A novel approach for the identification of protein–protein interaction with integral membrane proteins

Protein–protein interaction plays a major role in all biological processes. The currently available genetic methods such as the two-hybrid system and the protein recruitment system are relatively limited in their ability to identify interactions with integral membrane proteins. Here we describe the development of a reverse Ras recruitment system (reverse RRS), in which the bait used encodes a membrane protein. The bait is expressed in its natural environment, the membrane, whereas the protein partner (the prey) is fused to a cytoplasmic Ras mutant. Protein–protein interaction between the proteins encoded by the prey and the bait results in Ras membrane translocation and activation of a viability pathway in yeast. We devised the expression of the bait and prey proteins under the control of dual distinct inducible promoters, thus enabling a rapid selection of transformants in which growth is attributed solely to specific protein–protein interaction. The reverse RRS approach greatly extends the usefulness of the protein recruitment systems and the use of integral membrane proteins as baits. The system serves as an attractive approach to explore novel protein–protein interactions with high specificity and selectivity, where other methods fail.

A novel multiple affinity purification tag and its use in identification of proteins associated with a cyclin–CDK complex

A novel multiple affinity purification (MAFT) or tandem affinity purification (TAP) tag has been constructed. It consists of the calmodulin binding peptide, six histidine residues, and three copies of the hemagglutinin epitope. This ‘CHH’ MAFT tag allows two or three consecutive purification steps, giving high purity. Active Clb2–Cdc28 kinase complex was purified from yeast cells after inserting the CHH tag into Clb2. Associated proteins were identified using mass spectrometry. These included the known associated proteins Cdc28, Sic1 and Cks1. Several other proteins were found including the 70 kDa chaperone, Ssa1.

Breaksite batch mapping, a rapid method for assay and identification of DNA breaksites in mammalian cells

DNA breaks occur during many processes in mammalian cells, including recombination, repair, mutagenesis and apoptosis. Here we report a simple and rapid method for assaying DNA breaks and identifying DNA breaksites. Breaksites are first tagged and amplified by ligation-mediated PCR (LM-PCR), using nested PCR primers to increase the specificity and sensitivity of amplification. Breaksites are then mapped by batch sequencing LM-PCR products. This allows easy identification of multiple breaksites per reaction without tedious fractionation of PCR products by gel electrophoresis or cloning. Breaksite batch mapping requires little starting material and can be used to identify either single- or double-strand breaks.

Infrared identification of 2XMM J191043.4+091629.4

Context. We report the infrared identification of the X-ray source 2XMM J191043.4+091629.4, which was detected by XMM-Newton/EPIC in the vicinity of the Galactic supernova remnant W49B. Aims. The aim of this work is to establish the nature of the X-ray source 2XMM J191043.4+091629.4 studying both the infrared photometry and spectroscopy of the companion. Methods. We analysed UKIDSS images around the best position of the X-ray source and obtained spectra of the best candidate using NICS in the Telescopio Nazionale Galileo (TNG) 3.5-m telescope. We present photometric and spectroscopic TNG analyses of the infrared counterpart of the X-ray source, identifying emission lines in the K-band. The H-band spectra does not present any significant feature. Results. We have shown that the Brackett γ H i at 2.165 μm, and He i at 2.184 μm and at 2.058 μm are significantly present in the infrared spectrum. The CO bands are also absent from our spectrum. Based on these results and the X-ray characteristics of the source, we conclude that the infrared counterpart is an early B-type supergiant star with an E(B − V) = 7.6 ± 0.3 at a distance of 16.0 ± 0.5 kpc. This would be, therefore, the first high-mass X-ray binary in the Outer Arm at galactic longitudes of between 30° and 60°.

Identificación de minerales mediante difracción de rayos X utilizando bases de datos online de libre acceso

El artículo proporciona una metodología sencilla para la identificación de minerales mediante la técnica de difracción de rayos X de polvo utilizando bases de datos mineralógicos de libre acceso y online. Las bases de datos utilizadas son la base de datos mineralógicas webmineral y la base de datos de estructuras cristalinas de la American Mineralogist Crystal Structure Database, AMS. En el presente trabajo se han elaborado 3 actividades resueltas de estudios reales y en orden creciente de dificultad. Se ha pretendido hacer hincapié en puntos donde el profesor puede interactuar con el alumno y promover la capacidad de análisis, síntesis y razonamiento crítico del alumno ante un problema de investigación en geología. Finalmente se ha elaborado un Anexo donde se recogen recomendaciones para que el profesor desarrolle sus propias actividades.

