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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…

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

2011-01-01

2

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

2010-11-19

3

Interactive Key to Taiwan Grasses Using Characters of Leaf Anatomy - The ActKey Approach  

Microsoft Academic Search

ActKey is an online interactive key program and database for identification of organisms. It differs from traditional dichotomous keys in providing multi-access entry points. Rather than answering questions to key couplets while following a pre-defined path, ActKey provides a wider strategy for identifying an unknown plant. The program is web-based and supports most popular internet browsers. Visitors can use interactive

Chang-Sheng Kuoh; Hong Song

2005-01-01

4

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

5

EFFECTIVENESS OF REPTILE SPECIES IDENTIFICATION - A COMPARISON OF A DICHOTOMOUS KEY WITH AN IDENTIFICATION BOOK  

Microsoft Academic Search

Species identification tasks are a prerequisite for an understanding of biodiversity. Here, we focused on different educational materials to foster the identification of six European reptile species. Our educational training unit was based on natural plastic models of six species and pupils either used an illustrated identification book or a dichotomous key. 71 secondary school pupils (6th graders) from four

Christoph Randler; Irene Zehender

6

A multiple-entry polytomous computer key for identification of the Astragalus species (Fabaceae) of Siberia  

Microsoft Academic Search

A description is given of interactive multiple-entry polytomous computer key designed to identify 102 Siberia’s Astragalus species and subspecies. At each identification step the program reduces the species list, shortens the lists of qualitative\\u000a character states, recalculates the diagnostic value of characters, and rank the characters according to their diagnostic value.\\u000a In the process of identification, a user can return

I. A. Artemov

2010-01-01

7

XKey: A tool for the generation of identification keys  

Microsoft Academic Search

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

Miguel Delgado Calvo-flores; Waldo Fajardo Contreras; Eva Lucrecia Gibaja Galindo; Ramón Pérez-pérez

2006-01-01

8

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.

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

2012-01-01

9

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

10

Application of Cognitive Engineering Principles to the Redesign of a Dichotomous Identification Key for Parasitology  

Microsoft Academic Search

Dichotomous identification keys are used throughout biology for identification of plants, insects, and parasites. However, correct use of identification keys can be difficult as they are not usually intended for novice users who may not be familiar with the terminology used or with the morphology of the organism being identified. Therefore, we applied cognitive engineering principles to redesign a parasitology

Kimberly A. Smith-Akins; Sharon McLane; Thomas M. Craig; Todd R. Johnson

2006-01-01

11

A SINE-based dichotomous key for primate identification.  

PubMed

For DNA samples or 'divorced' tissues, identifying the organism from which they were taken generally requires some type of analytical method. The ideal approach would be robust even in the hands of a novice, requiring minimal equipment, time, and effort. Genotyping SINEs (Short INterspersed Elements) is such an approach as it requires only PCR-related equipment, and the analysis consists solely of interpreting fragment sizes in agarose gels. Modern primate genomes are known to contain lineage-specific insertions of Alu elements (a primate-specific SINE); thus, to demonstrate the utility of this approach, we used members of the Alu family to identify DNA samples from evolutionarily divergent primate species. For each node of a combined phylogenetic tree (56 species; n=8 [Hominids]; 11 [New World monkeys]; 21 [Old World monkeys]; 2 [Tarsiformes]; and, 14 [Strepsirrhines]), we tested loci (>400 in total) from prior phylogenetic studies as well as newly identified elements for their ability to amplify in all 56 species. Ultimately, 195 loci were selected for inclusion in this Alu-based key for primate identification. This dichotomous SINE-based key is best used through hierarchical amplification, with the starting point determined by the level of initial uncertainty regarding sample origin. With newly emerging genome databases, finding informative retrotransposon insertions is becoming much more rapid; thus, the general principle of using SINEs to identify organisms is broadly applicable. PMID:17056208

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

2006-08-30

12

A Non-interactive Public-Key Distribution System  

Microsoft Academic Search

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

Ueli M. Maurer; Yacov Yacobi

1996-01-01

13

Identification keys, the "natural method," and the development of plant identification manuals.  

PubMed

The origins of field guides and other plant identification manuals have been poorly understood until now because little attention has been paid to 18th century botanical identification guides. Identification manuals came to have the format we continue to use today when botanical instructors in post-Revolutionary France combined identification keys (step-wise analyses focusing on distinctions between plants) with the "natural method" (clustering of similar plants, allowing for identification by gestalt) and alphabetical indexes. Botanical works featuring multiple but linked techniques to enable plant identification became very popular in France by the first decade of the 19th century. British botanists, however, continued to use Linnaeus's sexual system almost exclusively for another two decades. Their reluctance to use other methods or systems of classification can be attributed to a culture suspicious of innovation, anti-French sentiment and the association of all things Linnaean with English national pride, fostered in particular by the President of the Linnean Society of London, Sir James Edward Smith. The British aversion to using multiple plant identification technologies in one text also helps explain why it took so long for English botanists to adopt the natural method, even after several Englishmen had tried to introduce it to their country. Historians of ornithology emphasize that the popularity of ornithological guides in the 19th and 20th centuries stems from their illustrations, illustrations made possible by printing technologies that improved illustration quality and reduced costs. Though illustrations are the most obvious features of late 19th century and 20th century guides, the organizational principles that make them functional as identification devices come from techniques developed in botanical works in the 18th century. PMID:19831202

Scharf, Sara T

2009-01-01

14

Identification of key recombinants in multiplex SMA families  

SciTech Connect

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

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

1994-07-01

15

SIKey: A tool to generate secondary identification keys for targeted diagnosis  

Microsoft Academic Search

Secondary identification key (SIK) is a new tool for species identification which enables users to identify possible specimens from a particular group of species (as rice insect pests). The SIK has proved more efficient and easier to be adapted than traditional keys for targeted diagnosis. Since it is hard and time-consuming for taxonomists to design SIK manually, a Web-based tool,

Xiao-bin Zhang; Xue-xin Chen; Jia-an Cheng

2008-01-01

16

New efficient user identification and key distribution scheme providing enhanced security  

Microsoft Academic Search

Apart from user identification and key distribution, it is very useful for the login process to achieve user anonymity. Recently, Wu and Hsu proposed an efficient user identification scheme with key distribution while preserving user anonymity by extending an earlier work of Lee and Chang. We however find out that the Wu and Hsu scheme has a serious weakness, which

Yanjiang Yang; Shuhong Wang; Feng Bao; Jie Wang; Robert Huijie Deng

2004-01-01

17

A Secure Identification and Key agreement protocol with user Anonymity (SIKA)  

Microsoft Academic Search

Anonymity is a desirable security feature in addition to providing user identification and key agreement during a user's login process. Recently, Yang et al., proposed an efficient user identification and key distribution protocol while preserving user anonymity. Their protocol addresses a weakness in the protocol proposed by Wu and Hsu. Unfortunately, Yang's protocol poses a vulnerability that can be exploited

Kumar Mangipudi; Rajendra S. Katti

2006-01-01

18

Application of Cognitive Engineering Principles to the Redesign of a Dichotomous Identification Key for Parasitology  

PubMed Central

Dichotomous identification keys are used throughout biology for identification of plants, insects, and parasites. However, correct use of identification keys can be difficult as they are not usually intended for novice users who may not be familiar with the terminology used or with the morphology of the organism being identified. Therefore, we applied cognitive engineering principles to redesign a parasitology identification key for the Internet. We addressed issues of visual clutter and spatial distance by displaying a single question couplet at a time and by switching to the appropriate next couplet after the user made a choice. Our analysis of the original paper-based key versus the Web-based approach found that of 26 applicable cognitive engineering principles, the paper key did not meet 4 (15%) and partially met 11 (42%). In contrast, the redesigned key met 100% of 32 applicable cognitive engineering principles.

Smith-Akin, Kimberly A.; McLane, Sharon; Craig, Thomas M.; Johnson, Todd R.

2006-01-01

19

Construction of a high-quality yeast two-hybrid (Y2H) library and its application in identification of interacting proteins with key vernalization regulator TaVRN-A1 in wheat  

PubMed Central

Background Low temperature is required for the competence of winter wheat to flowering (vernalization), and several key components in the vernalization-mediated flowering pathway have been isolated. A Y2H library is a very useful platform to further unravel novel regulators in the flowering pathway. Thus, there is a necessity to construct a high-quality Y2H library using vernalized winter wheat plants. Result We described the construction of a high-quality Y2H library using winter wheat plants with cold-treatment for different weeks to maximize pooling interacting proteins during vernalization. The resultant Y2H library contained ~2.5×106 independent clones, with a cell density of ~2.6×108 and an average insert size of ~ 1.5 kb. TaVRN-A1 was used as a “bait” to test the quality of the Y2H library. As a result, several cDNA clones encoding TaSOC1 and TaSVP1 that were known to have a direct binding with TaVRN-A1 were identified, demonstrating that the Y2H screen system constructed in this study was highly efficient. Additional proteins that were discovered but not characterized in previous studies could be novel partners of TaVRN-A1 in wheat. Conclusion We established a high-efficient Y2H screen system using the Matchmaker™ technology with several modifications in the critical steps. Ultimately, we provided a successful example to fast and economically create high-quality Y2H libraries for studies on protein interaction in hexaploid wheat.

2013-01-01

20

A new key to the identification of the Afrotropical nightjars (Caprimulgidae)  

Microsoft Academic Search

Jockson, H.D. 2000. A new key to the identification of the Afrotropicol nightjars (Caprimulgidae). Ostrich 71 (3&4): 371-379. A new dichotomous key to the identification of the Afrotropicol nightjars, based mainly on mensural Characters, is presented. This replaces the author's 1984 key to the nightjor species of Africa and its islands, which has been revised to incorporate extensive additional data

H. D. Jackson

2000-01-01

21

Statistical Mechanics Approach to Lock-Key Supramolecular Chemistry Interactions  

NASA Astrophysics Data System (ADS)

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

Odriozola, Gerardo; Lozada-Cassou, Marcelo

2013-03-01

22

Hash-Based RFID Security Protocol Using Randomly Key-Changed Identification Procedure  

Microsoft Academic Search

\\u000a Radio Frequency Identification (RFID) is considered to be a promising identification approach in ubiquitous sensing technology.\\u000a The operation of RFID systems in advanced applications may pose security and privacy risks to both organizations and individuals.\\u000a In this paper, using randomly Key-Changed Identification, we propose an eavesdropping-proof security protocol based on cryptographic\\u000a one way hash functions for passive RFID tags. Compared

Jia Zhai; Chang Mok Park; Gi-nam Wang

2006-01-01

23

Identification of Key Operational Risk Indicators for Banks  

Microsoft Academic Search

The aim of this article is to indetify what operational risk in banking institutions entails and to identify the various firm-wide key operational risk indicators in a typical South African retail bank. This article includes both internal and external operational risk events in the definition of operational risk. To indentify firm-wide operational risk indicators, questionnaires were completed by managers of

Andrea Saayman; Paul Styger; Janel Esterhuysen

2004-01-01

24

Key pairing interaction in layered doped ionic insulators.  

PubMed

A controversial issue on whether the electron-phonon interaction (EPI) is crucial for high-temperature superconductivity or it is weak and inessential has remained one of the most challenging problems of contemporary condensed matter physics. We employ a continuum random phase approximation for the dielectric response function allowing for a self-consistent semianalytical evaluation of the EPI strength, electron-electron attractions, and the carrier mass renormalization in layered high-temperature superconductors. We show that the Fröhlich EPI with high-frequency optical phonons in doped ionic lattices is the key pairing interaction, which is beyond the BCS-Migdal-Eliashberg approximation in underdoped superconductors, and it remains a significant player in overdoped compounds. PMID:21231408

Alexandrov, A S; Bratkovsky, A M

2010-11-24

25

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

Microsoft Academic Search

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 the method useful but not easy to perform. As an

Andrej Šorgo

2006-01-01

26

A dichotomous key for the identification of common British wild flower families  

Microsoft Academic Search

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 with wild flower families.

Piers Wood

2004-01-01

27

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…

Sorgo, Andrej

2006-01-01

28

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

NASA Astrophysics Data System (ADS)

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

Palotai, R.; Csermely, P.

2009-12-01

29

A molecular key for the identification of blow flies in southeastern Nebraska.  

PubMed

Immature blow flies (Calliphoridae) are typically the first colonizers of cadavers. Identification of the early instars using traditional, morphology-based keys is difficult because of their small size, similarity, and simplicity in external morphology. Information derived from molecular genetic data would augment the accurate identification of immature flies. Nine species of blow flies commonly found in southeastern Nebraska were used to examine the utility of molecular-based keys. Polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP) were investigated with 10 common, inexpensive, restriction enzymes from an amplicon of approximately 1500 bp spanning the mitochondrial cytochrome oxidase I gene. A simple molecular taxonomic key, comprising RFLP from the restriction enzymes HinfI and DraI, enabled the differentiation of all species used. Further development of PCR-RFLP, including more extensive and intensive examination of blow flies, would benefit forensic laboratories in the accurate identification of evidence consisting of immature blow flies. PMID:22563809

Samarakoon, Upeka; Skoda, Steven R; Baxendale, Frederick P; Foster, John E

2012-05-04

30

A novel user identification scheme with key distribution preserving user anonymity for distributed computer networks  

Microsoft Academic Search

Recently, Yang et al. proposed an efficient user identification scheme with key distribution, in which it is possible for the user to anonymously log into a system and establish a secret key shared with the system. Mangipudi and Katti later demonstrated a Deniable-of-Service (DoS) attack on the Yang et al. scheme and then proposed an improvement to withstand such an

Chien-lung Hsu; Yu-hao Chuang

2009-01-01

31

Pictorial Key for the Identification of the Mosquitoes Associated with Yellow Fever in Africa.  

National Technical Information Service (NTIS)

A pictorial key was developed as a training aid for the identification of the adults of 15 species of mosquitoes involved in the transmission of yellow fever virus in Africa. Included are 14 species of Aedes (subgenera Aedimorphus, Diceromyia and Stegomyi...

R. A. Ward Y. Huang

1981-01-01

32

Vulnerability of User Identification and Key Agreement Protocol with User Anonymity  

Microsoft Academic Search

In 2006, Kumar-Rajendra proposed a secure identification and key agreement protocol with user anonymity (SIKA). The current paper demonstrates the vulnerability of the SIKA protocol. Furthermore, we present an improvement to repair the security flaws of the SIKA protocol.

Eun-jun Yoon; Kee-young Yoo

2007-01-01

33

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.

Lopes-Andrade, Cristiano; Lawrence, John F.

2011-01-01

34

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

PubMed Central

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

Mandahl-Barth, G.

1962-01-01

35

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.

Leggett, Roxanne; Kirchoff, Bruce K.

2011-01-01

36

CCFA microbial-host interactions workshop: highlights and key observations.  

PubMed

This article provides a summary of the proceedings of the CCFA Microbial-Host Interactions Workshop that was held in St. Petersburg, Florida, on March 16-19, 2006. Approximately 75 senior and junior investigators from around the world shared their most current research findings through oral presentations, poster sessions, and active discussion. Because intestinal microbiota are significant contributors in the development of inflammatory bowel diseases (IBD), understanding the body's responses to and interactions with microbes, especially in the colon and distal small intestine, is critical to elucidating the etiology and pathogenesis of IBD and developing effective therapeutic interventions. Major advances have occurred recently in molecular detection of luminal bacterial species, identifying dominant microbial antigens that drive intestinal inflammation, the mechanisms of innate immune and epithelial responses to bacteria, and regulation of inflammation by innate and acquired immune cells. PMID:17294437

Sartor, R Balfour; Blumberg, Richard S; Braun, Jonathan; Elson, Charles O; Mayer, Lloyd F

2007-05-01

37

Children's wishful identification and parasocial interaction with favorite television characters  

Microsoft Academic Search

Children aged 7 to 12 were interviewed about their favorite TV character. Nearly all boys and about half of the girls selected same?sex favorites. Regression analyses used perceived character traits (attractiveness, strength, humor, intelligence, social behavior) to predict wishful identification and parasocial interaction with characters. For male characters, wishful identification was predicted by intelligence and (for girls only) humor; parasocial

Cynthia Hoffner

1996-01-01

38

A genetic ensemble approach for gene-gene interaction identification  

PubMed Central

Background It has now become clear that gene-gene interactions and gene-environment interactions are ubiquitous and fundamental mechanisms for the development of complex diseases. Though a considerable effort has been put into developing statistical models and algorithmic strategies for identifying such interactions, the accurate identification of those genetic interactions has been proven to be very challenging. Methods In this paper, we propose a new approach for identifying such gene-gene and gene-environment interactions underlying complex diseases. This is a hybrid algorithm and it combines genetic algorithm (GA) and an ensemble of classifiers (called genetic ensemble). Using this approach, the original problem of SNP interaction identification is converted into a data mining problem of combinatorial feature selection. By collecting various single nucleotide polymorphisms (SNP) subsets as well as environmental factors generated in multiple GA runs, patterns of gene-gene and gene-environment interactions can be extracted using a simple combinatorial ranking method. Also considered in this study is the idea of combining identification results obtained from multiple algorithms. A novel formula based on pairwise double fault is designed to quantify the degree of complementarity. Conclusions Our simulation study demonstrates that the proposed genetic ensemble algorithm has comparable identification power to Multifactor Dimensionality Reduction (MDR) and is slightly better than Polymorphism Interaction Analysis (PIA), which are the two most popular methods for gene-gene interaction identification. More importantly, the identification results generated by using our genetic ensemble algorithm are highly complementary to those obtained by PIA and MDR. Experimental results from our simulation studies and real world data application also confirm the effectiveness of the proposed genetic ensemble algorithm, as well as the potential benefits of combining identification results from different algorithms.

2010-01-01

39

Identification of multiple interacting bad data via power system decomposition  

SciTech Connect

This paper presents a new, highly robust bad data identification algorithm for electric power system state estimation. A system decomposition scheme is coupled with the least median of squares estimator to allow identification of multiple interacting bad data even in cases of conforming errors. The algorithm is inherently resistant to bad measurements in positions of leverage, makes no a priori measurement error probability distribution assumptions, and is applicable in a real-time environment.

Cheniae, M.G.; Mili, L. [Virginia Polytechnic Inst. and State Univ., Blacksburg, VA (United States). Bradley Dept. of Electrical Engineering; Rousseeuw, P.J. [Univ. Instelling Antwerpen (Belgium). Mathematics Dept.

1996-08-01

40

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

PubMed

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

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

2010-06-14

41

Remote teaching of arthropod species identification through interactive multimedia.  

PubMed

Remote teaching programs are effective means for providing entomologists with the knowledge they need to confidently identify medically important arthropods. Using interactive multimedia, these programs teach the morphology of ticks and larval and adult mosquitoes through tutorials, followed by practice identifications of collected arthropod specimens. Interactive multimedia programs are created in 3 phases: planning, design, and development. Species identification is one of the most important skills that entomologists must have, because recognition of disease vectors during field surveillance is an important component of overall troop protection. PMID:20084737

Schultz, George W; Robbins, Richard G

42

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...

43

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.

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

2012-01-01

44

Identification of Hidden Key Hepatitis C Populations: An Evaluation of Screening Practices Using Mixed Epidemiological Methods  

PubMed Central

Background Hepatitis C virus (HCV) is a major cause of liver diseases worldwide. Due to its asymptomatic nature, screening is necessary for identification. Because screening of the total population is not cost effective, it is important to identify which risk factors for positivity characterize the key populations in which targeting of screening yields the highest numbers of HCV positives, and assess which of these key populations have remained hidden to current care. Methods Laboratory registry data (2002–2008) were retrieved for all HCV tests (23,800) in the south of the Netherlands (adult population 500,000). Screening trends were tested using Poisson regression and chi-square tests. Risk factors for HCV positivity were assessed using a logistic regression. The hidden HCV-positive population was estimated by a capture-recapture approach. Results The number of tests increased over time (2,388 to 4,149, p<.01). Nevertheless, the positivity rate among those screened decreased between 2002 and 2008 (6.3% to 2.1%, p<.01). The population prevalence was estimated to be 0.49% (95%CI 0.41–0.59). Of all HCV-positive patients, 66% were hidden to current screening practices. Risk factors associated with positivity were low socio-economic status, male sex, and age between 36–55. In future screening 48% (95%CI 37–63) of total patients and 47% (95%CI 32–70) of hidden patients can be identified by targeting 9% (men with low socio-economic status, between 36–55 years old) of the total population. Conclusions Although the current HCV screening policy increasingly addresses high-risk populations, it only reaches one third of positive patients. This study shows that combining easily identifiable demographic risk factors can be used to identify key populations as a likely target for effective HCV screening. We recommend strengthening screening among middle-aged man, living in low socio-economic neighborhoods.

Vermeiren, Angelique P. A.; Dukers-Muijrers, Nicole H. T. M.; van Loo, Inge H. M.; Stals, Frans; van Dam, Dirk W.; Ambergen, Ton; Hoebe, Christian J. P. A.

2012-01-01

45

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

46

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

47

A Remark on a Non-interactive Public-Key Distribution System  

Microsoft Academic Search

An identity-based non-interactive public key distribution system was presented by these authors at Eurocrypt’ 91 [2]. It is based on the observation that for an appropriate choice of m, computing discrete logarithms in Z\\u000a m* is feasible if and only if the factorization of m is known. This observation allows one to set up an exponential key distribution system in

Ueli M. Maurer; Yacov Yacobi

1992-01-01

48

Study on the key problems of interaction between microwave and chemical reaction  

Microsoft Academic Search

Microwave has been found as an efficient heating method in chemical industry. However, in present days the interaction between\\u000a microwave and chemical reactions has not been deeply understood, which restricts a wider application of high power microwave\\u000a in chemical industry. In this paper, the key problems of interaction between microwave and chemical reaction are investigated,\\u000a such as complex effective permittivity

Xiaoqing Yang; Kama Huang

2007-01-01

49

Illustrated identification keys to strongylid parasites (Strongylidae: Nematoda) of horses, zebras and asses (Equidae).  

PubMed

The Equidae (the horse, Equus caballus, the ass, Equus asinus, zebras and their hybrids) are hosts to a great variety of nematode parasites, some of which can cause significant morbidity or mortality if individual hosts are untreated. Worldwide the nematode parasites of horses belong to 7 suborders, 12 families, 29 genera and 83 species. The great majority (19 of 29 genera and 64 of 83 species) are members of the family Strongylidae, which includes the most common and pathogenic nematode parasites of horses. Only the Strongylidae are included in this treatise. The Strongylidae (common name strongylids) of horses--nematodes with a well-developed buccal capsule, a mouth collar with two leaf-crowns, and a strongyloid (common name of superfamily Strongyloidea) copulatory bursa--can be separated into two subfamilies: Strongylinae (common name strongylins), usually large or medium-sized with a globular or funnel-shaped buccal capsule; and Cyathostominae (common name cyathostomins), usually small to medium-sized with a cylindrical buccal capsule. The increased attention to strongylid nematode parasites of horses has resulted in the need for updated diagnostic keys to these parasites using readily recognizable characters and the most recent literature on their systematics. Because the cyathostomins have been historically difficult to identify, and because they have emerged as the most significant nematode pathogens of horses, we provide a brief nomenclatural and taxonomic history and an introduction to the morphology of this group. This treatise is intended to serve as a basic working tool--providing easy identifications to genus and species of adult strongylid nematodes of equids. All strongylid nematodes normally parasitic in horses, the ass (and their hybrids), and zebras are included. The keys are illustrated with line drawings and halftone photomicrographs of each species. A short discussion of the systematics of the genus and species is provided for each genus following the species descriptions. Species diagnoses and a synonymy of each species is provided. Geographic distribution, prevalence, and location in host are also given for each species. PMID:18603375

Lichtenfels, J Ralph; Kharchenko, Vitaliy A; Dvojnos, Grigory M

2008-05-21

50

Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base-phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations.  

PubMed

RNA molecules are stabilized by a wide range of noncanonical interactions that are not present in DNA. Among them, the recently classified base-phosphate (BPh) interactions belong to the most important ones. Twelve percent of nucleotides in the ribosomal crystal structures are involved in BPh interactions. BPh interactions are highly conserved and provide major constraints on RNA sequence evolution. Here we provide assessment of the energetics of BPh interactions using MP2 computations extrapolated to the complete basis set of atomic orbitals and corrected for higher-order electron correlation effects. The reference computations are compared with DFT-D and DFT-D3 approaches, the SAPT method, and the molecular mechanics force field. The computations, besides providing the basic benchmark for the BPh interactions, allow some refinements of the original classification, including identification of some potential doubly bonded BPh patterns. The reference computations are followed by analysis of some larger RNA fragments that consider the context of the BPh interactions. The computations demonstrate the complexity of interaction patterns utilizing the BPh interactions in real RNA structures. The BPh interactions are often involved in intricate interaction networks. We studied BPh interactions of protonated adenine that can contribute to catalysis of hairpin ribozyme, the key BPh interaction in the S-turn motif of the sarcin-ricin loop, which may predetermine the S-turn topology and complex BPh patterns from the glmS riboswitch. Finally, the structural stability of BPh interactions in explicit solvent molecular dynamics simulations is assessed. The simulations well preserve key BPh interactions and allow dissection of structurally/functionally important water-meditated BPh bridges, which could not be considered in earlier bioinformatics classification of BPh interactions. PMID:21910417

Zgarbová, Marie; Jure?ka, Petr; Banáš, Pavel; Otyepka, Michal; Sponer, Judit E; Leontis, Neocles B; Zirbel, Craig L; Sponer, Ji?í

2011-09-12

51

Identification of the key LMO2-binding determinants on Ldb1.  

PubMed

The overexpression of LIM-only protein 2 (LMO2) in T-cells, as a result of chromosomal translocations, retroviral insertion during gene therapy, or in transgenic mice models, leads to the onset of T-cell leukemias. LMO2 comprises two protein-binding LIM domains that allow LMO2 to interact with multiple protein partners, including LIM domain-binding protein 1 (Ldb1, also known as CLIM2 and NLI), an essential cofactor for LMO proteins. Sequestration of Ldb1 by LMO2 in T-cells may prevent it binding other key partners, such as LMO4. Here, we show using protein engineering and enzyme-linked immunosorbent assay (ELISA) methodologies that LMO2 binds Ldb1 with a twofold lower affinity than does LMO4. Thus, excess LMO2 rather than an intrinsically higher binding affinity would lead to sequestration of Ldb1. Both LIM domains of LMO2 are required for high-affinity binding to Ldb1 (K(D) = 2.0 x 10(-8) M). However, the first LIM domain of LMO2 is primarily responsible for binding to Ldb1 (K(D) = 2.3 x 10(-7) M), whereas the second LIM domain increases binding by an order of magnitude. We used mutagenesis in combination with yeast two-hybrid analysis, and phage display selection to identify LMO2-binding "hot spots" within Ldb1 that locate to the LIM1-binding region. The delineation of this region reveals some specific differences when compared to the equivalent LMO4:Ldb1 interaction that hold promise for the development of reagents to specifically bind LMO2 in the treatment of leukemia. PMID:16616188

Ryan, Daniel P; Sunde, Margaret; Kwan, Ann H-Y; Marianayagam, Neelan J; Nancarrow, Amy L; Vanden Hoven, Rachel N; Thompson, Lyndal S; Baca, Manuel; Mackay, Joel P; Visvader, Jane E; Matthews, Jacqueline M

2006-03-20

52

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.

53

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

Microsoft Academic Search

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

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

2005-01-01

54

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

NASA Astrophysics Data System (ADS)

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

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

2011-07-01

55

Crystal structures of HIV-1 reverse transcriptase with picomolar inhibitors reveal key interactions for drug design.  

PubMed

X-ray crystal structures at 2.9 Å resolution are reported for two complexes of catechol diethers 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, José A; Gallardo-Macias, Ricardo; Jorgensen, William L; Anderson, Karen S

2012-11-19

56

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.

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

2012-01-01

57

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

PubMed

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

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

2013-10-02

58

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.

