WorldWideScience

Sample records for non-redundant signal components

  1. Micromorphic continua: non-redundant formulations

    Science.gov (United States)

    Romano, Giovanni; Barretta, Raffaele; Diaco, Marina

    2016-11-01

    The kinematics of generalized continua is investigated and key points concerning the definition of overall tangent strain measure are put into evidence. It is shown that classical measures adopted in the literature for micromorphic continua do not obey a constraint qualification requirement, to be fulfilled for well-posedness in optimization theory, and are therefore termed redundant. Redundancy of continua with latent microstructure and of constrained Cosserat continua is also assessed. A simplest, non-redundant, kinematic model of micromorphic continua, is proposed by dropping the microcurvature field. The equilibrium conditions and the related variational linear elastostatic problem are formulated and briefly discussed. The simplest model involves a reduced number of state variables and of elastic constitutive coefficients, when compared with other models of micromorphic continua, being still capable of enriching the Cauchy continuum model in a significant way.

  2. Imaging protoplanets: observing transition disks with non-redundant masking

    CERN Document Server

    Sallum, Steph; Close, Laird M; Hinz, Philip M; Follette, Katherine B; Kratter, Kaitlin; Skemer, Andrew J; Bailey, Vanessa P; Briguglio, Runa; Defrere, Denis; Macintosh, Bruce A; Males, Jared R; Morzinski, Katie M; Puglisi, Alfio T; Rodigas, Timothy J; Spalding, Eckhart; Tuthill, Peter G; Vaz, Amali; Weinberger, Alycia; Xomperio, Marco

    2016-01-01

    Transition disks, protoplanetary disks with inner clearings, are promising objects in which to directly image forming planets. The high contrast imaging technique of non-redundant masking is well posed to detect planetary mass companions at several to tens of AU in nearby transition disks. We present non-redundant masking observations of the T Cha and LkCa 15 transition disks, both of which host posited sub-stellar mass companions. However, due to a loss of information intrinsic to the technique, observations of extended sources (e.g. scattered light from disks) can be misinterpreted as moving companions. We discuss tests to distinguish between these two scenarios, with applications to the T Cha and LkCa 15 observations. We argue that a static, forward-scattering disk can explain the T Cha data, while LkCa 15 is best explained by multiple orbiting companions.

  3. Mining Non-Redundant High Order Correlations in Binary Data.

    Science.gov (United States)

    Zhang, Xiang; Pan, Feng; Wang, Wei; Nobel, Andrew

    2008-08-01

    Many approaches have been proposed to find correlations in binary data. Usually, these methods focus on pair-wise correlations. In biology applications, it is important to find correlations that involve more than just two features. Moreover, a set of strongly correlated features should be non-redundant in the sense that the correlation is strong only when all the interacting features are considered together. Removing any feature will greatly reduce the correlation.In this paper, we explore the problem of finding non-redundant high order correlations in binary data. The high order correlations are formalized using multi-information, a generalization of pairwise mutual information. To reduce the redundancy, we require any subset of a strongly correlated feature subset to be weakly correlated. Such feature subsets are referred to as Non-redundant Interacting Feature Subsets (NIFS). Finding all NIFSs is computationally challenging, because in addition to enumerating feature combinations, we also need to check all their subsets for redundancy. We study several properties of NIFSs and show that these properties are useful in developing efficient algorithms. We further develop two sets of upper and lower bounds on the correlations, which can be incorporated in the algorithm to prune the search space. A simple and effective pruning strategy based on pair-wise mutual information is also developed to further prune the search space. The efficiency and effectiveness of our approach are demonstrated through extensive experiments on synthetic and real-life datasets.

  4. Extra Solar Planet Science With a Non Redundant Mask

    Science.gov (United States)

    Minto, Stefenie Nicolet; Sivaramakrishnan, Anand; Greenbaum, Alexandra; St. Laurent, Kathryn; Thatte, Deeparshi

    2017-01-01

    To detect faint planetary companions near a much brighter star, at the Resolution Limit of the James Webb Space Telescope (JWST) the Near-Infrared Imager and Slitless Spectrograph (NIRISS) will use a non-redundant aperture mask (NRM) for high contrast imaging. I simulated NIRISS data of stars with and without planets, and run these through the code that measures interferometric image properties to determine how sensitive planetary detection is to our knowledge of instrumental parameters, starting with the pixel scale. I measured the position angle, distance, and contrast ratio of the planet (with respect to the star) to characterize the binary pair. To organize this data I am creating programs that will automatically and systematically explore multi-dimensional instrument parameter spaces and binary characteristics. In the future my code will also be applied to explore any other parameters we can simulate.

  5. Ion pairs in non-redundant protein structures

    Indian Academy of Sciences (India)

    B A Gowri Shankar; R Sarani; Daliah Michael; P Mridula; C Vasuki; G Sowmiya; B Vasundhar; P Sudha; J Jeyakanthan; D Velmurugan; K Sekar

    2007-06-01

    Ion pairs contribute to several functions including the activity of catalytic triads, fusion of viral membranes, stability in thermophilic proteins and solvent–protein interactions. Furthermore, they have the ability to affect the stability of protein structures and are also a part of the forces that act to hold monomers together. This paper deals with the possible ion pair combinations and networks in 25% and 90% non-redundant protein chains. Different types of ion pairs present in various secondary structural elements are analysed. The ion pairs existing between different subunits of multisubunit protein structures are also computed and the results of various analyses are presented in detail. The protein structures used in the analysis are solved using X-ray crystallography, whose resolution is better than or equal to 1.5 Å and R-factor better than or equal to 20%. This study can, therefore, be useful for analyses of many protein functions. It also provides insights into the better understanding of the architecture of protein structure.

  6. Autonomous control system reconfiguration for spacecraft with non-redundant actuators

    Science.gov (United States)

    Grossman, Walter

    1995-01-01

    The Small Satellite Technology Initiative (SSTI) 'CLARK' spacecraft is required to be single-failure tolerant, i.e., no failure of any single component or subsystem shall result in complete mission loss. Fault tolerance is usually achieved by implementing redundant subsystems. Fault tolerant systems are therefore heavier and cost more to build and launch than non-redundent, non fault-tolerant spacecraft. The SSTI CLARK satellite Attitude Determination and Control System (ADACS) achieves single-fault tolerance without redundancy. The attitude determination system system uses a Kalman Filter which is inherently robust to loss of any single attitude sensor. The attitude control system uses three orthogonal reaction wheels for attitude control and three magnetic dipoles for momentum control. The nominal six-actuator control system functions by projecting the attitude correction torque onto the reaction wheels while a slower momentum management outer loop removes the excess momentum in the direction normal to the local B field. The actuators are not redundant so the nominal control law cannot be implemented in the event of a loss of a single actuator (dipole or reaction wheel). The spacecraft dynamical state (attitude, angular rate, and momentum) is controllable from any five-element subset of the six actuators. With loss of an actuator the instantaneous control authority may not span R(3) but the controllability gramian integral(limits between t,0) Phi(t, tau)B(tau )B(prime)(tau) Phi(prime)(t, tau)d tau retains full rank. Upon detection of an actuator failure the control torque is decomposed onto the remaining active axes. The attitude control torque is effected and the over-orbit momentum is controlled. The resulting control system performance approaches that of the nominal system.

  7. Dynamics of social contagions with memory of non-redundant information

    CERN Document Server

    Wang, Wei; Zhang, Hai-Feng; Lai, Ying-Cheng

    2015-01-01

    A key ingredient in social contagion dynamics is reinforcement, as adopting a certain social behavior requires verification of its credibility and legitimacy. Memory of non-redundant information plays an important role in reinforcement, which so far has eluded theoretical analysis. We first propose a general social contagion model with reinforcement derived from non-redundant information memory. Then, we develop a unified edge-based compartmental theory to analyze this model, and a remarkable agreement with numerics is obtained on some specific models. Using a spreading threshold model as a specific example to understand the memory effect, in which each individual adopts a social behavior only when the cumulative pieces of information that the individual received from his/her neighbors exceeds an adoption threshold. Through analysis and numerical simulations, we find that the memory characteristic markedly affects the dynamics as quantified by the final adoption size. Strikingly, we uncover a transition pheno...

  8. Non-redundant unique interface structures as templates for modeling protein interactions

    OpenAIRE

    Engin Cukuroglu; Attila Gursoy; Ruth Nussinov; Ozlem Keskin

    2014-01-01

    Non-Redundant Unique Interface Structures as Templates for Modeling Protein Interactions Engin Cukuroglu1, Attila Gursoy1*, Ruth Nussinov2,3, Ozlem Keskin1* 1 Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Istanbul, Turkey, 2 National Cancer Institute, Cancer and Inflammation Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., National Cancer Institute, Frederick, Maryland, United States of ...

  9. Discovering Non-Redundant Association Rules using MinMax Approximation Rules

    OpenAIRE

    R. Vijaya Prakash; Dr. A. Govardhan3; Prof. SSVN. Sarma

    2012-01-01

    Frequent pattern mining is an important area of data mining used to generate the Association Rules. The extracted Frequent Patterns quality is a big concern, as it generates huge sets of rules and many of them are redundant. Mining Non-Redundant Frequent patterns is a big concern in the area of Association rule mining. In this paper we proposed a method to eliminate the redundant Frequent patterns using MinMax rule approach, to generate the quality Association Rules.

  10. Inhibitors targeting two-component signal transduction.

    Science.gov (United States)

    Watanabe, Takafumi; Okada, Ario; Gotoh, Yasuhiro; Utsumi, Ryutaro

    2008-01-01

    A two-component signal transduction system (TCS) is an attractive target for antibacterial agents. In this chapter, we review the TCS inhibitors developed during the past decade and introduce novel drug discovery systems to isolate the inhibitors of the YycG/YycF system, an essential TCS for bacterial growth, in an effort to develop a new class of antibacterial agents.

  11. Principal Component Analysis in ECG Signal Processing

    Directory of Open Access Journals (Sweden)

    Andreas Bollmann

    2007-01-01

    Full Text Available This paper reviews the current status of principal component analysis in the area of ECG signal processing. The fundamentals of PCA are briefly described and the relationship between PCA and Karhunen-Loève transform is explained. Aspects on PCA related to data with temporal and spatial correlations are considered as adaptive estimation of principal components is. Several ECG applications are reviewed where PCA techniques have been successfully employed, including data compression, ST-T segment analysis for the detection of myocardial ischemia and abnormalities in ventricular repolarization, extraction of atrial fibrillatory waves for detailed characterization of atrial fibrillation, and analysis of body surface potential maps.

  12. Planetary system, star formation, and black hole science with non-redundant masking on space telescopes

    CERN Document Server

    Sivaramakrishna, Anand; Ireland, Michael; Lloyd, James; Perrin, Marshall; Soummer, Remi; McKernan, Barry; Ford, Saavik

    2009-01-01

    Non-redundant masking (NRM) is a high contrast, high resolution technique relevant to future space missions concerned with extrasolar planetary system and star formation, as well as general high angular resolution galactic and extragalactic astronomy. NRM enables the highest angular resolution science possible given the telescope's diameter and operating wavelength. It also provides precise information on a telescope's optical state. We must assess NRM contrast limits realistically to understand the science yield of NRM in space, and, simultaneously, develop NRM science for planet and star formation and extragalactic science in the UV-NIR, to help steer high resolution space-based astronomy in the coming decade.

  13. Overlap and diversity in antimicrobial peptide databases: compiling a non-redundant set of sequences.

    Science.gov (United States)

    Aguilera-Mendoza, Longendri; Marrero-Ponce, Yovani; Tellez-Ibarra, Roberto; Llorente-Quesada, Monica T; Salgado, Jesús; Barigye, Stephen J; Liu, Jun

    2015-08-01

    The large variety of antimicrobial peptide (AMP) databases developed to date are characterized by a substantial overlap of data and similarity of sequences. Our goals are to analyze the levels of redundancy for all available AMP databases and use this information to build a new non-redundant sequence database. For this purpose, a new software tool is introduced. A comparative study of 25 AMP databases reveals the overlap and diversity among them and the internal diversity within each database. The overlap analysis shows that only one database (Peptaibol) contains exclusive data, not present in any other, whereas all sequences in the LAMP_Patent database are included in CAMP_Patent. However, the majority of databases have their own set of unique sequences, as well as some overlap with other databases. The complete set of non-duplicate sequences comprises 16 990 cases, which is almost half of the total number of reported peptides. On the other hand, the diversity analysis identifies the most and least diverse databases and proves that all databases exhibit some level of redundancy. Finally, we present a new parallel-free software, named Dover Analyzer, developed to compute the overlap and diversity between any number of databases and compile a set of non-redundant sequences. These results are useful for selecting or building a suitable representative set of AMPs, according to specific needs. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  14. Analysis of knockout mutants reveals non-redundant functions of poly(ADP-ribose)polymerase isoforms in Arabidopsis.

    Science.gov (United States)

    Pham, Phuong Anh; Wahl, Vanessa; Tohge, Takayuki; de Souza, Laise Rosado; Zhang, Youjun; Do, Phuc Thi; Olas, Justyna J; Stitt, Mark; Araújo, Wagner L; Fernie, Alisdair R

    2015-11-01

    The enzyme poly(ADP-ribose)polymerase (PARP) has a dual function being involved both in the poly(ADP-ribosyl)ation and being a constituent of the NAD(+) salvage pathway. To date most studies, both in plant and non-plant systems, have focused on the signaling role of PARP in poly(ADP-ribosyl)ation rather than any role that can be ascribed to its metabolic function. In order to address this question we here used a combination of expression, transcript and protein localization studies of all three PARP isoforms of Arabidopsis alongside physiological analysis of the corresponding mutants. Our analyses indicated that whilst all isoforms of PARP were localized to the nucleus they are also present in non-nuclear locations with parp1 and parp3 also localised in the cytosol, and parp2 also present in the mitochondria. We next isolated and characterized insertional knockout mutants of all three isoforms confirming a complete knockout in the full length transcript levels of the target genes as well as a reduced total leaf NAD hydrolase activity in the two isoforms (PARP1, PARP2) that are highly expressed in leaves. Physiological evaluation of the mutant lines revealed that they displayed distinctive metabolic and root growth characteristics albeit unaltered leaf morphology under optimal growth conditions. We therefore conclude that the PARP isoforms play non-redundant non-nuclear metabolic roles and that their function is highly important in rapidly growing tissues such as the shoot apical meristem, roots and seeds.

  15. A Frequent Closed Itemsets Lattice-based Approach for Mining Minimal Non-Redundant Association Rules

    CERN Document Server

    Vo, Bay

    2011-01-01

    There are many algorithms developed for improvement the time of mining frequent itemsets (FI) or frequent closed itemsets (FCI). However, the algorithms which deal with the time of generating association rules were not put in deep research. In reality, in case of a database containing many FI/FCI (from ten thousands up to millions), the time of generating association rules is much larger than that of mining FI/FCI. Therefore, this paper presents an application of frequent closed itemsets lattice (FCIL) for mining minimal non-redundant association rules (MNAR) to reduce a lot of time for generating rules. Firstly, we use CHARM-L for building FCIL. After that, based on FCIL, an algorithm for fast generating MNAR will be proposed. Experimental results show that the proposed algorithm is much faster than frequent itemsets lattice-based algorithm in the mining time.

  16. In-focus wavefront sensing using non-redundant mask-induced pupil diversity

    CERN Document Server

    Greenbaum, Alexandra

    2016-01-01

    Wavefront estimation using in-focus image data is critical to many applications. This data is invariant to a sign flip with complex conjugation of the complex amplitude in the pupil, making for a non-unique solution. Information from an in-focus image taken through a non-redundant pupil mask (NRM) can break this ambiguity, enabling the true aberration to be determined. We demonstrate this by priming a full pupil Gerchberg-Saxton phase retrieval with NRM fringe phase information. We apply our method to measure simulated aberrations on the segmented James Webb Space Telescope (JWST) mirror using full pupil and NRM data from its Near Infrared Imager and Slitless Spectrograph (NIRISS).

  17. In-focus phase retrieval using JWST-NIRISS's non-redundant mask

    Science.gov (United States)

    Greenbaum, Alexandra Z.; Gamper, Noah; Sivaramakrishnan, Anand

    2016-07-01

    The James Webb Space Telescope's Near InfraRed Imager and Slitless Spectrograph (NIRISS) contains a 7-hole non-redundant mask (NRM) in its pupil. NIRISS's Aperture Masking Interferometry (AMI) mode is useful both for science as well as wavefront sensing. In-focus science detector NRM and full pupil images of unresolved stars can be used to measure the wavefront without any dedicated wavefront sensing hardware or any moving mirrors. Using routine science operational sequences, these images can be taken before or after any science visit. NRM fringe phases constrain Gerchberg-Saxton phase retrieval to disambiguate the algorithm's two-fold degeneracy. We summarize how consecutive masked and unmasked exposures provide enough information to reconstruct a wavefront with up to ˜1-2 rms radians of error. We present our latest progress on using this approach on laboratory experiments, and discuss those results in the context of contingency for JWST segment phasing. We discuss extending our method to ground-based AO systems and future space telescopes.

  18. Non-redundant patent sequence databases with value-added annotations at two levels.

    Science.gov (United States)

    Li, Weizhong; McWilliam, Hamish; de la Torre, Ana Richart; Grodowski, Adam; Benediktovich, Irina; Goujon, Mickael; Nauche, Stephane; Lopez, Rodrigo

    2010-01-01

    The European Bioinformatics Institute (EMBL-EBI) provides public access to patent data, including abstracts, chemical compounds and sequences. Sequences can appear multiple times due to the filing of the same invention with multiple patent offices, or the use of the same sequence by different inventors in different contexts. Information relating to the source invention may be incomplete, and biological information available in patent documents elsewhere may not be reflected in the annotation of the sequence. Search and analysis of these data have become increasingly challenging for both the scientific and intellectual-property communities. Here, we report a collection of non-redundant patent sequence databases, which cover the EMBL-Bank nucleotides patent class and the patent protein databases and contain value-added annotations from patent documents. The databases were created at two levels by the use of sequence MD5 checksums. Sequences within a level-1 cluster are 100% identical over their whole length. Level-2 clusters were defined by sub-grouping level-1 clusters based on patent family information. Value-added annotations, such as publication number corrections, earliest publication dates and feature collations, significantly enhance the quality of the data, allowing for better tracking and cross-referencing. The databases are available format: http://www.ebi.ac.uk/patentdata/nr/.

  19. Non-redundant patent sequence databases with value-added annotations at two levels

    Science.gov (United States)

    Li, Weizhong; McWilliam, Hamish; de la Torre, Ana Richart; Grodowski, Adam; Benediktovich, Irina; Goujon, Mickael; Nauche, Stephane; Lopez, Rodrigo

    2010-01-01

    The European Bioinformatics Institute (EMBL-EBI) provides public access to patent data, including abstracts, chemical compounds and sequences. Sequences can appear multiple times due to the filing of the same invention with multiple patent offices, or the use of the same sequence by different inventors in different contexts. Information relating to the source invention may be incomplete, and biological information available in patent documents elsewhere may not be reflected in the annotation of the sequence. Search and analysis of these data have become increasingly challenging for both the scientific and intellectual-property communities. Here, we report a collection of non-redundant patent sequence databases, which cover the EMBL-Bank nucleotides patent class and the patent protein databases and contain value-added annotations from patent documents. The databases were created at two levels by the use of sequence MD5 checksums. Sequences within a level-1 cluster are 100% identical over their whole length. Level-2 clusters were defined by sub-grouping level-1 clusters based on patent family information. Value-added annotations, such as publication number corrections, earliest publication dates and feature collations, significantly enhance the quality of the data, allowing for better tracking and cross-referencing. The databases are available format: http://www.ebi.ac.uk/patentdata/nr/. PMID:19884134

  20. An image-plane algorithm for JWST's non-redundant aperture mask data

    CERN Document Server

    Greenbaum, Alexandra Z; Sivaramakrishnan, Anand; Lacour, Sylvestre

    2014-01-01

    The high angular resolution technique of non-redundant masking (NRM) or aperture masking interferometry (AMI) has yielded images of faint protoplanetary companions of nearby stars from the ground. AMI on James Webb Space Telescope (JWST)'s Near Infrared Imager and Slitless Spectrograph (NIRISS) has a lower thermal background than ground-based facilites and does not suffer from atmospheric instability. NIRISS AMI images are likely to have 90 - 95% Strehl ratio between 2.77 and 4.8 micron. In this paper we quantify factors that limit the raw point source contrast of JWST NRM. We develop an analytic model of the NRM point spread function which includes different optical path delays (pistons) between mask holes and fit the model parameters with image plane data. It enables a straightforward way to exclude bad pixels, is suited to limited fields of view, and can incorporate effects such as intra-pixel sensitivity variations. We simulate various sources of noise to estimate their effect on the standard deviation of...

  1. One-component systems dominate signal transduction in prokaryotes

    OpenAIRE

    Ulrich, Luke E; Koonin, Eugene V.; Zhulin, Igor B.

    2005-01-01

    Two-component systems that link environmental signals to cellular responses are viewed as the primary mode of signal transduction in prokaryotes. By analyz-ing information encoded by 145 prokaryotic genomes, we found that the majority of signal transduction systems consist of a single protein that contains input and output domains but lacks phosphotransfer domains typical of two-component systems. One-component systems are evolutionarily older, more widely distributed among bacteria and archa...

  2. Extracellular matrix component signaling in cancer

    DEFF Research Database (Denmark)

    Multhaupt, Hinke A. B.; Leitinger, Birgit; Gullberg, Donald

    2016-01-01

    Cell responses to the extracellular matrix depend on specific signaling events. These are important from early development, through differentiation and tissue homeostasis, immune surveillance, and disease pathogenesis. Signaling not only regulates cell adhesion cytoskeletal organization and motil...... as well as matrix constitution and protein crosslinking. Here we summarize roles of the three major matrix receptor types, with emphasis on how they function in tumor progression. [on SciFinder(R)]......Cell responses to the extracellular matrix depend on specific signaling events. These are important from early development, through differentiation and tissue homeostasis, immune surveillance, and disease pathogenesis. Signaling not only regulates cell adhesion cytoskeletal organization...... and motility but also provides survival and proliferation cues. The major classes of cell surface receptors for matrix macromols. are the integrins, discoidin domain receptors, and transmembrane proteoglycans such as syndecans and CD44. Cells respond not only to specific ligands, such as collagen, fibronectin...

  3. AN IMAGE-PLANE ALGORITHM FOR JWST'S NON-REDUNDANT APERTURE MASK DATA

    Energy Technology Data Exchange (ETDEWEB)

    Greenbaum, Alexandra Z. [Johns Hopkins University Department of Physics and Astronomy 3400 North Charles, Baltimore, MD 21218 (United States); Pueyo, Laurent; Sivaramakrishnan, Anand [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Lacour, Sylvestre [LESIA, CNRS/UMR-8109, Observatoire de Paris, UPMC, Université Paris Diderot 5 place Jules Janssen, 92195 Meudon (France)

    2015-01-10

    The high angular resolution technique of non-redundant masking (NRM) or aperture masking interferometry (AMI) has yielded images of faint protoplanetary companions of nearby stars from the ground. AMI on James Webb Space Telescope (JWST)'s Near Infrared Imager and Slitless Spectrograph (NIRISS) has a lower thermal background than ground-based facilities and does not suffer from atmospheric instability. NIRISS AMI images are likely to have 90%-95% Strehl ratio between 2.77 and 4.8 μm. In this paper we quantify factors that limit the raw point source contrast of JWST NRM. We develop an analytic model of the NRM point spread function which includes different optical path delays (pistons) between mask holes and fit the model parameters with image plane data. It enables a straightforward way to exclude bad pixels, is suited to limited fields of view, and can incorporate effects such as intra-pixel sensitivity variations. We simulate various sources of noise to estimate their effect on the standard deviation of closure phase, σ{sub CP} (a proxy for binary point source contrast). If σ{sub CP} < 10{sup –4} radians—a contrast ratio of 10 mag—young accreting gas giant planets (e.g., in the nearby Taurus star-forming region) could be imaged with JWST NIRISS. We show the feasibility of using NIRISS' NRM with the sub-Nyquist sampled F277W, which would enable some exoplanet chemistry characterization. In the presence of small piston errors, the dominant sources of closure phase error (depending on pixel sampling, and filter bandwidth) are flat field errors and unmodeled variations in intra-pixel sensitivity. The in-flight stability of NIRISS will determine how well these errors can be calibrated by observing a point source. Our results help develop efficient observing strategies for space-based NRM.

  4. Pentraxin 3, a non-redundant soluble pattern recognition receptor involved in innate immunity.

    Science.gov (United States)

    Mantovani, Alberto; Garlanda, Cecilia; Bottazzi, Barbara

    2003-06-01

    Pentraxin 3 (PTX3) is the first long pentraxin identified. Long pentraxins consist of a C-terminal pentraxin domain, which has sequence similarity to C-reactive protein (CRP) and serum amyloid P (SAP) component (the classic short pentraxins), and of an unrelated N-terminal portion. PTX3 is made by diverse cell types, most prominently endothelial cells, macrophages and dendritic cells, in response to primary inflammatory signals (e.g. interleukin-1 (IL-1), tumour necrosis factor (TNF), lipopolysaccharide (LPS)). It binds diverse ligands, including microbial moieties, C1q and apoptotic cells. Evidence suggests that PTX3 plays a role in the regulation of innate resistance to pathogens, inflammatory reactions, possibly clearance of self-components and female fertility.

  5. One-component systems dominate signal transduction in prokaryotes

    Science.gov (United States)

    Ulrich, Luke E.; Koonin, Eugene V.; Zhulin, Igor B.

    2009-01-01

    Two-component systems that link environmental signals to cellular responses are viewed as the primary mode of signal transduction in prokaryotes. By analyz-ing information encoded by 145 prokaryotic genomes, we found that the majority of signal transduction systems consist of a single protein that contains input and output domains but lacks phosphotransfer domains typical of two-component systems. One-component systems are evolutionarily older, more widely distributed among bacteria and archaea, and display a greater diversity of domains than two-component systems. PMID:15680762

  6. Engineering key components in a synthetic eukaryotic signal transduction pathway

    OpenAIRE

    Antunes, Mauricio S; Kevin J Morey; Tewari-Singh, Neera; Bowen, Tessa A.; Smith, J. Jeff; Webb, Colleen T.; Hellinga, Homme W.; Medford, June I.

    2009-01-01

    Signal transduction underlies how living organisms detect and respond to stimuli. A goal of synthetic biology is to rewire natural signal transduction systems. Bacteria, yeast, and plants sense environmental aspects through conserved histidine kinase (HK) signal transduction systems. HK protein components are typically comprised of multiple, relatively modular, and conserved domains. Phosphate transfer between these components may exhibit considerable cross talk between the otherwise apparent...

  7. Non-redundant Aperture Masking Interferometry (AMI) and segment phasing with JWST-NIRISS

    Science.gov (United States)

    Sivaramakrishnan, Anand; Lafrenière, David; Ford, K. E. Saavik; McKernan, Barry; Cheetham, Anthony; Greenbaum, Alexandra Z.; Tuthill, Peter G.; Lloyd, James P.; Ireland, Michael J.; Doyon, René; Beaulieu, Mathilde; Martel, André; Koekemoer, Anton; Martinache, Frantz; Teuben, Peter

    2012-09-01

    The Aperture Masked Interferometry (AMI) mode on JWST-NIRISS is implemented as a 7-hole, 15% throughput, non-redundant mask (NRM) that operates with 5-8% bandwidth filters at 3.8, 4.3, and 4.8 microns. We present refined estimates of AMI's expected point-source contrast, using realizations of noise matched to JWST pointing requirements, NIRISS detector noise, and Rev-V JWST wavefront error models for the telescope and instrument. We describe our point-source binary data reduction algorithm, which we use as a standardized method to compare different observational strategies. For a 7.5 magnitude star we report a 10-a detection at between 8.7 and 9.2 magnitudes of contrast between 100 mas to 400 mas respectively, using closure phases and squared visibilities in the absence of bad pixels, but with various other noise sources. With 3% of the pixels unusable, the expected contrast drops by about 0.5 magnitudes. AMI should be able to reach targets as bright as M=5. There will be significant overlap between Gemini-GPI and ESO-SPHERE targets and AMI's search space, and a complementarity with NIRCam's coronagraph. We also illustrate synthesis imaging with AMI, demonstrating an imaging dynamic range of 25 at 100 mas scales. We tailor existing radio interferometric methods to retrieve a faint bar across a bright nucleus, and explain the similarities to synthesis imaging at radio wavelengths. Modest contrast observations of dusty accretion flows around AGNs will be feasible for NIRISS AMI. We show our early results of image-plane deconvolution as well. Finally, we report progress on an NRM-inspired approach to mitigate mission-level risk associated with JWST's specialized wavefront sensing hardware. By combining narrow band and medium band Nyquist-sampled images taken with a science camera we can sense JWST primary mirror segment tip-tilt to lOmas, and piston to a few nm. We can sense inter-segment piston errors of up to 5 coherence lengths of the broadest bandpass filter used

  8. Two Component Signal Transduction in Desulfovibrio Species

    Energy Technology Data Exchange (ETDEWEB)

    Luning, Eric; Rajeev, Lara; Ray, Jayashree; Mukhopadhyay, Aindrila

    2010-05-17

    The environmentally relevant Desulfovibrio species are sulfate-reducing bacteria that are of interest in the bioremediation of heavy metal contaminated water. Among these, the genome of D. vulgaris Hildenborough encodes a large number of two component systems consisting of 72 putative response regulators (RR) and 64 putative histidinekinases (HK), the majority of which are uncharacterized. We classified the D. vulgaris Hildenborough RRs based on their output domains and compared the distribution of RRs in other sequenced Desulfovibrio species. We have successfully purified most RRs and several HKs as His-tagged proteins. We performed phospho-transfer experiments to verify relationships between cognate pairs of HK and RR, and we have also mapped a few non-cognate HK-RR pairs. Presented here are our discoveries from the Desulfovibrio RR categorization and results from the in vitro studies using purified His tagged D. vulgaris HKs and RRs.

  9. Receptor domains of two-component signal transduction systems.

    Science.gov (United States)

    Perry, Julie; Koteva, Kalinka; Wright, Gerard

    2011-05-01

    Two-component signal transduction systems are found ubiquitously in prokaryotes, and in archaea, fungi, yeast and some plants, where they regulate physiologic and molecular processes at both transcriptional and post-transcriptional levels. Two-component systems sense changes in environmental conditions when a specific ligand binds to the receptor domain of the histidine kinase sensory component. The structures of many histidine kinase receptors are known, including those which sense extracellular and cytoplasmic signals. In this review, we discuss the basic architecture of two-component signalling circuits, including known system ligands, structure and function of both receptor and signalling domains, the chemistry of phosphotransfer, and cross-talk between different two-component pathways. Given the importance of these systems in regulating cellular responses, many biochemical techniques have been developed for their study and analysis. We therefore also review current methods used to study two-component signalling, including a new affinity-based proteomics approach used to study inducible resistance to the antibiotic vancomycin through the VanSR two-component signal transduction system.

  10. ECG signals denoising using wavelet transform and independent component analysis

    Science.gov (United States)

    Liu, Manjin; Hui, Mei; Liu, Ming; Dong, Liquan; Zhao, Zhu; Zhao, Yuejin

    2015-08-01

    A method of two channel exercise electrocardiograms (ECG) signals denoising based on wavelet transform and independent component analysis is proposed in this paper. First of all, two channel exercise ECG signals are acquired. We decompose these two channel ECG signals into eight layers and add up the useful wavelet coefficients separately, getting two channel ECG signals with no baseline drift and other interference components. However, it still contains electrode movement noise, power frequency interference and other interferences. Secondly, we use these two channel ECG signals processed and one channel signal constructed manually to make further process with independent component analysis, getting the separated ECG signal. We can see the residual noises are removed effectively. Finally, comparative experiment is made with two same channel exercise ECG signals processed directly with independent component analysis and the method this paper proposed, which shows the indexes of signal to noise ratio (SNR) increases 21.916 and the root mean square error (MSE) decreases 2.522, proving the method this paper proposed has high reliability.

  11. Exploring fMRI Data for Periodic Signal Components

    DEFF Research Database (Denmark)

    Hansen, Lars Kai; Nielsen, Finn Årup; Larsen, Jan

    2002-01-01

    We use a Bayesian framework to detect periodic components in fMRI data. The resulting detector is sensitive to periodic components with a flexible number of harmonics and with arbitrary amplitude and phases of the harmonics. It is possible to detect the correct number of harmonics in periodic sig...... signals even if the fundamental frequency is beyond the Nyquist frequency. We apply the signal detector to locate regions that are highly affected by periodic physiological artifacts, such as cardiac pulsation....

  12. Engineering key components in a synthetic eukaryotic signal transduction pathway.

    Science.gov (United States)

    Antunes, Mauricio S; Morey, Kevin J; Tewari-Singh, Neera; Bowen, Tessa A; Smith, J Jeff; Webb, Colleen T; Hellinga, Homme W; Medford, June I

    2009-01-01

    Signal transduction underlies how living organisms detect and respond to stimuli. A goal of synthetic biology is to rewire natural signal transduction systems. Bacteria, yeast, and plants sense environmental aspects through conserved histidine kinase (HK) signal transduction systems. HK protein components are typically comprised of multiple, relatively modular, and conserved domains. Phosphate transfer between these components may exhibit considerable cross talk between the otherwise apparently linear pathways, thereby establishing networks that integrate multiple signals. We show that sequence conservation and cross talk can extend across kingdoms and can be exploited to produce a synthetic plant signal transduction system. In response to HK cross talk, heterologously expressed bacterial response regulators, PhoB and OmpR, translocate to the nucleus on HK activation. Using this discovery, combined with modification of PhoB (PhoB-VP64), we produced a key component of a eukaryotic synthetic signal transduction pathway. In response to exogenous cytokinin, PhoB-VP64 translocates to the nucleus, binds a synthetic PlantPho promoter, and activates gene expression. These results show that conserved-signaling components can be used across kingdoms and adapted to produce synthetic eukaryotic signal transduction pathways.

  13. Evolutionary conservation of plant gibberellin signalling pathway components

    Directory of Open Access Journals (Sweden)

    Reski Ralf

    2007-11-01

    Full Text Available Abstract Background: Gibberellins (GA are plant hormones that can regulate germination, elongation growth, and sex determination. They ubiquitously occur in seed plants. The discovery of gibberellin receptors, together with advances in understanding the function of key components of GA signalling in Arabidopsis and rice, reveal a fairly short GA signal transduction route. The pathway essentially consists of GID1 gibberellin receptors that interact with F-box proteins, which in turn regulate degradation of downstream DELLA proteins, suppressors of GA-controlled responses. Results: Arabidopsis sequences of the gibberellin signalling compounds were used to screen databases from a variety of plants, including protists, for homologues, providing indications for the degree of conservation of the pathway. The pathway as such appears completely absent in protists, the moss Physcomitrella patens shares only a limited homology with the Arabidopsis proteins, thus lacking essential characteristics of the classical GA signalling pathway, while the lycophyte Selaginella moellendorffii contains a possible ortholog for each component. The occurrence of classical GA responses can as yet not be linked with the presence of homologues of the signalling pathway. Alignments and display in neighbour joining trees of the GA signalling components confirm the close relationship of gymnosperms, monocotyledonous and dicotyledonous plants, as suggested from previous studies. Conclusion: Homologues of the GA-signalling pathway were mainly found in vascular plants. The GA signalling system may have its evolutionary molecular onset in Physcomitrella patens, where GAs at higher concentrations affect gravitropism and elongation growth.

  14. Rewiring the specificity of two-component signal transduction systems.

    Science.gov (United States)

    Skerker, Jeffrey M; Perchuk, Barrett S; Siryaporn, Albert; Lubin, Emma A; Ashenberg, Orr; Goulian, Mark; Laub, Michael T

    2008-06-13

    Two-component signal transduction systems are the predominant means by which bacteria sense and respond to environmental stimuli. Bacteria often employ tens or hundreds of these paralogous signaling systems, comprised of histidine kinases (HKs) and their cognate response regulators (RRs). Faithful transmission of information through these signaling pathways and avoidance of detrimental crosstalk demand exquisite specificity of HK-RR interactions. To identify the determinants of two-component signaling specificity, we examined patterns of amino acid coevolution in large, multiple sequence alignments of cognate kinase-regulator pairs. Guided by these results, we demonstrate that a subset of the coevolving residues is sufficient, when mutated, to completely switch the substrate specificity of the kinase EnvZ. Our results shed light on the basis of molecular discrimination in two-component signaling pathways, provide a general approach for the rational rewiring of these pathways, and suggest that analyses of coevolution may facilitate the reprogramming of other signaling systems and protein-protein interactions.

  15. Determinants of specificity in two-component signal transduction.

    Science.gov (United States)

    Podgornaia, Anna I; Laub, Michael T

    2013-04-01

    Maintaining the faithful flow of information through signal transduction pathways is critical to the survival and proliferation of organisms. This problem is particularly challenging as many signaling proteins are part of large, paralogous families that are highly similar at the sequence and structural levels, increasing the risk of unwanted cross-talk. To detect environmental signals and process information, bacteria rely heavily on two-component signaling systems comprised of sensor histidine kinases and their cognate response regulators. Although most species encode dozens of these signaling pathways, there is relatively little cross-talk, indicating that individual pathways are well insulated and highly specific. Here, we review the molecular mechanisms that enforce this specificity. Further, we highlight recent studies that have revealed how these mechanisms evolve to accommodate the introduction of new pathways by gene duplication. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. Single channel signal component separation using Bayesian estimation

    Institute of Scientific and Technical Information of China (English)

    Cai Quanwei; Wei Ping; Xiao Xianci

    2007-01-01

    A Bayesian estimation method to separate multicomponent signals with single channel observation is presented in this paper. By using the basis function projection, the component separation becomes a problem of limited parameter estimation. Then, a Bayesian model for estimating parameters is set up. The reversible jump MCMC (Monte Carlo Markov Chain) algorithmis adopted to perform the Bayesian computation. The method can jointly estimate the parameters of each component and the component number. Simulation results demonstrate that the method has low SNR threshold and better performance.

  17. Evolution of two-component signal transduction systems.

    Science.gov (United States)

    Capra, Emily J; Laub, Michael T

    2012-01-01

    To exist in a wide range of environmental niches, bacteria must sense and respond to a variety of external signals. A primary means by which this occurs is through two-component signal transduction pathways, typically composed of a sensor histidine kinase that receives the input stimuli and then phosphorylates a response regulator that effects an appropriate change in cellular physiology. Histidine kinases and response regulators have an intrinsic modularity that separates signal input, phosphotransfer, and output response; this modularity has allowed bacteria to dramatically expand and diversify their signaling capabilities. Recent work has begun to reveal the molecular basis by which two-component proteins evolve. How and why do orthologous signaling proteins diverge? How do cells gain new pathways and recognize new signals? What changes are needed to insulate a new pathway from existing pathways? What constraints are there on gene duplication and lateral gene transfer? Here, we review progress made in answering these questions, highlighting how the integration of genome sequence data with experimental studies is providing major new insights.

  18. The Evolution of Two-Component Signal Transduction Systems

    Science.gov (United States)

    Capra, Emily J.; Laub, Michael T.

    2014-01-01

    To exist in a wide range of environmental niches, bacteria must sense and respond to a myriad of external signals. A primary means by which this occurs is through two-component signal transduction pathways, typically comprised of a histidine kinase that receives the input stimuli and a response regulator that effects an appropriate change in cellular physiology. Histidine kinases and response regulators have an intrinsic modularity that separates signal input, phosphotransfer, and output response; this modularity has allowed bacteria to dramatically expand and diversify their signaling capabilities. Recent work has begun to reveal the molecular basis by which two-component proteins evolve. How and why do orthologous signaling proteins diverge? How do cells gain new pathways and recognize new signals? What changes are needed to insulate a new pathway from existing pathways? What constraints are there on gene duplication and lateral gene transfer? Here, we review progress made in answering these questions, highlighting how the integration of genome sequence data with experimental studies is providing major new insights. PMID:22746333

  19. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.

    Science.gov (United States)

    Pruitt, Kim D; Tatusova, Tatiana; Maglott, Donna R

    2005-01-01

    The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) provides a non-redundant collection of sequences representing genomic data, transcripts and proteins. Although the goal is to provide a comprehensive dataset representing the complete sequence information for any given species, the database pragmatically includes sequence data that are currently publicly available in the archival databases. The database incorporates data from over 2400 organisms and includes over one million proteins representing significant taxonomic diversity spanning prokaryotes, eukaryotes and viruses. Nucleotide and protein sequences are explicitly linked, and the sequences are linked to other resources including the NCBI Map Viewer and Gene. Sequences are annotated to include coding regions, conserved domains, variation, references, names, database cross-references, and other features using a combined approach of collaboration and other input from the scientific community, automated annotation, propagation from GenBank and curation by NCBI staff.

  20. The mechanism of signal transduction by two-component systems.

    Science.gov (United States)

    Casino, Patricia; Rubio, Vicente; Marina, Alberto

    2010-12-01

    Two-component systems, composed of a homodimeric histidine kinase (HK) and a response regulator (RR), are major signal transduction devices in bacteria. Typically the signal triggers HK autophosphorylation at one His residue, followed by phosphoryl transfer from the phospho-His to an Asp residue in the RR. Signal extinction frequently involves phospho-RR dephosphorylation by a phosphatase activity of the HK. Our understanding of these reactions and of the determinants of partner specificity among HK-RR couples has been greatly increased by recent crystal structures and biochemical experiments on HK-RR complexes. Cis-autophosphorylation (one subunit phosphorylates itself) occurs in some HKs while trans-autophosphorylation takes place in others. We review and integrate this new information, discuss the mechanism of the three reactions and propose a model for transmembrane signaling by these systems. Copyright © 2010 Elsevier Ltd. All rights reserved.

  1. Prognostic value of hedgehog signal component expressions in hepatoblastoma patients

    Directory of Open Access Journals (Sweden)

    Li Ying-Cun

    2010-11-01

    Full Text Available Abstract Objective Activation of hedgehog (Hh pathway has been implicated in the development of human malignancies. Hh as well as related downstream target genes has been extensively studied in many kinds of malignant tumours for clinical diagnostic or prognostic utilities. This study aimed at investigating whether Hh molecules provides a molecular marker of hepatoblastoma malignancy. Methods We obtained tissue sections from 32 patients with hepatoblastoma as well as cholestasis and normal control. Immunohistochemical analysis were performed to determine Hh signal components in human hepatoblastoma. The prognostic significance of single expression of Hh signal components were evaluated using Cox proportional hazards regression models and Kaplan-Meier survival analysis for statistical analysis. Results Expression of Hh signal components showed an increase in hepatoblastoma compared with chole stasis and normal tissues. There was a positive correlation between Smo or Gli1 expression and tumor clinicopathological features, such as histological type, tumor grade, tumor size and clinical stage. Both Smo or Gli1 protein high expression was significantly associated with poor prognosis by univariate analyses and multivariate analyses. Conclusions Abnormal Hh signaling activation plays important roles in the malignant potential of hepatoblastoma. Gli1 expression is an independent prognostic marker.

  2. Molecular Mechanisms of Two-Component Signal Transduction.

    Science.gov (United States)

    Zschiedrich, Christopher P; Keidel, Victoria; Szurmant, Hendrik

    2016-09-25

    Two-component systems (TCS) comprising sensor histidine kinases and response regulator proteins are among the most important players in bacterial and archaeal signal transduction and also occur in reduced numbers in some eukaryotic organisms. Given their importance to cellular survival, virulence, and cellular development, these systems are among the most scrutinized bacterial proteins. In the recent years, a flurry of bioinformatics, genetic, biochemical, and structural studies have provided detailed insights into many molecular mechanisms that underlie the detection of signals and the generation of the appropriate response by TCS. Importantly, it has become clear that there is significant diversity in the mechanisms employed by individual systems. This review discusses the current knowledge on common themes and divergences from the paradigm of TCS signaling. An emphasis is on the information gained by a flurry of recent structural and bioinformatics studies.

  3. Driving Electric Vehicle by EMG Signal Considering Frequency Components

    Science.gov (United States)

    Aso, Shinichi; Sasaki, Akinori; Hashimoto, Hiroshi; Ishii, Chiharu

    This paper proposes a useful method driving the electric vehicle by EMG signals (Electromyographic signals) which are filtered on the basis of frequency components which change with muscle contraction. This method estimates strength of muscular tension by a single EMG signal. By our method, user is able to control speed of the electric vehicle by strength of muscular tension. The method of speed control may give user good or bad operation feeling in the meaning of SD (Semantic Differential) method and factor analysis. The operation feeling is evaluated by experiment on EMG interface in cases of using filters or not. As a result, it is shown that operation feeling is influenced by this method.

  4. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.

    Science.gov (United States)

    Pruitt, Kim D; Tatusova, Tatiana; Maglott, Donna R

    2007-01-01

    NCBI's reference sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. The database includes 3774 organisms spanning prokaryotes, eukaryotes and viruses, and has records for 2,879,860 proteins (RefSeq release 19). RefSeq records integrate information from multiple sources, when additional data are available from those sources and therefore represent a current description of the sequence and its features. Annotations include coding regions, conserved domains, tRNAs, sequence tagged sites (STS), variation, references, gene and protein product names, and database cross-references. Sequence is reviewed and features are added using a combined approach of collaboration and other input from the scientific community, prediction, propagation from GenBank and curation by NCBI staff. The format of all RefSeq records is validated, and an increasing number of tests are being applied to evaluate the quality of sequence and annotation, especially in the context of complete genomic sequence.

  5. Rewiring two-component signal transduction with small RNAs.

    Science.gov (United States)

    Göpel, Yvonne; Görke, Boris

    2012-04-01

    Bacterial two-component systems (TCSs) and small regulatory RNAs (sRNAs) form densely interconnected networks that integrate and transduce information from the environment into fine-tuned changes of gene expression. Many TCSs control target genes indirectly through regulation of sRNAs, which in turn regulate gene expression by base-pairing with mRNAs or targeting a protein. Conversely, sRNAs may control TCS synthesis, thereby recruiting the TCS regulon to other regulatory networks. Several TCSs control expression of multiple homologous sRNAs providing the regulatory networks with further flexibility. These sRNAs act redundantly, additively or hierarchically on targets. The regulatory speed of sRNAs and their unique features in gene regulation make them ideal players extending the flexibility, dynamic range or timing of TCS signaling. Copyright © 2011 Elsevier Ltd. All rights reserved.

  6. Auxiliary phosphatases in two-component signal transduction.

    Science.gov (United States)

    Silversmith, Ruth E

    2010-04-01

    Signal termination in two-component systems occurs by loss of the phosphoryl group from the response regulator protein. This review explores our current understanding of the structures, catalytic mechanisms and means of regulation of the known families of phosphatases that catalyze response regulator dephosphorylation. The CheZ and CheC/CheX/FliY families, despite different overall structures, employ identical catalytic strategies using an amide side chain to orient a water molecule for in-line attack of the aspartyl phosphate. Spo0E phosphatases contain sequence and structural features that suggest a strategy similar to the chemotaxis phosphatases but the mechanism used by the Rap phosphatases is not yet elucidated. Identification of features shared by phosphatase families may aid in the identification of currently unrecognized classes of response regulator phosphatases. Copyright 2010 Elsevier Ltd. All rights reserved.

  7. HID-1, a New Component of the Peptidergic Signaling Pathway

    Science.gov (United States)

    Mesa, Rosana; Luo, Shuo; Hoover, Christopher M.; Miller, Kenneth; Minniti, Alicia; Inestrosa, Nibaldo; Nonet, Michael L.

    2011-01-01

    hid-1 was originally identified as a Caenorhabditis elegans gene encoding a novel conserved protein that regulates the decision to enter into the enduring dauer larval stage. We isolated a novel allele of hid-1 in a forward genetic screen for mutants mislocalizing RBF-1 rabphilin, a RAB-27 effector. Here we demonstrate that HID-1 functions in the nervous system to regulate neuromuscular signaling and in the intestine to regulate the defecation motor program. We further show that a conserved N-terminal myristoylated motif of both invertebrate and vertebrate HID-1 is essential for its association with intracellular membranes in nematodes and PC12 cells. C. elegans neuronal HID-1 resides on intracellular membranes in neuronal cell somas; however, the kinesin UNC-104 also transports HID-1 to synaptic regions. HID-1 accumulates in the axons of unc-13 and unc-31 mutants, suggesting it is associated with neurosecretory vesicles. Consistent with this, genetic studies place HID-1 in a peptidergic signaling pathway. Finally, a hid-1 null mutation reduces the levels of endogenous neuropeptides and alters the secretion of fluorescent-tagged cargos derived from neuronal and intestinal dense core vesicles (DCVs). Taken together, our findings indicate that HID-1 is a novel component of a DCV-based neurosecretory pathway and that it regulates one or more aspects of the biogenesis, maturation, or trafficking of DCVs. PMID:21115972

  8. Signaling Components Involved in Plant Responses to Phosphate Starvation

    Institute of Scientific and Technical Information of China (English)

    Hui Yuan; Dong Liu

    2008-01-01

    Phosphorus is one of the macronutrients essential for plant growth and development. Many soils around the world are deficient in phosphate (Pi) which is the form of phosphorus that plants can absorb and utilize. To cope with the stress of Pi starvation, plants have evolved many elaborate strategies to enhance the acquisition and utilization of Pi from the environment. These strategies include morphological, biochemical and physiological responses which ultimately enable plants to better survive under low Pi conditions. Though these adaptive responses have been well described because of their ecological and agricultural importance, our studies on the molecular mechanisms underlying these responses are still in their infancy. In the last decade, significant progresses have been made towards the identification of the molecular components which are involved in the control of plant responses to Pi starvation. In this article, we first provide an overview of some major responses of plants to Pi starvation, then summarize what we have known so tar about the signaling components involved in these responses, as well as the roles of sugar and phytohormones.

  9. A graph-theoretic approach for identifying non-redundant and relevant gene markers from microarray data using multiobjective binary PSO.

    Science.gov (United States)

    Mandal, Monalisa; Mukhopadhyay, Anirban

    2014-01-01

    The purpose of feature selection is to identify the relevant and non-redundant features from a dataset. In this article, the feature selection problem is organized as a graph-theoretic problem where a feature-dissimilarity graph is shaped from the data matrix. The nodes represent features and the edges represent their dissimilarity. Both nodes and edges are given weight according to the feature's relevance and dissimilarity among the features, respectively. The problem of finding relevant and non-redundant features is then mapped into densest subgraph finding problem. We have proposed a multiobjective particle swarm optimization (PSO)-based algorithm that optimizes average node-weight and average edge-weight of the candidate subgraph simultaneously. The proposed algorithm is applied for identifying relevant and non-redundant disease-related genes from microarray gene expression data. The performance of the proposed method is compared with that of several other existing feature selection techniques on different real-life microarray gene expression datasets.

  10. A graph-theoretic approach for identifying non-redundant and relevant gene markers from microarray data using multiobjective binary PSO.

    Directory of Open Access Journals (Sweden)

    Monalisa Mandal

    Full Text Available The purpose of feature selection is to identify the relevant and non-redundant features from a dataset. In this article, the feature selection problem is organized as a graph-theoretic problem where a feature-dissimilarity graph is shaped from the data matrix. The nodes represent features and the edges represent their dissimilarity. Both nodes and edges are given weight according to the feature's relevance and dissimilarity among the features, respectively. The problem of finding relevant and non-redundant features is then mapped into densest subgraph finding problem. We have proposed a multiobjective particle swarm optimization (PSO-based algorithm that optimizes average node-weight and average edge-weight of the candidate subgraph simultaneously. The proposed algorithm is applied for identifying relevant and non-redundant disease-related genes from microarray gene expression data. The performance of the proposed method is compared with that of several other existing feature selection techniques on different real-life microarray gene expression datasets.

  11. HARMONIC COMPONENT EXTRACTION FROM A CHAOTIC SIGNAL BASED ON EMPIRICAL MODE DECOMPOSITION METHOD

    Institute of Scientific and Technical Information of China (English)

    LI Hong-guang; MENG Guang

    2006-01-01

    A novel approach of signal extraction of a harmonic component from a chaotic signal generated by a Duffing oscillator was proposed. Based on empirical mode decomposition (EMD) and concept that any signal is composed of a series of the simple intrinsic modes, the harmonic components were extracted from the chaotic signals. Simulation results show the approach is satisfactory.

  12. Continuous Fourier transform method and apparatus. [for the analysis of simultaneous analog signal components

    Science.gov (United States)

    Munoz, R. M. (Inventor)

    1974-01-01

    An input analog signal to be frequency analyzed is separated into N number of simultaneous analog signal components each identical to the original but delayed relative to the original by a successively larger time delay. The separated and delayed analog components are combined together in a suitable number of adders and attenuators in accordance with at least one component product of the continuous Fourier transform and analog signal matrices to separate the analog input signal into at least one of its continuous analog frequency components of bandwidth 1/N times the bandwidth of the original input signal. The original analog input signal can be reconstituted by combining the separate analog frequency components in accordance with the component products of the continuous Fourier transform and analog frequency component matrices. The continuous Fourier transformation is useful for spectrum analysis, filtering, transfer function synthesis, and communications.

  13. Special Technology Area Review on Mixed-Signal Components

    Science.gov (United States)

    2000-04-01

    MEMS, mixed signal, physical-to-analog converters, and microwave applications. • Process reproducibility/design simplicity. Example: OPAMP 740. • Cost...Naval Surface Warfare Center OEM.................................................. Original Equipment Manufacturer OPAMP

  14. Signal integration by the two-component signal transduction response regulator CpxR.

    Science.gov (United States)

    Wolfe, Alan J; Parikh, Niyati; Lima, Bruno P; Zemaitaitis, Bozena

    2008-04-01

    The CpxAR two-component signal transduction system in Escherichia coli and other pathogens senses diverse envelope stresses and promotes the transcription of a variety of genes that remedy these stresses. An important member of the CpxAR regulon is cpxP. The CpxA-dependent transcription of cpxP has been linked to stresses such as misfolded proteins and alkaline pH. It also has been proposed that acetyl phosphate, the intermediate of the phosphotransacetylase (Pta)-acetate kinase (AckA) pathway, can activate the transcription of cpxP in a CpxA-independent manner by donating its phosphoryl group to CpxR. We tested this hypothesis by measuring the transcription of cpxP using mutants with mutations in the CpxAR pathway, mutants with mutations in the Pta-AckA pathway, and mutants with a combination of both types of mutations. From this epistasis analysis, we learned that CpxR integrates diverse stimuli. The stimuli that originate in the envelope depend on CpxA, while those associated with growth and central metabolism depend on the Pta-AckA pathway. While CpxR could receive a phosphoryl group from acetyl phosphate, this global signal was not the primary trigger for CpxR activation associated with the Pta-AckA pathway. On the strength of these results, we contend that the interactions between central metabolism and signal transduction can be quite complex and that successful investigations of such interactions must include a complete epistatic analysis.

  15. Multistep phosphorylation systems: tunable components of biological signaling circuits.

    Science.gov (United States)

    Valk, Evin; Venta, Rainis; Ord, Mihkel; Faustova, Ilona; Kõivomägi, Mardo; Loog, Mart

    2014-11-05

    Multisite phosphorylation of proteins is a powerful signal processing mechanism that plays crucial roles in cell division and differentiation as well as in disease. We recently demonstrated a novel phenomenon in cell cycle regulation by showing that cyclin-dependent kinase-dependent multisite phosphorylation of a crucial substrate is performed sequentially in the N-to-C terminal direction along the disordered protein. The process is controlled by key parameters, including the distance between phosphorylation sites, the distribution of serines and threonines in sites, and the position of docking motifs. According to our model, linear patterns of phosphorylation along disordered protein segments determine the signal-response function of a multisite phosphorylation switch. Here we discuss the general advantages and engineering principles of multisite phosphorylation networks as processors of kinase signals. We also address the idea of using the mechanistic logic of linear multisite phosphorylation networks to design circuits for synthetic biology applications.

  16. A novel "four-component" two-component signal transduction mechanism regulates developmental progression in Myxococcus xanthus.

    Science.gov (United States)

    Jagadeesan, Sakthimala; Mann, Petra; Schink, Christian W; Higgs, Penelope I

    2009-08-07

    Histidine-aspartate phosphorelays are employed by two-component signal transduction family proteins to mediate responses to specific signals or stimuli in microorganisms and plants. The RedCDEF proteins constitute a novel signaling system in which four two-component proteins comprising a histidine kinase, a histidine-kinase like protein, and two response regulators function together to regulate progression through the elaborate developmental program of Myxococcus xanthus. A combination of in vivo phenotypic analyses of in-frame deletions and non-functional point mutations in each gene as well as in vitro autophosphorylation and phosphotransfer analyses of recombinant proteins indicate that the RedC histidine kinase protein autophosphorylates and donates a phosphoryl group to the single domain response regulator, RedF, to repress progression through the developmental program. To relieve this developmental repression, RedC instead phosphorylates RedD, a dual receiver response regulator protein. Surprisingly, RedD transfers the phosphoryl group to the histidine kinase-like protein RedE, which itself appears to be incapable of autophosphorylation. Phosphorylation of RedE may render RedE accessible to RedF, where it removes the phosphoryl group from RedF-P, which is otherwise an unusually stable phosphoprotein. These analyses reveal a novel "four-component" signaling mechanism that has probably arisen to temporally coordinate signals controlling the developmental program in M. xanthus. The RedCDEF signaling system provides an important example of how the inherent plasticity and modularity of the basic two-component signaling domains comprise a highly adaptable framework well suited to expansion into complex signaling mechanisms.

  17. MATHEMATICAL SOLUTIONS OF VEHIULAR DELAY COMPONENTS AT SIGNALIZED INTERSECTIONS BASED ON APPROXIMATE CALCULATION METHOD

    Directory of Open Access Journals (Sweden)

    Halim CEYLAN

    2007-02-01

    Full Text Available This study develops approximate mathematical expressions for delay components at signalized intersections. Delay components are solved with the coordinate transformation method. The performance indicators for the signalized intersection are determined as an oversaturated and under saturated cases. During the analysis, the steady-state and the deterministic queuing theory are investigated first, and then time-dependent transformation is made. Developed model, called YHM, is applied to an example signalized intersection. Results are compared with the current situation and the Webster method. YHM is improved the intersection performance by about 500 % for this example. Moreover, signal parameters are significantly differs from the current and Webster signal control.

  18. WRKY Transcription Factors: Key Components in Abscisic Acid Signaling

    Science.gov (United States)

    2011-01-01

    2008). In cereals, upon imbibing, the embryos of nondormant seeds produce GA. This GA is transported to the aleurone, a thin layer of cells surround- ing...sensing, signaling and transport . Plant Cell Physiol. 51, 1821–1839. Urano, K., Kurihara, Y., Seki, M. and Shinozaki, K. (2010) ‘Omics’ analyses of...galactinol synthase (BhGolS1) promoter. Planta , 230, 1155–1166. Wu, F.-Q., Xin, Q., Cao, Z., Liu, Z.-Q., Du, S.-Y., Mei, C., Zhao, C.-X., Wang, X.-F

  19. TGF-β1 autocrine signalling and enamel matrix components.

    Science.gov (United States)

    Kobayashi-Kinoshita, Saeko; Yamakoshi, Yasuo; Onuma, Kazuo; Yamamoto, Ryuji; Asada, Yoshinobu

    2016-09-16

    Transforming growth factor-β1 (TGF-β1) is present in porcine enamel extracts and is critical for proper mineralization of tooth enamel. Here, we show that the mRNA of latent TGF-β1 is expressed throughout amelogenesis. Latent TGF-β1 is activated by matrix metalloproteinase 20 (MMP20), coinciding with amelogenin processing by the same proteinase. Activated TGF-β1 binds to the major amelogenin cleavage products, particularly the neutral-soluble P103 amelogenin, to maintain its activity. The P103 amelogenin-TGF-β1 complex binds to TGFBR1 to induce TGF-β1 signalling. The P103 amelogenin-TGF-β1 complex is slowly cleaved by kallikrein 4 (KLK4), which is secreted into the transition- and maturation-stage enamel matrix, thereby reducing TGF-β1 activity. To exert the multiple biological functions of TGF-β1 for amelogenesis, we propose that TGF-β1 is activated or inactivated by MMP20 or KLK4 and that the amelogenin cleavage product is necessary for the in-solution mobility of TGF-β1, which is necessary for binding to its receptor on ameloblasts and retention of its activity.

  20. TGF-β1 autocrine signalling and enamel matrix components

    Science.gov (United States)

    Kobayashi-Kinoshita, Saeko; Yamakoshi, Yasuo; Onuma, Kazuo; Yamamoto, Ryuji; Asada, Yoshinobu

    2016-01-01

    Transforming growth factor-β1 (TGF-β1) is present in porcine enamel extracts and is critical for proper mineralization of tooth enamel. Here, we show that the mRNA of latent TGF-β1 is expressed throughout amelogenesis. Latent TGF-β1 is activated by matrix metalloproteinase 20 (MMP20), coinciding with amelogenin processing by the same proteinase. Activated TGF-β1 binds to the major amelogenin cleavage products, particularly the neutral-soluble P103 amelogenin, to maintain its activity. The P103 amelogenin-TGF-β1 complex binds to TGFBR1 to induce TGF-β1 signalling. The P103 amelogenin-TGF-β1 complex is slowly cleaved by kallikrein 4 (KLK4), which is secreted into the transition- and maturation-stage enamel matrix, thereby reducing TGF-β1 activity. To exert the multiple biological functions of TGF-β1 for amelogenesis, we propose that TGF-β1 is activated or inactivated by MMP20 or KLK4 and that the amelogenin cleavage product is necessary for the in-solution mobility of TGF-β1, which is necessary for binding to its receptor on ameloblasts and retention of its activity. PMID:27633089

  1. Two-component systems and their co-option for eukaryotic signal transduction.

    Science.gov (United States)

    Schaller, G Eric; Shiu, Shin-Han; Armitage, Judith P

    2011-05-10

    Two-component signaling pathways involve histidine kinases, response regulators, and sometimes histidine-containing phosphotransfer proteins. Prevalent in prokaryotes, these signaling elements have also been co-opted to meet the needs of signal transduction in eukaryotes such as fungi and plants. Here we consider the evolution of such regulatory systems, with a particular emphasis on the roles they play in signaling by the plant hormones cytokinin and ethylene, in phytochrome-mediated perception of light, and as integral components of the circadian clock. Copyright © 2011 Elsevier Ltd. All rights reserved.

  2. A post-modification approach to independent component analysis for resolution of overlapping GC/MS signals: from independent components to chemical components

    Institute of Scientific and Technical Information of China (English)

    WANG Wei; CAI WenSheng; SHAO XueGuang

    2007-01-01

    Independent component analysis (ICA) has demonstrated its power to extract mass spectra from overlapping GC/MS signal. However, there is still a problem that mass spectra with negative peaks at some m/z will be obtained in the resolved results when there are overlapping peaks in the mass spectra of a mixture. Based on a detail theoretical analysis of the preconditions for ICA and the non-negative property of GC/MS signals, a post-modification based on chemical knowledge (PMBK) strategy is proposed to solve this problem. By both simulated and experimental GC/MS signals, it was proved that the PMBK strategy can improve the resolution effectively.

  3. Two-component signal transduction pathways regulating growth and cell cycle progression in a bacterium: a system-level analysis

    National Research Council Canada - National Science Library

    Skerker, Jeffrey M; Prasol, Melanie S; Perchuk, Barrett S; Biondi, Emanuele G; Laub, Michael T

    2005-01-01

    Two-component signal transduction systems, comprised of histidine kinases and their response regulator substrates, are the predominant means by which bacteria sense and respond to extracellular signals...

  4. Recurrence Quantification Analysis and Principal Components in the Detection of Short Complex Signals

    CERN Document Server

    Zbilut, J P; Webber, C L

    1998-01-01

    Recurrence plots were introduced to help aid the detection of signals in complicated data series. This effort was furthered by the quantification of recurrence plot elements. We now demonstrate the utility of combining recurrence quantification analysis with principal components analysis to allow for a probabilistic evaluation for the presence of deterministic signals in relatively short data lengths.

  5. Evolution and phyletic distribution of two-component signal transduction systems

    OpenAIRE

    Wuichet, Kristin; Cantwell, Brian J.; Zhulin, Igor B.

    2010-01-01

    Two-component signal transduction systems are abundant in prokaryotes. They enable cells to adjust multiple cellular functions in response to changing environmental conditions. These systems are also found, although in much smaller numbers, in lower eukaryotes and plants, where they appear to control a few very specific functions. Two-component systems have evolved in Bacteria from much simpler one-component systems bringing about the benefit of extracellular versus intracellular sensing. We ...

  6. Fatigue crack growth monitoring of idealized gearbox spline component using acoustic emission

    Science.gov (United States)

    Zhang, Lu; Ozevin, Didem; Hardman, William; Kessler, Seth; Timmons, Alan

    2016-04-01

    The spline component of gearbox structure is a non-redundant element that requires early detection of flaws for preventing catastrophic failures. The acoustic emission (AE) method is a direct way of detecting active flaws; however, the method suffers from the influence of background noise and location/sensor based pattern recognition method. It is important to identify the source mechanism and adapt it to different test conditions and sensors. In this paper, the fatigue crack growth of a notched and flattened gearbox spline component is monitored using the AE method in a laboratory environment. The test sample has the major details of the spline component on a flattened geometry. The AE data is continuously collected together with strain gauges strategically positions on the structure. The fatigue test characteristics are 4 Hz frequency and 0.1 as the ratio of minimum to maximum loading in tensile regime. It is observed that there are significant amount of continuous emissions released from the notch tip due to the formation of plastic deformation and slow crack growth. The frequency spectra of continuous emissions and burst emissions are compared to understand the difference of sudden crack growth and gradual crack growth. The predicted crack growth rate is compared with the AE data using the cumulative AE events at the notch tip. The source mechanism of sudden crack growth is obtained solving the inverse mathematical problem from output signal to input signal. The spline component of gearbox structure is a non-redundant element that requires early detection of flaws for preventing catastrophic failures. In this paper, the fatigue crack growth of a notched and flattened gearbox spline component is monitored using the AE method The AE data is continuously collected together with strain gauges. There are significant amount of continuous emissions released from the notch tip due to the formation of plastic deformation and slow crack growth. The source mechanism of

  7. A computational approach for ordering signal transduction pathway components from genomics and proteomics Data

    Directory of Open Access Journals (Sweden)

    Zhao Hongyu

    2004-10-01

    Full Text Available Abstract Background Signal transduction is one of the most important biological processes by which cells convert an external signal into a response. Novel computational approaches to mapping proteins onto signaling pathways are needed to fully take advantage of the rapid accumulation of genomic and proteomics information. However, despite their importance, research on signaling pathways reconstruction utilizing large-scale genomics and proteomics information has been limited. Results We have developed an approach for predicting the order of signaling pathway components, assuming all the components on the pathways are known. Our method is built on a score function that integrates protein-protein interaction data and microarray gene expression data. Compared to the individual datasets, either protein interactions or gene transcript abundance measurements, the integrated approach leads to better identification of the order of the pathway components. Conclusions As demonstrated in our study on the yeast MAPK signaling pathways, the integration analysis of high-throughput genomics and proteomics data can be a powerful means to infer the order of pathway components, enabling the transformation from molecular data into knowledge of cellular mechanisms.

  8. Evolution and phyletic distribution of two-component signal transduction systems.

    Science.gov (United States)

    Wuichet, Kristin; Cantwell, Brian J; Zhulin, Igor B

    2010-04-01

    Two-component signal transduction systems are abundant in prokaryotes. They enable cells to adjust multiple cellular functions in response to changing environmental conditions. These systems are also found, although in much smaller numbers, in lower eukaryotes and plants, where they appear to control a few very specific functions. Two-component systems have evolved in Bacteria from much simpler one-component systems bringing about the benefit of extracellular versus intracellular sensing. We review reports establishing the origins of two-component systems and documenting their occurrence in major lineages of Life. Copyright 2010 Elsevier Ltd. All rights reserved.

  9. Algorithm for Generating Non-Redundant Association Rules%一种无冗余的关联规则发现算法

    Institute of Scientific and Technical Information of China (English)

    高峰; 谢剑英

    2001-01-01

    关联规则是数据挖掘的重要研究内容之一,而传统算法生成的关联规则之间存在着大量的冗余规则.本文提出了一种通用的由最大频繁项目集生成无冗余关联规则的GNRR算法,利用规则之间的冗余关系,按一定顺序挖掘不同的规则,消除了规则之间的冗余性,使发现的规则数目呈指数倍减少.%The discovery of association rules is an important research topic in data mining, but the traditional association rules discovery algorithm produces too many redundant rules. This paper presented a general algorithm for mining non-redundant rules from the largest frequent itemsets using the redundant relationship of rules. The algorithm eliminates the redundancy between the rules and reduces the number of rules exponentially.

  10. Separating Fractal and Oscillatory Components in the Power Spectrum of Neurophysiological Signal.

    Science.gov (United States)

    Wen, Haiguang; Liu, Zhongming

    2016-01-01

    Neurophysiological field-potential signals consist of both arrhythmic and rhythmic patterns indicative of the fractal and oscillatory dynamics arising from likely distinct mechanisms. Here, we present a new method, namely the irregular-resampling auto-spectral analysis (IRASA), to separate fractal and oscillatory components in the power spectrum of neurophysiological signal according to their distinct temporal and spectral characteristics. In this method, we irregularly resampled the neural signal by a set of non-integer factors, and statistically summarized the auto-power spectra of the resampled signals to separate the fractal component from the oscillatory component in the frequency domain. We tested this method on simulated data and demonstrated that IRASA could robustly separate the fractal component from the oscillatory component. In addition, applications of IRASA to macaque electrocorticography and human magnetoencephalography data revealed a greater power-law exponent of fractal dynamics during sleep compared to wakefulness. The temporal fluctuation in the broadband power of the fractal component revealed characteristic dynamics within and across the eyes-closed, eyes-open and sleep states. These results demonstrate the efficacy and potential applications of this method in analyzing electrophysiological signatures of large-scale neural circuit activity. We expect that the proposed method or its future variations would potentially allow for more specific characterization of the differential contributions of oscillatory and fractal dynamics to distributed neural processes underlying various brain functions.

  11. Non-stationary component extraction in noisy multicomponent signal using polynomial chirping Fourier transform.

    Science.gov (United States)

    Lu, Wenlong; Xie, Junwei; Wang, Heming; Sheng, Chuan

    2016-01-01

    Inspired by track-before-detection technology in radar, a novel time-frequency transform, namely polynomial chirping Fourier transform (PCFT), is exploited to extract components from noisy multicomponent signal. The PCFT combines advantages of Fourier transform and polynomial chirplet transform to accumulate component energy along a polynomial chirping curve in the time-frequency plane. The particle swarm optimization algorithm is employed to search optimal polynomial parameters with which the PCFT will achieve a most concentrated energy ridge in the time-frequency plane for the target component. The component can be well separated in the polynomial chirping Fourier domain with a narrow-band filter and then reconstructed by inverse PCFT. Furthermore, an iterative procedure, involving parameter estimation, PCFT, filtering and recovery, is introduced to extract components from a noisy multicomponent signal successively. The Simulations and experiments show that the proposed method has better performance in component extraction from noisy multicomponent signal as well as provides more time-frequency details about the analyzed signal than conventional methods.

  12. A Novel Constrained Topographic Independent Component Analysis for Separation of Epileptic Seizure Signals

    Directory of Open Access Journals (Sweden)

    Min Jing

    2007-01-01

    Full Text Available Blind separation of the electroencephalogram signals (EEGs using topographic independent component analysis (TICA is an effective tool to group the geometrically nearby source signals. The TICA algorithm further improves the results if the desired signal sources have particular properties which can be exploited in the separation process as constraints. Here, the spatial-frequency information of the seizure signals is used to design a constrained TICA for the separation of epileptic seizure signal sources from the multichannel EEGs. The performance is compared with those from the TICA and other conventional ICA algorithms. The superiority of the new constrained TICA has been validated in terms of signal-to-interference ratio and correlation measurement.

  13. A post-modification approach to independent compo-nent analysis for resolution of overlapping GC/MS signals:from independent components to chemical components

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Independent component analysis (ICA) has demonstrated its power to extract mass spectra from over-lapping GC/MS signal. However, there is still a problem that mass spectra with negative peaks at some m/z will be obtained in the resolved results when there are overlapping peaks in the mass spectra of a mixture. Based on a detail theoretical analysis of the preconditions for ICA and the non-negative property of GC/MS signals, a post-modification based on chemical knowledge (PMBK) strategy is pro-posed to solve this problem. By both simulated and experimental GC/MS signals, it was proved that the PMBK strategy can improve the resolution effectively.

  14. Two-Component Signal Transduction Systems in the Cyanobacterium Synechocystis sp. PCC 6803

    Institute of Scientific and Technical Information of China (English)

    LIU Xingguo; HUANG Wei; WU Qingyu

    2006-01-01

    Two-component systems are signal transduction systems which enable bacteria to regulate cellular functions in response to changing environmental conditions. The unicellular Synechocystis sp. PCC 6803 has become a model organism for a range of biochemical and molecular biology studies aiming at investigating environmental stress response. The publication of the complete genome sequence of the cyanobacterium Synechocystis sp. PCC 6803 provided a tremendous stimulus for research in this field, and at least 80 open reading frames were identified as members of the two-component signal transduction systems in this single species of cyanobacteria. To date, functional roles have been determined for only a limited number of such proteins. This review summarizes our current knowledge about the two-component signal transduction systems in Synechocystis sp. PCC 6803 and describes recent achievements in elucidating the functional roles of these systems.

  15. Use of two-component signal transduction systems in the construction of synthetic genetic networks.

    Science.gov (United States)

    Ninfa, Alexander J

    2010-04-01

    Two-component signal transduction systems are a common type of signaling system in prokaryotes; the typical cell has dozens of systems regulating aspects of physiology and controlling responses to environmental conditions. In this review, I consider how these systems may be useful for engineering novel cell functions. Examples of successful incorporation of two-component systems into engineered systems are noted, and features of the systems that favor or hinder potential future use of these signaling systems for synthetic biology applications are discussed. The focus will be on the engineering of novel couplings of sensory functions to signaling outputs. Recent successes in this area are noted, such as the development of light-sensitive transmitter proteins and chemotactic receptors responsive to nitrate. Copyright 2010 Elsevier Ltd. All rights reserved.

  16. Multi-component LFM signal detection and parameter estimation based on Radon-HHT

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A new method is proposed to analyze multi-component linear frequency modulated (LFM) signals, which eliminates cross terms in conventional Wigner-Ville distribution (WVD). The approach is based on Radon transform and Hilbert-Huang transform (HHT), which is a recently developed method adaptive to non-linear and non-stationary signals. The complicated signal is decomposed into several intrinsic mode functions (IMF) by the empirical mode decomposition (EMD), which makes the consequent instantaneous frequency meaningful. After the instantaneous frequency and Hilbert spectrum are computed, multi-component LFM signals detection and parameter estimation are obtained using Radon transform on the Hilbert spectrum plane. The simulation results show its feasibility and effectiveness.

  17. Nonlinear real-life signal detection with a supervised principal components analysis.

    Science.gov (United States)

    Zhou, C T; Cai, T X; Cai, T F

    2007-03-01

    A novel strategy named supervised principal components analysis for the detection of a target signal of interest embedded in an unknown noisy environment has been investigated. There are two channels in our detection scheme. Each channel consists of a nonlinear phase-space reconstructor (for embedding a data matrix using the received time series) and a principal components analyzer (for feature extraction), respectively. The output error time series, which results from the difference of both eigenvectors of the correlation data matrices from these two channels, is then analyzed using time-frequency tools, for example, frequency spectrum or Wigner-Ville distribution. Experimental results based on real-life electromagnetic data are presented to demonstrate the detection performance of our algorithm. It is found that weak signals hidden beneath the noise floor can be detected. Furthermore, the robustness of the detection performance clearly illustrated that signal frequencies can be extracted when the signal power is not too low.

