved in some dytiscid lineages. The Australian species form a well-supported clade characterized by the presence of a short nasale, fewer natatory setae on the metatibia, and a marked shortening of the antennal sensorial appendage and the last abdominal segment. However, no larval characters were discovered to resolve relationships within that clade. The Palearctic H. hermanni (Fabricius, 1775) lacks a distinct nasale and is resolved as sister to the clade formed by the Australian species.  PMID:25081162

Michat, Mariano C; Alarie, Yves; Hendrich, Lars

2014-01-01

165

Transcriptional interactions during smallpox infection and identification of early infection biomarkers.  

PubMed

Smallpox is a deadly disease that can be intentionally reintroduced into the human population as a bioweapon. While host gene expression microarray profiling can be used to detect infection, the analysis of this information using unsupervised and supervised classification techniques can produce contradictory results. Here, we present a novel computational approach to incorporate molecular genome annotation features that are key for identifying early infection biomarkers (EIB). Our analysis identified 58 EIBs expressed in peripheral blood mononuclear cells (PBMCs) collected from 21 cynomolgus macaques (Macaca fascicularis) infected with two variola strains via aerosol and intravenous exposure. The level of expression of these EIBs was correlated with disease progression and severity. No overlap between the EIBs co-expression and protein interaction data reported in public databases was found. This suggests that a pathogen-specific re-organization of the gene expression and protein interaction networks occurs during infection. To identify potential genome-wide protein interactions between variola and humans, we performed a protein domain analysis of all smallpox and human proteins. We found that only 55 of the 161 protein domains in smallpox are also present in the human genome. These co-occurring domains are mostly represented in proteins involved in blood coagulation, complement activation, angiogenesis, inflammation, and hormone transport. Several of these proteins are within the EIBs category and suggest potential new targets for the development of therapeutic countermeasures. PMID:17992748

Valdivia-Granda, Willy A; Kann, Maricel G; Malaga, Jose

2007-01-01

166

Effective Identification of Akt Interacting Proteins by Two-Step Chemical Crosslinking, Co-Immunoprecipitation and Mass Spectrometry  

PubMed Central

Akt is a critical protein for cell survival and known to interact with various proteins. However, Akt binding partners that modulate or regulate Akt activation have not been fully elucidated. Identification of Akt-interacting proteins has been customarily achieved by co-immunoprecipitation combined with western blot and/or MS analysis. An intrinsic problem of the method is loss of interacting proteins during procedures to remove non-specific proteins. Moreover, antibody contamination often interferes with the detection of less abundant proteins. Here, we developed a novel two-step chemical crosslinking strategy to overcome these problems which resulted in a dramatic improvement in identifying Akt interacting partners. Akt antibody was first immobilized on protein A/G beads using disuccinimidyl suberate and allowed to bind to cellular Akt along with its interacting proteins. Subsequently, dithiobis[succinimidylpropionate], a cleavable crosslinker, was introduced to produce stable complexes between Akt and binding partners prior to the SDS-PAGE and nanoLC-MS/MS analysis. This approach enabled identification of ten Akt partners from cell lysates containing as low as 1.5 mg proteins, including two new potential Akt interacting partners. None of these but one protein was detectable without crosslinking procedures. The present method provides a sensitive and effective tool to probe Akt-interacting proteins. This strategy should also prove useful for other protein interactions, particularly those involving less abundant or weakly associating partners. PMID:23613850

Huang, Bill X.; Kim, Hee-Yong

2013-01-01

167

"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

168

On-line bioaffinity-electrospray mass spectrometry for simultaneous detection, identification, and quantification of protein-ligand interactions.  

PubMed

We describe here an on-line combination of a surface acoustic wave (SAW) biosensor with electrospray ionization mass spectrometry (SAW-ESI-MS) that enables the direct detection, identification, and quantification of affinity-bound ligands from a protein-ligand complex on a biosensor chip. A trapping column was used between the SAW-biosensor and the electrospray mass spectrometer equipped with a micro-guard column, which provides simultaneous sample concentration and desalting for the mass spectrometric analysis of the dissociated ligand. First applications of the on-line SAW-ESI-MS combination include (1), differentiation of ?-amyloid (A?) epitope peptides bound to anti-A? antibodies; (2), the identification of immobilized Substance P peptide-calmodulin complex; (3), identification and quantification of the interaction of 3-nitrotyrosine-modified peptides with nitrotyrosine-specific antibodies; and (4), identification of immobilized anti-?-synuclein-human ?-synuclein complex. Quantitative determinations of protein-ligand complexes by SAW yielded dissociation constants (K(D)) from micro-to low nanomolar sample concentrations. The on-line bioaffinity-ESI-MS combination presented here is expected to enable broad bioanalytical application to the simultaneous, label-free determination and quantification of biopolymer-ligand interactions, as diverse as antigen-antibody and lectin-carbohydrate complexes. PMID:20692851

Dragusanu, Mihaela; Petre, Brîndusa-Alina; Slamnoiu, Stefan; Vlad, Camelia; Tu, Tingting; Przybylski, Michael

2010-10-01

169

Identification of Genes Important for the Physical Interaction between Protein Pairs through Reverse PCA (rPCA).  

PubMed

Cells contain many important protein complexes involved in performing and regulating structural, metabolic, and signaling functions. Understanding physical and functional interactions between proteins in living systems is of vital importance in biology. The importance of protein-protein interactions (PPIs) has led to the development of several powerful methodologies and techniques to detect them. All of this information has enabled the creation of large protein-interaction networks. One important challenge in biology is to understand how protein complexes respond to genetic perturbations. Here we describe a systematic genetic assay termed "reverse PCA," which allows the identification of genes whose products are required for modulating the physical interaction between two given proteins. Our assay starts with a yeast strain in which the PPI of interest can be detected by resistance to the drug methotrexate, in the context of the protein-fragment complementation assay (PCA). By combining the synthetic genetic array (SGA) technology, we can systematically screen mutant libraries of the yeast Saccharomyces cerevisiae to identify trans-acting mutations that disrupt the physical interaction of interest. The identification of such mutants is valuable for unraveling important regulatory mechanisms, and for defining the response of the protein interactome to specific perturbations. Curr. Protoc. Cell Biol. 64:17.15.1-17.15.11. © 2014 by John Wiley & Sons, Inc. PMID:25181300

Lev, Ifat; Volpe, Marina; Ben-Aroya, Shay

2014-01-01

170

Experimental analysis of vehicle-bridge interaction using a wireless monitoring system and a two-stage system identification technique  

NASA Astrophysics Data System (ADS)

Deterioration of bridges under repeated traffic loading has called attention to the need for improvements in the understanding of vehicle-bridge interaction. While analytical and numerical models have been previously explored to describe the interaction that exists between a sprung mass (i.e., a moving vehicle) and an elastic beam (i.e., bridge), comparatively less research has been focused on the experimental observation of vehicle-bridge interaction. A wireless monitoring system with wireless sensors installed on both the bridge and moving vehicle is proposed to record the dynamic interaction between the bridge and vehicle. Time-synchronized vehicle-bridge response data is used within a two-stage system identification methodology. In the first stage, the free-vibration response of the bridge is used to identify the dynamic characteristics of the bridge. In the second stage, the vehicle-bridge response data is used to identify the time varying load imposed on the bridge from the vehicle. To test the proposed monitoring and system identification strategy, the 180 m long Yeondae Bridge (Icheon, Korea) was selected. A dense network of wireless sensors was installed on the bridge while wireless sensors were installed on a multi-axle truck. The truck was driven across the bridge at constant velocity with bridge and vehicle responses measured. Excellent agreement between the measured Yeondae Bridge response and that predicted by an estimated vehicle-bridge interaction model validates the proposed strategy.

Kim, Junhee; Lynch, Jerome P.

2012-04-01

171

Induced fit docking, pharmacophore modeling, and molecular dynamic simulations on thiazolidinedione derivatives to explore key interactions with Tyr48 in polyol pathway.  

PubMed

To obtain a scientific thought and expedition to explore key interactions with Tyr48 in aldose reductase (ALR), combined study of pharmacophore modeling, induced fit docking, and dynamics studies were performed on ALR. A stereo chemically and energetically valid model of ALR-NADP+ complex was developed using homology modeling technique. Statistically a significant five point pharmacophore model was designed on a set of 54 thiazolidinedione derivatives with good external and internal predictive ability. Rigid and induced fit docking protocols were applied on ALR protein for both with and without NADP+ cofactor to identify a suitable binding mode that facilitates the key hydrogen bond interactions with Tyr48. Docking of thiazolidinedione derivatives into ALR-NADP+ complex gave more promising results by reducing false positive binding of inhibitors into the co-factor binding site. Structural changes within Try48 and Asp43 during the binding process in enzyme inhibitor complex were analyzed using molecular dynamics (MD) simulations. The results obtained from dynamic simulations emphasized the role of Tyr48 in maintaining inter or intra molecular hydrogen bond interaction with the protein or inhibitor respectively. New molecules were designed and checked for their binding interactions and showed improved results compared to existing thiazolidinediones derivatives. Hence, these combined protocols will be helpful and cooperative to design and optimize molecules with better inhibitory activity against the biologically active target. PMID:24974084

Vijjulatha, Manga; Lingala, Yamini; Merugu, RaviRaja Tejaswi

2014-07-01

172

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

173

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

174

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

ERIC Educational Resources Information Center

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

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

2012-01-01

175

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

E-print Network

and artificial intelligence. A social robot is a robot that interacts with humans and participates in human purposed to study a pet robot and used small stuffed animal robots. Thus, it is difficult to apply powerfully influences a subjective evaluation of the robot's intelligence. Through the experiment, we have

Kanda, Takayuki

176

TNF-? promotes c-REL/?Np63? interaction and TAp73 dissociation from key genes that mediate growth arrest and apoptosis in head and neck cancer  

PubMed Central

Inflammation-induced activation of proto-oncogenic NF-?B/REL and dysfunction of tumor suppressor TP53/p63/p73 family transcription factors are key events in cancer progression. How inflammatory signaling coordinates dysregulation of these two transcription factor families during oncogenesis remains incompletely understood. Here, we observed that oncoprotein c-REL and tumor suppressor TAp73 are co-expressed and complex with ?Np63? in the nucleus of a subset of head and neck squamous cell carcinoma (HNSCC) cell lines with mutant (mt)TP53. TNF-? a pro-inflammatory cytokine, promoted nuclear translocation and c-REL/?Np63? interaction and dissociation of TAp73 from nuclear ?Np63? to the cytoplasm, while c-REL siRNA depletion attenuated this effect. Overexpression of c-REL or a c-REL ?B-site DNA binding mutant enhanced protein interaction with?Np63? and TAp73 dissociation, implicating c-REL/?Np63?-specific interactions in these effects. We discovered TNF-?- or genetic alteration of c-REL expression inversely modulates?Np63?/TAp73 interactions on distinct p63 DNA binding sites, including those for key growth arrest and apoptotic genes p21WAF1, NOXA, and PUMA. Functionally, c-REL repressed these genes and the anti-proliferative effects of TNF-? or TAp73. Conversely, c-REL siRNA depletion enhanced TAp73 promoter interaction, and expression of genes mediating growth arrest and apoptosis. Similar to TNF-? treated HNSCC lines, human HNSCC tumors and hyperplastic squamous epithelia of transgenic mice overexpressing ?Np63? that exhibit inflammation, also demonstrate increased nuclear c-REL/?Np63? and cytoplasmic TAp73 localization. These findings unveil a novel and reversible dynamic mechanism whereby pro-inflammatory cytokine TNF-?-induced c-REL/?Np63? interactions inactivate tumor suppressor TAp73 function, promoting TNF-? resistance and cell survival in cancers with mtTP53. PMID:21933882

Lu, Hai; Yang, Xinping; Duggal, Praveen; Allen, Clint T.; Yan, Bin; Cohen, Jonah; Nottingham, Liesl; Romano, Rose-Anne; Sinha, Satrajit; King, Kathryn E.; Weinberg, Wendy C.; Chen, Zhong; Van Waes, Carter

2011-01-01

177

The inflamed axis: the interaction between stress, hormones, and the expression of inflammatory-related genes within key structures comprising the hypothalamic-pituitary-adrenal axis.  

PubMed

Acute stress increases the expression of cytokines and other inflammatory-related factors in the CNS, plasma, and endocrine glands, and activation of inflammatory signaling pathways within the hypothalamic-pituitary-adrenal (HPA) axis may play a key role in later stress sensitization. In addition to providing a summary of stress effects on neuroimmune changes within the CNS, we present a series of experiments that characterize stress effects on members of the interleukin-1? (IL-1) super-family and other inflammatory-related genes in key structures comprising the HPA axis (PVN, pituitary and adrenal glands), followed by a series of experiments examining the impact of exogenous hormone administration (CRH and ACTH) and dexamethasone on the expression of inflammatory-related genes in adult male Sprague-Dawley rats. The results demonstrated robust, time-dependent, and asynchronous expression patterns for IL-1 and IL-1R2 in the PVN, with substantial increases in IL-6 and COX-2 in the adrenal glands emerging as key findings. The effects of exogenous CRH and ACTH were predominantly isolated within the adrenals. Finally, pretreatment with dexamethasone severely blunted neuroimmune changes in the adrenal glands, but not in the PVN. These findings provide novel insight into the relationship between stress, the expression of inflammatory signaling factors within key structures comprising the HPA axis, and their interaction with HPA hormones, and provide a foundation for better understanding the role of cytokines as modulators of hypothalamic, pituitary and adrenal sensitivity. PMID:24184413

Hueston, Cara M; Deak, Terrence

2014-01-30

178

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

179

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

PubMed Central

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

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

2007-01-01

180

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

NASA Astrophysics Data System (ADS)

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

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

2008-05-01

181

A network inference method for large-scale unsupervised identification of novel drug-drug interactions  

E-print Network

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

Guimera, Roger

2014-01-01

182

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

PubMed Central

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

Guimera, Roger; Sales-Pardo, Marta

2013-01-01

183

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.

184

Ascorbic acid is a key participant during the interactions between chloroplasts and mitochondria to optimize photosynthesis and protect against photoinhibition.  

PubMed

The possible role of L-ascorbate (AsA) as a biochemical signal during the interactions between photosynthesis and respiration was examined in leaf discs of Arabidopsis thaliana. AsA content was either decreased as in AsA-deficient vtc1 mutants or increased by treatment with L-galactono-1, 4-lactone (L-GalL, a precursor of AsA; EC 1.3.2.3). In mutants, photosynthesis was extremely sensitive to both antimycin A (inhibitor of the cytochrome c oxidase pathway [COX pathway]) and salicylhydroxamic acid (SHAM, inhibitor of the alternative pathway [AOX pathway]), particularly at high light conditions. Mitochondrial inhibitors lowered the ratio of reduced AsA to total AsA, at high light, indicating oxidative stress in leaf discs. Elevation of AsA by L-GalL decreased the sensitivity of photosynthesis at high light to antimycin A or SHAM, sustained photosynthesis at supraoptimal light and relieved the extent of photoinhibition. High ratios of reduced AsA to total AsA in L-GalL-treated leaf discs suggests that L-GalL lowers oxidative stress. The protection by L-GalL of photosynthesis against the mitochondrial inhibitors and photoinhibition was quite pronounced in vtc1 mutants. Our results suggest that the levels and redox state of AsA modify the pattern of modulation of photosynthesis by mitochondrial metabolism. The extent of the AOX pathway as a percentage of the total respiration in Arabidopsis mesophyll protoplasts was much higher in vtc1 than in wild type. We suggest that the role of AsA becomes pronounced at high light and/or when the AOX pathway is inhibited. While acknowledging the importance of the COX pathway, we hypothesize that AsA and the AOX pathway may complement each other to protect photosynthesis against photoinhibition. PMID:21451257

Talla, Saikrishna; Riazunnisa, Khateef; Padmavathi, Lolla; Sunil, Bobba; Rajsheel, Pidakala; Raghavendra, Agepati S

2011-03-01

185

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

186

Comparative Identification of Differential Interactions from Trajectories of Dynamic Biological Networks  

PubMed Central

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.

Ouyang, Zhengyu; Song, Mingzhou (Joe)

2010-01-01

187

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

188

[Identification and spatial distribution of key premises for Aedes aegypti in the Porto Dantas neighborhood, Aracaju, Sergipe State, Brazil, 2007-2008].  