2013-01-01

59

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

60

Identification of key success factors of functional dairy foods product development  

Microsoft Academic Search

The present study elucidates key success factors influencing the product development of functional dairy foods and examines if the studied products can be categorized as potential breakthrough products primarily in a domestic market. General conclusions are also made with reference to functional foods development in the international setting. Three functional dairy foods were studied with specific emphasis on the key

Mikaela Biström; Katrina Nordström

2002-01-01

61

Approach to key technologies identification for rocket powered single stage to orbit vehicles  

Microsoft Academic Search

A reusable vertical take off, vertical landing rocket powered single stage to orbit vehicle has been studied as a part of the Ae´rospatiale future launchers systematic study policy. The main goal of this study is to investigate the key points of this kind of configurations, especially identify, classify and quantify the specific problems, key technologies, tools and test facilities needed

F. Deneu; P. Terrenoire

1996-01-01

62

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

63

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

64

Automatic and Interactive Key Posture Design by Combing the PIK with Parametric Posture Splicing  

NASA Astrophysics Data System (ADS)

Key posture design is commonly needed in computer animation. This paper presents an automatic and interactive whole body posture designing technique by combining the PIK (prioritized inverse kinematics) with the proposed parametric human posture splicing technique. The key feature of PIK is that the user can design a posture by adding high level constraints with different priorities. However, the PIK is essentially a numerical IK algorithm which relies on the iterative optimization starting from a good enough initial posture to get the final result. To speed up the running efficiency and ensure the lifelikeness of the final posture, the parametric posture splicing technique is proposed to generate the initial guess of the PIK. According to the set of the high level constraints, the whole body is divided into some partial parts, whose postures are then generated by the parametric posture synthesis from a single posture database. Then an initial posture guess with some main characteristics of the finally acceptable posture can be generated approximately by splicing these partial body postures together. Starting from this initial guess and with all constraints considered at different priority levels, the PIK can be initialized with a bias defined by this particularly initial guess and iterated step by step to get a final posture. The total process of the whole body posture generation is automatic and interactive. The experimental results show that this combination method can not only improve the computation efficiency of the PIK but also can simultaneously ensure the naturalness of the final posture.

Li, Shilei; Wu, Bing; Liang, Jiahong; Su, Jiongming

65

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

66

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

NASA Astrophysics Data System (ADS)

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

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

2009-04-01

67

Identifying stabilizing key residues in proteins using interresidue interaction energy matrix.  

PubMed

We are proposing an interresidue interaction energy map (IEM)--a new tool for protein structure analysis and protein bioinformatics. This approach employs the sum of pair-wise interaction energies of a particular residue as a measure of its structural importance. We will show that the IEM can serve as a means for identifying key residues responsible for the stability of a protein. Our method can be compared with the interresidue contact map but has the advantage of weighting the contacts by the stabilization energy content which they bring to the protein structure. For the theoretical adjustment of the proposed method, we chose the Trp-cage mini protein as a model system to compare a spectrum of computational methods ranging from the ab initio MP2 level through the DFT method to empirical force-field methods. The IEM method correctly identifies Tryptophane 6 as the key residue in the Trp-cage. The other residues with the highest stabilizing contributions correspond to the structurally important positions in the protein. We have further tested our method on the Trp2Cage miniprotein--a P12W mutant of the Trp-cage and on two proteins from the rubredoxin family that differ in their thermostability. Our method correctly identified the thermodynamically more stable variants in both cases and therefore can also be used as a tool for the relative measurement of protein stability. Finally, we will point out the important role played by dispersion energy, which contributes significantly to the total stabilization energy and whose role in aromatic pairs is clearly dominant. Surprisingly, the dispersion energy plays an even more important role in the interaction of prolines with aromatic systems. PMID:18214960

Bendová-Biedermannová, Lada; Hobza, Pavel; Vondrásek, Jirí

2008-07-01

68

Excavating and endolithic sponge species (Porifera) from the Mediterranean: species descriptions and identification key  

Microsoft Academic Search

The present study is a review of the excavating and endolithic sponges present in the Mediterranean. A dichotomic key to 22 species is presented. Detailed species descriptions are provided based on newly collected material and previous descriptions from the literature. In the case of Cliona viridis (Schmidt, 1862), an in-depth histological study has also been performed. Discussions on problematic taxonomic

Dolors Rosell; María-J. Uriz

2002-01-01

69

Preliminary Keys to Waterfowl Age and Sex Identification by Means of Wing Plumage.  

National Technical Information Service (NTIS)

The paper describes characters in the wing plumage that are useful for determining age and sex of most common species of ducks. Each species is discussed briefly, and a key outlining a logical order in which to examine age and sex characters is presented....

S. M. Carney

1964-01-01

70

The Identification, Definition, and Measurement of Key Variables in Wait Time Research.  

ERIC Educational Resources Information Center

Wait time, or the pauses between questions and responses, has been demonstrated to be an important factor influencing classroom learning. This paper reviews the key variables that have emerged in wait time research over the past 20 years. Progress in defining and measuring wait time has resulted in improved methodology for wait time research.…

Gooding, C. Thomas; And Others

71

Identification of key radionuclides in a nuclear waste repository in basalt  

Microsoft Academic Search

Radionuclides were identified which appear to pose the greatest potential hazard to man during long term storage of nuclear waste in a repository mined in the Columbia Plateau basalt formation. The criteria used to select key radionuclides were as follows: quantity of radionuclide in stored waste; biological toxicity; leach rate of the wastes into groundwater; and transport rate via ground

G. S. Barney; B. J. Wood

1980-01-01

72

Provably secure and efficient identification and key agreement protocol with user anonymity  

Microsoft Academic Search

Many authentication and key agreement protocols were proposed for protecting communicated messages. In previous protocols, if the user?s identity is transmitted in plaintext, an adversary can tap the communications and employ it to launch some attacks. In most protocols with user anonymity, they focus on satisfaction of several security requirements. From a client?s point of view, those protocols are not

Ren-Chiun Wang; Wen-Shenq Juang; Chin-Laung Lei

2011-01-01

73

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

ERIC Educational Resources Information Center

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

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

2008-01-01

74

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.

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

2011-01-01

75

Identification of Protein Interacting Partners Using Tandem Affinity Purification  

PubMed Central

A critical and often limiting step in understanding the function of host and viral proteins is the identification of interacting cellular or viral protein partners. There are many approaches that allow the identification of interacting partners, including the yeast two hybrid system, as well as pull down assays using recombinant proteins and immunoprecipitation of endogenous proteins followed by mass spectrometry identification1. Recent studies have highlighted the utility of double-affinity tag mediated purification, coupled with two specific elution steps in the identification of interacting proteins. This approach, termed Tandem Affinity Purification (TAP), was initially used in yeast2,3 but more recently has been adapted to use in mammalian cells4-8. As proof-of-concept we have established a tandem affinity purification (TAP) method using the well-characterized eukaryotic translation initiation factor eIF4E9,10.The cellular translation factor eIF4E is a critical component of the cellular eIF4F complex involved in cap-dependent translation initiation10. The TAP tag used in the current study is composed of two Protein G units and a streptavidin binding peptide separated by a Tobacco Etch Virus (TEV) protease cleavage sequence. The TAP tag used in the current study is composed of two Protein G units and a streptavidin binding peptide separated by a Tobacco Etch Virus (TEV) protease cleavage sequence8. To forgo the need for the generation of clonal cell lines, we developed a rapid system that relies on the expression of the TAP-tagged bait protein from an episomally maintained plasmid based on pMEP4 (Invitrogen). Expression of tagged murine eIF4E from this plasmid was controlled using the cadmium chloride inducible metallothionein promoter. Lysis of the expressing cells and subsequent affinity purification via binding to rabbit IgG agarose, TEV protease cleavage, binding to streptavidin linked agarose and subsequent biotin elution identified numerous proteins apparently specific to the eIF4E pull-down (when compared to control cell lines expressing the TAP tag alone). The identities of the proteins were obtained by excision of the bands from 1D SDS-PAGE and subsequent tandem mass spectrometry. The identified components included the known eIF4E binding proteins eIF4G and 4EBP-1. In addition, other components of the eIF4F complex, of which eIF4E is a component were identified, namely eIF4A and Poly-A binding protein. The ability to identify not only known direct binding partners as well as secondary interacting proteins, further highlights the utility of this approach in the characterization of proteins of unknown function.

Thorne, Lucy; Goodfellow, Ian

2012-01-01

76

Identification of key radionuclides in a nuclear waste repository in basalt  

NASA Astrophysics Data System (ADS)

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

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

1980-05-01

77

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

2009-07-16

78

Helical peptide arrays for lead identification and interaction site mapping.  

PubMed

Libraries composed of linear and cyclic peptides cannot fully represent the higher order structures of most antigenic sites. To map the binding site of ligands or antibodies, a larger part of the three-dimensional space should be sampled. Because parallel synthesis of large arrays of peptides on hydrogels is restricted to relatively small peptides, a simple and robust homodimeric helical system was chosen for antigen presentation. First, it was established in an heterodimeric system that the 26-mer peptide could be synthesized and that the helical coiled-coil peptides interact in the hydrogel in a predictable manner. Next, libraries of homodimeric coiled coils were synthesized into which the epitope was grafted. Using dedicated helical dimeric and trimeric coiled-coil libraries, the epitopes of two anti-HIV-1 gp41 monoclonal antibodies known to interact with helical structures were mapped at high resolution. These mappings precisely reflect existing X-ray data, and the arrays can be applied to lead identification, epitope mapping, and systematic analysis of amino acid contribution to coiled-coil systems. PMID:21708118

Langedijk, Johannes P M; Zekveld, Maria J; Ruiter, Mariska; Corti, Davide; Back, Jaap W

2011-06-12

79

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

PubMed

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

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

1999-08-01

80

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

PubMed

Background:Breast cancer is a heterogeneous disease characterised by complex molecular alterations underlying the varied behaviour and response to therapy. However, translation of cancer genetic profiling for use in routine clinical practice remains elusive or prohibitively expensive. As an alternative, immunohistochemical analysis applied to routinely processed tissue samples could be used to identify distinct biological classes of breast cancer.Methods:In this study, 1073 archival breast tumours previously assessed for 25 key breast cancer biomarkers using immunohistochemistry and classified using clustering algorithms were further refined using naïve Bayes classification performance. Criteria for class membership were defined using the expression of a reduced panel of 10 proteins able to identify key molecular classes. We examined the association between these breast cancer classes with clinicopathological factors and patient outcome.Results:We confirm patient classification similar to established genotypic biological classes of breast cancer in addition to novel sub-divisions of luminal and basal tumours. Correlations between classes and clinicopathological parameters were in line with expectations and showed highly significant association with patient outcome. Furthermore, our novel biological class stratification provides additional prognostic information to the Nottingham Prognostic Index.Conclusion:This study confirms that distinct molecular phenotypes of breast cancer can be identified using robust and routinely available techniques and both the luminal and basal breast cancer phenotypes are heterogeneous and contain distinct subgroups. PMID:24008658

Green, A R; Powe, D G; Rakha, E A; Soria, D; Lemetre, C; Nolan, C C; Barros, F F T; Macmillan, R D; Garibaldi, J M; Ball, G R; Ellis, I O

2013-09-05

81

[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

82

A new species of the medicinal leech (Oligochaeta, Hirudinida, Hirudo) from Transcaucasia and an identification key for the genus Hirudo.  

PubMed

A recent molecular phylogenetic study has suggested that the genus Hirudo contains a neglected species previously known as the orientalis coloration type of the medicinal leech Hirudo medicinalis. In this paper, the new species is formally described as Hirudo orientalis sp. n. It can most readily be identified by the grass green coloration of the dorsum, segmentally arranged pairs of black quadrangular or rounded dots on its paramarginal dorsal stripes and similarly arranged, but less regular light-colored markings on the predominantly black venter. It has medium-sized epididymes and an evenly coiled vagina. H. orientalis is known from Transcaucasia, Iran, and Uzbekistan. It is widely used in medicine as the "medicinal leech." Very little is known about its exact distribution, specific habitat, and conservation status. The paper contains an identification key to all species of the genus Hirudo. PMID:16261357

Utevsky, Serge Y; Trontelj, Peter

2005-10-28

83

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

Microsoft Academic Search

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

Rodolfo Mendoza-Denton; Janina Pietrzak; Geraldine Downey

2008-01-01

84

Markerless identification of key events in gait cycle using image flow.  

PubMed

Gait analysis has been an interesting area of research for several decades. In this paper, we propose image-flow-based methods to compute the motion and velocities of different body segments automatically, using a single inexpensive video camera. We then identify and extract different events of the gait cycle (double-support, mid-swing, toe-off and heel-strike) from video images. Experiments were conducted in which four walking subjects were captured from the sagittal plane. Automatic segmentation was performed to isolate the moving body from the background. The head excursion and the shank motion were then computed to identify the key frames corresponding to different events in the gait cycle. Our approach does not require calibrated cameras or special markers to capture movement. We have also compared our method with the Optotrak 3D motion capture system and found our results in good agreement with the Optotrak results. The development of our method has potential use in the markerless and unencumbered video capture of human locomotion. Monitoring gait in homes and communities provides a useful application for the aged and the disabled. Our method could potentially be used as an assessment tool to determine gait symmetry or to establish the normal gait pattern of an individual. PMID:23367011

Vishnoi, Nalini; Duric, Zoran; Gerber, Naomi Lynn

2012-01-01

85

Identification of Key Residues Determining Species Differences in Inhibitor Binding of Microsomal Prostaglandin E Synthase-1*  

PubMed Central

Microsomal prostaglandin E synthase-1 (MPGES1) is induced during an inflammatory reaction from low basal levels by pro-inflammatory cytokines and subsequently involved in the production of the important mediator of inflammation, prostaglandin E2. Nonsteroidal anti-inflammatory drugs prevent prostaglandin E2 production by inhibiting the upstream enzymes cyclooxygenases 1 and 2. In contrast to these conventional drugs, a new generation of NSAIDs targets the terminal enzyme MPGES1. Some of these compounds potently inhibit human MPGES1 but do not have an effect on the rat orthologue. We investigated this interspecies difference in a rat/human chimeric form of the enzyme as well as in several mutants and identified key residues Thr-131, Leu-135, and Ala-138 in human MPGES1, which play a crucial role as gate keepers for the active site of MPGES1. These residues are situated in transmembrane helix 4, lining the entrance to the cleft between two subunits in the protein trimer, and regulate access of the inhibitor in the rat enzyme. Exchange toward the human residues in rat MPGES1 was accompanied with a gain of inhibitor activity, whereas exchange in human MPGES1 toward the residues found in rat abrogated inhibitor activity. Our data give evidence for the location of the active site at the interface between subunits in the homotrimeric enzyme and suggest a model of how the natural substrate PGH2, or competitive inhibitors of MPGES1, enter the active site via the phospholipid bilayer of the membrane.

Pawelzik, Sven-Christian; Uda, Narasimha Rao; Spahiu, Linda; Jegerschold, Caroline; Stenberg, Patric; Hebert, Hans; Morgenstern, Ralf; Jakobsson, Per-Johan

2010-01-01

86

A Key Interaction between the Alphavirus Envelope Proteins Responsible for Initial Dimer Dissociation during Fusion  

PubMed Central

Alphaviruses such as Semliki Forest virus (SFV) are enveloped viruses whose surface is covered by an organized lattice composed of trimers of E2-E1 heterodimers. The E1 envelope protein, a class II fusion protein, contains the hydrophobic fusion loop and refolds to drive virus fusion with the endosome membrane. The E2 protein is synthesized as a precursor p62, whose processing by furin primes the heterodimer for dissociation during virus entry. Dissociation of the E2-E1 heterodimer is an essential step during low-pH-triggered fusion, while the dissociation of the immature p62-E1 dimer is relatively pH resistant. Previous structural studies described an “acid-sensitive region” in E2 that becomes disordered at low pH. Within this region, the conserved E2 H170 is in position to form a hydrogen bond with the underlying E1 S57. Here we experimentally tested the role of this interaction in regulating dimer dissociation in mature and immature virus. Alanine substitutions of E1 S57 and E2 H170 destabilized the heterodimer and produced a higher pH threshold for exposure of the E1 fusion loop and for fusion of the immature virus. E1 S57K or S57D mutations were lethal and caused transport and assembly defects that were partially abrogated by neutralization of the exocytic pathway. The lethal phenotype of E1 S57K was rescued by second-site mutations at E2 H170/M171. Together, our results define a key role for the E1 S57-E2 H170 interaction in dimer stability and the pH dependence of fusion and provide evidence for stepwise dissociation of the E2-E1 dimer at low pH.

Fields, Whitney

2013-01-01

87

Disease candidate gene identification and prioritization using protein interaction networks  

PubMed Central

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 HITS algorithms, and the K-Step Markov method are applied to prioritize disease candidate genes in a training-test schema. Using a list of known disease-related genes from our earlier study as a training set ("seeds"), and the rest of the known genes as a test list, we perform large-scale cross validation to rank the candidate genes and also evaluate and compare the performance of our approach. Under appropriate settings – for example, a back probability of 0.3 for PageRank with Priors and HITS with Priors, and step size 6 for K-Step Markov method – the three methods achieved a comparable AUC value, suggesting a similar performance. Conclusion Even though network-based methods are generally not as effective as integrated functional annotation-based methods for disease candidate gene prioritization, in a one-to-one comparison, PPIN-based candidate gene prioritization performs better than all other gene features or annotations. Additionally, we demonstrate that methods used for studying both social and Web networks can be successfully used for disease candidate gene prioritization.

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

2009-01-01

88

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

2012-05-14

89

Identification of the key residues determining the product specificity of isomerohydrolase  

PubMed Central

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

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

2012-01-01

90

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

PubMed Central

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

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

2013-01-01

91

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

PubMed

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

Wang, Fangfang; Perry, Sharyn E

2013-01-11

92

Prevention or Identification of Web Intrusion via Human Computer Interaction Behaviour - A Proposal.  

National Technical Information Service (NTIS)

The present work proposes a new technique for the identification or prevention of intrusion in web applications via the monitoring of the user interaction behaviour. We report preliminary results in a verification task based on a user claiming his identit...

A. Fred A. A. Vieira H. Gamboa

2004-01-01

93

Perception of Interactivity: Affects of Four Key Variables in Mobile Advertising  

Microsoft Academic Search

There are indications that interactivity could benefit the effectiveness of mobile advertisements. But there are few guidelines on how to design interactive mobile advertisements. This study investigated the influences of various design features of mobile advertisements on perceived interactivity and the relationship between perceived interactivity and attitude toward mobile advertisements. An experiment consisting of 2 sessions was conducted to test

Qin Gao; Pei-Luen Patrick Rau; Gavriel Salvendy

2009-01-01

94

The genus Alterosa Blahnik, 2005 (Trichoptera, Philopotamidae, Philopotaminae) in northeastern Brazil, including the description of three new species and an identification key for the genus.  

PubMed

Alterosa Blahnik, 2005 contains 35 described species distributed in southern and southeastern Brazil. Three new species of Alterosa from northeastern Brazil are described and illustrated, Alterosa amadoi sp. n., Alterosa castroalvesi sp. n. and Alterosa caymmii sp. n., the first records of the genus from northeastern Brazil. An identification key for all known species of the genus is also presented. PMID:23950667

Dumas, Leandro Lourenço; Calor, Adolfo Ricardo; Nessimian, Jorge Luiz

2013-07-15

95

The genus Alterosa Blahnik, 2005 (Trichoptera, Philopotamidae, Philopotaminae) in northeastern Brazil, including the description of three new species and an identification key for the genus  

PubMed Central

Abstract Alterosa Blahnik, 2005 contains 35 described species distributed in southern and southeastern Brazil. Three new species of Alterosa from northeastern Brazil are described and illustrated, Alterosa amadoi sp. n., Alterosa castroalvesi sp. n. and Alterosa caymmii sp. n., the first records of the genus from northeastern Brazil. An identification key for all known species of the genus is also presented.

Dumas, Leandro Lourenco; Calor, Adolfo Ricardo; Nessimian, Jorge Luiz

2013-01-01

96

Identification of key mechanisms controlling gene expression in Leishmania infected macrophages using genome-wide promoter analysis.  

PubMed

The present study describes the in silico prediction of the regulatory network of Leishmania infected human macrophages. The construction of the gene regulatory network requires the identification of Transcription Factor Binding Sites (TFBSs) in the regulatory regions (promoters, enhancers) of genes that are regulated upon Leishmania infection. The promoters of human, mouse, rat, dog and chimpanzee genes were first identified in the whole genomes using available experimental data on full length cDNA sequences or deep CAGE tag data (DBTSS, FANTOM3, FANTOM4), mRNA models (ENSEMBL), or using hand annotated data (EPD, TRANSFAC). A phylogenetic footprinting analysis and a MATCH analysis of the promoter sequences were then performed to predict TFBS. Then, an SQL database that integrates all results of promoter analysis as well as other genome annotation information obtained from ENSEMBL, TRANSFAC, TRED (Transcription Regulatory Element Database), ORegAnno and the ENCODE project, was established. Finally publicly available expression data from human Leishmania infected macrophages were analyzed using the genome-wide information on predicted TFBS with the computer system ExPlain™. The gene regulatory network was constructed and activated signal transduction pathways were revealed. The Irak1 pathway was identified as a key pathway regulating gene expression changes in Leishmania infected macrophages. PMID:21093613

Ghedira, Kais; Hornischer, Klaus; Konovalova, Tatiana; Jenhani, Ahmed-Zaki; Benkahla, Alia; Kel, Alexander

2010-11-18

97

Identification of Key Residues in Virulent Canine Distemper Virus Hemagglutinin That Control CD150/SLAM-Binding Activity?  

PubMed Central

Morbillivirus cell entry is controlled by hemagglutinin (H), an envelope-anchored viral glycoprotein determining interaction with multiple host cell surface receptors. Subsequent to virus-receptor attachment, H is thought to transduce a signal triggering the viral fusion glycoprotein, which in turn drives virus-cell fusion activity. Cell entry through the universal morbillivirus receptor CD150/SLAM was reported to depend on two nearby microdomains located within the hemagglutinin. Here, we provide evidence that three key residues in the virulent canine distemper virus A75/17 H protein (Y525, D526, and R529), clustering at the rim of a large recessed groove created by ?-propeller blades 4 and 5, control SLAM-binding activity without drastically modulating protein surface expression or SLAM-independent F triggering.

Zipperle, Ljerka; Langedijk, Johannes P. M.; Orvell, Claes; Vandevelde, Marc; Zurbriggen, Andreas; Plattet, Philippe

2010-01-01

98

Key Interactions in Integrin Ectodomain Responsible for Global Conformational Change Detected by Elastic Network Normal-Mode Analysis  

PubMed Central

Integrin, a membrane protein with a huge extracellular domain, participates in cell-cell and cell-extracellular-matrix interactions for metazoan. A group of integrins is known to perform a large-scale structural change when the protein is activated, but the activation mechanism and generality of the conformational change remain to be elucidated. We performed normal-mode analysis of the elastic network model on integrin ?V?3 ectodomain in the bent form and identified key residues that influenced molecular motions. Iterative normal-mode calculations demonstrated that the specific nonbonded interactions involving the key residues work as a snap to keep integrin in the bent form. The importance of the key residues for the conformational change was further verified by mutation experiments, in which integrin ?IIb?3 was used. The conservation pattern of amino acid residues among the integrin family showed that the characteristic pattern of residues seen around these key residues is found in the limited groups of integrin ?-chains. This conservation pattern suggests that the molecular mechanism of the conformational change relying on the interactions found in integrin ?V?3 is unique to the limited types of integrins.

Matsumoto, Atsushi; Kamata, Tetsuji; Takagi, Junichi; Iwasaki, Kenji; Yura, Kei

2008-01-01

99

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.

Biondi, Maurizio; D'Alessandro, Paola

2012-01-01

100

Large-scale identification of yeast integral membrane protein interactions  

Microsoft Academic Search

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

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

2005-01-01

101

Key issues for the successful design of an intelligent, interactive playground  

Microsoft Academic Search

An Intelligent Playground is an environment with interactive objects that, using advanced technology such as sensors and actuators, react to the interaction with the children and actively encourage children to play. Thus, an intelligent playground stimulates children to move and play together. In this way, it provides for a healthy alternative for popular pastimes such as computer games and television.

Janienke Sturm; Tilde Bekker; Bas Groenendaal; Rik Wesselink; Berry Eggen

2008-01-01

102

CREATING AN INTERACTIVE AND DICHOTOMOUS KEY TO THE WORLD SUBFAMILIES OF BRACONIDAE  

Microsoft Academic Search

Members of Braconidae (Hymenoptera: Ichneumonoidea) are mostly parasitoids of other holometabolous insects. It is a large family with a little over 18,000 described species and many more to be described. Subfamily classification in this group has been unstable and resolution of phylogenetic history at the subfamily level has been problematic. Since 1993, no new keys to the subfamilies of Braconidae

Kacie Jo Johansen

2010-01-01

103

Modeling social interactions: Identification, empirical methods and policy implications  

Microsoft Academic Search

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

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

2008-01-01

104

Identification of a novel protein interacting with RPGR  

Microsoft Academic Search

A novel protein, called RPGRIP, has been identified as interacting with the RPGR protein, which is mutated in a severe form of human retinal degeneration, X-linked retinitis pigmentosa (RP3 type). The bovine RPGRIP was identified initially by screening for RPGR-interacting proteins with a bovine retina cDNA library using the yeast two-hybrid system. The specificity of the interaction was confirmed by

James P. Boylan; Alan F. Wright

2000-01-01

105

Symbolic optimization of interacting controllers based onredundancy identification and removal  

Microsoft Academic Search

This paper presents a binary decision diagram (BDD)-based algorithm for the optimization of the driven machine, M2, of a finite-state machine (FSM) network with cascade connection, M1 ?M2. The technique we propose relies on redundant faults identification and removal. A fault, f, located into machine M 2, is redundant with respect to the overall network if the driving machine M1

Fabrizio Ferrandi; Franco Fummi; Enrico Macii; Massimo Poncino; Donatella Sciuto

2000-01-01

106

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

NASA Astrophysics Data System (ADS)

The interaction of alkali adatoms with metal surfaces is reviewed.The relevance of the spectral properties in the bond formation is discussed.It is shown the role of the surface projected band gap in determining the alkali electronic resonance features.A critical overview of different theoretical models gives an unified picture of the alkali atom - metal surface bond.

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

2013-05-01

107

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

108

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

109

Identifying key electrostatic interactions in Rhizomucor miehei lipase: the influence of solvent dielectric  

Microsoft Academic Search

.   The conformational change associated with the interfacial activation of Rhizomucor miehei lipase involves the displacement of an ?-helical lid (residues 82–96) away from the active site on moving from water (high\\u000a dielectric) to lipid (low dielectric). The presence of two media of very different dielectric properties suggests that electrostatic\\u000a interactions play an important role in this process. We have

Sanna Jääskeläinen; Chandra S. Verma; Roderick E. Hubbard; Leo S. D. Caves

1999-01-01

110

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.

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

111

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

PubMed

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; Gaur, Deepak

2012-11-26

112

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.

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

2012-01-01

113

Anharmonic Resonance in Intense Laser-Matter Interaction: Key to Collisionless Absorption  

NASA Astrophysics Data System (ADS)

We show that anharmonic resonance is the leading mechanism of collisionless absorption in overdense matter (solids, droplets, clusters). It induces a finite phase shift between current density and laser field, produces the fast electrons in single events, in contrast to stochastic and diffusive processes, and creates the hot Maxwellian tail observed in simulations and measured in the experiment. Finally, the difference in interaction of p polarized and circularly polarized laser light follows in the most immediate way. Some of the proposed absorption mechanisms are critically analyzed.

Mulser, P.; Bauer, D.

2010-11-01

114

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

PubMed

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

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

2012-06-01

115

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

PubMed Central

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

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

2013-01-01

116

The plasma-wall interaction region: a key low temperature plasma for controlled fusion  

NASA Astrophysics Data System (ADS)

The plasma-wall interaction region of a fusion device provides the interface between the hot core plasma and the material surfaces. To obtain acceptably low levels of erosion from these surfaces requires most of the power leaving the core to be radiated. This is accomplished in existing devices by encouraging plasma detachment, in which the hot plasma arriving in the region is cooled by volume recombination and ion-neutral momentum transfer with a dense population of neutrals recycled from the surface. The result is a low temperature (1 eV1019 m-3) but weakly ionized (n0>1020 m-3, ne/n0<0.1) plasma found nowhere else in the fusion environment. This plasma provides many of the conditions found in industrial plasmas exploiting plasma chemistry and the presence of carbon in the region (in the form of carbon-fibre composite used in the plasma facing materials) can result in the formation of deposited hydrocarbon films. The plasma-wall interaction region is therefore among the most difficult in fusion to model, requiring an understanding of atomic, molecular and surface physics issues.