  18. Targeting two-component signal transduction: a novel drug discovery system.

    Science.gov (United States)

    Okada, Ario; Gotoh, Yasuhiro; Watanabe, Takafumi; Furuta, Eiji; Yamamoto, Kaneyoshi; Utsumi, Ryutaro

    2007-01-01

    We have developed two screening systems for isolating inhibitors that target bacterial two-component signal transduction: (1) a differential growth assay using a temperature-sensitive yycF mutant (CNM2000) of Bacillus subtilis, which is supersensitive to histidine kinase inhibitors, and (2) a high-throughput genetic system for targeting the homodimerization of histidine kinases essential for the bacterial two-component signal transduction. By using these methods, we have been able to identify various types of inhibitors that block the autophosphorylation of histidine kinases with different modes of actions.

  19. Role of functionality in two-component signal transduction: A stochastic study

    Science.gov (United States)

    Maity, Alok Kumar; Bandyopadhyay, Arnab; Chaudhury, Pinaki; Banik, Suman K.

    2014-03-01

    We present a stochastic formalism for signal transduction processes in a bacterial two-component system. Using elementary mass action kinetics, the proposed model takes care of signal transduction in terms of a phosphotransfer mechanism between the cognate partners of a two-component system, viz., the sensor kinase and the response regulator. Based on the difference in functionality of the sensor kinase, the noisy phosphotransfer mechanism has been studied for monofunctional and bifunctional two-component systems using the formalism of the linear noise approximation. Steady-state analysis of both models quantifies different physically realizable quantities, e.g., the variance, the Fano factor (variance/mean), and mutual information. The resultant data reveal that both systems reliably transfer information of extracellular environment under low external stimulus and in a high-kinase-and-phosphatase regime. We extend our analysis further by studying the role of the two-component system in downstream gene regulation.

  20. Highly Flexible Multimode Digital Signal Processing Systems Using Adaptable Components and Controllers

    Science.gov (United States)

    Kumar, Vinu Vijay; Lach, John

    2006-12-01

    Multimode systems have emerged as an area- and power-efficient platform for implementing multiple timewise mutually exclusive digital signal processing (DSP) applications in a single hardware space. This paper presents a design methodology for integrating flexible components and controllers into primarily fixed logic multimode DSP systems, thereby increasing their overall efficiency and implementation capabilities. The components are built using a technique called small-scale reconfigurability (SSR) that provides the necessary flexibility for both intermode and intramode reconfigurabilities, without the penalties associated with general-purpose reconfigurable logic. Using this methodology, area and power consumption are reduced beyond what is provided by current multimode systems, without sacrificing performance. The results show an average of 7% reduction in datapath component area, 26% reduction in register area, 36% reduction in interconnect MUX cost, and 68% reduction in the number of controller signals, with an average 38% increase in component utilization for a set of benchmark 32-bit DSP applications.

  1. Highly Flexible Multimode Digital Signal Processing Systems Using Adaptable Components and Controllers

    Directory of Open Access Journals (Sweden)

    Kumar Vinu Vijay

    2006-01-01

    Full Text Available Multimode systems have emerged as an area- and power-efficient platform for implementing multiple timewise mutually exclusive digital signal processing (DSP applications in a single hardware space. This paper presents a design methodology for integrating flexible components and controllers into primarily fixed logic multimode DSP systems, thereby increasing their overall efficiency and implementation capabilities. The components are built using a technique called small-scale reconfigurability (SSR that provides the necessary flexibility for both intermode and intramode reconfigurabilities, without the penalties associated with general-purpose reconfigurable logic. Using this methodology, area and power consumption are reduced beyond what is provided by current multimode systems, without sacrificing performance. The results show an average of 7% reduction in datapath component area, 26% reduction in register area, 36% reduction in interconnect MUX cost, and 68% reduction in the number of controller signals, with an average 38% increase in component utilization for a set of benchmark 32-bit DSP applications.

  2. Complex Signal Kurtosis and Independent Component Analysis for Wideband Radio Frequency Interference Detection

    Science.gov (United States)

    Schoenwald, Adam; Mohammed, Priscilla; Bradley, Damon; Piepmeier, Jeffrey; Wong, Englin; Gholian, Armen

    2016-01-01

    Radio-frequency interference (RFI) has negatively implicated scientific measurements across a wide variation passive remote sensing satellites. This has been observed in the L-band radiometers SMOS, Aquarius and more recently, SMAP [1, 2]. RFI has also been observed at higher frequencies such as K band [3]. Improvements in technology have allowed wider bandwidth digital back ends for passive microwave radiometry. A complex signal kurtosis radio frequency interference detector was developed to help identify corrupted measurements [4]. This work explores the use of ICA (Independent Component Analysis) as a blind source separation technique to pre-process radiometric signals for use with the previously developed real and complex signal kurtosis detectors.

  3. The Role of Cgrp-Receptor Component Protein (Rcp in Cgrp-Mediated Signal Transduction

    Directory of Open Access Journals (Sweden)

    M. A. Prado

    2001-01-01

    Full Text Available The calcitonin gene-related peptide (CGRP-receptor component protein (RCP is a 17-kDa intracellular peripheral membrane protein required for signal transduction at CGRP receptors. To determine the role of RCP in CGRP-mediated signal transduction, RCP was depleted from NIH3T3 cells using antisense strategy. Loss of RCP protein correlated with loss of cAMP production by CGRP in the antisense cells. In contrast, loss of RCP had no effect on CGRP-mediated binding; therefore RCP is not acting as a chaperone for the CGRP receptor. Instead, RCP is a novel signal transduction molecule that couples the CGRP receptor to the cellular signal transduction machinery. RCP thus represents a prototype for a new class of signal transduction proteins that are required for regulation of G protein-coupled receptors.

  4. Phosphate sink containing two-component signaling systems as tunable threshold devices

    DEFF Research Database (Denmark)

    Amin, Munia; Kothamachu, Varun B; Feliu, Elisenda

    2014-01-01

    -component signaling systems offer a rich diversity of sensory systems that are built around a core phosphotransfer reaction between histidine kinases and their output response regulator proteins, and thus are a good target for reengineering through synthetic biology. Here, we explore the signal-response relationship...... and define key parameters that control threshold levels and sensitivity of the signal-response curve. We confirm these findings experimentally, by in vitro reconstitution of the one HK-two RR motif found in the Sinorhizobium meliloti chemotaxis pathway and measuring the resulting signal-response curve. We...... to implement tunable switch-like signal processing and provides an ideal basis for developing threshold devices for synthetic biology applications....

  5. Cross-talk and specificity in two-component signal transduction pathways.

    Science.gov (United States)

    Agrawal, Ruchi; Sahoo, Bikash Kumar; Saini, Deepak Kumar

    2016-05-01

    Two-component signaling systems (TCSs) are composed of two proteins, sensor kinases and response regulators, which can cross-talk and integrate information between them by virtue of high-sequence conservation and modular nature, to generate concerted and diversified responses. However, TCSs have been shown to be insulated, to facilitate linear signal transmission and response generation. Here, we discuss various mechanisms that confer specificity or cross-talk among TCSs. The presented models are supported with evidence that indicate the physiological significance of the observed TCS signaling architecture. Overall, we propose that the signaling topology of any TCSs cannot be predicted using obvious sequence or structural rules, as TCS signaling is regulated by multiple factors, including spatial and temporal distribution of the participating proteins.

  6. A simple iterative independent component analysis algorithm for vibration source signal identification of complex structures

    Directory of Open Access Journals (Sweden)

    Lee Dong-Sup

    2015-01-01

    Full Text Available Independent Component Analysis (ICA, one of the blind source separation methods, can be applied for extracting unknown source signals only from received signals. This is accomplished by finding statistical independence of signal mixtures and has been successfully applied to myriad fields such as medical science, image processing, and numerous others. Nevertheless, there are inherent problems that have been reported when using this technique: instability and invalid ordering of separated signals, particularly when using a conventional ICA technique in vibratory source signal identification of complex structures. In this study, a simple iterative algorithm of the conventional ICA has been proposed to mitigate these problems. The proposed method to extract more stable source signals having valid order includes an iterative and reordering process of extracted mixing matrix to reconstruct finally converged source signals, referring to the magnitudes of correlation coefficients between the intermediately separated signals and the signals measured on or nearby sources. In order to review the problems of the conventional ICA technique and to validate the proposed method, numerical analyses have been carried out for a virtual response model and a 30 m class submarine model. Moreover, in order to investigate applicability of the proposed method to real problem of complex structure, an experiment has been carried out for a scaled submarine mockup. The results show that the proposed method could resolve the inherent problems of a conventional ICA technique.

  7. Phosphate sink containing two-component signaling systems as tunable threshold devices.

    Directory of Open Access Journals (Sweden)

    Munia Amin

    2014-10-01

    Full Text Available Synthetic biology aims to design de novo biological systems and reengineer existing ones. These efforts have mostly focused on transcriptional circuits, with reengineering of signaling circuits hampered by limited understanding of their systems dynamics and experimental challenges. Bacterial two-component signaling systems offer a rich diversity of sensory systems that are built around a core phosphotransfer reaction between histidine kinases and their output response regulator proteins, and thus are a good target for reengineering through synthetic biology. Here, we explore the signal-response relationship arising from a specific motif found in two-component signaling. In this motif, a single histidine kinase (HK phosphotransfers reversibly to two separate output response regulator (RR proteins. We show that, under the experimentally observed parameters from bacteria and yeast, this motif not only allows rapid signal termination, whereby one of the RRs acts as a phosphate sink towards the other RR (i.e. the output RR, but also implements a sigmoidal signal-response relationship. We identify two mathematical conditions on system parameters that are necessary for sigmoidal signal-response relationships and define key parameters that control threshold levels and sensitivity of the signal-response curve. We confirm these findings experimentally, by in vitro reconstitution of the one HK-two RR motif found in the Sinorhizobium meliloti chemotaxis pathway and measuring the resulting signal-response curve. We find that the level of sigmoidality in this system can be experimentally controlled by the presence of the sink RR, and also through an auxiliary protein that is shown to bind to the HK (yielding Hill coefficients of above 7. These findings show that the one HK-two RR motif allows bacteria and yeast to implement tunable switch-like signal processing and provides an ideal basis for developing threshold devices for synthetic biology applications.

  8. Climate signal detected in sub-fossil and living oak trees data. An analysis of signal frequency components

    Science.gov (United States)

    Constantin, Nechita; Francisca, Chiriloaei; Maria, Radoane; Ionel, Popa; Nicoae, Radoane

    2016-04-01

    This study is focused on analysis the frequency components of the signal detected in living and sub-fossil tree ring series from different time periods. The investigation is oriented to analyze signal frequency components (low and high) of the two categories of trees. The interpretation technique of tree ring width is the instrument most often used to elaborate past climatic reconstructions. The annual resolution, but also, the high capacity of trees to accumulate climatic information are attributes which confer to palaeo-environmental reconstructions the biggest credibility. The main objective of the study refers to the evaluation of climatic signal characteristics, both present day climate and palaeo-climate (last 7000 years BP). Modern dendrochronological methods were applied on 350 samples of sub-fossil trees and 400 living trees. The subfossil trunks were sampled from different fluvial environments (Siret, Suceava, Moldova). Their age was determined using radiocarbon, varying from under 100 years to almost 7000 years BP. The subfossil tree species investigated were Quercus, Alnus, Ulmus. Considering living trees, these were identified on eastern part of Romania, in different actual physico-geographical conditions. The studied living tree species consisted in Quercus species (robur and petraea). Each site was investigated regarding stress factors of the sampled tree. The working methods were applied to the total wood series, both late and early, to detect intra-annual level climate information. Each series has been tested to separate individual trees with climatic signal of other trees with different signals (noises determined by competition between individuals or site stress, or anthropic impact). Comparing dendrochronological series (sub-fossil and living trees) we want to identify what significant causes determined the difference in the signal frequencies. Especially, the human interventions registered in the last 2 centuries will be evaluated by these

  9. Chirp-Rate Resolution of Fractional Fourier Transform in Multi-component LFM Signal

    Institute of Scientific and Technical Information of China (English)

    LIU Feng; HUANG Yu; TAO Ran; WANG Yue

    2009-01-01

    Distinguishing close chirp-rates of different linear frequency modulation (LFM) signals under concentrated and complicated signal environment was studied.Firstly,detection and parameter estimation of multi-component LFM signal were used by discrete fast fractional Fourier transform (FrFT).Then the expression of chirp-rate resolution in fractional Fourier domain (FrFD) was deduced from discrete normalize time-frequency distribution,when multi-component LFM signal had only one center frequency.Furthermore,the detail influence of the sampling time,sampling frequeney and chirp-rate upon the resolution was analyzed by partial differential equation.Simulation results and analysis indicate that increasing the sampling time can enhance the resolution,but the influence of the sampling frequency can be omitted.What's more,in multi-component LFM signal,the chirp-rate resolution of FrFT is no less than a minimal value,and it mainly dependent on the biggest value of chirp-rates,with which it has an approximately positive exponential relationship.

  10. Efficient Low-Sensitivity Sampling of Multiband Signals with Bounded Components

    CERN Document Server

    Selva, J

    2010-01-01

    This paper presents an efficient method to sample multiband signals with bounded components, at a rate below the Nyquist limit, while keeping at the same time the numerical sensitivity at a low level. The method is based on band-limited windowing, followed by trigonometric approximation in consecutive time intervals. The key point is that the trigonometric approximation "inherits" the multiband property, that is, its coefficients are formed by bursts of non-zero elements corresponding to the multiband components. It is shown that this method can be well combined with the recently proposed synchronous multi-rate sampling (SMRS) scheme, given that the resulting linear system is sparse and formed by ones and zeroes. The proposed method allows one to trade sampling efficiency for noise sensitivity, and is specially well suited for bounded signals with unbounded energy like those in communications, navigation, audio systems, etc. Besides, it is also applicable to finite energy signals and periodic band-limited sig...

  11. Functional characterization and reconstitution of ABA signaling components using transient gene expression in rice protoplasts

    Directory of Open Access Journals (Sweden)

    Namhyo eKim

    2015-08-01

    Full Text Available The core component of ABA-dependent gene expression signaling have been identified in Arabidopsis and rice. This signaling pathway consists of four major components; group A OsbZIPs, SAPKs, subclass A OsPP2Cs and OsPYL/RCARs in rice. These might be able to make thousands of combinations through interaction networks resulting in diverse signaling responses. We tried to characterize those gene functions using transient gene expression for rice protoplasts (TGERP because it is instantaneous and convenient system. Firstly, in order to monitor the ABA signaling output, we developed reporter system named pRab16A-fLUC which consists of Rab16A promoter of rice and luciferase gene. It responses more rapidly and sensitively to ABA than pABRC3-fLUC that consists of ABRC3 of HVA1 promoter in TGERP. We screened the reporter responses for over-expression of each signaling components from group A OsbZIPs to OsPYL/RCARs with or without ABA in TGERP. OsbZIP46 induced reporter most strongly among OsbZIPs tested in the presence of ABA. SAPKs could activate the OsbZIP46 even in the ABA independence. Subclass A OsPP2C6 and -8 almost completely inhibited the OsbZIP46 activity in the different degree through the SAPK9. Lastly, OsPYL/RCAR2 and -5 rescued the OsbZIP46 activity in the presence of SAPK9 and OsPP2C6 dependent on ABA concentration and expression level. By using TGERP, we could characterize successfully the effects of ABA dependent gene expression signaling components in rice. In conclusion, TGERP represents very useful technology to study systemic functional genomics in rice or other monocots.

  12. Divergent receiver responses to components of multimodal signals in two foot-flagging frog species.

    Directory of Open Access Journals (Sweden)

    Doris Preininger

    Full Text Available Multimodal communication of acoustic and visual signals serves a vital role in the mating system of anuran amphibians. To understand signal evolution and function in multimodal signal design it is critical to test receiver responses to unimodal signal components versus multimodal composite signals. We investigated two anuran species displaying a conspicuous foot-flagging behavior in addition to or in combination with advertisement calls while announcing their signaling sites to conspecifics. To investigate the conspicuousness of the foot-flagging signals, we measured and compared spectral reflectance of foot webbings of Micrixalus saxicola and Staurois parvus using a spectrophotometer. We performed behavioral field experiments using a model frog including an extendable leg combined with acoustic playbacks to test receiver responses to acoustic, visual and combined audio-visual stimuli. Our results indicated that the foot webbings of S. parvus achieved a 13 times higher contrast against their visual background than feet of M. saxicola. The main response to all experimental stimuli in S. parvus was foot flagging, whereas M. saxicola responded primarily with calls but never foot flagged. Together these across-species differences suggest that in S. parvus foot-flagging behavior is applied as a salient and frequently used communicative signal during agonistic behavior, whereas we propose it constitutes an evolutionary nascent state in ritualization of the current fighting behavior in M. saxicola.

  13. Denoising of chaotic signal using independent component analysis and empirical mode decomposition with circulate translating

    Science.gov (United States)

    Wen-Bo, Wang; Xiao-Dong, Zhang; Yuchan, Chang; Xiang-Li, Wang; Zhao, Wang; Xi, Chen; Lei, Zheng

    2016-01-01

    In this paper, a new method to reduce noises within chaotic signals based on ICA (independent component analysis) and EMD (empirical mode decomposition) is proposed. The basic idea is decomposing chaotic signals and constructing multidimensional input vectors, firstly, on the base of EMD and its translation invariance. Secondly, it makes the independent component analysis on the input vectors, which means that a self adapting denoising is carried out for the intrinsic mode functions (IMFs) of chaotic signals. Finally, all IMFs compose the new denoised chaotic signal. Experiments on the Lorenz chaotic signal composed of different Gaussian noises and the monthly observed chaotic sequence on sunspots were put into practice. The results proved that the method proposed in this paper is effective in denoising of chaotic signals. Moreover, it can correct the center point in the phase space effectively, which makes it approach the real track of the chaotic attractor. Project supported by the National Science and Technology, China (Grant No. 2012BAJ15B04), the National Natural Science Foundation of China (Grant Nos. 41071270 and 61473213), the Natural Science Foundation of Hubei Province, China (Grant No. 2015CFB424), the State Key Laboratory Foundation of Satellite Ocean Environment Dynamics, China (Grant No. SOED1405), the Hubei Provincial Key Laboratory Foundation of Metallurgical Industry Process System Science, China (Grant No. Z201303), and the Hubei Key Laboratory Foundation of Transportation Internet of Things, Wuhan University of Technology, China (Grant No.2015III015-B02).

  14. Specificity residues determine binding affinity for two-component signal transduction systems.

    Science.gov (United States)

    Willett, Jonathan W; Tiwari, Nitija; Müller, Susanne; Hummels, Katherine R; Houtman, Jon C D; Fuentes, Ernesto J; Kirby, John R

    2013-11-05

    Two-component systems (TCS) comprise histidine kinases and their cognate response regulators and allow bacteria to sense and respond to a wide variety of signals. Histidine kinases (HKs) phosphorylate and dephosphorylate their cognate response regulators (RRs) in response to stimuli. In general, these reactions appear to be highly specific and require an appropriate association between the HK and RR proteins. The Myxococcus xanthus genome encodes one of the largest repertoires of signaling proteins in bacteria (685 open reading frames [ORFs]), including at least 127 HKs and at least 143 RRs. Of these, 27 are bona fide NtrC-family response regulators, 21 of which are encoded adjacent to their predicted cognate kinases. Using system-wide profiling methods, we determined that the HK-NtrC RR pairs display a kinetic preference during both phosphotransfer and phosphatase functions, thereby defining cognate signaling systems in M. xanthus. Isothermal titration calorimetry measurements indicated that cognate HK-RR pairs interact with dissociation constants (Kd) of approximately 1 µM, while noncognate pairs had no measurable binding. Lastly, a chimera generated between the histidine kinase, CrdS, and HK1190 revealed that residues conferring phosphotransfer and phosphatase specificity dictate binding affinity, thereby establishing discrete protein-protein interactions which prevent cross talk. The data indicate that binding affinity is a critical parameter governing system-wide signaling fidelity for bacterial signal transduction proteins. Using in vitro phosphotransfer and phosphatase profiling assays and isothermal titration calorimetry, we have taken a system-wide approach to demonstrate specificity for a family of two-component signaling proteins in Myxococcus xanthus. Our results demonstrate that previously identified specificity residues dictate binding affinity and that phosphatase specificity follows phosphotransfer specificity for cognate HK-RR pairs. The data

  15. A three-component model of the control error in manual tracking of continuous random signals.

    Science.gov (United States)

    Gerisch, Hans; Staude, Gerhard; Wolf, Werner; Bauch, Gerhard

    2013-10-01

    The performance of human operators acting within closed-loop control systems is investigated in a classic tracking task. The dependence of the control error (tracking error) on the parameters display gain, k(display), and input signal frequency bandwidth, f(g), which alter task difficulty and presumably the control delay, is studied with the aim of functionally specifying it via a model. The human operator as an element of a cascaded human-machine control system (e.g., car driving or piloting an airplane) codetermines the overall system performance. Control performance of humans in continuous tracking has been described in earlier studies. Using a handheld joystick, 10 participants tracked continuous random input signals. The parameters f(g) and k(display) were altered between experiments. Increased task difficulty promoted lengthened control delay and, consequently, increased control error.Tracking performance degraded profoundly with target deflection components above 1 Hz, confirming earlier reports. The control error is composed of a delay-induced component, a demand-based component, and a novel component: a human tracking limit. Accordingly, a new model that allows concepts of the observed control error to be split into these three components is suggested. To achieve optimal performance in control systems that include a human operator (e.g., vehicles, remote controlled rovers, crane control), (a) tasks should be kept as simple as possible to achieve shortest control delays, and (b) task components requiring higher-frequency (> 1 Hz) tracking actions should be avoided or automated by technical systems.

  16. Two-component mediated peroxide sensing and signal transduction in fission yeast.

    Science.gov (United States)

    Quinn, Janet; Malakasi, Panagiota; Smith, Deborah A; Cheetham, Jill; Buck, Vicky; Millar, Jonathan B A; Morgan, Brian A

    2011-07-01

    Two-component related proteins play a major role in regulating the oxidative stress response in the fission yeast, Schizosaccharomyces pombe. For example, the peroxide-sensing Mak2 and Mak3 histidine kinases regulate H(2)O(2)-induced activation of the Sty1 stress-activated protein kinase pathway, and the Skn7-related response regulator transcription factor, Prr1, is essential for activation of the core oxidative stress response genes. Here, we investigate the mechanism by which the S. pombe two-component system senses H(2)O(2), and the potential role of two-component signaling in the regulation of Prr1. Significantly, we demonstrate that PAS and GAF domains present in the Mak2 histidine kinase are essential for redox-sensing and activation of Sty1. In addition, we find that Prr1 is required for the transcriptional response to a wide range of H(2)O(2) concentrations and, furthermore, that two-component regulation of Prr1 is specifically required for the response of cells to high levels of H(2)O(2). Significantly, this provides the first demonstration that the conserved two-component phosphorylation site on Skn7-related proteins influences resistance to oxidative stress and oxidative stress-induced gene expression. Collectively, these data provide new insights into the two-component mediated sensing and signaling mechanisms underlying the response of S. pombe to oxidative stress.

  17. The evolution of multi-component visual signals in darters (genus Etheostoma

    Directory of Open Access Journals (Sweden)

    Jennifer M. GUMM, Tamra C. MENDELSON

    2011-04-01

    Full Text Available As complex traits evolve, each component of the trait may be under different selection pressures and could respond independently to distinct evolutionary forces. We used comparative methods to examine patterns of evolution in multiple components of a complex courtship signal in darters, specifically addressing the question of how nuptial coloration evolves across different areas of the body. Using spectral reflectance, we defined 4 broad color classes present on the body and fins of 17 species of freshwater fishes (genus Etheostoma and quantified differences in hue within each color class. Ancestral state reconstruction suggests that most color traits were expressed in the most recent common ancestor of sampled species and that differences among species are mostly due to losses in coloration. The evolutionary lability of coloration varied across body regions; we found significant phylogenetic signal for orange color on the body but not for most colors on fins. Finally, patterns of color evolution and hue of the colors were correlated among the two dorsal fins and between the anterior dorsal and anal fins, but not between any of the fins and the body. The observed patterns support the hypothesis that different components of complex signals may be subject to distinct evolutionary pressures, and suggests that the combination of behavioral displays and morphology in communication may have a strong influence on patterns of signal evolution [Current Zoology 57 (2: 125–139, 2011].

  18. Using structural information to change the phosphotransfer specificity of a two-component chemotaxis signalling complex.

    Directory of Open Access Journals (Sweden)

    Christian H Bell

    2010-02-01

    Full Text Available Two-component signal transduction pathways comprising histidine protein kinases (HPKs and their response regulators (RRs are widely used to control bacterial responses to environmental challenges. Some bacteria have over 150 different two-component pathways, and the specificity of the phosphotransfer reactions within these systems is tightly controlled to prevent unwanted crosstalk. One of the best understood two-component signalling pathways is the chemotaxis pathway. Here, we present the 1.40 A crystal structure of the histidine-containing phosphotransfer domain of the chemotaxis HPK, CheA(3, in complex with its cognate RR, CheY(6. A methionine finger on CheY(6 that nestles in a hydrophobic pocket in CheA(3 was shown to be important for the interaction and was found to only occur in the cognate RRs of CheA(3, CheY(6, and CheB(2. Site-directed mutagenesis of this methionine in combination with two adjacent residues abolished binding, as shown by surface plasmon resonance studies, and phosphotransfer from CheA(3-P to CheY(6. Introduction of this methionine and an adjacent alanine residue into a range of noncognate CheYs, dramatically changed their specificity, allowing protein interaction and rapid phosphotransfer from CheA(3-P. The structure presented here has allowed us to identify specificity determinants for the CheA-CheY interaction and subsequently to successfully reengineer phosphotransfer signalling. In summary, our results provide valuable insight into how cells mediate specificity in one of the most abundant signalling pathways in biology, two-component signal transduction.

  19. Extraction of pure components from overlapped signals in gas chromatography-mass spectrometry (GC-MS

    Directory of Open Access Journals (Sweden)

    Likić Vladimir A

    2009-10-01

    Full Text Available Abstract Gas chromatography-mass spectrometry (GC-MS is a widely used analytical technique for the identification and quantification of trace chemicals in complex mixtures. When complex samples are analyzed by GC-MS it is common to observe co-elution of two or more components, resulting in an overlap of signal peaks observed in the total ion chromatogram. In such situations manual signal analysis is often the most reliable means for the extraction of pure component signals; however, a systematic manual analysis over a number of samples is both tedious and prone to error. In the past 30 years a number of computational approaches were proposed to assist in the process of the extraction of pure signals from co-eluting GC-MS components. This includes empirical methods, comparison with library spectra, eigenvalue analysis, regression and others. However, to date no approach has been recognized as best, nor accepted as standard. This situation hampers general GC-MS capabilities, and in particular has implications for the development of robust, high-throughput GC-MS analytical protocols required in metabolic profiling and biomarker discovery. Here we first discuss the nature of GC-MS data, and then review some of the approaches proposed for the extraction of pure signals from co-eluting components. We summarize and classify different approaches to this problem, and examine why so many approaches proposed in the past have failed to live up to their full promise. Finally, we give some thoughts on the future developments in this field, and suggest that the progress in general computing capabilities attained in the past two decades has opened new horizons for tackling this important problem.

  20. Features of protein-protein interactions in two-component signaling deduced from genomic libraries.

    Science.gov (United States)

    White, Robert A; Szurmant, Hendrik; Hoch, James A; Hwa, Terence

    2007-01-01

    As more and more sequence data become available, new approaches for extracting information from these data become feasible. This chapter reports on one such method that has been applied to elucidate protein-protein interactions in bacterial two-component signaling pathways. The method identifies residues involved in the interaction through an analysis of over 2500 functionally coupled proteins and a precise determination of the substitutional constraints placed on one protein by its signaling mate. Once identified, a simple log-likelihood scoring procedure is applied to these residues to build a predictive tool for assigning signaling mates. The ability to apply this method is based on a proliferation of related domains within multiple organisms. Paralogous evolution through gene duplication and divergence of two-component systems has commonly resulted in tens of closely related interacting pairs within one organism with a roughly one-to-one correspondence between signal and response. This provides us with roughly an order of magnitude more protein pairs than there are unique, fully sequenced bacterial species. Consequently, this chapter serves as both a detailed exposition of the method that has provided more depth to our knowledge of bacterial signaling and a look ahead to what would be possible on a more widespread scale, that is, to protein-protein interactions that have only one example per genome, as the number of genomes increases by a factor of 10.

  1. Mixed-signal VLSI independent component analyzer for hearing aid applications.

    Science.gov (United States)

    Li, Shuo; Stanaćević, Milutin

    2014-01-01

    We present a mixed-signal architecture for implementation of independent component analysis designed for the task of blind source separation of acoustic sources interfacing miniature microphone array. The matrix-vector multiplication is implemented through integration of switched current sources controlled by the pulse-width modulated signals. The proposed architecture implementing 3×3 static ICA in 0.5μm CMOS technology occupies chip area of 0.49 mm(2) with the power consumption of 80μW at 5 V supply voltage.

  2. Independent Component Analysis of Complex Valued Signals Based on First-order Statistics

    Directory of Open Access Journals (Sweden)

    P.C. Xu

    2013-12-01

    Full Text Available This paper proposes a novel method based on first-order statistics, aims to solve the problem of the independent component extraction of complex valued signals in instantaneous linear mixtures. Single-step and iterative algorithms are proposed and discussed under the engineering practice. Theoretical performance analysis about asymptotic interference-to-signal ratio (ISR and probability of correct support estimation (PCE are accomplished. Simulation examples validate the theoretic analysis, and demonstrate that the single-step algorithm is extremely effective. Moreover, the iterative algorithm is more efficient than complex FastICA under certain circumstances.

  3. The Role of Cgrp-Receptor Component Protein (Rcp) in Cgrp-Mediated Signal Transduction

    OpenAIRE

    Prado, M.A.; B. Evans-Bain; Santi, S. L.; Dickerson, I M

    2001-01-01

    The calcitonin gene-related peptide (CGRP)-receptor component protein (RCP) is a 17-kDa intracellular peripheral membrane protein required for signal transduction at CGRP receptors. To determine the role of RCP in CGRP-mediated signal transduction, RCP was depleted from NIH3T3 cells using antisense strategy. Loss of RCP protein correlated with loss of cAMP production by CGRP in the antisense cells. In contrast, loss of RCP had no effect on CGRP-mediated binding; therefore RCP is not acting as...

  4. Two-component signal transduction system SaeRS positively regulates Staphylococcus epidermidis glucose metabolism.

    Science.gov (United States)

    Lou, Qiang; Qi, Yijun; Ma, Yuanfang; Qu, Di

    2014-01-01

    Staphylococcus epidermidis, which is a causative pathogen of nosocomial infection, expresses its virulent traits such as biofilm and autolysis regulated by two-component signal transduction system SaeRS. In this study, we performed a proteomic analysis of differences in expression between the S. epidermidis 1457 wild-type and saeRS mutant to identify candidates regulated by saeRS using two-dimensional gel electrophoresis (2-DE) combined with matrix-assisted laser desorption/lonization mass spectrometry (MALDI-TOF-MS). Of 55 identified proteins that significantly differed in expression between the two strains, 15 were upregulated and 40 were downregulated. The downregulated proteins included enzymes related to glycolysis and TCA cycle, suggesting that glucose is not properly utilized in S. epidermidis when saeRS was deleted. The study will be helpful for treatment of S. epidermidis infection from the viewpoint of metabolic modulation dependent on two-component signal transduction system SaeRS.

  5. Structural insight into partner specificity and phosphoryl transfer in two-component signal transduction.

    Science.gov (United States)

    Casino, Patricia; Rubio, Vicente; Marina, Alberto

    2009-10-16

    The chief mechanism used by bacteria for sensing their environment is based on two conserved proteins: a sensor histidine kinase (HK) and an effector response regulator (RR). The signal transduction process involves highly conserved domains of both proteins that mediate autokinase, phosphotransfer, and phosphatase activities whose output is a finely tuned RR phosphorylation level. Here, we report the structure of the complex between the entire cytoplasmic portion of Thermotoga maritima class I HK853 and its cognate, RR468, as well as the structure of the isolated RR468, both free and BeF(3)(-) bound. Our results provide insight into partner specificity in two-component systems, recognition of the phosphorylation state of each partner, and the catalytic mechanism of the phosphatase reaction. Biochemical analysis shows that the HK853-catalyzed autokinase reaction proceeds by a cis autophosphorylation mechanism within the HK subunit. The results suggest a model for the signal transduction mechanism in two-component systems.

  6. Expression of insulin signalling components in the sensory epithelium of the human saccule

    DEFF Research Database (Denmark)

    Degerman, Eva; Rauch, Uwe; Lindberg, Sven

    2013-01-01

    Several studies have demonstrated a link between diabetes and the dysfunction of the inner ear. Few studies, however, have reported the signalling mechanisms involved in metabolic control in human inner ear cells. Knowledge of the expression and role of the insulin receptor and downstream...... signalling components in the inner ear is sparce. Our immunohistochemistry approach has shown that the insulin receptor, insulin receptor substrate 1 (IRS1), protein kinase B (PKB) and insulin-sensitive glucose transporter (GLUT4) are expressed in the sensory epithelium of the human saccule, which also...... exhibits expression of a calcium-sensitive cAMP/cGMP phosphodiesterase 1C (PDE1C) and the vasopressin type 2 receptor. IRS1 and PDE1C are selectively expressed in sensory epithelial hair cells, whereas the other components are expressed in sensory epithelial supporting cells or in both cell types...

  7. Expression of canonical WNT/β-CATENIN signaling components in the developing human lung

    Directory of Open Access Journals (Sweden)

    Zhang Mingfeng

    2012-07-01

    Full Text Available Abstract Background The WNT/β-CATENIN signaling cascade is crucial for the patterning of the early lung morphogenesis in mice, but its role in the developing human lung remains to be determined. In this study, expression patterns of canonical WNT/β-CATENIN signaling components, including WNT ligands (WNT2, WNT7B, receptors ( FZD4, FZD7, LRP5, LRP6, transducers ( DVL2, DVL3, GSK-3β, β-CATENIN, APC, AXIN2, transcription factors ( TCF4, LEF1 and antagonists ( SOSTDC1 were examined in human embryonic lung at 7, 12, 17 and 21 weeks of gestation (W by real-time qRT-PCR and in situ hybridization. Results qRT-PCR analysis showed that some of these components were gradually upregulated, while some were significantly downregulated from the 7 W to the 12 W. However, most components reached a high level at 17 W, with a subsequent decrease at 21 W. In situ hybridization showed that the canonical WNT ligands and receptors were predominantly located in the peripheral epithelium, whereas the canonical WNT signal transducers and transcription factors were not only detected in the respiratory epithelium, but some were also scattered at low levels in the surrounding mesenchyme in the developing human lung. Furthermore, Western blot, qRT-PCR and histological analysis demonstrated that the β-CATENIN-dependent WNT signaling in embryonic human lung was activated in vitro by CHIR 99021 stimulation. Conclusions This study of the expression patterns and in vitro activity of the canonical WNT/β-CATENIN pathways suggests that these components play an essential role in regulation of human lung development.

  8. Dopamine reward prediction-error signalling: a two-component response

    Science.gov (United States)

    Schultz, Wolfram

    2017-01-01

    Environmental stimuli and objects, including rewards, are often processed sequentially in the brain. Recent work suggests that the phasic dopamine reward prediction-error response follows a similar sequential pattern. An initial brief, unselective and highly sensitive increase in activity unspecifically detects a wide range of environmental stimuli, then quickly evolves into the main response component, which reflects subjective reward value and utility. This temporal evolution allows the dopamine reward prediction-error signal to optimally combine speed and accuracy. PMID:26865020

  9. In vivo study of the two-component signaling network in Escherichia coli

    OpenAIRE

    Sommer, Erik

    2012-01-01

    Microorganisms commonly use ‘two-component’ signaling systems for sensing environmental conditions, with members being present in nearly all bacterial and archaeal genomes in different numbers. Prototypical two-component systems are comprised of a sensory histidine kinase and a response regulator protein that is phosphorylated by the kinase. The regulator typically acts as a transcription factor regulating gene expression. Due to their prevalence in microorganisms, a basic understanding of th...

  10. General aspects of two-component regulatory circuits in bacteria: Domains, signals and roles.

    Science.gov (United States)

    Padilla-Vaca, Felipe; Mondragón-Jaimes, Verónica; Franco, Bernardo

    2016-08-09

    All living organisms are subject to changing environments, which must be sensed in order to respond swiftly and efficiently. Two-component systems (TCS) are signal transduction regulatory circuits based typically on a membrane bound sensor kinase and a cytoplasmic response regulator, that is activated through a histidine to aspartate phosphorelay reactions. Activated response regulator acts usually as a transcription factor. The best known examples were identified in bacteria, but they are also found in fungi, algae and plants. Thus far, they are not found in mammals. Regulatory circuits coupled to two-component systems exhibit a myriad of responses to environmental stimuli such as: redox potential, pH, specific metabolites, pressure, light and more recently to specific antimicrobial peptides that activate a sensor kinase responsible for expressing virulence factors through the active response regulator. In this review we explore general aspects on two-component systems that ultimately can play a role on virulence regulation, also the intriguing domain properties of the sensor kinases that can be a potential target for antimicrobial compounds. Only a handful of sensor kinases are extensively characterized, the vast majority belong to what we call 'the dark matter of bacterial signal transduction' since no known signal, structure and biochemical properties are available. Regulatory circuits from vertebrate pathogenic organisms can explain virulence in terms of either response to environmental factors or specific niche occupancy. Hopefully, knowledge on these signal transduction systems can lead to identify novel molecules that target two-component systems, since the increase of drug resistant microorganisms is worrisome.

  11. Histidine Phosphotransfer Proteins in Fungal Two-Component Signal Transduction Pathways

    OpenAIRE

    2013-01-01

    The histidine phosphotransfer (HPt) protein Ypd1 is an important participant in the Saccharomyces cerevisiae multistep two-component signal transduction pathway and, unlike the expanded histidine kinase gene family, is encoded by a single gene in nearly all model and pathogenic fungi. Ypd1 is essential for viability in both S. cerevisiae and in Cryptococcus neoformans. These and other aspects of Ypd1 biology, combined with the availability of structural and mutational data in S. cerevisiae, s...

  12. REVIEW: Previous Deception detection methods and New proposed method using independent component analysis of EEG signals.

    Directory of Open Access Journals (Sweden)

    Roshni D. Tale

    2014-04-01

    Full Text Available Deception detection has important legal and medical applications, but the reliability of methods for the differentiation between truthful and deceptive responses is still limited. Deception detection can be more accurately achieved by measuring the brain correlates of lying in an individual. For the evaluation of the method, several participants were gone through the designed concealed information test paradigm and their respective brain signals were recorded. The electroencephalogram (EEG signals were recorded and separated into many single trials. To enhance signal noise ratio (SNR of P3 components, the independent component analysis (ICA method was adopted to separate non-P3 (i.e. artifacts and P3 components from every single trial. Then the P3 waveforms with high SNR were reconstructed. And then group of features based on time, frequency, and amplitude were extracted from the reconstructed P3 waveforms. Finally, two different class of feature samples were used to train a support vector machine (SVM classifier because it has higher performance compared with several other classifiers. The method presented in this paper improves the efficiency of CIT and deception detection in comparison with previous reported methods.

  13. Blind Extraction of Chaotic Signals by Using the Fast Independent Component Analysis Algorithm

    Institute of Scientific and Technical Information of China (English)

    CHEN Hong-Bin; FENG Jiu-Chao; FANG Yong

    2008-01-01

    We report the results of using the fast independent component analysis(FastICA)algorithm to realize blind extraction of chaotic signals.Two cases are taken into consideration:namely,the mixture is noiseless or contaminated by noise.Pre-whitening is employed to reduce the effect of noise before using the FastICA algorithm.The correlation coefficient criterion is adopted to evaluate the performance,and the success rate is defined as a new criterion to indicate the performance with respect to noise or different mixing matrices.Simulation results show that the FastICA algorithm can extract the chaotic signals effectively.The impact of noise,the length of a signal frame,the number of sources and the number of observed mixtures on the performance is investigated in detail.It is also shown that regarding a noise as an independent source is not always correct.

  14. Blind Separation of Acoustic Signals Combining SIMO-Model-Based Independent Component Analysis and Binary Masking

    Directory of Open Access Journals (Sweden)

    Hiekata Takashi

    2006-01-01

    Full Text Available A new two-stage blind source separation (BSS method for convolutive mixtures of speech is proposed, in which a single-input multiple-output (SIMO-model-based independent component analysis (ICA and a new SIMO-model-based binary masking are combined. SIMO-model-based ICA enables us to separate the mixed signals, not into monaural source signals but into SIMO-model-based signals from independent sources in their original form at the microphones. Thus, the separated signals of SIMO-model-based ICA can maintain the spatial qualities of each sound source. Owing to this attractive property, our novel SIMO-model-based binary masking can be applied to efficiently remove the residual interference components after SIMO-model-based ICA. The experimental results reveal that the separation performance can be considerably improved by the proposed method compared with that achieved by conventional BSS methods. In addition, the real-time implementation of the proposed BSS is illustrated.

  15. Relationship of oscillating and average components of laser Doppler flowmetry signal

    Science.gov (United States)

    Mizeva, Irina; Frick, Peter; Podtaev, Sergey

    2016-08-01

    Signals from laser Doppler flowmeters widely used in intravital studies of skin blood flow include, along with a slowly varying average component, an oscillating part. However, in most clinical studies, pulsations are usually smoothed by data preprocessing and only the mean blood flow is analyzed. To reveal the relationship between average and oscillating perfusion components measured by a laser Doppler flowmeter, we examined the microvascular response to the contralateral cold pressor test recorded at two different sites of the hand: dorsal part of the arm and finger pad. Such a protocol makes it possible to provide a wide range of perfusion. The average perfusion always decreases during cooling, while the oscillating component demonstrates a differently directed response. The wavelet analysis of laser Doppler flowmetry (LDF) signals shows that the pulsatile component is nonlinearly related to the average perfusion. Under low perfusion, the amplitude of pulsations is proportional to its mean value, but, as perfusion increases, the amplitude of pulsations becomes lower. The type of response is defined by the basal perfusion and the degree of vasoconstriction caused by cooling. Interpretation of the results is complicated by the nonlinear transfer function of the LDF device, the contribution of which is studied using artificial examples.

  16. Analysis and Classification of Acoustic Emission Signals During Wood Drying Using the Principal Component Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Ho Yang [Korea Research Institute of Standards and Science, Daejeon (Korea, Republic of); Kim, Ki Bok [Chungnam National University, Daejeon (Korea, Republic of)

    2003-06-15

    In this study, acoustic emission (AE) signals due to surface cracking and moisture movement in the flat-sawn boards of oak (Quercus Variablilis) during drying under the ambient conditions were analyzed and classified using the principal component analysis. The AE signals corresponding to surface cracking showed higher in peak amplitude and peak frequency, and shorter in rise time than those corresponding to moisture movement. To reduce the multicollinearity among AE features and to extract the significant AE parameters, correlation analysis was performed. Over 99% of the variance of AE parameters could be accounted for by the first to the fourth principal components. The classification feasibility and success rate were investigated in terms of two statistical classifiers having six independent variables (AE parameters) and six principal components. As a result, the statistical classifier having AE parameters showed the success rate of 70.0%. The statistical classifier having principal components showed the success rate of 87.5% which was considerably than that of the statistical classifier having AE parameters

  17. The role of the CGRP-receptor component protein (RCP) in adrenomedullin receptor signal transduction.

    Science.gov (United States)

    Prado, M A; Evans-Bain, B; Oliver, K R; Dickerson, I M

    2001-11-01

    G protein-coupled receptors are usually thought to act as monomer receptors that bind ligand and then interact with G proteins to initiate signal transduction. In this study we report an intracellular peripheral membrane protein named the calcitonin gene-related peptide (CGRP)-receptor component protein (RCP) required for signal transduction at the G protein-coupled receptor for adrenomedullin. Cell lines were made that expressed an antisense construct of the RCP cDNA, and in these cells diminished RCP expression correlated with loss of adrenomedullin signal transduction. In contrast, loss of RCP did not diminish receptor density or affinity, therefore RCP does not appear to act as a chaperone protein. Instead, RCP represents a novel class of protein required to couple the adrenomedullin receptor to the cellular signal transduction pathway. A candidate adrenomedullin receptor named the calcitonin receptor-like receptor (CRLR) has been described, which forms high affinity adrenomedullin receptors when co-expressed with the accessory protein receptor-activity modifying protein 2 (RAMP2). RCP co-immunoprecipitated with CRLR and RAMP2, indicating that a functional adrenomedullin receptor is composed of at least three proteins: the ligand binding protein (CRLR), an accessory protein (RAMP2), and a coupling protein for signal transduction (RCP).

  18. SNMP is a signaling component required for pheromone sensitivity in Drosophila.

    Science.gov (United States)

    Jin, Xin; Ha, Tal Soo; Smith, Dean P

    2008-08-05

    The only known volatile pheromone in Drosophila, 11-cis-vaccenyl acetate (cVA), mediates a variety of behaviors including aggregation, mate recognition, and sexual behavior. cVA is detected by a small set of olfactory neurons located in T1 trichoid sensilla on the antennae of males and females. Two components known to be required for cVA reception are the odorant receptor Or67d and the extracellular pheromone-binding protein LUSH. Using a genetic screen for cVA-insensitive mutants, we have identified a third component required for cVA reception: sensory neuron membrane protein (SNMP). SNMP is a homolog of CD36, a scavenger receptor important for lipoprotein binding and uptake of cholesterol and lipids in vertebrates. In humans, loss of CD36 is linked to a wide range of disorders including insulin resistance, dyslipidemia, and atherosclerosis, but how CD36 functions in lipid transport and signal transduction is poorly understood. We show that SNMP is required in pheromone-sensitive neurons for cVA sensitivity but is not required for sensitivity to general odorants. Using antiserum to SNMP infused directly into the sensillum lymph, we show that SNMP function is required on the dendrites of cVA-sensitive neurons; this finding is consistent with a direct role in cVA signal transduction. Therefore, pheromone perception in Drosophila should serve as an excellent model to elucidate the role of CD36 members in transmembrane signaling.

  19. [Equalization of whole-band signal's SNR in the blood components noninvasive measurement].

    Science.gov (United States)

    Li, Gang; Wang, Hui-quan; Zhang, Hao; Lin, Ling; Wu, Xiao-rong; Zhang, Bao-ju

    2012-02-01

    To fully extend the category of blood components that can be noninvasively measured by dynamic spectrum (DS) method and to increase its measuring precision, an overall consideration of light source, tissue absorption and sensor's sensitivity was made. Compensating the light source and adding the telecentric lens not only expand the spectral effective detecting range, but also balance the signal-to-noise ratio (SNR) of the photoelectric pulse in the whole band equalization. The integral SNR of DS signal was increased and the measurement bandwidth was expanded. The effectiveness of this method was validated by the quality evaluation criterion of DS data: the effective detecting range of visible DS was widened from 600-1 000 nm to 500-1 135 nm; the effective detecting range of near-infrared DS was widened from 900-1 100 nm to 900-1 700 nm. The results show that the design can create the condition for detection of new blood components noninvasively, and enhance the prediction accuracy of the blood components, for which noninvasive measuring using DS method has been achieved.

  20. An intimate link: two-component signal transduction systems and metal transport systems in bacteria.

    Science.gov (United States)

    Singh, Kamna; Senadheera, Dilani B; Cvitkovitch, Dennis G

    2014-01-01

    Bacteria have evolved various strategies to contend with high concentrations of environmental heavy metal ions for rapid, adaptive responses to maintain cell viability. Evidence gathered in the past two decades suggests that bacterial two-component signal transduction systems (TCSTSs) are intimately involved in monitoring cation accumulation, and can regulate the expression of related metabolic and virulence genes to elicit adaptive responses to changes in the concentration of these ions. Using examples garnered from recent studies, we summarize the cross-regulatory relationships between metal ions and TCSTSs. We present evidence of how bacterial TCSTSs modulate metal ion homeostasis and also how metal ions, in turn, function to control the activities of these signaling systems linked with bacterial survival and virulence.

  1. Using Heterologous COS-7 Cells to Identify Semaphorin-Signaling Components.

    Science.gov (United States)

    Sakurai, Atsuko; Doçi, Colleen L; Gutkind, J Silvio

    2017-01-01

    Semaphorins are a family of membrane-bound and secreted type of proteins which were initially identified as chemorepulsive axon guidance molecules. Plexins and neuropilins are two major receptor families of semaphorins, and their common downstream targets are the actin cytoskeleton and cell-to-extracellular matrix adhesions. Semaphorins promote the collapse of growth cones by inducing rapid changes in the cytoskeleton and disassembly of focal adhesion structures. When transfected with appropriate receptors, non-neuronal COS-7 cells exhibit a similar cell collapse phenotype upon semaphorin stimulation. This heterologous system using COS-7 cells has been developed and widely used to investigate semaphorin-signaling pathways. In this chapter, we describe a COS-7 collapse assay protocol used to identify semaphorin-signaling components and a method to produce recombinant class 3 semaphorin proteins.

  2. Electrical Signal Path Study and Component Assay for the MAJORANA N-Type Segmented Contact Detector

    Energy Technology Data Exchange (ETDEWEB)

    Amman, Mark; Bergevin, Marc; Chan, Yuen-Dat; Detwiler, Jason A.; Fujikawa, Brian .; Lesko, Kevin T.; Luke, Paul N.; Prior, Gersende; Poon, Alan W.; Smith, Alan R.; Vetter, Kai; Yaver, Harold; Zimmermann, Sergio

    2009-02-24

    The purpose of the present electrical signal path study is to explore the various issues related to the deployment of highly-segmented low-background Ge detectors for the MAJORANA double-beta decay experiment. A significant challenge is to simultaneously satisfy competing requirements for the mechanical design, electrical readout performance, and radiopurity specifications from the MAJORANA project. Common to all rare search experiments, there is a very stringent limit on the acceptable radioactivity level of all the electronics components involved. Some of the findings are summarized in this report.

  3. Genomic analysis of two-component signal transduction proteins in basidiomycetes.

    Science.gov (United States)

    Lavín, José L; Ramírez, Lucía; Ussery, David W; Pisabarro, Antonio G; Oguiza, José A

    2010-01-01

    Two-component system (TCS) proteins are components of complex signal transduction pathways in fungi, and play essential roles in the regulation of several cellular functions and responses. Species of basidiomycetes have a marked variation in their specific physiological traits, morphological complexity and lifestyles. In this study, we have used the available complete genomes of basidiomycetes to carry out a thorough identification and an extensive comparative analysis of the TCS proteins in this fungal phylum. In comparison with ascomycetes, basidiomycetes exhibit an intermediate number of TCS proteins. Several TCS proteins are highly conserved among all the basidiomycetes, and other TCS proteins appear to be specific to particular species of basidiomycetes. Moreover, some species appear to have developed a unique histidine kinase group with unusual domain architecture, the Dual-histidine kinases. The presence of differential sets of TCS proteins between basidiomycete species might reflect their adaptation to diverse environmental niches.

  4. GFExtractor:事件序列上有效挖掘无冗余情节规则的算法%GFExtractor:algorithm of mining non-redundant episode rules effectively in event sequence

    Institute of Scientific and Technical Information of China (English)

    袁红娟

    2013-01-01

    事件序列上挖掘情节规则,旨在发现情节之间的因果关系。基于非重叠的最小发生的支持度定义及深度优先搜索策略,提出在事件序列上挖掘无冗余情节规则的GFExtractor算法。利用非生成子情节的剪枝策略,淘汰非生成子情节;利用向前、向后扩展检查,淘汰非闭情节;最终在情节生成子集Gen与频繁闭情节集FCE之间产生无冗余的情节规则。实验结果证实了算法在事件序列上挖掘无冗余情节规则的有效性。%Mining episode rules in event sequence aims to discover the causal relationship between the episodes. To mine non-redundant episode rules in event sequence, the algorithm of GFExtractor is proposed in this paper, based on the support defi-nition of non-overlapping minimal occurrences and the depth-first search strategy. GFExtractor uses the pruning technology to eliminate non-generator episodes, and uses the forward and backward extension check to eliminate non-closed episodes. Non-redundant episode rules are generated between a superset of Gen and FCE. Experimental results confirm the validity of algo-rithm in mining non-redundant episode rules in event sequence.

  5. A Small G Protein as a Novel Component of the Rice Brassinosteroid Signal Transduction.

    Science.gov (United States)

    Zhang, Ge; Song, Xiaoguang; Guo, Hongyan; Wu, Yao; Chen, Xiaoying; Fang, Rongxiang

    2016-09-01

    Brassinosteroids (BRs) are a class of steroid hormones that are essential for plant growth and development. The BR signal transduction pathway in the dicot model plant Arabidopsis is well established, but the components connecting the BR signaling steps in rice have not been fully explored. For example, how the BR signaling is fine-tuned in rice, especially at the BR receptor level, is largely unknown. Here we show that OsPRA2, a rice small G protein, plays a repressive role in the BR signaling pathway. Lamina inclination, coleoptile elongation, and root inhibition assays indicated that rice plants with suppressed expression of OsPRA2 were more sensitive to exogenously applied brassinolide than the wild-type plants. Conversely, rice overexpressing OsPRA2 was less sensitive to exogenous brassinolide. Further study uncovered that OsPRA2 inhibited the dephosphorylation of, and thus inactivated the transcription factor BRASSINAZOLE-RESISTANT 1 (OsBZR1). More importantly, OsPRA2 was found to co-localize with and directly bind to rice BR receptor BRASSINOSTEROID-INSENSITIVE 1 (OsBRI1) at the plasma membrane. Additionally, the in vitro assays showed that OsPRA2 inhibits its autophosphorylation. This OsPRA2-OsBRI1 interaction led to the dissociation of OsBRI1 from its co-receptor OsBAK1, and abolished OsBRI1-mediated phosphorylation of OsBAK1. Together, these results reveal a possible working mechanism of OsPRA2 as a novel negative regulator on OsBRI1 and OsBZR1 and extend the knowledge about the regulatory mechanism of rice BR signaling.

  6. Comparative Analysis of Two-component Signal Transduction System in Two Streptomycete Genomes

    Institute of Scientific and Technical Information of China (English)

    Wu WEI; Yixue LI; Weihua WANG; Zhiwei CAO; Hong YU; Xiaojing WANG; Jing ZHAO; Hao TAN; Hao XU; Weihong JIANG

    2007-01-01

    Species of the genus Streptomyces are major bacteria responsible for producing most natural antibiotics. Streptomyces coelicolor A3(2) and Streptomyces avermitilis were sequenced in 2002 and 2003,respectively. Two-component signal transduction systems (TCSs), consisting of a histidine sensor kinase (SK) and a cognate response regulator (RR), form the most common mechanism of transmembrane signal transduction in prokaryotes. TCSs in S. coelicolor A3(2) have been analyzed in detail. Here, we identify and classify the SK and RR of S. avermitilis and compare the TCSs with those of S. coelicolor A3(2) by computational approaches. Phylogenetic analysis of the cognate SK-RR pairs of the two species indicated that the cognate SK-RR pairs fall into four classes according to the distribution of their orthologs in other organisms. In addition to the cognate SK-RR pairs, some potential partners of non-cognate SK-RR were found, including those of unpaired SK and orphan RR and the cross-talk between different components in either strain. Our study provides new clues for further exploration of the molecular regulation mechanism of streptomycetes with industrial importance.

  7. LINGO-1 is a component of the Nogo-66 receptor/p75 signaling complex.

    Science.gov (United States)

    Mi, Sha; Lee, Xinhua; Shao, Zhaohui; Thill, Greg; Ji, Benxiu; Relton, Jane; Levesque, Melissa; Allaire, Norm; Perrin, Steve; Sands, Bryan; Crowell, Thomas; Cate, Richard L; McCoy, John M; Pepinsky, R Blake

    2004-03-01

    Axon regeneration in the adult CNS is prevented by inhibitors in myelin. These inhibitors seem to modulate RhoA activity by binding to a receptor complex comprising a ligand-binding subunit (the Nogo-66 receptor NgR1) and a signal transducing subunit (the neurotrophin receptor p75). However, in reconstituted non-neuronal systems, NgR1 and p75 together are unable to activate RhoA, suggesting that additional components of the receptor may exist. Here we describe LINGO-1, a nervous system-specific transmembrane protein that binds NgR1 and p75 and that is an additional functional component of the NgR1/p75 signaling complex. In non-neuronal cells, coexpression of human NgR1, p75 and LINGO-1 conferred responsiveness to oligodendrocyte myelin glycoprotein, as measured by RhoA activation. A dominant-negative human LINGO-1 construct attenuated myelin inhibition in transfected primary neuronal cultures. This effect on neurons was mimicked using an exogenously added human LINGO-1-Fc fusion protein. Together these observations suggest that LINGO-1 has an important role in CNS biology.

  8. Delineation of downstream signalling components during acrosome reaction mediated by heat solubilized human zona pellucida

    Directory of Open Access Journals (Sweden)

    Talwar Pankaj

    2010-01-01

    Full Text Available Abstract Background Human egg is enveloped by a glycoproteinaceous matrix, zona pellucida (ZP, responsible for binding of the human spermatozoa to the egg and induction of acrosomal exocytosis in the spermatozoon bound to ZP. In the present manuscript, attempts have been made to delineate the downstream signalling components employed by human ZP to induce acrosome reaction. Methods Heat-solubilized human ZP (SIZP was used to study the induction of acrosome reaction in capacitated human spermatozoa using tetramethylrhodamine isothiocyanate conjugated Pisum sativum agglutinin (TRITC-PSA in absence or presence of various pharmacological inhibitors. In addition, intracellular calcium ([Ca2+]i levels in sperm using Fluo-3 acetoxymethyl ester as fluorescent probe were also estimated in response to SIZP. Results SIZP induces acrosomal exocytosis in capacitated human sperm in a dose dependent manner accompanied by an increase in [Ca2+]i. Human SIZP mediated induction of acrosome reaction depends on extracellular Ca2+ and involves activation of Gi protein-coupled receptor, tyrosine kinase, protein kinases A & C and phosphoinositide 3 (PI3- kinase. In addition, T-type voltage operated calcium channels and GABA-A receptor associated chloride (Cl- channels play an important role in SIZP mediated induction of acrosome reaction. Conclusions Results described in the present study provide a comprehensive account of the various downstream signalling components associated with human ZP mediated acrosome reaction.

  9. Two-Component Signal Transduction System SaeRS Positively Regulates Staphylococcus epidermidis Glucose Metabolism

    Directory of Open Access Journals (Sweden)

    Qiang Lou

    2014-01-01

    Full Text Available Staphylococcus epidermidis, which is a causative pathogen of nosocomial infection, expresses its virulent traits such as biofilm and autolysis regulated by two-component signal transduction system SaeRS. In this study, we performed a proteomic analysis of differences in expression between the S. epidermidis 1457 wild-type and saeRS mutant to identify candidates regulated by saeRS using two-dimensional gel electrophoresis (2-DE combined with matrix-assisted laser desorption/lonization mass spectrometry (MALDI-TOF-MS. Of 55 identified proteins that significantly differed in expression between the two strains, 15 were upregulated and 40 were downregulated. The downregulated proteins included enzymes related to glycolysis and TCA cycle, suggesting that glucose is not properly utilized in S. epidermidis when saeRS was deleted. The study will be helpful for treatment of S. epidermidis infection from the viewpoint of metabolic modulation dependent on two-component signal transduction system SaeRS.

  10. P2CS: a two-component system resource for prokaryotic signal transduction research

    Directory of Open Access Journals (Sweden)

    Méjean Vincent

    2009-07-01

    Full Text Available Abstract Background With the escalation of high throughput prokaryotic genome sequencing, there is an ever-increasing need for databases that characterise, catalogue and present data relating to particular gene sets and genomes/metagenomes. Two-component system (TCS signal transduction pathways are the dominant mechanisms by which micro-organisms sense and respond to external as well as internal environmental changes. These systems respond to a wide range of stimuli by triggering diverse physiological adjustments, including alterations in gene expression, enzymatic reactions, or protein-protein interactions. Description We present P2CS (Prokaryotic 2-Component Systems, an integrated and comprehensive database of TCS signal transduction proteins, which contains a compilation of the TCS genes within 755 completely sequenced prokaryotic genomes and 39 metagenomes. P2CS provides detailed annotation of each TCS gene including family classification, sequence features, functional domains, as well as genomic context visualization. To bypass the generic problem of gene underestimation during genome annotation, we also constituted and searched an ORFeome, which improves the recovery of TCS proteins compared to searches on the equivalent proteomes. Conclusion P2CS has been developed for computational analysis of the modular TCSs of prokaryotic genomes and metagenomes. It provides a complete overview of information on TCSs, including predicted candidate proteins and probable proteins, which need further curation/validation. The database can be browsed and queried with a user-friendly web interface at http://www.p2cs.org/.

  11. P2CS: a two-component system resource for prokaryotic signal transduction research.

    Science.gov (United States)

    Barakat, Mohamed; Ortet, Philippe; Jourlin-Castelli, Cécile; Ansaldi, Mireille; Méjean, Vincent; Whitworth, David E

    2009-07-15

    With the escalation of high throughput prokaryotic genome sequencing, there is an ever-increasing need for databases that characterise, catalogue and present data relating to particular gene sets and genomes/metagenomes. Two-component system (TCS) signal transduction pathways are the dominant mechanisms by which micro-organisms sense and respond to external as well as internal environmental changes. These systems respond to a wide range of stimuli by triggering diverse physiological adjustments, including alterations in gene expression, enzymatic reactions, or protein-protein interactions. We present P2CS (Prokaryotic 2-Component Systems), an integrated and comprehensive database of TCS signal transduction proteins, which contains a compilation of the TCS genes within 755 completely sequenced prokaryotic genomes and 39 metagenomes. P2CS provides detailed annotation of each TCS gene including family classification, sequence features, functional domains, as well as genomic context visualization. To bypass the generic problem of gene underestimation during genome annotation, we also constituted and searched an ORFeome, which improves the recovery of TCS proteins compared to searches on the equivalent proteomes. P2CS has been developed for computational analysis of the modular TCSs of prokaryotic genomes and metagenomes. It provides a complete overview of information on TCSs, including predicted candidate proteins and probable proteins, which need further curation/validation. The database can be browsed and queried with a user-friendly web interface at http://www.p2cs.org/.

  12. Component

    Directory of Open Access Journals (Sweden)

    Tibor Tot

    2011-01-01

    Full Text Available A unique case of metaplastic breast carcinoma with an epithelial component showing tumoral necrosis and neuroectodermal stromal component is described. The tumor grew rapidly and measured 9 cm at the time of diagnosis. No lymph node metastases were present. The disease progressed rapidly and the patient died two years after the diagnosis from a hemorrhage caused by brain metastases. The morphology and phenotype of the tumor are described in detail and the differential diagnostic options are discussed.

  13. Assignment of Empirical Mode Decomposition Components and Its Application to Biomedical Signals.

    Science.gov (United States)

    Schiecke, K; Schmidt, C; Piper, D; Putsche, P; Feucht, M; Witte, H; Leistritz, L

    2015-01-01

    Empirical mode decomposition (EMD) is a frequently used signal processing approach which adaptively decomposes a signal into a set of narrow-band components known as intrinsic mode functions (IMFs). For multi-trial, multivariate (multiple simultaneous recordings), and multi-subject analyses the number and signal properties of the IMFs can deviate from each other between trials, channels and subjects. A further processing of IMFs, e.g. a simple ensemble averaging, should determine which IMFs of one signal correspond to IMFs from another signal. When the signal properties have similar characteristics, the IMFs are assigned to each other. This problem is known as correspondence problem. From the mathematical point of view, in some cases the correspondence problem can be transformed into an assignment problem which can be solved e.g. by the Kuhn-Munkres algorithm (KMA) by which a minimal cost matching can be found. We use the KMA for solving classic assignment problems, i.e. the pairwise correspondence between two sets of IMFs of equal cardinalities, and for pairwise correspondences between two sets of IMFs with different cardinalities representing an unbalanced assignment problem which is a special case of the k-cardinality assignment problem. A KMA-based approach to solve the correspondence problem was tested by using simulated, heart rate variability (HRV), and EEG data. The KMA-based results of HRV decomposition are compared with those obtained from a hierarchical cluster analysis (state-of-the-art). The major difference between the two approaches is that there is a more consistent assignment pattern using KMA. Integrating KMA into complex analysis concepts enables a comprehensive exploitation of the key advantages of the EMD. This can be demonstrated by non-linear analysis of HRV-related IMFs and by an EMD-based cross-frequency coupling analysis of the EEG data. The successful application to HRV and EEG analysis demonstrates that our solutions can be used for

  14. Expression of SHH signaling pathway components in the developing human lung.

    Science.gov (United States)

    Zhang, Mingfeng; Wang, Hong; Teng, Hongqi; Shi, Jueping; Zhang, Yanding

    2010-10-01

    The Sonic hedgehog (Shh) cascade is crucial for the patterning of the early lung morphogenesis in mice, but its role in the developing human lung remains to be determined. In the present study, the expression patterns of SHH signaling pathway components, including SHH, PTCH1, SMO, GLI1, GLI2 and GLI3 were examined by in situ hybridization and immunohistochemistry, and compared with the equivalent patterns in mice. Our results showed that, as in mice, SHH was expressed in the epithelium of the developing human lung. However, SHH receptors (PTCH1 and SMO) and SHH signaling effectors (GLI1-3) were strongly detected in the human lung epithelium, but weakly in the mesenchyme, slightly different from their expressions in mice. Furthermore, the expression levels of SHH signaling pathway genes in human lung, but not that of GLI1, were subsequently downregulated at the canalicular stage evaluated by real-time PCR, coincident with a decline in the developing murine lung. In conclusion, in spite of slight differences, the considerable similarities of gene expression in human and mice suggest that conserved molecular networks regulate mammalian lung development.

  15. DELLA proteins are common components of symbiotic rhizobial and mycorrhizal signalling pathways

    Science.gov (United States)

    Jin, Yue; Liu, Huan; Luo, Dexian; Yu, Nan; Dong, Wentao; Wang, Chao; Zhang, Xiaowei; Dai, Huiling; Yang, Jun; Wang, Ertao

    2016-01-01

    Legumes form symbiotic associations with either nitrogen-fixing bacteria or arbuscular mycorrhizal fungi. Formation of these two symbioses is regulated by a common set of signalling components that act downstream of recognition of rhizobia or mycorrhizae by host plants. Central to these pathways is the calcium and calmodulin-dependent protein kinase (CCaMK)–IPD3 complex which initiates nodule organogenesis following calcium oscillations in the host nucleus. However, downstream signalling events are not fully understood. Here we show that Medicago truncatula DELLA proteins, which are the central regulators of gibberellic acid signalling, positively regulate rhizobial symbiosis. Rhizobia colonization is impaired in della mutants and we provide evidence that DELLAs can promote CCaMK–IPD3 complex formation and increase the phosphorylation state of IPD3. DELLAs can also interact with NSP2–NSP1 and enhance the expression of Nod-factor-inducible genes in protoplasts. We show that DELLA is able to bridge a protein complex containing IPD3 and NSP2. Our results suggest a transcriptional framework for regulation of root nodule symbiosis. PMID:27514472

  16. TRPM5, a taste-signaling transient receptor potential ion-channel, is a ubiquitous signaling component in chemosensory cells

    Directory of Open Access Journals (Sweden)

    Hofmann Thomas

    2007-07-01

    Full Text Available Abstract Background A growing number of TRP channels have been identified as key players in the sensation of smell, temperature, mechanical forces and taste. TRPM5 is known to be abundantly expressed in taste receptor cells where it participates in sweet, amino acid and bitter perception. A role of TRPM5 in other sensory systems, however, has not been studied so far. Results Here, we systematically investigated the expression of TRPM5 in rat and mouse tissues. Apart from taste buds, where we found TRPM5 to be predominantly localized on the basolateral surface of taste receptor cells, TRPM5 immunoreactivity was seen in other chemosensory organs – the main olfactory epithelium and the vomeronasal organ. Most strikingly, we found solitary TRPM5-enriched epithelial cells in all parts of the respiratory and gastrointestinal tract. Based on their tissue distribution, the low cell density, morphological features and co-immunostaining with different epithelial markers, we identified these cells as brush cells (also known as tuft, fibrillovesicular, multivesicular or caveolated cells. In terms of morphological characteristics, brush cells resemble taste receptor cells, while their origin and biological role are still under intensive debate. Conclusion We consider TRPM5 to be an intrinsic signaling component of mammalian chemosensory organs, and provide evidence for brush cells being an important cellular correlate in the periphery.

  17. Physiological modules for generating discrete and rhythmic movements: Component analysis of EMG signals.

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    Ana eBengoetxea

    2015-01-01

    Full Text Available A central question in Neuroscience is that of how the nervous system generates the spatiotemporal commands needed to realize complex gestures, such as handwriting. A key postulate is that the CNS builds up complex movements from a set of simpler motor primitives or control modules. In this study we examined the control modules underlying the generation of muscle activations when performing different types of movement: discrete, point-to-point movements in eight different directions and continuous figure-eight movements in both the normal, upright orientation and rotated 90°. To test for the effects of biomechanical constraints, movements were performed in the frontal-parallel or sagittal planes, corresponding to two different nominal flexion/abduction postures of the shoulder. In all cases we measured limb kinematics and surface EMG signals for seven different muscles acting around the shoulder.We first performed principal component analysis (PCA of the EMG signals on a movement-by-movement basis. We found a surprisingly consistent pattern of muscle groupings across movement types and movement planes, although we could detect systematic differences between the PCs derived from movements performed in each shoulder posture and between the principal components associated with the different orientations of the figure. Unexpectedly we found no systematic differences between the figure eights and the point-to-point movements. The first three principal components could be associated with a general co-contraction of all seven muscles plus two patterns of reciprocal activation. From these results, we surmise that both ‘discrete-rhythmic movements’ such as the figure eight, and discrete point-to-point movement may be constructed from three different fundamental modules, one regulating the impedance of the limb over the time span of the movement and two others operating to generate movement, one aligned with the vertical and the other aligned with the

  18. Combining RNA interference and kinase inhibitors against cell signalling components involved in cancer

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    Hanson Bonnie J

    2005-10-01

    Full Text Available Abstract Background The transcription factor activator protein-1 (AP-1 has been implicated in a large variety of biological processes including oncogenic transformation. The tyrosine kinases of the epidermal growth factor receptor (EGFR constitute the beginning of one signal transduction cascade leading to AP-1 activation and are known to control cell proliferation and differentiation. Drug discovery efforts targeting this receptor and other pathway components have centred on monoclonal antibodies and small molecule inhibitors. Resistance to such inhibitors has already been observed, guiding the prediction of their use in combination therapies with other targeted agents such as RNA interference (RNAi. This study examines the use of RNAi and kinase inhibitors for qualification of components involved in the EGFR/AP-1 pathway of ME180 cells, and their inhibitory effects when evaluated individually or in tandem against multiple components of this important disease-related pathway. Methods AP-1 activation was assessed using an ME180 cell line stably transfected with a beta-lactamase reporter gene under the control of AP-1 response element following epidermal growth factor (EGF stimulation. Immunocytochemistry allowed for further quantification of small molecule inhibition on a cellular protein level. RNAi and RT-qPCR experiments were performed to assess the amount of knockdown on an mRNA level, and immunocytochemistry was used to reveal cellular protein levels for the targeted pathway components. Results Increased potency of kinase inhibitors was shown by combining RNAi directed towards EGFR and small molecule inhibitors acting at proximal or distal points in the pathway. After cellular stimulation with EGF and analysis at the level of AP-1 activation using a β-lactamase reporter gene, a 10–12 fold shift or 2.5–3 fold shift toward greater potency in the IC50 was observed for EGFR and MEK-1 inhibitors, respectively, in the presence of RNAi

  19. Clustering of Dependent Components: A New Paradigm for fMRI Signal Detection

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    Hurdal Monica K

    2005-01-01

    Full Text Available Exploratory data-driven methods such as unsupervised clustering and independent component analysis (ICA are considered to be hypothesis-generating procedures and are complementary to the hypothesis-led statistical inferential methods in functional magnetic resonance imaging (fMRI. Recently, a new paradigm in ICA emerged, that of finding "clusters" of dependent components. This intriguing idea found its implementation into two new ICA algorithms: tree-dependent and topographic ICA. For fMRI, this represents the unifying paradigm of combining two powerful exploratory data analysis methods, ICA and unsupervised clustering techniques. For the fMRI data, a comparative quantitative evaluation between the two methods, tree-dependent and topographic ICA, was performed. The comparative results were evaluated by (1 task-related activation maps, (2 associated time courses, and (3 ROC study. The most important findings in this paper are that (1 both tree-dependent and topographic ICA are able to identify signal components with high correlation to the fMRI stimulus, and that (2 topographic ICA outperforms all other ICA methods including tree-dependent ICA for 8 and 9 ICs. However for 16 ICs, topographic ICA is outperformed by tree-dependent ICA (KGV using as an approximation of the mutual information the kernel generalized variance. The applicability of the new algorithm is demonstrated on experimental data.

  20. Precise periodic components estimation for chronobiological signals through Bayesian Inference with sparsity enforcing prior.

    Science.gov (United States)

    Dumitru, Mircea; Mohammad-Djafari, Ali; Sain, Simona Baghai

    2016-12-01

    The toxicity and efficacy of more than 30 anticancer agents present very high variations, depending on the dosing time. Therefore, the biologists studying the circadian rhythm require a very precise method for estimating the periodic component (PC) vector of chronobiological signals. Moreover, in recent developments, not only the dominant period or the PC vector present a crucial interest but also their stability or variability. In cancer treatment experiments, the recorded signals corresponding to different phases of treatment are short, from 7 days for the synchronization segment to 2 or 3 days for the after-treatment segment. When studying the stability of the dominant period, we have to consider very short length signals relative to the prior knowledge of the dominant period, placed in the circadian domain. The classical approaches, based on Fourier transform (FT) methods are inefficient (i.e., lack of precision) considering the particularities of the data (i.e., the short length). Another particularity of the signals considered in such experiments is the level of noise: such signals are very noisy and establishing the periodic components that are associated with the biological phenomena and distinguishing them from the ones associated with the noise are difficult tasks. In this paper, we propose a new method for the estimation of the PC vector of biomedical signals, using the biological prior informations and considering a model that accounts for the noise. The experiments developed in cancer treatment context are recording signals expressing a limited number of periods. This is a prior information that can be translated as the sparsity of the PC vector. The proposed method considers the PC vector estimation as an Inverse Problem (IP) using the general Bayesian inference in order to infer the unknown of our model, i.e. the PC vector but also the hyperparameters (i.e the variances). The sparsity prior information is modeled using a sparsity enforcing prior law

  1. Histidine phosphotransfer proteins in fungal two-component signal transduction pathways.

    Science.gov (United States)

    Fassler, Jan S; West, Ann H

    2013-08-01

    The histidine phosphotransfer (HPt) protein Ypd1 is an important participant in the Saccharomyces cerevisiae multistep two-component signal transduction pathway and, unlike the expanded histidine kinase gene family, is encoded by a single gene in nearly all model and pathogenic fungi. Ypd1 is essential for viability in both S. cerevisiae and in Cryptococcus neoformans. These and other aspects of Ypd1 biology, combined with the availability of structural and mutational data in S. cerevisiae, suggest that the essential interactions between Ypd1 and response regulator domains would be a good target for antifungal drug development. The goal of this minireview is to summarize the wealth of data on S. cerevisiae Ypd1 and to consider the potential benefits of conducting related studies in pathogenic fungi.