PubMed

Currently the best way to avoid new dengue epidemics is to control the mosquito vector Aedes aegypti. This study thus aimed to identify and analyze the spatial distribution of "key premises" for Ae. aegypti in Aracaju, Sergipe State, Brazil. Three entomological surveys were performed prior to, during, and after the dengue epidemic and in different conditions of precipitation: the end of the rainy season, beginning of the rainy season, and the dry season. Key premises were identified by positivity in more than one survey and presence of pupae. Spatial distribution and dispersal of mosquitoes used analysis of point patterns, with the kernel and buffer density estimator. Key premises were responsible for maintaining infestation of the area, independently of environmental conditions and the period in the epidemic, serving as foci generating mosquitoes that can spread to areas adjacent to the neighborhood. Thus, in order to be more effective, vector control measures should target these properties. PMID:23459822

Marteis, Letícia Silva; Steffler, Lizandra Makowski; Araújo, Karina Conceição Gomes Machado de; Santos, Roseli La Corte dos

2013-02-01

189

Answer Keys  

NSDL National Science Digital Library

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

2010-01-01

190

Rab11 Function in Trypanosoma brucei: Identification of Conserved and Novel Interaction Partners ? †  

PubMed Central

The Ras-like GTPase Rab11 is implicated in multiple aspects of intracellular transport, including maintenance of plasma membrane composition and cytokinesis. In metazoans, these functions are mediated in part via coiled-coil Rab11-interacting proteins (FIPs) acting as Rab11 effectors. Additional interaction between Rab11 and the exocyst subunit Sec15 connects Rab11 with exocytosis. We find that FIPs are metazoan specific, suggesting that other factors mediate Rab11 functions in nonmetazoans. We examined Rab11 interactions in Trypanosoma brucei, where endocytosis is well studied and the role of Rab11 in recycling well documented. TbSec15 and TbRab11 interact, demonstrating evolutionary conservation. By yeast two-hybrid screening, we identified additional Rab11 interaction partners. Tb927.5.1640 (designated RBP74) interacted with both Rab11 and Rab5. RBP74 shares a coiled-coil architecture with metazoan FIPs but is unrelated by sequence and appears to play a role in coordinating endocytosis and recycling. A second coiled-coil protein, Tb09.211.4830 (TbAZI1), orthologous to AZI1 in Homo sapiens, interacts exclusively with Rab11. AZI1 is restricted to taxa with motile cilia/flagella. These data suggest that Rab11 functions are mediated by evolutionarily conserved (i.e., AZI1 and Sec15) and potentially lineage-specific (RBP74) interactions essential for the integration of the endomembrane system. PMID:21642507

Gabernet-Castello, Carme; DuBois, Kelly N.; Nimmo, Camus; Field, Mark C.

2011-01-01

191

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

Microsoft Academic Search

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

Cory Batenchuk; Lioudmila Tepliakova; Mads Kærn

2010-01-01

192

Key interactions in the immunoglobulin-like structure of apo-neocarzinostatin: Evidence from nuclear magnetic resonance relaxation data and molecular dynamics simulations  

PubMed Central

The three-dimensional structure of apo-neocarzinostatin (apo-NCS, MW: ca.11000, antitumoral chromophore carrier protein) is based on a seven-stranded antiparallel ?-sandwich, very similar to the immunoglobulin folding domain. We investigated the backbone dynamics of apo-NCS by 13C-NMR relaxation measurements and molecular dynamics simulation. Model-free parameters determined from the experimental data are compared with a 1.5-nsec molecular simulation of apo-NCS in aqueous solution. This comparison provides an accurate description of both local and collective movements within the protein. This analysis enabled us to correlate dynamic processes with key interactions of this ?-protein. Local motions that could be relevant for the intermolecular association with the ligand are also described. PMID:11604530

Izadi-Pruneyre, Nadia; Quiniou, Éric; Blouquit, Yves; Perez, Javier; Minard, Philippe; Desmadril, Michel; Mispelter, Joël; Adjadj, Élisabeth

2001-01-01

193

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

194

Solution Structure of the LIM-Homeodomain Transcription Factor Complex Lhx3/Ldb1 and the Effects of a Pituitary Mutation on Key Lhx3 Interactions  

PubMed Central

Lhx3 is a LIM-homeodomain (LIM-HD) transcription factor that regulates neural cell subtype specification and pituitary development in vertebrates, and mutations in this protein cause combined pituitary hormone deficiency syndrome (CPHDS). The recently published structures of Lhx3 in complex with each of two key protein partners, Isl1 and Ldb1, provide an opportunity to understand the effect of mutations and posttranslational modifications on key protein-protein interactions. Here, we use small-angle X-ray scattering of an Ldb1-Lhx3 complex to confirm that in solution the protein is well represented by our previously determined NMR structure as an ensemble of conformers each comprising two well-defined halves (each made up of LIM domain from Lhx3 and the corresponding binding motif in Ldb1) with some flexibility between the two halves. NMR analysis of an Lhx3 mutant that causes CPHDS, Lhx3(Y114C), shows that the mutation does not alter the zinc-ligation properties of Lhx3, but appears to cause a structural rearrangement of the hydrophobic core of the LIM2 domain of Lhx3 that destabilises the domain and/or reduces the affinity of Lhx3 for both Ldb1 and Isl1. Thus the mutation would affect the formation of Lhx3-containing transcription factor complexes, particularly in the pituitary gland where these complexes are required for the production of multiple pituitary cell types and hormones. PMID:22848397

Jeffries, Cy M.; Kwan, Ann; Whitten, Andrew E.; Trewhella, Jill; Mackay, Joel P.; Matthews, Jacqueline M.

2012-01-01

195

Molecular interactions of Bcl-2 and Bcl-xL with mortalin: identification and functional characterization.  

PubMed

Bcl-2 family of proteins consists of both pro-apoptotic and anti-apoptotic members that control cellular apoptosis. They predominantly reside in the mitochondria and control the release of apoptotic factors from the mitochondria to the cytosol by regulating its membrane potential and opening the PT (permeability transition) pore. Here we report bioinformatics and biochemical evidence to demonstrate the interaction between Bcl-2 and Bcl-xL with a stress chaperone, mortalin. We demonstrate that such interaction results in the abrogation of mortalin-p53 interaction leading to nuclear translocation and transcriptional reactivation of p53 function that results in an induction of senescence in cancer cells. PMID:24050266

Saxena, Nishant; Katiyar, Shashank P; Liu, Ye; Grover, Abhinav; Gao, Ran; Sundar, Durai; Kaul, Sunil C; Wadhwa, Renu

2013-01-01

196

Structure–function studies of peptides for cell adhesion inhibition: Identification of key residues by alanine mutation and peptide-truncation approach  

Microsoft Academic Search

Blockage of the interaction of CD2 with its ligand CD58 is expected to bring out potential therapeutic value for autoimmune diseases and organ transplantation. Three series of peptides (cVL, cIL and cAQ series) were designed from ratCD2 and humanCD2 to modulate CD2–CD58 interaction. To determine the specific segments in parent peptides responsible for inhibitory activity as lead sequence, we generated

Cheng Li; Seetharama D. Satyanarayanajois

2007-01-01

197

Identification of receptor-interacting regions of vitellogenin within evolutionarily conserved ?-sheet structures by using a peptide array.  

PubMed

Vitellogenesis, a key process in oviparous animals, is characterized by enhanced synthesis of the lipoprotein vitellogenin, which serves as the major yolk-protein precursor. In most oviparous animals, and specifically in crustaceans, vitellogenin is mainly synthesized in the hepatopancreas, secreted to the hemolymph, and taken up into the ovary by receptor-mediated endocytosis. In the present study, localization of the vitellogenin receptor and its interaction with vitellogenin were investigated in the freshwater prawn Macrobrachium rosenbergii. The receptor was immuno-histochemically localized to the cell periphery and around yolk vesicles. A receptor blot assay revealed that the vitellogenin receptor interacts with most known vitellogenin subunits, the most prominent being the 79 kDa subunit. The receptor was, moreover, able to interact with trypsin-digested vitellogenin peptides. By combining a novel peptide-array approach with tandem mass spectrometry, eleven vitellogenin-derived peptides that interacted with the receptor were identified. A 3D model of vitellogenin indicated that four of the identified peptides are N-terminally localized. One of the peptides is homologous to the receptor-recognized site of vertebrate vitellogenin, and assumes a conserved ?-sheet structure. These findings suggest that this specific ?-sheet region in the vitellogenin N-terminal lipoprotein domain is the receptor-interacting site, with the rest of the protein serving to enhance affinity for the receptor. The conservation of the receptor recognition site in invertebrate and vertebrate vitellogenin might have vast implications for oviparous species reproduction, development, immunity, and pest management. PMID:23733483

Roth, Ziv; Weil, Simy; Aflalo, Eliahu D; Manor, Rivka; Sagi, Amir; Khalaila, Isam

2013-06-17

198

Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics  

PubMed Central

Quantitative proteomics combined with immuno-affinity purification, SILAC immunoprecipitation, represent a powerful means for the discovery of novel protein:protein interactions. By allowing the accurate relative quantification of protein abundance in both control and test samples, true interactions may be easily distinguished from experimental contaminants. Low affinity interactions can be preserved through the use of less-stringent buffer conditions and remain readily identifiable. This protocol discusses the labeling of tissue culture cells with stable isotope labeled amino acids, transfection and immunoprecipitation of an affinity tagged protein of interest, followed by the preparation for submission to a mass spectrometry facility. This protocol then discusses how to analyze and interpret the data returned from the mass spectrometer in order to identify cellular partners interacting with a protein of interest. As an example this technique is applied to identify proteins binding to the eukaryotic translation initiation factors: eIF4AI and eIF4AII. PMID:25046639

Emmott, Edward; Goodfellow, Ian

2014-01-01

199

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

PubMed Central

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

200

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

PubMed Central

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

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

2013-01-01

201

Optical key system  

DOEpatents

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

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

2000-01-01

202

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

PubMed Central

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

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

2014-01-01

203

Identification of interacting transcription factors regulating tissue gene expression in human  

PubMed Central

Background Tissue gene expression is generally regulated by multiple transcription factors (TFs). A major first step toward understanding how tissues achieve their specificity is to identify, at the genome scale, interacting TFs regulating gene expression in different tissues. Despite previous discoveries, the mechanisms that control tissue gene expression are not fully understood. Results We have integrated a function conservation approach, which is based on evolutionary conservation of biological function, and genes with highest expression level in human tissues to predict TF pairs controlling tissue gene expression. To this end, we have identified 2549 TF pairs associated with a certain tissue. To find interacting TFs controlling tissue gene expression in a broad spatial and temporal manner, we looked for TF pairs common to the same type of tissues and identified 379 such TF pairs, based on which TF-TF interaction networks were further built. We also found that tissue-specific TFs may play an important role in recruiting non-tissue-specific TFs to the TF-TF interaction network, offering the potential for coordinating and controlling tissue gene expression across a variety of conditions. Conclusion The findings from this study indicate that tissue gene expression is regulated by large sets of interacting TFs either on the same promoter of a gene or through TF-TF interaction networks. PMID:20085649

2010-01-01

204

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

205

A key gene of the RNA interference pathway in the black tiger shrimp, Penaeus monodon: Identification and functional characterisation of Dicer1  

Microsoft Academic Search

RNA interference (RNAi) is an evolutionarily conserved mechanism by which double-stranded RNA (dsRNA) initiates post-transcriptional silencing of homologous genes. Here we report the amplification and characterisation of a full length cDNA from black tiger shrimp (Penaeus monodon) that encodes the bidentate RNAase III Dicer, a key component of the RNAi pathway. The full length of the shrimp Dicer (Pm Dcr1)

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

2008-01-01

206

Quantification of ligand-regulated nuclear receptor corepressor and coactivator binding, key interactions determining ligand potency and efficacy for the thyroid hormone receptor.  

PubMed

The potency and efficacy of ligands for nuclear receptors (NR) result both from the affinity of the ligand for the receptor and from the affinity that various coregulatory proteins have for ligand-receptor complexes; the latter interaction, however, is rarely quantified. To understand the molecular basis for ligand potency and efficacy, we developed dual time-resolved fluorescence resonance energy transfer (tr-FRET) assays and quantified binding of both ligand and coactivator or corepressor to the thyroid hormone receptor (TR). Promoter-bound TR exerts dual transcriptional regulatory functions, recruiting corepressor proteins and repressing transcription in the absence of thyroid hormones (THs) and shedding corepressors in favor of coactivators upon binding agonists, activating transcription. Our tr-FRET assays involve a TRE sequence labeled with terbium (fluorescence donor), TRbeta.RXRalpha heterodimer, and fluorescein-labeled NR interaction domains of coactivator SRC3 or corepressor NCoR (fluorescence acceptors). Through coregulator titrations, we could determine the affinity of SRC3 or NCoR for TRE-bound TR.RXR heterodimers, unliganded or saturated with different THs. Alternatively, through ligand titrations, we could determine the relative potencies of different THs. The order of TR agonist potencies is as follows: GC-1 approximately T 3 approximately TRIAC approximately T 4 > rT 3 (for both coactivator recruitment and corepressor dissociation); the affinities of SRC3 binding to TR-ligand complexes followed a similar trend. This highlights the fact that the low activity of rT 3 is derived both from its low affinity for TR and from the low affinity of SRC for the TR-rT 3 complex. The TR antagonist NH-3 failed to induce SRC3 recruitment but did effect NCoR dissociation. These assays provide quantitative information about the affinity of two key interactions that are determinants of NR ligand potency and efficacy. PMID:18558711

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

2008-07-15

207

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

PubMed Central

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

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

2008-01-01

208

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

SciTech Connect

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

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

2008-07-15

209

Identification of microRNA-target interaction in APRIL-knockdown colorectal cancer cells  

Microsoft Academic Search

MicroRNAs (miRNAs) regulate mammalian gene expression by targeting mRNAs and have key roles in several cellular processes, including differentiation, development, apoptosis and cancer pathomechanisms. Our previous studies have confirmed that a proliferation-inducing ligand (APRIL) gene is overexpressed in colorectal cancer (CRC) tumors and SW480 cells. To study the potential mechanisms of APRIL gene in the occurrence and development of the

F Wang; W Ding; J Wang; R Jing; X Wang; H Cong; Y Wang; S Ju; H Wang

2011-01-01

210

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, Nuria; Arias Perez, JoseI.; Benitez, Javier; Flyger, Henrik; Nordestgaard, B?rge G.; Truong, Therese; Cordina-Duverger, Emilie; Menegaux, Florence; Silva, Isabel dos Santos; Fletcher, Olivia; Johnson, Nichola; Haberle, 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; Guenel, 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

211

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

212

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

213

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

214

Identification of Cellular Proteins Interacting with the Retroviral Restriction Factor SAMHD1  

PubMed Central

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

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

2014-01-01

215

Identification of proteins interacting with lactate dehydrogenase in claw muscle of the porcelain crab Petrolisthes cinctipes  

PubMed Central

Biochemical adaptation of enzymes involves conservation of activity, stability and affinity across a wide range of intracellular and environmental conditions. Enzyme adaptation by alteration of primary structure is well known, but the roles of protein-protein interactions in enzyme adaptation are less well understood. Interspecific differences in thermal stability of lactate dehydrogenase (LDH) in porcelain crabs (genus Petrolisthes) are related to intrinsic differences among LDH molecules and by interactions with other stabilizing proteins. Here, we identified proteins that interact with LDH in porcelain crab claw muscle tissue using co-immunoprecipitation, and showed LDH exists in high molecular weight complexes using size exclusion chromatography and Western blot analyses. Co-immunoprecipitated proteins were separated using 2D SDS PAGE and analyzed by LC/ESI using peptide MS/MS. Peptide MS/MS ions were compared to an EST database for Petrolisthes cinctipes to identify proteins. Identified proteins included cytoskeletal elements, glycolytic enzymes, a phosphagen kinase, and the respiratory protein hemocyanin. Our results support the hypothesis that LDH interacts with glycolytic enzymes in a metabolon structured by cytoskeletal elements that may also include the enzyme for transfer of the adenylate charge in glycolytically produced ATP. Those interactions may play specific roles in biochemical adaptation of glycolytic enzymes. PMID:21968246

Cayenne, Andrea P.; Gabert, Beverly; Stillman, Jonathon H.

2011-01-01

216

Identification of self consistent field interaction parameter from continuum Monte Carlo simulation of model polymer blends  

NASA Astrophysics Data System (ADS)

Monte Carlo simulations of binary AB polymer blends have been performed to evaluate the effective interaction parameter ?e of self consistent field theory, and to quantify corrections to RPA predictions for fluctuations. We consider a model with a non-bonded pair interaction vij(r) = ?ijf(r) for which f(r) is of the repulsive Lennard-Jones form, ?AA=?BB, and ?AB= ?AA+ ??. Using thermodynamic perturbation theory, to first order in ??, we obtain an interaction free energy with the composition dependence predicted by Flory-Huggins theory, with an effective interaction parameter ?e= ??zc. Here, zc is an effective coordination number given by the average of the sum of values of f(r) for interactions between a test monomer and nearby monomers on other chains, in a reference system with ??=0. Results for composition fluctuations in semigrand ensemble simulations of blends with a range of values of ??!=0, for several chain lengths, are compared to RPA predictions calculated using this perturbatively defined ?e parameter.