Counsell, G. F.

2002-08-01

117

Automatic Identification and Organization of Index Terms for Interactive Browsing.  

ERIC Educational Resources Information Center

The potential of automatically generated indexes for information access has been recognized for several decades, but the quantity of text and the ambiguity of natural language processing have made progress at this task more difficult than was originally foreseen. Recently, a body of work on development of interactive systems to support phrase…

Wacholder, Nina; Evans, David K.; Klavans, Judith L.

118

Identification of novel CBP interacting proteins in embryonic orofacial tissue  

Microsoft Academic Search

cAMP response element-binding protein (CREB)-binding protein (CBP) plays an important role as a general co-integrator of multiple signaling pathways and interacts with a large number of transcription factors and co-factors, through its numerous protein-binding domains. To identify nuclear factors associated with CBP in developing orofacial tissue, a yeast two-hybrid screen of a cDNA library derived from orofacial tissue from gestational

Xiaolong Yin; Dennis R. Warner; Emily A. Roberts; M. Michele Pisano; Robert M.. Greene

2005-01-01

119

Magnetic anisotropy, magnetostatic interactions and identification of magnetofossils  

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

120

Magnetic anisotropy, magnetostatic interactions and identification of magnetofossils  

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

121

Identification of interspecies interactions affecting Porphyromonas gingivalis virulence phenotypes  

PubMed Central

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

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

2011-01-01

122

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

PubMed

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

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

2010-11-17

123

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

PubMed

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

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

2013-05-03

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.

Flores, Ricardo; Ruiz-Ruiz, Susana; Soler, Nuria; Sanchez-Navarro, Jesus; Fagoaga, Carmen; Lopez, Carmelo; Navarro, Luis; Moreno, Pedro; Pena, Leandro

2013-01-01

125

A survey of electronic drug information resources and identification of problems associated with the differing vocabularies used to key them.  

PubMed

Drug information resources are increasingly becoming electronically available. They differ in scope, granularity, and purpose. These considerations have shaped the selection of dissimilar drug name keys, complicating access. An abbreviated and simplified historical context of the development of official controlled vocabularies and their relationships is followed by a review of the kinds of information available in several electronic drug information resources. The key vocabularies used are discussed with examples. Problems using the differing terms of the resource vocabularies are identified. PMID:8130551

Gnassi, J A; Barnett, G O

1993-01-01

126

Automated identification of pathways from quantitative genetic interaction data  

PubMed Central

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

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

2010-01-01

127

Identification of Genes That Interact With Drosophila liquid facets  

PubMed Central

We have performed mutagenesis screens of the Drosophila X chromosome and the autosomes for dominant enhancers of the rough eye resulting from overexpression of liquid facets. The liquid facets gene encodes the homolog of vertebrate endocytic Epsin, an endocytic adapter protein. In Drosophila, Liquid facets is a core component of the Notch signaling pathway required in the signaling cells for ligand endocytosis and signaling. Why ligand internalization by the signaling cells is essential for signaling is a mystery. The requirement for Liquid facets is a hint at the answer, and the genes identified in this screen provide further clues. Mutant alleles of clathrin heavy chain, Rala, split ends, and auxilin were identified as enhancers. We describe the mutant alleles and mutant phenotypes of Rala and aux. We discuss the relevance of all of these genetic interactions to the function of Liquid facets in Notch signaling.

Eun, Suk Ho; Lea, Kristi; Overstreet, Erin; Stevens, Samuel; Lee, Ji-Hoon; Fischer, Janice A.

2007-01-01

128

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

Microsoft Academic Search

The vast majority of physiological processes in living cells are mediated by protein–protein interactions often specified by particular protein sequence motifs. PDZ domains, composed of 80–100 amino acid residues, are an important class of interaction motif. Among the PDZ-containing proteins, glutaminase interacting protein (GIP), also known as Tax Interacting Protein TIP-1, is unique in being composed almost exclusively of a

Sevil Zencir; Mohiuddin Ovee; Melanie J. Dobson; Monimoy Banerjee; Zeki Topcu; Smita Mohanty

2011-01-01

129

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.

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

2012-01-01

130

Identification of minimally interacting modules in an intrinsically disordered protein.  

PubMed

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

2012-08-22

131

Identification of new G?? interaction sites in adenylyl cyclase 2.  

PubMed

The role of G?? in adenylyl cyclase (AC) signaling is complicated due to its role as a conditional activator (AC2, AC4 and AC7) and an inhibitor (AC1, AC3 and AC8). AC2 is stimulated by G?(s) and if G?? is present the stimulation is synergistic. The precise mechanism of this synergistic activation is still not known. In order to further elucidate the role of G?? in AC2 activation by G?(s), peptides derived from the C1 domains of AC2 were synthesized and the ability of the various peptides to regulate AC2 function was tested. Our results identify two new G??-binding sites in the AC2 C1 domain, AC2 C1a 339-360 and AC2 C1b 578-602 that are involved with stimulation of AC2 by G??. These two regions are different from the previously described QEHA motif in the C2 domain of AC2. Further, the recently discovered PFAHL motif was confirmed to bind and to be involved with stimulation of AC2 by G??. These functional studies indicate that multiple regions of AC2 are involved in the interaction with G??. PMID:21596131

Boran, Aislyn D W; Chen, Yibang; Iyengar, Ravi

2011-05-08

132

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.

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

2010-01-01

133

DEVELOPMENT OF MOLECULAR DIAGNOSTIC MARKERS FOR HOMALODISCA SHARPSHOOTERS PRESENT IN CALIFORNIA TO AID IN THE IDENTIFICATION OF KEY PREDATORS  

Technology Transfer Automated Retrieval System (TEKTRAN)

The aim of the present study was to develop molecular diagnostic markers to identify key predators of Homalodisca sharpshooter species present in California, H coagulata (Glassy-winged Sharpshooter, GWSS) and H liturata (Smoke-tree Sharpshooter, STSS). RAPD-PCR DNA fmgerprinting of several sharpshoo...

134

Identification of NPM-ALK interacting proteins by tandem mass spectrometry  

Microsoft Academic Search

Constitutive overexpression of nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) is a key oncogenic event in anaplastic large-cell lymphomas with the characteristic chromosomal aberration t(2;5)(p23;q35). Proteins that interact with ALK tyrosine kinase play important roles in mediating downstream cellular signals, and are potential targets for novel therapies. Using a functional proteomic approach, we determined the identity of proteins that interact with the ALK

David K Crockett; Zhaosheng Lin; Kojo SJ Elenitoba-Johnson; Megan S Lim

2004-01-01

135

Identification of Brain-Specific Angiogenesis Inhibitor 2 as an Interaction Partner of Glutaminase Interacting Protein  

PubMed Central

The vast majority of physiological processes in living cells are mediated by protein-protein interactions often specified by particular protein sequence motifs. PDZ domains, composed of 80–100 amino acid residues, are an important class of interaction motif. Among the PDZ-containing proteins, Glutaminase Interacting Protein (GIP), also known as Tax Interacting Protein TIP-1, is unique in being composed almost exclusively of a single PDZ domain. GIP has important roles in cellular signalling, protein scaffolding and modulation of tumor growth and interact with a number of physiological partner proteins, including Glutaminase L, ?-Catenin, FAS, HTLV Tax, HPV E6, Rhotekin and Kir 2.3. To identify the network of proteins that interact with GIP, a human fetal brain cDNA library was screened using a yeast two-hybrid assay with GIP as bait. We identified Brain-specific Angiogenesis Inhibitor 2 (BAI2), a member of the adhesion-G protein-coupled receptors (GPCRs), as a new partner of GIP. BAI2 is expressed primarily in neurons, further expanding GIP cellular functions. The interaction between GIP and the carboxy-terminus of BAI2 was characterized using fluorescence, Circular Dichroism (CD) and Nuclear Magnetic Resonance (NMR) spectroscopy assays. These biophysical analyses support the interaction identified in the yeast two-hybrid assay. This is the first study reporting BAI2 as an interaction partner of GIP.

Zencir, Sevil; Ovee, Mohiuddin; Dobson, Melanie J.; Banerjee, Monimoy; Topcu, Zeki; Mohanty, Smita

2011-01-01

136

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

2013-04-08

137

Identifying Key Juxtamembrane Interactions in Cell Membranes Using AraC-based Transcriptional Reporter Assay (AraTM)*  

PubMed Central

Dimerization is a key regulatory mechanism in activation of transmembrane (TM) receptors during signal transduction. This process involves a coordinated interplay between extracellular (EX), TM, and cytoplasmic (CYTO) regions to form a specific interface required for both ligand binding and intracellular signaling to occur. While several transcriptional activator-based methods exist for investigating TM interactions in bacterial membranes, expression of TM chimera in these methods occurs in a reverse orientation, and are limited to only TM domains for proper membrane trafficking and integration. We therefore developed a new, AraC-based transcriptional reporter assay (AraTM) that expresses EX-TM-CYTO chimera in their native orientation, thereby enabling membrane trafficking to occur independent of the TM chimera used as well as permitting analysis of EX-TM-CYTO interactions in biological membranes. Using integrin ?IIb TM-CYTO as a model, we observe a large increase in homodimerization for the constitutively active TM mutant L980A relative to wild-type in the TM-CYTO construct (A963-E1008). We also characterized the receptor for advanced glycation endproducts (RAGE), whose homooligomeric state is critical in ligand recognition, and find the specific juxtamembrane region within the CYTO (A375-P394) mediates homodimerization, and is dominant over effects observed when the extracellular C2 domain is included. Furthermore, we find good agreement between our AraTM measurements in bacterial membranes and BRET measurements made on corresponding RAGE constructs expressed in transfected HEK293 cells. Overall, the AraTM assay provides a new approach to identify specific interactions between receptor EX-TM-CYTO domains in biological membranes that are important in regulation of signal transduction.

Su, Pin-Chuan; Berger, Bryan W.

2012-01-01

138

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

PubMed Central

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

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

2012-01-01

139

Interactive Vision from the Top Down: Interactional Structure Applied to the Identification and Interpretation of Visual Interactive Behaviour  

Microsoft Academic Search

This paper considers the construction of machine vision systems for tracking interaction, informed by work from the human sciences1. The e mphasis is on the construction of what we refer to as 'global l evel systems' or 'global systems' f or short, which treat the unit of interaction as being relatively large (e.g. the script for a greeting, proceeding from

Bernard Ogden; Kerstin Dautenhahn

2001-01-01

140

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

2012-06-04

141

The Structure of the Human RNase H2 Complex Defines Key Interaction Interfaces Relevant to Enzyme Function and Human Disease*  

PubMed Central

Ribonuclease H2 (RNase H2) is the major nuclear enzyme involved in the degradation of RNA/DNA hybrids and removal of ribonucleotides misincorporated in genomic DNA. Mutations in each of the three RNase H2 subunits have been implicated in a human auto-inflammatory disorder, Aicardi-Goutières Syndrome (AGS). To understand how mutations impact on RNase H2 function we determined the crystal structure of the human heterotrimer. In doing so, we correct several key regions of the previously reported murine RNase H2 atomic model and provide biochemical validation for our structural model. Our results provide new insights into how the subunits are arranged to form an enzymatically active complex. In particular, we establish that the RNASEH2A C terminus is a eukaryotic adaptation for binding the two accessory subunits, with residues within it required for enzymatic activity. This C-terminal extension interacts with the RNASEH2C C terminus and both are necessary to form a stable, enzymatically active heterotrimer. Disease mutations cluster at this interface between all three subunits, destabilizing the complex and/or impairing enzyme activity. Altogether, we locate 25 out of 29 residues mutated in AGS patients, establishing a firm basis for future investigations into disease pathogenesis and function of the RNase H2 enzyme.

Reijns, Martin A. M.; Bubeck, Doryen; Gibson, Lucien C. D.; Graham, Stephen C.; Baillie, George S.; Jones, E. Yvonne; Jackson, Andrew P.

2011-01-01

142

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

PubMed

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

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

2013-09-01

143

Culture and identification of Desulfovibrio spp. from corals infected by black band disease on Dominican and Florida Keys reefs.  

PubMed

Black band disease (BBD) of corals is characterized as a pathogenic microbial consortium composed of a wide variety of microorganisms. Together, many of these microorganisms contribute to an active sulfur cycle that produces anoxia and high levels of sulfide adjacent to the coral surface, conditions that are lethal to coral tissue. Sulfate-reducing bacteria, as sulfide producers, are an important component of the sulfur cycle and the black band community. Previous molecular survey studies have shown multiple Desulfovibrio species present in BBD but with limited consistency between bacterial species and infections. In this study we compared 16S rRNA gene sequences of sulfate-reducing bacteria selectively cultured from 6 BBD bands on 4 coral species, Diploria clivosa, D. strigosa, D. labyrinthiformes, and Siderastrea siderea, in the Florida Keys and Dominica. The 16S rRNA gene sequences were obtained through direct sequencing of PCR products or by cloning. A BLAST search revealed that 8 out of 10 cultures sequenced were highly homologous to Desulfovibrio sp. strain TBP-1, a strain originally isolated from marine sediment. Although the remaining 2 sequences were less homologous to Desulfovibrio sp. strain TBP-1, they did not match any other sulfate-reducing (or other) species in GenBank. PMID:16703774

Viehman, S; Mills, D K; Meichel, G W; Richardson, L L

2006-03-23

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.

2011-01-01

145

Functional Identification of APIP as Human mtnB, a Key Enzyme in the Methionine Salvage Pathway  

PubMed Central

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

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

2012-01-01

146

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

PubMed

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

2013-09-05

147

Identification of key DNA elements involved in promoter recognition by Mxr1p, a master regulator of methanol utilization pathway in Pichia pastoris.  

PubMed

Mxr1p (methanol expression regulator 1) functions as a key regulator of methanol metabolism in the methylotrophic yeast Pichia pastoris. In this study, a recombinant Mxr1p protein containing the N-terminal zinc finger DNA binding domain was overexpressed and purified from E. coli cells and its ability to bind to promoter sequences of AOXI encoding alcohol oxidase was examined. In the AOX1 promoter, Mxr1p binds at six different regions. Deletions encompassing these regions result in a significant decrease in AOXI promoter activity in vivo. Based on the analysis of AOXI promoter sequences, a consensus sequence for Mxr1p binding consisting of a core 5' CYCC 3' motif was identified. When the core CYCC sequence is mutated to CYCA, CYCT or CYCM (M = 5-methylcytosine), Mxr1p binding is abolished. Though Mxr1p is the homologue of Saccharomyces cerevisiae Adr1p transcription factor, it does not bind to Adr1p binding site of S. cerevisiae alcohol dehydrogenase promoter (ADH2UAS1). However, two point mutations convert ADH2UAS1 into an Mxr1p binding site. The identification of key DNA elements involved in promoter recognition by Mxr1p is an important step in understanding its function as a master regulator of the methanol utilization pathway in P. pastoris. PMID:19450714

Kranthi, Balla Venkata; Kumar, Ritesh; Kumar, Nallani Vijay; Rao, Desirazu N; Rangarajan, Pundi N

2009-05-18

148

Identification and characterization of a mammalian protein interacting with 20S proteasome precursors  

PubMed Central

The assembly of individual mammalian proteasome subunits into catalytically active 20S proteasome is not well understood. Herein, we report the identification and characterization of human and mouse homologues of the yeast proteasome maturating factor Ump1p. We delineate the region of hUMP1 implicated in the specific interaction with proteasome precursors and show that hUMP1 protein is absent from the mature form of the 20S proteasome. We also show that the transcript level of mammalian UMP1 is increased after IFN-? treatment and that mammalian UMP1 is functionally related to but not interchangeable with its yeast homologue.

Burri, Lena; Hockendorff, Jorg; Boehm, Ulrich; Klamp, Thorsten; Dohmen, R. Jurgen; Levy, Frederic

2000-01-01

149

Identification and characterization of a mammalian protein interacting with 20S proteasome precursors.  

PubMed

The assembly of individual mammalian proteasome subunits into catalytically active 20S proteasome is not well understood. Herein, we report the identification and characterization of human and mouse homologues of the yeast proteasome maturating factor Ump1p. We delineate the region of hUMP1 implicated in the specific interaction with proteasome precursors and show that hUMP1 protein is absent from the mature form of the 20S proteasome. We also show that the transcript level of mammalian UMP1 is increased after IFN-gamma treatment and that mammalian UMP1 is functionally related to but not interchangeable with its yeast homologue. PMID:10973495

Burri, L; Höckendorff, J; Boehm, U; Klamp, T; Dohmen, R J; Lévy, F

2000-09-12

150

Chemical crosslinking and mass spectrometric identification of interaction sites within soluble aggregate of protein therapeutics.  

PubMed

Protein aggregation presents a major challenge to bioengineering. In the present study, chemical crosslinking and mass spectrometry are employed to probe the interaction amongst soluble oligomer formed by Fc molecule of monoclonal antibody. Aggregation was induced by thermal stress at 42°C for 6h under physiological pH. Contacting residues on adjacent molecules were captured with bifunctional crosslinker BS3, followed by mass spectrometric identification of the crosslinked sites. The approach provides site-specific information regarding the binding interface that would have broad application in the field. PMID:22677652

Zhao, Alan; Hao, Gang; Gu, Jane

2012-05-22

151

Sensor fault detection and identification in dead-reckoning system of mobile robot: interacting multiple model approach  

Microsoft Academic Search

An interacting multiple-model (IMM) approach to sensor fault detection and identification (FDI) in the dead reckoning of mobile robots is proposed Changes of sensor normal\\/failure modes are explicitly modeled as switching from one mode to another in a probabilistic manner; mode probabilities and robot states are estimated via a bank of Kalman filters with mutual interaction. To provide better fault

Masafumi Hashimoto; Hiroyuki Kawashima; Takashi Nakagami; Fuminori Oba

2001-01-01

152

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

SciTech Connect

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) 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 2D-LC/MS/MS; and stage 2 analysis of PIR-labeled peptides by multiplexed LC/FTICR-MS; (iii) data analysis: identification of cross-linked peptides and proteins of origin using accurate mass and other constraints. 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 S. 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 the PIR approach is particularly suited for studies of membrane protein-protein interactions, an area under-represented with current widely-used approaches.

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

2009-03-01

153

Identification of Direct Targets of FUSCA3, a Key Regulator of Arabidopsis Seed Development1[C][W][OA  

PubMed Central

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

Wang, Fangfang; Perry, Sharyn E.

2013-01-01

154

Modelling molecular interaction pathways using a two-stage identification algorithm.  

PubMed

In systems biology, molecular interactions are typically modelled using white-box methods, usually based on mass action kinetics. Unfortunately, problems with dimensionality can arise when the number of molecular species in the system is very large, which makes the system modelling and behavior simulation extremely difficult or computationally too expensive. As an alternative, this paper investigates the identification of two molecular interaction pathways using a black-box approach. This type of method creates a simple linear-in-the-parameters model using regression of data, where the output of the model at any time is a function of previous system states of interest. One of the main objectives in building black-box models is to produce an optimal sparse nonlinear one to effectively represent the system behavior. In this paper, it is achieved by applying an efficient iterative approach, where the terms in the regression model are selected and refined using a forward and backward subset selection algorithm. The method is applied to model identification for the MAPK signal transduction pathway and the Brusselator using noisy data of different sizes. Simulation results confirm the efficacy of the black-box modelling method which offers an alternative to the computationally expensive conventional approach. PMID:19003449

Gormley, Padhraig; Li, Kang; Irwin, George W

2008-03-04

155

Modelling molecular interaction pathways using a two-stage identification algorithm  

PubMed Central

In systems biology, molecular interactions are typically modelled using white-box methods, usually based on mass action kinetics. Unfortunately, problems with dimensionality can arise when the number of molecular species in the system is very large, which makes the system modelling and behavior simulation extremely difficult or computationally too expensive. As an alternative, this paper investigates the identification of two molecular interaction pathways using a black-box approach. This type of method creates a simple linear-in-the-parameters model using regression of data, where the output of the model at any time is a function of previous system states of interest. One of the main objectives in building black-box models is to produce an optimal sparse nonlinear one to effectively represent the system behavior. In this paper, it is achieved by applying an efficient iterative approach, where the terms in the regression model are selected and refined using a forward and backward subset selection algorithm. The method is applied to model identification for the MAPK signal transduction pathway and the Brusselator using noisy data of different sizes. Simulation results confirm the efficacy of the black-box modelling method which offers an alternative to the computationally expensive conventional approach.

Li, Kang; Irwin, George W.

2008-01-01

156

Structure and Mutagenesis Studies of the C-terminal Region of Licensing Factor Cdt1 Enable the Identification of Key Residues for Binding to Replicative Helicase Mcm Proteins  

PubMed Central

In eukaryotes, DNA replication is fired once in a single cell cycle before cell division starts to maintain stability of the genome. This event is tightly controlled by a series of proteins. Cdt1 is one of the licensing factors and is involved in recruiting replicative DNA helicase Mcm2–7 proteins into the pre-replicative complex together with Cdc6. In Cdt1, the C-terminal region serves as a binding site for Mcm2–7 proteins, although the details of these interactions remain largely unknown. Here, we report the structure of the region and the key residues for binding to Mcm proteins. We determined the solution structure of the C-terminal fragment, residues 450–557, of mouse Cdt1 by NMR. The structure consists of a winged-helix domain and shows unexpected similarity to those of the C-terminal domain of Cdc6 and the central fragment of Cdt1, thereby implying functional and evolutionary relationships. Structure-based mutagenesis and an in vitro binding assay enabled us to pinpoint the region that interacts with Mcm proteins. Moreover, by performing in vitro binding and budding yeast viability experiments, we showed that ?45 residues located in the N-terminal direction of the structural region are equally crucial for recognizing Mcm proteins. Our data suggest the possibility that winged-helix domain plays a role as a common module to interact with replicative helicase in the DNA replication-licensing process.

Jee, JunGoo; Mizuno, Takeshi; Kamada, Katsuhiko; Tochio, Hidehito; Chiba, Yasumasa; Yanagi, Ken-ichiro; Yasuda, Gentaro; Hiroaki, Hidekazu; Hanaoka, Fumio; Shirakawa, Masahiro

2010-01-01

157

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

PubMed Central

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

Randrianambinintsoa, Fano Jose; Leger, Nicole; Robert, Vincent; Depaquit, Jerome

2013-01-01

158

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

2013-08-02

159

Atom-Specific Interaction Quantification and Identification by 3D-SPM  

NASA Astrophysics Data System (ADS)

Entire scientific disciplines such as mechanics and chemistry are governed by the interactions between atoms and molecules. On surfaces, forces extending into the vacuum direct the behavior of phenomena such as thin film growth, nanotribology, and surface catalysis. To advance our knowledge of the fundamentals governing these topics, it is desirable to simultaneously map electron densities and quantify force interactions between the surface of interest and a probe with atomic resolution. Using the oxygen-reconstructed copper (100) surface as a model system, we demonstrate that much of this information can be derived from combining three-dimensional atomic force microscopy (3D-AFM) with simultaneous STM. The three-dimensional scanning probe microscopy (3D-SPM) variant resulting from this combination provides complementary information in the various interaction channels recorded. The surface oxide layer of copper (100) features defects and a distinct structure of the Cu and O sublattices that is ideally suited for such model investigations. The analysis of our experimental results allows for the identification of atomic species and defects on the sample surface through the comparison of simultaneously recorded force and current data.

Schwendemann, Todd C.; Baykara, Mehmet Z.; Monig, Harry; Todorovic, Milica; Gotzen, Jan; Unverdi, Ozhan; Perez, Ruben; Altman, Eric I.; Schwarz, Udo D.

2012-02-01

160

Identification and characterization of a novel folliculin-interacting protein FNIP2  

PubMed Central

Birt-Hogg-Dube’ syndrome characterized by increased risk for renal neoplasia is caused by germline mutations in the BHD/FLCN gene encoding a novel tumor suppressor protein, folliculin(FLCN), which interacts with FNIP1 and 5?-AMP-activated protein kinase(AMPK). Here we report the identification and characterization of a novel FNIP1 homolog FNIP2 that also interacts with FLCN and AMPK. C-terminally-deleted FLCN mutants, similar to those produced by naturally-occurring germline mutations in BHD patients, were unable to bind FNIP2. These data taken together with our previous results that demonstrated FNIP1 binding to the C-terminus of FLCN suggest that FLCN tumor suppressor function may be facilitated by interactions with both FNIP1 and FNIP2 through its C-terminus. Furthermore, we demonstrate that FNIP1 and FNIP2 are able to form homo- or heteromeric multimers suggesting that they may function independently or cooperatively with FLCN. Differential expression of FNIP1 and FNIP2 transcripts in some normal tissues may indicate tissue specificity for these homologs. Interestingly FNIP1 and FNIP2 were oppositely expressed in human clear cell renal cell carcinoma(RCC), and coordinately expressed in chromophobe RCC and oncocytoma, suggesting their differential function in different histologic variants of RCC.

Hasumi, Hisashi; Baba, Masaya; Hong, Seung-Beom; Hasumi, Yukiko; Huang, Ying; Yao, Masahiro; Valera, Vladimir A.; Linehan, W. Marston; Schmidt, Laura S.

2009-01-01

161

Identification of gene-environment interactions in cancer studies using penalization.  

PubMed

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

2013-08-29

162

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

SciTech Connect

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

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

2007-04-20

163

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

Microsoft Academic Search

The Freshwater Ecology Laboratory at Connecticut College has developed an interactive, Web-based identification key to freshwater algal genera using the Lucid Professional and Lucid 3 software developed by the Centre for Biological Information Technology at the University of Queensland, Brisbane, Australia. The Key to Freshwater Algae was funded by the National Science Foundation (Award #CCLI-0229531) to encourage awareness of microscopic

Hannah A. Shayler; Peter A. Siver

2006-01-01

164

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

Microsoft Academic Search

The Freshwater Ecology Laboratory at Connecticut College has developed an interactive, Web-based identification key to freshwater algal genera using the Lucid Professional and Lucid 3 software developed by the Centre for Biological Information Technology at the University of Queensland, Brisbane, Australia. The Key to Freshwater Algae was funded by the National Science Foundation (Award #CCLI-0229531) to encourage awareness of microscopic

Hannah A. Shayler; Peter A. Siver

2006-01-01

165

"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…

Shayler, Hannah A.; Siver, Peter A.

2006-01-01

166

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

167

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

168

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

PubMed Central

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

Kazanietz, Marcelo G.

2013-01-01

169

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.

Vashist, Surender; Urena, Luis; Chaudhry, Yasmin

2012-01-01

170

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

PubMed Central

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

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

2011-01-01

171

Key Inter-molecular Interactions in the E. Coli 70S Ribosome Revealed by Coarse-Grained Analysis  

PubMed Central

The ribosome is a very large complex, which consists of many RNA and protein molecules and plays a central role in protein biosynthesis in all organisms. Extensive interactions between different molecules are critical to ribosomal functional dynamics. In this work, inter-molecular interactions in the E. coli 70S ribosome are investigated by coarse-grained (CG) analysis. CG models are defined to preserve dynamic domains in RNAs and proteins, and capture functional motions in the ribosome, then the CG sites are connected by harmonic springs and spring constants are obtained by matching the computed fluctuations to those of an all-atom molecular dynamics (MD) simulation. Those spring constants indicate how strong the interactions are between the ribosomal components, which are in good agreement with various experimental data. Nearly all of bridges between the small and large ribosomal subunits are indicated by CG interactions with large spring constants. The head of the small subunit is very mobile because it has the minimal CG interactions with the rest of the subunit; However, a large number of small subunit proteins bind to maintain the internal structure of the head. The results show a clear connection between the inter-molecular interactions and the structural and functional properties of the ribosome because of the reduced complexity in domain-based CG models. The present approach also provides a useful strategy to map interactions between molecules within large biomolecular complexes since it is not straightforward to investigate these by either atomistic MD simulations or residue-based elastic network models.

Zhang, Zhiyong; Sanbonmatsu, Karissa Y.; Voth, Gregory A.

2011-01-01

172

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.