  2. Two-component signal transduction as potential drug targets in pathogenic bacteria.

    Science.gov (United States)

    Gotoh, Yasuhiro; Eguchi, Yoko; Watanabe, Takafumi; Okamoto, Sho; Doi, Akihiro; Utsumi, Ryutaro

    2010-04-01

    Gene clusters contributing to processes such as cell growth and pathogenicity are often controlled by two-component signal transduction systems (TCSs). Specific inhibitors against TCS systems work differently from conventional antibiotics, and developing them into new drugs that are effective against various drug-resistant bacteria may be possible. Furthermore, inhibitors of TCSs that control virulence factors may reduce virulence without killing the pathogenic bacteria. Previous TCS inhibitors targeting the kinase domain of the histidine kinase sensor suffered from poor selectivity. Recent TCS inhibitors, however, target the sensory domains of the sensors blocking the quorum sensing system, or target the essential response regulator. These new targets are introduced, together with several specific TCSs that have the potential to serve as effective drug targets. Copyright 2010 Elsevier Ltd. All rights reserved.

  3. Bioelectric signal classification using a recurrent probabilistic neural network with time-series discriminant component analysis.

    Science.gov (United States)

    Hayashi, Hideaki; Shima, Keisuke; Shibanoki, Taro; Kurita, Yuichi; Tsuji, Toshio

    2013-01-01

    This paper outlines a probabilistic neural network developed on the basis of time-series discriminant component analysis (TSDCA) that can be used to classify high-dimensional time-series patterns. TSDCA involves the compression of high-dimensional time series into a lower-dimensional space using a set of orthogonal transformations and the calculation of posterior probabilities based on a continuous-density hidden Markov model that incorporates a Gaussian mixture model expressed in the reduced-dimensional space. The analysis can be incorporated into a neural network so that parameters can be obtained appropriately as network coefficients according to backpropagation-through-time-based training algorithm. The network is considered to enable high-accuracy classification of high-dimensional time-series patterns and to reduce the computation time taken for network training. In the experiments conducted during the study, the validity of the proposed network was demonstrated for EEG signals.

  4. Molecular components underlying nongenomic thyroid hormone signaling in embryonic zebrafish neurons

    Directory of Open Access Journals (Sweden)

    Yonkers Marc A

    2009-06-01

    Full Text Available Abstract Background Neurodevelopment requires thyroid hormone, yet the mechanisms and targets of thyroid hormone action during embryonic stages remain ill-defined. We previously showed that the thyroid hormone thyroxine (T4 rapidly increases voltage-gated sodium current in zebrafish Rohon-Beard cells (RBs, a primary sensory neuron subtype present during embryonic development. Here, we determined essential components of the rapid T4 signaling pathway by identifying the involved intracellular messengers, the targeted sodium channel isotype, and the spatial and temporal expression pattern of the nongenomic αVβ3 integrin T4 receptor. Results We first tested which signaling pathways mediate T4's rapid modulation of sodium current (INa by perturbing specific pathways associated with nongenomic thyroid hormone signaling. We found that pharmacological blockade of protein phosphatase 1 and the mitogen-activated protein kinase p38 isoform decreased and increased tonic sodium current amplitudes, respectively, and blockade of either occluded rapid responses to acute T4 application. We next tested for the ion channel target of rapid T4 signaling via morpholino knock-down of specific sodium channel isotypes. We found that selective knock-down of the sodium channel α-subunit Nav1.6a, but not Nav1.1la, occluded T4's acute effects. We also determined the spatial and temporal distribution of a nongenomic T4 receptor, integrin αVβ3. At 24 hours post fertilization (hpf, immunofluorescent assays showed no specific integrin αVβ3 immunoreactivity in wild-type zebrafish embryos. However, by 48 hpf, embryos expressed integrin αVβ3 in RBs and primary motoneurons. Consistent with this temporal expression, T4 modulated RB INa at 48 but not 24 hpf. We next tested whether T4 rapidly modulated INa of caudal primary motoneurons, which express the receptor (αVβ3 and target (Nav1.6a of rapid T4 signaling. In response to T4, caudal primary motoneurons rapidly increased

  5. Non-Intrusive Load Monitoring of HVAC Components using Signal Unmixing

    Energy Technology Data Exchange (ETDEWEB)

    Rahimpour, Alireza [University of Tennessee, Knoxville (UTK); Qi, Hairong [ORNL; Fugate, David L [ORNL; Kuruganti, Teja [ORNL

    2015-01-01

    Heating, Ventilating and Air Conditioning units (HVAC) are a major electrical energy consumer in buildings. Monitoring of the operation and energy consumption of HVAC would increase the awareness of building owners and maintenance service providers of the condition and quality of performance of these units, enabling conditioned-based maintenance which would help achieving higher energy efficiency. In this paper, a novel non-intrusive load monitoring method based on group constrained non-negative matrix factorization is proposed for monitoring the different components of HVAC unit by only measuring the whole building aggregated power signal. At the first level of this hierarchical approach, power consumption of the building is decomposed to energy consumption of the HVAC unit and all the other electrical devices operating in the building such as lighting and plug loads. Then, the estimated power signal of the HVAC is used for estimating the power consumption profile of the HVAC major electrical loads such as compressors, condenser fans and indoor blower. Experiments conducted on real data collected from a building testbed maintained at the Oak Ridge National Laboratory (ORNL) demonstrate high accuracy on the disaggregation task.

  6. The Role of Two-Component Signal Transduction Systems in Staphylococcus aureus Virulence Regulation.

    Science.gov (United States)

    Haag, Andreas F; Bagnoli, Fabio

    2016-01-05

    Staphylococcus aureus is a versatile, opportunistic human pathogen that can asymptomatically colonize a human host but can also cause a variety of cutaneous and systemic infections. The ability of S. aureus to adapt to such diverse environments is reflected in the presence of complex regulatory networks fine-tuning metabolic and virulence gene expression. One of the most widely distributed mechanisms is the two-component signal transduction system (TCS) which allows a pathogen to alter its gene expression profile in response to environmental stimuli. The simpler TCSs consist of only a transmembrane histidine kinase (HK) and a cytosolic response regulator. S. aureus encodes a total of 16 conserved pairs of TCSs that are involved in diverse signalling cascades ranging from global virulence gene regulation (e.g. quorum sensing by the Agr system), the bacterial response to antimicrobial agents, cell wall metabolism, respiration and nutrient sensing. These regulatory circuits are often interconnected and affect each other's expression, thus fine-tuning staphylococcal gene regulation. This manuscript gives an overview of the current knowledge of staphylococcal environmental sensing by TCS and its influence on virulence gene expression and virulence itself. Understanding bacterial gene regulation by TCS can give major insights into staphylococcal pathogenicity and has important implications for knowledge-based drug design and vaccine formulation.

  7. [Two-component signal transduction as attractive drug targets in pathogenic bacteria].

    Science.gov (United States)

    Utsumi, Ryutaro; Igarashi, Masayuki

    2012-01-01

    Gene clusters contributing to processes such as cell growth and pathogenicity are often controlled by two-component signal transduction systems (TCSs). TCS consists of a histidine kinase (HK) and a response regulator (RR). TCSs are attractive as drug targets for antimicrobials because many HK and RR genes are coded on the bacterial genome though few are found in lower eukaryotes. The HK/RR signal transduction system is distinct from serine/threonine and tyrosine phosphorylation in higher eukaryotes. Specific inhibitors against TCS systems work differently from conventional antibiotics, and developing them into new drugs that are effective against various drug-resistant bacteria may be possible. Furthermore, inhibitors of TCSs that control virulence factors may reduce virulence without killing the pathogenic bacteria. Previous TCS inhibitors targeting the kinase domain of the histidine kinase sensor suffered from poor selectivity. Recent TCS inhibitors, however, target the sensory domains of the sensors blocking the quorum sensing system, or target the essential response regulator. These new targets are introduced, together with several specific TCSs that have the potential to serve as effective drug targets.

  8. Non-Intrusive Load Monitoring of HVAC Components using Signal Unmixing

    Energy Technology Data Exchange (ETDEWEB)

    Rahimpour, Alireza [University of Tennessee, Knoxville (UTK); Qi, Hairong [ORNL; Fugate, David L [ORNL; Kuruganti, Teja [ORNL

    2015-01-01

    Heating, Ventilating and Air Conditioning units (HVAC) are a major electrical energy consumer in buildings. Monitoring of the operation and energy consumption of HVAC would increase the awareness of building owners and maintenance service providers of the condition and quality of performance of these units, enabling conditioned-based maintenance which would help achieving higher energy efficiency. In this paper, a novel non-intrusive load monitoring method based on group constrained non-negative matrix factorization is proposed for monitoring the different components of HVAC unit by only measuring the whole building aggregated power signal. At the first level of this hierarchical approach, power consumption of the building is decomposed to energy consumption of the HVAC unit and all the other electrical devices operating in the building such as lighting and plug loads. Then, the estimated power signal of the HVAC is used for estimating the power consumption profile of the HVAC major electrical loads such as compressors, condenser fans and indoor blower. Experiments conducted on real data collected from a building testbed maintained at the Oak Ridge National Laboratory (ORNL) demonstrate high accuracy on the disaggregation task.

  9. Regulation of acid resistance by connectors of two-component signal transduction systems in Escherichia coli.

    Science.gov (United States)

    Eguchi, Yoko; Ishii, Eiji; Hata, Kensuke; Utsumi, Ryutaro

    2011-03-01

    Two-component signal transduction systems (TCSs), utilized extensively by bacteria and archaea, are involved in the rapid adaptation of the organisms to fluctuating environments. A typical TCS transduces the signal by a phosphorelay between the sensor histidine kinase and its cognate response regulator. Recently, small-sized proteins that link TCSs have been reported and are called "connectors." Their physiological roles, however, have remained elusive. SafA (sensor associating factor A) (formerly B1500), a small (65-amino-acid [65-aa]) membrane protein, is among such connectors and links Escherichia coli TCSs EvgS/EvgA and PhoQ/PhoP. Since the activation of the EvgS/EvgA system induces acid resistance, we examined whether the SafA-activated PhoQ/PhoP system is also involved in the acid resistance induced by EvgS/EvgA. Using a constitutively active evgS1 mutant for the activation of EvgS/EvgA, we found that SafA, PhoQ, and PhoP all contributed to the acid resistance phenotype. Moreover, EvgS/EvgA activation resulted in the accumulation of cellular RpoS in the exponential-phase cells in a SafA-, PhoQ-, and PhoP-dependent manner. This RpoS accumulation was caused by another connector, IraM, expression of which was induced by the activation of the PhoQ/PhoP system, thus preventing RpoS degradation by trapping response regulator RssB. Acid resistance assays demonstrated that IraM also participated in the EvgS/EvgA-induced acid resistance. Therefore, we propose a model of a signal transduction cascade proceeding from EvgS/EvgA to PhoQ/PhoP and then to RssB (connected by SafA and IraM) and discuss its contribution to the acid resistance phenotype.

  10. Negative control in two-component signal transduction by transmitter phosphatase activity.

    Science.gov (United States)

    Huynh, TuAnh Ngoc; Stewart, Valley

    2011-10-01

    Bifunctional sensor transmitter modules of two-component systems exert both positive and negative control on the receiver domain of the cognate response regulator. In negative control, the transmitter module accelerates the rate of phospho-receiver dephosphorylation. This transmitter phosphatase reaction serves the important physiological functions of resetting response regulator phosphorylation level and suppressing cross-talk. Although the biochemical reactions underlying positive control are reasonably well understood, the mechanism for transmitter phosphatase activity has been unknown. A recent hypothesis is that the transmitter phosphatase reaction is catalysed by a conserved Gln, Asn or Thr residue, via a hydrogen bond between the amide or hydroxyl group and the nucleophilic water molecule in acyl-phosphate hydrolysis. This hypothetical mechanism closely resembles the established mechanisms of auxiliary phosphatases such as CheZ and CheX, and may be widely conserved in two-component signal transduction. In addition to the proposed catalytic residues, transmitter phosphatase activity also requires the correct transmitter conformation and appropriate interactions with the receiver. Evidence suggests that the phosphatase-competent and autokinase-competent states are mutually exclusive, and the corresponding negative and positive activities are likely to be reciprocally regulated through dynamic control of transmitter conformations. © 2011 Blackwell Publishing Ltd.

  11. Mutations in components of the Wnt signaling pathway in gastric cancer

    Institute of Scientific and Technical Information of China (English)

    Kai-Feng Pan; Wan-Guo Liu; Lian Zhang; Wei-Cheng You; You-Yong Lu

    2008-01-01

    AIM:To explore the contribution of AXIN1,AXIN2 and beta-catenin,components of Wnt signaling pathway,to the carcinogenesis of gastric cancer(GC),we examined AXIN1,AXIN2 exon7 and CTNNB1(encoding betacatenin) exon3 mutations in 70 GCs.METHODS:The presence of mutations was identified by polymerase chain reaction(PCR)-based denaturing high-performance liquid chromatography and direct DNA sequencing.Beta-catenin expression was detected by immunohistochemical analysis.RESULTS:Among the 70 GCs,5(7.1%)had mutations in one or two of these three components.A frameshift mutation(1 bp deletion)in exon7 of AXIN2 was found in one case.Four cases,including the case with a mutation in AXIN2,had frameshift mutations and missense mutations in AXIN1.Five single nucleotide polymorphisms (SNPs),334 C>T,874 C>T,1396 G>A,1690 C>T and 1942 T>G,were identified in AXTN1.A frameshift mutation(27 bp deletion) spanning exon3 of CTNNB1 was observed in one case.All four cases with mutations in AXIN1 and AXIN2 showed nuclear betacatenin expression.CONCLUSION:These data indicate that the mutations in AXIN1 and AXIN2 may contribute to gastric carcinogenesis.

  12. Integration of multivariate empirical mode decomposition and independent component analysis for fetal ECG separation from abdominal signals.

    Science.gov (United States)

    Thanaraj, Palani; Roshini, Mable; Balasubramanian, Parvathavarthini

    2016-11-14

    The fetal electrocardiogram (FECG) signals are essential to monitor the health condition of the baby. Fetal heart rate (FHR) is commonly used for diagnosing certain abnormalities in the formation of the heart. Usually, non-invasive abdominal electrocardiogram (AbECG) signals are obtained by placing surface electrodes in the abdomen region of the pregnant woman. AbECG signals are often not suitable for the direct analysis of fetal heart activity. Moreover, the strength and magnitude of the FECG signals are low compared to the maternal electrocardiogram (MECG) signals. The MECG signals are often superimposed with the FECG signals that make the monitoring of FECG signals a difficult task. Primary goal of the paper is to separate the fetal electrocardiogram (FECG) signals from the unwanted maternal electrocardiogram (MECG) signals. A multivariate signal processing procedure is proposed here that combines the Multivariate Empirical Mode Decomposition (MEMD) and Independent Component Analysis (ICA). The proposed method is evaluated with clinical abdominal signals taken from three pregnant women (N= 3) recorded during the 38-41 weeks of the gestation period. The number of fetal R-wave detected (NEFQRS), the number of unwanted maternal peaks (NMQRS), the number of undetected fetal R-wave (NUFQRS) and the FHR detection accuracy quantifies the performance of our method. Clinical investigation with three test subjects shows an overall detection accuracy of 92.8%. Comparative analysis with benchmark signal processing method such as ICA suggests the noteworthy performance of our method.

  13. Imidazole as a Small Molecule Analogue in Two-Component Signal Transduction.

    Science.gov (United States)

    Page, Stephani C; Silversmith, Ruth E; Collins, Edward J; Bourret, Robert B

    2015-12-15

    In two-component signal transduction systems (TCSs), responses to stimuli are mediated through phosphotransfer between protein components. Canonical TCSs use His → Asp phosphotransfer in which phosphoryl groups are transferred from a conserved His on a sensory histidine kinase (HK) to a conserved Asp on a response regulator (RR). RRs contain the catalytic core of His → Asp phosphotransfer, evidenced by the ability of RRs to autophosphorylate with small molecule analogues of phospho-His proteins. Phosphorelays are a more complex variation of TCSs that additionally utilize Asp → His phosphotransfer through the use of an additional component, the histidine-containing phosphotransfer domain (Hpt), which reacts with RRs both as phosphodonors and phosphoacceptors. Here we show that imidazole has features of a rudimentary Hpt. Imidazole acted as a nucleophile and attacked phosphorylated RRs (RR-P) to produce monophosphoimidazole (MPI) and unphosphorylated RR. Phosphotransfer from RR-P to imidazole required the intact RR active site, indicating that the RR provided the core catalytic machinery for Asp → His phosphotransfer. Imidazole functioned in an artificial phosphorelay to transfer phosphoryl groups between unrelated RRs. The X-ray crystal structure of an activated RR·imidazole complex showed imidazole oriented in the RR active site similarly to the His of an Hpt. Imidazole interacted with RR nonconserved active site residues, which influenced the relative reactivity of RR-P with imidazole versus water. Rate constants for reaction of imidazole or MPI with chimeric RRs suggested that the RR active site contributes to the kinetic preferences exhibited by the YPD1 Hpt.

  14. Phosphoinositide-signaling is one component of a robust plant defense response.

    Directory of Open Access Journals (Sweden)

    Imara Yasmin Perera

    2014-06-01

    Full Text Available The phosphoinositide pathway and inositol-1,4,5-triphosphate (InsP3 have been implicated in plant responses to many abiotic stresses; however, their role in response to biotic stress is not well characterized. In the current study, we show that both basal defense and systemic acquired resistance responses are affected in transgenic plants constitutively expressing the human type I inositol polyphosphate 5-phosphatase (InsP 5-ptase which have greatly reduced InsP3 levels. Flagellin induced Ca2+-release as well as the expressions of some flg22 responsive genes were attenuated in the InsP 5-ptase plants. Furthermore, the InsP 5-ptase plants were more susceptible to virulent and avirulent strains of Pseudomonas syringae pv. tomato (PstDC3000. The InsP 5-ptase plants had lower basal salicylic acid (SA levels and the induction of SAR in systemic leaves was reduced and delayed. Reciprocal exudate experiments showed that although the InsP 5-ptase plants produced equally effective molecules that could trigger PR-1 gene expression in wild type plants, exudates collected from either wild type or InsP 5-ptase plants triggered less PR-1 gene expression in InsP 5-ptase plants. Additionally, expression profiles indicated that several defense genes including PR-1, PR-2, PR-5 and AIG1 were basally down regulated in the InsP 5-ptase plants compared with wild type. Upon pathogen attack, expression of these genes was either not induced or showed delayed induction in systemic leaves. Our study shows that phosphoinositide signaling is one component of the plant defense network and is involved in both basal and systemic responses. The dampening of InsP3-mediated signaling affects Ca2+ release, modulates defense gene expression and compromises plant defense responses.

  15. The Two-Component Signal Transduction System VxrAB Positively Regulates Vibrio cholerae Biofilm Formation.

    Science.gov (United States)

    Teschler, Jennifer K; Cheng, Andrew T; Yildiz, Fitnat H

    2017-09-15

    Two-component signal transduction systems (TCSs), typically composed of a sensor histidine kinase (HK) and a response regulator (RR), are the primary mechanism by which pathogenic bacteria sense and respond to extracellular signals. The pathogenic bacterium Vibrio cholerae is no exception and harbors 52 RR genes. Using in-frame deletion mutants of each RR gene, we performed a systematic analysis of their role in V. cholerae biofilm formation. We determined that 7 RRs impacted the expression of an essential biofilm gene and found that the recently characterized RR, VxrB, regulates the expression of key structural and regulatory biofilm genes in V. choleraevxrB is part of a 5-gene operon, which contains the cognate HK vxrA and three genes of unknown function. Strains carrying ΔvxrA and ΔvxrB mutations are deficient in biofilm formation, while the ΔvxrC mutation enhances biofilm formation. The overexpression of VxrB led to a decrease in motility. We also observed a small but reproducible effect of the absence of VxrB on the levels of cyclic di-GMP (c-di-GMP). Our work reveals a new function for the Vxr TCS as a regulator of biofilm formation and suggests that this regulation may act through key biofilm regulators and the modulation of cellular c-di-GMP levels.IMPORTANCE Biofilms play an important role in the Vibrio cholerae life cycle, providing protection from environmental stresses and contributing to the transmission of V. cholerae to the human host. V. cholerae can utilize two-component systems (TCS), composed of a histidine kinase (HK) and a response regulator (RR), to regulate biofilm formation in response to external cues. We performed a systematic analysis of V. cholerae RRs and identified a new regulator of biofilm formation, VxrB. We demonstrated that the VxrAB TCS is essential for robust biofilm formation and that this system may regulate biofilm formation via its regulation of key biofilm regulators and cyclic di-GMP levels. This research furthers our

  16. Principal components of hand kinematics and neurophysiological signals in motor cortex during reach to grasp movements.

    Science.gov (United States)

    Mollazadeh, Mohsen; Aggarwal, Vikram; Thakor, Nitish V; Schieber, Marc H

    2014-10-15

    A few kinematic synergies identified by principal component analysis (PCA) account for most of the variance in the coordinated joint rotations of the fingers and wrist used for a wide variety of hand movements. To examine the possibility that motor cortex might control the hand through such synergies, we collected simultaneous kinematic and neurophysiological data from monkeys performing a reach-to-grasp task. We used PCA, jPCA and isomap to extract kinematic synergies from 18 joint angles in the fingers and wrist and analyzed the relationships of both single-unit and multiunit spike recordings, as well as local field potentials (LFPs), to these synergies. For most spike recordings, the maximal absolute cross-correlations of firing rates were somewhat stronger with an individual joint angle than with any principal component (PC), any jPC or any isomap dimension. In decoding analyses, where spikes and LFP power in the 100- to 170-Hz band each provided better decoding than other LFP-based signals, the first PC was decoded as well as the best decoded joint angle. But the remaining PCs and jPCs were predicted with lower accuracy than individual joint angles. Although PCs, jPCs or isomap dimensions might provide a more parsimonious description of kinematics, our findings indicate that the kinematic synergies identified with these techniques are not represented in motor cortex more strongly than the original joint angles. We suggest that the motor cortex might act to sculpt the synergies generated by subcortical centers, superimposing an ability to individuate finger movements and adapt the hand to grasp a wide variety of objects.

  17. A signal-substrate match in the substrate-borne component of a multimodal courtship display

    Directory of Open Access Journals (Sweden)

    Damian O. ELIAS, Andrew C. MASON, Eileen A. HEBETS

    2010-06-01

    Full Text Available The environment can impose strong limitations on the efficacy of signal transmission. In particular, for vibratory communication, the signaling environment is often extremely heterogeneous at very small scales. Nevertheless, natural selection is expected to select for signals well-suited to effective transmission. Here, we test for substrate-dependent signal efficacy in the wolf spider Schizocosa stridulans Stratton 1991. We first explore the transmission characteristics of this important signaling modality by playing recorded substrate-borne signals through three different substrates (leaf litter, pine litter, and red clay and measuring the propagated signal. We found that the substrate-borne signal of S. stridulans attenuates the least on leaf litter, the substrate upon which the species is naturally found. Next, by assessing mating success with artificially muted and non-muted males across different signaling substrates (leaf litter, pine litter, and sand, we explored the relationship between substrate-borne signaling and substrate for mating success. We found that muted males were unsuccessful in obtaining copulations regardless of substrate, while mating success was dependent on the signaling substrate for non-muted males. For non-muted males, more males copulated on leaf litter than any other substrate. Taken together, these results confirm the importance of substrate-borne signaling in S. stridulans and suggest a match between signal properties and signal efficacy – leaf litter transmits the signal most effectively and males are most successful in obtaining copulations on leaf litter [Current Zoology 56 (3: 370–378, 2010].

  18. Early estrogen-induced gene 1, a novel RANK signaling component, is essential for osteoclastogenesis

    Institute of Scientific and Technical Information of China (English)

    Han Kyoung Choi; Hye Ri Kang; Eutteum Jung; Tae Eon Kim; Jing Jing Lin; Soo Young Lee

    2013-01-01

    The receptor activator of NF-kB (RANK) and immunoreceptor tyrosine-based activation motif (ITAM)-containing adaptors are essential factors involved in regulating osteoclast formation and bone remodeling.Here,we identify early estrogen-induced gene 1 (EEIG1) as a novel RANK ligand (RANKL)-inducible protein that physically interacts with RANK and further associates with Gab2,PLCγ2 and Tec/Btk kinases upon RANKL stimulation.EEIG1 positively regulates RANKL-induced osteoclast formation,likely due to its ability to facilitate RANKL-stimulated PLCγ2 phosphorylation and NFATc1 induction.In addition,an inhibitory peptide designed to block RANK-EEIG1 interaction inhibited RANKL-induced bone destruction by reducing osteoclast formation.Together,our results identify EEIG1 as a novel RANK signaling component controlling RANK-mediated osteoclast formation,and suggest that targeting EEIG1 might represent a new therapeutic strategy for the treatment of pathological bone resorption.

  19. Cell and Signal Components of the Microenvironment of Bone Metastasis Are Affected by Hypoxia

    Directory of Open Access Journals (Sweden)

    Paola Bendinelli

    2016-05-01

    Full Text Available Bone metastatic cells release bone microenvironment proteins, such as the matricellular protein SPARC (secreted protein acidic and rich in cysteine, and share a cell signaling typical of the bone metabolism controlled by Runx2. The megakaryocytes in the bone marrow engrafted by the metastases seem to be one of the principal microenvironment sources of the biological stimuli, implicated in the formation of an osteoblastic niche, and affecting metastasis phenotype and colonization. Educated platelets in the circulation might derive from megakaryocytes in bone metastasis. The evaluation of predictive markers in the circulating platelets might be useful for the stratification of patients for therapeutic purposes. The hypoxic environment in bone metastasis is one of the key regulators of the network of the biological soluble and structural components of the matrix. In bone metastatic cells under hypoxia, similar patterns of Runx2 and SPARC are observed, both showing downregulation. Conversely, hypoxia induces Endothelin 1, which upregulates SPARC, and these biological stimuli may be considered prognostic markers of bone metastasis in breast carcinoma patients.

  20. Cell and Signal Components of the Microenvironment of Bone Metastasis Are Affected by Hypoxia

    Science.gov (United States)

    Bendinelli, Paola; Maroni, Paola; Matteucci, Emanuela; Desiderio, Maria Alfonsina

    2016-01-01

    Bone metastatic cells release bone microenvironment proteins, such as the matricellular protein SPARC (secreted protein acidic and rich in cysteine), and share a cell signaling typical of the bone metabolism controlled by Runx2. The megakaryocytes in the bone marrow engrafted by the metastases seem to be one of the principal microenvironment sources of the biological stimuli, implicated in the formation of an osteoblastic niche, and affecting metastasis phenotype and colonization. Educated platelets in the circulation might derive from megakaryocytes in bone metastasis. The evaluation of predictive markers in the circulating platelets might be useful for the stratification of patients for therapeutic purposes. The hypoxic environment in bone metastasis is one of the key regulators of the network of the biological soluble and structural components of the matrix. In bone metastatic cells under hypoxia, similar patterns of Runx2 and SPARC are observed, both showing downregulation. Conversely, hypoxia induces Endothelin 1, which upregulates SPARC, and these biological stimuli may be considered prognostic markers of bone metastasis in breast carcinoma patients. PMID:27187355

  1. Physiological Role of Two-Component Signal Transduction Systems in Food-Associated Lactic Acid Bacteria.

    Science.gov (United States)

    Monedero, Vicente; Revilla-Guarinos, Ainhoa; Zúñiga, Manuel

    2017-01-01

    Two-component systems (TCSs) are widespread signal transduction pathways mainly found in bacteria where they play a major role in adaptation to changing environmental conditions. TCSs generally consist of sensor histidine kinases that autophosphorylate in response to a specific stimulus and subsequently transfer the phosphate group to their cognate response regulators thus modulating their activity, usually as transcriptional regulators. In this review we present the current knowledge on the physiological role of TCSs in species of the families Lactobacillaceae and Leuconostocaceae of the group of lactic acid bacteria (LAB). LAB are microorganisms of great relevance for health and food production as the group spans from starter organisms to pathogens. Whereas the role of TCSs in pathogenic LAB (most of them belonging to the family Streptococcaceae) has focused the attention, the roles of TCSs in commensal LAB, such as most species of Lactobacillaceae and Leuconostocaceae, have been somewhat neglected. However, evidence available indicates that TCSs are key players in the regulation of the physiology of these bacteria. The first studies in food-associated LAB showed the involvement of some TCSs in quorum sensing and production of bacteriocins, but subsequent studies have shown that TCSs participate in other physiological processes, such as stress response, regulation of nitrogen metabolism, regulation of malate metabolism, and resistance to antimicrobial peptides, among others. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Functional characterization of WalRK: A two-component signal transduction system from Bacillus anthracis

    Directory of Open Access Journals (Sweden)

    Alisha Dhiman

    2014-01-01

    Full Text Available Two-component signal transduction systems (TCS, consisting of a sensor histidine protein kinase and its cognate response regulator, are an important mode of environmental sensing in bacteria. Additionally, they have been found to regulate virulence determinants in several pathogens. Bacillus anthracis, the causative agent of anthrax and a bioterrorism agent, harbours 41 pairs of TCS. However, their role in its pathogenicity has remained largely unexplored. Here, we show that WalRK of B. anthracis forms a functional TCS which exhibits some species-specific functions. Biochemical studies showed that domain variants of WalK, the histidine kinase, exhibit classical properties of autophosphorylation and phosphotransfer to its cognate response regulator WalR. Interestingly, these domain variants also show phosphatase activity towards phosphorylated WalR, thereby making WalK a bifunctional histidine kinase/phosphatase. An in silico regulon determination approach, using a consensus binding sequence from Bacillus subtilis, provided a list of 30 genes that could form a putative WalR regulon in B. anthracis. Further, electrophoretic mobility shift assay was used to show direct binding of purified WalR to the upstream regions of three putative regulon candidates, an S-layer protein EA1, a cell division ABC transporter FtsE and a sporulation histidine kinase KinB3. Our work lends insight into the species-specific functions and mode of action of B. anthracis WalRK.

  3. Functional characterization of WalRK: A two-component signal transduction system from Bacillus anthracis.

    Science.gov (United States)

    Dhiman, Alisha; Bhatnagar, Sonika; Kulshreshtha, Parul; Bhatnagar, Rakesh

    2014-01-01

    Two-component signal transduction systems (TCS), consisting of a sensor histidine protein kinase and its cognate response regulator, are an important mode of environmental sensing in bacteria. Additionally, they have been found to regulate virulence determinants in several pathogens. Bacillus anthracis, the causative agent of anthrax and a bioterrorism agent, harbours 41 pairs of TCS. However, their role in its pathogenicity has remained largely unexplored. Here, we show that WalRK of B. anthracis forms a functional TCS which exhibits some species-specific functions. Biochemical studies showed that domain variants of WalK, the histidine kinase, exhibit classical properties of autophosphorylation and phosphotransfer to its cognate response regulator WalR. Interestingly, these domain variants also show phosphatase activity towards phosphorylated WalR, thereby making WalK a bifunctional histidine kinase/phosphatase. An in silico regulon determination approach, using a consensus binding sequence from Bacillus subtilis, provided a list of 30 genes that could form a putative WalR regulon in B. anthracis. Further, electrophoretic mobility shift assay was used to show direct binding of purified WalR to the upstream regions of three putative regulon candidates, an S-layer protein EA1, a cell division ABC transporter FtsE and a sporulation histidine kinase KinB3. Our work lends insight into the species-specific functions and mode of action of B. anthracis WalRK.

  4. Comparative Genomic Analysis of Two-Component Signal Transduction Systems in Probiotic Lactobacillus casei.

    Science.gov (United States)

    Yu, Shuijing; Peng, Yanping; Chen, Wanyi; Deng, Yangwu; Guo, Yanhua

    2014-09-01

    Lactobacillus casei has traditionally been recognized as a probiotic, thus needing to survive the industrial production processes and transit through the gastrointestinal tract before providing benefit to human health. The two-component signal transduction system (TCS) plays important roles in sensing and reacting to environmental changes, which consists of a histidine kinase (HK) and a response regulator (RR). In this study we identified HKs and RRs of six sequenced L. casei strains. Ortholog analysis revealed 15 TCS clusters (HK-RR pairs), one orphan HKs and three orphan RRs, of which 12 TCS clusters were common to all six strains, three were absent in one strain. Further classification of the predicted HKs and RRs revealed interesting aspects of their putative functions. Some TCS clusters are involved with the response under the stress of the bile salts, acid, or oxidative, which contribute to survive the difficult journey through the human gastrointestinal tract. Computational predictions of 15 TCSs were verified by PCR experiments. This genomic level study of TCSs should provide valuable insights into the conservation and divergence of TCS proteins in the L. casei strains.

  5. Identification of a two-component signal transduction system that regulates maltose genes in Clostridium perfringens.

    Science.gov (United States)

    Hiscox, Thomas J; Ohtani, Kaori; Shimizu, Tohru; Cheung, Jackie K; Rood, Julian I

    2014-12-01

    Clostridium perfringens is a Gram-positive rod that is widely distributed in nature and is the etiological agent of several human and animal diseases. The complete genome sequence of C. perfringens strain 13 has been determined and multiple two-component signal transduction systems identified. One of these systems, designated here as the MalNO system, was analyzed in this study. Microarray analysis was used to carry out functional analysis of a malO mutant. The results, which were confirmed by quantitative reverse-transcriptase PCR, indicated that genes putatively involved in the uptake and metabolism of maltose were up-regulated in the malO mutant. These effects were reversed by complementation with the wild-type malO gene. Growth of these isogenic strains in medium with and without maltose showed that the malO mutant recovered more quickly from maltose deprivation when compared to the wild-type and complemented strains, leading to the conclusion that the MalNO system regulates maltose utilization in C. perfringens. It is postulated that this regulatory network may allow this soil bacterium and opportunistic pathogen to respond to environmental conditions where there are higher concentrations of maltose or maltodextrins, such as in the presence of decaying plant material in rich soil. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Adaptation to environmental stimuli within the host: two-component signal transduction systems of Mycobacterium tuberculosis.

    Science.gov (United States)

    Bretl, Daniel J; Demetriadou, Chrystalla; Zahrt, Thomas C

    2011-12-01

    Pathogenic microorganisms encounter a variety of environmental stresses following infection of their respective hosts. Mycobacterium tuberculosis, the etiological agent of tuberculosis, is an unusual bacterial pathogen in that it is able to establish lifelong infections in individuals within granulomatous lesions that are formed following a productive immune response. Adaptation to this highly dynamic environment is thought to be mediated primarily through transcriptional reprogramming initiated in response to recognition of stimuli, including low-oxygen tension, nutrient depletion, reactive oxygen and nitrogen species, altered pH, toxic lipid moieties, cell wall/cell membrane-perturbing agents, and other environmental cues. To survive continued exposure to these potentially adverse factors, M. tuberculosis encodes a variety of regulatory factors, including 11 complete two-component signal transduction systems (TCSSs) and several orphaned response regulators (RRs) and sensor kinases (SKs). This report reviews our current knowledge of the TCSSs present in M. tuberculosis. In particular, we discuss the biochemical and functional characteristics of individual RRs and SKs, the environmental stimuli regulating their activation, the regulons controlled by the various TCSSs, and the known or postulated role(s) of individual TCSSs in the context of M. tuberculosis physiology and/or pathogenesis.

  7. Interaction of the Arabidopsis UV-B-Specific Signaling Component UVR8 with Chromatin

    Institute of Scientific and Technical Information of China (English)

    Catherine Cloix; Gareth I.Jenkins

    2008-01-01

    Arabidopsis UV RESISTANCE LOCUS8 (UVR8) is a UV-B-specific signaling component that regulates expression of a range of genes concerned with UV protection. Here, we investigate the interaction of UVR8 with chromatin. Using antibodies specific to UVR8 in chromatin immunoprecipitation (CHIP) assays with wild-type plants, we show that native UVR8 binds to chromatin in vivo. Similar experiments using an anti-GFP antibody with plants expressing a GFP-UVR8 fusion show that UVR8 associates with a relatively small region of chromatin containing the HY5 gene. UVR8 interacts with chromatin containing the promoter regions of other genes, but not with all the genes it regulates. UV-B is not required for the interaction of UVR8 with chromatin because association with several gene loci is observed in the absence of UV-B. Pulldown assays demonstrate that UVR8 associates with histones in vivo and competition experiments indicate that the interaction is preferentially with histone H2B. ChIP experiments using antibodies that recognize specific histone modifications indicate that the UV-B-stimulated transcription of some genes may be correlated with histone modification. In particular, the ELIP1 promoter showed a significant enrichment of diacetyl histone H3 (K9/K14) following UV-B exposure.These findings increase understanding of the interaction of the key UV-B-specific regulator UVR8 with chromatin.

  8. NARG Algorithm of Extracting Non-redundant Association Rule in Concept Lattice%概念格上无冗余关联规则的提取算法NARG

    Institute of Scientific and Technical Information of China (English)

    苗茹; 沈夏炯; 胡小华

    2009-01-01

    Association roles are the very valuable kind of law in data mining. A large number of rules arc usually generated from database using ordinary mining algorithms. Especially when the minimal support and minimal confidence are reduced, the number of association rules rise rapidly. The key of eliminating redundant association rules is to reduce rules without losing data information. This paper presents a new algorithm called NARG to extract non-redundant association rules based on concept lattice and properties of redundant association rules. This algorithm can gain the minimal non-redundant set of association rules while effectively improve efficiency of extracting rules without losing any information of data.%在数据挖掘中,关联规则是很有价值的一类规律.普通的挖掘算法会产生大量的规则,尤其是当最小支持度和最小可信度减少时,关联规则的数目急剧上升.如何对规则进行约减而又不丢失数据信息是消除冗余关联规则的关键.根据概念格的理论和冗余关联规则的性质,提出在概念格上提取无冗余关联规则的NARG算法.该算法可以得到最小的无冗余的关联规则集,而且不丢失任何信息,可有效提高关联规则生成的效率.

  9. Optimization of diagnostic strategy in non-redundant multi-fault system based on probability threshold%基于概率阈的非冗余多故障系统诊断策略优化

    Institute of Scientific and Technical Information of China (English)

    朱海鹏; 景博; 黄以锋; 苏俊阳

    2012-01-01

    针对传统的单故障假设无法诊断复杂系统多故障并发的情况,提出了一种基于概率阈的非冗余系统多故障诊断策略.首先对系统的相关性模型进行扩展,并删除低于概率阈的故障状态,建立非冗余系统的多故障测试诊断模型;其次在信息熵算法的基础上建立Rollout算法,获得了最优测试序列;然后建立故障诊断树并计算测试代价;最后以某机载电子系统为例验证了该方法的有效性.该方法可以在保证测试费用最小的情况下获得非冗余系统的最优测试序列.%This paper propsoed a multiple fault diagnostic strategy for non-redundant system based on probability threshold. Firstly,it expanded system dependency models, removed fault states which were below probability threshold, and established multiple fault diagnostic models of non-redundant system. Then using entropy algorithm as base algorithm, it presented Rollout algorithm to obtain best test sequence. At last.it built the fault diagnosis tree and calculated test cost. It put forward an airborne electronic system to prove its effectiveness. It can obtain the best test sequence by minimums cost test.

  10. Fluorescence signalling of the transition metal ions: Design strategy based on the choice of the fluorophore component

    Indian Academy of Sciences (India)

    N B Sankaran; S Banthia; A Samanta

    2002-12-01

    Transition metal ions are notorious for their fluorescence quenching abilities. In this paper, we discuss the design strategies for the development of efficient off-on fluorescence signalling systems for the transition metal ions. It is shown that even simple fluorophore-spacer-receptor systems can display excellent off-on fluorescence signalling towards the quenching metal ions when the fluorophore component is chosen judiciously.

  11. The human keratinocyte two-dimensional gel protein database (update 1995): mapping components of signal transduction pathways

    DEFF Research Database (Denmark)

    Celis, J E; Rasmussen, H H; Gromov, P

    1995-01-01

    )vaccinia virus expression of full length cDNAs, and (vi) in vitro transcription/translation of full-length cDNAs. This year, special emphasis has been given to the identification of signal transduction components by using 2-D gel immunoblotting of crude keratinocyte lysates in combination with enhanced......--through a systematic study of ekeratinocytes--qualitative and quantitative information on proteins and their genes that may allow us to identify abnormal patterns of gene expression and to pinpoint signaling pathways and components affected in various skin diseases, cancer included. Udgivelsesdato: 1995-Dec...

  12. Reversing-pulse electric birefringence of multicomponent systems: the formulation and signal simulation for two axially symmetric components in equilibrium and the appearance of unusual signal patterns.

    Science.gov (United States)

    Yamaoka, Kiwamu

    2007-04-15

    This paper consists of two parts on reversing-pulse electric birefringence (RPEB) signal patterns. The first is the theoretical formulation of two axially symmetric models coexisting in equilibrium in solution. The present RPEB theory is based on the original Tinoco-Yamaoka theory with classical electric dipole moments, which was recently modified and extended by Yamaoka, Sasai, and Kohno to include various electric and optical parameters and most importantly the ion-fluctuation dipole moment (1/2) along the longitudinal direction of axially symmetric molecules. The theory contains the electric polarizability anisotropy Deltaalpha', which can be either positive or negative in relation to the shape of components. The overall signal can be expressed as the sum of the fractions of two components in proportions to the coefficient F(1) or F(2) (=1-F(1)). The second part is the simulation of theoretical RPEB curves for the two-component system with various sets of electric and hydrodynamic parameters for hypothetical but interesting cases. In consideration of the decay behavior, calculated decay curves were compared with experimentally conceivable signals, classifying them into three categories according to cases: F(1)>1, 0signal in buildup and reverse transients reveals the mechanism of field orientation and electro-optic properties of molecules in solution. The ratio q=/ktDeltaalpha(') is the crucial factor that controls the pattern of RPEB signals. If q value of one component is positive and the other is negative, the simulated RPEB curves are characterized by three cases: q>0, q0 or qsignals. If -1signal patterns appears.

  13. Preliminary study on electron paramagnetic resonance (EPR) signal properties of mobile phone components for dose estimation in radiation accident

    Energy Technology Data Exchange (ETDEWEB)

    Park, Byeong Ryong; Ha, Wi Ho; Park, Sun Hoo; Lee, Jin Kyeong; Lee, Seung Sook [Korea Institute of Radiological and Medical Sciences, Seoul (Korea, Republic of)

    2015-12-15

    We have investigated the EPR signal properties in 12 components of two mobile phones (LCD, OLED) using electron paramagnetic resonance (EPR) spectrometer in this study.EPR measurements were performed at normal atmospheric conditions using Bruker EXEXSYS-II E500 spectrometer with X-band bridge, and samples were irradiated by {sup 137}C{sub s} gamma-ray source. To identify the presence of radiation-induced signal (RIS), the EPR spectra of each sample were measured unirradiated and irradiated at 50 Gy. Then, dose-response curve and signal intensity variating by time after irradiation were measured. As a result, the signal intensity increased after irradiation in all samples except the USIM plastic and IC chip. Among the samples, cover glass(CG), lens, light guide plate(LGP) and diffusion sheet have shown fine linearity (R{sup 2} > 0.99). Especially, the LGP had ideal characteristics for dosimetry because there were no signal in 0 Gy and high rate of increase in RIS. However, this sample showed weakness in fading. Signal intensity of LGP and Diffusion Sheet decreased by 50% within 72 hours after irradiation, while signals of Cover Glass and Lens were stably preserved during the short period of time. In order to apply rapidly EPR dosimetry using mobile phone components in large-scale radiation accidents, further studies on signal differences for same components of the different mobile phone, fading, pretreatment of samples and processing of background signal are needed. However, it will be possible to do dosimetry by dose-additive method or comparative method using unirradiated same product in small-scale accident.

  14. Expression and significance of sonic hedgehog signaling pathway-related components in brainstem and supratentorial astrocytomas

    Institute of Scientific and Technical Information of China (English)

    XIN Yu; HAO Shu-yu; TIAN Yong-ji; ZHANG Jun-ting; WU Zhen; WAN Hong; LI Jun-hua; JIANG Jian; ZHANG Li-wei

    2011-01-01

    Background Studies have shown that abnormal activation of the sonic hedgehog pathway is closely related to tumorigenesis in central nervous system.This study aimed to investigate the role of the sonic hedgehog signaling pathway in the occurrence of brainstem and supratentorial glioma.Methods Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) and immunohistochemistry were used to detect the expression of sonic hedgehog-related components in 5 specimens of normal brain tissue,10 of grade Ⅱ brainstem glioma,and 10 of grade Ⅱ supratentorial glioma.The significance of differences between two groups was determined using the Mann-Whitney U test or the two-sample test according to the results of normality distribution tests.Results The mRNA expression levels of sonic hedgehog-related genes were higher in brainstem astrocytomas than in supratentorial astrocytomas and normal brain tissue.The level of protein patched homolog 1 (PTCH1) was significantly higher in brainstem astrocytomas than in supratentorial astrocytomas and normal brain tissue (P <0.01).Immunohistochemistry semi-quantitative analysis was consistent with the qRT-PCR result that PTCH1 expression was increased significantly in brainstem astrocytomas at the protein level (P <0.05).Conclusions Enhanced PTCH1 expression and activation of the sonic hedgehog pathway are involved in brainstem glioma.This may be related to the difference in malignant biological behavior between brainstem and hemispheric glioma,and could be an ideal therapeutic target in brainstem glioma.

  15. Conformational transition of response regulator RR468 in a two-component system signal transduction process.

    Science.gov (United States)

    Banerjee, Rahul; Yan, Honggao; Cukier, Robert I

    2014-05-08

    Signal transduction can be accomplished via a two-component system (TCS) consisting of a histidine kinase (HK) and a response regulator (RR). In this work, we simulate the response regulator RR468 from Thermotoga maritima, in which phosphorylation and dephosphorylation of a conserved aspartate residue acts as a switch via a large conformational change concentrated in three proximal loops. A detailed view of the conformational transition is obscured by the lack of stability of the intermediate states, which are difficult to detect using common structural biology techniques. Molecular dynamics (MD) trajectories of the inactive and active conformations were run, and show that the inactive (or active) trajectories do not exhibit sampling of the active (or inactive) conformations on this time scale. Targeted MD (TMD) was used to generate trajectories that span the inactive and active conformations and provide a view of how a localized event like phosphorylation can lead to conformational changes elsewhere in the protein, especially in the three proximal loops. The TMD trajectories are clustered to identify stages along the transition path. Residue interaction networks are identified that point to key residues having to rearrange in the process of transition. These are identified using both hydrogen bond analysis and residue interaction strength measurements. Potentials of mean force are generated for key residue rearrangements to ascertain their free energy barriers. We introduce methods that attempt to extrapolate from one conformation to the other and find that the most fluctuating proximal loop can transit part way from one to the other, suggesting that this conformational information is embedded in the sequence.

  16. Cloning of a two-component signal transduction system of Xanthomonas campestris pv. phaseoli var. fuscans strain BXPF65

    DEFF Research Database (Denmark)

    Chan, JWYF; Maynard, Scott; Goodwin, PH

    1998-01-01

    A putative two-component signal transduction system was amplified and cloned from the plant pathogenic bacterium Xanthomonas campestris pv. phaseoli var. fuscans isolate BXPF65. The 620 bp amplified fragment was sequenced and analyzed with the BLAST Enhanced Alignment Utility (BEAUTY). BEAUTY ana...

  17. Comparative analysis of two-component signal transduction systems of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis

    NARCIS (Netherlands)

    Been, de M.W.H.J.; Francke, C.; Moezelaar, R.; Abee, T.; Siezen, R.J.

    2006-01-01

    Members of the Bacillus cereus group are ubiquitously present in the environment and can adapt to a wide range of environmental fluctuations. In bacteria, these adaptive responses are generally mediated by two-component signal transduction systems (TCSs), which consist of a histidine kinase (HK) and

  18. Comparative analysis of two-component signal transduction systems of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis

    NARCIS (Netherlands)

    Been, M.W.H.J. de; Francke, C.; Moezelaar, R.; Abee, T.; Siezen, R.J.

    2006-01-01

    Members of the Bacillus cereus group are ubiquitously present in the environment and can adapt to a wide range of environmental fluctuations. In bacteria, these adaptive responses are generally mediated by two-component signal transduction systems (TCSs), which consist of a histidine kinase (HK) and

  19. Purification and assays of Rhodobacter capsulatus RegB-RegA two-component signal transduction system.

    Science.gov (United States)

    Swem, Lee R; Swem, Danielle L; Wu, Jiang; Bauer, Carl E

    2007-01-01

    Two-component signal-transduction systems, composed of a histidine-sensor kinase and a DNA-binding response regulator, allow bacteria to detect environmental changes and adjust cellular physiology to live more efficiently in a broad distribution of niches. Although many two-component signal-transduction systems are known, a limited number of signals that stimulate these systems have been discovered. This chapter describes the purification and characterization of the predominant two-component signal-transduction system utilized by Rhodobacter capsulatus, a nonsulfur purple photosynthetic bacterium. Specifically, we explain the overexpression, detergent solubilization, and purification of the full-length membrane-spanning histidine-sensor kinase RegB. We also provide a method to measure autophosphorylation of RegB and discern the effect of its signal molecule, ubiquinone, on autophosphorylation levels. In addition we describe the overexpression and purification of the cognate response regulator RegA and a technique used to visualize the phosphotransfer reaction from RegB to RegA.

  20. Stochastic simulation of prokaryotic two-component signalling indicates stochasticity-induced active-state locking and growth-rate dependent bistability

    NARCIS (Netherlands)

    K. Wei (Katy); M. Moinat (Maxim); T.R. Maarleveld (Timo); F.J. Bruggeman (Frank)

    2014-01-01

    htmlabstractSignal transduction by prokaryotes almost exclusively relies on two-component systems for sensing and responding to (extracellular) signals. Here, we use stochastic models of two-component systems to better understand the impact of stochasticity on the fidelity and robustness of signal

  1. PSM/SH2-B distributes selected mitogenic receptor signals to distinct components in the PI3-kinase and MAP kinase signaling pathways.

    Science.gov (United States)

    Deng, Youping; Xu, Hu; Riedel, Heimo

    2007-02-15

    The Pro-rich, PH, and SH2 domain containing mitogenic signaling adapter PSM/SH2-B has been implicated as a cellular partner of various mitogenic receptor tyrosine kinases and related signaling mechanisms. Here, we report in a direct comparison of three peptide hormones, that PSM participates in the assembly of distinct mitogenic signaling complexes in response to insulin or IGF-I when compared to PDGF in cultured normal fibroblasts. The complex formed in response to insulin or IGF-I involves the respective peptide hormone receptor and presumably the established components leading to MAP kinase activation. However, our data suggest an alternative link from the PDGF receptor via PSM directly to MEK1/2 and consequently also to p44/42 activation, possibly through a scaffold protein. At least two PSM domains participate, the SH2 domain anticipated to link PSM to the respective receptor and the Pro-rich region in an association with an unidentified downstream component resulting in direct MEK1/2 and p44/42 regulation. The PDGF receptor signaling complex formed in response to PDGF involves PI 3-kinase in addition to the same components and interactions as described for insulin or IGF-I. PSM associates with PI 3-kinase via p85 and in addition the PSM PH domain participates in the regulation of PI 3-kinase activity, presumably through membrane interaction. In contrast, the PSM Pro-rich region appears to participate only in the MAP kinase signal. Both pathways contribute to the mitogenic response as shown by cell proliferation, survival, and focus formation. PSM regulates p38 MAP kinase activity in a pathway unrelated to the mitogenic response.

  2. Receptor component protein (RCP): a member of a multi-protein complex required for G-protein-coupled signal transduction.

    Science.gov (United States)

    Prado, M A; Evans-Bain, B; Dickerson, I M

    2002-08-01

    The calcitonin-gene-related peptide (CGRP) receptor component protein (RCP) is a 148-amino-acid intracellular protein that is required for G-protein-coupled signal transduction at receptors for the neuropeptide CGRP. RCP works in conjunction with two other proteins to constitute a functional CGRP receptor: calcitonin-receptor-like receptor (CRLR) and receptor-activity-modifying protein 1 (RAMP1). CRLR has the stereotypical seven-transmembrane topology of a G-protein-coupled receptor; it requires RAMP1 for trafficking to the cell surface and for ligand specificity, and requires RCP for coupling to the cellular signal transduction pathway. We have made cell lines that expressed an antisense construct of RCP and determined that CGRP-mediated signal transduction was reduced, while CGRP binding was unaffected. Furthermore, signalling at two other endogenous G-protein-coupled receptors was unaffected, suggesting that RCP was specific for a limited subset of receptors.

  3. Eye blink artifact rejection in single-channel electroencephalographic signals by complete ensemble empirical mode decomposition and independent component analysis.

    Science.gov (United States)

    Kanoga, Suguru; Mitsukura, Yasue

    2015-01-01

    To study an eye blink artifact rejection scheme from single-channel electroencephalographic (EEG) signals has been now a major challenge in the field of EEG signal processing. High removal performance is still needed to more strictly investigate pattern of EEG features. This paper proposes a new eye blink artifact rejection scheme from single-channel EEG signals by combining complete ensemble empirical mode decomposition (CEEMD) and independent component analysis (ICA). We compare the separation performance of our proposed scheme with existing schemes (wavelet-ICA, EMD-ICA, and EEMD-ICA) though real-life data by using signal-to-noise ratio. As a result, CEEMD-ICA showed high performance (11.86 dB) than all other schemes (10.78, 10.59, and 11.30 dB) in the ability of eye blink artifact removal.

  4. Stochastic kinetic model of two component system signalling reveals all-or-none, graded and mixed mode stochastic switching responses.

    Science.gov (United States)

    Kierzek, Andrzej M; Zhou, Lu; Wanner, Barry L

    2010-03-01

    Two-component systems (TCSs) are prevalent signal transduction systems in bacteria that control innumerable adaptive responses to environmental cues and host-pathogen interactions. We constructed a detailed stochastic kinetic model of two component signalling based on published data. Our model has been validated with flow cytometry data and used to examine reporter gene expression in response to extracellular signal strength. The model shows that, depending on the actual kinetic parameters, TCSs exhibit all-or-none, graded or mixed mode responses. In accordance with other studies, positively autoregulated TCSs exhibit all-or-none responses. Unexpectedly, our model revealed that TCSs lacking a positive feedback loop exhibit not only graded but also mixed mode responses, in which variation of the signal strength alters the level of gene expression in induced cells while the regulated gene continues to be expressed at the basal level in a substantial fraction of cells. The graded response of the TCS changes to mixed mode response by an increase of the translation initiation rate of the histidine kinase. Thus, a TCS is an evolvable design pattern capable of implementing deterministic regulation and stochastic switches associated with both graded and threshold responses. This has implications for understanding the emergence of population diversity in pathogenic bacteria and the design of genetic circuits in synthetic biology applications. The model is available in systems biology markup language (SBML) and systems biology graphical notation (SBGN) formats and can be used as a component of large-scale biochemical reaction network models.

  5. Principal component analysis of soft x-ray signals generated by the PF-1000 facility in experiments with solid targets

    Science.gov (United States)

    Kowalska-Strzęciwilk, Ewa; Skrzeczanowski, Wojciech; Czarnecka, Agata; Kubkowska, Monika; Paduch, Marian; Zielińska, Ewa

    2014-05-01

    The paper presents the analysis of soft x-ray signals generated in the PF-1000 facility equipped with a modified inner electrode with a central tungsten insert of 50 mm diameter in experiments with tungsten and carbon samples. The PF-1000 machine was operated with pure deuterium filling under the initial pressure of 1.3 hPa. The machine was powered using a condenser bank charged initially to 24 kV, corresponding to the stored energy of 380 kJ, with the maximum discharge current amounted to 1.8 MA. For investigation of plasma stream-sample interactions, we applied 16-frame laser interferometry, optical spectroscopy and soft x-ray measurements with the use of a system of four silicon pin-diodes. In this paper, we mainly focus on the principal component analysis (PCA) of the registered x-ray signals to find a corelation between the neutron yield and observed maxima in signals. X-ray signals collected by four pin-diodes covered a 9 cm range in front of the electrode ends. Each diode collected a signal from the circle of 3 cm diameter. The presented PCA analysis is based on 57 PF discharges and 16 parameters are taken into account in the analysis. The study of signals from the pin-diode system showed good correlation between the neutron yield and the maximum in the x-ray signal, which appeared about 1000-1300 ns after the maximum of plasma compression.

  6. Structure and mechanism of the essential two-component signal-transduction system WalKR in Staphylococcus aureus.

    Science.gov (United States)

    Ji, Quanjiang; Chen, Peter J; Qin, Guangrong; Deng, Xin; Hao, Ziyang; Wawrzak, Zdzislaw; Yeo, Won-Sik; Quang, Jenny Winjing; Cho, Hoonsik; Luo, Guan-Zheng; Weng, Xiaocheng; You, Qiancheng; Luan, Chi-Hao; Yang, Xiaojing; Bae, Taeok; Yu, Kunqian; Jiang, Hualiang; He, Chuan

    2016-03-18

    Most low GC Gram-positive bacteria possess an essential walKR two-component system (TCS) for signal transduction involved in regulating cell wall homoeostasis. Despite the well-established intracellular regulatory mechanism, the role of this TCS in extracellular signal recognition and factors that modulate the activity of this TCS remain largely unknown. Here we identify the extracellular receptor of the kinase 'WalK' (erWalK) as a key hub for bridging extracellular signal input and intracellular kinase activity modulation in Staphylococcus aureus. Characterization of the crystal structure of erWalK revealed a canonical Per-Arnt-Sim (PAS) domain for signal sensing. Single amino-acid mutation of potential signal-transduction residues resulted in severely impaired function of WalKR. A small molecule derived from structure-based virtual screening against erWalK is capable of selectively activating the walKR TCS. The molecular level characterization of erWalK will not only facilitate exploration of natural signal(s) but also provide a template for rational design of erWalK inhibitors.

  7. Use of independent component analysis to improve signal-to-noise ratio in multi-probe fluorescence microscopy.

    Science.gov (United States)

    Dao, L; Lucotte, B; Glancy, B; Chang, L-C; Hsu, L-Y; Balaban, R S

    2014-11-01

    In conventional multi-probe fluorescence microscopy, narrow bandwidth filters on detectors are used to avoid bleed-through artefacts between probes. The limited bandwidth reduces the signal-to-noise ratio of the detection, often severely compromising one or more channels. Herein, we describe a process of using independent component analysis to discriminate the position of different probes using only a dichroic mirror to differentiate the signals directed to the detectors. Independent component analysis was particularly effective in samples where the spatial overlap between the probes is minimal, a very common case in cellular microscopy. This imaging scheme collects nearly all of the emitted light, significantly improving the image signal-to-noise ratio. In this study, we focused on the detection of two fluorescence probes used in vivo, NAD(P)H and ANEPPS. The optimal dichroic mirror cutoff frequency was determined with simulations using the probes spectral emissions. A quality factor, defined as the cross-channel contrast-to-noise ratio, was optimized to maximize signals while maintaining spatial discrimination between the probes after independent component analysis post-processing. Simulations indicate that a ∼3 fold increase in signal-to-noise ratio using the independent component analysis approach can be achieved over the conventional narrow-band filtering approach without loss of spatial discrimination. We confirmed this predicted performance from experimental imaging of NAD(P)H and ANEPPS in mouse skeletal muscle, in vivo. For many multi-probe studies, the increased sensitivity of this 'full bandwidth' approach will lead to improved image quality and/or reduced excitation power requirements.

  8. Two-component signal transduction pathways regulating growth and cell cycle progression in a bacterium: a system-level analysis.

    Directory of Open Access Journals (Sweden)

    Jeffrey M Skerker

    2005-10-01

    Full Text Available Two-component signal transduction systems, comprised of histidine kinases and their response regulator substrates, are the predominant means by which bacteria sense and respond to extracellular signals. These systems allow cells to adapt to prevailing conditions by modifying cellular physiology, including initiating programs of gene expression, catalyzing reactions, or modifying protein-protein interactions. These signaling pathways have also been demonstrated to play a role in coordinating bacterial cell cycle progression and development. Here we report a system-level investigation of two-component pathways in the model organism Caulobacter crescentus. First, by a comprehensive deletion analysis we show that at least 39 of the 106 two-component genes are required for cell cycle progression, growth, or morphogenesis. These include nine genes essential for growth or viability of the organism. We then use a systematic biochemical approach, called phosphotransfer profiling, to map the connectivity of histidine kinases and response regulators. Combining these genetic and biochemical approaches, we identify a new, highly conserved essential signaling pathway from the histidine kinase CenK to the response regulator CenR, which plays a critical role in controlling cell envelope biogenesis and structure. Depletion of either cenK or cenR leads to an unusual, severe blebbing of cell envelope material, whereas constitutive activation of the pathway compromises cell envelope integrity, resulting in cell lysis and death. We propose that the CenK-CenR pathway may be a suitable target for new antibiotic development, given previous successes in targeting the bacterial cell wall. Finally, the ability of our in vitro phosphotransfer profiling method to identify signaling pathways that operate in vivo takes advantage of an observation that histidine kinases are endowed with a global kinetic preference for their cognate response regulators. We propose that this

  9. Systematic Dissection and Trajectory-Scanning Mutagenesis of the Molecular Interface That Ensures Specificity of Two-Component Signaling Pathways

    Science.gov (United States)

    Lubin, Emma A.; Ashenberg, Orr; Skerker, Jeffrey M.; Laub, Michael T.

    2010-01-01

    Two-component signal transduction systems enable bacteria to sense and respond to a wide range of environmental stimuli. Sensor histidine kinases transmit signals to their cognate response regulators via phosphorylation. The faithful transmission of information through two-component pathways and the avoidance of unwanted cross-talk require exquisite specificity of histidine kinase-response regulator interactions to ensure that cells mount the appropriate response to external signals. To identify putative specificity-determining residues, we have analyzed amino acid coevolution in two-component proteins and identified a set of residues that can be used to rationally rewire a model signaling pathway, EnvZ-OmpR. To explore how a relatively small set of residues can dictate partner selectivity, we combined alanine-scanning mutagenesis with an approach we call trajectory-scanning mutagenesis, in which all mutational intermediates between the specificity residues of EnvZ and another kinase, RstB, were systematically examined for phosphotransfer specificity. The same approach was used for the response regulators OmpR and RstA. Collectively, the results begin to reveal the molecular mechanism by which a small set of amino acids enables an individual kinase to discriminate amongst a large set of highly-related response regulators and vice versa. Our results also suggest that the mutational trajectories taken by two-component signaling proteins following gene or pathway duplication may be constrained and subject to differential selective pressures. Only some trajectories allow both the maintenance of phosphotransfer and the avoidance of unwanted cross-talk. PMID:21124821

  10. Two-Component Signal Transduction Pathways Regulating Growth and Cell Cycle Progression in a Bacterium: A System-Level Analysis

    Science.gov (United States)

    Skerker, Jeffrey M; Prasol, Melanie S; Perchuk, Barrett S; Biondi, Emanuele G

    2005-01-01

    Two-component signal transduction systems, comprised of histidine kinases and their response regulator substrates, are the predominant means by which bacteria sense and respond to extracellular signals. These systems allow cells to adapt to prevailing conditions by modifying cellular physiology, including initiating programs of gene expression, catalyzing reactions, or modifying protein–protein interactions. These signaling pathways have also been demonstrated to play a role in coordinating bacterial cell cycle progression and development. Here we report a system-level investigation of two-component pathways in the model organism Caulobacter crescentus. First, by a comprehensive deletion analysis we show that at least 39 of the 106 two-component genes are required for cell cycle progression, growth, or morphogenesis. These include nine genes essential for growth or viability of the organism. We then use a systematic biochemical approach, called phosphotransfer profiling, to map the connectivity of histidine kinases and response regulators. Combining these genetic and biochemical approaches, we identify a new, highly conserved essential signaling pathway from the histidine kinase CenK to the response regulator CenR, which plays a critical role in controlling cell envelope biogenesis and structure. Depletion of either cenK or cenR leads to an unusual, severe blebbing of cell envelope material, whereas constitutive activation of the pathway compromises cell envelope integrity, resulting in cell lysis and death. We propose that the CenK–CenR pathway may be a suitable target for new antibiotic development, given previous successes in targeting the bacterial cell wall. Finally, the ability of our in vitro phosphotransfer profiling method to identify signaling pathways that operate in vivo takes advantage of an observation that histidine kinases are endowed with a global kinetic preference for their cognate response regulators. We propose that this system

  11. Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: orphans and crosstalks.

    Directory of Open Access Journals (Sweden)

    Andrea Procaccini

    Full Text Available Predictive understanding of the myriads of signal transduction pathways in a cell is an outstanding challenge of systems biology. Such pathways are primarily mediated by specific but transient protein-protein interactions, which are difficult to study experimentally. In this study, we dissect the specificity of protein-protein interactions governing two-component signaling (TCS systems ubiquitously used in bacteria. Exploiting the large number of sequenced bacterial genomes and an operon structure which packages many pairs of interacting TCS proteins together, we developed a computational approach to extract a molecular interaction code capturing the preferences of a small but critical number of directly interacting residue pairs. This code is found to reflect physical interaction mechanisms, with the strongest signal coming from charged amino acids. It is used to predict the specificity of TCS interaction: Our results compare favorably to most available experimental results, including the prediction of 7 (out of 8 known interaction partners of orphan signaling proteins in Caulobacter crescentus. Surveying among the available bacterial genomes, our results suggest 15∼25% of the TCS proteins could participate in out-of-operon "crosstalks". Additionally, we predict clusters of crosstalking candidates, expanding from the anecdotally known examples in model organisms. The tools and results presented here can be used to guide experimental studies towards a system-level understanding of two-component signaling.

  12. Increased Expression of TGF-β Signaling Components in a Mouse Model of Fibrosis Induced by Submandibular Gland Duct Ligation.

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    Lucas T Woods

    Full Text Available Transforming growth factor-β (TGF-β is a multi-functional cytokine with a well-described role in the regulation of tissue fibrosis and regeneration in the liver, kidney and lung. Submandibular gland (SMG duct ligation and subsequent deligation in rodents is a classical model for studying salivary gland damage and regeneration. While previous studies suggest that TGF-β may contribute to salivary gland fibrosis, the expression of TGF-β signaling components has not been investigated in relation to mouse SMG duct ligation-induced fibrosis and regeneration following ductal deligation. Following a 7 day SMG duct ligation, TGF-β1 and TGF-β3 were significantly upregulated in the SMG, as were TGF-β receptor 1 and downstream Smad family transcription factors in salivary acinar cells, but not in ductal cells. In acinar cells, duct ligation also led to upregulation of snail, a Smad-activated E-cadherin repressor and regulator of epithelial-mesenchymal transition, whereas in ductal cells upregulation of E-cadherin was observed while snail expression was unchanged. Upregulation of these TGF-β signaling components correlated with upregulation of fibrosis markers collagen 1 and fibronectin, responses that were inhibited by administration of the TGF-β receptor 1 inhibitors SB431542 or GW788388. After SMG regeneration following a 28 day duct deligation, TGF-β signaling components and epithelial-mesenchymal transition markers returned to levels similar to non-ligated controls. The results from this study indicate that increased TGF-β signaling contributes to duct ligation-induced changes in salivary epithelium that correlate with glandular fibrosis. Furthermore, the reversibility of enhanced TGF-β signaling in acinar cells of duct-ligated mouse SMG after deligation indicates that this is an ideal model for studying TGF-β signaling mechanisms in salivary epithelium as well as mechanisms of fibrosis initiation and their resolution.

  13. Pentraxins as a key component of innate immunity.

    Science.gov (United States)

    Bottazzi, Barbara; Garlanda, Cecilia; Salvatori, Giovanni; Jeannin, Pascale; Manfredi, Angelo; Mantovani, Alberto

    2006-02-01

    Pentraxins are a complex superfamily of multifunctional molecules characterized by a multimeric structure. C-reactive protein and pentraxin 3 (PTX3) are prototypic molecules of the short and long pentraxin family, respectively. PTX3 is conserved in evolution and produced by innate immune cells. Evidence suggests that PTX3 acts as a non-redundant component of the humoral arm of innate immunity, downstream of, and complementary to, cellular recognition, as well as a tuner of inflammation.

  14. The periplasmic regulator ExoR inhibits ExoS/ChvI two-component signaling in Sinorhizobium meliloti

    OpenAIRE

    Chen, Esther J.; Sabio, Erich A.; Long, Sharon R

    2008-01-01

    Sinorhizobium meliloti requires ExoS/ChvI two-component signaling to establish a nitrogen-fixing symbiosis with legume hosts. The importance of ExoS/ChvI signaling in microbe-host interactions is underscored by the requirement of ExoS/ChvI orthologs for virulence of the related α-proteobacteria Agrobacterium tumefaciens and Brucella abortus. In S. meliloti, ExoS/ChvI is a key regulator of gene expression for exopolysaccharide synthesis, biofilm formation, motility, nutrient utilization, and f...

  15. Detection of the deterministic component in acoustic emission signals from mechanically loaded rock samples

    Science.gov (United States)

    Hilarov, V. L.

    2015-11-01

    Using the Takens theorem, the attractor was reconstructed for amplitudes of acoustic emission signals measured during fracture of granite samples. Systematic features of the temporal behavior of system dynamic characteristics, such as the embedding dimension, fractal dimensions, recurrence plots, and their numerical parameters, were determined. For a preliminarily water-saturated sample, an order-disorder phase transition was detected in the structure of acoustic emission signals.

  16. A proteomic analysis of LRRK2 binding partners reveals interactions with multiple signaling components of the WNT/PCP pathway.

    Science.gov (United States)

    Salašová, Alena; Yokota, Chika; Potěšil, David; Zdráhal, Zbyněk; Bryja, Vítězslav; Arenas, Ernest

    2017-07-11

    Autosomal-dominant mutations in the Park8 gene encoding Leucine-rich repeat kinase 2 (LRRK2) have been identified to cause up to 40% of the genetic forms of Parkinson's disease. However, the function and molecular pathways regulated by LRRK2 are largely unknown. It has been shown that LRRK2 serves as a scaffold during activation of WNT/β-catenin signaling via its interaction with the β-catenin destruction complex, DVL1-3 and LRP6. In this study, we examine whether LRRK2 also interacts with signaling components of the WNT/Planar Cell Polarity (WNT/PCP) pathway, which controls the maturation of substantia nigra dopaminergic neurons, the main cell type lost in Parkinson's disease patients. Co-immunoprecipitation and tandem mass spectrometry was performed in a mouse substantia nigra cell line (SN4741) and human HEK293T cell line in order to identify novel LRRK2 binding partners. Inhibition of the WNT/β-catenin reporter, TOPFlash, was used as a read-out of WNT/PCP pathway activation. The capacity of LRRK2 to regulate WNT/PCP signaling in vivo was tested in Xenopus laevis' early development. Our proteomic analysis identified that LRRK2 interacts with proteins involved in WNT/PCP signaling such as the PDZ domain-containing protein GIPC1 and Integrin-linked kinase (ILK) in dopaminergic cells in vitro and in the mouse ventral midbrain in vivo. Moreover, co-immunoprecipitation analysis revealed that LRRK2 binds to two core components of the WNT/PCP signaling pathway, PRICKLE1 and CELSR1, as well as to FLOTILLIN-2 and CULLIN-3, which regulate WNT secretion and inhibit WNT/β-catenin signaling, respectively. We also found that PRICKLE1 and LRRK2 localize in signalosomes and act as dual regulators of WNT/PCP and β-catenin signaling. Accordingly, analysis of the function of LRRK2 in vivo, in X. laevis revelaed that LRKK2 not only inhibits WNT/β-catenin pathway, but induces a classical WNT/PCP phenotype in vivo. Our study shows for the first time that LRRK2 activates the WNT

  17. Two-Component Signal Transduction Systems of Desulfovibrio Vulgaris: Structural and Phylogenetic Analysis and Deduction of Putative Cognate Pairs

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Weiwen; Culley, David E.; Wu, Gang; Brockman, Fred J.

    2006-01-20

    ABSTRACT-Two-component signal transduction systems (TCSTS) composed of sensory histidine kinases (HK) and response regulators (RR), constitute a key element of the mechanism by which bacteria sense and respond to changes in environments. A large number of TCSTSs including 59 putative HKs and 55 RRs were identified from the Desulfovibrio vulgaris genome, indicating their important roles in regulation of cellular metabolism. In this study, the structural and phylogenetic analysis of all putative TCSTSs in D. vulgaris was performed. The results showed D. vulgaris contained an unexpectedly large number of hybrid-type HKs, implying that multiple-step phosphorelay may be a common signal transduction mechanism in D. vulgaris. Most TCSTS components of D. vulgaris were found clustered into several subfamilies previously recognized in other bacteria and extensive co-evolution between D. vulgaris HKs and RRs was observed, suggesting that the concordance of HKs and RRs in cognate phylogenetic groups could be indicative of cognate TCSTSs...

  18. Investigation on Spectral Structure of Gearbox Vibration Signals by Principal Component Analysis for Condition Monitoring Purposes

    Energy Technology Data Exchange (ETDEWEB)

    Zimroz, Radoslaw [Wroclaw University of Technology, Diagnostics and Vibro-Acoustics Science Laboratory (Poland); Bartkowiak, Anna, E-mail: radoslaw.zimroz@pwr.wroc.pl, E-mail: aba@ii.uni.wroc.pl [University of Wroclaw, Institute of Computer Science, Wroclaw (Poland)

    2011-07-19

    Spectral analysis is well-established analysis of vibrations used in diagnostics both in academia and industry. In general, one may identify components related to particular stages in the gearbox and analyze amplitudes of these components with a simple rule for decision-making: if amplitudes are increasing the condition becomes worse. However, usually one should analyze not single amplitude but at least several components, but: how to analyze them simultaneously? We have provided an example (case study) for planetary gearboxes in good and bad conditions (case B and case A). As diagnostic features we have used 15 amplitudes of spectral components related to fundamental planetary mesh frequency and its harmonics. Using Principal Component Analysis (PCA), it has been shown that amplitudes don't vary in the same way; change of condition affects not only amplitudes of all components in that sense, but also relation between them. We have investigated geometry of the data and it has been shown that the proportions of the explained total inertia of the three data sets ('good', 'bad' and mixed good/bad) are different. We claim that it may be a novel diagnostic approach to employ multidimensional analysis for accounting not only directly observed values but also interrelations both within and between the two groups of data. Different structure of the data is associated with different condition of the machines and such assumption is specified for the first time in the literature. Obviously it requires more studies.

  19. Influence of two-component signal transduction systems of Lactobacillus casei BL23 on tolerance to stress conditions.

    Science.gov (United States)

    Alcántara, Cristina; Revilla-Guarinos, Ainhoa; Zúñiga, Manuel

    2011-02-01

    Lactobacillus casei BL23 carries 17 two-component signal transduction systems. Insertional mutations were introduced into each gene encoding the cognate response regulators, and their effects on growth under different conditions were assayed. Inactivation of systems TC01, TC06, and TC12 (LCABL_02080-LCABL_02090, LCABL_12050-LCABL_12060, and LCABL_19600-LCABL_19610, respectively) led to major growth defects under the conditions assayed.

  20. Separating movement and gravity components in an acceleration signal and implications for the assessment of human daily physical activity.