Chung, Jun Kyung; Morse, David

2008-03-01

217

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

PubMed

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

Wadhwa, Renu; Takano, Syuichi; Kaur, Kamaljit; Aida, Satoshi; Yaguchi, Tomoko; Kaul, Zeenia; Hirano, Takashi; Taira, Kazunari; Kaul, Sunil C

2005-10-15

218

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

219

The 3.2 ? 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

220

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

221

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

PubMed

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. PMID:22245583

Lupo, Julien; Conti, Audrey; Sueur, Charlotte; Coly, Pierre-Alain; Couté, Yohann; Hunziker, Walter; Burmeister, Wim P; Germi, Raphaelle; Manet, Evelyne; Gruffat, Henri; Morand, Patrice; Boyer, Véronique

2012-03-10

222

Identification of YidC Residues That Define Interactions with the Sec Apparatus  

PubMed Central

In bacteria, a subset of membrane proteins insert into the membrane via the Sec apparatus with the assistance of the widely conserved essential membrane protein insertase YidC. After threading into the SecYEG translocon, transmembrane segments of nascent proteins are thought to exit the translocon via a lateral gate in SecY, where YidC facilitates their transfer into the lipid bilayer. Interactions between YidC and components of the Sec apparatus are critical to its function. The first periplasmic loop of YidC interacts directly with SecF. We sought to identify the regions or residues of YidC that interact with SecY or with additional components of the Sec apparatus other than SecDF. Using a synthetic lethal screen, we identified residues of YidC that, when mutated, led to dependence on SecDF for viability. Each residue identified is highly conserved among YidC homologs; most lie within transmembrane domains. Overexpression of SecY in the presence of two YidC mutants partially rescued viability in the absence of SecDF, suggesting that the corresponding wild-type YidC residues (G355 and M471) participate in interactions, direct or indirect, with SecY. Staphylococcus aureus YidC complemented depletion of YidC, but not of SecDF, in Escherichia coli. G355 of E. coli YidC is invariant in S. aureus YidC, suggesting that this highly conserved glycine serves a conserved function in interactions with SecY. This study demonstrates that transmembrane residues are critical in YidC interactions with the Sec apparatus and provides guidance on YidC residues of interest for future structure-function analyses. PMID:24187090

Li, Zaoping; Boyd, Dana; Reindl, Martin

2014-01-01

223

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

Microsoft Academic Search

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

Fabio Coppedè; Enzo Grossi; Francesca Migheli; Lucia Migliore

2010-01-01

224

Structure of the RNA polymerase assembly factor Crl and identification of its interaction surface with sigma S.  

PubMed

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

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

2014-09-01

225

Plant Identification  

NSDL National Science Digital Library

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

226

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

PubMed Central

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

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

2012-01-01

227

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

PubMed

Direct IAP binding protein with low pI/second mitochondrial activator of caspases, HtrA2/Omi and GstPT/eRF3 are mammalian proteins that bind via N-terminal inhibitor of apoptosis protein (IAP) binding motifs (IBMs) to the baculoviral IAP repeat (BIR) domains of IAPs. These interactions can prevent IAPs from inhibiting caspases, or displace active caspases, thereby promoting cell death. We have identified several additional potential IAP antagonists, including glutamate dehydrogenase (GdH), Nipsnap 3 and 4, CLPX, leucine-rich pentatricopeptide repeat motif-containing protein and 3-hydroxyisobutyrate dehydrogenase. All are mitochondrial proteins from which N-terminal import sequences are removed generating N-terminal IBMs. Whereas most of these proteins have alanine at the N-terminal position, as observed for previously described antagonists, GdH has an N-terminal serine residue that is essential for X-linked IAP (XIAP) interaction. These newly described IAP binding proteins interact with XIAP mainly via BIR2, with binding eliminated or significantly reduced by a single point mutation (D214S) within this domain. Through this interaction, many are able to antagonise XIAP inhibition of caspase 3 in vitro. PMID:16794601

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

2007-02-01

228

Identification and characterization of multiple novel Rab-myosin Va interactions  

PubMed Central

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

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

2013-01-01

229

PAINT: A Promoter Analysis and Interaction Network Generation Tool for Gene Regulatory Network Identification  

Microsoft Academic Search

We have developed a bioinformatics tool named PAINT that automates the promoter analy- sis of a given set of genes for the presence of transcription factor binding sites. Based on co- incidence of regulatory sites, this tool produces an interaction matrix that represents a can- didate transcriptional regulatory network. This tool currently consists of (1) a database of promoter sequences

Rajanikanth Vadigepalli; Praveen Chakravarthula; Daniel E. Zak; James S. Schwaber; Gregory E. Gonye

2003-01-01

230

Identification of Functionally Important TonB-ExbD Periplasmic Domain Interactions In Vivo  

PubMed Central

In Gram-negative bacteria, the cytoplasmic membrane proton-motive force energizes the active transport of TonB-dependent ligands through outer membrane TonB-gated transporters. In Escherichia coli, cytoplasmic membrane proteins ExbB and ExbD couple the proton-motive force to conformational changes in TonB, which are hypothesized to form the basis of energy transduction through direct contact with the transporters. While the role of ExbB is not well understood, contact between periplasmic domains of TonB and ExbD is required, with the conformational response of TonB to presence or absence of proton motive force being modulated through ExbD. A region (residues 92 to 121) within the ExbD periplasmic domain was previously identified as being important for TonB interaction. Here, the specific sites of periplasmic domain interactions between that region and the TonB carboxy terminus were identified by examining 270 combinations of 45 TonB and 6 ExbD individual cysteine substitutions for disulfide-linked heterodimer formation. ExbD residues A92C, K97C, and T109C interacted with multiple TonB substitutions in four regions of the TonB carboxy terminus. Two regions were on each side of the TonB residues known to interact with the TonB box of TonB-gated transporters, suggesting that ExbD positions TonB for correct interaction at that site. A third region contained a functionally important glycine residue, and the fourth region involved a highly conserved predicted amphipathic helix. Three ExbD substitutions, F103C, L115C, and T121C, were nonreactive with any TonB cysteine substitutions. ExbD D25, a candidate to be on a proton translocation pathway, was important to support efficient TonB-ExbD heterodimerization at these specific regions. PMID:22493017

Ollis, Anne A.

2012-01-01

231

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

PubMed Central

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

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

2012-01-01

232

Identification of Key Residues Essential for the Structural Fold and Receptor Selectivity within the A-chain of Human Gene-2 (H2) Relaxin*  

PubMed Central

Human gene-2 (H2) relaxin is currently in Phase III clinical trials for the treatment of acute heart failure. It is a 53-amino acid insulin-like peptide comprising two chains and three disulfide bonds. It interacts with two of the relaxin family peptide (RXFP) receptors. Although its cognate receptor is RXFP1, it is also able to cross-react with RXFP2, the native receptor for a related peptide, insulin-like peptide 3. In order to understand the basis of this cross-reactivity, it is important to elucidate both binding and activation mechanisms of this peptide. The primary binding mechanism of this hormone has been extensively studied and well defined. H2 relaxin binds to the leucine-rich repeats of RXFP1 and RXFP2 using B-chain-specific residues. However, little is known about the secondary interaction that involves the A-chain of H2 relaxin and transmembrane exoloops of the receptors. We demonstrate here through extensive mutation of the A-chain that the secondary interaction between H2 relaxin and RXFP1 is not driven by any single amino acid, although residues Tyr-3, Leu-20, and Phe-23 appear to contribute. Interestingly, these same three residues are important drivers of the affinity and activity of H2 relaxin for RXFP2 with additional minor contributions from Lys-9, His-12, Lys-17, Arg-18, and Arg-22. Our results provide new insights into the mechanism of secondary activation interaction of RXFP1 and RXFP2 by H2 relaxin, leading to a potent and RXFP1-selective analog, H2:A(4–24)(F23A), which was tested in vitro and in vivo and found to significantly inhibit collagen deposition similar to native H2 relaxin. PMID:23024363

Chan, Linda J.; Rosengren, K. Johan; Layfield, Sharon L.; Bathgate, Ross A. D.; Separovic, Frances; Samuel, Chrishan S.; Hossain, Mohammed A.; Wade, John D.

2012-01-01

233

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

234

The APETALA-2-like transcription factor OsAP2-39 controls key interactions between abscisic acid and gibberellin in rice.  

PubMed

The interaction between phytohormones is an important mechanism which controls growth and developmental processes in plants. Deciphering these interactions is a crucial step in helping to develop crops with enhanced yield and resistance to environmental stresses. Controlling the expression level of OsAP2-39 which includes an APETALA 2 (AP2) domain leads to phenotypic changes in rice. Overexpression of OsAP2-39 leads to a reduction in yield by decreasing the biomass and the number of seeds in the transgenic rice lines. Global transcriptome analysis of the OsAP2-39 overexpression transgenic rice revealed the upregulation of a key abscisic acid (ABA) biosynthetic gene OsNCED-I which codes for 9-cis-epoxycarotenoid dioxygenase and leads to an increase in the endogenous ABA level. In addition to OsNCED-1, the gene expression analysis revealed the upregulation of a gene that codes for the Elongation of Upper most Internode (EUI) protein, an enzyme that catalyzes 16?, 17-epoxidation of non-13-hydroxylated GAs, which has been shown to deactivate gibberellins (GAs) in rice. The exogenous application of GA restores the wild-type phenotype in the transgenic line and ABA application induces the expression of EUI and suppresses the expression of OsAP2-39 in the wild-type line. These observations clarify the antagonistic relationship between ABA and GA and illustrate a mechanism that leads to homeostasis of these hormones. In vivo and in vitro analysis showed that the expression of both OsNCED-1 and EUI are directly controlled by OsAP2-39. Together, these results reveal a novel mechanism for the control of the ABA/GA balance in rice which is regulated by OsAP2-39 that in turn regulates plant growth and seed production. PMID:20838584

Yaish, Mahmoud W; El-Kereamy, Ashraf; Zhu, Tong; Beatty, Perrin H; Good, Allen G; Bi, Yong-Mei; Rothstein, Steven J

2010-09-01

235

Key Nutrients.  

ERIC Educational Resources Information Center

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

Federal Extension Service (USDA), Washington, DC.

236

Illustrated key for identification of the species included in the genus Leptoglossus (Hemiptera: Heteroptera: Coreidae: Coreinae: Anisoscelini), and descriptions of five new species and new synonyms.  

PubMed

Five new species of Leptoglossus are described: L.caicosensis from Turks and Caicos Island, L. egeri and L. impensus from Bolivia, L. franckei from Costa Rica, and L. polychromus from Ecuador, Cooperative Republic of Guiana (British Guiana), and French Guiana. Leptoglossus argentinus Bergroth is synonymized under L. chilensis chilensis (Spinola) and Narnia anaticula Brailovsky & Barrera under Leptoglossus occidentalis Heidemann. Dorsal view drawings and key to the 61 known species and 1 subspecies are included; a complete checklist, and the position of each species within the species-group defined herein, are given except for two species L. macrophylus Stål and L. polychromus sp.nov., that are insertae-sedis. The pronotal disk, hind legs, and male genital capsule of the new species here described are illustrated. PMID:24870317

Brailovsky, Harry

2014-01-01

237

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

238

Identification of Siah-interacting protein as a potential regulator of apoptosis and curcumin resistance  

Microsoft Academic Search

The mechanism underlying curcumin (diferuloylmethane) resistance is still largely unknown. Here we employed proteomic approach to identify the Siah-interacting protein (SIP) as a candidate for detailed study, because the spot intensity of SIP on a two-dimensional gel displayed 70–90% reduction in curcumin-sensitive cells, but remained unchanged in curcumin-resistant sublines, after curcumin treatment. Both gain- and loss-of-function studies revealed that SIP

J Luo; J Yang; B-Y Yu; W Liu; M Li; S-M Zhuang

2010-01-01

239

Identification of binding partners interacting with the ?1-N-propeptide of type V collagen.  

PubMed

The predominant form of type V collagen is the [?1(V)]??2(V) heterotrimer. Mutations in COL5A1 or COL5A2, encoding respectively the ?1(V)- and ?2(V)-collagen chain, cause classic EDS (Ehlers-Danlos syndrome), a heritable connective tissue disorder, characterized by fragile hyperextensible skin and joint hypermobility. Approximately half of the classic EDS cases remain unexplained. Type V collagen controls collagen fibrillogenesis through its conserved ?1(V)-N-propeptide domain. To gain an insight into the role of this domain, a yeast two-hybrid screen among proteins expressed in human dermal fibroblasts was performed utilizing the N-propeptide as a bait. We identified 12 interacting proteins, including extracellular matrix proteins and proteins involved in collagen biosynthesis. Eleven interactions were confirmed by surface plasmon resonance and/or co-immunoprecipitation: ?1(I)- and ?2(I)-collagen chains, ?1(VI)-, ?2(VI)- and ?3(VI)-collagen chains, tenascin-C, fibronectin, PCPE-1 (procollagen C-proteinase enhancer-1), TIMP-1 (tissue inhibitor of metalloproteinases-1), MMP-2 (matrix metalloproteinase 2) and TGF-?1 (transforming growth factor ?1). Solid-phase binding assays confirmed the involvement of the ?1(V)-N-propeptide in the interaction between native type V collagen and type VI collagen, suggesting a bridging function of this protein complex in the cell-matrix environment. Enzymatic studies showed that processing of the ?1(V)-N-propeptide by BMP-1 (bone morphogenetic protein 1)/procollagen C-proteinase is enhanced by PCPE-1. These interactions are likely to be involved in extracellular matrix homoeostasis and their disruption could explain the pathogenetic mechanism in unresolved classic EDS cases. PMID:20979576

Symoens, Sofie; Renard, Marjolijn; Bonod-Bidaud, Christelle; Syx, Delfien; Vaganay, Elisabeth; Malfait, Fransiska; Ricard-Blum, Sylvie; Kessler, Efrat; Van Laer, Lut; Coucke, Paul; Ruggiero, Florence; De Paepe, Anne

2011-01-15

240

Identification of Novel Contributions to High-affinity Glycoprotein–Receptor Interactions using Engineered Ligands  

PubMed Central

Engineered receptor fragments and glycoprotein ligands employed in different assay formats have been used to dissect the basis for the dramatic enhancement of binding of two model membrane receptors, dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin (DC-SIGN) and the macrophage galactose lectin, to glycoprotein ligands compared to simple sugars. These approaches make it possible to quantify the importance of two major factors that combine to enhance the affinity of single carbohydrate-recognition domains (CRDs) for glycoprotein ligands by 100-to 300-fold. First, the presence of extended binding sites within a single CRD can enhance interaction with branched glycans, resulting in increases of fivefold to 20-fold in affinity. Second, presentation of glycans on a glycoprotein surface increases affinity by 15-to 20-fold, possibly due to low-specificity interactions with the surface of the protein or restriction in the conformation of the glycans. In contrast, when solution-phase networking is avoided, enhancement due to binding of multiple branches of a glycan to multiple CRDs in the oligomeric forms of these receptors is minimal and binding of a receptor oligomer to multiple glycans on a single glycoprotein makes only a twofold contribution to overall affinity. Thus, in these cases, multivalent interactions of individual glycoproteins with individual receptor oligomers have a limited role in achieving high affinity. These findings, combined with considerations of membrane receptor geometry, are consistent with the idea that further enhancement of the binding to multivalent glycoprotein ligands requires interaction of multiple receptor oligomers with the ligands. PMID:20004209

Coombs, Peter J.; Harrison, Rebecca; Pemberton, Samantha; Quintero-Martinez, Adrián; Parry, Simon; Haslam, Stuart M.; Dell, Anne; Taylor, Maureen E.; Drickamer, Kurt

2010-01-01

241

Identification of a Brucella spp. secreted effector specifically interacting with human small GTPase Rab2  

E-print Network

GTPase Rab2 Marie de Barsy,1 Alexandre Jamet,1,2 Didier Filopon,1 Cécile Nicolas,1 Géraldine Laloux,1 the human small GTPase Rab2 and a Bru- cella spp. protein named RicA. This interaction was confirmed by GST-pull-down with the GDP-bound form of Rab2. A TEM-b-lactamase-RicA fusion was translocated from Brucella abortus to RAW264

242

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

243

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; Aragon, Pablo; Kaltenbrunner, Andreas

2013-01-01

244

Identification of a novel interacting partner of the chemosensory protein 1 from Plutella xylostella L.  