Huang, Bill X.; Kim, Hee-Yong

2013-01-01

173

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

PubMed Central

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

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

2013-01-01

174

Identification of Key Residues in Subgroup A Avian Leukosis Virus Envelope Determining Receptor Binding Affinity and Infectivity of Cells Expressing Chicken or Quail Tva Receptor  

PubMed Central

To better understand retroviral entry, we have characterized the interactions between subgroup A avian leukosis virus [ALV(A)] envelope glycoproteins and Tva, the receptor for ALV(A), that result in receptor interference. We have recently shown that soluble forms of the chicken and quail Tva receptor (sTva), expressed from genes delivered by retroviral vectors, block ALV(A) infection of cultured chicken cells (?200-fold antiviral effect) and chickens (>98% of the birds were not infected). We hypothesized that inhibition of viral replication by sTva would select virus variants with mutations in the surface glycoprotein (SU) that altered the binding affinity of the subgroup A SU for the sTva protein and/or altered the normal receptor usage of the virus. Virus propagation in the presence of quail sTva-mIgG, the quail Tva extracellular region fused to the constant region of the mouse immunoglobulin G (IgG) protein, identified viruses with three mutations in the subgroup A hr1 region of SU, E149K, Y142N, and Y142N/E149K. These mutations reduced the binding affinity of the subgroup A envelope glycoproteins for quail sTva-mIgG (32-, 324-, and 4,739-fold, respectively) but did not alter their binding affinity for chicken sTva-mIgG. The ALV(A) mutants efficiently infected cells expressing the chicken Tva receptor but were 2-fold (E149K), 10-fold (Y142N), and 600-fold (Y142N/E149K) less efficient at infecting cells expressing the quail Tva receptor. These mutations identify key determinants of the interaction between the ALV(A) glycoproteins and the Tva receptor. We also conclude from these results that, at least for the wild-type and variant ALV(A)s tested, the receptor binding affinity was directly related to infection efficiency.

Holmen, Sheri L.; Melder, Deborah C.; Federspiel, Mark J.

2001-01-01

175

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

PubMed Central

We recently reported the first crystal structure of a paramyxovirus hemagglutinin-neuraminidase (HN) from Newcastle disease virus. This multifunctional protein is responsible for binding to cellular sialyl-glycoconjugate receptors, promotion of fusion through interaction with the second viral surface fusion (F) glycoprotein, and processing progeny virions by removal of sialic acid from newly synthesized viral coat proteins. Our structural studies suggest that HN possesses a single sialic acid recognition site that can be switched between being a binding site and a catalytic site. Here we examine the effect of mutation of several conserved amino acids around the binding site on the hemagglutination, neuraminidase, and fusion functions of HN. Most mutations around the binding site result in loss of neuraminidase activity, whereas the effect on receptor binding is more variable. Residues E401, R416, and Y526 appear to be key for receptor binding. The increase in fusion promotion seen in some mutants that lack receptor binding activity presents a conundrum. We propose that in these cases HN may be switched into a fusion-promoting state through a series of conformational changes that propagate from the sialic acid binding site through to the HN dimer interface. These results further support the single-site model and suggest certain residues to be important for the triggering of fusion.

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

2002-01-01

176

Probing the sialic acid binding site of the hemagglutinin-neuraminidase of Newcastle disease virus: identification of key amino acids involved in cell binding, catalysis, and fusion.  

PubMed

We recently reported the first crystal structure of a paramyxovirus hemagglutinin-neuraminidase (HN) from Newcastle disease virus. This multifunctional protein is responsible for binding to cellular sialyl-glycoconjugate receptors, promotion of fusion through interaction with the second viral surface fusion (F) glycoprotein, and processing progeny virions by removal of sialic acid from newly synthesized viral coat proteins. Our structural studies suggest that HN possesses a single sialic acid recognition site that can be switched between being a binding site and a catalytic site. Here we examine the effect of mutation of several conserved amino acids around the binding site on the hemagglutination, neuraminidase, and fusion functions of HN. Most mutations around the binding site result in loss of neuraminidase activity, whereas the effect on receptor binding is more variable. Residues E401, R416, and Y526 appear to be key for receptor binding. The increase in fusion promotion seen in some mutants that lack receptor binding activity presents a conundrum. We propose that in these cases HN may be switched into a fusion-promoting state through a series of conformational changes that propagate from the sialic acid binding site through to the HN dimer interface. These results further support the single-site model and suggest certain residues to be important for the triggering of fusion. PMID:11799177

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

2002-02-01

177

Key Interactions in Integrin Ectodomain Responsible for Global Conformational Change Detected by Elastic Network Normal-Mode Analysis  

Microsoft Academic Search

Integrin, a membrane protein with a huge extracellular domain, participates in cell-cell and cell-extracellular-matrix interactions for metazoan. A group of integrins is known to perform a large-scale structural change when the protein is activated, but the activation mechanism and generality of the conformational change remain to be elucidated. We performed normal-mode analysis of the elastic network model on integrin ?V?3

Atsushi Matsumoto; Tetsuji Kamata; Junichi Takagi; Kenji Iwasaki; Kei Yura

2008-01-01

178

Illustrated key for the identification of brachyuran megalopae (Crustacea: Decapoda) in the plankton of Peter the Great Bay (Sea of Japan)  

Microsoft Academic Search

A dichotomous key for brachyuran megalopae from Peter the Great Bay (Russian waters of the Sea of Japan) is provided. The key covers 18 taxa identified to species level and uses only the external characters of larvae that are easy to observe with a stereomicroscope without specimen dissection. The key is mainly based on the new original descriptions of larvae

OLGA M. KORN; ELENA S. KORNIENKO

2010-01-01

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.

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

2007-01-01

180

An overlapping module identification method in protein-protein interaction networks  

PubMed Central

Background Previous studies have shown modular structures in PPI (protein-protein interaction) networks. More recently, many genome and metagenome investigations have focused on identifying modules in PPI networks. However, most of the existing methods are insufficient when applied to networks with overlapping modular structures. In our study, we describe a novel overlapping module identification method (OMIM) to address this problem. Results Our method is an agglomerative clustering method merging modules according to their contributions to modularity. Nodes that have positive effects on more than two modules are defined as overlapping parts. As well, we designed de-noising steps based on a clustering coefficient and hub finding steps based on nodal weight. Conclusions The low computational complexity and few control parameters prove that our method is suitable for large scale PPI network analysis. First, we verified OMIM on a small artificial word association network which was able to provide us with a comprehensive evaluation. Then experiments on real PPI networks from the MIPS Saccharomyces Cerevisiae dataset were carried out. The results show that OMIM outperforms several other popular methods in identifying high quality modular structures.

2012-01-01

181

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

PubMed Central

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

Wohlrab, Hartmut

2010-01-01

182

Study of ventricular interaction during pulmonary embolism using clinical identification in a minimum cardiovascular system model.  

PubMed

Cardiovascular disturbances are difficult to diagnose and treat because of the large range of possible underlying dysfunctions combined with regulatory reflex mechanisms that can result in conflicting clinical data. Thus, medical professionals often rely on experience and intuition to optimize hemodynamics in the critically ill. This paper combines an existing minimal cardiovascular system model with an extended integral based parameter identification method to track the evolution of induced pulmonary embolism in porcine data. The model accounts for ventricular interaction dynamics and is shown to predict an increase in the right ventricle expansion index and a decrease in septum volume consistent with known physiological response to pulmonary embolism. The full range of hemodynamic responses was captured with mean prediction errors of 4.1% in the pressures and 3.1% in the volumes for 6 sets of clinical data. Pulmonary resistance increased significantly with the onset of embolism in all cases, as expected, with the percentage increase ranging from 89.98% to 261.44% of the initial state. These results are an important first step towards model-based cardiac diagnosis in the Intensive Care Unit. PMID:18002620

Desaive, Thomas; Ghuysen, Alexandre; Lambermont, Bernard; Kolh, Philippe; Dauby, Pierre C; Starfinger, Christina; Hann, Christopher E; Chase, J; Shaw, Geoffrey M

2007-01-01

183

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

PubMed

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

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

2011-12-27

184

Protein folding rates and thermodynamic stability are key determinants for interaction with the Hsp70 chaperone system  

PubMed Central

The Hsp70 family of molecular chaperones participates in vital cellular processes including the heat shock response and protein homeostasis. E. coli's Hsp70, known as DnaK, works in concert with the DnaJ and GrpE co-chaperones (K/J/E chaperone system), and mediates cotranslational and post-translational protein folding in the cytoplasm. While the role of the K/J/E chaperones is well understood in the presence of large substrates unable to fold independently, it is not known if and how K/J/E modulates the folding of smaller proteins able to fold even in the absence of chaperones. Here, we combine experiments and computation to evaluate the significance of kinetic partitioning as a model to describe the interplay between protein folding and binding to the K/J/E chaperone system. First, we target three nonobligatory substrates, that is, proteins that do not require chaperones to fold. The experimentally observed chaperone association of these client proteins during folding is entirely consistent with predictions from kinetic partitioning. Next, we develop and validate a computational model (CHAMP70) that assumes kinetic partitioning of substrates between folding and interaction with K/J/E. CHAMP70 quantitatively predicts the experimentally measured interaction of RNase HD as it refolds in the presence of various chaperones. CHAMP70 shows that substrates are posed to interact with K/J/E only if they are slow-folding proteins with a folding rate constant kf <50 s?1, and/or thermodynamically unstable proteins with a folding free energy ?G0UN ??2 kcal mol?1. Hence, the K/J/E system is tuned to use specific protein folding rates and thermodynamic stabilities as substrate selection criteria.

Sekhar, Ashok; Lam, Hon Nam; Cavagnero, Silvia

2012-01-01

185

Nucleotide analogs and molecular modeling studies reveal key interactions involved in substrate recognition by the yeast RNA triphosphatase  

PubMed Central

RNA triphosphatases (RTPases) are involved in the addition of the distinctive cap structure found at the 5? ends of eukaryotic mRNAs. Fungi, protozoa and some DNA viruses possess an RTPase that belongs to the triphosphate tunnel metalloenzyme family of enzymes that can also hydrolyze nucleoside triphosphates. Previous crystallization studies revealed that the phosphohydrolase catalytic core is located in a hydrophilic tunnel composed of antiparallel ?-strands. However, all past efforts to obtain structural information on the interaction between RTPases and their substrates were unsuccessful. In the present study, we used computational molecular docking to model the binding of a nucleotide substrate into the yeast RTPase active site. In order to confirm the docking model and to gain additional insights into the molecular determinants involved in substrate recognition, we also evaluated both the phosphohydrolysis and the inhibitory potential of an important number of nucleotide analogs. Our study highlights the importance of specific amino acids for the binding of the sugar, base and triphosphate moieties of the nucleotide substrate, and reveals both the structural flexibility and complexity of the active site. These data illustrate the functional features required for the interaction of an RTPase with a ligand and pave the way to the use of nucleotide analogs as potential inhibitors of RTPases of pathogenic importance.

Issur, Moheshwarnath; Despins, Simon; Bougie, Isabelle; Bisaillon, Martin

2009-01-01

186

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

SciTech Connect

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

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

2008-10-20

187

Identification of T1D susceptibility genes within the MHC region by combining protein interaction networks and SNP genotyping data  

PubMed Central

Aim To develop novel methods for identifying new genes that contribute to the risk of developing type 1 diabetes within the Major Histocompatibility Complex (MHC) region on chromosome 6, independently of the known linkage disequilibrium (LD) between human leucocyte antigen (HLA)-DRB1, -DQA1, -DQB1 genes. Methods We have developed a novel method that combines single nucleotide polymorphism (SNP) genotyping data with protein–protein interaction (ppi) networks to identify disease-associated network modules enriched for proteins encoded from the MHC region. Approximately 2500 SNPs located in the 4 Mb MHC region were analysed in 1000 affected offspring trios generated by the Type 1 Diabetes Genetics Consortium (T1DGC). The most associated SNP in each gene was chosen and genes were mapped to ppi networks for identification of interaction partners. The association testing and resulting interacting protein modules were statistically evaluated using permutation. Results A total of 151 genes could be mapped to nodes within the protein interaction network and their interaction partners were identified. Five protein interaction modules reached statistical significance using this approach. The identified proteins are well known in the pathogenesis of T1D, but the modules also contain additional candidates that have been implicated in ?-cell development and diabetic complications. Conclusions The extensive LD within the MHC region makes it important to develop new methods for analysing genotyping data for identification of additional risk genes for T1D. Combining genetic data with knowledge about functional pathways provides new insight into mechanisms underlying T1D.

Brorsson, C.; Hansen, N. T.; Lage, K.; Bergholdt, R.; Brunak, S.; Pociot, F.

2009-01-01

188

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

Microsoft Academic Search

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)

M. Schweitzer; M. English; S. Schexnayder; J. Altman

1995-01-01

189

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.

190

Alkaline magma- oceanic lithosphere interaction: a key to understand the nephelinite-alkali basalt transition observed in oceanic islands  

NASA Astrophysics Data System (ADS)

An important question in the petrogenesis of oceanic island basalts is related to the location of the different mantle components which interact during their formation. Most models suggest that all components are located within the convecting mantle and therefore neglect the potential role of the oceanic lithosphere [e.g. 1]. Here we show that lithospheric mantle plays a fundamental role in the process responsible for the range of parental melt (i.e. from nephelinite to tholeiite) observed in intraplate volcanoes. Alkaline lavas from continental volcanoes or oceanic islands characterized by thick lithosphere (>50 km) define a compositional continuum from nephelinites to alkali olivine basalts and often to tholeiites. The decrease in incompatible trace-element concentrations from nephelinitic to tholeiitic magmas in single volcanoes is consistent with this continuum reflecting an increase in the degree of partial melting of a common source [2]; however, no experiments on mantle lithologies (peridotite, pyroxenite) have reproduced the observed compositional continuum (nor even the observed range of silica contents: ~40 to 48 wt. % SiO2). Alternatively, this continuum could be explained by reaction between nephelinitic/basanitic liquid and surrounding peridotite [3, 4, 5]. To test this latter hypothesis, 'sandwich' experiments were performed in which a layer of hornblendite (producing nephelinitic magmas [5]) was packed between layers of moderately depleted peridotite. Experiments were done at 1.5 and 2.5 GPa, with temperature ranging from 1225 to 1425° C. At the same temperature (1250-1300° C), the SiO2 contents of partial melts produced in the sandwich runs are up to 4-5 wt. % higher than liquids from the hornblendite-only experiments. This difference reflects the dissolution of orthopyroxene in the peridotite layers in the sandwich runs. For both major and trace elements, the compositional trends defined by glasses from the hornblendite-only melting experiments and from the sandwich experiments are similar to trends observed in natural basanite - alkali basalt suites. These results suggest that compositional trends from nephelinite/basanite to alkali basalt observed in intraplate setting are related to reaction between nephelinitic/basanitic liquids and peridotite rather than, for example, a pressure effect and/or an increase in the degree of partial melting of peridotitic sources. Although we do not exclude that the alkaline magma-peridotite interaction is an important process in the convecting mantle (i.e. at pressure higher that 2.5-3 GPa), we suggest that the main interaction which produces the nephelinite/basanite to alkali basalt/tholeiite composition ranges observed in oceanic islands appends in the lithospheric mantle. These experiments indicate also that the temperature at which alkali melts interact with peridotites could be significantly lower that the solidus temperature of theses peridotites. This provides an explanation for the implication of lithospheric components during the generation of alkaline lavas without requiring that these components reach their melting temperature. We conclude that lithospheric mantle needs to be considerate as an important component in the petrogenesis of alkaline lavas. [1] Ito and Mahoney (2005) EPSL 230, 29- 46; [2] Frey et al. (1978) J. Petrol. 19, 463-513; [3] Shaw et al. (1998) Contrib. Mineral. Petrol. 132, 354-370; [4] Lundstrom (2000) Nature 403, 527-530; [5] Pilet et al. (2008) Science 320, 916-919.

Pilet, Sebastien; Baker, Michael B.; Stolper, Edward M.; Muntener, Othmar

2010-05-01

191

Daxx is a key downstream component of receptor interacting protein kinase 3 mediating retinal ischemic cell death.  

PubMed

Receptor-interacting protein 3 (RIP3) has been implicated in ischemic necrosis of retinal cells. An in silico analysis followed by experimental validation identified death associated protein (Daxx) as a novel substrate of RIP3. In vitro binding studies revealed that RIP3 binds to the serine/proline/threonine-rich domain (amino acid 625-740) of Daxx. Upon ischemic insult, RIP3 phosphorylated Daxx at Ser-668 in the retinal ganglion cells, triggering nuclear export of Daxx. Depletion of RIP3 significantly inhibited nuclear export of Daxx and attenuated cell death to a great extent. Collectively, the findings of this study demonstrate that phosphorylation of Daxx by RIP3 comprises an important part of ischemic necrosis in rat retinal ganglion cells. PMID:23260419

Lee, Yun-Suk; Dayma, Yogesh; Park, Min-Young; Kim, Kyung Il; Yoo, Sung-Eun; Kim, Eunhee

2012-12-19

192

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

PubMed Central

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

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

2012-01-01

193

Genome-wide identification of DNA-protein interactions using chromatin immunoprecipitation coupled with flow cell sequencing  

Microsoft Academic Search

The transcriptional networks underlying mammalian cell development and function are largely unknown. The recently described use of flow cell sequencing devices in combination with chromatin immunoprecipitation (ChIP-seq) stands to revolutionize the identification of DNA-protein interactions. As such, ChIP-seq is rapidly becoming the method of choice for the genome-wide localization of histone modifications and transcription factor binding sites. As further studies

Brad G Hoffman; Steven J M Jones

2009-01-01

194

Rap1 Functions as a Key Regulator of T-Cell and Antigen-Presenting Cell Interactions and Modulates T-Cell Responses  

PubMed Central

Activation of T cells by antigen requires adhesive interactions with antigen-presenting cells (APC) in which leukocyte function-associated antigen 1 (LFA-1) and intercellular adhesion molecules (ICAMs) are important. However, it is not well understood what signaling molecules regulate this process and how the modulation of adhesive events influences T-cell activation. Here we show that Rap1 is activated in T cells in an antigen-dependent manner and accumulated at the contact site of T-cell and antigen-loaded APC. Inhibition of Rap1 activation by a dominant-negative Rap1 or SPA-1, a Rap1 GTPase-activating protein, abrogates LFA-1-ICAM-1-mediated adhesive interactions with antigen-pulsed APC and the subsequent T-cell-receptor triggering and interleukin-2 production. Conversely, augmented antigen-dependent Rap1 activation by the expression of wild-type Rap1 enhances these responses but culminates in apoptosis by Fas and FasL. Thus, Rap1 functions as a key regulator of T-cell and APC interactions and modulates T-cell responses from productive activation to activation-induced cell death by regulating the strength of adhesive interactions. Moreover, constitutive Rap1 activation rendered T cells unresponsive with accumulation of p27Kip1. Our study indicates that the activation state of Rap1 has a decisive effect on the T-cell response to antigen.

Katagiri, Koko; Hattori, Masakazu; Minato, Nagahiro; Kinashi, Tatsuo

2002-01-01

195

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

196

Identification and quantification of nucleosides and nucleobases in Geosaurus and Leech by hydrophilic-interaction chromatography.  

PubMed

A simple hydrophilic-interaction chromatography (HILIC) method was developed for the identification and quantification of 14 nucleosides and nucleobases, namely cytosine, uracil, cytidine, guanine, hypoxanthine, xanthine, uridine, thymine, inosine, guanosine, thymidine, 2'-deoxyadenosine, 2'-deoxyinosine and 2'-deoxyuridine in two traditional Chinese medicines, Geosaurus and Leech. The separation was achieved on a TSKgel Amide-80 column (150 mm × 2.0 mm, 3.0 ?m) with a mixture of acetonitrile and 10 mM aqueous ammonium acetate as the mobile phase at a flow rate of 0.2 mL/min. The temperature was set at 30°C and UV detection wavelength was set at 260 nm. All calibration curves showed good linearity (R(2)>0.9957) within the test ranges. The overall intra- and inter-day RSD ranged from 0.4 to 3.4% and from 0.7 to 3.3%, respectively. The LOD and LOQ were in the range of 0.07-30.49 ng/mL and 0.26-60.98 ng/mL, respectively. The repeatability of the method was in the range of 2.2-5.8% for Geosaurus and 1.4-5.5% for Leech. The recoveries of the samples were in the range of 91.4-100.9% for Geosaurus, and 91.9-99.3% for Leech. The established method was applied successfully for the analysis of nucleosides and nucleobases in 22 commercially available samples collected from different regions in China and Japan. Our data showed that HILIC had advantages as a useful tool for the study of the bioactive components in Geosaurus and Leech as well as their quality control, and could therefore be used for the determination of the analytes in pharmaceutical products and biological fluids. PMID:21807233

Chen, Pei; Li, Wei; Li, Qin; Wang, Yinghua; Li, Zhenguo; Ni, Yefeng; Koike, Kazuo

2011-06-29

197

Identification of a fibronectin interaction site in the extracellular matrix protein ameloblastin.  

PubMed

Mammalian teeth are composed of hydroxyapatite crystals that are embedded in a rich extracellular matrix. This matrix is produced by only two cell types, the mesenchymal odontoblasts and the ectodermal ameloblasts. Ameloblasts secrete the enamel proteins amelogenin, ameloblastin, enamelin and amelotin. Odontoblasts secrete collagen type I and several calcium-binding phosphoproteins including dentin sialophosphoprotein, dentin matrix protein, bone sialoprotein and osteopontin. The latter four proteins have recently been grouped in the family of the SIBLINGs (small integrin-binding ligand, N-linked glycoproteins) because they display similar gene structures and because they contain an RGD tripeptide sequence that binds to integrin receptors and thus mediates cell adhesion. We have prepared all the other tooth-specific proteins in recombinant form and examined whether they might also promote cell adhesion similar to the SIBLINGs. We found that only ameloblastin consistently mediated adhesion of osteoblastic and fibroblastic cells to plastic or titanium surfaces. The activity was dependent on the intact three-dimensional structure of ameloblastin and required de novo protein synthesis of the adhering cells. By deletion analysis and in vitro mutagenesis, the active site could be narrowed down to a sequence of 13 amino acid residues (VPIMDFADPQFPT) derived from exon 7 of the rat ameloblastin gene or exons 7-9 of the human gene. Kinetic studies and RNA interference experiments further demonstrated that this sequence does not directly bind to a cell surface receptor but that it interacts with cellular fibronectin, which in turn binds to integrin receptors. The identification of a fibronectin-binding domain in ameloblastin might permit interesting applications for dental implantology. Implants could be coated with peptides containing the active sequence, which in turn would recruit fibronectin from the patient's blood. The recruited fibronectin should then promote cell adhesion on the implant surface, thereby accelerating osseointegration of the implant. PMID:20043904

Beyeler, Michael; Schild, Christof; Lutz, Roman; Chiquet, Matthias; Trueb, Beat

2010-01-04

198

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

PubMed

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

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

2013-01-01

199

Optical key system  

SciTech Connect

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, K.G.; Clough, R.E.

2000-04-25

200

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.

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

2012-01-01

201

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

ERIC Educational Resources Information Center

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

Ginter, Earl J.; Bonney, Warren

1993-01-01

202

Eyewitness Identification  

Microsoft Academic Search

Eyewitness identifications play an important role in many police investigations and courtroom decisions. Identification decision accuracy is shaped not only by the quality of a witness’s memory but also by social-influence variables. Some variables can be categorized as general impairments, whereas others produce biases against a specific suspect. We review some of the key variables in each category and consider

Neil Brewer; Gary L. Wells

2011-01-01

203

Identification of GPCR-interacting cytosolic proteins using HDL particles and mass spectrometry-based proteomic approach.  

PubMed

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

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

2013-01-25

204

Análisis de dos conceptos clave en el estudio de las interacciones: formato y zona de desarrollo próximo Analysis of two key concepts in the study of interactions: formats and zone of proximal development  

Microsoft Academic Search

In this paper two key concepts of great relevance for the study of interactions are revised: format and zone of proximal development, one derived from Bruner and the other from the early works of Vygotsky. Traits and applications in family and scholar contexts are analysed when they are applied to dyads and in school interactions. Extending the analysis we go

205

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

2008-06-18

206

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.

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

2009-01-01

207

The Identification of Nucleic Acid-interacting Proteins Using a Simple Proteomics-based Approach That Directly Incorporates the Electrophoretic Mobility Shift Assay  

Microsoft Academic Search

Proteins that interact with nucleic acids are central to numerous cellular processes, and their continuing char- acterization represents one of the foremost challenges in the postgenomic era. Here we describe a simple pro- teomics-based approach for the identification by mass spectrometry of proteins in crude extracts that interact with nucleic acids. It incorporates the electrophoretic mobility shift assay and is

Jonathan A. Stead; Jeff N. Keen; Kenneth J. McDowall

2006-01-01

208

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.

209

Identification of dynein light chain road block-1 as a novel interaction partner with the human reduced folate carrier.  

PubMed

The reduced folate carrier (RFC) is a major folate transport system in mammalian cells. RFC is highly expressed in the intestine and believed to play a role in folate absorption. Studies from our laboratory and others have characterized different aspects of the intestinal folate absorption process, but little is known about possible existence of accessory protein(s) that interacts with RFC and influences its physiology and/or cell biology. We investigated this issue by employing a bacterial two-hybrid system to screen a BacterioMatch II human intestinal cDNA library using the large intracellular loop between transmembrane domains 6 and 7 of the human RFC (hRFC) as bait. Our screening has resulted in the identification of dynein light chain road block-1 (DYNLRB1) as an interacting partner with hRFC. Existence of a direct protein-protein interaction between hRFC and DYNLRB1 was confirmed by in vitro pull-down assay and in vivo mammalian two-hybrid luciferase assay and coimmunoprecipitation analysis. Furthermore, confocal imaging of live human intestinal epithelial HuTu-80 cells demonstrated colocalization of DYNLRB1 with hRFC. Coexpression of DYNLRB1 with hRFC led to a significant (P < 0.05) increase in folate uptake. On the other hand, inhibiting the endogenous DYNLRB1 with gene-specific small interfering RNA or pharmacologically with a specific inhibitor (vanadate) led to a significant (P < 0.05) decrease in folate uptake. This study demonstrates for the first time the identification of DYNLRB1 as an interacting protein partner with hRFC. Furthermore, DYNLRB1 appears to influence the function and cell biology of hRFC. PMID:19571232

Ashokkumar, Balasubramaniem; Nabokina, Svetlana M; Ma, Thomas Y; Said, Hamid M

2009-07-01

210

Identification of dynein light chain road block-1 as a novel interaction partner with the human reduced folate carrier  

PubMed Central

The reduced folate carrier (RFC) is a major folate transport system in mammalian cells. RFC is highly expressed in the intestine and believed to play a role in folate absorption. Studies from our laboratory and others have characterized different aspects of the intestinal folate absorption process, but little is known about possible existence of accessory protein(s) that interacts with RFC and influences its physiology and/or cell biology. We investigated this issue by employing a bacterial two-hybrid system to screen a BacterioMatch II human intestinal cDNA library using the large intracellular loop between transmembrane domains 6 and 7 of the human RFC (hRFC) as bait. Our screening has resulted in the identification of dynein light chain road block-1 (DYNLRB1) as an interacting partner with hRFC. Existence of a direct protein-protein interaction between hRFC and DYNLRB1 was confirmed by in vitro pull-down assay and in vivo mammalian two-hybrid luciferase assay and coimmunoprecipitation analysis. Furthermore, confocal imaging of live human intestinal epithelial HuTu-80 cells demonstrated colocalization of DYNLRB1 with hRFC. Coexpression of DYNLRB1 with hRFC led to a significant (P < 0.05) increase in folate uptake. On the other hand, inhibiting the endogenous DYNLRB1 with gene-specific small interfering RNA or pharmacologically with a specific inhibitor (vanadate) led to a significant (P < 0.05) decrease in folate uptake. This study demonstrates for the first time the identification of DYNLRB1 as an interacting protein partner with hRFC. Furthermore, DYNLRB1 appears to influence the function and cell biology of hRFC.

Ashokkumar, Balasubramaniem; Nabokina, Svetlana M.; Ma, Thomas Y.; Said, Hamid M.