    Science.gov (United States)

    van Hees, Vincent T; Gorzelniak, Lukas; Dean León, Emmanuel Carlos; Eder, Martin; Pias, Marcelo; Taherian, Salman; Ekelund, Ulf; Renström, Frida; Franks, Paul W; Horsch, Alexander; Brage, Søren

    2013-01-01

    Human body acceleration is often used as an indicator of daily physical activity in epidemiological research. Raw acceleration signals contain three basic components: movement, gravity, and noise. Separation of these becomes increasingly difficult during rotational movements. We aimed to evaluate five different methods (metrics) of processing acceleration signals on their ability to remove the gravitational component of acceleration during standardised mechanical movements and the implications for human daily physical activity assessment. An industrial robot rotated accelerometers in the vertical plane. Radius, frequency, and angular range of motion were systematically varied. Three metrics (Euclidian norm minus one [ENMO], Euclidian norm of the high-pass filtered signals [HFEN], and HFEN plus Euclidean norm of low-pass filtered signals minus 1 g [HFEN+]) were derived for each experimental condition and compared against the reference acceleration (forward kinematics) of the robot arm. We then compared metrics derived from human acceleration signals from the wrist and hip in 97 adults (22-65 yr), and wrist in 63 women (20-35 yr) in whom daily activity-related energy expenditure (PAEE) was available. In the robot experiment, HFEN+ had lowest error during (vertical plane) rotations at an oscillating frequency higher than the filter cut-off frequency while for lower frequencies ENMO performed better. In the human experiments, metrics HFEN and ENMO on hip were most discrepant (within- and between-individual explained variance of 0.90 and 0.46, respectively). ENMO, HFEN and HFEN+ explained 34%, 30% and 36% of the variance in daily PAEE, respectively, compared to 26% for a metric which did not attempt to remove the gravitational component (metric EN). In conclusion, none of the metrics as evaluated systematically outperformed all other metrics across a wide range of standardised kinematic conditions. However, choice of metric explains different degrees of variance in

  1. Separating movement and gravity components in an acceleration signal and implications for the assessment of human daily physical activity.

    Directory of Open Access Journals (Sweden)

    Vincent T van Hees

    Full Text Available INTRODUCTION: Human body acceleration is often used as an indicator of daily physical activity in epidemiological research. Raw acceleration signals contain three basic components: movement, gravity, and noise. Separation of these becomes increasingly difficult during rotational movements. We aimed to evaluate five different methods (metrics of processing acceleration signals on their ability to remove the gravitational component of acceleration during standardised mechanical movements and the implications for human daily physical activity assessment. METHODS: An industrial robot rotated accelerometers in the vertical plane. Radius, frequency, and angular range of motion were systematically varied. Three metrics (Euclidian norm minus one [ENMO], Euclidian norm of the high-pass filtered signals [HFEN], and HFEN plus Euclidean norm of low-pass filtered signals minus 1 g [HFEN+] were derived for each experimental condition and compared against the reference acceleration (forward kinematics of the robot arm. We then compared metrics derived from human acceleration signals from the wrist and hip in 97 adults (22-65 yr, and wrist in 63 women (20-35 yr in whom daily activity-related energy expenditure (PAEE was available. RESULTS: In the robot experiment, HFEN+ had lowest error during (vertical plane rotations at an oscillating frequency higher than the filter cut-off frequency while for lower frequencies ENMO performed better. In the human experiments, metrics HFEN and ENMO on hip were most discrepant (within- and between-individual explained variance of 0.90 and 0.46, respectively. ENMO, HFEN and HFEN+ explained 34%, 30% and 36% of the variance in daily PAEE, respectively, compared to 26% for a metric which did not attempt to remove the gravitational component (metric EN. CONCLUSION: In conclusion, none of the metrics as evaluated systematically outperformed all other metrics across a wide range of standardised kinematic conditions. However, choice

  2. The Nla28S/Nla28 two-component signal transduction system regulates sporulation in Myxococcus xanthus.

    Science.gov (United States)

    Sarwar, Zaara; Garza, Anthony G

    2012-09-01

    The response regulator Nla28 is a key component in a cascade of transcriptional activators that modulates expression of many important developmental genes in Myxococcus xanthus. In this study, we identified and characterized Nla28S, a histidine kinase that modulates the activity of this important regulator of M. xanthus developmental genes. We show that the putative cytoplasmic domain of Nla28S has the in vitro biochemical properties of a histidine kinase protein: it hydrolyzes ATP and undergoes an ATP-dependent autophosphorylation that is acid labile and base stable. We also show that the putative cytoplasmic domain of Nla28S transfers a phosphoryl group to Nla28 in vitro, that the phosphotransfer is specific, and that a substitution in the predicted site of Nla28 phosphorylation (aspartate 53) abolishes the phosphotransfer reaction. In phenotypic studies, we found that a mutation in nla28S produces a developmental phenotype similar to, but weaker than, that produced by a mutation in nla28; both mutations primarily affect sporulation. Together, these data indicate that Nla28S is the in vivo histidine kinase partner of Nla28 and that the primary function of the Nla28S/Nla28 two-component signal transduction system is to regulate sporulation genes. The results of genetic studies suggest that phosphorylation of Nla28S is important for the in vivo sporulation function of the Nla28S/Nla28 two-component system. In addition, the quorum signal known as A-signal is important for full developmental expression of the nla28S-nla28 operon, suggesting that quorum signaling regulates the availability of the Nla28S/Nla28 signal transduction circuit in developing cells.

  3. STAC--A New Domain Associated with Transmembrane Solute Transport and Two-Component Signal Transduction Systems.

    Science.gov (United States)

    Korycinski, Mateusz; Albrecht, Reinhard; Ursinus, Astrid; Hartmann, Marcus D; Coles, Murray; Martin, Jörg; Dunin-Horkawicz, Stanislaw; Lupas, Andrei N

    2015-10-09

    Transmembrane receptors are integral components of sensory pathways in prokaryotes. These receptors share a common dimeric architecture, consisting in its basic form of an N-terminal extracellular sensor, transmembrane helices, and an intracellular effector. As an exception, we have identified an archaeal receptor family--exemplified by Af1503 from Archaeoglobus fulgidus--that is C-terminally shortened, lacking a recognizable effector module. Instead, a HAMP domain forms the sole extension for signal transduction in the cytosol. Here, we examine the gene environment of Af1503-like receptors and find a frequent association with transmembrane transport proteins. Furthermore, we identify and define a closely associated new protein domain family, which we characterize structurally using Af1502 from A. fulgidus. Members of this family are found both as stand-alone proteins and as domains within extant receptors. In general, the latter appear as connectors between the solute carrier 5 (SLC5)-like transmembrane domains and two-component signal transduction (TCST) domains. This is seen, for example, in the histidine kinase CbrA, which is a global regulator of metabolism, virulence, and antibiotic resistance in Pseudomonads. We propose that this newly identified domain family mediates signal transduction in systems regulating transport processes and name it STAC, for SLC and TCST-Associated Component. Copyright © 2015 MRC Laboratory of Molecular Biology. Published by Elsevier Ltd.. All rights reserved.

  4. Influences of an acoustic signal with ultrasound components on the acquisition of a defensive conditioned reflex in Wistar rats.

    Science.gov (United States)

    Loseva, E V; Alekseeva, T G

    2007-06-01

    The effects of short (90 sec) exposures to a complex acoustic signal with ultrasound components on the acquisition of a defensive conditioned two-way avoidance reflex using an electric shock as the unconditioned stimulus in a shuttle box were studied in female Wistar rats. This stimulus induced audiogenic convulsions of different severities in 59% of the animals. A scale for assessing the ability of rats to acquire the conditioned two-way avoidance reflex was developed. Presentation of the complex acoustic signal was found to be a powerful stressor for Wistar rats, preventing the acquisition of the reflex in the early stages (four and six days) after presentation. This effect was independent of the presence and severity of audiogenic convulsions in the rats during presentation of the acoustic signal. On repeat training nine days after the acoustic signal (with the first session after four days), acquisition of the reflex was hindered (as compared with controls not presented with the acoustic signal). However, on repeat training at later time points (1.5 months after the complex acoustic signal, with the first session after six days), the rats rapidly achieved the learning criterion (10 correct avoidance responses in a row). On the other hand, if the acoustic signal was presented at different times (immediately or at three or 45 days) after the first training session, the animals' ability to acquire the reflex on repeat training was not impaired at either the early or late periods after exposure to the stressor. These results suggest that the complex acoustic signal impairs short-term memory (the process of acquisition of the conditioned two-way avoidance reflex at the early post-presentation time point) but has no effect on long-term memory or consolidation of the memory trace.

  5. 454 Transcriptome sequencing suggests a role for two-component signalling in cellularization and differentiation of barley endosperm transfer cells.

    Directory of Open Access Journals (Sweden)

    Johannes Thiel

    Full Text Available BACKGROUND: Cell specification and differentiation in the endosperm of cereals starts at the maternal-filial boundary and generates the endosperm transfer cells (ETCs. Besides the importance in assimilate transfer, ETCs are proposed to play an essential role in the regulation of endosperm differentiation by affecting development of proximate endosperm tissues. We attempted to identify signalling elements involved in early endosperm differentiation by using a combination of laser-assisted microdissection and 454 transcriptome sequencing. PRINCIPAL FINDINGS: 454 sequencing of the differentiating ETC region from the syncytial state until functionality in transfer processes captured a high proportion of novel transcripts which are not available in existing barley EST databases. Intriguingly, the ETC-transcriptome showed a high abundance of elements of the two-component signalling (TCS system suggesting an outstanding role in ETC differentiation. All components and subfamilies of the TCS, including distinct kinds of membrane-bound receptors, have been identified to be expressed in ETCs. The TCS system represents an ancient signal transduction system firstly discovered in bacteria and has previously been shown to be co-opted by eukaryotes, like fungi and plants, whereas in animals and humans this signalling route does not exist. Transcript profiling of TCS elements by qRT-PCR suggested pivotal roles for specific phosphorelays activated in a coordinated time flow during ETC cellularization and differentiation. ETC-specificity of transcriptionally activated TCS phosphorelays was assessed for early differentiation and cellularization contrasting to an extension of expression to other grain tissues at the beginning of ETC maturation. Features of candidate genes of distinct phosphorelays and transcriptional activation of genes putatively implicated in hormone signalling pathways hint at a crosstalk of hormonal influences, putatively ABA and ethylene, and

  6. Morphogenesis signaling components influence cell cycle regulation by cyclin dependent kinase

    Directory of Open Access Journals (Sweden)

    Bevis Brooke J

    2009-07-01

    Full Text Available Abstract Background The yeast cell cycle is largely controlled by the cyclin-dependent kinase (CDK Cdc28. Recent evidence suggests that both CDK complex stability as well as function during mitosis is determined by precise regulation of Swe1, a CDK inhibitory kinase and cyclin binding partner. A model of mitotic progression has been provided by study of filamentous yeast. When facing nutrient-limited conditions, Ras2-mediated PKA and MAPK signaling cascades induce a switch from round to filamentous morphology resulting in delayed mitotic progression. Results To delineate how the dimorphic switch contributes to cell cycle regulation, temperature sensitive cdc28 mutants exhibiting constitutive filamentation were subjected to epistasis analyses with RAS2 signaling effectors. It was found that Swe1-mediated inhibitory tyrosine phosphorylation of Cdc28 during filamentous growth is in part mediated by Ras2 activation of PKA, but not Kss1-MAPK, signaling. This pathway is further influenced by Cks1, a conserved CDK-binding partner of elusive function with multiple proposed roles in CDK activation, transcriptional regulation and ubiquitin-mediated proteasome degradation. Conclusion The dynamic balance between Cks1- and Swe1-dependent regulation of Cdc28 and, thereby, the timing of mitosis during yeast dimorphism is regulated in part by Ras2/cAMP-mediated PKA signaling, a key pathway controlling filamentous growth.

  7. Automatic Classification of Artifactual ICA-Components for Artifact Removal in EEG Signals

    Directory of Open Access Journals (Sweden)

    Tangermann Michael

    2011-08-01

    Full Text Available Abstract Background Artifacts contained in EEG recordings hamper both, the visual interpretation by experts as well as the algorithmic processing and analysis (e.g. for Brain-Computer Interfaces (BCI or for Mental State Monitoring. While hand-optimized selection of source components derived from Independent Component Analysis (ICA to clean EEG data is widespread, the field could greatly profit from automated solutions based on Machine Learning methods. Existing ICA-based removal strategies depend on explicit recordings of an individual's artifacts or have not been shown to reliably identify muscle artifacts. Methods We propose an automatic method for the classification of general artifactual source components. They are estimated by TDSEP, an ICA method that takes temporal correlations into account. The linear classifier is based on an optimized feature subset determined by a Linear Programming Machine (LPM. The subset is composed of features from the frequency-, the spatial- and temporal domain. A subject independent classifier was trained on 640 TDSEP components (reaction time (RT study, n = 12 that were hand labeled by experts as artifactual or brain sources and tested on 1080 new components of RT data of the same study. Generalization was tested on new data from two studies (auditory Event Related Potential (ERP paradigm, n = 18; motor imagery BCI paradigm, n = 80 that used data with different channel setups and from new subjects. Results Based on six features only, the optimized linear classifier performed on level with the inter-expert disagreement (10% Mean Squared Error (MSE on the RT data. On data of the auditory ERP study, the same pre-calculated classifier generalized well and achieved 15% MSE. On data of the motor imagery paradigm, we demonstrate that the discriminant information used for BCI is preserved when removing up to 60% of the most artifactual source components. Conclusions We propose a universal and efficient classifier of

  8. A procedure to correct the effects of a relative delay between the quadrature components of radar signals at base band

    Directory of Open Access Journals (Sweden)

    Grydeland

    2005-01-01

    Full Text Available The real and imaginary parts of baseband signals are obtained from a real narrow-band signal by quadrature mixing, i.e. by mixing with cosine and sine signals at the narrow band's selected center frequency. We address the consequences of a delay between the outputs of the quadrature mixer, which arise when digital samples of the quadrature baseband signals are not synchronised, i.e. when the real and imaginary components have been shifted by one or more samples with respect to each other. Through analytical considerations and simulations of such an error on different synthetic signals, we show how this error can be expected to afflict different measurements. In addition, we show the effect of the error on actual incoherent scatter radar data obtained by two different digital receiver systems used in parallel at the EISCAT Svalbard Radar (ESR. The analytical considerations indicate a procedure to correct the error, albeit with some limitations due to a small singular region. We demonstrate the correction procedure on actually afflicted data and compare the results to simultaneously acquired unafflicted data. We also discuss the possible data analysis strategies, including some that avoid dealing directly with the singular region mentioned above.

  9. Automatic classification of artifactual ICA-components for artifact removal in EEG signals.

    Science.gov (United States)

    Winkler, Irene; Haufe, Stefan; Tangermann, Michael

    2011-08-02

    Artifacts contained in EEG recordings hamper both, the visual interpretation by experts as well as the algorithmic processing and analysis (e.g. for Brain-Computer Interfaces (BCI) or for Mental State Monitoring). While hand-optimized selection of source components derived from Independent Component Analysis (ICA) to clean EEG data is widespread, the field could greatly profit from automated solutions based on Machine Learning methods. Existing ICA-based removal strategies depend on explicit recordings of an individual's artifacts or have not been shown to reliably identify muscle artifacts. We propose an automatic method for the classification of general artifactual source components. They are estimated by TDSEP, an ICA method that takes temporal correlations into account. The linear classifier is based on an optimized feature subset determined by a Linear Programming Machine (LPM). The subset is composed of features from the frequency-, the spatial- and temporal domain. A subject independent classifier was trained on 640 TDSEP components (reaction time (RT) study, n = 12) that were hand labeled by experts as artifactual or brain sources and tested on 1080 new components of RT data of the same study. Generalization was tested on new data from two studies (auditory Event Related Potential (ERP) paradigm, n = 18; motor imagery BCI paradigm, n = 80) that used data with different channel setups and from new subjects. Based on six features only, the optimized linear classifier performed on level with the inter-expert disagreement (EEG data. Based on linear methods, it is applicable for different electrode placements and supports the introspection of results. Trained on expert ratings of large data sets, it is not restricted to the detection of eye- and muscle artifacts. Its performance and generalization ability is demonstrated on data of different EEG studies.

  10. Processing of pulse oximeter signals using adaptive filtering and autocorrelation to isolate perfusion and oxygenation components

    Science.gov (United States)

    Ibey, Bennett; Subramanian, Hariharan; Ericson, Nance; Xu, Weijian; Wilson, Mark; Cote, Gerard L.

    2005-03-01

    A blood perfusion and oxygenation sensor has been developed for in situ monitoring of transplanted organs. In processing in situ data, motion artifacts due to increased perfusion can create invalid oxygenation saturation values. In order to remove the unwanted artifacts from the pulsatile signal, adaptive filtering was employed using a third wavelength source centered at 810nm as a reference signal. The 810 nm source resides approximately at the isosbestic point in the hemoglobin absorption curve where the absorbance of light is nearly equal for oxygenated and deoxygenated hemoglobin. Using an autocorrelation based algorithm oxygenation saturation values can be obtained without the need for large sampling data sets allowing for near real-time processing. This technique has been shown to be more reliable than traditional techniques and proven to adequately improve the measurement of oxygenation values in varying perfusion states.

  11. Independent Component Analysis for fMRI: What is Signal and What is Noise?

    DEFF Research Database (Denmark)

    McKeown, Martin; Hansen, Lars Kai; Sejnowski, Terrence J.

    2003-01-01

    Many sources of fluctuation contribute to the functional magnetic resonance imaging (fMRI) signal, complicating attempts to infer those changes that are truly related to brain activation. Unlike methods of analysis of fMRI data that test the time course of each voxel against a hypothesized waveform...... that are not time-locked to an easily specified sensory or motor event. These methods can be further improved by incorporating prior knowledge regarding the temporal and spatial extent of brain activation....

  12. The Signaling Role of CD40 Ligand in Platelet Biology and in Platelet Component Transfusion

    Directory of Open Access Journals (Sweden)

    Chaker Aoui

    2014-12-01

    Full Text Available The CD40 ligand (CD40L is a transmembrane molecule of crucial interest in cell signaling in innate and adaptive immunity. It is expressed by a variety of cells, but mainly by activated T-lymphocytes and platelets. CD40L may be cleaved into a soluble form (sCD40L that has a cytokine-like activity. Both forms bind to several receptors, including CD40. This interaction is necessary for the antigen specific immune response. Furthermore, CD40L and sCD40L are involved in inflammation and a panoply of immune related and vascular pathologies. Soluble CD40L is primarily produced by platelets after activation, degranulation and cleavage, which may present a problem for transfusion. Soluble CD40L is involved in adverse transfusion events including transfusion related acute lung injury (TRALI. Although platelet storage designed for transfusion occurs in sterile conditions, platelets are activated and release sCD40L without known agonists. Recently, proteomic studies identified signaling pathways activated in platelet concentrates. Soluble CD40L is a good candidate for platelet activation in an auto-amplification loop. In this review, we describe the immunomodulatory role of CD40L in physiological and pathological conditions. We will focus on the main signaling pathways activated by CD40L after binding to its different receptors.

  13. Hedgehog Signaling Components Are Expressed in Choroidal Neovascularization in Laser-induced Retinal Lesion

    Science.gov (United States)

    Nochioka, Katsunori; Okuda, Hiroaki; Tatsumi, Kouko; Morita, Shoko; Ogata, Nahoko; Wanaka, Akio

    2016-01-01

    Choroidal neovascularization is one of the major pathological changes in age-related macular degeneration, which causes devastating blindness in the elderly population. The molecular mechanism of choroidal neovascularization has been under extensive investigation, but is still an open question. We focused on sonic hedgehog signaling, which is implicated in angiogenesis in various organs. Laser-induced injuries to the mouse retina were made to cause choroidal neovascularization. We examined gene expression of sonic hedgehog, its receptors (patched1, smoothened, cell adhesion molecule down-regulated by oncogenes (Cdon) and biregional Cdon-binding protein (Boc)) and downstream transcription factors (Gli1-3) using real-time RT-PCR. At seven days after injury, mRNAs for Patched1 and Gli1 were upregulated in response to injury, but displayed no upregulation in control retinas. Immunohistochemistry revealed that Patched1 and Gli1 proteins were localized to CD31-positive endothelial cells that cluster between the wounded retina and the pigment epithelium layer. Treatment with the hedgehog signaling inhibitor cyclopamine did not significantly decrease the size of the neovascularization areas, but the hedgehog agonist purmorphamine made the areas significantly larger than those in untreated retina. These results suggest that the hedgehog-signaling cascade may be a therapeutic target for age-related macular degeneration. PMID:27239075

  14. Virtual and flexible digital signal processing system based on software PnP and component works

    Science.gov (United States)

    He, Tao; Wu, Qinghua; Zhong, Fei; Li, Wei

    2005-05-01

    An idea about software PnP (Plug & Play) is put forward according to the hardware PnP. And base on this idea, a virtual flexible digital signal processing system (FVDSPS) is carried out. FVDSPS is composed of a main control center, many sub-function modules and other hardware I/O modules. Main control center sends out commands to sub-function modules, and manages running orders, parameters and results of sub-functions. The software kernel of FVDSPS is DSP (Digital Signal Processing) module, which communicates with the main control center through some protocols, accept commands or send requirements. The data sharing and exchanging between the main control center and the DSP modules are carried out and managed by the files system of the Windows Operation System through the effective communication. FVDSPS real orients objects, orients engineers and orients engineering problems. With FVDSPS, users can freely plug and play, and fast reconfigure a signal process system according to engineering problems without programming. What you see is what you get. Thus, an engineer can orient engineering problems directly, pay more attention to engineering problems, and promote the flexibility, reliability and veracity of testing system. Because FVDSPS orients TCP/IP protocol, through Internet, testing engineers, technology experts can be connected freely without space. Engineering problems can be resolved fast and effectively. FVDSPS can be used in many fields such as instruments and meter, fault diagnosis, device maintenance and quality control.

  15. Two-component signal transduction in Corynebacterium glutamicum and other corynebacteria: on the way towards stimuli and targets.

    Science.gov (United States)

    Bott, Michael; Brocker, Melanie

    2012-06-01

    In bacteria, adaptation to changing environmental conditions is often mediated by two-component signal transduction systems. In the prototypical case, a specific stimulus is sensed by a membrane-bound histidine kinase and triggers autophosphorylation of a histidine residue. Subsequently, the phosphoryl group is transferred to an aspartate residue of the cognate response regulator, which then becomes active and mediates a specific response, usually by activating and/or repressing a set of target genes. In this review, we summarize the current knowledge on two-component signal transduction in Corynebacterium glutamicum. This Gram-positive soil bacterium is used for the large-scale biotechnological production of amino acids and can also be applied for the synthesis of a wide variety of other products, such as organic acids, biofuels, or proteins. Therefore, C. glutamicum has become an important model organism in industrial biotechnology and in systems biology. The type strain ATCC 13032 possesses 13 two-component systems and the role of five has been elucidated in recent years. They are involved in citrate utilization (CitAB), osmoregulation and cell wall homeostasis (MtrAB), adaptation to phosphate starvation (PhoSR), adaptation to copper stress (CopSR), and heme homeostasis (HrrSA). As C. glutamicum does not only face changing conditions in its natural environment, but also during cultivation in industrial bioreactors of up to 500 m(3) volume, adaptability can also be crucial for good performance in biotechnological production processes. Detailed knowledge on two-component signal transduction and regulatory networks therefore will contribute to both the application and the systemic understanding of C. glutamicum and related species.

  16. Quercetin modulates Wnt signaling components in prostate cancer cell line by inhibiting cell viability, migration, and metastases.

    Science.gov (United States)

    Baruah, Meghna M; Khandwekar, Anand P; Sharma, Neeti

    2016-10-01

    Epithelial-mesenchymal transition (EMT) is a plastic transition in tumor progression during which cancer cells undergo dramatic changes acquiring highly invasive properties. Transforming growth factor-β (TGF-β) is an inducer of EMT in epithelial cells and is obligatory for acquiring invasive phenotype in carcinoma. TGF-β plays a vital role in metastasis and tumorigenesis in prostate cancer, and mutations in the components of Wnt signaling pathways are associated with various kinds of cancers including prostate cancer. The purpose of this study was to identify alterations in Wnt signaling pathway components involved during prostate cancer progression and to determine the effect of quercetin on TGF-β-induced EMT in prostate cancer (PC-3) cell line. The expression of epithelial and mesenchymal markers and the components of Wnt signaling pathway were evaluated by real-time polymerase chain reaction. It was observed that quercetin prevented TGF-β-induced expression of vimentin and N-cadherin and increased the expression of E-cadherin in PC-3 cells, thus preventing TGF-β-induced EMT. Furthermore, the relative expression of Twist, Snail, and Slug showed that quercetin significantly decreased TGF-β-induced expression of Twist, Snail, and Slug. In the present study, the expression of epithelial markers were found to be upregulated in naive state and downregulated in induced state whereas the mesenchymal markers were found to be downregulated in naive state and upregulated in induced state. Thus, our study concludes that quercetin may prevent prostate cancer metastasis by regulating the components of Wnt pathway.

  17. Unmasking local activity within local field potentials (LFPs) by removing distal electrical signals using independent component analysis.

    Science.gov (United States)

    Whitmore, Nathan W; Lin, Shih-Chieh

    2016-05-15

    Local field potentials (LFPs) are commonly thought to reflect the aggregate dynamics in local neural circuits around recording electrodes. However, we show that when LFPs are recorded in awake behaving animals against a distal reference on the skull as commonly practiced, LFPs are significantly contaminated by non-local and non-neural sources arising from the reference electrode and from movement-related noise. In a data set with simultaneously recorded LFPs and electroencephalograms (EEGs) across multiple brain regions while rats perform an auditory oddball task, we used independent component analysis (ICA) to identify signals arising from electrical reference and from volume-conducted noise based on their distributed spatial pattern across multiple electrodes and distinct power spectral features. These sources of distal electrical signals collectively accounted for 23-77% of total variance in unprocessed LFPs, as well as most of the gamma oscillation responses to the target stimulus in EEGs. Gamma oscillation power was concentrated in volume-conducted noise and was tightly coupled with the onset of licking behavior, suggesting a likely origin of muscle activity associated with body movement or orofacial movement. The removal of distal signal contamination also selectively reduced correlations of LFP/EEG signals between distant brain regions but not within the same region. Finally, the removal of contamination from distal electrical signals preserved an event-related potential (ERP) response to auditory stimuli in the frontal cortex and also increased the coupling between the frontal ERP amplitude and neuronal activity in the basal forebrain, supporting the conclusion that removing distal electrical signals unmasked local activity within LFPs. Together, these results highlight the significant contamination of LFPs by distal electrical signals and caution against the straightforward interpretation of unprocessed LFPs. Our results provide a principled approach to

  18. Diversity of two-component systems: insights into the signal transduction mechanism by the  Staphylococcus aureus two-component system GraSR.

    Science.gov (United States)

    Muzamal, Uzma; Gomez, Daniel; Kapadia, Fenika; Golemi-Kotra, Dasantila

    2014-01-01

    The response to cationic antimicrobial peptides (CAMPs) in Staphylococcus aureus relies on a two-component system (TCS), GraSR, an auxiliary protein GraX and an ATP-binding cassette (ABC) transporter, VraF/G. To understand the signal transduction mechanism by GraSR, we investigated the kinase activity of the cytoplasmic domain of histidine kinase GraS and the interaction with its cognate response regulator GraR. We also investigated interactions among the auxiliary protein GraX, GraS/R and the ATPase protein of the ABC transporter, VraF. We found that GraS lacks autophosphorylation activity, unlike a similar histidine kinase, BceS, of Bacillus subtilis. In addition, the interaction between GraS and GraR is very weak in comparison to the stronger interaction observed between BceS and its conjugated response regulator, BceR, suggesting that CAMP signaling may not flow directly from GraS to GraR. We found that the auxiliary protein GraX interacts with VraF and GraR, and requires the histidine phosphotransfer and dimerization domain of GraS to interact with this protein. Further, VraF requires the GraS region that connects the membrane-bound domain with the cytoplasmic domain of this protein for interaction with GraS. The interactions of GraX with GraS/R and VraF indicate that GraX may serve as a scaffold to bring these proteins in close proximity to GraS, plausibly to facilitate activation of GraS to ultimately transduce the signal to GraR.

  19. Identification of damage in a suspension component using narrowband and broadband nonlinear signal processing techniques

    Science.gov (United States)

    Haroon, Muhammad; Adams, Douglas E.

    2007-04-01

    Fatigue tests on a stabilizer bar link of an automotive suspension system are used to initiate a crack and grow the crack size. During these tests, slow sine sweeps are used to extract narrowband restoring forces across the stabilizer bar link. The restoring forces are shown to characterize the nonlinear changes in component internal forces due to crack growth. Broadband frequency response domain techniques are used to analyze the durability response data. Nonlinear frequency domain models of the dynamic transmissibility across the cracked region are shown to change as a function of crack growth. Higher order spectra are used to show the increase in nonlinear coupling of response frequency components with the appearance and growth of the crack. It is shown that crack growth can be detected and characterized by the changes in nonlinear indicators.

  20. Comprehensive assessment of expression of insulin signaling pathway components in subcutaneous adipose tissue of women with and without polycystic ovary syndrome

    Directory of Open Access Journals (Sweden)

    Ning Xu

    2015-09-01

    Conclusions: Differential expression of core insulin signaling pathway components in subcutaneous adipose tissue is not a major contributor to the pathogenesis of PCOS. Correlation between clinical phenotypes and expression of several genes in the mitogenic limb of the insulin signaling pathway suggests mitogenic signaling by insulin may regulate steroidogenesis and glucose homeostasis.

  1. The phylogenetically-related pattern recognition receptors EFR and XA21 recruit similar immune signaling components in monocots and dicots.

    Directory of Open Access Journals (Sweden)

    Nicholas Holton

    2015-01-01

    Full Text Available During plant immunity, surface-localized pattern recognition receptors (PRRs recognize pathogen-associated molecular patterns (PAMPs. The transfer of PRRs between plant species is a promising strategy for engineering broad-spectrum disease resistance. Thus, there is a great interest in understanding the mechanisms of PRR-mediated resistance across different plant species. Two well-characterized plant PRRs are the leucine-rich repeat receptor kinases (LRR-RKs EFR and XA21 from Arabidopsis thaliana (Arabidopsis and rice, respectively. Interestingly, despite being evolutionary distant, EFR and XA21 are phylogenetically closely related and are both members of the sub-family XII of LRR-RKs that contains numerous potential PRRs. Here, we compared the ability of these related PRRs to engage immune signaling across the monocots-dicots taxonomic divide. Using chimera between Arabidopsis EFR and rice XA21, we show that the kinase domain of the rice XA21 is functional in triggering elf18-induced signaling and quantitative immunity to the bacteria Pseudomonas syringae pv. tomato (Pto DC3000 and Agrobacterium tumefaciens in Arabidopsis. Furthermore, the EFR:XA21 chimera associates dynamically in a ligand-dependent manner with known components of the EFR complex. Conversely, EFR associates with Arabidopsis orthologues of rice XA21-interacting proteins, which appear to be involved in EFR-mediated signaling and immunity in Arabidopsis. Our work indicates the overall functional conservation of immune components acting downstream of distinct LRR-RK-type PRRs between monocots and dicots.

  2. Identification and characterization of novel defence and PCD signalling components in Arabidopsis

    DEFF Research Database (Denmark)

    Xie, Wenjun

    Plants protect themselves from pathogens by activating a defence signalling network. The Arabidopsis double mutant syp121 syp122 is dwarfed and mimics a response as if it was attacked by pathogens. Using EMS as mutagen on syp121 syp122, a suppressor screen was performed. More than 200 partially...... a large protein with at least six domains with predicted functions, and mutations in five of these showed that they are important for the lesion mimic phenotype of syp121 syp122. Subcellular localization showed SSD6 to function on the ER. In the project, a split-GFP Gateway vector system was developed...

  3. FGFR-ERK signaling is an essential component of tissue separation.

    Science.gov (United States)

    Hasse, Christian; Holz, Oliver; Lange, Ellen; Pisowodzki, Lisa; Rebscher, Nicole; Christin Eder, Marie; Hobmayer, Bert; Hassel, Monika

    2014-11-01

    Formation of a constriction and tissue separation between parent and young polyp is a hallmark of the Hydra budding process and controlled by fibroblast growth factor receptor (FGFR) signaling. Appearance of a cluster of cells positive for double phosphorylated ERK (dpERK) at the late separation site indicated that the RAS/MEK/ERK pathway might be a downstream target of the Hydra Kringelchen FGFR. In fact, inhibition of ERK phosphorylation by the MEK inhibitor U0126 reversibly delayed bud detachment and prevented formation of the dpERK-positive cell cluster indicating de novo-phosphorylation of ERK at the late bud base. In functional studies, a dominant-negative Kringelchen FGFR prevented bud detachment as well as appearance of the dpERK-positive cell cluster. Ectopic expression of full length Kringelchen, on the other hand, induced a localized rearrangement of the actin cytoskeleton at sites of constriction, localized ERK-phosphorylation and autotomy of the body column. Our data suggest a model in which (i) the Hydra FGFR targets, via an unknown pathway, the actin cytoskeleton to induce a constriction and (ii) FGFR activates MEK/ERK signaling at the late separation site to allow tissue separation.

  4. Direct interactions between calcitonin-like receptor (CLR) and CGRP-receptor component protein (RCP) regulate CGRP receptor signaling.

    Science.gov (United States)

    Egea, Sophie C; Dickerson, Ian M

    2012-04-01

    Calcitonin gene-related peptide (CGRP) is a neuropeptide with multiple neuroendocrine roles, including vasodilation, migraine, and pain. The receptor for CGRP is a G protein-coupled receptor (GPCR) that requires three proteins for function. CGRP binds to a heterodimer composed of the GPCR calcitonin-like receptor (CLR) and receptor activity-modifying protein (RAMP1), a single transmembrane protein required for pharmacological specificity and trafficking of the CLR/RAMP1 complex to the cell surface. In addition, the CLR/RAMP1 complex requires a third protein named CGRP-receptor component protein (RCP) for signaling. Previous studies have demonstrated that depletion of RCP from cells inhibits CLR signaling, and in vivo studies have demonstrated that expression of RCP correlates with CLR signaling and CGRP efficacy. It is not known whether RCP interacts directly with CLR to exert its effect. The current studies identified a direct interaction between RCP and an intracellular domain of CLR using yeast two-hybrid analysis and coimmunoprecipitation. When this interacting domain of CLR was expressed as a soluble fusion protein, it coimmunoprecipitated with RCP and inhibited signaling from endogenous CLR. Expression of this dominant-negative domain of CLR did not significantly inhibit trafficking of CLR to the cell surface, and thus RCP may not have a chaperone function for CLR. Instead, RCP may regulate CLR signaling in the cell membrane, and direct interaction between RCP and CLR is required for CLR activation. To date, RCP has been found to interact only with CLR and represents a novel neuroendocrine regulatory step in GPCR signaling.

  5. Influence of a component of solar irradiance on radon signals at 1 km depth, Gran Sasso, Italy

    Directory of Open Access Journals (Sweden)

    G. Steinitz

    2012-12-01

    Full Text Available Exploratory monitoring of radon is conducted at one location at the deep underground Gran Sasso National Laboratory (LNGS. Measurements (15-min resolution are performed over a time span of ca. 600 days in the air of the surrounding calcareous country rock. Utilizing both alpha and gamma-ray detectors systematic and recurring radon signals are recorded. Two primary signal types are determined: (a non-periodic Multi-Day (MD signals lasting 2–10 days, and (b Daily Radon (DR signals – which are of a periodic nature exhibiting a primary 24-h cycle. The local ancillary environmental conditions (P, T seem not to affect radon in air monitored at the site. Long term patterns of day-time measurements are different from the pattern of night-time measurements indicating a day-night modulation of gamma radiation from radon in air. The phenomenology of the MD and DR signals is similar to situations encountered at other locations where radon is monitored with a high time resolution in geogas at upper crustal levels. In accordance with recent field and experimental results it is suggested that a components of solar irradiance is affecting the radiation from radon in air, and this influence is further modulated by the diurnal rotation of Earth. The occurrence of these radon signals in the 1 km deep low radiation underground geological environment of LNGS provides new information on the time variation of the local radiation environment. The observations and results place the LNGS facility as a high priority location for performing advanced investigations of these geophysical phenomena, due to its location and its infrastructure.

  6. Shocking fault component of abnormal sound signal in the fault engine extract method based on linear superposition method and cross-correlation analysis

    Directory of Open Access Journals (Sweden)

    Dayong Ning

    2015-08-01

    Full Text Available An extracted fault component of an abnormal sound is useful for faulty diagnosis. The existing fault component extracting approaches based on time–frequency analysis should filter the original signal to eliminate the background noise. However, these approaches will significantly change the fault component. In this article, a method for extracting the fault component of an abnormal sound signal is presented. This method is based on the linear superposition method and cross-correlation analysis. The method can eliminate the background noise and acquire the waveform of fault component. According to the feature of the shocking fault component, the acquired signal was intercepted into several segments, and the cross-correlation analysis was adopted to remove the wrong segment without the fault shocking component. The correct components were then linearly superposed together to eliminate the background noise. Finally, two experiments were performed to evaluate the effectiveness of the proposed fault component extracting method. The results show that the approach satisfactorily extracts the fault shocking component. The precise faulty component can be extracted by this method, which judges the engine condition precisely. The fault type can be diagnosed easily by this method. This method can be used in other fields to extract a particular component from a complicated signal.

  7. Model selection reveals control of cold signalling by evening-phased components of the plant circadian clock.

    Science.gov (United States)

    Keily, Jack; MacGregor, Dana R; Smith, Robert W; Millar, Andrew J; Halliday, Karen J; Penfield, Steven

    2013-10-01

    Circadian clocks confer advantages by restricting biological processes to certain times of day through the control of specific phased outputs. Control of temperature signalling is an important function of the plant oscillator, but the architecture of the gene network controlling cold signalling by the clock is not well understood. Here we use a model ensemble fitted to time-series data and a corrected Akaike Information Criterion (AICc) analysis to extend a dynamic model to include the control of the key cold-regulated transcription factors C-REPEAT BINDING FACTORs 1-3 (CBF1, CBF2, CBF3). AICc was combined with in silico analysis of genetic perturbations in the model ensemble, and selected a model that predicted mutant phenotypes and connections between evening-phased circadian clock components and CBF3 transcriptional control, but these connections were not shared by CBF1 and CBF2. In addition, our model predicted the correct gating of CBF transcription by cold only when the cold signal originated from the clock mechanism itself, suggesting that the clock has an important role in temperature signal transduction. Our data shows that model selection could be a useful method for the expansion of gene network models. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

  8. Expression patterns of Wnt signaling component, secreted frizzled-related protein 3 in astrocytoma and glioblastoma

    Science.gov (United States)

    PEĆINA-ŠLAUS, NIVES; KAFKA, ANJA; VAROŠANEC, ANA MARIA; MARKOVIĆ, LEON; KRSNIK, ŽELJKA; NJIRIĆ, NIKO; MRAK, GORAN

    2016-01-01

    Secreted frizzled-related protein 3 (SFRP3) is a member of the family of soluble proteins, which modulate the Wnt signaling cascade. Novel research has identified aberrant expression of SFRPs in different types of cancer. In the present study the expression intensities and localizations of the SFRP3 protein across different histopathological grades of astrocytic brain tumors were investigated by immunohistochemistry, digital scanning and image analysis. The results demonstrated that the differences between expression levels and malignancy grades were statistically significant. Tumors were classified into four malignancy grades according to the World Health Organization guidelines. Moderate (P=0.014) and strong (P=0.028) nuclear expression levels were significantly different in pilocytic (grade I) and diffuse (grade II) astrocytomas demonstrating higher expression values, as compared with anaplastic astrocytoma (grade III) and glioblastoma (grade IV). When the sample was divided into two groups, the moderate and high cytoplasmic expression levels were observed to be significantly higher in glioblastomas than in the group comprising astrocytoma II and III. Furthermore, the results indicated that high grade tumors were associated with lower values of moderate (P=0.002) and strong (P=0.018) nuclear expression in comparison to low grade tumors. Analysis of cytoplasmic staining demonstrated that strong cytoplasmic expression was significantly higher in the astrocytoma III and IV group than in the astrocytoma I and II group (P=0.048). Furthermore, lower grade astrocytomas exhibited reduced membranous SFRP3 staining when compared with higher grade astrocytomas and this difference was statistically significant (P=0.036). The present results demonstrated that SFRP3 protein expression levels were decreased in the nucleus in higher grade astrocytoma (indicating the expected behavior of an antagonist of Wnt signaling), whereas when the SFRP3 was located in the cytoplasm an

  9. Expression patterns of Wnt signaling component, secreted frizzled‑related protein 3 in astrocytoma and glioblastoma.

    Science.gov (United States)

    Pećina-Šlaus, Nives; Kafka, Anja; Varošanec, Ana Maria; Marković, Leon; Krsnik, Željka; Njirić, Niko; Mrak, Goran

    2016-05-01

    Secreted frizzled-related protein 3 (SFRP3) is a member of the family of soluble proteins, which modulate the Wnt signaling cascade. Novel research has identified aberrant expression of SFRPs in different types of cancer. In the present study the expression intensities and localizations of the SFRP3 protein across different histopathological grades of astrocytic brain tumors were investigated by immunohistochemistry, digital scanning and image analysis. The results demonstrated that the differences between expression levels and malignancy grades were statistically significant. Tumors were classified into four malignancy grades according to the World Health Organization guidelines. Moderate (P=0.014) and strong (P=0.028) nuclear expression levels were significantly different in pilocytic (grade I) and diffuse (grade II) astrocytomas demonstrating higher expression values, as compared with anaplastic astrocytoma (grade III) and glioblastoma (grade IV). When the sample was divided into two groups, the moderate and high cytoplasmic expression levels were observed to be significantly higher in glioblastomas than in the group comprising astrocytoma II and III. Furthermore, the results indicated that high grade tumors were associated with lower values of moderate (P=0.002) and strong (P=0.018) nuclear expression in comparison to low grade tumors. Analysis of cytoplasmic staining demonstrated that strong cytoplasmic expression was significantly higher in the astrocytoma III and IV group than in the astrocytoma I and II group (P=0.048). Furthermore, lower grade astrocytomas exhibited reduced membranous SFRP3 staining when compared with higher grade astrocytomas and this difference was statistically significant (P=0.036). The present results demonstrated that SFRP3 protein expression levels were decreased in the nucleus in higher grade astrocytoma (indicating the expected behavior of an antagonist of Wnt signaling), whereas when the SFRP3 was located in the

  10. Positive autoregulation shapes response timing and intensity in two-component signal transduction systems.

    Science.gov (United States)

    Mitrophanov, Alexander Y; Hadley, Tricia J; Groisman, Eduardo A

    2010-08-27

    Positive feedback loops are regulatory elements that can modulate expression output, kinetics and noise in genetic circuits. Transcriptional regulators participating in such loops are often expressed from two promoters, one constitutive and one autoregulated. Here, we investigate the interplay of promoter strengths and the intensity of the stimulus activating the transcriptional regulator in defining the output of a positively autoregulated genetic circuit. Using a mathematical model of two-component regulatory systems, which are present in all domains of life, we establish that positive feedback strongly affects the steady-state output levels at both low and high levels of stimulus if the constitutive promoter of the regulator is weak. By contrast, the effect of positive feedback is negligible when the constitutive promoter is sufficiently strong, unless the stimulus intensity is very high. Furthermore, we determine that positive feedback can affect both transient and steady state output levels even in the simplest genetic regulatory systems. We tested our modeling predictions by abolishing the positive feedback loop in the two-component regulatory system PhoP/PhoQ of Salmonella enterica, which resulted in diminished induction of PhoP-activated genes. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

  11. Calcium-signaling components in rat insulinoma β-cells (INS-1) and pancreatic islets are differentially influenced by melatonin.

    Science.gov (United States)

    Bazwinsky-Wutschke, Ivonne; Mühlbauer, Eckhard; Albrecht, Elke; Peschke, Elmar

    2014-05-01

    The pineal secretory product melatonin exerts its influence on the insulin secretion of pancreatic islets by different signaling pathways. The purpose of this study was to analyze the impact of melatonin on calcium-signaling components under different conditions. In a transfected INS-1 cell line overexpressing the human MT2 receptor (hMT2-INS-1), melatonin treatment induced even stronger depressive effects on calcium/calmodulin-dependent kinase 2d and IV (Camk2d, CamkIV) transcripts during 3-isobutyl-1-methylxanthine (IBMX) treatment than in normal INS-1 cells, indicating a crucial influence of melatonin receptor density on transcript-level regulation. In addition, melatonin induced a significant downregulation of calmodulin (Calm1) in IBMX-treated hMT2-INS-1 cells. Long-term administration of melatonin alone reduced CamkIV transcript levels in INS-1 cells; however, transcript levels of Camk2d remained unchanged. The release of insulin was diminished under long-term melatonin treatment. The impact of melatonin also involved reductions in CAMK2D protein during IBMX or forskolin treatments in INS-1 cells, as measured by an enzyme-linked immunosorbent assay, indicating a functional significance of transcriptional changes in pancreatic islets. Furthermore, analysis of melatonin receptor knockout mice showed that the transcript levels of Camk2d, CamkIV, and Calm1 were differentially influenced according to the melatonin receptor subtype deleted. In conclusion, this study provides evidence that melatonin has different impacts on the regulation of Calm1 and Camk. These calcium-signaling components are known as participants in the calcium/calmodulin pathway, which plays an important functional role in the modulation of the β-cell signaling pathways leading to insulin secretion.

  12. Rac-1 and Raf-1 kinases, components of distinct signaling pathways, activate myotonic dystrophy protein kinase

    Science.gov (United States)

    Shimizu, M.; Wang, W.; Walch, E. T.; Dunne, P. W.; Epstein, H. F.

    2000-01-01

    Myotonic dystrophy protein kinase (DMPK) is a serine-threonine protein kinase encoded by the myotonic dystrophy (DM) locus on human chromosome 19q13.3. It is a close relative of other kinases that interact with members of the Rho family of small GTPases. We show here that the actin cytoskeleton-linked GTPase Rac-1 binds to DMPK, and coexpression of Rac-1 and DMPK activates its transphosphorylation activity in a GTP-sensitive manner. DMPK can also bind Raf-1 kinase, the Ras-activated molecule of the MAP kinase pathway. Purified Raf-1 kinase phosphorylates and activates DMPK. The interaction of DMPK with these distinct signals suggests that it may play a role as a nexus for cross-talk between their respective pathways and may partially explain the remarkable pleiotropy of DM.

  13. A fast and accurate frequency estimation algorithm for sinusoidal signal with harmonic components

    Science.gov (United States)

    Hu, Jinghua; Pan, Mengchun; Zeng, Zhidun; Hu, Jiafei; Chen, Dixiang; Tian, Wugang; Zhao, Jianqiang; Du, Qingfa

    2016-10-01

    Frequency estimation is a fundamental problem in many applications, such as traditional vibration measurement, power system supervision, and microelectromechanical system sensors control. In this paper, a fast and accurate frequency estimation algorithm is proposed to deal with low efficiency problem in traditional methods. The proposed algorithm consists of coarse and fine frequency estimation steps, and we demonstrate that it is more efficient than conventional searching methods to achieve coarse frequency estimation (location peak of FFT amplitude) by applying modified zero-crossing technique. Thus, the proposed estimation algorithm requires less hardware and software sources and can achieve even higher efficiency when the experimental data increase. Experimental results with modulated magnetic signal show that the root mean square error of frequency estimation is below 0.032 Hz with the proposed algorithm, which has lower computational complexity and better global performance than conventional frequency estimation methods.

  14. Virus-induced gene silencing reveals signal transduction components required for the Pvr9-mediated hypersensitive response in Nicotiana benthamiana.

    Science.gov (United States)

    Tran, Phu-Tri; Choi, Hoseong; Choi, Doil; Kim, Kook-Hyung

    2016-08-01

    Resistance to pathogens mediated by plant resistance (R) proteins requires different signaling transduction components and pathways. Our previous studies revealed that a potyvirus resistance gene in pepper, Pvr9, confers a hypersensitive response (HR) to pepper mottle virus in Nicotiana benthamiana. Our results show that the Pvr9-mediated HR against pepper mottle virus infection requires HSP90, SGT1, NDR1, but not EDS1. These results suggest that the Pvr9-mediated HR is possibly related to the SA pathway but not the ET, JA, ROS or NO pathways.

  15. Functional characterization and developmental expression profiling of gibberellin signalling components in Vitis vinifera.

    Science.gov (United States)

    Acheampong, Atiako Kwame; Hu, Jianhong; Rotman, Ariel; Zheng, Chuanlin; Halaly, Tamar; Takebayashi, Yumiko; Jikumaru, Yusuke; Kamiya, Yuji; Lichter, Amnon; Sun, Tai-Ping; Or, Etti

    2015-03-01

    Gibberellins (GAs) regulate numerous developmental processes in grapevine (Vitis vinifera) such as rachis elongation, fruit set, and fruitlet abscission. The ability of GA to promote berry enlargement has led to its indispensable use in the sternospermocarpic ('seedless') table grape industry worldwide. However, apart from VvGAI1 (VvDELLA1), which regulates internode elongation and fruitfulness, but not berry size of seeded cultivars, little was known about GA signalling in grapevine. We have identified and characterized two additional DELLAs (VvDELLA2 and VvDELLA3), two GA receptors (VvGID1a and VvGID1b), and two GA-specific F-box proteins (VvSLY1a and VvSLY1b), in cv. Thompson seedless. With the exception of VvDELLA3-VvGID1b, all VvDELLAs interacted with the VvGID1s in a GA-dependent manner in yeast two-hybrid assays. Additionally, expression of these grape genes in corresponding Arabidopsis mutants confirmed their functions in planta. Spatiotemporal analysis of VvDELLAs showed that both VvDELLA1 and VvDELLA2 are abundant in most tissues, except in developing fruit where VvDELLA2 is uniquely expressed at high levels, suggesting a key role in fruit development. Our results further suggest that differential organ responses to exogenous GA depend on the levels of VvDELLA proteins and endogenous bioactive GAs. Understanding this interaction will allow better manipulation of GA signalling in grapevine. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  16. Identification of genes required for nonhost resistance to Xanthomonas oryzae pv. oryzae reveals novel signaling components.

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    Wen Li

    Full Text Available BACKGROUND: Nonhost resistance is a generalized, durable, broad-spectrum resistance exhibited by plant species to a wide variety of microbial pathogens. Although nonhost resistance is an attractive breeding strategy, the molecular basis of this form of resistance remains unclear for many plant-microbe pathosystems, including interactions with the bacterial pathogen of rice, Xanthomonas oryzae pv. oryzae (Xoo. METHODS AND FINDINGS: Virus-induced gene silencing (VIGS and an assay to detect the hypersensitive response (HR were used to screen for genes required for nonhost resistance to Xoo in N. benthamiana. When infiltrated with Xoo strain YN-1, N. benthamiana plants exhibited a strong necrosis within 24 h and produced a large amount of H(2O(2 in the infiltrated area. Expression of HR- and defense-related genes was induced, whereas bacterial numbers dramatically decreased during necrosis. VIGS of 45 ACE (Avr/Cf-elicited genes revealed identified seven genes required for nonhost resistance to Xoo in N. benthamiana. The seven genes encoded a calreticulin protein (ACE35, an ERF transcriptional factor (ACE43, a novel Solanaceous protein (ACE80, a hydrolase (ACE117, a peroxidase (ACE175 and two proteins with unknown function (ACE95 and ACE112. The results indicate that oxidative burst and calcium-dependent signaling pathways play an important role in nonhost resistance to Xoo. VIGS analysis further revealed that ACE35, ACE80, ACE95 and ACE175, but not the other three ACE genes, interfered with the Cf-4/Avr4-dependent HR. CONCLUSIONS/SIGNIFICANCE: N. benthamiana plants inoculated with Xoo respond by rapidly eliciting an HR and nonhost resistance. The oxidative burst and other signaling pathways are pivotal in Xoo-N. benthamiana nonhost resistance, and genes involved in this response partially overlap with those involved in Cf/Avr4-dependent HR. The seven genes required for N. benthamiana-mediated resistance to Xoo provide a basis for further dissecting

  17. Rhythmic Components in Extracranial Brain Signals Reveal Multifaceted Task Modulation of Overlapping Neuronal Activity.

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    Roemer van der Meij

    Full Text Available Oscillatory neuronal activity is implicated in many cognitive functions, and its phase coupling between sensors may reflect networks of communicating neuronal populations. Oscillatory activity is often studied using extracranial recordings and compared between experimental conditions. This is challenging, because there is overlap between sensor-level activity generated by different sources, and this can obscure differential experimental modulations of these sources. Additionally, in extracranial data, sensor-level phase coupling not only reflects communicating populations, but can also be generated by a current dipole, whose sensor-level phase coupling does not reflect source-level interactions. We present a novel method, which is capable of separating and characterizing sources on the basis of their phase coupling patterns as a function of space, frequency and time (trials. Importantly, this method depends on a plausible model of a neurobiological rhythm. We present this model and an accompanying analysis pipeline. Next, we demonstrate our approach, using magnetoencephalographic (MEG recordings during a cued tactile detection task as a case study. We show that the extracted components have overlapping spatial maps and frequency content, which are difficult to resolve using conventional pairwise measures. Because our decomposition also provides trial loadings, components can be readily contrasted between experimental conditions. Strikingly, we observed heterogeneity in alpha and beta sources with respect to whether their activity was suppressed or enhanced as a function of attention and performance, and this happened both in task relevant and irrelevant regions. This heterogeneity contrasts with the common view that alpha and beta amplitude over sensory areas are always negatively related to attention and performance.

  18. Evolutionary recycling of light signaling components in fleshy fruits: new insights on the role of pigments to monitor ripening

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    Briardo eLlorente

    2016-03-01

    Full Text Available Besides an essential source of energy, light provides environmental information to plants. Photosensory pathways are thought to have occurred early in plant evolution, probably at the time of the Archaeplastida ancestor, or perhaps even earlier. Manipulation of individual components of light perception and signaling networks in tomato (Solanum lycopersicum affects the metabolism of ripening fruit at several levels. Most strikingly, recent experiments have shown that some of the molecular mechanisms originally devoted to sense and respond to environmental light cues have been re-adapted during evolution to provide plants with useful information on fruit ripening progression. In particular, the presence of chlorophylls in green fruit can strongly influence the spectral composition of the light filtered through the fruit pericarp. The concomitant changes in light quality can be perceived and transduced by phytochromes and phytochrome-interacting factors, respectively, to regulate gene expression and in turn modulate the production of carotenoids, a family of metabolites that are relevant for the final pigmentation of ripe fruits. We raise the hypothesis that the evolutionary recycling of light-signaling components to finely adjust pigmentation to the actual ripening stage of the fruit may have represented a selective advantage for primeval fleshy-fruited plants even before the extinction of dinosaurs.

  19. An Overview of Two-Component Signal Transduction Systems Implicated in Extra-Intestinal Pathogenic E. coli Infections

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    Erin J. Breland

    2017-05-01

    Full Text Available Extra-intestinal pathogenic E. coli (ExPEC infections are common in mammals and birds. The predominant ExPEC types are avian pathogenic E. coli (APEC, neonatal meningitis causing E. coli/meningitis associated E. coli (NMEC/MAEC, and uropathogenic E. coli (UPEC. Many reviews have described current knowledge on ExPEC infection strategies and virulence factors, especially for UPEC. However, surprisingly little has been reported on the regulatory modules that have been identified as critical in ExPEC pathogenesis. Two-component systems (TCSs comprise the predominant method by which bacteria respond to changing environments and play significant roles in modulating bacterial fitness in diverse niches. Recent studies have highlighted the potential of manipulating signal transduction systems as a means to chemically re-wire bacterial pathogens, thereby reducing selective pressure and avoiding the emergence of antibiotic resistance. This review begins by providing a brief introduction to characterized infection strategies and common virulence factors among APEC, NMEC, and UPEC and continues with a comprehensive overview of two-component signal transduction networks that have been shown to influence ExPEC pathogenesis.

  20. An Overview of Two-Component Signal Transduction Systems Implicated in Extra-Intestinal Pathogenic E. coli Infections.

    Science.gov (United States)

    Breland, Erin J; Eberly, Allison R; Hadjifrangiskou, Maria

    2017-01-01

    Extra-intestinal pathogenic E. coli (ExPEC) infections are common in mammals and birds. The predominant ExPEC types are avian pathogenic E. coli (APEC), neonatal meningitis causing E. coli/meningitis associated E. coli (NMEC/MAEC), and uropathogenic E. coli (UPEC). Many reviews have described current knowledge on ExPEC infection strategies and virulence factors, especially for UPEC. However, surprisingly little has been reported on the regulatory modules that have been identified as critical in ExPEC pathogenesis. Two-component systems (TCSs) comprise the predominant method by which bacteria respond to changing environments and play significant roles in modulating bacterial fitness in diverse niches. Recent studies have highlighted the potential of manipulating signal transduction systems as a means to chemically re-wire bacterial pathogens, thereby reducing selective pressure and avoiding the emergence of antibiotic resistance. This review begins by providing a brief introduction to characterized infection strategies and common virulence factors among APEC, NMEC, and UPEC and continues with a comprehensive overview of two-component signal transduction networks that have been shown to influence ExPEC pathogenesis.

  1. Characterization of the Arc two-component signal transduction system of the capnophilic rumen bacterium Mannheimia succiniciproducens.

    Science.gov (United States)

    Jung, Won Seok; Jung, Young Ryul; Oh, Doo-Byoung; Kang, Hyun Ah; Lee, Sang Yup; Chavez-Canales, Maria; Georgellis, Dimitris; Kwon, Ohsuk

    2008-07-01

    The ArcB/A two-component signal transduction system of Escherichia coli modulates the expression of numerous operons in response to redox conditions of growth. We demonstrate that the putative arcA and arcB genes of Mannheimia succiniciproducens MBEL55E, a capnophilic (CO2-loving) rumen bacterium, encode functional proteins that specify a two-component system. The Arc proteins of the two bacterial species sufficiently resemble each other that they can participate in heterologous transphosphorylation in vitro, and the arcA and arcB genes of M. succiniciproducens confer toluidine blue resistance to E. coli arcA and arcB mutants. However, neither the quinone analogs (ubiquinone 0 and menadione) nor the cytosolic effectors (d-lactate, acetate, and pyruvate) affect the net phosphorylation of M. succiniciproducens ArcB. Our results indicate that different types of signaling molecules and distinct modes of kinase regulation are used by the ArcB proteins of E. coli and M. succiniciproducens.

  2. Applying independent component analysis to detect silent speech in magnetic resonance imaging signals.

    Science.gov (United States)

    Abe, Kazuhiro; Takahashi, Toshimitsu; Takikawa, Yoriko; Arai, Hajime; Kitazawa, Shigeru

    2011-10-01

    Independent component analysis (ICA) can be usefully applied to functional imaging studies to evaluate the spatial extent and temporal profile of task-related brain activity. It requires no a priori assumptions about the anatomical areas that are activated or the temporal profile of the activity. We applied spatial ICA to detect a voluntary but hidden response of silent speech. To validate the method against a standard model-based approach, we used the silent speech of a tongue twister as a 'Yes' response to single questions that were delivered at given times. In the first task, we attempted to estimate one number that was chosen by a participant from 10 possibilities. In the second task, we increased the possibilities to 1000. In both tasks, spatial ICA was as effective as the model-based method for determining the number in the subject's mind (80-90% correct per digit), but spatial ICA outperformed the model-based method in terms of time, especially in the 1000-possibility task. In the model-based method, calculation time increased by 30-fold, to 15 h, because of the necessity of testing 1000 possibilities. In contrast, the calculation time for spatial ICA remained as short as 30 min. In addition, spatial ICA detected an unexpected response that occurred by mistake. This advantage was validated in a third task, with 13 500 possibilities, in which participants had the freedom to choose when to make one of four responses. We conclude that spatial ICA is effective for detecting the onset of silent speech, especially when it occurs unexpectedly.

  3. Systematic profiling of Caenorhabditis elegans locomotive behaviors reveals additional components in G-protein Gαq signaling.

    Science.gov (United States)

    Yu, Hui; Aleman-Meza, Boanerges; Gharib, Shahla; Labocha, Marta K; Cronin, Christopher J; Sternberg, Paul W; Zhong, Weiwei

    2013-07-16

    Genetic screens have been widely applied to uncover genetic mechanisms of movement disorders. However, most screens rely on human observations of qualitative differences. Here we demonstrate the application of an automatic imaging system to conduct a quantitative screen for genes regulating the locomotive behavior in Caenorhabditis elegans. Two hundred twenty-seven neuronal signaling genes with viable homozygous mutants were selected for this study. We tracked and recorded each animal for 4 min and analyzed over 4,400 animals of 239 genotypes to obtain a quantitative, 10-parameter behavioral profile for each genotype. We discovered 87 genes whose inactivation causes movement defects, including 50 genes that had never been associated with locomotive defects. Computational analysis of the high-content behavioral profiles predicted 370 genetic interactions among these genes. Network partition revealed several functional modules regulating locomotive behaviors, including sensory genes that detect environmental conditions, genes that function in multiple types of excitable cells, and genes in the signaling pathway of the G protein Gαq, a protein that is essential for animal life and behavior. We developed quantitative epistasis analysis methods to analyze the locomotive profiles and validated the prediction of the γ isoform of phospholipase C as a component in the Gαq pathway. These results provided a system-level understanding of how neuronal signaling genes coordinate locomotive behaviors. This study also demonstrated the power of quantitative approaches in genetic studies.

  4. Plant signalling components EDS1 and SGT1 enhance disease caused by the necrotrophic pathogen Botrytis cinerea.

    Science.gov (United States)

    El Oirdi, Mohamed; Bouarab, Kamal

    2007-01-01

    * Botrytis cinerea is a necrotrophic fungus that causes grey mould on a wide range of food plants, especially grapevine, tomato, soft fruits and vegetables. This disease brings about important economic losses in both pre- and postharvest crops. Successful protection of host plants against this pathogen is severely hampered by a lack of resistance genes in the hosts and the considerable phenotypic diversity of the fungus. * The aim of this study was to test whether B. cinerea manipulates the immunity-signalling pathways in plants to restore its disease. * We showed that B. cinerea caused disease in Nicotiana benthamiana through the activation of two plant signalling genes, EDS1 and SGT1, which have been shown to be essential for resistance against biotrophic pathogens; and more interestingly, virus-induced gene silencing of these two plant signalling components enhanced N. benthamiana resistance to B. cinerea. Finally, plants expressing the baculovirus antiapoptotic protein p35 were more resistant to this necrotrophic pathogen than wild-type plants. * This work highlights a new strategy used by B. cinerea to establish disease. This information is important for the design of strategies to improve plant pathogen resistance.

  5. Fatigue study of ultra-runners: Presentation of a new approach for the separation of GRF signals components

    Science.gov (United States)

    Zakaria, F. A.; El Badaoui, M.; Lamraoui, M.; Khalil, M.

    2016-06-01

    In recent years, ultra-marathon running has become increasingly popular in many countries around the world. The ability to run for long hours has played a role in human evolution. It is known that the etiology of fatigue depends upon the exercise under consideration. In order to characterize and find a full description of the fatigue and its effects on the human locomotion mechanics, and to extract the relevant parameters and information for diagnosis, we have investigated the changes in running mechanics. More specifically, the ground reaction force (GRF) manifestations of fatigue, have been investigated by using advanced signal processing tools. GRF signals are composed of two parts: an active peak representing the propulsive force and a passive peak that represents the impact force. The impact force is the major factor indicating the reaction of muscle, that may reflects the fatigue state and performance of the muscle. In this article, we focused on the treatment of biomechanical signals for the purpose of GRF components separation where the aim is to separate the contribution of the active components and the passive components. For this reason, we proposed a new algorithm, based on the Gaussian decomposition and non-linear least squares method that will achieve the desired goal. We then compare the results of separation with a proposed BSS based method i.e. "FastICA algorithm". We also compare the results with that obtained by Sabri et al. [1-3] who used different BSS techniques which gave bad and fair results. The separated passive signal is then proved to contain a mixture of a deterministic phenomenon and a stationary random phenomenon, where both phenomena are separated using the cepstral editing procedure (CEP) method. CEP is applied after signal synchronization using method with maximization of the inter-correlation function. The random part is then proved to be cyclostationary of order 2. A real application examined the biomechanical changes occurring in

  6. Designing a robust feature extraction method based on optimum allocation and principal component analysis for epileptic EEG signal classification.

    Science.gov (United States)

    Siuly, Siuly; Li, Yan

    2015-04-01

    The aim of this study is to design a robust feature extraction method for the classification of multiclass EEG signals to determine valuable features from original epileptic EEG data and to discover an efficient classifier for the features. An optimum allocation based principal component analysis method named as OA_PCA is developed for the feature extraction from epileptic EEG data. As EEG data from different channels are correlated and huge in number, the optimum allocation (OA) scheme is used to discover the most favorable representatives with minimal variability from a large number of EEG data. The principal component analysis (PCA) is applied to construct uncorrelated components and also to reduce the dimensionality of the OA samples for an enhanced recognition. In order to choose a suitable classifier for the OA_PCA feature set, four popular classifiers: least square support vector machine (LS-SVM), naive bayes classifier (NB), k-nearest neighbor algorithm (KNN), and linear discriminant analysis (LDA) are applied and tested. Furthermore, our approaches are also compared with some recent research work. The experimental results show that the LS-SVM_1v1 approach yields 100% of the overall classification accuracy (OCA), improving up to 7.10% over the existing algorithms for the epileptic EEG data. The major finding of this research is that the LS-SVM with the 1v1 system is the best technique for the OA_PCA features in the epileptic EEG signal classification that outperforms all the recent reported existing methods in the literature. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  7. Modular and coordinated expression of immune system regulatory and signaling components in the developing and adult nervous system.

    Science.gov (United States)

    Monzón-Sandoval, Jimena; Castillo-Morales, Atahualpa; Crampton, Sean; McKelvey, Laura; Nolan, Aoife; O'Keeffe, Gerard; Gutierrez, Humberto

    2015-01-01

    During development, the nervous system (NS) is assembled and sculpted through a concerted series of neurodevelopmental events orchestrated by a complex genetic programme. While neural-specific gene expression plays a critical part in this process, in recent years, a number of immune-related signaling and regulatory components have also been shown to play key physiological roles in the developing and adult NS. While the involvement of individual immune-related signaling components in neural functions may reflect their ubiquitous character, it may also reflect a much wider, as yet undescribed, genetic network of immune-related molecules acting as an intrinsic component of the neural-specific regulatory machinery that ultimately shapes the NS. In order to gain insights into the scale and wider functional organization of immune-related genetic networks in the NS, we examined the large scale pattern of expression of these genes in the brain. Our results show a highly significant correlated expression and transcriptional clustering among immune-related genes in the developing and adult brain, and this correlation was the highest in the brain when compared to muscle, liver, kidney and endothelial cells. We experimentally tested the regulatory clustering of immune system (IS) genes by using microarray expression profiling in cultures of dissociated neurons stimulated with the pro-inflammatory cytokine TNF-alpha, and found a highly significant enrichment of immune system-related genes among the resulting differentially expressed genes. Our findings strongly suggest a coherent recruitment of entire immune-related genetic regulatory modules by the neural-specific genetic programme that shapes the NS.

  8. Two-Component Signal Transduction Systems That Regulate the Temporal and Spatial Expression of Myxococcus xanthus Sporulation Genes.

    Science.gov (United States)

    Sarwar, Zaara; Garza, Anthony G

    2015-09-14

    When starved for nutrients, Myxococcus xanthus produces a biofilm that contains a mat of rod-shaped cells, known as peripheral rods, and aerial structures called fruiting bodies, which house thousands of dormant and stress-resistant spherical spores. Because rod-shaped cells differentiate into spherical, stress-resistant spores and spore differentiation occurs only in nascent fruiting bodies, many genes and multiple levels of regulation are required. Over the past 2 decades, many regulators of the temporal and spatial expression of M. xanthus sporulation genes have been uncovered. Of these sporulation gene regulators, two-component signal transduction circuits, which typically contain a histidine kinase sensor protein and a transcriptional regulator known as response regulator, are among the best characterized. In this review, we discuss prototypical two-component systems (Nla6S/Nla6 and Nla28S/Nla28) that regulate an early, preaggregation phase of sporulation gene expression during fruiting body development. We also discuss orphan response regulators (ActB and FruA) that regulate a later phase of sporulation gene expression, which begins during the aggregation stage of fruiting body development. In addition, we summarize the research on a complex two-component system (Esp) that is important for the spatial regulation of sporulation. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  9. Signaling components of the 1α,25(OH)2D3-dependent Pdia3 receptor complex are required for Wnt5a calcium-dependent signaling.

    Science.gov (United States)

    Doroudi, Maryam; Olivares-Navarrete, Rene; Hyzy, Sharon L; Boyan, Barbara D; Schwartz, Zvi

    2014-11-01

    Wnt5a and 1α,25(OH)2D3 are important regulators of endochondral ossification. In osteoblasts and growth plate chondrocytes, 1α,25(OH)2D3 initiates rapid effects via its membrane-associated receptor protein disulfide isomerase A3 (Pdia3) in caveolae, activating phospholipase A2 (PLA2)-activating protein (PLAA), calcium/calmodulin-dependent protein kinase II (CaMKII), and PLA2, resulting in protein kinase C (PKC) activation. Wnt5a initiates its calcium-dependent effects via intracellular calcium release, activating PKC and CaMKII. We investigated the requirement for components of the Pdia3 receptor complex in Wnt5a calcium-dependent signaling. We determined that Wnt5a signals through a CaMKII/PLA2/PGE2/PKC cascade. Silencing or blocking Pdia3, PLAA, or vitamin D receptor (VDR), and inhibition of calmodulin (CaM), CaMKII, or PLA2 inhibited Wnt5a-induced PKC activity. Wnt5a activated PKC in caveolin-1-silenced cells, but methyl-beta-cyclodextrin reduced its stimulatory effect. 1α,25(OH)2D3 reduced stimulatory effects of Wnt5a on PKC in a dose-dependent manner. In contrast, Wnt5a had a biphasic effect on 1α,25(OH)2D3-stimulated PKC activation; 50ng/ml Wnt5a caused a 2-fold increase in 1α,25(OH)2D3-stimulated PKC but higher Wnt5a concentrations reduced 1α,25(OH)2D3-stimulated PKC activation. Western blots showed that Wnt receptors Frizzled2 (FZD2) and Frizzled5 (FZD5), and receptor tyrosine kinase-like orphan receptor 2 (ROR2) were localized to caveolae. Blocking ROR2, but not FZD2 or FZD5, abolished the stimulatory effects of 1α,25(OH)2D3 on PKC and CaMKII. 1α,25(OH)2D3 membrane receptor complex components (Pdia3, PLAA, caveolin-1, CaM) interacted with Wnt5a receptors/co-receptors (ROR2, FZD2, FZD5) in immunoprecipitation studies, interactions that changed with either 1α,25(OH)2D3 or Wnt5a treatment. This study demonstrates that 1α,25(OH)2D3 and Wnt5a mediate their effects via similar receptor components and suggests that these pathways may interact.

  10. G-protein signalling components GCR1 and GPA1 mediate responses to multiple abiotic stresses in Arabidopsis

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    Navjyoti eChakraborty

    2015-11-01

    Full Text Available G-protein signalling components have been implicated in some individual stress responses in Arabidopsis, but have not been comprehensively evaluated at the genetic and biochemical level. Stress emerged as the largest functional category in our whole transcriptome analyses of knock-out mutants of GCR1 and/or GPA1 in Arabidopsis (Chakraborty et al., 2015a, PloS one 10, e0117819 and Chakraborty et al., 2015b, Plant Mol. Biol., doi: 10.1007/s11103-015-0374-2. This led us to ask whether G-protein signalling components offer converging points in the plant’s response to multiple abiotic stresses. In order to test this hypothesis, we carried out detailed analysis of the stress category in the present study, which revealed 144 differentially expressed genes (DEGs, spanning a wide range of abiotic stresses, including heat, cold, salt, light stress etc. Only 10 of these DEGs are shared by all the three mutants, while the single mutants (GCR1/GPA1 shared more DEGs between themselves than with the double mutant (GCR1-GPA1. RT-qPCR validation of 28 of these genes spanning different stresses revealed identical regulation of the DEGs shared between the mutants. We also validated the effects of cold, heat and salt stresses in all the 3 mutants and WT on % germination, root and shoot length, relative water content, proline content, lipid peroxidation and activities of catalase, ascorbate peroxidase and superoxide dismutase. All the 3 mutants showed evidence of stress tolerance, especially to cold, followed by heat and salt, in terms of all the above parameters. This clearly shows the role of GCR1 and GPA1 in mediating the plant’s response to multiple abiotic stresses for the first time, especially cold, heat and salt stresses. This also implies a role for classical G-protein signalling pathways in stress sensitivity in the normal plants of Arabidopsis. This is also the first genetic and biochemical evidence of abiotic stress tolerance rendered by knock

  11. Stochastic simulation of prokaryotic two-component signalling indicates stochasticity-induced active-state locking and growth-rate dependent bistability.

    Science.gov (United States)

    Wei, Katy; Moinat, Maxim; Maarleveld, Timo R; Bruggeman, Frank J

    2014-07-29

    Signal transduction by prokaryotes almost exclusively relies on two-component systems for sensing and responding to (extracellular) signals. Here, we use stochastic models of two-component systems to better understand the impact of stochasticity on the fidelity and robustness of signal transmission, the outcome of autoregulatory gene expression and the influence of cell growth and division. We report that two-component systems are remarkably robust against copy number fluctuations of the signalling proteins they are composed of, which enhances signal transmission fidelity. Furthermore, we find that due to stochasticity these systems can get locked in an active state for extended time periods when (initially high) signal levels drop to zero. This behaviour can contribute to a bet-hedging adaptation strategy, aiding survival in fluctuating environments. Additionally, autoregulatory gene expression can cause two-component systems to become bistable at realistic parameter values. As a result, two sub-populations of cells can co-exist-active and inactive cells, which contributes to fitness in unpredictable environments. Bistability proved robust with respect to cell growth and division, and is tunable by the growth rate. In conclusion, our results indicate how single cells can cope with the inevitable stochasticity occurring in the activity of their two-component systems. They are robust to disadvantageous fluctuations that scramble signal transduction and they exploit beneficial stochasticity that generates fitness-enhancing heterogeneity across an isogenic population of cells.

  12. The Auditory-Evoked N2 and P3 Components in the Stop-Signal Task: Indices of Inhibition, Response-Conflict or Error-Detection?

    Science.gov (United States)

    Dimoska, Aneta; Johnstone, Stuart J.; Barry, Robert J.

    2006-01-01

    The N2 and P3 components have been separately associated with response inhibition in the stop-signal task, and more recently, the N2 has been implicated in the detection of response-conflict. To isolate response inhibition activity from early sensory processing, the present study compared processing of the stop-signal with that of a…

  13. Differences in two-component signal transduction proteins among the genus Brucella: implications for host preference and pathogenesis

    DEFF Research Database (Denmark)

    Binnewies, Tim Terence; Ussery, David; Lavín, JL

    2010-01-01

    Two-component systems (TCSs) are the predominant bacterial signal transduction mechanisms. Species of the genus Brucella are genetically highly related and differ mainly in mammalian host adaptation and pathogenesis. In this study, TCS proteins encoded in the available genome sequences of Brucella...... species have been identified using bioinformatic methods. All the Brucella species share an identical set of TCS proteins, and the number of TCS proteins in the closely related opportunistic human pathogen Ochrobactrum anthropi was higher than in Brucella species as expected from its lifestyle. O....... anthropi lacks orthologs of the Brucella TCSs NodVW, TceSR and TcfSR, suggesting that these TCS proteins could be necessary for the adaptation of Brucella as an intracellular pathogen. This genomic analysis revealed the presence of a differential distribution of TCS pseudogenes among Brucella species...