Identification of Acremonium isolates from grapevines and evaluation of their antagonism towards Plasmopara viticola

Some endophytic fungal genera in Vitis vinifera, including Acremonium, have been reported as antagonists of Plasmopara viticola. Endophytic Acremonium isolates from an asymptomatic grapevine cultivar Inzolia from Italy were identified by morphological features and multigene phylogenies of ITS, 18S and 28S genes, and their intra-specific genomic diversity was analyzed by RAPD analysis. Culture filtrates (CFs) obtained from Acremonium isolates were tested in vitro for their inhibitory activity against the P. viticola sporangia germination. Among 94 isolates, 68 belonged to the Acremonium persicinum and 26 to the Acremonium sclerotigenum. RAPD analysis grouped the A. persicinum isolates into 15 clusters and defined 31 different strains. The A. sclerotigenum isolates, instead, were clustered into 22 groups and represented 25 strains. All A. persicinum CFs inhibited sporangia germination of P. viticola, while not all those of A. sclerotigenum had inhibitory effect. A different degree of inhibition was observed between strains of the same species, while some strains of different species showed identical inhibitory effect. No correlation was found between RAPD groups and inhibitory activity in both Acremonium species.

COMUNICAÇÃO MERCADOLÓGICA EM MÍDIAS SOCIAIS ONLINE ANÁLISES PARA RELACIONAMENTOS EM REDES VIRTUAIS

Com o propósito de incrementar suas campanhas mercadológicas, muitas organizações, recorrem às ferramentas de mídias sociais hospedadas na Internet. Com isso, procuram o aumento de produtividade com adoção de sistemas automatizados de reprodução de mensagens, ou mesmo de recursos de acesso direto, inserindo mensagens de caráter persuasivo nos fóruns de discussões em comunidades online. Uma certa falta de sensibilidade para com o trato comunicacional, num meio potencialmente promissor, mas que pede uma outra interpretação, para posterior ação. Frequentemente implica em uma possibilidade de reverberação indicando ser imprescindível maior atenção na elaboração e no direcionamento desses fluxos comunicacionais, acentuadamente os de propósitos persuasivos. Nesse sentido, o presente trabalho propõe o estudo de comunidades online nas quais possamos a partir da identificação dos fatores que levem à sua formação, analisar e interpretar sua estrutura e seus fluxos comunicacionais, tais que, indiquem seus elementos agregadores. Para tal, com os preceitos metodológicos observados, objetivou-se demonstrar que, com esses componentes, as análises podem ser desenvolvidas para melhor adequação de estratégias de relacionamentos, possibilitando ações inerentes ao processo comunicacional mercadológico com essas comunidades. A metodologia ora empregada envolveu análise estrutural da rede com aplicações de softwares como UCINET, integrado com NetDraw, e dos fluxos comunicacionais, que formaram o corpora, analisado com a suíte Wordsmith Tools. Uma rede formada em comunidade hospedada na ferramenta orkut, por meio da obtenção dos conteúdos de fóruns temáticos, forneceu o corpora para as análises lexicais. Os resultados obtidos puderam caracterizar, não só a própria existência da rede social, como as potencialidades de relacionamento, a partir de interpretações de fluxos dialógicos de seus elementos agregadores, por meio de recursos visuais (grafos), estatísticos e lexicais.

Word of mouth communication within online communities:conceptualizing the online social network

Word of mouth (WOM) communication is a major part of online consumer interactions, particularly within the environment of online communities. Nevertheless, existing (offline) theory may be inappropriate to describe online WOM and its influence on evaluation and purchase.The authors report the results of a two-stage study aimed at investigating online WOM: a set of in-depth qualitative interviews followed by a social network analysis of a single online community. Combined, the results provide strong evidence that individuals behave as if Web sites themselves are primary "actors" in online social networks and that online communities can act as a social proxy for individual identification. The authors offer a conceptualization of online social networks which takes the Web site into account as an actor, an initial exploration of the concept of a consumer-Web site relationship, and a conceptual model of the online interaction and information evaluation process. © 2007 Wiley Periodicals, Inc. and Direct Marketing Educational Foundation, Inc.