2009-01-01

211

Identification of the Substrates and Interaction Proteins of Aurora Kinases from a Protein-Protein Interaction Model  

Microsoft Academic Search

The increasing use of high-throughput and large-scale bioinformatics-based studies has generated a massive amount of data stored in a number of different databases. The major need now is to explore this disparate data to find biologically relevant interactions and pathways. Thus, in the post-genomic era, there is clearly a need for the development of algorithms that can accurately predict novel

An-Chi Tien; Ming-Hong Lin; Li-Jen Su; Yi-Ren Hong; Tai-Shan Cheng; Yuan-Chii G. Lee; Wey-Jinq Lin; Ivan H. Still; Chi-Ying F. Huang

2003-01-01

212

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

PubMed Central

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.

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

2010-01-01

213

Identification of Gal80p-interacting proteins by Saccharomyces cerevisiae whole genome phage display  

Microsoft Academic Search

Networks of interacting proteins and protein interaction maps can help in functional annotation in genome analysis projects. We present the application of genomic phage display as a tool to identify interacting proteins in Saccharomyces cerevisiae. We have developed a large phagemid display library (?7.7×107 independent clones) of sheared S. cerevisiae genomic DNA (12.1 Mbp genome size) fused to gene III

Kirsten Hertveldt; Mekonnen Lemma Dechassa; Johan Robben; Guido Volckaert

2003-01-01

214

QUICK identification and SPR validation of signal transducers and activators of transcription 3 (Stat3) interacting proteins.  

PubMed

Signal transducers and activators of transcription 3 (Stat3) has been reported to be involved in the pathogenesis of various human diseases and is constitutively active in human multiple myeloma (MM) U266 cells. The Stat3-regulated mechanisms involved in these processes, however, are not fully defined. To further understand the regulation of Stat3 activity, we performed a systematic proteomic analysis of Stat3 interacting proteins in U266 cells. This analysis, termed quantitative immunoprecipitation combined with knockdown (QUICK), combines RNAi, stable isotope labeling with amino acids in cell culture (SILAC), immunoprecipitation, and quantitative MS. As a result, quantitative mass spectrometry analysis allowed us to distinguish specific Stat3 interacting proteins from background proteins and led to the identification of a total of 38 proteins. Three Stat3 interacting proteins - 14-3-3?, PRKCB and Hsp90 - were further confirmed by reciprocal co-immunoprecipitations and surface plasmon resonance (SPR) analysis. Our results therefore not only uncover a number of Stat3 interacting proteins that possess a variety of cellular functions, but also provide new insight into the mechanisms that regulate Stat3 activity and function in MM cells. PMID:22075167

Zheng, Peng; Zhong, Qiu; Xiong, Qian; Yang, Mingkun; Zhang, Jia; Li, Chongyang; Bi, Li-Jun; Ge, Feng

2011-10-30

215

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

216

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.

Duconge, F; Toulme, J J

1999-01-01

217

Learning in Three Keys.  

ERIC Educational Resources Information Center

Learning keys in human experience are (1) controlling the environment; (2) interacting with, understanding, and adapting one's relationship to the environment; and (3) liberating oneself from the environment. A learning-centered schooling model balances control, adaptive, and personal criteria. (SK)

Hill, John C.

1997-01-01

218

Identification of potential Plk1 targets in a cell-cycle specific proteome through structural dynamics of kinase and Polo box-mediated interactions.  

PubMed

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

Bibi, Nousheen; Parveen, Zahida; Rashid, Sajid

2013-08-15

219

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

PubMed Central

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

Bibi, Nousheen; Parveen, Zahida; Rashid, Sajid

2013-01-01

220

Identification of interaction patterns and classification with applications to microarray data  

Microsoft Academic Search

Emerging patterns represent a class of interaction structures which has been recently proposed as a tool in data mining. A new and more general definition referring to underlying probabilities is proposed. The defined interaction patterns (IP) carry information about the relevance of combinations of variables for distinguishing between classes. Since they are formally quite similar to the leaves of a

Anne-laure Boulesteix; Gerhard Tutz

2006-01-01

221

[Identification of the proteins interacting with neuroprotective peptide humanin in a yeast two-hybrid system].  

PubMed

Humanine is a human neuroprotective peptide with a wide action spectrum. To analyze molecular mechanisms of humanin functioning, a search for proteins interacting with this peptide was conducted using yeast two-hybrid system. Screening of human fetal brain cDNA library identified seven proteins with different functions that specifically interacted with humanin. PMID:16583711

Maksimov, V V; Arman, I P; Tarantul, V Z

2006-02-01

222

Identification of the proteins interacting with neuroprotective peptide humanin in a yeast two-hybrid system  

Microsoft Academic Search

Humanine is a human neuroprotective peptide with a wide action spectrum. To analyze molecular mechanisms of humanin functioning,\\u000a a search for proteins interacting with this peptide was conducted using yeast two-hybrid system. Screening of human fetal\\u000a brain cDNA library identified seven proteins with different functions that specifically interacted with humanin.

V. V. Maximov; I. P. Arman; V. Z. Tarantul

2006-01-01

223

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

2013-06-03

224

Identification of key residues essential for the structural fold and receptor selectivity within the A-chain of human gene-2 (H2) relaxin.  

PubMed

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

2012-09-28

225

Identification of expression quantitative trait loci by the interaction analysis using genetic algorithm.  

PubMed

Many genes with major effects on quantitative traits have been reported to interact with other genes. However, finding a group of interacting genes from thousands of SNPs is challenging. Hence, an efficient and robust algorithm is needed. The genetic algorithm (GA) is useful in searching for the optimal solution from a very large searchable space. In this study, we show that genome-wide interaction analysis using GA and a statistical interaction model can provide a practical method to detect biologically interacting loci. We focus our search on transcriptional regulators by analyzing gene x gene interactions for cancer-related genes. The expression values of three cancer-related genes were selected from the expression data of the Genetic Analysis Workshop 15 Problem 1 data set. We implemented a GA to identify the expression quantitative trait loci that are significantly associated with expression levels of the cancer-related genes. The time complexity of the GA was compared with that of an exhaustive search algorithm. As a result, our GA, which included heuristic methods, such as archive, elitism, and local search, has greatly reduced computational time in a genome-wide search for gene x gene interactions. In general, the GA took one-fifth the computation time of an exhaustive search for the most significant pair of single-nucleotide polymorphisms. PMID:18466570

Namkung, Junghyun; Nam, Jin-Wu; Park, Taesung

2007-12-18

226

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

PubMed Central

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.

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

2013-01-01

227

Identification of interaction partners of ?-thymosins: application of thymosin ?4 labeled by transglutaminase.  

PubMed

In this review, we identify potential interaction partners of the ?-thymosin family. The proteins of this family are highly conserved peptides in mammals and yet only one intracellular (G-actin) and one cell-surface protein (? subunit of F(1) -F(0) ATP synthase) were identified as interaction partners of thymosin ?4. Cross-linking experiments may be a possible approach to discover additional proteins that interact with the ?-thymosin family. It has previously been shown that thymosin ?4 can be labeled at its glutaminyl residues with various cadaverines using tissue transglutaminase. Here, we illuminate recent results and give an outlook on upcoming work in the field. PMID:23050824

App, Christine; Knop, Jana; Mannherz, Hans Georg; Hannappel, Ewald

2012-10-01

228

Classification and the Dichotomous Key  

NSDL National Science Digital Library

Classification is a vital science-process skill for all students to master. Understanding dichotomous keys as a means of classification enables students to better comprehend large amounts of information and understand how to organize, compare and contrast, and analyze that information. To biology students, mastering the dichotomous key provides an avenue through which they can identify any organism they come in contact with. This article discusses how to approach and teach the concepts of classification and identification in science classes.

Watson, Sandy; Miller, Ted

2009-03-01

229

Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining  

PubMed Central

Background Fever is one of the most common adverse events of vaccines. The detailed mechanisms of fever and vaccine-associated gene interaction networks are not fully understood. In the present study, we employed a genome-wide, Centrality and Ontology-based Network Discovery using Literature data (CONDL) approach to analyse the genes and gene interaction networks associated with fever or vaccine-related fever responses. Results Over 170,000 fever-related articles from PubMed abstracts and titles were retrieved and analysed at the sentence level using natural language processing techniques to identify genes and vaccines (including 186 Vaccine Ontology terms) as well as their interactions. This resulted in a generic fever network consisting of 403 genes and 577 gene interactions. A vaccine-specific fever sub-network consisting of 29 genes and 28 gene interactions was extracted from articles that are related to both fever and vaccines. In addition, gene-vaccine interactions were identified. Vaccines (including 4 specific vaccine names) were found to directly interact with 26 genes. Gene set enrichment analysis was performed using the genes in the generated interaction networks. Moreover, the genes in these networks were prioritized using network centrality metrics. Making scientific discoveries and generating new hypotheses were possible by using network centrality and gene set enrichment analyses. For example, our study found that the genes in the generic fever network were more enriched in cell death and responses to wounding, and the vaccine sub-network had more gene enrichment in leukocyte activation and phosphorylation regulation. The most central genes in the vaccine-specific fever network are predicted to be highly relevant to vaccine-induced fever, whereas genes that are central only in the generic fever network are likely to be highly relevant to generic fever responses. Interestingly, no Toll-like receptors (TLRs) were found in the gene-vaccine interaction network. Since multiple TLRs were found in the generic fever network, it is reasonable to hypothesize that vaccine-TLR interactions may play an important role in inducing fever response, which deserves a further investigation. Conclusions This study demonstrated that ontology-based literature mining is a powerful method for analyzing gene interaction networks and generating new scientific hypotheses.

2012-01-01

230

Identification of Connexin-Interacting Proteins: Application of the Yeast Two-Hybrid Screen  

Microsoft Academic Search

Protein–protein interactions are recognized as one of the fundamental mechanisms for relaying the intra- and intercellular signals that are required for normal cellular activities affecting growth, development, and maintenance of homeostasis in tissues and organs. The yeast two-hybrid screen has become a valuable tool for identifying protein–protein interactions. The gap junction protein connexin 43 (Cx43) has been implicated in a

Chengshi Jin; Alan F. Lau; Kendra Dean Martyn

2000-01-01

231

Proteomic-Based Identification of CD4Interacting Proteins in Human Primary Macrophages  

Microsoft Academic Search

BackgroundHuman macrophages (M?) express low levels of CD4 glycoprotein, which is constitutively recycled, and 40–50% of its localization is intracellular at steady-state. Although CD4-interacting proteins in lymphoid cells are well characterised, little is known about the CD4 protein interaction-network in human M?, which notably lack LCK, a Src family protein tyrosine kinase believed to stabilise CD4 at the surface of

Rui André Saraiva Raposo; Benjamin Thomas; Gabriela Ridlova; William James; Yang Cai

2011-01-01

232

Identification of new protein interactions between dengue fever virus and its hosts, human and mosquito.  

PubMed

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

2013-01-11

233

Transblot and cytochemical identification of avidin-interacting proteins in mitochondria of cultured cells  

Microsoft Academic Search

Cell lysates prepared from 3T3-L1 cells were analyzed by western blotting using the avidin-biotin complex system and anti-Bax antibody. The antibody interacted with bands of proteins with estimated molecular weights of 120, 74, 72, and 25 kDa. However, only the 25-kDa band was detected with the anti-Bax antibody when the direct immunoblotting method was used. Peroxidase-conjugated avidin interacted with the 120-,

Eiko Sasaki; Yoshifumi Okamoto; Kaya Yoshida; Hirohiko Okamura; Katsuhide Shimizu; Fumio Nasu; Hiroyuki Morimoto; Tatsuji Haneji

2003-01-01

234

Identification of three novel peptides that inhibit CD40–CD154 interaction  

Microsoft Academic Search

The CD40–CD154 interaction is an attractive target for therapeutic intervention in various autoimmune disorders, including\\u000a rheumatoid arthritis, systemic lupus erythematosus (SLE), multiple sclerosis, and myasthenia gravis. In this study, to develop\\u000a a new disruption strategy of the CD40–CD154 interaction, we screened for peptides with inhibitory effects on such ligation.\\u000a 2 × 1011 phage display libraries displaying liner peptides of 12-mer

Minetake Kitagawa; Daisuke Goto; Mizuko Mamura; Isao Matsumoto; Satoshi Ito; Akito Tsutsumi; Takayuki Sumida

2005-01-01

235

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.

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

2013-01-01

236

Identification of Neuroglobin-interacting Proteins Using Yeast Two-hybrid Screening  

PubMed Central

Neuroglobin (Ngb) is a globin protein that is highly and specifically expressed in brain neurons. A large volume of evidence has proven that Ngb is a neuroprotective molecule against hypoxic/ischemic brain injury and other related neurological disorder; however, the underlying mechanisms remain poorly understood. Aiming to provide more clues in understanding the molecular mechanisms of Ngb’s neuroprotection, we performed yeast two-hybrid screening to search for proteins that interact with Ngb. From a mouse brain cDNA library, we found totally 36 proteins that potentially interact with Ngb, and 10 of them were each identified in multiple positive clones. The shared sequences within these multiple clones are more likely to be Ngb-interacting domains. In primary cultured mouse cortical neurons, immuno-precipitation was performed to confirm the interactions of selected proteins with Ngb. The discovered Ngb-interacting proteins in this study include those involved in energy metabolism, mitochondria function and signaling pathways for cell survival and proliferation. Our findings provide molecular targets for investigating protein interaction-based biological functions and neuroprotective mechanisms of Ngb.

Yu, Zhanyang; Liu, Ning; Wang, Yi; Li, Xiaokun; Wang, Xiaoying

2011-01-01

237

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.

2010-01-01

238

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

PubMed Central

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

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

2012-01-01

239

Target identification by chromatographic co-elution: monitoring of drug-protein interactions without immobilization or chemical derivatization.  

PubMed

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

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

2012-02-22

240

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

241

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

PubMed

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

Prévost, M; Vertongen, P; Waelbroeck, M

2012-08-14

242

Identification and interaction of amino acids with leucine-anthracene reagent by TLC and spectrophotometry: experimental and theoretical studies.  

PubMed

A new reagent has been synthesized by coupling anthracene moiety to L-leucine. The reagent is characterized by different analytical techniques. It is capable for easy identification of various amino acids on thin-layer chromatography plates by developing distinguishable colors (detection limit between 0.1-0.5 ?g at cold condition and 0.1-0.4 ?g after heating). This reagent also binds with different amino acids very strongly in solution (methanol). Estimation of equilibrium binding constants of this new reagent with different amino acids has also been carried out. The values of the binding constants are lowest for L-Tyrosine (6.86 × 10³ dm³ mol(-1)) and highest for L-Arginine monohydrochloride (8.86 × 10? dm³ mol(-1)) at 25°C. A theoretical study (Hartree-Fock) has been performed to investigate the interaction of the reagent with a representative amino acid, glycine. PMID:21859542

Sahana, Animesh; Das, Sudipta; Saha, Raja; Gupta, Moumita; Laskar, Subrata; Das, Debasis

2011-09-01

243

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

PubMed

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

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

2012-07-30

244

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

PubMed Central

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

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

2012-01-01

245

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

2013-04-18

246

A novel mRNA affinity purification technique for the identification of interacting proteins and transcripts in ribonucleoprotein complexes.  

PubMed

Intracellular mRNA targeting and localized translation are potential determinants for protein localization. To facilitate targeting, mRNAs possess specific cis-acting sequence motifs that are recognized by trans-acting RNA-binding proteins (RBPs). While many mRNAs are trafficked, our knowledge of the RBPs involved and presence of additional transcripts within these ribonucleoprotein (RNP) complexes is limited. To facilitate the identification of RBPs and transcripts that bind to specific mRNAs, we developed RNA-binding protein purification and identification (RaPID), a novel technique that allows for the affinity purification of MS2 aptamer-tagged mRNAs and subsequent detection of bound RBPs and transcripts using mass-spectometry and RT-PCR, respectively. RaPID effectively isolated specific mRNAs from both yeast and mammalian cells, and identified known mRNA-RBP interactions (e.g., ASH1-She2; ?-Actin-IMP1). By isolating tagged OXA1 mRNA using RaPID, we could identify a yeast COPI subunit (i.e., Sec27) as a candidate interacting protein. This finding was strengthened by the observation that a portion of OXA1 mRNA was delocalized in a sec27-1 temperature-sensitive mutant at restrictive temperatures. Finally, RaPID could also be used to show biochemically the coexistence of different RNA species within the same RNP complex (e.g., coprecipitation of the yeast SRO7, WSC2, SEC3, and IST2 mRNAs with ASH1 mRNA) for the first time. PMID:20876833

Slobodin, Boris; Gerst, Jeffrey E

2010-09-28

247

A novel mRNA affinity purification technique for the identification of interacting proteins and transcripts in ribonucleoprotein complexes  

PubMed Central

Intracellular mRNA targeting and localized translation are potential determinants for protein localization. To facilitate targeting, mRNAs possess specific cis-acting sequence motifs that are recognized by trans-acting RNA-binding proteins (RBPs). While many mRNAs are trafficked, our knowledge of the RBPs involved and presence of additional transcripts within these ribonucleoprotein (RNP) complexes is limited. To facilitate the identification of RBPs and transcripts that bind to specific mRNAs, we developed RNA-binding protein purification and identification (RaPID), a novel technique that allows for the affinity purification of MS2 aptamer-tagged mRNAs and subsequent detection of bound RBPs and transcripts using mass-spectometry and RT–PCR, respectively. RaPID effectively isolated specific mRNAs from both yeast and mammalian cells, and identified known mRNA–RBP interactions (e.g., ASH1-She2; ?-Actin-IMP1). By isolating tagged OXA1 mRNA using RaPID, we could identify a yeast COPI subunit (i.e., Sec27) as a candidate interacting protein. This finding was strengthened by the observation that a portion of OXA1 mRNA was delocalized in a sec27-1 temperature-sensitive mutant at restrictive temperatures. Finally, RaPID could also be used to show biochemically the coexistence of different RNA species within the same RNP complex (e.g., coprecipitation of the yeast SRO7, WSC2, SEC3, and IST2 mRNAs with ASH1 mRNA) for the first time.

Slobodin, Boris; Gerst, Jeffrey E.

2010-01-01

248

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

PubMed Central

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

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

2012-01-01

249

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

250

Identification of insulin receptor substrate proteins as key molecules for the TbetaR-V/LRP-1-mediated growth inhibitory signaling cascade in epithelial and myeloid cells.  

PubMed

The type V TGF-beta receptor (TbetaR-V) mediates IGF-independent growth inhibition by IGFBP-3 and mediates growth inhibition by TGF-beta1 in concert with the other TGF-beta receptor types. TbetaR-V was recently found to be identical to LRP-1. Here we find that insulin and (Q3A4Y15L16) IGF-I (an IGF-I analog that has a low affinity for IGFBP-3) antagonize growth inhibition by IGFBP-3 in mink lung epithelial cells (Mv1Lu cells) stimulated by serum. In these cells, IGFBP-3 induces serine-specific dephosphorylation of IRS-1 and IRS-2. The IGFBP-3-induced dephosphorylation of IRS-2 is prevented by cotreatment of cells with insulin, (Q3A4Y15L16) IGF-I, or TbetaR-V/LRP-1 antagonists. The magnitude of the IRS-2 dephosphorylation induced by IGFBP-3 positively correlates with the degree of growth inhibition by IGFBP-3 in Mv1Lu cells and mutant cells derived from Mv1Lu cells. Stable transfection of murine 32D myeloid cells (which lack endogenous IRS proteins and are insensitive to growth inhibition by IGFBP-3) with IRS-1 or IRS-2 cDNA confers sensitivity to growth inhibition by IGFBP-3; this IRS-mediated growth inhibition can be completely reversed by insulin in 32D cells stably expressing IRS-2 and the insulin receptor. These results suggest that IRS-1 and IRS-2 are key molecules for the TbetaR-V/LRP-1-mediated growth inhibitory signaling cascade. PMID:15371331

Huang, Shuan Shian; Leal, Sandra M; Chen, Chun-Lin; Liu, I-Hua; Huang, Jung San

2004-09-15

251

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

PubMed

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

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

2005-01-01

252

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.

253

The 'system of pasta' - an introduction to dichotomous keys  

Microsoft Academic Search

Familiarity with species and species identification seems to be a prerequisite for understanding biodiversity and many syllabuses and practitioners emphasise the use of dichotomous keys. Previous studies revealed that pupils using illustrated identification books often coped better with identification tasks than pupils using dichotomous keys. One reason might be that pupils were confronted with two cognitive tasks simultaneously: how to

Christoph Randler; Anna Birtel

2008-01-01

254

Detection of Additional Gene Products Induced by the Interaction between Phytophthora capsici and its Host, Capsicum annuum, and the Identification of an Elicitin-Encoding Gene  

Microsoft Academic Search

Bailey, A.M., Muñoz-Sánchez, C.I., Martínez-Hernández, P. and Manríquez-Escamilla, M. 2001. Detection of additional gene products induced by the interaction between Phytophthora capsici and its host, Capsicum annuum, and the identification of an elicitin-encoding gene. Revista Mexicana de Fitopatología 19:23-31. Gene expression by Phytophthora capsici was analyzed during the early stages of interaction with pepper (Capsicum annuum) by differential display. Fungal

Ana María Bailey; Claudia Ivonne Muñoz-Sánchez; Pedro Martínez-Hernández; Manuel Manríquez-Escamilla

255

Identification of a Protein That Interacts with Tubulin Dimers and Increases the Catastrophe Rate of Microtubules  

Microsoft Academic Search

Using a polymerization inhibition assay, we have purified a small, heat stable protein that physically interacts with tubulin dimers and increases the catastrophe rate of microtubules. Sequence analysis identified this protein as oncoprotein 18 (Op18)\\/stathmin, a conserved phosphoprotein that is highly expressed in leukemia cells. Immunodepletion experiments in Xenopus egg extracts showed that Op18\\/stathmin is involved in physiological regulation of

Lisa D Belmont; Timothy J Mitchison

1996-01-01

256

Identification and characterization of multiple novel Rab-myosin Va interactions.  

PubMed

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, Graça; McCaffrey, Mary W; Goud, Bruno

2013-09-04

257

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.

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

2012-01-01

258

Functional Interaction Map of Lyssavirus Phosphoprotein: Identification of the Minimal Transcription Domains  

Microsoft Academic Search

Lyssaviruses, the causative agents of rabies encephalitis, are distributed in seven genotypes. The phyloge- netically distant rabies virus (PV strain, genotype 1) and Mokola virus (genotype 3) were used to develop a strategy to identify functional homologous interactive domains from two proteins (P and N) which participate in the viral ribonucleoprotein (RNP) transcription-replication complex. This strategy combined two-hybrid and green

YVES JACOB; ELEONORE REAL; NOEL TORDO

2001-01-01

259

Identification of a Small Molecule That Modulates Platelet Glycoprotein Ib-von Willebrand Factor Interaction*  

PubMed Central

The von Willebrand factor (VWF) A1-glycoprotein (GP) Ib? interaction is of major importance during thrombosis mainly at sites of high shear stress. Inhibitors of this interaction prevent platelet-dependent thrombus formation in vivo, without major bleeding complications. However, the size and/or protein nature of the inhibitors currently in development limit oral bioavailability and clinical development. We therefore aimed to search for a small molecule protein-protein interaction inhibitor interfering with the VWF-GPIb? binding. After determination of putative small molecule binding pockets on the surface of VWF-A1 and GPIb? using site-finding algorithms and molecular dynamics, high throughput molecular docking was performed on both binding partners. A selection of compounds showing good in silico docking scores into the predicted pockets was retained for testing their in vitro effect on VWF-GPIb? complex formation, by which we identified a compound that surprisingly stimulated the VWF-GPIb? binding in a ristocetin cofactor ELISA and increased platelet adhesion in whole blood to collagen under arterial shear rate but in contrast inhibited ristocetin-induced platelet aggregation. The selected compound adhering to the predicted binding partner GPIb? could be confirmed by saturation transfer difference NMR spectroscopy. We thus clearly identified a small molecule that modulates VWF-GPIb? binding and that will now serve as a starting point for further studies and chemical modifications to fully characterize the interaction and to manipulate specific activity of the compound.

Broos, Katleen; Trekels, Mieke; Jose, Rani Alphonsa; Demeulemeester, Jonas; Vandenbulcke, Aline; Vandeputte, Nele; Venken, Tom; Egle, Brecht; De Borggraeve, Wim M.; Deckmyn, Hans; De Maeyer, Marc

2012-01-01

260

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

PubMed

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

Bürmann, Frank; Sawant, Prachi; Bramkamp, Marc

2012-07-01

261

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

PubMed Central

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

Burmann, Frank; Sawant, Prachi; Bramkamp, Marc

2012-01-01

262

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

PubMed Central

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

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

2007-01-01

263

Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data  

Microsoft Academic Search

Mounting evidence shows that many protein complexes are conserved in evolution. Here we use conservation to find complexes that are common to yeast S. Cerevisiae and bacteria H. pylori. Our analysis combines protein interaction data, that are available for each of the two species, and orthology information based on protein sequence comparison. We develop a detailed probabilistic model for protein

Roded Sharan; Trey Ideker; Brian P. Kelley; Ron Shamir; Richard M. Karp

2004-01-01

264

Microenvironmental interactions in chronic lymphocytic leukemia: hints for pathogenesis and identification of targets for rational therapy.  

PubMed

Chronic lymphocytic leukemia (CLL) is a clinically heterogeneous disease characterized by the accumulation/expansion of a clonal population of small mature B lymphocytes in blood, bone marrow, and lymphoid organs. Although initial genetic events are considered primarily responsible for the first step(s) of neoplastic transformation, the development and progression of the CLL clone are thought to be affected by various micro-environmental signals that regulate proliferation and survival of malignant B cells. In the present review, we focus on specific interactions of CLL cells with the microenvironmental component, as they occur through the usage by CLL cells of specific molecular structures whose expression has been associated with prognosis, including: i) interactions of CLL cells via the surface BCR and dependent on specific molecular features of the BCR itself and/or the presence of the BCR-associated molecule ZAP- 70; ii) non-BCR-dependent proliferative and/or pro-survival interactions of CLL cells by CD49d and CD38. An overview of the putative drugs that could be employed to target specific molecules involved in CLL cells/tumor microenvironment interactions is also proposed in the closing chapter of the review. PMID:22591383

Dal Bo, Michele; Bomben, Riccardo; Zucchetto, Antonella; Del Poeta, Giovanni; Gaidano, Gianluca; Deaglio, Silvia; Efremov, Dimitar G; Gattei, Valter

2012-01-01

265

Identification of cellular proteins that interact with the adeno-associated virus rep protein.  

PubMed

Adeno-associated virus (AAV) codes for four related nonstructural Rep proteins. AAV both replicates and assembles in the nucleus and requires coinfection with a helper virus, either adenovirus (Ad) or herpesvirus, for a productive infection. Like other more complex DNA viruses, it is believed that AAV interacts or modifies host cell proteins to carry out its infection cycle. To date, relatively little is known about the host proteins that interact with the viral Rep proteins, which are known to be directly involved in DNA replication, control of viral and cellular transcription, splicing, and protein translation. In this study, we used affinity-tagged Rep protein to purify cellular protein complexes that were associated with Rep in cells that had been infected with Ad and AAV. In all, we identified 188 cellular proteins from 16 functional categories, including 14 transcription factors, 6 translation factors, 15 potential splicing proteins, 5 proteins involved in protein degradation, and 13 proteins involved in DNA replication or repair. This dramatically increases the number of potential interactions over the current number of approximately 26. Twelve of the novel proteins found were further tested by coimmunoprecipitation or colocalization using confocal immunomicroscopy. Of these, 10 were confirmed as proteins that formed complexes with Rep, including proteins of the MCM complex (DNA replication), RCN1 (membrane transport), SMC2 (chromatin dynamics), EDD1 (ubiquitin ligase), IRS4 (signal transduction), and FUS (splicing). Computer analysis suggested that 45 and 28 of the 188 proteins could be placed in a pathway of interacting proteins involved in DNA replication and protein synthesis, respectively. Of the proteins involved in DNA replication, all of the previously identified proteins involved in AAV DNA replication were found, except Ad DBP. The only Ad protein found to interact with Rep was the E1b55K protein. In addition, we confirmed that Rep interacts with Ku70/80 helicase. In vitro DNA synthesis assays demonstrated that although Ku helicase activity could substitute for MCM to promote strand displacement synthesis, its presence was not essential. Our study suggests that the interaction of AAV with cellular proteins is much more complex than previously suspected and provides a resource for further studies of the AAV life cycle. PMID:18971280

Nash, Kevin; Chen, Weijun; Salganik, Max; Muzyczka, Nicholas

2008-10-29

266

Identification and characterization of RHOA-interacting proteins in bovine spermatozoa.  