PubMed

Chemosensory proteins (CSPs) are small soluble proteins endowed with heterogeneous functions. The information so far available for CSPs suggested these well-defined and conserved proteins were involved in diverse activities, including chemical communication, feeding, development, mating, immune regulation, as well as circadian rhythms. However, the detailed mechanisms of these physiological functions remain elusive. To explore the underlying mechanisms of CSPs and their interaction partners, a cDNA library from the head of Plutella xylostella was screened against CSP1 to identify proteins involved in the PxylCSP1-related physiological activities. Protein kinase C (PKC) was screened out as a putative interacting protein of PxylCSP1. The full length of PxylPKC cDNA was obtained, and the results of semi-quantitative real-time PCR and quantitative real-time PCR revealed that PxylPKC showed similar expression pattern as PxylCSP1. In vivo and in vitro interactions between PxylCSP1 and PxylPKC were further confirmed by co-immunoprecipitation and GST pull-down assays, respectively. These findings extended our knowledge on the mechanisms of CSP-regulated functions, and providing new target proteins to facilitate the design of novel intervention strategies against the pest. PMID:24095714

Yi, Xin; Liu, XiaoLei; Zhao, HaiMing; Wang, PeiDan; Rizwan-ul-Haq, Muhammad; Hu, MeiYing; Zhong, GuoHua

2014-02-01

245

Identification of Nuclear Phosphatidylinositol 4,5-Bisphosphate-Interacting Proteins by Neomycin Extraction*  

PubMed Central

Considerable insight into phosphoinositide-regulated cytoplasmic functions has been gained by identifying phosphoinositide-effector proteins. Phosphoinositide-regulated nuclear functions however are fewer and less clear. To address this, we established a proteomic method based on neomycin extraction of intact nuclei to enrich for nuclear phosphoinositide-effector proteins. We identified 168 proteins harboring phosphoinositide-binding domains. Although the vast majority of these contained lysine/arginine-rich patches with the following motif, K/R-(Xn = 3–7)-K-X-K/R-K/R, we also identified a smaller subset of known phosphoinositide-binding proteins containing pleckstrin homology or plant homeodomain modules. Proteins with no prior history of phosphoinositide interaction were identified, some of which have functional roles in RNA splicing and processing and chromatin assembly. The remaining proteins represent potentially other novel nuclear phosphoinositide-effector proteins and as such strengthen our appreciation of phosphoinositide-regulated nuclear functions. DNA topology was exemplar among these: Biochemical assays validated our proteomic data supporting a direct interaction between phosphatidylinositol 4,5-bisphosphate and DNA Topoisomerase II?. In addition, a subset of neomycin extracted proteins were further validated as phosphatidyl 4,5-bisphosphate-interacting proteins by quantitative lipid pull downs. In summary, data sets such as this serve as a resource for a global view of phosphoinositide-regulated nuclear functions. PMID:21048195

Lewis, Aurélia E.; Sommer, Lilly; Arntzen, Magnus Ø.; Strahm, Yvan; Morrice, Nicholas A.; Divecha, Nullin; D'Santos, Clive S.

2011-01-01

246

Identification of interactions in fractional-order systems with high dimensions  

NASA Astrophysics Data System (ADS)

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; Lin, Wei

2014-06-01

247

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

248

In vitro selection identifies key determinants for loop-loop interactions: RNA aptamers selective for the TAR RNA element of HIV-1.  

PubMed Central

We selected RNA aptamers specific for the trans-activation responsive (TAR) RNA, a stem-loop structure crucial for the transcription of the integrated genome of the human immunodeficiency virus. Most of the selected sequences could be folded as imperfect hairpins and displayed a 5'-GUCCCAGA-3' consensus motif constituting the apical loop. The six central bases of this consensus sequence are complementary to the entire TAR loop, leading to the formation of TAR RNA-aptamer "kissing" complexes. The consensus G and A residues closing the aptamer loop contributed to the high affinity (Kd = 30 nM at 23 degrees C) of the aptamers for the TAR RNA. This G A pair was shown to be crucial for binding to TAR at a low magnesium concentration. The selection also identified 5'-PuPy and 5'-PyPu base pairs at alpha and beta positions of the stem, next to the loop, respectively. This strategy offered a way to identify key determinants of loop-loop interactions and to generate high affinity ligands of TAR RNA structure. PMID:10606271

Duconge, F; Toulme, J J

1999-01-01

249

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

250

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.

251

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

PubMed

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

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

2013-03-01

252

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

PubMed

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

Kumar, Abhay; Majeti, Narasimha Vara Prasad

2014-07-01

253

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

254

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

255

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

256

Functional dissection of the major structural protein of bluetongue virus: identification of key residues within VP7 essential for capsid assembly.  

PubMed

A lattice of VP7 trimers forms the surface of the icosahedral bluetongue virus (BTV) core. To investigate the role of VP7 oligomerization in core assembly, a series of residues for substitution were predicted based on crystal structures of BTV type 10 VP7 molecule targeting the monomer-monomer contacts within the trimer. Seven site-specific substitution mutations of VP7 have been created using cDNA clones and were employed to produce seven recombinant baculoviruses. The effects of these mutations on VP7 solubility, ability to trimerize and formation of core-like particles (CLPs) in the presence of the scaffolding VP3 protein, were investigated. Of the seven VP7 mutants examined, three severely affected the stability of CLP, while two other mutants had lesser effect on CLP stability. Only one mutant had no apparent effect on the formation of the stable capsid. One mutant in which the conserved tyrosine at residue 271 (lower domain helix 6) was replaced by arginine formed insoluble aggregates, implying an effect in the folding of the molecule despite the prediction that such a change would be accommodated. All six soluble VP7 mutants were purified, and their ability to trimerize was examined. All mutants, including those that did not form stable CLPs, assembled into stable trimers, implying that single substitution may not be sufficient to perturb the complex monomer-monomer contacts, although subtle changes within the VP7 trimer could destabilize the core. The study highlights some of the key residues that are crucial for BTV core assembly and illustrates how the structure of VP7 in isolation underrepresents the dynamic nature of the assembly process at the biological level. PMID:10954567

Limn, C K; Staeuber, N; Monastyrskaya, K; Gouet, P; Roy, P

2000-09-01

257

Functional Dissection of the Major Structural Protein of Bluetongue Virus: Identification of Key Residues within VP7 Essential for Capsid Assembly  

PubMed Central

A lattice of VP7 trimers forms the surface of the icosahedral bluetongue virus (BTV) core. To investigate the role of VP7 oligomerization in core assembly, a series of residues for substitution were predicted based on crystal structures of BTV type 10 VP7 molecule targeting the monomer-monomer contacts within the trimer. Seven site-specific substitution mutations of VP7 have been created using cDNA clones and were employed to produce seven recombinant baculoviruses. The effects of these mutations on VP7 solubility, ability to trimerize and formation of core-like particles (CLPs) in the presence of the scaffolding VP3 protein, were investigated. Of the seven VP7 mutants examined, three severely affected the stability of CLP, while two other mutants had lesser effect on CLP stability. Only one mutant had no apparent effect on the formation of the stable capsid. One mutant in which the conserved tyrosine at residue 271 (lower domain helix 6) was replaced by arginine formed insoluble aggregates, implying an effect in the folding of the molecule despite the prediction that such a change would be accommodated. All six soluble VP7 mutants were purified, and their ability to trimerize was examined. All mutants, including those that did not form stable CLPs, assembled into stable trimers, implying that single substitution may not be sufficient to perturb the complex monomer-monomer contacts, although subtle changes within the VP7 trimer could destabilize the core. The study highlights some of the key residues that are crucial for BTV core assembly and illustrates how the structure of VP7 in isolation underrepresents the dynamic nature of the assembly process at the biological level. PMID:10954567

Limn, Chang-Kwang; Staeuber, Norbert; Monastyrskaya, Katherine; Gouet, Patrice; Roy, Polly

2000-01-01

258

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

PubMed Central

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

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

2014-01-01

259

Identification of rabbit and mouse beta-glucuronidases in human fibroblasts following direct interaction with lymphocytes.  

PubMed

Human fibroblasts totally deficient in beta-glucuronidase acquired high levels of enzyme activity when co-cultured with mouse or rabbit lymphocytes. Direct cell-to-cell contact was obligatory for this process. The enzyme acquired by the fibroblasts was shown to be identical to beta-glucuronidase from donor lymphocytes by its position of elution from DEAE-cellulose, thermal stability, mobility on polyacrylamide gels and by its antigenic determinants. The enzyme extracted from deficient fibroblasts after co-culture with lymphocytes showed no evidence of any hybridisation between human and mouse or rabbit sub-units. It is concluded that during direct cell interaction, enzymically active beta-glucuronidase is transferred directly from donor lymphocytes to deficient fibroblasts by a mechanism, previously shown not to involve normal receptor mediated endocytosis. PMID:7159606

Dean, M F; Olsen, I; Muir, H

1982-12-30

260

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

PubMed

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

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

2007-10-12

261

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

NASA Astrophysics Data System (ADS)

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

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

2007-10-01

262

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

263

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

264

Identification, immunolocalization, and immunological characterization of nitric oxide synthase-interacting protein from Clonorchis sinensis.  

PubMed

Recently, accumulating evidences indicate that nitric oxide (NO) is a potent mediator with diverse roles in regulating cellular functions, signaling pathways, and variety of pathological processes. In the present study, using data from the published genomic for Clonorchis sinensis (C. sinensis), we investigated a gene encoding nitric oxide synthase-interacting protein (NOSIP) of C. sinensis. Recombinant CsNOSIP (rCsNOSIP) was expressed and purified from Escherichia coli BL21. The open reading frame of CsNOSIP comprises 867 bp which encodes 289 amino acids and shares 72.9, 45.2, 47, 46.4, and 45.8% identity with NOSIP from Schistosoma mansoni, Xenopus laevis, Rattus norvegicus, Mus musculus, and Homo sapiens, respectively. Bioinformatics analysis suggested that the full-length sequence contains an eNOS-interacting domain and numerous B-cell epitopes. Quantitative RT-PCR indicated that CsNOSIP differentially transcribed throughout the adult worms, metacercariae, and egg stages of C. sinensis, and were highly expressed in the adult worms. Moreover, western blot analysis showed that the rCsNOSIP could be detected by the serum from BALB/c mice infected with C. sinensis and the serum from BALB/c mice immunized with excretory/secretory products (ESPs). Furthermore, immunolocalization assay showed that CsNOSIP was specifically localized in the intestine, vitellarium, and eggs of adult worm. Both immunoblot and immunolocalization results demonstrated that CsNOSIP was one component of ESPs of C. sinensis, which could be supported by SignalP analysis. Moreover, analysis of the antibody subclass and cytokine profile demonstrated that subcutaneously immunized BALB/c mice with rCsNOSIP could significantly enhance serum IgG1 level and up-regulate expression of IL-4 and IL-6 in the splenocytes. Our results suggested that CsNOSIP was an important antigen exposed to host immune system and probably involved in immune regulation of host by inducing Th2-polarized immune response. PMID:24604383

Bian, Meng; Li, Shan; Wang, Xiaoyun; Xu, Yanquan; Chen, Wenjun; Zhou, Chenhui; Chen, Xueqing; He, Lei; Xu, Jin; Liang, Chi; Wu, Zhongdao; Huang, Yan; Li, Xuerong; Yu, Xinbing

2014-05-01

265

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

PubMed Central

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

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

1996-01-01

266

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

267

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

NASA Astrophysics Data System (ADS)

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

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

2010-12-01

268

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

PubMed

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

Lo, S H; Janmey, P A; Hartwig, J H; Chen, L B

1994-06-01

269

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

PubMed

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

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

2014-04-01

270

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

PubMed

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

Frost, Carol D; Toner, Rachel N

2004-01-01

271

Identification of ORC1/CDC6-Interacting Factors in Trypanosoma brucei Reveals Critical Features of Origin Recognition Complex Architecture  

PubMed Central

DNA Replication initiates by formation of a pre-replication complex on sequences termed origins. In eukaryotes, the pre-replication complex is composed of the Origin Recognition Complex (ORC), Cdc6 and the MCM replicative helicase in conjunction with Cdt1. Eukaryotic ORC is considered to be composed of six subunits, named Orc1–6, and monomeric Cdc6 is closely related in sequence to Orc1. However, ORC has been little explored in protists, and only a single ORC protein, related to both Orc1 and Cdc6, has been shown to act in DNA replication in Trypanosoma brucei. Here we identify three highly diverged putative T. brucei ORC components that interact with ORC1/CDC6 and contribute to cell division. Two of these factors are so diverged that we cannot determine if they are eukaryotic ORC subunit orthologues, or are parasite-specific replication factors. The other we show to be a highly diverged Orc4 orthologue, demonstrating that this is one of the most widely conserved ORC subunits in protists and revealing it to be a key element of eukaryotic ORC architecture. Additionally, we have examined interactions amongst the T. brucei MCM subunits and show that this has the conventional eukaryotic heterohexameric structure, suggesting that divergence in the T. brucei replication machinery is limited to the earliest steps in origin licensing. PMID:22412905

Tiengwe, Calvin; Marcello, Lucio; Farr, Helen; Gadelha, Catarina; Burchmore, Richard; Barry, J. David; Bell, Stephen D.; McCulloch, Richard

2012-01-01

272

Computer-assisted identification and volumetric quantification of dynamic contrast enhancement in brain MRI: an interactive system  

NASA Astrophysics Data System (ADS)

We present a dedicated segmentation system for tumor identification and volumetric quantification in dynamic contrast brain magnetic resonance (MR) scans. Our goal is to offer a practically useful tool at the end of clinicians in order to boost volumetric tumor assessment. The system is designed to work in an interactive mode such that maximizes the integration of computing capacity and clinical intelligence. We demonstrate the main functions of the system in terms of its functional flow and conduct preliminary validation using a representative pilot dataset. The system is inexpensive, user-friendly, easy to deploy and integrate with picture archiving and communication systems (PACS), and possible to be open-source, which enable it to potentially serve as a useful assistant for radiologists and oncologists. It is anticipated that in the future the system can be integrated into clinical workflow so that become routine available to help clinicians make more objective interpretations of treatment interventions and natural history of disease to best advocate patient needs.

Wu, Shandong; Avgeropoulos, Nicholas G.; Rippe, David J.

2013-03-01

273

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

PubMed Central

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

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

2012-01-01

274

Identification of a novel protein capable of interacting with the IL-3 receptor.  

PubMed

IL-3 has numerous functions in hematopoiesis yet its receptor has not been fully characterized. We have developed two mAb, 4G8 and 2F2, that markedly inhibited IL-3-dependent proliferation whereas only marginally affecting IL-2 or IL-4-induced proliferation. On Western blots, both antibodies identified the same protein, which varied in size from 115 to 145 kDa in six cell lines tested. The 4G8/2F2 Ag was detected at moderate density, on a wide variety of cells including IL-3-dependent cell lines and T lymphocytes. Radioligand binding studies revealed that 4G8, but not 2F2, could inhibit the binding of 125I-IL-3 to the high affinity IL-3R. These data suggest that the mAb 4G8 and 2F2 recognize different epitopes on the same Ag, and suggest furthermore that the inhibition of IL-3-dependent proliferation mediated by 2F2, in particular, does not occur via inhibition of ligand binding. Neither antibody showed an enhanced level of fluorescent staining of Cos 7 cells transfected with the low affinity IL-3R cDNA. In addition, 4G8 did not inhibit IL-3 binding to L cells transfected with the cloned IL-3R or IL-4R despite the fact that 4G8 was expressed on these cells. These data suggest that the 4G8/2F2 Ag is a unique cell surface protein that can interact with the endogenous functional IL-3R. PMID:2005398

Morel, P A; Schreurs, J; Townsend, K; Gross, M; Chiller, J M; Tweardy, D J

1991-04-01

275

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

276

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

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

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 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

279

Unnatural selection: talent identification and development in sport.  

PubMed

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

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

2005-01-01

280

Energetic characterization of the basic fibroblast growth factor-heparin interaction: identification of the heparin binding domain.  