Online trendy topics detection in microblogs with selective user monitoring under cost constraints

As microblog services such as Twitter become a fast and convenient communication approach, identification of trendy topics in microblog services has great academic and business value. However detecting trendy topics is very challenging due to huge number of users and short-text posts in microblog diffusion networks. In this paper we introduce a trendy topics detection system under computation and communication resource constraints. In stark contrast to retrieving and processing the whole microblog contents, we develop an idea of selecting a small set of microblog users and processing their posts to achieve an overall acceptable trendy topic coverage, without exceeding resource budget for detection. We formulate the selection operation of these subset users as mixed-integer optimization problems, and develop heuristic algorithms to compute their approximate solutions. The proposed system is evaluated with real-time test data retrieved from Sina Weibo, the dominant microblog service provider in China. It's shown that by monitoring 500 out of 1.6 million microblog users and tracking their microposts (about 15,000 daily) with our system, nearly 65% trendy topics can be detected, while on average 5 hours earlier before they appear in Sina Weibo official trends.

Towards the in silico identification of class II restricted T-cell epitopes:a partial least squares iterative self-consistent algorithm for affinity prediction

Motivation: The immunogenicity of peptides depends on their ability to bind to MHC molecules. MHC binding affinity prediction methods can save significant amounts of experimental work. The class II MHC binding site is open at both ends, making epitope prediction difficult because of the multiple binding ability of long peptides. Results: An iterative self-consistent partial least squares (PLS)-based additive method was applied to a set of 66 pep- tides no longer than 16 amino acids, binding to DRB1*0401. A regression equation containing the quantitative contributions of the amino acids at each of the nine positions was generated. Its predictability was tested using two external test sets which gave r pred =0.593 and r pred=0.655, respectively. Furthermore, it was benchmarked using 25 known T-cell epitopes restricted by DRB1*0401 and we compared our results with four other online predictive methods. The additive method showed the best result finding 24 of the 25 T-cell epitopes. Availability: Peptides used in the study are available from http://www.jenner.ac.uk/JenPep. The PLS method is available commercially in the SYBYL molecular modelling software package. The final model for affinity prediction of peptides binding to DRB1*0401 molecule is available at http://www.jenner.ac.uk/MHCPred. Models developed for DRB1*0101 and DRB1*0701 also are available in MHC- Pred

Individual identification via electrocardiogram analysis

Background: During last decade the use of ECG recordings in biometric recognition studies has increased. ECG characteristics made it suitable for subject identification: it is unique, present in all living individuals, and hard to forge. However, in spite of the great number of approaches found in literature, no agreement exists on the most appropriate methodology. This study aimed at providing a survey of the techniques used so far in ECG-based human identification. Specifically, a pattern recognition perspective is here proposed providing a unifying framework to appreciate previous studies and, hopefully, guide future research. Methods: We searched for papers on the subject from the earliest available date using relevant electronic databases (Medline, IEEEXplore, Scopus, and Web of Knowledge). The following terms were used in different combinations: electrocardiogram, ECG, human identification, biometric, authentication and individual variability. The electronic sources were last searched on 1st March 2015. In our selection we included published research on peer-reviewed journals, books chapters and conferences proceedings. The search was performed for English language documents. Results: 100 pertinent papers were found. Number of subjects involved in the journal studies ranges from 10 to 502, age from 16 to 86, male and female subjects are generally present. Number of analysed leads varies as well as the recording conditions. Identification performance differs widely as well as verification rate. Many studies refer to publicly available databases (Physionet ECG databases repository) while others rely on proprietary recordings making difficult them to compare. As a measure of overall accuracy we computed a weighted average of the identification rate and equal error rate in authentication scenarios. Identification rate resulted equal to 94.95 % while the equal error rate equal to 0.92 %. Conclusions: Biometric recognition is a mature field of research. Nevertheless, the use of physiological signals features, such as the ECG traits, needs further improvements. ECG features have the potential to be used in daily activities such as access control and patient handling as well as in wearable electronics applications. However, some barriers still limit its growth. Further analysis should be addressed on the use of single lead recordings and the study of features which are not dependent on the recording sites (e.g. fingers, hand palms). Moreover, it is expected that new techniques will be developed using fiducials and non-fiducial based features in order to catch the best of both approaches. ECG recognition in pathological subjects is also worth of additional investigations.