  14. Two-component signal transduction system SaeRS is involved in competence and penicillin susceptibility in Staphylococcus epidermidis.

    Science.gov (United States)

    Lou, Qiang; Ma, Yuanfang; Qu, Di

    2016-04-01

    Staphylococcus epidermidis, which is a causative pathogen of nosocomial infection, expresses its virulent traits such as biofilm and autolysis regulated by two-component signal transduction system SaeRS. In this study, the S. epidermidis SaeRS was identified to negatively regulate the expression of genes involved in competence (comF, murF), cytolysis (lrgA), and autolysis (lytS) by DNA microarray or real-time RT-PCR analysis. In addition, saeRS mutant showed increased competence and higher susceptibility to antibiotics such as penicillin and oxacillin than the wild-type strain. The study will be helpful for understanding the characterization of the SaeRS in S. epidermidis. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Two-component signal transduction in Synechocystis sp. PCC 6803 under phosphate limitation: role of acetyl phosphate.

    Science.gov (United States)

    Juntarajumnong, Waraporn; Eaton-Rye, Julian J; Incharoensakdi, Aran

    2007-09-30

    The two-component signal transduction, which typically consists of a histidine kinase and a response regulator, is used by bacterial cells to sense changes in their environment. Previously, the SphS-SphR histidine kinase and response regulator pair of phosphate sensing signal transduction has been identified in Synechocystis sp. PCC 6803. In addition, some response regulators in bacteria have been shown to be cross regulated by low molecular weight phosphorylated compounds in the absence of the cognate histidine kinase. The ability of an endogenous acetyl phosphate to phosphorylate the response regulator, SphR in the absence of the cognate histidine kinase, SphS was therefore tested in Synechocystis sp. PCC 6803. The mutant lacking functional SphS and acetate kinase showed no detectable alkaline phosphatase activity under phosphate-limiting growth conditions. The results suggested that the endogenous acetyl phosphate accumulated inside the mutants could not activate the SphR via phosphorylation. On the other hand, exogenous acetyl phosphate could allow the mutant lacking functional acetate kinase and phosphotransacetylase to grow under phosphate-limiting conditions suggesting the role of acetyl phosphate as an energy source. Reverse transcription PCR demonstrated that the transcripts of acetate kinase and phosphotransacetylase genes in Synechocystis sp. PCC 6803 is upregulated in response to phosphate limitation suggesting the importance of these two enzymes for energy metabolism in Synechocystis cells.

  16. Genetic analysis of the functions and interactions of components of the LevQRST signal transduction complex of Streptococcus mutans.

    Directory of Open Access Journals (Sweden)

    Lin Zeng

    Full Text Available Transcription of the genes for a fructan hydrolase (fruA and a fructose/mannose sugar:phosphotransferase permease (levDEFG in Streptococcus mutans is activated by a four-component regulatory system consisting of a histidine kinase (LevS, a response regulator (LevR and two carbohydrate-binding proteins (LevQT. The expression of the fruA and levD operons was at baseline in a levQ mutant and substantially decreased in a levT null mutant, with lower expression with the cognate inducers fructose or mannose, but slightly higher expression in glucose or galactose. A strain expressing levQ with two point mutations (E170A/F292S did not require inducers to activate gene expression and displayed altered levD expression when growing on various carbohydrates, including cellobiose. Linker-scanning (LS mutagenesis was used to generate three libraries of mutants of levQ, levS and levT that displayed various levels of altered substrate specificity and of fruA/levD gene expression. The data support that LevQ and LevT are intimately involved in the sensing of carbohydrate signals, and that LevQ appears to be required for the integrity of the signal transduction complex, apparently by interacting with the sensor kinase LevS.

  17. Oxidation-reduction signalling components in regulatory pathways of state transitions and photosystem stoichiometry adjustment in chloroplasts.

    Science.gov (United States)

    Puthiyaveetil, Sujith; Ibrahim, Iskander M; Allen, John F

    2012-02-01

    State transitions and photosystem stoichiometry adjustment are two oxidation-reduction (redox)-regulated acclimatory responses in photosynthesis. State transitions are short-term adaptations that, in chloroplasts, involve reversible post-translational modification by phosphorylation of light-harvesting complex II (LHC II). Photosystem stoichiometry adjustments are long-term responses involving transcriptional regulation of reaction centre genes. Both responses are initiated by changes in light quality and are regulated by the redox state of plastoquinone (PQ). The LHC II kinase involved in the state 2 transition is a serine/threonine kinase known as STT7 in Chlamydomonas, and as STN7 in Arabidopsis. The phospho-LHC II phosphatase that produces the state 1 transition is a PP2C-type protein phosphatase currently termed both TAP38 and PPH1. In plants and algae, photosystem stoichiometry adjustment is governed by a modified two-component sensor kinase of cyanobacterial origin - chloroplast sensor kinase (CSK). CSK is a sensor of the PQ redox state. Chloroplast sigma factor 1 (SIG1) and plastid transcription kinase (PTK) are the functional partners of CSK in chloroplast gene regulation. We suggest a signalling pathway for photosystem stoichiometry adjustment. The signalling pathways of state transitions and photosystem stoichiometry adjustments are proposed to be distinct, with the two pathways sensing PQ redox state independently of each other.

  18. Dysregulated Expression of Tensin 2 and Components of the PI3 Kinase/Akt Signaling Pathway in Human Thyroid Carcinoma

    Directory of Open Access Journals (Sweden)

    Nasrollah Erfani

    2016-01-01

    Full Text Available Background: The phosphatidylinositol 3-kinase/Akt signaling pathway is recognized as a key driver of cancer cell survival and proliferation, and is often contingent upon an impairment of expression/function of the PTEN tumor suppressor, a negative regulator of this pathway. In addition, the cytoskeletal signaling protein Tensin 2 has also been implicated as a negative regulator of this pathway. However, the PI3K pathway remains to be fully characterized in clinical thyroid carcinomas. The aim of this study is to determine the expression of components of the PI3K pathway in neoplastic and normal tissue sections obtained from patients with thyroid carcinoma. Methods: Tissues from 58 cases with thyroid carcinoma underwent immunohistochemistry for activated Akt (phosphorylated Akt, pAkt, Tensin 2 and PTEN. Results: A total of 100% of thyroid cancerous tissues were positive for pAkt staining compared to 67.9% of normal tissues. In contrast, 46.8% of cancer tissues were positive for Tensin 2 compared to 61.7% of normal tissues. For PTEN, 82.8% of cancerous tissues and 67.2% of normal tissues stained positive for this protein. There were no associations between the expression levels of the molecules with the patients’ clinicopathological characteristics. Conclusion:We have found evidence for an enhanced activation of the PI3K/Akt signaling pathway in clinical thyroid carcinoma tissues. This can be coupled with concomitant downregulation of Tensin 2. Further work is required to determine the relative significance of PTEN expression versus its activity in thyroid carcinoma in order to determine its role in the observed increased Akt activity.

  19. Automated resolution of chromatographic signals by independent component analysis-orthogonal signal deconvolution in comprehensive gas chromatography/mass spectrometry-based metabolomics.

    Science.gov (United States)

    Domingo-Almenara, Xavier; Perera, Alexandre; Ramírez, Noelia; Brezmes, Jesus

    2016-07-01

    Comprehensive gas chromatography-mass spectrometry (GC×GC-MS) provides a different perspective in metabolomics profiling of samples. However, algorithms for GC×GC-MS data processing are needed in order to automatically process the data and extract the purest information about the compounds appearing in complex biological samples. This study shows the capability of independent component analysis-orthogonal signal deconvolution (ICA-OSD), an algorithm based on blind source separation and distributed in an R package called osd, to extract the spectra of the compounds appearing in GC×GC-MS chromatograms in an automated manner. We studied the performance of ICA-OSD by the quantification of 38 metabolites through a set of 20 Jurkat cell samples analyzed by GC×GC-MS. The quantification by ICA-OSD was compared with a supervised quantification by selective ions, and most of the R(2) coefficients of determination were in good agreement (R(2)>0.90) while up to 24 cases exhibited an excellent linear relation (R(2)>0.95). We concluded that ICA-OSD can be used to resolve co-eluted compounds in GC×GC-MS.

  20. Classification of technical signals for noise diagnosis of machines and components; Klassifikation technischer Signale fuer die Geraeuschdiagnose von Maschinen und Bauteilen

    Energy Technology Data Exchange (ETDEWEB)

    Tschoepe, C.; Hentschel, D.; Frankenstein, B. [Fraunhofer-Institut fuer Zerstoerungsfreie Pruefverfahren, Dresden (Germany); Hirschfeld, D. [Voice INTER connect GmbH, Dresden (Germany); Hoffmann, R. [Technische Univ., Dresden (DD)

    2005-07-01

    For analysis and evaluation of acoustical signals from technical processes different approaches are used. In the field of non-destructive testing and acoustic diagnostics signals are increasingly complex. The following paper presents approaches for the automatic classification of technical signals for typical examples. Signals with higher complexity require more performant algorithms like DTW (Dynamic Time Warping) and HMM (Hidden-Markov-Models), which are already applied successfully in speech processing.

  1. The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling.

    Science.gov (United States)

    Schaap, Pauline; Barrantes, Israel; Minx, Pat; Sasaki, Narie; Anderson, Roger W; Bénard, Marianne; Biggar, Kyle K; Buchler, Nicolas E; Bundschuh, Ralf; Chen, Xiao; Fronick, Catrina; Fulton, Lucinda; Golderer, Georg; Jahn, Niels; Knoop, Volker; Landweber, Laura F; Maric, Chrystelle; Miller, Dennis; Noegel, Angelika A; Peace, Rob; Pierron, Gérard; Sasaki, Taeko; Schallenberg-Rüdinger, Mareike; Schleicher, Michael; Singh, Reema; Spaller, Thomas; Storey, Kenneth B; Suzuki, Takamasa; Tomlinson, Chad; Tyson, John J; Warren, Wesley C; Werner, Ernst R; Werner-Felmayer, Gabriele; Wilson, Richard K; Winckler, Thomas; Gott, Jonatha M; Glöckner, Gernot; Marwan, Wolfgang

    2015-11-27

    Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental model organisms. It has a sophisticated life cycle with several distinct stages including amoebal, flagellated, and plasmodial cells. It is unusual in switching between open and closed mitosis according to specific life-cycle stages. Here we present the analysis of the genome of this enigmatic and important model organism and compare it with closely related species. The genome is littered with simple and complex repeats and the coding regions are frequently interrupted by introns with a mean size of 100 bases. Complemented with extensive transcriptome data, we define approximately 31,000 gene loci, providing unexpected insights into early eukaryote evolution. We describe extensive use of histidine kinase-based two-component systems and tyrosine kinase signaling, the presence of bacterial and plant type photoreceptors (phytochromes, cryptochrome, and phototropin) and of plant-type pentatricopeptide repeat proteins, as well as metabolic pathways, and a cell cycle control system typically found in more complex eukaryotes. Our analysis characterizes P. polycephalum as a prototypical eukaryote with features attributed to the last common ancestor of Amorphea, that is, the Amoebozoa and Opisthokonts. Specifically, the presence of tyrosine kinases in Acanthamoeba and Physarum as representatives of two distantly related subdivisions of Amoebozoa argues against the later emergence of tyrosine kinase signaling in the opisthokont lineage and also against the acquisition by horizontal gene transfer. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  2. Minor abnormalities of testis development in mice lacking the gene encoding the MAPK signalling component, MAP3K1.

    Directory of Open Access Journals (Sweden)

    Nick Warr

    Full Text Available In mammals, the Y chromosome is a dominant male determinant, causing the bipotential gonad to develop as a testis. Recently, cases of familial and spontaneous 46,XY disorders of sex development (DSD have been attributed to mutations in the human gene encoding mitogen-activated protein kinase kinase kinase 1, MAP3K1, a component of the mitogen-activated protein kinase (MAPK signal transduction pathway. In individuals harbouring heterozygous mutations in MAP3K1, dysregulation of MAPK signalling was observed in lymphoblastoid cell lines, suggesting a causal role for these mutations in disrupting XY sexual development. Mice lacking the cognate gene, Map3k1, are viable and exhibit the eyes open at birth (EOB phenotype on a mixed genetic background, but on the C57BL/6J genetic background most mice die at around 14.5 dpc due to a failure of erythropoiesis in the fetal liver. However, no systematic examination of sexual development in Map3k1-deficient mice has been described, an omission that is especially relevant in the case of C57BL/6J, a genetic background that is sensitized to disruptions to testis determination. Here, we report that on a mixed genetic background mice lacking Map3k1 are fertile and exhibit no overt abnormalities of testis development. On C57BL/6J, significant non-viability is observed with very few animals surviving to adulthood. However, an examination of development in Map3k1-deficient XY embryos on this genetic background revealed no significant defects in testis determination, although minor abnormalities were observed, including an increase in gonadal length. Based on these observations, we conclude that MAP3K1 is not required for mouse testis determination. We discuss the significance of these data for the functional interpretation of sex-reversing MAP3K1 mutations in humans.

  3. Molecular characterization of banana NAC transcription factors and their interactions with ethylene signalling component EIL during fruit ripening.

    Science.gov (United States)

    Shan, Wei; Kuang, Jian-fei; Chen, Lei; Xie, Hui; Peng, Huan-huan; Xiao, Yun-yi; Li, Xue-ping; Chen, Wei-xin; He, Quan-guang; Chen, Jian-ye; Lu, Wang-jin

    2012-09-01

    The plant-specific NAC (NAM, ATAF1/2, and CUC2) transcription factors (TFs) play important roles in plant growth, development, and stress responses. However, the precise role of NAC TFs in relation to fruit ripening is poorly understood. In this study, six NAC genes, designated MaNAC1-MaNAC6, were isolated and characterized from banana fruit. Subcellular localization showed that MaNAC1-MaNAC5 proteins localized preferentially to the nucleus, while MaNAC6 was distributed throughout the entire cell. A transactivation assay in yeast demonstrated that MaNAC4 and MaNAC6, as well as their C-terminal regions, possessed trans-activation activity. Gene expression profiles in fruit with four different ripening characteristics, including natural, ethylene-induced, 1-methylcyclopropene (1-MCP)-delayed, and a combination of 1-MCP with ethylene treatment, revealed that the MaNAC genes were differentially expressed in peel and pulp during post-harvest ripening. MaNAC1 and MaNAC2 were apparently upregulated by ethylene in peel and pulp, consistent with the increase in ethylene production. In contrast, MaNAC3 in peel and pulp and MaNAC5 in peel were constitutively expressed, and transcripts of MaNAC4 in peel and pulp and MaNAC6 in peel decreased, while MaNAC5 or MaNAC6 in pulp increased slightly during fruit ripening. Furthermore, the MaNAC2 promoter was activated after ethylene application, further enhancing the involvement of MaNAC2 in fruit ripening. More importantly, yeast two-hybrid and bimolecular fluorescence complementation analyses confirmed that MaNAC1/2 physically interacted with a downstream component of ethylene signalling, ethylene insensitive 3 (EIN3)-like protein, termed MaEIL5, which was downregulated during ripening. Taken together, these results suggest that MaNACs such as MaNAC1/MaNAC2, may be involved in banana fruit ripening via interaction with ethylene signalling components.

  4. The VirSR two-component signal transduction system regulates NetB toxin production in Clostridium perfringens.

    Science.gov (United States)

    Cheung, Jackie K; Keyburn, Anthony L; Carter, Glen P; Lanckriet, Anouk L; Van Immerseel, Filip; Moore, Robert J; Rood, Julian I

    2010-07-01

    Clostridium perfringens causes several diseases in domestic livestock, including necrotic enteritis in chickens, which is of concern to the poultry industry due to its health implications and associated economic cost. The novel pore-forming toxin NetB is a critical virulence factor in the pathogenesis of this disease. In this study, we have examined the regulation of NetB toxin production. In C. perfringens, the quorum sensing-dependent VirSR two-component signal transduction system regulates genes encoding several toxins and extracellular enzymes. Analysis of the sequence upstream of the netB gene revealed the presence of potential DNA binding sites, or VirR boxes, that are recognized by the VirR response regulator. In vitro binding experiments showed that purified VirR was able to recognize and bind to these netB-associated VirR boxes. Furthermore, using a reporter gene assay, the netB VirR boxes were shown to be functional. Mutation of the virR gene in two avian C. perfringens strains was shown to significantly reduce the production of the NetB toxin; culture supernatants derived from these strains were no longer cytotoxic to Leghorn male hepatoma cells. Complementation with the virRS operon restored the toxin phenotypes to wild type. The results also showed that the VirSR two-component system regulates the expression of netB at the level of transcription. We postulate that in the gastrointestinal tract of infected birds, NetB production is upregulated when the population of C. perfringens cells reaches a threshold level that leads to activation of the VirSR system.

  5. The VirSR Two-Component Signal Transduction System Regulates NetB Toxin Production in Clostridium perfringens▿

    Science.gov (United States)

    Cheung, Jackie K.; Keyburn, Anthony L.; Carter, Glen P.; Lanckriet, Anouk L.; Van Immerseel, Filip; Moore, Robert J.; Rood, Julian I.

    2010-01-01

    Clostridium perfringens causes several diseases in domestic livestock, including necrotic enteritis in chickens, which is of concern to the poultry industry due to its health implications and associated economic cost. The novel pore-forming toxin NetB is a critical virulence factor in the pathogenesis of this disease. In this study, we have examined the regulation of NetB toxin production. In C. perfringens, the quorum sensing-dependent VirSR two-component signal transduction system regulates genes encoding several toxins and extracellular enzymes. Analysis of the sequence upstream of the netB gene revealed the presence of potential DNA binding sites, or VirR boxes, that are recognized by the VirR response regulator. In vitro binding experiments showed that purified VirR was able to recognize and bind to these netB-associated VirR boxes. Furthermore, using a reporter gene assay, the netB VirR boxes were shown to be functional. Mutation of the virR gene in two avian C. perfringens strains was shown to significantly reduce the production of the NetB toxin; culture supernatants derived from these strains were no longer cytotoxic to Leghorn male hepatoma cells. Complementation with the virRS operon restored the toxin phenotypes to wild type. The results also showed that the VirSR two-component system regulates the expression of netB at the level of transcription. We postulate that in the gastrointestinal tract of infected birds, NetB production is upregulated when the population of C. perfringens cells reaches a threshold level that leads to activation of the VirSR system. PMID:20457789

  6. Effects of exercise on AMPK signaling and downstream components to PI3K in rat with type 2 diabetes.

    Directory of Open Access Journals (Sweden)

    Shicheng Cao

    Full Text Available Exercise can increase skeletal muscle sensitivity to insulin, improve insulin resistance and regulate glucose homeostasis in rat models of type 2 diabetes. However, the potential mechanism remains poorly understood. In this study, we established a male Sprague-Dawley rat model of type 2 diabetes, with insulin resistance and β cell dysfunction, which was induced by a high-fat diet and low-dose streptozotocin to replicate the pathogenesis and metabolic characteristics of type 2 diabetes in humans. We also investigated the possible mechanism by which chronic and acute exercise improves metabolism, and the phosphorylation and expression of components of AMP-activated protein kinase (AMPK and downstream components of phosphatidylinositol 3-kinase (PI3K signaling pathways in the soleus. As a result, blood glucose, triglyceride, total cholesterol, and free fatty acid were significantly increased, whereas insulin level progressively declined in diabetic rats. Interestingly, chronic and acute exercise reduced blood glucose, increased phosphorylation and expression of AMPKα1/2 and the isoforms AMPKα1 and AMPKα2, and decreased phosphorylation and expression of AMPK substrate, acetyl CoA carboxylase (ACC. Chronic exercise upregulated phosphorylation and expression of AMPK upstream kinase, LKB1. But acute exercise only increased LKB1 expression. In particular, exercise reversed the changes in protein kinase C (PKCζ/λ phosphorylation, and PKCζ phosphorylation and expression. Additionally, exercise also increased protein kinase B (PKB/Akt1, Akt2 and GLUT4 expression, but AS160 protein expression was unchanged. Chronic exercise elevated Akt (Thr(308 and (Ser(473 and AS160 phosphorylation. Finally, we found that exercise increased peroxisome proliferator-activated receptor-γ coactivator 1 (PGC1 mRNA expression in the soleus of diabetic rats. These results indicate that both chronic and acute exercise influence the phosphorylation and expression of

  7. A Cyclic di-GMP-binding Adaptor Protein Interacts with Histidine Kinase to Regulate Two-component Signaling.

    Science.gov (United States)

    Xu, Linghui; Venkataramani, Prabhadevi; Ding, Yichen; Liu, Yang; Deng, Yinyue; Yong, Grace Lisi; Xin, Lingyi; Ye, Ruijuan; Zhang, Lianhui; Yang, Liang; Liang, Zhao-Xun

    2016-07-29

    The bacterial messenger cyclic di-GMP (c-di-GMP) binds to a diverse range of effectors to exert its biological effect. Despite the fact that free-standing PilZ proteins are by far the most prevalent c-di-GMP effectors known to date, their physiological function and mechanism of action remain largely unknown. Here we report that the free-standing PilZ protein PA2799 from the opportunistic pathogen Pseudomonas aeruginosa interacts directly with the hybrid histidine kinase SagS. We show that PA2799 (named as HapZ: histidine kinase associated PilZ) binds directly to the phosphoreceiver (REC) domain of SagS, and that the SagS-HapZ interaction is further enhanced at elevated c-di-GMP concentration. We demonstrate that binding of HapZ to SagS inhibits the phosphotransfer between SagS and the downstream protein HptB in a c-di-GMP-dependent manner. In accordance with the role of SagS as a motile-sessile switch and biofilm growth factor, we show that HapZ impacts surface attachment and biofilm formation most likely by regulating the expression of a large number of genes. The observations suggest a previously unknown mechanism whereby c-di-GMP mediates two-component signaling through a PilZ adaptor protein.

  8. Differences in two-component signal transduction proteins among the genus Brucella: implications for host preference and pathogenesis.

    Science.gov (United States)

    Lavín, José Luis; Binnewies, Tim T; Pisabarro, Antonio G; Ussery, David W; García-Lobo, Juan M; Oguiza, José A

    2010-08-26

    Two-component systems (TCSs) are the predominant bacterial signal transduction mechanisms. Species of the genus Brucella are genetically highly related and differ mainly in mammalian host adaptation and pathogenesis. In this study, TCS proteins encoded in the available genome sequences of Brucella species have been identified using bioinformatic methods. All the Brucella species share an identical set of TCS proteins, and the number of TCS proteins in the closely related opportunistic human pathogen Ochrobactrum anthropi was higher than in Brucella species as expected from its lifestyle. O. anthropi lacks orthologs of the Brucella TCSs NodVW, TceSR and TcfSR, suggesting that these TCS proteins could be necessary for the adaptation of Brucella as an intracellular pathogen. This genomic analysis revealed the presence of a differential distribution of TCS pseudogenes among Brucella species. Moreover, there were also differences in TCS pseudogenes between strains belonging to the same Brucella species, and in particular between B. suis biovars 1 and 2. Copyright 2010 Elsevier B.V. All rights reserved.

  9. Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm.

    Science.gov (United States)

    Kyriakidis, Dimitrios A; Tiligada, Ekaterini

    2009-09-01

    Adaptive signal transduction within microbial cells involves a multi-faceted regulated phosphotransfer mechanism that comprises structural rearrangements of sensor histidine kinases upon ligand-binding and phosphorylation-induced conformational changes in response regulators of versatile two-component systems (TCS), arisen early in bacterial evolution. In Escherichia coli, cross-talk between the AtoS histidine kinase and the AtoC response regulator, forming the AtoSC TCS, through His --> Asp phosphotransfer, activates AtoC directly to induce atoDAEB operon expression, thus modulating diverse fundamental cellular processes such as short-chain fatty acid catabolism, poly-(R)-3-hydroxybutyrate biosynthesis and chemotaxis. Among the inducers hitherto identified, acetoacetate is the classical activator. The AtoSC TCS functional modulation by polyamines, histamine and Ca(2+), as well as the role of AtoC as transcriptional regulator, add new promising perspectives in the physiological significance and potential pharmacological exploitation of this TCS in cell proliferation, bacteria-host interactions, chemotaxis, and adaptation.

  10. Analysis of protein expression regulated by the Helicobacter pylori ArsRS two-component signal transduction system.

    Science.gov (United States)

    Loh, John T; Gupta, Shobhana S; Friedman, David B; Krezel, Andrzej M; Cover, Timothy L

    2010-04-01

    Previous studies have shown that the Helicobacter pylori ArsRS two-component signal transduction system contributes to acid-responsive gene expression. To identify additional members of the ArsRS regulon and further investigate the regulatory role of the ArsRS system, we analyzed protein expression in wild-type and arsS null mutant strains. Numerous proteins were differentially expressed in an arsS mutant strain compared to a wild-type strain when the bacteria were cultured at pH 5.0 and also when they were cultured at pH 7.0. Genes encoding 14 of these proteins were directly regulated by the ArsRS system, based on observed binding of ArsR to the relevant promoter regions. The ArsRS-regulated proteins identified in this study contribute to acid resistance (urease and amidase), acetone metabolism (acetone carboxylase), resistance to oxidative stress (thioredoxin reductase), quorum sensing (Pfs), and several other functions. These results provide further definition of the ArsRS regulon and underscore the importance of the ArsRS system in regulating expression of H. pylori proteins during bacterial growth at both neutral pH and acidic pH.

  11. The two-component signal transduction system YvcPQ regulates the bacterial resistance to bacitracin in Bacillus thuringiensis.

    Science.gov (United States)

    Zhang, Shumeng; Li, Xinfeng; Wang, Xun; Li, Zhou; He, Jin

    2016-10-01

    YvcPQ is one of the two-component signal transduction systems that respond to specific stimuli and enable cells to adjust multiple cellular functions. It consists of a histidine kinase YvcQ and a response regulator YvcP. In this study, through searching the consensus sequence recognized by YvcP, we found four YvcP-binding motifs in the promoter regions of genes yvcR (BMB171_C4100), BMB171_C4385, kapD (BMB171_C4525) and BMB171_C4835 in Bacillus thuringiensis BMB171 which is a representative of Bacillus cereus group, and confirmed that these genes are regulated by YvcP. We compared the sequence of yvcPQ and its downstream genes in genus Bacillus, and found two different kinds of yvc locus, one was the yvcPQ-RS in B. subtilis species and the other was the yvcPQ-R-S1S2 in B. cereus group. Furthermore, we found that YvcP activates the transcription of yvcS1S2 (downstream of yvcR) to promote bacterial resistance to bacitracin and deletion of either yvcPQ operon or yvcS1S2 operon renders the bacterial cells more sensitive to bacitracin. This study enriched our understanding of both the YvcPQ's function and the mechanism of bacterial resistance to bacitracin.

  12. Single-cell analysis reveals that insulation maintains signaling specificity between two yeast MAPK pathways with common components.

    Science.gov (United States)

    Patterson, Jesse C; Klimenko, Evguenia S; Thorner, Jeremy

    2010-10-19

    Eukaryotic cells use multiple mitogen-activated protein kinase (MAPK) cascades to evoke appropriate responses to external stimuli. In Saccharomyces cerevisiae, the MAPK Fus3 is activated by pheromone-binding heterotrimeric guanosine triphosphate-binding protein (G protein)-coupled receptors to promote mating, whereas the MAPK Hog1 is activated by hyperosmotic stress to elicit the high-osmolarity glycerol (HOG) response. Although these MAPK pathways share several upstream components, exposure to either pheromone or osmolyte alone triggers only the appropriate response. We used fluorescence localization- and transcription-specific reporters to assess activation of these pathways in individual cells on the minute and hour time scale, respectively. Dual activation of these two MAPK pathways occurred over a broad range of stimulant concentrations and temporal regimes in wild-type cells subjected to costimulation. Thus, signaling specificity is achieved through an "insulation" mechanism, not a "cross-inhibition" mechanism. Furthermore, we showed that there was a critical period during which Hog1 activity had to occur for proper insulation of the HOG pathway.

  13. Cumulative and Synergistic Effects of Physical, Biological, and Acoustic Signals on Marine Mammal Habitat Use Physical Oceanography Component: Soundscapes Under Sea Ice: Can We Listen for Open Water?

    Science.gov (United States)

    2013-09-30

    disappear as these mammals begin their annual migration to the Arctic Ocean. The soundscape shows loud floe-banging conditions mixed with periods of...Physical, Biological, and Acoustic Signals on Marine Mammal Habitat Use Physical Oceanography Component: Soundscapes Under Sea Ice: Can we listen for...research effort is to enhance the understanding of how variability in physical, biological, and acoustic signals impact marine mammal habitat use. This is

  14. Analysis of the virulence-associated RevSR two-component signal transduction system of Clostridium perfringens.

    Science.gov (United States)

    Cheung, Jackie K; Wisniewski, Jessica A; Adams, Vicki M; Quinsey, Noelene S; Rood, Julian I

    2016-09-01

    Clostridium perfringens is a Gram-positive, anaerobic, spore-forming bacterium that causes human gas gangrene (clostridial myonecrosis) and food poisoning. Early studies showed that virulence was regulated by the VirSR two-component signal transduction system. However, our identification of the RevR orphan response regulator indicated that more than one system was involved in controlling virulence. To further characterize this virulence-associated regulator, gel mobility shift experiments, coupled with DNase I footprinting, were used to identify the RevR DNA binding sequence. Bioinformatics analysis suggested that an orphan sensor histidine kinase, CPE1757 (renamed RevS), was the cognate sensor of RevR. Interaction between RevS and RevR was demonstrated by use of a bacterial two-hybrid system and validated by protein-protein interaction studies using biolayer interferometry. To assess the involvement of RevS in virulence regulation, the revS gene was inactivated by Targetron insertion. When isogenic wild-type, revS and complemented revS strains were tested in a mouse myonecrosis model, the revS mutant was found to be attenuated in virulence, which was similar to the attenuation observed previously with the revR mutant. However, transcriptional analysis of selected RevR-regulated genes in the revS mutant revealed a different pattern of expression to a revR mutant, suggesting that the RevSR system is more complex than originally thought. Taken together, the results have led to the identification and characterization of the two essential parts of a new regulatory network that is involved in the regulation of virulence in C. perfringens.

  15. A genome-wide study of two-component signal transduction systems in eight newly sequenced mutans streptococci strains.

    Science.gov (United States)

    Song, Lifu; Sudhakar, Padhmanand; Wang, Wei; Conrads, Georg; Brock, Anke; Sun, Jibin; Wagner-Döbler, Irene; Zeng, An-Ping

    2012-04-04

    Mutans streptococci are a group of gram-positive bacteria including the primary cariogenic dental pathogen Streptococcus mutans and closely related species. Two component systems (TCSs) composed of a signal sensing histidine kinase (HK) and a response regulator (RR) play key roles in pathogenicity, but have not been comparatively studied for these oral bacterial pathogens. HKs and RRs of 8 newly sequenced mutans streptococci strains, including S. sobrinus DSM20742, S. ratti DSM20564 and six S. mutans strains, were identified and compared to the TCSs of S. mutans UA159 and NN2025, two previously genome sequenced S. mutans strains. Ortholog analysis revealed 18 TCS clusters (HK-RR pairs), 2 orphan HKs and 2 orphan RRs, of which 8 TCS clusters were common to all 10 strains, 6 were absent in one or more strains, and the other 4 were exclusive to individual strains. Further classification of the predicted HKs and RRs revealed interesting aspects of their putative functions. While TCS complements were comparable within the six S. mutans strains, S. sobrinus DSM20742 lacked TCSs possibly involved in acid tolerance and fructan catabolism, and S. ratti DSM20564 possessed 3 unique TCSs but lacked the quorum-sensing related TCS (ComDE). Selected computational predictions were verified by PCR experiments. Differences in the TCS repertoires of mutans streptococci strains, especially those of S. sobrinus and S. ratti in comparison to S. mutans, imply differences in their response mechanisms for survival in the dynamic oral environment. This genomic level study of TCSs should help in understanding the pathogenicity of these mutans streptococci strains.

  16. Identification of DNA binding motifs of the Mycobacterium tuberculosis PhoP/PhoR two-component signal transduction system.

    Science.gov (United States)

    Cimino, Mena; Thomas, Christophe; Namouchi, Amine; Dubrac, Sarah; Gicquel, Brigitte; Gopaul, Deshmukh N

    2012-01-01

    The Mycobacterium tuberculosis PhoP/PhoR two-component signal transduction system controls the expression of about 2% of the genome and plays a major role in pathogenicity. However, its regulon has not been well characterized. The binding site of PhoP transcription regulator was identified in the upstream regions of msl3, pks2, lipF and fadD21 genes, by using gene fusions, electrophoretic mobility shift assays and DNase I footprinting experiments. A consensus sequence for PhoP binding was deduced. It consists of two direct repeats, DR1/DR2, associated with a third repeat, DR3, important in some cases for PhoP binding to DR1/DR2 but located at a variable distance from these direct repeats. DR1/DR2 and DR3 consensus sequences were used to screen the whole-genome sequence for other putative binding sites potentially corresponding to genes directly regulated by PhoP. The identified 87 genes, encoding transcription regulators, and proteins involved in secondary metabolites biosynthesis, transport and catabolism are proposed to belong to the PhoP regulon. A consensus sequence derived from the analysis of PhoP binding to four gene promoter regions is proposed. We show for the first time the involvement of a third direct repeat motif in this binding reaction. The consensus sequence was instrumented to study the global regulation mediated by PhoP in M. tuberculosis. This analysis leads to the identification of several genes that are potentially regulated by this key player.

  17. Evolutionary history of the OmpR/IIIA family of signal transduction two component systems in Lactobacillaceae and Leuconostocaceae

    Directory of Open Access Journals (Sweden)

    González-Candelas Fernando

    2011-02-01

    Full Text Available Abstract Background Two component systems (TCS are signal transduction pathways which typically consist of a sensor histidine kinase (HK and a response regulator (RR. In this study, we have analyzed the evolution of TCS of the OmpR/IIIA family in Lactobacillaceae and Leuconostocaceae, two families belonging to the group of lactic acid bacteria (LAB. LAB colonize nutrient-rich environments such as foodstuffs, plant materials and the gastrointestinal tract of animals thus driving the study of this group of both basic and applied interest. Results The genomes of 19 strains belonging to 16 different species have been analyzed. The number of TCS encoded by the strains considered in this study varied between 4 in Lactobacillus helveticus and 17 in Lactobacillus casei. The OmpR/IIIA family was the most prevalent in Lactobacillaceae accounting for 71% of the TCS present in this group. The phylogenetic analysis shows that no new TCS of this family has recently evolved in these Lactobacillaceae by either lineage-specific gene expansion or domain shuffling. Furthermore, no clear evidence of non-orthologous replacements of either RR or HK partners has been obtained, thus indicating that coevolution of cognate RR and HKs has been prevalent in Lactobacillaceae. Conclusions The results obtained suggest that vertical inheritance of TCS present in the last common ancestor and lineage-specific gene losses appear as the main evolutionary forces involved in their evolution in Lactobacillaceae, although some HGT events cannot be ruled out. This would agree with the genomic analyses of Lactobacillales which show that gene losses have been a major trend in the evolution of this group.

  18. A novel two-component signaling system facilitates uropathogenic Escherichia coli's ability to exploit abundant host metabolites.

    Directory of Open Access Journals (Sweden)

    Wentong Cai

    Full Text Available Two-component signaling systems (TCSs are major mechanisms by which bacteria adapt to environmental conditions. It follows then that TCSs would play important roles in the adaptation of pathogenic bacteria to host environments. However, no pathogen-associated TCS has been identified in uropathogenic Escherichia coli (UPEC. Here, we identified a novel TCS, which we termed KguS/KguR (KguS: α-ketoglutarate utilization sensor; KguR: α-ketoglutarate utilization regulator in UPEC CFT073, a strain isolated from human pyelonephritis. kguS/kguR was strongly associated with UPEC but was found only rarely among other E. coli including commensal and intestinal pathogenic strains. An in vivo competition assay in a mouse UTI model showed that deletion of kguS/kguR in UPEC CFT073 resulted in a significant reduction in its colonization of the bladders and kidneys of mice, suggesting that KguS/KguR contributed to UPEC fitness in vivo. Comparative proteomics identified the target gene products of KguS/KguR, and sequence analysis showed that TCS KguS/KguR and its targeted-genes, c5032 to c5039, are encoded on a genomic island, which is not present in intestinal pathogenic E. coli. Expression of the target genes was induced by α-ketoglutarate (α-KG. These genes were further shown to be involved in utilization of α-KG as a sole carbon source under anaerobic conditions. KguS/KguR contributed to the regulation of the target genes with the direct regulation by KguR verified using an electrophoretic mobility shift assay. In addition, oxygen deficiency positively modulated expression of kguS/kguR and its target genes. Taken altogether, this study describes the first UPEC-associated TCS that functions in controlling the utilization of α-ketoglutarate in vivo thereby facilitating UPEC adaptation to life inside the urinary tract.

  19. A novel two-component signaling system facilitates uropathogenic Escherichia coli's ability to exploit abundant host metabolites.

    Science.gov (United States)

    Cai, Wentong; Wannemuehler, Yvonne; Dell'anna, Giuseppe; Nicholson, Bryon; Barbieri, Nicolle L; Kariyawasam, Subhashinie; Feng, Yaping; Logue, Catherine M; Nolan, Lisa K; Li, Ganwu

    2013-01-01

    Two-component signaling systems (TCSs) are major mechanisms by which bacteria adapt to environmental conditions. It follows then that TCSs would play important roles in the adaptation of pathogenic bacteria to host environments. However, no pathogen-associated TCS has been identified in uropathogenic Escherichia coli (UPEC). Here, we identified a novel TCS, which we termed KguS/KguR (KguS: α-ketoglutarate utilization sensor; KguR: α-ketoglutarate utilization regulator) in UPEC CFT073, a strain isolated from human pyelonephritis. kguS/kguR was strongly associated with UPEC but was found only rarely among other E. coli including commensal and intestinal pathogenic strains. An in vivo competition assay in a mouse UTI model showed that deletion of kguS/kguR in UPEC CFT073 resulted in a significant reduction in its colonization of the bladders and kidneys of mice, suggesting that KguS/KguR contributed to UPEC fitness in vivo. Comparative proteomics identified the target gene products of KguS/KguR, and sequence analysis showed that TCS KguS/KguR and its targeted-genes, c5032 to c5039, are encoded on a genomic island, which is not present in intestinal pathogenic E. coli. Expression of the target genes was induced by α-ketoglutarate (α-KG). These genes were further shown to be involved in utilization of α-KG as a sole carbon source under anaerobic conditions. KguS/KguR contributed to the regulation of the target genes with the direct regulation by KguR verified using an electrophoretic mobility shift assay. In addition, oxygen deficiency positively modulated expression of kguS/kguR and its target genes. Taken altogether, this study describes the first UPEC-associated TCS that functions in controlling the utilization of α-ketoglutarate in vivo thereby facilitating UPEC adaptation to life inside the urinary tract.

  20. The synthetic cationic lipid diC14 activates a sector of the Arabidopsis defence network requiring endogenous signalling components.

    Science.gov (United States)

    Cambiagno, Damián Alejandro; Lonez, Caroline; Ruysschaert, Jean-Marie; Alvarez, María Elena

    2015-12-01

    Natural and synthetic elicitors have contributed significantly to the study of plant immunity. Pathogen-derived proteins and carbohydrates that bind to immune receptors, allow the fine dissection of certain defence pathways. Lipids of a different nature that act as defence elicitors, have also been studied, but their specific effects have been less well characterized, and their receptors have not been identified. In animal cells, nanoliposomes of the synthetic cationic lipid 3-tetradecylamino-tert-butyl-N-tetradecylpropionamidine (diC14) activate the TLR4-dependent immune cascade. Here, we have investigated whether this lipid induces Arabidopsis defence responses. At the local level, diC14 activated early and late defence gene markers (FRK1, WRKY29, ICS1 and PR1), acting in a dose-dependent manner. This lipid induced the salicylic acid (SA)-dependent, but not jasmonic acid (JA)-dependent, pathway and protected plants against Pseudomonas syringae pv. tomato (Pst), but not Botrytis cinerea. diC14 was not toxic to plant or pathogen, and potentiated pathogen-induced callose deposition. At the systemic level, diC14 induced PR1 expression and conferred resistance against Pst. diC14-induced defence responses required the signalling protein EDS1, but not NDR1. Curiously, the lipid-induced defence gene expression was lower in the fls2/efr/cerk1 triple mutant, but still unchanged in the single mutants. The amidine headgroup and chain length were important for its activity. Given the robustness of the responses triggered by diC14, its specific action on a defence pathway and the requirement for well-known defence components, this synthetic lipid is emerging as a useful tool to investigate the initial events involved in plant innate immunity.

  1. Robust signal reconstruction for condition monitoring of industrial components via a modified Auto Associative Kernel Regression method

    Science.gov (United States)

    Baraldi, Piero; Di Maio, Francesco; Turati, Pietro; Zio, Enrico

    2015-08-01

    In this work, we propose a modification of the traditional Auto Associative Kernel Regression (AAKR) method which enhances the signal reconstruction robustness, i.e., the capability of reconstructing abnormal signals to the values expected in normal conditions. The modification is based on the definition of a new procedure for the computation of the similarity between the present measurements and the historical patterns used to perform the signal reconstructions. The underlying conjecture for this is that malfunctions causing variations of a small number of signals are more frequent than those causing variations of a large number of signals. The proposed method has been applied to real normal condition data collected in an industrial plant for energy production. Its performance has been verified considering synthetic and real malfunctioning. The obtained results show an improvement in the early detection of abnormal conditions and the correct identification of the signals responsible of triggering the detection.

  2. A subfamily of putative cytokinin receptors is revealed by an analysis of the evolution of the two-component signaling system of plants.

    Science.gov (United States)

    Gruhn, Nijuscha; Halawa, Mhyeddeen; Snel, Berend; Seidl, Michael F; Heyl, Alexander

    2014-05-01

    The two-component signaling system--the major signaling pathway of bacteria--is found among higher eukaryotes only in plants, where it regulates diverse processes, such as the signaling of the phytohormone cytokinin. Cytokinin is perceived by a hybrid histidine (His) kinase receptor, and the signal is transduced by a multistep phosphorelay system of His phosphotransfer proteins and different classes of response regulators (RRs). To shed light on the origin and evolution of the two-component signaling system members in plants, we conducted a comprehensive domain-based phylogenetic study across the relevant kingdoms, including Charophyceae algae, the group of green algae giving rise to land plants. Surprisingly, we identified a subfamily of cytokinin receptors with members only from the early diverging land plants Marchantia polymorpha and Physcomitrella patens and then experimentally characterized two members of this subfamily. His phosphotransfer proteins of Charophyceae seemed to be more closely related to land plants than to other groups of green algae. Farther down the signaling pathway, the type-B RRs were found across all plant clades, but many members lack either the canonical Asp residue or the DNA binding domain. In contrast, the type-A RRs seemed to be limited to land plants. Finally, the analysis provided hints that one additional group of RRs, the type-C RRs, might be degenerated receptors and thus, of a different evolutionary origin than bona fide RRs.

  3. HOIL-1L interacting protein (HOIP as an NF-kappaB regulating component of the CD40 signaling complex.

    Directory of Open Access Journals (Sweden)

    Bruce S Hostager

    Full Text Available The tumor necrosis factor receptor (TNFR superfamily mediates signals critical for regulation of the immune system. One family member, CD40, is important for the efficient activation of antibody-producing B cells and other antigen-presenting cells. The molecules and mechanisms that mediate CD40 signaling are only partially characterized. Proteins known to interact with the cytoplasmic domain of CD40 include members of the TNF receptor-associated factor (TRAF family, which regulate signaling and serve as links to other signaling molecules. To identify additional proteins important for CD40 signaling, we used a combined stimulation/immunoprecipitation procedure to isolate CD40 signaling complexes from B cells and characterized the associated proteins by mass spectrometry. In addition to known CD40-interacting proteins, we detected SMAC/DIABLO, HTRA2/Omi, and HOIP/RNF31/PAUL/ZIBRA. We found that these previously unknown CD40-interacting partners were recruited in a TRAF2-dependent manner. HOIP is a ubiquitin ligase capable of mediating NF-kappaB activation through the ubiquitin-dependent activation of IKKgamma. We found that a mutant HOIP molecule engineered to lack ubiquitin ligase activity inhibited the CD40-mediated activation of NF-kappaB. Together, our results demonstrate a powerful approach for the identification of signaling molecules associated with cell surface receptors and indicate an important role for the ubiquitin ligase activity of HOIP in proximal CD40 signaling.

  4. A two-component signal-transduction cascade in Carnobacterium piscicola LV17B : two signaling peptides and one sensor-transmitter

    NARCIS (Netherlands)

    Kleerebezem, M; Kuipers, OP; de Vos, WM; Stiles, ME; Quadri, LEN; Vos, Willem M. de; Stiles, Michael E.; Quadri, Luis E.N.

    2001-01-01

    In the lactic acid bacterium Carnobacterium piscicola LV17B a peptide-pheromone dependent quorum-sensing mode is involved in the regulation of bacteriocin production. Bacteriocin CB2 was identified as an environmental signal that induces bacteriocin production. Here, we demonstrate that a second 24

  5. A two-component signal-transduction cascade in Carnobacterium piscicola LV17B : two signaling peptides and one sensor-transmitter

    NARCIS (Netherlands)

    Kleerebezem, M; Kuipers, OP; de Vos, WM; Stiles, ME; Quadri, LEN; Vos, Willem M. de; Stiles, Michael E.; Quadri, Luis E.N.

    2001-01-01

    In the lactic acid bacterium Carnobacterium piscicola LV17B a peptide-pheromone dependent quorum-sensing mode is involved in the regulation of bacteriocin production. Bacteriocin CB2 was identified as an environmental signal that induces bacteriocin production. Here, we demonstrate that a second 24

  6. Characterizing near-surface firn using the scattered signal component of the glacier surface return from airborne radio-echo sounding

    Science.gov (United States)

    Rutishauser, Anja; Grima, Cyril; Sharp, Martin; Blankenship, Donald D.; Young, Duncan A.; Cawkwell, Fiona; Dowdeswell, Julian A.

    2016-12-01

    We derive the scattered component (hereafter referred to as the incoherent component) of glacier surface echoes from airborne radio-echo sounding measurements over Devon Ice Cap, Arctic Canada, and compare the scattering distribution to firn stratigraphy observations from ground-based radar data. Low scattering correlates to laterally homogeneous firn above 1800 m elevation containing thin, flat, and continuous ice layers and below 1200 m elevation where firn predominantly consists of ice. Increased scattering between elevations of 1200-1800 m corresponds to firn with inhomogeneous, undulating ice layers. No correlation was found to surface roughness and its theoretical incoherent backscattering values. This indicates that the scattering component is mainly influenced by the near-surface firn stratigraphy, whereas surface roughness effects are minor. Our results suggest that analyzing the scattered signal component of glacier surface echoes is a promising approach to characterize the spatial heterogeneity of firn that is affected by melting and refreezing processes.

  7. Fast removal of ocular artifacts from electroencephalogram signals using spatial constraint independent component analysis based recursive least squares in brain-computer interface

    Institute of Scientific and Technical Information of China (English)

    Bang-hua YANG; Liang-fei HE; Lin LIN; Qian WANG

    2015-01-01

    Ocular artifacts cause the main interfering signals within electroencephalogram (EEG) signal measurements. An adaptive filter based on reference signals from an electrooculogram (EOG) can reduce ocular interference, but collecting EOG signals during a long-term EEG recording is inconvenient and uncomfortable for the subject. To remove ocular artifacts from EEG in brain-computer interfaces (BCIs), a method named spatial constraint independent component analysis based recursive least squares (SCICA-RLS) is proposed. The method consists of two stages. In the first stage, independent component analysis (ICA) is used to decompose multiple EEG channels into an equal number of independent components (ICs). Ocular ICs are identified by an automatic artifact detection method based on kurtosis. Then empirical mode decomposition (EMD) is employed to remove any cerebral activity from the identified ocular ICs to obtain exact artifact ICs. In the second stage, first, SCICA applies exact artifact ICs obtained in the first stage as a constraint to extract artifact ICs from the given EEG signal. These extracted ICs are called spatial constraint ICs (SC-ICs). Then the RLS based adaptive filter uses SC-ICs as reference signals to reduce interference, which avoids the need for parallel EOG recordings. In addition, the proposed method has the ability of fast computation as it is not necessary for SCICA to identify all ICs like ICA. Based on the EEG data recorded from seven subjects, the new approach can lead to average classification accuracies of 3.3% and 12.6% higher than those of the standard ICA and raw EEG, respectively. In addition, the proposed method has 83.5% and 83.8% reduction in time-consumption compared with the standard ICA and ICA-RLS, respectively, which demonstrates a better and faster OA reduction.

  8. Dysregulated Expression of Tensin 2 and Components of the PI3 Kinase/Akt Signaling Pathway in Human Thyroid Carcinoma

    OpenAIRE

    Nasrollah Erfani; Mohammad Javad Fattahi; Mohammad Hossein Dabbaghmanesh; Mohammad Mehrazmay; Ahmad Monabati; Akbar Rasekhi Kazerouni; Sassan Hafizi; Abbas Ghaderi

    2016-01-01

    Background: The phosphatidylinositol 3-kinase/Akt signaling pathway is recognized as a key driver of cancer cell survival and proliferation, and is often contingent upon an impairment of expression/function of the PTEN tumor suppressor, a negative regulator of this pathway. In addition, the cytoskeletal signaling protein Tensin 2 has also been implicated as a negative regulator of this pathway. However, the PI3K pathway remains to be fully characterized in clinical thyroid carc...

  9. Screening for compounds that affect the interaction between bacterial two-component signal transduction response regulator protein and cognate promoter DNA.

    Science.gov (United States)

    Erickson, Matthew G; Ulijasz, Andrew T; Weisblum, Bernard

    2008-01-01

    Bacterial signal transduction systems can be used as drug targets. The signal transduction targets fall into two groups--sensor kinases and response regulators. Previously reported studies describe hits that were thought to inactivate sensor kinases but on closer examination were found to act elsewhere instead; a possible reason for this is that full-length sensor kinases are integral membrane proteins whose activity might reflect interaction with the cell membrane or with membrane components. We describe a model system that instead is based on the interaction between a test compound and a response regulator in a homogeneous phase reaction. In this system, response regulator-DNA complex formation and its inhibition by a test compound are measured by fluorescence polarization. The model system should be readily adaptable to drug discovery based on other bacterial two-component s transduction systems.

  10. Characterizing near-surface firn from the scattered signal component of glacier surface reflections detected in airborne radio-echo sounding measurements

    Science.gov (United States)

    Rutishauser, A.; Grima, C.; Sharp, M. J.; Blankenship, D. D.; Young, D. A.; Cawkwell, F.; Dowdeswell, J. A.

    2016-12-01

    With recent summer warming, surface melt on Canadian Arctic ice caps has intensified and extended to higher elevations in ice cap accumulation areas. Consequently, more meltwater percolates into the near-surface firn, and refreezes as ice layers where firn temperatures are below freezing. This process can increase firn densification rates, causing a lowering of the glacier surface height even in the absence of mass changes. Thus, knowledge of spatio-temporal variations in the near-surface firn stratigraphy is important for interpreting altimetrically-derived estimates of ice cap mass balance. We investigate the use of the scattering signal component of glacier surface reflections in airborne radio-echo sounding (RES) measurements to characterize the near-surface firn stratigraphy. The scattering signal distribution over Devon Ice Cap is compared to firn stratigraphy derived from ground-based radar data. We identify three distinct firn facies zones at different elevation ranges. The scattered signal component changes significantly between the different firn facies zones: low scattering correlates to laterally homogeneous firn containing thin, flat and continuous ice layers at elevations above 1800 m and below 1200 m, where firn consists mainly of ice. Higher scattering values are found from 1200-1800 m where the firn contains discrete, undulating ice layers. No correlation was found between the scattering component and surface roughness. Modelled scattering values for the measured roughness were significantly less than the observed values, and did not reproduce their observed spatial distribution. This indicates that the scattering component is determined mainly by the structure of near-surface firn. Our results suggest that the scattering component of surface reflections from airborne RES measurements has potential for characterizing heterogeneity in the spatial structure of firn that is affected by melting and refreezing processes.

  11. Evidence for a respiratory component, similar to mammalian respiratory sinus arrhythmia, in the heart rate variability signal from the rattlesnake, Crotalus durissus terrificus.

    Science.gov (United States)

    Campbell, Hamish A; Leite, Cleo A C; Wang, Tobias; Skals, Marianne; Abe, Augusto S; Egginton, Stuart; Rantin, F Tadeu; Bishop, Charles M; Taylor, Edwin W

    2006-07-01

    Autonomic control of heart rate variability and the central location of vagal preganglionic neurones (VPN) were examined in the rattlesnake (Crotalus durissus terrificus), in order to determine whether respiratory sinus arrhythmia (RSA) occurred in a similar manner to that described for mammals. Resting ECG signals were recorded in undisturbed snakes using miniature datalogging devices, and the presence of oscillations in heart rate (fh) was assessed by power spectral analysis (PSA). This mathematical technique provides a graphical output that enables the estimation of cardiac autonomic control by measuring periodic changes in the heart beat interval. At fh above 19 min(-1) spectra were mainly characterised by low frequency components, reflecting mainly adrenergic tonus on the heart. By contrast, at fh below 19 min(-1) spectra typically contained high frequency components, demonstrated to be cholinergic in origin. Snakes with a fh >19 min(-1) may therefore have insufficient cholinergic tonus and/or too high an adrenergic tonus acting upon the heart for respiratory sinus arrhythmia (RSA) to develop. A parallel study monitored fh simultaneously with the intraperitoneal pressures associated with lung inflation. Snakes with a fhrate (fv). Adrenergic blockade by propranolol infusion increased the variability of the ventilation cycle, and the oscillatory component of the fh spectrum broadened accordingly. Infusion of atropine to effect cholinergic blockade abolished this HF component, confirming a role for vagal control of the heart in matching fh and fv in the rattlesnake. A neuroanatomical study of the brainstem revealed two locations for vagal preganglionic neurones (VPN). This is consistent with the suggestion that generation of ventilatory components in the heart rate variability (HRV) signal are dependent on spatially distinct loci for cardiac VPN. Therefore, this study has demonstrated the presence of RSA in the HRV signal and a dual location for VPN in the

  12. Signal Decomposition of High Resolution Time Series River Data to Separate Local and Regional Components of Conductivity

    Science.gov (United States)

    Signal processing techniques were applied to high-resolution time series data obtained from conductivity loggers placed upstream and downstream of an oil and gas wastewater treatment facility along a river. Data was collected over 14-60 days. The power spectral density was us...

  13. : Signal Decomposition of High Resolution Time Series River data to Separate Local and Regional Components of Conductivity

    Science.gov (United States)

    Signal processing techniques were applied to high-resolution time series data obtained from conductivity loggers placed upstream and downstream of a wastewater treatment facility along a river. Data was collected over 14-60 days, and several seasons. The power spectral densit...

  14. Independent component analysis (ICA) algorithms for improved spectral deconvolution of overlapped signals in 1H NMR analysis: application to foods and related products.

    Science.gov (United States)

    Monakhova, Yulia B; Tsikin, Alexey M; Kuballa, Thomas; Lachenmeier, Dirk W; Mushtakova, Svetlana P

    2014-05-01

    The major challenge facing NMR spectroscopic mixture analysis is the overlapping of signals and the arising impossibility to easily recover the structures for identification of the individual components and to integrate separated signals for quantification. In this paper, various independent component analysis (ICA) algorithms [mutual information least dependent component analysis (MILCA); stochastic non-negative ICA (SNICA); joint approximate diagonalization of eigenmatrices (JADE); and robust, accurate, direct ICA algorithm (RADICAL)] as well as deconvolution methods [simple-to-use-interactive self-modeling mixture analysis (SIMPLISMA) and multivariate curve resolution-alternating least squares (MCR-ALS)] are applied for simultaneous (1)H NMR spectroscopic determination of organic substances in complex mixtures. Among others, we studied constituents of the following matrices: honey, soft drinks, and liquids used in electronic cigarettes. Good quality spectral resolution of up to eight-component mixtures was achieved (correlation coefficients between resolved and experimental spectra were not less than 0.90). In general, the relative errors in the recovered concentrations were below 12%. SIMPLISMA and MILCA algorithms were found to be preferable for NMR spectra deconvolution and showed similar performance. The proposed method was used for analysis of authentic samples. The resolved ICA concentrations match well with the results of reference gas chromatography-mass spectrometry as well as the MCR-ALS algorithm used for comparison. ICA deconvolution considerably improves the application range of direct NMR spectroscopy for analysis of complex mixtures. Copyright © 2014 John Wiley & Sons, Ltd.

  15. Detection of gear cracks in a complex gearbox of wind turbines using supervised bounded component analysis of vibration signals collected from multi-channel sensors

    Science.gov (United States)

    Li, Zhixiong; Yan, Xinping; Wang, Xuping; Peng, Zhongxiao

    2016-06-01

    In the complex gear transmission systems, in wind turbines a crack is one of the most common failure modes and can be fatal to the wind turbine power systems. A single sensor may suffer with issues relating to its installation position and direction, resulting in the collection of weak dynamic responses of the cracked gear. A multi-channel sensor system is hence applied in the signal acquisition and the blind source separation (BSS) technologies are employed to optimally process the information collected from multiple sensors. However, literature review finds that most of the BSS based fault detectors did not address the dependence/correlation between different moving components in the gear systems; particularly, the popular used independent component analysis (ICA) assumes mutual independence of different vibration sources. The fault detection performance may be significantly influenced by the dependence/correlation between vibration sources. In order to address this issue, this paper presents a new method based on the supervised order tracking bounded component analysis (SOTBCA) for gear crack detection in wind turbines. The bounded component analysis (BCA) is a state of art technology for dependent source separation and is applied limitedly to communication signals. To make it applicable for vibration analysis, in this work, the order tracking has been appropriately incorporated into the BCA framework to eliminate the noise and disturbance signal components. Then an autoregressive (AR) model built with prior knowledge about the crack fault is employed to supervise the reconstruction of the crack vibration source signature. The SOTBCA only outputs one source signal that has the closest distance with the AR model. Owing to the dependence tolerance ability of the BCA framework, interfering vibration sources that are dependent/correlated with the crack vibration source could be recognized by the SOTBCA, and hence, only useful fault information could be preserved in

  16. A Conserved Two-Component Signal Transduction System Controls the Response to Phosphate Starvation in Bifidobacterium breve UCC2003.

    NARCIS (Netherlands)

    Alvarez-Martin, P.; Fernandez, M.; O'Connell-Motherway, M.; O'Connell, K.J.; Sauvageot, N.; Fitzgerald, G.F.; Macsharry, J.; Zomer, A.L.; Sinderen, D. van

    2012-01-01

    This work reports on the identification and molecular characterization of the two-component regulatory system (2CRS) PhoRP, which controls the response to inorganic phosphate (P(i)) starvation in Bifidobacterium breve UCC2003. The response regulator PhoP was shown to bind to the promoter region of

  17. Expression of TGFbeta-family signalling components in ageing cartilage: age-related loss of TGFbeta and BMP receptors

    NARCIS (Netherlands)

    Caam, A.P.M. van; Madej, W.M.; Thijssen, E.; Garcia de Vinuesa, A.; Berg, W.B. van den; Goumans, M.J.; Dijke, P. Ten; Blaney Davidson, E.N.; Kraan, P.M. van der

    2016-01-01

    OBJECTIVE: Ageing is the main risk factor for osteoarthritis (OA). We investigated if expression of transforming growth factor beta (TGFbeta)-family components, a family which is crucial for the maintenance of healthy articular cartilage, is altered during ageing in cartilage. Moreover, we investiga

  18. On the solar origin of the signal at 220.7microHz: A possible component of a g mode?

    CERN Document Server

    Jiménez, A

    2009-01-01

    Gravity modes in the Sun have been the object of a long and difficult search in recent decades. Thanks to the data accumulated with the last generation of instruments (BiSON, GONG and three helioseismic instruments aboard SoHO), scientists have been able to find signatures of their presence. However, the individual detection of such modes remains evasive. In this article, we study the signal at 220.7 microHz which is a peak that is present in most of the helioseismic data of the last 10 years. This signal has already been identified as being one component of a g-mode candidate detected in the GOLF Doppler velocity signal. The nature of this peak is studied in particular using the VIRGO/SPM instrument aboard SoHO. First we analyse all the available instrumental data of VIRGO and SoHO (housekeeping) to reject any possible instrumental origin. No relation was found, implying that the signal has a solar origin. Using Monte Carlo simulations, we find, with more than 99% confidence level, that the signal found in V...

  19. miR-216a regulates snx5, a novel notch signaling pathway component, during zebrafish retinal development.

    Science.gov (United States)

    Olena, Abigail F; Rao, Mahesh B; Thatcher, Elizabeth J; Wu, Shu-Yu; Patton, James G

    2015-04-01

    Precise regulation of Notch signaling is essential for normal vertebrate development. Mind bomb (Mib) is a ubiquitin ligase that is required for activation of Notch by Notch׳s ligand, Delta. Sorting Nexin 5 (SNX5) co-localizes with Mib and Delta complexes and has been shown to directly bind to Mib. We show that microRNA-216a (miR-216a) is expressed in the retina during early development and regulates snx5 to precisely regulate Notch signaling. miR-216a and snx5 have complementary expression patterns. Knocking down miR-216a and/or overexpression of snx5 resulted in increased Notch activation. Conversely, knocking down snx5 and/or miR-216a overexpression caused a decrease in Notch activation. We propose a model in which SNX5, precisely controlled by miR-216a, is a vital partner of Mib in promoting endocytosis of Delta and subsequent activation of Notch signaling.

  20. Autoregulation of lantibiotic bovicin HJ50 biosynthesis by the BovK-BovR two-component signal transduction system in Streptococcus bovis HJ50.

    Science.gov (United States)

    Ni, Jianqiang; Teng, Kunling; Liu, Gang; Qiao, Caixia; Huan, Liandong; Zhong, Jin

    2011-01-01

    Streptococcus bovis HJ50 produces a lacticin 481-like 33-amino-acid-residue lantibiotic, designated bovicin HJ50. bovK-bovR in the bovicin HJ50 biosynthetic gene cluster is predicted to be a two-component signal transduction system involved in sensing signals and regulating gene expression. Disruption of bovK or bovR resulted in the abrogation of bovicin HJ50 production, suggesting both genes play important roles in bovicin HJ50 biosynthesis. Addition of exogenous bovicin HJ50 peptide to cultures of a bovM mutant that lost the capability for bovicin HJ50 production and structural gene bovA transcription in S. bovis HJ50 induced dose-dependent transcription of the bovA gene, demonstrating that bovicin HJ50 production was normally autoregulated. The transcription of bovA was no longer induced by bovicin HJ50 in bovK and bovR disruption mutants, suggesting that BovK-BovR plays an essential role in the signal transduction regulating bovicin HJ50 biosynthesis. A phosphorylation assay indicated that BovK has the ability to autophosphorylate and subsequently transfer the phosphoryl group to the downstream BovR protein to carry on signal transduction. Electromobility shift assays (EMSA) and green fluorescent protein (GFP) reporter gene expression assays showed the specific binding of BovR to the bovA promoter, indicating that BovR regulates bovA expression by direct binding between them. Taken together, bovicin HJ50 biosynthesis is induced by bovicin HJ50 itself and regulated via the two-component signal transduction system BovK-BovR.

  1. Single-Cell Analysis Reveals that Insulation Maintains Signaling Specificity between Two Yeast MAPK Pathways with Common Components

    OpenAIRE

    Patterson, Jesse C.; Klimenko, Evguenia S.; Thorner, Jeremy

    2010-01-01

    Eukaryotic cells use multiple mitogen-activated protein kinase (MAPK) cascades to evoke appropriate responses to external stimuli. In Saccharomyces cerevisiae, the MAPK Fus3 is activated by pheromone-binding G protein-coupled receptors to promote mating, whereas the MAPK Hog1 is activated by hyperosmotic stress to elicit the high osmolarity glycerol (HOG) response. Although these MAPK pathways share several upstream components, exposure to either pheromone or osmolyte alone triggers only the ...

  2. Searching for Potential Drug Targets in Two-component and Phosphorelay Signal-transduction Systems using Three-dimensional Cluster Analysis

    Institute of Scientific and Technical Information of China (English)

    Xiao-Hui CAI; Qing ZHANG; Shuo-Yong SHI; Da-Fu DING

    2005-01-01

    Two-component and phosphorelay signal transduction systems are central components in the virulence and antimicrobial resistance responses of a number of bacterial and fungal pathogens; in some cases, these systems are essential for bacterial growth and viability. Herein, we analyze in detail the conserved surface residue clusters in the phosphotransferase domain of histidine kinases and the regulatory domain of response regulators by using complex structure-based three-dimensional cluster analysis. We also investigatethe protein-protein interactions that these residue clusters participate in. The Spo0B-SpoOF complex structure was used as the reference structure, and the multiple aligned sequences of phosphotransferases and response regulators were paired correspondingly. The results show that a contiguous conserved residue cluster is formed around the active site, which crosses the interface of histidine kinases and response regulators. The conserved residue clusters of phosphotransferase and the regulatory domains are directly involved in the functional implementation of two-component signal transduction systems and are good targets for the development of novel antimicrobial agents.

  3. Crystal structure of the TRIM25 B30.2 (PRYSPRY) domain: a key component of antiviral signalling

    Science.gov (United States)

    D'Cruz, Akshay A.; Kershaw, Nadia J.; Chiang, Jessica J.; Wang, May K.; Nicola, Nicos A.; Babon, Jeffrey J.; Gack, Michaela U.; Nicholson, Sandra E.

    2014-01-01

    TRIM (tripartite motif) proteins primarily function as ubiquitin E3 ligases that regulate the innate immune response to infection. TRIM25 [also known as Efp (oestrogen-responsive finger protein)] has been implicated in the regulation of oestrogen receptor α signalling and in the regulation of innate immune signalling via RIG-I (retinoic acid-inducible gene-I). RIG-I senses cytosolic viral RNA and is subsequently ubiquitinated by TRIM25 at its N-terminal CARDs (caspase recruitment domains), leading to type I interferon production. The interaction with RIG-I is dependent on the TRIM25 B30.2 domain, a protein-interaction domain composed of the PRY and SPRY tandem sequence motifs. In the present study we describe the 1.8 Å crystal structure of the TRIM25 B30.2 domain, which exhibits a typical B30.2/SPRY domain fold comprising two N-terminal α-helices, thirteen β-strands arranged into two β-sheets and loop regions of varying lengths. A comparison with other B30.2/SPRY structures and an analysis of the loop regions identified a putative binding pocket, which is likely to be involved in binding target proteins. This was supported by mutagenesis and functional analyses, which identified two key residues (Asp488 and Trp621) in the TRIM25 B30.2 domain as being critical for binding to the RIG-I CARDs. PMID:24015671

  4. Identification of a second two-component signal transduction system that controls fosfomycin tolerance and glycerol-3-phosphate uptake.

    Science.gov (United States)

    Kurabayashi, Kumiko; Hirakawa, Yuko; Tanimoto, Koichi; Tomita, Haruyoshi; Hirakawa, Hidetada

    2015-03-01

    Particular interest in fosfomycin has resurfaced because it is a highly beneficial antibiotic for the treatment of refractory infectious diseases caused by pathogens that are resistant to other commonly used antibiotics. The biological cost to cells of resistance to fosfomycin because of chromosomal mutation is high. We previously found that a bacterial two-component system, CpxAR, induces fosfomycin tolerance in enterohemorrhagic Escherichia coli (EHEC) O157:H7. This mechanism does not rely on irreversible genetic modification and allows EHEC to relieve the fitness burden that results from fosfomycin resistance in the absence of fosfomycin. Here we show that another two-component system, TorSRT, which was originally characterized as a regulatory system for anaerobic respiration utilizing trimethylamine-N-oxide (TMAO), also induces fosfomycin tolerance. Activation of the Tor regulatory pathway by overexpression of torR, which encodes the response regulator, or addition of TMAO increased fosfomycin tolerance in EHEC. We also show that phosphorylated TorR directly represses the expression of glpT, a gene that encodes a symporter of fosfomycin and glycerol-3-phosphate, and activation of the TorR protein results in the reduced uptake of fosfomycin by cells. However, cells in which the Tor pathway was activated had an impaired growth phenotype when cultured with glycerol-3-phosphate as a carbon substrate. These observations suggest that the TorSRT pathway is the second two-component system to reversibly control fosfomycin tolerance and glycerol-3-phosphate uptake in EHEC, and this may be beneficial for bacteria by alleviating the biological cost. We expect that this mechanism could be a potential target to enhance the utility of fosfomycin as chemotherapy against multidrug-resistant pathogens. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  5. C. elegans EOR-1/PLZF and EOR-2 positively regulate Ras and Wnt signaling and function redundantly with LIN-25 and the SUR-2 Mediator component

    OpenAIRE

    Howard, Robyn M.; Sundaram, Meera V.

    2002-01-01

    In Caenorhabditis elegans, Ras/ERK and Wnt/β-catenin signaling pathways cooperate to induce P12 and vulval cell fates in a Hox-dependent manner. Here we describe eor-1 and eor-2, two new positively acting nuclear components of the Ras and Wnt pathways. eor-1 and eor-2 act downstream or in parallel to ERK and function redundantly with the Mediator complex gene sur-2 and the functionally related gene lin-25, such that removal of both eor-1/eor-2 and sur-2/lin-25 mimics the removal of a main Ras...

  6. ‘Forcing the issue’ - Aromatic tuning facilitates stimulus-independent modulation of a two-component signaling circuit

    DEFF Research Database (Denmark)

    Nørholm, Morten; von Heijne, Gunnar; Draheim, Roger R.

    2014-01-01

    desirable because particular physiological or developmental processes could be controlled for biotechnological purposes without the need to identify the stimulus itself. Here, we demonstrate that aromatic tuning, i.e., repositioning the aromatic residues commonly found at the cytoplasmic end of the receptor...... receptors were not locked in a single conformation. We also noted that circuits containing aromatically tuned variants became more sensitive to changes in the receptor concentration than their wild-type counterpart, suggesting a new way to study mechanisms underpinning receptor concentration......-dependent robustness. We believe that aromatic tuning has several advantages compared to previous methods aimed at stimulus-independent modulation of receptors and that it will be generally applicable to a wide-range of two-component circuits....

  7. NUC-2, a component of the phosphate-regulated signal transduction pathway in Neurospora crassa, is an ankyrin repeat protein.

    Science.gov (United States)

    Poleg, Y; Aramayo, R; Kang, S; Hall, J G; Metzenberg, R L

    1996-10-28

    In response to phosphorus limitation, the fungus Neurospora crassa synthesizes a number of enzymes that function to bring more phosphate into the cell. The NUC-2 protein appears to sense the availability of phosphate and transmits the signal downstream to the regulatory pathway. The nuc-2+ gene has been cloned by its ability to restore growth of a nuc-2 mutant under restrictive conditions of high pH and low phosphate concentration. We mapped the cloned gene to the right arm of linkage group II, consistent with the chromosomal position of the nuc-2 mutation as determined by classical genetic mapping. The nuc-2' open reading frame is interrupted by five introns and codes for a protein of 1066 amino acid residues. Its predicted amino acid sequence has high similarity to that of its homolog in Saccharomyces cerevisiae, PHO81. Both proteins contain six ankyrin repeats, which have been implicated in the cyclin-dependent kinase inhibitory activity of PHO81. The phenotypes of a nuc-2 mutant generated by repeat-induced point mutation and of a strain harboring a UV-induced nuc-2 allele are indistinguishable. Both are unable to grow under the restrictive conditions, a phenotype which is to some degree temperature dependent. The nuc-2+ gene is transcriptionally regulated. A 15-fold increase in the level of the nuc-2+ transcript occurs in response to a decrease in exogenous phosphate concentration.

  8. A conserved two-component signal transduction system controls the response to phosphate starvation in Bifidobacterium breve UCC2003.

    Science.gov (United States)

    Alvarez-Martin, Pablo; Fernández, Matilde; O'Connell-Motherway, Mary; O'Connell, Kerry Joan; Sauvageot, Nicolas; Fitzgerald, Gerald F; MacSharry, John; Zomer, Aldert; van Sinderen, Douwe

    2012-08-01

    This work reports on the identification and molecular characterization of the two-component regulatory system (2CRS) PhoRP, which controls the response to inorganic phosphate (P(i)) starvation in Bifidobacterium breve UCC2003. The response regulator PhoP was shown to bind to the promoter region of pstSCAB, specifying a predicted P(i) transporter system, as well as that of phoU, which encodes a putative P(i)-responsive regulatory protein. This interaction is assumed to cause transcriptional modulation under conditions of P(i) limitation. Our data suggest that the phoRP genes are subject to positive autoregulation and, together with pstSCAB and presumably phoU, represent the complete regulon controlled by the phoRP-encoded 2CRS in B. breve UCC2003. Determination of the minimal PhoP binding region combined with bioinformatic analysis revealed the probable recognition sequence of PhoP, designated here as the PHO box, which together with phoRP is conserved among many high-GC-content Gram-positive bacteria. The importance of the phoRP 2CRS in the response of B. breve to P(i) starvation conditions was confirmed by analysis of a B. breve phoP insertion mutant which exhibited decreased growth under phosphate-limiting conditions compared to its parent strain UCC2003.

  9. Evidence for the Induction of Key Components of the NOTCH Signaling Pathway via Deltamethrin and Azamethiphos Treatment in the Sea Louse Caligus rogercresseyi

    Directory of Open Access Journals (Sweden)

    Sebastian Boltaña

    2016-05-01

    Full Text Available The extensive use of organophosphates and pyrethroids in the aquaculture industry has negatively impacted parasite sensitivity to the delousing effects of these antiparasitics, especially among sea lice species. The NOTCH signaling pathway is a positive regulator of ABC transporter subfamily C expression and plays a key role in the generation and modulation of pesticide resistance. However, little is known about the molecular mechanisms behind pesticide resistance, partly due to the lack of genomic and molecular information on the processes involved in the resistance mechanism of sea lice. Next-generation sequencing technologies provide an opportunity for rapid and cost-effective generation of genome-scale data. The present study, through RNA-seq analysis, determined that the sea louse Caligus rogercresseyi (C. rogercresseyi specifically responds to the delousing drugs azamethiphos and deltamethrin at the transcriptomic level by differentially activating mRNA of the NOTCH signaling pathway and of ABC genes. These results suggest that frequent antiparasitic application may increase the activity of inhibitory mRNA components, thereby promoting inhibitory NOTCH output and conditions for increased resistance to delousing drugs. Moreover, data analysis underscored that key functions of NOTCH/ABC components were regulated during distinct phases of the drug response, thus indicating resistance modifications in C. rogercresseyi resulting from the frequent use of organophosphates and pyrethroids.

  10. Phosphoproteomic analysis of protein kinase C signaling in Saccharomyces cerevisiae reveals Slt2 mitogen-activated protein kinase (MAPK)-dependent phosphorylation of eisosome core components.