PubMed

Fibroblast growth factors (FGF's) interact on cell surfaces with "low-affinity" heparan sulfate proteoglycans (HSPG) and "high-affinity" FGF receptors (FGFR) to initiate cell proliferation. Previous reports have implicated the binding of heparin, or heparan sulfate, to FGF as essential for FGF-mediated signal transduction and mitogenicity. However, the molecular recognition events which dictate the specificity of this interaction have remained elusive. Amino acid residues on the surface of basic FGF (bFGF) were targeted as potential heparin contacts on the basis of the position of sulfate anions in the X-ray crystal structure of bFGF and of a modeled pentasaccharide heparin-bFGF complex. Each identified amino acid was replaced individually with alanine by site-directed mutagenesis, and the resulting mutant proteins were characterized for differences in binding to a low molecular weight heparin (approximately 3000) by isothermal titrating calorimetry and also for differences in [NaCl] elution from a heparin-Sepharose affinity resin. The combination of site-directed mutagenesis and titrating calorimetry permitted an analysis of the energetic contributions of individual bFGF residues in the binding of heparin to bFGF. The key amino acids which comprise the heparin binding domain on bFGF constitute a discontinuous binding epitope and include K26, N27, R81, K119, R120, T121, Q123, K125, K129, Q134, and K135. Addition of the observed delta delta G degrees of binding for each single site mutant accounts for 8.56 kcal/mol (> 95%) of the free energy of binding. The delta delta G degrees values for N27A, R120A, K125A, and Q134A are all greater than 1 kcal/mol each, and these four amino acids together contribute 4.8 kcal/mol (56%) to the total binding free energy. Amino acid residues K119 through K135 reside in the C-terminal domain of bFGF and collectively contribute 6.6 kcal/mol (76%) of the binding free energy. Although 7 out of the 11 identified amino acids in the heparin binding domain are positively charged, a 7-fold increase in [NaCl] decreases the affinity of wild-type bFGF binding to heparin only 37-fold (Kd at 0.1 M NaCl = 470 nM vs Kd at 0.7 M NaCl = 17.2 microM). This indicates that pure electrostatic interactions contribute only 30% of the binding free energy as analyzed by polyelectrolyte theory and that more specific nonionic interactions, such as hydrogen bonding and van der Waals packing, contribute the majority of the free energy for this binding reaction. PMID:8142385

Thompson, L D; Pantoliano, M W; Springer, B A

1994-04-01

281

Pax6 Interactions with Chromatin and Identification of Its Novel Direct Target Genes in Lens and Forebrain  

PubMed Central

Pax6 encodes a specific DNA-binding transcription factor that regulates the development of multiple organs, including the eye, brain and pancreas. Previous studies have shown that Pax6 regulates the entire process of ocular lens development. In the developing forebrain, Pax6 is expressed in ventricular zone precursor cells and in specific populations of neurons; absence of Pax6 results in disrupted cell proliferation and cell fate specification in telencephalon. In the pancreas, Pax6 is essential for the differentiation of ?-, ?- and ?-islet cells. To elucidate molecular roles of Pax6, chromatin immunoprecipitation experiments combined with high-density oligonucleotide array hybridizations (ChIP-chip) were performed using three distinct sources of chromatin (lens, forebrain and ?-cells). ChIP-chip studies, performed as biological triplicates, identified a total of 5,260 promoters occupied by Pax6. 1,001 (133) of these promoter regions were shared between at least two (three) distinct chromatin sources, respectively. In lens chromatin, 2,335 promoters were bound by Pax6. RNA expression profiling from Pax6+/? lenses combined with in vivo Pax6-binding data yielded 76 putative Pax6-direct targets, including the Gaa, Isl1, Kif1b, Mtmr2, Pcsk1n, and Snca genes. RNA and ChIP data were validated for all these genes. In lens cells, reporter assays established Kib1b and Snca as Pax6 activated and repressed genes, respectively. In situ hybridization revealed reduced expression of these genes in E14 cerebral cortex. Moreover, we examined differentially expressed transcripts between E9.5 wild type and Pax6?/? lens placodes that suggested Efnb2, Fat4, Has2, Nav1, and Trpm3 as novel Pax6-direct targets. Collectively, the present studies, through the identification of Pax6-direct target genes, provide novel insights into the molecular mechanisms of Pax6 gene control during mouse embryonic development. In addition, the present data demonstrate that Pax6 interacts preferentially with promoter regions in a tissue-specific fashion. Nevertheless, nearly 20% of the regions identified are accessible to Pax6 in multiple tissues. PMID:23342162

Huang, Jie; Ninkovic, Jovica; Walcher, Tessa; Wolf, Louise; Vitenzon, Ariel; Zheng, Deyou; Gotz, Magdalena; Beebe, David C.; Zavadil, Jiri; Cvekl, Ales

2013-01-01

282

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

283

The APETALA-2Like Transcription Factor OsAP2-39 Controls Key Interactions between Abscisic Acid and Gibberellin in Rice  

Microsoft Academic Search

The interaction between phytohormones is an important mechanism which controls growth and developmental processes in plants. Deciphering these interactions is a crucial step in helping to develop crops with enhanced yield and resistance to environmental stresses. Controlling the expression level of OsAP2-39 which includes an APETALA 2 (AP2) domain leads to phenotypic changes in rice. Overexpression of OsAP2-39 leads to

Mahmoud W. Yaish; Ashraf El-kereamy; Tong Zhu; Perrin H. Beatty; Allen G. Good; Yong-Mei Bi; Steven J. Rothstein

2010-01-01

284

Finding new protein interactions using the DUALhunter The identification of protein interactions has been greatly simplified by the invention of yeast-based  

E-print Network

anchors the protein in the endoplasmic reticulum (ER) membrane, and the C-terminal half of ubiquitin (CubDNA library, and the protein's interacting partners are isolated. No prior knowledge of the interaction

Cai, Long

285

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

286

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

287

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

PubMed Central

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

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

2013-01-01

288

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

289

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

290

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

291

Modern key agreement techniques  

Microsoft Academic Search

Abstract: We present a survey of modern key agreement techniques, and discuss distinguishing characteristics,including identity (entity) authentication, implicit key authentication, key confirmation, andkey freshness.

Rainer A. Rueppel; Paul C. Van Oorschot

1994-01-01

292

Identification of RNA Helicase A as a Cellular Factor That Interacts with Influenza A Virus NS1 Protein and Its Role in the Virus Life Cycle  

PubMed Central

Influenza A virus NS1 protein has multiple functions in the infected cell during the virus life cycle. Identification of novel cellular factors that interact with NS1 and understanding their functions in virus infection are of great interest. Recombinant viruses carrying a tagged NS1 are valuable for investigation of interactions between NS1 and cellular factors in the context of virus infection. Here, we report the generation of replication-competent recombinant influenza A viruses bearing a Strep tag in the NS1 protein. Purification of a protein complex associated with Strep-tagged NS1 from virus-infected cells followed by mass spectrometry revealed a number of attractive host factors. Among them, we focused our study on RNA helicase A (RHA) in this report. Through biomedical and functional analyses, we demonstrated that RHA interacts with NS1 in an RNA-dependent manner. Knockdown of RHA resulted in a significant reduction on virus yield and polymerase activity in a minigenome assay. Our cell-free viral genome replication assay showed that viral RNA replication and transcription can be enhanced by addition of RHA, and the enhanced effect of RHA required its ATP-dependent helicase activity. In summary, we established a system to identify cellular factors that interact with NS1 protein during virus infection and furthermore demonstrated that RHA interacts with NS1 and enhances viral replication and transcription. PMID:22171255

Lin, Li; Li, Yang; Pyo, Hyun-Mi; Lu, Xinya; Raman, Sathya N. Thulasi; Liu, Qiang; Brown, Earl G.

2012-01-01

293

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

294

Interaction of Penicillin-Binding Protein 2x and Ser/Thr protein kinase StkP, two key players in Streptococcus pneumoniae?R6 morphogenesis.  

PubMed

Bacterial cell growth and division require the co-ordinated action of peptidoglycan biosynthetic enzymes and cell morphogenesis proteins. However, the regulatory mechanisms that allow generating proper bacterial shape and thus preserving cell integrity remain largely uncharacterized, especially in ovococci. Recently, the conserved eukaryotic-like Ser/Thr protein kinase of Streptococcus pneumoniae (StkP) was demonstrated to play a major role in cell shape and division. Here, we investigate the molecular mechanisms underlying the regulatory function(s) of StkP and show that it involves one of the essential actors of septal peptidoglycan synthesis, Penicillin-Binding Protein 2x (PBP2x). We demonstrate that StkP and PBP2x interact directly and are present in the same membrane-associated complex in S.?pneumoniae. We further show that they both display a late-division localization pattern at the division site and that the positioning of PBP2x depends on the presence of the extracellular PASTA domains of StkP. We demonstrate that StkP and PBP2x interaction is mediated by their extracellular regions and that the complex formation is inhibited in vitro in the presence of cell wall fragments. These data suggest that the role of StkP in cell division is modulated by an interaction with PBP2x. PMID:23899042

Morlot, C; Bayle, L; Jacq, M; Fleurie, A; Tourcier, G; Galisson, F; Vernet, T; Grangeasse, C; Di Guilmi, A M

2013-10-01

295

Exploring novel strategies for AIDS protozoal pathogens: ?-helix mimetics targeting a key allosteric protein-protein interaction in C. hominis TS-DHFR  

PubMed Central

The bifunctional enzyme thymidylate synthase–dihydrofolate reductase (TS–DHFR) from the protozoal parasite Cryptosporidium hominis is a potential molecular target for the design of antiparasitic therapies for AIDS-related opportunistic infections. The enzyme exists as a homodimer with each monomer containing a unique swap domain known as a “crossover helix” that binds in a cleft on the adjacent DHFR active site. This crossover helix is absent in species containing monofunctional forms of DHFR such as human. An in-depth understanding of protein–protein interactions between the crossover helix and adjacent DHFR active site that might modulate enzyme integrity or function would allow for insights into rational design of species-specific allosteric inhibitors. Mutational analysis coupled with structural studies and biophysical and kinetic characterization of crossover helix mutants identifies this domain as essential for full enzyme stability and catalytic activity, and pinpoints these effects to distinct faces of the crossover helix important in protein–protein interactions. Moreover, targeting this helical protein interaction with ?-helix mimetics of the crossover helix leads to selective inhibition and destabilization of the C. hominis TS–DHFR enzyme, thus validating this region as a new avenue to explore for species-specific inhibitor design. PMID:24324854

Martucci, W. Edward; Rodriguez, Johanna M.; Vargo, Melissa A.; Marr, Matthew; Hamilton, Andrew D.

2013-01-01

296

Optimizing Requirements Decisions with KEYS  

NASA Technical Reports Server (NTRS)

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

Jalali, Omid; Menzies, Tim; Feather, Martin

2008-01-01

297

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

298

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

SciTech Connect

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

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

2009-12-18

299

The identification and characterisation of a functional interaction between arginyl-tRNA-protein transferase and topoisomerase II  

SciTech Connect

Topoisomerase II is required for the viability of all eukaryotic cells. It plays important roles in DNA replication, recombination, chromosome segregation, and the maintenance of the nuclear scaffold. Proteins that interact with and regulate this essential enzyme are of great interest. To investigate the role of proteins interacting with the N-terminal domain of the Saccharomyces cerevisiae topoisomerase II, we used a yeast two-hybrid protein interaction screen. We identified an interaction between arginyl-tRNA-protein transferase (Ate1) and the N-terminal domain of the S. cerevisiae topoisomerase II, including the potential site of interaction. Ate1 is a component of the N-end rule protein degradation pathway which targets proteins for degradation. We also propose a previously unidentified role for Ate1 in modulating the level of topoisomerase II through the cell cycle.

Barker, Catherine R. [University of Liverpool, School of Clinical Sciences, Division of Gastroenterology, Henry Wellcome Laboratory of Molecular and Cellular Gastroenterology, Crown Street, Liverpool L69 3BX (United Kingdom); Mouchel, Nathalie A.P. [Compton Paddock Laboratories, Frilsham Home Farm Business Unit, Yattendon, Thatcham RG 18 0XT (United Kingdom); Jenkins, John R. [University of Liverpool, School of Clinical Sciences, Division of Gastroenterology, Henry Wellcome Laboratory of Molecular and Cellular Gastroenterology, Crown Street, Liverpool L69 3BX (United Kingdom)]. E-mail: John.Jenkins@Liverpool.ac.uk

2006-04-07

300

Quantum identification system Miloslav Dusek,1  

E-print Network

identification system combining a classical identification procedure and quantum key distribution is proposed only once and the distribution of a common secret string is achieved by means of quantum keyQuantum identification system Miloslav Dusek,1 Ondrej Haderka,2,1 Martin Hendrych,2,1 and Robert

Dusek, Miloslav

301

Quantum identification system  

E-print Network

A secure quantum identification system combining a classical identification procedure and quantum key distribution is proposed. Each identification sequence is always used just once and new sequences are ``refuelled'' from a shared provably secret key transferred through the quantum channel. Two identification protocols are devised. The first protocol can be applied when legitimate users have an unjammable public channel at their disposal. The deception probability is derived for the case of a noisy quantum channel. The second protocol employs unconditionally secure authentication of information sent over the public channel, and thus it can be applied even in the case when an adversary is allowed to modify public communications. An experimental realization of a quantum identification system is described.

Miloslav Dusek; Ondrej Haderka; Martin Hendrych; Robert Myska

1998-09-10

302

Molecular basis of cannabinoid CB1 receptor coupling to the G protein heterotrimer G?i??: identification of key CB1 contacts with the C-terminal helix ?5 of G?i.  

PubMed

The cannabinoid (CB1) receptor is a member of the rhodopsin-like G protein-coupled receptor superfamily. The human CB1 receptor, which is among the most expressed receptors in the brain, has been implicated in several disease states, including drug addiction, anxiety, depression, obesity, and chronic pain. Different classes of CB1 agonists evoke signaling pathways through the activation of specific subtypes of G proteins. The molecular basis of CB1 receptor coupling to its cognate G protein is unknown. As a first step toward understanding CB1 receptor-mediated G protein signaling, we have constructed a ternary complex structural model of the CB1 receptor and Gi heterotrimer (CB1-Gi), guided by the x-ray structure of ?2-adrenergic receptor (?2AR) in complex with Gs (?2AR-Gs), through 824-ns duration molecular dynamics simulations in a fully hydrated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer environment. We identified a group of residues at the juxtamembrane regions of the intracellular loops 2 and 3 (IC2 and IC3) of the CB1 receptor, including Ile-218(3.54), Tyr-224(IC2), Asp-338(6.30), Arg-340(6.32), Leu-341(6.33), and Thr-344(6.36), as potential key contacts with the extreme C-terminal helix ?5 of G?i. Ala mutations of these residues at the receptor-Gi interface resulted in little G protein coupling activity, consistent with the present model of the CB1-Gi complex, which suggests tight interactions between CB1 and the extreme C-terminal helix ?5 of G?i. The model also suggests that unique conformational changes in the extreme C-terminal helix ?5 of G? play a crucial role in the receptor-mediated G protein activation. PMID:24092756

Shim, Joong-Youn; Ahn, Kwang H; Kendall, Debra A

2013-11-01

303

Mineral Identification  

NSDL National Science Digital Library

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

Rmesser

2010-11-16

304

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

PubMed

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

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

2011-07-01

305

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

Microsoft Academic Search

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

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

1996-01-01

306

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

NASA Astrophysics Data System (ADS)

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

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

2013-03-01

307

Assessing Effects and interactions among key variables affecting the growth of mixotrophic microalgae: pH, inoculum volume, and growth medium composition.  

PubMed

A 2(3) + 3 full factorial experimental design was used to evaluate growth rate and biomass productivity of four selected, high-biomass-yielding microalgae species,namely, Chlorella vulgaris (CV), Scenedesmus acutus (SA), Chlamydomonas reinhardtii (CR), and Chlamydomonas debaryana (CD), in mixtures of growth medium (MWC) and wastewater at different proportions (from 20 to 50% of MWC) and at different pH (from 7 to 9). Multilinear regression analysis of the biomass productivity data showed that for SA and CD the biomass productivity was independent of the proportion of medium (MWC), while the growth of CV and CR slowed down in mixtures with high proportions of wastewater. However, the biomass productivity of SA was dependent on pH, while the growth of the other microalgae was independent of pH (7-9). When evaluating the influence of pH and proportion of medium, CD appeared most robust among the algae species, despite its lower biomass productivity. All the four species reduced 80-90% of the nitrate [Formula: see text] and 60-70% of the ammonia [Formula: see text] initially present in the wastewater:medium mixture, although the extent of the reduction was dependent on the initial [Formula: see text] ratio. Both SA and CV reduced ?20-25% of the chemical oxygen demand (COD) contained in the wastewater. This study shows the remarkable influence of certain variables that are often ignored in the search for optimal conditions of microalgal growth and also reveals the importance of considering interactions among growth variables in potential applications at large scale, particularly in the field of bioremediation. PMID:24274013

Ale, M T; Pinelo, M; Meyer, A S

2014-01-01

308

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.