PubMed

In somatic cells, RHOA mediates actin dynamics through a GNA13-mediated signaling cascade involving RHO kinase (ROCK), LIM kinase (LIMK), and cofilin. RHOA can be negatively regulated by protein kinase A (PRKA), and it interacts with members of the A-kinase anchoring (AKAP) family via intermediary proteins. In spermatozoa, actin polymerization precedes the acrosome reaction, which is necessary for normal fertility. The present study was undertaken to determine whether the GNA13-mediated RHOA signaling pathway may be involved in acrosome reaction in bovine caudal sperm, and whether AKAPs may be involved in its targeting and regulation. GNA13, RHOA, ROCK2, LIMK2, and cofilin were all detected by Western blot in bovine caudal sperm. Overlay, immunoprecipitation, and subsequent mass spectrometry analysis identified several RHOA-interacting proteins, including proacrosin, angiotensin-converting enzyme, tubulin, aldolase C, and AKAP4. Using overlay and pulldown techniques, we demonstrate that phosphorylation of AKAP3 increases its interaction with the RHOA-interacting proteins PRKAR2 (the type II regulatory subunit of PRKA, formerly RII) and ropporin (ROPN1, a PRKAR2-like protein, or R2D2). Varying calcium concentrations in pulldown assays did not significantly alter binding to R2D2 proteins. These data suggest that the actin-regulating GNA13-mediated RHOA-ROCK-LIMK-cofilin pathway is present in bovine spermatozoa, that RHOA interacts with proteins involved in capacitation and the acrosome reaction, and that RHOA signaling in sperm may be targeted by AKAPs. Finally, AKAP3 binding to PRKAR2 and ROPN1 is regulated by phosphorylation in vitro. PMID:17928627

Fiedler, Sarah E; Bajpai, Malini; Carr, Daniel W

2007-10-10

267

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.

Ollis, Anne A.

2012-01-01

268

Rapid coupling of Surface Plasmon Resonance (SPR and SPRi) and ProteinChip(TM) based mass spectrometry for the identification of proteins in nucleoprotein interactions  

PubMed Central

We compared coupling approaches of SPR to LC-MS and ProteinChip™-based mass spectrometry (SELDI™) as a means of identifying proteins captured on DNA surfaces. The approach we outline has the potential to allow multiple, quantitative analysis of macromolecular interactions followed by rapid mass spectrometry identification of retained material.

Bouffartigues, Emeline; Leh, Herve; Anger-Leroy, Marielle; Rimsky, Sylvie; Buckle, Malcolm

2007-01-01

269

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

SciTech Connect

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

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

2008-04-01

270

Identification of MDP (muramyl dipeptide)-binding key domains in NOD2 (nucleotide-binding and oligomerization domain-2) receptor of Labeo rohita.  

PubMed

In lower eukaryotes-like fish, innate immunity contributed by various pattern recognition receptor (PRR) plays an essential role in protection against diseases. Nucleotide-binding and oligomerization domain (NOD)-2 is a cytoplasmic PRR that recognizes MDP (muramyl dipeptide) of the Gram positive and Gram negative bacteria as ligand and activates signalling to induce innate immunity. Hypothesizing a similar NOD2 signalling pathway of higher eukaryotes, the peripheral blood leucocytes (PBLs) of rohu (Labeo rohita) was stimulated with MDP. The data of quantitative real-time PCR (qRT-PCR) revealed MDP-mediated inductive expression of NOD2 and its down-stream molecule RICK/RIP2 (receptor-interacting serine-threonine protein kinase-2). This observation suggested the existence of MDP-binding sites in rohu NOD2 (rNOD2). To investigate it, 3D model of ligand-binding leucine-rich repeat (LRR) region of rNOD2 (rNOD2-LRR) was constructed following ab initio and threading approaches in I-TASSER web server. Structural refinement of the model was performed by energy minimization, and MD (molecular dynamics) simulation was performed in GROMACS (Groningen Machine for Chemical Simulations). The refined model of rNOD2-LRR was validated through SAVES, ProSA, ProQ, WHAT IF and MolProbity servers, and molecular docking with MDP was carried out in GOLD 4.1. The result of docking identified LRR3-7 comprising Lys820, Phe821, Asn822, Arg847, Gly849, Trp877, Trp901 and Trp931 as MDP-binding critical amino acids in rNOD2. This is the first study in fish to provide an insight into the 3D structure of NOD2-LRR region and its important motifs that are expected to be engaged in MDP binding and innate immunity. PMID:23255217

Maharana, Jitendra; Swain, Banikalyan; Sahoo, Bikash R; Dikhit, Manas R; Basu, Madhubanti; Mahapatra, Abhijit S; Jayasankar, Pallipuram; Samanta, Mrinal

2012-12-20

271

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

PubMed Central

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

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

2011-01-01

272

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

PubMed Central

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

2010-01-01

273

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

274

Data integration and exploration for the identification of molecular mechanisms in tumor-immune cells interaction  

PubMed Central

Cancer progression is a complex process involving host-tumor interactions by multiple molecular and cellular factors of the tumor microenvironment. Tumor cells that challenge immune activity may be vulnerable to immune destruction. To address this question we have directed major efforts towards data integration and developed and installed a database for cancer immunology with more than 1700 patients and associated clinical data and biomolecular data. Mining of the database revealed novel insights into the molecular mechanisms of tumor-immune cell interaction. In this paper we present the computational tools used to analyze integrated clinical and biomolecular data. Specifically, we describe a database for heterogenous data types, the interfacing bioinformatics and statistical tools including clustering methods, survival analysis, as well as visualization methods. Additionally, we discuss generic issues relevant to the integration of clinical and biomolecular data, as well as recent developments in integrative data analyses including biomolecular network reconstruction and mathematical modeling.

2010-01-01

275

Interaction between alginates and manganese cations: identification of preferred cation binding sites.  

PubMed

Algal and bacterial alginates have been studied by means of 13C NMR spectroscopy in presence of paramagnetic manganese ions in order to reveal the nature of their interaction with bivalent cations. It is found that the mannuronate blocks bind manganese cations externally near their carboxylate groups, while guluronate blocks show the capability to integrate Mn2+ into pocket-like structures formed by adjacent guluronate residues. In alternating mannuronate-guluronate blocks, manganese ions preferentially locate in a concave structure formed by guluronate-mannuronate pairs. Partial acetylation of the alginate generally reduces its capability to interact with bivalent cations, however, the selectivity of the binding geometry is conserved. The results may serve as a hint for the better understanding of the alginate gelation in presence of calcium ions. PMID:15178012

Emmerichs, N; Wingender, J; Flemming, H-C; Mayer, C

2004-04-01

276

Identification of a novel heteroglycan-interacting protein, HIP 1.3, from Arabidopsis thaliana  

Microsoft Academic Search

Plastidial degradation of transitory starch yields mainly maltose and glucose. Following the export into the cytosol, maltose acts as donor for a glucosyl transfer to cytosolic heteroglycans as mediated by a cytosolic transglucosidase (DPE2; EC 2.4.1.25) and the second glucosyl residue is liberated as glucose. The cytosolic phosphorylase (Pho2\\/PHS2; EC 2.4.1.1) also interacts with heteroglycans using the same intramolecular sites

Joerg Fettke; Adriano Nunes-Nesi; Alisdair R. Fernie; Martin Steup

2011-01-01

277

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

PubMed Central

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

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

2013-01-01

278

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

PubMed

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

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

2013-10-03

279

Identification of small-molecule antagonists that inhibit an activator:coactivator interaction  

Microsoft Academic Search

Phosphorylation of the cAMP response element binding protein (CREB) at Ser-133 in response to hormonal stimuli triggers cellular gene expression via the recruitment of the histone acetylase coactivator paralogs CREB binding protein (CBP) and p300 to the promoter. The NMR structure of the CREB:CBP complex, using relevant interaction domains called KID and KIX, respectively, reveals a shallow hydrophobic groove on

Jennifer L. Best; Carlos A. Amezcua; Bernhard Mayr; Lawrence Flechner; Christopher M. Murawsky; Beverly Emerson; Tsaffrir Zor; Kevin H. Gardner; Marc Montminy

2004-01-01

280

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

PubMed

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

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

2013-10-18

281

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

282

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

283

Identification of NIPSNAP1 as a Nocistatin-interacting Protein Involving Pain Transmission*  

PubMed Central

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

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

2012-01-01

284

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

PubMed

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

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

2012-08-17

285

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.

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

2013-01-01

286

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

PubMed Central

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

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

1990-01-01

287

Identification of novel small molecules that inhibit protein-protein interactions between MAGE and KAP-1  

PubMed Central

The Class I MAGE proteins are normally expressed only in developing germ cells but are often aberrantly expressed in malignancies, particularly melanoma, making them good therapeutic targets. MAGE proteins promote tumor survival by binding to the RBCC region of KAP-1 and suppressing p53. Although, suppression of MAGE expression, by RNA interference, relieves p53 suppression and inhibits tumor growth, its therapeutic uses are limited by lack of methods for systemic delivery of small interfering RNA. To overcome this barrier, we sought to discover chemical compounds that inhibit binding between MAGE and KAP-1 proteins. Based on previously published effects of MAGE suppression, we developed a strategy for screening a small molecule library based on selective death of MAGE positive cells, activation of p53 and lack of caspase activity. We screened the Maybridge HitFinder library of compounds and eight compounds fulfilled these criteria. Seven of these compounds interfered with co-precipitation of MAGE and KAP-1, and three interfered with binding of MAGE and KAP-1 in a mammalian two hybrid assay. We now report identification of three potential compounds that interfere with MAGE/KAP-1 binding and can be developed as novel chemo-therapeutic agents for treatment of advanced melanoma and other cancers.

Bhatia, Neehar; Yang, Bing; Xiao, Tony Z.; Peters, Noel; Hoffmann, Michael F.; Longley, B. Jack

2011-01-01

288

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

SciTech Connect

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

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

2008-07-18

289

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.

290

Identification of significant association and gene-gene interaction of GABA receptor subunit genes in autism.  

PubMed

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

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

2005-07-15

291

Improved hydrophilic interaction chromatography method for the identification and quantification of glucosinolates.  

PubMed

An improved hydrophilic interaction liquid chromatography (HILIC) method has been developed to separate members of a closely related family of chemoprotective phytochemicals called glucosinolates. This method exploits the emergence of a second generation of HILIC chemistry, using a silica-based permanently zwitterionic stationary phase. These columns are more robust, durable, and glucosinolates separations are more reproducible than with the original polyhydroxyethyl aspartamide columns. Furthermore, the HILIC system that we report herein permits much greater alteration of the mobile phase composition for customized separation of glucosinolates from plant extracts, across a wide spectrum of polarity. PMID:17482632

Wade, Kristina L; Garrard, Ian J; Fahey, Jed W

2007-04-20

292

Identification of severe potential drug-drug interactions using an Italian general-practitioner database  

Microsoft Academic Search

Objective  To analyze prescriptions in a general-practitioner database over 1 year to determine the frequency, the characteristics, and\\u000a the monitoring of the severe potential drug-drug interactions (DDIs).\\u000a \\u000a \\u000a \\u000a Methods  We retrospectively analyzed the clinical records from 16 general practitioners in the Veneto region, an area in northern Italy.\\u000a The study covered the period from January 1 to December 31, 2004. We selected all severe

L. Magro; A. Conforti; F. Del Zotti; R. Leone; M. L. Iorio; I. Meneghelli; D. Massignani; E. Visonà; U. Moretti

2008-01-01

293

Identification of adenovirus serotype 5 hexon regions that interact with scavenger receptors.  

PubMed

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. PMID:22156515

Khare, Reeti; Reddy, Vijay S; Nemerow, Glen R; Barry, Michael A

2011-12-07

294

Identification of mammalin cytosolic proteins that can interact specifically with FACC  

SciTech Connect

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

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

1994-09-01

295

Identification of metagenes and their Interactions through Large-scale Analysis of Arabidopsis Gene Expression Data  

PubMed Central

Background Many plant genes have been identified through whole genome and deep transcriptome sequencing and other methods; yet our knowledge on the function of many of these genes remains limited. The integration and analysis of large gene-expression datasets gives researchers the ability to formalize hypotheses concerning the functionality and interaction between different groups of correlated genes. Results We applied the non-negative matrix factorization (NMF) algorithm to the AtGenExpress dataset which consists of 783 microarray samples (29 separate experimental series) conducted on the model plant Arabidopsis thaliana. We identified 15 metagenes, which are groups of genes with correlated expression. Functional roles of these metagenes are established by observing the enriched gene ontology (GO) categories using gene set enrichment analyses (GSEA). Activity levels of these metagenes in various experimental conditions are also analyzed to associate metagenes with stimuli/conditions. A metagene correlation network, constructed based on the results of NMF analysis, revealed many new interactions between the metagenes. Comparison of these metagenes with an earlier large-scale clustering analysis indicates many statistically significant overlaps. Conclusions This study identifies a network of correlated metagenes composed of Arabidopsis genes acting in a highly correlated fashion across a broad spectrum of experimental stimuli, which may shed some light on the function of many of the un-annotated genes.

2012-01-01

296

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

PubMed Central

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

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

2010-01-01

297

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

PubMed

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

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

2010-01-25

298

Identification of domains in rubella virus genomic RNA and capsid protein necessary for specific interaction.  

PubMed Central

In rubella virus-infected cells, genomic 40S and subgenomic 24S RNAs are present in the cytoplasm of infected cells. However, encapsidation by rubella virus capsid protein is specific for 40S genomic RNA. As a first step toward understanding the assembly of rubella virus nucleocapsid at the molecular level, the interaction between capsid protein and genomic RNA was studied by Northwestern (RNA-protein) blot analysis. RNA probes prepared by in vitro transcription were used to localize the RNA sequence that participates in binding to the capsid protein. We have identified a 29-nucleotide RNA sequence (nucleotides 347 to 375) that is essential for the binding. By using overlapping synthetic peptides of capsid protein, a peptide domain (residues 28 to 56) that displays specific RNA-binding activity of capsid protein has been located. This result suggests that the specific recognition of viral RNA during rubella virus assembly involves, at least in part, the nucleocapsid protein.

Liu, Z; Yang, D; Qiu, Z; Lim, K T; Chong, P; Gillam, S

1996-01-01

299

The interaction of ?-chymotrypsin with one persistent organic pollutant (dicofol): spectroscope and molecular modeling identification.  

PubMed

Great attention is devoted to persistent organic pollutant (POP), among which the pesticide dicofol is critical related to food safety and might raise the risk of cancer incidence. To take a comprehensive evaluation of its toxicity, we investigated its interaction with a serine protease ?-chymotrypsin by multi-spectroscopic techniques and molecular modeling method. UV-vis absorption, synchronous fluorescence, and circular dichroism data elucidated that dicofol unfolded the framework of ?-chymotrypsin and led to secondary structure changes. The fluorescence and lifetime assay determined the static quenching mode and binding parameters. As an auxiliary method, molecular modeling has displayed the specific binding site and information about binding forces and drug-residues distances which were consistent with conclusions from above. Additional, enzyme activity assay gave evidence at the functional aspect to clarify the fact that dicofol could contribute to the conformational changes and furthermore alter the function of the enzyme. PMID:22771722

Liu, Ying; Liu, Rutao

2012-07-03

300

Aerosol generation and identification for model studies of particle-lung interactions.  

PubMed

This article discusses the idea and set-up of a laboratory system for generating reproducible concentrated occupational aerosols containing metal compounds. A dust representative for 2 metal-machining workstations (an electric grinder and an electric disc cutter) was released from a fluidized-bed generator, and then sampled and compared in respect to concentration, particle size distribution, particle morphology and the content of metal elements (Fe, Al, Cu, Mn, Cr, Ni, Pb, Zn, Mg). The results indicate the presence of a significant number of irregularly-shaped respirable particles. Those particles contained mainly Fe and Al, and their composition was shown to depend on particle size. The proposed system of aerosol generation and collection can be used in studies of interactions between airborne particles and a model lung surfactant. PMID:20331917

Kondej, Dorota; Sosnowski, Tomasz R

2010-01-01

301

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

PubMed Central

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

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

2005-01-01

302

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.

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

2012-01-01

303

Identification of ORC1/CDC6-interacting factors in Trypanosoma brucei reveals critical features of origin recognition complex architecture.  

PubMed

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

2012-03-08

304

Identification of Archaea-specific chemotaxis proteins which interact with the flagellar apparatus  

PubMed Central

Background Archaea share with bacteria the ability to bias their movement towards more favorable locations, a process known as taxis. Two molecular systems drive this process: the motility apparatus and the chemotaxis signal transduction system. The first consists of the flagellum, the flagellar motor, and its switch, which allows cells to reverse the rotation of flagella. The second targets the flagellar motor switch in order to modulate the switching frequency in response to external stimuli. While the signal transduction system is conserved throughout archaea and bacteria, the archaeal flagellar apparatus is different from the bacterial one. The proteins constituting the flagellar motor and its switch in archaea have not yet been identified, and the connection between the bacterial-like chemotaxis signal transduction system and the archaeal motility apparatus is unknown. Results Using protein-protein interaction analysis, we have identified three proteins in Halobacterium salinarum that interact with the chemotaxis (Che) proteins CheY, CheD, and CheC2, as well as the flagella accessory (Fla) proteins FlaCE and FlaD. Two of the proteins belong to the protein family DUF439, the third is a HEAT_PBS family protein. In-frame deletion strains for all three proteins were generated and analyzed as follows: a) photophobic responses were measured by a computer-based cell tracking system b) flagellar rotational bias was determined by dark-field microscopy, and c) chemotactic behavior was analyzed by a swarm plate assay. Strains deleted for the HEAT_PBS protein or one of the DUF439 proteins proved unable to switch the direction of flagellar rotation. In these mutants, flagella rotate only clockwise, resulting in exclusively forward swimming cells that are unable to respond to tactic signals. Deletion of the second DUF439 protein had only minimal effects. HEAT_PBS proteins could be identified in the chemotaxis gene regions of all motile haloarchaea sequenced so far, but not in those of other archaeal species. Genes coding for DUF439 proteins, however, were found to be integral parts of chemotaxis gene regions across the archaeal domain, and they were not detected in other genomic context. Conclusion Altogether, these results demonstrate that, in the archaeal domain, previously unrecognized archaea-specific Che proteins are essential for relaying taxis signaling to the flagellar apparatus.

2009-01-01

305

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

PubMed Central

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

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

2013-01-01

306

Identification of a redox-modulatory interaction between uncoupling protein 3 and thioredoxin 2 in the mitochondrial intermembrane space.  

PubMed

Uncoupling protein 3 (UCP3) is a member of the mitochondrial solute carrier superfamily that is enriched in skeletal muscle and controls mitochondrial reactive oxygen species (ROS) production, but the mechanisms underlying this function are unclear. Aims: The goal of this work focused on the identification of mechanisms underlying UCP3 functions. Results: Here we report that the N-terminal, intermembrane space (IMS)-localized hydrophilic domain of mouse UCP3 interacts with the N-terminal mitochondrial targeting signal of thioredoxin 2 (Trx2), a mitochondrial thiol reductase. Cellular immunoprecipitation and in vitro pull-down assays show that the UCP3-Trx2 complex forms directly, and that the Trx2?N-terminus is both necessary and sufficient to confer UCP3 binding. Mutation studies show that neither a catalytically inactivated Trx2 mutant, nor a mutant Trx2 bearing the N-terminal targeting sequence of cytochrome c oxidase (COXMTS-Trx2) bind UCP3. Biochemical analyses using permeabilized mitochondria, and live cell experiments using bimolecular fluorescence complementation show that the UCP3-Trx2 complex forms specifically in the IMS. Finally, studies in C2C12 myocytes stably overexpressing UCP3 (2.5-fold) and subjected to Trx2 knockdown show that Trx2 is required for the UCP3-dependent mitigation of complex III-driven mitochondrial ROS generation. UCP3 expression was increased in mice fed a high fat diet, leading to increased localization of Trx2 to the IMS. UCP3 overexpression also increased expression of the glucose transporter GLUT4 in a Trx2-dependent fashion. Innovation: This is the first report of a mitochondrial protein-protein interaction with UCP3 and the first demonstration that UCP3 binds directly, and in cells and tissues with mitochondrial thioredoxin 2. Conclusion: These studies identify a novel UCP3-Trx2 complex, a novel submitochondrial localization of Trx2, and a mechanism underlying UCP3-regulated mitochondrial ROS production. PMID:21619484

Hirasaka, Katsuya; Lago, Cory U; Kenaston, M Alexander; Fathe, Kristin; Nowinski, Sara M; Nikawa, Takeshi; Mills, Edward M

2011-07-12

307

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

308

Identification of binding sites of Lactobacillus plantarum enolase involved in the interaction with human plasminogen.  

PubMed

The enolase EnoA1 of Lactobacillus plantarum is here shown to interact with human plasminogen (Plg). By sequence alignment of EnoA1 with Streptococcus pneumoniae and Bifidobacterium lactis enolases, we identified BS1 and BS2 Plg-binding sites. A structure prediction of EnoA1 showed lysine residues in position 255 (BS2), and 422 (BS1) exposed on protein surface. A lysine residue in position 259 was as well identified as surface-exposed amino acid. The enoA1 gene was site directed-mutagenized to generate four mutated proteins, carrying K255A, K259A, K422A and K259A/K422A substitutions. The functional role of these lysine residues was assessed evaluating specific Plg-binding activity of the mutated proteins. While the binding activity of the mutated proteins was drastically reduced, the residual enzymatic activity was more than 50% of EnoA1. Our results show that L. plantarum EnoA1 exhibits the Plg-BS1, and the Plg-BS2 extending up to the lysine residue in position 259, therefore consisting of 12-aa residues instead of 9-aa residues described in S. pneumoniae. A test performed on whole cells of L. plantarum, demonstrated that after inducing conversion of the cell-bound plasminogen to plasmin, this was released into the medium, unlike the mechanism reported for most pathogens, that retained plasmin bound to the cell surface. PMID:23103380

Vastano, Valeria; Capri, Ugo; Candela, Marco; Siciliano, Rosa Anna; Russo, Luigi; Renda, Mario; Sacco, Margherita

2012-10-25

309

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

SciTech Connect

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

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

2006-04-28

310

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

311

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

PubMed

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

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

2013-08-09

312

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

Microsoft Academic Search

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

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

2010-01-01

313

Identification of an intracellular protein that specifically interacts with photoaffinity-labeled oncogenic p21 protein  

SciTech Connect

An oncogenic 21-kDa (p21) protein (Harvey RAS protein with Val-12) has been covalently modified with a functional reagent that contains a photoactivatable aromatic azide group. This modified p21 protein has been introduced quantitatively into NIH 3T3 cells using an erythrocyte-mediated fusion technique. The introduced p21 protein was capable of inducing enhanced pinocytosis and DNA synthesis in the recipient cells. To identify the putative intracellular protein(s) that specifically interact with modified p21 protein, the cells were pulsed with ({sup 35}S)methionine at selected times after fusion and then UV-irradiated to activate the azide group. The resulting nitrene covalently binds to amino acid residues in adjacent proteins, thus linking the p21 protein to these proteins. The cells were then lysed, and the lysate was immunoprecipitated with the anti-p21 monoclonal antibody Y13-259. The immunoprecipitate was analyzed by SDS/PAGE to identify p21 - protein complexes. By using this technique, the authors found that three protein complexes of 51, 64, and 82 kDa were labeled specifically and reproducibly. The most prominent band is the 64-kDa protein complex that shows a time-dependent rise and fall, peaking within a 5-hr period after introduction of the p21 protein the cells. These studies provide evidence that in vitro the p21 protein becomes associated with a protein whose mass is about 43 kDa. They suggest that the formation of this complex may play a role in mediating early events involved with cell transformation induced by RAS oncogenes.

Lee, G. (New York Univ., NY (USA) Columbia Univ. College of Physicians and Surgeons, New York, NY (USA)); Ronai, Z.A. (Columbia Univ. College of Physicians and Surgeons, New York, NY (USA) American Health Foundation, Valhalla, NY (USA)); Pincus, M.R. (New York Univ., NY (USA) State Univ. of New York Health Science Center, Syracuse (USA)); Brandt-Rauf, P.W.; Weinstein, I.B. (Columbia Univ. College of Physicians and Surgeons, New York, NY (USA)); Murphy, R.B. (New York Univ., NY (USA) Cornell Univ. Medical College, White Plains, NY (USA)); Delohery, T.M. (Columbia Univ. College of Physicians and Surgeons, New York, NY (USA)); Nishimura, S.; Yamaizumi. Z. (National Cancer Center Research Institute, Tokyo (Japan))

1989-11-01

314

Features analysis for identification of date and party hubs in protein interaction network of Saccharomyces Cerevisiae  

PubMed Central

Background It has been understood that biological networks have modular organizations which are the sources of their observed complexity. Analysis of networks and motifs has shown that two types of hubs, party hubs and date hubs, are responsible for this complexity. Party hubs are local coordinators because of their high co-expressions with their partners, whereas date hubs display low co-expressions and are assumed as global connectors. However there is no mutual agreement on these concepts in related literature with different studies reporting their results on different data sets. We investigated whether there is a relation between the biological features of Saccharomyces Cerevisiae's proteins and their roles as non-hubs, intermediately connected, party hubs, and date hubs. We propose a classifier that separates these four classes. Results We extracted different biological characteristics including amino acid sequences, domain contents, repeated domains, functional categories, biological processes, cellular compartments, disordered regions, and position specific scoring matrix from various sources. Several classifiers are examined and the best feature-sets based on average correct classification rate and correlation coefficients of the results are selected. We show that fusion of five feature-sets including domains, Position Specific Scoring Matrix-400, cellular compartments level one, and composition pairs with two and one gaps provide the best discrimination with an average correct classification rate of 77%. Conclusions We study a variety of known biological feature-sets of the proteins and show that there is a relation between domains, Position Specific Scoring Matrix-400, cellular compartments level one, composition pairs with two and one gaps of Saccharomyces Cerevisiae's proteins, and their roles in the protein interaction network as non-hubs, intermediately connected, party hubs and date hubs. This study also confirms the possibility of predicting non-hubs, party hubs and date hubs based on their biological features with acceptable accuracy. If such a hypothesis is correct for other species as well, similar methods can be applied to predict the roles of proteins in those species.

2010-01-01

315

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

316

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

317

Identification of the metabolites of lesogaberan using linear trap quadrupole orbitrap mass spectrometry and hydrophilic interaction liquid chromatography.  