A question of complexity:measuring the maturity of online enquiry communities

Online enquiry communities such as Question Answering (Q&A) websites allow people to seek answers to all kind of questions. With the growing popularity of such platforms, it is important for community managers to constantly monitor the performance of their communities. Although different metrics have been proposed for tracking the evolution of such communities, maturity, the process in which communities become more topic proficient over time, has been largely ignored despite its potential to help in identifying robust communities. In this paper, we interpret community maturity as the proportion of complex questions in a community at a given time. We use the Server Fault (SF) community, a Question Answering (Q&A) community of system administrators, as our case study and perform analysis on question complexity, the level of expertise required to answer a question. We show that question complexity depends on both the length of involvement and the level of contributions of the users who post questions within their community. We extract features relating to askers, answerers, questions and answers, and analyse which features are strongly correlated with question complexity. Although our findings highlight the difficulty of automatically identifying question complexity, we found that complexity is more influenced by both the topical focus and the length of community involvement of askers. Following the identification of question complexity, we define a measure of maturity and analyse the evolution of different topical communities. Our results show that different topical communities show different maturity patterns. Some communities show a high maturity at the beginning while others exhibit slow maturity rate. Copyright 2013 ACM.

Analysis and identification of spamming behaviors in Sina Weibo microblog

Spamming has been a widespread problem for social networks. In recent years there is an increasing interest in the analysis of anti-spamming for microblogs, such as Twitter. In this paper we present a systematic research on the analysis of spamming in Sina Weibo platform, which is currently a dominant microblogging service provider in China. Our research objectives are to understand the specific spamming behaviors in Sina Weibo and find approaches to identify and block spammers in Sina Weibo based on spamming behavior classifiers. To start with the analysis of spamming behaviors we devise several effective methods to collect a large set of spammer samples, including uses of proactive honeypots and crawlers, keywords based searching and buying spammer samples directly from online merchants. We processed the database associated with these spammer samples and interestingly we found three representative spamming behaviors: Aggressive advertising, repeated duplicate reposting and aggressive following. We extract various features and compare the behaviors of spammers and legitimate users with regard to these features. It is found that spamming behaviors and normal behaviors have distinct characteristics. Based on these findings we design an automatic online spammer identification system. Through tests with real data it is demonstrated that the system can effectively detect the spamming behaviors and identify spammers in Sina Weibo.

Native language identification (NLID) for forensic authorship analysis of weblogs

This chapter introduces Native Language Identification (NLID) and considers the casework applications with regard to authorship analysis of online material. It presents findings from research identifying which linguistic features were the best indicators of native (L1) Persian speakers blogging in English, and analyses how these features cope at distinguishing between native influences from languages that are linguistically and culturally related. The first chapter section outlines the area of Native Language Identification, and demonstrates its potential for application through a discussion of relevant case history. The next section discusses a development of methodology for identifying influence from L1 Persian in an anonymous blog author, and presents findings. The third part discusses the application of these features to casework situations as well as how the features identified can form an easily applicable model and demonstrates the application of this to casework. The research presented in this chapter can be considered a case study for the wider potential application of NLID.

ToPI - uma abordagem online para identificar locais de interesse utilizando fotografias geo-referenciadas

Due to the growing use of social networks people no longer just consume data, they also produce and share it. Geo-tagged information, i.e., data with geographical location, have been used in many attempts to identify popular places and help tourists that will visit unfamiliar cities. This Master Thesis presents an online strategy that uses geo-tagged photos and their metadata in order to identify places of interest inside a given geographical area and retrieve relevant related information. The whole process runs automatically in real time, returning updated information about places. The proposed strategy takes into account the inherent dynamism of social media, and thus is robust under inconsistencies and/or outdated information, a common issue in solutions that rely on previously stored data. The analysis of the results showed that our approach is very promising, returning places that present high agreement with those from a popular travel website.