309

Gene by Smoking Interaction in Hypertension: Identification of a Major QTL on Chromosome 15q for Systolic Blood Pressure in Mexican Americans  

PubMed Central

OBJECTIVE Our objective was to investigate the influence of gene by smoking (GxS) interaction on hypertension (HT) and blood pressure (BP) using genome-wide linkage analysis in Mexican Americans, followed by SNP fine mapping of candidate genes in the linked chromosomal region. METHODS We used nonparametric methods to test for linkage of microsatellites with HT and BP measures in smokers, non-smokers, and the combined group. To begin fine-mapping of a major QTL for SBP on chromosome 15q that showed strong evidence for GxS interaction, we genotyped 55 SNPs in 9 candidate genes for association studies using two population-based statistical methods. RESULTS The strongest evidence for GxS interaction (p = 0.0004) was found for SBP on chromosome 15q, where a major QTL (LOD = 3.36) was identified only in non-smokers. Follow-up studies identified three SNPs in three genes (ANPEP, IGF1R, and SLCO3A1) that showed associations with SBP only in non-smokers, cumulatively accounting for a 7 mmHg increase in SBP. However, conditional linkage analyses that accounted for phenotypic effects of these SNPs only slightly reduced the original LOD score. CONCLUSION The detection of a major QTL on chromosome 15q for SBP in non-smokers indicates the presence of loci that influence BP via GxS interactions. However, identification of the genes that underlie such QTL effects remains a challenge. Although we found three candidate genes that showed significant associations with SBP in non-smokers, further studies are required to identify the gene(s) that underlie the chromosome 15q QTL that influences SBP via GxS interactions. PMID:19330903

Montasser, May E.; Shimmin, Lawrence C.; Hanis, Craig L.; Boerwinkle, Eric; Hixson, James E.

2009-01-01

310

Computational identification of post-translational modification-based nuclear import regulations by characterizing nuclear localization signal-import receptor interaction.  

PubMed

The binding affinity between a nuclear localization signal (NLS) and its import receptor is closely related to corresponding nuclear import activity. PTM-based modulation of the NLS binding affinity to the import receptor is one of the most understood mechanisms to regulate nuclear import of proteins. However, identification of such regulation mechanisms is challenging due to the difficulty of assessing the impact of PTM on corresponding nuclear import activities. In this study we proposed NIpredict, an effective algorithm to predict nuclear import activity given its NLS, in which molecular interaction energy components (MIECs) were used to characterize the NLS-import receptor interaction, and the support vector regression machine (SVR) was used to learn the relationship between the characterized NLS-import receptor interaction and the corresponding nuclear import activity. Our experiments showed that nuclear import activity change due to NLS change could be accurately predicted by the NIpredict algorithm. Based on NIpredict, we developed a systematic framework to identify potential PTM-based nuclear import regulations for human and yeast nuclear proteins. Application of this approach has identified the potential nuclear import regulation mechanisms by phosphorylation of two nuclear proteins including SF1 and ORC6. Proteins 2014; 82:2783-2796. © 2014 Wiley Periodicals, Inc. PMID:25043850

Lin, Jhih-Rong; Liu, Zhonghao; Hu, Jianjun

2014-10-01

311

Identification of histone H4-like TAF in Schizosaccharomyces pombe as a protein that interacts with WD repeat-containing TAF.  

PubMed

The general transcription factor TFIID consists of the TATA-binding protein (TBP) and multiple TBP-associated factors (TAFs). We previously identified two distinct WD repeat-containing TAFs, spTAF72 and spTAF73, in the fission yeast Schizosaccharomyces pombe. Here we report the identification of another S.pombe TAF, spTAF50, which is the S.pombe homolog of histone H4-like TAFs such as human TAF80, Drosophila TAF60 and Saccharomyces cerevisiae TAF60. spTAF50 was identified in a two-hybrid screen as a protein that interacts with the C-terminal WD repeat-containing region of spTAF72. Gene disruption revealed that spTAF50 is essential for cell viability. In vitro, spTAF50 bound to spTAF72 but less efficiently to spTAF73. In S.pombe cells, spTAF50 was detected as a protein with an apparent molecular mass of approximately 50 kDa. Immunoprecipitation experiments demonstrated that spTAF50 is present in both the TFIID and SAGA-like complexes as in the case of spTAF72. These results indicate that the C-terminal region of spTAF72, which largely consists of WD repeats, interacts with spTAF50 in the TFIID and SAGA-like complexes, suggesting a role for the WD repeat domain in the interaction between TAFs. PMID:11972332

Mitsuzawa, Hiroshi; Ishihama, Akira

2002-05-01

312

Interaction of Mycobacterium leprae with human airway epithelial cells: adherence, entry, survival, and identification of potential adhesins by surface proteome analysis.  

PubMed

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

Silva, Carlos A M; Danelishvili, Lia; McNamara, Michael; Berredo-Pinho, Márcia; Bildfell, Robert; Biet, Franck; Rodrigues, Luciana S; Oliveira, Albanita V; Bermudez, Luiz E; Pessolani, Maria C V

2013-07-01

313

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

PubMed Central

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

2010-01-01

314

COURSE OUTLINE FOR 342--WOOD ANATOMY, PROPERTIES AND IDENTIFICATION  

E-print Network

1 COURSE OUTLINE FOR 342--WOOD ANATOMY, PROPERTIES AND IDENTIFICATION 3 Credits Instructor: Ed and identification (pgs. 127-160; 407- 501). Gross identification using keys. 5 Examination (Tuesday); Gymnosperm-501). Gross and microscopic identification using keys. Burke will be in Tennessee and Virginia teaching

Vonessen, Nikolaus

315

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

316

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

317

A Novel Genetic System Based on Zinc Finger Nucleases for the Identification of Interactions between Proteins In Vivo  

PubMed Central

Yeast two-hybrid (Y2H) methods are powerful tools for detecting protein–protein interactions. The traditional Y2H method has been widely applied to screen novel protein interactions since it was established two decades ago. The high false-positive rate of the traditional method drove the development of modified Y2H systems. Here, we describe a novel Y2H system using zinc-finger nucleases (ZFNs). ZFNs contain two functional domains, a zinc-finger DNA-binding domain (ZFP) and a non-specific nuclease domain (FokI). In this system, the bait is expressed as a fusion protein with a specific ZFP, and the prey is fused to the FokI. A reporter vector is designed such that the ZFN target site disrupts the Gal4 open reading frame. By transforming the three plasmids into a yeast strain (AH109), the interaction between the bait and prey proteins reconstitutes ZFN function and generates the double-strand break (DSB) on its target site. The DNA DSB repair restores Gal4 function, which activates the expression of the four reporter genes. We used p53-SV40LT interacting proteins to prove the concept. In addition, 80% positive rate was observed in a cDNA screening test against WDSV orfA protein. Our results strongly suggested that this Y2H system could increase screening reliability and reproducibility, and provide a novel approach for interactomics research. PMID:24392024

Lin, Juan; Shao, Simin; Zhang, Tingting; Xu, Huarong; Wei, Zehui; Zhang, Zhiying

2013-01-01

318

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

Microsoft Academic Search

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

Ronald D. Snyder; Marc R. Arnone

2002-01-01

319

379. Identification of Structural Aspects of Adenovirus Interactions with Host Factors In Vivo Using Tandem Mass Spectrometry  

Microsoft Academic Search

Intensive studies of adenovirus infectivity and bio-distribution in animal models demonstrated that liver tissue is responsible for clearance of the bulk of intravenously applied vector. We recently demonstrated that adenovirus binding to blood factors, specifically coagulation factor IX and C4 binding protein, leads to high level hepatocyte transduction and virus trapping by Kupffer cells. Apparently, virus interaction with the coxsackie-

Oleksandr Kalyuzhniy; Catalin Doneanu; Martin Sadilek; Dmitry M. Shayakhmetov

2006-01-01

320

Identification of multiple proteins that interact with functional regions of the human cardiac alpha-actin promoter.  

PubMed

5' Sequences of the human cardiac alpha-actin gene are involved in the tissue-specific and developmental regulation of the gene. Deletion analyses combined with transient expression experiments in muscle cells have demonstrated three primary regions of functional importance (A. Minty and L. Kedes, Mol. Cell. Biol. 6:2125-2136, 1986; T. Miwa and L. Kedes, Mol. Cell. Biol. 7:2803-2813, 1987), and we have previously demonstrated binding of a protein indistinguishable from serum response factor (SRF) to the most proximal region (T.A. Gustafson, T. Miwa, L.M. Boxer, and L. Kedes, Mol. Cell. Biol. 8:4110-4119, 1988). In this report, we examine protein interaction with the remainder of the promoter. Gel shift and footprinting assays revealed that at least seven distinct nuclear proteins interacted with known and putative regulatory regions of the promoter. The transcription factor Sp1 bound to eight sites, as demonstrated by footprinting assays and gel shift analysis with purified Sp1. Purified CCAAT box-binding transcription factor CTF/NF-I and Sp1 were shown to interact with the far-upstream regulatory element at -410, and footprint analysis showed extensive overlap of these two sites. Two unidentified proteins with similar but distinct footprints interacted with the second region of functional importance at -140, which contains the second CArG motif [CC(A + T rich)6GG], and these proteins were shown to be distinct from SRF. SRF was found to bind to the remaining three CArG boxes, two of which were closely interdigitated with Sp1 sites. In addition, CArG box 4 was found to interact with SRF and another distinct protein whose footprint was contained within the SRF-binding site. Sequences surrounding the TATA box were also shown to bind proteins. Sp1 was shown to bind to a site immediately downstream from the TATA box and to a site within the first exon. Thus, each of the three functional upstream regions, as defined by transfection assays, was shown to interact with five factors: Sp1 and CTF/NF-I at the upstream site, two unidentified proteins at the central site, and SRF at the most proximal site. These results suggest that expression of the cardiac actin gene in muscle cells is controlled by complex interactions among multiple upstream and intragenic elements. PMID:2796988

Gustafson, T A; Kedes, L

1989-08-01

321

Identification of multiple proteins that interact with functional regions of the human cardiac alpha-actin promoter.  

PubMed Central

5' Sequences of the human cardiac alpha-actin gene are involved in the tissue-specific and developmental regulation of the gene. Deletion analyses combined with transient expression experiments in muscle cells have demonstrated three primary regions of functional importance (A. Minty and L. Kedes, Mol. Cell. Biol. 6:2125-2136, 1986; T. Miwa and L. Kedes, Mol. Cell. Biol. 7:2803-2813, 1987), and we have previously demonstrated binding of a protein indistinguishable from serum response factor (SRF) to the most proximal region (T.A. Gustafson, T. Miwa, L.M. Boxer, and L. Kedes, Mol. Cell. Biol. 8:4110-4119, 1988). In this report, we examine protein interaction with the remainder of the promoter. Gel shift and footprinting assays revealed that at least seven distinct nuclear proteins interacted with known and putative regulatory regions of the promoter. The transcription factor Sp1 bound to eight sites, as demonstrated by footprinting assays and gel shift analysis with purified Sp1. Purified CCAAT box-binding transcription factor CTF/NF-I and Sp1 were shown to interact with the far-upstream regulatory element at -410, and footprint analysis showed extensive overlap of these two sites. Two unidentified proteins with similar but distinct footprints interacted with the second region of functional importance at -140, which contains the second CArG motif [CC(A + T rich)6GG], and these proteins were shown to be distinct from SRF. SRF was found to bind to the remaining three CArG boxes, two of which were closely interdigitated with Sp1 sites. In addition, CArG box 4 was found to interact with SRF and another distinct protein whose footprint was contained within the SRF-binding site. Sequences surrounding the TATA box were also shown to bind proteins. Sp1 was shown to bind to a site immediately downstream from the TATA box and to a site within the first exon. Thus, each of the three functional upstream regions, as defined by transfection assays, was shown to interact with five factors: Sp1 and CTF/NF-I at the upstream site, two unidentified proteins at the central site, and SRF at the most proximal site. These results suggest that expression of the cardiac actin gene in muscle cells is controlled by complex interactions among multiple upstream and intragenic elements. Images PMID:2796988

Gustafson, T A; Kedes, L

1989-01-01

322

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

323

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

PubMed

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

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

2013-10-01

324

Identification of a small molecule that modifies MglA/SspA interaction and impairs intramacrophage survival of Francisella tularensis.  

PubMed

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

325

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

326

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

PubMed

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

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

2014-01-01

327

Identification of structural determinants of ligand selectivity in 5-HT? receptor subtypes on the basis of protein-ligand interactions.  

PubMed

Drug selectivity is one of the most critical improvement steps in drug development. The 5-hydroxytryptamine 2 (5-HT?) receptor has 3 subtypes that exhibit different pharmacological functions. Because of their high amino acid sequence similarity, designing small molecules that selectively activate only 1 receptor among the 3 subtypes is difficult. We performed homology modeling of the 5-HT? receptor subtypes using the ??-adrenergic receptor as a template to identify differences in active sites that may influence 5-HT? receptor agonist selectivity. A subset of selective 5-HT? agonists was docked into the modeled protein structures to investigate their interactions with each receptor. Subtype-specific active site residues at positions xl2.54, 5.39, and 5.46 interacted differently with each ligand. Molecular dynamics simulations revealed that position 5.46 of the 5-HT(2A) receptor interacted more favorably with selective 5-HT(2A) agonists than with selective 5-HT(2B) agonists. These computationally obtained insights provided clues to improving agonist selectivity for specific pharmacological action at 5-HT? receptors. PMID:23085173

Jang, Jae Wan; Kim, Min Sup; Cho, Yong Seo; Cho, Art E; Pae, Ae Nim

2012-09-01

328

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; Levesque, Georges

2011-01-01

329

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

PubMed

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 with 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' 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 complementary 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 antianthrax and antiangiogenic diseases. PMID:23479355

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

2013-07-01

330

Identification of a Site in Sar1 Involved in the Interaction with the Cytoplasmic Tail of Glycolipid Glycosyltransferases*  

PubMed Central

Glycolipid glycosyltransferases (GGT) are transported from the endoplasmic reticulum (ER) to the Golgi, their site of residence, via COPII vesicles. An interaction of a (R/K)X(R/K) motif at their cytoplasmic tail (CT) with Sar1 is critical for the selective concentration in the transport vesicles. In this work using computational docking, we identify three putative binding pockets in Sar1 (sites A, B, and C) involved in the interaction with the (R/K)X(R/K) motif. Sar1 mutants with alanine replacement of amino acids in site A were tested in vitro and in cells. In vitro, mutant versions showed a reduced ability to bind immobilized peptides with the CT sequence of GalT2. In cells, Sar1 mutants (Sar1D198A) specifically affect the exiting of GGT from the ER, resulting in an ER/Golgi concentration ratio favoring the ER. Neither the typical Golgi localization of GM130 nor the exiting and transport of the G protein of the vesicular stomatitis virus were affected. The protein kinase inhibitor H89 produced accumulation of Sec23, Sar1, and GalT2 at the ER exit sites; Sar1D189A also accumulated at these sites, but in this case GalT2 remained disperse along ER membranes. The results indicate that amino acids in site A of Sar1 are involved in the interaction with the CT of GGT for concentration at ER exiting sites. PMID:20650895

Quintero, Cristián A.; Giraudo, Claudio G.; Villarreal, Marcos; Montich, Guillermo; Maccioni, Hugo J. F.

2010-01-01

331

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

332

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. [BMB Reports 2014; 47(11): 643-648]. PMID:25154718

Shin, Jihye; Sohn, Young Chang

2014-11-01

333

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

PubMed

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

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

2014-01-01

334

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

335

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

336

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

337

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

338

Identification of a cis-acting DNA–protein interaction implicated in singular var gene choice in Plasmodium falciparum  

PubMed Central

Plasmodium falciparum is responsible for the most severe form of malaria in humans. Antigenic variation of P. falciparum erythrocyte membrane protein 1 leads to immune evasion and occurs through switches in mutually exclusive var gene transcription. The recent progress in Plasmodium epigenetics notwithstanding, the mechanisms by which singularity of var activation is achieved are unknown. Here, we employed a functional approach to dissect the role of var gene upstream regions in mutually exclusive activation. Besides identifying sequence elements involved in activation and initiation of transcription, we mapped a region downstream of the transcriptional start site that is required to maintain singular var gene choice. Activation of promoters lacking this sequence occurs no longer in competition with endogenous var genes. Within this region we pinpointed a sequence-specific DNA–protein interaction involving a cis-acting sequence motif that is conserved in the majority of var loci. These results suggest an important role for this interaction in mutually exclusive locus recognition. Our findings are furthermore consistent with a novel mechanism for the control of singular gene choice in eukaryotes. In addition to their importance in P. falciparum antigenic variation, our results may also help to explain similar processes in other systems. PMID:22891919

Brancucci, Nicolas M B; Witmer, Kathrin; Schmid, Christoph D; Flueck, Christian; Voss, Till S

2012-01-01

339

Fast identification of novel lymphoid tyrosine phosphatase inhibitors using target-ligand interaction-based virtual screening.  