PubMed

1. In this study, hydrophilic interaction liquid chromatography (HILIC), radiochemical activity monitoring and linear trap quadrupole orbitrap mass spectrometry (MS) and tandem mass spectrometry (MS/MS) were used to identify the metabolites of a highly polar novel ?-aminobutyric acid type-B receptor agonist, lesogaberan, in rats. 2. Urine was collected from three male Wistar rats for 24 h after dosing with (14)C-labelled lesogaberan (170 mg/kg, 10 MBq/kg); plasma samples were taken 2 and 24 h after dosing. Pooled samples were separated by HILIC and eluents were analysed by radiochemical activity monitoring, MS and MS/MS. 3. Only the parent compound was detected in plasma, but six metabolites (M1-M6) were detected in urine. Analysis of MS and MS/MS data and comparison with synthetic reference standards enabled the identification of the structure of each metabolite. M1 was identified as the N-acetylated species [(2R)-3-acetamido-2-fluoropropyl]-phosphinic acid, and M6 as [(2R)-3-amino-2-fluoropropyl]-phosphonic acid. Metabolites M2 and M5 were the alcohol and carboxylic acid species 3-hydroxypropyl-phosphinic acid and 3-hydroxyphosphonoyl-propanoic acid, respectively, both of which had lost the fluorine atom present in the parent compound. M3 was the corresponding carboxylic acid species retaining the fluorine atom, (2R)-2-fluoro-3-hydroxyphosphonoyl-propanoic acid. Finally M4 was identified as [(2R)-2-fluoro-3-guanidino-propyl]-phosphinic acid. PMID:23030741

Ekdahl, Anja; Aurell-Holmberg, Ann; Castagnoli, Neal

2012-10-03

318

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

319

Identification of a Redox-Modulatory Interaction Between Uncoupling Protein 3 and Thioredoxin 2 in the Mitochondrial Intermembrane Space  

PubMed Central

Abstract Uncoupling protein 3 (UCP3) is a member of the mitochondrial solute carrier superfamily that is enriched in skeletal muscle and controls mitochondrial reactive oxygen species (ROS) production, but the mechanisms underlying this function are unclear. Aims The goal of this work focused on the identification of mechanisms underlying UCP3 functions. Results Here we report that the N-terminal, intermembrane space (IMS)-localized hydrophilic domain of mouse UCP3 interacts with the N-terminal mitochondrial targeting signal of thioredoxin 2 (Trx2), a mitochondrial thiol reductase. Cellular immunoprecipitation and in vitro pull-down assays show that the UCP3–Trx2 complex forms directly, and that the Trx2?N-terminus is both necessary and sufficient to confer UCP3 binding. Mutation studies show that neither a catalytically inactivated Trx2 mutant, nor a mutant Trx2 bearing the N-terminal targeting sequence of cytochrome c oxidase (COXMTS-Trx2) bind UCP3. Biochemical analyses using permeabilized mitochondria, and live cell experiments using bimolecular fluorescence complementation show that the UCP3–Trx2 complex forms specifically in the IMS. Finally, studies in C2C12 myocytes stably overexpressing UCP3 (2.5-fold) and subjected to Trx2 knockdown show that Trx2 is required for the UCP3-dependent mitigation of complex III-driven mitochondrial ROS generation. UCP3 expression was increased in mice fed a high fat diet, leading to increased localization of Trx2 to the IMS. UCP3 overexpression also increased expression of the glucose transporter GLUT4 in a Trx2-dependent fashion. Innovation This is the first report of a mitochondrial protein–protein interaction with UCP3 and the first demonstration that UCP3 binds directly, and in cells and tissues with mitochondrial thioredoxin 2. Conclusion These studies identify a novel UCP3–Trx2 complex, a novel submitochondrial localization of Trx2, and a mechanism underlying UCP3-regulated mitochondrial ROS production. Antioxid. Redox Signal. 15, 2645–2661.

Hirasaka, Katsuya; Lago, Cory U.; Kenaston, M. Alexander; Fathe, Kristin; Nowinski, Sara M.; Nikawa, Takeshi

2011-01-01

320

Identification of synaptic interactions  

Microsoft Academic Search

This paper studies the influence exerted by the presynaptic spike train on the postsynaptic one. It applies to synaptic exploration a novel method for characterization of point-process systems (Brillinger, 1974, 1975a), and draws from it physiologically meaningful conclusions. The departure point was a large data set of action potential trains from an Aplysia network whose neurons are connected by monosynaptic

David R. Brillinger; Hugh L. Bryant; José P. Segundo

1976-01-01

321

Oxyanion-steering and CH-? Interactions as Key Elements in a N-Heterocyclic Carbene-Catalyzed [4+2] Cycloaddition  

PubMed Central

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. In this communication, 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.

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

2012-01-01

322

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

2013-08-27

323

A combined database related and de novo MS-identification of yeast mannose-1-phosphate guanyltransferase PSA1 interaction partners at different phases of batch cultivation  

NASA Astrophysics Data System (ADS)

Mass spectrometry-based proteomic research has become one of the main methods in protein-protein interaction research. Several high throughput studies have established an interaction landscape of exponentially growing Baker's yeast culture. However, many of the protein-protein interactions are likely to change in different environmental conditions. In order to examine the dynamic nature of the protein interactions we isolated the protein complexes of mannose-1-phosphate guanyltransferase PSA1 from Saccharomyces cerevisiae at four different time points during batch cultivation. We used the tandem affinity purification (TAP)-method to purify the complexes and subjected the tryptic peptides to LC-MS/MS. The resulting peak lists were analyzed with two different methods: the database related protein identification program X!Tandem and the de novo sequencing program Lutefisk. We observed significant changes in the interactome of PSA1 during the batch cultivation and identified altogether 74 proteins interacting with PSA1 of which only six were found to interact during all time points. All the other proteins showed a more dynamic nature of binding activity. In this study we also demonstrate the benefit of using both database related and de novo methods in the protein interaction research to enhance both the quality and the quantity of observations.

Parviainen, Ville; Joenväärä, Sakari; Peltoniemi, Hannu; Mattila, Pirkko; Renkonen, Risto

2009-04-01

324

Characterization of the Interaction of Full-Length HIV-1 Vif Protein with its Key Regulator CBF? and CRL5 E3 Ubiquitin Ligase Components  

PubMed Central

Human immunodeficiency virus-1 (HIV-1) viral infectivity factor (Vif) is essential for viral replication because of its ability to eliminate the host's antiviral response to HIV-1 that is mediated by the APOBEC3 family of cellular cytidine deaminases. Vif targets these proteins, including APOBEC3G, for polyubiquitination and subsequent proteasome-mediated degradation via the formation of a Cullin5-ElonginB/C-based E3 ubiquitin ligase. Determining how the cellular components of this E3 ligase complex interact with Vif is critical to the intelligent design of new antiviral drugs. However, structural studies of Vif, both alone and in complex with cellular partners, have been hampered by an inability to express soluble full-length Vif protein. Here we demonstrate that a newly identified host regulator of Vif, core-binding factor-beta (CBF?), interacts directly with Vif, including various isoforms and a truncated form of this regulator. In addition, carboxyl-terminal truncations of Vif lacking the BC-box and cullin box motifs were sufficient for CBF? interaction. Furthermore, association of Vif with CBF?, alone or in combination with Elongin B/C (EloB/C), greatly increased the solubility of full-length Vif. Finally, a stable complex containing Vif-CBF?-EloB/C was purified in large quantity and shown to bind purified Cullin5 (Cul5). This efficient strategy for purifying Vif-Cul5-CBF?-EloB/C complexes will facilitate future structural and biochemical studies of Vif function and may provide the basis for useful screening approaches for identifying novel anti-HIV drug candidates.

Liu, Yayan; Yu, Xiao-Fang

2012-01-01

325

Characterization of the interaction of full-length HIV-1 Vif protein with its key regulator CBF? and CRL5 E3 ubiquitin ligase components.  

PubMed

Human immunodeficiency virus-1 (HIV-1) viral infectivity factor (Vif) is essential for viral replication because of its ability to eliminate the host's antiviral response to HIV-1 that is mediated by the APOBEC3 family of cellular cytidine deaminases. Vif targets these proteins, including APOBEC3G, for polyubiquitination and subsequent proteasome-mediated degradation via the formation of a Cullin5-ElonginB/C-based E3 ubiquitin ligase. Determining how the cellular components of this E3 ligase complex interact with Vif is critical to the intelligent design of new antiviral drugs. However, structural studies of Vif, both alone and in complex with cellular partners, have been hampered by an inability to express soluble full-length Vif protein. Here we demonstrate that a newly identified host regulator of Vif, core-binding factor-beta (CBF?), interacts directly with Vif, including various isoforms and a truncated form of this regulator. In addition, carboxyl-terminal truncations of Vif lacking the BC-box and cullin box motifs were sufficient for CBF? interaction. Furthermore, association of Vif with CBF?, alone or in combination with Elongin B/C (EloB/C), greatly increased the solubility of full-length Vif. Finally, a stable complex containing Vif-CBF?-EloB/C was purified in large quantity and shown to bind purified Cullin5 (Cul5). This efficient strategy for purifying Vif-Cul5-CBF?-EloB/C complexes will facilitate future structural and biochemical studies of Vif function and may provide the basis for useful screening approaches for identifying novel anti-HIV drug candidates. PMID:22479405

Zhou, Xiaohong; Evans, Sean L; Han, Xue; Liu, Yayan; Yu, Xiao-Fang

2012-03-30

326

Pax6 interactions with chromatin and identification of its novel direct target genes in lens and forebrain.  

PubMed

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

Xie, Qing; Yang, Ying; Huang, Jie; Ninkovic, Jovica; Walcher, Tessa; Wolf, Louise; Vitenzon, Ariel; Zheng, Deyou; Götz, Magdalena; Beebe, David C; Zavadil, Jiri; Cvekl, Ales

2013-01-14

327

RUNX1 Is a Key Target in t(4;11) Leukemias that Contributes to Gene Activation through an AF4-MLL Complex Interaction  

PubMed Central

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

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

2013-01-01

328

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

329

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.

330

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

NASA Astrophysics Data System (ADS)

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

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

2010-10-01

331

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

SciTech Connect

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

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

2010-10-08

332

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

Microsoft Academic Search

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

Sonja B Lauterbach; Roberto Lanzillotti; Theresa L Coetzer

2003-01-01

333

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

PubMed

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

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

2013-07-08

334

Identification of entomopathogenic fungi  

Technology Transfer Automated Retrieval System (TEKTRAN)

This chapter provides essential assistance for the identification of the most important genera (and main species) of fungal pathogens affecting insects, mites, and spiders. The key allows identifications regardless of which major spore types might be present with the specimen. The phylogenetic affi...

335

Regional-scale identification of groundwater-surface water interaction using hydrochemistry and multivariate statistical methods, Wairarapa Valley, New Zealand  

Microsoft Academic Search

Identifying areas of interaction between groundwater and surface water is crucial for effective environmental management, because this interaction is known to influence water quantity and quality. This paper applies hydrochemistry and multivariate statistics to identify locations and mechanisms of groundwater-surface water interaction in the pastorally dominated Wairarapa Valley, New Zealand. Hierarchical Cluster Analysis (HCA) and Principal Components Analysis (PCA) were

M. R. Guggenmos; C. J. Daughney; B. M. Jackson; U. Morgenstern

2011-01-01

336

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

PubMed Central

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

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

2002-01-01

337

Evaluating Key Statements Analysis  

Microsoft Academic Search

Key Statement Analysis extracts from a program, state- ments that form the core of the program's computation. A good set of key statements is small but has a large impact. Key statements form a useful starting point for understand- ing and manipulating a program. An empirical investigation of three kinds of key state- ments is presented. The three are based

David Binkley; Nicolas Gold; Mark Harman; Zheng Li; Kiarash Mahdavi

2008-01-01

338

Identification of Cell-Surface Molecular Interactions under Living Conditions by Using the Enzyme-Mediated Activation of Radical Sources (EMARS) Method  

PubMed Central

Important biological events associated with plasma membranes, such as signal transduction, cell adhesion, and protein trafficking, are mediated through the membrane microdomains. We have developed a novel method termed enzyme-mediated activation of radical sources (EMARS) to identify coclustering molecules on the cell surface under living conditions, which features a radical formation from an aryl azide reagent by horseradish peroxidase (HRP). For identification of molecules labeled by the EMARS reaction, antibody array system and mass spectrometry-based proteomics approaches are available. Spatio- temporally-regulated interaction between ?1 integrin and ErbB4 involved in fibronectin-dependent cell migration and therapeutic antibody-stimulated interaction between FGFR3 and CD20 were discovered using the EMARS method.

Honke, Koichi; Kotani, Norihiro

2012-01-01

339

Disrupting the Acyl Carrier Protein/SpoT Interaction In Vivo: Identification of ACP Residues Involved in the Interaction and Consequence on Growth  

PubMed Central

In bacteria, Acyl Carrier Protein (ACP) is the central cofactor for fatty acid biosynthesis. It carries the acyl chain in elongation and must therefore interact successively with all the enzymes of this pathway. Yet, ACP also interacts with proteins of diverse unrelated function. Among them, the interaction with SpoT has been proposed to be involved in regulating ppGpp levels in the cell in response to fatty acid synthesis inhibition. In order to better understand this mechanism, we screened for ACP mutants unable to interact with SpoT in vivo by bacterial two-hybrid, but still functional for fatty acid synthesis. The position of the selected mutations indicated that the helix II of ACP is responsible for the interaction with SpoT. This suggested a mechanism of recognition similar to one used for the enzymes of fatty acid synthesis. Consistently, the interactions tested by bacterial two-hybrid of ACP with fatty acid synthesis enzymes were also affected by the mutations that prevented the interaction with SpoT. Yet, interestingly, the corresponding mutant strains were viable, and the phenotypes of one mutant suggested a defect in growth regulation.

Angelini, Sandra; My, Laetitia; Bouveret, Emmanuelle

2012-01-01

340

Identification of a tobacco protein interacting with tomato mosaic virus coat protein and facilitating long-distance movement of virus  

Microsoft Academic Search

Summary. The protein–protein interaction of virus and host is essential for virus infection and host defense. The coat protein (CP) of tomato mosaic virus (ToMV) has been proved to be involved in cell-to-cell and long-distance movements of viruses that are presumably related with the protein–protein interactions. However, the host proteins that interact with the ToMV coat protein (ToCP) are largely

Y. Li; M. Y. Wu; H. H. Song; X. Hu; B. S. Qiu

2005-01-01

341

A benchmarked protein microarray-based platform for the identification of novel low-affinity extracellular protein interactions.  

PubMed

Low-affinity extracellular protein interactions are critical for cellular recognition processes, but existing methods to detect them are limited in scale, making genome-wide interaction screens technically challenging. To address this, we report here the miniaturization of the AVEXIS (avidity-based extracellular interaction screen) assay by using protein microarray technology. To achieve this, we have developed protein tags and sample preparation methods that enable the parallel purification of hundreds of recombinant proteins expressed in mammalian cells. We benchmarked the protein microarray-based assay against a set of known quantified receptor-ligand pairs and show that it is sensitive enough to detect even very weak interactions that are typical of this class of interactions. The increase in scale enables interaction screening against a dilution series of immobilized proteins on the microarray enabling the observation of saturation binding behaviors to show interaction specificity and also the estimation of interaction affinities directly from the primary screen. These methodological improvements now permit screening for novel extracellular receptor-ligand interactions on a genome-wide scale. PMID:22342946

Sun, Yi; Gallagher-Jones, Marcus; Barker, Colin; Wright, Gavin J

2012-02-17

342

A benchmarked protein microarray-based platform for the identification of novel low-affinity extracellular protein interactions  

PubMed Central

Low-affinity extracellular protein interactions are critical for cellular recognition processes, but existing methods to detect them are limited in scale, making genome-wide interaction screens technically challenging. To address this, we report here the miniaturization of the AVEXIS (avidity-based extracellular interaction screen) assay by using protein microarray technology. To achieve this, we have developed protein tags and sample preparation methods that enable the parallel purification of hundreds of recombinant proteins expressed in mammalian cells. We benchmarked the protein microarray-based assay against a set of known quantified receptor–ligand pairs and show that it is sensitive enough to detect even very weak interactions that are typical of this class of interactions. The increase in scale enables interaction screening against a dilution series of immobilized proteins on the microarray enabling the observation of saturation binding behaviors to show interaction specificity and also the estimation of interaction affinities directly from the primary screen. These methodological improvements now permit screening for novel extracellular receptor–ligand interactions on a genome-wide scale.

Sun, Yi; Gallagher-Jones, Marcus; Barker, Colin; Wright, Gavin J.

2012-01-01

343

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

344

An identification procedure for foodborne microbial hazards  

Microsoft Academic Search

A stepwise and interactive identification procedure for foodborne microbial hazards has been developed in which use is made of several levels of detail ranging from rough hazard identification to comprehensive hazard identification. This approach allows one to tackle the most obvious hazards first, before focusing on less obvious hazards. The interactive character of the identification procedure is based on the

Gerwen van S. J. C; Wit de J. C; S. Notermans; M. H. Zwietering

1997-01-01

345

Identification of key amino acids responsible for the substantially higher affinities of human type 1 3beta-hydroxysteroid dehydrogenase/isomerase (3beta-HSD1) for substrates, coenzymes, and inhibitors relative to human 3beta-HSD2.  

PubMed

The human type 1 (placenta, breast tumors, and prostate tumors) and type 2 (adrenals and gonads) isoforms of 3beta-hydroxysteroid dehydrogenase/isomerase (3beta-HSD1 and 3beta-HSD2) are encoded by two distinct genes that are expressed in a tissue-specific pattern. Our recent studies have shown that His156 contributes to the 14-fold higher affinity that 3beta-HSD1 exhibits for substrate and inhibitor steroids compared with human 3beta-HSD2 containing Tyr156 in the otherwise identical catalytic domain. Our structural model of human 3beta-HSD localizes His156 or Tyr156 in the subunit interface of the enzyme homodimer. The model predicts that Gln105 on one enzyme subunit has a higher probability of interacting with His156 on the other subunit in 3beta-HSD1 than with Tyr156 in 3beta-HSD2. The Q105M mutant of 3beta-HSD1 (Q105M1) shifts the Michaelis-Menten constant (Km) for 3beta-HSD substrate and inhibition constants (Ki) for epostane and trilostane to the much lower affinity profiles measured for wild-type 3beta-HSD2 and H156Y1. However, the Q105M2 mutant retains substrate and inhibitor kinetic profiles similar to those of 3beta-HSD2. Our model also predicts that Gln240 in 3beta-HSD1 and Arg240 in 3beta-HSD2 may be responsible for the 3-fold higher affinity of the type 1 isomerase activity for substrate steroid and cofactors. The Q240R1 mutation increases the isomerase substrate Km by 2.2-fold to a value similar to that of 3beta-HSD2 isomerase and abolishes the allosteric activation of isomerase by NADH. The R240Q2 mutation converts the isomerase substrate, cofactor, and inhibitor kinetic profiles to the 4-14-fold higher affinity profiles of 3beta-HSD1. Thus, key structural reasons for the substantially higher affinities of 3beta-HSD1 for substrates, coenzymes, and inhibitors have been identified. These structure and function relationships can be used in future docking studies to design better inhibitors of the 3beta-HSD1 that may be useful in the treatment of hormone-sensitive cancers and preterm labor. PMID:15797861

Thomas, James L; Boswell, Elizabeth L; Scaccia, Launa A; Pletnev, Vladimir; Umland, Timothy C

2005-03-28

346

IDENTIFICATION OF KEY AMINO ACIDS RESPONSIBLE FOR THE SUBSTANTIALLY HIGHER AFFINITIES OF HUMAN TYPE 1 3?-HYDROXYSTEROID DEHYDROGENASE/ISOMERASE (3?-HSD1) FOR SUBSTRATES, COENZYMES AND INHIBITORS RELATIVE TO HUMAN 3?-HSD2*  

PubMed Central

The human type 1 (placenta, breast tumors, prostate tumors) and type 2 (adrenals, gonads) isoforms of 3?-hydroxysteroid dehydrogenase/isomerase (3?-HSD1 and 3?-HSD2) are encoded by two distinct genes that are expressed in a tissue-specific pattern. Our recent studies have shown that His156 contributes to the 14-fold higher affinity that 3?-HSD1 exhibits for substrate and inhibitor steroids compared to human 3?-HSD2 containing Tyr156 in the otherwise identical catalytic domain. Our structural model of human 3?-HSD localizes His156 or Tyr156 in the subunit interface of the enzyme homodimer. The model predicts that Gln105 on one enzyme subunit has a higher probability of interacting with His156 on the other subunit in 3?-HSD1 than with Tyr156 in 3?-HSD2. The Q105M mutant of 3?-HSD1 (Q105M1) shifts the Michaelis-Menten constant (Km) for 3?-HSD substrate and inhibition constants (Ki) for epostane and trilostane to the much lower affinity profiles measured for wild-type 3?-HSD2 and H156Y1. However, the Q105M2 mutant retains substrate and inhibitor kinetic profiles similar to those of 3?-HSD2. Our model also predicts that Gln240 in 3?-HSD1 and Arg240 in 3?-HSD2 may be responsible for the 3-fold higher affinity of the type 1 isomerase activity for substrate steroid and cofactors. The Q240R1 mutation increases the isomerase substrate Km by 2.2-fold to a value similar to that of 3?-HSD2 isomerase and abolishes the allosteric activation of isomerase by NADH. The R240Q2 mutation converts the isomerase substrate, cofactor and inhibitor kinetic profiles to the 4- to 14-fold higher affinity profiles of 3?-HSD1. Thus, key structural reasons for the substantially higher affinities of 3?-HSD1 for substrates, coenzymes and inhibitors have been identified. These structure and function relationships can be used in future docking studies to design better inhibitors of the 3?-HSD1 that may be useful in the treatment hormone-sensitive cancers and preterm labor.

Thomas, James L.; Boswell, Elizabeth L.; Scaccia, Launa A.; Pletnev, Vladimir; Umland, Timothy C.

2005-01-01

347

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

348

The Key to Security.  

ERIC Educational Resources Information Center

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

Kennedy, Mike

2001-01-01

349

Keys for XML  

Microsoft Academic Search

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

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

2001-01-01

350

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

PubMed Central

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

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

2010-01-01

351

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

2010-03-17

352

Keys to Scholarship  

ERIC Educational Resources Information Center

Up ahead, a foreboding wooden door showing wear from passage of earlier travelers is spotted. As the old porch light emits a pale yellow glow, a key ring emerges from deep inside the coat pocket. Searching for just the right key, the voyager settles on one that also shows age. As the key enters its receptacle and begins to turn, a clicking noise…

Hebert, Terri

2011-01-01

353

Work Keys USA.  

ERIC Educational Resources Information Center

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

Work Keys USA, 1998

1998-01-01

354

Dynamic key for encryption  

Microsoft Academic Search

In this paper proposed a new secret-key block cipher method, in the proposed method, the plaintext and the ciphertext are 33152 bit blocks or multiple of 33152. The ciphertext are 33152 bit blocks or multiple of 33152. The secret key is dynamic key with 33152 bit long or multiple of 33152. The proposed method is combine of RSA, DES, TowFish,

M. S. Al Rababaa; M. A. Al Rababah

2009-01-01

355

Certificateless Public Key Cryptography  

Microsoft Academic Search

This paper introduces and makes concrete the concept of certiflcateless public key cryptography (CL-PKC), a model for the use of public key cryp- tography which avoids the inherent escrow of identity-based cryptography and yet which does not require certiflcates to guarantee the authenticity of public keys. The lack of certiflcates and the presence of an adversary who has access to

Sattam S. Al-riyami; Kenneth G. Paterson

2003-01-01

356

Keys to Scholarship  

ERIC Educational Resources Information Center

|Up ahead, a foreboding wooden door showing wear from passage of earlier travelers is spotted. As the old porch light emits a pale yellow glow, a key ring emerges from deep inside the coat pocket. Searching for just the right key, the voyager settles on one that also shows age. As the key enters its receptacle and begins to turn, a clicking noise…

Hebert, Terri

2011-01-01

357

Identification of transcriptional and phosphatase regulators as interaction partners of human ADA3, a component of histone acetyltransferase complexes.  

PubMed

ADA (alteration/deficiency in activation) 3 is a conserved component of several transcriptional adaptor and HAT (histone acetyltransferase) complexes that regulate RNA polymerase II-mediated gene expression. Within the HAT complexes ADA3 is associated with ADA2 and the HAT GCN5 (general control non-repressed 5). ADA3 plays roles in diverse cellular processes and also in malignancies by modulating GCN5 catalytic activity and/or by interactions with other regulators. To gain a better understanding of ADA3 function, we used a yeast two-hybrid approach to screen a human fetal cDNA library for proteins that interacted with hADA3 (human ADA3). We identified three novel hADA3-interacting partners, a transcriptional regulator, AATF (apoptosis-antagonizing transcription factor), and regulatory subunits of the PP1 (protein phosphatase 1) and PP2A (protein phosphatase 2A) [PPP1R7 (PP1 regulatory subunit 7) and PPP2R5D (PP2A 56 kDa regulatory subunit ? isoform) respectively]. Analysis of truncated versions of hADA3 indicated that the C-terminal ADA2-interacting domain was not required for these interactions. Fluorescent microscopy analysis and co-immunoprecipitation provided support for the co-localization and interaction of hADA3 with these proteins in human cells. Expression of the interacting proteins altered expression of an hADA3-regulated reporter gene, suggesting functional consequences for the interactions. The detected interactions of hADA3 might extend the spectrum of mechanisms by which ADA3 can contribute to the regulation of gene expression and shed light on processes mediated by these newly identified ADA3 partners. PMID:23167988

Zencir, Sevil; Sike, Adam; Dobson, Melanie J; Ayaydin, Ferhan; Boros, Imre; Topcu, Zeki

2013-03-01

358

Identification of protein-protein interaction inhibitors targeting vaccinia virus processivity factor for development of antiviral agents.  

PubMed

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

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

2011-08-15

359

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

PubMed Central

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

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

2011-01-01

360

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

361

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

PubMed Central

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

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

2012-01-01

362

Identification of a regulatory motif in Hsp70 that affects ATPase activity, substrate binding and interaction with HDJ-1.  

PubMed Central

The Hsp70 family of molecular chaperones has an essential role in the synthesis, folding and translocation of the nascent peptide chain. While the general features of these activities are well documented, less is understood about the regulation of these activities. The ATPase rate is stimulated by non-native proteins, furthermore, interaction with ATP leads to the release of protein substrate concurrent with a conformational change in Hsp70. One interpretation of these data is that the two domains of Hsp70 interact. In the process of mapping the carboxyl-terminal boundary of the substrate binding domain for human Hsp70, we identified a regulatory motif, EEVD, which is conserved at the extreme carboxyl terminus among nearly all cloned cytosolic eukaryotic Hsp70s. Deletion or mutation of EEVD affects the ATPase activity, the ability to interact with substrates, and interferes with the ability of the mutant Hsp70 to interact with HDJ-1 in the refolding of denatured firefly luciferase. Examination of the biophysical properties of the mutant Hsp70s reveals a change in the overall shape and conformation of the protein consistent with reduced interactions between the two domains. These data suggest that the EEVD motif is involved in the intramolecular regulation of Hsp70 function and intermolecular interactions with HDJ-1. Images

Freeman, B C; Myers, M P; Schumacher, R; Morimoto, R I

1995-01-01

363

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.

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

2012-01-01

364

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

2013-05-13

365

Identification of the tri-Al tricitrate complex in Plantago almogravensis by hydrophilic interaction LC with parallel ICP-MS and electrospray Orbitrap MS/MS detection.  

PubMed

The identification of the ligands binding Al is essential to understand the mechanisms by which plants detoxify Al internally. However, studies concerning the speciation of Al have been frustrated by its complex chemistry. This work describes the identification of the tri-Al tricitrate (Al3cit3) complex in Plantago almogravensis, encompassing an integrated mass spectrometry approach based on hydrophilic interaction liquid chromatography (HILIC) and parallel detection by ICP-MS and ESI-MS/MS. This work also reports that both Al and Fe are bound by tricitrate, sometimes simultaneously, and the consequences of this finding are discussed. Of the complexes separated by size exclusion chromatography, Al3cit3 is the most stable occurring in P. almogravensis as it was the only one recovered after HILIC. This approach provided new information on the mechanism of Al detoxification in P. almogravensis, namely that Al is bound by the organic acid citrate and that the relative concentration of the detected complexes is affected by the organ type and internal Al concentration, and has potential for studying the speciation of Al in less tolerant plants. PMID:23877102

Grevenstuk, Tomás; Flis, Paulina; Ouerdane, Laurent; Lobinski, Ryszard; Romano, Anabela

2013-09-01

366

Key Features of Successful Programs for the Gifted and Talented.  

ERIC Educational Resources Information Center

The Enrichment Triad Model (Triad) and the Revolving Door Identification model (RDIM) form the TRIAD/RDIM program model for gifted and talented students. The article outlines the key features of the program. (MD)

Reis, Sally M.; Renzulli, Joseph S.

1984-01-01

367

Excitation by flows in seals and clearances. Part 1: Introduction: Fluid-structure-interactions in rotordynamics. Part 2: Identification of rotordynamic coefficients of annular seals  

NASA Astrophysics Data System (ADS)

The fluid-structure interactions in rotor dynamics and the identification of rotor dynamic coefficients of annular seals are studied. The different fluid forces acting in the neck ring, the interstage seals, the balance pistons, the impellers and the oil film bearings of pumps are reviewed. These forces can have a large influence on the bending vibrations of a pump rotor. Theoretical and experimental models of fluid elements and of rotordynamics are presented. Simulations of the rotordynamic behavior show that the fluid forces of most elements can be described by linear-force relations. A theoretical model and an indentification procedure are presented to determine the dynamic coefficients of seals. The identified parameters confirm the assumptions in modeling and point out that the stiffness and damping characteristics of seals are significant for the stability behavior of pumps.