    Science.gov (United States)

    Mascaraque, Victoria; Hernáez, María Luisa; Jiménez-Sánchez, María; Hansen, Rasmus; Gil, Concha; Martín, Humberto; Cid, Víctor J; Molina, María

    2013-03-01

    The cell wall integrity (CWI) pathway of the model organism Saccharomyces cerevisiae has been thoroughly studied as a paradigm of the mitogen-activated protein kinase (MAPK) pathway. It consists of a classic MAPK module comprising the Bck1 MAPK kinase kinase, two redundant MAPK kinases (Mkk1 and Mkk2), and the Slt2 MAPK. This module is activated under a variety of stimuli related to cell wall homeostasis by Pkc1, the only member of the protein kinase C family in budding yeast. Quantitative phosphoproteomics based on stable isotope labeling of amino acids in cell culture is a powerful tool for globally studying protein phosphorylation. Here we report an analysis of the yeast phosphoproteome upon overexpression of a PKC1 hyperactive allele that specifically activates CWI MAPK signaling in the absence of external stimuli. We found 82 phosphopeptides originating from 43 proteins that showed enhanced phosphorylation in these conditions. The MAPK S/T-P target motif was significantly overrepresented in these phosphopeptides. Hyperphosphorylated proteins provide putative novel targets of the Pkc1-cell wall integrity pathway involved in diverse functions such as the control of gene expression, protein synthesis, cytoskeleton maintenance, DNA repair, and metabolism. Remarkably, five components of the plasma-membrane-associated protein complex known as eisosomes were found among the up-regulated proteins. We show here that Pkc1-induced phosphorylation of the eisosome core components Pil1 and Lsp1 was not exerted directly by Pkc1, but involved signaling through the Slt2 MAPK module.

  11. Gene expression analysis of rice seedling under potassium deprivation reveals major changes in metabolism and signaling components.

    Directory of Open Access Journals (Sweden)

    Alka Shankar

    Full Text Available Plant nutrition is one of the important areas for improving the yield and quality in crops as well as non-crop plants. Potassium is an essential plant nutrient and is required in abundance for their proper growth and development. Potassium deficiency directly affects the plant growth and hence crop yield and production. Recently, potassium-dependent transcriptomic analysis has been performed in the model plant Arabidopsis, however in cereals and crop plants; such a transcriptome analysis has not been undertaken till date. In rice, the molecular mechanism for the regulation of potassium starvation responses has not been investigated in detail. Here, we present a combined physiological and whole genome transcriptomic study of rice seedlings exposed to a brief period of potassium deficiency then replenished with potassium. Our results reveal that the expressions of a diverse set of genes annotated with many distinct functions were altered under potassium deprivation. Our findings highlight altered expression patterns of potassium-responsive genes majorly involved in metabolic processes, stress responses, signaling pathways, transcriptional regulation, and transport of multiple molecules including K(+. Interestingly, several genes responsive to low-potassium conditions show a reversal in expression upon resupply of potassium. The results of this study indicate that potassium deprivation leads to activation of multiple genes and gene networks, which may be acting in concert to sense the external potassium and mediate uptake, distribution and ultimately adaptation to low potassium conditions. The interplay of both upregulated and downregulated genes globally in response to potassium deprivation determines how plants cope with the stress of nutrient deficiency at different physiological as well as developmental stages of plants.

  12. Genome-wide survey of two-component signal transduction systems in the plant growth-promoting bacterium Azospirillum.

    Science.gov (United States)

    Borland, Stéphanie; Oudart, Anne; Prigent-Combaret, Claire; Brochier-Armanet, Céline; Wisniewski-Dyé, Florence

    2015-10-22

    Two-component systems (TCS) play critical roles in sensing and responding to environmental cues. Azospirillum is a plant growth-promoting rhizobacterium living in the rhizosphere of many important crops. Despite numerous studies about its plant beneficial properties, little is known about how the bacterium senses and responds to its rhizospheric environment. The availability of complete genome sequenced from four Azospirillum strains (A. brasilense Sp245 and CBG 497, A. lipoferum 4B and Azospirillum sp. B510) offers the opportunity to conduct a comprehensive comparative analysis of the TCS gene family. Azospirillum genomes harbour a very large number of genes encoding TCS, and are especially enriched in hybrid histidine kinases (HyHK) genes compared to other plant-associated bacteria of similar genome sizes. We gained further insight into HyHK structure and architecture, revealing an intriguing complexity of these systems. An unusual proportion of TCS genes were orphaned or in complex clusters, and a high proportion of predicted soluble HKs compared to other plant-associated bacteria are reported. Phylogenetic analyses of the transmitter and receiver domains of A. lipoferum 4B HyHK indicate that expansion of this family mainly arose through horizontal gene transfer but also through gene duplications all along the diversification of the Azospirillum genus. By performing a genome-wide comparison of TCS, we unraveled important 'genus-defining' and 'plant-specifying' TCS. This study shed light on Azospirillum TCS which may confer important regulatory flexibility. Collectively, these findings highlight that Azospirillum genomes have broad potential for adaptation to fluctuating environments.

  13. Electrical Excitation of the Pulmonary Venous Musculature May Contribute to the Formation of the Last Component of the High Frequency Signal of the P Wave

    Directory of Open Access Journals (Sweden)

    Junko Abe, MD

    2005-01-01

    Full Text Available Pulmonary veins (PVs have been shown to play an important role in the induction and perpetuation of focal AF. Fifty-one patients with AF, and 24 patients without AF as control subjects, were enrolled in this study. Signal-averaged P-wave recording was performed, and the filtered P wave duration (FPD, the root-mean-square voltage for the last 20, 30 and 40 ms (RMS20, 30, and 40, respectively were compared. In 7 patients with AF, these parameters were compared before and after the catheter ablation. The FPD was significantly longer and the RMS20 was smaller in the patients with AF than those without AF. Because RMS30 was widely distributed between 2 and 10 µV, the AF group was sub-divided into two groups; Group 1 was comprised of the patients with an RMS30 ≧5.0 µV, and group 2, <5.0 µV. In group 1, short-coupled PACs were more frequently documented on Holter monitoring, and exercise testing more readily induced AF. After successful electrical disconnection between the LA and PVs, each micropotential parameter was significantly attenuated. These results indicate that the high frequency signal amplitude of the last component of the P wave is relatively high in patients with AF triggered by focal repetitive excitations most likely originating from the PVs. That is, attenuation by the LA-PV electrical isolation, and thus the high frequency P signals of the last component, may contain the electrical excitation of the PV musculature.

  14. Identification of putative insulin-like peptides and components of insulin signaling pathways in parasitic platyhelminths by the use of genome-wide screening.

    Science.gov (United States)

    Wang, Shuai; Luo, Xuenong; Zhang, Shaohua; Yin, Cai; Dou, Yongxi; Cai, Xuepeng

    2014-02-01

    No endogenous insulin-like peptides in parasitic flatworms have been reported. Insulin receptors from flukes and tapeworms have been shown to interact directly with the host-derived insulin molecule, which suggests the exploitation of host-derived insulin. In this study, a strategy of genome-wide searches followed by comprehensive analyses of strictly conserved features of the insulin family was used to demonstrate the presence of putative insulin-like peptides in the genomes of six tapeworms and two flukes. In addition, whole insulin signaling pathways were annotated on a genome-wide scale. Two putative insulin-like peptide genes in each genome of tapeworms and one insulin-like peptide gene in each genome of flukes were identified. The comprehensive analyses revealed that all of these peptides showed the common features shared by other members of the insulin family, and the phylogenetic analysis implied a putative gene duplication event in the Cestoda during the evolution of insulin-like peptide genes. The quantitative expression analysis and immunolocalization results suggested a putative role of these peptides in reproduction. Entire sets of major components of the classic insulin signaling pathway were successfully identified, suggesting that this pathway in parasitic flatworms might also regulate many other important biological activities. We believe that the identification of the insulin-like peptides gives us a better understanding of the insulin signaling pathway in these parasites, as well as host-parasite interactions.

  15. Comparative analysis of the Spirulina platensis subcellular proteome in response to low- and high-temperature stresses: uncovering cross-talk of signaling components

    Science.gov (United States)

    2011-01-01

    The present study focused on comparative proteome analyses of low- and high-temperature stresses and potential protein-protein interaction networks, constructed by using a bioinformatics approach, in response to both stress conditions. The data revealed two important points: first, the results indicate that low-temperature stress is tightly linked with oxidative stress as well as photosynthesis; however, no specific mechanism is revealed in the case of the high-temperature stress response. Second, temperature stress was revealed to be linked with nitrogen and ammonia assimilation. Moreover, the data also highlighted the cross-talk of signaling pathways. Some of the detected signaling proteins, e.g., Hik14, Hik26 and Hik28, have potential interactions with differentially expressed proteins identified in both temperature stress conditions. Some differentially expressed proteins found in the Spirulina protein-protein interaction network were also examined for their physical interactions by a yeast two hybrid system (Y2H). The Y2H results obtained in this study suggests that the potential PPI network gives quite reliable potential interactions for Spirulina. Therefore, the bioinformatics approach employed in this study helps in the analysis of phenomena where proteome analyses of knockout mutants have not been carried out to directly examine for specificity or cross-talk of signaling components. PMID:21756373

  16. Comparative analysis of the Spirulina platensis subcellular proteome in response to low- and high-temperature stresses: uncovering cross-talk of signaling components

    Directory of Open Access Journals (Sweden)

    Roytrakul Sittiruk

    2011-07-01

    Full Text Available Abstract The present study focused on comparative proteome analyses of low- and high-temperature stresses and potential protein-protein interaction networks, constructed by using a bioinformatics approach, in response to both stress conditions. The data revealed two important points: first, the results indicate that low-temperature stress is tightly linked with oxidative stress as well as photosynthesis; however, no specific mechanism is revealed in the case of the high-temperature stress response. Second, temperature stress was revealed to be linked with nitrogen and ammonia assimilation. Moreover, the data also highlighted the cross-talk of signaling pathways. Some of the detected signaling proteins, e.g., Hik14, Hik26 and Hik28, have potential interactions with differentially expressed proteins identified in both temperature stress conditions. Some differentially expressed proteins found in the Spirulina protein-protein interaction network were also examined for their physical interactions by a yeast two hybrid system (Y2H. The Y2H results obtained in this study suggests that the potential PPI network gives quite reliable potential interactions for Spirulina. Therefore, the bioinformatics approach employed in this study helps in the analysis of phenomena where proteome analyses of knockout mutants have not been carried out to directly examine for specificity or cross-talk of signaling components.

  17. The disease resistance signaling components EDS1 and PAD4 are essential regulators of the cell death pathway controlled by LSD1 in Arabidopsis.

    Science.gov (United States)

    Rustérucci, C; Aviv, D H; Holt, B F; Dangl, J L; Parker, J E

    2001-10-01

    Specific recognition of pathogens is mediated by plant disease resistance (R) genes and translated into a successful defense response. The extent of associated hypersensitive cell death varies from none to an area encompassing cells surrounding an infection site, depending on the R gene activated. We constructed double mutants in Arabidopsis between positive regulators of R function and a negative regulator of cell death, LSD1, to address whether genes required for normal R function also regulate the runaway cell death observed in lsd1 mutants. We report here that EDS1 and PAD4, two signaling genes that mediate some but not all R responses, also are required for runaway cell death in the lsd1 mutant. Importantly, this novel function of EDS1 and PAD4 is operative when runaway cell death in lsd1 is initiated through an R gene that does not require EDS1 or PAD4 for disease resistance. NDR1, another component of R signaling, also contributes to the control of plant cell death. The roles of EDS1 and PAD4 in regulating lsd1 runaway cell death are related to the interpretation of reactive oxygen intermediate-derived signals at infection sites. We further demonstrate that the fate of superoxide at infection sites is different from that observed at the leading margins of runaway cell death lesions in lsd1 mutants.

  18. MAP4K3 is a component of the TORC1 signalling complex that modulates cell growth and viability in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Martín Resnik-Docampo

    Full Text Available BACKGROUND: MAP4K3 is a conserved Ser/Thr kinase that has being found in connection with several signalling pathways, including the Imd, EGFR, TORC1 and JNK modules, in different organisms and experimental assays. We have analyzed the consequences of changing the levels of MAP4K3 expression in the development of the Drosophila wing, a convenient model system to characterize gene function during epithelial development. METHODOLOGY AND PRINCIPAL FINDINGS: Using loss-of-function mutants and over-expression conditions we find that MAP4K3 activity affects cell growth and viability in the Drosophila wing. These requirements are related to the modulation of the TORC1 and JNK signalling pathways, and are best detected when the larvae grow in a medium with low protein concentration (TORC1 or are exposed to irradiation (JNK. We also show that MAP4K3 display strong genetic interactions with different components of the InR/Tor signalling pathway, and can interact directly with the GTPases RagA and RagC and with the multi-domain kinase Tor. CONCLUSIONS AND SIGNIFICANCE: We suggest that MAP4K3 has two independent functions during wing development, one related to the activation of the JNK pathway in response to stress and other in the assembling or activation of the TORC1 complex, being critical to modulate cellular responses to changes in nutrient availability.

  19. Proteomic mapping of stimulus-specific signaling pathways involved in THP-1 cells exposed to Porphyromonas gingivalis or its purified components.

    Science.gov (United States)

    Saba, Julian A; McComb, Mark E; Potts, Donna L; Costello, Catherine E; Amar, Salomon

    2007-06-01

    Periodontitis is an inflammatory disease initiated by host-parasite interactions which contributes to connective tissue destruction and alveolar bone resorption. Porphyromonas gingivalis (P.g.), a black-pigmented Gram-negative anaerobic bacterium, is a major pathogen in the development and progression of periodontitis. To characterize the role that P. gingivalis and its cell surface components play in disease processes, we investigated the differential expression of proteins induced by live P.g., P.g. LPS, and P.g. FimA, using two-dimensional gel electrophoresis in combination with mass spectrometry. We have tested whether, at the level of protein expression, unique signaling pathways are differentially induced by the bacterial components P.g. LPS and P.g. FimA, as compared to live P.g. We found that P.g. LPS stimulation of THP-1 up-regulated the expression of a set of proteins compared to control: deoxyribonuclease, actin, carbonic anhydrase 2, alpha enolase, adenylyl cyclase-associated protein (CAP1), protein disulfide isomerase (PDI), glucose regulated protein (grp78), and 70-kDa heat shock protein (HSP70), whereas FimA treatment did not result in statistically significant changes to protein levels versus the control. Live P.g. stimulation resulted in 12 differentially expressed proteins: CAP1, tubulin beta-2 chain, ATP synthase beta chain, tubulin alpha-6 chain, PDI, vimentin, 60-kDa heat shock protein, and nucleolin were found to be up-regulated, while carbonic anhydrase II, beta-actin, and HSP70 were down-regulated relative to control. These differential changes by the bacteria and its components are interpreted as preferential signal pathway activation in host immune/inflammatory responses to P.g. infection.

  20. A review of 1α,25(OH)2D3 dependent Pdia3 receptor complex components in Wnt5a non-canonical pathway signaling.

    Science.gov (United States)

    Doroudi, Maryam; Olivares-Navarrete, Rene; Boyan, Barbara D; Schwartz, Zvi

    2015-08-01

    Wnt5a and 1α,25-dihydroxyvitamin D3 [1α,25(OH)2D3] regulate endochondral ossification. 1α,25(OH)2D3 initiates its calcium-dependent effects via its membrane-associated receptor, protein disulfide isomerase A3 (Pdia3). 1α,25(OH)2D3 binding to Pdia3 triggers the interaction between Pdia3 and phospholipase A2 (PLA2)-activating protein (PLAA), resulting in downstream activation of calcium/calmodulin-dependent protein kinase II (CaMKII), PLA2, and protein kinase C (PKC). Wnt5a initiates its calcium-dependent effects via binding its receptors Frizzled2 (FZD2) and Frizzled5 (FZD5) and receptor tyrosine kinase-like orphan receptor 2 (ROR2), activating intracellular calcium release and stimulating PKC and CaMKII. Recent efforts to determine the inter-relation between Wnt5a and 1α,25(OH)2D3 signaling pathways have demonstrated that Wnt5a signals through a CaMKII/PLA2/PGE2/PKC cascade in chondrocytes and osteoblasts in which the components of the Pdia3 receptor complex were required. Furthermore, ROR2, but not FZD2 or FZD5, was required to mediate the calcium-dependent actions of 1α,25(OH)2D3. This review provides evidence that 1α,25(OH)2D3 and Wnt5a mediate their calcium-dependent pathways via similar receptor components and proposes that these pathways may interact since they are competing for the same receptor complex components.

  1. Histone Deacetylase 2 Is a Component of Influenza A Virus-Induced Host Antiviral Response

    Directory of Open Access Journals (Sweden)

    Prashanth T. Nagesh

    2017-07-01

    Full Text Available Host cells produce variety of antiviral factors that create an antiviral state and target various stages of influenza A virus (IAV life cycle to inhibit infection. However, IAV has evolved various strategies to antagonize those antiviral factors. Recently, we reported that a member of class I host histone deacetylases (HDACs, HDAC1 possesses an anti-IAV function. Herein, we provide evidence that HDAC2, another class I member and closely related to HDAC1 in structure and function, also possesses anti-IAV properties. In turn, IAV, like HDAC1, dysregulates HDAC2, mainly at the polypeptide level through proteasomal degradation to potentially minimize its antiviral effect. We found that IAV downregulated the HDAC2 polypeptide level in A549 cells in an H1N1 strain-independent manner by up to 47%, which was recovered to almost 100% level in the presence of proteasome-inhibitor MG132. A further knockdown in HDAC2 expression by up to 90% via RNA interference augmented the growth kinetics of IAV in A549 cells by more than four-fold after 24 h of infection. Furthermore, the knockdown of HDAC2 expression decreased the IAV-induced phosphorylation of the transcription factor, Signal Transducer and Activator of Transcription I (STAT1 and the expression of interferon-stimulated gene, viperin in infected cells by 41 and 53%, respectively. The role of HDAC2 in viperin expression was analogous to that of HDAC1, but it was not in the phosphorylation of STAT1. This indicated that, like HDAC1, HDAC2 is a component of IAV-induced host innate antiviral response and performs both redundant and non-redundant functions vis-a-vis HDAC1; however, IAV dysregulates them both in a redundant manner.

  2. Identification of potential genetic components involved in the deviant quorum-sensing signaling pathways of Burkholderia glumae through a functional genomics approach

    Directory of Open Access Journals (Sweden)

    Ruoxi eChen

    2015-03-01

    Full Text Available Burkholderia glumae is the chief causal agent for bacterial panicle blight of rice. The acyl-homoserine lactone (AHL-mediated quorum-sensing (QS system dependent on a pair of luxI and luxR homologs, tofI and tofR, is the primary cell-to-cell signaling mechanism determining the virulence of this bacterium. Production of toxoflavin, a major virulence factor of B. glumae, is known to be dependent on the tofI/tofR QS system. In our previous study, however, it was observed that B. glumae mutants defective in tofI or tofR produced toxoflavin if they grew on the surface of a solid medium, suggesting that alternative signaling pathways independent of tofI or tofR are activated in that growth condition for the production of toxoflavin. In this study, potential genetic components involved in the tofI- and tofR-independent signaling pathways for toxoflavin production were sought through screening random mini-Tn5 mutants of B. glumae to better understand the intercellular signaling pathways of this pathogen. Fifteen and three genes were initially identified as the potential genetic elements of the tofI- and tofR-independent pathways, respectively. Especially, the ORF (bglu_2g06320 divergently transcribed from toxJ, which encodes an orphan LuxR protein and controls toxoflavin biosynthesis, was newly identified in this study as a gene required for the tofR-independent toxoflavin production and named as toxK. Among those genes, flhD, dgcB, and wyzB were further studied to validate their functions in the tofI-independent toxoflavin production, and similar studies were also conducted with qsmR and toxK for their functions in the tofR-independent toxoflavin production. This work provides a foundation for future comprehensive studies of the intercellular signaling systems of B. glumae and other related pathogenic bacteria.

  3. Salinity-induced inhibition of growth in the aquatic pteridophyte Azolla microphylla primarily involves inhibition of photosynthetic components and signaling molecules as revealed by proteome analysis.

    Science.gov (United States)

    Thagela, Preeti; Yadav, Ravindra Kumar; Mishra, Vagish; Dahuja, Anil; Ahmad, Altaf; Singh, Pawan Kumar; Tiwari, Budhi Sagar; Abraham, Gerard

    2017-01-01

    Salinity stress causes adverse physiological and biochemical changes in the growth and productivity of a plant. Azolla, a symbiotic pteridophyte and potent candidate for biofertilizer due to its nitrogen fixation ability, shows reduced growth and nitrogen fixation during saline stress. To better understand regulatory components involved in salinity-induced physiological changes, in the present study, Azolla microphylla plants were exposed to NaCl (6.74 and 8.61 ds/m) and growth, photochemical reactions of photosynthesis, ion accumulation, and changes in cellular proteome were studied. Maximum dry weight was accumulated in control and untreated plant while a substantial decrease in dry weight was observed in the plants exposed to salinity. Exposure of the organism to different concentrations of salt in hydroponic conditions resulted in differential level of Na(+) and K(+) ion accumulation. Comparative analysis of salinity-induced proteome changes in A. microphylla revealed 58 salt responsive proteins which were differentially expressed during the salt exposure. Moreover, 42 % spots among differentially expressed proteins were involved in different signaling events. The identified proteins are involved in photosynthesis, energy metabolism, amino acid biosynthesis, protein synthesis, and defense. Downregulation of these key metabolic proteins appears to inhibit the growth of A. microphylla in response to salinity. Altogether, the study revealed that in Azolla, increased salinity primarily affected signaling and photosynthesis that in turn leads to reduced biomass.

  4. 一种基于PCA的MPSK信号码元速率估计方法%Symbol rate estimation method of MPSK signals using principal component analysis

    Institute of Scientific and Technical Information of China (English)

    王蒙; 汪伟; 于宏毅; 胡赟鹏

    2013-01-01

    Aiming at the symbol rate estimation of MPSK signals,this paper investigated the phenomenon that the peak features of cyclic spectrum were corrupted by colored background noise in the case of limited data,and proposed a symbol rate estimation algorithm which combined principal component analysis with cyclic spectrum.PCA transformation restrained the colored background noise in the cyclic spectrum,improved estimation precision,and decreased estimation variance.Simulation result shows that the algorithm acquires fine estimation precision under limited data,and is suitable for MPSK signals with distinct shaped filter coefficients.%针对MPSK信号的码元速率估计问题,研究了有限数据条件下循环谱的谱线特征受到背景色噪声干扰的现象,提出了一种基于主分量分析(PCA)的循环谱特征码元速率估计方法.PCA变换抑制了信号循环谱中的背景色噪声,提高了估计精度,减小了估计方差.仿真表明,该方法在有限数据条件下具有良好的估计性能,适用于不同成形滤波系数的MPSK信号.

  5. Clinical significance of both tumor and stromal expression of components of the IL-1 and TNF-α signaling pathways in prostate cancer.

    Science.gov (United States)

    Rodríguez-Berriguete, Gonzalo; Sánchez-Espiridión, Beatriz; Cansino, José R; Olmedilla, Gabriel; Martínez-Onsurbe, Pilar; Sánchez-Chapado, Manuel; Paniagua, Ricardo; Fraile, Benito; Royuela, Mar

    2013-11-01

    IL-1 and TNF-α, the two major proinflammatory cytokines, have been involved in initiation and progression of several malignancies. They could influence the biological behavior of prostatic tumors and patient outcome, and could be useful as prognostic factors. This study evaluated the prognostic capability for biochemical progression after radical prostatectomy of expression of IL-1, TNF-α and related signaling components, in the tumor and surrounding stroma, as well as its correlation with other clinicopathological features. Expression of IL-1α, IL-1β, IL-1Ra, IL-1RI, IL-1RII, IRAK-1, TRAF6, TNF-α, TNFRI and TRAF2 was analyzed by immunohistochemistry in radical prostatectomy samples from 93 prostate cancer patients. Spearman's test, Kaplan-Meier curves, and univariate and multivariate Cox proportional hazard regression analyses were performed. Expression of TNF-α, TNFRI, TRAF2, ILRI, IRAK-1 and TRAF6 correlated with at least one clinicopathological feature (clinical T stage, pathological T stage, preoperative serum PSA or Gleason score). Increased tumor expression of TNF-α, TNFRI and IL-1RI, and reduced tumor expression of IRAK-1 were significantly correlated with a poor prognosis in univariate analysis. Reduced stromal expression of IL-1β and IL-1RII, and increased stromal expression of IRAK-1 were also adverse prognostic factors in univariate analysis. Remarkably, tumor IL-1β and stromal IL-1RII and IRAK-1 remained as independent prognostic factors after adjustment for preoperative serum PSA, pathological T stage and Gleason score in multivariate Cox models. Our results suggest that prostatic expression of TNF-α, IL-1β and related signaling proteins (TNFRI, IL-1RI, IL-1RII and IRAK-1) predicts clinical outcome in prostate cancer, and support the involvement of TNF-α and IL-1β signaling in prostate cancer progression.

  6. The Arabidopsis KH-Domain RNA-Binding Protein ESR1 Functions in Components of Jasmonate Signalling, Unlinking Growth Restraint and Resistance to Stress.

    Directory of Open Access Journals (Sweden)

    Louise F Thatcher

    Full Text Available Glutathione S-transferases (GSTs play important roles in the protection of cells against toxins and oxidative damage where one Arabidopsis member, GSTF8, has become a commonly used marker gene for early stress and defense responses. A GSTF8 promoter fragment fused to the luciferase reporter gene was used in a forward genetic screen for Arabidopsis mutants with up-regulated GSTF8 promoter activity. This identified the esr1-1 (enhanced stress response 1 mutant which also conferred increased resistance to the fungal pathogen Fusarium oxysporum. Through positional cloning, the ESR1 gene was found to encode a KH-domain containing RNA-binding protein (At5g53060. Whole transcriptome sequencing of esr1-1 identified altered expression of genes involved in responses to biotic and abiotic stimuli, hormone signaling pathways and developmental processes. In particular was an overall significant enrichment for jasmonic acid (JA mediated processes in the esr1-1 down-regulated dataset. A subset of these genes were tested for MeJA inducibility and we found the expression of some but not all were reduced in esr1-1. The esr1-1 mutant was not impaired in other aspects of JA-signalling such as JA- sensitivity or development, suggesting ESR1 functions in specific components of the JA-signaling pathway. Examination of salicylic acid (SA regulated marker genes in esr1-1 showed no increase in basal or SA induced expression suggesting repression of JA-regulated genes is not due to antagonistic SA-JA crosstalk. These results define new roles for KH-domain containing proteins with ESR1 unlinking JA-mediated growth and defense responses.

  7. Conjugal transfer of the Sinorhizobium meliloti 1021 symbiotic plasmid is governed through the concerted action of one- and two-component signal transduction regulators.

    Science.gov (United States)

    Nogales, Joaquina; Blanca-Ordóñez, Helena; Olivares, José; Sanjuán, Juan

    2013-03-01

    Conjugal transfer of Sinorhizobium meliloti and Rhizobium etli symbiotic plasmids are repressed by the transcriptional regulator RctA. Here we report on new key players in the signal transduction cascade towards S. meliloti pSym conjugation. We have identified S. meliloti pSymA gene SMa0974 as an orthologue of the R. etli rctB gene which is required to antagonize repression by RctA. In S. meliloti two additional genes, rctR and rctC participate in control of rctB expression. rctR (SMa0955) encodes a protein of the GntR family of transcriptional regulators involved in repression of rctB. A rctR mutant promotes pSymA conjugal transfer and displays increased transcription of tra, virB and rctB genes even in presence of wild-type rctA gene. Among genes repressed by RctR, rctC (SMa0961) encodes a response regulator required to activate rctB transcription and therefore for derepression of plasmid conjugative functions. We conclude that in both R. etli and S. meliloti pSym conjugal transfer is derepressed via rctB, however the regulatory cascades to achieve activation of rctB are probably different. Upstream of rctB, the S. meliloti pSym conjugal transfer is regulated through the concerted action of genes representing one- (rctR) and two-component (rctC) signal transduction systems in response to yet unidentified signals.

  8. Systems level analysis of two-component signal transduction systems in Erwinia amylovora: Role in virulence, regulation of amylovoran biosynthesis and swarming motility

    Directory of Open Access Journals (Sweden)

    Sundin George W

    2009-05-01

    Full Text Available Abstract Background Two-component signal transduction systems (TCSTs, consisting of a histidine kinase (HK and a response regulator (RR, represent a major paradigm for signal transduction in prokaryotes. TCSTs play critical roles in sensing and responding to environmental conditions, and in bacterial pathogenesis. Most TCSTs in Erwinia amylovora have either not been identified or have not yet been studied. Results We used a systems approach to identify TCST and related signal transduction genes in the genome of E. amylovora. Comparative genomic analysis of TCSTs indicated that E. amylovora TCSTs were closely related to those of Erwinia tasmaniensis, a saprophytic enterobacterium isolated from apple flowers, and to other enterobacteria. Forty-six TCST genes in E. amylovora including 17 sensor kinases, three hybrid kinases, 20 DNA- or ligand-binding RRs, four RRs with enzymatic output domain (EAL-GGDEF proteins, and two kinases were characterized in this study. A systematic TCST gene-knockout experiment was conducted, generating a total of 59 single-, double-, and triple-mutants. Virulence assays revealed that five of these mutants were non-pathogenic on immature pear fruits. Results from phenotypic characterization and gene expression experiments indicated that several groups of TCST systems in E. amylovora control amylovoran biosynthesis, one of two major virulence factors in E. amylovora. Both negative and positive regulators of amylovoran biosynthesis were identified, indicating a complex network may control this important feature of pathogenesis. Positive (non-motile, EnvZ/OmpR, negative (hypermotile, GrrS/GrrA, and intermediate regulators for swarming motility in E. amylovora were also identified. Conclusion Our results demonstrated that TCSTs in E. amylovora played major roles in virulence on immature pear fruit and in regulating amylovoran biosynthesis and swarming motility. This suggested presence of regulatory networks governing

  9. Systems level analysis of two-component signal transduction systems in Erwinia amylovora: role in virulence, regulation of amylovoran biosynthesis and swarming motility.

    Science.gov (United States)

    Zhao, Youfu; Wang, Dongping; Nakka, Sridevi; Sundin, George W; Korban, Schuyler S

    2009-05-26

    Two-component signal transduction systems (TCSTs), consisting of a histidine kinase (HK) and a response regulator (RR), represent a major paradigm for signal transduction in prokaryotes. TCSTs play critical roles in sensing and responding to environmental conditions, and in bacterial pathogenesis. Most TCSTs in Erwinia amylovora have either not been identified or have not yet been studied. We used a systems approach to identify TCST and related signal transduction genes in the genome of E. amylovora. Comparative genomic analysis of TCSTs indicated that E. amylovora TCSTs were closely related to those of Erwinia tasmaniensis, a saprophytic enterobacterium isolated from apple flowers, and to other enterobacteria. Forty-six TCST genes in E. amylovora including 17 sensor kinases, three hybrid kinases, 20 DNA- or ligand-binding RRs, four RRs with enzymatic output domain (EAL-GGDEF proteins), and two kinases were characterized in this study. A systematic TCST gene-knockout experiment was conducted, generating a total of 59 single-, double-, and triple-mutants. Virulence assays revealed that five of these mutants were non-pathogenic on immature pear fruits. Results from phenotypic characterization and gene expression experiments indicated that several groups of TCST systems in E. amylovora control amylovoran biosynthesis, one of two major virulence factors in E. amylovora. Both negative and positive regulators of amylovoran biosynthesis were identified, indicating a complex network may control this important feature of pathogenesis. Positive (non-motile, EnvZ/OmpR), negative (hypermotile, GrrS/GrrA), and intermediate regulators for swarming motility in E. amylovora were also identified. Our results demonstrated that TCSTs in E. amylovora played major roles in virulence on immature pear fruit and in regulating amylovoran biosynthesis and swarming motility. This suggested presence of regulatory networks governing expression of critical virulence genes in E. amylovora.

  10. Equation-free analysis of two-component system signalling model reveals the emergence of co-existing phenotypes in the absence of multistationarity.

    Directory of Open Access Journals (Sweden)

    Rebecca B Hoyle

    Full Text Available Phenotypic differences of genetically identical cells under the same environmental conditions have been attributed to the inherent stochasticity of biochemical processes. Various mechanisms have been suggested, including the existence of alternative steady states in regulatory networks that are reached by means of stochastic fluctuations, long transient excursions from a stable state to an unstable excited state, and the switching on and off of a reaction network according to the availability of a constituent chemical species. Here we analyse a detailed stochastic kinetic model of two-component system signalling in bacteria, and show that alternative phenotypes emerge in the absence of these features. We perform a bifurcation analysis of deterministic reaction rate equations derived from the model, and find that they cannot reproduce the whole range of qualitative responses to external signals demonstrated by direct stochastic simulations. In particular, the mixed mode, where stochastic switching and a graded response are seen simultaneously, is absent. However, probabilistic and equation-free analyses of the stochastic model that calculate stationary states for the mean of an ensemble of stochastic trajectories reveal that slow transcription of either response regulator or histidine kinase leads to the coexistence of an approximate basal solution and a graded response that combine to produce the mixed mode, thus establishing its essential stochastic nature. The same techniques also show that stochasticity results in the observation of an all-or-none bistable response over a much wider range of external signals than would be expected on deterministic grounds. Thus we demonstrate the application of numerical equation-free methods to a detailed biochemical reaction network model, and show that it can provide new insight into the role of stochasticity in the emergence of phenotypic diversity.

  11. Active Components with Inhibitory Activities on IFN-γ/STAT1 and IL-6/STAT3 Signaling Pathways from Caulis Trachelospermi

    Directory of Open Access Journals (Sweden)

    Xiao-Ting Liu

    2014-08-01

    Full Text Available Initial investigation for new active herbal extract with inhibiting activity on JAK/STAT signaling pathway revealed that the extract of Caulis Trachelospermi, which was separated by 80% alcohol extraction and subsequent HP-20 macroporous resin column chromatography, was founded to strongly inhibit IFN-γ-induced STAT1-responsive luciferase activity (IFN-γ/STAT1 with IC50 value of 2.43 μg/mL as well as inhibiting IL-6-induced STAT3-responsive luciferase activity (IL-6/STAT3 with IC50 value of 1.38 μg/mL. Subsequent study on its active components led to the isolation and identification of two new dibenzylbutyrolactone lignans named 4-demethyltraxillaside (1 and nortrachelogenin 4-O-β-d-glucopyranoside (2, together with six known compounds. The lignan compounds 1–4 together with other lignan compounds isolated in previous study were tested the activities on IFN-γ/STAT1 and IL-6/STAT3 pathways. The following result showed that the main components trachelogenin and arctigenin had corresponding activities on IFN-γ/STAT1 pathway with IC50 values of 3.14 μM and 9.46 μM as well as trachelogenin, arctigenin and matairesinol strongly inhibiting IL-6/STAT3 pathway with IC50 values of 3.63 μM, 6.47 μM and 2.92 μM, respectively.

  12. Design and implementation of an SVM-based computer classification system for discriminating depressive patients from healthy controls using the P600 component of ERP signals.

    Science.gov (United States)

    Kalatzis, I; Piliouras, N; Ventouras, E; Papageorgiou, C C; Rabavilas, A D; Cavouras, D

    2004-07-01

    A computer-based classification system has been designed capable of distinguishing patients with depression from normal controls by event-related potential (ERP) signals using the P600 component. Clinical material comprised 25 patients with depression and an equal number of gender and aged-matched healthy controls. All subjects were evaluated by a computerized version of the digit span Wechsler test. EEG activity was recorded and digitized from 15 scalp electrodes (leads). Seventeen features related to the shape of the waveform were generated and were employed in the design of an optimum support vector machine (SVM) classifier at each lead. The outcomes of those SVM classifiers were selected by a majority-vote engine (MVE), which assigned each subject to either the normal or depressive classes. MVE classification accuracy was 94% when using all leads and 92% or 82% when using only the right or left scalp leads, respectively. These findings support the hypothesis that depression is associated with dysfunction of right hemisphere mechanisms mediating the processing of information that assigns a specific response to a specific stimulus, as those mechanisms are reflected by the P600 component of ERPs. Our method may aid the further understanding of the neurophysiology underlying depression, due to its potentiality to integrate theories of depression and psychophysiology.

  13. Response curves of the surface modules of the Pierre Auger Observatory and the contribution of the hadronic component to the total signal of extensive showers

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, Marcio Ap.; Chinellato, J.A. [Universidade Estadual de Campinas (UNICAMP), SP (Brazil). Inst. de Fisica

    2011-07-01

    Full text: At large distances from the shower's core, is generally said that the electromagnetic and muonic components are responsible for most of the signal detected and the contribution of hadrons is irrelevant. In fact, looking at the events generated by the simulations of showers, we see an average number of hadrons which is small compared to other components. On the other hand, the important factor to be considered is the fraction of energy they carry. Geant4 full simulations of shower particles interacting in the surface module are very time consuming. To overcome this difficulty, we produced a set of response curves that can replace the corresponding full simulations. To include albedo phenomena, we include a soil layer as a new target for hadronic interactions, with the detailed treatment of hadron interactions available in Geant4 tool kit. The response curves for each particle type were obtained with full runs of Geant4 in the new setup. We will present this parametrization, which reduce the processing time by factors larger than 1000 times. These response curves were implemented in the tool kit Offline, developed by the collaboration to simulate/reconstruct the development of air showers. The Geant4 class corresponding to the surface module was replaced by our parametrization, while the rest of the simulation chain remained unchanged. The main focus of this work are the interactions of the hadronic component, in the tank and in the soil target below the tank. Those were obtained with the new setup and compared to the results from the original version of Offline. To assess the contribution of hadrons, we also studied the contribution of other components under the same conditions, so we can to obtain always the effect of hadronic interactions compared with the other components. We make a comparison between the energy reconstructed by the original Offline (with no changes) and the Offline with the implementation of our parameterization. We can infer the

  14. Development and validation of a high-throughput cell-based screen to identify activators of a bacterial two-component signal transduction system.

    Science.gov (United States)

    van Rensburg, Julia J; Fortney, Kate R; Chen, Lan; Krieger, Andrew J; Lima, Bruno P; Wolfe, Alan J; Katz, Barry P; Zhang, Zhong-Yin; Spinola, Stanley M

    2015-07-01

    CpxRA is a two-component signal transduction system (2CSTS) found in many drug-resistant Gram-negative bacteria. In response to periplasmic stress, CpxA autophosphorylates and donates a phosphoryl group to its cognate response regulator, CpxR. Phosphorylated CpxR (CpxR-P) upregulates genes involved in membrane repair and downregulates multiple genes that encode virulence factors, which are trafficked across the cell membrane. Mutants that constitutively activate CpxRA in Salmonella enterica serovar Typhimurium and Haemophilus ducreyi are avirulent in mice and humans, respectively. Thus, the activation of CpxRA has high potential as a novel antimicrobial/antivirulence strategy. Using a series of Escherichia coli strains containing a CpxR-P-responsive lacZ reporter and deletions in genes encoding CpxRA system components, we developed and validated a novel cell-based high-throughput screen (HTS) for CpxRA activators. A screen of 36,000 compounds yielded one hit compound that increased reporter activity in wild-type cells. This is the first report of a compound that activates, rather than inhibits, a 2CSTS. The activity profile of the compound against CpxRA pathway mutants in the presence of glucose suggested that the compound inhibits CpxA phosphatase activity. We confirmed that the compound induced the accumulation of CpxR-P in treated cells. Although the hit compound contained a nitro group, a derivative lacking this group retained activity in serum and had lower cytotoxicity than that of the initial hit. This HTS is amenable for the screening of larger libraries to find compounds that activate CpxRA by other mechanisms, and it could be adapted to find activators of other two-component systems.

  15. A new three-component signal model to objectively select power Doppler wall filter cut-off velocity for quantitative microvascular imaging

    Science.gov (United States)

    Elfarnawany, Mai; Lacefield, James C.

    2013-03-01

    The wall-filter selection curve (WFSC) method was developed to automatically select cut-off velocities for high-frequency power Doppler imaging. Selection curves are constructed by plotting color pixel density (CPD) as a function of wall filter cut-off velocity. A new three-component mathematical model is developed to guide the design of an online implementation of the method for in vivo imaging. The model treats Doppler imaging as a signal detection task in which the scanner must distinguish intravascular pixels from perivascular and extravascular pixels and includes a cost function to identify the optimum cut-off velocity that provides accurate vascular quantification and minimizes the effect of color pixel artifacts on visualization of vascular structures. The goodness of fit of the three-component model to flow-phantom data is significantly improved compared to a previous two-component model (F test, p new model indicate that selection curves should be sampled using at least 100 cut-off velocities to ensure robust performance of the automated WFSC method and determine an upper bound on CPD variability that ensures reliable vascular quantification accuracy, defined as CPD within 5% of the reference vascular volume fraction. Results of the simulations also provide evidence that limiting the selection of the cut-off velocity to a binary choice between the middle and right end of the characteristic interval is sufficient to meet the quantification accuracy goal. The model provides an intuitive, empirical description of the relationship between system settings and blood-flow detection performance in power Doppler imaging.

  16. Perturbation of the two-component signal transduction system, BprRS, results in attenuated virulence and motility defects in Burkholderia pseudomallei.

    Science.gov (United States)

    Lazar Adler, Natalie R; Allwood, Elizabeth M; Deveson Lucas, Deanna; Harrison, Paul; Watts, Stephen; Dimitropoulos, Alexandra; Treerat, Puthayalai; Alwis, Priyangi; Devenish, Rodney J; Prescott, Mark; Govan, Brenda; Adler, Ben; Harper, Marina; Boyce, John D

    2016-05-04

    Burkholderia pseudomallei is the causative agent of melioidosis, a severe invasive disease of humans and animals. Initial screening of a B. pseudomallei signature-tagged mutagenesis library identified an attenuated mutant with a transposon insertion in a gene encoding the sensor component of an uncharacterised two-component signal transduction system (TCSTS), which we designated BprRS. Single gene inactivation of either the response regulator gene (bprR) or the sensor histidine kinase gene (bprS) resulted in mutants with reduced swarming motility and reduced virulence in mice. However, a bprRS double mutant was not attenuated for virulence and displayed wild-type levels of motility. The transcriptomes of the bprS, bprR and bprRS mutants were compared with the transcriptome of the parent strain K96243. Inactivation of the entire BprRS TCSTS (bprRS double mutant) resulted in altered expression of only nine genes, including both bprR and bprS, five phage-related genes and bpss0686, encoding a putative 5, 10-methylene tetrahydromethanopterin reductase involved in one carbon metabolism. In contrast, the transcriptomes of each of the bprR and bprS single gene mutants revealed more than 70 differentially expressed genes common to both mutants, including regulatory genes and those required for flagella assembly and for the biosynthesis of the cytotoxic polyketide, malleilactone. Inactivation of the entire BprRS TCSTS did not alter virulence or motility and very few genes were differentially expressed indicating that the definitive BprRS regulon is relatively small. However, loss of a single component, either the sensor histidine kinase BprS or its cognate response regulator BprR, resulted in significant transcriptomic and phenotypic differences from the wild-type strain. We hypothesize that the dramatically altered phenotypes of these single mutants are the result of cross-regulation with one or more other TCSTSs and concomitant dysregulation of other key regulatory genes.

  17. The Meckel syndrome- associated protein MKS1 functionally interacts with components of the BBSome and IFT complexes to mediate ciliary trafficking and hedgehog signaling

    Science.gov (United States)

    Barrington, Chloe L.; Katsanis, Nicholas

    2017-01-01

    The importance of primary cilia in human health is underscored by the link between ciliary dysfunction and a group of primarily recessive genetic disorders with overlapping clinical features, now known as ciliopathies. Many of the proteins encoded by ciliopathy-associated genes are components of a handful of multi-protein complexes important for the transport of cargo to the basal body and/or into the cilium. A key question is whether different complexes cooperate in cilia formation, and whether they participate in cilium assembly in conjunction with intraflagellar transport (IFT) proteins. To examine how ciliopathy protein complexes might function together, we have analyzed double mutants of an allele of the Meckel syndrome (MKS) complex protein MKS1 and the BBSome protein BBS4. We find that Mks1; Bbs4 double mutant mouse embryos exhibit exacerbated defects in Hedgehog (Hh) dependent patterning compared to either single mutant, and die by E14.5. Cells from double mutant embryos exhibit a defect in the trafficking of ARL13B, a ciliary membrane protein, resulting in disrupted ciliary structure and signaling. We also examined the relationship between the MKS complex and IFT proteins by analyzing double mutant between Mks1 and a hypomorphic allele of the IFTB component Ift172. Despite each single mutant surviving until around birth, Mks1; Ift172avc1 double mutants die at mid-gestation, and exhibit a dramatic failure of cilia formation. We also find that Mks1 interacts genetically with an allele of Dync2h1, the IFT retrograde motor. Thus, we have demonstrated that the MKS transition zone complex cooperates with the BBSome to mediate trafficking of specific trans-membrane receptors to the cilium. Moreover, the genetic interaction of Mks1 with components of IFT machinery suggests that the transition zone complex facilitates IFT to promote cilium assembly and structure. PMID:28291807

  18. The Hybrid Histidine Kinase LadS Forms a Multicomponent Signal Transduction System with the GacS/GacA Two-Component System in Pseudomonas aeruginosa

    Science.gov (United States)

    Redelberger, David; Fadel, Firas; Filloux, Alain; Sivaneson, Melissa; de Bentzmann, Sophie; Bordi, Christophe

    2016-01-01

    In response to environmental changes, Pseudomonas aeruginosa is able to switch from a planktonic (free swimming) to a sessile (biofilm) lifestyle. The two-component system (TCS) GacS/GacA activates the production of two small non-coding RNAs, RsmY and RsmZ, but four histidine kinases (HKs), RetS, GacS, LadS and PA1611, are instrumental in this process. RetS hybrid HK blocks GacS unorthodox HK autophosphorylation through the formation of a heterodimer. PA1611 hybrid HK, which is structurally related to GacS, interacts with RetS in P. aeruginosa in a very similar manner to GacS. LadS hybrid HK phenotypically antagonizes the function of RetS by a mechanism that has never been investigated. The four sensors are found in most Pseudomonas species but their characteristics and mode of signaling may differ from one species to another. Here, we demonstrated in P. aeruginosa that LadS controls both rsmY and rsmZ gene expression and that this regulation occurs through the GacS/GacA TCS. We additionally evidenced that in contrast to RetS, LadS signals through GacS/GacA without forming heterodimers, either with GacS or with RetS. Instead, we demonstrated that LadS is involved in a genuine phosphorelay, which requires both transmitter and receiver LadS domains. LadS signaling ultimately requires the alternative histidine-phosphotransfer domain of GacS, which is here used as an Hpt relay by the hybrid kinase. LadS HK thus forms, with the GacS/GacA TCS, a multicomponent signal transduction system with an original phosphorelay cascade, i.e. H1LadS→D1LadS→H2GacS→D2GacA. This highlights an original strategy in which a unique output, i.e. the modulation of sRNA levels, is controlled by a complex multi-sensing network to fine-tune an adapted biofilm and virulence response. PMID:27176226

  19. The Hybrid Histidine Kinase LadS Forms a Multicomponent Signal Transduction System with the GacS/GacA Two-Component System in Pseudomonas aeruginosa.

    Directory of Open Access Journals (Sweden)

    Gaël Chambonnier

    2016-05-01

    Full Text Available In response to environmental changes, Pseudomonas aeruginosa is able to switch from a planktonic (free swimming to a sessile (biofilm lifestyle. The two-component system (TCS GacS/GacA activates the production of two small non-coding RNAs, RsmY and RsmZ, but four histidine kinases (HKs, RetS, GacS, LadS and PA1611, are instrumental in this process. RetS hybrid HK blocks GacS unorthodox HK autophosphorylation through the formation of a heterodimer. PA1611 hybrid HK, which is structurally related to GacS, interacts with RetS in P. aeruginosa in a very similar manner to GacS. LadS hybrid HK phenotypically antagonizes the function of RetS by a mechanism that has never been investigated. The four sensors are found in most Pseudomonas species but their characteristics and mode of signaling may differ from one species to another. Here, we demonstrated in P. aeruginosa that LadS controls both rsmY and rsmZ gene expression and that this regulation occurs through the GacS/GacA TCS. We additionally evidenced that in contrast to RetS, LadS signals through GacS/GacA without forming heterodimers, either with GacS or with RetS. Instead, we demonstrated that LadS is involved in a genuine phosphorelay, which requires both transmitter and receiver LadS domains. LadS signaling ultimately requires the alternative histidine-phosphotransfer domain of GacS, which is here used as an Hpt relay by the hybrid kinase. LadS HK thus forms, with the GacS/GacA TCS, a multicomponent signal transduction system with an original phosphorelay cascade, i.e. H1LadS→D1LadS→H2GacS→D2GacA. This highlights an original strategy in which a unique output, i.e. the modulation of sRNA levels, is controlled by a complex multi-sensing network to fine-tune an adapted biofilm and virulence response.

  20. The Hybrid Histidine Kinase LadS Forms a Multicomponent Signal Transduction System with the GacS/GacA Two-Component System in Pseudomonas aeruginosa.

    Science.gov (United States)

    Chambonnier, Gaël; Roux, Lorène; Redelberger, David; Fadel, Firas; Filloux, Alain; Sivaneson, Melissa; de Bentzmann, Sophie; Bordi, Christophe

    2016-05-01

    In response to environmental changes, Pseudomonas aeruginosa is able to switch from a planktonic (free swimming) to a sessile (biofilm) lifestyle. The two-component system (TCS) GacS/GacA activates the production of two small non-coding RNAs, RsmY and RsmZ, but four histidine kinases (HKs), RetS, GacS, LadS and PA1611, are instrumental in this process. RetS hybrid HK blocks GacS unorthodox HK autophosphorylation through the formation of a heterodimer. PA1611 hybrid HK, which is structurally related to GacS, interacts with RetS in P. aeruginosa in a very similar manner to GacS. LadS hybrid HK phenotypically antagonizes the function of RetS by a mechanism that has never been investigated. The four sensors are found in most Pseudomonas species but their characteristics and mode of signaling may differ from one species to another. Here, we demonstrated in P. aeruginosa that LadS controls both rsmY and rsmZ gene expression and that this regulation occurs through the GacS/GacA TCS. We additionally evidenced that in contrast to RetS, LadS signals through GacS/GacA without forming heterodimers, either with GacS or with RetS. Instead, we demonstrated that LadS is involved in a genuine phosphorelay, which requires both transmitter and receiver LadS domains. LadS signaling ultimately requires the alternative histidine-phosphotransfer domain of GacS, which is here used as an Hpt relay by the hybrid kinase. LadS HK thus forms, with the GacS/GacA TCS, a multicomponent signal transduction system with an original phosphorelay cascade, i.e. H1LadS→D1LadS→H2GacS→D2GacA. This highlights an original strategy in which a unique output, i.e. the modulation of sRNA levels, is controlled by a complex multi-sensing network to fine-tune an adapted biofilm and virulence response.

  1. Functional characterization of the histidine kinase of the E. coli two-component signal transduction system AtoS-AtoC.

    Science.gov (United States)

    Filippou, Panagiota S; Kasemian, Lucy D; Panagiotidis, Christos A; Kyriakidis, Dimitrios A

    2008-09-01

    The Escherichia coli AtoS-AtoC two-component signal transduction system regulates the expression of the atoDAEB operon genes, whose products are required for short-chain fatty acid catabolism. In this study purified his-tagged wild-type and mutant AtoS proteins were used to prove that these proteins are true sensor kinases. The phosphorylated residue was identified as the histidine-398, which was located in a conserved Eta-box since AtoS carrying a mutation at this site failed to phosphorylate. This inability to phosphorylate was not due to gross structural alterations of AtoS since the H398L mutant retained its capability to bind ATP. Furthermore, the H398L mutant AtoS was competent to catalyze the trans-phosphorylation of an AtoS G-box (G565A) mutant protein which otherwise failed to autophosphorylate due to its inability to bind ATP. The formation of homodimers between the various AtoS proteins was also shown by cross-linking experiments both in vitro and in vivo.

  2. OmpR, a response regulator of the two-component signal transduction pathway, influences inv gene expression in Yersinia enterocolitica O9

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    Marta eBrzóstkowska

    2012-12-01

    Full Text Available The environmental control of invasin expression in Yersinia enterocolitica is mediated by a regulatory network composed of negative and positive regulators of inv gene transcription. Previously, we demonstrated that OmpR, a response regulator of the two-component signal transduction pathway EnvZ/OmpR, negatively regulates invasin gene expression in Y. enterocolitica O9 by direct interaction with the inv promoter region. This study was undertaken to clarify the role of OmpR in the inv regulatory circuit in which RovA protein has been shown to positively regulate inv transcription. Using ompR, rovA and ompR rovA Y. enterocolitica mutant backgrounds we showed that the inhibitory effect of OmpR on inv transcription may be observed only when RovA is present/active in Y. enterocolitica cells. To extend our research on inv regulation we examined the effect of OmpR on rovA gene expression. Analysis of rovA-lacZ transcriptional fusion in Y. enterocolitica wild-type and ompR background indicated that OmpR does not influence rovA expression. Thus, our results indicate that OmpR influences invasin expression directly via binding to the inv promoter, but not through modulation of rovA expression.

  3. Crosstalk of two-component signal transduction systems in regulating central carbohydrate and energy metabolism during autotrophic and photomixotrophic growth of Synechocystis sp. PCC 6803.

    Science.gov (United States)

    Pei, Guangsheng; Niu, Xiangfeng; Zhou, Yuqing; Chen, Lei; Zhang, Weiwen

    2017-05-22

    Unicellular model cyanobacterium Synechocystis sp. PCC 6803 has received considerable attention as a sustainable energy resource because of its photosynthetic machinery. However, two-component signal transduction systems (TCSTSs) in regulating central carbohydrate and energy metabolism of cyanobacteria are still poorly understood due to their diversity and functional complication. In this study, by comparing the growth of knockout mutants of 44 response regulators (RRs) of TCSTSs in Synechocystis, several RR mutants demonstrating differential growth patterns were identified under auto- or photomixotrophic conditions. However, in spite of no growth difference observed for the remaining RR mutants, liquid chromatography-mass spectrometry based metabolomic profile analysis showed that a widespread crosstalk of TCSTSs in regulating central carbohydrate and energy metabolism of Synechocystis was identified, while most of them showed diverse patterns during different trophic types or growth stages. Furthermore, an integrative analysis between evolutionary relationships and metabolomic profiles revealed some pairs of paralogous RRs with highly functional convergence, suggesting the possible conserved functions of Synechocystis TCSTSs during evolution. This study laid an important basis for understanding the function of TCSTSs in photosynthetic cyanobacteria.

  4. OmpR, a response regulator of the two-component signal transduction pathway, influences inv gene expression in Yersinia enterocolitica O9.

    Science.gov (United States)

    Brzóstkowska, Marta; Raczkowska, Adrianna; Brzostek, Katarzyna

    2012-01-01

    The environmental control of invasin (inv) expression in Yersinia enterocolitica is mediated by a regulatory network composed of negative and positive regulators of inv gene transcription. Previously, we demonstrated that OmpR, a response regulator of the two-component signal transduction pathway EnvZ/OmpR, negatively regulates inv gene expression in Y. enterocolitica O9 by direct interaction with the inv promoter region. This study was undertaken to clarify the role of OmpR in the inv regulatory circuit in which RovA protein has been shown to positively regulate inv transcription. Using ompR, rovA, and ompR rovA Y. enterocolitica mutant backgrounds we showed that the inhibitory effect of OmpR on inv transcription may be observed only when RovA is present/active in Y. enterocolitica cells. To extend our research on inv regulation we examined the effect of OmpR on rovA gene expression. Analysis of rovA-lacZ transcriptional fusion in Y. enterocolitica wild-type and ompR background indicated that OmpR does not influence rovA expression. Thus, our results indicate that OmpR influences inv expression directly via binding to the inv promoter, but not through modulation of rovA expression.

  5. Two-component signal transduction system CBO0787/CBO0786 represses transcription from botulinum neurotoxin promoters in Clostridium botulinum ATCC 3502.

    Science.gov (United States)

    Zhang, Zhen; Korkeala, Hannu; Dahlsten, Elias; Sahala, Elina; Heap, John T; Minton, Nigel P; Lindström, Miia

    2013-03-01

    Blocking neurotransmission, botulinum neurotoxin is the most poisonous biological substance known to mankind. Despite its infamy as the scourge of the food industry, the neurotoxin is increasingly used as a pharmaceutical to treat an expanding range of muscle disorders. Whilst neurotoxin expression by the spore-forming bacterium Clostridium botulinum appears tightly regulated, to date only positive regulatory elements, such as the alternative sigma factor BotR, have been implicated in this control. The identification of negative regulators has proven to be elusive. Here, we show that the two-component signal transduction system CBO0787/CBO0786 negatively regulates botulinum neurotoxin expression. Single insertional inactivation of cbo0787 encoding a sensor histidine kinase, or of cbo0786 encoding a response regulator, resulted in significantly elevated neurotoxin gene expression levels and increased neurotoxin production. Recombinant CBO0786 regulator was shown to bind to the conserved -10 site of the core promoters of the ha and ntnh-botA operons, which encode the toxin structural and accessory proteins. Increasing concentration of CBO0786 inhibited BotR-directed transcription from the ha and ntnh-botA promoters, demonstrating direct transcriptional repression of the ha and ntnh-botA operons by CBO0786. Thus, we propose that CBO0786 represses neurotoxin gene expression by blocking BotR-directed transcription from the neurotoxin promoters. This is the first evidence of a negative regulator controlling botulinum neurotoxin production. Understanding the neurotoxin regulatory mechanisms is a major target of the food and pharmaceutical industries alike.

  6. Crystallization and preliminary crystallographic analysis of Arabidopsis thaliana EDS1, a key component of plant immunity, in complex with its signalling partner SAG101.

    Science.gov (United States)

    Wagner, Stephan; Rietz, Steffen; Parker, Jane E; Niefind, Karsten

    2011-02-01

    In plants, the nucleocytoplasmic protein EDS1 (Enhanced disease susceptibility1) is an important regulator of innate immunity, coordinating host-cell defence and cell-death programs in response to pathogen attack. Arabidopsis thaliana EDS1 stabilizes and signals together with its partners PAD4 (Phytoalexin deficient4) and SAG101 (Senescence-associated gene101). Characterization of EDS1 molecular configurations in vitro and in vivo points to the formation of structurally and spatially distinct EDS1 homomeric dimers and EDS1 heteromeric complexes with either PAD4 or SAG101 as necessary components of the immune response. EDS1, PAD4 and SAG101 constitute a plant-specific protein family with a unique `EP' (EDS1-PAD4-specific) domain at their C-termini and an N-terminal domain resembling enzymes with an α/β-hydrolase fold. Here, the expression, purification and crystallization of a functional EDS1 complex formed by EDS1 and SAG101 from Arabidopsis thaliana are reported. The crystals belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 101.8, b = 115.9, c = 122.8 Å, and diffracted to 3.5 Å resolution.

  7. Evolutionary gradient of predicted nuclear localization signals (NLS)-bearing proteins in genomes of family Planctomycetaceae.

    Science.gov (United States)

    Guo, Min; Yang, Ruifu; Huang, Chen; Liao, Qiwen; Fan, Guangyi; Sun, Chenghang; Lee, Simon Ming-Yuen

    2017-04-04

    The nuclear envelope is considered a key classification marker that distinguishes prokaryotes from eukaryotes. However, this marker does not apply to the family Planctomycetaceae, which has intracellular spaces divided by lipidic intracytoplasmic membranes (ICMs). Nuclear localization signal (NLS), a short stretch of amino acid sequence, destines to transport proteins from cytoplasm into nucleus, and is also associated with the development of nuclear envelope. We attempted to investigate the NLS motifs in Planctomycetaceae genomes to demonstrate the potential molecular transition in the development of intracellular membrane system. In this study, we identified NLS-like motifs that have the same amino acid compositions as experimentally identified NLSs in genomes of 11 representative species of family Planctomycetaceae. A total of 15 NLS types and 170 NLS-bearing proteins were detected in the 11 strains. To determine the molecular transformation, we compared NLS-bearing protein abundances in the 11 representative Planctomycetaceae genomes with them in genomes of 16 taxonomically varied microorganisms: nine bacteria, two archaea and five fungi. In the 27 strains, 29 NLS types and 1101 NLS-bearing proteins were identified, principal component analysis showed a significant transitional gradient from bacteria to Planctomycetaceae to fungi on their NLS-bearing protein abundance profiles. Then, we clustered the 993 non-redundant NLS-bearing proteins into 181 families and annotated their involved metabolic pathways. Afterwards, we aligned the ten types of NLS motifs from the 13 families containing NLS-bearing proteins among bacteria, Planctomycetaceae or fungi, considering their diversity, length and origin. A transition towards increased complexity from non-planctomycete bacteria to Planctomycetaceae to archaea and fungi was detected based on the complexity of the 10 types of NLS-like motifs in the 13 NLS-bearing proteins families. The results of this study reveal that

  8. Role of the two component signal transduction system CpxAR in conferring cefepime and chloramphenicol resistance in Klebsiella pneumoniae NTUH-K2044.

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    Vijaya Bharathi Srinivasan

    Full Text Available BACKGROUND: Klebsiella pneumoniae is a gram-negative, non-motile, facultative anaerobe belonging to the Enterobacteriaceae family of the γ-Proteobacteria class in the phylum Proteobacteria. Multidrug resistant K. pneumoniae have caused major therapeutic problems worldwide due to emergence of extended-spectrum β-lactamase producing strains. Two-component systems serve as a basic stimulus-response coupling mechanism to allow organisms to sense and respond to changes in many different environmental conditions including antibiotic stress. PRINCIPAL FINDINGS: In the present study, we investigated the role of an uncharacterized cpxAR operon in bacterial physiology and antimicrobial resistance by generating isogenic mutant (ΔcpxAR deficient in the CpxA/CpxR component derived from the hyper mucoidal K1 strain K. pneumoniae NTUH-K2044. The behaviour of ΔcpxAR was determined under hostile conditions, reproducing stresses encountered in the gastrointestinal environment and deletion resulted in higher sensitivity to bile, osmotic and acid stresses. The ΔcpxAR was more susceptible to β-lactams and chloramphenicol than the wild-type strain, and complementation restored the altered phenotypes. The relative change in expression of acrB, acrD, eefB efflux genes were decreased in cpxAR mutant as evidenced by qRT-PCR. Comparison of outer membrane protein profiles indicated a conspicuous difference in the knock out background. Gel shift assays demonstrated direct binding of CpxR(KP to promoter region of ompC(KP in a concentration dependent manner. CONCLUSIONS AND SIGNIFICANCE: The Cpx envelope stress response system is known to be activated by alterations in pH, membrane composition and misfolded proteins, and this systematic investigation reveals its direct involvement in conferring antimicrobial resistance against clinically significant antibiotics for the very first time. Overall results displayed in this report reflect the pleiotropic role of the Cpx

  9. A model for peak and width of signaling windows: Ips duplicatus and Chilo partellus pheromone component proportions--does response have a wider window than production?

    Science.gov (United States)

    Schlyter, F; Svensson, M; Zhang, Q H; Knízek, M; Krokene, P; Ivarsson, P; Birgersson, G

    2001-07-01

    Pheromone communication systems have a reliable signal with a restricted window of amounts and ratios released and perceived. We propose a model based on a Gaussian response profile that allows a quantification of the response peak (location of optimum) and a measure of the peak width (response window). Interpreting the Gaussian curve, fitted by nonlinear regression (NLR), as a standard normal distribution, the peak location equals the mean (it) and the window width equals 2 x the standard deviation (2sigma). The NLR procedure can provide an objective measure for both peak location and width for a wide range of data sets. Four empirical data sets as well as 10 literature data sets were analyzed. The double-spined spruce engraver, Ips duplicatus, was field tested in four populations to find the optimum proportion for attraction to the two male aggregation pheromone components, ipsdienol (Id) and (E)-myrcenol(EM), ranging from 0 to 100% of Id. Tests in Norway and the Czech Republic confirmed the preference of western populations for a blend between 50 and 90% Id. A population in Inner Mongolia showed a preference for traps with the 10 and 50% Id baits. The NLR fitted values for response peak and width (mu; 2sigma) were: Norway 0.64, 0.73; Czech Republic 0.53, 0.73; NE China 0.77, 0.29; and Inner Mongolia 0.33, 0.50. The signal produced by Norwegian field-collected males had a narrower window width (2sigma = 0.12). Males of the maize stem borer, Chilo partellus, were tested in a flight tunnel for their response to variation in the two major female sex pheromone gland components, (Z)- l1-hexadecenal and the corresponding alcohol (OH). Variation of the alcohol in seven levels from 2 to 29% OH showed the highest male response for 17% OH. For all behavioral steps, the peak of male response was near mu = 0.14, while the window width fell from 2sigma = 0.5 to 0.2 for eight sequential behavioral steps from take-off to copulation. Female production had a similar peak location

  10. The essential yhcSR two-component signal transduction system directly regulates the lac and opuCABCD operons of Staphylococcus aureus.

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    Meiying Yan

    Full Text Available Our previous studies suggested that the essential two-component signal transduction system, YhcSR, regulates the opuCABCD operon at the transcriptional level, and the Pspac-driven opuCABCD partially complements the lethal effects of yhcS antisense RNA expression in Staphylococcus aureus. However, the reason why yhcSR regulon is required for growth is still unclear. In this report, we present that the lac and opuC operons are directly transcriptionally regulated by YhcSR. Using real-time RT-PCR we showed that the down-regulation of yhcSR expression affected the transcription of lacA encoding galactose-6-phosphotase isomerase subunit LacA, and opuCA encoding a subunit of a glycine betaine/carnitine/choline ABC transporter. Promoter-lux reporter fusion studies further confirmed the transcriptional regulation of lac by YhcSR. Gel shift assays revealed that YhcR binds to the promoter regions of the lac and opuC operons. Moreover, the Pspac-driven lacABC expression in trans was able to partially complement the lethal effect of induced yhcS antisense RNA. Likewise, the Pspac-driven opuCABCD expression in trans complemented the growth defect of S. aureus in a high osmotic strength medium during the depletion of YhcSR. Taken together, the above data indicate that the yhcSR system directly regulates the expression of lac and opuC operons, which, in turn, may be partially associated with the essentiality of yhcSR in S. aureus. These results provide a new insight into the biological functions of the yhcSR, a global regulator.

  11. The two-component signal transduction system ArlRS regulates Staphylococcus epidermidis biofilm formation in an ica-dependent manner.

    Directory of Open Access Journals (Sweden)

    Yang Wu

    Full Text Available Due to its ability to form biofilms on medical devices, Staphylococcus epidermidis has emerged as a major pathogen of nosocomial infections. In this study, we investigated the role of the two-component signal transduction system ArlRS in regulating S. epidermidis biofilm formation. An ArlRS-deficient mutant, WW06, was constructed using S. epidermidis strain 1457 as a parental strain. Although the growth curve of WW06 was similar to that of SE1457, the mutant strain was unable to form biofilms in vitro. In a rabbit subcutaneous infection model, sterile disks made of polymeric materials were implanted subcutaneously followed with inoculation of WW06 or SE1457. The viable bacteria cells of WW06 recovered from biofilms on the embedded disks were much lower than that of SE1457. Complementation of arlRS genes expression from plasmid in WW06 restored biofilm-forming phenotype both in vivo and in vitro. WW06 maintained the ability to undergo initial attachment. Transcription levels of several genes involved in biofilm formation, including icaADBC, sigB, and sarA, were decreased in WW06, compared to SE1457; and icaR expression was increased in WW06, detected by real-time reverse-transcription PCR. The biofilm-forming phenotype was restored by overexpressing icaADBC in WW06 but not by overexpressing sigB, indicating that ArlRS regulates biofilm formation through the regulation of icaADBC. Gel shift assay showed that ArlR can bind to the promoter region of the ica operon. In conclusion, ArlRS regulates S. epidermidis biofilm formation in an ica-dependent manner, distinct from its role in S. aureus.

  12. Expression and maintenance of ComD-ComE, the two-component signal-transduction system that controls competence of Streptococcus pneumoniae.

    Science.gov (United States)

    Martin, Bernard; Granadel, Chantal; Campo, Nathalie; Hénard, Vincent; Prudhomme, Marc; Claverys, Jean-Pierre

    2010-03-01

    A secreted competence-stimulating peptide (CSP), encoded by comC, constitutes, together with the two-component system ComD-ComE, the master switch for competence induction in Streptococcus pneumoniae. Interaction between CSP and its membrane-bound histidine-kinase receptor, ComD, is believed to lead to autophosphorylation of ComD, which then transphosphorylates the ComE response regulator to activate transcription of a limited set of genes, including the comCDE operon. This generates a positive feedback loop, amplifying the signal and co-ordinating competence throughout the population. On the other hand, the promoter(s) and proteins important for basal comCDE expression have not been defined. We now report that CSP-induced and basal comCDE transcription both initiate from the same promoter, P(E); that basal expression necessitates the presence of both ComD and a phosphate-accepting form of ComE, but not CSP; and that overexpression of ComE(R120S) triggers ComD-dependent transformation in the absence of CSP. These observations suggest that self-activation of ComD is required for basal comCDE expression. We also establish that transcriptional readthrough occurs across the tRNA(Arg5) terminator and contributes significantly to comCDE expression. Finally, we demonstrate by various means, including single-cell competence analysis with GFP, that readthrough is crucial to avoid the stochastic production of CSP non-responsive cells lacking ComD or ComE.

  13. The two-component signal transduction system ArlRS regulates Staphylococcus epidermidis biofilm formation in an ica-dependent manner.

    Science.gov (United States)

    Wu, Yang; Wang, Jiaxue; Xu, Tao; Liu, Jingran; Yu, Wenqi; Lou, Qiang; Zhu, Tao; He, Nianan; Ben, Haijing; Hu, Jian; Götz, Friedrich; Qu, Di

    2012-01-01

    Due to its ability to form biofilms on medical devices, Staphylococcus epidermidis has emerged as a major pathogen of nosocomial infections. In this study, we investigated the role of the two-component signal transduction system ArlRS in regulating S. epidermidis biofilm formation. An ArlRS-deficient mutant, WW06, was constructed using S. epidermidis strain 1457 as a parental strain. Although the growth curve of WW06 was similar to that of SE1457, the mutant strain was unable to form biofilms in vitro. In a rabbit subcutaneous infection model, sterile disks made of polymeric materials were implanted subcutaneously followed with inoculation of WW06 or SE1457. The viable bacteria cells of WW06 recovered from biofilms on the embedded disks were much lower than that of SE1457. Complementation of arlRS genes expression from plasmid in WW06 restored biofilm-forming phenotype both in vivo and in vitro. WW06 maintained the ability to undergo initial attachment. Transcription levels of several genes involved in biofilm formation, including icaADBC, sigB, and sarA, were decreased in WW06, compared to SE1457; and icaR expression was increased in WW06, detected by real-time reverse-transcription PCR. The biofilm-forming phenotype was restored by overexpressing icaADBC in WW06 but not by overexpressing sigB, indicating that ArlRS regulates biofilm formation through the regulation of icaADBC. Gel shift assay showed that ArlR can bind to the promoter region of the ica operon. In conclusion, ArlRS regulates S. epidermidis biofilm formation in an ica-dependent manner, distinct from its role in S. aureus.

  14. The two-component signal transduction system CopRS of Corynebacterium glutamicum is required for adaptation to copper-excess stress.

    Science.gov (United States)

    Schelder, Stephanie; Zaade, Daniela; Litsanov, Boris; Bott, Michael; Brocker, Melanie

    2011-01-01

    Copper is an essential cofactor for many enzymes but at high concentrations it is toxic for the cell. Copper ion concentrations ≥50 µM inhibited growth of Corynebacterium glutamicum. The transcriptional response to 20 µM Cu(2+) was studied using DNA microarrays and revealed 20 genes that showed a ≥ 3-fold increased mRNA level, including cg3281-cg3289. Several genes in this genomic region code for proteins presumably involved in the adaption to copper-induced stress, e. g. a multicopper oxidase (CopO) and a copper-transport ATPase (CopB). In addition, this region includes the copRS genes (previously named cgtRS9) which encode a two-component signal transduction system composed of the histidine kinase CopS and the response regulator CopR. Deletion of the copRS genes increased the sensitivity of C. glutamicum towards copper ions, but not to other heavy metal ions. Using comparative transcriptome analysis of the ΔcopRS mutant and the wild type in combination with electrophoretic mobility shift assays and reporter gene studies the CopR regulon and the DNA-binding motif of CopR were identified. Evidence was obtained that CopR binds only to the intergenic region between cg3285 (copR) and cg3286 in the genome of C. glutamicum and activates expression of the divergently oriented gene clusters cg3285-cg3281 and cg3286-cg3289. Altogether, our data suggest that CopRS is the key regulatory system in C. glutamicum for the extracytoplasmic sensing of elevated copper ion concentrations and for induction of a set of genes capable of diminishing copper stress.

  15. Two-component signal transduction in Agaricus bisporus: a comparative genomic analysis with other basidiomycetes through the web-based tool BASID2CS.

    Science.gov (United States)

    Lavín, José L; García-Yoldi, Alberto; Ramírez, Lucía; Pisabarro, Antonio G; Oguiza, José A

    2013-06-01

    Two-component systems (TCSs) are signal transduction mechanisms present in many eukaryotes, including fungi that play essential roles in the regulation of several cellular functions and responses. In this study, we carry out a genomic analysis of the TCS proteins in two varieties of the white button mushroom Agaricus bisporus. The genomes of both A. bisporus varieties contain eight genes coding for TCS proteins, which include four hybrid Histidine Kinases (HKs), a single histidine-containing phosphotransfer (HPt) protein and three Response Regulators (RRs). Comparison of the TCS proteins among A. bisporus and the sequenced basidiomycetes showed a conserved core complement of five TCS proteins including the Tco1/Nik1 hybrid HK, HPt protein and Ssk1, Skn7 and Rim15-like RRs. In addition, Dual-HKs, unusual hybrid HKs with 2 HK and 2 RR domains, are absent in A. bisporus and are limited to various species of basidiomycetes. Differential expression analysis showed no significant up- or down-regulation of the Agaricus TCS genes in the conditions/tissue analyzed with the exception of the Skn7-like RR gene (Agabi_varbisH97_2|198669) that is significantly up-regulated on compost compared to cultured mycelia. Furthermore, the pipeline web server BASID2CS (http://bioinformatics.unavarra.es:1000/B2CS/BASID2CS.htm) has been specifically designed for the identification, classification and functional annotation of putative TCS proteins from any predicted proteome of basidiomycetes using a combination of several bioinformatic approaches. Copyright © 2012 Elsevier Inc. All rights reserved.

  16. The essential yhcSR two-component signal transduction system directly regulates the lac and opuCABCD operons of Staphylococcus aureus.

    Science.gov (United States)

    Yan, Meiying; Hall, Jeffrey W; Yang, Junshu; Ji, Yinduo

    2012-01-01

    Our previous studies suggested that the essential two-component signal transduction system, YhcSR, regulates the opuCABCD operon at the transcriptional level, and the Pspac-driven opuCABCD partially complements the lethal effects of yhcS antisense RNA expression in Staphylococcus aureus. However, the reason why yhcSR regulon is required for growth is still unclear. In this report, we present that the lac and opuC operons are directly transcriptionally regulated by YhcSR. Using real-time RT-PCR we showed that the down-regulation of yhcSR expression affected the transcription of lacA encoding galactose-6-phosphotase isomerase subunit LacA, and opuCA encoding a subunit of a glycine betaine/carnitine/choline ABC transporter. Promoter-lux reporter fusion studies further confirmed the transcriptional regulation of lac by YhcSR. Gel shift assays revealed that YhcR binds to the promoter regions of the lac and opuC operons. Moreover, the Pspac-driven lacABC expression in trans was able to partially complement the lethal effect of induced yhcS antisense RNA. Likewise, the Pspac-driven opuCABCD expression in trans complemented the growth defect of S. aureus in a high osmotic strength medium during the depletion of YhcSR. Taken together, the above data indicate that the yhcSR system directly regulates the expression of lac and opuC operons, which, in turn, may be partially associated with the essentiality of yhcSR in S. aureus. These results provide a new insight into the biological functions of the yhcSR, a global regulator.