PubMed

Lymphoid-specific tyrosine phosphatase (Lyp), a critical signaling regulator of immune cells, is associated with various autoimmune diseases, including type 1 diabetes, rheumatoid arthritis, and systemic lupus erythematosus. Recent research suggests that Lyp is a potential drug target for autoimmune diseases. Herein, we applied a target-ligand interaction-based virtual screening method to identify novel Lyp inhibitors. Nine Lyp inhibitors with novel scaffolds were identified with eight reversible inhibitors (Ki values ranged from 2.87 to 28.03 ?M) and one covalent inhibitor (Ki = 40.98 ± 13.19 ?M). The top four compounds (A2, A15, A19, and A26) displayed selectivity over other phosphatases in preliminary experiments, and kinetic analysis indicated that these compounds are competitive inhibitors of Lyp. Compounds A15 and A19 up-regulated TCR (T cell receptor) mediated signaling and transcriptional activation through inhibition of Lyp activity in T cells. The new chemotypes of Lyp selective inhibitors identified through the target-ligand interaction-based virtual screening may provide new leads for Lyp targeted therapeutic development. PMID:25372368

Hou, Xuben; Li, Rong; Li, Kangshuai; Yu, Xiao; Sun, Jin-Peng; Fang, Hao

2014-11-26

340

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

PubMed Central

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

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

2013-01-01

341

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

342

Specimen specific parameter identification of ovine lumbar intervertebral discs: On the influence of fibre-matrix and fibre-fibre shear interactions.  

PubMed

Numerical models of the intervertebral disc, which address mechanical questions commonly make use of the difference in water content between annulus and nucleus, and thus fluid and solid parts are separated. Despite this simplification, models remain complex due to the anisotropy and nonlinearity of the annulus and regional variations of the collagen fibre density. Additionally, it has been shown that cross-links make a large contribution to the stiffness of the annulus. Because of this complex composite structure, it is difficult to reproduce several sets of experimental data with one single set of material parameters. This study addresses the question to which extent the ultrastructure of the intervertebral disc should be modelled so that its moment-angle behaviour can be adequately described. Therefore, a hyperelastic constitutive law, based on continuum mechanical principles was derived, which does not only consider the anisotropy from the collagen fibres, but also interactions among the fibres and between the fibres and the ground substance. Eight ovine lumbar intervertebral discs were tested on a custom made spinal loading simulator in flexion/extension, lateral bending and axial rotation. Specimen-specific geometrical models were generated using CT images and T2 maps to distinguish between annulus fibrosus and nucleus pulposus. For the identification of the material parameters the annulus fibrosus was described with two scenarios: with and without fibre-matrix and fibre-fibre interactions. Both scenarios showed a similar behaviour on a load displacement level. Comparing model predictions to the experimental data, the mean RMS of all specimens and all load cases was 0.54±0.15° without the interaction and 0.54±0.19° when the fibre-matrix and fibre-fibre interactions were included. However, due to the increased stiffness when cross-links effects were included, this scenario showed more physiological stress-strain relations in uniaxial and biaxial stress states. Thus, the present study suggests that fibre-matrix and fibre-fibre interactions should be considered in the constitutive law when the model addresses questions concerning the stress field of the annulus fibrosus. PMID:24361932

Reutlinger, Christoph; Bürki, Alexander; Brandejsky, Vaclav; Ebert, Lars; Büchler, Philippe

2014-02-01

343

Identification of a Skp1-like protein interacting with SFB, the pollen S determinant of the gametophytic self-incompatibility in Prunus.  

PubMed

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 SCF(SLF) 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

2012-07-01

344

Identification of a putative chromosomal replication origin from Helicobacter pylori and its interaction with the initiator protein DnaA  

PubMed Central

The key elements of the initiation of Helicobacter pylori chromosome replication, DnaA protein and putative oriC region, have been characterized. The gene arrangement in the H.pylori dnaA region differs from that found in many other eubacterial dnaA regions (rnpA-rmpH-dnaA-dnaN-recF-gyrB). Helicobacter pylori dnaA is flanked by two open reading frames with unknown function, while dnaN-gyrB and rnpA-rmpH loci are separated from the dnaA gene by 600 and 90 kb, respectively. We show that the dnaA gene encoding initiator protein DnaA is expressed in H.pylori cells. The H.pylori DnaA protein, like other DnaA proteins, can be divided into four domains. Here we demonstrate that the C-terminal domain of H.pylori DnaA protein is responsible for DNA binding. Using in silico and in vitro studies, the putative oriC region containing five DnaA boxes has been located upstream of the dnaA gene. DNase I and gel retardation analyses show that the C-terminal domain of H.pylori DnaA protein specifically binds each of five DnaA boxes. PMID:11376143

Zawilak, Anna; Cebrat, Stanislaw; Mackiewicz, Pawel; Krol-Hulewicz, Anna; Jakimowicz, Dagmara; Messer, Walter; Gosciniak, Grazyna; Zakrzewska-Czerwinska, Jolanta

2001-01-01

345

Identification of domains responsible for von Willebrand factor type VI collagen interaction mediating platelet adhesion under high flow.  

PubMed

We have identified type VI collagen (Col VI) as a primary subendothelial extracellular matrix component responsible for von Willebrand factor (vWF)-dependent platelet adhesion and aggregation under high tensile strength. Intact tetrameric Col VI was the form of the collagen found to be capable of promoting vWF-mediated platelet adhesion/aggregation under this shear condition, whereas removal of the predominant portion of the terminal globules by pepsin treatment abrogated its activity. The inability of the pepsin-digested Col VI to support any platelet interaction at high flow was because of the failure of the A3(vWF) domain to bind to this form of collagen, suggesting a stringent requirement of a tridimensional conformation or of intactness of its macromolecular structure. In contrast, the A1(vWF) domain bound to both intact and pepsin-digested Col VI tetramers but, in accordance with the cooperating function of the two vWF domains, failed to support platelet adhesion/aggregation under high shear onto Col VI by itself. The putative A1(vWF) binding site resided within the A7(VI) module (residues 413-613) of the globular amino-terminal portion of the alpha3(VI) chain. Soluble recombinant A7(VI) polypeptide strongly perturbed the vWF-mediated platelet adhesion to Col VI under high shear rates, without affecting the binding of the vWF platelet receptor glycoprotein Ibalpha to its cognate ligand A1(vWF). The findings provide evidence for a concerted action of the A1(vWF) and A3(vWF) domains in inducing platelet arrest on Col VI. This is accomplished via an interaction of the A1(vWF) domain with a site contained in the alpha3 chain A7(VI) domain and via a conformation-dependent interaction of the A3(vWF) domain with the intact tetrameric collagen. The data further emphasize that Col VI microfilaments linking the subendothelial basement membrane to the interstitial collagenous network may play a pivotal role in the hemostatic process triggered upon damage of the blood vessel wall. PMID:9915842

Mazzucato, M; Spessotto, P; Masotti, A; De Appollonia, L; Cozzi, M R; Yoshioka, A; Perris, R; Colombatti, A; De Marco, L

1999-01-29

346

Separation and identification of oligonucleotides by hydrophilic interaction liquid chromatography (HILIC) - inductively coupled plasma mass spectrometry (ICPMS)  

PubMed Central

A method for the separation and detection of oligonucleotides utilizing hydrophilic interaction liquid chromatography (HILIC) with inductively coupled plasma mass spectrometry (ICPMS) is described. Polythymidilic acids of various lengths (10, 15, 20 and 30 nucleotides) were separated under gradient HILIC conditions. Selective detection of oligonucleotides was possible through monitoring m/z 47, corresponding to 31P16O+, using ICPMS. Oxygen was used as a reaction gas in the collision/reaction cell to produce PO+ by reacting with phosphorus in the gas phase, thereby effectively eliminating the interferences for phosphorus normally seen at m/z 31. Limits of detection (LODs) were determined to be 1.69 pmol, 1.21 pmol, 1.0 pmol and 0.55 pmol loaded on column for the 10, 15, 20 and 30-mer, respectively. PMID:20830328

Easter, Renee N.; Kroning, Karolin K.; Caruso, Joseph A.; Limbach, Patrick A.

2012-01-01

347

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

348

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

349

Utility of peptide-protein affinity complexes in proteomics: identification of interaction partners of a tumor suppressor peptide.  

PubMed

We used a N-biotinylated peptide analog of the C-terminal domain of the tumor suppressor protein, p21cip1/waf1 to elucidate peptide/protein interacting partners. The C-terminal domain of p21cip1/waf1 protein spanning 141-160 amino acid residues is known to bind PCNA and this interaction is important in many biological processes including cell-cycle control. This C-terminal 20-mer efficiently extracts PCNA in the presence of a variety of N- or C-terminally attached affinity tags. Using difference silver stained 2D gels combined with in-gel tryptic digests, we identified the difference spots using MALDI-TOF mass spectrometry-based peptide mass fingerprinting followed by a database search using PROFOUND against NCBIs human nonredundant protein sequence data bank. Identified spots include the p48 subunit of chromatin assembly factor-1, the heat shock 70 protein analog BiP, calmodulin, nucleolin and a spot similar in size to dimeric PCNA. In contrast, microcapillary ion-trap LC-MS/MS analysis of a tryptic digest of entire affinity extracts derived from both control and experimental runs followed by database searches using SEQUEST confirmed the presence of most of the above proteins. This strategy also identified hnRNPA1, HPSP90alpha, HSP40 and T-complex protein 1, a protein similar to prothymosin, and a possible allelic variant of the p21cip1/waf1 protein. The use of N-biotinylated peptide derived from the C-terminal domain of p21cip1/waf1 protein in proteomic analysis exemplified here suggests that peptides obtained from intracellular functional screens could also potentially serve as efficient baits to discover new drug targets. PMID:12605602

Gururaja, T L; Li, W; Payan, D G; Anderson, D C

2003-04-01

350

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

PubMed Central

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

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

2012-01-01

351

Megabits secure key rate quantum key distribution  

E-print Network

Quantum cryptography (QC) can provide unconditional secure communication between two authorized parties based on the basic principles of quantum mechanics. However, imperfect practical conditions limit its transmission distance and communication speed. Here we implemented the differential phase shift (DPS) quantum key distribution (QKD) with up-conversion assisted hybrid photon detector (HPD) and achieved 1.3 M bits per second secure key rate over a 10-km fiber, which is tolerant against the photon number splitting (PNS) attack, general collective attacks on individual photons, and any other known sequential unambiguous state discrimination (USD) attacks.

Zhang, Q; Honjo, T; Wen, K; Hirohata, T; Suyama, M; Takiguchi, Y; Kamada, H; Tokura, Y; Tadanaga, O; Nishida, Y; Asobe, M; Yamamoto, Y

2008-01-01

352

Megabits secure key rate quantum key distribution  

E-print Network

Quantum cryptography (QC) can provide unconditional secure communication between two authorized parties based on the basic principles of quantum mechanics. However, imperfect practical conditions limit its transmission distance and communication speed. Here we implemented the differential phase shift (DPS) quantum key distribution (QKD) with up-conversion assisted hybrid photon detector (HPD) and achieved 1.3 M bits per second secure key rate over a 10-km fiber, which is tolerant against the photon number splitting (PNS) attack, general collective attacks on individual photons, and any other known sequential unambiguous state discrimination (USD) attacks.

Q. Zhang; H. Takesue; T. Honjo; K. Wen; T. Hirohata; M. Suyama; Y. Takiguchi; H. Kamada; Y. Tokura; O. Tadanaga; Y. Nishida; M. Asobe; Y. Yamamoto

2008-09-23

353

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

354

Metalloregulation of the cyanobacterial smt locus: identification of SmtB binding sites and direct interaction with metals.  

PubMed Central

The smtB gene of Synechococcus PCC 7942 encodes a trans-acting repressor of the metal-regulated smtA gene that encodes a class II metallothionein. Recombinant SmtB has been expressed in Escherichia coli and purified. Electrophoretic mobility shift assays using recombinant SmtB or a protein extract from Synechococcus PCC 6301 reveal the concentration-dependent formation of three specific complexes with the smt operator/promoter. SmtB is also capable of direct interaction with metals as evidenced by 65Zn binding to the SmtB protein as well as the inhibition of repressor-DNA complex formation in the presence of various metal ions. Methylation interference analysis of such complexes identifies four protein contact points within the smt operator/promoter DNA. The points of contact appear to represent two pairs of binding sites, one pair in each of two inverted repeats (nt 548-563, 589-602). The contact points within each pair lie on opposing DNA strands and are separated by 10 bp, placing the repressor binding sites on opposite sides of the DNA helix. Based on electrophoretic mobility shift assays, methylation interference and molecular size calculations we propose that recombinant SmtB binds to the smt operator/promoter in multimeric fashion. Images PMID:7630724

Erbe, J L; Taylor, K B; Hall, L M

1995-01-01

355

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

356

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

357

Identification and mapping of leaf, stem and stripe rust resistance quantitative trait loci and their interactions in durum wheat.  

PubMed

Leaf rust (Puccinia triticina Eriks.), stripe rust (Puccinia striiformis f. tritici Eriks.) and stem rust (Puccinia graminis f. sp. tritici) cause major production losses in durum wheat (Triticum turgidum L. var. durum). The objective of this research was to identify and map leaf, stripe and stem rust resistance loci from the French cultivar Sachem and Canadian cultivar Strongfield. A doubled haploid population from Sachem/Strongfield and parents were phenotyped for seedling reaction to leaf rust races BBG/BN and BBG/BP and adult plant response was determined in three field rust nurseries near El Batan, Obregon and Toluca, Mexico. Stripe rust response was recorded in 2009 and 2011 nurseries near Toluca and near Njoro, Kenya in 2010. Response to stem rust was recorded in field nurseries near Njoro, Kenya, in 2010 and 2011. Sachem was resistant to leaf, stripe and stem rust. A major leaf rust quantitative trait locus (QTL) was identified on chromosome 7B at Xgwm146 in Sachem. In the same region on 7B, a stripe rust QTL was identified in Strongfield. Leaf and stripe rust QTL around DArT marker wPt3451 were identified on chromosome 1B. On chromosome 2B, a significant leaf rust QTL was detected conferred by Strongfield, and at the same QTL, a Yr gene derived from Sachem conferred resistance. Significant stem rust resistance QTL were detected on chromosome 4B. Consistent interactions among loci for resistance to each rust type across nurseries were detected, especially for leaf rust QTL on 7B. Sachem and Strongfield offer useful sources of rust resistance genes for durum rust breeding. PMID:23396999

Singh, A; Pandey, M P; Singh, A K; Knox, R E; Ammar, K; Clarke, J M; Clarke, F R; Singh, R P; Pozniak, C J; Depauw, R M; McCallum, B D; Cuthbert, R D; Randhawa, H S; Fetch, T G

2013-02-01

358

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

PubMed

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

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

2014-09-01

359

The degradation (by distinct pathways) of human D-amino acid oxidase and its interacting partner pLG72--two key proteins in D-serine catabolism in the brain.  