Nordmann, R.

368

Finding the maximum a posteriori probability (MAP) in a Bayesian taxonomic key is NP-hard  

Microsoft Academic Search

As an alternative to dichotomous keys, tabular keys are used for taxonomic identification. With the use of computers, keys based on the Bayes formula can also be made available more widely. For the development of a key, the maximum a posterior probability (MAP) for a taxon is important because it allows to evaluate the quality of a key. If it

Urs Fischbacher

1996-01-01

369

Identification and analysis of stereoselective drug interactions with low-density lipoprotein by high-performance affinity chromatography.  

PubMed

Columns containing immobilized low-density lipoprotein (LDL) were prepared for the analysis of drug interactions with this agent by high-performance affinity chromatography (HPAC). R/S-Propranolol was used as a model drug for this study. The LDL columns gave reproducible binding to propranolol over 60 h of continuous use in the presence of pH 7.4 0.067 M potassium phosphate buffer. Experiments conducted with this type of column through frontal analysis indicated that two types of interactions were occurring between R-propranolol and LDL, while only a single type of interaction was observed between S-propranolol and LDL. The first type of interaction, which was seen for both enantiomers, involved non-saturable binding; this interaction had an overall affinity (nK(a)) of 1.9 (±0.1) × 10(5) M(-1) for R-propranolol and 2.7 (±0.2) × 10(5) M(-1) for S-propranolol at 37 °C. The second type of interaction was observed only for R-propranolol and involved saturable binding that had an association equilibrium constant (K(a)) of 5.2 (±2.3) × 10(5) M(-1) at 37 °C. Similar differences in binding behavior were found for the two enantiomers at 20 °C and 27 °C. This is the first known example of stereoselective binding of drugs by LDL or other lipoproteins. This work also illustrates the ability of HPAC to be used as a tool for characterizing mixed-mode interactions that involve LDL and related binding agents. PMID:22354572

Sobansky, Matthew R; Hage, David S

2012-02-22

370

Identification of novel protein-protein interactions of Yersinia pestis type III secretion system by yeast two hybrid system.  

PubMed

Type III secretion system (T3SS) of the plague bacterium Y. pestis encodes a syringe-like structure consisting of more than 20 proteins, which can inject virulence effectors into host cells to modulate the cellular functions. Here in this report, interactions among the possible components in T3SS of Yersinia pestis were identified using yeast mating technique. A total of 57 genes, including all the pCD1-encoded genes except those involved in plasmid replication and partition, pseudogenes, and the putative transposase genes, were subjected to yeast mating analysis. 21 pairs of interaction proteins were identified, among which 9 pairs had been previously reported and 12 novel pairs were identified in this study. Six of them were tested by GST pull down assay, and interaction pairs of YscG-SycD, YscG-TyeA, YscI-YscF, and YopN-YpCD1.09c were successfully validated, suggesting that these interactions might play potential roles in function of Yersinia T3SS. Several potential new interactions among T3SS components could help to understand the assembly and regulation of Yersinia T3SS. PMID:23349800

Yang, Huiying; Tan, Yafang; Zhang, Tingting; Tang, Liujun; Wang, Jian; Ke, Yuehua; Guo, Zhaobiao; Yang, Xiaoming; Yang, Ruifu; Du, Zongmin

2013-01-22

371

Establishment of a robust dengue virus NS3-NS5 binding assay for identification of protein-protein interaction inhibitors.  

PubMed

Whereas the dengue virus (DENV) non-structural (NS) proteins NS3 and NS5 have been shown to interact in vitro and in vivo, the biological relevance of this interaction in viral replication has not been fully clarified. Here, we first applied a simple and robust in vitro assay based on AlphaScreen technology in combination with the wheat-germ cell-free protein production system to detect the DENV-2 NS3-NS5 interaction in a 384-well plate. The cell-free-synthesized NS3 and NS5 recombinant proteins were soluble and in possession of their respective enzymatic activities in vitro. In addition, AlphaScreen assays using the recombinant proteins detected a specific interaction between NS3 and NS5 with a robust Z' factor of 0.71. By employing the AlphaScreen assay, we found that both the N-terminal protease and C-terminal helicase domains of NS3 are required for its association with NS5. Furthermore, a competition assay revealed that the binding of full-length NS3 to NS5 was significantly inhibited by the addition of an excess of NS3 protease or helicase domains. Our results demonstrate that the AlphaScreen assay can be used to discover novel antiviral agents targeting the interactions between DENV NS proteins. PMID:23072882

Takahashi, Hirotaka; Takahashi, Chikako; Moreland, Nicole J; Chang, Young-Tae; Sawasaki, Tatsuya; Ryo, Akihide; Vasudevan, Subhash G; Suzuki, Youichi; Yamamoto, Naoki

2012-10-13

372

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

PubMed

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 Thermotoga 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 form pseudo 6-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 (accompanying paper Piasta et al. (2013) Biochemistry, DOI: 10.1021/bi400385c) 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

2013-05-23

373

Identification and localization of the sperm CRISP family protein CiUrabin involved in gamete interaction in the ascidian Ciona intestinalis.  

PubMed

Ascidians are hermaphrodites, and most release sperm and eggs nearly simultaneously. Many species, including Halocynthia roretzi and Ciona intestinalis, are self-sterile. We previously reported that the interaction between a 12 EGF-like repeat-containing vitelline-coat (VC) protein, HrVC70, and a sperm GPI-anchored CRISP, HrUrabin, in lipid rafts plays a key role in self-/nonself-recognizable gamete interaction in H. roretzi. On the other hand, we recently identified two pairs of polymorphic genes responsible for self-incompatibility in C. intestinalis by positional cloning: The sperm polycystin 1-like receptors s-Themis-A/B and its fibrinogen-like ligand v-Themis-A/B on the VC. However, it is not known if the orthologs of HrVC70 and HrUrabin also participate in gamete interaction in C. intestinalis since they are from different orders. Here, we tested for a C. intestinalis ortholog (CiUrabin) of HrUrabin by searching the genome database and proteomes of sperm lipid rafts. The identified CiUrabin belongs to the CRISP family, with a PR domain and a GPI-anchor-attachment site. CiUrabin appears to be specifically expressed in the testis and localized at the surface of the sperm head, as revealed by Northern blotting and immunocytochemistry, respectively. The specific interaction between CiVC57, a C. intestinalis ortholog of HrVC70, and CiUrabin was confirmed by Far Western analysis, similarly to the interaction between HrVC70 and HrUrabin. The molecular interaction between CiVC57 and CiUrabin may be involved in the primary binding of sperm to the VC prior to the allorecognition process, mediated by v-Themis-A/B and s-Themis-A/B, during fertilization of C. intestinalis. PMID:21656869

Yamaguchi, Akira; Saito, Takako; Yamada, Lixy; Taniguchi, Hisaaki; Harada, Yoshito; Sawada, Hitoshi

2011-06-08

374

Identification and Characterization of the RLIP/RALBP1 Interacting Protein Xreps1 in Xenopus laevis Early Development  

PubMed Central

Background The FGF/Ras/Ral/RLIP pathway is required for the gastrulation process during the early development of vertebrates. The Ral Interacting Protein (RLIP also known as RalBP1) interacts with GTP-bound Ral proteins. RLIP/RalBP1 is a modular protein capable of participating in many cellular functions. Methodology/Principal Findings To investigate the role of RLIP in early development, a two-hybrid screening using a library of maternal cDNAs of the amphibian Xenopus laevis was performed. Xreps1 was isolated as a partner of RLIP/RalBP1 and its function was studied. The mutual interacting domains of Xreps1 and Xenopus RLIP (XRLIP) were identified. Xreps1 expressed in vivo, or synthesized in vitro, interacts with in vitro expressed XRLIP. Interestingly, targeting of Xreps1 or the Xreps1-binding domain of XRLIP (XRLIP(469–636)) to the plasma membrane through their fusion to the CAAX sequence induces a hyperpigmentation phenotype of the embryo. This hyperpigmented phenotype induced by XRLIP(469–636)-CAAX can be rescued by co-expression of a deletion mutant of Xreps1 restricted to the RLIP-binding domain (Xreps1(RLIP-BD)) but not by co-expression of a cDNA coding for a longer form of Xreps1. Conclusion/Significance We demonstrate here that RLIP/RalBP1, an effector of Ral involved in receptor-mediated endocytosis and in the regulation of actin dynamics during embryonic development, also interacts with Reps1. Although these two proteins are present early during embryonic development, they are active only at the end of gastrulation. Our results suggest that the interaction between RLIP and Reps1 is negatively controlled during the cleavage stage of development, which is characterized by rapid mitosis. Later in development, Reps1 is required for the normal function of the ectodermic cell, and its targeting into the plasma membrane affects the stability of the ectoderm.

Boissel, Laurent; Fillatre, Jonathan; Moreau, Jacques

2012-01-01

375

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

PubMed

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

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

2013-03-28

376

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

377

Deniable Group Key Agreement  

Microsoft Academic Search

Especially for key establishment protocols to be used in internet applications, the (privacy) concern of deniability arises: Can a protocol transcript be used—possibly by a participant—to prove the involvement of another party in the protocol?\\u000a For two party key establishment protocols, a common technique for achieving deniability is the replacement of signature-based\\u000a message authentication with authentication based on symmetric keys.

Jens-Matthias Bohli; Rainer Steinwandt

378

Identification of Factor Xa Residues Critical for Interaction with Protein Z-dependent Protease Inhibitor: Both Active-site and Exosite Interactions Are Required for Inhibition  

PubMed Central

Protein Z-dependent protease inhibitor (ZPI) is a plasma serpin which can rapidly inactivate factor Xa (fXa) in the presence of protein Z (PZ), negatively charged phospholipids and Ca2+. To investigate the mechanism by which ZPI inactivates fXa, we expressed the serpin in mammalian cells and characterized its reactivity with both wild-type and selected mutants of fXa which 1) contained substitutions in the autolysis loop and the heparin-binding exosite, 2) lacked the first EGF-like domain (fXa-des-EGF-1), or 3) contained the Gla domain of protein C (fXa/PC-Gla). Inhibition studies in both the presence and absence of PZ revealed that Arg-143, Lys-147 and Arg-154 of the autolysis loop and Lys-96, Lys-169 and Lys-236 of the heparin-binding exosite are required for recognition of ZPI, with Arg-143 being essential for the interaction. Similar studies with fXa-des-EGF-1 and fXa/PC-Gla suggested that protein-protein interaction with either the Gla or the EGF-1 domain may not play a dominant role in the PZ-dependent recognition of fXa by the serpin on phospholipid vesicles. Further studies showed that an inactive Ser-195 to Ala mutant of fXa effectively competes with wild-type fXa for binding to the non-serpin inhibitors, tissue factor pathway inhibitor and recombinant tick anticoagulant peptide, but does not compete for binding to ZPI. This suggests that the catalytic residue of fXa is required for interaction with ZPI.

Manithody, Chandrashekhara; Yang, Likui

2005-01-01

379

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.

Banerjee, Jayashree; Wedegaertner, Philip B.

2004-01-01

380

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

381

Gas chromatographic method of identification of n-aliphatic amines through the use of donor-acceptor interaction with phosphate  

Microsoft Academic Search

It has been found that sodium triphosphate can be used successfully instead of an alkali for the modification of a support in the gas chromatographic analysis of amines. A possible mechanism explaining the interaction of the salt with amines is discussed. The chromatographic behavior of primary, secondary and tertiary n-aliphatic amines for four columns prepared with the following liquid phases:

R. V. Golovnya; I. L. Zhuravleva

1973-01-01

382

Male Phyllotreta striolata (F.) Produce an Aggregation Pheromone: Identification of Male-specific compounds and Interaction with Host Plant Volatiles  

Microsoft Academic Search

The chrysomelid beetle Phyllotreta striolata is an important pest of Brassicaceae in Southeast Asia and North America. Here, we identified the aggregation pheromone of\\u000a a population of P. striolata from Taiwan, and host plant volatiles that interact with the pheromone. Volatiles emitted by feeding male P. striolata attracted males and females in the field. Headspace volatile analyses revealed that six

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

2011-01-01

383

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

PubMed Central

AvrRxv is a member of a family of pathogen effectors present in pathogens of both plant and mammalian species. Xanthomonas campestris pv. vesicatoria strains carrying AvrRxv induce a hypersensitive response (HR) in the tomato cultivar Hawaii 7998. Using a yeast two-hybrid screen, we identified a 14-3-3 protein from tomato that interacts with AvrRxv called AvrRxv Interactor 1 (ARI1). The interaction was confirmed in vitro with affinity chromatography. Using mutagenesis, we identified a 14-3-3-binding domain in AvrRxv and demonstrated that a mutant in that domain showed concomitant loss of interaction with ARI1 and HR-inducing activity in tomato. These results demonstrate that the AvrRxv bacterial effector recruits 14-3-3 proteins for its function within host cells. AvrRxv homologues YopP and YopJ from Yersinia do not have AvrRxv-specific HR-inducing activity when delivered into tomato host cells by Agrobacterium. Although YopP itself cannot induce HR, its C-terminal domain containing the catalytic residues can replace that of AvrRxv in an AvrRxv-YopP chimera for HR-inducing activity. Phylogenetic analysis indicates that the sequences encoding the C-termini of family members are evolving independently from those encoding the N-termini. Our results support a model in which there are three functional domains in proteins of the family, translocation, interaction, and catalytic.

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

2009-01-01

384

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

PubMed

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

Holcroft, James; Ganss, Bernhard

2011-12-01

385

Identification of the amino acid region involved in the intercellular interaction between the ?1 subunits of Na+/K+-ATPase  

PubMed Central

Epithelial junctions depend on intercellular interactions between ?1 subunits of the Na+/K+-ATPase molecules of neighboring cells. The interaction between dog and rat subunits is less effective than the interaction between two dog ?1 subunits, indicating the importance of species-specific regions for ?1–?1 binding. To identify these regions, the species-specific amino acid residues were mapped on a high-resolution structure of the Na+/K+-ATPase ?1 subunit to select those exposed towards the ?1 subunit of the neighboring cell. These exposed residues were mutated in both dog and rat YFP-linked ?1 subunits (YFP–?1) and also in the secreted extracellular domain of the dog ?1 subunit. Five rat-like mutations in the amino acid region spanning residues 198–207 of the dog YFP–?1 expressed in Madin–Darby canine kidney (MDCK) cells decreased co-precipitation of the endogenous dog ?1 subunit with YFP–?1 to the level observed between dog ?1 and rat YFP–?1. In parallel, these mutations impaired the recognition of YFP–?1 by the dog-specific antibody that inhibits cell adhesion between MDCK cells. Accordingly, dog-like mutations in rat YFP–?1 increased both the (YFP–?1)–?1 interaction in MDCK cells and recognition by the antibody. Conversely, rat-like mutations in the secreted extracellular domain of the dog ?1 subunit increased its interaction with rat YFP–?1 in vitro. In addition, these mutations resulted in a reduction of intercellular adhesion between rat lung epithelial cells following addition of the secreted extracellular domain of the dog ?1 subunit to a cell suspension. Therefore, the amino acid region 198–207 is crucial for both trans-dimerization of the Na+/K+-ATPase ?1 subunits and cell–cell adhesion.

Tokhtaeva, Elmira; Sachs, George; Sun, Haiying; Dada, Laura A.; Sznajder, Jacob I.; Vagin, Olga

2012-01-01

386

Prediction of drug-target interaction networks from the integration of chemical and genomic spaces  

Microsoft Academic Search

Motivation: The identification of interactions between drugs and target proteins is a key area in genomic drug discovery. Therefore, there is a strong incentive to develop new methods capable of detecting these potential drug-target interactions efficiently. Results: In this article, we characterize four classes of drug-target interaction networks in humans involving enzymes, ion channels, G-protein-coupled receptors (GPCRs) and nuclear receptors,

Yoshihiro Yamanishi; Michihiro Araki; Alex Gutteridge; Wataru Honda; Minoru Kanehisa

2008-01-01

387

Identification of expressed genes during compatible interaction between stripe rust (Puccinia striiformis) and wheat using a cDNA library  

PubMed Central

Background Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat worldwide. To establish compatibility with the host, Pst forms special infection structures to invade the plant with minimal damage to host cells. Although compatible interaction between wheat and Pst has been studied using various approaches, research on molecular mechanisms of the interaction is limited. The aim of this study was to develop an EST database of wheat infected by Pst in order to determine transcription profiles of genes involved in compatible wheat-Pst interaction. Results Total RNA, extracted from susceptible infected wheat leaves harvested at 3, 5 and 8 days post inoculation (dpi), was used to create a cDNA library, from which 5,793 ESTs with high quality were obtained and clustered into 583 contigs and 2,160 singletons to give a set of 2,743 unisequences (GenBank accessions: GR302385 to GR305127). The BLASTx program was used to search for homologous genes of the unisequences in the GenBank non-redundant protein database. Of the 2,743 unisequences, 52.8% (the largest category) were highly homologous to plant genes; 16.3% to fungal genes and 30% of no-hit. The functional classification of all ESTs was established based on the database entry giving the best E-value using the Bevan's classification categories. About 50% of the ESTs were significantly homologous to genes encoding proteins with known functions; 20% were similar to genes encoding proteins with unknown functions and 30% did not have significant homology to any sequence in the database. The quantitative real-time PCR (qRT-PCR) analysis determined the transcription profiles and their involvement in the wheat-Pst interaction for seven of the gene. Conclusion The cDNA library is useful for identifying the functional genes involved in the wheat-Pst compatible interaction, and established a new database for studying Pst pathogenesis genes and wheat defense genes. The transcription patterns of seven genes were confirmed by the qRT-PCR assay to be differentially expressed in wheat-Pst compatible and incompatible interaction.

2009-01-01

388

Identification of Proteins That Interact with Exon Sequences, Splice Sites, and the Branchpoint Sequence during Each Stage of Spliceosome Assembly  

Microsoft Academic Search

We have carried out a systematic analysis of the proteins that interact with specific intron and exon sequences during each stage of mammalian spliceosome assembly. This was achieved by site-specifically labeling individual nucleotides within the 5*and 3*splice sites, the branchpoint sequence (BPS), or the exons with 32 P and identifying UV-cross-linked proteins in the E, A, B, or C spliceosomal

MARIA DOLORES CHIARA; MARIA BENNETT; PATRICK CHAMPION-ARNAUD; LEON PALANDJIAN; ANDROBIN REED

1996-01-01

389

Identification of a novel BTB-zinc finger transcriptional repressor, CIBZ, that interacts with CtBP corepressor  

Microsoft Academic Search

The transcriptional corepressor C-terminal binding protein (CtBP) is thought to be involved in development and oncogenesis, but the regulation of its corepressor activity is largely unknown. We show here that a novel BTB-zinc finger protein, CIBZ (CtBP-interacting BTB zinc finger protein; a mouse ortholog of rat ZENON that was recently identified as an e-box\\/dyad binding protein), redistributes CtBP to pericentromeric

Nobuhiro Sasai; Eishou Matsuda; Emiko Sarashina; Yasumasa Ishida; Masashi Kawaichi

2005-01-01

390

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

PubMed

AvrRxv is a member of a family of pathogen effectors present in pathogens of both plant and mammalian species. Xanthomonas campestris pv. vesicatoria strains carrying AvrRxv induce a hypersensitive response (HR) in the tomato cultivar Hawaii 7998. Using a yeast two-hybrid screen, we identified a 14-3-3 protein from tomato that interacts with AvrRxv called AvrRxv Interactor 1 (ARI1). The interaction was confirmed in vitro with affinity chromatography. Using mutagenesis, we identified a 14-3-3-binding domain in AvrRxv and demonstrated that a mutant in that domain showed concomitant loss of interaction with ARI1 and HR-inducing activity in tomato. These results demonstrate that the AvrRxv bacterial effector recruits 14-3-3 proteins for its function within host cells. AvrRxv homologues YopP and YopJ from Yersinia do not have AvrRxv-specific HR-inducing activity when delivered into tomato host cells by Agrobacterium. Although YopP itself cannot induce HR, its C-terminal domain containing the catalytic residues can replace that of AvrRxv in an AvrRxv-YopP chimera for HR-inducing activity. Phylogenetic analysis indicates that the sequences encoding the C-termini of family members are evolving independently from those encoding the N-termini. Our results support a model in which there are three functional domains in proteins of the family, translocation, interaction, and catalytic. PMID:21796232

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

2008-01-01

391

An on-bead assay for the identification of non-natural peptides targeting the Androgen Receptor–cofactor interaction  

Microsoft Academic Search

An efficient and rapid on-bead screening method was established to identify non-natural peptides that target the Androgen Receptor–cofactor interaction. Binding of the Androgen Receptor ligand binding domain to peptide sequences displayed on beads in a One-Bead-One-Compound format could be screened using fluorescence microscopy. The method was applied to generate and screen both a focussed and a random peptide library. Resynthesis

Hülya Göksel; Dorothee Wasserberg; Sabine Möcklinghoff; Belen Vaz Araujo; Luc Brunsveld

2011-01-01

392

Identification of 14-3-3? as a Mieap-interacting protein and its role in mitochondrial quality control  

PubMed Central

Mieap, a p53-inducible protein, controls mitochondrial integrity by inducing the accumulation of lysosomal proteins within mitochondria. This phenomenon is designated MALM, for Mieap-induced accumulation of lysosome-like organelles within mitochondria. To identify this novel Mieap-interacting protein(s), we performed a two-dimensional image-converted analysis of liquid chromatography and mass spectrometry (2DICAL) on the proteins immunoprecipitated by an anti-Mieap antibody. We indentified 14-3-3? as one of the proteins that was included in the Mieap-binding protein complex when MALM was induced. The interaction between Mieap and 14-3-3? was confirmed on the exogenous and endogenous proteins. Interestingly, 14-3-3? was localized within mitochondria when MALM occurred. A 14-3-3? deficiency did not affect the accumulation of Mieap and lysosomal proteins within mitochondria, but dramatically inhibited the elimination of oxidized mitochondrial proteins. These results suggest that 14-3-3? plays a critical role in eliminating oxidized mitochondrial proteins during the MALM process by interacting with Mieap within mitochondria.

Miyamoto, Takafumi; Kitamura, Noriaki; Ono, Masaya; Nakamura, Yasuyuki; Yoshida, Masaki; Kamino, Hiroki; Murai, Ryuya; Yamada, Tesshi; Arakawa, Hirofumi

2012-01-01

393

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.

Koutras, Carolina; Levesque, Georges

2011-01-01

394

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

2011-10-14

395

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

2013-03-11

396

Identification of the polypeptide chains in Torpedo californica electroplax membranes that interact with a local anesthetic analog.  

PubMed Central

Procaine amide azide, a derivative of the local anesthetic procaine amide, was prepared and its interactions with acetylcholine receptor-rich membrane fragments from Torpedo californica electroplax were studied. Procaine amide azide was radiolabeled by a method that may be of general use for the preparation of other radioactive tertiary amines. When low concentrations of 3H-labeled procaine amide azide were photolyzed in the presence of receptor-rich membrane preparations, a simple pattern of incorporated radioactivity was seen after electrophoresis on sodium dodecyl sulfate/polyacrylamide gels. Only two major labeled bands were seen, corresponding to apparent Mr of about 43,000 and 90,000. When the length of the gels was increased, the labeled band of lower Mr was resolved into two labeled proteins, one major and one minor, with apparent Mr of 43,000 and 40,000, respectively. The radioactivity incorporated into the protein of Mr 40,000 could be attributed to interaction of [3H]procaine amide azide with cholinergic ligand-binding sites, whereas labeling of the polypeptide of Mr 43,000 appears to represent interaction of the photolabile derivative with another class of sites. The labeling component of 90,000 Mr could be removed by preparation of membrane fragments in iodoacetamide-containing buffer and therefore appeared unrelated to the acetylcholine receptor. Images

Blanchard, S G; Raftery, M A

1979-01-01

397

Identification and characterization of Alix/AIP1 interacting proteins from the black tiger shrimp, Penaeus monodon.  

PubMed

Apoptosis is proposed to be a major cause of death in shrimp viral infections. From our previous study, an apoptosis-related gene, Pm-Alix, was identified from the black tiger shrimp. Its expression was high in defence-related tissues including haemocytes and the lymphoid organ. To clarify its possible role in shrimp, we used Pm-Alix as bait in a yeast two-hybrid analysis to search for Alix interacting proteins in shrimp. Two cDNA sequences discovered had homology to a predicted ubiquitin C of the purple sea urchin, Strongylocentrotus purpuratus, and to a guanylyl cyclase of the red swamp crayfish, Procambarus clarkii. In vitro pull-down assays confirmed positive interaction between Pm-Alix and both proteins. Tissue distribution analysis revealed that Pm-Alix and the two binding partners were widely expressed in various tissues but more highly expressed in haemocytes. However, no significant positive or negative correlation was found in the expression of these genes as shrimp approached morbidity and death after challenge with white spot syndrome virus. Thus, the results suggested that Alix and its interacting partners did not play a direct role related to shrimp death. PMID:20412359

Sangsuriya, P; Rojtinnakorn, J; Senapin, S; Flegel, T W

2010-04-14

398

Identification of hemagglutinin structural domain and polymorphisms which may modulate swine H1N1 interactions with human receptor  

PubMed Central

Background The novel A/H1N1 influenza virus, which recently emerged in North America is most closely related to North American H1N1/N2 swine viruses. Until the beginning of 2009, North American swine H1N1/N2 viruses have only sporadically infected humans as dead-end hosts. In 2009 the A/H1N1 virus acquired the capacity to spread efficiently by human to human transmission. The novel A/H1N1 influenza virus has struck thousands of people in more than 70 countries and killed more than 140, representing a public health emergency of international concern. Here we have studied properties of hemagglutinin of A/H1N1 which may modulate virus/receptor interaction. Results Analyses by ISM bioinformatics platform of the HA1 protein of North American swine H1N1/N2 viruses and the new A/H1N1 showed that both groups of viruses differed in conserved characteristics that reflect a distinct propensity of these viruses to undergo a specific interaction with swine or human host proteins or receptors. Swine H1N1/N2 viruses that sporadically infected humans featured both the swine and the human interaction pattern. Substitutions F71S, T128S, E302K, M314L in HA1 of swine H1N1 viruses from North America are identified as critical for the human interaction pattern of A/H1N1 and residues D94, D196 and D274 are predicted to be "hot-spots" for polymorphisms which could increase infectivity of A/H1N1 virus. At least one of these residues has already emerged in the A/H1N1 isolates from Spain, Italy and USA. The domain 286-326 was identified to be involved in virus/receptor interaction. Conclusion Our results (i) contribute to better understanding of the origin of the novel A/H1N1 influenza virus, (ii) provide a tool for monitoring its molecular evolution (iii) predicts hotspots associated with enhanced infectivity in humans and (iv) identify therapeutic and diagnostic targets for prevention and treatment of A/H1N1 infection.

Veljkovic, Veljko; Niman, Henry L; Glisic, Sanja; Veljkovic, Nevena; Perovic, Vladimir; Muller, Claude P

2009-01-01

399

A key to the genera of medically important fungi  

Microsoft Academic Search

A simplified method for the rapid identification of medically important fungi is presented in the form of a dichotomous key. By noting the presence or absence of diagnostic features, one can effectively use the key to separate medically important fungi from other fungi. An unfamiliar fungus of medical importance in tissue or culture can be identified to genus within minutes

Michael R. McGinnis; Anthony E. Hilger

1971-01-01

400

Key Sectors: A New Proposal from Network Theory  

Microsoft Academic Search

García Muñiz A. S., Morillas Raya A. and Ramos Carvajal C. Key sectors: a new proposal from network theory, Regional Studies. There is a long tradition of studies in the input–output field for determining key sectors. Their analysis allows the identification of those sectors that affect the demand and supply system greatly, therefore constituting the basis for the growth and

Ana Salomé García Muñiz; Antonio Morillas Raya; Carmen Ramos Carvajal

2008-01-01