  17. Role of the CpxAR two-component signal transduction system in control of fosfomycin resistance and carbon substrate uptake.

    Science.gov (United States)

    Kurabayashi, Kumiko; Hirakawa, Yuko; Tanimoto, Koichi; Tomita, Haruyoshi; Hirakawa, Hidetada

    2014-01-01

    Although fosfomycin is an old antibiotic, it has resurfaced with particular interest. The antibiotic is still effective against many pathogens that are resistant to other commonly used antibiotics. We have found that fosfomycin resistance of enterohemorrhagic Escherichia coli (EHEC) O157:H7 is controlled by the bacterial two-component signal transduction system CpxAR. A cpxA mutant lacking its phosphatase activity results in constitutive activation of its cognate response regulator, CpxR, and fosfomycin resistance. We have shown that fosfomycin resistance requires CpxR because deletion of the cpxR gene in the cpxA mutant restores fosfomycin sensitivity. We have also shown that CpxR directly represses the expression of two genes, glpT and uhpT, which encode transporters that cotransport fosfomycin with their native substrates glycerol-3-phosphate and glucose-6-phosphate, and repression of these genes leads to a decrease in fosfomycin transport into the cpxA mutant. However, the cpxA mutant had an impaired growth phenotype when cultured with glycerol-3-phosphate or glucose-6-phosphate as a sole carbon substrate and was outcompeted by the parent strain, even in nutrient-rich medium. This suggests a trade-off between fosfomycin resistance and the biological fitness associated with carbon substrate uptake. We propose a role for the CpxAR system in the reversible control of fosfomycin resistance. This may be a beneficial strategy for bacteria to relieve the fitness burden that results from fosfomycin resistance in the absence of fosfomycin.

  18. A Moraxella catarrhalis two-component signal transduction system necessary for growth in liquid media affects production of two lysozyme inhibitors.

    Science.gov (United States)

    Joslin, Stephanie N; Pybus, Christine; Labandeira-Rey, Maria; Evans, Amanda S; Attia, Ahmed S; Brautigam, Chad A; Hansen, Eric J

    2015-01-01

    There are a paucity of data concerning gene products that could contribute to the ability of Moraxella catarrhalis to colonize the human nasopharynx. Inactivation of a gene (mesR) encoding a predicted response regulator of a two-component signal transduction system in M. catarrhalis yielded a mutant unable to grow in liquid media. This mesR mutant also exhibited increased sensitivity to certain stressors, including polymyxin B, SDS, and hydrogen peroxide. Inactivation of the gene (mesS) encoding the predicted cognate sensor (histidine) kinase yielded a mutant with the same inability to grow in liquid media as the mesR mutant. DNA microarray and real-time reverse transcriptase PCR analyses indicated that several genes previously shown to be involved in the ability of M. catarrhalis to persist in the chinchilla nasopharynx were upregulated in the mesR mutant. Two other open reading frames upregulated in the mesR mutant were shown to encode small proteins (LipA and LipB) that had amino acid sequence homology to bacterial adhesins and structural homology to bacterial lysozyme inhibitors. Inactivation of both lipA and lipB did not affect the ability of M. catarrhalis O35E to attach to a human bronchial epithelial cell line in vitro. Purified recombinant LipA and LipB fusion proteins were each shown to inhibit human lysozyme activity in vitro and in saliva. A lipA lipB deletion mutant was more sensitive than the wild-type parent strain to killing by human lysozyme in the presence of human apolactoferrin. This is the first report of the production of lysozyme inhibitors by M. catarrhalis. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  19. OsDMI3 Is a Novel Component of Abscisic Acid Signaling in the Induction of Antioxidant Defense in Leaves of Rice

    Institute of Scientific and Technical Information of China (English)

    Ben Shi; Lan Ni; Aying Zhang; Jianmei Cao; Hong Zhang; Tingting Qin; Mingpu Tan; Jianhua Zhang; Mingyi Jiang

    2012-01-01

    Ca2+ and calmodulin (CaM) have been shown to play an important role in abscisic acid (ABA)-induced antioxidant defense.However,it is unknown whether Ca2+/CaM-dependent protein kinase (CCaMK) is involved in the process.In the present study,the role of rice CCaMK,OsDMI3,in ABA-induced antioxidant defense was investigated in leaves of rice (Oryza sativa) plants.Treatments with ABA,H2O2,and polyethylene glycol (PEG) induced the expression of OsDMI3 and the activity of OsDMI3,and H2O2 is required for the ABA-induced increases in the expression and the activity of OsDMI3 under water stress.Subcellular localization analysis showed that OsDMI3 is located in the nucleus,the cytoplasm,and the plasma membrane.The analysis of the transient expression of OsDMI3 in rice protoplasts and the RNA interference (RNAi) silencing of OsDMI3 in rice protoplasts showed that OsDMI3 is required for ABA-induced increases in the expression and the activities of superoxide dismutase (SOD) and catalase (CAT).Further,the oxidative damage induced by higher concentrations of PEG and H2O2 was aggravated in the mutant of OsDMI3.Moreover,the analysis of the RNAi silencing of OsDMI3 in protoplasts and the mutant of OsDMI3 showed that higher levels of H2O2 accumulation require OsDMI3 activation in ABA signaling,but the initial H2O2 production induced by ABA is not dependent on the activation of OsDMI3 in leaves of rice plants.Our data reveal that OsDMI3 is an important component in ABA-induced antioxidant defense in rice.

  20. Two-component signal transduction system CBO0787/CBO0786 represses transcription from botulinum neurotoxin promoters in Clostridium botulinum ATCC 3502.

    Directory of Open Access Journals (Sweden)

    Zhen Zhang

    2013-03-01

    Full Text Available Blocking neurotransmission, botulinum neurotoxin is the most poisonous biological substance known to mankind. Despite its infamy as the scourge of the food industry, the neurotoxin is increasingly used as a pharmaceutical to treat an expanding range of muscle disorders. Whilst neurotoxin expression by the spore-forming bacterium Clostridium botulinum appears tightly regulated, to date only positive regulatory elements, such as the alternative sigma factor BotR, have been implicated in this control. The identification of negative regulators has proven to be elusive. Here, we show that the two-component signal transduction system CBO0787/CBO0786 negatively regulates botulinum neurotoxin expression. Single insertional inactivation of cbo0787 encoding a sensor histidine kinase, or of cbo0786 encoding a response regulator, resulted in significantly elevated neurotoxin gene expression levels and increased neurotoxin production. Recombinant CBO0786 regulator was shown to bind to the conserved -10 site of the core promoters of the ha and ntnh-botA operons, which encode the toxin structural and accessory proteins. Increasing concentration of CBO0786 inhibited BotR-directed transcription from the ha and ntnh-botA promoters, demonstrating direct transcriptional repression of the ha and ntnh-botA operons by CBO0786. Thus, we propose that CBO0786 represses neurotoxin gene expression by blocking BotR-directed transcription from the neurotoxin promoters. This is the first evidence of a negative regulator controlling botulinum neurotoxin production. Understanding the neurotoxin regulatory mechanisms is a major target of the food and pharmaceutical industries alike.

  1. Characterization of the mrgRS locus of the opportunistic pathogen Burkholderia pseudomallei: temperature regulates the expression of a two-component signal transduction system

    Directory of Open Access Journals (Sweden)

    Dance David AB

    2006-08-01

    Full Text Available Abstract Background Burkholderia pseudomallei is a saprophyte in tropical environments and an opportunistic human pathogen. This versatility requires a sensing mechanism that allows the bacterium to respond rapidly to altered environmental conditions. We characterized a two-component signal transduction locus from B. pseudomallei 204, mrgR and mrgS, encoding products with extensive homology with response regulators and histidine protein kinases of Escherichia coli, Bordetella pertussis, and Vibrio cholerae. Results The locus was present and expressed in a variety of B. pseudomallei human and environmental isolates but was absent from other Burkholderia species, B. cepacia, B. cocovenenans, B. plantarii, B. thailandensis, B. vandii, and B. vietnamiensis. A 2128 bp sequence, including the full response regulator mrgR, but not the sensor kinase mrgS, was present in the B. mallei genome. Restriction fragment length polymorphism downstream from mrgRS showed two distinct groups were present among B. pseudomallei isolates. Our analysis of the open reading frames in this region of the genome revealed that transposase and bacteriophage activity may help explain this variation. MrgR and MrgS proteins were expressed in B. pseudomallei 204 cultured at different pH, salinity and temperatures and the expression was substantially reduced at 25°C compared with 37°C or 42°C but was mostly unaffected by pH or salinity, although at 25°C and 0.15% NaCl a small increase in MrgR expression was observed at pH 5. MrgR was recognized by antibodies in convalescent sera pooled from melioidosis patients. Conclusion The results suggest that mrgRS regulates an adaptive response to temperature that may be essential for pathogenesis, particularly during the initial phases of infection. B. pseudomallei and B. mallei are very closely related species that differ in their capacity to adapt to changing environmental conditions. Modifications in this region of the genome may

  2. Interleukin-6-induced STAT3 transactivation and Ser(727) phosphorylation involves Vav, Rac-1 and the kinase SEK-1/MKK-4 as signal transduction components

    NARCIS (Netherlands)

    Schuringa, JJ; Jonk, LJC; Dokter, WHA; Vellenga, E; Kruijer, W

    2000-01-01

    In the present study, signal transducer and activator of transcription 3 (STAT3) Ser(727) phosphorylation and transactivation was investigated in relation to activation of mitogen-activated protein (MAP) kinase family members including extracellular-signal-regulated protein kinase (ERK)-1, c-Jun N-t

  3. The Wnt signaling pathway in cellular proliferation and differentiation: A tale of two coactivators.

    Science.gov (United States)

    Teo, Jia-Ling; Kahn, Michael

    2010-09-30

    Wnt signaling pathways play divergent roles during development, normal homeostasis and disease. The responses that result from the activation of the pathway control both proliferation and differentiation. Tight regulation and controlled coordination of the Wnt signaling cascade is required to maintain the balance between proliferation and differentiation. The non-redundant roles of the coactivator proteins CBP and p300, within the context of Wnt signaling are discussed. We highlight their roles as integrators of the various inputs that a cell receives to elicit the correct and coordinated response. We propose that essentially all cellular information - i.e. from other signaling pathways, nutrient levels, etc. - is funneled down into a choice of coactivators usage, either CBP or p300, by their interacting partner beta-catenin (or catenin-like molecules in the absence of beta-catenin) to make the critical decision to either remain quiescent, or once entering cycle to proliferate without differentiation or to initiate the differentiation process.

  4. Non-destructive testing of high heat flux components of fusion devices by infrared thermography: modeling and signal processing; Controle non destructif par thermographie infrarouge des composants face au plasma des machines de fusion controlee

    Energy Technology Data Exchange (ETDEWEB)

    Cismondi, F

    2007-07-01

    In Plasma Facing Components (PFCs) the joint of the CFC armour material onto the metallic CuCrZr heat sink needs to be significant defects free. Detection of material flaws is a major issue of the PFCs acceptance protocol. A Non-Destructive Technique (NDT) based upon active infrared thermography allows testing PFCs on SATIR tests bed in Cadarache. Up to now defect detection was based on the comparison of the surface temperature evolution of the inspected component with that of a supposed 'defect-free' one (used as a reference element). This work deals with improvement of thermal signal processing coming from SATIR. In particular the contributions of the thermal modelling and statistical signal processing converge in this work. As for thermal modelling, the identification of a sensitive parameter to defect presence allows improving the quantitative estimation of defect Otherwise Finite Element (FE) modeling of SATIR allows calculating the so called deterministic numerical tile. Statistical approach via the Monte Carlo technique extends the numerical tile concept to the numerical population concept. As for signal processing, traditional statistical treatments allow a better localization of the bond defect processing thermo-signal by itself, without utilising a reference signal. Moreover the problem of detection and classification of random signals can be solved by maximizing the signal-to-noise ratio. Two filters maximizing the signal-to-noise ratio are optimized: the stochastic matched filter aims at detects detection and the constrained stochastic matched filter aims at defects classification. Performances are quantified and methods are compared via the ROC curves. (author)

  5. Identification of p62/SQSTM1 as a component of non-canonical Wnt VANGL2-JNK signalling in breast cancer.

    Science.gov (United States)

    Puvirajesinghe, Tania M; Bertucci, François; Jain, Ashish; Scerbo, Pierluigi; Belotti, Edwige; Audebert, Stéphane; Sebbagh, Michael; Lopez, Marc; Brech, Andreas; Finetti, Pascal; Charafe-Jauffret, Emmanuelle; Chaffanet, Max; Castellano, Rémy; Restouin, Audrey; Marchetto, Sylvie; Collette, Yves; Gonçalvès, Anthony; Macara, Ian; Birnbaum, Daniel; Kodjabachian, Laurent; Johansen, Terje; Borg, Jean-Paul

    2016-01-12

    The non-canonical Wnt/planar cell polarity (Wnt/PCP) pathway plays a crucial role in embryonic development. Recent work has linked defects of this pathway to breast cancer aggressiveness and proposed Wnt/PCP signalling as a therapeutic target. Here we show that the archetypal Wnt/PCP protein VANGL2 is overexpressed in basal breast cancers, associated with poor prognosis and implicated in tumour growth. We identify the scaffold p62/SQSTM1 protein as a novel VANGL2-binding partner and show its key role in an evolutionarily conserved VANGL2-p62/SQSTM1-JNK pathway. This proliferative signalling cascade is upregulated in breast cancer patients with shorter survival and can be inactivated in patient-derived xenograft cells by inhibition of the JNK pathway or by disruption of the VANGL2-p62/SQSTM1 interaction. VANGL2-JNK signalling is thus a potential target for breast cancer therapy.

  6. On the suppression of background signals originating from NMR hardware components. Application to zero echo time imaging and relaxation time analysis.

    Science.gov (United States)

    Dreher, Wolfgang; Bardenhagen, Ingo; Huang, Li; Bäumer, Marcus

    2016-04-01

    Modern NMR imaging systems used for biomedical research are equipped with B0 gradient systems with strong maximum gradient strength and short switching time enabling (1)H NMR measurements of samples with very short transverse relaxation times. However, background signal originating from non-optimized RF coils may hamper experiments with ultrashort delays between RF excitation and signal reception. We demonstrate that two simple means, outer volume suppression and the use of shaped B0 fields produced by higher-order shim coils, allow a considerable suppression of disturbing background signals. Thus, the quality of NMR images acquired at ultrashort or zero echo time is improved and systematic errors in quantitative data evaluation are avoided. Fields of application comprise MRI with ultrashort echo time or relaxation time analysis, for both biomedical research and characterizing porous media filled with liquids or gases.

  7. Frizzled 2 is a key component in the regulation of TOR signaling-mediated egg production in the mosquito Aedes aegypti.

    Science.gov (United States)

    Weng, Shih-Che; Shiao, Shin-Hong

    2015-06-01

    The Wnt signaling pathway was first discovered as a key event in embryonic development and cell polarity in Drosophila. Recently, several reports have shown that Wnt stimulates translation and cell growth by activating the mTOR pathway in mammals. Previous studies have demonstrated that the Target of Rapamycin (TOR) pathway plays an important role in mosquito vitellogenesis. However, the interactions between these two pathways are poorly understood in the mosquito. In this study, we hypothesized that factors from the TOR and Wnt signaling pathways interacted synergistically in mosquito vitellogenesis. Our results showed that silencing Aedes aegypti Frizzled 2 (AaFz2), a transmembrane receptor of the Wnt signaling pathway, decreased the fecundity of mosquitoes. We showed that AaFz2 was highly expressed at the transcriptional and translational levels in the female mosquito 6 h after a blood meal, indicating amino acid-stimulated expression of AaFz2. Notably, the phosphorylation of S6K, a downstream target of the TOR pathway, and the expression of vitellogenin were inhibited in the absence of AaFz2. A direct link was found in this study between Wnt and TOR signaling in the regulation of mosquito reproduction.

  8. Phosphorylation of the Hippo Pathway Component AMOTL2 by the mTORC2 Kinase Promotes YAP Signaling, Resulting in Enhanced Glioblastoma Growth and Invasiveness*♦

    Science.gov (United States)

    Artinian, Nicholas; Cloninger, Cheri; Holmes, Brent; Benavides-Serrato, Angelica; Bashir, Tariq; Gera, Joseph

    2015-01-01

    The mechanistic target of rapamycin (mTOR) and Hippo signaling pathways are two major signaling cascades that coordinately regulate cell growth and proliferation. Dysregulation of these pathways plays a critical role in gliomagenesis. Recent reports have provided evidence of cross-talk between the mTOR and Hippo pathways; however, a complete description of the signaling relationships between these pathways remains to be elucidated. Utilizing a gene-trapping strategy in a mouse glioma model, we report the identification of AMOTL2 as a candidate substrate for mTORC2. AMOTL2 is phosphorylated at serine 760 by mTORC2. Mutation of AMOTL2 mimicking constitutive Ser760 phosphorylation blocks its ability to bind and repress YAP leading to increased relative expression of known YAP gene targets. Moreover, overexpression of AMOTL2 or a nonphosphorylatable AMOTL2-S760A mutant inhibited YAP-induced transcription, foci formation, growth, and metastatic properties, whereas overexpression of a phosphomimetic AMOTL2-S760E mutant negated these repressive effects of AMOTL2 in glioblastoma (GBM) cells in vitro. Similar effects on xenograft growth were observed in GBM cells expressing these AMOTL2 Ser760 mutants. YAP was also shown to be required for Rictor-mediated GBM growth and survival. Finally, an analysis of mTORC2/AMOTL2/YAP activities in primary GBM samples supported the clinical relevance of this signaling cascade, and we propose that pharmacological agents cotargeting these regulatory circuits may hold therapeutic potential. PMID:25998128

  9. The three-component signalling system HbpS-SenS-SenR as an example of a redox sensing pathway in bacteria

    NARCIS (Netherlands)

    Ortiz de Orué Lucana, Darío; Groves, Matthew R

    The two-component system SenS-SenR and the extracellular HbpS protein of the cellulose degrader Streptomyces reticuli have been shown to act in concert as a novel system which detects redox stress. In vivo and in vitro experiments have led to the hypothesis that HbpS binds and degrades heme,

  10. Impact of the Use of Object Request Broker Middleware for Inter-Component Communications in C6416 Digital Signal Processor Based Software Communications Architecture Radio Systems

    Directory of Open Access Journals (Sweden)

    Mohamed I. Yousef

    2012-01-01

    Full Text Available Problem statement: This study presents an in-depth analysis of the performance of Software Communications Architecture (SCA component-based waveform applications in terms of inter-component communications. The main limitation with SCA, in the context of embedded systems, is the additional cost introduced by the use of Object Request Broker (ORB middleware. The ORB middleware handles the interaction between components and objects in SCA distributed environment. This interaction should be highly efficient, due to the real time nature of SCA systems and transparent to the application programmer. Approach: We can achieve high efficiency in SCA systems by enhancing the Inter-Process Communications (IPC mechanisms in Operating systems (OS micro kernels, while we achieve transparency through Interface Definition Language (IDL. Different encoding mechanisms like “External Data Representation (XDR, Network Data Representation (NDR and Common Data Representation (CDR facilitate inter-component communication transparently and efficiently”. Marshalling procedures format data from the local machine representation to common network representations. A most common encoding mechanism for Common Object Request Broker Architecture (CORBA systems is CDR representation. Measurements have been performed with ORBExpress DSP as a CORBA distribution and Open Source SCA Implementation Embedded (OSSIE for SCA implementation. In order to perform these measurements we proposed two metrics for profiling the ORB that are invocation and marshalling. In addition, we propose three elements of data types to evaluate the performance of ORB middleware that are, Basic, Array and Sequence data types. Results: The CORBA bus is really the part, which brings an overhead to the SCA radio systems. This overhead is due to method invocations that have been carried out by ORB middleware. Conclusion: Performance benchmarks of ORBExpress DSP middleware show that, although using CORBA for

  11. Preliminary Crystallographic Studies of the Regulatory Domain of Response Regulator YycF from an Essential Two-Component Signal Transduction System

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, H.; Heroux, A; Sequeira, R; Tang, L

    2009-01-01

    YycGF is a crucial signal transduction system for the regulation of cell-wall metabolism in low-G+C Gram-positive bacteria, which include many important human pathogens. The response regulator YycF receives signals from its cognate histidine kinase YycG through a phosphotransfer reaction and elicits responses through regulation of gene expression. The N-terminal regulatory domain of YycF from Bacillus subtilis was overproduced and purified. The protein was crystallized and X-ray data were collected to 1.95 A resolution with a completeness of 97.7% and an overall Rmerge of 7.7%. The crystals belonged to space group P3121, with unit-cell parameters a = b = 59.50, c = 79.06 A.

  12. Identification of extracellular and intracellular signaling components of the mammary adipose tissue and its interstitial fluid in high risk breast cancer patients

    DEFF Research Database (Denmark)

    Celis, J.E.; Cabezón, T.; Gromov, P.

    2005-01-01

    carcinoma cells. Very little is known, however, about which factors adipocytes produce that may orchestrate these actions and how this may come about. In an effort to shed some light on these questions, we present here a detailed proteomic analysis, using two-dimensional gel-based technology, mass...... proteins were identified, including numerous signaling molecules, hormones, cytokines, and growth factors, involved in a variety of biological processes such as signal transduction and cell communication; energy metabolism; protein metabolism; cell growth and/or maintenance; immune response; transport...... of their molecular cellular circuitry. In addition, the results open new possibilities to the study of obesity, which has a strong association with type 2 diabetes, hypertension, and coronary heart disease. © 2005 by The American Society for Biochemistry and Molecular Biology, Inc....

  13. The epithelial αvβ3-integrin boosts the MYD88-dependent TLR2 signaling in response to viral and bacterial components.

    Directory of Open Access Journals (Sweden)

    Tatiana Gianni

    2014-11-01

    Full Text Available TLR2 is a cell surface receptor which elicits an immediate response to a wide repertoire of bacteria and viruses. Its response is usually thought to be proinflammatory rather than an antiviral. In monocytic cells TLR2 cooperates with coreceptors, e.g. CD14, CD36 and αMβ2-integrin. In an earlier work we showed that αvβ3-integrin acts in concert with TLR2 to elicit an innate response to HSV, and to lipopolysaccharide. This response is characterized by production of IFN-α and -β, a specific set of cytokines, and NF-κB activation. We investigated the basis of the cooperation between αvβ3-integrin and TLR2. We report that β3-integrin participates by signaling through Y residues located in the C-tail, known to be involved in signaling activity. αvβ3-integrin boosts the MYD88-dependent TLR2 signaling and IRAK4 phosphorylation in 293T and in epithelial, keratinocytic and neuronal cell lines. The replication of ICP0minus HSV is greatly enhanced by DN versions of MYD88, of Akt - a hub of this pathway, or by β3integrin-silencing. αvβ3-integrin enables the recruitment of TLR2, MAL, MYD88 at lipid rafts, the platforms from where the signaling starts. The PAMP of the HSV-induced innate response is the gH/gL virion glycoprotein, which interacts with αvβ3-integrin and TLR2 independently one of the other, and cross-links the two receptors. Given the preferential distribution of αvβ3-integrin to epithelial cells, we propose that αvβ3-integrin serves as coreceptor of TLR2 in these cells. The results open the possibility that TLR2 makes use of coreceptors in a variety of cells to broaden its spectrum of activity and tissue specificity.

  14. Identification of p62/SQSTM1 as a component of non-canonical Wnt VANGL2–JNK signalling in breast cancer

    Science.gov (United States)

    Puvirajesinghe, Tania M.; Bertucci, François; Jain, Ashish; Scerbo, Pierluigi; Belotti, Edwige; Audebert, Stéphane; Sebbagh, Michael; Lopez, Marc; Brech, Andreas; Finetti, Pascal; Charafe-Jauffret, Emmanuelle; Chaffanet, Max; Castellano, Rémy; Restouin, Audrey; Marchetto, Sylvie; Collette, Yves; Gonçalvès, Anthony; Macara, Ian; Birnbaum, Daniel; Kodjabachian, Laurent; Johansen, Terje; Borg, Jean-Paul

    2016-01-01

    The non-canonical Wnt/planar cell polarity (Wnt/PCP) pathway plays a crucial role in embryonic development. Recent work has linked defects of this pathway to breast cancer aggressiveness and proposed Wnt/PCP signalling as a therapeutic target. Here we show that the archetypal Wnt/PCP protein VANGL2 is overexpressed in basal breast cancers, associated with poor prognosis and implicated in tumour growth. We identify the scaffold p62/SQSTM1 protein as a novel VANGL2-binding partner and show its key role in an evolutionarily conserved VANGL2–p62/SQSTM1–JNK pathway. This proliferative signalling cascade is upregulated in breast cancer patients with shorter survival and can be inactivated in patient-derived xenograft cells by inhibition of the JNK pathway or by disruption of the VANGL2–p62/SQSTM1 interaction. VANGL2–JNK signalling is thus a potential target for breast cancer therapy. PMID:26754771

  15. PhoP-PhoR two-component signal transduction systems in pathogenesis of Mycobacterium tuberculosis%PhoPR双组份系统在结核分枝杆菌致病机制中的研究进展

    Institute of Scientific and Technical Information of China (English)

    邬博; 张万江

    2014-01-01

    Two-component signal transduction system (TCS) exists extensively in prokaryotic cell ,which plays a key role of regulation in the growth ,differentiation ,metabolism ,virulence ,persistence ,and pathogenicity .PhoPR two-component signal transduction system ,as one of two-component systems ,is the most basic and the most importantly sensitive to the envi-ronmental changes and makes corresponding certain reaction system adapt to changes in the host microenvironment .Therefore , PhoPR TCS which is an important regulatory system of Mycobacterium tuberculosis (MTB) to adapt to environmental change has been increasing concern ,even PhoPR TCS is becoming the new front-burner issue in the pathogenesis of M TB regulation of research .%双组份信号转导系统(Two-component signal transduction system ,TCS)广泛存在于原核生物细胞内,对细胞生长、分化、代谢、毒力、持留性、致病性等方面的调控发挥着重要作用。PhoPR TCS作为双组份系统中最基本、最重要的感应外界环境变化,并作出相应反应的调控系统,能够调控结核分枝杆菌(Mycobacterium Tuberculosis ,MTB)更好的适应宿主微环境变化。因此PhoPR TCS作为M TB适应环境变化的重要调控系统已愈来愈受关注,关于PhoPR TCS在M TB的致病机制调控方面的研究正在成为新的热点。

  16. Identification of a 60-kD tumor necrosis factor (TNF) receptor as the major signal transducing component in TNF responses

    OpenAIRE

    1990-01-01

    We describe here a monoclonal antibody (H398) that immunoprecipitates a human 60-kD tumor necrosis factor (TNF) membrane receptor (p60) and competes with TNF binding to p60 but not to p85 TNF receptors. Despite partial inhibition of TNF binding capacity of cells coexpressing both TNF receptor molecules, H398 uniformly and completely inhibits very distinct TNF responses on a variety of cell lines. These data suggest a limited structural heterogeneity in those components actually contributing t...

  17. An SVM-Based Classifier for Estimating the State of Various Rotating Components in Agro-Industrial Machinery with a Vibration Signal Acquired from a Single Point on the Machine Chassis

    Directory of Open Access Journals (Sweden)

    Ruben Ruiz-Gonzalez

    2014-11-01

    Full Text Available The goal of this article is to assess the feasibility of estimating the state of various rotating components in agro-industrial machinery by employing just one vibration signal acquired from a single point on the machine chassis. To do so, a Support Vector Machine (SVM-based system is employed. Experimental tests evaluated this system by acquiring vibration data from a single point of an agricultural harvester, while varying several of its working conditions. The whole process included two major steps. Initially, the vibration data were preprocessed through twelve feature extraction algorithms, after which the Exhaustive Search method selected the most suitable features. Secondly, the SVM-based system accuracy was evaluated by using Leave-One-Out cross-validation, with the selected features as the input data. The results of this study provide evidence that (i accurate estimation of the status of various rotating components in agro-industrial machinery is possible by processing the vibration signal acquired from a single point on the machine structure; (ii the vibration signal can be acquired with a uniaxial accelerometer, the orientation of which does not significantly affect the classification accuracy; and, (iii when using an SVM classifier, an 85% mean cross-validation accuracy can be reached, which only requires a maximum of seven features as its input, and no significant improvements are noted between the use of either nonlinear or linear kernels.

  18. Xiang-Qi-Tang and its active components exhibit anti-inflammatory and anticoagulant properties by inhibiting MAPK and NF-κB signaling pathways in LPS-treated rat cardiac microvascular endothelial cells.

    Science.gov (United States)

    He, Chang-Liang; Yi, Peng-Fei; Fan, Qiao-Jia; Shen, Hai-Qing; Jiang, Xiao-Lin; Qin, Qian-Qian; Song, Zhou; Zhang, Cui; Wu, Shuai-Cheng; Wei, Xu-Bin; Li, Ying-Lun; Fu, Ben-Dong

    2013-04-01

    Xiang-Qi-Tang (XQT) is a Chinese herbal formula containing Cyperus rotundus, Astragalus membranaceus and Andrographis paniculata. Alpha-Cyperone (CYP), astragaloside IV (AS-IV) and andrographolide (AND) are the three major active components in this formula. XQT may modulate the inflammatory or coagulant responses. We therefore assessed the effects of XQT on lipopolysaccharide (LPS)-induced inflammatory model of rat cardiac microvascular endothelial cells (RCMECs). XQT, CYP, AS-IV and AND inhibited the production of tumor necrosis factor alpha (TNF-α), intercellular cell adhesion molecule-1 (ICAM-1) and plasminogen activator inhibitor-1 (PAI-1), and up-regulated the mRNA expression of Kruppel-like factor 2 (KLF2). XQT and CYP inhibited the secretion of tissue factor (TF). To further explore the mechanism, we found that XQT, or its active components CYP, AS-IV and AND significantly inhibited extracellular signal-regulated kinase (ERK), c-jun NH2-terminal kinase (JNK) and p38 phosphorylation protein expression as well as decreased the phosphorylation levels of nuclear factor κB (NF-κB) p65 proteins in LPS-stimulated RCMECs. These results suggested that XQT and its active components inhibited the expression of inflammatory and coagulant mediators via mitogen-activated protein kinase (MAPKs) and NF-κB signaling pathways. These findings may contribute to future research on the action mechanisms of this formula, as well as therapy for inflammation- or coagulation-related diseases.

  19. Anti-wrinkle and anti-inflammatory effects of active garlic components and the inhibition of MMPs via NF-κB signaling.

    Directory of Open Access Journals (Sweden)

    So Ra Kim

    Full Text Available Skin aging is a multisystem degenerative process caused by several factors, such as, UV irradiation, stress, and smoke. Furthermore, wrinkle formation is a striking feature of photoaging and is associated with oxidative stress and inflammatory response. In the present study, we investigated whether caffeic acid, S-allyl cysteine, and uracil, which were isolated from garlic, modulate UVB-induced wrinkle formation and effect the expression of matrix-metalloproteinase (MMP and NF-κB signaling. The results obtained showed that all three compounds significantly inhibited the degradation of type І procollagen and the expressions of MMPs in vivo and attenuated the histological collagen fiber disorder and oxidative stress in vivo. Furthermore, caffeic acid and S-allyl cysteine were found to decrease oxidative stress and inflammation by modulating the activities of NF-κB and AP-1, and uracil exhibited an indirect anti-oxidant effect by suppressing cyclooxygenase-2 (COX-2 and inducible nitric oxide synthase (iNOS expressions levels and downregulating transcriptional factors. These results suggest that the anti-wrinkle effects of caffeic acid, S-allyl cysteine, and uracil are due to anti-oxidant and/or anti-inflammatory effects. Summarizing, caffeic acid, S-allyl cysteine, and uracil inhibited UVB-induced wrinkle formation by modulating MMP via NF-κB signaling.

  20. The role of temporal and dynamic signal components in the perception of syllable-final stop voicing by children and adults

    Science.gov (United States)

    Nittrouer, Susan

    2004-04-01

    Adults whose native languages permit syllable-final obstruents, and show a vocalic length distinction based on the voicing of those obstruents, consistently weight vocalic duration strongly in their perceptual decisions about the voicing of final stops, at least in laboratory studies using synthetic speech. Children, on the other hand, generally disregard such signal properties in their speech perception, favoring formant transitions instead. These age-related differences led to the prediction that children learning English as a native language would weight vocalic duration less than adults, but weight syllable-final transitions more in decisions of final-consonant voicing. This study tested that prediction. In the first experiment, adults and children (eight and six years olds) labeled synthetic and natural CVC words with voiced or voiceless stops in final C position. Predictions were strictly supported for synthetic stimuli only. With natural stimuli it appeared that adults and children alike weighted syllable-offset transitions strongly in their voicing decisions. The predicted age-related difference in the weighting of vocalic duration was seen for these natural stimuli almost exclusively when syllable-final transitions signaled a voiced final stop. A second experiment with adults and children (seven and five years old) replicated these results for natural stimuli with four new sets of natural stimuli. It was concluded that acoustic properties other than vocalic duration might play more important roles in voicing decisions for final stops than commonly asserted, sometimes even taking precedence over vocalic duration.

  1. Membrane-associated proteomics of chickpea identifies Sad1/UNC-84 protein (CaSUN1), a novel component of dehydration signaling

    Science.gov (United States)

    Jaiswal, Dinesh Kumar; Mishra, Poonam; Subba, Pratigya; Rathi, Divya; Chakraborty, Subhra; Chakraborty, Niranjan

    2014-02-01

    Dehydration affects almost all the physiological processes including those that result in the accumulation of misfolded proteins in the endoplasmic reticulum (ER), which in turn elicits a highly conserved signaling, the unfolded protein response (UPR). We investigated the dehydration-responsive membrane-associated proteome of a legume, chickpea, by 2-DE coupled with mass spectrometry. A total of 184 protein spots were significantly altered over a dehydration treatment of 120 h. Among the differentially expressed proteins, a non-canonical SUN domain protein, designated CaSUN1 (Cicer arietinum Sad1/UNC-84), was identified. CaSUN1 localized to the nuclear membrane and ER, besides small vacuolar vesicles. The transcripts were downregulated by both abiotic and biotic stresses, but not by abscisic acid treatment. Overexpression of CaSUN1 conferred stress tolerance in transgenic Arabidopsis. Furthermore, functional complementation of the yeast mutant, slp1, could rescue its growth defects. We propose that the function of CaSUN1 in stress response might be regulated via UPR signaling.

  2. Tyrosol and hydroxytyrosol, two main components of olive oil, protect N2a cells against amyloid-β-induced toxicity. Involvement of the NF-κB signaling.

    Science.gov (United States)

    St-Laurent-Thibault, C; Arseneault, M; Longpré, F; Ramassamy, C

    2011-08-01

    Alzheimer's disease (AD) is the most common form of dementia. Recently, a number of epidemiological studies have evidence that some dietary factors such as low antioxidants and vitamins intake could increase the risk of AD. In the opposite, diets rich in unsaturated fatty acids, in polyphenols, vitamins and antioxidants were identified as preventive factors. Several studies have reported that adherence to the Mediterranean diet (MeDi) was associated with a reduction in incident of dementia. The beneficial effect of MeDi may be the result of the association of some individual and non-identified food components and high consumption of olive oil. In this study we have investigated the protective effects of two components of olive oil, tyrosol (Tyr) and hydroxytyrosol (OH-Tyr), against Aβ-induced toxicity. In cultured neuroblastoma N2a cells, we found that Aβ(25-35) (100 µg/ml) treatment induced a decrease of glutathione (GSH) and the activation of the transcription factor NF-κB and cell death. Our results demonstrated that the number of cell death decreased when cells were co-treated with Aβ and Tyr or OH-Tyr. However, neither of these phenolic compounds was able to prevent the decrease of GSH induced by H(2)O(2) or Aβ. We found that the increase in the nuclear translocation of the NF-κB subunits after Aβ exposure was attenuated in the presence of Tyr or OH-Tyr. These results identified two individual food components of the MeDi as neuroprotective agent against Aβ and their potential involvement in the beneficial effect of the MeDi for the prevention of AD.

  3. Multi-signal components combining acquisition method based on padding zero for TD-AltBOC%补0的 TD-AltBOC 多信号分量联合捕获方法

    Institute of Scientific and Technical Information of China (English)

    杨建雷; 金天; 黄智刚; 秦红磊

    2014-01-01

    针对TD-AltBOC导频路和数据路码片时分复用,四信号分量码相位相同的特点,提出了补0的TD-AltBOC多信号分量联合捕获方法。该方法通过将本地复制的TD-AltBOC信号奇数和偶数码片伪随机码分别补0消除相邻码片数据跳变造成的相关峰损失,将4个信号分量的相关值进行多种相干组合,选取最优的相干组合相关值作为最终的统计判决量,解决了传统的单信号分量捕获方法损失信号能量的问题。从理论上分析了TD-AltBOC信号码片时分复用对传统FFT捕获方法性能的影响,推导了所提出方法的虚警概率和检测概率表达式。理论和仿真结果表明:所提出的方法比传统FFT 方法和GPS L2C CM码单信号分量捕获方法提高捕获灵敏度3~6 dB,降低平均捕获时间5%~35%,当载噪比为38 dB-Hz,虚警概率为0.1%时,检测概率可达80%。%In TD-AltBOC structure, the data and pilot chips are time-divisional and the four signal components have the same code phase.According to these characteristics, a multi-signal components combining acquisition method based on padding zero was proposed.In this method, the local replicated odd and even chip pseudorandom noise (PN) codes were padded with zero, respectively.This allows for the elimination of the correlation peak loss caused by bit transitions of ad-jacent chips.The correlation values of the four signal components were coherently combined and the optimal correlation value was selected as the final decision variable.This method can solve the signal energy loss problem in the traditional single signal component acquisition.The influence of the time-division multiplexing of TD-Alt BOC signal chips using a traditional FFT acquisition method was analyzed in theory, and the false probability and detection probability expression were deduced.The theoretical and simulated results showed that the proposed method can provide 3~6 dB acquisition

  4. The Combination of Three Components Derived from Sheng MaiSan Protects Myocardial Ischemic Diseases and Inhibits Oxidative Stress via Modulating MAPKs and JAK2-STAT3 Signaling Pathways Based on Bioinformatics Approach

    Science.gov (United States)

    Li, Fang; Zhang, Yu; Zeng, Donglin; Xia, Yu; Fan, Xiaoxue; Tan, Yisha; Kou, Junping; Yu, Boyang

    2017-01-01

    GRS is a drug combination of three components including ginsenoside Rb1, ruscogenin and schisandrin. It derived from the well-known TCM formula Sheng MaiSan, a widely used traditional Chinese medicine for the treatment of cardiovascular diseases in clinic. The present study illuminates its underlying mechanisms against myocardial ischemic diseases based on the combined methods of bioinformatic prediction and experimental verification. A protein database was established through constructing the drug-protein network. And the target-pathway interaction network clustered the potential signaling pathways and targets of GRS in treatment of myocardial ischemic diseases. Several target proteins, such as NFKB1, STAT3 and MAPK14, were identified as the candidate key proteins, and MAPKs and JAK-STAT signaling pathway were suggested as the most related pathways, which were in accordance with the gene ontology analysis. Then, the predictive results were further validated and we found that GRS treatment alleviated hypoxia/reoxygenation (H/R)-induced cardiomyocytes injury via suppression of MDA levels and ROS generation, and potential mechanisms might related to the suppression of activation of MAPKs and JAK2-STAT3 signaling pathways. Conclusively, our results offer the evidence that GRS attenuates myocardial ischemia injury via regulating oxidative stress and MAPKs and JAK2-STAT3 signaling pathways, which supplied some new insights for its prevention and treatment of myocardial ischemia diseases.

  5. Pseudomonas quinolone signalling system: a component of quorum sensing cascade is a crucial player in the acute urinary tract infection caused by Pseudomonas aeruginosa.

    Science.gov (United States)

    Bala, Anju; Chhibber, Sanjay; Harjai, Kusum

    2014-11-01

    Pseudomonas aeruginosa is an opportunistic pathogen which employs quorum sensing system to regulate several genes required for its survival and pathogenicity within the host. Besides acylhomoserine lactone (AHL) mediated las and rhl systems, this organism possesses Pseudomonas quinolone signalling (PQS) system based on alkyl quinolone signal molecules. The quinolone system represents another layer of sophistication in the complex quorum sensing cascade. Therefore, in the present study, we evaluated the contribution of the PQS system in the establishment of acute urinary tract infection (UTI) in the mouse model. For this, wild-type parent strain of P. aeruginosa MPAO1 and its isogenic single transposon mutant strains pqsH and pqsA were employed to induce UTI in mice. PQS molecules in the tissue homogenates of mice were detected by high performance thin layer chromatography (HP-TLC) method. Virulence of strains was assessed in terms of bacteriological count, histopathological lesions in the renal and bladder tissue and generation of pathological index markers like reactive nitrogen intermediates and malondialdehyde. HP-TLC analysis showed presence of PQS molecules in the renal and bladder tissue of mice infected with MPAO1 while no PQS was detected in case of pqsH and pqsA mutant strains. Results indicated that MPAO1 possessing fully functional PQS biosynthetic genes was highly virulent and caused acute pyelonephritis with severe inflammation and tissue destruction. On the contrary, significant reduction in the log count, mild tissue damage and declined levels of pathological markers were observed in mice infected with mutant strains as compared to MPAO1. Further among mutants, all these parameters were maximally impaired in the pqsA mutant in which synthesis of alkyl quinolones was completely abolished due to the transposon mutation in respective gene. Virulence of the pqsH mutant strain was lesser than that of the MPAO1 but higher than pqsA mutant. In addition, the

  6. Plasmodium falciparum signal recognition particle components and anti-parasitic effect of ivermectin in blocking nucleo-cytoplasmic shuttling of SRP.

    Science.gov (United States)

    Panchal, M; Rawat, K; Kumar, G; Kibria, K M; Singh, S; Kalamuddin, Md; Mohmmed, A; Malhotra, P; Tuteja, R

    2014-01-16

    Signal recognition particle (SRP) is a ubiquitous ribonucleoprotein complex that targets proteins to endoplasmic reticulum (ER) in eukaryotes. Here we report that Plasmodium falciparum SRP is composed of six polypeptides; SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72 and a 303nt long SRP RNA. We generated four transgenic parasite lines expressing SRP-GFP chimeric proteins and co-localization studies showed the nucleo-cytoplasmic localization for these proteins. The evaluation of the effect of known SRP and nuclear import/export inhibitors on P. falciparum revealed that ivermectin, an inhibitor of importin α/β mediated nuclear import inhibited the nuclear import of PfSRP polypeptides at submicromolar concentration, thereby killing the parasites. These findings provide insights into dynamic structure of P. falciparum SRP and also raise the possibility that ivermectin could be used in combination with other antimalarial agents to control the disease.

  7. Cytokinin Regulates the Etioplast-Chloroplast Transition through the Two-Component Signaling System and Activation of Chloroplast-Related Genes1

    Science.gov (United States)

    Cortleven, Anne; Marg, Ingke; Schlicke, Hagen; Hill, Kristine; Schmülling, Thomas

    2016-01-01

    One of the classical functions of the plant hormone cytokinin is the regulation of plastid development, but the underlying molecular mechanisms remain elusive. In this study, we employed a genetic approach to evaluate the role of cytokinin and its signaling pathway in the light-induced development of chloroplasts from etioplasts in Arabidopsis (Arabidopsis thaliana). Cytokinin increases the rate of greening and stimulates ultrastructural changes characteristic for the etioplast-to-chloroplast transition. The steady-state levels of metabolites of the tetrapyrrole biosynthesis pathway leading to the production of chlorophyll are enhanced by cytokinin. This effect of cytokinin on metabolite levels arises due to the modulation of expression for chlorophyll biosynthesis genes such as HEMA1, GUN4, GUN5, and CHLM. Increased expression of HEMA1 is reflected in an enhanced level of the encoded glutamyl-tRNA reductase, which catalyzes one of the rate-limiting steps of chlorophyll biosynthesis. Mutant analysis indicates that the cytokinin receptors ARABIDOPSIS HIS KINASE2 (AHK2) and AHK3 play a central role in this process. Furthermore, the B-type ARABIDOPSIS RESPONSE REGULATOR1 (ARR1), ARR10, and ARR12 play an important role in mediating the transcriptional output during etioplast-chloroplast transition. B-type ARRs bind to the promotors of HEMA1 and LHCB6 genes, indicating that cytokinin-dependent transcription factors directly regulate genes of chlorophyll biosynthesis and the light harvesting complex. Together, these results demonstrate an important role for the cytokinin signaling pathway in chloroplast development, with the direct transcriptional regulation of chlorophyll biosynthesis genes as a key aspect for this hormonal control. PMID:27388681

  8. Cytokinin Regulates the Etioplast-Chloroplast Transition through the Two-Component Signaling System and Activation of Chloroplast-Related Genes.

    Science.gov (United States)

    Cortleven, Anne; Marg, Ingke; Yamburenko, Maria V; Schlicke, Hagen; Hill, Kristine; Grimm, Bernhard; Schaller, G Eric; Schmülling, Thomas

    2016-09-01

    One of the classical functions of the plant hormone cytokinin is the regulation of plastid development, but the underlying molecular mechanisms remain elusive. In this study, we employed a genetic approach to evaluate the role of cytokinin and its signaling pathway in the light-induced development of chloroplasts from etioplasts in Arabidopsis (Arabidopsis thaliana). Cytokinin increases the rate of greening and stimulates ultrastructural changes characteristic for the etioplast-to-chloroplast transition. The steady-state levels of metabolites of the tetrapyrrole biosynthesis pathway leading to the production of chlorophyll are enhanced by cytokinin. This effect of cytokinin on metabolite levels arises due to the modulation of expression for chlorophyll biosynthesis genes such as HEMA1, GUN4, GUN5, and CHLM Increased expression of HEMA1 is reflected in an enhanced level of the encoded glutamyl-tRNA reductase, which catalyzes one of the rate-limiting steps of chlorophyll biosynthesis. Mutant analysis indicates that the cytokinin receptors ARABIDOPSIS HIS KINASE2 (AHK2) and AHK3 play a central role in this process. Furthermore, the B-type ARABIDOPSIS RESPONSE REGULATOR1 (ARR1), ARR10, and ARR12 play an important role in mediating the transcriptional output during etioplast-chloroplast transition. B-type ARRs bind to the promotors of HEMA1 and LHCB6 genes, indicating that cytokinin-dependent transcription factors directly regulate genes of chlorophyll biosynthesis and the light harvesting complex. Together, these results demonstrate an important role for the cytokinin signaling pathway in chloroplast development, with the direct transcriptional regulation of chlorophyll biosynthesis genes as a key aspect for this hormonal control. © 2016 American Society of Plant Biologists. All rights reserved.

  9. A two-component signal-transducing system is involved in competence and penicillin susceptibility in laboratory mutants of Streptococcus pneumoniae.

    Science.gov (United States)

    Guenzi, E; Gasc, A M; Sicard, M A; Hakenbeck, R

    1994-05-01

    Penicillin resistance in Streptococcus pneumoniae has been attributed so far to the production of penicillin-binding protein (PBP) variants with decreased affinities for beta-lactam antibiotics. Cefotaxime-resistant laboratory mutants, selected after several steps on increasing concentrations of this beta-lactam, become deficient in transformation as well. A DNA fragment conferring both cefotaxime resistance and transformation deficiency was isolated and cloned from the mutant C306. The cefotaxime resistance associated with this resistance determinant was not accompanied with apparent changes in PBP properties, and it mapped on the chromosome distinct from the known resistance determinants, genes encoding PBP2x, PBP1a or PBP2b. Determination of a 2265 bp DNA sequence of the resistance determinant revealed two open reading frames, ciaR and ciaH, whose deduced amino acid sequence identified the corresponding proteins as the response regulator and histidine kinase receptor, respectively (members of the two families of bacterial signal-transducing proteins). Two hydrophobic peptide regions divided the histidine kinase CiaH into two putative domains: an N-terminal extracellular sensor part, and an intracellular C-terminal domain with the conserved His-226 residue, the presumed phosphorylation site. The single point mutations responsible for cefotaxime-resistance and transformation deficiency of C306 and of another two independently isolated cefotaxime-resistant mutants were each located in the C-terminal half of CiaH. A small extracellular protein, the competence factor, is required for induction of competence. Neither C306 nor the transformants obtained with the mutated ciaH gene produced competence factor, and exogenous competence factor could not complement the transformation deficiency, indicating that the signal-transducing system cia is involved in early steps of competence regulation.

  10. OFD1 and flotillins are integral components of a ciliary signaling protein complex organized by polycystins in renal epithelia and odontoblasts.

    Directory of Open Access Journals (Sweden)

    Stephanie Jerman

    Full Text Available Mutation of the X-linked oral-facial-digital syndrome type 1 (OFD1 gene is embryonic lethal in males and results in craniofacial malformations and adult onset polycystic kidney disease in females. While the OFD1 protein localizes to centriolar satellites, centrosomes and basal bodies, its cellular function and how it relates to cystic kidney disease is largely unknown. Here, we demonstrate that OFD1 is assembled into a protein complex that is localized to the primary cilium and contains the epidermal growth factor receptor (EGFR and domain organizing flotillin proteins. This protein complex, which has similarity to a basolateral adhesion domain formed during cell polarization, also contains the polycystin proteins that when mutant cause autosomal dominant polycystic kidney disease (ADPKD. Importantly, in human ADPKD cells where mutant polycystin-1 fails to localize to cilia, there is a concomitant loss of localization of polycystin-2, OFD1, EGFR and flotillin-1 to cilia. Together, these data suggest that polycystins are necessary for assembly of a novel flotillin-containing ciliary signaling complex and provide a molecular rationale for the common renal pathologies caused by OFD1 and PKD mutations.

  11. Lipids as tumoricidal components of human α-lactalbumin made lethal to tumor cells (HAMLET): unique and shared effects on signaling and death.

    Science.gov (United States)

    Ho, James C S; Storm, Petter; Rydström, Anna; Bowen, Ben; Alsin, Fredrik; Sullivan, Louise; Ambite, Inès; Mok, K H; Northen, Trent; Svanborg, Catharina

    2013-06-14

    Long-chain fatty acids are internalized by receptor-mediated mechanisms or receptor-independent diffusion across cytoplasmic membranes and are utilized as nutrients, building blocks, and signaling intermediates. Here we describe how the association of long-chain fatty acids to a partially unfolded, extracellular protein can alter the presentation to target cells and cellular effects. HAMLET (human α-lactalbumin made lethal to tumor cells) is a tumoricidal complex of partially unfolded α-lactalbumin and oleic acid (OA). As OA lacks independent tumoricidal activity at concentrations equimolar to HAMLET, the contribution of the lipid has been debated. We show by natural abundance (13)C NMR that the lipid in HAMLET is deprotonated and by chromatography that oleate rather than oleic acid is the relevant HAMLET constituent. Compared with HAMLET, oleate (175 μm) showed weak effects on ion fluxes and gene expression. Unlike HAMLET, which causes metabolic paralysis, fatty acid metabolites were less strongly altered. The functional overlap increased with higher oleate concentrations (500 μm). Cellular responses to OA were weak or absent, suggesting that deprotonation favors cellular interactions of fatty acids. Fatty acids may thus exert some of their essential effects on host cells when in the deprotonated state and when presented in the context of a partially unfolded protein.

  12. Knockdown of SF-1 and RNF31 affects components of steroidogenesis, TGFβ, and Wnt/β-catenin signaling in adrenocortical carcinoma cells.

    Directory of Open Access Journals (Sweden)

    Anna Ehrlund

    Full Text Available The orphan nuclear receptor Steroidogenic Factor-1 (SF-1, NR5A1 is a critical regulator of development and homeostasis of the adrenal cortex and gonads. We recently showed that a complex containing E3 ubiquitin ligase RNF31 and the known SF-1 corepressor DAX-1 (NR0B1 interacts with SF-1 on target promoters and represses transcription of steroidogenic acute regulatory protein (StAR and aromatase (CYP19 genes. To further evaluate the role of SF-1 in the adrenal cortex and the involvement of RNF31 in SF-1-dependent pathways, we performed genome-wide gene-expression analysis of adrenocortical NCI-H295R cells where SF-1 or RNF31 had been knocked down using RNA interference. We find RNF31 to be deeply connected to cholesterol metabolism and steroid hormone synthesis, strengthening its role as an SF-1 coregulator. We also find intriguing evidence of negative crosstalk between SF-1 and both transforming growth factor (TGF β and Wnt/β-catenin signaling. This crosstalk could be of importance for adrenogonadal development, maintenance of adrenocortical progenitor cells and the development of adrenocortical carcinoma. Finally, the SF-1 gene profile can be used to distinguish malignant from benign adrenocortical tumors, a finding that implicates SF-1 in the development of malignant adrenocortical carcinoma.

  13. Ultrafine particles from diesel vehicle emissions at different driving cycles induce differential vascular pro-inflammatory responses: Implication of chemical components and NF-κB signaling

    Directory of Open Access Journals (Sweden)

    Jen Nelson

    2010-03-01

    Full Text Available Abstract Background Epidemiological evidence supports the association between exposure to ambient particulate matter (PM and cardiovascular diseases. Chronic exposure to ultrafine particles (UFP; Dp Results UFP2 contained a higher level of redox active organic compounds and metals on a per PM mass basis than UFP1. While both UFP1 and UFP2 induced superoxide production and up-regulated stress response genes such as heme oxygenease-1 (HO-1, OKL38, and tissue factor (TF, only UFP2 induced the expression of pro-inflammatory genes such as IL-8 (2.8 ± 0.3-fold, MCP-1 (3.9 ± 0.4-fold, and VCAM (6.5 ± 1.1-fold (n = 3, P P Conclusion While UFP1 induced higher level of oxidative stress and stress response gene expression, only UFP2, with higher levels of redox active organic compounds and metals, induced pro-inflammatory responses via NF-κB signaling. Thus, UFP with distinct chemical compositions caused differential response patterns in endothelial cells.

  14. Catechol, a major component of smoke, influences primary root growth and root hair elongation through reactive oxygen species-mediated redox signaling.

    Science.gov (United States)

    Wang, Ming; Schoettner, Matthias; Xu, Shuqing; Paetz, Christian; Wilde, Julia; Baldwin, Ian T; Groten, Karin

    2017-03-01

    Nicotiana attenuata germinates from long-lived seedbanks in native soils after fires. Although smoke signals have been known to break seed dormancy, whether they also affect seedling establishment and root development remains unclear. In order to test this, seedlings were treated with smoke solutions. Seedlings responded in a dose-dependent manner with significantly increased primary root lengths, due mainly to longitudinal cell elongation, increased numbers of lateral roots and impaired root hair development. Bioassay-driven fractionations and NMR were used to identify catechol as the main active compound for the smoke-induced root phenotype. The transcriptome analysis revealed that mainly genes related to auxin biosynthesis and redox homeostasis were altered after catechol treatment. However, histochemical analyses of reactive oxygen species (ROS) and the inability of auxin applications to rescue the phenotype clearly indicated that highly localized changes in the root's redox-status, rather than in levels of auxin, are the primary effector. Moreover, H2 O2 application rescued the phenotype in a dose-dependent manner. Chemical cues in smoke not only initiate seed germination, but also influence seedling root growth; understanding how these cues work provides new insights into the molecular mechanisms by which plants adapt to post-fire environments.

  15. Derivative of plant phenolic compound inhibits the type III secretion system of Dickeya dadantii via HrpX/HrpY two-component signal transduction and Rsm systems.

    Science.gov (United States)

    Li, Yan; Hutchins, William; Wu, Xiaogang; Liang, Cuirong; Zhang, Chengfang; Yuan, Xiaochen; Khokhani, Devanshi; Chen, Xin; Che, Yizhou; Wang, Qi; Yang, Ching-Hong

    2015-02-01

    The type III secretion system (T3SS) is a major virulence factor in many Gram-negative bacterial pathogens and represents a particularly appealing target for antimicrobial agents. Previous studies have shown that the plant phenolic compound p-coumaric acid (PCA) plays a role in the inhibition of T3SS expression of the phytopathogen Dickeya dadantii 3937. This study screened a series of derivatives of plant phenolic compounds and identified that trans-4-hydroxycinnamohydroxamic acid (TS103) has an eight-fold higher inhibitory potency than PCA on the T3SS of D. dadantii. The effect of TS103 on regulatory components of the T3SS was further elucidated. Our results suggest that TS103 inhibits HrpY phosphorylation and leads to reduced levels of hrpS and hrpL transcripts. In addition, through a reduction in the RNA levels of the regulatory small RNA RsmB, TS103 also inhibits hrpL at the post-transcriptional level via the rsmB-RsmA regulatory pathway. Finally, TS103 inhibits hrpL transcription and mRNA stability, which leads to reduced expression of HrpL regulon genes, such as hrpA and hrpN. To our knowledge, this is the first inhibitor to affect the T3SS through both the transcriptional and post-transcriptional pathways in the soft-rot phytopathogen D. dadantii 3937. © 2014 BSPP AND JOHN WILEY & SONS LTD.

  16. Chaotic signal denoising method based on independent component analysis and empirical mode decomposition∗%基于独立成分分析和经验模态分解的混沌信号降噪

    Institute of Scientific and Technical Information of China (English)

    王文波; 张晓东; 汪祥莉

    2013-01-01

    According to the characteristics of empirical mode decomposition and denoise of independent component analysis, an adaptive denoising method of chaotic signal is proposed based on independent component analysis and empirical mode decomposition. First, the chaotic signal is decomposed into a set of intrinsic mode functions by empirical mode decomposition;then, the multi-dimensional input vectors are constructed based on the translation invariant empirical mode decomposition, and the noise of each intrinsic mode function is removed through the constructed multi-dimensional input vectors and the independent component analysis; finally, the denoisied chaotic signal is obtained by accumulating and reconstructing all the processed intrinsic mode functions. Both the chaotic signal generated by Lorenz map with different level Gaussian noises, and the observed monthly series of sunspots are respectively used for noise reduction using the proposed method. The results of numerical experiments show that the proposed method is efficient. It can better correct the positions of data points in phase space and approximate the real chaotic attractor trajectories more closely.%  基于经验模态分解和独立成分分析去噪的特点,提出了一种联合独立成分分析和经验模态分解的混沌信号降噪方法。利用经验模态分解对混沌信号进行分解,根据平移不变经验模态分解的思想构造多维输入向量,通过所构造的多维输入向量和独立成分分析对混沌信号的各层内蕴模态函数进行自适应去噪处理;将处理后的所有内蕴模态函数进行累加重构,从而得到降噪后的混沌信号。仿真实验中分别对叠加不同强度高斯噪声的Lorenz混沌信号及实际观测的月太阳黑子混沌序列进行了研究,结果表明本文方法能够对混沌信号进行有效的降噪,而且能够较好地校正相空间中点的位置,逼近真实的混沌吸引子轨迹。

  17. Two-Component Signaling System VgrRS Directly Senses Extracytoplasmic and Intracellular Iron to Control Bacterial Adaptation under Iron Depleted Stress.

    Directory of Open Access Journals (Sweden)

    Li Wang

    2016-12-01

    Full Text Available Both iron starvation and excess are detrimental to cellular life, especially for animal and plant pathogens since they always live in iron-limited environments produced by host immune responses. However, how organisms sense and respond to iron is incompletely understood. Herein, we reveal that in the phytopathogenic bacterium Xanthomonas campestris pv. campestris, VgrS (also named ColS is a membrane-bound receptor histidine kinase that senses extracytoplasmic iron limitation in the periplasm, while its cognate response regulator, VgrR (ColR, detects intracellular iron excess. Under iron-depleted conditions, dissociation of Fe3+ from the periplasmic sensor region of VgrS activates the VgrS autophosphorylation and subsequent phosphotransfer to VgrR, an OmpR-family transcription factor that regulates bacterial responses to take up iron. VgrR-VgrS regulon and the consensus DNA binding motif of the transcription factor VgrR were dissected by comparative proteomic and ChIP-seq analyses, which revealed that in reacting to iron-depleted environments, VgrR directly or indirectly controls the expressions of hundreds of genes that are involved in various physiological cascades, especially those associated with iron-uptake. Among them, we demonstrated that the phosphorylated VgrR tightly represses the transcription of a special TonB-dependent receptor gene, tdvA. This regulation is a critical prerequisite for efficient iron uptake and bacterial virulence since activation of tdvA transcription is detrimental to these processes. When the intracellular iron accumulates, the VgrR-Fe2+ interaction dissociates not only the binding between VgrR and the tdvA promoter, but also the interaction between VgrR and VgrS. This relieves the repression in tdvA transcription to impede continuous iron uptake and avoids possible toxic effects of excessive iron accumulation. Our results revealed a signaling system that directly senses both extracytoplasmic and intracellular

  18. Comparative proteomics of oxalate downregulated tomatoes points towards cross talk of signal components and metabolic consequences during post-harvest storage

    Directory of Open Access Journals (Sweden)

    Kanika Narula

    2016-08-01

    Full Text Available Fruits of angiosperms evolved intricate regulatory machinery for sensorial attributes and storage quality after harvesting. Organic acid composition of storage organs forms the molecular and biochemical basis of organoleptic and nutritional qualities with metabolic specialization. Of these, oxalic acid (OA, determines the post-harvest quality in fruits. Tomato (Solanum lycopersicum fruit have distinctive feature to undergo a shift from heterotrophic metabolism to carbon assimilation partitioning during storage. We have earlier shown that decarboxylative degradation of OA by FvOXDC leads to acid homeostasis besides increased fungal tolerance in E8.2-OXDC tomato. Here, we elucidate the metabolic consequences of oxalate down-regulation and molecular mechanisms that determine organoleptic features, signaling and hormonal regulation in E8.2-OXDC fruit during post-harvest storage. A comparative proteomics approach has been applied between wild-type and E8.2-OXDC tomato in temporal manner. The MS/MS analyses led to the identification of 32 and 39 differentially abundant proteins associated with primary and secondary metabolism, assimilation, biogenesis, and development in wild-type and E8.2-OXDC tomatoes, respectively. Next, we interrogated the proteome data using correlation network analysis that identified significant functional hubs pointing toward storage related coinciding processes through a common mechanism of function and modulation. Furthermore, physiochemical analyses exhibited reduced oxalic acid content with concomitant increase in citric acid, lycopene and marginal decrease in malic acid in E8.2-OXDC fruit. Nevertheless, E8.2-OXDC fruit maintained an optimal pH and a steady state acid pool. These might contribute to reorganization of pectin constituent, reduced membrane leakage and improved fruit firmness in E8.2-OXDC fruit with that of wild-type tomato during storage. Collectively, our study provides insights into kinetically controlled

  19. Effect of histamine on the signal transduction of the AtoS-AtoC two component system and involvement in poly-(R)-3-hydroxybutyrate biosynthesis in Escherichia coli.

    Science.gov (United States)

    Kyriakidis, D A; Theodorou, M C; Filippou, P S; Kyriakidis, K D; Tiligada, E

    2008-06-01

    AtoS-AtoC two-component system acts directly on the atoDAEB operon transcription to regulate the biosynthesis of short-chain poly-(R)-3-hydroxybutyrate. This study sought to investigate the effect of histamine and compound 48/80 on the regulation of AtoS-AtoC two-component system in Escherichia coli K-12 MA255 (speC(-), speB(-)) and the isogenic E. coli strains BW25113 (atoSC(+)) and BW28878 (DeltaatoSC) transformed with plasmids carrying related genes. Histamine or compound 48/80 induced or tended to reduce atoC transcription, respectively, while neither compound showed any effect on atoDAEB operon transcription. Moreover, histamine down-regulated poly-(R)-3-hydroxybutyrate biosynthesis, whereas compound 48/80 up-regulated its biosynthesis, maximal induction being obtained in the presence of multiple copies of AtoS-AtoC. Interestingly, co-administration of histamine counteracted this inductive effect of compound 48/80. The reported data provide the first evidence for a differential modulator role of histamine and compound 48/80 on the AtoS-AtoC two-component system signaling in potentially pathogenic bacteria, leading to a new perspective on their symbiotic behavior.

  20. Progression on the research of two-component signal transduction system in fungus and its inhibitors%真菌双组分信号转导系统及其抑制剂研究进展

    Institute of Scientific and Technical Information of China (English)

    徐西光; 张子平; 程波

    2011-01-01

    双组分信号转导系统存在于包括真菌在内的大部分低等真核生物、原核生物及一些植物中.真菌双组分信号转导蛋白在细胞新陈代谢、毒力以及致病性等方面具有重要作用,且目前在人类细胞中尚未发现双组分信号转导系统.因此,探明真菌双组分信号转导系统的机制,可为抑制剂的设计和寻找提供多个“靶点”,从而研制出能够抗致病性真菌而不对宿主细胞造成损伤的新型抗真菌药物.本文就近年来真菌双组分信号转导系统及其潜在抑制剂进行综述.%Two-component signal transduction system, which plays an important role in cell metabolism, virulence and pathoge-nicity, has been found in most lower eukaryotes, prokaryotes and some plants, yet not in human cells. Well-understanding of the mechanism may be helpful for inhibitor designing, which has antifungal effect without damage to host cell. Recent literatures about two-component signal transduction system in fungi and potential inhibitors are reviewed.

  1. Electronic components

    CERN Document Server

    Colwell, Morris A

    1976-01-01

    Electronic Components provides a basic grounding in the practical aspects of using and selecting electronics components. The book describes the basic requirements needed to start practical work on electronic equipment, resistors and potentiometers, capacitance, and inductors and transformers. The text discusses semiconductor devices such as diodes, thyristors and triacs, transistors and heat sinks, logic and linear integrated circuits (I.C.s) and electromechanical devices. Common abbreviations applied to components are provided. Constructors and electronics engineers will find the book useful

  2. Estimación de las componentes simétricas instantáneas de señales eléctricas usando filtros sintonizados Instantaneous symmetrical components estimation of electrical signals using tuned filters

    Directory of Open Access Journals (Sweden)

    Johann F Petit Suárez

    2011-06-01

    Full Text Available En este artículo se propone un algoritmo basado en filtros sintonizados para extraer las componentes instantáneas de secuencia positiva, negativa y cero (+,-,0 de señales de tensión y/o corrientes desequilibradas y distorsionadas. El trabajo se encuentra justificado en la necesidad de disponer de nuevos algoritmos que puedan ser utilizados en la medición de parámetros que afectan a la calidad de la energía eléctrica con el fin de diagnosticar y compensar las perturbaciones presentes en las señales de tensión y/o corriente. El desempeño del algoritmo es evaluado mediante simulaciones en Matlab/Simulink y por medio de su implementación en tiempo real en la tarjeta de desarrollo dSPACE 1104. Los resultados obtenidos muestran la eficacia del algoritmo propuesto.In this paper a new algorithm based on tuned filters to extract the positive, negative and zero sequence instantaneous components of distorted and unbalanced electrical signals is shown. The new algorithm can be used in applications such as signal parameter estimation, power quality analysis and it can be useful for estimating the reference signal of some compensation devices used to improve the power quality. The algorithm performance is evaluated by simulations in Matlab/Simulink and through its implementation in real time on a dSPACE 1104 development board. In addition, the experimental setup results show an outstanding performance.

  3. Transcriptional regulation of abscisic acid signal core components during cucumber seed germination and under Cu²⁺, Zn²⁺, NaCl and simulated acid rain stresses.

    Science.gov (United States)

    Wang, Yanping; Wang, Ya; Kai, Wenbin; Zhao, Bo; Chen, Pei; Sun, Liang; Ji, Kai; Li, Qian; Dai, Shengjie; Sun, Yufei; Wang, Yidong; Pei, Yuelin; Leng, Ping

    2014-03-01

    Abscisic acid (ABA) is an important phytohormone that regulates lots of physiological and biochemical processes in plant life cycle, especially in seed germination and stress responses. For exploring the transcriptional regulation of ABA signal transduction during cucumber (Cucumis sativus L.) seed germination and under Cu(2+), Zn(2+), NaCl and simulated acid rain stresses, nine CsPYLs, three group A CsPP2Cs and two subclass III CsSnRK2s were identified from cucumber genome, which respectively showed high sequence similarities and highly conserved domains with homologous genes in Arabidopsis. Based on Real-time PCR analysis, most of the tested genes' expression decreased during cucumber seed germination, which was in accordance with the ABA level variation. In addition, according to the absolute expression, CsPYL1, CsPYL3, CsPP2C5, CsABI1, CsSnRK2.3 and CsSnRK2.4 were highly expressed, indicating that they may play more important roles in ABA signaling during cucumber seed germination. Moreover, most of these highly expressed genes, except CsPYL3, were up-regulated by ABA treatment. Meanwhile, most of the tested genes' expression dramatically changed at the initial water uptake phase, indicating that this period may be critical in the regulation of ABA on seed germination. Under Cu(2+), Zn(2+), NaCl and simulated acid rain stresses, cucumber seed germination percentage decreased and ABA content increased. Meanwhile, the expression of ABA signal transduction core components genes showed specific response to a particular stress and was not always consist with ABA variation. Generally, the expression of CsPYL1, CsPYL3, CsABI1, CsSnRK2.3 and CsSnRK2.4 was sensitive to 120 mM NaCl and 0.5 mM Cu(2+) treatments.

  4. Compressive Principal Component Pursuit

    CERN Document Server

    Wright, John; Min, Kerui; Ma, Yi

    2012-01-01

    We consider the problem of recovering a target matrix that is a superposition of low-rank and sparse components, from a small set of linear measurements. This problem arises in compressed sensing of structured high-dimensional signals such as videos and hyperspectral images, as well as in the analysis of transformation invariant low-rank recovery. We analyze the performance of the natural convex heuristic for solving this problem, under the assumption that measurements are chosen uniformly at random. We prove that this heuristic exactly recovers low-rank and sparse terms, provided the number of observations exceeds the number of intrinsic degrees of freedom of the component signals by a polylogarithmic factor. Our analysis introduces several ideas that may be of independent interest for the more general problem of compressed sensing and decomposing superpositions of multiple structured signals.

  5. SCOOP - Semiconductor COmponents for Optical signal Processing

    DEFF Research Database (Denmark)

    Mørk, Jesper; Yvind, Kresten; Oxenløwe, Leif Katsuo;

    2001-01-01

    Opto-electronic semiconductor devices operating at very high bitrates play a central role in the continued expansion of the transmission capacity of optical communication systems. A number of different devices based on quantum well structures have been manufactured within the framework of the nat......Opto-electronic semiconductor devices operating at very high bitrates play a central role in the continued expansion of the transmission capacity of optical communication systems. A number of different devices based on quantum well structures have been manufactured within the framework...... of the national SCOOP programme. Results for a high-speed modulator, a short-pulse laser and an all-optical switch are presented....

  6. Areca nut components affect COX-2, cyclin B1/cdc25C and keratin expression, PGE2 production in keratinocyte is related to reactive oxygen species, CYP1A1, Src, EGFR and Ras signaling.

    Directory of Open Access Journals (Sweden)

    Mei-Chi Chang

    Full Text Available Chewing of betel quid (BQ increases the risk of oral cancer and oral submucous fibrosis (OSF, possibly by BQ-induced toxicity and induction of inflammatory response in oral mucosa.Primary gingival keratinocytes (GK cells were exposed to areca nut (AN components with/without inhibitors. Cytotoxicity was measured by 3-(4,5-dimethyl- thiazol- 2-yl-2,5-diphenyl-tetrazolium bromide (MTT assay. mRNA and protein expression was evaluated by reverse transcriptase-polymerase chain reaction (RT-PCR and western blotting. PGE2/PGF2α production was measured by enzyme-linked immunosorbent assays.Areca nut extract (ANE stimulated PGE2/PGF2α production, and upregulated the expression of cyclooxygenase-2 (COX-2, cytochrome P450 1A1 (CYP1A1 and hemeoxygenase-1 (HO-1, but inhibited expression of keratin 5/14, cyclinB1 and cdc25C in GK cells. ANE also activated epidermal growth factor receptor (EGFR, Src and Ras signaling pathways. ANE-induced COX-2, keratin 5, keratin 14 and cdc25C expression as well as PGE2 production were differentially regulated by α-naphthoflavone (a CYP 1A1/1A2 inhibitor, PD153035 (EGFR inhibitor, pp2 (Src inhibitor, and manumycin A (a Ras inhibitor. ANE-induced PGE2 production was suppressed by piper betle leaf (PBL extract and hydroxychavicol (two major BQ components, dicoumarol (aQuinone Oxidoreductase--NQO1 inhibitor and curcumin. ANE-induced cytotoxicity was inhibited by catalase and enhanced by dicoumarol, suggesting that AN components may contribute to the pathogenesis of OSF and oral cancer via induction of aberrant differentiation, cytotoxicity, COX-2 expression, and PGE2/PGF2α production.CYP4501A1, reactive oxygen species (ROS, EGFR, Src and Ras signaling pathways could all play a role in ANE-induced pathogenesis of oral cancer. Addition of PBL into BQ and curcumin consumption could inhibit the ANE-induced inflammatory response.

  7. Multiplexing oscillatory biochemical signals.

    Science.gov (United States)

    de Ronde, Wiet; ten Wolde, Pieter Rein

    2014-04-01

    In recent years it has been increasingly recognized that biochemical signals are not necessarily constant in time and that the temporal dynamics of a signal can be the information carrier. Moreover, it is now well established that the protein signaling network of living cells has a bow-tie structure and that components are often shared between different signaling pathways. Here we show by mathematical modeling that living cells can multiplex a constant and an oscillatory signal: they can transmit these two signals simultaneously through a common signaling pathway, and yet respond to them specifically and reliably. We find that information transmission is reduced not only by noise arising from the intrinsic stochasticity of biochemical reactions, but also by crosstalk between the different channels. Yet, under biologically relevant conditions more than 2 bits of information can be transmitted per channel, even when the two signals are transmitted simultaneously. These observations suggest that oscillatory signals are ideal for multiplexing signals.

  8. Principal component analysis with pre-normalization improves the signal-to-noise ratio and image quality in positron emission tomography studies of amyloid deposits in Alzheimer's disease

    Energy Technology Data Exchange (ETDEWEB)

    Razifar, Pasha [Molecular Imaging and CT Research, GE Healthcare, WI 53188, Waukesha (United States); Engler, Henry [Department of Medical Science, Uppsala University, SE-751 85 Uppsala (Sweden); Blomquist, Gunnar [Department of Oncology, Radiology and Clinical Immunology, Uppsala University, SE-751 85 Uppsala (Sweden); Ringheim, Anna; Estrada, Sergio [Uppsala Imanet AB, GE Healthcare, Box 967, SE-751 09, Uppsala (Sweden); Laangstroem, Bengt [Department of Biochemistry and Organic Chemistry, Uppsala University, SE-751 24 Uppsala (Sweden); Bergstroem, Mats [Department of Pharmaceutical Biosciences, Uppsala University, SE-751 24 Uppsala (Sweden)

    2009-06-07

    This study introduces a new approach for the application of principal component analysis (PCA) with pre-normalization on dynamic positron emission tomography (PET) images. These images are generated using the amyloid imaging agent N-methyl [{sup 11}C]2-(4'-methylaminophenyl)-6-hydroxy-benzothiazole ([{sup 11}C]PIB) in patients with Alzheimer's disease (AD) and healthy volunteers (HVs). The aim was to introduce a method which, by using the whole dataset and without assuming a specific kinetic model, could generate images with improved signal-to-noise and detect, extract and illustrate changes in kinetic behavior between different regions in the brain. Eight AD patients and eight HVs from a previously published study with [{sup 11}C]PIB were used. The approach includes enhancement of brain regions where the kinetics of the radiotracer are different from what is seen in the reference region, pre-normalization for differences in noise levels and removal of negative values. This is followed by slice-wise application of PCA (SW-PCA) on the dynamic PET images. Results obtained using the new approach were compared with results obtained using reference Patlak and summed images. The new approach generated images with good quality in which cortical brain regions in AD patients showed high uptake, compared to cerebellum and white matter. Cortical structures in HVs showed low uptake as expected and in good agreement with data generated using kinetic modeling. The introduced approach generated images with enhanced contrast and improved signal-to-noise ratio (SNR) and discrimination power (DP) compared to summed images and parametric images. This method is expected to be an important clinical tool in the diagnosis and differential diagnosis of dementia.