PubMed

Human D-amino acid oxidase (EC 1.4.3.3; hDAAO) is a peroxisomal flavoenzyme significantly enriched in the mammalian brain. hDAAO has been proposed to play (with serine racemase; EC 5.1.1.18) an essential role in the catabolism of D-serine, an 'atypical' key signalling molecule that acts as allosteric activator of the N-methyl-D-aspartate-type glutamate receptor (NMDAr). hDAAO and its interacting partner pLG72 have been related to schizophrenia, a highly disabling psychiatric disorder in which a dysfunction of NMDA-mediated neurotransmission is widely assumed to occur. We previously demonstrated that the D-serine cellular concentration depends on hDAAO and pLG72 expression levels and that newly-synthesized hDAAO interacts with its modulator in the cytosol, being progressively destabilized and inactivated. To obtain insight into the mechanisms regulating cellular D-serine levels, we investigated the degradation pathways of hDAAO and pLG72 in U87 glioblastoma cells stably expressing enhanced yellow fluorescent protein-hDAAO (peroxisomal), hDAAO-enhanced yellow fluorescent protein (cytosolic) or pLG72-enhanced cyan fluorescent protein (mitochondrial) proteins. hDAAO is a long-lived protein: the peroxisomal fraction of this flavoprotein is degraded via the lysosomal/endosomal pathway (and blocking this pathway increases the cellular hDAAO activity and decreases D-serine levels), whereas the cytosolic portion is ubiquitinated and targeted to the proteasome. By contrast, pLG72 shows a rapid turnover (t(1/2) ? 25-40 min) and is degraded via the proteasome system, albeit not ubiquitinated. Overexpression of pLG72 increases the turnover of hDAAO, in turn playing a protective role against excessive D-serine depletion. PMID:24237903

Cappelletti, Pamela; Campomenosi, Paola; Pollegioni, Loredano; Sacchi, Silvia

2014-02-01

360

Exploiting likely-positive and unlabeled data to improve the identification of protein-protein interaction articles  

PubMed Central

Background Experimentally verified protein-protein interactions (PPI) cannot be easily retrieved by researchers unless they are stored in PPI databases. The curation of such databases can be made faster by ranking newly-published articles' relevance to PPI, a task which we approach here by designing a machine-learning-based PPI classifier. All classifiers require labeled data, and the more labeled data available, the more reliable they become. Although many PPI databases with large numbers of labeled articles are available, incorporating these databases into the base training data may actually reduce classification performance since the supplementary databases may not annotate exactly the same PPI types as the base training data. Our first goal in this paper is to find a method of selecting likely positive data from such supplementary databases. Only extracting likely positive data, however, will bias the classification model unless sufficient negative data is also added. Unfortunately, negative data is very hard to obtain because there are no resources that compile such information. Therefore, our second aim is to select such negative data from unlabeled PubMed data. Thirdly, we explore how to exploit these likely positive and negative data. And lastly, we look at the somewhat unrelated question of which term-weighting scheme is most effective for identifying PPI-related articles. Results To evaluate the performance of our PPI text classifier, we conducted experiments based on the BioCreAtIvE-II IAS dataset. Our results show that adding likely-labeled data generally increases AUC by 3~6%, indicating better ranking ability. Our experiments also show that our newly-proposed term-weighting scheme has the highest AUC among all common weighting schemes. Our final model achieves an F-measure and AUC 2.9% and 5.0% higher than those of the top-ranking system in the IAS challenge. Conclusion Our experiments demonstrate the effectiveness of integrating unlabeled and likely labeled data to augment a PPI text classification system. Our mixed model is suitable for ranking purposes whereas our hierarchical model is better for filtering. In addition, our results indicate that supervised weighting schemes outperform unsupervised ones. Our newly-proposed weighting scheme, TFBRF, which considers documents that do not contain the target word, avoids some of the biases found in traditional weighting schemes. Our experiment results show TFBRF to be the most effective among several other top weighting schemes. PMID:18315856

Tsai, Richard Tzong-Han; Hung, Hsi-Chuan; Dai, Hong-Jie; Lin, Yi-Wen; Hsu, Wen-Lian

2008-01-01

361

Beta-glucoside permease represses the bgl operon of Escherichia coli by phosphorylation of the antiterminator protein and also interacts with glucose-specific enzyme III, the key element in catabolite control.  

PubMed Central

The beta-glucoside (bgl) operon of Escherichia coli is subject to both positive control by transcriptional termination/antitermination and negative control by the beta-glucoside-specific transport protein, an integral membrane protein known as enzyme IIBgl. Previous results led us to speculate that enzyme IIBgl exerts its negative control by phosphorylating and thereby inactivating the antiterminator protein, BglG. Specifically, our model postulated that the transport protein enzyme IIBgl exhibits protein-phosphotransferase activity in the absence of beta-glucosides. We now present biochemical evidence that the phosphorylation of protein BglG does indeed occur in vivo and that it is accompanied by the loss of antitermination activity. BglG persists in the phosphorylated state in the absence of beta-glucosides but is rapidly dephosphorylated when beta-glucosides become available for transport. Our data also suggested specific interactions between the beta-glucoside transport protein and the glucose-specific enzyme III (enzyme IIIGlc), a component of glucose transport and a key element in regulation of catabolite repression. These observations indicate that enzyme IIIGlc may, in conjunction with enzyme IIBgl, modulate the transport of beta-glucosides and the phosphorylation of the antiterminator protein. In the absence of both sugars, when the catabolite-controlled promoter of the operon is derepressed, enzyme IIIGlc may mediate tight repression of antitermination. Images PMID:2195546

Schnetz, K; Rak, B

1990-01-01

362

Quantum dense key distribution  

SciTech Connect

This paper proposes a protocol for quantum dense key distribution. This protocol embeds the benefits of a quantum dense coding and a quantum key distribution and is able to generate shared secret keys four times more efficiently than the Bennet-Brassard 1984 protocol. We hereinafter prove the security of this scheme against individual eavesdropping attacks, and we present preliminary experimental results, showing its feasibility.

Degiovanni, I.P.; Ruo Berchera, I.; Castelletto, S.; Rastello, M.L.; Bovino, F.A.; Colla, A.M.; Castagnoli, G. [Istituto Elettrotecnico Nazionale G. Ferraris, Strada delle Cacce 91, 10135 Torino (Italy); ELSAG SpA, Via Puccini 2, 16154, Genova (Italy)

2004-03-01

363

Plant Identification, Abridged  

NSDL National Science Digital Library

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

364

Important issues concerning interactive user interfaces in grid based computational steering systems  

Microsoft Academic Search

This paper discusses a number of important issues concerning interactive user interfaces in grid based computational steering systems. The goal is to improve the scientist's efficiency and make the system more accessible to users who are not necessarily computer experts. A key step is the identification of critical factors that affect the performance of the user. Whilst it is easy

Roy S. Kalawsky; Simon P. Nee

365

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...

2010-07-20

366

How Is This Flower Pollinated? A Polyclave Key to Use in Teaching.  

ERIC Educational Resources Information Center

Presents an identification method which uses the process of elimination to identify pollination systems. Provides the polyclave key, methodology for using the key, a sample worksheet, and abbreviation codes for pollination systems. (MVL)

Tyrrell, Lucy

1989-01-01

367

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.; Jackson, Scott.; Mirick, Peter.

368

SCIENCE MATTERS KEY CHAIN  

NSDL National Science Digital Library

Brushed nickel key chain commemorating the launch of the new Science Matters initiative. Limited edition. All proceeds from the sale of this item go to fund the John Glenn Center for Science Education.

1900-01-01

369

Public-Key Steganography  

Microsoft Academic Search

Informally, a public-key steganography protocol allows two parties, who have never met or exchanged a secret, to send hidden mes- sages over a public channel so that an adversary cannot even detect that these hidden messages are being sent. Unlike previous settings in which provable security has been applied to steganography, public-key steganography is information-theoretically impossible. In this work we

Luis Von Ahn; Nicholas J. Hopper

2004-01-01

370

Key Regression: Enabling Efficient Key Distribution for Secure Distributed Storage  

Microsoft Academic Search

The Plutus file system introduced the notion of key rotation as a means to derive a sequence of temporally- related keys from the most recent key. In this paper we show that, despite natural intuition to the contrary, key rotation schemes cannot generically be used to key other cryptographic objects; in fact, keying an encryp- tion scheme with the output

Kevin Fu; Seny Kamara; Yoshi Kohno

2006-01-01

371

Systems pharmacology of the nerve growth factor pathway: use of a systems biology model for the identification of key drug targets using sensitivity analysis and the integration of physiology and pharmacology  

PubMed Central

The nerve growth factor (NGF) pathway is of great interest as a potential source of drug targets, for example in the management of certain types of pain. However, selecting targets from this pathway either by intuition or by non-contextual measures is likely to be challenging. An alternative approach is to construct a mathematical model of the system and via sensitivity analysis rank order the targets in the known pathway, with respect to an endpoint such as the diphosphorylated extracellular signal-regulated kinase concentration in the nucleus. Using the published literature, a model was created and, via sensitivity analysis, it was concluded that, after NGF itself, tropomyosin receptor kinase A (TrkA) was one of the most sensitive druggable targets. This initial model was subsequently used to develop a further model incorporating physiological and pharmacological parameters. This allowed the exploration of the characteristics required for a successful hypothetical TrkA inhibitor. Using these systems models, we were able to identify candidates for the optimal drug targets in the known pathway. These conclusions were consistent with clinical and human genetic data. We also found that incorporating appropriate physiological context was essential to drawing accurate conclusions about important parameters such as the drug dose required to give pathway inhibition. Furthermore, the importance of the concentration of key reactants such as TrkA kinase means that appropriate contextual data are required before clear conclusions can be drawn. Such models could be of great utility in selecting optimal targets and in the clinical evaluation of novel drugs. PMID:24427523

Benson, Neil; Matsuura, Tomomi; Smirnov, Sergey; Demin, Oleg; Jones, Hannah M.; Dua, Pinky; van der Graaf, Piet H.

2013-01-01

372

Optimizations for the EcoPod field identification tool  

PubMed Central

Background We sketch our species identification tool for palm sized computers that helps knowledgeable observers with census activities. An algorithm turns an identification matrix into a minimal length series of questions that guide the operator towards identification. Historic observation data from the census geographic area helps minimize question volume. We explore how much historic data is required to boost performance, and whether the use of history negatively impacts identification of rare species. We also explore how characteristics of the matrix interact with the algorithm, and how best to predict the probability of observing a previously unseen species. Results Point counts of birds taken at Stanford University's Jasper Ridge Biological Preserve between 2000 and 2005 were used to examine the algorithm. A computer identified species by correctly answering, and counting the algorithm's questions. We also explored how the character density of the key matrix and the theoretical minimum number of questions for each bird in the matrix influenced the algorithm. Our investigation of the required probability smoothing determined whether Laplace smoothing of observation probabilities was sufficient, or whether the more complex Good-Turing technique is required. Conclusion Historic data improved identification speed, but only impacted the top 25% most frequently observed birds. For rare birds the history based algorithms did not impose a noticeable penalty in the number of questions required for identification. For our dataset neither age of the historic data, nor the number of observation years impacted the algorithm. Density of characters for different taxa in the identification matrix did not impact the algorithms. Intrinsic differences in identifying different birds did affect the algorithm, but the differences affected the baseline method of not using historic data to exactly the same degree. We found that Laplace smoothing performed better for rare species than Simple Good-Turing, and that, contrary to expectation, the technique did not then adversely affect identification performance for frequently observed birds. PMID:18366649

Manoharan, Aswath; Stamberger, Jeannie; Yu, YuanYuan; Paepcke, Andreas

2008-01-01

373

Identification of a cAMP-response Element in the Regulator of G-protein Signaling-2 (RGS2) Promoter as a Key Cis-regulatory Element for RGS2 Transcriptional Regulation by Angiotensin II in Cultured Vascular Smooth Muscles*  

PubMed Central

Mice deficient in regulator of G-protein signaling-2 (RGS2) have severe hypertension, and RGS2 genetic variations occur in hypertensive humans. A potentially important negative feedback loop in blood pressure homeostasis is that angiotensin II (Ang II) increases vascular smooth muscle cell (VSMC) RGS2 expression. We reported that Group VIA phospholipase A2 (iPLA2?) is required for this response (Xie, Z., Gong, M. C., Su, W., Turk, J., and Guo, Z. (2007) J. Biol. Chem. 282, 25278–25289), but the specific molecular causes and consequences of iPLA2? activation are not known. Here we demonstrate that both protein kinases C (PKC) and A (PKA) participate in Ang II-induced VSMC RGS2 mRNA up-regulation, and that actions of PKC and PKA precede and follow iPLA2? activation, respectively. Moreover, we identified a conserved cAMP-response element (CRE) in the murine RGS2 promoter that is critical for cAMP-response element-binding protein (CREB) binding and RGS2 promoter activation. Forskolin-stimulated RGS2 mRNA up-regulation is inhibited by CREB sequestration or specific disruption of the CREB-RGS2 promoter interaction, and Ang II-induced CREB phosphorylation and nuclear localization are blocked by iPLA2? pharmacologic inhibition or genetic ablation. Ang II-induced intracellular cyclic AMP accumulation precedes CREB phosphorylation and is diminished by inhibiting iPLA2, cyclooxygenase, or lipoxygenase. Moreover, three single nucleotide polymorphisms identified in hypertensive patients are located in the human RGS2 promoter CREB binding site. Point mutations corresponding to these single nucleotide polymorphisms interfere with stimulation of human RGS2 promoter activity by forskolin. Our studies thus delineate a negative feedback loop to attenuate Ang II signaling in VSMC with potential importance in blood pressure homeostasis and the pathogenesis of human essential hypertension. PMID:22057271

Xie, Zhongwen; Liu, Dexiang; Liu, Shu; Calderon, Lindsay; Zhao, Guogang; Turk, John; Guo, Zhenheng

2011-01-01

374

Information Reconciliation for Quantum Key Distribution  

E-print Network

Quantum key distribution (QKD) relies on quantum and classical procedures in order to achieve the growing of a secret random string -the key- known only to the two parties executing the protocol. Limited intrinsic efficiency of the protocol, imperfect devices and eavesdropping produce errors and information leakage from which the set of measured signals -the raw key- must be stripped in order to distill a final, information theoretically secure, key. The key distillation process is a classical one in which basis reconciliation, error correction and privacy amplification protocols are applied to the raw key. This cleaning process is known as information reconciliation and must be done in a fast and efficient way to avoid cramping the performance of the QKD system. Brassard and Salvail proposed a very simple and elegant protocol to reconcile keys in the secret-key agreement context, known as Cascade, that has become the de-facto standard for all QKD practical implementations. However, it is highly interactive, requiring many communications between the legitimate parties and its efficiency is not optimal, imposing an early limit to the maximum tolerable error rate. In this paper we describe a low-density parity-check reconciliation protocol that improves significantly on these problems. The protocol exhibits better efficiency and limits the number of uses of the communications channel. It is also able to adapt to different error rates while remaining efficient, thus reaching longer distances or higher secure key rate for a given QKD system.

David Elkouss; Jesus Martinez-Mateo; Vicente Martin

2010-07-09

375

Comparison is key.  

PubMed

Several concepts from Georg Rasch's last papers are discussed. The key one is comparison because Rasch considered the method of comparison fundamental to science. From the role of comparison stems scientific inference made operational by a properly developed frame of reference producing specific objectivity. The exact specifications Rasch outlined for making comparisons are explicated from quotes, and the role of causality derived from making comparisons is also examined. Understanding causality has implications for what can and cannot be produced via Rasch measurement. His simple examples were instructive, but the implications are far reaching upon first establishing the key role of comparison. PMID:24518579

Stone, Mark H; Stenner, A Jackson

2014-01-01

376

Quantum Key Distribution  

E-print Network

This chapter describes the application of lasers, specifically diode lasers, in the area of quantum key distribution (QKD). First, we motivate the distribution of cryptographic keys based on quantum physical properties of light, give a brief introduction to QKD assuming the reader has no or very little knowledge about cryptography, and briefly present the state-of-the-art of QKD. In the second half of the chapter we describe, as an example of a real-world QKD system, the system deployed between the University of Calgary and SAIT Polytechnic. We conclude the chapter with a brief discussion of quantum networks and future steps.

Chan, Philip; Mo, Xiaofan; Tittel, Wolfgang

2011-01-01

377

Key Concepts in Algebra  

NSDL National Science Digital Library

The Key Concepts in Algebra collection provides quick and easy access to high-quality high school algebra resources. These resources have been selected by trusted educators to correlate with the Denver Public School's Algebra 1 and 2 instructional learning guides for teachers.

2012-08-14

378

Name ___KEY_______________ Due Date: __________________  

E-print Network

Name ___KEY_______________ Due Date: __________________ GEOL 106 Writing #1 ­ Intro & Overview 1 with interstellar (between star) dust that came from a supernovae star explosion, briefly explain how we think our solar system formed. Following the Big Bang, some first generation stars became supernovae, spreading

Kirby, Carl S.

379

Classifying Public Key Certificates  

Microsoft Academic Search

In spite of the fact that there are several companies that (try to) sell public key certificates, there is still no unified or standardized clas- sification scheme that can be used to compare and put into perspective the various oerings. In this paper, we try to start filling this gap and pro- pose a four-dimensional scheme that can be used

Javier Lopez; Rolf Oppliger; Günther Pernul

2005-01-01

380

Analytical blind channel identification  

Microsoft Academic Search

A novel analytical blind single-input single-output (SISO) identification algorithm is presented, based on the noncircular second-order statistics of the output. It is shown that statistics of order higher than two are not mandatory to restore identifiability. Our approach is valid, for instance, when the channel is excited by phase shift keying (PSK) inputs. It is shown that the channel taps

Olivier Grellier; P. Comon; B. Mourrain; P. Trebuchet

2002-01-01

381

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

ERIC Educational Resources Information Center

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

Keller, Johannes

2007-01-01