  9. 隐藏嗜酸菌Acidiphilium cryptum JF-5双组分信号转导系统%Two-component signal transduction system of Acidiphilium cryptum JF-5

    Institute of Scientific and Technical Information of China (English)

    余水静; 彭艳平; 邓扬悟; 郭燕华; 刘荷英

    2013-01-01

      为了探索隐藏嗜酸菌(Acidiphilium cryptum)对多变极端矿山环境条件的感知和反应分子机制,预测和分析了隐藏嗜酸菌JF-5菌株的双组分信号转导系统(Two-component signal transduction system, TCS)的分布、结构及功能。鉴定了9对成对TCSs、2个杂合结构TCSs、3个孤儿组氨酸蛋白激酶(HK)和5个孤儿反应调节蛋白(RR);发现5个TCSs参与隐藏嗜酸菌对重金属响应转录调控;大多数HKs的N-末端具有接受信号的跨膜区、HAMP或PAS等结构域,RRs主要是OmpR亚家族,占总RRs的40%以上;从进化关系上来看,一些处在进化树同一分支上的共同聚簇TCS基因可能具有相同的进化途径。本研究结果可为研究隐藏嗜酸菌在极端环境中适应性分子机制提供新的方向。%In order to explore the molecular mechanism of Acidiphilium cryptum response to extreme conditions in the mine environment, the distributions, structures and putative biological functions of two-component signal transduction systems (TCSs) in A. cryptum JF-5 are predicated and analyzed. And 9 TCSs, 2 hybrid histidine kinases (HK), 3 orphan HKs and 5 orphan response regulator proteins (RR) were identified. Five TCSs were involved in the transcription regulation of A. cryptum response to heavy metal. The most N-terminal regions of HKs were characterized by the presence of transmembrane helices, HAMPs, or PAS domains. More than 40 percent of putative RRs were classified into OmpR subfamily. From the evolutionary relationship, the common clustering TCS genes in the same branch of the evolutionary tree may have the same evolutionary pathway. Our results should open a novel research direction in A. cryptum for molecular mechanism of the adaptation in the extreme environment.

  10. Bioinformatics analysis of two-component signal transduction systems of Bacillus thuringiensis%苏云金芽孢杆菌双组份信号转导系统的生物信息学分析

    Institute of Scientific and Technical Information of China (English)

    张清仪; 王阶平; 程钢; 刘钟慧; 范文瑾; 何进

    2011-01-01

    苏云金芽孢杆菌(Bacillus thuringiensis)能产生杀虫晶体蛋白等多种活性成分,是目前应用最广泛的微生物杀虫剂.本文采用生物信息学方法,系统分析了由本实验室完成全基因组测序的苏云全芽孢杆菌YBT-1520、CT-43和BMB171 3个菌株的双组分信号转导系统(Two-component signal traducction system,TCS)的分布、结构及功能,并初步构建了部分TCS的调控网络关系图.本研究旨在为深入研究苏云金芽孢杆菌的生长、代谢以及毒力因子的表达与调控,全面了解伴孢晶体的形成机制开辟新的研究方向.%Bacillus thuringiensis (Bt) strains, which can produce insecticidal crystal proteins, were widely used as biological pesticides. In this paper, we comprehensively analyzed the distributions, structures and putative biological functions of two-component transduction systems (TCS) from the genomes of Bt strains YBT-1520, CT-43 and BMB171, which have been sequenced by our laboratory. And more importantly, we constructed a preliminary TCS regulatory networks. This study should open a novel research direction in Bt for the growth, metabolism, regulator of toxic gene expression, as well as the formation mechanism of parasporal crystals.

  11. Prosocial Signalling

    DEFF Research Database (Denmark)

    Kahsay, Goytom Abraha

    suggested that consumers pay price premium because this sends the signal that the consumer has prosocial preferences and a few empirical studies have documented that reputation plays a key role when consumers choose products containing prosocial components. However, little is known about consumers...... consumer goods and presents empirical evidences from a natural consumption data. This thesis also investigates consumers’ behaviour under a newly introduced pricing system called Pay-What-You-Want (PWYW) and investigates empirically whether reputation signalling can be used as a policy instrument in other...... on the role of social network in facilitating factor input transactions and the role of reputation in reducing enforcement. Finally, the third part consists of one paper which is concerned with investigating the effect of climate change and adaptation policy on agricultural production in Eastern Africa...

  12. Two-component signal transduction system and the virulence-related characteristics of Streptococcus mutans%双组分信号传导系统与变异链球菌的致病相关特性

    Institute of Scientific and Technical Information of China (English)

    陈娇

    2011-01-01

    Two-component signal transduction system (TCSTS) plays an important role in the expression of virulence factors of Streptococcus mutans, such as the competence development, the formation of biofilm, the stability of structure, the production of bacteriocin, and the properties of acid production and resistance. It provides many ecological advantages to compete and survive in the dental plaque. This article is a review about the composition of TCSTS of Streptococcus mutans, the effect of TCSTS on the virulence-related characteristics of Streptococcus mutans, and the application significance of TCSTS.%双组分信号传导系统(TCSTS)在变异链球菌感受态形成、生物膜形成、结构稳定、菌素产生、产酸耐酸特性等毒力因子表达方面起着重要的作用,为其在菌斑生物膜中的竞争和生存提供了诸多生态性优势.本文就变异链球菌TCSTS的组成、TCSTS对变异链球菌致病相关特性的影响、TCSTS的应用意义等作一综述.

  13. Novel pure component contribution, mean centering of ratio spectra and factor based algorithms for simultaneous resolution and quantification of overlapped spectral signals: An application to recently co-formulated tablets of chlorzoxazone, aceclofenac and paracetamol

    Science.gov (United States)

    Toubar, Safaa S.; Hegazy, Maha A.; Elshahed, Mona S.; Helmy, Marwa I.

    2016-06-01

    In this work, resolution and quantitation of spectral signals are achieved by several univariate and multivariate techniques. The novel pure component contribution algorithm (PCCA) along with mean centering of ratio spectra (MCR) and the factor based partial least squares (PLS) algorithms were developed for simultaneous determination of chlorzoxazone (CXZ), aceclofenac (ACF) and paracetamol (PAR) in their pure form and recently co-formulated tablets. The PCCA method allows the determination of each drug at its λmax. While, the mean centered values at 230, 302 and 253 nm, were used for quantification of CXZ, ACF and PAR, respectively, by MCR method. Partial least-squares (PLS) algorithm was applied as a multivariate calibration method. The three methods were successfully applied for determination of CXZ, ACF and PAR in pure form and tablets. Good linear relationships were obtained in the ranges of 2-50, 2-40 and 2-30 μg mL- 1 for CXZ, ACF and PAR, in order, by both PCCA and MCR, while the PLS model was built for the three compounds each in the range of 2-10 μg mL- 1. The results obtained from the proposed methods were statistically compared with a reported one. PCCA and MCR methods were validated according to ICH guidelines, while PLS method was validated by both cross validation and an independent data set. They are found suitable for the determination of the studied drugs in bulk powder and tablets.

  14. VicRK two-component signal transduction system of Streptococcus mutans%变异链球菌的VicRK双组分信号传导系统

    Institute of Scientific and Technical Information of China (English)

    田媛媛

    2012-01-01

    Streptococcus mutans(S.nuaans), which is considered as the chief pathogen of human caries, possesses the ability to form biofilm via sucrose-dependent adhesion, genesis and endure acids in the biofilm that may ultimately lead to dental caries. VicRK is one of the 13 putative two-component signal transduction systems of S.mutans that modulate the expression of cariogeneisis related virulence factors. This review summarized the mechanism, structural organization, physiological characteristics and the impact on the cariogenesis capabilities of VicRK, as well as the correlation between VicRK and VicX in S.mutans.%变异链球菌是人类龋病的主要病原菌,它通过蔗糖依赖性黏附形成生物膜并在其中产酸耐酸,最终导致龋病.VicRK是变异链球菌13种双组分信号传导系统之一,可调节变异链球菌致龋性毒力相关因子的表达.本文就VicRK的作用机制、结构组成、生理特性,及其对变异链球菌致龋性的影响,VicRK和VicX间的关系等研究进展作一综述.

  15. 穿戴式儿童情感识别系统中心电信号放大器的设计%Design for the ECG Signal Collection Component in the Wearable System for Child-Emotion Recognition

    Institute of Scientific and Technical Information of China (English)

    周洁; 魏丹丹; 赵力; 邹采荣

    2011-01-01

    Recent researches show that children's emotion ability can indicate their future achievement. Emotions are typically associated with observable physiological changing patterns as well as subjective appraisals and cognitive components representation. In order to prevent the devices from influencing the children's nature state,we proposed the concept of "Wearable" system. The emphasis of this paper is to realize the collecting part of ECG signal in this system.%研究表明儿童时期具有的情绪能力,是他们以后生活中能否成功的最好预示.虽然情绪是一种主观意识,但情绪状态的变化总会伴随一定的生理变化.从而我们可以从生理参数的角度,用一套客观的评价标准来研究情绪状态.为了让测试儿童处在一个相对自然的状态,使情绪识别结果的可信度更高,我们提出了"穿戴式"生理参数采集系统的概念.本文的研究重点就是实现这个系统中的心电信号采集部分.

  16. Limonin, a Component of Dictamni Radicis Cortex, Inhibits Eugenol-Induced Calcium and cAMP Levels and PKA/CREB Signaling Pathway in Non-Neuronal 3T3-L1 Cells

    Directory of Open Access Journals (Sweden)

    Yeo Cho Yoon

    2015-12-01

    Full Text Available Limonin, one of the major components in dictamni radicis cortex (DRC, has been shown to play various biological roles in cancer, inflammation, and obesity in many different cell types and tissues. Recently, the odorant-induced signal transduction pathway (OST has gained attention not only because of its function in the perception of smell but also because of its numerous physiological functions in non-neuronal cells. However, little is known about the effects of limonin and DRC on the OST pathway in non-neuronal cells. We investigated odorant-stimulated increases in Ca2+ and cAMP, major second messengers in the OST pathway, in non-neuronal 3T3-L1 cells pretreated with limonin and ethanol extracts of DRC. Limonin and the extracts significantly decreased eugenol-induced Ca2+ and cAMP levels and upregulated phosphorylation of CREB and PKA. Our results demonstrated that limonin and DRC extract inhibit the OST pathway in non-neuronal cells by modulating Ca2+ and cAMP levels and phosphorylation of CREB.

  17. Mechanism of activation of PhoQ/PhoP two-component signal transduction by SafA, an auxiliary protein of PhoQ histidine kinase in Escherichia coli.

    Science.gov (United States)

    Ishii, Eiji; Eguchi, Yoko; Utsumi, Ryutaro

    2013-01-01

    The PhoQ/PhoP two-component signal transduction system in Escherichia coli is activated by SafA, a small membrane protein that modifies the PhoQ histidine kinase. The SafA C-terminal domain (41-65 aa) interacts directly with the sensory domain of PhoQ at the periplasm. We used in vitro and in vivo strategies to elucidate the way SafA modifies the PhoQ/PhoP phosphorelay system. First, the enzymatic activities of membranes from cells overexpressing PhoQ and cells expressing both PhoQ and SafA were compared in vitro. Increased autophosphorylation of PhoQ was observed in the presence of SafA, but it did not increase the dephosphorylation of phospho-PhoP by PhoQ. In addition, SafA increased the phospho-PhoP level on the phosphotransfer assay. We confirmed that induction of SafA results in an accumulation of phospho-PhoP in vivo by the Phos-tag system. Our results suggest that the accumulation of phospho-PhoP is linked to activation of PhoQ autophosphorylation by SafA.

  18. Limonin, a Component of Dictamni Radicis Cortex, Inhibits Eugenol-Induced Calcium and cAMP Levels and PKA/CREB Signaling Pathway in Non-Neuronal 3T3-L1 Cells.

    Science.gov (United States)

    Yoon, Yeo Cho; Kim, Sung-Hee; Kim, Min Jung; Yang, Hye Jeong; Rhyu, Mee-Ra; Park, Jae-Ho

    2015-12-10

    Limonin, one of the major components in dictamni radicis cortex (DRC), has been shown to play various biological roles in cancer, inflammation, and obesity in many different cell types and tissues. Recently, the odorant-induced signal transduction pathway (OST) has gained attention not only because of its function in the perception of smell but also because of its numerous physiological functions in non-neuronal cells. However, little is known about the effects of limonin and DRC on the OST pathway in non-neuronal cells. We investigated odorant-stimulated increases in Ca(2+) and cAMP, major second messengers in the OST pathway, in non-neuronal 3T3-L1 cells pretreated with limonin and ethanol extracts of DRC. Limonin and the extracts significantly decreased eugenol-induced Ca(2+) and cAMP levels and upregulated phosphorylation of CREB and PKA. Our results demonstrated that limonin and DRC extract inhibit the OST pathway in non-neuronal cells by modulating Ca(2+) and cAMP levels and phosphorylation of CREB.

  19. The Drosophila gene Medea demonstrates the requirement for different classes of Smads in dpp signaling.

    Science.gov (United States)

    Das, P; Maduzia, L L; Wang, H; Finelli, A L; Cho, S H; Smith, M M; Padgett, R W

    1998-04-01

    Signals from transforming growth factor-beta (TGF-beta) ligands are transmitted within the cell by members of the Smad family, which can be grouped into three classes based on sequence similarities. Our previous identification of both class I and II Smads functioning in a single pathway in C. elegans, raised the issue of whether the requirement for Smads derived from different classes is a general feature of TGF-beta signaling. We report here the identification of a new Drosophila class II Smad, Medea, a close homolog of the human tumor-suppressor gene DPC4. Embryos from germline clones of both Medea and Mad (a class I Smad) are ventralized, as are embryos null for the TGF-beta-like ligand decapentaplegic (dpp). Loss of Medea also blocks dpp signaling during later development, suggesting that Medea, like Mad, is universally required for dpp signaling. Furthermore, we show that the necessity for these two closely related, non-redundant Smads, is due to their different signaling properties - upon activation of the Dpp pathway, Mad is required to actively translocate Medea into the nucleus. These results provide a paradigm for, and distinguish between, the requirement for class I and II Smads in Dpp/BMP signaling.

  20. Cognitive Component Analysis

    DEFF Research Database (Denmark)

    Feng, Ling

    2008-01-01

    of audio contexts along with pattern recognition methods to map components to known contexts. It also involves looking for the right representations for auditory inputs, i.e. the data analytic processing pipelines invoked by human brains. The main ideas refer to Cognitive Component Analysis, defined......This dissertation concerns the investigation of the consistency of statistical regularities in a signaling ecology and human cognition, while inferring appropriate actions for a speech-based perceptual task. It is based on unsupervised Independent Component Analysis providing a rich spectrum...... as the process of unsupervised grouping of generic data such that the ensuing group structure is well-aligned with that resulting from human cognitive activity. Its hypothesis runs ecologically: features which are essentially independent in a context defined ensemble, can be efficiently coded as sparse...

  1. Specific components of face perception in the human fusiform gyrus studied by tomographic estimates of magnetoencephalographic signals: a tool for the evaluation of non-verbal communication in psychosomatic paradigms.

    Science.gov (United States)

    Okazaki, Yuka; Ioannides, Andreas A

    2007-12-04

    The aim of this study was to determine the specific spatiotemporal activation patterns of face perception in the fusiform gyrus (FG). The FG is a key area in the specialized brain system that makes possible the recognition of face with ease and speed in our daily life. Characterization of FG response provides a quantitative method for evaluating the fundamental functions that contribute to non-verbal communication in various psychosomatic paradigms. The MEG signal was recorded during passive visual stimulus presentation with three stimulus types - Faces, Hands and Shoes. The stimuli were presented separately to the central and peripheral visual fields. We performed statistical parametric mapping (SPM) analysis of tomographic estimates of activity to compare activity between a pre- and post-stimulus period in the same object (baseline test), and activity between objects (active test). The time course of regional activation curves was analyzed for each stimulus condition. The SPM baseline test revealed a response to each stimulus type, which was very compact at the initial segment of main M(FG)170. For hands and shoes the area of significant change remains compact. For faces the area expanded widely within a few milliseconds and its boundaries engulfed the other object areas. The active test demonstrated that activity for faces was significantly larger than the activity for hands. The same face specific compact area as in the baseline test was identified, and then again expanded widely. For each stimulus type and presentation in each one of the visual fields locations, the analysis of the time course of FG activity identified three components in the FG: M(FG)100, M(FG)170, and M(FG)200 - all showed preference for faces. Early compact face-specific activity in the FG expands widely along the occipito-ventral brain within a few milliseconds. The significant difference between faces and the other object stimuli in M(FG)100 shows that processing of faces is already

  2. Specific components of face perception in the human fusiform gyrus studied by tomographic estimates of magnetoencephalographic signals: a tool for the evaluation of non-verbal communication in psychosomatic paradigms

    Directory of Open Access Journals (Sweden)

    Ioannides Andreas A

    2007-12-01

    Full Text Available Abstract Aims The aim of this study was to determine the specific spatiotemporal activation patterns of face perception in the fusiform gyrus (FG. The FG is a key area in the specialized brain system that makes possible the recognition of face with ease and speed in our daily life. Characterization of FG response provides a quantitative method for evaluating the fundamental functions that contribute to non-verbal communication in various psychosomatic paradigms. Methods The MEG signal was recorded during passive visual stimulus presentation with three stimulus types – Faces, Hands and Shoes. The stimuli were presented separately to the central and peripheral visual fields. We performed statistical parametric mapping (SPM analysis of tomographic estimates of activity to compare activity between a pre- and post-stimulus period in the same object (baseline test, and activity between objects (active test. The time course of regional activation curves was analyzed for each stimulus condition. Results The SPM baseline test revealed a response to each stimulus type, which was very compact at the initial segment of main MFG170. For hands and shoes the area of significant change remains compact. For faces the area expanded widely within a few milliseconds and its boundaries engulfed the other object areas. The active test demonstrated that activity for faces was significantly larger than the activity for hands. The same face specific compact area as in the baseline test was identified, and then again expanded widely. For each stimulus type and presentation in each one of the visual fields locations, the analysis of the time course of FG activity identified three components in the FG: MFG100, MFG170, and MFG200 – all showed preference for faces. Conclusion Early compact face-specific activity in the FG expands widely along the occipito-ventral brain within a few milliseconds. The significant difference between faces and the other object stimuli in MFG

  3. Systematic mutation analysis of two-component signal transduction systems reveals EsrA-EsrB and PhoP-PhoQ as the major virulence regulators in Edwardsiella tarda.

    Science.gov (United States)

    Lv, Yuanzhi; Xiao, Jingfan; Liu, Qin; Wu, Haizhen; Zhang, Yuanxing; Wang, Qiyao

    2012-05-25

    Edwardsiella tarda is a Gram-negative broad-host-range pathogen that causes hemorrhagic septicemia in many commercially important fish species. Its ability to adapt to and thrive in diverse environments outside and inside of its hosts prompts us to investigate the roles of the previously identified 33 putative two-component signal transduction systems (TCSs) in E. tarda. In this work, we successfully constructed deletion mutations in each of the response regulator genes, suggesting that none of the TCSs are essential for cell viability in E. tarda. The mutants were further examined for roles in biofilm formation, antibiotic resistance, stress response, expression and secretion of proteins involved in either the type III secretion system (T3SS) or type VI secretion system (T6SS), as well as virulence. Through these assays, we identified four regulators of biofilm development, two regulators of antibiotic resistance, and four regulators involved in stress responses. We found that two regulators, EsrB and PhoP, are essential for the pathogenicity of E. tarda and further demonstrated that these two regulators have codependent and independent contributions to E. tarda virulence. Mutation of EsrB resulted in the complete loss of both the T3SS and T6SS proteins, while PhoP partially regulated the expression of T3SS and T6SS genes through EsrB, and was essential for resistance to antimicrobial peptides. This work suggested that these two response regulators are involved in the regulation of the complex virulence network of this bacterium and merit as candidate genes for live attenuated vaccine construction. Copyright © 2011 Elsevier B.V. All rights reserved.

  4. A combination of four effective components derived from Sheng-mai san attenuates hydrogen peroxide-induced injury in PC12 cells through inhibiting Akt and MAPK signaling pathways.

    Science.gov (United States)

    Cao, Guo-Sheng; Li, Shao-Xia; Wang, Yan; Xu, Ying-Qiong; Lv, Yan-Ni; Kou, Jun-Ping; Yu, Bo-Yang

    2016-07-01

    The present study was designed to investigate whether a combination of four effective components derived from Sheng-mai san (SMXZF; ginsenoside Rb1: ginsenoside Rg1: DT-13: Schizandrol A as 6 : 9 : 4 : 5) could attenuate hydrogen peroxide (H2O2)-induced injury in PC12 cells, focusing on the Akt and MAPK pathways . The PC12 cells were exposed to H2O2 (400 μmol·L(-1)) for 1 h in the presence or absence of SMXZF pre-treatment for 24 h. Cell viability was measured by MTT assay. The efflux of lactate dehydrogenase (LDH), the intracellular content of malondialdehyde (MDA), the activities of superoxide dismutase (SOD), and caspase-3 were also determined. Cell apoptosis was measured by Hoechst 33342 staining and Annexin V-FITC/PI staining method. The expression of Bcl-2, Bax, cleaved caspase-3, Akt, and MAPKs were detected by Western blotting analyses. SMXZF pretreatment significantly increased the cell viability and SOD activity and improved the cell morphological changes, while reduced the levels of LDH and MDA at the concentrations of 0.1, 1 and 10 μg·mL(-1). SMXZF also inhibited H2O2-induced apoptosis in PC12 cells. Moreover, SMXZF reduced the activity of caspase-3, up-regulated the protein ratio of Bcl-2 and Bax and inhibited the expression of cleaved caspase-3, p-Akt, p-p38, p-JNK and p-ERK1/2 in H2O2-induced PC12 cells. Co-incubation of Akt inhibitor or p38 inhibitor partly attenuated the protection of SMXZF against H2O2-injured PC12 cells. In conclusion, our findings suggested that SMXZF attenuated H2O2-induced injury in PC12 cells by inhibiting Akt and MAPKs signaling pathways, which might shed insights on its neuroprotective mechanism.

  5. The effect of an aerobic training program on the electrical remodeling of the heart: high-frequency components of the signal-averaged electrocardiogram are predictors of the maximal aerobic power

    Directory of Open Access Journals (Sweden)

    M. Marocolo

    2007-02-01

    Full Text Available Increased heart rate variability (HRV and high-frequency content of the terminal region of the ventricular activation of signal-averaged ECG (SAECG have been reported in athletes. The present study investigates HRV and SAECG parameters as predictors of maximal aerobic power (VO2max in athletes. HRV, SAECG and VO2max were determined in 18 high-performance long-distance (25 ± 6 years; 17 males runners 24 h after a training session. Clinical visits, ECG and VO2max determination were scheduled for all athletes during thew training period. A group of 18 untrained healthy volunteers matched for age, gender, and body surface area was included as controls. SAECG was acquired in the resting supine position for 15 min and processed to extract average RR interval (Mean-RR and root mean squared standard deviation (RMSSD of the difference of two consecutive normal RR intervals. SAECG variables analyzed in the vector magnitude with 40-250 Hz band-pass bi-directional filtering were: total and 40-µV terminal (LAS40 duration of ventricular activation, RMS voltage of total (RMST and of the 40-ms terminal region of ventricular activation. Linear and multivariate stepwise logistic regressions oriented by inter-group comparisons were adjusted in significant variables in order to predict VO2max, with a P < 0.05 considered to be significant. VO2max correlated significantly (P < 0.05 with RMST (r = 0.77, Mean-RR (r = 0.62, RMSSD (r = 0.47, and LAS40 (r = -0.39. RMST was the independent predictor of VO2max. In athletes, HRV and high-frequency components of the SAECG correlate with VO2max and the high-frequency content of SAECG is an independent predictor of VO2max.

  6. Signaling in symbiosis

    NARCIS (Netherlands)

    Limpens, E.H.M.; Bisseling, T.

    2003-01-01

    In recent years, the major focus in nodulation research has been on the genetic dissection of Nod-factor signaling. Components of this pathway appear to be shared with signaling processes that are induced during the formation of mycorrhiza. With the cloning of orthologs of the NIN and DMI2 genes

  7. Signaling in symbiosis

    NARCIS (Netherlands)

    Limpens, E.H.M.; Bisseling, T.

    2003-01-01

    In recent years, the major focus in nodulation research has been on the genetic dissection of Nod-factor signaling. Components of this pathway appear to be shared with signaling processes that are induced during the formation of mycorrhiza. With the cloning of orthologs of the NIN and DMI2 genes fro

  8. E3 ubiquitin ligases Pellinos as regulators of pattern recognition receptor signaling and immune responses.

    Science.gov (United States)

    Medvedev, Andrei E; Murphy, Michael; Zhou, Hao; Li, Xiaoxia

    2015-07-01

    Pellinos are a family of E3 ubiquitin ligases discovered for their role in catalyzing K63-linked polyubiquitination of Pelle, an interleukin-1 (IL-1) receptor-associated kinase homolog in the Drosophila Toll pathway. Subsequent studies have revealed the central and non-redundant roles of mammalian Pellino-1, Pellino-2, and Pelino-3 in signaling pathways emanating from IL-1 receptors, Toll-like receptors, NOD-like receptors, T- and B-cell receptors. While Pellinos ability to interact with many signaling intermediates suggested their scaffolding roles, recent findings in mice expressing ligase-inactive Pellinos demonstrated the importance of Pellino ubiquitin ligase activity. Cell-specific functions of Pellinos have emerged, e.g. Pellino-1 being a negative regulator in T lymphocytes and a positive regulator in myeloid cells, and details of molecular regulation of receptor signaling by various members of the Pellino family have been revealed. In this review, we summarize current information about Pellino-mediated regulation of signaling by pattern recognition receptors, T-cell and B-cell receptors and tumor necrosis factor receptors, and discuss Pellinos roles in sepsis and infectious diseases, as well as in autoimmune, inflammatory, and allergic disorders. We also provide our perspective on the potential of targeting Pellinos with peptide- or small molecule-based drug compounds as a new therapeutic approach for septic shock and autoimmune pathologies.

  9. Transcriptional regulation of SlPYL, SlPP2C, and SlSnRK2 gene families encoding ABA signal core components during tomato fruit development and drought stress.

    Science.gov (United States)

    Sun, Liang; Wang, Yan-Ping; Chen, Pei; Ren, Jie; Ji, Kai; Li, Qian; Li, Ping; Dai, Sheng-Jie; Leng, Ping

    2011-11-01

    In order to characterize the potential transcriptional regulation of core components of abscisic acid (ABA) signal transduction in tomato fruit development and drought stress, eight SlPYL (ABA receptor), seven SlPP2C (type 2C protein phosphatase), and eight SlSnRK2 (subfamily 2 of SNF1-related kinases) full-length cDNA sequences were isolated from the tomato nucleotide database of NCBI GenBank. All SlPYL, SlPP2C, and SlSnRK2 genes obtained are homologous to Arabidopsis AtPYL, AtPP2C, and AtSnRK2 genes, respectively. Based on phylogenetic analysis, SlPYLs and SlSnRK2s were clustered into three subfamilies/subclasses, and all SlPP2Cs belonged to PP2C group A. Within the SlPYL gene family, SlPYL1, SlPYL2, SlPYL3, and SlPYL6 were the major genes involved in the regulation of fruit development. Among them, SlPYL1 and SlPYL2 were expressed at high levels throughout the process of fruit development and ripening; SlPYL3 was strongly expressed at the immature green (IM) and mature green (MG) stages, while SlPYL6 was expressed strongly at the IM and red ripe (RR) stages. Within the SlPP2C gene family, the expression of SlPP2C, SlPP2C3, and SlPP2C4 increased after the MG stage; SlPP2C1 and SlPP2C5 peaked at the B3 stage, while SlPP2C2 and SlPP2C6 changed little during fruit development. Within the SlSnRK2 gene family, the expression of SlSnRK2.2, SlSnRK2.3, SlSnRK2.4, and SlSnRK2C was higher than that of other members during fruit development. Additionally, most SlPYL genes were down-regulated, while most SlPP2C and SlSnRK2 genes were up-regulated by dehydration in tomato leaf.

  10. Structural characterization of the heme-based oxygen sensor, AfGcHK, its interactions with the cognate response regulator, and their combined mechanism of action in a bacterial two-component signaling system.

    Science.gov (United States)

    Stranava, Martin; Martínek, Václav; Man, Petr; Fojtikova, Veronika; Kavan, Daniel; Vaněk, Ondřej; Shimizu, Toru; Martinkova, Marketa

    2016-10-01

    The oxygen sensor histidine kinase AfGcHK from the bacterium Anaeromyxobacter sp. Fw 109-5 forms a two-component signal transduction system together with its cognate response regulator (RR). The binding of oxygen to the heme iron of its N-terminal sensor domain causes the C-terminal kinase domain of AfGcHK to autophosphorylate at His183 and then transfer this phosphate to Asp52 or Asp169 of the RR protein. Analytical ultracentrifugation revealed that AfGcHK and the RR protein form a complex with 2:1 stoichiometry. Hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) suggested that the most flexible part of the whole AfGcHK protein is a loop that connects the two domains and that the heme distal side of AfGcHK, which is responsible for oxygen binding, is the only flexible part of the sensor domain. HDX-MS studies on the AfGcHK:RR complex also showed that the N-side of the H9 helix in the dimerization domain of the AfGcHK kinase domain interacts with the helix H1 and the β-strand B2 area of the RR protein's Rec1 domain, and that the C-side of the H8 helix region in the dimerization domain of the AfGcHK protein interacts mostly with the helix H5 and β-strand B6 area of the Rec1 domain. The Rec1 domain containing the phosphorylable Asp52 of the RR protein probably has a significantly higher affinity for AfGcHK than the Rec2 domain. We speculate that phosphorylation at Asp52 changes the overall structure of RR such that the Rec2 area containing the second phosphorylation site (Asp169) can also interact with AfGcHK. Proteins 2016; 84:1375-1389. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  11. Florigen signaling.

    Science.gov (United States)

    Tsuji, Hiroyuki; Taoka, Ken-Ichiro

    2014-01-01

    Florigen is a systemic signal that promotes flowering. Its molecular nature is a conserved FLOWERING LOCUS T (FT) protein that belongs to the PEBP family. FT is expressed in the leaf phloem and transported to the shoot apical meristem where it initiates floral transition. In the cells of the meristem, FT binds 14-3-3 proteins and bZIP transcription factor FD to form the florigen activation complex, FAC, which activates floral meristem identity genes such as AP1. The FAC model provides molecular basis for multiple functions of FT beyond flowering through changes of its partners and transcriptional targets. The surface of FT protein includes several regions essential for transport and functions, suggesting the binding of additional components that support its function. FT expression is under photoperiodic control, involving a conserved GIGANTEA-CONSTANS-FT regulatory module with species-specific modifications that contribute variations of flowering time in natural populations.

  12. Digital Microrobotics based on bistable modules : Design of a non-redundant digital micropositioning robot.

    OpenAIRE

    Chalvet, Vincent; Zarycki, Artur; Haddab, Yassine; Lutz, Philippe

    2011-01-01

    International audience; High precision manipulation becomes a recurrent need in micro or nanoscale. Microrobots based on active material were designed to perform micromanipulation tasks in various environments such as microrobotic stations or electronic microscopes (SEM, TEM). These active materials are used to generate proportional actuation, but show some drawbacks we want to avoid (non linearity, integration of sensors, . . . ). In this paper we propose a new type of microrobot, called dig...

  13. 2H Singularity-Free Momentum Generation with Non-Redundant Single Gimbaled Control Moment Gyroscopes

    Science.gov (United States)

    2006-12-01

    Authorized licensed use limited to: Naval Postgraduate School. Downloaded on May 29, 2009 at 14:31 from IEEE Xplore . Restrictions apply. Proceedings...from IEEE Xplore . Restrictions apply. 45th IEEE CDC, San Diego, USA, Dec. 13-15, 2006 The Newton-Euler relation relates generated torque to the timed...May 29, 2009 at 14:31 from IEEE Xplore . Restrictions apply. 45th IEEE CDC, San Diego, USA, Dec. 13-15, 2006 20 40 60 80 CMG Skew Angle, ~ Fig. 3

  14. ‘JANE EYRE’:A SIMPLE EXPERIMENT WITH A NON-REDUNDANT BILINGUAL SIMPLIFIED TEXT

    Institute of Scientific and Technical Information of China (English)

    David; Kellogg

    1997-01-01

    What do film subtitles,airport announcements,labels on products for export,simultaneousinterpreters,and vocabulary glosses all have in common?All are bilingual texts,of course,but morethan that they are all redundant,at least for the truly bilingual.Yet there is something irresistiblyseductive about the redundant part of bilingual texts for the language student.To paraphrase OscarWilde,an English student of French can resist almost anything except the temptation to read Englishsubtitles during a French movie or to listen to all four sides of a simultaneously translated argument.Perhaps the temptation lies in our insecurity that we really can understand the original,or in thehopelessly naive quest for the"exact"meaning of language items.With a flick of the eyess.the road

  15. GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics.

    Science.gov (United States)

    Tabas-Madrid, Daniel; Nogales-Cadenas, Ruben; Pascual-Montano, Alberto

    2012-07-01

    Since its first release in 2007, GeneCodis has become a valuable tool to functionally interpret results from experimental techniques in genomics. This web-based application integrates different sources of information to finding groups of genes with similar biological meaning. This process, known as enrichment analysis, is essential in the interpretation of high-throughput experiments. The frequent feedbacks and the natural evolution of genomics and bioinformatics have allowed the growth of the tool and the development of this third release. In this version, a special effort has been made to remove noisy and redundant output from the enrichment results with the inclusion of a recently reported algorithm that summarizes significantly enriched terms and generates functionally coherent modules of genes and terms. A new comparative analysis has been added to allow the differential analysis of gene sets. To expand the scope of the application, new sources of biological information have been included, such as genetic diseases, drugs-genes interactions and Pubmed information among others. Finally, the graphic section has been renewed with the inclusion of new interactive graphics and filtering options. The application is freely available at http://genecodis.cnb.csic.es.

  16. On the structural basis of non-redundant acquisition: Evidence from Spanish bilingual L3 Portuguese.

    OpenAIRE

    Rothman, Jason; Giancaspro, David; Halloran, Becky

    2014-01-01

    This chapter has two goals: (a) to discuss the Spanish-Portuguese interface in current formal language acquisition research and (b) to highlight the contributions of this language pairing in the emerging field of formal third language acquisition. The authors discuss two L3 acquisition studies (Montrul, Dias, & Santos, 2011; Giancaspro, Halloran, & Iverson, in press) examining Differential Object Marking, a morphological case marker present in Spanish but not in Portuguese, ...

  17. Signal Words

    Science.gov (United States)

    SIGNAL WORDS TOPIC FACT SHEET NPIC fact sheets are designed to answer questions that are commonly asked by the ... making decisions about pesticide use. What are Signal Words? Signal words are found on pesticide product labels, ...

  18. Two component systems: physiological effect of a third component.

    Directory of Open Access Journals (Sweden)

    Baldiri Salvado

    Full Text Available Signal transduction systems mediate the response and adaptation of organisms to environmental changes. In prokaryotes, this signal transduction is often done through Two Component Systems (TCS. These TCS are phosphotransfer protein cascades, and in their prototypical form they are composed by a kinase that senses the environmental signals (SK and by a response regulator (RR that regulates the cellular response. This basic motif can be modified by the addition of a third protein that interacts either with the SK or the RR in a way that could change the dynamic response of the TCS module. In this work we aim at understanding the effect of such an additional protein (which we call "third component" on the functional properties of a prototypical TCS. To do so we build mathematical models of TCS with alternative designs for their interaction with that third component. These mathematical models are analyzed in order to identify the differences in dynamic behavior inherent to each design, with respect to functionally relevant properties such as sensitivity to changes in either the parameter values or the molecular concentrations, temporal responsiveness, possibility of multiple steady states, or stochastic fluctuations in the system. The differences are then correlated to the physiological requirements that impinge on the functioning of the TCS. This analysis sheds light on both, the dynamic behavior of synthetically designed TCS, and the conditions under which natural selection might favor each of the designs. We find that a third component that modulates SK activity increases the parameter space where a bistable response of the TCS module to signals is possible, if SK is monofunctional, but decreases it when the SK is bifunctional. The presence of a third component that modulates RR activity decreases the parameter space where a bistable response of the TCS module to signals is possible.

  19. Spatial Phosphoprotein Profiling Reveals a Compartmentalized Extracellular Signal-regulated Kinase Switch Governing Neurite Growth and Retraction

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yingchun; Yang, Feng; Fu, Yi; Huang, Xiahe; Wang, Wei; Jiang, Xining; Gritsenko, Marina A.; Zhao, Rui; Monroe, Matthew E.; Pertz, Olivier C.; Purvine, Samuel O.; Orton, Daniel J.; Jacobs, Jon M.; Camp, David G.; Smith, Richard D.; Klemke, Richard L.

    2011-05-20

    Abstract - Brain development and spinal cord regeneration require neurite sprouting and growth cone navigation in response to extension and collapsing factors present in the extracellular environment. These external guidance cues control neurite growth cone extension and retraction processes through intracellular protein phosphorylation of numerous cytoskeletal, adhesion, and polarity complex signaling proteins. However, the complex kinase/substrate signaling networks that mediate neuritogenesis have not been investigated. Here, we compare the neurite phosphoproteome under growth and retraction conditions using neurite purification methodology combined with mass spectrometry. More than 4000 non-redundant phosphorylation sites from 1883 proteins have been annotated and mapped to signaling pathways that control kinase/phosphatase networks, cytoskeleton remodeling, and axon/dendrite specification. Comprehensive informatics and functional studies revealed a compartmentalized ERK activation/deactivation cytoskeletal switch that governs neurite growth and retraction, respectively. Our findings provide the first system-wide analysis of the phosphoprotein signaling networks that enable neurite growth and retraction and reveal an important molecular switch that governs neuritogenesis.

  20. Spatial Phosphoprotein Profiling Reveals a Compartmentalized Extracellular Signal-regulated Kinase Switch Governing Neurite Growth and Retraction*

    Science.gov (United States)

    Wang, Yingchun; Yang, Feng; Fu, Yi; Huang, Xiahe; Wang, Wei; Jiang, Xinning; Gritsenko, Marina A.; Zhao, Rui; Monore, Matthew E.; Pertz, Olivier C.; Purvine, Samuel O.; Orton, Daniel J.; Jacobs, Jon M.; Camp, David G.; Smith, Richard D.; Klemke, Richard L.

    2011-01-01

    Brain development and spinal cord regeneration require neurite sprouting and growth cone navigation in response to extension and collapsing factors present in the extracellular environment. These external guidance cues control neurite growth cone extension and retraction processes through intracellular protein phosphorylation of numerous cytoskeletal, adhesion, and polarity complex signaling proteins. However, the complex kinase/substrate signaling networks that mediate neuritogenesis have not been investigated. Here, we compare the neurite phosphoproteome under growth and retraction conditions using neurite purification methodology combined with mass spectrometry. More than 4000 non-redundant phosphorylation sites from 1883 proteins have been annotated and mapped to signaling pathways that control kinase/phosphatase networks, cytoskeleton remodeling, and axon/dendrite specification. Comprehensive informatics and functional studies revealed a compartmentalized ERK activation/deactivation cytoskeletal switch that governs neurite growth and retraction, respectively. Our findings provide the first system-wide analysis of the phosphoprotein signaling networks that enable neurite growth and retraction and reveal an important molecular switch that governs neuritogenesis. PMID:21454597

  1. Spatial phosphoprotein profiling reveals a compartmentalized extracellular signal-regulated kinase switch governing neurite growth and retraction.

    Science.gov (United States)

    Wang, Yingchun; Yang, Feng; Fu, Yi; Huang, Xiahe; Wang, Wei; Jiang, Xinning; Gritsenko, Marina A; Zhao, Rui; Monore, Matthew E; Pertz, Olivier C; Purvine, Samuel O; Orton, Daniel J; Jacobs, Jon M; Camp, David G; Smith, Richard D; Klemke, Richard L

    2011-05-20

    Brain development and spinal cord regeneration require neurite sprouting and growth cone navigation in response to extension and collapsing factors present in the extracellular environment. These external guidance cues control neurite growth cone extension and retraction processes through intracellular protein phosphorylation of numerous cytoskeletal, adhesion, and polarity complex signaling proteins. However, the complex kinase/substrate signaling networks that mediate neuritogenesis have not been investigated. Here, we compare the neurite phosphoproteome under growth and retraction conditions using neurite purification methodology combined with mass spectrometry. More than 4000 non-redundant phosphorylation sites from 1883 proteins have been annotated and mapped to signaling pathways that control kinase/phosphatase networks, cytoskeleton remodeling, and axon/dendrite specification. Comprehensive informatics and functional studies revealed a compartmentalized ERK activation/deactivation cytoskeletal switch that governs neurite growth and retraction, respectively. Our findings provide the first system-wide analysis of the phosphoprotein signaling networks that enable neurite growth and retraction and reveal an important molecular switch that governs neuritogenesis.

  2. Separation of components of a broad 1H-NMR composite signal by means of nutation experiments under low amplitude radiofrequency fields. Application to the water signal in synthetic clays; Developpement et mise en oeuvre d'une nouvelle methode fondee sur le phenomene de nutation pour la decomposition d'un signal composite de resonance magnetique nucleaire. Application au signal 1h de l'eau dans des argiles synthetiques

    Energy Technology Data Exchange (ETDEWEB)

    Trausch, G

    2006-11-15

    Nowadays, geologic nuclear waste storage is envisioned according to a multi-layer model which implies clays. The latter exhibit retention capacities and low permeability to water; that is why they are considered as a good candidate for engineered barriers to radioactive waste disposal. The present work here aims at studying transport phenomena which involve water molecules in three samples of synthetic clays (two of them exhibiting a Pake doublet) by means of Nuclear Magnetic Resonance (NMR). The first chapter describes structural properties of clays and presents the state-of-art of NMR and other experimental techniques used for such systems. The second chapter deals with the interpretation and the simulation of each conventional proton spectrum. These simulations allow us to evidence and to characterize a chemical exchange phenomenon. The third chapter is dedicated to original nutation experiments performed under low radiofrequency field in the case of broad NMR signal. It is shown that this type of NMR experiment can yield the number and the proportion of each species contributing to the whole signal. These results are exploited in the fourth chapter for processing relaxation and diffusion experiments. Finally, the diffusion coefficients obtained by NMR are divided by a factor 4 with respect to pure water while relaxation rates are two orders of magnitude greater. (author)

  3. Molecular and Cellular Signaling

    CERN Document Server

    Beckerman, Martin

    2005-01-01

    A small number of signaling pathways, no more than a dozen or so, form a control layer that is responsible for all signaling in and between cells of the human body. The signaling proteins belonging to the control layer determine what kinds of cells are made during development and how they function during adult life. Malfunctions in the proteins belonging to the control layer are responsible for a host of human diseases ranging from neurological disorders to cancers. Most drugs target components in the control layer, and difficulties in drug design are intimately related to the architecture of the control layer. Molecular and Cellular Signaling provides an introduction to molecular and cellular signaling in biological systems with an emphasis on the underlying physical principles. The text is aimed at upper-level undergraduates, graduate students and individuals in medicine and pharmacology interested in broadening their understanding of how cells regulate and coordinate their core activities and how diseases ...

  4. Study of engine noise based on independent component analysis

    Institute of Scientific and Technical Information of China (English)

    HAO Zhi-yong; JIN Yan; YANG Chen

    2007-01-01

    Independent component analysis was applied to analyze the acoustic signals from diesel engine. First the basic principle of independent component analysis (ICA) was reviewed. Diesel engine acoustic signal was decomposed into several independent components (Ics); Fourier transform and continuous wavelet transform (CWT) were applied to analyze the independent components. Different noise sources of the diesel engine were separated, based on the characteristics of different component in time-frequency domain.

  5. Qualitatively different T cell phenotypic responses to IL-2 versus IL-15 are unified by identical dependences on receptor signal strength and duration.

    Science.gov (United States)

    Arneja, Abhinav; Johnson, Hannah; Gabrovsek, Laura; Lauffenburger, Douglas A; White, Forest M

    2014-01-01

    IL-2 and IL-15 are common γ-chain family cytokines involved in regulation of T cell differentiation and homeostasis. Despite signaling through the same receptors, IL-2 and IL-15 have non-redundant roles in T cell biology, both physiologically and at the cellular level. The mechanisms by which IL-2 and IL-15 trigger distinct phenotypes in T cells remain elusive. To elucidate these mechanisms, we performed a quantitative comparison of the phosphotyrosine signaling network and resulting phenotypes triggered by IL-2 and IL-15. This study revealed that the signaling networks activated by IL-2 or IL-15 are highly similar and that T cell proliferation and metabolism are controlled in a quantitatively distinct manner through IL-2/15R signal strength independent of the cytokine identity. Distinct phenotypes associated with IL-2 or IL-15 stimulation therefore arise through differential regulation of IL-2/15R signal strength and duration because of differences in cytokine-receptor binding affinity, receptor expression levels, physiological cytokine levels, and cytokine-receptor intracellular trafficking kinetics. These results provide important insights into the function of other shared cytokine and growth factor receptors, quantitative regulation of cell proliferation and metabolism through signal transduction, and improved design of cytokine based clinical immunomodulatory therapies for cancer and infectious diseases.

  6. 独立分量分析融合小波能量阈值的电子鼻信号去漂移方法%Drift elimination method of electronic nose signals based on independent component analysis coupled with wavelet energy threshold value

    Institute of Scientific and Technical Information of China (English)

    殷勇; 吴文凯; 于慧春

    2014-01-01

    -Gaussianity maximization of negentropy was used to decompose the e-nose signals and generated many corresponding independent components. Secondly, some independent components were selected by their wavelet energy with the help of wavelet analysis so as to eliminate those independent components corresponding to drift signals. The reason is that some independent components corresponding to the constituents of food samples should be mainstream, and they can reflect the quality characteristic of food, and their energy values are relatively larger than that of the independent components corresponding to drift signals, then these independent components can be selected by wavelet energy threshold value. Namely, the independent components for which wavelet energy values are greater than the threshold value will be selected, otherwise will be removed, and the removed independent components may be considered to correspond to the e-nose drift signals. Finally, the e-nose signals which did not contain drift signals were obtained by reconstructing these selected independent components so as to carry out subsequent discrimination works. In order to test the validity of the proposed method, six kinds of white spirit samples and six kinds of vinegar samples were selected as identification objects. These white spirit samples (or vinegar samples) belong to three product groups, and each product group has two grades samples which are close in quality so as to increase the degree of difficulty of discrimination work. By trial and error, the wavelet energy threshold value for white spirit samples and vinegar samples were 0.075 and 0.258, respectively. After the e-nose signals of white spirit and vinegar samples were handled by the proposed method and the corresponding reconstructed e-nose signals were also obtained, the integral values (INV) selected as a kind of feature of the original e-nose signals and the reconstructed e-nose signals could be extracted. When Fisher discriminant analysis (FDA) was employed

  7. ATP signals

    DEFF Research Database (Denmark)

    Novak, Ivana

    2016-01-01

    The Department of Biology at the University of Copenhagen explains the function of ATP signalling in the pancreas......The Department of Biology at the University of Copenhagen explains the function of ATP signalling in the pancreas...

  8. Geniposide, the component of the Chinese herbal formula Tongluojiunao, protects amyloid-βpeptide (1-42)-mediated death of hippocampal neurons via the non-classical estrogen signaling pathway

    Institute of Scientific and Technical Information of China (English)

    Jiao Li; Yan Tan; Qi Zhang; Xu Wang; Angran Fan; Qian Hua; Feng Wang; Haimin Ding; Chunyan Jin; Jinyan Chen; Yanan Zhao; Xiaojing Li; Wenju Chen; Ping Sun

    2014-01-01

    Tongluojiunao (TLJN) is an herbal medicine consisting of two main components, geniposide and ginsenoside Rg1. TLJN has been shown to protect primary cultured hippocampal neurons. How-ever, its mechanism of action remains unclear. In the present study, primary cultured hippocampal neurons treated with Aβ1-42 (10 µmol/L) signiifcantly increased the release of lactate dehydroge-nase, which was markedly reduced by TLJN (2 µL/mL), speciifcally by the component geniposide (26 µmol/L), but not ginsenoside Rg1 (2.5 µmol/L). hTe estrogen receptor inhibitor, ICI182780 (1 µmol/L), did not block TLJN-or geniposide-mediated decrease of lactate dehydrogenase under Aβ1-42-exposed conditions. However, the phosphatidyl inositol 3-kinase or mitogen-activated protein kinase pathway inhibitor, LY294002 (50 µmol/L) or U0126 (10 µmol/L), respectively blo cked the decrease of lactate dehydrogenase mediated by TLJN or geniposide. hTerefore, these results suggest that the non-classical estrogen pathway (i.e., phosphatidyl inositol 3-kinase or mitogen-activated protein kinase) is involved in the neuroprotective effect of TLJN, speciifcally its component, geniposide, against Aβ1-42-mediated cell death in primary cultured hippocampal neurons.

  9. On the Spectrum of Periodic Signals

    Science.gov (United States)

    Al-Smadi, Adnan

    2004-01-01

    In theory, there are many methods for the representation of signals. In practice, however, Fourier analysis involving the resolution of signals into sinusoidal components is used widely. There are several methods for Fourier analysis available for representation of signals. If the signal is periodic, then the Fourier series is used to represent…

  10. Gibberellin Signal Transduction in Rice

    Institute of Scientific and Technical Information of China (English)

    Liu-Min Fan; Xiaoyan Feng; Yu Wang; Xing Wang Deng

    2007-01-01

    In the past decade, significant knowledge has accumulated regarding gibberellin (GA) signal transduction in rice as a result of studies using multiple approaches, particularly molecular genetics. The present review highlights the recent developments in the identification of GA signaling pathway components, the discovery of GA-induced destruction of GA signaling represser (DELLA protein), and the possible mechanism underlying the regulation of GA-responsive gene expression in rice.

  11. Notch Signaling in Pancreatic Development

    OpenAIRE

    2015-01-01

    The Notch signaling pathway plays a significant role in embryonic cell fate determination and adult tissue homeostasis. Various studies have demonstrated the deep involvement of Notch signaling in the development of the pancreas and the lateral inhibition of Notch signaling in pancreatic progenitor differentiation and maintenance. The targeted inactivation of the Notch pathway components promotes premature differentiation of the endocrine pancreas. However, there is still the contrary opinion...

  12. 快速独立分量分析及其在脑电信号处理中的应用%Fast Independent Component Analysis and Its Application to EEG Signal Processing

    Institute of Scientific and Technical Information of China (English)

    雷江震; 邹俊忠; 张见; 李艳洪; 王行愚

    2006-01-01

    独立分量分析(Independent Component Analysis, ICA)是一种基于信号统计特性的盲源分离方法,由于其分离的信号之间是互相独立的,所以在生物电信号去除干扰和伪迹、信号分离以及特征提取等方面有很大的潜在价值.本文提出了一种改进的快速ICA方法,提高了收敛速度.通过仿真,证明这种方法的优越性.最后利用该方法去除脑电中眼动伪迹,达到了较好的效果.

  13. Variability and component composition

    NARCIS (Netherlands)

    Storm, T. van der

    2004-01-01

    In component-based product populations, feature models have to be described at the component level to be able to benefit from a product family approach. As a consequence, composition of components becomes very complex. We describe how component-level variability can be managed in the face of compone

  14. Signaling aggression.

    Science.gov (United States)

    van Staaden, Moira J; Searcy, William A; Hanlon, Roger T

    2011-01-01

    From psychological and sociological standpoints, aggression is regarded as intentional behavior aimed at inflicting pain and manifested by hostility and attacking behaviors. In contrast, biologists define aggression as behavior associated with attack or escalation toward attack, omitting any stipulation about intentions and goals. Certain animal signals are strongly associated with escalation toward attack and have the same function as physical attack in intimidating opponents and winning contests, and ethologists therefore consider them an integral part of aggressive behavior. Aggressive signals have been molded by evolution to make them ever more effective in mediating interactions between the contestants. Early theoretical analyses of aggressive signaling suggested that signals could never be honest about fighting ability or aggressive intentions because weak individuals would exaggerate such signals whenever they were effective in influencing the behavior of opponents. More recent game theory models, however, demonstrate that given the right costs and constraints, aggressive signals are both reliable about strength and intentions and effective in influencing contest outcomes. Here, we review the role of signaling in lieu of physical violence, considering threat displays from an ethological perspective as an adaptive outcome of evolutionary selection pressures. Fighting prowess is conveyed by performance signals whose production is constrained by physical ability and thus limited to just some individuals, whereas aggressive intent is encoded in strategic signals that all signalers are able to produce. We illustrate recent advances in the study of aggressive signaling with case studies of charismatic taxa that employ a range of sensory modalities, viz. visual and chemical signaling in cephalopod behavior, and indicators of aggressive intent in the territorial calls of songbirds.

  15. 甘遂中激活NF-κB信号通路的化学成分%Chemical Components from Euphorbia kansui Activate NF-κB Signaling Pathway

    Institute of Scientific and Technical Information of China (English)

    陈晓珍; 张婷婷; 李国友; 方冬梅; 张国林; 罗应刚

    2013-01-01

    采用95%乙醇对甘遂进行提取,溶剂回收后得总浸膏;然后采用不同极性的有机溶剂进行萃取得萃取物;将总浸膏和各萃取物进行激活NF-κB信号通路活性检测;选取激活作用最强的氯仿萃取物进行硅胶柱层析,TLC检测合并;将得到的各部位进行进一步的激活NF-κB信号通路测试;结果表明激活作用最强的部位为非极性部位,因此我们采用GC-MS技术分离并鉴定了56个化合物,占总量的99.72%,主要成分为脂肪酸及其衍生物、长链烷烃及其衍生物,还有单萜、倍半萜类、芳香族类和脂肪醛等.在激活NF-κB信号通路的指导下,我们从甘遂非极性部位分析并鉴定了其中的促炎成分如(Z)-7-Hexadecenal和7,11-Hexadecadienal等,这些成分激活NF-κB信号通路的表达,从而引起炎症因子的释放,导致炎症,从上述非极性部位中还分析了部分毒性物质,为阐明甘遂的毒效物质基础提供了参考.%Kansui Radix, the dried roots of Euphorbia kansui Liou. (Euphorbiaceae) ,are commonly used traditional Chinese medicine. It was reported that the usage of Kansuiwould cause inflammation. An NF-KB-LUC reporter system was established to evaluate the bioactivity of Kansuiin this study. The 95% ethanol crude extractand different solvent-soluble extracts of Kansui were obtained by solvent extraction and fractionation. Bioassay guided separation suggested that the first sub-fraction ( C1) of the CHCI3 -soluble fraction displayed strong bioactivity. GC-MS was introduced to separate and identify the chemical components of the nonpolar sub-fraction of Kansui ( C1). Totally 56 compounds were identified from the non-polar sub-fraction C1. The main components were aliphatic acids and derivatives, long-chain alkanes, monoterpenes, sesquiterpenes, aromatic compoundsand aldehydydes. The aliphatic aldehydes such as (Z)-7-hexadecenal and 7,11-hexadecadienal detected in the sample extract were reported to cause

  16. Polarized CMB recovery with sparse component separation

    CERN Document Server

    Bobin, Jerome; Starck, Jean-Luc

    2015-01-01

    The polarization modes of the cosmological microwave background are an invaluable source of information for cosmology, and a unique window to probe the energy scale of inflation. Extracting such information from microwave surveys requires disentangling between foreground emissions and the cosmological signal, which boils down to solving a component separation problem. Component separation techniques have been widely studied for the recovery of CMB temperature anisotropies but quite rarely for the polarization modes. In this case, most component separation techniques make use of second-order statistics to discriminate between the various components. More recent methods, which rather emphasize on the sparsity of the components in the wavelet domain, have been shown to provide low-foreground, full-sky estimate of the CMB temperature anisotropies. Building on sparsity, the present paper introduces a new component separation technique dubbed PolGMCA (Polarized Generalized Morphological Component Analysis), which r...

  17. Bayesian signaling

    OpenAIRE

    Hedlund, Jonas

    2014-01-01

    This paper introduces private sender information into a sender-receiver game of Bayesian persuasion with monotonic sender preferences. I derive properties of increasing differences related to the precision of signals and use these to fully characterize the set of equilibria robust to the intuitive criterion. In particular, all such equilibria are either separating, i.e., the sender's choice of signal reveals his private information to the receiver, or fully disclosing, i.e., the outcome of th...

  18. Reconstruction of harmonic signals based on bispectrum

    Institute of Scientific and Technical Information of China (English)

    FAN Yangyu; SUN Jincai; LI Pingan; XU Jiadong; SHANG Jiuhao

    2000-01-01

    A method for accurate reconstruction of the harmonic signals from bispectrum is presented. Based on the analysis of the measured harmonic signal, a sinusoid signal with 0phase, 1-amplitude and half of the fundamental frequency combines with the measured signal to form a combined signal, and then the bispectrum analysis is carried out to reconstruct the phase and the amplitude of the measured signal accurately. Without the zero-phase assumption of the fundamental component, using the new method eliminates the phase shifting between the calculated Fourier phase and the true Fourier phase in the existing signal retrieval methods based on bispectrum. The simulation results show the effectiveness of the new method.

  19. KORRIGAN1 Interacts Specifically with Integral Components of the Cellulose Synthase Machinery

    NARCIS (Netherlands)

    Mansoori Zangir, N.; Timmers, J.F.P.; Desprez, T.; Lessa Alvim Kamei, C.; Dees, D.C.T.; Vincken, J.P.; Visser, R.G.F.; Höfte, H.; Vernhettes, S.; Trindade, L.M.

    2014-01-01

    Cellulose is synthesized by the so called rosette protein complex and the catalytic subunits of this complex are the cellulose synthases (CESAs). It is thought that the rosette complexes in the primary and secondary cell walls each contains at least three different non-redundant cellulose synthases.

  20. Digital Signal Processor For GPS Receivers

    Science.gov (United States)

    Thomas, J. B.; Meehan, T. K.; Srinivasan, J. M.

    1989-01-01

    Three innovative components combined to produce all-digital signal processor with superior characteristics: outstanding accuracy, high-dynamics tracking, versatile integration times, lower loss-of-lock signal strengths, and infrequent cycle slips. Three components are digital chip advancer, digital carrier downconverter and code correlator, and digital tracking processor. All-digital signal processor intended for use in receivers of Global Positioning System (GPS) for geodesy, geodynamics, high-dynamics tracking, and ionospheric calibration.

  1. Current topics in signal transduction in bacteria

    NARCIS (Netherlands)

    Hellingwerf, K.J.; Crielaard, W.; Teixeira de mattos, M.J.; Hoff, W.D.; Kort, R.; Verhamme, D.T.; Avignone-Rossa, C

    1998-01-01

    Among the signal transfer systems in bacteria two types predominate: two-component regulatory systems and quorum sensing systems. Both types of system can mediate signal transfer across the bacterial cell envelope; however, the signalling molecule typically is not taken up into the cells in the

  2. Proteomics insights into plant signaling and development.

    NARCIS (Netherlands)

    Kaufmann, K.; Smaczniak, C.D.; Vries, de S.C.; Angenent, G.C.; Karlova, R.B.

    2011-01-01

    Mass spectrometry-based proteomics is used to gain insight into the abundance and subcellular localization of cellular signaling components, the composition of molecular complexes and the regulation of signaling pathways. Multicellular organisms have evolved signaling networks and fast responses to

  3. Microsystem for signal processing applications

    Science.gov (United States)

    Frankenstein, B.; Froehlich, K.-J.; Hentschel, D.; Reppe, G.

    2005-05-01

    Acoustic monitoring of technological processes requires methods that eliminate noise as much as possible. Sensor-near signal evaluation can contribute substantially. Frequently, a further necessity exists to integrate the measuring technique in the monitored structure. The solution described contains components for analog preprocessing of acoustic signals, their digitization, algorithms for data reduction, and digital communication. The core component is a digital signal processor (DSP). Digital signal processors perform the algorithms necessary for filtering, down sampling, FFT computation and correlation of spectral components particularly effective. A compact, sensor-near signal processing structure was realized. It meets the Match-X standard, which as specified by the German Association for Mechanical and Plant Engineering (VDMA) for development of micro-technical modules, which can be combined to applicaiton specific systems. The solution is based on AL2O3 ceramic components including different signal processing modules as ADC, as well as memory and power supply. An arbitrary waveform generator has been developed and combined with a power amplifier for piezoelectric transducers in a special module. A further module interfaces to these transducers. It contains a multi-channel preamplifier, some high-pass filters for analog signal processing and an ADC-driver. A Bluetooth communication chip for wireless data transmission and a DiscOnChip module are under construction. As a first application, the combustion behavior of safety-relevant contacts is monitored. A special waveform up to 5MHz is produced and sent to the monitored object. The resulting signal form is evaluated with special algorithms, which extract significant parameters of the signal, and transmitted via CAN-bus.

  4. Signal processing method and system for noise removal and signal extraction

    Science.gov (United States)

    Fu, Chi Yung; Petrich, Loren

    2009-04-14

    A signal processing method and system combining smooth level wavelet pre-processing together with artificial neural networks all in the wavelet domain for signal denoising and extraction. Upon receiving a signal corrupted with noise, an n-level decomposition of the signal is performed using a discrete wavelet transform to produce a smooth component and a rough component for each decomposition level. The n.sup.th level smooth component is then inputted into a corresponding neural network pre-trained to filter out noise in that component by pattern recognition in the wavelet domain. Additional rough components, beginning at the highest level, may also be retained and inputted into corresponding neural networks pre-trained to filter out noise in those components also by pattern recognition in the wavelet domain. In any case, an inverse discrete wavelet transform is performed on the combined output from all the neural networks to recover a clean signal back in the time domain.

  5. Reusable Component Services

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Reusable Component Services (RCS) is a super-catalog of components, services, solutions and technologies that facilitates search, discovery and collaboration in...

  6. Normalization of vibration signals generated under highly varying speed and load with application to signal separation

    Science.gov (United States)

    Urbanek, Jacek; Barszcz, Tomasz; Strączkiewicz, Marcin; Jablonski, Adam

    2017-01-01

    The paper presents a normalization dedicated to transform non-stationary vibration signals into signals characterized by purely stationary properties. For this purpose, a novel class of generalized periodic signals is defined followed by a proposition of a normalization technique, which takes advantage of available, instantaneous values of operational parameters. Within the paper, a well-known discrete-random separation (DRS) technique is recalled as an exemplary technique, which has been restricted to stationary signals so far. The authors present a step-by-step adoption of the DRS to non-stationary signals. The method is applied to simulated signal, test rig signal, and a vibration signal from industrial object. Additionally, for the purpose of synthesis of simulated signal, a new model of multi-component vibrations generated under varying regime is proposed. The presented method aims to expand existing solutions dealing with varying frequency to a more general solution dealing with independent, simultaneous varying frequency and amplitude of signal components.

  7. Glutamate signalling in bone.

    Directory of Open Access Journals (Sweden)

    Karen eBrakspear

    2012-08-01

    Full Text Available Mechanical loading plays a key role in the physiology of bone, allowing bone to functionally adapt to its environment, however characterisation of the signalling events linking load to bone formation is incomplete. A screen for genes associated with mechanical load-induced bone formation identified the glutamate transporter GLAST, implicating the excitatory amino acid, glutamate, in the mechanoresponse. When an osteogenic load (10N, 10Hz was externally applied to the rat ulna, GLAST (EAAT1 mRNA, was significantly down-regulated in osteocytes in the loaded limb. Functional components from each stage of the glutamate signalling pathway have since been identified within bone, including proteins necessary for calcium-mediated glutamate exocytosis, receptors, transporters and signal propagation. Activation of ionotropic glutamate receptors has been shown to regulate the phenotype of osteoblasts and osteoclasts in vitro and bone mass in vivo. Furthermore, glutamatergic nerves have been identified in the vicinity of bone cells expressing glutamate receptors in vivo. However, it is not yet known how a glutamate signalling event is initiated in bone or its physiological significance. This review will examine the role of the glutamate signalling pathway in bone, with emphasis on the functions of glutamate transporters in osteoblasts.

  8. IL-27 receptor signalling restricts the formation of pathogenic, terminally differentiated Th1 cells during malaria infection by repressing IL-12 dependent signals.

    Directory of Open Access Journals (Sweden)

    Ana Villegas-Mendez

    Full Text Available The IL-27R, WSX-1, is required to limit IFN-γ production by effector CD4⁺ T cells in a number of different inflammatory conditions but the molecular basis of WSX-1-mediated regulation of Th1 responses in vivo during infection has not been investigated in detail. In this study we demonstrate that WSX-1 signalling suppresses the development of pathogenic, terminally differentiated (KLRG-1⁺ Th1 cells during malaria infection and establishes a restrictive threshold to constrain the emergent Th1 response. Importantly, we show that WSX-1 regulates cell-intrinsic responsiveness to IL-12 and IL-2, but the fate of the effector CD4⁺ T cell pool during malaria infection is controlled primarily through IL-12 dependent signals. Finally, we show that WSX-1 regulates Th1 cell terminal differentiation during malaria infection through IL-10 and Foxp3 independent mechanisms; the kinetics and magnitude of the Th1 response, and the degree of Th1 cell terminal differentiation, were comparable in WT, IL-10R1⁻/⁻ and IL-10⁻/⁻ mice and the numbers and phenotype of Foxp3⁺ cells were largely unaltered in WSX-1⁻/⁻ mice during infection. As expected, depletion of Foxp3⁺ cells did not enhance Th1 cell polarisation or terminal differentiation during malaria infection. Our results significantly expand our understanding of how IL-27 regulates Th1 responses in vivo during inflammatory conditions and establishes WSX-1 as a critical and non-redundant regulator of the emergent Th1 effector response during malaria infection.

  9. Principal component analysis

    NARCIS (Netherlands)

    Bro, R.; Smilde, A.K.

    2014-01-01

    Principal component analysis is one of the most important and powerful methods in chemometrics as well as in a wealth of other areas. This paper provides a description of how to understand, use, and interpret principal component analysis. The paper focuses on the use of principal component analysis

  10. SA3654 Component characterization. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Meir, G.W.

    1996-06-01

    AlliedSignal Inc., Federal Manufacturing & Technologies (FM&T), was provided with production capability assurance program (PCAP) funding to develop, characterize, and qualify purchased product components for use on the PRESS-A program. The SA3654, N-Channel, Power MOSFET was identified as a component needing such activity to support PRESS-A. This report presents the characterization activities and results for the SA3654.

  11. A putative colR(XC1049)-colS(XC1050) two-component signal transduction system in Xanthomonas campestris positively regulates hrpC and hrpE operons and is involved in virulence, the hypersensitive response and tolerance to various stresses.

    Science.gov (United States)

    Zhang, Sui-Sheng; He, Yong-Qiang; Xu, Li-Ming; Chen, Bo-Wen; Jiang, Bo-Le; Liao, Jie; Cao, Jin-Rui; Liu, Dan; Huang, Yan-Qiang; Liang, Xiao-Xia; Tang, Dong-Jie; Lu, Guang-Tao; Tang, Ji-Liang

    2008-01-01

    The ColR-ColS two-component signal transduction system was originally characterized as a regulatory system involved in the capacity of root-colonizing biocontrol bacterium Pseudomonas fluorescens to colonize plant roots. There are three pairs of putative colR-colS two-component regulatory systems annotated in the phytopathogen Xanthomonas campestris pathovar campestris. Mutational studies revealed that one of them, named colR(XC1049) and colS(XC1050), is a global regulatory system involved in various cellular processes, including virulence, hypersensitive response and stress tolerance. Growth rate determination showed that, although the colR(XC1049) and colS(XC1050) mutants are not auxotrophic, colR(XC1049) and colS(XC1050) are required for the pathogen to proliferate well in standard media and host plants. Assays of beta-glucuronidase activities of plasmid-driven promoter-gusA reporters and/or semi-quantitative RT-PCR demonstrated that colR(XC1049) and colS(XC1050) positively regulate expression of hrpC and hrpE operons, and that expression of colR(XC1049) and colS(XC1050) is not controlled by key hrp regulators HrpG and HrpX.

  12. Mutations in different components of FGF signaling in LADD syndrome.

    NARCIS (Netherlands)

    Rohmann, E.; Brunner, H.G.; Kayserili, H.; Uyguner, O.; Nurnberg, G.; Lew, E.D.; Dobbie, A.; Eswarakumar, V.P.; Uzumcu, A.; Ulubil-Emeroglu, M.; Leroy, J.G.; Li, Y.; Becker, C.; Lehnerdt, K.; Cremers, C.W.R.J.; Yuksel-Apak, M.; Nurnberg, P.; Kubisch, C.; Schlessinger, J.; Bokhoven, J.H.L.M. van; Wollnik, B.

    2006-01-01

    Lacrimo-auriculo-dento-digital (LADD) syndrome is characterized by lacrimal duct aplasia, malformed ears and deafness, small teeth and digital anomalies. We identified heterozygous mutations in the tyrosine kinase domains of the genes encoding fibroblast growth factor receptors 2 and 3 (FGFR2, FGFR3

  13. Radiation Hard Wide Temperature Range Mixed-Signal Components Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Low temperature survivability, high performance and radiation tolerance of electronics in combination is required for NASA's surface missions. Modern sub-micron CMOS...

  14. Adaptive Signal Processing Testbed

    Science.gov (United States)

    Parliament, Hugh A.

    1991-09-01

    The design and implementation of a system for the acquisition, processing, and analysis of signal data is described. The initial application for the system is the development and analysis of algorithms for excision of interfering tones from direct sequence spread spectrum communication systems. The system is called the Adaptive Signal Processing Testbed (ASPT) and is an integrated hardware and software system built around the TMS320C30 chip. The hardware consists of a radio frequency data source, digital receiver, and an adaptive signal processor implemented on a Sun workstation. The software components of the ASPT consists of a number of packages including the Sun driver package; UNIX programs that support software development on the TMS320C30 boards; UNIX programs that provide the control, user interaction, and display capabilities for the data acquisition, processing, and analysis components of the ASPT; and programs that perform the ASPT functions including data acquisition, despreading, and adaptive filtering. The performance of the ASPT system is evaluated by comparing actual data rates against their desired values. A number of system limitations are identified and recommendations are made for improvements.

  15. Supply chain components

    Directory of Open Access Journals (Sweden)

    Vieraşu, T.

    2011-01-01

    Full Text Available In this article I will go through three main logistics components, which are represented by: transportation, inventory and facilities, and the three secondary logistical components: information, production location, price and how they determine performance of any supply chain. I will discuss then how these components are used in the design, planning and operation of a supply chain. I will also talk about some obstacles a supply chain manager may encounter.

  16. Independent multiresolution component analysis and matching pursuit

    NARCIS (Netherlands)

    E. Capobianco (Enrico)

    2001-01-01

    textabstractWe show that decomposing a class of signals with overcomplete dictionaries of functions and combining multiresolution and independent component analysis allow for feature detection in complex non-stationary high frequency time series. Computational learning techniques are then designed

  17. Hot gas path component

    Energy Technology Data Exchange (ETDEWEB)

    Lacy, Benjamin Paul; Kottilingam, Srikanth Chandrudu; Porter, Christopher Donald; Schick, David Edward

    2017-09-12

    Various embodiments of the disclosure include a turbomachine component. and methods of forming such a component. Some embodiments include a turbomachine component including: a first portion including at least one of a stainless steel or an alloy steel; and a second portion joined with the first portion, the second portion including a nickel alloy including an arced cooling feature extending therethrough, the second portion having a thermal expansion coefficient substantially similar to a thermal expansion coefficient of the first portion, wherein the arced cooling feature is located within the second portion to direct a portion of a coolant to a leakage area of the turbomachine component.

  18. Psychological Component of Infertility

    Science.gov (United States)

    ... Home FAQs Frequently Asked Questions Quick Facts About Infertility FAQs About Infertility FAQs About the Psychological Component of Infertility FAQs About Cloning and Stem Cell Research SART's ...

  19. 基于独立成分分析结合遗传算法的电子鼻蜜源检测特征信号挖掘%Analysis of feature signals of electronic nose in honey nectar detection based on independent components analysis combined with genetic algorithm

    Institute of Scientific and Technical Information of China (English)

    刘宁晶; 史波林; 赵镭; 庆兆珅; 籍保平; 周峰

    2015-01-01

    针对交叉敏感性传感器阵列电子鼻图谱含样品信息全、噪声杂、信号冗余等特点,该文根据盲信号处理原理,利用独立成分分析提取油菜蜜、椴树蜜、洋槐蜜电子鼻交叉信号中不同性质分离的独立信号。将各蜜源样本电子鼻信号矩阵延响应时间轴方向展开,统一了各样品间独立成分分解顺序的一致性,并保持了混合信号矩阵中蜂蜜样本的排序。根据不同独立成分数分离信号所带来的蜜源分类效果,8个独立成分为最优成分数。结合遗传算法筛选出各独立成分中代表蜜源样本间差异而无重复信息的特征响应点20个,来富集蜂蜜样本间的整体电子鼻差异信息,并发现大部分集中于信号的吸附阶段,少量出现于解析附阶段。油菜蜜、椴树蜜、洋槐蜜蜜源判别模型采用支持向量机算法建立,通过比较原始信号、电导变化最大值、主成分分析(principal component analysis, PCA)、独立成分分析(independent component analysis, ICA)、独立成分分析结合遗传算法(genetic algorithm, GA)这5种信号处理方式,发现ICA结合GA的特征信号挖掘效果最优,预测集判别率(95.0%)最高,其中油菜蜜、椴树蜜、洋槐蜜的预测集判别力分别为24/25、16/17、36/38;且与训练集判别率(96.3%)最接近,说明模型稳定性高、泛化能力强。结果表明该方法可以准确提取电子鼻信号中能代表蜂蜜蜜源差异信息的特征信号,并在保证蜜源分类效果的前提下,大幅减小电子鼻信号的数据量。该研究为去除电子鼻交叉信号中的冗余成分,并挖掘掩藏其下的差异信息提供了很好的指导意义,同时也拓宽了ICA的应用范围。%Focusing on the characteristics of electronic nose (e-nose), including fully, noisy and redundant, Independent Components Analysis (ICA) is proposed to extract differential signals of e

  20. Sema4C-Plexin B2 signalling modulates ureteric branching in developing kidney.

    Science.gov (United States)

    Perälä, Nina; Jakobson, Madis; Ola, Roxana; Fazzari, Pietro; Penachioni, Junia Y; Nymark, Mariann; Tanninen, Tiina; Immonen, Tiina; Tamagnone, Luca; Sariola, Hannu

    2011-02-01

    Semaphorins, originally identified as axon guidance molecules, have also been implicated in angiogenesis, function of the immune system and cancerous growth. Here we show that deletion of Plexin B2 (Plxnb2), a semaphorin receptor that is expressed